Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 266 of 322
Found at i:88104632 original size:29 final size:29
Alignment explanation
Indices: 88104590--88104646 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
88104580 ACCATTAATG
* *
88104590 AAAATATAAAAAAATTTAAAATTATTTTT
1 AAAAAATAAAAAAAATTAAAATTATTTTT
* *
88104619 AAAAAATATAAAAAATTATAATTATTTT
1 AAAAAATAAAAAAAATTAAAATTATTTT
88104647 AAATAATGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
AAAAAATAAAAAAAATTAAAATTATTTTT
Found at i:88104723 original size:22 final size:22
Alignment explanation
Indices: 88104698--88104748 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
88104688 AAATATGAGT
* *
88104698 TTGAGAGAATTTTGGAAGGAAG
1 TTGAGAGAATTTTAGAAGGAAA
88104720 TTGAGAGAATTTTAGAAGGAAA
1 TTGAGAGAATTTTAGAAGGAAA
88104742 TTGAGAG
1 TTGAGAG
88104749 GATTAGAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTAGAAGGAAA
Found at i:88106424 original size:23 final size:24
Alignment explanation
Indices: 88106377--88106422 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
88106367 GAAAAATATT
88106377 AAATATATATATTTTGTATTTTTA
1 AAATATATATATTTTGTATTTTTA
*
88106401 AAATATA-ATAGTTTTTTATTTT
1 AAATATATATA-TTTTGTATTTT
88106423 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
AAATATATATATTTTGTATTTTTA
Found at i:88106552 original size:59 final size:59
Alignment explanation
Indices: 88106489--88106665 Score: 255
Period size: 66 Copynumber: 2.9 Consensus size: 59
88106479 TCAAGTTTGT
*
88106489 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
88106548 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAA-T--T--AA-T-ACAATTAATAATTTGATAA
88106613 A
59 A
* * *
88106614 TTTACTAATTAAATGTTAGATTTTATTACAGCAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
88106666 AATAATTTGA
Statistics
Matches: 107, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
59 45 0.42
60 2 0.02
61 2 0.02
62 1 0.01
63 1 0.01
64 2 0.02
65 2 0.02
66 52 0.49
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.41
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:88106602 original size:66 final size:66
Alignment explanation
Indices: 88106519--88106687 Score: 293
Period size: 66 Copynumber: 2.5 Consensus size: 66
88106509 TTTTGTTACA
88106519 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATT-A-ACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
88106584 AAT
64 AAT
* *
88106587 ACAATTAACAATTAATAATTTGATAAATTTACTAATTAAATGTTAGATTTTATTACAGCAATTAA
1 ACAATTAACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAA
88106652 T
66 T
*
88106653 ACAATTAACAATTAATAATTTGATAATTTTACTAA
1 ACAATTAACAATTAATAATTTGATAAATTTACTAA
88106688 CAATTAGTTT
Statistics
Matches: 98, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
66 91 0.93
67 1 0.01
68 6 0.06
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (66 bp):
ACAATTAACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAA
T
Found at i:88106741 original size:5 final size:5
Alignment explanation
Indices: 88106731--88106760 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
88106721 TAATTAAAAA
88106731 CGGGC CGGGC CGGGC CGGGC CGGGC CGGGC
1 CGGGC CGGGC CGGGC CGGGC CGGGC CGGGC
88106761 TCGAGCCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.60, T:0.00
Consensus pattern (5 bp):
CGGGC
Found at i:88107254 original size:19 final size:19
Alignment explanation
Indices: 88107232--88107268 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
88107222 AGAAATTGAT
88107232 AAGAAG-AAAAG--AAAGA
1 AAGAAGAAAAAGAAAAAGA
88107248 AAGAAGAAAAAGAAAAAGA
1 AAGAAGAAAAAGAAAAAGA
88107267 AA
1 AA
88107269 AAAGTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
19 7 0.39
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (19 bp):
AAGAAGAAAAAGAAAAAGA
Found at i:88121605 original size:20 final size:21
Alignment explanation
Indices: 88121566--88121605 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
88121556 GGTATGCAAA
* *
88121566 TTTGTGAGAATTTGGGTTTTT
1 TTTGTGAGAATTTAGATTTTT
88121587 TTTG-GAGAATTTAGATTTT
1 TTTGTGAGAATTTAGATTTT
88121606 AAAAGGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (21 bp):
TTTGTGAGAATTTAGATTTTT
Found at i:88136163 original size:59 final size:59
Alignment explanation
Indices: 88136100--88136246 Score: 179
Period size: 59 Copynumber: 2.5 Consensus size: 59
88136090 CAAAAAGCTT
* *
88136100 AGTTTAGATACTTAATTGGACAAAAAAAAGTTCAAGTATCAATTTGAACCTTGACGCT-A
1 AGTTTAGATACCTAATTGGACAAAAAAAAGTTCAAGTATCAAATTGAACCTTGA-GCTCA
* * * * * *
88136159 AGTTTAGATACCCAATCGGATAAAAAAAGGTTTAAGTATCAAATTGAACCTTGAGGTCA
1 AGTTTAGATACCTAATTGGACAAAAAAAAGTTCAAGTATCAAATTGAACCTTGAGCTCA
** *
88136218 AGTTTAGGCACCTAATTAGACAAAAAAAA
1 AGTTTAGATACCTAATTGGACAAAAAAAA
88136247 ACACATTAGG
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
58 2 0.03
59 70 0.97
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (59 bp):
AGTTTAGATACCTAATTGGACAAAAAAAAGTTCAAGTATCAAATTGAACCTTGAGCTCA
Found at i:88136684 original size:20 final size:20
Alignment explanation
Indices: 88136637--88136685 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
88136627 TAAACTAATT
*
88136637 TTTAATTAATACTTATATAA
1 TTTAATAAATACTTATATAA
*
88136657 TTAAAATAAATA-TTATATAAA
1 TT-TAATAAATACTTATAT-AA
88136678 TTTAATAA
1 TTTAATAA
88136686 TCGGACATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAATAAATACTTATATAA
Found at i:88137170 original size:25 final size:26
Alignment explanation
Indices: 88137139--88137203 Score: 89
Period size: 25 Copynumber: 2.5 Consensus size: 26
88137129 TTTATAAATA
*
88137139 AATTTATTTAAAATTAGTGTTTT-TT
1 AATTTATTTAAAATTAATGTTTTGTT
*
88137164 ATTTTATTT-AAATTAATGTTTTGTT
1 AATTTATTTAAAATTAATGTTTTGTT
88137189 AATTTATTTATAAAT
1 AATTTATTTA-AAAT
88137204 AATAAATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.35
25 18 0.53
27 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (26 bp):
AATTTATTTAAAATTAATGTTTTGTT
Found at i:88138430 original size:19 final size:20
Alignment explanation
Indices: 88138398--88138435 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
88138388 AACCTATAAA
*
88138398 TATAGAAAATTATATAAAAG
1 TATAGAAAAATATATAAAAG
88138418 TATA-AAAAATATATAAAA
1 TATAGAAAAATATATAAAA
88138436 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
TATAGAAAAATATATAAAAG
Found at i:88138468 original size:12 final size:11
Alignment explanation
Indices: 88138450--88138499 Score: 75
Period size: 12 Copynumber: 4.5 Consensus size: 11
88138440 TTAAAATGAT
88138450 GAAAATTATAA
1 GAAAATTATAA
88138461 GAAAAATTATAA
1 G-AAAATTATAA
88138473 GAAAATATATAA
1 GAAAAT-TATAA
88138485 GAAAATTAT-A
1 GAAAATTATAA
88138495 GAAAA
1 GAAAA
88138500 GTTTGTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.16
11 9 0.24
12 22 0.59
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (11 bp):
GAAAATTATAA
Found at i:88138489 original size:23 final size:22
Alignment explanation
Indices: 88138442--88138499 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
88138432 AAAAATAATT
*
88138442 AAAATGAT-GAAAATTATAAGA
1 AAAATTATAGAAAATTATAAGA
88138463 AAAATTATAAGAAAATATATAAG-
1 AAAATTAT-AGAAAAT-TATAAGA
88138486 AAAATTATAGAAAA
1 AAAATTATAGAAAA
88138500 GTTTGTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 7 0.21
22 6 0.18
23 14 0.42
24 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (22 bp):
AAAATTATAGAAAATTATAAGA
Found at i:88138497 original size:10 final size:10
Alignment explanation
Indices: 88138398--88138499 Score: 75
Period size: 10 Copynumber: 9.9 Consensus size: 10
88138388 AACCTATAAA
88138398 TATAGAAAAT
1 TATAGAAAAT
* *
88138408 TATATAAAAG
1 TATAGAAAAT
*
88138418 TATAAAAAAT
1 TATAGAAAAT
88138428 ATATA-AAAAT
1 -TATAGAAAAT
* *
88138438 AAT-TAAAAT
1 TATAGAAAAT
*
88138447 GAT-GAAAAT
1 TATAGAAAAT
88138456 TATAAGAAAAAT
1 TAT-AG-AAAAT
88138468 TATAAGAAAAT
1 TAT-AGAAAAT
88138479 ATATAAGAAAAT
1 -TAT-AGAAAAT
88138491 TATAGAAAA
1 TATAGAAAA
88138500 GTTTGTTATT
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
9 16 0.21
10 27 0.35
11 13 0.17
12 22 0.28
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (10 bp):
TATAGAAAAT
Found at i:88157516 original size:125 final size:125
Alignment explanation
Indices: 88157292--88157670 Score: 623
Period size: 125 Copynumber: 3.0 Consensus size: 125
88157282 GATAAAATCA
*
88157292 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACATGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
88157357 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTATAAAAAATGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* *
88157417 AGGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCACTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
*
88157482 AGGTCCTGAAAAAATAATTTTGAGTTGACATTTCTGAGCAAATAGTATAAAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTAT--AAAAAACGCTTC
*
88157544 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * * *
88157609 TGGTCCTAAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAGCACTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
88157669 AA
1 AA
88157671 TCGACTAGCT
Statistics
Matches: 236, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
125 120 0.51
127 116 0.49
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:88157600 original size:127 final size:127
Alignment explanation
Indices: 88157292--88157661 Score: 627
Period size: 127 Copynumber: 2.9 Consensus size: 127
88157282 GATAAAATCA
*
88157292 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACATGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
88157357 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTAT--AAAAAATGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAAACGCTTC
* *
88157417 AGGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCACTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
*
88157482 AGGTCCTGAAAAAATAATTTTGAGTTGACATTTCTGAGCAAATAGTATAAAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAAACGCTTC
*
88157544 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * *
88157609 TGGTCCTAAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAA
66 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAA
88157662 GCACTTCAAT
Statistics
Matches: 229, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
125 108 0.47
127 121 0.53
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (127 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAAACGCTTC
Found at i:88158333 original size:51 final size:51
Alignment explanation
Indices: 88158262--88158358 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
88158252 AGTAATTAAC
*
88158262 AATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGGGCAAATTGAAATTA
1 AATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAAATTA
* * *
88158313 AATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAAATTGA
1 AATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGA
88158359 GAGGAAATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.27, T:0.26
Consensus pattern (51 bp):
AATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAAATTA
Found at i:88158347 original size:22 final size:22
Alignment explanation
Indices: 88158322--88158375 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
88158312 AAATATGGAT
88158322 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
88158344 TTGAGAGCAAA-TTGAGAGGAAA
1 TTGAGAG-AAATTTGAGAGGAAA
88158366 TTGAGA-AAAT
1 TTGAGAGAAAT
88158376 AATTGAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 3 0.10
22 22 0.76
23 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:88161973 original size:25 final size:23
Alignment explanation
Indices: 88161939--88161989 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
88161929 ATTATTTACG
*
88161939 ATTTTAATATTTAATTTTAAAAGTT
1 ATTTTAATA-TAAATTTTAAAA-TT
*
88161964 ATTTTGATATAAATTTTAAAATT
1 ATTTTAATATAAATTTTAAAATT
88161987 ATT
1 ATT
88161990 AAGTCCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.21
24 11 0.46
25 8 0.33
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
ATTTTAATATAAATTTTAAAATT
Found at i:88165801 original size:11 final size:13
Alignment explanation
Indices: 88165777--88165808 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
88165767 TAGTTTATTA
88165777 ATATTTTAATATG
1 ATATTTTAATATG
88165790 AT-TTTTAA-ATG
1 ATATTTTAATATG
88165801 ATATTTTA
1 ATATTTTA
88165809 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:88169864 original size:25 final size:25
Alignment explanation
Indices: 88169826--88169874 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
88169816 GATCACCGAT
** *
88169826 TTCAGCTCTTATGAGCTTCCTGTTA
1 TTCAGCTCACATGAGCTTACTGTTA
88169851 TTCAGCTCACATGAGCTTACTGTT
1 TTCAGCTCACATGAGCTTACTGTT
88169875 TACAACTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.41
Consensus pattern (25 bp):
TTCAGCTCACATGAGCTTACTGTTA
Found at i:88169888 original size:24 final size:25
Alignment explanation
Indices: 88169835--88169890 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
88169825 TTTCAGCTCT
* * *
88169835 TATGAGCTTCCTGTTATTCAGCTCA
1 TATGAGCTTACTGTTATACAACTCA
*
88169860 CATGAGCTTACTGTT-TACAACTCA
1 TATGAGCTTACTGTTATACAACTCA
88169884 TATGAGC
1 TATGAGC
88169891 ATACATGTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (25 bp):
TATGAGCTTACTGTTATACAACTCA
Found at i:88171382 original size:25 final size:24
Alignment explanation
Indices: 88171333--88171385 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
88171323 GTCATTAGGG
* * *
88171333 TTACCGATTCTAGCTCTTATGAGC
1 TTACCGATACTAACTCGTATGAGC
88171357 TTACCGATACTCAACTCGTATGAGC
1 TTACCGATACT-AACTCGTATGAGC
88171382 TTAC
1 TTAC
88171386 TGTTATTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (24 bp):
TTACCGATACTAACTCGTATGAGC
Found at i:88171875 original size:23 final size:23
Alignment explanation
Indices: 88171849--88171899 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
88171839 GAAAGGTATG
88171849 TGTAATATCCC-GAAAATTACTAC
1 TGTAATA-CCCTGAAAATTACTAC
*
88171872 TGTAATACCCTGAAAATTGCTAC
1 TGTAATACCCTGAAAATTACTAC
*
88171895 AGTAA
1 TGTAA
88171900 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (23 bp):
TGTAATACCCTGAAAATTACTAC
Found at i:88178031 original size:38 final size:40
Alignment explanation
Indices: 88177953--88178041 Score: 112
Period size: 41 Copynumber: 2.3 Consensus size: 40
88177943 CGACTTTGAG
*
88177953 TCGATAAGACACTGGGTGTCAATTTACTACTTCGGATTAAT
1 TCGATAAGACACTGGGTGCCAATTTA-TACTTCGGATTAAT
* *
88177994 TCGATAAGGCACTGGGTGCCAA-TT-TACTTCGGTTTAAT
1 TCGATAAGACACTGGGTGCCAATTTATACTTCGGATTAAT
*
88178032 T-GATGAGACA
1 TCGATAAGACA
88178042 TTGTGTGTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
37 7 0.16
38 14 0.33
40 2 0.05
41 20 0.47
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (40 bp):
TCGATAAGACACTGGGTGCCAATTTATACTTCGGATTAAT
Found at i:88180191 original size:12 final size:13
Alignment explanation
Indices: 88180164--88180196 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
88180154 TATAAGGGAA
*
88180164 AATAAAAACTAAT
1 AATAATAACTAAT
88180177 AATAATAAC-AAT
1 AATAATAACTAAT
88180189 AATAATAA
1 AATAATAA
88180197 TAACATCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAATAACTAAT
Found at i:88180193 original size:15 final size:15
Alignment explanation
Indices: 88180173--88180201 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
88180163 AAATAAAAAC
88180173 TAATAATAATAACAA
1 TAATAATAATAACAA
88180188 TAATAATAATAACA
1 TAATAATAATAACA
88180202 TCACATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATAATAATAACAA
Found at i:88180910 original size:13 final size:15
Alignment explanation
Indices: 88180879--88180914 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
88180869 GAAAAGAGAA
88180879 AAAAATA-AAGAAAG
1 AAAAATAGAAGAAAG
88180893 AAAAATAGAA-AAAG
1 AAAAATAGAAGAAAG
88180907 -AAAATAGA
1 AAAAATAGA
88180915 TATACCGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 11 0.52
15 2 0.10
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (15 bp):
AAAAATAGAAGAAAG
Found at i:88181830 original size:95 final size:95
Alignment explanation
Indices: 88181713--88181906 Score: 298
Period size: 95 Copynumber: 2.0 Consensus size: 95
88181703 AAGATCTGAA
**
88181713 ATCTTCAATCTATTCCACTGCCAACCAGGAAGATAGAATTATTGGCTTCAATATACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCCAACCAGGAAGATAGAATTATCAGCTTCAATATACTCCACTGTA
88181778 GTCACAGGGAGGTAAAATCTGCCATCTTTG
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
** * * * * *
88181808 ATCTTCAATCTATTCTTCTGCCAATCAGGGAGATAGAATTATCAGCTTCACTGTACTCTACTGTA
1 ATCTTCAATCTATTCCACTGCCAACCAGGAAGATAGAATTATCAGCTTCAATATACTCCACTGTA
*
88181873 GTCGCAGGGAGGTAAAATCTGCCATCTTTG
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
88181903 ATCT
1 ATCT
88181907 GCTCCGCTGC
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 89 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAACCAGGAAGATAGAATTATCAGCTTCAATATACTCCACTGTA
GTCACAGGGAGGTAAAATCTGCCATCTTTG
Found at i:88182078 original size:67 final size:67
Alignment explanation
Indices: 88181969--88182094 Score: 207
Period size: 67 Copynumber: 1.9 Consensus size: 67
88181959 GCCAGTGCAG
* * *
88181969 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTCAAGGC
1 GAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTCAAGGC
88182034 AA
66 AA
* *
88182036 GAAGGCAAGATCTATTGTCTTCAACTAGCTCCACCACTACCGAGAGAGGCAAGGTTTGT
1 GAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGT
88182095 GTCTTCGATC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.21
Consensus pattern (67 bp):
GAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTCAAGGC
AA
Found at i:88183250 original size:21 final size:21
Alignment explanation
Indices: 88183224--88183270 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
88183214 GGTAGAGCAA
*
88183224 GATCACCACATGCCCTAATCT
1 GATCACCACATGCCCCAATCT
** *
88183245 GATCACTTCATGCCCCATTCT
1 GATCACCACATGCCCCAATCT
88183266 GATCA
1 GATCA
88183271 ATATTTGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.36, G:0.11, T:0.28
Consensus pattern (21 bp):
GATCACCACATGCCCCAATCT
Found at i:88184217 original size:198 final size:194
Alignment explanation
Indices: 88183874--88184264 Score: 701
Period size: 198 Copynumber: 2.0 Consensus size: 194
88183864 TCATGCCAGT
*
88183874 CCTTATTCACCTCTAGGTAATTCGGTGACAAAATGTGGTGTCTGCTTCTAAATTGATTTCAGACC
1 CCTTATTCACCTCTAGGTAATTCGGTGACAAAACGTGGTGTCTGCTTCTAAATTGATTTCAGACC
*
88183939 TCAGTTATCGTGCTATCATTTAAGTTCAATGCATTTTCCAATACTATCCTCTCTGAAATTCTGTA
66 TCAGTTATCGTGCTATCATTTAAGTTCAATGCATTTTCCAATACCATCCTCTCTGAAATTCTGTA
88184004 TCGGTATAGGATGACCTTAATCCATGAAGTAGCCTCTAAAAAAAAATGAAGCAATGCCCATTAGA
131 TCGGTATAGGATGACCTTAATCCATGAAGTAGCCTCT----AAAAATGAAGCAATGCCCATTAGA
88184069 AGC
192 AGC
* *
88184072 CCTTGTTCACCTCTAGGTAATTCGGTGACAAAACGTGGTGTCTGCTTCTGAATTGATTTCAGACC
1 CCTTATTCACCTCTAGGTAATTCGGTGACAAAACGTGGTGTCTGCTTCTAAATTGATTTCAGACC
88184137 TCAGTTATCGTGCTATCATTTAAGTTCAATGCATTTTCCAATACCATCCTCTCTGAAATTCTGTA
66 TCAGTTATCGTGCTATCATTTAAGTTCAATGCATTTTCCAATACCATCCTCTCTGAAATTCTGTA
*
88184202 TCGGTATAGGATGACCTTAATCCATGAAGTAGCCTCTCAAAATGAAGCAATGCCCATTAGAAG
131 TCGGTATAGGATGACCTTAATCCATGAAGTAGCCTCTAAAAATGAAGCAATGCCCATTAGAAG
88184265 TCTTTGGTAA
Statistics
Matches: 188, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
194 25 0.13
198 163 0.87
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (194 bp):
CCTTATTCACCTCTAGGTAATTCGGTGACAAAACGTGGTGTCTGCTTCTAAATTGATTTCAGACC
TCAGTTATCGTGCTATCATTTAAGTTCAATGCATTTTCCAATACCATCCTCTCTGAAATTCTGTA
TCGGTATAGGATGACCTTAATCCATGAAGTAGCCTCTAAAAATGAAGCAATGCCCATTAGAAGC
Found at i:88184399 original size:6 final size:6
Alignment explanation
Indices: 88184388--88184448 Score: 99
Period size: 6 Copynumber: 10.3 Consensus size: 6
88184378 TTAACCTCTC
88184388 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT -TCTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CT-TTTT
88184436 -TTTTT CTTTTT CT
1 CTTTTT CTTTTT CT
88184449 CCTATTTTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.09
6 48 0.91
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
CTTTTT
Found at i:88184456 original size:18 final size:18
Alignment explanation
Indices: 88184388--88184463 Score: 86
Period size: 18 Copynumber: 4.2 Consensus size: 18
88184378 TTAACCTCTC
88184388 CTTTTTCT-TTTTCTTTTT
1 CTTTTTCTCTTTT-TTTTT
88184406 CTTTTTCT-TTTTCTTTTT
1 CTTTTTCTCTTTT-TTTTT
88184424 CTTTTT-TCTTTTTTTTT
1 CTTTTTCTCTTTTTTTTT
* *
88184441 CTTTTTCTCCTATTTTTGT
1 CTTTTTCT-CTTTTTTTTT
88184460 CTTT
1 CTTT
88184464 GATTTTTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
17 12 0.23
18 29 0.55
19 12 0.23
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (18 bp):
CTTTTTCTCTTTTTTTTT
Found at i:88184491 original size:20 final size:19
Alignment explanation
Indices: 88184461--88184534 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
88184451 TATTTTTGTC
88184461 TTTGATTTTTTTTTGATTT
1 TTTGATTTTTTTTTGATTT
88184480 TTTGATTTTTTTTTTGATTTT
1 TTTGA-TTTTTTTTTGA-TTT
*
88184501 TTTGA-TTTTTTTTGATAT
1 TTTGATTTTTTTTTGATTT
*
88184519 TTTGAATTTTTTTTGA
1 TTTGATTTTTTTTTGA
88184535 GTCTGAACTC
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
18 7 0.14
19 25 0.49
20 11 0.22
21 8 0.16
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.76
Consensus pattern (19 bp):
TTTGATTTTTTTTTGATTT
Found at i:88184492 original size:21 final size:21
Alignment explanation
Indices: 88184461--88184513 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
88184451 TATTTTTGTC
88184461 TTTGA-TTTTTTTTTGA-TTT
1 TTTGATTTTTTTTTTGATTTT
88184480 TTTGATTTTTTTTTTGATTTT
1 TTTGATTTTTTTTTTGATTTT
88184501 TTTGATTTTTTTT
1 TTTGATTTTTTTT
88184514 GATATTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 5 0.16
20 11 0.34
21 16 0.50
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.81
Consensus pattern (21 bp):
TTTGATTTTTTTTTTGATTTT
Found at i:88184513 original size:12 final size:12
Alignment explanation
Indices: 88184477--88184503 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
88184467 TTTTTTTTGA
88184477 TTTTTTGATTTT
1 TTTTTTGATTTT
88184489 TTTTTTGATTTT
1 TTTTTTGATTTT
88184501 TTT
1 TTT
88184504 GATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (12 bp):
TTTTTTGATTTT
Found at i:88184520 original size:12 final size:10
Alignment explanation
Indices: 88184461--88184534 Score: 68
Period size: 8 Copynumber: 7.5 Consensus size: 10
88184451 TATTTTTGTC
88184461 TTTGATTTTTT
1 TTTGA-TTTTT
88184472 TTTGA--TTT
1 TTTGATTTTT
88184480 TTTGATTTTTTT
1 TTTGA--TTTTT
88184492 TTTGA-TTTT
1 TTTGATTTTT
88184501 TTTGATTTTT
1 TTTGATTTTT
*
88184511 TTTGA--TAT
1 TTTGATTTTT
88184519 TTTGAATTTTT
1 TTTG-ATTTTT
88184530 TTTGA
1 TTTGA
88184535 GTCTGAACTC
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
8 14 0.26
9 10 0.19
10 10 0.19
11 11 0.21
12 8 0.15
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.76
Consensus pattern (10 bp):
TTTGATTTTT
Found at i:88185256 original size:21 final size:22
Alignment explanation
Indices: 88185223--88185263 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
88185213 TATGTACAAT
*
88185223 ATGATTATGAATGAATGAATGA
1 ATGATTATGAATGAAAGAATGA
88185245 ATGATT-TGAATGAAAGAAT
1 ATGATTATGAATGAAAGAAT
88185264 AAAAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGATTATGAATGAAAGAATGA
Found at i:88188815 original size:3 final size:3
Alignment explanation
Indices: 88188807--88188844 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
88188797 TTAAAAGAGT
88188807 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
88188845 TTGAAAACAT
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:88188957 original size:10 final size:11
Alignment explanation
Indices: 88188935--88188963 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
88188925 AAAAACTAAA
88188935 AATATATATAT
1 AATATATATAT
88188946 AATATA-ATAT
1 AATATATATAT
88188956 AATATATA
1 AATATATA
88188964 AAAAGGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATATATAT
Found at i:88190189 original size:15 final size:16
Alignment explanation
Indices: 88190163--88190192 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
88190153 TAGTGTTTAG
88190163 GTGGGTTATTGGGTTT
1 GTGGGTTATTGGGTTT
88190179 GTGGG-TATTGGGTT
1 GTGGGTTATTGGGTT
88190193 CTTTTGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.00, G:0.47, T:0.47
Consensus pattern (16 bp):
GTGGGTTATTGGGTTT
Found at i:88190603 original size:43 final size:43
Alignment explanation
Indices: 88190525--88191105 Score: 196
Period size: 44 Copynumber: 13.4 Consensus size: 43
88190515 CTACTGCCAA
* * * * *
88190525 TTCAGAGAGATAAGATTCTTTATTTTAATCCGCTCCACTGTAAC
1 TTCAGGGAGATAAGATTATGT-CTTTAATCTGCTCCACTGTAAC
* *
88190569 TTCAGGGAGATAGGATTATGTCTTTAATCTGCTCCGCTGTAAC
1 TTCAGGGAGATAAGATTATGTCTTTAATCTGCTCCACTGTAAC
* *** * *
88190612 CTCAGGGAGATAAGATCTGCAAT-TCTTCGGTCTACTCCGCTGTAAC
1 TTCAGGGAGATAAGAT-T---ATGTCTTTAATCTGCTCCACTGTAAC
* * * * * *
88190658 CTCAGGGAAATAAGACCTGATG-C---GATCTACTCTACTGTAAC
1 TTCAGGGAGATAAGA--TTATGTCTTTAATCTGCTCCACTGTAAC
* * * *
88190699 TTCAGAGAGATAAGATCCTTTAT-TTTAATCCGCTCCACTGTAAC
1 TTCAGGGAGATAAGAT--TATGTCTTTAATCTGCTCCACTGTAAC
* * * *
88190743 TTCAGGGAGATAGGATTATGTCTGTAATCTGCTCCGCTATAA-
1 TTCAGGGAGATAAGATTATGTCTTTAATCTGCTCCACTGTAAC
*** **
88190785 TCTCAGGGAGATAAGATCTGAAAT-TCTTCGGTCTATTCCACTGTAA-
1 T-TCAGGGAGATAAGAT-T---ATGTCTTTAATCTGCTCCACTGTAAC
* ** * *** * **
88190831 TCTCAGGGAAATAAGA-CCTGAC-ACGATCTACTCTGCTGTAAC
1 T-TCAGGGAGATAAGATTATGTCTTTAATCTGCTCCACTGTAAC
* ** *
88190873 TTCAGAGAGATAAGATCCT-TCATTTTAATCCGCTCCACTGTAA-
1 TTCAGGGAGATAAGATTATGTC--TTTAATCTGCTCCACTGTAAC
* * * **
88190916 TCTCAGGGGGATAGGATTACTAG-CTTCAATCTGCTCTGCTGTAA-
1 T-TCAGGGAGATAAGATTA-T-GTCTTTAATCTGCTCCACTGTAAC
* * *** * *
88190960 TCTCAGGGAGATAAGA-TCTGAC-ACGATCTACTCTACTGTAAC
1 T-TCAGGGAGATAAGATTATGTCTTTAATCTGCTCCACTGTAAC
* *
88191002 TTCAGAGAGATAAGATCCT-TCGT-TTTAATCCGCTCCACTGTAA-
1 TTCAGGGAGATAAGAT--TAT-GTCTTTAATCTGCTCCACTGTAAC
* * * *
88191045 TATCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAA-
1 T-TCAGGGAGATAAGATTA-TGTCTTTAATCTGCTCCACTGTAAC
88191089 TCTCAGGGAGATAAGAT
1 T-TCAGGGAGATAAGAT
88191106 CTGAAATTCT
Statistics
Matches: 401, Mismatches: 96, Indels: 80
0.69 0.17 0.14
Matches are distributed among these distances:
39 1 0.00
41 85 0.21
42 13 0.03
43 68 0.17
44 165 0.41
45 1 0.00
46 63 0.16
47 4 0.01
48 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
TTCAGGGAGATAAGATTATGTCTTTAATCTGCTCCACTGTAAC
Found at i:88190709 original size:87 final size:87
Alignment explanation
Indices: 88190595--88190889 Score: 269
Period size: 87 Copynumber: 3.4 Consensus size: 87
88190585 TATGTCTTTA
* * * * * *
88190595 ATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTACTCCGCTGTAACCT
1 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCT
88190660 CAGGGAAATAAGACCTGATGCG
66 CAGGGAAATAAGACCTGATGCG
* ** ** ** *
88190682 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATT-TT-AATCCGCTCCACTGTAACT
1 ATCTACTCTGCTGTAACTTCAGAGAGATAAGAT-CTGAAATTCTTCGGTCTACTCCACTGTAACC
* * *
88190744 TCAGGGAGATAGGA--TTATGTCTG
65 TCAGGGAAATAAGACCTGATG-C-G
* * * * *
88190767 TAATCTGCTCCGCTATAA-TCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAA
1 --ATCTACTCTGCTGTAACT-TCAGAGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAA
* **
88190831 TCTCAGGGAAATAAGACCTGACACG
63 CCTCAGGGAAATAAGACCTGATGCG
88190856 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATC
1 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATC
88190890 CTTCATTTTA
Statistics
Matches: 157, Mismatches: 39, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
83 4 0.03
84 1 0.01
85 26 0.17
86 5 0.03
87 88 0.56
88 5 0.03
89 25 0.16
90 1 0.01
91 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (87 bp):
ATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCT
CAGGGAAATAAGACCTGATGCG
Found at i:88190798 original size:174 final size:173
Alignment explanation
Indices: 88190508--88190980 Score: 736
Period size: 174 Copynumber: 2.7 Consensus size: 173
88190498 CTTGGACGTA
* *
88190508 ATCTACTCTACTGCCAA-TTCAGAGAGATAAGATTCTTTATTTTAATCCGCTCCACTGTAACTTC
1 ATCTACTCTACTG-TAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTC
* *
88190572 AGGGAGATAGGATTATGTCTTTAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTC
65 AGGGAGATAGGATTATGTC-TTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTC
* **
88190637 TTCGGTCTACTCCGCTGTAACCTCAGGGAAATAAGACCTGATGCG
129 TTCGGTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGACACG
88190682 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
*
88190747 GGGAGATAGGATTATGTCTGTAATCTGCTCCGCTATAATCTCAGGGAGATAAGATCTGAAATTCT
66 GGGAGATAGGATTATGTCT-TAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCT
* *
88190812 TCGGTCTATTCCACTGTAATCTCAGGGAAATAAGACCTGACACG
130 TCGGTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGACACG
* *
88190856 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCGCTCCACTGTAA-TCTC
1 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACT-TC
* *
88190920 AGGGGGATAGGATTACTAG-CTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAAGATCTGA
65 AGGGAGATAGGATTA-T-GTCTT-AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
88190981 CACGATCTAC
Statistics
Matches: 278, Mismatches: 15, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
173 4 0.01
174 234 0.84
175 39 0.14
176 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (173 bp):
ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA
GGGAGATAGGATTATGTCTTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTT
CGGTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGACACG
Found at i:88190975 original size:129 final size:129
Alignment explanation
Indices: 88190825--88191109 Score: 498
Period size: 129 Copynumber: 2.2 Consensus size: 129
88190815 GTCTATTCCA
* * *
88190825 CTGTAATCTCAGGGAAATAAGACCTGACACGATCTACTCTGCTGTAACTTCAGAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
* * *
88190890 CTTCATTTTAATCCGCTCCACTGTAATCTCAGGGGGATAGGATTACTAGCTTCAATCTGCTCTG
66 CTTCATTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCG
88190954 CTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
* *
88191019 CTTCGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTATCTTCAATCTGCTCCG
66 CTTCATTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCG
88191083 CTGTAATCTCAGGGAGATAAGATCTGA
1 CTGTAATCTCAGGGAGATAAGATCTGA
88191110 AATTCTTCGG
Statistics
Matches: 148, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 148 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (129 bp):
CTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
CTTCATTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCG
Found at i:88197493 original size:14 final size:15
Alignment explanation
Indices: 88197469--88197509 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
88197459 TTTCGAAAAG
88197469 AGAAA-AAAAATA-A
1 AGAAAGAAAAATAGA
88197482 AGAAAGAAAAATAGA
1 AGAAAGAAAAATAGA
88197497 A-AAAG-AAAATAGA
1 AGAAAGAAAAATAGA
88197510 TATACCGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.50
14 11 0.42
15 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (15 bp):
AGAAAGAAAAATAGA
Found at i:88201044 original size:18 final size:18
Alignment explanation
Indices: 88201011--88201045 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88201001 CTTATTTTTG
* *
88201011 CGAAAGCTACGTCTATTA
1 CGAAAGCTAAGACTATTA
88201029 CGAAAGCTAAGACTATT
1 CGAAAGCTAAGACTATT
88201046 CAATCTGGCC
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:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (18 bp):
CGAAAGCTAAGACTATTA
Found at i:88205719 original size:17 final size:17
Alignment explanation
Indices: 88205693--88205727 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
88205683 TTAAAAAACA
*
88205693 TTTTTCAAAAATATATT
1 TTTTTCAAAAATACATT
*
88205710 TTTTTTAAAAATACATT
1 TTTTTCAAAAATACATT
88205727 T
1 T
88205728 GAAAAGTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTTCAAAAATACATT
Found at i:88205971 original size:26 final size:27
Alignment explanation
Indices: 88205917--88205973 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
88205907 TAAGTAATTA
* *
88205917 ATATAAATTATTTGTAAAATTATTGAT
1 ATATAAAATATTTGTAAAATTATTAAT
88205944 ATATAAAATATTT-TAAAATT-TTAA-
1 ATATAAAATATTTGTAAAATTATTAAT
88205968 ATATAA
1 ATATAA
88205974 TAGTAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.21
25 3 0.11
26 7 0.25
27 12 0.43
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (27 bp):
ATATAAAATATTTGTAAAATTATTAAT
Found at i:88216487 original size:53 final size:54
Alignment explanation
Indices: 88216385--88216491 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 54
88216375 CCTTAAATGC
* **
88216385 TTACGAATTGATTAAATAATTTTTATTAAATTATTATAATAAATAATGTAAAAT
1 TTACGAATTGATCAAATAATTTTTATTAAATTACCATAATAAATAATGTAAAAT
* * *
88216439 TTACGAATTGATCAAATAA-TTTTATTTAATTACCATAATAATTCATGTAAAAT
1 TTACGAATTGATCAAATAATTTTTATTAAATTACCATAATAAATAATGTAAAAT
88216492 ATGAAATGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 29 0.62
54 18 0.38
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (54 bp):
TTACGAATTGATCAAATAATTTTTATTAAATTACCATAATAAATAATGTAAAAT
Found at i:88216885 original size:24 final size:24
Alignment explanation
Indices: 88216848--88216895 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
88216838 AAAAGAATAC
* *
88216848 AAAAATTATTAAAAATTACAAAAA
1 AAAAACTATAAAAAATTACAAAAA
* *
88216872 AAAAACTATAAAAATTTACTAAAA
1 AAAAACTATAAAAAATTACAAAAA
88216896 TTTCAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAACTATAAAAAATTACAAAAA
Found at i:88217128 original size:15 final size:14
Alignment explanation
Indices: 88217104--88217133 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
88217094 ATATAATAAA
88217104 TAAATAAATTGAAC
1 TAAATAAATTGAAC
88217118 TAAACTAAATTGAAC
1 TAAA-TAAATTGAAC
88217133 T
1 T
88217134 TCTTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (14 bp):
TAAATAAATTGAAC
Found at i:88217680 original size:3 final size:3
Alignment explanation
Indices: 88217674--88217699 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
88217664 GGAAAAAAAT
88217674 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
88217700 CTAATCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:88220700 original size:27 final size:27
Alignment explanation
Indices: 88220669--88220728 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
88220659 AAATTCTAAT
*
88220669 AAAAATCT-TTAAAAATGAAAAAAATTAC
1 AAAAATATATTAAAAAT--AAAAAATTAC
*
88220697 AAAAATATATTAAAAATATAAAATTAC
1 AAAAATATATTAAAAATAAAAAATTAC
88220724 AAAAA
1 AAAAA
88220729 AACTATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 14 0.48
28 7 0.24
29 8 0.28
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (27 bp):
AAAAATATATTAAAAATAAAAAATTAC
Found at i:88220737 original size:27 final size:27
Alignment explanation
Indices: 88220689--88220740 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
88220679 AAAAATGAAA
*
88220689 AAAATTACAAAAATATATTAAAAATAT
1 AAAATTACAAAAAAATATTAAAAATAT
88220716 AAAATTACAAAAAAACTA-TAAAAAT
1 AAAATTACAAAAAAA-TATTAAAAAT
88220741 TTACTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (27 bp):
AAAATTACAAAAAAATATTAAAAATAT
Found at i:88221495 original size:3 final size:3
Alignment explanation
Indices: 88221489--88221514 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
88221479 GGAAAAAAAT
88221489 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
88221515 CTAATCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:88229474 original size:186 final size:186
Alignment explanation
Indices: 88229160--88229534 Score: 750
Period size: 186 Copynumber: 2.0 Consensus size: 186
88229150 TTTAGATCAA
88229160 AATTTGGTGGAAATTGGAGGAAAATAGAAAATTACCAAAATGTCCCTAAATTTTGGTATTTCTGC
1 AATTTGGTGGAAATTGGAGGAAAATAGAAAATTACCAAAATGTCCCTAAATTTTGGTATTTCTGC
88229225 AATTTAGCCTGGTAAGTTCGTATGAACTATATTCTGTATAATTTTAATTAAAGAGAATGTTATTT
66 AATTTAGCCTGGTAAGTTCGTATGAACTATATTCTGTATAATTTTAATTAAAGAGAATGTTATTT
88229290 TGTGATGAATATTATATAAATATGTGTTTTATTATTGAAATTGAATTATTATTGGT
131 TGTGATGAATATTATATAAATATGTGTTTTATTATTGAAATTGAATTATTATTGGT
88229346 AATTTGGTGGAAATTGGAGGAAAATAGAAAATTACCAAAATGTCCCTAAATTTTGGTATTTCTGC
1 AATTTGGTGGAAATTGGAGGAAAATAGAAAATTACCAAAATGTCCCTAAATTTTGGTATTTCTGC
88229411 AATTTAGCCTGGTAAGTTCGTATGAACTATATTCTGTATAATTTTAATTAAAGAGAATGTTATTT
66 AATTTAGCCTGGTAAGTTCGTATGAACTATATTCTGTATAATTTTAATTAAAGAGAATGTTATTT
88229476 TGTGATGAATATTATATAAATATGTGTTTTATTATTGAAATTGAATTATTATTGGT
131 TGTGATGAATATTATATAAATATGTGTTTTATTATTGAAATTGAATTATTATTGGT
88229532 AAT
1 AAT
88229535 ATGTATAATT
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
186 189 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.41
Consensus pattern (186 bp):
AATTTGGTGGAAATTGGAGGAAAATAGAAAATTACCAAAATGTCCCTAAATTTTGGTATTTCTGC
AATTTAGCCTGGTAAGTTCGTATGAACTATATTCTGTATAATTTTAATTAAAGAGAATGTTATTT
TGTGATGAATATTATATAAATATGTGTTTTATTATTGAAATTGAATTATTATTGGT
Found at i:88231622 original size:37 final size:38
Alignment explanation
Indices: 88231569--88231661 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 38
88231559 AGTTCCACAT
* * * **
88231569 TGTGGTGTGTAAGGTGGATGATCCAATTATGGTTC-TA
1 TGTGGTGTGCAGGGTGGATGAGCCAATTATGGCCCTTA
* ** *
88231606 TGTGGTGTGCAGGGTGGATGGGCCTTTTGTGGCCCTTA
1 TGTGGTGTGCAGGGTGGATGAGCCAATTATGGCCCTTA
88231644 TGTGGTGTGCAGGGTGGA
1 TGTGGTGTGCAGGGTGGA
88231662 CGAAGCGGTG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 26 0.57
38 20 0.43
ACGTcount: A:0.14, C:0.11, G:0.41, T:0.34
Consensus pattern (38 bp):
TGTGGTGTGCAGGGTGGATGAGCCAATTATGGCCCTTA
Found at i:88233888 original size:3 final size:3
Alignment explanation
Indices: 88233880--88233910 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
88233870 ATAAATTTCA
88233880 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
88233911 GCTTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:88234065 original size:13 final size:13
Alignment explanation
Indices: 88234044--88234073 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
88234034 ATTTTTTAAA
*
88234044 ATATTTATTTTAT
1 ATATGTATTTTAT
88234057 ATATGTATTTTAT
1 ATATGTATTTTAT
88234070 ATAT
1 ATAT
88234074 TATGATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (13 bp):
ATATGTATTTTAT
Found at i:88234840 original size:108 final size:110
Alignment explanation
Indices: 88234549--88234842 Score: 441
Period size: 110 Copynumber: 2.7 Consensus size: 110
88234539 TCAAAAAAGG
*
88234549 AAAATATTTCTAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAA-ATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
* * * ** *
88234614 GGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
65 GGGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATATCCCCTTC
*
88234660 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCT-
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
88234724 GGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATA-CCCCTTC
66 GGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATATCCCCTTC
* * **
88234768 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCTTTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
*
88234832 GGTTTCGATTT
66 GGTGTCGATTT
88234843 CTCGTTTATC
Statistics
Matches: 168, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
107 15 0.09
108 57 0.34
109 34 0.20
110 58 0.35
111 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (110 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTCTCATTCAACCAAATAGCTAAATATCCCCTTC
Found at i:88237713 original size:32 final size:29
Alignment explanation
Indices: 88237654--88237726 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 29
88237644 GGGTCCAATT
*
88237654 AAAATTTTTAAATTTTTGTGAGATTAATG
1 AAAATTTTCAAATTTTTGTGAGATTAATG
* * *
88237683 AGAATTTTCAAATATTTTAAGTGAGCTTAATT
1 AAAATTTTCAAAT-TTTT--GTGAGATTAATG
88237715 AAAATTTTCAAA
1 AAAATTTTCAAA
88237727 AAAATTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 11 0.31
30 4 0.11
32 21 0.58
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (29 bp):
AAAATTTTCAAATTTTTGTGAGATTAATG
Found at i:88244948 original size:30 final size:30
Alignment explanation
Indices: 88244864--88244949 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
88244854 TAAGGTTATT
*
88244864 TTTACCAAAATATTACAAAAAAATAA-AAAA
1 TTTACCAAAATAATACAAAAAAA-AAGAAAA
** * * **
88244894 AATACCAAAATAATA-TACAAAAAAGATTA
1 TTTACCAAAATAATACAAAAAAAAAGAAAA
88244923 TTTACCAAAATAATACAAAAAAAAAGA
1 TTTACCAAAATAATACAAAAAAAAAGA
88244950 CGGCTGAATG
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
28 2 0.05
29 20 0.47
30 21 0.49
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.21
Consensus pattern (30 bp):
TTTACCAAAATAATACAAAAAAAAAGAAAA
Found at i:88248427 original size:18 final size:18
Alignment explanation
Indices: 88248385--88248427 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
88248375 GCCCATTCCG
* *
88248385 AAGTATATATATATACAT
1 AAGTATGTATATATACAC
88248403 ATA-TATGTATATATACAC
1 A-AGTATGTATATATACAC
88248421 AAGTATG
1 AAGTATG
88248428 CCCATTCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (18 bp):
AAGTATGTATATATACAC
Found at i:88248938 original size:28 final size:28
Alignment explanation
Indices: 88248900--88249109 Score: 341
Period size: 28 Copynumber: 7.5 Consensus size: 28
88248890 TAAATTGTAC
88248900 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
* *
88248928 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
88248956 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
* *
88248984 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
88249012 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
* *
88249040 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
88249068 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
88249095 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
88249110 GACTTAATAA
Statistics
Matches: 171, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
27 24 0.14
28 147 0.86
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTTGATTATGT
Found at i:88248966 original size:56 final size:56
Alignment explanation
Indices: 88248900--88249109 Score: 377
Period size: 56 Copynumber: 3.8 Consensus size: 56
88248890 TAAATTGTAC
88248900 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
88248956 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
88249012 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
88249068 AGCACTAAGTGTGCGAG-TTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCG
88249110 GACTTAATAA
Statistics
Matches: 150, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
55 23 0.15
56 127 0.85
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.32
Consensus pattern (56 bp):
AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:88251501 original size:33 final size:32
Alignment explanation
Indices: 88251464--88251541 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
88251454 TGGCCCTACC
** * *
88251464 ATGGTCTTACATTTGTAGTACCATAACCCAGTT
1 ATGGTCTTACATCAG-AATACCATAACCCAGCT
* *
88251497 ATGGTCTTATCATCAGAATGCCATAGCCCAGCT
1 ATGGTCTTA-CATCAGAATACCATAACCCAGCT
88251530 ATGGTCTTACAT
1 ATGGTCTTACAT
88251542 ATAAATACTG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.08
33 31 0.82
34 4 0.11
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (32 bp):
ATGGTCTTACATCAGAATACCATAACCCAGCT
Found at i:88251587 original size:68 final size:66
Alignment explanation
Indices: 88251515--88251640 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 66
88251505 ATCATCAGAA
* * * *
88251515 TGCCATAGCCCAGCTATGGTC-TTACATATAAATACTGCCATGGTCCAACCATGGTCTTACGTCC
1 TGCCATAACCCAGCTAAGGTCTTTACAT-TAAA-A-TGCCATAGACCAACCATGGTCTTACGTCC
88251579 AAGG
63 AAGG
* * *
88251583 TGCCATAACCCAGTTAAGGTCTTTTCATTAAAATGCCATAGACCAACTATGGTCTTAC
1 TGCCATAACCCAGCTAAGGTCTTTACATTAAAATGCCATAGACCAACCATGGTCTTAC
88251641 ATATAAATAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
66 22 0.44
67 1 0.02
68 22 0.44
69 5 0.10
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (66 bp):
TGCCATAACCCAGCTAAGGTCTTTACATTAAAATGCCATAGACCAACCATGGTCTTACGTCCAAG
G
Found at i:88251589 original size:101 final size:101
Alignment explanation
Indices: 88251484--88251677 Score: 316
Period size: 101 Copynumber: 1.9 Consensus size: 101
88251474 ATTTGTAGTA
* * * *
88251484 CCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAAATA
1 CCATAACCCAGTTAAGGTCTTATCATCAAAATGCCATAGACCAACTATGGTCTTACATATAAATA
88251549 CTGCCATGGTCCAACCATGGTCTTACGTCCAAGGTG
66 CTGCCATGGTCCAACCATGGTCTTACGTCCAAGGTG
* *
88251585 CCATAACCCAGTTAAGGTCTTTTCATTAAAATGCCATAGACCAACTATGGTCTTACATATAAATA
1 CCATAACCCAGTTAAGGTCTTATCATCAAAATGCCATAGACCAACTATGGTCTTACATATAAATA
* *
88251650 CTGTCATGGTCCTACCATGGTCTTACGT
66 CTGCCATGGTCCAACCATGGTCTTACGT
88251678 TCAATTCATC
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 85 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (101 bp):
CCATAACCCAGTTAAGGTCTTATCATCAAAATGCCATAGACCAACTATGGTCTTACATATAAATA
CTGCCATGGTCCAACCATGGTCTTACGTCCAAGGTG
Found at i:88255071 original size:26 final size:26
Alignment explanation
Indices: 88255042--88255123 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
88255032 TGATACAAAT
88255042 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
88255068 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88255094 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88255120 TGAT
1 TGAT
88255124 GGGAATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:88262551 original size:26 final size:26
Alignment explanation
Indices: 88262522--88262707 Score: 354
Period size: 26 Copynumber: 7.2 Consensus size: 26
88262512 TGATAAAAAT
88262522 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88262548 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88262574 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88262600 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88262626 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
88262652 TGATAATGGCTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
88262678 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
88262704 TGAT
1 TGAT
88262708 GGGCATTTCA
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 158 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:88275285 original size:10 final size:10
Alignment explanation
Indices: 88275262--88275313 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
88275252 ATGTGAATCT
*
88275262 ATCATAAATAA
1 ATCA-AAATTA
88275273 ATCAAAATTA
1 ATCAAAATTA
88275283 ATCAAAATTTA
1 ATCAAAA-TTA
*
88275294 ATATAAAATTA
1 AT-CAAAATTA
*
88275305 ATTAAAATT
1 ATCAAAATT
88275314 CAACATGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
10 19 0.51
11 14 0.38
12 4 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (10 bp):
ATCAAAATTA
Found at i:88281145 original size:25 final size:25
Alignment explanation
Indices: 88281102--88281199 Score: 96
Period size: 25 Copynumber: 4.0 Consensus size: 25
88281092 GTACATGTAT
* **
88281102 GCTCATATGAGCT-ATGAATCAATAA
1 GCTCATACGAGCTGA-GAATCGGTAA
*
88281127 GCTCATACGAGTTGAGAATCGGTAA
1 GCTCATACGAGCTGAGAATCGGTAA
*
88281152 GCTC-TCACAAGCTGA-AATCGGTAA
1 GCTCAT-ACGAGCTGAGAATCGGTAA
*
88281176 GCTCATACGAGCTGA-AATTGGTAA
1 GCTCATACGAGCTGAGAATCGGTAA
88281200 TCCCTAATGA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
24 30 0.48
25 31 0.50
26 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTGAGAATCGGTAA
Found at i:88281173 original size:24 final size:24
Alignment explanation
Indices: 88281124--88281199 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 24
88281114 TATGAATCAA
* *
88281124 TAAGCTCATACGAGTTGAGAATCGG
1 TAAGCTCATACAAGCTGA-AATCGG
88281149 TAAGCTC-TCACAAGCTGAAATCGG
1 TAAGCTCAT-ACAAGCTGAAATCGG
* *
88281173 TAAGCTCATACGAGCTGAAATTGG
1 TAAGCTCATACAAGCTGAAATCGG
88281197 TAA
1 TAA
88281200 TCCCTAATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
24 30 0.67
25 15 0.33
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (24 bp):
TAAGCTCATACAAGCTGAAATCGG
Found at i:88284898 original size:102 final size:104
Alignment explanation
Indices: 88284721--88284922 Score: 293
Period size: 102 Copynumber: 2.0 Consensus size: 104
88284711 ATATCGATAC
* * * *
88284721 AACTTCCCAAACTTGTATAAAACAAGTTTAAAACACTTAAAGACATTTTTGATTGACTCAAAAAT
1 AACTTCCCAAACTTGAATAAAACAAGTTTAAAACACTCAAAGACATTTTGGATTGACACAAAAAT
*
88284786 GTTTAGATAAATTAAAATACATTTAAAATA-AGTTATAT
66 ATTTAGATAAATTAAAATACATTTAAAATATAGTTATAT
** *
88284824 AACTTCCCAAACTTGAATAAAATGAGTTTAAAACAC-CAAA-ATCATTTTGGATTGGCACAAAAA
1 AACTTCCCAAACTTGAATAAAACAAGTTTAAAACACTCAAAGA-CATTTTGGATTGACACAAAAA
*
88284887 TATTTAGATAAATTAAAATACATTTAGAATATAGTT
65 TATTTAGATAAATTAAAATACATTTAAAATATAGTT
88284923 TTGAGTACTT
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 1 0.01
102 50 0.57
103 37 0.42
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33
Consensus pattern (104 bp):
AACTTCCCAAACTTGAATAAAACAAGTTTAAAACACTCAAAGACATTTTGGATTGACACAAAAAT
ATTTAGATAAATTAAAATACATTTAAAATATAGTTATAT
Found at i:88299247 original size:23 final size:24
Alignment explanation
Indices: 88299197--88299249 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
88299187 TTGTTTTATT
* *
88299197 TTTATTTTTATTTTTTTGCCCTTA
1 TTTATTTTTATTTTATTGCCATTA
88299221 -TTATTTTTATTTTATT-CCATTA
1 TTTATTTTTATTTTATTGCCATTA
88299243 TTTATTT
1 TTTATTT
88299250 ATTCATTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTATTTTTATTTTATTGCCATTA
Found at i:88299252 original size:16 final size:16
Alignment explanation
Indices: 88299218--88299257 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
88299208 TTTTTTGCCC
88299218 TTATT-ATT-TTTATT
1 TTATTCATTATTTATT
88299232 TTATTCCATTATTTA-T
1 TTATT-CATTATTTATT
88299248 TTATTCATTA
1 TTATTCATTA
88299258 CTTTTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 5 0.22
16 9 0.39
17 4 0.17
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTCATTATTTATT
Found at i:88304511 original size:13 final size:13
Alignment explanation
Indices: 88304493--88304535 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
88304483 TAGATTTTTC
88304493 CTAAATATTATTA
1 CTAAATATTATTA
88304506 CTAAATA--ATT-
1 CTAAATATTATTA
*
88304516 CTAAATATTATCA
1 CTAAATATTATTA
88304529 CTAAATA
1 CTAAATA
88304536 ATTCAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 2 0.08
13 14 0.54
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
CTAAATATTATTA
Found at i:88304523 original size:23 final size:23
Alignment explanation
Indices: 88304493--88304544 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
88304483 TAGATTTTTC
*
88304493 CTAAATATTATTACTAAATAATT
1 CTAAATATTATCACTAAATAATT
88304516 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
88304539 CAAAAT
1 CTAAAT
88304545 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:88306711 original size:11 final size:11
Alignment explanation
Indices: 88306680--88306721 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
88306670 AAGCATAGCT
88306680 TTAATTAAGTG
1 TTAATTAAGTG
88306691 ATTCAATTAAGTG
1 -TT-AATTAAGTG
88306704 TTAATTAA-TG
1 TTAATTAAGTG
88306714 TTATATTA
1 TTA-ATTA
88306722 TATCTGATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 5 0.18
11 10 0.36
12 4 0.14
13 9 0.32
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (11 bp):
TTAATTAAGTG
Found at i:88324563 original size:40 final size:37
Alignment explanation
Indices: 88324508--88324674 Score: 166
Period size: 35 Copynumber: 4.6 Consensus size: 37
88324498 CATGGCAAAG
*
88324508 TGTGAAATGTAGGTATGGTATCATC-T-ATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCATCATACTGAGT
* *
88324543 TGTGAAAAGTAGGTATGGTATTATC--CATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCATCATACTGAGT
88324578 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATC--AT-CATACTGAGT
** * * *
88324618 TAAGAAATGTAGGTATGGCATT-TC-CCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTATCATCATACTGAGT
** *
88324653 TGAAAAATATAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
88324675 TCAATGAGGA
Statistics
Matches: 112, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
35 82 0.73
39 2 0.02
40 28 0.25
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGGTATTATCATCATACTGAGT
Found at i:88324646 original size:75 final size:75
Alignment explanation
Indices: 88324508--88324678 Score: 194
Period size: 75 Copynumber: 2.4 Consensus size: 75
88324498 CATGGCAAAG
* ** *
88324508 TGTGAAATGTAGGTATGG---TATC--ATCTATACTGAGTTGTGAAAAGTAGGTATGGTATTATC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAAAGTAGGTATGGCATTATC
*
88324568 CATACTGAGC
66 CATACCGAGC
*
88324578 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAAAGTAGGTATGGCATTAT-
*
88324642 CCATACCGAGT
65 CCATACCGAGC
** *
88324653 TGAAAAATATAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
88324679 TGAGGAAAAC
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 58 0.68
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAAAGTAGGTATGGCATTATC
CATACCGAGC
Found at i:88329838 original size:23 final size:23
Alignment explanation
Indices: 88329812--88329857 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
88329802 AGATTTTTCT
* *
88329812 TAAATATTATTATTAAATAATTC
1 TAAATATTATCACTAAATAATTC
88329835 TAAATATTATCACTAAATAATTC
1 TAAATATTATCACTAAATAATTC
88329858 AAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAATATTATCACTAAATAATTC
Found at i:88330845 original size:19 final size:18
Alignment explanation
Indices: 88330812--88330848 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
88330802 AAAATATATT
*
88330812 TTTAATTTTGATAATTTA
1 TTTAATTTAGATAATTTA
88330830 TTTAACTTTAGATAATTTA
1 TTTAA-TTTAGATAATTTA
88330849 AAACATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTAATTTAGATAATTTA
Found at i:88353853 original size:25 final size:25
Alignment explanation
Indices: 88353820--88353902 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
88353810 AGTAAGTTGC
*
88353820 ATATGAATAAATATACAACAACAAT
1 ATATCAATAAATATACAACAACAAT
**
88353845 ATATCAAT--A-AT-CAACATA-GTT
1 ATATCAATAAATATACAACA-ACAAT
*
88353866 GCATATGAATAAATATACAACAACAAT
1 --ATATCAATAAATATACAACAACAAT
88353893 ATATCAATAA
1 ATATCAATAA
88353903 TCAACATACT
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 8 0.19
25 17 0.40
26 3 0.07
27 6 0.14
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (25 bp):
ATATCAATAAATATACAACAACAAT
Found at i:88353885 original size:48 final size:48
Alignment explanation
Indices: 88353814--88353910 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
88353804 AAGCTTAGTA
88353814 AGTTGCATATGAATAAATATACAACAACAATATATCAATAATCAACAT
1 AGTTGCATATGAATAAATATACAACAACAATATATCAATAATCAACAT
88353862 AGTTGCATATGAATAAATATACAACAACAATATATCAATAATCAACAT
1 AGTTGCATATGAATAAATATACAACAACAATATATCAATAATCAACAT
88353910 A
1 A
88353911 CTCATAATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.27
Consensus pattern (48 bp):
AGTTGCATATGAATAAATATACAACAACAATATATCAATAATCAACAT
Found at i:88354261 original size:46 final size:45
Alignment explanation
Indices: 88354165--88354381 Score: 188
Period size: 46 Copynumber: 4.6 Consensus size: 45
88354155 CATCTTAAGT
* *
88354165 CGATGCCATGTCCCAGACATGGTCTTACACT-GACTATTATCTAGTA-GC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAG-CT-TCATCTCG-AGGC
88354213 CGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTT-CATCTCGAGGC
* * * * * * *
88354259 CGATGCATATCCCAGAAAAGTCTTACACTAGCACTCGTCTCAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGC-TTCATCTCGAGGC
* * *
88354305 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TCAT-CTCGAGGC
* *
88354353 CGATGCATATCCCAAACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
88354382 GGCCCACATC
Statistics
Matches: 140, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
45 2 0.01
46 71 0.51
47 39 0.28
48 27 0.19
49 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTTCATCTCGAGGC
Found at i:88354355 original size:94 final size:92
Alignment explanation
Indices: 88354211--88354381 Score: 240
Period size: 94 Copynumber: 1.8 Consensus size: 92
88354201 TTATCTAGTA
*
88354211 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAGGCCGATGCATATCCCAGAA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATATCGAGGCCGATGCATATCCCA-AA
88354276 -AAGTCTTACACTAGCACTCGTCTCAAT
65 CAAGTCTTACACTAGCACTCGTCTCAAT
* *
88354303 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATATCCC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TACAT-ATCGAGGCCGATGCATATCCC
*
88354366 AAACATGTCTTACACT
62 AAACAAGTCTTACACT
88354382 GGCCCACATC
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
92 7 0.10
93 16 0.23
94 45 0.64
95 2 0.03
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATATCGAGGCCGATGCATATCCCAAAC
AAGTCTTACACTAGCACTCGTCTCAAT
Found at i:88361096 original size:22 final size:20
Alignment explanation
Indices: 88361060--88361106 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
88361050 ATGGGGCAAA
88361060 CGTGTGTATAGACACACGCC
1 CGTGTGTATAGACACACGCC
88361080 CGTGTGTATAGACACACGCC
1 CGTGTGTATAGACACACGCC
88361100 CGTGTGT
1 CGTGTGT
88361107 CTACCCGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (20 bp):
CGTGTGTATAGACACACGCC
Found at i:88362286 original size:7 final size:7
Alignment explanation
Indices: 88362274--88362299 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
88362264 ATAACTTATT
88362274 ACCCTAA
1 ACCCTAA
88362281 ACCCTAA
1 ACCCTAA
88362288 ACCCTAA
1 ACCCTAA
88362295 ACCCT
1 ACCCT
88362300 TTAATTCCAT
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:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (7 bp):
ACCCTAA
Found at i:88362796 original size:46 final size:46
Alignment explanation
Indices: 88362746--88362837 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
88362736 ACATTTGGGC
* *
88362746 GTTCGCATGCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAT
1 GTTCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGAT
88362792 GTTCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGAT
1 GTTCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGAT
88362838 ACCTAGTTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (46 bp):
GTTCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGAT
Found at i:88364278 original size:47 final size:47
Alignment explanation
Indices: 88364205--88364481 Score: 219
Period size: 47 Copynumber: 5.9 Consensus size: 47
88364195 TGGGTAAGGT
* *
88364205 GCCGATGCCATGTCTCAGACACGGTCTTACACTGGCTCACATCTCACA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCA-A
* * *
88364253 -TCGATGCCATGTCCCAGACATGGTCTTATACTGACT-ATCATCTCATA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCA-CATCTCA-A
* *
88364300 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACGTCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAA
* ** * * *
88364345 GGCCGATG-CATATCCCAGACAT-GTCTTACACTAACACTCATCTGAA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAA
* * * * * ***
88364391 TGCCGATGCCATATCCCAAACATGGTCTTATACTGGCTCTCATAATGTG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACAT-CTCAA
* * * *
88364440 GCCAATG-CATATCCCAAACAT-GTCTTACACTGGCCCACATCT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCT
88364482 TAAGTGACCC
Statistics
Matches: 190, Mismatches: 32, Indels: 17
0.79 0.13 0.07
Matches are distributed among these distances:
45 2 0.01
46 79 0.42
47 81 0.43
48 26 0.14
49 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.27
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAA
Found at i:88364332 original size:93 final size:92
Alignment explanation
Indices: 88364204--88364470 Score: 254
Period size: 94 Copynumber: 2.8 Consensus size: 92
88364194 ATGGGTAAGG
* * * *
88364204 TGCCGATGCCATGTCTCAGACACGGTCTTACACTGGCTCACATCTCACA-TCGATGCCATGTCCC
1 TGCCGATGCCATGTCCCAGACA-TGTCTTACACTGGCTCACATCTCA-AGCCGATG-CATATCCC
* *
88364268 AGACATGGTCTTATACTGACTA-TCATCTC-A
63 AGACAT-GTCTTACACTAAC-ACTCATCTCAA
* *
88364298 TAGCCGATG-CATGTCCCAGACATGTCTTACACTGGCTTACGTCTCAAGGCCGATGCATATCCCA
1 T-GCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCACATCTCAA-GCCGATGCATATCCCA
*
88364362 GACATGTCTTACACTAACACTCATCTGAA
64 GACATGTCTTACACTAACACTCATCTCAA
* * * * * *** *
88364391 TGCCGATGCCATATCCCAAACATGGTCTTATACTGGCTCTCATAATGTGGCCAATGCATATCCCA
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCACAT-CTCAAGCCGATGCATATCCCA
*
88364456 AACATGTCTTACACT
64 GACATGTCTTACACT
88364471 GGCCCACATC
Statistics
Matches: 144, Mismatches: 21, Indels: 16
0.80 0.12 0.09
Matches are distributed among these distances:
91 1 0.01
92 25 0.17
93 48 0.33
94 62 0.43
95 8 0.06
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27
Consensus pattern (92 bp):
TGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCACATCTCAAGCCGATGCATATCCCAGA
CATGTCTTACACTAACACTCATCTCAA
Found at i:88364472 original size:46 final size:46
Alignment explanation
Indices: 88364300--88364473 Score: 153
Period size: 46 Copynumber: 3.7 Consensus size: 46
88364290 TCATCTCATA
* *
88364300 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTC-TCAA---G
1 GCCGATGCATATCCCAAACATGTCTTACACTGGC-T-C-TCAT-AATGTG
* ** * *
88364346 GCCGATGCATATCCCAGACATGTCTTACACTAACACTCAT-CTGAAT-
1 GCCGATGCATATCCCAAACATGTCTTACACTGGCTCTCATAATG--TG
*
88364392 GCCGATGCCATATCCCAAACATGGTCTTATACTGGCTCTCATAATGTG
1 GCCGATG-CATATCCCAAACAT-GTCTTACACTGGCTCTCATAATGTG
*
88364440 GCCAATGCATATCCCAAACATGTCTTACACTGGC
1 GCCGATGCATATCCCAAACATGTCTTACACTGGC
88364474 CCACATCTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
43 2 0.02
44 2 0.02
46 50 0.48
47 28 0.27
48 21 0.20
49 2 0.02
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (46 bp):
GCCGATGCATATCCCAAACATGTCTTACACTGGCTCTCATAATGTG
Found at i:88367608 original size:11 final size:11
Alignment explanation
Indices: 88367592--88367617 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
88367582 TATTAATATA
88367592 TATTTATTTTT
1 TATTTATTTTT
88367603 TATTTATTTTT
1 TATTTATTTTT
88367614 TATT
1 TATT
88367618 AGTGATGCAT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TATTTATTTTT
Found at i:88373048 original size:3 final size:3
Alignment explanation
Indices: 88373040--88373071 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
88373030 GGTACGGTTA
*
88373040 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
88373072 AGAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:88375765 original size:25 final size:27
Alignment explanation
Indices: 88375722--88375793 Score: 87
Period size: 25 Copynumber: 2.8 Consensus size: 27
88375712 CAACTATCAC
* *
88375722 TTCTCGCTGAGCTTGCAGCTTTG-ACA
1 TTCTTGCTAAGCTTGCAGCTTTGCACA
88375748 -TCTTGCTAAGCTTGCAGC-TTGCACA
1 TTCTTGCTAAGCTTGCAGCTTTGCACA
* *
88375773 TTTTTGCTGAGCTTGCAGCTT
1 TTCTTGCTAAGCTTGCAGCTT
88375794 ACACATTAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 3 0.08
25 19 0.49
26 16 0.41
27 1 0.03
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.38
Consensus pattern (27 bp):
TTCTTGCTAAGCTTGCAGCTTTGCACA
Found at i:88375786 original size:26 final size:26
Alignment explanation
Indices: 88375722--88375800 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
88375712 CAACTATCAC
*
88375722 TTCTCGCTGAGCTTGCAGCTTTG-ACA
1 TTCTTGCTGAGCTTGCAGC-TTGCACA
*
88375748 -TCTTGCTAAGCTTGCAGCTTGCACA
1 TTCTTGCTGAGCTTGCAGCTTGCACA
* *
88375773 TTTTTGCTGAGCTTGCAGCTTACACA
1 TTCTTGCTGAGCTTGCAGCTTGCACA
88375799 TT
1 TT
88375801 AGAAAGCTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
24 3 0.07
25 19 0.41
26 24 0.52
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (26 bp):
TTCTTGCTGAGCTTGCAGCTTGCACA
Found at i:88376302 original size:25 final size:25
Alignment explanation
Indices: 88376274--88376330 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
88376264 TCAGTTTATT
88376274 TTGAACTAA-AAAACTAAACTAGT-GC
1 TTGAACTAACAAAA-TAAAC-AGTAGC
* *
88376299 TTGAAGTAACAAAATGAACAGTAGC
1 TTGAACTAACAAAATAAACAGTAGC
88376324 TTGAACT
1 TTGAACT
88376331 TTAGCCAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 3 0.11
25 20 0.74
26 4 0.15
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.25
Consensus pattern (25 bp):
TTGAACTAACAAAATAAACAGTAGC
Found at i:88380922 original size:16 final size:16
Alignment explanation
Indices: 88380901--88380931 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88380891 TTTCCCAAAG
*
88380901 CAAAGGAAGAGAAAAA
1 CAAAGGAAAAGAAAAA
88380917 CAAAGGAAAAGAAAA
1 CAAAGGAAAAGAAAA
88380932 CCCCCAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.06, G:0.23, T:0.00
Consensus pattern (16 bp):
CAAAGGAAAAGAAAAA
Found at i:88385480 original size:22 final size:22
Alignment explanation
Indices: 88385436--88385482 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
88385426 TATATATGAT
* *
88385436 AAATGGTAGCAACATAATAGTA
1 AAATGGTAGCAAAACAATAGTA
* *
88385458 AAATTGTAGCAAAACAATGGTA
1 AAATGGTAGCAAAACAATAGTA
88385480 AAA
1 AAA
88385483 AGTGGGAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (22 bp):
AAATGGTAGCAAAACAATAGTA
Found at i:88388600 original size:12 final size:12
Alignment explanation
Indices: 88388583--88388608 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
88388573 AAATAAAATT
88388583 AATTATATAATA
1 AATTATATAATA
88388595 AATTATATAATA
1 AATTATATAATA
88388607 AA
1 AA
88388609 GTAAGTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTATATAATA
Found at i:88399685 original size:9 final size:9
Alignment explanation
Indices: 88399662--88399754 Score: 58
Period size: 8 Copynumber: 10.9 Consensus size: 9
88399652 GAAAATAAGT
*
88399662 TAAAGAAAA
1 TAAATAAAA
88399671 TAAAATAAAA
1 T-AAATAAAA
88399681 TAAATAAAA
1 TAAATAAAA
*
88399690 -AACTAAAA
1 TAAATAAAA
*
88399698 -AAATTAAA
1 TAAATAAAA
* *
88399706 -AAAGAAGA
1 TAAATAAAA
88399714 TAAA-AAAA
1 TAAATAAAA
88399722 T-AATAAAA
1 TAAATAAAA
88399730 GTAAA-AATAA
1 -TAAATAA-AA
88399740 -AAATAAAA
1 TAAATAAAA
88399748 -AAATAAA
1 TAAATAAA
88399755 CTTAATGATA
Statistics
Matches: 69, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
7 2 0.03
8 38 0.55
9 17 0.25
10 12 0.17
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (9 bp):
TAAATAAAA
Found at i:88399705 original size:17 final size:16
Alignment explanation
Indices: 88399672--88399754 Score: 73
Period size: 16 Copynumber: 5.1 Consensus size: 16
88399662 TAAAGAAAAT
88399672 AAAATAAAATAAATAA
1 AAAATAAAATAAATAA
88399688 AAAACTAAAA-AAATTAA
1 AAAA-TAAAATAAA-TAA
* *
88399705 AAAAGAAGATAAA-AA
1 AAAATAAAATAAATAA
*
88399720 AATAATAAAAGTAAAAATA
1 AA-AATAAAA-TAAATA-A
88399739 AAAATAAAA-AAATAA
1 AAAATAAAATAAATAA
88399754 A
1 A
88399755 CTTAATGATA
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
15 6 0.11
16 19 0.35
17 19 0.35
18 8 0.15
19 3 0.05
ACGTcount: A:0.80, C:0.01, G:0.04, T:0.16
Consensus pattern (16 bp):
AAAATAAAATAAATAA
Found at i:88399705 original size:21 final size:20
Alignment explanation
Indices: 88399677--88399754 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 20
88399667 AAAATAAAAT
88399677 AAAATAAATAAAAA-ACTAAA
1 AAAATAAATAAAAAGA-TAAA
88399697 AAAATTAAA-AAAGAAGATAAA
1 AAAA-TAAATAAA-AAGATAAA
88399718 AAAAT-AAT-AAAAG-TAAA
1 AAAATAAATAAAAAGATAAA
*
88399735 AATAA-AAATAAAAAAATAAA
1 AA-AATAAATAAAAAGATAAA
88399755 CTTAATGATA
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
17 6 0.12
18 8 0.16
19 8 0.16
20 12 0.24
21 14 0.29
22 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.15
Consensus pattern (20 bp):
AAAATAAATAAAAAGATAAA
Found at i:88399716 original size:29 final size:29
Alignment explanation
Indices: 88399682--88399754 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
88399672 AAAATAAAAT
* *
88399682 AAATAAAAAACTAAAAAAATTAAAAA-AGA
1 AAATAAAAAAATAAAAAAAGTAAAAATA-A
* *
88399711 AGATAAAAAAATAATAAAAGTAAAAATAA
1 AAATAAAAAAATAAAAAAAGTAAAAATAA
88399740 AAATAAAAAAATAAA
1 AAATAAAAAAATAAA
88399755 CTTAATGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 36 0.97
30 1 0.03
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.15
Consensus pattern (29 bp):
AAATAAAAAAATAAAAAAAGTAAAAATAA
Found at i:88399858 original size:16 final size:16
Alignment explanation
Indices: 88399825--88399872 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
88399815 TAGAAATAGC
*
88399825 AAAATAATAATA-ATA
1 AAAATTATAATATATA
88399840 AAAATTATAATATATAA
1 AAAATTATAATATAT-A
*
88399857 AAAATTA-AAAATATA
1 AAAATTATAATATATA
88399872 A
1 A
88399873 GTATAAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 13 0.45
16 8 0.28
17 8 0.28
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTATAATATATA
Found at i:88399860 original size:18 final size:19
Alignment explanation
Indices: 88399828--88399872 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
88399818 AAATAGCAAA
88399828 ATAATA-ATAATAAAAATT
1 ATAATATATAATAAAAATT
88399846 ATAATATAT-A-AAAAATT
1 ATAATATATAATAAAAATT
*
88399863 A-AAAATATAA
1 ATAATATATAA
88399873 GTATAAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
18 7 0.29
19 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAATATATAATAAAAATT
Found at i:88399886 original size:25 final size:23
Alignment explanation
Indices: 88399838--88399923 Score: 68
Period size: 25 Copynumber: 3.5 Consensus size: 23
88399828 ATAATAATAA
88399838 TAAAAATTATAATATATAAA-AAAT
1 TAAAAA-TATAATATA-AAATAAAT
88399862 TAAAAATATAAGTATAAGAATAAAT
1 TAAAAATATAA-TATAA-AATAAAT
* *
88399887 TAATTAAT-TAATTAGTAAAATAAAA
1 TAA-AAATATAA-TA-TAAAATAAAT
88399912 TAAATAATATAA
1 TAAA-AATATAA
88399924 CAATTAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
23 6 0.12
24 12 0.24
25 24 0.47
26 9 0.18
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (23 bp):
TAAAAATATAATATAAAATAAAT
Found at i:88399912 original size:5 final size:5
Alignment explanation
Indices: 88399902--88399949 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
88399892 AATTAATTAG
*
88399902 TAAAA TAAAA T-AAA TAATA TAACAA TTAATAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAA-AA -TAA-AA TAAAA TAAAA TAAAA
88399949 T
1 T
88399950 TGGGGTGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 4 0.11
5 24 0.65
6 4 0.11
7 5 0.14
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (5 bp):
TAAAA
Found at i:88407075 original size:34 final size:34
Alignment explanation
Indices: 88407032--88407099 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
88407022 GTATTGAATG
88407032 GGGTATTGTTAAAGAAATAGTAGTTTAAAATTTT
1 GGGTATTGTTAAAGAAATAGTAGTTTAAAATTTT
88407066 GGGTATTGTTAAAGAAATAGTAGTTTAAAATTTT
1 GGGTATTGTTAAAGAAATAGTAGTTTAAAATTTT
88407100 TCTTTCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (34 bp):
GGGTATTGTTAAAGAAATAGTAGTTTAAAATTTT
Found at i:88411241 original size:33 final size:32
Alignment explanation
Indices: 88411189--88411254 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
88411179 AACAATCAAA
* *
88411189 TGTAGTTTGGGCCTAAGCCCATTTTAGTCTCAG
1 TGTAGTTCGGGCCTAAGCCCATTTCAGT-TCAG
* *
88411222 TGTAGTTCGGGCTTTAGCCCATTTCAGTTCAG
1 TGTAGTTCGGGCCTAAGCCCATTTCAGTTCAG
88411254 T
1 T
88411255 ATCAAATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (32 bp):
TGTAGTTCGGGCCTAAGCCCATTTCAGTTCAG
Found at i:88425077 original size:25 final size:25
Alignment explanation
Indices: 88425049--88425100 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
88425039 TTTGGCTTGA
*
88425049 CATTTACTAAGCAATATCAGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
88425074 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
88425099 CA
1 CA
88425101 AATTATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:88438606 original size:22 final size:24
Alignment explanation
Indices: 88438567--88438610 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
88438557 GTAGTTCAAA
*
88438567 ATTTTTCTATCAATTTATTAAAAG
1 ATTTTCCTATCAATTTATTAAAAG
88438591 ATTTTCCTA-CAA-TTATTAAA
1 ATTTTCCTATCAATTTATTAAA
88438611 TCTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTTTCCTATCAATTTATTAAAAG
Found at i:88440386 original size:12 final size:12
Alignment explanation
Indices: 88440366--88440398 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
88440356 CGTGTTAGGG
*
88440366 CACATGGCCTAC
1 CACACGGCCTAC
88440378 CACACGGCCTAC
1 CACACGGCCTAC
88440390 CACACGGCC
1 CACACGGCC
88440399 ATATGGCGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.48, G:0.18, T:0.09
Consensus pattern (12 bp):
CACACGGCCTAC
Found at i:88447754 original size:12 final size:12
Alignment explanation
Indices: 88447739--88447769 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
88447729 GACGCCACAC
*
88447739 GGCCGTGTTGTA
1 GGCCGTGTGGTA
88447751 GGCCGTGTGGTA
1 GGCCGTGTGGTA
88447763 GGCCGTG
1 GGCCGTG
88447770 CATAAAGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.19, G:0.48, T:0.26
Consensus pattern (12 bp):
GGCCGTGTGGTA
Found at i:88452685 original size:31 final size:31
Alignment explanation
Indices: 88452650--88452711 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
88452640 TCAACTTTGC
88452650 CACATAGATGGCCGGCCAAGGGGTGGCTCTT
1 CACATAGATGGCCGGCCAAGGGGTGGCTCTT
*
88452681 CACATAGATGGCTGGCCAAGGGGTGGCTCTT
1 CACATAGATGGCCGGCCAAGGGGTGGCTCTT
88452712 TGGCTACTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.21
Consensus pattern (31 bp):
CACATAGATGGCCGGCCAAGGGGTGGCTCTT
Found at i:88468215 original size:16 final size:16
Alignment explanation
Indices: 88468194--88468230 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
88468184 TTGGTTCGCT
*
88468194 GTAATGGAATAGAGGC
1 GTAATGGAACAGAGGC
88468210 GTAATGGAACAGAGGC
1 GTAATGGAACAGAGGC
88468226 GTAAT
1 GTAAT
88468231 AGGTAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.35, T:0.19
Consensus pattern (16 bp):
GTAATGGAACAGAGGC
Done.