Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 117 of 135
Found at i:35102510 original size:24 final size:24
Alignment explanation
Indices: 35102450--35102512 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
35102440 TAGATTAATA
* * *
35102450 AGAGTTTGACTCAAACAAATACAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
35102474 AGAGTTTATCTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
35102498 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
35102513 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:35108507 original size:19 final size:18
Alignment explanation
Indices: 35108473--35108518 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
35108463 ATAAAAAATT
*
35108473 AATTTTATATATTTTTAA
1 AATTTTAAATATTTTTAA
**
35108491 AATTTTAAATAATTTTTTG
1 AATTTTAAAT-ATTTTTAA
35108510 AATTTTAAA
1 AATTTTAAA
35108519 AAAATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
AATTTTAAATATTTTTAA
Found at i:35113868 original size:30 final size:30
Alignment explanation
Indices: 35113832--35113891 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
35113822 GACATCAACT
*
35113832 CAATTAAAAAATTACAAAAATATTTTTTCG
1 CAATTAAAAAATTACAAAAATATATTTTCG
*
35113862 CAATTAAAGAATTACAAAAATATATTTTCG
1 CAATTAAAAAATTACAAAAATATATTTTCG
35113892 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (30 bp):
CAATTAAAAAATTACAAAAATATATTTTCG
Found at i:35117501 original size:262 final size:262
Alignment explanation
Indices: 35117036--35117568 Score: 1034
Period size: 262 Copynumber: 2.0 Consensus size: 262
35117026 CTACTGCTAA
35117036 AATGATAGGTGCTAAGGGCTTGCTGGGGAGGTCGTGGCCTGACTTGGATATGTTACCATTGGGAT
1 AATGATAGGTGCTAAGGGCTTGCTGGGGAGGTCGTGGCCTGACTTGGATATGTTACCATTGGGAT
35117101 GGCTCACTGATCCAGGTTATACGCCCTGGCAAATAGCTACTCCTTTCATGCCCTTGTTGTCCCTA
66 GGCTCACTGATCCAGGTTATACGCCCTGGCAAATAGCTACTCCTTTCATGCCCTTGTTGTCCCTA
35117166 CCAGTTGTCTATGCAATGAATACTTTTTAGTTGTAAAATATTTGTTTTGAGTTGGGCATTTATAT
131 CCAGTTGTCTATGCAATGAATACTTTTTAGTTGTAAAATATTTGTTTTGAGTTGGGCATTTATAT
*
35117231 GGGAGGGCTAAGCTAGAATCAGTGAAGAACCAAAAATAATTAGATACTTTCCTGCACTATAGGTT
196 GGGAGGGCTAACCTAGAATCAGTGAAGAACCAAAAATAATTAGATACTTTCCTGCACTATAGGTT
35117296 CG
261 CG
35117298 AATGATAGGTGCTAAGGGCTTGCTGGGGAGGTCGTGGCCTGACTTGGATATGTTACCATTGGGAT
1 AATGATAGGTGCTAAGGGCTTGCTGGGGAGGTCGTGGCCTGACTTGGATATGTTACCATTGGGAT
35117363 GGCTCACTGATCCAGGTTATACGCCCTGGCAAATAGCTACTCCTTTCATGCCCTTGTTGTCCCTA
66 GGCTCACTGATCCAGGTTATACGCCCTGGCAAATAGCTACTCCTTTCATGCCCTTGTTGTCCCTA
35117428 CCAGTTGTCTATGCAATG-ATGACTTTTTAGTTGTAAAATATTTGTTTTGAGTTGGGCATTTATA
131 CCAGTTGTCTATGCAATGAAT-ACTTTTTAGTTGTAAAATATTTGTTTTGAGTTGGGCATTTATA
35117492 TGGGAGGGCTAACCTAGAATCAGTGAAGAACCAAAAATAATTAGATACTTTCCTGCACTATAGGT
195 TGGGAGGGCTAACCTAGAATCAGTGAAGAACCAAAAATAATTAGATACTTTCCTGCACTATAGGT
35117557 TCG
260 TCG
35117560 AATGA-AGGT
1 AATGATAGGT
35117569 CCACATAGAA
Statistics
Matches: 269, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
261 6 0.02
262 263 0.98
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (262 bp):
AATGATAGGTGCTAAGGGCTTGCTGGGGAGGTCGTGGCCTGACTTGGATATGTTACCATTGGGAT
GGCTCACTGATCCAGGTTATACGCCCTGGCAAATAGCTACTCCTTTCATGCCCTTGTTGTCCCTA
CCAGTTGTCTATGCAATGAATACTTTTTAGTTGTAAAATATTTGTTTTGAGTTGGGCATTTATAT
GGGAGGGCTAACCTAGAATCAGTGAAGAACCAAAAATAATTAGATACTTTCCTGCACTATAGGTT
CG
Found at i:35122551 original size:18 final size:18
Alignment explanation
Indices: 35122513--35122552 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
35122503 AACAAGCAGC
* *
35122513 TAAATAACAATAAATACA
1 TAAATAAAAATAAATAAA
*
35122531 TAAATAAAAATAATTAAA
1 TAAATAAAAATAAATAAA
35122549 TAAA
1 TAAA
35122553 GGAAAAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAATAAAAATAAATAAA
Found at i:35124608 original size:62 final size:62
Alignment explanation
Indices: 35124515--35124659 Score: 166
Period size: 62 Copynumber: 2.3 Consensus size: 62
35124505 TTGCACTATT
* * * * * * * *
35124515 ATAACATGTGCAATGTGATACCTGAATTATCAATTTGTGTATTAATTGA-TACTTGTACTTTT
1 ATAAAATGTCCAATGTGATACATGAACTATCAATTTGTATATT-ATTGAGTACATATACTTTC
* * * *
35124577 ATAGAATGTCTAATGTGGTACATGAACTATCAATTTGTATATTATTTAGTACATATACTTTC
1 ATAAAATGTCCAATGTGATACATGAACTATCAATTTGTATATTATTGAGTACATATACTTTC
35124639 ATAAAATGTCCAATGTGATAC
1 ATAAAATGTCCAATGTGATAC
35124660 TTATACTTTG
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
61 4 0.06
62 63 0.94
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (62 bp):
ATAAAATGTCCAATGTGATACATGAACTATCAATTTGTATATTATTGAGTACATATACTTTC
Found at i:35124846 original size:164 final size:168
Alignment explanation
Indices: 35124647--35124980 Score: 399
Period size: 169 Copynumber: 2.0 Consensus size: 168
35124637 TCATAAAATG
* *
35124647 TCCAATGTGATACTTATACTTTGAAAATGTTCAAGGTGGTACTTAAACTA-TCA-A-T-AATTAT
1 TCCAATGTGATACTTATACTTTGAAAATATTCAAGGTGGGACTTAAACTATTCATAGTGAATTAT
** ** * * *
35124708 TATGATAATTGGAGTAAACACCCGTAATAAATGTTAAA-CCACCAATGAAAATTCAACCTGTGGA
66 TATGATAATTGGAGTAAACACCAATAATAAATACTAAATCAACCAATGAAAATTCAACATGTGAA
* *
35124772 TTTTTTCTCCAAATCATTAATTTCACATGGGTGATATAA
131 TTTTTT-TACAAATCATTAATCTCACATGGGTGATATAA
* * * * *
35124811 TCCAATGTGGTGCTTATACTTTGAAAATATTCAAGGTGGGACTTAAGCTATTGATTAGTGTATTA
1 TCCAATGTGATACTTATACTTTGAAAATATTCAAGGTGGGACTTAAACTATTCA-TAGTGAATTA
* ** * * **
35124876 TTATGATCATTGGAGTAAACACCAATTGTAACTACTAAATCAATCAATGAAAATTCGGCATGTGA
65 TTATGATAATTGGAGTAAACACCAATAATAAATACTAAATCAACCAATGAAAATTCAACATGTGA
*
35124941 ATTTTTTTACAAATCATTAATCTCATATGGGTGATATAA
130 ATTTTTTTACAAATCATTAATCTCACATGGGTGATATAA
35124980 T
1 T
35124981 ATTATGTGAA
Statistics
Matches: 140, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
164 45 0.32
165 2 0.01
167 1 0.01
168 1 0.01
169 65 0.46
170 26 0.19
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (168 bp):
TCCAATGTGATACTTATACTTTGAAAATATTCAAGGTGGGACTTAAACTATTCATAGTGAATTAT
TATGATAATTGGAGTAAACACCAATAATAAATACTAAATCAACCAATGAAAATTCAACATGTGAA
TTTTTTTACAAATCATTAATCTCACATGGGTGATATAA
Found at i:35131681 original size:30 final size:28
Alignment explanation
Indices: 35131541--35131826 Score: 241
Period size: 30 Copynumber: 9.8 Consensus size: 28
35131531 GGGCAAGTTG
* * *
35131541 GTAATTTTGGGAAAGTTTAGGGTTAAAAC
1 GTAATTTT-TGAAAGTTTAGGGGTAAAAT
* *
35131570 ATGATTTTTGAAAGTTTAGGGGTAAAAAT
1 GTAATTTTTGAAAGTTTAGGGGT-AAAAT
*
35131599 GTAATTTTTGGAAGTTTAGGGG-AAAAT
1 GTAATTTTTGAAAGTTTAGGGGTAAAAT
*
35131626 GTAATTTTTGAGAAGTTTAAGGGTAAAAT
1 GTAATTTTTGA-AAGTTTAGGGGTAAAAT
**
35131655 GTAAAATTTGCAAAGTTTAGAGGGTAAAAAT
1 GTAATTTTTG-AAAGTTTAG-GGGT-AAAAT
* *
35131686 GTAATTTTTAAAAAGTTTAGGGTTAAAAT
1 GTAATTTTT-GAAAGTTTAGGGGTAAAAT
* *
35131715 GTAATTTTTGGGAAGTTTGGGGGTTAAAAT
1 GTAATTTTT-GAAAGTTTAGGGG-TAAAAT
* * *
35131745 ATAATTTTTGGAAAGTTTAAGAGTCAAAAT
1 GTAATTTTT-GAAAGTTTAGGGGT-AAAAT
* * *
35131775 ATAATTTTTGGAAAGTTTGGGGGTCAAAAC
1 GTAATTTTT-GAAAGTTTAGGGGT-AAAAT
* * *
35131805 ATGATTTTTGGATAGTTTAGGG
1 GTAATTTTT-GAAAGTTTAGGG
35131827 ACCTTCTGGG
Statistics
Matches: 214, Mismatches: 34, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
27 15 0.07
28 23 0.11
29 73 0.34
30 82 0.38
31 21 0.10
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (28 bp):
GTAATTTTTGAAAGTTTAGGGGTAAAAT
Found at i:35131702 original size:60 final size:60
Alignment explanation
Indices: 35131541--35131803 Score: 281
Period size: 60 Copynumber: 4.5 Consensus size: 60
35131531 GGGCAAGTTG
* * *
35131541 GTAATTTTGGGAAAGTTTAGGGTTAAAACATG--ATTTTTG-AAAGTTTAGGGGTAAAAAT
1 GTAATTTTTGGAAAGTTTAGGGGTAAAA-ATGTAATTTTTGAAAAGTTTAAGGGTAAAAAT
*
35131599 GTAATTTTTGG-AAGTTTAGGGG--AAAATGTAATTTTTGAGAAGTTTAAGGGT-AAAAT
1 GTAATTTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTTTAAGGGTAAAAAT
** * * *
35131655 GTAAAATTTGCAAAGTTTAGAGGGTAAAAATGTAATTTTTAAAAAGTTT-AGGGTTAAAAT
1 GTAATTTTTGGAAAGTTTAG-GGGTAAAAATGTAATTTTTGAAAAGTTTAAGGGTAAAAAT
* * * * * * *
35131715 GTAATTTTTGGGAAGTTTGGGGGTTAAAATATAATTTTTGGAAAGTTTAAGAGTCAAAAT
1 GTAATTTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTTTAAGGGTAAAAAT
* * *
35131775 ATAATTTTTGGAAAGTTTGGGGGTCAAAA
1 GTAATTTTTGGAAAGTTTAGGGGTAAAAA
35131804 CATGATTTTT
Statistics
Matches: 173, Mismatches: 23, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
54 3 0.02
55 3 0.02
56 20 0.12
57 29 0.17
58 13 0.08
59 29 0.17
60 76 0.44
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (60 bp):
GTAATTTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTTTAAGGGTAAAAAT
Found at i:35132858 original size:16 final size:15
Alignment explanation
Indices: 35132837--35132878 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
35132827 TTCAACTTCT
35132837 TTTATTAATATTAATA
1 TTTATTAATATTAA-A
35132853 TTTATTAAT-TATAAA
1 TTTATTAATAT-TAAA
35132868 TTTATT-ATATT
1 TTTATTAATATT
35132879 TTGAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 3 0.12
15 9 0.38
16 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTATTAATATTAAA
Found at i:35133535 original size:6 final size:6
Alignment explanation
Indices: 35133516--35133617 Score: 83
Period size: 6 Copynumber: 18.0 Consensus size: 6
35133506 TGGACATTAG
* * * *
35133516 TAAATT TAAA-- TAAATT TAAACT TAAATT T-ACTA TAAAAT TAAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA-TT
* * *
35133562 TAAA-- TAAATT TAAACT TAAA-A TAAATT TAAATT TAAA-A TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
35133606 TAAATT TAAATT
1 TAAATT TAAATT
35133618 CTGTTTGGGT
Statistics
Matches: 75, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
4 8 0.11
5 11 0.15
6 51 0.68
7 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:35133557 original size:17 final size:17
Alignment explanation
Indices: 35133532--35133615 Score: 114
Period size: 17 Copynumber: 4.9 Consensus size: 17
35133522 TAAATAAATT
* **
35133532 TAAACTTAAATTTACTA
1 TAAATTTAAATTTAAAA
* *
35133549 TAAAATTAAATTTTAAA
1 TAAATTTAAATTTAAAA
*
35133566 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
35133583 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
35133600 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
35133616 TTCTGTTTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 59 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:35133557 original size:23 final size:22
Alignment explanation
Indices: 35133516--35133616 Score: 66
Period size: 23 Copynumber: 4.5 Consensus size: 22
35133506 TGGACATTAG
*
35133516 TAAATTTAAATAAATTTAAACT
1 TAAATTTAAATAAAATTAAACT
* *
35133538 TAAATTTACTATAAAATTAAATTT
1 TAAATTTA-AATAAAATTAAA-CT
* *
35133562 TAAA--TAAATTTAAACTTAAA-A
1 TAAATTTAAA--TAAAATTAAACT
*
35133583 TAAATTTAAATTTAAAA-TAAATT
1 TAAATTTAAA--TAAAATTAAACT
35133606 TAAATTTAAAT
1 TAAATTTAAAT
35133617 TCTGTTTGGG
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
21 6 0.09
22 14 0.22
23 39 0.61
24 5 0.08
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATTTAAATAAAATTAAACT
Found at i:35133569 original size:28 final size:26
Alignment explanation
Indices: 35133523--35133593 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 26
35133513 TAGTAAATTT
35133523 AAATAAATTTAAACTTAAATTT-ACTATA
1 AAATAAATTTAAA--TAAATTTAACT-TA
35133551 AAATTAAATTTTAAATAAATTTAAACTTA
1 AAA-TAAA-TTTAAATAAATTT-AACTTA
35133580 AAATAAATTTAAAT
1 AAATAAATTTAAAT
35133594 TTAAAATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
27 7 0.18
28 14 0.36
29 9 0.23
30 9 0.23
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.39
Consensus pattern (26 bp):
AAATAAATTTAAATAAATTTAACTTA
Found at i:35133603 original size:11 final size:11
Alignment explanation
Indices: 35133549--35133609 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
35133539 AAATTTACTA
35133549 TAAAATTAAATT
1 TAAAA-TAAATT
*
35133561 TTAAATAAATT
1 TAAAATAAATT
* *
35133572 TAAACTTAAA-A
1 TAAA-ATAAATT
*
35133583 TAAATTTAAATT
1 TAAA-ATAAATT
35133595 TAAAATAAATT
1 TAAAATAAATT
35133606 TAAA
1 TAAA
35133610 TTTAAATTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
11 28 0.70
12 12 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAAATAAATT
Found at i:35134059 original size:39 final size:39
Alignment explanation
Indices: 35133993--35134603 Score: 394
Period size: 39 Copynumber: 15.7 Consensus size: 39
35133983 GATAACTACC
* * **
35133993 ATCTGCCCCATGATCGAAGTAAGAGATTGACTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* *
35134032 ATCTGCCCCAAGCTCGGGGTAAAAGATTGA---ATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGG-TG
*
35134069 CAATCTACCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * * *
35134110 ATCTACTCCAAGCTCGGGGTAAGAGATCGA---ATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGG-TG
* * *
35134147 CAATCTGCCCTAGGCTTGGGGTAAGAGATTGATTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * * * *
35134188 ATCTGCCTCAGGCTCGAGGTAAAAGATTTACTGATGTTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * * * *
35134227 ATTTGCCTCTGGCTCGAGGTAAGAGATCGA---ATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGG-TG
* *
35134264 CAATCTG-CCCAGGCTCGGGGTAAGAGATTTG-CTGACGCTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGA-TTGACTGATGGTG
* * * *
35134304 ATTTGCCCTAGGCTCGGGGTAAGAGATTTACTGATAGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * * ** * * *
35134343 ATCTACCCTAGGCTCGGGGTAAAAGATCAAATTGCT-GTA
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT-TGACTGATGGTG
* * * *
35134382 ATCTGCCCTAGGCTCGAGTTAAGAGATTAACTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * * **
35134421 ATCTGCCCCAAGCTAGGGGTAA-AGGATCAGAC-GACT-GCA
1 ATCTGCCCCAGGCTCGGGGTAAGA-GAT-TGACTGA-TGGTG
* * *
35134460 ATCTACCACAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * *
35134499 ATCTGCTCTAGGCTCGGGGTAAGAGATCGA---ATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGG-TG
* * *
35134536 CAATCTGTCCCTGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
** * **
35134577 ATCTATCCCAGACTCGAAGTAAGAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
35134604 CGAATGGCTG
Statistics
Matches: 443, Mismatches: 94, Indels: 70
0.73 0.15 0.12
Matches are distributed among these distances:
36 15 0.03
37 8 0.02
38 32 0.07
39 358 0.81
40 10 0.02
41 8 0.02
42 12 0.03
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
Found at i:35134127 original size:78 final size:77
Alignment explanation
Indices: 35133993--35134642 Score: 546
Period size: 78 Copynumber: 8.4 Consensus size: 77
35133983 GATAACTACC
* * **
35133993 ATCTGCCCCATGATCGAAGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTG-CCCAAGCTCGGGGTAAAAGA
*
35134058 TTGAATGGCTGCA
65 TCGAATGGCTGCA
* * *
35134071 ATCTACCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTACTCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGC-CCAAGCTCGGGGTAAAAGA
35134136 TCGAATGGCTGCA
65 TCGAATGGCTGCA
* * * * *
35134149 ATCTGCCCTAGGCTTGGGGTAAGAGATTGATTGATGGTGATCTGCCTCAGGCTCGAGGTAAAAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCC-CAAGCTCGGGGTAAAAGA
** * *
35134214 TTTACTGATGTTG--
65 TCGAATG--GCTGCA
* * * * * * *
35134227 ATTTGCCTCTGGCTCGAGGTAAGAGATCGA---ATGGCTGCAATCTGCCCAGGCTCGGGGTAAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGG-TG--ATCTGCCCAAGCTCGGGGTAAAA
* *
35134289 GATTTG-CTGACGCTG--
63 GA-TCGAATG--GCTGCA
* * * * * *
35134304 ATTTGCCCTAGGCTCGGGGTAAGAGATTTACTGATAGTGATCTACCCTAGGCTCGGGGTAAAAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCC-AAGCTCGGGGTAAAAGA
* * *
35134369 TCAAATTGCTGTA
65 TCGAATGGCTGCA
* * * * * *
35134382 ATCTGCCCTAGGCTCGAGTTAAGAGATTAACTGATGGTGATCTGCCCCAAGCTAGGGGTAAAGGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTG-CCCAAGCTCGGGGTAAAAGA
* *
35134447 TC-AGACGACTGCA
65 TCGA-ATGGCTGCA
* * * * * *
35134460 ATCTACCACAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCTCTAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGC-CCAAGCTCGGGGTAAAAGA
35134525 TCGAATGGCTGCA
65 TCGAATGGCTGCA
* * * * ** *
35134538 ATCTGTCCCTGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTATCCC-AGACTCGAAGTAAGAG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCT-GCCCAAG-CTCGGGGTAAAAG
35134602 ATCGAATGGCTGCA
64 ATCGAATGGCTGCA
* **
35134616 ATCTGTCCTTGGCTCGGGGTAAGAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
35134643 CTTCAATTTT
Statistics
Matches: 469, Mismatches: 82, Indels: 42
0.79 0.14 0.07
Matches are distributed among these distances:
75 4 0.01
76 6 0.01
77 60 0.13
78 386 0.82
79 7 0.01
80 6 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (77 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCAAGCTCGGGGTAAAAGAT
CGAATGGCTGCA
Found at i:35134221 original size:117 final size:115
Alignment explanation
Indices: 35134077--35134642 Score: 535
Period size: 117 Copynumber: 4.9 Consensus size: 115
35134067 TGCAATCTAC
*
35134077 CCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTACTCCAAGCTCGGGGTAAGAGATCGAAT
1 CCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTAC-CCAGGCTCGGGGTAAGAGATCGAAT
* *
35134142 GGCTGCAATCTGCCCTAGGCTTGGGGTAAGAGATTGATTGATGGTGATCTG
65 GGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTG
* * * * * * * *
35134193 CCTCAGGCTCGAGGTAAAAGATTTACTGATGTTGATTTGCCTCTGGCTCGAGGTAAGAGATCGAA
1 CC-CAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTACC-CAGGCTCGGGGTAAGAGATCGAA
* * *
35134258 TGGCTGCAATCTGCCC-AGGCTCGGGGTAAGAGATTTG-CTGACGCTGATTTG
64 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGA-TTGACTGATGGTGATCTG
* * * *
35134309 CCCTAGGCTCGGGGTAAGAGATTTACTGATAGTGATCTACCCTAGGCTCGGGGTAAAAGATCAAA
1 CCC-AGGCTCGGGGTAAGAGATTGACTGATGGTGATCTACCC-AGGCTCGGGGTAAGAGATCGAA
* * * * *
35134374 TTGCTGTAATCTGCCCTAGGCTCGAGTTAAGAGATTAACTGATGGTGATCTG
64 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTG
* * * **
35134426 CCCCAAGCTAGGGGTAA-AGGATCAGAC-GACT-GCAATCTACCACAGGCTCGGGGTAAGAGATT
1 -CCCAGGCTCGGGGTAAGA-GAT-TGACTGA-TGGTGATCTACC-CAGGCTCGGGGTAAGAGA-T
* *
35134488 GGCTG-ATGG-TG--ATCTGCTCTAGGCTCGGGGTAAGAGATCGA---ATGGCTGCAATCTG
60 --C-GAATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGACTGATGG-TG--ATCTG
* * * **
35134543 TCCCTGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTATCCCAGACTCGAAGTAAGAGATCGAA
1 -CCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTA-CCCAGGCTCGGGGTAAGAGATCGAA
* *
35134608 TGGCTGCAATCTGTCCTTGGCTCGGGGTAAGAGAT
64 TGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGAT
35134643 CTTCAATTTT
Statistics
Matches: 363, Mismatches: 60, Indels: 53
0.76 0.13 0.11
Matches are distributed among these distances:
113 1 0.00
114 9 0.02
115 6 0.02
116 101 0.28
117 229 0.63
118 11 0.03
119 2 0.01
120 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (115 bp):
CCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTACCCAGGCTCGGGGTAAGAGATCGAATG
GCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTG
Found at i:35145491 original size:29 final size:28
Alignment explanation
Indices: 35145401--35145661 Score: 146
Period size: 30 Copynumber: 8.8 Consensus size: 28
35145391 ATTCGAGGGC
35145401 AAAATGATAATTTTTGGATA-TCTTGGGGTA
1 AAAAT-ATAATTTTTGGA-AGT-TTGGGGTA
**** * ** *
35145431 AATCGGTAATTTTGGGAAGTTCAGGGTC
1 AAAATATAATTTTTGGAAGTTTGGGGTA
*
35145459 AAAATATGATTTTTGGAAGTTTGGGGATA
1 AAAATATAATTTTTGGAAGTTTGGGG-TA
* * **
35145488 AAAATGTAATTTTTTGAAGTTTAGGGGCG
1 AAAATATAATTTTTGGAAGTTT-GGGGTA
*
35145517 AAAATATAATTTTTAAGAAGTTTGAGGGTA
1 AAAATATAATTTTT-GGAAGTTTG-GGGTA
* * **
35145547 AAATTTTAAATTTTACGAAGTTTGAGAGGGTA
1 AAAATAT-AATTTTTGGAAGTTT--G-GGGTA
* * *
35145579 AAAATGTGATTTTTGGAAGTTCAGGGGGTA
1 AAAATATAATTTTTGGAAGTT--TGGGGTA
* * * *
35145609 AAAATGTATTTTTTGGAAACGTTTGGTGTT
1 AAAATATAATTTTTGG-AA-GTTTGGGGTA
35145639 AAAATATAATTTTTGGAAAGTTT
1 AAAATATAATTTTTGG-AAGTTT
35145662 AAGGGTTAAA
Statistics
Matches: 176, Mismatches: 43, Indels: 25
0.72 0.18 0.10
Matches are distributed among these distances:
28 24 0.14
29 49 0.28
30 68 0.39
31 20 0.11
32 15 0.09
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (28 bp):
AAAATATAATTTTTGGAAGTTTGGGGTA
Found at i:35145539 original size:30 final size:28
Alignment explanation
Indices: 35145437--35145544 Score: 83
Period size: 29 Copynumber: 3.7 Consensus size: 28
35145427 GGTAAATCGG
** * *
35145437 TAATTTTGGGAAGTTCAGGGTCAAAATA
1 TAATTTTTAGAAGTTTAGGGGCAAAATA
* * * *
35145465 TGATTTTTGGAAGTTT-GGGGATAAAAATG
1 TAATTTTTAGAAGTTTAGGGG--CAAAATA
*
35145494 TAATTTTTTGAAGTTTAGGGGCGAAAATA
1 TAATTTTTAGAAGTTTAGGGGC-AAAATA
35145523 TAATTTTTAAGAAGTTTGAGGG
1 TAATTTTT-AGAAGTTT-AGGG
35145545 TAAAATTTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.05
28 13 0.21
29 32 0.51
30 11 0.17
31 4 0.06
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (28 bp):
TAATTTTTAGAAGTTTAGGGGCAAAATA
Found at i:35147382 original size:6 final size:6
Alignment explanation
Indices: 35147363--35147447 Score: 67
Period size: 6 Copynumber: 15.0 Consensus size: 6
35147353 TAGACATTAA
* *
35147363 TAAATT TAAA-- TAAATT TAAACT TAAATT TACAA-- TAAAAT TAAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT TAAA-TT
* *
35147409 TAAA-- TAAATT TAAACT TAAA-A TAAATT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
35147448 CTATTTAGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
4 10 0.16
5 6 0.09
6 41 0.64
7 7 0.11
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:35147404 original size:17 final size:16
Alignment explanation
Indices: 35147361--35147446 Score: 86
Period size: 17 Copynumber: 5.2 Consensus size: 16
35147351 ATTAGACATT
35147361 AATAAATTTAAA--TA
1 AATAAATTTAAATTTA
*
35147375 AATTTAAACTTAAATTTA
1 AA--TAAATTTAAATTTA
*
35147393 CAATAAAATTAAATTTTA
1 -AATAAATTTAAA-TTTA
*
35147411 AATAAATTTAAACTTAA
1 AATAAATTTAAA-TTTA
35147428 AATAAATTTAAATTTA
1 AATAAATTTAAATTTA
35147444 AAT
1 AAT
35147447 TCTATTTAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
14 2 0.03
16 15 0.25
17 35 0.58
18 6 0.10
19 2 0.03
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAAATTTAAATTTA
Found at i:35147440 original size:10 final size:10
Alignment explanation
Indices: 35147361--35147422 Score: 67
Period size: 10 Copynumber: 6.2 Consensus size: 10
35147351 ATTAGACATT
35147361 AATAAATTTA
1 AATAAATTTA
35147371 AATAAATTTA
1 AATAAATTTA
35147381 AACTTAAATTTA
1 AA--TAAATTTA
*
35147393 CAATAAAATTA
1 -AATAAATTTA
35147404 AAT---TTTA
1 AATAAATTTA
35147411 AATAAATTTA
1 AATAAATTTA
35147421 AA
1 AA
35147423 CTTAAAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
7 6 0.14
10 21 0.48
11 7 0.16
12 8 0.18
13 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (10 bp):
AATAAATTTA
Found at i:35154060 original size:20 final size:20
Alignment explanation
Indices: 35154019--35154057 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35154009 TCACATATAC
35154019 TTCAAAAAAATATTTTAAAA
1 TTCAAAAAAATATTTTAAAA
*
35154039 TTCAACAAAAT-TTTTAAAA
1 TTCAAAAAAATATTTTAAAA
35154058 ATTTATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (20 bp):
TTCAAAAAAATATTTTAAAA
Found at i:35162387 original size:22 final size:22
Alignment explanation
Indices: 35162334--35162387 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
35162324 AAATTTTTTC
* *
35162334 TTGTTGTTGTTTTGCTACTATT
1 TTGTTGTTATATTGCTACTATT
** * *
35162356 TTACTATTATATTGTTACTATT
1 TTGTTGTTATATTGCTACTATT
35162378 TTGTTGTTAT
1 TTGTTGTTAT
35162388 TGTTTGAATA
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.07, G:0.13, T:0.63
Consensus pattern (22 bp):
TTGTTGTTATATTGCTACTATT
Found at i:35178522 original size:29 final size:28
Alignment explanation
Indices: 35178466--35178522 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
35178456 AATAACAACG
*
35178466 TTAAAAAAATCTTTTAAATAATTAAATT
1 TTAAAAAAATCTTTTAAAGAATTAAATT
* * *
35178494 TTAAAAAAATGTTTTTAAGATTTAGAATT
1 TTAAAAAAATCTTTTAAAGAATTA-AATT
35178523 AGTTGAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (28 bp):
TTAAAAAAATCTTTTAAAGAATTAAATT
Found at i:35179885 original size:21 final size:21
Alignment explanation
Indices: 35179848--35179887 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35179838 TTTTAATTTG
*
35179848 ATTTTTTTTAAAGAATTTATA
1 ATTTTTTATAAAGAATTTATA
35179869 ATTTTTTATAATA-AATTTA
1 ATTTTTTATAA-AGAATTTA
35179888 GTAAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
ATTTTTTATAAAGAATTTATA
Found at i:35183763 original size:11 final size:11
Alignment explanation
Indices: 35183747--35183787 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
35183737 AATTAAACTT
35183747 TTATTTTTATA
1 TTATTTTTATA
*
35183758 TTATTTTTAAA
1 TTATTTTTATA
35183769 TATATTTTTATA
1 T-TATTTTTATA
35183781 TT-TTTTT
1 TTATTTTT
35183788 CATTCATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 5 0.19
11 12 0.44
12 10 0.37
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:35185657 original size:9 final size:9
Alignment explanation
Indices: 35185643--35185851 Score: 63
Period size: 9 Copynumber: 22.4 Consensus size: 9
35185633 GACATGTAGC
35185643 AAAAATATA
1 AAAAATATA
35185652 AAAAATA-A
1 AAAAATATA
35185660 AAAACA-ATA
1 AAAA-ATATA
**
35185669 AAAGTTATA
1 AAAAATATA
*
35185678 AAAATTATTA
1 AAAAATA-TA
***
35185688 AATTTTAATA
1 AAAAAT-ATA
*
35185698 AAAATTATA
1 AAAAATATA
*
35185707 AAAATTATTA
1 AAAAATA-TA
** *
35185717 AAATTTTATT
1 AAA-AATATA
35185727 AAAAAT-TAA
1 AAAAATAT-A
*
35185736 AAAAATTGTAA
1 AAAAA-TAT-A
35185747 AAAAATTATA
1 AAAAA-TATA
*
35185757 GAAAATAT-
1 AAAAATATA
*
35185765 AGAAATATA
1 AAAAATATA
35185774 AAAAATAT-
1 AAAAATATA
** *
35185782 AAATTTTTA
1 AAAAATATA
*
35185791 TAAAATCATA
1 AAAAAT-ATA
*
35185801 AGAACAT-TA
1 A-AAAATATA
35185810 TAAAAATATA
1 -AAAAATATA
35185820 AATAAATAT-
1 AA-AAATATA
*
35185829 AAAATTCATA
1 AAAAAT-ATA
35185839 AAAAATATA
1 AAAAATATA
35185848 AAAA
1 AAAA
35185852 TTATTGTATA
Statistics
Matches: 152, Mismatches: 29, Indels: 38
0.69 0.13 0.17
Matches are distributed among these distances:
8 21 0.14
9 69 0.45
10 43 0.28
11 19 0.12
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAAATATA
Found at i:35185697 original size:29 final size:30
Alignment explanation
Indices: 35185665--35185742 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
35185655 AATAAAAAAC
*
35185665 AATAAAAGTTATAAAAATTATT-AAATTTT
1 AATAAAAATTATAAAAATTATTAAAATTTT
35185694 AATAAAAATTATAAAAATTATTAAAATTTT
1 AATAAAAATTATAAAAATTATTAAAATTTT
* *
35185724 ATTAAAAATTAAAAAAATT
1 AATAAAAATTATAAAAATT
35185743 GTAAAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 21 0.47
30 24 0.53
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (30 bp):
AATAAAAATTATAAAAATTATTAAAATTTT
Found at i:35185818 original size:37 final size:36
Alignment explanation
Indices: 35185767--35185852 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 36
35185757 GAAAATATAG
***
35185767 AAATATAAAAAATATAAATTTTTATAAAA-TCATAAGA
1 AAATAT-AAAAATATAAATAAATATAAAATTCATAA-A
*
35185804 ACATTATAAAAATATAAATAAATATAAAATTCATAAA
1 A-AATATAAAAATATAAATAAATATAAAATTCATAAA
35185841 AAATATAAAAAT
1 AAATATAAAAAT
35185853 TATTGTATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
36 10 0.24
37 22 0.52
38 10 0.24
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.30
Consensus pattern (36 bp):
AAATATAAAAATATAAATAAATATAAAATTCATAAA
Found at i:35185905 original size:21 final size:20
Alignment explanation
Indices: 35185871--35185923 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 20
35185861 AAAAAGAAAC
35185871 ATTTTTA-TATTTTTCTATA
1 ATTTTTATTATTTTTCTATA
35185890 ATTTTTATTGATTTTT-T-T-
1 ATTTTTATT-ATTTTTCTATA
*
35185908 ATTTTTTTTATTTTTC
1 ATTTTTATTATTTTTC
35185924 GCCATATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 6 0.20
18 8 0.27
19 8 0.27
20 2 0.07
21 6 0.20
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (20 bp):
ATTTTTATTATTTTTCTATA
Found at i:35186059 original size:20 final size:20
Alignment explanation
Indices: 35186026--35186064 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35186016 TCAAAAGGTC
*
35186026 TTTTTGATGCATTTTATAAT
1 TTTTTGATGAATTTTATAAT
*
35186046 TTTTTTATGAATTTTATAA
1 TTTTTGATGAATTTTATAA
35186065 AATTTTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTTGATGAATTTTATAAT
Found at i:35186070 original size:20 final size:21
Alignment explanation
Indices: 35186026--35186070 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
35186016 TCAAAAGGTC
* *
35186026 TTTTTGATGCATTTTAT-AAT
1 TTTTTGATGAATTTTATAAAA
*
35186046 TTTTTTATGAATTTTATAAAA
1 TTTTTGATGAATTTTATAAAA
35186067 TTTT
1 TTTT
35186071 ACTTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTTTGATGAATTTTATAAAA
Found at i:35186142 original size:29 final size:28
Alignment explanation
Indices: 35186084--35186142 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
35186074 TTTTTTTTAA
* *
35186084 TAATTTTTAATAAAATATCAATATTTTT
1 TAATTTTTAATAAAATATCAATAATATT
*
35186112 TAATATTTTAATTAAAAT-TTAATAATATT
1 TAAT-TTTTAA-TAAAATATCAATAATATT
35186141 TA
1 TA
35186143 TAGCTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 16 0.62
30 6 0.23
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TAATTTTTAATAAAATATCAATAATATT
Found at i:35186590 original size:21 final size:22
Alignment explanation
Indices: 35186560--35186603 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
35186550 ATTGAGTGAA
**
35186560 AAAAAGATTTAATTATTTTTTT
1 AAAAAGATTTAAAGATTTTTTT
35186582 AAAAA-ATTTAAAGATTTTTTT
1 AAAAAGATTTAAAGATTTTTTT
35186603 A
1 A
35186604 CATAGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
AAAAAGATTTAAAGATTTTTTT
Found at i:35194881 original size:6 final size:6
Alignment explanation
Indices: 35194872--35194896 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35194862 CTCACAATCA
35194872 CATGGC CATGGC CATGGC CATGGC C
1 CATGGC CATGGC CATGGC CATGGC C
35194897 GACTGTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (6 bp):
CATGGC
Found at i:35195227 original size:13 final size:13
Alignment explanation
Indices: 35195209--35195235 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35195199 ATGCCTACTT
35195209 TCACGTGTATATA
1 TCACGTGTATATA
35195222 TCACGTGTATATA
1 TCACGTGTATATA
35195235 T
1 T
35195236 ATATATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TCACGTGTATATA
Found at i:35198870 original size:14 final size:14
Alignment explanation
Indices: 35198851--35198889 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
35198841 CAGTATATTC
35198851 AAAAAAAAATTAAA
1 AAAAAAAAATTAAA
*
35198865 AAAAAAACA-TAAA
1 AAAAAAAAATTAAA
35198878 AGAAAAAAAATT
1 A-AAAAAAAATT
35198890 GCTCAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 5 0.24
14 15 0.71
15 1 0.05
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAAAAAAATTAAA
Found at i:35200118 original size:26 final size:27
Alignment explanation
Indices: 35200089--35200143 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
35200079 AGGGAGAAGC
*
35200089 AAAAGAGAAAGGAAAAT-AAAGAAAAA
1 AAAAGAGAAAAGAAAATAAAAGAAAAA
** *
35200115 AAAAGTTAAAAGAACATAAAAGAAAAA
1 AAAAGAGAAAAGAAAATAAAAGAAAAA
35200142 AA
1 AA
35200144 TAAATTGCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (27 bp):
AAAAGAGAAAAGAAAATAAAAGAAAAA
Found at i:35201036 original size:14 final size:14
Alignment explanation
Indices: 35201017--35201043 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35201007 TTAAATATTT
35201017 TAATTTGATAAAAA
1 TAATTTGATAAAAA
35201031 TAATTTGATAAAA
1 TAATTTGATAAAA
35201044 TGTTAACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
TAATTTGATAAAAA
Found at i:35204617 original size:21 final size:23
Alignment explanation
Indices: 35204582--35204636 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
35204572 TACAAAAAAA
35204582 TTATTTAGTT-TATTTA-TAAATT
1 TTATTTA-TTATATTTAGTAAATT
* *
35204604 TTA-TTATTATATTTAGTTATTT
1 TTATTTATTATATTTAGTAAATT
35204626 TTATTTATTAT
1 TTATTTATTAT
35204637 TTAATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 9 0.32
22 10 0.36
23 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTATTTATTATATTTAGTAAATT
Found at i:35204638 original size:13 final size:13
Alignment explanation
Indices: 35204603--35204645 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
35204593 ATTTATAAAT
35204603 TTTATTA-TTATA
1 TTTATTATTTATA
*
35204615 TTTAGTTATTTTTA
1 TTTA-TTATTTATA
35204629 TTTATTATTTA-A
1 TTTATTATTTATA
35204641 TTTAT
1 TTTAT
35204646 AAATAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.37
13 9 0.33
14 8 0.30
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTATTATTTATA
Found at i:35205856 original size:17 final size:17
Alignment explanation
Indices: 35205836--35205874 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
35205826 TTTATTATAA
*
35205836 ATTATATTTTAAATATT
1 ATTATATATTAAATATT
*
35205853 ATTATATATTAATTATT
1 ATTATATATTAAATATT
*
35205870 TTTAT
1 ATTAT
35205875 TAATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTATATATTAAATATT
Found at i:35208835 original size:3 final size:3
Alignment explanation
Indices: 35208827--35208852 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35208817 CCTACTTGCT
35208827 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
35208853 TACCTTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:35211163 original size:24 final size:26
Alignment explanation
Indices: 35211135--35211191 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 26
35211125 CGAAGTACTT
35211135 AACAGAAGC-GCA-TAAGTGCTGGGA
1 AACAGAAGCAGCACTAAGTGCTGGGA
35211159 AACAGAAGCTAGCACGTAAGTGCTGGGA
1 AACAGAAGC-AGCAC-TAAGTGCTGGGA
35211187 AACAG
1 AACAG
35211192 TAGGCACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.31
26 3 0.10
28 17 0.59
ACGTcount: A:0.39, C:0.18, G:0.32, T:0.12
Consensus pattern (26 bp):
AACAGAAGCAGCACTAAGTGCTGGGA
Found at i:35211221 original size:22 final size:23
Alignment explanation
Indices: 35211186--35211241 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
35211176 AAGTGCTGGG
*
35211186 AAACAGTAGGCACACACAGTGCT
1 AAACAGTAAGCACACACAGTGCT
* *
35211209 GAACAG-AAGCACACATAGTGCT
1 AAACAGTAAGCACACACAGTGCT
35211231 AAACAGTAAGC
1 AAACAGTAAGC
35211242 GCGCTAGCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.12
Consensus pattern (23 bp):
AAACAGTAAGCACACACAGTGCT
Found at i:35218244 original size:106 final size:106
Alignment explanation
Indices: 35218129--35218325 Score: 274
Period size: 106 Copynumber: 1.9 Consensus size: 106
35218119 TATATTTTTT
** * *
35218129 ATATGTCAAATATTTAT-TTTTTTCAAT-TACATTGT-GAGTATGGTAAATTTTAATATTATAAA
1 ATATGTCAAATATCAATATATTTTC-ATCTACATTGTGGA-TATGATAAATTTTAATATT-TAAA
*
35218191 ATCAAATAATTATTTTAAACATCATTATTATTTTAATATGTAAA
63 ATCAAATAATTATTTCAAACATCATTATTATTTTAATATGTAAA
*
35218235 ATATTTCAAATATCAATATATTTTCATCTACATTGTGGATATGATAAATTTTAATATTTAAAATC
1 ATATGTCAAATATCAATATATTTTCATCTACATTGTGGATATGATAAATTTTAATATTTAAAATC
* *
35218300 AATTAATTATTTCAAATATCATTATT
66 AAATAATTATTTCAAACATCATTATT
35218326 CTTAATAAAT
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
106 46 0.57
107 32 0.40
108 2 0.03
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.47
Consensus pattern (106 bp):
ATATGTCAAATATCAATATATTTTCATCTACATTGTGGATATGATAAATTTTAATATTTAAAATC
AAATAATTATTTCAAACATCATTATTATTTTAATATGTAAA
Found at i:35226237 original size:21 final size:21
Alignment explanation
Indices: 35226211--35226254 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35226201 TAAAATAACT
35226211 ATAATTATA-CTAAAATTTAAA
1 ATAATTATATCTAAAA-TTAAA
*
35226232 ATAATTATATTTAAAATTAAA
1 ATAATTATATCTAAAATTAAA
35226253 AT
1 AT
35226255 CTAGTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATTATATCTAAAATTAAA
Found at i:35230865 original size:6 final size:6
Alignment explanation
Indices: 35230854--35230884 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
35230844 TAAAATGAAT
35230854 GAAATG GAAATG GAAATG GAAATG GAAATG G
1 GAAATG GAAATG GAAATG GAAATG GAAATG G
35230885 CAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.16
Consensus pattern (6 bp):
GAAATG
Found at i:35231581 original size:2 final size:2
Alignment explanation
Indices: 35231569--35231606 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
35231559 TTTACATACG
35231569 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35231607 TCTTTTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:35240151 original size:20 final size:20
Alignment explanation
Indices: 35240119--35240159 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
35240109 AGTTTTTTAT
35240119 AAAACTCAATTAAAATATTA
1 AAAACTCAATTAAAATATTA
*
35240139 AAAAC-CAACTTAAAATTTTA
1 AAAACTCAA-TTAAAATATTA
35240159 A
1 A
35240160 GCAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAACTCAATTAAAATATTA
Found at i:35240569 original size:82 final size:82
Alignment explanation
Indices: 35240432--35240672 Score: 383
Period size: 82 Copynumber: 2.9 Consensus size: 82
35240422 AAACCTCATA
* **
35240432 TGATGGTCTGATAATTAAAGGTGTTCTCCGTCTCAAATATGATCTGAATTTGAGTCGTGCTAGTC
1 TGATGGTATGATGGTTAAAGGTGTTCTCCGTCTCAAATATGATCTGAATTTGAGTCGTGCTAGTC
35240497 ATGTTTGTTGTTCCATG
66 ATGTTTGTTGTTCCATG
* * * *
35240514 TGATGGTATGATGGTTGAAGGTGTTCTCCGTCTCAAATATAATTTGAATTTGAGTCGTGTTAGTC
1 TGATGGTATGATGGTTAAAGGTGTTCTCCGTCTCAAATATGATCTGAATTTGAGTCGTGCTAGTC
35240579 ATGTTTGTTGTTCCATG
66 ATGTTTGTTGTTCCATG
* * * *
35240596 TGATGGTCTGATGGTTAAAGGTGTTTTCCGTCTCAGATATGATCTGAATTTGAGTCGTGCTAGTA
1 TGATGGTATGATGGTTAAAGGTGTTCTCCGTCTCAAATATGATCTGAATTTGAGTCGTGCTAGTC
35240661 ATGTTTGTTGTT
66 ATGTTTGTTGTT
35240673 TGAATTTTAT
Statistics
Matches: 144, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 144 1.00
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42
Consensus pattern (82 bp):
TGATGGTATGATGGTTAAAGGTGTTCTCCGTCTCAAATATGATCTGAATTTGAGTCGTGCTAGTC
ATGTTTGTTGTTCCATG
Found at i:35267977 original size:82 final size:82
Alignment explanation
Indices: 35267839--35268083 Score: 400
Period size: 82 Copynumber: 3.0 Consensus size: 82
35267829 ATAAAATTCA
* * *
35267839 AACAACAAACATTACTAGCACGACTCAAATTCAGATCATATCTGAGACGGAAAACACCTTTAACC
1 AACAACAAACATGACTAGCACGACTCAAATTCAGATCATATTTGAGACGGAGAACACCTTTAACC
35267904 ATCAGACCATCACATGG
66 ATCAGACCATCACATGG
* * * *
35267921 AACAACAAACATGACTAACACGACTCAAATTCAAATTATATTTGAGACGGAGAACACCTTCAACC
1 AACAACAAACATGACTAGCACGACTCAAATTCAGATCATATTTGAGACGGAGAACACCTTTAACC
*
35267986 ATCATACCATCACATGG
66 ATCAGACCATCACATGG
**
35268003 AACAACAAACATGACTAGCACGACTCAAATTCAGATCATATTTGAGACGGAGAACACCTTTAATT
1 AACAACAAACATGACTAGCACGACTCAAATTCAGATCATATTTGAGACGGAGAACACCTTTAACC
35268068 ATCAGACCATCACATG
66 ATCAGACCATCACATG
35268084 AGGTTTGATT
Statistics
Matches: 148, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 148 1.00
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.21
Consensus pattern (82 bp):
AACAACAAACATGACTAGCACGACTCAAATTCAGATCATATTTGAGACGGAGAACACCTTTAACC
ATCAGACCATCACATGG
Found at i:35268380 original size:20 final size:20
Alignment explanation
Indices: 35268352--35268398 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
35268342 AAATTATTGC
35268352 TTAAAATTTTAAGTTG-GTTT
1 TTAAAATTTTAA-TTGAGTTT
*
35268372 TTAATATTTTAATTGAGTTT
1 TTAAAATTTTAATTGAGTTT
35268392 TATAAAA
1 T-TAAAA
35268399 AACTGTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 16 0.70
21 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (20 bp):
TTAAAATTTTAATTGAGTTT
Found at i:35269651 original size:15 final size:15
Alignment explanation
Indices: 35269631--35269659 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35269621 GTGGGAGGGT
35269631 TAATGGATCCCGTGG
1 TAATGGATCCCGTGG
35269646 TAATGGATCCCGTG
1 TAATGGATCCCGTG
35269660 ACAGGCCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.28
Consensus pattern (15 bp):
TAATGGATCCCGTGG
Found at i:35272059 original size:25 final size:26
Alignment explanation
Indices: 35271989--35272053 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
35271979 AATTTAGTAG
*
35271989 TTAGTAGGTGAAAGATGAAGAGTTTT
1 TTAGTAGGTGAAAGATCAAGAGTTTT
*
35272015 TTAGTAGATGAAAGATCAAGAG-TTT
1 TTAGTAGGTGAAAGATCAAGAGTTTT
35272040 TTAGTAGGTGAAAG
1 TTAGTAGGTGAAAG
35272054 GCCAAGGGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 16 0.44
26 20 0.56
ACGTcount: A:0.37, C:0.02, G:0.29, T:0.32
Consensus pattern (26 bp):
TTAGTAGGTGAAAGATCAAGAGTTTT
Found at i:35276415 original size:25 final size:26
Alignment explanation
Indices: 35276358--35276422 Score: 114
Period size: 26 Copynumber: 2.5 Consensus size: 26
35276348 AATTTAGTAG
35276358 TTAGTAGGTGAAAGATCAAGAGTTTT
1 TTAGTAGGTGAAAGATCAAGAGTTTT
*
35276384 TTAGTAGATGAAAGATCAAGAG-TTT
1 TTAGTAGGTGAAAGATCAAGAGTTTT
35276409 TTAGTAGGTGAAAG
1 TTAGTAGGTGAAAG
35276423 GCTAAGGGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
25 16 0.43
26 21 0.57
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (26 bp):
TTAGTAGGTGAAAGATCAAGAGTTTT
Found at i:35279806 original size:29 final size:29
Alignment explanation
Indices: 35279774--35279875 Score: 80
Period size: 29 Copynumber: 3.4 Consensus size: 29
35279764 TCTTTTGGTT
35279774 ACTCAACTATCAATATTTTTAATTTGATC
1 ACTCAACTATCAATATTTTTAATTTGATC
*** * ** *
35279803 ACTCAACTATTGTTCCTTTTCTTTTTTGGTC
1 ACTCAACTATCAAT-ATTTT-TAATTTGATC
* *
35279834 AC-CAACTATTAATTTTTTTAATTTGATC
1 ACTCAACTATCAATATTTTTAATTTGATC
*
35279862 ACCCAACTAATCAA
1 ACTCAACT-ATCAA
35279876 GATTGTTTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
28 9 0.16
29 20 0.36
30 17 0.31
31 9 0.16
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (29 bp):
ACTCAACTATCAATATTTTTAATTTGATC
Found at i:35279862 original size:59 final size:60
Alignment explanation
Indices: 35279747--35279870 Score: 180
Period size: 59 Copynumber: 2.1 Consensus size: 60
35279737 TAGGTTACCT
* *
35279747 AACTATTGTCCATTTTCTCTTTTGGTTACTCAACTATCAATATTTTTAATTTGATCACTC
1 AACTATTGTCCATTTTCTCTTTTGGTCACTCAACTATCAATATTTTTAATTTGATCACCC
* * *
35279807 AACTATTGTTCC-TTTTCTTTTTTGGTCAC-CAACTATTAATTTTTTTAATTTGATCACCC
1 AACTATTG-TCCATTTTCTCTTTTGGTCACTCAACTATCAATATTTTTAATTTGATCACCC
35279866 AACTA
1 AACTA
35279871 ATCAAGATTG
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
59 32 0.55
60 23 0.40
61 3 0.05
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.48
Consensus pattern (60 bp):
AACTATTGTCCATTTTCTCTTTTGGTCACTCAACTATCAATATTTTTAATTTGATCACCC
Found at i:35280841 original size:30 final size:31
Alignment explanation
Indices: 35280807--35280872 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
35280797 TTATAGGTGG
*
35280807 GTGACC-AAAAATAAAAGTGG-TAATAGTTGA
1 GTGACCAAAAAATAAAAG-GGACAATAGTTGA
35280837 GTGACCAAAAAATAAAAGGGACAATAGTTGA
1 GTGACCAAAAAATAAAAGGGACAATAGTTGA
*
35280868 ATGAC
1 GTGAC
35280873 TTGTGGTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.20
Consensus pattern (31 bp):
GTGACCAAAAAATAAAAGGGACAATAGTTGA
Found at i:35282347 original size:15 final size:17
Alignment explanation
Indices: 35282322--35282353 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
35282312 TAGATTTTAA
35282322 GATTGAAAAATA-AAAT
1 GATTGAAAAATAGAAAT
35282338 GATT-AAAAATAGAAAT
1 GATTGAAAAATAGAAAT
35282354 TTCGGTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (17 bp):
GATTGAAAAATAGAAAT
Found at i:35287839 original size:15 final size:17
Alignment explanation
Indices: 35287818--35287858 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
35287808 TAATTTTTTA
35287818 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
35287834 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
35287850 AAAATTATA
1 AAAATTATA
35287859 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:35288219 original size:31 final size:31
Alignment explanation
Indices: 35288184--35288259 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
35288174 ATATAATCCC
** *
35288184 AAAAAATCAATTAAATTCTCTAAAAATAATT
1 AAAAAATCAATTAAACCCTCAAAAAATAATT
* * *
35288215 AAAAAAACAATTAAGCCCTGAAAAAATAATT
1 AAAAAATCAATTAAACCCTCAAAAAATAATT
35288246 AAAAAATCAATTAA
1 AAAAAATCAATTAA
35288260 TCTTTCACTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.62, C:0.11, G:0.03, T:0.25
Consensus pattern (31 bp):
AAAAAATCAATTAAACCCTCAAAAAATAATT
Found at i:35292044 original size:52 final size:51
Alignment explanation
Indices: 35291958--35292100 Score: 178
Period size: 52 Copynumber: 2.8 Consensus size: 51
35291948 ATTTCACTTC
* * ** *
35291958 ATTCATATACTCACGATGACACATAGCCACCAGACCTTATAATTTGCAAGGG
1 ATTCATATACTCACGATGACACATAGTCATCAGACCTT-TAATCCGCAAAGG
* *
35292010 ATTCATATACTCACGATGACACAGAGTCATCAGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCAGACCT-TTAATCCGCAAAGG
* * *
35292062 ATTCATATACTCATGATGACACTTAGTCATCGGACCTTT
1 ATTCATATACTCACGATGACACATAGTCATCAGACCTTT
35292101 TCGTTTATGG
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
51 2 0.03
52 76 0.96
53 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACATAGTCATCAGACCTTTAATCCGCAAAGG
Found at i:35295372 original size:27 final size:27
Alignment explanation
Indices: 35295337--35295390 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
35295327 TAAATGATAT
*
35295337 TTTTATT-AAATTATAATTA-TTTAATA
1 TTTTATTAAAATAAT-ATTATTTTAATA
35295363 TTTTATTTAAAATAATATTATTTTAATA
1 TTTTA-TTAAAATAATATTATTTTAATA
35295391 AGTAATATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.21
27 6 0.25
28 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTATTAAAATAATATTATTTTAATA
Found at i:35295385 original size:15 final size:18
Alignment explanation
Indices: 35295358--35295399 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
35295348 TATAATTATT
*
35295358 TAATATTTTATTTAA-AA-
1 TAATATTAT-TTTAATAAG
35295375 TAATATTATTTTAATAAG
1 TAATATTATTTTAATAAG
35295393 TAATATT
1 TAATATT
35295400 GTAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 10 0.45
18 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATATTATTTTAATAAG
Found at i:35297084 original size:20 final size:20
Alignment explanation
Indices: 35297045--35297083 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35297035 TTTTTAAAAA
35297045 ATAAAAATTTTAGATTTTTT
1 ATAAAAATTTTAGATTTTTT
*
35297065 ATAAATATTTTA-ATTTTTT
1 ATAAAAATTTTAGATTTTTT
35297084 TTGTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
ATAAAAATTTTAGATTTTTT
Found at i:35297497 original size:24 final size:22
Alignment explanation
Indices: 35297423--35297512 Score: 67
Period size: 24 Copynumber: 4.0 Consensus size: 22
35297413 AAAATAATTT
*
35297423 ATGATAATTATACATTTATAAATA
1 ATGATAATT-TA-ATTTAAAAATA
* * * *
35297447 CTTATAAATTAA--TAAAAATT
1 ATGATAATTTAATTTAAAAATA
35297467 ATGATAATTGTATATTTAAAAATA
1 ATGATAATT-TA-ATTTAAAAATA
* *
35297491 ATTATAATTTAATTTACAAATA
1 ATGATAATTTAATTTAAAAATA
35297513 TTACTTAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
20 12 0.24
21 2 0.04
22 12 0.24
23 4 0.08
24 21 0.41
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (22 bp):
ATGATAATTTAATTTAAAAATA
Found at i:35298968 original size:5 final size:5
Alignment explanation
Indices: 35298960--35298985 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
35298950 ACAGCATATG
35298960 GCCAT GCCAT GCCAT GCCAT GCCAT G
1 GCCAT GCCAT GCCAT GCCAT GCCAT G
35298986 GATGTGGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.23, T:0.19
Consensus pattern (5 bp):
GCCAT
Found at i:35315242 original size:14 final size:15
Alignment explanation
Indices: 35315223--35315254 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
35315213 AGCATAATCT
35315223 AAATTTTAATAA-AA
1 AAATTTTAATAATAA
35315237 AAA-TTTAATAATAA
1 AAATTTTAATAATAA
35315251 AAAT
1 AAAT
35315255 AAAGGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATTTTAATAATAA
Found at i:35315782 original size:5 final size:5
Alignment explanation
Indices: 35315772--35315806 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
35315762 GTTGCTATCA
35315772 CCCAT CCCAT CCCAT CCCAT CCCAT CCCAT CCCAT
1 CCCAT CCCAT CCCAT CCCAT CCCAT CCCAT CCCAT
35315807 TTAACAGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
CCCAT
Found at i:35316202 original size:41 final size:41
Alignment explanation
Indices: 35316157--35316279 Score: 149
Period size: 41 Copynumber: 3.0 Consensus size: 41
35316147 GAACACTAGT
*
35316157 GGCGTTTATGGGAAAAGCACCGCTAAAGGTTAAGCAATAGC
1 GGCGTTTATGAGAAAAGCACCGCTAAAGGTTAAGCAATAGC
* * * * * * *
35316198 GGCGTTTATAAGAAAA-CGCTGCTAAAGATCAGAACACTAGC
1 GGCGTTTATGAGAAAAGCACCGCTAAAGGTTA-AGCAATAGC
*
35316239 GGTGTTTATGAGAAAAGCACCGCTAAAGGTTAAGCAATAGC
1 GGCGTTTATGAGAAAAGCACCGCTAAAGGTTAAGCAATAGC
35316280 TGTGTTTTCC
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
40 11 0.17
41 42 0.66
42 11 0.17
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (41 bp):
GGCGTTTATGAGAAAAGCACCGCTAAAGGTTAAGCAATAGC
Found at i:35316265 original size:82 final size:82
Alignment explanation
Indices: 35316128--35316279 Score: 259
Period size: 82 Copynumber: 1.9 Consensus size: 82
35316118 TGTTTTCTTA
* * *
35316128 AAAACGCCGTTAAAGATCAGAACACTAGTGGCGTTTATGGGAAAAGCACCGCTAAAGGTTAAGCA
1 AAAACGCCGCTAAAGATCAGAACACTAGCGGCGTTTATGAGAAAAGCACCGCTAAAGGTTAAGCA
35316193 ATAGCGGCGTTTATAAG
66 ATAGCGGCGTTTATAAG
* *
35316210 AAAACGCTGCTAAAGATCAGAACACTAGCGGTGTTTATGAGAAAAGCACCGCTAAAGGTTAAGCA
1 AAAACGCCGCTAAAGATCAGAACACTAGCGGCGTTTATGAGAAAAGCACCGCTAAAGGTTAAGCA
35316275 ATAGC
66 ATAGC
35316280 TGTGTTTTCC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (82 bp):
AAAACGCCGCTAAAGATCAGAACACTAGCGGCGTTTATGAGAAAAGCACCGCTAAAGGTTAAGCA
ATAGCGGCGTTTATAAG
Found at i:35324164 original size:15 final size:15
Alignment explanation
Indices: 35324144--35324174 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35324134 ACAAAGCTTA
*
35324144 AAAATAAAAAATCCT
1 AAAATAAAAAAACCT
35324159 AAAATAAAAAAACCT
1 AAAATAAAAAAACCT
35324174 A
1 A
35324175 GCAGTTGTCT
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:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATAAAAAAACCT
Found at i:35324723 original size:25 final size:25
Alignment explanation
Indices: 35324673--35324724 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
35324663 TTCATGTCAT
*
35324673 TTTATTATAATCTCATTTATTATTA
1 TTTATTATAATCTCATTTATCATTA
* *
35324698 TTTATT-TAATTTGCATTTATCGTTA
1 TTTATTATAATCT-CATTTATCATTA
35324723 TT
1 TT
35324725 ATCTTGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.62
Consensus pattern (25 bp):
TTTATTATAATCTCATTTATCATTA
Found at i:35330536 original size:2 final size:2
Alignment explanation
Indices: 35330515--35330566 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
35330505 CAGATTCTAC
35330515 TA TA -A TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35330554 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
35330567 GCCCCAATAG
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:35333623 original size:17 final size:17
Alignment explanation
Indices: 35333580--35333624 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
35333570 TTTTTATATC
35333580 ATAAAAAT-TAAATTAA
1 ATAAAAATATAAATTAA
* * *
35333596 ATTAAATTATATATTAA
1 ATAAAAATATAAATTAA
35333613 ATAAAAATATAA
1 ATAAAAATATAA
35333625 TTCAATTCGG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAAATATAAATTAA
Found at i:35339791 original size:176 final size:176
Alignment explanation
Indices: 35339494--35339847 Score: 681
Period size: 176 Copynumber: 2.0 Consensus size: 176
35339484 GCTGATGATT
*
35339494 TAACTAATCGTGTCTCAACTACTAGCTACATTGGTTTGAATTTGGTAAGCTGTTTCTCAAGAAAC
1 TAACTAATCGTGTCTCAACTACTAGCTACATTAGTTTGAATTTGGTAAGCTGTTTCTCAAGAAAC
35339559 AGACACAATGGCTCGATCTTCCACCGAAGCCGAGTTGCAAAAGCCACATGGGAAACATATTCTCA
66 AGACACAATGGCTCGATCTTCCACCGAAGCCGAGTTGCAAAAGCCACATGGGAAACATATTCTCA
35339624 TACCAAGGCCACTGTGACAATGTTAGTGTCATAACCCAATCTTTTA
131 TACCAAGGCCACTGTGACAATGTTAGTGTCATAACCCAATCTTTTA
*
35339670 TAACTAATCGTGTCTCAACTACTAGCTACATTAGTTTGAATTTGGTAAGCTGTTTTTCAAGAAAC
1 TAACTAATCGTGTCTCAACTACTAGCTACATTAGTTTGAATTTGGTAAGCTGTTTCTCAAGAAAC
*
35339735 AGACACAATGGCTCGATCTTCCACCGAAGCCGAGTTGCAAAAGCCACATTGGAAACATATTCTCA
66 AGACACAATGGCTCGATCTTCCACCGAAGCCGAGTTGCAAAAGCCACATGGGAAACATATTCTCA
35339800 TACCAAGGCCACTGTGACAATGTTAGTGTCATAACCCAATCTTTTA
131 TACCAAGGCCACTGTGACAATGTTAGTGTCATAACCCAATCTTTTA
35339846 TA
1 TA
35339848 GCCGCATGCA
Statistics
Matches: 175, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
176 175 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (176 bp):
TAACTAATCGTGTCTCAACTACTAGCTACATTAGTTTGAATTTGGTAAGCTGTTTCTCAAGAAAC
AGACACAATGGCTCGATCTTCCACCGAAGCCGAGTTGCAAAAGCCACATGGGAAACATATTCTCA
TACCAAGGCCACTGTGACAATGTTAGTGTCATAACCCAATCTTTTA
Found at i:35341362 original size:18 final size:18
Alignment explanation
Indices: 35341327--35341364 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
35341317 TGAATTTTTA
*
35341327 AATTCGAATAACTCGAAT
1 AATTCGAATAACTAGAAT
35341345 AATTCGAATAAAC-AGAAT
1 AATTCGAAT-AACTAGAAT
35341363 AA
1 AA
35341365 AATTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.24
Consensus pattern (18 bp):
AATTCGAATAACTAGAAT
Found at i:35355609 original size:2 final size:2
Alignment explanation
Indices: 35355602--35355646 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
35355592 CCAAAATCTA
35355602 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
35355644 AT A
1 AT A
35355647 GTGGGATTAA
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:35356176 original size:17 final size:18
Alignment explanation
Indices: 35356135--35356173 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
35356125 ATTGCTTCTC
*
35356135 AAAAGTACTTTTGAGACA
1 AAAAGCACTTTTGAGACA
*
35356153 AAAAGCACTTTTGAGATA
1 AAAAGCACTTTTGAGACA
35356171 AAA
1 AAA
35356174 GCATTACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (18 bp):
AAAAGCACTTTTGAGACA
Found at i:35359446 original size:17 final size:17
Alignment explanation
Indices: 35359390--35359450 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
35359380 ATTTATATCT
35359390 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
* *
35359407 ATTAAATTTTACATT-TTGT
1 ATT--A-TTTATATTATTGA
*
35359426 ATTATTTATATTATTAA
1 ATTATTTATATTATTGA
35359443 ATTATTTA
1 ATTATTTA
35359451 ATCATGATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 7 0.20
17 14 0.40
19 7 0.20
20 7 0.20
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:35359585 original size:18 final size:19
Alignment explanation
Indices: 35359542--35359586 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
35359532 GGTATCAATT
*
35359542 TCACATTTTATCTTTAAAAA
1 TCACATTTTA-CTTAAAAAA
35359562 T-A-ATTTTA-TTAAAAAA
1 TCACATTTTACTTAAAAAA
35359578 TCACATTTT
1 TCACATTTT
35359587 TTACATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 8 0.36
17 1 0.05
18 11 0.50
19 1 0.05
20 1 0.05
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (19 bp):
TCACATTTTACTTAAAAAA
Found at i:35360207 original size:2 final size:2
Alignment explanation
Indices: 35360200--35360224 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35360190 CCACTTTTGC
35360200 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
35360225 TATTTAATTT
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:35364200 original size:29 final size:29
Alignment explanation
Indices: 35364145--35364201 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
35364135 ATTTTTATAT
* * *
35364145 TAAATAAATATAATTATTTGAATATAAAA
1 TAAATAAATATAAATATGTCAATATAAAA
35364174 TAAATAAATATAAAATATGTCAA-ATAAA
1 TAAATAAATAT-AAATATGTCAATATAAA
35364202 TAACAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (29 bp):
TAAATAAATATAAATATGTCAATATAAAA
Found at i:35369343 original size:51 final size:51
Alignment explanation
Indices: 35369262--35369426 Score: 187
Period size: 51 Copynumber: 3.2 Consensus size: 51
35369252 GTCCGATGAC
* *
35369262 TCATCGTGAGTAAATGAATCCTTTACGGATTAGAA-GTCTGATGACTAAGTG
1 TCATCGTGAGTAAATGAATCCATGACGGATTA-AAGGTCTGATGACTAAGTG
* *
35369313 TCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTCTGATGACTTAGTG
1 TCATCGTGAGTAAATGAATCCATGACGGATTAAAGGTCTGATGACTAAGTG
** *
35369364 TCATCGTGAGT--ATGAATTCCTAT-ACGGAACAAGAGGTCCGATGACTATA-TG
1 TCATCGTGAGTAAATGAA-TCC-ATGACGGATTAA-AGGTCTGATGACTA-AGTG
35369415 TCATCGTGAGTA
1 TCATCGTGAGTA
35369427 TTAAATAAAA
Statistics
Matches: 99, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
49 5 0.05
50 11 0.11
51 82 0.83
52 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
TCATCGTGAGTAAATGAATCCATGACGGATTAAAGGTCTGATGACTAAGTG
Found at i:35371860 original size:29 final size:29
Alignment explanation
Indices: 35371828--35371968 Score: 110
Period size: 29 Copynumber: 4.8 Consensus size: 29
35371818 TTCGAGGAAA
35371828 TTCGGGGTTAAAAATGGGATTTTGGAAGG
1 TTCGGGGTTAAAAATGGGATTTTGGAAGG
* ** *
35371857 TTCGAGGG-T-AAAATGGTAATTTTGTTAGA
1 TTCG-GGGTTAAAAATGG-GATTTTGGAAGG
** *
35371886 ACCGGGGTTAAAAATGGGATTTTGGAAAG
1 TTCGGGGTTAAAAATGGGATTTTGGAAGG
* * *
35371915 TTCGGGGGT-AAAATGGTAATTTTTGGATA-T
1 TTCGGGGTTAAAAATGG-GA-TTTTGGA-AGG
*
35371945 TTCGGGGTCAAAAATGGGATTTTG
1 TTCGGGGTTAAAAATGGGATTTTG
35371969 AAATGTTCAA
Statistics
Matches: 85, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
28 17 0.20
29 35 0.41
30 25 0.29
31 8 0.09
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (29 bp):
TTCGGGGTTAAAAATGGGATTTTGGAAGG
Found at i:35371870 original size:58 final size:58
Alignment explanation
Indices: 35371815--35371995 Score: 208
Period size: 58 Copynumber: 3.1 Consensus size: 58
35371805 GCAAAAATGA
*
35371815 AATTTCGAGGAAATTCGGGGTTAAAAATGGGATTTTGGAAGGTTCGAGGGTAAAATGGT
1 AATTT-GAGGAAATTCGGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGT
* *
35371874 AATTTTGTTA-G-AA-CCGGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGT
1 AA-TTTG--AGGAAATTCGGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGT
** * * *
35371932 AATTTTTGGATATTTCGGGGTCAAAAATGGGATTTT-GAAATGTTCAAGGGTAAAATGGT
1 AATTTGAGGA-AATTCGGGGTTAAAAATGGGATTTTGGAAA-GTTCGAGGGTAAAATGGT
35371991 AATTT
1 AATTT
35371996 TTGGATGTTT
Statistics
Matches: 104, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
56 1 0.01
57 3 0.03
58 49 0.47
59 46 0.44
60 4 0.04
61 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (58 bp):
AATTTGAGGAAATTCGGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGT
Found at i:35371968 original size:59 final size:59
Alignment explanation
Indices: 35371828--35372016 Score: 242
Period size: 59 Copynumber: 3.2 Consensus size: 59
35371818 TTCGAGGAAA
* *
35371828 TTCGGGGTTAAAAATGGGATTTTGGAAGGTTCGAGGGTAAAATGGTAATTTTGTTAGA-A-
1 TTCGGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGTAA-TTT-TTGGATAT
* *
35371887 -CCGGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGATAT
1 TTCGGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGATAT
* * *
35371945 TTCGGGGTCAAAAATGGGATTTT-GAAATGTTCAAGGGTAAAATGGTAATTTTTGGATGT
1 TTCGGGGTTAAAAATGGGATTTTGGAAA-GTTCGAGGGTAAAATGGTAATTTTTGGATAT
* *
35372004 TTCAGGATTAAAA
1 TTCGGGGTTAAAA
35372017 TGTAATTTTT
Statistics
Matches: 114, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
56 4 0.04
57 4 0.04
58 48 0.42
59 58 0.51
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (59 bp):
TTCGGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGATAT
Found at i:35371995 original size:29 final size:28
Alignment explanation
Indices: 35371896--35372025 Score: 79
Period size: 30 Copynumber: 4.5 Consensus size: 28
35371886 ACCGGGGTTA
* * *
35371896 AAAATGG-GATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTGGAAATTTC-AGGGT
* *
35371924 AAAATGGTAATTTTTGGATATTTCGGGGT
1 AAAATGGTAA-TTTTGGAAATTTCAGGGT
*
35371953 CAAAAATGG-GATTTT-GAAATGTTCAAGGGT
1 --AAAATGGTAATTTTGGAAAT-TTC-AGGGT
** *
35371983 AAAATGGTAATTTTTGGATGTTTCAGGATT
1 AAAATGGTAA-TTTTGGAAATTTCAGG-GT
35372013 AAAAT-GTAATTTT
1 AAAATGGTAATTTT
35372026 TTGAAGTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
28 22 0.27
29 21 0.26
30 29 0.35
31 10 0.12
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (28 bp):
AAAATGGTAATTTTGGAAATTTCAGGGT
Found at i:35372016 original size:30 final size:29
Alignment explanation
Indices: 35371923--35372026 Score: 81
Period size: 29 Copynumber: 3.6 Consensus size: 29
35371913 AGTTCGGGGG
* *
35371923 TAAAATGGTAATTTTTGGATATTTCGGGGT
1 TAAAATGGTAATTTTTGGATGTTTC-AGGT
* * * *
35371953 CAAAAATGG-GA-TTTTGAAATG-TTCAAGGG
1 -TAAAATGGTAATTTTTG-GATGTTTC-AGGT
35371982 TAAAATGGTAATTTTTGGATGTTTCAGGAT
1 TAAAATGGTAATTTTTGGATGTTTCAGG-T
35372012 TAAAAT-GTAATTTTT
1 TAAAATGGTAATTTTT
35372027 TGAAGTTTTG
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 7 0.12
29 26 0.46
30 17 0.30
31 7 0.12
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (29 bp):
TAAAATGGTAATTTTTGGATGTTTCAGGT
Found at i:35372797 original size:18 final size:18
Alignment explanation
Indices: 35372776--35372812 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35372766 ATTAAAACAT
*
35372776 TACTAATTATTATTATTA
1 TACTAATTATTACTATTA
*
35372794 TACTTATTATTACTATTA
1 TACTAATTATTACTATTA
35372812 T
1 T
35372813 TATTACTGTT
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:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (18 bp):
TACTAATTATTACTATTA
Found at i:35372802 original size:12 final size:12
Alignment explanation
Indices: 35372783--35372819 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
35372773 CATTACTAAT
35372783 TATTATTATTA-
1 TATTATTATTAC
35372794 TACTTATTATTAC
1 TA-TTATTATTAC
35372807 TATTATTATTAC
1 TATTATTATTAC
35372819 T
1 T
35372820 GTTAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:35373533 original size:18 final size:18
Alignment explanation
Indices: 35373510--35373544 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35373500 TGGGCCTATA
35373510 TTTTGTAATTAGACTTTC
1 TTTTGTAATTAGACTTTC
* *
35373528 TTTTGTAGTTGGACTTT
1 TTTTGTAATTAGACTTT
35373545 TTAATTTATA
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:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (18 bp):
TTTTGTAATTAGACTTTC
Found at i:35374329 original size:200 final size:201
Alignment explanation
Indices: 35373976--35374413 Score: 628
Period size: 200 Copynumber: 2.2 Consensus size: 201
35373966 TGACCTGGTC
* * * *
35373976 TTCTTCTTTGTGTCTCATCAGGAAGATGACCGCGAT-AATCTGTTTTAATTCGCTTCTCTGGATC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGC-CTCAATCTGTTTTAATTCGCTTATCTGGATC
* * *
35374040 TCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAACTAACCTTTTTATTGCT
65 TCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAACTAACCATTTTATTGCT
* * * * *
35374105 TCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTTGCTTGCGTTGAGCATTGA
130 TCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGATTCGAAGATTGGCTCGCGTTGAGCATTGA
35374170 GTTGATA
195 GTTGATA
* ** *
35374177 TTCTTCTCTGTATCTCATCAGTAAGATGACCGCCTCGCT-TGTTTTGATTCGCTTATCTGGATCT
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCAATCTGTTTTAATTCGCTTATCTGGATCT
* * *
35374241 CCTTAGGAAGACGAATCTGGTCTACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
66 CCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAACTAACCATTTTATTGCTT
* * *
35374306 CGACCTGCTTCTCAATGTCTCATCAAGAAGCTGGATTCGAAGATTGGCTCGTGTTGAGCGTTGAG
131 CGACCTGCTTCTCAATATCTCATCAAGAAGCTGGATTCGAAGATTGGCTCGCGTTGAGCATTGAG
* *
35374371 TTGGTG
196 TTGATA
*
35374377 TTCTTCTCTGTATCTCATCAGGAAGATTACCGCCTCA
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCA
35374414 CTATTTTATT
Statistics
Matches: 209, Mismatches: 27, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
200 178 0.85
201 31 0.15
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (201 bp):
TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCAATCTGTTTTAATTCGCTTATCTGGATCT
CCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAACTAACCATTTTATTGCTT
CGACCTGCTTCTCAATATCTCATCAAGAAGCTGGATTCGAAGATTGGCTCGCGTTGAGCATTGAG
TTGATA
Found at i:35386618 original size:29 final size:27
Alignment explanation
Indices: 35386578--35386678 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 27
35386568 TTTAGGGTTA
*
35386578 AAAATGGGATTTTGGAAGGTTCGGGGGT
1 AAAATGGAATTTTGGAA-GTTCGGGGGT
* *
35386606 AAAATGGTAATTTTTGGTGAA-ATCGGGGTT
1 AAAATGG-AA-TTTT-G-GAAGTTCGGGGGT
*
35386636 AAAAATGGGATTTTGGAAAGTTCGGGGGT
1 -AAAATGGAATTTTGG-AAGTTCGGGGGT
35386665 AAAATGGTAATTTT
1 AAAATGG-AATTTT
35386679 TGGATGTTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
27 1 0.02
28 17 0.29
29 17 0.29
30 12 0.21
31 8 0.14
32 3 0.05
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.33
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAGTTCGGGGGT
Found at i:35386618 original size:59 final size:59
Alignment explanation
Indices: 35386555--35386678 Score: 196
Period size: 59 Copynumber: 2.1 Consensus size: 59
35386545 ACAAAAATGA
* *
35386555 AATTTTAGG-GAAATTTAGGGTTAAAAATGGGATTTTGGAAGGTTCGGGGGTAAAATGGT
1 AATTTTAGGTGAAA-TCAGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGT
* *
35386614 AATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGT
1 AATTTTAGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGT
35386673 AATTTT
1 AATTTT
35386679 TGGATGTTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
59 56 0.93
60 4 0.07
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.34
Consensus pattern (59 bp):
AATTTTAGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGT
Found at i:35386632 original size:30 final size:30
Alignment explanation
Indices: 35386598--35386681 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 30
35386588 TTTGGAAGGT
35386598 TCGGGGGTAAAATGGTAATTTTTGGTGAAA-
1 TCGGGGGTAAAATGGTAATTTTTGG-GAAAG
* *
35386628 TCGGGGTTAAAAATGG-GA-TTTT-GGAAAG
1 TCGGGGGT-AAAATGGTAATTTTTGGGAAAG
35386656 TTCGGGGGTAAAATGGTAATTTTTGG
1 -TCGGGGGTAAAATGGTAATTTTTGG
35386682 ATGTTTCAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
27 4 0.09
28 8 0.18
29 12 0.27
30 12 0.27
31 8 0.18
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (30 bp):
TCGGGGGTAAAATGGTAATTTTTGGGAAAG
Found at i:35386682 original size:30 final size:30
Alignment explanation
Indices: 35386587--35386682 Score: 110
Period size: 30 Copynumber: 3.2 Consensus size: 30
35386577 AAAAATGGGA
*
35386587 TTTTGGAAGGTTCGGGGGTAAAATGGTAAT
1 TTTTGGAAAGTTCGGGGGTAAAATGGTAAT
* *
35386617 TTTTGGTGAAA--TCGGGGTTAAAAATGG-GA-
1 TTTT-G-GAAAGTTCGGGGGT-AAAATGGTAAT
35386646 TTTTGGAAAGTTCGGGGGTAAAATGGTAAT
1 TTTTGGAAAGTTCGGGGGTAAAATGGTAAT
35386676 TTTTGGA
1 TTTTGGA
35386683 TGTTTCAAGG
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
27 4 0.07
28 8 0.15
29 12 0.22
30 19 0.35
31 8 0.15
32 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.34, T:0.34
Consensus pattern (30 bp):
TTTTGGAAAGTTCGGGGGTAAAATGGTAAT
Found at i:35386722 original size:28 final size:29
Alignment explanation
Indices: 35386661--35386739 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 29
35386651 GAAAGTTCGG
35386661 GGGT-AAAATGGTAATTTTTGGATGTTTCA
1 GGGTCAAAAT-GTAATTTTTGGATGTTTCA
* * *
35386690 AGGTCAAAATGTAATTTTTTGA-GTTTTA
1 GGGTCAAAATGTAATTTTTGGATGTTTCA
* *
35386718 GGGTCAAAATATAATTTCTGGA
1 GGGTCAAAATGTAATTTTTGGA
35386740 CAGTTCAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 23 0.55
29 14 0.33
30 5 0.12
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.41
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTTGGATGTTTCA
Found at i:35387080 original size:31 final size:32
Alignment explanation
Indices: 35387015--35387080 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
35387005 TTACAGGGCT
* * *
35387015 AAATTAAAATAAATTAAAGTACAAAAGGGACC
1 AAATTAAAACAAATAAAAATACAAAAGGGACC
*
35387047 AAATTAAAACAAATAAAAATACAGAA-GGACC
1 AAATTAAAACAAATAAAAATACAAAAGGGACC
35387078 AAA
1 AAA
35387081 GCAATAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 8 0.27
32 22 0.73
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.15
Consensus pattern (32 bp):
AAATTAAAACAAATAAAAATACAAAAGGGACC
Found at i:35387790 original size:3 final size:3
Alignment explanation
Indices: 35387730--35387773 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
35387720 ATATTAAAAC
*
35387730 ATT ATT AATT ATT ATT ATT A-T ACTT ATT ATT ACT ATT ATT ATT A
1 ATT ATT -ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT A
35387774 CTGTTAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 29 0.81
4 5 0.14
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:35388489 original size:18 final size:18
Alignment explanation
Indices: 35388466--35388500 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35388456 TGGGCCTATA
*
35388466 TTTTGTAATTGGACTTTC
1 TTTTGTAATTGAACTTTC
*
35388484 TTTTGTAGTTGAACTTT
1 TTTTGTAATTGAACTTT
35388501 TTAATTTATA
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:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (18 bp):
TTTTGTAATTGAACTTTC
Found at i:35390225 original size:7 final size:7
Alignment explanation
Indices: 35390210--35390242 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
35390200 ATATTTTAGT
*
35390210 ATTGGAA
1 ATTGAAA
35390217 ATTGAAA
1 ATTGAAA
35390224 ATTGAAA
1 ATTGAAA
35390231 ATTGAAA
1 ATTGAAA
35390238 ATTGA
1 ATTGA
35390243 GTATTGAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (7 bp):
ATTGAAA
Found at i:35391227 original size:10 final size:10
Alignment explanation
Indices: 35391195--35391250 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
35391185 TATTGCTATT
35391195 TTTTTTGCTG
1 TTTTTTGCTG
35391205 TTTTTGATG-TG
1 TTTTT--TGCTG
35391216 TTTTTTGCTG
1 TTTTTTGCTG
* *
35391226 TTTTAGTGCTA
1 TTTT-TTGCTG
*
35391237 TTTTTTGTTG
1 TTTTTTGCTG
35391247 TTTT
1 TTTT
35391251 GGTATCTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
9 2 0.05
10 18 0.49
11 15 0.41
12 2 0.05
ACGTcount: A:0.05, C:0.05, G:0.20, T:0.70
Consensus pattern (10 bp):
TTTTTTGCTG
Found at i:35391242 original size:33 final size:32
Alignment explanation
Indices: 35391205--35391325 Score: 106
Period size: 33 Copynumber: 3.7 Consensus size: 32
35391195 TTTTTTGCTG
35391205 TTTTTGATGTGTTTT-TTGCTGTTTTAGTGCTAT
1 TTTTTG-T-TGTTTTGTTGCTGTTTTAGTGCTAT
* *
35391238 TTTTTGTTGTTTTGGTAT-CTGTTTTAGTGTTGT
1 TTTTTGTTGTTTT-GT-TGCTGTTTTAGTGCTAT
* *
35391271 TTTTTGTTGTTTTGGTGCTGCTTT--TGCTATT
1 TTTTTGTTGTTTTGTTGCTGTTTTAGTGCTA-T
*
35391302 ATTTTTGTTGTTGTTTTTGCTGTT
1 -TTTTTGTTGTT-TTGTTGCTGTT
35391326 GTTTTGATTG
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
30 3 0.04
31 8 0.11
32 19 0.26
33 41 0.57
34 1 0.01
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.66
Consensus pattern (32 bp):
TTTTTGTTGTTTTGTTGCTGTTTTAGTGCTAT
Found at i:35391274 original size:12 final size:11
Alignment explanation
Indices: 35391203--35391345 Score: 80
Period size: 11 Copynumber: 12.8 Consensus size: 11
35391193 TTTTTTTTGC
35391203 TGTTTTTGATG-
1 TGTTTTTG-TGT
*
35391214 TGTTTTT-TGC
1 TGTTTTTGTGT
* *
35391224 TGTTTTAGTGC
1 TGTTTTTGTGT
*
35391235 TATTTTT-TGT
1 TGTTTTTGTGT
* *
35391245 TGTTTTGGTAT
1 TGTTTTTGTGT
*
35391256 CTGTTTTAGTGT
1 -TGTTTTTGTGT
35391268 TGTTTTT-TGT
1 TGTTTTTGTGT
* *
35391278 TGTTTTGGTGC
1 TGTTTTTGTGT
* *
35391289 TGCTTTTGCTAT
1 TGTTTTTG-TGT
*
35391301 TATTTTTGTTGT
1 TGTTTTTG-TGT
35391313 TGTTTTTGCTGT
1 TGTTTTTG-TGT
35391325 TG-TTTTGATTGT
1 TGTTTTTG--TGT
35391337 TGTTTTTGT
1 TGTTTTTGT
35391346 TATTTAGATG
Statistics
Matches: 101, Mismatches: 23, Indels: 16
0.72 0.16 0.11
Matches are distributed among these distances:
9 2 0.02
10 22 0.22
11 37 0.37
12 35 0.35
13 5 0.05
ACGTcount: A:0.06, C:0.05, G:0.23, T:0.66
Consensus pattern (11 bp):
TGTTTTTGTGT
Found at i:35391330 original size:24 final size:23
Alignment explanation
Indices: 35391194--35391344 Score: 84
Period size: 21 Copynumber: 6.7 Consensus size: 23
35391184 ATATTGCTAT
* * *
35391194 TTTTTTTGCTGTTTTTGATG-TG
1 TTTTGTTGTTGTTTTTGCTGTTG
* * * *
35391216 TTTT-TTGCTGTTTTAG-TGCTA
1 TTTTGTTGTTGTTTTTGCTGTTG
* *
35391237 TTTT-TTGTTG-TTTTGGTATCTG
1 TTTTGTTGTTGTTTTTGCTGT-TG
35391259 TTTTAG-TGTTGTTTTT--TGTTG
1 TTTT-GTTGTTGTTTTTGCTGTTG
* * * * *
35391280 TTTTGGTGCTGCTTTTGCTATTAT
1 TTTTGTTGTTGTTTTTGCTGTT-G
35391304 TTTTGTTGTTGTTTTTGCTGTTG
1 TTTTGTTGTTGTTTTTGCTGTTG
35391327 TTTTGATTGTTGTTTTTG
1 TTTTG-TTGTTGTTTTTG
35391345 TTATTTAGAT
Statistics
Matches: 101, Mismatches: 17, Indels: 20
0.73 0.12 0.14
Matches are distributed among these distances:
20 7 0.07
21 36 0.36
22 11 0.11
23 13 0.13
24 34 0.34
ACGTcount: A:0.05, C:0.05, G:0.23, T:0.67
Consensus pattern (23 bp):
TTTTGTTGTTGTTTTTGCTGTTG
Found at i:35391340 original size:15 final size:12
Alignment explanation
Indices: 35391265--35391346 Score: 64
Period size: 12 Copynumber: 7.1 Consensus size: 12
35391255 TCTGTTTTAG
35391265 TGTTG-TTTT-T
1 TGTTGTTTTTGT
*
35391275 TGTTG-TTTTGG
1 TGTTGTTTTTGT
* * *
35391286 TGCTGCTTTTGC
1 TGTTGTTTTTGT
* *
35391298 TATTATTTTTGT
1 TGTTGTTTTTGT
*
35391310 TGTTGTTTTTGC
1 TGTTGTTTTTGT
35391322 TGTTG-TTTTGAT
1 TGTTGTTTTTG-T
35391334 TGTTGTTTTTGT
1 TGTTGTTTTTGT
35391346 T
1 T
35391347 ATTTAGATGT
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
10 9 0.16
11 9 0.16
12 33 0.59
13 5 0.09
ACGTcount: A:0.04, C:0.05, G:0.23, T:0.68
Consensus pattern (12 bp):
TGTTGTTTTTGT
Found at i:35391346 original size:33 final size:32
Alignment explanation
Indices: 35391238--35391346 Score: 96
Period size: 33 Copynumber: 3.2 Consensus size: 32
35391228 TTAGTGCTAT
* *
35391238 TTTTTGTTGTTTTGGTATCTGTTTT-AGTGTTG
1 TTTTTGTTGTTTTGGTGT-TGTTTTGATTGTTG
* *
35391270 TTTTTTGTTGTTTTGGTGCTGCTTTTGCTATTATT-
1 -TTTTTGTTGTTTTGGTGTTG-TTTTG--ATTGTTG
*
35391305 TTTGTTGTTGTTTTTGCTGTTGTTTTGATTGTTG
1 TTT-TTGTTG-TTTTGGTGTTGTTTTGATTGTTG
35391339 TTTTTGTT
1 TTTTTGTT
35391347 ATTTAGATGT
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
32 2 0.03
33 30 0.48
34 6 0.10
35 11 0.18
36 13 0.21
ACGTcount: A:0.05, C:0.05, G:0.23, T:0.68
Consensus pattern (32 bp):
TTTTTGTTGTTTTGGTGTTGTTTTGATTGTTG
Found at i:35393614 original size:27 final size:25
Alignment explanation
Indices: 35393564--35393614 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
35393554 CACGGGACAT
*
35393564 TAATTTCTTCTTCTTTTTTCTTCCA
1 TAATTTCTTCTTCTTTTATCTTCCA
35393589 TAATTTCTCTGCTCTCTTTTAT-TTCC
1 TAATTTCT-T-CT-TCTTTTATCTTCC
35393615 TTCCTTCTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 8 0.36
26 1 0.05
27 6 0.27
28 7 0.32
ACGTcount: A:0.12, C:0.25, G:0.02, T:0.61
Consensus pattern (25 bp):
TAATTTCTTCTTCTTTTATCTTCCA
Found at i:35394556 original size:26 final size:26
Alignment explanation
Indices: 35394522--35394572 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
35394512 CAAATCTTAA
*
35394522 ACCAAACTTTTCAAAATCACTTTTCC
1 ACCAAACTTTTCAAAAGCACTTTTCC
* *
35394548 ACCACACTTTTTAAAAGCACTTTTC
1 ACCAAACTTTTCAAAAGCACTTTTC
35394573 AAAAACAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.35
Consensus pattern (26 bp):
ACCAAACTTTTCAAAAGCACTTTTCC
Found at i:35395581 original size:20 final size:20
Alignment explanation
Indices: 35395529--35395606 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
35395519 CATCAAGGGT
*
35395529 ACGAGTGTGCAAATAGGGGC
1 ACGAGTGTGCAAACAGGGGC
** *
35395549 AC-CTTAGTACAAACAGGGGC
1 ACGAGT-GTGCAAACAGGGGC
*
35395569 ACGAGTGTGCAAACAGGGGT
1 ACGAGTGTGCAAACAGGGGC
* *
35395589 AGGAGTGTGCAAATAGGG
1 ACGAGTGTGCAAACAGGG
35395607 TACTTCATCT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.37, T:0.15
Consensus pattern (20 bp):
ACGAGTGTGCAAACAGGGGC
Found at i:35397434 original size:9 final size:9
Alignment explanation
Indices: 35397422--35397564 Score: 58
Period size: 9 Copynumber: 14.8 Consensus size: 9
35397412 ATTTAATATT
35397422 TTTTTATAA
1 TTTTTATAA
35397431 TTTTTATAA
1 TTTTTATAA
*
35397440 GTTTATATTAA
1 -TTTTTA-TAA
* *
35397451 TTTTAATAT
1 TTTTTATAA
35397460 TGTTTTAT-A
1 T-TTTTATAA
* *
35397469 TTATTTGTGA
1 TT-TTTATAA
35397479 TTTTTATAA
1 TTTTTATAA
*
35397488 TTTTTTTAA
1 TTTTTATAA
*
35397497 TAATTTTAT-G
1 T--TTTTATAA
35397507 TTTTTATAAA
1 TTTTTAT-AA
*
35397517 ATTTTA-AA
1 TTTTTATAA
*
35397525 TATTTTAAATA
1 T-TTTTATA-A
35397536 TGTTTTATTAA
1 T-TTTTA-TAA
35397547 TTTGATTATAA
1 TTT--TTATAA
*
35397558 GTTTTAT
1 TTTTTAT
35397565 TTTTTTTAGT
Statistics
Matches: 101, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
8 9 0.09
9 40 0.40
10 26 0.26
11 22 0.22
12 4 0.04
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:35397436 original size:20 final size:20
Alignment explanation
Indices: 35397391--35397503 Score: 67
Period size: 20 Copynumber: 5.7 Consensus size: 20
35397381 TTATTAGATT
* *
35397391 TTTTTAATAAATTTTTATAG
1 TTTTTAATAATTTTTTATAA
* *
35397411 TATTTAATATTTTTTTATAA
1 TTTTTAATAATTTTTTATAA
* *
35397431 TTTTT-ATAAGTTTATATTAA
1 TTTTTAATAATTTTTTA-TAA
35397451 -TTTTAAT-ATTGTTTTAT-A
1 TTTTTAATAATT-TTTTATAA
* *
35397469 TTATTT-GTGA-TTTTTATAA
1 TT-TTTAATAATTTTTTATAA
35397488 TTTTTTTAATAATTTT
1 --TTTTTAATAATTTT
35397504 ATGTTTTTAT
Statistics
Matches: 69, Mismatches: 13, Indels: 20
0.68 0.13 0.20
Matches are distributed among these distances:
18 7 0.10
19 19 0.28
20 36 0.52
21 4 0.06
22 3 0.04
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTTAATAATTTTTTATAA
Found at i:35397521 original size:28 final size:27
Alignment explanation
Indices: 35397479--35397531 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
35397469 TTATTTGTGA
** *
35397479 TTTTTATAATTTTTTTAATAATTTTATG
1 TTTTTATAAAATTTTAAAT-ATTTTATG
35397507 TTTTTATAAAATTTTAAATATTTTA
1 TTTTTATAAAATTTTAAATATTTTA
35397532 AATATGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTTATAAAATTTTAAATATTTTATG
Found at i:35406962 original size:23 final size:25
Alignment explanation
Indices: 35406911--35406963 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
35406901 TTTAAAATTT
*
35406911 TAATGATTCTTTATTTTTTTTGTTGAA
1 TAATGATTCTTTA--TTTTTTGTTAAA
35406938 TAATGATTCTTTA-TTTTT-TTAAA
1 TAATGATTCTTTATTTTTTGTTAAA
35406961 TAA
1 TAA
35406964 CTTTTCTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 7 0.28
24 5 0.20
27 13 0.52
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (25 bp):
TAATGATTCTTTATTTTTTGTTAAA
Found at i:35410548 original size:23 final size:22
Alignment explanation
Indices: 35410521--35410578 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 22
35410511 TATATATCAA
*
35410521 TTTGGG-TTTAGATATTAATGGG
1 TTTGGGTTTTA-AAATTAATGGG
35410543 TATTGGGTTTTAAAATTAATGGG
1 T-TTGGGTTTTAAAATTAATGGG
35410566 TTTGGGCTTTTAA
1 TTTGGG-TTTTAA
35410579 GAGTATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 6 0.19
23 22 0.69
24 4 0.12
ACGTcount: A:0.24, C:0.02, G:0.28, T:0.47
Consensus pattern (22 bp):
TTTGGGTTTTAAAATTAATGGG
Found at i:35410748 original size:18 final size:18
Alignment explanation
Indices: 35410703--35410749 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
35410693 TAAAATGTCA
35410703 AAATAG-AAAA-TAAATC
1 AAATAGAAAAATTAAATC
35410719 AAATA-AATAAATTAAATC
1 AAATAGAA-AAATTAAATC
35410737 AAATAGAAAAATT
1 AAATAGAAAAATT
35410750 GATTAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.22
17 3 0.11
18 16 0.59
19 2 0.07
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.23
Consensus pattern (18 bp):
AAATAGAAAAATTAAATC
Done.