Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold9
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: 3883850
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 144036 characters in sequence are not A, C, G, or T
File 4 of 24
Found at i:510352 original size:13 final size:13
Alignment explanation
Indices: 510334--510390 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
510324 ATATTGCTTG
510334 GTATCGATACATT
1 GTATCGATACATT
510347 GTATCGATACATGTTCTT
1 GTATCGATACA-----TT
510365 GGTATCGATACATT
1 -GTATCGATACATT
*
510379 GTATCGGTACAT
1 GTATCGATACAT
510391 GTTCTTGGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
14 2 0.05
18 2 0.05
19 11 0.30
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:510371 original size:19 final size:18
Alignment explanation
Indices: 510314--510378 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
510304 ATACCCAGCT
510314 GTATCGATACATATTGCTTG
1 GTATCGATACAT-TT-CTTG
510334 GTATCGATACA----TT-
1 GTATCGATACATTTCTTG
510347 GTATCGATACATGTTCTTG
1 GTATCGATACAT-TTCTTG
510366 GTATCGATACATT
1 GTATCGATACATT
510379 GTATCGGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 2 0.05
18 3 0.08
19 12 0.31
20 11 0.28
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.40
Consensus pattern (18 bp):
GTATCGATACATTTCTTG
Found at i:510371 original size:32 final size:32
Alignment explanation
Indices: 510313--510408 Score: 156
Period size: 32 Copynumber: 3.0 Consensus size: 32
510303 CATACCCAGC
*
510313 TGTATCGATACATATTGCTTGGTATCGATACAT
1 TGTATCGATACATGTT-CTTGGTATCGATACAT
510346 TGTATCGATACATGTTCTTGGTATCGATACAT
1 TGTATCGATACATGTTCTTGGTATCGATACAT
* *
510378 TGTATCGGTACATGTTCTTGGTATTGATACA
1 TGTATCGATACATGTTCTTGGTATCGATACA
510409 CAGTGCATTG
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 45 0.75
33 15 0.25
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATGTTCTTGGTATCGATACAT
Found at i:510839 original size:20 final size:20
Alignment explanation
Indices: 510816--510889 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
510806 ACAATTCAAA
510816 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
510836 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
510857 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
510877 GTATCGATACATG
1 GTATCGATACATG
510890 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:510860 original size:21 final size:21
Alignment explanation
Indices: 510834--510909 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
510824 ACATGTTGCA
510834 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
510855 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
510875 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
510896 ATGTATCGATACAT
1 ATGTATCGATACAT
510910 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:510867 original size:41 final size:41
Alignment explanation
Indices: 510816--510909 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
510806 ACAATTCAAA
510816 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
510857 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
510898 GTATCGATACAT
1 GTATCGATACAT
510910 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:510966 original size:13 final size:13
Alignment explanation
Indices: 510948--510973 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
510938 TACAGCAAGT
510948 ATGTATCGATACA
1 ATGTATCGATACA
510961 ATGTATCGATACA
1 ATGTATCGATACA
510974 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:513220 original size:21 final size:21
Alignment explanation
Indices: 513187--513231 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
513177 TTGCAAGTTG
*
513187 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
513209 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
513229 AAA
1 AAA
513232 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:516705 original size:34 final size:35
Alignment explanation
Indices: 516667--516733 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
516657 CCTTACAACA
516667 CTATC-TTTC-AGGACTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAGGACTAAGATAG-AACCTCTCTCT
*
516701 CTATCTTTTTCAAGGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAGGACTAAGATAGAACCTCTC
516734 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAGGACTAAGATAGAACCTCTCTCT
Found at i:517200 original size:13 final size:13
Alignment explanation
Indices: 517182--517206 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
517172 CAATTTTTTG
517182 TGTATCGATACAT
1 TGTATCGATACAT
517195 TGTATCGATACA
1 TGTATCGATACA
517207 AACTTGCTGT
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:517954 original size:21 final size:21
Alignment explanation
Indices: 517913--517956 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
517903 CTCCCCTTTA
* *
517913 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
517934 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
517955 TC
1 TC
517957 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:522377 original size:34 final size:35
Alignment explanation
Indices: 522339--522405 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
522329 CCTTACAACA
522339 CTATC-TTTC-AGGACTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAGGACTAAGATAG-AACCTCTCTCT
*
522373 CTATCTTTTTCAAGGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAGGACTAAGATAGAACCTCTC
522406 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAGGACTAAGATAGAACCTCTCTCT
Found at i:522872 original size:13 final size:13
Alignment explanation
Indices: 522854--522878 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
522844 CAATTTTTTG
522854 TGTATCGATACAT
1 TGTATCGATACAT
522867 TGTATCGATACA
1 TGTATCGATACA
522879 AACTTGCTGT
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:531624 original size:1 final size:1
Alignment explanation
Indices: 531620--531685 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
531610 TTCTTTTTTC
* * * * * * * *
531620 AAAAAAAAAACAAAAAACAACAAAAAAACAAAAAAACAAAAAAAAACAGAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
531685 A
1 A
531686 GAAGAATATG
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:531646 original size:18 final size:17
Alignment explanation
Indices: 531621--531683 Score: 83
Period size: 18 Copynumber: 3.5 Consensus size: 17
531611 TCTTTTTTCA
531621 AAAAAAAAACAAAAAAC
1 AAAAAAAAACAAAAAAC
531638 AACAAAAAAACAAAAAAAC
1 AA-AAAAAAAC-AAAAAAC
531657 AAAAAAAAACAGAAAAA-
1 AAAAAAAAACA-AAAAAC
531674 AAGAAAAAAA
1 AA-AAAAAAA
531684 AAGAAGAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.12
18 28 0.67
19 9 0.21
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACAAAAAAC
Found at i:531688 original size:10 final size:10
Alignment explanation
Indices: 531620--531685 Score: 75
Period size: 10 Copynumber: 6.8 Consensus size: 10
531610 TTCTTTTTTC
531620 AAAAAAAA-A
1 AAAAAAAACA
*
531629 ACAAAAAACA
1 AAAAAAAACA
531639 ACAAAAAAAC-
1 A-AAAAAAACA
531649 -AAAAAAACA
1 AAAAAAAACA
531658 AAAAAAAACA
1 AAAAAAAACA
* *
531668 GAAAAAAAGA
1 AAAAAAAACA
531678 AAAAAAAA
1 AAAAAAAA
531686 GAAGAATATG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
8 8 0.17
9 7 0.15
10 26 0.54
11 7 0.15
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:532912 original size:61 final size:60
Alignment explanation
Indices: 532654--533497 Score: 996
Period size: 61 Copynumber: 14.4 Consensus size: 60
532644 CTTCTTCCAC
*
532654 TTTT-CAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACG-C-TTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
** * * * *
532714 CATCCCATTCCTCAAAGAGCAGGA----TGCCTTTT-AAAGCCCACACAAGCTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
532769 CTTT-CAGTCCTCAAAGAGCAGGACACCTTCTCCTTTGC-AAGCCCACATAAGCTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGAC-GCTT-TCCTTTTCAAAGCCCACACAAGTTGGTGGCA
** * *
532829 CCTT-CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACTCGAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACG-CTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
532889 TTTTCCAGTCCTCAAGGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACAAGTTGCTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACG-CTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
532950 TTTTCTAGTCCTCAAAGAGCAGGACGC---CC--TTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
533005 TTTTCCAGTCCTCAAAGAGCAGGACG----CC-TTTGAAAGCTCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
533060 TTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCTTTC-CTTTTCAAAGCCCACACAAGTTGGTGGCA
** * *
533121 CCTTCCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGACA
1 TTTTCCAGTCCTCAAAGAGCAGGACG-CTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
533182 TTTTCCAGTCCTCAAAGAGCAGGA--C--TCC-TTTCAAAGCCCACACCAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
533237 TTTTCCAGTCCTCAAAGAGCAGGACG---T-C-TTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
533292 TTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTT-GTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCTTTC-CTTTTCAAAGCCCACACAAGTTGGTGGCA
** * *
533352 CCTTCCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTCGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACG-CTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
** * **
533413 CCTTCCAGTCCTCAAAAAGCAGGACGCCTTTCCTTTTCAAAGCCCACATGAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACG-CTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
533474 CTTTT-TAGTCCTCAAAGAGCAGGA
1 -TTTTCCAGTCCTCAAAGAGCAGGA
533498 TGCACTTTAT
Statistics
Matches: 693, Mismatches: 61, Indels: 59
0.85 0.08 0.07
Matches are distributed among these distances:
54 20 0.03
55 231 0.33
56 4 0.01
57 2 0.00
58 2 0.00
59 9 0.01
60 127 0.18
61 291 0.42
62 7 0.01
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (60 bp):
TTTTCCAGTCCTCAAAGAGCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:533146 original size:232 final size:231
Alignment explanation
Indices: 532658--533497 Score: 1130
Period size: 232 Copynumber: 3.6 Consensus size: 231
532648 TTCCACTTTT
* * * *
532658 CAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACATCCCAT
1 CAGTCCTCAAAGAGCAGGACGCC-TTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAG
* * * * *
532722 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCACTTTCAGTCCTCAAAGAG
65 TCCTCAAAGAGCAGGACGCCCTTCAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAG
* * * * **
532787 CAGGACACCTTCTCCTTTGCAAGCCCACATAAGCTGGTGGCACCTT-CAGTCCTCAAAGAGCAGG
130 CAGG--A----CGCCTTTGAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGG
* * * * **
532851 ACGCCTTTC-CTTTTCAAAGCCCACTCGAGTTGGTGGCATTTTC
189 ATG-CTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
* * * *
532894 CAGTCCTCAAGGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACAAGTTGCTGGCATTTTCTAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGT
532959 CCTCAAAGAGCAGGACGCCCTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
66 CCTCAAAGAGCAGGACGCCCTTCAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAG
*
533024 CAGGACGCCTTTGAAAGCTCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTT
130 CAGGACGCCTTTGAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTT
533089 TCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
195 TCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
533126 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGACATTTTCCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGT
* * *
533191 CCTCAAAGAGCAGGACTCCTTTCAAAGCCCACACCAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
66 CCTCAAAGAGCAGGACGCCCTTCAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAG
* *
533256 CAGGACGTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTT
130 CAGGACGCCTTTGAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTT
533321 TCTCTTTGCAAAGCCCACACAAGTT-GTGGCACCTTC
195 TCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
533357 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTCGCACCTTCCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGT
* ** *
533422 CCTCAAAAAGCAGGACGCCTTTCCTTTTCAAAGCCCACATGAGTTGGTGGCACTTTTTAGTCCTC
66 CCTCAAAGAGCAGGACG-C---CC--TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTC
533487 AAAGAGCAGGA
124 AAAGAGCAGGA
533498 TGCACTTTAT
Statistics
Matches: 544, Mismatches: 49, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
231 118 0.22
232 259 0.48
235 11 0.02
236 92 0.17
237 60 0.11
238 4 0.01
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (231 bp):
CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGT
CCTCAAAGAGCAGGACGCCCTTCAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGC
AGGACGCCTTTGAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTT
CTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:534148 original size:16 final size:16
Alignment explanation
Indices: 534105--534148 Score: 60
Period size: 14 Copynumber: 3.0 Consensus size: 16
534095 AAAAGGAAAA
534105 AAAAAAATA-ATAA-T
1 AAAAAAATATATAATT
534119 AAAAAAAT-TA-AATT
1 AAAAAAATATATAATT
534133 AAAAAAATATATAATT
1 AAAAAAATATATAATT
534149 TTGTCCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.08
14 18 0.69
15 2 0.08
16 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAAAATATATAATT
Found at i:534274 original size:19 final size:18
Alignment explanation
Indices: 534250--534344 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
534240 AAACTGTAAA
534250 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
534269 TGTATCGATAC---A--T
1 TGTATCGATACATAAGTT
534282 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
534301 TGTATCGATAC---A--T
1 TGTATCGATACATAAGTT
*
534314 TGTATCGATACATATGTTT
1 TGTATCGATACATAAG-TT
534333 TGTATCGATACA
1 TGTATCGATACA
534345 ATGTATCGCT
Statistics
Matches: 63, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 24 0.38
16 3 0.05
19 36 0.57
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.39
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:534286 original size:13 final size:13
Alignment explanation
Indices: 534268--534326 Score: 64
Period size: 13 Copynumber: 4.1 Consensus size: 13
534258 TACATAAGTG
534268 TTGTATCGATACA
1 TTGTATCGATACA
534281 TTGTATCGATACATAA
1 TTGTATCGATAC---A
534297 GTGTTGTATCGATACA
1 ---TTGTATCGATACA
534313 TTGTATCGATACA
1 TTGTATCGATACA
534326 T
1 T
534327 ATGTTTTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 26 0.65
16 2 0.05
19 12 0.30
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:534291 original size:32 final size:32
Alignment explanation
Indices: 534250--534352 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
534240 AAACTGTAAA
534250 TGTATCGATACATAAGTGTTGTATCGATACAT
1 TGTATCGATACATAAGTGTTGTATCGATACAT
534282 TGTATCGATACATAAGTGTTGTATCGATACAT
1 TGTATCGATACATAAGTGTTGTATCGATACAT
* * *
534314 TGTATCGATACATATGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAT
534346 TGTATCG
1 TGTATCG
534353 CTACGAAGCT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAT
Found at i:536595 original size:11 final size:12
Alignment explanation
Indices: 536576--536613 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
536566 ACTGCCAGAA
536576 ATGTATCGATAC
1 ATGTATCGATAC
536588 AT-TATCGATAC
1 ATGTATCGATAC
536599 ATTGTATCGATAC
1 A-TGTATCGATAC
536612 AT
1 AT
536614 CGTCTTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.42
12 4 0.17
13 10 0.42
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:536608 original size:13 final size:13
Alignment explanation
Indices: 536577--536613 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
536567 CTGCCAGAAA
536577 TGTATCGATACA-
1 TGTATCGATACAT
536589 T-TATCGATACAT
1 TGTATCGATACAT
536601 TGTATCGATACAT
1 TGTATCGATACAT
536614 CGTCTTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.43
12 2 0.09
13 11 0.48
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:540634 original size:61 final size:60
Alignment explanation
Indices: 540546--540695 Score: 221
Period size: 61 Copynumber: 2.5 Consensus size: 60
540536 ACTTTTCAAC
* * * *
540546 CCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCACCTTTC-AGT
1 CCTCAAAGAGCAGGACG-CTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGT
540607 CCTCAAAGAGCAGGACGTCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGT
1 CCTCAAAGAGCAGGACG-CTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGT
540668 CCTCAAAGAGCAGGACGCTCTCTCCTTT
1 CCTCAAAGAGCAGGACGCT-TCTCCTTT
540696 CACCTTTTTG
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
60 6 0.07
61 76 0.93
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (60 bp):
CCTCAAAGAGCAGGACGCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGT
Found at i:540710 original size:100 final size:93
Alignment explanation
Indices: 540596--540778 Score: 233
Period size: 94 Copynumber: 1.9 Consensus size: 93
540586 AAGTTGGTGG
* *
540596 CACCTTTCAGTCCTCAAAGAGCAGGACGTCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-C
1 CACCTTTCAGTCCTCAAAGAGCAGGA-----T-GCCTTTTAAAGCCCACACAAGCTGGTGGCATC
* *
540660 TTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTT
60 TT-C-AGTCCTCAAAAAGCAAGACGCTCTCTCCTTT
**
540696 CACCTTTTTGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCATCTTCAGT
1 CACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCATCTTCAGT
540761 CCTCAAAAAGCAAGACGC
66 CCTCAAAAAGCAAGACGC
540779 CTGTCAAGGC
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
93 19 0.25
94 29 0.38
95 4 0.05
100 24 0.32
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (93 bp):
CACCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCATCTTCAGT
CCTCAAAAAGCAAGACGCTCTCTCCTTT
Found at i:540834 original size:55 final size:55
Alignment explanation
Indices: 540696--541057 Score: 449
Period size: 55 Copynumber: 6.5 Consensus size: 55
540686 TCTCTCCTTT
** * *
540696 CACCTTTTTGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGG
1 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
* * * * * *
540751 CATC-TTCAGTCCTCAAAAAGCAAGACGCCTGTCAAGGCCCACACAAGTTGGTGG
1 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
*
540805 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACGAGTTGGTGG
1 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
* * *
540860 CACCCTCCAATCCTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTCAGTCCTCAAAGAGCAGGACGCC----T-TTT-AAAGCCCACACAAGTTGGTGG
*
540921 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGTCCACACAAGTTGGTGG
1 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
** * *
540976 CATTTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGG
1 CA-CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
* *
541032 CA-CTTCCCAGTCCTCAAAGAGTAGGA
1 CACCTT-TCAGTCCTCAAAGAGCAGGA
541058 TGCTCTCTCT
Statistics
Matches: 264, Mismatches: 34, Indels: 18
0.84 0.11 0.06
Matches are distributed among these distances:
54 46 0.17
55 113 0.43
56 53 0.20
57 1 0.00
59 1 0.00
60 3 0.01
61 47 0.18
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (55 bp):
CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:540961 original size:28 final size:28
Alignment explanation
Indices: 540929--541014 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 28
540919 GGCACCTTTC
540929 AGTCCTCAAAGAGCAGGACGCCTTTTAA
1 AGTCCTCAAAGAGCAGGACGCCTTTTAA
* * ** ** * **
540957 AGTCCACACA-AGTTGGTGGCATTTTTTT
1 AGTCCTCAAAGAGCAGGACGC-CTTTTAA
*
540985 AGTCCTCAAAGAGCAGGATGCCTTTTAA
1 AGTCCTCAAAGAGCAGGACGCCTTTTAA
541013 AG
1 AG
541015 CCCACACAAG
Statistics
Matches: 38, Mismatches: 18, Indels: 4
0.63 0.30 0.07
Matches are distributed among these distances:
27 6 0.16
28 26 0.68
29 6 0.16
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (28 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTAA
Found at i:541029 original size:172 final size:170
Alignment explanation
Indices: 540725--541057 Score: 479
Period size: 172 Copynumber: 1.9 Consensus size: 170
540715 AGCAGGATGC
* * *
540725 CTTTTAAAGCCCACACAAGCTGGTGGCATCTTCAGTCCTCAAAAAGCAAGACGCCTGTCAAGGCC
1 CTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAAAGCAAGACGCCTGTCAAAGCC
*
540790 CACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACGAGTT
66 CACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTT
540855 GGTGGCACC-CTCCAATCCTCAAAGAGCAGGACGCCTTTTT
131 GGTGGCACCTC-CCAATCCTCAAAGAGCAGGACGCCTTTTT
* * * * * *
540895 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGT
1 CTTTCAAAGCCCACACAAGCTGGTGGCACC-TTCAGTCCTCAAAAAGCAAGACGCCTGTCAAAGC
** * *
540960 CCACACAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAG
65 CCACACAAGTTGGTGGCA-CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAG
* * *
541025 TTGGTGGCACTTCCCAGTCCTCAAAGAGTAGGA
129 TTGGTGGCACCTCCCAATCCTCAAAGAGCAGGA
541058 TGCTCTCTCT
Statistics
Matches: 143, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
170 27 0.19
171 46 0.32
172 69 0.48
173 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (170 bp):
CTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAAAGCAAGACGCCTGTCAAAGCC
CACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTT
GGTGGCACCTCCCAATCCTCAAAGAGCAGGACGCCTTTTT
Found at i:541070 original size:116 final size:109
Alignment explanation
Indices: 540696--541057 Score: 456
Period size: 116 Copynumber: 3.2 Consensus size: 109
540686 TCTCTCCTTT
** * *
540696 CACCTTTTTGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCATCTTCAGT
1 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATCTTCAGT
* * * * *
540761 CCTCAAAAAGCAAGACGCCTGTCAAGGCCCACACAAGTTGGTGG
66 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
* * * *
540805 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCCAA
1 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-TCTTCAG
540870 TCCTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGG
65 TCCTCAAAGAGCAGGACGCC----T-TTT-AAAGCCCACACAAGTTGGTGG
* * *
540921 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGTCCACACAAGTTGGTGGCATTTTTTTA
1 CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA--TCTTCA
*
540986 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGG
64 GTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
* *
541032 CA-CTTCCCAGTCCTCAAAGAGTAGGA
1 CACCTT-TCAGTCCTCAAAGAGCAGGA
541058 TGCTCTCTCT
Statistics
Matches: 220, Mismatches: 24, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
109 52 0.24
110 25 0.11
111 41 0.19
112 3 0.01
113 1 0.00
114 1 0.00
115 1 0.00
116 75 0.34
117 21 0.10
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (109 bp):
CACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATCTTCAGT
CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:541349 original size:61 final size:63
Alignment explanation
Indices: 541100--541338 Score: 294
Period size: 61 Copynumber: 3.9 Consensus size: 63
541090 AGCAGGACGC
* *
541100 CTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGCAGAACGCCTTT-T
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTCT
* * **
541161 CCTTTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGA-TACTTTCT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTCT
* * * * *
541222 CTTTGCAAAGCCCACACAAGTTGGTGGCAC-CTTCCAATCCTCAAAGAGCAGGATGCCTTTCT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTCT
* * * *
541284 -TTTTCAAAGCCCACACGAGTTAGTGGCACTTTT-TTGTCCTCAAAGAGTAGGACGC
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGC
541339 ATTTTATTTT
Statistics
Matches: 150, Mismatches: 23, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
60 4 0.03
61 116 0.77
62 30 0.20
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (63 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTCT
Found at i:541377 original size:375 final size:368
Alignment explanation
Indices: 540630--541344 Score: 923
Period size: 375 Copynumber: 1.9 Consensus size: 368
540620 GACGTCTTCT
*
540630 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTCTCTCCTT
* *
540695 TCACCTTTTTGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCATCTTCAG
66 TCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGCTGGTGGCATCTTCAG
*
540760 TCCTCAAAAAGCAAGACGCCTGTCAAGGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGA
131 TCCTCAAAAAGCAAGACGCCTGTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGA
* *
540825 GCAGGACGCCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCCAATCCTCAAAGAGCAGGACGCC
196 GCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCCAATCCTCAAAGAGCAGGACGCC
* *
540890 TTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
261 TTTTTCTTTCAAAGCCCACACAAGTTAGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCATTTT
*
540955 AAAGTCCACACAAGTTGGTGGCATTTTTTTAGTCCTCAAAGAGCAGGATG
326 AAAGTCCACAC-A--TGCT-GCA---TTTTAGTCCTCAAAGAGCAGGATG
* * *
541005 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGTAGGATGCTCTCTCTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTCTCTCCTT
** * * *
541070 TTGCCTTTTAGTCCTCGAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
66 TCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGCTGGTGGCA-TCTTC-
* * * * *
541135 AGTCCTTAAAGAGC-AGAACGCCTTTTCCTTTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCTAG
129 AGTCCTCAAAAAGCAAG-ACG------CCTGTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AG
* *
541198 TCCTCAAAGAGCAGGATACTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAATCCT
186 TCCTCAAAGAGCAGG--AC--GC-CTTT-CAAAGCCCACACAAGTTGGTGGCACCCTCCAATCCT
* * * **
541263 CAAAGAGCAGGATGCCTTTCTT-TTTCAAAGCCCACACGAGTTAGTGGCACTTTTTTGTCCTCAA
245 CAAAGAGCAGGACGCCTTT-TTCTTTCAAAGCCCACACAAGTTAGTGGCACCTTTCAGTCCTCAA
*
541327 AGAGTAGGACGCATTTTA
309 AGAGCAGGACGCATTTTA
541345 TTTTCCTCTC
Statistics
Matches: 294, Mismatches: 29, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
375 113 0.38
376 6 0.02
377 15 0.05
382 4 0.01
383 43 0.15
385 2 0.01
387 1 0.00
388 4 0.01
389 104 0.35
390 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (368 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCTCTCTCCTT
TCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGCTGGTGGCATCTTCAG
TCCTCAAAAAGCAAGACGCCTGTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGA
GCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCCAATCCTCAAAGAGCAGGACGCC
TTTTTCTTTCAAAGCCCACACAAGTTAGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCATTTT
AAAGTCCACACATGCTGCATTTTAGTCCTCAAAGAGCAGGATG
Found at i:541378 original size:42 final size:42
Alignment explanation
Indices: 541315--541480 Score: 170
Period size: 42 Copynumber: 3.9 Consensus size: 42
541305 AGTGGCACTT
* * *
541315 TTTTGTCCTCAAAGAGTAGGACGCATTTTATTTTCCTCTCTC
1 TTTTGTCCTCAAAGAGCAGGACGCACTTCATTTTCCTCTCTC
* * * ** *
541357 ATTTGTCCTCAAAGAGCAGGACACACCTCATTCCCTTATTTTCTC
1 TTTTGTCCTCAAAGAGCAGGACGCACTTCATT---TTCCTCTCTC
* * *
541402 TTTTGTCCTCAAAGACCAGGACGCACTTTATTTTCCTCTTTC
1 TTTTGTCCTCAAAGAGCAGGACGCACTTCATTTTCCTCTCTC
* * *
541444 TTTTGTCCTCAAAGAGTAGGAAGCATTTCATTTTCCT
1 TTTTGTCCTCAAAGAGCAGGACGCACTTCATTTTCCT
541481 TTTTTCCTTT
Statistics
Matches: 98, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
42 64 0.65
45 34 0.35
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (42 bp):
TTTTGTCCTCAAAGAGCAGGACGCACTTCATTTTCCTCTCTC
Found at i:541612 original size:40 final size:42
Alignment explanation
Indices: 541516--541615 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
541506 GATGTACTCT
* *
541516 TTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTTCTTC
1 TTTTC-CTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTTC
* * * *
541559 TCTTCCTTAGTCCTCAAGGAGCAAGAC-CTATTTC-ATTC-TC
1 TTTTCCTTTGTCCTCAAGAAGCAAGACACT-TTCCTATTCTTC
541599 TTTTCCTTTGTCCTCAA
1 TTTTCCTTTGTCCTCAA
541616 AAAGTGGGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
40 17 0.35
41 5 0.10
42 22 0.46
43 4 0.08
ACGTcount: A:0.19, C:0.29, G:0.11, T:0.41
Consensus pattern (42 bp):
TTTTCCTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTTC
Found at i:542350 original size:11 final size:12
Alignment explanation
Indices: 542331--542368 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
542321 TGCCAAGGAA
542331 ATGTATCGATAC
1 ATGTATCGATAC
542343 AT-TATCGATAC
1 ATGTATCGATAC
542354 ATTGTATCGATAC
1 A-TGTATCGATAC
542367 AT
1 AT
542369 CGATCTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.42
12 4 0.17
13 10 0.42
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:542363 original size:13 final size:13
Alignment explanation
Indices: 542332--542368 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
542322 GCCAAGGAAA
542332 TGTATCGATACA-
1 TGTATCGATACAT
542344 T-TATCGATACAT
1 TGTATCGATACAT
542356 TGTATCGATACAT
1 TGTATCGATACAT
542369 CGATCTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.43
12 2 0.09
13 11 0.48
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:542380 original size:20 final size:21
Alignment explanation
Indices: 542332--542389 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
542322 GCCAAGGAAA
542332 TGTATCGATACATTATCGATACAT
1 TGTATCGATAC---ATCGATACAT
*
542356 TGTATCGATACATCGAT-CTT
1 TGTATCGATACATCGATACAT
542376 TGTATCGATACATC
1 TGTATCGATACATC
542390 TAAGAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 6 0.18
24 11 0.33
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATCGATACAT
Found at i:545705 original size:11 final size:12
Alignment explanation
Indices: 545686--545747 Score: 92
Period size: 11 Copynumber: 5.2 Consensus size: 12
545676 TGCCAAGGAA
545686 ATGTATCGATAC
1 ATGTATCGATAC
545698 AT-TATCGATAC
1 ATGTATCGATAC
545709 ATTGTATCGATAC
1 A-TGTATCGATAC
545722 AT-TATCGATAC
1 ATGTATCGATAC
545733 ATTGTATCGATAC
1 A-TGTATCGATAC
545746 AT
1 AT
545748 CGATCTTTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
11 20 0.43
12 6 0.13
13 20 0.43
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:545718 original size:13 final size:13
Alignment explanation
Indices: 545687--545747 Score: 94
Period size: 13 Copynumber: 5.0 Consensus size: 13
545677 GCCAAGGAAA
545687 TGTATCGATACA-
1 TGTATCGATACAT
545699 T-TATCGATACAT
1 TGTATCGATACAT
545711 TGTATCGATACA-
1 TGTATCGATACAT
545723 T-TATCGATACAT
1 TGTATCGATACAT
545735 TGTATCGATACAT
1 TGTATCGATACAT
545748 CGATCTTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
11 20 0.44
12 4 0.09
13 21 0.47
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:545719 original size:24 final size:24
Alignment explanation
Indices: 545687--545767 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
545677 GCCAAGGAAA
545687 TGTATCGATACATTATCGATACAT
1 TGTATCGATACATTATCGATACAT
545711 TGTATCGATACATTATCGATACAT
1 TGTATCGATACATTATCGATACAT
*
545735 TGTATCGATAC---ATCGAT-CTT
1 TGTATCGATACATTATCGATACAT
545755 TGTATCGATACAT
1 TGTATCGATACAT
545768 CTAGGAAGTT
Statistics
Matches: 54, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
20 13 0.24
21 6 0.11
24 35 0.65
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (24 bp):
TGTATCGATACATTATCGATACAT
Found at i:548162 original size:51 final size:51
Alignment explanation
Indices: 548089--548270 Score: 267
Period size: 51 Copynumber: 3.6 Consensus size: 51
548079 TTAATTTTCT
* * *
548089 CAATTTTTCATAATTGGCGATACTCCAACTCCGATTTTATTTTCAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACAC
* *
548140 CAATTTTCCACAATCGGGGATACTCCAAC-CCTGGTTTTATTTTCAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACTCC-GATTTTATTTTCAAAACAC
* * *
548191 CAATTTTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACAC
*
548242 CAATTTTTCATAATCGGGGATACTCCAAC
1 CAATTTTCCATAATCGGGGATACTCCAAC
548271 CCTGTTAATC
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
50 2 0.02
51 112 0.97
52 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (51 bp):
CAATTTTCCATAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACAC
Found at i:548291 original size:28 final size:28
Alignment explanation
Indices: 548257--548328 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
548247 TTTCATAATC
548257 GGGGATACTCCAACCCTGTTA-ATCATCG-
1 GGGGATACTCCAACCCTGTTATATC--CGA
*
548285 GGGGATACTCCAACCCTGTTATTTCCGA
1 GGGGATACTCCAACCCTGTTATATCCGA
548313 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
548329 CAGCTTTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 2 0.05
28 37 0.90
29 2 0.05
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.24
Consensus pattern (28 bp):
GGGGATACTCCAACCCTGTTATATCCGA
Found at i:548368 original size:79 final size:79
Alignment explanation
Indices: 548285--548487 Score: 343
Period size: 79 Copynumber: 2.6 Consensus size: 79
548275 TTAATCATCG
*
548285 GGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTCCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTCCTAAAATATT
*
548350 GATTTCTCACAGTC
66 GATTTCTCACAATC
* *
548364 GGGGATACTCCAACCCCGTTATTTCCCAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTCCTAAAATATT
548429 GATTTCTCACAATC
66 GATTTCTCACAATC
* * *
548443 GGGGATACTTCAACCCCGTTATTTTCGCGGGGATACTCCAACCCC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCC
548488 GTTATTTTTG
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 116 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTCCTAAAATATT
GATTTCTCACAATC
Found at i:548484 original size:28 final size:28
Alignment explanation
Indices: 548442--548516 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
548432 TTCTCACAAT
*
548442 CGGGGATACTTCAACCCCGTTATTTTCG
1 CGGGGATACTCCAACCCCGTTATTTTCG
*
548470 CGGGGATACTCCAACCCCGTTATTTTTG
1 CGGGGATACTCCAACCCCGTTATTTTCG
*
548498 AGGGGATACTCCAACCCCG
1 CGGGGATACTCCAACCCCG
548517 ATTTTATTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.27
Consensus pattern (28 bp):
CGGGGATACTCCAACCCCGTTATTTTCG
Found at i:548580 original size:78 final size:79
Alignment explanation
Indices: 548472--548646 Score: 228
Period size: 78 Copynumber: 2.2 Consensus size: 79
548462 TATTTTCGCG
* *
548472 GGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTA-TTTCAAAACACCA
1 GGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCA
* *
548536 ATTTTCTATGATTA
66 ATTTTCTATAATCA
* * *
548550 GGGATACTCCAACCCTGTTA-TTTCGAAGGGGATACTCCAACCTCGATTTTATTTTCAGAACATC
1 GGGATACTCCAACCCTGTTATTTTCG-AGGGGATACTCCAACCCCGATTTTATTTTCAAAACACC
*
548614 GATTTTCTATAATCA
65 AATTTTCTATAATCA
* * *
548629 GGGGTACTTCAGCCCTGT
1 GGGATACTCCAACCCTGT
548647 CGTCATCTCC
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
77 4 0.05
78 43 0.51
79 37 0.44
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (79 bp):
GGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCA
ATTTTCTATAATCA
Found at i:556514 original size:48 final size:48
Alignment explanation
Indices: 556438--556562 Score: 169
Period size: 48 Copynumber: 2.6 Consensus size: 48
556428 GGTGTGTACA
* * *
556438 ATAGTCAAATGAGGGAAGAAAAGTGTTTGACTAGGCCCTAACACTAAT
1 ATAGTCAAACGAGGGAAGAAAAGAGTTTGACTAGGCCCTAACACCAAT
* * * *
556486 ATAGTCAAACGAGGGAAGACAAGAGTTTGATTAGGCCTTAACTCCAAT
1 ATAGTCAAACGAGGGAAGAAAAGAGTTTGACTAGGCCCTAACACCAAT
* *
556534 ATAGTCAAACAAGGGAGGAAAAGAGTTTG
1 ATAGTCAAACGAGGGAAGAAAAGAGTTTG
556563 GCCAGGTATA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.22
Consensus pattern (48 bp):
ATAGTCAAACGAGGGAAGAAAAGAGTTTGACTAGGCCCTAACACCAAT
Found at i:556913 original size:90 final size:91
Alignment explanation
Indices: 556794--556965 Score: 276
Period size: 90 Copynumber: 1.9 Consensus size: 91
556784 TCAAGATATC
556794 CTTGCCCCAAAGGAAATCAGGCTTAGTGATGCATCAATACCATCTAGTAATTGGATGAAAGG-GA
1 CTTGCCCCAAAGGAAATCAGGCTTAGTGATGCATCAATACCATCTAGTAATTGGATG-AAGGAGA
556858 TATGATTGGG-AATGTGTGGGTTGTAT
65 TATGATTGGGAAATGTGTGGGTTGTAT
* * * **
556884 CTTGCCCCAAAGGAAATTAGGCTTGGTGATGCATTAATACCATCTAGTGGTTGGATGAAGGAGAT
1 CTTGCCCCAAAGGAAATCAGGCTTAGTGATGCATCAATACCATCTAGTAATTGGATGAAGGAGAT
556949 ATGATTGGGAAATGTGT
66 ATGATTGGGAAATGTGT
556966 TTTCCTTGAA
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
89 4 0.05
90 64 0.85
91 7 0.09
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (91 bp):
CTTGCCCCAAAGGAAATCAGGCTTAGTGATGCATCAATACCATCTAGTAATTGGATGAAGGAGAT
ATGATTGGGAAATGTGTGGGTTGTAT
Found at i:558390 original size:11 final size:11
Alignment explanation
Indices: 558374--558404 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
558364 TCCATTTCTC
558374 TTTTTTCTTTT
1 TTTTTTCTTTT
558385 TTTTTTCTTTT
1 TTTTTTCTTTT
558396 TTTTCTTCT
1 TTTT-TTCT
558405 CTTTCACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:558689 original size:23 final size:24
Alignment explanation
Indices: 558663--558711 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
558653 TCTACACTTG
558663 TTCCA-TTTCATACTTTTTCTTTT
1 TTCCATTTTCATACTTTTTCTTTT
*
558686 TTCCATTTTTCATTCTTTTTCTTTT
1 TTCCA-TTTTCATACTTTTTCTTTT
558711 T
1 T
558712 CTTTTTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.22
25 18 0.78
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.69
Consensus pattern (24 bp):
TTCCATTTTCATACTTTTTCTTTT
Found at i:565267 original size:13 final size:13
Alignment explanation
Indices: 565249--565288 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
565239 ACAATGTTCT
565249 TTGTATCGATACA
1 TTGTATCGATACA
*
565262 TTGTATTGATACA
1 TTGTATCGATACA
*
565275 ATGTATCGATACA
1 TTGTATCGATACA
565288 T
1 T
565289 GGGTTACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:567815 original size:20 final size:19
Alignment explanation
Indices: 567792--567879 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 19
567782 CATTATGCTT
567792 TGTATCGATACATGAACAAA
1 TGTATCGATACATGAAC-AA
*
567812 TGTATTGATACAT------
1 TGTATCGATACATGAACAA
** *
567825 TGTATCGATACATGTTCAT
1 TGTATCGATACATGAACAA
*
567844 TGTATCGTTACATGAACAAA
1 TGTATCGATACATGAAC-AA
567864 TGTATCGATACATGAA
1 TGTATCGATACATGAA
567880 ACTGGCAGTA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
13 12 0.22
19 14 0.26
20 28 0.52
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (19 bp):
TGTATCGATACATGAACAA
Found at i:567846 original size:19 final size:19
Alignment explanation
Indices: 567821--567879 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
567811 ATGTATTGAT
*
567821 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGA
* *
567840 TCATTGTATCGTTACATGA
1 ACATTGTATCGATACATGA
*
567859 ACAAATGTATCGATACATGA
1 AC-ATTGTATCGATACATGA
567879 A
1 A
567880 ACTGGCAGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGA
Found at i:567856 original size:52 final size:53
Alignment explanation
Indices: 567772--567876 Score: 160
Period size: 52 Copynumber: 2.0 Consensus size: 53
567762 CACTTTCAAA
* *
567772 TGTATCGATACATTATGCTTTGTATCGATACATGAACAAATGTATTGATACAT
1 TGTATCGATACATTATGCATTGTATCGATACATGAACAAATGTATCGATACAT
*
567825 TGTATCGATACATGT-T-CATTGTATCGTTACATGAACAAATGTATCGATACAT
1 TGTATCGATACAT-TATGCATTGTATCGATACATGAACAAATGTATCGATACAT
567877 GAAACTGGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
52 33 0.69
53 14 0.29
54 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATTATGCATTGTATCGATACATGAACAAATGTATCGATACAT
Found at i:567941 original size:13 final size:13
Alignment explanation
Indices: 567923--567955 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
567913 GATACATGAC
567923 ACAATGTATCGAT
1 ACAATGTATCGAT
567936 ACAATGTATCGAT
1 ACAATGTATCGAT
567949 AC-ATGTA
1 ACAATGTA
567956 GAATTGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:567951 original size:33 final size:33
Alignment explanation
Indices: 567909--567971 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
567899 CCACTATTTA
567909 TATCGATACATG-ACACAATGTATCGATACAATG
1 TATCGATACATGTACA-AATGTATCGATACAATG
* *
567942 TATCGATACATGTAGAATTGTATCGATACA
1 TATCGATACATGTACAAATGTATCGATACA
567972 TTGCCTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (33 bp):
TATCGATACATGTACAAATGTATCGATACAATG
Found at i:572598 original size:157 final size:158
Alignment explanation
Indices: 572108--572660 Score: 514
Period size: 157 Copynumber: 3.5 Consensus size: 158
572098 TAAATTTAAG
* * * * * * *
572108 AAAAATTATGAAAATGCCCCTA-AAGGATA-CTTCGATGTAAAAGTA-CCCGATAACCTTAAAAG
1 AAAAAATATGAAAATGCCCCTATAAGTATACCTTCGATATAAAAGTACCCCAACAACCCTAAAGG
* * * * * ** * * *
572170 AC-TAAAAACAGATTATAAAT-GGGATAAACCTATT-TTAAATGTACACCTTCGACGTAGAAGCG
66 ACAT-AAAA-AGACTAGAAATAGTGATGAACCTATTCCTAAATGCCCACCTTCGGCATAAAAGCG
* * * *
572232 AA-CCTAGTGATAACCTAAGACTC-GATTTTA
129 AACCCGA-TGACAACCTAGGACTCAG-TTCTA
* * ** ** * * ** ***
572262 AAAAATTATGAAAATACCTTTATGTGTAGATCTTCGACGTAAAAGTACCTTGACAACCCTAAAGG
1 AAAAAATATGAAAATGCCCCTATAAGTATACCTTCGATATAAAAGTACCCCAACAACCCTAAAGG
*
572327 ACCTAAAAAGACTAGAAATAGTGATGAACCTATTCCTAAATGCCCACCTTCGGCATAAAAGCGAA
66 ACATAAAAAGACTAGAAATAGTGATGAACCTATTCCTAAATGCCCACCTTCGGCATAAAAGCGAA
* * *
572392 CCTGGTGACAACCTAGGACTTAGTTCTA
131 CCCGATGACAACCTAGGACTCAGTTCTA
572420 AAAAAATATGAAAATGCCCCTATAAGTATACCTTCGATATAAAAGTACCCCAACAACCCTAAAGG
1 AAAAAATATGAAAATGCCCCTATAAGTATACCTTCGATATAAAAGTACCCCAACAACCCTAAAGG
* * * *
572485 ACATAAAAAGAGTAGAAATGGTGATGAACCTA-TCCTAAATGCCCACTTTTGGCATAAAAGC-AG
66 ACATAAAAAGACTAGAAATAGTGATGAACCTATTCCTAAATGCCCACCTTCGGCATAAAAGCGA-
* *
572548 ACCCGATGACAACCTAGGACTCGGTTTTA
130 ACCCGATGACAACCTAGGACTCAGTTCTA
*** * * * * **
572577 GGGAAATATGAAAATGCCCCTATAGGTATACTTTTGATGTAAAAGTACCCCGGCAACCCTAAAGG
1 AAAAAATATGAAAATGCCCCTATAAGTATACCTTCGATATAAAAGTACCCCAACAACCCTAAAGG
572642 ACATAAAAAGACTAGAAAT
66 ACATAAAAAGACTAGAAAT
572661 TAAGATTTTT
Statistics
Matches: 327, Mismatches: 63, Indels: 15
0.81 0.16 0.04
Matches are distributed among these distances:
154 19 0.06
155 3 0.01
156 25 0.08
157 155 0.47
158 123 0.38
159 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.24
Consensus pattern (158 bp):
AAAAAATATGAAAATGCCCCTATAAGTATACCTTCGATATAAAAGTACCCCAACAACCCTAAAGG
ACATAAAAAGACTAGAAATAGTGATGAACCTATTCCTAAATGCCCACCTTCGGCATAAAAGCGAA
CCCGATGACAACCTAGGACTCAGTTCTA
Found at i:574436 original size:11 final size:10
Alignment explanation
Indices: 574416--574460 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
574406 TTTGCTTGGA
574416 TTTTTCT-TT
1 TTTTTCTCTT
*
574425 TTTCTCTCTT
1 TTTTTCTCTT
574435 TTCTTTCTCTT
1 TT-TTTCTCTT
*
574446 TTTTTTTCTT
1 TTTTTCTCTT
574456 TTTTT
1 TTTTT
574461 TTCTCACTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 6 0.19
10 16 0.52
11 9 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:574461 original size:11 final size:11
Alignment explanation
Indices: 574416--574462 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
574406 TTTGCTTGGA
574416 TTTTTCTTTTT
1 TTTTTCTTTTT
* * *
574427 TCTCTCTTTTC
1 TTTTTCTTTTT
*
574438 TTTCTC-TTTT
1 TTTTTCTTTTT
574448 TTTTTCTTTTT
1 TTTTTCTTTTT
574459 TTTT
1 TTTT
574463 CTCACTTGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:574927 original size:122 final size:124
Alignment explanation
Indices: 574773--575019 Score: 426
Period size: 122 Copynumber: 2.0 Consensus size: 124
574763 CAACAAACTA
* *
574773 GTCAAAATAATCAAATAAAAAATTAAACTAAATAAAATTTCAAAAATTCCAAG-AAATTAGGATT
1 GTCAAAATAATCAAATAAAAAATTAAACTAAATAAAATTCCAAAAATTCCAAGAAAATTAAGATT
* *
574837 AATATTAATTGGT-CCAAACAAAATTTTAGAAATCAAAAAAATAAGAAAAATCCTCATG
66 AATATTAATTAGTCCCAAACAAAATTTTAGAAATCAAAAAAATAAGAAAAATCCTAATG
*
574895 GTCAAAATAATCAAATAAAAAATTAAATTAAATAAAATTCCAAAAATTCCAAGAAAATTAAGATT
1 GTCAAAATAATCAAATAAAAAATTAAACTAAATAAAATTCCAAAAATTCCAAGAAAATTAAGATT
*
574960 ACTATTAATTAGTCCCAAACAAAATTTTAGAAATCAAAAAAATAAGAAAAATCCTAATG
66 AATATTAATTAGTCCCAAACAAAATTTTAGAAATCAAAAAAATAAGAAAAATCCTAATG
575019 G
1 G
575020 AAAGTTAAAA
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
122 51 0.44
123 21 0.18
124 45 0.38
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.26
Consensus pattern (124 bp):
GTCAAAATAATCAAATAAAAAATTAAACTAAATAAAATTCCAAAAATTCCAAGAAAATTAAGATT
AATATTAATTAGTCCCAAACAAAATTTTAGAAATCAAAAAAATAAGAAAAATCCTAATG
Found at i:575331 original size:165 final size:163
Alignment explanation
Indices: 575160--575881 Score: 622
Period size: 165 Copynumber: 4.4 Consensus size: 163
575150 TATTAGGTAC
** * * * * *
575160 ATTTTAAAAATTTTAAACCAA-AGAAAATCCCTCCGAAAATATTTATGGAATAGAAAACTCAGTT
1 ATTTTAAAAATTGAAAACCAAGA-AAAATCCCTCCAAAAAAATTTACGGAGTAGAAAACACA-TT
* * *
575224 TTTTGAAAAAAGGAAAATTTCAAAGAAAAATCTAAAACATATGAAAATAAATTAATTTTTGAAAA
64 TTTTGAAAAAAGGAAAATTTCAAAGAAAAAT-AAAAACATATGAAAATGAATGAATTTTTGAAAA
**
575289 ATGAATTAATATGAAATAAATAATGCTGTTTGATGA
128 ATGAATTAATATGAAATAAATAATAATGTTTGATGA
* *
575325 ATTTTAAAAAATGAAAACCAAGAAAAATCCC-CTCAAAAAAATTTACAGAGTA-AAAA-ACATTG
1 ATTTTAAAAATTGAAAACCAAGAAAAATCCCTC-CAAAAAAATTTACGGAGTAGAAAACACATT-
* * *
575387 TATTTCAAAAAA-AAAGAAGTTTCAAGGAAAAAATAAAAAACATATGAAAATGAATGAATTTTTG
64 T-TTTGAAAAAAGGAA-AA-TTTCAAAG-AAAAAT-AAAAACATATGAAAATGAATGAATTTTTG
* * * * *
575451 -AAACTGGATTAATATGAAATAAATAATAATGTATAATGC
124 AAAAATGAATTAATATGAAATAAATAATAATGTTTGATGA
* *
575490 ATTTTAAAAATTGAAAACCATGAAAAAT-CCTCCCAAAAAAATTTACGGAGTAGAAAACACTATA
1 ATTTTAAAAATTGAAAACCAAGAAAAATCCCT-CCAAAAAAATTTACGGAGTAGAAAACAC-ATT
* * * *
575554 TTTCGAAAAAAAAGG-AAATTTTAAAGAAAAATGAAAAGATCATGAAAATGAATGAATTTTTGAA
64 TTTTG--AAAAAAGGAAAATTTCAAAGAAAAATAAAAACAT-ATGAAAATGAATGAATTTTTGAA
* * * *
575618 AAATAAATTAATATGAAATAAGTAAAAATATTTGATGA
126 AAATGAATTAATATGAAATAAATAATAATGTTTGATGA
* * ** * * * * * *
575656 ATTGTAAAAATTAAAAATTAAGAAAAATCCC-CTCAAAAAGATTAACAGAGTAAAAAACATAGTA
1 ATTTTAAAAATTGAAAACCAAGAAAAATCCCTC-CAAAAAAATTTACGGAGTAGAAAACACA-TT
* * * * *
575720 TTTCGAAAAAAATGAAAGTTTCAAGGAAAAAATCAAAAGC-TCATGAAAATGAATGAATTTTT-A
64 TTTTG-AAAAAAGGAAAATTTCAAAG-AAAAAT-AAAAACAT-ATGAAAATGAATGAATTTTTGA
* * * ** *
575783 AGAACTGAATTACTATGAAATAAATAAAAATACTTGATAA
125 A-AAATGAATTAATATGAAATAAATAATAATGTTTGATGA
* ** * *
575823 ATTTTAAAAATTAAAAATTAAGAAAAAT-CCTCCTGAAAAAACTTTACGGAGAAGAAAAC
1 ATTTTAAAAATTGAAAACCAAGAAAAATCCCTCC--AAAAAAATTTACGGAGTAGAAAAC
575882 CGTAATTTAA
Statistics
Matches: 457, Mismatches: 73, Indels: 51
0.79 0.13 0.09
Matches are distributed among these distances:
162 2 0.00
163 5 0.01
164 24 0.05
165 160 0.35
166 141 0.31
167 95 0.21
168 30 0.07
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.27
Consensus pattern (163 bp):
ATTTTAAAAATTGAAAACCAAGAAAAATCCCTCCAAAAAAATTTACGGAGTAGAAAACACATTTT
TTGAAAAAAGGAAAATTTCAAAGAAAAATAAAAACATATGAAAATGAATGAATTTTTGAAAAATG
AATTAATATGAAATAAATAATAATGTTTGATGA
Found at i:575685 original size:331 final size:335
Alignment explanation
Indices: 575229--575881 Score: 888
Period size: 331 Copynumber: 2.0 Consensus size: 335
575219 CAGTTTTTTG
* * *
575229 AAAAAAGGAAAATTTCAAAGAAAAATCTAAAACATATGAAAATAAATTAATTTTTGAAAAATGAA
1 AAAAAAGGAAAATTTCAAAGAAAAATCGAAAACATATGAAAATAAATGAATTTTTGAAAAATAAA
*** * * *
575294 TTAATATGAAATAAATAATGCTGTTTGATGAATTTTAAAAAATGAAAACCAAGAAAAATCCCCTC
66 TTAATATGAAATAAATAAAAATATTTGATGAATTGTAAAAAATAAAAACCAAGAAAAATCCCCTC
* *
575359 AAAAAAATTTACAGAGTAAAAAACATTGTATTTCAAAAAAAAAG-AAGTTTCAAGGAAAAAATAA
131 AAAAAAATTAACAGAGTAAAAAACATAGTATTTCAAAAAAAAAGAAAGTTTCAAGGAAAAAATAA
* * * *
575423 AAAACAT-ATGAAAATGAATGAATTTTTGA-AACTGGATTAATATGAAATAAATAATAAT-GTAT
196 AAAAC-TCATGAAAATGAATGAATTTTTAAGAACTGAATTAATATGAAATAAATAAAAATACT-T
** * * *
575485 AATGCATTTTAAAAATTGAAAACCATGAAAAATCCTCC-CAAAAAAATTTACGGAGTAGAAAACA
259 AATAAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCTCAAAAAAATTTACGGAGAAGAAAACA
575549 CTATATTTCGAA
324 CTATATTTCGAA
* * *
575561 AAAAAAGG-AAATTTTAAAGAAAAAT-GAAAAGATCATGAAAATGAATGAATTTTTGAAAAATAA
1 AAAAAAGGAAAATTTCAAAGAAAAATCGAAAACAT-ATGAAAATAAATGAATTTTTGAAAAATAA
* * **
575624 ATTAATATGAAATAAGTAAAAATATTTGATGAATTGTAAAAATTAAAAATTAAGAAAAATCCCCT
65 ATTAATATGAAATAAATAAAAATATTTGATGAATTGTAAAAAATAAAAACCAAGAAAAATCCCCT
* * * *
575689 CAAAAAGATTAACAGAGTAAAAAACATAGTATTTCGAAAAAAATGAAAGTTTCAAGGAAAAAATC
130 CAAAAAAATTAACAGAGTAAAAAACATAGTATTTCAAAAAAAAAGAAAGTTTCAAGGAAAAAATA
* * *
575754 AAAAGCTCATGAAAATGAATGAATTTTTAAGAACTGAATTACTATGAAATAAATAAAAATACTTG
195 AAAAACTCATGAAAATGAATGAATTTTTAAGAACTGAATTAATATGAAATAAATAAAAATACTTA
** * *
575819 ATAAATTTTAAAAATTAAAAATTAAGAAAAATCCTCCTGAAAAAACTTTACGGAGAAGAAAAC
260 ATAAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCTCAAAAAAATTTACGGAGAAGAAAAC
575882 CGTAATTTAA
Statistics
Matches: 277, Mismatches: 38, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
330 6 0.02
331 138 0.50
332 52 0.19
333 58 0.21
334 23 0.08
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (335 bp):
AAAAAAGGAAAATTTCAAAGAAAAATCGAAAACATATGAAAATAAATGAATTTTTGAAAAATAAA
TTAATATGAAATAAATAAAAATATTTGATGAATTGTAAAAAATAAAAACCAAGAAAAATCCCCTC
AAAAAAATTAACAGAGTAAAAAACATAGTATTTCAAAAAAAAAGAAAGTTTCAAGGAAAAAATAA
AAAACTCATGAAAATGAATGAATTTTTAAGAACTGAATTAATATGAAATAAATAAAAATACTTAA
TAAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCTCAAAAAAATTTACGGAGAAGAAAACACT
ATATTTCGAA
Found at i:575724 original size:166 final size:168
Alignment explanation
Indices: 575229--575869 Score: 721
Period size: 166 Copynumber: 3.9 Consensus size: 168
575219 CAGTTTTTTG
** * *
575229 AAAAAAGGAAAATTTCAAAG-AAAAATCTAAAACATATGAAAATAAATTAATTTTTGAAAAATGA
1 AAAAAAGG-AAATTTCAAAGAAAAAATAAAAAACATATGAAAATGAATGAATTTTTGAAAAATGA
*** * * *
575293 ATTAATATGAAATAAATAATGCTGTTTGATGAATTTTAAAAAATGAAAACCAAGAAAAATCC-CC
65 ATTAATATGAAATAAATAAAAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCC
*
575357 TCAAAAAAATTTACAGAGTAAAAAACATTGTATTTC-AA
130 TCAAAAAAATTTACAGAGTAAAAAACATAGTATTTCGAA
* * * * *
575395 AAAAAAAGAAGTTTCAAGGAAAAAATAAAAAACATATGAAAATGAATGAATTTTTG-AAACTGGA
1 AAAAAAGGAAATTTCAAAGAAAAAATAAAAAACATATGAAAATGAATGAATTTTTGAAAAATGAA
* * * * * * *
575459 TTAATATGAAATAAATAATAATGTATAATGCATTTTAAAAATTGAAAACCATGAAAAATCCTCC-
66 TTAATATGAAATAAATAAAAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCT
* *
575523 CAAAAAAATTTACGGAGTAGAAAACACTA-TATTTCGAA
131 CAAAAAAATTTACAGAGTAAAAAACA-TAGTATTTCGAA
* * * *
575561 AAAAAAGGAAATTTTAAAG-AAAAAT-GAAAAGATCATGAAAATGAATGAATTTTTGAAAAATAA
1 AAAAAAGGAAATTTCAAAGAAAAAATAAAAAACAT-ATGAAAATGAATGAATTTTTGAAAAATGA
* * **
575624 ATTAATATGAAATAAGTAAAAATATTTGATGAATTGTAAAAATTAAAAATTAAGAAAAATCC-CC
65 ATTAATATGAAATAAATAAAAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCC
* *
575688 TCAAAAAGATTAACAGAGTAAAAAACATAGTATTTCG-A
130 TCAAAAAAATTTACAGAGTAAAAAACATAGTATTTCGAA
* * * * *
575726 AAAAAATGAAAGTTTCAAGGAAAAAATCAAAAGC-TCATGAAAATGAATGAATTTTT-AAGAACT
1 AAAAAAGGAAA-TTTCAAAGAAAAAATAAAAAACAT-ATGAAAATGAATGAATTTTTGAA-AAAT
* * * **
575789 GAATTACTATGAAATAAATAAAAATACTTGATAAATTTTAAAAATTAAAAATTAAGAAAAATCCT
63 GAATTAATATGAAATAAATAAAAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCT
* *
575854 CCTGAAAAAACTTTAC
128 CCTCAAAAAAATTTAC
575870 GGAGAAGAAA
Statistics
Matches: 402, Mismatches: 60, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
164 6 0.01
165 141 0.35
166 151 0.38
167 89 0.22
168 15 0.04
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.27
Consensus pattern (168 bp):
AAAAAAGGAAATTTCAAAGAAAAAATAAAAAACATATGAAAATGAATGAATTTTTGAAAAATGAA
TTAATATGAAATAAATAAAAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCT
CAAAAAAATTTACAGAGTAAAAAACATAGTATTTCGAA
Found at i:579664 original size:85 final size:82
Alignment explanation
Indices: 579515--579741 Score: 249
Period size: 83 Copynumber: 2.7 Consensus size: 82
579505 GAAAAGTAGC
* * * * *
579515 CCACACATTCCTAATCATCTCCCTTTCTTTTAACCACTAGATGATATTGATGCATCATATGACCA
1 CCACACATTCCCAATCATAT-CCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACATGA-C-
* * *
579580 CAAAAAAATGAGGGTGCATA
63 CAAAAAAAGGAGGGTGAAAA
* * *
579600 CCTCATATTCCCAATCATATCACTTTCTTTTAGCCACTAGATGGTATTGATACATCACATGACCA
1 CCACACATTCCCAATCATATC-CTTTCTTTTAGCCACTAGATGGTATTGATGCATCACATGACCA
* **
579665 TAAAGGGGAGGGTGAAAA
65 AAAAAAGGAGGGTGAAAA
* *
579683 CCACACATTCCCAATCATATCCTTT-TTATCCAGCCACTAAATGGTATTGATGCATCACA
1 CCACACATTCCCAATCATATCCTTTCTT-T-TAGCCACTAGATGGTATTGATGCATCACA
579742 AAGCTTGATT
Statistics
Matches: 120, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
81 2 0.02
82 5 0.04
83 59 0.49
84 2 0.02
85 52 0.43
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.30
Consensus pattern (82 bp):
CCACACATTCCCAATCATATCCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACATGACCAA
AAAAAGGAGGGTGAAAA
Found at i:580792 original size:44 final size:43
Alignment explanation
Indices: 580452--580823 Score: 219
Period size: 44 Copynumber: 8.4 Consensus size: 43
580442 TTTTTATACT
* *
580452 TGTTTGACGTGATGATTTAGCCCTAGTCAAACTGCTTTGATACTTC
1 TGTTTGACATGATGGTTTAGCCCTAGTCAAACT-CTTT--TACTTC
* * *
580498 -ATCTGACGTGATGGTTCTTA-CCCTAGTCAAACTCTTTTGA-TTCC
1 TGTTTGACATGATGG-T-TTAGCCCTAGTCAAACTCTTTT-ACTT-C
* * * *
580542 TTGTTTGATATGATGGTTTTTA-CCTTGGTCAAACT-TTTT-TTTC
1 -TGTTTGACATGATGG--TTTAGCCCTAGTCAAACTCTTTTACTTC
* * *
580585 TCATTTGACATGATGGTTTACCCCTAGTTAAACTCTTTATA-TTC
1 T-GTTTGACATGATGGTTTAGCCCTAGTCAAACTCTTT-TACTTC
* *
580629 TGTTTGACATGATGGTTCATGCCCTGGTCAAACT-TTTTCAATCTT-
1 TGTTTGACATGATGGTTTA-GCCCTAGTCAAACTCTTTT--A-CTTC
* * * * * * * *
580674 TGTTTGACGTGATAGTTTTCGCCATGGTTAAACCCCTTTCACTT-
1 TGTTTGACATGAT-GGTTTAGCCCTAGTCAAA-CTCTTTTACTTC
* *
580718 TCGTTTGACGTGATGGTTCTA-CCCTTGTCAAACTCTGTTTACTTC
1 T-GTTTGACATGATGGTT-TAGCCCTAGTCAAACTCT-TTTACTTC
* *
580763 TATTTGACATGATGGTTTAGCCCTAGTCAAACTCTTTT-CATCC
1 TGTTTGACATGATGGTTTAGCCCTAGTCAAACTCTTTTAC-TTC
580806 TCGTTTGACATGATGGTT
1 T-GTTTGACATGATGGTT
580824 CAACCCTCAT
Statistics
Matches: 259, Mismatches: 39, Indels: 58
0.73 0.11 0.16
Matches are distributed among these distances:
41 4 0.02
42 13 0.05
43 49 0.19
44 85 0.33
45 56 0.22
46 44 0.17
47 8 0.03
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (43 bp):
TGTTTGACATGATGGTTTAGCCCTAGTCAAACTCTTTTACTTC
Found at i:580824 original size:88 final size:86
Alignment explanation
Indices: 580492--580830 Score: 271
Period size: 88 Copynumber: 3.9 Consensus size: 86
580482 ACTGCTTTGA
* * * * *
580492 TACTTC-ATCTGACGTGATGGTTCTTA-CCCTAGTCAAACTCTTTTGATTCCTTGTTTGATATGA
1 TACTTCTATTTGACATGATGG-T-TTAGCCCTAGTCAAACTCTTTTCA-TCCTCGTTTGACATGA
*
580555 TGGTTTTTA-CCTTGGTCAAACTTTT
63 TGG-TTCTACCCTT-GTCAAACTTTT
* * * *
580580 T-TTTCTCATTTGACATGATGGTTTACCCCTAGTTAAACTCTTTAT-ATTCT-GTTTGACATGAT
1 TACTTCT-ATTTGACATGATGGTTTAGCCCTAGTCAAACTCTTT-TCATCCTCGTTTGACATGAT
* *
580642 GGTTCATGCCCTGGTCAAACTTTT
64 GGTTC-TACCCTTGTCAAACTTTT
* * * * * * * * * * *
580666 TCAATCTT-TGTTTGACGTGATAGTTTTCGCCATGGTTAAACCCCTTTCA-CTTTCGTTTGACGT
1 T--A-CTTCTATTTGACATGAT-GGTTTAGCCCTAGTCAAACTCTTTTCATC-CTCGTTTGACAT
580729 GATGGTTCTACCCTTGTCAAACTCTGTT
61 GATGGTTCTACCCTTGTCAAACT-T-TT
580757 TACTTCTATTTGACATGATGGTTTAGCCCTAGTCAAACTCTTTTCATCCTCGTTTGACATGATGG
1 TACTTCTATTTGACATGATGGTTTAGCCCTAGTCAAACTCTTTTCATCCTCGTTTGACATGATGG
*
580822 TTCAACCCT
66 TTCTACCCT
580831 CATTGAACTT
Statistics
Matches: 197, Mismatches: 36, Indels: 36
0.73 0.13 0.13
Matches are distributed among these distances:
85 2 0.01
86 26 0.13
87 12 0.06
88 76 0.39
89 59 0.30
90 19 0.10
91 3 0.02
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.43
Consensus pattern (86 bp):
TACTTCTATTTGACATGATGGTTTAGCCCTAGTCAAACTCTTTTCATCCTCGTTTGACATGATGG
TTCTACCCTTGTCAAACTTTT
Found at i:583988 original size:13 final size:13
Alignment explanation
Indices: 583970--583995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
583960 CAATTTTTTG
583970 TGTATCGATACAT
1 TGTATCGATACAT
583983 TGTATCGATACAT
1 TGTATCGATACAT
583996 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:584080 original size:20 final size:20
Alignment explanation
Indices: 584055--584127 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
584045 CAACTTTTTT
584055 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
584075 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
584096 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
584116 ATGTATCGATAC
1 ATGTATCGATAC
584128 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:584093 original size:41 final size:41
Alignment explanation
Indices: 584034--584127 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
584024 CTGCCAAGAA
*
584034 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
584075 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
584116 ATGTATCGATAC
1 ATGTATCGATAC
584128 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:584109 original size:21 final size:21
Alignment explanation
Indices: 584034--584109 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
584024 CTGCCAAGAA
* *
584034 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
584055 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
584075 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
584096 ATGTATCGATACAT
1 ATGTATCGATACAT
584110 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:586570 original size:13 final size:13
Alignment explanation
Indices: 586552--586578 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
586542 ACATGCTGCT
586552 TTGTATCGATACA
1 TTGTATCGATACA
586565 TTGTATCGATACA
1 TTGTATCGATACA
586578 T
1 T
586579 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:586575 original size:33 final size:32
Alignment explanation
Indices: 586533--586597 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
586523 CACACCTAGA
* *
586533 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATG-TGCATTGTATCAATACAT
*
586566 TGTATCGATACATGTTCATTGTATCAATACAT
1 TGTATCGATACATGTGCATTGTATCAATACAT
586598 GGACAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCAATACAT
Found at i:586587 original size:19 final size:19
Alignment explanation
Indices: 586562--586619 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
586552 TTGTATCGAT
*
586562 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
586581 TCATTGTATCAATACATGG
1 ACATTGTATCGATACATGG
586600 ACAAATTGTATCGATACATG
1 AC--ATTGTATCGATACATG
586620 AAACTGGTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:586692 original size:32 final size:31
Alignment explanation
Indices: 586651--586713 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
586641 TCACTATTTG
586651 TATCGATACATG-GTATAATGTATCGATACATT
1 TATCGATACATGAG-A-AATGTATCGATACATT
586683 TATCGATACATGAAGAAATGTATCGATACAT
1 TATCGATACATG-AGAAATGTATCGATACAT
586714 AGCTTGTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 27 0.93
33 1 0.03
34 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (31 bp):
TATCGATACATGAGAAATGTATCGATACATT
Found at i:592879 original size:13 final size:13
Alignment explanation
Indices: 592861--592885 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
592851 CAACATTCCT
592861 TGTATCGATACAA
1 TGTATCGATACAA
592874 TGTATCGATACA
1 TGTATCGATACA
592886 TTGGGTAATA
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:594097 original size:17 final size:18
Alignment explanation
Indices: 594072--594113 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
594062 ATTTTTACAT
*
594072 AAGGGGGAGAT-TTGTTA
1 AAGGAGGAGATATTGTTA
594089 AAGGAGGAGATAATTGTTA
1 AAGGAGGAGAT-ATTGTTA
594108 AAGGAG
1 AAGGAG
594114 TATGTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
19 12 0.55
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (18 bp):
AAGGAGGAGATATTGTTA
Found at i:594151 original size:65 final size:65
Alignment explanation
Indices: 594047--594176 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
594037 AAGGGGGAGA
* *
594047 AGTATGTGAAAATAAATTTTTACATAAGGGGGAGATTTGTTAAAGGAGGAGATAATTGTTAAAGG
1 AGTATGTGAAAATAAATTTTTACATAAGGAGGAGATTTGTTAAAGGAGGAGATAATCGTTAAAGG
* *
594112 AGTATGTGAAAATAAATTTTTACATAAGGAGGAGATTTGTTAAATGAGGAGATAATCGTTTAAGG
1 AGTATGTGAAAATAAATTTTTACATAAGGAGGAGATTTGTTAAAGGAGGAGATAATCGTTAAAGG
594177 GGGAGAATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.32
Consensus pattern (65 bp):
AGTATGTGAAAATAAATTTTTACATAAGGAGGAGATTTGTTAAAGGAGGAGATAATCGTTAAAGG
Found at i:594755 original size:13 final size:13
Alignment explanation
Indices: 594737--594763 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
594727 ACATGCTACT
594737 TTGTATCGATACA
1 TTGTATCGATACA
594750 TTGTATCGATACA
1 TTGTATCGATACA
594763 T
1 T
594764 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:594760 original size:33 final size:32
Alignment explanation
Indices: 594718--594782 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
594708 CACACCCAGA
*
594718 TGTATCGATACATGCTACTTTGTATCGATACAT
1 TGTATCGATACATG-TACATTGTATCGATACAT
*
594751 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTACATTGTATCGATACAT
594783 GGACAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGTACATTGTATCGATACAT
Found at i:594877 original size:32 final size:31
Alignment explanation
Indices: 594836--594898 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
594826 TCACTATGTG
594836 TATCGATACATG-GTATAATGTATCGATACATT
1 TATCGATACATGAG-A-AATGTATCGATACATT
594868 TATCGATACATGAAGAAATGTATCGATACAT
1 TATCGATACATG-AGAAATGTATCGATACAT
594899 AGCTTGTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 27 0.93
33 1 0.03
34 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (31 bp):
TATCGATACATGAGAAATGTATCGATACATT
Found at i:602117 original size:2 final size:2
Alignment explanation
Indices: 602112--602144 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
602102 TGTGTGTGTG
602112 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
602145 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:604057 original size:2 final size:2
Alignment explanation
Indices: 604050--604091 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
604040 ATTGCAGCAG
604050 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
604092 AATTATGGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:605945 original size:31 final size:31
Alignment explanation
Indices: 605907--606004 Score: 196
Period size: 31 Copynumber: 3.2 Consensus size: 31
605897 GTCATCTGAA
605907 ATTATAGAATGAAGCTTTTTAGGCTTAGTGG
1 ATTATAGAATGAAGCTTTTTAGGCTTAGTGG
605938 ATTATAGAATGAAGCTTTTTAGGCTTAGTGG
1 ATTATAGAATGAAGCTTTTTAGGCTTAGTGG
605969 ATTATAGAATGAAGCTTTTTAGGCTTAGTGG
1 ATTATAGAATGAAGCTTTTTAGGCTTAGTGG
606000 ATTAT
1 ATTAT
606005 TTGGTGCTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (31 bp):
ATTATAGAATGAAGCTTTTTAGGCTTAGTGG
Found at i:606621 original size:2 final size:2
Alignment explanation
Indices: 606614--606657 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
606604 TCCTTAAATC
606614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
606656 TA
1 TA
606658 AATGCACGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:607907 original size:27 final size:28
Alignment explanation
Indices: 607844--607908 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 28
607834 TTGTGTATAG
607844 ATATTAA-TTA-TTTTTTAATTAACATT
1 ATATTAATTTATTTTTTTAATTAACATT
* *
607870 TTA-T-ATCTTATTTTTTTCATTAA-ATT
1 ATATTAAT-TTATTTTTTTAATTAACATT
607896 ATATTAATTTATT
1 ATATTAATTTATT
607909 GAATTTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
24 1 0.03
25 1 0.03
26 10 0.32
27 17 0.55
28 2 0.06
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATTAATTTATTTTTTTAATTAACATT
Found at i:610232 original size:16 final size:16
Alignment explanation
Indices: 610206--610245 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
610196 TTTCTCTACT
610206 AATTA-TAAATA-ATA
1 AATTATTAAATATATA
610220 AATATATTAAATATATA
1 AAT-TATTAAATATATA
610237 AATTATTAA
1 AATTATTAA
610246 GTTAATGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.13
15 2 0.09
16 12 0.52
17 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTATTAAATATATA
Found at i:610349 original size:11 final size:11
Alignment explanation
Indices: 610335--610365 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
610325 ATAATGATTG
610335 AATTAAATTAA
1 AATTAAATTAA
610346 AATTAAATTAA
1 AATTAAATTAA
*
610357 ATTTAAATT
1 AATTAAATT
610366 TTTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTAAATTAA
Found at i:610356 original size:16 final size:16
Alignment explanation
Indices: 610335--610365 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
610325 ATAATGATTG
610335 AATTAAATTAAAATTA
1 AATTAAATTAAAATTA
*
610351 AATTAAATTTAAATT
1 AATTAAATTAAAATT
610366 TTTTTTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTAAATTAAAATTA
Found at i:611248 original size:16 final size:16
Alignment explanation
Indices: 611216--611278 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 16
611206 TATTAAAAAA
*
611216 TAAAA-AATGTGAATT
1 TAAAATAATTTGAATT
*
611231 TAAAATAATTTTAATT
1 TAAAATAATTTGAATT
* *
611247 TAACATAGTTTGAATT
1 TAAAATAATTTGAATT
* *
611263 TGAGATAATTTGAATT
1 TAAAATAATTTGAATT
611279 CGAAAAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
15 5 0.13
16 34 0.87
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (16 bp):
TAAAATAATTTGAATT
Found at i:611288 original size:16 final size:16
Alignment explanation
Indices: 611217--611299 Score: 62
Period size: 16 Copynumber: 5.2 Consensus size: 16
611207 ATTAAAAAAT
*
611217 AAAAAATGTGAATTT-
1 AAAAAATTTGAATTTG
*
611232 AAAATAATTTTAATTT-
1 AAAA-AATTTGAATTTG
* *
611248 AACATAGTTTGAATTTG
1 AA-AAAATTTGAATTTG
* * *
611265 AGATAATTTGAATTCG
1 AAAAAATTTGAATTTG
*
611281 AAAAAATTTAAATTTG
1 AAAAAATTTGAATTTG
611297 AAA
1 AAA
611300 GTATTTAAAC
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
15 4 0.08
16 47 0.89
17 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (16 bp):
AAAAAATTTGAATTTG
Found at i:612005 original size:2 final size:2
Alignment explanation
Indices: 611998--612040 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
611988 CTCGAAATTC
611998 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
612039 TA
1 TA
612041 ACAAATGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:613275 original size:17 final size:17
Alignment explanation
Indices: 613239--613297 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
613229 AACTAAGCTT
* * *
613239 GAACCTGACAAAGGCAC
1 GAACCTGAAAAAGTCCC
613256 GAACCTGAAAAAGTCCC
1 GAACCTGAAAAAGTCCC
* *
613273 GAACCCGAATAAGT-CC
1 GAACCTGAAAAAGTCCC
*
613289 GAATCTGAA
1 GAACCTGAA
613298 CAAGCTTGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
16 9 0.26
17 26 0.74
ACGTcount: A:0.41, C:0.27, G:0.20, T:0.12
Consensus pattern (17 bp):
GAACCTGAAAAAGTCCC
Found at i:613350 original size:16 final size:16
Alignment explanation
Indices: 613304--613351 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
613294 TGAACAAGCT
*
613304 TGAACTCGAATGAGTC
1 TGAACTCGAATGAGCC
*
613320 TGAACAT-TAATGAGCC
1 TGAAC-TCGAATGAGCC
*
613336 TGAACTCGAACGAGCC
1 TGAACTCGAATGAGCC
613352 CGAATCTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (16 bp):
TGAACTCGAATGAGCC
Found at i:617588 original size:166 final size:163
Alignment explanation
Indices: 617289--617839 Score: 485
Period size: 166 Copynumber: 3.3 Consensus size: 163
617279 TTTTTTCTAG
* * * *
617289 TTTC-AAAATACGAAATTTTCTACTT-CGTAAATATTTTTGGAGGGATTTTTC-TCGATTTTAAT
1 TTTCTAAAATACG-AGTTTTCTA-TTCCGTAAATATTTTCGGA-AGATTTTTCTTAG-TTTTAAT
* * * * * *
617351 TTTTAAAATTCATAAAATAGTATTATTTAACTCACATTAAATCAGTTTTTAAAAACTT-ATTCAT
62 TTTTAAAATTCATCAAATAATATTATTTGATTCACATTAAATCAG-TTTTGAAAATTTAATTCAT
* * * *
617415 CTTCATGAGTTTTTGAATTTTTTCCTTGAAATTCTCCTGT
126 TTTCATGAG-TTTTGGATTTTTTCTTTGAAATTC-CCTCT
*
617455 TTTC-AAAATACAGAGTTTTCTATTCCGTAAATTTTTTCGCGAAGATTTTTCTTAGTTTTAATTT
1 TTTCTAAAATAC-GAGTTTTCTATTCCGTAAATATTTTCG-GAAGATTTTTCTTAGTTTTAATTT
* *
617519 TTAAAATTCATCAAATATTATTATTTGATTCATATTAAAAT-AGTTTTGAAAATTTAATTCATTT
64 TTAAAATTCATCAAATAATATTATTTGATTCACATT-AAATCAGTTTTGAAAATTTAATTCATTT
617583 TCATGAGTTTTGGATATTTTTCTTTGAAA-TCCCTCT
128 TCATGAGTTTTGGAT-TTTTTCTTTGAAATTCCCTCT
* * * * * * **
617619 TTTCTTAAAAAATCGAGTTTTTTATTCCATAAATATTTCCGGGGAGATTTTGT-TTGGTCTAAAA
1 TTTC-TAAAATA-CGAGTTTTCTATTCCGTAAATATTTTC-GGAAGATTTT-TCTTAGT-TTTAA
* * * * *
617683 TTTTTAAAATGT-ATCTAATAATGTCA-TGGAATTCCCATTAAATCAGTTTTGAAAATTTAATTC
61 TTTTTAAAAT-TCATCAAATAATATTATTTG-ATTCACATTAAATCAGTTTTGAAAATTTAATTC
* * * * *
617746 ATTTTCATGAGTATTGGATTTTTTCTTTAAAATACCATTTT
124 ATTTTCATGAGTTTTGGATTTTTTCTTTGAAATTCC-CTCT
* * * *
617787 TTTCGAAAA-ATTGAGTTTTCTAGTCCGTAAATATTTTCGAAAGGATTTTTCTT
1 TTTCTAAAATA-CGAGTTTTCTATTCCGTAAATATTTTCGGAA-GATTTTTCTT
617840 GATTTAAAAA
Statistics
Matches: 320, Mismatches: 45, Indels: 40
0.79 0.11 0.10
Matches are distributed among these distances:
164 8 0.03
165 24 0.08
166 196 0.61
167 85 0.27
168 7 0.02
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (163 bp):
TTTCTAAAATACGAGTTTTCTATTCCGTAAATATTTTCGGAAGATTTTTCTTAGTTTTAATTTTT
AAAATTCATCAAATAATATTATTTGATTCACATTAAATCAGTTTTGAAAATTTAATTCATTTTCA
TGAGTTTTGGATTTTTTCTTTGAAATTCCCTCT
Found at i:622940 original size:96 final size:96
Alignment explanation
Indices: 622775--623040 Score: 324
Period size: 96 Copynumber: 2.8 Consensus size: 96
622765 ACGGATGGAT
* * * *
622775 TATCCCCTTGAAGGAATGGGGTTGGTA-TG-CCCTCGATGATGATAATTTAAGCAAAAATAAGAT
1 TATCCCCTAGGAGGAATGGGGTTGG-AGTGTCCCT-GATGATGACAATTTAAG-AAAAATAAAAT
* * ***
622838 TTAAATCTTTACGAGTTTAAAGACGGGGTTAGAA
63 TTAAATCTTGACAAGTTTAAAGACAACGTTAGAA
*
622872 TATCCCCTAGGAGGAAT-GGGTTGGAGTGTCCCTAATGATGACAATTTAAGTAAAAATAAAATTT
1 TATCCCCTAGGAGGAATGGGGTTGGAGTGTCCCTGATGATGACAATTTAAG-AAAAATAAAATTT
*
622936 AAATCTTGACAAGTTTAAAGATAACGTTAGAA
65 AAATCTTGACAAGTTTAAAGACAACGTTAGAA
* ** *
622968 TATCCTCTCA-GAGGAATGGGGTTGGAGTGTCTTTGATGATGACAATTTAAGAAAAATAATATTT
1 TATCCCCT-AGGAGGAATGGGGTTGGAGTGTCCCTGATGATGACAATTTAAGAAAAATAAAATTT
623032 AAATCTTGA
65 AAATCTTGA
623041 AAATGTTCAT
Statistics
Matches: 148, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
95 1 0.01
96 97 0.66
97 50 0.34
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (96 bp):
TATCCCCTAGGAGGAATGGGGTTGGAGTGTCCCTGATGATGACAATTTAAGAAAAATAAAATTTA
AATCTTGACAAGTTTAAAGACAACGTTAGAA
Found at i:626021 original size:33 final size:32
Alignment explanation
Indices: 625984--626051 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
625974 TGTTACAAGC
**
625984 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATACTATG-TGTATCGATA
*
626017 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
626049 CAA
1 CAA
626052 ATTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:626024 original size:13 final size:13
Alignment explanation
Indices: 626006--626031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
625996 ACATTTTATG
626006 ATGTATCGATACA
1 ATGTATCGATACA
626019 ATGTATCGATACA
1 ATGTATCGATACA
626032 TACTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:626109 original size:20 final size:20
Alignment explanation
Indices: 626084--626134 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
626074 CCAATGACTT
**
626084 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
626104 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
626124 GTATCGATACA
1 GTATCGATACA
626135 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:626140 original size:13 final size:13
Alignment explanation
Indices: 626122--626150 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
626112 ACATTTAGTC
626122 ATGTATCGATACA
1 ATGTATCGATACA
626135 ATGTATCGATACA
1 ATGTATCGATACA
626148 ATG
1 ATG
626151 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:626161 original size:20 final size:20
Alignment explanation
Indices: 626136--626186 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
626126 ATCGATACAA
*
626136 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
626156 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
626176 TGTATCGATAC
1 TGTATCGATAC
626187 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:626730 original size:22 final size:22
Alignment explanation
Indices: 626703--626747 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
626693 TTTTCTTTTC
626703 TCTCCCCCTTAATCAAAA-AATT
1 TCTCCCCCTTAAT-AAAATAATT
626725 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
626747 T
1 T
626748 GACAATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:628480 original size:20 final size:21
Alignment explanation
Indices: 628451--628491 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
628441 TGTTTTTATT
628451 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
628470 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
628492 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:628641 original size:13 final size:13
Alignment explanation
Indices: 628623--628660 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
628613 ATAAACCCCT
628623 TGTATCGATACAC
1 TGTATCGATACAC
* *
628636 TGTATCGATATAT
1 TGTATCGATACAC
628649 TGTATCGATACA
1 TGTATCGATACA
628661 GAAAATACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:630656 original size:20 final size:20
Alignment explanation
Indices: 630633--630705 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
630623 ACAATTCAAA
630633 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
630653 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
630674 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
630694 GTATCGATACAT
1 GTATCGATACAT
630706 AAAAAAAGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:630684 original size:41 final size:42
Alignment explanation
Indices: 630633--630727 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 42
630623 ACAATTCAAA
*
630633 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
*
630674 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
630716 GTATCGATACAT
1 GTATCGATACAT
630728 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 32 0.63
42 19 0.37
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:630784 original size:13 final size:13
Alignment explanation
Indices: 630766--630791 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
630756 TACAGCAAGT
630766 ATGTATCGATACA
1 ATGTATCGATACA
630779 ATGTATCGATACA
1 ATGTATCGATACA
630792 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:634871 original size:15 final size:15
Alignment explanation
Indices: 634851--634881 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
634841 TAAAAATGTC
634851 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
634866 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
634881 C
1 C
634882 CAAACGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:636966 original size:20 final size:21
Alignment explanation
Indices: 636887--636965 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
636877 AATGTCCAAA
*
636887 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
636907 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
636932 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
636952 TTGTATCGATACAT
1 ATGTATCGATACAT
636966 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:636970 original size:13 final size:13
Alignment explanation
Indices: 636952--636990 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
636942 ACATTTTTCT
636952 TTGTATCGATACA
1 TTGTATCGATACA
636965 TTGTATCGATACA
1 TTGTATCGATACA
*
636978 CTGTATCGATACA
1 TTGTATCGATACA
636991 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:638804 original size:23 final size:23
Alignment explanation
Indices: 638774--638820 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
638764 GTGCAAATAA
638774 ATTTTGATATGAATTACTTGATT
1 ATTTTGATATGAATTACTTGATT
638797 ATTTTGATATGAATTACTTGATT
1 ATTTTGATATGAATTACTTGATT
638820 A
1 A
638821 AGGGGGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (23 bp):
ATTTTGATATGAATTACTTGATT
Found at i:639480 original size:20 final size:20
Alignment explanation
Indices: 639457--639529 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
639447 ACAATTCAAA
639457 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
639477 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
639498 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
639518 GTATCGATACAT
1 GTATCGATACAT
639530 AAAAAAAGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:639508 original size:41 final size:42
Alignment explanation
Indices: 639457--639551 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 42
639447 ACAATTCAAA
*
639457 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
*
639498 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
639540 GTATCGATACAT
1 GTATCGATACAT
639552 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 32 0.63
42 19 0.37
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:639608 original size:13 final size:13
Alignment explanation
Indices: 639590--639615 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
639580 TACAGCAAGT
639590 ATGTATCGATACA
1 ATGTATCGATACA
639603 ATGTATCGATACA
1 ATGTATCGATACA
639616 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:640866 original size:18 final size:17
Alignment explanation
Indices: 640843--640876 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
640833 TAATGTTTTA
640843 GTCGAATATGTTGTCTTC
1 GTCGAATATGTT-TCTTC
640861 GTCGAATATGTTTCTT
1 GTCGAATATGTTTCTT
640877 GGATAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.47
Consensus pattern (17 bp):
GTCGAATATGTTTCTTC
Found at i:641082 original size:21 final size:22
Alignment explanation
Indices: 641047--641089 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
641037 AATTATATAG
641047 TAATTATATAAGATAAATTAAA
1 TAATTATATAAGATAAATTAAA
*
641069 TAATT-TATTAGATAAATTAAA
1 TAATTATATAAGATAAATTAAA
641090 AGTTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
TAATTATATAAGATAAATTAAA
Found at i:643998 original size:16 final size:16
Alignment explanation
Indices: 643977--644010 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
643967 GATAAAGTGT
643977 TTGAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAA
643993 TTGAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAA
644009 TT
1 TT
644011 TAAATGTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (16 bp):
TTGAAAAAAAAAAAAA
Found at i:644037 original size:21 final size:21
Alignment explanation
Indices: 644013--644069 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
644003 AAAAAATTTA
644013 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
644034 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
644055 AATGTATCGATACAT
1 AATGTATCGATACAT
644070 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:644149 original size:19 final size:19
Alignment explanation
Indices: 644125--644192 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
644115 AATTCAACAA
644125 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
644144 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
644159 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
* *
644176 ATTGTATCAATACATAA
1 TTTGTATCGATACATAA
644193 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:644164 original size:13 final size:13
Alignment explanation
Indices: 644146--644170 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
644136 ACATAAGTTT
644146 TGTATCGATACAA
1 TGTATCGATACAA
644159 TGTATCGATACA
1 TGTATCGATACA
644171 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:644168 original size:32 final size:32
Alignment explanation
Indices: 644127--644189 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
644117 TTCAACAATT
* *
644127 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCAATACAA
644159 TGTATCGATACATAAGTATTGTATCAATACA
1 TGTATCGATACATAAGTATTGTATCAATACA
644190 TAATTAGCTA
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:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCAATACAA
Found at i:644250 original size:13 final size:13
Alignment explanation
Indices: 644232--644257 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
644222 CATTTTTCTG
644232 TGTATCGATACAT
1 TGTATCGATACAT
644245 TGTATCGATACAT
1 TGTATCGATACAT
644258 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
Done.