Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022584.1 Corchorus olitorius cultivar O-4 contig22617, 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: 19377
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2632 original size:20 final size:20
Alignment explanation
Indices: 2594--2633 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2584 TTTTCAAAAA
*
2594 AAAAACGCAAACACAAAATT
1 AAAAACGCAAAAACAAAATT
* *
2614 AAAAACGGAAAAACCAAATT
1 AAAAACGCAAAAACAAAATT
2634 TTTTTTAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.65, C:0.17, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAACGCAAAAACAAAATT
Found at i:6530 original size:7 final size:7
Alignment explanation
Indices: 6520--6578 Score: 100
Period size: 7 Copynumber: 8.4 Consensus size: 7
6510 TTTTGAGCCA
6520 TGAATTT
1 TGAATTT
6527 TGAATTT
1 TGAATTT
*
6534 TGAGTTT
1 TGAATTT
*
6541 TGAGTTT
1 TGAATTT
6548 TGAATTT
1 TGAATTT
6555 TGAATTT
1 TGAATTT
6562 TGAATTT
1 TGAATTT
6569 TGAATTT
1 TGAATTT
6576 TGA
1 TGA
6579 GCAATGAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (7 bp):
TGAATTT
Found at i:6530 original size:28 final size:28
Alignment explanation
Indices: 6496--6571 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
6486 GAAATGCAGG
* *
6496 TTTTGAAATTTGATTTTTGAGCCATGAA
1 TTTTGAATTTTGAATTTTGAGCCATGAA
* ***
6524 TTTTGAATTTTGAGTTTTGAGTTTTGAA
1 TTTTGAATTTTGAATTTTGAGCCATGAA
6552 TTTTGAATTTTGAATTTTGA
1 TTTTGAATTTTGAATTTTGA
6572 ATTTTGAGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (28 bp):
TTTTGAATTTTGAATTTTGAGCCATGAA
Found at i:6548 original size:21 final size:21
Alignment explanation
Indices: 6495--6579 Score: 107
Period size: 21 Copynumber: 4.0 Consensus size: 21
6485 TGAAATGCAG
* *
6495 GTTTTGAAATTTGATTTTTGA
1 GTTTTGAATTTTGAATTTTGA
***
6516 GCCATGAATTTTGAATTTTGA
1 GTTTTGAATTTTGAATTTTGA
*
6537 GTTTTGAGTTTTGAATTTTGA
1 GTTTTGAATTTTGAATTTTGA
*
6558 ATTTTGAATTTTGAATTTTGA
1 GTTTTGAATTTTGAATTTTGA
6579 G
1 G
6580 CAATGAAATG
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.25, C:0.02, G:0.20, T:0.53
Consensus pattern (21 bp):
GTTTTGAATTTTGAATTTTGA
Found at i:6752 original size:33 final size:33
Alignment explanation
Indices: 6712--6789 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
6702 AGAAACTGTG
* * *
6712 GATTTTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
6745 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
6778 AATTTTGAACTT
1 GATTTTGAACTT
6790 CTTAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:7009 original size:54 final size:54
Alignment explanation
Indices: 6893--7153 Score: 330
Period size: 54 Copynumber: 4.8 Consensus size: 54
6883 AGATCATCGT
* * * ** *
6893 AAACTTCT-TGGAATGACCACACTGGATCAACTTTAAGATCAACTTAGATTTTTGA
1 AAACTTCTAT-GAAAGACCACACTGGGTCATC-TTAAGATCAACTTAGACCTCTGA
* * * *
6948 AAACTTCTATGGAAGACCACACAGGGTCGTCTGAAGATCAACTTAGACCTCT-A
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACCTCTGA
*
7001 AAAGCTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA
1 AAA-CTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACCTCTGA
* *
7056 AAACTTCTATAAAAGACCACACTGAGTCATCTTAAGATCAACTTAGACCTCT-A
1 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACCTCTGA
* *
7109 AAAGCTTTTATGAAAGACCACACTGGATCATCTTAAGATCAACTT
1 AAA-CTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTT
7154 TCTGGAAAGA
Statistics
Matches: 180, Mismatches: 22, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
53 8 0.04
54 144 0.80
55 27 0.15
56 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (54 bp):
AAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCAACTTAGACCTCTGA
Found at i:7093 original size:108 final size:108
Alignment explanation
Indices: 6907--7153 Score: 386
Period size: 108 Copynumber: 2.3 Consensus size: 108
6897 TTCTTGGAAT
* * * **
6907 GACCACACTGGATCAACTTTAAGATCAACTTAGATTTTTGAAAACTTCTATGGAAGACCACACAG
1 GACCACACTGGATCATC-TTAAGATCAACTTAGATCTCTGAAAACTTCTATAAAAGACCACACAG
* *
6972 GGTCGTCTGAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAA
65 AGTCATCTGAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAA
* *
7016 GACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATAAAAGACCACACTGA
1 GACCACACTGGATCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATAAAAGACCACACAGA
* *
7081 GTCATCTTAAGATCAACTTAGACCTCTAAAAGCTTTTATGAAA
66 GTCATCTGAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAA
7124 GACCACACTGGATCATCTTAAGATCAACTT
1 GACCACACTGGATCATCTTAAGATCAACTT
7154 TCTGGAAAGA
Statistics
Matches: 126, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
108 111 0.88
109 15 0.12
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (108 bp):
GACCACACTGGATCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATAAAAGACCACACAGA
GTCATCTGAAGATCAACTTAGACCTCTAAAAGCTTCTATGAAA
Found at i:7338 original size:74 final size:74
Alignment explanation
Indices: 7250--7642 Score: 425
Period size: 74 Copynumber: 5.3 Consensus size: 74
7240 CCTAAACTGG
* * * *
7250 GATTTTGAAGAGACACCTAAACAGGTACCTTAAATTAGGATTTAATAGGAAACCTAAACAGGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAAT
*
7315 TTTGAACAA
66 CTTGAACAA
* * *
7324 GATTTTGATGAGACACCTAAATAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAAT
*
7389 CTTAAACAA
66 CTTGAACAA
* * *
7398 GATTTTGATGAGACACCTAAATAGGGACCTTAAATAAAGATTTAATAAGAAACCTAAACAAGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAAT
7463 CTTGAACAA
66 CTTGAACAA
* * * * ** * * * *
7472 AATTTTGATGAGACACCTAAACAAGGATCTTGAACCA-GATTTCGATGAGACACCTAAACAGG-G
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTT-AATAAGAAACCTAAACAGGAA
* *
7535 TCCTTAAATAA
65 T-CTTGAACAA
** * * *
7546 GGA-TTTGAAAAGACACCTAAACAGAGACCTTAAATAAGGATTTAATAAGACACCTAAACAGGGA
1 -GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAA
* *
7610 CCTTAAACAA
65 TCTTGAACAA
* *
7620 GGA-TTTGATAAAACACCTAAACA
1 -GATTTTGATGAGACACCTAAACA
7643 TGAATCTTGA
Statistics
Matches: 270, Mismatches: 44, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
73 6 0.02
74 258 0.96
75 6 0.02
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (74 bp):
GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAAT
CTTGAACAA
Found at i:7718 original size:148 final size:148
Alignment explanation
Indices: 7260--7718 Score: 550
Period size: 148 Copynumber: 3.1 Consensus size: 148
7250 GATTTTGAAG
* * *
7260 AGACACCTAAACAG-GTACCTTAAATTAGGATTTAATAGGAAACCTAAACAGGAATTTTGAACAA
1 AGACACCTAAACAGAG-ACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAA
* * * * * *
7324 GATTTTGATGAGACACCTAAATAGGGACCTTAAATAAGGA-TTTGAT-AAGAAACCTAAACAGGG
65 GATTTTGATGAGACACCTAAACAAGGATCTTGAACAA-GATTTTGATGAA-ACACCTAAACAGGG
* * *
7387 ATCTTAAACAA-GATTTTGATG
128 ACCTTAAATAAGGA-TTTGATA
* * * * *
7408 AGACACCTAAATAGGGACCTTAAATAAAGATTTAATAAGAAACCTAAACAAGAATCTTGAACAAA
1 AGACACCTAAACAGAGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAG
* * * *
7473 ATTTTGATGAGACACCTAAACAAGGATCTTGAACCAGATTTCGATGAGACACCTAAACAGGGTCC
66 ATTTTGATGAGACACCTAAACAAGGATCTTGAACAAGATTTTGATGAAACACCTAAACAGGGACC
*
7538 TTAAATAAGGATTTGAAA
131 TTAAATAAGGATTTGATA
* * * *
7556 AGACACCTAAACAGAGACCTTAAATAAGGATTTAATAAGACACCTAAACAGGGACCTTAAACAAG
1 AGACACCTAAACAGAGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAA-
* * * * *
7621 GA-TTTGATAAAACACCTAAACATGAATCTTGAACAAGATTTTTATGAAACACCTAAACAGGGAC
65 GATTTTGATGAGACACCTAAACAAGGATCTTGAACAAGATTTTGATGAAACACCTAAACAGGGAC
7685 CTTAAATAAGGATTTGATA
130 CTTAAATAAGGATTTGATA
*
7704 AGACACCTACACAGA
1 AGACACCTAAACAGA
7719 AATCTTGAAC
Statistics
Matches: 265, Mismatches: 41, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
147 2 0.01
148 258 0.97
149 5 0.02
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (148 bp):
AGACACCTAAACAGAGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAG
ATTTTGATGAGACACCTAAACAAGGATCTTGAACAAGATTTTGATGAAACACCTAAACAGGGACC
TTAAATAAGGATTTGATA
Found at i:7738 original size:37 final size:36
Alignment explanation
Indices: 7260--7744 Score: 380
Period size: 37 Copynumber: 13.1 Consensus size: 36
7250 GATTTTGAAG
* * * * *
7260 AGACACCTAAACAGGTACCTTAAATTAGGATTTAATA
1 AGACACCTAAACAGGGATCTTAAA-CAAGATTTGATA
* * * * * *
7297 GGAAACCTAAACAGGAATTTTGAACAAGATTTTGATG
1 AGACACCTAAACAGGGATCTTAAACAAGA-TTTGATA
* * *
7334 AGACACCTAAATAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGATCTTAAACAA-GATTTGATA
* *
7371 AGAAACCTAAACAGGGATCTTAAACAAGATTTTGATG
1 AGACACCTAAACAGGGATCTTAAACAAGA-TTTGATA
* * * *
7408 AGACACCTAAATAGGGACCTTAAATAAAGATTTAATA
1 AGACACCTAAACAGGGATCTTAAA-CAAGATTTGATA
* * * * * *
7445 AGAAACCTAAACAAGAATCTTGAACAAAATTTTGATG
1 AGACACCTAAACAGGGATCTTAAACAAGA-TTTGATA
* * * *
7482 AGACACCTAAACAAGGATCTTGAACCAGATTTCGATG
1 AGACACCTAAACAGGGATCTTAAACAAGATTT-GATA
* *
7519 AGACACCTAAACAGGG-TCCTTAAATAAGGATTTGAAA
1 AGACACCTAAACAGGGAT-CTTAAACAA-GATTTGATA
* * * *
7556 AGACACCTAAACAGAGACCTTAAATAAGGATTTAATA
1 AGACACCTAAACAGGGATCTTAAACAA-GATTTGATA
*
7593 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
1 AGACACCTAAACAGGGATCTTAAACAA-GATTTGATA
* * * * *
7630 AAACACCTAAACATGAATCTTGAACAAGATTTTTATGA
1 AGACACCTAAACAGGGATCTTAAACAAGA-TTTGAT-A
* *
7668 A-ACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGATCTTAAACAA-GATTTGATA
* ** * *
7704 AGACACCTACACAGAAATCTTGAACAAGATTTTGATG
1 AGACACCTAAACAGGGATCTTAAACAAGA-TTTGATA
7741 AGAC
1 AGAC
7745 TGAATTTTGT
Statistics
Matches: 358, Mismatches: 76, Indels: 28
0.77 0.16 0.06
Matches are distributed among these distances:
36 18 0.05
37 325 0.91
38 15 0.04
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (36 bp):
AGACACCTAAACAGGGATCTTAAACAAGATTTGATA
Found at i:12074 original size:6 final size:6
Alignment explanation
Indices: 12063--12116 Score: 81
Period size: 6 Copynumber: 8.5 Consensus size: 6
12053 TCTTTGCATA
12063 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTATTATT TTTAAT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTA--A-T TTTAAT
12114 TTT
1 TTT
12117 TACACTAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
6 38 0.84
7 1 0.02
8 1 0.02
9 5 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:13683 original size:18 final size:18
Alignment explanation
Indices: 13662--13698 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13652 AAAGGGTAAT
*
13662 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
13680 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
13698 T
1 T
13699 GGTAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:14568 original size:19 final size:18
Alignment explanation
Indices: 14544--14579 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14534 TGAAGATTTA
14544 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
14563 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
14580 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:16118 original size:32 final size:32
Alignment explanation
Indices: 16077--16175 Score: 171
Period size: 32 Copynumber: 3.0 Consensus size: 32
16067 AGACCGATCA
*
16077 AGCGGCGTCTATAGAACAAAACGCCCTTATTT
1 AGCGGCGTCTACAGAACAAAACGCCCTTATTT
16109 AGCGGCGTCTACAGAACAAAACGCCCTTATTT
1 AGCGGCGTCTACAGAACAAAACGCCCTTATTT
16141 AGCGGCGTCTACAGAACAAAACGCCGCTATATTT
1 AGCGGCGTCTACAGAACAAAACGCC-CT-TATTT
16175 A
1 A
16176 ACTGCTTTTA
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
32 56 0.88
33 2 0.03
34 6 0.09
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (32 bp):
AGCGGCGTCTACAGAACAAAACGCCCTTATTT
Done.