Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014789.1 Corchorus olitorius cultivar O-4 contig14822, 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: 14028
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:932 original size:24 final size:24
Alignment explanation
Indices: 866--940 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
856 ATGTTTAATT
* * *
866 GTGGGCGCGCTGCCACTTCGGATG
1 GTGGGTGCGCTCCCACTTCCGATG
* * **
890 GGGGGTGTGCTCCTGCTTCCGATG
1 GTGGGTGCGCTCCCACTTCCGATG
*
914 GTGGGTGCGCTCCCACTTCTGATG
1 GTGGGTGCGCTCCCACTTCCGATG
938 GTG
1 GTG
941 AGCATTCTAC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.07, C:0.27, G:0.40, T:0.27
Consensus pattern (24 bp):
GTGGGTGCGCTCCCACTTCCGATG
Found at i:1429 original size:55 final size:55
Alignment explanation
Indices: 1210--1577 Score: 429
Period size: 55 Copynumber: 6.6 Consensus size: 55
1200 CTTCGAGAGC
* * * * * *
1210 GTACTACCTTTTCGCGATCTTTGGTAGCGTACTACCGCTTCGCAG-TCGTTGG-GAGC
1 GTACTACCATTTCGCGAACTTTGG-GGCGTACTACCGCTTCG-AGAGC-TTGGAGGGA
* * *
1266 GTACTACC-TCTTTGCGATCTTTGGGAGCGTACTACCGCTTCGAGAGCTTGGAGGGGGT
1 GTACTACCAT-TTCGCGAACTTTGGG-GCGTACTACCGCTTCGAGAGCTTGGA--GGGA
* * *
1324 GTTCTACCAATTCGCGAGA-TTTGGGAGCGTACTACCGCTTCAAGAGCTTGGAGGGA
1 GTACTACCATTTCGCGA-ACTTTGGG-GCGTACTACCGCTTCGAGAGCTTGGAGGGA
*
1380 GTACTACCATTTCGCGAACTTTGGGGCGTACTACCACTTCGAGAGCTTGGAGGGA
1 GTACTACCATTTCGCGAACTTTGGGGCGTACTACCGCTTCGAGAGCTTGGAGGGA
* * * *
1435 ATACTACCAATTCGCGAGCTTTGGGAGCGTACTACCGCTTCAAGAGCTTGGAGGGA
1 GTACTACCATTTCGCGAACTTTGGG-GCGTACTACCGCTTCGAGAGCTTGGAGGGA
* *
1491 GTACTACCATTTCGCAAACTTTGGGGCGTACTACCACTTCGAGAGCTTGGAGGGA
1 GTACTACCATTTCGCGAACTTTGGGGCGTACTACCGCTTCGAGAGCTTGGAGGGA
* *
1546 GTACTACCATTTCGTGAACTTTGAGGCGTACT
1 GTACTACCATTTCGCGAACTTTGGGGCGTACT
1578 TCCACTTTGC
Statistics
Matches: 273, Mismatches: 29, Indels: 21
0.85 0.09 0.07
Matches are distributed among these distances:
55 115 0.42
56 111 0.41
58 47 0.17
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (55 bp):
GTACTACCATTTCGCGAACTTTGGGGCGTACTACCGCTTCGAGAGCTTGGAGGGA
Found at i:1454 original size:83 final size:81
Alignment explanation
Indices: 1347--1657 Score: 295
Period size: 83 Copynumber: 3.8 Consensus size: 81
1337 GCGAGATTTG
* * * *
1347 GGAGCGTACTACCGCTTCAAGAGCTTGGAGGGAGTACTACCATTTCGCGAACTTTGGGGCGTACT
1 GGAGGGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGCGAACTTTGAGGCGTACT
*
1412 ACCACTTCGAGAGCTT
66 ACCACTTCGAGAACTT
* * * * ** ** * * *
1428 GGAGGGAATACTACCAATTCGCGAGCTTTGG-GAGCGTACTACCGCTTCAAGAGCTTGGAGGGAG
1 GGAGGG--TACTACCACTTCGAGAGC-TTGGAGGGAGTACTACCATTTCGCGAACTTTGA-GGCG
*
1492 TACTACCATTTCGCA-AACTTT
62 TACTACCACTTCG-AGAAC-TT
*
1513 GG-GGCGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGTGAACTTTGAGGCGTAC
1 GGAGG-GTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGCGAACTTTGAGGCGTAC
* * * *
1577 TTCCACTTTGCGATCCTT
65 TACCACTTCGAGA-ACTT
* * *
1595 GAGAGTGTACTACCACCTCGGGAGCTTGGAGGGAGTACTACCATTTCGCGAACTTTGAGGCGT
1 G-GAGGGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGCGAACTTTGAGGCGT
1658 GTTCTACGCC
Statistics
Matches: 181, Mismatches: 37, Indels: 22
0.75 0.15 0.09
Matches are distributed among these distances:
81 5 0.03
82 21 0.12
83 125 0.69
84 24 0.13
85 6 0.03
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (81 bp):
GGAGGGTACTACCACTTCGAGAGCTTGGAGGGAGTACTACCATTTCGCGAACTTTGAGGCGTACT
ACCACTTCGAGAACTT
Found at i:1469 original size:111 final size:111
Alignment explanation
Indices: 1210--1577 Score: 476
Period size: 111 Copynumber: 3.3 Consensus size: 111
1200 CTTCGAGAGC
** * * * *
1210 GTACTACCTTTTCGCGATCTTTGGTAGCGTACTACCGCTTC--GCAGTCGTTGG-GAGCGTACTA
1 GTACTACCAATTCGCGAGCTTTGGGAGCGTACTACCGCTTCAAG-AG-C-TTGGAGGGAGTACTA
* * * *
1272 CC-TCTTTGCGATCTTTGGGAGCGTACTACCGCTTCGAGAGCTTGGAGGGGGT
63 CCAT-TTCGCGAACTTTGGG-GCGTACTACCACTTCGAGAGCTTGGA--GGGA
* *
1324 GTTCTACCAATTCGCGAGATTTGGGAGCGTACTACCGCTTCAAGAGCTTGGAGGGAGTACTACCA
1 GTACTACCAATTCGCGAGCTTTGGGAGCGTACTACCGCTTCAAGAGCTTGGAGGGAGTACTACCA
1389 TTTCGCGAACTTTGGGGCGTACTACCACTTCGAGAGCTTGGAGGGA
66 TTTCGCGAACTTTGGGGCGTACTACCACTTCGAGAGCTTGGAGGGA
*
1435 ATACTACCAATTCGCGAGCTTTGGGAGCGTACTACCGCTTCAAGAGCTTGGAGGGAGTACTACCA
1 GTACTACCAATTCGCGAGCTTTGGGAGCGTACTACCGCTTCAAGAGCTTGGAGGGAGTACTACCA
*
1500 TTTCGCAAACTTTGGGGCGTACTACCACTTCGAGAGCTTGGAGGGA
66 TTTCGCGAACTTTGGGGCGTACTACCACTTCGAGAGCTTGGAGGGA
* * * *
1546 GTACTACCATTTCGTGAACTTTGAG-GCGTACT
1 GTACTACCAATTCGCGAGCTTTGGGAGCGTACT
1578 TCCACTTTGC
Statistics
Matches: 229, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
110 7 0.03
111 130 0.57
113 29 0.13
114 59 0.26
115 3 0.01
116 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (111 bp):
GTACTACCAATTCGCGAGCTTTGGGAGCGTACTACCGCTTCAAGAGCTTGGAGGGAGTACTACCA
TTTCGCGAACTTTGGGGCGTACTACCACTTCGAGAGCTTGGAGGGA
Found at i:1481 original size:28 final size:28
Alignment explanation
Indices: 1206--1621 Score: 222
Period size: 28 Copynumber: 14.9 Consensus size: 28
1196 TTGTCTTCGA
** * *
1206 GAGCGTACTACCTTTTCGCGATCTTTGG
1 GAGCGTACTACCACTTCGAGAGCTTTGG
* * * *
1234 TAGCGTACTACCGCTTCGCAG-TCGTTGG
1 GAGCGTACTACCACTTCG-AGAGCTTTGG
* * * *
1262 GAGCGTACTACCTCTTTGCGATCTTTGG
1 GAGCGTACTACCACTTCGAGAGCTTTGG
* *
1290 GAGCGTACTACCGCTTCGAGAGCTTGGAGG
1 GAGCGTACTACCACTTCGAGAGCTT--TGG
* * * * * *
1320 GGGTGTTCTACCAATTCGCGAGATTTGG
1 GAGCGTACTACCACTTCGAGAGCTTTGG
* *
1348 GAGCGTACTACCGCTTCAAGAGC-TTGG
1 GAGCGTACTACCACTTCGAGAGCTTTGG
* * * * *
1375 AGGGAGTACTACCATTTCGCGAACTTTGG
1 -GAGCGTACTACCACTTCGAGAGCTTTGG
1404 G-GCGTACTACCACTTCGAGAGC-TT-G
1 GAGCGTACTACCACTTCGAGAGCTTTGG
* * *
1429 GAGGGAATACTACCAATTCGCGAGCTTTGG
1 GAGCG--TACTACCACTTCGAGAGCTTTGG
* *
1459 GAGCGTACTACCGCTTCAAGAGC-TTGG
1 GAGCGTACTACCACTTCGAGAGCTTTGG
* * * *
1486 AGGGAGTACTACCATTTCGCA-AACTTTGG
1 -GAGCGTACTACCACTTCG-AGAGCTTTGG
1515 G-GCGTACTACCACTTCGAGAGC-TTGG
1 GAGCGTACTACCACTTCGAGAGCTTTGG
* * * * * *
1541 AGGGAGTACTACCATTTCGTGAACTTTGA
1 -GAGCGTACTACCACTTCGAGAGCTTTGG
* * * * * *
1570 G-GCGTACTTCCACTTTGCGATCCTTGA
1 GAGCGTACTACCACTTCGAGAGCTTTGG
* * *
1597 GAGTGTACTACCACCTCGGGAGCTT
1 GAGCGTACTACCACTTCGAGAGCTT
1622 GGAGGGAGTA
Statistics
Matches: 291, Mismatches: 78, Indels: 38
0.71 0.19 0.09
Matches are distributed among these distances:
25 2 0.01
26 9 0.03
27 63 0.22
28 177 0.61
29 15 0.05
30 25 0.09
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.27
Consensus pattern (28 bp):
GAGCGTACTACCACTTCGAGAGCTTTGG
Found at i:2644 original size:17 final size:18
Alignment explanation
Indices: 2622--2657 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2612 TCATTGGGAT
*
2622 TACTTC-AATTCTTCAAA
1 TACTTCAAACTCTTCAAA
2639 TACTTCAAACTCTTCAAA
1 TACTTCAAACTCTTCAAA
2657 T
1 T
2658 TCAAGGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (18 bp):
TACTTCAAACTCTTCAAA
Found at i:3854 original size:307 final size:307
Alignment explanation
Indices: 3300--3900 Score: 1121
Period size: 307 Copynumber: 2.0 Consensus size: 307
3290 ACAATGGTTC
3300 TGATGCCTCTAGGTGTTGTGAGTTTTTCCCTCATTGGCATCATTCTTGATCTAGACTTATTTGCA
1 TGATGCCTCTAGGTGTTGTGAGTTTTTCCCTCATTGGCATCATTCTTGATCTAGACTTATTTGCA
3365 TACAACTTGTTGAGTTTCTCCCATGCAACAAAGGAAGAAGTGGCTGATGCAAGGTGAGAAACCAC
66 TACAACTTGTTGAGTTTCTCCCATGCAACAAAGGAAGAAGTGGCTGATGCAAGGTGAGAAACCAC
*
3430 ACTTTCGGTGGATGATGCTAATCATTCCATGAAAAAGCAAGTGATCTTGCTTTATCCAGTGTTCA
131 ACTTTCGGTGGATGATGCTAATCATTCCATGAAAAAGCAAGCGATCTTGCTTTATCCAGTGTTCA
*
3495 TACGCTTGATTTGGAACCATGTCGGTGGTTCCTGTTTTCTGAATTTCCTTTGATGGGGATTTATT
196 TACGCTTGATTTGGAACCATGTCGGTGGTTCCTGTTTTCTGAATTTCCTTTGATGGGCATTTATT
3560 CGACCCATCCACATACCCAAGTAGATCGAATCCAGTGTTCATACGCT
261 CGACCCATCCACATACCCAAGTAGATCGAATCCAGTGTTCATACGCT
*
3607 TGATGCCTCTAGGTGTTGTGAGTTTTTCCCTCATTGGCATCATTCTTGATCTAGACTTATTTGTA
1 TGATGCCTCTAGGTGTTGTGAGTTTTTCCCTCATTGGCATCATTCTTGATCTAGACTTATTTGCA
* *
3672 TACAACTTGTTGAGTTTCTCCCATGCAGCAAATGAAGAAGTGGCTGATGCAAGGTGAGAAACCAC
66 TACAACTTGTTGAGTTTCTCCCATGCAACAAAGGAAGAAGTGGCTGATGCAAGGTGAGAAACCAC
* *
3737 ACTTTCGGTGGATGATGCTAATCATTCCATGAAGAAGCAGGCGATCTTGCTTTATCCAGTGTTCA
131 ACTTTCGGTGGATGATGCTAATCATTCCATGAAAAAGCAAGCGATCTTGCTTTATCCAGTGTTCA
*
3802 TACGCTTGATTTGGAACCATGTCGGTTGTTCCTGTTTTCTGAATTTCCTTTGATGGGCATTTATT
196 TACGCTTGATTTGGAACCATGTCGGTGGTTCCTGTTTTCTGAATTTCCTTTGATGGGCATTTATT
*
3867 CGACCCATCTACATACCCAAGTAGATCGAATCCA
261 CGACCCATCCACATACCCAAGTAGATCGAATCCA
3901 ATGAGAAGGG
Statistics
Matches: 285, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
307 285 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (307 bp):
TGATGCCTCTAGGTGTTGTGAGTTTTTCCCTCATTGGCATCATTCTTGATCTAGACTTATTTGCA
TACAACTTGTTGAGTTTCTCCCATGCAACAAAGGAAGAAGTGGCTGATGCAAGGTGAGAAACCAC
ACTTTCGGTGGATGATGCTAATCATTCCATGAAAAAGCAAGCGATCTTGCTTTATCCAGTGTTCA
TACGCTTGATTTGGAACCATGTCGGTGGTTCCTGTTTTCTGAATTTCCTTTGATGGGCATTTATT
CGACCCATCCACATACCCAAGTAGATCGAATCCAGTGTTCATACGCT
Found at i:5156 original size:31 final size:31
Alignment explanation
Indices: 5121--5179 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
5111 TTCGGCTCAT
*
5121 CTGGATTCA-GGTCATTCAGGTCTCGGGTCTG
1 CTGGATTCAGGGTCATGCAGGT-TCGGGTCTG
*
5152 CTGGATTTAGGGTCATGCAGGTTCGGGT
1 CTGGATTCAGGGTCATGCAGGTTCGGGT
5180 TTTGGTCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.14, C:0.19, G:0.36, T:0.32
Consensus pattern (31 bp):
CTGGATTCAGGGTCATGCAGGTTCGGGTCTG
Found at i:6781 original size:31 final size:28
Alignment explanation
Indices: 6745--6805 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
6735 AAATAATATA
*
6745 AATATA-ATAA-ATGACATATTATAATTTGT
1 AATATATATAAGATGAC-TAAT-TAATTT-T
6774 AATATATATAAGATGACTAATTAATTTT
1 AATATATATAAGATGACTAATTAATTTT
6802 AATA
1 AATA
6806 AAAAATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.17
29 12 0.41
30 7 0.24
31 5 0.17
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (28 bp):
AATATATATAAGATGACTAATTAATTTT
Found at i:11917 original size:21 final size:21
Alignment explanation
Indices: 11893--11933 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11883 AATATCAAAG
*
11893 AAATAATATCAACAACAACTC
1 AAATAACATCAACAACAACTC
* *
11914 AAATACCATTAACAACAACT
1 AAATAACATCAACAACAACT
11934 TATTAACCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATAACATCAACAACAACTC
Found at i:12739 original size:17 final size:17
Alignment explanation
Indices: 12717--12764 Score: 78
Period size: 19 Copynumber: 2.7 Consensus size: 17
12707 TATATAACTA
12717 TAAAATAACTATGGTCC
1 TAAAATAACTATGGTCC
12734 TAAAATAAAGCTATGGTCC
1 TAAAAT-AA-CTATGGTCC
12753 TAAAATAACTAT
1 TAAAATAACTAT
12765 AAAGGTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.34
18 4 0.14
19 15 0.52
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (17 bp):
TAAAATAACTATGGTCC
Found at i:13183 original size:2 final size:2
Alignment explanation
Indices: 13176--13207 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
13166 ATAATCTACA
*
13176 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13208 TATTTGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.