Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015895.1 Corchorus olitorius cultivar O-4 contig15928, 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: 180237
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:451 original size:23 final size:23
Alignment explanation
Indices: 425--473 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
415 CTAAATTTCT
* * *
425 AAGTTTAAATAGTCATCTCTATA
1 AAGTTTAAACAATCAACTCTATA
448 AAGTTTAAACAATCAACTCTATA
1 AAGTTTAAACAATCAACTCTATA
471 AAG
1 AAG
474 CTAAATTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (23 bp):
AAGTTTAAACAATCAACTCTATA
Found at i:3255 original size:2 final size:2
Alignment explanation
Indices: 3248--3273 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3238 TAATAGTATG
3248 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
3274 GTGTACTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8458 original size:17 final size:17
Alignment explanation
Indices: 8436--8483 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
8426 CATACCATAT
*
8436 GACTAGTAATGTTTTAG
1 GACTAGTAATGTTTTAA
*
8453 GACTAGTTATGTTTTAA
1 GACTAGTAATGTTTTAA
*
8470 TACTAGTAATGTTT
1 GACTAGTAATGTTT
8484 CTTAAATCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (17 bp):
GACTAGTAATGTTTTAA
Found at i:10524 original size:22 final size:22
Alignment explanation
Indices: 10496--10934 Score: 207
Period size: 22 Copynumber: 19.9 Consensus size: 22
10486 TGATAATCAC
10496 TATAAAATTTTGATAACCTCCA
1 TATAAAATTTTGATAACCTCCA
* *
10518 TATAAAATTTTGATAA-TTACA
1 TATAAAATTTTGATAACCTCCA
* * * *
10539 CTATAAAATTTTTATGACGGTAC-
1 -TATAAAATTTTGATAAC-CTCCA
* * *
10562 TATAAAATTTCGAGAACTTCCA
1 TATAAAATTTTGATAACCTCCA
* * * *
10584 TATAAAATTGTGTTAACTTCCC
1 TATAAAATTTTGATAACCTCCA
*
10606 TATAAAATTTTG-TTACACTACC-
1 TATAAAATTTTGATAAC-CT-CCA
** *
10628 TATAAAATTTAAATAACCACC-
1 TATAAAATTTTGATAACCTCCA
* * *
10649 TAATGAAATTTTGATAACCACCC
1 T-ATAAAATTTTGATAACCTCCA
*
10672 TATGAAATTTTGATAACCTCTCA
1 TATAAAATTTTGATAACCTC-CA
* * * * *
10695 -ATGAAATGTTGGTAAGC-GCA
1 TATAAAATTTTGATAACCTCCA
10715 TATTATGAAATTTTGATAACCTTCCAA
1 TA-TA--AAATTTTGATAACC-TCC-A
* * *
10742 TAAAAAATATTGGTAA--TCACA
1 TATAAAATTTTGATAACCTC-CA
10763 TTATAAAATTTTGATAACCAT--A
1 -TATAAAATTTTGATAACC-TCCA
* *
10785 TCATGAAATTGTGAT-ACCT-CA
1 T-ATAAAATTTTGATAACCTCCA
10806 CTATGAAAATTTTGATAACCTCCA
1 -TAT-AAAATTTTGATAACCTCCA
* *
10830 TTTGAAATTTTGATAACCT-C-
1 TATAAAATTTTGATAACCTCCA
*
10850 -ATGAAATTTTGATAACCATCC-
1 TATAAAATTTTGATAACC-TCCA
*
10871 TATAAAATTTTGATAACATACC-
1 TATAAAATTTTGATAACCT-CCA
* *
10893 TAT-AAATTCTCT-ATAACTTCCT
1 TATAAAATT-T-TGATAACCTCCA
*
10915 TATAAAATTTTGTTAACCTC
1 TATAAAATTTTGATAACCTC
10935 TTAGAGAACT
Statistics
Matches: 325, Mismatches: 55, Indels: 74
0.72 0.12 0.16
Matches are distributed among these distances:
19 16 0.05
20 4 0.01
21 33 0.10
22 221 0.68
23 19 0.06
24 26 0.08
25 1 0.00
26 2 0.01
27 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (22 bp):
TATAAAATTTTGATAACCTCCA
Found at i:10545 original size:44 final size:44
Alignment explanation
Indices: 10484--10931 Score: 248
Period size: 44 Copynumber: 10.2 Consensus size: 44
10474 TCTTATGAAA
10484 TTTGATAA-T-CACTATAAAATTTTGATAACCTCCATATAAAAT
1 TTTGATAACTACACTATAAAATTTTGATAACCTCCATATAAAAT
* * * * *
10526 TTTGATAATTACACTATAAAATTTTTATGACGGTAC-TATAAAAT
1 TTTGATAACTACACTATAAAATTTTGATAAC-CTCCATATAAAAT
* * * * * * *
10570 TTCGAGAACTTC-CATATAAAATTGTGTTAACTTCCCTATAAAAT
1 TTTGATAACTACAC-TATAAAATTTTGATAACCTCCATATAAAAT
* ** * *
10614 TTTGTTACACTAC-CTATAAAATTTAAATAACCACC-TAATGAAAT
1 TTTGATA-ACTACACTATAAAATTTTGATAACCTCCAT-ATAAAAT
* * * *
10658 TTTGATAACCACCCTATGAAATTTTGATAACCTCTCA-ATGAAAT
1 TTTGATAACTACACTATAAAATTTTGATAACCTC-CATATAAAAT
* * * * * * *
10702 GTTGGTAAGCGCATATTATGAAATTTTGATAACCTTCCAATAAAAAAT
1 TTTGATAA-C-TACACTATAAAATTTTGATAACC-TCC-ATATAAAAT
* * * *
10750 ATTGGTAA-TCACATTATAAAATTTTGATAACCAT--ATCATGAAAT
1 TTTGATAACT-ACACTATAAAATTTTGATAACC-TCCAT-ATAAAAT
* * * *
10794 TGTGATACCT-CACTATGAAAATTTTGATAACCTCCATTTGAAAT
1 TTTGATAACTACACTAT-AAAATTTTGATAACCTCCATATAAAAT
* *
10838 TTTGATAAC--CTC-ATGAAATTTTGATAACCATCC-TATAAAAT
1 TTTGATAACTACACTATAAAATTTTGATAACC-TCCATATAAAAT
* *
10879 TTTGATAACATAC-CTAT-AAATTCTCT-ATAACTTCCTTATAAAAT
1 TTTGATAAC-TACACTATAAAATT-T-TGATAACCTCCATATAAAAT
*
10923 TTTGTTAAC
1 TTTGATAAC
10932 CTCTTAGAGA
Statistics
Matches: 318, Mismatches: 59, Indels: 56
0.73 0.14 0.13
Matches are distributed among these distances:
41 29 0.09
42 13 0.04
43 28 0.09
44 178 0.56
45 13 0.04
46 42 0.13
47 3 0.01
48 12 0.04
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (44 bp):
TTTGATAACTACACTATAAAATTTTGATAACCTCCATATAAAAT
Found at i:10766 original size:46 final size:45
Alignment explanation
Indices: 10672--10781 Score: 125
Period size: 46 Copynumber: 2.4 Consensus size: 45
10662 ATAACCACCC
* * *
10672 TATGAAATTTTGATAACCTCTCAATGAAATGTTGGTAAGCGCATAT
1 TATGAAATTTTGATAACCTCTCAATAAAATATTGGTAA-CGCACAT
*
10718 TATGAAATTTTGATAACCT-TCCAATAAAAAATATTGGTAA-TCACAT
1 TATGAAATTTTGATAACCTCT-CAAT--AAAATATTGGTAACGCACAT
*
10764 TATAAAATTTTGATAACC
1 TATGAAATTTTGATAACC
10782 ATATCATGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
45 1 0.02
46 44 0.79
48 11 0.20
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (45 bp):
TATGAAATTTTGATAACCTCTCAATAAAATATTGGTAACGCACAT
Found at i:10909 original size:63 final size:63
Alignment explanation
Indices: 10768--10889 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
10758 TCACATTATA
* *
10768 AAATTTTGATAACCATATCATGAAATTGTGATACCTCACTATGAAAATTTTGATAACCTCCATTT
1 AAATTTTGATAACC---TCATGAAATTGTGATACCTCACTATGAAAATTTTGATAACATCCATAT
10833 G
63 G
*
10834 AAATTTTGATAACCTCATGAAATTTTGATAACCATC-CTAT-AAAATTTTGATAACAT
1 AAATTTTGATAACCTCATGAAATTGTGAT-ACC-TCACTATGAAAATTTTGATAACAT
10890 ACCTATAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
63 29 0.56
64 7 0.13
65 2 0.04
66 14 0.27
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (63 bp):
AAATTTTGATAACCTCATGAAATTGTGATACCTCACTATGAAAATTTTGATAACATCCATATG
Found at i:12220 original size:7 final size:7
Alignment explanation
Indices: 12210--12274 Score: 65
Period size: 6 Copynumber: 10.4 Consensus size: 7
12200 AATTTAAAAT
*
12210 TAAATCA
1 TAAATAA
12217 TAAATAA
1 TAAATAA
12224 T-AATAA
1 TAAATAA
12230 T-AATAA
1 TAAATAA
12236 T-AATAA
1 TAAATAA
12242 T-AATAA
1 TAAATAA
12248 T-AATAA
1 TAAATAA
12254 T-AATAA
1 TAAATAA
12260 T-AATAA
1 TAAATAA
12266 T-AATAA
1 TAAATAA
12272 TAA
1 TAA
12275 TATATGATAG
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
6 48 0.86
7 8 0.14
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (7 bp):
TAAATAA
Found at i:12227 original size:3 final size:3
Alignment explanation
Indices: 12219--12276 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
12209 TTAAATCATA
12219 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12267 AAT AAT AAT A
1 AAT AAT AAT A
12277 TATGATAGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19718 original size:69 final size:69
Alignment explanation
Indices: 19602--19739 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
19592 ACAATATTGA
* *
19602 AATCCCCCTAACACCCACGAAATATTATAACCTGATAAAGTGAGCCTTACCTCCTCAAATAAAAT
1 AATCCCCCTAACACCCACAAAATATTATAACCCGATAAAGTGAGCCTTACCTCCTCAAATAAAAT
19667 TTCC
66 TTCC
*
19671 AATCTCCCTAACACCCACAAAATATTATAACCCGATAAAGTGAGCCTTACCTCCTCAAATAAAAT
1 AATCCCCCTAACACCCACAAAATATTATAACCCGATAAAGTGAGCCTTACCTCCTCAAATAAAAT
19736 TTCC
66 TTCC
19740 CTTCGCCAAC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.38, C:0.30, G:0.07, T:0.25
Consensus pattern (69 bp):
AATCCCCCTAACACCCACAAAATATTATAACCCGATAAAGTGAGCCTTACCTCCTCAAATAAAAT
TTCC
Found at i:21686 original size:22 final size:22
Alignment explanation
Indices: 21658--21711 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
21648 ACATTAAAAA
* *
21658 TGGGTCGTGCTGCGTCGGCACG
1 TGGGTCGTGCTGCGCCAGCACG
*
21680 TGGGTCGTGCTGTGCCAGCACG
1 TGGGTCGTGCTGCGCCAGCACG
21702 TGGGTCGTGC
1 TGGGTCGTGC
21712 CGTGCCATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.06, C:0.26, G:0.44, T:0.24
Consensus pattern (22 bp):
TGGGTCGTGCTGCGCCAGCACG
Found at i:21716 original size:22 final size:22
Alignment explanation
Indices: 21675--21718 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21665 TGCTGCGTCG
*
21675 GCACGTGGGTCGTGCTGTGCCA
1 GCACGTGGGTCGTGCCGTGCCA
21697 GCACGTGGGTCGTGCCGTGCCA
1 GCACGTGGGTCGTGCCGTGCCA
21719 TGGCATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.30, G:0.41, T:0.20
Consensus pattern (22 bp):
GCACGTGGGTCGTGCCGTGCCA
Found at i:22030 original size:3 final size:3
Alignment explanation
Indices: 22024--22049 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
22014 GTTGCAAGAA
22024 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
22050 ATCTATTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:33843 original size:14 final size:14
Alignment explanation
Indices: 33824--33856 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
33814 TAACCGAGAA
33824 AACCGACACATTTC
1 AACCGACACATTTC
*
33838 AACCGACCCATTTC
1 AACCGACACATTTC
33852 AACCG
1 AACCG
33857 TTTTCTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.39, G:0.09, T:0.18
Consensus pattern (14 bp):
AACCGACACATTTC
Found at i:35667 original size:104 final size:102
Alignment explanation
Indices: 35519--35709 Score: 276
Period size: 104 Copynumber: 1.9 Consensus size: 102
35509 TTGTTTAAAT
* * * **
35519 TTTTATAATTTTACTTAACCAAAAACTCTATTTTTATTTGATTAAATCTAATATTTTTATAAGTA
1 TTTTATAAGTTTACTCAACCAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-A--A
35584 CTATTTTATTTTTACCATTTTACTATTTAAATTAAAATAC
63 CTATTTTATTTTTACCATTTTACTATTTAAATTAAAATAC
* *
35624 TTTTAT-AGTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAAGTTTACTCAACCAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
35688 TTTTATTTTTATCATTTTACTA
66 TTTTATTTTTACCATTTTACTA
35710 ATTTTTTTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 24 0.31
103 1 0.01
104 47 0.60
105 6 0.08
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.52
Consensus pattern (102 bp):
TTTTATAAGTTTACTCAACCAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTTACTATTTAAATTAAAATAC
Found at i:36626 original size:22 final size:22
Alignment explanation
Indices: 36601--36642 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
36591 AATTATAGTA
*
36601 TTCTTGGATCATCCGGGTTAAC
1 TTCTCGGATCATCCGGGTTAAC
* *
36623 TTCTCGGGTCATTCGGGTTA
1 TTCTCGGATCATCCGGGTTA
36643 CAGGTTTGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.38
Consensus pattern (22 bp):
TTCTCGGATCATCCGGGTTAAC
Found at i:39729 original size:21 final size:22
Alignment explanation
Indices: 39703--39745 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
39693 AAACTTTTCA
39703 TTTAATAAAATAA-AAAATATT
1 TTTAATAAAATAATAAAATATT
* *
39724 TTTAATAATATAATAATATATT
1 TTTAATAAAATAATAAAATATT
39746 ATTTTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAATAAAATAATAAAATATT
Found at i:40059 original size:105 final size:106
Alignment explanation
Indices: 39918--40166 Score: 319
Period size: 107 Copynumber: 2.3 Consensus size: 106
39908 TGACATCCCT
* * * **
39918 ATTAGTTATATATTTTATTTCTAAAACTCTATAACAAT-ATTATTAATTATGGAATTTACCCTTA
1 ATTAGTTTTGTATTTTATTTCAAAAACTCTATAACAATAATTATTAATTATCAAATTTACCCTTA
39982 AAATAAAAATAAAATTTTAATTT-GGAGCTAAACTT-AGTGAA
66 AAATAAAAATAAAATTTTAATTTAGG-GCTAAACTTGA-TGAA
*
40023 ATTAGTTTTGTATTTTATTTCAAAAAC-CTTATAACAATAAATTATTAATTTTCAAATTTACCCT
1 ATTAGTTTTGTATTTTATTTCAAAAACTC-TATAACAAT-AATTATTAATTATCAAATTTACCCT
**
40087 TAAAATAAAAATTCAATTTTAATTTAGGGCTAAACTTGATGAA
64 TAAAATAAAAATAAAATTTTAATTTAGGGCTAAACTTGATGAA
40130 ATTAGTTTTATAGTATTTTATTTCTAAAAA-TCTATAA
1 ATTAG-TTT-T-GTATTTTATTTC-AAAAACTCTATAA
40167 TAAAAAACCT
Statistics
Matches: 126, Mismatches: 8, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
104 1 0.01
105 33 0.26
107 62 0.49
108 6 0.05
109 1 0.01
110 17 0.13
111 6 0.05
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (106 bp):
ATTAGTTTTGTATTTTATTTCAAAAACTCTATAACAATAATTATTAATTATCAAATTTACCCTTA
AAATAAAAATAAAATTTTAATTTAGGGCTAAACTTGATGAA
Found at i:40105 original size:107 final size:106
Alignment explanation
Indices: 39918--40201 Score: 312
Period size: 107 Copynumber: 2.6 Consensus size: 106
39908 TGACATCCCT
* * * * **
39918 ATTAGTTATATATTTTATTTCTAAAACTCTATAACAAT--ATTATTAATTATGGAATTTACCCTT
1 ATTAGTTTTGTATTTTATTTCAAAAACT-TATAACAATAAATTATTAATTTTCAAATTTACCCTT
39981 AAAATAAAAATAAAATTTTAATTT-GGAGCTAAACTT-AGTGAA
65 AAAATAAAAATAAAATTTTAATTTAGG-GCTAAACTTGA-TGAA
40023 ATTAGTTTTGTATTTTATTTCAAAAACCTTATAACAATAAATTATTAATTTTCAAATTTACCCTT
1 ATTAGTTTTGTATTTTATTTCAAAAA-CTTATAACAATAAATTATTAATTTTCAAATTTACCCTT
**
40088 AAAATAAAAATTCAATTTTAATTTAGGGCTAAACTTGATGAA
65 AAAATAAAAATAAAATTTTAATTTAGGGCTAAACTTGATGAA
* * *
40130 ATTAGTTTTATAGTATTTTATTTCTAAAAA-TCTATAATAAAAAACCT-TTAA-TTTCATAATTT
1 ATTAG-TTT-T-GTATTTTATTTC-AAAAACT-TATAACAATAAA-TTATTAATTTTCA-AATTT
*
40192 ACTCTTAAAA
59 ACCCTTAAAA
40202 ATTAAATTTC
Statistics
Matches: 155, Mismatches: 12, Indels: 19
0.83 0.06 0.10
Matches are distributed among these distances:
105 32 0.21
106 2 0.01
107 62 0.40
108 6 0.04
109 7 0.05
110 40 0.26
111 6 0.04
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.43
Consensus pattern (106 bp):
ATTAGTTTTGTATTTTATTTCAAAAACTTATAACAATAAATTATTAATTTTCAAATTTACCCTTA
AAATAAAAATAAAATTTTAATTTAGGGCTAAACTTGATGAA
Found at i:40260 original size:15 final size:16
Alignment explanation
Indices: 40240--40278 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
40230 AATAATAACT
*
40240 AAAAAGAATGAA-AAA
1 AAAAAGAATAAAGAAA
40255 AAAAAGAAATAAAGAAA
1 AAAAAG-AATAAAGAAA
40272 AAAAAGA
1 AAAAAGA
40279 CACGTCACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 6 0.29
17 9 0.43
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (16 bp):
AAAAAGAATAAAGAAA
Found at i:42253 original size:24 final size:22
Alignment explanation
Indices: 42198--42254 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
42188 TACTCCACCT
42198 TTTGTATTTTCCTCATCGTTTTC
1 TTTG-ATTTTCCTCATCGTTTTC
*
42221 TTATCGATTTTCACTCATCTTTTTTC
1 TT-T-GATTTTC-CTCATC-GTTTTC
42247 TTTGATTT
1 TTTGATTT
42255 ATGTCATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 12 0.41
25 8 0.28
26 7 0.24
ACGTcount: A:0.12, C:0.19, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTGATTTTCCTCATCGTTTTC
Found at i:44031 original size:32 final size:33
Alignment explanation
Indices: 43969--44037 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 33
43959 AATTAAAACT
* ***
43969 AAAACAAATATACTTACTTTCCCTCAAAAAAA-
1 AAAACAAATATACTTACTTACAAACAAAAAAAG
44001 AAAACAAATATACTTACTCTACAAAC-AAAAAAG
1 AAAACAAATATACTTACT-TACAAACAAAAAAAG
44034 AAAA
1 AAAA
44038 AGAAAAGTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 24 0.77
33 7 0.23
ACGTcount: A:0.59, C:0.19, G:0.01, T:0.20
Consensus pattern (33 bp):
AAAACAAATATACTTACTTACAAACAAAAAAAG
Found at i:44600 original size:30 final size:31
Alignment explanation
Indices: 44552--44612 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
44542 ATAACGTGTC
44552 ACATTAATTACTTTTTTTATTTTGAGATAAT
1 ACATTAATTACTTTTTTTATTTTGAGATAAT
44583 ACATTAATTAC-TTTTTTATTTTGAGATAAT
1 ACATTAATTACTTTTTTTATTTTGAGATAAT
44613 GTGAACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (31 bp):
ACATTAATTACTTTTTTTATTTTGAGATAAT
Found at i:45091 original size:14 final size:14
Alignment explanation
Indices: 45074--45120 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
45064 CTCATTTATT
45074 ACTTTTTATTTGTA
1 ACTTTTTATTTGTA
*
45088 ACTTTTTTTTTGGCATA
1 ACTTTTTATTT-G--TA
45105 A-TTTTTATTTGTA
1 ACTTTTTATTTGTA
45118 ACT
1 ACT
45121 CTAAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
13 3 0.11
14 11 0.41
15 2 0.07
16 8 0.30
17 3 0.11
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (14 bp):
ACTTTTTATTTGTA
Found at i:50976 original size:35 final size:36
Alignment explanation
Indices: 50926--50993 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
50916 CTCTTCTGCG
*
50926 TCATATTTTTGTTGTTGTTTTTCTGAAACTCTTGCT
1 TCATATTTTTGTTGTTGGTTTTCTGAAACTCTTGCT
*
50962 TCATATTTTT-TTGTTGGTTTTCTGTAACTCTT
1 TCATATTTTTGTTGTTGGTTTTCTGAAACTCTT
50994 ACTTTCTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60
Consensus pattern (36 bp):
TCATATTTTTGTTGTTGGTTTTCTGAAACTCTTGCT
Found at i:51098 original size:113 final size:112
Alignment explanation
Indices: 50882--51098 Score: 251
Period size: 113 Copynumber: 1.9 Consensus size: 112
50872 TGTCTCTCTC
*
50882 CTTTCTTTGAAGCTTCTGCCTTTTGCTCTTTCTGCTCTTCTGCGTCATATTTTTGTTGTTGTTTT
1 CTTTCTTTGAAGATTCTGCCTTTTGCTCTTTCTGCTCTTCTGCGTCATATTTTTGTTGTTGTTTT
* ** * * **
50947 TCTGAAACTCTTGCTTCATATTTTTTTGTTGGTTTTCTGTAACTCTTA
66 TCTGAAACTCTTGATT-ATATTTTGCTATTAGAATTCTGTAACTCTTA
* * *
50995 CTTTCTTTGAAGATTCTGCCTTTTGCTCTTTTTGCTCTTCTGCTTCATTTTTTTTGTTGTTGTTT
1 CTTTCTTTGAAGATTCTGCCTTTTGCTCTTTCTGCTCTTCTGCGTCA-TATTTTTGTTGTTGTTT
* *
51060 TTCTG-CAC-CTTAGGATT-TGCTTTTGCTATTAGAATTCTG
65 TTCTGAAACTCTT--GATTAT-ATTTTGCTATTAGAATTCTG
51099 GGTTTGAAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
112 4 0.05
113 59 0.68
114 24 0.28
ACGTcount: A:0.11, C:0.19, G:0.15, T:0.56
Consensus pattern (112 bp):
CTTTCTTTGAAGATTCTGCCTTTTGCTCTTTCTGCTCTTCTGCGTCATATTTTTGTTGTTGTTTT
TCTGAAACTCTTGATTATATTTTGCTATTAGAATTCTGTAACTCTTA
Found at i:66472 original size:121 final size:123
Alignment explanation
Indices: 66322--66555 Score: 312
Period size: 124 Copynumber: 1.9 Consensus size: 123
66312 AGAAATTGAG
* * ** *
66322 GTGGGGTGACTTAATTTTATAGGGGAGGAGTCT-CTT-TATTACAATTAA-TGTTAAATCACATA
1 GTGGGGTGACTTAATTTTATAAGGGAGGAGTCTCCTTAAATTA-AAGGAAGTGCTAAATCACATA
** *
66384 ATTTGTAAGTCGAGTAATTATTCTAATGGCAAGTAAATCTCCAAGGAAGTACAAATGAA
65 ATTTGTAACCCAAGTAATTATTCTAATGGCAAGTAAATCTCCAAGGAAGTACAAATGAA
** * * *
66443 GTGGGGTGACTTCTTTTTATAATGGAGGAGTCTCCTTACAATTAAGGGAAGTGCTAAATCACCTA
1 GTGGGGTGACTTAATTTTATAAGGGAGGAGTCTCCTTA-AATTAAAGGAAGTGCTAAATCACATA
66508 ATTTGTAACCCAAGTAATTATTCTAATGGCAAGTAAATCTCCAAGGAA
65 ATTTGTAACCCAAGTAATTATTCTAATGGCAAGTAAATCTCCAAGGAA
66556 ACTTATAAGT
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
121 29 0.30
122 3 0.03
123 3 0.03
124 61 0.64
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (123 bp):
GTGGGGTGACTTAATTTTATAAGGGAGGAGTCTCCTTAAATTAAAGGAAGTGCTAAATCACATAA
TTTGTAACCCAAGTAATTATTCTAATGGCAAGTAAATCTCCAAGGAAGTACAAATGAA
Found at i:66711 original size:86 final size:86
Alignment explanation
Indices: 66562--66727 Score: 251
Period size: 86 Copynumber: 1.9 Consensus size: 86
66552 GGAAACTTAT
* * * *
66562 AAGTAATTTCCAAGACAACCTCCAAGTAATCTCTCTTAATGTGATTTTTCTTGATTCTCTCATTA
1 AAGTAATTTCCAAGACAACCTCCAAATAATCTCTCTTAATGTGATTTTCCTTAAATCTCTCATTA
66627 TTAATTCTCTTGATTCACTCC
66 TTAATTCTCTTGATTCACTCC
* * * * *
66648 AAGTAATTTCTAAGACAACCTCCAAATAATCTCTCTTGATTTGATTTTCCTTAAATCTTTCATTG
1 AAGTAATTTCCAAGACAACCTCCAAATAATCTCTCTTAATGTGATTTTCCTTAAATCTCTCATTA
66713 TTAATTCTCTTGATT
66 TTAATTCTCTTGATT
66728 AACCCCCCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (86 bp):
AAGTAATTTCCAAGACAACCTCCAAATAATCTCTCTTAATGTGATTTTCCTTAAATCTCTCATTA
TTAATTCTCTTGATTCACTCC
Found at i:73272 original size:62 final size:62
Alignment explanation
Indices: 73171--73291 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 62
73161 AATTGGGAAA
* *
73171 GTGCTGGAAACTGGGAAGCTTTAGATTTTCCATACGGGACTA-ATGAAAGCTGGAATTTTAAT
1 GTGCTGGAAACTGGAAAGCCTTAGATTTTCCATACGGGACTACA-GAAAGCTGGAATTTTAAT
* * *
73233 GTGCTGGAAATTGGAAAGCCTTATATTTTCCTTGA-GGGACTACAGAAAGCTGGAATTTT
1 GTGCTGGAAACTGGAAAGCCTTAGATTTTCCAT-ACGGGACTACAGAAAGCTGGAATTTT
73292 GCTGATAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 50 0.96
63 2 0.04
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (62 bp):
GTGCTGGAAACTGGAAAGCCTTAGATTTTCCATACGGGACTACAGAAAGCTGGAATTTTAAT
Found at i:94981 original size:2 final size:2
Alignment explanation
Indices: 94974--94999 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
94964 ACATGACATA
94974 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
95000 GTCATATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99767 original size:16 final size:14
Alignment explanation
Indices: 99727--99768 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 14
99717 ACAGAGGTTG
99727 ACAGAAAACAATTA
1 ACAGAAAACAATTA
99741 ACAGAAAAACAATTAA
1 ACAG-AAAACAATT-A
99757 ACTAGAAAACAA
1 AC-AGAAAACAA
99769 AACAGAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.16
15 9 0.36
16 10 0.40
17 2 0.08
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (14 bp):
ACAGAAAACAATTA
Found at i:107845 original size:8 final size:9
Alignment explanation
Indices: 107831--107857 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
107821 AAAAATATTG
107831 AAAAAAATC
1 AAAAAAATC
107840 AAAAAAATC
1 AAAAAAATC
107849 AAAAAAATC
1 AAAAAAATC
107858 TGTGTCGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:108069 original size:21 final size:21
Alignment explanation
Indices: 108043--108083 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
108033 TTTAAACCCT
108043 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
108064 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
108084 GGGTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:109184 original size:33 final size:33
Alignment explanation
Indices: 109138--109218 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 33
109128 GTGTTTTAGA
*
109138 TGTTG-TTAGTGATGATACTAAAACTAATTTGA-G
1 TGTTGTTTA-TGATGACACTAAAACT-ATTTGAGG
* * *
109171 TGTTGTTTATGATGACACTAAATCTTTTTTAGG
1 TGTTGTTTATGATGACACTAAAACTATTTGAGG
*
109204 TGTTGTTTGTGATGA
1 TGTTGTTTATGATGA
109219 AACAAATTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 4 0.10
33 34 0.83
34 3 0.07
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (33 bp):
TGTTGTTTATGATGACACTAAAACTATTTGAGG
Found at i:109659 original size:29 final size:30
Alignment explanation
Indices: 109591--109648 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
109581 TTCAAGGGGG
*
109591 AGGGAATGATGCGCCCAAGGCTTATCATGC
1 AGGGAATGATGCGCCCAAGGATTATCATGC
109621 AGGGAATGATGCG-CCAAGGATTATCATG
1 AGGGAATGATGCGCCCAAGGATTATCATG
109649 GAGAGGATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (30 bp):
AGGGAATGATGCGCCCAAGGATTATCATGC
Found at i:109661 original size:15 final size:15
Alignment explanation
Indices: 109637--109666 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
109627 TGATGCGCCA
*
109637 AGGATTATCATGGAG
1 AGGATGATCATGGAG
109652 AGGATGATCATGGAG
1 AGGATGATCATGGAG
109667 TGCAAGGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.37, T:0.23
Consensus pattern (15 bp):
AGGATGATCATGGAG
Found at i:111942 original size:12 final size:12
Alignment explanation
Indices: 111917--111953 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
111907 AGCCAAGACT
*
111917 ACGACCACGGCC
1 ACGACCACGTCC
*
111929 ACGTCCACGTCC
1 ACGACCACGTCC
111941 ACGACCACGTCC
1 ACGACCACGTCC
111953 A
1 A
111954 TAAGTATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.49, G:0.19, T:0.08
Consensus pattern (12 bp):
ACGACCACGTCC
Found at i:112929 original size:33 final size:33
Alignment explanation
Indices: 112884--112952 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
112874 TTTAATAATA
* *
112884 AAAGAAATGTAGAAGAAGGAGATTATGCATGAT
1 AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
112917 AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
1 AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
112950 AAA
1 AAA
112953 TAAACTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.51, C:0.04, G:0.28, T:0.17
Consensus pattern (33 bp):
AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
Found at i:113624 original size:27 final size:25
Alignment explanation
Indices: 113559--113631 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 25
113549 ATCTGCCTAT
*
113559 ATTTAAAATTTTAAAAATAAAATATA
1 ATTTAAAA-TTTAAAAATTAAATATA
* *
113585 ATTTAAAATATTTAAAAATTAAGTTTA
1 ATTT-AAA-ATTTAAAAATTAAATATA
113612 GAGTTTAAAATTTAAAAATT
1 -A-TTTAAAATTTAAAAATT
113632 TTAATAACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.10
27 28 0.70
28 5 0.12
29 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
ATTTAAAATTTAAAAATTAAATATA
Found at i:114757 original size:33 final size:33
Alignment explanation
Indices: 114715--114778 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
114705 CTTCTAAACA
*
114715 CTTTTGGGTATTTTTACCTTTGAGCTTACATCT
1 CTTTTGGGTATTTCTACCTTTGAGCTTACATCT
*
114748 CTTTTGGGTATTTCTACCTTTGGGCTTACAT
1 CTTTTGGGTATTTCTACCTTTGAGCTTACAT
114779 TTGGGCAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.14, C:0.19, G:0.17, T:0.50
Consensus pattern (33 bp):
CTTTTGGGTATTTCTACCTTTGAGCTTACATCT
Found at i:116297 original size:17 final size:17
Alignment explanation
Indices: 116275--116308 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
116265 AGCTTGCTGC
116275 AAAGTTTCGACGATATT
1 AAAGTTTCGACGATATT
116292 AAAGTTTCGACGATATT
1 AAAGTTTCGACGATATT
116309 GAAGCTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
AAAGTTTCGACGATATT
Found at i:117388 original size:52 final size:52
Alignment explanation
Indices: 117326--117832 Score: 533
Period size: 52 Copynumber: 10.1 Consensus size: 52
117316 ATTTCACTCA
*
117326 AGTTTTCAAAGTATTCAATTTAACTCTTTTTCAAGTCGGGAAAGTTCCCATC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCATC
117378 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCATC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCATC
* * * * * *
117430 AATTGTCAAAGTATTTAATTTAACTC---TT----T-GGTAAAGTTCCCACC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCATC
*
117474 AGTTCTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCATC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCATC
* * * * *
117526 AGTTGTCAAAGTATTTAATTTAACTC---TT----T-GGGAAAGTTTCCACC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCATC
* *
117570 AGTTCTCAAAGTATTCAATTTATCTCTTTTTCAAGTTC-GGAAAGTTCCCATC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAG-TCGGGAAAGTTCCCATC
* * * *
117622 AGTTGTCAAAGTATTTAATTTAACTC---TT----T-GGGAAAGTTCCCACC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCATC
* *
117666 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTTGGGAAAGTTCCCACC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCATC
* *
117718 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTTTTACAAGTTGGGAAAGTTCCCATT
1 AGTTTTCAAAGTATTCAATTTAGCTC---TTTTT-CAAGTCGGGAAAGTTCCCATC
* ** * *
117774 AGTTTTCAAAGTACTCAATTTAGCTGGTTTTCAAATTGGGAAAGTTCCCATC
1 AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCATC
117826 AGGTTTT
1 A-GTTTT
117833 AGTTTTCAAT
Statistics
Matches: 387, Mismatches: 37, Indels: 61
0.80 0.08 0.13
Matches are distributed among these distances:
44 108 0.28
45 2 0.01
47 6 0.02
49 6 0.02
51 2 0.01
52 206 0.53
53 9 0.02
55 5 0.01
56 43 0.11
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (52 bp):
AGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCATC
Found at i:117532 original size:96 final size:96
Alignment explanation
Indices: 117363--117746 Score: 644
Period size: 96 Copynumber: 4.0 Consensus size: 96
117353 TTTTCAAGTC
* *
117363 GGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCA
1 GGGAAAGTTCCCACCAGTTCTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCA
*
117428 TCAATTGTCAAAGTATTTAATTTAACTCTTT
66 TCAGTTGTCAAAGTATTTAATTTAACTCTTT
*
117459 GGTAAAGTTCCCACCAGTTCTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCA
1 GGGAAAGTTCCCACCAGTTCTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCA
117524 TCAGTTGTCAAAGTATTTAATTTAACTCTTT
66 TCAGTTGTCAAAGTATTTAATTTAACTCTTT
* *
117555 GGGAAAGTTTCCACCAGTTCTCAAAGTATTCAATTTATCTCTTTTTCAAGTTC-GGAAAGTTCCC
1 GGGAAAGTTCCCACCAGTTCTCAAAGTATTCAATTTAGCTCTTTTTCAAG-TCGGGAAAGTTCCC
117619 ATCAGTTGTCAAAGTATTTAATTTAACTCTTT
65 ATCAGTTGTCAAAGTATTTAATTTAACTCTTT
* *
117651 GGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTTGGGAAAGTTCCCA
1 GGGAAAGTTCCCACCAGTTCTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCA
* * * *
117716 CCAGTTTTCAAAGTATTCAATTTAGCTCTTT
66 TCAGTTGTCAAAGTATTTAATTTAACTCTTT
117747 TTTTTACAAG
Statistics
Matches: 271, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
95 1 0.00
96 268 0.99
97 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (96 bp):
GGGAAAGTTCCCACCAGTTCTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCA
TCAGTTGTCAAAGTATTTAATTTAACTCTTT
Found at i:119290 original size:14 final size:13
Alignment explanation
Indices: 119245--119295 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
119235 TTTAAATCAT
**
119245 AATTAAAATTTTT
1 AATTAAAATTTAA
* *
119258 AATGAAAA-ATAA
1 AATTAAAATTTAA
119270 AATTAAAATTTAA
1 AATTAAAATTTAA
119283 ACATTAAAATTTA
1 A-ATTAAAATTTA
119296 TATAATCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 8 0.27
13 11 0.37
14 11 0.37
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (13 bp):
AATTAAAATTTAA
Found at i:122638 original size:18 final size:19
Alignment explanation
Indices: 122602--122639 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
122592 CTAAGCAAGA
*
122602 ATATAAATAAAAACTAATT
1 ATATAAATAAAAACAAATT
*
122621 ATAT-AATAACAACAAATT
1 ATATAAATAAAAACAAATT
122639 A
1 A
122640 AAGAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
ATATAAATAAAAACAAATT
Found at i:126741 original size:16 final size:17
Alignment explanation
Indices: 126720--126751 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
126710 TTAAAAATAC
126720 CAATTATAAAG-AAAAG
1 CAATTATAAAGCAAAAG
126736 CAATTATAAAGCAAAA
1 CAATTATAAAGCAAAA
126752 CTAAATTAAA
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:0.62, C:0.09, G:0.09, T:0.19
Consensus pattern (17 bp):
CAATTATAAAGCAAAAG
Found at i:128237 original size:30 final size:31
Alignment explanation
Indices: 128203--128264 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
128193 GTTCTTTCTC
* *
128203 CTTGAAATATTTCTTCAA-TGATCTTC-ATGA
1 CTTGAAATA-ATCTTCAATTAATCTTCAATGA
128233 CTTGAAATAATCTTCAATTAATCTTCAATGA
1 CTTGAAATAATCTTCAATTAATCTTCAATGA
128264 C
1 C
128265 GAACTTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.25
30 16 0.57
31 5 0.18
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (31 bp):
CTTGAAATAATCTTCAATTAATCTTCAATGA
Found at i:142094 original size:11 final size:11
Alignment explanation
Indices: 142078--142102 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
142068 TAAACAAACA
142078 TAAACGAACTT
1 TAAACGAACTT
142089 TAAACGAACTT
1 TAAACGAACTT
142100 TAA
1 TAA
142103 CCGAGCTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (11 bp):
TAAACGAACTT
Found at i:143325 original size:19 final size:19
Alignment explanation
Indices: 143288--143328 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
143278 CTTTCACTTG
*
143288 CTTCAATTGCAGTTTGTGT
1 CTTCAATTGCAGTTAGTGT
143307 CTTCATATTGCA-TTAGTGT
1 CTTCA-ATTGCAGTTAGTGT
143326 CTT
1 CTT
143329 TAACTGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (19 bp):
CTTCAATTGCAGTTAGTGT
Found at i:149752 original size:2 final size:2
Alignment explanation
Indices: 149745--149783 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
149735 TTGCACTGCT
149745 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
149784 CCAATAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:168072 original size:2 final size:2
Alignment explanation
Indices: 168065--168092 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
168055 GTAAACCTAC
168065 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
168093 GTGGATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:168566 original size:40 final size:40
Alignment explanation
Indices: 168511--168590 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
168501 AAGAGGTTAG
168511 AATTCTAGATAATTAAGGGGGATAGGATTTTAT-ATAACAT
1 AATTCTAGATAATTAAGGGGGATAGGA-TTTATCATAACAT
*
168551 AATTCTAGATAATTAAGGGGGATATGATTTATCATAACAT
1 AATTCTAGATAATTAAGGGGGATAGGATTTATCATAACAT
168591 TTATGTGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 5 0.13
40 33 0.87
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (40 bp):
AATTCTAGATAATTAAGGGGGATAGGATTTATCATAACAT
Found at i:175819 original size:15 final size:15
Alignment explanation
Indices: 175799--175832 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
175789 TTAGATAGGT
175799 TATTAATTTATCGAG
1 TATTAATTTATCGAG
175814 TATTAATTTATCGAG
1 TATTAATTTATCGAG
175829 -ATTA
1 TATTA
175833 TATTGTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (15 bp):
TATTAATTTATCGAG
Found at i:178649 original size:4 final size:4
Alignment explanation
Indices: 178640--178679 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
178630 AAATTTAGTA
* * *
178640 ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATAT GTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
178680 GAGTAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:178651 original size:6 final size:6
Alignment explanation
Indices: 178640--178679 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
178630 AAATTTAGTA
* * *
178640 ATATAT ATATAT ATATAT ATATGT ATGTAT ATGTAT ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
178680 GAGTAATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:178655 original size:10 final size:10
Alignment explanation
Indices: 178640--178679 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
178630 AAATTTAGTA
178640 ATATATATAT
1 ATATATATAT
178650 ATATATATAT
1 ATATATATAT
* *
178660 ATGTATGTAT
1 ATATATATAT
*
178670 ATGTATATAT
1 ATATATATAT
178680 GAGTAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Done.