Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 2 of 182
Found at i:389172 original size:27 final size:27
Alignment explanation
Indices: 389139--389351 Score: 264
Period size: 27 Copynumber: 7.6 Consensus size: 27
389129 TAAATTGTGC
* *
389139 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
389166 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGATTATGT
*
389194 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
389221 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGATTATGT
*
389249 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
389276 AGCACTGAGTGTGCGGACTCAAGTTTGATTATGT
1 AGCACTAAGTGTGC-G-----AG-TTGATTATGT
* *
389310 AGCACTAACTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
389337 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
389352 GACTTAATAT
Statistics
Matches: 167, Mismatches: 10, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
27 87 0.52
28 56 0.34
33 3 0.02
34 21 0.13
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:389203 original size:55 final size:55
Alignment explanation
Indices: 389139--389351 Score: 291
Period size: 55 Copynumber: 3.8 Consensus size: 55
389129 TAAATTGTGC
* * *
389139 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATATAGCACTAAGTGTGCGAGTTTGATTATGT
*
389194 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATATAGCACTAAGTGTGCGAGTTTGATTATGT
* *
389249 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCGGACTCAAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATATAGCACTAAGTGTGC-G-----AGTTTGATTATGT
* * *
389310 AGCACTAACTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATATAGCACTAAGTGTGCG
389352 GACTTAATAT
Statistics
Matches: 146, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
55 91 0.62
56 1 0.01
60 1 0.01
61 53 0.36
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATATAGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:397318 original size:29 final size:28
Alignment explanation
Indices: 397282--397359 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
397272 TCATGAGATT
397282 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
397312 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
397339 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
397360 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:397577 original size:174 final size:174
Alignment explanation
Indices: 397312--397639 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
397302 AAATTGTACA
*
397312 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
397377 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCAAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCAAGTCAA
397442 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
397486 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
397551 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCAAGTCAA
397616 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
397640 ACCTTGAGTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCAAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:399558 original size:20 final size:20
Alignment explanation
Indices: 399533--399578 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
399523 ATTAGGCCTT
399533 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
399553 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
399572 GCCCATA
1 GCCCATA
399579 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:399587 original size:19 final size:20
Alignment explanation
Indices: 399545--399588 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
399535 CCATATTAAC
** *
399545 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
399565 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
399584 ACAGT
1 ACAGT
399589 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:401061 original size:25 final size:22
Alignment explanation
Indices: 401007--401061 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 22
400997 TTTTGGCTAG
401007 AGAAGAAAAGAAGGAGAAAAGA
1 AGAAGAAAAGAAGGAGAAAAGA
* *
401029 AAATAGAAGAAGAGAGGAGAAGAGA
1 AGA-AGAA-AAGA-AGGAGAAAAGA
401054 AGGAAGAA
1 A-GAAGAA
401062 TTCGGCACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 2 0.08
23 4 0.15
24 4 0.15
25 15 0.58
26 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.02
Consensus pattern (22 bp):
AGAAGAAAAGAAGGAGAAAAGA
Found at i:403051 original size:21 final size:20
Alignment explanation
Indices: 403027--403065 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
403017 CCTTGTTGAA
403027 TTCGTAATTTGGCCCATTTTC
1 TTCGT-ATTTGGCCCATTTTC
*
403048 TTCGTTTTTGGCCCATTT
1 TTCGTATTTGGCCCATTT
403066 CTCGTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.10, C:0.23, G:0.15, T:0.51
Consensus pattern (20 bp):
TTCGTATTTGGCCCATTTTC
Found at i:404796 original size:27 final size:27
Alignment explanation
Indices: 404766--404943 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
404756 ATATTGAGCC
* *
404766 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
404793 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
404820 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
404848 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
404875 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
404902 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
404929 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
404944 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:404905 original size:82 final size:81
Alignment explanation
Indices: 404787--404942 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
404777 TGCTATATAA
* * * *
404787 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCA-AATCGCA
404852 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
404869 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCA
*
404933 CCCTTAGTGC
65 CACTTAGTGC
404943 TGTACAATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 17 0.27
82 47 0.73
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:407666 original size:17 final size:17
Alignment explanation
Indices: 407644--407678 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
407634 CAATCAAAAT
407644 TTATCCTAAATATGATA
1 TTATCCTAAATATGATA
407661 TTATCCTAAATATGATA
1 TTATCCTAAATATGATA
407678 T
1 T
407679 GAGAGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (17 bp):
TTATCCTAAATATGATA
Found at i:410904 original size:39 final size:39
Alignment explanation
Indices: 410740--410922 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
410730 TTGAATGCTG
* * * * * * *
410740 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
410780 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
410820 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
410860 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
410899 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
410923 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:410942 original size:79 final size:80
Alignment explanation
Indices: 410776--410957 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
410766 GCTAAGTGAA
* * * *
410776 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
410840 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
410856 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
410920 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
410935 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
410958 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:416309 original size:88 final size:88
Alignment explanation
Indices: 416160--416337 Score: 347
Period size: 88 Copynumber: 2.0 Consensus size: 88
416150 AGAAACTAGC
416160 TGAATTGTACGTTTATCAAATTGTGAGATTACACGGGGTACCTGTTTCTATCGTGTCGGATAGAG
1 TGAATTGTACGTTTATCAAATTGTGAGATTACACGGGGTACCTGTTTCTATCGTGTCGGATAGAG
416225 ATCCGAGATTCACCTCACGATTT
66 ATCCGAGATTCACCTCACGATTT
*
416248 TGAATTGTACGTTTATCAAATTGTGAGTTTACACGGGGTACCTGTTTCTATCGTGTCGGATAGAG
1 TGAATTGTACGTTTATCAAATTGTGAGATTACACGGGGTACCTGTTTCTATCGTGTCGGATAGAG
416313 ATCCGAGATTCACCTCACGATTT
66 ATCCGAGATTCACCTCACGATTT
416336 TG
1 TG
416338 GAAGAAATTG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (88 bp):
TGAATTGTACGTTTATCAAATTGTGAGATTACACGGGGTACCTGTTTCTATCGTGTCGGATAGAG
ATCCGAGATTCACCTCACGATTT
Found at i:418778 original size:40 final size:40
Alignment explanation
Indices: 418695--418997 Score: 387
Period size: 40 Copynumber: 7.6 Consensus size: 40
418685 TTGAATGCTG
* * * * * *
418695 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
418735 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
418775 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
418815 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
418855 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
418895 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
418935 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
418974 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
418998 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:424760 original size:206 final size:206
Alignment explanation
Indices: 424406--424814 Score: 676
Period size: 206 Copynumber: 2.0 Consensus size: 206
424396 AATAACGTCT
*
424406 AATCCCTAGATTGAATAATTGATACTTTTCTCTAATTAACACCCTAGGGTTGCATTAACTCAAGC
1 AATCCCTAGATTGAATAATTGAAACTTTTCTCTAATTAACACCCTAGGGTTGCATTAACTCAAGC
*
424471 TATGAATCCCCTTATTAGGTTTCACCCTAATCCGACAAAATCTTGTCACCCTATCTCTAGGCGCG
66 TATGAATCCCCTTATTAGGTTTCACCCTAATCCGACAAAATCTTGTCACCCTATCTCTAGGCACG
* *
424536 CAATCAACTCCGCTTAATTATTACAAATGTACTCTTAGACAGGGTCTATTTCTCTCTA-AATAAG
131 CAATCAACTCCGCTTAATTATGACAAATGTACTCTTAGACAGGGTCTATTCCTC-CTAGAATAAG
424600 AGCTTATCATCG
195 AGCTTATCATCG
* * *
424612 AATCCCTAGATTGAATAATTGAAACTTTTCTCTAATTAACACTCTAGGGTTGCATTAACTCGATC
1 AATCCCTAGATTGAATAATTGAAACTTTTCTCTAATTAACACCCTAGGGTTGCATTAACTCAAGC
* * * * *
424677 TATGGATCCCCTTATTAGGTTTTACCCTAATCTGGCAAAATCTTGTCACCCTATCTTTAGGCACG
66 TATGAATCCCCTTATTAGGTTTCACCCTAATCCGACAAAATCTTGTCACCCTATCTCTAGGCACG
*
424742 CAATCAACTCCGCTTAATTATGACAAATGTTCTCTTAGACAGGGTCTATTCCTCCTATGAATAAG
131 CAATCAACTCCGCTTAATTATGACAAATGTACTCTTAGACAGGGTCTATTCCTCCTA-GAATAAG
424807 AGCTTATC
195 AGCTTATC
424815 TTGAATCAGT
Statistics
Matches: 188, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
205 3 0.02
206 171 0.91
207 14 0.07
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (206 bp):
AATCCCTAGATTGAATAATTGAAACTTTTCTCTAATTAACACCCTAGGGTTGCATTAACTCAAGC
TATGAATCCCCTTATTAGGTTTCACCCTAATCCGACAAAATCTTGTCACCCTATCTCTAGGCACG
CAATCAACTCCGCTTAATTATGACAAATGTACTCTTAGACAGGGTCTATTCCTCCTAGAATAAGA
GCTTATCATCG
Found at i:427216 original size:38 final size:38
Alignment explanation
Indices: 427165--427240 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
427155 AAATTGGCTT
*
427165 TTAATTTTGTTTTTAATTCATTTTAACTACTAAATGAC
1 TTAATTTTGTTTTTAATTCATTTTAACAACTAAATGAC
427203 TTAATTTTGTTTTTAATTCATTTTAACAACTAAATGAC
1 TTAATTTTGTTTTTAATTCATTTTAACAACTAAATGAC
427241 CAAAATGTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.51
Consensus pattern (38 bp):
TTAATTTTGTTTTTAATTCATTTTAACAACTAAATGAC
Found at i:431971 original size:14 final size:16
Alignment explanation
Indices: 431947--431978 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
431937 AGTAGAAACC
431947 TAGAGATATATGA-AT
1 TAGAGATATATGATAT
431962 TAGA-ATATATGATAT
1 TAGAGATATATGATAT
431977 TA
1 TA
431979 TGTTAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (16 bp):
TAGAGATATATGATAT
Found at i:435173 original size:343 final size:343
Alignment explanation
Indices: 434547--435575 Score: 1871
Period size: 343 Copynumber: 3.0 Consensus size: 343
434537 ATAAGTCCTT
* * * *
434547 TTCACCGATTGTGCTACTGAGGTAAGTTTGCATGTAAATAAGATATCGTTTTTACTTATGTTATA
1 TTCACCGATTGTTCTACCGAGGTAATTTTGTATGTAAATAAGATATCGTTTTTACTTATGTTATA
*
434612 ATATTTTGTTATTATATGAAAGGTGGTTGCATATTGAATGATCACTTGATGTAAATTATGAATTG
66 ATATTTTGTTATTATATAAAAGGTGGTTGCATATTGAATGATCACTTGATGTAAATTATGAATTG
434677 AAATTGATTATGGATGAATTGATATAATGTTGAACAGTGAGGAATTTCCCGGTTGGACCATCGGA
131 AAATTGATTATGGATGAATTGATATAATGTTGAACAGTGAGGAATTTCCCGGTTGGACCATCGGA
434742 ATAGAAAAGATACGGATGATCCATTGCGAAAACACATGTGTAGTACTATGTGCAGGCTACTATGT
196 ATAGAAAAGATACGGATGATCCATTGCGAAAACACATGTGTAGTACTATGTGCAGGCTACTATGT
434807 GTTTAAAATTGTTTTAGGTCACGTGTGTCGTCCTAAGTGCAGGCTACTATGCGTACTCGATAGCT
261 GTTTAAAATTGTTTTAGGTCACGTGTGTCGTCCTAAGTGCAGGCTACTATGCGTACTCGATAGCT
434872 TCGATCACATGTGTGGTA
326 TCGATCACATGTGTGGTA
434890 TTCACCGATTGTTCTACCGAGGTAATTTTGTATGTAAATAAGATATCGTTTTTACTTATGTTATA
1 TTCACCGATTGTTCTACCGAGGTAATTTTGTATGTAAATAAGATATCGTTTTTACTTATGTTATA
434955 ATATTTTGTTATTATATAAAAGGTGGTTGCATATTGAATGATCACTTGATGTAAATTATGAATTG
66 ATATTTTGTTATTATATAAAAGGTGGTTGCATATTGAATGATCACTTGATGTAAATTATGAATTG
435020 AAATTGATTATGGATGAATTGATATAATGTTGAACAGTGAGGAATTTCCCGGTTGGACCATCGGA
131 AAATTGATTATGGATGAATTGATATAATGTTGAACAGTGAGGAATTTCCCGGTTGGACCATCGGA
435085 ATAGAAAAGATACGGATGATCCATTGCGAAAACACATGTGTAGTACTATGTGCAGGCTACTATGT
196 ATAGAAAAGATACGGATGATCCATTGCGAAAACACATGTGTAGTACTATGTGCAGGCTACTATGT
435150 GTTTAAAATTGTTTTAGGTCACGTGTGTCGTCCTAAGTGCAGGCTACTATGCGTACTCGATAGCT
261 GTTTAAAATTGTTTTAGGTCACGTGTGTCGTCCTAAGTGCAGGCTACTATGCGTACTCGATAGCT
435215 TCGATCACATGTGTGGTA
326 TCGATCACATGTGTGGTA
435233 TTCACCGATTGTTCTACCGAGGTAATTTTGTATGTAAATAAGATATCGTTTTTACTTATGTTATA
1 TTCACCGATTGTTCTACCGAGGTAATTTTGTATGTAAATAAGATATCGTTTTTACTTATGTTATA
435298 ATATTTTGTTATTATATAAAAGGTGGTTGCATATTGAATGATCACTTGATGTAAATTATGAATTG
66 ATATTTTGTTATTATATAAAAGGTGGTTGCATATTGAATGATCACTTGATGTAAATTATGAATTG
* * *
435363 AAATTGATTATGGATGAATTGATAAAATGTTGAACAGTGAGGAATTTTCTGGTTGGACC-TCCGG
131 AAATTGATTATGGATGAATTGATATAATGTTGAACAGTGAGGAATTTCCCGGTTGGACCAT-CGG
* * * *
435427 AATAGAAAAGATACGAATGATCCGTTGTGAAAACATATGTGTAGTACTATGTGCAGGCTACTATG
195 AATAGAAAAGATACGGATGATCCATTGCGAAAACACATGTGTAGTACTATGTGCAGGCTACTATG
* * * * *
435492 TGTTTAAAATGGTTTTAGGTCACGTGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCGATAGC
260 TGTTTAAAATTGTTTTAGGTCACGTGTGTCGTCCTAAGTGCAGGCTACTATGCGTACTCGATAGC
* *
435557 TTCAATCACATGTTTGGTA
325 TTCGATCACATGTGTGGTA
435576 AGTGTAAGCC
Statistics
Matches: 666, Mismatches: 19, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
342 1 0.00
343 665 1.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (343 bp):
TTCACCGATTGTTCTACCGAGGTAATTTTGTATGTAAATAAGATATCGTTTTTACTTATGTTATA
ATATTTTGTTATTATATAAAAGGTGGTTGCATATTGAATGATCACTTGATGTAAATTATGAATTG
AAATTGATTATGGATGAATTGATATAATGTTGAACAGTGAGGAATTTCCCGGTTGGACCATCGGA
ATAGAAAAGATACGGATGATCCATTGCGAAAACACATGTGTAGTACTATGTGCAGGCTACTATGT
GTTTAAAATTGTTTTAGGTCACGTGTGTCGTCCTAAGTGCAGGCTACTATGCGTACTCGATAGCT
TCGATCACATGTGTGGTA
Found at i:441838 original size:46 final size:46
Alignment explanation
Indices: 441775--441899 Score: 137
Period size: 47 Copynumber: 2.7 Consensus size: 46
441765 AACTCGTAGT
* ** *
441775 CGATGCATGTCCTAGGCATGTCTTACACTAGCT-TACATCTTG-AGGC
1 CGATGCATGTCCCAGGCATGTCTTACACTAGCTCT-CATAATGTA-CC
* * *
441821 TGATGCATGTCCCAGGCATGGTCTTACACTGGCTCTCGTAATGTACC
1 CGATGCATGTCCCAGGCAT-GTCTTACACTAGCTCTCATAATGTACC
*
441868 CGATGCATGTCCCAGACATGTCTTACACTAGC
1 CGATGCATGTCCCAGGCATGTCTTACACTAGC
441900 ACACAATAAC
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
46 29 0.44
47 35 0.53
48 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (46 bp):
CGATGCATGTCCCAGGCATGTCTTACACTAGCTCTCATAATGTACC
Found at i:443859 original size:17 final size:18
Alignment explanation
Indices: 443837--443870 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
443827 TAAGAGTTGA
*
443837 TAAA-TTTATTTTTCTAT
1 TAAATTTTATTATTCTAT
443854 TAAATTTTATTATTCTA
1 TAAATTTTATTATTCTA
443871 GAAAGTAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (18 bp):
TAAATTTTATTATTCTAT
Found at i:447375 original size:49 final size:49
Alignment explanation
Indices: 447303--447527 Score: 189
Period size: 49 Copynumber: 4.7 Consensus size: 49
447293 TGATATATGT
* *
447303 GCTAGTGCAAAACCTGTCTGGGACATGGCATCGGCATCGATAGATGAGA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATCGATAGATGAGA
* * * * * *
447352 GCTAGTGTAAGACCTGTCTGGGACACGGCATCAGCCTCAAGATATGCA-A
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATCGATAGATG-AGA
* * * * * *
447401 GCTAGTGTAAGATCTGTCTGGGACATGGCATTGGC-TTG--GGGTGTG-
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATCGATAGATGAGA
* * *
447446 TC-ACTGTAAGACCTGTCTGGGACATGGCATCGACA-CAGATA-AGTGAGA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATC-GATAGA-TGAGA
* *
447494 GCTAGTGTAAGACTTGTCTGGGACAAGG-ATCGGC
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGC
447528 CTTAGTGTAA
Statistics
Matches: 135, Mismatches: 32, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
44 28 0.21
45 2 0.01
46 2 0.01
47 3 0.02
48 7 0.05
49 92 0.68
50 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (49 bp):
GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATCGATAGATGAGA
Found at i:447566 original size:34 final size:34
Alignment explanation
Indices: 447496--447566 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
447486 AAGTGAGAGC
* * **
447496 TAGTGTAAGACTTGTCTGGGACAAGGATCGGCCT
1 TAGTGTAAGACCTGACTGGGACAAGGATCGAACT
*
447530 TAGTGTAAGACCTGACTGGGACATGGCATC-AACT
1 TAGTGTAAGACCTGACTGGGACAAGG-ATCGAACT
447564 TAG
1 TAG
447567 ATGTGAGATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 28 0.90
35 3 0.10
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (34 bp):
TAGTGTAAGACCTGACTGGGACAAGGATCGAACT
Found at i:448700 original size:40 final size:41
Alignment explanation
Indices: 448656--448751 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 41
448646 TCAAGGTTTT
*
448656 TGGACACGGGCGTGTCACGGTCGTGTGAAGGACACGAG-CA
1 TGGACACGGGCGTGTCACGGCCGTGTGAAGGACACGAGCCA
* * * *
448696 TGGACACGGGCGTGTCATGGCCGTGTGAGGGACATGGGCCA
1 TGGACACGGGCGTGTCACGGCCGTGTGAAGGACACGAGCCA
448737 TGGACACGGGCGTGT
1 TGGACACGGGCGTGT
448752 GCCAGAGCGT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.19, C:0.22, G:0.43, T:0.17
Consensus pattern (41 bp):
TGGACACGGGCGTGTCACGGCCGTGTGAAGGACACGAGCCA
Found at i:467619 original size:73 final size:73
Alignment explanation
Indices: 467495--467680 Score: 302
Period size: 73 Copynumber: 2.5 Consensus size: 73
467485 NNNNNNNNNN
467495 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATGTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATGTC
* * *
467560 TGTTTTCC
66 TATTGTCA
** *
467568 AAATTTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATGTC
467633 TATTGTCA
66 TATTGTCA
467641 AAAAATCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCAG
1 AAAAATCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCAG
467681 TTCACATGCT
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 3 0.03
73 101 0.97
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATGTC
TATTGTCA
Found at i:469045 original size:22 final size:23
Alignment explanation
Indices: 469001--469048 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
468991 AAAATACGAC
* * *
469001 AAATATACGAAAATATAATATAA
1 AAATATAAGAAAATAAAAAATAA
469024 AAATATAAG-AAATAAAAAATAA
1 AAATATAAGAAAATAAAAAATAA
469046 AAA
1 AAA
469049 AAATTAGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (23 bp):
AAATATAAGAAAATAAAAAATAA
Found at i:469144 original size:37 final size:37
Alignment explanation
Indices: 469103--469178 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
469093 GCACCGGCGA
* *
469103 GGCTCCGGTGGCCGTCCGGTGACCGGCCCCCGTGGCC
1 GGCTCCGGTGGCCATCCGGTGACCGGCCCCCATGGCC
*
469140 GGCTCCGGTGGCCATCCGGTGACCGGCCCCTATGGCC
1 GGCTCCGGTGGCCATCCGGTGACCGGCCCCCATGGCC
469177 GG
1 GG
469179 AGCTCCCCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.05, C:0.41, G:0.39, T:0.14
Consensus pattern (37 bp):
GGCTCCGGTGGCCATCCGGTGACCGGCCCCCATGGCC
Found at i:469150 original size:13 final size:13
Alignment explanation
Indices: 469103--469152 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
469093 GCACCGGCGA
469103 GGCTCCGGTGGCC
1 GGCTCCGGTGGCC
*
469116 -G-TCCGGTGACC
1 GGCTCCGGTGGCC
* *
469127 GGCCCCCGTGGCC
1 GGCTCCGGTGGCC
469140 GGCTCCGGTGGCC
1 GGCTCCGGTGGCC
469153 ATCCGGTGAC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
11 9 0.31
12 2 0.07
13 18 0.62
ACGTcount: A:0.02, C:0.42, G:0.42, T:0.14
Consensus pattern (13 bp):
GGCTCCGGTGGCC
Found at i:469727 original size:20 final size:20
Alignment explanation
Indices: 469693--469739 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
469683 ATATTGTTAC
469693 TATTATTTTTATTAATA-TAT
1 TATTATTTTTATTAA-AGTAT
469713 TAATTATTTTT-TTAAAGTAT
1 T-ATTATTTTTATTAAAGTAT
469733 TATTATT
1 TATTATT
469740 ACTAATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.28
20 9 0.36
21 9 0.36
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTATTTTTATTAAAGTAT
Found at i:469736 original size:23 final size:21
Alignment explanation
Indices: 469694--469739 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
469684 TATTGTTACT
469694 ATTATTTTTATTAATATATTA
1 ATTATTTTTATTAATATATTA
469715 ATTATTTTT-TTAA-AGTATT-
1 ATTATTTTTATTAATA-TATTA
469734 ATTATT
1 ATTATT
469740 ACTAATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.29
20 8 0.33
21 9 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTATTTTTATTAATATATTA
Found at i:469802 original size:13 final size:14
Alignment explanation
Indices: 469778--469808 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
469768 ATTATTATCA
469778 ATATTAATATATGT
1 ATATTAATATATGT
469792 ATATT-ATATATGT
1 ATATTAATATATGT
469805 ATAT
1 ATAT
469809 ATTCATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
ATATTAATATATGT
Found at i:469905 original size:12 final size:12
Alignment explanation
Indices: 469890--469921 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
469880 TATATTTCAT
*
469890 TATTATTTTTAA
1 TATTATTATTAA
469902 TATTATTATTAA
1 TATTATTATTAA
469914 TATTATTA
1 TATTATTA
469922 GATGTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:470101 original size:21 final size:20
Alignment explanation
Indices: 470068--470110 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
470058 TTTTATATAC
470068 TATTACATGTATACTTCTAA
1 TATTACATGTATACTTCTAA
* *
470088 TATTATATCGTATATTTCTAA
1 TATTACAT-GTATACTTCTAA
470109 TA
1 TA
470111 CCATCATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (20 bp):
TATTACATGTATACTTCTAA
Found at i:471267 original size:43 final size:43
Alignment explanation
Indices: 471149--471254 Score: 203
Period size: 43 Copynumber: 2.5 Consensus size: 43
471139 NNNNNNNNNN
*
471149 GGCCTTCGTGCCTAGCAGGCTTCGTGCTGGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCG
471192 GGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCG
471235 GGCCTTCGTGCCTAGCAGGC
1 GGCCTTCGTGCCTAGCAGGC
471255 GTAATGCCGG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.09, C:0.26, G:0.35, T:0.29
Consensus pattern (43 bp):
GGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCG
Found at i:475399 original size:42 final size:42
Alignment explanation
Indices: 475335--475489 Score: 168
Period size: 42 Copynumber: 3.7 Consensus size: 42
475325 CTAAAACTAT
*
475335 GTGTAAGACCATATCTGGGATATGGCATCAATGTAAGATTTC
1 GTGTAAGACCATATCTGAGATATGGCATCAATGTAAGATTTC
* *
475377 GTGTAAGACCATATTTGAGATATGGCATCAATGTGAGATTTC
1 GTGTAAGACCATATCTGAGATATGGCATCAATGTAAGATTTC
* * * *** **
475419 GTGTAAGACCATAGT-TGGGCTATTGGCATCGATACGAGATCCC
1 GTGTAAGACCATA-TCTGAGATA-TGGCATCAATGTAAGATTTC
* *
475462 ATGTAAGACCATATCTGGGATATGGCAT
1 GTGTAAGACCATATCTGAGATATGGCAT
475490 TGGTATGGTA
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
42 64 0.65
43 34 0.35
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATATCTGAGATATGGCATCAATGTAAGATTTC
Found at i:475687 original size:15 final size:16
Alignment explanation
Indices: 475661--475690 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
475651 ATGAACCCTC
475661 AGTAAGGTTATGATTG
1 AGTAAGGTTATGATTG
475677 AGTAA-GTTATGATT
1 AGTAAGGTTATGATT
475691 ATAAGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (16 bp):
AGTAAGGTTATGATTG
Found at i:486015 original size:29 final size:29
Alignment explanation
Indices: 485976--486054 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
485966 CTTAATAATC
*
485976 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
486006 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
486035 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
486055 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:493593 original size:47 final size:47
Alignment explanation
Indices: 493542--493736 Score: 223
Period size: 47 Copynumber: 4.1 Consensus size: 47
493532 TTAGGATTTT
*
493542 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCA
* * *
493589 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCA
* * * * *
493636 ATGTGGTGAATATGAACATGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCA
** * * *
493683 ATGTGAAAAATGTATGAGAAATG--TATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATG--TGA-ACATGCATATATGTGATAAAGCCGAATGGCCA
493731 ATGTGA
1 ATGTGA
493737 AATATGTATG
Statistics
Matches: 130, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
47 92 0.71
48 31 0.24
49 3 0.02
50 4 0.03
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAAGCCGAATGGCCA
Found at i:493644 original size:25 final size:25
Alignment explanation
Indices: 493569--493644 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
493559 ATGCATATAT
493569 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
493594 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
493616 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
493641 GTGA
1 GTGA
493645 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:493721 original size:48 final size:48
Alignment explanation
Indices: 493658--493766 Score: 191
Period size: 48 Copynumber: 2.3 Consensus size: 48
493648 TGAACATGTA
493658 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATGTATGAGAAATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATGTATGAGAAATG
* *
493706 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATGTATGAGAAATG
*
493754 CATATGTGGTAAA
1 TATATGTGGTAAA
493767 TGTAACACCC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.38, C:0.06, G:0.27, T:0.29
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATGTATGAGAAATG
Found at i:507585 original size:108 final size:108
Alignment explanation
Indices: 507396--507611 Score: 335
Period size: 108 Copynumber: 2.0 Consensus size: 108
507386 TCCGAACGGG
* * *
507396 TAATTCAGATACTCGAGGACATGTTGAGATGCTGCGTCTTAGAGTTCTGTGGTTCATGGGAAAGA
1 TAATTCAGATACTCGAGGACATGTTGAGATGCTGCATCCTAGAGTTCTGTGGTTCATGCGAAAGA
* *
507461 TATTTGCCTTTGATTGAATTCGCTTATAACAATAGCTTTCAAT
66 AATTTGCCTTTGATTGAATTCGCTTACAACAATAGCTTTCAAT
* * * *
507504 TAATTCAGATACTTGAGGATATGTTGAGATGTTGCATCCTCGAGTT-TAGTGGTTCATGCGAAAG
1 TAATTCAGATACTCGAGGACATGTTGAGATGCTGCATCCTAGAGTTCT-GTGGTTCATGCGAAAG
507568 AAATTTGCCTTTGATTGAATTCGCTTACAACAATAGCTTTCAAT
65 AAATTTGCCTTTGATTGAATTCGCTTACAACAATAGCTTTCAAT
507612 CAAGCATTAA
Statistics
Matches: 98, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
107 1 0.01
108 97 0.99
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (108 bp):
TAATTCAGATACTCGAGGACATGTTGAGATGCTGCATCCTAGAGTTCTGTGGTTCATGCGAAAGA
AATTTGCCTTTGATTGAATTCGCTTACAACAATAGCTTTCAAT
Found at i:513403 original size:29 final size:29
Alignment explanation
Indices: 513369--513654 Score: 502
Period size: 29 Copynumber: 9.9 Consensus size: 29
513359 TAATCAACCG
* * *
513369 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTCAGTGCCATGCA-TTTCAAGCT
* *
513398 CGCACACTTAGTGCCATGCATTTCAAGCC
1 CGCACACTCAGTGCCATGCATTTCAAGCT
*
513427 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTCAGTGCCATGCATTTCAAGCT
513456 CGCACACTCAGTGCCATGCATTTCAAGCT
1 CGCACACTCAGTGCCATGCATTTCAAGCT
513485 CGCACACTCAGTGCCATGCATTTCAAGCT
1 CGCACACTCAGTGCCATGCATTTCAAGCT
513514 CGCACACTCAGTGCCATGCATTTCAAGCT
1 CGCACACTCAGTGCCATGCATTTCAAGCT
513543 CGCACACTCAGTGCCATGCATTTCAAGCT
1 CGCACACTCAGTGCCATGCATTTCAAGCT
513572 CGCACACTCAGTGCCATGCATTTCAAGCT
1 CGCACACTCAGTGCCATGCATTTCAAGCT
513601 CGCACACTCAGTGCCATGCATTTCAAGCT
1 CGCACACTCAGTGCCATGCATTTCAAGCT
513630 CGCACACTCAGTGCCATGCATTTCA
1 CGCACACTCAGTGCCATGCATTTCA
513655 GGCAACACCC
Statistics
Matches: 251, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
28 3 0.01
29 248 0.99
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTCAGTGCCATGCATTTCAAGCT
Found at i:515056 original size:22 final size:22
Alignment explanation
Indices: 515030--515075 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
515020 GCAAGGTAGT
* *
515030 ATGTGTTAAATGCTTTAATATA
1 ATGTGATAAATGATTTAATATA
*
515052 ATGTGATAAATGATTTATTATA
1 ATGTGATAAATGATTTAATATA
515074 AT
1 AT
515076 TATGAGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (22 bp):
ATGTGATAAATGATTTAATATA
Found at i:521958 original size:32 final size:32
Alignment explanation
Indices: 521922--522015 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
521912 TTTTTGAGTG
**
521922 GTACACACAAAGTATACCTTTCCTTTTCAAGT
1 GTACACACAAAGTATACCTAACCTTTTCAAGT
* * * * *
521954 GTACATATAAAGTGTACATAACCTTTTCATGT
1 GTACACACAAAGTATACCTAACCTTTTCAAGT
* *
521986 GATATACACAAAGTATACCCAACCTTTTCA
1 G-TACACACAAAGTATACCTAACCTTTTCA
522016 CATTTGATAG
Statistics
Matches: 48, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
32 26 0.54
33 22 0.46
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (32 bp):
GTACACACAAAGTATACCTAACCTTTTCAAGT
Found at i:522050 original size:29 final size:29
Alignment explanation
Indices: 522008--522103 Score: 129
Period size: 29 Copynumber: 3.3 Consensus size: 29
521998 GTATACCCAA
522008 CCTTTTCACATTTGATAGCCAAAGCTATC
1 CCTTTTCACATTTGATAGCCAAAGCTATC
**
522037 CCTTTTCACATTTGATAGCTGAAGCTATC
1 CCTTTTCACATTTGATAGCCAAAGCTATC
** *
522066 CCTTTTCACATTCAATAGCCTAAGCTATC
1 CCTTTTCACATTTGATAGCCAAAGCTATC
* *
522095 ACTATTCAC
1 CCTTTTCAC
522104 TGATTAGGTA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.27, C:0.28, G:0.09, T:0.35
Consensus pattern (29 bp):
CCTTTTCACATTTGATAGCCAAAGCTATC
Found at i:522075 original size:58 final size:58
Alignment explanation
Indices: 522008--522261 Score: 163
Period size: 62 Copynumber: 4.2 Consensus size: 58
521998 GTATACCCAA
** * * *
522008 CCTTTTCACATTTGATAGCCAAAGCTATCCCTTTTCAC-ATTTGATAGCTGAAGCTATC
1 CCTTTTCACATTCAATAGCCAAAGCTATCACTATTCACGATTAGATAGCTGAAGCTA-C
* * *
522066 CCTTTTCACATTCAATAGCCTAAGCTATCACTATTCACTGATTAGGTAGCTGGAGCTAC
1 CCTTTTCACATTCAATAGCCAAAGCTATCACTATTCAC-GATTAGATAGCTGAAGCTAC
* * * * * *
522125 CACTTTTCACTAATCAAGTAGCCGAAGCTA-CTACTTTTCACTGATCAGGTAGCCGAAGCTAAC
1 C-CTTTTCAC-ATTCAA-TAGCCAAAGCTATC-ACTATTCAC-GATTAGATAGCTGAAGCT-AC
* * * * * * * * *
522188 ACTTTTCAC-TGATCAGGTAGCCGAAGTTACCACTTTTCACTGATCAGGTAGCCGAAGCTAC
1 CCTTTTCACAT--TCA-ATAGCCAAAGCTATCACTATTCAC-GATTAGATAGCTGAAGCTAC
522249 CACTTTTCACATT
1 C-CTTTTCACATT
522262 GTACGCACAA
Statistics
Matches: 164, Mismatches: 19, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
58 33 0.20
59 2 0.01
60 23 0.14
61 9 0.05
62 93 0.57
63 4 0.02
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (58 bp):
CCTTTTCACATTCAATAGCCAAAGCTATCACTATTCACGATTAGATAGCTGAAGCTAC
Found at i:522123 original size:31 final size:31
Alignment explanation
Indices: 522081--522258 Score: 257
Period size: 31 Copynumber: 5.7 Consensus size: 31
522071 TCACATTCAA
* * * *
522081 TAGCCTAAGCTATCACTATTCACTGATTAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
* * * *
522112 TAGCTGGAGCTACCACTTTTCACTAATCAAG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
*
522143 TAGCCGAAGCTACTACTTTTCACTGATCAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
*
522174 TAGCCGAAGCTAACACTTTTCACTGATCAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
*
522205 TAGCCGAAGTTACCACTTTTCACTGATCAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
522236 TAGCCGAAGCTACCACTTTTCAC
1 TAGCCGAAGCTACCACTTTTCAC
522259 ATTGTACGCA
Statistics
Matches: 129, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 129 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (31 bp):
TAGCCGAAGCTACCACTTTTCACTGATCAGG
Found at i:522168 original size:62 final size:62
Alignment explanation
Indices: 522052--522258 Score: 260
Period size: 62 Copynumber: 3.4 Consensus size: 62
522042 TCACATTTGA
* * * * *
522052 TAGCTGAAGCTATCC-CTTTTCAC-ATTCAA-TAGCCTAAGCTA-TCACTATTCACTGATTAGG
1 TAGCCGAAGCTA-CCACTTTTCACTAATCAAGTAGCCGAAGCTACT-ACTTTTCACTGATCAGG
* *
522112 TAGCTGGAGCTACCACTTTTCACTAATCAAGTAGCCGAAGCTACTACTTTTCACTGATCAGG
1 TAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGAAGCTACTACTTTTCACTGATCAGG
* * * * *
522174 TAGCCGAAGCTAACACTTTTCACTGATCAGGTAGCCGAAGTTACCACTTTTCACTGATCAGG
1 TAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGAAGCTACTACTTTTCACTGATCAGG
522236 TAGCCGAAGCTACCACTTTTCAC
1 TAGCCGAAGCTACCACTTTTCAC
522259 ATTGTACGCA
Statistics
Matches: 130, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.02
60 19 0.15
61 5 0.04
62 103 0.79
63 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (62 bp):
TAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGAAGCTACTACTTTTCACTGATCAGG
Found at i:528655 original size:18 final size:17
Alignment explanation
Indices: 528612--528656 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
528602 TATTTATTAT
528612 AATATTTATT--TTTTA
1 AATATTTATTAATTTTA
*
528627 AA-ATTTTTTAATATTTA
1 AATATTTATTAAT-TTTA
528644 AATATTTATTAAT
1 AATATTTATTAAT
528657 GTGACACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 6 0.25
15 2 0.08
16 1 0.04
17 6 0.25
18 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATATTTATTAATTTTA
Found at i:531506 original size:16 final size:18
Alignment explanation
Indices: 531477--531511 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
531467 GTAACTTTTC
531477 TTTCTTCTTCTTTTTATT
1 TTTCTTCTTCTTTTTATT
531495 TTTCTT-TT-TTTTTATT
1 TTTCTTCTTCTTTTTATT
531511 T
1 T
531512 CTCTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 2 0.12
18 6 0.35
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTCTTCTTCTTTTTATT
Found at i:535823 original size:86 final size:86
Alignment explanation
Indices: 535678--535885 Score: 353
Period size: 86 Copynumber: 2.4 Consensus size: 86
535668 TTAAGGTATG
* * *
535678 GATTTTGTTCGGTTCTTGATAATTTCTAGGTTTTTGTAATTGTTGCTTCGTATACTATCTTCGGC
1 GATTTTGTTCGGTTTTTGATAATTTCTACGTTTTTGTAATGGTTGCTTCGTATACTATCTTCGGC
535743 TATATAAGGCACTAAATGTGC
66 TATATAAGGCACTAAATGTGC
* *
535764 GATTTTGTTCAGTTTTTGATAATTTCTACGTTTTTGTAATGGTTGCTTTGTATACTATCTTCGGC
1 GATTTTGTTCGGTTTTTGATAATTTCTACGTTTTTGTAATGGTTGCTTCGTATACTATCTTCGGC
535829 TATATAAGGCACTAAATGTGC
66 TATATAAGGCACTAAATGTGC
* *
535850 GATTTTGTTCGGTTTTTGATCATTTCTACGTATTTG
1 GATTTTGTTCGGTTTTTGATAATTTCTACGTTTTTG
535886 GCACTAAGTG
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 114 1.00
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (86 bp):
GATTTTGTTCGGTTTTTGATAATTTCTACGTTTTTGTAATGGTTGCTTCGTATACTATCTTCGGC
TATATAAGGCACTAAATGTGC
Found at i:536015 original size:44 final size:44
Alignment explanation
Indices: 535967--536073 Score: 153
Period size: 44 Copynumber: 2.4 Consensus size: 44
535957 GTTAATTGAG
*
535967 AAAGCACTAAGTGTGCGGAATTATTAAGGCTTC-AGCTAATCTTT
1 AAAGCATTAAGTGTGCGGAATTATTAAGGCTTCGAG-TAATCTTT
* * **
536011 AAAGCATTAAGTATACAAAATTATTAAGGCTTCGAGTAATCTTT
1 AAAGCATTAAGTGTGCGGAATTATTAAGGCTTCGAGTAATCTTT
536055 AAAGCATTAAGTGTGCGGA
1 AAAGCATTAAGTGTGCGGA
536074 TGTTTAAAGC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 51 0.96
45 2 0.04
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (44 bp):
AAAGCATTAAGTGTGCGGAATTATTAAGGCTTCGAGTAATCTTT
Found at i:550945 original size:12 final size:12
Alignment explanation
Indices: 550928--550953 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
550918 ATCGGGCTGT
550928 TACAGGTATCGA
1 TACAGGTATCGA
550940 TACAGGTATCGA
1 TACAGGTATCGA
550952 TA
1 TA
550954 TTCGTGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (12 bp):
TACAGGTATCGA
Found at i:551821 original size:15 final size:15
Alignment explanation
Indices: 551789--551817 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
551779 ATTTTATGTG
551789 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
551804 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
551818 ATTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:553055 original size:56 final size:56
Alignment explanation
Indices: 552956--553064 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 56
552946 CATGGCATCA
* * * *
552956 ATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGATTCTG
1 ATATATGTGTGCGAGTAAGACCACGTCTGAGACGTTGGCATCGATATGCGATTCTG
* *
553012 ATATATGTGTGCGAGTAAGACC-CTGTCTGGGACAG-TGGTATCGATATGCGATT
1 ATATATGTGTGCGAGTAAGACCAC-GTCTGAGAC-GTTGGCATCGATATGCGATT
553065 ACATGTAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 1 0.02
56 43 0.96
57 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (56 bp):
ATATATGTGTGCGAGTAAGACCACGTCTGAGACGTTGGCATCGATATGCGATTCTG
Found at i:571060 original size:21 final size:21
Alignment explanation
Indices: 571031--571098 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
571021 TTCAAGGGTA
*
571031 TGTCATGACACCCTCAGTCTG
1 TGTCGTGACACCCTCAGTCTG
571052 TGTCGTGACACCCTCAGTCTG
1 TGTCGTGACACCCTCAGTCTG
*
571073 TGTCGTGACACCCTCAATCTG
1 TGTCGTGACACCCTCAGTCTG
571094 TGTCG
1 TGTCG
571099 CAACATCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.16, C:0.32, G:0.22, T:0.29
Consensus pattern (21 bp):
TGTCGTGACACCCTCAGTCTG
Found at i:572149 original size:17 final size:17
Alignment explanation
Indices: 572129--572164 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
572119 GTTTTAAGAG
572129 AAAAAATAGATTAATGT
1 AAAAAATAGATTAATGT
572146 AAAAAATAGATTAATGT
1 AAAAAATAGATTAATGT
572163 AA
1 AA
572165 CACCTGGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (17 bp):
AAAAAATAGATTAATGT
Found at i:578768 original size:25 final size:24
Alignment explanation
Indices: 578734--578780 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
578724 CAACAATGTT
*
578734 AAAACATATATAAATAATAATATGA
1 AAAAAATATATAAAT-ATAATATGA
*
578759 AAAAAATATATATATATAATAT
1 AAAAAATATATAAATATAATAT
578781 AGTGTTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
AAAAAATATATAAATATAATATGA
Found at i:578930 original size:3 final size:3
Alignment explanation
Indices: 578916--578969 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
578906 AATACTAGCG
* *
578916 ATA ATG ATA ATA ATA ATT ATA ATA ATA ATA ATA ATA ATAA ATCA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A ATA
578963 A-A ATA AT
1 ATA ATA AT
578970 GGTAACAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:582495 original size:46 final size:46
Alignment explanation
Indices: 582428--582575 Score: 226
Period size: 46 Copynumber: 3.2 Consensus size: 46
582418 ATAAAATCCT
* * *
582428 ATAATAT-CTATTAGGAATCAAATTTCTAAAAGATAATATCTAATA
1 ATAATATCCTATTAAGAATCAAATTGCTAAAAAATAATATCTAATA
*
582473 ATAATATCCTATTAAGAATCAAATTGCTAAAAAATAGTATCTAATA
1 ATAATATCCTATTAAGAATCAAATTGCTAAAAAATAATATCTAATA
* * *
582519 ATAATATCCTATTATGAATCAAATTGGTAAAAAATAAAATCTAATA
1 ATAATATCCTATTAAGAATCAAATTGCTAAAAAATAATATCTAATA
582565 ATAATATCCTA
1 ATAATATCCTA
582576 ACAACACTAT
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 7 0.07
46 87 0.93
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (46 bp):
ATAATATCCTATTAAGAATCAAATTGCTAAAAAATAATATCTAATA
Found at i:585672 original size:14 final size:14
Alignment explanation
Indices: 585653--585680 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
585643 TGATAGTGAT
585653 CTAGACACCTTGCC
1 CTAGACACCTTGCC
585667 CTAGACACCTTGCC
1 CTAGACACCTTGCC
585681 GTATCAGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.14, T:0.21
Consensus pattern (14 bp):
CTAGACACCTTGCC
Found at i:587362 original size:45 final size:45
Alignment explanation
Indices: 587165--587458 Score: 148
Period size: 45 Copynumber: 6.5 Consensus size: 45
587155 AGGAAATGAT
* * *
587165 TAAGACCATAGTTGAAAGACACTATGGCA-CTA-TACTAGAAACGAG
1 TAAGACCATAGTTGAAAGACACTATGGCATC-ACGAATA-AAACGAA
* *** * ** *
587210 TAAGACTATAGTTGAAAGATGTTATGGCATCACGATTGTATC-AA
1 TAAGACCATAGTTGAAAGACACTATGGCATCACGAATAAAACGAA
* * * * ** ** *
587254 GTAAGACCATAGCTGAAAGACGCTATGGCATCATGATTTTATTGAG
1 -TAAGACCATAGTTGAAAGACACTATGGCATCACGAATAAAACGAA
* ** ** *
587300 TAAAATAATAGCCGAAAGACACTATGGCATCACGAATCAAACGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCACGAATAAAACGAA
* * *
587345 TAAGACCATAGTTGAAAGGCACTATGGCAAT-AAG-ATGGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGC-ATCACGAAT--AAAACGAA
* * * * * * *
587391 TAAGACCAAAGTTGAAAGACACAATGACAACATGACAAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCACGA-ATAAAACGAA
* *
587437 TAAGACCATGGCTGAAAGACAC
1 TAAGACCATAGTTGAAAGACAC
587459 CACGGAATTA
Statistics
Matches: 190, Mismatches: 49, Indels: 19
0.74 0.19 0.07
Matches are distributed among these distances:
44 3 0.02
45 121 0.64
46 65 0.34
48 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.21
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCATCACGAATAAAACGAA
Found at i:587404 original size:46 final size:46
Alignment explanation
Indices: 587342--587458 Score: 126
Period size: 46 Copynumber: 2.5 Consensus size: 46
587332 CGAATCAAAC
* * * * * ***
587342 GAATAAGACCATAGTTGAAAGGCACTATGGCAATAAGATGGAAAAT
1 GAATAAGACCAAAGTTGAAAGACACAATGACAACAAGACAAAAAAT
*
587388 GAATAAGACCAAAGTTGAAAGACACAATGACAACATGACAAAAAAT
1 GAATAAGACCAAAGTTGAAAGACACAATGACAACAAGACAAAAAAT
** *
587434 GAATAAGACCATGGCTGAAAGACAC
1 GAATAAGACCAAAGTTGAAAGACAC
587459 CACGGAATTA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.50, C:0.15, G:0.21, T:0.15
Consensus pattern (46 bp):
GAATAAGACCAAAGTTGAAAGACACAATGACAACAAGACAAAAAAT
Found at i:587883 original size:26 final size:26
Alignment explanation
Indices: 587847--587897 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
587837 AATGAAAAAG
587847 GAACAAATTGAGTAATAGATTGAGGC
1 GAACAAATTGAGTAATAGATTGAGGC
587873 GAACAAATTGAGTAATAGATTGAGG
1 GAACAAATTGAGTAATAGATTGAGG
587898 AATAAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.06, G:0.27, T:0.24
Consensus pattern (26 bp):
GAACAAATTGAGTAATAGATTGAGGC
Found at i:590685 original size:26 final size:26
Alignment explanation
Indices: 590656--590737 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
590646 TGATACAAAT
590656 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
590682 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
590708 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
590734 TGAT
1 TGAT
590738 GGGAATTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:597185 original size:35 final size:35
Alignment explanation
Indices: 597146--597217 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
597136 GTTTTTAAGG
*
597146 TTAGGGTTTTGCCAAAATAAGTTAAGGTTTAGTGT
1 TTAGGGTTTTGCCAAAATAAGTTAAGGTTTAGAGT
* ** *
597181 TTAGGTTTTTGTTAAAATAAGTTAGGGTTTAGAGT
1 TTAGGGTTTTGCCAAAATAAGTTAAGGTTTAGAGT
597216 TT
1 TT
597218 TAGTAGATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (35 bp):
TTAGGGTTTTGCCAAAATAAGTTAAGGTTTAGAGT
Found at i:597327 original size:34 final size:33
Alignment explanation
Indices: 597267--597422 Score: 146
Period size: 34 Copynumber: 4.8 Consensus size: 33
597257 AAATTTATTC
* *
597267 AAATTAGGGTTTAGGATTTTTTAATAAATTAAGT
1 AAATTAGGGTTTAGG-GTTTTAAATAAATTAAGT
* *
597301 AAATTAGGATTCTAGGGTTTTAAATAAATTAGGGT
1 AAATTAGGGTT-TAGGGTTTTAAATAAATTA-AGT
* *
597336 ---TTAGGGTTTATAGTTTTTAAATAAATTAAGT
1 AAATTAGGGTTTA-GGGTTTTAAATAAATTAAGT
597367 AAATTAGGGTTTTAGGGTTTTAAATAAA-T---T
1 AAATTAGGG-TTTAGGGTTTTAAATAAATTAAGT
**
597397 AAATTAGGGTTTAGTTTTTTAAATAA
1 AAATTAGGGTTTAGGGTTTTAAATAA
597423 CATTGTGTTT
Statistics
Matches: 103, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
29 15 0.15
30 10 0.10
31 4 0.04
32 22 0.21
33 1 0.01
34 41 0.40
35 10 0.10
ACGTcount: A:0.37, C:0.01, G:0.19, T:0.44
Consensus pattern (33 bp):
AAATTAGGGTTTAGGGTTTTAAATAAATTAAGT
Found at i:597328 original size:25 final size:24
Alignment explanation
Indices: 597295--597344 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
597285 TTTTAATAAA
*
597295 TTAAGTAAATTAGGATTCTAGGGTT
1 TTAAATAAATTAGGATT-TAGGGTT
*
597320 TTAAATAAATTAGGGTTTAGGGTT
1 TTAAATAAATTAGGATTTAGGGTT
597344 T
1 T
597345 ATAGTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.42
Consensus pattern (24 bp):
TTAAATAAATTAGGATTTAGGGTT
Found at i:597353 original size:66 final size:66
Alignment explanation
Indices: 597270--597422 Score: 206
Period size: 66 Copynumber: 2.4 Consensus size: 66
597260 TTTATTCAAA
* *
597270 TTAGGGTTTAGGATTTTTTAATAAATTAAGTAAATTAGGATTCTAGGGTTTTAAATAAATTAGGG
1 TTAGGGTTTAAGATTTTTAAATAAATTAAGTAAATTAGGATTCTAGGGTTTTAAATAAATTAGGG
597335 T
66 T
* *
597336 TTAGGGTTTATAG-TTTTTAAATAAATTAAGTAAATTAGGGTTTTAGGGTTTTAAATAAATTA--
1 TTAGGGTTTA-AGATTTTTAAATAAATTAAGTAAATTAGGATTCTAGGGTTTTAAATAAATTAGG
**
597398 AA
65 GT
*
597400 TTAGGGTTT-AGTTTTTTAAATAA
1 TTAGGGTTTAAGATTTTTAAATAA
597423 CATTGTGTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
62 2 0.03
63 11 0.14
64 9 0.11
66 56 0.71
67 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (66 bp):
TTAGGGTTTAAGATTTTTAAATAAATTAAGTAAATTAGGATTCTAGGGTTTTAAATAAATTAGGG
T
Found at i:597451 original size:24 final size:24
Alignment explanation
Indices: 597405--597451 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
597395 TTAAATTAGG
* *
597405 GTTTAGTTTTTTAAATAACATTGT
1 GTTTAGTTTTTTAAACAAAATTGT
* *
597429 GTTTATTTTTTTTAACAAAATTG
1 GTTTAGTTTTTTAAACAAAATTG
597452 ACTATTTGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (24 bp):
GTTTAGTTTTTTAAACAAAATTGT
Found at i:600148 original size:15 final size:14
Alignment explanation
Indices: 600124--600157 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
600114 CTATTTTAAT
*
600124 GTTTATGGATTATGG
1 GTTTAGGGATTAT-G
600139 GTTTAGGGATTATG
1 GTTTAGGGATTATG
600153 GTTTA
1 GTTTA
600158 AGGGTTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (14 bp):
GTTTAGGGATTATG
Found at i:600197 original size:7 final size:7
Alignment explanation
Indices: 600137--600257 Score: 57
Period size: 7 Copynumber: 17.0 Consensus size: 7
600127 TATGGATTAT
600137 GGGTTTA
1 GGGTTTA
*
600144 GGGATTA
1 GGGTTTA
*
600151 TGGTTTAA
1 GGGTTT-A
600159 GGG-TT-
1 GGGTTTA
*
600164 GTGATTTA
1 G-GGTTTA
*
600172 AGGTTTA
1 GGGTTTA
*
600179 GGGGTTA
1 GGGTTTA
600186 TGGGTTTA
1 -GGGTTTA
600194 GGGTTTA
1 GGGTTTA
***
600201 AATTTTA
1 GGGTTTA
*
600208 GGATTTA
1 GGGTTTA
**
600215 ATGTTTA
1 GGGTTTA
*
600222 TGGTTTA
1 GGGTTTA
*
600229 GGGATTA
1 GGGTTTA
* *
600236 AGGATTA
1 GGGTTTA
600243 GGAGTTTA
1 GG-GTTTA
600251 GGGTTTA
1 GGGTTTA
600258 AATTAATTAA
Statistics
Matches: 82, Mismatches: 26, Indels: 12
0.68 0.22 0.10
Matches are distributed among these distances:
5 1 0.01
6 1 0.01
7 65 0.79
8 15 0.18
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Found at i:600905 original size:15 final size:16
Alignment explanation
Indices: 600887--600925 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
600877 AAAAAAATTT
600887 AAAATTTAAA-AATAA
1 AAAATTTAAACAATAA
*
600902 AAAA-TAAAACAATAA
1 AAAATTTAAACAATAA
600917 AAAATTTAA
1 AAAATTTAA
600926 TATTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 4 0.20
15 13 0.65
16 3 0.15
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATTTAAACAATAA
Found at i:605342 original size:46 final size:46
Alignment explanation
Indices: 605280--605411 Score: 176
Period size: 46 Copynumber: 2.9 Consensus size: 46
605270 CAACTCATGT
* * * *
605280 AATTGAGGTGTATAAATGTTGTTAATTG-AGATGTTAAAGTGCTGCA
1 AATTGAAGTGTTTAAATGCTGTAAATTGAAG-TGTTAAAGTGCTGCA
605326 AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGCTGCA
1 AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGCTGCA
* * * *
605372 AATTGAAGTGTTTGAATGCAGTAAATTGGAGTGTTTAAGT
1 AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGT
605412 ACTTATTTTG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
46 75 0.97
47 2 0.03
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (46 bp):
AATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGCTGCA
Found at i:605407 original size:23 final size:23
Alignment explanation
Indices: 605280--605409 Score: 131
Period size: 23 Copynumber: 5.7 Consensus size: 23
605270 CAACTCATGT
* * * *
605280 AATTGAGGTGTATAAATGTTGTT
1 AATTGAAGTGTTTAAATGCTGTA
*
605303 AATTG-AGATG-TTAAAGTGCTGCA
1 AATTGAAG-TGTTTAAA-TGCTGTA
605326 AATTGAAGTGTTTAAATGCTGTA
1 AATTGAAGTGTTTAAATGCTGTA
*
605349 AATTGAAGTG-TTAAAGTGCTGCA
1 AATTGAAGTGTTTAAA-TGCTGTA
* *
605372 AATTGAAGTGTTTGAATGCAGTA
1 AATTGAAGTGTTTAAATGCTGTA
*
605395 AATTGGAGTGTTTAA
1 AATTGAAGTGTTTAA
605410 GTACTTATTT
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.11
23 68 0.76
24 11 0.12
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (23 bp):
AATTGAAGTGTTTAAATGCTGTA
Found at i:606604 original size:56 final size:56
Alignment explanation
Indices: 606543--606719 Score: 147
Period size: 56 Copynumber: 3.2 Consensus size: 56
606533 TAAATTAGTT
606543 AATTATTTAGTAAGTTAAAATGTGTAAAAAATTATCTCTCATCAATAAAAAAATTA
1 AATTATTTAGTAAGTTAAAATGTGTAAAAAATTATCTCTCATCAATAAAAAAATTA
* * * * * **
606599 AATTATTTA--AACG---AGA--T-TAATAAAA-TAACATATAATAAATACTATGTAAATTA
1 AATTATTTAGTAA-GTTAAAATGTGTAA-AAAATTATC-TCTCATCAATA--A-AAAAATTA
606652 GTTAATTATTTAGTAAGTTAAAATGTGTAAAAAATTATCTCTCATCAATAAAAAAATTA
1 ---AATTATTTAGTAAGTTAAAATGTGTAAAAAATTATCTCTCATCAATAAAAAAATTA
606711 AATTATTTA
1 AATTATTTA
606720 AACGAGATTA
Statistics
Matches: 89, Mismatches: 14, Indels: 36
0.64 0.10 0.26
Matches are distributed among these distances:
49 6 0.07
50 13 0.15
52 3 0.03
53 6 0.07
54 2 0.02
55 1 0.01
56 27 0.30
57 1 0.01
58 2 0.02
59 6 0.07
60 3 0.03
62 13 0.15
63 6 0.07
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (56 bp):
AATTATTTAGTAAGTTAAAATGTGTAAAAAATTATCTCTCATCAATAAAAAAATTA
Found at i:606651 original size:112 final size:112
Alignment explanation
Indices: 606517--606746 Score: 451
Period size: 112 Copynumber: 2.1 Consensus size: 112
606507 ATACATAATT
606517 TATAATAAATACTATGTAAATTAGTTAATTATTTAGTAAGTTAAAATGTGTAAAAAATTATCTCT
1 TATAATAAATACTATGTAAATTAGTTAATTATTTAGTAAGTTAAAATGTGTAAAAAATTATCTCT
606582 CATCAATAAAAAAATTAAATTATTTAAACGAGATTAATAAAATAACA
66 CATCAATAAAAAAATTAAATTATTTAAACGAGATTAATAAAATAACA
606629 TATAATAAATACTATGTAAATTAGTTAATTATTTAGTAAGTTAAAATGTGTAAAAAATTATCTCT
1 TATAATAAATACTATGTAAATTAGTTAATTATTTAGTAAGTTAAAATGTGTAAAAAATTATCTCT
*
606694 CATCAATAAAAAAATTAAATTATTTAAACGAGATTAATAAAATAATA
66 CATCAATAAAAAAATTAAATTATTTAAACGAGATTAATAAAATAACA
606741 TATAAT
1 TATAAT
606747 CATATTTTAA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 117 1.00
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.37
Consensus pattern (112 bp):
TATAATAAATACTATGTAAATTAGTTAATTATTTAGTAAGTTAAAATGTGTAAAAAATTATCTCT
CATCAATAAAAAAATTAAATTATTTAAACGAGATTAATAAAATAACA
Found at i:611228 original size:20 final size:20
Alignment explanation
Indices: 611200--611241 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
611190 TAAAAAAATA
* *
611200 AAATATAAAAATTTAAATTT
1 AAATATAAAAACTAAAATTT
*
611220 AAATTTAAAAACTAAAATTT
1 AAATATAAAAACTAAAATTT
611240 AA
1 AA
611242 TCATTATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATATAAAAACTAAAATTT
Found at i:617206 original size:9 final size:9
Alignment explanation
Indices: 617188--617227 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
617178 ATTTCTAATA
617188 TATATATTT
1 TATATATTT
*
617197 TATGTATTT
1 TATATATTT
617206 TATATATTAT
1 TATATATT-T
617216 GTATATATTT
1 -TATATATTT
617226 TA
1 TA
617228 ATGTTATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 17 0.63
10 2 0.07
11 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (9 bp):
TATATATTT
Found at i:617224 original size:20 final size:20
Alignment explanation
Indices: 617122--617227 Score: 62
Period size: 20 Copynumber: 5.2 Consensus size: 20
617112 ATCATTATTA
*
617122 TTTATATATATATGTATGTA-
1 TTTATATAT-TATGTATATAT
*
617142 TTTATATAGCGTATG-A-ATAGT
1 TTTATATA--TTATGTATATA-T
617163 TTT-TATATTAT-TATA-AT
1 TTTATATATTATGTATATAT
* *
617180 TTCTAATATATATATTTTATGTAT
1 TT-T-ATATAT-TA-TGTATATAT
617204 TTTATATATTATGTATATAT
1 TTTATATATTATGTATATAT
617224 TTTA
1 TTTA
617228 ATGTTATTAG
Statistics
Matches: 67, Mismatches: 6, Indels: 26
0.68 0.06 0.26
Matches are distributed among these distances:
17 3 0.04
18 6 0.09
19 3 0.04
20 29 0.43
21 11 0.16
22 7 0.10
23 4 0.06
24 4 0.06
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (20 bp):
TTTATATATTATGTATATAT
Found at i:617304 original size:24 final size:24
Alignment explanation
Indices: 617277--617322 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
617267 ATATATTTTT
*
617277 ATATCATCTTATGTACATATATAA
1 ATATCATCTTATATACATATATAA
* *
617301 ATATTATGTTATATACATATAT
1 ATATCATCTTATATACATATAT
617323 GCAATATGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (24 bp):
ATATCATCTTATATACATATATAA
Found at i:617653 original size:25 final size:24
Alignment explanation
Indices: 617625--617680 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
617615 GTTATATTTT
*
617625 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
617650 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
617673 CACTATTA
1 CACTATTA
617681 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:628805 original size:75 final size:75
Alignment explanation
Indices: 627833--629647 Score: 2353
Period size: 75 Copynumber: 24.3 Consensus size: 75
627823 TTCTATTTTC
* * * *
627833 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTT-TATTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGT-ATTTTCAATTT
* *
627897 CTAT-TTTC--
65 TTGTCTTTCAA
* * * * * *
627905 AAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGCTAATTTT-TATTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGT-ATTTTCAATTT
* *
627969 CTAT-TTTC--
65 TTGTCTTTCAA
* * * * * *
627977 AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGCTAATTTT-TATTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGT-ATTTTCAATTT
* *
628041 CTAT-TTTC--
65 TTGTCTTTCAA
* * * * * *
628049 AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGCTAATTTT-TATTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGT-ATTTTCAATTT
* *
628113 CTAT-TTTC--
65 TTGTCTTTCAA
* * * * * *
628121 AAAATTCAACTCATATTGCGAGAAATGAGTTGACCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
628186 TGT-TTTC--
66 TGTCTTTCAA
* * * *
628193 AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGATATGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
*
628258 TGTTTTTCAAAA
66 TGTCTTTC--AA
** * ** * * * * *
628270 AAAAATCGGCTCATATTACGAGAGGTGAGTTGAGCTTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
628335 TGT-TTTC--
66 TGTCTTTCAA
* * * * * *
628342 AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
628407 TGT-TTTC--
66 TGTCTTTCAA
* * * * * *
628414 AAAATTCAACTCATATTGCGAGTAATGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATTTA
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
628479 TGT-TTTC--
66 TGTCTTTCAA
* ** *
628486 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG---ACATGCTGAGGTATTTTCAAT
* *
628550 TTCTATCTTTCAAAAAA
63 TTTTGTCTTTC----AA
* ** ** * * ***
628567 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTGGAAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
*
628632 TGT-TTCTTAA
66 TGTCTT-TCAA
* * *
628642 TTTATGTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAA
1 ---A------AAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTAT
*
628707 TTTCAATTTCTGT-TTTCAA
56 TTTCAATTTTTGTCTTTCAA
628726 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
628791 TGTCTTTCAA
66 TGTCTTTCAA
628801 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
628866 TGTCTTTCAA
66 TGTCTTTCAA
628876 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
628941 TGTCTTTCAA
66 TGTCTTTCAA
628951 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
629016 TGTCTTTCAA
66 TGTCTTTCAA
629026 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
629091 TGTCTTTCAA
66 TGTCTTTCAA
629101 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
629166 TGTCTTTCAA
66 TGTCTTTCAA
629176 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
629241 TGTCTTTCAA
66 TGTCTTTCAA
629251 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
629316 TGTCTTTCAA
66 TGTCTTTCAA
629326 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
629391 TGTCTTTCAA
66 TGTCTTTCAA
629401 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
629466 TGTCTTTCAA
66 TGTCTTTCAA
629476 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
629541 TGTCTTTCAA
66 TGTCTTTCAA
** * * * **
629551 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGTGGTAACTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
* *
629616 TGT-TGTAAA
66 TGTCTTTCAA
629625 AAAAATCAACTCATATTGCGAGA
1 AAAAATCAACTCATATTGCGAGA
629648 GGCGACTTGA
Statistics
Matches: 1624, Mismatches: 90, Indels: 56
0.92 0.05 0.03
Matches are distributed among these distances:
71 5 0.00
72 496 0.31
73 4 0.00
74 109 0.07
75 827 0.51
76 4 0.00
77 56 0.03
78 3 0.00
79 21 0.01
81 37 0.02
82 2 0.00
84 7 0.00
85 53 0.03
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
TGTCTTTCAA
Found at i:629763 original size:93 final size:89
Alignment explanation
Indices: 629622--629878 Score: 272
Period size: 93 Copynumber: 2.9 Consensus size: 89
629612 TTTTTGTTGT
* * * *
629622 AAAAAAAATCAACTCATATTGCGAGAGGCGACTTGAGTCTTAGGTCACACGCTGAGGTATTTTCA
1 AAAAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTGA-GTCACACGCTGAGGTATTTTCA
* * **
629687 ATTTCCGTTTTTCAATTTCTGCCTTTC
65 ATTTCTGTTTTTCAAGTTAAG--TTTC
* **
629714 AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACA-TATCGAGGTATTTT
1 -AAAAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCT-GAGTCACACGCT-GAGGTATTTT
** *
629778 CAAAATCTGCTTTTCAAGTTAAGTTTC
63 CAATTTCTGTTTTTCAAGTTAAGTTTC
*
629805 ---AAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTTG-GCTCACACGCTGAGCTATTTTC
1 AAAAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCC-TGAG-TCACACGCTGAGGTATTTTC
629866 AATTTCTGTTTTT
64 AATTTCTGTTTTT
629879 AGAGAGTCAA
Statistics
Matches: 139, Mismatches: 20, Indels: 16
0.79 0.11 0.09
Matches are distributed among these distances:
86 1 0.01
87 61 0.44
88 2 0.01
91 4 0.03
92 1 0.01
93 69 0.50
94 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (89 bp):
AAAAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTGAGTCACACGCTGAGGTATTTTCAA
TTTCTGTTTTTCAAGTTAAGTTTC
Found at i:634603 original size:14 final size:12
Alignment explanation
Indices: 634576--634600 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
634566 CACAACATGC
634576 ATGGTATTAAAA
1 ATGGTATTAAAA
634588 ATGGTATTAAAA
1 ATGGTATTAAAA
634600 A
1 A
634601 AATATAATAC
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGGTATTAAAA
Found at i:634962 original size:12 final size:12
Alignment explanation
Indices: 634899--634964 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
634889 ATATACACTA
*
634899 ATATACAATAAT
1 ATATATAATAAT
634911 A-ATAGTAATAAT
1 ATATA-TAATAAT
*
634923 A-ATATTAA-AAG
1 ATATA-TAATAAT
*
634934 CTAT-TAATAAT
1 ATATATAATAAT
634945 ACTATATAATAAT
1 A-TATATAATAAT
634958 ATATATA
1 ATATATA
634965 TAAGCATCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
10 3 0.07
11 7 0.16
12 25 0.58
13 8 0.19
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (12 bp):
ATATATAATAAT
Found at i:637117 original size:43 final size:43
Alignment explanation
Indices: 637032--637113 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
637022 AGGAGACAAA
* *
637032 ATCTGTAATTTTCAGCCTATTACCCTACGGCTTAGGGGTTAAG
1 ATCTGTAAATTTCAACCTATTACCCTACGGCTTAGGGGTTAAG
* * * *
637075 ATCTGTAAATTT-AACCTCTTACCCTCCTGCTTATGGGTT
1 ATCTGTAAATTTCAACCTATTACCCTACGGCTTAGGGGTT
637114 TAAGGCTTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 22 0.67
43 11 0.33
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (43 bp):
ATCTGTAAATTTCAACCTATTACCCTACGGCTTAGGGGTTAAG
Found at i:647604 original size:3 final size:3
Alignment explanation
Indices: 647590--647725 Score: 50
Period size: 3 Copynumber: 45.0 Consensus size: 3
647580 AAATATACAC
* * *
647590 TAA TATA TAA TAA TAA TAG TAA TAA TAA TAA TAT TAA -AA GCTAT TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA TAA
* * ** *
647637 TAA TAC TATA TAA T-A TATA TATA TGTA TAA GCA TCA -AA TAA -AA TAA
1 TAA TAA TA-A TAA TAA TA-A TA-A T-AA TAA TAA TAA TAA TAA TAA TAA
* * * * *
647683 TAA TAA T-A GAA CAC TAA TAA AAA T-A TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
647726 ATGTAATAGC
Statistics
Matches: 98, Mismatches: 23, Indels: 24
0.68 0.16 0.17
Matches are distributed among these distances:
2 10 0.10
3 74 0.76
4 13 0.13
5 1 0.01
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:651647 original size:17 final size:17
Alignment explanation
Indices: 651625--651658 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
651615 AATATTTTCC
* *
651625 CATAAAATATTAAAAAA
1 CATAAAAAATCAAAAAA
651642 CATAAAAAATCAAAAAA
1 CATAAAAAATCAAAAAA
651659 ATTATAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (17 bp):
CATAAAAAATCAAAAAA
Found at i:651843 original size:13 final size:13
Alignment explanation
Indices: 651825--651851 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
651815 AAAAAAATTT
651825 AAAATATTATAAA
1 AAAATATTATAAA
651838 AAAATATTATAAA
1 AAAATATTATAAA
651851 A
1 A
651852 GTATTAAAAT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATATTATAAA
Found at i:651886 original size:9 final size:9
Alignment explanation
Indices: 651808--651889 Score: 51
Period size: 9 Copynumber: 8.7 Consensus size: 9
651798 AAATTTTCTT
651808 TAAAAA-TA
1 TAAAAATTA
*
651816 AAAAAATT-
1 TAAAAATTA
651824 TAAAATATTA
1 TAAAA-ATTA
*
651834 TAAAAAAATA
1 T-AAAAATTA
*
651844 TTATAAAAGTA
1 -TA-AAAATTA
*
651855 TTAAAATTGA
1 TAAAAATT-A
*
651865 TATAAATTTA
1 TA-AAAATTA
651875 TAAAAATTA
1 TAAAAATTA
651884 TAAAAA
1 TAAAAA
651890 AAAATCTTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
8 9 0.16
9 21 0.37
10 11 0.19
11 16 0.28
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:657839 original size:8 final size:8
Alignment explanation
Indices: 657826--657852 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
657816 TAGGCCTGTC
657826 ATCTTATG
1 ATCTTATG
657834 ATCTTATG
1 ATCTTATG
657842 ATCTTATG
1 ATCTTATG
657850 ATC
1 ATC
657853 CCATGACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (8 bp):
ATCTTATG
Found at i:664837 original size:25 final size:24
Alignment explanation
Indices: 664800--664920 Score: 134
Period size: 25 Copynumber: 4.8 Consensus size: 24
664790 ACGAGCTGTA
* *
664800 AACGGAAAGCTCATTCGAGCTGAAT
1 AACGG-AAGCTCATACGAGCTAAAT
*
664825 AACTGGAAGCTCATGCGAGCTAAAT
1 AAC-GGAAGCTCATACGAGCTAAAT
*
664850 AACGGGAAGCTCATGCGAGCTAAAT
1 AAC-GGAAGCTCATACGAGCTAAAT
* *
664875 AACAAGAAGCTCATACGAGCTATAT
1 AAC-GGAAGCTCATACGAGCTAAAT
*
664900 ATCGAGAAGCTCATACGAGCT
1 AACG-GAAGCTCATACGAGCT
664921 GTGGTGTGTC
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
25 83 0.98
26 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (24 bp):
AACGGAAGCTCATACGAGCTAAAT
Found at i:664869 original size:50 final size:50
Alignment explanation
Indices: 664800--664921 Score: 154
Period size: 50 Copynumber: 2.4 Consensus size: 50
664790 ACGAGCTGTA
* * ** *
664800 AACGGAAAGCTCATTCGAGCTGAATAACTGGAAGCTCATGCGAGCTAAAT
1 AACGGGAAGCTCATACGAGCTGAATAACAAGAAGCTCATACGAGCTAAAT
* * *
664850 AACGGGAAGCTCATGCGAGCTAAATAACAAGAAGCTCATACGAGCTATAT
1 AACGGGAAGCTCATACGAGCTGAATAACAAGAAGCTCATACGAGCTAAAT
* *
664900 ATCGAGAAGCTCATACGAGCTG
1 AACGGGAAGCTCATACGAGCTG
664922 TGGTGTGTCC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (50 bp):
AACGGGAAGCTCATACGAGCTGAATAACAAGAAGCTCATACGAGCTAAAT
Found at i:665110 original size:22 final size:21
Alignment explanation
Indices: 665060--665112 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
665050 TTATGGCTAT
665060 TGTACAATTTACAAACAATAAA
1 TGTACAATTTA-AAACAATAAA
*
665082 --T-CAATTTAACACATATAAA
1 TGTACAATTTAAAACA-ATAAA
665101 TGTACAATTTAA
1 TGTACAATTTAA
665113 TTACACGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 1 0.04
21 1 0.04
22 8 0.31
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (21 bp):
TGTACAATTTAAAACAATAAA
Found at i:674855 original size:17 final size:17
Alignment explanation
Indices: 674813--674856 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
674803 CAAAATTATG
* *
674813 GGCCCACATGCCCGTGT
1 GGCCCACACGCCCGTAT
*
674830 GGACCCACACGTCCGTAT
1 GG-CCCACACGCCCGTAT
674848 GGCCCACAC
1 GGCCCACAC
674857 AACCACACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.18, C:0.43, G:0.25, T:0.14
Consensus pattern (17 bp):
GGCCCACACGCCCGTAT
Found at i:676422 original size:15 final size:16
Alignment explanation
Indices: 676397--676426 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
676387 ACCCAAGAAC
676397 ACAATAAGAGAAAAAT
1 ACAATAAGAGAAAAAT
676413 ACAA-AAGAGAAAAA
1 ACAATAAGAGAAAAA
676427 GATAATAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.07, G:0.13, T:0.07
Consensus pattern (16 bp):
ACAATAAGAGAAAAAT
Found at i:678458 original size:15 final size:15
Alignment explanation
Indices: 678438--678479 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
678428 AATTTTAAAG
*
678438 AAATGTGATTATTTA
1 AAATGTGATTATTAA
*
678453 AAATGTGACTATTAA
1 AAATGTGATTATTAA
678468 AAATGTGATTAT
1 AAATGTGATTAT
678480 CGAGAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.40
Consensus pattern (15 bp):
AAATGTGATTATTAA
Found at i:678919 original size:13 final size:13
Alignment explanation
Indices: 678901--678927 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
678891 TAATAAACTT
678901 TATTCTTGACAAA
1 TATTCTTGACAAA
678914 TATTCTTGACAAA
1 TATTCTTGACAAA
678927 T
1 T
678928 TTAATTGATA
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:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TATTCTTGACAAA
Found at i:684147 original size:16 final size:15
Alignment explanation
Indices: 684121--684151 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
684111 TACCAATTTT
684121 TAAAAAAAAATAAAA
1 TAAAAAAAAATAAAA
684136 TAAAATAAAAATAAAA
1 TAAAA-AAAAATAAAA
684152 AATACACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAAAAAATAAAA
Found at i:691465 original size:16 final size:16
Alignment explanation
Indices: 691444--691477 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
691434 TGGGAGAAAA
691444 AACCCGATATTTATGG
1 AACCCGATATTTATGG
691460 AACCCGATATTTATGG
1 AACCCGATATTTATGG
691476 AA
1 AA
691478 ATACATCACC
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:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (16 bp):
AACCCGATATTTATGG
Found at i:696031 original size:19 final size:19
Alignment explanation
Indices: 696007--696125 Score: 188
Period size: 19 Copynumber: 6.2 Consensus size: 19
695997 AATCTTTAAG
696007 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
696026 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
696045 GATATGTGCAATCTTAGATAT
1 GATA--TGCAATCTTAGATAT
696066 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
696083 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
696102 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
696123 GAT
1 GAT
696126 CTTGTAATCT
Statistics
Matches: 94, Mismatches: 0, Indels: 10
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.18
19 49 0.52
21 28 0.30
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:696679 original size:26 final size:24
Alignment explanation
Indices: 696635--696683 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
696625 GTGCATAGTT
696635 TTATTTTTTTATATGCTATGTTTAA
1 TTATTTTTTTATATGCTAT-TTTAA
* *
696660 TTATTTCTTTTATGTTCTATTTTA
1 TTATTT-TTTTATATGCTATTTTA
696684 TGATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.67
Consensus pattern (24 bp):
TTATTTTTTTATATGCTATTTTAA
Found at i:699410 original size:37 final size:38
Alignment explanation
Indices: 699352--699429 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 38
699342 TTACGAAGTC
* * *
699352 TTACCCGGACATAATCTCCACACAAAGTTATCGGGT-T
1 TTACCCGGACAAAATCCCCACACAAAGTCATCGGGTCT
**
699389 TTACCCGGACAAAATCCCCACACGTAGTCATCGGGTCT
1 TTACCCGGACAAAATCCCCACACAAAGTCATCGGGTCT
699427 TTA
1 TTA
699430 GAGCTCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 31 0.89
38 4 0.11
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (38 bp):
TTACCCGGACAAAATCCCCACACAAAGTCATCGGGTCT
Found at i:699624 original size:47 final size:47
Alignment explanation
Indices: 699548--699662 Score: 158
Period size: 47 Copynumber: 2.4 Consensus size: 47
699538 CTTCGGGACT
* * * *
699548 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
* * * *
699595 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
699642 TATCACATATATACACTTTCA
1 TATCACATATATACACTTTCA
699663 TGTATACACA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
Found at i:705243 original size:1 final size:1
Alignment explanation
Indices: 705237--705297 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
705227 CTTCTATCTC
* * * * * * * *
705237 AAAAAAAAAGAAAAAGAAAAAGAAAAAGAAAAAAATAATAAAAAGAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
705298 TGGAGAGGCG
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (1 bp):
A
Found at i:705252 original size:6 final size:6
Alignment explanation
Indices: 705237--705296 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
705227 CTTCTATCTC
* *
705237 AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AAAA-A ATAATA AAAAG-
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
705282 AAAA-A AAAAGA AAAA
1 AAAAGA AAAAGA AAAA
705297 ATGGAGAGGC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
5 16 0.33
6 32 0.67
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:706334 original size:88 final size:88
Alignment explanation
Indices: 706185--707033 Score: 1518
Period size: 88 Copynumber: 9.6 Consensus size: 88
706175 AAACAAGATT
706185 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
706250 GAAGCAGATCGAAGATTTCAGCA
66 GAAGCAGATCGAAGATTTCAGCA
706273 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
706338 GAAGCAGATCGAAGATTTCAGCA
66 GAAGCAGATCGAAGATTTCAGCA
706361 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
706426 GAAGCAGATCGAAGATTTCAGCA
66 GAAGCAGATCGAAGATTTCAGCA
706449 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
706514 GAAGCAGATCGAAGATTTCAGCA
66 GAAGCAGATCGAAGATTTCAGCA
706537 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
706602 GAAGCAGATCGAAGATTTCAGCA
66 GAAGCAGATCGAAGATTTCAGCA
706625 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
706690 GAAGCAGATCGAAGATTTCAGCA
66 GAAGCAGATCGAAGATTTCAGCA
706713 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
706778 GAAGCAGATCGAAGATTTCAGCA
66 GAAGCAGATCGAAGATTTCAGCA
* * * *
706801 TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATTTGACATTCCTATGCTTATAGC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
* **
706866 AAAAAAGATCGAAGATTTCAGCA
66 GAAGCAGATCGAAGATTTCAGCA
* *
706889 TGGCATATCCCTGTGTTTATAGGGAAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTAC
1 TGGC--ATCCCTGTGTTTATAGGG-AACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTAT
* *
706954 AGTGAAACAGATCGAAGATTTCAGCA
63 AGCGAAGCAGATCGAAGATTTCAGCA
* * * * *
706980 TGGCATCCCTATGTTTATAGGGAACAAATTGAAGATAACAGATCTGACATCTCC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACA-CTCC
707034 ATTTCGACGG
Statistics
Matches: 738, Mismatches: 19, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
88 637 0.86
89 21 0.03
90 18 0.02
91 62 0.08
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (88 bp):
TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGC
GAAGCAGATCGAAGATTTCAGCA
Found at i:707713 original size:47 final size:47
Alignment explanation
Indices: 707635--707922 Score: 486
Period size: 47 Copynumber: 6.1 Consensus size: 47
707625 CCCTTCGGGA
* * * * * *
707635 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
707682 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
707729 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
707776 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
707825 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
707872 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
707919 CTTA
1 CTTA
707923 CTATCATTTC
Statistics
Matches: 229, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
47 182 0.79
49 47 0.21
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:707832 original size:96 final size:94
Alignment explanation
Indices: 707635--707922 Score: 486
Period size: 96 Copynumber: 3.0 Consensus size: 94
707625 CCCTTCGGGA
* * * * * * * *
707635 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
707700 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
707729 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
707794 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
707825 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
707890 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
707919 CTTA
1 CTTA
707923 CTATCATTTC
Statistics
Matches: 184, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
94 90 0.49
96 94 0.51
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:707904 original size:143 final size:141
Alignment explanation
Indices: 707635--707922 Score: 495
Period size: 143 Copynumber: 2.0 Consensus size: 141
707625 CCCTTCGGGA
* * * *
707635 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
707700 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
707765 GGCCATTAGGC
131 GGCCATTAGGC
* * *
707776 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACAT-T-TATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATAC
707841 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
707906 TCGGCCATTAGGC
129 TCGGCCATTAGGC
707919 CTTA
1 CTTA
707923 CTATCATTTC
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
141 10 0.07
142 1 0.01
143 127 0.92
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (141 bp):
CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:713494 original size:1 final size:1
Alignment explanation
Indices: 713488--713548 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
713478 CTTCTATCTC
* * * * * * * *
713488 AAAAAAAAAGAAAAAGAAAAAGAAAAAGAAAAAAATAATAAAAAGAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
713549 TGGAGAGGCG
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (1 bp):
A
Found at i:713503 original size:6 final size:6
Alignment explanation
Indices: 713488--713547 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
713478 CTTCTATCTC
* *
713488 AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AAAA-A ATAATA AAAAG-
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
713533 AAAA-A AAAAGA AAAA
1 AAAAGA AAAAGA AAAA
713548 ATGGAGAGGC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
5 16 0.33
6 32 0.67
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:714587 original size:88 final size:88
Alignment explanation
Indices: 714436--715200 Score: 663
Period size: 88 Copynumber: 8.7 Consensus size: 88
714426 AAACAAGATT
*
714436 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAAC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAGC
*
714501 AAAGCAGATCGAAGATTTCAGCA
66 GAAGCAGATCGAAGATTTCAGCA
* *
714524 TCGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAAC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAGC
*
714589 AAAGCAGATCGAAGATTTCAGCA
66 GAAGCAGATCGAAGATTTCAGCA
* * * * * *
714612 TCGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGGCA-TCCCTGTGTTTATA
1 TGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGACACT-CCTGTGCTTACA
* **
714675 GGGAA-CAGATCGAAGATAGCAG-A
64 GCGAAGCAGATCGAAGATTTCAGCA
* * ** * *
714698 TGTGACA-CTCCTGTGCTTATAGCGAAGCAGATCGAAGATTTCAG--CATGGCA-TCCCTGTGTT
1 TG-G-CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGACACT-CCTGTGCT
* * * ***
714759 TATAGGGAA-CA-AGTTGAAGACAGCAG-A
60 TACAGCGAAGCAGA-TCGAAGATTTCAGCA
714786 TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACA
1 --TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACA
714851 GCGAAGCAGATCGAAGATTTCAGCA
64 GCGAAGCAGATCGAAGATTTCAGCA
* * * * * * *
714876 TGGCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGCAGATCTGACATTCTTGTGATTATAGT
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAGC
714941 GAAGCAGATCGAAGATTTCAGCA
66 GAAGCAGATCGAAGATTTCAGCA
* * * * * *
714964 TGGCATCCCTATGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGGCA-TCCCTGTGTTTATA
1 TGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGACACT-CCTGTGCTTACA
* * **
715027 GGGAA-CAAATCGAAGATAGCAG-A
64 GCGAAGCAGATCGAAGATTTCAGCA
* * * * *** ** *
715050 TCTGACATTCCTGTGCTTACAACAAAGCAGATCGAAGATTTCAGCATC-G-CA-TCCCTGTGTTT
1 --TGGCATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAG-ATCTGACACT-CCTGTGCTT
* * * **
715112 ATAGGGAA-CA-AGTTGAAGATAGCAG-A
61 ACAGCGAAGCAGA-TCGAAGATTTCAGCA
*
715138 TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTA
1 --TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTA
715201 NNNNNNNNNN
Statistics
Matches: 575, Mismatches: 73, Indels: 58
0.81 0.10 0.08
Matches are distributed among these distances:
86 5 0.01
87 68 0.12
88 453 0.79
89 41 0.07
90 8 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (88 bp):
TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAGC
GAAGCAGATCGAAGATTTCAGCA
Found at i:714662 original size:132 final size:132
Alignment explanation
Indices: 714526--714956 Score: 736
Period size: 132 Copynumber: 3.3 Consensus size: 132
714516 TTTCAGCATC
* *
714526 GCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAACAA
1 GCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAGCGA
*
714591 AGCAGATCGAAGATTTCAGCATCGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
66 AGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
714656 TG
131 TG
* *
714658 GCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGCGA
1 GCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAGCGA
*
714723 AGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGACAGCAGATT
66 AGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
714788 TG
131 TG
714790 GCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAGCGA
1 GCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAGCGA
* *
714855 AGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGCAGATC
66 AGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
714920 TG
131 TG
* * * * *
714922 ACATTCTTGTGATTATAGTGAAGCAGATCGAAGAT
1 GCATCCCTGTGTTTATAGGGAA-CAGATCGAAGAT
714957 TTCAGCATGG
Statistics
Matches: 282, Mismatches: 16, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
132 270 0.96
133 12 0.04
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
GCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAGCGA
AGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
TG
Found at i:714882 original size:220 final size:219
Alignment explanation
Indices: 714436--715175 Score: 960
Period size: 220 Copynumber: 3.4 Consensus size: 219
714426 AAACAAGATT
* *
714436 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAAC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTATAGC
* * *
714501 AAAGCAGATCGAAGATTTCAGCATCGCATCCCTGTGTTTATAGGGAAC-AGATCGAAGATAGCAG
66 GAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAG-TTGAAGATAGCAG
* * * * *** ** *
714565 ATCTGACA-CTCCTGTGCTTACAACAAAGCAGATCGAAGATTTCAGCATC-G-CATCCCTGTGTT
130 ATTTGGCATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAG-ATCTGACAT-CCTGTGCT
* * * **
714627 TATAGGGAA-CA-AGTTGAAGATAGCAG-A
191 TACAGCGAAGCAGA-TCGAAGATTTCAGCA
*
714654 TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATA
1 --TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTATA
*
714719 GCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGACAGCA
64 GCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCA
714784 GATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTA
129 GATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACA-TCCTGTGCTTA
714849 CAGCGAAGCAGATCGAAGATTTCAGCA
193 CAGCGAAGCAGATCGAAGATTTCAGCA
* * * * * *
714876 TGGCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGCAGATCTGACATTCTTGTGATTATAGT
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTATAGC
*
714941 GAAGCAGATCGAAGATTTCAGCATGGCATCCCTATGTTTATAGGGAACAAGTTGAAGATAGCAGA
66 GAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGA
*
715006 TTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACA
131 TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACA-TCCTGTGCTTACA
* *
715071 ACAAAGCAGATCGAAGATTTCAGCA
195 GCGAAGCAGATCGAAGATTTCAGCA
* * * * *
715096 TCGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGGCA-TCCCTGTGTTTATA
1 TGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGACACT-CCTGTGCTTATA
*
715159 GGGAA-CAGATCGAAGAT
64 GCGAAGCAGATCGAAGAT
715176 AGCAGATGTG
Statistics
Matches: 469, Mismatches: 41, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
218 3 0.01
219 30 0.06
220 418 0.89
221 16 0.03
222 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (219 bp):
TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTATAGC
GAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGA
TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATCCTGTGCTTACAG
CGAAGCAGATCGAAGATTTCAGCA
Found at i:715012 original size:132 final size:130
Alignment explanation
Indices: 714527--715196 Score: 692
Period size: 132 Copynumber: 5.1 Consensus size: 130
714517 TTCAGCATCG
* * * *
714527 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAACAAA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGA--TGGCACTCCTGTGCTTATAGCGAA
** * * *
714592 GCAGATCGAAGATTTCAGCATCGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTT
64 GCAGATCGAAGATAGCAGCATGGCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGCAGATCT
*
714657 GG
129 GA
714659 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGTGACACTCCTGTGCTTATAGCGAA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATG-G-CACTCCTGTGCTTATAGCGAA
** * * *
714724 GCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGACAGCAGATTT
64 GCAGATCGAAGATAGCAGCATGGCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGCAGATCT
*
714789 GG
129 GA
* *
714791 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAGCGAA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGA--TGGCACTCCTGTGCTTATAGCGAA
**
714856 GCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGCAGATCT
64 GCAGATCGAAGATAGCAGCATGGCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGCAGATCT
714921 GA
129 GA
* * * * ** * * *
714923 CATTCTTGTGATTATAGTGAAGCAGATCGAAGATTTCAGCATGGCA-TCCCTATGTTTATAGGGA
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAG-ATGGCACT-CCTGTGCTTATAGCGA
* *
714987 A-CA-AGTTGAAGATAGCAG-ATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAG
63 AGCAGA-TCGAAGATAGCAGCA--TGGCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGCAG
715049 ATCTGA
125 ATCTGA
* * * *** ** * * *
715055 CATTCCTGTGCTTACAACAAAGCAGATCGAAGATTTCAGCATCGCA-TCCCTGTGTTTATAGGGA
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAG-ATGGCACT-CCTGTGCTTATAGCGA
* * *
715119 A-CA-AGTTGAAGATAGCAG-ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAG
63 AGCAGA-TCGAAGATAGCAGCA--TGGCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGCAG
*
715181 ATGTGA
125 ATCTGA
715187 CA-CTCCTGTG
1 CATC-CCTGTG
715197 CTTANNNNNN
Statistics
Matches: 489, Mismatches: 38, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
130 4 0.01
131 13 0.03
132 454 0.93
133 15 0.03
134 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (130 bp):
CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATGGCACTCCTGTGCTTATAGCGAAGC
AGATCGAAGATAGCAGCATGGCATCCCTGTGTTTATAGGGAACAAATTGAAGATAGCAGATCTGA
Found at i:719024 original size:18 final size:19
Alignment explanation
Indices: 718994--719032 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
718984 CCTCAATGCC
*
718994 AAAACATAAATAAAACCAT
1 AAAACATAAATAAAACAAT
719013 AAAACA-AAATAAAACAAT
1 AAAACATAAATAAAACAAT
719031 AA
1 AA
719033 TAGCAAGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (19 bp):
AAAACATAAATAAAACAAT
Found at i:722896 original size:43 final size:43
Alignment explanation
Indices: 722844--722985 Score: 205
Period size: 43 Copynumber: 3.3 Consensus size: 43
722834 TTTTTGAAAA
*
722844 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCAC
*
722887 AAACGCCGCTAAA-AGCCATGACCTTTAGCGGCGCTTTTTTTAC
1 AAACGCCGCTAAAGA-CCATGACCTTTAGCGGCGCTTTTTTCAC
* * * * *
722930 AAACGCCGCTAAAGATCATAACCTTTAGCTGCACTTTTCTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCAC
722973 AAACGCCGCTAAA
1 AAACGCCGCTAAA
722986 AATAATGGTA
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
42 1 0.01
43 87 0.98
44 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCAC
Found at i:723115 original size:67 final size:63
Alignment explanation
Indices: 723043--723170 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 63
723033 TTTCTATGAT
*
723043 AAATATTATATTATGTTTAATTTTTAAAATTTAAACTTTAAACTATATACTTTTAAGGATAAATA
1 AAATATTATATTA--TTTAATTTTTAAAATTTAAACTTTAAACTATATACATTTAAGGATAAATA
* *
723108 AAA-A--ATATTATTTAATTTTTGAAATTTGAACTTTAAACTATATACATTTAAGGATAAATA
1 AAATATTATATTATTTAATTTTTAAAATTTAAACTTTAAACTATATACATTTAAGGATAAATA
723168 AAA
1 AAA
723171 AATATTAATT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
60 50 0.83
62 6 0.10
64 1 0.02
65 3 0.05
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (63 bp):
AAATATTATATTATTTAATTTTTAAAATTTAAACTTTAAACTATATACATTTAAGGATAAATA
Done.