Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013844.1 Corchorus capsularis cultivar CVL-1 contig13865, 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: 22009
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--31 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32 ATTTACCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:846 original size:22 final size:22
Alignment explanation
Indices: 816--915 Score: 112
Period size: 22 Copynumber: 4.5 Consensus size: 22
806 AAAAGATTAT
*
816 CAAAATTTCATAGT-GTGGTTAC
1 CAAAATTTCATA-TAGAGGTTAC
* *
838 CAAAGTTTCATATAGAGGTTAT
1 CAAAATTTCATATAGAGGTTAC
* * *
860 CAAAATTTCATACAAAGATTAC
1 CAAAATTTCATATAGAGGTTAC
* *
882 CAAAATTTCATAAAAAGGTTAC
1 CAAAATTTCATATAGAGGTTAC
904 CAAAATTTCATA
1 CAAAATTTCATA
916 GGGAGGGAGG
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
21 1 0.01
22 66 0.99
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATATAGAGGTTAC
Found at i:985 original size:22 final size:22
Alignment explanation
Indices: 946--1000 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
936 TTGTGCTTAT
** *
946 CAAAATTTCCTAGGGAGGTTAA
1 CAAAATTTTATAGAGAGGTTAA
*
968 CAAAATTTTATAGAGAGGTTAT
1 CAAAATTTTATAGAGAGGTTAA
*
990 GAAAATTTTAT
1 CAAAATTTTAT
1001 GAATGAAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (22 bp):
CAAAATTTTATAGAGAGGTTAA
Found at i:1190 original size:66 final size:66
Alignment explanation
Indices: 1120--1253 Score: 171
Period size: 66 Copynumber: 2.0 Consensus size: 66
1110 TAGTTTTATT
** * * **
1120 TAGTGCGATTATTAAAATTTTATAG-GTAGATTATCAAATTTTCATATTGAGGTTATCGAAATTT
1 TAGTGCGATTACCAAAATTTCACAGTGT-GATTATCAAATTTTCATAGGGAGGTTATCGAAATTT
1184 CA
65 CA
* * *
1186 TAGTGTGATTACCAAGATTTCACAGTGTGGTTATCAAATTTTCATAGGGAGGTTATCGAAATTTC
1 TAGTGCGATTACCAAAATTTCACAGTGTGATTATCAAATTTTCATAGGGAGGTTATCGAAATTTC
1251 A
66 A
1252 TA
1 TA
1254 ATGAGCTTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 56 0.97
67 2 0.03
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (66 bp):
TAGTGCGATTACCAAAATTTCACAGTGTGATTATCAAATTTTCATAGGGAGGTTATCGAAATTTC
A
Found at i:1271 original size:44 final size:43
Alignment explanation
Indices: 1050--1273 Score: 148
Period size: 44 Copynumber: 5.1 Consensus size: 43
1040 AGTTTCATTC
* *
1050 TCATAGGGAGGTTATCGAAATTTCATTATGTGGTTATCAAAATTT
1 TCATAGGGAGGTTATC-AAATTTCATAATGAGGTTATC-AAATTT
* * * * * * * * *
1095 TCATAGTGCGGTTA-CTAGTTTTATTTAGTGCGATTATTAAAATTT
1 TCATAGGGAGGTTATCAAATTTCA--TAATGAGGTTA-TCAAATTT
* * *
1140 T-ATAGGTAGATTATCAAATTTTCATATTGAGGTTATCGAAA-TT
1 TCATAGGGAGGTTATCAAA-TTTCATAATGAGGTTATC-AAATTT
* * * * * * *
1183 TCATAGTGTGATTACCAAGATTTCACAGTGTGGTTATCAAATTT
1 TCATAGGGAGGTTATCAA-ATTTCATAATGAGGTTATCAAATTT
*
1227 TCATAGGGAGGTTATCGAAATTTCATAATGAGCTTATCAAATTT
1 TCATAGGGAGGTTATC-AAATTTCATAATGAGGTTATCAAATTT
1271 TCA
1 TCA
1274 AAATATGGTT
Statistics
Matches: 133, Mismatches: 36, Indels: 21
0.70 0.19 0.11
Matches are distributed among these distances:
43 12 0.09
44 85 0.64
45 31 0.23
46 5 0.04
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (43 bp):
TCATAGGGAGGTTATCAAATTTCATAATGAGGTTATCAAATTT
Found at i:1273 original size:22 final size:21
Alignment explanation
Indices: 1050--1270 Score: 124
Period size: 22 Copynumber: 10.0 Consensus size: 21
1040 AGTTTCATTC
*
1050 TCATAGGGAGGTTATCGAAATT
1 TCATAGTGAGGTTATC-AAATT
*
1072 TCATTA-TGTGGTTATCAAAATTT
1 TCA-TAGTGAGGTTATC-AAA-TT
* * *
1095 TCATAGTGCGGTTA-CTAGTT
1 TCATAGTGAGGTTATCAAATT
* * * *
1115 TTATTTAGTGCGATTATTAAAATT
1 TCA--TAGTGAGGTTA-TCAAATT
* *
1139 TTATAG-GTAGATTATCAAATTT
1 TCATAGTG-AGGTTATCAAA-TT
*
1161 TCATATTGAGGTTATCGAAATT
1 TCATAGTGAGGTTATC-AAATT
* * *
1183 TCATAGTGTGATTACCAAGATT
1 TCATAGTGAGGTTATCAA-ATT
* *
1205 TCACAGTGTGGTTATCAAATTT
1 TCATAGTGAGGTTATCAAA-TT
*
1227 TCATAGGGAGGTTATCGAAATT
1 TCATAGTGAGGTTATC-AAATT
* *
1249 TCATAATGAGCTTATCAAATT
1 TCATAGTGAGGTTATCAAATT
1270 T
1 T
1271 TCAAAATATG
Statistics
Matches: 156, Mismatches: 29, Indels: 29
0.73 0.14 0.14
Matches are distributed among these distances:
20 4 0.03
21 15 0.10
22 110 0.71
23 21 0.13
24 6 0.04
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (21 bp):
TCATAGTGAGGTTATCAAATT
Found at i:1273 original size:66 final size:66
Alignment explanation
Indices: 1150--1293 Score: 182
Period size: 66 Copynumber: 2.2 Consensus size: 66
1140 TATAGGTAGA
** * * * * *
1150 TTATCAAATTTTCATATTGAGGTTATCGAAATTTCATAGTGTGATTACCAAGATTTCACAGTGTG
1 TTATCAAATTTTCATAGGGAGGTTATCGAAATTTCATAATGAGATTACCAAGATTTCAAAATATG
1215 G
66 G
* *
1216 TTATCAAATTTTCATAGGGAGGTTATCGAAATTTCATAATGAGCTTATCAA-ATTTTCAAAATAT
1 TTATCAAATTTTCATAGGGAGGTTATCGAAATTTCATAATGAGATTACCAAGA-TTTCAAAATAT
1280 GG
65 GG
1282 TTATCAATATTT
1 TTATCAA-ATTT
1294 CTACATTGGA
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
65 1 0.01
66 62 0.93
67 4 0.06
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.40
Consensus pattern (66 bp):
TTATCAAATTTTCATAGGGAGGTTATCGAAATTTCATAATGAGATTACCAAGATTTCAAAATATG
G
Found at i:1285 original size:22 final size:21
Alignment explanation
Indices: 1214--1293 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 21
1204 TTCACAGTGT
***
1214 GGTTATCAAATTTTCATAGGGA
1 GGTTATCAAATTTTCA-AAATA
*
1236 GGTTATCGAAA-TTTCATAATGA
1 GGTTATC-AAATTTTCAAAAT-A
*
1258 GCTTATCAAATTTTCAAAATA
1 GGTTATCAAATTTTCAAAATA
1279 TGGTTATCAATATTT
1 -GGTTATCAA-ATTT
1294 CTACATTGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
21 4 0.09
22 35 0.76
23 7 0.15
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (21 bp):
GGTTATCAAATTTTCAAAATA
Found at i:2884 original size:16 final size:17
Alignment explanation
Indices: 2858--2890 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2848 TTTTTATTGG
2858 TTAATATATAATATATA
1 TTAATATATAATATATA
*
2875 TTAA-ATATAATTTATA
1 TTAATATATAATATATA
2891 AGTACACCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATATATAATATATA
Found at i:6009 original size:102 final size:100
Alignment explanation
Indices: 5820--6355 Score: 474
Period size: 99 Copynumber: 5.4 Consensus size: 100
5810 TCTTTATATA
* * * * **
5820 GAGAATCGTCATTTATACCTTTGTTT-TCTGGAGCATTATCATGACCTCTAGAATT-TTTCTTAT
1 GAGAATCATCATTTACACCTTTGTTTATTTGGAGCATTATCATGACCTCTAG-ATTCCTTCGAAT
** *
5883 CTTTATTATATAGAGAATTGTATCCATCATCGGCATACT
65 CTTTA-TATA-A-AGAATCATATCCATCATCAGCATACT
*
5922 GAGAATCATCATTTACACCTTTGTTATAATTTGGAGCATTATCATGACCTCTAGATTCCTTCAAA
1 GAGAATCATCATTTACACCTTTGTT-T-ATTTGGAGCATTATCATGACCTCTAGATTCCTTCGAA
* *
5987 TCTTCATACAAAGAATCATATCCATCATCAGCATACT
64 TCTTTATATAAAGAATCATATCCATCATCAGCATACT
* * * * * * *
6024 GGGAATCATCATTCACACCCTTG-TTACTTGGAACATCT-TCAT---CTTTAG-CTCCTTTCGCT
1 GAGAATCATCATTTACACCTTTGTTTATTTGGAGCAT-TATCATGACCTCTAGATTCC-TT--C-
*
6083 GAATCTTTATATAGAGAATCATATCCATCATCAGCATACT
61 GAATCTTTATATAAAGAATCATATCCATCATCAGCATACT
* *
6123 GAGAATCATCATTTATACCTTTG-TTATTTGGAGCATTATCATGACCTCTAGATTCTTTCGAATC
1 GAGAATCATCATTTACACCTTTGTTTATTTGGAGCATTATCATGACCTCTAGATTCCTTCGAATC
6187 TTTATATAAAGAATCATATCCATCATCAGCATACT
66 TTTATATAAAGAATCATATCCATCATCAGCATACT
* * * * * * * * * *
6222 GGGAATCATCGTTTACATCTTTG-TCACTTCGAACATCT-CCAT---CTCTAG-CTCCTTTAATT
1 GAGAATCATCATTTACACCTTTGTTTATTTGGAGCAT-TATCATGACCTCTAGATTCC--T--TC
* * * *
6281 GAATCTTTATATAGAGAGTCGTATCCATCATCAGCATATT
61 GAATCTTTATATAAAGAATCATATCCATCATCAGCATACT
* *
6321 GAGAATCATCGTTTACACCTTTG-TTATTCGGAGCA
1 GAGAATCATCATTTACACCTTTGTTTATTTGGAGCA
6356 CTTCTAGATA
Statistics
Matches: 360, Mismatches: 55, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
95 5 0.01
96 13 0.04
97 1 0.00
98 2 0.01
99 218 0.61
100 4 0.01
101 1 0.00
102 73 0.20
103 4 0.01
104 6 0.02
105 33 0.09
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (100 bp):
GAGAATCATCATTTACACCTTTGTTTATTTGGAGCATTATCATGACCTCTAGATTCCTTCGAATC
TTTATATAAAGAATCATATCCATCATCAGCATACT
Found at i:6229 original size:198 final size:198
Alignment explanation
Indices: 5888--6355 Score: 702
Period size: 198 Copynumber: 2.3 Consensus size: 198
5878 CTTATCTTTA
* *
5888 TTATATAGAGAATTGTATCCATCATCGGCATACTGAGAATCATCATTTACACCTTTGTTATAATT
1 TTATATAGAGAATCGTATCCATCATCAGCATACTGAGAATCATCATTTACACCTTTG-T-T-ATT
5953 TGGAGCATTATCATGACCTCTAGATTCCTTCAAATCTTCATACAAAGAATCATATCCATCATCAG
63 TGGAGCATTATCATGACCTCTAGATTCCTTCAAATCTTCATACAAAGAATCATATCCATCATCAG
* * * * **
6018 CATACTGGGAATCATCATTCACACCCTTGTTACTTGGAACATCTTCATCTTTAGCTCCTTTCGCT
128 CATACTGGGAATCATCATTCACACCCTTGTCACTTCGAACATCTCCATCTCTAGCTCCTTTAACT
6083 GAATCT
193 GAATCT
* *
6089 TTATATAGAGAATCATATCCATCATCAGCATACTGAGAATCATCATTTATACCTTTGTTATTTGG
1 TTATATAGAGAATCGTATCCATCATCAGCATACTGAGAATCATCATTTACACCTTTGTTATTTGG
* * * *
6154 AGCATTATCATGACCTCTAGATTCTTTCGAATCTTTATATAAAGAATCATATCCATCATCAGCAT
66 AGCATTATCATGACCTCTAGATTCCTTCAAATCTTCATACAAAGAATCATATCCATCATCAGCAT
* * * * *
6219 ACTGGGAATCATCGTTTACATCTTTGTCACTTCGAACATCTCCATCTCTAGCTCCTTTAATTGAA
131 ACTGGGAATCATCATTCACACCCTTGTCACTTCGAACATCTCCATCTCTAGCTCCTTTAACTGAA
6284 TCT
196 TCT
* * * *
6287 TTATATAGAGAGTCGTATCCATCATCAGCATATTGAGAATCATCGTTTACACCTTTGTTATTCGG
1 TTATATAGAGAATCGTATCCATCATCAGCATACTGAGAATCATCATTTACACCTTTGTTATTTGG
6352 AGCA
66 AGCA
6356 CTTCTAGATA
Statistics
Matches: 242, Mismatches: 25, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
198 187 0.77
199 1 0.00
200 1 0.00
201 53 0.22
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (198 bp):
TTATATAGAGAATCGTATCCATCATCAGCATACTGAGAATCATCATTTACACCTTTGTTATTTGG
AGCATTATCATGACCTCTAGATTCCTTCAAATCTTCATACAAAGAATCATATCCATCATCAGCAT
ACTGGGAATCATCATTCACACCCTTGTCACTTCGAACATCTCCATCTCTAGCTCCTTTAACTGAA
TCT
Found at i:9715 original size:99 final size:99
Alignment explanation
Indices: 9602--9882 Score: 451
Period size: 99 Copynumber: 2.9 Consensus size: 99
9592 GAGTAGTTCG
* *
9602 TCTAGGTTCTTTTGCTGAATCTTTATATTCATAATCATAACCATAAGCACCAAACTCTGGGTCAT
1 TCTAGATTCTTTTGCTGAATCTTTATATTCATAATCATATCCATAAGCACCAAACTCTGGGTCAT
*
9667 TTACACCTTTGTTGTTTGGATCACTATCATGACC
66 TTACACCTTTGTTATTTGGATCACTATCATGACC
9701 TCTAGATTCTTTTGCTGAATCTTTATATTCATAATCATATCCATAAGCACCAAACTCTGGGTCAT
1 TCTAGATTCTTTTGCTGAATCTTTATATTCATAATCATATCCATAAGCACCAAACTCTGGGTCAT
* *
9766 TTACACCTTTGTTATTTGGATCACTATTATGGCC
66 TTACACCTTTGTTATTTGGATCACTATCATGACC
* * *
9800 TCTAGATTCTTTTGCTG-A--GTTATATTCATCATCATATCCATAAGCACCAAACTCTGGATCAT
1 TCTAGATTCTTTTGCTGAATCTTTATATTCATAATCATATCCATAAGCACCAAACTCTGGGTCAT
* *
9862 TTACTCCTTTGTTATTCGGAT
66 TTACACCTTTGTTATTTGGAT
9883 GATCTTCAGC
Statistics
Matches: 172, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
96 60 0.35
98 1 0.01
99 111 0.65
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (99 bp):
TCTAGATTCTTTTGCTGAATCTTTATATTCATAATCATATCCATAAGCACCAAACTCTGGGTCAT
TTACACCTTTGTTATTTGGATCACTATCATGACC
Found at i:16978 original size:6 final size:6
Alignment explanation
Indices: 16967--16996 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
16957 GAAGAAAGGG
16967 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
16997 AATAGGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:17535 original size:27 final size:27
Alignment explanation
Indices: 17505--17558 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
17495 AATTATTTTA
17505 AGAAAATTAAGTTAAGAAATGAAATTT
1 AGAAAATTAAGTTAAGAAATGAAATTT
*
17532 AGAAAATTCAGTTAAGAAATGAAATTT
1 AGAAAATTAAGTTAAGAAATGAAATTT
17559 TGTTGTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.30
Consensus pattern (27 bp):
AGAAAATTAAGTTAAGAAATGAAATTT
Found at i:17551 original size:13 final size:14
Alignment explanation
Indices: 17502--17550 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
17492 ATAAATTATT
17502 TTAAGAAAATTAAG
1 TTAAGAAAATTAAG
* *
17516 TTAAG-AAATGAAA
1 TTAAGAAAATTAAG
* *
17529 TTTAGAAAATTCAG
1 TTAAGAAAATTAAG
17543 TTAAGAAA
1 TTAAGAAA
17551 TGAAATTTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.29
Consensus pattern (14 bp):
TTAAGAAAATTAAG
Found at i:17877 original size:11 final size:11
Alignment explanation
Indices: 17863--17900 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
17853 ATTCATAACA
17863 AATTTATAATT
1 AATTTATAATT
17874 AATTTATAATT
1 AATTTATAATT
17885 -ATTTGATAATT
1 AATTT-ATAATT
*
17896 TATTT
1 AATTT
17901 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:18479 original size:13 final size:13
Alignment explanation
Indices: 18461--18488 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18451 AAGATGGTTT
18461 CTCACAGTTAGAC
1 CTCACAGTTAGAC
18474 CTCACAGTTAGAC
1 CTCACAGTTAGAC
18487 CT
1 CT
18489 GTTCAAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (13 bp):
CTCACAGTTAGAC
Done.