Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014298.1 Corchorus capsularis cultivar CVL-1 contig14319, 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: 24121
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2312 original size:27 final size:27
Alignment explanation
Indices: 2282--2353 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
2272 GTGAACTCAT
*
2282 AATGACCAAAATGCCCCTGAATGTAAG
1 AATGACCAAAATGCCCCTGAATGTAAA
*
2309 AATGACAAAAATGCCCCTGAATGTAAA
1 AATGACCAAAATGCCCCTGAATGTAAA
2336 AATGACCAAAATGCCCCT
1 AATGACCAAAATGCCCCT
2354 AGGTGACCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (27 bp):
AATGACCAAAATGCCCCTGAATGTAAA
Found at i:5784 original size:32 final size:32
Alignment explanation
Indices: 5744--5842 Score: 146
Period size: 32 Copynumber: 3.1 Consensus size: 32
5734 ATAACAAACT
*
5744 CCAC-AAATAGTGGCGCTTTATTCTACAAATG
1 CCACGAAATAGTGGCGCTTTATTCTATAAATG
* *
5775 CCACGAAATAGTGGAGCTTTATTCTATAAACG
1 CCACGAAATAGTGGCGCTTTATTCTATAAATG
* *
5807 CCACGAAATAGTGGCGCTTTATACAATAAATG
1 CCACGAAATAGTGGCGCTTTATTCTATAAATG
5839 CCAC
1 CCAC
5843 TAATTTAAGT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
31 4 0.07
32 56 0.93
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (32 bp):
CCACGAAATAGTGGCGCTTTATTCTATAAATG
Found at i:8883 original size:15 final size:16
Alignment explanation
Indices: 8856--8890 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
8846 ATGATCGAAT
*
8856 CAAAGAGAAACCTTAC
1 CAAAGAGAAACCTCAC
8872 CAAAGA-AAACCTCAC
1 CAAAGAGAAACCTCAC
8887 CAAA
1 CAAA
8891 AAGGGGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.54, C:0.29, G:0.09, T:0.09
Consensus pattern (16 bp):
CAAAGAGAAACCTCAC
Found at i:10592 original size:12 final size:12
Alignment explanation
Indices: 10575--10617 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
10565 GTTGTGGCCG
*
10575 GATGGCCCGTGC
1 GATGGCCCATGC
10587 GATGGCCCATGC
1 GATGGCCCATGC
*
10599 GATGTCCCATGC
1 GATGGCCCATGC
*
10611 GTTGGCC
1 GATGGCC
10618 GGTTGCCCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.12, C:0.33, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGGCCCATGC
Found at i:13054 original size:9 final size:9
Alignment explanation
Indices: 13040--13068 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
13030 AAAATATCAG
13040 AAAAATAAA
1 AAAAATAAA
13049 AAAAAT-AA
1 AAAAATAAA
13057 AAAAATAAA
1 AAAAATAAA
13066 AAA
1 AAA
13069 TTTCGACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:14295 original size:19 final size:18
Alignment explanation
Indices: 14271--14306 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14261 TGAAGATTTC
14271 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
14290 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
14307 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:15611 original size:15 final size:16
Alignment explanation
Indices: 15591--15624 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15581 GATTGCTTTC
*
15591 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
15606 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
15622 TTA
1 TTA
15625 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:16474 original size:26 final size:26
Alignment explanation
Indices: 16435--16489 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
16425 GCTTATTCAT
* *
16435 GGGCATTTTAGTCATTTTTACATTAG
1 GGGCATTTTAGTCATCTCTACATTAG
* *
16461 GGGCATTTTGGTCATCTCTACATTGG
1 GGGCATTTTAGTCATCTCTACATTAG
16487 GGG
1 GGG
16490 GGGGGGATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (26 bp):
GGGCATTTTAGTCATCTCTACATTAG
Found at i:23752 original size:6 final size:6
Alignment explanation
Indices: 23741--23767 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
23731 TTAATTCTGC
23741 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
23768 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Done.