Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012569.1 Corchorus capsularis cultivar CVL-1 contig12590, 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: 29851
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1055 original size:24 final size:24
Alignment explanation
Indices: 1023--1071 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1013 TTGTTTATTC
1023 AAGTAGGGAGTTATAAAAATTTCT
1 AAGTAGGGAGTTATAAAAATTTCT
1047 AAGTAGGGAGTTATAAAAATTTCT
1 AAGTAGGGAGTTATAAAAATTTCT
1071 A
1 A
1072 TAAAAATGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (24 bp):
AAGTAGGGAGTTATAAAAATTTCT
Found at i:8239 original size:26 final size:26
Alignment explanation
Indices: 8210--8259 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
8200 GCCATCGGTA
8210 AGTTCATCTCAAGTTTTTCCTGCGTG
1 AGTTCATCTCAAGTTTTTCCTGCGTG
**
8236 AGTTCATCTCCGGTTTTTCCTGCG
1 AGTTCATCTCAAGTTTTTCCTGCG
8260 GTAATTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.12, C:0.26, G:0.20, T:0.42
Consensus pattern (26 bp):
AGTTCATCTCAAGTTTTTCCTGCGTG
Found at i:10238 original size:8 final size:8
Alignment explanation
Indices: 10225--10249 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
10215 TGGACACGTT
10225 TTGTACTA
1 TTGTACTA
10233 TTGTACTA
1 TTGTACTA
10241 TTGTACTA
1 TTGTACTA
10249 T
1 T
10250 GTAATCTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (8 bp):
TTGTACTA
Found at i:12091 original size:28 final size:29
Alignment explanation
Indices: 12059--12134 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
12049 ACTTGCAGCG
*
12059 TTTGGTCGTTTTGCCCCCGAACT-TCAAT
1 TTTGGACGTTTTGCCCCCGAACTCTCAAT
* **
12087 TTTGGACATTTTGCTCCCTTAACTCTCAAT
1 TTTGGACGTTTTGC-CCCCGAACTCTCAAT
*
12117 TTTGAACGTTTTGCCCCC
1 TTTGGACGTTTTGCCCCC
12135 TCTCAAACGA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 12 0.31
29 10 0.26
30 17 0.44
ACGTcount: A:0.16, C:0.29, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCCGAACTCTCAAT
Found at i:18110 original size:34 final size:33
Alignment explanation
Indices: 18061--18127 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
18051 TCAATTAATT
*
18061 GTTTTACTTAAATTGTTTTCTTAGTCATTAGTTTA
1 GTTTTACTTAAATTGTTTTCCTAGT--TTAGTTTA
*
18096 GTTTTA-TTCAATTGTTTTCCTAGTTTAGTTTA
1 GTTTTACTTAAATTGTTTTCCTAGTTTAGTTTA
18128 ATTATTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 8 0.27
34 16 0.53
35 6 0.20
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (33 bp):
GTTTTACTTAAATTGTTTTCCTAGTTTAGTTTA
Found at i:18795 original size:12 final size:12
Alignment explanation
Indices: 18778--18807 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
18768 CTGGCAATCT
18778 GTGTTTCGTGTC
1 GTGTTTCGTGTC
18790 GTGTTTCGTGTC
1 GTGTTTCGTGTC
18802 GTGTTT
1 GTGTTT
18808 ACATAGGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.33, T:0.53
Consensus pattern (12 bp):
GTGTTTCGTGTC
Found at i:19028 original size:16 final size:16
Alignment explanation
Indices: 19009--19055 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
18999 GTTTGAGTTC
19009 GGGTATTTTCGGGCTT
1 GGGTATTTTCGGGCTT
** *
19025 GGGTTAAGTT-GGGTTT
1 GGG-TATTTTCGGGCTT
19041 GGGTATTTTCGGGCT
1 GGGTATTTTCGGGCT
19056 CGGCTTATGT
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
15 4 0.17
16 15 0.65
17 4 0.17
ACGTcount: A:0.09, C:0.09, G:0.40, T:0.43
Consensus pattern (16 bp):
GGGTATTTTCGGGCTT
Found at i:19112 original size:23 final size:23
Alignment explanation
Indices: 19084--19127 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19074 GGTGATTTCA
*
19084 GGTTCGGTCTCGGGTAGGGTTTG
1 GGTTCGGGCTCGGGTAGGGTTTG
*
19107 GGTTCGGGCTCGGGTCGGGTT
1 GGTTCGGGCTCGGGTAGGGTT
19128 CGGGCTCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.02, C:0.16, G:0.50, T:0.32
Consensus pattern (23 bp):
GGTTCGGGCTCGGGTAGGGTTTG
Found at i:20312 original size:166 final size:167
Alignment explanation
Indices: 19919--20362 Score: 551
Period size: 166 Copynumber: 2.7 Consensus size: 167
19909 TGAGTCATTT
*
19919 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGAACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * * * * *
19984 TTAAGTAATCTGCTAAGTAGGTAAAA-ACGAAAAAGATTAGTTCTCTAGTTCATATCATCAATCC
65 TTAAGTAATCTGCAAAGTAGG-AAAAGACGAAAAAAATAAGTTCTCTACTCCATATAAGCAAGCC
* * * *
20048 TTGATGGGGATCTTTTATTAATTCTACTACTCTATTCAA
129 TTGATAGAGATCTTTTAGTAATTCTACTACTCTATTAAA
* * * *
20087 GTCCATTAAGAAATGACCAAAAAGATTA-CTATTTAATCCCCTCAAGAATCAATAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * *
20151 TTAAATAATCCGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCA-A-AAGCAAGCC
65 TTAAGTAATCTGCAAAGTAGGAAAAGACGAAAAAAATAAGTTCTCT-ACTCCATATAAGCAAGCC
*
20214 TTGGTAGAGATCTTTTAGTAATT-TCACTACTCTATTAAA
129 TTGATAGAGATCTTTTAGTAATTCT-ACTACTCTATTAAA
*
20253 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAAT-CCCTCAAGAATTAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
** *
20317 TTAAGTAATCTTAAAAGTGGGAAAAGACGAAAAAAATTAA-TTCTCT
65 TTAAGTAATCTGCAAAGTAGGAAAAGACGAAAAAAA-TAAGTTCTCT
20363 CGCTCCTCAT
Statistics
Matches: 238, Mismatches: 32, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
165 2 0.01
166 126 0.53
167 81 0.34
168 29 0.12
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (167 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCAAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTACTCCATATAAGCAAGCCTT
GATAGAGATCTTTTAGTAATTCTACTACTCTATTAAA
Found at i:20481 original size:2 final size:2
Alignment explanation
Indices: 20476--20502 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20466 TTATATAAGT
20476 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20503 TTTGTAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22286 original size:30 final size:30
Alignment explanation
Indices: 22250--22310 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
22240 GCGACCCACC
*
22250 AAGAACAAGATAGAGATGACAGAGTGAAGG
1 AAGAACAAGATAGACATGACAGAGTGAAGG
*
22280 AAGAACAAGGTAGACATGACAGAGTGAAGG
1 AAGAACAAGATAGACATGACAGAGTGAAGG
22310 A
1 A
22311 GGAAACAGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.49, C:0.08, G:0.33, T:0.10
Consensus pattern (30 bp):
AAGAACAAGATAGACATGACAGAGTGAAGG
Found at i:22877 original size:8 final size:8
Alignment explanation
Indices: 22864--22889 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
22854 TGAAGATATT
22864 TTGAAGAA
1 TTGAAGAA
22872 TTGAAGAA
1 TTGAAGAA
22880 TTGAAGAA
1 TTGAAGAA
22888 TT
1 TT
22890 AATTCAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (8 bp):
TTGAAGAA
Found at i:24267 original size:6 final size:6
Alignment explanation
Indices: 24256--24282 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
24246 TATAATCTGT
24256 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
24283 GCTTTACTTT
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:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Done.