Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022523.1 Corchorus olitorius cultivar O-4 contig22556, 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: 51316
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1299 original size:19 final size:19
Alignment explanation
Indices: 1275--1312 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1265 ATGCACTTAA
1275 AACTTTCTTATGATACTAT
1 AACTTTCTTATGATACTAT
1294 AACTTTCTTATGATACTAT
1 AACTTTCTTATGATACTAT
1313 GCATTAGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (19 bp):
AACTTTCTTATGATACTAT
Found at i:8652 original size:17 final size:17
Alignment explanation
Indices: 8630--8666 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
8620 GAGAAAGTTT
8630 TAAAATAGTCATAATAG
1 TAAAATAGTCATAATAG
8647 TAAAATAGTCATAATAG
1 TAAAATAGTCATAATAG
8664 TAA
1 TAA
8667 TCAGAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.11, T:0.30
Consensus pattern (17 bp):
TAAAATAGTCATAATAG
Found at i:12089 original size:8 final size:8
Alignment explanation
Indices: 12067--12113 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
12057 TTTAATATTA
12067 TTATTAAG
1 TTATTAAG
12075 ATTATTAAG
1 -TTATTAAG
12084 TTATTATA-
1 TTATTA-AG
12092 TTATTAAG
1 TTATTAAG
*
12100 TTA-TAAT
1 TTATTAAG
12107 TTATTAA
1 TTATTAA
12114 ATCTAAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
7 7 0.21
8 18 0.53
9 9 0.26
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (8 bp):
TTATTAAG
Found at i:12096 original size:16 final size:16
Alignment explanation
Indices: 12075--12113 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12065 TATTATTAAG
*
12075 ATTATTAAGTTATTAT
1 ATTATTAAGTTATAAT
12091 ATTATTAAGTTATAAT
1 ATTATTAAGTTATAAT
12107 -TTATTAA
1 ATTATTAA
12114 ATCTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
ATTATTAAGTTATAAT
Found at i:18988 original size:24 final size:24
Alignment explanation
Indices: 18956--19004 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
18946 CATTTTCCAG
18956 ATATCCAATATATAATGACAAAGC
1 ATATCCAATATATAATGACAAAGC
18980 ATATCCAATATATAATGACAAAGC
1 ATATCCAATATATAATGACAAAGC
19004 A
1 A
19005 CGTTGCTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.24
Consensus pattern (24 bp):
ATATCCAATATATAATGACAAAGC
Found at i:23763 original size:19 final size:19
Alignment explanation
Indices: 23735--23772 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23725 GAAACAGGGG
* *
23735 AAAACCAAAAAAGAAAAAA
1 AAAACAAAAAAACAAAAAA
23754 AAAACAAAAAAACAAAAAA
1 AAAACAAAAAAACAAAAAA
23773 GACTCTCTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (19 bp):
AAAACAAAAAAACAAAAAA
Found at i:24704 original size:28 final size:30
Alignment explanation
Indices: 24649--24709 Score: 88
Period size: 33 Copynumber: 2.0 Consensus size: 30
24639 GCTGTTGACG
24649 ATTTCAGGTAAACTAAACGAATATAATAATAAA
1 ATTTCAGGTAAACTAAACGAA-AT-AT-ATAAA
24682 ATTTCAGGTAAACTAAACG-AATATATAA
1 ATTTCAGGTAAACTAAACGAAATATATAA
24710 GCATGTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 4 0.14
30 2 0.07
31 2 0.07
32 1 0.04
33 19 0.68
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (30 bp):
ATTTCAGGTAAACTAAACGAAATATATAAA
Found at i:25204 original size:25 final size:24
Alignment explanation
Indices: 25170--25223 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
25160 GTTCCTGTTT
*
25170 TTTTTCTTTCCATTTTTTTTCCTTA
1 TTTTTCTTTCCA-TTTCTTTCCTTA
* *
25195 TTTTTCTTTCTATTTCTTTCCTTT
1 TTTTTCTTTCCATTTCTTTCCTTA
25219 TTTTT
1 TTTTT
25224 GTTTTCTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTCTTTCCATTTCTTTCCTTA
Found at i:37410 original size:31 final size:31
Alignment explanation
Indices: 37375--37437 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
37365 GGAGCTCAAC
37375 TTCGTAACGAGTCGAGCACGAGCTTGAAAAA
1 TTCGTAACGAGTCGAGCACGAGCTTGAAAAA
37406 TTCGTAACGAGTCGAGCACGAGCTTGAAAAA
1 TTCGTAACGAGTCGAGCACGAGCTTGAAAAA
37437 T
1 T
37438 AGAAGATCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (31 bp):
TTCGTAACGAGTCGAGCACGAGCTTGAAAAA
Found at i:37503 original size:32 final size:32
Alignment explanation
Indices: 37458--37530 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
37448 CAAGTTCGAG
37458 TCGAGC-TTCGAGTTTTTCCATCGAGTCAAGC
1 TCGAGCTTTCGAGTTTTTCCATCGAGTCAAGC
*
37489 TCGAGCTTTCGAGTTTTTCCATCGAGTCGAGC
1 TCGAGCTTTCGAGTTTTTCCATCGAGTCAAGC
37521 TCGAGCTTTC
1 TCGAGCTTTC
37531 CAAAACTCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 6 0.15
32 34 0.85
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.34
Consensus pattern (32 bp):
TCGAGCTTTCGAGTTTTTCCATCGAGTCAAGC
Found at i:37582 original size:34 final size:34
Alignment explanation
Indices: 37534--37602 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
37524 AGCTTTCCAA
*
37534 AACTCGACTTGGCTCATTTACAGCCCTAATTACT
1 AACTCGACTCGGCTCATTTACAGCCCTAATTACT
*
37568 AACTCGACTCGGCTCATTTACAGCCCTAGTTACT
1 AACTCGACTCGGCTCATTTACAGCCCTAATTACT
37602 A
1 A
37603 CTATAATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.30
Consensus pattern (34 bp):
AACTCGACTCGGCTCATTTACAGCCCTAATTACT
Found at i:37667 original size:33 final size:33
Alignment explanation
Indices: 37625--37694 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
37615 GGGTCGGTAG
37625 CAAGGTTAGGTGAAACCCATTCATCCCTAATAA
1 CAAGGTTAGGTGAAACCCATTCATCCCTAATAA
37658 CAAGGTTAGGTGAAACCCATTCATCCCTAATAA
1 CAAGGTTAGGTGAAACCCATTCATCCCTAATAA
37691 CAAG
1 CAAG
37695 CTTAAGCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (33 bp):
CAAGGTTAGGTGAAACCCATTCATCCCTAATAA
Found at i:37942 original size:42 final size:42
Alignment explanation
Indices: 37895--37978 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
37885 ACAACTAAAA
* * *
37895 AATATATTTTTGTATCCAAACACCTAAATATCTTTTATATTT
1 AATATATTCTTGTATCAAAACACCTAAATATCCTTTATATTT
37937 AATATATTCTTGTATCAAAACACCTAAATATCCTTTATATTT
1 AATATATTCTTGTATCAAAACACCTAAATATCCTTTATATTT
37979 GGAAGTCCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.45
Consensus pattern (42 bp):
AATATATTCTTGTATCAAAACACCTAAATATCCTTTATATTT
Found at i:43423 original size:14 final size:14
Alignment explanation
Indices: 43404--43433 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
43394 TGGCAACACC
43404 ATGCCAACAGATTG
1 ATGCCAACAGATTG
43418 ATGCCAACAGATTG
1 ATGCCAACAGATTG
43432 AT
1 AT
43434 TGTTGAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (14 bp):
ATGCCAACAGATTG
Found at i:45096 original size:91 final size:89
Alignment explanation
Indices: 44902--45083 Score: 283
Period size: 91 Copynumber: 2.0 Consensus size: 89
44892 GGTAAGTTTA
* * *
44902 ATGAGCTTCAATTATGGCTGAAGCTCAAACATTCCCTCTACTTGGCTATTGTAAATATTTTTGTC
1 ATGAGCTTCATTTATGGCTGAAGCTCAAACATTCCCCCTACTTGGCTATTGTAAATATTTTTGGC
*
44967 TGTAGAATTCTAACCATGCATTAT
66 TCTAGAATTCTAACCATGCATTAT
44991 ATGAGCTTCATTTATGGCTGAAGCTCTCAAACATTCCCCCTACTTGGCTATTGTAAATATTTTTG
1 ATGAGCTTCATTTATGGCTGAAG--CTCAAACATTCCCCCTACTTGGCTATTGTAAATATTTTTG
* * *
45056 GGTCTAGGATTCTGACCATGCATTAT
64 GCTCTAGAATTCTAACCATGCATTAT
45082 AT
1 AT
45084 TCTTTTGTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
89 22 0.26
91 62 0.74
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (89 bp):
ATGAGCTTCATTTATGGCTGAAGCTCAAACATTCCCCCTACTTGGCTATTGTAAATATTTTTGGC
TCTAGAATTCTAACCATGCATTAT
Found at i:46564 original size:8 final size:8
Alignment explanation
Indices: 46548--46579 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
46538 TAAATAACAA
*
46548 CTATTAAT
1 CTATAAAT
46556 CTATAAAT
1 CTATAAAT
46564 CTATAAAT
1 CTATAAAT
46572 CTATAAAT
1 CTATAAAT
46580 GGAAAACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (8 bp):
CTATAAAT
Found at i:47151 original size:2 final size:2
Alignment explanation
Indices: 47144--47176 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
47134 TAATATTTAG
*
47144 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47177 TTAGAAGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:49056 original size:20 final size:20
Alignment explanation
Indices: 49031--49080 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
49021 GCAAGAAGGC
49031 TATTAAAAAATTTAAAAGAT
1 TATTAAAAAATTTAAAAGAT
*
49051 TATTAAAAAATTTATAAGAT
1 TATTAAAAAATTTAAAAGAT
49071 TATTAAAAAA
1 TATTAAAAAA
49081 AACTTATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
TATTAAAAAATTTAAAAGAT
Found at i:49080 original size:22 final size:22
Alignment explanation
Indices: 49035--49101 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
49025 GAAGGCTATT
*
49035 AAAAAATTTAAAAGATTATT--
1 AAAAAATTTATAAGATTATTAA
49055 AAAAAATTTATAAGATTATTAA
1 AAAAAATTTATAAGATTATTAA
* * *
49077 AAAAAACTTATAAGGTTACTAA
1 AAAAAATTTATAAGATTATTAA
49099 AAA
1 AAA
49102 TGCTTAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 19 0.46
22 22 0.54
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (22 bp):
AAAAAATTTATAAGATTATTAA
Done.