Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014012.1 Corchorus capsularis cultivar CVL-1 contig14033, 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: 33982
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3579 original size:72 final size:72
Alignment explanation
Indices: 3458--3959 Score: 702
Period size: 72 Copynumber: 7.0 Consensus size: 72
3448 AGTAATACGT
* * * *
3458 ATGAAGAGCCCTTTTAAGGGTCCAGAGATACTGGCTGGCAGGCGGTGGAGAGCTGATCTTGACCA
1 ATGAAGAGCCCTCTTAAGGGTCCAGAGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCA
3523 AGCACGG
66 AGCACGG
* * *
3530 ATGAAGAGCCCTCTTAAGGGTCCAGAGATACCGGTTGGCAGGCGATGGAGAGCTGACCTTGACCA
1 ATGAAGAGCCCTCTTAAGGGTCCAGAGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCA
3595 AGCACGG
66 AGCACGG
* * * ** *
3602 ATGAAGAACCCTCTTAAGGGTCCAGTGAGACCGGCTGGCAGGCAATGAAGAGCCGACCTTGACCA
1 ATGAAGAGCCCTCTTAAGGGTCCAGAGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCA
* *
3667 ACCACAG
66 AGCACGG
* *
3674 ATGAAGAGCCTTTTTAAGGGTCCAGAGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCA
1 ATGAAGAGCCCTCTTAAGGGTCCAGAGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCA
3739 AGCACGG
66 AGCACGG
* * *
3746 ATGAAGAGCCCTCTTAAGGGTCCAGAGATACGGGCTGGCAGGCGGTGGAGAGCCGACATTTACCA
1 ATGAAGAGCCCTCTTAAGGGTCCAGAGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCA
3811 AGCACGG
66 AGCACGG
* * * * *
3818 ATGAAGAGTCCTCTTAAGAGTTC--AGATACCGGCTGGCAGGCAGTGGAGAGCCAACCTTGACCA
1 ATGAAGAGCCCTCTTAAGGGTCCAGAGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCA
*
3881 AGGACGG
66 AGCACGG
* * * * *
3888 ATGAAGAACCCTCTTAAGGGTCCAGTGAGACCGGCTGGCAGGCGGTGGAGAGCCAACCTCGACCA
1 ATGAAGAGCCCTCTTAAGGGTCCAGAGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCA
*
3953 AACACGG
66 AGCACGG
3960 CACTGGCTAG
Statistics
Matches: 380, Mismatches: 48, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
70 60 0.16
72 320 0.84
ACGTcount: A:0.27, C:0.24, G:0.33, T:0.16
Consensus pattern (72 bp):
ATGAAGAGCCCTCTTAAGGGTCCAGAGATACCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCA
AGCACGG
Found at i:6806 original size:3 final size:3
Alignment explanation
Indices: 6800--6837 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6790 CTTTTAAATC
6800 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6838 AGATTCTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:8352 original size:79 final size:78
Alignment explanation
Indices: 8257--8406 Score: 273
Period size: 79 Copynumber: 1.9 Consensus size: 78
8247 CTATTGGAAC
8257 GGCATGCCGCCCCAGGAGGGAGGCAATGTCCATGGCATACCGCCCTCCCAGAGAGGCAGCAGTTT
1 GGCATGCCGCCCCAGGAGGGAGGCAATGTCCATGGCATACCGCCCTCCCAGAGAGGCAGCA-TTT
8322 TTTTTTGGACACAT
65 TTTTTTGGACACAT
* *
8336 GGCATGCCGCCCCAGGAGGGAGGCAATGTCCATGGCATGCCGCCCTCCCAGAGAGGCAGTATTTT
1 GGCATGCCGCCCCAGGAGGGAGGCAATGTCCATGGCATACCGCCCTCCCAGAGAGGCAGCATTTT
8401 TTTTTG
66 TTTTTG
8407 ACAAAATGGC
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
78 10 0.14
79 59 0.86
ACGTcount: A:0.20, C:0.29, G:0.30, T:0.21
Consensus pattern (78 bp):
GGCATGCCGCCCCAGGAGGGAGGCAATGTCCATGGCATACCGCCCTCCCAGAGAGGCAGCATTTT
TTTTTGGACACAT
Found at i:26330 original size:3 final size:3
Alignment explanation
Indices: 26317--26359 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
26307 CTGATCATTG
* * **
26317 TCA TGA TCA TCA TCA TCA TGA TGT TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
26360 GGTTGGGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:27895 original size:2 final size:2
Alignment explanation
Indices: 27885--27915 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
27875 CATGCAAAAA
*
27885 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27916 GAAGATCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28674 original size:21 final size:23
Alignment explanation
Indices: 28630--28675 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
28620 AATCTTATTA
28630 GTGACCTTATTAATTGAGCTTTTTT
1 GTGACCTTATTAA-T-AGCTTTTTT
28655 GTGACCTTATTAA-A-CTTTTTT
1 GTGACCTTATTAATAGCTTTTTT
28676 TTTCTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
25 13 0.62
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.52
Consensus pattern (23 bp):
GTGACCTTATTAATAGCTTTTTT
Found at i:28719 original size:21 final size:21
Alignment explanation
Indices: 28689--28759 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
28679 CTTTTTTGGC
* *
28689 CTTATAAAGTTTTTTAGTCAT
1 CTTATTAAGTTTTTTAGTAAT
* *
28710 CTTATTAAGTTTTTTTACCTAAC
1 CTTATTAAG-TTTTTTA-GTAAT
*
28733 CTTATTAAGATTTTTAGTAAT
1 CTTATTAAGTTTTTTAGTAAT
28754 CTTATT
1 CTTATT
28760 GTGGATTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 17 0.41
22 13 0.32
23 11 0.27
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.54
Consensus pattern (21 bp):
CTTATTAAGTTTTTTAGTAAT
Found at i:28896 original size:18 final size:18
Alignment explanation
Indices: 28873--28918 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
28863 AGAGTTACCA
28873 TTTTCGTAGTGTACATCG
1 TTTTCGTAGTGTACATCG
*
28891 TTTTCGTAGTGTACATTG
1 TTTTCGTAGTGTACATCG
28909 TTTTCGTAGT
1 TTTTCGTAGT
28919 ATATCACGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.13, G:0.22, T:0.50
Consensus pattern (18 bp):
TTTTCGTAGTGTACATCG
Found at i:29022 original size:21 final size:21
Alignment explanation
Indices: 28997--29063 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
28987 TTTTGACTAA
28997 TTTTAGTAACCTTATAAATAT
1 TTTTAGTAACCTTATAAATAT
* *
29018 TTTTAATAA--TAATAAA-ACT
1 TTTTAGTAACCTTATAAATA-T
*
29037 TTTT-GTAACCTTATTAAGT-T
1 TTTTAGTAACCTTA-TAAATAT
29057 TTTTAGT
1 TTTTAGT
29064 GACCATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
18 4 0.11
19 11 0.31
20 7 0.20
21 13 0.37
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (21 bp):
TTTTAGTAACCTTATAAATAT
Found at i:29302 original size:85 final size:87
Alignment explanation
Indices: 29166--29346 Score: 258
Period size: 86 Copynumber: 2.1 Consensus size: 87
29156 AAAACCTTGT
* * * *
29166 AAATTTTCTTGATAAGTTTATAAATTTTTCATTAAAGTTAAAAGCTTTTTAAATAGTTTT-CTTA
1 AAATTTT-TTGATAAGCTTATAAATTTGTCAATAAACTTAAAAGCTTTTTAAATAGTTTTCCTTA
*
29230 AATTTATTCAATCACCTCGTTTA
65 AATTTATTCAATAACCTCGTTTA
* *
29253 AAATTTTTTGGTAAGCTTATAAA-TTGTCAATAAACTTAACAGCTTTTTAAATAGTTTTCCTTAA
1 AAATTTTTTGATAAGCTTATAAATTTGTCAATAAACTTAAAAGCTTTTTAAATAGTTTTCCTTAA
*
29317 ATTTATTCAATAACCTCTTTTA
66 ATTTATTCAATAACCTCGTTTA
*
29339 AGATTTTT
1 AAATTTTT
29347 AGTCATCTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
85 31 0.37
86 46 0.55
87 7 0.08
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (87 bp):
AAATTTTTTGATAAGCTTATAAATTTGTCAATAAACTTAAAAGCTTTTTAAATAGTTTTCCTTAA
ATTTATTCAATAACCTCGTTTA
Found at i:29359 original size:85 final size:86
Alignment explanation
Indices: 29178--29359 Score: 242
Period size: 85 Copynumber: 2.1 Consensus size: 86
29168 ATTTTCTTGA
* * * * *
29178 TAAGTTTATAAATTTTTCATTAAAGTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAATC
1 TAAGCTTATAAATTTGTCAATAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAATA
*
29243 ACCTCGTTTAAAATTTTTTGG
66 ACCTCGTTTAAAATTTTTTAG
*
29264 TAAGCTTATAAA-TTGTCAATAAACTTAACAGCTTTTTAAATAGTTTTCCTTAAATTTATTCAAT
1 TAAGCTTATAAATTTGTCAATAAACTTAAAAGCTTTTTAAATAGTTTT-CTTAAATTTATTCAAT
* *
29328 AACCTCTTTTAAGA-TTTTTAG
65 AACCTCGTTTAAAATTTTTTAG
* *
29349 TCATCTTATAA
1 TAAGCTTATAA
29360 CATGTTTTAG
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
85 46 0.55
86 38 0.45
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (86 bp):
TAAGCTTATAAATTTGTCAATAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAATA
ACCTCGTTTAAAATTTTTTAG
Found at i:29431 original size:20 final size:20
Alignment explanation
Indices: 29408--29445 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29398 CCTTGTAAGA
29408 TTTATAGTTAA-CTTATGAAT
1 TTTATAG-TAACCTTATGAAT
29428 TTTATAGTAACCTTATGA
1 TTTATAGTAACCTTATGA
29446 CGTTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (20 bp):
TTTATAGTAACCTTATGAAT
Found at i:29944 original size:20 final size:20
Alignment explanation
Indices: 29907--29945 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29897 TATTATTCTT
* *
29907 TTTTAGTAACATTGTTAAGC
1 TTTTAATAACATTATTAAGC
*
29927 TTTTAATAACTTTATTAAG
1 TTTTAATAACATTATTAAG
29946 ACTACTTTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (20 bp):
TTTTAATAACATTATTAAGC
Found at i:30096 original size:21 final size:20
Alignment explanation
Indices: 30058--30107 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
30048 TTTCAATATA
30058 TAACTTAGTAAGCATTTTAG
1 TAACTTAGTAAGCATTTTAG
* *
30078 TAACTTTATTAAGCTTTTTAG
1 TAAC-TTAGTAAGCATTTTAG
30099 TAACCTTAG
1 TAA-CTTAG
30108 AAAGTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 20 0.80
22 1 0.04
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (20 bp):
TAACTTAGTAAGCATTTTAG
Found at i:30156 original size:21 final size:20
Alignment explanation
Indices: 30066--30158 Score: 59
Period size: 21 Copynumber: 4.5 Consensus size: 20
30056 TATAACTTAG
* *
30066 TAAGCATTTTAGTAACTTTA
1 TAAGCTTTTTAGTAACTTGA
30086 TTAAGCTTTTTAGTAACCTTAGA
1 -TAAGCTTTTTAGTAA-CTT-GA
*
30109 -AAG--TTTTA-TATACTCCTGT
1 TAAGCTTTTTAGTA-ACT--TGA
*
30128 TAAACTTTTTAGTAACTTGGA
1 TAAGCTTTTTAGTAACTT-GA
30149 TAAGCTTTTT
1 TAAGCTTTTT
30159 TATCATCTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
18 4 0.07
19 7 0.12
20 4 0.07
21 27 0.48
22 11 0.20
23 3 0.05
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (20 bp):
TAAGCTTTTTAGTAACTTGA
Found at i:31527 original size:10 final size:10
Alignment explanation
Indices: 31501--31538 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
31491 CCCAAAAAAC
*
31501 TATATATATA
1 TATATACATA
31511 TATATACATA
1 TATATACATA
31521 TATATACATA
1 TATATACATA
31531 -ATA-ACATA
1 TATATACATA
31539 AAATAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 5 0.19
9 3 0.11
10 19 0.70
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (10 bp):
TATATACATA
Found at i:33639 original size:2 final size:2
Alignment explanation
Indices: 33632--33662 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33622 AGAAGGCATG
33632 TA TA 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 TA TA T
33663 TTGTATACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.