Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000989.1 Hibiscus syriacus cultivar Beakdansim tig00001980_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 949177
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 3 of 3
Found at i:648230 original size:33 final size:33
Alignment explanation
Indices: 648116--648230 Score: 124
Period size: 35 Copynumber: 3.3 Consensus size: 33
648106 ATACAATCTG
* *
648116 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCA-TATCACGCCAATAACATCACC--AT
* *
648152 TCCATCACCATATCACGCCTATATCATCACCATAT
1 TCCATCACCATATCACGCCAATAACATCACC--AT
648187 TCCATCACCATATCACGCCAATAACATCATCC-T
1 TCCATCACCATATCACGCCAATAACATCA-CCAT
*
648220 TCCATTACCAT
1 TCCATCACCAT
648231 TTCATCACCA
Statistics
Matches: 75, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
33 11 0.15
35 52 0.69
36 12 0.16
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCACCAT
Found at i:650996 original size:6 final size:6
Alignment explanation
Indices: 650967--651016 Score: 66
Period size: 6 Copynumber: 8.2 Consensus size: 6
650957 AAAAGCAACA
*
650967 AAAAGAG AAAAAG AAAGAAG AAAAAT AAAAAG -AAAAG AAAAAG AAAAAG
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
651016 A
1 A
651017 CTCCTACATC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 5 0.13
6 24 0.62
7 10 0.26
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:651006 original size:17 final size:18
Alignment explanation
Indices: 650967--651016 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 18
650957 AAAAGCAACA
650967 AAAAGAGAAAAAGAAAGAAG
1 AAAA-AGAAAAAG-AAGAAG
*
650987 AAAAATAAAAAGAA-AAG
1 AAAAAGAAAAAGAAGAAG
651004 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
651017 CTCCTACATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.54
18 2 0.07
19 7 0.25
20 4 0.14
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAAGAAGAAG
Found at i:651007 original size:11 final size:11
Alignment explanation
Indices: 650975--651013 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
650965 CAAAAAGAGA
650975 AAAAGAAAGAAG
1 AAAAGAAA-AAG
*
650987 AAAAATAAAAAG
1 -AAAAGAAAAAG
650999 AAAAGAAAAAG
1 AAAAGAAAAAG
651010 AAAA
1 AAAA
651014 AGACTCCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 3 0.12
13 7 0.29
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:651014 original size:12 final size:12
Alignment explanation
Indices: 650967--651016 Score: 66
Period size: 13 Copynumber: 4.1 Consensus size: 12
650957 AAAAGCAACA
650967 AAAAGAGAAAAAG
1 AAAA-AGAAAAAG
*
650980 AAAGAAGAAAAAT
1 AAA-AAGAAAAAG
650993 AAAAAG-AAAAG
1 AAAAAGAAAAAG
651004 AAAAAGAAAAAG
1 AAAAAGAAAAAG
651016 A
1 A
651017 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 10 0.30
12 9 0.27
13 13 0.39
14 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:656276 original size:13 final size:12
Alignment explanation
Indices: 656257--656317 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
656247 ATATAGGCGT
656257 GATATGGTGATG
1 GATATGGTGATG
656269 GAATATGGTGAT-
1 G-ATATGGTGATG
*
656281 GATATAGGCG-T-
1 GATAT-GGTGATG
656292 GATAATGGTGATG
1 GAT-ATGGTGATG
656305 GACTATGGTGATG
1 GA-TATGGTGATG
656318 ATTTAGGCGT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
11 11 0.27
12 8 0.20
13 21 0.51
14 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:656312 original size:36 final size:36
Alignment explanation
Indices: 656239--656343 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
656229 ATTTAGAAGT
*
656239 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
656274 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
656310 TGGTGATGATTTAGGCGTGATAATGGTGATGGAA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
656344 GATTGTATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:657621 original size:21 final size:21
Alignment explanation
Indices: 657595--657636 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
657585 ACATGGCATC
*
657595 AATGGGGCAGCAACTATTTAT
1 AATGGGGCAACAACTATTTAT
657616 AATGGGGCAACAACTATTTAT
1 AATGGGGCAACAACTATTTAT
657637 GAAAGGTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (21 bp):
AATGGGGCAACAACTATTTAT
Found at i:662623 original size:13 final size:12
Alignment explanation
Indices: 662604--662664 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
662594 ATATAGGCGT
662604 GATATGGTGATG
1 GATATGGTGATG
662616 GAATATGGTGAT-
1 G-ATATGGTGATG
*
662628 GATATAGGCG-T-
1 GATAT-GGTGATG
662639 GATAATGGTGATG
1 GAT-ATGGTGATG
662652 GACTATGGTGATG
1 GA-TATGGTGATG
662665 ATTTAGGCGT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
11 11 0.27
12 8 0.20
13 21 0.51
14 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:662659 original size:36 final size:36
Alignment explanation
Indices: 662586--662690 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
662576 ATTTAGAAGT
*
662586 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
662621 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
662657 TGGTGATGATTTAGGCGTGATAATGGTGATGGAA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
662691 GATTGTATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:663342 original size:21 final size:21
Alignment explanation
Indices: 663313--663354 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
663303 ACATGGCATC
663313 AATGAGGCAGCAACTATTTAT
1 AATGAGGCAGCAACTATTTAT
*
663334 AATGGGGCAGCAACTATTTAT
1 AATGAGGCAGCAACTATTTAT
663355 GAAAGGTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (21 bp):
AATGAGGCAGCAACTATTTAT
Found at i:665096 original size:20 final size:22
Alignment explanation
Indices: 665067--665106 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
665057 GGGAGAGCTT
665067 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
665087 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
665107 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:668822 original size:20 final size:22
Alignment explanation
Indices: 668793--668832 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
668783 GGGAGAGCTT
668793 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
668813 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
668833 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:672092 original size:17 final size:15
Alignment explanation
Indices: 672072--672127 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 15
672062 ATTGGAGTGT
672072 AAAAAGAAAGAAAAGAC
1 AAAAAG-AAGAAAA-AC
*
672089 AAAAAGAAGAAAATTC
1 AAAAAGAAGAAAA-AC
*
672105 ATAAAAGAAGAAAAAG
1 A-AAAAGAAGAAAAAC
672121 AAAAAGA
1 AAAAAGA
672128 TTTCAAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.18
16 10 0.29
17 18 0.53
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.05
Consensus pattern (15 bp):
AAAAAGAAGAAAAAC
Found at i:672118 original size:26 final size:25
Alignment explanation
Indices: 672082--672143 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
672072 AAAAAGAAAG
*
672082 AAAAGACAAAAAGAAGAAA-A-TTCA
1 AAAAGAGAAAAAGAA-AAAGATTTCA
672106 TAAAAGAAGAAAAAGAAAAAGATTTCA
1 -AAAAG-AGAAAAAGAAAAAGATTTCA
672133 AAAAGAGAAAA
1 AAAAGAGAAAA
672144 GCAAGCCAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 14 0.42
26 15 0.45
27 4 0.12
ACGTcount: A:0.71, C:0.05, G:0.15, T:0.10
Consensus pattern (25 bp):
AAAAGAGAAAAAGAAAAAGATTTCA
Found at i:683719 original size:19 final size:18
Alignment explanation
Indices: 683677--683722 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
683667 GACGTCATAT
*
683677 GCAGCTCACAAAGTACAG
1 GCAGCTCACAAAGTAAAG
683695 GACAGCTCACAAAGTATAAG
1 G-CAGCTCACAAAGTA-AAG
683715 GCAGCTCA
1 GCAGCTCA
683723 TGGAACACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 21 0.84
20 3 0.12
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.13
Consensus pattern (18 bp):
GCAGCTCACAAAGTAAAG
Found at i:685649 original size:22 final size:21
Alignment explanation
Indices: 685612--685652 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
685602 CCATCTCTAT
685612 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
685633 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
685653 ATTCCGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:685983 original size:10 final size:9
Alignment explanation
Indices: 685967--686028 Score: 61
Period size: 10 Copynumber: 6.2 Consensus size: 9
685957 ATTGGAGTGC
685967 AAAAAGAAA
1 AAAAAGAAA
685976 AGAAAAGACAA
1 A-AAAAGA-AA
*
685987 AAATCAGAAA
1 AAA-AAGAAA
685997 AAAATCAGAAA
1 AAAA--AGAAA
686008 AAAAAGAAA
1 AAAAAGAAA
686017 AGAAAAGAAA
1 A-AAAAGAAA
686027 AA
1 AA
686029 TAAATTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
9 8 0.18
10 22 0.49
11 15 0.33
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:686012 original size:12 final size:11
Alignment explanation
Indices: 685985--686011 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
685975 AAGAAAAGAC
685985 AAAAATCAGAA
1 AAAAATCAGAA
685996 AAAAATCAGAA
1 AAAAATCAGAA
686007 AAAAA
1 AAAAA
686012 AGAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.07, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAATCAGAA
Found at i:686162 original size:29 final size:29
Alignment explanation
Indices: 686122--686190 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
686112 GATAACCTTA
686122 TTGTTTCTTGAGAAAGGTTGCAGTAAGTG
1 TTGTTTCTTGAGAAAGGTTGCAGTAAGTG
686151 TTGTTTCTTGAGAAAGGTTGCAGTAAGTG
1 TTGTTTCTTGAGAAAGGTTGCAGTAAGTG
686180 TTGTTTCTTGA
1 TTGTTTCTTGA
686191 ATTGTAAGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.22, C:0.07, G:0.29, T:0.42
Consensus pattern (29 bp):
TTGTTTCTTGAGAAAGGTTGCAGTAAGTG
Found at i:691186 original size:22 final size:21
Alignment explanation
Indices: 691149--691189 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
691139 CCATCTCCAT
691149 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
691170 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
691190 ATTCCACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:692003 original size:25 final size:25
Alignment explanation
Indices: 691973--692030 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 25
691963 AAAATTAGCA
691973 AAGAAAAAGTCAAGCACTCCAAAAG
1 AAGAAAAAGTCAAGCACTCCAAAAG
691998 AAG-AAAAGTCAAGCACTCCAAAAG
1 AAGAAAAAGTCAAGCACTCCAAAAG
*
692022 AACAAAAAG
1 AAGAAAAAG
692031 AAAAAGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 23 0.74
25 8 0.26
ACGTcount: A:0.59, C:0.19, G:0.16, T:0.07
Consensus pattern (25 bp):
AAGAAAAAGTCAAGCACTCCAAAAG
Found at i:712766 original size:338 final size:338
Alignment explanation
Indices: 712093--712769 Score: 918
Period size: 338 Copynumber: 2.0 Consensus size: 338
712083 TCATCTTGAT
*
712093 ACTTCTAGTTCTTAGTTCATATAAATAGTGCGTCAAAGTACTTATCACCACCCCTTGAAGAAACA
1 ACTTCTAGTTCCTAGTTCATATAAATAGTGCGTCAAAGTACTTATCACCACCCCTTGAAGAAACA
*
712158 ATATAAAGATTGGGTCTTTGCTCTCTATAGCATTGGTTCTTCTTTGAGCGTTCTTCAAGATACTA
66 ATATAAAGATTGGGTCTTTGCTCTCTATAGCATTGGTTCTTCTATGAGCGTTCTTCAAGATACTA
* * * * *
712223 TCCTCACAACCATCCTTTTGTTTCATCGCCATAACCATAACCATTTCAATCATCTTCTGCTTCCA
131 TCCACACAACCATCCCTTTGTTTCATCGCCATAACCATAACCATATCAACCATCTTCCGCTTCCA
* * *
712288 TCTCTCATTTATTAAATAGCCTACCTATTAAACCATACGTTTAACACCCTTATCCATTCTGTTTT
196 TCTCTCATTTATTAAATAGCCTACCTAATAAACCATACATTTAACACCCTTAACCATTCTGTTTT
* *
712353 GAGCCATTCACTTGTGCAGGTTATTTTGCTTCCTTCCTAGATCCATAATCAAACGAGAAGGTAGA
261 GAGCCATTCACTTGTGCAGGTTATTTTGCTTCCTTCCTAGATCCATAATCAAACGAGAAGGCACA
*
712418 ATTACCTTACATC
326 AGTACCTTACATC
* * * * * *
712431 ACTTCTGGTTCCTAGTTCTTATAACTAGTGGGTCAAAGTCCTTAAT-ACCACCCCTTGAAGAAGC
1 ACTTCTAGTTCCTAGTTCATATAAATAGTGCGTCAAAGTACTT-ATCACCACCCCTTGAAGAAAC
*
712495 AATATAAAGTTTGGGTCTTTGCTCTCTATAGCATTGGTTCTTCTATGAGAC-TTCTTCAAGATAC
65 AATATAAAGATTGGGTCTTTGCTCTCTATAGCATTGGTTCTTCTATGAG-CGTTCTTCAAGATAC
* ***
712559 TATCCACACTACCATCCCTTTGTTTCATCGCCATAACCATAGTTATATCAACCATCTTCCGCTTC
129 TATCCACACAACCATCCCTTTGTTTCATCGCCATAACCATAACCATATCAACCATCTTCCGCTTC
* * * * * *
712624 CATCAT-TTA-TTATTTAAATAGCCTACCTAATCACCCATACATTTACCACCTTTAACTATCTCT
194 CATC-TCTCATTTA-TTAAATAGCCTACCTAATAAACCATACATTTAACACCCTTAACCAT-TCT
* * * **
712687 -TTTTGATCCATTCACTTGTGTAGGTTGTTTTGCTTCCTTCCTAGATCCACT-ATCAATTGA-AG
256 GTTTTGAGCCATTCACTTGTGCAGGTTATTTTGCTTCCTTCCTAGATCCA-TAATCAAACGAGA-
*
712749 AGGCACAAGTGCCTTACATC
319 AGGCACAAGTACCTTACATC
712769 A
1 A
712770 AATAAAGTCA
Statistics
Matches: 296, Mismatches: 36, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
337 4 0.01
338 284 0.96
339 8 0.03
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (338 bp):
ACTTCTAGTTCCTAGTTCATATAAATAGTGCGTCAAAGTACTTATCACCACCCCTTGAAGAAACA
ATATAAAGATTGGGTCTTTGCTCTCTATAGCATTGGTTCTTCTATGAGCGTTCTTCAAGATACTA
TCCACACAACCATCCCTTTGTTTCATCGCCATAACCATAACCATATCAACCATCTTCCGCTTCCA
TCTCTCATTTATTAAATAGCCTACCTAATAAACCATACATTTAACACCCTTAACCATTCTGTTTT
GAGCCATTCACTTGTGCAGGTTATTTTGCTTCCTTCCTAGATCCATAATCAAACGAGAAGGCACA
AGTACCTTACATC
Found at i:723914 original size:35 final size:37
Alignment explanation
Indices: 723868--723947 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
723858 TTTGAGAATT
*
723868 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
723903 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
723940 TGGTGATG
1 TGGTGATG
723948 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:730266 original size:11 final size:11
Alignment explanation
Indices: 730248--730335 Score: 56
Period size: 11 Copynumber: 7.6 Consensus size: 11
730238 AGAATTTGGT
730248 GATGATATAGGC
1 GATGATAT-GGC
*
730260 G-TGATATGGT
1 GATGATATGGC
*
730270 GATGGACTATGGT
1 GAT-GA-TATGGC
730283 GATGATATAGGC
1 GATGATAT-GGC
*
730295 G-TGATATGGT
1 GATGATATGGC
*
730305 GATGGACTATGGT
1 GAT-GA-TATGGC
730318 GATGATATAGGC
1 GATGATAT-GGC
730330 G-TGATA
1 GATGATA
730336 ATGGAAGATG
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
10 6 0.09
11 25 0.39
12 15 0.23
13 18 0.28
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.31
Consensus pattern (11 bp):
GATGATATGGC
Found at i:730272 original size:22 final size:22
Alignment explanation
Indices: 730244--730335 Score: 73
Period size: 24 Copynumber: 4.0 Consensus size: 22
730234 TTTGAGAATT
730244 TGGTGATGATATAGGCG-TGATA
1 TGGTGATGATAT-GGCGATGATA
*
730266 TGGTGATGGACTATGGTGATGATA
1 TGGTGAT-GA-TATGGCGATGATA
* *
730290 TAGGCG-TGATATGGTGATGGACTA
1 T-GGTGATGATATGGCGAT-GA-TA
730314 TGGTGATGATATAGGCG-TGATA
1 TGGTGATGATAT-GGCGATGATA
730336 ATGGAAGATG
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
22 18 0.31
23 14 0.24
24 20 0.34
25 6 0.10
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (22 bp):
TGGTGATGATATGGCGATGATA
Found at i:730282 original size:13 final size:12
Alignment explanation
Indices: 730262--730360 Score: 66
Period size: 13 Copynumber: 8.2 Consensus size: 12
730252 ATATAGGCGT
730262 GATATGGTGATG
1 GATATGGTGATG
730274 GACTATGGTGAT-
1 GA-TATGGTGATG
*
730286 GATATAGGCG-T-
1 GATAT-GGTGATG
730297 GATATGGTGATG
1 GATATGGTGATG
730309 GACTATGGTGAT-
1 GA-TATGGTGATG
*
730321 GATATAGGCG-T-
1 GATAT-GGTGATG
*
730332 GATAATGGAAGATG
1 GAT-ATGG-TGATG
730346 GATTATGGTGATG
1 GA-TATGGTGATG
730359 GA
1 GA
730361 AATAGTATCT
Statistics
Matches: 71, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.04
11 19 0.27
12 17 0.24
13 25 0.35
14 6 0.08
15 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:730290 original size:35 final size:35
Alignment explanation
Indices: 730244--730358 Score: 194
Period size: 35 Copynumber: 3.2 Consensus size: 35
730234 TTTGAGAATT
730244 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
730279 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
* *
730314 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
730351 TGGTGATG
1 TGGTGATG
730359 GAAATAGTAT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
35 56 0.74
36 4 0.05
37 16 0.21
ACGTcount: A:0.27, C:0.04, G:0.37, T:0.31
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGACTA
Found at i:750595 original size:13 final size:13
Alignment explanation
Indices: 750573--750602 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
750563 ACTAAACACC
750573 TTTC-ACATACCT
1 TTTCAACATACCT
750585 TTTCAACATACCT
1 TTTCAACATACCT
750598 TTTCA
1 TTTCA
750603 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:762711 original size:14 final size:14
Alignment explanation
Indices: 762693--762732 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
762683 TTTCAAAAAA
*
762693 AAAAACAAAAAAGGC
1 AAAAA-AAAAACGGC
762708 AAAAAAAAAACGGC
1 AAAAAAAAAACGGC
762722 AAAAAAAAAAC
1 AAAAAAAAAAC
762733 AAAAAAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACGGC
Found at i:762717 original size:15 final size:15
Alignment explanation
Indices: 762692--762731 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
762682 TTTTCAAAAA
762692 AAAAAACAAAAAAGGC
1 AAAAAA-AAAAAAGGC
*
762708 -AAAAAAAAAACGGC
1 AAAAAAAAAAAAGGC
762722 AAAAAAAAAA
1 AAAAAAAAAA
762732 CAAAAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGGC
Found at i:770678 original size:10 final size:10
Alignment explanation
Indices: 770665--770707 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
770655 AAATTTTGGC
770665 TTTTTTGTTT
1 TTTTTTGTTT
**
770675 TTTTTTGCCT
1 TTTTTTGTTT
770685 TTTTTTG--T
1 TTTTTTGTTT
770693 TTTTTTGTTT
1 TTTTTTGTTT
770703 TTTTT
1 TTTTT
770708 AAAAAAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 8 0.28
10 21 0.72
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:773067 original size:13 final size:13
Alignment explanation
Indices: 773049--773073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
773039 GATACTATCT
773049 TTCCATTACCATC
1 TTCCATTACCATC
773062 TTCCATTACCAT
1 TTCCATTACCAT
773074 TTCACGCCTA
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:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCCATTACCATC
Found at i:773602 original size:16 final size:17
Alignment explanation
Indices: 773576--773607 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
773566 CTATCCACCC
773576 TATCATAACCATTTCTA
1 TATCATAACCATTTCTA
773593 TATC-TAACCATTTCT
1 TATCATAACCATTTCT
773608 TTTAAGCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (17 bp):
TATCATAACCATTTCTA
Found at i:780363 original size:19 final size:20
Alignment explanation
Indices: 780316--780366 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
780306 GAAACCCCTT
**
780316 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
780336 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
780355 TGAAGATACATG
1 TGAAAATACATG
780367 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:784374 original size:19 final size:20
Alignment explanation
Indices: 784327--784377 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
784317 GAAACCCCTT
**
784327 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
784347 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
784366 TGAAGATACATG
1 TGAAAATACATG
784378 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:797866 original size:23 final size:24
Alignment explanation
Indices: 797838--797891 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
797828 AAAATTCGCA
*
797838 AAGAAAA-TCAAAGTACTC-AAAAG
1 AAGAAAATTC-AAGCACTCAAAAAG
*
797861 AAGAAAATTCCAGCACTCAAAAAG
1 AAGAAAATTCAAGCACTCAAAAAG
797885 AAGAAAA
1 AAGAAAA
797892 GAAAAGCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.61, C:0.15, G:0.13, T:0.11
Consensus pattern (24 bp):
AAGAAAATTCAAGCACTCAAAAAG
Found at i:800440 original size:20 final size:20
Alignment explanation
Indices: 800415--800461 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
800405 CACTACGTGG
800415 GAAGAAATGAATGCCATTTT
1 GAAGAAATGAATGCCATTTT
800435 GAAGAAATGAATGCCATTTT
1 GAAGAAATGAATGCCATTTT
*
800455 GAGGAAA
1 GAAGAAA
800462 CGTTTGTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.26
Consensus pattern (20 bp):
GAAGAAATGAATGCCATTTT
Found at i:805413 original size:11 final size:13
Alignment explanation
Indices: 805381--805410 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
805371 TGGCCAAAGA
805381 TGAAAAGGTATGT
1 TGAAAAGGTATGT
805394 TGAAAAGGTATG-
1 TGAAAAGGTATGT
805406 TGAAA
1 TGAAA
805411 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:810895 original size:2 final size:2
Alignment explanation
Indices: 810888--810939 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
810878 ATACTATAGC
810888 TA 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 TA
*
810930 TA TA TC TA TA
1 TA TA TA TA TA
810940 GTTATTATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:811025 original size:17 final size:17
Alignment explanation
Indices: 810992--811031 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
810982 GTTATTATTA
810992 TATAATATAGTCACATTCT
1 TATAATATAG-CACATT-T
811011 TATAATATA-CACATTT
1 TATAATATAGCACATTT
811027 TATAA
1 TATAA
811032 GTTTATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 6 0.29
19 9 0.43
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
TATAATATAGCACATTT
Found at i:814554 original size:2 final size:2
Alignment explanation
Indices: 814547--814624 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
814537 ATATGGCAGC
814547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
814589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
814625 GTTGGTGATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:814839 original size:47 final size:47
Alignment explanation
Indices: 814786--814907 Score: 244
Period size: 47 Copynumber: 2.6 Consensus size: 47
814776 AGGGGTGGTA
814786 AACAAGGACTTTGACCCACTATCTATAAAGATATAGGAACCAGAAGT
1 AACAAGGACTTTGACCCACTATCTATAAAGATATAGGAACCAGAAGT
814833 AACAAGGACTTTGACCCACTATCTATAAAGATATAGGAACCAGAAGT
1 AACAAGGACTTTGACCCACTATCTATAAAGATATAGGAACCAGAAGT
814880 AACAAGGACTTTGACCCACTATCTATAA
1 AACAAGGACTTTGACCCACTATCTATAA
814908 GCTTGATAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 75 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (47 bp):
AACAAGGACTTTGACCCACTATCTATAAAGATATAGGAACCAGAAGT
Found at i:817780 original size:22 final size:20
Alignment explanation
Indices: 817755--817794 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
817745 ATGTTTGTTT
817755 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
817777 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
817795 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:819147 original size:13 final size:13
Alignment explanation
Indices: 819125--819154 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
819115 ACTAAACACC
819125 TTTC-ACATACCT
1 TTTCAACATACCT
819137 TTTCAACATACCT
1 TTTCAACATACCT
819150 TTTCA
1 TTTCA
819155 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:823077 original size:22 final size:20
Alignment explanation
Indices: 823052--823091 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
823042 ATGTTTGTTT
823052 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
823074 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
823092 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:836095 original size:9 final size:9
Alignment explanation
Indices: 836081--836106 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
836071 CAAGGTAACC
836081 TTGATGCCT
1 TTGATGCCT
836090 TTGATGCCT
1 TTGATGCCT
836099 TTGATGCC
1 TTGATGCC
836107 AAAAGTGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (9 bp):
TTGATGCCT
Found at i:841643 original size:22 final size:22
Alignment explanation
Indices: 841586--841644 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
841576 AAAATCCAGC
*
841586 AAAGAAAATCAAAGCACTCAAA
1 AAAGAAAATGAAAGCACTCAAA
* **
841608 AGAAGAAATTGAAAGCACTTGAA
1 A-AAGAAAATGAAAGCACTCAAA
*
841631 AAAGAAAAAGAAAG
1 AAAGAAAATGAAAG
841645 AAAGAAAAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 12 0.40
23 18 0.60
ACGTcount: A:0.63, C:0.10, G:0.17, T:0.10
Consensus pattern (22 bp):
AAAGAAAATGAAAGCACTCAAA
Found at i:846134 original size:338 final size:338
Alignment explanation
Indices: 845507--846156 Score: 959
Period size: 338 Copynumber: 1.9 Consensus size: 338
845497 TCATCTTGAT
*
845507 ACTTCTGGTTCTTAGTTCATATAACTAGTGCGTCAAAGTACTTATCACCACCCCTTGAAGAAACA
1 ACTTCTGGTTCCTAGTTCATATAACTAGTGCGTCAAAGTACTTATCACCACCCCTTGAAGAAACA
845572 ATATAAAGATTGGGTCTTTGCTCTCTATAGCATTGGTTCTTCTTTGAGCGTTCTTCAAGATACTA
66 ATATAAAGATTGGGTCTTTGCTCTCTATAGCATTGGTTCTTCTTTGAGCGTTCTTCAAGATACTA
* * * * *
845637 TCCTCACAACCATCCTTTTGTTTCATCGCCATAACCATAACCATTTCAATCATCTTCTGCTTCCA
131 TCCACACAACCATCCCTTTGTTTCATCGCCATAACCATAACCATATCAACCATCTTCCGCTTCCA
* *
845702 TCTCTCATTTATTAAATAGCCTACCTATTAAACCATACATTTAACACCCTTATCCATTCTGTTTT
196 TCTCTCATTTATTAAATAGCCTACCTAATAAACCATACATTTAACACCCTTAACCATTCTGTTTT
*
845767 GAGCCATTCACTTGTGCAGGTTATTTTGCTTCCTTTCTAGATCCACAATCAAATGAGAAGGTAGA
261 GAGCCATTCACTTGTGCAGGTTATTTTGCTTCCTTCCTAGATCCACAATCAAATGAGAAGGTAGA
845832 ATTACCTTACATC
326 ATTACCTTACATC
* * * *
845845 ACTTCTGGTTCCTAGTTCTTATAACTAGTGGGTCAAAGTCCTTAAT-ACCACCCCTTGAAGAAGC
1 ACTTCTGGTTCCTAGTTCATATAACTAGTGCGTCAAAGTACTT-ATCACCACCCCTTGAAGAAAC
* *
845909 AATATAAAGTTTGGGTCTTTGCTCTCTATATCATTGGTTCTTCTTTGAGAC-TTCTTCAAGATAC
65 AATATAAAGATTGGGTCTTTGCTCTCTATAGCATTGGTTCTTCTTTGAG-CGTTCTTCAAGATAC
* ***
845973 TATCCACACTACCATCCCTTTGTTTCATCGCCATAACCATAGTTATATCAACCATCTTCCGCTTC
129 TATCCACACAACCATCCCTTTGTTTCATCGCCATAACCATAACCATATCAACCATCTTCCGCTTC
* * * * * *
846038 CATCAT-TTA-TTATTTAAATAGCCTACCTAATCACCCATATATTTACCACCTTTAACCATCTCT
194 CATC-TCTCATTTA-TTAAATAGCCTACCTAATAAACCATACATTTAACACCCTTAACCAT-TCT
* * * *
846101 -TTTTGAGCCATTCACTTGTGTATGTTGTTTTGCTTCCTTCCTAGATCCACTATCAA
256 GTTTTGAGCCATTCACTTGTGCAGGTTATTTTGCTTCCTTCCTAGATCCACAATCAA
846157 TTGAAGAGGC
Statistics
Matches: 278, Mismatches: 29, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
337 3 0.01
338 268 0.96
339 7 0.03
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.37
Consensus pattern (338 bp):
ACTTCTGGTTCCTAGTTCATATAACTAGTGCGTCAAAGTACTTATCACCACCCCTTGAAGAAACA
ATATAAAGATTGGGTCTTTGCTCTCTATAGCATTGGTTCTTCTTTGAGCGTTCTTCAAGATACTA
TCCACACAACCATCCCTTTGTTTCATCGCCATAACCATAACCATATCAACCATCTTCCGCTTCCA
TCTCTCATTTATTAAATAGCCTACCTAATAAACCATACATTTAACACCCTTAACCATTCTGTTTT
GAGCCATTCACTTGTGCAGGTTATTTTGCTTCCTTCCTAGATCCACAATCAAATGAGAAGGTAGA
ATTACCTTACATC
Found at i:851545 original size:35 final size:37
Alignment explanation
Indices: 851499--851578 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
851489 TTTGAGAATT
*
851499 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
851534 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
851571 TGGTGATG
1 TGGTGATG
851579 GAAATAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:856029 original size:35 final size:37
Alignment explanation
Indices: 855983--856062 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
855973 TTTGAGAATT
*
855983 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
856018 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
856055 TGGTGATG
1 TGGTGATG
856063 GAAATAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:873214 original size:28 final size:29
Alignment explanation
Indices: 873172--873233 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
873162 TCTTTTACAA
*
873172 TTTTTTTGAA-ATTTTGGCTTTTCTGTTT
1 TTTTTTTGAATATTTTGCCTTTTCTGTTT
* * *
873200 TTTTTTTGACTTTTTTTGCCTTTTTTGTTT
1 TTTTTTTGA-ATATTTTGCCTTTTCTGTTT
873230 TTTT
1 TTTT
873234 AAAATAGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 9 0.32
30 19 0.68
ACGTcount: A:0.06, C:0.08, G:0.11, T:0.74
Consensus pattern (29 bp):
TTTTTTTGAATATTTTGCCTTTTCTGTTT
Found at i:875592 original size:13 final size:13
Alignment explanation
Indices: 875574--875598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
875564 GATGCTATCT
875574 TTCCATTACCATC
1 TTCCATTACCATC
875587 TTCCATTACCAT
1 TTCCATTACCAT
875599 TTCACGCTAT
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:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCCATTACCATC
Found at i:878687 original size:19 final size:20
Alignment explanation
Indices: 878640--878690 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
878630 GAAACCCCTT
**
878640 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
878660 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
878679 TGAAGATACATG
1 TGAAAATACATG
878691 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:880095 original size:23 final size:24
Alignment explanation
Indices: 880067--880120 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
880057 AAATTCCGCA
*
880067 AAGAAAA-TCAAAGTACTC-AAAAG
1 AAGAAAATTC-AAGCACTCAAAAAG
*
880090 AAGAAAATTCCAGCACTCAAAAAG
1 AAGAAAATTCAAGCACTCAAAAAG
880114 AAGAAAA
1 AAGAAAA
880121 GAAAAGCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.61, C:0.15, G:0.13, T:0.11
Consensus pattern (24 bp):
AAGAAAATTCAAGCACTCAAAAAG
Found at i:887739 original size:16 final size:15
Alignment explanation
Indices: 887718--887747 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
887708 AAGACCAGAA
887718 TTCTTTTTCTTTTTTT
1 TTCTTTTT-TTTTTTT
887734 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
887748 AATTTTCGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTCTTTTTTTTTTTT
Found at i:887746 original size:11 final size:10
Alignment explanation
Indices: 887721--887745 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
887711 ACCAGAATTC
887721 TTTTTCTTTT
1 TTTTTCTTTT
887731 TTTTTCTTTT
1 TTTTTCTTTT
887741 TTTTT
1 TTTTT
887746 TTAATTTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:892440 original size:26 final size:26
Alignment explanation
Indices: 892410--892461 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
892400 GTACACTGGA
892410 GTGTGATGCACGATGAGGCAGCTTGG
1 GTGTGATGCACGATGAGGCAGCTTGG
892436 GTGTGATGCACGATGAGGCAGCTTGG
1 GTGTGATGCACGATGAGGCAGCTTGG
892462 TAGAGTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.42, T:0.23
Consensus pattern (26 bp):
GTGTGATGCACGATGAGGCAGCTTGG
Found at i:894814 original size:17 final size:17
Alignment explanation
Indices: 894781--894820 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
894771 GTTATTATTA
894781 TATAATATAGTCACATTCT
1 TATAATATAG-CACATT-T
894800 TATAATATA-CACATTT
1 TATAATATAGCACATTT
894816 TATAA
1 TATAA
894821 GTTTATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 6 0.29
19 9 0.43
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
TATAATATAGCACATTT
Found at i:898557 original size:47 final size:47
Alignment explanation
Indices: 898488--898609 Score: 244
Period size: 47 Copynumber: 2.6 Consensus size: 47
898478 AGGAGTGGTA
898488 AACAAGGACTTTGACCCACTATCTATAAAGATATAGGAACCAGAAGT
1 AACAAGGACTTTGACCCACTATCTATAAAGATATAGGAACCAGAAGT
898535 AACAAGGACTTTGACCCACTATCTATAAAGATATAGGAACCAGAAGT
1 AACAAGGACTTTGACCCACTATCTATAAAGATATAGGAACCAGAAGT
898582 AACAAGGACTTTGACCCACTATCTATAA
1 AACAAGGACTTTGACCCACTATCTATAA
898610 GCTTGATAAG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 75 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (47 bp):
AACAAGGACTTTGACCCACTATCTATAAAGATATAGGAACCAGAAGT
Found at i:908714 original size:11 final size:13
Alignment explanation
Indices: 908682--908711 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
908672 TGGCCAAAGA
908682 TGAAAAGGTATGT
1 TGAAAAGGTATGT
908695 TGAAAAGGTATG-
1 TGAAAAGGTATGT
908707 TGAAA
1 TGAAA
908712 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:922184 original size:11 final size:11
Alignment explanation
Indices: 922162--922241 Score: 65
Period size: 11 Copynumber: 6.7 Consensus size: 11
922152 TTTGAGAATT
922162 TGGTGATGATA
1 TGGTGATGATA
922173 TAGGTG-TGATA
1 T-GGTGATGATA
922184 TGGTGATGGACTA
1 TGGTGAT-GA-TA
922197 TGGTGATGATA
1 TGGTGATGATA
922208 TAGGTG-TGATAA
1 T-GGTGATGAT-A
*
922220 TGGAAGATGGATTA
1 TGG-TGAT-GA-TA
922234 TGGTGATG
1 TGGTGATG
922242 GAAATAGTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
10 4 0.07
11 17 0.30
12 16 0.28
13 13 0.23
14 6 0.11
15 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.38, T:0.34
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:922190 original size:22 final size:22
Alignment explanation
Indices: 922162--922241 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 22
922152 TTTGAGAATT
922162 TGGTGATGATATAGGTG-TGATA
1 TGGTGATGATAT-GGTGATGATA
922184 TGGTGATGGACTATGGTGATGATA
1 TGGTGAT-GA-TATGGTGATGATA
*
922208 TAGGTG-TGATAATGGAAGATGGATTA
1 T-GGTGATGAT-ATGG-TGAT-GA-TA
922234 TGGTGATG
1 TGGTGATG
922242 GAAATAGTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
22 8 0.17
23 12 0.25
24 13 0.27
25 10 0.21
26 5 0.10
ACGTcount: A:0.28, C:0.01, G:0.38, T:0.34
Consensus pattern (22 bp):
TGGTGATGATATGGTGATGATA
Found at i:922208 original size:35 final size:37
Alignment explanation
Indices: 922162--922241 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
922152 TTTGAGAATT
*
922162 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGTGTGATAATGGAAGATGGACTA
*
922197 TGGTGATGATATAGGTGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGTGTGATAATGGAAGATGGACTA
922234 TGGTGATG
1 TGGTGATG
922242 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.01, G:0.38, T:0.34
Consensus pattern (37 bp):
TGGTGATGATATAGGTGTGATAATGGAAGATGGACTA
Found at i:922243 original size:13 final size:13
Alignment explanation
Indices: 922182--922243 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
922172 ATAGGTGTGA
*
922182 TATGGTGATGGAC
1 TATGGTGATGGAT
922195 TATGGTGAT-GA-
1 TATGGTGATGGAT
922206 TATAGGTG-T-GAT
1 TAT-GGTGATGGAT
* *
922218 AATGGAAGATGGAT
1 TATGG-TGATGGAT
922232 TATGGTGATGGA
1 TATGGTGATGGA
922244 AATAGTATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
11 8 0.20
12 9 0.22
13 16 0.40
14 7 0.17
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.32
Consensus pattern (13 bp):
TATGGTGATGGAT
Found at i:922604 original size:20 final size:19
Alignment explanation
Indices: 922579--922629 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
922569 GAAACCCCTT
*
922579 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTAT-A
*
922599 TGAAAATATATGATTTATA
1 TGAAAATACATGATTTATA
*
922618 TGAAGATACATG
1 TGAAAATACATG
922630 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (19 bp):
TGAAAATACATGATTTATA
Found at i:930180 original size:16 final size:16
Alignment explanation
Indices: 930159--930191 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
930149 TAGTTAGCTC
930159 ATTTGCATCCTAACAT
1 ATTTGCATCCTAACAT
*
930175 ATTTGCATTCTAACAT
1 ATTTGCATCCTAACAT
930191 A
1 A
930192 GGTGGCAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTTGCATCCTAACAT
Found at i:944361 original size:15 final size:15
Alignment explanation
Indices: 944337--944372 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
944327 TTTGATAACT
*
944337 ATTCTATCCATTTCA
1 ATTCTTTCCATTTCA
944352 ATTCTTTCCATTTCA
1 ATTCTTTCCATTTCA
*
944367 TTTCTT
1 ATTCTT
944373 AATTATTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTCTTTCCATTTCA
Done.