Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014597.1 Corchorus capsularis cultivar CVL-1 contig14618, 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: 28845
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:3435 original size:203 final size:203
Alignment explanation
Indices: 3085--3477 Score: 741
Period size: 203 Copynumber: 1.9 Consensus size: 203
3075 AGTTGAGATG
3085 AGAAAGGGTATACCCCCAGTTTCCAAGTAAATAAATCAAGGAAAAATGAATATGGGAGGAACTGA
1 AGAAAGGGTATACCCCCAGTTTCCAAGTAAATAAATCAAGGAAAAATGAATATGGGAGGAACTGA
3150 ACCTATAGAGAAAGGATAAGGTTTGAAGTCATGATTACCTTCATTTAGTCGAGGTTTAGGGGACC
66 ACCTATAGAGAAAGGATAAGGTTTGAAGTCATGATTACCTTCATTTAGTCGAGGTTTAGGGGACC
*
3215 TTGTTTCTCTTTCATTGCTTTCATTCTCAGAATGTTGATTTTGGTTATGTGAGCATGGTACCCTT
131 TTGTTTCTCTGTCATTGCTTTCATTCTCAGAATGTTGATTTTGGTTATGTGAGCATGGTACCCTT
3280 TCATTCTC
196 TCATTCTC
*
3288 AGAAAGGGTATACGCCCAGTTTCCAAGTAAATAAATCAAGGAAAAATGAATATGGGAGGAACTGA
1 AGAAAGGGTATACCCCCAGTTTCCAAGTAAATAAATCAAGGAAAAATGAATATGGGAGGAACTGA
* **
3353 ACCTATAGAGAAAGGATAAGGTTTGAGGTCATGATTACCTTTGTTTAGTCGAGGTTTAGGGGACC
66 ACCTATAGAGAAAGGATAAGGTTTGAAGTCATGATTACCTTCATTTAGTCGAGGTTTAGGGGACC
3418 TTGTTTCTCTGTCATTGCTTTCATTCTCAGAATGTTGATTTTGGTTATGTGAGCATGGTA
131 TTGTTTCTCTGTCATTGCTTTCATTCTCAGAATGTTGATTTTGGTTATGTGAGCATGGTA
3478 TCTCCACAAA
Statistics
Matches: 185, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
203 185 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (203 bp):
AGAAAGGGTATACCCCCAGTTTCCAAGTAAATAAATCAAGGAAAAATGAATATGGGAGGAACTGA
ACCTATAGAGAAAGGATAAGGTTTGAAGTCATGATTACCTTCATTTAGTCGAGGTTTAGGGGACC
TTGTTTCTCTGTCATTGCTTTCATTCTCAGAATGTTGATTTTGGTTATGTGAGCATGGTACCCTT
TCATTCTC
Found at i:3562 original size:1 final size:1
Alignment explanation
Indices: 3556--3585 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3546 TCTTCTCTTC
3556 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3586 GTCCTTCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15732 original size:39 final size:39
Alignment explanation
Indices: 15689--15772 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
15679 TTTTTCTCCG
15689 GTTATTACTGTTCTTGTTTAGCTGTTTGGGTGATATGAT
1 GTTATTACTGTTCTTGTTTAGCTGTTTGGGTGATATGAT
15728 GTTATTACTGTTCTTGTTTAGCTGTTTGGGTGATATGAT
1 GTTATTACTGTTCTTGTTTAGCTGTTTGGGTGATATGAT
*
15767 TTTATT
1 GTTATT
15773 TGTTTAGTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.15, C:0.07, G:0.24, T:0.54
Consensus pattern (39 bp):
GTTATTACTGTTCTTGTTTAGCTGTTTGGGTGATATGAT
Found at i:21014 original size:31 final size:30
Alignment explanation
Indices: 20911--21016 Score: 85
Period size: 31 Copynumber: 3.5 Consensus size: 30
20901 TGTCTAATAT
**
20911 CCAATTTGGGTCTAAACCTTTTTCAACTTGC-
1 CCAATTTGGGTCTAAACC--TTTCAAAATGCA
* * *
20942 TCAATTTGAGG-CTAAACCTTT--AGATGAA
1 CCAATTTG-GGTCTAAACCTTTCAAAATGCA
* *
20970 CCAAATTGAGTCTAAACCTTATCAAAATGCA
1 CCAATTTGGGTCTAAACCTT-TCAAAATGCA
21001 CCAATTTGGGTCTAAA
1 CCAATTTGGGTCTAAA
21017 TTTGACAAGA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
27 4 0.07
28 15 0.26
29 4 0.07
31 33 0.57
32 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (30 bp):
CCAATTTGGGTCTAAACCTTTCAAAATGCA
Found at i:21198 original size:64 final size:64
Alignment explanation
Indices: 21097--21224 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
21087 GTTTAAACGG
* *
21097 TGCTTATATAAGTGAAAATTACTTAAAGTCACTGTAAGGAAACCATTCTAGTGATACAAAGCCA
1 TGCTTATATAAGTGAAAATTACTTAAAGCCACTGTAAGGAAACCATTCTAGTGATAAAAAGCCA
21161 TGCTTATATAAGTGAAAATTACTTAAAGCCACTGTAAGGAAACCATTCTAGTGATAAAAAGCCA
1 TGCTTATATAAGTGAAAATTACTTAAAGCCACTGTAAGGAAACCATTCTAGTGATAAAAAGCCA
21225 ACCAATTACA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (64 bp):
TGCTTATATAAGTGAAAATTACTTAAAGCCACTGTAAGGAAACCATTCTAGTGATAAAAAGCCA
Found at i:27692 original size:16 final size:16
Alignment explanation
Indices: 27671--27704 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
27661 TAATGACCAA
27671 TGAAATTTGAACCCAG
1 TGAAATTTGAACCCAG
27687 TGAAATTTGAACCCAG
1 TGAAATTTGAACCCAG
27703 TG
1 TG
27705 TTACGTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (16 bp):
TGAAATTTGAACCCAG
Found at i:27753 original size:2 final size:2
Alignment explanation
Indices: 27748--27798 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
27738 TACATACATT
* * * * *
27748 TA TA TA TA CA TA TA TA TA TA TA TG TA TG TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27790 TA TA TA TA T
1 TA TA TA TA T
27799 GAAAAATTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27758 original size:16 final size:16
Alignment explanation
Indices: 27737--27770 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27727 CACACACACC
*
27737 ATACATACATTTATAT
1 ATACATACATATATAT
*
27753 ATACATATATATATAT
1 ATACATACATATATAT
27769 AT
1 AT
27771 GTATGTATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
ATACATACATATATAT
Done.