Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 3 of 25
Found at i:310325 original size:79 final size:79
Alignment explanation
Indices: 310128--310348 Score: 245
Period size: 79 Copynumber: 2.8 Consensus size: 79
310118 ACAAAGGGGC
* *
310128 TGGAGTATCCCTGATTATGGAAAATCG--GTGTTCTAGAAATAAAATTGAGGTTGGAGTATCCCC
1 TGGAGTATCCCTGATTATGGAAAATCGAAGTCTTC-A-AAATAAAATCGAGGTTGGAGTATCCCC
310191 TCGAAAATAACAGGGT
64 TCGAAAATAACAGGGT
* * * * * *
310207 TAGAGCATCCCTAATTATAGG-AAATTGACA-TTTTGAAAATAAAATCGAGGTTGGAGTATCCCC
1 TGGAGTATCCCTGATTAT-GGAAAATCGA-AGTCTTCAAAATAAAATCGAGGTTGGAGTATCCCC
310270 TCGAAAATAAC-GGGAT
64 TCGAAAATAACAGGG-T
* * ** *
310286 TGGAGTATCCCTGATTGTGGAAAATCGAAGCCTTCAAAATAAGGTCGGGGTTGGAGTATCCCC
1 TGGAGTATCCCTGATTATGGAAAATCGAAGTCTTCAAAATAAAATCGAGGTTGGAGTATCCCC
310349 GCCAAACCCC
Statistics
Matches: 117, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
78 6 0.05
79 105 0.90
80 3 0.03
81 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (79 bp):
TGGAGTATCCCTGATTATGGAAAATCGAAGTCTTCAAAATAAAATCGAGGTTGGAGTATCCCCTC
GAAAATAACAGGGT
Found at i:310534 original size:50 final size:50
Alignment explanation
Indices: 310456--310579 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
310446 AACGAGATTG
* * * *
310456 GAGTATCCCCGATCATGAAAAATTAATATTTTGGAAATAAAACA-AGGGTTA
1 GAGTATCCCCGA-GATGAAAAATCAATATTTTAGAAATAAAACAGA-GGTCA
* * *
310507 GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAGCCGAGGTCG
1 GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAACAGAGGTCA
*
310557 GAGTATCCCCAAGATGAAAAATC
1 GAGTATCCCCGAGATGAAAAATC
310580 TAGAACTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 51 0.80
51 13 0.20
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (50 bp):
GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAAACAGAGGTCA
Found at i:312932 original size:50 final size:50
Alignment explanation
Indices: 312867--312985 Score: 168
Period size: 50 Copynumber: 2.4 Consensus size: 50
312857 ATTGACACAT
* *
312867 TGAAAAATGTGTCGATACATCTGGGT-AAACCCAAAATGTATCGATAATAA
1 TGAAAAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGAT-ATAA
* *
312917 TGAACAATGTATCGATACATCTAGGTAAAACCCAGAATGTATCGATATAA
1 TGAAAAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGATATAA
* *
312967 TGAATAATGTATTGATACA
1 TGAAAAATGTATCGATACA
312986 AATTGTGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 44 0.71
51 18 0.29
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (50 bp):
TGAAAAATGTATCGATACATCTAGGTAAAACCCAAAATGTATCGATATAA
Found at i:313783 original size:62 final size:61
Alignment explanation
Indices: 313614--314194 Score: 672
Period size: 62 Copynumber: 9.7 Consensus size: 61
313604 AATAAAATGG
* * * ** * *
313614 GTCCTGCTCTTTGGGGACT-AGAAGGTGCCACCAACATGTGTTGGCTTTGCAAGGAGAATGC
1 GTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * * *
313675 ATCTTGCTTTTTGAAGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * *
313736 GTCCTACTCCTTGAGGACTGAAAAGTGCCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTG-CCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * *
313798 ATCTTGCTATTTGAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * *
313858 GTCCTGCTCTTTAAGGACTAAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* *
313920 GTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAGCTTATGTGGGCTTT-----G-AAAGGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * * *
313974 GTCGTGCTCTTTAAGGACTGGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGT
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* *
314035 GTCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * *
314097 ATCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGCCTTT------AAAAGGT
1 GTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* **
314152 GTCTTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGG
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGG
314195 TATTTGAAAG
Statistics
Matches: 445, Mismatches: 61, Indels: 34
0.82 0.11 0.06
Matches are distributed among these distances:
54 24 0.05
55 68 0.15
56 1 0.00
60 74 0.17
61 118 0.27
62 160 0.36
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (61 bp):
GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
Found at i:313846 original size:122 final size:122
Alignment explanation
Indices: 313614--314150 Score: 644
Period size: 122 Copynumber: 4.4 Consensus size: 122
313604 AATAAAATGG
** * * * ** * *
313614 GTCCTGCTCTTTGGGGACT-AGAAGGTGCCACCAACATGTGTTGGCTTTGCAAGGAGAATGCATC
1 GTCCTGCTCTTTAAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
* * * *
313678 TTGCTTTTTGAAGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
65 CTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * *
313736 GTCCTACTCCTTGAGGACTGAAAAGTGCCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
1 GTCCTGCTCTTTAAGGACTGAAAAGTG-CCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
* * *
313801 TTGCTATTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAGGC
65 CTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* *
313858 GTCCTGCTCTTTAAGGACTAAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
1 GTCCTGCTCTTTAAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
* *
313923 CTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTATGTGGGCTTT-----G-AAAGGC
65 CTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * * **
313974 GTCGTGCTCTTTAAGGACTGGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGTGTCC
1 GTCCTGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* *
314039 TACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
66 TGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * *
314097 ATCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGCCTTTAAAAGG
1 GTCCTGCTCTTTAAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
314151 TGTCTTGCTC
Statistics
Matches: 366, Mismatches: 37, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
115 55 0.15
116 25 0.07
117 25 0.07
122 155 0.42
123 106 0.29
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (122 bp):
GTCCTGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
TGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
Found at i:314069 original size:177 final size:177
Alignment explanation
Indices: 313699--314190 Score: 698
Period size: 177 Copynumber: 2.7 Consensus size: 177
313689 AGACTGGAAG
* * *
313699 GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCCTTGAGGACTGAAAAGTGC
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTG-AAGGTG-
* *
313764 CCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCTTGCTATTTGAGGACT-GAAGGTGCCAC
64 CCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCTTGCTCTTTGAGGACTGGAAGGTGCCAC
* * *
313828 CAGCTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTAAGGACTAAAAAA
123 CAACTTGTATGGGCTTTAAAAGGAAAAGGCGTCCTACTCTTTAAGGACTAAAAAA
313883 GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCC
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCC
* * * *
313948 ACCAGCTTATGTGGGCTTTGAAAGGCGTCGTGCTCTTTAAGGACTGGAAGGTGCCACCAACTTGT
66 ACCAACTTGTGTGGGCTTTGAAAGGCGTCTTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGT
* * *
314013 ATGGGCTTTAAAAGGAAAAGGTGTCCTACTCTTTGAGGACTAGAAAA
131 ATGGGCTTTAAAAGGAAAAGGCGTCCTACTCTTTAAGGACTAAAAAA
*
314060 GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGC
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGC
* * * * **
314125 CACCAACTTGTGTGGCCTTTAAAAGGTGTCTTGCTCTTTGAGGACTGAAAAATGCCACCAACTTG
65 CACCAACTTGTGTGGGCTTTGAAAGGCGTCTTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTG
314190 T
130 T
314191 GTGGTATTTG
Statistics
Matches: 280, Mismatches: 26, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
176 21 0.08
177 116 0.41
178 64 0.23
182 19 0.07
183 5 0.02
184 55 0.20
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (177 bp):
GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCC
ACCAACTTGTGTGGGCTTTGAAAGGCGTCTTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGT
ATGGGCTTTAAAAGGAAAAGGCGTCCTACTCTTTAAGGACTAAAAAA
Found at i:315318 original size:8 final size:8
Alignment explanation
Indices: 315300--315359 Score: 59
Period size: 8 Copynumber: 7.4 Consensus size: 8
315290 AAGCAGGTTC
*
315300 TTTTCTTT
1 TTTTGTTT
*
315308 TTTT-TTG
1 TTTTGTTT
315315 TTTTGTTT
1 TTTTGTTT
315323 TTTTGTTTCT
1 TTTTG-TT-T
*
315333 TTTTATTT
1 TTTTGTTT
315341 TTTTGTTT
1 TTTTGTTT
*
315349 TTTTATTT
1 TTTTGTTT
315357 TTT
1 TTT
315360 AAAAAAGAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
7 6 0.14
8 29 0.66
9 4 0.09
10 5 0.11
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.87
Consensus pattern (8 bp):
TTTTGTTT
Found at i:315333 original size:32 final size:32
Alignment explanation
Indices: 315297--315358 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
315287 CTTAAGCAGG
*
315297 TTCTTTTCTTTTTTTTTGTTTTGTT-TTTTTGT
1 TTCTTTT-TATTTTTTTGTTTTGTTATTTTTGT
*
315329 TTCTTTTTATTTTTTTGTTTTTTTATTTTT
1 TTCTTTTTATTTTTTTGTTTTGTTATTTTT
315359 TAAAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.03, C:0.05, G:0.06, T:0.85
Consensus pattern (32 bp):
TTCTTTTTATTTTTTTGTTTTGTTATTTTTGT
Found at i:315336 original size:18 final size:17
Alignment explanation
Indices: 315305--315359 Score: 69
Period size: 16 Copynumber: 3.3 Consensus size: 17
315295 GGTTCTTTTC
* *
315305 TTTTTT-TTTGTTTTGT
1 TTTTTTGTTTTTTTTAT
315321 TTTTTTGTTTCTTTTTAT
1 TTTTTTGTTT-TTTTTAT
315339 TTTTTTG-TTTTTTTAT
1 TTTTTTGTTTTTTTTAT
315355 TTTTT
1 TTTTT
315360 AAAAAAGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 18 0.51
17 5 0.14
18 12 0.34
ACGTcount: A:0.04, C:0.02, G:0.07, T:0.87
Consensus pattern (17 bp):
TTTTTTGTTTTTTTTAT
Found at i:315344 original size:26 final size:27
Alignment explanation
Indices: 315301--315352 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
315291 AGCAGGTTCT
*
315301 TTTCTTTTTTTTTGTTTTGTTTTTTTG
1 TTTCTTTTTATTTGTTTTGTTTTTTTG
315328 TTTCTTTTTATTT-TTTTGTTTTTTT
1 TTTCTTTTTATTTGTTTTGTTTTTTT
315353 ATTTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.87
Consensus pattern (27 bp):
TTTCTTTTTATTTGTTTTGTTTTTTTG
Found at i:315360 original size:23 final size:25
Alignment explanation
Indices: 315300--315360 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
315290 AAGCAGGTTC
*
315300 TTTTCTTTTTT-TTTGTTTTGTTTT
1 TTTTATTTTTTATTTGTTTTGTTTT
*
315324 TTTGTTTCTTTTTATTT-TTTTG-TTT
1 TTT-TAT-TTTTTATTTGTTTTGTTTT
315349 TTTTATTTTTTA
1 TTTTATTTTTTA
315361 AAAAAGAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
23 6 0.19
24 5 0.16
25 8 0.25
26 10 0.31
27 3 0.09
ACGTcount: A:0.05, C:0.03, G:0.07, T:0.85
Consensus pattern (25 bp):
TTTTATTTTTTATTTGTTTTGTTTT
Found at i:327097 original size:30 final size:28
Alignment explanation
Indices: 327061--327118 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
327051 AATCGGTGTT
* *
327061 CTAGAAATAAAATCGGGGTTGGAGTATCCC
1 CTAGAAA-AAAAT-AGGGTTGGAGCATCCC
*
327091 CTAGAAAATAATAGGGTTGGAGCATCCC
1 CTAGAAAAAAATAGGGTTGGAGCATCCC
327119 TGATTATAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.56
29 4 0.16
30 7 0.28
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.22
Consensus pattern (28 bp):
CTAGAAAAAAATAGGGTTGGAGCATCCC
Found at i:327407 original size:79 final size:78
Alignment explanation
Indices: 327030--327390 Score: 309
Period size: 79 Copynumber: 4.6 Consensus size: 78
327020 AACAGGGCTA
* * * * *
327030 GAGTATCCTCTAATTACGAAAAATCGGTGTTCTAGAAATAAAATCGGGGTTGGAGTATCCCCT-A
1 GAGTATCC-CTGATTATGAAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCA
*
327094 GAAAATAATAGGGTTG
65 G-AAATAA-CGGGTTG
* * * * * *
327110 GAGCATCCCTGATTAT-AGGAAATCAACGTTTT-GAAAATAAAATCGAGGTTGGAGTATCCCCTC
1 GAGTATCCCTGATTATGA-AAAATCGATGTTTTAG-AAATAAAACCGGGGTTGGAGTATCCCCTC
*
327173 AAAAATAACAGGGTTG
64 AGAAATAAC-GGGTTG
* * * * * * ** * *
327189 GAGCATCCCCGATTGTGGAAAATCGAAGCTTTAGAAATAAGGCCGGGGTTGAAGTATCCCCACCA
1 GAGTATCCCTGATTATGAAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC-TCA
*
327254 -AAATAACGGGGTTA
65 GAAATAAC-GGGTTG
* * * * * *
327268 GAGTAT-CCTCGCTTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTCA
1 GAGTATCCCT-GATTATGAAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCA
327332 GAAATAACGGGATTG
65 GAAATAACGGG-TTG
* *
327347 GAGTATCCCTGATTATGAAAAATTGATGTTTTGGAAATAAAACC
1 GAGTATCCCTGATTATGAAAAATCGATGTTTTAGAAATAAAACC
327391 AAGGTTAGAG
Statistics
Matches: 223, Mismatches: 47, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
78 9 0.04
79 200 0.90
80 14 0.06
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.26
Consensus pattern (78 bp):
GAGTATCCCTGATTATGAAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAG
AAATAACGGGTTG
Found at i:330975 original size:13 final size:13
Alignment explanation
Indices: 330957--330986 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
330947 ATAAACCCAG
*
330957 AATGTATCGATAC
1 AATGTATCAATAC
330970 AATGTATCAATAC
1 AATGTATCAATAC
330983 AATG
1 AATG
330987 AATAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:335278 original size:20 final size:20
Alignment explanation
Indices: 335245--335282 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
335235 GTAAAAAGAT
* *
335245 AGAATGTATCGATACATTGA
1 AGAATCTATAGATACATTGA
335265 AGAATCTATAGATACATT
1 AGAATCTATAGATACATT
335283 CATACATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATCTATAGATACATTGA
Found at i:339863 original size:19 final size:20
Alignment explanation
Indices: 339819--339870 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
339809 TTACAAGCCA
339819 ATGTATCGATACATTTGGTC
1 ATGTATCGATACATTTGGTC
*
339839 ATGTATTGATACATCTT-GT-
1 ATGTATCGATACAT-TTGGTC
339858 ATGTATCGATACA
1 ATGTATCGATACA
339871 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.41
20 15 0.52
21 2 0.07
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTGGTC
Found at i:339962 original size:20 final size:21
Alignment explanation
Indices: 339912--339964 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
339902 GCCAATCATC
*
339912 TGTATCGATACACTTTTTGCA
1 TGTATCGATACACTTTGTGCA
* *
339933 AGTATTGATACA-TTTG-GTCA
1 TGTATCGATACACTTTGTG-CA
339953 TGTATCGATACA
1 TGTATCGATACA
339965 ATGTATCGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.04
20 15 0.58
21 10 0.38
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
TGTATCGATACACTTTGTGCA
Found at i:339970 original size:13 final size:13
Alignment explanation
Indices: 339952--339976 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
339942 ACATTTGGTC
339952 ATGTATCGATACA
1 ATGTATCGATACA
339965 ATGTATCGATAC
1 ATGTATCGATAC
339977 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:340562 original size:22 final size:22
Alignment explanation
Indices: 340536--340577 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
340526 CTTTTCTCTC
340536 CCCCTTAATCAAAA-AATTTCTG
1 CCCCTTAAT-AAAACAATTTCTG
340558 CCCCTTAATAAAACAATTTC
1 CCCCTTAATAAAACAATTTC
340578 CTGTAATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (22 bp):
CCCCTTAATAAAACAATTTCTG
Found at i:342651 original size:8 final size:8
Alignment explanation
Indices: 342633--342663 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
342623 ATTTCAACAT
342633 CAAACATCA
1 CAAA-ATCA
342642 CAAAATCA
1 CAAAATCA
342650 CAAAATCA
1 CAAAATCA
342658 CAAAAT
1 CAAAAT
342664 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:348614 original size:13 final size:13
Alignment explanation
Indices: 348596--348621 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
348586 ACATTTGGTC
348596 ATGTATCGATACA
1 ATGTATCGATACA
348609 ATGTATCGATACA
1 ATGTATCGATACA
348622 TCTTGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:348616 original size:33 final size:32
Alignment explanation
Indices: 348574--348641 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
348564 CGTTACAAGC
348574 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
348607 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
348639 CAA
1 CAA
348642 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:350057 original size:155 final size:154
Alignment explanation
Indices: 349759--350271 Score: 464
Period size: 155 Copynumber: 3.3 Consensus size: 154
349749 GCTAAGTTTA
* * * * * * * *
349759 AAAAAATTACGAAAATGCCCCTACGGAATACCTTCAATGTAAAAGTA-CCTGATACCCCTAAATG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTAAAAGTATCCCGGTA-CCCTAAAAG
* * * *
349823 ACTTAAAAAGGACTACAAAAGGGATGAACCTATCCTAAATGCCCACTTTTGGCATAAAA--ATGA
65 ACTTAAAAA-GATTACAAAAGGGATGAACCTATCCTAAATACCCACCTTTGACATAAAAGCA-G-
* * *
349886 ACTTGGTT-ATAACCTAGGATTTGGTTCT
127 AC-TCGTTGATAGCCTAGGAATTGGTTCT
* * * *
349914 AAAAAATTATGAAAATACCCCTAGGGGATACCTTCGACGTGAAAGTATCCCGGTACCTTTAAAGG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTAAAAGTATCCCGGTACC-CTAAAAG
* * *
349979 ACTTAAAAAGATTATAAAAGGGATAAAACTATCCTAAATACCCACCTTTGACATAAAAGCAGACT
65 ACTTAAAAAGATTACAAAAGGGATGAACCTATCCTAAATACCCACCTTTGACATAAAAGCAGACT
* * *
350044 CGTTGATAGCCTAGGACTAGGTTTT
130 CGTTGATAGCCTAGGAATTGGTTCT
* * * * * *
350069 GAAAAATTATGAAAATGCCCTTATGGGTATACCTTCGACGTAAAAGTATCTCGGTAACCCTAAAA
1 AAAAAATTACGAAAATACCCCTA-GGGGATACCTTCGACGTAAAAGTATCCCGGT-ACCCTAAAA
* * * * ** *
350134 GACTTAAAGAA-ATTAGAGATGGGATGAACCTATCCTAAATACCCACCTTCGATGTAAAAGCGGA
64 GACTTAAA-AAGATTACAAAAGGGATGAACCTATCCTAAATACCCACCTTTGACATAAAAGCAGA
* *
350198 CCCAG-TGAT-GACCTAGGAATTAGTTCT
128 CTC-GTTGATAG-CCTAGGAATTGGTTCT
* * * * * *
350225 GAAAAATTACGAAAATATCCCTAAGGGATACTTTCGATGAAAAAGTA
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTAAAAGTA
350272 CCTAATATCC
Statistics
Matches: 294, Mismatches: 54, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
154 4 0.01
155 142 0.48
156 141 0.48
157 7 0.02
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (154 bp):
AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTAAAAGTATCCCGGTACCCTAAAAGA
CTTAAAAAGATTACAAAAGGGATGAACCTATCCTAAATACCCACCTTTGACATAAAAGCAGACTC
GTTGATAGCCTAGGAATTGGTTCT
Found at i:350213 original size:156 final size:154
Alignment explanation
Indices: 349760--350271 Score: 437
Period size: 156 Copynumber: 3.3 Consensus size: 154
349750 CTAAGTTTAA
* * * * * * * * * *
349760 AAAAATTACGAAAATGCCCCTACGGAATACCTTCAATGTAAAAGTA-CCTGATACCCCTAAATGA
1 AAAAATTATGAAAATACCCCTAGGGGATACCTTCGACGTAAAAGTATCCCGGTACCTCTAAAAGA
* * * * * * * *
349824 CTTAAAAAGGACTACAAAAGGGATGAACCTATCCTAAATGCCCACTTTTGGCATAAAA--ATGAA
66 CTTAAAAA-GATTAGAAAAGGGATAAAACTATCCTAAATACCCACCTTCGACATAAAAGCA-G-A
** * *
349887 CTTGGTT-ATAACCTAGGATTTGGTTCTA
128 C-CCGTTGAT-ACCTAGGATTAGGTTCTG
* * *
349915 AAAAATTATGAAAATACCCCTAGGGGATACCTTCGACGTGAAAGTATCCCGGTACCTTTAAAGGA
1 AAAAATTATGAAAATACCCCTAGGGGATACCTTCGACGTAAAAGTATCCCGGTACCTCTAAAAGA
* * *
349980 CTTAAAAAGATTATAAAAGGGATAAAACTATCCTAAATACCCACCTTTGACATAAAAGCAGACTC
66 CTTAAAAAGATTAGAAAAGGGATAAAACTATCCTAAATACCCACCTTCGACATAAAAGCAGACCC
* *
350045 GTTGATAGCCTAGGACTAGGTTTTG
131 GTTGATA-CCTAGGATTAGGTTCTG
* * * *
350070 AAAAATTATGAAAATGCCCTTATGGGTATACCTTCGACGTAAAAGTATCTCGGTAACC-CTAAAA
1 AAAAATTATGAAAATACCCCTA-GGGGATACCTTCGACGTAAAAGTATCCCGGT-ACCTCTAAAA
* * * * ** *
350134 GACTTAAAGAA-ATTAGAGATGGGATGAACCTATCCTAAATACCCACCTTCGATGTAAAAGCGGA
64 GACTTAAA-AAGATTAGAAAAGGGATAAAACTATCCTAAATACCCACCTTCGACATAAAAGCAGA
350198 CCCAG-TGATGACCTAGGAATTA-GTTCTG
128 CCC-GTTGAT-ACCTAGG-ATTAGGTTCTG
* * * * * *
350226 AAAAATTACGAAAATATCCCTAAGGGATACTTTCGATGAAAAAGTA
1 AAAAATTATGAAAATACCCCTAGGGGATACCTTCGACGTAAAAGTA
350272 CCTAATATCC
Statistics
Matches: 294, Mismatches: 52, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
154 5 0.02
155 137 0.47
156 141 0.48
157 11 0.04
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (154 bp):
AAAAATTATGAAAATACCCCTAGGGGATACCTTCGACGTAAAAGTATCCCGGTACCTCTAAAAGA
CTTAAAAAGATTAGAAAAGGGATAAAACTATCCTAAATACCCACCTTCGACATAAAAGCAGACCC
GTTGATACCTAGGATTAGGTTCTG
Found at i:356720 original size:32 final size:32
Alignment explanation
Indices: 356664--356726 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
356654 CACACGCAGA
*
356664 TGTATCGATACATATTGCTTGTATCCATACAT
1 TGTATCGATACATATTGCTAGTATCCATACAT
* *
356696 TGTATCGATACATGTT-CATAGTATCGATACA
1 TGTATCGATACATATTGC-TAGTATCCATACA
356727 CCTTGAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATATTGCTAGTATCCATACAT
Found at i:361892 original size:13 final size:13
Alignment explanation
Indices: 361874--361912 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
361864 ATAATCCCCC
*
361874 TGTATCGATACAG
1 TGTATCGATACAA
361887 TGTATCGATACAA
1 TGTATCGATACAA
361900 TGTATCGATACAA
1 TGTATCGATACAA
361913 AGAATGCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:363996 original size:15 final size:15
Alignment explanation
Indices: 363976--364016 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
363966 GTTCATCAAT
363976 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
363991 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
*
364006 CTCAATTTGGA
1 TTC-ATTTGGA
364017 CATTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:368107 original size:13 final size:13
Alignment explanation
Indices: 368089--368113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
368079 CATTTTATGG
368089 TGTATCGATACAA
1 TGTATCGATACAA
368102 TGTATCGATACA
1 TGTATCGATACA
368114 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:368129 original size:32 final size:33
Alignment explanation
Indices: 368066--368133 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
368056 CGTTACAAGC
**
368066 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
368099 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
368131 CAA
1 CAA
368134 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:372853 original size:33 final size:33
Alignment explanation
Indices: 372811--372876 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
372801 AAAACTCAGA
372811 TGTATCGATACTGCATTC-TTAGTATCGATACAT
1 TGTATCGATACTGCATTCTTTA-TATCGATACAT
*
372844 TGTATCGATACTGCGTTCTTTATATCGATACAT
1 TGTATCGATACTGCATTCTTTATATCGATACAT
372877 AAGTACTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (33 bp):
TGTATCGATACTGCATTCTTTATATCGATACAT
Found at i:376711 original size:79 final size:79
Alignment explanation
Indices: 376628--376797 Score: 195
Period size: 79 Copynumber: 2.2 Consensus size: 79
376618 CATAATTGGA
* * * * *
376628 GATACTCCAATCCCGTTCTTTCCT-AAGG-GATACTCTAACCCC-GACTTTATTTCT-AAGATAT
1 GATACTCCAACCCCGTTATTT--TGAAGGAGATACTCCAACCCCAG-CCTTATTTCTAAAG-CAT
*
376689 TGATTTCTCACAATCGGG
62 CGATTTCTCACAATCGGG
**
376707 GATACTCCAACCCCGTTATTTTGGCGGAGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGAT
1 GATACTCCAACCCCGTTATTTTGAAGGAGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGAT
*
376772 TTTTCACAATCGGG
66 TTCTCACAATCGGG
376786 GATACTCCAACC
1 GATACTCCAACC
376798 TCGATTTTAT
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
77 1 0.01
78 2 0.03
79 71 0.91
80 4 0.05
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.31
Consensus pattern (79 bp):
GATACTCCAACCCCGTTATTTTGAAGGAGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGAT
TTCTCACAATCGGG
Found at i:381193 original size:85 final size:84
Alignment explanation
Indices: 381093--381696 Score: 347
Period size: 85 Copynumber: 7.1 Consensus size: 84
381083 CTTTTATCCT
* * * * * * *
381093 TTGTCTACCTATCGGCTTAGTCCCGGCAGACACCTTCACCCTTATGGAGACTTGTCAGCTTAGTC
1 TTGTTTACCTGTCGGCTCAGTCCCGG-ATAAACCTT-ACCCTTATGGTGACCTGTCAGCTTAGTC
*
381158 TCT-AGTCAACCTTCATCTCA
64 TCTCAGTCAACCTCCATCTCA
* * * *
381178 TTGTTTACCTGTCGGCTTAGTCCTC-AATAAACCCACTACCCCTATGGTGACCTGTCAGCTTAGT
1 TTGTTTACCTGTCGGCTCAGTCC-CGGATAAA-CC-TTACCCTTATGGTGACCTGTCAGCTTAGT
*
381242 CT-TCAATCAACCTCCATCTCA
63 CTCTCAGTCAACCTCCATCTCA
* * * * * *
381263 TTATTTACCTGTCAGCTCAGTCCCTGATAAACCATTACCTTTATGGTGACTTGTCAGCATAGTC-
1 TTGTTTACCTGTCGGCTCAGTCCCGGATAAACC-TTACCCTTATGGTGACCTGTCAGCTTAGTCT
381327 CTTCAGTCAACCTCCATCTCA
65 C-TCAGTCAACCTCCATCTCA
* * ** * * *
381348 TTGTTTACCTATCAGCTCAGTCTTGGGA-AACACCCTTACCCATATGGTGACCTATCAACTTAGT
1 TTGTTTACCTGTCGGCTCAGTC-CCGGATAA-A-CCTTACCCTTATGGTGACCTGTCAGCTTAGT
* ***
381412 TTCT-AGTCAACCTTTGTCTCA
63 CTCTCAGTCAACCTCCATCTCA
* * * * * * **
381433 TTGTTTACCAGTCGGCTCAATCCC-TAGTAAACTCTTTACCCTTATGGTGACCTGCCAACTCAAC
1 TTGTTTACCTGTCGGCTCAGTCCCGGA-TAAAC-C-TTACCCTTATGGTGACCTGTCAGCTTAGT
* *
381497 CTCT-AATCAACCTTCATCTCA
63 CTCTCAGTCAACCTCCATCTCA
* * * * * * *
381518 TTATTTACCTATTGGCTCAGTCCTTGG-TAAACCCTTTATCCATT-CGGTGACCTGGT-GGCTTA
1 TTGTTTACCTGTCGGCTCAGTCC-CGGATAAA-CC-TTA-CCCTTATGGTGACCT-GTCAGCTTA
* * *
381580 GTC-CTCGGTCAACACTTCATC-CC
61 GTCTCTCAGTCAAC-CTCCATCTCA
* * * * * * *
381603 TTATTTACTTGTCAGCTCAGTCCACGGCA-AACCCCTTACCCTTTTGGTGACCTATCAGCTCAGT
1 TTGTTTACCTGTCGGCTCAGTCC-CGG-ATAA-ACCTTACCCTTATGGTGACCTGTCAGCTTAGT
** *
381667 CT-TTGGTCGACCTCCATCTCA
63 CTCTCAGTCAACCTCCATCTCA
* *
381688 CTATTTACC
1 TTGTTTACC
381697 CGTTGGCCTA
Statistics
Matches: 401, Mismatches: 89, Indels: 58
0.73 0.16 0.11
Matches are distributed among these distances:
83 2 0.00
84 48 0.12
85 302 0.75
86 46 0.11
87 3 0.01
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (84 bp):
TTGTTTACCTGTCGGCTCAGTCCCGGATAAACCTTACCCTTATGGTGACCTGTCAGCTTAGTCTC
TCAGTCAACCTCCATCTCA
Found at i:381620 original size:255 final size:255
Alignment explanation
Indices: 381098--381696 Score: 566
Period size: 255 Copynumber: 2.3 Consensus size: 255
381088 ATCCTTTGTC
* * * * * * * * *
381098 TACCTATCGGCTTAGTCC-CGGCAGACACCTTCACCCTTATGGAGACTTGTCAGCTTAGTCTCTA
1 TACCTATCAGCTCAGTCCACGGCAAACCCCTT-ACCCATATGGTGACCTATCAACTTAGTCTCTA
* * *
381162 GTCAACCTTCATCTCATTGTTTACCTGTCGGCTTAGTCCTCAATAAACCCACTACCCCTATGGTG
65 GTCAACCTTCATCTCATTGTTTACCAGTCGGCTCAATCCTCAATAAACCCACTACCCCTATGGTG
* * * ** *
381227 ACCTGTCAGCTTAGTCTTCAATCAACCTCCATCTCATTATTTACCTGTCAGCTCAGTCCCTGATA
130 ACCTGCCAACTCAACCTTCAATCAACCTCCATCTCATTATTTACCTATCAGCTCAGTCCCTGATA
* * * *
381292 AACCATTACCTTTATGGTGACTTGTCAGCATAGTCCTTCAGTCAACCTCCATCTCATTGTT
195 AACCATTACCATTACGGTGACTGGTCAGCATAGTCCTTCAGTCAACCTCCATCTCATTATT
** * *
381353 TACCTATCAGCTCAGT-CTTGGGAAACACCCTTACCCATATGGTGACCTATCAACTTAGTTTCTA
1 TACCTATCAGCTCAGTCCACGGCAAAC-CCCTTACCCATATGGTGACCTATCAACTTAGTCTCTA
** * * ** *
381417 GTCAACCTTTGTCTCATTGTTTACCAGTCGGCTCAATCC-CTAGTAAACTCTTTACCCTTATGGT
65 GTCAACCTTCATCTCATTGTTTACCAGTCGGCTCAATCCTC-AATAAACCCACTACCCCTATGGT
* ** * *
381481 GACCTGCCAACTCAACC-TCTAATCAACCTTCATCTCATTATTTACCTATTGGCTCAGTCCTTGG
129 GACCTGCCAACTCAACCTTC-AATCAACCTCCATCTCATTATTTACCTATCAGCTCAGTCCCTGA
* * * * * *
381545 TAAACCCTTTATCCATT-CGGTGACCTGGT-GGCTTAGTCC-TCGGTCAACACTTCATC-CCTTA
193 TAAA-CCATTA-CCATTACGGTGA-CTGGTCAGCATAGTCCTTCAGTCAAC-CTCCATCTCATTA
381606 TT
254 TT
* * * * * * * *
381608 TACTTGTCAGCTCAGTCCACGGCAAACCCCTTACCCTTTTGGTGACCTATCAGCTCAGTCTTTGG
1 TACCTATCAGCTCAGTCCACGGCAAACCCCTTACCCATATGGTGACCTATCAACTTAGTCTCTAG
* * * *
381673 TCGACCTCCATCTCACTATTTACC
66 TCAACCTTCATCTCATTGTTTACC
381697 CGTTGGCCTA
Statistics
Matches: 274, Mismatches: 61, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
254 4 0.01
255 227 0.83
256 35 0.13
257 8 0.03
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (255 bp):
TACCTATCAGCTCAGTCCACGGCAAACCCCTTACCCATATGGTGACCTATCAACTTAGTCTCTAG
TCAACCTTCATCTCATTGTTTACCAGTCGGCTCAATCCTCAATAAACCCACTACCCCTATGGTGA
CCTGCCAACTCAACCTTCAATCAACCTCCATCTCATTATTTACCTATCAGCTCAGTCCCTGATAA
ACCATTACCATTACGGTGACTGGTCAGCATAGTCCTTCAGTCAACCTCCATCTCATTATT
Found at i:382940 original size:127 final size:126
Alignment explanation
Indices: 382709--382944 Score: 307
Period size: 127 Copynumber: 1.9 Consensus size: 126
382699 TCAAATTACG
* * * * ** *
382709 GAGTTTTCTACTCTGTAATTTTTTTGGGGGAATTTTTCTTGGTTTTCAATTTTTTAAATTCATCA
1 GAGTTTTCTACTCTGTAATATTTTCGGGGGAATTTTTCTCGATTTAAAATTTTTAAAATTCATCA
* *
382774 AATATTATTATTTAATTCATATTAAATCTATTTTCAAAAATTCATTCATTTTCGAAATATT
66 AATATTATTATTAAATTCATATTAAATCTATTTACAAAAATTCATTCATTTTCGAAATATT
*
382835 GAGTTTTCTACTTTGTGAATATTTTCGAGGGG-ATTTTTCTCGATTTAAAATTTTTAAAATTCAT
1 GAGTTTTCTACTCTGT-AATATTTTCG-GGGGAATTTTTCTCGATTTAAAATTTTTAAAATTCAT
* *
382899 CTAATATT-TTCATTAAATTCATATTAAATC-AGTTTAGAAAAATTCA
64 CAAATATTATT-ATTAAATTCATATTAAATCTA-TTTACAAAAATTCA
382945 AATTATTTCA
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
126 18 0.19
127 72 0.77
128 4 0.04
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (126 bp):
GAGTTTTCTACTCTGTAATATTTTCGGGGGAATTTTTCTCGATTTAAAATTTTTAAAATTCATCA
AATATTATTATTAAATTCATATTAAATCTATTTACAAAAATTCATTCATTTTCGAAATATT
Found at i:383366 original size:17 final size:17
Alignment explanation
Indices: 383324--383359 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
383314 AAATGTGGTG
*
383324 AAAGGAAAT-AAAATGA
1 AAAGAAAATGAAAATGA
383340 AAAGAAAATGAAAATGA
1 AAAGAAAATGAAAATGA
383357 AAA
1 AAA
383360 AACAATGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (17 bp):
AAAGAAAATGAAAATGA
Found at i:384561 original size:164 final size:160
Alignment explanation
Indices: 384366--384742 Score: 431
Period size: 164 Copynumber: 2.3 Consensus size: 160
384356 AGGGTATAAA
*
384366 AAAAGATCTC-AAAACTTTTCGTATCTTTTTGGGTTTCCATTAAGGTACAAAATGGTATTTTTCA
1 AAAAGATTTCAAAAACTTTTCGTATCTTTTTGGGTTTCCATTAAGGTACAAAATGGTATTTTTCA
* * * *
384430 AAAATAAATAAATTAAATTAAATTAAAAATTTCATAAT-C-AAAATAAATATTAATCATTTTTCT
66 AAAACAAATAAATAAAATTAAACTAAAAATTTCAT-ATCCGAAAAGAAAT-TTAAT--TTTTT-T
* * *
384493 AATCTTTTATATTCCTATAGGG-GTCCGTAGGGGTAT
126 -ATCTCTTATACTCCTAT-GGGTATCCGTAGGGGTAT
* * *
384529 AAAAGATTTCAAAAACTTTTCGTATTTTTTTGGGTTTCCATTAAGGTATGAAAA-GGTATTTTTT
1 AAAAGATTTCAAAAACTTTTCGTATCTTTTTGGGTTTCCATTAAGGTA-CAAAATGGTATTTTTC
* * * * * * *
384593 GAAAACAAATAAATAAAATTAAGCTAATACTTTCATATCCGAGAGGAACTTTAATTTTTTTATCT
65 AAAAACAAATAAATAAAATTAAACTAAAAATTTCATATCCGAAAAGAAATTTAATTTTTTTATCT
384658 CTTATACTCCTATGGGTATCCGTAGGGGTAT
130 CTTATACTCCTATGGGTATCCGTAGGGGTAT
* * * * * *
384689 AAAAGGTTTTAAAAACTTTTCATATCTTTTTAGGCTTCCATTAAGGTACCAAAT
1 AAAAGATTTCAAAAACTTTTCGTATCTTTTTGGGTTTCCATTAAGGTACAAAAT
384743 AAAATTTTCA
Statistics
Matches: 182, Mismatches: 26, Indels: 15
0.82 0.12 0.07
Matches are distributed among these distances:
159 6 0.03
160 70 0.38
161 1 0.01
162 5 0.03
163 11 0.06
164 80 0.44
165 9 0.05
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (160 bp):
AAAAGATTTCAAAAACTTTTCGTATCTTTTTGGGTTTCCATTAAGGTACAAAATGGTATTTTTCA
AAAACAAATAAATAAAATTAAACTAAAAATTTCATATCCGAAAAGAAATTTAATTTTTTTATCTC
TTATACTCCTATGGGTATCCGTAGGGGTAT
Found at i:385496 original size:156 final size:154
Alignment explanation
Indices: 385154--385716 Score: 484
Period size: 156 Copynumber: 3.6 Consensus size: 154
385144 TTTTATCATT
*
385154 CTTTTTTAAGTCCTTTAGGGTATCGGGTACTTCTACGTCGAAGATAT-CTCC-TAGGGGTATTTT
1 CTTTTTTAAGTCCTTTAGGGTATCGGGTACTTCTACGTCGAAGGTATAC-CCATA-GGGTATTTT
* * * * *
385217 CATAATTTTTTAGAACCAACTCCTAGGTAATCACCGGGTCCACTTTTATGCTAAAGGTGCATATT
64 CGTAATTTTTTAGAGCCAAGTCCTAGGTTATCACCGGGTCTACTTTTATGCTAAAGGTGCATATT
385282 TAGGATAGGTTCATCCCATCTTAAAC
129 TAGGATAGGTTCATCCCATCTTAAAC
* * *** *
385308 CTTTTTTAAATCTTTTAGGGGTATCAAATACTTCTACGTCGAAGGTATACCCATAGAGGCATTTT
1 CTTTTTTAAGTCCTTTA-GGGTATCGGGTACTTCTACGTCGAAGGTATACCCATAG-GGTATTTT
* * * * * * * *
385373 TGTAATTTTCTAGAGTCAAGTCTTAGGTTGTCACCGGGTCTGCTTTTATGTTAGAGGTGGGCA-A
64 CGTAATTTTTTAGAGCCAAGTCCTAGGTTATCACCGGGTCTACTTTTATGCTAAAGGT--GCATA
*
385437 -TTAGGATAGGTTCATCCCATCTCT-AAT
127 TTTAGGATAGGTTCATCCCATCT-TAAAC
* * * *
385464 C-TTTTTAAGTCCTTTAGGGTAACCGGGGTACTT-TCATGTTGAAAGTATACCCATATGGGTATT
1 CTTTTTTAAGTCCTTTAGGGT-ATC-GGGTACTTCT-ACGTCGAAGGTATACCCATA-GGGTATT
* * * * * * ** **
385527 TTCGTAATTTTTTAAAGCCGAGTCCTAAGTTCTCATCGGGTCTTCTTTTATGCCGAAGGTGGGTA
62 TTCGTAATTTTTTAGAGCCAAGTCCTAGGTTATCACCGGGTCTACTTTTATGCTAAAGGTGCATA
* *
385592 TTTGGGAT-GTGTTCATCCC-TTTTAAAATC
127 TTTAGGATAG-GTTCATCCCATCTT-AAA-C
* * * * *
385621 C-TTTTTAAGTCCTTTGGGGTATCAGATACTTTTACGTCAAAGGTAT-CTCC-TAGGGGTATTTT
1 CTTTTTTAAGTCCTTTAGGGTATCGGGTACTTCTACGTCGAAGGTATAC-CCATA-GGGTATTTT
* * * *
385683 CATAATTTTTTAGAACCAAGTCCTAAGTTGTCAC
64 CGTAATTTTTTAGAGCCAAGTCCTAGGTTATCAC
385717 TAGGTCTGTT
Statistics
Matches: 325, Mismatches: 65, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
154 61 0.19
155 66 0.20
156 173 0.53
157 22 0.07
158 3 0.01
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (154 bp):
CTTTTTTAAGTCCTTTAGGGTATCGGGTACTTCTACGTCGAAGGTATACCCATAGGGTATTTTCG
TAATTTTTTAGAGCCAAGTCCTAGGTTATCACCGGGTCTACTTTTATGCTAAAGGTGCATATTTA
GGATAGGTTCATCCCATCTTAAAC
Found at i:390593 original size:19 final size:20
Alignment explanation
Indices: 390539--390593 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 20
390529 TTTGTGGAAA
* *
390539 AAAAG-AAAAATGAGATGAC
1 AAAAGAAAAAATGAAAAGAC
*
390558 AAAAGAAAACAA-AAAAAG-C
1 AAAAGAAAA-AATGAAAAGAC
390577 AAAAGAAAAAATGAAAA
1 AAAAGAAAAAATGAAAA
390594 ATCAAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 2 0.07
19 19 0.66
20 6 0.21
21 2 0.07
ACGTcount: A:0.75, C:0.05, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAAATGAAAAGAC
Found at i:392129 original size:90 final size:90
Alignment explanation
Indices: 391840--392170 Score: 385
Period size: 90 Copynumber: 3.7 Consensus size: 90
391830 TCTTACCTCA
* * * * * *
391840 TTCATGCAACCACTAGATGGTACTGATGTATATCATAAAGCCTGATATCCTTGGAGCAAGGGTGC
1 TTCATCCAACCACTAGATGGTATTGATG--CATCACAAAGCCTAATATCCTTGGGGCAAGGGTGC
* *
391905 AGCCCACACATTCCTAATCATATTCCT
64 AGCCCACACATTCCCAATCATATTCCC
* * * * * * *
391932 TTCATCCAACTAGTAGACGGTATTGATGTATCACAAAGCCTGATATCCTTAGGGCGAGGGTGCAG
1 TTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTAATATCCTTGGGGCAAGGGTGCAG
**
391997 CCCATGCATTCCCAATCATATTCCC
66 CCCACACATTCCCAATCATATTCCC
* * ** *
392022 TTCATCCAACCACTAGATGATATTGATGCATCACAAAGCCTAATTTCCTTGGGGCAAAAGTGTAG
1 TTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTAATATCCTTGGGGCAAGGGTGCAG
392087 CCCACACATTCCCAATCATATTCCC
66 CCCACACATTCCCAATCATATTCCC
* * ** *
392112 TTCACCCAACCATTAGATGGTACCGATGCATCATAAAG-CTCAATATCCTTGGGGCAAGG
1 TTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCT-AATATCCTTGGGGCAAGG
392171 ATATCCCGAC
Statistics
Matches: 202, Mismatches: 36, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
89 2 0.01
90 177 0.88
92 23 0.11
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (90 bp):
TTCATCCAACCACTAGATGGTATTGATGCATCACAAAGCCTAATATCCTTGGGGCAAGGGTGCAG
CCCACACATTCCCAATCATATTCCC
Found at i:392442 original size:35 final size:35
Alignment explanation
Indices: 392403--392539 Score: 186
Period size: 35 Copynumber: 3.9 Consensus size: 35
392393 GAATATTCTC
*
392403 TCAAACTCTTTCTATCATCATTTGACTATATTTGA
1 TCAAACTCTTTCCATCATCATTTGACTATATTTGA
* * *
392438 TCAAACTCTTTCCATCACCATTTGACTGTATTTGG
1 TCAAACTCTTTCCATCATCATTTGACTATATTTGA
* *
392473 TTAAACTCTTTCCATCATCATTTGACTATATCT-A
1 TCAAACTCTTTCCATCATCATTTGACTATATTTGA
* *
392507 GTCAAACTCTTTCCATCATCGTTTGATTATATT
1 -TCAAACTCTTTCCATCATCATTTGACTATATT
392540 GGCGTTAGGA
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 88 1.00
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (35 bp):
TCAAACTCTTTCCATCATCATTTGACTATATTTGA
Found at i:395033 original size:13 final size:13
Alignment explanation
Indices: 395015--395040 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
395005 CAATTTTTTG
395015 TGTATCGATACAT
1 TGTATCGATACAT
395028 TGTATCGATACAT
1 TGTATCGATACAT
395041 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:395105 original size:21 final size:21
Alignment explanation
Indices: 395079--395154 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
395069 CTGCCAAGAA
395079 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
395100 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
395120 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
395141 ATGTATCGATACAT
1 ATGTATCGATACAT
395155 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:395124 original size:20 final size:20
Alignment explanation
Indices: 395099--395172 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
395089 ACATCTTTTT
395099 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
395119 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
395140 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
395160 CATGTATCGATAC
1 CATGTATCGATAC
395173 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:395136 original size:41 final size:41
Alignment explanation
Indices: 395079--395172 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
395069 CTGCCAAGAA
395079 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
395120 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
395161 ATGTATCGATAC
1 ATGTATCGATAC
395173 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:397642 original size:13 final size:13
Alignment explanation
Indices: 397624--397675 Score: 86
Period size: 13 Copynumber: 4.0 Consensus size: 13
397614 ATAATCACCC
* *
397624 TGTATCGATATAG
1 TGTATCGATACAA
397637 TGTATCGATACAA
1 TGTATCGATACAA
397650 TGTATCGATACAA
1 TGTATCGATACAA
397663 TGTATCGATACAA
1 TGTATCGATACAA
397676 AGAAAAATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:397686 original size:20 final size:20
Alignment explanation
Indices: 397661--397739 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
397651 GTATCGATAC
397661 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
397681 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
397706 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
397726 CATGTATCGATACA
1 AATGTATCGATACA
397740 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:401619 original size:21 final size:21
Alignment explanation
Indices: 401590--401634 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
401580 AAGTTTTCAT
*
401590 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
401610 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
401632 TTT
1 TTT
401635 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:403907 original size:21 final size:21
Alignment explanation
Indices: 403881--403956 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
403871 CTGCCAAGAA
403881 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
403902 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
403922 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
403943 ATGTATCGATACAT
1 ATGTATCGATACAT
403957 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:403926 original size:20 final size:20
Alignment explanation
Indices: 403901--403974 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
403891 ACATCTTTTT
403901 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
403921 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
403942 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
403962 CATGTATCGATAC
1 CATGTATCGATAC
403975 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:403938 original size:41 final size:41
Alignment explanation
Indices: 403881--403974 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
403871 CTGCCAAGAA
403881 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
403922 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
403963 ATGTATCGATAC
1 ATGTATCGATAC
403975 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:415281 original size:52 final size:51
Alignment explanation
Indices: 415143--415291 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
415133 CGAAATATAA
*
415143 AAATTTGCCTGCATGTATCGATACATTCATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTCATAGTGTATCGATACATCTGGGC
*
415194 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTCATAGTGTATCGATACATCTGGGC
***
415246 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTCAT-AGTGTATCGATACAT
415292 TTGAGTAATG
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
51 26 0.29
52 64 0.71
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTCATAGTGTATCGATACATCTGGGC
Found at i:416266 original size:39 final size:39
Alignment explanation
Indices: 416194--416353 Score: 106
Period size: 39 Copynumber: 3.9 Consensus size: 39
416184 GTGATAAAGA
* *
416194 TGCCAATATGCTGATTCACGGCCAACGATATTGGACTTG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTG
* ** *
416233 TGCCAATGTGCTGATTCAAGGCCAGTGGCATTGGACTTAAAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTT---------G
* * * *
416281 TGCCAATACGCTGATTCAAAGCCAACGATATTAGG-CTTA
1 TGCCAATATGCTGATTCAAGGCCAACGACATT-GGACTTG
* * *
416320 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGG
416354 TCTTAAAGTT
Statistics
Matches: 91, Mismatches: 20, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
38 2 0.02
39 58 0.64
48 29 0.32
49 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (39 bp):
TGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTG
Found at i:416352 original size:87 final size:88
Alignment explanation
Indices: 416194--416406 Score: 277
Period size: 87 Copynumber: 2.4 Consensus size: 88
416184 GTGATAAAGA
* *
416194 TGCCAATATGCTGATTCACGGCCAACGATATT-GGACTTGTGCCAATGTGCTGATTCAAGGCCAG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTAGG-CTTATGCCAATGTGCTGATTCAAGGCCAG
***
416258 TGGCATTGGACTTAAAG-ACAAGG
65 CAACATTGGACTTAAAGTACAAGG
* *
416281 TGCCAATACGCTGATTCAAAGCCAACGATATTAGGCTTATGCCAATGTGCTGATTCAAGGCCAGC
1 TGCCAATATGCTGATTCAAGGCCAACGATATTAGGCTTATGCCAATGTGCTGATTCAAGGCCAGC
* ****
416346 AACATTGGTCTTAAAGTTGTCGG
66 AACATTGGACTTAAAGTACAAGG
* *
416369 TGCCAATATGTTGATTCAAGGCCATCGATATTAGGCTT
1 TGCCAATATGCTGATTCAAGGCCAACGATATTAGGCTT
416407 TAAAGATAAA
Statistics
Matches: 108, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
87 70 0.65
88 38 0.35
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (88 bp):
TGCCAATATGCTGATTCAAGGCCAACGATATTAGGCTTATGCCAATGTGCTGATTCAAGGCCAGC
AACATTGGACTTAAAGTACAAGG
Found at i:416478 original size:138 final size:136
Alignment explanation
Indices: 416242--416543 Score: 401
Period size: 138 Copynumber: 2.2 Consensus size: 136
416232 GTGCCAATGT
* ** *
416242 GCTGATTCAAGGCCAGTGGCATT-GGAC-TTAAAGACAAGGTGCCAATACGCTGATTCAAAGCCA
1 GCTGATTCAAGGCCAGCGATATTAGG-CTTTAAAGAAAAGGTGCCAATACGCTGATTCAAAGCCA
* ** *
416305 ACGATATTAGGCTTATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGTTGTCGGT
65 ACGATATTAGGCTTATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGAT-AAGAT
* *
416370 GCCAATAT
129 GCCAACAC
* * * * *
416378 GTTGATTCAAGGCCATCGATATTAGGCTTTAAAGATAAAGGTGCCAATATGCTGGTTCAAGGCCA
1 GCTGATTCAAGGCCAGCGATATTAGGCTTTAAAGA-AAAGGTGCCAATACGCTGATTCAAAGCCA
* *
416443 GCGATATTAGGCTTATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGATAAGATG
65 ACGATATTAGGCTTATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGATAAGATG
*
416508 CCAACGC
130 CCAACAC
416515 GCTGATTCAAGGCCAGCGATATTAGGCTT
1 GCTGATTCAAGGCCAGCGATATTAGGCTT
416544 AGAAGAAGAC
Statistics
Matches: 143, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
136 19 0.13
137 43 0.30
138 81 0.57
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (136 bp):
GCTGATTCAAGGCCAGCGATATTAGGCTTTAAAGAAAAGGTGCCAATACGCTGATTCAAAGCCAA
CGATATTAGGCTTATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGATAAGATGC
CAACAC
Found at i:416533 original size:87 final size:89
Alignment explanation
Indices: 416369--416544 Score: 239
Period size: 87 Copynumber: 2.0 Consensus size: 89
416359 AAGTTGTCGG
* * * * * * * *
416369 TGCCAATATGTTGATTCAAGGCCATCGATATTAGGCTTTAAAGATAAAGGTGCCAATATGCTGGT
1 TGCCAATATGCTGATTCAAGGCCAGCAACATTAGGCTTTAAAGATAAAGATGCCAACACGCTGAT
416434 TCAAGGCCAGCGATATTAGGCTTA
66 TCAAGGCCAGCGATATTAGGCTTA
* * *
416458 TGCCAATGTGCTGATTCAAGGCCAGCAACATT-GGTTTTAAAGAT-AAGATGCCAACGCGCTGAT
1 TGCCAATATGCTGATTCAAGGCCAGCAACATTAGGCTTTAAAGATAAAGATGCCAACACGCTGAT
416521 TCAAGGCCAGCGATATTAGGCTTA
66 TCAAGGCCAGCGATATTAGGCTTA
416545 GAAGAAGACG
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
87 38 0.50
88 11 0.14
89 27 0.36
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (89 bp):
TGCCAATATGCTGATTCAAGGCCAGCAACATTAGGCTTTAAAGATAAAGATGCCAACACGCTGAT
TCAAGGCCAGCGATATTAGGCTTA
Found at i:416633 original size:27 final size:27
Alignment explanation
Indices: 416566--416683 Score: 94
Period size: 29 Copynumber: 4.2 Consensus size: 27
416556 CACCAACTTG
* *
416566 TGTGGGCTTTTGAAAGGGTTG-CATCAACT
1 TGTGGGC-TTTG-AAGGG-TGCCACCGACT
* * *
416595 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGC-TTTGAAGGGTGCCACCGACT
416623 TGTGGGCTTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTG-AA-GGGTGCCACCGACT
** * *
416652 TGTGGGCTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAGGGTGCCACCGACT
416679 TGTGG
1 TGTGG
416684 ACTTAAAAGG
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
27 23 0.31
28 19 0.26
29 32 0.43
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.31
Consensus pattern (27 bp):
TGTGGGCTTTGAAGGGTGCCACCGACT
Found at i:416654 original size:29 final size:30
Alignment explanation
Indices: 416566--416660 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 30
416556 CACCAACTTG
* * *
416566 TGTGGGCTTTTGAAAGGGTTG-CATCAACT
1 TGTGGGCTTTTGAAAGGGGTGCCACCGACT
* * *
416595 TGTGTGCTTTTG-AA-GGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGGGTGCCACCGACT
416623 TGTGGGC-TTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTTGAAAGGGGTGCCACCGACT
416652 TGTGGGCTT
1 TGTGGGCTT
416661 AAAAGGGTGC
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
27 9 0.16
28 15 0.27
29 30 0.55
30 1 0.02
ACGTcount: A:0.16, C:0.17, G:0.34, T:0.34
Consensus pattern (30 bp):
TGTGGGCTTTTGAAAGGGGTGCCACCGACT
Found at i:416682 original size:56 final size:57
Alignment explanation
Indices: 416566--416683 Score: 132
Period size: 56 Copynumber: 2.1 Consensus size: 57
416556 CACCAACTTG
* * * ** * *
416566 TGTGGGCTTTTGAAAGGGTTGCATCAACTTGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGGGTGCACCAACTTGTGGGCTTTAAAAGGGTGCCACGGACT
* *
416623 TGTGGGC-TTTGAAAGGGGTGCCACCGACTTGTGGGC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTTGAAAGGGGTG-CACCAACTTGTGGGCTTTAAAAGGGTGCCACGGACT
416679 TGTGG
1 TGTGG
416684 ACTTAAAAGG
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
56 32 0.63
57 19 0.37
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.31
Consensus pattern (57 bp):
TGTGGGCTTTTGAAAGGGGTGCACCAACTTGTGGGCTTTAAAAGGGTGCCACGGACT
Found at i:416688 original size:27 final size:27
Alignment explanation
Indices: 416607--416693 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
416597 TGTGCTTTTG
* * *
416607 AAGGTTGCCACTGACTTGTGGGCTTTGAA
1 AAGGGTGCCACCGACTTGTGGAC-TT-AA
* *
416636 AGGGGTGCCACCGACTTGTGGGCTTAA
1 AAGGGTGCCACCGACTTGTGGACTTAA
* *
416663 AAGGGTGCCACGGAGTTGTGGACTTAA
1 AAGGGTGCCACCGACTTGTGGACTTAA
416690 AAGG
1 AAGG
416694 AAAAAGAGTG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 29 0.57
28 2 0.04
29 20 0.39
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (27 bp):
AAGGGTGCCACCGACTTGTGGACTTAA
Found at i:416699 original size:34 final size:34
Alignment explanation
Indices: 416661--416789 Score: 170
Period size: 34 Copynumber: 3.8 Consensus size: 34
416651 TTGTGGGCTT
*
416661 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
416695 AAAAGAGTGCCATGGAGTTGTGGGCTTAAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTT-AAAAGGA
* * *
416730 AAAAGAGTGCCATGGAGTTGTGGGCTTAAAAGTA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
416764 AAAAG-GTGCCACGGACTCGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
416790 TTGACAGGGT
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
33 17 0.20
34 35 0.41
35 34 0.40
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.20
Consensus pattern (34 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:416725 original size:27 final size:28
Alignment explanation
Indices: 416694--416760 Score: 71
Period size: 35 Copynumber: 2.1 Consensus size: 28
416684 ACTTAAAAGG
416694 AAAAAGAGTGCCATGGAGTTGTGGGCTT
1 AAAAAGAGTGCCATGGAGTTGTGGGCTT
416722 AAAAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTT
1 -------AAAAAGAGTGCCATGGAGTTGTGGGCTT
416757 AAAA
1 AAAA
416761 GTAAAAAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
28 4 0.12
35 28 0.88
ACGTcount: A:0.37, C:0.09, G:0.33, T:0.21
Consensus pattern (28 bp):
AAAAAGAGTGCCATGGAGTTGTGGGCTT
Found at i:416734 original size:35 final size:34
Alignment explanation
Indices: 416661--416774 Score: 176
Period size: 34 Copynumber: 3.4 Consensus size: 34
416651 TTGTGGGCTT
* * *
416661 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCATGGAGTTGTGGGCTTAAAAGGA
416695 AAAAGAGTGCCATGGAGTTGTGGGCTTAAAAAGGA
1 AAAAGAGTGCCATGGAGTTGTGGGCTT-AAAAGGA
*
416730 AAAAGAGTGCCATGGAGTTGTGGGCTTAAAAGTA
1 AAAAGAGTGCCATGGAGTTGTGGGCTTAAAAGGA
416764 AAAAG-GTGCCA
1 AAAAGAGTGCCA
416775 CGGACTCGTG
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
33 6 0.08
34 35 0.47
35 34 0.45
ACGTcount: A:0.37, C:0.11, G:0.33, T:0.19
Consensus pattern (34 bp):
AAAAGAGTGCCATGGAGTTGTGGGCTTAAAAGGA
Found at i:418242 original size:1 final size:1
Alignment explanation
Indices: 418238--418393 Score: 123
Period size: 1 Copynumber: 156.0 Consensus size: 1
418228 CTTTTTGTTG
* * * * * * *
418238 TTTTTTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTTTTTTTTTGTTTTTTCTTTGTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * * *
418303 TTTGTTTTTTTTCTTTTGTTTGTTTTGTTTTTTTTTTGTTTTTTCTTTGTTTTCTTTTCTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
418368 TTTTTTCTTTTGTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
418394 GTGGAGGACG
Statistics
Matches: 113, Mismatches: 42, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 113 1.00
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (1 bp):
T
Found at i:418256 original size:13 final size:13
Alignment explanation
Indices: 418240--418392 Score: 162
Period size: 13 Copynumber: 10.9 Consensus size: 13
418230 TTTTGTTGTT
418240 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
*
418253 TTTTTTTGTTTTG
1 TTTTTTTTTTTTG
*
418266 TTTTTTTTTTTTT
1 TTTTTTTTTTTTG
418279 TTTGTTTTTTCTTTG
1 TTT-TTTTTT-TTTG
*
418294 TTTTTTTTCTTTG
1 TTTTTTTTTTTTG
418307 TTTTTTTTCTTTTG
1 TTTTTTTT-TTTTG
*
418321 TTTGTTTTGTTTTTTT
1 -TT-TTTT-TTTTTTG
418337 TTTGTTTTTTCTTTG
1 TTT-TTTTTT-TTTG
*
418352 TTTTCTTTTCTTTG
1 TTTT-TTTTTTTTG
418366 TTTTTTTTCTTTTG
1 TTTTTTTT-TTTTG
418380 TTTGTTTTTTTTT
1 TTT-TTTTTTTTT
418393 TGTGGAGGAC
Statistics
Matches: 119, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
13 42 0.35
14 39 0.33
15 28 0.24
16 8 0.07
17 2 0.02
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:418287 original size:41 final size:39
Alignment explanation
Indices: 418229--418393 Score: 154
Period size: 41 Copynumber: 4.2 Consensus size: 39
418219 ATCCGGACCC
* * * *
418229 TTTTTGTTGTTTTTT-TTTTTTTTGTTTTTTTGTTTTGT
1 TTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTGT
*
418267 TTTTTTTTTTTTTTTGTTTTTTCTTTGTTTTTTTTCTTTGT
1 TTTTTTTTTTTTTTTGTTTTTT-TTT-TTTTTTTTTTTTGT
* * *
418308 TTTTTTTCTTTTGTTTGTTTTGTTTTTTTTTTGTTTTTTCT
1 TTTTTTT-TTTTTTTTGTTTT-TTTTTTTTTTTTTTTTTGT
* * * * *
418349 TTGTTTTCTTTTCTTTGTTTTTTTTCTTTTGTTTGTTT-T
1 TT-TTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTGT
418388 TTTTTT
1 TTTTTT
418394 GTGGAGGACG
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
38 17 0.16
39 9 0.08
40 15 0.14
41 44 0.42
42 19 0.18
43 2 0.02
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (39 bp):
TTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTGT
Found at i:418298 original size:54 final size:55
Alignment explanation
Indices: 418240--418393 Score: 238
Period size: 58 Copynumber: 2.7 Consensus size: 55
418230 TTTTGTTGTT
* *
418240 TTTTTTTTTTTTG-TTTTTTTGTTTTGTTTTTTTTTTTTTTTTGTTTTTTCTTTG
1 TTTTTTTTCTTTGTTTTTTTTCTTTTGTTTTTTTTTTTTTTTTGTTTTTTCTTTG
418294 TTTTTTTTCTTTGTTTTTTTTCTTTTGTTTGTTTTGTTTTTTTTTTGTTTTTTCTTTG
1 TTTTTTTTCTTTGTTTTTTTTCTTTTG-TT-TTTT-TTTTTTTTTTGTTTTTTCTTTG
*
418352 TTTTCTTTTCTTTGTTTTTTTTCTTTTGTTTGTTTTTTTTTT
1 TTTT-TTTTCTTTGTTTTTTTTCTTTTGTTTTTTTTTTTTTT
418394 GTGGAGGACG
Statistics
Matches: 92, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
54 12 0.13
55 12 0.13
56 10 0.11
57 7 0.08
58 28 0.30
59 23 0.25
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (55 bp):
TTTTTTTTCTTTGTTTTTTTTCTTTTGTTTTTTTTTTTTTTTTGTTTTTTCTTTG
Found at i:418328 original size:59 final size:59
Alignment explanation
Indices: 418231--418393 Score: 253
Period size: 59 Copynumber: 2.8 Consensus size: 59
418221 CCGGACCCTT
418231 TTTGTTGTTTTTT-TTT-TTTTTGTTT-TTTTGTTTTGTTTTTTTTTTTTTTTTGTTTTTTC
1 TTTGTT-TTTTTTCTTTGTTTTT-TTTCTTTTG-TTTGTTTTTTTTTTTTTTTTGTTTTTTC
*
418290 TTTGTTTTTTTTCTTTGTTTTTTTTCTTTTGTTTG-TTTTGTTTTTTTTTTGTTTTTTC
1 TTTGTTTTTTTTCTTTGTTTTTTTTCTTTTGTTTGTTTTTTTTTTTTTTTTGTTTTTTC
418348 TTTGTTTTCTTTTCTTTGTTTTTTTTCTTTTGTTTGTTTTTTTTTT
1 TTTGTTTT-TTTTCTTTGTTTTTTTTCTTTTGTTTGTTTTTTTTTT
418394 GTGGAGGACG
Statistics
Matches: 97, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
58 36 0.37
59 43 0.44
60 18 0.19
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (59 bp):
TTTGTTTTTTTTCTTTGTTTTTTTTCTTTTGTTTGTTTTTTTTTTTTTTTTGTTTTTTC
Found at i:418394 original size:54 final size:53
Alignment explanation
Indices: 418240--418395 Score: 206
Period size: 54 Copynumber: 2.8 Consensus size: 53
418230 TTTTGTTGTT
* * *
418240 TTTTTTTTTTTTGTTTTTTTGT-TTTGTTTTTTTTTTTTTTTTGTTTTTTCTTTG
1 TTTTTTTTCTTTGTTTTTTT-TCTTT-TGTTTGTTTTTTTTTTGTTTTTTCTTTG
418294 TTTTTTTTCTTTGTTTTTTTTCTTTTGTTTGTTTTGTTTTTTTTTTGTTTTTTCTTTG
1 TTTTTTTTCTTTGTTTTTTTTC---T-TTTG-TTTGTTTTTTTTTTGTTTTTTCTTTG
418352 TTTTCTTTTCTTTGTTTTTTTTCTTTTGTTTGTTTTTTTTTTGT
1 TTTT-TTTTCTTTGTTTTTTTTCTTTTGTTTGTTTTTTTTTTGT
418396 GGAGGACGCC
Statistics
Matches: 92, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
53 1 0.01
54 35 0.38
55 4 0.04
56 1 0.01
57 2 0.02
58 31 0.34
59 18 0.20
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (53 bp):
TTTTTTTTCTTTGTTTTTTTTCTTTTGTTTGTTTTTTTTTTGTTTTTTCTTTG
Found at i:432364 original size:52 final size:51
Alignment explanation
Indices: 432263--432373 Score: 152
Period size: 52 Copynumber: 2.2 Consensus size: 51
432253 AAAATTTGCC
* * **
432263 TCGATACATCTGGCAAATTTGCCTGTATGTATCGATACATTTCATAGTGTA
1 TCGATACATCTGGCAAATTTGCCTGCATGTATCAATACATAACATAGTGTA
*
432314 TCGATACATCTGGGCAAATTTGCCTGCATGTATCAATACA-AAGATCAGTGTA
1 TCGATACATCT-GGCAAATTTGCCTGCATGTATCAATACATAACAT-AGTGTA
432366 TCGATACA
1 TCGATACA
432374 ATGTATCGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
51 13 0.25
52 40 0.75
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (51 bp):
TCGATACATCTGGCAAATTTGCCTGCATGTATCAATACATAACATAGTGTA
Found at i:432380 original size:13 final size:13
Alignment explanation
Indices: 432362--432386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
432352 CAAAGATCAG
432362 TGTATCGATACAA
1 TGTATCGATACAA
432375 TGTATCGATACA
1 TGTATCGATACA
432387 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:432502 original size:32 final size:33
Alignment explanation
Indices: 432434--432502 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
432424 TTCGTAACTG
*
432434 TACATTGTATCGATACAAAACTTTATGTGTCAA
1 TACATTGTATCGATACAAAACTTTATGTATCAA
* *
432467 TACATTGTATCGATACAACAC-TTATGTATCGA
1 TACATTGTATCGATACAAAACTTTATGTATCAA
432499 TACA
1 TACA
432503 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
TACATTGTATCGATACAAAACTTTATGTATCAA
Found at i:437910 original size:10 final size:10
Alignment explanation
Indices: 437892--437953 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
437882 TCCTTCGTAC
437892 CAAAAAAAAA
1 CAAAAAAAAA
*
437902 CAAAGAAAAA
1 CAAAAAAAAA
437912 CAAACAAACAAA
1 CAAA-AAA-AAA
437924 CAAACAAAAAA
1 CAAA-AAAAAA
* *
437935 -ACAAATAAA
1 CAAAAAAAAA
*
437944 TAAAAAAAAA
1 CAAAAAAAAA
437954 GGTCCAGATG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 5 0.12
10 22 0.51
11 5 0.12
12 11 0.26
ACGTcount: A:0.82, C:0.13, G:0.02, T:0.03
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:437916 original size:4 final size:4
Alignment explanation
Indices: 437909--437939 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
437899 AAACAAAGAA
*
437909 AAAC AAAC AAAC AAAC AAAC AAAA AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
437940 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:437924 original size:12 final size:12
Alignment explanation
Indices: 437893--437939 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
437883 CCTTCGTACC
437893 AAAAAA-AAACAA
1 AAAAAACAAAC-A
437905 AGAAAAACAAACA
1 A-AAAAACAAACA
*
437918 AACAAACAAACA
1 AAAAAACAAACA
437930 AAAAAACAAA
1 AAAAAACAAA
437940 TAAATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 20 0.65
13 7 0.23
14 4 0.13
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAAACAAACA
Found at i:439259 original size:29 final size:28
Alignment explanation
Indices: 439164--439656 Score: 622
Period size: 28 Copynumber: 17.5 Consensus size: 28
439154 GGTACATCTC
439164 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
439192 TTCAAAGCCCATAAATTAGTGGCA-CACT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
* **
439220 TTCAAAGCCCACAAGTCAGTTGCATTTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
439248 TCTCAAAACCCACAAGTCAGTGGCATCCT
1 T-TCAAAGCCCACAAGTCAGTGGCATCCT
439277 TCTCAAAGCCCACAAGTCAGTGGCATCC-
1 T-TCAAAGCCCACAAGTCAGTGGCATCCT
* * *
439305 TTCTATAAGCCCATAAGCCAGTGGCGTCCT
1 TTC-A-AAGCCCACAAGTCAGTGGCATCCT
* *
439335 TTCAAAGCCCACAAGCCTAGTGGCGTCCT
1 TTCAAAGCCCACAAGTC-AGTGGCATCCT
*
439364 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
439392 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
439420 TTCAAAGCCCACAAGTCAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
439449 TTCAAAGCCCACAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* **
439476 TTGCATAGCCCATGAGTCAGTGGCA-CCTT
1 TT-CAAAGCCCACAAGTCAGTGGCATCC-T
*
439505 TTCAAAGCCTACAAGTCAGTGGCATCC-
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
439532 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
439560 TTCAAAGCCCACGAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
439588 TTCAAAGCCCGCAAGTCAGAGGCA-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
439615 TCTCAAAACCCACAAGTCAGTGGCATCCTT
1 T-TCAAAGCCCACAAGTCAGTGGCATCC-T
439645 TTC-AAGCCCACA
1 TTCAAAGCCCACA
439657 CAAGTCGATG
Statistics
Matches: 405, Mismatches: 44, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
27 35 0.09
28 233 0.58
29 132 0.33
30 5 0.01
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:439432 original size:85 final size:84
Alignment explanation
Indices: 439164--439656 Score: 602
Period size: 85 Copynumber: 5.8 Consensus size: 84
439154 GGTACATCTC
* * * *
439164 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAATTAGTGGCACACTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* **
439229 CACAAGTCAGTTGCATTTT
66 CACAAGTCAGTGGCATCCT
* *
439248 TCTCAAAACCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATCC-TTCTATA
1 T-TCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGCCCACAAGTCAGTGGCACCCTTTC-A-A
* * *
439312 AGCCCATAAGCCAGTGGCGTCCT
62 AGCCCACAAGTCAGTGGCATCCT
* *
439335 TTCAAAGCCCACAAGCCTAGTGGCGTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTC-AGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
439400 CCACAAGTCAGTGGCATCCT
65 CCACAAGTCAGTGGCATCCT
* * *
439420 TTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTGCATAG
1 TTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTT-CAAAG
**
439484 CCCATGAGTCAGTGGCA-CCTT
64 CCCACAAGTCAGTGGCATCC-T
* *
439505 TTCAAAGCCTACAAGTCAGTGGCATCC-TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* * *
439569 CACGAGTTAGTGGCATCTT
66 CACAAGTCAGTGGCATCCT
* * * *
439588 TTCAAAGCCCGCAAGTCAGAGGCA-CCTTCTCAAAACCCACAAGTCAGTGGCATCCTTTTC-AAG
1 TTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAG
439651 CCCACA
64 CCCACA
439657 CAAGTCGATG
Statistics
Matches: 355, Mismatches: 40, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
82 2 0.01
83 66 0.19
84 50 0.14
85 142 0.40
86 62 0.17
87 33 0.09
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (84 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
CACAAGTCAGTGGCATCCT
Found at i:443483 original size:47 final size:46
Alignment explanation
Indices: 443340--443903 Score: 281
Period size: 47 Copynumber: 12.0 Consensus size: 46
443330 GATATGACTA
* * * *
443340 TATTGGCGTTAGGACCTGGTCAAACTCAAATTCCACTCTCGTTTGACTG
1 TATTGGCGTTAGGACCTAGTCAAACTC--TTTCCA-TCTTGTTTAACTG
* * ** * *
443389 TA-T--CGATTACCGCCCTAGTCAAACTC-TTCCATCATCATTTGATTG
1 TATTGGCG-TTA-GGACCTAGTCAAACTCTTTCCATC-TTGTTTAACTG
* *
443434 TATTGGCGTTAGGATCTAGTCAAATTCTTTCCATTCTTGTTTAACTG
1 TATTGGCGTTAGGACCTAGTCAAACTCTTTCCA-TCTTGTTTAACTG
* * * * *
443481 TATTAGCGTTAGGAGCTGGTCAAACT-TAAATTCCACTCTCGTTTAGCTG
1 TATTGGCGTTAGGACCTAGTCAAACTCT---TTCCA-TCTTGTTTAACTG
** * * *
443530 TATT-G-GTTATTACCCTTGTCAAACTC-TTCCATCATCGTTTGACTG
1 TATTGGCGTTAGGA-CCTAGTCAAACTCTTTCCATC-TTGTTTAACTG
* * * * *
443575 TATTGGCATTAAGACCTAGTCAAACTCTTTTCACCCTT-ATTATACTG
1 TATTGGCGTTAGGACCTAGTCAAACTCTTTCCA-TCTTGTTTA-ACTG
* * *
443622 TATTGGAGTTAGGACCTAGTCAAACTCTTTCCACCTTCGTTTGACTG
1 TATTGGCGTTAGGACCTAGTCAAACTCTTTCCATCTT-GTTTAACTG
* * * ** *
443669 TATTGGCGTTAAGACCTGGTCAAACTCAAATTCCACTCTCATTTGACTG
1 TATTGGCGTTAGGACCTAGTCAAACTC--TTTCCA-TCTTGTTTAACTG
* ** * ** *
443718 TA-TCG-GTTACCACCCTGGTCAAACTC-TTCCATCATCATTTGACTG
1 TATTGGCGTTAGGA-CCTAGTCAAACTCTTTCCATC-TTGTTTAACTG
* * ** * *
443763 TATTGGCGTTATGACCAAGTCAAACTCTTTCCATCCTCATTTGATTG
1 TATTGGCGTTAGGACCTAGTCAAACTCTTTCCAT-CTTGTTTAACTG
* * * * *
443810 TATTGGCATTAGGACCTAGTCAAACTCTTTCCAACCATGTTTGATTG
1 TATTGGCGTTAGGACCTAGTCAAACTCTTTCC-ATCTTGTTTAACTG
* * * * *
443857 CATTGGCGTTAGGGCCTGGTTAAACT-TTTCTTATCCTTGTTTAACTG
1 TATTGGCGTTAGGACCTAGTCAAACTCTTTC-CAT-CTTGTTTAACTG
443904 CTTCAGCATT
Statistics
Matches: 408, Mismatches: 74, Indels: 68
0.74 0.13 0.12
Matches are distributed among these distances:
44 6 0.01
45 52 0.13
46 53 0.13
47 209 0.51
48 49 0.12
49 37 0.09
50 2 0.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (46 bp):
TATTGGCGTTAGGACCTAGTCAAACTCTTTCCATCTTGTTTAACTG
Found at i:443604 original size:141 final size:141
Alignment explanation
Indices: 443340--443671 Score: 395
Period size: 141 Copynumber: 2.4 Consensus size: 141
443330 GATATGACTA
* *
443340 TATTGGCGTTAGGACCTGGTCAAACTCAAATTCCACTCTCGTTTGACTGTATCGATTACCGCCCT
1 TATTAGCGTTAGGACCTGGTCAAACTCAAATTCCACTCTCGTTTGACTGTATCGATTACCACCCT
* * * * *
443405 AGTCAAACTCTTCCATCATCATTTGATTGTATTGGCGTTAGGATCTAGTCAAATTCTTTCCATTC
66 AGTCAAACTCTTCCATCATCATTTGACTGTATTGGCATTAAGACCTAGTCAAACTCTTTCCATTC
443470 TTGTTTAACTG
131 TTGTTTAACTG
* * * * **
443481 TATTAGCGTTAGGAGCTGGTCAAACTTAAATTCCACTCTCGTTT-AGCTGTATTGGTTATTACCC
1 TATTAGCGTTAGGACCTGGTCAAACTCAAATTCCACTCTCGTTTGA-CTGTATCGATTACCACCC
* * * **
443545 TTGTCAAACTCTTCCATCATCGTTTGACTGTATTGGCATTAAGACCTAGTCAAACTCTTTTCACC
65 TAGTCAAACTCTTCCATCATCATTTGACTGTATTGGCATTAAGACCTAGTCAAACTCTTTCCATT
*
443610 CTT-ATTATACTG
130 CTTGTTTA-ACTG
* * * *
443622 TATTGGAGTTAGGACCTAGTCAAACTC--TTTCCAC-CTTCGTTTGACTGTAT
1 TATTAGCGTTAGGACCTGGTCAAACTCAAATTCCACTC-TCGTTTGACTGTAT
443672 TGGCGTTAAG
Statistics
Matches: 162, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
138 1 0.01
139 18 0.11
140 5 0.03
141 138 0.85
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (141 bp):
TATTAGCGTTAGGACCTGGTCAAACTCAAATTCCACTCTCGTTTGACTGTATCGATTACCACCCT
AGTCAAACTCTTCCATCATCATTTGACTGTATTGGCATTAAGACCTAGTCAAACTCTTTCCATTC
TTGTTTAACTG
Found at i:443749 original size:188 final size:187
Alignment explanation
Indices: 443405--443882 Score: 604
Period size: 188 Copynumber: 2.5 Consensus size: 187
443395 TTACCGCCCT
* * * * * * *
443405 AGTCAAACTC-TTCCATCATCATTTGATTGTATTGGCGTTAGGATCTAGTCAAATTCTTTCCATT
1 AGTCAAACTCTTTCCACCCTCATTTGACTGTATTGGAGTTAGGACCTAGTCAAACTCTTTCCA-C
* * * * * *
443469 CTTGTTTAACTGTATTAGCGTTAGGAGCTGGTCAAACTTAAATTCCACTCTCGTTTAGCTGTATT
65 CTTGTTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCAAATTCCACTCTCATTTAGCTGTATC
** * * *
443534 GGTTATTACCCTTGTCAAACTCTTCCATCATCGTTTGACTGTATTGGCATTAAGACCT
130 GGTTACCACCCTGGTCAAACTCTTCCATCATCATTTGACTGTATTGGCATTAAGACCA
* *
443592 AGTCAAACTCTTTTCACCCTTATTAT-ACTGTATTGGAGTTAGGACCTAGTCAAACTCTTTCCAC
1 AGTCAAACTCTTTCCACCCTCATT-TGACTGTATTGGAGTTAGGACCTAGTCAAACTCTTTCCAC
*
443656 CTTCGTTTGACTGTATTGGCGTTAAGACCTGGTCAAACTCAAATTCCACTCTCATTT-GACTGTA
65 CTT-GTTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCAAATTCCACTCTCATTTAG-CTGTA
* *
443720 TCGGTTACCACCCTGGTCAAACTCTTCCATCATCATTTGACTGTATTGGCGTTATGACCA
128 TCGGTTACCACCCTGGTCAAACTCTTCCATCATCATTTGACTGTATTGGCATTAAGACCA
* *
443780 AGTCAAACTCTTTCCATCCTCATTTGATTGTATTGGCA-TTAGGACCTAGTCAAACTCTTTCCAA
1 AGTCAAACTCTTTCCACCCTCATTTGACTGTATTGG-AGTTAGGACCTAGTCAAACTCTTTCC-A
* * * * *
443844 CCATGTTTGATTGCATTGGCGTTAGGGCCTGGTTAAACT
64 CCTTGTTTGACTGTATTGGCGTTAGGACCTGGTCAAACT
443883 TTTCTTATCC
Statistics
Matches: 251, Mismatches: 33, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
187 15 0.06
188 230 0.92
189 6 0.02
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (187 bp):
AGTCAAACTCTTTCCACCCTCATTTGACTGTATTGGAGTTAGGACCTAGTCAAACTCTTTCCACC
TTGTTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCAAATTCCACTCTCATTTAGCTGTATCG
GTTACCACCCTGGTCAAACTCTTCCATCATCATTTGACTGTATTGGCATTAAGACCA
Found at i:443882 original size:94 final size:92
Alignment explanation
Indices: 443406--443886 Score: 390
Period size: 94 Copynumber: 5.1 Consensus size: 92
443396 TACCGCCCTA
* * * * *
443406 GTCAAACTC-TTCCATCATCATTTGATTGTATTGGCGTTAGGATCTAGTCAAATTCTTTCCATTC
1 GTCAAACTCTTTCCA-CCTCATTTGACTGTATTGG-ATTAGGACCTAGTCAAACTCTTTCCA-TC
* * * * *
443470 -TTGTTTAACTGTATTAGCGTTAGGAGCTG
63 ATCGTTTGACTGTATTGGCGTTAAGACCTG
* ** *
443499 GTCAAACT-TAAATTCCACTCTCGTTT-AGCTGTATTGG-TTATTACCCTTGTCAAACTC-TTCC
1 GTCAAACTCT---TTCCAC-CTCATTTGA-CTGTATTGGATTAGGA-CCTAGTCAAACTCTTTCC
* *
443560 ATCATCGTTTGACTGTATTGGCATTAAGACCTA
60 ATCATCGTTTGACTGTATTGGCGTTAAGACCTG
* * *
443593 GTCAAACTCTTTTCACCCTTATTAT-ACTGTATTGGAGTTAGGACCTAGTCAAACTCTTTCCACC
1 GTCAAACTCTTTCCA-CCTCATT-TGACTGTATTGGA-TTAGGACCTAGTCAAACTCTTTCCATC
*
443657 TTCGTTTGACTGTATTGGCGTTAAGACCTG
63 ATCGTTTGACTGTATTGGCGTTAAGACCTG
* * ** *
443687 GTCAAACTCAAATTCCACTCTCATTTGACTGTATCGG-TTACCACCCTGGTCAAACTC-TTCCAT
1 GTCAAACTC--TTTCCAC-CTCATTTGACTGTATTGGATTAGGA-CCTAGTCAAACTCTTTCCAT
* * **
443750 CATCATTTGACTGTATTGGCGTTATGACCAA
62 CATCGTTTGACTGTATTGGCGTTAAGACCTG
* *
443781 GTCAAACTCTTTCCATCCTCATTTGATTGTATTGGCATTAGGACCTAGTCAAACTCTTTCCAACC
1 GTCAAACTCTTTCCA-CCTCATTTGACTGTATTGG-ATTAGGACCTAGTCAAACTCTTTCC-ATC
* * * *
443846 AT-GTTTGATTGCATTGGCGTTAGGGCCTG
63 ATCGTTTGACTGTATTGGCGTTAAGACCTG
*
443875 GTTAAACT-TTTC
1 GTCAAACTCTTTC
443887 TTATCCTTGT
Statistics
Matches: 311, Mismatches: 53, Indels: 48
0.75 0.13 0.12
Matches are distributed among these distances:
92 38 0.12
93 42 0.14
94 164 0.53
95 31 0.10
96 36 0.12
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (92 bp):
GTCAAACTCTTTCCACCTCATTTGACTGTATTGGATTAGGACCTAGTCAAACTCTTTCCATCATC
GTTTGACTGTATTGGCGTTAAGACCTG
Found at i:444196 original size:85 final size:86
Alignment explanation
Indices: 444005--444196 Score: 233
Period size: 86 Copynumber: 2.2 Consensus size: 86
443995 GTATCGCTTT
* * *
444005 TCATCCCTTATTTACTTGTCTGCTCTATCCCTAGTAAACCTCTTTATCCCCTTGGTGACCCATAA
1 TCATCCCTTATTTACTTGTCGGCTATATCCCTAGTAAACCCCTTTATCCCCTTGGTGACCCATAA
*
444070 GCTTAGTCCCCAGACAACTTG
66 GCTTAGTACCCAGACAACTTG
* * * * ** **
444091 CCATCCCTTATTTACTTGTCGGCTATATCCTTGGTAAACCCCTTTATCCCTTTGGTGACCTGTTG
1 TCATCCCTTATTTACTTGTCGGCTATATCCCTAGTAAACCCCTTTATCCCCTTGGTGACCCATAA
** *
444156 GCTT-GTACCTGGTCAACTTG
66 GCTTAGTACCCAGACAACTTG
*
444176 TCATCCCTTATTTACCTGTCG
1 TCATCCCTTATTTACTTGTCG
444197 ACTCTGTCCC
Statistics
Matches: 89, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
85 31 0.35
86 58 0.65
ACGTcount: A:0.18, C:0.31, G:0.14, T:0.38
Consensus pattern (86 bp):
TCATCCCTTATTTACTTGTCGGCTATATCCCTAGTAAACCCCTTTATCCCCTTGGTGACCCATAA
GCTTAGTACCCAGACAACTTG
Found at i:444638 original size:13 final size:13
Alignment explanation
Indices: 444620--444644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
444610 ATCACTTAAA
444620 TGTATCGATACAT
1 TGTATCGATACAT
444633 TGTATCGATACA
1 TGTATCGATACA
444645 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:444695 original size:52 final size:51
Alignment explanation
Indices: 444633--444781 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
444623 ATCGATACAT
**
444633 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGAAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGAAAATTTGCCCAGA
* * *
444685 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGAAAATTTGCCCAGA
*
444737 TGTATCGATACACTATTCAATGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGAAAATTT
444782 TCATATTTCG
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.97
53 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGAAAATTTGCCCAGA
Found at i:449303 original size:164 final size:160
Alignment explanation
Indices: 448973--449468 Score: 471
Period size: 164 Copynumber: 3.0 Consensus size: 160
448963 TTAAACATAA
* * * * **
448973 AAATTCTCCAAATATTATCATTTAATAAT-ACCATCAAATCATTTTTGAAAAATTC-TTTTTATT
1 AAATTCT-CAAATATCATCATTTAAT--TCA-TATTAAATCAGTTTTGAAAAATTCATTCAT-TT
* * * * * * * *
449036 TCATGAGTTATTAA-TTTTCCTTTAAAAATCTCTTGTTTTCGAAATATGGAGTCTTCTATTCCGT
61 TCATGAGTTTTTAATTTTTTC-TTGAAATTCTC-TATTTTCGAAATATAGAATTTTCTATTCCGT
* * **
449100 AAATTTTTTCGAGGAGATTTTTCTTGGTTTTAATTTTT
124 AAA-TTTTTCGGGGGGATTTTTCTTATTTTTAATTTTT
* * * *
449138 AAATTC-CAAAATATTATTATTTATTTCATATTAAATCAGTTTTTAAAAATTCATTCATTTTCAT
1 AAATTCTC-AAATATCATCATTTAATTCATATTAAATCAGTTTTGAAAAATTCATTCATTTTCAT
* * * * *
449202 GAGTTTTTCATTTTTTCTTTGAATTTTTTCTATTTTCGAAATATAGAATTTTCTACTCTGTAAAT
65 GAGTTTTTAATTTTTTC-TTGAA-ATTCTCTATTTTCGAAATATAGAATTTTCTATTCCGTAAAT
449267 GTTTTCGGGGGGATTTTTCTTAATTTTTAATTTTT
128 -TTTTCGGGGGGATTTTTCTT-ATTTTTAATTTTT
* *
449302 AAAATTCTTCAAATATCATCATTTAATTCATATTAAATCAGTTTTGAAATATTCATTTATTTTCA
1 -AAATTC-TCAAATATCATCATTTAATTCATATTAAATCAGTTTTGAAAAATTCATTCATTTTCA
* * *
449367 TGAGTTTTTAATTTTTTCTTGAAATTCTCTATTTTCCAAA-AAACTGAATTTTCTATTCCATAAA
64 TGAGTTTTTAATTTTTTCTTGAAATTCTCTATTTTCGAAATATA--GAATTTTCTATTCCGTAAA
* * **
449431 TTTTTTGGGGGGATTTTTCTCGATTTAAAATTTTT
127 TTTTTCGGGGGGATTTTTCT-TATTTTTAATTTTT
449466 AAA
1 AAA
449469 ATTTATCTAA
Statistics
Matches: 275, Mismatches: 43, Indels: 28
0.79 0.12 0.08
Matches are distributed among these distances:
162 36 0.13
163 66 0.24
164 72 0.26
165 34 0.12
166 66 0.24
167 1 0.00
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.50
Consensus pattern (160 bp):
AAATTCTCAAATATCATCATTTAATTCATATTAAATCAGTTTTGAAAAATTCATTCATTTTCATG
AGTTTTTAATTTTTTCTTGAAATTCTCTATTTTCGAAATATAGAATTTTCTATTCCGTAAATTTT
TCGGGGGGATTTTTCTTATTTTTAATTTTT
Found at i:449358 original size:166 final size:161
Alignment explanation
Indices: 449008--449471 Score: 479
Period size: 166 Copynumber: 2.8 Consensus size: 161
448998 TAATACCATC
* ** * * * * *
449008 AAATCATTTTTGAAAAATTC-TTTTTATTTCATGAGTTATTAA-TTTTCCTTTAAAAATCTCTTG
1 AAATCAGTTTTGAAAAATTCATTCAT-TTTCATGAGTTTTTAATTTTTTC-TTGAAATTCTC-TA
* * * * * **
449071 TTTTCGAAATATGGAGTCTTCTATTCCGTAAATTTTTTCGAGGAGATTTTTCTTGGTTTTAATTT
63 TTTTCGAAATATAGAATTTTCTATTCCGTAAA-TTTTTCGGGGGGATTTTTCTTATTTTTAATTT
* * *
449136 TT-AAATTCCAAAATATTATTATTTATTTCATATT
127 TTAAAATTCCAAAATATCATCATTTAATTCATATT
* * * *
449170 AAATCAGTTTTTAAAAATTCATTCATTTTCATGAGTTTTTCATTTTTTCTTTGAATTTTTTCTAT
1 AAATCAGTTTTGAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTC-TTGAA-ATTCTCTAT
* *
449235 TTTCGAAATATAGAATTTTCTACTCTGTAAATGTTTTCGGGGGGATTTTTCTTAATTTTTAATTT
64 TTTCGAAATATAGAATTTTCTATTCCGTAAAT-TTTTCGGGGGGATTTTTCTT-ATTTTTAATTT
449300 TTAAAATTCTTC-AAATATCATCATTTAATTCATATT
127 TTAAAATTC--CAAAATATCATCATTTAATTCATATT
* *
449336 AAATCAGTTTTGAAATATTCATTTATTTTCATGAGTTTTTAATTTTTTCTTGAAATTCTCTATTT
1 AAATCAGTTTTGAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTCTTGAAATTCTCTATTT
* * * * * **
449401 TCCAAA-AAACTGAATTTTCTATTCCATAAATTTTTTGGGGGGATTTTTCTCGATTTAAAATTTT
66 TCGAAATATA--GAATTTTCTATTCCGTAAATTTTTCGGGGGGATTTTTCT-TATTTTTAATTTT
449465 TAAAATT
128 TAAAATT
449472 TATCTAATAT
Statistics
Matches: 252, Mismatches: 39, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
162 33 0.13
163 61 0.24
164 63 0.25
165 28 0.11
166 66 0.26
167 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (161 bp):
AAATCAGTTTTGAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTCTTGAAATTCTCTATTT
TCGAAATATAGAATTTTCTATTCCGTAAATTTTTCGGGGGGATTTTTCTTATTTTTAATTTTTAA
AATTCCAAAATATCATCATTTAATTCATATT
Found at i:449507 original size:164 final size:165
Alignment explanation
Indices: 448972--449547 Score: 421
Period size: 164 Copynumber: 3.5 Consensus size: 165
448962 TTTAAACATA
* * * * * *
448972 AAAATTCTCCAAATATTATCATTTAATAATACCAT-CAAATCATTTTTGAAAAATTC-TTTTTAT
1 AAAATTCTTCAAATATCATCATTTAAT--T--CATATAAATCAGTTTTGAAATATTCATTTAT-T
* * * * * * * * * * *
449035 TTCATGAGTTATTAA-TTTTCCTTT-AAAAATCTCTTGTTTTCGAAATATGGAGTCTTCTATTCC
61 TTCATGAGTTTTTAATTTTTTCTTTGAATATTCTC-TATTTTCAAAAAATAGAATTTTCTACTCC
* * * * *** *
449098 GTAAATTTTTTCGAGGAGATTTTTCTTGGTTT-TAATTTTT
125 ATAAATGTTTTCGGGGGGATTTTTCTCAATTTAAAATTTTT
* * * * * *
449138 -AAATTC--CAAAATATTATTATTTATTTCATATTAAATCAGTTTTTAAAAATTCATTCATTTTC
1 AAAATTCTTC-AAATATCATCATTTAATTCATA-TAAATCAGTTTTGAAATATTCATTTATTTTC
* * * * * **
449200 ATGAGTTTTTCATTTTTTCTTTGAATTTTTTCTATTTTCGAAATATAGAATTTTCTACTCTGTAA
64 ATGAGTTTTTAATTTTTTCTTTGAATATTCTCTATTTTCAAAAAATAGAATTTTCTACTCCATAA
* **
449265 ATGTTTTCGGGGGGATTTTTCTTAATTTTTAATTTTT
129 ATGTTTTCGGGGGGATTTTTCTCAATTTAAAATTTTT
449302 AAAATTCTTCAAATATCATCATTTAATTCATATTAAATCAGTTTTGAAATATTCATTTATTTTCA
1 AAAATTCTTCAAATATCATCATTTAATTCATA-TAAATCAGTTTTGAAATATTCATTTATTTTCA
*
449367 TGAGTTTTTAATTTTTTC-TTGAA-ATTCTCTATTTTCCAAAAAACT-GAATTTTCTATTCCATA
65 TGAGTTTTTAATTTTTTCTTTGAATATTCTCTATTTT-CAAAAAA-TAGAATTTTCTACTCCATA
* *
449429 AAT-TTTTTGGGGGGATTTTTCTCGATTTAAAATTTTT
128 AATGTTTTCGGGGGGATTTTTCTCAATTTAAAATTTTT
* ** * * *
449466 AAAATT-TATCTAATATTGTTA-TTAAGCTCTCATA-AAATCAGTTTCAAGAAAT-TTAATTTA-
1 AAAATTCT-TCAAATATCATCATTTAA--T-TCATATAAATCAGTTT--TGAAATATTCATTTAT
*
449526 TTTCATGAGTTTTGAATTTTTT
60 TTTCATGAGTTTTTAATTTTTT
449548 TGTATATATT
Statistics
Matches: 341, Mismatches: 51, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
160 3 0.01
162 33 0.10
163 67 0.20
164 113 0.33
165 47 0.14
166 77 0.23
167 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.50
Consensus pattern (165 bp):
AAAATTCTTCAAATATCATCATTTAATTCATATAAATCAGTTTTGAAATATTCATTTATTTTCAT
GAGTTTTTAATTTTTTCTTTGAATATTCTCTATTTTCAAAAAATAGAATTTTCTACTCCATAAAT
GTTTTCGGGGGGATTTTTCTCAATTTAAAATTTTT
Found at i:449885 original size:11 final size:11
Alignment explanation
Indices: 449871--449921 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
449861 TCAGCTGGAA
449871 AAAAAAAAGAG
1 AAAAAAAAGAG
*
449882 AAAAAAGAGAG
1 AAAAAAAAGAG
* *
449893 AAAGAAAAG-C
1 AAAAAAAAGAG
* *
449903 AAGAAAAATAG
1 AAAAAAAAGAG
449914 AAAAAAAA
1 AAAAAAAA
449922 ATAGGTAAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
10 6 0.20
11 24 0.80
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:450597 original size:13 final size:13
Alignment explanation
Indices: 450579--450603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
450569 CATAAAATGT
450579 TGTATCGATACAA
1 TGTATCGATACAA
450592 TGTATCGATACA
1 TGTATCGATACA
450604 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:450687 original size:13 final size:13
Alignment explanation
Indices: 450669--450693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
450659 ATTACTCACA
450669 TGTATCGATACAT
1 TGTATCGATACAT
450682 TGTATCGATACA
1 TGTATCGATACA
450694 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:450830 original size:52 final size:52
Alignment explanation
Indices: 450702--450822 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
450692 CACTGATCTT
*
450702 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
450754 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
450806 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
450823 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:457779 original size:1 final size:1
Alignment explanation
Indices: 457775--457799 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
457765 AAAGAGAGTC
457775 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
457800 GGGTGCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:458070 original size:16 final size:16
Alignment explanation
Indices: 458040--458070 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
458030 TTCTTTTCCA
*
458040 AAAAAAGAAACAAAAC
1 AAAAAAGAAAAAAAAC
458056 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
458071 GAGAGGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAC
Found at i:459139 original size:27 final size:27
Alignment explanation
Indices: 459101--459152 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
459091 TTAATTCGTC
*
459101 TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAGCCCACAACTCCGTGGCACCCG
459128 TTTAAGCCCACAACTCCGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
459153 TTCTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCG
Found at i:459203 original size:35 final size:35
Alignment explanation
Indices: 459131--459739 Score: 663
Period size: 35 Copynumber: 17.8 Consensus size: 35
459121 GCACCCGTTT
* *
459131 AAGCCCACAACTCCGTGGCACC-TTCTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
459165 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
* * *
459200 AAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-TCTTTTTA
459237 AAGCCCACAACTCCGTGGCACC-TTTTTC-TTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
* *
459270 AAGCCCACAACTCTGTGGCACTCTTTTTTCCTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTTT-CTTTTTA
*
459307 AAGCCCACAACTCTGTGGCACC-TTTTTC-TTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
** **
459340 AAGCCCACAACTCCGTGGCACTCTTTTACCCGTTT-
1 AAGCCCACAACTCCGTGGCAC-CTTTTTTCTTTTTA
459375 AAGCCCACAACTCCGTGGCACC-TTTTTC-TTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
* ** *
459408 AAGCCCACAATTCCGTGGCA-CTTAATTCGTCTTT-
1 AAGCCCACAACTCCGTGGCACCTTTTTTC-TTTTTA
* *
459442 AAGTCCACAACTCCGTGGCACC------C-GTTT-
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
* *
459469 AAGCCCACAACTCCGTGGCACC-TTCTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
459503 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
* * *
459538 AAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-TCTTTTTA
459575 AAGCCCACAACTCCGTGGCACC-TTTTTC-TTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
* *
459608 AAGCCCACAACTCTGTGGCACTCTTTTTTCCTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTTT-CTTTTTA
*
459645 AAGCCCACAACTCTGTGGCACC-TTTTTC-TTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
** *
459678 AAGCCCACAACTCCGTGGCACTCTTTTACCCTTTT-
1 AAGCCCACAACTCCGTGGCAC-CTTTTTTCTTTTTA
* * *
459713 AAGTCCACAACTTCGTGGCATCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTT
459740 CCCTTCCCAA
Statistics
Matches: 497, Mismatches: 46, Indels: 64
0.82 0.08 0.11
Matches are distributed among these distances:
27 24 0.05
29 1 0.00
32 5 0.01
33 125 0.25
34 76 0.15
35 139 0.28
36 25 0.05
37 102 0.21
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (35 bp):
AAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTA
Found at i:459303 original size:70 final size:70
Alignment explanation
Indices: 459034--459740 Score: 862
Period size: 70 Copynumber: 10.4 Consensus size: 70
459024 CAATCTCTTC
* * * **
459034 TCAAAGTCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAATTCCGTGGCA--CTTAATT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
*
459097 CGTCTT
66 CCT-TT
* * *
459103 T--AAGTCCACAACTCCGTGGCACC-----CGTTT-AAGCCCACAACTCCGTGGCAC-C-TTCTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
459158 -CTTT
66 CCTTT
*
459162 TCAAAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTT
1 TCAAAGCCCACAACTCCGTGGCACC-TTTTTC-TTTTAAAGCCCACAACTCCGTGGCACTCTTTT
*
459227 TCCCTTT
64 TTCCTTT
*
459234 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
459299 CCTTT
66 CCTTT
* **
459304 TCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTAC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
*
459369 CCGTT
66 CCTTT
* **
459374 T--AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAATTCCGTGGCA--CTTAATT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
*
459435 CGTCTT
66 CCT-TT
* * *
459441 T--AAGTCCACAACTCCGTGGCACC-----CGTTT-AAGCCCACAACTCCGTGGCAC-C-TTCTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
459496 -CTTT
66 CCTTT
*
459500 TCAAAGCCCACAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTT
1 TCAAAGCCCACAACTCCGTGGCACC-TTTTTC-TTTTAAAGCCCACAACTCCGTGGCACTCTTTT
*
459565 TCCCTTT
64 TTCCTTT
*
459572 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTT
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
459637 CCTTT
66 CCTTT
* **
459642 TCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTAC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
459707 CCTTT
66 CCTTT
* * *
459712 T--AAGTCCACAACTTCGTGGCATCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACCTTTTTC
459741 CCTTCCCAAA
Statistics
Matches: 564, Mismatches: 45, Indels: 59
0.84 0.07 0.09
Matches are distributed among these distances:
59 6 0.01
60 2 0.00
61 86 0.15
62 10 0.02
66 4 0.01
67 47 0.08
68 81 0.14
69 41 0.07
70 211 0.37
71 18 0.03
72 58 0.10
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (70 bp):
TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
CCTTT
Found at i:459477 original size:27 final size:27
Alignment explanation
Indices: 459439--459490 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
459429 TTAATTCGTC
*
459439 TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAGCCCACAACTCCGTGGCACCCG
459466 TTTAAGCCCACAACTCCGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
459491 TTCTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCG
Found at i:459657 original size:338 final size:338
Alignment explanation
Indices: 459041--459740 Score: 1355
Period size: 338 Copynumber: 2.1 Consensus size: 338
459031 TTCTCAAAGT
*
459041 CCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAATTCCGTGGCACTTAATTCGTCTTTAA
1 CCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAATTCCGTGGCACTTAATTCGTCTTTAA
459106 GTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCC
66 GTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCC
459171 ACAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTC
131 ACAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTC
459236 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTTCC
196 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTTCC
459301 TTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
261 TTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
459366 TACCCGTTTAAGC
326 TACCCGTTTAAGC
459379 CCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAATTCCGTGGCACTTAATTCGTCTTTAA
1 CCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAATTCCGTGGCACTTAATTCGTCTTTAA
459444 GTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCC
66 GTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCC
459509 ACAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTC
131 ACAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTC
459574 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTTCC
196 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTTCC
459639 TTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
261 TTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
* *
459704 TACCCTTTTAAGT
326 TACCCGTTTAAGC
* *
459717 CCACAACTTCGTGGCATCTTTTTC
1 CCACAACTCCGTGGCACCTTTTTC
459741 CCTTCCCAAA
Statistics
Matches: 357, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
338 357 1.00
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (338 bp):
CCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAATTCCGTGGCACTTAATTCGTCTTTAA
GTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCC
ACAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTC
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTTCC
TTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
TACCCGTTTAAGC
Found at i:459783 original size:103 final size:102
Alignment explanation
Indices: 459131--459789 Score: 489
Period size: 106 Copynumber: 6.4 Consensus size: 102
459121 GCACCCGTTT
* * * *
459131 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTTCTT
1 AAGCCCACAACTCGGTGGCAACTTCTTC-TCT-AAAGCCCACAACTCCGTGGCACC--TTTTCCT
**
459196 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCA
62 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTCCCA
* * * * *
459237 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTTCCT
1 AAGCCCACAACTCGGTGGCAACTTCTTC-TCTAAAGCCCACAACTCCGTGGCAC-C--TTTTCCT
**
459302 TTTCAAAGCCCACAACTCTGTGGCAC-CTTTTT--CTT-TTA
62 TTT-AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTCCCA
* * * * *
459340 AAGCCCACAACTCCGTGGC-ACTCTTTTACCCGTTTAAGCCCACAACTCCGTGGCACCTTTTTCT
1 AAGCCCACAACTCGGTGGCAACT-TCTT-CTC--TAAAGCCCACAACTCCGTGGCACCTTTTCCT
* * ** * *
459404 TTTAAAGCCCACAATTCCGTGGCACT-TAATTCGTCTT---T
62 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTC-CCTTCCCA
* * * *
459442 AAGTCCACAACTCCGTGGC-AC-CCGT-T-T-AAGCCCACAACTCCGTGGCACCTTCTT-CTTTT
1 AAGCCCACAACTCGGTGGCAACTTCTTCTCTAAAGCCCACAACTCCGTGGCACCTT-TTCCTTTT
* * ***
459501 CAAAGCCCACAACTCCGTGGCAC-CTTTTT-TCTTTTTA
65 -AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTCCCA
* * * * *
459538 AAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
1 AAGCCCACAACTCGGTGGCA-ACTTCTT--C-TCT-AAAGCCCACAACTCCGTGGCACCTTTTCC
* **
459603 TTTTAAAGCCCACAACTCTGTGGCACTCTTTTTTCCTTTTCA
61 TTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTCCCA
* * * *
459645 AAGCCCACAACTCTGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTACCCT
1 AAGCCCACAACTCGGTGGCAACTTCTTC-TCTAAAGCCCACAACTCCGTGGCAC-CTTTT--CCT
*
459710 TTT-AAGTCCACAACT-TCGTGGCA-TCTTTTTCCCTTCCCA
62 TTTAAAGCCCACAACTCT-GTGGCACTCTTTTTCCCTTCCCA
*
459749 AAGCCCACACAAGTCGGTGGCAAC-TCTTC-CTAAAGCCCACA
1 AAG-CC-CACAACTCGGTGGCAACTTCTTCTCTAAAGCCCACA
459790 CAAGTCGGTG
Statistics
Matches: 474, Mismatches: 44, Indels: 73
0.80 0.07 0.12
Matches are distributed among these distances:
93 4 0.01
94 29 0.06
95 27 0.06
96 17 0.04
98 1 0.00
99 1 0.00
100 1 0.00
101 23 0.05
102 31 0.07
103 59 0.12
104 36 0.08
105 88 0.19
106 109 0.23
107 48 0.10
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.32
Consensus pattern (102 bp):
AAGCCCACAACTCGGTGGCAACTTCTTCTCTAAAGCCCACAACTCCGTGGCACCTTTTCCTTTTA
AAGCCCACAACTCTGTGGCACTCTTTTTCCCTTCCCA
Found at i:459784 original size:32 final size:32
Alignment explanation
Indices: 459742--459850 Score: 161
Period size: 32 Copynumber: 3.4 Consensus size: 32
459732 ATCTTTTTCC
*
459742 CTTCCCAAAGCCCACACAAGTCGGTGGCAACT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACT
459774 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAA-C-T
*
459808 CTTCC-AAAGCCCACACAAGTCGGTGGCAACC
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACT
459839 CTT-CT-AAGCCCA
1 CTTCCTAAAGCCCA
459851 ATATAGCTGG
Statistics
Matches: 72, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
30 8 0.11
31 3 0.04
32 30 0.42
33 25 0.35
34 6 0.08
ACGTcount: A:0.28, C:0.38, G:0.17, T:0.17
Consensus pattern (32 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACT
Found at i:459822 original size:33 final size:33
Alignment explanation
Indices: 459746--459843 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
459736 TTTTCCCTTC
459746 CCAAAGCCCACACAAGTCGGTGGCAA-C-TCTT
1 CCAAAGCCCACACAAGTCGGTGGCAACCTTCTT
459777 CCTAAAGCCCACACAAGTCGGTGGCAACCTTCTT
1 CC-AAAGCCCACACAAGTCGGTGGCAACCTTCTT
459811 CCAAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 CCAAAGCCCACACAAGTCGGTGGCAA-CCTTCT
459844 AAGCCCAATA
Statistics
Matches: 63, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
31 2 0.03
32 24 0.38
33 25 0.40
34 12 0.19
ACGTcount: A:0.28, C:0.37, G:0.18, T:0.17
Consensus pattern (33 bp):
CCAAAGCCCACACAAGTCGGTGGCAACCTTCTT
Found at i:459961 original size:49 final size:49
Alignment explanation
Indices: 459843--460610 Score: 926
Period size: 49 Copynumber: 15.8 Consensus size: 49
459833 GCAACCCTTC
*
459843 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* *
459895 TAAGTCCAATGTAGCTGGCCTT-AACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAA-TCAGCATATTGGCACCTTCATCTT
* *
459944 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C-T-TT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
459987 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * * *
460036 TAAGTCCAATGTAGTTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
460085 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
460134 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
460183 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
460232 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
460281 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * *
460330 GAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
460373 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
460422 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
460465 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTT
* * ** *
460517 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC----T-TCATCTT
* * * * *
460572 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
460611 TCTTTATCAC
Statistics
Matches: 621, Mismatches: 66, Indels: 55
0.84 0.09 0.07
Matches are distributed among these distances:
43 116 0.19
44 1 0.00
45 3 0.00
47 1 0.00
48 1 0.00
49 382 0.62
50 5 0.01
51 2 0.00
52 72 0.12
53 1 0.00
55 36 0.06
56 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:460591 original size:55 final size:55
Alignment explanation
Indices: 460462--461493 Score: 327
Period size: 55 Copynumber: 18.7 Consensus size: 55
460452 ACATTGGCAC
* *
460462 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
460514 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
460569 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-CTTTT-TC-TCAT
* *
460633 CATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCAT
1 C--TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
460684 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * * * * * *
460739 CTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATC-CT-T---TTTCTCAT
* * **
460799 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCA-CCTTCATCATC-T
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTC-TCAT
** ** * * * * * *
460853 CTAAAAACCCAATGA-CGCTGGTCATGAATCAGCACATTG---TCATTTTTCGCAT
1 CTTTAAGTCCAAT-ATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
** * * ** * ** *
460905 CTTCGAG-CCTAATATCGCTAGCC--GCATATTGGC-TCTT-TTATCCTTCTTCTCAT
1 CTTTAAGTCC-AATATAGCTGGCCTTG-A-ATCAGCATATTGACATCCTTTTTCTCAT
* * * * * * * *
460958 CTTTCAA-CCCAATATCGTTGGCCGTGAATCAACGTATTG--GTCC-TTTTATCA-
1 CTTT-AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
461009 CTTTCCA-TCC--TCATCACCTTTAAGTCC--AATATC-GC-TGGCCTTGA-ATCAGCATATTGG
1 CTTT-AAGTCCAAT-AT-AGC--T--GGCCTTGA-ATCAGCAT---ATTGACATC--C-T-TT--
*
461066 CATCTTCAT
49 -TTC-TCAT
* * *
461075 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----------C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* *
461118 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
461170 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
461225 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-CTTTT-TC-TCAT
* *
461289 CATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCAT
1 C--TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
461340 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * * * * * *
461395 CTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATC-CT-T---TTTCTCAT
*
461455 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
461494 GCACCTTCAT
Statistics
Matches: 723, Mismatches: 152, Indels: 202
0.67 0.14 0.19
Matches are distributed among these distances:
43 40 0.06
45 1 0.00
49 73 0.10
50 6 0.01
51 25 0.03
52 103 0.14
53 35 0.05
54 55 0.08
55 148 0.20
56 6 0.01
57 5 0.01
58 6 0.01
59 1 0.00
60 87 0.12
61 8 0.01
62 16 0.02
63 10 0.01
64 15 0.02
65 6 0.01
66 75 0.10
67 1 0.00
68 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
Found at i:460751 original size:170 final size:164
Alignment explanation
Indices: 460462--461504 Score: 1019
Period size: 170 Copynumber: 6.3 Consensus size: 164
460452 ACATTGGCAC
*
460462 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTTCAAT
460527 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
63 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
460592 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
128 ATGAATCAACATATTGGCATCTTTATCAC-TTT-T--TCAT
*
460633 CATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATG
1 C--TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATG
*
460698 TAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCA
64 TAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCA
460763 TGAATCAACATATTGGCATCTTTATCACTTTTTCAT
129 TGAATCAACATATTGGCATCTTTATCACTTTTTCAT
* * ***
460799 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTCTAAAAACCCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC-T-T-T--AAGTTCA
* * * * * ** * * *
460864 ATG-ACGCTGGTCATGAATCAGCACATTG---TCATTTTTCGCATCTTCGAGCCTAATATCGCTA
61 ATGTA-GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTG
460925 GCC--G------CATATTGGC-TCTTTTATC-CTTCTTCTCAT
125 GCCATGAATCAACATATTGGCATC-TTTATCACTT-TT-TCAT
* * * * * *
460958 CTTTCAA-CCCAATATCGTTGGCCGTGAATCAACGTATTGGTCCTTTTATCACTTTCCATCCTCA
1 CTTT-AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG---------CA---T-C-T--TCA
* * * ** *
461022 TCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCATCTTTAA
49 T---CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAA
* * * * * * *
461081 GTCCAATGTAGCTGGCCTTGAATCAGCACATTGG---------CA------C--
111 GCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTTCAT
*
461118 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTTCAAT
461183 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
63 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
461248 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
128 ATGAATCAACATATTGGCATCTTTATCAC-TTT-T--TCAT
*
461289 CATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATG
1 C--TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATG
*
461354 TAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCA
64 TAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCA
461419 TGAATCAACATATTGGCATCTTTATCACTTTTTCAT
129 TGAATCAACATATTGGCATCTTTATCACTTTTTCAT
* *
461455 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
461505 ATCTCTAAAA
Statistics
Matches: 727, Mismatches: 70, Indels: 157
0.76 0.07 0.16
Matches are distributed among these distances:
144 37 0.05
145 1 0.00
146 1 0.00
147 3 0.00
148 1 0.00
149 1 0.00
150 38 0.05
153 2 0.00
157 5 0.01
158 17 0.02
159 39 0.05
160 33 0.05
162 1 0.00
164 95 0.13
165 1 0.00
166 39 0.05
167 1 0.00
168 5 0.01
169 35 0.05
170 237 0.33
171 13 0.02
172 2 0.00
173 104 0.14
175 5 0.01
176 2 0.00
177 1 0.00
178 8 0.01
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (164 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
AATCAACATATTGGCATCTTTATCACTTTTTCAT
Found at i:460801 original size:60 final size:61
Alignment explanation
Indices: 460730--460849 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 61
460720 TTGACATCCT
* * * *
460730 TTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCAC
1 TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCAC
* * * *
460791 TTTT-TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCA
1 TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCA
460850 TCTCTAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 47 0.92
61 4 0.08
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (61 bp):
TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCAC
Found at i:461095 original size:49 final size:48
Alignment explanation
Indices: 461026--461203 Score: 231
Period size: 49 Copynumber: 3.7 Consensus size: 48
461016 TCCTCATCAC
*
461026 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAT-TTCAT
* *
461075 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATTTCAT
461118 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CA-TTT-CAT
* *
461170 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCA
461204 CGTTGACATC
Statistics
Matches: 113, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
43 38 0.34
45 3 0.03
49 39 0.35
50 1 0.01
52 32 0.28
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (48 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATTTCAT
Found at i:461136 original size:43 final size:43
Alignment explanation
Indices: 461075--461160 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
461065 GCATCTTCAT
* *
461075 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
461118 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
461161 ATTTTCCATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:461232 original size:656 final size:656
Alignment explanation
Indices: 460367--461710 Score: 2643
Period size: 656 Copynumber: 2.0 Consensus size: 656
460357 AGCACATTGG
460367 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
460432 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
460497 ATTGGCACATTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTT
131 ATTGGCACATTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTT
460562 TTCTCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCT
196 TTCTCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCT
460627 CATCATCATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
261 CATCATCATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
460692 TCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGT
326 TCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGT
460757 TGGCCATGAATCAACATATTGGCATCTTTATCACTTTTTCATCTTTAAGTCCAATATTGCTGGCC
391 TGGCCATGAATCAACATATTGGCATCTTTATCACTTTTTCATCTTTAAGTCCAATATTGCTGGCC
460822 TTGAATCAGCATATTGGCACCTTCATCATCTCTAAAAACCCAATGACGCTGGTCATGAATCAGCA
456 TTGAATCAGCATATTGGCACCTTCATCATCTCTAAAAACCCAATGACGCTGGTCATGAATCAGCA
460887 CATTGTCATTTTTCGCATCTTCGAGCCTAATATCGCTAGCCGCATATTGGCTCTTTTATCCTTCT
521 CATTGTCATTTTTCGCATCTTCGAGCCTAATATCGCTAGCCGCATATTGGCTCTTTTATCCTTCT
460952 TCTCATCTTTCAACCCAATATCGTTGGCCGTGAATCAACGTATTGGTCCTTTTATCACTTTCCAT
586 TCTCATCTTTCAACCCAATATCGTTGGCCGTGAATCAACGTATTGGTCCTTTTATCACTTTCCAT
461017 CCTCAT
651 CCTCAT
461023 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
461088 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
461153 ATTGGCACATTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTT
131 ATTGGCACATTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTT
461218 TTCTCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCT
196 TTCTCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCT
461283 CATCATCATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
261 CATCATCATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
461348 TCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGT
326 TCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGT
461413 TGGCCATGAATCAACATATTGGCATCTTTATCACTTTTTCATCTTTAAGTCCAATATTGCTGGCC
391 TGGCCATGAATCAACATATTGGCATCTTTATCACTTTTTCATCTTTAAGTCCAATATTGCTGGCC
461478 TTGAATCAGCATATTGGCACCTTCATCATCTCTAAAAACCCAATGACGCTGGTCATGAATCAGCA
456 TTGAATCAGCATATTGGCACCTTCATCATCTCTAAAAACCCAATGACGCTGGTCATGAATCAGCA
461543 CATTGTCATTTTTCGCATCTTCGAGCCTAATATCGCTAGCCGCATATTGGCTCTTTTATCCTTCT
521 CATTGTCATTTTTCGCATCTTCGAGCCTAATATCGCTAGCCGCATATTGGCTCTTTTATCCTTCT
461608 TCTCATCTTTCAACCCAATATCGTTGGCCGTGAATCAACGTATTGGTCCTTTTATCACTTTCCAT
586 TCTCATCTTTCAACCCAATATCGTTGGCCGTGAATCAACGTATTGGTCCTTTTATCACTTTCCAT
461673 CCTCAT
651 CCTCAT
* * * * *
461679 CATCTTTAAGTCCAGTGTGGCAGGCCTTGAAT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAAT
461711 TTGCACAGTG
Statistics
Matches: 683, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
656 683 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.35
Consensus pattern (656 bp):
CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
GTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
ATTGGCACATTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTT
TTCTCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCT
CATCATCATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
TCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGT
TGGCCATGAATCAACATATTGGCATCTTTATCACTTTTTCATCTTTAAGTCCAATATTGCTGGCC
TTGAATCAGCATATTGGCACCTTCATCATCTCTAAAAACCCAATGACGCTGGTCATGAATCAGCA
CATTGTCATTTTTCGCATCTTCGAGCCTAATATCGCTAGCCGCATATTGGCTCTTTTATCCTTCT
TCTCATCTTTCAACCCAATATCGTTGGCCGTGAATCAACGTATTGGTCCTTTTATCACTTTCCAT
CCTCAT
Found at i:461457 original size:60 final size:61
Alignment explanation
Indices: 461386--461505 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 61
461376 TTGACATCCT
* * * *
461386 TTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCAC
1 TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCAC
* * * *
461447 TTTT-TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCA
1 TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCA
461506 TCTCTAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 47 0.92
61 4 0.08
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (61 bp):
TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCAC
Found at i:462341 original size:13 final size:13
Alignment explanation
Indices: 462323--462347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
462313 CATAAAATGT
462323 TGTATCGATACAA
1 TGTATCGATACAA
462336 TGTATCGATACA
1 TGTATCGATACA
462348 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:462431 original size:13 final size:13
Alignment explanation
Indices: 462413--462437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
462403 ATTACTCACA
462413 TGTATCGATACAT
1 TGTATCGATACAT
462426 TGTATCGATACA
1 TGTATCGATACA
462438 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:462574 original size:52 final size:52
Alignment explanation
Indices: 462446--462566 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
462436 CACTGATCTT
*
462446 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
462498 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
462550 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
462567 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:466237 original size:11 final size:11
Alignment explanation
Indices: 466221--466258 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
466211 CAAAAATAAA
466221 TAAATTCAAAT
1 TAAATTCAAAT
466232 TAAATT-AACA-
1 TAAATTCAA-AT
466242 TAAATTCAAAT
1 TAAATTCAAAT
466253 TAAATT
1 TAAATT
466259 AACACTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (11 bp):
TAAATTCAAAT
Found at i:466273 original size:26 final size:21
Alignment explanation
Indices: 466220--466262 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
466210 TCAAAAATAA
466220 ATAAATTCAAATTAAATTAAC
1 ATAAATTCAAATTAAATTAAC
466241 ATAAATTCAAATTAAATTAAC
1 ATAAATTCAAATTAAATTAAC
466262 A
1 A
466263 CTTTCATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATTCAAATTAAATTAAC
Found at i:467431 original size:20 final size:20
Alignment explanation
Indices: 467391--467444 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
467381 TTCTATGATC
* *
467391 TGTATTGATACAATTAGTGAA
1 TGTATCGATAC-ATAAGTGAA
467412 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
*
467432 TGTATCAATACAT
1 TGTATCGATACAT
467445 GTCTCAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:467517 original size:20 final size:20
Alignment explanation
Indices: 467492--467543 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
467482 GGCCAAAAAT
**
467492 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAACCAAA
**
467512 TGTATCGATACATTTCCAAA
1 TGTATCGATACATAACCAAA
467532 TGTATCGATACA
1 TGTATCGATACA
467544 ATTTGTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAACCAAA
Found at i:468326 original size:21 final size:20
Alignment explanation
Indices: 468301--468353 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
468291 TACAAGCCAA
**
468301 TGTATCGATACAATTTTTTTG
1 TGTATCGATACAA-TACTTTG
468322 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
468341 TGTATCGATACAA
1 TGTATCGATACAA
468354 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
20 2 0.07
21 11 0.38
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:469095 original size:21 final size:21
Alignment explanation
Indices: 469054--469097 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
469044 CTCCCCTTTA
* *
469054 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
469075 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
469096 TC
1 TC
469098 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:470907 original size:13 final size:13
Alignment explanation
Indices: 470889--470926 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
470879 ATAATCCCCC
470889 TGTATCGATACAG
1 TGTATCGATACAG
*
470902 TGTATCGATACAT
1 TGTATCGATACAG
470915 TGTATCGATACA
1 TGTATCGATACA
470927 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:476568 original size:156 final size:157
Alignment explanation
Indices: 476273--476610 Score: 402
Period size: 156 Copynumber: 2.2 Consensus size: 157
476263 TAGTGGGTAT
* * *
476273 TTAGGATAGGCTCATCCCATCTTAAACCTTTTTTAAGTCCTTTAGGGGTATCAGGTACTTCTATG
1 TTAGGATAGGTTCATCCCATCTTAAACCTTTTTTAAGTCCTTTAGGGCTATCAGATACTTCTATG
* * * * *
476338 TTGAAGGTATACCCATTAGGGGCATTTTCGTAATTCCTCAGAGTCAAGTCCTAGGTTGCCACCGG
66 TCGAAGGTATACCCATTAGGGGCATTTTCATAATTCCTCAGAGCCAAGTCCTAAGTTGCCACCGA
* *
476403 GCCTACTTTTATGCCGAATGTAGGCAA
131 GCCTACTTTTATACCGAAGGTAGGCAA
* *
476430 TTAGGATAGGTTCATCCCATCTCT-AATC-TTTTTAAGTCCTTTAGGGCTATCGAGATGCTT-TA
1 TTAGGATAGGTTCATCCCATCT-TAAACCTTTTTTAAGTCCTTTAGGGCTATC-AGATACTTCT-
* *
476492 ATGTCGAAGGTATACCCA-TAGGGGCATTTTCATAATTTCCT-AGAGCCGAGTCCTAAGTTGTCA
63 ATGTCGAAGGTATACCCATTAGGGGCATTTTCATAA-TTCCTCAGAGCCAAGTCCTAAGTTGCCA
* * * * *
476555 CTGAGTCTGCTTTTATACCGAAGGTAGGTAT
127 CCGAGCCTACTTTTATACCGAAGGTAGGCAA
*
476586 TTCA-GATAGGTTCAT-CCATTTTAAA
1 TT-AGGATAGGTTCATCCCATCTTAAA
476611 ATCCTTTGTA
Statistics
Matches: 155, Mismatches: 20, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
154 1 0.01
155 7 0.05
156 93 0.60
157 53 0.34
158 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (157 bp):
TTAGGATAGGTTCATCCCATCTTAAACCTTTTTTAAGTCCTTTAGGGCTATCAGATACTTCTATG
TCGAAGGTATACCCATTAGGGGCATTTTCATAATTCCTCAGAGCCAAGTCCTAAGTTGCCACCGA
GCCTACTTTTATACCGAAGGTAGGCAA
Found at i:476654 original size:156 final size:156
Alignment explanation
Indices: 476273--476660 Score: 394
Period size: 156 Copynumber: 2.5 Consensus size: 156
476263 TAGTGGGTAT
* * * * *
476273 TTAGGATAGGCTCATCCCATCT-TAAACCTTTTTTAAGTCCTTTAGGGGTATC-AGGTACTTCTA
1 TTAGGATAGGTTCATCCCATCTCT-AATC-TTTGTAAATCCTTTAGGGGTATCGA-GTACTTTTA
* * * *
476336 TGTTGAAGGTATACCCATTAGGGGCATTTTCGTAATTCCTCAGAGTCAAGTCCTAGGTTGCCACC
63 TGTCGAAGGTATACCCATTAGGGGCATTTTCATAATTCCTCAGAGCCAAGTCCTAAGTTGCCACC
* * *
476401 GGGCCTACTTTTATGCCGAATGTAGGCAA
128 GAGCCTACTTTTATACCGAAGGTAGGCAA
* * * * *
476430 TTAGGATAGGTTCATCCCATCTCTAATCTTTTTAAGTCCTTTAGGGCTATCGAGATGCTTTAATG
1 TTAGGATAGGTTCATCCCATCTCTAATCTTTGTAAATCCTTTAGGGGTATCGAG-TACTTTTATG
* * *
476495 TCGAAGGTATACCCA-TAGGGGCATTTTCATAATTTCCT-AGAGCCGAGTCCTAAGTTGTCACTG
65 TCGAAGGTATACCCATTAGGGGCATTTTCATAA-TTCCTCAGAGCCAAGTCCTAAGTTGCCACCG
* * * *
476558 AGTCTGCTTTTATACCGAAGGTAGGTAT
129 AGCCTACTTTTATACCGAAGGTAGGCAA
* * *
476586 TTCA-GATAGGTTCAT-CCAT-TTTAAAATCCTTTGTAAATGCTTTAGGGGTATCGAGTAATTTT
1 TT-AGGATAGGTTCATCCCATCTCT--AAT-CTTTGTAAATCCTTTAGGGGTATCGAGTACTTTT
*
476648 ACGTCGAAGGTAT
62 ATGTCGAAGGTAT
476661 CCTTTAAGGG
Statistics
Matches: 194, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
154 2 0.01
155 4 0.02
156 112 0.58
157 75 0.39
158 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (156 bp):
TTAGGATAGGTTCATCCCATCTCTAATCTTTGTAAATCCTTTAGGGGTATCGAGTACTTTTATGT
CGAAGGTATACCCATTAGGGGCATTTTCATAATTCCTCAGAGCCAAGTCCTAAGTTGCCACCGAG
CCTACTTTTATACCGAAGGTAGGCAA
Done.