Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008197.1 Corchorus capsularis cultivar CVL-1 contig08218, 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: 24385
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:4605 original size:43 final size:44
Alignment explanation
Indices: 4534--4620 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
4524 TGATTTGCCT
* *
4534 TCACACCGCCTTGGTCAAATTGAAAAG-CCAACATGGCTTTTTA
1 TCACACCACCTTGGTCAAATTGAAAAGCCCAACATGGCCTTTTA
*
4577 TCACAGCCACCTTGGTCAAATTG-AAAGCCCGACATGGCCTTTTA
1 TCACA-CCACCTTGGTCAAATTGAAAAGCCCAACATGGCCTTTTA
4621 AAATTCTCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 9 0.23
44 30 0.77
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (44 bp):
TCACACCACCTTGGTCAAATTGAAAAGCCCAACATGGCCTTTTA
Found at i:6238 original size:45 final size:45
Alignment explanation
Indices: 6172--6259 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
6162 GATTACTTCT
6172 CCAGCTCATCATTAATCCGGGGTAAGGATCTTTTAGTAATTCCTC
1 CCAGCTCATCATTAATCCGGGGTAAGGATCTTTTAGTAATTCCTC
* * *
6217 CCAGCTTATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCC
1 CCAGCTCATCATTAATCCGGGGTAAGGATCTTTTAGTAATTCC
6260 ACAACTCTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGGGGTAAGGATCTTTTAGTAATTCCTC
Found at i:10542 original size:15 final size:15
Alignment explanation
Indices: 10516--10556 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
10506 AAGAAGGGGG
10516 AAGAAAAGAAAGAAAA
1 AAGAAAA-AAAGAAAA
10532 AAGAAAAAAAGAAAA
1 AAGAAAAAAAGAAAA
**
10547 GGGAAAAAAA
1 AAGAAAAAAA
10557 TTTAATGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAGAAAA
Found at i:15947 original size:30 final size:29
Alignment explanation
Indices: 15889--15969 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 29
15879 GTTTAATATC
*
15889 CAAATTAGCCCCTTAA-TTATTCTTTTTGGGA
1 CAAATTGGCCCCTTAACTT-TT-TTTTT-GGA
* *
15920 CAAATTGGCTCCTTACCTTTTTTTTTGGA
1 CAAATTGGCCCCTTAACTTTTTTTTTGGA
15949 CAAATTGGCCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
15970 AAAAACGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
29 22 0.50
30 5 0.11
31 15 0.34
32 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (29 bp):
CAAATTGGCCCCTTAACTTTTTTTTTGGA
Found at i:16712 original size:31 final size:29
Alignment explanation
Indices: 16632--16690 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
16622 TCTCGTTTTT
16632 AAAAGTTAA-GGAGCCAATTTGTCCAAAAA
1 AAAAGTTAAGGGA-CCAATTTGTCCAAAAA
*
16661 AAAAGTTAAGGGACCAATTTGTCCCAAAA
1 AAAAGTTAAGGGACCAATTTGTCCAAAAA
16690 A
1 A
16691 GGATAGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.20
Consensus pattern (29 bp):
AAAAGTTAAGGGACCAATTTGTCCAAAAA
Found at i:22196 original size:14 final size:14
Alignment explanation
Indices: 22177--22204 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22167 GTAGCTGTAC
22177 AAGAAGAAAAGGAA
1 AAGAAGAAAAGGAA
22191 AAGAAGAAAAGGAA
1 AAGAAGAAAAGGAA
22205 CCACCGGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAAGGAA
Found at i:23199 original size:315 final size:314
Alignment explanation
Indices: 22628--23258 Score: 1088
Period size: 315 Copynumber: 2.0 Consensus size: 314
22618 AAAGCCACGT
* * *
22628 TAGCATGTCACGTGTTTTGAAAATACCATTCAATTTAGGATAAATTTTTTTAAAATTAAAAAAAA
1 TAGCATGCCACGTGTTTTGAAAATACCATGCAATTTAGGATAAATTTTTTGAAAATTAAAAAAAA
* * *
22693 TGATTGATGGTAGCATGAAAGTAAACTTTTTGAAAATGAATTCAGATTGTTTTTTAAATTTTTTT
66 TGATTGATAGCAGCATGAAAGTAAACTTTCTGAAAATGAATTCAGATTGTTTTTTAAATTTTTTT
* *
22758 TCTTTTCTGGAAAATTTACCTTAAGATGAGGTGGCATTTTTAGGTTATAGGGCATGCTGGCATGA
131 TCTTTTCTGGAAAATTTACCTTAAGATGAGGTGACATTTTTAGGTCATAGGGCATGCTGGCATGA
22823 CTTTTTCTCACAACAAGATGACTAATCTAGCCAAATTTGAGAGTTCAAGGGTGAAATTGGTTAAA
196 CTTTTTCTCACAACAAGATGACTAATCTAGCCAAATTTGAGAGTTCAAGGGTGAAATTGGTTAAA
* *
22888 ATAGAAGTTCATGGATTTTTTTGACTGTTTGCATAAAGTTCAGGGATGAAAAAG
261 ATAAAAGTTCATGAATTTTTTTGACTGTTTGCATAAAGTTCAGGGATGAAAAAG
22942 TAGCATGCCACGTGTTTTGAAAATACCATGCAATTTAGGATAAATTTTTTGAAAATTAAAAAAAA
1 TAGCATGCCACGTGTTTTGAAAATACCATGCAATTTAGGATAAATTTTTTGAAAATT---AAAAA
23007 TAAATGATTGATAGCAGCATGAAAGTAAACTTTCTGAAAATGAATTCAGATTG-TTTTT-AA-TT
63 -AAATGATTGATAGCAGCATGAAAGTAAACTTTCTGAAAATGAATTCAGATTGTTTTTTAAATTT
*
23069 TTTTTCTTTTCTGGAAAATTTACCTTAAGATGAGGTGACATTTTTAGGTCATATGGCATGCTGGC
127 TTTTTCTTTTCTGGAAAATTTACCTTAAGATGAGGTGACATTTTTAGGTCATAGGGCATGCTGGC
* *
23134 ATGATTTTTTCTCACAACAGGATGACTAATCTAGCCAAATTTGAGAGTTCAAGGGTGAAATTGGT
192 ATGACTTTTTCTCACAACAAGATGACTAATCTAGCCAAATTTGAGAGTTCAAGGGTGAAATTGGT
23199 TAAAATAAAAGTTCATGAATTTTTTTGACTGTTTGCATAAAGTTCAGGGATGAAAAAG
257 TAAAATAAAAGTTCATGAATTTTTTTGACTGTTTGCATAAAGTTCAGGGATGAAAAAG
23257 TA
1 TA
23259 TATTAAGCCA
Statistics
Matches: 300, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
314 54 0.18
315 185 0.62
316 2 0.01
317 10 0.03
318 49 0.16
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (314 bp):
TAGCATGCCACGTGTTTTGAAAATACCATGCAATTTAGGATAAATTTTTTGAAAATTAAAAAAAA
TGATTGATAGCAGCATGAAAGTAAACTTTCTGAAAATGAATTCAGATTGTTTTTTAAATTTTTTT
TCTTTTCTGGAAAATTTACCTTAAGATGAGGTGACATTTTTAGGTCATAGGGCATGCTGGCATGA
CTTTTTCTCACAACAAGATGACTAATCTAGCCAAATTTGAGAGTTCAAGGGTGAAATTGGTTAAA
ATAAAAGTTCATGAATTTTTTTGACTGTTTGCATAAAGTTCAGGGATGAAAAAG
Found at i:23503 original size:16 final size:16
Alignment explanation
Indices: 23482--23518 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
23472 GGTAGTTTTC
23482 TCGGGTCAATC-GGGTT
1 TCGGGTC-ATCTGGGTT
23498 TCGGGTCATCTGGGTT
1 TCGGGTCATCTGGGTT
23514 T-GGGT
1 TCGGGT
23519 TATTCGAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.08, C:0.16, G:0.41, T:0.35
Consensus pattern (16 bp):
TCGGGTCATCTGGGTT
Done.