Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022308.1 Corchorus olitorius cultivar O-4 contig22341, 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: 21805
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1681 original size:12 final size:13
Alignment explanation
Indices: 1656--1688 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
1646 CTGACTATTT
1656 TTTTTTAAATATA
1 TTTTTTAAATATA
1669 TTTTTTAAA-ATA
1 TTTTTTAAATATA
1681 TTTTTTAA
1 TTTTTTAA
1689 TAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTAAATATA
Found at i:4233 original size:6 final size:6
Alignment explanation
Indices: 4224--4250 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4214 TTTTCTTTTA
4224 TAATTT TAATTT TAATTT TAATTT TAA
1 TAATTT TAATTT TAATTT TAATTT TAA
4251 ATAATAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TAATTT
Found at i:7835 original size:36 final size:36
Alignment explanation
Indices: 7788--7859 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
7778 GGGAAGCCAA
*
7788 GATTGAGCTGAATAATCGTGTGGTGCGGGACTATTC
1 GATTGAGCTGAATAATCGTGTGGTGCAGGACTATTC
7824 GATTGAGCTGAATAATCGTGTGGTGCAGGACTATTC
1 GATTGAGCTGAATAATCGTGTGGTGCAGGACTATTC
7860 CTCCCGCCGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.31
Consensus pattern (36 bp):
GATTGAGCTGAATAATCGTGTGGTGCAGGACTATTC
Found at i:8948 original size:43 final size:43
Alignment explanation
Indices: 8807--9093 Score: 227
Period size: 41 Copynumber: 6.8 Consensus size: 43
8797 CTCTCTCCTC
* * *
8807 AAAGTTCC-CAAACACATTTATAACACAGGGGCAATTCC-CTTTCTA
1 AAAG-TCCTCAAACACATTTATAACACAGGGGC-A--CCTCTATATT
* * * *
8852 AAAGTCCTCAAACACATTTATAACACAGAGACA-TTC-ATATC
1 AAAGTCCTCAAACACATTTATAACACAGGGGCACCTCTATATT
* * * *
8893 AAAGTCCCCAAGCACAATTATAACACAGGGGCACCTCTATTTT
1 AAAGTCCTCAAACACATTTATAACACAGGGGCACCTCTATATT
* * * *
8936 AAAGTCCTCAAGCACATTTATAACACA-GAG-ACATCTATATC
1 AAAGTCCTCAAACACATTTATAACACAGGGGCACCTCTATATT
* * * *
8977 AAAGTCCCCAAACACAATTATAACACAGGGACAATCCTCTCTA--
1 AAAGTCCTCAAACACATTTATAACACAGGGGC-A-CCTCTATATT
* *
9020 AAAGTCCTCAAACACATTTATAACACATGGGCA--TCTATACT
1 AAAGTCCTCAAACACATTTATAACACAGGGGCACCTCTATATT
* *
9061 AAAGTCC-CTAAACACAATTATAACACAAGGGCA
1 AAAGTCCTC-AAACACATTTATAACACAGGGGCA
9094 ATTTCTATTT
Statistics
Matches: 197, Mismatches: 34, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
39 5 0.03
40 1 0.01
41 91 0.46
42 7 0.04
43 56 0.28
44 5 0.03
45 32 0.16
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.23
Consensus pattern (43 bp):
AAAGTCCTCAAACACATTTATAACACAGGGGCACCTCTATATT
Found at i:8964 original size:84 final size:81
Alignment explanation
Indices: 8805--9093 Score: 341
Period size: 84 Copynumber: 3.4 Consensus size: 81
8795 TTCTCTCTCC
* *
8805 TCAAAGTTCCCAAACACATTTATAACACAGGGGCAATTCC-CTTTCTAAAAGTCCTCAAACACAT
1 TCAAAGTCCCCAAACACAATTATAACACAGGGGC-A--CCTCTTT-T-AAAGTCCTCAAACACAT
8869 TTATAACACAGAGACATTCATA
61 TTATAACACAGAGACA-TCATA
* *
8891 TCAAAGTCCCCAAGCACAATTATAACACAGGGGCACCTCTATTTTAAAGTCCTCAAGCACATTTA
1 TCAAAGTCCCCAAACACAATTATAACACAGGGGCACCTC--TTTTAAAGTCCTCAAACACATTTA
8956 TAACACAGAGACATCTATA
64 TAACACAGAGACATC-ATA
* * *
8975 TCAAAGTCCCCAAACACAATTATAACACAGGGACAATCCTCTCTAAAAGTCCTCAAACACATTTA
1 TCAAAGTCCCCAAACACAATTATAACACAGGGGC-A-CCTCTTTTAAAGTCCTCAAACACATTTA
*
9040 TAACACATG-GGCATC-TA
64 TAACACA-GAGACATCATA
* *
9057 TACTAAAGTCCCTAAACACAATTATAACACAAGGGCA
1 T-C-AAAGTCCCCAAACACAATTATAACACAGGGGCA
9094 ATTTCTATTT
Statistics
Matches: 181, Mismatches: 13, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
82 3 0.02
83 6 0.03
84 130 0.72
85 4 0.02
86 38 0.21
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.23
Consensus pattern (81 bp):
TCAAAGTCCCCAAACACAATTATAACACAGGGGCACCTCTTTTAAAGTCCTCAAACACATTTATA
ACACAGAGACATCATA
Found at i:10961 original size:25 final size:25
Alignment explanation
Indices: 10927--10977 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
10917 AGTTTGTACT
10927 TTTATATAGTAGTAAGATAGTAAGA
1 TTTATATAGTAGTAAGATAGTAAGA
10952 TTTATATAGTAGTAAGATAGTAAGA
1 TTTATATAGTAGTAAGATAGTAAGA
10977 T
1 T
10978 AAAATAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
TTTATATAGTAGTAAGATAGTAAGA
Found at i:18832 original size:16 final size:15
Alignment explanation
Indices: 18794--18835 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
18784 ACAGAGGTTG
*
18794 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
18809 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
18824 ACTAGAAAACAA
1 AC-AGAAAACAA
18836 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:20218 original size:18 final size:19
Alignment explanation
Indices: 20197--20237 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
20187 CCCTTGAAAT
20197 AAATCTTCAA-TGGTCTTC
1 AAATCTTCAATTGGTCTTC
*
20215 AAATCTTCAATTTGTCTTC
1 AAATCTTCAATTGGTCTTC
20234 AAAT
1 AAAT
20238 GGTCTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (19 bp):
AAATCTTCAATTGGTCTTC
Found at i:20234 original size:11 final size:11
Alignment explanation
Indices: 20200--20247 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
20190 TTGAAATAAA
20200 TCTTC-AATGG
1 TCTTCAAATGG
20210 TCTTCAAA---
1 TCTTCAAATGG
* *
20218 TCTTCAATTTG
1 TCTTCAAATGG
20229 TCTTCAAATGG
1 TCTTCAAATGG
20240 TCTTCAAA
1 TCTTCAAA
20248 CACGAACTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
8 7 0.23
10 5 0.16
11 19 0.61
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (11 bp):
TCTTCAAATGG
Found at i:20635 original size:2 final size:2
Alignment explanation
Indices: 20628--20652 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20618 TCTACAACAA
20628 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 A
20653 GTTCATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21338 original size:16 final size:16
Alignment explanation
Indices: 21305--21408 Score: 97
Period size: 16 Copynumber: 6.6 Consensus size: 16
21295 GGGCGGGTTT
*
21305 GGGTTCAGGTAC-TTC
1 GGGTTCGGGTACTTTC
21320 GGGTTCGGGTACTTTC
1 GGGTTCGGGTACTTTC
* **
21336 GGGCTCGGGTTA-AGTC
1 GGGTTCGGG-TACTTTC
*
21352 GGGTTCGGGTATTTTC
1 GGGTTCGGGTACTTTC
*
21368 GGGTTCGGGTTA-TGTC
1 GGGTTCGGG-TACTTTC
*
21384 GAGTTCGGGTACTTTC
1 GGGTTCGGGTACTTTC
*
21400 GAGTTCGGG
1 GGGTTCGGG
21409 CTCGGGTAGG
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
15 15 0.20
16 55 0.74
17 4 0.05
ACGTcount: A:0.10, C:0.16, G:0.39, T:0.35
Consensus pattern (16 bp):
GGGTTCGGGTACTTTC
Found at i:21354 original size:32 final size:32
Alignment explanation
Indices: 21318--21400 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
21308 TTCAGGTACT
21318 TCGGGTTCGGGTACTTTCGGGCTCGGGTTAAG
1 TCGGGTTCGGGTACTTTCGGGCTCGGGTTAAG
* * *
21350 TCGGGTTCGGGTATTTTCGGGTTCGGGTTATG
1 TCGGGTTCGGGTACTTTCGGGCTCGGGTTAAG
*
21382 TCGAGTTCGGGTACTTTCG
1 TCGGGTTCGGGTACTTTCG
21401 AGTTCGGGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.08, C:0.17, G:0.39, T:0.36
Consensus pattern (32 bp):
TCGGGTTCGGGTACTTTCGGGCTCGGGTTAAG
Done.