Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 106 of 131
Found at i:35211522 original size:13 final size:13
Alignment explanation
Indices: 35211506--35211540 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
35211496 TTTAAACAAA
*
35211506 TTAATTAACTTAT
1 TTAATTAACTAAT
35211519 TTAATTAACTAAT
1 TTAATTAACTAAT
*
35211532 TTAACTAAC
1 TTAATTAAC
35211541 AACAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Found at i:35214039 original size:45 final size:44
Alignment explanation
Indices: 35213969--35214060 Score: 121
Period size: 45 Copynumber: 2.1 Consensus size: 44
35213959 GCTACCGAAT
* *
35213969 TTTAAAGGATGTATAATGCTTTCCTTTAAATGATATAACGACTCC
1 TTTAAAGGATGTATAATGCTCTCCTTTAAATGATATAACAAC-CC
* * * *
35214014 TTTAAATGATGTATAATTCTCTCCTTTAATTGATGTAACAACCC
1 TTTAAAGGATGTATAATGCTCTCCTTTAAATGATATAACAACCC
35214058 TTT
1 TTT
35214061 GTATGTAACC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 5 0.12
45 36 0.88
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (44 bp):
TTTAAAGGATGTATAATGCTCTCCTTTAAATGATATAACAACCC
Found at i:35214042 original size:24 final size:23
Alignment explanation
Indices: 35213969--35214050 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 23
35213959 GCTACCGAAT
* *
35213969 TTTAAAGGATGTATAATGCTTTCC
1 TTTAAATGATGTATAAT-CTCTCC
*
35213993 TTTAAATGA--TATAA-CGACTCC
1 TTTAAATGATGTATAATC-TCTCC
35214014 TTTAAATGATGTATAATTCTCTCC
1 TTTAAATGATGTATAA-TCTCTCC
*
35214038 TTTAATTGATGTA
1 TTTAAATGATGTA
35214051 ACAACCCTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.02
21 12 0.25
22 5 0.10
23 5 0.10
24 24 0.50
25 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (23 bp):
TTTAAATGATGTATAATCTCTCC
Found at i:35214182 original size:20 final size:20
Alignment explanation
Indices: 35214153--35214203 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
35214143 ACCTAAAAAC
*
35214153 AAACACATTAAAAACACATT
1 AAACATATTAAAAACACATT
* **
35214173 AAACATATTAAACACATTTT
1 AAACATATTAAAAACACATT
35214193 AACACATATTA
1 AA-ACATATTA
35214204 GACTTAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (20 bp):
AAACATATTAAAAACACATT
Found at i:35214356 original size:54 final size:54
Alignment explanation
Indices: 35214294--35214419 Score: 173
Period size: 54 Copynumber: 2.3 Consensus size: 54
35214284 CAACAATAAA
* * *
35214294 TTATTCCAGCAACTAAATTGACTAAGA-AGAACTTAATTAACTAAGATGAGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATA-AACTCAATTAAATAAGATGAGTAAT
* *
35214348 TTATTCCAGCAACTTAATTAACTAAGATAAACTCAATTAAATAATATGAGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATAAACTCAATTAAATAAGATGAGTAAT
* *
35214402 TTATTCGAACAACTAAAT
1 TTATTCCAGCAACTAAAT
35214420 ACTTATTCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 62 0.98
55 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (54 bp):
TTATTCCAGCAACTAAATTAACTAAGATAAACTCAATTAAATAAGATGAGTAAT
Found at i:35215850 original size:24 final size:25
Alignment explanation
Indices: 35215812--35215904 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
35215802 GCATCAGGGA
* *
35215812 TTACCGATTCTTAGCTTGTATGAGC
1 TTACCAATTCTCAGCTTGTATGAGC
* *
35215837 TTACCAATT-TTAGCTTGTGA-GATC
1 TTACCAATTCTCAGCTTGT-ATGAGC
*
35215861 TTACCAATTCTCAGCTCGTATGAGC
1 TTACCAATTCTCAGCTTGTATGAGC
35215886 TTACCAATT-TACAGCTTGT
1 TTACCAATTCT-CAGCTTGT
35215905 GAGAGCATAC
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
24 23 0.40
25 35 0.60
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (25 bp):
TTACCAATTCTCAGCTTGTATGAGC
Found at i:35215871 original size:49 final size:50
Alignment explanation
Indices: 35215812--35215935 Score: 169
Period size: 49 Copynumber: 2.5 Consensus size: 50
35215802 GCATCAGGGA
* * *
35215812 TTACCGATTCTTAGCTTGTATGAGCTTACCAATTT-TAGCTTGTGAGATC
1 TTACCGATTCTTAGCTCGTATGAGCTTACCAATTTACAGCTTGTGAGAGC
* *
35215861 TTACCAATTCTCAGCTCGTATGAGCTTACCAATTTACAGCTTGTGAGAGC
1 TTACCGATTCTTAGCTCGTATGAGCTTACCAATTTACAGCTTGTGAGAGC
* * *
35215911 ATACCGATTCATAGCTCGTTTGAGC
1 TTACCGATTCTTAGCTCGTATGAGC
35215936 ATACATGTAC
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
49 32 0.50
50 32 0.50
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (50 bp):
TTACCGATTCTTAGCTCGTATGAGCTTACCAATTTACAGCTTGTGAGAGC
Found at i:35215888 original size:25 final size:25
Alignment explanation
Indices: 35215812--35215894 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 25
35215802 GCATCAGGGA
*
35215812 TTACCGATTCTTAGCTTGTATGAGC
1 TTACCAATTCTTAGCTTGTATGAGC
*
35215837 TTACCAATT-TTAGCTTGTGA-GATC
1 TTACCAATTCTTAGCTTGT-ATGAGC
* *
35215861 TTACCAATTCTCAGCTCGTATGAGC
1 TTACCAATTCTTAGCTTGTATGAGC
35215886 TTACCAATT
1 TTACCAATT
35215895 TACAGCTTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
24 22 0.44
25 28 0.56
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (25 bp):
TTACCAATTCTTAGCTTGTATGAGC
Found at i:35215926 original size:25 final size:25
Alignment explanation
Indices: 35215812--35215935 Score: 94
Period size: 25 Copynumber: 5.0 Consensus size: 25
35215802 GCATCAGGGA
* *
35215812 TTACCGATTCTTAGCTTGTATGAGC
1 TTACCAATTCATAGCTTGTATGAGC
* *
35215837 TTACCAATT-TTAGCTTGTGA-GATC
1 TTACCAATTCATAGCTTGT-ATGAGC
*
35215861 TTACCAATTC-TCAGCTCGTATGAGC
1 TTACCAATTCAT-AGCTTGTATGAGC
* *
35215886 TTACCAATTTACAGCTTGTGA-GAGC
1 TTACCAATTCATAGCTTGT-ATGAGC
* * * *
35215911 ATACCGATTCATAGCTCGTTTGAGC
1 TTACCAATTCATAGCTTGTATGAGC
35215936 ATACATGTAC
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
24 23 0.29
25 55 0.70
26 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (25 bp):
TTACCAATTCATAGCTTGTATGAGC
Found at i:35215927 original size:50 final size:48
Alignment explanation
Indices: 35215813--35215935 Score: 156
Period size: 50 Copynumber: 2.5 Consensus size: 48
35215803 CATCAGGGAT
* * * *
35215813 TACCGATTCTTAGCTTGTATGAGCTTACCAATTTTAGCTTGTGAGATCT
1 TACCGATTC-TAGCTCGTATGAGCTTACCAATTTCAGCTTGTGAGAGCA
*
35215862 TACCAATTCTCAGCTCGTATGAGCTTACCAATTTACAGCTTGTGAGAGCA
1 TACCGATTCT-AGCTCGTATGAGCTTACCAATTT-CAGCTTGTGAGAGCA
*
35215912 TACCGATTCATAGCTCGTTTGAGC
1 TACCGATTC-TAGCTCGTATGAGC
35215936 ATACATGTAC
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
48 1 0.02
49 30 0.47
50 32 0.50
51 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (48 bp):
TACCGATTCTAGCTCGTATGAGCTTACCAATTTCAGCTTGTGAGAGCA
Found at i:35217775 original size:50 final size:50
Alignment explanation
Indices: 35217647--35217888 Score: 155
Period size: 50 Copynumber: 4.7 Consensus size: 50
35217637 GATAATAACA
* * * ** * * *
35217647 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTACA-
1 TGCCAACGCCATGTCCCAAACATGGTCTTACGTGGGAACTCTCATAT-CAG
* * * * * *
35217697 -GCCAATGCCATATCCCAGATATGGTCTTACTTGGGAATTCTCATATCAG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACGTGGGAACTCTCATATCAG
* * * * * * *
35217746 TGCCCATGTCATGTCCCAAACATGGTCTTACGAGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACGTGGGAACTCTCATATCAG
* ** *
35217796 TGCCAACGCCATGTCCCATACATGGTCTTACGTGGGGCCTCTCATAAGCTCAATAA
1 TGCCAACGCCATGTCCCAAACATGGTCTTACGTGGGAACTCTCAT-A--TC---AG
* * *
35217852 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAACGCCATGTCCCAAACATGGTCTTACGTGGGA
35217889 TCTCATTCCT
Statistics
Matches: 151, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
48 2 0.01
49 37 0.25
50 77 0.51
53 2 0.01
56 33 0.22
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAAACATGGTCTTACGTGGGAACTCTCATATCAG
Found at i:35224387 original size:25 final size:25
Alignment explanation
Indices: 35224359--35224424 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
35224349 ATGATCTATG
* * *
35224359 AATCGGTATGCTCTTAAGAGCTAAA
1 AATCAGTAAGCTCATAAGAGCTAAA
*
35224384 AATCAGTAAGCTCATACGAGCTAAA
1 AATCAGTAAGCTCATAAGAGCTAAA
35224409 AATCAGTAAGCTCATA
1 AATCAGTAAGCTCATA
35224425 CGAGTTATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (25 bp):
AATCAGTAAGCTCATAAGAGCTAAA
Found at i:35224425 original size:25 final size:25
Alignment explanation
Indices: 35224376--35224428 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
35224366 ATGCTCTTAA
35224376 GAGCTAAAAATCAGTAAGCTCATAC
1 GAGCTAAAAATCAGTAAGCTCATAC
35224401 GAGCTAAAAATCAGTAAGCTCATAC
1 GAGCTAAAAATCAGTAAGCTCATAC
35224426 GAG
1 GAG
35224429 TTATGTTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (25 bp):
GAGCTAAAAATCAGTAAGCTCATAC
Found at i:35229621 original size:15 final size:15
Alignment explanation
Indices: 35229601--35229632 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35229591 CTCTATCATT
35229601 TTCTTTCTCTTTTTC
1 TTCTTTCTCTTTTTC
*
35229616 TTCTTTTTCTTTTTC
1 TTCTTTCTCTTTTTC
35229631 TT
1 TT
35229633 AATTTTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTCTTTCTCTTTTTC
Found at i:35229666 original size:39 final size:39
Alignment explanation
Indices: 35229615--35229689 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
35229605 TTCTCTTTTT
* *
35229615 CTTCTTTTTCTTTTTCTTAATTTTCAATTTCTTTTTTAA
1 CTTCTTTTTCTTTTTCCTAATTTTCAATCTCTTTTTTAA
**
35229654 CTTCTTTTTCTTTTTCCTCTTTTTCAATCTCTTTTT
1 CTTCTTTTTCTTTTTCCTAATTTTCAATCTCTTTTT
35229690 CTTTTTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (39 bp):
CTTCTTTTTCTTTTTCCTAATTTTCAATCTCTTTTTTAA
Found at i:35232513 original size:204 final size:204
Alignment explanation
Indices: 35232160--35232563 Score: 745
Period size: 204 Copynumber: 2.0 Consensus size: 204
35232150 CAGGCCTAAG
* *
35232160 AGATGTTTCATCTTGCACTTGGGCTCTTCAAGTTTAGGCTAATCCCAATGTCGTCGAGATGTATC
1 AGATGTTTCATCTTGCACTTGGGCCCTTCAAGTTTAGGCCAATCCCAATGTCGTCGAGATGTATC
*
35232225 GAAACATGATGCGACCAGGTTCGTACCACATAGCTAGGGTGAAGGAGATTTGGTTTTCTTATTTT
66 GAAACATGATGCGACCAGGTTCGCACCACATAGCTAGGGTGAAGGAGATTTGGTTTTCTTATTTT
*
35232290 CATTGGATGTAAGTGAATTTTGATGTTCATTTGTTGTAATTTTTATATTTTTGAGATCATTGCAG
131 CATTGGATGTAAATGAATTTTGATGTTCATTTGTTGTAATTTTTATATTTTTGAGATCATTGCAG
35232355 CTAGGGTTA
196 CTAGGGTTA
*
35232364 AGATGTTTCATCTTGCACTTGGGCCCTTCAAGTTTAGGCCAATCCCGATGTCGTCGAGATGTATC
1 AGATGTTTCATCTTGCACTTGGGCCCTTCAAGTTTAGGCCAATCCCAATGTCGTCGAGATGTATC
35232429 GAAACATGATGCGACCAGGTTCGCACCACATAGCTAGGGTGAAGGAGATTTGGTTTTCTTATTTT
66 GAAACATGATGCGACCAGGTTCGCACCACATAGCTAGGGTGAAGGAGATTTGGTTTTCTTATTTT
* *
35232494 CATTGGATGTAAATGAATTTTGATGTTCATTTGTTGTAATTTTTATATTTTTGAGATCGTTGCAT
131 CATTGGATGTAAATGAATTTTGATGTTCATTTGTTGTAATTTTTATATTTTTGAGATCATTGCAG
35232559 CTAGG
196 CTAGG
35232564 TTCAACTAGC
Statistics
Matches: 193, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
204 193 1.00
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (204 bp):
AGATGTTTCATCTTGCACTTGGGCCCTTCAAGTTTAGGCCAATCCCAATGTCGTCGAGATGTATC
GAAACATGATGCGACCAGGTTCGCACCACATAGCTAGGGTGAAGGAGATTTGGTTTTCTTATTTT
CATTGGATGTAAATGAATTTTGATGTTCATTTGTTGTAATTTTTATATTTTTGAGATCATTGCAG
CTAGGGTTA
Found at i:35233425 original size:36 final size:36
Alignment explanation
Indices: 35233380--35233498 Score: 121
Period size: 36 Copynumber: 3.3 Consensus size: 36
35233370 ATAAGCATTT
*
35233380 GTGTATTTTGGAGCGATTGGCTCGTGTGAGCATCTG
1 GTGTATTTTGGAGCGATTGGCTCATGTGAGCATCTG
* *
35233416 GTGTATTTTGGTGGGATTGGCTCATGTGAGCATCTG
1 GTGTATTTTGGAGCGATTGGCTCATGTGAGCATCTG
* * * ** * * *
35233452 TTGTGTCTTACAGGGATTAGCTCATGTGACCATCTG
1 GTGTATTTTGGAGCGATTGGCTCATGTGAGCATCTG
* *
35233488 CTGTGTTTTGG
1 GTGTATTTTGG
35233499 TTGGACTGAC
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.14, C:0.14, G:0.33, T:0.39
Consensus pattern (36 bp):
GTGTATTTTGGAGCGATTGGCTCATGTGAGCATCTG
Found at i:35237030 original size:30 final size:30
Alignment explanation
Indices: 35236994--35237158 Score: 115
Period size: 30 Copynumber: 5.6 Consensus size: 30
35236984 CTTTGGTTAT
*
35236994 AAATTATGAAAAGGGATGGTGACTAACATC
1 AAATTATGAAAAGGGATGGTGACGAACATC
*
35237024 AAATTATGAAAAGGGATGGTGACGACCATC
1 AAATTATGAAAAGGGATGGTGACGAACATC
* * * * ***
35237054 GAACTATGAAATGGGATGGCT-TCGGTTAT-
1 AAATTATGAAAAGGGATGG-TGACGAACATC
** * *
35237083 TGATCTATGAAAAGGGAT--AGCCG-ACTATC
1 AAAT-TATGAAAAGGGATGGTGACGAAC-ATC
* * *
35237112 GAATTATGAAAATGGATGGTGACGACCATC
1 AAATTATGAAAAGGGATGGTGACGAACATC
*
35237142 AAATTATGGAAAGGGAT
1 AAATTATGAAAAGGGAT
35237159 AGCTTCAGCT
Statistics
Matches: 101, Mismatches: 26, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
28 16 0.16
29 3 0.03
30 80 0.79
31 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.24
Consensus pattern (30 bp):
AAATTATGAAAAGGGATGGTGACGAACATC
Found at i:35237117 original size:88 final size:88
Alignment explanation
Indices: 35237025--35237189 Score: 233
Period size: 88 Copynumber: 1.9 Consensus size: 88
35237015 ACTAACATCA
* * * * * *
35237025 AATTATGAAAAGGGATGGTGACGACCATCGAACTAT-GAAATGGGATGGCTTCGGTTATTGATCT
1 AATTATGAAAAGGGATGGTGACGACCATCAAACTATGGAAA-GGGATAGCTTCAGCTATCGAACT
*
35237089 ATGAAAAGGGATAGCCGACTATCG
65 ATCAAAAGGGATAGCCGACTATCG
* *
35237113 AATTATGAAAATGGATGGTGACGACCATCAAATTATGGAAAGGGATAGCTTCAGCTATCGAACTA
1 AATTATGAAAAGGGATGGTGACGACCATCAAACTATGGAAAGGGATAGCTTCAGCTATCGAACTA
35237178 TCAAAAGGGATA
66 TCAAAAGGGATA
35237190 ACTTTGGTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
88 63 0.94
89 4 0.06
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.24
Consensus pattern (88 bp):
AATTATGAAAAGGGATGGTGACGACCATCAAACTATGGAAAGGGATAGCTTCAGCTATCGAACTA
TCAAAAGGGATAGCCGACTATCG
Found at i:35244304 original size:30 final size:31
Alignment explanation
Indices: 35244264--35244345 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
35244254 GGTGACAACC
35244264 ATCAAA-CTATGAAAAGGGATGGCTTC-GACT
1 ATCAAATCTATGAAAAGGGATGGCTTCAG-CT
** *
35244294 AT-TGATCTATGAAAAGGGATAGCTTCAGCT
1 ATCAAATCTATGAAAAGGGATGGCTTCAGCT
35244324 ATCAAAT-TATGAAAAGGGATGG
1 ATCAAATCTATGAAAAGGGATGG
35244346 TGACACCCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 1 0.02
30 39 0.91
31 3 0.07
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (31 bp):
ATCAAATCTATGAAAAGGGATGGCTTCAGCT
Found at i:35249540 original size:28 final size:29
Alignment explanation
Indices: 35249493--35249547 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
35249483 AATAATGAAT
35249493 TCTTTTTTTTTCATTGTATT-TTTTGTAG
1 TCTTTTTTTTTCATTGTATTCTTTTGTAG
35249521 TCTTTTTTATATTC-TT-TATTCTTTTGT
1 TCTTTTTT-T-TTCATTGTATTCTTTTGT
35249548 CAACTCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 12 0.50
29 9 0.38
30 3 0.12
ACGTcount: A:0.11, C:0.09, G:0.07, T:0.73
Consensus pattern (29 bp):
TCTTTTTTTTTCATTGTATTCTTTTGTAG
Found at i:35252231 original size:32 final size:32
Alignment explanation
Indices: 35252178--35252283 Score: 115
Period size: 32 Copynumber: 3.1 Consensus size: 32
35252168 TTATGCTCAA
*
35252178 CTTTTATTTTTTTAGACTTTGAGCAAACTTTG
1 CTTTTATTTTTTTAGAATTTGAGCAAACTTTG
*
35252210 CTCTTTA-TTTTTTAGAATTTGAGCAATCTTTTATTTG
1 CT-TTTATTTTTTTAGAATTTGAGCAAAC-----TTTG
*
35252247 CTTTTATTTTTTCTAGAATTTGAGCAAACTTTT
1 CTTTTATTTTTT-TAGAATTTGAGCAAACTTTG
35252280 CTTT
1 CTTT
35252284 GTTCTTTAGT
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
32 21 0.34
33 11 0.18
36 4 0.06
37 11 0.18
38 15 0.24
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.56
Consensus pattern (32 bp):
CTTTTATTTTTTTAGAATTTGAGCAAACTTTG
Found at i:35252247 original size:37 final size:39
Alignment explanation
Indices: 35252180--35252291 Score: 125
Period size: 38 Copynumber: 3.1 Consensus size: 39
35252170 ATGCTCAACT
*
35252180 TTTATTTTTT-TAGACTTTGAGCAAAC-----TTTGCTC
1 TTTATTTTTTCTAGAATTTGAGCAAACTTTTATTTGCTC
*
35252213 TTTA-TTTTT-TAGAATTTGAGCAATCTTTTATTTGCT-
1 TTTATTTTTTCTAGAATTTGAGCAAACTTTTATTTGCTC
* *
35252249 TTTATTTTTTCTAGAATTTGAGCAAACTTTTCTTTGTTC
1 TTTATTTTTTCTAGAATTTGAGCAAACTTTTATTTGCTC
35252288 TTTA
1 TTTA
35252292 GTCATTTTCT
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
32 19 0.29
33 4 0.06
36 4 0.06
37 11 0.17
38 24 0.36
39 4 0.06
ACGTcount: A:0.21, C:0.12, G:0.11, T:0.56
Consensus pattern (39 bp):
TTTATTTTTTCTAGAATTTGAGCAAACTTTTATTTGCTC
Found at i:35254257 original size:20 final size:20
Alignment explanation
Indices: 35254234--35254280 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
35254224 GGGTTAAAAT
*
35254234 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
35254254 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
35254274 TGAGCTG
1 TGAGCTG
35254281 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:35257302 original size:25 final size:25
Alignment explanation
Indices: 35257273--35257322 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
35257263 GAAACATACT
*
35257273 TTAAAAATTCATGTGAAATGCCTTA
1 TTAAAAATTCAGGTGAAATGCCTTA
35257298 TTAAAAATTCAGGTGAAATGCCTTA
1 TTAAAAATTCAGGTGAAATGCCTTA
35257323 CCCCTCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (25 bp):
TTAAAAATTCAGGTGAAATGCCTTA
Found at i:35259462 original size:6 final size:6
Alignment explanation
Indices: 35259453--35259512 Score: 66
Period size: 6 Copynumber: 9.7 Consensus size: 6
35259443 TAAACAAATT
* * *
35259453 AAATAA AAATAA AAAGTAA AGATAA AAATGAA AAAGAA AAATAA AACTAA
1 AAATAA AAATAA AAA-TAA AAATAA AAAT-AA AAATAA AAATAA AAATAA
*
35259503 AAATAT AAAT
1 AAATAA AAAT
35259513 TTTCTTAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
6 35 0.78
7 10 0.22
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:35259472 original size:13 final size:12
Alignment explanation
Indices: 35259453--35259512 Score: 66
Period size: 13 Copynumber: 4.8 Consensus size: 12
35259443 TAAACAAATT
35259453 AAATAAAAATAA
1 AAATAAAAATAA
*
35259465 AAAGTAAAGATAA
1 AAA-TAAAAATAA
*
35259478 AAATGAAAAAGAA
1 AAAT-AAAAATAA
*
35259491 AAATAAAACTAA
1 AAATAAAAATAA
*
35259503 AAATATAAAT
1 AAATAAAAAT
35259513 TTTCTTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
12 18 0.46
13 21 0.54
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.17
Consensus pattern (12 bp):
AAATAAAAATAA
Found at i:35259477 original size:19 final size:18
Alignment explanation
Indices: 35259453--35259505 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
35259443 TAAACAAATT
35259453 AAATAAAAATAAAAAGTAA
1 AAATAAAAATAAAAAG-AA
*
35259472 AGATAAAAATGAAAAAGAA
1 AAATAAAAAT-AAAAAGAA
*
35259491 AAATAAAACTAAAAA
1 AAATAAAAATAAAAA
35259506 TATAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.17
19 19 0.63
20 6 0.20
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (18 bp):
AAATAAAAATAAAAAGAA
Found at i:35270809 original size:42 final size:42
Alignment explanation
Indices: 35270732--35270819 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
35270722 GTGCCAGATA
*
35270732 GTGTACCCTTCGAAGTAGCCTCACACACCCATGTG-CATGGCC
1 GTGTACCCTTCAAAGTAGCCTCACACACCCATGTGCCA-GGCC
** *
35270774 GTGTACCCTTCAAAGTAGCCTCACATGCCCGTGTGCCAGGCC
1 GTGTACCCTTCAAAGTAGCCTCACACACCCATGTGCCAGGCC
35270816 GTGT
1 GTGT
35270820 GGTAGGACAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 39 0.95
43 2 0.05
ACGTcount: A:0.19, C:0.34, G:0.24, T:0.23
Consensus pattern (42 bp):
GTGTACCCTTCAAAGTAGCCTCACACACCCATGTGCCAGGCC
Found at i:35272071 original size:25 final size:25
Alignment explanation
Indices: 35272035--35272090 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
35272025 AAGCTATAAA
*
35272035 CGGTAAGATCATAAT-AGTTGAATAT
1 CGGTAAGATCAT-ATGAGCTGAATAT
* *
35272060 CGGTAAGCTCATGTGAGCTGAATAT
1 CGGTAAGATCATATGAGCTGAATAT
35272085 CGGTAA
1 CGGTAA
35272091 TTGTAATGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (25 bp):
CGGTAAGATCATATGAGCTGAATAT
Found at i:35280658 original size:20 final size:20
Alignment explanation
Indices: 35280620--35280658 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35280610 TGAATTTAAG
*
35280620 TGACCATTTGCTTATCTTAT
1 TGACCATTTGCTTAGCTTAT
35280640 TGACCATTTGGC-TAGCTTA
1 TGACCATTT-GCTTAGCTTA
35280659 GCTTTTAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (20 bp):
TGACCATTTGCTTAGCTTAT
Found at i:35282262 original size:12 final size:10
Alignment explanation
Indices: 35282237--35282276 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
35282227 GAACATGATG
35282237 AATTTTAATT
1 AATTTTAATT
35282247 AATTTTATAGTT
1 AATTTTA-A-TT
*
35282259 AATTTTGATT
1 AATTTTAATT
35282269 AATTTTAA
1 AATTTTAA
35282277 CTATTTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 16 0.62
11 2 0.08
12 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (10 bp):
AATTTTAATT
Found at i:35289175 original size:19 final size:20
Alignment explanation
Indices: 35289134--35289178 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
35289124 GTGAAAATGC
* *
35289134 AAAAGAAAAGAAAAATGAGA
1 AAAAGAAAAGAAAAATCAAA
*
35289154 AAAAGAAAGGAAAAA-CAAA
1 AAAAGAAAAGAAAAATCAAA
35289173 AAAAGA
1 AAAAGA
35289179 GAGTGAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:35289217 original size:15 final size:18
Alignment explanation
Indices: 35289183--35289220 Score: 55
Period size: 15 Copynumber: 2.3 Consensus size: 18
35289173 AAAAGAGAGT
35289183 GAAAAGAGAGTGAGAAAA
1 GAAAAGAGAGTGAGAAAA
35289201 GAAAAG-GA-TGA-AAAA
1 GAAAAGAGAGTGAGAAAA
35289216 GAAAA
1 GAAAA
35289221 AGATTGACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 3 0.15
17 2 0.10
18 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (18 bp):
GAAAAGAGAGTGAGAAAA
Found at i:35300996 original size:20 final size:20
Alignment explanation
Indices: 35300971--35301047 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
35300961 CTTGTATGGG
35300971 TTTGCACTTTGATGCCTCTA
1 TTTGCACTTTGATGCCTCTA
*
35300991 TTTGCACTTTGGTGCCTCTGA
1 TTTGCACTTTGATGCCTCT-A
* *
35301012 -TTGCACATTCATGCCTCTA
1 TTTGCACTTTGATGCCTCTA
*
35301031 TTTGCACTTTGGTGCCT
1 TTTGCACTTTGATGCCT
35301048 TTGTTCTACA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.43
Consensus pattern (20 bp):
TTTGCACTTTGATGCCTCTA
Found at i:35301027 original size:40 final size:40
Alignment explanation
Indices: 35300972--35301047 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
35300962 TTGTATGGGT
* *
35300972 TTGCACTTTGATGCCTCTATTTGCACTTTGGTGCCTCTGA
1 TTGCACATTCATGCCTCTATTTGCACTTTGGTGCCTCTGA
35301012 TTGCACATTCATGCCTCTATTTGCACTTTGGTGCCT
1 TTGCACATTCATGCCTCTATTTGCACTTTGGTGCCT
35301048 TTGTTCTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.42
Consensus pattern (40 bp):
TTGCACATTCATGCCTCTATTTGCACTTTGGTGCCTCTGA
Found at i:35313707 original size:22 final size:22
Alignment explanation
Indices: 35313677--35313721 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
35313667 CCCACTAGCA
35313677 CTAAGACCAATCACTCATATAT
1 CTAAGACCAATCACTCATATAT
* *
35313699 CTAATACCAATCAGTCATATAT
1 CTAAGACCAATCACTCATATAT
35313721 C
1 C
35313722 AGGGGATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.27, G:0.04, T:0.29
Consensus pattern (22 bp):
CTAAGACCAATCACTCATATAT
Found at i:35317452 original size:15 final size:15
Alignment explanation
Indices: 35317432--35317461 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35317422 GCCCTCGAGG
35317432 CATTAGCAAGTGGTT
1 CATTAGCAAGTGGTT
*
35317447 CATTAGGAAGTGGTT
1 CATTAGCAAGTGGTT
35317462 TTTCAATGAC
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:0.27, C:0.10, G:0.30, T:0.33
Consensus pattern (15 bp):
CATTAGCAAGTGGTT
Found at i:35325859 original size:9 final size:9
Alignment explanation
Indices: 35325845--35325907 Score: 63
Period size: 9 Copynumber: 6.3 Consensus size: 9
35325835 TTATTTAATC
35325845 TTTCTTTCT
1 TTTCTTTCT
35325854 TTTCTTTCT
1 TTTCTTTCT
*
35325863 TTTCTCTCT
1 TTTCTTTCT
35325872 TTTCTCTTCTT
1 TTTCT-TTC-T
35325883 CGTTTCATTTCT
1 --TTTC-TTTCT
35325895 TTTCTCTTCT
1 TTTCT-TTCT
35325905 TTT
1 TTT
35325908 TATCTAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
9 23 0.50
10 13 0.28
11 1 0.02
12 1 0.02
13 7 0.15
14 1 0.02
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:35325876 original size:23 final size:24
Alignment explanation
Indices: 35325849--35325906 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
35325839 TTAATCTTTC
* *
35325849 TTTCTTTTCTTTCTTTTC-TCTCT
1 TTTCTCTTCTTTCGTTTCATCTCT
*
35325872 TTTCTCTTC-TTCGTTTCATTTCT
1 TTTCTCTTCTTTCGTTTCATCTCT
35325895 TTTCTCTTCTTT
1 TTTCTCTTCTTT
35325907 TTATCTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.23
23 21 0.70
24 2 0.07
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTCTCTTCTTTCGTTTCATCTCT
Found at i:35330119 original size:2 final size:2
Alignment explanation
Indices: 35330112--35330144 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35330102 AAGTGAAAAT
35330112 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 A
35330145 AAATGGAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35337472 original size:20 final size:20
Alignment explanation
Indices: 35337414--35337478 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
35337404 CTTTCAATTC
*
35337414 TTTTCCTTTAC-TACTATTT
1 TTTTCCTTTACTTACTTTTT
*
35337433 TTTTCC---A-TT-CTTTTC
1 TTTTCCTTTACTTACTTTTT
*
35337448 CTTTCCTTTACTTACTTTTT
1 TTTTCCTTTACTTACTTTTT
35337468 TTTTCCTTTAC
1 TTTTCCTTTAC
35337479 AAATATTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
15 9 0.26
16 2 0.06
18 1 0.03
19 8 0.23
20 15 0.43
ACGTcount: A:0.11, C:0.25, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTCCTTTACTTACTTTTT
Found at i:35339832 original size:20 final size:20
Alignment explanation
Indices: 35339807--35339847 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
35339797 TCAAGCTTAA
35339807 AGTAGTAATTTATTAT-TTTT
1 AGTAGT-ATTTATTATATTTT
*
35339827 AGTAGTTTTTATTATATTTT
1 AGTAGTATTTATTATATTTT
35339847 A
1 A
35339848 TATATCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (20 bp):
AGTAGTATTTATTATATTTT
Found at i:35345344 original size:15 final size:15
Alignment explanation
Indices: 35345324--35345355 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35345314 TTATTGACAC
35345324 TTCTTCTTGTTCTTG
1 TTCTTCTTGTTCTTG
*
35345339 TTCTTCTTGTTTTTG
1 TTCTTCTTGTTCTTG
35345354 TT
1 TT
35345356 TTTATTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.12, T:0.72
Consensus pattern (15 bp):
TTCTTCTTGTTCTTG
Found at i:35358492 original size:3 final size:3
Alignment explanation
Indices: 35358486--35358526 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
35358476 AATAGTTCCC
35358486 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35358527 TTTTATGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:35359536 original size:18 final size:18
Alignment explanation
Indices: 35359503--35359537 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35359493 TGATAACTGC
*
35359503 ATTTGTATATGGGGTGGG
1 ATTTGTATATAGGGTGGG
*
35359521 ATTTGTATATATGGTGG
1 ATTTGTATATAGGGTGG
35359538 AAGTATTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (18 bp):
ATTTGTATATAGGGTGGG
Found at i:35364011 original size:49 final size:49
Alignment explanation
Indices: 35363939--35364038 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
35363929 AAACATGGTG
* * *
35363939 GTTATAATTCTTTTTGGAAAGAATATAACTTTTTTAGTACTTTCCATAT
1 GTTATAATTCTTTTTGGAAAGAATATAACATGTTTAATACTTTCCATAT
* *
35363988 GTTATATTTCTTTTTGGAAAGAATATAACATGTTTAATGCTTTCCATAT
1 GTTATAATTCTTTTTGGAAAGAATATAACATGTTTAATACTTTCCATAT
35364037 GT
1 GT
35364039 GCTTTATAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (49 bp):
GTTATAATTCTTTTTGGAAAGAATATAACATGTTTAATACTTTCCATAT
Found at i:35369160 original size:26 final size:27
Alignment explanation
Indices: 35369105--35369158 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
35369095 ATTGAATATA
35369105 CAAGGGGTTGCTAAGTGCTGATTCCCC
1 CAAGGGGTTGCTAAGTGCTGATTCCCC
*
35369132 CAAGGGTTTGCTAAGTGCTGATTCCCC
1 CAAGGGGTTGCTAAGTGCTGATTCCCC
35369159 AAATCATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (27 bp):
CAAGGGGTTGCTAAGTGCTGATTCCCC
Found at i:35369246 original size:27 final size:27
Alignment explanation
Indices: 35369208--35369260 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
35369198 TTAAATGAAA
35369208 AAGGGGTTGCTAACTGCTGATCCCCCC
1 AAGGGGTTGCTAACTGCTGATCCCCCC
* *
35369235 AAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAACTGCTGATCCCCC
35369261 AAATCATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (27 bp):
AAGGGGTTGCTAACTGCTGATCCCCCC
Found at i:35369330 original size:102 final size:102
Alignment explanation
Indices: 35369106--35369330 Score: 396
Period size: 102 Copynumber: 2.2 Consensus size: 102
35369096 TTGAATATAC
* *
35369106 AAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGTTTGCTAAGTGCTGATTCCCCAAATCATTGGTG
1 AAGGGGTTGCTAAGTGCTGATCCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTG
*
35369171 GTTGCTAAGTGCTGATTCCACCTTATCTTAAATGAAA
66 GTTGCTAAGTGCTGATTCCACCATATCTTAAATGAAA
*
35369208 AAGGGGTTGCTAACTGCTGATCCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTG
1 AAGGGGTTGCTAAGTGCTGATCCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTG
35369273 GTTGCTAAGTGCTGATTCCACCATATCTTAAATGAAA
66 GTTGCTAAGTGCTGATTCCACCATATCTTAAATGAAA
* *
35369310 AAGGGGCTGCTAAGTACTGAT
1 AAGGGGTTGCTAAGTGCTGAT
35369331 TCCCTGAATT
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 116 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (102 bp):
AAGGGGTTGCTAAGTGCTGATCCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTG
GTTGCTAAGTGCTGATTCCACCATATCTTAAATGAAA
Found at i:35369358 original size:75 final size:74
Alignment explanation
Indices: 35369235--35369435 Score: 321
Period size: 75 Copynumber: 2.7 Consensus size: 74
35369225 TGATCCCCCC
*
35369235 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATT-CCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
35369300 TTAAATGAAA
65 TTAAATGAAA
* * * * *
35369310 AAGGGGCTGCTAAGTACTGATTCCCTGAATTATTGGTGGTTGCTAAGTGCTGATTCCTCCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCC-GAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
35369375 TTAAATGAAA
65 TTAAATGAAA
35369385 AAGGGGTTGCTAAGTGCTGATTTCCCGAATCATTGGTGGTTGCTAAGTGCT
1 AAGGGGTTGCTAAGTGCTGA-TTCCCGAATCATTGGTGGTTGCTAAGTGCT
35369436 AAATCCATCG
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
74 3 0.03
75 107 0.93
76 5 0.04
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (74 bp):
AAGGGGTTGCTAAGTGCTGATTCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATCT
TAAATGAAA
Found at i:35380184 original size:57 final size:57
Alignment explanation
Indices: 35380116--35380243 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 57
35380106 TCTCACCACG
* * *
35380116 AAGGCATCCTTTTAACAGAGTTTACCTTAAGGCATCCTTTTAACAGAGATAGACATA
1 AAGGCATCCTTTAAACAGAGTTTACCATAAGGCATCCTTTTAACAAAGATAGACATA
* * * *
35380173 AAGGCATCCTTTAAATAGAGTTTGCCATAAGGCATCCTTTTAACAAAGATAGCCACA
1 AAGGCATCCTTTAAACAGAGTTTACCATAAGGCATCCTTTTAACAAAGATAGACATA
* *
35380230 AAAGCTTCCTTTAA
1 AAGGCATCCTTTAA
35380244 TAGAGATCGT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (57 bp):
AAGGCATCCTTTAAACAGAGTTTACCATAAGGCATCCTTTTAACAAAGATAGACATA
Found at i:35380192 original size:29 final size:29
Alignment explanation
Indices: 35380144--35380387 Score: 235
Period size: 29 Copynumber: 8.5 Consensus size: 29
35380134 AGTTTACCTT
* * * *
35380144 AAGGCATCCTTTTAACAGAGATAGACATA
1 AAGGCTTCCTTTTAATAGAGATAGCCACA
* * * * *
35380173 AAGGCATCCTTTAAATAGAGTTTGCCA-T
1 AAGGCTTCCTTTTAATAGAGATAGCCACA
* * *
35380201 AAGGCATCCTTTTAACAAAGATAGCCACA
1 AAGGCTTCCTTTTAATAGAGATAGCCACA
* * *
35380230 AAAGCTTCC-TTTAATAGAGATCGTCACA
1 AAGGCTTCCTTTTAATAGAGATAGCCACA
35380258 AAGGCTTCCTTTTACA-A-AGATAGCCACA
1 AAGGCTTCCTTTTA-ATAGAGATAGCCACA
*
35380286 ATGGCTTCCTTTTAATAGAGATAGCCACA
1 AAGGCTTCCTTTTAATAGAGATAGCCACA
*
35380315 AAGGTTTCCTTTTAATAGAGATAGCCACA
1 AAGGCTTCCTTTTAATAGAGATAGCCACA
* * * * *
35380344 AAGGCGTTCTTTTTAAAAGAAAAAGCTACA
1 AAGGC-TTCCTTTTAATAGAGATAGCCACA
*
35380374 AAGGCATCCTTTTA
1 AAGGCTTCCTTTTA
35380388 CAAAAATTGG
Statistics
Matches: 177, Mismatches: 32, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
27 1 0.01
28 68 0.38
29 83 0.47
30 25 0.14
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (29 bp):
AAGGCTTCCTTTTAATAGAGATAGCCACA
Found at i:35380227 original size:28 final size:28
Alignment explanation
Indices: 35380116--35380341 Score: 163
Period size: 28 Copynumber: 8.0 Consensus size: 28
35380106 TCTCACCACG
* *
35380116 AAGGCATCCTTTTAACAGAGTTTA-CCTT
1 AAGGCATCCTTTTAACAGAG-ATAGCCAT
*
35380144 AAGGCATCCTTTTAACAGAGATAGACAT
1 AAGGCATCCTTTTAACAGAGATAGCCAT
* * * *
35380172 AAAGGCATCCTTTAAATAGAGTTTGCCAT
1 -AAGGCATCCTTTTAACAGAGATAGCCAT
* *
35380201 AAGGCATCCTTTTAACAAAGATAGCCACA
1 AAGGCATCCTTTTAACAGAGATAGCCA-T
* * * *
35380230 AAAGCTTCC-TTTAATAGAGATCGTCACA-
1 AAGGCATCCTTTTAACAGAGATAG-C-CAT
* * *
35380258 AAGGCTTCCTTTT-ACAAAGATAGCCAC
1 AAGGCATCCTTTTAACAGAGATAGCCAT
* * *
35380285 AATGGCTTCCTTTTAATAGAGATAGCCACA
1 AA-GGCATCCTTTTAACAGAGATAGCCA-T
** *
35380315 AAGGTTTCCTTTTAATAGAGATAGCCA
1 AAGGCATCCTTTTAACAGAGATAGCCA
35380342 CAAAGGCGTT
Statistics
Matches: 161, Mismatches: 27, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
26 2 0.01
27 5 0.03
28 81 0.50
29 69 0.43
30 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (28 bp):
AAGGCATCCTTTTAACAGAGATAGCCAT
Found at i:35380262 original size:57 final size:56
Alignment explanation
Indices: 35380144--35380391 Score: 241
Period size: 57 Copynumber: 4.3 Consensus size: 56
35380134 AGTTTACCTT
* * * * * *
35380144 AAGGCATCCTTTTAACAGAGATAGACATAAAGGCATCCTTTAAATAGAGTTTGC-CA
1 AAGGCATCCTTTTAACAAAGATAGCCACAAAGGCTTCCTTT-AATAGAGATAGCACA
* *
35380200 TAAGGCATCCTTTTAACAAAGATAGCCACAAAAGCTTCCTTTAATAGAGATCGTCACA
1 -AAGGCATCCTTTTAACAAAGATAGCCACAAAGGCTTCCTTTAATAGAGATAG-CACA
* *
35380258 AAGGCTTCCTTTT-ACAAAGATAGCCACAATGGCTTCCTTTTAATAGAGATAGCCACA
1 AAGGCATCCTTTTAACAAAGATAGCCACAAAGGCTTCC-TTTAATAGAGATAG-CACA
** * * * * * *
35380315 AAGGTTTCCTTTTAATAGAGATAGCCACAAAGGCGTTCTTTTTAAAAGAAAAAGCTACA
1 AAGGCATCCTTTTAACAAAGATAGCCACAAAGGC-TTC-CTTTAATAGAGATAGC-ACA
35380374 AAGGCATCCTTTT-ACAAA
1 AAGGCATCCTTTTAACAAA
35380392 AATTGGTGTT
Statistics
Matches: 160, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
56 31 0.19
57 78 0.49
58 23 0.14
59 28 0.17
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (56 bp):
AAGGCATCCTTTTAACAAAGATAGCCACAAAGGCTTCCTTTAATAGAGATAGCACA
Found at i:35385658 original size:18 final size:18
Alignment explanation
Indices: 35385635--35385677 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
35385625 TACGATCGGA
35385635 CACATCAACAACTCGACT
1 CACATCAACAACTCGACT
* * *
35385653 CACATCACCAAGTCGATT
1 CACATCAACAACTCGACT
35385671 CACATCA
1 CACATCA
35385678 GACATGGTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.37, G:0.07, T:0.19
Consensus pattern (18 bp):
CACATCAACAACTCGACT
Found at i:35385809 original size:50 final size:50
Alignment explanation
Indices: 35385730--35385850 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
35385720 TATCCTAGAT
* * ** * * **
35385730 ATGGTCTTACATGAGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACAGGGGACCTCTCATATCGGTACCAACACCATGTCCCAGAC
*
35385780 ATGGTCTTACAGGGGACCTCTCATCTCGGTACCAACACCATGTCCCAGAC
1 ATGGTCTTACAGGGGACCTCTCATATCGGTACCAACACCATGTCCCAGAC
*
35385830 ATGGTCTCAC-GTGGGACCTCT
1 ATGGTCTTACAG-GGGACCTCT
35385851 GATAACCTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 1 0.02
50 59 0.98
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACAGGGGACCTCTCATATCGGTACCAACACCATGTCCCAGAC
Found at i:35396266 original size:5 final size:5
Alignment explanation
Indices: 35396256--35396286 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
35396246 ATTGAGTTAG
35396256 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A
35396287 ATCTCATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:35398864 original size:45 final size:45
Alignment explanation
Indices: 35398813--35398898 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
35398803 AGAAGTGAGA
* *
35398813 GAAAAAGAAAACGAAAAAGAGAAGATTGAAAAGGAAATTGATATT
1 GAAAAAGAAAACGAAAAAGAGAAAATTGAAAAAGAAATTGATATT
* * *
35398858 GAAAAAGGAAATGAAAAGGAGAAAATTGAAAAAGAAATTGA
1 GAAAAAGAAAACGAAAAAGAGAAAATTGAAAAAGAAATTGA
35398899 AGAACGAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (45 bp):
GAAAAAGAAAACGAAAAAGAGAAAATTGAAAAAGAAATTGATATT
Found at i:35401586 original size:16 final size:17
Alignment explanation
Indices: 35401555--35401592 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
35401545 AAAAAACCCA
35401555 AATTTATTTCCCAATTT
1 AATTTATTTCCCAATTT
35401572 AATTTATTT-CCAATTT
1 AATTTATTTCCCAATTT
35401588 -ATTTA
1 AATTTA
35401593 ATTGTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 7 0.33
17 9 0.43
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTATTTCCCAATTT
Found at i:35405479 original size:97 final size:97
Alignment explanation
Indices: 35405310--35405518 Score: 337
Period size: 97 Copynumber: 2.2 Consensus size: 97
35405300 GTCCCTTAGT
* * * * *
35405310 TTAAAATTTCATAGCCATTTGACTCTTTTAACTAATAGAACTTAACTTTTACCATTTTTATGATT
1 TTAAAATTTCATAACCACTTGACCCTTTTAACTAACAGAACTTAACTTTTACCATTTTTACGATT
*
35405375 TAGTCCTTTTAATTTAATTAACCATTTAAACA
66 TAATCCTTTTAATTTAATTAACCATTTAAACA
* *
35405407 TTAAAATTTCATAACCACTTGACCCTTTTAACTAACAGAACTTAACTTTTTCTATTTTTACGATT
1 TTAAAATTTCATAACCACTTGACCCTTTTAACTAACAGAACTTAACTTTTACCATTTTTACGATT
*
35405472 TAATCCTTTTCATTTAATTAACCATTTAAACA
66 TAATCCTTTTAATTTAATTAACCATTTAAACA
35405504 TTAAAATTTCATAAC
1 TTAAAATTTCATAAC
35405519 AAAAATTTAA
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 103 1.00
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (97 bp):
TTAAAATTTCATAACCACTTGACCCTTTTAACTAACAGAACTTAACTTTTACCATTTTTACGATT
TAATCCTTTTAATTTAATTAACCATTTAAACA
Found at i:35407661 original size:27 final size:27
Alignment explanation
Indices: 35407630--35407745 Score: 114
Period size: 27 Copynumber: 4.4 Consensus size: 27
35407620 CCCGATATTT
*
35407630 GTAAAATGACCATAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* * * **
35407657 GTAAAATAACTG-AAAACCCCCATAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
35407683 GTAAAATGACCGTAATGACCCC-GTAAG
1 GTAAAATGACCGTAAT-ACCCCTGTAGG
*
35407710 GTAAAATGACCGTAATGCCCCTAG-AGG
1 GTAAAATGACCGTAATACCCCT-GTAGG
35407737 GT-AAATGAC
1 GTAAAATGAC
35407746 TATTTTTCCC
Statistics
Matches: 72, Mismatches: 13, Indels: 9
0.77 0.14 0.10
Matches are distributed among these distances:
26 32 0.44
27 34 0.47
28 6 0.08
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.19
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTGTAGG
Found at i:35407742 original size:26 final size:28
Alignment explanation
Indices: 35407630--35407745 Score: 97
Period size: 26 Copynumber: 4.4 Consensus size: 28
35407620 CCCGATATTT
*
35407630 GTAAAATGACCATAAT-ACCCCTGT-AGG
1 GTAAAATGACCGTAATGACCCC-GTAAGG
* * * *
35407657 GTAAAATAACTG-AA-AACCCC-CATAGG
1 GTAAAATGACCGTAATGACCCCGTA-AGG
35407683 GTAAAATGACCGTAATGACCCCGTAA-G
1 GTAAAATGACCGTAATGACCCCGTAAGG
35407710 GTAAAATGACCGTAATG-CCCC-TAGAGG
1 GTAAAATGACCGTAATGACCCCGTA-AGG
35407737 GT-AAATGAC
1 GTAAAATGAC
35407746 TATTTTTCCC
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
25 2 0.03
26 32 0.44
27 32 0.44
28 6 0.08
29 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.19
Consensus pattern (28 bp):
GTAAAATGACCGTAATGACCCCGTAAGG
Found at i:35407793 original size:24 final size:24
Alignment explanation
Indices: 35407762--35407872 Score: 118
Period size: 24 Copynumber: 4.6 Consensus size: 24
35407752 TCCCCTCGAG
* *
35407762 TGTAAATGATTGATTTGTCCGTGA
1 TGTAAATGACTGATTTGTCTGTGA
*
35407786 TGTAAATGACTAATTTGTCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
*
35407810 TTTAAATGACTGATTTGTCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
*
35407834 TTGGT--ATGATTGATTTGTCTGTGA
1 -T-GTAAATGACTGATTTGTCTGTGA
* **
35407858 TTTGTATGACTGATT
1 TGTAAATGACTGATT
35407873 CTGAGCATGG
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 70 0.95
25 1 0.01
26 1 0.01
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.46
Consensus pattern (24 bp):
TGTAAATGACTGATTTGTCTGTGA
Found at i:35407824 original size:48 final size:48
Alignment explanation
Indices: 35407764--35407872 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
35407754 CCCTCGAGTG
*
35407764 TAAATGATTGATTTGTCCGTGA-T-GTAAATGACTAATTTGTCTGTGATT
1 TAAATGACTGATTTGTCCGTGATTGGT--ATGACTAATTTGTCTGTGATT
* * *
35407812 TAAATGACTGATTTGTCTGTGATTGGTATGATTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCCGTGATTGGTATGACTAATTTGTCTGTGATT
**
35407860 TGTATGACTGATT
1 TAAATGACTGATT
35407873 CTGAGCATGG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 50 0.94
49 1 0.02
50 2 0.04
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (48 bp):
TAAATGACTGATTTGTCCGTGATTGGTATGACTAATTTGTCTGTGATT
Found at i:35407860 original size:11 final size:11
Alignment explanation
Indices: 35407820--35407862 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
35407810 TTTAAATGAC
35407820 TGATTTGTCTG
1 TGATTTGTCTG
* *
35407831 TGATTGGTATG
1 TGATTTGTCTG
35407842 ATTGATTTGTCTG
1 --TGATTTGTCTG
35407855 TGATTTGT
1 TGATTTGT
35407863 ATGACTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.14, C:0.05, G:0.28, T:0.53
Consensus pattern (11 bp):
TGATTTGTCTG
Found at i:35407997 original size:27 final size:27
Alignment explanation
Indices: 35407941--35407997 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
35407931 GGAAGTACTG
* *
35407941 TACTGGTGGCTCTGCCACAATCACTGT
1 TACTAGTGGCTCTGCCACAATCACTAT
35407968 TACTAGTGGCT-TGGCCACATAT-ACTAT
1 TACTAGTGGCTCT-GCCACA-ATCACTAT
35407995 TAC
1 TAC
35407998 AGGAAGCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 1 0.04
27 23 0.88
28 2 0.08
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (27 bp):
TACTAGTGGCTCTGCCACAATCACTAT
Found at i:35408085 original size:32 final size:32
Alignment explanation
Indices: 35408044--35408214 Score: 204
Period size: 32 Copynumber: 5.4 Consensus size: 32
35408034 GCTGCGATTC
*
35408044 TACTGATGGCTTTGTGTCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
35408076 TACTGATGGCTTTGTGTCGATCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
35408108 TACT-AGTGGCTTTGTGCCGATCATATTACCAT
1 TACTGA-TGGCTTTGTGCCGATCATATTACCGT
* * * *
35408140 TATTGATGG-TTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTT-TGTGCCGATCATATTACCGT
* *
35408172 TACTGATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
35408203 TACTTATGGCTT
1 TACTGATGGCTT
35408215 GTAGCCATTC
Statistics
Matches: 124, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
31 14 0.11
32 107 0.86
33 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:35408816 original size:14 final size:14
Alignment explanation
Indices: 35408797--35408826 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35408787 AAGTCCTCAA
*
35408797 AAATTTTGGATTTT
1 AAATTTGGGATTTT
35408811 AAATTTGGGATTTT
1 AAATTTGGGATTTT
35408825 AA
1 AA
35408827 TGATTGTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (14 bp):
AAATTTGGGATTTT
Found at i:35411401 original size:42 final size:43
Alignment explanation
Indices: 35411322--35411420 Score: 132
Period size: 42 Copynumber: 2.3 Consensus size: 43
35411312 TCTCGGACGT
*
35411322 GGTCTTACATGTAATCAACTATCGATGCCACTGTCCCAAACAG
1 GGTCTTACATGTAATCAACTATCGATGCCAATGTCCCAAACAG
*
35411365 GGTCTTACAT-TAAATC-A-TATACGATGCCAATGTCCCAAACAT
1 GGTCTTACATGT-AATCAACTAT-CGATGCCAATGTCCCAAACAG
*
35411407 GGTCTTACACGTAA
1 GGTCTTACATGTAA
35411421 ATCTCAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
41 3 0.06
42 32 0.64
43 15 0.30
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (43 bp):
GGTCTTACATGTAATCAACTATCGATGCCAATGTCCCAAACAG
Found at i:35411423 original size:43 final size:45
Alignment explanation
Indices: 35411321--35411518 Score: 184
Period size: 43 Copynumber: 4.6 Consensus size: 45
35411311 GTCTCGGACG
* * * *
35411321 TGGTCTTACATGT-AATCAAC-TATCGATGCCACTGTCCCAAACA
1 TGGTCTTACACGTAAATCATCAAATCGATGCCAATGTCCCAAACA
* * *
35411364 GGGTCTTACA-TTAAATCAT-ATA-CGATGCCAATGTCCCAAACA
1 TGGTCTTACACGTAAATCATCAAATCGATGCCAATGTCCCAAACA
* ** * *
35411406 TGGTCTTACACGTAAATC-TCAAATTGATGCCAACATCCCAGACG
1 TGGTCTTACACGTAAATCATCAAATCGATGCCAATGTCCCAAACA
*
35411450 TGGTCTTACAC--AAATTC-TCAAATCGATGCCAATGTCCCAGACA
1 TGGTCTTACACGTAAA-TCATCAAATCGATGCCAATGTCCCAAACA
*
35411493 TGGTCTTACACG-AAATCA-CATATCGA
1 TGGTCTTACACGTAAATCATCAAATCGA
35411519 AGTCCTATTT
Statistics
Matches: 130, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
42 33 0.25
43 68 0.52
44 29 0.22
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (45 bp):
TGGTCTTACACGTAAATCATCAAATCGATGCCAATGTCCCAAACA
Found at i:35411454 original size:44 final size:43
Alignment explanation
Indices: 35411342--35411518 Score: 189
Period size: 43 Copynumber: 4.1 Consensus size: 43
35411332 GTAATCAACT
* * * ** *
35411342 ATCGATGCCACTGTCCCAAACAGGGTCTTACATTAAA--TCAT
1 ATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCTCAA
*
35411383 ATACGATGCCAATGTCCCAAACATGGTCTTACACGTAAATCTCAA
1 AT-CGATGCCAATGTCCCAGACATGGTCTTACACG-AAATCTCAA
* ** *
35411428 ATTGATGCCAACATCCCAGACGTGGTCTTACAC-AAATTCTCAA
1 ATCGATGCCAATGTCCCAGACATGGTCTTACACGAAA-TCTCAA
* *
35411471 ATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCACAT
1 ATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCTCAA
35411514 ATCGA
1 ATCGA
35411519 AGTCCTATTT
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
41 2 0.02
42 31 0.27
43 47 0.41
44 29 0.25
45 5 0.04
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (43 bp):
ATCGATGCCAATGTCCCAGACATGGTCTTACACGAAATCTCAA
Found at i:35413802 original size:16 final size:15
Alignment explanation
Indices: 35413783--35413818 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
35413773 TCACTTTTTT
35413783 TATATGTTAAATATAG
1 TATAT-TTAAATATAG
35413799 TATAATTTAAATATAG
1 TAT-ATTTAAATATAG
35413815 TATA
1 TATA
35413819 GTCTAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.05
16 16 0.84
17 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (15 bp):
TATATTTAAATATAG
Found at i:35413825 original size:16 final size:16
Alignment explanation
Indices: 35413790--35413825 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
35413780 TTTTATATGT
*
35413790 TAAATATAGTATAATT
1 TAAATATAGTATAATC
*
35413806 TAAATATAGTATAGTC
1 TAAATATAGTATAATC
35413822 TAAA
1 TAAA
35413826 ACACCTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (16 bp):
TAAATATAGTATAATC
Found at i:35414283 original size:26 final size:26
Alignment explanation
Indices: 35414239--35414289 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
35414229 TTGAACCTCG
* * *
35414239 AGGTTCAAGGTTTGGGTTTGGATTTA
1 AGGTTCAAGGCTTGAGTTTGAATTTA
*
35414265 AGGTTCAGGGCTTGAGTTTGAATTT
1 AGGTTCAAGGCTTGAGTTTGAATTT
35414290 TGAGTTCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.06, G:0.33, T:0.41
Consensus pattern (26 bp):
AGGTTCAAGGCTTGAGTTTGAATTTA
Found at i:35420976 original size:35 final size:35
Alignment explanation
Indices: 35420925--35421014 Score: 117
Period size: 35 Copynumber: 2.6 Consensus size: 35
35420915 CAGTGGCATA
** *
35420925 CTTAACATACGAATCAGAATCAAAATAGTAACATG
1 CTTAACATGTGAATCAGAATCAAAATAATAACATG
* * **
35420960 GTTAACATGTGTATCAGAATCAAAATAATGGCATG
1 CTTAACATGTGAATCAGAATCAAAATAATAACATG
35420995 CTTAACATGTGAATCAGAAT
1 CTTAACATGTGAATCAGAAT
35421015 ATCAACAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (35 bp):
CTTAACATGTGAATCAGAATCAAAATAATAACATG
Found at i:35421140 original size:27 final size:26
Alignment explanation
Indices: 35421089--35421141 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
35421079 TGAGTATTAG
**
35421089 GAAAACGTATATCAACATATTTAATA
1 GAAAACGTATATCAACATACATAATA
35421115 GAAAATCGTATAATC-ACATACATAATA
1 GAAAA-CGTAT-ATCAACATACATAATA
35421142 TTACAGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 15 0.65
28 3 0.13
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (26 bp):
GAAAACGTATATCAACATACATAATA
Found at i:35423342 original size:14 final size:14
Alignment explanation
Indices: 35423322--35423357 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
35423312 TAGTGGTGGT
35423322 GAAAGAAAGGAAAA
1 GAAAGAAAGGAAAA
* *
35423336 TAAAGAAAGTAAAA
1 GAAAGAAAGGAAAA
35423350 GAAAGAAA
1 GAAAGAAA
35423358 AAAACAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (14 bp):
GAAAGAAAGGAAAA
Found at i:35429978 original size:23 final size:22
Alignment explanation
Indices: 35429935--35429978 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
35429925 TTCTAAGTTG
35429935 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
35429958 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
35429979 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:35430180 original size:51 final size:50
Alignment explanation
Indices: 35430122--35430308 Score: 214
Period size: 51 Copynumber: 3.7 Consensus size: 50
35430112 TCAGTTCACA
*
35430122 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCTGGTACACG
* * * * ***
35430173 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCTGGTACGTA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATCTGGTACACG
* * * *
35430224 TAGTAGGCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCTGGTACACG
* *
35430274 TAGTAGCTTACACATAGTACTACACATGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
35430309 CACTTTCCCT
Statistics
Matches: 110, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
49 2 0.02
50 37 0.34
51 69 0.63
52 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCTGGTACACG
Found at i:35430298 original size:101 final size:101
Alignment explanation
Indices: 35430121--35430304 Score: 271
Period size: 101 Copynumber: 1.8 Consensus size: 101
35430111 TTCAGTTCAC
* * *
35430121 ATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTGATACACGTAGTAGCCTGCAC
1 ATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTACAC
35430186 ATAGTACTACACACGTGATCGAAACTATCTGGTACGT
65 ATAGTACTACACACGTGATCGAAACTATCTGGTACGT
* * * *
35430223 ATAGTAGGCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCTTACAC
1 ATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTACAC
*
35430287 ATAGTACTACACATGTGA
65 ATAGTACTACACACGTGA
35430305 CCATCACTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
100 4 0.05
101 37 0.51
102 32 0.44
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (101 bp):
ATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTACACA
TAGTACTACACACGTGATCGAAACTATCTGGTACGT
Found at i:35433214 original size:20 final size:19
Alignment explanation
Indices: 35433159--35433203 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
35433149 CATTTCATTG
*
35433159 AGCTCCAATTAGCTCATTTCC
1 AGCTCC-ATGAGCTCATTT-C
*
35433180 AGCTCCATGAACTCATTTC
1 AGCTCCATGAGCTCATTTC
35433199 AGCTC
1 AGCTC
35433204 ATTTGAGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.31
Consensus pattern (19 bp):
AGCTCCATGAGCTCATTTC
Found at i:35438428 original size:33 final size:35
Alignment explanation
Indices: 35438342--35438431 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 35
35438332 ATACATACTA
35438342 CCATGGTCCAACCATGGTCTTACATCTGAAAAACTG
1 CCATGGTCCAACCATGGTCTTACA-CTGAAAAACTG
* * * * * *
35438378 CCATAG-CCTCACTATGGTCTTAC-GT-AAACATTG
1 CCATGGTCC-AACCATGGTCTTACACTGAAAAACTG
35438411 CCATGGTCCAACCATGGTCTT
1 CCATGGTCCAACCATGGTCTT
35438432 GTACTTTTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
33 21 0.49
34 3 0.07
35 2 0.05
36 17 0.40
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (35 bp):
CCATGGTCCAACCATGGTCTTACACTGAAAAACTG
Found at i:35442257 original size:17 final size:18
Alignment explanation
Indices: 35442215--35442250 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35442205 AATCAAAATC
*
35442215 ATGATTTTGAAATGGAAA
1 ATGATATTGAAATGGAAA
35442233 ATGATATTGAAATGGAAA
1 ATGATATTGAAATGGAAA
35442251 TGGTATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (18 bp):
ATGATATTGAAATGGAAA
Found at i:35443187 original size:23 final size:23
Alignment explanation
Indices: 35443160--35443206 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
35443150 CACTATAAAT
35443160 ACCCACCTCTATTCTTCATTTTC
1 ACCCACCTCTATTCTTCATTTTC
35443183 ACCCACCTCTATTCTTCATTTTC
1 ACCCACCTCTATTCTTCATTTTC
35443206 A
1 A
35443207 TGATCATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.43
Consensus pattern (23 bp):
ACCCACCTCTATTCTTCATTTTC
Found at i:35444180 original size:29 final size:29
Alignment explanation
Indices: 35444132--35444188 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
35444122 GCTAGGGACT
*
35444132 AAATTGTAATAAATGTAAAAGTTTAGGGA
1 AAATTGTAATAAATGTAAAAGTTAAGGGA
*
35444161 AAATGTGTAATTAATG-AAAAGTTAAGGG
1 AAAT-TGTAATAAATGTAAAAGTTAAGGG
35444189 TCAAATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (29 bp):
AAATTGTAATAAATGTAAAAGTTAAGGGA
Found at i:35447646 original size:39 final size:38
Alignment explanation
Indices: 35447527--35447679 Score: 143
Period size: 38 Copynumber: 4.0 Consensus size: 38
35447517 AGTTTAAGTC
* *
35447527 TTTAATTATGTCATAATTTGAACATCATTAATATGA-GT
1 TTTAATTATGTCATAATTTGAACATCTTTAATA-CATGT
* *
35447565 TTTAATTATGTCATAATCTGAACATCTTTAATA-AGGGTT
1 TTTAATTATGTCATAATTTGAACATCTTTAATACA-TG-T
* * *
35447604 TTTAATTATGTCATAGTTTAGGACATCTTAAATACATGT
1 TTTAATTATGTCATAATTT-GAACATCTTTAATACATGT
* *
35447643 TTT-ATATATGTCCTAGTTT-AGACATCTTTAATACATG
1 TTTAAT-TATGTCATAATTTGA-ACATCTTTAATACATG
35447680 CCTTTAGCTC
Statistics
Matches: 98, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
36 1 0.01
38 49 0.50
39 34 0.35
40 13 0.13
41 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.44
Consensus pattern (38 bp):
TTTAATTATGTCATAATTTGAACATCTTTAATACATGT
Found at i:35451471 original size:22 final size:22
Alignment explanation
Indices: 35451443--35451497 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
35451433 TAATGCCTAG
*
35451443 CAGGCTTAGTGTCGGTGTTAGT
1 CAGGCTTAGTGTCGATGTTAGT
*
35451465 CAGGCTTAGTGTCGATGTTATT
1 CAGGCTTAGTGTCGATGTTAGT
35451487 CAGGCTTAGTG
1 CAGGCTTAGTG
35451498 CCTAGCAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.16, C:0.15, G:0.33, T:0.36
Consensus pattern (22 bp):
CAGGCTTAGTGTCGATGTTAGT
Found at i:35455562 original size:26 final size:26
Alignment explanation
Indices: 35455510--35455562 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
35455500 CACCAATATC
* * *
35455510 GCAGTATAGGTGCCAGTAGTAATAAT
1 GCAGTAGAGCTGCCAGTAGTAAGAAT
* *
35455536 GCAGTAGAGCTGCTAGTAGTCAGAAT
1 GCAGTAGAGCTGCCAGTAGTAAGAAT
35455562 G
1 G
35455563 GCTAAGACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (26 bp):
GCAGTAGAGCTGCCAGTAGTAAGAAT
Found at i:35455670 original size:32 final size:32
Alignment explanation
Indices: 35455612--35455845 Score: 213
Period size: 32 Copynumber: 7.4 Consensus size: 32
35455602 GAATGGCTAC
* * *
35455612 AAGCCATAAGT-ACAGTAATGTGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
35455643 AAGCCATCAGTAGCAGTGATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * * *
35455675 CAGCCATCAGCAACGGTAACATGATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
35455707 AAGCCAT-AGTAGCAGTGATATGATCAGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
35455738 CAGCCATCAGTAACAGTGAA-ATGATCGGCACA
1 AAGCCATCAGTAACAGT-AATATGATCGGCACA
* * * *
35455770 TAGCCACCAGTAATAGTAATATGATCAGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * * *
35455802 AAGCCATTAGTAACGGTACTATGACCGGAACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
35455834 AAGCCATCAGTA
1 AAGCCATCAGTA
35455846 GCATCGCAGC
Statistics
Matches: 161, Mismatches: 38, Indels: 7
0.78 0.18 0.03
Matches are distributed among these distances:
31 36 0.22
32 124 0.77
33 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:35455898 original size:27 final size:26
Alignment explanation
Indices: 35455863--35455927 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
35455853 AGCAAAGTTG
*
35455863 CCAGCAACAGTATATGTGGCCA-AGCCA
1 CCAGTAACAGTAT-TGTGG-CAGAGCCA
35455890 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGT-ATTGTGGCAGAGCCA
*
35455917 CCAAT-ACAGTA
1 CCAGTAACAGTA
35455928 CTTCCTCCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 7 0.21
27 24 0.71
28 2 0.06
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGTAACAGTATTGTGGCAGAGCCA
Found at i:35456024 original size:24 final size:23
Alignment explanation
Indices: 35455997--35456059 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
35455987 TCAGAATCAA
*
35455997 TCATTCAAATCACAGACAAACCAG
1 TCATTCAAA-CACAAACAAACCAG
* *
35456021 TCATACCAAACACAAACAAATCAG
1 TCAT-TCAAACACAAACAAACCAG
* *
35456045 TCATTTAACCACAAA
1 TCATTCAAACACAAA
35456060 TAAAACAATC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 8 0.25
24 20 0.62
25 4 0.12
ACGTcount: A:0.49, C:0.29, G:0.05, T:0.17
Consensus pattern (23 bp):
TCATTCAAACACAAACAAACCAG
Found at i:35456071 original size:23 final size:23
Alignment explanation
Indices: 35456031--35456077 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
35456021 TCATACCAAA
* *
35456031 CACAAACAAATCAGTCATTTAAC
1 CACAAACAAAACAATCATTTAAC
*
35456054 CACAAATAAAACAATCATTTAAC
1 CACAAACAAAACAATCATTTAAC
35456077 C
1 C
35456078 TTGGGAGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.51, C:0.26, G:0.02, T:0.21
Consensus pattern (23 bp):
CACAAACAAAACAATCATTTAAC
Found at i:35456151 original size:27 final size:27
Alignment explanation
Indices: 35456112--35456289 Score: 126
Period size: 27 Copynumber: 6.6 Consensus size: 27
35456102 CCACCAGGGC
35456112 ATTACAGTCATTTTACCCTATAGGGGT
1 ATTACAGTCATTTTACCCTATAGGGGT
* *
35456139 GTTACTGTCATTTTACCCTAT-GGGGT
1 ATTACAGTCATTTTACCCTATAGGGGT
** * * *
35456165 ATT-TTGATTATTTTACCCTATGGGGGC
1 ATTACAG-TCATTTTACCCTATAGGGGT
** * *
35456192 ATTTTAGTCATTCTACCCTATGGGGGT
1 ATTACAGTCATTTTACCCTATAGGGGT
* * *
35456219 ATTTCAGACATTTTTCCCTATAGGGGT
1 ATTACAGTCATTTTACCCTATAGGGGT
*** * * *
35456246 ATTTTGGTCATTTTATCTTATAGAGGT
1 ATTACAGTCATTTTACCCTATAGGGGT
***
35456273 ATTTTGGTCATTTTACC
1 ATTACAGTCATTTTACC
35456290 TATTTTAGGG
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
25 2 0.02
26 20 0.16
27 101 0.81
28 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (27 bp):
ATTACAGTCATTTTACCCTATAGGGGT
Found at i:35456178 original size:53 final size:53
Alignment explanation
Indices: 35456119--35456289 Score: 166
Period size: 54 Copynumber: 3.2 Consensus size: 53
35456109 GGCATTACAG
*
35456119 TCATTTTACCCTATAGGGGTGTTACTGTCATTTTACCCTAT-GGGGTATTTTGA
1 TCATTTTACCCTATAGGGGTATTA-TGTCATTTTACCCTATAGGGGTATTTTGA
* * * * * * *
35456172 TTATTTTACCCTATGGGGGCATTTTAGTCATTCTACCCTATGGGGGTATTTCAGA
1 TCATTTTACCCTATAGGGGTATTAT-GTCATTTTACCCTATAGGGGTATTT-TGA
* * * * * *
35456227 -CATTTTTCCCTATAGGGGTATTTTGGTCATTTTATCTTATAGAGGTATTTTGG
1 TCATTTTACCCTATAGGGGTATTAT-GTCATTTTACCCTATAGGGGTATTTTGA
35456280 TCATTTTACC
1 TCATTTTACC
35456290 TATTTTAGGG
Statistics
Matches: 94, Mismatches: 20, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
52 1 0.01
53 34 0.36
54 57 0.61
55 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.20, T:0.44
Consensus pattern (53 bp):
TCATTTTACCCTATAGGGGTATTATGTCATTTTACCCTATAGGGGTATTTTGA
Found at i:35456209 original size:80 final size:81
Alignment explanation
Indices: 35456108--35456260 Score: 200
Period size: 80 Copynumber: 1.9 Consensus size: 81
35456098 TTACCCACCA
* * * *
35456108 GGGCATTACAGTCATTTTACCCTATAGGGGTGTTACTGTCATTTTACCCTAT-GGGGTATTTTGA
1 GGGCATTACAGTCATTCTACCCTATAGGGGTATTACAGACATTTTACCCTATAGGGGTATTTTGA
*
35456172 TTATTTTACCCTATGG
66 TCATTTTACCCTATGG
** * * * *
35456188 GGGCATTTTAGTCATTCTACCCTATGGGGGTATTTCAGACATTTTTCCCTATAGGGGTATTTTGG
1 GGGCATTACAGTCATTCTACCCTATAGGGGTATTACAGACATTTTACCCTATAGGGGTATTTTGA
35456253 TCATTTTA
66 TCATTTTA
35456261 TCTTATAGAG
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
80 43 0.70
81 18 0.30
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.42
Consensus pattern (81 bp):
GGGCATTACAGTCATTCTACCCTATAGGGGTATTACAGACATTTTACCCTATAGGGGTATTTTGA
TCATTTTACCCTATGG
Found at i:35459442 original size:16 final size:16
Alignment explanation
Indices: 35459421--35459454 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
35459411 GACGAGTGAA
35459421 TTATTATTTATTTATT
1 TTATTATTTATTTATT
35459437 TTATTATTTATTTATT
1 TTATTATTTATTTATT
35459453 TT
1 TT
35459455 CTACGAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTATTTATTTATT
Found at i:35460534 original size:22 final size:22
Alignment explanation
Indices: 35460509--35460561 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
35460499 TAGTGCCTAG
35460509 CAGGCTTAGTACCGGTGCTATT
1 CAGGCTTAGTACCGGTGCTATT
* * *
35460531 CAGGCTTAGTGCCGGTGTTGTT
1 CAGGCTTAGTACCGGTGCTATT
35460553 CAGGCTTAG
1 CAGGCTTAG
35460562 AGTCTAGCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (22 bp):
CAGGCTTAGTACCGGTGCTATT
Found at i:35460596 original size:60 final size:60
Alignment explanation
Indices: 35460488--35460620 Score: 176
Period size: 60 Copynumber: 2.2 Consensus size: 60
35460478 AATCATACTA
* * *
35460488 TTATTCAAGCTTAGTGCCTAGCAGGCTTAGTACCGGTGCTATTCAGGCTTAGTGCCGGTG
1 TTATTCAAGCTTAGAGCCTAGCAAGCTTAGTACCGGTGCTATTCAGGCTTAGTGCCAGTG
* * * * * * *
35460548 TTGTTCAGGCTTAGAGTCTAGCAAGCTTAGTGCCGGTGTTATTTAGGCTTTGTGCCAGTG
1 TTATTCAAGCTTAGAGCCTAGCAAGCTTAGTACCGGTGCTATTCAGGCTTAGTGCCAGTG
35460608 TTATTCAAGCTTA
1 TTATTCAAGCTTA
35460621 TTGTGGGTAT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (60 bp):
TTATTCAAGCTTAGAGCCTAGCAAGCTTAGTACCGGTGCTATTCAGGCTTAGTGCCAGTG
Found at i:35460619 original size:22 final size:22
Alignment explanation
Indices: 35460569--35460620 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
35460559 TAGAGTCTAG
*
35460569 CAAGCTTAGTGCCGGTGTTATT
1 CAAGCTTAGTGCCAGTGTTATT
* * *
35460591 TAGGCTTTGTGCCAGTGTTATT
1 CAAGCTTAGTGCCAGTGTTATT
35460613 CAAGCTTA
1 CAAGCTTA
35460621 TTGTGGGTAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (22 bp):
CAAGCTTAGTGCCAGTGTTATT
Found at i:35464698 original size:23 final size:22
Alignment explanation
Indices: 35464672--35464714 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
35464662 AAATGGTTTA
35464672 TTTA-CCATTTAAGTCCATTTACT
1 TTTATCCA-TTAAGT-CATTTACT
*
35464695 TTTATTCATTAAGTCATTTA
1 TTTATCCATTAAGTCATTTA
35464715 ATCATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.33
23 10 0.56
24 2 0.11
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTATCCATTAAGTCATTTACT
Found at i:35468522 original size:19 final size:20
Alignment explanation
Indices: 35468477--35468522 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
35468467 CTTGTACGGG
35468477 ATTGCACTTCAGTGCCACTA
1 ATTGCACTTCAGTGCCACTA
* * *
35468497 TTTGCACTTCGGTGCCTC-A
1 ATTGCACTTCAGTGCCACTA
35468516 ATTGCAC
1 ATTGCAC
35468523 AATCATGCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (20 bp):
ATTGCACTTCAGTGCCACTA
Found at i:35473008 original size:21 final size:22
Alignment explanation
Indices: 35472946--35473044 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 22
35472936 CTAAATTATT
* *
35472946 CCCTAAATTGCACATAC-GTGC
1 CCCTGAATTGCACATACAGTAC
* * *
35472967 CCCT-ATTTGTAC-TTCAGTAC
1 CCCTGAATTGCACATACAGTAC
*
35472987 CCTTGAATTGCACATACA-TAC
1 CCCTGAATTGCACATACAGTAC
* * *
35473008 CCCTG-TTTGTAC-TTCAGTAC
1 CCCTGAATTGCACATACAGTAC
35473028 CCCTGAATTGCACATAC
1 CCCTGAATTGCACATAC
35473045 GTGCCCATGT
Statistics
Matches: 57, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
19 5 0.09
20 25 0.44
21 22 0.39
22 5 0.09
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.31
Consensus pattern (22 bp):
CCCTGAATTGCACATACAGTAC
Found at i:35473011 original size:41 final size:41
Alignment explanation
Indices: 35472951--35473117 Score: 201
Period size: 41 Copynumber: 4.1 Consensus size: 41
35472941 TTATTCCCTA
*
35472951 AATTGCACATACGTGCCCCTATTTGTACTTCAGTACCCTTG
1 AATTGCACATACGTGCCCCTGTTTGTACTTCAGTACCCTTG
* * *
35472992 AATTGCACATACATACCCCTGTTTGTACTTCAGTACCCCTG
1 AATTGCACATACGTGCCCCTGTTTGTACTTCAGTACCCTTG
* *
35473033 AATTGCACATACGTGCCCATGTTTGTACTT-TGATACCCTTG
1 AATTGCACATACGTGCCCCTGTTTGTACTTCAG-TACCCTTG
* * * * * * *
35473074 AATAGCACATATGTGCCCTTGTTTATACTCCGGTAACCTTG
1 AATTGCACATACGTGCCCCTGTTTGTACTTCAGTACCCTTG
35473115 AAT
1 AAT
35473118 CGAGTAAAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
40 1 0.01
41 106 0.98
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (41 bp):
AATTGCACATACGTGCCCCTGTTTGTACTTCAGTACCCTTG
Found at i:35474100 original size:54 final size:54
Alignment explanation
Indices: 35474040--35474212 Score: 145
Period size: 54 Copynumber: 3.2 Consensus size: 54
35474030 CAACTCAAAG
*
35474040 TGTTACACGGGTACAGACACGGGCTGGGACACGGCCATGTGTCCCTATTTTGAT
1 TGTTACACGGGTACAGACACGGGCTGGGACATGGCCATGTGTCCCTATTTTGAT
** * * * * * ** *
35474094 TGTTACACAGCCTAGCAG--ACGGTCTTGTGG-CTTGGCCATGTGGCCCAACTTAAAG
1 TGTTACAC-GGGTA-CAGACACGGGC-TG-GGACATGGCCATGTGTCCCTATTTTGAT
* * * * *
35474149 AGTTGCACGGGCACAGACACGGGCTGAGACATGGCCATGTGTCCCTCTTTTGAT
1 TGTTACACGGGTACAGACACGGGCTGGGACATGGCCATGTGTCCCTATTTTGAT
35474203 TGTTACACGG
1 TGTTACACGG
35474213 CCTGGCCACA
Statistics
Matches: 84, Mismatches: 28, Indels: 14
0.67 0.22 0.11
Matches are distributed among these distances:
53 4 0.05
54 42 0.50
55 33 0.39
56 5 0.06
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (54 bp):
TGTTACACGGGTACAGACACGGGCTGGGACATGGCCATGTGTCCCTATTTTGAT
Found at i:35474133 original size:109 final size:109
Alignment explanation
Indices: 35473985--35474215 Score: 336
Period size: 109 Copynumber: 2.1 Consensus size: 109
35473975 CATTTTTTAG
** * *
35473985 TGTTACATTGCCTGGCACACGGGCTTGTGGCTTGGCCATGTGACCCAACTCAAAGTGTTACACGG
1 TGTTACACAGCCTAGCACACGGGCTTGTGGCTTGGCCATGTGACCCAACTCAAAGAGTTACACGG
* *
35474050 GTACAGACACGGGCTGGGACACGGCCATGTGTCCCTATTTTGAT
66 GCACAGACACGGGCTGAGACACGGCCATGTGTCCCTATTTTGAT
* * * * *
35474094 TGTTACACAGCCTAGCAGACGGTCTTGTGGCTTGGCCATGTGGCCCAACTTAAAGAGTTGCACGG
1 TGTTACACAGCCTAGCACACGGGCTTGTGGCTTGGCCATGTGACCCAACTCAAAGAGTTACACGG
* *
35474159 GCACAGACACGGGCTGAGACATGGCCATGTGTCCCTCTTTTGAT
66 GCACAGACACGGGCTGAGACACGGCCATGTGTCCCTATTTTGAT
*
35474203 TGTTACACGGCCT
1 TGTTACACAGCCT
35474216 GGCCACACAG
Statistics
Matches: 108, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (109 bp):
TGTTACACAGCCTAGCACACGGGCTTGTGGCTTGGCCATGTGACCCAACTCAAAGAGTTACACGG
GCACAGACACGGGCTGAGACACGGCCATGTGTCCCTATTTTGAT
Found at i:35477293 original size:29 final size:29
Alignment explanation
Indices: 35477220--35477337 Score: 155
Period size: 29 Copynumber: 3.9 Consensus size: 29
35477210 AATGGTAAGA
*
35477220 ACCATCCCTTTTCATTAATCGATGGTCGTCATC
1 ACCATCCCTTTTCA-TAATTGATGGTCG---TC
* *
35477253 ACCATCCATTTTCATAGTTGATGGTCGTC
1 ACCATCCCTTTTCATAATTGATGGTCGTC
35477282 ACCATCCCTTTTCATAATTGATGGTCGTC
1 ACCATCCCTTTTCATAATTGATGGTCGTC
* *
35477311 ACCATCCCTTTTCATAATCGATAGTCG
1 ACCATCCCTTTTCATAATTGATGGTCG
35477338 AAGCTATACC
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
29 54 0.69
32 11 0.14
33 13 0.17
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (29 bp):
ACCATCCCTTTTCATAATTGATGGTCGTC
Found at i:35477349 original size:29 final size:28
Alignment explanation
Indices: 35477317--35477379 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
35477307 CGTCACCATC
*
35477317 CCTTTTCATAATCGATAGTCGAAGCTAT
1 CCTTTTCATAATCGATAGCCGAAGCTAT
* * *
35477345 ACCTTTTCATATTTGATTGCCGAAGCTAT
1 -CCTTTTCATAATCGATAGCCGAAGCTAT
35477374 CCTTTT
1 CCTTTT
35477380 TCATTGGTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (28 bp):
CCTTTTCATAATCGATAGCCGAAGCTAT
Found at i:35477350 original size:58 final size:59
Alignment explanation
Indices: 35477219--35477361 Score: 146
Period size: 58 Copynumber: 2.4 Consensus size: 59
35477209 CAATGGTAAG
* * * * *
35477219 AACCATCCCTTTTCATTAATCGATGGTCGTCATCACCATCCATTTTCATAGTTGATGGTCGT
1 AACCATACCTTTTCA-TAATTGATGGTCG--ATCACCATCCATTTTCATAATCGATAGTCGT
* * *
35477281 CACCATCCCTTTTCATAATTGATGGTCG-TCACCATCCCTTTTCATAATCGATAGTCG-
1 AACCATACCTTTTCATAATTGATGGTCGATCACCATCCATTTTCATAATCGATAGTCGT
* *
35477338 AAGCTATACCTTTTCATATTTGAT
1 AA-CCATACCTTTTCATAATTGAT
35477362 TGCCGAAGCT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
57 1 0.01
58 43 0.61
61 12 0.17
62 14 0.20
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.38
Consensus pattern (59 bp):
AACCATACCTTTTCATAATTGATGGTCGATCACCATCCATTTTCATAATCGATAGTCGT
Found at i:35479261 original size:91 final size:91
Alignment explanation
Indices: 35479106--35479293 Score: 376
Period size: 91 Copynumber: 2.1 Consensus size: 91
35479096 TGGCCATATC
35479106 TTTGGTAATTTTTTTATTGATGGGTTTAGGCATGAATGATTAACTAATGATAAAACTTATTTCTT
1 TTTGGTAATTTTTTTATTGATGGGTTTAGGCATGAATGATTAACTAATGATAAAACTTATTTCTT
35479171 ATTTGTAACTTTATTCTTAAATTGAA
66 ATTTGTAACTTTATTCTTAAATTGAA
35479197 TTTGGTAATTTTTTTATTGATGGGTTTAGGCATGAATGATTAACTAATGATAAAACTTATTTCTT
1 TTTGGTAATTTTTTTATTGATGGGTTTAGGCATGAATGATTAACTAATGATAAAACTTATTTCTT
35479262 ATTTGTAACTTTATTCTTAAATTGAA
66 ATTTGTAACTTTATTCTTAAATTGAA
35479288 TTTGGT
1 TTTGGT
35479294 GTGTGGATTG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 97 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (91 bp):
TTTGGTAATTTTTTTATTGATGGGTTTAGGCATGAATGATTAACTAATGATAAAACTTATTTCTT
ATTTGTAACTTTATTCTTAAATTGAA
Found at i:35479694 original size:43 final size:43
Alignment explanation
Indices: 35479647--35479729 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
35479637 AACTCGACTA
* *
35479647 TGTGACCCAACTTCGAATACACACATGGTTTGACACACAGCCG
1 TGTGACCCAACTTCGAATACACACATGGGTAGACACACAGCCG
* * *
35479690 TGTGACCCTATTTCGAATATACACATGGGTAGACACACAG
1 TGTGACCCAACTTCGAATACACACATGGGTAGACACACAG
35479730 GTTGGAACAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (43 bp):
TGTGACCCAACTTCGAATACACACATGGGTAGACACACAGCCG
Found at i:35483383 original size:48 final size:48
Alignment explanation
Indices: 35483331--35483426 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
35483321 GCTTGGACGG
35483331 GTAACCTGACACATTTAATTTGTATCTGATTAGCTCTTAGGAGCATTA
1 GTAACCTGACACATTTAATTTGTATCTGATTAGCTCTTAGGAGCATTA
35483379 GTAACCTGACACATTTAATTTGTATCTGATTAGCTCTTAGGAGCATTA
1 GTAACCTGACACATTTAATTTGTATCTGATTAGCTCTTAGGAGCATTA
35483427 TCTATTTCTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (48 bp):
GTAACCTGACACATTTAATTTGTATCTGATTAGCTCTTAGGAGCATTA
Found at i:35485086 original size:10 final size:10
Alignment explanation
Indices: 35485071--35485124 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
35485061 CATGTGGTTC
35485071 AGCTCATTCG
1 AGCTCATTCG
35485081 AGCTCAAGTT--
1 AGCTC-A-TTCG
35485091 AGCTCATTCG
1 AGCTCATTCG
35485101 AGCTCAATTC-
1 AGCTC-ATTCG
35485111 AGCTCATT-G
1 AGCTCATTCG
35485120 AGCTC
1 AGCTC
35485125 GTTATTAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
8 2 0.05
9 9 0.24
10 20 0.53
11 5 0.13
12 2 0.05
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (10 bp):
AGCTCATTCG
Found at i:35485096 original size:20 final size:20
Alignment explanation
Indices: 35485068--35485124 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
35485058 TTTCATGTGG
35485068 TTCAGCTCATTCGAGCTCAA
1 TTCAGCTCATTCGAGCTCAA
35485088 GTT-AGCTCATTCGAGCTCAA
1 -TTCAGCTCATTCGAGCTCAA
35485108 TTCAGCTCATT-GAGCTC
1 TTCAGCTCATTCGAGCTC
35485125 GTTATTAGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.23
20 25 0.71
21 2 0.06
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.32
Consensus pattern (20 bp):
TTCAGCTCATTCGAGCTCAA
Found at i:35495616 original size:77 final size:76
Alignment explanation
Indices: 35495484--35495677 Score: 236
Period size: 77 Copynumber: 2.6 Consensus size: 76
35495474 TTTTTCCCTT
* * * * *
35495484 AAATCAGTTCCACC-CCCTAAAATCCCTAA-TTGTTTTCCCAATCCCTTTCTTTTTTTCCCCAAT
1 AAATCAGTTCCCCCTCCCTGAAATCCCTAATTTTTTTTCCCAATCCCTTTCTCTTTTTCCCCAAC
35495547 TTATTTTCACC
66 TTATTTTCACC
35495558 AAATCAGTTCCCCCTCCCTGAAATCCCTAACTTTTTTTTCCCAATTCCCTTTC-CTTTTTCCCCA
1 AAATCAGTTCCCCCTCCCTGAAATCCCTAA-TTTTTTTTCCCAA-TCCCTTTCTCTTTTTCCCCA
* *
35495622 ACTTCTTTTCCCC
64 ACTTATTTTCACC
* *
35495635 AAATTC-GTTCCCCCTCTCC-GAAATCCCTAATTCTTTTCCCCAA
1 AAA-TCAGTTCCCCCTC-CCTGAAATCCCTAATTTTTTTTCCCAA
35495678 AGCGCGTCTA
Statistics
Matches: 105, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
74 13 0.12
75 14 0.13
76 11 0.10
77 55 0.52
78 12 0.11
ACGTcount: A:0.21, C:0.38, G:0.03, T:0.39
Consensus pattern (76 bp):
AAATCAGTTCCCCCTCCCTGAAATCCCTAATTTTTTTTCCCAATCCCTTTCTCTTTTTCCCCAAC
TTATTTTCACC
Found at i:35500679 original size:30 final size:30
Alignment explanation
Indices: 35500639--35500698 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
35500629 AAAATCGTCG
* *
35500639 CTAAAGGTCTTGTTTTACAGCGGCGTTTGT
1 CTAAAGGTCTTGTTCTACAGCGGCATTTGT
* *
35500669 CTAAATGTCTTGTTCTATAGCGGCATTTGT
1 CTAAAGGTCTTGTTCTACAGCGGCATTTGT
35500699 GGAAAAACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.18, C:0.17, G:0.23, T:0.42
Consensus pattern (30 bp):
CTAAAGGTCTTGTTCTACAGCGGCATTTGT
Found at i:35500731 original size:42 final size:43
Alignment explanation
Indices: 35500669--35500777 Score: 139
Period size: 43 Copynumber: 2.6 Consensus size: 43
35500659 CGGCGTTTGT
* *
35500669 CTAAATGTCTTGTTCTATAGCGGCATTTGT-GGAAAAACACCA
1 CTAAAAGTCATGTTCTATAGCGGCATTTGTGGGAAAAACACCA
* * * * *
35500711 CTAAAAGTCATGTTTTATAGCGGCGTTTGTGGGAAAAGCGCCG
1 CTAAAAGTCATGTTCTATAGCGGCATTTGTGGGAAAAACACCA
*
35500754 CTAAAGGTCATGTTCTATAGCGGC
1 CTAAAAGTCATGTTCTATAGCGGC
35500778 TTTTTTATAT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
42 26 0.46
43 31 0.54
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (43 bp):
CTAAAAGTCATGTTCTATAGCGGCATTTGTGGGAAAAACACCA
Found at i:35501892 original size:13 final size:13
Alignment explanation
Indices: 35501876--35501902 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35501866 TAATTAAAGG
35501876 GTTAAAATTTAAA
1 GTTAAAATTTAAA
35501889 GTTAAAATTTAAA
1 GTTAAAATTTAAA
35501902 G
1 G
35501903 ATGATAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (13 bp):
GTTAAAATTTAAA
Found at i:35501967 original size:9 final size:9
Alignment explanation
Indices: 35501953--35502079 Score: 67
Period size: 9 Copynumber: 15.0 Consensus size: 9
35501943 AACTTTGGAT
35501953 CATAACTTA
1 CATAACTTA
35501962 CATAACTTA
1 CATAACTTA
35501971 CATAA--TA
1 CATAACTTA
*
35501978 CATAA-ATA
1 CATAACTTA
* * *
35501986 TATATCATA
1 CATAACTTA
35501995 TCAT-A-TT-
1 -CATAACTTA
35502002 -ATAACTTA
1 CATAACTTA
*
35502010 CATAACCTA
1 CATAACTTA
*
35502019 TATAACTTA
1 CATAACTTA
35502028 CATAACTTA
1 CATAACTTA
*
35502037 CATAA--TG
1 CATAACTTA
*
35502044 CATAA-ATA
1 CATAACTTA
* * *
35502052 TATATCATA
1 CATAACTTA
35502061 TCATAACTTA
1 -CATAACTTA
35502071 CATAACTTA
1 CATAACTTA
35502080 ATTATACTTA
Statistics
Matches: 92, Mismatches: 16, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
5 2 0.02
6 1 0.01
7 15 0.16
8 10 0.11
9 56 0.61
10 8 0.09
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:35502068 original size:61 final size:62
Alignment explanation
Indices: 35501954--35502076 Score: 194
Period size: 66 Copynumber: 1.9 Consensus size: 62
35501944 ACTTTGGATC
35501954 ATAACTTACATAACTTACATAATACATAAATATATATCATATCATATTATAACTTACATAACCTA
1 ATAACTTACATAACTTACATAATACATAAATATATATCATATC----TATAACTTACATAACCTA
35502019 T
62 T
*
35502020 ATAACTTACATAACTTACATAATGCATAAATATATATCATATC-ATAACTTACATAAC
1 ATAACTTACATAACTTACATAATACATAAATATATATCATATCTATAACTTACATAAC
35502077 TTAATTATAC
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
61 14 0.25
66 42 0.75
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.35
Consensus pattern (62 bp):
ATAACTTACATAACTTACATAATACATAAATATATATCATATCTATAACTTACATAACCTAT
Done.