Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007575.1 Corchorus capsularis cultivar CVL-1 contig07596, 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: 34330
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:1844 original size:17 final size:17
Alignment explanation
Indices: 1822--1889 Score: 66
Period size: 17 Copynumber: 3.8 Consensus size: 17
1812 ATTATTTCTT
1822 TTCTTCTTCTTCTCGAC
1 TTCTTCTTCTTCTCGAC
* *
1839 TTCTTCATCTTCTCCAC
1 TTCTTCTTCTTCTCGAC
*
1856 TCCTTCCTTC-TCGTCGAGC
1 TTCTT-CTTCTTC-TCGA-C
1875 TTCTTCTTTCTTCTC
1 TTCTTC-TTCTTCTC
1890 ATTATGGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
17 21 0.52
18 7 0.17
19 10 0.25
20 2 0.05
ACGTcount: A:0.06, C:0.38, G:0.06, T:0.50
Consensus pattern (17 bp):
TTCTTCTTCTTCTCGAC
Found at i:2191 original size:29 final size:29
Alignment explanation
Indices: 2147--2214 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
2137 TTAATTTAGG
* *
2147 TGTTCTTGCAAGTTTATGGTTGTTGAGTT
1 TGTTCTTGCAAATTTATGGCTGTTGAGTT
2176 TGTTCTTGCAAATTTATGGCTGTTGAGTT
1 TGTTCTTGCAAATTTATGGCTGTTGAGTT
2205 TGTTCTTGCA
1 TGTTCTTGCA
2215 CGATAAACCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.15, C:0.10, G:0.25, T:0.50
Consensus pattern (29 bp):
TGTTCTTGCAAATTTATGGCTGTTGAGTT
Found at i:2686 original size:64 final size:64
Alignment explanation
Indices: 2581--2709 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
2571 CCTTACCTTG
* *
2581 ACTCTGTTTTAGTGTTGGTTTTAAAGTTGAAATGAATGAAAAAATGTAGCCTTCTTGTTCATAA
1 ACTCTGTTTTAATGTTGGTTTTAAAGTTGAAATGAAGGAAAAAATGTAGCCTTCTTGTTCATAA
* *
2645 ACTCTGTTTTAATGTTGGTTTTAAAGTTGGAATGAAGGAAAATATGTAGCCTTCTTGTTCATAA
1 ACTCTGTTTTAATGTTGGTTTTAAAGTTGAAATGAAGGAAAAAATGTAGCCTTCTTGTTCATAA
2709 A
1 A
2710 TTATGTCAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (64 bp):
ACTCTGTTTTAATGTTGGTTTTAAAGTTGAAATGAAGGAAAAAATGTAGCCTTCTTGTTCATAA
Found at i:6107 original size:27 final size:27
Alignment explanation
Indices: 6049--6100 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
6039 ATTAAAAAAA
6049 CCAGCCTCATCCCCAACATTTGAAGGT
1 CCAGCCTCATCCCCAACATTTGAAGGT
* *
6076 CCAGCCTTATCCCCACCATTTGAAG
1 CCAGCCTCATCCCCAACATTTGAAG
6101 TCCCAGCAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.38, G:0.13, T:0.23
Consensus pattern (27 bp):
CCAGCCTCATCCCCAACATTTGAAGGT
Found at i:6909 original size:39 final size:39
Alignment explanation
Indices: 6855--6939 Score: 170
Period size: 39 Copynumber: 2.2 Consensus size: 39
6845 CAACTTAAGT
6855 AGAGAAGCTTTGAATAACCTCATATTATTCATATATAAC
1 AGAGAAGCTTTGAATAACCTCATATTATTCATATATAAC
6894 AGAGAAGCTTTGAATAACCTCATATTATTCATATATAAC
1 AGAGAAGCTTTGAATAACCTCATATTATTCATATATAAC
6933 AGAGAAG
1 AGAGAAG
6940 TTAAAAGACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (39 bp):
AGAGAAGCTTTGAATAACCTCATATTATTCATATATAAC
Found at i:7605 original size:171 final size:171
Alignment explanation
Indices: 7264--7609 Score: 604
Period size: 173 Copynumber: 2.0 Consensus size: 171
7254 CAGCCCAGAA
*
7264 AACACACAGGAAAACCCTTGATTTCGCTCGCAATGAAGTTTACAAGTGAATTAACGGTAAAAAAC
1 AACACACAGGAAAACCCTCGATTTCGCTCGCAATGAAGTTTACAAGTGAATTAACGGTAAAAAAC
7329 CTAAAAACTACAAATGATAGGAGATTCAGATGGCTTTTCGAAGAAATTTCGAAGAACCCTAACTC
66 CTAAAAACTACAAATGATAGGAGATTCAGATGGCTTTTCGAAGAAATTTCGAAGAACCCTAACTC
*
7394 TGGAATTTGGGGGTTTTTTTTTCCCTCGATGAATTTTTTTT
131 TGGAATTTGGGGGTGTTTTTTTCCCTCGATGAATTTTTTTT
7435 AACACACAGGAAAACCCTCGATTTCGCTCGCAATGAAGTTTACAAGTGAATTAACGGTGAAAAAA
1 AACACACAGGAAAACCCTCGATTTCGCTCGCAATGAAGTTTACAAGTGAATTAACGGT--AAAAA
* * * *
7500 ACCTAAAAACTACATATTATAGGAGATTCAGATGGGTTTTCGAAGAAATTTCGAAGAACCCTAAT
64 ACCTAAAAACTACAAATGATAGGAGATTCAGATGGCTTTTCGAAGAAATTTCGAAGAACCCTAAC
*
7565 TCTGGAATTTGGGGG-GTTTTTTTCCCTCGATGGATTTTTTTT
129 TCTGGAATTTGGGGGTGTTTTTTTCCCTCGATGAATTTTTTTT
7607 AAC
1 AAC
7610 TAACGATTTT
Statistics
Matches: 166, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
171 57 0.34
172 28 0.17
173 81 0.49
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (171 bp):
AACACACAGGAAAACCCTCGATTTCGCTCGCAATGAAGTTTACAAGTGAATTAACGGTAAAAAAC
CTAAAAACTACAAATGATAGGAGATTCAGATGGCTTTTCGAAGAAATTTCGAAGAACCCTAACTC
TGGAATTTGGGGGTGTTTTTTTCCCTCGATGAATTTTTTTT
Found at i:7840 original size:29 final size:30
Alignment explanation
Indices: 7784--7841 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
7774 GTGATTTGGT
* **
7784 CGTTTCATGTAACGTTATATCCTTAATTGC
1 CGTTTCATGAAACGTTATATCCCAAATTGC
7814 CGTTTC-TGAAACGTTATATCCCAAATTG
1 CGTTTCATGAAACGTTATATCCCAAATTG
7842 ATCCGCGCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (30 bp):
CGTTTCATGAAACGTTATATCCCAAATTGC
Found at i:8001 original size:19 final size:19
Alignment explanation
Indices: 7977--8013 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
7967 TAACATAGTT
*
7977 TAATTTAGTCACGTGGATA
1 TAATTTAGCCACGTGGATA
7996 TAATTTAGCCACGTGGAT
1 TAATTTAGCCACGTGGAT
8014 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (19 bp):
TAATTTAGCCACGTGGATA
Found at i:10472 original size:6 final size:6
Alignment explanation
Indices: 10456--10505 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
10446 GCAGTGCAAC
*
10456 AAAAC- AAAACG AAAACG -AAACA AAAACAG AAAACAG AAAAACG AAAACG
1 AAAACG AAAACG AAAACG AAAACG AAAAC-G AAAAC-G -AAAACG AAAACG
10505 A
1 A
10506 TGCCAAACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 9 0.23
6 17 0.44
7 8 0.21
8 5 0.13
ACGTcount: A:0.72, C:0.16, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAACG
Found at i:15299 original size:145 final size:147
Alignment explanation
Indices: 15032--15306 Score: 491
Period size: 145 Copynumber: 1.9 Consensus size: 147
15022 TATTTTGAAG
* *
15032 CAAATTTGTCACCAGTTTTGTCACTTTCACCACCTTTGAAGCAATCTGAGCTACGTACATTGATG
1 CAAATTCGTCACCAGTTTTGTCACTTTCACCACCTTTGAAGCAATCCGAG--ACGTACATTGATG
15097 CATATGGGCTTGATGAATTTCGAAATTGGCAATTATTTGATGATACTTAACATATTTCCATTATA
64 CATATGGGCTTGATGAATTTCGAAATTGGCAATTATTTGATGATACTTAACATATTTCCATTATA
15162 AATTTCTACGAATACTTGA
129 AATTTCTACGAATACTTGA
15181 CAAATTCGTCACCAGTTTTGTCACTTTCACCACCTTTGAAGCAATCCGAG-C-TACATTGATGCA
1 CAAATTCGTCACCAGTTTTGTCACTTTCACCACCTTTGAAGCAATCCGAGACGTACATTGATGCA
*
15244 TATGGGCTTGATGAATTTCGAAATTGGCAATTATTTGATGATACTTAACATATTTCTATTATA
66 TATGGGCTTGATGAATTTCGAAATTGGCAATTATTTGATGATACTTAACATATTTCCATTATA
15307 TGTGGCGTTT
Statistics
Matches: 123, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
145 74 0.60
146 1 0.01
149 48 0.39
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (147 bp):
CAAATTCGTCACCAGTTTTGTCACTTTCACCACCTTTGAAGCAATCCGAGACGTACATTGATGCA
TATGGGCTTGATGAATTTCGAAATTGGCAATTATTTGATGATACTTAACATATTTCCATTATAAA
TTTCTACGAATACTTGA
Found at i:23769 original size:6 final size:6
Alignment explanation
Indices: 23758--23786 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
23748 TAATCGTGGA
23758 GAGATC GAGATC GAGATC GAGAT- GAGATC
1 GAGATC GAGATC GAGATC GAGATC GAGATC
23787 ATTTTCTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.17
Consensus pattern (6 bp):
GAGATC
Found at i:24741 original size:6 final size:6
Alignment explanation
Indices: 24730--24756 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
24720 CTTGTTCTTC
24730 CTCCAT CTCCAT CTCCAT CTCCAT CTC
1 CTCCAT CTCCAT CTCCAT CTCCAT CTC
24757 GAACCCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.52, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCAT
Found at i:29327 original size:16 final size:16
Alignment explanation
Indices: 29306--29336 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29296 TGAAAAATAT
29306 AAGAGAATAGAGAGAG
1 AAGAGAATAGAGAGAG
*
29322 AAGAGAATATAGAGA
1 AAGAGAATAGAGAGA
29337 AGGGGAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.10
Consensus pattern (16 bp):
AAGAGAATAGAGAGAG
Found at i:34178 original size:17 final size:18
Alignment explanation
Indices: 34164--34197 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34154 TAATTATTGG
34164 AAAT-AAAATATTATTAA
1 AAATAAAAATATTATTAA
34181 AAATAAAAATATTATTA
1 AAATAAAAATATTATTA
34198 TATTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATAAAAATATTATTAA
Done.