Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013708.1 Corchorus olitorius cultivar O-4 contig13741, 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: 45673
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:524 original size:21 final size:21
Alignment explanation
Indices: 500--545 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
490 CTTAGACAAT
500 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
521 TCCAGTGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
542 TCCA
1 TCCA
546 TTGATCTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:1608 original size:10 final size:10
Alignment explanation
Indices: 1593--1622 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1583 GTAGAGATTC
1593 TTATTTTTTT
1 TTATTTTTTT
*
1603 TTATTTTTTA
1 TTATTTTTTT
1613 TTATTTTTTT
1 TTATTTTTTT
1623 GCATCTCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:10457 original size:24 final size:24
Alignment explanation
Indices: 10430--10516 Score: 70
Period size: 24 Copynumber: 3.5 Consensus size: 24
10420 TCCAATCAAG
10430 TTTTCAAAGTGTTCAATTTAGGTC
1 TTTTCAAAGTGTTCAATTTAGGTC
* ***
10454 TTTTGAAAGTGAGAAAGTTCCCAATAGGT-
1 TTTTCAAAGTGTTCAA-TT-----TAGGTC
10483 -TTTCAAAGTGTTCAATTTAGGTC
1 TTTTCAAAGTGTTCAATTTAGGTC
10506 TTTTCAAAGTG
1 TTTTCAAAGTG
10517 GGAAAGTTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
22 5 0.11
24 22 0.47
25 2 0.04
27 2 0.04
28 11 0.23
30 5 0.11
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (24 bp):
TTTTCAAAGTGTTCAATTTAGGTC
Found at i:10470 original size:52 final size:52
Alignment explanation
Indices: 10402--10555 Score: 238
Period size: 52 Copynumber: 3.0 Consensus size: 52
10392 TCCTTCAAAG
*
10402 TTTTCAAAGTGGGAAAGTTCCAATCAAGTTTTCAAAGTGTTCAATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCAATCAGGTTTTCAAAGTGTTCAATTTAGGTC
* *
10454 TTTTGAAAGTGAGAAAGTTCCCAAT-AGGTTTTCAAAGTGTTCAATTTAGGTC
1 TTTTCAAAGTGGGAAAGTT-CCAATCAGGTTTTCAAAGTGTTCAATTTAGGTC
* * *
10506 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAGCGTTCAACTTAGG
1 TTTTCAAAGTGGGAAAGTTCCAATCAGGTTTTCAAAGTGTTCAATTTAGG
10556 GAAAGTTCTC
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 4 0.04
52 83 0.90
53 5 0.05
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (52 bp):
TTTTCAAAGTGGGAAAGTTCCAATCAGGTTTTCAAAGTGTTCAATTTAGGTC
Found at i:13448 original size:22 final size:22
Alignment explanation
Indices: 13405--13458 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
13395 ATCAGAAAAG
*
13405 AAAAAGAATAAAGTGAAAAGAAT
1 AAAAAGAA-AAAGAGAAAAGAAT
13428 AAAAAGAAAAA-AGAAAGAGAAT
1 AAAAAGAAAAAGAGAAA-AGAAT
13450 AAAAAGAAA
1 AAAAAGAAA
13459 TGCAACGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.14
22 17 0.59
23 8 0.28
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (22 bp):
AAAAAGAAAAAGAGAAAAGAAT
Found at i:13545 original size:14 final size:15
Alignment explanation
Indices: 13512--13547 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
13502 CAAGAGACGT
*
13512 TTTTCAAGAAAATTG
1 TTTTCAAGAAAATGG
13527 TTTTCAAGAAAA-GG
1 TTTTCAAGAAAATGG
13541 TTTTCAA
1 TTTTCAA
13548 AAATGAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (15 bp):
TTTTCAAGAAAATGG
Found at i:16423 original size:16 final size:15
Alignment explanation
Indices: 16404--16433 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16394 TTTATTGATT
16404 AATTAATAACTCTCTA
1 AATTAATAAC-CTCTA
16420 AATTAATAACCTCT
1 AATTAATAACCTCT
16434 CGTGGTCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTAATAACCTCTA
Found at i:17288 original size:54 final size:54
Alignment explanation
Indices: 17173--17555 Score: 457
Period size: 54 Copynumber: 7.1 Consensus size: 54
17163 TTAGCCGAAT
* * *
17173 TTCAAGTGATCCAGTGCGGTCAGTCAA-AAAGTTTCTAGTGGTTTAACTTTATC
1 TTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* * *
17226 GTCAAAGTGATCCAGTGCGATCAATCAATAAAGTTTCCAGTGGTTTAAGTTTATC
1 TTC-AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* *
17281 TTCAAGTGATCCAGTGCGGTCAATCAAGAAAATCTCCAGTGGTTTAAGTTTATC
1 TTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* ** *
17335 TTCAAATGATCCAGTGCGGTCAATCAAGAAAGTTTATAGTGGTTTAGGTTTATC
1 TTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* * * ** *
17389 TTCAAGTGATCTAGTGCGATC-GTTGAGAAAGTCTCCAGTGGTTTAAGTTTATC
1 TTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* * ** * *
17442 TTCAAGTGATGCACTGCGGTCAATCAAGAAAGTTTATAGTGGCTTAGGTTTATC
1 TTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* * ** * **
17496 TTCAAGTGATCCAGTGTGATCGTTC-AGAAAGATTCCAGTGGTTTAAAATTATC
1 TTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
17549 TTCAAGT
1 TTCAAGT
17556 TATTGATCGA
Statistics
Matches: 276, Mismatches: 51, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
53 72 0.26
54 178 0.64
55 26 0.09
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (54 bp):
TTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
Found at i:17469 original size:107 final size:108
Alignment explanation
Indices: 17173--17555 Score: 497
Period size: 107 Copynumber: 3.6 Consensus size: 108
17163 TTAGCCGAAT
* * * * * *
17173 TTCAAGTGATCCAGTGCGGTCAG-TCAAAAAGTTTCTAGTGGTTTAACTTTATCGTCAAAGTGAT
1 TTCAAGTGATCCAGTGCGATCAGTTCAGAAAGTCTCCAGTGGTTTAAGTTTATCTTC-AAGTGAT
* * ** *
17237 CCAGTGCGATCAATCAATAAAGTTTCCAGTGGTTTAAGTTTATC
65 CCAGTGCGGTCAATCAAGAAAGTTTATAGTGGTTTAGGTTTATC
* * * *
17281 TTCAAGTGATCCAGTGCGGTCA-ATCAAGAAAATCTCCAGTGGTTTAAGTTTATCTTCAAATGAT
1 TTCAAGTGATCCAGTGCGATCAGTTC-AGAAAGTCTCCAGTGGTTTAAGTTTATCTTCAAGTGAT
17345 CCAGTGCGGTCAATCAAGAAAGTTTATAGTGGTTTAGGTTTATC
65 CCAGTGCGGTCAATCAAGAAAGTTTATAGTGGTTTAGGTTTATC
* * *
17389 TTCAAGTGATCTAGTGCGATC-GTTGAGAAAGTCTCCAGTGGTTTAAGTTTATCTTCAAGTGATG
1 TTCAAGTGATCCAGTGCGATCAGTTCAGAAAGTCTCCAGTGGTTTAAGTTTATCTTCAAGTGATC
* *
17453 CACTGCGGTCAATCAAGAAAGTTTATAGTGGCTTAGGTTTATC
66 CAGTGCGGTCAATCAAGAAAGTTTATAGTGGTTTAGGTTTATC
* **
17496 TTCAAGTGATCCAGTGTGATC-GTTCAGAAAGAT-TCCAGTGGTTTAAAATTATCTTCAAGT
1 TTCAAGTGATCCAGTGCGATCAGTTCAGAAAG-TCTCCAGTGGTTTAAGTTTATCTTCAAGT
17556 TATTGATCGA
Statistics
Matches: 245, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
107 130 0.53
108 90 0.37
109 25 0.10
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (108 bp):
TTCAAGTGATCCAGTGCGATCAGTTCAGAAAGTCTCCAGTGGTTTAAGTTTATCTTCAAGTGATC
CAGTGCGGTCAATCAAGAAAGTTTATAGTGGTTTAGGTTTATC
Found at i:18256 original size:27 final size:27
Alignment explanation
Indices: 18224--18309 Score: 109
Period size: 28 Copynumber: 3.1 Consensus size: 27
18214 AATTTACTTC
*
18224 TTTTGGTCATTTGCATGTCCAGGGGCA
1 TTTTGGTCATTTGCACGTCCAGGGGCA
* *
18251 TTTTGGTCATTTTGCACATCTAGGGGCA
1 TTTTGGTCA-TTTGCACGTCCAGGGGCA
* *
18279 TTTTGGACATTTGCACGACCAGGGGGCA
1 TTTTGGTCATTTGCACGTCCA-GGGGCA
18307 TTT
1 TTT
18310 CAGTCATCTC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 18 0.36
28 32 0.64
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (27 bp):
TTTTGGTCATTTGCACGTCCAGGGGCA
Found at i:19467 original size:40 final size:40
Alignment explanation
Indices: 19404--19486 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
19394 CATAGGGGCA
*
19404 GCAAGCATCTCAAAGTCAGCATGTTGCAAACAGATTGAGG
1 GCAAGCATCTCAAAGTCAACATGTTGCAAACAGATTGAGG
* **
19444 GCAAGCATTTCAGGGTCAACATGTTGCAAACAGATTGAGG
1 GCAAGCATCTCAAAGTCAACATGTTGCAAACAGATTGAGG
19484 GCA
1 GCA
19487 CAGGAGCTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (40 bp):
GCAAGCATCTCAAAGTCAACATGTTGCAAACAGATTGAGG
Found at i:37073 original size:28 final size:28
Alignment explanation
Indices: 37036--37139 Score: 83
Period size: 24 Copynumber: 3.7 Consensus size: 28
37026 CTGTTTTAGA
*
37036 TGTTGTGTGATGATACTAAACCATGAGTT
1 TGTT-TGTGATGACACTAAACCATGAGTT
* *
37065 TGTTTGTGATGACA-TAAATC-T-AG-A
1 TGTTTGTGATGACACTAAACCATGAGTT
*
37089 TGTTTG-GATGATACTAAACCTAATTTGAGTGT
1 TGTTTGTGATGACACTAAACC--A--TGAGT-T
37121 TGTTTGTGATGACACTAAA
1 TGTTTGTGATGACACTAAA
37140 TCTGTTTTAG
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
23 6 0.10
24 11 0.19
25 2 0.03
26 1 0.02
27 5 0.09
28 9 0.16
29 5 0.09
30 2 0.03
32 6 0.10
33 11 0.19
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (28 bp):
TGTTTGTGATGACACTAAACCATGAGTT
Found at i:37133 original size:56 final size:54
Alignment explanation
Indices: 37032--37142 Score: 156
Period size: 56 Copynumber: 2.0 Consensus size: 54
37022 AAATCTGTTT
37032 TAGATGTTGTGTGATGATACTAAACCATGAGTTTGTTTGTGATGACA-TAAATC
1 TAGATGTTGTGTGATGATACTAAACCATGAGTTTGTTTGTGATGACACTAAATC
37085 TAGATGTT-TG-GATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGACACTAAATC
1 TAGATGTTGTGTGATGATACTAAACC--A--TGAGT-TTGTTTGTGATGACACTAAATC
37142 T
1 T
37143 GTTTTAGGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
51 14 0.27
52 2 0.04
53 9 0.17
55 5 0.10
56 15 0.29
57 7 0.13
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.39
Consensus pattern (54 bp):
TAGATGTTGTGTGATGATACTAAACCATGAGTTTGTTTGTGATGACACTAAATC
Found at i:37138 original size:33 final size:33
Alignment explanation
Indices: 37089--37165 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
37079 TAAATCTAGA
*
37089 TGTTTG-GATGATACTAAACCTAATTTGA-GTGT
1 TGTTTGTGATGACACTAAACCT-ATTTGAGGTGT
* * *
37121 TGTTTGTGATGACACTAAATCTGTTTTAGGTGT
1 TGTTTGTGATGACACTAAACCTATTTGAGGTGT
37154 TGTTTGTGATGA
1 TGTTTGTGATGA
37166 AACAAATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
32 10 0.26
33 29 0.74
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (33 bp):
TGTTTGTGATGACACTAAACCTATTTGAGGTGT
Found at i:37179 original size:33 final size:32
Alignment explanation
Indices: 37112--37216 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 32
37102 CTAAACCTAA
* *
37112 TTTGAGTGTTGTTTGTGATGACACTAAA-TCTGT
1 TTTG-GTGTTGTTTGTGATGAAAC-AAATTATGT
37145 TTTAGGTGTTGTTTGTGATGAAACAAATTATGT
1 TTT-GGTGTTGTTTGTGATGAAACAAATTATGT
* ** *
37178 TTTGGATGCTAATTGTGATGAAAACAAA-TCTGT
1 TTTGG-TGTTGTTTGTGATG-AAACAAATTATGT
37211 TTTGGT
1 TTTGGT
37217 TGATCATAGC
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
32 6 0.10
33 48 0.77
34 8 0.13
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.44
Consensus pattern (32 bp):
TTTGGTGTTGTTTGTGATGAAACAAATTATGT
Found at i:40572 original size:35 final size:35
Alignment explanation
Indices: 40517--40714 Score: 315
Period size: 35 Copynumber: 5.7 Consensus size: 35
40507 AGGGATCCAA
* * *
40517 ATGACTCGGTGCAGCGTCTTCAAAGTTGAATTCTG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAATTCTG
*
40552 ATGACTCGGTGTAGCATCTTCAAAGATGAATTCTA
1 ATGACTCGGTGTAGCATCTTCAAAGATGAATTCTG
*
40587 ATGACTCGGTGTACCATCTTCAAAGATGAATTCTG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAATTCTG
* * *
40622 ATGACTCGGTGTAGCATCTTCAAAGATTAACTCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAATTCTG
*
40657 ATGACTCGGTGTAGCATCTTCAAAGATGAATTCAG
1 ATGACTCGGTGTAGCATCTTCAAAGATGAATTCTG
40692 ATGACTCGGTGTAGCATCTTCAA
1 ATGACTCGGTGTAGCATCTTCAA
40715 TATGGACTCA
Statistics
Matches: 151, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 151 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (35 bp):
ATGACTCGGTGTAGCATCTTCAAAGATGAATTCTG
Found at i:40834 original size:90 final size:89
Alignment explanation
Indices: 40708--40971 Score: 386
Period size: 90 Copynumber: 3.0 Consensus size: 89
40698 CGGTGTAGCA
* * * * **
40708 TCTTCAATATGGACTCAGTGGGCTCGATGCAACAAATCTTCAAATAGATCAAAGTGATTCGGTGA
1 TCTTCAATGTGGACTCAGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGGTGATTCGGTGA
*
40773 ATCAGGCTAATGCGGTGCATTACT
66 ATCAAGCTAATGCGGTGCATTACT
*
40797 TCTTCAATGTGGGGCTCAGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGGTGATTCGGTG
1 TCTTCAATGT-GGACTCAGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGGTGATTCGGTG
*
40862 AATCAAGCTAATGCGGTGCTTTACT
65 AATCAAGCTAATGCGGTGCATTACT
* *
40887 TCTTCAATGTTGGACTCAGTGAGCTCGGTGCAGCAAATCTTCAAATAGGTTAGGGTGATTCGGTG
1 TCTTCAATG-TGGACTCAGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGGTGATTCGGTG
**
40952 AATCAAG-GGATGCGGTGCAT
65 AATCAAGCTAATGCGGTGCAT
40972 CTCTTCAAAG
Statistics
Matches: 158, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
89 19 0.12
90 138 0.87
91 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (89 bp):
TCTTCAATGTGGACTCAGTGAGCTCGGTGCAGCAAATCTTCAAATAGATCAGGGTGATTCGGTGA
ATCAAGCTAATGCGGTGCATTACT
Found at i:41318 original size:28 final size:27
Alignment explanation
Indices: 41269--41363 Score: 145
Period size: 28 Copynumber: 3.4 Consensus size: 27
41259 AATTTACTTC
**
41269 TTTTGGTCATTTGCGGGTCCAGGGGCA
1 TTTTGGTCATTTGCACGTCCAGGGGCA
41296 TTTTGGTCATTTTGCACGTCCAGGGGCA
1 TTTTGGTCA-TTTGCACGTCCAGGGGCA
41324 TTTTGGTCATTTGCACGTCCATGGGGCA
1 TTTTGGTCATTTGCACGTCCA-GGGGCA
*
41352 TTTTAGTCATTT
1 TTTTGGTCATTT
41364 CAAGTACATT
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
27 21 0.33
28 42 0.67
ACGTcount: A:0.14, C:0.19, G:0.28, T:0.39
Consensus pattern (27 bp):
TTTTGGTCATTTGCACGTCCAGGGGCA
Found at i:42513 original size:40 final size:40
Alignment explanation
Indices: 42450--42532 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 40
42440 CATAGGGGCA
* *
42450 GCAAGCATCTCAAAGTCAGCATGTTGCAAACAGATTGAGG
1 GCAAGCATCTCAAAGTCAACATGTTGCAAACAGATTGAAG
* **
42490 GCAAGCATTTCAGGGTCAACATGTTGCAAACAGATTGAAG
1 GCAAGCATCTCAAAGTCAACATGTTGCAAACAGATTGAAG
42530 GCA
1 GCA
42533 CATGAGCTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.20
Consensus pattern (40 bp):
GCAAGCATCTCAAAGTCAACATGTTGCAAACAGATTGAAG
Done.