Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007192.1 Corchorus capsularis cultivar CVL-1 contig07213, 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: 19261
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:122 original size:10 final size:11
Alignment explanation
Indices: 104--132 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
94 TCGAAAATTT
104 TTATTTTTTTA
1 TTATTTTTTTA
115 TT-TTTTTTTA
1 TTATTTTTTTA
125 TTATTTTT
1 TTATTTTT
133 CGATATAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (11 bp):
TTATTTTTTTA
Found at i:123 original size:13 final size:14
Alignment explanation
Indices: 100--132 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
90 CTGGTCGAAA
*
100 ATTTTTATTTTTTT
1 ATTTTTATTTTATT
114 ATTTTT-TTTTATT
1 ATTTTTATTTTATT
127 ATTTTT
1 ATTTTT
133 CGATATAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
ATTTTTATTTTATT
Found at i:233 original size:8 final size:8
Alignment explanation
Indices: 205--238 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
195 GAATCGGCTA
205 TGAATTTT
1 TGAATTTT
*
213 TGAAGTTTC
1 TGAA-TTTT
222 TGAATTTT
1 TGAATTTT
230 TGAATTTT
1 TGAATTTT
238 T
1 T
239 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:1218 original size:33 final size:33
Alignment explanation
Indices: 1147--1265 Score: 134
Period size: 33 Copynumber: 3.5 Consensus size: 33
1137 AAAGGATCGT
* * *
1147 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCGT
1 GTGGCCGGTTGTGGCCGGACATGTCC-ATGTCGC
* * *
1180 TTGGCCGGTTGTAGCCGGCCATGTCCATGTCGC
1 GTGGCCGGTTGTGGCCGGACATGTCCATGTCGC
1213 GTGGCCGG-TGATGGCCGGACATGTCCATGTCGC
1 GTGGCCGGTTG-TGGCCGGACATGTCCATGTCGC
1246 GTGGCCGGTCTTGTGGCCGG
1 GTGGCCGG--TTGTGGCCGG
1266 TGTTGCGCGG
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
32 3 0.04
33 61 0.84
35 7 0.10
36 2 0.03
ACGTcount: A:0.08, C:0.27, G:0.42, T:0.24
Consensus pattern (33 bp):
GTGGCCGGTTGTGGCCGGACATGTCCATGTCGC
Found at i:5665 original size:30 final size:29
Alignment explanation
Indices: 5631--5699 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
5621 ACCGAGTGCG
* *
5631 AACCCACACTCAAAACAATCCCAAGTGCAC
1 AACCCGCACTCAAAACAA-CACAAGTGCAC
** *
5661 AACCCGCACTTGAATCAACACAAGTGCAC
1 AACCCGCACTCAAAACAACACAAGTGCAC
5690 AACCCGCACT
1 AACCCGCACT
5700 TGATACACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.39, C:0.39, G:0.10, T:0.12
Consensus pattern (29 bp):
AACCCGCACTCAAAACAACACAAGTGCAC
Found at i:14009 original size:51 final size:48
Alignment explanation
Indices: 13895--14712 Score: 323
Period size: 49 Copynumber: 16.7 Consensus size: 48
13885 TCTTTACCTA
* * * ** * *
13895 CTTTTTCCCAAAACGCCCTTCCCCGATGGAAGGCGTTTATTTTTATTAA
1 CTTTTTCCCTAAACGCCCTTCCCGGACGGAAGGCACTCATTTTTATT-G
*
13944 CTTTTT-CCTAAAACGCCTTTCCCGGACGGAAGGCACTCAATTTTTATTTG
1 CTTTTTCCCT-AAACGCCCTTCCCGGACGGAAGGCACTC-ATTTTTA-TTG
* * *
13994 CCTTTTTCCCTAAACGCCCTTCCTGGACGGAAGCCATTCATTTTTACTTG
1 -CTTTTTCCCTAAACGCCCTTCCCGGACGGAAGGCACTCATTTTTA-TTG
* * ** * * * *
14044 CTATTTCCC-AAAGTGCCCTTCCCAAACGGAAGCCATTCATCTTTACGTG
1 CTTTTTCCCTAAA-CGCCCTTCCCGGACGGAAGGCACTCATTTTTA-TTG
* * * * * * * *
14093 CTATCTCCCAAAACACCCTTCCCAGACGGAAGCCATTTATTTTTACTTG
1 CTTTTTCCCTAAACGCCCTTCCCGGACGGAAGGCACTCATTTTTA-TTG
* * ** * * *
14142 CTATTTCCC-AAAGCGCCCTGCCTAGACGGACGCCACT--TATTTACTTG
1 CTTTTTCCCTAAA-CGCCCTTCCCGGACGGAAGGCACTCATTTTTA-TTG
* * * * * **
14189 CTATTTCCC-AAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTCGCTTG
1 CTTTTTCCCTAAA-CGCCCTTCCCGGACGGAAGGCACTCATTTT-TATTG
* * * * * **
14238 CTATTT-CCTAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTCGCTTG
1 CTTTTTCCCTAAA-CGCCCTTCCCGGACGGAAGGCACTCATTTT-TATTG
* * * * * *
14287 CTATTTCCC-AAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTGCTTG
1 CTTTTTCCCTAAA-CGCCCTTCCCGGACGGAAGGCACTCATTTTT-ATTG
*** * * * ** * *
14336 CTATCCCCCCAAAACGCCCTTCTCGGACGGAAGCCGTTTATCTTTACTTG
1 CT-TTTTCCCTAAACGCCCTTCCCGGACGGAAGGCACTCATTTTTA-TTG
* * * * **
14386 CTATTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTATTA-CC
1 CTTTTTCCCTAAACGCCCTTCCCGGACGGAAGGCACTCATTTTTATTG
* * * * *
14433 CATTTTTCCCAAAACGCCCTTCCCGTACGGAAGGCACTAATCTTTACCTG
1 C-TTTTTCCCTAAACGCCCTTCCCGGACGGAAGGCACTCATTTTTA-TTG
* * * *
14483 -TTTTTCCCAAAATGCCCTTCCCGGACAGAAGGCACTTA-TTTTATTTG
1 CTTTTTCCCTAAACGCCCTTCCCGGACGGAAGGCACTCATTTTTA-TTG
** ** * * * * **
14530 CTATTTTCCAAAAATACCCTTCCCGGATGGAAGACGCTTATTTTTA-CC
1 CT-TTTTCCCTAAACGCCCTTCCCGGACGGAAGGCACTCATTTTTATTG
* * * * * *
14578 CACTTTTCCCCAAAGTGTCCTTCCCCGACGGAAGGCACTGATTTTTACTTG
1 C-TTTTTCCCTAAA-CGCCCTTCCCGGACGGAAGGCACTCATTTTTA-TTG
** * * * * *
14629 CTTTTTTTCTAAAACACCCTTCCCGGATGGAAGGCGCT-AGTTTTACTCG
1 CTTTTTCCCT-AAACGCCCTTCCCGGACGGAAGGCACTCATTTTTA-TTG
* * * *
14678 CTTTTT-CTTAAAATGCCCTTTCCGGACGAAAGGCA
1 CTTTTTCCCT-AAACGCCCTTCCCGGACGGAAGGCA
14713 AGTTCGCTTT
Statistics
Matches: 623, Mismatches: 118, Indels: 57
0.78 0.15 0.07
Matches are distributed among these distances:
47 49 0.08
48 115 0.18
49 332 0.53
50 85 0.14
51 39 0.06
52 3 0.00
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (48 bp):
CTTTTTCCCTAAACGCCCTTCCCGGACGGAAGGCACTCATTTTTATTG
Found at i:14455 original size:48 final size:48
Alignment explanation
Indices: 14389--14663 Score: 212
Period size: 48 Copynumber: 5.6 Consensus size: 48
14379 TTACTTGCTA
14389 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTATTACCCATT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTATTACCCATT
* * **
14437 TTTCCCAAAACGCCCTTCCCGTACGGAAGGCACTAATCT-TTACCTGTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGAT-TATTACCCATT
* * * ** *
14485 TTTCCCAAAATGCCCTTCCCGGACAGAAGGCACTTATTTTATTTGCTA-T
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGA--TTATTACCCATT
* ** * * * * *
14534 TTTCCAAAAATACCCTTCCCGGATGGAAGACGCTTATTTTTACCCACTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTATTACCCA-TT
* ** * * * * *
14583 TTCCCCAAAGTGTCCTTCCCCGACGGAAGGCACTGATTTTTACTTGCTTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTATTAC--CCATT
* * * *
14633 TTTTCTAAAACACCCTTCCCGGATGGAAGGC
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGC
14664 GCTAGTTTTA
Statistics
Matches: 177, Mismatches: 42, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
47 6 0.03
48 74 0.42
49 67 0.38
50 29 0.16
51 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.31
Consensus pattern (48 bp):
TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTATTACCCATT
Found at i:14633 original size:49 final size:49
Alignment explanation
Indices: 13898--14630 Score: 579
Period size: 49 Copynumber: 15.0 Consensus size: 49
13888 TTACCTACTT
* * * ** * *
13898 TTTCCCAAAACGCCCTTCCCCGATGGAAGGCGTTTATTTTTA-TTAACTT
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTT-GCTA
* * * * * * *
13947 TTTCCTAAAACGCCTTTCCCGGACGGAAGGCACTCAATTTTTATTTGCCTT
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACT-TATTTTTACTTG-CTA
* **
13998 TTTCCCTAAACGCCCTTCCTGGACGGAAGCCA-TTCATTTTTACTTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTT-ATTTTTACTTGCTA
** * * *
14047 TTTCCCAAAGTGCCCTTCCCAAACGGAAGCCA-TTCATCTTTACGTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTT-ATTTTTACTTGCTA
* * *
14096 TCTCCCAAAACACCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTTGCTA
* * * *
14145 TTTCCCAAAGCGCCCTGCCTAGACGGACGCCACTTA--TTTACTTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTTGCTA
* * **
14192 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTCGCTTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTTGCTA
* * * **
14241 TTTCCTAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTCGCTTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTTGCTA
* * *
14290 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTGCTTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTTGCTA
** * * ** *
14339 TCCCCCCAAAACGCCCTTCTCGGACGGAAGCCGTTTATCTTTACTTGCTA
1 T-TTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTTGCTA
* * * * * *
14389 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTATTAC--CCATT
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTTGC-TA
* * * * *
14437 TTTCCCAAAACGCCCTTCCC-GTACGGAAGGCACTAATCTTTACCTG-TT
1 TTTCCCAAAACGCCCTTCCCAG-ACGGAAGCCACTTATTTTTACTTGCTA
* * * * *
14485 TTTCCCAAAATGCCCTTCCCGGACAGAAGGCACTTA-TTTTATTTGCTA
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTTGCTA
* ** * * * * ***
14533 TTTTCCAAAAATACCCTTCCCGGATGGAAGACGCTTATTTTTACCCACT-
1 -TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTTGCTA
** * * * *
14582 TTTCCCCAAAGTGTCCTTCCCCGACGGAAGGCACTGATTTTTACTTGCT
1 TTT-CCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTTGCT
14631 TTTTTTCTAA
Statistics
Matches: 568, Mismatches: 99, Indels: 34
0.81 0.14 0.05
Matches are distributed among these distances:
47 51 0.09
48 76 0.13
49 341 0.60
50 68 0.12
51 32 0.06
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.31
Consensus pattern (49 bp):
TTTCCCAAAACGCCCTTCCCAGACGGAAGCCACTTATTTTTACTTGCTA
Done.