Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003231.1 Corchorus capsularis cultivar CVL-1 contig03239, 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: 2283
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:901 original size:35 final size:35
Alignment explanation
Indices: 856--1188 Score: 418
Period size: 35 Copynumber: 9.5 Consensus size: 35
846 GAATTTCTTG
* * * *
856 AAATGAGATCACCTCTGATTGTTTGAAACTACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
** * * *
891 AAATATGATCAACTCTGATCGTTGCAAAATATTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
*
926 AAATGCGGTCAACTCTGATCGTTGGAAACTACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
961 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
* * *
996 AAATGCGATCACCCCTGATCGTTGGAAACGACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
*
1031 AAATGCGATCAACTCTGATCGTTGGAAACTTCTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
* *
1066 AAATGTGATCAACTCTGATCGTTGGAAAATACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
* *
1101 AAATACGATCAACTCTGATCGTTGGAAAATACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
* * * * *
1136 AAATGAGATCAAATCTGA-CCTCTGAAAACTTCTTG-
1 AAATGCGATCAACTCTGATCGT-TGGAAACTAC-TGA
*
1171 AAATGAGATCAACTCTGA
1 AAATGCGATCAACTCTGA
1189 CCTCTTAAAA
Statistics
Matches: 261, Mismatches: 35, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
34 2 0.01
35 257 0.98
36 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (35 bp):
AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
Found at i:1181 original size:70 final size:71
Alignment explanation
Indices: 1031--1682 Score: 627
Period size: 70 Copynumber: 9.0 Consensus size: 71
1021 AAACGACTGA
* * * * *
1031 AAATGCGATCAACTCTGATCGT-TGGAAACTTC-TGAAAATGTGATCAACTCTGATCGT-TGGAA
1 AAATGAGATCAACTCTGATCCTCTGAAAACTTCTTG-AAATGAGATCAACTCTGA-CCTCT-GAA
*
1093 AA-TAC-TG
63 AACTTCTTG
* * *
1100 AAAAT-ACGATCAACTCTGATCGT-TGGAAAA-TAC-TGAAAATGAGATCAAATCTGACCTCTGA
1 -AAATGA-GATCAACTCTGATCCTCT-GAAAACTTCTTG-AAATGAGATCAACTCTGACCTCTGA
1161 AAACTTCTTG
62 AAACTTCTTG
*
1171 AAATGAGATCAACTCTGA-CCTCTTAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAAC
1 AAATGAGATCAACTCTGATCCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAAC
1235 TTCTTG
66 TTCTTG
*
1241 AAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGAGATCAACTATGACCTCTGAAAAC
1 AAATGAGATCAACTCTGATCCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAAC
*
1305 TGCTTG
66 TTCTTG
* * * * **
1311 GAATGAGATCAAATCTGA-CCTCTGAAAACTGCTTGGAATGAGAACTGCTTGGAA-TGAGATCAA
1 AAATGAGATCAACTCTGATCCTCTGAAAACTTCTTGAAATGAG-A-T-C----AACTCTGA-C--
***
1374 CTCTGACCTCTGAAAACTGCTTG
56 CTCTGAAAACT------T-CTTG
* *
1397 GAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTCTGAAA
1 AAATGAGATCAACTCTGATCCTCTGAAAACTTCTTGAAATGAGATCAACTCTGA-C-CTCTGAAA
*
1461 ACTTTTTG
64 ACTTCTTG
* * * *
1469 GAATGAGATCAACTCTG-GCCTCTGGAAACTTCTTGCAATGAGATCAACTCTGACCTCTGAAAAC
1 AAATGAGATCAACTCTGATCCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAAC
1533 TTCTTG
66 TTCTTG
* * * * * *
1539 GAATGAGATCAACTCTGACCTCTCTGAAAACTTTTTGGAATGAGATCAACTCTGGCCTCTGGAAA
1 AAATGAGATCAACTCTGATC-CTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAA
1604 CTTCTTG
65 CTTCTTG
*
1611 AAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAAC
1 AAATGAGATCAACTCTGATCCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAAC
1675 TTC-TG
66 TTCTTG
1680 AAA
1 AAA
1683 ATGACCGCAG
Statistics
Matches: 505, Mismatches: 47, Indels: 61
0.82 0.08 0.10
Matches are distributed among these distances:
69 18 0.04
70 280 0.55
71 13 0.03
72 117 0.23
73 2 0.00
76 3 0.01
77 3 0.01
79 18 0.04
80 4 0.01
83 1 0.00
84 1 0.00
85 1 0.00
86 44 0.09
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (71 bp):
AAATGAGATCAACTCTGATCCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAAC
TTCTTG
Found at i:1189 original size:35 final size:35
Alignment explanation
Indices: 1137--1353 Score: 344
Period size: 35 Copynumber: 6.2 Consensus size: 35
1127 AAATACTGAA
* *
1137 AATGAGATCAAATCTGACCTCTGAAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
* *
1172 AATGAGATCAACTCTGACCTCTTAAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
*
1207 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
*
1242 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
* *
1277 AATGAGATCAACTATGACCTCTGAAAACTGCTTGG
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
* *
1312 AATGAGATCAAATCTGACCTCTGAAAACTGCTTGG
1 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
1347 AATGAGA
1 AATGAGA
1354 ACTGCTTGGA
Statistics
Matches: 174, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 174 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (35 bp):
AATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
Found at i:1216 original size:105 final size:105
Alignment explanation
Indices: 827--1682 Score: 594
Period size: 105 Copynumber: 8.0 Consensus size: 105
817 AACTCTTTTG
* * * * ** * *
827 GATCAACTCTGATCATC-GGGAATTTCTTGAAATGAGATCACCTCTGATTGTTTG-AAACTAC-T
1 GATCAACTCTGA-CCTCTGGAAACTTCTTGAAATGAGATCAACTCTGA-CCTCTGAAAACTTCTT
* *
889 GAAAAT-ATGATCAACTCTGATCGT-TGCAAAA-TATTGAAAATGC
64 G-AAATGA-GATCAACTCTGATCGTCTG-AAAACTACTG-AAATGA
* * * * * * *
932 GGTCAACTCTGATCGT-TGGAAACTAC-TGAAAATGCGATCAACTCTGATCGT-TGGAAACTAC-
1 GATCAACTCTGA-CCTCTGGAAACTTCTTG-AAATGAGATCAACTCTGA-CCTCTGAAAACTTCT
* * * * * *
993 TGAAAATGCGATCACCCCTGATCGT-TGGAAACGACTGAAAATGC
63 TG-AAATGAGATCAACTCTGATCGTCTGAAAACTACTG-AAATGA
* * * *
1037 GATCAACTCTGATCGT-TGGAAACTTC-TGAAAATGTGATCAACTCTGATCGT-TGGAAAA-TAC
1 GATCAACTCTGA-CCTCTGGAAACTTCTTG-AAATGAGATCAACTCTGA-CCTCT-GAAAACTTC
1098 -TGAAAAT-ACGATCAACTCTGATCGT-TGGAAAA-TACTGAAAATGA
62 TTG-AAATGA-GATCAACTCTGATCGTCT-GAAAACTACTG-AAATGA
* * *
1142 GATCAAATCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTTAAAACTTCTTGA
1 GATCAACTCTGACCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGA
* *
1207 AATGAGATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
66 AATGAGATCAACTCTGATCGTCTGAAAACTAC-TGAAATGA
* * * *
1247 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTATGACCTCTGAAAACTGCTTGG
1 GATCAACTCTGACCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGA
* * * *
1312 AATGAGATCAAATCTGA-CCTCTGAAAACTGCTTGGAATGA
66 AATGAGATCAACTCTGATCGTCTGAAAACTAC-TGAAATGA
** * * *
1352 GAACTGCTTGGAA-TGAGATCAACTCT-GACCTCTGAAAACTGCTTGGAATGAGATCAACTCTGA
1 G-A-T-C----AACTCTGA-C--CTCTGGA------AAC--TTCTTGAAATGAGATCAACTCTGA
* ** *
1415 CCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTC-TCTGAAAACTTTTTGGAATGA
48 CCTCTGAAAACTTCTTGAAATGAGATCAACTCTGA--TCGTCTGAAAAC-TACTGAAATGA
* * *
1475 GATCAACTCTGGCCTCTGGAAACTTCTTGCAATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
1 GATCAACTCTGACCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGA
** *
1540 AATGAGATCAACTCTGACCTC-TCTGAAAACTTTTTGGAATGA
66 AATGAGATCAACTCTGA--TCGTCTGAAAAC-TACTGAAATGA
* *
1582 GATCAACTCTGGCCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
1 GATCAACTCTGACCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGA
* *
1647 AATGAGATCAACTCTGA-CCTCTGAAAACTTCTGAAA
66 AATGAGATCAACTCTGATCGTCTGAAAACTACTGAAA
1683 ATGACCGCAG
Statistics
Matches: 648, Mismatches: 61, Indels: 85
0.82 0.08 0.11
Matches are distributed among these distances:
104 29 0.04
105 335 0.52
106 16 0.02
107 164 0.25
108 1 0.00
109 2 0.00
111 3 0.00
112 3 0.00
113 1 0.00
114 8 0.01
115 2 0.00
116 3 0.00
117 2 0.00
119 2 0.00
120 1 0.00
121 55 0.08
122 1 0.00
123 18 0.03
124 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (105 bp):
GATCAACTCTGACCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGA
AATGAGATCAACTCTGATCGTCTGAAAACTACTGAAATGA
Found at i:1358 original size:16 final size:16
Alignment explanation
Indices: 1337--1369 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1327 GACCTCTGAA
1337 AACTGCTTGGAATGAG
1 AACTGCTTGGAATGAG
1353 AACTGCTTGGAATGAG
1 AACTGCTTGGAATGAG
1369 A
1 A
1370 TCAACTCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.24
Consensus pattern (16 bp):
AACTGCTTGGAATGAG
Found at i:1379 original size:51 final size:51
Alignment explanation
Indices: 1302--1404 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
1292 GACCTCTGAA
1302 AACTGCTTGGAATGAGATCAAATCTGACCTCTGAAAACTGCTTGGAATGAG
1 AACTGCTTGGAATGAGATCAAATCTGACCTCTGAAAACTGCTTGGAATGAG
*
1353 AACTGCTTGGAATGAGATCAACTCTGACCTCTGAAAACTGCTTGGAATGAG
1 AACTGCTTGGAATGAGATCAAATCTGACCTCTGAAAACTGCTTGGAATGAG
1404 A
1 A
1405 TCAACTCTGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (51 bp):
AACTGCTTGGAATGAGATCAAATCTGACCTCTGAAAACTGCTTGGAATGAG
Found at i:1422 original size:86 final size:86
Alignment explanation
Indices: 1267--1439 Score: 301
Period size: 86 Copynumber: 2.0 Consensus size: 86
1257 GACCTCTGAA
*
1267 AACTTCTTGAAATGAGATCAACTATGACCTCTGAAAACTGCTTGGAATGAGATCAAATCTGACCT
1 AACTGCTTGAAATGAGATCAACTATGACCTCTGAAAACTGCTTGGAATGAGATCAAATCTGACCT
1332 CTGAAAACTGCTTGGAATGAG
66 CTGAAAACTGCTTGGAATGAG
* * *
1353 AACTGCTTGGAATGAGATCAACTCTGACCTCTGAAAACTGCTTGGAATGAGATCAACTCTGACCT
1 AACTGCTTGAAATGAGATCAACTATGACCTCTGAAAACTGCTTGGAATGAGATCAAATCTGACCT
*
1418 CTGAAAACTTCTTGGAATGAG
66 CTGAAAACTGCTTGGAATGAG
1439 A
1 A
1440 TCAACTCTGA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (86 bp):
AACTGCTTGAAATGAGATCAACTATGACCTCTGAAAACTGCTTGGAATGAGATCAAATCTGACCT
CTGAAAACTGCTTGGAATGAG
Found at i:1686 original size:35 final size:35
Alignment explanation
Indices: 1353--1678 Score: 526
Period size: 35 Copynumber: 9.2 Consensus size: 35
1343 TTGGAATGAG
*
1353 AACTGCTTGGAATGAGATCAACTCTGACCTCTGAA
1 AACTTCTTGGAATGAGATCAACTCTGACCTCTGAA
*
1388 AACTGCTTGGAATGAGATCAACTCTGACCTCTGAA
1 AACTTCTTGGAATGAGATCAACTCTGACCTCTGAA
1423 AACTTCTTGGAATGAGATCAACTCTGACCTCTCTGAA
1 AACTTCTTGGAATGAGATCAACTCTGA-C-CTCTGAA
* * *
1460 AACTTTTTGGAATGAGATCAACTCTGGCCTCTGGA
1 AACTTCTTGGAATGAGATCAACTCTGACCTCTGAA
*
1495 AACTTCTTGCAATGAGATCAACTCTGACCTCTGAA
1 AACTTCTTGGAATGAGATCAACTCTGACCTCTGAA
1530 AACTTCTTGGAATGAGATCAACTCTGACCTCTCTGAA
1 AACTTCTTGGAATGAGATCAACTCTGA-C-CTCTGAA
* * *
1567 AACTTTTTGGAATGAGATCAACTCTGGCCTCTGGA
1 AACTTCTTGGAATGAGATCAACTCTGACCTCTGAA
*
1602 AACTTCTTGAAATGAGATCAACTCTGACCTCTGAA
1 AACTTCTTGGAATGAGATCAACTCTGACCTCTGAA
1637 AACTTCTTGGAATGAGATCAACTCTGACCTCTGAA
1 AACTTCTTGGAATGAGATCAACTCTGACCTCTGAA
1672 AACTTCT
1 AACTTCT
1679 GAAAATGACC
Statistics
Matches: 270, Mismatches: 17, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
35 202 0.75
36 4 0.01
37 64 0.24
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (35 bp):
AACTTCTTGGAATGAGATCAACTCTGACCTCTGAA
Found at i:1686 original size:142 final size:142
Alignment explanation
Indices: 1137--1678 Score: 718
Period size: 142 Copynumber: 3.7 Consensus size: 142
1127 AAATACTGAA
* *
1137 AATGAGATCAAATCTGA-C-CTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTTAAAAC
1 AATGAGATCAACTCTGACCTCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAAC
* *
1200 TTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTG
66 TTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTG
*
1265 AAAACTTCTTGA
131 AAAACTTCTTGG
* * * *
1277 AATGAGATCAACTATGA-C-CTCTGAAAACTGCTTGGAATGAGATCAAATCTGACCTCTGAAAAC
1 AATGAGATCAACTCTGACCTCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAA-
*
1340 TGCTTGGAATGAGAACTGCTTGGAATGAGATCAACTCTGACCTCTGAAAACTGCTTGGAATGAGA
65 --C------T------T-CTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGA
1405 TCAACTCTGACCTCTGAAAACTTCTTGG
115 TCAACTCTGACCTCTGAAAACTTCTTGG
* * * *
1433 AATGAGATCAACTCTGACCTCTCTGAAAACTTTTTGGAATGAGATCAACTCTGGCCTCTGGAAAC
1 AATGAGATCAACTCTGACCTCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAAC
*
1498 TTCTTGCAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTC
66 TTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGA-C-CTC
*
1563 TGAAAACTTTTTGG
129 TGAAAACTTCTTGG
* *
1577 AATGAGATCAACTCTG-GC-CTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAAC
1 AATGAGATCAACTCTGACCTCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAAC
1640 TTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCT
66 TTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCT
1679 GAAAATGACC
Statistics
Matches: 356, Mismatches: 26, Indels: 38
0.85 0.06 0.09
Matches are distributed among these distances:
140 56 0.16
142 133 0.37
143 4 0.01
144 32 0.09
149 2 0.01
155 2 0.01
156 87 0.24
157 1 0.00
158 39 0.11
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (142 bp):
AATGAGATCAACTCTGACCTCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAAC
TTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGAGATCAACTCTGACCTCTG
AAAACTTCTTGG
Done.