Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011265.1 Corchorus capsularis cultivar CVL-1 contig11286, 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: 2884
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:368 original size:22 final size:23
Alignment explanation
Indices: 340--385 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
330 TACGCTTGAG
*
340 GTTTCAAAAAAAAAA-AGGAAAA
1 GTTTCAAAAAAAAAAGAGAAAAA
362 GTTTCAAAAAAAAAAGAGAAAAA
1 GTTTCAAAAAAAAAAGAGAAAAA
385 G
1 G
386 GGAGGGGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.67, C:0.04, G:0.15, T:0.13
Consensus pattern (23 bp):
GTTTCAAAAAAAAAAGAGAAAAA
Found at i:372 original size:21 final size:23
Alignment explanation
Indices: 340--383 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
330 TACGCTTGAG
340 GTTTCAAAAAAAAAAAG-GAAAA
1 GTTTCAAAAAAAAAAAGAGAAAA
362 GTTTC-AAAAAAAAAAGAGAAAA
1 GTTTCAAAAAAAAAAAGAGAAAA
384 AGGGAGGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.68, C:0.05, G:0.14, T:0.14
Consensus pattern (23 bp):
GTTTCAAAAAAAAAAAGAGAAAA
Found at i:1281 original size:35 final size:35
Alignment explanation
Indices: 1242--1526 Score: 430
Period size: 35 Copynumber: 8.1 Consensus size: 35
1232 TCCAGTGCGG
1242 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
1277 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
1312 TCATTGCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
1347 TCATTCCAAGGAGTTTTTAGAGGTCAGAGTTGATC
1 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
1382 TCATTCCAAGCAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
1417 TCATTCCAAGCAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
1452 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* * * *
1487 ACATGTTC-AGAAGTTTCCA-ACGATCAGAGTTGATC
1 TCAT-TCCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
*
1522 GCATT
1 TCATT
1527 TTCAGTAGTT
Statistics
Matches: 235, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
34 2 0.01
35 230 0.98
36 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (35 bp):
TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
Found at i:1527 original size:70 final size:69
Alignment explanation
Indices: 1242--1766 Score: 439
Period size: 70 Copynumber: 7.5 Consensus size: 69
1232 TCCAGTGCGG
* * * * *
1242 TCATTCCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAG
1 TCATTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCATTTC-AGTAGTTTCCA-AGATCAGAG
1306 TTGATC
64 TTGATC
* * * * ** *
1312 TCATTGCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCATTCCAAGGAGTTTTTAGAGGTCAGAG
1 TCATTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCATTTC-AGTAGTTTCCA-AGATCAGAG
1376 TTGATC
64 TTGATC
* * * * * * *
1382 TCATTCCAAGCAGTTTTCAGA-GGTCAGAGTTGATCTCATTCCAAGCAGTTTTCAGAGGTCAGAG
1 TCATTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCATTTC-AGTAGTTTCCA-AGATCAGAG
1446 TTGATC
64 TTGATC
* * *
1452 TCATTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCACATGTTCAGAAGTTTCCAACGATCAGAG
1 TCATTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCAT-TTCAGTAGTTTCCAA-GATCAGAG
1516 TTGATC
64 TTGATC
* * * * *
1522 GCATTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACAATCAGA
1 TCA-TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA-TTTCAGTAGTTTCCAA-GATCAGA
1585 GTTGATC
63 GTTGATC
* * *
1592 GCATTTTC-AGTA-TTTTGCA-ACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGATCAG
1 TCA-TTTCAAGAAGTTTT-CAGACGATCAGAGTTGATCTCA-TTTCAGTAGTTTCCAA-GATCAG
1654 AGTTGATC
62 AGTTGATC
* * * *
1662 ACATTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATCACATTTTCAGTAGTTTCCTATA-ATCAG
1 TCA-TTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCA-TTTCAGTAGTTTCC-A-AGATCAG
1724 A-TGTGATC
62 AGT-TGATC
* * *
1732 TCATTTCAAGAA-ATTTCCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGACGATCAGAGTTGATC
1767 CAGAGGAGTT
Statistics
Matches: 410, Mismatches: 33, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
69 13 0.03
70 385 0.94
71 11 0.03
72 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (69 bp):
TCATTTCAAGAAGTTTTCAGACGATCAGAGTTGATCTCATTTCAGTAGTTTCCAAGATCAGAGTT
GATC
Found at i:1531 original size:35 final size:35
Alignment explanation
Indices: 1440--1766 Score: 410
Period size: 35 Copynumber: 9.3 Consensus size: 35
1430 TTTTCAGAGG
* * * *
1440 TCAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GG
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCA-ACGA
* * *
1475 TCAGAGTTGATCACATGTTCAGAAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1510 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
1545 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACAA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* *
1580 TCAGAGTTGATCGCATTTTCAGTATTTTGCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1615 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
1650 TCAGAGTTGATCACATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * **
1685 TCAGAGTTGATCACATTTTCAGTAGTTTCCTATAA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * * * *
1720 TCAGA-TGTGATCTCA-TTTCAAGAAATTTCCGATGA
1 TCAGAGT-TGATCGCATTTTC-AGTAGTTTCCAACGA
1755 TCAGAGTTGATC
1 TCAGAGTTGATC
1767 CAGAGGAGTT
Statistics
Matches: 265, Mismatches: 22, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
34 6 0.02
35 255 0.96
36 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (35 bp):
TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
Found at i:1537 original size:105 final size:104
Alignment explanation
Indices: 1242--1766 Score: 435
Period size: 105 Copynumber: 5.0 Consensus size: 104
1232 TCCAGTGCGG
* * * *
1242 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGT
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCACATTTC-AGAAGTTTCCAGAGATCAGAGT
* * * * *
1307 TGATCTCATTGCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
65 TGATCGCATTTCAAGTAGTTTCCA-ACGATCAGAGTTGATC
* * * * * * * *
1347 TCATTCCAAGGAGTTTTTAGAGGTCAGAGTTGATCTCATTCCAAGCAGTTTTCAGAGGTCAGAGT
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCACATTTC-AGAAGTTTCCAGAGATCAGAGT
* * * * *
1412 TGATCTCATTCCAAGCAGTTTTCAGA-GGTCAGAGTTGATC
65 TGATCGCATTTCAAGTAGTTTCCA-ACGATCAGAGTTGATC
1452 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCACATGTTCAGAAGTTTCCA-ACGATCAGAG
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCACAT-TTCAGAAGTTTCCAGA-GATCAGAG
1516 TTGATCGCATTTTC-AGTAGTTTCCAACGATCAGAGTTGATC
64 TTGATCGCA-TTTCAAGTAGTTTCCAACGATCAGAGTTGATC
* * * ** * * * *
1557 GCATTTTC-AGTAGTTTCCA-ACAATCAGAGTTGATCGCATTTTCAGTATTTTGCA-ACGATCAG
1 TCA-TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCACA-TTTCAGAAGTTTCCAGA-GATCAG
1619 AGTTGATCGCATTTTC-AGTAGTTTCCAACGATCAGAGTTGATC
62 AGTTGATCGCA-TTTCAAGTAGTTTCCAACGATCAGAGTTGATC
* * * * * *
1662 ACATTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATCACATTTTCAGTAGTTTCCTATA-ATCAG
1 TCA-TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCACA-TTTCAGAAGTTTCC-AGAGATCAG
* * * * *
1724 A-TGTGATCTCATTTCAAGAAATTTCCGATGATCAGAGTTGATC
62 AGT-TGATCGCATTTCAAGTAGTTTCCAACGATCAGAGTTGATC
1767 CAGAGGAGTT
Statistics
Matches: 371, Mismatches: 38, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
104 8 0.02
105 351 0.95
106 11 0.03
107 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (104 bp):
TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCACATTTCAGAAGTTTCCAGAGATCAGAGTT
GATCGCATTTCAAGTAGTTTCCAACGATCAGAGTTGATC
Done.