Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015775.1 Corchorus capsularis cultivar CVL-1 contig15796, 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: 21797
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:6085 original size:27 final size:27
Alignment explanation
Indices: 6055--6108 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
6045 AGCTTCAGAG
6055 GGAAACTCTTGAATTAATATGTATTTT
1 GGAAACTCTTGAATTAATATGTATTTT
6082 GGAAACTCTTGAATTAATATGTATTTT
1 GGAAACTCTTGAATTAATATGTATTTT
6109 CTTTTCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (27 bp):
GGAAACTCTTGAATTAATATGTATTTT
Found at i:12659 original size:33 final size:33
Alignment explanation
Indices: 12605--12722 Score: 184
Period size: 33 Copynumber: 3.5 Consensus size: 33
12595 CCCATGGTGA
* *
12605 AGCCGCCCCAGTGGGAGAGGCTCCGCCGTGGTTG
1 AGCCTCCCTAGTGGG-GAGGCTCCGCCGTGGTTG
12639 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
*
12672 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGCTG
1 AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
12705 AGCCAT-CCTAGTGGGGAG
1 AGCC-TCCCTAGTGGGGAG
12723 ACTCAGTGTA
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
33 66 0.82
34 14 0.17
ACGTcount: A:0.12, C:0.31, G:0.40, T:0.18
Consensus pattern (33 bp):
AGCCTCCCTAGTGGGGAGGCTCCGCCGTGGTTG
Found at i:12668 original size:16 final size:16
Alignment explanation
Indices: 12615--12701 Score: 61
Period size: 17 Copynumber: 5.2 Consensus size: 16
12605 AGCCGCCCCA
12615 GTGGGAGAGGCTCCGCC
1 GTGGG-GAGGCTCCGCC
* * *
12632 GTGGTTGAGCCTCC-CTA
1 GTGG-GGAGGCTCCGC-C
12649 GTGGGGAGGCTCCGCC
1 GTGGGGAGGCTCCGCC
* * *
12665 GTGGTTGAGCCTCC-CTA
1 GTGG-GGAGGCTCCGC-C
12682 GTGGGGAGGCTCCGCC
1 GTGGGGAGGCTCCGCC
12698 GTGG
1 GTGG
12702 CTGAGCCATC
Statistics
Matches: 52, Mismatches: 12, Indels: 13
0.68 0.16 0.17
Matches are distributed among these distances:
16 24 0.46
17 28 0.54
ACGTcount: A:0.09, C:0.29, G:0.43, T:0.20
Consensus pattern (16 bp):
GTGGGGAGGCTCCGCC
Found at i:12797 original size:21 final size:21
Alignment explanation
Indices: 12773--12816 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12763 AAAAGTGTAA
* *
12773 AAAAATGGGGCGGTATTTAGC
1 AAAAATAGGGCGATATTTAGC
*
12794 AAAACTAGGGCGATATTTAGC
1 AAAAATAGGGCGATATTTAGC
12815 AA
1 AA
12817 CTCCCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (21 bp):
AAAAATAGGGCGATATTTAGC
Found at i:13224 original size:26 final size:26
Alignment explanation
Indices: 13184--13235 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
13174 ACTGAGACTA
*
13184 GACTCGAAACTGACTAAAAAACAAACT
1 GACTCGAAACCGACTAAAAAA-AAACT
*
13211 GACTC-AAACCGACTAAGAAAAAACT
1 GACTCGAAACCGACTAAAAAAAAACT
13236 CAAATAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 13 0.57
27 5 0.22
ACGTcount: A:0.52, C:0.23, G:0.12, T:0.13
Consensus pattern (26 bp):
GACTCGAAACCGACTAAAAAAAAACT
Found at i:13384 original size:13 final size:14
Alignment explanation
Indices: 13358--13389 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
13348 ACGAGAACTA
13358 GAGAGGGAGAAGGG
1 GAGAGGGAGAAGGG
13372 GAGAGGG-GAAGGG
1 GAGAGGGAGAAGGG
13385 GAGAG
1 GAGAG
13390 AGAGGAGCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (14 bp):
GAGAGGGAGAAGGG
Found at i:17109 original size:11 final size:11
Alignment explanation
Indices: 17093--17123 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
17083 TATAAAGAAG
17093 TAATTCAATTA
1 TAATTCAATTA
17104 TAATTCAATTA
1 TAATTCAATTA
*
17115 GAATTCAAT
1 TAATTCAAT
17124 AACCGATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (11 bp):
TAATTCAATTA
Found at i:18211 original size:20 final size:20
Alignment explanation
Indices: 18186--18225 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
18176 AAGCGAACTA
18186 GAGAGAGAAGGAGAAAGAAATC
1 GAGAG-GAA-GAGAAAGAAATC
*
18208 GAGAGGAAGAGAGAGAAA
1 GAGAGGAAGAGAAAGAAA
18226 GGATAAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.55, C:0.03, G:0.40, T:0.03
Consensus pattern (20 bp):
GAGAGGAAGAGAAAGAAATC
Found at i:18329 original size:18 final size:21
Alignment explanation
Indices: 18285--18345 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 21
18275 TTTTAGGAAT
18285 ATAATATATATATATATATATA
1 ATAATAT-TATATATATATATA
*
18307 TTAATATTA-ATA-ATA-ATA
1 ATAATATTATATATATATATA
18325 ATAATATTAT-TATTATATATA
1 ATAATATTATATA-TATATATA
18346 GTTAAATAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 13 0.39
19 3 0.09
20 6 0.18
21 5 0.15
22 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATATTATATATATATATA
Found at i:19843 original size:24 final size:24
Alignment explanation
Indices: 19816--19863 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
19806 CCTTACCGTC
19816 GTCGAGAGAGAGAGAG-GAGAGAAA
1 GTCGAGAGA-AGAGAGTGAGAGAAA
19840 GTCGAGAGAAGAGAGTGAGAGAAA
1 GTCGAGAGAAGAGAGTGAGAGAAA
19864 ATTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.46, C:0.04, G:0.44, T:0.06
Consensus pattern (24 bp):
GTCGAGAGAAGAGAGTGAGAGAAA
Found at i:20277 original size:18 final size:19
Alignment explanation
Indices: 20251--20295 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
20241 TAAATACTAA
*
20251 AAAGCCCACTA-TTTCCAC
1 AAAGCCCACTACTTTACAC
*
20269 AAGGCCCACTACTTTACAC
1 AAAGCCCACTACTTTACAC
20288 AAAGCCCA
1 AAAGCCCA
20296 TTATACAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.36, C:0.38, G:0.09, T:0.18
Consensus pattern (19 bp):
AAAGCCCACTACTTTACAC
Found at i:21112 original size:18 final size:19
Alignment explanation
Indices: 21075--21112 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
21065 ACTTTACTCA
* *
21075 CCCAATCAAATTCATTAAG
1 CCCAATCAAATTAATCAAG
21094 CCCAATC-AATTAATCAAG
1 CCCAATCAAATTAATCAAG
21112 C
1 C
21113 TATCACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.42, C:0.29, G:0.05, T:0.24
Consensus pattern (19 bp):
CCCAATCAAATTAATCAAG
Done.