Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009847.1 Corchorus capsularis cultivar CVL-1 contig09868, 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: 73681
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:768 original size:29 final size:28
Alignment explanation
Indices: 734--788 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
724 TTAAAATTGG
* *
734 AAGTTTAATGGACAAAATGTCCAAAATTA
1 AAGTTTAAGGGACAAAAAGT-CAAAATTA
*
763 AAGTTTAGGGGACAAAAAGTCAAAAT
1 AAGTTTAAGGGACAAAAAGTCAAAAT
789 CATGAGGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (28 bp):
AAGTTTAAGGGACAAAAAGTCAAAATTA
Found at i:1334 original size:26 final size:26
Alignment explanation
Indices: 1305--1357 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1295 TGGGCTATTA
*
1305 CGAAATTTAGAATGCAGATCGAATTC
1 CGAAATTTAGAATACAGATCGAATTC
1331 CGAAATTTAGAATACAGATCGAATTC
1 CGAAATTTAGAATACAGATCGAATTC
1357 C
1 C
1358 TATTGTTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (26 bp):
CGAAATTTAGAATACAGATCGAATTC
Found at i:17256 original size:27 final size:27
Alignment explanation
Indices: 17213--17266 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
17203 TAACCTTTAC
*
17213 AGGATTTCCTTTATATAAAGGGATTCT
1 AGGATTTCCTCTATATAAAGGGATTCT
* *
17240 AGGATTTCCTCTGTATAAAGTGATTCT
1 AGGATTTCCTCTATATAAAGGGATTCT
17267 CCGACCAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41
Consensus pattern (27 bp):
AGGATTTCCTCTATATAAAGGGATTCT
Found at i:22214 original size:16 final size:16
Alignment explanation
Indices: 22193--22223 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22183 GACAAAGCCT
22193 GGGTCGAATCCGGATA
1 GGGTCGAATCCGGATA
*
22209 GGGTCGGATCCGGAT
1 GGGTCGAATCCGGAT
22224 GAGTCATGGC
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:0.19, C:0.19, G:0.42, T:0.19
Consensus pattern (16 bp):
GGGTCGAATCCGGATA
Found at i:24215 original size:28 final size:29
Alignment explanation
Indices: 24162--24216 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
24152 TTCAAATTGC
* *
24162 AATTTTAAGGGACAAAATGTCCAAAATTA
1 AATTTTAAGGGACAAAACGTACAAAATTA
*
24191 AATTTTAGGGGACAAAACG-ACAAAAT
1 AATTTTAAGGGACAAAACGTACAAAAT
24217 CATACAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (29 bp):
AATTTTAAGGGACAAAACGTACAAAATTA
Found at i:31163 original size:84 final size:81
Alignment explanation
Indices: 31003--31187 Score: 219
Period size: 84 Copynumber: 2.2 Consensus size: 81
30993 TGTCGAAGAC
* * * *
31003 AGAGATCATTATCATCATCATTATGATCATGATTCCCAAGGAAGATATTATCAACCTAACCATCA
1 AGAGATCATTATCATCATCATTATGATCATCATTCCCAAGGAAGATATTAGCAACCGAACCAGCA
31068 AACTGCACTTGAAAAG
66 AACTGCACTTGAAAAG
* * * * *
31084 AGAGATCCTTATCATCATTATTATGATGATCCCCATTCCCAAGGAAGATATTGGC-ATCGAACCC
1 AGAGATCATTATCATCATCATTATGATCAT---CATTCCCAAGGAAGATATTAGCAACCGAA-CC
* *
31148 AGCAATCTGCTCTTGAAAAG
62 AGCAAACTGCACTTGAAAAG
*
31168 AGAGATCATTATTATCATCA
1 AGAGATCATTATCATCATCA
31188 CTACAATGAT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
81 27 0.31
83 4 0.05
84 55 0.64
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (81 bp):
AGAGATCATTATCATCATCATTATGATCATCATTCCCAAGGAAGATATTAGCAACCGAACCAGCA
AACTGCACTTGAAAAG
Found at i:36862 original size:27 final size:28
Alignment explanation
Indices: 36808--36864 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
36798 CGGTCAAAAT
* *
36808 AGAATCTATGATATATTTTTTTTTAGGTA
1 AGAATCTATGA-ATATTTTTATTGAGGTA
36837 AGAATCTATG-ATATTTTTATTGAGGTA
1 AGAATCTATGAATATTTTTATTGAGGTA
36864 A
1 A
36865 ATAAATCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 16 0.62
29 10 0.38
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (28 bp):
AGAATCTATGAATATTTTTATTGAGGTA
Found at i:36871 original size:29 final size:29
Alignment explanation
Indices: 36804--36880 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
36794 TTGTCGGTCA
* *
36804 AAATAGAATCTATGATATATTTTTTTTTAGGT
1 AAATA-AATCTATG--ATATTTTTATTGAGGT
*
36836 -AA-GAATCTATGATATTTTTATTGAGGT
1 AAATAAATCTATGATATTTTTATTGAGGT
*
36863 AAATAAATCTATAATATT
1 AAATAAATCTATGATATT
36881 AATAATTCGT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 14 0.37
28 2 0.05
29 20 0.53
31 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (29 bp):
AAATAAATCTATGATATTTTTATTGAGGT
Found at i:48944 original size:53 final size:54
Alignment explanation
Indices: 48882--48983 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 54
48872 TTCTTTTTTC
* *
48882 TTTCAAATTTTGATGGATGAATCCGTATATTTTTAGGATTCATTAGGAAGCAAT
1 TTTCAAATTTTGATGGATGAATCCGAATATTTCTAGGATTCATTAGGAAGCAAT
* *
48936 TTTC-AATTTTGATTGATGAATCCGAATATTTCTAGGATTCATTTGGAA
1 TTTCAAATTTTGATGGATGAATCCGAATATTTCTAGGATTCATTAGGAA
48984 CTCTTATGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 40 0.91
54 4 0.09
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (54 bp):
TTTCAAATTTTGATGGATGAATCCGAATATTTCTAGGATTCATTAGGAAGCAAT
Found at i:53884 original size:33 final size:35
Alignment explanation
Indices: 53842--53927 Score: 110
Period size: 33 Copynumber: 2.6 Consensus size: 35
53832 ACTGATTGGT
* *
53842 ATCTATGTATATATATATATTTTTTT-T-TAGAGA
1 ATCTATGTATATATATATATTTTTTTATGGAAAGA
*
53875 ATCTATGTATACAT-TAT-TTTTTTTATGGAAAGA
1 ATCTATGTATATATATATATTTTTTTATGGAAAGA
53908 ATCTATGTATATATAT-TATT
1 ATCTATGTATATATATATATT
53928 GATAGTCATA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
31 7 0.16
32 4 0.09
33 31 0.69
34 3 0.07
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (35 bp):
ATCTATGTATATATATATATTTTTTTATGGAAAGA
Found at i:56321 original size:13 final size:13
Alignment explanation
Indices: 56301--56351 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
56291 AACAGATTAA
56301 AGAA-AAAAACAG
1 AGAACAAAAACAG
56313 AGAACAAAAACAG
1 AGAACAAAAACAG
* *
56326 AGCAGAAAAACAG
1 AGAACAAAAACAG
*
56339 AGAACGAAAACAG
1 AGAACAAAAACAG
56352 GGAAAAACAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
12 4 0.12
13 29 0.88
ACGTcount: A:0.67, C:0.14, G:0.20, T:0.00
Consensus pattern (13 bp):
AGAACAAAAACAG
Found at i:56341 original size:26 final size:23
Alignment explanation
Indices: 56305--56364 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 23
56295 GATTAAAGAA
56305 AAAAACAGAGAACAAAAACAGAGCAG
1 AAAAACAGAGAACAAAAACAG-G--G
*
56331 AAAAACAGAGAACGAAAACAGGG
1 AAAAACAGAGAACAAAAACAGGG
56354 AAAAACAGAGA
1 AAAAACAGAGA
56365 CACTAACCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 12 0.36
25 1 0.03
26 20 0.61
ACGTcount: A:0.65, C:0.13, G:0.22, T:0.00
Consensus pattern (23 bp):
AAAAACAGAGAACAAAAACAGGG
Found at i:73359 original size:56 final size:52
Alignment explanation
Indices: 73262--73365 Score: 154
Period size: 56 Copynumber: 1.9 Consensus size: 52
73252 TGGGAACCAT
*
73262 TGCAGCTTTTATAATCTTTACAAAAAAAATGTAGAGTATTGGGAACCATTAA
1 TGCAGCTTTTATAATCTTTACAAAAAAAATGTAAAGTATTGGGAACCATTAA
*
73314 TGCAGCTTTTATAATATTCTTTTCAAAAAAAAATGTAAAGTATTGGGAACCA
1 TGCAGCTTTTAT-A-A-TCTTTAC-AAAAAAAATGTAAAGTATTGGGAACCA
73366 ACCATAAGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
52 12 0.26
53 1 0.02
54 1 0.02
55 6 0.13
56 26 0.57
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (52 bp):
TGCAGCTTTTATAATCTTTACAAAAAAAATGTAAAGTATTGGGAACCATTAA
Done.