Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012913.1 Corchorus capsularis cultivar CVL-1 contig12934, 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: 35965
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1691 original size:3 final size:3
Alignment explanation
Indices: 1683--1717 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1673 TTGATAAAAA
1683 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1718 ATAATATAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5003 original size:12 final size:12
Alignment explanation
Indices: 4986--5010 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4976 TGCAAAGAAG
4986 GTTCCACTGCTT
1 GTTCCACTGCTT
4998 GTTCCACTGCTT
1 GTTCCACTGCTT
5010 G
1 G
5011 CTATTGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.32, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTCCACTGCTT
Found at i:5045 original size:19 final size:18
Alignment explanation
Indices: 5021--5056 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
5011 CTATTGCAAT
5021 TTAAGGGATTTTAGTTTTA
1 TTAAGGGATTTTA-TTTTA
5040 TTAAGGGATTTTATTTT
1 TTAAGGGATTTTATTTT
5057 CATTTTACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (18 bp):
TTAAGGGATTTTATTTTA
Found at i:5077 original size:21 final size:18
Alignment explanation
Indices: 5051--5098 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 18
5041 TAAGGGATTT
5051 TATTTTCATTTTACTTCGTAA
1 TATTTTCATTTTA-TT-G-AA
5072 TATTTT-AGTTTTATTGAA
1 TATTTTCA-TTTTATTGAA
5090 TATTTTCAT
1 TATTTTCAT
5099 CCTTTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
18 9 0.36
19 2 0.08
20 3 0.12
21 11 0.44
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.60
Consensus pattern (18 bp):
TATTTTCATTTTATTGAA
Found at i:5617 original size:119 final size:119
Alignment explanation
Indices: 5511--6008 Score: 552
Period size: 120 Copynumber: 4.2 Consensus size: 119
5501 ATCTATACCC
* *
5511 GTGACGTTCTGACTTTT-GTCACGAATAATGATAA-A-CTTCCTCATATTTTTTGACAATCAACA
1 GTGACGTTC-CACTTTTCGTCACGAATAATGA-AATATTTTCCTCAT-TTTTTTGACAATCAACA
* * * * *
5573 ATTATGAGTGACGTTATATTGTAGTATTTTATGACGTACA-TTACGTCACCTATACAT
63 ATTTTGAGTGACGTTTTATTTTAATATTTTATGACG-AAATTTACGTCACCTATACAT
* *
5630 GTGACGTTCCAATTTTCGTCACGAATAATGAAATATTTTCCTCATTTTTGTGACAATCAACAATT
1 GTGACGTTCCACTTTTCGTCACGAATAATGAAATATTTTCCTCATTTTTTTGACAATCAACAATT
*
5695 GTTG-GTGACGTTTTATTTTAATATTTTATGACGAAATTTACGTCACCGATACAT
66 -TTGAGTGACGTTTTATTTTAATATTTTATGACGAAATTTACGTCACCTATACAT
*
5749 GTGACGTTCCACTTTTCGTCACGAATAATGAAATATTTTCCTCATTTTTTGTGACAATAAACAAT
1 GTGACGTTCCACTTTTCGTCACGAATAATGAAATATTTTCCTCATTTTTT-TGACAATCAACAAT
* * * *
5814 TTTTAGTGACATTTTATTTTAATATTTTATGACGAAATTTGCGTCACCGATACAT
65 TTTGAGTGACGTTTTATTTTAATATTTTATGACGAAATTTACGTCACCTATACAT
* * * *
5869 GTGACGTT-CACATTTTTGTCAC-ATATAACT-ACACATTTTCCTCATGTTTTGTGACAATCAAC
1 GTGACGTTCCAC-TTTTCGTCACGA-ATAA-TGAAATATTTTCCTCAT-TTTTTTGACAATCAAC
* * * **
5931 AACTTTT-TGTGACGTTATAATTTAATATTTTATGAC-AACATTTGTGTCACC--TACAT
62 AA-TTTTGAGTGACGTTTTATTTTAATATTTTATGACGAA-ATTTACGTCACCTATACAT
** * *
5987 GTGATATTTCAATTTTCGTCAC
1 GTGACGTTCCACTTTTCGTCAC
6009 ATATAACTAA
Statistics
Matches: 335, Mismatches: 30, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
118 29 0.09
119 143 0.43
120 154 0.46
121 9 0.03
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (119 bp):
GTGACGTTCCACTTTTCGTCACGAATAATGAAATATTTTCCTCATTTTTTTGACAATCAACAATT
TTGAGTGACGTTTTATTTTAATATTTTATGACGAAATTTACGTCACCTATACAT
Found at i:5860 original size:120 final size:120
Alignment explanation
Indices: 5410--6008 Score: 584
Period size: 119 Copynumber: 5.0 Consensus size: 120
5400 TACTCATCTT
* * * * *
5410 GTCACGAATAACT-AAACA-TTTACT-ATTTTTTATGACGATCAACAATTGTTAGTGACGTTATA
1 GTCACGAATAA-TGAAATATTTTCCTCATTTTTTGTGACAATCAACAATTTTTAGTGACGTTAT-
* * ** * * * * * * ** *
5472 ATCTCAA-ATTGCATAATGAAACTTACGTTATCTATACCCGTGACGTTCTGACTTTT-
64 ATTTTAATATTTTATGACGAAATTTACGTCACCGATACATGTGACGTTC-CACTTTTC
* * *
5528 GTCACGAATAATGATAA-A-CTTCCTCATATTTTT-TGACAATCAACAATTATGAGTGACGTTAT
1 GTCACGAATAATGA-AATATTTTCCTCAT-TTTTTGTGACAATCAACAATTTTTAGTGACGTTAT
* * * * *
5590 ATTGTAGTATTTTATGACGTACA-TTACGTCACCTATACATGTGACGTTCCAATTTTC
64 ATTTTAATATTTTATGACG-AAATTTACGTCACCGATACATGTGACGTTCCACTTTTC
* * *
5647 GTCACGAATAATGAAATATTTTCCTCA-TTTTTGTGACAATCAACAATTGTTGGTGACGTTTTAT
1 GTCACGAATAATGAAATATTTTCCTCATTTTTTGTGACAATCAACAATTTTTAGTGACGTTATAT
5711 TTTAATATTTTATGACGAAATTTACGTCACCGATACATGTGACGTTCCACTTTTC
66 TTTAATATTTTATGACGAAATTTACGTCACCGATACATGTGACGTTCCACTTTTC
* * *
5766 GTCACGAATAATGAAATATTTTCCTCATTTTTTGTGACAATAAACAATTTTTAGTGACATTTTAT
1 GTCACGAATAATGAAATATTTTCCTCATTTTTTGTGACAATCAACAATTTTTAGTGACGTTATAT
* *
5831 TTTAATATTTTATGACGAAATTTGCGTCACCGATACATGTGACGTT-CACATTTTT
66 TTTAATATTTTATGACGAAATTTACGTCACCGATACATGTGACGTTCCAC-TTTTC
* * *
5886 GTCAC-ATATAACT-ACACATTTTCCTCATGTTTTGTGACAATCAACAACTTTTT-GTGACGTTA
1 GTCACGA-ATAA-TGAAATATTTTCCTCATTTTTTGTGACAATCAACAA-TTTTTAGTGACGTTA
* ** ** * *
5948 TAATTTAATATTTTATGAC-AACATTTGTGTCACC--TACATGTGATATTTCAATTTTC
63 TATTTTAATATTTTATGACGAA-ATTTACGTCACCGATACATGTGACGTTCCACTTTTC
6004 GTCAC
1 GTCAC
6009 ATATAACTAA
Statistics
Matches: 415, Mismatches: 48, Indels: 36
0.83 0.10 0.07
Matches are distributed among these distances:
117 1 0.00
118 54 0.13
119 183 0.44
120 171 0.41
121 6 0.01
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (120 bp):
GTCACGAATAATGAAATATTTTCCTCATTTTTTGTGACAATCAACAATTTTTAGTGACGTTATAT
TTTAATATTTTATGACGAAATTTACGTCACCGATACATGTGACGTTCCACTTTTC
Found at i:5869 original size:239 final size:237
Alignment explanation
Indices: 5511--6008 Score: 602
Period size: 239 Copynumber: 2.1 Consensus size: 237
5501 ATCTATACCC
* *
5511 GTGACGTTCTGACTTTT-GTCACGAATAATGATAAACTTCCTCATATTTTTTGACAATCAACAAT
1 GTGACGTTC-CACTTTTCGTCACGAATAATGATAAACTTCCTCATATTTTTTGACAATAAACAAT
* * * *
5575 TATGAGTGACGTTATATTGTAGTATTTTATGACGTACATTACGTCACCTATACATGTGACGTTC-
65 TATGAGTGACATTATATTGTAATATTTTATGACGTAAATTACGTCACCGATACATGTGACGTTCA
*
5639 CAATTTTCGTCACGA-ATAA-TGAAATATTTTCCTCAT-TTTTGTGACAATCAACAA-TTGTTGG
130 C-ATTTTCGTCAC-ATATAACT-AAACATTTTCCTCATGTTTTGTGACAATCAACAACTT-TTGG
* *
5700 TGACGTTTTATTTTAATATTTTATGACGAA-ATTTACGTCACCGATACAT
191 TGACGTTATAATTTAATATTTTATGAC-AACATTTACGTCACC--TACAT
*
5749 GTGACGTTCCACTTTTCGTCACGAATAATGA-AATATTTTCCTCAT-TTTTTGTGACAATAAACA
1 GTGACGTTCCACTTTTCGTCACGAATAATGATAA-A-CTTCCTCATATTTTT-TGACAATAAACA
* * * * *
5812 ATTTTTAGTGACATTTTATTTTAATATTTTATGACG-AAATTTGCGTCACCGATACATGTGACGT
63 ATTATGAGTGACATTATATTGTAATATTTTATGACGTAAA-TTACGTCACCGATACATGTGACGT
* * *
5876 TCACATTTTTGTCACATATAACTACACATTTTCCTCATGTTTTGTGACAATCAACAACTTTTTGT
127 TCACATTTTCGTCACATATAACTAAACATTTTCCTCATGTTTTGTGACAATCAACAACTTTTGGT
**
5941 GACGTTATAATTTAATATTTTATGACAACATTTGTGTCACCTACAT
192 GACGTTATAATTTAATATTTTATGACAACATTTACGTCACCTACAT
** * *
5987 GTGATATTTCAATTTTCGTCAC
1 GTGACGTTCCACTTTTCGTCAC
6009 ATATAACTAA
Statistics
Matches: 225, Mismatches: 24, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
237 8 0.04
238 55 0.24
239 102 0.45
240 58 0.26
241 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (237 bp):
GTGACGTTCCACTTTTCGTCACGAATAATGATAAACTTCCTCATATTTTTTGACAATAAACAATT
ATGAGTGACATTATATTGTAATATTTTATGACGTAAATTACGTCACCGATACATGTGACGTTCAC
ATTTTCGTCACATATAACTAAACATTTTCCTCATGTTTTGTGACAATCAACAACTTTTGGTGACG
TTATAATTTAATATTTTATGACAACATTTACGTCACCTACAT
Found at i:12107 original size:13 final size:13
Alignment explanation
Indices: 12089--12115 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12079 AAACAACTGA
12089 AAAGCACTTCTGG
1 AAAGCACTTCTGG
12102 AAAGCACTTCTGG
1 AAAGCACTTCTGG
12115 A
1 A
12116 TATTCTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:16985 original size:1 final size:1
Alignment explanation
Indices: 16979--17022 Score: 79
Period size: 1 Copynumber: 44.0 Consensus size: 1
16969 TCGGGGAAGG
*
16979 TTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17023 CTTTCTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.02, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:17007 original size:20 final size:20
Alignment explanation
Indices: 16979--17026 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
16969 TCGGGGAAGG
16979 TTTTT-TTTTTTTTTTTTTT
1 TTTTTCTTTTTTTTTTTTTT
16998 TTTTTCTTTTTTTTTTTTTT
1 TTTTTCTTTTTTTTTTTTTT
17018 TTTTTCTTT
1 TTTTTCTTT
17027 CTATTTTGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.00, C:0.04, G:0.00, T:0.96
Consensus pattern (20 bp):
TTTTTCTTTTTTTTTTTTTT
Found at i:17012 original size:24 final size:24
Alignment explanation
Indices: 16980--17033 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
16970 CGGGGAAGGT
*
16980 TTTTTTTTTTTTTTTTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTCTTTC
17004 TTTTTTTTTTTTTTTTTTTCTTTC
1 TTTTTTTTTTTTTTTTTTTCTTTC
*
17028 TATTTT
1 TTTTTT
17034 GCCTTTCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.02, C:0.06, G:0.00, T:0.93
Consensus pattern (24 bp):
TTTTTTTTTTTTTTTTTTTCTTTC
Found at i:20306 original size:18 final size:18
Alignment explanation
Indices: 20283--20325 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
20273 TCACTTCCTC
20283 CTTTTTCATCATTTTTTT
1 CTTTTTCATCATTTTTTT
**
20301 CTTTTTCATTTTTTTTTT
1 CTTTTTCATCATTTTTTT
20319 CATTTTT
1 C-TTTTT
20326 TCAGAGGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (18 bp):
CTTTTTCATCATTTTTTT
Found at i:20325 original size:12 final size:12
Alignment explanation
Indices: 20296--20326 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
20286 TTTCATCATT
20296 TTTTTCTTTTTCA
1 TTTTT-TTTTTCA
20309 TTTTTTTTTTCA
1 TTTTTTTTTTCA
20321 TTTTTT
1 TTTTTT
20327 CAGAGGGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:20940 original size:18 final size:18
Alignment explanation
Indices: 20919--20954 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20909 TTGAAAATTT
20919 TCTCTTTTTCCACGTAAA
1 TCTCTTTTTCCACGTAAA
20937 TCTCTTTTTCCACGTAAA
1 TCTCTTTTTCCACGTAAA
20955 ACTATCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.06, T:0.44
Consensus pattern (18 bp):
TCTCTTTTTCCACGTAAA
Found at i:20964 original size:20 final size:18
Alignment explanation
Indices: 20921--20964 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
20911 GAAAATTTTC
*
20921 TCTTTTTCCACGTAAATC
1 TCTTTTTCCACGTAAATA
20939 TCTTTTTCCACGTAAAACTA
1 TCTTTTTCCACGT-AAA-TA
20959 TCTTTT
1 TCTTTT
20965 AGAAAGTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
19 3 0.13
20 7 0.30
ACGTcount: A:0.23, C:0.25, G:0.05, T:0.48
Consensus pattern (18 bp):
TCTTTTTCCACGTAAATA
Found at i:35534 original size:27 final size:27
Alignment explanation
Indices: 35504--35564 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
35494 TCGAATTAGC
* * * *
35504 ATTTTGGTCTTTTTTGCATTTAGGGGT
1 ATTTTGGTCATTCTGGCATTCAGGGGT
*
35531 ATTTTTGTCATTCTGGCATTCAGGGGT
1 ATTTTGGTCATTCTGGCATTCAGGGGT
35558 ATTTTGG
1 ATTTTGG
35565 GGTTTAGGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.13, C:0.10, G:0.26, T:0.51
Consensus pattern (27 bp):
ATTTTGGTCATTCTGGCATTCAGGGGT
Done.