Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012256.1 Corchorus olitorius cultivar O-4 contig12289, 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: 36044
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:441 original size:33 final size:33
Alignment explanation
Indices: 378--441 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
368 ATACTGAATA
**
378 ATATTGCCCCTGAAGAGGCATAAATTCATGAGC
1 ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
* *
411 ATATTGCCCCTGTAGTGGCATAAACCCATGA
1 ATATTGCCCCTGAAGAGGCATAAACCCATGA
442 AAAGATCATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (33 bp):
ATATTGCCCCTGAAGAGGCATAAACCCATGAGC
Found at i:3028 original size:48 final size:48
Alignment explanation
Indices: 2957--3049 Score: 170
Period size: 48 Copynumber: 1.9 Consensus size: 48
2947 AAAATTTTAT
2957 TTAGAATTGAAATTACCAAGTTTCAATCATAAACCGAAAGACCCGCGA
1 TTAGAATTGAAATTACCAAGTTTCAATCATAAACCGAAAGACCCGCGA
3005 TTAGAATTGAAATTACTC-AGTTTCAATCATAAACCGAAAGACCCG
1 TTAGAATTGAAATTAC-CAAGTTTCAATCATAAACCGAAAGACCCG
3050 AAGCTAATGC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 43 0.98
49 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (48 bp):
TTAGAATTGAAATTACCAAGTTTCAATCATAAACCGAAAGACCCGCGA
Found at i:6971 original size:3 final size:3
Alignment explanation
Indices: 6963--6990 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6953 TGCAGTCTCT
6963 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
6991 AAGCACCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9787 original size:19 final size:20
Alignment explanation
Indices: 9753--9790 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
9743 AAATTCTAAA
9753 TTAAATAAATACTATCCATC
1 TTAAATAAATACTATCCATC
9773 TTAAATAAA-ACTATCCAT
1 TTAAATAAATACTATCCAT
9791 TAGAGGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAAATAAATACTATCCATC
Found at i:11118 original size:19 final size:18
Alignment explanation
Indices: 11081--11125 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
11071 CAAAATTTAT
11081 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
11099 TAATTATTT-TTCAGAATAA
1 TAATTATTTATT-A-AATAA
*
11118 TTATTATT
1 TAATTATT
11126 AATTTTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 10 0.42
19 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:13323 original size:2 final size:2
Alignment explanation
Indices: 13318--13353 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13308 CTCTATATTT
13318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13354 CACGTGAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24229 original size:24 final size:24
Alignment explanation
Indices: 24182--24257 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
24172 GAGGAAAATC
*
24182 AAACGGCCACATAGTTGGTCGTGAG
1 AAACGGCCACAT-GGTGGTCGTGAG
*
24207 AAACGGCTACATGGTGGTCGTGAG
1 AAACGGCCACATGGTGGTCGTGAG
** * *
24231 ATTCGACCACATAGTGGTCGTGAG
1 AAACGGCCACATGGTGGTCGTGAG
24255 AAA
1 AAA
24258 AAAAACAAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 31 0.74
25 11 0.26
ACGTcount: A:0.29, C:0.18, G:0.32, T:0.21
Consensus pattern (24 bp):
AAACGGCCACATGGTGGTCGTGAG
Found at i:25369 original size:11 final size:11
Alignment explanation
Indices: 25353--25387 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
25343 TTTTTCTGTA
25353 TTTTGTTTTTG
1 TTTTGTTTTTG
*
25364 TTTTGTTTTCG
1 TTTTGTTTTTG
25375 TTTTGTTTTTG
1 TTTTGTTTTTG
25386 TT
1 TT
25388 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:26392 original size:130 final size:133
Alignment explanation
Indices: 26095--26396 Score: 336
Period size: 130 Copynumber: 2.3 Consensus size: 133
26085 AAATTGTTAA
* * *
26095 GGAGGTTATCAAAATTTAATGGGAGGTTACCAAAAATTTCTTAGAGAGGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATGTGTGGTTACC-AAAATTTCTTAGAGAGGTTATCAAAATTTCATA
* * *
26160 GAGAGACGATCGAAATTTCATAGGGAGCTTAGCAAAATTTCATAGTGTGGTTTATCAAAAATTTT
65 GAGAGACGATCGAAATTTCATAAGGAGATTAGCAAAATTTCATAGTGTGGTTTATCAAAAATTTA
**
26225 ATGG
130 ACAG
* * * *
26229 GGAGTTTATCAAAATTACAT-TGTAGTTATCAAAA-TT-TTATGA-AGGTTGA-CAAAATTTCAT
1 GGAGGTTATCAAAATTTCATGTGTGGTTACCAAAATTTCTTA-GAGAGGTT-ATCAAAATTTCAT
* *
26289 A-AG-GAGGTTATCGAAATTTCATAAGGAGATT-GTCGAAATTTCATAGTGTGG-TTATC-AAAA
64 AGAGAGACG--ATCGAAATTTCATAAGGAGATTAG-CAAAATTTCATAGTGTGGTTTATCAAAAA
26349 TTTAACAG
126 TTTAACAG
*
26357 GGAGGTTATCAACATTTCATAGTGTGGTTACCAAAATTTC
1 GGAGGTTATCAAAATTTCAT-GTGTGGTTACCAAAATTTC
26397 ATTGTGTGAT
Statistics
Matches: 140, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
128 29 0.21
129 8 0.06
130 69 0.49
131 7 0.05
132 4 0.03
133 6 0.04
134 17 0.12
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (133 bp):
GGAGGTTATCAAAATTTCATGTGTGGTTACCAAAATTTCTTAGAGAGGTTATCAAAATTTCATAG
AGAGACGATCGAAATTTCATAAGGAGATTAGCAAAATTTCATAGTGTGGTTTATCAAAAATTTAA
CAG
Found at i:26394 original size:66 final size:66
Alignment explanation
Indices: 26032--26559 Score: 297
Period size: 66 Copynumber: 7.9 Consensus size: 66
26022 TTCATAATGT
* * * * * ** *
26032 GGTTATCAAAATTTCATAGTGTGGTTACGAAAATTT-AGTAGTGCT-ATTACCAAAAATTGTTAA
1 GGTTATCAAAATTTCATAGTGAGGTTACCAAAATTTCA-TAGTG-TGGTTATCAAAATTTCATAG
26095 GGA
64 GGA
* * * * * *
26098 GGTTATCAAAATTTAAT-GGGAGGTTACCAAAAATTTCTTAGAGAGGTTATCAAAATTTCATAGA
1 GGTTATCAAAATTTCATAGTGAGGTTACC-AAAATTTCATAGTGTGGTTATCAAAATTTCATAGG
26162 GA
65 GA
*** * * * * * *
26164 GACGATCGAAATTTCATAGGGAGCTTAGCAAAATTTCATAGTGTGGTTTATCAAAAATTTTATGG
1 GGTTATCAAAATTTCATAGTGAGGTTACCAAAATTTCATAGTGTGG-TTATC-AAAATTTCATAG
26229 GGA
64 GGA
* * * * * *
26232 GTTTATCAAAATTACATTGT-A-GTTATCAAAATTT--TA-TGAAGGTTGA-CAAAATTTCATAA
1 GGTTATCAAAATTTCATAGTGAGGTTACCAAAATTTCATAGTG-TGGTT-ATCAAAATTTCATAG
26291 GGA
64 GGA
* * ** * * *
26294 GGTTATCGAAATTTCATAAG-GAGATTGTCGAAATTTCATAGTGTGGTTATCAAAATTTAACAGG
1 GGTTATCAAAATTTCAT-AGTGAGGTTACCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGG
26358 GA
65 GA
* * *
26360 GGTTATCAACATTTCATAGTGTGGTTACCAAAATTTCATTGTGTGATTATGAGGTTATCAAAATT
1 GGTTATCAAAATTTCATAGTGAGGTTACCAAAATTTCA-T-AGTG----T--GGTTATCAAAATT
*
26425 TCATAGGAA
58 TCATAGGGA
* * **
26434 GGTTGA-CAAAATTTCATTG-GTAGGTTATCAAAATTTCATAGCGTGTAATTATCAAAATTTCAT
1 GGTT-ATCAAAATTTCATAGTG-AGGTTACCAAAATTTCATA--GTGTGGTTATCAAAATTTCAT
26497 AGGGA
62 AGGGA
* * * * * * ** * *
26502 GATTAACGAAATTTCAAAATAGAGGTTATCAAAAAATCATATTGAGGTTATCAAAATT
1 GGTTATCAAAATTTCATAGT-GAGGTTACCAAAATTTCATAGTGTGGTTATCAAAATT
26560 GATAAGGACC
Statistics
Matches: 350, Mismatches: 81, Indels: 61
0.71 0.16 0.12
Matches are distributed among these distances:
62 26 0.07
63 7 0.02
64 15 0.04
65 11 0.03
66 125 0.36
67 32 0.09
68 59 0.17
69 17 0.05
70 2 0.01
72 1 0.00
73 2 0.01
74 52 0.15
75 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.34
Consensus pattern (66 bp):
GGTTATCAAAATTTCATAGTGAGGTTACCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGGG
A
Found at i:26403 original size:22 final size:22
Alignment explanation
Indices: 26010--26409 Score: 180
Period size: 22 Copynumber: 18.3 Consensus size: 22
26000 TTTATTAGGA
* * *
26010 GGTTATCATAGTTTCATAATGT
1 GGTTATCAAAATTTCATAGTGT
26032 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
26054 GGTTA-CGAAAATTT-AGTAGTGCT
1 GGTTATC-AAAATTTCA-TAGTG-T
* * * *
26077 -ATTACCAAAAATTGTTA-AG-GA
1 GGTTATC-AAAATT-TCATAGTGT
* * *
26098 GGTTATCAAAATTTAAT-GGGA
1 GGTTATCAAAATTTCATAGTGT
* * * *
26119 GGTTACCAAAAATTTCTTAGAGA
1 GGTTATC-AAAATTTCATAGTGT
* *
26142 GGTTATCAAAATTTCATAGAGA
1 GGTTATCAAAATTTCATAGTGT
*** * * *
26164 GACGATCGAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAGTGT
* *
26186 GCTTAGCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* * * *
26208 GGTTTATCAAAAATTTTATGGGGA
1 GG-TTATC-AAAATTTCATAGTGT
* *
26232 GTTTATCAAAATTACAT--TGT
1 GGTTATCAAAATTTCATAGTGT
* *
26252 AGTTATCAAAATTT--TA-TGAA
1 GGTTATCAAAATTTCATAGTG-T
*
26272 GGTTGA-CAAAATTTCATAAG-GA
1 GGTT-ATCAAAATTTCAT-AGTGT
* *
26294 GGTTATCGAAATTTCATAAG-GA
1 GGTTATCAAAATTTCAT-AGTGT
* * *
26316 GATTGTCGAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* * * *
26338 GGTTATCAAAATTTAACAGGGA
1 GGTTATCAAAATTTCATAGTGT
*
26360 GGTTATCAACATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
26382 GGTTACCAAAATTTCATTGTGT
1 GGTTATCAAAATTTCATAGTGT
*
26404 GATTAT
1 GGTTAT
26410 GAGGTTATCA
Statistics
Matches: 292, Mismatches: 64, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.00
19 2 0.01
20 26 0.09
21 20 0.07
22 199 0.68
23 30 0.10
24 13 0.04
25 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:26443 original size:22 final size:22
Alignment explanation
Indices: 26411--26559 Score: 99
Period size: 22 Copynumber: 6.6 Consensus size: 22
26401 TGTGATTATG
26411 AGGTTATCAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
* *
26433 AGGTTGA-CAAAATTTCATTGGT
1 AGGTT-ATCAAAATTTCATAGGA
26455 AGGTTATCAAAATTTCATAGCGTGTA
1 AGGTTATCAAAATTTCATA--G-G-A
*
26481 A--TTATCAAAATTTCATAGGG
1 AGGTTATCAAAATTTCATAGGA
* * * * **
26501 AGATTAACGAAATTTCAAAATA
1 AGGTTATCAAAATTTCATAGGA
** *
26523 GAGGTTATCAAAAAATCATATTG-
1 -AGGTTATCAAAATTTCATA-GGA
26546 AGGTTATCAAAATT
1 AGGTTATCAAAATT
26560 GATAAGGACC
Statistics
Matches: 96, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 60 0.62
23 14 0.15
24 17 0.18
25 1 0.01
26 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:26864 original size:22 final size:22
Alignment explanation
Indices: 26800--26954 Score: 114
Period size: 22 Copynumber: 7.0 Consensus size: 22
26790 TTATTAAAAC
*
26800 TTATAGTGTGGTTACCAAAATT
1 TTATAGTGTGGTTATCAAAATT
* * * *
26822 TTGTAGGGAGGTTATCGAAATT
1 TTATAGTGTGGTTATCAAAATT
* *
26844 TTATAGTCTGGTTATTAAAATT
1 TTATAGTGTGGTTATCAAAATT
* **
26866 GTATAAG-GAAGTTATCAAAATT
1 TTAT-AGTGTGGTTATCAAAATT
* ** **
26888 TTGTTCTGTGGTTATTTAAATT
1 TTATAGTGTGGTTATCAAAATT
* * * *
26910 GTATAGAGAGATTATCAAAATT
1 TTATAGTGTGGTTATCAAAATT
*
26932 TTATAGTGTAGTTATCAAAATT
1 TTATAGTGTGGTTATCAAAATT
26954 T
1 T
26955 CATTATTTTG
Statistics
Matches: 93, Mismatches: 38, Indels: 4
0.69 0.28 0.03
Matches are distributed among these distances:
22 91 0.98
23 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.43
Consensus pattern (22 bp):
TTATAGTGTGGTTATCAAAATT
Found at i:29510 original size:36 final size:37
Alignment explanation
Indices: 29433--29510 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 37
29423 TCGTCCACAT
29433 TTGTATGGACTTGAGTCCTTTTTTTTTTTAGGCACCA
1 TTGTATGGACTTGAGTCCTTTTTTTTTTTAGGCACCA
29470 -TGTATGGACTTGAGT-CTTTTTTTTTTT-GGCACCTA
1 TTGTATGGACTTGAGTCCTTTTTTTTTTTAGGCACC-A
29505 TTGTAT
1 TTGTAT
29511 TCCAATCTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
34 6 0.15
35 13 0.33
36 20 0.51
ACGTcount: A:0.15, C:0.14, G:0.19, T:0.51
Consensus pattern (37 bp):
TTGTATGGACTTGAGTCCTTTTTTTTTTTAGGCACCA
Found at i:29853 original size:19 final size:20
Alignment explanation
Indices: 29833--29868 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
29823 ATTTAATTAT
29833 TTTA-ATATTA-ATTTTTTA
1 TTTATATATTATATTTTTTA
29851 TTTATATATTATATTTTT
1 TTTATATATTATATTTTT
29869 ACTTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATATATTATATTTTTTA
Done.