Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012920.1 Corchorus capsularis cultivar CVL-1 contig12941, 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: 59515
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Found at i:1309 original size:53 final size:53
Alignment explanation
Indices: 1216--1368 Score: 195
Period size: 53 Copynumber: 2.9 Consensus size: 53
1206 ATTTATAAGT
* * *
1216 CCCTAGACACAGAGGCAATTCTATATCAAAAGTCCTCAAACACAAGGGTATTCAC
1 CCCTAAACACAAAGGC-A-TCTACATCAAAAGTCCTCAAACACAAGGGTATTCAC
* *
1271 CCCTAAACACAGAGGCACCTCT-C-TCAAAAGTCCTCAAACACAAGGGTATTCAT
1 CCCTAAACACAAAGGCA--TCTACATCAAAAGTCCTCAAACACAAGGGTATTCAC
*
1324 CCCTAAACACAAAGGCATCTACATC-AAAGTCCTCAAGCACAAGGG
1 CCCTAAACACAAAGGCATCTACATCAAAAGTCCTCAAACACAAGGG
1369 CATCTATATT
Statistics
Matches: 89, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
51 3 0.03
52 20 0.22
53 47 0.53
54 1 0.01
55 18 0.20
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.18
Consensus pattern (53 bp):
CCCTAAACACAAAGGCATCTACATCAAAAGTCCTCAAACACAAGGGTATTCAC
Found at i:1403 original size:30 final size:29
Alignment explanation
Indices: 1323--1424 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 29
1313 AGGGTATTCA
* *
1323 TCCCTAAACACAAAGGCATCTACATCAAAG
1 TCCCTAAACAC-AAGGCATCTATATTAAAG
*
1353 T-CCTCAAGCACAAGGGCATCTATATTAAAG
1 TCCCT-AAACACAA-GGCATCTATATTAAAG
* *
1383 TCCCTAAACACAGAGCCATCTATACTAAAG
1 TCCCTAAACACA-AGGCATCTATATTAAAG
*
1413 TCCCCAAACACA
1 TCCCTAAACACA
1425 TATAATACAG
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
29 5 0.08
30 52 0.85
31 4 0.07
ACGTcount: A:0.40, C:0.30, G:0.11, T:0.19
Consensus pattern (29 bp):
TCCCTAAACACAAGGCATCTATATTAAAG
Found at i:10350 original size:15 final size:15
Alignment explanation
Indices: 10327--10359 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10317 CCGACCGAGC
*
10327 CAGCGGCATCCCTAG
1 CAGCAGCATCCCTAG
10342 CAGCAGCATCCCTAG
1 CAGCAGCATCCCTAG
10357 CAG
1 CAG
10360 GCATGAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.39, G:0.24, T:0.12
Consensus pattern (15 bp):
CAGCAGCATCCCTAG
Found at i:13754 original size:53 final size:53
Alignment explanation
Indices: 13685--13818 Score: 202
Period size: 53 Copynumber: 2.5 Consensus size: 53
13675 CAAAGGCAAT
*
13685 TCTATATCAAAAGTCCTCAAACACAAGGGTATTCACCCCTAAACACAGAGGCA
1 TCTACATCAAAAGTCCTCAAACACAAGGGTATTCACCCCTAAACACAGAGGCA
*
13738 CCTCT-C-TCAAAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCA
1 --TCTACATCAAAAGTCCTCAAACACAAGGGTATTCACCCCTAAACACAGAGGCA
*
13791 TCTACATC-AAAGTCCTCAAGCACAAGGG
1 TCTACATCAAAAGTCCTCAAACACAAGGG
13819 CATCTATATT
Statistics
Matches: 74, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
51 3 0.04
52 20 0.27
53 48 0.65
55 3 0.04
ACGTcount: A:0.37, C:0.30, G:0.14, T:0.19
Consensus pattern (53 bp):
TCTACATCAAAAGTCCTCAAACACAAGGGTATTCACCCCTAAACACAGAGGCA
Found at i:13853 original size:30 final size:30
Alignment explanation
Indices: 13773--13874 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
13763 AGGGTATTCA
* *
13773 TCCCTAAACACAGAGGCATCTACATCAAAG
1 TCCCTAAACACAGAGGCATCTATATTAAAG
*
13803 T-CCTCAAGCACA-AGGGCATCTATATTAAAG
1 TCCCT-AAACACAGA-GGCATCTATATTAAAG
* *
13833 TCCCTAAACACAGAGACATCTATACTAAAG
1 TCCCTAAACACAGAGGCATCTATATTAAAG
*
13863 TCCCGAAACACA
1 TCCCTAAACACA
13875 TATAACACAG
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
29 4 0.07
30 53 0.87
31 4 0.07
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (30 bp):
TCCCTAAACACAGAGGCATCTATATTAAAG
Found at i:14236 original size:144 final size:144
Alignment explanation
Indices: 13976--14261 Score: 563
Period size: 144 Copynumber: 2.0 Consensus size: 144
13966 AATAAAGCCC
*
13976 ATATCACATATATATCACACTTGGGGGCTTGCCTTTCAAAGTCCACTTTCGGCCTAACAAAACAG
1 ATATCACATATATATCACACTTGGGGGCTCGCCTTTCAAAGTCCACTTTCGGCCTAACAAAACAG
14041 GCCCAAGACGTTGGGGCCTTGCCAACTAATCTCACAAACAATAGCATGGAGACAAAAGGCACAAA
66 GCCCAAGACGTTGGGGCCTTGCCAACTAATCTCACAAACAATAGCATGGAGACAAAAGGCACAAA
14106 ACTCAATTCCCTAT
131 ACTCAATTCCCTAT
14120 ATATCACATATATATCACACTTGGGGGCTCGCCTTTCAAAGTCCACTTTCGGCCTAACAAAACAG
1 ATATCACATATATATCACACTTGGGGGCTCGCCTTTCAAAGTCCACTTTCGGCCTAACAAAACAG
14185 GCCCAAGACGTTGGGGCCTTGCCAACTAATCTCACAAACAATAGCATGGAGACAAAAGGCACAAA
66 GCCCAAGACGTTGGGGCCTTGCCAACTAATCTCACAAACAATAGCATGGAGACAAAAGGCACAAA
14250 ACTCAATTCCCT
131 ACTCAATTCCCT
14262 GCTGCAGCAT
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 141 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.22
Consensus pattern (144 bp):
ATATCACATATATATCACACTTGGGGGCTCGCCTTTCAAAGTCCACTTTCGGCCTAACAAAACAG
GCCCAAGACGTTGGGGCCTTGCCAACTAATCTCACAAACAATAGCATGGAGACAAAAGGCACAAA
ACTCAATTCCCTAT
Found at i:18916 original size:11 final size:11
Alignment explanation
Indices: 18900--18931 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
18890 GAAGTTCGTG
18900 TTTGAAGATTA
1 TTTGAAGATTA
*
18911 TTTGAAGATAA
1 TTTGAAGATTA
18922 TTTGAAGATT
1 TTTGAAGATT
18932 TGAAGACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:20319 original size:19 final size:18
Alignment explanation
Indices: 20292--20327 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20282 TTAGATTTAA
*
20292 TTTACATTGCTTTGCTTAG
1 TTTAAATTGCTTT-CTTAG
20311 TTTAAATTGCTTTCTTA
1 TTTAAATTGCTTTCTTA
20328 AAATCCCCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (18 bp):
TTTAAATTGCTTTCTTAG
Found at i:22553 original size:1 final size:1
Alignment explanation
Indices: 22522--22546 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
22512 CTCAAAGAGC
22522 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
22547 GCTTTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:22754 original size:21 final size:19
Alignment explanation
Indices: 22723--22766 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 19
22713 AATATAAAGG
22723 GAGTTTTGGGAA-AGAGAAA
1 GAGTTTTGGGAAGAG-GAAA
22742 GAGTTTTCCGGGAAGAGGAAA
1 GAGTTTT--GGGAAGAGGAAA
22763 GAGT
1 GAGT
22767 AAGTAAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.32
21 13 0.59
22 2 0.09
ACGTcount: A:0.36, C:0.05, G:0.39, T:0.20
Consensus pattern (19 bp):
GAGTTTTGGGAAGAGGAAA
Found at i:29975 original size:30 final size:30
Alignment explanation
Indices: 29916--29975 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
29906 AATATGCGCT
*
29916 GACGTGGATGACACGTGGAAGAAATGTGTA
1 GACGTGGATGACACGTGGAAGAAACGTGTA
*
29946 GACGTGGATGACACGTGGAAGATACGTGTA
1 GACGTGGATGACACGTGGAAGAAACGTGTA
29976 TGCAAACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.12, G:0.37, T:0.20
Consensus pattern (30 bp):
GACGTGGATGACACGTGGAAGAAACGTGTA
Found at i:30108 original size:34 final size:33
Alignment explanation
Indices: 30070--30139 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 33
30060 CCTATTTTAT
30070 CATGAACTATTATGAACACAAACAACATTCAACA
1 CATGAACTATTATGAACACAAACAACATTCAA-A
* *
30104 CATGAACTATTATGAACACCAAGAACATTCAAA
1 CATGAACTATTATGAACACAAACAACATTCAAA
30137 CAT
1 CAT
30140 TGCAGCCACC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 4 0.12
34 30 0.88
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.21
Consensus pattern (33 bp):
CATGAACTATTATGAACACAAACAACATTCAAA
Found at i:30335 original size:15 final size:17
Alignment explanation
Indices: 30300--30335 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
30290 AACTAAGACC
30300 GAAAATATCAGAAAACA
1 GAAAATATCAGAAAACA
30317 -AAAAT-TCAG-AAACA
1 GAAAATATCAGAAAACA
30331 GAAAA
1 GAAAA
30336 AAATTCCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.28
15 8 0.44
16 5 0.28
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (17 bp):
GAAAATATCAGAAAACA
Found at i:40762 original size:18 final size:19
Alignment explanation
Indices: 40739--40777 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
40729 CCTAAATTTA
40739 TTTTCGACAC-AATTTTTT
1 TTTTCGACACAAATTTTTT
*
40757 TTTTCGACGCAAATTTTTT
1 TTTTCGACACAAATTTTTT
40776 TT
1 TT
40778 CGTTTTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (19 bp):
TTTTCGACACAAATTTTTT
Found at i:40773 original size:17 final size:17
Alignment explanation
Indices: 40732--40779 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
40722 CGCAAACCCT
*
40732 AAATTTATTTTCGACAC
1 AAATTTTTTTTCGACAC
* *
40749 AATTTTTTTTTTCGACGC
1 AA-ATTTTTTTTCGACAC
40767 AAATTTTTTTTCG
1 AAATTTTTTTTCG
40780 TTTTAGAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.52
Consensus pattern (17 bp):
AAATTTTTTTTCGACAC
Found at i:46881 original size:30 final size:30
Alignment explanation
Indices: 46845--46904 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
46835 AAAGTTCGTG
* * *
46845 TTTGAAGATTTATTG-AAGATAATTTGAAGA
1 TTTGAAGA-CTATTGAAAAATAATTTCAAGA
46875 TTTGAAGACTATTGAAAAATAATTTCAAGA
1 TTTGAAGACTATTGAAAAATAATTTCAAGA
46905 AGCAAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (30 bp):
TTTGAAGACTATTGAAAAATAATTTCAAGA
Found at i:48976 original size:156 final size:155
Alignment explanation
Indices: 48679--49073 Score: 419
Period size: 156 Copynumber: 2.5 Consensus size: 155
48669 TTGGTTAAGT
* * * * *
48679 TTCATCTCAAACGGACTTAAGATGAAAAACTTATGCATGTTTTTCAGTTAATGACAGTTTGGGGT
1 TTCAGCTCAATCGGACTTAAGATGAAAAACTTATGCAAGTTTTTCATTTAATGACAATTTGGGGT
* * * ** * *
48744 GTGAAACCA-ACTTCACTATGATAGGGAGTTTGGTTTTACTTAGAATCTTTTCTATAGTTTTATG
66 GTGAAACCATACTTCACCATCATAGGGAGCTCCGTTTTACTTAGAATCTTTTCCATAGTCTTATG
* *
48808 GGAATAATCTAAG-CCTACTGGTGGAAAA
131 GGAAGAACCTAAGTCC--CT--TGGAAAA
* *
48836 -TCAGCTTC-ATTGGACTTAAGATGAAAAACTTATGCAAGTTTTTCATTTAATGACAATTTAGGG
1 TTCAGC-TCAATCGGACTTAAGATGAAAAACTTATGCAAGTTTTTCATTTAATGACAATTTGGGG
* * * *
48899 AGAGAAACCATA-TTCACCATCA-AGGGGAGCTCCGTTTTACTTAGAATTTTTTCCATAGTCTTG
65 TGTGAAACCATACTTCACCATCATA-GGGAGCTCCGTTTTACTTAGAATCTTTTCCATAGTCTTA
*
48962 T-TGACAGAACCTAAGTCCCTTGGAAAA
129 TGGGA-AGAACCTAAGTCCCTTGGAAAA
* * * *
48989 GTTTCATCTCAATCAGACTTAAGGTGAAAAACTTATGCAAGTTTTTCATTTAAGGACAATTTGGG
1 --TTCAGCTCAATCGGACTTAAGATGAAAAACTTATGCAAGTTTTTCATTTAATGACAATTTGGG
*
49054 GTGTGAAACC-TAGTTCACCA
64 GTGTGAAACCATACTTCACCA
49074 AGAAGGAGGG
Statistics
Matches: 199, Mismatches: 29, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
153 7 0.04
155 9 0.05
156 178 0.89
157 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (155 bp):
TTCAGCTCAATCGGACTTAAGATGAAAAACTTATGCAAGTTTTTCATTTAATGACAATTTGGGGT
GTGAAACCATACTTCACCATCATAGGGAGCTCCGTTTTACTTAGAATCTTTTCCATAGTCTTATG
GGAAGAACCTAAGTCCCTTGGAAAA
Found at i:49423 original size:28 final size:28
Alignment explanation
Indices: 49389--49464 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
49379 CAGAAGGACA
49389 ACGCCTGATACATCAGAGGGAAGATTTT
1 ACGCCTGATACATCAGAGGGAAGATTTT
*
49417 ATGCCTGATACATCAGAGGGAAGATTTT
1 ACGCCTGATACATCAGAGGGAAGATTTT
**
49445 ACGCCTGATATGTCAGAGGG
1 ACGCCTGATACATCAGAGGG
49465 TGACGTCCTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (28 bp):
ACGCCTGATACATCAGAGGGAAGATTTT
Found at i:55479 original size:6 final size:6
Alignment explanation
Indices: 55460--55499 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
55450 ATTAATTTGT
55460 TTTAGA TTTAAGA TTTAGA TTTAGA TTTAGA TTT-GA TTTA
1 TTTAGA TTT-AGA TTTAGA TTTAGA TTTAGA TTTAGA TTTA
55500 CTTTGCTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (6 bp):
TTTAGA
Found at i:57748 original size:20 final size:20
Alignment explanation
Indices: 57723--57800 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
57713 AATACAAGAA
57723 ATTTGATTTACAAATTGGAC
1 ATTTGATTTACAAATTGGAC
*
57743 ATTTGATTTGCAAATTGGAC
1 ATTTGATTTACAAATTGGAC
57763 ATTTGATTTACAAATTGGAC
1 ATTTGATTTACAAATTGGAC
*
57783 ATTTGATTTGCAAATTGG
1 ATTTGATTTACAAATTGG
57801 TGCTCTTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTTGATTTACAAATTGGAC
Found at i:57778 original size:40 final size:40
Alignment explanation
Indices: 57723--57800 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
57713 AATACAAGAA
57723 ATTTGATTTACAAATTGGACATTTGATTTGCAAATTGGAC
1 ATTTGATTTACAAATTGGACATTTGATTTGCAAATTGGAC
57763 ATTTGATTTACAAATTGGACATTTGATTTGCAAATTGG
1 ATTTGATTTACAAATTGGACATTTGATTTGCAAATTGG
57801 TGCTCTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (40 bp):
ATTTGATTTACAAATTGGACATTTGATTTGCAAATTGGAC
Done.