Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold33
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: 2032796
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 48244 characters in sequence are not A, C, G, or T
File 2 of 13
Found at i:200095 original size:20 final size:20
Alignment explanation
Indices: 200060--200100 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
200050 CAAATTTCTT
200060 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
200082 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
200101 AACAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:200404 original size:20 final size:21
Alignment explanation
Indices: 200364--200415 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
200354 TTCCTAGGCA
**
200364 GCACCCACCAGGTCGTGACC-G
1 GCACCC-CCAGGTCGCAACCGG
200385 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCGCAACCGG
200406 GCAGCCCCCA
1 GCA-CCCCCA
200416 CACTAGCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 11 0.41
21 10 0.37
22 6 0.22
ACGTcount: A:0.19, C:0.48, G:0.27, T:0.06
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCGG
Found at i:201801 original size:22 final size:21
Alignment explanation
Indices: 201775--201818 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
201765 TGAAAGTGTT
*
201775 AAATTATTTTACTAAGGGGGAG
1 AAATT-TTTGACTAAGGGGGAG
*
201797 AAATTTTTGATTAAGGGGGAG
1 AAATTTTTGACTAAGGGGGAG
201818 A
1 A
201819 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.32
Consensus pattern (21 bp):
AAATTTTTGACTAAGGGGGAG
Found at i:202396 original size:20 final size:21
Alignment explanation
Indices: 202373--202425 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
202363 CAGGTTGCAT
**
202373 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
202393 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
202414 TGTATCGATACA
1 TGTATCGATACA
202426 AGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:202499 original size:20 final size:20
Alignment explanation
Indices: 202458--202509 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
202448 TAGCCAAACT
**
202458 TGTATCGATACA-CATAGTA
1 TGTATCGATACATCATAAAA
202477 TGTATCGATACATCATAAAA
1 TGTATCGATACATCATAAAA
202497 TGTATCGATACAT
1 TGTATCGATACAT
202510 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATCATAAAA
Found at i:203398 original size:24 final size:24
Alignment explanation
Indices: 203350--203445 Score: 131
Period size: 24 Copynumber: 3.9 Consensus size: 24
203340 GATTGATCTC
203350 TTTATAACAATTATTT-TTTATAT
1 TTTATAACAATTATTTCTTTATAT
*
203373 TTTATAACAATTATTCCTTTATAT
1 TTTATAACAATTATTTCTTTATAT
*
203397 TTTATAACAATTGCTATTTTTTTATAT
1 TTTATAACAA-T--TATTTCTTTATAT
*
203424 TTTATAACAATTGTTTCTTTAT
1 TTTATAACAATTATTTCTTTAT
203446 GTTATGTAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
23 15 0.23
24 26 0.41
25 1 0.02
26 1 0.02
27 21 0.33
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTATAACAATTATTTCTTTATAT
Found at i:203422 original size:27 final size:26
Alignment explanation
Indices: 203350--203437 Score: 114
Period size: 27 Copynumber: 3.5 Consensus size: 26
203340 GATTGATCTC
203350 TTTATAACAA-T-TA-TTTTTTATAT
1 TTTATAACAATTGTATTTTTTTATAT
**
203373 TTTATAACAA-T-TATTCCTTTATAT
1 TTTATAACAATTGTATTTTTTTATAT
203397 TTTATAACAATTGCTATTTTTTTATAT
1 TTTATAACAATTG-TATTTTTTTATAT
203424 TTTATAACAATTGT
1 TTTATAACAATTGT
203438 TTCTTTATGT
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
23 13 0.23
24 18 0.32
25 1 0.02
26 1 0.02
27 24 0.42
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTATAACAATTGTATTTTTTTATAT
Found at i:206567 original size:2 final size:2
Alignment explanation
Indices: 206560--206587 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
206550 TTTTCATCAA
206560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
206588 CAATTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:209985 original size:32 final size:30
Alignment explanation
Indices: 209949--210007 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
209939 GAAATCAAAT
209949 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
209981 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
210008 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:210305 original size:13 final size:13
Alignment explanation
Indices: 210287--210312 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
210277 CAATTTTTTG
210287 TGTATCGATACAT
1 TGTATCGATACAT
210300 TGTATCGATACAT
1 TGTATCGATACAT
210313 ACTTTGTGTA
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:210324 original size:32 final size:33
Alignment explanation
Indices: 210267--210330 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
210257 TACAAGCCAA
**
210267 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
210300 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
210331 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:211107 original size:79 final size:78
Alignment explanation
Indices: 210971--211349 Score: 377
Period size: 79 Copynumber: 4.8 Consensus size: 78
210961 AAAACGGGGC
* * * * * *
210971 TGGAGTATCCCCGACTATGAAAAATCGGTGTTCTGGAAATAAAATCGGGGTTAGAGTATCCCCTT
1 TGGAGTATCCCCGATTATG-AAAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCC-T
*
211036 AG-AAAGAAC-AGGGT
64 AGAAAATAACGA-GGT
* * * *
211050 TGGAGTATCCCTGATAATAGAAAATTGATGTTTT-GAAAATAAAATCGGGGTTGGAGTATCCCCT
1 TGGAGTATCCCCGATTAT-GAAAATTGATGTTTTAG-AAATAAAACCGGGGTTAGAGTATCCCCT
*
211114 CGAAAATAACGAGGT
64 AGAAAATAACGAGGT
* ** * * **
211129 TGGAGAATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAGGCCGAGGTTGGAGTATCCCCGC
1 TGGAGTATCCCCGATTAT-GAAAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCCTA
* * *
211194 CAAAATAATGGGGT
65 GAAAATAACGAGGT
* ** * * *
211208 TGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTAGAGTATCCCCTC
1 TGGAGTATCCCCGATTATGA-AAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCCTA
*
211273 GAAAATAACGAGAT
65 GAAAATAACGAGGT
* **
211287 TGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACTAGGGTTAGAGTATCCCC
1 TGGAGTATCCCCGATTATG-AAAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCC
211350 GAGATGAAAA
Statistics
Matches: 251, Mismatches: 42, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
78 5 0.02
79 242 0.96
80 4 0.02
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (78 bp):
TGGAGTATCCCCGATTATGAAAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCCTAG
AAAATAACGAGGT
Found at i:211344 original size:158 final size:159
Alignment explanation
Indices: 210971--211350 Score: 439
Period size: 158 Copynumber: 2.4 Consensus size: 159
210961 AAAACGGGGC
* * * * *
210971 TGGAGTATCCCCGACTATGAAAAATCGGTGTTCTGGAAATAAAA-TCGGGGTTAGAGTATCCCC-
1 TGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACT-AGGGTTAGAGTATCCCCG
** * ** * *
211034 TTAGAAAGAACAGGGTTGGAGTATCCCTGATAATAGAAAATTGATGTTTTGAAAATAAAATCGGG
65 CCAGAAAGAACAGGGTTGGAGTATCCCCGATAATAGAAAATCAATATTTTGAAAATAAAACCGGG
* *
211099 GTTGGAGTATCCCCTCGAAAATAACGAGGT
130 GTTAGAGTATCCCCTCGAAAATAACGAGAT
* * * ** * *
211129 TGGAGAATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAGGC-CGAGGTTGGAGTATCCCCG
1 TGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACTAG-GGTTAGAGTATCCCCG
* ** ** *
211193 CCA-AAATAATGGGGTTGGAGTATCCCCGATTGT-GAGAAATCAATATTTT-AGAAATAAAGCCG
65 CCAGAAAGAACAGGGTTGGAGTATCCCCGATAATAGA-AAATCAATATTTTGA-AAATAAAACCG
211255 GGGTTAGAGTATCCCCTCGAAAATAACGAGAT
128 GGGTTAGAGTATCCCCTCGAAAATAACGAGAT
211287 TGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACTAGGGTTAGAGTATCCCCG
1 TGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACTAGGGTTAGAGTATCCCCG
211351 AGATGAAAAA
Statistics
Matches: 183, Mismatches: 33, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
157 4 0.02
158 177 0.97
159 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (159 bp):
TGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACTAGGGTTAGAGTATCCCCGC
CAGAAAGAACAGGGTTGGAGTATCCCCGATAATAGAAAATCAATATTTTGAAAATAAAACCGGGG
TTAGAGTATCCCCTCGAAAATAACGAGAT
Found at i:211376 original size:50 final size:50
Alignment explanation
Indices: 211289--211412 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 50
211279 AACGAGATTG
* ** * *
211289 GAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACTAG-GGTTA
1 GAGTATCCCCGA-GATGAAAAATCAATATTTTAGAAAT-AAACTAGAGGTTA
* * *
211340 GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAATTCGAGGTTG
1 GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAACTAGAGGTTA
*
211390 GAGTATCCCTGAGATGAAAAATC
1 GAGTATCCCCGAGATGAAAAATC
211413 TAGAAATTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 5 0.08
50 46 0.73
51 12 0.19
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (50 bp):
GAGTATCCCCGAGATGAAAAATCAATATTTTAGAAATAAACTAGAGGTTA
Found at i:214872 original size:154 final size:156
Alignment explanation
Indices: 214623--214914 Score: 385
Period size: 154 Copynumber: 1.9 Consensus size: 156
214613 TGAGTTTTAG
* * *
214623 GTCATCACCGGGTCACTTTTATGTCAAAGGTATGCATTTAGGATATATTCACTCTCCTAGCTTCA
1 GTCATCACCGAGTCACTTTTATGTCAAAGGTATGCATTTAGGATAGATTCACTCTCCTAACTTCA
* * * * * *
214688 TTTTTATGTCTTTTAAGGTTACTAAGATACTTTCACATCAATA-TATACCTT-ATGGATATTTTG
66 TTTTTATGTCCTTTAAGGTTACCAAAATACTTTCACATCAAAAGTATACCTTAAGGGATACTTTG
214751 GTAATTTCCTTAGAACCGACTACTAA
131 GTAATTTCCTTAGAACCGACTACTAA
* * *
214777 GTCATCACTGAGTCATTTTTATG-CTAAAGGTATGCATTTAGGATAGGTTCACTCTCCTAACTTC
1 GTCATCACCGAGTCACTTTTATGTC-AAAGGTATGCATTTAGGATAGATTCACTCTCCTAACTTC
* * ** *
214841 TTTTTTGTGTCCTTT-AGAGTTACCAAAATACTTTCATGTCAAAAGTATACCTTAAGGGGTACTT
65 ATTTTTATGTCCTTTAAG-GTTACCAAAATACTTTCACATCAAAAGTATACCTTAAGGGATACTT
214905 TGGTAATTTC
129 TGGTAATTTC
214915 ATCAAAACCA
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
153 3 0.03
154 89 0.76
155 8 0.07
156 17 0.15
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (156 bp):
GTCATCACCGAGTCACTTTTATGTCAAAGGTATGCATTTAGGATAGATTCACTCTCCTAACTTCA
TTTTTATGTCCTTTAAGGTTACCAAAATACTTTCACATCAAAAGTATACCTTAAGGGATACTTTG
GTAATTTCCTTAGAACCGACTACTAA
Found at i:215306 original size:155 final size:159
Alignment explanation
Indices: 215142--215495 Score: 416
Period size: 159 Copynumber: 2.3 Consensus size: 159
215132 TCCTTTTCTA
** *
215142 TTCATTTTTGTGTCATTTAGGGTTACCATTATACTTTT-ACGTCGAA-G-ATATAT-TC-TAAGC
1 TTCATTTTTGTGTCATTTAGGGTTACCAGGATA-TTTTCACATCGAAGGTATATATATCTTAAGC
* * * * *
215202 GCATTCTGGTAATTTCTTTGGAA-TAAAGTCTTACGTCATCAC-TAGGTCACTTTTCTGCCAAAG
65 GCATTCTGCTAATTTCCTTAGAACT-AAGTCTTAAGTCATCACAT-GGTCACTTTTATGCCAAAG
* * *
215265 ATATGCATTTAGGATAGGTTCACTCTCCTAGC
128 ATATACATTTAAGATAGGTTCACTCTACTAGC
* * * * *
215297 TTTATTTTTGTGTCTTTTAGGGTTACCAGGATATTTTCACATTGAAGGTATATATATCTTAGGGG
1 TTCATTTTTGTGTCATTTAGGGTTACCAGGATATTTTCACATCGAAGGTATATATATCTTAAGCG
* * *
215362 CATTTTGCTAATTTCCTTAGAACTGAGTCTTAAGTCATCACATGGTCACTTTTATGCCAAAGGTA
66 CATTCTGCTAATTTCCTTAGAACTAAGTCTTAAGTCATCACATGGTCACTTTTATGCCAAAGATA
* *
215427 TACATTTAAGATAGGTTTAGTCTACTAGC
131 TACATTTAAGATAGGTTCACTCTACTAGC
* * *
215456 TTCATTTTTGTGTCCTTTAAGGTTACGAGGATATTTTCAC
1 TTCATTTTTGTGTCATTTAGGGTTACCAGGATATTTTCAC
215496 GTTGAAGATA
Statistics
Matches: 167, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
154 4 0.02
155 35 0.21
156 1 0.01
157 6 0.04
158 2 0.01
159 117 0.70
160 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (159 bp):
TTCATTTTTGTGTCATTTAGGGTTACCAGGATATTTTCACATCGAAGGTATATATATCTTAAGCG
CATTCTGCTAATTTCCTTAGAACTAAGTCTTAAGTCATCACATGGTCACTTTTATGCCAAAGATA
TACATTTAAGATAGGTTCACTCTACTAGC
Found at i:216767 original size:62 final size:63
Alignment explanation
Indices: 216695--216822 Score: 152
Period size: 63 Copynumber: 2.0 Consensus size: 63
216685 TTTACATGCT
*
216695 TTTATCTATTGGA-TAATTTCAATATCTTGTTTAAATTA-CTTGTGATGTTCATTGCTTTGAAA
1 TTTATCTATTGGATTAATTTCAATATCTTATTTAAA-TAGCTTGTGATGTTCATTGCTTTGAAA
* ** * * * * *
216757 TTTATGTATTGGATTAATTTTGATATTTTATTTGAATAGTTTGTGATTTTCATTGTTTTGAAA
1 TTTATCTATTGGATTAATTTCAATATCTTATTTAAATAGCTTGTGATGTTCATTGCTTTGAAA
216820 TTT
1 TTT
216823 TATTTAAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
62 14 0.25
63 41 0.75
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.55
Consensus pattern (63 bp):
TTTATCTATTGGATTAATTTCAATATCTTATTTAAATAGCTTGTGATGTTCATTGCTTTGAAA
Found at i:217813 original size:20 final size:21
Alignment explanation
Indices: 217790--217828 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
217780 CAAAGCAATA
217790 TGTATCGATAC-TTCTAGGCC
1 TGTATCGATACTTTCTAGGCC
217810 TGTATCGATACTTTCTAGG
1 TGTATCGATACTTTCTAGG
217829 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (21 bp):
TGTATCGATACTTTCTAGGCC
Found at i:220198 original size:12 final size:12
Alignment explanation
Indices: 220181--220205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
220171 AATAAAATCT
220181 ATTTTTGATGAA
1 ATTTTTGATGAA
220193 ATTTTTGATGAA
1 ATTTTTGATGAA
220205 A
1 A
220206 AAAGAAAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (12 bp):
ATTTTTGATGAA
Found at i:220369 original size:13 final size:13
Alignment explanation
Indices: 220351--220378 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
220341 CATAGTGCCC
220351 TTGTATCGATACA
1 TTGTATCGATACA
220364 TTGTATCGATACA
1 TTGTATCGATACA
220377 TT
1 TT
220379 CTAGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:224850 original size:3 final size:3
Alignment explanation
Indices: 224842--224867 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
224832 CAAGTCAACT
224842 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
224868 TTTATTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:225449 original size:20 final size:20
Alignment explanation
Indices: 225424--225700 Score: 178
Period size: 20 Copynumber: 12.8 Consensus size: 20
225414 TTTTACCATG
225424 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
* * *
225444 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTTA
* *
225464 ATGTATCGATATATTTTTCA
1 ATGTATCGATACATTTTTTA
* *
225484 ATATATCGATGCATTCTGTCTTTGTACCTA
1 ATGTATCGAT--A--C-AT-TTT-T---TA
*
225514 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTTA
* * * *
225535 ATGAATCGATACATGTATGA
1 ATGTATCGATACATTTTTTA
225555 ATGTATCGATAC-TTTTTTCA
1 ATGTATCGATACATTTTTT-A
* *
225575 ATGTATCGATGCATTTTTGA
1 ATGTATCGATACATTTTTTA
225595 ATGTATCGATACATTCTGTCTTTTTACCCA
1 ATGTATCGATACA-----T-TTTTT----A
*
225625 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTTA
* * *
225646 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTTA
225666 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
225686 ATGTATCGATACATT
1 ATGTATCGATACATT
225701 CTGTCTTTTT
Statistics
Matches: 200, Mismatches: 33, Indels: 48
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.01
20 143 0.71
21 7 0.04
22 1 0.00
24 1 0.00
25 9 0.05
26 9 0.05
27 2 0.01
29 1 0.00
30 2 0.01
31 22 0.11
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTA
Found at i:225582 original size:91 final size:91
Alignment explanation
Indices: 225423--225589 Score: 291
Period size: 91 Copynumber: 1.8 Consensus size: 91
225413 TTTTTACCAT
* *
225423 GATGTATCGATACATTTTTTAATGTATCGATACATGTATGAATGTATCGATATATTTTTCAATAT
1 GATGTATCGATACATTTTTCAATGAATCGATACATGTATGAATGTATCGATATATTTTTCAATAT
225488 ATCGATGCATTCTGTCTTTGTACCTA
66 ATCGATGCATTCTGTCTTTGTACCTA
*
225514 GATGTATCGATACATTTTTCAATGAATCGATACATGTATGAATGTATCGATACT-TTTTTCAATG
1 GATGTATCGATACATTTTTCAATGAATCGATACATGTATGAATGTATCGATA-TATTTTTCAATA
225578 TATCGATGCATT
65 TATCGATGCATT
225590 TTTGAATGTA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 71 0.99
92 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (91 bp):
GATGTATCGATACATTTTTCAATGAATCGATACATGTATGAATGTATCGATATATTTTTCAATAT
ATCGATGCATTCTGTCTTTGTACCTA
Found at i:225628 original size:111 final size:110
Alignment explanation
Indices: 225428--225700 Score: 393
Period size: 111 Copynumber: 2.5 Consensus size: 110
225418 ACCATGATGT
* * * * * * *
225428 ATCGATACATTTTTTAATGTATCGATACATGTATGAATGTATCGATATATTTTTCAATATATCGA
1 ATCGATACATGTATGAATGTATCGATAC-TTTTTTAATGTATCGATACATTTTTCAATATATCGA
* *
225493 TGCATTCTGTCTTTGTACCTAGATGTATCGATACATTTTTCAATGA
65 TACATTCTGTCTTTGTACCCAGATGTATCGATACATTTTTCAATGA
* * *
225539 ATCGATACATGTATGAATGTATCGATACTTTTTTCAATGTATCGATGCATTTTTGAATGTATCGA
1 ATCGATACATGTATGAATGTATCGATACTTTTTT-AATGTATCGATACATTTTTCAATATATCGA
* *
225604 TACATTCTGTCTTTTTACCCAGATGTATCGATACATTTTTCAATGT
65 TACATTCTGTCTTTGTACCCAGATGTATCGATACATTTTTCAATGA
225650 ATCGATACATGTATGAATGTATCGATACATTTTTTAATGTATCGATACATT
1 ATCGATACATGTATGAATGTATCGATAC-TTTTTTAATGTATCGATACATT
225701 CTGTCTTTTT
Statistics
Matches: 145, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
110 3 0.02
111 136 0.94
112 6 0.04
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (110 bp):
ATCGATACATGTATGAATGTATCGATACTTTTTTAATGTATCGATACATTTTTCAATATATCGAT
ACATTCTGTCTTTGTACCCAGATGTATCGATACATTTTTCAATGA
Found at i:225634 original size:91 final size:91
Alignment explanation
Indices: 225534--225750 Score: 301
Period size: 91 Copynumber: 2.4 Consensus size: 91
225524 TACATTTTTC
* * * * * *
225534 AATGAATCGATACATGTATGAATGTATCGATACTTTTTTCAATGTATCGATGCATTTTTGAATGT
1 AATGTATCGATACATGTATCAATGTATCGATACATGTATCAATGTATCGATACATTTTTGAATGT
225599 ATCGATACATTCTGTCTTTTTACCCA
66 ATCGATACATTCTGTCTTTTTACCCA
* * * * *
225625 GATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATTTTTTAATGT
1 AATGTATCGATACATGTATCAATGTATCGATACATGTATCAATGTATCGATACATTTTTGAATGT
225690 ATCGATACATTCTGTCTTTTTACCCA
66 ATCGATACATTCTGTCTTTTTACCCA
* *
225716 AATGTATCGATACAT-TTTACAATGTATCGACACAT
1 AATGTATCGATACATGTAT-CAATGTATCGATACAT
225751 CTAGTTAAAA
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 3 0.03
91 109 0.97
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (91 bp):
AATGTATCGATACATGTATCAATGTATCGATACATGTATCAATGTATCGATACATTTTTGAATGT
ATCGATACATTCTGTCTTTTTACCCA
Found at i:225641 original size:51 final size:50
Alignment explanation
Indices: 225573--225750 Score: 205
Period size: 51 Copynumber: 3.7 Consensus size: 50
225563 ATACTTTTTT
* *
225573 CAATGTATCGATGCATTTTTGAATGTATCGATACATTCTGTCTTTTTACC
1 CAATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTTTACC
*
225623 CAGATGTATCGATACATTTTTCAATGTATCGATACA---TG------TA-T
1 CA-ATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTTTACC
* *
225664 GAATGTATCGATACATTTTTTAATGTATCGATACATTCTGTCTTTTTACC
1 CAATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTTTACC
* *
225714 CAAATGTATCGATACATTTTACAATGTATCGACACAT
1 C-AATGTATCGATACATTTTTCAATGTATCGATACAT
225751 CTAGTTAAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
40 32 0.30
41 1 0.01
42 2 0.02
43 2 0.02
48 2 0.02
49 2 0.02
50 2 0.02
51 63 0.59
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (50 bp):
CAATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTTTACC
Found at i:230450 original size:13 final size:13
Alignment explanation
Indices: 230432--230456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230422 CATTTTACTA
230432 TGTATCGATACAT
1 TGTATCGATACAT
230445 TGTATCGATACA
1 TGTATCGATACA
230457 ATGCCCCATG
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:234719 original size:21 final size:21
Alignment explanation
Indices: 234693--234769 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
234683 AAAAATTCCA
234693 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
234714 AATGTATCGATACATTTGT-G
1 AATGTATCGATACATTTGTAG
* *
234734 AAATGTATCGATACA-TTCTACA
1 -AATGTATCGATACATTTGTA-G
234756 AATGTATCGATACA
1 AATGTATCGATACA
234770 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.08
21 47 0.92
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:234829 original size:19 final size:19
Alignment explanation
Indices: 234805--234872 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
234795 AATTCAACGA
234805 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
234824 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
234839 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
234856 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
234873 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:234843 original size:32 final size:32
Alignment explanation
Indices: 234807--234869 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
234797 TTCAACGATT
*
234807 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
234839 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
234870 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:234844 original size:13 final size:13
Alignment explanation
Indices: 234826--234850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234816 ACATAAGTTT
234826 TGTATCGATACAA
1 TGTATCGATACAA
234839 TGTATCGATACA
1 TGTATCGATACA
234851 TAAGTATTGT
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:234930 original size:13 final size:13
Alignment explanation
Indices: 234912--234937 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
234902 CATTTTTCTG
234912 TGTATCGATACAT
1 TGTATCGATACAT
234925 TGTATCGATACAT
1 TGTATCGATACAT
234938 GGATCTTTGT
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:234934 original size:33 final size:33
Alignment explanation
Indices: 234892--234958 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
234882 GCCAAGGAAA
***
234892 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
234925 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
234958 T
1 T
234959 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:237611 original size:53 final size:52
Alignment explanation
Indices: 237395--237615 Score: 225
Period size: 52 Copynumber: 4.2 Consensus size: 52
237385 ATTTTCGAGA
* * * * * * *
237395 GGATACTCCAACCCCTACTTTA-TTCTTAAAATATTGA-TTTCTCATAATCGG
1 GGATACTCCAACCCCGATTTTATTTC-TAAAACACTAATTTTTTCACAATCGG
* *
237446 GGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTCCACAATCGG
1 GGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTTCACAATCGG
* * *
237498 GGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTTTCCTT--TAATCGG
1 GGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTT--TTCACAATCGG
* * * *
237550 GGATACTCCAGCTCCGATTTTATTTCCAAAAACACTAATTTTTTCACAATCGA
1 GGATACTCCAACCCCGATTTTATTT-CTAAAACACTAATTTTTTCACAATCGG
*
237603 GGACACTCCAACC
1 GGATACTCCAACC
237616 TCGTTATTTC
Statistics
Matches: 139, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
51 30 0.22
52 80 0.58
53 28 0.20
54 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.33
Consensus pattern (52 bp):
GGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTTCACAATCGG
Found at i:244052 original size:55 final size:55
Alignment explanation
Indices: 243966--244903 Score: 1071
Period size: 55 Copynumber: 16.5 Consensus size: 55
243956 CGCCTTCTCT
*
243966 TTTTAAAGCCCACACAAGTTGGTGGC-GCTTCCTAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCC-AGTCCTCAAAGAGCAGGACGCC
*
244021 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGATGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTT-CCAGTCCTCAAAGAGCAGGACGCC
* *
244076 TTTTCTATTAAAGCCCACACAAGTTGGTGGC-GCTTCCTAGTCCTCAAAGAGTAGGACGCC
1 ---T-T-TTAAAGCCCACACAAGTTGGTGGCATCTTCC-AGTCCTCAAAGAGCAGGACGCC
244136 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTT-CCAGTCCTCAAAGAGCAGGACGCC
* * *
244191 TTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGCC
1 ---T-TTT-AAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCC
* * * *
244251 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCC
* * * *
244306 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGC-----C
244366 TTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCC
1 -TTTTAAAGCCCACACAAGTTGGTGGCATCTT-CCAGTCCTCAAAGAGCAGGACGCC
* * *
244422 TTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGCC
1 ---T-TTT-AAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCC
* * *
244482 TTTTAAAGCCCACCCAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGCTTTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGC-----C
* * * * *
244541 TTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGACCATGACACC
1 TTTT-AAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCC
* * *
244597 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCC
* * * *
244652 TCTTAAAGCCCACCCAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGCTTTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGC-----C
* * *
244711 TTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGACACC
1 TTTT-AAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCC
* * *
244767 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCC
* * * * *
244822 TCTTAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCC
* *
244877 TTTCAAAGCCCACACGAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
244904 CTTTTTACTC
Statistics
Matches: 779, Mismatches: 61, Indels: 86
0.84 0.07 0.09
Matches are distributed among these distances:
54 41 0.05
55 419 0.54
56 19 0.02
57 3 0.00
58 4 0.01
59 18 0.02
60 188 0.24
61 87 0.11
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (55 bp):
TTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGCC
Found at i:244135 original size:115 final size:114
Alignment explanation
Indices: 243932--244927 Score: 1192
Period size: 115 Copynumber: 8.7 Consensus size: 114
243922 TCTTTTAGCC
* * **
243932 CTTCCCAGTCCTCAAAAAGCAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGC-GCTT
1 CTTCCCAGTCCTCAAAGAGCAGGACGCCTT-T-TCTTTAAAGCCCACACAAGTTGGTGGCATTTT
243996 CCTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
64 CC-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* **
244048 CTTCCCAGTCCTCAAAGAGCAGGATGCCTTTTCTATTAAAGCCCACACAAGTTGGTGGC-GCTTC
1 CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCT-TTAAAGCCCACACAAGTTGGTGGCATTTTC
*
244112 CTAGTCCTCAAAGAGTAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
65 C-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
244163 CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTT-AAAGCCCACACAAGTTGGTGGCATTTTC
* * *
244228 CAATCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
65 CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
244278 TTTTCCAATCCTCAAAGAGCAGGATGCC-TTTC---AAAGCCCACACAAGTTGGTGGCATTTTCT
1 CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
244339 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
66 AGTCCTCAAAGAGCAGGACGC-----C-TTTTAAAGCCCACACAAGTTGGTGGCA
244394 CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTT-AAAGCCCACACAAGTTGGTGGCATTTTC
* * *
244459 CAATCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCA
65 CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
244509 CCTT--CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTT
1 -CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTC-TTT-AAAGCCCACACAAGTTGGTGGCATTT
* * * * *
244572 TCCAGTCCCCAAAGACCATGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
63 TCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * **
244624 TTTTCCAGTCCTCAAAGAGCAGGACACC---TC-TTAAAGCCCACCCAAGTTGGTGGCACCTT-C
1 CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
244684 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
66 AGTCCTCAAAGAGCAGGACGC-----CTTTT-AAAGCCCACACAAGTTGGTGGCA
* * * *
244739 TTTTCCAGTCCCCAAAGAGCAGGACACC-TTTC---AAAGCCCACACAAGTTGGTGGCATTTTCC
1 CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
244800 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCTACACAAGTTGGTGGCA
66 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
244849 CCTT-TCAGTCCTCAAAGAGTAGGACGCC-TTTC---AAAGCCCACACGAGTTGGTGGCACTTTT
1 -CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTAAAGCCCACACAAGTTGGTGGCA-TTTT
* * *
244909 -TACTCCTCAATGAGCAGGA
64 CCAGTCCTCAAAGAGCAGGA
244928 TACACTTTAT
Statistics
Matches: 786, Mismatches: 65, Indels: 64
0.86 0.07 0.07
Matches are distributed among these distances:
109 17 0.02
110 156 0.20
111 12 0.02
113 2 0.00
114 40 0.05
115 379 0.48
116 126 0.16
117 6 0.01
121 48 0.06
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (114 bp):
CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:244254 original size:27 final size:27
Alignment explanation
Indices: 244224--244309 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
244214 TTGGTGGCAT
244224 TTTCCAATCCTCAAAGAGCAGGATGCC
1 TTTCCAATCCTCAAAGAGCAGGATGCC
* * ** *
244251 TTTCAAAGCC-CACACA-AGTTGG-TGGCAT
1 TTTCCAATCCTCA-A-AGAGCAGGAT-GC-C
244279 TTTCCAATCCTCAAAGAGCAGGATGCC
1 TTTCCAATCCTCAAAGAGCAGGATGCC
244306 TTTC
1 TTTC
244310 AAAGCCCACA
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
26 3 0.07
27 20 0.48
28 16 0.38
29 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (27 bp):
TTTCCAATCCTCAAAGAGCAGGATGCC
Found at i:244261 original size:170 final size:171
Alignment explanation
Indices: 243966--244927 Score: 1260
Period size: 170 Copynumber: 5.7 Consensus size: 171
243956 CGCCTTCTCT
*
243966 TTTTAAAGCCCACACAAGTTGGTGGC-GCTTCCTAGTCCTCAAAGAGCAGGACG-C----CTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCC-AGTCCTCAAAGAGCAGGACGCCTTTTCTTTT
* * *
244025 -AAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGATGCCTTTTCTATTAAAG
65 CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC-TTTC----AAAG
** *
244089 CCCACACAAGTTGGTGGC-GCTTCCTAGTCCTCAAAGAGTAGGACGCC
125 CCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACGCC
244136 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTC-TTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT
* *
244199 CAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGCCTTTCAAAGCCCAC
65 CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
* *
244264 ACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGCC
130 ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
* ** * * * *
244306 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTC
* *
244371 AAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGC
66 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG-C----CTTTCAAAGC
* *
244436 CCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGCC
126 CCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
* * *
244482 TTTTAAAGCCCACCCAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTC
* * * *
244546 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGACCATGACACCTTTCAAAGCCCACA
66 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACA
*
244611 CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC
131 CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
* * * *
244652 TCTTAAAGCCCACCCAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTC
* *
244716 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACA
66 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACA
*
244781 CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC
131 CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
* * * *
244822 TCTTAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACG-C----C-TTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTC
* * * *
244881 AAAGCCCACACGAGTTGGTGGCACTTTT-TACTCCTCAATGAGCAGGA
66 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
244928 TACACTTTAT
Statistics
Matches: 728, Mismatches: 46, Indels: 41
0.89 0.06 0.05
Matches are distributed among these distances:
165 41 0.06
166 5 0.01
170 391 0.54
171 76 0.10
172 1 0.00
174 8 0.01
175 123 0.17
176 83 0.11
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (171 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTC
AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACA
CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC
Found at i:245735 original size:19 final size:19
Alignment explanation
Indices: 245711--245778 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
245701 AATTCAACGA
245711 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
245730 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
245745 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
245762 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
245779 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:245749 original size:32 final size:32
Alignment explanation
Indices: 245713--245775 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
245703 TTCAACGATT
*
245713 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
245745 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
245776 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:245750 original size:13 final size:13
Alignment explanation
Indices: 245732--245756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
245722 ACATAAGTTT
245732 TGTATCGATACAA
1 TGTATCGATACAA
245745 TGTATCGATACA
1 TGTATCGATACA
245757 TAAGTATTGT
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:245836 original size:13 final size:13
Alignment explanation
Indices: 245818--245843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
245808 CATTTTTCTG
245818 TGTATCGATACAT
1 TGTATCGATACAT
245831 TGTATCGATACAT
1 TGTATCGATACAT
245844 GATCTTTGTA
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:245859 original size:32 final size:33
Alignment explanation
Indices: 245798--245863 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
245788 GCCAAGGAAA
**
245798 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTGATCTGTGTATCGATACAT
*
245831 TGTATCGATACA-TGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCTGTGTATCGATACAT
245863 T
1 T
245864 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (33 bp):
TGTATCGATACATTGATCTGTGTATCGATACAT
Found at i:247454 original size:51 final size:52
Alignment explanation
Indices: 247378--247600 Score: 193
Period size: 52 Copynumber: 4.3 Consensus size: 52
247368 TTATTTTCGA
* * * * *
247378 GGGGATACTCCAACCCCTG-CTTTATTCTTAAAATATTGATTTCT-CATAATC
1 GGGGATACTCCAACCCC-GATTTTATTCTTAAAACACTAATTTCTCCACAATC
* *
247429 GGGGATACTCCAACCTCGATTTTATTGC-TAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATT-CTTAAAACACTAATTTCTCCACAATC
* * **
247481 GGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTT-TCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTCTTAAAACACTAATTTCTCC-ACAATC
* * * ** * * *
247533 GGGGATACTCTAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTA-TTCTTAAAACACTAATTTCTCCACAATC
* *
247586 GAGGACACTCCAACC
1 GGGGATACTCCAACC
247601 TCGTTATTTC
Statistics
Matches: 139, Mismatches: 26, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
50 1 0.01
51 37 0.27
52 70 0.50
53 29 0.21
54 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGATTTTATTCTTAAAACACTAATTTCTCCACAATC
Found at i:247494 original size:52 final size:52
Alignment explanation
Indices: 247425--247603 Score: 200
Period size: 52 Copynumber: 3.4 Consensus size: 52
247415 GATTTCTCAT
* *
247425 AATCGGGGATACTCCAACCTCGATTTTATTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCTCGATTTTATTCCTAAAACACCAATTTTTCCAC
* ** **
247477 AATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAA-TTTTCCTTT
1 AATCGGGGATACTCCAACCTCGATTTTATTCCTAAAACACCAATTTTTCC-AC
* * * *
247529 AATCGGGGATACT-CTAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCAC
1 AATCGGGGATACTCCAACCT-CGATTTTA-TTCCTAAAACACCAATTTTTCCAC
* *
247582 AATCGAGGACACTCCAACCTCG
1 AATCGGGGATACTCCAACCTCG
247604 TTATTTCATC
Statistics
Matches: 103, Mismatches: 19, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
51 9 0.09
52 60 0.58
53 25 0.24
54 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
AATCGGGGATACTCCAACCTCGATTTTATTCCTAAAACACCAATTTTTCCAC
Found at i:247829 original size:78 final size:78
Alignment explanation
Indices: 247679--247829 Score: 196
Period size: 78 Copynumber: 1.9 Consensus size: 78
247669 CCAAAATATT
* ** * * * *
247679 GATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTT
1 GATTTCTCACAACCGGGGATACTCCAACCCCGTTATTTTCAAGGGAACACTCCAACCCCGATTTT
* *
247744 TTTTCTAATCATC
66 ATCTCTAATCATC
*
247757 GATTTCTCACAACCGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG-TTAT
1 GATTTCTCACAACCGGGGATACTCCAACCCCGTTATTTTCAAGGGAACACTCCAACCCCGATT-T
247821 TATCTCTAA
65 TATCTCTAA
247830 AAACATTAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
77 2 0.03
78 60 0.97
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (78 bp):
GATTTCTCACAACCGGGGATACTCCAACCCCGTTATTTTCAAGGGAACACTCCAACCCCGATTTT
ATCTCTAATCATC
Found at i:250925 original size:139 final size:139
Alignment explanation
Indices: 250670--250938 Score: 351
Period size: 139 Copynumber: 1.9 Consensus size: 139
250660 GGAGATACTT
* * * *
250670 GCAAGGAGATTAGTCAGTCTATCAATGTCAATGGCAAGAAAGACAGGTATGGATTGGGTATCTAG
1 GCAAGGAGATTAGTCAGTCCATCAATGTCAATGGCAAGAAAGACAGGCATAGATTGGGTATCAAG
* * * * * * *
250735 CCAAAGTGGGTTTAGAAGAAGAAAATTAAGAATAGTTATCAAAAGAAGAAGTCAGCCCGAGCCAT
66 CCAAAATAGGTTCAAAAGAACAAAATTAAGAATAGATATCAAAAGAAGAAGTCAGCCCAAGCCAT
250800 TAGTCAATG
131 TAGTCAATG
* ** * * *
250809 GCAAGGGGATTAGTTGGTCCATCAATGTCAATGGCAAGAAAGATAGGCCTAGATTGGGTTTCAAG
1 GCAAGGAGATTAGTCAGTCCATCAATGTCAATGGCAAGAAAGACAGGCATAGATTGGGTATCAAG
* *
250874 CCAAAATAAGG-TCAAAAGAACAAAATTGAGAATAGATATCAAAAGATGAAGTCAGCCCAAGCCA
66 CCAAAAT-AGGTTCAAAAGAACAAAATTAAGAATAGATATCAAAAGAAGAAGTCAGCCCAAGCCA
250938 T
130 T
250939 CAACAGTCAA
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
139 108 0.98
140 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (139 bp):
GCAAGGAGATTAGTCAGTCCATCAATGTCAATGGCAAGAAAGACAGGCATAGATTGGGTATCAAG
CCAAAATAGGTTCAAAAGAACAAAATTAAGAATAGATATCAAAAGAAGAAGTCAGCCCAAGCCAT
TAGTCAATG
Found at i:257304 original size:13 final size:13
Alignment explanation
Indices: 257286--257311 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
257276 CAATTTGGGA
257286 TGTATCGATACAT
1 TGTATCGATACAT
257299 TGTATCGATACAT
1 TGTATCGATACAT
257312 CTTGTGTGTA
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:257308 original size:33 final size:32
Alignment explanation
Indices: 257266--257329 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
257256 TACAAGCTAA
257266 TGTATCGATACAAT-TTGGGATGTATCGATACAT
1 TGTATCGATAC-ATCTTGGG-TGTATCGATACAT
*
257299 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
257330 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:261569 original size:19 final size:19
Alignment explanation
Indices: 261545--261608 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
261535 TTTCAACGAT
261545 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
261564 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
261578 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
261596 TTGTATCGATACA
1 TTGTATCGATACA
261609 ATGTATCGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:261582 original size:32 final size:32
Alignment explanation
Indices: 261546--261616 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
261536 TTCAACGATT
261546 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
261578 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
261610 TGTATCG
1 TGTATCG
261617 CTAGGAAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:261583 original size:13 final size:13
Alignment explanation
Indices: 261565--261589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
261555 ACATAAGTGT
261565 TGTATCGATACAA
1 TGTATCGATACAA
261578 TGTATCGATACA
1 TGTATCGATACA
261590 TAAGTGTTGT
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:261657 original size:48 final size:48
Alignment explanation
Indices: 261597--261738 Score: 284
Period size: 48 Copynumber: 3.0 Consensus size: 48
261587 ACATAAGTGT
261597 TGTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGTTG
1 TGTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGTTG
261645 TGTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGTTG
1 TGTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGTTG
261693 TGTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGT
1 TGTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGT
261739 ATCGATACAT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 94 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (48 bp):
TGTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGTTG
Found at i:261774 original size:13 final size:13
Alignment explanation
Indices: 261756--261781 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
261746 CATTTTTCTG
261756 TGTATCGATACAT
1 TGTATCGATACAT
261769 TGTATCGATACAT
1 TGTATCGATACAT
261782 CTAGGAAGTT
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:262326 original size:11 final size:11
Alignment explanation
Indices: 262295--262328 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
262285 AATCCTTTAG
*
262295 CAAAAAAAAAA
1 CAAAAAAAACA
*
262306 CCAAAAAAACA
1 CAAAAAAAACA
262317 CAAAAAAAACA
1 CAAAAAAAACA
262328 C
1 C
262329 TATTCCCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAAAAAACA
Found at i:264191 original size:51 final size:51
Alignment explanation
Indices: 264131--264247 Score: 147
Period size: 51 Copynumber: 2.4 Consensus size: 51
264121 AATTCTCTGC
264131 AATCGGGGATA-TCCCAACTCCGATTTCATTT-TCAAAACA-CTAATTTTCTAT
1 AATCGGGGATACT-CCAACTCCGATTTCATTTCT-AAAACATC-AATTTTCTAT
*
264182 AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAA-TTT-T-T
1 AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTAT
*
264230 CATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
264248 CCCGTTAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
48 18 0.30
49 1 0.02
50 3 0.05
51 36 0.59
52 3 0.05
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTAT
Found at i:264267 original size:27 final size:27
Alignment explanation
Indices: 264229--264305 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
264219 CATCAATTTT
264229 TCATCGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
*
264256 TCATCGGGGATACTCCAACCCCGTTAT
1 TCATCGGGGATACTCCAACCCCGTTAA
** *
264283 TTTTGAGGGGATACTCCAACCCC
1 TCAT-CGGGGATACTCCAACCCC
264306 CGGATTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 28 0.62
28 17 0.38
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:264434 original size:79 final size:80
Alignment explanation
Indices: 264258--264435 Score: 236
Period size: 80 Copynumber: 2.2 Consensus size: 80
264248 CCCGTTAATC
* **
264258 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCCGGATTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGATTTATTTCTAAAA
* * *
264323 TATTAATTTCTTATA
66 TATGAATTTCTCACA
* *
264338 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAA-CCCCGGTTTTATTTC-CAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGATTTATTTCTAAAA
*
264401 TCATCGATTTTC-CACA
66 T-AT-GAATTTCTCACA
264417 ATCGGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
264436 TATCTTTATT
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 4 0.05
79 37 0.43
80 46 0.53
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGATTTATTTCTAAAA
TATGAATTTCTCACA
Found at i:264496 original size:52 final size:50
Alignment explanation
Indices: 264369--264538 Score: 187
Period size: 52 Copynumber: 3.3 Consensus size: 50
264359 TTATCTCCGA
* * * *
264369 GGGGATACTCCAACCCCGGTTTTATTTCCAAATCATCGATTTTCCACAATC
1 GGGGATACTCCAA-CCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
* * **
264420 GGGGATACTCCAACCCTATCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCGAT-TTTATTTCCAAAACACCAATTTTCC-ACAATC
* * *
264472 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCGCAATT
1 GGGGATACTCCAAC-CCGATTTTATTTCC-AAAACACCAATTTTCCACAATC
*
264524 GAGGATACTCCAACC
1 GGGGATACTCCAACC
264539 TCGTTATTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
50 4 0.04
51 35 0.35
52 42 0.42
53 19 0.19
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:266772 original size:13 final size:12
Alignment explanation
Indices: 266754--266787 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
266744 AAATCTTCAC
266754 TTTTTTTTTCTGT
1 TTTTTTTTTCT-T
*
266767 TTTTTTCTTCTT
1 TTTTTTTTTCTT
266779 TTTTTTTTT
1 TTTTTTTTT
266788 TAGAATTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:287414 original size:21 final size:20
Alignment explanation
Indices: 287390--287446 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 20
287380 ACCTTCTCTT
*
287390 CAAAAAAAATAAAAAAAAAAG
1 CAAAAAAAA-AAAAAAAAAAA
287411 CAAAAAAAAAAAACAAAAAAA
1 CAAAAAAAAAAAA-AAAAAAA
287432 CAAAACAAAGAAAAA
1 CAAAA-AAA-AAAAA
287447 GAGAGAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 4 0.12
21 20 0.62
22 3 0.09
23 5 0.16
ACGTcount: A:0.86, C:0.09, G:0.04, T:0.02
Consensus pattern (20 bp):
CAAAAAAAAAAAAAAAAAAA
Found at i:287417 original size:14 final size:13
Alignment explanation
Indices: 287391--287446 Score: 69
Period size: 13 Copynumber: 4.3 Consensus size: 13
287381 CCTTCTCTTC
*
287391 AAAAAAAA-TAAA
1 AAAAAAAACAAAA
*
287403 AAAAAAAGCAAAA
1 AAAAAAAACAAAA
287416 AAAAAAAACAAAA
1 AAAAAAAACAAAA
*
287429 AAACAAAACAAAGA
1 AAAAAAAACAAA-A
287443 AAAA
1 AAAA
287447 GAGAGAAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 7 0.19
13 26 0.70
14 4 0.11
ACGTcount: A:0.88, C:0.07, G:0.04, T:0.02
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:287420 original size:26 final size:26
Alignment explanation
Indices: 287391--287446 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
287381 CCTTCTCTTC
* *
287391 AAAAAAAATAAAAAAA-AAAGCAAAA
1 AAAAAAAACAAAAAAACAAAACAAAA
*
287416 AAAAAAAACAAAAAAACAAAACAAAG
1 AAAAAAAACAAAAAAACAAAACAAAA
287442 AAAAA
1 AAAAA
287447 GAGAGAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.88, C:0.07, G:0.04, T:0.02
Consensus pattern (26 bp):
AAAAAAAACAAAAAAACAAAACAAAA
Found at i:288589 original size:55 final size:54
Alignment explanation
Indices: 288461--288842 Score: 530
Period size: 55 Copynumber: 6.9 Consensus size: 54
288451 TTCCTTTTAA
** *
288461 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTC
1 AAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGA---C---ACCTTTC
* *
288521 AAAGCCCATACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTTTC
1 AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACACCTTTC
* *
288576 AAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACACCTTTT
1 AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACACCTTTC
* *
288631 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTC
1 AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACACCTTTC
288686 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTC
1 AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACACCTTTC
* *
288741 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
1 AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACACCTTTC
* * *
288796 AAAGCCTACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGA
288843 TACACTTTAT
Statistics
Matches: 297, Mismatches: 21, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
54 3 0.01
55 245 0.82
56 6 0.02
58 1 0.00
60 24 0.08
61 18 0.06
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (54 bp):
AAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACACCTTTC
Found at i:288656 original size:29 final size:29
Alignment explanation
Indices: 288623--288768 Score: 85
Period size: 28 Copynumber: 5.2 Consensus size: 29
288613 AAGAGCAGGA
288623 CACCTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTTTAAAGCCCACACAAGTTGGTGG
* * **
288652 CACC-TTT-CAGTCCC-CA-AAG-AGCAGG
1 CACCTTTTAAAG-CCCACACAAGTTGGTGG
*
288677 ACACCTTTCAAAGCCCACACAAGTTGGTGG
1 -CACCTTTTAAAGCCCACACAAGTTGGTGG
** * * * **
288707 CA--TTTTCCAGTCCTCA-AAG-AGCAGG
1 CACCTTTTAAAGCCCACACAAGTTGGTGG
*
288732 ACACCTTTCAAAGCCCACACAAGTTGGTGG
1 -CACCTTTTAAAGCCCACACAAGTTGGTGG
288762 CACCTTT
1 CACCTTT
288769 CAGTCCTCAA
Statistics
Matches: 80, Mismatches: 25, Indels: 24
0.62 0.19 0.19
Matches are distributed among these distances:
25 6 0.08
26 12 0.15
27 18 0.22
28 19 0.24
29 19 0.24
30 6 0.08
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (29 bp):
CACCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:288693 original size:26 final size:26
Alignment explanation
Indices: 288611--288693 Score: 60
Period size: 26 Copynumber: 3.1 Consensus size: 26
288601 TTCCAATCCT
*
288611 CAAAGAGCAGGACACCTTTTAAAGCC
1 CAAAGAGCAGGACACCTTTCAAAGCC
** * ***
288637 CACACA-AGTTGGTGGCACCTTTCAGTCCC
1 CA-A-AGAG-CAG-GACACCTTTCAAAGCC
288666 CAAAGAGCAGGACACCTTTCAAAGCC
1 CAAAGAGCAGGACACCTTTCAAAGCC
288692 CA
1 CA
288694 CACAAGTTGG
Statistics
Matches: 39, Mismatches: 13, Indels: 10
0.63 0.21 0.16
Matches are distributed among these distances:
26 16 0.41
27 5 0.13
28 5 0.13
29 13 0.33
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (26 bp):
CAAAGAGCAGGACACCTTTCAAAGCC
Found at i:288740 original size:27 final size:27
Alignment explanation
Indices: 288710--288795 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
288700 TTGGTGGCAT
288710 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * **
288737 TTTCAAAGCCCACACAAGTTGGTGG-CACC
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
*
288766 TTT-CAGTCCTCAAAGAGCAGGACGCC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
288792 TTTC
1 TTTC
288796 AAAGCCTACA
Statistics
Matches: 41, Mismatches: 13, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
25 3 0.07
26 9 0.22
27 10 0.24
28 6 0.15
29 10 0.24
30 3 0.07
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:289688 original size:19 final size:16
Alignment explanation
Indices: 289662--289760 Score: 66
Period size: 19 Copynumber: 6.0 Consensus size: 16
289652 AATTTCAGCG
289662 ATTTGTATCGATACATA
1 ATTTGTATCGATACA-A
289679 AGTGTTGTATCGATAC-A
1 A-T-TTGTATCGATACAA
*
289696 A--TGTATCAATACATAA
1 ATTTGTATCGATAC--AA
289712 ATGTTGTATCGATAC-A
1 AT-TTGTATCGATACAA
289728 A--TGTATCGATACACA
1 ATTTGTATCGATACA-A
289743 AGTTTTGTATCGATACAA
1 A--TTTGTATCGATACAA
289761 TGTATCGCTA
Statistics
Matches: 66, Mismatches: 2, Indels: 27
0.69 0.02 0.28
Matches are distributed among these distances:
13 21 0.32
15 2 0.03
16 4 0.06
17 3 0.05
18 2 0.03
19 34 0.52
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (16 bp):
ATTTGTATCGATACAA
Found at i:289701 original size:32 final size:32
Alignment explanation
Indices: 289665--289767 Score: 170
Period size: 32 Copynumber: 3.2 Consensus size: 32
289655 TTCAGCGATT
289665 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
289697 TGTATCAATACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
289729 TGTATCGATACACAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
289761 TGTATCG
1 TGTATCG
289768 CTAGGAAGCT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:289767 original size:13 final size:13
Alignment explanation
Indices: 289684--289740 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
289674 ACATAAGTGT
289684 TGTATCGATACAA
1 TGTATCGATACAA
*
289697 TGTATCAATACATAAA
1 TGTATCGATAC---AA
289713 TGTTGTATCGATACAA
1 ---TGTATCGATACAA
289729 TGTATCGATACA
1 TGTATCGATACA
289741 CAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
16 4 0.11
19 10 0.28
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:289835 original size:21 final size:21
Alignment explanation
Indices: 289791--289847 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
289781 GCCAAGGAAA
*
289791 TGTATCGATACAT-TTTTCTG
1 TGTATCGATACATCTATTCTG
*
289811 TGTATCGATACATCTATTCTT
1 TGTATCGATACATCTATTCTG
289832 TGTATCGATACATCTA
1 TGTATCGATACATCTA
289848 GGAAGTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (21 bp):
TGTATCGATACATCTATTCTG
Found at i:290379 original size:11 final size:11
Alignment explanation
Indices: 290350--290381 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
290340 AATCCTTTAG
290350 CAAAAAAAAC-
1 CAAAAAAAACA
290360 C-AAAAAAACA
1 CAAAAAAAACA
290370 CAAAAAAAACA
1 CAAAAAAAACA
290381 C
1 C
290382 TATTTCCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.40
10 2 0.10
11 10 0.50
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAAAAAACA
Found at i:292224 original size:51 final size:51
Alignment explanation
Indices: 292164--292281 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 51
292154 CAGTTCTCCG
292164 TAATCGGGGATA-TCCCAACTCCGATTTCATTT-TCAAAACA-CTAATTTTCTA
1 TAATCGGGGATACT-CCAACTCCGATTTCATTTCT-AAAACATC-AATTTTCTA
*
292215 TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAA-TTT-T-
1 TAATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTA
*
292263 TCATCGGGGATACTCCAAC
1 TAATCGGGGATACTCCAAC
292282 CCCGTTAATC
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
48 18 0.29
49 1 0.02
50 3 0.05
51 37 0.60
52 3 0.05
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (51 bp):
TAATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTA
Found at i:292335 original size:28 final size:27
Alignment explanation
Indices: 292263--292339 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
292253 CATCAATTTT
*
292263 TCATCGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCATTAA
292290 TCATCGGGGATACTCCAACCCCATT-A
1 TCATCGGGGATACTCCAACCCCATTAA
**
292316 TTTTCGAGGGGATACTCCAACCCC
1 TCATC--GGGGATACTCCAACCCC
292340 CGGCTTTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.09
27 24 0.53
28 17 0.38
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCATTAA
Found at i:292468 original size:79 final size:80
Alignment explanation
Indices: 292292--292472 Score: 242
Period size: 80 Copynumber: 2.3 Consensus size: 80
292282 CCCGTTAATC
* * *
292292 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
* *
292357 TATTAATTTCTCATA
66 TATGAATTTCTCACA
* * *
292372 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCTAA-CCCCGGTTTTATTTC-CAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
*
292435 TCATCGATTTTC-CACA
66 T-AT-GAATTTCTCACA
292451 ATCGGGGATACTCCAACCCCGT
1 ATCGGGGATACTCCAACCCCGT
292473 CTTTATTTTC
Statistics
Matches: 90, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
78 4 0.04
79 41 0.46
80 45 0.50
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
TATGAATTTCTCACA
Found at i:292530 original size:52 final size:50
Alignment explanation
Indices: 292403--292577 Score: 197
Period size: 52 Copynumber: 3.4 Consensus size: 50
292393 TTATCTCCGA
* * * *
292403 GGGGATACTCTAACCCCGGTTTTATTTCCAAATCATCGATTTTCCACAATC
1 GGGGATACTCCAACCCC-GTTTTATTTCCAAAACACCAATTTTCCACAATC
* **
292454 GGGGATACTCCAACCCCGTCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGT-TTTATTTCCAAAACACCAATTTTCC-ACAATC
* * *
292506 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATT
1 GGGGATACTCCAACCCCG-TTTTATTTCC-AAAACACCAATTTTCCACAATC
* *
292558 GAGGATACTCCAACCTCGTT
1 GGGGATACTCCAACCCCGTT
292578 ATTTCATCGG
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
50 2 0.02
51 39 0.38
52 47 0.45
53 16 0.15
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGTTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:292583 original size:31 final size:30
Alignment explanation
Indices: 292548--292634 Score: 101
Period size: 28 Copynumber: 3.0 Consensus size: 30
292538 AACACCAATT
*
292548 TTTCACAATTGAGGATACTCCAACCTCGTTA
1 TTTCAC-ATCGAGGATACTCCAACCTCGTTA
*
292579 TTT--CATCGGGGATACTCCAACCTCGTTA
1 TTTCACATCGAGGATACTCCAACCTCGTTA
* *
292607 TTT--CATCGGGGATACTCCAACCCCGTTA
1 TTTCACATCGAGGATACTCCAACCTCGTTA
292635 CCTCCGAGGG
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
28 49 0.92
29 1 0.02
31 3 0.06
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (30 bp):
TTTCACATCGAGGATACTCCAACCTCGTTA
Found at i:292592 original size:28 final size:28
Alignment explanation
Indices: 292560--292634 Score: 141
Period size: 28 Copynumber: 2.7 Consensus size: 28
292550 TCACAATTGA
292560 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCTCGTTATTTCATCGG
292588 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCTCGTTATTTCATCGG
*
292616 GGATACTCCAACCCCGTTA
1 GGATACTCCAACCTCGTTA
292635 CCTCCGAGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (28 bp):
GGATACTCCAACCTCGTTATTTCATCGG
Found at i:292645 original size:28 final size:28
Alignment explanation
Indices: 292560--292659 Score: 101
Period size: 28 Copynumber: 3.6 Consensus size: 28
292550 TCACAATTGA
* ** **
292560 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACCTCAGAGG
* ** **
292588 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACCTCAGAGG
*
292616 GGATACTCCAACCCCGTTACCTCCGAGG
1 GGATACTCCAACCCCGTTACCTCAGAGG
292644 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
292660 GCTTTATTCC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACCTCAGAGG
Found at i:292793 original size:78 final size:78
Alignment explanation
Indices: 292613--292834 Score: 223
Period size: 78 Copynumber: 2.8 Consensus size: 78
292603 GTTATTTCAT
** *
292613 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * *
292678 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * * * * ** *
292692 TGGGGATACTCCAACCTCATTATTTCCGAGGGGATACTCCAATCCCGATTTTTTTTC-TAATCAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTATTCCCAAAAT-AT
292756 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* * * * *
292770 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGGACACTCCAACCCCGTTATTA-TCTCCAAAATA
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGAT-TTATTC-CCAAAATA
292834 T
64 T
292835 TAAATTTCTC
Statistics
Matches: 112, Mismatches: 27, Indels: 8
0.76 0.18 0.05
Matches are distributed among these distances:
77 3 0.03
78 61 0.54
79 45 0.40
80 3 0.03
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:297958 original size:13 final size:13
Alignment explanation
Indices: 297940--297965 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
297930 TACAAGCCAA
297940 TGTATCGATACAT
1 TGTATCGATACAT
297953 TGTATCGATACAT
1 TGTATCGATACAT
297966 CTTGTGTGTA
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:298072 original size:20 final size:21
Alignment explanation
Indices: 298025--298077 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
298015 GCCAATCACC
*
298025 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
298046 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
298066 TGTATCGATACA
1 TGTATCGATACA
298078 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:298083 original size:13 final size:13
Alignment explanation
Indices: 298065--298089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
298055 ACATTTGGTC
298065 ATGTATCGATACA
1 ATGTATCGATACA
298078 ATGTATCGATAC
1 ATGTATCGATAC
298090 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:298141 original size:20 final size:20
Alignment explanation
Indices: 298101--298137 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
298091 GTGCATTATG
298101 TATCGATACATTTGAAGGTT
1 TATCGATACATTTGAAGGTT
*
298121 TATCGATATATTT-AAGG
1 TATCGATACATTTGAAGG
298138 GTTTTGACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (20 bp):
TATCGATACATTTGAAGGTT
Found at i:298427 original size:20 final size:20
Alignment explanation
Indices: 298402--298439 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
298392 ACAATAAATA
298402 TATCGATACATTTACTTATG
1 TATCGATACATTTACTTATG
*
298422 TATCGATACATTTCCTTA
1 TATCGATACATTTACTTA
298440 GCAGTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (20 bp):
TATCGATACATTTACTTATG
Found at i:298502 original size:20 final size:21
Alignment explanation
Indices: 298462--298532 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
298452 GTGGTTTTGA
* *
298462 ATTGATACATTTCA-AGCATGT
1 ATTGATACA-TTCATTGTATGT
298483 ATTGATACATTCATT-TATGT
1 ATTGATACATTCATTGTATGT
* * * *
298503 ATCGATACATTTATTGTTTAT
1 ATTGATACATTCATTGTATGT
298524 ATTGATACA
1 ATTGATACA
298533 AATTATAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 21 0.51
21 20 0.49
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (21 bp):
ATTGATACATTCATTGTATGT
Found at i:300146 original size:31 final size:32
Alignment explanation
Indices: 300111--300271 Score: 129
Period size: 31 Copynumber: 5.2 Consensus size: 32
300101 AACTCGTTCA
*
300111 GGCTTTGA-TAAGGGTGCTACCAACTTGTGTG
1 GGCTTTGACTAAGGGTGCCACCAACTTGTGTG
* * **
300142 GGCTTTGACTCAA--GTGCCGCCAACTCGTGCA
1 GGCTTTGACT-AAGGGTGCCACCAACTTGTGTG
* *
300173 GGCTTTGACT-AGGTTGCCATCAACTTGTGTG
1 GGCTTTGACTAAGGGTGCCACCAACTTGTGTG
* * * **
300204 GGCTTTGACTTA-GGTGTCGCCAA-TTCGTGCA
1 GGCTTTGACTAAGGGTGCCACCAACTT-GTGTG
* *
300235 GGCTTTGACTAA-GGTGCCACTAACATGTGTG
1 GGCTTTGACTAAGGGTGCCACCAACTTGTGTG
300266 GGCTTT
1 GGCTTT
300272 TAACAAAAAG
Statistics
Matches: 99, Mismatches: 24, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
29 1 0.01
30 2 0.02
31 91 0.92
32 3 0.03
33 2 0.02
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (32 bp):
GGCTTTGACTAAGGGTGCCACCAACTTGTGTG
Found at i:300176 original size:62 final size:63
Alignment explanation
Indices: 300099--300271 Score: 235
Period size: 62 Copynumber: 2.8 Consensus size: 63
300089 AATCATGAAT
* *
300099 CCAACTCGTTCAGGCTTTGA-TAAGGGTGCTACCAACTTGTGTGGGCTTTGACTCAAGTGCCG
1 CCAACTCGTGCAGGCTTTGACTAAGGGTGCCACCAACTTGTGTGGGCTTTGACTCAAGTGCCG
* * * * *
300161 CCAACTCGTGCAGGCTTTGACT-AGGTTGCCATCAACTTGTGTGGGCTTTGACTTAGGTGTCG
1 CCAACTCGTGCAGGCTTTGACTAAGGGTGCCACCAACTTGTGTGGGCTTTGACTCAAGTGCCG
* * *
300223 CCAATTCGTGCAGGCTTTGACTAA-GGTGCCACTAACATGTGTGGGCTTT
1 CCAACTCGTGCAGGCTTTGACTAAGGGTGCCACCAACTTGTGTGGGCTTT
300272 TAACAAAAAG
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
62 95 0.98
63 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (63 bp):
CCAACTCGTGCAGGCTTTGACTAAGGGTGCCACCAACTTGTGTGGGCTTTGACTCAAGTGCCG
Found at i:300364 original size:62 final size:63
Alignment explanation
Indices: 300245--300596 Score: 370
Period size: 62 Copynumber: 5.5 Consensus size: 63
300235 GGCTTTGACT
* * * * * * *
300245 AAGGTGCCACTAACATGTGTGGGCTTTTAACAA-AAAGGAAAGGCGTCTTGCTCTTTGAGGACTA
1 AAGGTGCCACCAACTTGTGTGGGC-TTTAA-AAGAAA-AAAAGGCATCCTACTTTTTGAGGACTA
300309 A
63 A
* * *
300310 AAGGAGCCACCAACTTGTGTGTGCTTTAAAA-AAGAAAAGGCATCCTACTTTTTGAGGACTAA
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAAGGCATCCTACTTTTTGAGGACTAA
** * ** *
300372 AAGGT-CCACCAACTTGTGTGGGCTTTAAAAGAGAAAAAAGAAATGTGCCCTGCACTTTGAAGAC
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA-AAAAAAGGCA--T--CCTACTTTTTGAGGAC
300436 TAA
61 TAA
* *
300439 AAGGTGCCACCAACTTGTGTGGGCTTTAAAA-AGAAAAAGGCATCCTACTTTTTGAGGACTAT
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAAGGCATCCTACTTTTTGAGGACTAA
* * *
300501 AAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCAAGGCATCTTGCTTTTTGAGGACTA
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA---AAGGCATCCTACTTTTTGAGGACTA
300566 A
63 A
* *
300567 AAAGTGCCACCAACTTGTGTGGGTTTTAAA
1 AAGGTGCCACCAACTTGTGTGGGCTTTAAA
300597 GGGATTGTCA
Statistics
Matches: 241, Mismatches: 35, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
61 24 0.10
62 72 0.30
63 15 0.06
64 6 0.02
65 21 0.09
66 57 0.24
67 21 0.09
68 25 0.10
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (63 bp):
AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAAGGCATCCTACTTTTTGAGGACTAA
Found at i:300588 original size:128 final size:127
Alignment explanation
Indices: 300244--300596 Score: 471
Period size: 129 Copynumber: 2.8 Consensus size: 127
300234 AGGCTTTGAC
* * * *
300244 TAAGGTGCCACTAACATGTGTGGGCTTT-TAACAAAAAGGAAAGGCGTCTTGCTCTTTGAGGACT
1 TAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGAAAGGC-TCTTGCTCTTTGAGGACT
* *
300308 AAAAGGAGCCACCAACTTGTGTGTGCTTTAAAAAAGAAAAGGCATCCTACTTTTTGAGGACTA
65 AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCCTACTTTTTGAGGACTA
* * * * *
300371 AAAGGT-CCACCAACTTGTGTGGGCTTTAAAAGAGAAAAAAGAAATGTGC-CCTGCACTTTGAAG
1 TAAGGTGCCACCAACTTGTGTGGGCTTT-AAA-AGAAAAAGGAAA-G-GCTCTTGCTCTTTGAGG
300434 ACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAAGAAAAAGGCATCCTACTTTTTGAGGAC
62 ACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAG-AAAAGGCATCCTACTTTTTGAGGAC
300498 TA
126 TA
* * *
300500 TAAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCAAGGCATCTTGCTTTTTGAGGACT
1 TAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGAAAGGC-TCTTGCTCTTTGAGGACT
* *
300565 AAAAAGTGCCACCAACTTGTGTGGGTTTTAAA
65 AAAAGGTGCCACCAACTTGTGTGGGCTTTAAA
300597 GGGATTGTCA
Statistics
Matches: 195, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
126 21 0.11
127 6 0.03
128 57 0.29
129 88 0.45
130 21 0.11
131 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (127 bp):
TAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGAAAGGCTCTTGCTCTTTGAGGACTA
AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCCTACTTTTTGAGGACTA
Found at i:300657 original size:33 final size:31
Alignment explanation
Indices: 300571--300847 Score: 277
Period size: 31 Copynumber: 8.7 Consensus size: 31
300561 GACTAAAAAG
* *
300571 TGCCACCAACTTGTGTGGGTTTTA-AAGGGAT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGG-T
* * *
300602 TGTCATCGACTCGTGTGGGCTTTAGAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAG--AAGGGT
* * *
300635 TGCCACAGACTTGTGTAGGCTTTAGAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* *
300666 TGCCACCGAATTATGTGGGCTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
300697 TGCCACCGACTTATATGGGCTTTAGAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
*
300728 TGCCACCGACTTGTGTGGGCTTTAGAATGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
300759 TGCCACTGACTTATGTGGACTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
* * *
300792 TGCCACCGACTTGTATGGGTTTTAGAAAATGGT
1 TGCCACCGACTTGTGTGGGCTTTAG--AAGGGT
* * *
300825 TGCCACTGACTAGTGTGGACTTT
1 TGCCACCGACTTGTGTGGGCTTT
300848 TAAAAGAAAT
Statistics
Matches: 202, Mismatches: 37, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
31 128 0.63
33 69 0.34
34 5 0.02
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (31 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
Found at i:300683 original size:95 final size:94
Alignment explanation
Indices: 300571--300840 Score: 303
Period size: 95 Copynumber: 2.8 Consensus size: 94
300561 GACTAAAAAG
* * * * *
300571 TGCCACC-AACTTGTGTGGGTTTTA-AAGGGATTGTCATCGACTCGTGTGGGCTTTAGAAAAGGG
1 TGCCACCGAA-TTATGTGGGTTTTAGAAGGG-TTGCCACCGACTTGTATGGGCTTTAGAAAA-GG
*
300634 TTGCCACAGACTTGTGTAGGCTTTAGAGGGGT
63 TTGCCACAGACTTGTGTAGGCTTTAGAAGGGT
* *
300666 TGCCACCGAATTATGTGGGCTTTAGAAGGGTTGCCACCGACTTATATGGGCTTTAG-AAAGGTTG
1 TGCCACCGAATTATGTGGGTTTTAGAAGGGTTGCCACCGACTTGTATGGGCTTTAGAAAAGGTTG
* * *
300730 CCACCGACTTGTGTGGGCTTTAGAATGGT
66 CCACAGACTTGTGTAGGCTTTAGAAGGGT
* * * * *
300759 TGCCACTGACTTATGTGGACTTTAGAGAAGGGTTGCCACCGACTTGTATGGGTTTTAGAAAATGG
1 TGCCACCGAATTATGTGG-GTTT-TAGAAGGGTTGCCACCGACTTGTATGGGCTTTAGAAAA-GG
* *
300824 TTGCCACTGACTAGTGT
63 TTGCCACAGACTTGTGT
300841 GGACTTTTAA
Statistics
Matches: 149, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
93 46 0.31
94 5 0.03
95 71 0.48
96 10 0.07
97 17 0.11
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (94 bp):
TGCCACCGAATTATGTGGGTTTTAGAAGGGTTGCCACCGACTTGTATGGGCTTTAGAAAAGGTTG
CCACAGACTTGTGTAGGCTTTAGAAGGGT
Found at i:300977 original size:63 final size:63
Alignment explanation
Indices: 300902--301279 Score: 250
Period size: 63 Copynumber: 6.0 Consensus size: 63
300892 GATTGTGGAA
* * * *
300902 TTAAGAAGAAAAAAGGTACCATAGAGTTGTGGACTTTAAAAAAGATGCAATGGAGTTGTGAAC
1 TTAAAAAGAAAAAAGGTGCCATAGAGTTGTGGACTTTAAAAAAGATGCCATGGAGTTATGAAC
* * * * * * * * ** *
300965 TTAAAAAGAAAAAGGGGGCAATAGAGTTTTGAACTTTAAAAAGGGTGCTACAGAGTTATGGAC
1 TTAAAAAGAAAAAAGGTGCCATAGAGTTGTGGACTTTAAAAAAGATGCCATGGAGTTATGAAC
* * * ** *
301028 TTAAAAAGATAAAAGATGCCATAGAGTTGTGGACTTAAAAAGAAAAAGGGGGCCATAGAGTTATG
1 TTAAAAAGAAAAAAGGTGCCATAGAGTTGTGGACTT---TA-AAAAA-GATGCCATGGAGTTATG
*
301093 AAT
61 AAC
* * * * * *
301096 TTTAAAAG-----AGGTGCCACAGAGTTATGGACTTAAAATGATAAAGAGTGCCACGGAGTTGTG
1 TTAAAAAGAAAAAAGGTGCCATAGAGTTGTGGACTT-TAA--A-AAAGA-TGCCATGGAGTTATG
301156 AAC
61 AAC
* * * ** *
301159 TTAAAAAG-AAAAAGTGGGCCATGGAGTTGGGGAC-TTAAAAGGGA-GCCATGGAGTTATGGAC
1 TTAAAAAGAAAAAAG-GTGCCATAGAGTTGTGGACTTTAAAAAAGATGCCATGGAGTTATGAAC
* * * * *
301220 TTAAAAAGAAATAGGGTGCCATAGAGTTGTGGACTTTAAAAAGGGTGCCACGGAGTTATG
1 TTAAAAAGAAAAAAGGTGCCATAGAGTTGTGGACTTTAAAAAAGATGCCATGGAGTTATG
301280 GACTATAAGA
Statistics
Matches: 240, Mismatches: 58, Indels: 34
0.72 0.17 0.10
Matches are distributed among these distances:
60 1 0.00
61 41 0.17
62 14 0.06
63 137 0.57
64 1 0.00
66 3 0.01
67 7 0.03
68 36 0.15
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (63 bp):
TTAAAAAGAAAAAAGGTGCCATAGAGTTGTGGACTTTAAAAAAGATGCCATGGAGTTATGAAC
Found at i:300986 original size:34 final size:34
Alignment explanation
Indices: 300954--301262 Score: 159
Period size: 34 Copynumber: 9.6 Consensus size: 34
300944 AGATGCAATG
*
300954 GAGTTGTGAACTTAAAAAGAAAAAGGGGGCAATA
1 GAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATA
* * * * *
300988 GAGTTTTGAACTT-----TAAAAAGGGTGCTACA
1 GAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATA
* * **
301017 GAGTTATGGACTTAAAAAGATAAAA-GATGCCATA
1 GAGTTGTGAACTTAAAAAGA-AAAAGGGGGCCATA
*
301051 GAGTTGTGGACTTAAAAAGAAAAAGGGGGCCATA
1 GAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATA
* * * * *
301085 GAGTTATGAATTTTAAAAG----A-GGTGCCACA
1 GAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATA
* * * * * * **
301114 GAGTTATGGACTTAAAATGATAAAGAGTGCCACG
1 GAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATA
* *
301148 GAGTTGTGAACTTAAAAAGAAAAAGTGGGCCATG
1 GAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATA
* * * *
301182 GAGTTGGGGACTT-------AAAAGGGAGCCATG
1 GAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATA
* * * *
301209 GAGTTATGGACTTAAAAAGAAATAGGGTGCCATA
1 GAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATA
*
301243 GAGTTGTGGACTTTAAAAAG
1 GAGTTGTGAAC-TTAAAAAG
301263 GGTGCCACGG
Statistics
Matches: 212, Mismatches: 43, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
27 23 0.11
29 45 0.21
30 1 0.00
33 5 0.02
34 126 0.59
35 12 0.06
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (34 bp):
GAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATA
Found at i:301032 original size:28 final size:29
Alignment explanation
Indices: 300973--301035 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
300963 ACTTAAAAAG
* *
300973 AAAAAGGGGGCAATAGAGTTTTGAACTTT
1 AAAAAGGGGGCAACAGAGTTATGAACTTT
* * *
301002 AAAAAGGGTGCTACAGAGTTATGGAC-TT
1 AAAAAGGGGGCAACAGAGTTATGAACTTT
301030 AAAAAG
1 AAAAAG
301036 ATAAAAGATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (29 bp):
AAAAAGGGGGCAACAGAGTTATGAACTTT
Found at i:301071 original size:97 final size:96
Alignment explanation
Indices: 300941--301262 Score: 389
Period size: 97 Copynumber: 3.3 Consensus size: 96
300931 TGGACTTTAA
* * * *
300941 AAAAGATGCAATGGAGTTGTGAACTTAAAAAGAAAAAGGGGGCAATAGAGTTTTGAACTTTAAAA
1 AAAAGATGCCATAGAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATAGAGTTATGAACTTT-AAA
*
301006 AGGGTGCTACAGAGTTATGGACTTAAAAAGAT
65 AGGGTGCCACAGAGTTATGGACTTAAAAAGAT
* *
301038 AAAAGATGCCATAGAGTTGTGGACTTAAAAAGAAAAAGGGGGCCATAGAGTTATGAATTTTAAAA
1 AAAAGATGCCATAGAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATAGAGTTATGAACTTTAAAA
*
301103 GAGGTGCCACAGAGTTATGGACTTAAAATGAT
66 G-GGTGCCACAGAGTTATGGACTTAAAAAGAT
** * * ** *
301135 -AAAGAGTGCCACGGAGTTGTGAACTTAAAAAGAAAAAGTGGGCCATGGAGTTGGGGAC-TTAAA
1 AAAAGA-TGCCATAGAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATAGAGTTATGAACTTTAAA
* **
301198 AGGGAGCCATGGAGTTATGGACTTAAAAAGA-
65 AGGGTGCCACAGAGTTATGGACTTAAAAAGAT
* * *
301229 AATAGGGTGCCATAGAGTTGTGGACTTTAAAAAG
1 AA-AAGATGCCATAGAGTTGTGAAC-TTAAAAAG
301263 GGTGCCACGG
Statistics
Matches: 194, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
95 41 0.21
96 27 0.14
97 126 0.65
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (96 bp):
AAAAGATGCCATAGAGTTGTGAACTTAAAAAGAAAAAGGGGGCCATAGAGTTATGAACTTTAAAA
GGGTGCCACAGAGTTATGGACTTAAAAAGAT
Found at i:301128 original size:28 final size:28
Alignment explanation
Indices: 301071--301130 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
301061 CTTAAAAAGA
* *
301071 AAAAGGGGGCCATAGAGTTATGAATTTT
1 AAAAGGGGGCCACAGAGTTATGAATCTT
* *
301099 AAAAGAGGTGCCACAGAGTTATGGA-CTT
1 AAAAG-GGGGCCACAGAGTTATGAATCTT
301127 AAAA
1 AAAA
301131 TGATAAAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (28 bp):
AAAAGGGGGCCACAGAGTTATGAATCTT
Found at i:301206 original size:27 final size:27
Alignment explanation
Indices: 301168--301225 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
301158 CTTAAAAAGA
*
301168 AAAAGTGGGCCATGGAGTTGGGGACTT
1 AAAAGTGGGCCATGGAGTTAGGGACTT
*
301195 AAAAG-GGAGCCATGGAGTTATGGACTT
1 AAAAGTGG-GCCATGGAGTTAGGGACTT
301222 AAAA
1 AAAA
301226 AGAAATAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.34, C:0.10, G:0.34, T:0.21
Consensus pattern (27 bp):
AAAAGTGGGCCATGGAGTTAGGGACTT
Found at i:301222 original size:61 final size:63
Alignment explanation
Indices: 300857--301283 Score: 232
Period size: 63 Copynumber: 6.8 Consensus size: 63
300847 TTAAAAGAAA
* * * * * * * *
300857 TGCCATAGAATTGTGGACTTT-GAAA-GGTGCCAC-GAGATTGTGGAATTAAGAAGAAAAAAGG
1 TGCCATAGAGTTGGGGACTTTAAAAAGGGAGCCACGGAG-TTATGGACTTAAAAAGAAAAAGGG
* * * * * * *
300918 TACCATAGAGTTGTGGACTTTAAAAA-AGATGCAATGGAGTTGTGAACTTAAAAAGAAAAAGGG
1 TGCCATAGAGTTGGGGACTTTAAAAAGGGA-GCCACGGAGTTATGGACTTAAAAAGAAAAAGGG
* * ** * * * * *
300981 GGCAATAGAGTTTTGAACTTTAAAAAGGGTGCTACAGAGTTATGGACTTAAAAAGATAAAA-GA
1 TGCCATAGAGTTGGGGACTTTAAAAAGGGAGCCACGGAGTTATGGACTTAAAAAGA-AAAAGGG
* * * ** * * *
301044 TGCCATAGAGTTGTGGACTTAAAAAGAAAAAGGGGGCCATAGAGTTATGAATTTTAAAAG----A
1 TGCCATAGAGTTGGGGACTT-----TAAAAAGGGAGCCACGGAGTTATGGACTTAAAAAGAAAAA
301105 -GG
61 GGG
* ** * * * * *
301107 TGCCACAGAGTTATGGACTTAAAATGATAAAGAGTGCCACGGAGTTGTGAACTTAAAAAGAAAAA
1 TGCCATAGAGTTGGGGACTT----T-AAAAAGGGAGCCACGGAGTTATGGACTTAAAAAGAAAAA
301172 GTGG
61 G-GG
* * *
301176 -GCCATGGAGTTGGGGAC-TT-AAAAGGGAGCCATGGAGTTATGGACTTAAAAAGAAATAGGG
1 TGCCATAGAGTTGGGGACTTTAAAAAGGGAGCCACGGAGTTATGGACTTAAAAAGAAAAAGGG
* *
301236 TGCCATAGAGTTGTGGACTTTAAAAAGGGTGCCACGGAGTTATGGACT
1 TGCCATAGAGTTGGGGACTTTAAAAAGGGAGCCACGGAGTTATGGACT
301284 ATAAGAAGGT
Statistics
Matches: 284, Mismatches: 62, Indels: 38
0.74 0.16 0.10
Matches are distributed among these distances:
60 2 0.01
61 66 0.23
62 10 0.04
63 153 0.54
64 8 0.03
67 2 0.01
68 41 0.14
69 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.23
Consensus pattern (63 bp):
TGCCATAGAGTTGGGGACTTTAAAAAGGGAGCCACGGAGTTATGGACTTAAAAAGAAAAAGGG
Found at i:301275 original size:29 final size:29
Alignment explanation
Indices: 301167--301334 Score: 110
Period size: 29 Copynumber: 5.7 Consensus size: 29
301157 ACTTAAAAAG
* *
301167 AAAAAGTGG-GCCATGGAGTTGGGGAC-TT
1 AAAAAG-GGTGCCACGGAGTTGTGGACTTT
* * * *
301195 -AAAAGGGAGCCATGGAGTTATGGACTTAAAA
1 AAAAAGGGTGCCACGGAGTTGTGGACTT---T
**
301226 AGAAATAGGGTGCCATAGAGTTGTGGACTTT
1 A-AAA-AGGGTGCCACGGAGTTGTGGACTTT
* *
301257 AAAAAGGGTGCCACGGAGTTATGGACTAT
1 AAAAAGGGTGCCACGGAGTTGTGGACTTT
* **
301286 AAGAA-GGTGCCACGGAGTTGTGCTCTTT
1 AAAAAGGGTGCCACGGAGTTGTGGACTTT
* *
301314 AGAAAATGGTGCCACAGAGTT
1 A-AAAAGGGTGCCACGGAGTT
301335 ATAGGCTTTG
Statistics
Matches: 112, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
26 2 0.02
27 20 0.18
28 21 0.19
29 28 0.25
30 16 0.14
31 1 0.01
33 3 0.03
34 21 0.19
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.23
Consensus pattern (29 bp):
AAAAAGGGTGCCACGGAGTTGTGGACTTT
Found at i:308360 original size:21 final size:20
Alignment explanation
Indices: 308310--308363 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
308300 CATTTGAGAC
* *
308310 ATGTATCGGTACATTCACTT
1 ATGTATCGATACATTCACTA
*
308330 ATGCATCGATACATTCACTA
1 ATGTATCGATACATTCACTA
308350 ATTGTATCGATACA
1 A-TGTATCGATACA
308364 AATTGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:310974 original size:16 final size:16
Alignment explanation
Indices: 310942--310975 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
310932 AAATATTTAT
*
310942 TTATTATTTTATTTTA
1 TTATTATTTTATATTA
*
310958 TTATTATTTTGTATTA
1 TTATTATTTTATATTA
310974 TT
1 TT
310976 GAAAATTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTATTATTTTATATTA
Found at i:312016 original size:22 final size:21
Alignment explanation
Indices: 311991--312035 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
311981 TGCTAACAAA
*
311991 TTTTCTCATTTTTCTTGCTTTT
1 TTTTCTC-TTTCTCTTGCTTTT
*
312013 TTTTCTCTTTCTCTTTCTTTT
1 TTTTCTCTTTCTCTTGCTTTT
312034 TT
1 TT
312036 GCTGAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTCTCTTTCTCTTGCTTTT
Found at i:314840 original size:163 final size:165
Alignment explanation
Indices: 314460--314978 Score: 370
Period size: 163 Copynumber: 3.1 Consensus size: 165
314450 AATTAAAATG
* * * * * ** *
314460 TTCAAAACTGATTTAATAGGAGTTAAATAATAATATTAGATAAATTTTAAAAATTTTAAATCAAG
1 TTCAAAACTAATTTAATATGAATCAAATAATAAT-TT-GATCAATTTTAAAAATTAGAAACCAAG
* * * * * * * * **
314525 AAAAATCCTCCC-AAAATATTTATGGAGTAAAAAACTCGGTTTTTTCGAAA-AAAAGGTTCATTC
64 AAAAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTGGAAACAAGAGAAT--TTC
* * *
314588 AAACGAAAAAAATTCAAACTCACT-ATAAAAATGAATTAAATTT
127 AAA-G-AAAAAACTCAAA--AACTCATGAAAATGAA-TAAATTT
* * * * * ** *
314631 TT-AAAACTGATTTAAT-GGAATTC-CATGACAT-GTTAGAT-ACATTTTAAAAATTTTAGACCA
1 TTCAAAACTAATTTAATATGAA-TCAAAT-A-ATAATTTGATCA-ATTTTAAAAATTAGAAACCA
* * *
314691 A-AGAAAATCC-CTTCAAAAATATTTATGGAA-TAGAAAACT-CG-ATTTTTGAGAAA-ATAG-G
62 AGA-AAAATCCTC-CCAAAAAAATTTA-CGAAGTAGAAAACTCCGTA-TTTTG-GAAACA-AGAG
* * *
314749 GATTTTAAAG-AAAAACTCCAAAACTCATGAAAATGAGATAAA-TT
121 AATTTCAAAGAAAAAACTCAAAAACTCATGAAAATGA-ATAAATTT
**
314793 TTCAAAACTGTTTTAATATGAATCAAATAATAATTTGATCAATTTTAAAAATTAGAAACCAAGAA
1 TTCAAAACTAATTTAATATGAATCAAATAATAATTTGATCAATTTTAAAAATTAGAAACCAAGAA
*
314858 AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTGGAAACAAGAGAATTTCAAGG
66 AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTGGAAACAAGAGAATTTCAAAG
* *
314923 AAAAAATTCAAAAACTCATGAAGATGAATAAATTT
131 AAAAAACTCAAAAACTCATGAAAATGAATAAATTT
*
314958 TTGAAAACTAATTTAATATGA
1 TTCAAAACTAATTTAATATGA
314979 GTTAAATCCT
Statistics
Matches: 280, Mismatches: 41, Indels: 60
0.73 0.11 0.16
Matches are distributed among these distances:
162 12 0.04
163 85 0.30
164 39 0.14
165 44 0.16
166 1 0.00
167 8 0.03
168 35 0.12
169 32 0.11
170 20 0.07
171 4 0.01
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (165 bp):
TTCAAAACTAATTTAATATGAATCAAATAATAATTTGATCAATTTTAAAAATTAGAAACCAAGAA
AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTGGAAACAAGAGAATTTCAAAG
AAAAAACTCAAAAACTCATGAAAATGAATAAATTT
Found at i:315042 original size:123 final size:124
Alignment explanation
Indices: 314858--315089 Score: 313
Period size: 123 Copynumber: 1.9 Consensus size: 124
314848 AAACCAAGAA
** * *
314858 AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTGGAAACAAGAGAATTTCAAGG
1 AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTAAAAAAAAGAGAATTTCAAGA
*
314923 AAAAAATTCAAAAACTCATGAAGATGAATAAATTTTTGAAAACTAATTTAATATGAGTT
66 AAAAAATTCAAAAACTCATGAAAATGAATAAATTTTTGAAAACTAATTTAATATGAGTT
* * * * * * *
314982 AAATCCTTCCAAAAACATTTATGGAGTAG-AAATTTCGTATTTTAAAAAAAAGAGAGTTTCAAGA
1 AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTAAAAAAAAGAGAATTTCAAGA
* * * *
315046 AAAAAATTCAAGAATTTATGAAAATGAATGAATTTTTGAAAACT
66 AAAAAATTCAAAAACTCATGAAAATGAATAAATTTTTGAAAACT
315090 GATTAACTGT
Statistics
Matches: 92, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
123 67 0.73
124 25 0.27
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (124 bp):
AAATCCTCCCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTAAAAAAAAGAGAATTTCAAGA
AAAAAATTCAAAAACTCATGAAAATGAATAAATTTTTGAAAACTAATTTAATATGAGTT
Found at i:319903 original size:46 final size:48
Alignment explanation
Indices: 319786--319925 Score: 250
Period size: 49 Copynumber: 3.0 Consensus size: 48
319776 ACATAAGTGT
319786 TGTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGTTG
1 TGTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGTTG
319834 TGGTATCGATACAATGTATCGCTAGGAAGCTACTGCC-AGGAAAT-TTG
1 T-GTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGTTG
319881 TGTATCGATACAATGTATCGCTA-GAAGCTACTGCCAAGGAAATGT
1 TGTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGT
319926 ATCGATACAT
Statistics
Matches: 89, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
45 12 0.13
46 29 0.33
47 5 0.06
48 8 0.09
49 35 0.39
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (48 bp):
TGTATCGATACAATGTATCGCTAGGAAGCTACTGCCAAGGAAATGTTG
Found at i:319961 original size:13 final size:13
Alignment explanation
Indices: 319943--319968 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
319933 CATTTTTCTG
319943 TGTATCGATACAT
1 TGTATCGATACAT
319956 TGTATCGATACAT
1 TGTATCGATACAT
319969 CTATTCTTTG
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:319986 original size:34 final size:33
Alignment explanation
Indices: 319923--319987 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
319913 GCCAAGGAAA
*
319923 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
319956 TGTATCGATACATCTATTCTTTGTATCGATAC
1 TGTATCGATACAT-TATTCTGTGTATCGATAC
319988 TCTAGGAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.45
34 16 0.55
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:322394 original size:51 final size:51
Alignment explanation
Indices: 322334--322450 Score: 147
Period size: 51 Copynumber: 2.4 Consensus size: 51
322324 AATTCTCCGC
322334 AATCGGGGATA-TCCCAACTCCGATTTCATTT-TCAAAACA-CTAATTTTCTAT
1 AATCGGGGATACT-CCAACTCCGATTTCATTTCT-AAAACATC-AATTTTCTAT
*
322385 AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAA-TTT-T-T
1 AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTAT
*
322433 CATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
322451 CCCGTTAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
48 18 0.30
49 1 0.02
50 3 0.05
51 36 0.59
52 3 0.05
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTAT
Found at i:322470 original size:27 final size:27
Alignment explanation
Indices: 322432--322508 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
322422 CATCAATTTT
322432 TCATCGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
*
322459 TCATCGGGGATACTCCAACCCCGTTAT
1 TCATCGGGGATACTCCAACCCCGTTAA
** *
322486 TTTTGAGGGGATACTCCAACCCC
1 TCAT-CGGGGATACTCCAACCCC
322509 CGGATTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 28 0.62
28 17 0.38
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:322632 original size:51 final size:52
Alignment explanation
Indices: 322572--322718 Score: 192
Period size: 51 Copynumber: 2.8 Consensus size: 52
322562 TTATCTCCGA
* * * *
322572 GGGGATACTCCAACCCTGGTTTTATTTCCAAATCATCGATTTTCC-ATAATC
1 GGGGATACTCCAACCCTGATTTTATTTCCAAAACACCAATTTTCCTATAATC
* *
322623 GGGGATACTCCAACCCT-ATCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCTGAT-TTTATTTCCAAAACACCAATTTTCCTATAATC
322675 GGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAATTTT
1 GGGGATACTCCAAC-CCTGATTTTATTTCC-AAAACACCAATTTT
322719 TCGCAATTGA
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
50 1 0.01
51 38 0.45
52 27 0.32
53 18 0.21
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.35
Consensus pattern (52 bp):
GGGGATACTCCAACCCTGATTTTATTTCCAAAACACCAATTTTCCTATAATC
Found at i:322699 original size:52 final size:50
Alignment explanation
Indices: 322572--322741 Score: 187
Period size: 52 Copynumber: 3.3 Consensus size: 50
322562 TTATCTCCGA
* * * *
322572 GGGGATACTCCAACCCTGGTTTTATTTCCAAATCATCGATTTTCCATAATC
1 GGGGATACTCCAACCC-GATTTTATTTCCAAAACACCAATTTTCCATAATC
* * *
322623 GGGGATACTCCAACCCTATCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCGAT-TTTATTTCCAAAACACCAATTTTCC-ATAATC
* ** *
322675 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCGCAATT
1 GGGGATACTCCAAC-CCGATTTTATTTCC-AAAACACCAATTTTCCATAATC
*
322727 GAGGATACTCCAACC
1 GGGGATACTCCAACC
322742 TCGTTATTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
50 1 0.01
51 38 0.38
52 43 0.43
53 19 0.19
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTCCAAAACACCAATTTTCCATAATC
Found at i:324976 original size:13 final size:12
Alignment explanation
Indices: 324958--324991 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
324948 AAATCTTCAC
324958 TTTTTTTTTCTAT
1 TTTTTTTTTCT-T
*
324971 TTTTTTCTTCTT
1 TTTTTTTTTCTT
324983 TTTTTTTTT
1 TTTTTTTTT
324992 TTAGAATTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:345612 original size:12 final size:12
Alignment explanation
Indices: 345595--345650 Score: 76
Period size: 12 Copynumber: 4.6 Consensus size: 12
345585 CCTTCTCTTC
*
345595 AAAAAAAAATAA
1 AAAAAAAAACAA
*
345607 AAAAAAAAGCAA
1 AAAAAAAAACAA
345619 AAAAAAAAACAA
1 AAAAAAAAACAA
345631 AAAAACAAAACAA
1 AAAAA-AAAACAA
*
345644 AGAAAAA
1 AAAAAAA
345651 GAGAGAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
12 28 0.72
13 11 0.28
ACGTcount: A:0.88, C:0.07, G:0.04, T:0.02
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:346793 original size:55 final size:54
Alignment explanation
Indices: 346665--347046 Score: 539
Period size: 55 Copynumber: 6.9 Consensus size: 54
346655 TTCCTTTTAA
** *
346665 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTC
1 AAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGA---C---ACCTTTC
* *
346725 AAAGCCCATACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTTTC
1 AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACACCTTTC
* *
346780 AAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACACCTTTT
1 AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACACCTTTC
* *
346835 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTC
1 AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACACCTTTC
346890 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTC
1 AAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGACACCTTTC
* *
346945 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTC
1 AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACACCTTTC
* *
347000 AAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGA
347047 TACACTTTAT
Statistics
Matches: 298, Mismatches: 20, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
54 3 0.01
55 246 0.83
56 6 0.02
58 1 0.00
60 24 0.08
61 18 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (54 bp):
AAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACACCTTTC
Found at i:346860 original size:29 final size:29
Alignment explanation
Indices: 346827--346972 Score: 85
Period size: 28 Copynumber: 5.2 Consensus size: 29
346817 AAGAGCAGGA
346827 CACCTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTTTAAAGCCCACACAAGTTGGTGG
* * **
346856 CACC-TTT-CAGTCCC-CA-AAG-AGCAGG
1 CACCTTTTAAAG-CCCACACAAGTTGGTGG
*
346881 ACACCTTTCAAAGCCCACACAAGTTGGTGG
1 -CACCTTTTAAAGCCCACACAAGTTGGTGG
** * * * **
346911 CA--TTTTCCAGTCCTCA-AAG-AGCAGG
1 CACCTTTTAAAGCCCACACAAGTTGGTGG
*
346936 ACACCTTTCAAAGCCCACACAAGTTGGTGG
1 -CACCTTTTAAAGCCCACACAAGTTGGTGG
346966 CACCTTT
1 CACCTTT
346973 CAGTCCTCAA
Statistics
Matches: 80, Mismatches: 25, Indels: 24
0.62 0.19 0.19
Matches are distributed among these distances:
25 6 0.08
26 12 0.15
27 18 0.22
28 19 0.24
29 19 0.24
30 6 0.08
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (29 bp):
CACCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:346897 original size:26 final size:26
Alignment explanation
Indices: 346815--346897 Score: 60
Period size: 26 Copynumber: 3.1 Consensus size: 26
346805 TTCCAATCCT
*
346815 CAAAGAGCAGGACACCTTTTAAAGCC
1 CAAAGAGCAGGACACCTTTCAAAGCC
** * ***
346841 CACACA-AGTTGGTGGCACCTTTCAGTCCC
1 CA-A-AGAG-CAG-GACACCTTTCAAAGCC
346870 CAAAGAGCAGGACACCTTTCAAAGCC
1 CAAAGAGCAGGACACCTTTCAAAGCC
346896 CA
1 CA
346898 CACAAGTTGG
Statistics
Matches: 39, Mismatches: 13, Indels: 10
0.63 0.21 0.16
Matches are distributed among these distances:
26 16 0.41
27 5 0.13
28 5 0.13
29 13 0.33
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (26 bp):
CAAAGAGCAGGACACCTTTCAAAGCC
Found at i:346944 original size:27 final size:27
Alignment explanation
Indices: 346914--346999 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
346904 TTGGTGGCAT
346914 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * **
346941 TTTCAAAGCCCACACAAGTTGGTGG-CACC
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
*
346970 TTT-CAGTCCTCAAAGAGCAGGACGCC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
346996 TTTC
1 TTTC
347000 AAAGCCCACA
Statistics
Matches: 41, Mismatches: 13, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
25 3 0.07
26 9 0.22
27 10 0.24
28 6 0.15
29 10 0.24
30 3 0.07
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:347891 original size:19 final size:19
Alignment explanation
Indices: 347867--347949 Score: 79
Period size: 19 Copynumber: 4.7 Consensus size: 19
347857 ATTCAGCGAT
347867 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
347886 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
* *
347900 -TGTATCAATACATAAATG
1 TTGTATCGATACATAAGTG
* *
347918 TTGTATCGATACACAAGTT
1 TTGTATCGATACATAAGTG
*
347937 TTGTATTGATACA
1 TTGTATCGATACA
347950 ATGTATCGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
13 10 0.19
15 2 0.04
17 2 0.04
19 38 0.73
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:347904 original size:32 final size:32
Alignment explanation
Indices: 347868--347930 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
347858 TTCAGCGATT
* *
347868 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAATGTTGTATCGATACAA
347900 TGTATCAATACATAAATGTTGTATCGATACA
1 TGTATCAATACATAAATGTTGTATCGATACA
347931 CAAGTTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCAATACATAAATGTTGTATCGATACAA
Done.