Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007358.1 Corchorus capsularis cultivar CVL-1 contig07379, 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: 24268
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:220 original size:32 final size:32
Alignment explanation
Indices: 184--252 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
174 TTTAGTAATG
**
184 ACAATTTAGAAATATAATTTTTTAAA-AAGGGT
1 ACAATTTAGAAATAT-ATTTTAAAAATAAGGGT
* *
216 ACAA-TTGGAAATATGTTTTAAAAATAAGGGT
1 ACAATTTAGAAATATATTTTAAAAATAAGGGT
247 ACAATT
1 ACAATT
253 GGAAAACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 7 0.23
31 19 0.61
32 5 0.16
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.35
Consensus pattern (32 bp):
ACAATTTAGAAATATATTTTAAAAATAAGGGT
Found at i:228 original size:31 final size:31
Alignment explanation
Indices: 192--257 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
182 TGACAATTTA
**
192 GAAATATAATTTTTTAAA-AAGGGTACAATTG
1 GAAATAT-ATTTTAAAAATAAGGGTACAATTG
*
223 GAAATATGTTTTAAAAATAAGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATTG
254 GAAA
1 GAAA
258 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATTG
Found at i:293 original size:2 final size:2
Alignment explanation
Indices: 286--334 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
276 TTCGTACTTT
*
286 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
329 TA TA TA
1 TA TA TA
335 GAACTTCAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4181 original size:33 final size:33
Alignment explanation
Indices: 4129--4234 Score: 119
Period size: 33 Copynumber: 3.2 Consensus size: 33
4119 GATGACCCAT
* *
4129 GCCGTCCCAAGAGGGCGGCTTCACCATGGGCAG
1 GCCGCCCCATGAGGGCGGCTTCACCATGGGCAG
* ***
4162 GCCGCCCCATGAGGGCGGCTTCCCCATGAAAAG
1 GCCGCCCCATGAGGGCGGCTTCACCATGGGCAG
4195 GCCGCCCCACTG-GGGCGGCTT-AGCCA-GGGCAG
1 GCCGCCCCA-TGAGGGCGGCTTCA-CCATGGGCAG
4227 GCCGCCCC
1 GCCGCCCC
4235 GGTGGGGCGG
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
32 11 0.18
33 48 0.79
34 2 0.03
ACGTcount: A:0.16, C:0.39, G:0.35, T:0.10
Consensus pattern (33 bp):
GCCGCCCCATGAGGGCGGCTTCACCATGGGCAG
Found at i:4188 original size:17 final size:17
Alignment explanation
Indices: 4134--4190 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
4124 CCCATGCCGT
*
4134 CCCAAGAGGGCGGCTTC
1 CCCATGAGGGCGGCTTC
* **
4151 ACCAT--GGGCAGGCCGC
1 CCCATGAGGGC-GGCTTC
4167 CCCATGAGGGCGGCTTC
1 CCCATGAGGGCGGCTTC
4184 CCCATGA
1 CCCATGA
4191 AAAGGCCGCC
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
15 4 0.13
16 8 0.27
17 14 0.47
18 4 0.13
ACGTcount: A:0.18, C:0.37, G:0.33, T:0.12
Consensus pattern (17 bp):
CCCATGAGGGCGGCTTC
Found at i:4234 original size:32 final size:31
Alignment explanation
Indices: 4141--4246 Score: 106
Period size: 33 Copynumber: 3.3 Consensus size: 31
4131 CGTCCCAAGA
4141 GGGCGGCTTCACCATGGGCAGGCCGCCCCATG
1 GGGCGGCTT-ACCATGGGCAGGCCGCCCCATG
* ***
4173 AGGGCGGCTTCCCCATGAAAAGGCCGCCCCACTG
1 -GGGCGGCTT-ACCATGGGCAGGCCGCCCCA-TG
*
4207 GGGCGGCTTAGCCA-GGGCAGGCCGCCCCGGTG
1 GGGCGGCTTA-CCATGGGCAGGCCGCCCC-ATG
4239 GGGCGGCT
1 GGGCGGCT
4247 CGGCTAGTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
32 21 0.34
33 38 0.62
34 2 0.03
ACGTcount: A:0.13, C:0.36, G:0.40, T:0.11
Consensus pattern (31 bp):
GGGCGGCTTACCATGGGCAGGCCGCCCCATG
Found at i:4389 original size:33 final size:33
Alignment explanation
Indices: 4326--4401 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
4316 GTGCCGTCCT
* *
4326 CCTGGGGCGGCACTACCATGGCCAGGCCGCCTC
1 CCTGGGGCGGCACTACCATGGACAGACCGCCTC
* *
4359 CCTGGGGCGGCCCTACCATGGATAGACCG---C
1 CCTGGGGCGGCACTACCATGGACAGACCGCCTC
4389 CCTGGGGCGGCAC
1 CCTGGGGCGGCAC
4402 CGGTACTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 13 0.34
33 25 0.66
ACGTcount: A:0.13, C:0.39, G:0.36, T:0.12
Consensus pattern (33 bp):
CCTGGGGCGGCACTACCATGGACAGACCGCCTC
Found at i:4518 original size:33 final size:33
Alignment explanation
Indices: 4457--4548 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
4447 AAAGCCTTGT
* *
4457 CGTCCTAGTGGGGCGGCT-AGCCGTGGCAGAGC
1 CGTCCTAGTGGGGAGGCTCCGCCGTGGCAGAGC
4489 CGTCCTAGTGGGGAGGCTCCGCCGTGGCAGAGC
1 CGTCCTAGTGGGGAGGCTCCGCCGTGGCAGAGC
4522 CGTCCTAGTGGGGAGGCTCCG-CGTGGC
1 CGTCCTAGTGGGGAGGCTCCGCCGTGGC
4549 TAAGGGCAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 23 0.40
33 34 0.60
ACGTcount: A:0.11, C:0.29, G:0.43, T:0.16
Consensus pattern (33 bp):
CGTCCTAGTGGGGAGGCTCCGCCGTGGCAGAGC
Found at i:7342 original size:12 final size:12
Alignment explanation
Indices: 7325--7350 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7315 TTATACTATT
7325 ATTATTATAGTA
1 ATTATTATAGTA
7337 ATTATTATAGTA
1 ATTATTATAGTA
7349 AT
1 AT
7351 AAAATAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTATTATAGTA
Found at i:8924 original size:17 final size:18
Alignment explanation
Indices: 8876--8953 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 18
8866 AGTCAGCTCG
8876 GGTTGAATTTGGGTGATCA
1 GGTTGAATTTGGGT-ATCA
*
8895 GGTT-AATTCGGGT-TC-
1 GGTTGAATTTGGGTATCA
8910 GAGTTGAATTTGGG--TCA
1 G-GTTGAATTTGGGTATCA
* *
8927 GGTT-AATTCGGGT-TCT
1 GGTTGAATTTGGGTATCA
*
8943 GGTTTAATTTG
1 GGTTGAATTTG
8954 TGTTTTGGCC
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
15 8 0.16
16 16 0.33
17 13 0.27
18 8 0.16
19 4 0.08
ACGTcount: A:0.18, C:0.08, G:0.33, T:0.41
Consensus pattern (18 bp):
GGTTGAATTTGGGTATCA
Found at i:8933 original size:32 final size:35
Alignment explanation
Indices: 8877--8941 Score: 109
Period size: 32 Copynumber: 1.9 Consensus size: 35
8867 GTCAGCTCGG
8877 GTTGAATTTGGGTGATCAGGTTAATTCGGGTTCGA
1 GTTGAATTTGGGTGATCAGGTTAATTCGGGTTCGA
8912 GTTGAATTT-GG-G-TCAGGTTAATTCGGGTTC
1 GTTGAATTTGGGTGATCAGGTTAATTCGGGTTC
8942 TGGTTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 18 0.60
33 1 0.03
34 2 0.07
35 9 0.30
ACGTcount: A:0.18, C:0.09, G:0.34, T:0.38
Consensus pattern (35 bp):
GTTGAATTTGGGTGATCAGGTTAATTCGGGTTCGA
Found at i:9172 original size:16 final size:16
Alignment explanation
Indices: 9094--9174 Score: 90
Period size: 16 Copynumber: 5.1 Consensus size: 16
9084 TTTTCATAAA
*
9094 TTTTCGGATTCGGGTT
1 TTTTCGGGTTCGGGTT
* * *
9110 TTTTCAGGTTCTGATT
1 TTTTCGGGTTCGGGTT
* *
9126 TTTTCGGGTTAGGGCT
1 TTTTCGGGTTCGGGTT
* *
9142 TTTTCGGATTAGGGTT
1 TTTTCGGGTTCGGGTT
9158 TTTTCGGGTTCGGGTT
1 TTTTCGGGTTCGGGTT
9174 T
1 T
9175 GGGTTCAGAC
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.07, C:0.11, G:0.31, T:0.51
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTT
Found at i:21263 original size:74 final size:75
Alignment explanation
Indices: 21185--21341 Score: 266
Period size: 74 Copynumber: 2.1 Consensus size: 75
21175 TGGTCTTTTC
*
21185 ACACTTTTCAGG-TGA-CTAAAAAGCCCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCT
1 ACACTTTTCAGGATGACCTAAAAA-CCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCT
21248 TTTTCGTAATT
65 TTTTCGTAATT
21259 ACACTTTT-AGGATGACCTAAAAACCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTT
1 ACACTTTTCAGGATGACCTAAAAACCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTT
21323 TTTCGTAATT
66 TTTCGTAATT
*
21333 ACACATTTC
1 ACACTTTTC
21342 CCTTCCTTAA
Statistics
Matches: 78, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
73 3 0.04
74 68 0.87
75 7 0.09
ACGTcount: A:0.22, C:0.31, G:0.08, T:0.39
Consensus pattern (75 bp):
ACACTTTTCAGGATGACCTAAAAACCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTT
TTTCGTAATT
Found at i:21379 original size:20 final size:21
Alignment explanation
Indices: 21348--21386 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
21338 TTTCCCTTCC
21348 TTAATGGTTTTTAATTAATGT
1 TTAATGGTTTTTAATTAATGT
21369 TTAAT-GTTTTTAATTAAT
1 TTAATGGTTTTTAATTAAT
21387 TGCTTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (21 bp):
TTAATGGTTTTTAATTAATGT
Done.