Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006610.1 Corchorus capsularis cultivar CVL-1 contig06631, 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, 850
Length: 1417
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Found at i:881 original size:427 final size:426
Alignment explanation
Indices: 1--1417 Score: 2455
Period size: 427 Copynumber: 3.3 Consensus size: 426
*
1 CGAAAGGCT-ATTCCAGATGCTTTTTTGCGCAATGAGTACTCAAATGTCGTGCGTCGAATTGCGA
1 CGAAAGGCTCATTCCAGATGCTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATTGCGA
* * *
65 TGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCGTCAATTTTGCA
66 TGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCG
* * *
130 CATTTTTGTGCTAAACATAGTTCTTAGCAGAACTCTTGT-TGGATGCGTTTTTTCGCGAAACTAG
131 CGTTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTT-TCTGGATGCGTTTTTTCGCGAAACGAG
194 TGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTACACACAAACAAAGCTC
195 TGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTACACACAAACAAAGCTC
259 TCCTCGAAGTCTAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCGTTCTTAGTGGTTTGTC
260 TCCTCGAAGTCTAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCGTTCTTAGTGGTTTGTC
* *
324 GGAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAAGCTTACCAAGATGCCCAAAACC
325 GGAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAAC-AAAGCTTTCCTAGATGCCCAAAACC
389 TCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAG
389 TCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAG
427 CGAAAGGCTCATTCCAGATGCTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATTGCGA
1 CGAAAGGCTCATTCCAGATGCTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATTGCGA
492 TGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCG
66 TGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCG
** * *
557 CGTTTTTGTGCTATTCATAGTTCTTAGCAAAACTCTTTCTGGATGCGCTTTTTCGCGCAACGAGT
131 CGTTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTGGATGCGTTTTTTCGCGAAACGAGT
* * **
622 GCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAAAGAGCGCTATGCACAAACAAAGCTCT
196 GCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTACACACAAACAAAGCTCT
* * *
687 CCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCG
261 CCTCGAAGTCTAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCGTTCTTAGTGGTTTGTCG
*
752 GAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTTCCTAGAAGCCCAAAACCTC
326 GAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTTCCTAGATGCCCAAAACCTC
817 AACTTTGAGCGGTTGTATGCAAAACATCATTTTTAG
391 AACTTTGAGCGGTTGTATGCAAAACATCATTTTTAG
*
853 CGAAAGGCTCATTCCAGATGCTTTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCG
1 CGAAAGGCTCATTCCAGATGC-TTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATTGCG
* * *
918 ATGACATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTGAAGAAGTCCAAAGCCTCAACTTTGC
65 ATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGC
* *
983 GCGTTTTTGTGTTAAACATAGTTCTTAGCAAAATTCTTTCTGGATGCGTTTTTTCGCGAAACGAG
130 GCGTTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTGGATGCGTTTTTTCGCGAAACGAG
*
1048 TGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTACACATAAACAAAGCTC
195 TGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTACACACAAACAAAGCTC
*
1113 TCCTCGAAGTCTAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCGTTTTTAGTGGTTTGTC
260 TCCTCGAAGTCTAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCGTTCTTAGTGGTTTGTC
* * *
1178 GGAGTGAGATGAACTTTTTTGACAGCCCTGTGCAGCAACAAAGATTTCCTAGATGCCCAAAACCT
325 GGAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTTCCTAGATGCCCAAAACCT
*
1243 CAAGTTTGA-CGGTTGTATGCAAAACATCATTTTTAG
390 CAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAG
* *
1279 CGAAACGCTCATTCCAGATGCTTTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCG
1 CGAAAGGCTCATTCCAGATGC-TTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATTGCG
1344 ATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAG-CTCAACTTTGC
65 ATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGC
1408 GCGTTTTTGT
130 GCGTTTTTGT
Statistics
Matches: 939, Mismatches: 49, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
425 21 0.02
426 232 0.25
427 686 0.73
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (426 bp):
CGAAAGGCTCATTCCAGATGCTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATTGCGA
TGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCG
CGTTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTGGATGCGTTTTTTCGCGAAACGAGT
GCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTACACACAAACAAAGCTCT
CCTCGAAGTCTAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCGTTCTTAGTGGTTTGTCG
GAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTTCCTAGATGCCCAAAACCTC
AACTTTGAGCGGTTGTATGCAAAACATCATTTTTAG
Found at i:979 original size:269 final size:268
Alignment explanation
Indices: 500--988 Score: 594
Period size: 269 Copynumber: 1.8 Consensus size: 268
490 GATGAGATTG
* * * * * *
500 TTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTG
1 TTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGCCCAAAACCTCAACTTTGAGCGGTTGTA
* ** * **
565 TGCTATTCATAGTTCTTAGCAAAACTCTTTCTGGATGCGCTTTTTCGCGCAACGAGTGCTCAAAA
66 TGCAAAACATAGTTCTTAGCAAAACTCATTCCAGATGCGCTTTTTCGCGCAACGAGTGCTCAAAA
* * * **
630 GTCGTGTGTCGGAATGAGATGAGCTTGTTAAAGAGCGCTATGCACAAACAAAGCTCTCCTCGAAG
131 GTCGTGCGTCGGAATGAGATGAGCTTGTTAAACAGCCCTATGCACAAACAAAGCTCTCCAAGAAG
695 TCCAAAGCATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGA
196 TCCAAAGCATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGA
760 TGAACTTT
261 TGAACTTT
*
768 TTGGACAGCCCTGTGCAGAAACAAAGCTTTC-CTAGAAGCCCAAAACCTCAACTTTGAGCGGTTG
1 TTGGACAGCCCTGTGCACAAACAAAGCTTTCAC--GAAGCCCAAAACCTCAACTTTGAGCGGTTG
* * * *
832 TATGCAAAACATCA-TTTTTAGCGAAAGGCTCATTCCAGATGC-TTTTTTTGCGCAACGAGTGCT
64 TATGCAAAACAT-AGTTCTTAGC-AAA-ACTCATTCCAGATGCGCTTTTTCGCGCAACGAGTGCT
* * ** * *
895 CAAATGTCGTGCGTC-GAATTGCGATGA-CATTGTTGGACAGCCCTGTGCACAAACAAAGCT-TT
126 CAAAAGTCGTGCGTCGGAA-TGAGATGAGC-TTGTTAAACAGCCCTATGCACAAACAAAGCTCTC
* * *
957 GAAGAAGTCCAAAGCCTCAACTTTGCGCGTTT
189 CAAGAAGTCCAAAGCATCAACTTTGCGAGTTT
989 TTGTGTTAAA
Statistics
Matches: 183, Mismatches: 31, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
267 1 0.01
268 30 0.16
269 72 0.39
270 69 0.38
271 11 0.06
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (268 bp):
TTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGCCCAAAACCTCAACTTTGAGCGGTTGTA
TGCAAAACATAGTTCTTAGCAAAACTCATTCCAGATGCGCTTTTTCGCGCAACGAGTGCTCAAAA
GTCGTGCGTCGGAATGAGATGAGCTTGTTAAACAGCCCTATGCACAAACAAAGCTCTCCAAGAAG
TCCAAAGCATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGA
TGAACTTT
Found at i:1091 original size:157 final size:158
Alignment explanation
Indices: 747--1092 Score: 378
Period size: 157 Copynumber: 2.2 Consensus size: 158
737 CTTAGCGGTT
* * * *
747 TGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTTCCTAGAAGCCCAAA
1 TGTCGGAATGAGATG-ACTTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCAAGAAGCCCAAA
* *
812 ACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCTTT
65 ACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTCTTAGCGAAAGACTCATTCCAGATGCTTT
* * *
877 TTTTGCGCAACGAGTGCTCAAATGTCGTG
130 TTTCGCGAAACGAGTGCTCAAAAGTCGTG
* * * *
906 CGTC-GAATTGCGATGACATTGTTGGACAGCCCTGTGCACAAACAAAGCTTT-GAAGAAGTCCAA
1 TGTCGGAA-TGAGATGAC-TTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCAAGAAGCCCAA
* * * * * ** * * **
969 AGCCTCAACTTTGCGCGTTTTTGTGTTAAACAT-AGTTCTTAGC-AAA-ATTCTTTCTGGATGCG
64 AACCTCAACTTTGAGCGGTTGTATGCAAAACATCA-TTCTTAGCGAAAGACTCATTCCAGATGC-
1031 TTTTTTCGCGAAACGAGTGCTCAAAAGTCGTG
127 TTTTTTCGCGAAACGAGTGCTCAAAAGTCGTG
*
1063 TGTCGGAATGAGATGAGCTTGTTAGACAGC
1 TGTCGGAATGAGATGA-CTTGTTGGACAGC
1093 GCTACACATA
Statistics
Matches: 154, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
156 10 0.06
157 54 0.35
158 50 0.32
159 40 0.26
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (158 bp):
TGTCGGAATGAGATGACTTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCAAGAAGCCCAAAA
CCTCAACTTTGAGCGGTTGTATGCAAAACATCATTCTTAGCGAAAGACTCATTCCAGATGCTTTT
TTCGCGAAACGAGTGCTCAAAAGTCGTG
Done.