Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011523.1 Corchorus capsularis cultivar CVL-1 contig11544, 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: 52151
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:12107 original size:21 final size:22
Alignment explanation
Indices: 12081--12124 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
12071 GATCGGTGCT
12081 GAAAAGAGCAAC-AAAAGCTTG
1 GAAAAGAGCAACAAAAAGCTTG
12102 GAAAAGAGCAACAAAAAGCTTG
1 GAAAAGAGCAACAAAAAGCTTG
12124 G
1 G
12125 TTTGGTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.52, C:0.14, G:0.25, T:0.09
Consensus pattern (22 bp):
GAAAAGAGCAACAAAAAGCTTG
Found at i:16321 original size:18 final size:18
Alignment explanation
Indices: 16298--16339 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16288 TGGAGAGGCT
16298 TAAGGTACAATTGAAAAA
1 TAAGGTACAATTGAAAAA
* *
16316 TAAGGTATAGTTGAAAAA
1 TAAGGTACAATTGAAAAA
*
16334 TTAGGT
1 TAAGGT
16340 GGAGGAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.21, T:0.29
Consensus pattern (18 bp):
TAAGGTACAATTGAAAAA
Found at i:20096 original size:213 final size:214
Alignment explanation
Indices: 19615--20150 Score: 844
Period size: 213 Copynumber: 2.5 Consensus size: 214
19605 AAACCTGTTG
19615 TAAAGTGGTAATATCCCACATCGGTTATGTTTGACATGACTGGGTGCGTTATATACATGAAAGGC
1 TAAAGTGGTAATATCCCACATCGGTTATGTTTGACATGACTGGGTGC-TTATATACATGAAAGGC
* *
19680 CTCTCCACCTATTGCAAATTGGTTTTAGGTTGGACGCTTAACATGGTATCAGAGCTCAAGTCTGT
65 CTCTCCACCTATTGCCAATTGGTTTTAGGTTGGACGCTTAACATGGTATCAGAGCTCAAGTCCGT
*
19745 CCTGTTGCGCCCCAGACCCGGTTGTGTCCACGTGTAGGCCCGTTCTGTTTCGGTGTTGTCCTAGG
130 CCTGTTGCGCCCCAGACCCGGTTGTGTCCACGTGTAGGCCCGTTCTGTTTCGGTGTTGTCCCAGG
19810 CTACACGTGAGGGGGCGTGT
195 CTACACGTGAGGGGGCGTGT
* * * * *
19830 TAGAGTGGTAATATCCCACATTGGTTATGTTTGACATGACTGGGTGCCTTATATAGATGAAGGGT
1 TAAAGTGGTAATATCCCACATCGGTTATGTTTGACATGACTGGGTG-CTTATATACATGAAAGGC
* * * * *
19895 CTCTCCACCTATAGCCAATTGGTTTTTGGTTGGA-TCTGTGACATGGTATCAGAGCTCAGGTCCG
65 CTCTCCACCTATTGCCAATTGGTTTTAGGTTGGACGCT-TAACATGGTATCAGAGCTCAAGTCCG
* * * *
19959 TCCTGTTGCGCCCCATACTCGG-T-TGTCCACGTGTAGGCCCGTTCTGTTTCGGTGTTTTCCCGG
129 TCCTGTTGCGCCCCAGACCCGGTTGTGTCCACGTGTAGGCCCGTTCTGTTTCGGTGTTGTCCCAG
*
20022 GCTACACGTGAGGGGGTGTGT
194 GCTACACGTGAGGGGGCGTGT
*
20043 TAAAGTGGTAATATCCCACATCGGCTATGTTTGACATGACTGGGTGTCTTATATACATGAAAGGC
1 TAAAGTGGTAATATCCCACATCGGTTATGTTTGACATGACTGGGTG-CTTATATACATGAAAGGC
20108 CTCTCCACCTATTGCCAATTGGTTTTAGGTTGGACGCTTAACA
65 CTCTCCACCTATTGCCAATTGGTTTTAGGTTGGACGCTTAACA
20151 CCTGCAATGA
Statistics
Matches: 289, Mismatches: 29, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
213 151 0.52
214 5 0.02
215 132 0.46
216 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.32
Consensus pattern (214 bp):
TAAAGTGGTAATATCCCACATCGGTTATGTTTGACATGACTGGGTGCTTATATACATGAAAGGCC
TCTCCACCTATTGCCAATTGGTTTTAGGTTGGACGCTTAACATGGTATCAGAGCTCAAGTCCGTC
CTGTTGCGCCCCAGACCCGGTTGTGTCCACGTGTAGGCCCGTTCTGTTTCGGTGTTGTCCCAGGC
TACACGTGAGGGGGCGTGT
Found at i:22789 original size:15 final size:14
Alignment explanation
Indices: 22752--22790 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
22742 TAGGTTTCTA
22752 TAGGAGAGTGATTC
1 TAGGAGAGTGATTC
*
22766 TTGGGAGAGTGATTC
1 -TAGGAGAGTGATTC
22781 TAGGTAGAGT
1 TAGG-AGAGT
22791 AACTCTAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.26, C:0.05, G:0.38, T:0.31
Consensus pattern (14 bp):
TAGGAGAGTGATTC
Found at i:23702 original size:36 final size:36
Alignment explanation
Indices: 23655--23799 Score: 263
Period size: 36 Copynumber: 4.0 Consensus size: 36
23645 ATATCTCTCG
23655 CAAGGAGAGAGATGAGTCTCCACCAAGTTTGCCTCC
1 CAAGGAGAGAGATGAGTCTCCACCAAGTTTGCCTCC
* *
23691 CAAGGAGAGAGATGAGCCTCCACCAAGTTCGCCTCC
1 CAAGGAGAGAGATGAGTCTCCACCAAGTTTGCCTCC
*
23727 CAAGGAGAGAGATGAATCTCCACCAAGTTTGCCTCC
1 CAAGGAGAGAGATGAGTCTCCACCAAGTTTGCCTCC
23763 CAAGGAGAGAGATGAGTCTCCACCAAGTTTGCCTCC
1 CAAGGAGAGAGATGAGTCTCCACCAAGTTTGCCTCC
23799 C
1 C
23800 GCAAAGAGTA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 103 1.00
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (36 bp):
CAAGGAGAGAGATGAGTCTCCACCAAGTTTGCCTCC
Found at i:24574 original size:63 final size:63
Alignment explanation
Indices: 24463--24593 Score: 199
Period size: 63 Copynumber: 2.1 Consensus size: 63
24453 CCGAGACACA
* * * *
24463 TGAAGAGGCTTTCAACAACTATGTCATGAAATTGCAGGATGCGGTAGAAAATGGAAATGTTGG
1 TGAAGAGGATTTCAACAACTATGCCATGAAAGTGCAGGATGCGATAGAAAATGGAAATGTTGG
* * *
24526 TGAAGAGGATTTCATCAACTATGCCATGAAAGTGCTGGCTGCGATAGAAAATGGAAATGTTGG
1 TGAAGAGGATTTCAACAACTATGCCATGAAAGTGCAGGATGCGATAGAAAATGGAAATGTTGG
24589 TGAAG
1 TGAAG
24594 GAGTAACTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.25
Consensus pattern (63 bp):
TGAAGAGGATTTCAACAACTATGCCATGAAAGTGCAGGATGCGATAGAAAATGGAAATGTTGG
Found at i:33364 original size:90 final size:90
Alignment explanation
Indices: 33249--33491 Score: 297
Period size: 90 Copynumber: 2.7 Consensus size: 90
33239 GATGATTTTA
* ** * * *
33249 CATAGACCTTTAACATTGAAAGTTGCGGCAAAAATAGAACGAGTCCAGTTTTTGCCTTTGGTTTG
1 CATAGACATTTAATGTTGAAAGTTGCGGCAAAAATAGAACGAGTCCAGTTTCTGCCTTGGGTTCG
* *
33314 AACTTCAAGGTCGGAAACTATTTGG
66 AACTTCAAGGGCGGAAACGATTTGG
* * * *
33339 CTTAGACATTTAATGTTGAATGTTGCGGCTAAAATAGAACGAGTCTAGTTTCTGCCTTGGGTTCG
1 CATAGACATTTAATGTTGAAAGTTGCGGCAAAAATAGAACGAGTCCAGTTTCTGCCTTGGGTTCG
*
33404 AACTTCAAGGGCGGAAACGATTTTG
66 AACTTCAAGGGCGGAAACGATTTGG
* * * * * * *
33429 CATGGACCTTTTATGGTAAAAGTTGCGGCATAAAATGGAACGAGTCCAGTTTCTACCTTGGGT
1 CATAGACATTTAATGTTGAAAGTTGCGGCA-AAAATAGAACGAGTCCAGTTTCTGCCTTGGGT
33492 GAGTTTGCAT
Statistics
Matches: 128, Mismatches: 24, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
90 99 0.77
91 29 0.23
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (90 bp):
CATAGACATTTAATGTTGAAAGTTGCGGCAAAAATAGAACGAGTCCAGTTTCTGCCTTGGGTTCG
AACTTCAAGGGCGGAAACGATTTGG
Found at i:33540 original size:70 final size:70
Alignment explanation
Indices: 33425--33561 Score: 204
Period size: 70 Copynumber: 2.0 Consensus size: 70
33415 CGGAAACGAT
* * *
33425 TTTGCATGGACCTTTTATGGTAAAAGTTGCGGCATAAAATGGAACGAGTCCAGTTTCT-ACCTTG
1 TTTGCATAGACCTTTTATGGTAAAAGTTGCGGCATAAAATAGAACGAGTCCACTTTCTGA-CTTG
33489 GGTGAG
65 GGTGAG
* **
33495 TTTGCATAGACCTTTTATGTTAAAAGTTTTGGCATAAAATAGAACGAGTCCACTTTCTGACTTGG
1 TTTGCATAGACCTTTTATGGTAAAAGTTGCGGCATAAAATAGAACGAGTCCACTTTCTGACTTGG
33560 GT
66 GT
33562 TCGAACTTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 59 0.98
71 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (70 bp):
TTTGCATAGACCTTTTATGGTAAAAGTTGCGGCATAAAATAGAACGAGTCCACTTTCTGACTTGG
GTGAG
Found at i:37643 original size:38 final size:39
Alignment explanation
Indices: 37566--37641 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
37556 CGGATGTAAG
*
37566 TGAAGTATTTTTTTTTCCTTCTTACTTTTTCTTTTTTTA
1 TGAAGTATTTTTTTTCCCTTCTTACTTTTTCTTTTTTTA
*
37605 TGAAGTATTTTTTTTCCCTTCTTGCTTTTTCTTTTTT
1 TGAAGTATTTTTTTTCCCTTCTTACTTTTTCTTTTTT
37642 ATTTCAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.11, C:0.14, G:0.07, T:0.68
Consensus pattern (39 bp):
TGAAGTATTTTTTTTCCCTTCTTACTTTTTCTTTTTTTA
Found at i:37792 original size:15 final size:15
Alignment explanation
Indices: 37772--37801 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
37762 TTTTGACATC
37772 CATTATAAGTATGGA
1 CATTATAAGTATGGA
37787 CATTATAAGTATGGA
1 CATTATAAGTATGGA
37802 GAGGGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (15 bp):
CATTATAAGTATGGA
Found at i:39918 original size:29 final size:29
Alignment explanation
Indices: 39886--39945 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
39876 ATTTATTTTC
*
39886 ATGAGACTTGTTTTTGGTTATAATTGGAA
1 ATGAGACTTGTTTTTGATTATAATTGGAA
39915 ATGAGACTTGTTTTTGATTATAATTGGAA
1 ATGAGACTTGTTTTTGATTATAATTGGAA
39944 AT
1 AT
39946 TATATTATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.45
Consensus pattern (29 bp):
ATGAGACTTGTTTTTGATTATAATTGGAA
Found at i:40907 original size:87 final size:86
Alignment explanation
Indices: 40794--41008 Score: 229
Period size: 87 Copynumber: 2.5 Consensus size: 86
40784 GAGTCAGGCA
* * * *
40794 CAAAAATCCTCCACCAAATCAGTTTCCAAAGATTTTGCATCATTACTAACTAAAACTCCATTAGG
1 CAAAAATCCTCCACCAAATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGG
40859 AAGATCACTGAAATTTGAATT
66 AAGATCACTGAAATTTGAATT
* * * *
40880 CAAAATATCCTCTACCATAAT-ATTTTCCAAAGATTTTGCACCATAACCACCCATAACTCCATTA
1 CAAAA-ATCCTCCACCA-AATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTA
*
40944 GGAAGATCAC--AATCAATTGAATT
64 GGAAGATCACTGAA--ATTTGAATT
* * ** * *
40967 CAAATTATTCTCCACCCTATCAGTTTCCATAGAATTTGCACC
1 CAAA-AATCCTCCACCAAATCAGTTTCCAAAGATTTTGCACC
41009 TAAAAATCCT
Statistics
Matches: 106, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
85 2 0.02
86 7 0.07
87 94 0.89
88 3 0.03
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (86 bp):
CAAAAATCCTCCACCAAATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGG
AAGATCACTGAAATTTGAATT
Done.