Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015281.1 Corchorus olitorius cultivar O-4 contig15314, 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: 5828
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:3000 original size:66 final size:67
Alignment explanation
Indices: 2894--3024 Score: 151
Period size: 66 Copynumber: 2.0 Consensus size: 67
2884 TCTTGTCTCT
* * * * *
2894 GTGTGGTTATCAAAATTTCATAAGATGCTTATTATAATTTCATGAGG-C-GGTTATCAAAATTTC
1 GTGTGATTACCAAAATTTCATAAGAAGCTTATCAAAATTTCAT-AGGACAGGTTATCAAAATTTC
2957 ATA
65 ATA
* *
2960 GTGTGATTACCAAAATTTCATATGAAAG-TTATCAAAATTTCATAGGATCAGGTTATTAAAATTT
1 GTGTGATTACCAAAATTTCATAAG-AAGCTTATCAAAATTTCATAGGA-CAGGTTATCAAAATTT
3024 C
64 C
3025 TTAGGAAAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
65 3 0.06
66 34 0.63
67 3 0.06
68 14 0.26
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (67 bp):
GTGTGATTACCAAAATTTCATAAGAAGCTTATCAAAATTTCATAGGACAGGTTATCAAAATTTCA
TA
Found at i:3037 original size:90 final size:88
Alignment explanation
Indices: 2898--3085 Score: 218
Period size: 90 Copynumber: 2.1 Consensus size: 88
2888 GTCTCTGTGT
* **
2898 GGTTATCAAAATTTCATAAGATGCTTATTATAATTTCATGAGGCGGTTATCAAAATTTCATAGTG
1 GGTTATCAAAATTTCATAAGATGCTTATTAAAATTTCATGAGGAAGTTATCAAAATTTCATAGTG
2963 TGATTACCAAAATTTCATATGAAA
66 TGATTACCAAAATTTCATA-GAAA
* * * **
2987 -GTTATCAAAATTTCATAGGATCAGGTTATTAAAATTTC-TTAGGAAAGTTATTGAAATTTCATA
1 GGTTATCAAAATTTCATAAGAT--GCTTATTAAAATTTCATGAGG-AAGTTATCAAAATTTCATA
* * * *
3050 GTGTGGTTATCACAATTTTATAGAAA
63 GTGTGATTACCAAAATTTCATAGAAA
3076 GGTTATCAAA
1 GGTTATCAAA
3086 GAGATTATCA
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
88 20 0.24
89 8 0.10
90 55 0.66
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (88 bp):
GGTTATCAAAATTTCATAAGATGCTTATTAAAATTTCATGAGGAAGTTATCAAAATTTCATAGTG
TGATTACCAAAATTTCATAGAAA
Found at i:3066 original size:22 final size:21
Alignment explanation
Indices: 2896--3072 Score: 111
Period size: 22 Copynumber: 8.0 Consensus size: 21
2886 TTGTCTCTGT
2896 GTGGTTATCAAAATTTCATAAG
1 GTGGTTATCAAAATTTCAT-AG
* * * *
2918 ATGCTTATTATAATTTCATGAG
1 GTGGTTATCAAAATTTCAT-AG
*
2940 GCGGTTATCAAAATTTCATAG
1 GTGGTTATCAAAATTTCATAG
* *
2961 TGTGATTACCAAAATTTCATATG
1 -GTGGTTATCAAAATTTCATA-G
***
2984 AAAGTTATCAAAATTTCATAG
1 GTGGTTATCAAAATTTCATAG
* *
3005 GATCAGGTTATTAAAATTTCTTAG
1 G-T--GGTTATCAAAATTTCATAG
** **
3029 GAAAGTTATTGAAATTTCATAG
1 G-TGGTTATCAAAATTTCATAG
* *
3051 TGTGGTTATCACAATTTTATAG
1 -GTGGTTATCAAAATTTCATAG
3073 AAAGGTTATC
Statistics
Matches: 116, Mismatches: 33, Indels: 12
0.72 0.20 0.07
Matches are distributed among these distances:
21 3 0.03
22 93 0.80
23 2 0.02
24 18 0.16
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (21 bp):
GTGGTTATCAAAATTTCATAG
Found at i:3115 original size:22 final size:21
Alignment explanation
Indices: 3090--3504 Score: 146
Period size: 22 Copynumber: 18.8 Consensus size: 21
3080 ATCAAAGAGA
*
3090 TTATCAAAATGTCATATCGAGG
1 TTATCAAAATTTCATAT-GAGG
*
3112 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATA-TGAGG
* *
3134 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-ATGAGG
* **
3156 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-ATGAGG
*
3178 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATA-TGAGG
3200 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATG-AGG
* *
3222 TTAT-AAAAGTCTCAATTTCATAAGG
1 TTATCAAAA-TTTC-A--T-ATGAGG
* * * *
3247 AGTACCAAAATATGATA-GAAGG
1 -TTATCAAAATTTCATATG-AGG
*
3269 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATATGAG-G
* * * *
3289 ATTGTCGATATTTCATAGAGATTGG
1 -TTATCAAAATTTCATA-TGA--GG
* *
3314 ATTATCAAAATTT-ATAGGAAGA
1 -TTATCAAAATTTCATATG-AGG
**
3336 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATA-TGAGG
* *
3358 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATA-TGAGG
* * * *
3380 TTATCAAAATTACACAATGTGA
1 TTATCAAAATTTCA-TATGAGG
*
3402 TCATCAAAATTTCATA-GAGGGG
1 TTATCAAAATTTCATATGA--GG
* * *
3424 TCAACAAAATTTTATA-GAGAG
1 TTATCAAAATTTCATATGAG-G
*
3445 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-ATGAGG
* * * *
3467 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTC-ATATGAGG
*
3489 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
3505 GTGGTATTTA
Statistics
Matches: 298, Mismatches: 62, Indels: 67
0.70 0.15 0.16
Matches are distributed among these distances:
19 2 0.01
20 12 0.04
21 44 0.15
22 192 0.64
23 15 0.05
24 6 0.02
25 16 0.05
26 7 0.02
27 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATATGAGG
Found at i:3225 original size:44 final size:42
Alignment explanation
Indices: 3090--4030 Score: 228
Period size: 44 Copynumber: 21.8 Consensus size: 42
3080 ATCAAAGAGA
* * *
3090 TTATCAAAATGTCATATCGAGGTTAT-AAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATA-GGAGGTTATCAA-AATTTCATA-TGAGG
* * **
3134 TTAACAAAATTTCATAAGGAGGTTA-CTAATATTTCATGGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTATC-AAAATTTCAT-ATGAGG
*
3178 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATATG-AGG
* * * *
3222 TTATAAAAGTCTCAATTTCATAAGGA-G-TACCAAAATATGATA-GAAGG
1 TTAT-CAA-----AATTTCAT-AGGAGGTTATCAAAATTTCATATG-AGG
* * * * *
3269 TTATC-AAATCTCATA-GAGTGATTGTCGATATTTCATAGAGATTGG
1 TTATCAAAATTTCATAGGAG-G-TTATCAAAATTTCATA-TGA--GG
* **
3314 ATTATCAAAATTT-ATAGGAAGATTATCAAAATTTCATAGTGTTG
1 -TTATCAAAATTTCATAGG-AGGTTATCAAAATTTCATA-TGAGG
* * * * *
3358 TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACACAATGTGA
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCA-TATGAGG
* * * * *
3402 TCATCAAAATTTCATAGAGGGGTCAACAAAATTTTATA-GAGAG
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATATGAG-G
* * * * *
3445 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTC-ATATGAGG
* * *
3489 TTACCAAAATTTCATA-GTGG---T----ATTT-ATAGGGAGG
1 TTATCAAAATTTCATAGGAGGTTATCAAAATTTCATA-TGAGG
* * *
3523 TTATCAAAATTTCATAGTATGGTTA-CCAAA--T--TAGGAAGG
1 TTATCAAAATTTCATAGGA-GGTTATCAAAATTTCATATG-AGG
* * * * * *
3562 TTATTAAACTTTTATTATGGA-GTAATCAAAATTTCATAGTTTA-C
1 TTATCAAAATTTCA-TA-GGAGGTTATCAAAATTTCATA--TGAGG
* * *
3606 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATA-GTATG
1 TTATCAAAATTTCATAGGA-GGTTATCAAAATTTCATATG-AGG
* * * *
3649 TAGACCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG
1 T-TATCAAAATTTCATA-GGAGGTTATCAAAATTTCAT-ATGAGG
* ** *
3694 TTATAAAAAAATCATAGGGAGGTTATCAAAA-TT--TGT-A-G
1 TTATCAAAATTTCATA-GGAGGTTATCAAAATTTCATATGAGG
* * * * *
3732 TCATCAAGATTTCATAAGGAGGTTATAAAAATTTTATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATA-TGAGG
* * *
3776 TTTATTAAAATTTTATAGGAAGGTTTATC-AAA-TTCATAGCGAGG
1 -TTATCAAAATTTCATAGG-AGG-TTATCAAAATTTCATA-TGAGG
* * * * * * *
3820 TTATCACAATTTCATAGTGTGATTATCAAAATTCCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATA-TGAGG
** * * * * *
3864 TTA-CTAACAA-TTCATATAAAGGTTTTTAAATTTTCATAACGTGG
1 TTATC-AA-AATTTCATA-GGAGGTTATCAAAATTTCAT-ATGAGG
* * * * * *
3908 TTATTAATATATCATATGAAGGTTATCAACATCTCATAGTGTTA-G
1 TTATCAAAATTTCATA-GGAGGTTATCAAAATTTCATA-TG--AGG
* * *
3953 TTATCAAAATTTCATCGGGAAGTTATCAAAATTTCATAGTGCGG
1 TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATA-TGAGG
* * *
3997 TCT-TCAAAATTCCTTAGAGAGGTTAACAAAATTT
1 T-TATCAAAATTTCATAG-GAGGTTATCAAAATTT
4031 TATAAAAAGA
Statistics
Matches: 646, Mismatches: 164, Indels: 174
0.66 0.17 0.18
Matches are distributed among these distances:
33 2 0.00
34 17 0.03
35 3 0.00
36 2 0.00
38 28 0.04
39 25 0.04
40 16 0.02
41 4 0.01
42 24 0.04
43 72 0.11
44 310 0.48
45 74 0.11
46 28 0.04
47 15 0.02
48 14 0.02
49 1 0.00
50 9 0.01
51 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (42 bp):
TTATCAAAATTTCATAGGAGGTTATCAAAATTTCATATGAGG
Found at i:3785 original size:23 final size:23
Alignment explanation
Indices: 3740--3803 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
3730 AGTCATCAAG
* *
3740 ATTTCATAAGGAGG-TTATAAAA
1 ATTTTATAGGGAGGTTTATAAAA
*
3762 ATTTTATAGGGAGGTTTATTAAA
1 ATTTTATAGGGAGGTTTATAAAA
*
3785 ATTTTATAGGAAGGTTTAT
1 ATTTTATAGGGAGGTTTAT
3804 CAAATTCATA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 12 0.32
23 25 0.68
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.41
Consensus pattern (23 bp):
ATTTTATAGGGAGGTTTATAAAA
Found at i:3820 original size:21 final size:22
Alignment explanation
Indices: 3740--3836 Score: 67
Period size: 23 Copynumber: 4.4 Consensus size: 22
3730 AGTCATCAAG
* *
3740 ATTTCATAAG-GAGGTTATAAAA
1 ATTTCAT-AGCGAGGTTATCACA
* * * *
3762 ATTTTATAGGGAGGTTTATTAAA
1 ATTTCATAGCGAGG-TTATCACA
*
3785 ATTTTATAG-GAAGGTTTATCA-A
1 ATTTCATAGCG-AGG-TTATCACA
3807 A-TTCATAGCGAGGTTATCACA
1 ATTTCATAGCGAGGTTATCACA
3828 ATTTCATAG
1 ATTTCATAG
3837 TGTGATTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
20 6 0.09
21 13 0.20
22 21 0.32
23 25 0.38
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (22 bp):
ATTTCATAGCGAGGTTATCACA
Found at i:4129 original size:22 final size:22
Alignment explanation
Indices: 3510--4122 Score: 129
Period size: 22 Copynumber: 28.4 Consensus size: 22
3500 TCATAGTGGT
*
3510 ATTT-ATAGGGAGGTTATCAAA
1 ATTTCATAGGAAGGTTATCAAA
* * *
3531 ATTTCATAGTATGGTTA-CCAA
1 ATTTCATAGGAAGGTTATCAAA
*
3552 A--T--TAGGAAGGTTATTAAA
1 ATTTCATAGGAAGGTTATCAAA
* * *
3570 CTTTTATTATGG-A-GTAATCAAA
1 ATTTCA-TA-GGAAGGTTATCAAA
** * *
3592 ATTTCATAGTTTA-CTTTTCAAA
1 ATTTCATAG-GAAGGTTATCAAA
* *
3614 ATTTCATAAGAGGGTTATCAAA
1 ATTTCATAGGAAGGTTATCAAA
* * * *
3636 ATTTCATA-GTATGTAGACCAAA
1 ATTTCATAGGAAGGT-TATCAAA
* * *
3658 ATTTCATAGGGAGATTAACAAA
1 ATTTCATAGGAAGGTTATCAAA
* *
3680 ATTTCATAATG-AGGTTATAAAA
1 ATTTCAT-AGGAAGGTTATCAAA
** *
3702 AAATCATAGGGAGGTTATCAAA
1 ATTTCATAGGAAGGTTATCAAA
* * *
3724 A-TT--T--GTA-GTCATCAAG
1 ATTTCATAGGAAGGTTATCAAA
*
3740 ATTTCATAAGG-AGGTTATAAAA
1 ATTTCAT-AGGAAGGTTATCAAA
* * *
3762 ATTTTATAGGGAGGTTTATTAAA
1 ATTTCATAGGAAGG-TTATCAAA
*
3785 ATTTTATAGGAAGGTTTATC-AA
1 ATTTCATAGGAAGG-TTATCAAA
*
3807 A-TTCATAGCG-AGGTTATCACA
1 ATTTCATAG-GAAGGTTATCAAA
* *
3828 ATTTCATAGTG-TGATTATCAAA
1 ATTTCATAG-GAAGGTTATCAAA
* * * *
3850 ATTCCAGAGTG-TGATTA-CTAACA
1 ATTTCATAG-GAAGGTTATC-AA-A
** * *
3873 A-TTCATATAAAGGTTTTTAAA
1 ATTTCATAGGAAGGTTATCAAA
* * * * *
3894 TTTTCATAACG-TGGTTATTAAT
1 ATTTCAT-AGGAAGGTTATCAAA
* * *
3916 ATATCATATGAAGGTTATCAAC
1 ATTTCATAGGAAGGTTATCAAA
* *
3938 ATCTCATAGTGTTA-GTTATCAAA
1 ATTTCATAG-G-AAGGTTATCAAA
*
3961 ATTTCATCGGGAA-GTTATCAAA
1 ATTTCAT-AGGAAGGTTATCAAA
*
3983 ATTTCATAGTG-CGGTCT-TCAAA
1 ATTTCATAG-GAAGGT-TATCAAA
* * *
4005 ATTCCTTA-GAGAGGTTAACAAA
1 ATTTCATAGGA-AGGTTATCAAA
* ** * * *
4027 ATTTTATAAAAAGATTTTAAAA
1 ATTTCATAGGAAGGTTATCAAA
** * **
4049 ACTTT-ATAAAAAGGTTCTTGAA
1 A-TTTCATAGGAAGGTTATCAAA
* * **
4071 ATTCCATAGTATCGTTATCAAA
1 ATTTCATAGGAAGGTTATCAAA
4093 ATTTCATAGGAAGGTTATCAAA
1 ATTTCATAGGAAGGTTATCAAA
*
4115 CTTTCATA
1 ATTTCATA
4123 AGGAGGTCAT
Statistics
Matches: 428, Mismatches: 118, Indels: 91
0.67 0.19 0.14
Matches are distributed among these distances:
16 8 0.02
17 13 0.03
18 2 0.00
19 3 0.01
20 8 0.02
21 39 0.09
22 294 0.69
23 57 0.13
24 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATTTCATAGGAAGGTTATCAAA
Done.