Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 128 of 235
Found at i:43393583 original size:16 final size:15
Alignment explanation
Indices: 43393556--43393593 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
43393546 ATAATATCAC
43393556 TAATTAAAAATAAAA
1 TAATTAAAAATAAAA
*
43393571 TAATTAAATAATAAAT
1 TAATTAAA-AATAAAA
43393587 TAATTAA
1 TAATTAA
43393594 TTTGATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATTAAAAATAAAA
Found at i:43397269 original size:21 final size:21
Alignment explanation
Indices: 43397223--43397312 Score: 84
Period size: 21 Copynumber: 4.6 Consensus size: 21
43397213 TCAGCTCTGG
43397223 TGTGCTTCAG-TTAGC-CTT-
1 TGTGCTTCAGTTTAGCACTTA
* * *
43397241 CGGGCTTCCGTTTAGCACTTA
1 TGTGCTTCAGTTTAGCACTTA
43397262 TGTGCTTCAG-TTAGC-CTT-
1 TGTGCTTCAGTTTAGCACTTA
* * *
43397280 CGGGCTTCTGTTTAGCACTTA
1 TGTGCTTCAGTTTAGCACTTA
43397301 TGTGCTTCAGTT
1 TGTGCTTCAGTT
43397313 AGACTTCGGG
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
18 14 0.26
19 13 0.24
20 11 0.20
21 16 0.30
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.41
Consensus pattern (21 bp):
TGTGCTTCAGTTTAGCACTTA
Found at i:43397269 original size:39 final size:39
Alignment explanation
Indices: 43397223--43397326 Score: 190
Period size: 39 Copynumber: 2.7 Consensus size: 39
43397213 TCAGCTCTGG
43397223 TGTGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTA
1 TGTGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTA
*
43397262 TGTGCTTCAGTTAGCCTTCGGGCTTCTGTTTAGCACTTA
1 TGTGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTA
*
43397301 TGTGCTTCAGTTAGACTTCGGGCTTC
1 TGTGCTTCAGTTAGCCTTCGGGCTTC
43397327 AGATCACAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.39
Consensus pattern (39 bp):
TGTGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTA
Found at i:43397327 original size:18 final size:18
Alignment explanation
Indices: 43397226--43397328 Score: 80
Period size: 18 Copynumber: 5.4 Consensus size: 18
43397216 GCTCTGGTGT
*
43397226 GCTTCAGTTAGCCTTCGG
1 GCTTCAGTTAGACTTCGG
* * *
43397244 GCTTCCGTTTAGCACTTATGT
1 GCTTCAG-TTAG-ACTT-CGG
*
43397265 GCTTCAGTTAGCCTTCGG
1 GCTTCAGTTAGACTTCGG
* * *
43397283 GCTTCTGTTTAGCACTTATGT
1 GCTTCAG-TTAG-ACTT-CGG
43397304 GCTTCAGTTAGACTTCGG
1 GCTTCAGTTAGACTTCGG
43397322 GCTTCAG
1 GCTTCAG
43397329 ATCACAATGT
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
18 21 0.33
19 15 0.23
20 14 0.22
21 14 0.22
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.38
Consensus pattern (18 bp):
GCTTCAGTTAGACTTCGG
Found at i:43400075 original size:28 final size:28
Alignment explanation
Indices: 43400022--43400079 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
43400012 AGTGATAAAA
* *
43400022 TATAAATTTATAATTATTAATTTAAAATT
1 TATAAATTTAAAAATATTAA-TTAAAATT
43400051 TATAAATTATAAAAATATTAA-TAAAATT
1 TATAAATT-TAAAAATATTAATTAAAATT
43400079 T
1 T
43400080 TTTTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.31
29 8 0.31
30 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TATAAATTTAAAAATATTAATTAAAATT
Found at i:43400647 original size:61 final size:61
Alignment explanation
Indices: 43400582--43400706 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 61
43400572 GAAATTAAAT
43400582 AAATAATATTTAACTTTTTAAAAAATTAAAATATCAGTGTCTGGTTAATATTTCCCATTAA
1 AAATAATATTTAACTTTTTAAAAAATTAAAATATCAGTGTCTGGTTAATATTTCCCATTAA
*
43400643 AAATAATATTTAACTTTTTTAAAAATTAAAATATCAGTGTCTGGTTAATATTTCCCATTAA
1 AAATAATATTTAACTTTTTAAAAAATTAAAATATCAGTGTCTGGTTAATATTTCCCATTAA
43400704 AAA
1 AAA
43400707 AAGAGAGATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (61 bp):
AAATAATATTTAACTTTTTAAAAAATTAAAATATCAGTGTCTGGTTAATATTTCCCATTAA
Found at i:43406794 original size:24 final size:23
Alignment explanation
Indices: 43406758--43406803 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
43406748 CTTTAAGAAT
* *
43406758 ATTGAAATAATTACCTAGTTCAG
1 ATTGAAACAATTACCAAGTTCAG
*
43406781 ATTGAGAACAATTATCAAGTTCA
1 ATTGA-AACAATTACCAAGTTCA
43406804 AGACTCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (23 bp):
ATTGAAACAATTACCAAGTTCAG
Found at i:43419626 original size:30 final size:30
Alignment explanation
Indices: 43419592--43419651 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
43419582 AACATTTCCC
* *
43419592 CTAGTTTTTGTGGCTAAACTAAAGCCCTTT
1 CTAGTTTTTGTAGCTAAACTAAAACCCTTT
*
43419622 CTAGTTTTTGTAGCTTAACTAAAACCCTTT
1 CTAGTTTTTGTAGCTAAACTAAAACCCTTT
43419652 ACAAATTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (30 bp):
CTAGTTTTTGTAGCTAAACTAAAACCCTTT
Found at i:43424848 original size:58 final size:56
Alignment explanation
Indices: 43424779--43424963 Score: 150
Period size: 58 Copynumber: 3.2 Consensus size: 56
43424769 TTCAACTATT
* * *
43424779 ATTAAACTTAATCACTTTAATATTCAATTAATATAATACTTATCAAGATAAATATTAG
1 ATTAAATTTAATCACTTTAATATTAAATTAATA-AATACTTATCAA-ATAAATATTAA
* * *
43424837 ATTAAATTTAAT-A-TTAAATTTATTAAATTAATAGAATATTTATCTTAATTAAA-ATTAA
1 ATTAAATTTAATCACTTTAA--TATTAAATTAATA-AATACTTATC--AAATAAATATTAA
*
43424895 TATTAAGA--TAATCACTTTAATATTAAATTAATAAAGTAC-TAT-TAATATAATAATTAA
1 -ATTAA-ATTTAATCACTTTAATATTAAATTAATAAA-TACTTATCAAATA-AAT-ATTAA
43424952 ATTAAATTTAAT
1 ATTAAATTTAAT
43424964 AGTAAATTTA
Statistics
Matches: 102, Mismatches: 11, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
54 3 0.03
55 3 0.03
56 9 0.09
57 15 0.15
58 55 0.54
59 10 0.10
60 7 0.07
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (56 bp):
ATTAAATTTAATCACTTTAATATTAAATTAATAAATACTTATCAAATAAATATTAA
Found at i:43426533 original size:86 final size:86
Alignment explanation
Indices: 43426373--43426540 Score: 230
Period size: 86 Copynumber: 2.0 Consensus size: 86
43426363 TAATTAAACA
* *
43426373 AAATAGTTAATATCGTTAACTTTCTGATTAAAATGTTACGTGGTTACATATAATTTGAATGTCCT
1 AAATAATTAATATCGTTAACTTTCTGATTAAAATGTTACGTAGTTACATATAATTTGAATGTCCT
* *
43426438 AAAGCTCCTAGATATTACTCC
66 AAAGATCCTAGAGATTACTCC
* * ** *
43426459 AAATAATTAATATCGTTAACTTTTTTATTAAAATGTTACGTAGTTATGTATAATTTGTATG-CCT
1 AAATAATTAATATCGTTAACTTTCTGATTAAAATGTTACGTAGTTACATATAATTTGAATGTCC-
*
43426523 TTAAGATCCTAGAGATTA
65 TAAAGATCCTAGAGATTA
43426541 ACACGTGGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 2 0.03
86 69 0.97
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (86 bp):
AAATAATTAATATCGTTAACTTTCTGATTAAAATGTTACGTAGTTACATATAATTTGAATGTCCT
AAAGATCCTAGAGATTACTCC
Found at i:43434476 original size:31 final size:30
Alignment explanation
Indices: 43434417--43434479 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
43434407 ACGTGGAGCT
* *
43434417 TAAATTAAAATTTTTTTTATTTTTGGTGAC
1 TAAATTAAAATTTTTTTTATGTTGGGTGAC
*
43434447 TAAATTGAAATTTTTTTTATAGTTGGGTGAC
1 TAAATTAAAATTTTTTTTAT-GTTGGGTGAC
43434478 TA
1 TA
43434480 TCTGTATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.30, C:0.03, G:0.14, T:0.52
Consensus pattern (30 bp):
TAAATTAAAATTTTTTTTATGTTGGGTGAC
Found at i:43434648 original size:33 final size:33
Alignment explanation
Indices: 43434608--43434673 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
43434598 TATGCTTGAG
43434608 GAAATAATGTATTTAAAACTCATATTTGTGTTT
1 GAAATAATGTATTTAAAACTCATATTTGTGTTT
43434641 GAAATAATGTATTTAAAACTCATATTTGTGTTT
1 GAAATAATGTATTTAAAACTCATATTTGTGTTT
43434674 AAAAATAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (33 bp):
GAAATAATGTATTTAAAACTCATATTTGTGTTT
Found at i:43434676 original size:19 final size:19
Alignment explanation
Indices: 43434619--43434677 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
43434609 AAATAATGTA
43434619 TTTAAAACTCATATTTGTG
1 TTTAAAACTCATATTTGTG
* *
43434638 TTTGAAA-T-A-A--TGTA
1 TTTAAAACTCATATTTGTG
43434652 TTTAAAACTCATATTTGTG
1 TTTAAAACTCATATTTGTG
43434671 TTTAAAA
1 TTTAAAA
43434678 ATAACACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.52
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (19 bp):
TTTAAAACTCATATTTGTG
Found at i:43436593 original size:13 final size:13
Alignment explanation
Indices: 43436575--43436600 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43436565 TTCTTCATAG
43436575 ATGAATGTAAATT
1 ATGAATGTAAATT
43436588 ATGAATGTAAATT
1 ATGAATGTAAATT
43436601 TTACACTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
ATGAATGTAAATT
Found at i:43437514 original size:16 final size:15
Alignment explanation
Indices: 43437495--43437525 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
43437485 TTACAACTAA
43437495 AATTTTTAATTATTTT
1 AATTTTTAA-TATTTT
43437511 AATTTTTAATATTTT
1 AATTTTTAATATTTT
43437526 GAATAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
AATTTTTAATATTTT
Found at i:43444305 original size:15 final size:15
Alignment explanation
Indices: 43444285--43444318 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
43444275 AGATTTATCA
43444285 ATATTTAAAATATAT
1 ATATTTAAAATATAT
* *
43444300 ATATTTAATATATGT
1 ATATTTAAAATATAT
43444315 ATAT
1 ATAT
43444319 AAAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATATTTAAAATATAT
Found at i:43451469 original size:43 final size:43
Alignment explanation
Indices: 43451407--43451492 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
43451397 CGACTCCCAC
*
43451407 GTGACCTCTTCAACGCTAGGTTTCGCCATGGGAGTTTCACTAA
1 GTGACCTCTTCAACCCTAGGTTTCGCCATGGGAGTTTCACTAA
43451450 GTGACCTCTTCAACCCTAGGTTTCGCCATGGGAGTTTCACTAA
1 GTGACCTCTTCAACCCTAGGTTTCGCCATGGGAGTTTCACTAA
43451493 CGACATGCGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (43 bp):
GTGACCTCTTCAACCCTAGGTTTCGCCATGGGAGTTTCACTAA
Found at i:43455419 original size:17 final size:17
Alignment explanation
Indices: 43455371--43455424 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
43455361 AAAAAAGATA
*
43455371 AATTTAAATTTG-AATT
1 AATTTGAATTTGAAATT
* **
43455387 GATTTGAATTCAAAATT
1 AATTTGAATTTGAAATT
43455404 AATTTGAATTTGAAA-T
1 AATTTGAATTTGAAATT
43455420 AATTT
1 AATTT
43455425 AAGGGTCTGT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (17 bp):
AATTTGAATTTGAAATT
Found at i:43455967 original size:14 final size:15
Alignment explanation
Indices: 43455945--43456021 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
43455935 CAATCAAACA
43455945 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
43455959 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
43455974 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
43455994 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
43456008 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
43456022 ACTGGGAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:43455986 original size:20 final size:20
Alignment explanation
Indices: 43455961--43456000 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43455951 AATATTTTCC
*
43455961 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
43455981 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
43456001 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:43456006 original size:34 final size:35
Alignment explanation
Indices: 43455949--43456015 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
43455939 CAAACACCAG
*
43455949 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
43455984 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
43456016 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:43459515 original size:97 final size:97
Alignment explanation
Indices: 43459349--43459543 Score: 381
Period size: 97 Copynumber: 2.0 Consensus size: 97
43459339 CATGTATTCA
43459349 ATCGATGATGCAGACTGCCCCTCTCAACAACCAGATGTTAGCCAATGAAAAAAATTACTCCCTCA
1 ATCGATGATGCAGACTGCCCCTCTCAACAACCAGATGTTAGCCAATGAAAAAAATTACTCCCTCA
43459414 GATGTGATTGGAGTAGGCCATCGTAAGACCCC
66 GATGTGATTGGAGTAGGCCATCGTAAGACCCC
*
43459446 ATCGATGATGTAGACTGCCCCTCTCAACAACCAGATGTTAGCCAATGAAAAAAATTACTCCCTCA
1 ATCGATGATGCAGACTGCCCCTCTCAACAACCAGATGTTAGCCAATGAAAAAAATTACTCCCTCA
43459511 GATGTGATTGGAGTAGGCCATCGTAAGACCCC
66 GATGTGATTGGAGTAGGCCATCGTAAGACCCC
43459543 A
1 A
43459544 AGAAGACCAG
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (97 bp):
ATCGATGATGCAGACTGCCCCTCTCAACAACCAGATGTTAGCCAATGAAAAAAATTACTCCCTCA
GATGTGATTGGAGTAGGCCATCGTAAGACCCC
Found at i:43462703 original size:27 final size:27
Alignment explanation
Indices: 43462622--43462704 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 27
43462612 AACTCCCTGG
43462622 GTGGAGGGAAGCAGGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
****
43462649 AACAAGGGAAGCAGGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
*
43462676 GTGGAGGGAACCAGGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
43462703 GT
1 GT
43462705 CCTGCCAACC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.25, C:0.20, G:0.43, T:0.11
Consensus pattern (27 bp):
GTGGAGGGAAGCAGGTTGGCGGCACCA
Found at i:43462714 original size:27 final size:27
Alignment explanation
Indices: 43462633--43462727 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
43462623 TGGAGGGAAG
** * ** *
43462633 CAGGTTGGCGGCACCAAACAAGGGAAG
1 CAGGTTGGCGGCACCAGTCCAGCCAAC
** **
43462660 CAGGTTGGCGGCACCAGTGGAGGGAAC
1 CAGGTTGGCGGCACCAGTCCAGCCAAC
*
43462687 CAGGTTGGCGGCACCAGTCCTGCCAAC
1 CAGGTTGGCGGCACCAGTCCAGCCAAC
*
43462714 CAGATTGGCGGCAC
1 CAGGTTGGCGGCAC
43462728 TACTCGTGTT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.24, C:0.27, G:0.37, T:0.12
Consensus pattern (27 bp):
CAGGTTGGCGGCACCAGTCCAGCCAAC
Found at i:43462722 original size:54 final size:54
Alignment explanation
Indices: 43462622--43462727 Score: 131
Period size: 54 Copynumber: 2.0 Consensus size: 54
43462612 AACTCCCTGG
* ** * *
43462622 GTGGAGGGAAGCAGGTTGGCGGCACCAAACAAGGGAAGCAGGTTGGCGGCACCA
1 GTGGAGGGAACCAGGTTGGCGGCACCAAACAAGCCAACCAGATTGGCGGCACCA
** **
43462676 GTGGAGGGAACCAGGTTGGCGGCACCAGTCCTGCCAACCAGATTGGCGGCAC
1 GTGGAGGGAACCAGGTTGGCGGCACCAAACAAGCCAACCAGATTGGCGGCAC
43462728 TACTCGTGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.25, C:0.25, G:0.40, T:0.11
Consensus pattern (54 bp):
GTGGAGGGAACCAGGTTGGCGGCACCAAACAAGCCAACCAGATTGGCGGCACCA
Found at i:43463787 original size:18 final size:18
Alignment explanation
Indices: 43463759--43463803 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
43463749 TTGATATGGT
* *
43463759 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
*
43463777 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
43463795 TGGTGGCGA
1 TGGTGGCGA
43463804 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:43466194 original size:15 final size:15
Alignment explanation
Indices: 43466170--43466208 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
43466160 CAATATGCAC
*
43466170 AATAACTAAAACTAG
1 AATAATTAAAACTAG
*
43466185 AATAATT-AAATTAG
1 AATAATTAAAACTAG
43466199 AATAATTAAA
1 AATAATTAAA
43466209 TTGATACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (15 bp):
AATAATTAAAACTAG
Found at i:43466201 original size:14 final size:14
Alignment explanation
Indices: 43466182--43466210 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43466172 TAACTAAAAC
43466182 TAGAATAATTAAAT
1 TAGAATAATTAAAT
43466196 TAGAATAATTAAAT
1 TAGAATAATTAAAT
43466210 T
1 T
43466211 GATACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGAATAATTAAAT
Found at i:43467196 original size:17 final size:17
Alignment explanation
Indices: 43467174--43467210 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
43467164 AGTAAGATGT
43467174 CATGAATATTAGAATAG
1 CATGAATATTAGAATAG
43467191 CATGAATATTAGAATAG
1 CATGAATATTAGAATAG
43467208 CAT
1 CAT
43467211 CTTACCCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (17 bp):
CATGAATATTAGAATAG
Found at i:43468540 original size:16 final size:17
Alignment explanation
Indices: 43468521--43468552 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43468511 TTTTTTCCTT
43468521 TTTTTTA-TTTTTTTTA
1 TTTTTTACTTTTTTTTA
43468537 TTTTTTACTTTTTTTT
1 TTTTTTACTTTTTTTT
43468553 GATATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTACTTTTTTTTA
Found at i:43468584 original size:27 final size:27
Alignment explanation
Indices: 43468554--43468649 Score: 167
Period size: 27 Copynumber: 3.5 Consensus size: 27
43468544 CTTTTTTTTG
43468554 ATATATTTTGGTAAATAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAATTAT
43468581 ATATATTTTGGTAAATAAAAAAAATTAT
1 ATATATTTTGGTAAAT-AAAAAAATTAT
43468609 ATATATTTTGGTAAATAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAA-TTAT
43468637 A-ATATTTTGGTAA
1 ATATATTTTGGTAA
43468650 TTTTTTATTT
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
27 35 0.52
28 32 0.48
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (27 bp):
ATATATTTTGGTAAATAAAAAAATTAT
Found at i:43468610 original size:28 final size:28
Alignment explanation
Indices: 43468554--43468649 Score: 169
Period size: 28 Copynumber: 3.5 Consensus size: 28
43468544 CTTTTTTTTG
43468554 ATATATTTTGGTAAAT-AAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAATTAT
43468581 ATATATTTTGGTAAATAAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAATTAT
*
43468609 ATATATTTTGGTAAATAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAATTAT
43468637 A-ATATTTTGGTAA
1 ATATATTTTGGTAA
43468650 TTTTTTATTT
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
27 28 0.42
28 39 0.58
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAATTAT
Found at i:43468672 original size:13 final size:13
Alignment explanation
Indices: 43468654--43468679 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43468644 TGGTAATTTT
43468654 TTATTTTTTTATA
1 TTATTTTTTTATA
43468667 TTATTTTTTTATA
1 TTATTTTTTTATA
43468680 AAACCCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTTTTTATA
Found at i:43469472 original size:10 final size:10
Alignment explanation
Indices: 43469459--43469608 Score: 66
Period size: 10 Copynumber: 15.1 Consensus size: 10
43469449 TCCTTCCCTC
43469459 TTCTTCTTCT
1 TTCTTCTTCT
* *
43469469 TTCTTTTTTT
1 TTCTTCTTCT
43469479 TCTCTTC-TCAT
1 T-TCTTCTTC-T
43469490 TTCATT-TTCT
1 TTC-TTCTTCT
*
43469500 TTC--CTTAT
1 TTCTTCTTCT
43469508 TT-TTCTTTCT
1 TTCTTC-TTCT
* **
43469518 TTCCTCCCCT
1 TTCTTCTTCT
43469528 TTCCTT-TTCT
1 TT-CTTCTTCT
43469538 TTC--CTTCT
1 TTCTTCTTCT
43469546 TT-TTCTTTCT
1 TTCTTC-TTCT
* *
43469556 TTCCTCTCCT
1 TTCTTCTTCT
* *
43469566 TTCTTTTTCC
1 TTCTTCTTCT
*
43469576 TTCTTTTTCT
1 TTCTTCTTCT
43469586 TTCTTCCTTTCT
1 TTCTT-C-TTCT
43469598 TTCTTCTTCT
1 TTCTTCTTCT
43469608 T
1 T
43469609 CCCCTCTCAT
Statistics
Matches: 103, Mismatches: 20, Indels: 34
0.66 0.13 0.22
Matches are distributed among these distances:
8 11 0.11
9 3 0.03
10 63 0.61
11 17 0.17
12 9 0.09
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:43469538 original size:38 final size:38
Alignment explanation
Indices: 43469489--43469590 Score: 149
Period size: 38 Copynumber: 2.8 Consensus size: 38
43469479 TCTCTTCTCA
* *
43469489 TTTCATTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCC
1 TTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCCCC
*
43469527 TTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCC
1 TTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCCCC
43469565 TTT-C--TT-TTTCCTTCTTTTTCTTTCTT
1 TTTCCTTTTCTTTCCTTCTTTTTCTTTCTT
43469591 CCTTTCTTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 20 0.33
35 2 0.03
37 1 0.02
38 38 0.62
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (38 bp):
TTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCCCC
Found at i:43469549 original size:14 final size:14
Alignment explanation
Indices: 43469532--43469605 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
43469522 TCCCCTTTCC
43469532 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
43469546 TTTTCTTTCTTTCCT
1 TTTTCTTTCCTT-CT
43469561 CTCCTTTCTTTTTCCTTCT
1 -T--TTTC--TTTCCTTCT
43469580 TTTTCTTT-CTTC-
1 TTTTCTTTCCTTCT
*
43469592 CTTTCTTT-CTTCT
1 TTTTCTTTCCTTCT
43469605 T
1 T
43469606 CTTCCCCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
12 11 0.22
13 4 0.08
14 14 0.29
15 2 0.04
16 5 0.10
18 5 0.10
19 2 0.04
20 6 0.12
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:43469557 original size:28 final size:28
Alignment explanation
Indices: 43469526--43469605 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
43469516 CTTTCCTCCC
43469526 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
1 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
43469554 CTTTCCTCTCCTTTCTTTTTCCTTCTTTTTCTTT
1 CTTT-C-CT--TTTC--TTTCCTTCTTTTTCTTT
43469588 C-TTCC-TTTCTTT-CTTCTT
1 CTTTCCTTTTCTTTCCTTCTT
43469606 CTTCCCCTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 6 0.13
26 3 0.07
28 8 0.17
29 1 0.02
30 2 0.04
31 1 0.02
32 5 0.11
33 2 0.04
34 18 0.39
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (28 bp):
CTTTCCTTTTCTTTCCTTCTTTTTCTTT
Found at i:43469599 original size:18 final size:18
Alignment explanation
Indices: 43469435--43469610 Score: 81
Period size: 18 Copynumber: 10.0 Consensus size: 18
43469425 ATTACCTTAT
*
43469435 TTTCTTTTT-TTCCTTCC
1 TTTCTTTTTCTTTCTTCC
* * *
43469452 TTCCCTCTTC-TTCTT-C
1 TTTCTTTTTCTTTCTTCC
*
43469468 TTTCTTTTTTTTCTCTTCTC
1 TTTCTTTTTCTT-TCTTC-C
* *
43469488 ATTTCATTTTCTTTCCTT-A
1 -TTTCTTTTTCTTT-CTTCC
*
43469507 TTT-TTCTTTCTTTCCTCCCC
1 TTTCTT-TTTCTTT-CT-TCC
*
43469527 TTTCCTTTTC--T-TTCC
1 TTTCTTTTTCTTTCTTCC
43469542 -TTCTTTTTCTTTCTTTCC
1 TTTCTTTTTCTTTC-TTCC
* *
43469560 TCTC-CTTTCTTT-TTCC
1 TTTCTTTTTCTTTCTTCC
43469576 -TTCTTTTTCTTTCTTCC
1 TTTCTTTTTCTTTCTTCC
43469593 TTTCTTTCTTC-TTCTTCC
1 TTTCTTT-TTCTTTCTTCC
43469611 CCTCTCATTC
Statistics
Matches: 118, Mismatches: 21, Indels: 39
0.66 0.12 0.22
Matches are distributed among these distances:
14 8 0.07
15 4 0.03
16 20 0.17
17 16 0.14
18 42 0.36
19 5 0.04
20 9 0.08
21 14 0.12
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCTTTTTCTTTCTTCC
Found at i:43469606 original size:28 final size:30
Alignment explanation
Indices: 43469528--43469609 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 30
43469518 TTCCTCCCCT
*
43469528 TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TTCC-TTTCTTT-CTTCTTCTTCTTTCTTTCC
43469560 TCTCCTTTCTTT-TTCCTTCTT-TTTCTTT-C
1 T-TCCTTTCTTTCTT-CTTCTTCTTTCTTTCC
43469589 TTCCTTTCTTTCTTCTTCTTC
1 TTCCTTTCTTTCTTCTTCTTC
43469610 CCCTCTCATT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
28 16 0.36
29 4 0.09
30 9 0.20
31 5 0.11
32 8 0.18
33 3 0.07
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (30 bp):
TTCCTTTCTTTCTTCTTCTTCTTTCTTTCC
Found at i:43469695 original size:27 final size:27
Alignment explanation
Indices: 43469657--43469710 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
43469647 AATTCAAGGG
*
43469657 TGGTGCCGCCAACCTGGTTCCCTCCAC
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
43469684 TGGTGCCGCCAACCTGCTTCCCTCCAC
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
43469711 CCAGGGAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.11, C:0.46, G:0.20, T:0.22
Consensus pattern (27 bp):
TGGTGCCGCCAACCTGCTTCCCTCCAC
Found at i:43469784 original size:25 final size:24
Alignment explanation
Indices: 43469750--43469816 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
43469740 TTTTTCTTTT
43469750 TTATATATTTTGGTAAATAAAAAAA
1 TTATATATTTTGGTAAA-AAAAAAA
*
43469775 TTATATATTTTTTGGT-AAAAAAAAG
1 TTATATA--TTTTGGTAAAAAAAAAA
*
43469800 TTATAACATTTTGGTAA
1 TTAT-ATATTTTGGTAA
43469817 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
24 7 0.19
25 18 0.50
26 4 0.11
27 7 0.19
ACGTcount: A:0.45, C:0.01, G:0.10, T:0.43
Consensus pattern (24 bp):
TTATATATTTTGGTAAAAAAAAAA
Found at i:43469811 original size:24 final size:26
Alignment explanation
Indices: 43469751--43469817 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
43469741 TTTTCTTTTT
*
43469751 TATATATTTTGGTAAATAAAAAAATTA
1 TATACATTTTGGT-AATAAAAAAATTA
** *
43469778 TATATTTTTTGGTAA-AAAAAAGTTA
1 TATACATTTTGGTAATAAAAAAATTA
43469803 TA-ACATTTTGGTAAT
1 TATACATTTTGGTAAT
43469818 TTTTTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 10 0.29
25 11 0.31
26 2 0.06
27 12 0.34
ACGTcount: A:0.45, C:0.01, G:0.10, T:0.43
Consensus pattern (26 bp):
TATACATTTTGGTAATAAAAAAATTA
Found at i:43473716 original size:16 final size:15
Alignment explanation
Indices: 43473690--43473721 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
43473680 TAAGTATTAA
43473690 ATTTAATTTAATATT
1 ATTTAATTTAATATT
43473705 ATTTATATTTAATATT
1 ATTTA-ATTTAATATT
43473721 A
1 A
43473722 AATAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTAATTTAATATT
Found at i:43482176 original size:35 final size:35
Alignment explanation
Indices: 43482136--43482207 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
43482126 CATTACGCAT
43482136 ATCGGTTTCTATGGTGAACACCATTAGTTTTTTTA
1 ATCGGTTTCTATGGTGAACACCATTAGTTTTTTTA
43482171 ATCGGTTTCTATGGTGAACACCATTAGTTTTTTTA
1 ATCGGTTTCTATGGTGAACACCATTAGTTTTTTTA
43482206 AT
1 AT
43482208 GCTTAATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.46
Consensus pattern (35 bp):
ATCGGTTTCTATGGTGAACACCATTAGTTTTTTTA
Found at i:43482828 original size:21 final size:22
Alignment explanation
Indices: 43482804--43482845 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
43482794 CTCTAAAAAG
*
43482804 TTAACCAAATTT-ATTTATTTT
1 TTAAACAAATTTAATTTATTTT
*
43482825 TTAAACATATTTAATTTATTT
1 TTAAACAAATTTAATTTATTT
43482846 ATTTTCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
TTAAACAAATTTAATTTATTTT
Found at i:43482917 original size:20 final size:19
Alignment explanation
Indices: 43482888--43482941 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
43482878 ATTTATATAC
43482888 TTTTATATTTTTTAACTTCTT
1 TTTTA-ATTTTTTAACTT-TT
*
43482909 TTTTAA-TTTTTAAGTTTT
1 TTTTAATTTTTTAACTTTT
*
43482927 TGTTAAATTTTTTAA
1 T-TTTAATTTTTTAA
43482942 AAAATGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 3 0.10
19 13 0.45
20 8 0.28
21 5 0.17
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTTAATTTTTTAACTTTT
Found at i:43483123 original size:23 final size:24
Alignment explanation
Indices: 43483074--43483121 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
43483064 ACATGTCAAC
43483074 TTTAGGGATCAATATGATAAAAAAA
1 TTTAGGGATCAATATGA-AAAAAAA
43483099 TTTA-GGAGTCAATATGAAAAAAA
1 TTTAGGGA-TCAATATGAAAAAAA
43483122 TTACCAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.27
Consensus pattern (24 bp):
TTTAGGGATCAATATGAAAAAAAA
Found at i:43486973 original size:17 final size:18
Alignment explanation
Indices: 43486953--43486986 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43486943 TTAATATTTT
43486953 AAATATT-TTAAAATAAA
1 AAATATTATTAAAATAAA
*
43486970 AAATATTATTAATATAA
1 AAATATTATTAAAATAA
43486987 CAATATTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTATTAAAATAAA
Found at i:43492459 original size:61 final size:61
Alignment explanation
Indices: 43492331--43492466 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
43492321 CCTAAAAAAG
* * * ** *
43492331 GAAAGCTTTTATGGTAAGTACTTAATGTTAAGGAATGCCTTCGTGACAAAAATTTAGACAT
1 GAAAGCCTTTGTGGTAAGTACTAAATGTTAAGGAATGCCTTCGTGACAAAAATCAAGAAAT
* * * *
43492392 GAAAGCCTTTGTGGTGAGTACTAAATGTTAAGGAATGCCTTTGTGGCAAAACTCAAGAAAT
1 GAAAGCCTTTGTGGTAAGTACTAAATGTTAAGGAATGCCTTCGTGACAAAAATCAAGAAAT
* *
43492453 GTAAGCCTATGTGG
1 GAAAGCCTTTGTGG
43492467 AGAACCTCTG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (61 bp):
GAAAGCCTTTGTGGTAAGTACTAAATGTTAAGGAATGCCTTCGTGACAAAAATCAAGAAAT
Found at i:43499222 original size:3 final size:3
Alignment explanation
Indices: 43499214--43499251 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
43499204 GATGGAAATC
43499214 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
43499252 TTCCTTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43500746 original size:10 final size:9
Alignment explanation
Indices: 43500731--43500771 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
43500721 AAACTTTTAT
43500731 TAAAATAGTA
1 TAAAATA-TA
43500741 TAAAAT-TA
1 TAAAATATA
43500749 TAAAATATA
1 TAAAATATA
*
43500758 TAGAA-ATA
1 TAAAATATA
43500766 TAAAAT
1 TAAAAT
43500772 TTTATAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 15 0.56
9 6 0.22
10 6 0.22
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (9 bp):
TAAAATATA
Found at i:43500767 original size:17 final size:18
Alignment explanation
Indices: 43500731--43500771 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
43500721 AAACTTTTAT
43500731 TAAAATAGTATAAAATTA
1 TAAAATAGTATAAAATTA
43500749 TAAAATA-TATAGAAA-TA
1 TAAAATAGTATA-AAATTA
43500766 TAAAAT
1 TAAAAT
43500772 TTTATAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
TAAAATAGTATAAAATTA
Found at i:43500775 original size:46 final size:44
Alignment explanation
Indices: 43500688--43500827 Score: 117
Period size: 46 Copynumber: 3.1 Consensus size: 44
43500678 AACAGTTAAA
* * *
43500688 AAAATA-TAAAAATCATAAAA-ATATA-AAATTTGTAAACTTTTATT
1 AAAATAGTAAAAATTATAAAATATATAGAAA--TATAAAATTTTA-T
43500732 AAAATAGTATAAAATTATAAAATATATAGAAATATAAAATTTTAT
1 AAAATAGTA-AAAATTATAAAATATATAGAAATATAAAATTTTAT
* * * * * *
43500777 AAAGTCGTAAGAAAATTATACAATGTAAAGAAATAT-AAATTTCAT
1 AAAATAGT-A-AAAATTATAAAATATATAGAAATATAAAATTTTAT
43500822 AAAATA
1 AAAATA
43500828 ATTTATAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
44 6 0.08
45 21 0.27
46 44 0.56
47 5 0.06
48 3 0.04
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.33
Consensus pattern (44 bp):
AAAATAGTAAAAATTATAAAATATATAGAAATATAAAATTTTAT
Found at i:43501016 original size:20 final size:21
Alignment explanation
Indices: 43500993--43501041 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
43500983 AAAATATTCT
43500993 ATTTTTTAAT-AAATTTGAA-A
1 ATTTTTTAATAAAATTT-AATA
*
43501013 A-TTTTTATTAAAATTTAATA
1 ATTTTTTAATAAAATTTAATA
43501033 ATTTTTTAA
1 ATTTTTTAA
43501042 AATTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 9 0.38
20 9 0.38
21 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTTTTAATAAAATTTAATA
Found at i:43501017 original size:19 final size:20
Alignment explanation
Indices: 43500995--43501047 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
43500985 AATATTCTAT
43500995 TTTTTAAT-AAATTTGAA-AA
1 TTTTTAATAAAATTT-AATAA
*
43501014 TTTTTATTAAAATTTAATAA
1 TTTTTAATAAAATTTAATAA
43501034 TTTTT--TAAAATTTA
1 TTTTTAATAAAATTTA
43501048 TTTTTTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 9 0.29
19 9 0.29
20 13 0.42
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTTAATAAAATTTAATAA
Found at i:43501043 original size:18 final size:17
Alignment explanation
Indices: 43500993--43501047 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 17
43500983 AAAATATTCT
43500993 ATTTTTTAATAAATTTGAAA
1 ATTTTTT-A-AAATTT-AAA
43501013 ATTTTTATTAAAATTTAATA
1 A-TTTT-TTAAAATTTAA-A
43501033 ATTTTTTAAAATTTA
1 ATTTTTTAAAATTTA
43501048 TTTTTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 10 0.31
19 6 0.19
20 9 0.28
21 5 0.16
22 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTTTTAAAATTTAAA
Found at i:43504088 original size:13 final size:13
Alignment explanation
Indices: 43504070--43504096 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43504060 AAGCATGTTA
43504070 TAAGCATGAGAGT
1 TAAGCATGAGAGT
43504083 TAAGCATGAGAGT
1 TAAGCATGAGAGT
43504096 T
1 T
43504097 TGGGATAGCT
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:0.07, G:0.30, T:0.26
Consensus pattern (13 bp):
TAAGCATGAGAGT
Found at i:43515110 original size:12 final size:12
Alignment explanation
Indices: 43515093--43515117 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43515083 AGTTATGGCT
43515093 TGAATTTTAACA
1 TGAATTTTAACA
43515105 TGAATTTTAACA
1 TGAATTTTAACA
43515117 T
1 T
43515118 TTATTATTAA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGAATTTTAACA
Found at i:43515140 original size:15 final size:15
Alignment explanation
Indices: 43515120--43515171 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
43515110 TTTAACATTT
43515120 ATTATTAAACAATAA
1 ATTATTAAACAATAA
* *
43515135 ATTATTAAA-ATTTA
1 ATTATTAAACAATAA
43515149 A-TATTAAACAATAA
1 ATTATTAAACAATAA
43515163 ATTATTAAA
1 ATTATTAAA
43515172 ATTTATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 7 0.23
14 8 0.26
15 16 0.52
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTATTAAACAATAA
Found at i:43515155 original size:13 final size:14
Alignment explanation
Indices: 43515107--43515176 Score: 56
Period size: 15 Copynumber: 5.1 Consensus size: 14
43515097 TTTTAACATG
*
43515107 AATT-TTAACATTT
1 AATTATTAAAATTT
* *
43515120 -ATTATTAAACAATA
1 AATTATTAAA-ATTT
43515134 AATTATTAAAATTT
1 AATTATTAAAATTT
* *
43515148 AA-TATTAAACAATA
1 AATTATTAAA-ATTT
43515162 AATTATTAAAATTT
1 AATTATTAAAATTT
43515176 A
1 A
43515177 TTTTTTAATA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
12 3 0.07
13 11 0.26
14 13 0.30
15 16 0.37
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATTAAAATTT
Found at i:43515189 original size:28 final size:28
Alignment explanation
Indices: 43515107--43515178 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
43515097 TTTTAACATG
*
43515107 AATT-TTAACATTTATTATTAAACAATA
1 AATTATTAAAATTTATTATTAAACAATA
*
43515134 AATTATTAAAATTTAATATTAAACAATA
1 AATTATTAAAATTTATTATTAAACAATA
43515162 AATTATTAAAATTTATT
1 AATTATTAAAATTTATT
43515179 TTTTAATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 4 0.10
28 37 0.90
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
AATTATTAAAATTTATTATTAAACAATA
Found at i:43517180 original size:17 final size:17
Alignment explanation
Indices: 43517160--43517204 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
43517150 AAAAAGTATT
43517160 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
43517177 TTAAAAA-ATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
43517193 ATAAATATATTT
1 TTAAAAATATTT
43517205 ATTATATCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:43519233 original size:11 final size:12
Alignment explanation
Indices: 43519210--43519242 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
43519200 TTTCTATTAG
43519210 AATTTCTAGAAA
1 AATTTCTAGAAA
43519222 AATTTC-AGAAA
1 AATTTCTAGAAA
*
43519233 AATTTTTAGA
1 AATTTCTAGA
43519243 GATGTGCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (12 bp):
AATTTCTAGAAA
Found at i:43519595 original size:16 final size:16
Alignment explanation
Indices: 43519574--43519625 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
43519564 TTTGGTTCGC
43519574 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
43519590 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
43519606 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
43519622 TGTA
1 TGTA
43519626 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:43519672 original size:45 final size:44
Alignment explanation
Indices: 43519606--43519700 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
43519596 GGATTAGAGG
* * *
43519606 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
43519651 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
43519695 TGTAAT
1 TGTAAT
43519701 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:43519883 original size:18 final size:17
Alignment explanation
Indices: 43519862--43519896 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43519852 TTATTATTTA
*
43519862 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
43519880 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
43519897 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:43519890 original size:28 final size:27
Alignment explanation
Indices: 43519820--43519892 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
43519810 TTTATTATCA
*
43519820 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
43519848 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
43519875 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
43519893 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:43520755 original size:16 final size:16
Alignment explanation
Indices: 43520734--43520769 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
43520724 TAAGAAATCA
43520734 CAGCCATGTACTCCTG
1 CAGCCATGTACTCCTG
43520750 CAGCCATGTACTCCTG
1 CAGCCATGTACTCCTG
43520766 CAGC
1 CAGC
43520770 TCCTGAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.39, G:0.19, T:0.22
Consensus pattern (16 bp):
CAGCCATGTACTCCTG
Found at i:43529774 original size:22 final size:22
Alignment explanation
Indices: 43529726--43529775 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
43529716 GATGTCAGTC
43529726 AGAAAAGATTTGAAGATTTAGA
1 AGAAAAGATTTGAAGATTTAGA
**
43529748 A-AAAAGATATTGCGGA-TTAGA
1 AGAAAAGAT-TTGAAGATTTAGA
43529769 AGAAAAG
1 AGAAAAG
43529776 TATGTGAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.52, C:0.02, G:0.24, T:0.22
Consensus pattern (22 bp):
AGAAAAGATTTGAAGATTTAGA
Found at i:43536808 original size:16 final size:17
Alignment explanation
Indices: 43536781--43536813 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
43536771 ATCTAAATTC
*
43536781 ATTTTAAAATTTTAAAT
1 ATTTTAAAATTTAAAAT
43536798 ATTTT-AAATTTAAAAT
1 ATTTTAAAATTTAAAAT
43536814 TTAATAGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTTAAAATTTAAAAT
Found at i:43541288 original size:31 final size:31
Alignment explanation
Indices: 43541235--43541293 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
43541225 AAATTATTTT
* * *
43541235 AAATTAAAATTTATTAGTAAAATTCAATTAG
1 AAATAAAAATTTATGAGTAAAATCCAATTAG
43541266 AAATAAAAATTTAATGAG-AAAATCCAAT
1 AAATAAAAATTT-ATGAGTAAAATCCAAT
43541294 CAAACAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (31 bp):
AAATAAAAATTTATGAGTAAAATCCAATTAG
Found at i:43545300 original size:4 final size:4
Alignment explanation
Indices: 43545291--43545316 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
43545281 TATTGACGAT
43545291 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
43545317 AAGTGGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:43549548 original size:40 final size:40
Alignment explanation
Indices: 43549512--43549590 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 40
43549502 CACTAAAGAT
*
43549512 TGAGCATTAGTGGCGTTTTT-AAAAAAATGCCGCTAAAAA
1 TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA
* *
43549551 TGAGCATTAGCGGCGTTTTTCAAAAAAACGCCGCAAAAAA
1 TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA
43549591 CCTTAGCCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 19 0.53
40 17 0.47
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (40 bp):
TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA
Found at i:43549566 original size:39 final size:39
Alignment explanation
Indices: 43549437--43549590 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 39
43549427 AGCGGCACTT
** * *
43549437 TTAGCGGCGTTTGGACAAAAAACGCCGGTAAAAATCAAGCA
1 TTAGCGGCGTTTTTA-AAAAAACGCCGCTAAAAAT-GAGCA
* ** * * *
43549478 TTAGCGGCGCTTTCT-GGAAATCGCCACTAAAGATTGAGCA
1 TTAGCGGCG-TTTTTAAAAAAACGCCGCTAAA-AATGAGCA
* *
43549518 TTAGTGGCGTTTTTAAAAAAATGCCGCTAAAAATGAGCA
1 TTAGCGGCGTTTTTAAAAAAACGCCGCTAAAAATGAGCA
*
43549557 TTAGCGGCGTTTTTCAAAAAAACGCCGCAAAAAA
1 TTAGCGGCGTTTTT-AAAAAAACGCCGCTAAAAA
43549591 CCTTAGCCCA
Statistics
Matches: 89, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
39 24 0.27
40 51 0.57
41 11 0.12
42 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (39 bp):
TTAGCGGCGTTTTTAAAAAAACGCCGCTAAAAATGAGCA
Found at i:43549693 original size:41 final size:40
Alignment explanation
Indices: 43549626--43549741 Score: 153
Period size: 41 Copynumber: 2.8 Consensus size: 40
43549616 AACATTTCGT
* *
43549626 GGCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCCT-GG
1 GGCTTTAGCGGCGTTTTT-GATAAGCGCCGCTAATG-CTAGG
* *
43549667 GTCTTTAGCGGCGTTTTTGGATAAGCGCCGCTAATGGTAGG
1 GGCTTTAGCGGCGTTTTT-GATAAGCGCCGCTAATGCTAGG
43549708 GGCTTTAGCGGCGTTTTTGATAAAGCGCCGCTAA
1 GGCTTTAGCGGCGTTTTTGAT-AAGCGCCGCTAA
43549742 AAACATTTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 4 0.06
41 63 0.94
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (40 bp):
GGCTTTAGCGGCGTTTTTGATAAGCGCCGCTAATGCTAGG
Found at i:43549983 original size:22 final size:22
Alignment explanation
Indices: 43549958--43550032 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
43549948 GAGTTACTGT
43549958 TTTAAGGTTTATGGAGTATGGA
1 TTTAAGGTTTATGGAGTATGGA
* * *
43549980 TTTAAGGATTATGGATTAGGGA
1 TTTAAGGTTTATGGAGTATGGA
* *
43550002 -TTATGGTTTAAGG-GT-TGAGA
1 TTTAAGGTTTATGGAGTATG-GA
43550022 TTTAAGGTTTA
1 TTTAAGGTTTA
43550033 GGGGTTAGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 19 0.45
22 19 0.45
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (22 bp):
TTTAAGGTTTATGGAGTATGGA
Found at i:43550004 original size:14 final size:15
Alignment explanation
Indices: 43549974--43550014 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
43549964 GTTTATGGAG
43549974 TATGGATTTAAGGAT
1 TATGGATTTAAGGAT
*
43549989 TATGGA-TTAGGGAT
1 TATGGATTTAAGGAT
43550003 TATGG-TTTAAGG
1 TATGGATTTAAGG
43550015 GTTGAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TATGGATTTAAGGAT
Found at i:43550053 original size:22 final size:22
Alignment explanation
Indices: 43550027--43550089 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
43550017 TGAGATTTAA
*
43550027 GGTTTAGGGGTT-AGTGGTTAGG
1 GGTTTAGGGGTTAAG-AGTTAGG
43550049 GGTTTAGGGGTTAAGAGTTAGG
1 GGTTTAGGGGTTAAGAGTTAGG
* * *
43550071 GATTTAGGGTTTATGAGTT
1 GGTTTAGGGGTTAAGAGTT
43550090 CATGGGTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 34 0.94
23 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.43, T:0.38
Consensus pattern (22 bp):
GGTTTAGGGGTTAAGAGTTAGG
Found at i:43550141 original size:12 final size:12
Alignment explanation
Indices: 43550120--43550162 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
43550110 TGGGTTTAGA
43550120 TTAA-TTATTTT
1 TTAATTTATTTT
43550131 TTAATTTATTTT
1 TTAATTTATTTT
* *
43550143 TAAATAT-TTTT
1 TTAATTTATTTT
43550154 TTAATTTAT
1 TTAATTTAT
43550163 ATATTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 13 0.50
12 13 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTAATTTATTTT
Found at i:43550157 original size:23 final size:24
Alignment explanation
Indices: 43550119--43550172 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
43550109 TTGGGTTTAG
*
43550119 ATTAATTA-TTTTTTAATTTAT-T
1 ATTAAATATTTTTTTAATTTATAT
*
43550141 TTTAAATATTTTTTTAATTTATAT
1 ATTAAATATTTTTTTAATTTATAT
43550165 ATTAAATA
1 ATTAAATA
43550173 ATTTCATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 6 0.22
23 13 0.48
24 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTAAATATTTTTTTAATTTATAT
Found at i:43550394 original size:21 final size:21
Alignment explanation
Indices: 43550370--43550410 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
43550360 GATTTAAGGT
43550370 TTAGGGATTAAGAGTTAGGGG
1 TTAGGGATTAAGAGTTAGGGG
*
43550391 TTAGGGGTTAAGAGTTAGGG
1 TTAGGGATTAAGAGTTAGGG
43550411 ATTTAGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.44, T:0.29
Consensus pattern (21 bp):
TTAGGGATTAAGAGTTAGGGG
Found at i:43550419 original size:21 final size:20
Alignment explanation
Indices: 43550367--43550420 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 20
43550357 TAGGATTTAA
43550367 GGTTTAGGGATTAAGAGTTAG
1 GGTTTAGGG-TTAAGAGTTAG
*
43550388 GGGTTAGGGGTTAAGAGTTAG
1 GGTTTA-GGGTTAAGAGTTAG
43550409 GGATTTAGGGTT
1 GG-TTTAGGGTT
43550421 TCAAGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (20 bp):
GGTTTAGGGTTAAGAGTTAG
Found at i:43555030 original size:42 final size:43
Alignment explanation
Indices: 43554970--43555194 Score: 157
Period size: 43 Copynumber: 5.3 Consensus size: 43
43554960 ATGGCACTTT
** * *
43554970 TAGCGGCGTTTGCAAAAAAAACGTCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTATAAAAAAAGCGCCGCTAAAAGTCATGATCTA
* * *
43555013 TAGTGGCGTTTATAAAAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTATAAAAAAAGCGCCGCTAAAAGTCATGATCTA
* ** * * * * *
43555056 TAGCGGCGTTTGT-GTAAAAGTGCCACTAAAGGTCCTGATTTA
1 TAGCGGCGTTTATAAAAAAAGCGCCGCTAAAAGTCATGATCTA
* *** * * *
43555098 TAGCGGCGTTTGTGGGAAAAGTGTCGCTAAAGGTTC-TGATCTA
1 TAGCGGCGTTTATAAAAAAAGCGCCGCTAAAAG-TCATGATCTA
* *** * * * *
43555141 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTT
1 TAGCGGCGTTTATAAAAAAAGCGCCGCTAAAAGTCATGATCTA
43555184 TAGCGGCGTTT
1 TAGCGGCGTTT
43555195 TTGGCGGCGC
Statistics
Matches: 156, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
42 38 0.24
43 116 0.74
44 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTATAAAAAAAGCGCCGCTAAAAGTCATGATCTA
Found at i:43555106 original size:85 final size:86
Alignment explanation
Indices: 43554996--43555194 Score: 233
Period size: 85 Copynumber: 2.3 Consensus size: 86
43554986 AAAAACGTCG
* * * *
43554996 CTAAAAGTCATGATCTATAGTGGCGTTTATAAAAAAAGCGCCGCTAAAGG-TCTTGATCTATAGC
1 CTAAAGGTCCTGATTTATAGCGGCGTTTATAAAAAAAGCGCCGCTAAAGGTTC-TGATCTATAGC
* *
43555060 GGCGTTTGT-GTAAAAGTGCCA
65 GGCGTTTGTGGGAAAAGCGCCA
* *** * *
43555081 CTAAAGGTCCTGATTTATAGCGGCGTTTGTGGGAAAAGTGTCGCTAAAGGTTCTGATCTATAGCG
1 CTAAAGGTCCTGATTTATAGCGGCGTTTATAAAAAAAGCGCCGCTAAAGGTTCTGATCTATAGCG
*
43555146 GCGTTTGTGGGAAAAGCGCCG
66 GCGTTTGTGGGAAAAGCGCCA
*
43555167 CTAAAGGTCCTGGTCTT-TAGCGGCGTTT
1 CTAAAGGTCCTGAT-TTATAGCGGCGTTT
43555195 TTGGCGGCGC
Statistics
Matches: 97, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
85 60 0.62
86 35 0.36
87 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (86 bp):
CTAAAGGTCCTGATTTATAGCGGCGTTTATAAAAAAAGCGCCGCTAAAGGTTCTGATCTATAGCG
GCGTTTGTGGGAAAAGCGCCA
Found at i:43555137 original size:43 final size:43
Alignment explanation
Indices: 43554994--43555194 Score: 242
Period size: 43 Copynumber: 4.7 Consensus size: 43
43554984 AAAAAAACGT
* * * * *** *
43554994 CGCTAAAAGTCATGATCTATAGTGGCGTTTATAAAAAAAGCGC
1 CGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGTGC
* *
43555037 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GTAAAAGTGC
1 CGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGTGC
* * *
43555079 CACTAAAGGTCCTGATTTATAGCGGCGTTTGTGGGAAAAGTGT
1 CGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGTGC
* *
43555122 CGCTAAAGGTTCTGATCTATAGCGGCGTTTGTGGGAAAAGCGC
1 CGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGTGC
* *
43555165 CGCTAAAGGTCCTGGTCTTTAGCGGCGTTT
1 CGCTAAAGGTCCTGATCTATAGCGGCGTTT
43555195 TTGGCGGCGC
Statistics
Matches: 137, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
42 36 0.26
43 101 0.74
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (43 bp):
CGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGTGC
Found at i:43560625 original size:3 final size:3
Alignment explanation
Indices: 43560617--43560649 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
43560607 TCTTCGTCTT
43560617 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43560650 GTTGTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:43562848 original size:39 final size:39
Alignment explanation
Indices: 43562804--43562881 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
43562794 AAACTATAAT
* *
43562804 TTTGTTTCAATGTACATATATATTTTTGACAAAAGATCA
1 TTTGTTTCAATGTACAAATATATTTTTGACAAAAAATCA
* *
43562843 TTTGTTTCAGTGTTCAAATATATTTTTGACAAAAAATCA
1 TTTGTTTCAATGTACAAATATATTTTTGACAAAAAATCA
43562882 AGACATACGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (39 bp):
TTTGTTTCAATGTACAAATATATTTTTGACAAAAAATCA
Found at i:43584994 original size:15 final size:16
Alignment explanation
Indices: 43584964--43585002 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
43584954 TAGTAAAAAT
43584964 ATAATTTTACTATTTTA
1 ATAA-TTTACTATTTTA
*
43584981 ATAATTTA-TATTTTT
1 ATAATTTACTATTTTA
43584996 ATAATTT
1 ATAATTT
43585003 TTAAAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAATTTACTATTTTA
Found at i:43594430 original size:15 final size:15
Alignment explanation
Indices: 43594389--43594433 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
43594379 CCCCATTATT
43594389 TTGTTGATATTTTTA
1 TTGTTGATATTTTTA
*
43594404 TT-TTAGAT-TTTTTG
1 TTGTT-GATATTTTTA
43594418 TTGTTGATATTTTTA
1 TTGTTGATATTTTTA
43594433 T
1 T
43594434 ATGGGTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (15 bp):
TTGTTGATATTTTTA
Found at i:43604376 original size:29 final size:29
Alignment explanation
Indices: 43604343--43604398 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
43604333 TTTGGTCTCT
* *
43604343 ATATTTTTATAATGTTATTAATTAGTTTA
1 ATATTTTTACAATGTAATTAATTAGTTTA
43604372 ATATTTTTACAATGTAATTAATTAGTT
1 ATATTTTTACAATGTAATTAATTAGTT
43604399 CAAATAGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (29 bp):
ATATTTTTACAATGTAATTAATTAGTTTA
Found at i:43611036 original size:3 final size:3
Alignment explanation
Indices: 43611028--43611074 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
43611018 TTTATACACT
*
43611028 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
43611075 TGAAACTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:43618512 original size:27 final size:27
Alignment explanation
Indices: 43618455--43618509 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
43618445 CCAAACCTAG
*
43618455 CAAAACCAAATAACCGAAAGCAGTAAC
1 CAAAACCAAATAACCAAAAGCAGTAAC
*
43618482 CAAAACCAAATAACCCAAAATCAGTAAC
1 CAAAACCAAATAA-CCAAAAGCAGTAAC
43618510 AAACAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.56, C:0.27, G:0.07, T:0.09
Consensus pattern (27 bp):
CAAAACCAAATAACCAAAAGCAGTAAC
Found at i:43620262 original size:18 final size:19
Alignment explanation
Indices: 43620239--43620277 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
43620229 ACATCAACTA
*
43620239 ATTTTTTTATATATT-TTT
1 ATTTTTATATATATTATTT
43620257 ATTTTTATATATATTATTT
1 ATTTTTATATATATTATTT
43620276 AT
1 AT
43620278 ATGTCAGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTTATATATATTATTT
Found at i:43625753 original size:46 final size:45
Alignment explanation
Indices: 43625654--43625845 Score: 325
Period size: 46 Copynumber: 4.3 Consensus size: 45
43625644 TATGTATGAT
*
43625654 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
*
43625697 CACTTATCACTTTGTCACTTTATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
*
43625743 CACTTATCACTTTGTCACTTTATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
43625789 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
43625834 CACTTATCACTT
1 CACTTATCACTT
43625846 GATCAGATAA
Statistics
Matches: 143, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
43 10 0.07
44 5 0.03
45 38 0.27
46 90 0.63
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (45 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
Found at i:43625847 original size:37 final size:38
Alignment explanation
Indices: 43625803--43625878 Score: 127
Period size: 37 Copynumber: 2.0 Consensus size: 38
43625793 TATCACTTTG
* *
43625803 TCACTTGATCAGATAAGTGTAGCT-AGGCTACCACTTA
1 TCACTTGATCAGATAAGTGCAGCTAAAGCTACCACTTA
43625840 TCACTTGATCAGATAAGTGCAGCTAAAGCTACCACTTA
1 TCACTTGATCAGATAAGTGCAGCTAAAGCTACCACTTA
43625878 T
1 T
43625879 GTAACAGCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 23 0.64
38 13 0.36
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (38 bp):
TCACTTGATCAGATAAGTGCAGCTAAAGCTACCACTTA
Found at i:43628449 original size:46 final size:46
Alignment explanation
Indices: 43628382--43628736 Score: 473
Period size: 46 Copynumber: 8.1 Consensus size: 46
43628372 TTTGAGTACT
43628382 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
43628428 TCTGATCAAGTGACAAAGTGAT-A-----AG---T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
43628464 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
43628510 TCTGATCAAGTGACAAAGTGAT-A-----AG---TA-CTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
43628546 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
43628592 TCTGATCAAGTGACAAAGTGATAAGTGTTAACTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
43628638 TCTGATCAAGTGACAAAGTGATAAGTGGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGT-GGTAGCTTTAGCTACACTTA
* * *
43628685 TCTAATCAAGTGACAAAGTGATAAGTGGTAG-TCTTACCTACACTAA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCT-TTAGCTACACTTA
43628731 TCTGAT
1 TCTGAT
43628737 TAGGGACAAG
Statistics
Matches: 273, Mismatches: 14, Indels: 44
0.82 0.04 0.13
Matches are distributed among these distances:
36 61 0.22
37 5 0.02
40 4 0.01
42 4 0.01
45 5 0.02
46 152 0.56
47 42 0.15
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:43628485 original size:82 final size:82
Alignment explanation
Indices: 43628382--43628711 Score: 516
Period size: 82 Copynumber: 3.9 Consensus size: 82
43628372 TTTGAGTACT
*
43628382 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
43628447 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
43628464 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
*
43628529 GATAAGTACTACACTTA
66 GATAAGTGCTACACTTA
43628546 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
43628611 GATAAGTGTTAACTTTAGCTACACTTA
66 GATAA--G-------T-GCTACACTTA
* * *
43628638 TCTGATCAAGTGACAAAGTGATAAGTGGGTAGCCTTAGCTACACTTATCTAATCAAGTGACAAAG
1 TCTGATCAAGAGACAAAGTGATAAGT-GGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAG
43628703 TGATAAGTG
65 TGATAAGTG
43628712 GTAGTCTTAC
Statistics
Matches: 231, Mismatches: 6, Indels: 21
0.90 0.02 0.08
Matches are distributed among these distances:
82 150 0.65
83 1 0.00
84 2 0.01
91 2 0.01
92 34 0.15
93 42 0.18
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
GATAAGTGCTACACTTA
Found at i:43628702 original size:93 final size:92
Alignment explanation
Indices: 43628537--43628711 Score: 314
Period size: 93 Copynumber: 1.9 Consensus size: 92
43628527 GTGATAAGTA
* *
43628537 CTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAG
1 CTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTAATCAAG
43628602 TGACAAAGTGATAAGTGTTAACTTTAG
66 TGACAAAGTGATAAGTGTTAACTTTAG
*
43628629 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGGTAGCCTTAGCTACACTTATCTAATCAA
1 CTACACTTATCTGATCAAGAGACAAAGTGATAAGT-GGTAGCCTTAGCTACACTTATCTAATCAA
43628694 GTGACAAAGTGATAAGTG
65 GTGACAAAGTGATAAGTG
43628712 GTAGTCTTAC
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 34 0.43
93 45 0.57
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (92 bp):
CTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTAATCAAG
TGACAAAGTGATAAGTGTTAACTTTAG
Found at i:43628726 original size:93 final size:92
Alignment explanation
Indices: 43628537--43628736 Score: 312
Period size: 93 Copynumber: 2.2 Consensus size: 92
43628527 GTGATAAGTA
* *
43628537 CTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAG
1 CTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTAATCAAG
* *
43628602 TGACAAAGTGATAAGTGTTAACTTTAG
66 TGACAAAGTGATAAGTGGTAACTTTAC
*
43628629 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGGTAGCCTTAGCTACACTTATCTAATCAA
1 CTACACTTATCTGATCAAGAGACAAAGTGATAAGT-GGTAGCCTTAGCTACACTTATCTAATCAA
*
43628694 GTGACAAAGTGATAAGTGGT-AGTCTTAC
65 GTGACAAAGTGATAAGTGGTAACT-TTAC
*
43628722 CTACACTAATCTGAT
1 CTACACTTATCTGAT
43628737 TAGGGACAAG
Statistics
Matches: 99, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
92 36 0.36
93 63 0.64
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (92 bp):
CTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTAATCAAG
TGACAAAGTGATAAGTGGTAACTTTAC
Found at i:43632019 original size:15 final size:15
Alignment explanation
Indices: 43631999--43632036 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
43631989 TCACNTCAGC
43631999 AGGATTCAAATTTAT
1 AGGATTCAAATTTAT
* *
43632014 AGGATTCAGATTTGT
1 AGGATTCAAATTTAT
43632029 AGGATTCA
1 AGGATTCA
43632037 CAGCAACCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (15 bp):
AGGATTCAAATTTAT
Found at i:43633901 original size:29 final size:28
Alignment explanation
Indices: 43633869--43633960 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
43633859 AAGTCCATCA
*
43633869 ACCAAACATAATCTTGAAAACATAAATAT
1 ACCAAACATAAT-TTCAAAACATAAATAT
** * *
43633898 ACCAAAGCACCATTACAAAACAT-CATAT
1 ACCAAA-CATAATTTCAAAACATAAATAT
43633926 ACCAAACATAATTCTCAAAACATAAATAT
1 ACCAAACATAATT-TCAAAACATAAATAT
43633955 ACCAAA
1 ACCAAA
43633961 ATACACAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 5 0.10
28 18 0.35
29 24 0.47
30 4 0.08
ACGTcount: A:0.54, C:0.23, G:0.02, T:0.21
Consensus pattern (28 bp):
ACCAAACATAATTTCAAAACATAAATAT
Found at i:43666483 original size:22 final size:23
Alignment explanation
Indices: 43666436--43666484 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
43666426 AATATTTTTA
*
43666436 AATA-AATATAAAATACTATCTT
1 AATATAATATAAAATACTATCTG
43666458 AATATAATA-AAAATAC-ATCATG
1 AATATAATATAAAATACTATC-TG
43666480 AATAT
1 AATAT
43666485 TATTAAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 3 0.12
22 17 0.71
23 4 0.17
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (23 bp):
AATATAATATAAAATACTATCTG
Found at i:43667508 original size:17 final size:17
Alignment explanation
Indices: 43667483--43667525 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
43667473 TTTAAAAATG
43667483 TATAATTTTATT-TAAAA
1 TATAATTTT-TTGTAAAA
*
43667500 TATATTTTTTTGTAAAA
1 TATAATTTTTTGTAAAA
*
43667517 TTTAATTTT
1 TATAATTTT
43667526 GACATGATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TATAATTTTTTGTAAAA
Found at i:43668845 original size:14 final size:14
Alignment explanation
Indices: 43668826--43668855 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
43668816 ACGTGTCAAG
43668826 GTATTGTTAACTAT
1 GTATTGTTAACTAT
43668840 GTATTGTTAACTAT
1 GTATTGTTAACTAT
43668854 GT
1 GT
43668856 CAAGCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.50
Consensus pattern (14 bp):
GTATTGTTAACTAT
Found at i:43674385 original size:34 final size:34
Alignment explanation
Indices: 43674335--43674429 Score: 129
Period size: 34 Copynumber: 2.8 Consensus size: 34
43674325 GGTGTCTATA
* * *
43674335 GCTACTTTATTTATTTGTTATAAGCATATTAATT
1 GCTACTGTATTGATTTGTTATAAGCATACTAATT
*
43674369 GCTACTGTATTGATTTGTTATAAGCATGCTAATT
1 GCTACTGTATTGATTTGTTATAAGCATACTAATT
*
43674403 GCTA-TAGTATTGATATGTTATAAGCAT
1 GCTACT-GTATTGATTTGTTATAAGCAT
43674430 GTCATATTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 1 0.02
34 54 0.98
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.46
Consensus pattern (34 bp):
GCTACTGTATTGATTTGTTATAAGCATACTAATT
Found at i:43675525 original size:97 final size:96
Alignment explanation
Indices: 43675345--43675544 Score: 240
Period size: 97 Copynumber: 2.1 Consensus size: 96
43675335 TCCTCTCCGT
* * ** *
43675345 CGACTCCATCCAGTACTTGCCATAGTAGGCGTCGTTCCAACAATACCTTTAAATATTTCTTCCCC
1 CGACTCCATCCAGTACTCGCCACAGTAGGCGTCGTTCCAACAATACCTTTAAATATTTCCACCAC
* * **
43675410 ATTCAATCAGAGCATCTCCATAATTGATTTA
66 ATTCAATCAGAACATCTCCATAATAGATCCA
*
43675441 CGACTCCATCCAGTACTCGACCACAGTAGGCGTCGTTCCAA-AATCATCTTTAAATATTTCCACC
1 CGACTCCATCCAGTACTCG-CCACAGTAGGCGTCGTTCCAACAAT-ACCTTTAAATATTTCCACC
* ** * *
43675505 ATATTCAATTGGAACCTCTCCGTAATAGATCCA
64 ACATTCAATCAGAACATCTCCATAATAGATCCA
43675538 CGACTCC
1 CGACTCC
43675545 CCAATCCAGT
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
96 21 0.24
97 66 0.76
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.29
Consensus pattern (96 bp):
CGACTCCATCCAGTACTCGCCACAGTAGGCGTCGTTCCAACAATACCTTTAAATATTTCCACCAC
ATTCAATCAGAACATCTCCATAATAGATCCA
Found at i:43677696 original size:37 final size:33
Alignment explanation
Indices: 43677615--43677715 Score: 89
Period size: 38 Copynumber: 2.9 Consensus size: 33
43677605 AGCAAGTTTC
* * *
43677615 TTGCTACTGTCA-TGATCTGTTATAAGCATGATAA
1 TTGCTACTGT-ATTAATTTGTTATAAACATG-TAA
*
43677649 TTGCTACTGTATATATATATTTGTTATAAACATGTTA
1 TTGCTACTG--TAT-TA-ATTTGTTATAAACATGTAA
*
43677686 TTGCTGCTGTATTAATTTGTTAT-AACATGT
1 TTGCTACTGTATTAATTTGTTATAAACATGT
43677716 CATGTTGCAT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
32 7 0.12
33 9 0.16
34 11 0.19
35 4 0.07
36 1 0.02
37 11 0.19
38 14 0.25
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.46
Consensus pattern (33 bp):
TTGCTACTGTATTAATTTGTTATAAACATGTAA
Found at i:43679127 original size:19 final size:19
Alignment explanation
Indices: 43679096--43679132 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
43679086 ATTTAGAATT
43679096 TTAAGAAATATATAAAATA
1 TTAAGAAATATATAAAATA
43679115 TTAA-AAATAATATAAAAT
1 TTAAGAAAT-ATATAAAAT
43679133 TGCAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TTAAGAAATATATAAAATA
Found at i:43679177 original size:9 final size:9
Alignment explanation
Indices: 43679136--43679214 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
43679126 ATAAAATTGC
*
43679136 AAAATTTTA
1 AAAATTATA
*
43679145 CAAAATTACA
1 -AAAATTATA
*
43679155 AAAAGTATA
1 AAAATTATA
43679164 AAAATTATA
1 AAAATTATA
* *
43679173 GAAATTACAA
1 AAAATTA-TA
**
43679183 AAAAAAATA
1 AAAATTATA
43679192 AAAATTATA
1 AAAATTATA
*
43679201 TAAAATTGTA
1 -AAAATTATA
43679211 AAAA
1 AAAA
43679215 AGAGTTTGCA
Statistics
Matches: 53, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
9 33 0.62
10 20 0.38
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.27
Consensus pattern (9 bp):
AAAATTATA
Found at i:43679194 original size:27 final size:27
Alignment explanation
Indices: 43679147--43679200 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
43679137 AAATTTTACA
**
43679147 AAATTACAAAAAGTATAAAAATTATAG
1 AAATTACAAAAAAAATAAAAATTATAG
43679174 AAATTACAAAAAAAAATAAAAATTATA
1 AAATTAC-AAAAAAAATAAAAATTATA
43679201 TAAAATTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (27 bp):
AAATTACAAAAAAAATAAAAATTATAG
Found at i:43679212 original size:19 final size:19
Alignment explanation
Indices: 43679104--43679214 Score: 75
Period size: 19 Copynumber: 5.9 Consensus size: 19
43679094 TTTTAAGAAA
43679104 TATATAAAA-TATTAAAAAT
1 TATATAAAATTA-TAAAAAT
* **
43679123 AATATAAAATT-GCAAAAT
1 TATATAAAATTATAAAAAT
* * * *
43679141 TTTACAAAATTACAAAAAG
1 TATATAAAATTATAAAAAT
*
43679160 TATA-AAAATTATAGAAAT
1 TATATAAAATTATAAAAAT
* * **
43679178 TACAAAAAAAAATAAAAAT
1 TATATAAAATTATAAAAAT
*
43679197 TATATAAAATTGTAAAAA
1 TATATAAAATTATAAAAA
43679215 AGAGTTTGCA
Statistics
Matches: 67, Mismatches: 22, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
18 27 0.40
19 39 0.58
20 1 0.01
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
TATATAAAATTATAAAAAT
Found at i:43680100 original size:17 final size:17
Alignment explanation
Indices: 43680052--43680108 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
43680042 TTGAAGTTCA
43680052 AATTAAATTT-ATATTTT
1 AATTAAATTTAAT-TTTT
*
43680069 AAATAAATTTAAATTTTT
1 AATTAAATTT-AATTTTT
*
43680087 ACTTAAATTTAATTTTTT
1 AATTAAATTTAA-TTTTT
43680105 AATT
1 AATT
43680109 TAATATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 11 0.33
18 20 0.61
19 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTAAATTTAATTTTT
Found at i:43680531 original size:33 final size:34
Alignment explanation
Indices: 43680494--43680557 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
43680484 AGTTTAATTA
43680494 TATTTAATAT-AAAATAATTTAA-ATATATTTTAT
1 TATTTAATATGAAAATAATTTAACA-ATATTTTAT
* *
43680527 TATTTATTATGAATATAATTTAACAATATTT
1 TATTTAATATGAAAATAATTTAACAATATTT
43680558 ACATTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 9 0.33
34 17 0.63
35 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (34 bp):
TATTTAATATGAAAATAATTTAACAATATTTTAT
Found at i:43680638 original size:6 final size:6
Alignment explanation
Indices: 43680627--43680685 Score: 118
Period size: 6 Copynumber: 9.8 Consensus size: 6
43680617 TATATTATGT
43680627 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
43680675 AATATA AATAT
1 AATATA AATAT
43680686 TTATTTATTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:43680845 original size:44 final size:45
Alignment explanation
Indices: 43680761--43680853 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 45
43680751 ATTGATGTGT
*
43680761 AATGGAATAGAGACGTAATAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAGACGTAACAGTAATTCAATTGTTTGGTTGAATGG
*
43680806 AATGGAATAGA-ACTGTAACAGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGAC-GTAACAGTAATTCAAT-TGTTTGGTTGAATGG
43680850 AATG
1 AATG
43680854 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 1 0.02
44 25 0.57
45 18 0.41
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (45 bp):
AATGGAATAGAGACGTAACAGTAATTCAATTGTTTGGTTGAATGG
Found at i:43681651 original size:59 final size:59
Alignment explanation
Indices: 43681554--43681669 Score: 214
Period size: 59 Copynumber: 2.0 Consensus size: 59
43681544 TAAACTACCG
*
43681554 CATCAGAGGCAATCCTCCTACTGATTTGTTTGCCAATGGCCCGCATGTTTTCCGCCACA
1 CATCAGAGGCAATACTCCTACTGATTTGTTTGCCAATGGCCCGCATGTTTTCCGCCACA
*
43681613 CATCGGAGGCAATACTCCTACTGATTTGTTTGCCAATGGCCCGCATGTTTTCCGCCA
1 CATCAGAGGCAATACTCCTACTGATTTGTTTGCCAATGGCCCGCATGTTTTCCGCCA
43681670 ATAAAGTGGC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (59 bp):
CATCAGAGGCAATACTCCTACTGATTTGTTTGCCAATGGCCCGCATGTTTTCCGCCACA
Found at i:43682545 original size:49 final size:49
Alignment explanation
Indices: 43682475--43682578 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
43682465 AGAAAAAAAT
* * * *
43682475 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACATTATA
43682524 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACATTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACATTATA
43682573 AAATTA
1 AAATTA
43682579 TAACATTTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACATTATA
Found at i:43687141 original size:30 final size:30
Alignment explanation
Indices: 43687105--43687165 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
43687095 AGGCATGTTT
43687105 CATATTAAAAAATTATTCCGGAGTACTTGG
1 CATATTAAAAAATTATTCCGGAGTACTTGG
* *
43687135 CATATTAAAAAATTCTTGCGGAGTACTTGG
1 CATATTAAAAAATTATTCCGGAGTACTTGG
43687165 C
1 C
43687166 TGATAACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (30 bp):
CATATTAAAAAATTATTCCGGAGTACTTGG
Found at i:43690118 original size:34 final size:34
Alignment explanation
Indices: 43690080--43690147 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
43690070 TCTGAAATTC
43690080 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
1 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
43690114 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
1 AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
43690148 CTACATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (34 bp):
AATCTCGATCTGCTTTGGGCAAAACCCAAATGTT
Found at i:43690420 original size:78 final size:78
Alignment explanation
Indices: 43690291--43690434 Score: 207
Period size: 78 Copynumber: 1.8 Consensus size: 78
43690281 TATCAGCCAA
* * *
43690291 GGGGTTAACAAGGAGTGAATTTGCAATTGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAA
1 GGGGTTAACAAGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAA
43690356 GGCAGTGGCACTC
66 GGCAGTGGCACTC
** * * * *
43690369 GGGGTTAATGAGGACTGAATTCGCAATGGTGATTCTATCTTATTTGGCTTAGCTTCCTTTGGTAA
1 GGGGTTAACAAGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAA
43690434 G
66 G
43690435 ATAGCAACAC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 57 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (78 bp):
GGGGTTAACAAGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAA
GGCAGTGGCACTC
Done.