Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007193.1 Corchorus capsularis cultivar CVL-1 contig07214, 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: 26199
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Found at i:7619 original size:28 final size:27
Alignment explanation
Indices: 7583--7639 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
7573 AGTATCAATA
*
7583 CAGACTCAGACTAGTCTTAT-TCAATTT
1 CAGACTCAGACGAGTCTT-TCTCAATTT
*
7610 CAGACCTCAGACGGGTCTTTCTCAATTT
1 CAGA-CTCAGACGAGTCTTTCTCAATTT
7638 CA
1 CA
7640 TTTATCAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (27 bp):
CAGACTCAGACGAGTCTTTCTCAATTT
Found at i:7726 original size:102 final size:102
Alignment explanation
Indices: 7589--7773 Score: 307
Period size: 102 Copynumber: 1.8 Consensus size: 102
7579 AATACAGACT
* *
7589 CAGACTAGTCTTATTCAATTTCAGACCTCAGACGGGTCTTTCTCAATTTCATTTATCAAAGTTGA
1 CAGACTAGTCTTATTCAATTCCAGACCTCAGACGGGTCTTTCTCAATTTCAATTATCAAAGTTGA
*
7654 CCTCGGACAGGTCTTTCTTAGTTTTTCATATCGACCA
66 CCTCAGACAGGTCTTTCTTAGTTTTTCATATCGACCA
* * *
7691 CAGACTGGTCTTCTTCAATTCCAGACCTCATACGGGTCTTTCTCAATTTCAATTATCAAAGTTGA
1 CAGACTAGTCTTATTCAATTCCAGACCTCAGACGGGTCTTTCTCAATTTCAATTATCAAAGTTGA
*
7756 CCTCAGATAGGTCTTTCT
66 CCTCAGACAGGTCTTTCT
7774 CAATTTCAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 76 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (102 bp):
CAGACTAGTCTTATTCAATTCCAGACCTCAGACGGGTCTTTCTCAATTTCAATTATCAAAGTTGA
CCTCAGACAGGTCTTTCTTAGTTTTTCATATCGACCA
Found at i:7951 original size:60 final size:62
Alignment explanation
Indices: 7815--7965 Score: 198
Period size: 60 Copynumber: 2.5 Consensus size: 62
7805 TTGTCAGATA
* *
7815 TTCAGTTTCAGACCTCAGATAGGTCTTTCTCAATTTTCAAAATCGACCACAAACTGGTCTTC
1 TTCAGTTCCAGACCTCAGACAGGTCTTTCTCAATTTTCAAAATCGACCACAAACTGGTCTTC
* * * **
7877 TTCAGTTTCAGACCTCAGACAGGTCTTTCTCGA-TTTC-AATTCGACCACTGACTGGTCTTC
1 TTCAGTTCCAGACCTCAGACAGGTCTTTCTCAATTTTCAAAATCGACCACAAACTGGTCTTC
* * *
7937 TTCTGTTCCGGACCTCAAACAGGTCTTTC
1 TTCAGTTCCAGACCTCAGACAGGTCTTTC
7966 ATAGTTTTCA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 45 0.56
61 4 0.05
62 31 0.39
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (62 bp):
TTCAGTTCCAGACCTCAGACAGGTCTTTCTCAATTTTCAAAATCGACCACAAACTGGTCTTC
Found at i:11695 original size:197 final size:196
Alignment explanation
Indices: 11334--11868 Score: 504
Period size: 197 Copynumber: 2.8 Consensus size: 196
11324 TTACCAACTT
* * * * *
11334 TTTCCCAAAACGCCCTTCCTGGATGGAAGGCGTTTATTTTTATTAACTTTTTCCCAAAACGCCCT
1 TTTCCCAAAACGCCCTTCC-GGACGGAAGCCATTTATTTTTACTAACTATTTCCCAAAACGCCCT
* * * * * ** *
11399 TCCCGGACGGAAGGCACTCAATTTTTATTTGGTTTTTTCCCTAAAGGCCCTTCATGGACGGAAGG
65 TCCCAGACGGAAGCCACTCAATTTTTACTTGGCTATTTCCCTAAAGGCCCTTCACAGACGGAAGC
* * * * *
11464 CACTTCTTTTATTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTGCTAGC
130 CACTTATTTTATTTGCTATTCCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATCTTTACTAGC
11529 TA
195 TA
* * **
11531 TTTCCCAAAACGCCCTTCACAGACGGAAGCCATTTATTTTTGCTAACTATTTCCCAAAGTGCCCT
1 TTTCCCAAAACGCCCTTC-CGGACGGAAGCCATTTATTTTTACTAACTATTTCCCAAAACGCCCT
* *
11596 TCCCAGACGGAAGCCATTC-ATTTTTACTT-GCTATTTCCC-AAAGCGCCCTTCCCAGACGGAAG
65 TCCCAGACGGAAGCCACTCAATTTTTACTTGGCTATTTCCCTAAAG-GCCCTTCACAGACGGAAG
* * *
11658 CCATTTATTTT-TGCTTGCTATCTCCCCAAAACGCCCTTCCCGGACGGAAGCCGTTTATCTTTAC
129 CCACTTATTTTAT--TTGCTAT-TCCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATCTTTAC
*
11722 TTGCTA
191 TAGCTA
* * * * *
11728 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTATTAC---CTATTTTTCCAAAACGCCC
1 TTTCCCAAAACGCCCTT-CCGGACGGAAGCCATTTATTTTTACTAACTA-TTTCCCAAAACGCCC
* * * * * * * * *
11790 TT-CC---CGGAAGGCACT-AATCTTTACCT-G-TTTTTCCCAAAATGCCTTTCCCGGACGGAAG
64 TTCCCAGACGGAAGCCACTCAATTTTTACTTGGCTATTTCCCTAAAGGCCCTTCACAGACGGAAG
* *
11848 ACACTTATTTTACTTGCTATT
129 CCACTTATTTTATTTGCTATT
11869 TTCCAAAAAT
Statistics
Matches: 280, Mismatches: 48, Indels: 29
0.78 0.13 0.08
Matches are distributed among these distances:
188 1 0.00
189 7 0.03
190 32 0.11
191 21 0.08
194 10 0.04
195 45 0.16
196 16 0.06
197 146 0.52
198 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (196 bp):
TTTCCCAAAACGCCCTTCCGGACGGAAGCCATTTATTTTTACTAACTATTTCCCAAAACGCCCTT
CCCAGACGGAAGCCACTCAATTTTTACTTGGCTATTTCCCTAAAGGCCCTTCACAGACGGAAGCC
ACTTATTTTATTTGCTATTCCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATCTTTACTAGCT
A
Found at i:11814 original size:43 final size:44
Alignment explanation
Indices: 11728--11841 Score: 133
Period size: 43 Copynumber: 2.5 Consensus size: 44
11718 TTACTTGCTA
*
11728 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTATTACCTATT
1 TTTCCCAAAACGCCCTT-CC---CGGAAGGCACTAATTATTACCTATT
*
11776 TTT-CCAAAACGCCCTTCCCGGAAGGCACTAATCT-TTACCTGTT
1 TTTCCCAAAACGCCCTTCCCGGAAGGCACTAAT-TATTACCTATT
* *
11819 TTTCCCAAAATGCCTTTCCCGGA
1 TTTCCCAAAACGCCCTTCCCGGA
11842 CGGAAGACAC
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
43 24 0.40
44 18 0.30
46 2 0.03
47 13 0.22
48 3 0.05
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (44 bp):
TTTCCCAAAACGCCCTTCCCGGAAGGCACTAATTATTACCTATT
Found at i:11884 original size:49 final size:50
Alignment explanation
Indices: 11333--12045 Score: 511
Period size: 49 Copynumber: 14.7 Consensus size: 50
11323 TTTACCAACT
* * ** *
11333 TTTTCCCAAAACGCCCTTCCTGGATGGAAGGCGTTTATTTTTA-TTAACT-
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTT-GCTA
* * * *
11382 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTCAATTTTTATTTGGTT
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACT-TATTTTTACTTGCTA
* * ** * *
11433 TTTTCCCTAAAGGCCCTTCATGGACGGAAGGCACTT-CTTTTATTTGCTA
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
* * * * * *
11482 -TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTGCTAGCTA
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
* * * * * **
11531 -TTTCCCAAAACGCCCTTCACAGACGGAAGCCATTTATTTTTGCTAACTA
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
** * *
11580 -TTTCCCAAAGTGCCCTTCCCAGACGGAAGCCA-TTCATTTTTACTTGCTA
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTT-ATTTTTACTTGCTA
* * * * *
11629 -TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTGCTTGCTA
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
* * * ** *
11678 TCTCCCCAAAACGCCCTTCCCGGACGGAAGCCGTTTATCTTTACTTGCTA
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
* *
11728 -TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTATTAC---CTA
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
* * * *
11774 TTTTTCCAAAACGCCCTT-CC---CGGAAGGCACTAATCTTTACCTG-T-
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
* * *
11818 TTTTCCCAAAATGCCTTTCCCGGACGGAAGACACTTA-TTTTACTTGCTA
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
* ** * * * * **
11867 TTTTCCAAAAATACCTTTCCCGGATGGAAGACGCTTATTTTTACCCGC--
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
** * * *
11915 TTTTCTCCAAAGTGCCCTTCCCCGACGGAAGGCACTAATTTTTACATGCT-
1 TTTTC-CCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
* * * * * * *
11965 TTTTTCTAAAACACCCTTCCCGGATGGAAGGCGC-TAGTTTTACTCGCT-
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
** * * * *
12013 TTTTCTTAAAATGCCTTTTCCGGACGAAAGGCA
1 TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCA
12046 AGCTCGCTTT
Statistics
Matches: 542, Mismatches: 102, Indels: 41
0.79 0.15 0.06
Matches are distributed among these distances:
43 17 0.03
44 15 0.03
45 3 0.01
46 5 0.01
47 23 0.04
48 80 0.15
49 302 0.56
50 64 0.12
51 33 0.06
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (50 bp):
TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTA
Found at i:11950 original size:189 final size:190
Alignment explanation
Indices: 11629--11988 Score: 429
Period size: 189 Copynumber: 1.9 Consensus size: 190
11619 TTACTTGCTA
* * * * * *
11629 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTGCTTGCTATCTCCCCAAAACGCCC
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGACACTTATTTTTACTTGCTATCTCCCAAAAACACCC
* * ** *
11694 TTCCCGGACGGAAGCCGTTTATCTTTACTTGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGGC
66 TTCCCGGACGGAAGACGCTTATCTTTACCCGCTATTTCCCAAAACGCCCTTCCCCGACGGAAGGC
* *
11759 ACTGATTATTAC-CTATTTTTCCAAAACGCCCTTCCCGGAAGGCACTAATCTTTACCTGTT
131 ACTAATTATTACACT-TTTTTCCAAAACACCCTTCCCGGAAGGCACTAATCTTTACCTGTT
* * * * * * *
11819 TTTCCCAAAATGCCTTTCCCGGACGGAAGACACTTA-TTTTACTTGCTATTTTCCAAAAATACCT
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGACACTTATTTTTACTTGCTATCTCCCAAAAACACCC
* * **
11883 TTCCCGGATGGAAGACGCTTATTTTTACCCGCT-TTTCTCCAAAGTGCCCTTCCCCGACGGAAGG
66 TTCCCGGACGGAAGACGCTTATCTTTACCCGCTATTTC-CCAAAACGCCCTTCCCCGACGGAAGG
* *
11947 CACTAATTTTTACATGCTTTTTTCTAAAACACCCTTCCCGGA
130 CACTAATTATTACA--CTTTTTTCCAAAACACCCTTCCCGGA
11989 TGGAAGGCGC
Statistics
Matches: 140, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
188 4 0.03
189 82 0.59
190 30 0.21
191 22 0.16
192 2 0.01
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (190 bp):
TTTCCCAAAACGCCCTTCCCAGACGGAAGACACTTATTTTTACTTGCTATCTCCCAAAAACACCC
TTCCCGGACGGAAGACGCTTATCTTTACCCGCTATTTCCCAAAACGCCCTTCCCCGACGGAAGGC
ACTAATTATTACACTTTTTTCCAAAACACCCTTCCCGGAAGGCACTAATCTTTACCTGTT
Found at i:16277 original size:49 final size:49
Alignment explanation
Indices: 16205--16323 Score: 229
Period size: 49 Copynumber: 2.4 Consensus size: 49
16195 CTGCACACTC
16205 ACAAGATTCATTAGTCATCATACTTAGGGTTATTTTGTTATCATCAAAA
1 ACAAGATTCATTAGTCATCATACTTAGGGTTATTTTGTTATCATCAAAA
16254 ACAAGATTCATTAGTCATCATACTTAGGGTTATTTTGTTATCATCAAAA
1 ACAAGATTCATTAGTCATCATACTTAGGGTTATTTTGTTATCATCAAAA
*
16303 ACAAGATTCATTAGTCTTCAT
1 ACAAGATTCATTAGTCATCAT
16324 TCCATTTCAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 69 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (49 bp):
ACAAGATTCATTAGTCATCATACTTAGGGTTATTTTGTTATCATCAAAA
Found at i:17674 original size:2 final size:2
Alignment explanation
Indices: 17667--17701 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
17657 TGAATATAAA
* *
17667 AT AT AT AT AT AT AT AT AT TT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17702 GCGGCATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:22356 original size:32 final size:32
Alignment explanation
Indices: 22304--22371 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
22294 GCAGGATAAT
* * * *
22304 GGCGTCTAATGAATCGAACGCCACCATTTAGC
1 GGCGCCTAATGAAGCAAACGCCACCATATAGC
* *
22336 GGCGCCTAATGAAGCAAACGCCGCTATATAGC
1 GGCGCCTAATGAAGCAAACGCCACCATATAGC
22368 GGCG
1 GGCG
22372 TCTATAAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (32 bp):
GGCGCCTAATGAAGCAAACGCCACCATATAGC
Found at i:23062 original size:11 final size:11
Alignment explanation
Indices: 23046--23070 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23036 AATTTTAGGG
23046 TTCTCCTTTCC
1 TTCTCCTTTCC
23057 TTCTCCTTTCC
1 TTCTCCTTTCC
23068 TTC
1 TTC
23071 CGTTCGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (11 bp):
TTCTCCTTTCC
Found at i:23517 original size:23 final size:23
Alignment explanation
Indices: 23487--23531 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
23477 AGCTGAGTTC
23487 TGTTTTTATTCTTGCTGTTTTAT
1 TGTTTTTATTCTTGCTGTTTTAT
23510 TGTTTTTATTCTTGCTGTTTTA
1 TGTTTTTATTCTTGCTGTTTTA
23532 CTGATAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.09, C:0.09, G:0.13, T:0.69
Consensus pattern (23 bp):
TGTTTTTATTCTTGCTGTTTTAT
Found at i:24511 original size:24 final size:24
Alignment explanation
Indices: 24479--24533 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
24469 GGATTTAGCA
24479 GCAAATGACGAACCAATTGAGGCT
1 GCAAATGACGAACCAATTGAGGCT
* *
24503 GCAAATGACGACCCCATTGAGGCT
1 GCAAATGACGAACCAATTGAGGCT
24527 GCAAATG
1 GCAAATG
24534 GAGAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (24 bp):
GCAAATGACGAACCAATTGAGGCT
Found at i:24597 original size:27 final size:27
Alignment explanation
Indices: 24560--24646 Score: 131
Period size: 27 Copynumber: 3.3 Consensus size: 27
24550 TCCGGCCCTC
24560 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
* * *
24587 CCCACTGCGACCCAAGCAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
*
24614 CCCACTTCGACCCCAGTAGTGGA-CCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
24640 CCCACTT
1 CCCACTT
24647 TGCCTCGGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
26 10 0.19
27 44 0.81
ACGTcount: A:0.21, C:0.43, G:0.18, T:0.18
Consensus pattern (27 bp):
CCCACTTCGACCCCAGAAGTGGATCCT
Done.