Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 7 of 433
Found at i:2068577 original size:80 final size:80
Alignment explanation
Indices: 2068444--2068604 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
2068434 AATCTCACTA
2068444 TCAAAAAGTAGAGAACCTGGCGGGTTTCTTCTAGTCATAAACTATAAAAACCTATCAGAAGTAAA
1 TCAAAAAGTAGAGAACCTGGCGGGTTTCTTCTAGTCATAAACTATAAAAACCTATCAGAAGTAAA
2068509 TAAAAGAAAATTTAG
66 TAAAAGAAAATTTAG
2068524 TCAAAAAGTAGAGAACCTGGCGGGTTTCTTCTAGTCATAAACTATAAAAACCTATCAGAAGTAAA
1 TCAAAAAGTAGAGAACCTGGCGGGTTTCTTCTAGTCATAAACTATAAAAACCTATCAGAAGTAAA
2068589 TAAAAGAAAATTTAG
66 TAAAAGAAAATTTAG
2068604 T
1 T
2068605 AATATAAGCA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (80 bp):
TCAAAAAGTAGAGAACCTGGCGGGTTTCTTCTAGTCATAAACTATAAAAACCTATCAGAAGTAAA
TAAAAGAAAATTTAG
Found at i:2070434 original size:42 final size:43
Alignment explanation
Indices: 2070338--2070452 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 43
2070328 CTTCGTTTTC
** * *
2070338 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAA
** *
2070381 T-GATGTTATAGCCCAGCTATGGTCTTACACATATTCATAT-A
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAA
*
2070422 TCGATGCCATAGCCTAGCTATGGTCTTACAC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC
2070453 GAATCACATA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 2 0.03
42 58 0.95
43 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (43 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAA
Found at i:2070526 original size:47 final size:46
Alignment explanation
Indices: 2070423--2070546 Score: 140
Period size: 47 Copynumber: 2.7 Consensus size: 46
2070413 ATTCATATAT
* * * * * *
2070423 CGATGCCATAGCCTAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * * *
2070469 TGATGTCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
*
2070516 CGATGCCATATACCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
2070547 GAAATCACTT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 25 0.39
47 39 0.61
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:2070606 original size:31 final size:31
Alignment explanation
Indices: 2070571--2070684 Score: 174
Period size: 31 Copynumber: 3.7 Consensus size: 31
2070561 CTTGTCACTT
*
2070571 GTAGCTGAAGCTACCACTATTCACTGATCAG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
* *
2070602 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
* * *
2070633 GTAACAGAACCTACCACTTTTCACTGATCAG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAG
2070664 GTAGCTGAAGCTACCACTTTT
1 GTAGCTGAAGCTACCACTTTT
2070685 TACTTGTCAT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (31 bp):
GTAGCTGAAGCTACCACTTTTCACTGATCAG
Found at i:2070762 original size:50 final size:51
Alignment explanation
Indices: 2070664--2070785 Score: 183
Period size: 50 Copynumber: 2.4 Consensus size: 51
2070654 CACTGATCAG
* * * * *
2070664 GTAGCTGAAGCTACCACTTTTTACTTGTCATTTTTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTTTCATTGATCAGATAAGT
*
2070715 GTAGCCGAAGCTATCACTTATCACTT-TCACTTTTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTTTCATTGATCAGATAAGT
2070765 GTAGCCGAAGCTATCACTTAT
1 GTAGCCGAAGCTATCACTTAT
2070786 TGTAACGACC
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
50 43 0.66
51 22 0.34
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTTTCATTGATCAGATAAGT
Found at i:2071130 original size:12 final size:12
Alignment explanation
Indices: 2071085--2071140 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
2071075 TGTGTTAAAA
*
2071085 TATATATTAAAT
1 TATATATTATAT
2071097 TAT-TATTATATT
1 TATATATTATA-T
2071109 ATAGTATATTATAT
1 -TA-TATATTATAT
*
2071123 TATATATTATAC
1 TATATATTATAT
2071135 TATATA
1 TATATA
2071141 AATAAGTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 6 0.16
12 19 0.50
13 4 0.11
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (12 bp):
TATATATTATAT
Found at i:2071133 original size:5 final size:5
Alignment explanation
Indices: 2071087--2071127 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
2071077 TGTTAAAATA
* *
2071087 TATAT TAAAT TATTAT TATAT TATAG TATAT TATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT
2071128 ATTATACTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:2072427 original size:18 final size:19
Alignment explanation
Indices: 2072406--2072444 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
2072396 ATATATAGAT
2072406 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
2072424 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
2072443 AT
1 AT
2072445 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:2072793 original size:39 final size:39
Alignment explanation
Indices: 2072683--2072817 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
2072673 GACCTCGAGT
* * * *
2072683 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
2072724 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
2072762 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
2072801 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
2072818 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:2072961 original size:18 final size:19
Alignment explanation
Indices: 2072940--2072980 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2072930 AATGAAATGA
2072940 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
2072958 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
2072977 GAAA
1 GAAA
2072981 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:2076128 original size:30 final size:30
Alignment explanation
Indices: 2076093--2076150 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2076083 CACGGCCATG
* *
2076093 ACACACGGGCGTGTGGTAT-ACCCGTGTGTC
1 ACACACGGACGTGT-GAATCACCCGTGTGTC
2076123 ACACACGGACGTGTGAATCACCCGTGTG
1 ACACACGGACGTGTGAATCACCCGTGTG
2076151 GAAGTGCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.21, C:0.28, G:0.31, T:0.21
Consensus pattern (30 bp):
ACACACGGACGTGTGAATCACCCGTGTGTC
Found at i:2079536 original size:457 final size:460
Alignment explanation
Indices: 2078867--2079776 Score: 1459
Period size: 457 Copynumber: 2.0 Consensus size: 460
2078857 TCTTTTAAAT
* *
2078867 TGTGCAAGTCAATATGCTCACACAATCTAGCACACGGGCGTGTGGCTTGGCTGTGTGGCCCAAGT
1 TGTGCAAGTCAATATGCTCACACAATCTAACACACGGGCATGTGGCTTGGCTGTGTGGCCCAAGT
* * * * *
2078932 CAAGGAGTTACACAAGTACAGGTACGGGCTGGGACATAGCCGTGTGTCTCTATTTCGAATGTCCA
66 CAAGGAGTTACACAAGTACAGGCACGGGCTGGGAAACAACCGTGTGTCTCTATTTCGAATATCCA
2078997 CACGGTCTAAGACACGAACGTGTCTCTTGGTCGTGTGAATCAACGGCCTAGCCACACAGCCGTGT
131 CACGGTCTAAGACACGAACGTGTCTCTTGGTCGTGTGAATCAACGGCCTAGCCACACAGCCGTGT
* * * *
2079062 GACCCCTACAGCTTTGAAAAATTTTAATGTTTTTTGAAATATTCTTTGAGTACCTGATTTAGTCT
196 AACCCCTACAACTTTGAAAAATTTTAATGTTTTCTGAAATATTCTTTGAGTACCTAATTTAGTCT
*
2079127 CGACTTGTTTTTAATGCATATTATGGGCCTCGAGGGCTTGCATAAAGGA-AA-A-TATGTTTGAT
261 CGACTTGTTTTTAATGCATATTATGGGCCTCGAGGGCTCGCATAAAGGACAATATTATGTTTGAT
*
2079189 TTCTATTGGTTTCTGACATGAATGTTATATAATATGAAATGTCTTTTTAATTGATCTATAAACTC
326 TTCTATTGGTTTCTGACATGAATGTTATATAATATGAAATGTCTGTTTAATTGATCTATAAACTC
* ** *
2079254 TAGTAATACTCTGTAACTCTGTTCTGACGATGGATATGGGTTAGGGGTGTTACAGCAACATAGCA
391 TAGTAACACTCCATAACTCTGTTCCGACGATGGATATGGGTTAGGGGTGTTACAGCAACATAGCA
2079319 TAGGG
456 TAGGG
* *
2079324 TGTGCAAGTCAATATGCTCATACGATCTAACACACGGGCATGTGGCTTGGCTGTGTGGCCCAAGT
1 TGTGCAAGTCAATATGCTCACACAATCTAACACACGGGCATGTGGCTTGGCTGTGTGGCCCAAGT
* * *
2079389 CAGGGAGTTACACAGGTAC-GGACACGGGCTGGGAAACAACCGTGTGTCTCTATTTCGAATATCT
66 CAAGGAGTTACACAAGTACAGG-CACGGGCTGGGAAACAACCGTGTGTCTCTATTTCGAATATCC
** * *
2079453 ACACGGTCTAAGACACGGGCGTGTCTCTTGGTTGTGTGAATCAACGGCCTAGCCACACGGCCGTG
130 ACACGGTCTAAGACACGAACGTGTCTCTTGGTCGTGTGAATCAACGGCCTAGCCACACAGCCGTG
*
2079518 TAACCCCTGCAACTTTGAAAAATTTTAATGTTTTCTGAAATATTCTTTGAGTACCTAATTTAGTC
195 TAACCCCTACAACTTTGAAAAATTTTAATGTTTTCTGAAATATTCTTTGAGTACCTAATTTAGTC
* * * *
2079583 TCGACTTGTTTTTAATGCATATTATGGGCCTCGAGGGCTCGTATAAAGGACAATATTTTTTTTTT
260 TCGACTTGTTTTTAATGCATATTATGGGCCTCGAGGGCTCGCATAAAGGACAATA-TTATGTTTG
*
2079648 ATTTCTATTGGTTTCTGACATTAATGTTATATAATATGAAATGTCTGTTTAATTGATCTATAAAC
324 ATTTCTATTGGTTTCTGACATGAATGTTATATAATATGAAATGTCTGTTTAATTGATCTATAAAC
* * *
2079713 TCTAGTAACGCTCCATAACTCTGTTCCGATGATGGATATGGGTTAGGGGTGTTACAGCCACATA
389 TCTAGTAACACTCCATAACTCTGTTCCGACGATGGATATGGGTTAGGGGTGTTACAGCAACATA
2079777 ACCTAAGGTA
Statistics
Matches: 413, Mismatches: 35, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
456 2 0.00
457 283 0.69
458 2 0.00
459 1 0.00
461 125 0.30
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (460 bp):
TGTGCAAGTCAATATGCTCACACAATCTAACACACGGGCATGTGGCTTGGCTGTGTGGCCCAAGT
CAAGGAGTTACACAAGTACAGGCACGGGCTGGGAAACAACCGTGTGTCTCTATTTCGAATATCCA
CACGGTCTAAGACACGAACGTGTCTCTTGGTCGTGTGAATCAACGGCCTAGCCACACAGCCGTGT
AACCCCTACAACTTTGAAAAATTTTAATGTTTTCTGAAATATTCTTTGAGTACCTAATTTAGTCT
CGACTTGTTTTTAATGCATATTATGGGCCTCGAGGGCTCGCATAAAGGACAATATTATGTTTGAT
TTCTATTGGTTTCTGACATGAATGTTATATAATATGAAATGTCTGTTTAATTGATCTATAAACTC
TAGTAACACTCCATAACTCTGTTCCGACGATGGATATGGGTTAGGGGTGTTACAGCAACATAGCA
TAGGG
Found at i:2080925 original size:15 final size:15
Alignment explanation
Indices: 2080907--2080936 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2080897 TTTTGGATTA
*
2080907 TAATTTATTGGACTG
1 TAATTTATTAGACTG
2080922 TAATTTATTAGACTG
1 TAATTTATTAGACTG
2080937 GACTGTGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (15 bp):
TAATTTATTAGACTG
Found at i:2089186 original size:60 final size:61
Alignment explanation
Indices: 2089068--2089186 Score: 143
Period size: 62 Copynumber: 1.9 Consensus size: 61
2089058 TTGGCATAAT
* * *
2089068 AACAAATTTAACTCTCCAATATTTACATATTCTATCAATTTGGTTGTAATTCTAAAAAAATC
1 AACAAATTTAACCCTCCAATATTTACACATTATATCAATTTGGTTG-AATTCTAAAAAAATC
* * *
2089130 AACAAATTTAACCCT-CAAT-TTTACACATTATGTCAATTTAGCGTTGATTTTTAAAAA
1 AACAAATTTAACCCTCCAATATTTACACATTATATCAATTT-G-GTTGAATTCTAAAAA
2089187 TTCTAAAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
60 17 0.35
61 14 0.29
62 18 0.37
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (61 bp):
AACAAATTTAACCCTCCAATATTTACACATTATATCAATTTGGTTGAATTCTAAAAAAATC
Found at i:2101610 original size:14 final size:14
Alignment explanation
Indices: 2101587--2101623 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2101577 GAACACACAC
*
2101587 ATACATATACATAT
1 ATACATATACATAA
*
2101601 ATATATATACATAA
1 ATACATATACATAA
2101615 ATACATATA
1 ATACATATA
2101624 TATACATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (14 bp):
ATACATATACATAA
Found at i:2101624 original size:18 final size:18
Alignment explanation
Indices: 2101587--2101633 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
2101577 GAACACACAC
*
2101587 ATACATATACATATATATAT
1 ATACATA-A-ATACATATAT
2101607 ATACATAAATACATATAT
1 ATACATAAATACATATAT
2101625 ATACATAAA
1 ATACATAAA
2101634 GCTTGTGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 18 0.69
19 1 0.04
20 7 0.27
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (18 bp):
ATACATAAATACATATAT
Found at i:2108754 original size:46 final size:46
Alignment explanation
Indices: 2108687--2108913 Score: 339
Period size: 46 Copynumber: 5.0 Consensus size: 46
2108677 GGAGTGTGCT
2108687 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
2108733 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
2108779 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-
1 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
2108824 CTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * * *
2108870 ATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
2108914 TCATGTCAAA
Statistics
Matches: 167, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 42 0.25
46 125 0.75
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (46 bp):
CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:2108882 original size:91 final size:93
Alignment explanation
Indices: 2108694--2108913 Score: 329
Period size: 91 Copynumber: 2.4 Consensus size: 93
2108684 GCTCTGATAT
***
2108694 AAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGG
1 AAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGAACAAGACCATGG
* *
2108759 TTGAAAGATACCATGGCAACCTGATATG
66 TTGAAAGATACCATGGCAACATGACATG
*
2108787 -AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-CTGATATGAAATGAACAAGACCATGG
1 AAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGAACAAGACCATGG
2108850 TTGAAAGATACCATGGCAACATGACA-G
66 TTGAAAGATACCATGGCAACATGACATG
* * * *
2108877 AAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 AAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
2108914 TCATGTCAAA
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
90 1 0.01
91 78 0.67
92 37 0.32
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (93 bp):
AAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGAACAAGACCATGG
TTGAAAGATACCATGGCAACATGACATG
Found at i:2112539 original size:28 final size:28
Alignment explanation
Indices: 2112503--2112572 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 28
2112493 TAAAATACTC
2112503 TAAAAATAAATATAATATAATAATGTTG
1 TAAAAATAAATATAATATAATAATGTTG
* *
2112531 TAAATATAAATAT--T-TATTAATGTTG
1 TAAAAATAAATATAATATAATAATGTTG
* *
2112556 AAAAAATATATATAATA
1 TAAAAATAAATATAATA
2112573 ATATTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 20 0.59
26 1 0.03
27 1 0.03
28 12 0.35
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (28 bp):
TAAAAATAAATATAATATAATAATGTTG
Found at i:2116523 original size:15 final size:16
Alignment explanation
Indices: 2116505--2116534 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2116495 GGGGAGAGAA
2116505 GGGGGTG-AATAAAAG
1 GGGGGTGAAATAAAAG
2116520 GGGGGTGAAATAAAA
1 GGGGGTGAAATAAAA
2116535 AGCGCCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.13
Consensus pattern (16 bp):
GGGGGTGAAATAAAAG
Found at i:2117756 original size:2 final size:2
Alignment explanation
Indices: 2117749--2117774 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2117739 AGCACAAAAG
2117749 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
2117775 TGAAACAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2119271 original size:33 final size:34
Alignment explanation
Indices: 2119203--2119271 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 34
2119193 AGTCAAACGC
* **
2119203 ATAAAGAAATTACATATTTATTTACTTTAAAATA
1 ATAAAAAAATTACATATTTATTTAAATTAAAATA
*
2119237 ATAAAAAAATTA-AT-TATTATTTAAATTAAGATA
1 ATAAAAAAATTACATAT-TTATTTAAATTAAAATA
2119270 AT
1 AT
2119272 TTTAACATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
32 1 0.03
33 18 0.60
34 11 0.37
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (34 bp):
ATAAAAAAATTACATATTTATTTAAATTAAAATA
Found at i:2119426 original size:16 final size:17
Alignment explanation
Indices: 2119405--2119438 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2119395 TGGTATAATA
2119405 TTAA-TTTTACTAAAAT
1 TTAATTTTTACTAAAAT
*
2119421 TTAATTTTTACTATAAT
1 TTAATTTTTACTAAAAT
2119438 T
1 T
2119439 ATGCACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATTTTTACTAAAAT
Found at i:2124643 original size:20 final size:18
Alignment explanation
Indices: 2124595--2124645 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
2124585 TGAATATTAA
2124595 TATTAA-TTATTATAATT
1 TATTAATTTATTATAATT
*
2124612 TAAATAATTTTATTATATATAT
1 T-ATTAA-TTTATTATA-AT-T
2124634 TATTAATTTATT
1 TATTAATTTATT
2124646 TTATTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.04
18 4 0.15
20 14 0.52
21 6 0.22
22 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTAATTTATTATAATT
Found at i:2125498 original size:20 final size:20
Alignment explanation
Indices: 2125473--2125515 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2125463 ATGAAGAATG
2125473 TTGTAAGATATAAGCTATTT
1 TTGTAAGATATAAGCTATTT
2125493 TTGTAAGATATAAGCTATTT
1 TTGTAAGATATAAGCTATTT
2125513 TTG
1 TTG
2125516 GCACTTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.47
Consensus pattern (20 bp):
TTGTAAGATATAAGCTATTT
Found at i:2129596 original size:39 final size:39
Alignment explanation
Indices: 2129542--2129623 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
2129532 AGTCCCTCAG
2129542 ACTCAATTAATTTTCATTTCCCTATTCTATCTCCCCCCA
1 ACTCAATTAATTTTCATTTCCCTATTCTATCTCCCCCCA
2129581 ACTCAATTAATTTTCATTTCCCTATTCTATCTCCCCCCA
1 ACTCAATTAATTTTCATTTCCCTATTCTATCTCCCCCCA
2129620 ACTC
1 ACTC
2129624 CTAAAGGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.23, C:0.37, G:0.00, T:0.40
Consensus pattern (39 bp):
ACTCAATTAATTTTCATTTCCCTATTCTATCTCCCCCCA
Found at i:2139629 original size:51 final size:51
Alignment explanation
Indices: 2139553--2139655 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
2139543 TTATGCAAAT
2139553 AGTACACATGAGGTATATAATTCCATAATTATGAATGAAGACATTTATCAA
1 AGTACACATGAGGTATATAATTCCATAATTATGAATGAAGACATTTATCAA
2139604 AGTACACATGAGGTATATAATTCCATAATTATGAATGAAGACATTTATCAA
1 AGTACACATGAGGTATATAATTCCATAATTATGAATGAAGACATTTATCAA
2139655 A
1 A
2139656 CATTTTCCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (51 bp):
AGTACACATGAGGTATATAATTCCATAATTATGAATGAAGACATTTATCAA
Found at i:2140037 original size:42 final size:42
Alignment explanation
Indices: 2139988--2140115 Score: 168
Period size: 42 Copynumber: 3.0 Consensus size: 42
2139978 CTTCGTTTTC
** *
2139988 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACAT-A
*
2140031 T-GATGCCATAGCCCAACTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
* * * *
2140072 TCGATGCCATAGCCCAGCTATAGTCTTACACGTAATCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
2140114 TC
1 TC
2140116 ACATATCGAT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
41 2 0.03
42 72 0.96
43 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
Found at i:2140131 original size:49 final size:49
Alignment explanation
Indices: 2140058--2140195 Score: 165
Period size: 49 Copynumber: 2.8 Consensus size: 49
2140048 TATGGTCTTA
* * * * *
2140058 CACATATTCATATATCGATGCCATAGCCCAGCTATAGTCTTACAC-GTAAT
1 CACATA-TCACATATCGATGCCATATCCCAGATATGGTCTTACACAGT-AG
*
2140108 CACATATCACATATCGATGCCATATCCCAGATATGGTCTTATACAGTAG
1 CACATATCACATATCGATGCCATATCCCAGATATGGTCTTACACAGTAG
* *
2140157 CATATATCAC--AGCGATGCCATATCCCAGATATGGTCTTA
1 CACATATCACATATCGATGCCATATCCCAGATATGGTCTTA
2140196 TATGGAAATC
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
47 28 0.35
49 43 0.54
50 8 0.10
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (49 bp):
CACATATCACATATCGATGCCATATCCCAGATATGGTCTTACACAGTAG
Found at i:2140263 original size:31 final size:31
Alignment explanation
Indices: 2140217--2140365 Score: 208
Period size: 31 Copynumber: 4.8 Consensus size: 31
2140207 CTTGCCACTT
* *
2140217 GTAGCCGAAGTTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
** * * *
2140248 GTAGTTGGAGCTACCATTTTTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
2140279 GTAGCCGGAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
2140310 GTAGCCGAAGCTAACACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
2140341 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
2140366 TGTCATTTGT
Statistics
Matches: 102, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:2140451 original size:50 final size:50
Alignment explanation
Indices: 2140346--2140517 Score: 247
Period size: 50 Copynumber: 3.4 Consensus size: 50
2140336 ATCAGGTAGC
* * * * *
2140346 CGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATTAGATAAGTGTAAC-
1 CGAAGCTATCACTTATCACTT-TCACTTGTCCTTGATCAGATAAATGT-ACT
*
2140397 CGAAGCTAACACTTATCACTTTCACTTGTCCTTGATCAGATAAATGTACT
1 CGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAATGTACT
* *
2140447 CGAAGCTATCACTTATTACTTTCACTTGTCCTTGATCAGATAAATGTAGT
1 CGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAATGTACT
2140497 CGAAGCTATCACTTATCACTT
1 CGAAGCTATCACTTATCACTT
2140518 GTTGCCATGG
Statistics
Matches: 111, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
49 2 0.02
50 90 0.81
51 19 0.17
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (50 bp):
CGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAATGTACT
Found at i:2148261 original size:15 final size:15
Alignment explanation
Indices: 2148241--2148274 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2148231 GTTAGACGTA
2148241 TAGTATAACACTTGC
1 TAGTATAACACTTGC
2148256 TAGTATAACACTTGC
1 TAGTATAACACTTGC
2148271 TAGT
1 TAGT
2148275 TTTTATAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (15 bp):
TAGTATAACACTTGC
Found at i:2158778 original size:18 final size:18
Alignment explanation
Indices: 2158755--2158800 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2158745 TTTGTTCACA
* * *
2158755 GGTTTTGGTGTTGGGTGT
1 GGTTTTGGAGTTGGATGG
2158773 GGTTTTGGAGTTGGATGG
1 GGTTTTGGAGTTGGATGG
2158791 GGTTTTGGAG
1 GGTTTTGGAG
2158801 GTCTGTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.07, C:0.00, G:0.50, T:0.43
Consensus pattern (18 bp):
GGTTTTGGAGTTGGATGG
Found at i:2165892 original size:18 final size:18
Alignment explanation
Indices: 2165868--2165907 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2165858 CTAAGGAAAA
*
2165868 TAAATTTTTAAAAAT-TT
1 TAAAATTTTAAAAATATT
*
2165885 TAAAATTTTAAAAGTATT
1 TAAAATTTTAAAAATATT
2165903 TAAAA
1 TAAAA
2165908 GTTATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TAAAATTTTAAAAATATT
Found at i:2165908 original size:10 final size:9
Alignment explanation
Indices: 2165873--2165916 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
2165863 GAAAATAAAT
*
2165873 TTTTAAAAA
1 TTTTAAAAG
2165882 TTTTAAAA-
1 TTTTAAAAG
2165890 TTTTAAAAG
1 TTTTAAAAG
2165899 TATTTAAAAG
1 T-TTTAAAAG
*
2165909 TTATAAAA
1 TTTTAAAA
2165917 TTGATACAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 8 0.25
9 15 0.47
10 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (9 bp):
TTTTAAAAG
Found at i:2166044 original size:99 final size:99
Alignment explanation
Indices: 2165873--2166072 Score: 364
Period size: 99 Copynumber: 2.0 Consensus size: 99
2165863 GAAAATAAAT
2165873 TTTTAAAAATTTTAAAATTTTAAAAGTATTTAAAAGTTATAAAATTGATACAATCGGTTTAACTA
1 TTTTAAAAATTTTAAAATTTTAAAAGTATTTAAAAGTTATAAAATTGATACAATCGGTTTAACTA
* *
2165938 GTTTTTTTAGCTCAATTCAATCCATTCATATTGG
66 GTTTTTTTAACTCAATTCAATCCATTCATACTGG
* *
2165972 TTTTAAAATTTTTAAAATTTTAAAAGTATTTAAAAGTTATAAAATTGATACAATCGGTTTATCTA
1 TTTTAAAAATTTTAAAATTTTAAAAGTATTTAAAAGTTATAAAATTGATACAATCGGTTTAACTA
2166037 GTTTTTTTAACTCAATTCAATCCATTCATACTGG
66 GTTTTTTTAACTCAATTCAATCCATTCATACTGG
2166071 TT
1 TT
2166073 CACGAGTCAA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.45
Consensus pattern (99 bp):
TTTTAAAAATTTTAAAATTTTAAAAGTATTTAAAAGTTATAAAATTGATACAATCGGTTTAACTA
GTTTTTTTAACTCAATTCAATCCATTCATACTGG
Found at i:2166807 original size:20 final size:20
Alignment explanation
Indices: 2166769--2166807 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2166759 GATAAGTATG
*
2166769 TATGTGTTTGTAATTTGATT
1 TATGTGTTTGTAATATGATT
2166789 TATGTGTTT-TAAATATGAT
1 TATGTGTTTGT-AATATGAT
2166808 AAACATAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (20 bp):
TATGTGTTTGTAATATGATT
Found at i:2170059 original size:63 final size:60
Alignment explanation
Indices: 2169977--2170112 Score: 159
Period size: 60 Copynumber: 2.2 Consensus size: 60
2169967 TTTGGACAAA
* * *
2169977 AAAGTCAAGCTCACGTACCTAATTGGACCAAGAAAAAAAACTTTATG-TACTC-AATTGAACCTT
1 AAAGTCAAGTTCAAGTACCTAATTAGACC-A-AAAAAAAAC-TTA-GATAC-CAAATTGAACCTT
*
2170040 AAAGTCAAGTTCAAGTACCTAATTAGACCAAAAAAGAACTTAGATACCAAATTGAACCTT
1 AAAGTCAAGTTCAAGTACCTAATTAGACCAAAAAAAAACTTAGATACCAAATTGAACCTT
* *
2170100 CAAGCCAAGTTCA
1 AAAGTCAAGTTCA
2170113 GGTGCCAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 2 0.03
60 28 0.43
61 8 0.12
62 1 0.02
63 26 0.40
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (60 bp):
AAAGTCAAGTTCAAGTACCTAATTAGACCAAAAAAAAACTTAGATACCAAATTGAACCTT
Found at i:2171874 original size:15 final size:15
Alignment explanation
Indices: 2171839--2171881 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
2171829 TTTGTGGGCT
*
2171839 TTTTAAAAAATATTT
1 TTTTAAAAAATATTA
*
2171854 TATTTAAAAAGTATTA
1 T-TTTAAAAAATATTA
*
2171870 TTTTAATAAATA
1 TTTTAAAAAATA
2171882 AATTTCATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TTTTAAAAAATATTA
Found at i:2172635 original size:60 final size:60
Alignment explanation
Indices: 2172542--2172661 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
2172532 TGACTACTTC
* *
2172542 GGTCATCACTGCGAAAGACAATTTACTTGTCATACTTGAAGTTGTCTATTTTTAAAATAA
1 GGTCATCACTACGAAAGACAATTTACTTGTCATACTTGAAGTTGACTATTTTTAAAATAA
2172602 GGTCATCACTACGAAAGACAATTTACTTGTCATACTTGAAGTTGACTATTTTTAAAATAA
1 GGTCATCACTACGAAAGACAATTTACTTGTCATACTTGAAGTTGACTATTTTTAAAATAA
2172662 AATTTATGGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (60 bp):
GGTCATCACTACGAAAGACAATTTACTTGTCATACTTGAAGTTGACTATTTTTAAAATAA
Found at i:2180057 original size:25 final size:24
Alignment explanation
Indices: 2180006--2180058 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
2179996 TTTATATATA
** *
2180006 TTTTTAATTAATTTGGTTTTTATT
1 TTTTTAATTAATTTGGTTACTAAT
*
2180030 TTTTTAATTAAATTTTGTTACTAAT
1 TTTTTAATT-AATTTGGTTACTAAT
2180055 TTTT
1 TTTT
2180059 CAAAAGAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.68
Consensus pattern (24 bp):
TTTTTAATTAATTTGGTTACTAAT
Found at i:2187925 original size:20 final size:19
Alignment explanation
Indices: 2187900--2187947 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
2187890 ATACAAAATA
*
2187900 TTTATAATAATATAACTAAT
1 TTTATAATAAAATAA-TAAT
2187920 TTTATATATAAAATAATAAT
1 TTTATA-ATAAAATAATAAT
*
2187940 TTAATAAT
1 TTTATAAT
2187948 TTTTCAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 8 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTATAATAAAATAATAAT
Found at i:2210292 original size:22 final size:22
Alignment explanation
Indices: 2210264--2210308 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2210254 TAACCTCGCT
2210264 ACTATTACCAACTCAAATATGA
1 ACTATTACCAACTCAAATATGA
2210286 ACTATTACCAACTCAAATATGA
1 ACTATTACCAACTCAAATATGA
2210308 A
1 A
2210309 TTATGAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (22 bp):
ACTATTACCAACTCAAATATGA
Found at i:2212495 original size:19 final size:20
Alignment explanation
Indices: 2212457--2212496 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2212447 GAATATGTTG
2212457 TAAATAATAATTAATGGAAT
1 TAAATAATAATTAATGGAAT
* *
2212477 TAAATAA-ATTTAATTGAAT
1 TAAATAATAATTAATGGAAT
2212496 T
1 T
2212497 GAGCCGACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
TAAATAATAATTAATGGAAT
Found at i:2213890 original size:17 final size:15
Alignment explanation
Indices: 2213850--2213891 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
2213840 CTTTTAATTT
2213850 TTTATATTATTTAAAA
1 TTTATA-TATTTAAAA
2213866 TTTA-ATATTTAATAA
1 TTTATATATTTAA-AA
2213881 TATTATATATT
1 T-TTATATATT
2213892 ACTGTAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.30
15 4 0.17
16 7 0.30
17 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATATATTTAAAA
Found at i:2215855 original size:15 final size:16
Alignment explanation
Indices: 2215827--2215856 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2215817 AATGAATCAA
2215827 GTCTTAATTTATTACT
1 GTCTTAATTTATTACT
2215843 GTCTTAA-TTATTAC
1 GTCTTAATTTATTAC
2215857 CTTTACAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (16 bp):
GTCTTAATTTATTACT
Found at i:2222125 original size:14 final size:14
Alignment explanation
Indices: 2222108--2222135 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2222098 GCTAGTGTGT
2222108 TGCTATGAGTGAGC
1 TGCTATGAGTGAGC
2222122 TGCTATGAGTGAGC
1 TGCTATGAGTGAGC
2222136 CTTTGAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (14 bp):
TGCTATGAGTGAGC
Found at i:2224727 original size:22 final size:22
Alignment explanation
Indices: 2224695--2224738 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2224685 TATATAAAAA
2224695 GAGCTTAAATACAAATGAGTTT
1 GAGCTTAAATACAAATGAGTTT
* *
2224717 GAGCTTGAATACTAATGAGTTT
1 GAGCTTAAATACAAATGAGTTT
2224739 AATTGAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (22 bp):
GAGCTTAAATACAAATGAGTTT
Found at i:2229774 original size:36 final size:37
Alignment explanation
Indices: 2229734--2229818 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 37
2229724 AAGAATTTGC
*
2229734 TATTGTGACAAAATTAACTA-TCACAAAA-AAAAAAGT
1 TATTGTGACAAAATTAA-TAGTCACAAAAGAAAAAAGA
* * * **
2229770 TATTGTGATAAAGTTAATAGTTACAAAAGAATGAAGA
1 TATTGTGACAAAATTAATAGTCACAAAAGAAAAAAGA
2229807 TATTGTGACAAA
1 TATTGTGACAAA
2229819 GACGAAAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
35 2 0.05
36 22 0.55
37 16 0.40
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (37 bp):
TATTGTGACAAAATTAATAGTCACAAAAGAAAAAAGA
Found at i:2230495 original size:9 final size:9
Alignment explanation
Indices: 2230481--2230505 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2230471 TTAAGTCAAT
2230481 AGATGATTC
1 AGATGATTC
2230490 AGATGATTC
1 AGATGATTC
2230499 AGATGAT
1 AGATGAT
2230506 CGTTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (9 bp):
AGATGATTC
Found at i:2230654 original size:17 final size:17
Alignment explanation
Indices: 2230632--2230669 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2230622 TTTTTTTTTT
2230632 CTAAACTACCATTACAA
1 CTAAACTACCATTACAA
2230649 CTAAACTACCATTACAA
1 CTAAACTACCATTACAA
2230666 CTAA
1 CTAA
2230670 CTTTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (17 bp):
CTAAACTACCATTACAA
Found at i:2234515 original size:24 final size:23
Alignment explanation
Indices: 2234470--2234551 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 23
2234460 TATATTTTTC
* *
2234470 ATTTAAATTAA-AATTTACAAAT
1 ATTTAAATTAATATTTTAAAAAT
*
2234492 AATTTATATTAAT-TGTTTAAAAAT
1 -ATTTAAATTAATAT-TTTAAAAAT
2234516 ATTTAAAATTAATATTTTAAAATAT
1 ATTT-AAATTAATATTTTAAAA-AT
2234541 CATTTAAATTA
1 -ATTTAAATTA
2234552 TTATCTTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 14 0.29
24 22 0.45
25 9 0.18
26 4 0.08
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (23 bp):
ATTTAAATTAATATTTTAAAAAT
Found at i:2241783 original size:17 final size:18
Alignment explanation
Indices: 2241748--2241798 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
2241738 AAATAGTGCT
*
2241748 AAAAAAAAAGAAAATAAC
1 AAAAAAAAAGAAAAGAAC
*
2241766 AAAAAAAAAG-TAAGAAC
1 AAAAAAAAAGAAAAGAAC
2241783 AGGAAAAAAAAAGAAA
1 ---AAAAAAAAAGAAA
2241799 GCAGCAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 5 0.19
18 10 0.38
20 10 0.38
21 1 0.04
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (18 bp):
AAAAAAAAAGAAAAGAAC
Found at i:2242385 original size:30 final size:30
Alignment explanation
Indices: 2242344--2242404 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2242334 TACTTTAATT
* * *
2242344 TGATCAGTTTTAATCTTTATATTTTTTGAA
1 TGATCAATTTTAATCTCTATACTTTTTGAA
*
2242374 TGATCAATTTTAGTCTCTATACTTTTTGAA
1 TGATCAATTTTAATCTCTATACTTTTTGAA
2242404 T
1 T
2242405 TATGAAATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (30 bp):
TGATCAATTTTAATCTCTATACTTTTTGAA
Found at i:2247229 original size:26 final size:26
Alignment explanation
Indices: 2247200--2247251 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2247190 ACAAACATAG
2247200 CAACAAATTTAGACCATAAAATAAAT
1 CAACAAATTTAGACCATAAAATAAAT
2247226 CAACAAATTTAGACCATAAAATAAAT
1 CAACAAATTTAGACCATAAAATAAAT
2247252 TAACTAGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.04, T:0.23
Consensus pattern (26 bp):
CAACAAATTTAGACCATAAAATAAAT
Found at i:2247461 original size:23 final size:23
Alignment explanation
Indices: 2247394--2247461 Score: 54
Period size: 23 Copynumber: 3.0 Consensus size: 23
2247384 CAAACAAATG
2247394 CACAAGTATAGCAAGCTCTC-AA
1 CACAAGTATAGCAAGCTCTCAAA
* * * *
2247416 CGAGAAATTTA--AAGCAT-TGAAA
1 C-ACAAGTATAGCAAGC-TCTCAAA
2247438 CACAAGTATAGCAAGCTCTCAAA
1 CACAAGTATAGCAAGCTCTCAAA
2247461 C
1 C
2247462 TTGAAAGAGA
Statistics
Matches: 32, Mismatches: 8, Indels: 11
0.63 0.16 0.22
Matches are distributed among these distances:
21 11 0.34
22 6 0.19
23 15 0.47
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (23 bp):
CACAAGTATAGCAAGCTCTCAAA
Found at i:2249367 original size:20 final size:19
Alignment explanation
Indices: 2249333--2249370 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2249323 GTTAATCTTG
*
2249333 ATTAAATAAATTATTAAAA
1 ATTAAAAAAATTATTAAAA
2249352 ATTAAAAAATATTATTAAA
1 ATTAAAAAA-ATTATTAAA
2249371 GATTTTACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTAAAAAAATTATTAAAA
Found at i:2250231 original size:20 final size:20
Alignment explanation
Indices: 2250172--2250224 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2250162 TTGACTTGTG
* *
2250172 GAATTTCAATTTTAAATTTT
1 GAATCTCAATTTCAAATTTT
2250192 GAATCTCAATTTCAAATTTT
1 GAATCTCAATTTCAAATTTT
2250212 GAATCTCAATTTC
1 GAATCTCAATTTC
2250225 CCTTTTTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (20 bp):
GAATCTCAATTTCAAATTTT
Found at i:2255026 original size:20 final size:20
Alignment explanation
Indices: 2254993--2255031 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2254983 GGATTTTGTC
2254993 GATTGCACACGACCTAGGGAG
1 GATTGCACACGACCT-GGGAG
*
2255014 GATT-CACATGACCTGGGA
1 GATTGCACACGACCTGGGA
2255032 CACGACCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.28, C:0.23, G:0.31, T:0.18
Consensus pattern (20 bp):
GATTGCACACGACCTGGGAG
Found at i:2255427 original size:21 final size:21
Alignment explanation
Indices: 2255377--2255427 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2255367 CACACAGTCT
** *
2255377 TGTACCTCAGTCACACGGTCG
1 TGTACCTCAACCACACGATCG
2255398 TGT-CTCTCAACCACACGATCG
1 TGTAC-CTCAACCACACGATCG
2255419 TGTACCTCA
1 TGTACCTCA
2255428 GCTATACAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (21 bp):
TGTACCTCAACCACACGATCG
Found at i:2255656 original size:2 final size:2
Alignment explanation
Indices: 2255640--2255681 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2255630 TACTGTTAGA
2255640 AT AT -T AT AT -T 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
2255680 AT
1 AT
2255682 GTATTCTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2255935 original size:25 final size:25
Alignment explanation
Indices: 2255907--2255958 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2255897 TATGCATTAT
2255907 GGTTTGGATTTGGTTATGAGGATAA
1 GGTTTGGATTTGGTTATGAGGATAA
2255932 GGTTTGGATTTGGTTATGAGGATAA
1 GGTTTGGATTTGGTTATGAGGATAA
2255957 GG
1 GG
2255959 AAGTTAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (25 bp):
GGTTTGGATTTGGTTATGAGGATAA
Found at i:2261592 original size:1 final size:1
Alignment explanation
Indices: 2261545--2261578 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
2261535 AACCTAACCC
* *
2261545 AAAAAAAAAAAAAAAAAAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2261579 CTTACCCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:2262449 original size:3 final size:3
Alignment explanation
Indices: 2262407--2262435 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2262397 TTATTGTAGA
2262407 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2262436 CATACTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2269576 original size:71 final size:69
Alignment explanation
Indices: 2269382--2269645 Score: 323
Period size: 71 Copynumber: 3.7 Consensus size: 69
2269372 GAGTTAAGCC
* *
2269382 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
2269447 GAGGTAT
63 GAGGTAT
* * ** * *
2269454 TTTCAATTTTTGTGTTTTAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTG
1 TTTTAATTTTTGT-TTTAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCGGGGCACGCTG
2269518 AGGTAT
64 AGGTAT
*
2269524 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
1 TTTTAATTTTTGTTTT--AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
2269589 AGGTAT
64 AGGTAT
* * ** * *
2269595 TTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
2269646 TTTAATTTTT
Statistics
Matches: 166, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
69 35 0.21
70 56 0.34
71 59 0.36
72 16 0.10
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAG
GTAT
Found at i:2269690 original size:122 final size:124
Alignment explanation
Indices: 2269524--2269770 Score: 383
Period size: 122 Copynumber: 2.0 Consensus size: 124
2269514 GTTGAGGTAT
2269524 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
1 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
* *
2269589 AGGTATTTT-TA-GTTTATGTTTTAAATT-GACTCATATTGCGAGAGGTGAGTTAAGCC
66 AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
* * *
2269645 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTG-TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACT
* * * *
2269710 GAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCC
65 GAGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
2269770 T
1 T
2269771 CAGGTCACGC
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
121 12 0.11
122 59 0.52
123 1 0.01
124 13 0.12
125 28 0.25
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (124 bp):
TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
Found at i:2269731 original size:263 final size:257
Alignment explanation
Indices: 2269215--2269807 Score: 1033
Period size: 263 Copynumber: 2.3 Consensus size: 257
2269205 TTTCAAGGAA
*
2269215 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTGTTGT
1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
*
2269280 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT
66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACACTGAGGTATTTTTAGT
2269345 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
131 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
2269410 CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
196 CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
2269472 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
*
2269537 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTGAGGTATTTTTAGT
66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACACTGAGGTA---TT--T
2269602 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA
126 TTA-GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA
2269667 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT
190 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT
2269732 TTT
255 TTT
* * * * * *
2269735 AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCT
1 AA--TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
2269800 GTTTTCAA
64 GTTTTCAA
2269808 TTTACGTTGT
Statistics
Matches: 319, Mismatches: 9, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
257 119 0.37
260 2 0.01
262 4 0.01
263 131 0.41
265 63 0.20
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (257 bp):
AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACACTGAGGTATTTTTAGT
TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
Found at i:2269766 original size:72 final size:71
Alignment explanation
Indices: 2269645--2270084 Score: 288
Period size: 72 Copynumber: 6.1 Consensus size: 71
2269635 GAGTTAAGCC
*
2269645 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTGTTTTT-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
2269709 TGAGGTA
65 TGAGGTA
** * *
2269716 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTCAATTTTTGT-TTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
2269781 TGAGGTA
65 TGAGGTA
* * ** * * * * ** * *** *
2269788 TTTTCAATTTCTG-TTTT-CAATTTACGT--TGTT-CAAGA-ATCAACTCATATTGCGAGAGGTA
1 TTTTCAATTTTTGTTTTTAAAATCAAC-TCATATTGCGAGAGGTGAGTTGAGCCT-CG-G-GGCA
* * ***
2269847 GGTTGA-ACC
62 CGCTGAGGTA
** * * *
2269856 TTTT-AATTTCTACTTTTTCAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTTCAATTT-TTGTTTTT-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
2269920 CTGAGGTA
64 CTGAGGTA
* * ** * *
2269928 ATTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTACTAGAGGTGAGTTGAGCCTC-GGGCAC
1 TTTTCAATTTTTGTT-T--TTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
2269992 GCTGAGGTA
63 GCTGAGGTA
* ** * * **
2270001 TTTTCAATTTTTATGTTTTAATTTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
1 TTTTCAATTTTTGT-TTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-GGCAC
*
2270066 GCCGAGGTA
63 GCTGAGGTA
2270075 TTTTCAATTT
1 TTTTCAATTT
2270085 CCGTTTTTCA
Statistics
Matches: 268, Mismatches: 78, Indels: 43
0.69 0.20 0.11
Matches are distributed among these distances:
66 5 0.02
67 10 0.04
68 8 0.03
69 13 0.05
70 6 0.02
71 46 0.17
72 78 0.29
73 41 0.15
74 61 0.23
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (71 bp):
TTTTCAATTTTTGTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCT
GAGGTA
Found at i:2270098 original size:74 final size:72
Alignment explanation
Indices: 2269856--2270095 Score: 254
Period size: 74 Copynumber: 3.3 Consensus size: 72
2269846 AGGTTGAACC
* *
2269856 TTTT-AATTTCTACTTTTTCAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTTCAATTTCT-GTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
2269920 CTGAGGTA
65 CTGAGGTA
* * * * *
2269928 ATTTCAATTTCTG-TTGTCAAAAAAATCAACTCATATTACTAGAGGTGAGTTGAGCCTC-GGGCA
1 TTTTCAATTTCTGTTTTTC---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
2269991 CGCTGAGGTA
63 CGCTGAGGTA
* * ** * *
2270001 TTTTCAATTTTTATGTTTT-AATTTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACA
1 TTTTCAATTTCTGT-TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACA
*
2270065 CGCCGAGGTA
63 CGCTGAGGTA
*
2270075 TTTTCAATTTCCGTTTTTCAA
1 TTTTCAATTTCTGTTTTTCAA
2270096 TTTTGTCTTT
Statistics
Matches: 136, Mismatches: 22, Indels: 18
0.77 0.12 0.10
Matches are distributed among these distances:
71 35 0.26
72 5 0.04
73 35 0.26
74 58 0.43
75 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (72 bp):
TTTTCAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTA
Found at i:2270185 original size:75 final size:76
Alignment explanation
Indices: 2270090--2270782 Score: 229
Period size: 79 Copynumber: 8.8 Consensus size: 76
2270080 AATTTCCGTT
* *
2270090 TTTCAATTT-TGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-AC
1 TTTCAATTTCTGTCTGTC-AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCAC
*
2270153 ACGCTGAGGTAA
65 ACGCCGAGGTAA
* *
2270165 TTTCAATTTCTGT-TGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCAC
1 TTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-CAC
*
2270229 ACGCCGAGGTAT
65 ACGCCGAGGTAA
* * * *** * *
2270241 TTTCAATTTCCGTTTTTCAATTTTTGCCTTTCAAAAA--AA-TCAACTCATATTGCGAGAGGTGA
1 TTTCAATTTCTGTCTGTCAA------------AAAAATCAACTC-A-T-ATTGCGAGAG--GCGA
*
2270303 GTTGAGCCTCAGG-ACACGCTGAGGTAA
49 GTTGAGCCTCAGGCACACGCCGAGGTAA
* * * *
2270330 TTTCAATTTCTGT-TGTCAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCAC
1 TTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAG-GCAC
* *
2270394 ACGTCGAGGTAT
65 ACGCCGAGGTAA
* * * *** * * *
2270406 TTTCAATTTCCATTTTTCAATTTCTGCATTTCAAAAA--AAAAAATCAACT-C-ATATTGCGAGA
1 TTTCAATTT-C---TGTC----TGT-CA---AAAAAATCAACTCAT--ATTGCGAGA-GGCGA--
* *
2270467 GGTGAGTTGAGCCTC-GGGACACGCTGAGGTAA
49 -----GTTGAGCCTCAGGCACACGCCGAGGTAA
* * *** *
2270499 TTTCAATTTCTGT-TTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACA
1 TTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCACA
** *
2270560 CGTTGAGGTAT
66 CGCCGAGGTAA
* * * * * * *
2270571 TTTTAATTTCTGT-TTTC-AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCT-TGGCTCA
1 TTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCACA
* * *
2270633 TGCGCTGAGCTAT
66 --CGCCGAGGTAA
* * * * *
2270646 TTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCAC
1 TTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAG-GCAC
* * *
2270711 ACACTGAGGTATTT
65 ACGCCGAGGTA--A
* * * * * * *
2270725 TTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTC
1 TTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTC
2270783 GGGTTACATG
Statistics
Matches: 468, Mismatches: 86, Indels: 124
0.69 0.13 0.18
Matches are distributed among these distances:
72 39 0.08
73 35 0.07
74 56 0.12
75 32 0.07
76 61 0.13
77 50 0.11
78 9 0.02
79 62 0.13
80 8 0.02
83 1 0.00
84 2 0.00
85 2 0.00
86 4 0.01
87 7 0.01
88 10 0.02
89 42 0.09
91 16 0.03
92 1 0.00
93 20 0.04
94 1 0.00
95 10 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (76 bp):
TTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCACA
CGCCGAGGTAA
Found at i:2270214 original size:74 final size:77
Alignment explanation
Indices: 2270090--2270250 Score: 231
Period size: 74 Copynumber: 2.1 Consensus size: 77
2270080 AATTTCCGTT
* *
2270090 TTTCAATTT-TGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-AC
1 TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCAC
*
2270153 ACGCTGAGGTAA
66 ACGCCGAGGTAA
* *
2270165 TTTCAATTTCTGT-TGTC-AAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCA
1 TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-CA
*
2270228 CACGCCGAGGTAT
65 CACGCCGAGGTAA
2270241 TTTCAATTTC
1 TTTCAATTTC
2270251 CGTTTTTCAA
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
74 40 0.52
75 12 0.16
76 25 0.32
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (77 bp):
TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCAC
ACGCCGAGGTAA
Found at i:2270226 original size:165 final size:165
Alignment explanation
Indices: 2269929--2270725 Score: 921
Period size: 165 Copynumber: 4.9 Consensus size: 165
2269919 GCTGAGGTAA
* * * *
2269929 TTTCAATTTCTGT-TGTCAAAAAAATCAACTCATATTACTAGAGGTGAGTTGAGCCTC-GGGCAC
1 TTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* *** *
2269992 GCTGAGGTATTTTCAATTT-T-TATGT-TTTAATTTCAACTCGTATTGCGAGAGGCGAGTTGAGC
66 GCTGAGGTAATTTCAATTTCTGT-TGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGC
2270054 CTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
130 CTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
2270090 TTTCAATTT-TGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTCAATTTCTGTCTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* *
2270154 CGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGC
65 CGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGC
2270219 CTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
130 CTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
* *
2270255 TTTCAATTTTTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* *
2270320 GCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCC
66 GCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGCC
* * *
2270385 TCAGATCACACGTCGAGGTATTTTCAATTTCCATT
131 TCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
*
2270420 TTTCAATTTCTG-CATTTCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 TTTCAATTTCTGTC-TTTC----AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
* * ***
2270484 GACACGCTGAGGTAATTTCAATTTCTGTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTT
61 GACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTT
* **
2270547 GAGCCTCAAG--ACACGTTGAGG-----T--A------TT
126 GAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
* * * *
2270572 TTT-AATTTCTGT-TTTC-AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCT-TGGCTCA
1 TTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACA
* * * * * * *
2270633 TGCGCTGAGCTATTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
65 --CGCTGAGGTAATTTCAATTTCTGT-TGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTG
* * * *
2270698 AGCTTCAGATCACACACTGAGGTATTTT
127 AGCCTCAGGTCACACGCCGAGGTATTTT
2270726 TTCAATTTAT
Statistics
Matches: 567, Mismatches: 43, Indels: 56
0.85 0.06 0.08
Matches are distributed among these distances:
144 2 0.00
145 38 0.07
147 21 0.04
148 4 0.01
150 39 0.07
151 8 0.01
152 14 0.02
157 1 0.00
158 1 0.00
160 4 0.01
161 12 0.02
162 38 0.07
163 23 0.04
164 5 0.01
165 243 0.43
166 7 0.01
167 35 0.06
169 72 0.13
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (165 bp):
TTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGCC
TCAGGTCACACGCCGAGGTATTTTCAATTTCCGTT
Found at i:2270249 original size:76 final size:76
Alignment explanation
Indices: 2270089--2270807 Score: 242
Period size: 77 Copynumber: 9.1 Consensus size: 76
2270079 CAATTTCCGT
* *
2270089 TTTTCAATTT-TGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGAC
*
2270153 ACGCTGAGGTA
66 ACGCCGAGGTA
* * *
2270164 ATTTCAATTTCTGT-TGTC-AAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTC
1 TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG--
2270227 ACACGCCGAGGTA
64 ACACGCCGAGGTA
* * * * * * *
2270240 TTTTCAATTTCCGTTTTTCAATTTTTGCCTTTCAAAAA--AA-TCAACTCATAT-TGCGAGAGGT
1 TTTTCAATTTCTGTCTGTCAA-----------AAAAAATCAACTC-A-T-AT-TGCGAGA--GGC
*
2270301 GAGTTGAGCCTCAGGACACGCTGAGGTA
49 GAGTTGAGCCTCAGGACACGCCGAGGTA
* * * * *
2270329 ATTTCAATTTCTGT-TGTC-AAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATC
1 TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAG--G
*
2270392 ACACGTCGAGGTA
64 ACACGCCGAGGTA
* * * ** * * * *
2270405 TTTTCAATTTCCATTTTTCAATTTCTGCATTTCAAAAAAAAAAATCA-ACT-C-ATATTGCGAGA
1 TTTTCAATTT-C---TGTC----TGT-CA---AAAAAAATCAACTCATATTGCGAGA--G-GCG-
* *
2270467 GGTGAGTTGAGCCTCGGGACACGCTGAGGTA
50 ----AGTTGAGCCTCAGGACACGCCGAGGTA
* * * *** *
2270498 ATTTCAATTTCTGT-TTTC---AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
1 TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGAC
**
2270559 ACGTTGAGGTA
66 ACGCCGAGGTA
* * * * * * *
2270570 TTTTTAATTTCTGT-TTTC--AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCT-TGGCT
1 TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-A
* *
2270631 CATGCGCTGAGCTA
65 CA--CGCCGAGGTA
* * * *
2270645 TTTTCAATTTCTATCTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCA-GAT
1 TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGA-
*
2270708 CACACACTGAGGTA
65 CACGC-C-GAGGTA
* * * * * * * *
2270722 TTTTTTCAATTTATATTTTTC-AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGG
1 --TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG
* *
2270786 TTACATGTCGAGGTA
64 --ACACGCCGAGGTA
2270801 TTTTCAA
1 TTTTCAA
2270808 AATCTATTTT
Statistics
Matches: 487, Mismatches: 89, Indels: 134
0.69 0.13 0.19
Matches are distributed among these distances:
72 41 0.08
73 34 0.07
74 57 0.12
75 35 0.07
76 60 0.12
77 65 0.13
78 5 0.01
79 63 0.13
80 6 0.01
81 2 0.00
82 1 0.00
83 1 0.00
84 2 0.00
85 2 0.00
86 3 0.01
87 5 0.01
88 5 0.01
89 38 0.08
90 12 0.02
91 17 0.03
92 1 0.00
93 20 0.04
95 12 0.02
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (76 bp):
TTTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGAC
ACGCCGAGGTA
Found at i:2270766 original size:79 final size:76
Alignment explanation
Indices: 2270442--2270949 Score: 411
Period size: 72 Copynumber: 6.5 Consensus size: 76
2270432 CATTTCAAAA
** *
2270442 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACGCTGAGGTAATTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
2270505 TTTCTGTTTTC
66 TTTCTGTTTTC
* ** * * *
2270516 --AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-A-GACACGTTGAGGTATTTTTAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
2270577 TTTCTGTTTTC
66 TTTCTGTTTTC
* * ** * ** *
2270588 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
*
2270652 TTTCTATCTTTC
66 TTTCTGT-TTTC
* *
2270664 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTA--TTTTC
* *
2270729 AATTTATATTTTTC
64 AATTTCT-GTTTTC
* * * * * *
2270743 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACATG-TCGAGGTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCT-GAGGTATTTTCA
** *
2270807 AAATCTATTTTTC
65 ATTTCT-GTTTTC
* ** * **
2270820 AAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGA
1 -AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGA
*
2270885 GCTATTTTCAATTTCTGTTTTTTTTTC
55 GGTATTTTCAATTTCTG-----TTTTC
2270912 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
2270950 TTTTTAATTT
Statistics
Matches: 350, Mismatches: 55, Indels: 50
0.77 0.12 0.11
Matches are distributed among these distances:
72 64 0.18
73 32 0.09
75 21 0.06
76 4 0.01
77 63 0.18
78 3 0.01
79 63 0.18
80 1 0.00
81 5 0.01
82 29 0.08
88 57 0.16
89 1 0.00
91 2 0.01
92 5 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (76 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
TTTCTGTTTTC
Found at i:2270967 original size:30 final size:30
Alignment explanation
Indices: 2270931--2270992 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2270921 CAACTCATAT
2270931 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
2270961 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
2270991 TG
1 TG
2270993 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:2271700 original size:16 final size:16
Alignment explanation
Indices: 2271681--2271716 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2271671 AACCTAACCC
*
2271681 AAAAAAAAA-ACAAAG
1 AAAAAAAAAGAAAAAG
2271696 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
2271712 AAAAA
1 AAAAA
2271717 CTACCCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:2271729 original size:14 final size:15
Alignment explanation
Indices: 2271712--2271745 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2271702 AAAGAAAAAG
2271712 AAAAACT-ACCCCAA
1 AAAAACTAACCCCAA
*
2271726 AAAACCTAACCCCAA
1 AAAAACTAACCCCAA
2271741 AAAAA
1 AAAAA
2271746 AAAAGAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.62, C:0.32, G:0.00, T:0.06
Consensus pattern (15 bp):
AAAAACTAACCCCAA
Found at i:2272058 original size:11 final size:11
Alignment explanation
Indices: 2272042--2272080 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2272032 TTCTTTCGAA
2272042 TCTTTTTTCTT
1 TCTTTTTTCTT
*
2272053 TCTTTTTTGTGT
1 TCTTTTTTCT-T
*
2272065 TTTTTTTTCTT
1 TCTTTTTTCTT
2272076 TCTTT
1 TCTTT
2272081 ATATATACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:2272582 original size:3 final size:3
Alignment explanation
Indices: 2272534--2272568 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2272524 TTATTGTAGA
2272534 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2272569 CATACTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2274060 original size:16 final size:16
Alignment explanation
Indices: 2274041--2274072 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2274031 AATTAAAATC
*
2274041 TAAAATGATTTAAACT
1 TAAAATGATCTAAACT
2274057 TAAAATGATCTAAACT
1 TAAAATGATCTAAACT
2274073 ATAATCAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (16 bp):
TAAAATGATCTAAACT
Found at i:2274972 original size:23 final size:25
Alignment explanation
Indices: 2274945--2274998 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 25
2274935 TTAGATAAAC
2274945 TTATTTTATTTT-TTAAAAATAT-T
1 TTATTTTATTTTATTAAAAATATCT
2274968 TTATTTTATTTTAATTAAAAATATCT
1 TTATTTTATTTT-ATTAAAAATATCT
2274994 TTATT
1 TTATT
2274999 AATTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 12 0.43
25 10 0.36
26 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TTATTTTATTTTATTAAAAATATCT
Found at i:2275011 original size:18 final size:19
Alignment explanation
Indices: 2274978--2275013 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2274968 TTATTTTATT
2274978 TTAATTAAAAATATCTTTA
1 TTAATTAAAAATATCTTTA
2274997 TTAATTAAAAA-ATCTTT
1 TTAATTAAAAATATCTTT
2275014 CACTATCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATTAAAAATATCTTTA
Found at i:2276391 original size:14 final size:14
Alignment explanation
Indices: 2276366--2276402 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2276356 TTCTCATTTT
2276366 TCATTTTCTTTCTC
1 TCATTTTCTTTCTC
* *
2276380 TCGTTTTTTTTCTC
1 TCATTTTCTTTCTC
2276394 TCATTTTCT
1 TCATTTTCT
2276403 CCTATTATCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.68
Consensus pattern (14 bp):
TCATTTTCTTTCTC
Found at i:2283110 original size:22 final size:22
Alignment explanation
Indices: 2283082--2283128 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2283072 AGCCATGTCA
2283082 TTATCTACTTGAACAATTATGC
1 TTATCTACTTGAACAATTATGC
2283104 TTATCTACTTGAACAATTATGC
1 TTATCTACTTGAACAATTATGC
2283126 TTA
1 TTA
2283129 GTTTTTCGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43
Consensus pattern (22 bp):
TTATCTACTTGAACAATTATGC
Found at i:2283909 original size:24 final size:22
Alignment explanation
Indices: 2283860--2283914 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
2283850 TTTAAAATTT
**
2283860 TAAAAATATAATAAATGATAGT
1 TAAAAATATAATAAATGATACA
*
2283882 TAAATAATTTAATATAATGATACA
1 TAAA-AATATAATA-AATGATACA
2283906 T-AAAATATA
1 TAAAAATATA
2283915 CATTAATCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 9 0.33
23 10 0.37
24 8 0.30
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (22 bp):
TAAAAATATAATAAATGATACA
Found at i:2286641 original size:17 final size:17
Alignment explanation
Indices: 2286619--2286661 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
2286609 TGTCTTTGAG
2286619 TAGAAAAAAAAAAGAAA
1 TAGAAAAAAAAAAGAAA
2286636 TAGAAAAAAAAAAGAAA
1 TAGAAAAAAAAAAGAAA
*
2286653 AAGAAAAAA
1 TAGAAAAAA
2286662 GAGCATTGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.05
Consensus pattern (17 bp):
TAGAAAAAAAAAAGAAA
Found at i:2286642 original size:11 final size:12
Alignment explanation
Indices: 2286620--2286660 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 12
2286610 GTCTTTGAGT
2286620 AGAAAAA-AAAA
1 AGAAAAAGAAAA
*
2286631 AGAAATAGAAAA
1 AGAAAAAGAAAA
2286643 A-AAAAAGAAAA
1 AGAAAAAGAAAA
2286654 AGAAAAA
1 AGAAAAA
2286661 AGAGCATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (12 bp):
AGAAAAAGAAAA
Found at i:2291853 original size:21 final size:21
Alignment explanation
Indices: 2291814--2291854 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2291804 AAAATAAAAA
*
2291814 AATTAATTTATTTAGTTTAAT
1 AATTAATTAATTTAGTTTAAT
2291835 AATTAATTCAATTTA-TTTAA
1 AATTAATT-AATTTAGTTTAA
2291855 CTTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTAATTAATTTAGTTTAAT
Found at i:2292265 original size:18 final size:18
Alignment explanation
Indices: 2292219--2292266 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2292209 ATATGAACCT
2292219 TTTTATAATTTCTTTTTAA
1 TTTTATAATTT-TTTTTAA
* * *
2292238 ATTT-TGATTTTTTTTTA
1 TTTTATAATTTTTTTTAA
2292255 TTTTATAATTTT
1 TTTTATAATTTT
2292267 AAATTATTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
17 9 0.39
18 11 0.48
19 3 0.13
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTATAATTTTTTTTAA
Found at i:2297257 original size:21 final size:22
Alignment explanation
Indices: 2297216--2297257 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2297206 TTAATTTAGG
2297216 GAGCCATTGATTACTAGAAAAA
1 GAGCCATTGATTACTAGAAAAA
* *
2297238 GAGCTATTGA-TACTATAAAA
1 GAGCCATTGATTACTAGAAAA
2297258 TTGGTAATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (22 bp):
GAGCCATTGATTACTAGAAAAA
Found at i:2299989 original size:23 final size:23
Alignment explanation
Indices: 2299940--2299999 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
2299930 ATCATCACCT
* *
2299940 AAAAATTAAAAAAATATTTATATA
1 AAAAATT-TAAAAATATTAATATA
**
2299964 AAATCTTTAAAAATATATAATA-A
1 AAAAATTTAAAAATAT-TAATATA
2299987 AAAAATTTAAAAA
1 AAAAATTTAAAAA
2300000 GTTTCATTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAAATTTAAAAATATTAATATA
Found at i:2300485 original size:29 final size:28
Alignment explanation
Indices: 2300434--2300488 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
2300424 GTTTTTTGTA
* **
2300434 ATTTTATAATTTTTTTATTTTTTAAATG
1 ATTTTATAATTTTTGTAAATTTTAAATG
2300462 ATTTTAATAATTTTTGTAAATTTTAAA
1 ATTTT-ATAATTTTTGTAAATTTTAAA
2300489 ATATTTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (28 bp):
ATTTTATAATTTTTGTAAATTTTAAATG
Found at i:2300494 original size:29 final size:28
Alignment explanation
Indices: 2300434--2300495 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
2300424 GTTTTTTGTA
* * *
2300434 ATTTTATAATTTTTTTATTTTTTAAATG
1 ATTTTATAATTTTTTAAATTTTAAAATG
2300462 ATTTTAATAATTTTTGTAAATTTTAAAAT-
1 ATTTT-ATAATTTTT-TAAATTTTAAAATG
2300491 ATTTT
1 ATTTT
2300496 TTCATCCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 5 0.17
29 14 0.48
30 10 0.34
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (28 bp):
ATTTTATAATTTTTTAAATTTTAAAATG
Found at i:2301080 original size:37 final size:37
Alignment explanation
Indices: 2301030--2301104 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
2301020 ACGGTAGAGA
*
2301030 TATTACAGAAACTCTTGTACTAATTGTCAGATTGCAT
1 TATTACAGAAACTCTTGTACTAATTATCAGATTGCAT
2301067 TATTACAGAAACTCTTGTACTAATTATCAGATTGCAT
1 TATTACAGAAACTCTTGTACTAATTATCAGATTGCAT
2301104 T
1 T
2301105 TTGCCCCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (37 bp):
TATTACAGAAACTCTTGTACTAATTATCAGATTGCAT
Found at i:2316818 original size:182 final size:183
Alignment explanation
Indices: 2316316--2316831 Score: 680
Period size: 184 Copynumber: 2.8 Consensus size: 183
2316306 AGACAAGACC
* * * * * *
2316316 TGATTGTACATAAAAAATATACATTAGATACCATACAACAATCGAACCAGAACTAGAGACATAAT
1 TGATTGCACATGAAAAATATACATTAGATACCATACGACAATCGAACCGGAACTAGAG-CCTAAC
* * *
2316381 GACCATAAACACAATTTATATGCATTTTTGTATCCCACAACAAACCAGCAGATACAGCATAACTG
65 GACCATAAACACAATTTATATGCATTTTTCTATCCCACAACAAACCAGCAGATACTGCATAAATG
* * *
2316446 CATCA-TCACTAAGATATTTAGGAAATATTTAACAGAACTGGAACCTAAGGTTCT
130 CAT-AGTCACTAAGATCTTTAAGAAATATTTAACAAAACTGGAACCTAAGGTTCT
* *
2316500 TGATTGCACATGAAAAATATACATTAGATACCATACGACAATCAAACAGGAACTCA-AGCCATAA
1 TGATTGCACATGAAAAATATACATTAGATACCATACGACAATCGAACCGGAACT-AGAGCC-TAA
* * * **
2316564 CGACCATAAACACAATTTATATGCACTTTTCTATCCCACAACGATCCAGCAGATACTGTGTAAAT
64 CGACCATAAACACAATTTATATGCATTTTTCTATCCCACAACAAACCAGCAGATACTGCATAAAT
* *
2316629 GCATAGTCACTAAGATCTTTAAGAAATATTTAA-AAAACTGGCATCTAAGGTTCT
129 GCATAGTCACTAAGATCTTTAAGAAATATTTAACAAAACTGGAACCTAAGGTTCT
* *
2316683 TGATTGCACATGAAAAATATACATTAGATGCCATAGGGA-AATCGAACCGGAACTAGAGCCTAAC
1 TGATTGCACATGAAAAATATACATTAGATACCATA-CGACAATCGAACCGGAACTAGAGCCTAAC
* * * * * *
2316747 AACCATTAGCACAATTTATATGCATTTTTCTATCCCACAATAAACCAGCAAATACTGCATAAGTG
65 GACCATAAACACAATTTATATGCATTTTTCTATCCCACAACAAACCAGCAGATACTGCATAAATG
* *
2316812 CATAGTCATTAACATCTTTA
130 CATAGTCACTAAGATCTTTA
2316832 GGCCACTTAT
Statistics
Matches: 289, Mismatches: 38, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
182 77 0.27
183 71 0.25
184 140 0.48
185 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (183 bp):
TGATTGCACATGAAAAATATACATTAGATACCATACGACAATCGAACCGGAACTAGAGCCTAACG
ACCATAAACACAATTTATATGCATTTTTCTATCCCACAACAAACCAGCAGATACTGCATAAATGC
ATAGTCACTAAGATCTTTAAGAAATATTTAACAAAACTGGAACCTAAGGTTCT
Found at i:2320543 original size:9 final size:9
Alignment explanation
Indices: 2320531--2320583 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
2320521 AAAAATTCAA
2320531 AAAAATTTT
1 AAAAATTTT
2320540 -AAAATTTT
1 AAAAATTTT
2320548 AAAATATTTAT
1 AAAA-ATTT-T
2320559 AAAAATTTT
1 AAAAATTTT
* *
2320568 TAAAATTCT
1 AAAAATTTT
2320577 AAAAATT
1 AAAAATT
2320584 ATATAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
8 8 0.21
9 17 0.45
10 8 0.21
11 5 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
AAAAATTTT
Found at i:2320562 original size:29 final size:30
Alignment explanation
Indices: 2320530--2320614 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 30
2320520 AAAAAATTCA
2320530 AAAAAATTTTAAAATTTTAAAATATT-TAT
1 AAAAAATTTTAAAATTTTAAAATATTATAT
* *
2320559 AAAAATTTTTAAAATTCTAAAA-ATTATAT
1 AAAAAATTTTAAAATTTTAAAATATTATAT
** *
2320588 AAAAAAAGTTAAGATTTTAAAAATATT
1 AAAAAATTTTAAAATTTT-AAAATATT
2320615 CTAAAATGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 3 0.07
29 36 0.78
30 4 0.09
31 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (30 bp):
AAAAAATTTTAAAATTTTAAAATATTATAT
Found at i:2323336 original size:2 final size:2
Alignment explanation
Indices: 2323329--2323355 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2323319 TGGGTTTCTT
2323329 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2323356 TTCAAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2328187 original size:17 final size:17
Alignment explanation
Indices: 2328150--2328198 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
2328140 TGATTCGAAC
*
2328150 ATAAAATAATCT-AAAT
1 ATAAAATAATATAAAAT
* *
2328166 TTAAAATAATTTAAAAT
1 ATAAAATAATATAAAAT
2328183 ATAAAATAATATAAAA
1 ATAAAATAATATAAAA
2328199 ATTTCAAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 10 0.36
17 18 0.64
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAATAATATAAAAT
Found at i:2333412 original size:2 final size:2
Alignment explanation
Indices: 2333407--2333431 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2333397 ACACACACAC
2333407 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
2333432 AACTTTAAAA
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:2336019 original size:75 final size:75
Alignment explanation
Indices: 2335900--2336071 Score: 205
Period size: 75 Copynumber: 2.4 Consensus size: 75
2335890 CATGGCAAAG
** *
2335900 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
2335959 CCATACTGAGC
65 CCATACCGAGC
2335970 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
2336035 CATACCGAGT
66 CATACCGAGC
***
2336045 TAAAAAAATGTAGGTATGGTATT-TCAA
1 T-GTGAAATGTAGGTATGGTATTATCAA
2336072 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 1 0.01
75 46 0.53
76 18 0.21
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:2336038 original size:35 final size:35
Alignment explanation
Indices: 2335903--2336069 Score: 167
Period size: 35 Copynumber: 4.6 Consensus size: 35
2335893 GGCAAAGTGT
* **
2335903 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
2335938 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
2335973 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
2336013 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTT-AA
*
2336049 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
2336070 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
35 64 0.55
36 21 0.18
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:2336061 original size:36 final size:35
Alignment explanation
Indices: 2335999--2336069 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
2335989 ATTATCAAAT
* *
2335999 CCATACTGAGTTAAGAAATGTAGGTATGGCATTTC
1 CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
*
2336034 CCATACCGAGTTAAAAAAATGTAGGTATGGTATTTC
1 CCATACCGAGTT-AAAAAATGTAGGTATGGCATTTC
2336070 AATGAGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (35 bp):
CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
Found at i:2346296 original size:20 final size:19
Alignment explanation
Indices: 2346273--2346311 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2346263 ATTTTTTAAA
*
2346273 TAAATAAAGCAAAATATTTT
1 TAAA-AAAGCAAAAGATTTT
*
2346293 TAAAAAATCAAAAGATTTT
1 TAAAAAAGCAAAAGATTTT
2346312 GAATGGGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (19 bp):
TAAAAAAGCAAAAGATTTT
Found at i:2346743 original size:28 final size:28
Alignment explanation
Indices: 2346711--2346788 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
2346701 ATTTTTTTAA
2346711 TTTAAAATTTTAAAATATATAAAAATAT
1 TTTAAAATTTTAAAATATATAAAAATAT
* ** **
2346739 TTTAAAAGTCAAAAAT-TATTAAATTTAT
1 TTTAAAATTTTAAAATATA-TAAAAATAT
*
2346767 TTTAAATTTTTTAAAATATATA
1 TTTAAA-ATTTTAAAATATATA
2346789 TTTTTAATAT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
27 2 0.05
28 26 0.68
29 8 0.21
30 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
TTTAAAATTTTAAAATATATAAAAATAT
Found at i:2349693 original size:3 final size:3
Alignment explanation
Indices: 2349685--2349718 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2349675 TGGTGTTTTA
*
2349685 GGT GGT GGT GGT GGT GGT GGT GGT GGT TGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
2349719 TAATAGCCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
GGT
Found at i:2352275 original size:83 final size:83
Alignment explanation
Indices: 2352136--2352302 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
2352126 TATGTGAAAC
2352136 GACAAAGGGTTGAATCTTAGATCATGATAATTCAATAACGAAAAGCATAGGTAGCTTATAGTGGT
1 GACAAAGGGTTGAATCTTAGATCATGATAATTCAATAACGAAAAGCATAGGTAGCTTATAGTGGT
2352201 ACGTAAATAACATGGGGG
66 ACGTAAATAACATGGGGG
2352219 GACAAAGGGTTGAATCTTAGATCATGATAATTCAATAACGAAAAGCATAGGTAGCTTATAGTGGT
1 GACAAAGGGTTGAATCTTAGATCATGATAATTCAATAACGAAAAGCATAGGTAGCTTATAGTGGT
2352284 ACGTAAATAACATGGGGG
66 ACGTAAATAACATGGGGG
2352302 G
1 G
2352303 CACGTAGAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (83 bp):
GACAAAGGGTTGAATCTTAGATCATGATAATTCAATAACGAAAAGCATAGGTAGCTTATAGTGGT
ACGTAAATAACATGGGGG
Found at i:2354898 original size:14 final size:14
Alignment explanation
Indices: 2354863--2354919 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
2354853 GTTTGCCAGT
*
2354863 AAAATGTTTTCTCGG
1 AAAATGATTTCT-GG
*
2354878 TAAATGATTTCTGG
1 AAAATGATTTCTGG
2354892 AAAATGATTTACT-G
1 AAAATGATTT-CTGG
2354906 AAAAT-ATTTTCTGG
1 AAAATGA-TTTCTGG
2354920 TGTTTGGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
13 3 0.08
14 21 0.58
15 12 0.33
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:2355020 original size:20 final size:20
Alignment explanation
Indices: 2354992--2355035 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2354982 CGTAAAAGTT
* *
2354992 ATTTTTACATATATTAATAA
1 ATTTATACACATATTAATAA
2355012 ATTTATACACATATTAATAA
1 ATTTATACACATATTAATAA
2355032 ATTT
1 ATTT
2355036 TTATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTATACACATATTAATAA
Found at i:2358099 original size:19 final size:19
Alignment explanation
Indices: 2358077--2358115 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2358067 TATTTATTTA
2358077 TTATATTTAAATTTAATAT
1 TTATATTTAAATTTAATAT
* *
2358096 TTATATTTTAATTTGATAT
1 TTATATTTAAATTTAATAT
2358115 T
1 T
2358116 ATTTTATTAT
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:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTATATTTAAATTTAATAT
Found at i:2364379 original size:20 final size:20
Alignment explanation
Indices: 2364356--2364394 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2364346 CGATTTAAAA
2364356 TATAAAAAATTATTAATATG
1 TATAAAAAATTATTAATATG
* * *
2364376 TATATATATTTATTAATAT
1 TATAAAAAATTATTAATAT
2364395 ATGTAAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAAATTATTAATATG
Found at i:2364544 original size:13 final size:14
Alignment explanation
Indices: 2364515--2364552 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2364505 CTAAAAAAAT
2364515 AAATTATTTTTCAA
1 AAATTATTTTTCAA
*
2364529 AAATTATTTTTTAA
1 AAATTATTTTTCAA
*
2364543 AAAATATTTT
1 AAATTATTTT
2364553 ACTGAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
AAATTATTTTTCAA
Found at i:2368823 original size:10 final size:9
Alignment explanation
Indices: 2368808--2368872 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
2368798 AAAATTATTA
2368808 TTTTAAAGTT
1 TTTTAAA-TT
*
2368818 TTTTAAAGT
1 TTTTAAATT
*
2368827 TTTTAACTT
1 TTTTAAATT
2368836 TTTTATATATT
1 TTTTA-A-ATT
* *
2368847 CTTTAGATTT
1 TTTTA-AATT
2368857 TTTTAAATT
1 TTTTAAATT
2368866 TTTTAAA
1 TTTTAAA
2368873 AATATAAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
9 23 0.52
10 14 0.32
11 7 0.16
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (9 bp):
TTTTAAATT
Found at i:2376198 original size:13 final size:14
Alignment explanation
Indices: 2376175--2376203 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2376165 AGGTTTTGGA
2376175 TAAAAATATAAGTT
1 TAAAAATATAAGTT
2376189 TAAAAA-ATAAGTT
1 TAAAAATATAAGTT
2376202 TA
1 TA
2376204 GACAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (14 bp):
TAAAAATATAAGTT
Found at i:2377169 original size:20 final size:20
Alignment explanation
Indices: 2377144--2377185 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2377134 CAATATCAAG
2377144 TTGAATTAATCTGAGATCCA
1 TTGAATTAATCTGAGATCCA
*
2377164 TTGAATTAATTTGAGATCCA
1 TTGAATTAATCTGAGATCCA
2377184 TT
1 TT
2377186 TATAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (20 bp):
TTGAATTAATCTGAGATCCA
Found at i:2377991 original size:2 final size:2
Alignment explanation
Indices: 2377984--2378011 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2377974 ATACACATAA
2377984 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
2378012 CAGCATCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2382671 original size:18 final size:16
Alignment explanation
Indices: 2382649--2382687 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 16
2382639 GATATGACAA
2382649 AAAAAATATTAATTTTTT
1 AAAAAA-ATT-ATTTTTT
2382667 CAAAAAAATTATTTTTT
1 -AAAAAAATTATTTTTT
2382684 AAAA
1 AAAA
2382688 TTTATTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 3 0.15
19 6 0.30
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAAAAATTATTTTTT
Found at i:2382874 original size:2 final size:2
Alignment explanation
Indices: 2382869--2382914 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2382859 CTTTCTCTCT
2382869 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2382911 CA CA
1 CA CA
2382915 TCAGCACGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2387565 original size:15 final size:15
Alignment explanation
Indices: 2387545--2387627 Score: 57
Period size: 15 Copynumber: 5.5 Consensus size: 15
2387535 TGGGGCAATA
2387545 TAATTAAAAAATACG
1 TAATTAAAAAATACG
**
2387560 TAATTAATTTGAATA--
1 TAATTAA--AAAATACG
2387575 TAATTAAAAAATACG
1 TAATTAAAAAATACG
**
2387590 TAATTAATTTGAATA--
1 TAATTAA--AAAATACG
2387605 TAATTAAAAAATGACG
1 TAATTAAAAAAT-ACG
2387621 TAATTAA
1 TAATTAA
2387628 TATGAATTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 17
0.67 0.11 0.22
Matches are distributed among these distances:
13 7 0.14
14 1 0.02
15 28 0.55
16 7 0.14
17 8 0.16
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (15 bp):
TAATTAAAAAATACG
Found at i:2387643 original size:30 final size:30
Alignment explanation
Indices: 2387541--2387634 Score: 170
Period size: 30 Copynumber: 3.1 Consensus size: 30
2387531 CTTTTGGGGC
2387541 AATATAATTAAAAAATACGTAATTAATTTG
1 AATATAATTAAAAAATACGTAATTAATTTG
2387571 AATATAATTAAAAAATACGTAATTAATTTG
1 AATATAATTAAAAAATACGTAATTAATTTG
*
2387601 AATATAATTAAAAAATGACGTAATTAATATG
1 AATATAATTAAAAAAT-ACGTAATTAATTTG
2387632 AAT
1 AAT
2387635 TTAGTAAAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 46 0.74
31 16 0.26
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.35
Consensus pattern (30 bp):
AATATAATTAAAAAATACGTAATTAATTTG
Done.