Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005734.1 Corchorus capsularis cultivar CVL-1 contig05752, 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: 2405
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.40
Found at i:452 original size:44 final size:43
Alignment explanation
Indices: 284--737 Score: 521
Period size: 44 Copynumber: 10.4 Consensus size: 43
274 GGCTGACCAC
* * * *
284 CTAGTTCTTGTCTTCTTGGTTTGATTGTGGTGTGGTCGATCGA
1 CTAGTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGA
* * * * *
327 CTTGTTGTTTACTTCTTGCTTTGAGTGTGATGTGGTCTATCGA
1 CTAGTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGA
* * * * * * *
370 CTTGTTGTTTACTTCTTGCTTTGAGTGTAATGTAGTCGATTGA
1 CTAGTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGA
*
413 CTTGTTCTTGTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGA
1 CTAGTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGA
*
457 CTAGTTACTTCTCTTCTTGCTTTGAATGTGATGTGGTCGATCGA
1 CTAGTT-CTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGA
** **
501 CCGGTTCTTTTCTTCTCACTTCTGAATGTGATGTGGTCGATCGA
1 CTAGTTCTTTTCTTCTTGCTT-TGAATGTGATGTGGTCGATCGA
* *
545 CTAGTTATTTCTCTTCTTGGTTTGAATGTGATGTGGTCGATCGA
1 CTAGTTCTTT-TCTTCTTGCTTTGAATGTGATGTGGTCGATCGA
* *
589 CTAGTTACTTCTCTTCTTGCTTTGAATGTGATGTGGTCGATTGA
1 CTAGTT-CTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGA
** ** *
633 CCGGTTCTTTTCTTCTCACTTTTGAATCTGATGTGGTCGATCGA
1 CTAGTTCTTTTCTTCTTGC-TTTGAATGTGATGTGGTCGATCGA
* * *
677 CTAGTTACTTCTCTTCTTGGTTTAAATGTGATGTGGTCGATCGA
1 CTAGTT-CTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGA
**
721 CCGGTTCTTTTCTTCTT
1 CTAGTTCTTTTCTTCTT
738 TGTTTAGATT
Statistics
Matches: 351, Mismatches: 53, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
43 114 0.32
44 215 0.61
45 22 0.06
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.46
Consensus pattern (43 bp):
CTAGTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGA
Found at i:586 original size:132 final size:131
Alignment explanation
Indices: 294--721 Score: 592
Period size: 132 Copynumber: 3.3 Consensus size: 131
284 CTAGTTCTTG
* * * * *
294 TCTTCTTGGTTTGATTGTGGTGTGGTCGATCGACTTGTT-GTT-TACTTCTTGCTTTGAGTGTGA
1 TCTTCTTGGTTTGAATGTGATGTGGTCGATCGACTAGTTACTTCT-CTTCTTGCTTTGAATGTGA
* ** * * ** * * * * * *
357 TGTGGTCTATCGACTTGTTGTTTACTTCTTGCTTTGAGTGTAATGTAGTCGATTGACTTGTTCTT
65 TGTGGTCGATCGACCGGTTCTTTTCTTCTCACTTTGAATGTGATGTGGTCGATCGACTAGTTATT
422 GT-
130 -TC
*
424 TCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTAGTTACTTCTCTTCTTGCTTTGAATGTGAT
1 TCTTCTTGGTTTGAATGTGATGTGGTCGATCGACTAGTTACTTCTCTTCTTGCTTTGAATGTGAT
489 GTGGTCGATCGACCGGTTCTTTTCTTCTCACTTCTGAATGTGATGTGGTCGATCGACTAGTTATT
66 GTGGTCGATCGACCGGTTCTTTTCTTCTCACTT-TGAATGTGATGTGGTCGATCGACTAGTTATT
554 TC
130 TC
556 TCTTCTTGGTTTGAATGTGATGTGGTCGATCGACTAGTTACTTCTCTTCTTGCTTTGAATGTGAT
1 TCTTCTTGGTTTGAATGTGATGTGGTCGATCGACTAGTTACTTCTCTTCTTGCTTTGAATGTGAT
* * *
621 GTGGTCGATTGACCGGTTCTTTTCTTCTCACTTTTGAATCTGATGTGGTCGATCGACTAGTTACT
66 GTGGTCGATCGACCGGTTCTTTTCTTCTCAC-TTTGAATGTGATGTGGTCGATCGACTAGTTATT
686 TC
130 TC
*
688 TCTTCTTGGTTTAAATGTGATGTGGTCGATCGAC
1 TCTTCTTGGTTTGAATGTGATGTGGTCGATCGAC
722 CGGTTCTTTT
Statistics
Matches: 269, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
130 35 0.13
131 48 0.18
132 184 0.68
133 2 0.01
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (131 bp):
TCTTCTTGGTTTGAATGTGATGTGGTCGATCGACTAGTTACTTCTCTTCTTGCTTTGAATGTGAT
GTGGTCGATCGACCGGTTCTTTTCTTCTCACTTTGAATGTGATGTGGTCGATCGACTAGTTATTT
C
Found at i:1203 original size:21 final size:20
Alignment explanation
Indices: 1164--1233 Score: 56
Period size: 22 Copynumber: 3.4 Consensus size: 20
1154 CATTTTTCTT
1164 TCTTTGGAGAGCA--CTCCTC
1 TCTTTGG-GAGCATTCTCCTC
1183 TCTTTGGGTAGTC-TTCTCCTCC
1 TCTTTGGG-AG-CATTCTCCT-C
* *
1205 CCTTTGTGGAGCATTCTTCTC
1 TCTTTG-GGAGCATTCTCCTC
1226 TCTTTGGG
1 TCTTTGGG
1234 GGGCATTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
18 1 0.02
19 9 0.22
20 3 0.07
21 12 0.29
22 14 0.34
23 2 0.05
ACGTcount: A:0.09, C:0.29, G:0.21, T:0.41
Consensus pattern (20 bp):
TCTTTGGGAGCATTCTCCTC
Found at i:1575 original size:135 final size:130
Alignment explanation
Indices: 1350--1691 Score: 451
Period size: 126 Copynumber: 2.6 Consensus size: 130
1340 GGACGAAGTC
*
1350 GATTCATGTCGATCGCCACTTAATCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
1 GATTCATGTCGATCGCCACTTAGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGC-
* * * *
1415 GTTGGC-GATCGCCTATTGGCGTTGGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATT
65 -TCGCCTG-TTGGC--TTGGC-TTGGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATT
**
1479 GGGGAT
125 AAGGAT
* * * *
1485 GATTCAAGTCGATCGCCACTTTGTCGATGACCATACTAGGTCGAGCTCGCCCTTGCCTGATCGCT
1 GATTCATGTCGATCGCCACTTAGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
* *
1550 CGCCTGTTGGC---G-TTGGGCCCCTTGGGGGCATCATCATCATTTCTCGTATTTGATTAAGGAT
66 CGCCTGTTGGCTTGGCTTGGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTAAGGAT
* *
1611 GATTCATGTCGATCGTCACTTAGTCGATGGCCATACTAGGTCGAGCTCGGCATTGCCTGATCGCT
1 GATTCATGTCGATCGCCACTTAGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
1676 CGCCTGTTGGCGTTGG
66 CGCCTGTTGGC-TTGG
1692 GCCCTTTGAG
Statistics
Matches: 183, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
126 115 0.63
128 1 0.01
130 1 0.01
133 6 0.03
134 1 0.01
135 59 0.32
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (130 bp):
GATTCATGTCGATCGCCACTTAGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
CGCCTGTTGGCTTGGCTTGGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTAAGGAT
Found at i:1592 original size:126 final size:126
Alignment explanation
Indices: 1423--1712 Score: 454
Period size: 126 Copynumber: 2.3 Consensus size: 126
1413 CTGTTGGCGA
* **
1423 TCGCCTATTGGCGTTGGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTGGGGATGAT
1 TCGCCTGTTGGCGTTGGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTAAGGATGAT
* *
1488 TCAAGTCGATCGCCACTTTGTCGATGACCATACTAGGTCGAGCTCGCCCTTGCCTGATCGC
66 TCAAGTCGATCGCCACTTAGTCGATGACCATACTAGGTCGAGCTCGCCATTGCCTGATCGC
* *
1549 TCGCCTGTTGGCGTTGGGCCCCTTGGGGGCATCATCATCATTTCTCGTATTTGATTAAGGATGAT
1 TCGCCTGTTGGCGTTGGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTAAGGATGAT
* * * *
1614 TCATGTCGATCGTCACTTAGTCGATGGCCATACTAGGTCGAGCTCGGCATTGCCTGATCGC
66 TCAAGTCGATCGCCACTTAGTCGATGACCATACTAGGTCGAGCTCGCCATTGCCTGATCGC
* * *
1675 TCGCCTGTTGGCGTTGGGCCCTTTGAGGGCATCTTCAT
1 TCGCCTGTTGGCGTTGGGCCCCTTGGGGGCATCATCAT
1713 TTCCCATACT
Statistics
Matches: 150, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 150 1.00
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.31
Consensus pattern (126 bp):
TCGCCTGTTGGCGTTGGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTAAGGATGAT
TCAAGTCGATCGCCACTTAGTCGATGACCATACTAGGTCGAGCTCGCCATTGCCTGATCGC
Found at i:2177 original size:44 final size:44
Alignment explanation
Indices: 2104--2339 Score: 273
Period size: 44 Copynumber: 5.4 Consensus size: 44
2094 GATGTGGTGA
* * * * * *
2104 GGTCAGTCGACTTGTTGTTGACTTCCTTGCTTTGAATATGATGT
1 GGTCGGTCGACCTATTGTTTACTTTCTTGCGTTGAATATGATGT
* *
2148 GGTCGGTCGACCTATTGTTTGCTTGCTTGCGTT-AGATATGATGT
1 GGTCGGTCGACCTATTGTTTACTTTCTTGCGTTGA-ATATGATGT
* * *
2192 TGTCGATCGACCTATTGTTTACTTT-TTG-GCTTCAA-ATGATGT
1 GGTCGGTCGACCTATTGTTTACTTTCTTGCG-TTGAATATGATGT
* * *
2234 GGTCGGTCGACCTATTATTTGCTTTCTTGCGTTAAATATGATGT
1 GGTCGGTCGACCTATTGTTTACTTTCTTGCGTTGAATATGATGT
* *
2278 GGTCGGTCGACCTGTTGTTTACTTTCTTGCTTTGAATATGATGT
1 GGTCGGTCGACCTATTGTTTACTTTCTTGCGTTGAATATGATGT
*
2322 GGTCGGCCGACCTATTGT
1 GGTCGGTCGACCTATTGT
2340 CCTCTATCTC
Statistics
Matches: 163, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
42 29 0.18
43 14 0.09
44 120 0.74
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.42
Consensus pattern (44 bp):
GGTCGGTCGACCTATTGTTTACTTTCTTGCGTTGAATATGATGT
Found at i:2242 original size:86 final size:88
Alignment explanation
Indices: 2118--2339 Score: 315
Period size: 86 Copynumber: 2.5 Consensus size: 88
2108 AGTCGACTTG
* * * *
2118 TTGTTGACTTCCTTGCTTTGAATATGATGTGGTCGGTCGACCTATTGTTTGCTTGCTTGCGTTAG
1 TTGTTTACTTTCTTGCTTTCAATATGATGTGGTCGGTCGACCTATTGTTTGCTTGCTTGCGTTAA
*
2183 ATATGATGTTGTCGATCGACCTA
66 ATATGATGTGGTCGATCGACCTA
* *
2206 TTGTTTACTTT-TTGGC-TTCAA-ATGATGTGGTCGGTCGACCTATTATTTGCTTTCTTGCGTTA
1 TTGTTTACTTTCTT-GCTTTCAATATGATGTGGTCGGTCGACCTATTGTTTGCTTGCTTGCGTTA
* *
2268 AATATGATGTGGTCGGTCGACCTG
65 AATATGATGTGGTCGATCGACCTA
* *
2292 TTGTTTACTTTCTTGCTTTGAATATGATGTGGTCGGCCGACCTATTGT
1 TTGTTTACTTTCTTGCTTTCAATATGATGTGGTCGGTCGACCTATTGT
2340 CCTCTATCTC
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
86 72 0.61
87 12 0.10
88 34 0.29
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (88 bp):
TTGTTTACTTTCTTGCTTTCAATATGATGTGGTCGGTCGACCTATTGTTTGCTTGCTTGCGTTAA
ATATGATGTGGTCGATCGACCTA
Done.