Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006932.1 Corchorus capsularis cultivar CVL-1 contig06953, 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: 15767
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:316 original size:81 final size:81
Alignment explanation
Indices: 226--390 Score: 294
Period size: 81 Copynumber: 2.0 Consensus size: 81
216 CTGCAAGTTT
* *
226 TTATTTTCTTCCTTTCTTTTTCTTTAAAAGCATTAATCATTATTTCTTTCTGTAATTCTGTTTAT
1 TTATTTTCTTCCTTTCTTTTTCTTTAAAAGCATTAATCATTATTTATTTCTGTAATTCTGTTCAT
291 TGGTCTTGACGTCTTG
66 TGGTCTTGACGTCTTG
* *
307 TTATTTTCTTCCTTTTTTTTTCTTTAAATGCATTAATCATTATTTATTTCTGTAATTCTGTTCAT
1 TTATTTTCTTCCTTTCTTTTTCTTTAAAAGCATTAATCATTATTTATTTCTGTAATTCTGTTCAT
372 TGGTCTTGACGTCTTG
66 TGGTCTTGACGTCTTG
388 TTA
1 TTA
391 ATTTAAGTCT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.58
Consensus pattern (81 bp):
TTATTTTCTTCCTTTCTTTTTCTTTAAAAGCATTAATCATTATTTATTTCTGTAATTCTGTTCAT
TGGTCTTGACGTCTTG
Found at i:2001 original size:18 final size:18
Alignment explanation
Indices: 1978--2012 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1968 ATTTGACTCT
*
1978 TAAAGTTTCTACATCTAC
1 TAAAGTTACTACATCTAC
*
1996 TAAAGTTACTTCATCTA
1 TAAAGTTACTACATCTA
2013 ACTTGCTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (18 bp):
TAAAGTTACTACATCTAC
Found at i:5069 original size:29 final size:29
Alignment explanation
Indices: 5050--5108 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
5040 TGGAATAATT
*
5050 ATTGGAAGTAGAATAATTTTAAGATTTTG
1 ATTGGAAGTAGAATAATTTTAAGATATTG
*
5079 ATTGGAAGTAGAATAATTTTAAGATTTTG
1 ATTGGAAGTAGAATAATTTTAAGATATTG
5108 A
1 A
5109 GTACTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (29 bp):
ATTGGAAGTAGAATAATTTTAAGATATTG
Found at i:5477 original size:92 final size:92
Alignment explanation
Indices: 5315--5553 Score: 451
Period size: 92 Copynumber: 2.6 Consensus size: 92
5305 CTTTGTACTA
*
5315 TTTGCATTATTGGAGACAATTTCTGCATAGATTCTTCATGATAACTTTGCAGACCTTCATAATTT
1 TTTGCATTATTGGAGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACCTTCATAATTT
*
5380 GGCTTTCTCTTCATCCAATGAGTCAGC
66 CGCTTTCTCTTCATCCAATGAGTCAGC
5407 TTTGCATTATTGGAGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACCTTCATAATTT
1 TTTGCATTATTGGAGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACCTTCATAATTT
5472 CGCTTTCTCTTCATCCAATGAGTCAGC
66 CGCTTTCTCTTCATCCAATGAGTCAGC
*
5499 TTTGCATTATTGGAGACAATATCTGCAGAGATTCTTCATGATAACTTTGCAGACC
1 TTTGCATTATTGGAGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACC
5554 ATTATTTTTT
Statistics
Matches: 144, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 144 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (92 bp):
TTTGCATTATTGGAGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACCTTCATAATTT
CGCTTTCTCTTCATCCAATGAGTCAGC
Found at i:5569 original size:21 final size:21
Alignment explanation
Indices: 5543--5609 Score: 125
Period size: 21 Copynumber: 3.2 Consensus size: 21
5533 TTCATGATAA
5543 CTTTGCAGACCATTATTTTTT
1 CTTTGCAGACCATTATTTTTT
5564 CTTTGCAGACCATTATTTTTT
1 CTTTGCAGACCATTATTTTTT
*
5585 CTTTGCAGACCATTATTTTTA
1 CTTTGCAGACCATTATTTTTT
5606 CTTT
1 CTTT
5610 TTTTTTTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.52
Consensus pattern (21 bp):
CTTTGCAGACCATTATTTTTT
Found at i:7257 original size:156 final size:154
Alignment explanation
Indices: 6954--7465 Score: 581
Period size: 156 Copynumber: 3.3 Consensus size: 154
6944 CAGATTTAAG
* * *
6954 ATGAAAAACTTATGCTAGTTTTTCAATTAAAGACAATTTGGTGTGAGAAACC-ACTTCACTATGA
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAAGACAGTTTGGGGTGAGAAACCAACTTCACTATG-
* *
7018 TAGGGAGTTCGGTTTTACTTAGAA-TTTTTTCCATAGTCTTATGGAGATAGTCTAAGTCTC-GTG
65 TAGGGAGTTCGGTTTTACTTAGAATTTTTTTCCATAGTCTTATGGAGATAATCTAAGCCTCTGTG
* * * *
7081 GCTAAGTTTCATCTCAATTGGACTTAGT
130 GC-AA-ATTCAGCT-TATTGGACTTAGA
* * * * ** *
7109 ATGAAAAACTTATGCAAGTTTTTCAGTTAATGACGGTTTGGGGTGTCAAACCAACTTCTCTATGC
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAAGACAGTTTGGGGTGAGAAACCAACTTCACTATG-
7174 TAGGGAGTTCGGTTTTACTTAGAATTTTTTTCCATAGTCTTATGGAGATAATCTAAGCCTACTGT
65 TAGGGAGTTCGGTTTTACTTAGAATTTTTTTCCATAGTCTTATGGAGATAATCTAAGCCT-CTGT
* * *
7239 GG-AAAATCAGGCTTATTGGGCATAGA
129 GGCAAATTCA-GCTTATTGGACTTAGA
* * *
7265 ATGAAAAACTTATGCTAGTTTTTCATTTAAAGACAGTTTGGGGAGAGAAACCAAGTTCACCAT-T
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAAGACAGTTTGGGGTGAGAAACCAACTTCACTATGT
* * * * *
7329 AAGGAGAGCTCGGTTTTACTT-GTATTTTTTTCCATAGTCTTGTGGAGAGAATATAAGTCC-CT-
66 -AGG-GAGTTCGGTTTTACTTAGAATTTTTTTCCATAGTCTTATGGAGATAATCTAAG-CCTCTG
*
7391 TGGCAAAGTTTCAGCTTATTCAGACTTAGA
128 TGGCAAA--TTCAGCTTATT-GGACTTAGA
* *
7421 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTG
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAAGACAGTTTGGGGTG
7466 TGAAGTATAG
Statistics
Matches: 304, Mismatches: 41, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
153 3 0.01
154 6 0.02
155 86 0.28
156 167 0.55
157 37 0.12
158 1 0.00
159 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (154 bp):
ATGAAAAACTTATGCTAGTTTTTCATTTAAAGACAGTTTGGGGTGAGAAACCAACTTCACTATGT
AGGGAGTTCGGTTTTACTTAGAATTTTTTTCCATAGTCTTATGGAGATAATCTAAGCCTCTGTGG
CAAATTCAGCTTATTGGACTTAGA
Found at i:7838 original size:17 final size:17
Alignment explanation
Indices: 7816--7849 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7806 TATCCAGCAT
7816 CTCATGCTACCTAGTAC
1 CTCATGCTACCTAGTAC
*
7833 CTCATGCTACCTGGTAC
1 CTCATGCTACCTAGTAC
7850 TATGAGGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.35, G:0.15, T:0.29
Consensus pattern (17 bp):
CTCATGCTACCTAGTAC
Found at i:9241 original size:134 final size:135
Alignment explanation
Indices: 9002--9354 Score: 537
Period size: 134 Copynumber: 2.6 Consensus size: 135
8992 ATAGACTTGG
* * * *
9002 GGGGCAAAACCAATAACTGCTTGGTGCCCAGCCCAGTGCTCTACCTTTTCAACAAGTCAACCATC
1 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTCTTCAACAAGTCAACCATC
* * *
9067 AGGTGAATAACCAACAAGTCATGGCTTAGATTGGTCTCATCGATGAAAGACTTGGGGGGCAAGGA
66 AGGTGAACAACCAACAAGTCATGGCTCAGATTGGTCTCATCGATGAAAGACTCGGGGGGCAAGGA
9132 CTCG-
131 CTCGA
**
9136 GGGGGGAAACCAACAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTCTTCAACAAGTCAACCATC
1 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTCTTCAACAAGTCAACCATC
* *
9201 AGGTGAACAACCAACAAGTCATGGCTCGGATTTGTCTCATCGATGAAAGACTCGGGGGGCAAGGA
66 AGGTGAACAACCAACAAGTCATGGCTCAGATTGGTCTCATCGATGAAAGACTCGGGGGGCAAGGA
9266 CTCGA
131 CTCGA
* ** * * * *
9271 GGGGCAAAACCAACAGCCACTTGGTGCCCAGCCCGATGCTCTGCCTCTGCAACAAGTCAACAATG
1 GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTCTTCAACAAGTCAACCATC
9336 AGGTGAACAACCAACAAGT
66 AGGTGAACAACCAACAAGT
9355 TCCACCTCCA
Statistics
Matches: 198, Mismatches: 20, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
134 123 0.62
135 75 0.38
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (135 bp):
GGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTCTTCAACAAGTCAACCATC
AGGTGAACAACCAACAAGTCATGGCTCAGATTGGTCTCATCGATGAAAGACTCGGGGGGCAAGGA
CTCGA
Found at i:10723 original size:33 final size:33
Alignment explanation
Indices: 10652--10739 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
10642 AAAGGATCAT
* *
10652 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCAT
1 GTGGTCGGTTGTGGCCGGGCATGGCCGAGTCAC
* *
10685 TTGGTCGGTTGTGGCCGGGCATGGCC-ATGTCGC
1 GTGGTCGGTTGTGGCCGGGCATGGCCGA-GTCAC
10718 GTGGTCGG-TGATGGCCGGGCAT
1 GTGGTCGGTTG-TGGCCGGGCAT
10740 CTCCAAGTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 3 0.06
33 45 0.94
ACGTcount: A:0.08, C:0.23, G:0.45, T:0.24
Consensus pattern (33 bp):
GTGGTCGGTTGTGGCCGGGCATGGCCGAGTCAC
Done.