Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 23 of 182
Found at i:9482930 original size:4 final size:4
Alignment explanation
Indices: 9482923--9482949 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
9482913 AGAGAGAGCT
9482923 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
9482950 TTGAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:9492877 original size:3 final size:3
Alignment explanation
Indices: 9492869--9492899 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
9492859 GTGTTTTGCA
9492869 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9492900 TAGAGAGTAA
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:9502545 original size:18 final size:18
Alignment explanation
Indices: 9502522--9502556 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9502512 TTTCAAAAAC
9502522 TTTTAAAAAAAACTTTTG
1 TTTTAAAAAAAACTTTTG
**
9502540 TTTTAAAGTAAACTTTT
1 TTTTAAAAAAAACTTTT
9502557 AAATTTACCT
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:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (18 bp):
TTTTAAAAAAAACTTTTG
Found at i:9506074 original size:57 final size:58
Alignment explanation
Indices: 9505982--9506092 Score: 129
Period size: 57 Copynumber: 1.9 Consensus size: 58
9505972 ATAATTTTTT
* * * *
9505982 TTTATAATTTTTTTAGATTTTTTCACAAAACTTAAA-TATTTTAAC-AATTTTTAAAAC
1 TTTATAATATTTTTAGATTCTTTCAAAAAACTTAAACT-TTTTAACTAAATTTTAAAAC
* *
9506039 TTTATAATATTTTTATATTCTTT-AAATAAATTTAAACTTTTTAACTAAATTTTA
1 TTTATAATATTTTTAGATTCTTTCAAA-AAACTTAAACTTTTTAACTAAATTTTA
9506093 CAATTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
56 2 0.04
57 35 0.78
58 8 0.18
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (58 bp):
TTTATAATATTTTTAGATTCTTTCAAAAAACTTAAACTTTTTAACTAAATTTTAAAAC
Found at i:9518136 original size:19 final size:19
Alignment explanation
Indices: 9518114--9518150 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9518104 TTTTTATGAA
9518114 AATTTTGACATTTTAAAGG
1 AATTTTGACATTTTAAAGG
**
9518133 AATTTTGAGTTTTTAAAG
1 AATTTTGACATTTTAAAG
9518151 AACCATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (19 bp):
AATTTTGACATTTTAAAGG
Found at i:9518627 original size:1 final size:1
Alignment explanation
Indices: 9518621--9518645 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
9518611 AGTATTTGGC
9518621 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
9518646 GCGGATACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9519636 original size:5 final size:5
Alignment explanation
Indices: 9519626--9519650 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9519616 TCAATGGTGG
9519626 CTCCC CTCCC CTCCC CTCCC CTCCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC
9519651 TTTTCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCCC
Found at i:9521585 original size:2 final size:2
Alignment explanation
Indices: 9521578--9521602 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9521568 GTAGTTTAGA
9521578 AT 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 A
9521603 AAAGGAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9527597 original size:30 final size:31
Alignment explanation
Indices: 9527552--9527614 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
9527542 TCAACTTTTA
9527552 TATATTATTTTGAAA-TT-TAAAATTTATATT
1 TATATTATTTTGAAATTTATAAAATTT-TATT
9527582 TATA-TATTTTAGAAATTTATAAAATTTTATT
1 TATATTATTTT-GAAATTTATAAAATTTTATT
9527613 TA
1 TA
9527615 AAAATTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 6 0.20
30 8 0.27
31 8 0.27
32 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (31 bp):
TATATTATTTTGAAATTTATAAAATTTTATT
Found at i:9535832 original size:18 final size:16
Alignment explanation
Indices: 9535804--9535844 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
9535794 TTTCCTTTTT
9535804 AATTGTAATTAATTTAAA
1 AATT-TAATTAA-TTAAA
9535822 ATATTTAATTAATTAAA
1 A-ATTTAATTAATTAAA
9535839 AATTTA
1 AATTTA
9535845 TTCTTATCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.23
17 6 0.27
18 8 0.36
19 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AATTTAATTAATTAAA
Found at i:9538546 original size:28 final size:28
Alignment explanation
Indices: 9538508--9538567 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
9538498 AGAAAATAAA
*
9538508 AAAAAATTCTTTTAATATAATTTAATAT
1 AAAAAAGTCTTTTAATATAATTTAATAT
*
9538536 AAAAAAGTCTTTTAATATAATTTAATGT
1 AAAAAAGTCTTTTAATATAATTTAATAT
9538564 AAAA
1 AAAA
9538568 TATTATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (28 bp):
AAAAAAGTCTTTTAATATAATTTAATAT
Found at i:9538580 original size:28 final size:28
Alignment explanation
Indices: 9538521--9538581 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
9538511 AAATTCTTTT
* *
9538521 AATATAATTTAATATAAAAAAGTCTTTT
1 AATATAATTTAATATAAAAAAGTATTTA
* * *
9538549 AATATAATTTAATGTAAAATATTATTTA
1 AATATAATTTAATATAAAAAAGTATTTA
9538577 AATAT
1 AATAT
9538582 TATTCTTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (28 bp):
AATATAATTTAATATAAAAAAGTATTTA
Found at i:9544513 original size:17 final size:17
Alignment explanation
Indices: 9544493--9544529 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
9544483 TAAAAATTGG
9544493 ATTGAAAAAA-TAATTTA
1 ATTGAAAAAATTAA-TTA
9544510 ATTGAAAAAATTAATTA
1 ATTGAAAAAATTAATTA
9544527 ATT
1 ATT
9544530 TTTTAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
ATTGAAAAAATTAATTA
Found at i:9545176 original size:71 final size:68
Alignment explanation
Indices: 9545120--9545311 Score: 194
Period size: 71 Copynumber: 2.7 Consensus size: 68
9545110 CATATACCTG
* * *
9545120 AAAATTAAAAAATATATAATTTAAATTAAAAAGACATATTTAAAGAATAAATCAA-TTCAAAGAA
1 AAAATTTAAAAATATATAATTTAAATTAAAAAGACATATTTAAAGAATAAATCAATTTTAAA-AT
*
9545184 ATAAA
65 AT-AT
* * *
9545189 ATAAATTTTAAAA-ATATAATTT-AATTAAGAATACATATTTAAAGAATAATAAATCAA-TTTAA
1 A-AAATTTAAAAATATATAATTTAAATTAAAAAGACATATTTAAAG---AATAAATCAATTTTAA
9545251 AATAATAAAT
62 AAT-AT--AT
*
9545261 TAAATTTAAAAATATATAATTTAAATTAAATAAGACATATTTAAAGAATAA
1 AAAATTTAAAAATATATAATTTAAATTAAA-AAGACATATTTAAAGAATAA
9545312 TAAATTATTT
Statistics
Matches: 103, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
68 20 0.19
69 10 0.10
70 10 0.10
71 32 0.31
72 11 0.11
73 6 0.06
74 14 0.14
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (68 bp):
AAAATTTAAAAATATATAATTTAAATTAAAAAGACATATTTAAAGAATAAATCAATTTTAAAATA
TAT
Found at i:9545241 original size:53 final size:54
Alignment explanation
Indices: 9545157--9545285 Score: 124
Period size: 53 Copynumber: 2.4 Consensus size: 54
9545147 AAAAAGACAT
* * * *
9545157 ATTTAAAGAATAAATCAATTCAAAG-A-AATAAAATAAATTTTAAA-AATATAATTTA
1 ATTTAAA-AATACAT-AATTTAAAGAATAAT-AAATAAATTTAAAATAATA-AATTAA
* *
9545212 A-TTAAGAATACAT-ATTTAAAGAATAATAAATCAATTTAAAATAATAAATTAA
1 ATTTAAAAATACATAATTTAAAGAATAATAAATAAATTTAAAATAATAAATTAA
*
9545264 ATTTAAAAATATATAATTTAAA
1 ATTTAAAAATACATAATTTAAA
9545286 TTAAATAAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
51 7 0.11
52 19 0.31
53 23 0.38
54 11 0.18
55 1 0.02
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (54 bp):
ATTTAAAAATACATAATTTAAAGAATAATAAATAAATTTAAAATAATAAATTAA
Found at i:9545284 original size:21 final size:19
Alignment explanation
Indices: 9545233--9545287 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
9545223 ATATTTAAAG
*
9545233 AATAATAAA-TCAATTTAA
1 AATAATAAATTAAATTTAA
9545251 AATAATAAATTAAATTTAAA
1 AATAATAAATTAAATTT-AA
*
9545271 AATATATAATTTAAATT
1 AATA-ATAAATTAAATT
9545288 AAATAAGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 9 0.28
19 6 0.19
20 6 0.19
21 11 0.34
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAATAAATTAAATTTAA
Found at i:9545323 original size:20 final size:19
Alignment explanation
Indices: 9545225--9545342 Score: 84
Period size: 20 Copynumber: 6.2 Consensus size: 19
9545215 AAGAATACAT
*
9545225 ATTTAAAGAATAATAAATCA
1 ATTTAAA-AATAATAAATTA
9545245 ATTT-AAAATAATAAATTAA
1 ATTTAAAAATAATAAATT-A
*
9545264 ATTTAAAAATATATAATTTA
1 ATTTAAAAATA-ATAAATTA
* * *
9545284 AATT--AAATAAGACA-T-
1 ATTTAAAAATAATAAATTA
9545299 ATTTAAAGAATAATAAATTA
1 ATTTAAA-AATAATAAATTA
* **
9545319 TTTTAAAAGCAATAAATTTA
1 ATTTAAAAATAATAAA-TTA
9545339 ATTT
1 ATTT
9545343 TTTTTAAAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
15 3 0.04
16 1 0.01
17 3 0.04
18 22 0.29
19 15 0.20
20 26 0.34
21 6 0.08
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (19 bp):
ATTTAAAAATAATAAATTA
Found at i:9545355 original size:23 final size:24
Alignment explanation
Indices: 9545319--9545364 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
9545309 TAATAAATTA
*
9545319 TTTTAAAAGCAATAAATTTAATTTT
1 TTTTAAAA-CAATAAAATTAATTTT
9545344 TTTTAAAA-AATAAAATTAATT
1 TTTTAAAACAATAAAATTAATT
9545365 GAAAGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTTAAAACAATAAAATTAATTTT
Found at i:9548476 original size:23 final size:22
Alignment explanation
Indices: 9548412--9548485 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 22
9548402 TTCGCACCTC
* * *
9548412 GTGTGCCTACTGATTTACGCTAT
1 GTGTGCCTACTGA-TTGCACTGT
**
9548435 GTACGCCTACTGATTGCACTGT
1 GTGTGCCTACTGATTGCACTGT
9548457 GTGTGCCTACTGGATTGCACTGT
1 GTGTGCCTACT-GATTGCACTGT
9548480 GTGTGC
1 GTGTGC
9548486 TTATTGTTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.35
23 28 0.65
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTGT
Found at i:9549551 original size:22 final size:21
Alignment explanation
Indices: 9549504--9549551 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
9549494 GATTTTCATA
9549504 ATTAACTTAATTAATCATATT
1 ATTAACTTAATTAATCATATT
* * * *
9549525 TTTAACCTTGATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
9549547 ATTAA
1 ATTAA
9549552 TCAATATTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:9556555 original size:26 final size:27
Alignment explanation
Indices: 9556509--9556561 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
9556499 AAAATATTCC
*
9556509 TTTTTTATTTTATAACTATTTT-TAAT
1 TTTTTTATTTTATAACGATTTTATAAT
9556535 TTTTTTATTTTTATAA-GATTTTATAAT
1 TTTTTTA-TTTTATAACGATTTTATAAT
9556562 ATATATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTTTATTTTATAACGATTTTATAAT
Found at i:9562789 original size:250 final size:250
Alignment explanation
Indices: 9562348--9562849 Score: 995
Period size: 250 Copynumber: 2.0 Consensus size: 250
9562338 AATATATATG
9562348 TATGTCATGAAAATTGAATCATCTCTTACCTTTATTCTTGAATTTCCAAATTCTAATTCAATCCC
1 TATGTCATGAAAATTGAATCATCTCTTACCTTTATTCTTGAATTTCCAAATTCTAATTCAATCCC
9562413 TATTCACTTTAACACTTCAAAGTGGACTTTATAAAGAAATTAAGGTGTCTACTAACTCCCCTATA
66 TATTCACTTTAACACTTCAAAGTGGACTTTATAAAGAAATTAAGGTGTCTACTAACTCCCCTATA
9562478 TGCCTTTCTTAAGGAAATTAAGGAAATTTCAAAGAAAATGGAGGATTTTGAAGCTTGGAGGGCTT
131 TGCCTTTCTTAAGGAAATTAAGGAAATTTCAAAGAAAATGGAGGATTTTGAAGCTTGGAGGGCTT
9562543 AACAATGGTGAAGGGACTCAATTGGAATAAAAATAAAAGTTGGAAATGGGGAATA
196 AACAATGGTGAAGGGACTCAATTGGAATAAAAATAAAAGTTGGAAATGGGGAATA
*
9562598 TATGTCATGAAAATTGAATCATCTCTTACCTTTATTCTTGAATTTCCAAATTCTAATTCAATCCG
1 TATGTCATGAAAATTGAATCATCTCTTACCTTTATTCTTGAATTTCCAAATTCTAATTCAATCCC
9562663 TATTCACTTTAACACTTCAAAGTGGACTTTATAAAGAAATTAAGGTGTCTACTAACTCCCCTATA
66 TATTCACTTTAACACTTCAAAGTGGACTTTATAAAGAAATTAAGGTGTCTACTAACTCCCCTATA
9562728 TGCCTTTCTTAAGGAAATTAAGGAAATTTCAAAGAAAATGGAGGATTTTGAAGCTTGGAGGGCTT
131 TGCCTTTCTTAAGGAAATTAAGGAAATTTCAAAGAAAATGGAGGATTTTGAAGCTTGGAGGGCTT
9562793 AACAATGGTGAAGGGACTCAATTGGAATAAAAATAAAAGTTGGAAATGGGGAATA
196 AACAATGGTGAAGGGACTCAATTGGAATAAAAATAAAAGTTGGAAATGGGGAATA
9562848 TA
1 TA
9562850 GGCATGGACA
Statistics
Matches: 251, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
250 251 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (250 bp):
TATGTCATGAAAATTGAATCATCTCTTACCTTTATTCTTGAATTTCCAAATTCTAATTCAATCCC
TATTCACTTTAACACTTCAAAGTGGACTTTATAAAGAAATTAAGGTGTCTACTAACTCCCCTATA
TGCCTTTCTTAAGGAAATTAAGGAAATTTCAAAGAAAATGGAGGATTTTGAAGCTTGGAGGGCTT
AACAATGGTGAAGGGACTCAATTGGAATAAAAATAAAAGTTGGAAATGGGGAATA
Found at i:9583580 original size:33 final size:33
Alignment explanation
Indices: 9583538--9583606 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
9583528 TTGAGGTGAG
9583538 AAGGGTATGAACAATTATCTTTAATCATCTGGA
1 AAGGGTATGAACAATTATCTTTAATCATCTGGA
9583571 AAGGGTATGAACAATTATCTTTAATCATCTGGA
1 AAGGGTATGAACAATTATCTTTAATCATCTGGA
9583604 AAG
1 AAG
9583607 CTGACGGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.32
Consensus pattern (33 bp):
AAGGGTATGAACAATTATCTTTAATCATCTGGA
Found at i:9585971 original size:39 final size:39
Alignment explanation
Indices: 9585928--9586003 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
9585918 AGCTATGGAT
* *
9585928 TAAGTGTACAAGGTTGAAAGTA-TCGGTTCAAGGACCCAG
1 TAAGTGTACAAGGTGGAAAGTACT-GCTTCAAGGACCCAG
*
9585967 TAAGTGTATAAGGTGGAAAGTACTGCTTCAAGGACCC
1 TAAGTGTACAAGGTGGAAAGTACTGCTTCAAGGACCC
9586004 CTAGTAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.24
Consensus pattern (39 bp):
TAAGTGTACAAGGTGGAAAGTACTGCTTCAAGGACCCAG
Found at i:9602704 original size:28 final size:28
Alignment explanation
Indices: 9602660--9602715 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
9602650 TTTATTTAAT
*
9602660 TTTTTAAAAATTTAAAA-AATATAAAATA
1 TTTTTAAAAATTAAAAATAAT-TAAAATA
*
9602688 TTTTTAAACATTAAAAATAATTAAAATA
1 TTTTTAAAAATTAAAAATAATTAAAATA
9602716 ATATATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
TTTTTAAAAATTAAAAATAATTAAAATA
Found at i:9609879 original size:18 final size:18
Alignment explanation
Indices: 9609839--9609890 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
9609829 TTTTTAGTTG
*
9609839 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
9609857 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
9609875 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
9609891 CTCATCCCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:9616545 original size:30 final size:30
Alignment explanation
Indices: 9616495--9616551 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
9616485 AGAAAATCAT
*
9616495 AAAATATATAAGTGTAAATTCTAAAAAAAAC
1 AAAATATATAAGTGAAAATTC-AAAAAAAAC
*
9616526 AAAATA-ATATGTGAAAATTCAAAAAA
1 AAAATATATAAGTGAAAATTCAAAAAA
9616552 TATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.25
30 12 0.50
31 6 0.25
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.25
Consensus pattern (30 bp):
AAAATATATAAGTGAAAATTCAAAAAAAAC
Found at i:9616704 original size:29 final size:27
Alignment explanation
Indices: 9616645--9616704 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 27
9616635 GCAACCCCCT
*
9616645 AAAATATATTAAAACTATTAAAATATC
1 AAAATATATTAAAACTATTAAAAAATC
*
9616672 AAAATATTATATAAAAC-ATTCAAAAAATG
1 AAAATA-TAT-TAAAACTATT-AAAAAATC
9616701 AAAA
1 AAAA
9616705 CTTTAGTCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.21
28 6 0.21
29 16 0.57
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAATATATTAAAACTATTAAAAAATC
Found at i:9617889 original size:29 final size:28
Alignment explanation
Indices: 9617825--9617891 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 28
9617815 TTAAAAAATT
9617825 AAATTAAATCAGATAAATAAAAAATAAA
1 AAATTAAATCAGATAAATAAAAAATAAA
*
9617853 AAATTTAAAT-ATGA-AAATGAAAAATAAA
1 AAA-TTAAATCA-GATAAATAAAAAATAAA
9617881 TATAATTAAAT
1 -A-AATTAAAT
9617892 TATGTACTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 17 0.50
29 15 0.44
30 2 0.06
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.27
Consensus pattern (28 bp):
AAATTAAATCAGATAAATAAAAAATAAA
Found at i:9622253 original size:11 final size:12
Alignment explanation
Indices: 9622201--9622259 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
9622191 TATTTTTAAT
*
9622201 TTTTTAGAACAC
1 TTTTTAAAACAC
*
9622213 TTTTTAAAATTAC
1 TTTTTAAAA-CAC
*
9622226 TTTTTTACAACAC
1 -TTTTTAAAACAC
9622239 TTTTTAAAACA-
1 TTTTTAAAACAC
9622250 TTTTTCAAAA
1 TTTTT-AAAA
9622260 GAATGCTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 5 0.13
12 22 0.56
13 4 0.10
14 8 0.21
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (12 bp):
TTTTTAAAACAC
Found at i:9627653 original size:174 final size:174
Alignment explanation
Indices: 9627363--9627713 Score: 675
Period size: 174 Copynumber: 2.0 Consensus size: 174
9627353 CAGGAAAGAA
9627363 GAAGCTCACAACCGACACCCTGGGACTGATCCGTCCTGCCAGCACCCTGTGCCCCACGCTTTTGA
1 GAAGCTCACAACCGACACCCTGGGACTGATCCGTCCTGCCAGCACCCTGTGCCCCACGCTTTTGA
9627428 ATTTGCCATTGCTGATCAGCTTCAATCACAGAAAATGGTCATAGTTAACTAAGTAATGCATACAG
66 ATTTGCCATTGCTGATCAGCTTCAATCACAGAAAATGGTCATAGTTAACTAAGTAATGCATACAG
9627493 TAACACATCATCAATGTTTTGAACTTTATATTTGTTTTATTAAT
131 TAACACATCATCAATGTTTTGAACTTTATATTTGTTTTATTAAT
* *
9627537 GAAGCTCACAACCGACACCTTGGGACTGATCCGTCCTGCCAGCACCCTGTGCTCCACGCTTTTGA
1 GAAGCTCACAACCGACACCCTGGGACTGATCCGTCCTGCCAGCACCCTGTGCCCCACGCTTTTGA
9627602 ATTTGCCATTGCTGATCAGCTTCAATCACAGAAAATGGTCATAGTTAACTAAGTAATGCATACAG
66 ATTTGCCATTGCTGATCAGCTTCAATCACAGAAAATGGTCATAGTTAACTAAGTAATGCATACAG
*
9627667 TAACATATCATCAATGTTTTGAACTTTATATTTGTTTTATTAAT
131 TAACACATCATCAATGTTTTGAACTTTATATTTGTTTTATTAAT
9627711 GAA
1 GAA
9627714 TTTACACTTG
Statistics
Matches: 174, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (174 bp):
GAAGCTCACAACCGACACCCTGGGACTGATCCGTCCTGCCAGCACCCTGTGCCCCACGCTTTTGA
ATTTGCCATTGCTGATCAGCTTCAATCACAGAAAATGGTCATAGTTAACTAAGTAATGCATACAG
TAACACATCATCAATGTTTTGAACTTTATATTTGTTTTATTAAT
Found at i:9636850 original size:22 final size:21
Alignment explanation
Indices: 9636815--9636862 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
9636805 CGCCCCACAC
9636815 TCATATATTCAAATATATATA
1 TCATATATTCAAATATATATA
*
9636836 TCATATTTGTCAAATATATATA
1 TCATATAT-TCAAATATATATA
9636858 T-ATAT
1 TCATAT
9636863 CATAACAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (21 bp):
TCATATATTCAAATATATATA
Found at i:9639060 original size:5 final size:5
Alignment explanation
Indices: 9639046--9639086 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
9639036 ATTTATTTGT
*
9639046 AAAA- AAAAG AAAAG AAAAG AAAAG AAAAG AAATG -AAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
9639087 TAAAAAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
4 7 0.21
5 26 0.79
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:9644346 original size:6 final size:6
Alignment explanation
Indices: 9644336--9644370 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
9644326 TTCACAGACG
* *
9644336 AGGAGG AGGAGG AGGAGC AGGAGC AGGAGC AGGAG
1 AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAG
9644371 AAGAAGAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.57, T:0.00
Consensus pattern (6 bp):
AGGAGC
Found at i:9656121 original size:37 final size:37
Alignment explanation
Indices: 9656078--9656156 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
9656068 ATGATGATGA
9656078 GAAAAAGTAAACAAAACACGATACGAATAATATATGT
1 GAAAAAGTAAACAAAACACGATACGAATAATATATGT
9656115 GAAAAAGTAAACAAAACACGATACGAATAATATATGT
1 GAAAAAGTAAACAAAACACGATACGAATAATATATGT
*
9656152 CAAAA
1 GAAAA
9656157 TCTATATGGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (37 bp):
GAAAAAGTAAACAAAACACGATACGAATAATATATGT
Found at i:9657007 original size:24 final size:24
Alignment explanation
Indices: 9656975--9657022 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
9656965 GTAAGCAACA
9656975 AAACTTGGGCATTTTCCAATCTTT
1 AAACTTGGGCATTTTCCAATCTTT
9656999 AAACTTGGGCATTTTCCAATCTTT
1 AAACTTGGGCATTTTCCAATCTTT
9657023 TTCCAATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (24 bp):
AAACTTGGGCATTTTCCAATCTTT
Found at i:9661277 original size:110 final size:110
Alignment explanation
Indices: 9661079--9661279 Score: 294
Period size: 110 Copynumber: 1.8 Consensus size: 110
9661069 AGCTAATAAT
* * ** * * *
9661079 TCCTATTAACAAGCTAACAATCTCCCAAGGACTTAGTCATCTTAATGATAAAAAAGACTTTGCAG
1 TCCTACTAACAAACTAACAATCTCCCAACAACTTAATCATCTTAATGACAAAAAAGACTTTGCAA
** *
9661144 CCCTTGAGGCACTACCAAAGTTAGCTAACAAACTTATCTTCCAAC
66 CCCTTGAAACACTAACAAAGTTAGCTAACAAACTTATCTTCCAAC
*
9661189 TCCTACTAACAAACTAACAATCTCCCTACAACTTAATCATCTTAATGACAAAAAAGACTTTGCAA
1 TCCTACTAACAAACTAACAATCTCCCAACAACTTAATCATCTTAATGACAAAAAAGACTTTGCAA
*
9661254 CCCTTGAAACACTAACAAGGTTAGCT
66 CCCTTGAAACACTAACAAAGTTAGCT
9661280 TGCATAAATA
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
110 79 1.00
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (110 bp):
TCCTACTAACAAACTAACAATCTCCCAACAACTTAATCATCTTAATGACAAAAAAGACTTTGCAA
CCCTTGAAACACTAACAAAGTTAGCTAACAAACTTATCTTCCAAC
Found at i:9663483 original size:23 final size:23
Alignment explanation
Indices: 9663334--9663471 Score: 138
Period size: 23 Copynumber: 5.9 Consensus size: 23
9663324 CGAAGTACTT
9663334 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
9663360 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * *
9663382 ATCAGTAAGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
9663404 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
9663428 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
9663451 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
9663472 TGAACGGTAA
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
22 20 0.21
23 53 0.56
24 3 0.03
26 14 0.15
27 5 0.05
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:9666345 original size:16 final size:16
Alignment explanation
Indices: 9666306--9666348 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
9666296 CTTGGTTTAA
* *
9666306 GGTTTGGGTTTAATGG
1 GGTTTGGGTTAAAAGG
*
9666322 GTTATTGGGTTAAAAGG
1 GGT-TTGGGTTAAAAGG
9666339 GGTTTGGGTT
1 GGTTTGGGTT
9666349 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (16 bp):
GGTTTGGGTTAAAAGG
Found at i:9667203 original size:22 final size:22
Alignment explanation
Indices: 9667167--9667232 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
9667157 TATCACTTTA
* *
9667167 GCATAAATTCGCATATCACATG
1 GCATAAGTTCACATATCACATG
* * *
9667189 GCATAGGTTCACATATCACTTA
1 GCATAAGTTCACATATCACATG
9667211 GCATAAGTTCACATATCACATG
1 GCATAAGTTCACATATCACATG
9667233 ATAGTCACAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (22 bp):
GCATAAGTTCACATATCACATG
Found at i:9667291 original size:32 final size:33
Alignment explanation
Indices: 9667211--9667291 Score: 78
Period size: 32 Copynumber: 2.5 Consensus size: 33
9667201 ATATCACTTA
* *
9667211 GCATAAGTTCACATATCACATGATAGTCACACT
1 GCATAAGTTCACACATCACATGATACTCACACT
* * *
9667244 GTATAGGGT-AGCACATCACAT-ATACTCACAC-
1 GCATAAGTTCA-CACATCACATGATACTCACACT
9667275 GACATAAGTTCACACAT
1 G-CATAAGTTCACACAT
9667292 AGGTAGGGCA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
31 1 0.03
32 20 0.54
33 16 0.43
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (33 bp):
GCATAAGTTCACACATCACATGATACTCACACT
Found at i:9667488 original size:21 final size:21
Alignment explanation
Indices: 9667462--9667520 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
9667452 TCGTATCAAG
9667462 GTATGGTGATAGGGTTCGCAT
1 GTATGGTGATAGGGTTCGCAT
* *
9667483 GTATGGTGATAGGGTCCGTAT
1 GTATGGTGATAGGGTTCGCAT
*
9667504 GTAAGGTGATAGGGTTC
1 GTATGGTGATAGGGTTC
9667521 ACATACTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.08, G:0.39, T:0.32
Consensus pattern (21 bp):
GTATGGTGATAGGGTTCGCAT
Found at i:9667539 original size:42 final size:42
Alignment explanation
Indices: 9667466--9667565 Score: 96
Period size: 42 Copynumber: 2.4 Consensus size: 42
9667456 ATCAAGGTAT
* * * *
9667466 GGTGATAGGGTTCGCATGTATGGTGATAGGGTCCGT-ATGTAA
1 GGTGATAGGGTTCACATCTATGATGAGAGGGTCC-TCATGTAA
*
9667508 GGTGATAGGGTTCACATACTA-GATGAGAGGGTTCTCATGTAA
1 GGTGATAGGGTTCACAT-CTATGATGAGAGGGTCCTCATGTAA
** *
9667550 CATGATAAGGTTCACA
1 GGTGATAGGGTTCACA
9667566 AGTTAGGTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.02
42 45 0.94
43 2 0.04
ACGTcount: A:0.27, C:0.12, G:0.32, T:0.29
Consensus pattern (42 bp):
GGTGATAGGGTTCACATCTATGATGAGAGGGTCCTCATGTAA
Found at i:9689397 original size:2 final size:2
Alignment explanation
Indices: 9689390--9689432 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
9689380 TGGTAGAATT
9689390 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9689432 T
1 T
9689433 AACTTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:9694140 original size:21 final size:22
Alignment explanation
Indices: 9694102--9694150 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
9694092 ACTCCACCAA
* *
9694102 AAAAAATAAATTTAAAAT-TTT
1 AAAAAATAAATATAAAATAATT
9694123 AAAAAATAAATA-ATAAATAATT
1 AAAAAATAAATATA-AAATAATT
9694145 AAAAAA
1 AAAAAA
9694151 ACTAACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 15 0.62
22 8 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAATAAATATAAAATAATT
Found at i:9697038 original size:18 final size:18
Alignment explanation
Indices: 9696998--9697038 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
9696988 TGTTATATTT
9696998 TATATTATTATATAATAA
1 TATATTATTATATAATAA
*
9697016 AATATTATTAT-TAATTAA
1 TATATTATTATATAA-TAA
9697034 TATAT
1 TATAT
9697039 CCTTTGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATTATTATATAATAA
Found at i:9704160 original size:31 final size:31
Alignment explanation
Indices: 9704102--9704160 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
9704092 GCACCAACTT
* * * *
9704102 AAAAAAATGTCAAATTTATGTATTAAATTAA
1 AAAAAAATATCAAATTCAAGTACTAAATTAA
*
9704133 AAAAAAATATCAAATTCAAGTGCTAAAT
1 AAAAAAATATCAAATTCAAGTACTAAAT
9704161 ATTATATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (31 bp):
AAAAAAATATCAAATTCAAGTACTAAATTAA
Found at i:9705413 original size:29 final size:30
Alignment explanation
Indices: 9705378--9705448 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
9705368 ATTAGTAAAG
* *
9705378 ATAAAATTATACTTTGATCTCTT-AAAATA
1 ATAAAATTATAATTTAATCTCTTAAAAATA
* * *
9705407 ATAAAATTTTAATTTAATCTTTTAAAAATT
1 ATAAAATTATAATTTAATCTCTTAAAAATA
*
9705437 ATAAAAATATAA
1 ATAAAATTATAA
9705449 ATTATTTAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (30 bp):
ATAAAATTATAATTTAATCTCTTAAAAATA
Found at i:9706180 original size:54 final size:53
Alignment explanation
Indices: 9706063--9706199 Score: 166
Period size: 54 Copynumber: 2.6 Consensus size: 53
9706053 TCTTTTGCTT
* * * * * *
9706063 TTGAGAGTTAGGATTAGGGATTTAGTTGAGAGTTAGATTAGGCTCCCTTATGG
1 TTGAGAGTTAGGGTTAGAGATTTAGATGGGAGTTAGATTAAGCTCCCTTATAG
* * * *
9706116 TTGATAGTTAGGGTTAGAGATTTAGCTGGGAGTTAAGGTTAAGCTCCTTTATAG
1 TTGAGAGTTAGGGTTAGAGATTTAGATGGGAGTT-AGATTAAGCTCCCTTATAG
*
9706170 TTGAGAGTTAGTGTTAGAGATTTAGATGGG
1 TTGAGAGTTAGGGTTAGAGATTTAGATGGG
9706200 GTTTGAGAGT
Statistics
Matches: 71, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
53 29 0.41
54 42 0.59
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.36
Consensus pattern (53 bp):
TTGAGAGTTAGGGTTAGAGATTTAGATGGGAGTTAGATTAAGCTCCCTTATAG
Found at i:9706482 original size:31 final size:31
Alignment explanation
Indices: 9706444--9706509 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
9706434 AATTAACTAA
*
9706444 TTTTTTAAAATAAAAAATAATTTTTATACTT
1 TTTTTTAAAATAAAAAATAATTTTTATAATT
* ** *
9706475 TTTTTTAAATTTTAAAATTATTTTTATAATT
1 TTTTTTAAAATAAAAAATAATTTTTATAATT
9706506 TTTT
1 TTTT
9706510 GAATTTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTTTAAAATAAAAAATAATTTTTATAATT
Found at i:9706782 original size:38 final size:36
Alignment explanation
Indices: 9706710--9706789 Score: 97
Period size: 38 Copynumber: 2.2 Consensus size: 36
9706700 TCACTTAATT
* * *
9706710 TTTAAAAAAAATATAATTTTGTTTTATTCCTTAAGA
1 TTTAAAAAAAATATAATTTGGTTTAATTCATTAAGA
* *
9706746 TTTATAAAAAATATATATTTGGTTCTAATTTATTAAGA
1 TTTAAAAAAAATATA-ATTTGGTT-TAATTCATTAAGA
9706784 TTTAAA
1 TTTAAA
9706790 TATGTCAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
36 14 0.39
37 7 0.19
38 15 0.42
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (36 bp):
TTTAAAAAAAATATAATTTGGTTTAATTCATTAAGA
Found at i:9725127 original size:21 final size:21
Alignment explanation
Indices: 9725101--9725151 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
9725091 CATACCAGAT
*
9725101 AATTAAAATGA-TTAAATTAAA
1 AATTAAAATGAGTT-AATAAAA
*
9725122 AATTAATATGAGTTAATAAAA
1 AATTAAAATGAGTTAATAAAA
*
9725143 AATCAAAAT
1 AATTAAAAT
9725152 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (21 bp):
AATTAAAATGAGTTAATAAAA
Found at i:9733247 original size:200 final size:201
Alignment explanation
Indices: 9732857--9733699 Score: 1297
Period size: 200 Copynumber: 4.2 Consensus size: 201
9732847 TGACCTGGCC
* * * * *
9732857 TTCTTCTCTGTGTCTCATCAAGAGGATGGCCGCAGTC-ATCTGTTTTAATTCGCTTCTCTGGATC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCA-TCGCT-TGTTTTAATTCGCTTCTCTGGATC
* * *
9732921 TTCTCAGGAAGACAAATTTGGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGC
64 TCCTCAGGAAGACGAATTTGGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTTTATTGC
** *
9732986 TTCGACCTGCTTCTCAGTACCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCGTTGAGCGTTG
129 TTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCATTGAGCGTTG
9733051 AGTTGGTA
194 AGTTGGTA
* * *
9733059 TTCTTCTCTGTATCTCATCAGGAAGATGACCGTATCGCTTGTTTCAATTCGCTTCTCTAGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTTAATTCGCTTCTCTGGATCTC
*
9733124 CTCAGGAAGACGAATTT-GGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTTTATTGTTT
66 CTCAGGAAGACGAATTTGGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTTTATTGCTT
* *
9733188 CGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGTTCGGAGATTTGCTCGCATTGAGCGTTTGA
131 CGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCATTGAGCG-TTGA
9733253 GTTGGTA
195 GTTGGTA
* * * *
9733260 CTCTTCTCTATATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTTGCTTCTCTGGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTTAATTCGCTTCTCTGGATCTC
* * *
9733325 CTCAAGAAGACGAATTTGGGTCCACTTCTCTGTGTCTCATCTGGAAGCTAACCATTTTATTGTTT
66 CTCAGGAAGACGAATTTGGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTTTATTGCTT
*
9733390 CGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGTTCGAAGATTTGCTCGCATTGAGCGTTGAG
131 CGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCATTGAGCGTTGAG
9733455 TTGGTA
196 TTGGTA
* * *
9733461 TTCCTCTCTGTATCTCATCAGGAAGATGACCGCTTCGCTTGTTTTAATTCGCTTCTATGGATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTTAATTCGCTTCTCTGGATCTC
* * * *
9733526 CTTAGGAAGACGAATTT-GGTCCTCTTCTCTGTGTCTCATCATGAAGCTAGCCATTTTATTGCTT
66 CTCAGGAAGACGAATTTGGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTTTATTGCTT
*
9733590 CGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCATTGAGCGTCGAG
131 CGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCATTGAGCGTTGAG
9733655 TTGGTA
196 TTGGTA
*
9733661 TTCTTCTCTGTAT-T-A--A-GAAGATGACCGCCTCGCTTGTTT
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCGCTTGTTT
9733700 GTTGAACTAC
Statistics
Matches: 592, Mismatches: 46, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
195 22 0.04
196 1 0.00
198 1 0.00
199 1 0.00
200 223 0.38
201 211 0.36
202 133 0.22
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (201 bp):
TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTTAATTCGCTTCTCTGGATCTC
CTCAGGAAGACGAATTTGGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCATTTTATTGCTT
CGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCATTGAGCGTTGAG
TTGGTA
Found at i:9733641 original size:402 final size:396
Alignment explanation
Indices: 9732897--9733699 Score: 1311
Period size: 402 Copynumber: 2.0 Consensus size: 396
9732887 CGCAGTCATC
* *
9732897 TGTTTTAATTCGCTTCTCTGGATCTTCTCAGGAAGACAAATTTGGGTCCACTTCTCTGTGTCTCA
1 TGTTTTAATTCGCTTCTCTGGATCTCCTCAAGAAGACAAATTTGGGTCCACTTCTCTGTGTCTCA
* *
9732962 TCAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGCTGGGTTCG
66 TCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAAGAAGCTGGGTTCG
* *
9733027 AAGATTTGCTCGCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGT
131 AAGATTTGCTCGCATTGAGCGTTGAGTTGGTATTCCTCTCTGTATCTCATCAGGAAGATGACCGT
*
9733092 ATCGCTTGTTTCAATTCGCTTCTCTAGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTG
196 ATCGCTTGTTTCAATTCGCTTCTATAGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTG
* *
9733157 TCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGG
261 TCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGG
* *
9733222 GTTCGGAGATTTGCTCGCATTGAGCGTTTGAGTTGGTACTCTTCTCTATATCTCATCAGGAAGAT
326 GTTCGAAGATTTGCTCGCATTGAGCG-TCGAGTTGGTACTCTTCTCTATAT-T-A--A-GAAGAT
9733287 GACCGCCTCGCT
385 GACCGCCTCGCT
* *
9733299 TGTTTTAATTTGCTTCTCTGGATCTCCTCAAGAAGACGAATTTGGGTCCACTTCTCTGTGTCTCA
1 TGTTTTAATTCGCTTCTCTGGATCTCCTCAAGAAGACAAATTTGGGTCCACTTCTCTGTGTCTCA
* * **
9733364 TCTGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGTTCG
66 TCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAAGAAGCTGGGTTCG
9733429 AAGATTTGCTCGCATTGAGCGTTGAGTTGGTATTCCTCTCTGTATCTCATCAGGAAGATGACCGC
131 AAGATTTGCTCGCATTGAGCGTTGAGTTGGTATTCCTCTCTGTATCTCATCAGGAAGATGACCG-
* * * *
9733494 T-TCGCTTGTTTTAATTCGCTTCTATGGATCTCCTTAGGAAGACGAATTTGGTCCTCTTCTCTGT
195 TATCGCTTGTTTCAATTCGCTTCTATAGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGT
* *
9733558 GTCTCATCATGAAGCTAGCCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTG
260 GTCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTG
* *
9733623 GGTTCGAAGATTTGCTCGCATTGAGCGTCGAGTTGGTATTCTTCTCTGTATTAAGAAGATGACCG
325 GGTTCGAAGATTTGCTCGCATTGAGCGTCGAGTTGGTACTCTTCTCTATATTAAGAAGATGACCG
9733688 CCTCGCT
390 CCTCGCT
9733695 TGTTT
1 TGTTT
9733700 GTTGAACTAC
Statistics
Matches: 375, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
396 23 0.06
397 1 0.00
399 1 0.00
400 1 0.00
401 21 0.06
402 327 0.87
403 1 0.00
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (396 bp):
TGTTTTAATTCGCTTCTCTGGATCTCCTCAAGAAGACAAATTTGGGTCCACTTCTCTGTGTCTCA
TCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAAGAAGCTGGGTTCG
AAGATTTGCTCGCATTGAGCGTTGAGTTGGTATTCCTCTCTGTATCTCATCAGGAAGATGACCGT
ATCGCTTGTTTCAATTCGCTTCTATAGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTG
TCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGG
GTTCGAAGATTTGCTCGCATTGAGCGTCGAGTTGGTACTCTTCTCTATATTAAGAAGATGACCGC
CTCGCT
Found at i:9745796 original size:30 final size:31
Alignment explanation
Indices: 9745757--9745841 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 31
9745747 TGACGTTCGG
9745757 GGTAAAAATGTAATTTTTGGTAAAATT-A-A
1 GGTAAAAATGTAATTTTTGGTAAAATTCAGA
* * *
9745786 GGTCAAAAATGGAA-TTTAGG-AAAGTTCAGA
1 GGT-AAAAATGTAATTTTTGGTAAAATTCAGA
**
9745816 GGTAAAACGGTAATTTTTGGTAAAAT
1 GGTAAAAATGTAATTTTTGGTAAAAT
9745842 GGGGCTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
28 5 0.12
29 16 0.37
30 18 0.42
31 4 0.09
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (31 bp):
GGTAAAAATGTAATTTTTGGTAAAATTCAGA
Found at i:9745829 original size:59 final size:59
Alignment explanation
Indices: 9745761--9746255 Score: 467
Period size: 59 Copynumber: 8.5 Consensus size: 59
9745751 GTTCGGGGTA
*** *
9745761 AAAAT-GTAATTTTTGGTAAAATTAAGGTCAAAAATGGAATTTAGGAAAGTTCAGAGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCAGAGGT
* * * * *
9745819 AAAACGGTAATTTTTGGTAAAAT-GGGGCTAAAAAATAGG-GTTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGG-TCAAAAAT-GGAATTTTGGAAAGTTCAGAGGT
* * * * * *
9745878 AAAATGGTAATTTTTGATGAAATCGAGGT-TAAAATGGGATTTTGGAAAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCAGAGGT
** * *
9745936 AAAATGGTAATTTTTGTGTAAAATCAAGGTTAAATTAA--G-ATTTTGGAAAGTT-AAAGGGT
1 AAAATGGTAATTTTTG-GTAAAATCGGGGTCAAA--AATGGAATTTTGGAAAGTTCAGA-GGT
* * * *
9745995 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCAGAGGT
* * *
9746053 AAAATGGTAA-TTTGGGTAAAATTGGGGTC-AAAATGGAATTTTGGAAGGTTC-GAGGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCAGA-GGT
* * * *
9746110 AAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAGGTTCGGAGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCAGAGGT
* * * * * ** *
9746169 GAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATTGG-ATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCAGAGGT
** *
9746227 AAAATGGTAATTTTTAATGAAATCGGGGT
1 AAAATGGTAATTTTTGGTAAAATCGGGGT
9746256 TAATACGAGA
Statistics
Matches: 372, Mismatches: 47, Indels: 36
0.82 0.10 0.08
Matches are distributed among these distances:
55 2 0.01
56 1 0.00
57 51 0.14
58 151 0.41
59 155 0.42
60 10 0.03
62 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCAGAGGT
Found at i:9745926 original size:117 final size:116
Alignment explanation
Indices: 9745755--9746258 Score: 552
Period size: 117 Copynumber: 4.3 Consensus size: 116
9745745 TTTGACGTTC
* *** * *
9745755 GGGGTAAAAAT-GTAATTTTTGGTAAAATTAAGGTCAAAAATGGAATTTAGGAAAGTTCAGAGGT
1 GGGGT-AAAATGGTAATTTTTGGTGAAATCGGGGT-TAAAATGGAATTTTGGAAAGTTCAGAGGT
* * * *
9745819 AAAACGGTAATTTTTGGTAAAAT-GGGGCTAAAAAATAGGGTTTTGGAAAGTTTA
64 AAAATGGTAATTTTTGGTAAAATCAGGG-T-TAAAATAGGATTTTGGAAAGTTTA
* * * *
9745873 GGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAATGGGATTTTGGAAAGTTCAGGGGTAA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTCAGAGGTAA
* * * *
9745938 AATGGTAATTTTTGTGTAAAATCAAGGTTAAATTAAGATTTTGGAAAGTTAA
66 AATGGTAATTTTTG-GTAAAATCAGGGTTAAAATAGGATTTTGGAAAGTTTA
* * *
9745990 AGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAGTTCAGAGGTA
* ** * * *
9746054 AAATGGTAA-TTTGGGTAAAATTGGGGTCAAAAT-GGAATTTTGG-AAGGTTC
65 AAATGGTAATTTTTGGTAAAATCAGGGTTAAAATAGG-ATTTTGGAAAGTTTA
* * * *
9746104 GAGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAGGTTCGGAGGT
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGT-TAAAATGGAATTTTGGAAAGTTCAGAGGT
* * * *
9746169 GAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATTGGATTTTGGAAAGTTTG
64 AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAATAGGATTTTGGAAAGTTTA
**
9746222 GGGGTAAAATGGTAATTTTTAATGAAATCGGGGTTAA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAA
9746259 TACGAGATTT
Statistics
Matches: 327, Mismatches: 48, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
114 5 0.02
115 35 0.11
116 75 0.23
117 170 0.52
118 40 0.12
119 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (116 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTCAGAGGTAA
AATGGTAATTTTTGGTAAAATCAGGGTTAAAATAGGATTTTGGAAAGTTTA
Found at i:9745934 original size:58 final size:58
Alignment explanation
Indices: 9745751--9746273 Score: 504
Period size: 58 Copynumber: 9.0 Consensus size: 58
9745741 AATTTTTGAC
* *** * * *
9745751 GTTC-GGGGTAAAAAT-GTAATTTTTGGTAAAATTAAGGTCAAAAATGGAATTTAGGAAA
1 GTTCAGGGGT-AAAATGGTAATTTTTGGTGAAATCGGGGT-TAAAATGGGATTTTGGAAA
* * * *
9745809 GTTCAGAGGTAAAACGGTAATTTTTGGTAAAAT-GGGGCTAAAAAATAGGG-TTTTGGAAA
1 GTTCAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGG-T-TAAAAT-GGGATTTTGGAAA
* * *
9745868 GTTTAGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAATGGGATTTTGGAAA
1 GTTCAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAA
* ** * **
9745926 GTTCAGGGGTAAAATGGTAATTTTTGTGTAAAATCAAGGTTAAATTAAGATTTTGGAAA
1 GTTCAGGGGTAAAATGGTAATTTTTG-GTGAAATCGGGGTTAAAATGGGATTTTGGAAA
* * *
9745985 GTTAAAGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAA
1 GTTCAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGGATTTTGGAAA
* * * * * * *
9746043 GTTCGGGGGTAAAATGGTAA-TTTGGGTAAAATTGGGGTCAAAATGGAATTTTGGAAG
1 GTTCAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAA
* * * *
9746100 GTTC-GAGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAG
1 GTTCAG-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGT-TAAAATGGGATTTTGGAAA
* * *
9746159 GTTC-GGAGGTGAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATTGGATTTTGGAAA
1 GTTCAGG-GGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAA
** ** * * *
9746217 GTTTGGGGGTAAAATGGTAATTTTTAATGAAATCGGGGTTAATACGAGATTTTGGAA
1 GTTCAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAA
9746274 GTTTCGGGGT
Statistics
Matches: 395, Mismatches: 57, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
56 1 0.00
57 49 0.12
58 177 0.45
59 163 0.41
60 5 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (58 bp):
GTTCAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAA
Found at i:9746992 original size:14 final size:14
Alignment explanation
Indices: 9746969--9747014 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
9746959 GTTTGTCCAT
*
9746969 TTATTCCCTTTTTC
1 TTATTTCCTTTTTC
9746983 TTATTTCC-TTTTC
1 TTATTTCCTTTTTC
* *
9746996 TTTTTTCGTTTTT-
1 TTATTTCCTTTTTC
9747009 TTATTT
1 TTATTT
9747015 TTAAAAAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (14 bp):
TTATTTCCTTTTTC
Found at i:9748195 original size:17 final size:17
Alignment explanation
Indices: 9748173--9748238 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
9748163 CCCAATAAAA
*
9748173 TAAATTTAGATTTATTT
1 TAAATTTAAATTTATTT
***
9748190 TAAATTTAAATTTGCAT
1 TAAATTTAAATTTATTT
* *
9748207 AAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
9748224 TAAATTTAAAATTTA
1 TAAATTT-AAATTTA
9748239 AAATTAAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 31 0.82
18 7 0.18
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:9748197 original size:6 final size:6
Alignment explanation
Indices: 9748173--9748252 Score: 53
Period size: 6 Copynumber: 13.8 Consensus size: 6
9748163 CCCAATAAAA
* * ** *
9748173 TAAATT TAGATT T-ATTT TAAATT TAAATT TGCA-T AAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
9748219 T--ATT ATAAATT TAAAATT TAAAAT TAAA-T TAAAT
1 TAAATT -TAAATT T-AAATT TAAATT TAAATT TAAAT
9748253 GTCCATTAAC
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
4 3 0.05
5 11 0.20
6 33 0.59
7 9 0.16
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:9750199 original size:29 final size:29
Alignment explanation
Indices: 9750167--9750378 Score: 81
Period size: 29 Copynumber: 7.2 Consensus size: 29
9750157 CAGAAATTAT
9750167 ATTTTTACCCTCAAACTTTCCAAAATCTC
1 ATTTTTACCCTCAAACTTTCCAAAATCTC
*
9750196 ATTTTTAACCC-C-GA-TTTCACCAAAAAT-TGCC
1 ATTTTT-ACCCTCAAACTTT--CC-AAAATCT--C
* *
9750227 A-TTTTACCCCCAAACTTTCCAAAATCCC
1 ATTTTTACCCTCAAACTTTCCAAAATCTC
* **
9750255 ATTTTTA-ACTCCGA-TTTCACCAAAAAT-TACC
1 ATTTTTACCCTCAAACTTT--CC-AAAATCT--C
* *
9750286 ATTTTT-CCCTCGAACTTTCCAAAATCCC
1 ATTTTTACCCTCAAACTTTCCAAAATCTC
* *
9750314 ATTTTTAACCTC-GA-TTTCACTAAAAAT-TACC
1 ATTTTTACCCTCAAACTTTC-C--AAAATCT--C
* *
9750345 A-CTTTACCCTCAAACTTTCCAAAATCCC
1 ATTTTTACCCTCAAACTTTCCAAAATCTC
9750373 ATTTTT
1 ATTTTT
9750379 TAACCCCGAT
Statistics
Matches: 134, Mismatches: 20, Indels: 58
0.63 0.09 0.27
Matches are distributed among these distances:
27 10 0.07
28 17 0.13
29 43 0.32
30 36 0.27
31 18 0.13
32 10 0.07
ACGTcount: A:0.32, C:0.31, G:0.02, T:0.35
Consensus pattern (29 bp):
ATTTTTACCCTCAAACTTTCCAAAATCTC
Found at i:9750223 original size:59 final size:59
Alignment explanation
Indices: 9750169--9750591 Score: 650
Period size: 59 Copynumber: 7.2 Consensus size: 59
9750159 GAAATTATAT
* * *
9750169 TTTTACCCTCAAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAAATTGCCA
1 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
*
9750228 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACTCCGATTTCACCAAAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* * * * *
9750287 TTTTTCCCTCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACTAAAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* *
9750346 CTTTACCCTCAAACTTTCCAAAATCCCATTTTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATCCCA-TTTTTAACCCCGATTTCACCAAAAATTACCA
* * * *
9750406 TTTTACCCCCAAACTTTTCAAAATCCCA-TTTTAACCCCAATTTCACTAAAAATTAGCA
1 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* * * *
9750464 TTTTACCCCCGAATTTTCCAAAATCTCATTTTTAACCCCAATTTCACCAAAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
*
9750523 TTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
9750582 TTTTACCCCC
1 TTTTACCCCC
9750592 GAAAGTCAAA
Statistics
Matches: 329, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
58 51 0.16
59 224 0.68
60 54 0.16
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.34
Consensus pattern (59 bp):
TTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
Found at i:9750428 original size:29 final size:26
Alignment explanation
Indices: 9750396--9750591 Score: 79
Period size: 30 Copynumber: 6.7 Consensus size: 26
9750386 GATTTCACCA
9750396 AAAATTACCATTTTACCCCCAAACTTTTC
1 AAAA-TACCATTTTACCCCC-AA-TTTTC
* * *
9750425 AAAATCCCATTTTAACCCCAATTTCACTA
1 AAAATACCATTTTACCCCCAATTT---TC
*
9750454 AAAATTAGCATTTTACCCCCGAATTTTCC
1 AAAA-TACCATTTTACCCCC-AATTTT-C
* *
9750483 AAAAT-CTCATTTTTAACCCCAATTTCACC
1 AAAATAC-CA-TTTTACCCCCAATTT--TC
* *
9750512 AAAAATTACCATTTTACCCCTAAACTTTCC
1 -AAAA-TACCATTTTACCCC-CAA-TTTTC
* * * *
9750542 AAAATCCCATTTTTAACCCCGATTTCACC
1 AAAATACCA-TTTTACCCCCAATTT--TC
9750571 AAAAATTACCATTTTACCCCC
1 -AAAA-TACCATTTTACCCCC
9750592 GAAAGTCAAA
Statistics
Matches: 129, Mismatches: 18, Indels: 39
0.69 0.10 0.21
Matches are distributed among these distances:
26 3 0.02
27 5 0.04
28 27 0.21
29 37 0.29
30 39 0.30
31 14 0.11
32 4 0.03
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAATACCATTTTACCCCCAATTTTC
Found at i:9758041 original size:26 final size:24
Alignment explanation
Indices: 9758004--9758051 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
9757994 AAGTGTTGAC
9758004 AAAAAATAAATTAAATTAAAATTTT
1 AAAAAATAAATTAAA-TAAAATTTT
*
9758029 AAAACAATTAATTAAATAAAATT
1 AAAA-AATAAATTAAATAAAATT
9758052 CTATTTCCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAAAATAAATTAAATAAAATTTT
Found at i:9759979 original size:17 final size:19
Alignment explanation
Indices: 9759957--9759993 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
9759947 TAGAAAAAAT
9759957 TAAATAAAT-A-TAATTTA
1 TAAATAAATAATTAATTTA
9759974 TAAATAAATAATTAATTTA
1 TAAATAAATAATTAATTTA
9759993 T
1 T
9759994 TATATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATAAATAATTAATTTA
Found at i:9760006 original size:19 final size:18
Alignment explanation
Indices: 9759957--9760007 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
9759947 TAGAAAAAAT
9759957 TAAATAAATA-TAATTTA
1 TAAATAAATATTAATTTA
9759974 TAAATAAATAATTAATTTA
1 TAAATAAAT-ATTAATTTA
* *
9759993 TTATATTAATATTAA
1 -TAAATAAATATTAA
9760008 AAAACTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 9 0.31
18 1 0.03
19 12 0.41
20 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATAAATATTAATTTA
Found at i:9776005 original size:33 final size:33
Alignment explanation
Indices: 9775937--9776002 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
9775927 AATAAAAATA
9775937 TTAAAAATATTTATATTGTTTTTAATTTAATTT
1 TTAAAAATATTTATATTGTTTTTAATTTAATTT
*
9775970 TTAAAAATTTTTATATT-TTATTT-A-TTAATTT
1 TTAAAAATATTTATATTGTT-TTTAATTTAATTT
9776001 TT
1 TT
9776003 TTATATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 9 0.29
32 3 0.10
33 19 0.61
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (33 bp):
TTAAAAATATTTATATTGTTTTTAATTTAATTT
Found at i:9776105 original size:17 final size:17
Alignment explanation
Indices: 9776083--9776116 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9776073 TGTGTTATAA
*
9776083 ATTACATAATATAAAAC
1 ATTACAAAATATAAAAC
*
9776100 ATTACAAAATTTAAAAC
1 ATTACAAAATATAAAAC
9776117 GGATCAAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTACAAAATATAAAAC
Found at i:9791981 original size:34 final size:34
Alignment explanation
Indices: 9791938--9792008 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
9791928 TGAGGAGGGG
9791938 GAGTTTTTACAACCCAAAATTCATAGTGGGTCTA
1 GAGTTTTTACAACCCAAAATTCATAGTGGGTCTA
9791972 GAGTTTTTACAACCCAAAATTCATAGTGGGTCTA
1 GAGTTTTTACAACCCAAAATTCATAGTGGGTCTA
9792006 GAG
1 GAG
9792009 ATCTTATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (34 bp):
GAGTTTTTACAACCCAAAATTCATAGTGGGTCTA
Found at i:9792165 original size:110 final size:110
Alignment explanation
Indices: 9791972--9792176 Score: 392
Period size: 110 Copynumber: 1.9 Consensus size: 110
9791962 AGTGGGTCTA
9791972 GAGTTTTTACAACCCAAAATTCATAGTGGGTCTAGAGATCTTATAATTGGGCCTGCTACAATTGT
1 GAGTTTTTACAACCCAAAATTCATAGTGGGTCTAGAGATCTTATAATTGGGCCTGCTACAATTGT
9792037 GATCCACTGAAAGATATAGAAGCAAACTTCTGTAATGAGGAGGGG
66 GATCCACTGAAAGATATAGAAGCAAACTTCTGTAATGAGGAGGGG
*
9792082 GAGTTTTTACAACCCAAAATTCATAGTGGGTCTAGAGATCTTATAATTGGGCGTGCTACAATTGT
1 GAGTTTTTACAACCCAAAATTCATAGTGGGTCTAGAGATCTTATAATTGGGCCTGCTACAATTGT
*
9792147 GATCCACTGAAAGATATAGAAGCACACTTC
66 GATCCACTGAAAGATATAGAAGCAAACTTC
9792177 ATAGTGGATG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 93 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (110 bp):
GAGTTTTTACAACCCAAAATTCATAGTGGGTCTAGAGATCTTATAATTGGGCCTGCTACAATTGT
GATCCACTGAAAGATATAGAAGCAAACTTCTGTAATGAGGAGGGG
Found at i:9796331 original size:19 final size:19
Alignment explanation
Indices: 9796307--9796344 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9796297 TGAAATTTTC
* *
9796307 ATTTTAATTCAATTGTACA
1 ATTTTAAATCAATTATACA
9796326 ATTTTAAATCAATTATACA
1 ATTTTAAATCAATTATACA
9796345 CGTTCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTTTAAATCAATTATACA
Found at i:9796584 original size:20 final size:19
Alignment explanation
Indices: 9796546--9796595 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
9796536 CGTAAAAAGT
*
9796546 ATTTGAAATTGATATTATAA
1 ATTT-AAATTGATAATATAA
*
9796566 ATTTAAATTGCATAATATAT
1 ATTTAAATTG-ATAATATAA
9796586 ATTATAAATT
1 ATT-TAAATT
9796596 ATTTATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 6 0.23
20 14 0.54
21 6 0.23
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (19 bp):
ATTTAAATTGATAATATAA
Found at i:9799450 original size:21 final size:21
Alignment explanation
Indices: 9799424--9799466 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
9799414 AGATCAAAAA
*
9799424 AAATGTTGGTTATATCTTTAT
1 AAATGTTCGTTATATCTTTAT
9799445 AAATGTTCGTTATATCTTTAT
1 AAATGTTCGTTATATCTTTAT
9799466 A
1 A
9799467 GTTAATGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (21 bp):
AAATGTTCGTTATATCTTTAT
Found at i:9799738 original size:22 final size:24
Alignment explanation
Indices: 9799702--9799754 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
9799692 AAAAATTACC
9799702 AAAATTATGTATAAATGACATGAA
1 AAAATTATGTATAAATGACATGAA
* *
9799726 AAAATTAT-T-TAAATGTCATTAA
1 AAAATTATGTATAAATGACATGAA
*
9799748 ATAATTA
1 AAAATTA
9799755 AAAAAGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 17 0.65
23 1 0.04
24 8 0.31
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.36
Consensus pattern (24 bp):
AAAATTATGTATAAATGACATGAA
Found at i:9801401 original size:2 final size:2
Alignment explanation
Indices: 9801396--9801428 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9801386 GTGTGTATGT
*
9801396 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
9801429 TGTGGGGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9804709 original size:19 final size:19
Alignment explanation
Indices: 9804670--9804705 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9804660 AAATAAGCAA
*
9804670 AAATTCAAGTAAACAACAT
1 AAATCCAAGTAAACAACAT
9804689 AAATCCAAGT-AACAACA
1 AAATCCAAGTAAACAACA
9804706 ATAACACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.19, G:0.06, T:0.17
Consensus pattern (19 bp):
AAATCCAAGTAAACAACAT
Found at i:9805139 original size:57 final size:58
Alignment explanation
Indices: 9805041--9805153 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 58
9805031 AAGGAGTTGC
* *
9805041 TTATGAGTGTTATTTAGGAATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTAAT
1 TTATGAGTGTTATTTAAGAATAAAATTACATTTGAGTTTAAAAATATTTGGGTTTAAT
*
9805099 TTATGAGTGTT-TTTGAAGAAT-AAATTACATTTGGGTTTAAAAATATTTGGGTTTA
1 TTATGAGTGTTATTT-AAGAATAAAATTACATTTGAGTTTAAAAATATTTGGGTTTA
9805154 GTTTGTTGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
57 35 0.69
58 16 0.31
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.46
Consensus pattern (58 bp):
TTATGAGTGTTATTTAAGAATAAAATTACATTTGAGTTTAAAAATATTTGGGTTTAAT
Found at i:9808855 original size:30 final size:29
Alignment explanation
Indices: 9808812--9808896 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 29
9808802 TTATTTATAT
* *
9808812 TTTTATAATTTTTAAAATATTAAATTAAA
1 TTTTATTATTTTTAAAATATTAAAATAAA
* *
9808841 TTATTATTATTTTTAAAGTGATTAAAATATA
1 TT-TTATTATTTTTAAAAT-ATTAAAATAAA
*
9808872 TTTT-TTATTAATTTAAAATTTTAAA
1 TTTTATTATT--TTTAAAATATTAAA
9808897 GAGTCAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 7 0.15
30 21 0.46
31 18 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
TTTTATTATTTTTAAAATATTAAAATAAA
Found at i:9808866 original size:39 final size:39
Alignment explanation
Indices: 9808794--9808870 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
9808784 TTAGGGATCA
**
9808794 AAATTAAATTATTTATATTTTTATAATTTTTAAAATATT
1 AAATTAAATTATTTATATTTTTATAATGATTAAAATATT
9808833 AAATTAAATTA-TTATTATTTTTA-AAGTGATTAAAATAT
1 AAATTAAATTATTTA-TATTTTTATAA-TGATTAAAATAT
9808871 ATTTTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 5 0.15
39 29 0.85
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (39 bp):
AAATTAAATTATTTATATTTTTATAATGATTAAAATATT
Found at i:9809745 original size:20 final size:18
Alignment explanation
Indices: 9809695--9809751 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
9809685 AAATTACAAA
* *
9809695 AAAAATCAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
9809714 AAAATTCAAAATATTTAT
1 AAAATTCAAAATATTTAT
*
9809732 ACAAATTCCAAAATTTTTAT
1 A-AAATT-CAAAATATTTAT
9809752 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.18
19 16 0.48
20 11 0.33
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:9816974 original size:15 final size:15
Alignment explanation
Indices: 9816954--9816984 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9816944 TTATGACATT
*
9816954 ATTTATGTAAAATAA
1 ATTTATCTAAAATAA
9816969 ATTTATCTAAAATAA
1 ATTTATCTAAAATAA
9816984 A
1 A
9816985 AAAAACATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATTTATCTAAAATAA
Found at i:9817242 original size:13 final size:15
Alignment explanation
Indices: 9817197--9817248 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 15
9817187 TTTACTTTTG
*
9817197 TATATATAT-ATATA
1 TATATATATAAAATA
*
9817211 TATATATATATAATA
1 TATATATATAAAATA
9817226 TATATAT-TAAAAT-
1 TATATATATAAAATA
*
9817239 TATAAATATA
1 TATATATATA
9817249 TTAGTTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 6 0.19
14 16 0.50
15 10 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATATATATAAAATA
Found at i:9817249 original size:2 final size:2
Alignment explanation
Indices: 9817197--9817232 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
9817187 TTTACTTTTG
9817197 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9817233 TAAAATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9819790 original size:2 final size:2
Alignment explanation
Indices: 9819779--9819824 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
9819769 TAAATTTTAT
9819779 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9819820 TA TA T
1 TA TA T
9819825 CAACTAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9845181 original size:37 final size:37
Alignment explanation
Indices: 9845140--9845219 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
9845130 CCTAGAAGAC
* * *
9845140 AAAAGATAGAA-AAGAATAATAATA-ATTCTCTGTAAAG
1 AAAAGAT-GAAGAAGAAGAATAA-AGATCCTCTGTAAAA
*
9845177 AAAAGATGAAGATGAAGAATAAAGATCCTCTGTAAAA
1 AAAAGATGAAGAAGAAGAATAAAGATCCTCTGTAAAA
9845214 AAAAGA
1 AAAAGA
9845220 CAAAGATACA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 4 0.11
37 33 0.89
ACGTcount: A:0.57, C:0.06, G:0.16, T:0.20
Consensus pattern (37 bp):
AAAAGATGAAGAAGAAGAATAAAGATCCTCTGTAAAA
Found at i:9847765 original size:14 final size:14
Alignment explanation
Indices: 9847746--9847775 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9847736 ATTGAAAAAA
9847746 ATACACATTTAAAC
1 ATACACATTTAAAC
9847760 ATACACATTTAAAC
1 ATACACATTTAAAC
9847774 AT
1 AT
9847776 GTTCAACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (14 bp):
ATACACATTTAAAC
Found at i:9860237 original size:2 final size:2
Alignment explanation
Indices: 9860232--9860260 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9860222 TCTCTCTCTC
9860232 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9860261 TTCTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9874185 original size:33 final size:33
Alignment explanation
Indices: 9874085--9874168 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
9874075 TTGAAGAAAC
*
9874085 AAATCATGAAGATTTGATTATTATC-AAAAAAA
1 AAATCATGAAGATTGGATTATTATCAAAAAAAA
9874117 AAATCATGAAGATTGGATTATTATCAAAAAAAA
1 AAATCATGAAGATTGGATTATTATCAAAAAAAA
9874150 AAATCATGAAGATTGGATT
1 AAATCATGAAGATTGGATT
9874169 GAATTTGACT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 24 0.48
33 26 0.52
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (33 bp):
AAATCATGAAGATTGGATTATTATCAAAAAAAA
Found at i:9876705 original size:34 final size:31
Alignment explanation
Indices: 9876666--9876754 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
9876656 AAATAACAGC
* *
9876666 AAAACAATATTAATAACAACAAAAACAGTAATAA
1 AAAACAACATCAA-AACAACAAAAACAGT-A-AA
*
9876700 AAAACAACATGAAAACAACAACCAAAACAGTAAA
1 AAAACAACATCAAAACAAC-A--AAAACAGTAAA
9876734 AAAACAACATCAAAACAACAA
1 AAAACAACATCAAAACAACAA
9876755 TATAATTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
31 1 0.02
33 7 0.14
34 32 0.65
35 1 0.02
36 8 0.16
ACGTcount: A:0.69, C:0.18, G:0.03, T:0.10
Consensus pattern (31 bp):
AAAACAACATCAAAACAACAAAAACAGTAAA
Found at i:9879600 original size:14 final size:16
Alignment explanation
Indices: 9879581--9879612 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
9879571 TTTTTAAAGT
9879581 TTATAA-TTAA-AATA
1 TTATAATTTAATAATA
9879595 TTATAATTTAATAATA
1 TTATAATTTAATAATA
9879611 TT
1 TT
9879613 TAAATTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 4 0.25
16 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATAATTTAATAATA
Found at i:9879616 original size:25 final size:23
Alignment explanation
Indices: 9879587--9879642 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
9879577 AAGTTTATAA
*
9879587 TTAAAATATTATAATTTAATAATAT
1 TTAAAATA-TAT-ATTTAATAAAAT
* *
9879612 TTAAATTATATCTTTAATAAAAT
1 TTAAAATATATATTTAATAAAAT
9879635 TTATAAAT
1 TTA-AAAT
9879643 GTAATTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 13 0.50
24 6 0.23
25 7 0.27
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAAATATATATTTAATAAAAT
Found at i:9889939 original size:153 final size:154
Alignment explanation
Indices: 9889734--9890038 Score: 409
Period size: 153 Copynumber: 2.0 Consensus size: 154
9889724 TTTTAAAAGA
* * ** *
9889734 TTAAATTAAAATTTTATCATTTTTAGGAAAATCAAAATACAATTTCACTTTTATTAATTAAAATT
1 TTAAATTAAAATTTTATCAATTTAAAAAAAATCAAAATACAATTTCACTTTTACTAATTAAAATT
* * * *
9889799 TT-AAAAACTTAAATGATATTTTTTAAAATTTTAGGGGCAGCCCCTGCCAGCCAATTAATGGTTA
66 TTAAAAAACTTAAATAAAATTTTTT-AAATTTTAAGGGCAGACCCTGCCAGCCAATTAATGGTTA
9889863 ATGTAAAATATTTCTACTTTTTAAT
130 ATGTAAAATATTTCTACTTTTTAAT
* * *
9889888 TTAAATT-AAATTTTATCACATTTAAAAAAAAT-AAAATATAATTTTATTTTTACTAATTAAAAT
1 TTAAATTAAAATTTTATCA-ATTTAAAAAAAATCAAAATACAATTTCACTTTTACTAATTAAAAT
** *
9889951 TTTAAAAAACTTAAATAAAATTTTTTTCATTTTAAGGGCAGACCCTGCCAGCCCATTAATGGTTA
65 TTTAAAAAACTTAAATAAAATTTTTTAAATTTTAAGGGCAGACCCTGCCAGCCAATTAATGGTTA
* * *
9890016 ATGTAGAATATTTTTGCTTTTTA
130 ATGTAAAATATTTCTACTTTTTA
9890039 CAATATCCAG
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
153 95 0.73
154 36 0.27
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (154 bp):
TTAAATTAAAATTTTATCAATTTAAAAAAAATCAAAATACAATTTCACTTTTACTAATTAAAATT
TTAAAAAACTTAAATAAAATTTTTTAAATTTTAAGGGCAGACCCTGCCAGCCAATTAATGGTTAA
TGTAAAATATTTCTACTTTTTAAT
Found at i:9897035 original size:29 final size:29
Alignment explanation
Indices: 9897003--9897071 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
9896993 TTAACAATTA
*
9897003 AACTTAAATTT-TAAAATCTGAAATATA-AT
1 AACTTAAATTTCTAAAA-AT-AAATATACAT
9897032 AAC-TAAATTTCTAAAAATAAATATACAT
1 AACTTAAATTTCTAAAAATAAATATACAT
*
9897060 AAATTAAATTTC
1 AACTTAAATTTC
9897072 AAATTTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 7 0.20
28 12 0.34
29 16 0.46
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (29 bp):
AACTTAAATTTCTAAAAATAAATATACAT
Found at i:9898420 original size:16 final size:16
Alignment explanation
Indices: 9898388--9898441 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
9898378 AGTTTTTTTT
*
9898388 TTTTTAATTATTG-AA
1 TTTTTAATTTTTGTAA
*
9898403 TTTTTAGTTTTTGTAA
1 TTTTTAATTTTTGTAA
* * *
9898419 TTATTAATTTATGTTA
1 TTTTTAATTTTTGTAA
9898435 TTTTTAA
1 TTTTTAA
9898442 ATATTATATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 11 0.35
16 20 0.65
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (16 bp):
TTTTTAATTTTTGTAA
Found at i:9898446 original size:23 final size:23
Alignment explanation
Indices: 9898386--9898447 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
9898376 TTAGTTTTTT
*
9898386 TTTTTTTAATTATTGAATTTTTAG
1 TTTTTTTAATTATT-AATTTATAG
*
9898410 TTTTTGTAATTATTAATTTAT-G
1 TTTTTTTAATTATTAATTTATAG
*
9898432 TTATTTTTAAATATTA
1 TT-TTTTTAATTATTA
9898448 TATTACAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 3 0.09
23 17 0.52
24 13 0.39
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (23 bp):
TTTTTTTAATTATTAATTTATAG
Found at i:9908814 original size:37 final size:39
Alignment explanation
Indices: 9908744--9908819 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 39
9908734 TAAACAATAT
* *
9908744 ACTTATTTATATAAAAAAAGTTTTATAACTTTTATTATA
1 ACTTATTTATATAAAAAAAGTGTTATAACTTTTACTATA
*
9908783 ACTTA-TT-TATAAAAAAA-TGTTATAATTTTTTACTATA
1 ACTTATTTATATAAAAAAAGTGTTATAA-CTTTTACTATA
9908820 GTGCTAGCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 7 0.21
37 19 0.58
38 2 0.06
39 5 0.15
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (39 bp):
ACTTATTTATATAAAAAAAGTGTTATAACTTTTACTATA
Found at i:9911572 original size:165 final size:165
Alignment explanation
Indices: 9911300--9911625 Score: 546
Period size: 165 Copynumber: 2.0 Consensus size: 165
9911290 TATACTTAAT
* * *
9911300 TCAAAGGAAGAATAGACTCTGTTTAAGTATAGATCTAGCATAATTAAGTGGAATTGCATGCAATC
1 TCAAAGGAAGAATAAACCCTGTTTAAGTATAAATCTAGCATAATTAAGTGGAATTGCATGCAATC
*
9911365 CTAAAAATAGGATGACATAAATCTATCGGATTAGAGTCAAATCTAATAGGAAAATCTATATATCG
66 CTAAAAATAGGATGACATAAATCTATCCGATTAGAGTCAAATCTAATAGGAAAATCTATATATCG
9911430 AATTAATGCGACAATA-AGAGTTTTAATTAGATAAA
131 AATTAATGCGACAATAGA-AGTTTTAATTAGATAAA
* *
9911465 TCAAAGGAGGAATAAACCCTGTTTAAGTATAAATCTTGCATAATTAAGTGGAATTGCATGCAATC
1 TCAAAGGAAGAATAAACCCTGTTTAAGTATAAATCTAGCATAATTAAGTGGAATTGCATGCAATC
* * * *
9911530 CTAAAAATAGGATGACATAATTCTATCCTATTAGAGTCAAATCTAATAGGGAAATTTATATATCG
66 CTAAAAATAGGATGACATAAATCTATCCGATTAGAGTCAAATCTAATAGGAAAATCTATATATCG
9911595 AATTAATGCGACAATAGAAGTTTTAATTAGA
131 AATTAATGCGACAATAGAAGTTTTAATTAGA
9911626 AAGAAATTTA
Statistics
Matches: 150, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
165 149 0.99
166 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (165 bp):
TCAAAGGAAGAATAAACCCTGTTTAAGTATAAATCTAGCATAATTAAGTGGAATTGCATGCAATC
CTAAAAATAGGATGACATAAATCTATCCGATTAGAGTCAAATCTAATAGGAAAATCTATATATCG
AATTAATGCGACAATAGAAGTTTTAATTAGATAAA
Found at i:9913890 original size:14 final size:13
Alignment explanation
Indices: 9913859--9913897 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
9913849 GAATAATATA
* *
9913859 AAATATAATAATT
1 AAATATTATTATT
9913872 AAATATTATTATT
1 AAATATTATTATT
9913885 ATAATATTATTAT
1 A-AATATTATTAT
9913898 AAAACTGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AAATATTATTATT
Found at i:9918395 original size:25 final size:26
Alignment explanation
Indices: 9918351--9918399 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
9918341 GTCGAGTTTT
9918351 ATTATTAGTCTTTAAAAAAAAATTAA
1 ATTATTAGTCTTTAAAAAAAAATTAA
* *
9918377 ATTATTA-TTTTTAATAAAAAATT
1 ATTATTAGTCTTTAAAAAAAAATT
9918400 GATTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTATTAGTCTTTAAAAAAAAATTAA
Found at i:9919031 original size:11 final size:11
Alignment explanation
Indices: 9918964--9919031 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
9918954 TGTTGTTTAC
*
9918964 TTTTGTTATTG
1 TTTTGTTATTA
*
9918975 TTTTGTCA-TA
1 TTTTGTTATTA
*
9918985 GTTTTGTTATCA
1 -TTTTGTTATTA
* *
9918997 TTTCGCTATTA
1 TTTTGTTATTA
*
9919008 TATTGTTATTA
1 TTTTGTTATTA
*
9919019 TTTTGTTGTTA
1 TTTTGTTATTA
9919030 TT
1 TT
9919032 ATTTAGATAT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
10 1 0.02
11 41 0.95
12 1 0.02
ACGTcount: A:0.16, C:0.06, G:0.13, T:0.65
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:9927659 original size:13 final size:13
Alignment explanation
Indices: 9927641--9927674 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
9927631 CTGACTTTGG
9927641 AAAATTATAAAAA
1 AAAATTATAAAAA
*
9927654 AAAATTGTAAAAA
1 AAAATTATAAAAA
9927667 AATAATTA
1 AA-AATTA
9927675 GAGGCTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (13 bp):
AAAATTATAAAAA
Found at i:9937445 original size:21 final size:24
Alignment explanation
Indices: 9937399--9937445 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
9937389 ATGAAAATGA
*
9937399 AATTATTTTTTATATAACTTTCAT
1 AATTATTTTTTATATAACATTCAT
9937423 AATT-TTTTTTATA-AACATT-AT
1 AATTATTTTTTATATAACATTCAT
9937444 AA
1 AA
9937446 AAAAGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 5 0.23
23 9 0.41
24 4 0.18
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTATTTTTTATATAACATTCAT
Found at i:9954323 original size:30 final size:31
Alignment explanation
Indices: 9954270--9954358 Score: 126
Period size: 30 Copynumber: 2.9 Consensus size: 31
9954260 GGTAGTCTAG
* * *
9954270 TGACATAAATAAAAACTTTTGAATAGTTTAA
1 TGACTTAAATGAAAACTTTTGAATAGTTCAA
9954301 TGACTTAAATGAAAAC-TTTGAATAGTTCAA
1 TGACTTAAATGAAAACTTTTGAATAGTTCAA
* *
9954331 TGATTTAAATGAAAACTTTTAAATAGTT
1 TGACTTAAATGAAAACTTTTGAATAGTT
9954359 AAGTGACCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
30 28 0.54
31 24 0.46
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTTGAATAGTTCAA
Found at i:9954376 original size:30 final size:29
Alignment explanation
Indices: 9954270--9954378 Score: 112
Period size: 30 Copynumber: 3.6 Consensus size: 29
9954260 GGTAGTCTAG
9954270 TGACATAAATAAAAACTTTTGAATAGTTTAA
1 TGAC-TAAATAAAAACTTTTGAATAG-TTAA
*
9954301 TGACTTAAATGAAAAC-TTTGAATAGTTCAA
1 TGAC-TAAATAAAAACTTTTGAATAGTT-AA
* * *
9954331 TGATTTAAATGAAAACTTTTAAATAGTTAA
1 TGA-CTAAATAAAAACTTTTGAATAGTTAA
*
9954361 GTGACCAAATAAAAACTT
1 -TGACTAAATAAAAACTT
9954379 ACCAATATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
29 2 0.03
30 38 0.57
31 27 0.40
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (29 bp):
TGACTAAATAAAAACTTTTGAATAGTTAA
Found at i:9956140 original size:17 final size:17
Alignment explanation
Indices: 9956118--9956165 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
9956108 TTTTAAAAGA
9956118 GATATTTATTTTATTTT
1 GATATTTATTTTATTTT
* *
9956135 GATATTTA-ATAATTTT
1 GATATTTATTTTATTTT
*
9956151 -ATATTTTTTTTATTT
1 GATATTTATTTTATTT
9956166 ATTGAAAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 6 0.24
16 11 0.44
17 8 0.32
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (17 bp):
GATATTTATTTTATTTT
Found at i:9959017 original size:20 final size:19
Alignment explanation
Indices: 9958992--9959029 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
9958982 GCATCTCCAT
*
9958992 TTCTTTTATTGTTCTTGTTC
1 TTCTTTTACTGTT-TTGTTC
9959012 TTCTTTTACTGTTTTGTT
1 TTCTTTTACTGTTTTGTT
9959030 TGGTTTTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (19 bp):
TTCTTTTACTGTTTTGTTC
Found at i:9970988 original size:72 final size:72
Alignment explanation
Indices: 9970869--9971004 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 72
9970859 ATGCATTCCT
** *
9970869 CCATGATGGGGTGAAACATGAGCAGGAGAGGGAGACTGAGATAAAACAGGACCAGGTGAGGCAGT
1 CCATGATGGGGTGAAACATGAGCAGGAGAGACAGACTGAGATAAAACAGGACCAGGTGAAGCAGT
9970934 CCTACCA
66 CCTACCA
* * * *
9970941 CCATGATGGGGTGAAATA-GAAGCAGGAGAGACAGGCTGAGGTGAAACAGGACCAGGTGAAGCAG
1 CCATGATGGGGTGAAACATG-AGCAGGAGAGACAGACTGAGATAAAACAGGACCAGGTGAAGCAG
9971005 GCAGGTATTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 1 0.02
72 55 0.98
ACGTcount: A:0.35, C:0.16, G:0.37, T:0.12
Consensus pattern (72 bp):
CCATGATGGGGTGAAACATGAGCAGGAGAGACAGACTGAGATAAAACAGGACCAGGTGAAGCAGT
CCTACCA
Found at i:9983215 original size:16 final size:15
Alignment explanation
Indices: 9983190--9983221 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
9983180 GTGTGTATAT
9983190 ATTGATATTCTAATC
1 ATTGATATTCTAATC
9983205 ATTGCATATTCTAATC
1 ATTG-ATATTCTAATC
9983221 A
1 A
9983222 CTTATTCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTGATATTCTAATC
Found at i:9989290 original size:92 final size:92
Alignment explanation
Indices: 9989133--9989312 Score: 324
Period size: 92 Copynumber: 2.0 Consensus size: 92
9989123 AGTTGTATAT
*
9989133 ATTATTAGATGAATTTAGCTGCATCTATGTATCTATATGATGCTTTTATTCTGTTGTTCATGATG
1 ATTATTAGATGAATTTAGCTGCATCTATGTATCTATATGATGCTTTTATTCTGTTGGTCATGATG
* *
9989198 GATGAGATGGAGTTGCCTAGCACAGCC
66 GATGAGATGGAGATGACTAGCACAGCC
*
9989225 ATTATTAGATGAATTTAGCTGCATTTATGTATCTATATGATGCTTTTATTCTGTTGGTCATGATG
1 ATTATTAGATGAATTTAGCTGCATCTATGTATCTATATGATGCTTTTATTCTGTTGGTCATGATG
9989290 GATGAGATGGAGATGACTAGCAC
66 GATGAGATGGAGATGACTAGCAC
9989313 TGCTATGAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 84 1.00
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.39
Consensus pattern (92 bp):
ATTATTAGATGAATTTAGCTGCATCTATGTATCTATATGATGCTTTTATTCTGTTGGTCATGATG
GATGAGATGGAGATGACTAGCACAGCC
Found at i:10026218 original size:9 final size:9
Alignment explanation
Indices: 10026206--10026230 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
10026196 AATATATATT
10026206 ATTCGTTTC
1 ATTCGTTTC
10026215 ATTCGTTTC
1 ATTCGTTTC
10026224 ATTCGTT
1 ATTCGTT
10026231 GTTTTCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.56
Consensus pattern (9 bp):
ATTCGTTTC
Found at i:10028054 original size:14 final size:15
Alignment explanation
Indices: 10028035--10028063 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10028025 TGAATTTAGT
10028035 AGTTAAA-TTTATTA
1 AGTTAAATTTTATTA
10028049 AGTTAAATTTTATTA
1 AGTTAAATTTTATTA
10028064 TTCATGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (15 bp):
AGTTAAATTTTATTA
Found at i:10032481 original size:17 final size:17
Alignment explanation
Indices: 10032431--10032481 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
10032421 TATAATACGT
* *
10032431 AATATATGAATTTATTA
1 AATATATAAAATTATTA
10032448 AA-A-ATAAAAGTTA-TA
1 AATATATAAAA-TTATTA
10032463 AATATATAAAATTATTA
1 AATATATAAAATTATTA
10032480 AA
1 AA
10032482 AAGCATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 8 0.29
16 8 0.29
17 12 0.43
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (17 bp):
AATATATAAAATTATTA
Found at i:10037960 original size:44 final size:44
Alignment explanation
Indices: 10037912--10038002 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
10037902 GCCTAAAGTC
10037912 TTTATACTCTTTTAAAATTTAAAATTTAGTTATGATACTTTTAA
1 TTTATACTCTTTTAAAATTTAAAATTTAGTTATGATACTTTTAA
10037956 TTTATACTCTTTTAAAATTTAAAATTTAGTTATGATACTTTTAA
1 TTTATACTCTTTTAAAATTTAAAATTTAGTTATGATACTTTTAA
10038000 TTT
1 TTT
10038003 TGGGACATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (44 bp):
TTTATACTCTTTTAAAATTTAAAATTTAGTTATGATACTTTTAA
Found at i:10053859 original size:27 final size:27
Alignment explanation
Indices: 10053829--10053897 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
10053819 TTTGATACTA
10053829 TTATAATAATATTTAG-ATATT-TCAATT
1 TTAT-ATAATATTTAGAAT-TTGTCAATT
* * *
10053856 TTATTTAATTATTTGGAATTTGTCATTT
1 TTATATAA-TATTTAGAATTTGTCAATT
10053884 TTATATAATATTTA
1 TTATATAATATTTA
10053898 ATCGTAATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 3 0.09
27 17 0.50
28 14 0.41
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.57
Consensus pattern (27 bp):
TTATATAATATTTAGAATTTGTCAATT
Found at i:10054485 original size:70 final size:67
Alignment explanation
Indices: 10054386--10054518 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
10054376 TCCGAATAAG
* * *
10054386 AAAAGGCAAAACTACATCATTTTGATAAATGTTTACCCTTTCTAAAGTTAAAAGTCAAAATCATT
1 AAAAGGCAAAACTACATCATTTTGATAAATGTTTACCC-AT-T-AAGTTAAAAGGCAAAACCATT
10054451 AAGTT
63 AAGTT
* * * *
10054456 AAAAGGTAAAATTATATCTTTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGGCAAAACTACATCATTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTA
10054519 TATTATTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 20 0.36
68 1 0.02
69 1 0.02
70 34 0.61
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.33
Consensus pattern (67 bp):
AAAAGGCAAAACTACATCATTTTGATAAATGTTTACCCATTAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:10055372 original size:18 final size:18
Alignment explanation
Indices: 10055351--10055392 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
10055341 TGCAATTGGT
* *
10055351 ATTGGGGTGACGATTAGA
1 ATTGAGGTGACGATTAAA
*
10055369 ATTGAGGTGGCGATTAAA
1 ATTGAGGTGACGATTAAA
10055387 ATTGAG
1 ATTGAG
10055393 TTAAGCTCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.29
Consensus pattern (18 bp):
ATTGAGGTGACGATTAAA
Found at i:10057206 original size:21 final size:22
Alignment explanation
Indices: 10057143--10057206 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
10057133 TAAATTATAA
*
10057143 AAATAATATAAAATAATTAAAT
1 AAATAATATAAAATAATAAAAT
* *
10057165 -ATTATTATAAAATAA-ATAAAT
1 AAATAATATAAAATAATA-AAAT
10057186 AAATAATATAAAA-AATAAAAT
1 AAATAATATAAAATAATAAAAT
10057207 TAACTCTTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
21 23 0.68
22 11 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATAATATAAAATAATAAAAT
Found at i:10057206 original size:25 final size:26
Alignment explanation
Indices: 10057150--10057206 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
10057140 TAAAAATAAT
* * *
10057150 ATAAAATAATTAAATATTATTATAAA
1 ATAAAATAAATAAATAATATTAAAAA
10057176 AT-AAATAAATAAATAATA-TAAAAA
1 ATAAAATAAATAAATAATATTAAAAA
10057200 ATAAAAT
1 ATAAAAT
10057207 TAACTCTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 7 0.26
25 18 0.67
26 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (26 bp):
ATAAAATAAATAAATAATATTAAAAA
Found at i:10057814 original size:7 final size:7
Alignment explanation
Indices: 10057802--10057830 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
10057792 GCTGGACATC
10057802 AAGTATA
1 AAGTATA
10057809 AAGTATA
1 AAGTATA
10057816 AAGTATA
1 AAGTATA
10057823 AAG-ATA
1 AAGTATA
10057829 AA
1 AA
10057831 AGAAAAAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (7 bp):
AAGTATA
Done.