Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 34 of 199
Found at i:9625908 original size:46 final size:46
Alignment explanation
Indices: 9625839--9625927 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
9625829 GTTATTGATC
* *
9625839 AGTGGTAGTTACGGCTACATATCAGTGGTAGCTTCAGCTACATTTT
1 AGTGGTAGCTACGACTACATATCAGTGGTAGCTTCAGCTACATTTT
* *
9625885 AGTGGTAGCTACGACTACGTATCAGTGGTAGCTTCGGCTACAT
1 AGTGGTAGCTACGACTACATATCAGTGGTAGCTTCAGCTACAT
9625928 ATCAGTGTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (46 bp):
AGTGGTAGCTACGACTACATATCAGTGGTAGCTTCAGCTACATTTT
Found at i:9628004 original size:44 final size:45
Alignment explanation
Indices: 9627931--9628158 Score: 189
Period size: 45 Copynumber: 5.1 Consensus size: 45
9627921 GTGTTACAGA
*
9627931 CAAGATCTGCTATCTTTAGTCTGCTTCGCTGCAAACTCAGGGAGG
1 CAAGATCTGCTATCTTCAGTCTGCTTCGCTGCAAACTCAGGGAGG
* * * * * *
9627976 CAAGAT-TGGTGTCTTC-GATCTGTTTCGCTGCCAA-TACAGGAAGA
1 CAAGATCTGCTATCTTCAG-TCTGCTTCGCTGCAAACT-CAGGGAGG
* * * *
9628020 TAAGATCTGCTATCTTCAGTCTGCTCCGCTTCAAACTTAGGGAGG
1 CAAGATCTGCTATCTTCAGTCTGCTTCGCTGCAAACTCAGGGAGG
* * * * * * * *
9628065 CAAG-GCTGGTGTCTTC-GATCTCCTTTGCTGCCAA-TACAGGAAGA
1 CAAGATCTGCTATCTTCAG-TCTGCTTCGCTGCAAACT-CAGGGAGG
* *
9628109 CAAGATCTGCTATCTTCAGTCTGCTCCGCTGTAAACTCAGGGAGG
1 CAAGATCTGCTATCTTCAGTCTGCTTCGCTGCAAACTCAGGGAGG
9628154 CAAGA
1 CAAGA
9628159 CTTGTAGCTT
Statistics
Matches: 134, Mismatches: 39, Indels: 20
0.69 0.20 0.10
Matches are distributed among these distances:
43 4 0.03
44 61 0.46
45 65 0.49
46 4 0.03
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (45 bp):
CAAGATCTGCTATCTTCAGTCTGCTTCGCTGCAAACTCAGGGAGG
Found at i:9628083 original size:89 final size:89
Alignment explanation
Indices: 9627928--9628160 Score: 362
Period size: 89 Copynumber: 2.6 Consensus size: 89
9627918 GGGGTGTTAC
* * * *
9627928 AGACAAGATCTGCTATCTTTAGTCTGCTTCGCTGCAAACTCAGGGAGGCAAGATTGGTGTCTTCG
1 AGACAAGATCTGCTATCTTCAGTCTGCTCCGCTTCAAACTCAGGGAGGCAAGACTGGTGTCTTCG
*
9627993 ATCT-GTTTCGCTGCCAATACAGGA
66 ATCTCCTTT-GCTGCCAATACAGGA
* * *
9628017 AGATAAGATCTGCTATCTTCAGTCTGCTCCGCTTCAAACTTAGGGAGGCAAGGCTGGTGTCTTCG
1 AGACAAGATCTGCTATCTTCAGTCTGCTCCGCTTCAAACTCAGGGAGGCAAGACTGGTGTCTTCG
9628082 ATCTCCTTTGCTGCCAATACAGGA
66 ATCTCCTTTGCTGCCAATACAGGA
9628106 AGACAAGATCTGCTATCTTCAGTCTGCTCCGCTGT-AAACTCAGGGAGGCAAGACT
1 AGACAAGATCTGCTATCTTCAGTCTGCTCCGCT-TCAAACTCAGGGAGGCAAGACT
9628161 TGTAGCTTTC
Statistics
Matches: 131, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
89 127 0.97
90 4 0.03
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (89 bp):
AGACAAGATCTGCTATCTTCAGTCTGCTCCGCTTCAAACTCAGGGAGGCAAGACTGGTGTCTTCG
ATCTCCTTTGCTGCCAATACAGGA
Found at i:9628309 original size:44 final size:44
Alignment explanation
Indices: 9628212--9628640 Score: 245
Period size: 44 Copynumber: 9.7 Consensus size: 44
9628202 GTCTGATGCG
* * ***
9628212 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATT-TT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGT--TTCTTCA
* *
9628256 AT-TCGCTCCACTACAACTTCAGGGAGATATGATTGGTTTCTTCA
1 ATCT-GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
* * *
9628300 ATCTACTCCACTGCAACTTCAAGGAGATAAGATTGGTTTATTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
* * *
9628344 GTCTGCTCCACTGCAACTTCAAGGAGATAAGACTT-GTAAT-TTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGT-TTCTTCA
* * * * *
9628388 TTCTACTTCACTGCAACTTCAAGGAGAT-A-A--GGTTTACTAT-G
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTT-CT-TCA
* * * * *
9628429 ATCTGCTCTATTGCAACTCCAGAGAGATAAAATCTGTGATTTATAGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-G--TT-T--CTTCA
* * ** * * *
9628480 ATCTGTTCTACTATAACTTCAGGGAAATAAGATTCGCTATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GGTTTCTTCA
* * * *
9628525 GTCTGCTCCACTGCAACTTCAGGGGGATAAGACT--TTACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
* * * * * *
9628567 ATCCGCTCCACTGTAACTTCAGGGAGATAGGATT-ATTGGCTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTT-TCTTCA
* *
9628611 ATCTACTCCACTACAACTTCAGGGAGATAA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAA
9628641 AATTTTCCAT
Statistics
Matches: 298, Mismatches: 63, Indels: 48
0.73 0.15 0.12
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 21 0.07
42 39 0.13
43 7 0.02
44 156 0.52
45 35 0.12
46 1 0.00
47 2 0.01
48 1 0.00
49 2 0.01
50 3 0.01
51 28 0.09
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCA
Found at i:9628579 original size:42 final size:44
Alignment explanation
Indices: 9628520--9628640 Score: 138
Period size: 42 Copynumber: 2.8 Consensus size: 44
9628510 GATTCGCTAT
* *
9628520 CTTCAGTCTGCTCCACTGCAACTTCAGGGGGATAAGACT-TT-A
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTATTGA
* * * * *
9628562 CTTCAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTATTGA
* * *
9628606 CTTTAATCTACTCCACTACAACTTCAGGGAGATAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
9628641 AATTTTCCAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 33 0.52
43 2 0.03
44 29 0.45
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTATTGA
Found at i:9635867 original size:23 final size:22
Alignment explanation
Indices: 9635841--9635883 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9635831 TATAAATCTC
9635841 TAAGATTACAAAATCATATCTTT
1 TAAGATTAC-AAATCATATCTTT
* *
9635864 TAAGATTGCATATCATATCT
1 TAAGATTACAAATCATATCT
9635884 AAAATTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (22 bp):
TAAGATTACAAATCATATCTTT
Found at i:9635877 original size:17 final size:17
Alignment explanation
Indices: 9635855--9635906 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
9635845 ATTACAAAAT
9635855 CATATCTTTTAAGATTG
1 CATATCTTTTAAGATTG
* *
9635872 CATATCATATCTAAAATTG
1 CATATC-T-TTTAAGATTG
* *
9635891 CATATCCTTGAAGATT
1 CATATCTTTTAAGATT
9635907 ATATTTCCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 12 0.44
18 1 0.04
19 14 0.52
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (17 bp):
CATATCTTTTAAGATTG
Found at i:9636383 original size:12 final size:12
Alignment explanation
Indices: 9636366--9636390 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9636356 CTTTTATTAC
9636366 AAAAAAAAAAAG
1 AAAAAAAAAAAG
9636378 AAAAAAAAAAAG
1 AAAAAAAAAAAG
9636390 A
1 A
9636391 GTGGCGTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:9636663 original size:46 final size:46
Alignment explanation
Indices: 9636611--9636704 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
9636601 ATTATTAATT
9636611 TTTTGGATAAGTTTAAAACAAAAAAATTCACTTCATATCTATATAA
1 TTTTGGATAAGTTTAAAACAAAAAAATTCACTTCATATCTATATAA
* *
9636657 TTTTGGATAAGTTTAAAATAAAAAAATTCACTTCGTATCTATATAA
1 TTTTGGATAAGTTTAAAACAAAAAAATTCACTTCATATCTATATAA
9636703 TT
1 TT
9636705 AAACACTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (46 bp):
TTTTGGATAAGTTTAAAACAAAAAAATTCACTTCATATCTATATAA
Found at i:9644613 original size:30 final size:30
Alignment explanation
Indices: 9644551--9644615 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
9644541 AATAGTCTAT
**
9644551 ATTTTTATAATTTTCAAAGGATTAAATCAA
1 ATTTTTATAATTTTCAAAGGACCAAATCAA
* *
9644581 ATTTTTATAATTTT-AAAGGGCCAAAGTGAA
1 ATTTTTATAATTTTCAAAGGACCAAA-TCAA
9644611 ATTTT
1 ATTTT
9644616 ACCTTTACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (30 bp):
ATTTTTATAATTTTCAAAGGACCAAATCAA
Found at i:9652508 original size:50 final size:51
Alignment explanation
Indices: 9652440--9652567 Score: 172
Period size: 50 Copynumber: 2.6 Consensus size: 51
9652430 GAGATTATGT
* * *
9652440 GAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGA
1 GAGGTCCCATCGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGA
*
9652490 GAGGTCCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGA
1 GAGGTCCCATCGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGA
** *
9652540 GAACTCCCATC-TAAGACCATATCTGGGA
1 GAGGTCCCATCGTAAGACCATGTCTGGGA
9652568 TATGACATTG
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 66 0.96
51 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (51 bp):
GAGGTCCCATCGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGA
Found at i:9654101 original size:13 final size:13
Alignment explanation
Indices: 9654083--9654113 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
9654073 GGAATTAAAA
9654083 CTTCTATAAAAGC
1 CTTCTATAAAAGC
9654096 CTTCTATAAAAGC
1 CTTCTATAAAAGC
9654109 CTTCT
1 CTTCT
9654114 TATTCGAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (13 bp):
CTTCTATAAAAGC
Found at i:9655648 original size:38 final size:38
Alignment explanation
Indices: 9655596--9655731 Score: 166
Period size: 38 Copynumber: 3.6 Consensus size: 38
9655586 TGTAGTCATG
* * *
9655596 GTGTCACCCTAAAGGACCATTAGATAATCGTCATCACA
1 GTGTCGCCCCAAAGGACCAGTAGATAATCGTCATCACA
* * *
9655634 GTGTCGCCCCAAAGGACTAGTAGATAATTGTTATCACA
1 GTGTCGCCCCAAAGGACCAGTAGATAATCGTCATCACA
* *
9655672 GTGTCGCCCCAAAGGACAAGTAGATAA-CTGTCGTCACA
1 GTGTCGCCCCAAAGGACCAGTAGATAATC-GTCATCACA
**
9655710 GTGTCGCCCTGAAGGACCAGTA
1 GTGTCGCCCCAAAGGACCAGTA
9655732 CATATCTGTT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
38 84 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (38 bp):
GTGTCGCCCCAAAGGACCAGTAGATAATCGTCATCACA
Found at i:9657693 original size:20 final size:21
Alignment explanation
Indices: 9657668--9657706 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
9657658 AGGTCTGCCA
9657668 TTAATC-TAGAAAAT-AATGAG
1 TTAATCAT-GAAAATCAATGAG
9657688 TTAATCATGAAAATCAATG
1 TTAATCATGAAAATCAATG
9657707 GCGAGATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.31
Consensus pattern (21 bp):
TTAATCATGAAAATCAATGAG
Found at i:9660996 original size:26 final size:26
Alignment explanation
Indices: 9660960--9661026 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
9660950 ACTCTCGTTA
9660960 TTGCCATTACATTTCTACTTTCACTT
1 TTGCCATTACATTTCTACTTTCACTT
9660986 TTGCCATTACATTTCTACTTTCACTT
1 TTGCCATTACATTTCTACTTTCACTT
9661012 TTGCCA-TAGCATTTC
1 TTGCCATTA-CATTTC
9661027 CAATCACTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 2 0.05
26 38 0.95
ACGTcount: A:0.19, C:0.27, G:0.06, T:0.48
Consensus pattern (26 bp):
TTGCCATTACATTTCTACTTTCACTT
Found at i:9668107 original size:13 final size:13
Alignment explanation
Indices: 9668089--9668113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9668079 ACAAAGAATT
9668089 AAATATCAATTTA
1 AAATATCAATTTA
9668102 AAATATCAATTT
1 AAATATCAATTT
9668114 TTACTGTCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATATCAATTTA
Found at i:9669135 original size:111 final size:111
Alignment explanation
Indices: 9668941--9669166 Score: 373
Period size: 111 Copynumber: 2.0 Consensus size: 111
9668931 ATTTTTATCT
* * *
9668941 CTTCCAACCTTGAAGGGAGCAATATCTTTACAACGATAGGGTCTTTAATTGTCTCTTTCTCTAGT
1 CTTCCAACCTTGAAGGGAACAATATCTTTACAACGATAGGGTCTTTAATTGTCTCTTTCTCCAAT
*
9669006 TCAACTACCGGTGCAACTACTTCCTCTAGTTTTGGTTCATCATCAG
66 TCAACTACCGGTGCAACTACTTCCACTAGTTTTGGTTCATCATCAG
*
9669052 CTTCCAACCTTGAAGGGAACAATATCTTTACCAC-AGTAGGGTCTTTAATTGTCTCTTTCTCCAA
1 CTTCCAACCTTGAAGGGAACAATATCTTTACAACGA-TAGGGTCTTTAATTGTCTCTTTCTCCAA
* *
9669116 TTCAACTACCGGTGTAACTACTTTCACTAGTTTTGGTTCATCATCAG
65 TTCAACTACCGGTGCAACTACTTCCACTAGTTTTGGTTCATCATCAG
9669163 CTTC
1 CTTC
9669167 TAAGGGTCCT
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
110 1 0.01
111 106 0.99
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (111 bp):
CTTCCAACCTTGAAGGGAACAATATCTTTACAACGATAGGGTCTTTAATTGTCTCTTTCTCCAAT
TCAACTACCGGTGCAACTACTTCCACTAGTTTTGGTTCATCATCAG
Found at i:9677858 original size:13 final size:13
Alignment explanation
Indices: 9677840--9677877 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
9677830 CGAGGCTCAT
9677840 TCGCTTCTTTGCG
1 TCGCTTCTTTGCG
9677853 TCGCTTCTTTGCG
1 TCGCTTCTTTGCG
* *
9677866 TTGCTCCTTTGC
1 TCGCTTCTTTGC
9677878 TGATGGCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.00, C:0.32, G:0.21, T:0.47
Consensus pattern (13 bp):
TCGCTTCTTTGCG
Found at i:9683527 original size:28 final size:28
Alignment explanation
Indices: 9683386--9683540 Score: 175
Period size: 30 Copynumber: 5.2 Consensus size: 28
9683376 ATACAACATT
* * *
9683386 CAGTAACAGTCTGGGCCTGAGCCCTATA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
*
9683414 CAGTAATAGTACAGTGTGGGCCTTAGCCCATTA
1 CAG---TA--ACAGTGTGGGCCTTAGCCCAATA
9683447 CAGTAACAGTATGTGGGCCTTAGCCCAATA
1 CAGTAACAG--TGTGGGCCTTAGCCCAATA
*
9683477 TAGTAACAATGTGTGGGCCTTAGCCCAATA
1 CAGTAAC-A-GTGTGGGCCTTAGCCCAATA
*
9683507 CAGTAACAGTGTGAGCCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
9683535 CAGTAA
1 CAGTAA
9683541 TCAATACAAT
Statistics
Matches: 110, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
28 32 0.29
29 1 0.01
30 51 0.46
31 3 0.03
32 1 0.01
33 22 0.20
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (28 bp):
CAGTAACAGTGTGGGCCTTAGCCCAATA
Found at i:9683677 original size:26 final size:26
Alignment explanation
Indices: 9683648--9683728 Score: 128
Period size: 26 Copynumber: 3.1 Consensus size: 26
9683638 AACACACCAA
9683648 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
9683674 TATCGCAGCAAAGCTGTCAGTAACTA-
1 TATCGCAGCAAAGCTGCCAGTAAC-AG
*
9683700 TATCGCAGTAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
9683726 TAT
1 TAT
9683729 ACTTCCTCCA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
25 1 0.02
26 48 0.96
27 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:9683930 original size:27 final size:27
Alignment explanation
Indices: 9683898--9684574 Score: 574
Period size: 27 Copynumber: 25.2 Consensus size: 27
9683888 AACAGTTATT
* *
9683898 ATTTTACCCTATGGGGGTAATTCAATC
1 ATTTTACCCTATGGGGGTATTTCGATC
* *
9683925 ATTTTACCCTATAGGGGTAATTT-GTTC
1 ATTTTACCCTATGGGGGT-ATTTCGATC
* * * *
9683952 ATTTTACCCTACGAGGGTAATTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGATC
* * * *
9683979 ATTTTACCCTA-CGAGGTAATTC-AGTT
1 ATTTTACCCTATGGGGGTATTTCGA-TC
* * *
9684005 ATTTTATCCTACGGGGGTAATTCGATC
1 ATTTTACCCTATGGGGGTATTTCGATC
* **
9684032 ATTTTACCCTACGGGGGTAACTCGATC
1 ATTTTACCCTATGGGGGTATTTCGATC
* * *
9684059 ATTTTACCCTATAGAGGTAATTC-AGTC
1 ATTTTACCCTATGGGGGTATTTCGA-TC
* * * *
9684086 ATTTTACCCTACGAGGGTAATTCAATC
1 ATTTTACCCTATGGGGGTATTTCGATC
* *** *
9684113 ATTTTATCCT-TCGACAGTATTTC-AGTT
1 ATTTTACCCTAT-GGGGGTATTTCGA-TC
* *
9684140 ATTTAACCCTATAGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGATC
* *
9684167 ATTTTACCCT-TCGAGGGTATTTTGATC
1 ATTTTACCCTAT-GGGGGTATTTCGATC
* *
9684194 ATTTTACCCT-TCAGGGGTATTTTGATC
1 ATTTTACCCTAT-GGGGGTATTTCGATC
* * *
9684221 ATTTTAACTTATGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGATC
*
9684248 ATTTTACCCTATGGGGGTATTTCAATC
1 ATTTTACCCTATGGGGGTATTTCGATC
* *
9684275 ATTCTACCCTATGAGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGATC
* *
9684302 ATTCTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGATC
* * *
9684329 ATTCTACCTTAT-GGGGTATTTCCATC
1 ATTTTACCCTATGGGGGTATTTCGATC
*
9684355 ATTTTA-CCTATGAGGGTATTTC-AGTC
1 ATTTTACCCTATGGGGGTATTTCGA-TC
* *
9684381 ATTTTACCTTATGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGATC
* *
9684408 ATTCTACCCAATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGATC
* * *
9684435 ATTCTACCTTAT-GGGGTATTT-AAGTC
1 ATTTTACCCTATGGGGGTATTTCGA-TC
* *
9684461 ATTCTACCCTATGAGGGTATTTC-AGTC
1 ATTTTACCCTATGGGGGTATTTCGA-TC
9684488 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGATC
* *
9684515 -TTTCTACCCTATAGGGGTATTTCGGTC
1 ATTT-TACCCTATGGGGGTATTTCGATC
* ** * *
9684542 ACTTTACCCTATCAGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGATC
9684569 ATTTTA
1 ATTTTA
9684575 ACTATTTTGG
Statistics
Matches: 539, Mismatches: 88, Indels: 46
0.80 0.13 0.07
Matches are distributed among these distances:
25 6 0.01
26 84 0.16
27 438 0.81
28 11 0.02
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGATC
Found at i:9689416 original size:20 final size:20
Alignment explanation
Indices: 9689391--9689451 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
9689381 ATAATATTTC
9689391 GAAAAATAAAAATATTTTTA
1 GAAAAATAAAAATATTTTTA
* *
9689411 GAAAAAT-----TAATTTCA
1 GAAAAATAAAAATATTTTTA
9689426 -AAAAATAAAAATATTTTTA
1 GAAAAATAAAAATATTTTTA
9689445 GAAAAAT
1 GAAAAAT
9689452 TAATTTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
14 6 0.19
15 6 0.19
19 6 0.19
20 13 0.42
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (20 bp):
GAAAAATAAAAATATTTTTA
Found at i:9689430 original size:34 final size:34
Alignment explanation
Indices: 9689386--9689457 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
9689376 GTTAAATAAT
*
9689386 ATTTCGAAAAATAAAAATATTTTTAGAAAAATTA
1 ATTTCAAAAAATAAAAATATTTTTAGAAAAATTA
9689420 ATTTCAAAAAATAAAAATATTTTTAGAAAAATTA
1 ATTTCAAAAAATAAAAATATTTTTAGAAAAATTA
9689454 ATTT
1 ATTT
9689458 TATGGTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.38
Consensus pattern (34 bp):
ATTTCAAAAAATAAAAATATTTTTAGAAAAATTA
Found at i:9689922 original size:2 final size:2
Alignment explanation
Indices: 9689915--9689992 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
9689905 NNNNCTCGTA
9689915 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9689957 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9689993 TTGCTTATTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9690747 original size:21 final size:21
Alignment explanation
Indices: 9690723--9690769 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
9690713 CAAATCAGAA
9690723 TTGAAGCCCAAACTTGCTTGT
1 TTGAAGCCCAAACTTGCTTGT
9690744 TTGAAGCCCAAACTTGCTTGT
1 TTGAAGCCCAAACTTGCTTGT
9690765 TTGAA
1 TTGAA
9690770 CACTTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (21 bp):
TTGAAGCCCAAACTTGCTTGT
Found at i:9691681 original size:35 final size:35
Alignment explanation
Indices: 9691635--9691711 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
9691625 TAACATGTTG
9691635 TGACTGAAAATTTAATGCTTAATTGCTTTGATTTA
1 TGACTGAAAATTTAATGCTTAATTGCTTTGATTTA
9691670 TGACTGAAAATTTAATGCTTAATTGCTTTGATTTA
1 TGACTGAAAATTTAATGCTTAATTGCTTTGATTTA
*
9691705 TGCCTGA
1 TGACTGA
9691712 TTGGGTACAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (35 bp):
TGACTGAAAATTTAATGCTTAATTGCTTTGATTTA
Found at i:9694799 original size:22 final size:22
Alignment explanation
Indices: 9694765--9694815 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
9694755 AAAATTGAAA
*
9694765 TAACAATGGCAATGTCTTATAT
1 TAACAACGGCAATGTCTTATAT
*
9694787 TAACAACGTCAATGTCTTATAT
1 TAACAACGGCAATGTCTTATAT
9694809 TAACAAC
1 TAACAAC
9694816 AAGGTAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACAACGGCAATGTCTTATAT
Found at i:9698506 original size:31 final size:30
Alignment explanation
Indices: 9698441--9698514 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
9698431 ATTGTATAAA
9698441 GAAACTTTAATTTGGTGCAATTATACATGT
1 GAAACTTTAATTTGGTGCAATTATACATGT
* *
9698471 GAAACTCTAATTGTGGTTCAAATATATAC-T-T
1 GAAACTTTAATT-TGGTGC-AAT-TATACATGT
9698502 GAAACTTTAATTT
1 GAAACTTTAATTT
9698515 TGATTAATCG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 12 0.32
31 17 0.45
32 4 0.11
33 5 0.13
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (30 bp):
GAAACTTTAATTTGGTGCAATTATACATGT
Found at i:9698686 original size:29 final size:29
Alignment explanation
Indices: 9698655--9698711 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
9698645 AAATTGGATC
9698655 AAATCAAAATTTTATATATAAAATTATACA
1 AAATCAAAA-TTTATATATAAAATTATACA
*
9698685 AAATCAAAATTTATATATATAATTATA
1 AAATCAAAATTTATATATAAAATTATA
9698712 TATTAAACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (29 bp):
AAATCAAAATTTATATATAAAATTATACA
Found at i:9699753 original size:12 final size:12
Alignment explanation
Indices: 9699733--9699808 Score: 89
Period size: 12 Copynumber: 6.3 Consensus size: 12
9699723 TTTTAAGGTT
*
9699733 TATATATACATA
1 TATACATACATA
9699745 TATACATACATA
1 TATACATACATA
* * *
9699757 TATATATGCATG
1 TATACATACATA
9699769 TATACATACATA
1 TATACATACATA
* * *
9699781 TATATATGCATG
1 TATACATACATA
9699793 TATACATACATA
1 TATACATACATA
9699805 TATA
1 TATA
9699809 AGCACAGACA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (12 bp):
TATACATACATA
Found at i:9699772 original size:24 final size:24
Alignment explanation
Indices: 9699733--9699808 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 24
9699723 TTTTAAGGTT
* *
9699733 TATATATACATATATACATACATA
1 TATATATGCATGTATACATACATA
9699757 TATATATGCATGTATACATACATA
1 TATATATGCATGTATACATACATA
9699781 TATATATGCATGTATACATACATA
1 TATATATGCATGTATACATACATA
9699805 TATA
1 TATA
9699809 AGCACAGACA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (24 bp):
TATATATGCATGTATACATACATA
Found at i:9706116 original size:20 final size:20
Alignment explanation
Indices: 9706093--9706134 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
9706083 TATGTTTCAG
*
9706093 TGGTGAGTTTAGTGTTTAAA
1 TGGTGAGTTTAGTGTCTAAA
*
9706113 TGGTGGGTTTAGTGTCTAAA
1 TGGTGAGTTTAGTGTCTAAA
9706133 TG
1 TG
9706135 TAGCATCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.43
Consensus pattern (20 bp):
TGGTGAGTTTAGTGTCTAAA
Found at i:9707258 original size:10 final size:10
Alignment explanation
Indices: 9707228--9707267 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
9707218 AAAAGTTAAG
9707228 TATAT-ATAT
1 TATATAATAT
9707237 TATATATTATAT
1 TATATA--ATAT
9707249 TATATAATAT
1 TATATAATAT
9707259 TATATAATA
1 TATATAATA
9707268 AAAGAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.18
10 13 0.46
12 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TATATAATAT
Found at i:9708450 original size:22 final size:22
Alignment explanation
Indices: 9708424--9708504 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
9708414 TATTATTCCG
9708424 GGTGTGTTAGGTTGGATATTCT
1 GGTGTGTTAGGTTGGATATTCT
*
9708446 GGTGTGTTTGGTTGG--ATTC-
1 GGTGTGTTAGGTTGGATATTCT
* *
9708465 GTGTATCTTAGGTTGGATATTCT
1 G-GTGTGTTAGGTTGGATATTCT
*
9708488 GGTGTGTTTGGTTGGAT
1 GGTGTGTTAGGTTGGAT
9708505 TCGTGTATCC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.02
20 15 0.31
22 31 0.65
23 1 0.02
ACGTcount: A:0.11, C:0.05, G:0.37, T:0.47
Consensus pattern (22 bp):
GGTGTGTTAGGTTGGATATTCT
Found at i:9708489 original size:42 final size:42
Alignment explanation
Indices: 9708430--9708513 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
9708420 TCCGGGTGTG
9708430 TTAGGTTGGATATTCTGGTGTGTTTGGTTGGATTCGTGTATC
1 TTAGGTTGGATATTCTGGTGTGTTTGGTTGGATTCGTGTATC
9708472 TTAGGTTGGATATTCTGGTGTGTTTGGTTGGATTCGTGTATC
1 TTAGGTTGGATATTCTGGTGTGTTTGGTTGGATTCGTGTATC
9708514 CGTCAAGGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.12, C:0.07, G:0.33, T:0.48
Consensus pattern (42 bp):
TTAGGTTGGATATTCTGGTGTGTTTGGTTGGATTCGTGTATC
Found at i:9712127 original size:24 final size:24
Alignment explanation
Indices: 9712100--9712146 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
9712090 TTTGAAATGG
9712100 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
9712124 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
9712147 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:9712426 original size:40 final size:40
Alignment explanation
Indices: 9712307--9712444 Score: 129
Period size: 40 Copynumber: 3.5 Consensus size: 40
9712297 CTTCGAGTCA
* * * *
9712307 ATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTCG
1 ATGAGACACTGGGTGCCAAATTATTACTTCGGATT-ATCCG
* * * * * *
9712348 ATGGGGCACTGGGT-CCCAA-T-TTACTTAGGTTTAACCG
1 ATGAGACACTGGGTGCCAAATTATTACTTCGGATTATCCG
* *
9712385 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCCG
1 ATGAGACACTGGGTGCCAAATTATTACTTCGGATTATCCG
*
9712425 ATGAGGCACTGGGTGCCAAA
1 ATGAGACACTGGGTGCCAAA
9712445 CTGGTGTGTT
Statistics
Matches: 74, Mismatches: 20, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
37 15 0.20
38 12 0.16
39 2 0.03
40 33 0.45
41 12 0.16
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (40 bp):
ATGAGACACTGGGTGCCAAATTATTACTTCGGATTATCCG
Found at i:9734746 original size:35 final size:35
Alignment explanation
Indices: 9734696--9734780 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
9734686 TTTCAAGGTA
* * * *
9734696 TCACCACGAAAGACCTGTATACCATTTACATGGTG
1 TCACCCCGAAGGACCTATATACCATTTACACGGTG
* *
9734731 TCACCCTGAAGGACCTATATACTATTTACACGGTG
1 TCACCCCGAAGGACCTATATACCATTTACACGGTG
**
9734766 TTGCCCCGAAGGACC
1 TCACCCCGAAGGACC
9734781 AGTAGATAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (35 bp):
TCACCCCGAAGGACCTATATACCATTTACACGGTG
Found at i:9739418 original size:12 final size:12
Alignment explanation
Indices: 9739401--9739449 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
9739391 AAGAAATATG
*
9739401 AAATAAAAATAA
1 AAATAAAAAGAA
*
9739413 AAATAAGAAGAA
1 AAATAAAAAGAA
*
9739425 AAAGAAAAAGAA
1 AAATAAAAAGAA
*
9739437 AAAAAACAAAGAA
1 AAATAA-AAAGAA
9739450 GTGTCAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
12 25 0.81
13 6 0.19
ACGTcount: A:0.82, C:0.02, G:0.10, T:0.06
Consensus pattern (12 bp):
AAATAAAAAGAA
Found at i:9745681 original size:2 final size:2
Alignment explanation
Indices: 9745674--9745700 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9745664 GCGGTTCGCT
9745674 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
9745701 TCCCCCCCCC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9757015 original size:70 final size:70
Alignment explanation
Indices: 9756900--9757107 Score: 240
Period size: 70 Copynumber: 3.0 Consensus size: 70
9756890 GGCTCGTAAG
* **
9756900 TTCAATACCACAGCCTCCAAAATAGTTAGTGAGAGCTCAAACTCCCAGCTATAATCTTAGAA-CT
1 TTCAATACCGCAGCCTCCAAAATAGTTAGTGAGAGCTCAGGCTCCCAGCTATAATCTTA-AAGCT
***
9756964 CACGGG
65 CACAAA
* ** * * *
9756970 TTCAGTATTGTAGCCTCCAAAATAGTTAGCGAGAGCT-ACGGCTCCCAACTATAATCTTAAAGCT
1 TTCAATACCGCAGCCTCCAAAATAGTTAGTGAGAGCTCA-GGCTCCCAGCTATAATCTTAAAGCT
9757034 CACAAA
65 CACAAA
* * * *
9757040 TTCAATACCGCAGCCTCCAAAATAATTAGTGAGAGCTCAGGCTCCCAGATGTAATCTTAAGGCTC
1 TTCAATACCGCAGCCTCCAAAATAGTTAGTGAGAGCTCAGGCTCCCAGCTATAATCTTAAAGCTC
9757105 ACA
66 ACA
9757108 GCCTCTAAAA
Statistics
Matches: 113, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
69 3 0.03
70 109 0.96
71 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (70 bp):
TTCAATACCGCAGCCTCCAAAATAGTTAGTGAGAGCTCAGGCTCCCAGCTATAATCTTAAAGCTC
ACAAA
Found at i:9757140 original size:56 final size:56
Alignment explanation
Indices: 9757050--9757159 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 56
9757040 TTCAATACCG
* * *
9757050 CAGCCTCCAAAATAATTAGTGAGAGCTCAGGCTCCCAGATGTAATCTTAAGGCTCA
1 CAGCCTCCAAAATAATTAGTCAAAGCTCAAGCTCCCAGATGTAATCTTAAGGCTCA
* * *
9757106 CAGCCTCTAAAATAGTTAGTCAAAGCTCAAGCTCCCAGCTGTAATCTTAAGGCT
1 CAGCCTCCAAAATAATTAGTCAAAGCTCAAGCTCCCAGATGTAATCTTAAGGCT
9757160 TGTAGGTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (56 bp):
CAGCCTCCAAAATAATTAGTCAAAGCTCAAGCTCCCAGATGTAATCTTAAGGCTCA
Found at i:9760378 original size:20 final size:20
Alignment explanation
Indices: 9760355--9760392 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9760345 GAATAGTAGG
*
9760355 GTCAAGTCATGAACAGTGGA
1 GTCAAATCATGAACAGTGGA
9760375 GTCAAATCATGAACAGTG
1 GTCAAATCATGAACAGTG
9760393 ATAATATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (20 bp):
GTCAAATCATGAACAGTGGA
Found at i:9762008 original size:23 final size:23
Alignment explanation
Indices: 9761978--9762054 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
9761968 ACTTCCGTGT
9761978 ATTCATTCTAGCACTTAGGTGCA
1 ATTCATTCTAGCACTTAGGTGCA
9762001 ATTCATTCTAGCAC-TATGGTGCAA
1 ATTCATTCTAGCACTTA-GGTGC-A
* * *
9762025 ATTTATTCTGGCACTTCGGTGCA
1 ATTCATTCTAGCACTTAGGTGCA
*
9762048 ATACATT
1 ATTCATT
9762055 TTGTGGAGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
22 2 0.04
23 25 0.54
24 18 0.39
25 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (23 bp):
ATTCATTCTAGCACTTAGGTGCA
Found at i:9762032 original size:24 final size:24
Alignment explanation
Indices: 9761978--9762048 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
9761968 ACTTCCGTGT
9761978 ATTCATTCTAGCACTTAGGTGC-A
1 ATTCATTCTAGCACTTAGGTGCAA
9762001 ATTCATTCTAGCAC-TATGGTGCAA
1 ATTCATTCTAGCACTTA-GGTGCAA
* * *
9762025 ATTTATTCTGGCACTTCGGTGCAA
1 ATTCATTCTAGCACTTAGGTGCAA
9762049 TACATTTTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.05
23 19 0.45
24 20 0.48
25 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Consensus pattern (24 bp):
ATTCATTCTAGCACTTAGGTGCAA
Found at i:9767295 original size:25 final size:25
Alignment explanation
Indices: 9767258--9767307 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
9767248 ATTTAATTTC
* *
9767258 AAAAAGTTTAGTGA-CTAAATAAAA
1 AAAAAGTTAAGTGACCAAAATAAAA
9767282 AAAATAGTTAAGTGACCAAAATAAAA
1 AAAA-AGTTAAGTGACCAAAATAAAA
9767308 TGAAAGGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 9 0.41
26 9 0.41
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.22
Consensus pattern (25 bp):
AAAAAGTTAAGTGACCAAAATAAAA
Found at i:9769717 original size:16 final size:15
Alignment explanation
Indices: 9769677--9769717 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
9769667 TTTCAATTTT
9769677 ATTTT-AATAATAAA
1 ATTTTAAATAATAAA
9769691 A-TTTAAA-AATAATA
1 ATTTTAAATAATAA-A
9769705 ATTTTAAATAATA
1 ATTTTAAATAATA
9769718 TTCTTTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.35
14 5 0.22
15 6 0.26
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATAATAAA
Found at i:9771357 original size:40 final size:39
Alignment explanation
Indices: 9771297--9771446 Score: 106
Period size: 40 Copynumber: 3.7 Consensus size: 39
9771287 GGCACTTTTT
*
9771297 GCGGCGTTTGGAACAAAAGCGCCACAAAAAATAGAGCATTA
1 GCGGCGTTT--AACCAAAGCGCCACAAAAAATAGAGCATTA
* * * ** *
9771338 GCGGCGATTTAGCCAAAGCGCCGCTAAAGGTAGAGCATCA
1 GCGGCG-TTTAACCAAAGCGCCACAAAAAATAGAGCATTA
** * * *
9771378 GCGGCGTTTATACGGAAGCGCCGCTAAAAATAG-GAATTA
1 GCGGCGTTTA-ACCAAAGCGCCACAAAAAATAGAGCATTA
* *
9771417 ACGGCGTTTTATA-TAAAGCGCCACAAAAAA
1 GCGGCG-TTTA-ACCAAAGCGCCACAAAAAA
9771447 CCTAAGACGA
Statistics
Matches: 87, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
39 26 0.30
40 52 0.60
41 6 0.07
42 3 0.03
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (39 bp):
GCGGCGTTTAACCAAAGCGCCACAAAAAATAGAGCATTA
Found at i:9771546 original size:41 final size:41
Alignment explanation
Indices: 9771489--9771808 Score: 406
Period size: 41 Copynumber: 7.7 Consensus size: 41
9771479 TTTAAACATT
* *
9771489 TAGCGGCGTTTTTGTCTAAGCGTCGCTAATGCTCGGGTCTA
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCGGGTCTA
*
9771530 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCGGGTCTA
*
9771571 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCGGGTCTA
* * *
9771612 TAGCGGCGTTTTCGTATAAGCGCCGCTAATGCTCCGAGTCTT
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCT-CGGGTCTA
* * * *
9771654 TAGCGGCGCTTTCGTCTAAGCGCCGTTAATGCTCCGAGTCTT
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCT-CGGGTCTA
* * * *
9771696 TAGTGGCGTTTTCGTCTAAGCGCTGATAATGCTCTGTGTCTA
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTC-GGGTCTA
* * * *
9771738 TAGTGGCGTTTTCGCCTATGCGCCGCTAATGCTCGGGTCTT
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCGGGTCTA
** * *
9771779 TAGCGGCGTTTTTATATATGCGCCGCTAAT
1 TAGCGGCGTTTTCGTCTAAGCGCCGCTAAT
9771809 TCTCCTGTAT
Statistics
Matches: 252, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
41 143 0.57
42 109 0.43
ACGTcount: A:0.15, C:0.24, G:0.28, T:0.33
Consensus pattern (41 bp):
TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCGGGTCTA
Found at i:9771632 original size:82 final size:82
Alignment explanation
Indices: 9771489--9771850 Score: 420
Period size: 82 Copynumber: 4.4 Consensus size: 82
9771479 TTTAAACATT
* * *
9771489 TAGCGGCGTTTTTGTCTAAGCGTCGCTAATGCTCGGGTCTATAGCGGCGTTTTTGTCTAAGCGCC
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTATAGCGGCGTTTTCGTATAAGCGCC
*
9771554 GCTAATGCTCGGGTCTA
66 GCTAATGCTCGTGTCTA
9771571 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTATAGCGGCGTTTTCGTATAAGCGCC
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTATAGCGGCGTTTTCGTATAAGCGCC
* *
9771636 GCTAATGCTCCGAGTCTT
66 GCTAATGCT-CGTGTCTA
* * * * * * *
9771654 TAGCGGCGCTTTCGTCTAAGCGCCGTTAATGCTCCGAGTCTTTAGTGGCGTTTTCGTCTAAGCGC
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCT-CGGGTCTATAGCGGCGTTTTCGTATAAGCGC
* *
9771719 TGATAATGCTCTGTGTCTA
65 CGCTAATGCTC-GTGTCTA
* * * * * ** *
9771738 TAGTGGCGTTTTCGCCTATGCGCCGCTAATGCTCGGGTCTTTAGCGGCGTTTTTATATATGCGCC
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTATAGCGGCGTTTTCGTATAAGCGCC
* * *
9771803 GCTAATTCTCCTGTAT-
66 GCTAATGCTCGTGTCTA
* * *
9771819 TCAGCGGCGTTTGTATCTAAGCGCCGCGAATG
1 T-AGCGGCGTTTTTGTCTAAGCGCCGCTAATG
9771851 TATTAATCTT
Statistics
Matches: 237, Mismatches: 39, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
81 1 0.00
82 98 0.41
83 70 0.30
84 68 0.29
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.33
Consensus pattern (82 bp):
TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTATAGCGGCGTTTTCGTATAAGCGCC
GCTAATGCTCGTGTCTA
Found at i:9771825 original size:41 final size:41
Alignment explanation
Indices: 9771512--9771850 Score: 124
Period size: 41 Copynumber: 8.2 Consensus size: 41
9771502 GTCTAAGCGT
* * * * * *
9771512 CGCTAATGCTCGGGTCTAT-AGCGGCGTTTTTGTCTAAGCGC
1 CGCTAATGCTCCGGTAT-TCAGCGGCGTTTGTATATATGCGC
* * * * * *
9771553 CGCTAATGCTCGGGTCTAT-AGCGGCGTTTTTGTCTAAGCGC
1 CGCTAATGCTCCGGTAT-TCAGCGGCGTTTGTATATATGCGC
* *
9771594 CGCTAATGCTCGGGTCTAT-AGCGGCGTTTTCGTATA-A-GCGC
1 CGCTAATGCTCCGGTAT-TCAGCGGCG-TTT-GTATATATGCGC
* * *
9771635 CGCTAATGCTCCGAGTCTTTAGCGGCGCTTTCGTCTA-A-GCGC
1 CGCTAATGCTCCG-GTATTCAGCGGCG-TTT-GTATATATGCGC
* * * * *
9771677 CGTTAATGCTCCGAGTCTTTAGTGGCGTTTTCGTCTA-A-GCGC
1 CGCTAATGCTCCG-GTATTCAGCGGCG-TTT-GTATATATGCGC
* * * * * ***
9771719 TGATAATGCTCTGTGTCTAT-AGTGGCGTTT-TCGCCTATGCGC
1 CGCTAATGCTCCG-GTAT-TCAGCGGCGTTTGT-ATATATGCGC
* * * *
9771761 CGCTAATGCTCGGGTCTTTAGCGGCGTTTTTATATATGCGC
1 CGCTAATGCTCCGGTATTCAGCGGCGTTTGTATATATGCGC
* * * *
9771802 CGCTAATTCTCCTGTATTCAGCGGCGTTTGTATCTAAGCGC
1 CGCTAATGCTCCGGTATTCAGCGGCGTTTGTATATATGCGC
*
9771843 CGCGAATG
1 CGCTAATG
9771851 TATTAATCTT
Statistics
Matches: 255, Mismatches: 33, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 147 0.58
42 103 0.40
43 3 0.01
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (41 bp):
CGCTAATGCTCCGGTATTCAGCGGCGTTTGTATATATGCGC
Found at i:9780939 original size:43 final size:42
Alignment explanation
Indices: 9780891--9781053 Score: 166
Period size: 43 Copynumber: 3.7 Consensus size: 42
9780881 ATCTGCCAAA
* *
9780891 TTTAGCGGCGTTTTTGGTAAAAGAGCCGCTATAGATTAGGGTC
1 TTTAGCGGCGTTTTTGG-AAAAGCGCCGCTATAGATAAGGGTC
** * *
9780934 TTTAGCGGCGTTTTTGCGCGAAGCGCCGCTATATAGACAAAGGGTA
1 TTTAGCGGCGTTTTTG-GAAAAGCGCCGC--TATAGA-TAAGGGTC
* *
9780980 TTTAGCGGCGTTTTCTGGATAAGCGCCGCTATAGATCAGGGTC
1 TTTAGCGGCGTTTT-TGGAAAAGCGCCGCTATAGATAAGGGTC
*
9781023 GATT-GCGGCGTTTTTGGCAAAAGCGCCGCTA
1 -TTTAGCGGCGTTTTTGG-AAAAGCGCCGCTA
9781054 AAGGCCATGA
Statistics
Matches: 100, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
42 3 0.03
43 51 0.51
44 9 0.09
45 6 0.06
46 29 0.29
47 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTATAGATAAGGGTC
Found at i:9781047 original size:89 final size:89
Alignment explanation
Indices: 9780890--9781053 Score: 235
Period size: 89 Copynumber: 1.8 Consensus size: 89
9780880 AATCTGCCAA
* * *
9780890 ATTTAGCGGCGTTTTTGGTAAAAGAGCCGCTATAGATTAGGGTCTTTAGCGGCGTTTTTGCGCGA
1 ATTTAGCGGCGTTTTTGGTAAAAGAGCCGCTATAGATCAGGGTCATTAGCGGCGTTTTTGCGCAA
9780955 AGCGCCGCTATATAGACAAAGGGT
66 AGCGCCGCTATATAGACAAAGGGT
* *
9780979 ATTTAGCGGCGTTTTCTGG-ATAAGCGCCGCTATAGATCAGGGTCGATT-GCGGCGTTTTTG-GC
1 ATTTAGCGGCGTTTT-TGGTAAAAGAGCCGCTATAGATCAGGGTC-ATTAGCGGCGTTTTTGCGC
9781041 AAAAGCGCCGCTA
64 -AAAGCGCCGCTA
9781054 AAGGCCATGA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
88 2 0.03
89 60 0.90
90 5 0.07
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (89 bp):
ATTTAGCGGCGTTTTTGGTAAAAGAGCCGCTATAGATCAGGGTCATTAGCGGCGTTTTTGCGCAA
AGCGCCGCTATATAGACAAAGGGT
Found at i:9781074 original size:43 final size:43
Alignment explanation
Indices: 9780982--9781074 Score: 98
Period size: 43 Copynumber: 2.2 Consensus size: 43
9780972 AAAGGGTATT
* * * *
9780982 TAGCGGCGTTTTCTGGATAAGCGCCGCTATAGATCAGGGTCGA
1 TAGCGGCGTTTTCTGGAAAAGCGCCGCTAAAGACCAGGATCGA
* * * *
9781025 TTGCGGCGTTTT-TGGCAAAAGCGCCGCTAAAGGCCATGATCTA
1 TAGCGGCGTTTTCTGG-AAAAGCGCCGCTAAAGACCAGGATCGA
9781068 TAGCGGC
1 TAGCGGC
9781075 ACTTATATAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
42 3 0.08
43 37 0.93
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTTCTGGAAAAGCGCCGCTAAAGACCAGGATCGA
Found at i:9781093 original size:43 final size:43
Alignment explanation
Indices: 9781041--9781185 Score: 159
Period size: 43 Copynumber: 3.4 Consensus size: 43
9781031 CGTTTTTGGC
* * *
9781041 AAAAGCGCCGCTAAAGGCCATGATCTATAGCGGCACTTATATA
1 AAAAACGCCGCTAAAGACCATGATCTATAGCGGCGCTTATATA
* * **
9781084 AAAAACGCCGCTAAAGACCCTGATCTATAGTGGCGCTTATCCA
1 AAAAACGCCGCTAAAGACCATGATCTATAGCGGCGCTTATATA
* * * *
9781127 GAAAACGCTGCTAAAGACACCA--ATCTATAGCGGCGGTTATATT
1 AAAAACGCCGCTAAAG--ACCATGATCTATAGCGGCGCTTATATA
9781170 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
9781186 CTCTTAGTCT
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
43 80 0.96
45 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCATGATCTATAGCGGCGCTTATATA
Found at i:9781371 original size:22 final size:22
Alignment explanation
Indices: 9781343--9781385 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
9781333 TTGCGGCGCT
*
9781343 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
9781365 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
9781386 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:9783417 original size:47 final size:47
Alignment explanation
Indices: 9783347--9783440 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
9783337 CCGCCACAGG
*
9783347 CCTATCTTAAACTATGCAGGGAATTAATTGAGTCGAATCTATGCTTA
1 CCTATCTTAAACTATGCACGGAATTAATTGAGTCGAATCTATGCTTA
* *
9783394 CCTATCTTGAACTATGCACGGAATTAATTGAGTCGAATCTGTGCTTA
1 CCTATCTTAAACTATGCACGGAATTAATTGAGTCGAATCTATGCTTA
9783441 GAAACTGGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (47 bp):
CCTATCTTAAACTATGCACGGAATTAATTGAGTCGAATCTATGCTTA
Found at i:9785448 original size:3 final size:3
Alignment explanation
Indices: 9785442--9785472 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
9785432 AAAAAAAAAG
9785442 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
9785473 AATCAAGGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9802323 original size:26 final size:26
Alignment explanation
Indices: 9802294--9802380 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 26
9802284 AGTCCTTATG
* *
9802294 GACTTCCACAAAAGATAGTCCTCACA
1 GACTTCCACAAAAGATAGTCATGACA
*
9802320 GACTTTCCACAAAAGATAGTCATGATA
1 GAC-TTCCACAAAAGATAGTCATGACA
** * *
9802347 GACTTCCACATTAGATTGTCTTGACA
1 GACTTCCACAAAAGATAGTCATGACA
9802373 GACTTCCA
1 GACTTCCA
9802381 TATTTGCGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 29 0.56
27 23 0.44
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.26
Consensus pattern (26 bp):
GACTTCCACAAAAGATAGTCATGACA
Found at i:9809295 original size:27 final size:27
Alignment explanation
Indices: 9809264--9809569 Score: 336
Period size: 27 Copynumber: 11.4 Consensus size: 27
9809254 CTAATAGATG
9809264 AAAATGACTGAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
9809291 AAAATGACTGAAATACTCCCATAGAGT
1 AAAATGACTGAAATACCCCCATAGGGT
* * *
9809318 AAAATGACTGAAATACTCTCATAAGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
9809345 AAAATAACCGAAATA-CCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* * * *
9809371 AAAGTGACCGAAATACCCTCATAGAGT
1 AAAATGACTGAAATACCCCCATAGGGT
**
9809398 AAAATGACCAAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
*
9809425 AAAATGA-TCAAAATACCCCCATTA-GGT
1 AAAATGACT-GAAATACCCCCA-TAGGGT
*
9809452 AAAAT-AATCGAAATACCCCCATAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
* *
9809479 AAAATGACCGAAATACCCCTATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
9809506 AAAATGACTGAAATACCCTCATAGGAT
1 AAAATGACTGAAATACCCCCATAGGGT
**
9809533 AAAATGACTGTTATA-CCCC-TAGGAGAT
1 AAAATGACTGAAATACCCCCATAGG-G-T
9809560 AAAATGACTG
1 AAAATGACTG
9809570 TTATGGCCTT
Statistics
Matches: 240, Mismatches: 31, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
25 4 0.02
26 27 0.11
27 206 0.86
28 3 0.01
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (27 bp):
AAAATGACTGAAATACCCCCATAGGGT
Found at i:9809946 original size:28 final size:28
Alignment explanation
Indices: 9809915--9810131 Score: 305
Period size: 28 Copynumber: 7.8 Consensus size: 28
9809905 ACTGTTACTA
*
9809915 TATTGGGCTAAGACCCACACTGATTCTG
1 TATTGGGCTAAGGCCCACACTGATTCTG
9809943 TATTGGGCTAAGGCCCACACTG-TTACTG
1 TATTGGGCTAAGGCCCACACTGATT-CTG
* *
9809971 TATTGGGCTAAGGCCCACACTGATTTTT
1 TATTGGGCTAAGGCCCACACTGATTCTG
* * *
9809999 TATTGGGCTAAGGCTCACACTGGTTCTA
1 TATTGGGCTAAGGCCCACACTGATTCTG
*
9810027 TATTGGGCTAAGGCTCACACTGATTCTG
1 TATTGGGCTAAGGCCCACACTGATTCTG
* *
9810055 TATTAGGCTAAGGCCCACACTGATTTTG
1 TATTGGGCTAAGGCCCACACTGATTCTG
9810083 TATTGGGCTAAGGCCCACACTG-TTACTG
1 TATTGGGCTAAGGCCCACACTGATT-CTG
*
9810111 -ATTGGGCTAAAGCCCACACTG
1 TATTGGGCTAAGGCCCACACTG
9810132 TACTGCCACT
Statistics
Matches: 171, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
27 24 0.14
28 145 0.85
29 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (28 bp):
TATTGGGCTAAGGCCCACACTGATTCTG
Found at i:9813316 original size:22 final size:20
Alignment explanation
Indices: 9813259--9813317 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
9813249 TCTTTGTTCC
*
9813259 TAATCCTAAAACAAAATTAAA
1 TAATCCTAAAA-GAAATTAAA
* *
9813280 TCATCCTTAAAGAAATTAATA
1 TAATCCTAAAAGAAATTAA-A
9813301 TAATCCATAAAAGAAAT
1 TAATCC-TAAAAGAAAT
9813318 ATTCAATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 7 0.23
21 15 0.48
22 9 0.29
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.27
Consensus pattern (20 bp):
TAATCCTAAAAGAAATTAAA
Found at i:9814118 original size:20 final size:20
Alignment explanation
Indices: 9814091--9814150 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
9814081 TTTTTGATGT
*
9814091 GTTAAAATAATTTTAACTTG
1 GTTAAAATCATTTTAACTTG
* *
9814111 GTTGAAATCATTTTGACTTG
1 GTTAAAATCATTTTAACTTG
9814131 GTTAAAATCATTTTAACTTG
1 GTTAAAATCATTTTAACTTG
9814151 ATTTTAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (20 bp):
GTTAAAATCATTTTAACTTG
Found at i:9816056 original size:2 final size:2
Alignment explanation
Indices: 9816049--9816092 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
9816039 GTTATTTTAA
9816049 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9816090 AT A
1 AT A
9816093 CTNNNNNNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9816206 original size:2 final size:2
Alignment explanation
Indices: 9816199--9816238 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9816189 NNNNNNTTAT
9816199 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9816239 AACATATCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9816614 original size:138 final size:138
Alignment explanation
Indices: 9816434--9816712 Score: 540
Period size: 138 Copynumber: 2.0 Consensus size: 138
9816424 CAAATTCTTT
9816434 AAACATATATGATGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAATATATATCCATAC
1 AAACATATATGATGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAATATATATCCATAC
*
9816499 CGTAAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTAACATAAAATCATAATTGAATCC
66 CGAAAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTAACATAAAATCATAATTGAATCC
9816564 ATAAAAAA
131 ATAAAAAA
9816572 AAACATATATGATGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAATATATATCCATAC
1 AAACATATATGATGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAATATATATCCATAC
*
9816637 CGAAAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTAACATAAAATCATAATTGAATTC
66 CGAAAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTAACATAAAATCATAATTGAATCC
9816702 ATAAAAAA
131 ATAAAAAA
9816710 AAA
1 AAA
9816713 AAGTATCAAC
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.27
Consensus pattern (138 bp):
AAACATATATGATGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAATATATATCCATAC
CGAAAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTAACATAAAATCATAATTGAATCC
ATAAAAAA
Found at i:9816633 original size:69 final size:69
Alignment explanation
Indices: 9816434--9816635 Score: 155
Period size: 64 Copynumber: 2.9 Consensus size: 69
9816424 CAAATTCTTT
*
9816434 AAACATATATGATGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAATATATATCCATAC
1 AAACATATATGATGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAATATATATCCATAA
***
9816499 CGTA
66 AAAA
** ** * * * * * * * **
9816503 AAA-ATA-ACAACT--TCAACA--AATGTCCATCAAACCAATTTAACATAAAATCATAATTGAAT
1 AAACATATATGA-TGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAAT-AT-A-T--AT
9816562 CCATAAAAAA
60 CCATAAAAAA
9816572 AAACATATATGATGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAATATATATCCATA
1 AAACATATATGATGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAATATATATCCATA
9816636 CCGAAAAAAT
Statistics
Matches: 91, Mismatches: 30, Indels: 24
0.63 0.21 0.17
Matches are distributed among these distances:
64 21 0.23
65 2 0.02
66 5 0.05
67 3 0.03
68 4 0.04
69 21 0.23
70 4 0.04
71 3 0.03
72 5 0.05
73 2 0.02
74 21 0.23
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.28
Consensus pattern (69 bp):
AAACATATATGATGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAATATATATCCATAA
AAAA
Found at i:9816688 original size:69 final size:69
Alignment explanation
Indices: 9816477--9816688 Score: 163
Period size: 69 Copynumber: 3.1 Consensus size: 69
9816467 AAAGCACTTA
*
9816477 AAAATTGAATATATATCCATACCGTAAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTA
1 AAAATTGAATATATATCCATACCGAAAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTA
9816542 ACAT
66 ACAT
*** ** ** * * *
9816546 AAAATCAT-AAT-TGA-ATCCATAAAAAAAAACATATATGA-TGATGGACATGAATTTACTTCAA
1 AAAAT--TGAATAT-ATATCCATACCGAAAAA-ATA-ACAACT--TCAACA--AATGTCCATCAA
* *
9816607 AGC-ACTT---A-
57 ACCAATTTAACAT
9816615 AAAATTGAATATATATCCATACCGAAAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTA
1 AAAATTGAATATATATCCATACCGAAAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTA
9816680 ACAT
66 ACAT
9816684 AAAAT
1 AAAAT
9816689 CATAATTGAA
Statistics
Matches: 100, Mismatches: 25, Indels: 36
0.62 0.16 0.22
Matches are distributed among these distances:
64 11 0.11
65 3 0.03
66 4 0.04
67 3 0.03
68 9 0.09
69 40 0.40
70 9 0.09
71 3 0.03
72 4 0.04
73 3 0.03
74 11 0.11
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.26
Consensus pattern (69 bp):
AAAATTGAATATATATCCATACCGAAAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTA
ACAT
Found at i:9816713 original size:69 final size:69
Alignment explanation
Indices: 9816502--9816713 Score: 175
Period size: 69 Copynumber: 3.1 Consensus size: 69
9816492 TCCATACCGT
9816502 AAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTAACATAAAATCATAATTGAATCCATA
1 AAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTAACATAAAATCATAATTGAATCCATA
9816567 AAAA
66 AAAA
** ** * * * * * * * **
9816571 AAAACATATATGA-TGATGGACATGAATTTACTTCAAAGCACTTAAAAATTGAAT-AT-A-T--A
1 AAAA-ATA-ACAACT--TCAACA--AATGTCCATCAAACCAATTTAACATAAAATCATAATTGAA
***
9816630 TCCATACCGA
60 TCCATAAAAA
*
9816640 AAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTAACATAAAATCATAATTGAATTCATA
1 AAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTAACATAAAATCATAATTGAATCCATA
9816705 AAAA
66 AAAA
9816709 AAAAA
1 AAAAA
9816714 AGTATCAACA
Statistics
Matches: 98, Mismatches: 33, Indels: 24
0.63 0.21 0.15
Matches are distributed among these distances:
64 21 0.21
65 2 0.02
66 5 0.05
67 3 0.03
68 4 0.04
69 28 0.29
70 4 0.04
71 3 0.03
72 5 0.05
73 2 0.02
74 21 0.21
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (69 bp):
AAAAATAACAACTTCAACAAATGTCCATCAAACCAATTTAACATAAAATCATAATTGAATCCATA
AAAA
Found at i:9816752 original size:138 final size:137
Alignment explanation
Indices: 9816466--9816752 Score: 380
Period size: 138 Copynumber: 2.1 Consensus size: 137
9816456 GAATTTACTT
*
9816466 CAAAGCACTTAAAAATTGAATATATATCCATACCGTAAAAATAACAACTTCAACAAATGTCCATC
1 CAAA-CACTTAAAAATTGAATATATATCCATACCGAAAAAATAACAACTTCAACAAATGTCCATC
* ** * ** *
9816531 AAACCAATTTAACATAAAATCATAATTGAATCCATAAAAAAAAACATATATGATGATGGACATGA
65 AAACCAATTTAACATAAAATCATAATTGAATCCATAAAAAAAAAAATATACAATCATAAACATAA
*** *
9816596 ATTTACTT
130 AAACACTA
9816604 CAAAGCACTTAAAAATTGAATATATATCCATACCGAAAAAATAACAACTTCAACAAATGTCCATC
1 CAAA-CACTTAAAAATTGAATATATATCCATACCGAAAAAATAACAACTTCAACAAATGTCCATC
* * *
9816669 AAACCAATTTAACATAAAATCATAATTGAATTCATAAAAAAAAAAAGTATCAACAATCTTAAATA
65 AAACCAATTTAACATAAAATCATAATTGAATCCATAAAAAAAAAAA-TAT--ACAATCATAAACA
9816734 TAAAAACAC-A
127 TAAAAACACTA
9816744 CAAA-ACTTA
1 CAAACACTTA
9816753 GACCATAAAT
Statistics
Matches: 131, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
138 113 0.86
139 3 0.02
140 4 0.03
141 11 0.08
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.25
Consensus pattern (137 bp):
CAAACACTTAAAAATTGAATATATATCCATACCGAAAAAATAACAACTTCAACAAATGTCCATCA
AACCAATTTAACATAAAATCATAATTGAATCCATAAAAAAAAAAATATACAATCATAAACATAAA
AACACTA
Found at i:9817857 original size:9 final size:9
Alignment explanation
Indices: 9817843--9817879 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
9817833 TGGTTAAAAA
9817843 TTAACCGAT
1 TTAACCGAT
9817852 TTAACCGA-
1 TTAACCGAT
9817860 TTAACCGAT
1 TTAACCGAT
*
9817869 TTAATCGAT
1 TTAACCGAT
9817878 TT
1 TT
9817880 GAATCACTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (9 bp):
TTAACCGAT
Found at i:9817864 original size:17 final size:17
Alignment explanation
Indices: 9817842--9817878 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
9817832 TTGGTTAAAA
9817842 ATTAACCGATTTAACCG
1 ATTAACCGATTTAACCG
*
9817859 ATTAACCGATTTAATCG
1 ATTAACCGATTTAACCG
9817876 ATT
1 ATT
9817879 TGAATCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (17 bp):
ATTAACCGATTTAACCG
Found at i:9817918 original size:37 final size:37
Alignment explanation
Indices: 9817877--9818026 Score: 273
Period size: 37 Copynumber: 4.1 Consensus size: 37
9817867 ATTTAATCGA
*
9817877 TTTGAATCACTACATAATTAAAAAAATTACATAAGTC
1 TTTGAATCACTACATAATTAAAAACATTACATAAGTC
9817914 TTTGAATCACTACATAATTAAAAACATTACATAAGTC
1 TTTGAATCACTACATAATTAAAAACATTACATAAGTC
9817951 TTTGAATCACTACATAATTAAAAACATTACATAAGTC
1 TTTGAATCACTACATAATTAAAAACATTACATAAGTC
* *
9817988 TTTAAATCACTATATAATTAAAAACATTACATAAGTC
1 TTTGAATCACTACATAATTAAAAACATTACATAAGTC
9818025 TT
1 TT
9818027 AAAATTAACA
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 110 1.00
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.34
Consensus pattern (37 bp):
TTTGAATCACTACATAATTAAAAACATTACATAAGTC
Found at i:9817946 original size:17 final size:17
Alignment explanation
Indices: 9817887--9818021 Score: 72
Period size: 17 Copynumber: 7.4 Consensus size: 17
9817877 TTTGAATCAC
*
9817887 TACATAATTAAAAAAAT
1 TACATAATTAAAAACAT
** * *
9817904 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
9817924 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
9817941 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
9817961 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
* * *
9817978 TACATAAGTCTTTAAATCAC
1 TACATAA---TTAAAAACAT
*
9817998 TATATAATTAAAAACAT
1 TACATAATTAAAAACAT
9818015 TACATAA
1 TACATAA
9818022 GTCTTAAAAT
Statistics
Matches: 84, Mismatches: 25, Indels: 18
0.66 0.20 0.14
Matches are distributed among these distances:
17 46 0.55
20 38 0.45
ACGTcount: A:0.50, C:0.14, G:0.04, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:9818030 original size:20 final size:20
Alignment explanation
Indices: 9817894--9818030 Score: 94
Period size: 20 Copynumber: 7.3 Consensus size: 20
9817884 CACTACATAA
*
9817894 TTAAAAAAATTACATAAGTC
1 TTAAAAACATTACATAAGTC
** * *
9817914 TTTGAATCACTACATAA---
1 TTAAAAACATTACATAAGTC
9817931 TTAAAAACATTACATAAGTC
1 TTAAAAACATTACATAAGTC
** * *
9817951 TTTGAATCACTACATAA---
1 TTAAAAACATTACATAAGTC
9817968 TTAAAAACATTACATAAGTC
1 TTAAAAACATTACATAAGTC
* * * *
9817988 TTTAAATCACTATATAA---
1 TTAAAAACATTACATAAGTC
9818005 TTAAAAACATTACATAAGTC
1 TTAAAAACATTACATAAGTC
9818025 TTAAAA
1 TTAAAA
9818031 TTAACACATA
Statistics
Matches: 83, Mismatches: 25, Indels: 18
0.66 0.20 0.14
Matches are distributed among these distances:
17 39 0.47
20 44 0.53
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (20 bp):
TTAAAAACATTACATAAGTC
Found at i:9818040 original size:74 final size:74
Alignment explanation
Indices: 9817885--9818043 Score: 248
Period size: 74 Copynumber: 2.1 Consensus size: 74
9817875 GATTTGAATC
*
9817885 ACTACATAATTAAAAAAATTACATAAGTCTTTGAATCACTACATAATTAAAAACATTACATAAGT
1 ACTACATAATTAAAAAAATTACATAAGTCTTTAAATCACTACATAATTAAAAACATTACATAAGT
** *
9817950 CTTTGAATC
66 CTTAAAATA
* *
9817959 ACTACATAATTAAAAACATTACATAAGTCTTTAAATCACTATATAATTAAAAACATTACATAAGT
1 ACTACATAATTAAAAAAATTACATAAGTCTTTAAATCACTACATAATTAAAAACATTACATAAGT
9818024 CTTAAAATTA
66 CTTAAAA-TA
9818034 AC-ACATAATT
1 ACTACATAATT
9818044 GAAATGTAAG
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 75 0.96
75 3 0.04
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (74 bp):
ACTACATAATTAAAAAAATTACATAAGTCTTTAAATCACTACATAATTAAAAACATTACATAAGT
CTTAAAATA
Found at i:9821975 original size:13 final size:13
Alignment explanation
Indices: 9821957--9821985 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
9821947 TGTTAGAGAC
9821957 TTAGACTTTAGTT
1 TTAGACTTTAGTT
9821970 TTAGACTTTAGTT
1 TTAGACTTTAGTT
9821983 TTA
1 TTA
9821986 TTGGGTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGACTTTAGTT
Found at i:9822009 original size:19 final size:19
Alignment explanation
Indices: 9821985--9822057 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 19
9821975 CTTTAGTTTT
9821985 ATTGGGTTGGTAAATGGTA
1 ATTGGGTTGGTAAATGGTA
* * *
9822004 ATTGGGTTTGGGTAGACTTTAGTTT
1 ATTGGG-TT-GGTA-A--AT-GGTA
9822029 ATTGGGTTGGTAAATGGTA
1 ATTGGGTTGGTAAATGGTA
9822048 ATTGGGTTGG
1 ATTGGGTTGG
9822058 GTAATTGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 18 0.43
20 3 0.07
21 4 0.10
22 2 0.05
23 4 0.10
24 3 0.07
25 8 0.19
ACGTcount: A:0.21, C:0.01, G:0.37, T:0.41
Consensus pattern (19 bp):
ATTGGGTTGGTAAATGGTA
Found at i:9822038 original size:44 final size:44
Alignment explanation
Indices: 9821971--9822060 Score: 164
Period size: 44 Copynumber: 2.0 Consensus size: 44
9821961 ACTTTAGTTT
9821971 TAGACTTTAGTTTTATTGGGTTGGTAAATGGTAATTGGGTTTGGG
1 TAGACTTTAGTTTTATTGGGTTGGTAAATGGTAATTGGG-TTGGG
9822016 TAGACTTTAG-TTTATTGGGTTGGTAAATGGTAATTGGGTTGGG
1 TAGACTTTAGTTTTATTGGGTTGGTAAATGGTAATTGGGTTGGG
9822059 TA
1 TA
9822061 ATTGGGTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 7 0.16
44 28 0.62
45 10 0.22
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.43
Consensus pattern (44 bp):
TAGACTTTAGTTTTATTGGGTTGGTAAATGGTAATTGGGTTGGG
Found at i:9822062 original size:13 final size:13
Alignment explanation
Indices: 9822044--9822068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9822034 GTTGGTAAAT
9822044 GGTAATTGGGTTG
1 GGTAATTGGGTTG
9822057 GGTAATTGGGTT
1 GGTAATTGGGTT
9822069 TATTAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (13 bp):
GGTAATTGGGTTG
Found at i:9823646 original size:25 final size:25
Alignment explanation
Indices: 9823612--9823682 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
9823602 TATGCACATT
*
9823612 TATGCTCACACGAGCTGTGTATCAG
1 TATGCTCACACGAGCTGTGAATCAG
* * *
9823637 TATGCTCACACGAGCTATAAATCGG
1 TATGCTCACACGAGCTGTGAATCAG
*
9823662 TATGCTCGCACGAGCTGTGAA
1 TATGCTCACACGAGCTGTGAA
9823683 AATAGGCCTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (25 bp):
TATGCTCACACGAGCTGTGAATCAG
Found at i:9831302 original size:27 final size:25
Alignment explanation
Indices: 9831244--9831307 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
9831234 TCTTTTATAT
* * *
9831244 GTATGCTCACACGAGCTGTGTATCG
1 GTATGCTCACACAAGCTGTGAATAG
9831269 GTATGCTCACACAAGCTGTGAAAATAG
1 GTATGCTCACACAAGCTGTG--AATAG
*
9831296 GTCTGCTCACAC
1 GTATGCTCACAC
9831308 GAGTTATGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 19 0.58
27 14 0.42
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (25 bp):
GTATGCTCACACAAGCTGTGAATAG
Found at i:9841298 original size:75 final size:75
Alignment explanation
Indices: 9841213--9841363 Score: 257
Period size: 75 Copynumber: 2.0 Consensus size: 75
9841203 ATCTACTTGA
*
9841213 ACAAAAAACTTATAGCTCTTAGACTGATGGGTGAAGAATACTGGAATTTAATGTTGGATATCACC
1 ACAAAAAACTTATAGCTCTTAGACTGATGGGTGAAGAATACTAGAATTTAATGTTGGATATCACC
*
9841278 AGGATGATAT
66 AGAATGATAT
* *
9841288 ACAAAAAACTTATAGCTCTTAGACTGATGGTTGAAGAATACTAGAATTTGATGTTGGATATCACC
1 ACAAAAAACTTATAGCTCTTAGACTGATGGGTGAAGAATACTAGAATTTAATGTTGGATATCACC
*
9841353 ATAATGATAT
66 AGAATGATAT
9841363 A
1 A
9841364 AATGAAGAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (75 bp):
ACAAAAAACTTATAGCTCTTAGACTGATGGGTGAAGAATACTAGAATTTAATGTTGGATATCACC
AGAATGATAT
Found at i:9843425 original size:18 final size:18
Alignment explanation
Indices: 9843402--9843437 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
9843392 CCACCCCAAT
9843402 CTGATTTTATCACTAAAA
1 CTGATTTTATCACTAAAA
9843420 CTGATTTTATCACTAAAA
1 CTGATTTTATCACTAAAA
9843438 GAATTAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (18 bp):
CTGATTTTATCACTAAAA
Found at i:9846277 original size:44 final size:44
Alignment explanation
Indices: 9846214--9846320 Score: 205
Period size: 44 Copynumber: 2.4 Consensus size: 44
9846204 TTTGAGTATT
*
9846214 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
9846258 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
9846302 TCTGATCAGTGACAAGTGA
1 TCTGATCAGTGACAAGTGA
9846321 CAAGCGATAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:9846364 original size:57 final size:58
Alignment explanation
Indices: 9846271--9846394 Score: 223
Period size: 57 Copynumber: 2.2 Consensus size: 58
9846261 GATCAGTGAC
9846271 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGCGAT
1 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGCGAT
* *
9846329 AAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACAAGTGATAAGTGAT
1 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGCGAT
9846386 AAGTGATAA
1 AAGTGATAA
9846395 ATGATAAGTG
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
57 47 0.73
58 17 0.27
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (58 bp):
AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGCGAT
Found at i:9846382 original size:7 final size:7
Alignment explanation
Indices: 9846361--9846406 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
9846351 TACACTTATC
*
9846361 TGATCAG
1 TGATAAG
*
9846368 TGACAAG
1 TGATAAG
9846375 TGATAAG
1 TGATAAG
9846382 TGATAAG
1 TGATAAG
*
9846389 TGATAAA
1 TGATAAG
9846396 TGATAAG
1 TGATAAG
9846403 TGAT
1 TGAT
9846407 TCCGTGTAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.41, C:0.04, G:0.26, T:0.28
Consensus pattern (7 bp):
TGATAAG
Found at i:9847640 original size:16 final size:16
Alignment explanation
Indices: 9847610--9847652 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
9847600 TTTTAATTAA
9847610 AATTAAAATTAATTGT
1 AATTAAAATTAATTGT
*
9847626 TATTAAAATTAATTGT
1 AATTAAAATTAATTGT
*
9847642 AAGTAAAATTA
1 AATTAAAATTA
9847653 TCAAATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (16 bp):
AATTAAAATTAATTGT
Found at i:9847683 original size:59 final size:66
Alignment explanation
Indices: 9847643--9847839 Score: 318
Period size: 66 Copynumber: 3.1 Consensus size: 66
9847633 ATTAATTGTA
*
9847643 AGTAAAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGAT
1 AGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGAT
9847708 T
66 T
9847709 AGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGAT
1 AGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGAT
9847774 T
66 T
* *
9847775 AGTAAATTTATC-AA--ATT-A---TTAATTGTATCAATTGTTGTAACAAAATCTAACATTTGAT
1 AGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGAT
9847833 T
66 T
9847834 AGTAAA
1 AGTAAA
9847840 ACAAACTTGA
Statistics
Matches: 128, Mismatches: 3, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
59 45 0.35
62 1 0.01
63 3 0.02
65 2 0.02
66 77 0.60
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (66 bp):
AGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGAT
T
Found at i:9859429 original size:3 final size:3
Alignment explanation
Indices: 9859415--9859466 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
9859405 TTTTAAAAGC
* *
9859415 ATA ATA ACA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9859463 ATA A
1 ATA A
9859467 GATATTTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:9859586 original size:24 final size:23
Alignment explanation
Indices: 9859543--9859605 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
9859533 ATATATTTTT
*
9859543 TAGATTTTTTAAAAA-AAAATTA
1 TAGAATTTTTAAAAATAAAATTA
*
9859565 TA-ATATTTTTAAAAATACAAATTT
1 TAGA-ATTTTTAAAAATA-AAATTA
*
9859589 TAGAATTTTTATAAATA
1 TAGAATTTTTAAAAATA
9859606 TTTTGAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.03
22 12 0.35
23 1 0.03
24 19 0.56
25 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (23 bp):
TAGAATTTTTAAAAATAAAATTA
Found at i:9859615 original size:19 final size:19
Alignment explanation
Indices: 9859585--9859655 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
9859575 AAAAATACAA
9859585 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTA-AAATT
*
9859605 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTTAAAATT
*
9859624 ATTTTTAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAATT
9859644 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
9859656 TTTGTAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 3 0.07
19 26 0.58
20 16 0.36
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:9859636 original size:20 final size:20
Alignment explanation
Indices: 9859585--9859655 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
9859575 AAAAATACAA
*
9859585 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTAAAAATT
9859605 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
* *
9859624 ATTTTTAATTTTTGAAAATT
1 ATTTTGAATTTTTAAAAATT
9859644 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
9859656 TTTGTAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 8 0.18
19 17 0.38
20 20 0.44
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:9863048 original size:3 final size:3
Alignment explanation
Indices: 9863029--9863067 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
9863019 ACATGACATG
* * *
9863029 TTA TCA TTA TCA TTA TTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9863068 AGTACTTGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:9863068 original size:15 final size:15
Alignment explanation
Indices: 9863040--9863068 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9863030 TATCATTATC
9863040 ATTATTATTATTAAT
1 ATTATTATTATTAAT
9863055 ATTATTATTATTAA
1 ATTATTATTATTAA
9863069 GTACTTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATTATTATTAAT
Found at i:9865278 original size:21 final size:22
Alignment explanation
Indices: 9865252--9865298 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
9865242 AAATGGTAGC
** *
9865252 AAAATAGTGAAAAAAAA-TAAG
1 AAAATAGCAAAAAAAAAGTAAA
9865273 AAAATAGCAAAAAAAAAGTAAA
1 AAAATAGCAAAAAAAAAGTAAA
9865295 AAAA
1 AAAA
9865299 AAAAGCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.11
Consensus pattern (22 bp):
AAAATAGCAAAAAAAAAGTAAA
Found at i:9865860 original size:77 final size:77
Alignment explanation
Indices: 9865768--9865915 Score: 215
Period size: 77 Copynumber: 1.9 Consensus size: 77
9865758 TTACACATAA
* * * * *
9865768 TTTACTTGAATGTAATATATAACTACTTCGAAATTTGACACATTTGTTTTATCTGTTCTACTTCT
1 TTTACTTCAATGTAATACATAACTACTTCGAAATTTGACACACTTGTCTTATCTATTCTACTTCT
9865833 AAATGGTTCATT
66 AAATGGTTCATT
* * * *
9865845 TTTACTTCAATGTAATACATAGCTTCTTTGAAATTTGACACACTTGTCTTATCTATTCTACTTTT
1 TTTACTTCAATGTAATACATAACTACTTCGAAATTTGACACACTTGTCTTATCTATTCTACTTCT
9865910 AAATGG
66 AAATGG
9865916 GCTTCCAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 62 1.00
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (77 bp):
TTTACTTCAATGTAATACATAACTACTTCGAAATTTGACACACTTGTCTTATCTATTCTACTTCT
AAATGGTTCATT
Found at i:9870397 original size:37 final size:37
Alignment explanation
Indices: 9870356--9870430 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
9870346 CATTTTCGTA
9870356 AACCAGACTTGTATTAAATATTTACGAGAGTTATTTT
1 AACCAGACTTGTATTAAATATTTACGAGAGTTATTTT
9870393 AACCAGACTTGTATTAAATATTTACGAGAGTTATTTT
1 AACCAGACTTGTATTAAATATTTACGAGAGTTATTTT
9870430 A
1 A
9870431 GAAATGAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (37 bp):
AACCAGACTTGTATTAAATATTTACGAGAGTTATTTT
Found at i:9870659 original size:32 final size:32
Alignment explanation
Indices: 9870623--9870684 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
9870613 GATAACTTAA
*
9870623 TATATATATGT-TATAATAAATAACATGAAATG
1 TATATATAT-TATATAATAAATAAAATGAAATG
9870655 TATATATATTATATAATAAATAAAATGAAA
1 TATATATATTATATAATAAATAAAATGAAA
9870685 CATAAATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (32 bp):
TATATATATTATATAATAAATAAAATGAAATG
Found at i:9882968 original size:18 final size:18
Alignment explanation
Indices: 9882945--9882999 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 18
9882935 TGTCCATGGG
9882945 AGATTTATGGACTAAGTT
1 AGATTTATGGACTAAGTT
9882963 AGATTTGAGATGGTTTACTAAGTT
1 AGATTT---ATGG---ACTAAGTT
9882987 AGATTTATGGACT
1 AGATTTATGGACT
9883000 TTATTATTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
18 9 0.29
21 8 0.26
24 14 0.45
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (18 bp):
AGATTTATGGACTAAGTT
Found at i:9884406 original size:30 final size:30
Alignment explanation
Indices: 9884370--9884429 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
9884360 TTGTTGAGAG
*
9884370 TTAGGCTGACTTAGGCGTTTCTGTAACGAA
1 TTAGGCTGACTTAGGCATTTCTGTAACGAA
9884400 TTAGGCTGACTTAGGCATTTCTGTAACGAA
1 TTAGGCTGACTTAGGCATTTCTGTAACGAA
9884430 AAATTGCCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (30 bp):
TTAGGCTGACTTAGGCATTTCTGTAACGAA
Found at i:9886323 original size:91 final size:89
Alignment explanation
Indices: 9886155--9886362 Score: 258
Period size: 91 Copynumber: 2.3 Consensus size: 89
9886145 TGGACACTCC
* * * ** *
9886155 AATTTGTGGTTAAACCACCAGTG-TTGCAGGTTAATACGTTATTAGTAGCTTGAATACACAACGG
1 AATTTGTGGATAAATCACTAGTGTTTGCAGGTTAATACGTTACCAGTAGCTTGAATACACAACAG
*
9886219 GTTTGCAGATAAAAGCTACCAGTA
66 GTTTACAGATAAAAGCTACCAGTA
*
9886243 AATTTGTGGATAAATCACTAGTGTTTGCAGGTTAATACGCTT-CCAGTAGGTTGGGAATACACAA
1 AATTTGTGGATAAATCACTAGTGTTTGCAGGTTAATACG-TTACCAGTAGCTT--GAATACACAA
* * * *
9886307 CATGTTTACAGATAAAAGTTGCCTGTA
63 CAGGTTTACAGATAAAAGCTACCAGTA
*
9886334 AATTTGTGGATAAATCACTGGTGTTTGCA
1 AATTTGTGGATAAATCACTAGTGTTTGCA
9886363 AATAAACTGC
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
88 20 0.19
89 22 0.21
90 2 0.02
91 59 0.57
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (89 bp):
AATTTGTGGATAAATCACTAGTGTTTGCAGGTTAATACGTTACCAGTAGCTTGAATACACAACAG
GTTTACAGATAAAAGCTACCAGTA
Found at i:9890188 original size:18 final size:18
Alignment explanation
Indices: 9890165--9890202 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
9890155 ACCGTGTTAT
9890165 TTTGTGT-TCTATGCTATA
1 TTTGTGTAT-TATGCTATA
*
9890183 TTTGTGTATTATGTTATA
1 TTTGTGTATTATGCTATA
9890201 TT
1 TT
9890203 GTGACAGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (18 bp):
TTTGTGTATTATGCTATA
Found at i:9890993 original size:17 final size:17
Alignment explanation
Indices: 9890979--9891038 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
9890969 TATGATGTGA
9890979 TATGAACTGTTATGTAG
1 TATGAACTGTTATGTAG
* *
9890996 TATGAATTGCTAT-TCAG
1 TATGAACTGTTATGT-AG
* *
9891013 TATGAATTGTTATCTTA-
1 TATGAACTGTTAT-GTAG
9891030 TATGAACTG
1 TATGAACTG
9891039 ACATTTGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 1 0.03
17 33 0.92
18 1 0.03
19 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.43
Consensus pattern (17 bp):
TATGAACTGTTATGTAG
Found at i:9905380 original size:24 final size:25
Alignment explanation
Indices: 9905328--9905379 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
9905318 ACTGTTATAA
*
9905328 AAAATTATA-AAATAAAAATTAATT
1 AAAATTATATAAATAAAAAATAATT
9905352 AAAATTATATAAATGAAAAAAT-ATT
1 AAAATTATATAAAT-AAAAAATAATT
9905377 AAA
1 AAA
9905380 TAATATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 10 0.40
26 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAATTATATAAATAAAAAATAATT
Found at i:9905586 original size:32 final size:32
Alignment explanation
Indices: 9905550--9905610 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
9905540 ATTTAATTAA
*
9905550 AGAGA-GCTTTGAGAAATTTAGGGAGAAATTTG
1 AGAGATGCTTTGAGAAATTT-GGAAGAAATTTG
**
9905582 AGAGATTTTTTGAGAAATTTGGAAGAAAT
1 AGAGATGCTTTGAGAAATTTGGAAGAAAT
9905611 GTTGTGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 13 0.52
33 12 0.48
ACGTcount: A:0.39, C:0.02, G:0.28, T:0.31
Consensus pattern (32 bp):
AGAGATGCTTTGAGAAATTTGGAAGAAATTTG
Found at i:9908632 original size:16 final size:15
Alignment explanation
Indices: 9908597--9908643 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
9908587 TTAAACATAC
*
9908597 ATATTTAATTATAT-
1 ATATTTAATCATATA
9908611 ATATTTAATCATATA
1 ATATTTAATCATATA
* *
9908626 ATAATTTATTGATATA
1 AT-ATTTAATCATATA
9908642 AT
1 AT
9908644 TTATTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 13 0.46
15 2 0.07
16 13 0.46
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
ATATTTAATCATATA
Found at i:9911571 original size:13 final size:13
Alignment explanation
Indices: 9911553--9911581 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
9911543 ACTTTACAGA
9911553 AAAATTAATGAAT
1 AAAATTAATGAAT
9911566 AAAATTAATGAAT
1 AAAATTAATGAAT
9911579 AAA
1 AAA
9911582 TGAATAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (13 bp):
AAAATTAATGAAT
Found at i:9914033 original size:3 final size:3
Alignment explanation
Indices: 9914027--9914073 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
9914017 CTGAGTGGCT
9914027 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
9914074 TTCTTCTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:9914078 original size:3 final size:3
Alignment explanation
Indices: 9914072--9914120 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
9914062 ATCATCATCA
*
9914072 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
9914120 T
1 T
9914121 GTTCCAACAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:9915585 original size:15 final size:16
Alignment explanation
Indices: 9915565--9915598 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9915555 TTAAGAAACT
*
9915565 AAACAAA-GAAATTAA
1 AAACAAAGGAAATGAA
9915580 AAACAAAGGAAATGAA
1 AAACAAAGGAAATGAA
9915596 AAA
1 AAA
9915599 AATAGTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.74, C:0.06, G:0.12, T:0.09
Consensus pattern (16 bp):
AAACAAAGGAAATGAA
Found at i:9918270 original size:33 final size:33
Alignment explanation
Indices: 9918228--9918294 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
9918218 TTGTTACCTC
9918228 ACATAGTCTTTTATGTTCTTATTAAATCGAGCT
1 ACATAGTCTTTTATGTTCTTATTAAATCGAGCT
9918261 ACATAGTCTTTTATGTTCTTATTAAATCGAGCT
1 ACATAGTCTTTTATGTTCTTATTAAATCGAGCT
9918294 A
1 A
9918295 ATTGTTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (33 bp):
ACATAGTCTTTTATGTTCTTATTAAATCGAGCT
Found at i:9921419 original size:15 final size:15
Alignment explanation
Indices: 9921399--9921427 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9921389 GTATTGTTAT
9921399 TTGATAACACGGTGA
1 TTGATAACACGGTGA
9921414 TTGATAACACGGTG
1 TTGATAACACGGTG
9921428 TGTGAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:9924255 original size:56 final size:56
Alignment explanation
Indices: 9924169--9924280 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
9924159 GGCGGTGACC
9924169 TTGTTAATATAACTTGTTACACCCTAATGCTGTCACAGGTTATAATAACGAGGTCA
1 TTGTTAATATAACTTGTTACACCCTAATGCTGTCACAGGTTATAATAACGAGGTCA
*
9924225 TTGTTAGTATAACTTGTTACACCCTAATGCTGTCACAGGTTATAATAACGAGGTCA
1 TTGTTAATATAACTTGTTACACCCTAATGCTGTCACAGGTTATAATAACGAGGTCA
9924281 CCACTGTCGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (56 bp):
TTGTTAATATAACTTGTTACACCCTAATGCTGTCACAGGTTATAATAACGAGGTCA
Found at i:9925146 original size:3 final size:3
Alignment explanation
Indices: 9925138--9925199 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
9925128 CATGATCAAG
9925138 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
9925186 AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AA
9925200 TAATAATAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:9925438 original size:22 final size:21
Alignment explanation
Indices: 9925399--9925442 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
9925389 AAAATTATAA
*
9925399 AATATAAAAATATATATATGT
1 AATATAAAAAAATATATATGT
9925420 AATATAAGAAAAATATATATGT
1 AATATAA-AAAAATATATATGT
9925442 A
1 A
9925443 TGTGAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (21 bp):
AATATAAAAAAATATATATGT
Found at i:9925444 original size:26 final size:25
Alignment explanation
Indices: 9925404--9925458 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
9925394 TATAAAATAT
9925404 AAAAATATATATATGT-AA-TATAA
1 AAAAATATATATATGTGAATTATAA
9925427 GAAAAATATATATGTATGTGAATTATAA
1 -AAAAATATATA--TATGTGAATTATAA
9925455 AAAA
1 AAAA
9925459 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.41
26 5 0.19
27 6 0.22
28 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (25 bp):
AAAAATATATATATGTGAATTATAA
Found at i:9926193 original size:19 final size:19
Alignment explanation
Indices: 9926169--9926242 Score: 112
Period size: 19 Copynumber: 3.8 Consensus size: 19
9926159 AATCATATCT
*
9926169 TCTAAGAATGCATATCATA
1 TCTAAGATTGCATATCATA
9926188 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
9926209 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
9926228 TCTAAGATTTCATAT
1 TCTAAGATTGCATAT
9926243 TCTTGAAGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 32 0.63
21 19 0.37
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:9926206 original size:21 final size:21
Alignment explanation
Indices: 9926180--9926242 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
9926170 CTAAGAATGC
9926180 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
9926201 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
*
9926220 ATATCATATCTAAGATTTCAT
1 ATATCATATCTAAGATTGCAT
9926241 AT
1 AT
9926243 TCTTGAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 18 0.46
21 21 0.54
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:9926825 original size:44 final size:44
Alignment explanation
Indices: 9926776--9926978 Score: 175
Period size: 44 Copynumber: 4.7 Consensus size: 44
9926766 TTCTGATCCA
* * * * *
9926776 CTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCAATCTG
1 CTCCACTGCAACCTCAGGGAGATAAGATTGGCTTATTCAATCTG
*
9926820 TTCCACTGCAACCTCAGGGAGATAAGATTGGCTTATTCAATCTG
1 CTCCACTGCAACCTCAGGGAGATAAGATTGGCTTATTCAATCTG
* * * *
9926864 CTCCACTGCAACCTCGGGGAGATGAGACTGG---ATGC-ATCTG
1 CTCCACTGCAACCTCAGGGAGATAAGATTGGCTTATTCAATCTG
* * * * * * *
9926904 CTCTACTGCAACTTCAGAGAGACAAGATATGTGGTT-TT-AACCCG
1 CTCCACTGCAACCTCAGGGAGATAAGAT-TG-GCTTATTCAATCTG
* *
9926948 CTCCACTGCAACTTCAGGGAGATAGGATTGG
1 CTCCACTGCAACCTCAGGGAGATAAGATTGG
9926979 TTACTTCTGT
Statistics
Matches: 128, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
40 26 0.20
41 5 0.04
42 2 0.02
43 2 0.02
44 93 0.73
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (44 bp):
CTCCACTGCAACCTCAGGGAGATAAGATTGGCTTATTCAATCTG
Done.