Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, whole genome shotgun sequence
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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 13 of 100
Found at i:3360551 original size:5 final size:5
Alignment explanation
Indices: 3360541--3360579 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
3360531 AATAAGCATC
*
3360541 AAAAT AAAAT AAAA- AACAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
3360580 CCAAAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 28 0.90
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:3360587 original size:24 final size:24
Alignment explanation
Indices: 3360541--3360587 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3360531 AATAAGCATC
*
3360541 AAAATAAAATAAAAAACATAAAAT
1 AAAATAAAATAAAAAACAAAAAAT
**
3360565 AAAATAAAATAAAATCCAAAAAA
1 AAAATAAAATAAAAAACAAAAAA
3360588 ACTAAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (24 bp):
AAAATAAAATAAAAAACAAAAAAT
Found at i:3376868 original size:18 final size:18
Alignment explanation
Indices: 3376812--3376874 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
3376802 TATATATTTG
3376812 ATATTTTTATATT-AATA
1 ATATTTTTATATTAAATA
* *
3376829 A-ATTATTGAAAGTATAAA-A
1 ATATT-TTTATA-T-TAAATA
3376848 ATATTTTTATATTAAATA
1 ATATTTTTATATTAAATA
*
3376866 ATAATTTTA
1 ATATTTTTA
3376875 GTCATAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
16 3 0.09
17 9 0.26
18 11 0.31
19 7 0.20
20 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATATTTTTATATTAAATA
Found at i:3377703 original size:18 final size:18
Alignment explanation
Indices: 3377682--3377750 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
3377672 CATCATAATT
3377682 TATTTTATCATTATATTA
1 TATTTTATCATTATATTA
*
3377700 TA-TTTAT-ATTTAAATATA
1 TATTTTATCA-TTATAT-TA
* *
3377718 TATTTTATTATTA-ATTT
1 TATTTTATCATTATATTA
3377735 TAATTTTATCATTATA
1 T-ATTTTATCATTATA
3377751 ATAATTAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
16 1 0.02
17 12 0.29
18 19 0.45
19 9 0.21
20 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTTATCATTATATTA
Found at i:3377770 original size:27 final size:25
Alignment explanation
Indices: 3377727--3377797 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 25
3377717 ATATTTTATT
*
3377727 ATTAATTTTAATT-TTATCATTATAATA
1 ATTAATTTT-ATTATTAT-AATA-AATA
3377754 ATTAATTTTATTATTATAATAAATA
1 ATTAATTTTATTATTATAATAAATA
*
3377779 ATTTTATTTTTATTATTAT
1 A--TTAATTTTATTATTAT
3377798 TTTTAATCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
25 5 0.13
26 6 0.15
27 28 0.72
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTAATTTTATTATTATAATAAATA
Found at i:3377786 original size:21 final size:21
Alignment explanation
Indices: 3377735--3377791 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
3377725 TTATTAATTT
* *
3377735 TAATTTTATCATTATAATAAT
1 TAATTTTATTATTATAATAAA
3377756 TAATTTTATTATTATAATAAA
1 TAATTTTATTATTATAATAAA
*
3377777 TAATTTTATTTTTAT
1 TAATTTTATTATTAT
3377792 TATTATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TAATTTTATTATTATAATAAA
Found at i:3379424 original size:76 final size:78
Alignment explanation
Indices: 3379334--3379491 Score: 266
Period size: 76 Copynumber: 2.0 Consensus size: 78
3379324 TTTCCTTTAC
* *
3379334 TCATTTTATTTGTCCAAACGAAAGAATGAATTATCATTCTCTTTCCTTTAAAAA-C-CTTTTTTT
1 TCATTTTAATTGTCCAAACAAAAGAATGAATTATCATTCTCTTTCCTTTAAAAACCTCTTTTTTT
3379397 TTTTCCTTTTCTT
66 TTTTCCTTTTCTT
*
3379410 TCATTTTAATTGTCCAATCAAAAGAATGAATTATCATTCTCTTTCCTTTAAAAACCTTCTTTTTT
1 TCATTTTAATTGTCCAAACAAAAGAATGAATTATCATTCTCTTTCCTTTAAAAACC-TCTTTTTT
3379475 TTTTTCCTTTTCTT
65 TTTTTCCTTTTCTT
3379489 TCA
1 TCA
3379492 GTTCTTTTAC
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
76 51 0.67
77 1 0.01
79 24 0.32
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.51
Consensus pattern (78 bp):
TCATTTTAATTGTCCAAACAAAAGAATGAATTATCATTCTCTTTCCTTTAAAAACCTCTTTTTTT
TTTTCCTTTTCTT
Found at i:3389601 original size:3 final size:3
Alignment explanation
Indices: 3389593--3389633 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3389583 TTTCGTTTAT
3389593 TTA 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 TTA TT
3389634 GATTGATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3390130 original size:11 final size:13
Alignment explanation
Indices: 3390110--3390142 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3390100 AAAATTGCCT
3390110 AGAGAGAGAA-GG
1 AGAGAGAGAAGGG
3390122 AGA-AGAGAAGGG
1 AGAGAGAGAAGGG
3390134 AGAGAGAGA
1 AGAGAGAGA
3390143 GTTAGGGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.32
12 8 0.42
13 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (13 bp):
AGAGAGAGAAGGG
Found at i:3390548 original size:58 final size:57
Alignment explanation
Indices: 3390484--3390617 Score: 162
Period size: 56 Copynumber: 2.3 Consensus size: 57
3390474 TTTTTTAAAT
* *
3390484 AATTTTCCTAAAATAAAAATTCTAAAAAATATATTTTTGAGTAAAAGTTGAAAGTATC
1 AATTTTCCTAAAATAAAAATTCTAAAAAA-ATATTTTTAAGGAAAAGTTGAAAGTATC
** * * **
3390542 AATTTTCCTTGAA-AATAATTTTTTAAAAATATTTTTAAGGAAAAGTTGAAAGTATC
1 AATTTTCCTAAAATAAAAATTCTAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATC
*
3390598 AATTTCCCTGAAAATAAAAA
1 AATTTTCCT-AAAATAAAAA
3390618 AGTTTTAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
56 34 0.55
57 13 0.21
58 15 0.24
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (57 bp):
AATTTTCCTAAAATAAAAATTCTAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATC
Found at i:3390654 original size:58 final size:56
Alignment explanation
Indices: 3390509--3390661 Score: 175
Period size: 56 Copynumber: 2.7 Consensus size: 56
3390499 AAAATTCTAA
* * **
3390509 AAAATATATTTTTGAGTAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAATTTTTT
1 AAAA-ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCCTGAAAATAAAGTTTT
* *
3390566 AAAAATATTTTTAAGGAAAAGTTGAAAGTATCAA-TTTCCCTGAAAATAAAAAAGTTTT
1 AAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCCTGAAAAT---AAAGTTTT
* *
3390624 -AAAATATTTTTGAGAAAAAAATTGAAAGTATCAGTTTT
1 AAAAATATTTTTGAG-AAAAAGTTGAAAGTATCAATTTT
3390662 TTTAAAAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
55 12 0.15
56 28 0.34
57 17 0.21
58 22 0.27
59 3 0.04
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (56 bp):
AAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCCTGAAAATAAAGTTTT
Found at i:3390749 original size:59 final size:57
Alignment explanation
Indices: 3390676--3390817 Score: 160
Period size: 59 Copynumber: 2.4 Consensus size: 57
3390666 AAAAATAAAG
** * *
3390676 TTTCTAAAATAAAAATTTCCAAA-AATATTTTGGGAGGAGAAAGTTGAAAGTATTAATT
1 TTTCTAAAATAAAAATTTAAAAATAATATTTT--GAGGAAAAAGTTGAAAGTATCAATT
*
3390734 TTTCTGAAAATAAAAAGTTTAAAAATAATATTTTTAGGAAAAAGTTGAAAGTATCAATT
1 TTTCT-AAAATAAAAA-TTTAAAAATAATATTTTGAGGAAAAAGTTGAAAGTATCAATT
*
3390793 TTCTTTAAAAATAAAATATTTAAAA
1 TT-TCT-AAAATAAAA-ATTTAAAA
3390818 TAAAAATTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
58 5 0.07
59 34 0.47
60 24 0.33
61 9 0.12
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (57 bp):
TTTCTAAAATAAAAATTTAAAAATAATATTTTGAGGAAAAAGTTGAAAGTATCAATT
Found at i:3401285 original size:11 final size:11
Alignment explanation
Indices: 3401264--3401293 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
3401254 TATTATGCTA
3401264 AAAAAATAAAAT
1 AAAAAA-AAAAT
3401276 AAAAAAAAAAT
1 AAAAAAAAAAT
3401287 AAAAAAA
1 AAAAAAA
3401294 TTGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:3401305 original size:26 final size:24
Alignment explanation
Indices: 3401262--3401330 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 24
3401252 AGTATTATGC
*
3401262 TAAAAAAAT-AAAATAAAAAAAAAA
1 TAAAAAAATGAAAA-AAAAATAAAA
3401286 TAAAAAAATTGAAAAAAAAATAAAGA
1 TAAAAAAA-TGAAAAAAAAATAAA-A
3401312 -AGGAAAAAATGAAAAAAAA
1 TA--AAAAAATGAAAAAAAA
3401331 GACTCAAAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
24 8 0.21
25 10 0.26
26 15 0.38
27 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (24 bp):
TAAAAAAATGAAAAAAAAATAAAA
Found at i:3401922 original size:24 final size:24
Alignment explanation
Indices: 3401889--3401953 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
3401879 ATTTTTAGCA
3401889 AAAGA-ATGTGAGAATTAAATGAG
1 AAAGATATGTGAGAATTAAATGAG
3401912 AAAGATATGTGAGAATTAAATGAG
1 AAAGATATGTGAGAATTAAATGAG
3401936 AAAGATGAT-TGAGAATTA
1 AAAGAT-ATGTGAGAATTA
3401954 TGCTGACTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
23 5 0.12
24 33 0.82
25 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25
Consensus pattern (24 bp):
AAAGATATGTGAGAATTAAATGAG
Found at i:3402080 original size:16 final size:16
Alignment explanation
Indices: 3402059--3402090 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3402049 TATTTACATA
3402059 GCATGCATTGAATTTC
1 GCATGCATTGAATTTC
*
3402075 GCATGCATTGCATTTC
1 GCATGCATTGAATTTC
3402091 ACATAGCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (16 bp):
GCATGCATTGAATTTC
Found at i:3402424 original size:42 final size:42
Alignment explanation
Indices: 3402365--3402485 Score: 170
Period size: 42 Copynumber: 2.8 Consensus size: 42
3402355 ATTTATTTTT
3402365 TTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGTAAATTA
1 TTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGTAAATTA
* *
3402407 TTTTTTCAAATTTGTGGTGCCTCTGTTTAGAGGAGTAATTTA
1 TTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGTAAATTA
* * * *
3402449 TTTTTTAAAAAAGTTATTGAGCCTCTGTTTAGAGGAG
1 TTTTTT--CAAAGTTGTGGTGCCTCTGTTTAGAGGAG
3402486 CCTTATTTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 46 0.66
44 24 0.34
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (42 bp):
TTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGTAAATTA
Found at i:3402506 original size:44 final size:44
Alignment explanation
Indices: 3402351--3402709 Score: 257
Period size: 44 Copynumber: 8.2 Consensus size: 44
3402341 GATTGTCAAT
* * * * *
3402351 GAGCATTTATTTTTTTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAG
1 GAGC-TTTA-TTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAGAG
* * * * * * *
3402397 GAG--TAAATTATTTTTTCAAATTTGTGGTGCCTCTGTTTAGAG
1 GAGCTTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAGAG
* ** **
3402439 GAG--TAATTTATTTTTTAAAAAAGTTATTGAGCCTCTGTTTAGAG
1 GAGCTTTATTTA-TTTTT-CCAAAGTCGTTGAGCCTCTGTTTAGAG
* * *
3402483 GAGCCTTATTTATTTGTCCAAAGTCATTGAGCCTCT-TATTAGAG
1 GAGCTTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGT-TTAGAG
* *
3402527 GAGCTTTATTT-TTCTTTCCAAAGTCGTT-ATGCCTTTGCTTAGAG
1 GAGCTTTATTTATT-TTTCCAAAGTCGTTGA-GCCTCTGTTTAGAG
* *
3402571 AAGCTTTGTTTATTTTT-CAAAGTCGTTGAGCCTCTGTTTAGAG
1 GAGCTTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAGAG
* * * * * ** *
3402614 GAGCCTTGTTAATTTTTCAAAAGTCGTTTAGCCTCTACTTAGAT
1 GAGCTTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAGAG
* * * * *
3402658 GAGCTTTATCTATTTTTCTAAAAGTTGTTGAGCCTCTGATTAGAT
1 GAGCTTTATTTATTTTTC-CAAAGTCGTTGAGCCTCTGTTTAGAG
3402703 GAGCTTT
1 GAGCTTT
3402710 GATTAAGATT
Statistics
Matches: 260, Mismatches: 41, Indels: 25
0.80 0.13 0.08
Matches are distributed among these distances:
42 42 0.16
43 47 0.18
44 127 0.49
45 35 0.13
46 9 0.03
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (44 bp):
GAGCTTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAGAG
Found at i:3402617 original size:87 final size:86
Alignment explanation
Indices: 3402425--3402715 Score: 241
Period size: 87 Copynumber: 3.3 Consensus size: 86
3402415 AATTTGTGGT
* ** ** * ** *
3402425 GCCTCTGTTTAGAGGAGTAATTTATT--TTTTAAAAAAGTTATTGAGCCTCTGTTTAGAGGAGCC
1 GCCTCTGTTTAGAGGAG--CTTTATTAATTTTTCAAAAGTCGTTTAGCCTCTACTTAGA-GAGCT
* *
3402488 TTATTTATTTGTCCAAAGTCATTGA
63 TTATTTATTT-TTCAAAGTCGTTGA
* * * *
3402513 GCCTCT-TATTAGAGGAGCTTTATT-TTTCTTTCCAAAGTCG-TTATGCCTTTGCTTAGAGAAGC
1 GCCTCTGT-TTAGAGGAGCTTTATTAATT-TTTCAAAAGTCGTTTA-GCCTCTACTTAGAG-AGC
*
3402575 TTTGTTTATTTTTCAAAGTCGTTGA
62 TTTATTTATTTTTCAAAGTCGTTGA
* *
3402600 GCCTCTGTTTAGAGGAGCCTTGTTAATTTTTCAAAAGTCGTTTAGCCTCTACTTAGATGAGCTTT
1 GCCTCTGTTTAGAGGAGCTTTATTAATTTTTCAAAAGTCGTTTAGCCTCTACTTAGA-GAGCTTT
* *
3402665 ATCTATTTTTCTAAAAGTTGTTGA
65 ATTTATTTTTC--AAAGTCGTTGA
* *
3402689 GCCTCTGATTAGATGAGCTTTGATTAA
1 GCCTCTGTTTAGAGGAGCTTT-ATTAA
3402716 GATTAAAAAA
Statistics
Matches: 165, Mismatches: 26, Indels: 22
0.77 0.12 0.10
Matches are distributed among these distances:
86 6 0.04
87 75 0.45
88 52 0.32
89 28 0.17
90 4 0.02
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (86 bp):
GCCTCTGTTTAGAGGAGCTTTATTAATTTTTCAAAAGTCGTTTAGCCTCTACTTAGAGAGCTTTA
TTTATTTTTCAAAGTCGTTGA
Found at i:3402941 original size:28 final size:27
Alignment explanation
Indices: 3402904--3402971 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 27
3402894 TTTTTTATCT
*
3402904 TTTTA-TTATTATTTTGTT-GTTATTTTA
1 TTTTATTTATTATTTT-TTCGTT-TATTA
*
3402931 TTTTATTTATTGTTTTTTCGTTTATTA
1 TTTTATTTATTATTTTTTCGTTTATTA
*
3402958 TTTATTTTTATTAT
1 TTT-TATTTATTAT
3402972 GTACTATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 14 0.41
28 20 0.59
ACGTcount: A:0.18, C:0.01, G:0.06, T:0.75
Consensus pattern (27 bp):
TTTTATTTATTATTTTTTCGTTTATTA
Found at i:3402969 original size:13 final size:13
Alignment explanation
Indices: 3402951--3403013 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
3402941 TGTTTTTTCG
3402951 TTTATTATTTATT
1 TTTATTATTTATT
*
3402964 TTTATTATGTACTAT
1 TTTATTATTTA-T-T
*
3402979 TATATTA-TTATT
1 TTTATTATTTATT
*
3402991 TATATTATTTATT
1 TTTATTATTTATT
*
3403004 ATTATTATTT
1 TTTATTATTT
3403014 TGATTGATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
12 8 0.19
13 24 0.57
14 3 0.07
15 7 0.17
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (13 bp):
TTTATTATTTATT
Found at i:3402971 original size:3 final size:3
Alignment explanation
Indices: 3402952--3403012 Score: 54
Period size: 3 Copynumber: 19.7 Consensus size: 3
3402942 GTTTTTTCGT
* *
3402952 TTA TTA TTTA TTT TTA TTA TGTA CTA TTA -TA TTA TTA TT- TATA TTA
1 TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA T-TA TTA
3402998 TTTA TTA TTA TTA TT
1 -TTA TTA TTA TTA TT
3403013 TTGATTGATT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
2 3 0.06
3 36 0.75
4 9 0.19
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3402997 original size:27 final size:28
Alignment explanation
Indices: 3402953--3403008 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
3402943 TTTTTTCGTT
*
3402953 TATTATTTATTTTTATTATGTACTATTA
1 TATTATTTATTTATATTATGTACTATTA
* *
3402981 TATTA-TTATTTATATTATTTATTATTA
1 TATTATTTATTTATATTATGTACTATTA
3403008 T
1 T
3403009 TATTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (28 bp):
TATTATTTATTTATATTATGTACTATTA
Found at i:3403984 original size:60 final size:60
Alignment explanation
Indices: 3403901--3404096 Score: 238
Period size: 60 Copynumber: 3.3 Consensus size: 60
3403891 TGATTTTCCT
* * *
3403901 AAAATAAAATTTTCAAAAAATATATTTTTGAGAAAAAGTTGAAAGCATCAATTTTTCTTG
1 AAAATAAAATTTTTAAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTACTTG
** * *
3403961 AAAATAATTTTTTTAAAAAATATATTTTTAAGAAAAAGTTGAAAGTATCAA-TTTCCTTG
1 AAAATAAAATTTTTAAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTACTTG
** *
3404020 AAAATAAAAAAGTTT--AAAA-ATATTTTTGAGAAAAAGTTGAAAAGTATCAATTTTACTTA
1 AAAAT-AAAATTTTTAAAAAATATATTTTTGAGAAAAAGTTG-AAAGTATCAATTTTACTTG
* *
3404079 AAAATAAAGTTTCTAAAA
1 AAAATAAAATTTTTAAAA
3404097 TAAAAATTTT
Statistics
Matches: 114, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
57 19 0.17
58 19 0.17
59 23 0.20
60 53 0.46
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.36
Consensus pattern (60 bp):
AAAATAAAATTTTTAAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTACTTG
Found at i:3403996 original size:16 final size:17
Alignment explanation
Indices: 3403960--3403996 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
3403950 AATTTTTCTT
*
3403960 GAAAATAATTTTTTTAA
1 GAAAATAATATTTTTAA
3403977 -AAAAT-ATATTTTTAA
1 GAAAATAATATTTTTAA
3403992 GAAAA
1 GAAAA
3403997 AGTTGAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
GAAAATAATATTTTTAA
Found at i:3404298 original size:18 final size:17
Alignment explanation
Indices: 3404275--3404308 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
3404265 ATCATTATTT
3404275 TTTTATTATTTTATTTTA
1 TTTTATT-TTTTATTTTA
3404293 TTTTATTTTTTATTTT
1 TTTTATTTTTTATTTT
3404309 CTTTCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTATTTTTTATTTTA
Found at i:3404317 original size:16 final size:15
Alignment explanation
Indices: 3404269--3404319 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 15
3404259 GGGTGAATCA
3404269 TTATTTTTTTATTATT
1 TTATTTTTTTATT-TT
3404285 TTATTTTATTTTATTTT
1 TTA-TTT-TTTTATTTT
*
3404302 TTATTTTCTTTCTTTT
1 TTATTTT-TTTATTTT
3404318 TT
1 TT
3404320 GTAATTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 1 0.03
16 15 0.48
17 8 0.26
18 7 0.23
ACGTcount: A:0.14, C:0.04, G:0.00, T:0.82
Consensus pattern (15 bp):
TTATTTTTTTATTTT
Found at i:3404318 original size:17 final size:15
Alignment explanation
Indices: 3404269--3404331 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 15
3404259 GGGTGAATCA
*
3404269 TTATTTTTTTATTATT
1 TTATTTTTTT-TTTTT
3404285 TTATTTTATTTTATTTT
1 TTATTTT-TTTT-TTTT
3404302 TTATTTTCTTTCTTTTT
1 TTATTTT-TTT-TTTTT
3404319 TGTAATTTTTTTT
1 T-T-ATTTTTTTT
3404332 GTTAAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 8 0.20
17 22 0.55
18 5 0.12
19 5 0.12
ACGTcount: A:0.14, C:0.03, G:0.02, T:0.81
Consensus pattern (15 bp):
TTATTTTTTTTTTTT
Found at i:3418376 original size:29 final size:29
Alignment explanation
Indices: 3418344--3418404 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
3418334 ATTTTGATAT
*
3418344 AAATTAAAAT-TTTATTTAAATGTCAATAA
1 AAATTAAAATGTTTATTTAAATG-CAACAA
*
3418373 AAA-TAAAATGTTTATTTAACTGCAACAA
1 AAATTAAAATGTTTATTTAAATGCAACAA
3418401 AAAT
1 AAAT
3418405 GCAAAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (29 bp):
AAATTAAAATGTTTATTTAAATGCAACAA
Found at i:3418414 original size:29 final size:28
Alignment explanation
Indices: 3418348--3418416 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
3418338 TGATATAAAT
* *
3418348 TAAAATTTTATTTAAATGTCAATAAAAA
1 TAAAAGTTTATTTAAATGTCAACAAAAA
*
3418376 TAAAATGTTTATTTAACTG-CAACAAAAA
1 TAAAA-GTTTATTTAAATGTCAACAAAAA
3418404 TGCAAAAGTTTAT
1 T--AAAAGTTTAT
3418417 AAATTCAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 14 0.40
29 17 0.49
30 4 0.11
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.36
Consensus pattern (28 bp):
TAAAAGTTTATTTAAATGTCAACAAAAA
Found at i:3426245 original size:24 final size:23
Alignment explanation
Indices: 3426218--3426264 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
3426208 CTTCACAAGT
3426218 TTTATA-TCTTTCAAACAAACCAAA
1 TTTATATTC-TTCAAA-AAACCAAA
*
3426242 TTTATATTCTTCAAAATACCAAA
1 TTTATATTCTTCAAAAAACCAAA
3426265 AAATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 12 0.57
25 2 0.10
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (23 bp):
TTTATATTCTTCAAAAAACCAAA
Found at i:3426698 original size:20 final size:21
Alignment explanation
Indices: 3426659--3426701 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3426649 ATACAATTTT
**
3426659 TAAAAAACAAAAAATTAAAAA
1 TAAAAAACAAAAAACAAAAAA
3426680 TAAAAAA-AAAAAACAAAAAA
1 TAAAAAACAAAAAACAAAAAA
3426700 TA
1 TA
3426702 TTTTCTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.12
Consensus pattern (21 bp):
TAAAAAACAAAAAACAAAAAA
Found at i:3436986 original size:43 final size:43
Alignment explanation
Indices: 3436935--3437034 Score: 182
Period size: 43 Copynumber: 2.3 Consensus size: 43
3436925 ATTCTACCAT
* *
3436935 TTGGGTGATATTTTATGGAAACATGAATGTTTGTATTCTCAAA
1 TTGGGTGATATTTTATGGAAACATGAATGCTTCTATTCTCAAA
3436978 TTGGGTGATATTTTATGGAAACATGAATGCTTCTATTCTCAAA
1 TTGGGTGATATTTTATGGAAACATGAATGCTTCTATTCTCAAA
3437021 TTGGGTGATATTTT
1 TTGGGTGATATTTT
3437035 GGGGTAACTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (43 bp):
TTGGGTGATATTTTATGGAAACATGAATGCTTCTATTCTCAAA
Found at i:3437360 original size:22 final size:22
Alignment explanation
Indices: 3437335--3437381 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
3437325 AATTGTGCCT
3437335 ATTCTTTCTCGCCTTCTATAAG
1 ATTCTTTCTCGCCTTCTATAAG
* *
3437357 ATTCTTTCTTGCCTTGTATAAG
1 ATTCTTTCTCGCCTTCTATAAG
3437379 ATT
1 ATT
3437382 ATATTATCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (22 bp):
ATTCTTTCTCGCCTTCTATAAG
Found at i:3444379 original size:18 final size:18
Alignment explanation
Indices: 3444356--3444392 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3444346 TTAATACTTT
*
3444356 TAAATATAATTTTATTTA
1 TAAATATAATATTATTTA
3444374 TAAATATAATATTATTTA
1 TAAATATAATATTATTTA
3444392 T
1 T
3444393 TTATATTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAATATAATATTATTTA
Found at i:3444398 original size:18 final size:18
Alignment explanation
Indices: 3444359--3444470 Score: 59
Period size: 18 Copynumber: 5.9 Consensus size: 18
3444349 ATACTTTTAA
* **
3444359 ATATAATTTTATTTATAA
1 ATATAATATTATTTATTT
3444377 ATATAATATTATTTATTT
1 ATATAATATTATTTATTT
3444395 ATATTACTATATTATTATAATATTT
1 ATA-TA--ATATTA-T-T--TATTT
*
3444420 ATTTATAATAATATTTA-TT
1 A--TATAATATTATTTATTT
* *
3444439 A-AT-ATATTAATTATTA
1 ATATAATATTATTTATTT
*
3444455 ATATAATATTACTTAT
1 ATATAATATTATTTAT
3444471 GTTAATAAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
15 8 0.11
16 4 0.05
17 2 0.03
18 28 0.38
19 5 0.07
20 2 0.03
21 6 0.08
22 2 0.03
23 2 0.03
24 5 0.07
25 6 0.08
26 2 0.03
27 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATAATATTATTTATTT
Found at i:3444425 original size:16 final size:16
Alignment explanation
Indices: 3444360--3444464 Score: 69
Period size: 15 Copynumber: 6.6 Consensus size: 16
3444350 TACTTTTAAA
3444360 TATAAT-TTTATTTAT
1 TATAATATTTATTTAT
3444375 AAATATAATA-TTATTTAT
1 ---TATAATATTTATTTAT
3444393 T-T-ATATTACTATATTAT
1 TATAATATT--TAT-TTAT
3444410 TATAATATTTATTTAT
1 TATAATATTTATTTAT
* *
3444426 AATAATATTTA-TTAA
1 TATAATATTTATTTAT
* * *
3444441 TATATTAATTA-TTAA
1 TATAATATTTATTTAT
3444456 TATAATATT
1 TATAATATT
3444465 ACTTATGTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
13 3 0.04
14 2 0.03
15 23 0.32
16 17 0.23
17 8 0.11
18 15 0.21
19 5 0.07
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (16 bp):
TATAATATTTATTTAT
Found at i:3444477 original size:45 final size:45
Alignment explanation
Indices: 3444378--3444470 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
3444368 TATTTATAAA
* * * *
3444378 TATAATATTATTTATTTATATTACTATATTATTATAATATTTATT
1 TATAATAATATTTATTTATATTAATATATTAATATAATATTTACT
3444423 TATAATAATATTTATTAATATATTAAT-TATTAATATAATA-TTACT
1 TATAATAATATTTATT--TATATTAATATATTAATATAATATTTACT
3444468 TAT
1 TAT
3444471 GTTAATAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 22 0.52
46 12 0.29
47 8 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (45 bp):
TATAATAATATTTATTTATATTAATATATTAATATAATATTTACT
Found at i:3444596 original size:26 final size:26
Alignment explanation
Indices: 3444556--3444628 Score: 105
Period size: 25 Copynumber: 2.9 Consensus size: 26
3444546 AATTATTTTT
*
3444556 TAATATTAATA-ATTTTAATAATAAA
1 TAATTTTAATATATTTTAATAATAAA
*
3444581 TCATTTTAATATATTTTAATAATAAA
1 TAATTTTAATATATTTTAATAATAAA
*
3444607 TAATTTTTA-ATATTTTAATAAT
1 TAATTTTAATATATTTTAATAAT
3444629 TATATTAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 22 0.51
26 21 0.49
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TAATTTTAATATATTTTAATAATAAA
Found at i:3444773 original size:15 final size:14
Alignment explanation
Indices: 3444740--3444775 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
3444730 AAAATATAAA
3444740 TATTTTTTCAAAAT
1 TATTTTTTCAAAAT
3444754 TATTTTTTCAAAAT
1 TATTTTTTCAAAAT
3444768 TAATTTTT
1 T-ATTTTT
3444776 ACGAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTTTTCAAAAT
Found at i:3456292 original size:18 final size:19
Alignment explanation
Indices: 3456259--3456296 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3456249 GGTTTCAATT
3456259 TAAAAAATTATTTTTAAAA
1 TAAAAAATTATTTTTAAAA
*
3456278 TAAATAATT-TTTTTAAAA
1 TAAAAAATTATTTTTAAAA
3456296 T
1 T
3456297 TTTTAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAAAATTATTTTTAAAA
Found at i:3472551 original size:2 final size:2
Alignment explanation
Indices: 3472539--3472578 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
3472529 GATGCTAAAT
3472539 TC TC ATC TC TC 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 TC TC TC TC TC T
3472579 TTTTCCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3474660 original size:17 final size:17
Alignment explanation
Indices: 3474625--3474666 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3474615 GCAGGTAATA
3474625 TTCCTCTTTTTGCTACT
1 TTCCTCTTTTTGCTACT
*
3474642 TTCCTTCTTTTT-CTTCT
1 TTCC-TCTTTTTGCTACT
*
3474659 TTTCTCTT
1 TTCCTCTT
3474667 CCTCATCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 11 0.50
18 7 0.32
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.67
Consensus pattern (17 bp):
TTCCTCTTTTTGCTACT
Found at i:3474886 original size:2 final size:2
Alignment explanation
Indices: 3474879--3474903 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3474869 TTTTTGAACC
3474879 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 T
3474904 TGAACCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3476547 original size:2 final size:2
Alignment explanation
Indices: 3476540--3476566 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3476530 CATTATTGTA
3476540 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 A
3476567 GATAGATAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3482733 original size:21 final size:23
Alignment explanation
Indices: 3482699--3482742 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
3482689 TATGTAGAAG
3482699 AAAAAAAGTGACTT-AAAAAAAT
1 AAAAAAAGTGACTTGAAAAAAAT
* *
3482721 AAAAAAA-TTACTTGATAAAAAT
1 AAAAAAAGTGACTTGAAAAAAAT
3482743 TTTAAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.23
Consensus pattern (23 bp):
AAAAAAAGTGACTTGAAAAAAAT
Found at i:3500849 original size:13 final size:13
Alignment explanation
Indices: 3500831--3500855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3500821 GACAAACCCC
3500831 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
3500844 TCTTTTTTTTTT
1 TCTTTTTTTTTT
3500856 GTTTTCCATC
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:3517357 original size:147 final size:147
Alignment explanation
Indices: 3517090--3517377 Score: 540
Period size: 147 Copynumber: 2.0 Consensus size: 147
3517080 TATCCTAGAT
3517090 GAACCTCTATGACAAAAGTAATTTCTCCAAACTGAAATAGCCTTGCATGAAAAATCATGGACTGC
1 GAACCTCTATGACAAAAGTAATTTCTCCAAACTGAAATAGCCTTGCATGAAAAATCATGGACTGC
* *
3517155 TTCAATATCCCAATGAATCCTGACGTTCCAAGAAATATTCCACATAAAATTATTCCATGTCCACC
66 ATCAATATCCCAATGAATCCCGACGTTCCAAGAAATATTCCACATAAAATTATTCCATGTCCACC
3517220 AATGAAAACTTTCCCAA
131 AATGAAAACTTTCCCAA
* *
3517237 GAACCTCTATGACCAAAGTAATTTCTCCAAACTGAAATATCCTTGCATGAAAAATCATGGACTGC
1 GAACCTCTATGACAAAAGTAATTTCTCCAAACTGAAATAGCCTTGCATGAAAAATCATGGACTGC
3517302 ATCAATATCCCAATGAATCCCGACGTTCCAAGAAATATTCCACATAAAATTATTCCATGTCCACC
66 ATCAATATCCCAATGAATCCCGACGTTCCAAGAAATATTCCACATAAAATTATTCCATGTCCACC
3517367 AATGAAAACTT
131 AATGAAAACTT
3517378 GCATGCAAAT
Statistics
Matches: 137, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 137 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (147 bp):
GAACCTCTATGACAAAAGTAATTTCTCCAAACTGAAATAGCCTTGCATGAAAAATCATGGACTGC
ATCAATATCCCAATGAATCCCGACGTTCCAAGAAATATTCCACATAAAATTATTCCATGTCCACC
AATGAAAACTTTCCCAA
Found at i:3523921 original size:25 final size:24
Alignment explanation
Indices: 3523887--3523959 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 24
3523877 TATTACTATA
3523887 ATTATTAAAATATTAAAATATATTT
1 ATTATTAAAATATTAAAAT-TATTT
*
3523912 ATTATTAAAATATATTGAAATTATTT
1 ATTATT-AAA-ATATTAAAATTATTT
* *
3523938 ACTATTAAAATTATTAATATTA
1 ATTATTAAAA-TATTAAAATTA
3523960 AAAATAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 1 0.02
25 18 0.44
26 13 0.32
27 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (24 bp):
ATTATTAAAATATTAAAATTATTT
Found at i:3523960 original size:15 final size:16
Alignment explanation
Indices: 3523923--3523962 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
3523913 TTATTAAAAT
*
3523923 ATATTGAAATTATTTA
1 ATATTAAAATTATTTA
*
3523939 CTATTAAAATTA-TTA
1 ATATTAAAATTATTTA
3523954 ATATTAAAA
1 ATATTAAAA
3523963 ATAATTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
ATATTAAAATTATTTA
Found at i:3524118 original size:108 final size:109
Alignment explanation
Indices: 3523991--3524199 Score: 246
Period size: 108 Copynumber: 1.9 Consensus size: 109
3523981 TAATATTTAA
* * ** *
3523991 TATTAAAATATTATGTTAATATAAA-AAATACTTAAAATAAAACTATTTATT-ATTCT-TTATAT
1 TATTAAAATATTATATTAAT-TAAATAAATA-ATAAAATAAAACTA-TTATTAATAATATAATAT
* *
3524053 TATTTATTAATATGTTATATTAATAGTATGTTATTTATTAATAATAC
63 TATTTATTAATATATTATATTAATAGTATATTATTTATTAATAATAC
* * ** * *
3524100 TATTATAATATT-TATTAATTAAATTAATAATATTATTATACTATTATTAATAATATAATATTAT
1 TATTAAAATATTATATTAATTAAATAAATAATAAAATAAAACTATTATTAATAATATAATATTAT
3524164 TTATTAATATATTATATTAATAGTATATTATTTATT
66 TTATTAATATATTATATTAATAGTATATTATTTATT
3524200 TGTATAATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
106 5 0.06
107 16 0.19
108 52 0.62
109 11 0.13
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (109 bp):
TATTAAAATATTATATTAATTAAATAAATAATAAAATAAAACTATTATTAATAATATAATATTAT
TTATTAATATATTATATTAATAGTATATTATTTATTAATAATAC
Found at i:3524126 original size:33 final size:32
Alignment explanation
Indices: 3524089--3524150 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
3524079 TATGTTATTT
3524089 ATTAATAATACTATTATAATATTTATTAATTAA
1 ATTAATAATACTATTATAATA-TTATTAATTAA
* *
3524122 ATTAATAATATTATTATACTATTATTAAT
1 ATTAATAATACTATTATAATATTATTAAT
3524151 AATATAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 8 0.30
33 19 0.70
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
ATTAATAATACTATTATAATATTATTAATTAA
Found at i:3524148 original size:28 final size:27
Alignment explanation
Indices: 3524087--3524199 Score: 90
Period size: 28 Copynumber: 4.1 Consensus size: 27
3524077 AGTATGTTAT
* *
3524087 TTATTAA-TAATACTATTATAATATTTA
1 TTATTAATTAATAATATTATTATA-TTA
*
3524114 TTAATTAAATTAATAATATTATTATACTA
1 TT-ATT-AATTAATAATATTATTATATTA
*
3524143 TTATTAATAATATAATATTATT-TATTAA
1 TTATTAATTA-ATAATATTATTATATT-A
*
3524171 TATATTATATTAATAGTA-TATTAT-TTA
1 T-TATTA-ATTAATAATATTATTATATTA
3524198 TT
1 TT
3524200 TGTATAATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
26 1 0.01
27 11 0.15
28 25 0.35
29 17 0.24
30 17 0.24
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (27 bp):
TTATTAATTAATAATATTATTATATTA
Found at i:3524152 original size:23 final size:23
Alignment explanation
Indices: 3524122--3524180 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
3524112 TATTAATTAA
3524122 ATTAATAATATTATTATACTA-TT
1 ATTAATAATATTA-TATACTATTT
*
3524145 ATTAATAATA-TA-ATATTATTT
1 ATTAATAATATTATATACTATTT
3524166 ATTAAT-ATATTATAT
1 ATTAATAATATTATAT
3524181 TAATAGTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.25
21 10 0.31
22 4 0.12
23 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTAATAATATTATATACTATTT
Found at i:3524170 original size:49 final size:50
Alignment explanation
Indices: 3524103--3524235 Score: 130
Period size: 49 Copynumber: 2.7 Consensus size: 50
3524093 ATAATACTAT
*
3524103 TATAATATTTATTAATTAAATTAATAATATTATTA-TACTATTA-TTAATAA
1 TATAATA-TTATTTATTAAATTAATAATATTATTAGTA-TATTATTTAATAA
* * * **
3524153 TATAATATTATTTATT-AA-TATATTATATTAATAGTATATTATTTATTTG
1 TATAATATTATTTATTAAATTA-ATAATATTATTAGTATATTATTTAATAA
* *
3524202 TATAATATCATTTATTAATATAAATAATATTATT
1 TATAATATTATTTATTAA-ATTAATAATATTATT
3524236 TATAAGTAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
47 2 0.03
48 17 0.25
49 29 0.43
50 8 0.12
51 10 0.15
52 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (50 bp):
TATAATATTATTTATTAAATTAATAATATTATTAGTATATTATTTAATAA
Found at i:3524185 original size:31 final size:32
Alignment explanation
Indices: 3524112--3524199 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 32
3524102 TTATAATATT
* *
3524112 TATTA-ATTAA-ATTAATAATA-TTATTATAC
1 TATTATATTAATAGTAATATTATTTATTATAC
*
3524141 TATTATTAATAATA-TAATATTATTTATTAATA-
1 TATTA-TATTAATAGTAATATTATTTATT-ATAC
3524173 TATTATATTAATAGT-ATATTATTTATT
1 TATTATATTAATAGTAATATTATTTATT
3524200 TGTATAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
29 5 0.10
31 30 0.60
32 12 0.24
33 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (32 bp):
TATTATATTAATAGTAATATTATTTATTATAC
Found at i:3524234 original size:18 final size:18
Alignment explanation
Indices: 3524104--3524235 Score: 59
Period size: 18 Copynumber: 7.6 Consensus size: 18
3524094 TAATACTATT
3524104 ATAATATTTATTAAT-TAA
1 ATAATA-TTATTAATATAA
*
3524122 ATTAATAATATT-AT-T--
1 A-TAATATTATTAATATAA
* *
3524137 ATACTATTATTAATA-AT
1 ATAATATTATTAATATAA
*
3524154 ATAATATTATTTAT-TAA
1 ATAATATTATTAATATAA
* *
3524171 TATATTA-TATTAATAGTAT
1 -ATAATATTATTAATA-TAA
* **
3524190 ATTAT-TTATTTGTATAA
1 ATAATATTATTAATATAA
*
3524207 TATCAT-TTATTAATATAA
1 -ATAATATTATTAATATAA
3524225 ATAATATTATT
1 ATAATATTATT
3524236 TATAAGTAAA
Statistics
Matches: 84, Mismatches: 18, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
17 28 0.33
18 38 0.45
19 7 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
ATAATATTATTAATATAA
Found at i:3540626 original size:17 final size:17
Alignment explanation
Indices: 3540604--3540650 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
3540594 TTGGCTCTTC
3540604 AATTTTTAAAATTAAAA
1 AATTTTTAAAATTAAAA
**
3540621 AA-TTTTAAAATTTTAA
1 AATTTTTAAAATTAAAA
*
3540637 AATTTTTAATATTA
1 AATTTTTAAAATTA
3540651 TTTTTTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTTTAAAATTAAAA
Found at i:3540630 original size:8 final size:8
Alignment explanation
Indices: 3540607--3540642 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
3540597 GCTCTTCAAT
3540607 TTTTAAAA
1 TTTTAAAA
**
3540615 TTAAAAAA
1 TTTTAAAA
3540623 TTTTAAAA
1 TTTTAAAA
3540631 TTTTAAAA
1 TTTTAAAA
3540639 TTTT
1 TTTT
3540643 TAATATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTTAAAA
Found at i:3540722 original size:17 final size:18
Alignment explanation
Indices: 3540695--3540728 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3540685 TTATTTTATT
3540695 TTATGAAAAATAAAATTA
1 TTATGAAAAATAAAATTA
*
3540713 TTAT-AAAAATACAATT
1 TTATGAAAAATAAAATT
3540729 TTCTTCCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
TTATGAAAAATAAAATTA
Found at i:3542636 original size:384 final size:384
Alignment explanation
Indices: 3541915--3542637 Score: 801
Period size: 384 Copynumber: 1.9 Consensus size: 384
3541905 TAGGTGTGGA
* * *
3541915 AGAATGTCACGGACTTAAGAGAGAGTCTTAAATCTCACATCGAACATAATAGGAGGGTCACTGAG
1 AGAATGTCACGGACTTAAGAGAGAGTCATAAATCCCACATCGAACATAATAGGAGAGTCACTGAG
* * * ***
3541980 GTATAAAAAGATTCACACCATATCTTACTTGTGAGGTGCCTTTTGTAGGACAAAATTGTGAGGCC
66 GTACAAAAAGATTCACACCATATCTTACTTATGAGGTGCCTTTTGTAAGACAAAACCATGAGGCC
* * * * *
3542045 AAGTGGTCAGAGCGGACAATACCTTACAAGAGTATGAACCGTCACGGTTAGGCTGATCTGAGACG
131 AAGGGGTCAGAGCAGACAATACCTCACAAGAGTATGAACCGTCACGGTCAAGCTGATCTGAGACG
* * * ** * * * * * **
3542110 CTGGATGAGTGGATGCTCGGGTCTCAGAGTCGCGTGGGTTCGGAGCTTAAGTTTCGACCTGTGAC
196 CAGAAAGAGTAAATGCCCGGGTCCCAGAGTCGCGCGGGTTCAGAGCTTAAGTCTCGACCCATGAC
* * * * *
3542175 AAATGATATCAGAGCCAACCCTAAACCATTCGACCCACATCAAGTGTCTCGAGGGAGGTAGGCAG
261 AAATGATATAAGAGCCAACCCTAAACCATTCAACCCACACCAAGTGCCTCGAGGGAGGTAGGCAA
3542240 GGTGACCAGCCTCTCACGAGGTTGGGTGGAGGAGAATGTTACGGACCTATGGGTGGAGG
326 GGTGACCAGCCTCTCACGAGGTTGGGTGGAGGAGAATGTTACGGACCTATGGGTGGAGG
* *
3542299 AGAATGTCATGGACTTAAG-GAGGAGTCATGAATCCCACATCGAACATAATAGGAGAGTCACTGA
1 AGAATGTCACGGACTTAAGAGA-GAGTCATAAATCCCACATCGAACATAATAGGAGAGTCACTGA
* * * * *
3542363 GGTACAAAAGGGTTCACACCATCTCTTCCTTATGAGGCT-CCTTTTGTAAGATAAAACCATGAGG
65 GGTACAAAAAGATTCACACCATATCTTACTTATGAGG-TGCCTTTTGTAAGACAAAACCATGAGG
* ** *** *
3542427 TC-AGGGGATCAGAGCAGACAATACCTCACAAGAGTATGAATTGTGGTGGTCAAGCTGATCTGGG
129 CCAAGGGG-TCAGAGCAGACAATACCTCACAAGAGTATGAACCGTCACGGTCAAGCTGATCTGAG
* * * *
3542491 ACGCCAGAAAG-GTAAATGCCCGGGTCCCAGAGTTGTGCGGGTTTAGAGTTTAAGTCTCGACCCA
193 ACG-CAGAAAGAGTAAATGCCCGGGTCCCAGAGTCGCGCGGGTTCAGAGCTTAAGTCTCGACCCA
* * * * ** * * *
3542555 TGATAAGT-AGTATAAGAGCCAGCCCTATACTGTTTAATCCACGCCAAGAT-CCTCGAGGGAGGT
257 TGACAAATGA-TATAAGAGCCAACCCTAAACCATTCAACCCACACCAAG-TGCCTCGAGGGAGGT
* **
3542618 AGGTAAGGTGGTCAGCCTCT
320 AGGCAAGGTGACCAGCCTCT
3542638 GTGACGAAAG
Statistics
Matches: 272, Mismatches: 61, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
383 7 0.03
384 259 0.95
385 6 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (384 bp):
AGAATGTCACGGACTTAAGAGAGAGTCATAAATCCCACATCGAACATAATAGGAGAGTCACTGAG
GTACAAAAAGATTCACACCATATCTTACTTATGAGGTGCCTTTTGTAAGACAAAACCATGAGGCC
AAGGGGTCAGAGCAGACAATACCTCACAAGAGTATGAACCGTCACGGTCAAGCTGATCTGAGACG
CAGAAAGAGTAAATGCCCGGGTCCCAGAGTCGCGCGGGTTCAGAGCTTAAGTCTCGACCCATGAC
AAATGATATAAGAGCCAACCCTAAACCATTCAACCCACACCAAGTGCCTCGAGGGAGGTAGGCAA
GGTGACCAGCCTCTCACGAGGTTGGGTGGAGGAGAATGTTACGGACCTATGGGTGGAGG
Found at i:3542763 original size:110 final size:110
Alignment explanation
Indices: 3542570--3542791 Score: 381
Period size: 110 Copynumber: 2.0 Consensus size: 110
3542560 AGTAGTATAA
* * *
3542570 GAGCCAGCCCTATACTGTTTAATCCACGCCAAGATCCTCGAGGGAGGTAGGTAAGGTGGTCAGCC
1 GAGCCAGCCCTATACTGTTCAATCCACGCCAAGATCCTCGAGGGAGGAAGGCAAGGTGGTCAGCC
* *
3542635 TCTGTGACGAAAGCGTTACGAGGTTGGGTGGGAGAGAATGTCACG
66 TCCGTGACGAAAGCGTTACGAGGTTAGGTGGGAGAGAATGTCACG
*
3542680 GAGCCAGCCCTATACTGTTCAATCCACGCCAAGCTCCTCGAGGGAGGAAGGCAAGGTGGTCAGCC
1 GAGCCAGCCCTATACTGTTCAATCCACGCCAAGATCCTCGAGGGAGGAAGGCAAGGTGGTCAGCC
*
3542745 TCCGTGACGAAGGCGTTACGAGGTTAGGTGGGAGAGAATGTCACG
66 TCCGTGACGAAAGCGTTACGAGGTTAGGTGGGAGAGAATGTCACG
3542790 GA
1 GA
3542792 CCTAAGGAAG
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 105 1.00
ACGTcount: A:0.25, C:0.23, G:0.34, T:0.19
Consensus pattern (110 bp):
GAGCCAGCCCTATACTGTTCAATCCACGCCAAGATCCTCGAGGGAGGAAGGCAAGGTGGTCAGCC
TCCGTGACGAAAGCGTTACGAGGTTAGGTGGGAGAGAATGTCACG
Found at i:3543050 original size:2 final size:2
Alignment explanation
Indices: 3543043--3543078 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3543033 GACTCGTGAC
3543043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3543079 GAGATCCGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3543850 original size:2 final size:2
Alignment explanation
Indices: 3543843--3543880 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3543833 AATCAGTTGA
* *
3543843 AT AT AT AT AT CT AT AT -T AT TT 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
3543881 GTTTTGTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3561766 original size:30 final size:30
Alignment explanation
Indices: 3561728--3561805 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
3561718 ATTAATTATT
* *
3561728 TAAT-TTTTTATTTATATATATTTATATAA
1 TAATATTTTTATTTATATATATTTAAAAAA
* ** *
3561757 TGATATTTTTAAATATTTATATTTAAAAAA
1 TAATATTTTTATTTATATATATTTAAAAAA
3561787 TAATATTTTATATTT-TATA
1 TAATATTTT-TATTTATATA
3561806 AAATAATATT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
29 3 0.08
30 31 0.84
31 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
TAATATTTTTATTTATATATATTTAAAAAA
Found at i:3561798 original size:21 final size:22
Alignment explanation
Indices: 3561768--3561819 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
3561758 GATATTTTTA
3561768 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
*
3561788 AATATTTTATATTTTATAAAAT
1 AATATTTTATATTTTAAAAAAT
3561810 AATATTTTAT
1 AATATTTTAT
3561820 TAATTTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 19 0.66
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:3590766 original size:21 final size:21
Alignment explanation
Indices: 3590736--3590783 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
3590726 AAACAGTGAC
3590736 AATAGATAAATA-TTAAAATAA
1 AATA-ATAAATATTTAAAATAA
*
3590757 TAATAATAAATATTTAATATAA
1 -AATAATAAATATTTAAAATAA
3590779 AATAA
1 AATAA
3590784 ATTAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AATAATAAATATTTAAAATAA
Found at i:3592190 original size:2 final size:2
Alignment explanation
Indices: 3592183--3592218 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3592173 ATAGGGTGTA
3592183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3592219 GTAGAGGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3598216 original size:153 final size:153
Alignment explanation
Indices: 3597938--3598244 Score: 492
Period size: 153 Copynumber: 2.0 Consensus size: 153
3597928 GCCGCATTAT
* * *
3597938 GGATCATATGTTTGTGCAATGTTTCTGATTCTAATTTAATTGCATCATGATGAAACTTCTTGTCT
1 GGATCATATGTTTGTGAAATGTTTCTGATTCTAATTTAATTGCATCATGATGAAACTACATGTCT
3598003 TGTTTATGAAACAATTTAACCTACCTAATAGCTAAGAATCATTTCTCTGCAAAATTTTTGTTCAT
66 TGTTTATGAAACAATTTAACCTACCTAATAGCTAAGAATCATTTCTCTGCAAAATTTTTGTTCAT
3598068 ATCA-CAATACTAATGGAAAAATG
131 ATCATC-ATACTAATGGAAAAATG
* *
3598091 GGATCATATGTTTGTGAAATGTTTCTGATTCTAATTTAATTGCATCATGATGAAAGTACATGTTT
1 GGATCATATGTTTGTGAAATGTTTCTGATTCTAATTTAATTGCATCATGATGAAACTACATGTCT
* * * *
3598156 TGTTTATGAAACGATTTAACCTGCCTAATCA-TTTAGAATCATTTCTCTGCAAAATTTTTGTTCA
66 TGTTTATGAAACAATTTAACCTACCTAAT-AGCTAAGAATCATTTCTCTGCAAAATTTTTGTTCA
*
3598220 TATCATCATACTAATGGAAGAATG
130 TATCATCATACTAATGGAAAAATG
3598244 G
1 G
3598245 AATTAGATAA
Statistics
Matches: 142, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
153 140 0.99
154 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (153 bp):
GGATCATATGTTTGTGAAATGTTTCTGATTCTAATTTAATTGCATCATGATGAAACTACATGTCT
TGTTTATGAAACAATTTAACCTACCTAATAGCTAAGAATCATTTCTCTGCAAAATTTTTGTTCAT
ATCATCATACTAATGGAAAAATG
Found at i:3599037 original size:47 final size:48
Alignment explanation
Indices: 3598959--3599055 Score: 169
Period size: 47 Copynumber: 2.0 Consensus size: 48
3598949 TTGTTGTAGC
*
3598959 CAGTATATCCTTAGTTTGATATGAATTTCATAAAGCAAGCTTGTTTAA
1 CAGTATATCCTTAGTTTGATACGAATTTCATAAAGCAAGCTTGTTTAA
*
3599007 CAGTATATCCTTAG-TTGATACGAATTTCATAAATCAAGCTTGTTTAA
1 CAGTATATCCTTAGTTTGATACGAATTTCATAAAGCAAGCTTGTTTAA
3599054 CA
1 CA
3599056 TTTATCTAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 33 0.70
48 14 0.30
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (48 bp):
CAGTATATCCTTAGTTTGATACGAATTTCATAAAGCAAGCTTGTTTAA
Found at i:3607861 original size:2 final size:2
Alignment explanation
Indices: 3607854--3607888 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3607844 ATGTAATCTA
3607854 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 A
3607889 AAATAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3607993 original size:17 final size:17
Alignment explanation
Indices: 3607971--3608008 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3607961 CAAATTAGAT
* *
3607971 AATTTTAAATTTATTTA
1 AATTTTAAAATTATTCA
3607988 AATTTTAAAATTATTCA
1 AATTTTAAAATTATTCA
3608005 AATT
1 AATT
3608009 ATAATTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTAAAATTATTCA
Found at i:3616698 original size:13 final size:13
Alignment explanation
Indices: 3616640--3616698 Score: 57
Period size: 13 Copynumber: 4.3 Consensus size: 13
3616630 TTTAAATAAA
3616640 TTAAATAAAAA-T
1 TTAAATAAAAATT
*
3616652 ATATAATAAAAATAT
1 TTA-AATAAAAAT-T
*
3616667 TTAAATATCAAAATG
1 TTAAATA--AAAATT
3616682 TTAAATAAAAATT
1 TTAAATAAAAATT
3616695 TTAA
1 TTAA
3616699 TAACTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
12 2 0.05
13 17 0.45
14 4 0.11
15 10 0.26
16 5 0.13
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (13 bp):
TTAAATAAAAATT
Found at i:3617380 original size:18 final size:20
Alignment explanation
Indices: 3617347--3617387 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
3617337 TAACAAGACT
3617347 TTTTAATTTATTAATTTTGA
1 TTTTAATTTATTAATTTTGA
3617367 TTTTAA-TT-TTAATTTTGA
1 TTTTAATTTATTAATTTTGA
3617385 TTT
1 TTT
3617388 AATCATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 13 0.62
19 2 0.10
20 6 0.29
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTAATTTATTAATTTTGA
Found at i:3623646 original size:27 final size:26
Alignment explanation
Indices: 3623593--3623647 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
3623583 TCCTCTTAAT
* *
3623593 TTCTGATTTTTTTTTTTTTGTATTTA
1 TTCTGATTTTTTTTTTTTTGAAATTA
3623619 TTCTG-TTTATTTTTTTTTCTGAAATTA
1 TTCTGATTT-TTTTTTTTT-TGAAATTA
3623646 TT
1 TT
3623648 TCGGAAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 3 0.12
26 14 0.56
27 8 0.32
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.73
Consensus pattern (26 bp):
TTCTGATTTTTTTTTTTTTGAAATTA
Found at i:3625725 original size:14 final size:14
Alignment explanation
Indices: 3625706--3625733 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3625696 ACCATCAGAT
3625706 AAGAAAAGAAAAAA
1 AAGAAAAGAAAAAA
3625720 AAGAAAAGAAAAAA
1 AAGAAAAGAAAAAA
3625734 GATGACCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAAAAA
Found at i:3636139 original size:22 final size:23
Alignment explanation
Indices: 3636097--3636144 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
3636087 TTTTTTTTTG
3636097 TTTTTATATATTATTCTAATATGA
1 TTTTTATATATTATTCTAATA-GA
3636121 TTTTTA-ATA-TATT-TAAATAGA
1 TTTTTATATATTATTCT-AATAGA
3636142 TTT
1 TTT
3636145 AAGTATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.26
22 8 0.35
23 3 0.13
24 6 0.26
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTTTATATATTATTCTAATAGA
Found at i:3639149 original size:33 final size:33
Alignment explanation
Indices: 3639107--3639172 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
3639097 TGTTGTCTAA
3639107 ACTTAGGAAGCAGTAGATTTACCTTCTTTCCAC
1 ACTTAGGAAGCAGTAGATTTACCTTCTTTCCAC
3639140 ACTTAGGAAGCAGTAGATTTACCTTCTTTCCAC
1 ACTTAGGAAGCAGTAGATTTACCTTCTTTCCAC
3639173 TTTATGATGT
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:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (33 bp):
ACTTAGGAAGCAGTAGATTTACCTTCTTTCCAC
Found at i:3643731 original size:181 final size:181
Alignment explanation
Indices: 3643427--3643788 Score: 661
Period size: 181 Copynumber: 2.0 Consensus size: 181
3643417 AGATGGAATT
* *
3643427 GGATCTAGTGGGAGAGCGCATCTGTGTCTGCATCACTCGCTACAATTGGTACTATCTAGCCTATA
1 GGATCTAGTGGGAGAGCGCATCTGTGTCTGCATCAATCGCCACAATTGGTACTATCTAGCCTATA
*
3643492 CAGCTGTACTCTCTTCTTTGCATTCTCACTAAACCCACTTTTTCTTTTCATAGTACTTGATGTGT
66 CAACTGTACTCTCTTCTTTGCATTCTCACTAAACCCACTTTTTCTTTTCATAGTACTTGATGTGT
3643557 TGGTATTTTTTGGATTTAATTTATTAAATTGGTGTTATTTCAATGATAAAA
131 TGGTATTTTTTGGATTTAATTTATTAAATTGGTGTTATTTCAATGATAAAA
* * *
3643608 GGATCTAGTGGGAGAGTGCATCTGTGTCTGCATCAATCGCCACTATTGGTACTATCTAGCTTATA
1 GGATCTAGTGGGAGAGCGCATCTGTGTCTGCATCAATCGCCACAATTGGTACTATCTAGCCTATA
*
3643673 CAACTGTACTCTCTTCTTTGCATTCTCACTAAACCCACTTTTTCTTTTCATGGTACTTGATGTGT
66 CAACTGTACTCTCTTCTTTGCATTCTCACTAAACCCACTTTTTCTTTTCATAGTACTTGATGTGT
3643738 TGGTATTTTTTGGATTTAATTTATTAAATTGGTGTTATTTCAATGATAAAA
131 TGGTATTTTTTGGATTTAATTTATTAAATTGGTGTTATTTCAATGATAAAA
3643789 ATTCTCTACT
Statistics
Matches: 174, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
181 174 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (181 bp):
GGATCTAGTGGGAGAGCGCATCTGTGTCTGCATCAATCGCCACAATTGGTACTATCTAGCCTATA
CAACTGTACTCTCTTCTTTGCATTCTCACTAAACCCACTTTTTCTTTTCATAGTACTTGATGTGT
TGGTATTTTTTGGATTTAATTTATTAAATTGGTGTTATTTCAATGATAAAA
Found at i:3646012 original size:1 final size:1
Alignment explanation
Indices: 3646006--3646031 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3645996 GCAAGAGAGG
3646006 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3646032 CCTCACACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3650643 original size:31 final size:31
Alignment explanation
Indices: 3650580--3650642 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
3650570 AAAAAATGTG
*
3650580 AATGAAAATATGTTTGATAATTGAAAATAAA
1 AATGAAAATAAGTTTGATAATTGAAAATAAA
3650611 AATGAAAATAAG-TTGA-AATTTGAAAATAAA
1 AATGAAAATAAGTTTGATAA-TTGAAAATAAA
3650641 AA
1 AA
3650643 AATATTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 2 0.07
30 17 0.57
31 11 0.37
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.29
Consensus pattern (31 bp):
AATGAAAATAAGTTTGATAATTGAAAATAAA
Found at i:3650734 original size:22 final size:24
Alignment explanation
Indices: 3650691--3650734 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
3650681 TTTTTTATAT
**
3650691 TTTTTAAATTATCATTTTTTAACA
1 TTTTTAAATTATCATTAATTAACA
3650715 TTTTT-AA-TATCATTAATTAA
1 TTTTTAAATTATCATTAATTAA
3650735 TAAATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 2 0.11
24 5 0.28
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTTAAATTATCATTAATTAACA
Found at i:3650807 original size:18 final size:18
Alignment explanation
Indices: 3650776--3650810 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3650766 ATTAATAATA
3650776 TTATTATTAAATTTTTAT
1 TTATTATTAAATTTTTAT
* *
3650794 TTATTTTTACATTTTTA
1 TTATTATTAAATTTTTA
3650811 AAAAATAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTATTAAATTTTTAT
Found at i:3652554 original size:21 final size:22
Alignment explanation
Indices: 3652528--3652568 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3652518 GAATTCCACT
*
3652528 TATAATT-TTTTACTATAATCA
1 TATAATTATTTAACTATAATCA
3652549 TATAATTATTTAACTATAAT
1 TATAATTATTTAACTATAAT
3652569 AAGAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TATAATTATTTAACTATAATCA
Found at i:3658920 original size:105 final size:106
Alignment explanation
Indices: 3658714--3658926 Score: 356
Period size: 105 Copynumber: 2.0 Consensus size: 106
3658704 CCTCAATGGC
*
3658714 TTGAATTGATCCTTAGGAGTGTATATAAAATTAGATTTAGTTATACTGTATTGTATGTTTTGTAT
1 TTGAATTGATCCTTAGGAGTGTATATAAAATTAGATTTAGTTATACTGTATTGTATGTCTTGTAT
* **
3658779 TGGATTTCTATGGTTGCTTTATTGCCTTTGATATTCTTGGA
66 TGGATTTCTATGGTTGCTCTAGAGCCTTTGATATTCTTGGA
*
3658820 TTGAATTGATCCTTAGGAGTGTATATAAAATTAGATTTAGTTTTAC-GTATTGTATGTCTTGTAT
1 TTGAATTGATCCTTAGGAGTGTATATAAAATTAGATTTAGTTATACTGTATTGTATGTCTTGTAT
* *
3658884 TGGATTTCTATGGTTGCTCTAGAGCTTTTTATATTCTTGGA
66 TGGATTTCTATGGTTGCTCTAGAGCCTTTGATATTCTTGGA
3658925 TT
1 TT
3658927 TCCTATCCTA
Statistics
Matches: 100, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
105 55 0.55
106 45 0.45
ACGTcount: A:0.23, C:0.08, G:0.20, T:0.49
Consensus pattern (106 bp):
TTGAATTGATCCTTAGGAGTGTATATAAAATTAGATTTAGTTATACTGTATTGTATGTCTTGTAT
TGGATTTCTATGGTTGCTCTAGAGCCTTTGATATTCTTGGA
Found at i:3660628 original size:23 final size:23
Alignment explanation
Indices: 3660602--3660648 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3660592 CTAGGACTTA
* * *
3660602 CCCATCCGAGGAGTATACTTTTG
1 CCCATCCAACGAGTACACTTTTG
3660625 CCCATCCAACGAGTACACTTTTG
1 CCCATCCAACGAGTACACTTTTG
3660648 C
1 C
3660649 GATAAACTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (23 bp):
CCCATCCAACGAGTACACTTTTG
Found at i:3673100 original size:75 final size:75
Alignment explanation
Indices: 3672977--3673136 Score: 311
Period size: 75 Copynumber: 2.1 Consensus size: 75
3672967 CGATAATATA
*
3672977 TAGAAATGTTGCTGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAGCAGTATGGCCT
1 TAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAGCAGTATGGCCT
3673042 AATTAATTTT
66 AATTAATTTT
3673052 TAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAGCAGTATGGCCT
1 TAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAGCAGTATGGCCT
3673117 AATTAATTTT
66 AATTAATTTT
3673127 TAGAAATGTT
1 TAGAAATGTT
3673137 AATTAATTTT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 84 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (75 bp):
TAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAGCAGTATGGCCT
AATTAATTTT
Found at i:3673165 original size:19 final size:20
Alignment explanation
Indices: 3673116--3673156 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3673106 CAGTATGGCC
3673116 TAATTAATTTTTAGAAATGT
1 TAATTAATTTTTAGAAATGT
3673136 TAATTAATTTTTAGAAATGT
1 TAATTAATTTTTAGAAATGT
3673156 T
1 T
3673157 GATGATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
TAATTAATTTTTAGAAATGT
Found at i:3673209 original size:95 final size:95
Alignment explanation
Indices: 3673041--3673313 Score: 376
Period size: 95 Copynumber: 3.0 Consensus size: 95
3673031 CAGTATGGCC
3673041 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAG
1 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAG
*
3673106 CAGTATGGCCTAATTAATTTTTAGAAATGT
66 CAGGATGGCCTAATTAATTTTTAGAAATGT
3673136 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAG
1 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAG
3673201 CAGGATGGCCTAATTAATTTTTAGAAATGT
66 CAGGATGGCCTAATTAATTTTTAGAAATGT
* * * * * *
3673231 TGA-TGA-TTTTGGTAA-G--GA--ATCATT--T-----CTCATTTCTTGAACCTAAATTACTTA
1 TAATTAATTTTTAGAAATGTTGATGAT-TTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTA
3673282 GCAGGATGGCCTAATTAATTTTTAGAAATGT
65 GCAGGATGGCCTAATTAATTTTTAGAAATGT
3673313 T
1 T
3673314 GATGATTTTG
Statistics
Matches: 170, Mismatches: 7, Indels: 15
0.89 0.04 0.08
Matches are distributed among these distances:
82 57 0.34
87 1 0.01
88 2 0.01
89 2 0.01
90 2 0.01
92 1 0.01
93 7 0.04
94 2 0.01
95 96 0.56
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (95 bp):
TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAG
CAGGATGGCCTAATTAATTTTTAGAAATGT
Found at i:3673216 original size:75 final size:78
Alignment explanation
Indices: 3673136--3673461 Score: 502
Period size: 82 Copynumber: 4.2 Consensus size: 78
3673126 TTAGAAATGT
3673136 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGG-A-A-TCATTTCTTGAACCTAAATTACT
1 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAACATTCATTTCTTGAACCTAAATTACT
3673198 TAGCAGGATGGCC
66 TAGCAGGATGGCC
3673211 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTCATTTCTTGAACCTAAAT
1 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAA-CA--T-TCATTTCTTGAACCTAAAT
3673276 TACTTAGCAGGATGGCC
62 TACTTAGCAGGATGGCC
3673293 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTCATTTCTTGAACCTAAAT
1 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAA-CA--T-TCATTTCTTGAACCTAAAT
* *
3673358 TATTTAGCAGTATGGCC
62 TACTTAGCAGGATGGCC
*
3673375 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGG-A-A-TCCTTTCTTGAACCTAAATTACT
1 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAACATTCATTTCTTGAACCTAAATTACT
*
3673437 TAGCAGTATGGCC
66 TAGCAGGATGGCC
3673450 TAATTAATTTTT
1 TAATTAATTTTT
3673462 CTTTCTATGG
Statistics
Matches: 240, Mismatches: 4, Indels: 14
0.93 0.02 0.05
Matches are distributed among these distances:
75 83 0.35
76 1 0.00
78 1 0.00
79 1 0.00
81 1 0.00
82 153 0.64
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (78 bp):
TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAACATTCATTTCTTGAACCTAAATTACT
TAGCAGGATGGCC
Found at i:3673437 original size:157 final size:155
Alignment explanation
Indices: 3673136--3673461 Score: 509
Period size: 157 Copynumber: 2.1 Consensus size: 155
3673126 TTAGAAATGT
3673136 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAG
1 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAG
3673201 CAGGATGGCCTAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTCATTTCTT
66 CAGGATGGCCTAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAA-CA-TTCTCATTTCTT
3673266 GAACCTAAATTACTTAGCAGGATGGCC
129 GAACCTAAATTACTTAGCAGGATGGCC
3673293 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTCATTTCTTGAACCTAAAT
1 TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGG-A--A----TCATTTCTTGAACCTAAAT
* *
3673358 TATTTAGCAGTATGGCCTAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGG-A-A-TC-C-T
59 TACTTAGCAGGATGGCCTAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAACATTCTCAT
*
3673418 TTCTTGAACCTAAATTACTTAGCAGTATGGCC
124 TTCTTGAACCTAAATTACTTAGCAGGATGGCC
3673450 TAATTAATTTTT
1 TAATTAATTTTT
3673462 CTTTCTATGG
Statistics
Matches: 159, Mismatches: 3, Indels: 14
0.90 0.02 0.08
Matches are distributed among these distances:
157 81 0.51
158 2 0.01
159 2 0.01
160 1 0.01
161 1 0.01
163 1 0.01
164 71 0.45
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (155 bp):
TAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAATCATTTCTTGAACCTAAATTACTTAG
CAGGATGGCCTAATTAATTTTTAGAAATGTTGATGATTTTGGTAAGGAACATTCTCATTTCTTGA
ACCTAAATTACTTAGCAGGATGGCC
Found at i:3675364 original size:176 final size:176
Alignment explanation
Indices: 3674889--3675417 Score: 972
Period size: 176 Copynumber: 3.0 Consensus size: 176
3674879 AAGTACAAAA
*
3674889 TAAGCAAAAAAAAATAAAATGAACCACTTTAATTAGCTCTATTAGTTGATTTGTTTTCACATATT
1 TAAGCAAAAAAAAAAAAAATGAACCACTTTAATTAGCTCTATTAGTTGATTTGTTTTCACATATT
3674954 ATTTTCGTATAATAGCTTAAGAAATCTCTCAAAGTAGGATGATTTGTTTTACTTAGCTGGAACTT
66 ATTTTCGTATAATAGCTTAAGAAATCTCTCAAAGTAGGATGATTTGTTTTACTTAGCTGGAACTT
* *
3675019 TGTGAATTTAGAAAGTAAATTCACATATTTATTTGAAATTCTTAAT
131 TGTGAATTTAGAAAGTAAATGCACATATTTATTCGAAATTCTTAAT
* *
3675065 TAAGC--AAAAAAAAAAAATGAACCATTTTAATTAGCTCTATTAGTTGATTTGTTTTCGCATATT
1 TAAGCAAAAAAAAAAAAAATGAACCACTTTAATTAGCTCTATTAGTTGATTTGTTTTCACATATT
3675128 ATTTTCGTATAATAGCTTAAGAAATCTCTCAAAGTAGGATGATTTGTTTTACTTAGCTGGAACTT
66 ATTTTCGTATAATAGCTTAAGAAATCTCTCAAAGTAGGATGATTTGTTTTACTTAGCTGGAACTT
*
3675193 TGTGAAATTAGAAAGTAAATGCACATATTTATTCGAAATTCTTAAT
131 TGTGAATTTAGAAAGTAAATGCACATATTTATTCGAAATTCTTAAT
3675239 TAAGCAAAAAAAAAAAAAATGAACCACTTTAATTAGCTCTATTAGTTGATTTGTTTTCACATATT
1 TAAGCAAAAAAAAAAAAAATGAACCACTTTAATTAGCTCTATTAGTTGATTTGTTTTCACATATT
*
3675304 ATTCTCGTATAATAGCTTAAGAAATCTCTCAAAGTAGGATGATTTGTTTTACTTAGCTGGAACTT
66 ATTTTCGTATAATAGCTTAAGAAATCTCTCAAAGTAGGATGATTTGTTTTACTTAGCTGGAACTT
*
3675369 TGTGAATTTAGAAAGTAAGTGCACATATTTATTCGAAATTCTTAAT
131 TGTGAATTTAGAAAGTAAATGCACATATTTATTCGAAATTCTTAAT
3675415 TAA
1 TAA
3675418 TATAAATTCA
Statistics
Matches: 340, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
174 168 0.49
176 172 0.51
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (176 bp):
TAAGCAAAAAAAAAAAAAATGAACCACTTTAATTAGCTCTATTAGTTGATTTGTTTTCACATATT
ATTTTCGTATAATAGCTTAAGAAATCTCTCAAAGTAGGATGATTTGTTTTACTTAGCTGGAACTT
TGTGAATTTAGAAAGTAAATGCACATATTTATTCGAAATTCTTAAT
Found at i:3675895 original size:2 final size:2
Alignment explanation
Indices: 3675888--3675914 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3675878 GACACGAAGA
3675888 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 A
3675915 ATAAAGAAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3690035 original size:21 final size:19
Alignment explanation
Indices: 3690011--3690066 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 19
3690001 TTTATTATTA
3690011 ATATATTAATATTAAAAAATT
1 ATAT-TTAATA-TAAAAAATT
*
3690032 ATATTTTAATA-ATAATAATT
1 ATA-TTTAATATA-AAAAATT
3690052 -TATTTAATATAAAAA
1 ATATTTAATATAAAAA
3690067 TAAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 10 0.33
19 4 0.13
20 6 0.20
21 9 0.30
22 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATTTAATATAAAAAATT
Found at i:3690104 original size:23 final size:23
Alignment explanation
Indices: 3690094--3690170 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
3690084 ATTATTCTTT
* *
3690094 ATATTATTTATGAATATATTATA
1 ATATTATTTATTAATATATTTTA
3690117 ATATTATTTATTAATATATTATTA
1 ATATTATTTATTAATATATT-TTA
* * *
3690141 ATAGTATATTATTTAT-TA-TATA
1 ATATTAT-TTATTAATATATTTTA
3690163 ATATTATT
1 ATATTATT
3690171 ATAAGTAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.02
22 8 0.17
23 20 0.43
24 10 0.22
25 7 0.15
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (23 bp):
ATATTATTTATTAATATATTTTA
Found at i:3690124 original size:11 final size:11
Alignment explanation
Indices: 3690094--3690174 Score: 62
Period size: 11 Copynumber: 7.1 Consensus size: 11
3690084 ATTATTCTTT
3690094 ATATTATTTATGA
1 ATATTA-TTAT-A
3690107 ATA-TATTATA
1 ATATTATTATA
3690117 ATATTATTTATTA
1 ATATTA-TTA-TA
3690130 ATA-TATTATTA
1 ATATTATTA-TA
3690141 ATAGTATATTAT-
1 ATA-T-TATTATA
*
3690153 TTATTA-TATA
1 ATATTATTATA
3690163 ATATTATTATA
1 ATATTATTATA
3690174 A
1 A
3690175 GTAAATTATG
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
9 3 0.05
10 11 0.19
11 21 0.36
12 9 0.16
13 9 0.16
14 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
ATATTATTATA
Found at i:3690483 original size:13 final size:14
Alignment explanation
Indices: 3690451--3690495 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
3690441 GCACCTTTTG
3690451 TTTTGTAAAAAATGA
1 TTTT-TAAAAAATGA
*
3690466 TTTTTAAAATATGA
1 TTTTTAAAAAATGA
*
3690480 TTTTTGAAAAAT-A
1 TTTTTAAAAAATGA
3690493 TTT
1 TTT
3690496 GCATTTTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 4 0.15
14 19 0.70
15 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (14 bp):
TTTTTAAAAAATGA
Found at i:3690492 original size:16 final size:16
Alignment explanation
Indices: 3690451--3690493 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3690441 GCACCTTTTG
3690451 TTTTGTAAAAA-ATGAT
1 TTTTG-AAAAATATGAT
3690467 TTTT--AAAATATGAT
1 TTTTGAAAAATATGAT
3690481 TTTTGAAAAATAT
1 TTTTGAAAAATAT
3690494 TTGCATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.17
14 9 0.38
16 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (16 bp):
TTTTGAAAAATATGAT
Found at i:3690641 original size:26 final size:25
Alignment explanation
Indices: 3690610--3690676 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
3690600 CATTAATATA
3690610 ATTATTAAAAATTTAAAAAAATATTT
1 ATTATTAAAAATTT-AAAAAATATTT
* *
3690636 ATTATTAAAATATATT-GAAATTATTT
1 ATTATTAAAA-AT-TTAAAAAATATTT
*
3690662 ATTATTAAAATTTTA
1 ATTATTAAAAATTTA
3690677 TGTTAATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
24 2 0.06
25 1 0.03
26 28 0.80
27 2 0.06
28 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (25 bp):
ATTATTAAAAATTTAAAAAATATTT
Found at i:3690738 original size:15 final size:15
Alignment explanation
Indices: 3690720--3690916 Score: 147
Period size: 15 Copynumber: 12.8 Consensus size: 15
3690710 TATTATTCTT
3690720 TATATTATTTATTAA
1 TATATTATTTATTAA
*
3690735 TATATGATTTATTAATA
1 TATATTATTTATT-A-A
3690752 TAATATTATTTATTAA
1 T-ATATTATTTATTAA
* *
3690768 -A-ATTAATATATTAT
1 TATATT-ATTTATTAA
* *
3690782 TATAATAGTTATTAA
1 TATATTATTTATTAA
3690797 TATATTATTTATTAGCA
1 TATATTATTTATTA--A
*
3690814 TAATATTATATATTAA
1 T-ATATTATTTATTAA
*
3690830 TATAATA-TTATT--
1 TATATTATTTATTAA
* *
3690842 TAT-TAATATATT-A
1 TATATTATTTATTAA
3690855 TAATATTATTTATTAA
1 T-ATATTATTTATTAA
*
3690871 TATATTATATTAATAA
1 TATATTAT-TTATTAA
3690887 TATATTATTTATTTATA
1 TATATTATTTA-TTA-A
3690904 TACTATTATTTAT
1 TA-TATTATTTAT
3690917 AAGTAAAATT
Statistics
Matches: 144, Mismatches: 20, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
11 1 0.01
12 7 0.05
13 4 0.03
14 14 0.10
15 53 0.37
16 24 0.17
17 9 0.06
18 32 0.22
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (15 bp):
TATATTATTTATTAA
Found at i:3690762 original size:18 final size:18
Alignment explanation
Indices: 3690721--3690916 Score: 143
Period size: 18 Copynumber: 10.6 Consensus size: 18
3690711 ATTATTCTTT
3690721 ATATTATTTATT-A-AT-
1 ATATTATTTATTAATATA
*
3690736 ATATGATTTATTAATATA
1 ATATTATTTATTAATATA
*
3690754 ATATTATTTATTAAAATTAA
1 ATATTATTTATTAATA-T-A
* *
3690774 TATATTATTATAATAGTTATTAA
1 -ATATTATT-TATTA-ATA-T-A
**
3690797 TATATTATTTATTAGCATA
1 -ATATTATTTATTAATATA
*
3690816 ATATTATATATTAATATA
1 ATATTATTTATTAATATA
3690834 ATATTATTTATTAATATA
1 ATATTATTTATTAATATA
* * *
3690852 TTATAATATTATTTAT-TA
1 ATATTAT-TTATTAATATA
3690870 ATA-TATTATATTAATA-A
1 ATATTATT-TATTAATATA
*
3690887 TATATTATTTATTTATATA
1 -ATATTATTTATTAATATA
*
3690906 CTATTATTTAT
1 ATATTATTTAT
3690917 AAGTAAAATT
Statistics
Matches: 146, Mismatches: 21, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
15 11 0.08
16 2 0.01
17 11 0.08
18 75 0.51
19 14 0.10
20 2 0.01
21 9 0.06
22 8 0.05
23 14 0.10
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (18 bp):
ATATTATTTATTAATATA
Found at i:3690796 original size:62 final size:61
Alignment explanation
Indices: 3690710--3690913 Score: 183
Period size: 62 Copynumber: 3.4 Consensus size: 61
3690700 TAAAACTATT
* *
3690710 TATTATTCT-TTATATTATTTATTAATATATGATTTATTAATATAATATTATTTATTAAAATTAA
1 TATTATT-TATTATAATA-TTATTAATATAT-ATTTATTAATATAATATTATATATTAAAA-TAA
** *
3690774 TA-TA-TTATTATAATAGTTATTAATATATTATTTATTAGCATAATATTATATATTAATATAA
1 TATTATTTATTATAATA-TTATTAATATA-TATTTATTAATATAATATTATATATTAAAATAA
* * * *
3690835 TATTATTTATTA-ATATATTA-TAATAT-TATTTATTAATATATTA-TAT-TAATAATATAT
1 TATTATTTATTATA-ATATTATTAATATATATTTATTAATATAATATTATATATTAAAATAA
*
3690892 TATTTATTTA-TATACTATTATT
1 TA-TTATTTATTATAATATTATT
3690914 TATAAGTAAA
Statistics
Matches: 120, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
57 18 0.15
58 12 0.10
59 14 0.12
61 12 0.10
62 50 0.42
63 12 0.10
64 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (61 bp):
TATTATTTATTATAATATTATTAATATATATTTATTAATATAATATTATATATTAAAATAA
Found at i:3690799 original size:23 final size:23
Alignment explanation
Indices: 3690741--3690878 Score: 102
Period size: 23 Copynumber: 5.7 Consensus size: 23
3690731 TTAATATATG
* *
3690741 ATTTATTAATATAATATTAT-TT
1 ATTTATTAATATATTATTATAAT
*
3690763 ATTAAAATTAATATATTATTATAAT
1 ATT--TATTAATATATTATTATAAT
*
3690788 AGTTATTAATATATTATTTATTAGCAT
1 ATTTATTAATATATTA-TTA-TA--AT
* *
3690815 A-ATATT-ATATATTAATATAATATT
1 ATTTATTAATATATT-AT-T-ATAAT
* *
3690839 ATTTATTAATATATTATAATATT
1 ATTTATTAATATATTATTATAAT
3690862 ATTTATTAATATATTAT
1 ATTTATTAATATATTAT
3690879 ATTAATAATA
Statistics
Matches: 95, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
22 3 0.03
23 34 0.36
24 20 0.21
25 19 0.20
26 15 0.16
27 4 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
ATTTATTAATATATTATTATAAT
Found at i:3690890 original size:11 final size:13
Alignment explanation
Indices: 3690725--3690893 Score: 84
Period size: 13 Copynumber: 13.8 Consensus size: 13
3690715 TTCTTTATAT
3690725 TATT-TATTAATA
1 TATTATATTAATA
*
3690737 TATGATTTATTAATA
1 TAT--TATATTAATA
*
3690752 TA--ATATT-ATT
1 TATTATATTAATA
*
3690762 TATTAAAATTAATA
1 TATT-ATATTAATA
3690776 TA-T-TATT-ATAA
1 TATTATATTAAT-A
*
3690787 TAGT-TATTAATA
1 TATTATATTAATA
*
3690799 TATTAT-TTATTA
1 TATTATATTAATA
* *
3690811 GCATAATATT-ATA
1 -TATTATATTAATA
3690824 TATTA-ATATAATA
1 TATTATAT-TAATA
3690837 TTATT-TATTAATA
1 -TATTATATTAATA
*
3690850 TATTATAAT-AT-
1 TATTATATTAATA
3690861 TATT-TATTAATA
1 TATTATATTAATA
3690873 TATTATATTAATA
1 TATTATATTAATA
3690886 -A-TATATTA
1 TATTATATTA
3690894 TTTATTTATA
Statistics
Matches: 122, Mismatches: 14, Indels: 43
0.68 0.08 0.24
Matches are distributed among these distances:
10 9 0.07
11 25 0.20
12 32 0.26
13 33 0.27
14 13 0.11
15 10 0.08
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (13 bp):
TATTATATTAATA
Found at i:3692546 original size:17 final size:17
Alignment explanation
Indices: 3692505--3692548 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3692495 ATATATTTTT
* * *
3692505 TTTTATTTAAATTTATA
1 TTTTATTAAAAATAATA
3692522 TTTATATTAAAAATAATA
1 TTT-TATTAAAAATAATA
3692540 TTTTATTAA
1 TTTTATTAA
3692549 TTTTAGATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTATTAAAAATAATA
Found at i:3695271 original size:268 final size:268
Alignment explanation
Indices: 3694794--3695336 Score: 1077
Period size: 268 Copynumber: 2.0 Consensus size: 268
3694784 GAACACCAAA
3694794 AGAATCTTAGTACCATAGTGAGGAATCTTAATTAGTGACTTCATAAAAGGAATCTCAATTAGTGA
1 AGAATCTTAGTACCATAGTGAGGAATCTTAATTAGTGACTTCATAAAAGGAATCTCAATTAGTGA
3694859 GGTAGGCCAATAGAATATGCTGATGATAAAAGACTATAAGAATAAAAGAACAAAATAAAAAATAA
66 GGTAGGCCAATAGAATATGCTGATGATAAAAGACTATAAGAATAAAAGAACAAAATAAAAAATAA
3694924 TTTAAAAAACGATTTAACTTTTTCATGCTTTTCTAGAACACTTCAACAGCGGGAGAATCTACATG
131 TTTAAAAAACGATTTAACTTTTTCATGCTTTTCTAGAACACTTCAACAGCGGGAGAATCTACATG
*
3694989 AACGAGGTTGAGAACTTAGAACAATAAGTAAGGAAATTAGCAGATTCCTTTAGCATCACAACAAT
196 AACGAGGGTGAGAACTTAGAACAATAAGTAAGGAAATTAGCAGATTCCTTTAGCATCACAACAAT
3695054 AAATGATC
261 AAATGATC
3695062 AGAATCTTAGTACCATAGTGAGGAATCTTAATTAGTGACTTCATAAAAGGAATCTCAATTAGTGA
1 AGAATCTTAGTACCATAGTGAGGAATCTTAATTAGTGACTTCATAAAAGGAATCTCAATTAGTGA
3695127 GGTAGGCCAATAGAATATGCTGATGATAAAAGACTATAAGAATAAAAGAACAAAATAAAAAATAA
66 GGTAGGCCAATAGAATATGCTGATGATAAAAGACTATAAGAATAAAAGAACAAAATAAAAAATAA
3695192 TTTAAAAAACGATTTAACTTTTTCATGCTTTTCTAGAACACTTCAACAGCGGGAGAATCTACATG
131 TTTAAAAAACGATTTAACTTTTTCATGCTTTTCTAGAACACTTCAACAGCGGGAGAATCTACATG
3695257 AACGAGGGTGAGAACTTAGAACAATAAGTAAGGAAATTAGCAGATTCCTTTAGCATCACAACAAT
196 AACGAGGGTGAGAACTTAGAACAATAAGTAAGGAAATTAGCAGATTCCTTTAGCATCACAACAAT
3695322 AAATGATC
261 AAATGATC
3695330 AGAATCT
1 AGAATCT
3695337 ATAATTTAAG
Statistics
Matches: 274, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
268 274 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (268 bp):
AGAATCTTAGTACCATAGTGAGGAATCTTAATTAGTGACTTCATAAAAGGAATCTCAATTAGTGA
GGTAGGCCAATAGAATATGCTGATGATAAAAGACTATAAGAATAAAAGAACAAAATAAAAAATAA
TTTAAAAAACGATTTAACTTTTTCATGCTTTTCTAGAACACTTCAACAGCGGGAGAATCTACATG
AACGAGGGTGAGAACTTAGAACAATAAGTAAGGAAATTAGCAGATTCCTTTAGCATCACAACAAT
AAATGATC
Found at i:3696649 original size:4 final size:4
Alignment explanation
Indices: 3696640--3696666 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3696630 ATTTTAAATT
3696640 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
3696667 TAATTATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:3696680 original size:13 final size:14
Alignment explanation
Indices: 3696636--3696672 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
3696626 CATAATTTTA
*
3696636 AATTTTAATTAATT
1 AATTATAATTAATT
3696650 AA-T-TAATTAATT
1 AATTATAATTAATT
3696662 AATTATAATTA
1 AATTATAATTA
3696673 TTAGTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 11 0.52
13 2 0.10
14 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTATAATTAATT
Found at i:3698362 original size:8 final size:8
Alignment explanation
Indices: 3698332--3698390 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 8
3698322 ACAAATGTAC
3698332 TATTTTAT
1 TATTTTAT
3698340 TAATTATTAAT
1 T-ATT-TT-AT
3698351 TATTTTAT
1 TATTTTAT
3698359 TATTTTATT
1 TATTTTA-T
3698368 TATTTT-T
1 TATTTTAT
3698375 ATATTTT-T
1 -TATTTTAT
*
3698383 TCTTTTAT
1 TATTTTAT
3698391 CCAAAACTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
7 6 0.14
8 18 0.41
9 12 0.27
10 5 0.11
11 3 0.07
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
TATTTTAT
Found at i:3698379 original size:20 final size:19
Alignment explanation
Indices: 3698332--3698383 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
3698322 ACAAATGTAC
**
3698332 TATTTTATTAATTATTAAT
1 TATTTTATTTTTTATTAAT
*
3698351 TATTTTATTATTTTATTTAT
1 TATTTTATT-TTTTATTAAT
3698371 T-TTTATATTTTTT
1 TATTT-TATTTTTT
3698384 CTTTTATCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTTTATTTTTTATTAAT
Found at i:3711851 original size:28 final size:28
Alignment explanation
Indices: 3711820--3711879 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
3711810 TTGATTTTTT
* * *
3711820 TATATAGTTTGTATTTGTAATTTTTACA
1 TATATAATTTGTATTTGTAATTTATAAA
* *
3711848 TATATAATTTTTATTTTTAATTTATAAA
1 TATATAATTTGTATTTGTAATTTATAAA
3711876 TATA
1 TATA
3711880 ATTTCATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (28 bp):
TATATAATTTGTATTTGTAATTTATAAA
Found at i:3713260 original size:55 final size:54
Alignment explanation
Indices: 3713158--3713275 Score: 123
Period size: 55 Copynumber: 2.2 Consensus size: 54
3713148 AAAGCCAAAT
* * * *
3713158 AAAAAATATAATAGTCATATAGACAATATAATAAAGCCTAAACTAAAAGAG-CA
1 AAAAAATATAATACTCAAATAGAAAATATAATAAAGCCTAAACTAAAAAAGTCA
* * * *
3713211 AAAAAATATAATAAACTCAAATAGAAAATATAATAATA-TCTACAGTAAAAAAGTGA
1 AAAAAATATAAT--ACTCAAATAGAAAATATAATAA-AGCCTAAACTAAAAAAGTCA
3713267 AAAAAATAT
1 AAAAAATAT
3713276 GATTGTTTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
53 12 0.23
55 30 0.57
56 11 0.21
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.22
Consensus pattern (54 bp):
AAAAAATATAATACTCAAATAGAAAATATAATAAAGCCTAAACTAAAAAAGTCA
Found at i:3718540 original size:2 final size:2
Alignment explanation
Indices: 3718533--3718577 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3718523 GATTAGGGTC
3718533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3718575 AT A
1 AT A
3718578 CAAAGAGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3724724 original size:21 final size:21
Alignment explanation
Indices: 3724700--3724741 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3724690 TTATGTTAGA
* *
3724700 GATTATCAGAATTTAAATTTT
1 GATTATCAAAATTAAAATTTT
*
3724721 GATTATTAAAATTAAAATTTT
1 GATTATCAAAATTAAAATTTT
3724742 AATATTCTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (21 bp):
GATTATCAAAATTAAAATTTT
Found at i:3724747 original size:20 final size:21
Alignment explanation
Indices: 3724709--3724747 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3724699 AGATTATCAG
* *
3724709 AATTTAAATTTTGATTATTAA
1 AATTAAAATTTTGAATATTAA
3724730 AATTAAAATTTT-AATATT
1 AATTAAAATTTTGAATATT
3724748 CTACCAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
AATTAAAATTTTGAATATTAA
Found at i:3735562 original size:22 final size:22
Alignment explanation
Indices: 3735499--3735563 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
3735489 ATTTTAATTT
*
3735499 AATAATAAAAAACT-AAAAAATA
1 AATAA-AAAATACTAAAAAAATA
*
3735521 AAT--AAAATGCTTAAATAAAATA
1 AATAAAAAATAC-TAAA-AAAATA
3735543 AATAAAAAATACTAAAAAAAT
1 AATAAAAAATACTAAAAAAAT
3735564 TTTGAAACGG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
19 5 0.14
20 1 0.03
21 2 0.06
22 17 0.49
23 4 0.11
24 6 0.17
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.22
Consensus pattern (22 bp):
AATAAAAAATACTAAAAAAATA
Found at i:3739914 original size:53 final size:52
Alignment explanation
Indices: 3739848--3739953 Score: 119
Period size: 53 Copynumber: 2.0 Consensus size: 52
3739838 TTTAAATAAT
* *
3739848 TTTAATATGAATTTGATATTT-A-TTATATATATATACA-TAATATGATTAATATA
1 TTTAAAATGAATTT-ATATTTAACTAATATA-ATATA-ATTAATATGATT-ATATA
* *
3739901 TTTAAAATTAATTTATGTTTAACTAATATAATATAATTAATATGATTATATA
1 TTTAAAATGAATTTATATTTAACTAATATAATATAATTAATATGATTATATA
3739953 T
1 T
3739954 GAATAACATG
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
52 12 0.26
53 28 0.61
54 6 0.13
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (52 bp):
TTTAAAATGAATTTATATTTAACTAATATAATATAATTAATATGATTATATA
Found at i:3746198 original size:18 final size:17
Alignment explanation
Indices: 3746172--3746206 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3746162 AATCATTTTA
3746172 TTTAATTTTAATAAATTT
1 TTTAATTTT-ATAAATTT
*
3746190 TTTATTTTTATAAATTT
1 TTTAATTTTATAAATTT
3746207 AATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAATTTTATAAATTT
Found at i:3750159 original size:13 final size:15
Alignment explanation
Indices: 3750139--3750169 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3750129 ATTTTGATAG
3750139 ATATTTTT-ATATAA
1 ATATTTTTAATATAA
3750153 ATATTTTTAATATAA
1 ATATTTTTAATATAA
3750168 AT
1 AT
3750170 TTAGATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTTTTAATATAA
Found at i:3751269 original size:16 final size:16
Alignment explanation
Indices: 3751248--3751307 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
3751238 TAAAATTTTA
3751248 AATTTAAATTAAAATC
1 AATTTAAATTAAAATC
* *
3751264 AATTTAAATTATAATGA
1 AATTTAAATTAAAAT-C
**
3751281 AATTT-CTTTAAAAATC
1 AATTTAAATT-AAAATC
3751297 AATTTAAATTA
1 AATTTAAATTA
3751308 TAATGAAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
16 22 0.67
17 11 0.33
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (16 bp):
AATTTAAATTAAAATC
Done.