Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold14
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: 2879421
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 64274 characters in sequence are not A, C, G, or T
File 16 of 17
Found at i:2599035 original size:16 final size:16
Alignment explanation
Indices: 2599009--2599046 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2598999 TTAAAATATT
*
2599009 AAATA-AAATATGATA
1 AAATATAAATATAATA
*
2599024 TAATATAAATATAATA
1 AAATATAAATATAATA
2599040 AAATATA
1 AAATATA
2599047 TGTAACACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATATAAATATAATA
Found at i:2599045 original size:21 final size:22
Alignment explanation
Indices: 2599003--2599046 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2598993 AAAAAATTAA
**
2599003 AATATTAAATAAAATATGATAT
1 AATATTAAATAAAATAAAATAT
*
2599025 AATA-TAAATATAATAAAATAT
1 AATATTAAATAAAATAAAATAT
2599046 A
1 A
2599047 TGTAACACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
AATATTAAATAAAATAAAATAT
Found at i:2599492 original size:2 final size:2
Alignment explanation
Indices: 2599485--2599522 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2599475 TGACTACAAC
2599485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2599523 GTGAGAACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2599847 original size:10 final size:10
Alignment explanation
Indices: 2599832--2599863 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2599822 TCCAAGAGAT
2599832 AAAAAAGAAA
1 AAAAAAGAAA
*
2599842 AAAAAAGAAT
1 AAAAAAGAAA
2599852 AAAAAAGAAA
1 AAAAAAGAAA
2599862 AA
1 AA
2599864 GAATGCTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:2599862 original size:19 final size:21
Alignment explanation
Indices: 2599825--2599863 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2599815 ATAAAGTTCC
2599825 AAGAGATAAAAAAGAAAAAAA
1 AAGAGATAAAAAAGAAAAAAA
2599846 AAGA-ATAAAAAAGAAAAA
1 AAGAGATAAAAAAGAAAAA
2599864 GAATGCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (21 bp):
AAGAGATAAAAAAGAAAAAAA
Found at i:2601478 original size:22 final size:23
Alignment explanation
Indices: 2601453--2601498 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
2601443 ATTTAGTTTG
2601453 AGTTACTATTTAAA-TT-ATAAAA
1 AGTT-CTATTTAAATTTAATAAAA
*
2601475 AGTTTTATTTAAATTTAATAAAA
1 AGTTCTATTTAAATTTAATAAAA
2601498 A
1 A
2601499 TATTAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 6 0.29
23 7 0.33
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
AGTTCTATTTAAATTTAATAAAA
Found at i:2601507 original size:23 final size:21
Alignment explanation
Indices: 2601460--2601508 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
2601450 TTGAGTTACT
*
2601460 ATTTAAATTATAAAAAGTTTT
1 ATTTAAATTATAAAAAGTTTA
2601481 ATTTAAATTTAATAAAAA-TATTA
1 ATTTAAA-TT-ATAAAAAGT-TTA
2601504 ATTTA
1 ATTTA
2601509 TATAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
22 3 0.12
23 14 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTAAATTATAAAAAGTTTA
Found at i:2601540 original size:18 final size:18
Alignment explanation
Indices: 2601486--2601525 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2601476 GTTTTATTTA
* *
2601486 AATTTA-ATAAAAATATT
1 AATTTATATAAAATTTTT
2601503 AATTTATATAAAATTTTT
1 AATTTATATAAAATTTTT
2601521 AATTT
1 AATTT
2601526 TTAAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTTATATAAAATTTTT
Found at i:2602012 original size:22 final size:23
Alignment explanation
Indices: 2601987--2602058 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 23
2601977 AATTTTTATA
2601987 AAAAACAT-TTTTATTAAGTTTT
1 AAAAACATCTTTTATTAAGTTTT
* *
2602009 AAAAAATATCTTTTAATAA--TTT
1 -AAAAACATCTTTTATTAAGTTTT
2602031 AATAAATC-TCTTTTATTAAGTTTT
1 AA-AAA-CATCTTTTATTAAGTTTT
2602055 AAAA
1 AAAA
2602059 TATAAATAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
21 2 0.05
22 16 0.40
23 9 0.22
24 13 0.32
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (23 bp):
AAAAACATCTTTTATTAAGTTTT
Found at i:2602059 original size:22 final size:22
Alignment explanation
Indices: 2601995--2602061 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
2601985 TAAAAAACAT
2601995 TTTTATTAAGTTTTAAAAAATATC
1 TTTTATTAAGTTTT--AAAATATC
* * *
2602019 TTTTAATAA-TTTAATAAATCTC
1 TTTTATTAAGTTTTA-AAATATC
2602041 TTTTATTAAGTTTTAAAATAT
1 TTTTATTAAGTTTTAAAATAT
2602062 AAATAACTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 1 0.03
22 19 0.54
23 7 0.20
24 8 0.23
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (22 bp):
TTTTATTAAGTTTTAAAATATC
Found at i:2604248 original size:37 final size:38
Alignment explanation
Indices: 2604146--2604258 Score: 106
Period size: 37 Copynumber: 3.0 Consensus size: 38
2604136 TAATAAAAAT
*
2604146 TTAATTAATCTTAAAATTATTTTTAATT--AATGTTAAA
1 TTAAATAAT-TTAAAATTATTTTTAATTCAAATGTTAAA
* * * * *
2604183 TTGAATTATTATTAAGTTATATTTTAATTCAAATG-TATA
1 TTAAATAATT-TAAAATTAT-TTTTAATTCAAATGTTAAA
* *
2604222 TTAAATAATTTAAACTTATTTTTAATTCAAATTTTAA
1 TTAAATAATTTAAAATTATTTTTAATTCAAATGTTAA
2604259 TTTATTTTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
36 1 0.02
37 26 0.44
38 17 0.29
39 11 0.19
40 4 0.07
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (38 bp):
TTAAATAATTTAAAATTATTTTTAATTCAAATGTTAAA
Found at i:2604487 original size:17 final size:18
Alignment explanation
Indices: 2604452--2604491 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2604442 TAAAAATATA
*
2604452 TTTTTTTGTTTTAATAAC
1 TTTTTTTATTTTAATAAC
*
2604470 TTTTTTTATTTTTA-AAC
1 TTTTTTTATTTTAATAAC
2604487 TTTTT
1 TTTTT
2604492 AAAATAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTTTATTTTAATAAC
Found at i:2606255 original size:15 final size:17
Alignment explanation
Indices: 2606230--2606271 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2606220 TGTTTCATAA
2606230 AAAATATTATTTTTA-AT
1 AAAA-ATTATTTTTATAT
2606247 -AAAATTA-TTTTATAT
1 AAAAATTATTTTTATAT
2606262 AAAAATTATT
1 AAAAATTATT
2606272 CGTTACTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.23
15 6 0.27
16 10 0.45
17 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAAATTATTTTTATAT
Found at i:2607348 original size:27 final size:25
Alignment explanation
Indices: 2607318--2607382 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 25
2607308 ATAATATAAA
*
2607318 ATATAATTATATAAATATTTTAAATTT
1 ATATAA-TATA-AAATATATTAAATTT
* *
2607345 ATATAATATAAGATATATTAAATATA
1 ATATAATATAAAATATATTAAAT-TT
2607371 ATTATAATATAA
1 A-TATAATATAA
2607383 TCAATACGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.33
26 6 0.18
27 16 0.48
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
ATATAATATAAAATATATTAAATTT
Found at i:2609483 original size:18 final size:18
Alignment explanation
Indices: 2609457--2609498 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2609447 TTATTATAAA
* *
2609457 TTATTTAACAAATTGATT
1 TTATATAACAAATTAATT
2609475 TTATATAACAAATTAATT
1 TTATATAACAAATTAATT
2609493 TTATAT
1 TTATAT
2609499 TTTTTTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (18 bp):
TTATATAACAAATTAATT
Found at i:2609759 original size:19 final size:19
Alignment explanation
Indices: 2609737--2609775 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2609727 TTTCGAATCC
2609737 AAAAAAATAAAAATCTAAA
1 AAAAAAATAAAAATCTAAA
* *
2609756 AAAAAAATACAAATTTAAA
1 AAAAAAATAAAAATCTAAA
2609775 A
1 A
2609776 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAAAATAAAAATCTAAA
Found at i:2609785 original size:16 final size:16
Alignment explanation
Indices: 2609766--2609821 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
2609756 AAAAAAATAC
2609766 AAATTTAAAATAATTT
1 AAATTTAAAATAATTT
*
2609782 AAATTTATTAA-AATTT
1 AAATTTA-AAATAATTT
**
2609798 AAACATAAAATAATTT
1 AAATTTAAAATAATTT
2609814 -AATTTAAA
1 AAATTTAAA
2609822 TTTATCTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 8 0.25
16 22 0.69
17 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTAAAATAATTT
Found at i:2609795 original size:32 final size:31
Alignment explanation
Indices: 2609759--2609819 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
2609749 ATCTAAAAAA
**
2609759 AAAATACAAATTTAAAATAATTTAAATTTATT
1 AAAATACAAACATAAAATAATTT-AATTTATT
**
2609791 AAAATTTAAACATAAAATAATTTAATTTA
1 AAAATACAAACATAAAATAATTTAATTTA
2609820 AATTTATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 6 0.24
32 19 0.76
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (31 bp):
AAAATACAAACATAAAATAATTTAATTTATT
Found at i:2610146 original size:32 final size:32
Alignment explanation
Indices: 2610110--2610177 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 32
2610100 TATTAAATAT
*
2610110 TTATATAAATTTTAATA-AATTA-ATAATTTATA
1 TTATA-AAAATTTAATATAATTATAT-ATTTATA
2610142 TTATAAAAATTTAATATAATTATATATTTATA
1 TTATAAAAATTTAATATAATTATATATTTATA
2610174 TTAT
1 TTAT
2610178 TTCATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
31 10 0.30
32 21 0.64
33 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TTATAAAAATTTAATATAATTATATATTTATA
Found at i:2613441 original size:54 final size:54
Alignment explanation
Indices: 2613382--2613509 Score: 186
Period size: 54 Copynumber: 2.4 Consensus size: 54
2613372 AGGAACCTGT
* * *** *
2613382 ATCACTCCATTTTGAACCAGTCCATGAGTTGTTCACATCATTTGAAGCAT-AAGC
1 ATCACTCCATTTTGGACCAGTCCAGGAACAGTCCACATCATTTGAAGCATCAA-C
2613436 ATCACTCCATTTTGGACCAGTCCAGGAACAGTCCACATCATTTGAAGCATCAAC
1 ATCACTCCATTTTGGACCAGTCCAGGAACAGTCCACATCATTTGAAGCATCAAC
2613490 ATCACTCCATTTTGGACCAG
1 ATCACTCCATTTTGGACCAG
2613510 CCCAAGGTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 65 0.97
55 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (54 bp):
ATCACTCCATTTTGGACCAGTCCAGGAACAGTCCACATCATTTGAAGCATCAAC
Found at i:2619865 original size:18 final size:18
Alignment explanation
Indices: 2619844--2619884 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2619834 AAGACGAGAG
2619844 AAAAAGAAAAAAAAACAA
1 AAAAAGAAAAAAAAACAA
* * *
2619862 AAAAAGAAATAGAAATAA
1 AAAAAGAAAAAAAAACAA
2619880 AAAAA
1 AAAAA
2619885 AAATAGAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAAAAAACAA
Found at i:2619869 original size:24 final size:23
Alignment explanation
Indices: 2619842--2619887 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
2619832 GGAAGACGAG
2619842 AGAAAAAGAAAAAAAAACAAAAAA
1 AGAAAAAGAAAAAAAAA-AAAAAA
* *
2619866 AGAAATAGAAATAAAAAAAAAA
1 AGAAAAAGAAAAAAAAAAAAAA
2619888 TAGAGGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.85, C:0.02, G:0.09, T:0.04
Consensus pattern (23 bp):
AGAAAAAGAAAAAAAAAAAAAAA
Found at i:2620396 original size:21 final size:19
Alignment explanation
Indices: 2620372--2620418 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2620362 ATTTTCGTAA
*
2620372 AATTTTGGTTTTTAGTTTTT
1 AATTTTGG-TTTTACTTTTT
2620392 CAATTTTGGTTTTACTTTTT
1 -AATTTTGGTTTTACTTTTT
2620412 AATTTTG
1 AATTTTG
2620419 TTATCAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.28
20 10 0.40
21 8 0.32
ACGTcount: A:0.17, C:0.04, G:0.13, T:0.66
Consensus pattern (19 bp):
AATTTTGGTTTTACTTTTT
Found at i:2624785 original size:21 final size:22
Alignment explanation
Indices: 2624759--2624804 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
2624749 GCTAGAAAAG
2624759 AATGGAG-ATTTGAAGCCTAAT
1 AATGGAGAATTTGAAGCCTAAT
2624780 AATGGAGAATTTGAAGCCTAAT
1 AATGGAGAATTTGAAGCCTAAT
2624802 AAT
1 AAT
2624805 AATGGAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (22 bp):
AATGGAGAATTTGAAGCCTAAT
Found at i:2625572 original size:29 final size:30
Alignment explanation
Indices: 2625529--2625588 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
2625519 TTCACAAAAG
2625529 TATATTGCACTTGTTATCACTGATATACTT
1 TATATTGCACTTGTTATCACTGATATACTT
2625559 TATA-TGCACTTGTTATCACTGATATACTT
1 TATATTGCACTTGTTATCACTGATATACTT
2625588 T
1 T
2625589 TTCATAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.47
Consensus pattern (30 bp):
TATATTGCACTTGTTATCACTGATATACTT
Found at i:2625671 original size:13 final size:13
Alignment explanation
Indices: 2625655--2625681 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2625645 AATGATAGAA
2625655 GAAAAAAGAAAAT
1 GAAAAAAGAAAAT
2625668 GAAAAAAGAAAAT
1 GAAAAAAGAAAAT
2625681 G
1 G
2625682 CCAGTAACTC
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:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (13 bp):
GAAAAAAGAAAAT
Found at i:2625884 original size:17 final size:17
Alignment explanation
Indices: 2625862--2625895 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2625852 CGTGCTATAA
2625862 AAAATCATTCTCCTAAT
1 AAAATCATTCTCCTAAT
*
2625879 AAAATCATTCTTCTAAT
1 AAAATCATTCTCCTAAT
2625896 GACTTTCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATCATTCTCCTAAT
Found at i:2626095 original size:21 final size:21
Alignment explanation
Indices: 2626046--2626097 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
2626036 ATGATCGATT
* * *
2626046 TTAATTTCATTATTACAATAT
1 TTAATTTTATTAATACAATAA
*
2626067 TTAATTTTATTAATATAATAA
1 TTAATTTTATTAATACAATAA
2626088 TTAATTTTAT
1 TTAATTTTAT
2626098 CGTTATCGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAATTTTATTAATACAATAA
Found at i:2626490 original size:20 final size:20
Alignment explanation
Indices: 2626467--2626504 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2626457 AAAATACTCA
2626467 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
2626487 AATGTATCGATACATTAT
1 AATGTATCGATACATTAT
2626505 GTGTTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:2628377 original size:10 final size:10
Alignment explanation
Indices: 2628362--2628395 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2628352 GCACTAGGAA
2628362 AAAGATTTTT
1 AAAGATTTTT
2628372 AAAGATTTTT
1 AAAGATTTTT
*
2628382 AAAATATTTTT
1 -AAAGATTTTT
2628393 AAA
1 AAA
2628396 ACGATCCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (10 bp):
AAAGATTTTT
Found at i:2628390 original size:11 final size:11
Alignment explanation
Indices: 2628361--2628396 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
2628351 TGCACTAGGA
2628361 AAAAGATTTTT
1 AAAAGATTTTT
2628372 -AAAGATTTTT
1 AAAAGATTTTT
*
2628382 AAAATATTTTT
1 AAAAGATTTTT
2628393 AAAA
1 AAAA
2628397 CGATCCTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (11 bp):
AAAAGATTTTT
Found at i:2635005 original size:28 final size:28
Alignment explanation
Indices: 2634904--2635008 Score: 131
Period size: 27 Copynumber: 3.7 Consensus size: 28
2634894 CTGTGACCTC
* * * *
2634904 TTCAAAGTCCACGATTCAGTGGCATTTCTT
1 TTCAAAGTCCACAACTCCGTGGCA--TCCT
*
2634934 TTTAAAGTCCACAACTCCGTGGCATCCT
1 TTCAAAGTCCACAACTCCGTGGCATCCT
*
2634962 TT-TAAGTCCACAACTCCGTGGCATCCT
1 TTCAAAGTCCACAACTCCGTGGCATCCT
2634989 TTCAAAGTCCACAACTCCGT
1 TTCAAAGTCCACAACTCCGT
2635009 AAGTCCACAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
27 26 0.39
28 21 0.31
30 20 0.30
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.30
Consensus pattern (28 bp):
TTCAAAGTCCACAACTCCGTGGCATCCT
Found at i:2635028 original size:44 final size:44
Alignment explanation
Indices: 2634964--2635050 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
2634954 GGCATCCTTT
*
2634964 TAAGTCCACAACTCCGTGGCATCCTTTCAAAGTCCACAACTCCG
1 TAAGTCCACAACTCCATGGCATCCTTTCAAAGTCCACAACTCCG
* *
2635008 TAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCATAACTCC
1 TAAGTCCACAACTCCATGGCATCCTTTCAAAGTCCACAACTCC
2635051 ATGGCACCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.29, C:0.34, G:0.11, T:0.25
Consensus pattern (44 bp):
TAAGTCCACAACTCCATGGCATCCTTTCAAAGTCCACAACTCCG
Found at i:2635078 original size:72 final size:71
Alignment explanation
Indices: 2634938--2635080 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 71
2634928 TTTCTTTTTA
* *
2634938 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTCAAAGTCCACAA
1 AAGTCCACAACTCCATGGCATCCTTTTAAGTCCACAACTCCATGGCATCCTTTCAAAGTCCACAA
2635003 CTCCGT
66 CTCCGT
* *
2635009 AAGTCCACAACTCCATGGCATCCTTTTAAAGTCCATAACTCCATGGCA-CCTTTTTAAAGTCCAC
1 AAGTCCACAACTCCATGGCATCCTTTT-AAGTCCACAACTCCATGGCATCC-TTTCAAAGTCCAC
2635073 AACTCCGT
64 AACTCCGT
2635081 GGCACCCTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
71 28 0.42
72 38 0.58
ACGTcount: A:0.27, C:0.34, G:0.13, T:0.27
Consensus pattern (71 bp):
AAGTCCACAACTCCATGGCATCCTTTTAAGTCCACAACTCCATGGCATCCTTTCAAAGTCCACAA
CTCCGT
Found at i:2635099 original size:27 final size:27
Alignment explanation
Indices: 2635008--2635411 Score: 468
Period size: 27 Copynumber: 14.9 Consensus size: 27
2634998 CACAACTCCG
* *
2635008 TAAGTCCACAACTCCATGGCATCCTTT
1 TAAGTCCACAACTCCGTGGCACCCTTT
* * *
2635035 TAAAGTCCATAACTCCATGGCACCTTTT
1 T-AAGTCCACAACTCCGTGGCACCCTTT
2635063 TAAAGTCCACAACTCCGTGGCACCCTTT
1 T-AAGTCCACAACTCCGTGGCACCCTTT
* * *
2635091 AAAGTCCACAACTCTGTAGCACCCTTT
1 TAAGTCCACAACTCCGTGGCACCCTTT
* *
2635118 TAAGTCCACAACTCCGTGGCATCATTT
1 TAAGTCCACAACTCCGTGGCACCCTTT
* **
2635145 TAAGTCGACAACTCCGTGGCATTCTTT
1 TAAGTCCACAACTCCGTGGCACCCTTT
* *
2635172 TAAGTCCACAACTCTGTGGTA-CCTTT
1 TAAGTCCACAACTCCGTGGCACCCTTT
* ** *
2635198 TAAAGTCCACAATTCCGTGTTACCTTTT
1 T-AAGTCCACAACTCCGTGGCACCCTTT
* * *
2635226 TAAGTCAACAACCCCGTGGTACCCTTT
1 TAAGTCCACAACTCCGTGGCACCCTTT
* * *
2635253 TAAGTCCATAACCCCGTGGTACCCTTT
1 TAAGTCCACAACTCCGTGGCACCCTTT
* *
2635280 TAAGTCCATAACCCCGTGGCACCCTTT
1 TAAGTCCACAACTCCGTGGCACCCTTT
2635307 TAAGTCCACAACTCCGTGGCACCCTTT
1 TAAGTCCACAACTCCGTGGCACCCTTT
* **
2635334 TAAGTCCACAACTCCATGGCATTCTTT
1 TAAGTCCACAACTCCGTGGCACCCTTT
* * *
2635361 TAAAATCCACAACTCCGTTGCATCCTTT
1 T-AAGTCCACAACTCCGTGGCACCCTTT
2635389 TAAGTCCACAACTCCGTGGCACC
1 TAAGTCCACAACTCCGTGGCACC
2635412 TTTCAAAGCC
Statistics
Matches: 328, Mismatches: 45, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
26 5 0.02
27 247 0.75
28 76 0.23
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.29
Consensus pattern (27 bp):
TAAGTCCACAACTCCGTGGCACCCTTT
Found at i:2635424 original size:27 final size:28
Alignment explanation
Indices: 2635380--2636159 Score: 627
Period size: 28 Copynumber: 26.7 Consensus size: 28
2635370 CAACTCCGTT
* * * *
2635380 GCATCCTTT-TAAGTCCACAACTCCGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
*
2635407 GCA-CCTTTCAAAGCCCACCAGTCAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
2635434 GCATCCTTCTCAAAGCCCACAAGTCAGTG
1 GCATCCTT-TCAAAGCCCACAAGTCAGTG
* * *
2635463 GCATCTTTTCAAAGCCCCATAAGTTAGTG
1 GCATCCTTTCAAAG-CCCACAAGTCAGTG
* *
2635492 GCATCCTTTCAAAACCCACAAGTCAGTA
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
2635520 GCA-CCATTTCAAAGCCCACAAGTCAGTG
1 GCATCC-TTTCAAAGCCCACAAGTCAGTG
*
2635548 GCATCCTTTCAAAGCCCACAAGTTAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
*
2635576 GCATCAC-TTCAAAGCCCACACAAGTCGGTG
1 GCATC-CTTTCAAAG-CC-CACAAGTCAGTG
*
2635606 GCAGCCCATTTCAAAGCCCACAAGTC-GCTG
1 GCA-TCC-TTTCAAAGCCCACAAGTCAG-TG
* *
2635636 GCATCTTTTCAAAGTCCACACAAGTCGGTG
1 GCATCCTTTCAAAG-CC-CACAAGTCAGTG
*
2635666 GCACCCTTTCAAAGCCCACACAAGTCAGTG
1 GCATCCTTTCAAAG-CC-CACAAGTCAGTG
* ** **
2635696 GCAACTCATTTGGAAGCCCACACAAGTTGGTG
1 GC-A-TCCTTTCAAAG-CC-CACAAGTCAGTG
* **
2635728 GCAACCTATTTCAAAGCCCACACAAGTTGGTG
1 GCATCC--TTTCAAAG-CC-CACAAGTCAGTG
* * *
2635760 GCAACCCATTTGAAAGCCCACACAAGTCGGTG
1 GC-ATCC-TTTCAAAG-CC-CACAAGTCAGTG
* **
2635792 GCAACTCATTTCAAAGCCTACACAAGTTGGTG
1 GC-A-TCCTTTCAAAGCC--CACAAGTCAGTG
* * **
2635824 GTAACCCATTTCAAAGCCCACACAAGTTGGTG
1 G-CATCC-TTTCAAAG-CC-CACAAGTCAGTG
* * *
2635856 GTAACCCATTTCAAAGCCCACACAAGTCGGTG
1 G-CATCC-TTTCAAAG-CC-CACAAGTCAGTG
* * *
2635888 GTATCTTTTCAAAGCCTACAAGTCAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
*
2635916 GCACCCTTTCAAAGCCCACAAGTCAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
* * * *
2635944 GCATCCTTTCAATGTCCATAAGTCGGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
* * *
2635972 GCATCTTTTCAAAGCCCACAAGTCAATA
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
* * *
2636000 GTATCTTTTCCAAGCCCACAAGTCAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
* * *
2636028 GCAACTTTTCAAAGCCCACGAGTCAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
* * *
2636056 GCAACTTTTCAAAGCCCACGAGTCAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
* *
2636084 GCATCCTTCCAAAGCCTACAAGTCAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
**
2636112 GCATCCTTTCAAAGCAAACAAGTCAGTG
1 GCATCCTTTCAAAGCCCACAAGTCAGTG
2636140 GCAT-CTCTTCAAAGCCCACA
1 GCATCCT-TTCAAAGCCCACA
2636160 GAAGTTAGTG
Statistics
Matches: 640, Mismatches: 86, Indels: 53
0.82 0.11 0.07
Matches are distributed among these distances:
26 5 0.01
27 23 0.04
28 305 0.48
29 61 0.10
30 74 0.12
31 11 0.02
32 155 0.24
33 6 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (28 bp):
GCATCCTTTCAAAGCCCACAAGTCAGTG
Found at i:2635624 original size:32 final size:31
Alignment explanation
Indices: 2635395--2635991 Score: 441
Period size: 32 Copynumber: 20.1 Consensus size: 31
2635385 CTTTTAAGTC
* *
2635395 CACAACTCCGTGGCA-CC-TTTCAAAGCCCA
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
* *
2635424 C-C-AGTCAGTGGCATCC-TTCTCAAAG-CC-
1 CACAAGTCGGTGGCACCCATT-TCAAAGCCCA
* * *
2635451 CACAAGTCAGTGGCA-TCTTTTCAAAGCCC-
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
* ** * *
2635480 CATAAGTTAGTGGCATCC-TTTCAAA-ACC-
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
* *
2635508 CACAAGTCAGTAGCA-CCATTTCAAAG-CC-
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
* *
2635536 CACAAGTCAGTGGCATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
** * *
2635564 CACAAGTTAGTGGCA-TCACTTCAAAGCCCA
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
2635594 CACAAGTCGGTGGCAGCCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCA-CCCATTTCAAAGCCCA
* * * *
2635624 CACAAGTCGCTGGCA-TCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
2635654 CACAAGTCGGTGGCACCC-TTTCAAAGCCCA
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
* * **
2635684 CACAAGTCAGTGGCAACTCATTTGGAAGCCCA
1 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
* *
2635716 CACAAGTTGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
* *
2635748 CACAAGTTGGTGGCAACCCATTTGAAAGCCCA
1 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
* *
2635780 CACAAGTCGGTGGCAACTCATTTCAAAGCCTA
1 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCA
* *
2635812 CACAAGTTGGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGG-CACCCATTTCAAAGCCCA
* *
2635844 CACAAGTTGGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGG-CACCCATTTCAAAGCCCA
* * *
2635876 CACAAGTCGGTGGTA-TCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
* *
2635904 TACAAGTCAGTGGCACCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
* * * *
2635932 CACAAGTCAGTGGCATCC-TTTCAATG-TC-
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
* * *
2635960 CATAAGTCGGTGGCA-TCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCA
2635990 CA
1 CA
2635992 AGTCAATAGT
Statistics
Matches: 482, Mismatches: 61, Indels: 49
0.81 0.10 0.08
Matches are distributed among these distances:
27 14 0.03
28 158 0.33
29 52 0.11
30 77 0.16
31 7 0.01
32 174 0.36
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (31 bp):
CACAAGTCGGTGGCACCCATTTCAAAGCCCA
Found at i:2636300 original size:45 final size:45
Alignment explanation
Indices: 2636249--2636414 Score: 163
Period size: 45 Copynumber: 3.6 Consensus size: 45
2636239 TTAAAATCCG
*
2636249 ATATCGCTGGCATTGAATCAGCATATTGGCACCTTTATTAGCCCA
1 ATATCGCTGGCATTGAATCAGCACATTGGCACCTTTATTAGCCCA
* * * *
2636294 ATATCGCTGGCATTGAATAAGCACATTGGTCCACTTTTCCCTTAGCTCA
1 ATATCGCTGGCATTGAATCAGCACATTGG--CACCTTT--ATTAGCCCA
* * * **
2636343 ATGTTGCTGGCCTTGAATCAGCACATTATC-CACTTTATTAGCCCA
1 ATATCGCTGGCATTGAATCAGCACATTGGCAC-CTTTATTAGCCCA
* * *
2636388 ATGTCGCTGGCCTTGAATCAACACATT
1 ATATCGCTGGCATTGAATCAGCACATT
2636415 AATCCATTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
45 59 0.59
46 1 0.01
47 10 0.10
49 30 0.30
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (45 bp):
ATATCGCTGGCATTGAATCAGCACATTGGCACCTTTATTAGCCCA
Found at i:2636359 original size:49 final size:48
Alignment explanation
Indices: 2636286--2636464 Score: 170
Period size: 49 Copynumber: 3.8 Consensus size: 48
2636276 GGCACCTTTA
* * * *
2636286 TTAGCCCAATATCGCTGGCATTGAATAAGCACATTGGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATAAGCACATTGATCCACTTTT-CC
* * *
2636335 TTAGCTCAATGTTGCTGGCCTTGAATCAGCACATT-ATCCAC-TTT-A
1 TTAGCTCAATGTCGCTGGCCTTGAATAAGCACATTGATCCACTTTTCC
* * *
2636380 TTAGCCCAATGTCGCTGGCCTTGAATCAA-CACATTAATCCATTTTTCTC
1 TTAGCTCAATGTCGCTGGCCTTGAAT-AAGCACATTGATCCACTTTTC-C
* **
2636429 TTAG-TCCAATGTCGCTGACCTTGAATTGGCACATTG
1 TTAGCT-CAATGTCGCTGGCCTTGAATAAGCACATTG
2636465 GCAATCCTCT
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
45 30 0.28
46 6 0.06
47 6 0.06
48 5 0.05
49 59 0.56
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (48 bp):
TTAGCTCAATGTCGCTGGCCTTGAATAAGCACATTGATCCACTTTTCC
Found at i:2636365 original size:94 final size:94
Alignment explanation
Indices: 2636252--2636463 Score: 250
Period size: 94 Copynumber: 2.3 Consensus size: 94
2636242 AAATCCGATA
* * *
2636252 TCGCTGGCATTGAATCAGCATATT-GGCACCTTTATTAGCCCAATATCGCTGGCATTGAAT-AAG
1 TCGCTGGCCTTGAATCAGCACATTAGCCA-CTTTATTAGCCCAATATCGCTGGCATTGAATCAA-
**
2636315 CACATTGGTCCACTTTTCCCTTAG-CTCAATG
64 CACATTAATCCACTTTTCCCTTAGTC-CAATG
* * * *
2636346 TTGCTGGCCTTGAATCAGCACATTATCCACTTTATTAGCCCAATGTCGCTGGCCTTGAATCAACA
1 TCGCTGGCCTTGAATCAGCACATTAGCCACTTTATTAGCCCAATATCGCTGGCATTGAATCAACA
* *
2636411 CATTAATCCATTTTTCTCTTAGTCCAATG
66 CATTAATCCACTTTTCCCTTAGTCCAATG
* **
2636440 TCGCTGACCTTGAATTGGCACATT
1 TCGCTGGCCTTGAATCAGCACATT
2636464 GGCAATCCTC
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
94 95 0.95
95 5 0.05
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (94 bp):
TCGCTGGCCTTGAATCAGCACATTAGCCACTTTATTAGCCCAATATCGCTGGCATTGAATCAACA
CATTAATCCACTTTTCCCTTAGTCCAATG
Found at i:2636857 original size:20 final size:20
Alignment explanation
Indices: 2636834--2636871 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2636824 AAAATACCCA
2636834 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
2636854 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
2636872 GTGTTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:2637826 original size:18 final size:20
Alignment explanation
Indices: 2637786--2637826 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2637776 GACCACGCAT
*
2637786 TTTTTATTATGTTTCATGCA
1 TTTTTAATATGTTTCATGCA
2637806 TTTTTAATATG-TTCA-GCA
1 TTTTTAATATGTTTCATGCA
2637824 TTT
1 TTT
2637827 CATTGAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 4 0.20
20 10 0.50
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (20 bp):
TTTTTAATATGTTTCATGCA
Found at i:2644497 original size:18 final size:20
Alignment explanation
Indices: 2644474--2644525 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 20
2644464 ATTGTTTATA
2644474 TTATTAAAAATTTAT-T-TT
1 TTATTAAAAATTTATATATT
*
2644492 TTATT-AATATTTATATATT
1 TTATTAAAAATTTATATATT
*
2644511 TTATAATAAAATTTA
1 TTATTA-AAAATTTA
2644526 AATAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 8 0.30
18 6 0.22
19 6 0.22
21 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTAAAAATTTATATATT
Found at i:2649066 original size:22 final size:22
Alignment explanation
Indices: 2649038--2649083 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2649028 TTTTTTTTAT
2649038 TATTTAAAT-TTAATTATAAAAA
1 TATTTAAATATTAA-TATAAAAA
2649060 TATTTAAATATTAATATAAAAA
1 TATTTAAATATTAATATAAAAA
2649082 TA
1 TA
2649084 ATAGCTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTTAAATATTAATATAAAAA
Found at i:2651154 original size:10 final size:9
Alignment explanation
Indices: 2651139--2651174 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
2651129 AAGGTCTTTC
2651139 TTTGTTTTT
1 TTTGTTTTT
2651148 GTTTGTTTTT
1 -TTTGTTTTT
*
2651158 TTTTTTTTT
1 TTTGTTTTT
2651167 TTTGTTTT
1 TTTGTTTT
2651175 AAATTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (9 bp):
TTTGTTTTT
Found at i:2654225 original size:15 final size:16
Alignment explanation
Indices: 2654185--2654226 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2654175 ATGGACAAAT
2654185 ATATAATT-ATATATA
1 ATATAATTAATATATA
*
2654200 ATAAAAATTAAT-TATA
1 AT-ATAATTAATATATA
2654216 ATATAATTAAT
1 ATATAATTAAT
2654227 CAATTTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 10 0.43
16 11 0.48
17 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAATTAATATATA
Found at i:2657559 original size:37 final size:37
Alignment explanation
Indices: 2657512--2657606 Score: 147
Period size: 37 Copynumber: 2.5 Consensus size: 37
2657502 ATAGAATTTT
*
2657512 ATTAATTTTTTATAAATAATTTTATTAATCTTTTATAA
1 ATTAAATTTTTATAAATAATTTTATTAAT-TTTTATAA
2657550 A-TAAATTTTTATAAATAATTTTATTAATTTTTATAA
1 ATTAAATTTTTATAAATAATTTTATTAATTTTTATAA
*
2657586 ATTAATTGTTTTATAAATAAT
1 ATTAAAT-TTTTATAAATAAT
2657607 AGTAATAGGC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
36 9 0.17
37 30 0.57
38 14 0.26
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (37 bp):
ATTAAATTTTTATAAATAATTTTATTAATTTTTATAA
Found at i:2657561 original size:25 final size:24
Alignment explanation
Indices: 2657476--2657558 Score: 118
Period size: 23 Copynumber: 3.5 Consensus size: 24
2657466 TTTGGGTTTA
*
2657476 ATAAATTAA-TTT-TTAATTTTTT
1 ATAAATAAATTTTATTAATTTTTT
2657498 ATAAATAGAATTTTATTAATTTTTT
1 ATAAATA-AATTTTATTAATTTTTT
*
2657523 ATAAAT-AATTTTATTAATCTTTT
1 ATAAATAAATTTTATTAATTTTTT
2657546 ATAAATAAATTTT
1 ATAAATAAATTTT
2657559 TATAAATAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
22 6 0.11
23 24 0.44
24 9 0.16
25 16 0.29
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (24 bp):
ATAAATAAATTTTATTAATTTTTT
Found at i:2657565 original size:10 final size:10
Alignment explanation
Indices: 2657550--2657588 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
2657540 TCTTTTATAA
2657550 ATAAATTTTT
1 ATAAATTTTT
2657560 ATAAATAATTTT
1 ATAAAT--TTTT
*
2657572 ATTAATTTTT
1 ATAAATTTTT
2657582 ATAAATT
1 ATAAATT
2657589 AATTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 16 0.64
12 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATAAATTTTT
Found at i:2657792 original size:23 final size:21
Alignment explanation
Indices: 2657726--2657792 Score: 52
Period size: 23 Copynumber: 3.1 Consensus size: 21
2657716 TATTTAATTA
*
2657726 TTATAT-A-TTTATTTTATAAT
1 TTATATAATTTTATTTGAT-AT
2657746 TT-TATAATTTATATTTGGAT-T
1 TTATATAATTT-TATTT-GATAT
2657767 TTATAATAATGTTTATTTGATAT
1 TTAT-ATAAT-TTTATTTGATAT
2657790 TTA
1 TTA
2657793 CATTTTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 5 0.13
22 9 0.24
23 16 0.42
24 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (21 bp):
TTATATAATTTTATTTGATAT
Found at i:2658091 original size:3 final size:3
Alignment explanation
Indices: 2658083--2658121 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2658073 TGAATTTTTA
2658083 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2658122 ATAATACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2661729 original size:18 final size:19
Alignment explanation
Indices: 2661706--2661754 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
2661696 ATCAACCCCC
2661706 AATGTATCCT-CTACCACA
1 AATGTATCCTCCTACCACA
*
2661724 AATGTAT-CTCCTACCTCA
1 AATGTATCCTCCTACCACA
*
2661742 AATGTATCATCCT
1 AATGTATCCTCCT
2661755 CAAATCTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 21 0.78
19 4 0.15
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.33
Consensus pattern (19 bp):
AATGTATCCTCCTACCACA
Found at i:2664311 original size:15 final size:15
Alignment explanation
Indices: 2664293--2664343 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2664283 TTTTTTGCAG
2664293 TATAAGTTTTGCTAC
1 TATAAGTTTTGCTAC
* *
2664308 TATATTAGTCTTG-TCAG
1 TATA--AGTTTTGCT-AC
2664325 TATAAGTTTTGCTAC
1 TATAAGTTTTGCTAC
2664340 TATA
1 TATA
2664344 TTAGTCTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 15 0.54
16 2 0.07
17 11 0.39
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (15 bp):
TATAAGTTTTGCTAC
Found at i:2664331 original size:32 final size:32
Alignment explanation
Indices: 2664290--2664353 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2664280 TCTTTTTTTG
2664290 CAGTATAAGTTTTGCTACTATATTAGTCTTGT
1 CAGTATAAGTTTTGCTACTATATTAGTCTTGT
2664322 CAGTATAAGTTTTGCTACTATATTAGTCTTGT
1 CAGTATAAGTTTTGCTACTATATTAGTCTTGT
2664354 TTCTTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (32 bp):
CAGTATAAGTTTTGCTACTATATTAGTCTTGT
Found at i:2665999 original size:14 final size:14
Alignment explanation
Indices: 2665972--2666013 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2665962 AATTTGGAGA
2665972 AAAAAGAAAG--GG
1 AAAAAGAAAGAAGG
2665984 AAAAAGAAAGAAGG
1 AAAAAGAAAGAAGG
2665998 AAATAA-AAAGAAGG
1 AAA-AAGAAAGAAGG
2666012 AA
1 AA
2666014 GGAGAGAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 10 0.37
14 15 0.56
15 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAGAAGG
Found at i:2666007 original size:18 final size:18
Alignment explanation
Indices: 2665983--2666031 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
2665973 AAAAGAAAGG
2665983 GAAAAAGAAAGAAGGAAA
1 GAAAAAGAAAGAAGGAAA
* * *
2666001 TAAAAAGAAGGAAGGAGA
1 GAAAAAGAAAGAAGGAAA
*
2666019 GAAGAAGAAAGAA
1 GAAAAAGAAAGAA
2666032 AAAAAAAAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (18 bp):
GAAAAAGAAAGAAGGAAA
Found at i:2667859 original size:70 final size:69
Alignment explanation
Indices: 2667707--2667867 Score: 174
Period size: 70 Copynumber: 2.4 Consensus size: 69
2667697 TTTTGGGTTT
* *
2667707 TATAATCAAATAAAAAACTTAAATTTTTATAAATAAAATAAATTACACCATCAAAAATTTAAACA
1 TATAATCAAATAAAAAACTTAAATTTTTACAAATAAAATAAATTACACCATCAAAAATTGAAACA
2667772 TATG
66 TATG
* * * * *
2667776 T-TATGTCTAAA-AAACACATTTAAATTTTTACAAATCAAAATAAATTATA-CTTCAAAAATTGA
1 TATA-ATC-AAATAAA-AAACTTAAATTTTTACAAAT-AAAATAAATTACACCATCAAAAATTGA
2667838 AAC-TA-G
62 AACATATG
2667844 TATAATCAAATAAAAAA--TAAATTT
1 TATAATCAAATAAAAAACTTAAATTT
2667868 AAACTTTATA
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
65 7 0.09
67 5 0.06
68 9 0.12
69 10 0.13
70 34 0.44
71 12 0.16
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (69 bp):
TATAATCAAATAAAAAACTTAAATTTTTACAAATAAAATAAATTACACCATCAAAAATTGAAACA
TATG
Found at i:2667949 original size:18 final size:17
Alignment explanation
Indices: 2667923--2667962 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2667913 CTCATAAATA
2667923 AAAAT-AAATTATACTTT
1 AAAATAAAATTA-ACTTT
2667940 AAAATAAAATTAACTTT
1 AAAATAAAATTAACTTT
2667957 AAAATA
1 AAAATA
2667963 TCTACAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATAAAATTAACTTT
Found at i:2668241 original size:31 final size:34
Alignment explanation
Indices: 2668205--2668295 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 34
2668195 TTTTTATTTT
*
2668205 TTTAATTTATTATTTTTTAAAAAATTTAA-T-AA
1 TTTAATTTATTATTTATTAAAAAATTTAATTAAA
*
2668237 -TTAATATT-TTGATTTGTTAATATAAATTTAATTAAA
1 TTTAAT-TTATT-ATTTATTAA-A-AAATTTAATTAAA
2668273 TTTAATTTTATT-TTTATTAAAAA
1 TTTAA-TTTATTATTTATTAAAAA
2668296 TAATAATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
31 7 0.15
32 10 0.21
33 1 0.02
34 10 0.21
35 2 0.04
36 9 0.19
37 6 0.12
38 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (34 bp):
TTTAATTTATTATTTATTAAAAAATTTAATTAAA
Found at i:2668728 original size:16 final size:17
Alignment explanation
Indices: 2668699--2668731 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2668689 ACTTACCCTC
*
2668699 TAATGTTAAGTATTTTA
1 TAATGTTAAATATTTTA
2668716 TAAT-TTAAATATTTTA
1 TAATGTTAAATATTTTA
2668732 ATAAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
TAATGTTAAATATTTTA
Found at i:2672502 original size:12 final size:12
Alignment explanation
Indices: 2672485--2672509 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2672475 TTAAAAAAAA
2672485 TTAAAATTTAAT
1 TTAAAATTTAAT
2672497 TTAAAATTTAAT
1 TTAAAATTTAAT
2672509 T
1 T
2672510 CAATTAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAAATTTAAT
Found at i:2673053 original size:6 final size:6
Alignment explanation
Indices: 2673042--2673092 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
2673032 CAATTATATG
* *
2673042 ATATAA ATATAA A-ATAA AAATAA TTA-AA ATAT-A ATATAAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATAT-AA ATATAA
2673088 ATATA
1 ATATA
2673093 TAAAATTAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 14 0.37
6 19 0.50
7 5 0.13
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATATAA
Found at i:2673058 original size:11 final size:12
Alignment explanation
Indices: 2673037--2673092 Score: 64
Period size: 11 Copynumber: 4.8 Consensus size: 12
2673027 AAATACAATT
*
2673037 ATATGATAT-AA
1 ATATAATATAAA
*
2673048 ATATAAAATAAA
1 ATATAATATAAA
2673060 A-ATAAT-TAAA
1 ATATAATATAAA
2673070 ATATAATATAAA
1 ATATAATATAAA
2673082 ATATAAATATA
1 ATAT-AATATA
2673093 TAAAATTAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 5 0.13
11 16 0.42
12 11 0.29
13 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:2673072 original size:22 final size:22
Alignment explanation
Indices: 2673046--2673120 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 22
2673036 TATATGATAT
2673046 AAATATAAAATAAAAATAATTA
1 AAATATAAAATAAAAATAATTA
*
2673068 AAATATAATAT-AAAAT-A-TA
1 AAATATAAAATAAAAATAATTA
*
2673087 AATATATAAAATTAAGAATATATTA
1 AA-ATATAAAA-TAAAAATA-ATTA
*
2673112 AAATGTAAA
1 AAATATAAA
2673121 TTATTATCGT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 4 0.09
20 8 0.19
21 6 0.14
22 14 0.33
24 7 0.16
25 4 0.09
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (22 bp):
AAATATAAAATAAAAATAATTA
Found at i:2673077 original size:27 final size:28
Alignment explanation
Indices: 2673042--2673098 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
2673032 CAATTATATG
2673042 ATATAAATATAAAATAAAAATA-ATTAAA
1 ATATAAATATAAAATAAAAATATA-TAAA
*
2673070 ATAT-AATATAAAATATAAATATATAAA
1 ATATAAATATAAAATAAAAATATATAAA
2673097 AT
1 AT
2673099 TAAGAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (28 bp):
ATATAAATATAAAATAAAAATATATAAA
Found at i:2673090 original size:33 final size:33
Alignment explanation
Indices: 2673036--2673121 Score: 88
Period size: 34 Copynumber: 2.5 Consensus size: 33
2673026 AAAATACAAT
2673036 TATATGATATAAATATAAA-ATAAAAATAATTAA-AA
1 TATAT-ATA-AAATATAAATAT-AAAA-AATTAAGAA
*
2673071 TATAATATAAAATATAAATATATAAAATTAAGAA
1 TAT-ATATAAAATATAAATATAAAAAATTAAGAA
*
2673105 TATAT-TAAAATGTAAAT
1 TATATATAAAATATAAAT
2673122 TATTATCGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
32 11 0.24
33 8 0.17
34 17 0.37
35 8 0.17
36 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (33 bp):
TATATATAAAATATAAATATAAAAAATTAAGAA
Found at i:2673108 original size:16 final size:16
Alignment explanation
Indices: 2673075--2673115 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2673065 TTAAAATATA
2673075 ATATAAAA-TATAAAT
1 ATATAAAATTATAAAT
2673090 ATATAAAATTA-AGAAT
1 ATATAAAATTATA-AAT
2673106 ATATTAAAAT
1 ATA-TAAAAT
2673116 GTAAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.39
16 8 0.35
17 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATATAAAATTATAAAT
Found at i:2673553 original size:24 final size:23
Alignment explanation
Indices: 2673509--2673553 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
2673499 ATATAAATTT
***
2673509 TAAAATTTTAAATATTTAATATC
1 TAAAATTTTAAATAACAAATATC
2673532 TAAAATTTTTAAATAACAAATA
1 TAAAA-TTTTAAATAACAAATA
2673554 AAGAAGGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAAATTTTAAATAACAAATATC
Found at i:2677109 original size:2 final size:2
Alignment explanation
Indices: 2677104--2677132 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2677094 TATATATATT
2677104 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2677133 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2677137 original size:2 final size:2
Alignment explanation
Indices: 2677132--2677163 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2677122 TCTCTCTCTC
2677132 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2677164 CAAAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2677456 original size:20 final size:21
Alignment explanation
Indices: 2677431--2677470 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2677421 CATTTTTAAT
2677431 TATATA-ATATAT-TAATTTTG
1 TATATACAT-TATGTAATTTTG
2677451 TATATACATTATGTAATTTT
1 TATATACATTATGTAATTTT
2677471 TAGCATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (21 bp):
TATATACATTATGTAATTTTG
Found at i:2677574 original size:18 final size:18
Alignment explanation
Indices: 2677539--2677580 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
2677529 TTATTTATAT
2677539 TTTAAAATTTAATAAAAA
1 TTTAAAATTTAATAAAAA
*
2677557 TTATAAAA-TTATTAAAAA
1 TT-TAAAATTTAATAAAAA
2677575 TTTAAA
1 TTTAAA
2677581 TATATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 13 0.59
19 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAAATTTAATAAAAA
Found at i:2677601 original size:20 final size:20
Alignment explanation
Indices: 2677551--2677602 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
2677541 TAAAATTTAA
*
2677551 TAAAAATTATAA-A-ATTAT
1 TAAAAATTAAAATATATTAT
*
2677569 TAAAAATTTAAATATATTATT
1 TAAAAATTAAAATATATTA-T
2677590 TAAAAA-TAAAATA
1 TAAAAATTAAAATA
2677603 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 10 0.36
19 1 0.04
20 10 0.36
21 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATTAAAATATATTAT
Found at i:2677760 original size:32 final size:32
Alignment explanation
Indices: 2677719--2677781 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2677709 TAATTAATTC
*
2677719 TTTAAATAAATTATTTAAATATAAAATAAAAA
1 TTTAAATAAATCATTTAAATATAAAATAAAAA
2677751 TTTAAATAAATCATTTAAATATAAAATAAAA
1 TTTAAATAAATCATTTAAATATAAAATAAAA
2677782 TCTAAAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (32 bp):
TTTAAATAAATCATTTAAATATAAAATAAAAA
Found at i:2690619 original size:20 final size:20
Alignment explanation
Indices: 2690590--2690664 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
2690580 AAAAAGACAT
*
2690590 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAA
*
2690610 AATATATCGATACATT-CATA
1 AATGTATCGATACATTGCA-A
* * *
2690630 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGCAA
2690650 AATGTATCGATACAT
1 AATGTATCGATACAT
2690665 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:2690658 original size:40 final size:39
Alignment explanation
Indices: 2690587--2690664 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2690577 GGTAAAAAGA
* *
2690587 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
2690626 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
2690665 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:2691785 original size:18 final size:18
Alignment explanation
Indices: 2691764--2691820 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
2691754 ATTATTTGAA
2691764 AAATTAATTTTATATAAT
1 AAATTAATTTTATATAAT
2691782 AAATTAATTTTATATAAT
1 AAATTAATTTTATATAAT
2691800 AAATTAATTTTATAT-AT
1 AAATTAATTTTATATAAT
2691817 AAAT
1 AAAT
2691821 ATAGATTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
17 6 0.15
18 33 0.85
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTAATTTTATATAAT
Found at i:2691844 original size:36 final size:36
Alignment explanation
Indices: 2691764--2691844 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 36
2691754 ATTATTTGAA
*
2691764 AAATTAATTTTATATAATAAATTAATTTTATATAAT
1 AAATTAATTTTATATAATAAATTAATTTAATATAAT
2691800 AAATTAATTTTATAT-ATAAATATAGATTTCAATA-AAT
1 AAATTAATTTTATATAATAAAT-TA-ATTT-AATATAAT
2691837 AAA-TAATT
1 AAATTAATT
2691845 AAATATATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
35 6 0.15
36 22 0.54
37 10 0.24
38 3 0.07
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (36 bp):
AAATTAATTTTATATAATAAATTAATTTAATATAAT
Found at i:2692928 original size:19 final size:19
Alignment explanation
Indices: 2692900--2692946 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
2692890 ATTTATATTC
*
2692900 TAAATTTATTTTTAAATTT
1 TAAATATATTTTTAAATTT
* **
2692919 TACATATATTTTTATCTTT
1 TAAATATATTTTTAAATTT
2692938 TAAATATAT
1 TAAATATAT
2692947 AATTATTTAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
TAAATATATTTTTAAATTT
Found at i:2692953 original size:25 final size:25
Alignment explanation
Indices: 2692904--2692954 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
2692894 ATATTCTAAA
*
2692904 TTTATTTTTAAATTTTACATATATT
1 TTTATTTTTAAATTATACATATATT
2692929 TTTATCTTTTAAATATATA-AT-TATT
1 TTTAT-TTTTAAAT-TATACATATATT
2692954 T
1 T
2692955 ACATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 10 0.43
26 10 0.43
27 3 0.13
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTATTTTTAAATTATACATATATT
Found at i:2699785 original size:3 final size:3
Alignment explanation
Indices: 2699777--2699827 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
2699767 ATATGAAAAC
2699777 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2699825 ATA
1 ATA
2699828 GAAACAACAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2700800 original size:2 final size:2
Alignment explanation
Indices: 2700793--2700831 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2700783 CATCTAAGAA
2700793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2700832 ATGTCAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2706577 original size:34 final size:34
Alignment explanation
Indices: 2706532--2706681 Score: 194
Period size: 34 Copynumber: 4.4 Consensus size: 34
2706522 ATCCCTTAAA
* * *
2706532 TGTTGATTAAATGGGTGATTTGGTGGTTTGTCAT
1 TGTTGACTAAATGGGTGATTTGATAGTTTGTCAT
2706566 TGTTGACTAAATGGGTGATTTGATAGTTTG-CTAT
1 TGTTGACTAAATGGGTGATTTGATAGTTTGTC-AT
* * * * *
2706600 TGTTGATTAAATGAGTGATTCGGTAGTTTGCCAT
1 TGTTGACTAAATGGGTGATTTGATAGTTTGTCAT
*
2706634 TGTTGACTAAATGGGTGATTTGATGGTTTGTCAT
1 TGTTGACTAAATGGGTGATTTGATAGTTTGTCAT
*
2706668 TGTTGGCTAAATGG
1 TGTTGACTAAATGG
2706682 CTAAAAGAGA
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
33 1 0.01
34 98 0.98
35 1 0.01
ACGTcount: A:0.21, C:0.06, G:0.29, T:0.43
Consensus pattern (34 bp):
TGTTGACTAAATGGGTGATTTGATAGTTTGTCAT
Found at i:2706641 original size:68 final size:68
Alignment explanation
Indices: 2706532--2706672 Score: 221
Period size: 68 Copynumber: 2.1 Consensus size: 68
2706522 ATCCCTTAAA
* * * *
2706532 TGTTGATTAAATGGGTGATTTGGTGGTTTGTCATTGTTGACTAAATGGGTGATTTGATAGTTTG-
1 TGTTGATTAAATGAGTGATTCGGTAGTTTGCCATTGTTGACTAAATGGGTGATTTGATAGTTTGT
2706596 CTAT
66 C-AT
*
2706600 TGTTGATTAAATGAGTGATTCGGTAGTTTGCCATTGTTGACTAAATGGGTGATTTGATGGTTTGT
1 TGTTGATTAAATGAGTGATTCGGTAGTTTGCCATTGTTGACTAAATGGGTGATTTGATAGTTTGT
2706665 CAT
66 CAT
2706668 TGTTG
1 TGTTG
2706673 GCTAAATGGC
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
68 66 0.99
69 1 0.01
ACGTcount: A:0.21, C:0.06, G:0.29, T:0.45
Consensus pattern (68 bp):
TGTTGATTAAATGAGTGATTCGGTAGTTTGCCATTGTTGACTAAATGGGTGATTTGATAGTTTGT
CAT
Found at i:2711183 original size:34 final size:34
Alignment explanation
Indices: 2711138--2711202 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
2711128 AAGTAAGAGA
* *
2711138 ATTGTTGATTAAATGAGTGATTTGGTAGTTTACT
1 ATTGTTGATTAAATAAGTGATTTGATAGTTTACT
*
2711172 ATTGTTTATTAAATAAGTGATTTGATAGTTT
1 ATTGTTGATTAAATAAGTGATTTGATAGTTT
2711203 GTCATTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (34 bp):
ATTGTTGATTAAATAAGTGATTTGATAGTTTACT
Found at i:2712094 original size:23 final size:22
Alignment explanation
Indices: 2712052--2712096 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2712042 ATATATTATT
*
2712052 TTTATATTTAAATATTATGTAA
1 TTTATATTTAAATATAATGTAA
2712074 TTTATATTTTATAA-ATAATGTAA
1 TTTATA-TTTA-AATATAATGTAA
2712097 CATTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 12 0.60
24 2 0.10
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTATATTTAAATATAATGTAA
Found at i:2712207 original size:20 final size:20
Alignment explanation
Indices: 2712170--2712207 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2712160 TAGATTAAAC
**
2712170 TAAAAAAATATTTTAAAAAT
1 TAAAAAAATATTAAAAAAAT
2712190 TAAAAAAATATTAAAAAA
1 TAAAAAAATATTAAAAAA
2712208 TATATTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAAAATATTAAAAAAAT
Found at i:2712494 original size:2 final size:2
Alignment explanation
Indices: 2712487--2712513 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2712477 AGATTTAATT
2712487 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
2712514 GGCGATCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2712669 original size:19 final size:19
Alignment explanation
Indices: 2712625--2712671 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2712615 TAATTGGTAT
2712625 TAATTATAATTAATTATGA
1 TAATTATAATTAATTATGA
* *
2712644 TAA-TATATTTTATTTATG-
1 TAATTATA-ATTAATTATGA
2712662 TAATTATAAT
1 TAATTATAAT
2712672 AAATAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TAATTATAATTAATTATGA
Found at i:2713381 original size:18 final size:18
Alignment explanation
Indices: 2713355--2713391 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2713345 ATTTTTAAAT
*
2713355 TATTGTTATAAATATTTA
1 TATTATTATAAATATTTA
*
2713373 TATTATTATTAATATTTA
1 TATTATTATAAATATTTA
2713391 T
1 T
2713392 CTAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TATTATTATAAATATTTA
Found at i:2713584 original size:2 final size:2
Alignment explanation
Indices: 2713577--2713607 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2713567 TGGTTAATTT
2713577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2713608 CTTAGGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2715199 original size:19 final size:19
Alignment explanation
Indices: 2715175--2715218 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
2715165 ATGAATATTT
*
2715175 GAAAAATAA-GATTTTTGGA
1 GAAAAATAAGGA-ATTTGGA
2715194 GAAAAATAAGGAATTTGGA
1 GAAAAATAAGGAATTTGGA
2715213 GAAAAA
1 GAAAAA
2715219 ATGACGATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (19 bp):
GAAAAATAAGGAATTTGGA
Found at i:2716594 original size:24 final size:24
Alignment explanation
Indices: 2716567--2716614 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2716557 TTAATAATTC
**
2716567 ATATATTTGTATATTTTGTTATAT
1 ATATATTTGTATATCATGTTATAT
2716591 ATATATTTGTATATCATGTTATAT
1 ATATATTTGTATATCATGTTATAT
2716615 TCGTATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.58
Consensus pattern (24 bp):
ATATATTTGTATATCATGTTATAT
Found at i:2718523 original size:13 final size:13
Alignment explanation
Indices: 2718505--2718530 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2718495 CAATTTTTTG
2718505 TGTATCGATACAT
1 TGTATCGATACAT
2718518 TGTATCGATACAT
1 TGTATCGATACAT
2718531 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2718595 original size:21 final size:21
Alignment explanation
Indices: 2718569--2718644 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2718559 CTGCCAAGAA
*
2718569 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
2718590 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2718610 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2718631 ATGTATCGATACAT
1 ATGTATCGATACAT
2718645 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2718615 original size:20 final size:20
Alignment explanation
Indices: 2718590--2718662 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2718580 CATCTTTTTT
2718590 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2718610 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2718631 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2718651 ATGTATCGATAC
1 ATGTATCGATAC
2718663 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2718626 original size:41 final size:41
Alignment explanation
Indices: 2718569--2718662 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2718559 CTGCCAAGAA
*
2718569 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2718610 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2718651 ATGTATCGATAC
1 ATGTATCGATAC
2718663 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2719322 original size:31 final size:31
Alignment explanation
Indices: 2719284--2719344 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
2719274 CCCGTTTATT
2719284 AAAAAATCTCCCCCTTAATCAAGTAATTCAA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCAA
2719315 AAAAAATCTCCCCCTTAATCAAGTAATTCA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCA
2719345 TATCAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.26, G:0.03, T:0.26
Consensus pattern (31 bp):
AAAAAATCTCCCCCTTAATCAAGTAATTCAA
Found at i:2721146 original size:50 final size:50
Alignment explanation
Indices: 2721087--2721196 Score: 211
Period size: 50 Copynumber: 2.2 Consensus size: 50
2721077 TTTGGGTGAA
*
2721087 TGTATCGATAGAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
1 TGTATCGATAAAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
2721137 TGTATCGATAAAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
1 TGTATCGATAAAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
2721187 TGTATCGATA
1 TGTATCGATA
2721197 CAGTGTATCG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (50 bp):
TGTATCGATAAAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
Found at i:2721205 original size:13 final size:13
Alignment explanation
Indices: 2721187--2721224 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2721177 ATAAACACCC
2721187 TGTATCGATACAG
1 TGTATCGATACAG
*
2721200 TGTATCGATACAT
1 TGTATCGATACAG
2721213 TGTATCGATACA
1 TGTATCGATACA
2721225 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2723324 original size:15 final size:15
Alignment explanation
Indices: 2723304--2723334 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2723294 ATTTCGTTTG
*
2723304 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2723319 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2723334 G
1 G
2723335 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2728149 original size:52 final size:52
Alignment explanation
Indices: 2728016--2728156 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
2728006 TGAAAAGTTA
2728016 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
2728068 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
2728120 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
2728157 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:2728163 original size:13 final size:13
Alignment explanation
Indices: 2728145--2728169 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2728135 CAAAAATCAG
2728145 TGTATCGATACAA
1 TGTATCGATACAA
2728158 TGTATCGATACA
1 TGTATCGATACA
2728170 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2728253 original size:13 final size:13
Alignment explanation
Indices: 2728235--2728259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2728225 CAAAAAAATA
2728235 TGTATCGATACAT
1 TGTATCGATACAT
2728248 TGTATCGATACA
1 TGTATCGATACA
2728260 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2728255 original size:33 final size:33
Alignment explanation
Indices: 2728213--2728279 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2728203 AGTAGCTTAA
2728213 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2728246 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2728279 A
1 A
2728280 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2728358 original size:21 final size:21
Alignment explanation
Indices: 2728317--2728358 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2728307 GTTGGGACCT
*
2728317 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
2728338 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
2728359 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:2731063 original size:13 final size:13
Alignment explanation
Indices: 2731045--2731070 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2731035 CAATTTTTTG
2731045 TGTATCGATACAT
1 TGTATCGATACAT
2731058 TGTATCGATACAT
1 TGTATCGATACAT
2731071 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2731135 original size:21 final size:21
Alignment explanation
Indices: 2731109--2731184 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2731099 CTGCCAAGAA
*
2731109 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
2731130 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2731150 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2731171 ATGTATCGATACAT
1 ATGTATCGATACAT
2731185 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2731155 original size:20 final size:20
Alignment explanation
Indices: 2731130--2731202 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2731120 CATCTTTTTT
2731130 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2731150 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2731171 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2731191 ATGTATCGATAC
1 ATGTATCGATAC
2731203 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2731166 original size:41 final size:41
Alignment explanation
Indices: 2731109--2731202 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2731099 CTGCCAAGAA
*
2731109 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2731150 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2731191 ATGTATCGATAC
1 ATGTATCGATAC
2731203 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2731862 original size:31 final size:31
Alignment explanation
Indices: 2731824--2731884 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
2731814 CCCGTTTATT
2731824 AAAAAATCTCCCCCTTAATCAAGTAATTCAA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCAA
2731855 AAAAAATCTCCCCCTTAATCAAGTAATTCA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCA
2731885 TATCAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.26, G:0.03, T:0.26
Consensus pattern (31 bp):
AAAAAATCTCCCCCTTAATCAAGTAATTCAA
Found at i:2733686 original size:50 final size:50
Alignment explanation
Indices: 2733627--2733736 Score: 220
Period size: 50 Copynumber: 2.2 Consensus size: 50
2733617 TTTGGGTGAA
2733627 TGTATCGATAGAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
1 TGTATCGATAGAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
2733677 TGTATCGATAGAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
1 TGTATCGATAGAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
2733727 TGTATCGATA
1 TGTATCGATA
2733737 CAGTGTATCG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (50 bp):
TGTATCGATAGAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
Found at i:2733745 original size:13 final size:13
Alignment explanation
Indices: 2733727--2733764 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2733717 ATAAACACCC
2733727 TGTATCGATACAG
1 TGTATCGATACAG
*
2733740 TGTATCGATACAT
1 TGTATCGATACAG
2733753 TGTATCGATACA
1 TGTATCGATACA
2733765 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2735864 original size:15 final size:15
Alignment explanation
Indices: 2735844--2735874 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2735834 ATTTCGTTTG
*
2735844 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2735859 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2735874 G
1 G
2735875 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2739954 original size:13 final size:13
Alignment explanation
Indices: 2739936--2739961 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2739926 CAATTTTTTG
2739936 TGTATCGATACAT
1 TGTATCGATACAT
2739949 TGTATCGATACAT
1 TGTATCGATACAT
2739962 ACTTGCTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2740026 original size:21 final size:21
Alignment explanation
Indices: 2740000--2740075 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2739990 CTGCCAAGAA
*
2740000 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
2740021 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2740041 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2740062 ATGTATCGATACAT
1 ATGTATCGATACAT
2740076 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2740046 original size:20 final size:20
Alignment explanation
Indices: 2740021--2740093 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2740011 CATCTTTTTT
2740021 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2740041 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2740062 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2740082 ATGTATCGATAC
1 ATGTATCGATAC
2740094 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2740057 original size:41 final size:41
Alignment explanation
Indices: 2740000--2740093 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2739990 CTGCCAAGAA
*
2740000 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2740041 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2740082 ATGTATCGATAC
1 ATGTATCGATAC
2740094 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2740753 original size:31 final size:31
Alignment explanation
Indices: 2740715--2740775 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
2740705 CCCGTTTATT
2740715 AAAAAATCTCCCCCTTAATCAAGTAATTCAA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCAA
2740746 AAAAAATCTCCCCCTTAATCAAGTAATTCA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCA
2740776 TATCAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.26, G:0.03, T:0.26
Consensus pattern (31 bp):
AAAAAATCTCCCCCTTAATCAAGTAATTCAA
Found at i:2742578 original size:50 final size:50
Alignment explanation
Indices: 2742519--2742628 Score: 220
Period size: 50 Copynumber: 2.2 Consensus size: 50
2742509 TTTGGGTGAA
2742519 TGTATCGATAGAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
1 TGTATCGATAGAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
2742569 TGTATCGATAGAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
1 TGTATCGATAGAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
2742619 TGTATCGATA
1 TGTATCGATA
2742629 CAGTGTATCG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (50 bp):
TGTATCGATAGAATGAAGGAGGGTGGTTCGAACTGTTCAAATAAACACCC
Done.