Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009952.1 Corchorus capsularis cultivar CVL-1 contig09973, 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: 2439
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Found at i:394 original size:2 final size:2
Alignment explanation
Indices: 383--413 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
373 TATAAATTAT
383 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
414 ATCATCAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:733 original size:6 final size:6
Alignment explanation
Indices: 722--746 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
712 TGTCTCTCTT
722 TGTCTA TGTCTA TGTCTA TGTCTA T
1 TGTCTA TGTCTA TGTCTA TGTCTA T
747 TGCTTGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTCTA
Found at i:1261 original size:35 final size:35
Alignment explanation
Indices: 1193--1517 Score: 367
Period size: 35 Copynumber: 9.3 Consensus size: 35
1183 AACTCCTCTG
* * * *
1193 GATCAACTCTGATCATCGGAAATTTCTTG-AAATGA
1 GATCAACTCTGATCGTTGGAAAATAC-TGAAAATGA
* * * * *
1228 GATCACCTCTAATTGTTGGAAACTACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGA
* *
1263 GATCAACTCTGATCGTTGG-AACTACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGA
*
1297 GATCAACTCTGATCGTTGGAAAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGA
* * **
1332 GATCAACTCCGATCATTGGAAACCACTGAAAAT-A
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGA
*
1366 CGATCAACTCTGATC-ATGGAAAATACTGAAAATGCA
1 -GATCAACTCTGATCGTTGGAAAATACTGAAAATG-A
*
1402 -ATCAACTCTGATCGTTGGAAAATACTGAAAATGC
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGA
*
1436 GATCAACTATGATCGTTGGAAAATACTGAAAAT-A
1 GATCAACTCTGATCGTTGGAAAATACTGAAAATGA
* *
1470 TGATCAACTCTGATCGTTGGAAACTTCTTG-AAATGA
1 -GATCAACTCTGATCGTTGGAAAATAC-TGAAAATGA
1506 GATCAACTCTGA
1 GATCAACTCTGA
1518 CCCCTGAAAA
Statistics
Matches: 252, Mismatches: 28, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
34 64 0.25
35 184 0.73
36 4 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCGTTGGAAAATACTGAAAATGA
Found at i:1315 original size:69 final size:70
Alignment explanation
Indices: 1193--1517 Score: 415
Period size: 69 Copynumber: 4.7 Consensus size: 70
1183 AACTCCTCTG
* * * * * * * * *
1193 GATCAACTCTGATCATCGGAAATTTCTTG-AAATGAGATCACCTCTAATTGTTGGAAACTACTGA
1 GATCAACTCTGATCGTTGGAAACTAC-TGAAAATGCGATCAACTCTGATCGTTGGAAAATACTGA
1257 AAATGC
65 AAATGC
1263 GATCAACTCTGATCGTTGG-AACTACTGAAAATGCGATCAACTCTGATCGTTGGAAAATACTGAA
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGCGATCAACTCTGATCGTTGGAAAATACTGAA
1327 AATGC
66 AATGC
* * * * *
1332 GATCAACTCCGATCATTGGAAACCACTGAAAATACGATCAACTCTGATC-ATGGAAAATACTGAA
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGCGATCAACTCTGATCGTTGGAAAATACTGAA
1396 AATGC
66 AATGC
* * *
1401 AATCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTATGATCGTTGGAAAATACTGAA
1 GATCAACTCTGATCGTTGGAAACTACTGAAAATGCGATCAACTCTGATCGTTGGAAAATACTGAA
**
1466 AATAT
66 AATGC
* *
1471 GATCAACTCTGATCGTTGGAAACTTCTTG-AAATGAGATCAACTCTGA
1 GATCAACTCTGATCGTTGGAAACTAC-TGAAAATGCGATCAACTCTGA
1518 CCCCTGAAAA
Statistics
Matches: 222, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
68 2 0.01
69 118 0.53
70 100 0.45
71 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (70 bp):
GATCAACTCTGATCGTTGGAAACTACTGAAAATGCGATCAACTCTGATCGTTGGAAAATACTGAA
AATGC
Found at i:1373 original size:104 final size:105
Alignment explanation
Indices: 1243--1517 Score: 412
Period size: 104 Copynumber: 2.6 Consensus size: 105
1233 CCTCTAATTG
*
1243 TTGGAAACTACTGAAAATGCGATCAACTCTGATCGTTGG-AACTACTGAAAATGCGATCAACTCT
1 TTGGAAACTACTGAAAATACGATCAACTCTGATCGTTGGAAACTACTGAAAATGCGATCAACTCT
*
1307 GATCGTTGGAAAATACTGAAAATGCGATCAACTCCGATCA
66 GATCGTTGGAAAATACTGAAAATGCGATCAACTACGATCA
* * * *
1347 TTGGAAACCACTGAAAATACGATCAACTCTGATC-ATGGAAAATACTGAAAATGCAATCAACTCT
1 TTGGAAACTACTGAAAATACGATCAACTCTGATCGTTGGAAACTACTGAAAATGCGATCAACTCT
* *
1411 GATCGTTGGAAAATACTGAAAATGCGATCAACTATGATCG
66 GATCGTTGGAAAATACTGAAAATGCGATCAACTACGATCA
* * * *
1451 TTGGAAAATACTGAAAATATGATCAACTCTGATCGTTGGAAACTTCTTG-AAATGAGATCAACTC
1 TTGGAAACTACTGAAAATACGATCAACTCTGATCGTTGGAAACTAC-TGAAAATGCGATCAACTC
1515 TGA
65 TGA
1518 CCCCTGAAAA
Statistics
Matches: 152, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
103 3 0.02
104 123 0.81
105 24 0.16
106 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (105 bp):
TTGGAAACTACTGAAAATACGATCAACTCTGATCGTTGGAAACTACTGAAAATGCGATCAACTCT
GATCGTTGGAAAATACTGAAAATGCGATCAACTACGATCA
Found at i:1510 original size:139 final size:139
Alignment explanation
Indices: 1193--1517 Score: 458
Period size: 139 Copynumber: 2.3 Consensus size: 139
1183 AACTCCTCTG
* * * * ** *
1193 GATCAACTCTGATCATCGGAAATTTCTTGAAATGAGATCACCTCTAATTGTTGGAAACTACTGAA
1 GATCAACTCTGATCATTGGAAACTTCTTGAAATGAGATCAACTCTGATTCATGGAAAATACTGAA
* * *
1258 AATGCGATCAACTCTGATCGTTGGAACTACTGAAAATGCGATCAACTCTGATCGTTGGAAAATAC
66 AATGCAATCAACTCTGATCGTTGGAAATACTGAAAATGCGATCAACTATGATCGTTGGAAAATAC
*
1323 TGAAAATGC
131 TGAAAATAC
* **
1332 GATCAACTCCGATCATTGGAAACCAC-TGAAAAT-ACGATCAACTCTGA-TCATGGAAAATACTG
1 GATCAACTCTGATCATTGGAAACTTCTTG-AAATGA-GATCAACTCTGATTCATGGAAAATACTG
1394 AAAATGCAATCAACTCTGATCGTTGGAAAATACTGAAAATGCGATCAACTATGATCGTTGGAAAA
64 AAAATGCAATCAACTCTGATCGTTGG-AAATACTGAAAATGCGATCAACTATGATCGTTGGAAAA
*
1459 TACTGAAAATAT
128 TACTGAAAATAC
*
1471 GATCAACTCTGATCGTTGGAAACTTCTTGAAATGAGATCAACTCTGA
1 GATCAACTCTGATCATTGGAAACTTCTTGAAATGAGATCAACTCTGA
1518 CCCCTGAAAA
Statistics
Matches: 162, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
138 40 0.25
139 119 0.73
140 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (139 bp):
GATCAACTCTGATCATTGGAAACTTCTTGAAATGAGATCAACTCTGATTCATGGAAAATACTGAA
AATGCAATCAACTCTGATCGTTGGAAATACTGAAAATGCGATCAACTATGATCGTTGGAAAATAC
TGAAAATAC
Found at i:1529 original size:35 final size:35
Alignment explanation
Indices: 1471--1753 Score: 410
Period size: 35 Copynumber: 8.0 Consensus size: 35
1461 CTGAAAATAT
* *
1471 GATCAACTCTGATCGT-TGGAAACTTCTTGAAATGA
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGA
* *
1506 GATCAACTCTGACCCCTGAAAACTT-TTGATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
1540 GATCAACTCTGACCTCTGAAAACTTCTTGGAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1575 GATCAACTCTGACCTCTGAAAACTTCTTGGAACAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTT-G-A-AATGA
*
1613 GATCAACTCTGAACCTCTG-AAACTTCTTGAATACGA
1 GATCAACTCTG-ACCTCTGAAAACTTCTTGAA-ATGA
1649 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
1684 GATCAACTCTGACCTCTGAAAACTTCTTGATATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
* *
1719 GATCAACTCTGACCTCTGAAAGCTTCTTAAAATGA
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1754 CCGCTCTGGA
Statistics
Matches: 226, Mismatches: 14, Indels: 16
0.88 0.05 0.06
Matches are distributed among these distances:
34 33 0.15
35 132 0.58
36 28 0.12
37 1 0.00
38 25 0.11
39 7 0.03
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (35 bp):
GATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
Found at i:1544 original size:104 final size:104
Alignment explanation
Indices: 1222--1739 Score: 357
Period size: 104 Copynumber: 4.9 Consensus size: 104
1212 AAATTTCTTG
* * ** * * *
1222 AAATGAGATCACCTCTAATTGTTGGAAACTACTGAAAATGCGATCAACTCTGATCGTTGG-AACT
1 AAATGAGATCAACTCTGATCCTTGGAAAATACTGAAAAT-AGATCAACTCTGATCCTTGGAAACT
* * * * *
1286 AC-TGAAAATGCGATCAACTCTGATCGTTGGAAAATACTGA
65 TCTTGAAAATGAGATCAACTCTGACCGCT-GAAAATATTGA
* * * ** * *
1326 AAATGCGATCAACTCCGATCATTGGAAACCACTGAAAATACGATCAACTCTGAT-CATGGAAAAT
1 AAATGAGATCAACTCTGATCCTTGGAAAATACTGAAAATA-GATCAACTCTGATCCTTGGAAACT
* * * *
1390 AC-TGAAAATGCA-ATCAACTCTGATCGTTGGAAAATACTGA
65 TCTTGAAAATG-AGATCAACTCTGACCGCT-GAAAATATTGA
* * * *
1430 AAATGCGATCAACTATGATCGTTGGAAAATACTGAAAATATGATCAACTCTGATCGTTGGAAACT
1 AAATGAGATCAACTCTGATCCTTGGAAAATACTGAAAATA-GATCAACTCTGATCCTTGGAAACT
* *
1495 TCTTG-AAATGAGATCAACTCTGACCCCTGAAAACTTTTG-
65 TCTTGAAAATGAGATCAACTCTGACCGCTGAAAA-TATTGA
* * * *
1534 ATATGAGATCAACTCTGA-CCTCT-GAAAACTTCTTG-GAATGAGATCAACTCTGA-CCTCTGAA
1 AAATGAGATCAACTCTGATCCT-TGGAAAA-TAC-TGAAAAT-AGATCAACTCTGATCCT-TGGA
* * *
1595 AACTTCTTGGAACAATGAGATCAACTCTGAACCTCTGAAACTTCTTGA
61 AACTTCTT-GAA-AATGAGATCAACTCTG-ACCGCTGAAA-ATATTGA
* * * *
1643 ATACGAGATCAACTCTGA-CCTCT-GAAAACTTCTTG-AAATGAGATCAACTCTGA-CCTCTGAA
1 AAATGAGATCAACTCTGATCCT-TGGAAAA-TAC-TGAAAAT-AGATCAACTCTGATCCT-TGGA
* *
1704 AACTTCTTG-ATATGAGATCAACTCTGACCTCTGAAA
61 AACTTCTTGAAAATGAGATCAACTCTGACCGCTGAAA
1740 GCTTCTTAAA
Statistics
Matches: 355, Mismatches: 41, Indels: 35
0.82 0.10 0.08
Matches are distributed among these distances:
103 12 0.03
104 184 0.52
105 43 0.12
106 18 0.05
107 17 0.05
108 14 0.04
109 67 0.19
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (104 bp):
AAATGAGATCAACTCTGATCCTTGGAAAATACTGAAAATAGATCAACTCTGATCCTTGGAAACTT
CTTGAAAATGAGATCAACTCTGACCGCTGAAAATATTGA
Found at i:1669 original size:109 final size:104
Alignment explanation
Indices: 1471--1746 Score: 412
Period size: 109 Copynumber: 2.6 Consensus size: 104
1461 CTGAAAATAT
* * *
1471 GATCAACTCTGATCGT-TGGAAACTTCTTGAAATGAGATCAACTCTGACCCCTGAAAACTT-TTG
1 GATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTG-AAACTTCTTG
* *
1534 ATATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATGA
64 ATACGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
1575 GATCAACTCTGACCTCTGAAAACTTCTTGGAACAATGAGATCAACTCTGAACCTCTGAAACTTCT
1 GATCAACTCTGACCTCTGAAAACTTCTT-G-A-AATGAGATCAACTCTG-ACCTCTGAAACTTCT
1640 TGAATACGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
62 TG-ATACGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
*
1684 GATCAACTCTGACCTCTGAAAACTTCTTGATATGAGATCAACTCTGACCTCTGAAAGCTTCTT
1 GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAA-CTTCTT
1747 AAAATGACCG
Statistics
Matches: 158, Mismatches: 6, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
103 2 0.01
104 23 0.15
105 11 0.07
106 22 0.14
107 23 0.15
108 10 0.06
109 67 0.42
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (104 bp):
GATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAACTTCTTGAT
ACGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGA
Found at i:1705 original size:144 final size:142
Alignment explanation
Indices: 1471--1746 Score: 448
Period size: 144 Copynumber: 1.9 Consensus size: 142
1461 CTGAAAATAT
* * * *
1471 GATCAACTCTGATCGTTGGAAACTTCTTGAAATGAGATCAACTCTGACCCCTGAAAACTTTTGAT
1 GATCAACTCTGAACCTTGGAAACTTCTTGAAACGAGATCAACTCTGACCCCTGAAAACTTTTGAA
1536 ATGAGATCAACTCTGACCTCTGAAAACTTCTTGGA-ATGAGATCAACTCTGACCTCTGAAAACTT
66 ATGAGATCAACTCTGACCTCTGAAAACTTCTT-GATATGAGATCAACTCTGACCTCTGAAAACTT
1600 CTTGGAACAATGA
130 CTTGGAACAATGA
*
1613 GATCAACTCTGAACCTCT-GAAACTTCTTGAATACGAGATCAACTCTGACCTCTGAAAACTTCTT
1 GATCAACTCTGAACCT-TGGAAACTTCTTGAA-ACGAGATCAACTCTGACCCCTGAAAACTT-TT
*
1677 GAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGATATGAGATCAACTCTGACCTCTGAAAGC
63 GAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGATATGAGATCAACTCTGACCTCTGAAAAC
1742 TTCTT
128 TTCTT
1747 AAAATGACCG
Statistics
Matches: 124, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
142 27 0.22
143 30 0.24
144 67 0.54
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (142 bp):
GATCAACTCTGAACCTTGGAAACTTCTTGAAACGAGATCAACTCTGACCCCTGAAAACTTTTGAA
ATGAGATCAACTCTGACCTCTGAAAACTTCTTGATATGAGATCAACTCTGACCTCTGAAAACTTC
TTGGAACAATGA
Done.