Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017717.1 Corchorus olitorius cultivar O-4 contig17750, 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: 34597
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:2353 original size:3 final size:3
Alignment explanation
Indices: 2338--2413 Score: 66
Period size: 3 Copynumber: 25.7 Consensus size: 3
2328 AAGTGATGGC
* * * *
2338 GAT GAT GAG GAT GAT GAC GAG GAT GAT GAT GAT GAT GACG GA- GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA-T GAT GAT
* * *
2383 GA- AAT GAG GAT GAT GAT GAT GAT GGT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
2414 CCATGAGGAG
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.05
3 53 0.91
4 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.39, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:2719 original size:2 final size:2
Alignment explanation
Indices: 2712--2737 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2702 TCTGTTTTGC
2712 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2738 TGGTGACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3675 original size:45 final size:45
Alignment explanation
Indices: 3624--3727 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
3614 AGGCAGCCTC
* * * **
3624 TTATTTTGTATAGGTC-CTTAATTTGCCATTATCTAGACGAGACAT
1 TTATTTTGTATAGGTCAC-TAACTTGCAATGATCTAGAAAAGACAT
* * *
3669 TTATTTTGTATAGATCACTAACTTGCAATGATCTAGAAAAGGCCT
1 TTATTTTGTATAGGTCACTAACTTGCAATGATCTAGAAAAGACAT
3714 TTATTTTGTATAGG
1 TTATTTTGTATAGG
3728 GTTTAGTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 48 0.98
46 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (45 bp):
TTATTTTGTATAGGTCACTAACTTGCAATGATCTAGAAAAGACAT
Found at i:9933 original size:24 final size:24
Alignment explanation
Indices: 9901--9974 Score: 121
Period size: 24 Copynumber: 3.1 Consensus size: 24
9891 TCATAGATAG
9901 AATTCCGTTTTTGATTCTATTGCA
1 AATTCCGTTTTTGATTCTATTGCA
*
9925 AATTCCGTTTTTAATTCTATTGCA
1 AATTCCGTTTTTGATTCTATTGCA
**
9949 AATTCCGTTTTTGATTCCGTTGCA
1 AATTCCGTTTTTGATTCTATTGCA
9973 AA
1 AA
9975 GTACTCAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (24 bp):
AATTCCGTTTTTGATTCTATTGCA
Found at i:11163 original size:10 final size:10
Alignment explanation
Indices: 11148--11180 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
11138 AACCTTTCAC
11148 CCCGTCCTGT
1 CCCGTCCTGT
11158 CCCGTCCTGT
1 CCCGTCCTGT
*
11168 CCCGTCCCGT
1 CCCGTCCTGT
11178 CCC
1 CCC
11181 TTACTAGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.00, C:0.58, G:0.18, T:0.24
Consensus pattern (10 bp):
CCCGTCCTGT
Found at i:11519 original size:15 final size:15
Alignment explanation
Indices: 11499--11552 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
11489 ATCAAATGAG
11499 GGGTGGGGTGGGGAA
1 GGGTGGGGTGGGGAA
11514 GGGTGGGGT-----A
1 GGGTGGGGTGGGGAA
11524 GGGTGGGGTGGGGAA
1 GGGTGGGGTGGGGAA
*
11539 GGGTGGGGTAGGGA
1 GGGTGGGGTGGGGA
11553 GGGGGAGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
10 10 0.30
15 23 0.70
ACGTcount: A:0.13, C:0.00, G:0.72, T:0.15
Consensus pattern (15 bp):
GGGTGGGGTGGGGAA
Found at i:11532 original size:25 final size:25
Alignment explanation
Indices: 11499--11556 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
11489 ATCAAATGAG
11499 GGGTGGGGTGGGGAAGGGTGGGGTA
1 GGGTGGGGTGGGGAAGGGTGGGGTA
11524 GGGTGGGGTGGGGAAGGGTGGGGTA
1 GGGTGGGGTGGGGAAGGGTGGGGTA
*
11549 GGGAGGGG
1 GGGTGGGG
11557 GAGGATTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.12, C:0.00, G:0.74, T:0.14
Consensus pattern (25 bp):
GGGTGGGGTGGGGAAGGGTGGGGTA
Found at i:11556 original size:10 final size:10
Alignment explanation
Indices: 11498--11532 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
11488 GATCAAATGA
*
11498 GGGGTGGGGT
1 GGGGTAGGGT
*
11508 GGGGAAGGGT
1 GGGGTAGGGT
11518 GGGGTAGGGT
1 GGGGTAGGGT
11528 GGGGT
1 GGGGT
11533 GGGGAAGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.09, C:0.00, G:0.74, T:0.17
Consensus pattern (10 bp):
GGGGTAGGGT
Found at i:12125 original size:13 final size:13
Alignment explanation
Indices: 12109--12156 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
12099 TCATATAAAA
*
12109 ATTATATTATATT
1 ATTATATTATTTT
12122 ATTATATTTATTTT
1 ATTATA-TTATTTT
*
12136 ATTATTTTATTTT
1 ATTATATTATTTT
*
12149 ATTTTATT
1 ATTATATT
12157 CATTAAGGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTATATTATTTT
Found at i:12133 original size:17 final size:18
Alignment explanation
Indices: 12113--12161 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
12103 ATAAAAATTA
*
12113 TATTATATTATTATA-TT
1 TATTTTATTATTATATTT
*
12130 TATTTTATTATTTTATTT
1 TATTTTATTATTATATTT
12148 TATTTTATTCATTA
1 TATTTTATT-ATTA
12162 AGGACAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 13 0.48
18 11 0.41
19 3 0.11
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTTATTATTATATTT
Found at i:12161 original size:22 final size:25
Alignment explanation
Indices: 12113--12161 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
12103 ATAAAAATTA
*
12113 TATTATATTATTATATTTATTTTAT
1 TATTATATTATTATATTTATTTCAT
*
12138 TATTTTATT-TTAT-TTTA-TTCAT
1 TATTATATTATTATATTTATTTCAT
12160 TA
1 TA
12162 AGGACAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 6 0.27
23 4 0.18
24 4 0.18
25 8 0.36
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TATTATATTATTATATTTATTTCAT
Found at i:12867 original size:25 final size:24
Alignment explanation
Indices: 12821--12867 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
12811 CACTACTTAC
* * *
12821 TTCAATTTTAACAAGTTCTTAAAT
1 TTCAATCTTAACAAGATATTAAAT
12845 TTCAATCTTACACAAGATATTAA
1 TTCAATCTTA-ACAAGATATTAA
12868 TTGATTCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.40
Consensus pattern (24 bp):
TTCAATCTTAACAAGATATTAAAT
Found at i:12930 original size:25 final size:25
Alignment explanation
Indices: 12896--12943 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
12886 TATGTGCCCG
12896 GTTACTAATCAATACTAATTTGTCA
1 GTTACTAATCAATACTAATTTGTCA
12921 GTTACTAATCAATACTAATTTGT
1 GTTACTAATCAATACTAATTTGT
12944 TCAAATGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (25 bp):
GTTACTAATCAATACTAATTTGTCA
Found at i:20106 original size:214 final size:213
Alignment explanation
Indices: 19738--20122 Score: 655
Period size: 214 Copynumber: 1.8 Consensus size: 213
19728 TTATATATTT
* * * *
19738 TACATATTATTTTTTTAATTAGGTGAAATTACTAAATGCTCCTTCTAATTTTTAACCTGAGACGA
1 TACATATTATTTTTGTAATCAGGTGAAATTACTAAATGCTCCTTCTAACTTTTAACATGAGACGA
* * * *
19803 TCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATTGATTCGTATTTCATCAC
66 CCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCGATTCATATTCCATCAC
*
19868 TCTATAACCTCATAAATCATATTTATTATATTTGAACCCACTCACATTTACAGAGCAAAAAAAAA
131 TCTATAACCTCATAAATCATATTTATTATATTTAAACCCACTCACATTTACAGAGCAAAAAAAAA
19933 ATCTATAAAAATTGACTC
196 ATCTATAAAAATTGACTC
*
19951 TACATATTATTTTTGTAATCAGGTGAAAATTACTAAATGCTCCTTCTAACTTTTAACATGGGACG
1 TACATATTATTTTTGTAATCAGGTG-AAATTACTAAATGCTCCTTCTAACTTTTAACATGAGACG
20016 ACCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCGATTCATATTCCATCA
65 ACCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCGATTCATATTCCATCA
20081 -TGCTATAACCTCATAAATCATATTTATTATATTTAAACCCAC
130 CT-CTATAACCTCATAAATCATATTTATTATATTTAAACCCAC
20123 AGAAAACGTG
Statistics
Matches: 160, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
213 24 0.15
214 136 0.85
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (213 bp):
TACATATTATTTTTGTAATCAGGTGAAATTACTAAATGCTCCTTCTAACTTTTAACATGAGACGA
CCTTATCGCCCCGTTTTAGTCATTTCTCACATGCGGTTACACTGAATCGATTCATATTCCATCAC
TCTATAACCTCATAAATCATATTTATTATATTTAAACCCACTCACATTTACAGAGCAAAAAAAAA
ATCTATAAAAATTGACTC
Found at i:20899 original size:15 final size:14
Alignment explanation
Indices: 20874--20903 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
20864 TCTATTTTGA
20874 ATGATATATATATT
1 ATGATATATATATT
20888 ATGATGATATATATT
1 ATGAT-ATATATATT
20903 A
1 A
20904 CATTATTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
ATGATATATATATT
Found at i:20953 original size:19 final size:20
Alignment explanation
Indices: 20929--20976 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 20
20919 TTAGGTATGG
20929 AAACAAGTATACACATGCA-
1 AAACAAGTATACACATGCAT
*
20948 AAACAA--ATA-ACATGTAT
1 AAACAAGTATACACATGCAT
20965 AAACAAGTATAC
1 AAACAAGTATAC
20977 CCACATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
19 9 0.38
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.19
Consensus pattern (20 bp):
AAACAAGTATACACATGCAT
Found at i:21854 original size:53 final size:55
Alignment explanation
Indices: 21796--21899 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 55
21786 GACGTTGAAA
* *
21796 GAAACCAT-GAAA-TTTATTGTTACCATTAGCTGATCTCAGCCTACTATTCCATT
1 GAAACCATCAAAATTTTATTGTTACCATTAGCTGATCTCAGCCTACAATTCCATT
* * * *
21849 GAAACCATCAAAATTTTTTTTTTACCATTAGTTGATCTCAGCTTACAATTC
1 GAAACCATCAAAATTTTATTGTTACCATTAGCTGATCTCAGCCTACAATTC
21900 GTATTGAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 8 0.19
54 3 0.07
55 32 0.74
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (55 bp):
GAAACCATCAAAATTTTATTGTTACCATTAGCTGATCTCAGCCTACAATTCCATT
Found at i:30459 original size:33 final size:33
Alignment explanation
Indices: 30417--30493 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
30407 GATGGCAGCC
30417 CATGGTTTTGAAAAAAATATTTGGATTATGATA
1 CATGGTTTTGAAAAAAATATTTGGATTATGATA
* *
30450 CATGGTTTTGAAAGAAATATTTGGATTCTGATA
1 CATGGTTTTGAAAAAAATATTTGGATTATGATA
30483 CATGGTTTTGA
1 CATGGTTTTGA
30494 TATCACTGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (33 bp):
CATGGTTTTGAAAAAAATATTTGGATTATGATA
Found at i:31491 original size:13 final size:13
Alignment explanation
Indices: 31473--31508 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
31463 ACTATTTATT
31473 TTAATTTTGCATA
1 TTAATTTTGCATA
*
31486 TTAATTTTGTATA
1 TTAATTTTGCATA
31499 TTAATTTTGC
1 TTAATTTTGC
31509 CAGATGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (13 bp):
TTAATTTTGCATA
Found at i:32824 original size:35 final size:35
Alignment explanation
Indices: 32770--32837 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
32760 GAAAAAAGTT
32770 TAAGCTGGGCCAAACGGAAAATCCAGAAGTGCTAA
1 TAAGCTGGGCCAAACGGAAAATCCAGAAGTGCTAA
* * *
32805 TAAGTTGGGCCAAATGGAAATTCCAGAAGTGCT
1 TAAGCTGGGCCAAACGGAAAATCCAGAAGTGCT
32838 TTCCAGAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (35 bp):
TAAGCTGGGCCAAACGGAAAATCCAGAAGTGCTAA
Found at i:32843 original size:13 final size:13
Alignment explanation
Indices: 32825--32853 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
32815 CAAATGGAAA
32825 TTCCAGAAGTGCT
1 TTCCAGAAGTGCT
32838 TTCCAGAAGTGCT
1 TTCCAGAAGTGCT
32851 TTC
1 TTC
32854 AGTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (13 bp):
TTCCAGAAGTGCT
Done.