Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016760.1 Corchorus olitorius cultivar O-4 contig16793, 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: 14930
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:484 original size:29 final size:30
Alignment explanation
Indices: 452--518 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
442 ATGCAATTTG
452 GGATATAACGTTAC-AAAACAAACAATTAA
1 GGATATAACGTTACAAAAACAAACAATTAA
* *
481 GGATATAACGTTACTAAAAACGAGCAATTAA
1 GGATATAACGTTAC-AAAAACAAACAATTAA
512 GGATATA
1 GGATATA
519 GTCCGTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
31 20 0.59
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22
Consensus pattern (30 bp):
GGATATAACGTTACAAAAACAAACAATTAA
Found at i:685 original size:31 final size:31
Alignment explanation
Indices: 650--724 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
640 CTTACTGATT
* *
650 ATATCCTTAATTGCTTGAAATCAAAAACGTC
1 ATATCCTTAATTGCTTAAAATCAAAAAAGTC
*
681 ATATCCTTAATTGCTTAAAATCAAAAAAGTT
1 ATATCCTTAATTGCTTAAAATCAAAAAAGTC
712 ATATCCTTAATTG
1 ATATCCTTAATTG
725 TTTGTTTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (31 bp):
ATATCCTTAATTGCTTAAAATCAAAAAAGTC
Found at i:1807 original size:31 final size:30
Alignment explanation
Indices: 1766--1902 Score: 134
Period size: 31 Copynumber: 4.5 Consensus size: 30
1756 GTCAAATAAT
* * *
1766 CAATTTAGGATATAACGTTTGC-TGCCACAAG
1 CAATTAAGGATATAACGTTTTCAT--TACAAG
* **
1797 CAATTAAGGATATAACG-TTACAAAACAAG
1 CAATTAAGGATATAACGTTTTCATTACAAG
* *
1826 CAATTAATGATATAACGTTTTCTATTTCAAG
1 CAATTAAGGATATAACGTTTTC-ATTACAAG
* *
1857 CAATTAAGGATATGACGTTTTCGATTTCAAG
1 CAATTAAGGATATAACGTTTTC-ATTACAAG
1888 CAATTAAGGATATAA
1 CAATTAAGGATATAA
1903 TCAGTTAGGC
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
29 21 0.23
30 6 0.07
31 63 0.70
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (30 bp):
CAATTAAGGATATAACGTTTTCATTACAAG
Found at i:2105 original size:29 final size:31
Alignment explanation
Indices: 2031--2097 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
2021 TCTAACGGAC
2031 TATATCCTTAATTGCTCTCTTTTCGTAACGT
1 TATATCCTTAATTGCTCTCTTTTCGTAACGT
*
2062 TATATCCTTAATTGCT-TGTTTT-GTAACGT
1 TATATCCTTAATTGCTCTCTTTTCGTAACGT
2091 TATATCC
1 TATATCC
2098 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 5 0.14
31 16 0.46
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.49
Consensus pattern (31 bp):
TATATCCTTAATTGCTCTCTTTTCGTAACGT
Found at i:9782 original size:29 final size:29
Alignment explanation
Indices: 9708--9784 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
9698 CGTTTAAGAG
*
9708 GAGGCAAAAACGTCCAAAATTAGGAATTTAT
1 GAGGC-AAAACGTCCAAAATTA-GAATTAAT
* **
9739 GATGCAAAATATCCAAAATT-GAAGTTAAT
1 GAGGCAAAACGTCCAAAATTAGAA-TTAAT
9768 GAGGCAAAACGTCCAAA
1 GAGGCAAAACGTCCAAA
9785 CGTTTCAAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 3 0.08
29 18 0.47
30 13 0.34
31 4 0.11
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.21
Consensus pattern (29 bp):
GAGGCAAAACGTCCAAAATTAGAATTAAT
Found at i:12838 original size:18 final size:18
Alignment explanation
Indices: 12815--12850 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12805 TATGGATCAC
12815 AGTAAAACTCATTGTGGG
1 AGTAAAACTCATTGTGGG
12833 AGTAAAACTCATTGTGGG
1 AGTAAAACTCATTGTGGG
12851 TGTCAATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (18 bp):
AGTAAAACTCATTGTGGG
Found at i:13068 original size:13 final size:14
Alignment explanation
Indices: 13050--13094 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
13040 CTAAATTGAC
13050 ATTATTAAAATTT-
1 ATTATTAAAATTTA
13063 ATTATTTAAAATTTA
1 ATTA-TTAAAATTTA
13078 ATTA-TAAAATTTCA
1 ATTATTAAAATTT-A
13092 ATT
1 ATT
13095 TAGACCGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.41
14 13 0.45
15 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTATTAAAATTTA
Found at i:13263 original size:26 final size:24
Alignment explanation
Indices: 13208--13265 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
13198 TTATATTTCT
*
13208 AAATTTCTATTATTAAAATTTAGTA
1 AAATTT-TATTATTAAAATTAAGTA
* *
13233 TAATTTTATTATTTAAAAATTAATTA
1 AAATTTTATTA-TT-AAAATTAAGTA
13259 AAATTTT
1 AAATTTT
13266 CAATTTAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 5 0.19
25 7 0.26
26 15 0.56
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
AAATTTTATTATTAAAATTAAGTA
Found at i:13599 original size:22 final size:21
Alignment explanation
Indices: 13550--13774 Score: 128
Period size: 22 Copynumber: 10.1 Consensus size: 21
13540 TGTGGTTAAA
* *
13550 AAAATTTCATAAGATGGTTATT
1 AAAATTTCATAGGA-GGTTATC
*
13572 ATAATTTCATGAGGAGGTTATC
1 AAAATTTCAT-AGGAGGTTATC
* * * *
13594 AAAATTCCATCGTGTGGTTACC
1 AAAATTTCATAG-GAGGTTATC
* *
13616 AAAATTTCATATGGAAGTTAAC
1 AAAATTTCATA-GGAGGTTATC
*
13638 AAAATTTCATGGGAAGGTTA-C
1 AAAATTTCATAGG-AGGTTATC
* *
13659 TAAAATTTCATAGTGTGGTTACC
1 -AAAATTTCATAG-GAGGTTATC
*
13682 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGG---AGGTTATC
* * *
13706 AAAATTTCTTAGAAAGGTTATT
1 AAAATTTCATAG-GAGGTTATC
* * *
13728 GAAATTTCATAATGTGGTTATC
1 AAAATTTCAT-AGGAGGTTATC
* * *
13750 ACAATTTTATAGAAAGGTTATC
1 AAAATTTCATAG-GAGGTTATC
13772 AAA
1 AAA
13775 GAAATTATCA
Statistics
Matches: 155, Mismatches: 35, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
21 6 0.04
22 126 0.81
23 7 0.05
24 16 0.10
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
AAAATTTCATAGGAGGTTATC
Found at i:13688 original size:44 final size:44
Alignment explanation
Indices: 13539--13713 Score: 142
Period size: 44 Copynumber: 3.9 Consensus size: 44
13529 TCTTGTCTCT
* * * * *
13539 GTGTGGTTAAAAAAATTTCATAAGATGGTTATTATAATTTCATGA
1 GTGTGGTTAACAAAATTTCATAGGAAGGTTACTAAAATTTCAT-A
* * * * * *
13584 G-GAGGTTATCAAAATTCCATCGTG-TGGTTACCAAAATTTCATA
1 GTGTGGTTAACAAAATTTCATAG-GAAGGTTACTAAAATTTCATA
*
13627 -TG-GAAGTTAACAAAATTTCATGGGAAGGTTACTAAAATTTCATA
1 GTGTG--GTTAACAAAATTTCATAGGAAGGTTACTAAAATTTCATA
* *
13671 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTC
1 GTGTGGTTAACAAAATTTCATAGGA--AGGTTACTAAAATTTC
13714 TTAGAAAGGT
Statistics
Matches: 104, Mismatches: 17, Indels: 17
0.75 0.12 0.12
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 80 0.77
45 4 0.04
46 16 0.15
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (44 bp):
GTGTGGTTAACAAAATTTCATAGGAAGGTTACTAAAATTTCATA
Found at i:13948 original size:19 final size:20
Alignment explanation
Indices: 13924--13961 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13914 CTTTTACTAT
13924 GGAGGA-ATCAAAATTTCAG
1 GGAGGATATCAAAATTTCAG
13943 GGAGGATATCAAAATTTCA
1 GGAGGATATCAAAATTTCA
13962 TAGTTTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
GGAGGATATCAAAATTTCAG
Found at i:14126 original size:23 final size:22
Alignment explanation
Indices: 13779--14457 Score: 242
Period size: 22 Copynumber: 31.4 Consensus size: 22
13769 ATCAAAGAAA
* **
13779 TTATCAAAATGTCATAGCAAGG
1 TTATCAAAATTTCATAGGGAGG
* *
13801 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGGGAGG
* * *
13823 TTAACAAAATTTCATAAGAAGG
1 TTATCAAAATTTCATAGGGAGG
* *
13845 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGGGAGG
**
13867 TTATCAAAATTTCATA-CTATGG
1 TTATCAAAATTTCATAGGGA-GG
* * *
13889 TTA-CTAAA--T--TAGGAAGC
1 TTATCAAAATTTCATAGGGAGG
* * * *
13906 TTATTAAACTTTTACTATGGAGG
1 TTATCAAAATTTCA-TAGGGAGG
*
13929 -AATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATAGGGAGG
* **
13948 ATATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG-GGAGG
* * *
13970 TTTTCAAAATTTCATA-GTATG
1 TTATCAAAATTTCATAGGGAGG
* * *
13991 TAGATCAAAATTTTATAGGGAGA
1 T-TATCAAAATTTCATAGGGAGG
* **
14014 TTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGGGAGG
** *
14036 TTATCAAAACATCATAGAGAGG
1 TTATCAAAATTTCATAGGGAGG
*
14058 TTATCAAAA-TT--T--GTA-G
1 TTATCAAAATTTCATAGGGAGG
* *
14074 TTATCAAGATTTCATAAGGAGG
1 TTATCAAAATTTCATAGGGAGG
*
14096 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATAGGGAGG
* *
14118 TTTATCAAAATTTTATAGTGAGG
1 -TTATCAAAATTTCATAGGGAGG
* * * *
14141 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGGGAGG
* * * *
14163 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGGGAGG
*
14185 TTA-CTAACAA-TTCATATGGAGG
1 TTATC-AA-AATTTCATAGGGAGG
* * * ** * *
14207 TTTTTAAATTTTCATAACGTGA
1 TTATCAAAATTTCATAGGGAGG
* * **
14229 TTATCAATATATCATATAGAGG
1 TTATCAAAATTTCATAGGGAGG
* * **
14251 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAG-GGAGG
** *
14274 TTATCAAAATTTCATTCGGAAG
1 TTATCAAAATTTCATAGGGAGG
*
14296 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAGGGAGG
* *
14318 TCT-TCAAAA-TTCTTTAGGGATG
1 T-TATCAAAATTTC-ATAGGGAGG
* * *
14340 TTAACAAAATTTCATAAGAAGG
1 TTATCAAAATTTCATAGGGAGG
** **
14362 TTAAAAAAATTT-ATA-AAAGGG
1 TTATCAAAATTTCATAGGGA-GG
* * *
14383 TTCTCAAAA-TTCGATA-GTATCG
1 TTATCAAAATTTC-ATAGGGA-GG
* * *
14405 TTATTAAAGTTTCATAGGAAGG
1 TTATCAAAATTTCATAGGGAGG
* * *
14427 TTATTAAAATTTTATAAGGAGG
1 TTATCAAAATTTCATAGGGAGG
*
14449 TCATCAAAA
1 TTATCAAAA
14458 ATAGTGTAAT
Statistics
Matches: 481, Mismatches: 136, Indels: 80
0.69 0.20 0.11
Matches are distributed among these distances:
16 9 0.02
17 9 0.02
18 3 0.01
19 9 0.02
20 18 0.04
21 30 0.06
22 344 0.72
23 59 0.12
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGAGG
Found at i:14146 original size:83 final size:82
Alignment explanation
Indices: 13994--14152 Score: 192
Period size: 82 Copynumber: 1.9 Consensus size: 82
13984 TAGTATGTAG
* * *
13994 ATCAAAATTTTATAGGGAGATTAACAAAATTTCATAATGAGGTTATCAAAACATCATAGAGAGGT
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTATCAAAACATCATAGAGAGGT
14059 TATCAAAATTTGTAGTT
66 TATCAAAATTTGTAGTT
* * * * * ** * *
14076 ATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGTGAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGG-TTATCAAAACATCATAGAGAGG
*
14141 TTATCACAATTT
65 TTATCAAAATTT
14153 CATAGTGTGA
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
82 34 0.54
83 29 0.46
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (82 bp):
ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGAGGTTATCAAAACATCATAGAGAGGT
TATCAAAATTTGTAGTT
Found at i:14157 original size:22 final size:22
Alignment explanation
Indices: 13779--14355 Score: 255
Period size: 22 Copynumber: 26.7 Consensus size: 22
13769 ATCAAAGAAA
* **
13779 TTATCAAAATGTCATAGCAAGG
1 TTATCAAAATTTCATAGTGAGG
*
13801 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
13823 TTAACAAAATTTCATAAG-AAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * *
13845 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
13867 TTATCAAAATTTCATACT-ATGG
1 TTATCAAAATTTCATAGTGA-GG
* *
13889 TTA-CTAAA--T--TAG-GAAGC
1 TTATCAAAATTTCATAGTG-AGG
* * *
13906 TTATTAAACTTTTACTA-TGGAGG
1 TTATCAAAATTTCA-TAGT-GAGG
* *
13929 -AATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
13948 ATATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG-TGAGG
* *
13970 TTTTCAAAATTTCATAGT-ATG
1 TTATCAAAATTTCATAGTGAGG
* * * *
13991 TAGATCAAAATTTTATAGGGAGA
1 T-TATCAAAATTTCATAGTGAGG
* *
14014 TTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
** *
14036 TTATCAAAACATCATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
14058 TTATCAAAA-TT--T-GT-A-G
1 TTATCAAAATTTCATAGTGAGG
*
14074 TTATCAAGATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* *
14096 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
*
14118 TTTATCAAAATTTTATAGTGAGG
1 -TTATCAAAATTTCATAGTGAGG
* * *
14141 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
14163 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
14185 TTA-CTAACAA-TTCATA-TGGAGG
1 TTATC-AA-AATTTCATAGT-GAGG
* * *
14207 TTTTTAAATTTTCATAACGTGA--
1 TTATCAAAATTTCAT-A-GTGAGG
* *
14229 TTATCAATATATCATA-TAGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * *
14251 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAGTG-AGG
* *
14274 TTATCAAAATTTCATTCG-GAAG
1 TTATCAAAATTTCA-TAGTGAGG
14296 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
14318 TCT-TCAAAA-TTCTTTAGGGATG
1 T-TATCAAAATTTC-ATAGTGAGG
*
14340 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
14356 AGAAGGTTAA
Statistics
Matches: 416, Mismatches: 86, Indels: 106
0.68 0.14 0.17
Matches are distributed among these distances:
16 9 0.02
17 9 0.02
18 4 0.01
19 9 0.02
20 15 0.04
21 27 0.06
22 281 0.68
23 56 0.13
24 5 0.01
25 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:14871 original size:39 final size:40
Alignment explanation
Indices: 14815--14895 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
14805 TTTAATTCCT
14815 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
14855 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
14894 AT
1 AT
14896 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Done.