Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007097.1 Corchorus capsularis cultivar CVL-1 contig07118, 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: 19975
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:641 original size:21 final size:21
Alignment explanation
Indices: 617--660 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
607 CCAAACTGGA
617 TTGCTAAAT-ACCGTCCCATTT
1 TTGCT-AATCACCGTCCCATTT
* *
638 TTGCTATTCACCGTCTCATTT
1 TTGCTAATCACCGTCCCATTT
659 TT
1 TT
661 TATACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (21 bp):
TTGCTAATCACCGTCCCATTT
Found at i:1003 original size:32 final size:32
Alignment explanation
Indices: 962--1035 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
952 AATTTGGTCT
* *
962 AGCCGCCCCACAG-GGGCGGCCTGCCTTGGCGA
1 AGCCGCCCCA-AGAGGGCGGCCTACCATGGCGA
*
994 AGCCGCCCCATGAGGGCGGCCTACCATGGCGA
1 AGCCGCCCCAAGAGGGCGGCCTACCATGGCGA
1026 AGCCGCCCCA
1 AGCCGCCCCA
1036 GTGGGGAGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 1 0.03
32 37 0.97
ACGTcount: A:0.16, C:0.42, G:0.34, T:0.08
Consensus pattern (32 bp):
AGCCGCCCCAAGAGGGCGGCCTACCATGGCGA
Found at i:1127 original size:33 final size:33
Alignment explanation
Indices: 1026--1142 Score: 137
Period size: 33 Copynumber: 3.5 Consensus size: 33
1016 ACCATGGCGA
* *
1026 AGCCGCCCCAGTGGGGAGGCTCCGCCGTGGTTA
1 AGCCTCCCCAGTGGGGAGGCTCCGCCGTGGTTG
* * *
1059 AGCCTCCCCAATAGGGAAGCTCCGCCGTGGTTG
1 AGCCTCCCCAGTGGGGAGGCTCCGCCGTGGTTG
* * *
1092 AGCCTCCCTAGTGGGGAGGTTCCGCCGTGGCTG
1 AGCCTCCCCAGTGGGGAGGCTCCGCCGTGGTTG
*
1125 AGCCGT-CCTAGTGGGGAG
1 AGCC-TCCCCAGTGGGGAG
1143 ACTCAGTGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
33 71 0.99
34 1 0.01
ACGTcount: A:0.14, C:0.31, G:0.38, T:0.18
Consensus pattern (33 bp):
AGCCTCCCCAGTGGGGAGGCTCCGCCGTGGTTG
Found at i:2340 original size:31 final size:31
Alignment explanation
Indices: 2302--2363 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
2292 AGTTTTGTAA
*
2302 AACTTTTGAAACGCCTATTGTACCCTTATTT
1 AACTTTTGAAACGCCTATTATACCCTTATTT
*
2333 AACTTTTGAAACGCCTATTATATCCTTATTT
1 AACTTTTGAAACGCCTATTATACCCTTATTT
2364 GTCTAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (31 bp):
AACTTTTGAAACGCCTATTATACCCTTATTT
Found at i:2867 original size:13 final size:13
Alignment explanation
Indices: 2849--2873 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2839 TAATCCGTTG
2849 ACTATTTTTTTCT
1 ACTATTTTTTTCT
2862 ACTATTTTTTTC
1 ACTATTTTTTTC
2874 CTTTTTCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (13 bp):
ACTATTTTTTTCT
Found at i:7272 original size:30 final size:30
Alignment explanation
Indices: 7238--7295 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
7228 AAATAAGAAA
7238 ATTAAAATGTAAATTTATTAGTATTAGTCT
1 ATTAAAATGTAAATTTATTAGTATTAGTCT
7268 ATTAAAATGTAAATTTATTAGTATTAGT
1 ATTAAAATGTAAATTTATTAGTATTAGT
7296 ATTAGTCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (30 bp):
ATTAAAATGTAAATTTATTAGTATTAGTCT
Found at i:7659 original size:31 final size:31
Alignment explanation
Indices: 7615--7673 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
7605 GTTAGAAAAA
* *
7615 TAAGGATATAATAGACGTTTCAAAAGTTAAT
1 TAAGGATACAATAGACATTTCAAAAGTTAAT
* *
7646 TAAGGGTACAATAGGCATTTCAAAAGTT
1 TAAGGATACAATAGACATTTCAAAAGTT
7674 TTACAAAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (31 bp):
TAAGGATACAATAGACATTTCAAAAGTTAAT
Found at i:7747 original size:3 final size:3
Alignment explanation
Indices: 7739--7768 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
7729 ATATATATAT
7739 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7769 TATACAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8005 original size:42 final size:42
Alignment explanation
Indices: 7935--8039 Score: 183
Period size: 42 Copynumber: 2.5 Consensus size: 42
7925 TTCCTACCCT
7935 ACTCACCCAATACAAATACTCACCTGGTGAGATACTCACCCAC
1 ACTCACCCAATAC-AATACTCACCTGGTGAGATACTCACCCAC
* *
7978 ACTCACCCAATACAATACTCACCTGGTGAGATACTCACTCAT
1 ACTCACCCAATACAATACTCACCTGGTGAGATACTCACCCAC
8020 ACTCACCCAATACAATACTC
1 ACTCACCCAATACAATACTC
8040 TCCTAATGAG
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
42 47 0.78
43 13 0.22
ACGTcount: A:0.35, C:0.36, G:0.08, T:0.21
Consensus pattern (42 bp):
ACTCACCCAATACAATACTCACCTGGTGAGATACTCACCCAC
Found at i:9388 original size:22 final size:22
Alignment explanation
Indices: 9357--9400 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
9347 GATGAGAAAG
*
9357 TCTTGACCGAAGCCAAGCCTAA
1 TCTTGACCGAAACCAAGCCTAA
*
9379 TCTTGGCCGAAACCAAGCCTAA
1 TCTTGACCGAAACCAAGCCTAA
9401 AGAAGGGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (22 bp):
TCTTGACCGAAACCAAGCCTAA
Found at i:9519 original size:249 final size:249
Alignment explanation
Indices: 9075--9576 Score: 909
Period size: 249 Copynumber: 2.0 Consensus size: 249
9065 ATAGAGAAAG
9075 GGATGGGAAATCAGAGAGAAAGAGATGAGAAAGTCTTGACCGAAGCCAAGCCTAATCTTGGACGA
1 GGATGGGAAATCAGAGAGAAAGAGATGAGAAAGTCTTGACCGAAGCCAAGCCTAATCTTGGACGA
* *
9140 AACCAAGCCTAAAGAAGGGGATGGGAAACTAGAATTTTTTTCCTTAACATTGTTCTTGATCTTCA
66 AACCAAGCCTAAAGAAGGGGATGAGAAACTAGAATTTTTTTCCTTAACATTCTTCTTGATCTTCA
9205 TTCGTTACATAACATATATATAGTAGCTAGGGCATAATTCTTTGGATCTAAATACAATGGGCTTA
131 TTCGTTACATAACATATATATAGTAGCTAGGGCATAATTCTTTGGATCTAAATACAATGGGCTTA
*
9270 CAAAGACTATTATAAAATTAAACCAAAGACTATTAATTTAGG-TATTTGTCTCTT
196 CAAAGACCATTATAAAATTAAACCAAAGACTATTAATTT-GGATATTTGTCTCTT
*
9324 GGATGGGAAA-CTAGAGAGAAAGAGATGAGAAAGTCTTGACCGAAGCCAAGCCTAATCTTGGCCG
1 GGATGGGAAATC-AGAGAGAAAGAGATGAGAAAGTCTTGACCGAAGCCAAGCCTAATCTTGGACG
*
9388 AAACCAAGCCTAAAGAAGGGGATGAGAAACTATAATTTTTTTCCTTAACATTCTTCTTGATCTTC
65 AAACCAAGCCTAAAGAAGGGGATGAGAAACTAGAATTTTTTTCCTTAACATTCTTCTTGATCTTC
* *
9453 ATTCGTTACATAACATATATATAGTAGCTAGGGCATAATTCTTTGGGTCTAAATACAATTGGCTT
130 ATTCGTTACATAACATATATATAGTAGCTAGGGCATAATTCTTTGGATCTAAATACAATGGGCTT
9518 ACAAAGACCATTATAAAATTAAACCAAAGACTATTAATTTGGATATTTGTCTCTT
195 ACAAAGACCATTATAAAATTAAACCAAAGACTATTAATTTGGATATTTGTCTCTT
9573 GGAT
1 GGAT
9577 TGGCCGGCTA
Statistics
Matches: 244, Mismatches: 7, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
248 3 0.01
249 241 0.99
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (249 bp):
GGATGGGAAATCAGAGAGAAAGAGATGAGAAAGTCTTGACCGAAGCCAAGCCTAATCTTGGACGA
AACCAAGCCTAAAGAAGGGGATGAGAAACTAGAATTTTTTTCCTTAACATTCTTCTTGATCTTCA
TTCGTTACATAACATATATATAGTAGCTAGGGCATAATTCTTTGGATCTAAATACAATGGGCTTA
CAAAGACCATTATAAAATTAAACCAAAGACTATTAATTTGGATATTTGTCTCTT
Found at i:11471 original size:38 final size:38
Alignment explanation
Indices: 11412--11596 Score: 264
Period size: 38 Copynumber: 4.9 Consensus size: 38
11402 CACAATCTAG
* *
11412 CCAACAG-TTGACCCCCTGAGGCACGAGTCAACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGAGTCCACTCTTA
* *
11449 CCAACAGTTTAACCCCCCGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGAGTCCACTCTTA
*
11487 CCAACAGTTTAACCCCCTGAGACACGAGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGAGTCCACTCTTA
* * * *
11525 CCATCAGTTTAACCCCCTGAGACGCGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGAGTCCACTCTTA
* *
11563 CCATCAGTTTAACCCCCTGAGGCACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGAGTCCACT
11597 ATGCACAGCC
Statistics
Matches: 135, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
37 7 0.05
38 128 0.95
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGAGTCCACTCTTA
Found at i:19216 original size:47 final size:44
Alignment explanation
Indices: 19158--19246 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
19148 TTTGGGCAAG
* *
19158 TTCTCTTGGTGATCATAGTGAATTGTTAGATTATTATCAATCCATGT
1 TTCTCGTGGTGATCATAGT-AA--ATTAGATTATTATCAATCCATGT
* *
19205 TTCTCGTGGTGATGATAGTAAATTAGATTATTATCTATCCAT
1 TTCTCGTGGTGATCATAGTAAATTAGATTATTATCAATCCAT
19247 TTCGGAAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 19 0.50
46 2 0.05
47 17 0.45
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (44 bp):
TTCTCGTGGTGATCATAGTAAATTAGATTATTATCAATCCATGT
Done.