Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 225 of 320
Found at i:74851596 original size:18 final size:18
Alignment explanation
Indices: 74851562--74851598 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
74851552 TTTTATATTT
**
74851562 TTTTAAAAATTTTTTAAA
1 TTTTAAAAATTAATTAAA
74851580 TTTTAAAAATTAATTAAA
1 TTTTAAAAATTAATTAAA
74851598 T
1 T
74851599 ATTGGCATGC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAAAATTAATTAAA
Found at i:74858997 original size:18 final size:18
Alignment explanation
Indices: 74858970--74859004 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
74858960 GATAAATCCT
74858970 AATCAAGGATTTACTCCC
1 AATCAAGGATTTACTCCC
*
74858988 AATCAGGGATTTACTCC
1 AATCAAGGATTTACTCC
74859005 TATATTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (18 bp):
AATCAAGGATTTACTCCC
Found at i:74865351 original size:18 final size:18
Alignment explanation
Indices: 74865328--74865362 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
74865318 TGTTAATATA
74865328 GGAGTAAATCCCTGATTG
1 GGAGTAAATCCCTGATTG
*
74865346 GGAGTAAATCCTTGATT
1 GGAGTAAATCCCTGATT
74865363 AGGATTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (18 bp):
GGAGTAAATCCCTGATTG
Found at i:74870889 original size:18 final size:18
Alignment explanation
Indices: 74870866--74870900 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
74870856 TGTTAATATA
74870866 GGAGTAAATCCCTGATTG
1 GGAGTAAATCCCTGATTG
*
74870884 GGAGTAAATCCTTGATT
1 GGAGTAAATCCCTGATT
74870901 AGGATTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (18 bp):
GGAGTAAATCCCTGATTG
Found at i:74871678 original size:15 final size:15
Alignment explanation
Indices: 74871654--74871683 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
74871644 AACCTAAAAA
*
74871654 TTCTATTTCTATTTT
1 TTCTAATTCTATTTT
74871669 TTCTAATTCTATTTT
1 TTCTAATTCTATTTT
74871684 CTTAGGGCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (15 bp):
TTCTAATTCTATTTT
Found at i:74875714 original size:2 final size:2
Alignment explanation
Indices: 74875702--74875737 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
74875692 TTGGAATGAA
*
74875702 GT GT AT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
74875738 TTAGTACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
GT
Found at i:74883475 original size:29 final size:29
Alignment explanation
Indices: 74883431--74883502 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
74883421 TTTTTCTTTT
* *
74883431 TCAGAATAACATGAAAATAAA-ATTATTTA
1 TCAGAATAATATGAAAA-AAATATTAATTA
*
74883460 -CTAGAATAATATGAAAAAAATTTTAATTA
1 TC-AGAATAATATGAAAAAAATATTAATTA
74883489 TCAGAATAATATGA
1 TCAGAATAATATGA
74883503 CCTCTGGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.11
29 32 0.86
30 1 0.03
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (29 bp):
TCAGAATAATATGAAAAAAATATTAATTA
Found at i:74883735 original size:21 final size:21
Alignment explanation
Indices: 74883702--74883766 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 21
74883692 AGAGTTTATC
74883702 TTTTTATAATTTTATTTTAAAAA
1 TTTTTAT--TTTTATTTTAAAAA
*
74883725 TATTTT-TTTTTATTTTTTTAAAA
1 T-TTTTATTTTTA--TTTTAAAAA
74883748 TTTTTATTTTTA-TTTAAAA
1 TTTTTATTTTTATTTTAAAA
74883767 TGTGAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
20 6 0.17
21 5 0.14
22 4 0.11
23 17 0.47
24 4 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTATTTTTATTTTAAAAA
Found at i:74883747 original size:23 final size:23
Alignment explanation
Indices: 74883716--74883762 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
74883706 TATAATTTTA
74883716 TTTTAAAAATATTTT-TTTTTATT
1 TTTTAAAAAT-TTTTATTTTTATT
*
74883739 TTTTTAAAATTTTTATTTTTATT
1 TTTTAAAAATTTTTATTTTTATT
74883762 T
1 T
74883763 AAAATGTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTTAAAAATTTTTATTTTTATT
Found at i:74883751 original size:19 final size:19
Alignment explanation
Indices: 74883731--74883767 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
74883721 AAAATATTTT
74883731 TTTTTA-TTTT-TTTAAAA
1 TTTTTATTTTTATTTAAAA
74883748 TTTTTATTTTTATTTAAAA
1 TTTTTATTTTTATTTAAAA
74883767 T
1 T
74883768 GTGAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTATTTTTATTTAAAA
Found at i:74884253 original size:11 final size:11
Alignment explanation
Indices: 74884237--74884262 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
74884227 CATATCAAAA
74884237 AATAAATATAT
1 AATAAATATAT
74884248 AATAAATATAT
1 AATAAATATAT
74884259 AATA
1 AATA
74884263 CTACTCTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAAATATAT
Found at i:74885345 original size:27 final size:26
Alignment explanation
Indices: 74885307--74885370 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
74885297 TTATACACAG
* *
74885307 TTTATATTATTTC-AGTAATTAAATTTT
1 TTTATATTATTTCGA-TAAAT-AATATT
74885334 TTTATATTATTTCGATAAATAATATT
1 TTTATATTATTTCGATAAATAATATT
74885360 TTTATATTATT
1 TTTATATTATT
74885371 CCAGGACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 16 0.47
27 17 0.50
28 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (26 bp):
TTTATATTATTTCGATAAATAATATT
Found at i:74885368 original size:26 final size:27
Alignment explanation
Indices: 74885307--74885370 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
74885297 TTATACACAG
* *
74885307 TTTATATTATTTCAGTAATTAAATTTT
1 TTTATATTATTTCAGTAAATAAATATT
74885334 TTTATATTATTTC-GATAAAT-AATATT
1 TTTATATTATTTCAG-TAAATAAATATT
74885360 TTTATATTATT
1 TTTATATTATT
74885371 CCAGGACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 17 0.50
27 17 0.50
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (27 bp):
TTTATATTATTTCAGTAAATAAATATT
Found at i:74889140 original size:41 final size:41
Alignment explanation
Indices: 74889036--74889126 Score: 157
Period size: 41 Copynumber: 2.2 Consensus size: 41
74889026 AATGAACGAC
*
74889036 AAAATCTTT-TACTACATCTATTTTTACAATATCATTTCTTT
1 AAAAT-TTTCTACGACATCTATTTTTACAATATCATTTCTTT
74889077 AAAATTTTCTACGACATCTATTTTTACAATATCATTTCTTT
1 AAAATTTTCTACGACATCTATTTTTACAATATCATTTCTTT
74889118 AAAATTTTC
1 AAAATTTTC
74889127 ACTTTTAGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 3 0.06
41 45 0.94
ACGTcount: A:0.33, C:0.16, G:0.01, T:0.49
Consensus pattern (41 bp):
AAAATTTTCTACGACATCTATTTTTACAATATCATTTCTTT
Found at i:74895602 original size:18 final size:18
Alignment explanation
Indices: 74895579--74895614 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
74895569 AGAATTAAAA
*
74895579 AATAAAAATATATAAATT
1 AATAAAAAAATATAAATT
74895597 AATAAAAAAATATAAATT
1 AATAAAAAAATATAAATT
74895615 TTTTTCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAAAAAATATAAATT
Found at i:74896652 original size:5 final size:6
Alignment explanation
Indices: 74896636--74896661 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
74896626 AGATCGGACC
74896636 ATTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT
74896662 CGAATTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:74897653 original size:16 final size:16
Alignment explanation
Indices: 74897632--74897684 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 16
74897622 TTTGCATTGC
74897632 AAACGAAAGAGATGAG
1 AAACGAAAGAGATGAG
*
74897648 AAACGAAGAAGTGATGGAG
1 AAACG-A-AAGAGAT-GAG
74897667 AAAACGAAAGAGAT-AG
1 -AAACGAAAGAGATGAG
74897683 AA
1 AA
74897685 GAGAAAAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 2 0.06
16 7 0.23
17 1 0.03
18 12 0.39
19 4 0.13
20 5 0.16
ACGTcount: A:0.57, C:0.06, G:0.30, T:0.08
Consensus pattern (16 bp):
AAACGAAAGAGATGAG
Found at i:74898686 original size:82 final size:82
Alignment explanation
Indices: 74898581--74898782 Score: 260
Period size: 82 Copynumber: 2.5 Consensus size: 82
74898571 CAAGAAATAA
** * * *
74898581 CCTTAAAATAAATGTAAGAGGATTGAATTCTAAAAATAATTGAATTTGTATTTTCAAATCCAGAA
1 CCTTAAAATAAATAAAAGAGGATTAAATTCTAAAAATAATTGAATTTATATTTTCAAATCCAAAA
74898646 AATAAAGAGACTAAATT
66 AATAAAGAGACTAAATT
* * * *
74898663 CCTTAAAATAAATAAAAGGGGATTAAATTCTAATAATAATTGAATTTATATTTTTAAATTCAAAA
1 CCTTAAAATAAATAAAAGAGGATTAAATTCTAAAAATAATTGAATTTATATTTTCAAATCCAAAA
**
74898728 AATAAAGAGGTTAAATT
66 AATAAAGAGACTAAATT
* ** * *
74898745 TCTTAAAATAAATGTAAGAGAATTAAATTCCAAAAATA
1 CCTTAAAATAAATAAAAGAGGATTAAATTCTAAAAATA
74898783 CAAAGAATTC
Statistics
Matches: 102, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
82 102 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (82 bp):
CCTTAAAATAAATAAAAGAGGATTAAATTCTAAAAATAATTGAATTTATATTTTCAAATCCAAAA
AATAAAGAGACTAAATT
Found at i:74902496 original size:11 final size:11
Alignment explanation
Indices: 74902482--74902520 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
74902472 GTTTTCTCCC
74902482 TATTTTGCTAT
1 TATTTTGCTAT
*
74902493 TATTTTACTAT
1 TATTTTGCTAT
* *
74902504 TATGTTGCTAC
1 TATTTTGCTAT
74902515 TATTTT
1 TATTTT
74902521 ATTGTTATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.21, C:0.10, G:0.08, T:0.62
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:74902766 original size:12 final size:12
Alignment explanation
Indices: 74902745--74902778 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
74902735 TATATATTTT
*
74902745 AAAATTATATAA
1 AAAATAATATAA
74902757 AAAATAATATAA
1 AAAATAATATAA
*
74902769 AAATTAATAT
1 AAAATAATAT
74902779 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:74905259 original size:40 final size:40
Alignment explanation
Indices: 74905222--74905406 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
74905212 GCTACTCGTT
*
74905222 CAATTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAATTGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
74905262 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAATTGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
74905302 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAATTGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
74905341 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAATTGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
74905382 CAA-AGCCTTCGGGACTTAGCCCGGA
1 CAATTGCCTTCGGGACTTAGCCCGGA
74905407 CATCATTCAA
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.26
40 78 0.62
41 12 0.10
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAATTGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:74905325 original size:79 final size:81
Alignment explanation
Indices: 74905226--74905406 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 81
74905216 CTCGTTCAAT
* * *
74905226 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCCGGAT
1 TGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGAT
* *
74905289 TTAGTAAC-TCGCACAAA
64 ATAGTAACTTAGCACAAA
* **
74905306 TGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATAT
1 TGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATAT
* *
74905370 GGTCACTTAGCACAAA
66 AGTAACTTAGCACAAA
74905386 -GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGACTTAGCCCGGA
74905407 CATCATTCAA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 54 0.62
80 30 0.34
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
TGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATAT
AGTAACTTAGCACAAA
Found at i:74908687 original size:19 final size:20
Alignment explanation
Indices: 74908663--74908700 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
74908653 TTTCTAAGAT
74908663 AGAATATCT-TGTAATTATA
1 AGAATATCTATGTAATTATA
*
74908682 AGAATATGTATGTAATTAT
1 AGAATATCTATGTAATTAT
74908701 CATTTAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (20 bp):
AGAATATCTATGTAATTATA
Found at i:74914515 original size:21 final size:21
Alignment explanation
Indices: 74914491--74914550 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 21
74914481 TATTCCCTTC
74914491 AAAAGTCTATCAAATTTC-ATT
1 AAAAGTCTATCAAATTTCTA-T
* * * *
74914512 AAAATTTTCTCAAAATTCTAT
1 AAAAGTCTATCAAATTTCTAT
*
74914533 CAAAGTTCTATCAAATTT
1 AAAAG-TCTATCAAATTT
74914551 GTTTGTTTAA
Statistics
Matches: 28, Mismatches: 9, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (21 bp):
AAAAGTCTATCAAATTTCTAT
Found at i:74914535 original size:11 final size:11
Alignment explanation
Indices: 74914489--74914547 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
74914479 AATATTCCCT
*
74914489 TCAAAAGTCTA
1 TCAAAATTCTA
*
74914500 TCAAATTTC-A
1 TCAAAATTCTA
* * *
74914510 TTAAAATTTTC
1 TCAAAATTCTA
74914521 TCAAAATTCTA
1 TCAAAATTCTA
*
74914532 TCAAAGTTCTA
1 TCAAAATTCTA
74914543 TCAAA
1 TCAAA
74914548 TTTGTTTGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
10 7 0.19
11 30 0.81
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.37
Consensus pattern (11 bp):
TCAAAATTCTA
Found at i:74914805 original size:49 final size:48
Alignment explanation
Indices: 74914671--74914806 Score: 161
Period size: 48 Copynumber: 2.8 Consensus size: 48
74914661 AGTGATAATT
* *
74914671 TTAAATTTTCAAAACTA-TTCGATATTTTTTTCATTTATGCAAATTTAA
1 TTAAATTTGCAATACTACTT-GATATTTTTTTCATTTATGCAAATTTAA
* *
74914719 TTAAATTTGCAATACTATTTGATATTTTATTCATTTATGC-AATTATAA
1 TTAAATTTGCAATACTACTTGATATTTTTTTCATTTATGCAAATT-TAA
* *
74914767 TTACAATTT-CAATACTGCTTGATTTTTTTTTTCATTTATG
1 TTA-AATTTGCAATACTACTTGA-TATTTTTTTCATTTATG
74914807 ATGTTTGCAT
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
47 4 0.05
48 51 0.66
49 22 0.29
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (48 bp):
TTAAATTTGCAATACTACTTGATATTTTTTTCATTTATGCAAATTTAA
Found at i:74915825 original size:14 final size:15
Alignment explanation
Indices: 74915793--74915825 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
74915783 TTCATATTCA
74915793 GTATTTAGTATTTAT
1 GTATTTAGTATTTAT
74915808 -TATTTAGTA-TTAT
1 GTATTTAGTATTTAT
74915821 GTATT
1 GTATT
74915826 ATGTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (15 bp):
GTATTTAGTATTTAT
Found at i:74920395 original size:126 final size:125
Alignment explanation
Indices: 74919900--74920404 Score: 608
Period size: 125 Copynumber: 4.0 Consensus size: 125
74919890 ATTTATAACC
* ** * * *
74919900 TTATTTTTCTATGAACTACTGTAGCAAAA-AAAGTCTACGTGGGAGCTTTTTTTTC-GAAATTTT
1 TTATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGT-GGAGC--TTTTTCCAAAAATTTT
* * * * * *
74919963 CCTGATAGTGCATCATCCTTGAAGCGTTTTCAACAC--TTTGTTCAGAAACGTCTA-TCAAAA
63 GCTGACAATGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTCAAAA
* * * *
74920023 TTATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGAGAGTTTTTTACAGAAATTTTAC
1 TTATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTG-GAGCTTTTTCCAAAAATTTTGC
* * *
74920088 TGACAATGCATCCTACTTGAAGCTTTTTCGACACTATTTGTTCAGAAATGTCTACTCAAAA
65 TGACAATGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTCAAAA
** * * *
74920149 TT-TTTTTCTATAAATTATTGTAGCAAAAGAGCATCCACGTGGGAGCTTTTTCCAAAAATTTTGC
1 TTATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGT-GGAGCTTTTTCCAAAAATTTTGC
* *
74920213 TGACAATACATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAA
65 TGACAATGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTCAAAA
* *
74920274 TTATTTTTCTACGAACTACTGTAACAAAAGAGCGTCCATGTGGAGCTTTTTCCAAAAATTTTGCT
1 TTATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGAGCTTTTTCCAAAAATTTTGCT
* * * * * *
74920339 GACAGTGCATTCTGCTTGAATCGTTTTTCGACACTATTTGTTCAAAAACGTTTACTCAGAA
66 GACAATGCATCCTGCTTGAAGCG-TTTTCGACACTATTTGTTCAGAAACGTCTACTCAAAA
74920400 TTATT
1 TTATT
74920405 CTTGCAAAAA
Statistics
Matches: 332, Mismatches: 41, Indels: 15
0.86 0.11 0.04
Matches are distributed among these distances:
122 6 0.02
123 66 0.20
124 11 0.03
125 169 0.51
126 80 0.24
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (125 bp):
TTATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGAGCTTTTTCCAAAAATTTTGCT
GACAATGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTCAAAA
Found at i:74920979 original size:38 final size:39
Alignment explanation
Indices: 74920937--74921015 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 39
74920927 ATTATGTATC
*
74920937 AATTAA-CCTTAAATTTAATCAATTAACCTTAA-ACCCTA
1 AATTAATCCTT-AATTTAATCAATTAACCCTAATACCCTA
*
74920975 AATTAATTCTTAATTTAATCAATTAACCCTAATACCCTA
1 AATTAATCCTTAATTTAATCAATTAACCCTAATACCCTA
74921014 AA
1 AA
74921016 CTCTAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 26 0.70
39 11 0.30
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.35
Consensus pattern (39 bp):
AATTAATCCTTAATTTAATCAATTAACCCTAATACCCTA
Found at i:74926951 original size:15 final size:16
Alignment explanation
Indices: 74926925--74926958 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
74926915 TTTAGCTCTG
*
74926925 TTTTCTTTTTTTTTTC
1 TTTTCTTTTTTTTTCC
74926941 TTTTC-TTTTTTTTCC
1 TTTTCTTTTTTTTTCC
74926956 TTT
1 TTT
74926959 CTACTGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTCTTTTTTTTTCC
Found at i:74928285 original size:31 final size:29
Alignment explanation
Indices: 74928207--74928300 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 29
74928197 CTATGGGTCA
* *
74928207 TTTTCTTTTTTAGTCACTCAACTAT-ATT
1 TTTTCTTTTTTGGTCACCCAACTATGATT
* *
74928235 TTTT-TTTATATTGGCCACCCAACAATGGATT
1 TTTTCTTT-T-TTGGTCACCCAACTAT-GATT
74928266 TGTTTCTTTTTTGGTCACCCAACTATGAATT
1 T-TTTCTTTTTTGGTCACCCAACTATG-ATT
74928297 TTTT
1 TTTT
74928301 AAATTTGGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.06
28 5 0.09
29 12 0.23
30 4 0.08
31 22 0.42
32 4 0.08
33 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.51
Consensus pattern (29 bp):
TTTTCTTTTTTGGTCACCCAACTATGATT
Found at i:74928905 original size:17 final size:19
Alignment explanation
Indices: 74928868--74928905 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
74928858 TGTTATATTT
*
74928868 TTTTGAAGATGTTTATGTA
1 TTTTGAAGATGTTTATATA
74928887 TTTT-AAGAT-TTTATATA
1 TTTTGAAGATGTTTATATA
74928904 TT
1 TT
74928906 ATTATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 5 0.28
19 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (19 bp):
TTTTGAAGATGTTTATATA
Found at i:74928955 original size:17 final size:17
Alignment explanation
Indices: 74928923--74928965 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
74928913 ATTGTCAACA
**
74928923 ATATTTTTTATTTATAT
1 ATATTTTTTAAGTATAT
74928940 ATATTTTTTAAGTATAT
1 ATATTTTTTAAGTATAT
74928957 -TATTATTTT
1 ATATT-TTTT
74928966 GAAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
ATATTTTTTAAGTATAT
Found at i:74929832 original size:21 final size:21
Alignment explanation
Indices: 74929806--74929849 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
74929796 TCGTACTAGA
74929806 ATCAAATTGTAAACACAGTGT
1 ATCAAATTGTAAACACAGTGT
74929827 ATCAAATTGTAAACACAGTGT
1 ATCAAATTGTAAACACAGTGT
74929848 AT
1 AT
74929850 ACGTACCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (21 bp):
ATCAAATTGTAAACACAGTGT
Found at i:74934446 original size:24 final size:24
Alignment explanation
Indices: 74934378--74934450 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
74934368 GTTATGTAGA
* *
74934378 TAAAAAATGTTAACATTTTAAAAT
1 TAAAAAATATTCACATTTTAAAAT
*** *
74934402 T-AATTTTACTCA-ATTTTAAAAT
1 TAAAAAATATTCACATTTTAAAAT
74934424 TAAAAAATATTCACATTTTAAAAT
1 TAAAAAATATTCACATTTTAAAAT
74934448 TAA
1 TAA
74934451 TTTACTTTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
22 11 0.30
23 12 0.32
24 14 0.38
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (24 bp):
TAAAAAATATTCACATTTTAAAAT
Found at i:74948118 original size:13 final size:14
Alignment explanation
Indices: 74948100--74948133 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
74948090 TCAAGTTCGT
74948100 TTAATTGAA-AAAA
1 TTAATTGAACAAAA
74948113 TTAATTGAATCAAAA
1 TTAATTGAA-CAAAA
74948128 TTAATT
1 TTAATT
74948134 TGATTTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
15 10 0.53
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (14 bp):
TTAATTGAACAAAA
Found at i:74948948 original size:31 final size:32
Alignment explanation
Indices: 74948913--74948991 Score: 124
Period size: 31 Copynumber: 2.5 Consensus size: 32
74948903 AAGATCAGTA
74948913 AAAAGATTCGATTAATACAATATTTACACT-T
1 AAAAGATTCGATTAATACAATATTTACACTAT
*
74948944 AAAAGATTAGATTAATACAATATTTACACTAT
1 AAAAGATTCGATTAATACAATATTTACACTAT
*
74948976 AAAATGATTCAATTAA
1 AAAA-GATTCGATTAA
74948992 AATGTTTCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 29 0.67
32 5 0.12
33 9 0.21
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.34
Consensus pattern (32 bp):
AAAAGATTCGATTAATACAATATTTACACTAT
Found at i:74959768 original size:30 final size:30
Alignment explanation
Indices: 74959734--74959802 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
74959724 TCATGTTGGA
74959734 GCTTAAACT-AGCAATTGTTCCCATATTGAG
1 GCTTAAACTAAGCAATTGTTCCCATATT-AG
**
74959764 GCTTAAGTTAAGCAATTGTTCCCATATTAG
1 GCTTAAACTAAGCAATTGTTCCCATATTAG
*
74959794 GCTTGAACT
1 GCTTAAACT
74959803 TTAAGGTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (30 bp):
GCTTAAACTAAGCAATTGTTCCCATATTAG
Found at i:74965215 original size:23 final size:21
Alignment explanation
Indices: 74965164--74965215 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
74965154 TTTAATAAGT
74965164 TAATATTTACTGTTTGAAAAA
1 TAATATTTACTGTTTGAAAAA
74965185 T-ATCATTTACTGTTTGATATAAA
1 TAAT-ATTTACTGTTTGA-A-AAA
74965208 TAATATTT
1 TAATATTT
74965216 TTATCGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.07
21 14 0.52
22 1 0.04
23 8 0.30
24 2 0.07
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (21 bp):
TAATATTTACTGTTTGAAAAA
Found at i:74965422 original size:25 final size:25
Alignment explanation
Indices: 74965394--74965443 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
74965384 GATCTATCAG
74965394 CTTTCATAGTTTTAATAAATTTAAC
1 CTTTCATAGTTTTAATAAATTTAAC
74965419 CTTTCATAGTTTTAATAAATTTAAC
1 CTTTCATAGTTTTAATAAATTTAAC
74965444 TTATTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (25 bp):
CTTTCATAGTTTTAATAAATTTAAC
Found at i:74967950 original size:39 final size:40
Alignment explanation
Indices: 74967896--74968030 Score: 209
Period size: 40 Copynumber: 3.4 Consensus size: 40
74967886 GACTTATAGT
* *
74967896 CCGCAGGCTTTGTGCTGGCAATAGATATCCAGGTTAAATC
1 CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
*
74967936 CCACAGGC-TTGTGCTGGTAATAGATATCCGGGTTAAATC
1 CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
* *
74967975 CCGCAGGCTTTGTGTTGGTAATAGATATCTGGGTTAAATC
1 CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
*
74968015 CCGTAGGCTTTGTGCT
1 CCGCAGGCTTTGTGCT
74968031 AGAAATTGGA
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 36 0.42
40 50 0.58
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (40 bp):
CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
Found at i:74970606 original size:16 final size:16
Alignment explanation
Indices: 74970587--74970654 Score: 66
Period size: 16 Copynumber: 4.1 Consensus size: 16
74970577 AATTAATCTT
*
74970587 TTAAAAATTA-AAAATT
1 TTAAAAATTATAAAA-A
*
74970603 TTAAAAAATATAAAAA
1 TTAAAAATTATAAAAA
*
74970619 TTAGAAATTATTAAAAA
1 TTAAAAATTA-TAAAAA
74970636 GTATAAAAATTATAAAAA
1 -T-TAAAAATTATAAAAA
74970654 T
1 T
74970655 ATTTTTAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
16 17 0.40
17 11 0.26
18 7 0.16
19 8 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
TTAAAAATTATAAAAA
Found at i:74970632 original size:26 final size:25
Alignment explanation
Indices: 74970588--74970652 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 25
74970578 ATTAATCTTT
74970588 TAAAAATTAAAAATTTTAAAAAATA
1 TAAAAATTAAAAATTTTAAAAAATA
* *
74970613 TAAAAATTAGAAATTATTAAAAAGTA
1 TAAAAATTAAAAATT-TTAAAAAATA
74970639 TAAAAATTATAAAA
1 TAAAAATTA-AAAA
74970653 ATATTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 14 0.40
26 18 0.51
27 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (25 bp):
TAAAAATTAAAAATTTTAAAAAATA
Found at i:74971363 original size:8 final size:8
Alignment explanation
Indices: 74971340--74971369 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
74971330 ACAATATTTT
74971340 AATTTAAA
1 AATTTAAA
74971348 ATATTTAAA
1 A-ATTTAAA
74971357 AATTTAAA
1 AATTTAAA
74971365 AATTT
1 AATTT
74971370 GATTCATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AATTTAAA
Found at i:74977222 original size:18 final size:18
Alignment explanation
Indices: 74977189--74977223 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
74977179 TATAAGCCTC
*
74977189 AAATATGAACAGTAAAAT
1 AAATATGAACAATAAAAT
*
74977207 AAATATGAAGAATAAAA
1 AAATATGAACAATAAAA
74977224 AAAAATAGTA
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:0.66, C:0.03, G:0.11, T:0.20
Consensus pattern (18 bp):
AAATATGAACAATAAAAT
Found at i:74977230 original size:19 final size:18
Alignment explanation
Indices: 74977189--74977227 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
74977179 TATAAGCCTC
* *
74977189 AAATATGAACAGTAAAAT
1 AAATATGAACAATAAAAA
*
74977207 AAATATGAAGAATAAAAA
1 AAATATGAACAATAAAAA
74977225 AAA
1 AAA
74977228 ATAGTATAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (18 bp):
AAATATGAACAATAAAAA
Found at i:74978230 original size:25 final size:25
Alignment explanation
Indices: 74978167--74978231 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
74978157 TCTGAAATAA
*
74978167 ATATTTGAAATGTTTTATAATATAT
1 ATATTTGAAATATTTTATAATATAT
* **
74978192 ATTTTTCTAA-ATTTTA-AATATAT
1 ATATTTGAAATATTTTATAATATAT
74978215 ATATTTGAAATTATTTT
1 ATATTTGAAA-TATTTT
74978232 TGAAATTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
23 14 0.45
24 5 0.16
25 12 0.39
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (25 bp):
ATATTTGAAATATTTTATAATATAT
Found at i:74978264 original size:33 final size:32
Alignment explanation
Indices: 74978191--74978286 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 32
74978181 TTATAATATA
* *
74978191 TATTTTTCTAAATTTTAAATATATATATTTGAAAT
1 TATTTTT-AAAATTTTAAATAT-TAT-TTTAAAAT
*
74978226 TATTTTTGAAATTTTAAATATTAGTTTTAAAAT
1 TATTTTTAAAATTTTAAATATTA-TTTTAAAAT
74978259 TATTTTTTAAAATTTTAAATATTATTTT
1 TA-TTTTTAAAATTTTAAATATTATTTT
74978287 TTAAATATTA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
33 15 0.27
34 34 0.61
35 7 0.12
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (32 bp):
TATTTTTAAAATTTTAAATATTATTTTAAAAT
Found at i:74978285 original size:22 final size:22
Alignment explanation
Indices: 74978250--74978310 Score: 92
Period size: 21 Copynumber: 2.9 Consensus size: 22
74978240 TAAATATTAG
74978250 TTTTAAA-ATTATTTTTTAAAA
1 TTTTAAATATTATTTTTTAAAA
74978271 TTTTAAATATTATTTTTT-AAA
1 TTTTAAATATTATTTTTTAAAA
*
74978292 TATTAAATA-TATTTTTTAA
1 TTTTAAATATTATTTTTTAA
74978311 TAATATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 8 0.22
21 19 0.51
22 10 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTAAATATTATTTTTTAAAA
Found at i:74978290 original size:14 final size:13
Alignment explanation
Indices: 74978237--74978296 Score: 58
Period size: 12 Copynumber: 4.9 Consensus size: 13
74978227 ATTTTTGAAA
*
74978237 TTTTAAATATTAG
1 TTTTAAATATTAT
74978250 TTTTAAA-ATTAT
1 TTTTAAATATTAT
*
74978262 TTTTTAA-A--A-
1 TTTTAAATATTAT
74978271 TTTTAAATATTATT
1 TTTTAAATATTA-T
74978285 TTTTAAATATTA
1 TTTTAAATATTA
74978297 AATATATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 6 0.15
10 2 0.05
12 12 0.31
13 7 0.18
14 12 0.31
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
TTTTAAATATTAT
Found at i:74978307 original size:20 final size:20
Alignment explanation
Indices: 74978255--74978310 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
74978245 ATTAGTTTTA
*
74978255 AAAT-TATTTTTTAAAATTTT
1 AAATATATTTTTT-AAATATT
74978275 AAATATTATTTTTTAAATATT
1 AAATA-TATTTTTTAAATATT
74978296 AAATATATTTTTTAA
1 AAATATATTTTTTAA
74978311 TAATATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 14 0.42
21 11 0.33
22 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATATATTTTTTAAATATT
Found at i:74978315 original size:22 final size:21
Alignment explanation
Indices: 74978255--74978316 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
74978245 ATTAGTTTTA
*
74978255 AAAT-TATTTTTTAAAATTTT
1 AAATATATTTTTTAAAATATT
74978275 AAATATTATTTTTT-AAATATT
1 AAATA-TATTTTTTAAAATATT
74978296 AAATATATTTTTTAATAATAT
1 AAATATATTTTTTAA-AATAT
74978317 AAAACATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 12 0.32
21 12 0.32
22 13 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATATATTTTTTAAAATATT
Found at i:74978319 original size:21 final size:20
Alignment explanation
Indices: 74978255--74978319 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 20
74978245 ATTAGTTTTA
*
74978255 AAAT-TATTTTTTAAAATTTT
1 AAATATATTTTTTAAAA-TAT
74978275 AAATATTATTTTTT-AAATATT
1 AAATA-TATTTTTTAAAATA-T
74978296 AAATATATTTTTTAATAATAT
1 AAATATATTTTTTAA-AATAT
74978317 AAA
1 AAA
74978320 ACATTTAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
20 13 0.33
21 14 0.36
22 12 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATATATTTTTTAAAATAT
Found at i:74978501 original size:20 final size:20
Alignment explanation
Indices: 74978458--74978501 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
74978448 TATTTAAAAG
* * *
74978458 TTAAAAAAATAATATTTTAT
1 TTAAAAAAATAAAATTTGAA
*
74978478 TTAAAAAAGTAAAATTTGAA
1 TTAAAAAAATAAAATTTGAA
74978498 TTAA
1 TTAA
74978502 TTTGAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
TTAAAAAAATAAAATTTGAA
Found at i:74978554 original size:16 final size:16
Alignment explanation
Indices: 74978531--74978578 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
74978521 GAAAAGATTT
74978531 ATTT-TTTAAAAATAA
1 ATTTATTTAAAAATAA
*
74978546 ATTTATTTAAAAATAT
1 ATTTATTTAAAAATAA
*
74978562 ATATA-TTAAAAAGTAA
1 ATTTATTTAAAAA-TAA
74978578 A
1 A
74978579 AATCTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTTATTTAAAAATAA
Found at i:74978591 original size:20 final size:20
Alignment explanation
Indices: 74978553--74978612 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
74978543 TAAATTTATT
74978553 TAAAAATATATATATTAAAAAG
1 TAAAAATATA-A-ATTAAAAAG
* *
74978575 TAAAAATCTAAATTAAAAAT
1 TAAAAATATAAATTAAAAAG
*
74978595 TAAAAATATATATTAAAA
1 TAAAAATATAAATTAAAA
74978613 TTTTATATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 24 0.71
21 1 0.03
22 9 0.26
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAAAATATAAATTAAAAAG
Found at i:74978722 original size:21 final size:21
Alignment explanation
Indices: 74978684--74978772 Score: 54
Period size: 21 Copynumber: 3.9 Consensus size: 21
74978674 CCACCAAATA
**
74978684 AAATATTAATTTTTAAAATTTT
1 AAAT-TTAATTTAAAAAATTTT
74978706 AAATTTAATTTAAAAAATGTTT
1 AAATTTAATTTAAAAAAT-TTT
* * *
74978728 GAATAT-CTTTAAAATTAATTTT
1 AAATTTAATTTAAAA--AATTTT
74978750 AAAATTAATAATTTATAAAAATT
1 -AAATT--TAATTTA-AAAAATT
74978773 ATATTTAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
21 19 0.37
22 14 0.27
23 6 0.12
25 5 0.10
26 4 0.08
27 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATTTAATTTAAAAAATTTT
Found at i:74978876 original size:14 final size:15
Alignment explanation
Indices: 74978859--74978941 Score: 64
Period size: 14 Copynumber: 5.3 Consensus size: 15
74978849 TATATGTTAA
74978859 ATAATTTAAAA-ATT
1 ATAATTTAAAATATT
74978873 ATAATTTAAAATATT
1 ATAATTTAAAATATT
74978888 ATAAAATAAATTAAAAATATTT
1 AT--AAT---TT-AAAATA-TT
*
74978910 AAAATTTAAAATA-T
1 ATAATTTAAAATATT
*
74978924 A-CATTTAAAATATT
1 ATAATTTAAAATATT
74978938 ATAA
1 ATAA
74978942 AACTAATAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.18
14 15 0.27
15 6 0.11
16 6 0.11
17 5 0.09
20 5 0.09
21 6 0.11
22 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTTAAAATATT
Found at i:74978904 original size:21 final size:20
Alignment explanation
Indices: 74978875--74978914 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
74978865 TAAAAATTAT
*
74978875 AATTTAAAATATTATAAAATA
1 AATTAAAAATATT-TAAAATA
74978896 AATTAAAAATATTTAAAAT
1 AATTAAAAATATTTAAAAT
74978915 TTAAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTAAAAATATTTAAAATA
Found at i:74978912 original size:30 final size:29
Alignment explanation
Indices: 74978876--74978943 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
74978866 AAAAATTATA
74978876 ATTTAAAATATTATAAA-ATAAATTAAAAAT
1 ATTTAAAAT-TTA-AAATATAAATTAAAAAT
* *
74978906 ATTTAAAATTTAAAATATACATTTAAAAT
1 ATTTAAAATTTAAAATATAAATTAAAAAT
74978935 ATTATAAAA
1 ATT-TAAAA
74978944 CTAATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 3 0.09
29 17 0.50
30 14 0.41
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (29 bp):
ATTTAAAATTTAAAATATAAATTAAAAAT
Found at i:74979013 original size:133 final size:130
Alignment explanation
Indices: 74978773--74979045 Score: 333
Period size: 133 Copynumber: 2.1 Consensus size: 130
74978763 TATAAAAATT
*
74978773 ATATTTAAAAATTTAAAAATATTTAAAAAATTATAAAACAAATAATAAATTTGAAAGGTCATATC
1 ATATTT-AAAATTTAAAAATATTTAAAAAATTATAAAACAAATAATAAATTTGAAAGGTCATAAC
*
74978838 TTTAAAAATATTATATGTTAAATAATTTAAAAATTATAATTTAAAATATTATAAAA-TAA-ATTA
65 TTTAAAAATATTATATGTTAAATAATTTAAAAAATATAATTT--AATATTATAAAACTAATATTA
74978901 AAA
128 AAA
* * *
74978904 ATATTTAAAATTTAAAATATACATTTAAAATATTATAAAACTAATAATAAATTTGAACGGTCATA
1 ATATTTAAAATTTAAAA-AT--ATTTAAAAAATTATAAAACAAATAATAAATTTGAAAGGTCATA
* * * *
74978969 ACTTT-AAAATATTAAAATATTTTATATTA-TTAAAAAATAT-ATTTAATATTTTAAAACTAATA
63 ACTTTAAAAATATT---ATATGTTAAATAATTTAAAAAATATAATTTAATATTATAAAACTAATA
*
74979031 TTTAAA
125 TTAAAA
74979037 AT-TTTAAAA
1 ATATTTAAAA
74979046 AATAATTTCA
Statistics
Matches: 124, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
130 11 0.09
131 19 0.15
132 18 0.15
133 56 0.45
134 10 0.08
135 10 0.08
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (130 bp):
ATATTTAAAATTTAAAAATATTTAAAAAATTATAAAACAAATAATAAATTTGAAAGGTCATAACT
TTAAAAATATTATATGTTAAATAATTTAAAAAATATAATTTAATATTATAAAACTAATATTAAAA
Found at i:74979022 original size:21 final size:21
Alignment explanation
Indices: 74978982--74979053 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
74978972 TTAAAATATT
74978982 AAAATAT-TTT-ATATTATTAA
1 AAAATATATTTAATATT-TTAA
74979002 AAAATATATTTAATATTTT-A
1 AAAATATATTTAATATTTTAA
* *
74979022 AAACTAATATTTAAAATTTTAA
1 AAAAT-ATATTTAATATTTTAA
74979044 AAAATA-ATTT
1 AAAATATATTT
74979054 CAAATATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
20 16 0.36
21 19 0.42
22 10 0.22
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAATATATTTAATATTTTAA
Found at i:74979195 original size:31 final size:30
Alignment explanation
Indices: 74979136--74979194 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
74979126 TAAGGATAAA
74979136 GACAAAACTTAAAAAAAGTAAAAAAAAAAG
1 GACAAAACTTAAAAAAAGTAAAAAAAAAAG
*
74979166 GACAAAAGTTAAAAAAAGTAAAAAAAAAA
1 GACAAAACTTAAAAAAAGTAAAAAAAAAA
74979195 AAACCAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.75, C:0.05, G:0.10, T:0.10
Consensus pattern (30 bp):
GACAAAACTTAAAAAAAGTAAAAAAAAAAG
Found at i:74984660 original size:9 final size:9
Alignment explanation
Indices: 74984648--74984674 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
74984638 CATTTCTCTC
74984648 TCTTTTCTT
1 TCTTTTCTT
74984657 TCTTTTCTT
1 TCTTTTCTT
74984666 TCTTTTCTT
1 TCTTTTCTT
74984675 CGTGTTCCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (9 bp):
TCTTTTCTT
Found at i:74984728 original size:13 final size:13
Alignment explanation
Indices: 74984710--74984764 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
74984700 TTCTATTCTT
74984710 TTTATTTTCTTTA
1 TTTATTTTCTTTA
74984723 TTTA-TTTCATTTA
1 TTTATTTTC-TTTA
*
74984736 CTTATTTGT-TTTA
1 TTTATTT-TCTTTA
*
74984749 TTATATTTACTTTA
1 TT-TATTTTCTTTA
74984763 TT
1 TT
74984765 ATTATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
12 4 0.12
13 16 0.47
14 13 0.38
15 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTATTTTCTTTA
Found at i:74984766 original size:26 final size:24
Alignment explanation
Indices: 74984705--74984767 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 24
74984695 GTTCTTTCTA
74984705 TTCTTT-TTATTTTCTTTATTTAT
1 TTCTTTATTATTTTCTTTATTTAT
74984728 TTCATTTACTTATTTGT-TTTATTATAT
1 TTC-TTTA-TTATTT-TCTTTATT-TAT
74984755 TTACTTTATTATT
1 TT-CTTTATTATT
74984768 ATATTATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
23 3 0.09
24 3 0.09
26 17 0.50
27 10 0.29
28 1 0.03
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (24 bp):
TTCTTTATTATTTTCTTTATTTAT
Found at i:74985761 original size:34 final size:33
Alignment explanation
Indices: 74985723--74985834 Score: 118
Period size: 34 Copynumber: 3.3 Consensus size: 33
74985713 TGTAATGATA
*
74985723 TGTTATAAGCATGATAATTGTTA-CTATATCAATT
1 TGTTATAAGCATGAT-ATTGCTATC-ATATCAATT
* **
74985757 TGTTATAAGCATGCTATTGCTATCATATTGATT
1 TGTTATAAGCATGATATTGCTATCATATCAATT
* * **
74985790 TGTTATAAGCATGTCTATTGCTATCGTATTGATT
1 TGTTATAAGCATG-ATATTGCTATCATATCAATT
74985824 TGTTATAAGCA
1 TGTTATAAGCA
74985835 CGTAAACATG
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
33 26 0.37
34 45 0.63
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTTATAAGCATGATATTGCTATCATATCAATT
Found at i:74985902 original size:34 final size:35
Alignment explanation
Indices: 74985863--74985947 Score: 129
Period size: 34 Copynumber: 2.5 Consensus size: 35
74985853 ACTATACTGA
* *
74985863 CTTGTTATAAGCATGTCTATTGCTACCGTATTGAT
1 CTTGTTATAAGCATGTCTATTACTACCATATTGAT
74985898 -TTGTTATAAGCATGTCTATTACTACCATATTGAT
1 CTTGTTATAAGCATGTCTATTACTACCATATTGAT
*
74985932 CTT-CTATAAGCATGTC
1 CTTGTTATAAGCATGTC
74985948 ATGTCTAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 44 0.96
35 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (35 bp):
CTTGTTATAAGCATGTCTATTACTACCATATTGAT
Found at i:74988574 original size:40 final size:40
Alignment explanation
Indices: 74988510--74988616 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
74988500 AAATCAAAGT
* * *
74988510 TATCTCAATATCACACACTTAGTGCCACATATAGCCGAAGT
1 TATCTCCA-ATCACACACTAAGTGCCACATATAGCCGAAGC
* *
74988551 TAT-TCCAACTCACACACTAAGTGCTATATATAGCCGAAGC
1 TATCTCCAA-TCACACACTAAGTGCCACATATAGCCGAAGC
* * *
74988591 TATCTCGAAACGCACACTAAGTGCCA
1 TATCTCCAATCACACACTAAGTGCCA
74988617 AACATAGTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
39 1 0.02
40 47 0.85
41 7 0.13
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (40 bp):
TATCTCCAATCACACACTAAGTGCCACATATAGCCGAAGC
Found at i:74990122 original size:40 final size:40
Alignment explanation
Indices: 74990001--74990114 Score: 126
Period size: 40 Copynumber: 2.8 Consensus size: 40
74989991 TCACATTAAA
74990001 TCGAAGCTATCTTAATATCGCACACCT-AGTGCCACATATAG
1 TCGAAGCTATCTTAATA-CGCACA-CTAAGTGCCACATATAG
* * * * *
74990042 TCGAAGCTAT-TCCAATTCGCACACTAAATGCTATATATAG
1 TCGAAGCTATCT-TAATACGCACACTAAGTGCCACATATAG
74990082 TCGAAGCTATCTTGAA-ACGCACACTAAGTGCCA
1 TCGAAGCTATCTT-AATACGCACACTAAGTGCCA
74990115 AGCATAGTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
39 2 0.03
40 42 0.70
41 16 0.27
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (40 bp):
TCGAAGCTATCTTAATACGCACACTAAGTGCCACATATAG
Found at i:74990852 original size:27 final size:27
Alignment explanation
Indices: 74990814--74990867 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
74990804 CCCTAGAATG
*
74990814 CCTTAAATCTCTCTTTTCTTATTTATT
1 CCTTAAATCTCTCTTTCCTTATTTATT
74990841 CCTTAAATCTCTCTTTCCTTATTTATT
1 CCTTAAATCTCTCTTTCCTTATTTATT
74990868 TTCGATTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (27 bp):
CCTTAAATCTCTCTTTCCTTATTTATT
Found at i:74999795 original size:13 final size:14
Alignment explanation
Indices: 74999779--74999814 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
74999769 CAATCTCATA
74999779 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
74999792 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
74999805 TCTC-ATTTCA
1 TCTCAATTTCA
74999815 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:74999804 original size:18 final size:19
Alignment explanation
Indices: 74999766--74999806 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
74999756 TGGTTCATGT
74999766 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
74999785 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
74999803 TTTC
1 TTTC
74999807 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:74999996 original size:39 final size:38
Alignment explanation
Indices: 74999929--75000063 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
74999919 ACCAATATGG
* * *
74999929 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
74999968 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
75000006 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
75000047 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
75000064 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:75000332 original size:18 final size:19
Alignment explanation
Indices: 75000306--75000344 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
75000296 TTTCAATTCA
75000306 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
75000325 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
75000343 AT
1 AT
75000345 ATTTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:75001639 original size:10 final size:10
Alignment explanation
Indices: 75001612--75001649 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
75001602 TTATTTCTTC
*
75001612 TCTGTTTCGT
1 TCTGTTTCAT
75001622 T-TGCTTTCAT
1 TCTG-TTTCAT
75001632 TCTGTTTCAT
1 TCTGTTTCAT
75001642 TCTGTTTC
1 TCTGTTTC
75001650 TTTACTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.05, C:0.21, G:0.13, T:0.61
Consensus pattern (10 bp):
TCTGTTTCAT
Found at i:75001671 original size:5 final size:5
Alignment explanation
Indices: 75001661--75001713 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
75001651 TTACTTATTT
* *
75001661 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
75001709 ATATA
1 ATATA
75001714 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:75001677 original size:12 final size:12
Alignment explanation
Indices: 75001660--75001715 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
75001650 TTTACTTATT
75001660 TATATAATATAA
1 TATATAATATAA
75001672 TATATAATATAATA
1 TATATAATAT-A-A
75001686 TACTATAATATAA
1 TA-TATAATATAA
*
75001699 TA-ATAATTTAA
1 TATATAATATAA
75001710 TATATA
1 TATATA
75001716 TTTTAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:75004121 original size:41 final size:40
Alignment explanation
Indices: 75004073--75004182 Score: 136
Period size: 40 Copynumber: 2.7 Consensus size: 40
75004063 TCACATTAAA
75004073 TCGAAGCTATCTCAATATCGCACACCT-AGTGCCACATATAG
1 TCGAAGCTATCTCAAT-TCGCACA-CTAAGTGCCACATATAG
* *
75004114 TCGAAGCTAT-TCCAATTCGCACACTAAGTGCTATATATAG
1 TCGAAGCTATCT-CAATTCGCACACTAAGTGCCACATATAG
*
75004154 TCGAAGCTATCTCGAA-ACGCACACTAAGT
1 TCGAAGCTATCTC-AATTCGCACACTAAGT
75004183 ACCAAACATA
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
39 2 0.03
40 43 0.69
41 17 0.27
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (40 bp):
TCGAAGCTATCTCAATTCGCACACTAAGTGCCACATATAG
Found at i:75010953 original size:25 final size:26
Alignment explanation
Indices: 75010897--75010953 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 26
75010887 CAACAAATGA
*
75010897 GAATTCTTTAAATTAAATAATCTTAT
1 GAATTCTTTAAATTAAATAATCATAT
* * *
75010923 G-GTTCTTT-AATTGAATATTCATAT
1 GAATTCTTTAAATTAAATAATCATAT
75010947 GAATTCT
1 GAATTCT
75010954 CAATTAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 14 0.56
25 10 0.40
26 1 0.04
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (26 bp):
GAATTCTTTAAATTAAATAATCATAT
Found at i:75020229 original size:3 final size:3
Alignment explanation
Indices: 75020221--75020250 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
75020211 GGTGAAGCAA
75020221 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
75020251 GGAAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:75021848 original size:11 final size:10
Alignment explanation
Indices: 75021822--75021855 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
75021812 TCATGTCTTG
75021822 AAAATTTTAA
1 AAAATTTTAA
*
75021832 AAAATTTATAT
1 AAAATTT-TAA
75021843 AAAATTTTAA
1 AAAATTTTAA
75021853 AAA
1 AAA
75021856 TACGAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:75022730 original size:13 final size:13
Alignment explanation
Indices: 75022714--75022774 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
75022704 ACCAAATTTT
75022714 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
75022727 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* *
75022740 TCCACAGCACTTC
1 TCAAAAGCACTTC
* *
75022753 TCAAAAGTACTTT
1 TCAAAAGCACTTC
75022766 TCAAAAGCA
1 TCAAAAGCA
75022775 TTGCCAAACT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:75022774 original size:26 final size:26
Alignment explanation
Indices: 75022711--75022774 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
75022701 TAAACCAAAT
75022711 TTTTCAAAAGCACTTCTCAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
* * *
75022737 TTTTCCACAGCACTTCTCAAAAGTAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
75022763 TTTTCAAAAGCA
1 TTTTCAAAAGCA
75022775 TTGCCAAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.30
Consensus pattern (26 bp):
TTTTCAAAAGCACTTCTCAAAAGCAC
Found at i:75029895 original size:29 final size:31
Alignment explanation
Indices: 75029863--75029926 Score: 89
Period size: 29 Copynumber: 2.1 Consensus size: 31
75029853 AATAGTCTAT
75029863 ATTTTTATAATTTTTAAATAA-TT-AAAT-TA
1 ATTTTTATAATTTTTAAA-AAGTTAAAATATA
*
75029892 ATTTTTATCATTTTTAAAAAGTTAAAATATA
1 ATTTTTATAATTTTTAAAAAGTTAAAATATA
75029923 ATTT
1 ATTT
75029927 CACTAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 2 0.06
29 19 0.61
30 4 0.13
31 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (31 bp):
ATTTTTATAATTTTTAAAAAGTTAAAATATA
Found at i:75030608 original size:18 final size:20
Alignment explanation
Indices: 75030566--75030610 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
75030556 GTCTTATCTT
* *
75030566 ACATATTTATAATTTTATCA
1 ACATATTTATAAATATATCA
75030586 ACATATTT-TAAATATAT-A
1 ACATATTTATAAATATATCA
75030604 ACATATT
1 ACATATT
75030611 GTCAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 7 0.30
20 8 0.35
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (20 bp):
ACATATTTATAAATATATCA
Found at i:75030943 original size:35 final size:35
Alignment explanation
Indices: 75030904--75030973 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
75030894 GGTCAAACTG
75030904 GTTGTCACCTTAACATCATTGAAAGTTGATGTTTT
1 GTTGTCACCTTAACATCATTGAAAGTTGATGTTTT
75030939 GTTGTCACCTTAACATCATTGAAAGTTGATGTTTT
1 GTTGTCACCTTAACATCATTGAAAGTTGATGTTTT
75030974 AGTCAATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (35 bp):
GTTGTCACCTTAACATCATTGAAAGTTGATGTTTT
Found at i:75033026 original size:30 final size:29
Alignment explanation
Indices: 75032960--75033029 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
75032950 ATTTTAAAAT
75032960 ATTTAAAAAATAATTTTAATAATTCTTAA
1 ATTTAAAAAATAATTTTAATAATTCTTAA
* * * *
75032989 TTCTTAAAAAATAATTTTTATATGTTTTTAA
1 AT-TTAAAAAATAATTTTAATA-ATTCTTAA
75033020 ATTTAAAAAA
1 ATTTAAAAAA
75033030 AATAAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 1 0.03
30 26 0.76
31 7 0.21
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (29 bp):
ATTTAAAAAATAATTTTAATAATTCTTAA
Found at i:75034179 original size:20 final size:23
Alignment explanation
Indices: 75034144--75034195 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
75034134 GATACCCCCG
75034144 TACAATTTTTTAATAATT-TTTT
1 TACAATTTTTTAATAATTCTTTT
75034166 TACAA-TTTTT-ATAATTCTTTT
1 TACAATTTTTTAATAATTCTTTT
75034187 T-CTAATTTT
1 TAC-AATTTT
75034196 CAATAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 7 0.26
21 12 0.44
22 8 0.30
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (23 bp):
TACAATTTTTTAATAATTCTTTT
Found at i:75037077 original size:23 final size:24
Alignment explanation
Indices: 75037048--75037103 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
75037038 AAAAATAAAT
* *
75037048 ATAAAAACAGA-GTATGGTTTTGA
1 ATAAAAAAAGATGTAAGGTTTTGA
* *
75037071 ATAAAAAAATATTTAAGGTTTTGA
1 ATAAAAAAAGATGTAAGGTTTTGA
75037095 ATAAAAAAA
1 ATAAAAAAA
75037104 AGAAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.54, C:0.02, G:0.14, T:0.30
Consensus pattern (24 bp):
ATAAAAAAAGATGTAAGGTTTTGA
Found at i:75043230 original size:16 final size:16
Alignment explanation
Indices: 75043209--75043239 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
75043199 GAGAATATAG
75043209 AATAAATTTACTAAAA
1 AATAAATTTACTAAAA
75043225 AATAAATTTACTAAA
1 AATAAATTTACTAAA
75043240 TTTCTAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAATTTACTAAAA
Found at i:75067838 original size:40 final size:39
Alignment explanation
Indices: 75067721--75067844 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 39
75067711 GCATGATACT
*
75067721 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
75067760 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
* * * * *
75067799 TGGAAATATATCCGGGCTTAAAGTTCCGCAGGCTTTGTGC
1 TGGAAACATATCCGGACTT-GAGGTCCGCAGGCTATGTGC
*
75067839 TAGAAA
1 TGGAAA
75067845 TTGGACTCGG
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 55 0.71
40 22 0.29
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
Found at i:75075724 original size:40 final size:39
Alignment explanation
Indices: 75075600--75075723 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 39
75075590 GCATGATACT
*
75075600 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
75075639 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
* * * * *
75075678 TGGAAATATATCCGGGCTTAAAGTCCCGCAGGCTTTGTGC
1 TGGAAACATATCCGGACTTGAGGT-CCGCAGGCTATGTGC
*
75075718 TAGAAA
1 TGGAAA
75075724 TTGGACTCGG
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 58 0.75
40 19 0.25
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTGC
Found at i:75078607 original size:43 final size:42
Alignment explanation
Indices: 75078550--75078658 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
75078540 AATGCCAACA
75078550 TCCCAGACATGGTCTTACATGTAATCAAACATCGATG-CCACTG
1 TCCCAGACATGGTCTTACATGTAATCAAACA-CGATGTCCA-TG
* * * * * * *
75078593 TCCCAAACAGGGTCTTACACGAAATCAGATACGATGTCGATG
1 TCCCAGACATGGTCTTACATGTAATCAAACACGATGTCCATG
75078635 TCCCAGACATGGTCTTACATGTAA
1 TCCCAGACATGGTCTTACATGTAA
75078659 AATAGAAGTC
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
42 27 0.50
43 27 0.50
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACATGTAATCAAACACGATGTCCATG
Found at i:75078649 original size:42 final size:43
Alignment explanation
Indices: 75078550--75078700 Score: 123
Period size: 44 Copynumber: 3.5 Consensus size: 43
75078540 AATGCCAACA
* *
75078550 TCCCAGACATGGTCTTACATGTAATCAAACATCGATGCCACTG
1 TCCCAGACATGGTCTTACACGAAATCAAACATCGATGCCACTG
* * * * *
75078593 TCCCAAACAGGGTCTTACACGAAATCAGATA-CGATGTCGA-TG
1 TCCCAGACATGGTCTTACACGAAATCAAACATCGATG-CCACTG
* *
75078635 TCCCAGACATGGTCTTACATGTAAAAT-AGAA-GTCGATGCCAAC-G
1 TCCCAGACATGGTCTTACACG--AAATCA-AACATCGATGCC-ACTG
* *
75078679 TCCTAGACGTGGTCTTACACGA
1 TCCCAGACATGGTCTTACACGA
75078701 TAACACATAT
Statistics
Matches: 85, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
42 26 0.31
43 29 0.34
44 30 0.35
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGAAATCAAACATCGATGCCACTG
Found at i:75080262 original size:23 final size:25
Alignment explanation
Indices: 75080216--75080265 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
75080206 TCAGTTTGTT
75080216 TAGTTAATTTTATCATTTATTTTAAAA
1 TAGTTAATTTTATC--TTATTTTAAAA
75080243 TAGTTAATTTTATC-T-TTTTAAAA
1 TAGTTAATTTTATCTTATTTTAAAA
75080266 CTTTATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.35
24 1 0.04
27 14 0.61
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (25 bp):
TAGTTAATTTTATCTTATTTTAAAA
Found at i:75082306 original size:33 final size:32
Alignment explanation
Indices: 75082269--75082331 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
75082259 CAAAAAAAAT
*
75082269 TTGTTGTTTGT-TTGTTGTTTTACTACTATTTTA
1 TTGTTGTTT-TCTCGTTGTTTT-CTACTATTTTA
*
75082302 TTGTTGTTTTCTCGTTGTTTTCTATTATTT
1 TTGTTGTTTTCTCGTTGTTTTCTACTATTT
75082332 CACTATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 9 0.33
33 18 0.67
ACGTcount: A:0.10, C:0.08, G:0.14, T:0.68
Consensus pattern (32 bp):
TTGTTGTTTTCTCGTTGTTTTCTACTATTTTA
Found at i:75085560 original size:29 final size:28
Alignment explanation
Indices: 75085506--75085565 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
75085496 TTTGTTTTAT
** *
75085506 TATACATTAATTAATTAATATTATAATA
1 TATACATTAATTAATTAATAAGATAACA
* *
75085534 TATACATTTACTTAATTATTAAGATAACA
1 TATACA-TTAATTAATTAATAAGATAACA
75085563 TAT
1 TAT
75085566 TTTAACATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (28 bp):
TATACATTAATTAATTAATAAGATAACA
Found at i:75085983 original size:11 final size:11
Alignment explanation
Indices: 75085964--75086005 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
75085954 ACAAAAAAGC
75085964 TGTTATTTTAT
1 TGTTATTTTAT
* *
75085975 TGTTGTTTTAA
1 TGTTATTTTAT
75085986 TGTTATTTTAT
1 TGTTATTTTAT
*
75085997 TGTTGTTTT
1 TGTTATTTT
75086006 CTCCCTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (11 bp):
TGTTATTTTAT
Found at i:75085992 original size:22 final size:22
Alignment explanation
Indices: 75085964--75086005 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
75085954 ACAAAAAAGC
75085964 TGTTATTTTATTGTTGTTTTAA
1 TGTTATTTTATTGTTGTTTTAA
75085986 TGTTATTTTATTGTTGTTTT
1 TGTTATTTTATTGTTGTTTT
75086006 CTCCCTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (22 bp):
TGTTATTTTATTGTTGTTTTAA
Found at i:75090025 original size:143 final size:140
Alignment explanation
Indices: 75089745--75090082 Score: 478
Period size: 142 Copynumber: 2.4 Consensus size: 140
75089735 TTTACAGTAT
* * * * *
75089745 TTACATTATTTACATTTAATGATTGGGTCTATGAGTGGAGGCATGAATGTAACTTATAGTGTATG
1 TTACATTATTTACATTTAATGTTTGGGTCGATGAGTGAAGGCATGAATGTAACTTATAATATATG
* *
75089810 CTGTTTATGTTTCTAGTCTATATTTGGTTTAAAATGTTGAGGCATGGATAAATGGTGATCACATG
66 CTGTTTATGTTTCTAGTCTATATTTGGTTTAAAATGTTGAGGCATGGATAAATGCTGATCACATA
75089875 AAGGACTACAA
131 AAGGACTA-AA
* *
75089886 GTTACATTATTTACATTTAATGTTTGGGTCGATGGGTGAAGGCATGTATGTAACTTATAATATAT
1 -TTACATTATTTACATTTAATGTTTGGGTCGATGAGTGAAGGCATGAATGTAACTTATAATATAT
* * *
75089951 GCTGTTTATTTTTTCTATTCTATATTTGGTTTAAAATGTTGAGGCATGGATAAATGCTGATCACT
65 GCTGTTTA-TGTTTCTAGTCTATATTTGGTTTAAAATGTTGAGGCATGGATAAATGCTGATCACA
75090016 TAAAGGACTAAA
129 TAAAGGACTAAA
** * * * * *
75090028 AAACATTATTTACATTTAATGTTTGGCTCGACGAGTGGAGGCTTGATTGTAACTT
1 TTACATTATTTACATTTAATGTTTGGGTCGATGAGTGAAGGCATGAATGTAACTT
75090083 GTGTCAAAAG
Statistics
Matches: 174, Mismatches: 21, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
141 46 0.26
142 67 0.39
143 61 0.35
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (140 bp):
TTACATTATTTACATTTAATGTTTGGGTCGATGAGTGAAGGCATGAATGTAACTTATAATATATG
CTGTTTATGTTTCTAGTCTATATTTGGTTTAAAATGTTGAGGCATGGATAAATGCTGATCACATA
AAGGACTAAA
Found at i:75091883 original size:144 final size:144
Alignment explanation
Indices: 75091623--75091916 Score: 446
Period size: 144 Copynumber: 2.0 Consensus size: 144
75091613 TTCTGCACGG
** *
75091623 TTTTGTCACTTATTGGGAACTTATCTGATTAAGAGAGTCACATGCTAAGAATTATTGAAATATTG
1 TTTTGTCACTTATTAAGAACTTATCTGATTAAAAGAGTCACATGCTAAGAATTATTGAAATATTG
** * * *
75091688 AACTTAAATCAGTAGAAAGTAAGTTGAAGGGATTGTTATTGGCAGGCAGAAAGGTGAAATTAAAC
66 AACTTAAATCAGTAGAAAGTAAGTTGAAAAGACTGTTATCGGCAGGCAGAAAGGTGAAAGTAAAC
*
75091753 GTGTAGAATCTTTA
131 GTGTAGAATCATTA
75091767 TTTTGTCACTTATTAAGAACTTATCTGATTAAAAGAGTCACATGCTAAGAACTT-TTGAAATATT
1 TTTTGTCACTTATTAAGAACTTATCTGATTAAAAGAGTCACATGCTAAGAA-TTATTGAAATATT
* * *
75091831 GAACTTAAATCTGTAGAAAGTAAGTTGAAAAGACTGTTATCGGCGGGCAGAAAGGTGATAGTAAA
65 GAACTTAAATCAGTAGAAAGTAAGTTGAAAAGACTGTTATCGGCAGGCAGAAAGGTGAAAGTAAA
* *
75091896 TGTTTAGAATCATTA
130 CGTGTAGAATCATTA
75091911 TTTTGT
1 TTTTGT
75091917 TTACTTTTTC
Statistics
Matches: 135, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
144 133 0.99
145 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.34
Consensus pattern (144 bp):
TTTTGTCACTTATTAAGAACTTATCTGATTAAAAGAGTCACATGCTAAGAATTATTGAAATATTG
AACTTAAATCAGTAGAAAGTAAGTTGAAAAGACTGTTATCGGCAGGCAGAAAGGTGAAAGTAAAC
GTGTAGAATCATTA
Found at i:75097531 original size:21 final size:20
Alignment explanation
Indices: 75097487--75097531 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
75097477 TTTGAACTTT
* *
75097487 TTTTCCCCATTTTCCCTTTG
1 TTTTCCCCATTTTCCATTTC
*
75097507 TTTTCCTCCCTTTTCCATTTC
1 TTTTCC-CCATTTTCCATTTC
75097528 TTTT
1 TTTT
75097532 AGCGTAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.04, C:0.33, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTCCCCATTTTCCATTTC
Found at i:75101203 original size:39 final size:39
Alignment explanation
Indices: 75101160--75101237 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
75101150 AACCAAGGCC
75101160 CAACCCAAACCTAAATAACACCTAAAAAGACTAAAACCT
1 CAACCCAAACCTAAATAACACCTAAAAAGACTAAAACCT
75101199 CAACCCAAACCTAAATAACACCTAAAAAGACTAAAACCT
1 CAACCCAAACCTAAATAACACCTAAAAAGACTAAAACCT
75101238 AATTTCTCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.54, C:0.31, G:0.03, T:0.13
Consensus pattern (39 bp):
CAACCCAAACCTAAATAACACCTAAAAAGACTAAAACCT
Found at i:75102732 original size:39 final size:39
Alignment explanation
Indices: 75102684--75102776 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 39
75102674 TTACATGTTA
* * *
75102684 TAACAAGATCTAGCATTTGTTTC-AGATTCTTGGGTTATT
1 TAACGAGATCTAGCATTTGTTGCAAG-TTCTCGGGTTATT
* *
75102723 TAATGAGATCTAGC-CTTGTTGCAAGTTCTCGGGTTATT
1 TAACGAGATCTAGCATTTGTTGCAAGTTCTCGGGTTATT
*
75102761 TAACGTGATCTAGCAT
1 TAACGAGATCTAGCAT
75102777 CGTTGTAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
38 30 0.68
39 14 0.32
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (39 bp):
TAACGAGATCTAGCATTTGTTGCAAGTTCTCGGGTTATT
Found at i:75105471 original size:91 final size:91
Alignment explanation
Indices: 75105316--75105496 Score: 344
Period size: 91 Copynumber: 2.0 Consensus size: 91
75105306 CTGACTTGTA
75105316 ACACACAGCCGGTCACACGCCCGTATGTAAGCCCGTGTAGAGCATACTGACTTCATTTTAATTTC
1 ACACACAGCCGGTCACACGCCCGTATGTAAGCCCGTGTAGAGCATACTGACTTCATTTTAATTTC
75105381 AACACCAGAGGACACACGGCCATGTT
66 AACACCAGAGGACACACGGCCATGTT
* *
75105407 ACACACAGCCGGTCACACGCCCGTATGTAAGCCTGTGTAGAGCATACTGACTTTATTTTAATTTC
1 ACACACAGCCGGTCACACGCCCGTATGTAAGCCCGTGTAGAGCATACTGACTTCATTTTAATTTC
75105472 AACACCAGAGGACACACGGCCATGT
66 AACACCAGAGGACACACGGCCATGT
75105497 AACATGATCG
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (91 bp):
ACACACAGCCGGTCACACGCCCGTATGTAAGCCCGTGTAGAGCATACTGACTTCATTTTAATTTC
AACACCAGAGGACACACGGCCATGTT
Found at i:75113678 original size:40 final size:40
Alignment explanation
Indices: 75113623--75113700 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
75113613 TGCAGTACCT
*
75113623 TATGGTGTGTAGGGATGGACGGGTCGATTTTATCCCCATA
1 TATGGTGTGCAGGGATGGACGGGTCGATTTTATCCCCATA
**
75113663 TATGGTGTGCAGGGATGGGTGGGTCGATTTTATCCCCA
1 TATGGTGTGCAGGGATGGACGGGTCGATTTTATCCCCA
75113701 CATGGTGTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.18, C:0.15, G:0.35, T:0.32
Consensus pattern (40 bp):
TATGGTGTGCAGGGATGGACGGGTCGATTTTATCCCCATA
Found at i:75117827 original size:17 final size:17
Alignment explanation
Indices: 75117768--75117827 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
75117758 TTTCAAGTCA
* *
75117768 TTTGGGTTAGTATTAAT
1 TTTGGGTTTGTATCAAT
* *
75117785 TTTGAGTTTGTTTC-AT
1 TTTGGGTTTGTATCAAT
* * *
75117801 ATTGGATTTGTGTCAAT
1 TTTGGGTTTGTATCAAT
75117818 TTTGGGTTTG
1 TTTGGGTTTG
75117828 AATTACTTGA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
16 12 0.38
17 20 0.62
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.55
Consensus pattern (17 bp):
TTTGGGTTTGTATCAAT
Found at i:75124661 original size:12 final size:12
Alignment explanation
Indices: 75124644--75124677 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
75124634 CAGCCCACCC
75124644 ATATTAATTTTT
1 ATATTAATTTTT
*
75124656 ATATTATTTTTT
1 ATATTAATTTTT
75124668 ATA-TAATTTT
1 ATATTAATTTT
75124678 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:75124837 original size:31 final size:30
Alignment explanation
Indices: 75124799--75124864 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
75124789 TAACTTAACA
*
75124799 AACAAATGCCTCTGAAATAATAACAAAATTT
1 AACAAATGCCTCTAAAATAATAACAAAA-TT
* *
75124830 AACAAATGTCTTTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
75124860 AACAA
1 AACAA
75124865 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.26
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:75130818 original size:14 final size:14
Alignment explanation
Indices: 75130799--75130827 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
75130789 GTAGTGTTTG
75130799 AGAATTTGGAATTT
1 AGAATTTGGAATTT
75130813 AGAATTTGGAATTT
1 AGAATTTGGAATTT
75130827 A
1 A
75130828 TAAGTAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (14 bp):
AGAATTTGGAATTT
Found at i:75134419 original size:17 final size:17
Alignment explanation
Indices: 75134397--75134431 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
75134387 CATTATTTCA
75134397 GGAACCTAGCATGTTTT
1 GGAACCTAGCATGTTTT
75134414 GGAACCTAGCATGTTTT
1 GGAACCTAGCATGTTTT
75134431 G
1 G
75134432 TTACTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (17 bp):
GGAACCTAGCATGTTTT
Found at i:75136652 original size:15 final size:17
Alignment explanation
Indices: 75136622--75136655 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
75136612 TAAATTATAA
75136622 TTTATATTATTTTTTAT
1 TTTATATTATTTTTTAT
75136639 TTTATA-TA-TTTTTAT
1 TTTATATTATTTTTTAT
75136654 TT
1 TT
75136656 ATTAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 2 0.12
17 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATATTATTTTTTAT
Found at i:75138642 original size:14 final size:14
Alignment explanation
Indices: 75138625--75138659 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
75138615 TGATTAATTG
*
75138625 AAAATGATTTCTGA
1 AAAATGATTTATGA
*
75138639 AAAATGATTTATGG
1 AAAATGATTTATGA
75138653 AAAATGA
1 AAAATGA
75138660 CTTGTTTTTC
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:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (14 bp):
AAAATGATTTATGA
Found at i:75139593 original size:49 final size:48
Alignment explanation
Indices: 75139508--75139603 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 48
75139498 TATCACTTTA
*
75139508 GAAAATGTTTTACGAAAAAAATTTGATAAGACATTTTACGAGAATAAG
1 GAAAATGTTTTACAAAAAAAATTTGATAAGACATTTTACGAGAATAAG
* *
75139556 GAAAATGTTTTACAAAAAAAAATTTGATAAGATATTTTACGGGAATAA
1 GAAAATGTTTTAC-AAAAAAAATTTGATAAGACATTTTACGAGAATAA
75139604 TGGGACAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 13 0.30
49 31 0.70
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (48 bp):
GAAAATGTTTTACAAAAAAAATTTGATAAGACATTTTACGAGAATAAG
Found at i:75145135 original size:91 final size:91
Alignment explanation
Indices: 75144997--75145204 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
75144987 TTGATTTTAG
* *
75144997 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
75145062 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
75145089 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
75145154 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
75145180 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
75145205 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:75145173 original size:26 final size:28
Alignment explanation
Indices: 75145119--75145179 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
75145109 TATTATCAAG
* *
75145119 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
75145147 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
75145173 AATTATA
1 AATTATA
75145180 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:75145179 original size:44 final size:43
Alignment explanation
Indices: 75145037--75145179 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
75145027 GAATTTTATG
* *
75145037 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
75145081 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
75145128 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
75145172 AAATTATA
1 AAATTATA
75145180 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:75145297 original size:59 final size:57
Alignment explanation
Indices: 75145231--75145419 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
75145221 ATTTTATTAA
75145231 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
75145290 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
75145351 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
75145410 ATCATATATT
1 ATCATATATT
75145420 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:75145328 original size:66 final size:64
Alignment explanation
Indices: 75145258--75145456 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
75145248 AAATATATTT
75145258 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
75145323 G
64 G
* * * * * **
75145324 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
75145378 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
75145443 G
64 G
*
75145444 AATATTGATTATT
1 AATATTAATTATT
75145457 AAGAATTTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.27
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Done.