Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012004.1 Corchorus olitorius cultivar O-4 contig12037, 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: 36197
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:12517 original size:3 final size:3
Alignment explanation
Indices: 12509--12535 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12499 GTTCTAGTTG
12509 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
12536 TTGACAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:14585 original size:89 final size:89
Alignment explanation
Indices: 14434--14665 Score: 394
Period size: 89 Copynumber: 2.6 Consensus size: 89
14424 ACATATAGGT
14434 TTTATCAGTCAGACATATTTCAGAGCCCCTTCACCTCACCCAGGAGTAAGCCAGTATCGAGACAA
1 TTTATCAGTCAGACATATTTCAGAGCCCCTTCACCTCACCCAGGAGTAAGCCAGTATCGAGACAA
14499 GTGACAAGATGGAGTCATAGAAGG
66 GTGACAAGATGGAGTCATAGAAGG
14523 TTTATCAGTCAGACATATTTCAGAGCCCCTTCACCTCACCCAGGAGTAAGCCAGTATCGAGACAA
1 TTTATCAGTCAGACATATTTCAGAGCCCCTTCACCTCACCCAGGAGTAAGCCAGTATCGAGACAA
14588 GTGACAAGATGGAGTCATAGAAGG
66 GTGACAAGATGGAGTCATAGAAGG
* * * * * * *
14612 TTTATCAATCGGTCATATTTCAAAGCCCCTTTACCTCAACTAGGAGTAA-CCAGT
1 TTTATCAGTCAGACATATTTCAGAGCCCCTTCACCTCACCCAGGAGTAAGCCAGT
14666 TTTGAGAGTG
Statistics
Matches: 136, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
88 5 0.04
89 131 0.96
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (89 bp):
TTTATCAGTCAGACATATTTCAGAGCCCCTTCACCTCACCCAGGAGTAAGCCAGTATCGAGACAA
GTGACAAGATGGAGTCATAGAAGG
Found at i:20405 original size:11 final size:11
Alignment explanation
Indices: 20391--20445 Score: 76
Period size: 11 Copynumber: 5.1 Consensus size: 11
20381 TTTCATAACA
20391 AATTTATAATT
1 AATTTATAATT
20402 AATTTATAATT
1 AATTTATAATT
* **
20413 -ATTTGTAACA
1 AATTTATAATT
20423 AATTTATAATT
1 AATTTATAATT
20434 AATTTATAATT
1 AATTTATAATT
20445 A
1 A
20446 TTTGATGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
10 7 0.19
11 30 0.81
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
AATTTATAATT
Found at i:20416 original size:21 final size:22
Alignment explanation
Indices: 20391--20445 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
20381 TTTCATAACA
20391 AATTTATAATTAATTTATAATT
1 AATTTATAATTAATTTATAATT
* **
20413 -ATTTGTAACAAATTTATAATT
1 AATTTATAATTAATTTATAATT
20434 AATTTATAATTA
1 AATTTATAATTA
20446 TTTGATGATT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTTATAATTAATTTATAATT
Found at i:20422 original size:32 final size:32
Alignment explanation
Indices: 20386--20449 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
20376 TGTATTTTCA
20386 TAACAAATTTATAATTAATTTATAATTATTTG
1 TAACAAATTTATAATTAATTTATAATTATTTG
20418 TAACAAATTTATAATTAATTTATAATTATTTG
1 TAACAAATTTATAATTAATTTATAATTATTTG
20450 ATGATTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (32 bp):
TAACAAATTTATAATTAATTTATAATTATTTG
Found at i:23612 original size:207 final size:207
Alignment explanation
Indices: 23257--23674 Score: 818
Period size: 207 Copynumber: 2.0 Consensus size: 207
23247 TGTAAATTGA
23257 CTTTGGTTTTCGGCCAACAACGTTAACATCAACTGCGATATCCTCTGTGTCACAAAGAACTTAAG
1 CTTTGGTTTTCGGCCAACAACGTTAACATCAACTGCGATATCCTCTGTGTCACAAAGAACTTAAG
23322 ATCCTTCCTTGCATTAACAGTATCTTTGATCTTCCCCAGCACATCCATAACGGTCCCAAACACAT
66 ATCCTTCCTTGCATTAACAGTATCTTTGATCTTCCCCAGCACATCCATAACGGTCCCAAACACAT
*
23387 TATTTTCTATATGCATCACATCCAAATTATGTCGGATCAAATTGTTTTTCCAATACGGTAACTCC
131 CATTTTCTATATGCATCACATCCAAATTATGTCGGATCAAATTGTTTTTCCAATACGGTAACTCC
23452 CAAAATATACTC
196 CAAAATATACTC
*
23464 CTTTGGTTTTTGGCCAACAACGTTAACATCAACTGCGATATCCTCTGTGTCACAAAGAACTTAAG
1 CTTTGGTTTTCGGCCAACAACGTTAACATCAACTGCGATATCCTCTGTGTCACAAAGAACTTAAG
23529 ATCCTTCCTTGCATTAACAGTATCTTTGATCTTCCCCAGCACATCCATAACGGTCCCAAACACAT
66 ATCCTTCCTTGCATTAACAGTATCTTTGATCTTCCCCAGCACATCCATAACGGTCCCAAACACAT
23594 CATTTTCTATATGCATCACATCCAAATTATGTCGGATCAAATTGTTTTTCCAATACGGTAACTCC
131 CATTTTCTATATGCATCACATCCAAATTATGTCGGATCAAATTGTTTTTCCAATACGGTAACTCC
23659 CAAAATATACTC
196 CAAAATATACTC
23671 CTTT
1 CTTT
23675 TCATCCATTT
Statistics
Matches: 209, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
207 209 1.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (207 bp):
CTTTGGTTTTCGGCCAACAACGTTAACATCAACTGCGATATCCTCTGTGTCACAAAGAACTTAAG
ATCCTTCCTTGCATTAACAGTATCTTTGATCTTCCCCAGCACATCCATAACGGTCCCAAACACAT
CATTTTCTATATGCATCACATCCAAATTATGTCGGATCAAATTGTTTTTCCAATACGGTAACTCC
CAAAATATACTC
Found at i:28235 original size:32 final size:33
Alignment explanation
Indices: 28144--28237 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 33
28134 TAATCAATAT
28144 ATACATGAAAAATTCAAATAGTTTGGAAAATTC
1 ATACATGAAAAATTCAAATAGTTTGGAAAATTC
* * * *
28177 GATAGATG-TAAA--GAAAGAGTTTGGAAAATT-
1 -ATACATGAAAAATTCAAATAGTTTGGAAAATTC
* *
28207 TTTCATGAAAAATTCAAATAGTTTGGAAAAT
1 ATACATGAAAAATTCAAATAGTTTGGAAAAT
28238 CAATTTTGAA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
29 4 0.09
30 3 0.06
31 16 0.34
32 15 0.32
33 3 0.06
34 6 0.13
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.31
Consensus pattern (33 bp):
ATACATGAAAAATTCAAATAGTTTGGAAAATTC
Found at i:29706 original size:21 final size:22
Alignment explanation
Indices: 29680--29720 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
29670 GACTTCCTTT
29680 AGTCGACTTC-TCCCTTGCTCA
1 AGTCGACTTCTTCCCTTGCTCA
*
29701 AGTCGACTTCTTCTCTTGCT
1 AGTCGACTTCTTCCCTTGCT
29721 TCAACCGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.12, C:0.34, G:0.15, T:0.39
Consensus pattern (22 bp):
AGTCGACTTCTTCCCTTGCTCA
Found at i:35514 original size:19 final size:19
Alignment explanation
Indices: 35490--35528 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
35480 CAGTCAATGA
35490 ATATATTGACTCTGCTGTC
1 ATATATTGACTCTGCTGTC
35509 ATATATTGACTCTGCTGTC
1 ATATATTGACTCTGCTGTC
35528 A
1 A
35529 GACATGTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (19 bp):
ATATATTGACTCTGCTGTC
Done.