Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006102.1 Corchorus capsularis cultivar CVL-1 contig06120, 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: 1786
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Found at i:541 original size:159 final size:157
Alignment explanation
Indices: 256--760 Score: 643
Period size: 159 Copynumber: 3.2 Consensus size: 157
246 GATGAACTTT
* * *
256 TTGGATAGCCCTGTGCACAAACAAAGCTTTGCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGT
1 TTGGACAGCCCTGTGCACAAACAAAGCTTT-CTCGAAGTCCAAAACCTCAACTTTGAGCGGTTGT
* * * *
321 ATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCATATGCATTTTTTGGGCTACGAGTGCTCAA
65 ATGCAAAACATCATTTTTAGCGAAA-GCTCATTCTAGATGCATTTTTTGCGCAACGAGTGCTCAA
386 ATGTCGTGCGTCGAATTGCGATGAGATTG
129 ATGTCGTGCGTCGAATTGCGATGAGATTG
*
415 TTGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAACCTCAACTCTGAGCGGTTGT
1 TTGGACAGCCCTGTGCACAAACAAAGCTTT-CTCGAAGTCCAAAACCTCAACTTTGAGCGGTTGT
* *
480 ATGCAAAACATCATTTTTAGCGAAAGACTCATTCTAGATGCATTTTTTGCGCGACGTGTGCTCAA
65 ATGCAAAACATCATTTTTAGCGAAAG-CTCATTCTAGATGCATTTTTTGCGCAACGAGTGCTCAA
545 ATGTCGTGCGTCGAATTGCGATGAGATTG
129 ATGTCGTGCGTCGAATTGCGATGAGATTG
* * * * * *
574 TTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTG
1 TTGGACAGCCCTGTGCACAAACAAAGCTTTCTCGAAGTCCAAAACCTCAACTTTGAGCGGTTGTA
** * ** * * * * *
639 TGTTAAACTTTGTTCTTAGC-AAAGGTCTTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAA
66 TGCAAAACATCATTTTTAGCGAAAGCTCATTCTAGATGCATTTTTT-GCGCAACGAGTGCTCAAA
* * * * * *
703 AGTCGTGTGTCGGAGTGAGATGAGCTTG
130 TGTCGTGCGTCGAATTGCGATGAGATTG
* * *
731 TTAGACAGCGCTATGCACAAACAAAGCTTT
1 TTGGACAGCCCTGTGCACAAACAAAGCTTT
761 GCGTGTTTGT
Statistics
Matches: 306, Mismatches: 38, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
156 17 0.06
157 69 0.23
158 43 0.14
159 177 0.58
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (157 bp):
TTGGACAGCCCTGTGCACAAACAAAGCTTTCTCGAAGTCCAAAACCTCAACTTTGAGCGGTTGTA
TGCAAAACATCATTTTTAGCGAAAGCTCATTCTAGATGCATTTTTTGCGCAACGAGTGCTCAAAT
GTCGTGCGTCGAATTGCGATGAGATTG
Found at i:1088 original size:159 final size:160
Alignment explanation
Indices: 817--1216 Score: 394
Period size: 161 Copynumber: 2.5 Consensus size: 160
807 GATGAACTTT
* * * * * *
817 TTGGATAGCCCTGTGCACAATCAAAGCTTTCCTAGAAGCCCAAAGCCTCAACTTTGAGCGTTTGT
1 TTGGAAAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCCTCAACTTTCAGCATTTGT
* * * * *
882 GTGCAAAACATCGTTTTGAGGAACAGGCTCATTCCAGTTGCG-TTTTTTGCGCAATGAGTGCTCA
66 GTGCAAAACATCGTTTTGAGCAAAACGCTCATTCCAGATGCGATTTTTTGCGAAATGAGTGCTCA
** ** * * *
946 AATGTCATGTGTCGGAGTGAGTTGAGCATG
131 AAACTCATGTGTCAAAGTAAGATGAGCAAG
* * * *
976 TTGGAAAGCCCTGTGCACAAACAAAGATTTCCCCGAAGTCCAAAACCTCAACTTATCATCATTT-
1 TTGGAAAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCCTCAACTT-TCAGCATTTG
* ** * *
1040 TGTGCAAAACATCGTTCTT-AGCAAAACTCTTTTTCCGGATGCGATTTTTTTGTGAAATGAGTGC
65 TGTGCAAAACATCGTT-TTGAGCAAAACGCTCATTCCAGATGCGA-TTTTTTGCGAAATGAGTGC
* *
1104 TCAAAACTCGTTTGTCAAAGTAAGATGAGCAAG
128 TCAAAACTCATGTGTCAAAGTAAGATGAGCAAG
* * * * * * *
1137 ATGGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCTAAAGCATCAACTTTGC-GCATATG
1 TTGGAAAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCCTCAACTTT-CAGCATTTG
* *
1201 TATGCCAAACATCGTT
65 TGTGCAAAACATCGTT
1217 CTTAGCGGTT
Statistics
Matches: 193, Mismatches: 42, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
159 79 0.41
160 13 0.07
161 101 0.52
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (160 bp):
TTGGAAAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCCTCAACTTTCAGCATTTGT
GTGCAAAACATCGTTTTGAGCAAAACGCTCATTCCAGATGCGATTTTTTGCGAAATGAGTGCTCA
AAACTCATGTGTCAAAGTAAGATGAGCAAG
Found at i:1584 original size:158 final size:159
Alignment explanation
Indices: 1404--1781 Score: 431
Period size: 160 Copynumber: 2.4 Consensus size: 159
1394 TGCAATGAGA
* * *
1404 TTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCGTCAATTTTGCA-CAT
1 TTGTTGGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAATTTTGCATCA-
* * * * * *
1468 TTTTGTGCTAAACATAGTTCTTAGTAGAACTC-TTTCTGGATGC-CTTTTTTCGCACAACGAGAG
65 TTTTGTGCAAAACATAGTTCTTAGCAAAACTCTTTTCCGGATACGATTTTTT-GCACAACGAGAG
* **
1531 CTCAAAAGGCGTGTGTCGGAGTGAGATGAAC
129 CTCAAAAGGCGTGTCTCAAAGTGAGATGAAC
* * *
1562 TTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTAT-CATCA
1 TTGTTGGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAA-TTTTGCATCA
* ** * *
1626 TTTTGTGCAAAACATCGTTCTTAGCAAAACTCTTTTTCCGGATACGATTTTTTGTGCAATGAGTG
65 TTTTGTGCAAAACATAGTTCTTAGCAAAACTC-TTTTCCGGATACGATTTTTTGCACAACGAGAG
* * *
1691 CTCAAAAGTCGTTTCTCAAAGTGAGATGAGC
129 CTCAAAAGGCGTGTCTCAAAGTGAGATGAAC
** * * * *
1722 AAGATGGACAGCCCTATGAACAAACAGAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGC
1 TTGTTGGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAATTTTGC
1782 GCGTA
Statistics
Matches: 182, Mismatches: 32, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
158 79 0.43
159 7 0.04
160 90 0.49
161 6 0.03
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (159 bp):
TTGTTGGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAATTTTGCATCAT
TTTGTGCAAAACATAGTTCTTAGCAAAACTCTTTTCCGGATACGATTTTTTGCACAACGAGAGCT
CAAAAGGCGTGTCTCAAAGTGAGATGAAC
Done.