Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011193.1 Corchorus olitorius cultivar O-4 contig11226, 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: 20698
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1960 original size:44 final size:44
Alignment explanation
Indices: 1897--1980 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
1887 TGACAATAAA
* *
1897 ACCAAAATTACATAGGAAGGCTATCTAAATTTAATAGTGTTGTT
1 ACCAAAATTACATAGGAAGGCTATCAAAACTTAATAGTGTTGTT
* * * * *
1941 ACCAAAATTTCGTATGAAGGTTATCAAAACTTCATAGTGT
1 ACCAAAATTACATAGGAAGGCTATCAAAACTTAATAGTGT
1981 AATTTTCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (44 bp):
ACCAAAATTACATAGGAAGGCTATCAAAACTTAATAGTGTTGTT
Found at i:1963 original size:22 final size:22
Alignment explanation
Indices: 1938--2130 Score: 133
Period size: 22 Copynumber: 8.8 Consensus size: 22
1928 TAATAGTGTT
* *
1938 GTTACCAAAATTTCGTATGAAG
1 GTTATCAAAATTTCATATGAAG
*
1960 GTTATCAAAACTTCATAGTGTAA-
1 GTTATCAAAATTTCATA-TG-AAG
* *
1983 -TTTTCAAAATTTCACAT-AGAG
1 GTTATCAAAATTTCATATGA-AG
* * **
2004 GTTACCAAGATTTCATAAAAAG
1 GTTATCAAAATTTCATATGAAG
* * *
2026 GTTATCAAAATTTCTTAGGGAG
1 GTTATCAAAATTTCATATGAAG
* * *
2048 GTTAACAAAATTTCATACGAAA
1 GTTATCAAAATTTCATATGAAG
* *
2070 GTTATCAAAATTTTATAGTG-TG
1 GTTATCAAAATTTCATA-TGAAG
* * *
2092 GTTATTAAAATTTTATAAGAAG
1 GTTATCAAAATTTCATATGAAG
*
2114 GTTAACAAAATTTCATA
1 GTTATCAAAATTTCATA
2131 GGGAGGAAAT
Statistics
Matches: 130, Mismatches: 33, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 2 0.02
22 120 0.92
23 4 0.03
24 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATATGAAG
Found at i:2436 original size:22 final size:22
Alignment explanation
Indices: 2391--2470 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
2381 CATAGGGAGA
* * **
2391 TTATCAAAATTTCACACTAAGG
1 TTATCAAAATTTCTCAGTGTGG
**
2413 TTATCAAAATTTCTTTGTGTGG
1 TTATCAAAATTTCTCAGTGTGG
*
2435 TTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCTCAGTGTGG
*
2457 TTATCCAAATTTCT
1 TTATCAAAATTTCT
2471 ATGTTGGAGC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCTCAGTGTGG
Found at i:2459 original size:44 final size:44
Alignment explanation
Indices: 2293--2469 Score: 153
Period size: 44 Copynumber: 4.0 Consensus size: 44
2283 AGTTTCATTA
* * *
2293 TCATAGGGAGGTTATCGAAATTTCAAAGTATGGTTATCAAAATTT
1 TCATAGTGAGGTTATCAAAATTTCACAGTATGGTTATCAAAA-TT
* * * * *
2338 TCATAGTGCA-GCTATC-AACTTT-ATAGTGTGATTATCAAAATT
1 TCATAGTG-AGGTTATCAAAATTTCACAGTATGGTTATCAAAATT
* * * * *
2380 CCATAGGGAGATTATCAAAATTTCACACTAAGGTTATCAAAATT
1 TCATAGTGAGGTTATCAAAATTTCACAGTATGGTTATCAAAATT
* * * * *
2424 TCTTTGTGTGGTTATCAAAATTTCACAGTGTGGTTATCCAAATT
1 TCATAGTGAGGTTATCAAAATTTCACAGTATGGTTATCAAAATT
2468 TC
1 TC
2470 TATGTTGGAG
Statistics
Matches: 102, Mismatches: 26, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
41 1 0.01
42 12 0.12
43 20 0.20
44 56 0.55
45 12 0.12
46 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (44 bp):
TCATAGTGAGGTTATCAAAATTTCACAGTATGGTTATCAAAATT
Found at i:3404 original size:37 final size:38
Alignment explanation
Indices: 3333--3408 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
3323 TTGACAAATG
*
3333 ATATAATGAATGGTTTTAAATTTTTTCGTAAATATATA
1 ATATAATAAATGGTTTTAAATTTTTTCGTAAATATATA
3371 ATATAATAAATGGTTTTAAA-TTTTT-GATAAATATATA
1 ATATAATAAATGGTTTTAAATTTTTTCG-TAAATATATA
3408 A
1 A
3409 ATTATTTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 1 0.03
37 16 0.44
38 19 0.53
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.46
Consensus pattern (38 bp):
ATATAATAAATGGTTTTAAATTTTTTCGTAAATATATA
Found at i:3934 original size:2 final size:2
Alignment explanation
Indices: 3927--3956 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3917 AAAGTACTAG
3927 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
3957 ATTAATGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4937 original size:27 final size:27
Alignment explanation
Indices: 4907--4982 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
4897 CAAGGGGGTT
4907 ATGGAGGGTATGGTGGACGTGGAGGTA
1 ATGGAGGGTATGGTGGACGTGGAGGTA
* *
4934 ATGGAGGGTATGGTGGACGTGGCGGTT
1 ATGGAGGGTATGGTGGACGTGGAGGTA
* *
4961 ATGGAGGGTACGGTGGCCGTGG
1 ATGGAGGGTATGGTGGACGTGG
4983 TGGCTACGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.17, C:0.08, G:0.53, T:0.22
Consensus pattern (27 bp):
ATGGAGGGTATGGTGGACGTGGAGGTA
Found at i:4996 original size:18 final size:18
Alignment explanation
Indices: 4969--5003 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4959 TTATGGAGGG
*
4969 TACGGTGGCCGTGGTGGC
1 TACGGAGGCCGTGGTGGC
4987 TACGGAGGCCGTGGTGG
1 TACGGAGGCCGTGGTGG
5004 ATATGGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.20, G:0.51, T:0.20
Consensus pattern (18 bp):
TACGGAGGCCGTGGTGGC
Found at i:17221 original size:138 final size:138
Alignment explanation
Indices: 16973--17249 Score: 527
Period size: 138 Copynumber: 2.0 Consensus size: 138
16963 CGTGTACAGT
16973 GTTTTAGTGTCTGGAGACAAGATTGAAAAAAGAGAAAAACACTAAAAAAGTGTTTGAATATCCTG
1 GTTTTAGTGTCTGGAGACAAGATTGAAAAAAGAGAAAAACACTAAAAAAGTGTTTGAATATCCTG
*
17038 AGACAAGATCTAAACAAGGAAAATTTGATGAATGAGTAAGAACTCGTGATGAACAAGATGAAAAT
66 AGACAAGATCTAAACAAGGAAAATTTGATGAACGAGTAAGAACTCGTGATGAACAAGATGAAAAT
17103 GGCGCAGA
131 GGCGCAGA
* *
17111 GTTTTTGTGTCTGGAGACAAGATTGAAAAAAGAGAAAAACACTAAAAGAGTGTTTGAATATCCTG
1 GTTTTAGTGTCTGGAGACAAGATTGAAAAAAGAGAAAAACACTAAAAAAGTGTTTGAATATCCTG
17176 AGACAAGATCTAAACAAGGAAAATTTGATGAACGAGTAAGAACTCGTGATGAACAAGATGAAAAT
66 AGACAAGATCTAAACAAGGAAAATTTGATGAACGAGTAAGAACTCGTGATGAACAAGATGAAAAT
17241 GGCGCAGA
131 GGCGCAGA
17249 G
1 G
17250 CCAGAGAAAA
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 136 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (138 bp):
GTTTTAGTGTCTGGAGACAAGATTGAAAAAAGAGAAAAACACTAAAAAAGTGTTTGAATATCCTG
AGACAAGATCTAAACAAGGAAAATTTGATGAACGAGTAAGAACTCGTGATGAACAAGATGAAAAT
GGCGCAGA
Found at i:17381 original size:28 final size:28
Alignment explanation
Indices: 17317--17422 Score: 140
Period size: 28 Copynumber: 3.7 Consensus size: 28
17307 AGGAGCTGGT
* * *
17317 TTTTGAGATGAGTGATATCTCTGAGAAAATG
1 TTTTGAGATGTG-GA-ATCTGTGAG-ACATG
*
17348 TTTTGAGATATGGAATCTGTGAGACATG
1 TTTTGAGATGTGGAATCTGTGAGACATG
*
17376 TTTTGAGATGTGGAATCTGTGAGAGATG
1 TTTTGAGATGTGGAATCTGTGAGACATG
17404 TTTTGAGATGTGGAATCTG
1 TTTTGAGATGTGGAATCTG
17423 CCTTCAAGCC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
28 49 0.71
29 8 0.12
30 2 0.03
31 10 0.14
ACGTcount: A:0.27, C:0.06, G:0.30, T:0.37
Consensus pattern (28 bp):
TTTTGAGATGTGGAATCTGTGAGACATG
Done.