Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013057.1 Corchorus olitorius cultivar O-4 contig13090, 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: 45455
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:33 original size:13 final size:12
Alignment explanation
Indices: 15--59 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
5 ATTTTATTAC
15 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
28 TGTTTTATAAAT
1 TGTTTTATAAAT
*
40 AGTTTTAAATAAAT
1 TGTTTT--ATAAAT
54 TGTTTT
1 TGTTTT
60 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:2662 original size:3 final size:3
Alignment explanation
Indices: 2654--2717 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
2644 AGCATTTGTC
2654 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2702 ATT ATT ATT A-T ATT AT
1 ATT ATT ATT ATT ATT AT
2718 ATCTAATAAC
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4097 original size:12 final size:12
Alignment explanation
Indices: 4080--4104 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4070 TTATTTTATT
4080 ATATAATATATA
1 ATATAATATATA
4092 ATATAATATATA
1 ATATAATATATA
4104 A
1 A
4105 CAATAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATAATATATA
Found at i:7701 original size:291 final size:292
Alignment explanation
Indices: 6958--7840 Score: 1305
Period size: 291 Copynumber: 3.0 Consensus size: 292
6948 TTTTTAATGA
* *
6958 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTACCTCCTTTTGGC----TTTTTT
1 CTATGGAAATTACCTAAAGGCCAAATTGAGGATTAATGTGG----TGCTTTTGGCTTTTTTTTTT
* * * *
7019 TGGTCTTTTCTCAATTTTCGGGTGACTAAAAAGGCCCTTGATAAATTTCCT-CCTTACTTTTCCT
62 TGGTCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTTCT
* * * * *
7083 CCTGCCCTCTTTTGTAATTTACTATTTTTGTATTTATGATTAAGTGTGTTTTAATTATGTATTAA
127 GCTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTATATATTGA
* *
7148 TTGTGTGTGGATATTAGGATTTACAGGTTCAACTCCTCTGCTGGAATTCCAAAGGATTGGTGCTA
192 TTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGC-CGAATTCCAAAGGATTGGTGCTA
*
7213 TAAATGTATCTACCCGAGTTTATTAATTTAACAATTG
256 TAAATGTATCTACCCGAGTTCATTAATTTAACAATTG
*
7250 CTATGGAAATTACCTAAAAGGCCAAATTGAGTATTAATGTGGTGCTTCCTTTTGGCTTTTTTTCT
1 CTATGGAAATTACCT-AAAGGCCAAATTGAGGATTAATGTGGTG----CTTTTGGCTTTTTTT-T
* * *
7315 TTCT-GTCTTTTCTTACTTTTCGGGTGACTAAAAAGACCCTCAATGAATTTCCTCCCTTACTTTC
60 TT-TGGTCTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTT-
7379 TT-TGCTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTATATA
123 TTCTGCTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTATATA
7443 TTGATTGTGTGTGGATATTAGGATTTACCGGTTCAA-TCCTCTGCCGAATTCCAAAGGATTGGTG
188 TTGATTGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGAATTCCAAAGGATTGGTG
*
7507 CTATAAATGTATCTACCCGAGTCCATTAATTTAACAATTG
253 CTATAAATGTATCTACCCGAGTTCATTAATTTAACAATTG
*
7547 CTATGGAAATTACCTATAGGCCAAATTGAGGATTAATGTGGTGCTTTTGGCTTTTTTTTTTTGGT
1 CTATGGAAATTACCTAAAGGCCAAATTGAGGATTAATGTGGTGCTTTTGGCTTTTTTTTTTTGGT
* **
7612 CTTTTCTCACTTTTCGGTTGACTAAAAAGGTTCTCGATGAATTTCCTCCCTTACTTTTTCTGCTG
66 CTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTTCTGCTG
* *
7677 CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGCGTTTTAATTACATATTGATTGT
131 CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTATATATTGATTGT
* * * *
7742 GTGTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGGAATTCCAAAGGATTAGTGTTGTAAA
196 GTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCC-GAATTCCAAAGGATTGGTGCTATAAA
* *
7807 TGTGTTTACCCGAGTTCATTAATTTAACAATTG
260 TGTATCTACCCGAGTTCATTAATTTAACAATTG
7840 C
1 C
7841 AATCAAGATT
Statistics
Matches: 538, Mismatches: 36, Indels: 33
0.89 0.06 0.05
Matches are distributed among these distances:
289 1 0.00
290 3 0.01
291 152 0.28
292 37 0.07
293 87 0.16
296 26 0.05
297 75 0.14
298 54 0.10
299 102 0.19
300 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (292 bp):
CTATGGAAATTACCTAAAGGCCAAATTGAGGATTAATGTGGTGCTTTTGGCTTTTTTTTTTTGGT
CTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTTCTGCTG
CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTATATATTGATTGT
GTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGAATTCCAAAGGATTGGTGCTATAAAT
GTATCTACCCGAGTTCATTAATTTAACAATTG
Found at i:7965 original size:45 final size:42
Alignment explanation
Indices: 7916--8006 Score: 130
Period size: 45 Copynumber: 2.1 Consensus size: 42
7906 AACAATTAAA
*
7916 ATTAGTTTTATTTTGATGAATTATCTAGAGATAGAGGAGTAGAAT
1 ATTAGTTTTATTTTGATGAATTACCTAGAGAT---GGAGTAGAAT
*
7961 ATTAGTTTTATTTTGATGAATTACCTATAGATGGAGTAGAAT
1 ATTAGTTTTATTTTGATGAATTACCTAGAGATGGAGTAGAAT
8003 -TTAG
1 ATTAG
8007 GTAATGCACT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 10 0.23
45 30 0.68
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.42
Consensus pattern (42 bp):
ATTAGTTTTATTTTGATGAATTACCTAGAGATGGAGTAGAAT
Found at i:8797 original size:151 final size:151
Alignment explanation
Indices: 8624--8904 Score: 438
Period size: 151 Copynumber: 1.9 Consensus size: 151
8614 GGTCAATCAC
* * * * *
8624 AATAACCTTTTAAATTAAAATGGTAAA-AATAAAATAATTATAAAAATATTGAATTTGATTCAAT
1 AATAAACTTTAAAATTAAAATGGTAAATAATAAAATAATTAT-AAAATATCGAATTTAATTAAAT
* * *
8688 GAAAATACAATTTTTAATAGAATAAAACTGTATATTAAAAAATTTTAATATATCCAAGTTTTTAA
65 GAAAATACAATTTTTAATAAAATAAAAATGTATATTAAAAAATTTTAATATATCCAAGTTCTTAA
8753 TGAAAATTAGTAAAATGGTAAA
130 TGAAAATTAGTAAAATGGTAAA
8775 AATAAACTTTAAAATTAAAATGGTAAATAATAAAATAATTATAAAATATCGAATTTAATTAAATG
1 AATAAACTTTAAAATTAAAATGGTAAATAATAAAATAATTATAAAATATCGAATTTAATTAAATG
* * * *
8840 AAAATAGAGTTTTTAGTAAAATAAAAATGTATATTAAAACATTTTAATATATCCAAGTTCTTAAT
66 AAAATACAATTTTTAATAAAATAAAAATGTATATTAAAAAATTTTAATATATCCAAGTTCTTAAT
8905 AGAGTTTTTT
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
151 103 0.88
152 14 0.12
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (151 bp):
AATAAACTTTAAAATTAAAATGGTAAATAATAAAATAATTATAAAATATCGAATTTAATTAAATG
AAAATACAATTTTTAATAAAATAAAAATGTATATTAAAAAATTTTAATATATCCAAGTTCTTAAT
GAAAATTAGTAAAATGGTAAA
Found at i:13226 original size:20 final size:20
Alignment explanation
Indices: 13189--13226 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13179 TAATTTAGTT
*
13189 TTGCTTTATTTTTAAATTAA
1 TTGCTTTATCTTTAAATTAA
13209 TTGCTTT-TCTTTATAATT
1 TTGCTTTATCTTTA-AATT
13227 GGTACTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (20 bp):
TTGCTTTATCTTTAAATTAA
Found at i:29205 original size:1 final size:1
Alignment explanation
Indices: 29201--29257 Score: 87
Period size: 1 Copynumber: 57.0 Consensus size: 1
29191 TTTTGTCTTG
***
29201 TTTTTTTTTTTTTTTTTTTTTTTTGCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29258 CTAACTTGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.02, C:0.02, G:0.02, T:0.95
Consensus pattern (1 bp):
T
Found at i:29224 original size:30 final size:30
Alignment explanation
Indices: 29190--29254 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
29180 TTTCTCTCTC
29190 TTTTTGTC-TTGTTTTTTTTTTTTTTTTTTT
1 TTTTTG-CATTGTTTTTTTTTTTTTTTTTTT
*
29220 TTTTTGCATTTTTTTTTTTTTTTTTTTTTT
1 TTTTTGCATTGTTTTTTTTTTTTTTTTTTT
29250 TTTTT
1 TTTTT
29255 TTTCTAACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.02, C:0.03, G:0.05, T:0.91
Consensus pattern (30 bp):
TTTTTGCATTGTTTTTTTTTTTTTTTTTTT
Found at i:29385 original size:28 final size:29
Alignment explanation
Indices: 29331--29396 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
29321 AAAGAATGTG
*
29331 TAAACAGTTTTTCTTTTGGCCATGAAGTA
1 TAAACTGTTTTTCTTTTGGCCATGAAGTA
* *
29360 TAAACTGTTTTTTTTTTGGTCA-GAAGTA
1 TAAACTGTTTTTCTTTTGGCCATGAAGTA
29388 TAAACTGTT
1 TAAACTGTT
29397 GATGAACATC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 15 0.44
29 19 0.56
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (29 bp):
TAAACTGTTTTTCTTTTGGCCATGAAGTA
Found at i:37716 original size:30 final size:30
Alignment explanation
Indices: 37680--37738 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
37670 GAGGTTTAGA
*
37680 ATTTGAAAATGCTGCACTTGTTGAAAATGT
1 ATTTGAAAATGCTGCACCTGTTGAAAATGT
*
37710 ATTTGAAAATGCTGCCCCTGTTGAAAATG
1 ATTTGAAAATGCTGCACCTGTTGAAAATG
37739 GTGAAGAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (30 bp):
ATTTGAAAATGCTGCACCTGTTGAAAATGT
Found at i:37961 original size:60 final size:60
Alignment explanation
Indices: 37868--37991 Score: 212
Period size: 60 Copynumber: 2.1 Consensus size: 60
37858 CCAGATCCAG
*
37868 TTGGTGAAAGAGTTGAGGAAGTTCCTCAAGTTCCTGAGGTCAATGATAATACTACTGATA
1 TTGGTGAAAGAGTTGAGGAAGTTCCTCAAGTTCCTGAAGTCAATGATAATACTACTGATA
* * *
37928 TTGGTGAAAGAGTTGAGGAAGTTCCTGAAGTTCCTGAAGTCAATGATAATGCTGCTGATA
1 TTGGTGAAAGAGTTGAGGAAGTTCCTCAAGTTCCTGAAGTCAATGATAATACTACTGATA
37988 TTGG
1 TTGG
37992 CCAAGGTGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (60 bp):
TTGGTGAAAGAGTTGAGGAAGTTCCTCAAGTTCCTGAAGTCAATGATAATACTACTGATA
Found at i:40763 original size:24 final size:24
Alignment explanation
Indices: 40736--40800 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
40726 CCAGCTTCTC
40736 CCTCAAACACTGCAACAACCCCTA
1 CCTCAAACACTGCAACAACCCCTA
*
40760 CCTCAAACACTGCAACAACCCCTG
1 CCTCAAACACTGCAACAACCCCTA
* *
40784 CTTCAAACACTGAAACA
1 CCTCAAACACTGCAACA
40801 GCCCATCCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.38, C:0.42, G:0.06, T:0.14
Consensus pattern (24 bp):
CCTCAAACACTGCAACAACCCCTA
Done.