Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 130 of 240
Found at i:40401527 original size:111 final size:110
Alignment explanation
Indices: 40401364--40401690 Score: 539
Period size: 110 Copynumber: 3.0 Consensus size: 110
40401354 GAAATTCGAG
* * *
40401364 AGGATATTTGGCTATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTCCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTCCTC
* *
40401429 AAATTTCCCAAATGCAAAACATTGCCTTATTTCGAAAATTTTTAAA
66 GAATTTCCCAAACGCAAAACATTGCCTTATTT-GAAAATTTTTAAA
40401475 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACG-TTCTCT
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTC-CT
40401539 CGAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTAAA
65 CGAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTAAA
* * * *
40401585 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCGCATTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTCCTC
*
40401650 GAATTTTCCAAACGCAAAACATTGCCTTATTTGAAAATTTT
66 GAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAATTTT
40401691 GTTTTTGATA
Statistics
Matches: 204, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
110 114 0.56
111 90 0.44
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (110 bp):
AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTCCTC
GAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTAAA
Found at i:40402049 original size:39 final size:39
Alignment explanation
Indices: 40401998--40402072 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
40401988 AAGCATATAC
* *
40401998 ATATATATATATATGTAACTATCATAAAATAAAAAGTAT
1 ATATATAGATATATGTAACAATCATAAAATAAAAAGTAT
** *
40402037 ATATATAGATATATGTATGAATCATAAAATATAAAG
1 ATATATAGATATATGTAACAATCATAAAATAAAAAG
40402073 AACACATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (39 bp):
ATATATAGATATATGTAACAATCATAAAATAAAAAGTAT
Found at i:40402082 original size:39 final size:39
Alignment explanation
Indices: 40402000--40402082 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
40401990 GCATATACAT
* * * * *
40402000 ATATATATATATGTAACTATCATAAAATAAAAAGTATAT
1 ATATAGATATATGTAACAATCATAAAATAAAAAGAACAC
** *
40402039 ATATAGATATATGTATGAATCATAAAATATAAAGAACAC
1 ATATAGATATATGTAACAATCATAAAATAAAAAGAACAC
40402078 ATATA
1 ATATA
40402083 TAAAATAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (39 bp):
ATATAGATATATGTAACAATCATAAAATAAAAAGAACAC
Found at i:40402180 original size:25 final size:25
Alignment explanation
Indices: 40402123--40402187 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
40402113 GTAAGTGTAC
* *
40402123 ATATATAT-TACAAAAAGTATGTGT
1 ATATATATATACAAAAAATATATGT
*
40402147 GTA-AGTATATACAAAAAATATATGT
1 ATATA-TATATACAAAAAATATATGT
40402172 ATATATATATA-AAAAA
1 ATATATATATACAAAAA
40402188 CGTATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 1 0.03
24 10 0.29
25 22 0.65
26 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (25 bp):
ATATATATATACAAAAAATATATGT
Found at i:40402197 original size:23 final size:23
Alignment explanation
Indices: 40402152--40402197 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40402142 TGTGTGTAAG
* *
40402152 TATATACAAAAAATATATGTATA
1 TATATACAAAAAACATATATATA
* *
40402175 TATATATAAAAAACGTATATATA
1 TATATACAAAAAACATATATATA
40402198 AGGGCAATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
TATATACAAAAAACATATATATA
Found at i:40402271 original size:3 final size:3
Alignment explanation
Indices: 40402209--40402254 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
40402199 GGGCAATTAC
* *
40402209 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40402255 TTATTAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:40404723 original size:22 final size:22
Alignment explanation
Indices: 40404698--40404793 Score: 100
Period size: 19 Copynumber: 4.6 Consensus size: 22
40404688 TACAAATTAA
* *
40404698 ATCTTTAAGATTACAAAATCAT
1 ATCTTTAAGATTGCAATATCAT
40404720 ATCTTTTAAGATTGC-ATATCAT
1 ATC-TTTAAGATTGCAATATCAT
40404742 ATC--TAAGATTGCATATATCAT
1 ATCTTTAAGATTGCA-ATATCAT
40404763 ATC--TAAGATTGC-ATATCAT
1 ATCTTTAAGATTGCAATATCAT
40404782 ATC--TAAGATTGC
1 ATCTTTAAGATTGC
40404794 CTATCCTTGA
Statistics
Matches: 69, Mismatches: 2, Indels: 9
0.86 0.03 0.11
Matches are distributed among these distances:
19 28 0.41
21 19 0.28
22 12 0.17
23 10 0.14
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
ATCTTTAAGATTGCAATATCAT
Found at i:40404731 original size:23 final size:22
Alignment explanation
Indices: 40404688--40404745 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40404678 AAAGGGTATC
* *
40404688 TACAAATTAAATC-TTTAAGAT
1 TACAAATCATATCTTTTAAGAT
40404709 TACAAAATCATATCTTTTAAGAT
1 TAC-AAATCATATCTTTTAAGAT
* *
40404732 TGCATATCATATCT
1 TACAAATCATATCT
40404746 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (22 bp):
TACAAATCATATCTTTTAAGAT
Found at i:40404761 original size:21 final size:19
Alignment explanation
Indices: 40404726--40404798 Score: 119
Period size: 19 Copynumber: 3.7 Consensus size: 19
40404716 TCATATCTTT
40404726 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
40404745 TAAGATTGCATATATCATATC
1 TAAGATTGC--ATATCATATC
40404766 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
*
40404785 TAAGATTGCCTATC
1 TAAGATTGCATATC
40404799 CTTGAAGATT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 32 0.63
21 19 0.37
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TAAGATTGCATATCATATC
Found at i:40407645 original size:17 final size:17
Alignment explanation
Indices: 40407623--40407656 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40407613 TAAAAAAATT
40407623 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
40407640 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
40407657 ACTAGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTTAAAA
Found at i:40407654 original size:11 final size:11
Alignment explanation
Indices: 40407561--40407657 Score: 69
Period size: 11 Copynumber: 8.6 Consensus size: 11
40407551 AAAATACAAA
40407561 TTAAAAAAGTATT
1 TTAAAAAA--ATT
*
40407574 TTAAAAATATT
1 TTAAAAAAATT
**
40407585 TTAAAATTAAAAAA
1 TT-AAA--AAAATT
40407599 TTAAAAAAGTATT
1 TTAAAAAA--ATT
40407612 TTAAAAAAATT
1 TTAAAAAAATT
40407623 TTAAAAAAATT
1 TTAAAAAAATT
40407634 TT---AAAA--
1 TTAAAAAAATT
40407640 TTAAAAAAATT
1 TTAAAAAAATT
40407651 TTAAAAA
1 TTAAAAA
40407658 CTAGTATTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
6 2 0.03
8 4 0.06
9 4 0.06
11 31 0.46
12 3 0.04
13 19 0.28
14 5 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
TTAAAAAAATT
Found at i:40409255 original size:50 final size:50
Alignment explanation
Indices: 40409192--40409345 Score: 146
Period size: 50 Copynumber: 3.0 Consensus size: 50
40409182 ACATGAGAGT
* * * *
40409192 TCTCATATAGGTGCCCATGCCGTGTCCCAGACATGGTCTTACGGGGGACC
1 TCTCATATAGGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACC
* * * *
40409242 TCTCATCTTGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATC
1 TCTCATATAGGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACC
* * * *
40409292 TCTCATAATCTCAATGATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA
1 TCTCAT-A--T--A-GGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGA
40409346 TCTCATCCTC
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 48 0.56
53 1 0.01
56 36 0.42
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TCTCATATAGGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACC
Found at i:40409314 original size:56 final size:52
Alignment explanation
Indices: 40409214--40409349 Score: 168
Period size: 56 Copynumber: 2.6 Consensus size: 52
40409204 GCCCATGCCG
** * *
40409214 TGTCCCAGACATGGTCTTACGGGGGA-C-CTCTCATCTTGGTGCCAACGCCA
1 TGTCCCAGACATGGTCTTACATGGGATCTCTCTAATCTTGATGCCAACGCCA
*
40409264 TGTCCCAGACATGGTCTTACATGGGATCTCTCATAATCTCAATGATGCCAATGCCA
1 TGTCCCAGACATGGTCTTACATGGGATCTCTC-TAATCT---TGATGCCAACGCCA
*
40409320 TGTCCCAAACATGGTCTTACATGGGATCTC
1 TGTCCCAGACATGGTCTTACATGGGATCTC
40409350 ATCCTCTTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
50 24 0.32
51 1 0.01
52 3 0.04
53 5 0.07
56 41 0.55
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (52 bp):
TGTCCCAGACATGGTCTTACATGGGATCTCTCTAATCTTGATGCCAACGCCA
Found at i:40415490 original size:50 final size:50
Alignment explanation
Indices: 40415365--40415657 Score: 223
Period size: 50 Copynumber: 5.8 Consensus size: 50
40415355 TGAATATAAC
* * * * * * *
40415365 ATGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGA-TGTTTCTTGTA-
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACT-TCTCATATAG
* * * * * *
40415414 CTGCCAATGCCATATCCTAAATATGGTCTTACATGAGAGTTCTCATATAG
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACTTCTCATATAG
* * * ** * * *
40415464 GTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTG
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACTTCTCATATAG
* * * * * *
40415514 ATGCCAACGCCATGTCCCAAACATGGTCTTACATGTGACCTCTTATCTCG
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACTTCTCATATAG
* * *
40415564 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-TCTCTCATAATCTCAATG
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACT-TCTCAT-A--T--A-G
40415620 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA
40415658 TCTCATCTTC
Statistics
Matches: 191, Mismatches: 44, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
49 35 0.18
50 119 0.62
53 1 0.01
56 36 0.19
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACTTCTCATATAG
Found at i:40415540 original size:100 final size:104
Alignment explanation
Indices: 40415415--40415654 Score: 299
Period size: 100 Copynumber: 2.3 Consensus size: 104
40415405 TTTCTTGTAC
* * * ** * *
40415415 TGCCAATGCCATATCCTAAATATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGCCATGTC
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTC
* *
40415480 CCAGACATGGTCTTACGGGGGA-C-CTC-TCATCT-TGA
66 CCAGACATGGTCTTACAGGGGATCTCTCATAATCTATGA
* * * * *
40415515 TGCCAACGCCATGTCCCAAACATGGTCTTACATGTGACCTCTTATCTCGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTC
*
40415580 CCAGACATGGTCTTACATGGGATCTCTCATAATCTCAATGA
66 CCAGACATGGTCTTACAGGGGATCTCTCATAATCT--ATGA
40415621 TGCCAATGCCATGTCCCAAACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATG
40415655 GGATCTCATC
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
100 73 0.62
101 1 0.01
102 3 0.03
103 5 0.04
106 36 0.31
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (104 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTC
CCAGACATGGTCTTACAGGGGATCTCTCATAATCTATGA
Found at i:40415661 original size:56 final size:51
Alignment explanation
Indices: 40415472--40415657 Score: 232
Period size: 50 Copynumber: 3.6 Consensus size: 51
40415462 AGGTGCCCAT
* ** *
40415472 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCT-TGATGCCAAC
1 GCCATGTCCCAAACATGGTCTTACATGGGACCTCTAATCTCTGATGCCAAC
* * *
40415522 GCCATGTCCCAAACATGGTCTTACATGTGACCTCTTATCTC-GGTGCCAAC
1 GCCATGTCCCAAACATGGTCTTACATGGGACCTCTAATCTCTGATGCCAAC
* *
40415572 GCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATAATCTCAATGATGCCAAT
1 GCCATGTCCCAAACATGGTCTTACATGGGA-C-CTC-TAATCTC--TGATGCCAAC
40415628 GCCATGTCCCAAACATGGTCTTACATGGGA
1 GCCATGTCCCAAACATGGTCTTACATGGGA
40415658 TCTCATCTTC
Statistics
Matches: 117, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
50 71 0.61
51 1 0.01
52 3 0.03
53 6 0.05
56 36 0.31
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (51 bp):
GCCATGTCCCAAACATGGTCTTACATGGGACCTCTAATCTCTGATGCCAAC
Found at i:40423555 original size:18 final size:18
Alignment explanation
Indices: 40423528--40423563 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40423518 TTTTAAATAC
*
40423528 TTTTTATGAAAATAATTA
1 TTTTTATGAAAAGAATTA
*
40423546 TTTTTTTGAAAAGAATTA
1 TTTTTATGAAAAGAATTA
40423564 CAAAAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (18 bp):
TTTTTATGAAAAGAATTA
Found at i:40428061 original size:20 final size:20
Alignment explanation
Indices: 40428026--40428063 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40428016 GATGCATAAT
* *
40428026 AGAGGCACCGATGTGCAACC
1 AGAGGCACCAAAGTGCAACC
40428046 AGAGGCACCAAAGTGCAA
1 AGAGGCACCAAAGTGCAA
40428064 ACCTCGTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.26, G:0.29, T:0.08
Consensus pattern (20 bp):
AGAGGCACCAAAGTGCAACC
Found at i:40435056 original size:33 final size:33
Alignment explanation
Indices: 40435019--40435082 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
40435009 AAATGGTAAG
40435019 TTTTATATGTTGTGATAAT-A-TGAAATGTTTAAA
1 TTTTATAT-TTGT-ATAATAAGTGAAATGTTTAAA
*
40435052 TTTTATGTTTGTATAATAAGTGAAATGTTTA
1 TTTTATATTTGTATAATAAGTGAAATGTTTA
40435083 GAAATTGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 5 0.18
32 5 0.18
33 18 0.64
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (33 bp):
TTTTATATTTGTATAATAAGTGAAATGTTTAAA
Found at i:40436593 original size:16 final size:17
Alignment explanation
Indices: 40436566--40436603 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
40436556 AAAAGTAACA
40436566 ACATATTAATGTGGTTT
1 ACATATTAATGTGGTTT
40436583 ACATA-TAATGTGGTTT
1 ACATATTAATGTGGTTT
40436599 ACATA
1 ACATA
40436604 GCAAGCGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (17 bp):
ACATATTAATGTGGTTT
Found at i:40451942 original size:18 final size:18
Alignment explanation
Indices: 40451909--40451943 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40451899 AAAAATCATA
40451909 AATAATTTAAAATATTTC
1 AATAATTTAAAATATTTC
40451927 AATAATTTAAAATATTT
1 AATAATTTAAAATATTT
40451944 GTAAACTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAATTTAAAATATTTC
Found at i:40452381 original size:13 final size:13
Alignment explanation
Indices: 40452363--40452387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40452353 AAATGGAAGA
40452363 GAAAGTAAGCAAG
1 GAAAGTAAGCAAG
40452376 GAAAGTAAGCAA
1 GAAAGTAAGCAA
40452388 TCATGAAAGT
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:0.56, C:0.08, G:0.28, T:0.08
Consensus pattern (13 bp):
GAAAGTAAGCAAG
Found at i:40455197 original size:19 final size:19
Alignment explanation
Indices: 40455173--40455254 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
40455163 CACATACGTG
*
40455173 CCCCTGTTGTACTTCGGTA
1 CCCCTGTTGTACTTCAGTA
* * * *
40455192 CCCCTGATGCACATGC-GTG
1 CCCCTGTTGTAC-TTCAGTA
*
40455211 CCCCTGTTGTACTTCAGTG
1 CCCCTGTTGTACTTCAGTA
*
40455230 CCCCTATTGTACTTCAGTA
1 CCCCTGTTGTACTTCAGTA
40455249 CCCCTG
1 CCCCTG
40455255 ATGCACATAC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
18 2 0.04
19 47 0.92
20 2 0.04
ACGTcount: A:0.13, C:0.35, G:0.20, T:0.32
Consensus pattern (19 bp):
CCCCTGTTGTACTTCAGTA
Found at i:40455203 original size:38 final size:38
Alignment explanation
Indices: 40455159--40455234 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
40455149 AATTATACCC
*
40455159 GATGCACATACGTGCCCCTGTTGTACTTCGGTACCCCT
1 GATGCACATACGTGCCCCTGTTGTACTTCAGTACCCCT
* *
40455197 GATGCACATGCGTGCCCCTGTTGTACTTCAGTGCCCCT
1 GATGCACATACGTGCCCCTGTTGTACTTCAGTACCCCT
40455235 ATTGTACTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.14, C:0.34, G:0.22, T:0.29
Consensus pattern (38 bp):
GATGCACATACGTGCCCCTGTTGTACTTCAGTACCCCT
Found at i:40455430 original size:43 final size:43
Alignment explanation
Indices: 40455382--40455680 Score: 363
Period size: 43 Copynumber: 7.0 Consensus size: 43
40455372 TTTGCGGTGT
* *
40455382 TTTTCCCACAAACGCCGCTATAGACCATGACTTTTAGCGGCGC
1 TTTTCCCACAAACGCCGCTATAGACCAAGACCTTTAGCGGCGC
* * * *
40455425 TTTT-CCACAAACGCCGCTACAGATCAAGACCTTTAACGGCAC
1 TTTTCCCACAAACGCCGCTATAGACCAAGACCTTTAGCGGCGC
* ** *
40455467 TTTTCCCCCAAACGCCGCTATAGACCGTGACCTTTAGCGGCAC
1 TTTTCCCACAAACGCCGCTATAGACCAAGACCTTTAGCGGCGC
* * *
40455510 TTTTACCACAAACGCTGCTATAGACCAAGACCTTTAGCGACGC
1 TTTTCCCACAAACGCCGCTATAGACCAAGACCTTTAGCGGCGC
* * * * *
40455553 TTTTTCCACAAATGCCACTATAGATCTAGACCTTTAGCGGCGC
1 TTTTCCCACAAACGCCGCTATAGACCAAGACCTTTAGCGGCGC
*
40455596 -TTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGC
1 TTTTCCCACAAACGCCGCTATAGACCAAGACCTTTAGCGGCGC
* * * *
40455638 TTTT-TCACAAAAGCCGCTATAGAACAA-ACCTTTAGCGACGC
1 TTTTCCCACAAACGCCGCTATAGACCAAGACCTTTAGCGGCGC
40455679 TT
1 TT
40455681 CTCGCTAAAA
Statistics
Matches: 220, Mismatches: 34, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
41 15 0.07
42 94 0.43
43 111 0.50
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (43 bp):
TTTTCCCACAAACGCCGCTATAGACCAAGACCTTTAGCGGCGC
Found at i:40455491 original size:85 final size:84
Alignment explanation
Indices: 40455382--40455680 Score: 375
Period size: 85 Copynumber: 3.5 Consensus size: 84
40455372 TTTGCGGTGT
* *
40455382 TTTTCCCACAAACGCCGCTATAGACCATGACTTTTAGCGGCGCTTTTCCACAAACGCCGCTACAG
1 TTTTCCCACAAACGCCGCTATAGACC-TGACCTTTAGCGGCGCTTTTCCACAAACGCCGCTATAG
* *
40455447 ATCAAGACCTTTAACGGCAC
65 ATCAAGACCTTTAGCGGCGC
* * *
40455467 TTTTCCCCCAAACGCCGCTATAGACCGTGACCTTTAGCGGCACTTTTACCACAAACGCTGCTATA
1 TTTTCCCACAAACGCCGCTATAGACC-TGACCTTTAGCGGCGCTTTT-CCACAAACGCCGCTATA
* *
40455532 GACCAAGACCTTTAGCGACGC
64 GATCAAGACCTTTAGCGGCGC
* * * * *
40455553 TTTTTCCACAAATGCCACTATAGATCTAGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTATAG
1 TTTTCCCACAAACGCCGCTATAGACCT-GACCTTTAGCGGCGCTTTTCCACAAACGCCGCTATAG
40455618 ATCAAGACCTTTAGCGGCGC
65 ATCAAGACCTTTAGCGGCGC
* * * ** *
40455638 TTTT-TCACAAAAGCCGCTATAGAACAAACCTTTAGCGACGCTT
1 TTTTCCCACAAACGCCGCTATAGACCTGACCTTTAGCGGCGCTT
40455681 CTCGCTAAAA
Statistics
Matches: 185, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
83 15 0.08
84 17 0.09
85 83 0.45
86 70 0.38
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (84 bp):
TTTTCCCACAAACGCCGCTATAGACCTGACCTTTAGCGGCGCTTTTCCACAAACGCCGCTATAGA
TCAAGACCTTTAGCGGCGC
Found at i:40470120 original size:19 final size:20
Alignment explanation
Indices: 40470098--40470138 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40470088 TTAGTATTAC
40470098 TTTTAAG-ACATTTTATTTA
1 TTTTAAGAACATTTTATTTA
* *
40470117 TTTTAGGAATATTTTATTTA
1 TTTTAAGAACATTTTATTTA
40470137 TT
1 TT
40470139 GCATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTTAAGAACATTTTATTTA
Found at i:40474554 original size:25 final size:25
Alignment explanation
Indices: 40474525--40474578 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
40474515 TGGTGAATTA
* * *
40474525 GGTTCGCCAGGTAAGTTGCGAACTG
1 GGTTCACCAAGTAAGTTGCAAACTG
* *
40474550 GGTTCACCAATTGAGTTGCAAACTG
1 GGTTCACCAAGTAAGTTGCAAACTG
40474575 GGTT
1 GGTT
40474579 TGCCGGTCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (25 bp):
GGTTCACCAAGTAAGTTGCAAACTG
Found at i:40475096 original size:14 final size:14
Alignment explanation
Indices: 40475073--40475107 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40475063 TGTTTGACTG
*
40475073 AAAATAATTTCCGA
1 AAAATGATTTCCGA
*
40475087 AAAATGATTTCTGA
1 AAAATGATTTCCGA
40475101 AAAATGA
1 AAAATGA
40475108 CTTACTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (14 bp):
AAAATGATTTCCGA
Found at i:40477519 original size:6 final size:7
Alignment explanation
Indices: 40477485--40477516 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
40477475 TGACAAGGAT
40477485 GGGGGAA
1 GGGGGAA
40477492 GGGGGAA
1 GGGGGAA
40477499 GGGGGAA
1 GGGGGAA
40477506 GGGGGAA
1 GGGGGAA
40477513 GGGG
1 GGGG
40477517 AAGAGGCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (7 bp):
GGGGGAA
Found at i:40479742 original size:13 final size:13
Alignment explanation
Indices: 40479724--40479749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40479714 AAAGCGAGCC
40479724 TTTTTAAAGAAAG
1 TTTTTAAAGAAAG
40479737 TTTTTAAAGAAAG
1 TTTTTAAAGAAAG
40479750 GATTAATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
TTTTTAAAGAAAG
Found at i:40479781 original size:36 final size:37
Alignment explanation
Indices: 40479734--40479803 Score: 133
Period size: 36 Copynumber: 1.9 Consensus size: 37
40479724 TTTTTAAAGA
40479734 AAGTTTTTAAAGAAAGGATTAATAA-CATTCTTTAGC
1 AAGTTTTTAAAGAAAGGATTAATAAGCATTCTTTAGC
40479770 AAGTTTTTAAAGAAAGGATTAATAAGCATTCTTT
1 AAGTTTTTAAAGAAAGGATTAATAAGCATTCTTT
40479804 TAACACTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 25 0.76
37 8 0.24
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.37
Consensus pattern (37 bp):
AAGTTTTTAAAGAAAGGATTAATAAGCATTCTTTAGC
Found at i:40480374 original size:16 final size:17
Alignment explanation
Indices: 40480343--40480375 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40480333 GTTTATCACA
40480343 TGCGAACCACTATTTAC
1 TGCGAACCACTATTTAC
*
40480360 TGCGAATCA-TATTTAC
1 TGCGAACCACTATTTAC
40480376 AAGCGCACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (17 bp):
TGCGAACCACTATTTAC
Found at i:40482009 original size:21 final size:20
Alignment explanation
Indices: 40481947--40482009 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
40481937 GTTTGTTTTA
*
40481947 TTAAAC-TTAGTTAATTAAC
1 TTAAACTTTAATTAATTAAC
*
40481966 TT-AA-TTATAATTAATTAGGC
1 TTAAACTT-TAATTAATTA-AC
40481986 TTAAACTTTAATTAATTAATC
1 TTAAACTTTAATTAATTAA-C
40482007 TTA
1 TTA
40482010 TGATAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
18 3 0.09
19 11 0.31
20 3 0.09
21 16 0.46
22 2 0.06
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (20 bp):
TTAAACTTTAATTAATTAAC
Found at i:40503780 original size:19 final size:20
Alignment explanation
Indices: 40503758--40503798 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40503748 TTAGTATTAC
40503758 TTTTAAG-ACATTTTATTTA
1 TTTTAAGAACATTTTATTTA
* *
40503777 TTTTAGGAATATTTTATTTA
1 TTTTAAGAACATTTTATTTA
40503797 TT
1 TT
40503799 GCATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTTAAGAACATTTTATTTA
Found at i:40508778 original size:14 final size:14
Alignment explanation
Indices: 40508755--40508789 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40508745 TGTTTGACTG
*
40508755 AAAATAATTTCCGA
1 AAAATGATTTCCGA
*
40508769 AAAATGATTTCTGA
1 AAAATGATTTCCGA
40508783 AAAATGA
1 AAAATGA
40508790 CTTACTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (14 bp):
AAAATGATTTCCGA
Found at i:40511217 original size:6 final size:7
Alignment explanation
Indices: 40511183--40511214 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
40511173 TGACAAGGAT
40511183 GGGGGAA
1 GGGGGAA
40511190 GGGGGAA
1 GGGGGAA
40511197 GGGGGAA
1 GGGGGAA
40511204 GGGGGAA
1 GGGGGAA
40511211 GGGG
1 GGGG
40511215 AAGAGGCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (7 bp):
GGGGGAA
Found at i:40513443 original size:13 final size:13
Alignment explanation
Indices: 40513425--40513450 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40513415 AAAGCGAGCC
40513425 TTTTTAAAGAAAG
1 TTTTTAAAGAAAG
40513438 TTTTTAAAGAAAG
1 TTTTTAAAGAAAG
40513451 GATTAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
TTTTTAAAGAAAG
Found at i:40513477 original size:37 final size:37
Alignment explanation
Indices: 40513435--40513505 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
40513425 TTTTTAAAGA
40513435 AAGTTTTTAAAGAAAGGATTAATAAACATTCTTTAGC
1 AAGTTTTTAAAGAAAGGATTAATAAACATTCTTTAGC
*
40513472 AAGTTTTTAAAGAAAGGATTAATAAGCATTCTTT
1 AAGTTTTTAAAGAAAGGATTAATAAACATTCTTT
40513506 TAACACTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (37 bp):
AAGTTTTTAAAGAAAGGATTAATAAACATTCTTTAGC
Found at i:40514078 original size:16 final size:17
Alignment explanation
Indices: 40514047--40514079 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40514037 TTTATTCACA
40514047 TGCGAACCACTATTTAC
1 TGCGAACCACTATTTAC
*
40514064 TGCGAATCA-TATTTAC
1 TGCGAACCACTATTTAC
40514080 AAGCGCACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (17 bp):
TGCGAACCACTATTTAC
Found at i:40524442 original size:70 final size:69
Alignment explanation
Indices: 40524313--40524645 Score: 275
Period size: 70 Copynumber: 4.9 Consensus size: 69
40524303 TACTGCTGGT
* * * * * * * * *
40524313 TAACTATTTTGGAGGTCGTAATATTGAATTAGCAAGCCTTAAGAATATAGCTGGCAGCTTAAGCT
1 TAACAATTTTGGAGGCCGCAATATTGAATCAGCGAGCCTTAAGAGTACAGTTGGGAGCTTAAGCT
40524378 CCCGC
66 -CCGC
** * * ** * *
40524383 TAACTGTTTTGGGGGCTGCGGTATTGAATCAACGAGCCTTAAGAGTACAGTTGGGAGCTTGAGCT
1 TAACAATTTTGGAGGCCGCAATATTGAATCAGCGAGCCTTAAGAGTACAGTTGGGAGCTTAAGC-
**
40524448 TGTGC
65 TCCGC
** * *
40524453 TAACAATTTTAAAGGCCGCAATATTGAATTAGCAAGCCTTAAGAGTACAGCTT--GAGCTT--G-
1 TAACAATTTTGGAGGCCGCAATATTGAATCAGCGAGCCTTAAGAGTACAG-TTGGGAGCTTAAGC
40524513 T--GC
65 TCCGC
* *
40524516 TAACAATTTTGGAGGCCGCAATATTGAATCAGTGAGCCTTAAGAGTACAGTTGAGAGCTTAAGCT
1 TAACAATTTTGGAGGCCGCAATATTGAATCAGCGAGCCTTAAGAGTACAGTTGGGAGCTTAAGCT
*
40524581 CACAC
66 C-CGC
* *** * * * *
40524586 TAACTATTTTGGAGGCCATGATATTAAATCAGTGAGCCTTAAGAGTACAGCTAGGAGCTT
1 TAACAATTTTGGAGGCCGCAATATTGAATCAGCGAGCCTTAAGAGTACAGTTGGGAGCTT
40524646 GATGCGATCT
Statistics
Matches: 211, Mismatches: 42, Indels: 20
0.77 0.15 0.07
Matches are distributed among these distances:
62 2 0.01
63 47 0.22
64 6 0.03
65 1 0.00
66 1 0.00
67 2 0.01
69 6 0.03
70 143 0.68
71 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (69 bp):
TAACAATTTTGGAGGCCGCAATATTGAATCAGCGAGCCTTAAGAGTACAGTTGGGAGCTTAAGCT
CCGC
Found at i:40524537 original size:63 final size:63
Alignment explanation
Indices: 40524438--40524570 Score: 214
Period size: 63 Copynumber: 2.1 Consensus size: 63
40524428 TACAGTTGGG
*
40524438 AGCTTGAGCTTGTGCTAACAATTTTAAAGGCCGCAATATTGAATTAGCAAGCCTTAAGAGTAC
1 AGCTTGAGCTTGTGCTAACAATTTTAAAGGCCGCAATATTGAATCAGCAAGCCTTAAGAGTAC
** **
40524501 AGCTTGAGCTTGTGCTAACAATTTTGGAGGCCGCAATATTGAATCAGTGAGCCTTAAGAGTAC
1 AGCTTGAGCTTGTGCTAACAATTTTAAAGGCCGCAATATTGAATCAGCAAGCCTTAAGAGTAC
40524564 AG-TTGAG
1 AGCTTGAG
40524571 AGCTTAAGCT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
62 5 0.08
63 60 0.92
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (63 bp):
AGCTTGAGCTTGTGCTAACAATTTTAAAGGCCGCAATATTGAATCAGCAAGCCTTAAGAGTAC
Found at i:40524563 original size:133 final size:137
Alignment explanation
Indices: 40524332--40524580 Score: 326
Period size: 133 Copynumber: 1.8 Consensus size: 137
40524322 TGGAGGTCGT
* ** *
40524332 AATATTGAATTAGCAAGCCTTAAGAATATAGCTGGCAGCTTAAGCTCCCGCTAACTGTTTTGGGG
1 AATATTGAATTAGCAAGCCTTAAGAATACAGCTGGCAGCTT-AGCT--CGCTAACAATTTTGGAG
* ** * *
40524397 GCTGCGGTATTGAATCAACGAGCCTTAAGAGTACAGTTGGGAGCTTGAGCTTGTGCTAACAATTT
63 GCCGCAATATTGAATCAACGAGCCTTAAGAGTACAGTTGAGAGCTTAAGCTTGTGCTAACAATTT
40524462 TAAAGGCCGC
128 TAAAGGCCGC
* *
40524472 AATATTGAATTAGCAAGCCTTAAGAGTACAGCTTG-AGCTT-G-T-GCTAACAATTTTGGAGGCC
1 AATATTGAATTAGCAAGCCTTAAGAATACAGCTGGCAGCTTAGCTCGCTAACAATTTTGGAGGCC
**
40524533 GCAATATTGAATCAGTGAGCCTTAAGAGTACAGTTGAGAGCTTAAGCT
66 GCAATATTGAATCAACGAGCCTTAAGAGTACAGTTGAGAGCTTAAGCT
40524581 CACACTAACT
Statistics
Matches: 96, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
133 57 0.59
136 1 0.01
137 1 0.01
139 5 0.05
140 32 0.33
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (137 bp):
AATATTGAATTAGCAAGCCTTAAGAATACAGCTGGCAGCTTAGCTCGCTAACAATTTTGGAGGCC
GCAATATTGAATCAACGAGCCTTAAGAGTACAGTTGAGAGCTTAAGCTTGTGCTAACAATTTTAA
AGGCCGC
Found at i:40524589 original size:133 final size:135
Alignment explanation
Indices: 40524332--40524646 Score: 319
Period size: 133 Copynumber: 2.3 Consensus size: 135
40524322 TGGAGGTCGT
* * ** *
40524332 AATATTGAATTAGCAAGCCTTAAGAATATAGCTGGCAGCTTAAGCTCCCGCTAACTGTTTTGGGG
1 AATATTGAATTAGCAAGCCTTAAGAGTACAGCTGG-AGCTT--GCT--CGCTAACAATTTTGGAG
* ** * * ****
40524397 GCTGCGGTATTGAATCAACGAGCCTTAAGAGTACAGTTGGGAGCTTGAGCTTGTGCTAACAATTT
61 GCCGCAATATTGAATCAACGAGCCTTAAGAGTACAGTTGAGAGCTTAAGCTCACACTAACAATTT
*
40524462 TAAAGGCCGC
126 TAAAGGCCAC
*
40524472 AATATTGAATTAGCAAGCCTTAAGAGTACAGCTTGAGCTTG-T-GCTAACAATTTTGGAGGCCGC
1 AATATTGAATTAGCAAGCCTTAAGAGTACAGCTGGAGCTTGCTCGCTAACAATTTTGGAGGCCGC
** * **
40524535 AATATTGAATCAGTGAGCCTTAAGAGTACAGTTGAGAGCTTAAGCTCACACTAACTATTTTGGAG
66 AATATTGAATCAACGAGCCTTAAGAGTACAGTTGAGAGCTTAAGCTCACACTAACAATTTTAAAG
*
40524600 GCCAT
131 GCCAC
* * * **
40524605 GATATTAAATCAGTGAGCCTTAAGAGTACAGCTAGGAGCTTG
1 AATATTGAATTAGCAAGCCTTAAGAGTACAGCT-GGAGCTTG
40524647 ATGCGATCTG
Statistics
Matches: 146, Mismatches: 28, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
133 100 0.68
134 7 0.05
136 1 0.01
137 1 0.01
139 5 0.03
140 32 0.22
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (135 bp):
AATATTGAATTAGCAAGCCTTAAGAGTACAGCTGGAGCTTGCTCGCTAACAATTTTGGAGGCCGC
AATATTGAATCAACGAGCCTTAAGAGTACAGTTGAGAGCTTAAGCTCACACTAACAATTTTAAAG
GCCAC
Found at i:40526188 original size:20 final size:20
Alignment explanation
Indices: 40526144--40526191 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
40526134 GAGCTCAAAC
* * *
40526144 GAGCTAAATTAAGCTCATGT
1 GAGCTGAATTAAACTCATAT
*
40526164 AAGCTGAATTAAACTCATAT
1 GAGCTGAATTAAACTCATAT
40526184 GAGCTGAA
1 GAGCTGAA
40526192 CCGAGCTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (20 bp):
GAGCTGAATTAAACTCATAT
Found at i:40527971 original size:10 final size:9
Alignment explanation
Indices: 40527920--40528070 Score: 62
Period size: 9 Copynumber: 16.6 Consensus size: 9
40527910 TTAAAATGTT
40527920 TAAAAAATCA
1 TAAAAAAT-A
*
40527930 TAATAAATTA
1 TAA-AAAATA
*
40527940 TCAAAAATCA
1 TAAAAAAT-A
*
40527950 -GAAAAATA
1 TAAAAAATA
40527958 TAAAAAATA
1 TAAAAAATA
* *
40527967 TTAAATAT-
1 TAAAAAATA
*
40527975 TAGAAAATA
1 TAAAAAATA
* *
40527984 TGAAAATTGA
1 TAAAAAAT-A
* *
40527994 TATAAACT-
1 TAAAAAATA
*
40528002 TAAAAATTA
1 TAAAAAATA
40528011 -AAAAAAT-
1 TAAAAAATA
40528018 TAAAAAA-A
1 TAAAAAATA
40528026 TCATAAAAATA
1 T-A-AAAAATA
* *
40528037 TAAAAATTC
1 TAAAAAATA
*
40528046 TAATAAATTA
1 TAA-AAAATA
40528056 TAAAAATATA
1 TAAAAA-ATA
40528066 TAAAA
1 TAAAA
40528071 TTAACAAAAC
Statistics
Matches: 105, Mismatches: 23, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
8 25 0.24
9 40 0.38
10 34 0.32
11 6 0.06
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.28
Consensus pattern (9 bp):
TAAAAAATA
Found at i:40528120 original size:22 final size:22
Alignment explanation
Indices: 40528094--40528137 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40528084 TTTAAAATAT
*
40528094 TTAAAATTTTATAAAAAACATA
1 TTAAAATTCTATAAAAAACATA
*
40528116 TTAAAATTCTATAAAAACCATA
1 TTAAAATTCTATAAAAAACATA
40528138 AAATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (22 bp):
TTAAAATTCTATAAAAAACATA
Found at i:40528323 original size:3 final size:3
Alignment explanation
Indices: 40528315--40528349 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
40528305 GGTTGAATCA
*
40528315 ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40528350 TAATTGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:40528668 original size:21 final size:22
Alignment explanation
Indices: 40528635--40528702 Score: 54
Period size: 23 Copynumber: 3.1 Consensus size: 22
40528625 TTTATATCAA
*
40528635 TTTTAATATATTTTAATAATTTT
1 TTTTAACA-ATTTTAATAATTTT
40528658 TTTT-ACAATTTT--T-ATTCTT
1 TTTTAACAATTTTAATAATT-TT
* *
40528677 TTTTAAGAATTCTAATACATTTT
1 TTTTAACAATTTTAATA-ATTTT
40528700 TTT
1 TTT
40528703 AATTTTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
18 3 0.08
19 7 0.19
20 6 0.17
21 5 0.14
22 3 0.08
23 9 0.25
24 3 0.08
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.63
Consensus pattern (22 bp):
TTTTAACAATTTTAATAATTTT
Found at i:40529548 original size:3 final size:3
Alignment explanation
Indices: 40529540--40529577 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
40529530 TTTTTCGGTG
40529540 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
40529578 TGTCGAAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40530842 original size:20 final size:21
Alignment explanation
Indices: 40530803--40530843 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
40530793 AAATATTAGT
40530803 TAAAAAAATAAATATGTACATG
1 TAAAAAAATAAATA-GTACATG
40530825 TAAAAAAATAAATA-TACAT
1 TAAAAAAATAAATAGTACAT
40530844 AAATATAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
22 14 0.74
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (21 bp):
TAAAAAAATAAATAGTACATG
Found at i:40532545 original size:87 final size:87
Alignment explanation
Indices: 40532400--40532930 Score: 875
Period size: 87 Copynumber: 6.1 Consensus size: 87
40532390 CTCCACATCC
*
40532400 TCGATCTGCTCCACTACTG-TTAGGGAGATAAGATCGGTAATTTTCAACCTACTCCACTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
*
40532464 CAGGGAGACAAGGCTGGGGATT
66 CAGGGAGACAAGGCTGGGGACT
* *
40532486 TCGATCTGCTCCACTACCGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTACT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
40532551 CAGGGAGACAAGGCTGGGGACT
66 CAGGGAGACAAGGCTGGGGACT
* *
40532573 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCTACTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
* *
40532638 CAGGGAGACAAAGTTGGGGACT
66 CAGGGAGACAAGGCTGGGGACT
* ** *
40532660 TCGATCTGCTCCACTACTGCTTAGGAAGATAAGATCTGTAATTTTTGACATACTCCACTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
*
40532725 CAGGGAGACAAGGCTGAGGACT
66 CAGGGAGACAAGGCTGGGGACT
* * **
40532747 TTGATCTGCTACACTACTGCTTAGGGAGATAAGATCTGTAATTTTTGACCTACTCCACTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
*
40532812 CAGGGAGATAAGGCTGGGGACT
66 CAGGGAGACAAGGCTGGGGACT
*
40532834 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTTCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
*
40532899 CAGAGAGACAAGGCTGGGGACT
66 CAGGGAGACAAGGCTGGGGACT
40532921 TCGATCTGCT
1 TCGATCTGCT
40532931 TCGCTGTCGG
Statistics
Matches: 412, Mismatches: 32, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
86 18 0.04
87 394 0.96
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (87 bp):
TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
CAGGGAGACAAGGCTGGGGACT
Found at i:40532994 original size:44 final size:44
Alignment explanation
Indices: 40532944--40533166 Score: 162
Period size: 44 Copynumber: 5.1 Consensus size: 44
40532934 CTGTCGGTAT
40532944 AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCC
1 AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCC
* * * * ** * * ** ****
40532988 AGGAAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGC
1 AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTG-CAACCC
*
40533032 AGGAAGGCAATATCTGCTATTTTTAACCTGCTCCACTGCAACCC
1 AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCC
* * * * * * * *** ** *
40533076 AGGGAGGCAAG-GCTGATGTCTTTGATCTGCTTTGCTGTCGTCGC
1 AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTG-CAACCC
40533120 AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCC
1 AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCC
40533164 AGG
1 AGG
40533167 GAGACAAGGC
Statistics
Matches: 119, Mismatches: 56, Indels: 8
0.65 0.31 0.04
Matches are distributed among these distances:
43 33 0.28
44 53 0.45
45 33 0.28
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (44 bp):
AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCC
Found at i:40532999 original size:88 final size:88
Alignment explanation
Indices: 40532864--40533231 Score: 508
Period size: 88 Copynumber: 4.2 Consensus size: 88
40532854 TTAGGGAGAT
* * ** * * * *
40532864 AAGATCTG-TAATTTTCAACCTACTCCACTGCTTCTCAGAGAGACAAGGCTGGGGACTTCGATCT
1 AAGATCTGCT-ATTTTTAACCTGCTCCACTGCAACCCAGGGAGACAAGGCTGGTGTCTTCGATCT
**
40532928 GCTTCGCTGTCGGTATAGGAAGGC
65 GCTTCGCTGTCGGTGCAGGAAGGC
* *
40532952 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGAAGGCAAGGCTGGTGTCTTCGATCTG
1 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGACAAGGCTGGTGTCTTCGATCTG
*
40533017 CTTCGTTGTCGGTGCAGGAAGGC
66 CTTCGCTGTCGGTGCAGGAAGGC
* * * *
40533040 AATATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGCTGATGTCTTTGATCTG
1 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGACAAGGCTGGTGTCTTCGATCTG
*
40533105 CTTTGCTGTC-GTCGCAGGAAGGC
66 CTTCGCTGTCGGT-GCAGGAAGGC
*
40533128 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGACAAGGCTGGTGTCTTTGATCTG
1 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGACAAGGCTGGTGTCTTCGATCTG
*
40533193 CTTCGTTGTCGGTGCAGGAAGGC
66 CTTCGCTGTCGGTGCAGGAAGGC
*
40533216 AAGATCTACT-TTTTTA
1 AAGATCTGCTATTTTTA
40533232 TTGATCTGCT
Statistics
Matches: 252, Mismatches: 25, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
87 8 0.03
88 241 0.96
89 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (88 bp):
AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGACAAGGCTGGTGTCTTCGATCTG
CTTCGCTGTCGGTGCAGGAAGGC
Found at i:40534440 original size:5 final size:5
Alignment explanation
Indices: 40534430--40534490 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
40534420 TTTTCCCTTT
* *
40534430 TTTTG TTTTG TTTCAT- TTTTG TTTTG TTTTT TTTTG TTTT- TTTGTT
1 TTTTG TTTTG TTT--TG TTTTG TTTTG TTTTG TTTTG TTTTG TTT-TG
*
40534476 TTTTG TTTTT TTTTG
1 TTTTG TTTTG TTTTG
40534491 AAATATTTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
4 4 0.09
5 35 0.76
6 6 0.13
7 1 0.02
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.84
Consensus pattern (5 bp):
TTTTG
Found at i:40534469 original size:7 final size:7
Alignment explanation
Indices: 40534445--40534486 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
40534435 TTTTGTTTCA
40534445 TTTTTGT
1 TTTTTGT
*
40534452 TTTGTTTT
1 TTT-TTGT
40534460 TTTTTGTT
1 TTTTTG-T
40534468 TTTTTGT
1 TTTTTGT
40534475 TTTTTGT
1 TTTTTGT
40534482 TTTTT
1 TTTTT
40534487 TTTGAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTGT
Found at i:40534477 original size:15 final size:15
Alignment explanation
Indices: 40534427--40534489 Score: 85
Period size: 15 Copynumber: 4.2 Consensus size: 15
40534417 TTCTTTTCCC
40534427 TTTTTTTGTTTTGTT
1 TTTTTTTGTTTTGTT
*
40534442 TCATTTTTGTTTTGTT
1 T-TTTTTTGTTTTGTT
40534458 TTTTTTTGTTTT-TT
1 TTTTTTTGTTTTGTT
40534472 TGTTTTTTGTTTT-TT
1 T-TTTTTTGTTTTGTT
40534487 TTT
1 TTT
40534490 GAAATATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
14 5 0.11
15 25 0.57
16 14 0.32
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (15 bp):
TTTTTTTGTTTTGTT
Found at i:40534589 original size:14 final size:15
Alignment explanation
Indices: 40534566--40534598 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
40534556 ATTGACGCTT
40534566 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
40534580 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
40534595 TTCC
1 TTCC
40534599 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:40538871 original size:20 final size:21
Alignment explanation
Indices: 40538832--40538872 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
40538822 AAATATTAGT
40538832 TAAAAAAATAAATATGTACATG
1 TAAAAAAATAAATA-GTACATG
40538854 TAAAAAAATAAATA-TACAT
1 TAAAAAAATAAATAGTACAT
40538873 ATATATAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
22 14 0.74
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (21 bp):
TAAAAAAATAAATAGTACATG
Found at i:40540248 original size:3 final size:3
Alignment explanation
Indices: 40540240--40540264 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40540230 ATTGGGTATT
40540240 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
40540265 TAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:40540461 original size:19 final size:18
Alignment explanation
Indices: 40540416--40540462 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
40540406 TATTAATCAC
*
40540416 ATAAATTTTAAGTAATTA
1 ATAAATTTTCAGTAATTA
*
40540434 ATAAATTTTCAGTATATTG
1 ATAAATTTTCAGTA-ATTA
*
40540453 ATTAATTTTC
1 ATAAATTTTC
40540463 TAAGATGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (18 bp):
ATAAATTTTCAGTAATTA
Found at i:40545211 original size:18 final size:18
Alignment explanation
Indices: 40545185--40545231 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
40545175 GAGACATTAG
40545185 AAAATAAAAATTA-AACTA
1 AAAATAAAAATTATAA-TA
*
40545203 AAAACAAAAATTATAATA
1 AAAATAAAAATTATAATA
40545221 AAAATAAAAAT
1 AAAATAAAAAT
40545232 AACTAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 24 0.92
19 2 0.08
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAATAAAAATTATAATA
Found at i:40545226 original size:6 final size:6
Alignment explanation
Indices: 40545185--40545233 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
40545175 GAGACATTAG
* * * * *
40545185 AAAATA AAAATT AAACTA AAAACA AAAATT ATAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
40545233 A
1 A
40545234 CTAATTTAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:40545228 original size:24 final size:24
Alignment explanation
Indices: 40545201--40545249 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
40545191 AAAATTAAAC
40545201 TAAAAACAA-AAATTATAATAAAAA
1 TAAAAACAACAAATT-TAATAAAAA
* *
40545225 TAAAAATAACTAATTTAATAAAAA
1 TAAAAACAACAAATTTAATAAAAA
40545249 T
1 T
40545250 TTAGTGTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
TAAAAACAACAAATTTAATAAAAA
Found at i:40547881 original size:30 final size:30
Alignment explanation
Indices: 40547804--40547883 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
40547794 GAATAAATTA
* *
40547804 CTCACACAAGCTGACAATATATTAGGGTTG
1 CTCACACAAGCTGACATTATATTAGGATTG
* *
40547834 CTCACACAAGCTAACATTATAATT-GTATTG
1 CTCACACAAGCTGACATTAT-ATTAGGATTG
*
40547864 CTCACATAAGCTGACATTAT
1 CTCACACAAGCTGACATTAT
40547884 TTCGAAGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 40 0.93
31 3 0.07
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (30 bp):
CTCACACAAGCTGACATTATATTAGGATTG
Found at i:40549863 original size:21 final size:21
Alignment explanation
Indices: 40549838--40549879 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40549828 AATTTTAATG
*
40549838 AAAA-TATATTAATTTAAATTT
1 AAAATTAT-TTAATGTAAATTT
40549859 AAAATTATTTAATGTAAATTT
1 AAAATTATTTAATGTAAATTT
40549880 TGATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATTATTTAATGTAAATTT
Found at i:40550578 original size:11 final size:11
Alignment explanation
Indices: 40550562--40550598 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
40550552 AAGATGGAAG
40550562 AAAATTAATAT
1 AAAATTAATAT
40550573 AAAATTAATAT
1 AAAATTAATAT
*
40550584 AAAATAAATAGT
1 AAAATTAATA-T
40550596 AAA
1 AAA
40550599 TACATAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:40551166 original size:14 final size:14
Alignment explanation
Indices: 40551147--40551177 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
40551137 ATTTTACACC
40551147 AAACTTCACGGAGT
1 AAACTTCACGGAGT
40551161 AAACTTCACGGAGT
1 AAACTTCACGGAGT
40551175 AAA
1 AAA
40551178 TTTATCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (14 bp):
AAACTTCACGGAGT
Found at i:40551224 original size:20 final size:21
Alignment explanation
Indices: 40551194--40551232 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40551184 CATTATCATT
40551194 TATTATTTTTATCACTTTGAC
1 TATTATTTTTATCACTTTGAC
*
40551215 TATT-TTTTTATCATTTTG
1 TATTATTTTTATCACTTTG
40551233 GTTCCCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.21, C:0.10, G:0.05, T:0.64
Consensus pattern (21 bp):
TATTATTTTTATCACTTTGAC
Found at i:40555380 original size:40 final size:40
Alignment explanation
Indices: 40555197--40555392 Score: 225
Period size: 40 Copynumber: 4.9 Consensus size: 40
40555187 GTATATATAG
*
40555197 GAATGCACATAAGTGCCATTGTTTGTACTTCTG-TACCCCT
1 GAATGCACATAAGTGCCACTGTTTGTACTTC-GATACCCCT
*
40555237 GAATGCACATAAGTGCCACTGTTTGTACTTTGATACCCCT
1 GAATGCACATAAGTGCCACTGTTTGTACTTCGATACCCCT
* **
40555277 AAATGCACATAAGTGCC-CATGTTTGTACTTCGGCACCCCT
1 GAATGCACATAAGTGCCAC-TGTTTGTACTTCGATACCCCT
* * *** *
40555317 GAATGCACTTAAATGCTTTTATTTGTACTTCGATACCCCT
1 GAATGCACATAAGTGCCACTGTTTGTACTTCGATACCCCT
* * * *
40555357 GAATGCACATACGTGCCCCTATTTGTACTACGATAC
1 GAATGCACATAAGTGCCACTGTTTGTACTTCGATAC
40555393 TCCTAAATTC
Statistics
Matches: 132, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
39 2 0.02
40 130 0.98
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (40 bp):
GAATGCACATAAGTGCCACTGTTTGTACTTCGATACCCCT
Found at i:40560860 original size:21 final size:22
Alignment explanation
Indices: 40560820--40560861 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
40560810 TTTATATATT
*
40560820 TTTTCTTTTTGATTCTTTTTTC
1 TTTTCTTTTTGATTCATTTTTC
*
40560842 TTTT-TTTTTGATTGATTTTT
1 TTTTCTTTTTGATTCATTTTT
40560862 TTAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (22 bp):
TTTTCTTTTTGATTCATTTTTC
Found at i:40571317 original size:13 final size:13
Alignment explanation
Indices: 40571299--40571323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40571289 TTAAAACTAA
40571299 AATTAACTAAATT
1 AATTAACTAAATT
40571312 AATTAACTAAAT
1 AATTAACTAAAT
40571324 AACACGACAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAACTAAATT
Found at i:40579188 original size:51 final size:51
Alignment explanation
Indices: 40579112--40579213 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
40579102 TAGGCTATAG
* * *
40579112 GATGCCTATTTTGAGTCAGCACAGCCTCAATACCTATACCTGAGGCATCAC
1 GATGCCCATCTTGAGTCAGCACAGCCCCAATACCTATACCTGAGGCATCAC
40579163 GATGCCCATCTTGAGTCAGCACAGCCCCAATACCTATACCTGAGGCATCAC
1 GATGCCCATCTTGAGTCAGCACAGCCCCAATACCTATACCTGAGGCATCAC
40579214 ACTAAATCTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (51 bp):
GATGCCCATCTTGAGTCAGCACAGCCCCAATACCTATACCTGAGGCATCAC
Found at i:40581545 original size:27 final size:27
Alignment explanation
Indices: 40581515--40581692 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
40581505 ATATCGAGTC
* * * *
40581515 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
40581542 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40581569 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40581597 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40581624 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40581651 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40581678 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40581693 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40581654 original size:82 final size:81
Alignment explanation
Indices: 40581536--40581691 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
40581526 TGCTATATAA
*
40581536 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40581601 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40581618 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40581682 CACTTAGTGC
65 CACTTAGTGC
40581692 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40589451 original size:27 final size:27
Alignment explanation
Indices: 40589421--40589598 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
40589411 ATATCGAGTC
* * * *
40589421 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
40589448 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40589475 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40589503 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40589530 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40589557 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40589584 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40589599 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40589560 original size:82 final size:81
Alignment explanation
Indices: 40589442--40589597 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
40589432 TGCTATATAA
*
40589442 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40589507 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40589524 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40589588 CACTTAGTGC
65 CACTTAGTGC
40589598 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40592059 original size:18 final size:18
Alignment explanation
Indices: 40592038--40592074 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40592028 TTGGAGAGGG
*
40592038 ATTTTAATTTTTTTTTTC
1 ATTTTAATTTTTCTTTTC
*
40592056 ATTTTCATTTTTCTTTTC
1 ATTTTAATTTTTCTTTTC
40592074 A
1 A
40592075 GCTATATAAG
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:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTAATTTTTCTTTTC
Found at i:40594812 original size:25 final size:26
Alignment explanation
Indices: 40594784--40594833 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
40594774 TACCTCTTGT
40594784 TTTCCTTTTGTTTTTCCA-CTTTTCC
1 TTTCCTTTTGTTTTTCCATCTTTTCC
40594809 TTTCCTTTTGTTTTTCCATCTTTTC
1 TTTCCTTTTGTTTTTCCATCTTTTC
40594834 TTTTTGCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.04, C:0.26, G:0.04, T:0.66
Consensus pattern (26 bp):
TTTCCTTTTGTTTTTCCATCTTTTCC
Found at i:40600337 original size:47 final size:47
Alignment explanation
Indices: 40600285--40600641 Score: 525
Period size: 47 Copynumber: 7.6 Consensus size: 47
40600275 GATAATTGTG
* * *
40600285 ATGTGAATGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40600332 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGAGGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40600379 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40600426 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40600475 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40600522 ATGTGAAAGTGTATATACGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
40600569 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40600616 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
40600642 TCCCGAAGGG
Statistics
Matches: 279, Mismatches: 29, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
47 234 0.84
49 45 0.16
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:40600439 original size:143 final size:143
Alignment explanation
Indices: 40600285--40600641 Score: 533
Period size: 143 Copynumber: 2.5 Consensus size: 143
40600275 GATAATTGTG
*
40600285 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * * *
40600348 ATGTGATGAGGCCTAATGGCCGAGGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATG
66 ATGTGATAAGGCCTAATAGCCGAGGCGATGAATGTGAAAGTGTATATACGTGATAAGGCCGAATG
40600413 GCCAATGTGATGA
131 GCCAATGTGATGA
40600426 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * *
40600491 ATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATACGTGATGAGGCCTAATG
66 ATGTGATAAGGCCTAATAGCCGAGGCGATGAATGTGAAAGTGTATATACGTGATAAGGCCGAATG
*
40600556 GCCGATGTGATGA
131 GCCAATGTGATGA
* * * * * * * *
40600569 ATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
40600632 ATGTGATAAG
66 ATGTGATAAG
40600642 TCCCGAAGGG
Statistics
Matches: 197, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
141 59 0.30
142 2 0.01
143 136 0.69
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (143 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCTAATAGCCGAGGCGATGAATGTGAAAGTGTATATACGTGATAAGGCCGAATG
GCCAATGTGATGA
Found at i:40600574 original size:190 final size:188
Alignment explanation
Indices: 40600285--40600641 Score: 606
Period size: 190 Copynumber: 1.9 Consensus size: 188
40600275 GATAATTGTG
* * *
40600285 ATGTGAATGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATAC
*
40600350 GTGATGAGGCCTAATGGCCGAGGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGC
66 GTGATGAGGCCTAATGGCCGAGGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGC
*
40600415 CAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
131 CAACGTGATGAATGTGAAAGTGTATA-A-ATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40600475 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATAC
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATAC
* * *
40600540 GTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGC
66 GTGATGAGGCCTAATGGCCGAGGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGC
*
40600605 CAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
131 CAACGTGATGAATGTGAAAGTGTATAAATGTGATAAG
40600642 TCCCGAAGGG
Statistics
Matches: 157, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
188 10 0.06
189 1 0.01
190 146 0.93
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (188 bp):
ATGTGAAAGTATATATATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATAC
GTGATGAGGCCTAATGGCCGAGGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGC
CAACGTGATGAATGTGAAAGTGTATAAATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:40603145 original size:40 final size:40
Alignment explanation
Indices: 40602866--40603133 Score: 389
Period size: 40 Copynumber: 6.7 Consensus size: 40
40602856 AGGTCTCGAC
40602866 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
40602905 GATGTACCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
40602945 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
40602985 GATGTATCTGGACTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
40603025 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * *
40603065 -ATTATATCCGTGCTAA-ACCTCGAAGAGCATTCGTGCTGGT
1 GA-TGTATCCGGGCTAAGTCC-CGAAGAGCATTCGTGCTAGT
* * *
40603105 GTTATATCCGGGCTAGGTCCCGAAGAGCA
1 GATGTATCCGGGCTAAGTCCCGAAGAGCA
40603134 ATCATGCTGG
Statistics
Matches: 206, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
39 6 0.03
40 198 0.96
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:40603414 original size:58 final size:57
Alignment explanation
Indices: 40603345--40603453 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 57
40603335 CGAATGATTA
* *
40603345 GAGGCACTGTGTGTGCAAATTCTTTTAACCGAGCACTATGTGTGCGAAATCGGTAATT
1 GAGGCACTGTGTGTGCAAATTC-TTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
* * *
40603403 GAGGCACTGTGTGTGCGAGTTCTTCAACCAAGCACTATGTGTGCGAGATCG
1 GAGGCACTGTGTGTGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCG
40603454 ATCAGTGGGC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 26 0.57
58 20 0.43
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (57 bp):
GAGGCACTGTGTGTGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
Found at i:40607355 original size:47 final size:47
Alignment explanation
Indices: 40607303--40607659 Score: 534
Period size: 47 Copynumber: 7.6 Consensus size: 47
40607293 GATAATTGTG
* * *
40607303 ATGTGAATGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40607350 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40607397 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40607444 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40607493 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
40607540 ATGTGAAAGTGTATATACGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
40607587 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40607634 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
40607660 TCCCGAAGGG
Statistics
Matches: 281, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
47 236 0.84
49 45 0.16
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:40607457 original size:143 final size:143
Alignment explanation
Indices: 40607303--40607659 Score: 542
Period size: 143 Copynumber: 2.5 Consensus size: 143
40607293 GATAATTGTG
*
40607303 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * * *
40607366 ATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATG
66 ATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATACGTGATAAGGCCGAATG
40607431 GCCAATGTGATGA
131 GCCAATGTGATGA
40607444 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* *
40607509 ATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATACGTGATGAGGCCTAATG
66 ATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATACGTGATAAGGCCGAATG
*
40607574 GCCGATGTGATGA
131 GCCAATGTGATGA
* * * * * * * *
40607587 ATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
40607650 ATGTGATAAG
66 ATGTGATAAG
40607660 TCCCGAAGGG
Statistics
Matches: 198, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
141 59 0.30
142 2 0.01
143 137 0.69
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (143 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATACGTGATAAGGCCGAATG
GCCAATGTGATGA
Found at i:40607592 original size:190 final size:188
Alignment explanation
Indices: 40607303--40607659 Score: 615
Period size: 190 Copynumber: 1.9 Consensus size: 188
40607293 GATAATTGTG
* * *
40607303 ATGTGAATGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATAC
*
40607368 GTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGC
66 GTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGC
*
40607433 CAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
131 CAACGTGATGAATGTGAAAGTGTATA-A-ATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40607493 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATAC
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATAC
* *
40607558 GTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGC
66 GTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGC
*
40607623 CAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
131 CAACGTGATGAATGTGAAAGTGTATAAATGTGATAAG
40607660 TCCCGAAGGG
Statistics
Matches: 158, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
188 10 0.06
189 1 0.01
190 147 0.93
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (188 bp):
ATGTGAAAGTATATATATGTGATAAGGCCTAATAGCCGATGCGATGAATGTGAAAGTGTATATAC
GTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGC
CAACGTGATGAATGTGAAAGTGTATAAATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:40609754 original size:99 final size:100
Alignment explanation
Indices: 40609571--40609761 Score: 242
Period size: 99 Copynumber: 1.9 Consensus size: 100
40609561 CTTGGAAGGG
* * *
40609571 AGCATACAACAGCTCTTGGTGCATGTATGTCCAGGCGCATGTCCTCCCTTAGTTGACATCCAATG
1 AGCAAACAACAGCTCTTGGTGCATGTAGGTCCAGGCGCATGTCCTCCCTTAGATGACATCCAATG
*
40609636 AACCTATTGGTGAGCAGCCAATACATTCAGCTATA
66 AACCTATTGATGAGCAGCCAATACATTCAGCTATA
* * * * * *
40609671 AGCAAACAGCAGCTTCTTGGTGCATGT-GGTCCAGGTGCATGTCTTCCTTTA-ATGCCGTCCAAT
1 AGCAAACAACAGC-TCTTGGTGCATGTAGGTCCAGGCGCATGTCCTCCCTTAGATGACATCCAAT
* * *
40609734 GAATCTGTTGATGAGCAGCCAATGCATT
65 GAACCTATTGATGAGCAGCCAATACATT
40609762 TAGCCTACAA
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
99 33 0.43
100 31 0.40
101 13 0.17
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (100 bp):
AGCAAACAACAGCTCTTGGTGCATGTAGGTCCAGGCGCATGTCCTCCCTTAGATGACATCCAATG
AACCTATTGATGAGCAGCCAATACATTCAGCTATA
Found at i:40619140 original size:24 final size:24
Alignment explanation
Indices: 40619092--40619138 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40619082 ACTGGTCATA
*
40619092 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
40619116 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
40619139 GGGATTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:40619934 original size:81 final size:81
Alignment explanation
Indices: 40619799--40620022 Score: 304
Period size: 81 Copynumber: 2.8 Consensus size: 81
40619789 GAGAGGTCAA
* * * * * *
40619799 TAAAATGACTGAAATACCCCCATAGGGTAAAATGACTAAAATACCACTATAGGGTAAAATGATCG
1 TAAAATGACTAAAATACCCCAATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGATCA
40619864 AAATACCCTCATAGGG
66 AAATACCCTCATAGGG
* * ** *
40619880 TAAAATGATTTAAATACCCTTATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGATTA
1 TAAAATGACTAAAATACCCCAATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGATCA
*
40619945 AAATACTCTCATAGGG
66 AAATACCCTCATAGGG
** * *
40619961 TAAAATGACTAAAATACCCCAATAGGGTAGGATGACCGAAATACCCCCATAGGGTACAATGA
1 TAAAATGACTAAAATACCCCAATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGA
40620023 CTGTTATACC
Statistics
Matches: 125, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 125 1.00
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (81 bp):
TAAAATGACTAAAATACCCCAATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAAATGATCA
AAATACCCTCATAGGG
Found at i:40620033 original size:27 final size:27
Alignment explanation
Indices: 40619799--40620024 Score: 265
Period size: 27 Copynumber: 8.4 Consensus size: 27
40619789 GAGAGGTCAA
*
40619799 TAAAATGACTGAAATACCCCCATAGGG
1 TAAAATGACTAAAATACCCCCATAGGG
* *
40619826 TAAAATGACTAAAATACCACTATAGGG
1 TAAAATGACTAAAATACCCCCATAGGG
* *
40619853 TAAAATGA-TCGAAATACCCTCATAGGG
1 TAAAATGACT-AAAATACCCCCATAGGG
* * **
40619880 TAAAATGATTTAAATACCCTTATAGGG
1 TAAAATGACTAAAATACCCCCATAGGG
*
40619907 TAAAATGACCAAAATACCCCCATAGGG
1 TAAAATGACTAAAATACCCCCATAGGG
* * *
40619934 TAAAATGATTAAAATACTCTCATAGGG
1 TAAAATGACTAAAATACCCCCATAGGG
*
40619961 TAAAATGACTAAAATACCCCAATAGGG
1 TAAAATGACTAAAATACCCCCATAGGG
** **
40619988 TAGGATGACCGAAATACCCCCATAGGG
1 TAAAATGACTAAAATACCCCCATAGGG
*
40620015 TACAATGACT
1 TAAAATGACT
40620025 GTTATACCCT
Statistics
Matches: 167, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 165 0.99
28 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (27 bp):
TAAAATGACTAAAATACCCCCATAGGG
Found at i:40630385 original size:37 final size:35
Alignment explanation
Indices: 40630314--40630402 Score: 110
Period size: 37 Copynumber: 2.5 Consensus size: 35
40630304 CAACTATAAG
40630314 TGCCGAATGC-ACATAT-TCACTTATACCCACCTA
1 TGCCGAATGCTACATATATCACTTATACCCACCTA
* *
40630347 TGCCGAATGCATACATATATACACTTATATCCAGCTA
1 TGCCGAATGC-TACATATAT-CACTTATACCCACCTA
*
40630384 TGACGAATGCGTACATATA
1 TGCCGAATGC-TACATATA
40630403 CACATTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 10 0.21
35 6 0.12
36 1 0.02
37 31 0.65
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (35 bp):
TGCCGAATGCTACATATATCACTTATACCCACCTA
Found at i:40630659 original size:41 final size:41
Alignment explanation
Indices: 40630587--40630787 Score: 160
Period size: 41 Copynumber: 4.9 Consensus size: 41
40630577 ATTTAAACAG
* * * * * *
40630587 ATTCACTAGCACTTCA-CCTGATAGACTTATAGTCTAATTCC
1 ATTCACCAGCACTT-AGCCTGCTAGGCGTATAGTCTGATTCA
* *
40630628 GTTCACCAGCACTTAGCCTGCTAGGCCTATAG-CATGATTCA
1 ATTCACCAGCACTTAGCCTGCTAGGCGTATAGTC-TGATTCA
* * * * *
40630669 GTTCA-CAGGCACTTAGCCTACT-GGACATATAATCCGATTCA
1 ATTCACCA-GCACTTAGCCTGCTAGG-CGTATAGTCTGATTCA
* *
40630710 ATTCACCGGCACTTAGCCTGCT-GGACGTATAGTCCGATTCA
1 ATTCACCAGCACTTAGCCTGCTAGG-CGTATAGTCTGATTCA
* * *
40630751 ATTCATCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 ATTCACCAGCACTTAGCCTGCTAGGCGTATAGTCTGA
40630788 ACAATTTCAC
Statistics
Matches: 134, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
40 6 0.04
41 125 0.93
42 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (41 bp):
ATTCACCAGCACTTAGCCTGCTAGGCGTATAGTCTGATTCA
Found at i:40630797 original size:82 final size:82
Alignment explanation
Indices: 40630629--40630781 Score: 186
Period size: 82 Copynumber: 1.9 Consensus size: 82
40630619 TCTAATTCCG
* * * *
40630629 TTCACCAGCACTTAGCCTGCTAGGCCTATAGCATGATTCAGTTCACAGGCACTTAGCCTACTGGA
1 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCACGATTCAATTCACAGGCACTTAGCCTACTAGA
*
40630694 CATATAATCCGATTCAA
66 CATATAATCCGATACAA
* *
40630711 TTCACCGGCACTTAGCCTGCT-GGACGTATAGTC-CGATTCAATTCATC-GGCACTTAGCCTGCT
1 TTCACCGGCACTTAGCCTGCTAGG-CCTATAG-CACGATTCAATTCA-CAGGCACTTAGCCTACT
*
40630773 AGACGTATA
63 AGACATATA
40630782 GTCTGAACAA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
81 2 0.03
82 57 0.93
83 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (82 bp):
TTCACCGGCACTTAGCCTGCTAGGCCTATAGCACGATTCAATTCACAGGCACTTAGCCTACTAGA
CATATAATCCGATACAA
Found at i:40637565 original size:54 final size:54
Alignment explanation
Indices: 40637502--40637734 Score: 234
Period size: 54 Copynumber: 4.1 Consensus size: 54
40637492 AGTATCATAT
*
40637502 ATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
*
40637556 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * * *
40637610 ATTATATATTTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTATATTTTATAGTATCAT
1 ATTAT-GA-TTTGAGTA-AAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTT-TA-T-T-A-
40637674 A
54 A
*
40637675 TATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
40637730 ATTAT
1 ATTAT
40637735 ATATTTTAAT
Statistics
Matches: 143, Mismatches: 22, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
54 62 0.43
55 2 0.01
56 7 0.05
57 12 0.08
58 5 0.03
59 4 0.03
60 16 0.11
61 4 0.03
62 5 0.03
63 12 0.08
64 7 0.05
65 2 0.01
66 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.48
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:40637602 original size:28 final size:27
Alignment explanation
Indices: 40637517--40637602 Score: 63
Period size: 28 Copynumber: 3.1 Consensus size: 27
40637507 GATTTGAGTA
*
40637517 AATTCATATAAAAATATTAATTATTAAG
1 AATTCATAT-AAAATATTGATTATTAAG
* * *
40637545 AATT-TTATTAAAT-TATGA-T-TTGAG
1 AATTCATATAAAATAT-TGATTATTAAG
40637569 TAAATTCATATAAGAATATTGATTATTAAG
1 --AATTCATATAA-AATATTGATTATTAAG
40637599 AATT
1 AATT
40637603 TTATTAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
24 4 0.09
25 2 0.05
26 10 0.23
27 7 0.16
28 14 0.33
29 2 0.05
30 4 0.09
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (27 bp):
AATTCATATAAAATATTGATTATTAAG
Found at i:40637639 original size:15 final size:15
Alignment explanation
Indices: 40637604--40637655 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40637594 TTAAGAATTT
*
40637604 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40637618 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40637632 TATTTAATAATAAT-
1 TATTTAATTATAATA
40637646 TATGTTAATT
1 TAT-TTAATT
40637656 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40637681 original size:120 final size:120
Alignment explanation
Indices: 40637556--40637771 Score: 432
Period size: 120 Copynumber: 1.8 Consensus size: 120
40637546 ATTTTATTAA
40637556 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
40637621 TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
66 TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
40637676 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
40637741 TAATTATAATATATTTAATAATAATTATGTT
66 TAATTATAATATATTTAATAATAATTATGTT
40637772 TAAATATGAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 96 1.00
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (120 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
Found at i:40637754 original size:16 final size:16
Alignment explanation
Indices: 40637733--40637774 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40637723 TTATTAAATT
*
40637733 ATATATTTTAATTATA
1 ATATATTTTAATAATA
40637749 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
40637764 AT-TATGTTTAA
1 ATATAT-TTTAA
40637775 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:40637759 original size:15 final size:15
Alignment explanation
Indices: 40637724--40637765 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40637714 TTAAGAATTT
*
40637724 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40637738 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40637752 TATTTAATAATAAT
1 TATTTAATTATAAT
40637766 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40638011 original size:16 final size:16
Alignment explanation
Indices: 40637990--40638025 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
40637980 GATCTGCTAT
40637990 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40638006 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40638022 TACA
1 TACA
40638026 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:40645993 original size:11 final size:11
Alignment explanation
Indices: 40645977--40646007 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
40645967 TCAATTATTT
40645977 TCTCAATTTGC
1 TCTCAATTTGC
40645988 TCTCAATTTGC
1 TCTCAATTTGC
40645999 TCTCAATTT
1 TCTCAATTT
40646008 CCTTCCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.06, T:0.48
Consensus pattern (11 bp):
TCTCAATTTGC
Found at i:40647230 original size:7 final size:7
Alignment explanation
Indices: 40647218--40647243 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40647208 TAGTCGATTG
40647218 GTATTTA
1 GTATTTA
40647225 GTATTTA
1 GTATTTA
40647232 GTATTTA
1 GTATTTA
40647239 GTATT
1 GTATT
40647244 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:40647917 original size:17 final size:19
Alignment explanation
Indices: 40647885--40647927 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
40647875 TGTCAGGTGC
*
40647885 GTATCCTAGCCCCTTA-AT
1 GTATCCTAGACCCTTATAT
40647903 GTATCCTA-ACCCTTATAT
1 GTATCCTAGACCCTTATAT
*
40647921 GTTTCCT
1 GTATCCT
40647928 TTTTCGAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.40
Consensus pattern (19 bp):
GTATCCTAGACCCTTATAT
Found at i:40648430 original size:7 final size:7
Alignment explanation
Indices: 40648410--40648448 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
40648400 ATTTATTAAA
40648410 AATTTAT
1 AATTTAT
40648417 AAATTTAT
1 -AATTTAT
40648425 AATTTAT
1 AATTTAT
40648432 AA-TTA-
1 AATTTAT
40648437 AATTTAT
1 AATTTAT
40648444 AATTT
1 AATTT
40648449 TGTTGACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 2 0.07
6 6 0.21
7 14 0.48
8 7 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATTTAT
Found at i:40648501 original size:21 final size:21
Alignment explanation
Indices: 40648477--40648522 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
40648467 AACCCTAACT
*
40648477 CTAACCTTTAACTTAAAAACC
1 CTAACCCTTAACTTAAAAACC
*
40648498 CTAACCCTTAATTTAAAAACC
1 CTAACCCTTAACTTAAAAACC
40648519 CTAA
1 CTAA
40648523 ACTAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.28
Consensus pattern (21 bp):
CTAACCCTTAACTTAAAAACC
Found at i:40648537 original size:21 final size:21
Alignment explanation
Indices: 40648484--40648531 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
40648474 ACTCTAACCT
* *
40648484 TTAACTTAAAAACCCTAACCC
1 TTAATTTAAAAACCCTAACAC
40648505 TTAATTTAAAAACCCTAA-AC
1 TTAATTTAAAAACCCTAACAC
40648525 -TAATTTA
1 TTAATTTA
40648532 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.28
20 1 0.04
21 17 0.68
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAATTTAAAAACCCTAACAC
Found at i:40648621 original size:22 final size:22
Alignment explanation
Indices: 40648596--40648711 Score: 127
Period size: 22 Copynumber: 5.4 Consensus size: 22
40648586 CCCTAACCCT
*
40648596 AACCCTAACACTTTAACTTAAA
1 AACCCTAACACCTTAACTTAAA
40648618 AACCCTAA-ACCCTTAACTTAAA
1 AACCCTAACA-CCTTAACTTAAA
*
40648640 AACCCTAACAAAC--AACTTAAA
1 AACCCTAAC-ACCTTAACTTAAA
*
40648661 AACCTTAA-ACCCTTAACTTAAA
1 AACCCTAACA-CCTTAACTTAAA
*
40648683 AACCCTAAC-CTTTAACTT-AA
1 AACCCTAACACCTTAACTTAAA
40648703 AACCCTAAC
1 AACCCTAAC
40648712 CCTAAACCTA
Statistics
Matches: 81, Mismatches: 6, Indels: 16
0.79 0.06 0.16
Matches are distributed among these distances:
19 1 0.01
20 12 0.15
21 24 0.30
22 42 0.52
23 1 0.01
24 1 0.01
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (22 bp):
AACCCTAACACCTTAACTTAAA
Found at i:40648700 original size:43 final size:43
Alignment explanation
Indices: 40648596--40648714 Score: 170
Period size: 43 Copynumber: 2.8 Consensus size: 43
40648586 CCCTAACCCT
40648596 AACCCTAACACTTTAACTTAAAAACCCTAAACCCTTAACTTAAA
1 AACCCTAAC-CTTTAACTTAAAAACCCTAAACCCTTAACTTAAA
**** *
40648640 AACCCTAACAAACAACTTAAAAACCTTAAACCCTTAACTTAAA
1 AACCCTAACCTTTAACTTAAAAACCCTAAACCCTTAACTTAAA
40648683 AACCCTAACCTTTAACTT-AAAACCCT-AACCCT
1 AACCCTAACCTTTAACTTAAAAACCCTAAACCCT
40648715 AAACCTAGCC
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 6 0.09
42 7 0.11
43 43 0.66
44 9 0.14
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (43 bp):
AACCCTAACCTTTAACTTAAAAACCCTAAACCCTTAACTTAAA
Found at i:40648850 original size:59 final size:58
Alignment explanation
Indices: 40648778--40648901 Score: 212
Period size: 59 Copynumber: 2.1 Consensus size: 58
40648768 TTAACAATTA
40648778 ATAATTTTACTAACAAACTATAGCATTTTTACAAAATGTTTCGATTGGTACAAAAAAAT
1 ATAATTTTACTAACAAACTATAGCATTTTTACAAAATGTTTCGATTGGTAC-AAAAAAT
* * *
40648837 ATAATTTTACTAACAAACTCTTGCATTTTTACAAAATGTTTTGATTGGTACAAAAAAT
1 ATAATTTTACTAACAAACTATAGCATTTTTACAAAATGTTTCGATTGGTACAAAAAAT
40648895 ATAATTT
1 ATAATTT
40648902 GTTTACAATG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 14 0.23
59 48 0.77
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (58 bp):
ATAATTTTACTAACAAACTATAGCATTTTTACAAAATGTTTCGATTGGTACAAAAAAT
Found at i:40652210 original size:22 final size:22
Alignment explanation
Indices: 40652170--40652212 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40652160 TTTTATCTAA
*
40652170 AACCCTAAAAATCTTAAACCTT
1 AACCCTAAAAATCTAAAACCTT
40652192 AACCCTAAAAA-CTCAAAACCT
1 AACCCTAAAAATCT-AAAACCT
40652213 AAATCTAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (22 bp):
AACCCTAAAAATCTAAAACCTT
Found at i:40653167 original size:20 final size:21
Alignment explanation
Indices: 40653108--40653166 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
40653098 TTATGAAAAT
40653108 TTTTAAAAAATATTTTTTAAA
1 TTTTAAAAAATATTTTTTAAA
40653129 TTTTAAAAAATATTTTTTAAA
1 TTTTAAAAAATATTTTTTAAA
40653150 TTTTAAAAAATATTTTT
1 TTTTAAAAAATATTTTT
40653167 ATTTTAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTAAAAAATATTTTTTAAA
Found at i:40653430 original size:19 final size:19
Alignment explanation
Indices: 40653406--40653518 Score: 145
Period size: 19 Copynumber: 5.8 Consensus size: 19
40653396 AATTTTTGAG
40653406 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
40653425 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
* *
40653444 GATATATGCAATATTAGATAC
1 G--ATATGCAATCTTAGATAT
*
40653465 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
40653484 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40653503 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
40653519 ATATATGATT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 63 0.81
21 15 0.19
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.34
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40653451 original size:40 final size:40
Alignment explanation
Indices: 40653407--40653513 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 40
40653397 ATTTTTGAGG
*
40653407 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
* * **
40653447 ATATGCAATATTAGATACGATATGCAATCTTAGAGATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
40653487 ATAT--AATCTTAGATATGATATGCAATC
1 ATATGCAATCTTAGATATGATATGCAATC
40653514 TTAGAATATA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 21 0.35
40 39 0.65
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
Found at i:40654186 original size:22 final size:23
Alignment explanation
Indices: 40654149--40654192 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
40654139 CATATATATA
40654149 TTTTTTTAAAACGAATATTTTCC
1 TTTTTTTAAAACGAATATTTTCC
*
40654172 TTTTTTT-AAATGAATATTTTC
1 TTTTTTTAAAACGAATATTTTC
40654193 ATATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTTTTTAAAACGAATATTTTCC
Found at i:40654942 original size:98 final size:98
Alignment explanation
Indices: 40654822--40655018 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
40654812 TTGAAAATAA
* *
40654822 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
40654887 TTAAATCTTGGATAAGTTGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
40654920 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
* *
40654985 TTGAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
40655018 T
1 T
40655019 TTTATTGTAC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:40656227 original size:17 final size:18
Alignment explanation
Indices: 40656201--40656247 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
40656191 TTTGAAATTA
*
40656201 AAAATATATAAAATT-TT
1 AAAATATATAAAATTAAT
*
40656218 AAAATGTAT-AAATTAAT
1 AAAATATATAAAATTAAT
40656235 AAAATATATAAAA
1 AAAATATATAAAA
40656248 AAATTTACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 5 0.20
17 17 0.68
18 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAATATATAAAATTAAT
Found at i:40656399 original size:15 final size:16
Alignment explanation
Indices: 40656372--40656401 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40656362 AAATCTTAAT
40656372 TATTTTTATTATATTG
1 TATTTTTATTATATTG
40656388 TATTTTTA-TATATT
1 TATTTTTATTATATT
40656402 TTTTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TATTTTTATTATATTG
Found at i:40668186 original size:41 final size:40
Alignment explanation
Indices: 40668141--40668242 Score: 141
Period size: 41 Copynumber: 2.5 Consensus size: 40
40668131 TGATTCAGTA
40668141 CACCGGCACTTAGCCTGCTAGACATATAGTCTGAAATATTT
1 CACCGGCA-TTAGCCTGCTAGACATATAGTCTGAAATATTT
* * *
40668182 CACCGGCATTAAGCCTGCTAGACATATAGTTTGAAGTGTTT
1 CACCGGCATT-AGCCTGCTAGACATATAGTCTGAAATATTT
*
40668223 CACCGGCAATAAGCCTGCTA
1 CACCGGC-ATTAGCCTGCTA
40668243 AGCGCTATGC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
40 2 0.04
41 51 0.93
42 2 0.04
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (40 bp):
CACCGGCATTAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:40674187 original size:51 final size:50
Alignment explanation
Indices: 40674084--40674269 Score: 174
Period size: 51 Copynumber: 3.7 Consensus size: 50
40674074 TGTCTGCGAA
* * * * * ****
40674084 CACGTGTGTAGTACTAAGTGCAGGCTACCACGTGTATCGATAAATAACGGT
1 CACGTGTGTAGTACTATGTGTAGGCTACTACGTGAACCGA-AAAGCGTGGT
* * * * * * *
40674135 CACATGTGTAGTACTAAGTGTAGGCTATTATGTGAACCGGAAGGCCTTGGT
1 CACGTGTGTAGTACTATGTGTAGGCTACTACGTGAACCGAAAAG-CGTGGT
* *
40674186 CATGTGTGTAGTACTATGTGTAGGCTACTACGTGAACCGAAAAGCGTGAT
1 CACGTGTGTAGTACTATGTGTAGGCTACTACGTGAACCGAAAAGCGTGGT
* *
40674236 CACGTGTGTAGTACTATGTGAAGGCTACTGCGTG
1 CACGTGTGTAGTACTATGTGTAGGCTACTACGTG
40674270 TATCGAATGA
Statistics
Matches: 109, Mismatches: 25, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
50 37 0.34
51 72 0.66
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGTAGGCTACTACGTGAACCGAAAAGCGTGGT
Done.