Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 17 of 125
Found at i:5428554 original size:17 final size:17
Alignment explanation
Indices: 5428532--5428570 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5428522 AAAAAATTAT
5428532 TAAAAATTAGAAAAAAA
1 TAAAAATTAGAAAAAAA
** *
5428549 TAAAAATTTTAAAAATA
1 TAAAAATTAGAAAAAAA
5428566 TAAAA
1 TAAAA
5428571 TTTTATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
TAAAAATTAGAAAAAAA
Found at i:5428562 original size:16 final size:17
Alignment explanation
Indices: 5428543--5428582 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
5428533 AAAAATTAGA
5428543 AAAAAATA-AAAATTTT
1 AAAAAATATAAAATTTT
5428559 -AAAAATATAAAATTTT
1 AAAAAATATAAAATTTT
5428575 ATAAAAAT
1 A-AAAAAT
5428583 CGTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
18 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAAATATAAAATTTT
Found at i:5428598 original size:10 final size:10
Alignment explanation
Indices: 5428520--5428599 Score: 55
Period size: 10 Copynumber: 8.6 Consensus size: 10
5428510 TTAAATTTTA
5428520 ATAAAAAATT
1 ATAAAAAATT
*
5428530 ATTAAAAATT
1 ATAAAAAATT
*
5428540 AGAAAAAA--
1 ATAAAAAATT
5428548 AT-AAAAATT
1 ATAAAAAATT
*
5428557 -TTAAAAA-T
1 ATAAAAAATT
**
5428565 ATAAAATTTT
1 ATAAAAAATT
*
5428575 AT-AAAAATC
1 ATAAAAAATT
*
5428584 GTAAAAAATT
1 ATAAAAAATT
5428594 ATAAAA
1 ATAAAA
5428600 TATATAGAAA
Statistics
Matches: 51, Mismatches: 13, Indels: 12
0.67 0.17 0.16
Matches are distributed among these distances:
7 5 0.10
8 3 0.06
9 14 0.27
10 29 0.57
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:5428599 original size:9 final size:9
Alignment explanation
Indices: 5428523--5428700 Score: 75
Period size: 9 Copynumber: 19.1 Consensus size: 9
5428513 AATTTTAATA
5428523 AAAAATTATT
1 AAAAATTA-T
*
5428533 AAAAATTAG
1 AAAAATTAT
*
5428542 AAAAA-AAT
1 AAAAATTAT
*
5428550 AAAAATTTT
1 AAAAATTAT
5428559 AAAAA-TAT
1 AAAAATTAT
*
5428567 AAAATTTTAT
1 AAAA-ATTAT
5428577 AAAAATCGTA-
1 AAAAAT--TAT
5428587 AAAAATTAT
1 AAAAATTAT
5428596 -AAAATATAT
1 AAAAAT-TAT
*
5428605 AGAAA-TAT
1 AAAAATTAT
*
5428613 AAAATTTTAT
1 AAAA-ATTAT
*
5428623 AAAAGTT-T
1 AAAAATTAT
*
5428631 ATAAAGTCGTA-
1 A-AAAAT--TAT
5428642 AGAAAATTAT
1 A-AAAATTAT
5428652 ACAAAA-TAT
1 A-AAAATTAT
*
5428661 AAATAAATAT
1 AAA-AATTAT
* *
5428671 AAAATTCGTAA
1 AAAAAT--TAT
5428682 AAAAATTAT
1 AAAAATTAT
5428691 AAAAATTAT
1 AAAAATTAT
5428700 A
1 A
5428701 GTACCAAAAG
Statistics
Matches: 129, Mismatches: 20, Indels: 39
0.69 0.11 0.21
Matches are distributed among these distances:
8 29 0.22
9 43 0.33
10 42 0.33
11 15 0.12
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:5428648 original size:56 final size:57
Alignment explanation
Indices: 5428564--5428676 Score: 158
Period size: 58 Copynumber: 2.0 Consensus size: 57
5428554 ATTTTAAAAA
* *
5428564 TATAAAATTTTATAAAAATCGTAAAAAATTAT-AAAATATATAGAAATATAAAATTT
1 TATAAAAGTTTATAAAAATCGTAAAAAATTATAAAAATATAAAGAAATATAAAATTT
* *
5428620 TATAAAAGTTTAT-AAAGTCGTAAGAAAATTATACAAAATATAAATAAATATAAAATT
1 TATAAAAGTTTATAAAAATCGTAA-AAAATTATA-AAAATATAAAGAAATATAAAATT
5428677 CGTAAAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
55 9 0.18
56 20 0.40
58 21 0.42
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (57 bp):
TATAAAAGTTTATAAAAATCGTAAAAAATTATAAAAATATAAAGAAATATAAAATTT
Found at i:5428691 original size:58 final size:55
Alignment explanation
Indices: 5428564--5428694 Score: 138
Period size: 58 Copynumber: 2.3 Consensus size: 55
5428554 ATTTTAAAAA
** * *
5428564 TATAAAATTTTATAAAAATCGTAAAAAATTATAAAATATATAGAAATATAAAATTT
1 TATAAAAAATTAT-AAAATCGTAAAAAATTATAAAATATAAAGAAATATAAAATTG
** * *
5428620 TATAAAAGTTTATAAAGTCGTAAGAAAATTATACAAAATATAAATAAATATAAAATTCG
1 TATAAAAAATTATAAAATCGTAA-AAAATTAT--AAAATATAAAGAAATATAAAATT-G
5428679 TA-AAAAAATTATAAAA
1 TATAAAAAATTATAAAA
5428695 ATTATAGTAC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
55 9 0.14
56 20 0.32
58 32 0.51
59 2 0.03
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (55 bp):
TATAAAAAATTATAAAATCGTAAAAAATTATAAAATATAAAGAAATATAAAATTG
Found at i:5428883 original size:19 final size:19
Alignment explanation
Indices: 5428861--5428918 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
5428851 TTTTCAATGC
*
5428861 ATTTTATGATTTTTATAAA
1 ATTTTACGATTTTTATAAA
* * * *
5428880 ATTTTACAATTTTTTTTAT
1 ATTTTACGATTTTTATAAA
*
5428899 TTTTTACGATTTTTATAAA
1 ATTTTACGATTTTTATAAA
5428918 A
1 A
5428919 AAGTTTGAAT
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
ATTTTACGATTTTTATAAA
Found at i:5429220 original size:88 final size:88
Alignment explanation
Indices: 5429053--5429243 Score: 208
Period size: 88 Copynumber: 2.2 Consensus size: 88
5429043 TTTTTTAAAT
* * *
5429053 TTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTATCCAATCAAGTGAGGAAAAAAATAGGG
1 TTTGAGGG-CTTTTTGATGCATTTTGAAAGTTCAAGTATCAAATCAAGTGAGAAAAAAAAGAGGG
** *
5429118 ACTTTATTG-CTTTTTTGAAGAAC
65 ACTCAATTGTCTTTTTTGAAAAAC
* * *
5429141 TTTGAGGGCCTTTTTTATGCATTTTGAAAGTTGAAGTACTCAAAT-GAGTGCA-AAAAAAAAGAG
1 TTTGAGGG-CTTTTTGATGCATTTTGAAAGTTCAAGTA-TCAAATCAAGTG-AGAAAAAAAAGAG
* * *
5429204 GGGCTCAATTGTTTTTTTTGAAAAAG
63 GGACTCAATTGTCTTTTTTGAAAAAC
*
5429230 TGTGAGGGCTTTTT
1 TTTGAGGGCTTTTT
5429244 ACACCCTTAA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
88 62 0.72
89 24 0.28
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (88 bp):
TTTGAGGGCTTTTTGATGCATTTTGAAAGTTCAAGTATCAAATCAAGTGAGAAAAAAAAGAGGGA
CTCAATTGTCTTTTTTGAAAAAC
Found at i:5433152 original size:3 final size:3
Alignment explanation
Indices: 5433144--5433171 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5433134 AAAGCTTGAT
5433144 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
5433172 AGGGGATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:5441466 original size:56 final size:56
Alignment explanation
Indices: 5441406--5441518 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
5441396 CAAAAACAAA
5441406 ATCATATTTTACAAAAGCTAAAAGCATAAATAAATTATTAATAAACACATTAATTC
1 ATCATATTTTACAAAAGCTAAAAGCATAAATAAATTATTAATAAACACATTAATTC
5441462 ATCATATTTTACAAAAGCTAAAAGCATAAATAAATTATTAATAAACACATTAATTC
1 ATCATATTTTACAAAAGCTAAAAGCATAAATAAATTATTAATAAACACATTAATTC
5441518 A
1 A
5441519 AACTAGTATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (56 bp):
ATCATATTTTACAAAAGCTAAAAGCATAAATAAATTATTAATAAACACATTAATTC
Found at i:5454639 original size:23 final size:23
Alignment explanation
Indices: 5454613--5454685 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
5454603 ATGAATAGAG
*
5454613 AAGATTCTTTGCT-ATGAACAATA
1 AAGATTCTCTG-TAATGAACAATA
5454636 AAGATTCTCTGTAATGAACAATA
1 AAGATTCTCTGTAATGAACAATA
* * *
5454659 AATA-T-T-TGAAATGAACAGTA
1 AAGATTCTCTGTAATGAACAATA
5454679 AAGATTC
1 AAGATTC
5454686 CTTGCAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 15 0.36
21 2 0.05
22 2 0.05
23 23 0.55
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (23 bp):
AAGATTCTCTGTAATGAACAATA
Found at i:5454727 original size:22 final size:22
Alignment explanation
Indices: 5454691--5454732 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5454681 GATTCCTTGC
5454691 AATTAATAGTGAAGATTCTCAA
1 AATTAATAGTGAAGATTCTCAA
5454713 AATTCAATAGT-AAGATTCTC
1 AATT-AATAGTGAAGATTCTC
5454733 CATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
AATTAATAGTGAAGATTCTCAA
Found at i:5460958 original size:11 final size:11
Alignment explanation
Indices: 5460947--5460995 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
5460937 TTTGTTGTTG
*
5460947 TTTTACTATTG
1 TTTTACTATTA
* *
5460958 TTTCACTATCA
1 TTTTACTATTA
*
5460969 TTTCACTATTA
1 TTTTACTATTA
*
5460980 TATTACTATTA
1 TTTTACTATTA
5460991 TTTTA
1 TTTTA
5460996 TTGTTATTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.27, C:0.14, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTACTATTA
Found at i:5463352 original size:9 final size:8
Alignment explanation
Indices: 5463320--5463349 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5463310 CAGCATTTAA
*
5463320 TTAATATT
1 TTAAAATT
5463328 TTAAAATT
1 TTAAAATT
5463336 TTAAAATT
1 TTAAAATT
5463344 TTAAAA
1 TTAAAA
5463350 ATTCAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTAAAATT
Found at i:5464409 original size:27 final size:27
Alignment explanation
Indices: 5464378--5464429 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5464368 AGGAGCCTTT
5464378 AAATCAAATTGAATAGAATCAAATCGA
1 AAATCAAATTGAATAGAATCAAATCGA
* * *
5464405 AAATCAATTTGATTGGAATCAAATC
1 AAATCAAATTGAATAGAATCAAATC
5464430 AAATTGAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.27
Consensus pattern (27 bp):
AAATCAAATTGAATAGAATCAAATCGA
Found at i:5466700 original size:17 final size:17
Alignment explanation
Indices: 5466678--5466715 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
5466668 TTTAGAATTT
5466678 TTTTTTAAAAATATAAA
1 TTTTTTAAAAATATAAA
5466695 TTTTTTAAAAATATAAA
1 TTTTTTAAAAATATAAA
5466712 TTTT
1 TTTT
5466716 AAAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTTAAAAATATAAA
Found at i:5466742 original size:19 final size:19
Alignment explanation
Indices: 5466721--5466757 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5466711 ATTTTAAAAT
*
5466721 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
5466739 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
5466758 CTTATTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:5472820 original size:29 final size:30
Alignment explanation
Indices: 5472767--5472827 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
5472757 ACATATGATA
*
5472767 TTTAGTCTTTATGTTTTAATTTGACA-TAG
1 TTTAGTCTTTATGTTTTAATATGACATTAG
5472796 TTTAGTCTTTTAT-TTTTACA-ATGACATTAG
1 TTTAGTC-TTTATGTTTTA-ATATGACATTAG
5472826 TT
1 TT
5472828 ACTCCAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (30 bp):
TTTAGTCTTTATGTTTTAATATGACATTAG
Found at i:5473437 original size:19 final size:18
Alignment explanation
Indices: 5473400--5473439 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
5473390 CTTTAATAAG
5473400 TATATTTCTTATATATAT
1 TATATTTCTTATATATAT
* *
5473418 TATATTTGTGTATCTATAT
1 TATATTTCT-TATATATAT
5473437 TAT
1 TAT
5473440 TTACTATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (18 bp):
TATATTTCTTATATATAT
Found at i:5473965 original size:30 final size:31
Alignment explanation
Indices: 5473920--5473977 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
5473910 TGAAAGGAGT
* *
5473920 TCAAAATATTATTTTTTAATTTTTAAGGGAC
1 TCAAAATAATATTTTTTAATTTTAAAGGGAC
*
5473951 TCAAAA-AATATTTTTTAGTTTTAAAGG
1 TCAAAATAATATTTTTTAATTTTAAAGG
5473978 ATCCAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (31 bp):
TCAAAATAATATTTTTTAATTTTAAAGGGAC
Found at i:5479800 original size:72 final size:72
Alignment explanation
Indices: 5479703--5480023 Score: 498
Period size: 72 Copynumber: 4.5 Consensus size: 72
5479693 TTTTATATTC
*
5479703 AAAATCAAATATAAACAACTATTGATAAAACTAAAATACACATAAATAAGTAGAACATAAATTCA
1 AAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACATAAATTCA
5479768 ATATCCA
66 ATATCCA
* * * * * *
5479775 AAAACCAAACATAAATAACTATTGATAAAACTAGATTGCACATAAATAAGTAGAACAAAAATTCA
1 AAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACATAAATTCA
*
5479840 ATATTCA
66 ATATCCA
* * * *
5479847 AGAATCAAATATAAGCAACTATTGATAAAATTAGATTACACATAAATAAGTAGAACATAAATTCA
1 AAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACATAAATTCA
5479912 ATATCCA
66 ATATCCA
* * *
5479919 AGAACCAAATATAAGCAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACATAAATTCA
1 AAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACATAAATTCA
5479984 ATATCCA
66 ATATCCA
*
5479991 AAAATCAAACATAAACAACTATTGATAAAACTA
1 AAAATCAAATATAAACAACTATTGATAAAACTA
5480024 GTTTAGACCC
Statistics
Matches: 225, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 225 1.00
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.24
Consensus pattern (72 bp):
AAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACATAAATTCA
ATATCCA
Found at i:5480419 original size:18 final size:18
Alignment explanation
Indices: 5480390--5480459 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
5480380 CGTTTCCATC
5480390 AATGTTAACATCATTTAA
1 AATGTTAACATCATTTAA
*
5480408 AAT-TTGAACATCATTTGA
1 AATGTT-AACATCATTTAA
*
5480426 AGTGTTAACATCATTTAA
1 AATGTTAACATCATTTAA
5480444 AATGTTAACATCATTT
1 AATGTTAACATCATTT
5480460 CCTGCATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.04
18 42 0.91
19 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (18 bp):
AATGTTAACATCATTTAA
Found at i:5483683 original size:40 final size:38
Alignment explanation
Indices: 5483615--5483749 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
5483605 ACCAGAATGG
* *
5483615 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
5483655 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
5483692 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
5483733 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
5483750 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:5483747 original size:41 final size:38
Alignment explanation
Indices: 5483647--5483750 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
5483637 TTCGAAGCAA
* *
5483647 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
5483684 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
5483722 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
5483751 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:5484582 original size:25 final size:24
Alignment explanation
Indices: 5484543--5484594 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
5484533 TAGCTCTCTG
*
5484543 TTCTTTCTTCTTTTATTTCTTTTGT
1 TTCTTTCTTCTTTTA-TTCTTTTAT
5484568 TTCTTTCTT-TCTTTATTCTTTTAT
1 TTCTTTCTTCT-TTTATTCTTTTAT
5484592 TTC
1 TTC
5484595 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (24 bp):
TTCTTTCTTCTTTTATTCTTTTAT
Found at i:5489808 original size:40 final size:38
Alignment explanation
Indices: 5489740--5489874 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
5489730 ACCAGAATGG
* *
5489740 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
5489780 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
5489817 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
5489858 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
5489875 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:5489872 original size:41 final size:38
Alignment explanation
Indices: 5489772--5489875 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
5489762 TTCGAAGCAA
* *
5489772 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
5489809 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
5489847 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
5489876 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:5490751 original size:3 final size:3
Alignment explanation
Indices: 5490743--5490781 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
5490733 TATATATAGT
*
5490743 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAC TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5490782 TAAATAGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5490824 original size:8 final size:9
Alignment explanation
Indices: 5490742--5490825 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 9
5490732 ATATATATAG
5490742 TTAATAATA
1 TTAATAATA
*
5490751 ATAATAATA
1 TTAATAATA
*
5490760 ATAATAATA
1 TTAATAATA
*
5490769 AT-ATAATA
1 TTAATAATA
*
5490777 CTAATTAAATA
1 TTAA-T-AATA
* *
5490788 GTAATTTATA
1 TTAA-TAATA
*
5490798 TT-ATTATA
1 TTAATAATA
5490806 TT-ATAATA
1 TTAATAATA
5490814 TTAATAA-A
1 TTAATAATA
5490822 TTAA
1 TTAA
5490826 AAACAATCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
8 26 0.40
9 25 0.38
10 5 0.08
11 9 0.14
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (9 bp):
TTAATAATA
Found at i:5492740 original size:20 final size:21
Alignment explanation
Indices: 5492715--5492755 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5492705 TTTAATCTAA
* *
5492715 TATTTTTAA-TAAAATTAATT
1 TATTTTAAATTAAAATAAATT
5492735 TATTTTAAATTAAAATAAATT
1 TATTTTAAATTAAAATAAATT
5492756 AATATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTTTAAATTAAAATAAATT
Found at i:5498489 original size:51 final size:50
Alignment explanation
Indices: 5498407--5498511 Score: 174
Period size: 51 Copynumber: 2.1 Consensus size: 50
5498397 GTAGCTATAA
* *
5498407 ATCATTTGTTTATATTAAGTGTCCATGTGTTGTATGTATCAAGATAGGGT
1 ATCATTTGTTCATATTAAGTGTCCATGTGTTGCATGTATCAAGATAGGGT
*
5498457 ATCATTTGTTCATATTTAAGTGTCCATTTGTTGCATGTATCAAGATAGGGT
1 ATCATTTGTTCATA-TTAAGTGTCCATGTGTTGCATGTATCAAGATAGGGT
5498508 ATCA
1 ATCA
5498512 AAACCAGCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 13 0.25
51 38 0.75
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (50 bp):
ATCATTTGTTCATATTAAGTGTCCATGTGTTGCATGTATCAAGATAGGGT
Found at i:5501656 original size:32 final size:31
Alignment explanation
Indices: 5501603--5501666 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 31
5501593 AACAATATGT
5501603 AAAAATTAAATCAAATCAAAA-TTATATATA
1 AAAAATTAAATCAAATCAAAATTTATATATA
5501633 AAAAATTATATATCAAA-CTAAAATTTATATATA
1 AAAAATTA-A-ATCAAATC-AAAATTTATATATA
5501666 A
1 A
5501667 TTTTAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 8 0.27
31 2 0.07
32 10 0.33
33 10 0.33
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAAATTAAATCAAATCAAAATTTATATATA
Found at i:5502482 original size:18 final size:18
Alignment explanation
Indices: 5502459--5502498 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
5502449 TATTCAATTT
5502459 TATTATTATTCTAATAAA
1 TATTATTATTCTAATAAA
5502477 TATTATTATTCTAATAAA
1 TATTATTATTCTAATAAA
5502495 TATT
1 TATT
5502499 GGAATTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTATTATTCTAATAAA
Found at i:5502643 original size:21 final size:21
Alignment explanation
Indices: 5502619--5502660 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5502609 AGTAAATTAC
5502619 TAAA-AAAATTAATACATAAAA
1 TAAATAAAA-TAATACATAAAA
* *
5502640 TAAATACAATAATAGATAAAA
1 TAAATAAAATAATACATAAAA
5502661 CGAGATGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAATAAAATAATACATAAAA
Found at i:5506141 original size:15 final size:15
Alignment explanation
Indices: 5506121--5506151 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5506111 GACGGTTCCG
5506121 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
5506136 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
5506151 T
1 T
5506152 ACTGATACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
TGTGCTCTGATTCAT
Found at i:5509390 original size:9 final size:9
Alignment explanation
Indices: 5509373--5509410 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
5509363 TGAATTTCAC
5509373 AATTCGAAT
1 AATTCGAAT
*
5509382 AATTTGAAT
1 AATTCGAAT
*
5509391 AACTCGAAT
1 AATTCGAAT
5509400 AATTCGAAT
1 AATTCGAAT
5509409 AA
1 AA
5509411 CATATTGGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5513535 original size:21 final size:22
Alignment explanation
Indices: 5513509--5513550 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5513499 ACTGTCTCTG
5513509 TAAATT-TAAAAATAAGTAAAA
1 TAAATTATAAAAATAAGTAAAA
**
5513530 TAAATTATAAATTTAAGTAAA
1 TAAATTATAAAAATAAGTAAA
5513551 CAAGATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
TAAATTATAAAAATAAGTAAAA
Found at i:5516803 original size:28 final size:28
Alignment explanation
Indices: 5516748--5516803 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
5516738 TTTTAAAAAA
**
5516748 TATTAAACTTTATAATTTTTTTATTTTT
1 TATTAAACTTTATAATTTTCATATTTTT
*
5516776 TATTAAATTTTAATAATTTTCATATTTT
1 TATTAAACTTT-ATAATTTTCATATTTT
5516804 ATAATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (28 bp):
TATTAAACTTTATAATTTTCATATTTTT
Found at i:5516914 original size:22 final size:24
Alignment explanation
Indices: 5516864--5516908 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
5516854 ATATTATTTT
*
5516864 ATTTTTATTTTTTGTAATTTTATC
1 ATTTTTATTTTTTCTAATTTTATC
5516888 ATTTTTA-TTTTTCT-ATTTTAT
1 ATTTTTATTTTTTCTAATTTTAT
5516909 AGTTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 7 0.35
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (24 bp):
ATTTTTATTTTTTCTAATTTTATC
Found at i:5517874 original size:16 final size:16
Alignment explanation
Indices: 5517853--5517892 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
5517843 ACTTTTGCAG
5517853 AAGACTTTCTTGATTC
1 AAGACTTTCTTGATTC
5517869 AAGACTTTCTTGATTC
1 AAGACTTTCTTGATTC
5517885 AAGACTTT
1 AAGACTTT
5517893 GAGCCTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (16 bp):
AAGACTTTCTTGATTC
Found at i:5519240 original size:26 final size:27
Alignment explanation
Indices: 5519199--5519250 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
5519189 CGACACCTAA
5519199 CCCCTGCTGCCTCTGCCG-TGCCATGC
1 CCCCTGCTGCCTCTGCCGTTGCCATGC
*
5519225 CCCCTGCTG-CTGCTGCTGTTGCCATG
1 CCCCTGCTGCCT-CTGCCGTTGCCATG
5519251 TGTTGTCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.09
26 14 0.61
27 7 0.30
ACGTcount: A:0.04, C:0.44, G:0.25, T:0.27
Consensus pattern (27 bp):
CCCCTGCTGCCTCTGCCGTTGCCATGC
Found at i:5520277 original size:15 final size:16
Alignment explanation
Indices: 5520252--5520286 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
5520242 TATTTAATTC
5520252 ATTTGATATATTAAAT
1 ATTTGATATATTAAAT
5520268 ATTT-ATATATTAAAT
1 ATTTGATATATTAAAT
5520283 ATTT
1 ATTT
5520287 TTTAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTTGATATATTAAAT
Found at i:5521563 original size:17 final size:18
Alignment explanation
Indices: 5521541--5521581 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
5521531 ATATACTATA
*
5521541 TGGAGGATACATTGA-GG
1 TGGAGGATACATCGACGG
5521558 TGGAGGATACATCGACGG
1 TGGAGGATACATCGACGG
5521576 TGGAGG
1 TGGAGG
5521582 TGGGTGATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.27, C:0.10, G:0.44, T:0.20
Consensus pattern (18 bp):
TGGAGGATACATCGACGG
Found at i:5525244 original size:6 final size:6
Alignment explanation
Indices: 5525233--5525279 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
5525223 TAGAATTAAA
*
5525233 TATGTT TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
5525280 ATGCAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 1 0.03
6 35 0.95
7 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:5525400 original size:26 final size:26
Alignment explanation
Indices: 5525353--5525409 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5525343 GCTAAACCTC
* *
5525353 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATCCAAACATAAAAATA
** *
5525379 ATTAAATAAATCCAAATTTAAATATA
1 ATTAAATAAATCCAAACATAAAAATA
5525405 ATTAA
1 ATTAA
5525410 TTCCAAATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (26 bp):
ATTAAATAAATCCAAACATAAAAATA
Found at i:5529552 original size:27 final size:27
Alignment explanation
Indices: 5529522--5529588 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
5529512 AAAATATATA
5529522 TTTATATTATTTAAGT-TATTAATTTTT
1 TTTATATTATTTAAGTGTA-TAATTTTT
**
5529549 TTTAT-TATATTTTGGTGTATAATTTTT
1 TTTATAT-TATTTAAGTGTATAATTTTT
*
5529576 TTTGTATTATTTA
1 TTTATATTATTTA
5529589 GGTAATAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 1 0.03
27 29 0.88
28 3 0.09
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.67
Consensus pattern (27 bp):
TTTATATTATTTAAGTGTATAATTTTT
Found at i:5530484 original size:21 final size:23
Alignment explanation
Indices: 5530458--5530504 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
5530448 TTTTTACATG
*
5530458 TTTGTTTCT-TTTTTACTTTT-T
1 TTTGTTTATCTTTTTACTTTTAT
*
5530479 TTTGTTTATCTTTTTAGTTTTAT
1 TTTGTTTATCTTTTTACTTTTAT
5530502 TTT
1 TTT
5530505 ATTTTTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 10 0.45
23 4 0.18
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.79
Consensus pattern (23 bp):
TTTGTTTATCTTTTTACTTTTAT
Found at i:5532036 original size:23 final size:25
Alignment explanation
Indices: 5532017--5532065 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
5532007 AATTTAATTT
5532017 TTATAGAT-TTTA-ATAATTAATAA
1 TTATAGATATTTATATAATTAATAA
5532040 TTATAGATATTTATTATAATT-ATAA
1 TTATAGATATTTA-TATAATTAATAA
5532065 T
1 T
5532066 ATTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.35
24 4 0.17
25 5 0.22
26 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
TTATAGATATTTATATAATTAATAA
Found at i:5533940 original size:15 final size:15
Alignment explanation
Indices: 5533922--5533968 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
5533912 AAAATTTAAT
5533922 AAATAAAAATATATA
1 AAATAAAAATATATA
*
5533937 AAATTATTAAATAT-TA
1 AAA-TA-AAAATATATA
5533953 AAATAAAAA-ATATA
1 AAATAAAAATATATA
5533967 AA
1 AA
5533969 TATTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
13 2 0.07
14 7 0.26
15 5 0.19
16 7 0.26
17 6 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAAAAATATATA
Found at i:5533962 original size:23 final size:22
Alignment explanation
Indices: 5533910--5533981 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 22
5533900 GATTATATAA
5533910 AAAAAATTTAATAAATA--AAAAT
1 AAAAAA-TT-ATAAATATTAAAAT
5533932 ATATAAAATTATTAAATATTAAAAT
1 A-A-AAAATTA-TAAATATTAAAAT
*
5533957 AAAAAA-TATAAATATTTAAA-
1 AAAAAATTATAAATATTAAAAT
5533977 AAAAA
1 AAAAA
5533982 CTTAAAAAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
20 5 0.11
21 11 0.25
22 4 0.09
23 13 0.30
24 5 0.11
25 6 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAAATTATAAATATTAAAAT
Found at i:5535231 original size:15 final size:14
Alignment explanation
Indices: 5535211--5535242 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
5535201 AAAGAATATT
5535211 TTTAATATTTAAATA
1 TTTAATATTT-AATA
5535226 TTTAATATTTAATA
1 TTTAATATTTAATA
5535240 TTT
1 TTT
5535243 TTATTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATATTTAATA
Found at i:5535232 original size:7 final size:7
Alignment explanation
Indices: 5535211--5535242 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
5535201 AAAGAATATT
5535211 TTTAATA
1 TTTAATA
5535218 TTTAAATA
1 TTT-AATA
5535226 TTTAATA
1 TTTAATA
5535233 TTTAATA
1 TTTAATA
5535240 TTT
1 TTT
5535243 TTATTTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAATA
Found at i:5537112 original size:19 final size:20
Alignment explanation
Indices: 5537072--5537112 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
5537062 TTATATCTAT
*
5537072 AAATAATTTAAAAATTATAA
1 AAATAATTTAAAAATTAAAA
5537092 AAAT-ATTT-AAAATTAAAA
1 AAATAATTTAAAAATTAAAA
5537110 AAA
1 AAA
5537113 CCATAACTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 4 0.20
20 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATTTAAAAATTAAAA
Found at i:5545960 original size:17 final size:17
Alignment explanation
Indices: 5545938--5546041 Score: 145
Period size: 17 Copynumber: 6.1 Consensus size: 17
5545928 TAATTTCAAA
*
5545938 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
5545955 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
5545972 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
5545989 ATTTTTGAGTTTAAATTT
1 A-TTTTAAATTTAAATTT
5546007 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
5546024 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
5546041 A
1 A
5546042 AAATTTAATT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
17 62 0.82
18 14 0.18
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:5545966 original size:6 final size:6
Alignment explanation
Indices: 5545940--5546049 Score: 75
Period size: 6 Copynumber: 18.8 Consensus size: 6
5545930 ATTTCAAAAT
* * * *
5545940 TTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * * * * *
5545986 CTTATT TTTGAG TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
5546032 TTTAAA TTTAAAA TTTAA
1 TTTAAA TTT-AAA TTTAA
5546050 TTAAAAAATC
Statistics
Matches: 79, Mismatches: 20, Indels: 10
0.72 0.18 0.09
Matches are distributed among these distances:
5 16 0.20
6 57 0.72
7 6 0.08
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:5546007 original size:35 final size:34
Alignment explanation
Indices: 5545938--5546041 Score: 163
Period size: 34 Copynumber: 3.0 Consensus size: 34
5545928 TAATTTCAAA
* *
5545938 ATTTTAAATTTTAATTTATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTTATTTTGAGTTTAAATTT
*
5545972 ATTTTAAATTTAAACTTATTTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTTA-TTTTGAGTTTAAATTT
*
5546007 ATTTTAAATTTAAATTTATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTTATTTTGAGTTTAAATTT
5546041 A
1 A
5546042 AAATTTAATT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
34 32 0.50
35 32 0.50
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.59
Consensus pattern (34 bp):
ATTTTAAATTTAAATTTATTTTGAGTTTAAATTT
Found at i:5547830 original size:29 final size:29
Alignment explanation
Indices: 5547790--5548098 Score: 180
Period size: 29 Copynumber: 10.8 Consensus size: 29
5547780 CTCTACATTT
*
5547790 TTCT-AAAAATCACATTTTGACCCTAAAC
1 TTCTCAAAAATTACATTTTGACCCTAAAC
* * * *
5547818 TTCTCAAAAATCACATTTTAACCCCAATC
1 TTCTCAAAAATTACATTTTGACCCTAAAC
*
5547847 TTCTCAAAAATTACATTTTG-CCCTTGAAC
1 TTCTCAAAAATTACATTTTGACCC-TAAAC
*
5547876 TTCT-AAAAATTACATTTTTACCCCTAAAC
1 TTCTCAAAAATTACATTTTGA-CCCTAAAC
* ** **
5547905 TTC-CCAAAATTA-AGTTTTTCCCCGGAAC
1 TTCTCAAAAATTACA-TTTTGACCCTAAAC
* * **
5547933 TT-TCAAAAATCACATTTTTGTCCCCGAAC
1 TTCTCAAAAATTACA-TTTTGACCCTAAAC
*
5547962 TTC-C-AAAATTACATTTTTG-CCCTCGAAC
1 TTCTCAAAAATTACA-TTTTGACCCT-AAAC
*
5547990 TT-TCAAAAATCACATTTT-ACCCTAAA-
1 TTCTCAAAAATTACATTTTGACCCTAAAC
* * * *
5548016 TTTTCCTAAAATGACATTTTTACCCCTAAAAC
1 TTCT-CAAAAATTACATTTTGA-CCCT-AAAC
* * *
5548048 TT-TCTAAAATTATATTTTAACCCTAAAC
1 TTCTCAAAAATTACATTTTGACCCTAAAC
*
5548076 TATC-CAAAACTT-CATTTTTGACC
1 T-TCTCAAAAATTACA-TTTTGACC
5548099 TCATTTTTTT
Statistics
Matches: 226, Mismatches: 33, Indels: 43
0.75 0.11 0.14
Matches are distributed among these distances:
26 2 0.01
27 6 0.03
28 85 0.38
29 106 0.47
30 21 0.09
31 4 0.02
32 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
TTCTCAAAAATTACATTTTGACCCTAAAC
Found at i:5548036 original size:57 final size:56
Alignment explanation
Indices: 5547815--5548100 Score: 235
Period size: 57 Copynumber: 5.0 Consensus size: 56
5547805 TTTGACCCTA
* * *
5547815 AACTTCTCAAAAATCACATTTTAACCCCAATCTTCTCAAAAATTACA-TTTTGCCCTTG
1 AACTT-TCAAAAATCACATTTTAACCCTAAACTTC-C-AAAATTACATTTTTGCCCTCG
* *
5547873 AAC-TTCTAAAAATTACATTTTTACCCCTAAACTTCCCAAAATTA-AGTTTTT-CCC-CGG
1 AACTTTC-AAAAATCACA-TTTTAACCCTAAACTT-CCAAAATTACA-TTTTTGCCCTC-G
** **
5547930 AACTTTCAAAAATCACATTTTTGTCCCCGAACTTCCAAAATTACATTTTTGCCCTCG
1 AACTTTCAAAAATCACA-TTTTAACCCTAAACTTCCAAAATTACATTTTTGCCCTCG
* * * **
5547987 AACTTTCAAAAATCACATTTT-ACCCTAAATTTTCCTAAAATGACATTTTTACCCCTAA
1 AACTTTCAAAAATCACATTTTAACCCTAAA-CTTCC-AAAATTACATTTTT-GCCCTCG
* * * *
5548045 AACTTTCTAAAATTATATTTTAACCCTAAACTATCCAAAACTT-CATTTTTGACCTC
1 AACTTTCAAAAATCACATTTTAACCCTAAACT-TCCAAAA-TTACATTTTTGCCCTC
5548101 ATTTTTTTTT
Statistics
Matches: 186, Mismatches: 26, Indels: 33
0.76 0.11 0.13
Matches are distributed among these distances:
55 5 0.03
56 25 0.13
57 84 0.45
58 59 0.32
59 13 0.07
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (56 bp):
AACTTTCAAAAATCACATTTTAACCCTAAACTTCCAAAATTACATTTTTGCCCTCG
Found at i:5548301 original size:19 final size:19
Alignment explanation
Indices: 5548255--5548301 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5548245 TTATTTAACT
*
5548255 TTATTATTAATTGCATAGC
1 TTATTTTTAATTGCATAGC
* *
5548274 TCATATTTAATTTGCAT-GC
1 TTATTTTTAA-TTGCATAGC
5548293 TTATTTTTA
1 TTATTTTTA
5548302 TCTCTATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.53
Consensus pattern (19 bp):
TTATTTTTAATTGCATAGC
Found at i:5553797 original size:16 final size:18
Alignment explanation
Indices: 5553766--5553803 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
5553756 ATAGATTTTA
5553766 AATTAAATAAATTTAATT
1 AATTAAATAAATTTAATT
5553784 AATTAAA-AAA-TTAATT
1 AATTAAATAAATTTAATT
5553800 AATT
1 AATT
5553804 GCACTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 3 0.15
18 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTAAATAAATTTAATT
Found at i:5562514 original size:2 final size:2
Alignment explanation
Indices: 5562501--5562531 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5562491 TTTCAAAATA
*
5562501 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5562532 AACCTTTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5564824 original size:14 final size:15
Alignment explanation
Indices: 5564800--5564832 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5564790 ATGCATGTTC
5564800 ATTTAATTGAATAGT
1 ATTTAATTGAATAGT
*
5564815 ATTT-ATTGAATGGT
1 ATTTAATTGAATAGT
5564829 ATTT
1 ATTT
5564833 GAAATAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (15 bp):
ATTTAATTGAATAGT
Found at i:5566868 original size:23 final size:23
Alignment explanation
Indices: 5566815--5566873 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
5566805 AACAAATTTA
*
5566815 AAAATTTCATAATTTAAAATATT
1 AAAATTTTATAATTTAAAATATT
* * *
5566838 -AAATTTTATATTTTAGAATCTT
1 AAAATTTTATAATTTAAAATATT
5566860 AAAATTTTATAATT
1 AAAATTTTATAATT
5566874 CAATTTTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (23 bp):
AAAATTTTATAATTTAAAATATT
Found at i:5569337 original size:20 final size:20
Alignment explanation
Indices: 5569314--5569381 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
5569304 GTATGATATT
5569314 AAGTTAATGTGTAATAAATA
1 AAGTTAATGTGTAATAAATA
*
5569334 AAGTCATAA-AT-TAATAATGATA
1 AAGT--TAATGTGTAATAA--ATA
5569356 TTAAGTTAATGTGTAATAAATA
1 --AAGTTAATGTGTAATAAATA
5569378 AAGT
1 AAGT
5569382 CATAAATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
20 14 0.37
21 1 0.03
22 12 0.32
23 1 0.03
24 10 0.26
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.35
Consensus pattern (20 bp):
AAGTTAATGTGTAATAAATA
Found at i:5569402 original size:12 final size:12
Alignment explanation
Indices: 5569383--5569490 Score: 68
Period size: 12 Copynumber: 9.0 Consensus size: 12
5569373 AAATAAAGTC
5569383 ATAA-ATTAATA
1 ATAATATTAATA
* *
5569394 ATGATATTAATG
1 ATAATATTAATA
5569406 ATAATATTAATA
1 ATAATATTAATA
5569418 ATAAATAATGGTAATAA
1 AT-AAT-AT--TAAT-A
*
5569435 ATAGA-CTTAAT-
1 ATA-ATATTAATA
5569446 A-AATATTAATA
1 ATAATATTAATA
*
5569457 A-AA-A-TATTA
1 ATAATATTAATA
5569466 ATAATATTAATA
1 ATAATATTAATA
5569478 ATTAATATTAATA
1 A-TAATATTAATA
5569491 TTAAATAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 24
0.70 0.07 0.22
Matches are distributed among these distances:
9 6 0.08
10 9 0.12
11 8 0.11
12 23 0.30
13 18 0.24
14 2 0.03
15 1 0.01
16 5 0.07
17 4 0.05
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (12 bp):
ATAATATTAATA
Found at i:5569418 original size:44 final size:44
Alignment explanation
Indices: 5569306--5569403 Score: 196
Period size: 44 Copynumber: 2.2 Consensus size: 44
5569296 TTTTAAGTGT
5569306 ATGATATTAAGTTAATGTGTAATAAATAAAGTCATAAATTAATA
1 ATGATATTAAGTTAATGTGTAATAAATAAAGTCATAAATTAATA
5569350 ATGATATTAAGTTAATGTGTAATAAATAAAGTCATAAATTAATA
1 ATGATATTAAGTTAATGTGTAATAAATAAAGTCATAAATTAATA
5569394 ATGATATTAA
1 ATGATATTAA
5569404 TGATAATATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (44 bp):
ATGATATTAAGTTAATGTGTAATAAATAAAGTCATAAATTAATA
Found at i:5569466 original size:22 final size:23
Alignment explanation
Indices: 5569387--5569490 Score: 77
Period size: 22 Copynumber: 4.3 Consensus size: 23
5569377 AAAGTCATAA
*
5569387 ATTAATAATGATATTAATGATAATATT
1 ATTAATAA--ATATTAATAATAA-A-T
* * **
5569414 AATAATAAATAATGGTAATAAAT
1 ATTAATAAATATTAATAATAAAT
5569437 AGACTTAATAAATATTAATAA-AAAT
1 --A-TTAATAAATATTAATAATAAAT
*
5569462 ATTAAT-AATATTAATAATTAAT
1 ATTAATAAATATTAATAATAAAT
5569484 ATTAATA
1 ATTAATA
5569491 TTAAATAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
21 11 0.18
22 14 0.23
23 2 0.03
24 1 0.02
25 14 0.23
26 13 0.21
27 7 0.11
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (23 bp):
ATTAATAAATATTAATAATAAAT
Found at i:5570742 original size:29 final size:29
Alignment explanation
Indices: 5570710--5570913 Score: 148
Period size: 29 Copynumber: 7.0 Consensus size: 29
5570700 AGAATTCCAT
*
5570710 TTTTGACCCTAAACTTTCCAAAAATTACA
1 TTTTGACCCTGAACTTTCCAAAAATTACA
* * *
5570739 TTTTTACCCTCGAA-TTTCCTAAAATTCCA
1 TTTTGACCCT-GAACTTTCCAAAAATTACA
* *
5570768 TTTTTGACCCCGAACCTTCCAAAAATTACCA
1 -TTTTGACCCTGAACTTTCCAAAAATTA-CA
* * * *
5570799 TTTT-ACCCCTGGA-TGTCTAAAAATTCCA
1 TTTTGA-CCCTGAACTTTCCAAAAATTACA
* *
5570827 TTTTGACCCCGAACCTTCCAAAAATTACCA
1 TTTTGACCCTGAACTTTCCAAAAATTA-CA
* * *
5570857 TTTT-ACCCCTGAA-TGTCTAAAAATTCCA
1 TTTTGA-CCCTGAACTTTCCAAAAATTACA
* **
5570885 TTTTTGACCCTAAACCATCCAAAAATTAC
1 -TTTTGACCCTGAACTTTCCAAAAATTAC
5570914 CATCTTACCC
Statistics
Matches: 132, Mismatches: 31, Indels: 23
0.71 0.17 0.12
Matches are distributed among these distances:
28 13 0.10
29 65 0.49
30 52 0.39
31 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (29 bp):
TTTTGACCCTGAACTTTCCAAAAATTACA
Found at i:5570794 original size:59 final size:58
Alignment explanation
Indices: 5570702--5570997 Score: 373
Period size: 59 Copynumber: 5.0 Consensus size: 58
5570692 AACTTTTTAG
** * *
5570702 AATTCCATTTTTGACCCTAAACTTTCCAAAAATTA-CATTTTTACCCTCGAATTTCCT-AA
1 AATTCCATTTTTGACCCCGAACCTTCCAAAAATTACCA-TTTTACCC-CGAATGT-CTAAA
*
5570761 AATTCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCTGGATGTCTAAA
1 AATTCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCC-GAATGTCTAAA
5570820 AATTCCA-TTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCTGAATGTCTAAA
1 AATTCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCC-GAATGTCTAAA
** * * *
5570878 AATTCCATTTTTGACCCTAAACCATCCAAAAATTACCATCTTACCCCTAGATGTCTAAA
1 AATTCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCGA-ATGTCTAAA
* * * *
5570937 AATTCCATTTTTTGACCTCGAACCTTCCAAAAATTACCATTTTGCCCTCGAGTGTCCAAA
1 AATTCCA-TTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCC-CGAATGTCTAAA
5570997 A
1 A
5570998 TTACCGTTTT
Statistics
Matches: 210, Mismatches: 20, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
58 61 0.29
59 104 0.50
60 43 0.20
61 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.33
Consensus pattern (58 bp):
AATTCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCGAATGTCTAAA
Found at i:5570909 original size:117 final size:118
Alignment explanation
Indices: 5570702--5570999 Score: 417
Period size: 117 Copynumber: 2.5 Consensus size: 118
5570692 AACTTTTTAG
** * *
5570702 AATTCCATTTTTGACCCTAAACTTTCCAAAAATTA-CATTTTTACCCTCGAATTTCCTAAAATTC
1 AATTCCATTTTTGACCCCGAACCTTCCAAAAATTACCA-TTTTACCCTCGAATGTCCTAAAATTC
* * * *
5570766 CATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCTGGATGTCTAAA
65 CATTTTTGACCCCAAACCATCCAAAAATTACCATCTTACCCCTAGATGTCTAAA
5570820 AATTCCA-TTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCC-CTGAATGT-CTAAAAATT
1 AATTCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTC-GAATGTCCT-AAAATT
*
5570882 CCATTTTTGACCCTAAACCATCCAAAAATTACCATCTTACCCCTAGATGTCTAAA
64 CCATTTTTGACCCCAAACCATCCAAAAATTACCATCTTACCCCTAGATGTCTAAA
* * *
5570937 AATTCCATTTTTTGACCTCGAACCTTCCAAAAATTACCATTTTGCCCTCGAGTGTCC-AAAATT
1 AATTCCA-TTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCCTAAAATT
5571000 ACCGTTTTAC
Statistics
Matches: 161, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
116 3 0.02
117 100 0.62
118 15 0.09
119 41 0.25
120 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.34
Consensus pattern (118 bp):
AATTCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAATGTCCTAAAATTCC
ATTTTTGACCCCAAACCATCCAAAAATTACCATCTTACCCCTAGATGTCTAAA
Found at i:5570938 original size:29 final size:28
Alignment explanation
Indices: 5570788--5570947 Score: 130
Period size: 29 Copynumber: 5.5 Consensus size: 28
5570778 CGAACCTTCC
*
5570788 AAAAATTACCATTTTACCCCTGGATGTCT
1 AAAAATT-CCATTTTACCCCTAGATGTCT
* *
5570817 AAAAATTCCATTTTGACCCCGA-ACCT-TCC
1 AAAAATTCCATTTT-ACCCCTAGA--TGTCT
5570846 AAAAATTACCATTTTACCCCT-GAATGTCT
1 AAAAATT-CCATTTTACCCCTAG-ATGTCT
* ** *
5570875 AAAAATTCCATTTTTGA-CCCTAAACCATCC
1 AAAAATTCCA-TTTT-ACCCCTAGA-TGTCT
*
5570905 AAAAATTACCATCTTACCCCTAGATGTCT
1 AAAAATT-CCATTTTACCCCTAGATGTCT
5570934 AAAAATTCCATTTT
1 AAAAATTCCATTTT
5570948 TTGACCTCGA
Statistics
Matches: 103, Mismatches: 15, Indels: 27
0.71 0.10 0.19
Matches are distributed among these distances:
28 18 0.17
29 54 0.52
30 28 0.27
31 3 0.03
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (28 bp):
AAAAATTCCATTTTACCCCTAGATGTCT
Found at i:5571007 original size:28 final size:28
Alignment explanation
Indices: 5570966--5571025 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
5570956 GAACCTTCCA
* *
5570966 AAAATTACCATTTT-GCCCTCGAGTGTCC
1 AAAATTACCATTTTACCCCT-GAGTATCC
*
5570994 AAAATTACCGTTTTACCCCTGAGTATCC
1 AAAATTACCATTTTACCCCTGAGTATCC
5571022 AAAA
1 AAAA
5571026 ATCACATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.30
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCTGAGTATCC
Found at i:5571027 original size:29 final size:29
Alignment explanation
Indices: 5570785--5571035 Score: 85
Period size: 29 Copynumber: 8.6 Consensus size: 29
5570775 CCCCGAACCT
* *
5570785 TCCAAAAATTACCATTTTACCCCTGGA-TG
1 TCCAAAAATTACCATTTT-CCCCTCGAGTA
* * *
5570814 TCTAAAAATT-CCATTTTGACCC-CGAACCT-
1 TCCAAAAATTACCATTTT-CCCCTCG-A-GTA
* *
5570843 TCCAAAAATTACCATTTTACCCCT-GAATG
1 TCCAAAAATTACCATTTT-CCCCTCGAGTA
* * ** **
5570872 TCTAAAAATT-CCATTTTTGACCCTAAACCA
1 TCCAAAAATTACCA-TTTT-CCCCTCGAGTA
* * *
5570902 TCCAAAAATTACCATCTTACCCCTAGA-TG
1 TCCAAAAATTACCAT-TTTCCCCTCGAGTA
* ** *
5570931 TCTAAAAATT-CCATTTTTTGACCTCGAACCT-
1 TCCAAAAATTACCA--TTTTCCCCTCG-A-GTA
* *
5570962 TCCAAAAATTACCATTTTGCCCTCGAGTG
1 TCCAAAAATTACCATTTTCCCCTCGAGTA
*
5570991 TCC-AAAATTACCGTTTTACCCCT-GAGTA
1 TCCAAAAATTACCATTTT-CCCCTCGAGTA
*
5571019 TCCAAAAATCA-CATTTT
1 TCCAAAAATTACCATTTT
5571036 AACTCTGTCT
Statistics
Matches: 169, Mismatches: 34, Indels: 39
0.70 0.14 0.16
Matches are distributed among these distances:
27 1 0.01
28 44 0.26
29 65 0.38
30 41 0.24
31 14 0.08
32 4 0.02
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTCCCCTCGAGTA
Found at i:5571356 original size:97 final size:97
Alignment explanation
Indices: 5571254--5571447 Score: 250
Period size: 97 Copynumber: 2.0 Consensus size: 97
5571244 AAAACCTTTA
* * * *
5571254 AAATCGAGGTAATA-TTCTTTTATTTCGTG-TTTTGAAAATTTGTGTCTTAACTTACTAGGCACG
1 AAATCGAGGCAATATTTC-TTTATCTC-TGATTCTGAAAATTTGTGCCTTAACTTACTAGGCACG
*
5571317 ATTTTTCTTCAAATCG-GAATAATCGAATACCCTT
64 ACTTTTCTTCAAATCGAG-ATAATCGAATACCCTT
* * **
5571351 AAATCGAGGCAATGTTTCTTTATCTCTGATTCTGAAAATTTGTGCCTTAATTTACTAGGTGCGAC
1 AAATCGAGGCAATATTTCTTTATCTCTGATTCTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
*
5571416 TTTTCTTCAAATCGAGATAATCGAATATCCTT
66 TTTTCTTCAAATCGAGATAATCGAATACCCTT
5571448 TTCCAAGGTT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
96 2 0.02
97 78 0.93
98 4 0.05
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (97 bp):
AAATCGAGGCAATATTTCTTTATCTCTGATTCTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
TTTTCTTCAAATCGAGATAATCGAATACCCTT
Found at i:5573318 original size:22 final size:22
Alignment explanation
Indices: 5573278--5573338 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
5573268 TGATCTAAGG
* *
5573278 AAAAGTAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
5573299 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
5573321 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
5573339 GAAAGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.29
22 24 0.69
23 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:5573329 original size:15 final size:16
Alignment explanation
Indices: 5573304--5573333 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5573294 GAATTAAAAA
5573304 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
5573320 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
5573334 AATAGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:5575859 original size:13 final size:13
Alignment explanation
Indices: 5575841--5575865 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5575831 TAGTATGATG
5575841 AAATTTATTAAGA
1 AAATTTATTAAGA
5575854 AAATTTATTAAG
1 AAATTTATTAAG
5575866 GTATCCTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
AAATTTATTAAGA
Found at i:5586896 original size:18 final size:19
Alignment explanation
Indices: 5586863--5586898 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5586853 CAAATGAATC
*
5586863 ATTTCTCATTTTCATTTTT
1 ATTTCTCATTTCCATTTTT
5586882 ATTTC-CATTTCCATTTT
1 ATTTCTCATTTCCATTTT
5586899 AAGAAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTCTCATTTCCATTTTT
Found at i:5586985 original size:25 final size:25
Alignment explanation
Indices: 5586957--5587015 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
5586947 AAAACTATAA
*
5586957 TCATTTCTAAATGTTTTCTATTTCT
1 TCATTTCTAAATGTTTTCCATTTCT
5586982 TCATTTCTAAATGTTTTCCATTTCT
1 TCATTTCTAAATGTTTTCCATTTCT
5587007 TCATTTCTA
1 TCATTTCTA
5587016 TTCATTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.20, C:0.19, G:0.03, T:0.58
Consensus pattern (25 bp):
TCATTTCTAAATGTTTTCCATTTCT
Found at i:5588603 original size:21 final size:22
Alignment explanation
Indices: 5588563--5588603 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5588553 AATTTTTAAA
* *
5588563 TTTTATATTTTTATTCAAATCT
1 TTTTATATTTTGAATCAAATCT
5588585 TTTTATATTTTGAAT-AAAT
1 TTTTATATTTTGAATCAAAT
5588604 ATTTGGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTATATTTTGAATCAAATCT
Found at i:5589913 original size:18 final size:18
Alignment explanation
Indices: 5589892--5589953 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
5589882 TATGAAATCA
5589892 ATATTTATATTACCATAT
1 ATATTTATATTACCATAT
5589910 ATATTTATATGTTACCGTATAT
1 ATATTTATA--TTACC--ATAT
** *
5589932 ATAGATATTTTACCATAT
1 ATATTTATATTACCATAT
5589950 ATAT
1 ATAT
5589954 ATTTTACCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 16 0.44
20 10 0.28
22 10 0.28
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (18 bp):
ATATTTATATTACCATAT
Found at i:5589930 original size:20 final size:19
Alignment explanation
Indices: 5589892--5589953 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
5589882 TATGAAATCA
5589892 ATATTTATA-TTACCATAT
1 ATATTTATATTTACCATAT
*
5589910 ATATTTATATGTTACCGTAT
1 ATATTTATAT-TTACCATAT
**
5589930 ATATAGATATTTTACCATAT
1 ATATTTATA-TTTACCATAT
5589950 ATAT
1 ATAT
5589954 ATTTTACCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 9 0.24
20 27 0.73
21 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (19 bp):
ATATTTATATTTACCATAT
Found at i:5589969 original size:16 final size:16
Alignment explanation
Indices: 5589930--5589961 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5589920 GTTACCGTAT
*
5589930 ATATAGATATTTTACC
1 ATATATATATTTTACC
5589946 ATATATATATTTTACC
1 ATATATATATTTTACC
5589962 TTGTATATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (16 bp):
ATATATATATTTTACC
Found at i:5589969 original size:20 final size:18
Alignment explanation
Indices: 5589909--5589969 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 18
5589899 TATTACCATA
* *
5589909 TATATTTATATGTTACCGT
1 TATATATATATTTTACC-T
*
5589928 ATATATAGATATTTTACC-
1 -TATATATATATTTTACCT
5589946 -ATATATATATTTTACCT
1 TATATATATATTTTACCT
*
5589963 TGTATAT
1 TATATAT
5589970 CAATTGATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 15 0.44
18 5 0.15
20 14 0.41
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.51
Consensus pattern (18 bp):
TATATATATATTTTACCT
Found at i:5592333 original size:6 final size:6
Alignment explanation
Indices: 5592324--5592356 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5592314 AAAATAAAAT
*
5592324 AAAAGA AAAAGA AAAAGA AAAA-A AAAATA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
5592357 TGGAAGAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:5592339 original size:17 final size:17
Alignment explanation
Indices: 5592319--5592357 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5592309 ATTGAAAAAT
*
5592319 AAAATAAAAGAAAAAGA
1 AAAATAAAAAAAAAAGA
* *
5592336 AAAAGAAAAAAAAAATA
1 AAAATAAAAAAAAAAGA
5592353 AAAAT
1 AAAAT
5592358 GGAAGAGGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAATAAAAAAAAAAGA
Found at i:5593137 original size:27 final size:25
Alignment explanation
Indices: 5593091--5593140 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
5593081 TTAAACTGTG
5593091 TTTTTTTTTTATGTTGATTTTGAGT
1 TTTTTTTTTTATGTTGATTTTGAGT
* *
5593116 TTTTGTTTTTTCTGATTTATTTTGA
1 TTTT-TTTTTTATG-TTGATTTTGA
5593141 CAAAATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 8 0.38
27 9 0.43
ACGTcount: A:0.12, C:0.02, G:0.14, T:0.72
Consensus pattern (25 bp):
TTTTTTTTTTATGTTGATTTTGAGT
Found at i:5593429 original size:28 final size:29
Alignment explanation
Indices: 5593382--5593438 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
5593372 TTTGATTTAA
* * *
5593382 TGTGTAATTGTATGCATG-AATTTTAATT
1 TGTGTAATTATATACATGAAACTTTAATT
*
5593410 TGTGTAATTATATACGTGAAACTTTAATT
1 TGTGTAATTATATACATGAAACTTTAATT
5593439 GTGATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (29 bp):
TGTGTAATTATATACATGAAACTTTAATT
Found at i:5593440 original size:28 final size:27
Alignment explanation
Indices: 5593377--5593441 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
5593367 TAAATTTTGA
* * *
5593377 TTTAA-TGTGTAATTGTATGCATGAAT
1 TTTAATTGTGTAATTATATACATGAAC
*
5593403 TTTAATTTGTGTAATTATATACGTGAAAC
1 TTTAA-TTGTGTAATTATATACATG-AAC
5593432 TTTAATTGTG
1 TTTAATTGTG
5593442 ATTTAAATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 5 0.16
28 20 0.62
29 7 0.22
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (27 bp):
TTTAATTGTGTAATTATATACATGAAC
Found at i:5593550 original size:29 final size:29
Alignment explanation
Indices: 5593496--5593564 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
5593486 TATTTAAAGA
* * *
5593496 AATAAATAT-ATCAATTTATTTTTATATT
1 AATAAATATAATCAATTTATATATATAAT
*
5593524 GAATAAATATAAT-TATTTATATATATAAT
1 -AATAAATATAATCAATTTATATATATAAT
5593553 ATATAAATATAA
1 A-ATAAATATAA
5593565 AATGATATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 31 0.91
30 2 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
AATAAATATAATCAATTTATATATATAAT
Found at i:5593638 original size:29 final size:28
Alignment explanation
Indices: 5593598--5593659 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
5593588 ATTGATAATT
**
5593598 TATAAAAATTAAATTAAATAAAAATTTA
1 TATAAAAATTAAACAAAATAAAAATTTA
*
5593626 TATATAAAATTAAACAAAATTAAAATTTA
1 TATA-AAAATTAAACAAAATAAAAATTTA
5593655 TATAA
1 TATAA
5593660 TTCATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
TATAAAAATTAAACAAAATAAAAATTTA
Found at i:5593927 original size:7 final size:7
Alignment explanation
Indices: 5593911--5593948 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
5593901 TGCCCTTTTT
*
5593911 CTTCTTC
1 CTTCTCC
5593918 CTTCTCC
1 CTTCTCC
5593925 CTTCTCC
1 CTTCTCC
5593932 CTTCTCC
1 CTTCTCC
5593939 CTTCTCC
1 CTTCTCC
5593946 CTT
1 CTT
5593949 TTTCACAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (7 bp):
CTTCTCC
Found at i:5596303 original size:175 final size:174
Alignment explanation
Indices: 5595980--5596333 Score: 475
Period size: 175 Copynumber: 2.0 Consensus size: 174
5595970 TAGTTGCTCA
** * *
5595980 TGGAACTGGTTAAATGTTAAAGCATAATAACTGCTTACTGATCTGGAAAGTTCGGGATGCATACT
1 TGGAACTGGTTAAATGTTAAAGCATAATAACTGCTTACTGATCCAGAAAGTTCGGCATGAATACT
* * *
5596045 TTTGTTTGTCTTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGGACCGCTCAGATAAACT
66 TTTGTTTGTCGTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGCACCGCTCAGAT-AACT
* *
5596110 GTAACACTAACGGTTGATTGATTGGTGAAACGTGTTAGTAATTAT
130 GTAACACTAACAGTTGATTGATTGGAGAAACGTGTTAGTAATTAT
* *
5596155 TGGAACTGGTTAAATGTTAAAGCATTATAACTGTTTA-TGGATCCAGAAAGTTCGGCATGAATAC
1 TGGAACTGGTTAAATGTTAAAGCATAATAACTGCTTACT-GATCCAGAAAGTTCGGCATGAATAC
*
5596219 TTGTT-TTTGAT-GTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACGGCTCAGAGT
65 TT-TTGTTTG-TCGTCCATGTGTTTCTTTCTCATTTTGTTCTTTCC-ATATGCACCGCTCAGA-T
* * *
5596282 -ACTAGTTA-TCTGACAGTTGATTGATTGGAGAAACGTGTTAGTAATTAT
126 AACT-GTAACACTAACAGTTGATTGATTGGAGAAACGTGTTAGTAATTAT
5596330 TGGA
1 TGGA
5596334 TAGTAGTTAT
Statistics
Matches: 158, Mismatches: 15, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
174 1 0.01
175 136 0.86
176 20 0.13
177 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (174 bp):
TGGAACTGGTTAAATGTTAAAGCATAATAACTGCTTACTGATCCAGAAAGTTCGGCATGAATACT
TTTGTTTGTCGTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGCACCGCTCAGATAACTG
TAACACTAACAGTTGATTGATTGGAGAAACGTGTTAGTAATTAT
Found at i:5596410 original size:36 final size:36
Alignment explanation
Indices: 5596365--5596435 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
5596355 GTCATTGATC
* * *
5596365 GCTTGAGTAGATATGACCATGTG-TTAGTAATCAACA
1 GCTTAAGTAGATATGAACACGTGCTT-GTAATCAACA
*
5596401 GCTTAAGTAGATTTGAACACGTGCTTGTAATCAAC
1 GCTTAAGTAGATATGAACACGTGCTTGTAATCAAC
5596436 TGATTATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 28 0.93
37 2 0.07
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (36 bp):
GCTTAAGTAGATATGAACACGTGCTTGTAATCAACA
Found at i:5596924 original size:175 final size:175
Alignment explanation
Indices: 5596647--5596999 Score: 486
Period size: 175 Copynumber: 2.0 Consensus size: 175
5596637 AGTTGCACAC
* *
5596647 GGAACTGGTTAAATGTTAGAGCATAATAACTGCTTACTGATCCGAAAAGTTCGGGATGCATACTT
1 GGAACTGGTTAAATGTTAAAGCATAATAACTGCTTACTGATCCGAAAAGTTCGGGATGAATACTT
* *
5596712 TTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCC-ATATGGACCGCTCAGA-TAAAC
66 TTGTTTGTCGTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACCGCTCAGAGT--AC
* *
5596775 T-GTAACACTGACGGTTGATTGATTGGTGAAACGTGTTAGTAATTATT
129 TAGTAA-ACTGACAGTTGATTGATTGGAGAAACGTGTTAGTAATTATT
* *
5596822 GGAACTGGTTAAATGTTAAAGCATTATAACTGTTTA-TGGATCC-AGAAAGTTCGGGATGAATAC
1 GGAACTGGTTAAATGTTAAAGCATAATAACTGCTTACT-GATCCGA-AAAGTTCGGGATGAATAC
**
5596885 TTGTT-TTTGAT-GTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCATGGCTCAGAGT
64 TT-TTGTTTG-TCGTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACCGCTCAGAGT
* *
5596948 ACTAGTTATCTGACAGTTGATTGATTGGAGAAACGTGTTAGTAATTATT
127 ACTAGTAAACTGACAGTTGATTGATTGGAGAAACGTGTTAGTAATTATT
5596997 GGA
1 GGA
5597000 TAGTAGTTAT
Statistics
Matches: 159, Mismatches: 12, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
174 2 0.01
175 137 0.86
176 19 0.12
177 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.39
Consensus pattern (175 bp):
GGAACTGGTTAAATGTTAAAGCATAATAACTGCTTACTGATCCGAAAAGTTCGGGATGAATACTT
TTGTTTGTCGTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACCGCTCAGAGTACTA
GTAAACTGACAGTTGATTGATTGGAGAAACGTGTTAGTAATTATT
Found at i:5596925 original size:666 final size:666
Alignment explanation
Indices: 5595648--5597491 Score: 3068
Period size: 666 Copynumber: 2.8 Consensus size: 666
5595638 GTACTAGTTC
* * * * * *
5595648 TAGTAATTATTGGATAGTAGTTATGAGCTTTGTTAATCATTGATCGGTTAAGTAGATATGACTAC
1 TAGTAATTATTGGATAGTAGTTATGAGCTCTGTTAGTCATTGATCGCTTGAGTAGATATGACCAT
* * * * **
5595713 GTGTTACTAATCAACCGGTTAAGTAGATATGAACACATGCTTGTAATCAACTGATCGTGTAGCTC
66 GTGTTAGTAATCAACAGCTTAAGTAGATATGAACACGTGCTTGTAATCAACTGATTATGTAGCTC
* * * * * * *
5595778 TGAGCGAATGTTGTAAAGTAACGGATTGAGTAGTTCCAAGCGCCTTTTAGACATTAACGGTTAAG
131 TGAGTGCATG-T-T--ATTAACGGATTGAGTAGTTCCAAGCACCTTTTAGAAATTAATGGTCAAG
*
5595843 TACTGAGCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGAT
192 TACTGATCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGAT
* *
5595908 GAAGTAGTTATGAGCATGTGACCATGCTTGAGCTACTATCCTTGGACTATCAGTACTTGTTATAG
257 TAAGTAGTTATGAGCATGTGACCATGCTTCAGCTACTATCCTTGGACTATCAGTACTTG-T-TAG
* * *
5595973 TTGCTCATGGAACTGGTTAAATGTTAAAGCATAATAACTGCTTACTGATCTGGAAAGTTCGGGAT
320 TTGCTCATGGAACTGGTTAAATGTTAGAGCATAATAACTGCTTACTGATCCGAAAAGTTCGGGAT
*
5596038 GCATACTTTTGTTTGTCTTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGGACCGCTCAG
385 GCATACTTTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGGACCGCTCAG
*
5596103 ATAAACTGTAACACTAACGGTTGATTGATTGGTGAAACGTGTTAGTAATTATTGGAACTGGTTAA
450 ATAAACTGTAACACTGACGGTTGATTGATTGGTGAAACGTGTTAGTAATTATTGGAACTGGTTAA
5596168 ATGTTAAAGCATTATAACTGTTTATGGATCCAGAAAGTTCGGCATGAATACTTGTTTTTGATGTC
515 ATGTTAAAGCATTATAACTGTTTATGGATCCAGAAAGTTCGGCATGAATACTTGTTTTTGATGTC
5596233 CATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACGGCTCAGAGTACTAGTTATCTGACAG
580 CATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACGGCTCAGAGTACTAGTTATCTGACAG
5596298 TTGATTGATTGGAGAAACGTGT
645 TTGATTGATTGGAGAAACGTGT
5596320 TAGTAATTATTGGATAGTAGTTATGAGCTCTGTTAGTCATTGATCGCTTGAGTAGATATGACCAT
1 TAGTAATTATTGGATAGTAGTTATGAGCTCTGTTAGTCATTGATCGCTTGAGTAGATATGACCAT
*
5596385 GTGTTAGTAATCAACAGCTTAAGTAGATTTGAACACGTGCTTGTAATCAACTGATTATGTAGCTC
66 GTGTTAGTAATCAACAGCTTAAGTAGATATGAACACGTGCTTGTAATCAACTGATTATGTAGCTC
*
5596450 TGAGTGCATGTTATTAACGGATTGAGTAGTTCCAAGCACCTTTTAGAAATTAATGGTCAAGCACT
131 TGAGTGCATGTTATTAACGGATTGAGTAGTTCCAAGCACCTTTTAGAAATTAATGGTCAAGTACT
* * * *
5596515 GATCACGTTTTAGCAATTAGCAGTTTGAGTAGTTCTGATCACATGCTAGTAATTGATGGATTAAG
196 GATCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGATTAAG
** * *
5596580 TAGTTATGAGCATGTGACTGTGCTTCAGCTACTATCCTTGGACTATCAGTACATGTTAGTTGCAC
261 TAGTTATGAGCATGTGACCATGCTTCAGCTACTATCCTTGGACTATCAGTACTTGTTAGTTGCTC
*
5596645 ACGGAACTGGTTAAATGTTAGAGCATAATAACTGCTTACTGATCCGAAAAGTTCGGGATGCATAC
326 ATGGAACTGGTTAAATGTTAGAGCATAATAACTGCTTACTGATCCGAAAAGTTCGGGATGCATAC
5596710 TTTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGGACCGCTCAGATAAAC
391 TTTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGGACCGCTCAGATAAAC
5596775 TGTAACACTGACGGTTGATTGATTGGTGAAACGTGTTAGTAATTATTGGAACTGGTTAAATGTTA
456 TGTAACACTGACGGTTGATTGATTGGTGAAACGTGTTAGTAATTATTGGAACTGGTTAAATGTTA
*
5596840 AAGCATTATAACTGTTTATGGATCCAGAAAGTTCGGGATGAATACTTGTTTTTGATGTCCATGTG
521 AAGCATTATAACTGTTTATGGATCCAGAAAGTTCGGCATGAATACTTGTTTTTGATGTCCATGTG
*
5596905 TTTCTTTCTCATTTTGTTCTTTCCAATATGCATGGCTCAGAGTACTAGTTATCTGACAGTTGATT
586 TTTCTTTCTCATTTTGTTCTTTCCAATATGCACGGCTCAGAGTACTAGTTATCTGACAGTTGATT
5596970 GATTGGAGAAACGTGT
651 GATTGGAGAAACGTGT
5596986 TAGTAATTATTGGATAGTAGTTATGAGCTCTGTTAGTCATTGATCGCTTGAGTAGATATGACCAT
1 TAGTAATTATTGGATAGTAGTTATGAGCTCTGTTAGTCATTGATCGCTTGAGTAGATATGACCAT
5597051 GTGTTAGTAATCAACAGCTTAAGTAGATATGAACACGTGCTTGTAATCAACTGATTATGTAGCTC
66 GTGTTAGTAATCAACAGCTTAAGTAGATATGAACACGTGCTTGTAATCAACTGATTATGTAGCTC
* *
5597116 TGAGTGCATGTTATTAACGGATTGAGTAGTTCCAAACACCTTTTAGAAATTAATCGTCAAGTACT
131 TGAGTGCATGTTATTAACGGATTGAGTAGTTCCAAGCACCTTTTAGAAATTAATGGTCAAGTACT
5597181 GATCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGATTAAG
196 GATCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGATTAAG
*
5597246 TAGTTATGAGCACGTGACCATGCTTCAGCTACTATCCTTGGACTATCAGTACTTGTTAGTTGCTC
261 TAGTTATGAGCATGTGACCATGCTTCAGCTACTATCCTTGGACTATCAGTACTTGTTAGTTGCTC
* * * *
5597311 ATGGAACTGGTTAAATGTTAGAGCATAATAACTGTTTACTTATCC-AGAAAGCTCTGGATGCATA
326 ATGGAACTGGTTAAATGTTAGAGCATAATAACTGCTTACTGATCCGA-AAAGTTCGGGATGCATA
* * * *
5597375 CTTTTGTTTCTTGTGTATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGCACCGCTCAGATAAA
390 CTTTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGGACCGCTCAGATAAA
* *
5597440 CTGTACTAGTTCACTGACAGTTGATTGA----TGAAACGTGTTAATAATTATTGGA
455 CTGTA--A---CACTGACGGTTGATTGATTGGTGAAACGTGTTAGTAATTATTGGA
5597492 TGGTAGTTTT
Statistics
Matches: 1102, Mismatches: 64, Indels: 17
0.93 0.05 0.01
Matches are distributed among these distances:
665 1 0.00
666 776 0.70
667 24 0.02
668 158 0.14
670 1 0.00
671 17 0.02
672 125 0.11
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (666 bp):
TAGTAATTATTGGATAGTAGTTATGAGCTCTGTTAGTCATTGATCGCTTGAGTAGATATGACCAT
GTGTTAGTAATCAACAGCTTAAGTAGATATGAACACGTGCTTGTAATCAACTGATTATGTAGCTC
TGAGTGCATGTTATTAACGGATTGAGTAGTTCCAAGCACCTTTTAGAAATTAATGGTCAAGTACT
GATCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGATTAAG
TAGTTATGAGCATGTGACCATGCTTCAGCTACTATCCTTGGACTATCAGTACTTGTTAGTTGCTC
ATGGAACTGGTTAAATGTTAGAGCATAATAACTGCTTACTGATCCGAAAAGTTCGGGATGCATAC
TTTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGGACCGCTCAGATAAAC
TGTAACACTGACGGTTGATTGATTGGTGAAACGTGTTAGTAATTATTGGAACTGGTTAAATGTTA
AAGCATTATAACTGTTTATGGATCCAGAAAGTTCGGCATGAATACTTGTTTTTGATGTCCATGTG
TTTCTTTCTCATTTTGTTCTTTCCAATATGCACGGCTCAGAGTACTAGTTATCTGACAGTTGATT
GATTGGAGAAACGTGT
Found at i:5597076 original size:36 final size:36
Alignment explanation
Indices: 5597031--5597101 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
5597021 GTCATTGATC
* * *
5597031 GCTTGAGTAGATATGACCATGTG-TTAGTAATCAACA
1 GCTTAAGTAGATATGAACACGTGCTT-GTAATCAACA
5597067 GCTTAAGTAGATATGAACACGTGCTTGTAATCAAC
1 GCTTAAGTAGATATGAACACGTGCTTGTAATCAAC
5597102 TGATTATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 29 0.94
37 2 0.06
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (36 bp):
GCTTAAGTAGATATGAACACGTGCTTGTAATCAACA
Found at i:5597610 original size:36 final size:35
Alignment explanation
Indices: 5597565--5597661 Score: 92
Period size: 36 Copynumber: 2.8 Consensus size: 35
5597555 AACTGATTGT
*
5597565 GTAGCTCTGAGCACATGTTAGTAATTAACGGATCGA
1 GTAG-TCTGAGCACATGTTAGAAATTAACGGATCGA
* * * *
5597601 GTAGTTCTGAGCACTTTTTTGAAATTAA-TGATCGA
1 GTAG-TCTGAGCACATGTTAGAAATTAACGGATCGA
* *
5597636 GTA--CTGAGCACGTGTTAGCAATTAAC
1 GTAGTCTGAGCACATGTTAGAAATTAAC
5597662 ATTTTGAGTA
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
32 18 0.36
35 9 0.18
36 23 0.46
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (35 bp):
GTAGTCTGAGCACATGTTAGAAATTAACGGATCGA
Found at i:5598120 original size:97 final size:100
Alignment explanation
Indices: 5597936--5598126 Score: 219
Period size: 97 Copynumber: 1.9 Consensus size: 100
5597926 TAGTAAAAGT
* * *
5597936 AAGTAGTTCTGTTTGTTCTTTGGTTTTATCTCTAGATAGCGCGAGTGATAAACACGTGCCAGTGG
1 AAGTAGTTCTGCTTGTTCTTTGATTTTATCTCTAGATAGCGCGAGTGACAAACACGTGCCAGTGG
* * ** *
5598001 CCATTGAAGGCAGGATGCGTGCCTGTGAAAAGTAA
66 CCATTCAAGGCAAGACACGTGCCTCTGAAAAGTAA
* * * * *
5598036 AAGTAGTTTTGCTTGTTCTTTCTATTTTATCTTTAG-T-GCG-G-GTGACAAACACGTGTCAGTT
1 AAGTAGTTCTGCTTGTTCTTT-GATTTTATCTCTAGATAGCGCGAGTGACAAACACGTGCCAGTG
*
5598097 GCCATTCAAGGCAAGACATGTGCCTCTGAA
65 GCCATTCAAGGCAAGACACGTGCCTCTGAA
5598127 TAGGCTGAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
97 41 0.54
98 1 0.01
99 3 0.04
100 20 0.26
101 11 0.14
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (100 bp):
AAGTAGTTCTGCTTGTTCTTTGATTTTATCTCTAGATAGCGCGAGTGACAAACACGTGCCAGTGG
CCATTCAAGGCAAGACACGTGCCTCTGAAAAGTAA
Found at i:5614971 original size:7 final size:7
Alignment explanation
Indices: 5614959--5615001 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
5614949 TGAGACTTAA
5614959 ACCCGTT
1 ACCCGTT
5614966 ACCCGTT
1 ACCCGTT
5614973 ACCCGTT
1 ACCCGTT
5614980 ACCCGTT
1 ACCCGTT
5614987 ACCCGTT
1 ACCCGTT
5614994 ACCCGTT
1 ACCCGTT
5615001 A
1 A
5615002 TCCTAAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.16, C:0.42, G:0.14, T:0.28
Consensus pattern (7 bp):
ACCCGTT
Found at i:5615020 original size:14 final size:13
Alignment explanation
Indices: 5615003--5615050 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
5614993 TACCCGTTAT
*
5615003 CCTAAATCATAAAC
1 CCTAAATC-TAAAA
5615017 CCTAAAATCTAAAA
1 CCT-AAATCTAAAA
*
5615031 CCTAAAACCTAAAA
1 CCT-AAATCTAAAA
5615045 CCTAAA
1 CCTAAA
5615051 CCTTATCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 3 0.10
14 23 0.74
15 5 0.16
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (13 bp):
CCTAAATCTAAAA
Found at i:5615028 original size:21 final size:21
Alignment explanation
Indices: 5615003--5615050 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5614993 TACCCGTTAT
* *
5615003 CCTAAATCATAAACCCTAAAA
1 CCTAAAACATAAAACCTAAAA
* *
5615024 TCTAAAACCTAAAACCTAAAA
1 CCTAAAACATAAAACCTAAAA
5615045 CCTAAA
1 CCTAAA
5615051 CCTTATCTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (21 bp):
CCTAAAACATAAAACCTAAAA
Found at i:5615053 original size:6 final size:7
Alignment explanation
Indices: 5615012--5615050 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
5615002 TCCTAAATCA
*
5615012 TAAACCC
1 TAAAACC
*
5615019 TAAAATC
1 TAAAACC
5615026 TAAAACC
1 TAAAACC
5615033 TAAAACC
1 TAAAACC
5615040 TAAAACC
1 TAAAACC
5615047 TAAA
1 TAAA
5615051 CCTTATCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAAACC
Found at i:5616414 original size:13 final size:13
Alignment explanation
Indices: 5616392--5616429 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5616382 TAAAGTGACC
5616392 TAACGAATTTTGT
1 TAACGAATTTTGT
*
5616405 TAACGGATTTTGT
1 TAACGAATTTTGT
*
5616418 TAA-GATTTTTGT
1 TAACGAATTTTGT
5616430 AATTTTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.50
Consensus pattern (13 bp):
TAACGAATTTTGT
Found at i:5624593 original size:15 final size:15
Alignment explanation
Indices: 5624575--5624605 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5624565 AATACCTAAA
5624575 ATATAAAAAATTAAT
1 ATATAAAAAATTAAT
5624590 ATATAAAAAATTAAT
1 ATATAAAAAATTAAT
5624605 A
1 A
5624606 AACACAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATATAAAAAATTAAT
Found at i:5627806 original size:14 final size:14
Alignment explanation
Indices: 5627787--5627814 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5627777 AAAAATTTGA
5627787 ATAATTAATGATAT
1 ATAATTAATGATAT
5627801 ATAATTAATGATAT
1 ATAATTAATGATAT
5627815 GTCGAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
ATAATTAATGATAT
Found at i:5637010 original size:37 final size:37
Alignment explanation
Indices: 5636964--5637039 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
5636954 CTCCATCGAA
*
5636964 TAATGAACGCACATTGCGTCTCGCTCACCACATCCCC
1 TAATAAACGCACATTGCGTCTCGCTCACCACATCCCC
* * *
5637001 TAATAAACGCACATTTCGTCTCGTTCACCACATCTCC
1 TAATAAACGCACATTGCGTCTCGCTCACCACATCCCC
5637038 TA
1 TA
5637040 TTATCTCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.26, C:0.37, G:0.11, T:0.26
Consensus pattern (37 bp):
TAATAAACGCACATTGCGTCTCGCTCACCACATCCCC
Found at i:5657048 original size:22 final size:23
Alignment explanation
Indices: 5657008--5657050 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5656998 AAATTTAGAT
* *
5657008 ATAATTAAATTATATATTTTACA
1 ATAATAAAAATATATATTTTACA
5657031 ATAATAAAAATATA-ATTTTA
1 ATAATAAAAATATATATTTTA
5657051 TCATTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAATAAAAATATATATTTTACA
Found at i:5657078 original size:18 final size:17
Alignment explanation
Indices: 5657042--5657081 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5657032 TAATAAAAAT
5657042 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
5657059 ATAA-TTTAT-ATCTTT-
1 ATAATTTTATCAT-TTTA
5657074 ATAATTTT
1 ATAATTTT
5657082 TAAATGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTATCATTTTA
Found at i:5658646 original size:29 final size:28
Alignment explanation
Indices: 5658614--5658678 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
5658604 CCAGATATAT
5658614 TATATTATAAAAAATAATTATATCAATTA
1 TATATTATAAAAAATAATTATAT-AATTA
* *
5658643 TATATGT-TAAATAATAATTATATATTTA
1 TATAT-TATAAAAAATAATTATATAATTA
5658671 TAT-TTATA
1 TATATTATA
5658679 TTAACTCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 1 0.03
27 3 0.09
28 7 0.22
29 20 0.62
30 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
TATATTATAAAAAATAATTATATAATTA
Found at i:5662493 original size:52 final size:52
Alignment explanation
Indices: 5662413--5662592 Score: 315
Period size: 52 Copynumber: 3.5 Consensus size: 52
5662403 GTAAATGCAA
*
5662413 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
5662465 AAGGTCCGATGATTATGTGTCATTGTGAGTATATGAATCCTTTACGAATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
5662517 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
*
5662569 GAGGTCCGATGACTATGTGTCATC
1 AAGGTCCGATGACTATGTGTCATC
5662593 CGATGACTAT
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 120 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:5662596 original size:18 final size:18
Alignment explanation
Indices: 5662573--5662628 Score: 112
Period size: 18 Copynumber: 3.1 Consensus size: 18
5662563 GATTATGAGG
5662573 TCCGATGACTATGTGTCA
1 TCCGATGACTATGTGTCA
5662591 TCCGATGACTATGTGTCA
1 TCCGATGACTATGTGTCA
5662609 TCCGATGACTATGTGTCA
1 TCCGATGACTATGTGTCA
5662627 TC
1 TC
5662629 ATGAGTATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (18 bp):
TCCGATGACTATGTGTCA
Found at i:5662691 original size:52 final size:52
Alignment explanation
Indices: 5662609--5662737 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
5662599 CTATGTGTCA
*
5662609 TCCGATGACTATGTGTCATCATGAGTATATGAATCTTTTACGGATTATGAGG
1 TCCGATGACTATGTGTCATCATGAGCATATGAATCTTTTACGGATTATGAGG
* *
5662661 TCCGATGACTATGTGTCATCGTGAGCATATGAATCTTTTTCGGATTATGAGG
1 TCCGATGACTATGTGTCATCATGAGCATATGAATCTTTTACGGATTATGAGG
* *
5662713 TCCGATGACTATGTGCCATCTTGAG
1 TCCGATGACTATGTGTCATCATGAG
5662738 TATCAAATGA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (52 bp):
TCCGATGACTATGTGTCATCATGAGCATATGAATCTTTTACGGATTATGAGG
Found at i:5662721 original size:140 final size:140
Alignment explanation
Indices: 5662469--5662732 Score: 438
Period size: 140 Copynumber: 1.9 Consensus size: 140
5662459 GATTATAAGG
* **
5662469 TCCGATGATTATGTGTCATTGTGAGTATATGAATCCTTTACGAATTATAAGGTCCGATGACTATG
1 TCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATAAGGTCCGATGACTATG
* *
5662534 TGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCCGATGA
66 TGTCATCGTGAGCATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGCCATCCGATGA
5662599 CTATGTGTCA
131 CTATGTGTCA
* * *
5662609 TCCGATGACTATGTGTCATCATGAGTATATGAATCTTTTACGGATTATGAGGTCCGATGACTATG
1 TCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATAAGGTCCGATGACTATG
* *
5662674 TGTCATCGTGAGCATATGAATCTTTTTCGGATTATGAGGTCCGATGACTATGTGCCATC
66 TGTCATCGTGAGCATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGCCATC
5662733 TTGAGTATCA
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
140 114 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (140 bp):
TCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATAAGGTCCGATGACTATG
TGTCATCGTGAGCATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGCCATCCGATGA
CTATGTGTCA
Found at i:5664110 original size:16 final size:17
Alignment explanation
Indices: 5664080--5664115 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
5664070 CAGATGTCAC
*
5664080 ATTTCTTTTATATATTT
1 ATTTCTTTTAAATATTT
5664097 ATTT-TTTTAAATATTT
1 ATTTCTTTTAAATATTT
5664113 ATT
1 ATT
5664116 AACCTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTCTTTTAAATATTT
Found at i:5664889 original size:79 final size:79
Alignment explanation
Indices: 5664731--5664882 Score: 232
Period size: 79 Copynumber: 1.9 Consensus size: 79
5664721 CATTCAAAAC
* * *
5664731 TAATATTTCATTCAATCAATAAAAAATGAATATCGCATGAAAATCCTAATCTATCACCAGAAAAG
1 TAATATTTCATTCAATCAATAAAAAATGAATATCGAATGAAAATCCTAATCTATCACAAGAAAAA
* *
5664796 TCATAATTAGAATT
66 TCACAATCAGAATT
* * *
5664810 TAATATTTCATTCAATCAATAAAAATTGAATATTGAATGAAAATCCTAATTTATCACAAGAAAAA
1 TAATATTTCATTCAATCAATAAAAAATGAATATCGAATGAAAATCCTAATCTATCACAAGAAAAA
5664875 TCACAATC
66 TCACAATC
5664883 CAAATTTCTT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (79 bp):
TAATATTTCATTCAATCAATAAAAAATGAATATCGAATGAAAATCCTAATCTATCACAAGAAAAA
TCACAATCAGAATT
Found at i:5665092 original size:19 final size:18
Alignment explanation
Indices: 5665068--5665137 Score: 74
Period size: 19 Copynumber: 4.0 Consensus size: 18
5665058 ATGAAGAGAG
5665068 ATTAATTTATTTTATATAA
1 ATTAATTTATTTTATA-AA
*
5665087 ATTAATTTGTTTTATAAA
1 ATTAATTTATTTTATAAA
* * *
5665105 ATAAATTT-TCTCATAAA
1 ATTAATTTATTTTATAAA
5665122 A-TAATTT-TTTTATAAA
1 ATTAATTTATTTTATAAA
5665138 GTTTTTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.27
17 8 0.18
18 9 0.20
19 15 0.34
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (18 bp):
ATTAATTTATTTTATAAA
Found at i:5665104 original size:17 final size:16
Alignment explanation
Indices: 5665077--5665137 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
5665067 GATTAATTTA
*
5665077 TTTTATATAAATTAAT
1 TTTTTTATAAATTAAT
*
5665093 TTGTTTTATAAAATAAAT
1 TT-TTTTAT-AAATTAAT
* * *
5665111 TTTCTCATAAAATAAT
1 TTTTTTATAAATTAAT
5665127 TTTTTTATAAA
1 TTTTTTATAAA
5665138 GTTTTTTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
16 17 0.49
17 9 0.26
18 9 0.26
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (16 bp):
TTTTTTATAAATTAAT
Found at i:5665231 original size:15 final size:15
Alignment explanation
Indices: 5665204--5665245 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
5665194 GTTTGATAAA
*
5665204 TTGAAAAATTAAGTG
1 TTGAAAAAATAAGTG
5665219 CTT-AAAAAATAAGTG
1 -TTGAAAAAATAAGTG
5665234 TTGAAAAAATAA
1 TTGAAAAAATAA
5665246 ATATTGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 2 0.08
15 20 0.83
16 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.29
Consensus pattern (15 bp):
TTGAAAAAATAAGTG
Found at i:5669263 original size:13 final size:13
Alignment explanation
Indices: 5669245--5669307 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
5669235 GCATCATGTG
* *
5669245 AGCTCAATCTGTA
1 AGCTCAATATGCA
*
5669258 AGCTCATTATGCA
1 AGCTCAATATGCA
* **
5669271 AGCTCAATTTGTG
1 AGCTCAATATGCA
*
5669284 AGCTCATTATGCA
1 AGCTCAATATGCA
5669297 AGCTCAATATG
1 AGCTCAATATG
5669308 GATCCGGTCT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (13 bp):
AGCTCAATATGCA
Done.