Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006513.1 Corchorus capsularis cultivar CVL-1 contig06534, 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: 20392
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:720 original size:19 final size:18
Alignment explanation
Indices: 696--731 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
686 TGAAGATTTC
696 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
715 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
732 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:2809 original size:156 final size:156
Alignment explanation
Indices: 2461--2818 Score: 388
Period size: 157 Copynumber: 2.3 Consensus size: 156
2451 TCATCTCAAA
* * *
2461 TAGACTTAGCATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGCTTGGGGAGACAAACCAAC
1 TAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTGGGGAGACAAACCAAC
* * * * * * *
2526 TTCTCCATGCTAGAGAGTTCGGTTTCACTTGGATTTTTTTCCCATAACCTTATGATGATAATCTA
66 TTCACCATGCAAGAGAGCTCGGTTTCACTTAGAATTTTTTCCCACAACCTTATGATGATAATATA
*
2591 AGTATACTGGTGGAAAATCAGCTTCAT
131 AGTACACT-GTGGAAAATCAGCTTCAT
* * * * *
2618 TGGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTAGGGGTG-GAAACCTA
1 TAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTT-GGGGAGACAAACCAA
* * * * *
2682 GTTCACCAT-CAAGGGGAGCTCGGTTTTACTTAGAATTTTTT-CCACAATCTTATG-TGGATATT
65 CTTCACCATGCAA-GAGAGCTCGGTTTCACTTAGAATTTTTTCCCACAACCTTATGAT-GATAAT
*
2744 ATAAG-ACCCT-TGGAAAAATTTCAGC-TCAT
128 ATAAGTACACTGTGG-AAAA--TCAGCTTCAT
*
2773 TCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAAGACA
1 T-AGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
2819 GTTTGAGGTG
Statistics
Matches: 170, Mismatches: 24, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
153 3 0.02
154 4 0.02
155 9 0.05
156 68 0.40
157 81 0.48
158 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (156 bp):
TAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTGGGGAGACAAACCAAC
TTCACCATGCAAGAGAGCTCGGTTTCACTTAGAATTTTTTCCCACAACCTTATGATGATAATATA
AGTACACTGTGGAAAATCAGCTTCAT
Found at i:3198 original size:17 final size:17
Alignment explanation
Indices: 3178--3210 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3168 GCAGCCTATC
3178 ACCTCATACTACCTAGT
1 ACCTCATACTACCTAGT
3195 ACCTCATACTACCTAG
1 ACCTCATACTACCTAG
3211 GTACTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.27
Consensus pattern (17 bp):
ACCTCATACTACCTAGT
Found at i:4005 original size:23 final size:23
Alignment explanation
Indices: 3970--4049 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
3960 CCTCGCTATG
3970 AAATTTTGATAAATCTTCTTATA
1 AAATTTTGATAAATCTTCTTATA
* * * * *
3993 AAGTTTTGTTAAACCTCCCTATA
1 AAATTTTGATAAATCTTCTTATA
* *
4016 AAATTTTGAT-AATTTTCTTATG
1 AAATTTTGATAAATCTTCTTATA
*
4038 AAATCTTGATAA
1 AAATTTTGATAA
4050 CTACAAATTT
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
22 16 0.37
23 27 0.63
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCTTATA
Found at i:4083 original size:22 final size:22
Alignment explanation
Indices: 3958--4238 Score: 145
Period size: 22 Copynumber: 13.0 Consensus size: 22
3948 TCACACTATG
*
3958 AACCTCGCTATGAAATTTTGAT
1 AACCTCCCTATGAAATTTTGAT
* * * *
3980 AAATCTTCTTAT-AAAGTTTTGTT
1 -AACCTCCCTATGAAA-TTTTGAT
*
4003 AAACCTCCCTATAAAATTTTGAT
1 -AACCTCCCTATGAAATTTTGAT
** * * *
4026 AATTTTCTTATGAAATCTTGAT
1 AACCTCCCTATGAAATTTTGAT
*
4048 AA-----CTA-CAAATTTTGAT
1 AACCTCCCTATGAAATTTTGAT
**
4064 AACCTCCCTATGATTTTTTGAT
1 AACCTCCCTATGAAATTTTGAT
** *
4086 AACCTCATTATGAAATTTTGTT
1 AACCTCCCTATGAAATTTTGAT
*
4108 AATCTCCCTATGAAATTTTGATT
1 AACCTCCCTATGAAATTTTGA-T
* ** * *
4131 TATAT-ACTATAAAATTTTGAT
1 AACCTCCCTATGAAATTTTGAT
*
4152 AACC-CTCTTATGAAATTTTGA-
1 AACCTC-CCTATGAAATTTTGAT
* ** *
4173 AAACTAAACAATGAAATTTTGAT
1 AACCT-CCCTATGAAATTTTGAT
* *
4196 AACCTTCATATGAAATTTTGAT
1 AACCTCCCTATGAAATTTTGAT
*
4218 ATCCT-CC-ATGAAATTTTGAT
1 AACCTCCCTATGAAATTTTGAT
4238 A
1 A
4239 TCTCCGTTTC
Statistics
Matches: 192, Mismatches: 52, Indels: 31
0.70 0.19 0.11
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
20 14 0.07
21 9 0.05
22 117 0.61
23 36 0.19
24 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.42
Consensus pattern (22 bp):
AACCTCCCTATGAAATTTTGAT
Found at i:4212 original size:66 final size:63
Alignment explanation
Indices: 4054--4236 Score: 161
Period size: 66 Copynumber: 2.8 Consensus size: 63
4044 TGATAACTAC
* ** * * ** *
4054 AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTAT
1 AAATTTTGATAACCT-ACTATGAAATTTTGATAACCTC-TTATGAAATTTTG-AAAACTAACAAT
4119 G
63 G
* ** *
4120 AAATTTTGATTTATATACTATAAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAACAAT
1 AAATTTTGA-TAACCTACTATGAAATTTTGATAA-CCTCTTATGAAATTTTGAAAACT-AACAAT
4185 G
63 G
* * *
4186 AAATTTTGATAACCTTCATATGAAATTTTGATATCCTC-CATGAAATTTTGA
1 AAATTTTGATAACCTAC-TATGAAATTTTGATAACCTCTTATGAAATTTTGA
4237 TATCTCCGTT
Statistics
Matches: 94, Mismatches: 19, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
64 12 0.13
65 12 0.13
66 63 0.67
67 7 0.07
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.42
Consensus pattern (63 bp):
AAATTTTGATAACCTACTATGAAATTTTGATAACCTCTTATGAAATTTTGAAAACTAACAATG
Found at i:4230 original size:20 final size:22
Alignment explanation
Indices: 4183--4240 Score: 84
Period size: 20 Copynumber: 2.7 Consensus size: 22
4173 AAACTAAACA
* *
4183 ATGAAATTTTGATAACCTTCAT
1 ATGAAATTTTGATATCCTTCAC
4205 ATGAAATTTTGATATCC-TC-C
1 ATGAAATTTTGATATCCTTCAC
4225 ATGAAATTTTGATATC
1 ATGAAATTTTGATATC
4241 TCCGTTTCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 16 0.47
21 2 0.06
22 16 0.47
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
ATGAAATTTTGATATCCTTCAC
Found at i:4291 original size:22 final size:22
Alignment explanation
Indices: 4257--4306 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
4247 TCGGTGGACG
*
4257 ATTTTATAAAGAGGTTATCAAA
1 ATTTCATAAAGAGGTTATCAAA
*
4279 ATTTCATAGAGAGGTTATCAAA
1 ATTTCATAAAGAGGTTATCAAA
4301 ATTTCA
1 ATTTCA
4307 AAATGTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (22 bp):
ATTTCATAAAGAGGTTATCAAA
Found at i:4549 original size:22 final size:22
Alignment explanation
Indices: 4425--4672 Score: 111
Period size: 22 Copynumber: 11.4 Consensus size: 22
4415 AGAATTCTAA
* **
4425 GAGGATATCAAAATTTCATATA
1 GAGGTTATCAAAATTTCATAGG
* * *
4447 AAGTTTATCAAAATTTCATAGTT
1 GAGGTTATCAAAATTTCATAG-G
* * *
4470 TA-GTTTTCAAAATTTCATA-A
1 GAGGTTATCAAAATTTCATAGG
4490 GAGGGTTATCAAAATTAATTCATA-G
1 GA-GGTTATCAAAA-T--TTCATAGG
* * *
4515 TATGTAGATCAAAATTTCATAGG
1 GAGGT-TATCAAAATTTCATAGG
* * * **
4538 GAGATTAACAAAGTTTCATAAT
1 GAGGTTATCAAAATTTCATAGG
*
4560 GAGGTTATCAATAA-ATCATAGG
1 GAGGTTATCAA-AATTTCATAGG
4582 GAGGTTATCAAAATTT--T---
1 GAGGTTATCAAAATTTCATAGG
* * *
4599 TA-GTTATCAAGATTTCATAAG
1 GAGGTTATCAAAATTTCATAGG
* * * *
4620 AAAGTTATCAAAATTTTATAAG
1 GAGGTTATCAAAATTTCATAGG
* *
4642 GAGGTTTATCAAAATTTTATAGC
1 GAGG-TTATCAAAATTTCATAGG
4665 GAGGTTAT
1 GAGGTTAT
4673 AATCACAATT
Statistics
Matches: 170, Mismatches: 39, Indels: 34
0.70 0.16 0.14
Matches are distributed among these distances:
16 12 0.07
17 1 0.01
18 1 0.01
20 2 0.01
21 3 0.02
22 108 0.64
23 26 0.15
24 3 0.02
25 14 0.08
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.36
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGG
Found at i:4683 original size:25 final size:23
Alignment explanation
Indices: 4602--4670 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
4592 AAATTTTTAG
* * * *
4602 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTTATAAGGAGGT
4624 TTATCAAAATTTTATAAGGAGGT
1 TTATCAAAATTTTATAAGGAGGT
4647 TTATCAAAATTTTAT-AGCGAGGT
1 TTATCAAAATTTTATAAG-GAGGT
4670 T
1 T
4671 ATAATCACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
22 20 0.49
23 21 0.51
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAAGGAGGT
Found at i:5932 original size:22 final size:23
Alignment explanation
Indices: 5877--5933 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
5867 TATAGTGTTT
*
5877 GTTATCAAAATTTCATTTGTGAA
1 GTTATCAAAATTTCATATGTGAA
*
5900 GTTATCAAAATTTCATAT-TGAG
1 GTTATCAAAATTTCATATGTGAA
5922 GTCT-TCAAAATT
1 GT-TATCAAAATT
5934 CCTTAGGGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (23 bp):
GTTATCAAAATTTCATATGTGAA
Found at i:9720 original size:28 final size:28
Alignment explanation
Indices: 9679--9732 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
9669 GTGGGGTCAC
*
9679 TTGACCCCATTGAAATGGTAAAATTGTT
1 TTGACCCCACTGAAATGGTAAAATTGTT
9707 TTGACCCCACTGAAATGGTAAAATTG
1 TTGACCCCACTGAAATGGTAAAATTG
9733 CTTATAGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (28 bp):
TTGACCCCACTGAAATGGTAAAATTGTT
Found at i:12759 original size:45 final size:45
Alignment explanation
Indices: 12708--12797 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
12698 TAATCCCCTG
12708 GCAATTTCAGATAGACATTAACATTTGTTATTATTGATTACTATT
1 GCAATTTCAGATAGACATTAACATTTGTTATTATTGATTACTATT
12753 GCAATTTCAGATAGACATTAACATTTGTTATTATTGATTACTATT
1 GCAATTTCAGATAGACATTAACATTTGTTATTATTGATTACTATT
12798 ACTACATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (45 bp):
GCAATTTCAGATAGACATTAACATTTGTTATTATTGATTACTATT
Done.