Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006093.1 Corchorus capsularis cultivar CVL-1 contig06111, 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: 12712
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Found at i:2400 original size:16 final size:16
Alignment explanation
Indices: 2379--2413 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2369 AAAATTGTAA
2379 TTAAAATT-ATCATATC
1 TTAAAATTAAT-ATATC
2395 TTAAAATTAATATATC
1 TTAAAATTAATATATC
2411 TTA
1 TTA
2414 CATTCAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAAATTAATATATC
Found at i:6715 original size:30 final size:29
Alignment explanation
Indices: 6681--6746 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
6671 CTTTGTGTTG
*
6681 AAAGATGAAGTCTTTAAGTAATTTGTCAAC
1 AAAGATGAA-TCTTTAAGTAATTTGTAAAC
* * *
6711 AAAGATTGGATTTTTAAGTAATTTGTAAAT
1 AAAGA-TGAATCTTTAAGTAATTTGTAAAC
6741 AAAGAT
1 AAAGAT
6747 TAAATGTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 27 0.87
31 3 0.10
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (29 bp):
AAAGATGAATCTTTAAGTAATTTGTAAAC
Found at i:6757 original size:30 final size:30
Alignment explanation
Indices: 6693--6759 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
6683 AGATGAAGTC
* ** *
6693 TTTAAGTAATTTGTCAACAAAGATTGGATT
1 TTTAAGTAATTTGTAAACAAAGATTAAATG
*
6723 TTTAAGTAATTTGTAAATAAAGATTAAATG
1 TTTAAGTAATTTGTAAACAAAGATTAAATG
6753 TTTAAGT
1 TTTAAGT
6760 GAAAGATCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (30 bp):
TTTAAGTAATTTGTAAACAAAGATTAAATG
Found at i:6974 original size:51 final size:50
Alignment explanation
Indices: 6860--7023 Score: 129
Period size: 51 Copynumber: 3.2 Consensus size: 50
6850 ACTTTTAAGT
* * * * * *
6860 TAAAAGATTGAACTTTT-GAATAACTTGTAAAT-AAAATGAGATCTTTGAGC
1 TAAAAGA-TGAAATTTTGGATTAATTTGTAAATAAAAATGA-AACCTTGAAC
* *
6910 TAAAA-ATTAGAAATTTTTGATTGATTTGTAAATAAAAATGAAACCCTTGAAC
1 TAAAAGA-T-GAAATTTTGGATTAATTTGTAAATAAAAATGAAA-CCTTGAAC
* ** *
6962 TAAAAGATGAAATTTTGGATTAATTTGGT-GATAAAGGTGAAACCTTTAAGC
1 TAAAAGATGAAATTTTGGATTAATTT-GTAAATAAAAATGAAACCTTGAA-C
7013 TAAAAGATGAA
1 TAAAAGATGAA
7024 TTCTTGAATA
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
49 3 0.03
50 18 0.19
51 51 0.54
52 21 0.22
53 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (50 bp):
TAAAAGATGAAATTTTGGATTAATTTGTAAATAAAAATGAAACCTTGAAC
Found at i:7831 original size:39 final size:39
Alignment explanation
Indices: 7736--7848 Score: 163
Period size: 39 Copynumber: 2.9 Consensus size: 39
7726 AGTTGCTTAA
* *
7736 TCCCAGTTTACCCTTCCTCATCGGGAGGTGTTGTTTAAAT
1 TCCCAGTTTACCCTTCCTCATCGGAAGGTGTTG-TCAAAT
*
7776 TCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCAAAT
1 TCCCAGTTTACCCTTCCTCATCGGAAGGTGTTGTCAAAT
* * *
7815 TCCCAATTTACTCTTCCCCATCGGAAGGTGTTGT
1 TCCCAGTTTACCCTTCCTCATCGGAAGGTGTTGT
7849 TTAGTTTTCT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
39 35 0.53
40 31 0.47
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.35
Consensus pattern (39 bp):
TCCCAGTTTACCCTTCCTCATCGGAAGGTGTTGTCAAAT
Found at i:7884 original size:41 final size:40
Alignment explanation
Indices: 7693--8316 Score: 345
Period size: 41 Copynumber: 14.9 Consensus size: 40
7683 GTCTGATTCC
* *
7693 CAGTTTGCCCTTCCTCATCGGAAGGTATTGTTTAGTTGCTTAATCC
1 CAGTTTGCCCTTCC-CATCGGAAGGTGTTGTTTAG-T--TT--TCT
* * ** *
7739 CAGTTTACCCTTCCTCATCGGGAGGTGTTGTTTA-AATTCC
1 CAGTTTGCCCTTCC-CATCGGAAGGTGTTGTTTAGTTTTCT
* ** *
7779 CAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TCA-AATTCC
1 CAGTTTGCCCTTCC-CATCGGAAGGTGTTGTTTAGTTTTCT
* * *
7818 CAATTTACTCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCT
1 CAGTTTGCCCTT-CCCATCGGAAGGTGTTGTTTAGTTTTCT
*
7859 CA-TCTTGCCCTTCCCAGTCGGAAGGTGTTGTCTAGTTGTCAAATTCT
1 CAGT-TTGCCCTTCCCA-TCGGAAGGTGTTGTTTAG-T-T----TTCT
* * * * *
7906 CAATTGGCCCTTCCTTATCGGAAGGTTTTGTTTAG-TCTC-
1 CAGTTTGCCCTTCC-CATCGGAAGGTGTTGTTTAGTTTTCT
**
7945 CAGTTTGCCCTTCCCCATCGGAAGACGTTG-TTAG-TTTCT
1 CAGTTTGCCCTT-CCCATCGGAAGGTGTTGTTTAGTTTTCT
* ** *
7984 CAGTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTACATTTCC
1 CAGTTTGCCCTTCCC-ATCGGAAGGTGTTGTTTAGTTTTCT
* * *
8025 CAGTTTGCCCTTACCCACCGGAAGGTGTTGTCTAAGTCTATATTT
1 CAGTTTGCCCTT-CCCATCGGAAGGTGTTGT-TTAGT-T-T-TCT
* * *
8070 CCAGTTTGCCCTTCTCCACCGGAAGATGTTGTTTAGATTTAC-
1 -CAGTTTGCCCTTC-CCATCGGAAGGTGTTGTTTAG-TTTTCT
* * *
8112 CAGTTTGTCCTTCCC-TACGGGAAAGCGTTG-TTAG-TTTCT
1 CAGTTTGCCCTTCCCAT-C-GGAAGGTGTTGTTTAGTTTTCT
** * *
8151 CAGTTTGCCCTTCTCGGTCGGAAGGTGTTGTTTACTTTTCC
1 CAGTTTGCCCTTC-CCATCGGAAGGTGTTGTTTAGTTTTCT
* * ** *
8192 CAGTTTTCCATTCCCCATCGGAAGGTGTTGTTTAGCATTCC
1 CAGTTTGCCCTT-CCCATCGGAAGGTGTTGTTTAGTTTTCT
* * * * *
8233 CAGTTTGTCCTTCCTCACCGGAAGTTGTTGTTTTGTTGTCTAATT
1 CAGTTTGCCCTTCC-CATCGGAAGGTGTTGTTTAGTT-T-T--CT
* *
8278 ACCAGTTTGCCCTTCCCTACCGGAACGTGTTGTTTAGTT
1 --CAGTTTGCCCTTCCC-ATCGGAAGGTGTTGTTTAGTT
8317 GCCTTATTCC
Statistics
Matches: 457, Mismatches: 79, Indels: 83
0.74 0.13 0.13
Matches are distributed among these distances:
38 13 0.03
39 97 0.21
40 61 0.13
41 140 0.31
42 9 0.02
43 3 0.01
44 3 0.01
45 6 0.01
46 61 0.13
47 62 0.14
48 2 0.00
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (40 bp):
CAGTTTGCCCTTCCCATCGGAAGGTGTTGTTTAGTTTTCT
Found at i:7950 original size:166 final size:167
Alignment explanation
Indices: 7689--8222 Score: 410
Period size: 167 Copynumber: 3.2 Consensus size: 167
7679 CTTTGTCTGA
* * * * * * **
7689 TTCCCAGTTTGCCCTT-CCTCATCGGAAGGTATTGTTTAGTTG-CTTAA-TCCCAGTTTACCCTT
1 TTCCCAGTTTGCCCTTACC-CACCGGAAGGTGTTGTCTAGTTGTC-AAATTCTCAATTGGCCCTT
* * **
7751 CCTCATCGGGAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCAAATT
64 CCTCATCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCCCATCGGAAGACGTTGTCAAATT
* **
7816 CCCAATTTACTCTTCCCCATCGGAAGGTGTTGTTTAGTT
129 CCCAATTTACCCTTCCCCATCGGAAGGTGTTGTTTACAT
* *
7855 TTCTCA-TCTTGCCCTT-CCCAGTCGGAAGGTGTTGTCTAGTTGTCAAATTCTCAATTGGCCCTT
1 TTCCCAGT-TTGCCCTTACCCA-CCGGAAGGTGTTGTCTAGTTGTCAAATTCTCAATTGGCCCTT
* * * * **
7918 CCTTATCGGAAGGTTTTGTTT--AGTCTCCAGTTTGCCCTTCCCCATCGGAAGACGTTGTTAGTT
64 CCTCATCGGAAGGTGTTGTTTAAATTC-CCAGTTTGCCCTTCCCCATCGGAAGACGTTGTCAAAT
* * * **
7981 TCTCAGTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTACAT
128 TCCCAATTTACCCTTCCCCATCGGAAGGTGTTGTTTACAT
* * * *
8021 TTCCCAGTTTGCCCTTACCCACCGGAAGGTGTTGTCTA--AGTCTATATT-TCCAGTTTGCCCTT
1 TTCCCAGTTTGCCCTTACCCACCGGAAGGTGTTGTCTAGTTGTC-AAATTCT-CAATTGGCCCTT
* * * * * * *
8083 -CTCCACCGGAAGATGTTGTTTAGATTTACCAGTTTGTCCTTCCCTA-CGGGAA-AGCGTTGTTA
64 CCT-CATCGGAAGGTGTTGTTTA-AATTCCCAGTTTGCCCTTCCCCATC-GGAAGA-CGTTGTCA
** * * * * ** *
8145 GTTTCTCAGTTTGCCCTTCTCGGTCGGAAGGTGTTGTTTACTT
125 AATTCCCAATTTACCCTTCCCCATCGGAAGGTGTTGTTTACAT
* * * *
8188 TTCCCAGTTTTCCATTCCCCATCGGAAGGTGTTGT
1 TTCCCAGTTTGCCCTTACCCACCGGAAGGTGTTGT
8223 TTAGCATTCC
Statistics
Matches: 306, Mismatches: 47, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
164 6 0.02
165 34 0.11
166 130 0.42
167 135 0.44
168 1 0.00
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (167 bp):
TTCCCAGTTTGCCCTTACCCACCGGAAGGTGTTGTCTAGTTGTCAAATTCTCAATTGGCCCTTCC
TCATCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCCCATCGGAAGACGTTGTCAAATTCC
CAATTTACCCTTCCCCATCGGAAGGTGTTGTTTACAT
Found at i:8142 original size:87 final size:88
Alignment explanation
Indices: 7979--8197 Score: 208
Period size: 87 Copynumber: 2.6 Consensus size: 88
7969 ACGTTGTTAG
** * *
7979 TTTCTCAGTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTACATTTCCCAGTTTGCCCTTACCCACC
1 TTTCTCAGTTTGCCCTTCCCGACCGGAAGATGTTGTTTACATTTACCAGTTTGCCCTTACCCACC
* *
8044 GGAAGGTGTTGTCTAAGTCTATA
66 GGAAAGCGTTGTCTAAGTCTATA
* *
8067 TTTC-CAGTTTGCCCTTCTCC-ACCGGAAGATGTTGTTTAGATTTACCAGTTTGTCCTT-CCCTA
1 TTTCTCAGTTTGCCCTTC-CCGACCGGAAGATGTTGTTTACATTTACCAGTTTGCCCTTACCC-A
*
8129 CGGGAAAGCGTTGT-T-AG------
64 CCGGAAAGCGTTGTCTAAGTCTATA
* ** * * *
8146 TTTCTCAGTTTGCCCTTCTCGGTCGGAAGGTGTTGTTTACTTTTCCCAGTTT
1 TTTCTCAGTTTGCCCTTCCCGACCGGAAGATGTTGTTTACATTTACCAGTTT
8198 TCCATTCCCC
Statistics
Matches: 111, Mismatches: 16, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
79 5 0.05
80 38 0.34
85 2 0.02
86 4 0.04
87 56 0.50
88 6 0.05
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (88 bp):
TTTCTCAGTTTGCCCTTCCCGACCGGAAGATGTTGTTTACATTTACCAGTTTGCCCTTACCCACC
GGAAAGCGTTGTCTAAGTCTATA
Found at i:8222 original size:80 final size:79
Alignment explanation
Indices: 8067--8265 Score: 197
Period size: 80 Copynumber: 2.5 Consensus size: 79
8057 TAAGTCTATA
* *
8067 TTTCCAGTTTGCCCTTCTCCACCGGAAGATGTTGTTTAGATTTACCAGTTTGTCCTTCCCTACGG
1 TTTCCAGTTTGCCCTTCTCCACCGGAAGATGTTGTTTACATTTACCAGTTTGTCCTTCCCCACGG
8132 GAAAGCGTTGTTAG
66 GAAAGCGTTGTTAG
*** * * *
8146 TTTCTCAGTTTGCCCTTCTCGGTCGGAAGGTGTTGTTTACTTTTCCCAGTTT-TCCATTCCCCAT
1 TTTC-CAGTTTGCCCTTCTCCACCGGAAGATGTTGTTTACATTTACCAGTTTGTCC-TTCCCCA-
* *
8210 C-GGAAGGTGTTGTTTAG
63 CGGGAAAGCGTTG-TTAG
* * *
8227 CATTCCCAGTTTGTCCTTC-CTCACCGGAAGTTGTTGTTT
1 --TTTCCAGTTTGCCCTTCTC-CACCGGAAGATGTTGTTT
8266 TGTTGTCTAA
Statistics
Matches: 97, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
79 7 0.07
80 55 0.57
81 6 0.06
82 26 0.27
83 3 0.03
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.40
Consensus pattern (79 bp):
TTTCCAGTTTGCCCTTCTCCACCGGAAGATGTTGTTTACATTTACCAGTTTGTCCTTCCCCACGG
GAAAGCGTTGTTAG
Found at i:8292 original size:47 final size:45
Alignment explanation
Indices: 8232--8453 Score: 164
Period size: 47 Copynumber: 4.7 Consensus size: 45
8222 TTTAGCATTC
* * *
8232 CCAGTTTGTCCTTCCTCACCGGAAGTTGTTGTTTTGTTGTCTAATT
1 CCAGTTTGCCCTTCCTCACCGGAAG-TGTTGTTTAGTTGCCTAATT
*
8278 ACCAGTTTGCCCTTCC-CTACCGGAACGTGTTGTTTAGTTGCCTTATT
1 -CCAGTTTGCCCTTCCTC-ACCGGAA-GTGTTGTTTAGTTGCCTAATT
* * *
8325 CCCGTTTTGCCCTTCCTCA-CGGAAGGTGTTGTCTAAGTTGCCTTATT
1 CCAG-TTTGCCCTTCCTCACCGGAA-GTGTTGT-TTAGTTGCCTAATT
** * * * ** *
8372 CTTGTTTCGCCCTTCCCCATCAGAAGGTGTTGTTTAGTTATCTCATT
1 CCAGTTT-GCCCTTCCTCACCGGAA-GTGTTGTTTAGTTGCCTAATT
8419 CTC-GTTTTGCCCTTCC-CTACCGGAAGATGTTGTTT
1 C-CAG-TTTGCCCTTCCTC-ACCGGAAG-TGTTGTTT
8454 GATTTTGTCT
Statistics
Matches: 146, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
46 21 0.14
47 108 0.74
48 17 0.12
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.41
Consensus pattern (45 bp):
CCAGTTTGCCCTTCCTCACCGGAAGTGTTGTTTAGTTGCCTAATT
Done.