Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014658.1 Corchorus capsularis cultivar CVL-1 contig14679, 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: 55920
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:483 original size:56 final size:53
Alignment explanation
Indices: 416--530 Score: 167
Period size: 54 Copynumber: 2.1 Consensus size: 53
406 GAAAGGGGGC
416 AATCAGTAATTAAGTAAAAAGAGATTAATCAAGAGTCAAAGTAACAGTAATCAGT
1 AATCAGTAATTAAGT-AAAAGAGATTAATC-AGAGTCAAAGTAACAGTAATCAGT
* * **
471 AAATCAGTAATTAAGTAAAAGAGATTAATCAGAGTTAAGGTAGTAGTAATCAGT
1 -AATCAGTAATTAAGTAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGT
525 AATCAG
1 AATCAG
531 GTAAAAGATA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
53 6 0.11
54 20 0.36
55 14 0.25
56 15 0.27
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25
Consensus pattern (53 bp):
AATCAGTAATTAAGTAAAAGAGATTAATCAGAGTCAAAGTAACAGTAATCAGT
Found at i:890 original size:22 final size:22
Alignment explanation
Indices: 844--891 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
834 ATCTAAAAGG
* * *
844 GTAAAATGGTAATTAGCAAAGA
1 GTAAAATAGTAATCAGCAAAAA
*
866 GTAAAATAGTAATCAGTAAAAA
1 GTAAAATAGTAATCAGCAAAAA
888 GTAA
1 GTAA
892 GACGGTAGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.19, T:0.23
Consensus pattern (22 bp):
GTAAAATAGTAATCAGCAAAAA
Found at i:1016 original size:43 final size:42
Alignment explanation
Indices: 933--1092 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 42
923 AGTAAATAGT
* **
933 AATCAGTAAGAGTAAAAAGGGTAATAAGT-AAGAAGCAAAAGGA
1 AATCAGTAAAAGTAAAAA-GGTAACCAGTAAAG-AGCAAAAGGA
* * * **
976 AATTAGTAAGAGTAAAAAGGTAACCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAAGTAAAAAGGTAACCAGTAAAGAG-CAAAAGGA
* * * *
1019 AATCAGCAAAAAGTAAAAAGGTAATC-GATAAAAAGCAAAAGGC
1 AATCAG-TAAAAGTAAAAAGGTAACCAG-TAAAGAGCAAAAGGA
1062 AATCAGTAAAAAGTAAAAA-GTAACCAGTAAA
1 AATCAGT-AAAAGTAAAAAGGTAACCAGTAAA
1093 AAAGGGAGTA
Statistics
Matches: 95, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
42 19 0.20
43 54 0.57
44 22 0.23
ACGTcount: A:0.57, C:0.08, G:0.20, T:0.15
Consensus pattern (42 bp):
AATCAGTAAAAGTAAAAAGGTAACCAGTAAAGAGCAAAAGGA
Found at i:1096 original size:22 final size:21
Alignment explanation
Indices: 923--1094 Score: 125
Period size: 22 Copynumber: 8.0 Consensus size: 21
913 AATCATAGAC
* *
923 AGTAAATAGTAATCAGT-AAG
1 AGTAAAAAGTAATCAGTAAAA
* *
943 AGTAAAAAGGGTAATAAGTAAGA
1 AGTAAAAA--GTAATCAGTAAAA
* * * * *
966 AGCAAAAGGAAATTAGT-AAG
1 AGTAAAAAGTAATCAGTAAAA
* *
986 AGTAAAAAGGTAACCAGTAAAG
1 AGTAAAAA-GTAATCAGTAAAA
*
1008 AGTAAAAAGCTAATCAGCAAAA
1 AGTAAAAAG-TAATCAGTAAAA
1030 AGTAAAAAGGTAATC-GATAAAA
1 AGTAAAAA-GTAATCAG-TAAAA
* * *
1052 AGCAAAAGGCAATCAGTAAAA
1 AGTAAAAAGTAATCAGTAAAA
*
1073 AGTAAAAAGTAACCAGTAAAA
1 AGTAAAAAGTAATCAGTAAAA
1094 A
1 A
1095 AGGGAGTAGA
Statistics
Matches: 117, Mismatches: 26, Indels: 17
0.73 0.16 0.11
Matches are distributed among these distances:
20 14 0.12
21 43 0.37
22 52 0.44
23 8 0.07
ACGTcount: A:0.57, C:0.08, G:0.20, T:0.16
Consensus pattern (21 bp):
AGTAAAAAGTAATCAGTAAAA
Found at i:1162 original size:21 final size:21
Alignment explanation
Indices: 1124--1176 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
1114 TCAGTAATTC
* *
1124 AAAAAGTGAAATGGTAATCAGT
1 AAAAAGT-AAAAGATAATCAGT
1146 AAAAAGTAAAAGATAATCAGT
1 AAAAAGTAAAAGATAATCAGT
1167 AAAATAGTAA
1 AAAA-AGTAA
1177 TCAGTAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAAAGTAAAAGATAATCAGT
Found at i:1179 original size:15 final size:14
Alignment explanation
Indices: 1150--1197 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
1140 ATCAGTAAAA
1150 AGTAAAAGATAATC
1 AGTAAAAGATAATC
*
1164 AGTAAAATAGTAATC
1 AGTAAAAGA-TAATC
1179 AGTAAAAGATAATC
1 AGTAAAAGATAATC
1193 AGTAA
1 AGTAA
1198 GAGTAAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.23
Consensus pattern (14 bp):
AGTAAAAGATAATC
Found at i:1197 original size:21 final size:20
Alignment explanation
Indices: 1172--1245 Score: 51
Period size: 21 Copynumber: 3.5 Consensus size: 20
1162 TCAGTAAAAT
1172 AGTAATCAGTAAAAGATAATC
1 AGTAA-CAGTAAAAGATAATC
* *
1193 AGTAAGAGTAAAACAGTAATC
1 AGTAACAGTAAAAGA-TAATC
* * *
1214 GGTAAGAGCAAAAGCGATAAT-
1 AGTAACAGTAAAA--GATAATC
1235 AGTAATCAGTA
1 AGTAA-CAGTA
1246 GAGAGTAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
20 8 0.20
21 25 0.61
22 7 0.17
23 1 0.02
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.20
Consensus pattern (20 bp):
AGTAACAGTAAAAGATAATC
Found at i:1343 original size:29 final size:28
Alignment explanation
Indices: 1318--1382 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
1308 GTAAAAAGTG
1318 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
***
1346 GTAATTGGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
1373 GTAA-AAATAA
1 GTAATAAATAA
1383 TAAAAGTAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 3 0.10
27 18 0.58
28 10 0.32
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:4087 original size:70 final size:70
Alignment explanation
Indices: 4005--4236 Score: 304
Period size: 70 Copynumber: 3.2 Consensus size: 70
3995 TTGTTTAGGT
* *
4005 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT
4069 ATTTTA
65 ATTTTA
4075 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAGCTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-TA--TA
*
4140 TTATATTTTACCA
62 AT-TATTTT---A
* * *
4153 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
4218 TTATA
66 TTTTA
*
4223 TTTTACAATTTTAC
1 TTTTACTATTTTAC
4237 AATTTTAGTT
Statistics
Matches: 144, Mismatches: 9, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
70 63 0.44
71 5 0.03
72 2 0.01
73 5 0.03
74 5 0.03
75 6 0.04
76 2 0.01
77 2 0.01
78 54 0.38
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:4236 original size:78 final size:77
Alignment explanation
Indices: 4005--4243 Score: 341
Period size: 78 Copynumber: 3.2 Consensus size: 77
3995 TTGTTTAGGT
* *
4005 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
4065 AAT-TATTTT--A
65 ATTATATTTTACA
*
4075 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAGCTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
4140 TTATATTTTACCA
66 TTATATTTTA-CA
*
4153 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
4218 TTATATTTTACAA
66 TTATATTTTAC-A
*
4231 TTTTACAATTTTA
1 TTTTACTATTTTA
4244 GTTAAAAAAA
Statistics
Matches: 152, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
70 49 0.32
71 5 0.03
72 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 87 0.57
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACA
Found at i:5599 original size:6 final size:6
Alignment explanation
Indices: 5590--5632 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
5580 ATTATCATTA
* * *
5590 TTATTG TTATTG TTATTG TTATTG TTGTTG TTGTTG TCATTG T
1 TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG TTATTG T
5633 CGTCGTTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.12, C:0.02, G:0.21, T:0.65
Consensus pattern (6 bp):
TTATTG
Found at i:6320 original size:103 final size:99
Alignment explanation
Indices: 6205--6402 Score: 333
Period size: 103 Copynumber: 2.0 Consensus size: 99
6195 ATTTTTATAG
6205 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATATGTACTATTTTA
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA---ACTATTTTA
*
6270 TTTTTACCATTTTACTATTTTAATTAAAATAAAAATAT
63 TTTTTACCATTTTACTAATTTAATTAAAA-AAAAATAT
*
6308 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTT
*
6373 TTATCATTTTACTAATTTAATTAAAAAAAA
66 TTACCATTTTACTAATTTAATTAAAAAAAA
6403 CTTAGATATA
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
99 4 0.04
100 35 0.38
103 53 0.58
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.49
Consensus pattern (99 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTT
TTACCATTTTACTAATTTAATTAAAAAAAAATAT
Found at i:7878 original size:22 final size:22
Alignment explanation
Indices: 7839--7880 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
7829 GTTTATAATA
* *
7839 TTCTTGGGTCATCCGGGTTATC
1 TTCTCGGGTCATCAGGGTTATC
*
7861 TTCTCGGGTCATTAGGGTTA
1 TTCTCGGGTCATCAGGGTTA
7881 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:0.12, C:0.19, G:0.29, T:0.40
Consensus pattern (22 bp):
TTCTCGGGTCATCAGGGTTATC
Found at i:9678 original size:11 final size:11
Alignment explanation
Indices: 9664--9701 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9654 ATTCATAACA
9664 AATTTATAATT
1 AATTTATAATT
9675 AATTTATAATT
1 AATTTATAATT
9686 -ATTTGATAATT
1 AATTT-ATAATT
*
9697 TATTT
1 AATTT
9702 TATATAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:11741 original size:33 final size:33
Alignment explanation
Indices: 11668--11741 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 33
11658 AAAATTGCTC
*
11668 ATGCCGCCCTAGGGGGGGCAGCTGAGCCATGGTA
1 ATGCCGCCCCAGGGGGGGCA-CTGAGCCATGGTA
**
11702 GGGCCGCCCCAGGGGAGCGGC-CTG-GCCATGGTA
1 ATGCCGCCCCAGGGG-G-GGCACTGAGCCATGGTA
11735 ATGCCGC
1 ATGCCGC
11742 ACCGAAGGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
33 14 0.42
34 15 0.45
35 1 0.03
36 3 0.09
ACGTcount: A:0.15, C:0.31, G:0.42, T:0.12
Consensus pattern (33 bp):
ATGCCGCCCCAGGGGGGGCACTGAGCCATGGTA
Found at i:11830 original size:66 final size:63
Alignment explanation
Indices: 11760--11920 Score: 180
Period size: 66 Copynumber: 2.4 Consensus size: 63
11750 GGACGGCTTG
* * * *
11760 CCATGGCTAGGCCGTCCCCGTGGGGCGGCTGAGTCATGGCCAGGCTGCCTCCTTGGGGC-GGCAC
1 CCATGGCTAGGCCG-CCCCCTGGGGCGGCT-A-CCATGGCCAGGCCGCCTCCCTGGGGCGGGC-C
11824 TA
62 TA
*
11826 CCATGGCCAGGCCGCCTCCCTGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGGCCT
1 CCATGGCTAGGCCGCC-CCCTGGGGCGG--CTACCATGGCCAGGCCGCCTCCCTGGGGCGGGCCT
11891 A
63 A
* *
11892 CCATGGATAGACCGCCCCCCTGGGGCGGC
1 CCATGGCTAGGCCG-CCCCCTGGGGCGGC
11921 ACCGGTACTA
Statistics
Matches: 82, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
64 1 0.01
65 2 0.02
66 71 0.87
67 6 0.07
68 2 0.02
ACGTcount: A:0.11, C:0.39, G:0.36, T:0.14
Consensus pattern (63 bp):
CCATGGCTAGGCCGCCCCCTGGGGCGGCTACCATGGCCAGGCCGCCTCCCTGGGGCGGGCCTA
Found at i:11831 original size:33 final size:33
Alignment explanation
Indices: 11794--11922 Score: 188
Period size: 33 Copynumber: 3.9 Consensus size: 33
11784 GCGGCTGAGT
* *
11794 CATGGCCAGGCTGCCTCCTTGGGGCGGCACTAC
1 CATGGCCAGGCCGCCTCCCTGGGGCGGCACTAC
11827 CATGGCCAGGCCGCCTCCCTGGGGCGGCACTAC
1 CATGGCCAGGCCGCCTCCCTGGGGCGGCACTAC
11860 CATGGCCAGGCCGCCTCCCTGGGGCGGGC-CTAC
1 CATGGCCAGGCCGCCTCCCTGGGGC-GGCACTAC
** * *
11893 CATGGATAGACCGCCCCCCTGGGGCGGCAC
1 CATGGCCAGGCCGCCTCCCTGGGGCGGCAC
11923 CGGTACTAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
32 3 0.03
33 82 0.93
34 3 0.03
ACGTcount: A:0.12, C:0.40, G:0.34, T:0.13
Consensus pattern (33 bp):
CATGGCCAGGCCGCCTCCCTGGGGCGGCACTAC
Found at i:12106 original size:33 final size:32
Alignment explanation
Indices: 11986--12102 Score: 171
Period size: 32 Copynumber: 3.6 Consensus size: 32
11976 AAAAAGCCTT
*
11986 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTAGCCGTGGCAGA
* * *
12018 GCCGTCCTAGTGGGGCGGCTAGCTGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTAGCCGTGGCAGA
*
12050 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCT-AGCCGTGGCAGA
*
12083 GCCGTCCTAGTGGGGAGGCT
1 GCCGCCCTAGTGGGGAGGCT
12103 CCGCGTGGCT
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
32 48 0.62
33 29 0.38
ACGTcount: A:0.12, C:0.29, G:0.44, T:0.15
Consensus pattern (32 bp):
GCCGCCCTAGTGGGGAGGCTAGCCGTGGCAGA
Found at i:12442 original size:11 final size:11
Alignment explanation
Indices: 12414--12456 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
12404 TAGGTTGATG
*
12414 TAAAAAAATCTT
1 TAAAAAAA-ATT
*
12426 TTAAAAAAATT
1 TAAAAAAAATT
12437 TAAAAAAAAGTT
1 TAAAAAAAA-TT
12449 TAAAAAAA
1 TAAAAAAA
12457 TGGCGGAGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (11 bp):
TAAAAAAAATT
Found at i:12634 original size:15 final size:14
Alignment explanation
Indices: 12583--12675 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
12573 TTATGATTAG
*
12583 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
12597 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
12610 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
12623 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
12636 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
12649 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
12662 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
12675 T
1 T
12676 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:12643 original size:26 final size:26
Alignment explanation
Indices: 12614--12681 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
12604 TACTTAGTTT
12614 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
12640 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
12666 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
12682 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:12725 original size:24 final size:25
Alignment explanation
Indices: 12691--12749 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
12681 AAATGAAGGA
*
12691 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAATTGTTAG
12714 AAATGAAGTTTGAAGAAATTGTTAG
1 AAATGAAGTTTGAAGAAATTGTTAG
12739 AAATGAAGTTT
1 AAATGAAGTTT
12750 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 19 0.58
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAATTGTTAG
Found at i:15771 original size:18 final size:19
Alignment explanation
Indices: 15736--15777 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
15726 AACTAACTCG
15736 AACT-AACTGACTCAAAAA
1 AACTGAACTGACTCAAAAA
*
15754 AACTGAACTGACT-GAAAA
1 AACTGAACTGACTCAAAAA
15772 AACTGA
1 AACTGA
15778 CTAAACCCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.52, C:0.19, G:0.12, T:0.17
Consensus pattern (19 bp):
AACTGAACTGACTCAAAAA
Found at i:17798 original size:83 final size:80
Alignment explanation
Indices: 17648--17809 Score: 218
Period size: 83 Copynumber: 2.0 Consensus size: 80
17638 TAATAATACC
* *
17648 CTAAATTAATTCCATTTAATCAAAAACATATATATTCTATTAAAAAATCAAACATAATGATTTAA
1 CTAAATTAATTCCATTTAATCAAAAACATATATATACTATTAAAAAATCAAACATAATGATTGAA
*
17713 ATAGAATTTATAGAG
66 ATAGAATTCATAGAG
* * *
17728 CTAAATTAATTCCATTTAATGAAAAACATTTATTATATAAC-GTTACAAAATCAAACATAATGAT
1 CTAAATTAATTCCATTTAATCAAAAACA--TA-TATAT-ACTATTAAAAAATCAAACATAATGAT
*
17792 TGAAATAGGATTCATAGA
62 TGAAATAGAATTCATAGA
17810 ATGAAACTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
80 27 0.38
82 2 0.03
83 41 0.58
84 1 0.01
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (80 bp):
CTAAATTAATTCCATTTAATCAAAAACATATATATACTATTAAAAAATCAAACATAATGATTGAA
ATAGAATTCATAGAG
Found at i:19749 original size:22 final size:21
Alignment explanation
Indices: 19722--19765 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
19712 CCTCAAGTAC
19722 AAAAAAGGAAAAAAAAAAGAAA
1 AAAAAAGG-AAAAAAAAAGAAA
* *
19744 AAAAAAGGAGAAAACAAGAAA
1 AAAAAAGGAAAAAAAAAGAAA
19765 A
1 A
19766 TAAGCTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAAAAGGAAAAAAAAAGAAA
Found at i:19757 original size:12 final size:11
Alignment explanation
Indices: 19722--19757 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
19712 CCTCAAGTAC
19722 AAAAAAGGAAA
1 AAAAAAGGAAA
*
19733 AAAAAAAGAAA
1 AAAAAAGGAAA
*
19744 AAAAAAGGAGA
1 AAAAAAGGAAA
19755 AAA
1 AAA
19758 CAAGAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAGGAAA
Found at i:19796 original size:16 final size:16
Alignment explanation
Indices: 19772--19802 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19762 AAAATAAGCT
19772 TAAACTAATTAATTAA
1 TAAACTAATTAATTAA
*
19788 TAAAGTAATTAATTA
1 TAAACTAATTAATTA
19803 TTAATTAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
TAAACTAATTAATTAA
Found at i:31912 original size:156 final size:156
Alignment explanation
Indices: 31625--31924 Score: 433
Period size: 156 Copynumber: 1.9 Consensus size: 156
31615 TAGGTCATCT
31625 TGGCCAAGTTTCATCTCAAACAGACTTAAGATGAAAAACTTATGCAAGTTTTCCAGTTAAGGACA
1 TGGCCAAGTTTCATCTCAAACAGACTTAAGATGAAAAACTTATGCAAGTTTTCCAGTTAAGGACA
* *
31690 ATTTGGGGGTGAGAAACCACTTCACTATGATAGAAAGTCCGATTTTACTTACAATTTTTTCTATA
66 ATTTGGGGGTGACAAACCACTTCACTATGATAGAAAGTCCGATTTTACTTACAATTTTTTCCATA
31755 GTCTTATGGAGATAGTCTAAGTCTCG
131 GTCTTATGGAGATAGTCTAAGTCTCG
*** *
31781 TGGCCAAGTTTCATCTCAATTGGACTT-AGTATGAAAAACTTATGCAAGTTTTTCAGTTAAGGAC
1 TGGCCAAGTTTCATCTCAAACAGACTTAAG-ATGAAAAACTTATGCAAGTTTTCCAGTTAAGGAC
* * ** ** * * *
31845 AGTTT-GGGGTGTCAAACCAACTTCTTTATGATAGGGAGTTCGGTTTTACTTAGAATTTTTTCCA
65 AATTTGGGGGTGACAAACC-ACTTCACTATGATAGAAAGTCCGATTTTACTTACAATTTTTTCCA
31909 TAGTCTTATGGAGATA
129 TAGTCTTATGGAGATA
31925 ATATAAGCCT
Statistics
Matches: 127, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
155 13 0.10
156 114 0.90
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (156 bp):
TGGCCAAGTTTCATCTCAAACAGACTTAAGATGAAAAACTTATGCAAGTTTTCCAGTTAAGGACA
ATTTGGGGGTGACAAACCACTTCACTATGATAGAAAGTCCGATTTTACTTACAATTTTTTCCATA
GTCTTATGGAGATAGTCTAAGTCTCG
Found at i:32098 original size:147 final size:145
Alignment explanation
Indices: 31826--32116 Score: 302
Period size: 147 Copynumber: 2.0 Consensus size: 145
31816 AAACTTATGC
* * *** * * *
31826 AAGTTTTTCAGTTAAGGACAGTTTGGGGTGTCAAACCAACTTCTTTATGATAGGGAGTTCGGTTT
1 AAGTTTTTCAGTTAAGGACAGTTTGGGGAGACAAACCAACTTCACCATCATAGGAAGCTCGGTTT
* * * * *
31891 TACTTAGAATTTTTTCCATAGTCTTATGGAGATAATATAAGCCTAGTGGTGGAAAATCAGCCTTA
66 TACATAGAATTTTTTCCATAGTCTTATGGAAAGAATATAAGCC-ACT-GTGGAAAATCAG-CTCA
*
31956 TT-GGACTTAGAATGCAT
128 TTCAGACTTAGAATGCAT
* * *
31973 AAGTTTTTCATTTAAGGACAGTTTGGGGAGAGAAACCAAGTTCACCATCA-AGGAAAGCTCGGTT
1 AAGTTTTTCAGTTAAGGACAGTTTGGGGAGACAAACCAACTTCACCATCATAGG-AAGCTCGGTT
* * *
32037 TTACATAGAATTTTTTCCATAGTGTTTTGGAAAGAATCTAAGTCC-CT-TGGAAAATTTTCAGCT
65 TTACATAGAATTTTTTCCATAGTCTTATGGAAAGAATATAAG-CCACTGTGGAAAA---TCAGCT
32100 CATTCAGACTTAGAATG
126 CATTCAGACTTAGAATG
32117 AAAAACTTAT
Statistics
Matches: 118, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
144 7 0.06
146 9 0.08
147 100 0.85
148 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (145 bp):
AAGTTTTTCAGTTAAGGACAGTTTGGGGAGACAAACCAACTTCACCATCATAGGAAGCTCGGTTT
TACATAGAATTTTTTCCATAGTCTTATGGAAAGAATATAAGCCACTGTGGAAAATCAGCTCATTC
AGACTTAGAATGCAT
Found at i:35973 original size:26 final size:27
Alignment explanation
Indices: 35937--35989 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
35927 CAAAAAAAAA
*
35937 AAAAAAACAATAAAGGAAAT-AATTCT
1 AAAAAAACAATAAAAGAAATAAATTCT
35963 AAAAAAACAATAAAAGAAATAAATTCT
1 AAAAAAACAATAAAAGAAATAAATTCT
35990 CCAAAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.68, C:0.08, G:0.06, T:0.19
Consensus pattern (27 bp):
AAAAAAACAATAAAAGAAATAAATTCT
Found at i:36001 original size:27 final size:25
Alignment explanation
Indices: 35939--36001 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
35929 AAAAAAAAAA
*
35939 AAAAAC-AATAAAGGAAATAATTCT
1 AAAAACAAATAAAAGAAATAATTCT
*
35963 AAAAAAACAATAAAAGAAATAAATTCT
1 AAAAACA-AATAAAAGAAAT-AATTCT
*
35990 CCAAAACAAATA
1 -AAAAACAAATA
36002 TAAAAGAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 5 0.16
26 11 0.35
27 10 0.32
28 5 0.16
ACGTcount: A:0.67, C:0.11, G:0.05, T:0.17
Consensus pattern (25 bp):
AAAAACAAATAAAAGAAATAATTCT
Found at i:46563 original size:2 final size:2
Alignment explanation
Indices: 46552--46582 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
46542 AAAAAAAAAC
*
46552 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46583 ATTATATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:49703 original size:2 final size:2
Alignment explanation
Indices: 49690--49728 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
49680 ACTTGTGTCA
*
49690 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49729 AACAATATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:51074 original size:16 final size:16
Alignment explanation
Indices: 51050--51087 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
51040 GGAGAGAGGG
*
51050 TCTCGCAGGCGAAGCC
1 TCTCCCAGGCGAAGCC
51066 TCTCCCAGGCGAAGCC
1 TCTCCCAGGCGAAGCC
51082 TCTCCC
1 TCTCCC
51088 TGGTCGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.45, G:0.24, T:0.16
Consensus pattern (16 bp):
TCTCCCAGGCGAAGCC
Found at i:54643 original size:2 final size:2
Alignment explanation
Indices: 54636--54665 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54626 ACTTTTACTT
54636 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
54666 CTTTTTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.