Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 79 of 129
Found at i:12513959 original size:52 final size:51
Alignment explanation
Indices: 12513891--12514044 Score: 182
Period size: 51 Copynumber: 3.0 Consensus size: 51
12513881 AAAATTTCAA
* * * *
12513891 ATTCGCAAGACTTTTTAGCTTCGTAAAAATTCATATTCATAAGATTTTAAG
1 ATTCACAAGATTTTTTAGCTTCGTAAAAATTCAAATTCGTAAGATTTTAAG
* * * * * * *
12513942 ATTCATAAGAGTTTTTTAGTTTCATAAGAATTTAGATTCGTAAGATTTCAAG
1 ATTCACAAGA-TTTTTTAGCTTCGTAAAAATTCAAATTCGTAAGATTTTAAG
* *
12513994 ATTCGCAAGATTTTTCAGCTTCGTAAAAATTCAAATTCGTAAGATTTTAAG
1 ATTCACAAGATTTTTTAGCTTCGTAAAAATTCAAATTCGTAAGATTTTAAG
12514045 TTTACATTTG
Statistics
Matches: 83, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
51 42 0.51
52 41 0.49
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (51 bp):
ATTCACAAGATTTTTTAGCTTCGTAAAAATTCAAATTCGTAAGATTTTAAG
Found at i:12513965 original size:19 final size:17
Alignment explanation
Indices: 12513925--12514007 Score: 78
Period size: 17 Copynumber: 4.8 Consensus size: 17
12513915 AAAAATTCAT
12513925 ATTCATAAGATTTTAAG
1 ATTCATAAGATTTTAAG
*
12513942 ATTCATAAGAGTTTTTTAG
1 ATTCATAAGA--TTTTAAG
* *
12513961 TTTCATAAGAATTT-AG
1 ATTCATAAGATTTTAAG
* *
12513977 ATTCGTAAGATTTCAAG
1 ATTCATAAGATTTTAAG
**
12513994 ATTCGCAAGATTTT
1 ATTCATAAGATTTT
12514008 TCAGCTTCGT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
16 12 0.22
17 27 0.50
19 15 0.28
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.42
Consensus pattern (17 bp):
ATTCATAAGATTTTAAG
Found at i:12513985 original size:16 final size:16
Alignment explanation
Indices: 12513956--12514042 Score: 50
Period size: 16 Copynumber: 5.2 Consensus size: 16
12513946 ATAAGAGTTT
* *
12513956 TTTAGTTTCATAAGAA
1 TTTAGATTCGTAAGAA
12513972 TTTAGATTCGTAAG-A
1 TTTAGATTCGTAAGAA
* *
12513987 TTTCAAGATTCGCAAGATT
1 TTT--AGATTCGTAAGA-A
* *
12514006 TTTCAGCTTCGTAAAAA
1 TTT-AGATTCGTAAGAA
* * *
12514023 TTCAAATTCGTAAGAT
1 TTTAGATTCGTAAGAA
12514039 TTTA
1 TTTA
12514043 AGTTTACATT
Statistics
Matches: 52, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
15 4 0.08
16 24 0.46
17 12 0.23
18 9 0.17
19 3 0.06
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (16 bp):
TTTAGATTCGTAAGAA
Found at i:12514037 original size:51 final size:51
Alignment explanation
Indices: 12513884--12514040 Score: 183
Period size: 52 Copynumber: 3.1 Consensus size: 51
12513874 GATTCACAAA
* *
12513884 ATTTCAA-ATTCGCAAGACTTTTTAGCTTCGTAAAAATTCATATTCATAAG
1 ATTTCAAGATTCGCAAGACTTTTTAGCTTCGTAAAAATTCAAATTCGTAAG
* ** * * * * * *
12513934 ATTTTAAGATTCATAAGAGTTTTTTAGTTTCATAAGAATTTAGATTCGTAAG
1 ATTTCAAGATTCGCAAGA-CTTTTTAGCTTCGTAAAAATTCAAATTCGTAAG
12513986 ATTTCAAGATTCGCAAGA-TTTTTCAGCTTCGTAAAAATTCAAATTCGTAAG
1 ATTTCAAGATTCGCAAGACTTTTT-AGCTTCGTAAAAATTCAAATTCGTAAG
12514037 ATTT
1 ATTT
12514041 TAAGTTTACA
Statistics
Matches: 86, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
50 11 0.13
51 34 0.40
52 41 0.48
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (51 bp):
ATTTCAAGATTCGCAAGACTTTTTAGCTTCGTAAAAATTCAAATTCGTAAG
Found at i:12514037 original size:103 final size:101
Alignment explanation
Indices: 12513854--12514044 Score: 294
Period size: 103 Copynumber: 1.9 Consensus size: 101
12513844 ATTCCCAAAA
12513854 TTTTAGTTTCACAAGAATTTGATTCACAAAATTTCAAATTCGCAAGACTTTTTAGCTTCGTAAAA
1 TTTTAGTTTCACAAGAATTTGATTCACAAAATTTCAAATTCGCAAGACTTTTTAGCTTCGTAAAA
*
12513919 ATTCATATTCATAAGATTTTAAGATTCATAAGAGTT
66 ATTCAAATTCATAAGATTTTAAGATTCATAAGAGTT
* ** *
12513955 TTTTAGTTTCATAAGAATTTAGATTCGTAAGATTTCAAGATTCGCAAGA-TTTTTCAGCTTCGTA
1 TTTTAGTTTCACAAGAATTT-GATTCACAAAATTTCAA-ATTCGCAAGACTTTTT-AGCTTCGTA
*
12514019 AAAATTCAAATTCGTAAGATTTTAAG
63 AAAATTCAAATTCATAAGATTTTAAG
12514045 TTTACATTTG
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
101 19 0.23
102 19 0.23
103 43 0.53
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (101 bp):
TTTTAGTTTCACAAGAATTTGATTCACAAAATTTCAAATTCGCAAGACTTTTTAGCTTCGTAAAA
ATTCAAATTCATAAGATTTTAAGATTCATAAGAGTT
Found at i:12514153 original size:21 final size:21
Alignment explanation
Indices: 12514127--12514167 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12514117 ACATTTAAAG
12514127 ATTCGAATTCTAGAGATTCAC
1 ATTCGAATTCTAGAGATTCAC
* *
12514148 ATTCGAATTTTGGAGATTCA
1 ATTCGAATTCTAGAGATTCA
12514168 TACCCAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (21 bp):
ATTCGAATTCTAGAGATTCAC
Found at i:12514389 original size:44 final size:44
Alignment explanation
Indices: 12514297--12514404 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
12514287 CTCCTTATTC
* * *
12514297 AAGTTCAAAGATTCACATTCAATAAATCTTAGAGTTTCACATCT
1 AAGTTCAAAGATTCTCATTCAATAAATCTTAGAGATTCACATCA
*
12514341 AAGTTCAAAGGTTCTCATTCAA-AAAT-TTAGAGATTCACATCCAA
1 AAGTTCAAAGATTCTCATTCAATAAATCTTAGAGATTCACAT-C-A
* *
12514385 AAGTTCAAAGTTTCTTATTC
1 AAGTTCAAAGATTCTCATTC
12514405 GAGTTTGAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
42 13 0.23
43 5 0.09
44 38 0.68
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (44 bp):
AAGTTCAAAGATTCTCATTCAATAAATCTTAGAGATTCACATCA
Found at i:12514492 original size:22 final size:22
Alignment explanation
Indices: 12514447--12514600 Score: 192
Period size: 21 Copynumber: 7.2 Consensus size: 22
12514437 GGTTTCACAT
12514447 CTCAAAGATTCTCATTT-AAAA
1 CTCAAAGATTCTCATTTGAAAA
12514468 CTCAAAGATTCTCATTTGAAAA
1 CTCAAAGATTCTCATTTGAAAA
*
12514490 CTCAAA-ATTTTCATTTTG-AAA
1 CTCAAAGATTCTCA-TTTGAAAA
*
12514511 TTCAAAGATTCTCATTTGAAAA
1 CTCAAAGATTCTCATTTGAAAA
*
12514533 CTCAAATATTCTCATTTG-AAA
1 CTCAAAGATTCTCATTTGAAAA
* * *
12514554 CTTAAAAATTCTTATTTGAAAA
1 CTCAAAGATTCTCATTTGAAAA
* *
12514576 CTAAAATATTCTCATTTG-AAA
1 CTCAAAGATTCTCATTTGAAAA
12514597 CTCA
1 CTCA
12514601 TAATTTTATC
Statistics
Matches: 116, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
21 59 0.51
22 57 0.49
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (22 bp):
CTCAAAGATTCTCATTTGAAAA
Found at i:12514597 original size:43 final size:43
Alignment explanation
Indices: 12514454--12514598 Score: 197
Period size: 43 Copynumber: 3.4 Consensus size: 43
12514444 CATCTCAAAG
* *
12514454 ATTCTCATTTAAAACTCAAAGATTCTCATTTGAAAACTCAAAAT
1 ATTCTCATTTGAAACTTAAAGATTCTCATTTGAAAACT-AAAAT
*
12514498 -TT-TCATTTTGAAA-TTCAAAGATTCTCATTTGAAAACTCAAAT
1 ATTCTCA-TTTGAAACTT-AAAGATTCTCATTTGAAAACTAAAAT
* *
12514540 ATTCTCATTTGAAACTTAAAAATTCTTATTTGAAAACTAAAAT
1 ATTCTCATTTGAAACTTAAAGATTCTCATTTGAAAACTAAAAT
12514583 ATTCTCATTTGAAACT
1 ATTCTCATTTGAAACT
12514599 CATAATTTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
42 8 0.09
43 77 0.86
44 5 0.06
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (43 bp):
ATTCTCATTTGAAACTTAAAGATTCTCATTTGAAAACTAAAAT
Found at i:12515164 original size:77 final size:79
Alignment explanation
Indices: 12515023--12515193 Score: 213
Period size: 77 Copynumber: 2.2 Consensus size: 79
12515013 GGCTTATTAA
* * ** **
12515023 CACTAGTAATTTCAGCATAAATTTCATTCACTGATCCACATTATTTGCATCATTTGATTGTAACT
1 CACTAGCAATTTCAGCATAAATTTCATTCACTGATCCACATCATTTGCATCACCTGATCATAACT
*
12515088 CA-A-ACTTCTCAG
66 CACAGACTTCACAG
* *
12515100 CACTAGCAATTTTAGCATAAATTTCATAT-ACTGATCCACATCATTTTCATCACCTGATCATAAC
1 CACTAGCAATTTCAGCATAAATTTCAT-TCACTGATCCACATCATTTGCATCACCTGATCATAAC
*
12515164 TCACAGGCTTCACAG
65 TCACAGACTTCACAG
*
12515179 CACTGGCAATTTCAG
1 CACTAGCAATTTCAG
12515194 AACAAACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
77 57 0.72
78 2 0.03
79 20 0.25
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.34
Consensus pattern (79 bp):
CACTAGCAATTTCAGCATAAATTTCATTCACTGATCCACATCATTTGCATCACCTGATCATAACT
CACAGACTTCACAG
Found at i:12515848 original size:15 final size:15
Alignment explanation
Indices: 12515805--12515848 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
12515795 TCAATTTGAT
12515805 TTTTCATTTTTTTTCC
1 TTTT-ATTTTTTTTCC
*
12515821 TTTTATATTTTTTCC
1 TTTTATTTTTTTTCC
12515836 TTTT-TTTTATTTT
1 TTTTATTTT-TTTT
12515849 TTATCCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 18 0.72
16 4 0.16
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTTTTTTCC
Found at i:12516224 original size:14 final size:15
Alignment explanation
Indices: 12516205--12516237 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12516195 ATTTATGGCA
12516205 TTATTTCTTATT-TT
1 TTATTTCTTATTATT
*
12516219 TTATTTTTTATTATT
1 TTATTTCTTATTATT
12516234 TTAT
1 TTAT
12516238 AAAATGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTATTTCTTATTATT
Found at i:12520133 original size:15 final size:16
Alignment explanation
Indices: 12520115--12520145 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
12520105 TTTTAACCAA
12520115 AATTTTTTA-ATTTTT
1 AATTTTTTATATTTTT
12520130 AATTTTTTATATTTTT
1 AATTTTTTATATTTTT
12520146 TTATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
AATTTTTTATATTTTT
Found at i:12522259 original size:2 final size:2
Alignment explanation
Indices: 12522252--12522282 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12522242 TGTCTCATTA
12522252 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12522283 TGGAGGGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:12522564 original size:2 final size:2
Alignment explanation
Indices: 12522557--12522591 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12522547 TAATTTAAGT
12522557 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12522592 AAACCCTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12524526 original size:9 final size:9
Alignment explanation
Indices: 12524494--12524524 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12524484 TTGTTACAAA
12524494 ATTAATATT
1 ATTAATATT
12524503 ATTAATATT
1 ATTAATATT
*
12524512 ATTATTATT
1 ATTAATATT
12524521 ATTA
1 ATTA
12524525 TTTCGTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTAATATT
Found at i:12525524 original size:19 final size:20
Alignment explanation
Indices: 12525489--12525532 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
12525479 TAATATCATA
12525489 AAAAATCAACATAAAAAAAT
1 AAAAATCAACATAAAAAAAT
12525509 AAAAATCAA-A-ACAAAAAAT
1 AAAAATCAACATA-AAAAAAT
12525528 AAAAA
1 AAAAA
12525533 GAAAAAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.04
19 13 0.57
20 9 0.39
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAATCAACATAAAAAAAT
Found at i:12525538 original size:19 final size:19
Alignment explanation
Indices: 12525502--12525538 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12525492 AATCAACATA
**
12525502 AAAAAATAAAAATCAAAAC
1 AAAAAATAAAAAGAAAAAC
12525521 AAAAAATAAAAAGAAAAA
1 AAAAAATAAAAAGAAAAA
12525539 ACCTACGAAA
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:0.84, C:0.05, G:0.03, T:0.08
Consensus pattern (19 bp):
AAAAAATAAAAAGAAAAAC
Found at i:12525922 original size:51 final size:53
Alignment explanation
Indices: 12525779--12525940 Score: 156
Period size: 51 Copynumber: 3.1 Consensus size: 53
12525769 TCAGTAGTCG
* * * * *
12525779 AAAACTTCAACGG-CGCTGAAAAATTCAAAGA-TCCTCGGATTCTGGTGGCCA
1 AAAAATTCAACGGTCGCTGAAAAATTCAAACATTTCTCAGTTTCTGGTGGCCA
* * * * *
12525830 AAAAATTCAACGGTC-ATCGAAAAATTTAAAC-TTTTTCAGTTTTTGGT-GTCA
1 AAAAATTCAACGGTCGCT-GAAAAATTCAAACATTTCTCAGTTTCTGGTGGCCA
* *
12525881 AAAAATTCAACGGTCGCTGAAAAATTCAAACATTTCT-AGTTTCCGGTGACCCA
1 AAAAATTCAACGGTCGCTGAAAAATTCAAACATTTCTCAGTTTCTGGTG-GCCA
12525934 AAAAATT
1 AAAAATT
12525941 TTTCAAAATT
Statistics
Matches: 87, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
51 51 0.59
52 27 0.31
53 9 0.10
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (53 bp):
AAAAATTCAACGGTCGCTGAAAAATTCAAACATTTCTCAGTTTCTGGTGGCCA
Found at i:12526632 original size:41 final size:40
Alignment explanation
Indices: 12526571--12526742 Score: 197
Period size: 40 Copynumber: 4.3 Consensus size: 40
12526561 TTATGTAAAT
**
12526571 TTTAAATTTAAAAGGG-TCCTCTCATTAGAGGCAACAAAC
1 TTTAAATTTAAAAGGGCTCCTCTCACCAGAGGCAACAAAC
* *
12526610 TTTAAATGATAAAAGGGCTCCTCTCACCAAAGGCAACAAAC
1 TTTAAAT-TTAAAAGGGCTCCTCTCACCAGAGGCAACAAAC
* * *
12526651 TTTAGATTCAAAAGGGCTCCTCTCACCAGAAGCAACAAAC
1 TTTAAATTTAAAAGGGCTCCTCTCACCAGAGGCAACAAAC
* * * *
12526691 TTTAAATGTTAAAA--GCTTCTTTAACCAAAGGCAACAAAC
1 TTTAAAT-TTAAAAGGGCTCCTCTCACCAGAGGCAACAAAC
*
12526730 TTTAAATTAAAAA
1 TTTAAATTTAAAA
12526743 TATGAGAGGA
Statistics
Matches: 113, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
38 5 0.04
39 34 0.30
40 43 0.38
41 31 0.27
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (40 bp):
TTTAAATTTAAAAGGGCTCCTCTCACCAGAGGCAACAAAC
Found at i:12526932 original size:40 final size:40
Alignment explanation
Indices: 12526849--12527111 Score: 300
Period size: 40 Copynumber: 6.6 Consensus size: 40
12526839 CTCTGATAAG
* * * * *
12526849 AGGCAACGAACTTTAAAT-TCAAAAGGTTCCTCTCACCAA
1 AGGCAACAAACTTTAAATGTTAAAAAGCTCTTCTCACCAA
*
12526888 AGGCAACAAATTTTAAATGTTAAAAAGCTCTTCTCACCAA
1 AGGCAACAAACTTTAAATGTTAAAAAGCTCTTCTCACCAA
* * *
12526928 AGGCAACAAACTTTAAATGTTAAAAAGCTCCTCTGA-TAA
1 AGGCAACAAACTTTAAATGTTAAAAAGCTCTTCTCACCAA
* * * * * *
12526967 GAGGCAACGAACTTTAAAT-TCAAAAGGTTCCTCTCACCCA
1 -AGGCAACAAACTTTAAATGTTAAAAAGCTCTTCTCACCAA
*
12527007 AGGCAACAAATTTTAAATGTTAAAAAGCTCTTCTCACCAA
1 AGGCAACAAACTTTAAATGTTAAAAAGCTCTTCTCACCAA
** *
12527047 AGATAACAAACTTTAAATGTTAAAAAGCTCCTT-TAACCAA
1 AGGCAACAAACTTTAAATGTTAAAAAGCT-CTTCTCACCAA
*
12527087 AGGTAACAAACTTTAAATGTTAAAA
1 AGGCAACAAACTTTAAATGTTAAAA
12527112 TATGAGAGGC
Statistics
Matches: 190, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
39 47 0.25
40 140 0.74
41 3 0.02
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (40 bp):
AGGCAACAAACTTTAAATGTTAAAAAGCTCTTCTCACCAA
Found at i:12526978 original size:119 final size:119
Alignment explanation
Indices: 12526828--12527078 Score: 475
Period size: 119 Copynumber: 2.1 Consensus size: 119
12526818 GCTCTTAAAA
12526828 TTAAAAAGCTCCTCTGATAAGAGGCAACGAACTTTAAATTCAAAAGGTTCCTCTCACCAAAGGCA
1 TTAAAAAGCTCCTCTGATAAGAGGCAACGAACTTTAAATTCAAAAGGTTCCTCTCACCAAAGGCA
*
12526893 ACAAATTTTAAATGTTAAAAAGCTCTTCTCACCAAAGGCAACAAACTTTAAATG
66 ACAAATTTTAAATGTTAAAAAGCTCTTCTCACCAAAGACAACAAACTTTAAATG
*
12526947 TTAAAAAGCTCCTCTGATAAGAGGCAACGAACTTTAAATTCAAAAGGTTCCTCTCACCCAAGGCA
1 TTAAAAAGCTCCTCTGATAAGAGGCAACGAACTTTAAATTCAAAAGGTTCCTCTCACCAAAGGCA
*
12527012 ACAAATTTTAAATGTTAAAAAGCTCTTCTCACCAAAGATAACAAACTTTAAATG
66 ACAAATTTTAAATGTTAAAAAGCTCTTCTCACCAAAGACAACAAACTTTAAATG
12527066 TTAAAAAGCTCCT
1 TTAAAAAGCTCCT
12527079 TTAACCAAAG
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 129 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (119 bp):
TTAAAAAGCTCCTCTGATAAGAGGCAACGAACTTTAAATTCAAAAGGTTCCTCTCACCAAAGGCA
ACAAATTTTAAATGTTAAAAAGCTCTTCTCACCAAAGACAACAAACTTTAAATG
Found at i:12527002 original size:79 final size:80
Alignment explanation
Indices: 12526828--12527111 Score: 324
Period size: 79 Copynumber: 3.6 Consensus size: 80
12526818 GCTCTTAAAA
* * * * * *
12526828 TTAAAAAGCTCCTCTGA-TAAGAGGCAACGAACTTTAAAT-TCAAAAGGTTCCTCTCACCAAAGG
1 TTAAAAAGCTCCTCTCACCAA-AGGCAACAAACTTTAAATGTTAAAAAGCTCCTCTCACCAAAGG
*
12526891 CAACAAATTTTAAATG
65 CAACAAACTTTAAATG
* * *
12526907 TTAAAAAGCTCTTCTCACCAAAGGCAACAAACTTTAAATGTTAAAAAGCTCCTCTGA-TAAGAGG
1 TTAAAAAGCTCCTCTCACCAAAGGCAACAAACTTTAAATGTTAAAAAGCTCCTCTCACCAA-AGG
*
12526971 CAACGAACTTTAAAT-
65 CAACAAACTTTAAATG
* * * * * * **
12526986 TCAAAAGGTTCCTCTCACCCAAGGCAACAAATTTTAAATGTTAAAAAGCTCTTCTCACCAAAGAT
1 TTAAAAAGCTCCTCTCACCAAAGGCAACAAACTTTAAATGTTAAAAAGCTCCTCTCACCAAAGGC
12527051 AACAAACTTTAAATG
66 AACAAACTTTAAATG
* * *
12527066 TTAAAAAGCTCCTTTAACCAAAGGTAACAAACTTTAAATGTTAAAA
1 TTAAAAAGCTCCTCTCACCAAAGGCAACAAACTTTAAATGTTAAAA
12527112 TATGAGAGGC
Statistics
Matches: 169, Mismatches: 31, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
79 98 0.58
80 71 0.42
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (80 bp):
TTAAAAAGCTCCTCTCACCAAAGGCAACAAACTTTAAATGTTAAAAAGCTCCTCTCACCAAAGGC
AACAAACTTTAAATG
Found at i:12539653 original size:12 final size:12
Alignment explanation
Indices: 12539633--12539670 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12539623 AAATAACAAT
*
12539633 AATATCATAAAA
1 AATAACATAAAA
12539645 AATAACAT-AAA
1 AATAACATAAAA
12539656 AATCAACATAAAA
1 AAT-AACATAAAA
12539669 AA
1 AA
12539671 ATAAAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 6 0.26
12 12 0.52
13 5 0.22
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (12 bp):
AATAACATAAAA
Found at i:12539654 original size:26 final size:24
Alignment explanation
Indices: 12539620--12539676 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
12539610 TAGTAATAAT
*
12539620 ATAAAATAACAATAATATCATAAAAA
1 ATAAAATAAAAATAA-A-CATAAAAA
* *
12539646 ATAACATAAAAATCAACATAAAAAA
1 ATAAAATAAAAATAAACAT-AAAAA
12539671 ATAAAA
1 ATAAAA
12539677 ATCAAAACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 3 0.12
25 11 0.42
26 12 0.46
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (24 bp):
ATAAAATAAAAATAAACATAAAAA
Found at i:12539676 original size:20 final size:20
Alignment explanation
Indices: 12539651--12539696 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
12539641 AAAAAATAAC
* *
12539651 ATAAAAATCAACATAAAAAA
1 ATAAAAATCAAAACAAAAAA
12539671 ATAAAAATCAAAACAAAAAA
1 ATAAAAATCAAAACAAAAAA
12539691 A-AAAAA
1 ATAAAAA
12539697 AAGAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (20 bp):
ATAAAAATCAAAACAAAAAA
Found at i:12539998 original size:18 final size:18
Alignment explanation
Indices: 12539958--12539991 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12539948 AGCTAGAAAC
12539958 TTCAACGGCACCGAAAAA
1 TTCAACGGCACCGAAAAA
*
12539976 TTCAACGTCACC-AAAA
1 TTCAACGGCACCGAAAA
12539992 GTTTCAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (18 bp):
TTCAACGGCACCGAAAAA
Found at i:12567930 original size:10 final size:10
Alignment explanation
Indices: 12567916--12567969 Score: 90
Period size: 10 Copynumber: 5.3 Consensus size: 10
12567906 ATTTATTTAA
12567916 TTTTTTTCTT
1 TTTTTTTCTT
*
12567926 CTTTTTTCTT
1 TTTTTTTCTT
12567936 TTTTTTTCTT
1 TTTTTTTCTT
12567946 TTTTTTTCTT
1 TTTTTTTCTT
12567956 TTTTTTTCCTT
1 TTTTTTT-CTT
12567967 TTT
1 TTT
12567970 CTTCCTTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
10 35 0.85
11 6 0.15
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:12568692 original size:26 final size:26
Alignment explanation
Indices: 12568655--12568724 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
12568645 GCGGCCAAAA
* *
12568655 CCCAAAATGACGTCGTTTCACTAATG
1 CCCAAAACGACGTCGTTTCACCAATG
*
12568681 CCCAAAACGACGTCATTTCACCAATG
1 CCCAAAACGACGTCGTTTCACCAATG
*
12568707 CCCAAAACGACATCGTTT
1 CCCAAAACGACGTCGTTT
12568725 TGAGACCTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.23
Consensus pattern (26 bp):
CCCAAAACGACGTCGTTTCACCAATG
Found at i:12568956 original size:11 final size:11
Alignment explanation
Indices: 12568937--12568988 Score: 90
Period size: 10 Copynumber: 4.9 Consensus size: 11
12568927 TAGGTAAAAA
12568937 AAATTTTTTTT
1 AAATTTTTTTT
12568948 -AATTTTTTTT
1 AAATTTTTTTT
12568958 AAA-TTTTTTT
1 AAATTTTTTTT
12568968 AAATTTTTTTT
1 AAATTTTTTTT
12568979 AAATTTTTTT
1 AAATTTTTTT
12568989 ATATATATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
10 20 0.51
11 19 0.49
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
AAATTTTTTTT
Found at i:12568961 original size:21 final size:21
Alignment explanation
Indices: 12568937--12568989 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
12568927 TAGGTAAAAA
*
12568937 AAATTTTTTTTAATTTTTTTT
1 AAATTTTTTTAAATTTTTTTT
12568958 AAATTTTTTTAAATTTTTTTT
1 AAATTTTTTTAAATTTTTTTT
12568979 AAATTTTTTTA
1 AAATTTTTTTA
12568990 TATATATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
AAATTTTTTTAAATTTTTTTT
Found at i:12569020 original size:21 final size:23
Alignment explanation
Indices: 12568985--12569031 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
12568975 TTTTAAATTT
* *
12568985 TTTTATATATATTATTTTTGTTA
1 TTTTATATATATTATTATTGATA
12569008 TTTTA-AT-TATTATTATTGATA
1 TTTTATATATATTATTATTGATA
12569029 TTT
1 TTT
12569032 ATGCATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 2 0.09
23 5 0.23
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTTATATATATTATTATTGATA
Found at i:12570257 original size:15 final size:16
Alignment explanation
Indices: 12570237--12570274 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
12570227 ATTTTTAACC
*
12570237 AAAAAACAAGT-AAAA
1 AAAAAACAAATCAAAA
12570252 AAAAAACAAATCAAAA
1 AAAAAACAAATCAAAA
12570268 ACAAAAA
1 A-AAAAA
12570275 AGTTCACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 5 0.25
17 5 0.25
ACGTcount: A:0.82, C:0.11, G:0.03, T:0.05
Consensus pattern (16 bp):
AAAAAACAAATCAAAA
Found at i:12572680 original size:208 final size:208
Alignment explanation
Indices: 12572322--12572729 Score: 656
Period size: 208 Copynumber: 2.0 Consensus size: 208
12572312 AACCATAAAA
* * *
12572322 GAATAAGATGTGACTAATAGTGATTTAAAATATCTACACCAGAAAAACAAAAGGTTACGAATCTA
1 GAATAAGATGTGACTAACAGTGATTTAAAATATCTACACCAAAAAAACAAAAGGTTACGAATCCA
* * *
12572387 ATTCAAAATTAAAAAAGTCACTAAGTCTTACCTTAGTCGGTAACACGAAGTGGATGAACTCTAAG
66 ATTCAAAACTAAAAAAGTCACTAAGTCTTACCTTAGTCGGTAACACAAAGTGGATGAACTCCAAG
*
12572452 AAAAAATAAACCAATGAAAAGGCAAAGCTCAAGAAAAGTAAG-AGAAGACCACTAAAATTTATCA
131 AAAAAATAAACCAATGAAAAGGCAAAGCTCAAGAAAAGCAAGAAG-AGACCACTAAAATTTATCA
12572516 AGAATGTCATAATT
195 AGAATGTCATAATT
* * *
12572530 GAATAAGATGTGACTAACAGTGATTTGAAATATCTACACCAAAAAAATAAGAGGTTACGAATCCA
1 GAATAAGATGTGACTAACAGTGATTTAAAATATCTACACCAAAAAAACAAAAGGTTACGAATCCA
*
12572595 ATTCAAAACTGAAAAAGTCACTAAGTCTTACCTTAGTCGGTAACACAAAGTGGATGAACTCCAAG
66 ATTCAAAACTAAAAAAGTCACTAAGTCTTACCTTAGTCGGTAACACAAAGTGGATGAACTCCAAG
* * * * *
12572660 AAGAAATAAACTAATGAAAAGGCAAAGCTCAAGAAAAGCAATAAGAGACCACTAGAATTTCTCAA
131 AAAAAATAAACCAATGAAAAGGCAAAGCTCAAGAAAAGCAAGAAGAGACCACTAAAATTTATCAA
12572725 GAATG
196 GAATG
12572730 CTAGAATTGG
Statistics
Matches: 183, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
208 181 0.99
209 2 0.01
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (208 bp):
GAATAAGATGTGACTAACAGTGATTTAAAATATCTACACCAAAAAAACAAAAGGTTACGAATCCA
ATTCAAAACTAAAAAAGTCACTAAGTCTTACCTTAGTCGGTAACACAAAGTGGATGAACTCCAAG
AAAAAATAAACCAATGAAAAGGCAAAGCTCAAGAAAAGCAAGAAGAGACCACTAAAATTTATCAA
GAATGTCATAATT
Found at i:12575146 original size:8 final size:8
Alignment explanation
Indices: 12575133--12575200 Score: 57
Period size: 8 Copynumber: 8.2 Consensus size: 8
12575123 ACATTTTTAT
12575133 AATTAAAA
1 AATTAAAA
**
12575141 AATTAATT
1 AATTAAAA
12575149 AATT-AAA
1 AATTAAAA
12575156 AATTAAAAA
1 AATT-AAAA
12575165 AGATTAAAA
1 A-ATTAAAA
**
12575174 TTTTAAAA
1 AATTAAAA
*
12575182 TATTTAAAA
1 -AATTAAAA
12575191 AATTAAAA
1 AATTAAAA
12575199 AA
1 AA
12575201 AAAGAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
7 5 0.10
8 25 0.52
9 15 0.31
10 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (8 bp):
AATTAAAA
Found at i:12575153 original size:16 final size:15
Alignment explanation
Indices: 12575132--12575161 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
12575122 TACATTTTTA
12575132 TAATTAAAAAATTAAT
1 TAATT-AAAAATTAAT
12575148 TAATTAAAAATTAA
1 TAATTAAAAATTAA
12575162 AAAAGATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAATTAAAAATTAAT
Found at i:12575170 original size:17 final size:16
Alignment explanation
Indices: 12575149--12575201 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
12575139 AAAATTAATT
12575149 AATTAAAAATTAAAAA
1 AATTAAAAATTAAAAA
* *
12575165 AGATTAAAATTTTAAAAT
1 A-ATTAAAA-ATTAAAAA
*
12575183 ATTTAAAAAATTAAAAA
1 AATT-AAAAATTAAAAA
12575200 AA
1 AA
12575202 AAGAAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
16 1 0.04
17 16 0.57
18 11 0.39
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
AATTAAAAATTAAAAA
Found at i:12590330 original size:18 final size:17
Alignment explanation
Indices: 12590307--12590340 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
12590297 GCCTTCGAAG
12590307 TTTTTTATCTTTTTTTTT
1 TTTTTTA-CTTTTTTTTT
12590325 TTTTTTACTTTTTTTT
1 TTTTTTACTTTTTTTT
12590341 GGACGACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTACTTTTTTTTT
Found at i:12590789 original size:9 final size:9
Alignment explanation
Indices: 12590775--12590815 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
12590765 TTAAAAATAT
12590775 TTTTTTAAA
1 TTTTTTAAA
12590784 TTTTTTAAA
1 TTTTTTAAA
*
12590793 -TTTTTAATC
1 TTTTTTAA-A
12590802 TTTTTTAAA
1 TTTTTTAAA
12590811 TTTTT
1 TTTTT
12590816 AATTAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 7 0.25
9 14 0.50
10 7 0.25
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:12590805 original size:18 final size:18
Alignment explanation
Indices: 12590784--12590818 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12590774 TTTTTTTAAA
12590784 TTTTTTAAATTTTTAATC
1 TTTTTTAAATTTTTAATC
12590802 TTTTTTAAATTTTTAAT
1 TTTTTTAAATTTTTAAT
12590819 TAATTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTTAAATTTTTAATC
Found at i:12590833 original size:8 final size:8
Alignment explanation
Indices: 12590775--12590835 Score: 59
Period size: 8 Copynumber: 7.2 Consensus size: 8
12590765 TTAAAAATAT
12590775 TTTTTTAAA
1 TTTTTT-AA
12590784 TTTTTTAA
1 TTTTTTAA
*
12590792 ATTTTTAA
1 TTTTTTAA
12590800 TCTTTTTTAA
1 --TTTTTTAA
*
12590810 ATTTTTAA
1 TTTTTTAA
**
12590818 TTAATTAA
1 TTTTTTAA
12590826 TTTTTTAA
1 TTTTTTAA
12590834 TT
1 TT
12590836 ATAGAAATGT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
8 29 0.69
9 6 0.14
10 7 0.17
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTTTAA
Found at i:12591313 original size:171 final size:170
Alignment explanation
Indices: 12591001--12591543 Score: 716
Period size: 171 Copynumber: 3.2 Consensus size: 170
12590991 CTATAGGAAT
* * *
12591001 GACTGGAATTAAACCGCAAGTTAGAAGATGACGTTAACTTGGATTGAATCACAAGTCTG-AAATA
1 GACTGGGATTAAACCGCAAGTTAGAAAATGACGTTAACTTGGATTGAATCACAAGTCCGAAAATA
* * * * *
12591065 AGAAGACCGGGATTGGACCACGAGTCAGAAGATAATAACAATCGAGATTAAACTACGATTTTAAA
66 AGAAGACCGGGATTGAACCACGAGTCAGAGGATAACAATAATCGAGATTAAACTACGATTTTAGA
*
12591130 TTAAAGAGATCGGGATTGAATCACGAATCGAAAGATAAAGC
131 TTAAAGAGATCGGGATTGAATCACGAATC-AAAGATAAAGA
* * * * *
12591171 GACTGGGATTAAATCACAAGTTAGAAAATAATGTTAACTTCGATTGAATCACAAGTCCGAAAATA
1 GACTGGGATTAAACCGCAAGTTAGAAAATGACGTTAACTTGGATTGAATCACAAGTCCGAAAATA
* *
12591236 AGAAGACCAGGATTGAACCACGAGTCAGAGGATAACAATAATCGATG-TTAAACTATGATTTTAG
66 AGAAGACCGGGATTGAACCACGAGTCAGAGGATAACAATAATCGA-GATTAAACTACGATTTTAG
* *** * *
12591300 ATTAAAAAGATCGGGATTGAATCGTAAATTAGAGGATAAAGA
130 ATTAAAGAGATCGGGATTGAATCACGAATCA-AAGATAAAGA
* * * *
12591342 GA-TCGGGATTAAACCGCAAGTCAAAAAATGACATTAACTTGGATTGAATCATAAGTCCGAAAAT
1 GACT-GGGATTAAACCGCAAGTTAGAAAATGACGTTAACTTGGATTGAATCACAAGTCCGAAAAT
* *
12591406 AAGAAGACTGGGATTGAACCACGAGTAAGAGGATAACAATAATCGAGATTAAACTACGATTTTAG
65 AAGAAGACCGGGATTGAACCACGAGTCAGAGGATAACAATAATCGAGATTAAACTACGATTTTAG
* *
12591471 ATTAAAGAGATCGGGATTAAACCACGAATCAAAGATAAAGA
130 ATTAAAGAGATCGGGATTGAATCACGAATCAAAGATAAAGA
* * *
12591512 GA-TCGAGATTAAACCGTAAGTAAGAAAATGAC
1 GACT-GGGATTAAACCGCAAGTTAGAAAATGAC
12591544 AACAATCGAG
Statistics
Matches: 321, Mismatches: 47, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
170 91 0.28
171 229 0.71
172 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.22
Consensus pattern (170 bp):
GACTGGGATTAAACCGCAAGTTAGAAAATGACGTTAACTTGGATTGAATCACAAGTCCGAAAATA
AGAAGACCGGGATTGAACCACGAGTCAGAGGATAACAATAATCGAGATTAAACTACGATTTTAGA
TTAAAGAGATCGGGATTGAATCACGAATCAAAGATAAAGA
Found at i:12591553 original size:101 final size:99
Alignment explanation
Indices: 12591427--12591821 Score: 363
Period size: 101 Copynumber: 3.9 Consensus size: 99
12591417 GATTGAACCA
* * *
12591427 CGAGT-AAGAGGATAACAATAATCGAGATTAAACTACGA-TTTTAGATTAAAGAGATCGGGATTA
1 CGAGTCAAGA-GATAACAACAATCGAGATTAAACTATGACTTTGA-ATTAAAGAGATCGGGATTA
12591490 AACCACGAATC-AAAGATAAAGAGATCGAGATTAAAC
64 AACCACGAATCAAAAGATAAA-AGATCGAGATTAAAC
* * *
12591526 CGTAAGT-AAGAAAATGACAACAATCGAGATTAAACTGTGACTTTGAATTAAAGAGATCGGGATT
1 CG--AGTCAAG-AGATAACAACAATCGAGATTAAACTATGACTTTGAATTAAAGAGATCGGGATT
**** * *
12591590 AAACTGTAAATCGAAGAGATAAAAGATCAAGATTAAATC
63 AAACCACGAATC-AAAAGATAAAAGATCGAGATTAAA-C
* * * *
12591629 ACGAGTCAA-AGGATAACAACAATTGAGATTAAACTATGACTTTGAATTAAAAAGATCGAGATTG
1 -CGAGTCAAGA-GATAACAACAATCGAGATTAAACTATGACTTTGAATTAAAGAGATCGGGATTA
* * * *
12591693 AATCACGAATCAAAAAATATAAGATCGGGATTAAAC
64 AACCACGAATCAAAAGATAAAAGATCGAGATTAAAC
* * * *
12591729 TGCGAGTCAATG-GATAACAACAATCGAGATTAAACTATGATTTTAAATTAAAGAAATTGGGATT
1 --CGAGTCAA-GAGATAACAACAATCGAGATTAAACTATGACTTTGAATTAAAGAGATCGGGATT
* * *
12591793 GAATCACGAATC-GAAGAATAAAAAGATCG
63 AAACCACGAATCAAAAG-AT-AAAAGATCG
12591822 GAAACAAATC
Statistics
Matches: 241, Mismatches: 40, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
99 2 0.01
100 3 0.01
101 142 0.59
102 81 0.34
103 11 0.05
104 2 0.01
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (99 bp):
CGAGTCAAGAGATAACAACAATCGAGATTAAACTATGACTTTGAATTAAAGAGATCGGGATTAAA
CCACGAATCAAAAGATAAAAGATCGAGATTAAAC
Found at i:12591780 original size:203 final size:202
Alignment explanation
Indices: 12591425--12591792 Score: 465
Period size: 203 Copynumber: 1.8 Consensus size: 202
12591415 GGGATTGAAC
* * * *
12591425 CACGAGTAAGAGGATAACAATAATCGAGATTAAACTACGATTTTAGATTAAAGAGATCGGGATTA
1 CACGAGTAAGAGGATAACAACAATCGAGATTAAACTACGATTTGAGATTAAAAAGATCGAGATTA
* * *
12591490 AACCACGAATCAAAGATAAAGAGATCGAGATTAAACCGTAAGTAAGAAAATGACAACAATCGAGA
66 AACCACGAATCAAAAATAAAGAGATCGAGATTAAACCGCAAGTAAG-AAATAACAACAATCGAGA
* * *
12591555 TTAAACTGTGACTTTGAATTAAAGAGATCGGGATTAAACTGTAAATCGAAGAGATAAAAGATCAA
130 TTAAACTATGACTTTAAATTAAAGAAATCGGGATTAAACTGTAAATCGAAGAGATAAAAGATCAA
12591620 GATTAAAT
195 GATTAAAT
* *
12591628 CACGAGTCAA-AGGATAACAACAATTGAGATTAAACTATGACTTTGA-ATTAAAAAGATCGAGAT
1 CACGAGT-AAGAGGATAACAACAATCGAGATTAAACTACGA-TTTGAGATTAAAAAGATCGAGAT
* * * * * * *
12591691 TGAATCACGAATCAAAAAATATA-AGATCGGGATTAAACTGCGAGTCAATG-GATAACAACAATC
64 TAAACCACGAATC-AAAAATAAAGAGATCGAGATTAAACCGCAAGT-AA-GAAATAACAACAATC
* *
12591754 GAGATTAAACTATGATTTTAAATTAAAGAAATTGGGATT
126 GAGATTAAACTATGACTTTAAATTAAAGAAATCGGGATT
12591793 GAATCACGAA
Statistics
Matches: 139, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
203 123 0.88
204 15 0.11
205 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (202 bp):
CACGAGTAAGAGGATAACAACAATCGAGATTAAACTACGATTTGAGATTAAAAAGATCGAGATTA
AACCACGAATCAAAAATAAAGAGATCGAGATTAAACCGCAAGTAAGAAATAACAACAATCGAGAT
TAAACTATGACTTTAAATTAAAGAAATCGGGATTAAACTGTAAATCGAAGAGATAAAAGATCAAG
ATTAAAT
Found at i:12592296 original size:18 final size:18
Alignment explanation
Indices: 12592263--12592298 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12592253 TCGCTCAACA
*
12592263 ATCCCTTTTTTATTCTTT
1 ATCCCTTTTCTATTCTTT
*
12592281 ATCCCTTTTCTCTTCTTT
1 ATCCCTTTTCTATTCTTT
12592299 GTCTTTAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (18 bp):
ATCCCTTTTCTATTCTTT
Found at i:12592842 original size:21 final size:21
Alignment explanation
Indices: 12592817--12592857 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12592807 TACATATAGG
12592817 ATTTATAAATTTTACAATTTA
1 ATTTATAAATTTTACAATTTA
** *
12592838 ATTTATTTATTTTACTATTT
1 ATTTATAAATTTTACAATTT
12592858 TTAAATTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTATAAATTTTACAATTTA
Found at i:12595615 original size:177 final size:178
Alignment explanation
Indices: 12595279--12595633 Score: 685
Period size: 177 Copynumber: 2.0 Consensus size: 178
12595269 TTTTAAAAGT
12595279 ATAAGTAATTTGCTTGTCCCTTAAAATTTTAAAAATTTTATTTTGTGGAATAAGTTATTTGAATT
1 ATAAGTAATTTGCTTGTCCCTTAAAATTTTAAAAATTTTATTTTGTGGAATAAGTTATTTGAATT
12595344 TTTATGCCATATTAAAATATTAAAGAAGTTCTGTTATAACAAATATTTAATTAAAATTTCTATAT
66 TTTATGCCATATT-AAATATTAAAGAAGTTCTGTTATAACAAATATTTAATTAAAATTTCTATAT
*
12595409 ATTCTAATTTTATCCTCTAATAATTCATAAAGTTATAATAAGAATTATA
130 ATTCTAATTTTATCCTCTAATAATTCATAAAATTATAATAAGAATTATA
12595458 ATAAGTAATTTGCTTGTCCCTTAAAATTTTAAAAATTTTATTTTGTGGAATAAGTTATTTGAATT
1 ATAAGTAATTTGCTTGTCCCTTAAAATTTTAAAAATTTTATTTTGTGGAATAAGTTATTTGAATT
12595523 TTTATGCCATATT-AATATTAAAGAAGTTCTGTTATAACAAATATTTAATTAAAATTTCTATATA
66 TTTATGCCATATTAAATATTAAAGAAGTTCTGTTATAACAAATATTTAATTAAAATTTCTATATA
12595587 TTCTAATTTTATCCTCTAATAATTCATAAAATTATAATAAGAATTAT
131 TTCTAATTTTATCCTCTAATAATTCATAAAATTATAATAAGAATTAT
12595634 TTTTTTACAT
Statistics
Matches: 175, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
177 97 0.55
179 78 0.45
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (178 bp):
ATAAGTAATTTGCTTGTCCCTTAAAATTTTAAAAATTTTATTTTGTGGAATAAGTTATTTGAATT
TTTATGCCATATTAAATATTAAAGAAGTTCTGTTATAACAAATATTTAATTAAAATTTCTATATA
TTCTAATTTTATCCTCTAATAATTCATAAAATTATAATAAGAATTATA
Found at i:12601556 original size:21 final size:22
Alignment explanation
Indices: 12601532--12601575 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
12601522 TATATCCAAT
12601532 AGATATATAGAATA-AA-AAATA
1 AGATATATA-AATACAATAAATA
12601553 AGATATATAAATACAATAAATA
1 AGATATATAAATACAATAAATA
12601575 A
1 A
12601576 TATAAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (22 bp):
AGATATATAAATACAATAAATA
Found at i:12629435 original size:21 final size:22
Alignment explanation
Indices: 12629395--12629438 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
12629385 TGTATTTATA
12629395 TTATTTATTGTATTTATATATC
1 TTATTTATTGTATTTATATATC
12629417 TTATTT-TT-TATTCTATATATC
1 TTATTTATTGTATT-TATATATC
12629438 T
1 T
12629439 ATTGGATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (22 bp):
TTATTTATTGTATTTATATATC
Found at i:12635758 original size:79 final size:80
Alignment explanation
Indices: 12635594--12635759 Score: 174
Period size: 79 Copynumber: 2.1 Consensus size: 80
12635584 GGTTTTTTTA
* * * * *
12635594 GCTTTCTTTACCTTTTC-GTTTTTTAAGTTTTAAAAATAATATTTATCTATTAATTGTAATAATT
1 GCTTTATTTATCTTTTCAATTTTTTAAGTTTTAAAAATAATATTTAGCTATTAATTATAATAATT
* * **
12635658 AATTATGTATTTTTT
66 AATTACGCATTTTGG
* * *
12635673 GCTTTATTTATCTTTTCAATTTTTTTA-TTTTAAAAATAATATTTAGCTATTAATTATGATCATT
1 GCTTTATTTATCTTTTCAATTTTTTAAGTTTTAAAAATAATATTTAGCTATTAATTATAATAATT
* * *
12635737 GATTGCGCCTTTTGG
66 AATTACGCATTTTGG
*
12635752 GTTTTATT
1 GCTTTATT
12635760 GTCTTATGGT
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
79 63 0.90
80 7 0.10
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.56
Consensus pattern (80 bp):
GCTTTATTTATCTTTTCAATTTTTTAAGTTTTAAAAATAATATTTAGCTATTAATTATAATAATT
AATTACGCATTTTGG
Found at i:12641919 original size:66 final size:66
Alignment explanation
Indices: 12641839--12641975 Score: 229
Period size: 66 Copynumber: 2.1 Consensus size: 66
12641829 ATTCAAAAAT
* *
12641839 CAATATAAAATTTATTATGCATTATAACAAAATCAAAGTGATAACATTTATTTTGCAATATTATA
1 CAATATAAAATTTATTATGCATTATAACAAAATCAAAGTGATAACATTTATTTTGCAATATCAGA
12641904 A
66 A
* * *
12641905 CAATATAACATTTATTTTGCATTATAACAAAATCAGAGTGATAACATTTATTTTGCAATATCAGA
1 CAATATAAAATTTATTATGCATTATAACAAAATCAAAGTGATAACATTTATTTTGCAATATCAGA
12641970 A
66 A
12641971 CAATA
1 CAATA
12641976 GAAACCCATA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (66 bp):
CAATATAAAATTTATTATGCATTATAACAAAATCAAAGTGATAACATTTATTTTGCAATATCAGA
A
Found at i:12641956 original size:36 final size:35
Alignment explanation
Indices: 12641834--12641961 Score: 144
Period size: 36 Copynumber: 3.8 Consensus size: 35
12641824 ACATCATTCA
* *
12641834 AAAATCAA-T-ATAAAATTTATTATGCATTATAAC
1 AAAATCAAGTGATAACATTTATTTTGCATTATAAC
**
12641867 AAAATCAAAGTGATAACATTTATTTTGCA--ATATT
1 AAAATC-AAGTGATAACATTTATTTTGCATTATAAC
*
12641901 ATAA-CAA-T-ATAACATTTATTTTGCATTATAAC
1 AAAATCAAGTGATAACATTTATTTTGCATTATAAC
12641933 AAAATCAGAGTGATAACATTTATTTTGCA
1 AAAATCA-AGTGATAACATTTATTTTGCA
12641962 ATATCAGAAC
Statistics
Matches: 78, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
30 17 0.22
31 1 0.01
32 8 0.10
33 9 0.12
34 9 0.12
35 2 0.03
36 32 0.41
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (35 bp):
AAAATCAAGTGATAACATTTATTTTGCATTATAAC
Found at i:12642283 original size:146 final size:146
Alignment explanation
Indices: 12642023--12642288 Score: 381
Period size: 146 Copynumber: 1.8 Consensus size: 146
12642013 AATCATCTTG
* * * *
12642023 TCAACACAAGAACAATAGAAAACATAAGCATTCACGTATGTTCCTATGTTTAATTACCGCAATGC
1 TCAACACAAGAACAATAAAAAACATAAGCATTCAAGCATGCTCCTATGTTTAATTACCGCAATGC
* * *
12642088 AGGGAGCAAAAACTTTGGAAATTCCAGTAGCTCTAACTGCAACAACAGTTGCATCCTCTTTTACC
66 AGGGAGCAAAAACATAGGAAATTCCAGTAGCTCTAACTCCAACAACAGTTGCATCCTCTTTTACC
12642153 ACAATGAATCATCCCA
131 ACAATGAATCATCCCA
* *
12642169 TCAACATAAGAACAATAAAAAACATAAGCATTCAAGCATGCTCCTGTGTTTAATTACCGCAATGC
1 TCAACACAAGAACAATAAAAAACATAAGCATTCAAGCATGCTCCTATGTTTAATTACCGCAATGC
** * * * *
12642234 ATTGAGCAAAAACATAGGAAATTTCTA-TAGCTCTAACTCCGATAGCAGTTGCATC
66 AGGGAGCAAAAACATAGGAAA-TTCCAGTAGCTCTAACTCCAACAACAGTTGCATC
12642289 TCCAATCTTC
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
146 100 0.96
147 4 0.04
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (146 bp):
TCAACACAAGAACAATAAAAAACATAAGCATTCAAGCATGCTCCTATGTTTAATTACCGCAATGC
AGGGAGCAAAAACATAGGAAATTCCAGTAGCTCTAACTCCAACAACAGTTGCATCCTCTTTTACC
ACAATGAATCATCCCA
Found at i:12645350 original size:1 final size:1
Alignment explanation
Indices: 12645346--12645379 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
12645336 GAAAAACCTT
12645346 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12645380 TCCTTTCTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12645937 original size:19 final size:19
Alignment explanation
Indices: 12645910--12645984 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 19
12645900 AAAATTAGGG
*
12645910 ATAGTTATTATATAATGTT
1 ATAGATATTATATAATGTT
* *
12645929 ATAGATATTTATATTAT-AT
1 ATAGATA-TTATATAATGTT
12645948 ATAGAGTAGATTAAATATAATGTT
1 ATAGA-T--ATT--ATATAATGTT
12645972 ATAGATATT-TATA
1 ATAGATATTATATA
12645985 TTATATATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
18 4 0.09
19 12 0.27
20 9 0.20
21 5 0.11
22 1 0.02
23 7 0.16
24 6 0.14
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (19 bp):
ATAGATATTATATAATGTT
Found at i:12646024 original size:3 final size:3
Alignment explanation
Indices: 12646018--12646075 Score: 57
Period size: 3 Copynumber: 19.0 Consensus size: 3
12646008 GTTCTTTTTT
* *
12646018 TTA TTA TTA TATA GTT- TTG TTTA TTA TTA TTA TCA TTA -TA TTA TTA
1 TTA TTA TTA T-TA -TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
12646064 TTA TTA TTA TTA
1 TTA TTA TTA TTA
12646076 ATCTTTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 5 0.11
5 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:12646059 original size:17 final size:17
Alignment explanation
Indices: 12646039--12646073 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12646029 TAGTTTTGTT
12646039 TATTATTATTATCATTA
1 TATTATTATTATCATTA
*
12646056 TATTATTATTATTATTA
1 TATTATTATTATCATTA
12646073 T
1 T
12646074 TAATCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTATTATTATCATTA
Found at i:12646061 original size:20 final size:20
Alignment explanation
Indices: 12646038--12646075 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12646028 ATAGTTTTGT
12646038 TTATTATTATTATCATTATA
1 TTATTATTATTATCATTATA
*
12646058 TTATTATTATTATTATTA
1 TTATTATTATTATCATTA
12646076 ATCTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTATTATTATCATTATA
Found at i:12646479 original size:12 final size:11
Alignment explanation
Indices: 12646452--12646482 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
12646442 TCATTTGGGG
12646452 AATTTTTGAAA
1 AATTTTTGAAA
12646463 AATTTTTGAAA
1 AATTTTTGAAA
12646474 ATATTTTTG
1 A-ATTTTTG
12646483 GGTCATCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (11 bp):
AATTTTTGAAA
Found at i:12646908 original size:12 final size:12
Alignment explanation
Indices: 12646893--12646936 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
12646883 TACCCTTTTC
*
12646893 TTTTTTTTTTTA
1 TTTTTTTTTTGA
12646905 TTTTTTGTTTTGA
1 TTTTTT-TTTTGA
**
12646918 TTTTGATTTTGA
1 TTTTTTTTTTGA
12646930 TTTTTTT
1 TTTTTTT
12646937 ATGTTATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTTGA
Found at i:12647020 original size:4 final size:4
Alignment explanation
Indices: 12647013--12647063 Score: 50
Period size: 4 Copynumber: 11.8 Consensus size: 4
12647003 TTTCTAAAAA
12647013 AAAT AAAT AAAT AAAT AAAT AGAAT AAA- AAAT GAAACT GAAAT AAAAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT -AAA-T -AAAT -AAAT
12647061 AAA
1 AAA
12647064 GACCTAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
3 3 0.07
4 22 0.52
5 12 0.29
6 5 0.12
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:12647256 original size:13 final size:14
Alignment explanation
Indices: 12647240--12647268 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12647230 AAATAAATTG
12647240 TTTAAATG-AATCT
1 TTTAAATGCAATCT
12647253 TTTAAATGCAATCT
1 TTTAAATGCAATCT
12647267 TT
1 TT
12647269 AAAGAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (14 bp):
TTTAAATGCAATCT
Found at i:12652232 original size:208 final size:208
Alignment explanation
Indices: 12651874--12652294 Score: 815
Period size: 208 Copynumber: 2.0 Consensus size: 208
12651864 TTCATTGTTT
*
12651874 TCAAGATAATCTTACTGAATCAACTGTCAGATGGTATATTCAACTAGACAGGAGTCGTATTTAGT
1 TCAAGATAATCTTACTGAATCAACTATCAGATGGTATATTCAACTAGACAGGAGTCGTATTTAGT
12651939 CATGAAAAGATCTAGCCAAAGAATTTATTACTCAATATAAGCATGTCACAGACATGGCTCCAAAT
66 CATGAAAAGATCTAGCCAAAGAATTTATTACTCAATATAAGCATGTCACAGACATGGCTCCAAAT
12652004 AGACTATCATTGCAAAACATGAAAAAAAAACTAATGAAAATTTAAAGAATATGCCCAAAGATGGC
131 AGACTATCATTGCAAAACATGAAAAAAAAACTAATGAAAATTTAAAGAATATGCCCAAAGATGGC
12652069 AAGACGTTTTCAC
196 AAGACGTTTTCAC
*
12652082 TCAAGATAGTCTTACTGAATCAACTATCAGATGGTATATTCAACTAGACAGGAGTCGTATTTAGT
1 TCAAGATAATCTTACTGAATCAACTATCAGATGGTATATTCAACTAGACAGGAGTCGTATTTAGT
12652147 CATGAAAAGATCTAGCCAAAGAATTTATTACTCAATATAAGCATGTCACAGACATGGCTCCAAAT
66 CATGAAAAGATCTAGCCAAAGAATTTATTACTCAATATAAGCATGTCACAGACATGGCTCCAAAT
*
12652212 AGACTATCATTGCAAAACATGAAAAAAAAATTAATGAAAATTTAAAGAATATGCCCAAAGATGGC
131 AGACTATCATTGCAAAACATGAAAAAAAAACTAATGAAAATTTAAAGAATATGCCCAAAGATGGC
12652277 AAGACGTTTTCAC
196 AAGACGTTTTCAC
12652290 TCAAG
1 TCAAG
12652295 TTCAACTTAT
Statistics
Matches: 210, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
208 210 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (208 bp):
TCAAGATAATCTTACTGAATCAACTATCAGATGGTATATTCAACTAGACAGGAGTCGTATTTAGT
CATGAAAAGATCTAGCCAAAGAATTTATTACTCAATATAAGCATGTCACAGACATGGCTCCAAAT
AGACTATCATTGCAAAACATGAAAAAAAAACTAATGAAAATTTAAAGAATATGCCCAAAGATGGC
AAGACGTTTTCAC
Found at i:12658722 original size:7 final size:8
Alignment explanation
Indices: 12658708--12658737 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
12658698 GTATTATGCT
12658708 TAAAAAAA
1 TAAAAAAA
12658716 TAAAAAAA
1 TAAAAAAA
12658724 TAAAAAAA
1 TAAAAAAA
12658732 GTAAAA
1 -TAAAA
12658738 TGAGTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (8 bp):
TAAAAAAA
Found at i:12659742 original size:39 final size:39
Alignment explanation
Indices: 12659607--12660010 Score: 391
Period size: 40 Copynumber: 10.3 Consensus size: 39
12659597 GCCTCTCATA
** * * *
12659607 TTTTT-AATTTAAAGTTTGTTTTCTTTGGTTAAAAGAGC
1 TTTTTAAATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGC
* * * *
12659645 CTTTCAACATTTAAAGTTCGTTGCCTCTGGTCAGAGGAGC
1 TTTTTAA-ATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGC
* * * *
12659685 TTTTCAACATTTAAAGTTTGTTACCTTTGGTTAAAGGAGC
1 TTTTTAA-ATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGC
* * *
12659725 TTTTTGAATTTAAAGTTTGTTGCCTCTGATCAGAGGAGC
1 TTTTTAAATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGC
* * *
12659764 TTTTTAACATTTAAAGTATGTTGCCTTTGGTTAAAGGAGC
1 TTTTTAA-ATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGC
* * * *
12659804 TTTTTGAATTTAAAGTTCGTTGCCTCTGATCAGAGGAGC
1 TTTTTAAATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGC
* * * *
12659843 TTTTGAAATTTAAAATTTGTTGCCTTTGGTGAGAGGAGC
1 TTTTTAAATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGC
* * * * *
12659882 -TTTTGAATTTAAAGTTTGTTGTCTCTGATGAGTGGAGC
1 TTTTTAAATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGC
* * *
12659920 TTTTCAACATTTAAAGTTCGTTGCCTCTGGTTAGAGAAGC
1 TTTTTAA-ATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGC
*
12659960 TTTTTAAATTTAAAGTTT-TATAGCCTCTGTTTAGAGGAGC
1 TTTTTAAATTTAAAGTTTGT-T-GCCTCTGGTTAGAGGAGC
* *
12660000 CTTTCAAATTT
1 TTTTTAAATTT
12660011 TCTCCTAAAA
Statistics
Matches: 296, Mismatches: 63, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
38 35 0.12
39 107 0.36
40 154 0.52
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (39 bp):
TTTTTAAATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGC
Found at i:12659758 original size:79 final size:79
Alignment explanation
Indices: 12659613--12660010 Score: 498
Period size: 79 Copynumber: 5.1 Consensus size: 79
12659603 CATATTTTTA
** * * ** * *
12659613 ATTTAAAGTTTGTTTTCTTTGGTTAAAAGAGCCTTTCAACATTTAAAGTTCGTTGCCTCTGGTCA
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGA-ATTTAAAGTTTGTTGCCTCTGATCA
12659678 GAGGAGCTTTTCAAC
65 GAGGAGCTTTTCAAC
*
12659693 ATTTAAAGTTTGTTACCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTTGTTGCCTCTGATCAG
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTTGTTGCCTCTGATCAG
*
12659758 AGGAGCTTTTTAAC
66 AGGAGCTTTTCAAC
* *
12659772 ATTTAAAGTATGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTCGTTGCCTCTGATCAG
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTTGTTGCCTCTGATCAG
*
12659837 AGGAGCTTTTGAA-
66 AGGAGCTTTTCAAC
* * * * *
12659850 ATTTAAAATTTGTTGCCTTTGGTGAGAGGAGC-TTTTGAATTTAAAGTTTGTTGTCTCTGATGAG
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTTGTTGCCTCTGATCAG
*
12659914 TGGAGCTTTTCAAC
66 AGGAGCTTTTCAAC
* * * * * * *
12659928 ATTTAAAGTTCGTTGCCTCTGGTTAGAGAAGCTTTTTAAATTTAAAGTTT-TATAGCCTCTGTTT
1 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTTGT-T-GCCTCTGATC
*
12659992 AGAGGAGCCTTTCAA-
64 AGAGGAGCTTTTCAAC
12660007 ATTT
1 ATTT
12660011 TCTCCTAAAA
Statistics
Matches: 281, Mismatches: 33, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
77 40 0.14
78 56 0.20
79 132 0.47
80 53 0.19
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (79 bp):
ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTTGAATTTAAAGTTTGTTGCCTCTGATCAG
AGGAGCTTTTCAAC
Found at i:12660163 original size:3 final size:3
Alignment explanation
Indices: 12660157--12660227 Score: 99
Period size: 3 Copynumber: 23.0 Consensus size: 3
12660147 TTTATTTTTT
*
12660157 TTA TTA TTA TATA GTT- TTG TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA -TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
12660204 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
12660228 ATCTTTAAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
2 2 0.03
3 55 0.87
4 5 0.08
5 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12661014 original size:19 final size:19
Alignment explanation
Indices: 12660988--12661035 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
12660978 AGGTTTTCCC
* *
12660988 TTTT-TTTTTTCTTTTTAT
1 TTTTATTTTTTATTTTGAT
12661006 TTTTATTTTTTATTTTGAT
1 TTTTATTTTTTATTTTGAT
*
12661025 TTTGATTTTTT
1 TTTTATTTTTT
12661036 TATGTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.10, C:0.02, G:0.04, T:0.83
Consensus pattern (19 bp):
TTTTATTTTTTATTTTGAT
Found at i:12661034 original size:7 final size:6
Alignment explanation
Indices: 12660988--12661047 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
12660978 AGGTTTTCCC
* * *
12660988 TTTTT- TTTTTC TTTTTA TTTTTA TTTTTTA TTTTGA TTTTGA TTTTT-
1 TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA
12661035 TTATGTTA TTTTT
1 TT-T-TTA TTTTT
12661048 TTATGATGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
5 7 0.15
6 29 0.62
7 9 0.19
8 2 0.04
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:12661045 original size:19 final size:18
Alignment explanation
Indices: 12661002--12661046 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
12660992 TTTTTTCTTT
* *
12661002 TTATTTTTATTTTTTATT
1 TTATTTTGATTTTTTATG
12661020 TTGATTTTGATTTTTTTATG
1 TT-ATTTTGA-TTTTTTATG
12661040 TTATTTT
1 TTATTTT
12661047 TTTATGATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 10 0.43
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.78
Consensus pattern (18 bp):
TTATTTTGATTTTTTATG
Found at i:12661088 original size:28 final size:28
Alignment explanation
Indices: 12660999--12661092 Score: 72
Period size: 28 Copynumber: 3.5 Consensus size: 28
12660989 TTTTTTTTTC
* *
12660999 TTTT-TATTTTTATT-TT-TTATTTTGA
1 TTTTGTATTATTATTGTTATTATTTTAA
* * *
12661024 TTTTG-ATTTTTTTATGTTATT-TTTTTA
1 TTTTGTATTATTAT-TGTTATTATTTTAA
**
12661051 TGATGTTATTATTATTGTTATTATTTTAA
1 TTTTG-TATTATTATTGTTATTATTTTAA
12661080 TTTTGTATTATTA
1 TTTTGTATTATTA
12661093 CTGGTAATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
25 11 0.21
26 1 0.02
27 10 0.19
28 17 0.32
29 14 0.26
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (28 bp):
TTTTGTATTATTATTGTTATTATTTTAA
Found at i:12661348 original size:13 final size:14
Alignment explanation
Indices: 12661328--12661356 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12661318 AAATAAATTG
12661328 TTTAAATG-AATCT
1 TTTAAATGCAATCT
12661341 TTTAAATGCAATCT
1 TTTAAATGCAATCT
12661355 TT
1 TT
12661357 AGAGAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (14 bp):
TTTAAATGCAATCT
Found at i:12662383 original size:21 final size:21
Alignment explanation
Indices: 12662357--12662396 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12662347 ACTTGATTAA
*
12662357 ATATAATCAAGTATTACATTC
1 ATATAATCAACTATTACATTC
12662378 ATATAATCAACTATTACAT
1 ATATAATCAACTATTACAT
12662397 CACTAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.38
Consensus pattern (21 bp):
ATATAATCAACTATTACATTC
Found at i:12663948 original size:22 final size:21
Alignment explanation
Indices: 12663920--12663974 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
12663910 TTTTCTCTTC
**
12663920 TTACATTTTTACTAATTTTTT
1 TTACATTTTTACTAATAATTT
*
12663941 TTATCATTTTTATTAATAATTT
1 TTA-CATTTTTACTAATAATTT
12663963 TTACTATTTTTA
1 TTAC-ATTTTTA
12663975 TTTTTAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.65
Consensus pattern (21 bp):
TTACATTTTTACTAATAATTT
Found at i:12663975 original size:22 final size:22
Alignment explanation
Indices: 12663920--12663985 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
12663910 TTTTCTCTTC
* **
12663920 TTAC-ATTTTTACTAATTTTTT
1 TTACTATTTTTATTAATAATTT
12663941 TTA-TCATTTTTATTAATAATTT
1 TTACT-ATTTTTATTAATAATTT
**
12663963 TTACTATTTTTATTTTTAATTT
1 TTACTATTTTTATTAATAATTT
12663985 T
1 T
12663986 AAAAATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.08
22 33 0.89
23 1 0.03
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (22 bp):
TTACTATTTTTATTAATAATTT
Found at i:12665295 original size:3 final size:3
Alignment explanation
Indices: 12665289--12665322 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
12665279 AAAAACTATG
12665289 ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12665323 TTAGGTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:12665870 original size:167 final size:168
Alignment explanation
Indices: 12665581--12665906 Score: 419
Period size: 167 Copynumber: 1.9 Consensus size: 168
12665571 GAAGAAGCTT
* * **
12665581 AACAATTTTGAAAGGCTTTTCTAAGAAAAACCTCCATAACTTTTTATCAATTTAAATATTCTACT
1 AACAATTTTGAAAGGCTCTTCTAAGAAAAACCTCCACAAAGTTTTATCAATTTAAATATTCTACT
*
12665646 AAAAGGACTTACGAATCTTAATGATAAAAGCTCCTCTAAGTAAAGGTTAATCAA-TTTTT-AAAA
66 AAAAGGACTTACGAATCTTAATGATAAAAGCTCCTCTAAGTAAAGCTTAATCAATTTTTTCAAAA
12665709 AAAATTCATCTT-GAAAAAACTCCTCTAAATAGGGGCTC
131 AAAATTCATCTTAG-AAAAACTCCTCTAAATAGGGGCTC
* ** * * *
12665747 AACAATTTT-AAAGAGCTCTTCTAAGAATAGGCTCCACAAAGTTTTCTCAATTTACAATATTTTG
1 AACAATTTTGAAAG-GCTCTTCTAAGAAAAACCTCCACAAAGTTTTATCAATTTA-AATATTCTA
* * * * * *
12665811 GTTAAAGGACTTACGAATCTTGATGATGAAAGTTCCTCTAAGTAGAGACTTAA-CAATTTTTTTC
64 CTAAAAGGACTTACGAATCTTAATGATAAAAGCTCCTCTAAGTAAAG-CTTAATCAA-TTTTTTC
12665875 AAAAAAAATTCATCTTAGAAAAACTCCTCTAA
127 AAAAAAAATTCATCTTAGAAAAACTCCTCTAA
12665907 GTAAAGGCTC
Statistics
Matches: 136, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
165 4 0.03
166 41 0.30
167 51 0.38
168 4 0.03
169 5 0.04
170 30 0.22
171 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (168 bp):
AACAATTTTGAAAGGCTCTTCTAAGAAAAACCTCCACAAAGTTTTATCAATTTAAATATTCTACT
AAAAGGACTTACGAATCTTAATGATAAAAGCTCCTCTAAGTAAAGCTTAATCAATTTTTTCAAAA
AAAATTCATCTTAGAAAAACTCCTCTAAATAGGGGCTC
Found at i:12665954 original size:52 final size:51
Alignment explanation
Indices: 12665875--12666010 Score: 148
Period size: 52 Copynumber: 2.6 Consensus size: 51
12665865 AATTTTTTTC
* * * * * *
12665875 AAAAAAAATTCATCTTAGAAAAACTCCTCTAAGTAAAGGCTCAATAACTTTT
1 AAAAAAAATTTATATGA-AAAAACTCCTCTAAGCAAAGGCTCAACAACTTTA
* * *
12665927 AATAAAAATCCTTAT-TGCAAAAACTCCTCTAAGCAAAGGCTGAACAACTTTA
1 AAAAAAAAT--TTATATGAAAAAACTCCTCTAAGCAAAGGCTCAACAACTTTA
12665979 AAAAAAAATTTATCATGAAAAAACTCCTCTAA
1 AAAAAAAATTTAT-ATGAAAAAACTCCTCTAA
12666011 ACAACTCCTC
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
50 4 0.06
52 62 0.89
53 1 0.01
54 3 0.04
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.26
Consensus pattern (51 bp):
AAAAAAAATTTATATGAAAAAACTCCTCTAAGCAAAGGCTCAACAACTTTA
Found at i:12666018 original size:65 final size:64
Alignment explanation
Indices: 12665948--12666074 Score: 164
Period size: 65 Copynumber: 2.0 Consensus size: 64
12665938 TTATTGCAAA
* *
12665948 AACTCCTCTAAGCAAAGGCTGAACAACTTTAAAAAAAAATTTATCATGAAAAAACTCCTCTAAAC
1 AACTCCTCTAAGCAAAGGCTCAACAACTTTAAAAAAAAATTGATCATGAAAAAA-TCCTCTAAAC
** * * * * *
12666013 AACTCCTCTAAGCAGGGGCTCAATAACTTTTAATAAAAATTGATCTTGAAAAAATCTTCTAA
1 AACTCCTCTAAGCAAAGGCTCAACAACTTTAAAAAAAAATTGATCATGAAAAAATCCTCTAA
12666075 GCAAATGCTC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
64 7 0.13
65 46 0.87
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (64 bp):
AACTCCTCTAAGCAAAGGCTCAACAACTTTAAAAAAAAATTGATCATGAAAAAATCCTCTAAAC
Found at i:12666976 original size:16 final size:16
Alignment explanation
Indices: 12666957--12666993 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
12666947 TTTTTCTTAC
12666957 TTTTTTTTTTTTTTGT
1 TTTTTTTTTTTTTTGT
*
12666973 TTTTGTTTTTTTTTGT
1 TTTTTTTTTTTTTTGT
12666989 TTTTT
1 TTTTT
12666994 CATTCTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (16 bp):
TTTTTTTTTTTTTTGT
Found at i:12667027 original size:1 final size:1
Alignment explanation
Indices: 12666957--12667009 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
12666947 TTTTTCTTAC
* * * ** *
12666957 TTTTTTTTTTTTTTGTTTTTGTTTTTTTTTGTTTTTTCATTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12667010 CAAGCAAAGT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.02, C:0.04, G:0.06, T:0.89
Consensus pattern (1 bp):
T
Found at i:12678390 original size:21 final size:21
Alignment explanation
Indices: 12678356--12678418 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
12678346 TAAAAAAATT
12678356 TTTTTCTTATATTTTT-TCTAA
1 TTTTTCTTATATTTTTAT-TAA
12678377 TTTTT-TTATCATTTTTATTAA
1 TTTTTCTTAT-ATTTTTATTAA
*
12678398 TTTTGT-TAATAATTTTTATTA
1 TTTT-TCTTAT-ATTTTTATTA
12678419 TTTATTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
20 4 0.11
21 18 0.49
22 15 0.41
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTCTTATATTTTTATTAA
Found at i:12678412 original size:22 final size:21
Alignment explanation
Indices: 12678366--12678418 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
12678356 TTTTTCTTAT
* *
12678366 ATTTTT-TCTAATTTTTTTATC
1 ATTTTTAT-TAATTTTTTAATA
12678387 ATTTTTATTAATTTTGTTAATA
1 ATTTTTATTAATTTT-TTAATA
12678409 ATTTTTATTA
1 ATTTTTATTA
12678419 TTTATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (21 bp):
ATTTTTATTAATTTTTTAATA
Found at i:12678565 original size:38 final size:38
Alignment explanation
Indices: 12678522--12678599 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
12678512 TTTTATAAGG
*
12678522 CTTATTTCAAATTTTTACAAAATTATAAAAAATTTTAA
1 CTTATTTCAAATTTTAACAAAATTATAAAAAATTTTAA
*
12678560 CTTATTTCAAATTTTAACAAAATTATCAAAAATTTTAA
1 CTTATTTCAAATTTTAACAAAATTATAAAAAATTTTAA
12678598 CT
1 CT
12678600 ATGGATTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (38 bp):
CTTATTTCAAATTTTAACAAAATTATAAAAAATTTTAA
Found at i:12678592 original size:21 final size:21
Alignment explanation
Indices: 12678530--12678598 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 21
12678520 GGCTTATTTC
* *
12678530 AAATTTTTACAAAATTATAAA
1 AAATTTTAACAAAATTATCAA
**
12678551 AAATTTTAAC-TTATT-TC--
1 AAATTTTAACAAAATTATCAA
12678568 AAATTTTAACAAAATTATCAA
1 AAATTTTAACAAAATTATCAA
12678589 AAATTTTAAC
1 AAATTTTAAC
12678599 TATGGATTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
17 10 0.26
18 3 0.08
19 3 0.08
20 3 0.08
21 19 0.50
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATTTTAACAAAATTATCAA
Found at i:12679474 original size:20 final size:21
Alignment explanation
Indices: 12679445--12679484 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12679435 AGAGCCTTTT
12679445 TTTTTATTTTGGTAAGGTTTC
1 TTTTTATTTTGGTAAGGTTTC
**
12679466 TTTTT-TTTTTTTAAGGTTT
1 TTTTTATTTTGGTAAGGTTT
12679485 TGCTTGGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.12, C:0.03, G:0.15, T:0.70
Consensus pattern (21 bp):
TTTTTATTTTGGTAAGGTTTC
Found at i:12685442 original size:11 final size:11
Alignment explanation
Indices: 12685426--12685459 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12685416 TTCGTAAATT
12685426 ATTTAAATTTA
1 ATTTAAATTTA
**
12685437 ATTTAAATAAA
1 ATTTAAATTTA
12685448 ATTTAAATTTA
1 ATTTAAATTTA
12685459 A
1 A
12685460 ATAATTTGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:12685458 original size:17 final size:16
Alignment explanation
Indices: 12685430--12685463 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
12685420 TAAATTATTT
12685430 AAATTTAATTTAAATA
1 AAATTTAATTTAAATA
12685446 AAATTTAAATTTAAATA
1 AAATTT-AATTTAAATA
12685463 A
1 A
12685464 TTTGATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTAATTTAAATA
Found at i:12686120 original size:19 final size:19
Alignment explanation
Indices: 12686098--12686134 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12686088 TGATTTAAAA
*
12686098 TTAATTTAATAATTTTAAT
1 TTAATATAATAATTTTAAT
*
12686117 TTAATATAATATTTTTAA
1 TTAATATAATAATTTTAA
12686135 AATATTATTA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATATAATAATTTTAAT
Found at i:12686196 original size:28 final size:27
Alignment explanation
Indices: 12686148--12686201 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
12686138 ATTATTATGT
*
12686148 AATATAAATTATATCTTAGTTATATATA
1 AATATAAATTATATCTAAGTTA-ATATA
*
12686176 AATATAAATTTTTAT-TAAGTTAATAT
1 AATATAAA-TTATATCTAAGTTAATAT
12686202 TTTAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 14 0.61
29 5 0.22
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (27 bp):
AATATAAATTATATCTAAGTTAATATA
Found at i:12686236 original size:12 final size:12
Alignment explanation
Indices: 12686196--12686239 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
12686186 TTTATTAAGT
12686196 TAATATTTTAAA
1 TAATATTTTAAA
* *
12686208 TTAAAATATTAAA
1 -TAATATTTTAAA
*
12686221 TAATATTTTTAA
1 TAATATTTTAAA
12686233 TAATATT
1 TAATATT
12686240 ATACATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATATTTTAAA
Found at i:12690156 original size:22 final size:23
Alignment explanation
Indices: 12690130--12690177 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
12690120 CTTTCATCTT
* *
12690130 ATTTTTAATCTAT-TTTTTGAAC
1 ATTTTAAATATATATTTTTGAAC
*
12690152 ATTTTAAATATATATTTTTTAAC
1 ATTTTAAATATATATTTTTGAAC
12690175 ATT
1 ATT
12690178 AATTTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTTTAAATATATATTTTTGAAC
Found at i:12690206 original size:28 final size:27
Alignment explanation
Indices: 12690168--12690233 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 27
12690158 AATATATATT
12690168 TTTTAACATTAATTTTCT-TTTTTTTATA
1 TTTTAACATTAATTTT-TATTTTTTTA-A
12690196 TTTTGAA-ATT-ATTTTTATTTTTTTAA
1 TTTT-AACATTAATTTTTATTTTTTTAA
12690222 TTTTAACATTAA
1 TTTTAACATTAA
12690234 AAATCATGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
25 2 0.06
26 9 0.26
27 14 0.41
28 7 0.21
29 2 0.06
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTAACATTAATTTTTATTTTTTTAA
Found at i:12691968 original size:20 final size:21
Alignment explanation
Indices: 12691932--12691983 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12691922 CCCGAAATTA
12691932 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
12691954 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
12691975 AT-AAATATT
1 ATAAAATATT
12691984 TTAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:12691974 original size:21 final size:22
Alignment explanation
Indices: 12691932--12691983 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
12691922 CCCGAAATTA
12691932 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
12691954 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
12691975 AT-AAATATT
1 ATAAAATATT
12691984 TTAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:12691990 original size:30 final size:30
Alignment explanation
Indices: 12691955--12692012 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12691945 TTTTAAAATA
* * *
12691955 TAAAATATTATTTTTTAAATATAAATATTT
1 TAAAATATCATTATATAAATATAAATATTT
*
12691985 TAAAATATCATTATATAAATATATATAT
1 TAAAATATCATTATATAAATATAAATAT
12692013 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAATATCATTATATAAATATAAATATTT
Found at i:12697655 original size:22 final size:23
Alignment explanation
Indices: 12697630--12697678 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
12697620 TAATTTTATT
*
12697630 AATATAATAA-TAAATATAT-ATA
1 AATATAA-AATTAAATAAATAATA
12697652 AATATAAAATTAAATAAATAATA
1 AATATAAAATTAAATAAATAATA
12697675 AATA
1 AATA
12697679 ATATTTTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 2 0.08
22 15 0.62
23 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AATATAAAATTAAATAAATAATA
Found at i:12703791 original size:11 final size:11
Alignment explanation
Indices: 12703770--12703805 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
12703760 TTTTAAATTG
12703770 TATTATTTTTA
1 TATTATTTTTA
12703781 TA-TATTTTTTA
1 TATTA-TTTTTA
12703792 TATTATTTTTA
1 TATTATTTTTA
12703803 TAT
1 TAT
12703806 CATATCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.09
11 19 0.83
12 2 0.09
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:12705988 original size:18 final size:17
Alignment explanation
Indices: 12705965--12706019 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
12705955 ATTGGAGTGT
12705965 TTTTAATAAAATAAAAA
1 TTTTAATAAAATAAAAA
*
12705982 CTTTTAAT-AAATAAAAT
1 -TTTTAATAAAATAAAAA
*
12705999 TTTTAATACAATAAAAA
1 TTTTAATAAAATAAAAA
12706016 TTTT
1 TTTT
12706020 CTTTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 7 0.21
17 19 0.58
18 7 0.21
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTAATAAAATAAAAA
Found at i:12707070 original size:14 final size:15
Alignment explanation
Indices: 12707052--12707090 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
12707042 ATTTGTCTAA
12707052 AAAAATTAAAAAAA-T
1 AAAAA-TAAAAAAATT
*
12707067 AAAAACAAAAAAATT
1 AAAAATAAAAAAATT
12707082 AAAAATAAA
1 AAAAATAAA
12707091 TTTAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAATAAAAAAATT
Found at i:12707653 original size:19 final size:17
Alignment explanation
Indices: 12707626--12707675 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
12707616 AAAAGAAGGC
* *
12707626 AAAATAAAAAAAAATGAA
1 AAAACAAAAAAAAA-CAA
12707644 AGAAACAAAAAAAAACAA
1 A-AAACAAAAAAAAACAA
*
12707662 AAGACAAAAAAAAA
1 AAAACAAAAAAAAA
12707676 AGATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 12 0.43
18 4 0.14
19 12 0.43
ACGTcount: A:0.84, C:0.06, G:0.06, T:0.04
Consensus pattern (17 bp):
AAAACAAAAAAAAACAA
Found at i:12707676 original size:19 final size:19
Alignment explanation
Indices: 12707631--12707675 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
12707621 AAGGCAAAAT
**
12707631 AAAAAAAAATGAAAGAAAC
1 AAAAAAAAACAAAAGAAAC
12707650 AAAAAAAAACAAAAG--AC
1 AAAAAAAAACAAAAGAAAC
12707667 AAAAAAAAA
1 AAAAAAAAA
12707676 AGATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.46
19 13 0.54
ACGTcount: A:0.84, C:0.07, G:0.07, T:0.02
Consensus pattern (19 bp):
AAAAAAAAACAAAAGAAAC
Found at i:12718176 original size:16 final size:15
Alignment explanation
Indices: 12718150--12718194 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 15
12718140 GTAACATGAA
12718150 AGAATGAAAAAAATG
1 AGAATGAAAAAAATG
*
12718165 AGAATAGAAAAAAATT
1 AGAAT-GAAAAAAATG
12718181 A-AA-GAAAAAAATG
1 AGAATGAAAAAAATG
12718194 A
1 A
12718195 TATTCCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 10 0.37
15 7 0.26
16 10 0.37
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (15 bp):
AGAATGAAAAAAATG
Found at i:12718691 original size:48 final size:48
Alignment explanation
Indices: 12718625--12718776 Score: 187
Period size: 48 Copynumber: 3.2 Consensus size: 48
12718615 GGCATTTAAT
** ** * *
12718625 AGAAGAGCCTTTTGTTATTTCATTTTTAAAGTTGTCAACCCTCTGATG
1 AGAAGAGCCTTTCATTATTTTGTTTTTAAAATTGTCAAACCTCTGATG
* * * *
12718673 AGAGGAGCCTTTCATTATTTTGTTTTTAAAATGGTCAAACTTTTGATG
1 AGAAGAGCCTTTCATTATTTTGTTTTTAAAATTGTCAAACCTCTGATG
* * *
12718721 AGAAGAGCCTTTCATTATTTTGCTTTTAAAATTGTCAAGCCTCTAATG
1 AGAAGAGCCTTTCATTATTTTGTTTTTAAAATTGTCAAACCTCTGATG
12718769 AGAAGAGC
1 AGAAGAGC
12718777 ATAAAAAAGA
Statistics
Matches: 87, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 87 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Consensus pattern (48 bp):
AGAAGAGCCTTTCATTATTTTGTTTTTAAAATTGTCAAACCTCTGATG
Found at i:12720176 original size:5 final size:5
Alignment explanation
Indices: 12720166--12720211 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
12720156 GTTTCTATAT
12720166 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTA -TTTA -TTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
12720212 GCAATTTATC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 16 0.40
5 24 0.60
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:12720196 original size:4 final size:4
Alignment explanation
Indices: 12720167--12720209 Score: 50
Period size: 4 Copynumber: 9.8 Consensus size: 4
12720157 TTTCTATATT
12720167 TTTA TTTTA TTTTA TTTTA TTTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA -TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTT
12720210 TAGCAATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 19 0.50
5 19 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:12720200 original size:8 final size:9
Alignment explanation
Indices: 12720167--12720211 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
12720157 TTTCTATATT
12720167 TTTATTTTA
1 TTTATTTTA
12720176 TTTTATTTTA
1 -TTTATTTTA
12720186 TTT-TATTTA
1 TTTAT-TTTA
12720195 TTTA-TTTA
1 TTTATTTTA
12720203 TTTATTTTA
1 TTTATTTTA
12720212 GCAATTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 9 0.28
9 14 0.44
10 9 0.28
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTTA
Found at i:12720857 original size:5 final size:5
Alignment explanation
Indices: 12720847--12720872 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12720837 ACCAATGAAT
12720847 TAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA T
12720873 GTGTGCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:12721857 original size:29 final size:27
Alignment explanation
Indices: 12721825--12721903 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 27
12721815 TAATATATAA
* *
12721825 AAAAATTATTAAAAATATTGTTTATAATT
1 AAAAATTA-TAAAAATATT-TTTAAAAAT
* *
12721854 AAAATTTAATCAAAAT-TTATTTAAAAAT
1 AAAAATT-ATAAAAATATT-TTTAAAAAT
*
12721882 AAAAATTATATAAATATTTTTA
1 AAAAATTATAAAAATATTTTTA
12721904 CTAAAAATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
27 10 0.25
28 17 0.43
29 12 0.30
30 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
AAAAATTATAAAAATATTTTTAAAAAT
Found at i:12726035 original size:68 final size:68
Alignment explanation
Indices: 12725948--12726081 Score: 187
Period size: 68 Copynumber: 2.0 Consensus size: 68
12725938 ACGAATTTTT
* * *
12725948 TGTGAATATTATCGGTTTTTATTTATTTATGTTTATTTATTAAACTTAAAAAATAATCTTAAATA
1 TGTGAACATTATCGATTTTTATTTATTTATATTTATTTATTAAACTTAAAAAATAATCTTAAATA
12726013 AGA
66 AGA
* ** * * *
12726016 TGTGAACATTATCGATTTTTATTTTTTTATATTTATTTATTAAGTTTAACAAATAATTTTGAATA
1 TGTGAACATTATCGATTTTTATTTATTTATATTTATTTATTAAACTTAAAAAATAATCTTAAATA
12726081 A
66 A
12726082 TATTTTTATA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 57 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (68 bp):
TGTGAACATTATCGATTTTTATTTATTTATATTTATTTATTAAACTTAAAAAATAATCTTAAATA
AGA
Found at i:12726351 original size:15 final size:15
Alignment explanation
Indices: 12726320--12726361 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
12726310 TACATTTAGG
*
12726320 ATTTATTTGTTTA-A
1 ATTTATTTGATTATA
12726334 ATTTATTTGATTATA
1 ATTTATTTGATTATA
12726349 ATTTATTT-ATTAT
1 ATTTATTTGATTAT
12726362 TCATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (15 bp):
ATTTATTTGATTATA
Found at i:12730084 original size:12 final size:12
Alignment explanation
Indices: 12730055--12730095 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
12730045 TAAGATTCTT
*
12730055 ATTTAA-AAATA
1 ATTTAATAAAAA
12730066 ATTTAATAAAAA
1 ATTTAATAAAAA
*
12730078 TTTTAATAAAAA
1 ATTTAATAAAAA
12730090 ATTTAA
1 ATTTAA
12730096 ATTGATAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATTTAATAAAAA
Found at i:12731337 original size:198 final size:198
Alignment explanation
Indices: 12730999--12731398 Score: 800
Period size: 198 Copynumber: 2.0 Consensus size: 198
12730989 GCATAAGCTT
12730999 ATTTGTGTTATGATCTTAACCCTTTTTTTCATGTACATAGTTGCGGAAGAAAATTGTGATTGTTT
1 ATTTGTGTTATGATCTTAACCCTTTTTTTCATGTACATAGTTGCGGAAGAAAATTGTGATTGTTT
12731064 TAATTTTCCCACTGATAATCTTGATTTTTTCTGCAATTGGGGAAGTAGTTCAAACTTTGACAGCC
66 TAATTTTCCCACTGATAATCTTGATTTTTTCTGCAATTGGGGAAGTAGTTCAAACTTTGACAGCC
12731129 ATGAACATGATGGAAATTAAAGAAATTTAGAGGCCTTTTATGTATGGATTGTGTTTCAAGGGTCC
131 ATGAACATGATGGAAATTAAAGAAATTTAGAGGCCTTTTATGTATGGATTGTGTTTCAAGGGTCC
12731194 ACA
196 ACA
12731197 ATTTGTGTTATGATCTTAACCCTTTTTTTCATGTACATAGTTGCGGAAGAAAATTGTGATTGTTT
1 ATTTGTGTTATGATCTTAACCCTTTTTTTCATGTACATAGTTGCGGAAGAAAATTGTGATTGTTT
12731262 TAATTTTCCCACTGATAATCTTGATTTTTTCTGCAATTGGGGAAGTAGTTCAAACTTTGACAGCC
66 TAATTTTCCCACTGATAATCTTGATTTTTTCTGCAATTGGGGAAGTAGTTCAAACTTTGACAGCC
12731327 ATGAACATGATGGAAATTAAAGAAATTTAGAGGCCTTTTATGTATGGATTGTGTTTCAAGGGTCC
131 ATGAACATGATGGAAATTAAAGAAATTTAGAGGCCTTTTATGTATGGATTGTGTTTCAAGGGTCC
12731392 ACA
196 ACA
12731395 ATTT
1 ATTT
12731399 TCCCCACTTT
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
198 202 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (198 bp):
ATTTGTGTTATGATCTTAACCCTTTTTTTCATGTACATAGTTGCGGAAGAAAATTGTGATTGTTT
TAATTTTCCCACTGATAATCTTGATTTTTTCTGCAATTGGGGAAGTAGTTCAAACTTTGACAGCC
ATGAACATGATGGAAATTAAAGAAATTTAGAGGCCTTTTATGTATGGATTGTGTTTCAAGGGTCC
ACA
Found at i:12734717 original size:21 final size:21
Alignment explanation
Indices: 12734687--12734734 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
12734677 TCCTTATCAC
*
12734687 CTTGAATATCAATATCACCAA
1 CTTGAATATCAACATCACCAA
* * *
12734708 CTTGAGTATCAGCATCACTAA
1 CTTGAATATCAACATCACCAA
12734729 CTTGAA
1 CTTGAA
12734735 GAATACAAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (21 bp):
CTTGAATATCAACATCACCAA
Found at i:12737607 original size:22 final size:22
Alignment explanation
Indices: 12737582--12737631 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
12737572 CTTTTTAGAG
*
12737582 ATTATTT-AAGACATTTTTGCCT
1 ATTATTTAAAG-CATTTTTGCCC
12737604 ATTATTTAAAGCATTTTTGCCC
1 ATTATTTAAAGCATTTTTGCCC
12737626 ATTATT
1 ATTATT
12737632 CAAAACGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (22 bp):
ATTATTTAAAGCATTTTTGCCC
Found at i:12737643 original size:23 final size:22
Alignment explanation
Indices: 12737582--12737643 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
12737572 CTTTTTAGAG
* * *
12737582 ATTATTTAAGACATTTTTGCCT
1 ATTATTCAAAACATTTTTGCCC
* *
12737604 ATTATTTAAAGCATTTTTGCCC
1 ATTATTCAAAACATTTTTGCCC
*
12737626 ATTATTCAAAACGTTTTT
1 ATTATTCAAAACATTTTT
12737644 AACCAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (22 bp):
ATTATTCAAAACATTTTTGCCC
Found at i:12737737 original size:103 final size:102
Alignment explanation
Indices: 12737627--12737916 Score: 253
Period size: 103 Copynumber: 2.8 Consensus size: 102
12737617 TTTTTGCCCA
12737627 TTATTCAAAACGTTTTTAACCAAAAATACCTTCAATAATCTCTTTTAATTTCTATGAAGAGATTA
1 TTATTCAAAACGTTTTT-ACCAAAAATACCTTCAATAATCTCTTTTAATTTCTATG-AGAGATTA
12737692 TTCAAAGTGTTTTTTGTCAAAAATACCTTAAATAAT-CC
64 TTCAAAGTGTTTTTTGTCAAAAATACCTTAAATAATACC
** * * * *
12737730 TCT-TTCAATAA-GTTTTCTAGTAAAAATACCTTCAATAATCCCTTCTAATTTTTTATTAGAGAT
1 T-TATTCAA-AACGTTTT-TACCAAAAATACCTTCAATAATCTCTTTTAA-TTTCTATGAGAGAT
* * * *** * * * * **
12737793 TATTGAAGGCGTTTTTAACCATATATGCCTTGAATAATAGGG
62 TATTCAAAGTGTTTTTTGTCAAAAATACCTTAAATAATA-CC
** * ** *
12737835 TTATTCAAGGCGTTTCTGACCAAAAACGCCTTCAATAATCTTTTTTAATTTCTATGAGAGGATTA
1 TTATTCAAAACGTTT-TTACCAAAAATACCTTCAATAATCTCTTTTAATTTCTATGAGA-GATTA
*
12737900 TTCAAAGTATTTTTTGT
64 TTCAAAGTGTTTTTTGT
12737917 TAGAAACGCC
Statistics
Matches: 140, Mismatches: 37, Indels: 18
0.72 0.19 0.09
Matches are distributed among these distances:
103 71 0.51
104 20 0.14
105 48 0.34
106 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (102 bp):
TTATTCAAAACGTTTTTACCAAAAATACCTTCAATAATCTCTTTTAATTTCTATGAGAGATTATT
CAAAGTGTTTTTTGTCAAAAATACCTTAAATAATACC
Found at i:12737866 original size:43 final size:43
Alignment explanation
Indices: 12737792--12737873 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 43
12737782 TTATTAGAGA
* * * * * *
12737792 TTATTGAAGGCGTTTTTAACCATATATGCCTTGAATAATAGGG
1 TTATTCAAGGCGTTTCTAACCAAAAACGCCTTCAATAATAGGG
*
12737835 TTATTCAAGGCGTTTCTGACCAAAAACGCCTTCAATAAT
1 TTATTCAAGGCGTTTCTAACCAAAAACGCCTTCAATAAT
12737874 CTTTTTTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (43 bp):
TTATTCAAGGCGTTTCTAACCAAAAACGCCTTCAATAATAGGG
Found at i:12738711 original size:118 final size:116
Alignment explanation
Indices: 12738501--12738711 Score: 243
Period size: 118 Copynumber: 1.8 Consensus size: 116
12738491 ACCAAAAATA
* * *
12738501 CCTTGAATAATCAGTTATTCAATGCATTTTTTATCAAAACAACCTTCAATAATCTACTTCAATTT
1 CCTTGAATAATCAGTTATTCAAGGCATTTTTGATCAAAACAACCTTCAATAATCTACTTCAATGT
* * *
12738566 TTTATTGGAGATTATTGAAGGTATTTTTAGCCAGAAATACCTTGAATAATG
66 TTTATAGGAGATTATTCAAGGCATTTTTAGCCAGAAATACCTTGAATAATG
*
12738617 CCTTGAATAACCTCA-TTATTCAAGGCATTTTCTGA-CAAAA-AAGGCCTTCAATAATC-CCTTT
1 CCTTGAATAA--TCAGTTATTCAAGGCATTTT-TGATCAAAACAA--CCTTCAATAATCTAC-TT
* *
12738678 CAA-GTTTTATGAGGGGATTATTCAAGGCGTTTTT
60 CAATGTTTTAT-AGGAGATTATTCAAGGCATTTTT
12738712 TTCTATAATC
Statistics
Matches: 79, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
116 12 0.15
117 27 0.34
118 40 0.51
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (116 bp):
CCTTGAATAATCAGTTATTCAAGGCATTTTTGATCAAAACAACCTTCAATAATCTACTTCAATGT
TTTATAGGAGATTATTCAAGGCATTTTTAGCCAGAAATACCTTGAATAATG
Found at i:12739855 original size:15 final size:15
Alignment explanation
Indices: 12739821--12739855 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12739811 TTTAAAATTC
12739821 GTTTAAAATTTATTA
1 GTTTAAAATTTATTA
* *
12739836 ATTTAAAATTTATTT
1 GTTTAAAATTTATTA
12739851 GTTTA
1 GTTTA
12739856 TTATTCATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (15 bp):
GTTTAAAATTTATTA
Done.