Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 1 of 226
Found at i:4533 original size:23 final size:23
Alignment explanation
Indices: 4490--4533 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4480 AATATCCAAA
*
4490 ATTTTCGTAACTCATTATTTATT
1 ATTTTCGTAACTCATGATTTATT
* *
4513 ATTTTCTTAACTCATGCTTTA
1 ATTTTCGTAACTCATGATTTA
4534 GGGACTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.55
Consensus pattern (23 bp):
ATTTTCGTAACTCATGATTTATT
Found at i:12194 original size:16 final size:16
Alignment explanation
Indices: 12173--12204 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12163 TAAGTTATAA
12173 TTTTTTTATTTTTTAT
1 TTTTTTTATTTTTTAT
12189 TTTTTTTATTTTTTAT
1 TTTTTTTATTTTTTAT
12205 AAAATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTATTTTTTAT
Found at i:17948 original size:46 final size:46
Alignment explanation
Indices: 17884--18065 Score: 319
Period size: 46 Copynumber: 4.0 Consensus size: 46
17874 GGAAAAATGT
* *
17884 GAAAAGTAGGTATGGTGTTTCAGTAAAGAAAACCATACTGAGTTGT
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
17930 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
* *
17976 AAAAAGTAGGTATGGTGTTTTAGTGAAGAAAACCATACTGAGTTGC
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
*
18022 GAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGTT
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTT
18066 ATAGCAATGT
Statistics
Matches: 129, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 129 1.00
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.27
Consensus pattern (46 bp):
GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
Found at i:18530 original size:29 final size:29
Alignment explanation
Indices: 18497--18556 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
18487 GGGAATTGAA
18497 ATAAAAAGTATTAGTATGAATGACTAAGT
1 ATAAAAAGTATTAGTATGAATGACTAAGT
18526 ATAAAAAGTATTAGTATGAATGACTAAGT
1 ATAAAAAGTATTAGTATGAATGACTAAGT
18555 AT
1 AT
18557 GCAAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.17, T:0.32
Consensus pattern (29 bp):
ATAAAAAGTATTAGTATGAATGACTAAGT
Found at i:23997 original size:17 final size:16
Alignment explanation
Indices: 23969--24021 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
23959 TTTGGTTCGC
23969 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
23985 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
24002 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
24018 TGTA
1 TGTA
24022 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:24453 original size:121 final size:121
Alignment explanation
Indices: 24239--24742 Score: 902
Period size: 121 Copynumber: 4.2 Consensus size: 121
24229 ATCATATTTA
* * *
24239 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
*
24304 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
24360 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
24425 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
24481 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
24546 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* * * *
24602 AACATAATATATGATTAAATATATTTTAATTGAACAATATAATTTAATAAAATTCTTAATAATTA
1 AACATAAT-TATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTA
* *
24667 ATATTC-TTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
24723 AACATAATTATTATTAAATA
1 AACATAATTATTATTAAATA
24743 TATAACTTGA
Statistics
Matches: 371, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
120 11 0.03
121 302 0.81
122 58 0.16
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (121 bp):
AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:29020 original size:14 final size:14
Alignment explanation
Indices: 29001--29031 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
28991 AAAATATTAA
29001 CAACAAATAGTTCC
1 CAACAAATAGTTCC
29015 CAACAAATAGTTCC
1 CAACAAATAGTTCC
29029 CAA
1 CAA
29032 TTGCCAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.19
Consensus pattern (14 bp):
CAACAAATAGTTCC
Found at i:32606 original size:27 final size:27
Alignment explanation
Indices: 32553--32641 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 27
32543 GTGACGACGA
* * *
32553 CACTTCGGTGCAAATTAGCGATTGTGG
1 CACTTCGGTGCAAATCAGTGATAGTGG
*
32580 CACTTCGGTGCAACTCAGTGATAGTGG
1 CACTTCGGTGCAAATCAGTGATAGTGG
* ** * *
32607 CACCTCAATGCAATTCGGTGATAGTGG
1 CACTTCGGTGCAAATCAGTGATAGTGG
*
32634 CTCTTCGG
1 CACTTCGG
32642 AGCATTTCAT
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.28
Consensus pattern (27 bp):
CACTTCGGTGCAAATCAGTGATAGTGG
Found at i:32808 original size:11 final size:11
Alignment explanation
Indices: 32792--32816 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
32782 TGTAAGTGGA
32792 AATGATCATTT
1 AATGATCATTT
32803 AATGATCATTT
1 AATGATCATTT
32814 AAT
1 AAT
32817 TAATTTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
AATGATCATTT
Found at i:33695 original size:12 final size:11
Alignment explanation
Indices: 33662--33745 Score: 54
Period size: 12 Copynumber: 7.9 Consensus size: 11
33652 AAATAGAAGG
*
33662 GAAAG-AAAGG
1 GAAAGAAAAGA
33672 GAAA-AAAA-A
1 GAAAGAAAAGA
33681 GAAAGAAAATGA
1 GAAAGAAAA-GA
33693 GAAAG-AAA-A
1 GAAAGAAAAGA
33702 GAAAGAAAAGGA
1 GAAAGAAAA-GA
*
33714 AAAAGAAAA-A
1 GAAAGAAAAGA
* *
33724 GAGAGAGAGAGA
1 GAAAGA-AAAGA
*
33736 GAGAGAAAAG
1 GAAAGAAAAG
33746 TAAAATCACT
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
9 10 0.17
10 19 0.32
11 8 0.14
12 22 0.37
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (11 bp):
GAAAGAAAAGA
Found at i:33701 original size:21 final size:21
Alignment explanation
Indices: 33662--33722 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
33652 AAATAGAAGG
*
33662 GAAAG-AAAGG-GAAAAAAAA
1 GAAAGAAAAGGAGAAAGAAAA
*
33681 GAAAGAAAATGAGAAAGAAAA
1 GAAAGAAAAGGAGAAAGAAAA
*
33702 GAAAGAAAAGGAAAAAGAAAA
1 GAAAGAAAAGGAGAAAGAAAA
33723 AGAGAGAGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.14
20 4 0.11
21 27 0.75
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (21 bp):
GAAAGAAAAGGAGAAAGAAAA
Found at i:38980 original size:41 final size:40
Alignment explanation
Indices: 38935--39022 Score: 131
Period size: 41 Copynumber: 2.2 Consensus size: 40
38925 CGACTTTGAG
*
38935 TCGATGAAACACTGGGTGTCAATTTACTACTTCGGATTAAT
1 TCGATGAAACACTGGGTGTCAATTTACTACTTCGAATT-AT
** *
38976 TCGATGAGGCACTGGGTGTCAATTTATTACTTCGAATTAT
1 TCGATGAAACACTGGGTGTCAATTTACTACTTCGAATTAT
39016 TCGATGA
1 TCGATGA
39023 GGCACTAGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 9 0.21
41 34 0.79
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (40 bp):
TCGATGAAACACTGGGTGTCAATTTACTACTTCGAATTAT
Found at i:42872 original size:20 final size:21
Alignment explanation
Indices: 42843--42888 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
42833 ATATTTGATA
*
42843 ATTA-TTTAATTAGATA-AAT
1 ATTATTTTAATGAGATATAAT
*
42862 ATTATTTTAATGAGATATATT
1 ATTATTTTAATGAGATATAAT
42883 ATTATT
1 ATTATT
42889 ATTTTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 11 0.48
21 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
ATTATTTTAATGAGATATAAT
Found at i:44727 original size:101 final size:100
Alignment explanation
Indices: 44552--44781 Score: 336
Period size: 101 Copynumber: 2.3 Consensus size: 100
44542 TGAATTGACA
*
44552 GATAAGACCATAACT-GAGTTATGACACTATGAACGTAAAACCATGGTTGGACCATGGCAGTGTT
1 GATAAGACAAT-ACTAG-GTTATGACACTATGAACGTAAAACCATGGTTGGACCATGGCAGTGTT
* *
44616 TATATATAAGACCATAGCTGGGTTATGTCATTCTGAT
64 TATATATAAGACCATAGCTGGGCTATGGCATTCTGAT
* * * *
44653 GATAATACAATATCTAGGTTATGGCACTATGAACGTAAGACCATGGTTGGACTATGGCAGTGTTT
1 GATAAGACAATA-CTAGGTTATGACACTATGAACGTAAAACCATGGTTGGACCATGGCAGTGTTT
*
44718 ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
65 ATATATAAGACCATAGCTGGGCTATGGCATTCTGAT
* *
44754 GATAAGACCATACTGGGTTATGACACTA
1 GATAAGACAATACTAGGTTATGACACTA
44782 CAAATGTAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
100 15 0.13
101 99 0.86
102 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.30
Consensus pattern (100 bp):
GATAAGACAATACTAGGTTATGACACTATGAACGTAAAACCATGGTTGGACCATGGCAGTGTTTA
TATATAAGACCATAGCTGGGCTATGGCATTCTGAT
Found at i:44765 original size:33 final size:33
Alignment explanation
Indices: 44621--44775 Score: 118
Period size: 33 Copynumber: 4.7 Consensus size: 33
44611 GTGTTTATAT
*
44621 ATAAGACCATAGCTGGGTTATGTCATTCTGATG
1 ATAAGACCATAGCTGGGTTATGGCATTCTGATG
* * * * * * *
44654 ATAATACAATATCTAGGTTATGGCACTATGAACG
1 ATAAGACCATAGCTGGGTTATGGCATTCTG-ATG
* * ** * *
44688 -TAAGACCATGGTTGGACTATGGCAGTGTTTATATG
1 ATAAGACCATAGCTGGGTTATGGCA-T-TCT-GATG
*
44723 -TAAGACCATAGCTGGGCTATGGCATTCTGATG
1 ATAAGACCATAGCTGGGTTATGGCATTCTGATG
44755 ATAAGACCATA-CTGGGTTATG
1 ATAAGACCATAGCTGGGTTATG
44776 ACACTACAAA
Statistics
Matches: 91, Mismatches: 26, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
32 12 0.13
33 51 0.56
34 3 0.03
35 25 0.27
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (33 bp):
ATAAGACCATAGCTGGGTTATGGCATTCTGATG
Found at i:47428 original size:39 final size:40
Alignment explanation
Indices: 47293--47429 Score: 118
Period size: 40 Copynumber: 3.4 Consensus size: 40
47283 CGCTTGGACA
* **
47293 AAAAACGCCGA-TAAAAATCGAGCATTAGCGGCGCTTCAAG
1 AAAAACGCC-ACTAAAAATCGAGCATTAGCGGCGTTTTTAG
* * * * * *
47333 GAAAATGCCACTAAAGATCGAGCATTAGTGGAGTTTTTTG
1 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGTTTTTAG
**
47373 AAAAGTG-CAGCTAAAAAT-GAGCATTAGCGGCGTTTTTAG
1 AAAAACGCCA-CTAAAAATCGAGCATTAGCGGCGTTTTTAG
*
47412 AAAAAACGCCACAAAAAA
1 -AAAAACGCCACTAAAAA
47430 CCAAAGCCCA
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
39 21 0.28
40 52 0.69
41 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (40 bp):
AAAAACGCCACTAAAAATCGAGCATTAGCGGCGTTTTTAG
Found at i:48419 original size:17 final size:17
Alignment explanation
Indices: 48397--48439 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
48387 AATATATAAT
48397 ATTATAATGAAAAATTA
1 ATTATAATGAAAAATTA
*
48414 ATTATAATGCAAAATTA
1 ATTATAATGAAAAATTA
48431 ATATATAAT
1 AT-TATAAT
48440 ATTATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (17 bp):
ATTATAATGAAAAATTA
Found at i:48752 original size:104 final size:104
Alignment explanation
Indices: 48572--48780 Score: 409
Period size: 104 Copynumber: 2.0 Consensus size: 104
48562 CGTGTTTAAG
48572 AAATAAATTCATTTAGTTACAGATTATATGTAACACCCCTTACCCGAATTATCAAACTCTGACTG
1 AAATAAATTCATTTAGTTACAGATTATATGTAACACCCCTTACCCGAATTATCAAACTCTGACTG
*
48637 ATGTTTTTGACGTGGTTGCATCTGTAACTTTCAACAGAT
66 ACGTTTTTGACGTGGTTGCATCTGTAACTTTCAACAGAT
48676 AAATAAATTCATTTAGTTACAGATTATATGTAACACCCCTTACCCGAATTATCAAACTCTGACTG
1 AAATAAATTCATTTAGTTACAGATTATATGTAACACCCCTTACCCGAATTATCAAACTCTGACTG
48741 ACGTTTTTGACGTGGTTGCATCTGTAACTTTCAACAGAT
66 ACGTTTTTGACGTGGTTGCATCTGTAACTTTCAACAGAT
48780 A
1 A
48781 TCTATTTCCC
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (104 bp):
AAATAAATTCATTTAGTTACAGATTATATGTAACACCCCTTACCCGAATTATCAAACTCTGACTG
ACGTTTTTGACGTGGTTGCATCTGTAACTTTCAACAGAT
Found at i:54204 original size:14 final size:13
Alignment explanation
Indices: 54178--54227 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
54168 ATTTATTTGA
54178 AATATAATAATAT
1 AATATAATAATAT
54191 AATATAATTAATAT
1 AATATAA-TAATAT
* *
54205 AAT-TTACAATAT
1 AATATAATAATAT
54217 AATA-AATAATA
1 AATATAATAATA
54228 ATATACTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 13 0.42
13 9 0.29
14 9 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:64652 original size:32 final size:32
Alignment explanation
Indices: 64616--64681 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
64606 CTTGTGAATC
64616 ATGCACTTTGCTATATTTTGTTCCAAGTGATG
1 ATGCACTTTGCTATATTTTGTTCCAAGTGATG
64648 ATGCACTTTGCTATATTTTGTTCCAAGTGATG
1 ATGCACTTTGCTATATTTTGTTCCAAGTGATG
64680 AT
1 AT
64682 CTTGCATCGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (32 bp):
ATGCACTTTGCTATATTTTGTTCCAAGTGATG
Found at i:67682 original size:22 final size:22
Alignment explanation
Indices: 67637--67683 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
67627 CAAAATGCTG
* *
67637 TAAGAGAAATTATGAAGAATTC
1 TAAGAGAAATTAAGAAGAACTC
*
67659 TAAGAGAAATTAAGATGAACTC
1 TAAGAGAAATTAAGAAGAACTC
67681 TAA
1 TAA
67684 TGTAGCTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (22 bp):
TAAGAGAAATTAAGAAGAACTC
Found at i:68424 original size:47 final size:48
Alignment explanation
Indices: 68332--68427 Score: 142
Period size: 47 Copynumber: 2.0 Consensus size: 48
68322 CCAACTTGCC
68332 AATGATCACTTGAAATGAAGCATCGGCTAACCCCTTACATAATATGTCT
1 AATGATCACTTGAAATGAAGCA-CGGCTAACCCCTTACATAATATGTCT
* *
68381 AATGATCTCTTGATATGAAGCA-GGCTAACCCCTTAGC-TAATATGTCT
1 AATGATCACTTGAAATGAAGCACGGCTAACCCCTTA-CATAATATGTCT
68428 GCCATCTACC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 23 0.52
48 1 0.02
49 20 0.45
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (48 bp):
AATGATCACTTGAAATGAAGCACGGCTAACCCCTTACATAATATGTCT
Found at i:77219 original size:171 final size:171
Alignment explanation
Indices: 76934--77280 Score: 676
Period size: 171 Copynumber: 2.0 Consensus size: 171
76924 GCTATATAAT
*
76934 ATTCAGGAAAGGTCAATTGCATTGATTCTCTTTTGAGAAAAAGCCTTCCTTGTGATATTCAAGAC
1 ATTCAGGAAAGGTCAATTGCATTGATTCTCTTCTGAGAAAAAGCCTTCCTTGTGATATTCAAGAC
76999 TTCCTGTAACTAAGTAGGAGGATTTGGGTTTCATTCCCCACTAGCATGAAAGAACTTGATTCATT
66 TTCCTGTAACTAAGTAGGAGGATTTGGGTTTCATTCCCCACTAGCATGAAAGAACTTGATTCATT
77064 TCCATCCTCAATAATTCTGAATCATGTATACTTGATAATCA
131 TCCATCCTCAATAATTCTGAATCATGTATACTTGATAATCA
77105 ATTCAGGAAAGGTCAATTGCATTGATTCTCTTCTGAGAAAAAGCCTTCCTTGTGATATTCAAGAC
1 ATTCAGGAAAGGTCAATTGCATTGATTCTCTTCTGAGAAAAAGCCTTCCTTGTGATATTCAAGAC
77170 TTCCTGTAACTAAGTAGGAGGATTTGGGTTTCATTCCCCACTAGCATGAAAGAACTTGATTCATT
66 TTCCTGTAACTAAGTAGGAGGATTTGGGTTTCATTCCCCACTAGCATGAAAGAACTTGATTCATT
*
77235 TCCATCCTCAATACTTCTGAATCATGTATACTTGATAATCA
131 TCCATCCTCAATAATTCTGAATCATGTATACTTGATAATCA
77276 ATTCA
1 ATTCA
77281 AGCTTGGACA
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 174 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (171 bp):
ATTCAGGAAAGGTCAATTGCATTGATTCTCTTCTGAGAAAAAGCCTTCCTTGTGATATTCAAGAC
TTCCTGTAACTAAGTAGGAGGATTTGGGTTTCATTCCCCACTAGCATGAAAGAACTTGATTCATT
TCCATCCTCAATAATTCTGAATCATGTATACTTGATAATCA
Found at i:80040 original size:20 final size:21
Alignment explanation
Indices: 80011--80051 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
80001 TATATTAAAT
80011 TTTATAAAAG-TACAAAATAA
1 TTTATAAAAGTTACAAAATAA
* *
80031 TTTATCAAAGTTTCAAAATAA
1 TTTATAAAAGTTACAAAATAA
80052 AATTCATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (21 bp):
TTTATAAAAGTTACAAAATAA
Found at i:87452 original size:14 final size:14
Alignment explanation
Indices: 87433--87459 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
87423 CATTTGCTCA
87433 TCTCTTGTGGTTTG
1 TCTCTTGTGGTTTG
87447 TCTCTTGTGGTTT
1 TCTCTTGTGGTTT
87460 TTTCAAGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.26, T:0.59
Consensus pattern (14 bp):
TCTCTTGTGGTTTG
Found at i:89973 original size:48 final size:45
Alignment explanation
Indices: 89921--90077 Score: 163
Period size: 48 Copynumber: 3.4 Consensus size: 45
89911 TTACATCAAT
* *
89921 TTGGACAGCATTTATATACCAAACTAGACAGCATTTTCACACCAAAA
1 TTGGACAGCATATATATACCAAA-TAGACAGCATTTT-ACAACAAAA
* * * *
89968 TTTGGACAGCATATATACAACAAATTGGACAGCATATATACAAC-AAA
1 -TTGGACAGCATATATATACCAAA-TAGACAGCAT-TTTACAACAAAA
* * *
90015 TTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAAA
1 TTGGACAGCATATATATACCAAATAGA-CAGCA-TTTTACAACAAAA
90062 TTGGACAGCATATATA
1 TTGGACAGCATATATA
90078 CAACAATTTG
Statistics
Matches: 91, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
45 3 0.03
46 31 0.34
47 22 0.24
48 33 0.36
49 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (45 bp):
TTGGACAGCATATATATACCAAATAGACAGCATTTTACAACAAAA
Found at i:89979 original size:25 final size:24
Alignment explanation
Indices: 89897--90385 Score: 246
Period size: 23 Copynumber: 20.7 Consensus size: 24
89887 ATCTATCCTG
* *
89897 TTTGGACAGC-TCTTTTACATC-AA
1 TTTGGACAGCAT-TTATACACCAAA
*
89920 TTTGGACAGCATTTATATACCAAA
1 TTTGGACAGCATTTATACACCAAA
* *
89944 -CTAGACAGCATTT-TCACACCAAAA
1 TTTGGACAGCATTTAT-ACACC-AAA
* *
89968 TTTGGACAGCATATATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* *
89992 -TTGGACAGCATATATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* * *
90015 -TTGGGCAGCATATATATACCAAA
1 TTTGGACAGCATTTATACACCAAA
* *
90038 -TT-GAGCAGCATTTTTACATCAAA
1 TTTGGA-CAGCATTTATACACCAAA
* * *
90061 ATTGGACAGCATATATACAAC-AA
1 TTTGGACAGCATTTATACACCAAA
* ** *
90084 TTTGGGCAGCATAAATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
*
90108 -TT-GAGCAGCATTTTTACACCAAAA
1 TTTGGA-CAGCATTTATACACC-AAA
* * *
90132 ATTGGACAGCATTTTTACATCAAA
1 TTTGGACAGCATTTATACACCAAA
* * *
90156 ATTGGA-AGACATATATACAAC-AA
1 TTTGGACAG-CATTTATACACCAAA
* ** *
90179 TTTGGGCAGCATAAATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* *
90203 -TT-GAGCAACATTTTTACACCAAAA
1 TTTGGA-CAGCATTTATACACC-AAA
* * *
90227 ATTGGACAGCATATATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
* * *
90251 -TTGGGCAGCATATATATACC-AA
1 TTTGGACAGCATTTATACACCAAA
* * *
90273 TTT-GAGCAGCATTTTTGCATCAAA
1 TTTGGA-CAGCATTTATACACCAAA
* * * *
90297 ATTGGACAACATATATACAAC-AA
1 TTTGGACAGCATTTATACACCAAA
** *
90320 TTTGGACAGCATAAATACAACAAA
1 TTTGGACAGCATTTATACACCAAA
*
90344 -TT-GAGCAGCATTTTTACACCAAAAA
1 TTTGGA-CAGCATTTATACACC--AAA
*
90369 TTTGGACAGCATATATA
1 TTTGGACAGCATTTATA
90386 TAACAATTTG
Statistics
Matches: 365, Mismatches: 70, Indels: 59
0.74 0.14 0.12
Matches are distributed among these distances:
22 9 0.02
23 216 0.59
24 72 0.20
25 50 0.14
26 16 0.04
27 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (24 bp):
TTTGGACAGCATTTATACACCAAA
Found at i:89999 original size:23 final size:23
Alignment explanation
Indices: 89969--90396 Score: 328
Period size: 23 Copynumber: 18.2 Consensus size: 23
89959 ACACCAAAAT
89969 TTGGACAGCATATATACAACAAA
1 TTGGACAGCATATATACAACAAA
89992 TTGGACAGCATATATACAACAAA
1 TTGGACAGCATATATACAACAAA
* * *
90015 TTGGGCAGCATATATATACCAAA
1 TTGGACAGCATATATACAACAAA
* * *
90038 TT-GAGCAGCATTTTTACATCAAAA
1 TTGGA-CAGCATATATACAAC-AAA
*
90062 TTGGACAGCATATATACAACAAT
1 TTGGACAGCATATATACAACAAA
* *
90085 TTGGGCAGCATAAATACAACAAA
1 TTGGACAGCATATATACAACAAA
* * *
90108 TT-GAGCAGCATTTTTACACCAAAAA
1 TTGGA-CAGCATATATACA--ACAAA
* * *
90133 TTGGACAGCATTTTTACATCAAAA
1 TTGGACAGCATATATACAAC-AAA
*
90157 TTGGA-AGACATATATACAACAAT
1 TTGGACAG-CATATATACAACAAA
* *
90180 TTGGGCAGCATAAATACAACAAA
1 TTGGACAGCATATATACAACAAA
* * * *
90203 TT-GAGCAACATTTTTACACCAAAAA
1 TTGGA-CAGCATATATACA--ACAAA
90228 TTGGACAGCATATATACAACAAA
1 TTGGACAGCATATATACAACAAA
* * *
90251 TTGGGCAGCATATATA-TACCAA
1 TTGGACAGCATATATACAACAAA
* * * * *
90273 TTTGAGCAGCATTTTTGCATCAAAA
1 TTGGA-CAGCATATATACAAC-AAA
* *
90298 TTGGACAACATATATACAACAAT
1 TTGGACAGCATATATACAACAAA
*
90321 TTGGACAGCATAAATACAACAAA
1 TTGGACAGCATATATACAACAAA
* * *
90344 TT-GAGCAGCATTTTTACACCAAAAA
1 TTGGA-CAGCATATATACA--ACAAA
* *
90369 TTTGGACAGCATATATATAACAAT
1 -TTGGACAGCATATATACAACAAA
90393 TTGG
1 TTGG
90397 GTAGCATTTA
Statistics
Matches: 314, Mismatches: 69, Indels: 44
0.74 0.16 0.10
Matches are distributed among these distances:
22 12 0.04
23 187 0.60
24 50 0.16
25 47 0.15
26 16 0.05
27 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (23 bp):
TTGGACAGCATATATACAACAAA
Found at i:90169 original size:95 final size:95
Alignment explanation
Indices: 89947--90284 Score: 461
Period size: 95 Copynumber: 3.6 Consensus size: 95
89937 TACCAAACTA
* * * * *
89947 GACAGCATTTTCACACCAAAATTTGGACAGCATATATACAACAAATTGGACAGCATATATACAAC
1 GACAGCATTTTTACATCAAAA-TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAAC
* * * *
90012 AAATTGGGCAGCATATATATACC--AAATT-
65 AAATTGAGCAGCATTTTTACACCAAAAATTG
90040 GAGCAGCATTTTTACATCAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAAC
1 GA-CAGCATTTTTACATCAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAAC
90105 AAATTGAGCAGCATTTTTACACCAAAAATTG
65 AAATTGAGCAGCATTTTTACACCAAAAATTG
90136 GACAGCATTTTTACATCAAAATTGGA-AGACATATATACAACAATTTGGGCAGCATAAATACAAC
1 GACAGCATTTTTACATCAAAATTGGACAG-CATATATACAACAATTTGGGCAGCATAAATACAAC
*
90200 AAATTGAGCAACATTTTTACACCAAAAATTG
65 AAATTGAGCAGCATTTTTACACCAAAAATTG
* * * * * * *
90231 GACAGCATATATACAAC-AAATTGGGCAGCATATATATACCAATTTGAGCAGCAT
1 GACAGCATTTTTACATCAAAATTGGACAGCATATATACAACAATTTGGGCAGCAT
90285 TTTTGCATCA
Statistics
Matches: 222, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
93 61 0.27
94 49 0.22
95 110 0.50
96 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (95 bp):
GACAGCATTTTTACATCAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACA
AATTGAGCAGCATTTTTACACCAAAAATTG
Found at i:90220 original size:70 final size:71
Alignment explanation
Indices: 89966--90403 Score: 383
Period size: 70 Copynumber: 6.2 Consensus size: 71
89956 TTCACACCAA
* * * * * *
89966 AATTTGGACAGCATATATACAACAAATTG-GACAGCATATATACA--ACAAATTGGGCAGCATAT
1 AATTTGGGCAGCATAAATACAACAAATTGAG-CAGCATTTTTACACCAAAAATTGGACAGCATAT
* *
90028 ATATACC
65 ATACAAC
* * *** * * * * * *
90035 AAATTGAGCAGCATTTTTACATCAAAATTG-GACAGCATATATACA--ACAATTTGGGCAGCATA
1 AATTTGGGCAGCATAAATACAAC-AAATTGAG-CAGCATTTTTACACCAAAAATTGGACAGCATA
*
90097 AATACAAC
64 TATACAAC
* * *** * *
90105 AAATTGAGCAGCATTTTTACACCAAAAATTG-GACAGCATTTTTACATC-AAAATTGGA-AGACA
1 AATTTGGGCAGCATAAATACA--ACAAATTGAG-CAGCATTTTTACACCAAAAATTGGACAG-CA
90167 TATATACAAC
62 TATATACAAC
*
90177 AATTTGGGCAGCATAAATACAACAAATTGAGCAACATTTTTACACCAAAAATTGGACAGCATATA
1 AATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATA
90242 TACAAC
66 TACAAC
* * * * * * * *
90248 AAATTGGGCAGCATATATATACCAATTTGAGCAGCATTTTTGCATC-AAAATTGGACAACATATA
1 AATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATA
90312 TACAAC
66 TACAAC
*
90318 AATTTGGACAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAATTTGGACAGCATAT
1 AATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAA-TTGGACAGCATAT
*
90383 ATATAAC
65 ATACAAC
*
90390 AATTTGGGTAGCAT
1 AATTTGGGCAGCAT
90404 TTAAGCATCA
Statistics
Matches: 311, Mismatches: 47, Indels: 19
0.82 0.12 0.05
Matches are distributed among these distances:
69 17 0.05
70 144 0.46
71 85 0.27
72 65 0.21
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (71 bp):
AATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATATA
TACAAC
Found at i:90299 original size:95 final size:94
Alignment explanation
Indices: 89969--90354 Score: 381
Period size: 95 Copynumber: 4.1 Consensus size: 94
89959 ACACCAAAAT
* * * * * * * * *
89969 TTGGACAGCATATATACAACAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATATAC
1 TTGGGCAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAACATTTTTACAC
* * *
90034 C--AAATT-GAGCAGCATTTTTACATCAAAA
66 CAAAAATTGGA-CAGCATATATACAAC-AAA
* *
90062 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACAC
1 TTGGGCAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAACATTTTTACAC
* * *
90127 CAAAAATTGGACAGCATTTTTACATCAAAA
66 CAAAAATTGGACAGCATATATACAAC-AAA
*
90157 TT-GGAAGACATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAACATTTTTACA
1 TTGGGCAG-CATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAACATTTTTACA
90221 CCAAAAATTGGACAGCATATATACAACAAA
65 CCAAAAATTGGACAGCATATATACAACAAA
* * * *** * * * *
90251 TTGGGCAGCATATATATACCAATTTGAGCAGCATTTTTGCATCAAAATTG-GACAACATATATAC
1 TTGGGCAGCATATATACAACAATTTGGGCAGCATAAATACAAC-AAATTGAG-CAACATTTTTAC
* * *
90315 A--ACAATTTGGACAGCATAAATACAACAAA
64 ACCAAAAATTGGACAGCATATATACAACAAA
*
90344 TTGAGCAGCAT
1 TTGGGCAGCAT
90355 TTTTACACCA
Statistics
Matches: 258, Mismatches: 28, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
93 94 0.36
94 36 0.14
95 126 0.49
96 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (94 bp):
TTGGGCAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAACATTTTTACAC
CAAAAATTGGACAGCATATATACAACAAA
Found at i:90356 original size:141 final size:143
Alignment explanation
Indices: 90082--90403 Score: 472
Period size: 141 Copynumber: 2.3 Consensus size: 143
90072 TATATACAAC
* * * * *
90082 AATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCATTTT
1 AATTTGGACAGCATATATACAACAAATTGGGCAGCATATATACACC-AAAATTGGACAGCATTTT
*
90147 TACATCAAAATTGGAAGACATATATACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAAC
65 TACATCAAAATTGGAAGACATATATACAACAATTTGGACAGCATAAATACAACAAATTGAGCAAC
90212 ATTTTTACACCAAA
130 ATTTTTACACCAAA
* *
90226 AA-TTGGACAGCATATATACAACAAATTGGGCAGCATATATATACC--AATTTGAGCAGCATTTT
1 AATTTGGACAGCATATATACAACAAATTGGGCAGCATATATACACCAAAATTGGA-CAGCATTTT
* *
90288 TGCATCAAAATTGGACA-ACATATATACAACAATTTGGACAGCATAAATACAACAAATTGAGCAG
65 TACATCAAAATTGGA-AGACATATATACAACAATTTGGACAGCATAAATACAACAAATTGAGCAA
90352 CATTTTTACACCAAA
129 CATTTTTACACCAAA
* * *
90367 AATTTGGACAGCATATATATAACAATTTGGGTAGCAT
1 AATTTGGACAGCATATATACAACAAATTGGGCAGCAT
90404 TTAAGCATCA
Statistics
Matches: 162, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
140 6 0.04
141 85 0.52
142 32 0.20
143 37 0.23
144 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.27
Consensus pattern (143 bp):
AATTTGGACAGCATATATACAACAAATTGGGCAGCATATATACACCAAAATTGGACAGCATTTTT
ACATCAAAATTGGAAGACATATATACAACAATTTGGACAGCATAAATACAACAAATTGAGCAACA
TTTTTACACCAAA
Found at i:90416 original size:49 final size:49
Alignment explanation
Indices: 90082--90405 Score: 201
Period size: 48 Copynumber: 6.8 Consensus size: 49
90072 TATATACAAC
* *
90082 AATTTGGGCAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAA
1 AATTTGGACAGCATAAATACAACAAATTGAGCAGCATTTTAACACCAAA
*** * * * * *
90131 AA-TTGGACAGCATTTTTACATCAAAATTG-GAAGACA-TAT-ATA-CAAC
1 AATTTGGACAGCATAAATACAAC-AAATTGAGCAG-CATTTTAACACCAAA
* * *
90177 AATTTGGGCAGCATAAATACAACAAATTGAGCAACATTTTTACACCAAA
1 AATTTGGACAGCATAAATACAACAAATTGAGCAGCATTTTAACACCAAA
* * * *
90226 AA-TTGGACAGCATATATACAACAAATTGGGCAGCA-TATATATACC---
1 AATTTGGACAGCATAAATACAACAAATTGAGCAGCATTTTA-ACACCAAA
*** * * * * * *
90271 AATTT-GAGCAGCATTTTTGCATCAAAATTG-GACAACA-TAT-ATA-CAAC
1 AATTTGGA-CAGCATAAATACAAC-AAATTGAG-CAGCATTTTAACACCAAA
*
90318 AATTTGGACAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAA
1 AATTTGGACAGCATAAATACAACAAATTGAGCAGCATTTTAACACCAAA
* * * * *
90367 AATTTGGACAGCATATATATAACAATTTGGGTAGCATTT
1 AATTTGGACAGCATAAATACAACAAATTGAGCAGCATTT
90406 AAGCATCAAA
Statistics
Matches: 210, Mismatches: 45, Indels: 40
0.71 0.15 0.14
Matches are distributed among these distances:
44 1 0.00
45 7 0.03
46 37 0.18
47 54 0.26
48 59 0.28
49 52 0.25
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (49 bp):
AATTTGGACAGCATAAATACAACAAATTGAGCAGCATTTTAACACCAAA
Found at i:91159 original size:28 final size:28
Alignment explanation
Indices: 91127--91224 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
91117 TTTAATAAGT
*
91127 TCGCACACCTAGTGTTTAATAATCAATC
1 TCGCACACTTAGTGTTTAATAATCAATC
*
91155 TCGCACACTTAGTGCTTAATAATCAATC
1 TCGCACACTTAGTGTTTAATAATCAATC
* * * *
91183 TCGCATACTTAGTGATTT-ACAATTAAAC
1 TCGCACACTTAGTG-TTTAATAATCAATC
91211 TCGCACACTTAGTG
1 TCGCACACTTAGTG
91225 CTAATCTCAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 59 0.97
29 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (28 bp):
TCGCACACTTAGTGTTTAATAATCAATC
Found at i:92333 original size:14 final size:15
Alignment explanation
Indices: 92314--92342 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
92304 TCACGAAACT
92314 TTCACACAT-ATAAA
1 TTCACACATAATAAA
92328 TTCACACATAATAAA
1 TTCACACATAATAAA
92343 CACAGAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:99297 original size:23 final size:23
Alignment explanation
Indices: 99267--99324 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
99257 TCATGACTAC
*
99267 TTAA-TGAATATATTCAAGTATA
1 TTAATTGAATATATTCAAGAATA
* * *
99289 TTAATTGAACATGTTCATGAATA
1 TTAATTGAATATATTCAAGAATA
*
99312 TATAATCGAATAT
1 T-TAATTGAATAT
99325 GTTTGTGAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 4 0.14
23 15 0.54
24 9 0.32
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (23 bp):
TTAATTGAATATATTCAAGAATA
Found at i:120639 original size:3 final size:3
Alignment explanation
Indices: 120633--120685 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
120623 GAAGCAAAGC
120633 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
120681 TAA TA
1 TAA TA
120686 CTTGGCCGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:129248 original size:19 final size:18
Alignment explanation
Indices: 129220--129255 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
129210 GCAAAAAAGC
*
129220 ATAAAGTAAATAAGAATAG
1 ATAAAATAAATAA-AATAG
129239 ATAAAATAAATAAAATA
1 ATAAAATAAATAAAATA
129256 TTTACTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (18 bp):
ATAAAATAAATAAAATAG
Found at i:134876 original size:22 final size:22
Alignment explanation
Indices: 134848--134925 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
134838 ATCTGAAGCA
134848 TAAGCTCTCATGTTTAACGTAC
1 TAAGCTCTCATGTTTAACGTAC
*
134870 TAAGCTCTCATGTTTAACGAAC
1 TAAGCTCTCATGTTTAACGTAC
* * **
134892 TAAACCCTCATGGCTAACGTAC
1 TAAGCTCTCATGTTTAACGTAC
134914 TAAGCTCTCATG
1 TAAGCTCTCATG
134926 GCTAACGCAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (22 bp):
TAAGCTCTCATGTTTAACGTAC
Found at i:135364 original size:2 final size:2
Alignment explanation
Indices: 135357--135398 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
135347 ATCAGAAGTA
135357 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
135399 TTTCTTGACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:137088 original size:41 final size:41
Alignment explanation
Indices: 137031--137113 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
137021 TATAAAACCT
137031 TAGTTTTGATTTTAGTAGTTTGCTTTACTTTTGAAATTTTC
1 TAGTTTTGATTTTAGTAGTTTGCTTTACTTTTGAAATTTTC
*
137072 TAGTTTTGATTTTAGTATTTTGCTTTACTTTTGAAATTTTC
1 TAGTTTTGATTTTAGTAGTTTGCTTTACTTTTGAAATTTTC
137113 T
1 T
137114 TTTTATTTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.19, C:0.07, G:0.13, T:0.60
Consensus pattern (41 bp):
TAGTTTTGATTTTAGTAGTTTGCTTTACTTTTGAAATTTTC
Found at i:142465 original size:2 final size:2
Alignment explanation
Indices: 142458--142482 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
142448 TCACATGTGA
142458 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
142483 GTGGGGTGTG
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:149580 original size:60 final size:57
Alignment explanation
Indices: 149472--149607 Score: 143
Period size: 59 Copynumber: 2.3 Consensus size: 57
149462 TTTTCAAAGA
* *
149472 TTAACTTGGA-CAAAAAAATTCTAATCCCAATGTGAGAACATTTATCAAGTTCTAGGG
1 TTAACTTGGACCAAAAAAATTCTAATCCCAATGTGAGAACAATTATCAAGTT-TAAGG
* * *
149529 CTTAACTTGGACCAAAAAAAGTAT-TAGTCCTAATGTG-GAAACAATTGTCAAGTTTAAGG
1 -TTAACTTGGACCAAAAAAA-T-TCTAATCCCAATGTGAG-AACAATTATCAAGTTTAAGG
*
149588 TCTAACTTGGACAAAAAAAA
1 T-TAACTTGGACCAAAAAAA
149608 AAATTTAAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
58 11 0.16
59 30 0.45
60 25 0.37
61 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (57 bp):
TTAACTTGGACCAAAAAAATTCTAATCCCAATGTGAGAACAATTATCAAGTTTAAGG
Found at i:149605 original size:59 final size:58
Alignment explanation
Indices: 149472--149606 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 58
149462 TTTTCAAAGA
*
149472 TTAACTTGGACAAAAAAATTCTAATCCCAATGTGAGAACATTTATCAAGTTCTAGGGC
1 TTAACTTGGACAAAAAAATTCTAATCCCAATGTGAGAACAATTATCAAGTTCTAGGGC
* * * *
149530 TTAACTTGGACCAAAAAAAGTAT-TAGTCCTAATGTG-GAAACAATTGTCAAGTT-TAAGG-
1 TTAACTTGGA-CAAAAAAA-T-TCTAATCCCAATGTGAG-AACAATTATCAAGTTCTAGGGC
149588 TCTAACTTGGACAAAAAAA
1 T-TAACTTGGACAAAAAAA
149607 AAAATTTAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
58 19 0.28
59 22 0.33
60 25 0.37
61 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (58 bp):
TTAACTTGGACAAAAAAATTCTAATCCCAATGTGAGAACAATTATCAAGTTCTAGGGC
Found at i:155303 original size:6 final size:6
Alignment explanation
Indices: 155292--155378 Score: 129
Period size: 6 Copynumber: 14.5 Consensus size: 6
155282 CAACGATGGG
* *
155292 TCCGGT TCCGGT TCCGGT TCTGGT TCCGAT TCCGGT TCCGGT TCCGGT
1 TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT
* * *
155340 TCCGGT TCTGGT TACGAT TCCGGT TCCGGT TCCGGT TCC
1 TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCCGGT TCC
155379 AGCTCCAAGA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.03, C:0.31, G:0.30, T:0.36
Consensus pattern (6 bp):
TCCGGT
Found at i:155332 original size:36 final size:36
Alignment explanation
Indices: 155292--155378 Score: 165
Period size: 36 Copynumber: 2.4 Consensus size: 36
155282 CAACGATGGG
*
155292 TCCGGTTCCGGTTCCGGTTCTGGTTCCGATTCCGGT
1 TCCGGTTCCGGTTCCGGTTCTGGTTACGATTCCGGT
155328 TCCGGTTCCGGTTCCGGTTCTGGTTACGATTCCGGT
1 TCCGGTTCCGGTTCCGGTTCTGGTTACGATTCCGGT
155364 TCCGGTTCCGGTTCC
1 TCCGGTTCCGGTTCC
155379 AGCTCCAAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.03, C:0.31, G:0.30, T:0.36
Consensus pattern (36 bp):
TCCGGTTCCGGTTCCGGTTCTGGTTACGATTCCGGT
Found at i:157847 original size:6 final size:6
Alignment explanation
Indices: 157836--157865 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
157826 AAACGAGAGC
157836 GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA
1 GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA
157866 ATAGACAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (6 bp):
GTGGCA
Found at i:163653 original size:17 final size:17
Alignment explanation
Indices: 163628--163661 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
163618 ACTATCAATT
*
163628 ATTTAGAAAAATTCGAA
1 ATTTAGAAAAAGTCGAA
*
163645 ATTTTGAAAAAGTCGAA
1 ATTTAGAAAAAGTCGAA
163662 CGAAACCATT
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:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (17 bp):
ATTTAGAAAAAGTCGAA
Found at i:165911 original size:34 final size:35
Alignment explanation
Indices: 165851--165917 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
165841 CAAACACCAG
* *
165851 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
165886 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
165918 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:167282 original size:24 final size:24
Alignment explanation
Indices: 167250--167300 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
167240 ATGCTTCCCA
167250 TTAATTGCTCTTCAAAGCTACCCG
1 TTAATTGCTCTTCAAAGCTACCCG
**
167274 TTAATTGCTCTTTGAAGCTACCCG
1 TTAATTGCTCTTCAAAGCTACCCG
167298 TTA
1 TTA
167301 TAGGCTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (24 bp):
TTAATTGCTCTTCAAAGCTACCCG
Found at i:167307 original size:24 final size:26
Alignment explanation
Indices: 167264--167328 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 26
167254 TTGCTCTTCA
*
167264 AAGCTACCCGTTA-ATTGCTCTTTG-
1 AAGCTACCCGTTATATGGCTCTTTGT
167288 AAGCTACCCGTTATA-GGCTCTTTGT
1 AAGCTACCCGTTATATGGCTCTTTGT
* *
167313 GAGCTTCCCGTTATAT
1 AAGCTACCCGTTATAT
167329 TGCCCGGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 21 0.60
25 14 0.40
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (26 bp):
AAGCTACCCGTTATATGGCTCTTTGT
Found at i:178100 original size:15 final size:15
Alignment explanation
Indices: 178080--178125 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
178070 ACAAAATAAT
178080 AACATAAGTGACTAA
1 AACATAAGTGACTAA
* *
178095 AACATAA-T-ATTTCA
1 AACATAAGTGA-CTAA
178109 AACATAAGTGACTAA
1 AACATAAGTGACTAA
178124 AA
1 AA
178126 TGTAACCTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.42
15 12 0.50
16 1 0.04
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (15 bp):
AACATAAGTGACTAA
Found at i:181302 original size:2 final size:2
Alignment explanation
Indices: 181292--181339 Score: 87
Period size: 2 Copynumber: 23.5 Consensus size: 2
181282 CATATCACAC
181292 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
181335 AT AT A
1 AT AT A
181340 ACACATAACC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:182114 original size:16 final size:17
Alignment explanation
Indices: 182093--182124 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
182083 AAATATGCAA
182093 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
182109 TCACATAACTTCATAT
1 TCACATAACTTCATAT
182125 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:182419 original size:43 final size:43
Alignment explanation
Indices: 182368--182450 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 43
182358 GAATCAAATA
*
182368 CGATGCCAATGTCCCAGACATGGTCTTACACG-TAAACACAAGT
1 CGATGCCAACGTCCCAGACATGGTCTTACACGAT-AACACAAGT
*
182411 CGATGCCAACGTCCCAGACGTGGTCTTACACGATAACACA
1 CGATGCCAACGTCCCAGACATGGTCTTACACGATAACACA
182451 TATCGGAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.19
Consensus pattern (43 bp):
CGATGCCAACGTCCCAGACATGGTCTTACACGATAACACAAGT
Found at i:183841 original size:7 final size:7
Alignment explanation
Indices: 183829--183853 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
183819 AGAGAGCACT
183829 GATATGA
1 GATATGA
183836 GATATGA
1 GATATGA
183843 GATATGA
1 GATATGA
183850 GATA
1 GATA
183854 GTAGTGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (7 bp):
GATATGA
Found at i:186186 original size:34 final size:34
Alignment explanation
Indices: 186148--186226 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
186138 CAAATGACCT
*
186148 ATGTAAATCATGTATTCCATGTAGTTTATAAACC
1 ATGTAAATCATGTATTCCATGTAATTTATAAACC
* *
186182 ATGTAAATCATGTATTTCATGTAATTTATAATCC
1 ATGTAAATCATGTATTCCATGTAATTTATAAACC
*
186216 TTGTAAATCAT
1 ATGTAAATCAT
186227 ATAACTCTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (34 bp):
ATGTAAATCATGTATTCCATGTAATTTATAAACC
Found at i:186465 original size:23 final size:23
Alignment explanation
Indices: 186403--186493 Score: 96
Period size: 23 Copynumber: 4.0 Consensus size: 23
186393 TTGAGCTGGT
*
186403 AAACGGTAAGCTC-TATCGAGCTG
1 AAACGGTAAGCTCGTA-AGAGCTG
*
186426 -AACGATAAGCTCGTAAGAGCTG
1 AAACGGTAAGCTCGTAAGAGCTG
* * *
186448 AAATGGTAATCTCGTAAGAGGTG
1 AAACGGTAAGCTCGTAAGAGCTG
* *
186471 AAACGGTAAGCTCATACGAGCTG
1 AAACGGTAAGCTCGTAAGAGCTG
186494 TTGTGAGTCC
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
22 17 0.31
23 38 0.69
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (23 bp):
AAACGGTAAGCTCGTAAGAGCTG
Found at i:191628 original size:30 final size:30
Alignment explanation
Indices: 191584--191646 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
191574 ACTTAACAAG
191584 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
191614 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
191644 CAA
1 CAA
191647 TAAAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:213854 original size:19 final size:19
Alignment explanation
Indices: 213830--213868 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
213820 TATAAAAACA
*
213830 ACGGTAGCGGTGAGATTAG
1 ACGGTAGCAGTGAGATTAG
213849 ACGGTAGCAGTGAGATTAG
1 ACGGTAGCAGTGAGATTAG
213868 A
1 A
213869 TACTGGCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.38, T:0.21
Consensus pattern (19 bp):
ACGGTAGCAGTGAGATTAG
Found at i:215350 original size:4 final size:4
Alignment explanation
Indices: 215343--215368 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
215333 GAGCATATGT
215343 ATGG ATGG ATGG ATGG ATGG ATGG AT
1 ATGG ATGG ATGG ATGG ATGG ATGG AT
215369 ACCTGAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.46, T:0.27
Consensus pattern (4 bp):
ATGG
Found at i:229590 original size:18 final size:18
Alignment explanation
Indices: 229567--229604 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
229557 TTTTATTTTT
229567 TTTTTAAAAAAAATTGAG
1 TTTTTAAAAAAAATTGAG
* *
229585 TTTTTATACAAAATTGAG
1 TTTTTAAAAAAAATTGAG
229603 TT
1 TT
229605 ACTCAGCTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTTTAAAAAAAATTGAG
Found at i:230350 original size:23 final size:25
Alignment explanation
Indices: 230320--230380 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 25
230310 ATAAAAAATA
230320 ACCAAAATAT-T-ATTTTTTTATTT
1 ACCAAAATATATAATTTTTTTATTT
230343 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATA-TAT-AATTTTTTTATTT
230370 ACCAAAATATA
1 ACCAAAATATA
230381 CCCAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.26
24 1 0.03
25 1 0.03
26 2 0.06
27 21 0.62
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (25 bp):
ACCAAAATATATAATTTTTTTATTT
Found at i:230452 original size:27 final size:27
Alignment explanation
Indices: 230422--230473 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
230412 GGCCAATCAC
230422 ATTGGCGGCACCAAAGGTGCCAATGTG
1 ATTGGCGGCACCAAAGGTGCCAATGTG
*
230449 ATTGGCGGCACCAATGGTGCCAATG
1 ATTGGCGGCACCAAAGGTGCCAATG
230474 GACTAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.19
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAATGTG
Found at i:231025 original size:82 final size:82
Alignment explanation
Indices: 230929--231093 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
230919 AAAAGGAACC
230929 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
1 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
230994 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
*
231011 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
1 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
231076 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
231093 A
1 A
231094 TTTTAATTAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.38
Consensus pattern (82 bp):
AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
CATAAACATGTTAGACT
Found at i:231184 original size:18 final size:19
Alignment explanation
Indices: 231145--231240 Score: 124
Period size: 19 Copynumber: 5.2 Consensus size: 19
231135 ATTTTATATT
231145 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
231164 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
231182 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
231201 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
231219 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
231238 TTA
1 TTA
231241 CTTAATTAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 30 0.47
19 34 0.53
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:231193 original size:37 final size:37
Alignment explanation
Indices: 231145--231240 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
231135 ATTTTATATT
*
231145 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
231182 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
231219 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
231241 CTTAATTAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:232579 original size:25 final size:24
Alignment explanation
Indices: 232478--232603 Score: 127
Period size: 22 Copynumber: 5.3 Consensus size: 24
232468 CACTAATGAA
*
232478 CAGAGAGCACTAAAGTGCTAT-A-
1 CAGAGAGCACTAACGTGCTATAAT
*
232500 CAGAGAGCAC-AGATGTGCTA-AA-
1 CAGAGAGCACTA-ACGTGCTATAAT
* *
232522 CAGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACTAACGTGCTATAAT
* * *
232546 CAGATAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACTAACGTGCTA-TAAT
232571 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCT-ATAAT
232596 CAGAGAGC
1 CAGAGAGC
232604 GCGCTAAAGT
Statistics
Matches: 86, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.01
22 35 0.41
23 2 0.02
24 17 0.20
25 30 0.35
26 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.17
Consensus pattern (24 bp):
CAGAGAGCACTAACGTGCTATAAT
Found at i:232610 original size:27 final size:26
Alignment explanation
Indices: 232534--232610 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 26
232524 GAGAGCACTG
* *
232534 ACGTGCTAA-AATCAGATAGCACC-A
1 ACGTGCTAATAATCAGAGAGCGCCTA
* * *
232558 ACGTGCTAGTAGTCAGAGAGC-ACTA
1 ACGTGCTAATAATCAGAGAGCGCCTA
232583 ACGTGCTAATAATCAGAGAGCGCGCTA
1 ACGTGCTAATAATCAGAGAGCGC-CTA
232610 A
1 A
232611 AGTTCCTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
24 9 0.21
25 29 0.69
27 4 0.10
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
ACGTGCTAATAATCAGAGAGCGCCTA
Found at i:235868 original size:26 final size:28
Alignment explanation
Indices: 235839--235899 Score: 101
Period size: 26 Copynumber: 2.3 Consensus size: 28
235829 TTTTTTTGGT
235839 ATATTTTGA-TAAATAAAAAAA-TTATA
1 ATATTTTGAGTAAATAAAAAAAGTTATA
235865 ATATTTT-AGTAAATAAAAAAAGTTATA
1 ATATTTTGAGTAAATAAAAAAAGTTATA
235892 ATATTTTG
1 ATATTTTG
235900 GTTATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 1 0.03
26 19 0.59
27 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (28 bp):
ATATTTTGAGTAAATAAAAAAAGTTATA
Found at i:254808 original size:6 final size:6
Alignment explanation
Indices: 254794--254828 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
254784 ATTATTGAGT
*
254794 GAGGGG GAGGCG GAGGCG GAGGCG GAAGGCG GAGG
1 GAGGCG GAGGCG GAGGCG GAGGCG G-AGGCG GAGG
254829 GAGGAAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.20, C:0.11, G:0.69, T:0.00
Consensus pattern (6 bp):
GAGGCG
Found at i:268630 original size:13 final size:13
Alignment explanation
Indices: 268614--268640 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
268604 TAAAAAATAA
268614 ATATTTATTATAT
1 ATATTTATTATAT
268627 ATATTTATTATAT
1 ATATTTATTATAT
268640 A
1 A
268641 AGTACTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTTATTATAT
Found at i:269960 original size:70 final size:71
Alignment explanation
Indices: 269886--270020 Score: 229
Period size: 70 Copynumber: 1.9 Consensus size: 71
269876 AATTAATCTC
* *
269886 ATTTTATTACATCAAATAATATCAAAA-TAACTCAAAAAAA-TTTCTATTTTATTACGTCAAATA
1 ATTTTATTACATCAAATAATATCAAAATTAA-TCAAAAAAATTTTCTATTTTATTACATAAAATA
269949 AACTTCT
65 AACTTCT
269956 ATTTTATTACATCAAATAATATCAAAATTAATCAAAAAAATTTTCTATTTTATTACATAAAATAA
1 ATTTTATTACATCAAATAATATCAAAATTAATCAAAAAAATTTTCTATTTTATTACATAAAATAA
270021 TATCAAAATA
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
70 36 0.59
71 25 0.41
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (71 bp):
ATTTTATTACATCAAATAATATCAAAATTAATCAAAAAAATTTTCTATTTTATTACATAAAATAA
ACTTCT
Found at i:269972 original size:25 final size:25
Alignment explanation
Indices: 269917--269974 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
269907 TCAAAATAAC
* * *
269917 TCAAAAAAATTTCTATTTTATTACG
1 TCAAATAAACTTCTATTTTATTACA
269942 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAACTTCTATTTTATTACA
269967 TCAAATAA
1 TCAAATAA
269975 TATCAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (25 bp):
TCAAATAAACTTCTATTTTATTACA
Found at i:270010 original size:25 final size:25
Alignment explanation
Indices: 269917--270017 Score: 88
Period size: 25 Copynumber: 4.2 Consensus size: 25
269907 TCAAAATAAC
*
269917 TCAAAAAAATTTCTATTTTATTACG
1 TCAAAAAAATTTCTATTTTATTACA
* *
269942 TCAAATAAACTTCTATTTTATTACA
1 TCAAAAAAATTTCTATTTTATTACA
* * **
269967 TC-AAATAATATC-A--AAATTA-A
1 TCAAAAAAATTTCTATTTTATTACA
269987 TCAAAAAAATTTTCTATTTTATTACA
1 TCAAAAAAA-TTTCTATTTTATTACA
270013 T-AAAA
1 TCAAAA
270018 TAATATCAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
20 3 0.05
21 9 0.16
22 3 0.05
23 2 0.04
24 6 0.11
25 32 0.56
26 2 0.04
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.41
Consensus pattern (25 bp):
TCAAAAAAATTTCTATTTTATTACA
Found at i:270204 original size:21 final size:21
Alignment explanation
Indices: 270163--270207 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
270153 GACGGTTGTT
*
270163 GTTCCTCCGGTAGGGATTCTG
1 GTTCCTCCGGTAGGCATTCTG
*
270184 GTTCTTCCGGTACGGCA-TCTG
1 GTTCCTCCGGTA-GGCATTCTG
270205 GTT
1 GTT
270208 GTCAGACTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.09, C:0.24, G:0.31, T:0.36
Consensus pattern (21 bp):
GTTCCTCCGGTAGGCATTCTG
Found at i:271726 original size:23 final size:23
Alignment explanation
Indices: 271700--271798 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
271690 ATAAGTGCAA
271700 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
271723 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
271746 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
271769 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
271792 CACTGAT
1 CACTGAT
271799 CAATAACACT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:273868 original size:20 final size:20
Alignment explanation
Indices: 273831--273868 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
273821 TTTATTTTTA
*
273831 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
273851 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
273869 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:274645 original size:22 final size:25
Alignment explanation
Indices: 274590--274645 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
274580 CTTTTATAAC
*
274590 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAATTAAAAATTATCTAA
*
274615 AAATGAATAAA-TAAAAATT-TCT-T
1 AAAT-AATAAATTAAAAATTATCTAA
274638 AAATAATA
1 AAATAATA
274646 TTTAGAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 4 0.14
23 4 0.14
24 3 0.11
25 11 0.39
26 6 0.21
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.34
Consensus pattern (25 bp):
AAATAATAAATTAAAAATTATCTAA
Found at i:274831 original size:11 final size:11
Alignment explanation
Indices: 274817--274893 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
274807 TTAAATATGG
274817 ATTTGAGAGAA
1 ATTTGAGAGAA
*
274828 ATTTG-GAAGGA
1 ATTTGAG-AGAA
274839 ATTTGAGAGCAA
1 ATTTGAGAG-AA
274851 A-TTGAGAGGAA
1 ATTTGAGA-GAA
274862 ATTT-AGAGGAA
1 ATTTGAGA-GAA
274873 A-TTGAGAGGAA
1 ATTTGAGA-GAA
274884 ATTTGAGAGA
1 ATTTGAGAGA
274894 GGATTAGTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
10 3 0.05
11 42 0.74
12 12 0.21
ACGTcount: A:0.43, C:0.01, G:0.31, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:274842 original size:22 final size:22
Alignment explanation
Indices: 274817--274893 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
274807 TTAAATATGG
274817 ATTTGAGAGAAATTTG-GAAGG-A
1 ATTTGAGAGAAA-TTGAG-AGGAA
274839 ATTTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
274862 ATTT-AGAGGAAATTGAGAGGAA
1 ATTTGAGA-GAAATTGAGAGGAA
274884 ATTTGAGAGA
1 ATTTGAGAGA
274894 GGATTAGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
22 37 0.74
23 13 0.26
ACGTcount: A:0.43, C:0.01, G:0.31, T:0.25
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:274872 original size:33 final size:35
Alignment explanation
Indices: 274817--274892 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 35
274807 TTAAATATGG
* *
274817 ATTTGAGA-GAAATTTGGAAGGAATTTGAGAGCAA
1 ATTTGAGAGGAAATTTAGAAGGAAATTGAGAGCAA
*
274851 A-TTGAGAGGAAATTTAG-AGGAAATTGAGAGGAA
1 ATTTGAGAGGAAATTTAGAAGGAAATTGAGAGCAA
274884 ATTTGAGAG
1 ATTTGAGAG
274893 AGGATTAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.42, C:0.01, G:0.32, T:0.25
Consensus pattern (35 bp):
ATTTGAGAGGAAATTTAGAAGGAAATTGAGAGCAA
Found at i:281836 original size:7 final size:7
Alignment explanation
Indices: 281824--281848 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
281814 GCTGCTTGCT
281824 TTTTGGC
1 TTTTGGC
281831 TTTTGGC
1 TTTTGGC
281838 TTTTGGC
1 TTTTGGC
281845 TTTT
1 TTTT
281849 AGGATCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.24, T:0.64
Consensus pattern (7 bp):
TTTTGGC
Found at i:282590 original size:21 final size:21
Alignment explanation
Indices: 282566--282607 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
282556 TTGCCGAAAG
*
282566 ATTAAATGAAAGCCGGGTAAT
1 ATTAAATGAAAGCCGGCTAAT
282587 ATTAAATGAAAGCCGGCTAAT
1 ATTAAATGAAAGCCGGCTAAT
282608 CACCTATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (21 bp):
ATTAAATGAAAGCCGGCTAAT
Found at i:295158 original size:6 final size:6
Alignment explanation
Indices: 295147--295180 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
295137 GTACAATAAT
295147 CTACAC CTACAC CTACAC CTACAC CTACAC CTAC
1 CTACAC CTACAC CTACAC CTACAC CTACAC CTAC
295181 TAGTGGGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CTACAC
Found at i:296238 original size:19 final size:19
Alignment explanation
Indices: 296214--296252 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
296204 AATATTTTCT
*
296214 AGTAAATCATTTTACAGAA
1 AGTAAAACATTTTACAGAA
*
296233 AGTAAAACATTTTCCAGAA
1 AGTAAAACATTTTACAGAA
296252 A
1 A
296253 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (19 bp):
AGTAAAACATTTTACAGAA
Found at i:296255 original size:33 final size:34
Alignment explanation
Indices: 296202--296266 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
296192 CAAACAGCAG
* *
296202 AAAATATTTTCTAGTAAATCATTTTACAGAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAGT
*
296236 AAAACATTTTCCAG-AAATCATTTTACGGAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAA
296267 ACATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAGT
Found at i:296259 original size:14 final size:14
Alignment explanation
Indices: 296236--296275 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
296226 TACAGAAAGT
*
296236 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
296250 AAATCATTTTACGG
1 AAAACATTTTACAG
296264 AAAACATTTTAC
1 AAAACATTTTAC
296276 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:302882 original size:48 final size:49
Alignment explanation
Indices: 302824--302923 Score: 184
Period size: 48 Copynumber: 2.1 Consensus size: 49
302814 CACCTCGGCT
*
302824 TCTTTTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCC-A
1 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCTA
302872 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCTA
1 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCTA
302921 TCT
1 TCT
302924 GTCCGTTCTT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 46 0.92
49 4 0.08
ACGTcount: A:0.18, C:0.32, G:0.10, T:0.40
Consensus pattern (49 bp):
TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCTA
Found at i:314526 original size:15 final size:16
Alignment explanation
Indices: 314503--314558 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
314493 TTTTTATGTT
*
314503 TTATATATATTATTTTA
1 TTATATATA-TATTATA
*
314520 TTATATAATATAATATA
1 TTATAT-ATATATTATA
*
314537 TTATAT-TGTATTATA
1 TTATATATATATTATA
314552 TTATATA
1 TTATATA
314559 AATTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 13 0.39
17 17 0.52
18 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTATATATATATTATA
Found at i:314542 original size:5 final size:5
Alignment explanation
Indices: 314503--314557 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
314493 TTTTTATGTT
* *
314503 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATA TTGTA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
314552 TTATA T
1 TTATA T
314558 AAATTAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 28 0.68
7 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:314543 original size:27 final size:29
Alignment explanation
Indices: 314504--314559 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
314494 TTTTATGTTT
*
314504 TATATATATTATTTTATTATATAATATAA
1 TATATATATTATTGTATTATATAATATAA
*
314533 TATAT-TA-TATTGTATTATATTATATAA
1 TATATATATTATTGTATTATATAATATAA
314560 ATTAAATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.72
28 2 0.08
29 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
TATATATATTATTGTATTATATAATATAA
Found at i:316039 original size:2 final size:2
Alignment explanation
Indices: 316032--316060 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
316022 TAGTATGTAA
316032 AT AT 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 AT AT A
316061 AATTTAAGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:317404 original size:24 final size:23
Alignment explanation
Indices: 317377--317421 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
317367 GCCAAATGGA
* *
317377 GGATAGCGATGAAGATGATGAAGC
1 GGATAACGAGGAAGAT-ATGAAGC
317401 GGATAACGAGGAAGATATGAA
1 GGATAACGAGGAAGATATGAA
317422 AGAAAGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.42, C:0.07, G:0.36, T:0.16
Consensus pattern (23 bp):
GGATAACGAGGAAGATATGAAGC
Found at i:317529 original size:24 final size:22
Alignment explanation
Indices: 317481--317529 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 22
317471 ATTATTTTAA
317481 ATTATATTTTATAATATTATAT
1 ATTATATTTTATAATATTATAT
317503 ATTATGATTTTAGTAA-ATTCATAT
1 ATTAT-ATTTTA-TAATATT-ATAT
317527 ATT
1 ATT
317530 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.21
23 9 0.38
24 10 0.42
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTATATTTTATAATATTATAT
Found at i:317804 original size:16 final size:16
Alignment explanation
Indices: 317785--317830 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
317775 CTATTAGGCC
*
317785 TCTATTCCATTACGCA
1 TCTATTCCATTACACA
* *
317801 TCTATTCTATTACACC
1 TCTATTCCATTACACA
317817 TCTATTCCATTACA
1 TCTATTCCATTACA
317831 GCGAACCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.41
Consensus pattern (16 bp):
TCTATTCCATTACACA
Found at i:318774 original size:8 final size:8
Alignment explanation
Indices: 318761--318785 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
318751 AGATCTAAAC
318761 AGGCAGTA
1 AGGCAGTA
318769 AGGCAGTA
1 AGGCAGTA
318777 AGGCAGTA
1 AGGCAGTA
318785 A
1 A
318786 AGGAGCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.36, T:0.12
Consensus pattern (8 bp):
AGGCAGTA
Found at i:320042 original size:123 final size:123
Alignment explanation
Indices: 319818--320042 Score: 378
Period size: 123 Copynumber: 1.8 Consensus size: 123
319808 CTATTTCGAG
* *
319818 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTGGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTGGAGAAGAAATTATG
* *
319883 AAATCGCGCCCTCGTGGACGTGATTTTGTTACAGTAGGTCATGTAAGAAATATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTT
* * *
319941 TTGACGTTTCTGAGCAAATAGTATAAAATTGCTTCTACCAGGATGTTATTTGAGAAGAAATTATG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTGGAGAAGAAATTATG
*
320006 AAATCGCGCCCTCGTGGACGCGATTTTGCTATAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
320043 CAAGTTTGGG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 94 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTGGAGAAGAAATTATG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTT
Found at i:323712 original size:55 final size:54
Alignment explanation
Indices: 323577--323756 Score: 229
Period size: 55 Copynumber: 3.2 Consensus size: 54
323567 ATGTAAAATT
* * * *
323577 AAAATTATTAAGTCAAAAATTTGTGTTAATGGTTATTAAAATTATCATGCACA-CA-GT
1 AAAATTATTAAGT-AAAAAATTGTGTTAATGGTTAGTAAAATTATCA---A-ATTATGA
*
323634 AAAATTATTAAGTCAAAAAATTGTGTTAATGATTAGTAAAATTATCAAATTATGA
1 AAAATTATTAAGT-AAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGA
*
323689 AAAATTATTAAGTGTAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGA
1 AAAATTATTAAGT-AAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGA
323744 AAAATTATTAAGT
1 AAAATTATTAAGT
323757 TAGGTTAGGG
Statistics
Matches: 113, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
53 1 0.01
54 2 0.02
55 66 0.58
57 44 0.39
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.37
Consensus pattern (54 bp):
AAAATTATTAAGTAAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGA
Found at i:323806 original size:29 final size:29
Alignment explanation
Indices: 323750--324058 Score: 371
Period size: 29 Copynumber: 10.7 Consensus size: 29
323740 ATGAAAAATT
323750 ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
* *
323779 ATTAGGTTAGGGTTATGGTTAGGGTTTTTA
1 ATTAAGTTA-GGTTAGGGTTAGGGTTTTTA
*
323809 ATTAAATTAGGTT-GGAGTTAGGGTTTTTA
1 ATTAAGTTAGGTTAGG-GTTAGGGTTTTTA
* ** *
323838 AATGGGTTATGTTAGGGTTAGGGTTTTTA
1 ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
* * *
323867 ATTAATTTAGGTTAGGGTTAAGGTTTGTA
1 ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
*
323896 ATTAAATTAGGTTAGGGTTAGGGTTTTTTA
1 ATTAAGTTAGGTTAGGGTTAGGG-TTTTTA
*
323926 ATTAAGTTAGGTTAGGGTTAGTGTTTTTA
1 ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
*
323955 ATTAAATTAGGTT-GGAGTTAGGGTTTTTA
1 ATTAAGTTAGGTTAGG-GTTAGGGTTTTTA
*
323984 ATTAGGGTTTAGGTTAGGGTTAGGGTTTTTA
1 ATTA-AG-TTAGGTTAGGGTTAGGGTTTTTA
324015 ATT-AG---GGTTTA-GGTTAGGGTTTTTA
1 ATTAAGTTAGG-TTAGGGTTAGGGTTTTTA
*
324040 ATTAAATTAGGTTAGGGTT
1 ATTAAGTTAGGTTAGGGTT
324059 TTTATTACAT
Statistics
Matches: 238, Mismatches: 28, Indels: 28
0.81 0.10 0.10
Matches are distributed among these distances:
25 19 0.08
26 4 0.02
28 6 0.03
29 130 0.55
30 54 0.23
31 23 0.10
32 2 0.01
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
Found at i:323819 original size:59 final size:58
Alignment explanation
Indices: 323750--324058 Score: 362
Period size: 59 Copynumber: 5.3 Consensus size: 58
323740 ATGAAAAATT
* * *
323750 ATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAGGTTAGGGTTATGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTA-GGTTAGGGTTAGGGTTTTTA
* ** *
323809 ATTAAATTAGGTT-GGAGTTAGGGTTTTTAAATGGGTTATGTTAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGG-GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTA
* * * *
323867 ATTAATTTAGGTTAGGGTTAAGGTTTGTAATTAAATTAGGTTAGGGTTAGGGTTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGG-TTTTTA
* * *
323926 ATTAAGTTAGGTTAGGGTTAGTGTTTTTAATTAAATTAGGTT-GGAGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGG-GTTAGGGTTTTTA
**
323984 ATTAGGGTTTAGGTTAGGGTTAGGGTTTTTAATT-AG---GGTTTA-GGTTAGGGTTTTTA
1 ATTA--AATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGG-TTAGGGTTAGGGTTTTTA
324040 ATTAAATTAGGTTAGGGTT
1 ATTAAATTAGGTTAGGGTT
324059 TTTATTACAT
Statistics
Matches: 219, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
54 13 0.06
56 19 0.09
57 3 0.01
58 73 0.33
59 86 0.39
60 25 0.11
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (58 bp):
ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTA
Found at i:323856 original size:88 final size:87
Alignment explanation
Indices: 323755--324058 Score: 379
Period size: 88 Copynumber: 3.5 Consensus size: 87
323745 AAATTATTAA
** *
323755 GTTAGGTTAGGGTTAGGGTTTTTAATTAGGTTAGGGTTATGGTTAGGGTTTTTAATTAAATTAGG
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTAGGGTTTTTAATTAAATTAGG
*
323820 TT-GGAGTTAGGGTTTTTAAATGG
65 TTAGG-GTTAGGGTTTTTAATTGG
* * * *
323843 GTTATGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAAGGTTTGTAATTAAATTAGGT
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGT
**
323908 TAGGGTTAGGGTTTTTTAATTAA
66 TAGGGTTAGGG-TTTTTAATTGG
* **
323931 GTTAGGTTAGGGTTAGTGTTTTTAATTAAATTAGGTT-GGAGTTAGGGTTTTTAATTAGGGTTTA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG-GTTAGGGTTTTTAATTA--AATTA
323995 GGTTAGGGTTAGGGTTTTTAATTAGG
63 GGTTAGGGTTAGGGTTTTTAATT-GG
324021 G-T---TTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
324059 TTTATTACAT
Statistics
Matches: 190, Mismatches: 19, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
85 29 0.15
86 5 0.03
87 39 0.21
88 89 0.47
89 10 0.05
90 18 0.09
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.46
Consensus pattern (87 bp):
GTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGT
TAGGGTTAGGGTTTTTAATTGG
Found at i:323984 original size:25 final size:26
Alignment explanation
Indices: 323959--324043 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 26
323949 TTTTTAATTA
323959 AATTA-GGTTGGA-GTTAGGGTTTTT
1 AATTAGGGTTGGAGGTTAGGGTTTTT
323983 AATTAGGGTTTAGGTTAGGGTTAGGGTTTTT
1 AATTAGGG-TT-GG--A-GGTTAGGGTTTTT
*
324014 AATTAGGGTT-TAGGTTAGGGTTTTT
1 AATTAGGGTTGGAGGTTAGGGTTTTT
324039 AATTA
1 AATTA
324044 AATTAGGTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
24 5 0.09
25 20 0.38
26 3 0.06
27 2 0.04
29 1 0.02
30 2 0.04
31 20 0.38
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (26 bp):
AATTAGGGTTGGAGGTTAGGGTTTTT
Found at i:324053 original size:23 final size:24
Alignment explanation
Indices: 324001--324062 Score: 90
Period size: 25 Copynumber: 2.6 Consensus size: 24
323991 TTTAGGTTAG
**
324001 GGTTAGGGTTTTTAATTAGGGTTTA
1 GGTTAGGGTTTTTAATTA-GAATTA
324026 GGTTAGGGTTTTTAATTA-AATTA
1 GGTTAGGGTTTTTAATTAGAATTA
324049 GGTTAGGGTTTTTA
1 GGTTAGGGTTTTTA
324063 TTACATCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 17 0.49
25 18 0.51
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (24 bp):
GGTTAGGGTTTTTAATTAGAATTA
Found at i:324142 original size:36 final size:36
Alignment explanation
Indices: 324102--324214 Score: 90
Period size: 36 Copynumber: 3.2 Consensus size: 36
324092 ATCAAATAAT
324102 ATCAAAATAACTCGAAAAACTTTCTATGCGTATTAC
1 ATCAAAATAACTCGAAAAACTTTCTATGCGTATTAC
* *** * ** * *
324138 ATC-AAATAAACTTCTATTTTA-TTAC-AT-CAAATAAT
1 ATCAAAAT-AAC-TCGA-AAAACTTTCTATGCGTATTAC
324173 ATCAAAATAACTCGAAAAACTTTCTATGCGTATTAC
1 ATCAAAATAACTCGAAAAACTTTCTATGCGTATTAC
324209 ATCAAA
1 ATCAAA
324215 TAAACTTCTA
Statistics
Matches: 52, Mismatches: 18, Indels: 14
0.62 0.21 0.17
Matches are distributed among these distances:
33 1 0.02
34 6 0.12
35 16 0.31
36 22 0.42
37 6 0.12
38 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
ATCAAAATAACTCGAAAAACTTTCTATGCGTATTAC
Found at i:324177 original size:71 final size:71
Alignment explanation
Indices: 324061--324242 Score: 355
Period size: 71 Copynumber: 2.6 Consensus size: 71
324051 TTAGGGTTTT
*
324061 TATTACATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAACTTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAACTTTC
324126 TATGCG
66 TATGCG
324132 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAACTTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAACTTTC
324197 TATGCG
66 TATGCG
324203 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAA
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAA
324243 ACTTCTATTT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 110 1.00
ACGTcount: A:0.44, C:0.16, G:0.03, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAACTTTC
TATGCG
Found at i:324234 original size:96 final size:96
Alignment explanation
Indices: 324132--324338 Score: 405
Period size: 96 Copynumber: 2.2 Consensus size: 96
324122 TTTCTATGCG
324132 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAACTTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAACTTTC
*
324197 TATGCGTATTACATCAAATAAACTTCTATTT
66 TATGCATATTACATCAAATAAACTTCTATTT
324228 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAACTTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAACTTTC
324293 TATGCATATTACATCAAATAAACTTCTATTT
66 TATGCATATTACATCAAATAAACTTCTATTT
324324 TATTACATCAAATAA
1 TATTACATCAAATAA
324339 TAAATTTAAA
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 110 1.00
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.37
Consensus pattern (96 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAACTTTC
TATGCATATTACATCAAATAAACTTCTATTT
Found at i:327788 original size:50 final size:50
Alignment explanation
Indices: 327673--327838 Score: 251
Period size: 50 Copynumber: 3.3 Consensus size: 50
327663 GATAATAACA
* ** *
327673 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
327724 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
327774 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
327824 TGCCAATGCCATGTC
1 TGCCAATGCCATGTC
327839 TCATCTCGGT
Statistics
Matches: 103, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 70 0.68
51 33 0.32
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:327845 original size:24 final size:24
Alignment explanation
Indices: 327813--327862 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
327803 ACATGGGACC
327813 TCTCATCTCGGTGCCAATGCCATG
1 TCTCATCTCGGTGCCAATGCCATG
327837 TCTCATCTCGGTGCCAATGCCATG
1 TCTCATCTCGGTGCCAATGCCATG
327861 TC
1 TC
327863 CCAGACATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.34, G:0.20, T:0.30
Consensus pattern (24 bp):
TCTCATCTCGGTGCCAATGCCATG
Found at i:327884 original size:74 final size:74
Alignment explanation
Indices: 327763--327912 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 74
327753 ACGGGGGACC
327763 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCC
1 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCC
327828 AATGCCATG
66 AATGCCATG
*
327837 TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCC
1 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCC
327902 AATGCCATG
66 AATGCCATG
327911 TC
1 TC
327913 CCAGATATGG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.19, C:0.33, G:0.21, T:0.27
Consensus pattern (74 bp):
TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCC
AATGCCATG
Found at i:327912 original size:50 final size:50
Alignment explanation
Indices: 327837--327939 Score: 197
Period size: 50 Copynumber: 2.1 Consensus size: 50
327827 CAATGCCATG
327837 TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACC
1 TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACC
*
327887 TCTCATCTCGGTGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACC
1 TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACC
327937 TCT
1 TCT
327940 TTACCCAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.28
Consensus pattern (50 bp):
TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACC
Found at i:327933 original size:124 final size:124
Alignment explanation
Indices: 327713--327939 Score: 400
Period size: 124 Copynumber: 1.8 Consensus size: 124
327703 CATGGGATGT
* *
327713 TCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCC
1 TCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCC
327778 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATG
66 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATG
* *
327837 TCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCC
1 TCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCC
* *
327902 AATGCCATGTCCCAGATATGGTCTTACATGGGACCTCT
66 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
327940 TTACCCAAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 97 1.00
ACGTcount: A:0.19, C:0.32, G:0.22, T:0.26
Consensus pattern (124 bp):
TCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCC
AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATG
Found at i:328055 original size:13 final size:13
Alignment explanation
Indices: 328034--328064 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
328024 GCTTAGATCA
*
328034 TCATCAAATAAAT
1 TCATAAAATAAAT
328047 TCATAAAATAAAT
1 TCATAAAATAAAT
328060 TCATA
1 TCATA
328065 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:328311 original size:30 final size:31
Alignment explanation
Indices: 328277--328334 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
328267 CCTTGACTTT
*
328277 AACTTTTTCAAAATTACAATTTT-ACCCTTA
1 AACTTTTACAAAATTACAATTTTGACCCTTA
* *
328307 AACTTTTACATAATTACATTTTTGACCC
1 AACTTTTACAAAATTACAATTTTGACCC
328335 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (31 bp):
AACTTTTACAAAATTACAATTTTGACCCTTA
Found at i:329490 original size:51 final size:51
Alignment explanation
Indices: 329355--329478 Score: 171
Period size: 51 Copynumber: 2.4 Consensus size: 51
329345 TATTTTAAAA
* *
329355 AAGGAAATTGAGAGCAAATTGAAATTAAATATGGATTTGAGAGATTTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGAATTTGAGAGATTTTTGG
* * *
329406 AATGAAATTGAAAGGAAATTGAAATTAAATATGAATTT-ATGAGAATTTTT-G
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGAATTTGA-GAG-ATTTTTGG
329457 AAGGAAATTGAGAGAAAATTGA
1 AAGGAAATTGAGAGAAAATTGA
329479 GAGGAAATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
50 1 0.02
51 57 0.89
52 6 0.09
ACGTcount: A:0.46, C:0.01, G:0.23, T:0.31
Consensus pattern (51 bp):
AAGGAAATTGAGAGAAAATTGAAATTAAATATGAATTTGAGAGATTTTTGG
Found at i:329491 original size:12 final size:11
Alignment explanation
Indices: 329454--329493 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
329444 ATGAGAATTT
329454 TTGA-AGGAAA
1 TTGAGAGGAAA
*
329464 TTGAGAGAAAA
1 TTGAGAGGAAA
329475 TTGAGAGGAAA
1 TTGAGAGGAAA
329486 TATGAGAG
1 T-TGAGAG
329494 AGGATTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 4 0.15
11 16 0.62
12 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:329964 original size:101 final size:102
Alignment explanation
Indices: 329850--330053 Score: 331
Period size: 101 Copynumber: 2.0 Consensus size: 102
329840 ATTTTTATCA
* * *
329850 TTTTATTTTACCCTTTTCACTATTCATCATTTTTTACTCGTAAAATA-TTTTTTATTTAAATCTT
1 TTTTATTTCACCCTTTTCACTATTCATCATTTTTTACTCGTAAAAAAGTTTTCTATTTAAATCTT
329914 TTAAAAAGTTTAAAAT-AATAAAAATAAAATTATATTT
66 TTAAAAA-TTTAAAATGAATAAAAATAAAATTATATTT
329951 TTTTATTTCACCCTTTTCACTATTCATCATTTTTTACTCGTAAAAAAGTTTTCTATTTAAATCTT
1 TTTTATTTCACCCTTTTCACTATTCATCATTTTTTACTCGTAAAAAAGTTTTCTATTTAAATCTT
* * *
330016 TTAAAGATTTTAAATGGATAAAAATAAAATTATATTT
66 TTAAAAATTTAAAATGAATAAAAATAAAATTATATTT
330053 T
1 T
330054 AATTTCACTA
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
101 52 0.55
102 43 0.45
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (102 bp):
TTTTATTTCACCCTTTTCACTATTCATCATTTTTTACTCGTAAAAAAGTTTTCTATTTAAATCTT
TTAAAAATTTAAAATGAATAAAAATAAAATTATATTT
Found at i:340737 original size:163 final size:163
Alignment explanation
Indices: 340467--340793 Score: 645
Period size: 163 Copynumber: 2.0 Consensus size: 163
340457 CAGGGATCAC
340467 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
1 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
340532 TACAAATTCTAAATATCTATAGGATTCAAATTTATATCAGTCAATTAGAAGTAATATTAAATTCC
66 TACAAATTCTAAATATCTATAGGATTCAAATTTATATCAGTCAATTAGAAGTAATATTAAATTCC
*
340597 TTTCAAACATAGGACGACACAATTAATGCTATA
131 TTTCAAACATAGGACAACACAATTAATGCTATA
340630 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
1 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
340695 TACAAATTCTAAATATCTATAGGATTCAAATTTATATCAGTCAATTAGAAGTAATATTAAATTCC
66 TACAAATTCTAAATATCTATAGGATTCAAATTTATATCAGTCAATTAGAAGTAATATTAAATTCC
340760 TTTCAAACATAGGACAACACAATTAATGCTATA
131 TTTCAAACATAGGACAACACAATTAATGCTATA
340793 T
1 T
340794 TTGAACTGAA
Statistics
Matches: 163, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 163 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (163 bp):
TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
TACAAATTCTAAATATCTATAGGATTCAAATTTATATCAGTCAATTAGAAGTAATATTAAATTCC
TTTCAAACATAGGACAACACAATTAATGCTATA
Found at i:343305 original size:21 final size:23
Alignment explanation
Indices: 343269--343312 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
343259 TAATAAATGA
343269 AAATTATAAAACTATTAAATATT
1 AAATTATAAAACTATTAAATATT
*
343292 AAATTA-AAAA-TATTATATATT
1 AAATTATAAAACTATTAAATATT
343313 TTCTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 4 0.20
23 6 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATTATAAAACTATTAAATATT
Found at i:346697 original size:94 final size:95
Alignment explanation
Indices: 346571--346770 Score: 217
Period size: 95 Copynumber: 2.1 Consensus size: 95
346561 GTTTGTCAAT
* * * * * * * **
346571 TAAATTAATTAAAAAATTTTCAAAACTGGATTA-GTTTTCGTGTTTATTATTTTTAAGAAAAAAT
1 TAAATTAATTAAAAAAATTTAAAAACTAGATTAGGATTTAGAGTTAAGGATTTTTAAGAAAAAAT
* * *
346635 CAATTAAATT-AGAGTTTAGGGTTACTTGAG
66 CAAATAAATTAAG-GTTCAGGGTTACTAGAG
** * *
346665 TACTTTAATTAAAAAAATTTAAAAA-TCAGATTAGGATTTAGAGTTAAGGGTTTTTAAGGAAAAA
1 TAAATTAATTAAAAAAATTTAAAAACT-AGATTAGGATTTAGAGTTAAGGATTTTTAAGAAAAAA
346729 TCAAATAAATTAAGGTTCAGGGTTACTAGAG
65 TCAAATAAATTAAGGTTCAGGGTTACTAGAG
346760 TAAATTAATTA
1 TAAATTAATTA
346771 TAAATTTATA
Statistics
Matches: 85, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
93 1 0.01
94 26 0.31
95 56 0.66
96 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (95 bp):
TAAATTAATTAAAAAAATTTAAAAACTAGATTAGGATTTAGAGTTAAGGATTTTTAAGAAAAAAT
CAAATAAATTAAGGTTCAGGGTTACTAGAG
Done.