Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015679.1 Corchorus olitorius cultivar O-4 contig15712, 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: 22001
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--53 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
* **
1 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA CCC 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
43 TA TA T- TA TA TA
1 TA TA TA TA TA TA
54 AACCCTAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:41 original size:22 final size:24
Alignment explanation
Indices: 9--60 Score: 86
Period size: 26 Copynumber: 2.1 Consensus size: 24
1 TATATATA
9 TATATATATATATATATTATAAACCC
1 TATATATATATAT-TA-TATAAACCC
35 TATATATATATATTATATAAACCC
1 TATATATATATATTATATAAACCC
59 TA
1 TA
61 ATACCCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 11 0.42
25 2 0.08
26 13 0.50
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (24 bp):
TATATATATATATTATATAAACCC
Found at i:625 original size:22 final size:21
Alignment explanation
Indices: 594--643 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
584 AATTTAGTGA
594 CAAATTAAGGGCGCCTAATTGCT
1 CAAA-TAAGGG-GCCTAATTGCT
617 CAAATAA-GGGCCTAATTGCT
1 CAAATAAGGGGCCTAATTGCT
637 -AAA-AAGG
1 CAAATAAGG
644 AAGGTTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.08
19 4 0.15
20 11 0.42
21 2 0.08
22 3 0.12
23 4 0.15
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
CAAATAAGGGGCCTAATTGCT
Found at i:6219 original size:11 final size:11
Alignment explanation
Indices: 6199--6227 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6189 CTTGGTCTTG
6199 AATT-GATAAT
1 AATTCGATAAT
6209 AATTCGATAAT
1 AATTCGATAAT
6220 AATTCGAT
1 AATTCGAT
6228 TCAAGAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (11 bp):
AATTCGATAAT
Found at i:6279 original size:41 final size:41
Alignment explanation
Indices: 6226--6337 Score: 170
Period size: 41 Copynumber: 2.7 Consensus size: 41
6216 TAATAATTCG
* *
6226 ATTCAAGAGTCTCGATAACTTGTTCTTGAATTGATAATTTA
1 ATTCAAGAGTCTCGATGACTTGATCTTGAATTGATAATTTA
* **
6267 ATTCAAGGGTCTCGATGACTCAATCTTGAATTGATAATTTA
1 ATTCAAGAGTCTCGATGACTTGATCTTGAATTGATAATTTA
*
6308 ATTCAAGCGTCTCGATGACTTGATCTTGAA
1 ATTCAAGAGTCTCGATGACTTGATCTTGAA
6338 CAAACGAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (41 bp):
ATTCAAGAGTCTCGATGACTTGATCTTGAATTGATAATTTA
Found at i:6450 original size:16 final size:16
Alignment explanation
Indices: 6431--6461 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6421 CATCTGAAAA
6431 TACTTCAGAGCTTTTC
1 TACTTCAGAGCTTTTC
6447 TACTTCAGAGCTTTT
1 TACTTCAGAGCTTTT
6462 TTGGTTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (16 bp):
TACTTCAGAGCTTTTC
Found at i:8353 original size:19 final size:19
Alignment explanation
Indices: 8342--8378 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
8332 AATTTTTAAG
8342 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
8361 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
8379 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:8630 original size:19 final size:23
Alignment explanation
Indices: 8575--8629 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
8565 TCCCTAAGCA
8575 GAGAAGAAAGAAATTAGATCTTG
1 GAGAAGAAAGAAATTAGATCTTG
8598 GAGAAGAAAGAAATTAGATCTTG
1 GAGAAGAAAGAAATTAGATCTTG
8621 GAGAAGAAA
1 GAGAAGAAA
8630 TCAAAATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.51, C:0.04, G:0.27, T:0.18
Consensus pattern (23 bp):
GAGAAGAAAGAAATTAGATCTTG
Found at i:10640 original size:94 final size:95
Alignment explanation
Indices: 10541--10713 Score: 294
Period size: 94 Copynumber: 1.8 Consensus size: 95
10531 TAGTAATATC
*
10541 GTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGA-G
1 GTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACA
10605 TAAAACTATAAAAGTAAAATATGTGAAATT
66 TAAAACTATAAAAGTAAAATATGTGAAATT
* * *
10635 GTAAAAATAAATTAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT
1 GTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAC-
10700 ATAAAACTATAAAA
65 ATAAAACTATAAAA
10714 ATTTAAAACA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
94 60 0.82
96 13 0.18
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34
Consensus pattern (95 bp):
GTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACA
TAAAACTATAAAAGTAAAATATGTGAAATT
Found at i:10755 original size:81 final size:78
Alignment explanation
Indices: 10661--10819 Score: 282
Period size: 81 Copynumber: 2.0 Consensus size: 78
10651 TATAAGGATA
*
10661 TTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTATAAAACTATAAAAATTTAAAACAAT
1 TTAGATATAATTAAATAAAAATAGAGTTTTTAGTTGAC--TAAAACTATAAAAATTT-AAACAAT
10726 GACATTTAAGAAATAT
63 GACATTTAAGAAATAT
10742 TTAGATATAATTAAATAAAAATAGAGTTTTTAGTTGACTAAAACTATAAAAATTTAAACAATGAC
1 TTAGATATAATTAAATAAAAATAGAGTTTTTAGTTGACTAAAACTATAAAAATTTAAACAATGAC
10807 ATTTAAGAAATAT
66 ATTTAAGAAATAT
10820 ATTCAAAAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
78 23 0.30
79 17 0.22
81 37 0.48
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (78 bp):
TTAGATATAATTAAATAAAAATAGAGTTTTTAGTTGACTAAAACTATAAAAATTTAAACAATGAC
ATTTAAGAAATAT
Found at i:10871 original size:31 final size:31
Alignment explanation
Indices: 10828--10889 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
10818 ATATTCAAAA
* *
10828 AATACAGGTATAATAGGTGATTCAAAAGTTT
1 AATAAAGGTATAATAGGCGATTCAAAAGTTT
10859 AATAAAGGTATAATAGGCGATTCAAAAGTTT
1 AATAAAGGTATAATAGGCGATTCAAAAGTTT
10890 TACAAAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (31 bp):
AATAAAGGTATAATAGGCGATTCAAAAGTTT
Found at i:12552 original size:20 final size:21
Alignment explanation
Indices: 12512--12552 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12502 GATTATCATG
*
12512 TTTTGCAAATTTTACTCTTTT
1 TTTTGCAAATTTTAATCTTTT
*
12533 TTTTGCAATTTTTAAT-TTTT
1 TTTTGCAAATTTTAATCTTTT
12553 CTAATTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTTGCAAATTTTAATCTTTT
Found at i:13625 original size:20 final size:20
Alignment explanation
Indices: 13596--13666 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
13586 ATTGTGTTGC
13596 ATTATTATATTATAATAATT
1 ATTATTATATTATAATAATT
* * *
13616 ATTATAATATAATAATAATA
1 ATTATTATATTATAATAATT
*
13636 ATTA-T-TATTATCATAATT
1 ATTATTATATTATAATAATT
*
13654 ATTCTTATATTAT
1 ATTATTATATTAT
13667 CCCTTAGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 13 0.32
19 1 0.02
20 27 0.66
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTATTATATTATAATAATT
Found at i:13637 original size:23 final size:24
Alignment explanation
Indices: 13607--13652 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
13597 TTATTATATT
13607 ATAATAATTATTATAAT-ATAATA
1 ATAATAATTATTATAATCATAATA
*
13630 ATAATAATTATTATTATCATAAT
1 ATAATAATTATTATAATCATAAT
13653 TATTCTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAATAATTATTATAATCATAATA
Found at i:17662 original size:21 final size:21
Alignment explanation
Indices: 17638--17720 Score: 60
Period size: 22 Copynumber: 3.8 Consensus size: 21
17628 AATTTTGAAA
*
17638 GTTATCAAAATTCATTGTGTG
1 GTTATCAAAATTCATAGTGTG
*
17659 GTTA-CTAAAATTTTATAGTGTG
1 GTTATC-AAAA-TTCATAGTGTG
* *
17681 GTTCTCAAAATCTTATAGTGTG
1 GTTATCAAAAT-TCATAGTGTG
** *
17703 CCTACCAAAATTTCATAG
1 GTTATCAAAA-TTCATAG
17721 GTAGCATGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 9 0.18
22 37 0.76
23 2 0.04
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (21 bp):
GTTATCAAAATTCATAGTGTG
Found at i:17682 original size:22 final size:22
Alignment explanation
Indices: 17654--17720 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
17644 AAAATTCATT
17654 GTGTGGTTACTAAAATTTTATA
1 GTGTGGTTACTAAAATTTTATA
*
17676 GTGTGGTT-CTCAAAATCTTATA
1 GTGTGGTTACT-AAAATTTTATA
** * *
17698 GTGTGCCTACCAAAATTTCATA
1 GTGTGGTTACTAAAATTTTATA
17720 G
1 G
17721 GTAGCATGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
21 2 0.05
22 34 0.92
23 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (22 bp):
GTGTGGTTACTAAAATTTTATA
Found at i:17793 original size:22 final size:22
Alignment explanation
Indices: 17768--18006 Score: 168
Period size: 22 Copynumber: 10.8 Consensus size: 22
17758 TCCATGGAAT
*
17768 GTTATTAAAATTTCATAAGGAG
1 GTTATCAAAATTTCATAAGGAG
* *
17790 GTTATTAAAATAAAATTTCATAAGGAT
1 GTTA-T----CAAAATTTCATAAGGAG
*
17817 GTTATCAAAATTTCATATGGAG
1 GTTATCAAAATTTCATAAGGAG
*
17839 GTTATAAAAATTTCATAAGGAG
1 GTTATCAAAATTTCATAAGGAG
* *
17861 GTTATCGAAA-TTCAT-GGGAAG
1 GTTATCAAAATTTCATAAGG-AG
* * *
17882 GTTGTCAAAATTTCACAGGGAG
1 GTTATCAAAATTTCATAAGGAG
****
17904 GTTA-CTAAAATTTCATACTCTG
1 GTTATC-AAAATTTCATAAGGAG
* *
17926 GTTATCAAAATTTCATAGGGCG
1 GTTATCAAAATTTCATAAGGAG
* * *
17948 ATTATCGAAATCTT-ATATGGAG
1 GTTATCAAAAT-TTCATAAGGAG
17970 GTT-T-AAAATTTCAT-AGGAAG
1 GTTATCAAAATTTCATAAGG-AG
*
17990 ATTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
18007 GTGTGCTTAT
Statistics
Matches: 171, Mismatches: 30, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
19 4 0.02
20 12 0.07
21 18 0.11
22 109 0.64
23 7 0.04
26 1 0.01
27 20 0.12
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAG
Found at i:18016 original size:22 final size:22
Alignment explanation
Indices: 17801--18035 Score: 100
Period size: 22 Copynumber: 10.8 Consensus size: 22
17791 TTATTAAAAT
17801 AAAATTTCATAAG-GATG-TTATC
1 AAAATTTCAT-AGTGA-GATTATC
* *
17823 AAAATTTCATA-TGGAGGTTATA
1 AAAATTTCATAGT-GAGATTATC
*
17845 AAAATTTCATAAG-GAGGTTATC
1 AAAATTTCAT-AGTGAGATTATC
* * * *
17867 GAAA-TTCAT-GGGAAGGTTGTC
1 AAAATTTCATAGTG-AGATTATC
* * *
17888 AAAATTTCACAGGGAGGTTA-C
1 AAAATTTCATAGTGAGATTATC
* ** *
17909 TAAAATTTCATACTCTGGTTATC
1 -AAAATTTCATAGTGAGATTATC
* *
17932 AAAATTTCATAGGGCGATTATC
1 AAAATTTCATAGTGAGATTATC
* *
17954 GAAATCTT-ATA-TGGAGGTT-T-
1 AAAAT-TTCATAGT-GAGATTATC
17974 AAAATTTCATAG-GAAGATTATC
1 AAAATTTCATAGTG-AGATTATC
* *
17996 AAAATTTCATAGTGTGCTTAT-
1 AAAATTTCATAGTGAGATTATC
*
18017 AGAAATTACATAGTGAGAT
1 A-AAATTTCATAGTGAGAT
18036 AGAGTGAGCT
Statistics
Matches: 165, Mismatches: 28, Indels: 40
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.02
20 12 0.07
21 21 0.13
22 120 0.73
23 8 0.05
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (22 bp):
AAAATTTCATAGTGAGATTATC
Found at i:18283 original size:21 final size:22
Alignment explanation
Indices: 18238--18336 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
18228 TGTGGCAGTT
* *
18238 AAAATTTCAT-GATGAGTTTATC
1 AAAATTTCATAG-TGAGATTAAC
18260 AAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAGTGAGATTAAC
* * * * **
18281 AAAATTTGATATTGTGGTTCTC
1 AAAATTTCATAGTGAGATTAAC
* *
18303 AAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAGTGAGATTAAC
18325 AAAATTTCATAG
1 AAAATTTCATAG
18337 GTAAGTCATA
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 17 0.28
22 43 0.72
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAGTGAGATTAAC
Done.