Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022858.1 Corchorus olitorius cultivar O-4 contig22891, 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: 8042
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:787 original size:50 final size:50
Alignment explanation
Indices: 712--1027 Score: 551
Period size: 50 Copynumber: 6.3 Consensus size: 50
702 CATTAAACTC
* **
712 GGCTTATGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTTT
1 GGCTTGTGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTT
*
762 GGCTTGTGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTC
1 GGCTTGTGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTT
* *
812 GGCTTGTGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTC
1 GGCTTGTGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTT
*
862 GGCTTGTGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTT
1 GGCTTGTGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTT
*
912 GGCTTGTGGAAAAGCCGGTGTTGATAATTGATTCGTATGGAAACGAGTTT
1 GGCTTGTGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTT
962 GGCTTGTGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTT
1 GGCTTGTGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTT
*
1012 GGCTTATGGAAAAGCC
1 GGCTTGTGGAAAAGCC
1028 AAAGCATTCG
Statistics
Matches: 256, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 256 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (50 bp):
GGCTTGTGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTT
Found at i:1695 original size:50 final size:50
Alignment explanation
Indices: 1549--1698 Score: 239
Period size: 50 Copynumber: 3.0 Consensus size: 50
1539 CTTAAATGCC
* *
1549 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATA-CAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAA-AGCAATTTTA
*
1599 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* *
1649 CTTTGAAAAGCGAATTTTGATCTTAAACTCATAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1699 TTGTAAAACT
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
49 1 0.01
50 92 0.99
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
Found at i:2304 original size:6 final size:6
Alignment explanation
Indices: 2293--2335 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
2283 TCCATTCTCC
2293 TTTGAT TTTGA- TTTGAT TTT-ATT TTTGAT TTTGA- TTTGAT TTT
1 TTTGAT TTTGAT TTTGAT TTTGA-T TTTGAT TTTGAT TTTGAT TTT
2336 TTTGATTGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 11 0.33
6 21 0.64
7 1 0.03
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (6 bp):
TTTGAT
Found at i:2309 original size:5 final size:5
Alignment explanation
Indices: 2293--2358 Score: 55
Period size: 5 Copynumber: 12.6 Consensus size: 5
2283 TCCATTCTCC
* *
2293 TTTGA TTTTGA TTTGA TTTTA TTTTTGA TTTTGA TTTGA TTT-T TTTGA
1 TTTGA -TTTGA TTTGA TTTGA --TTTGA -TTTGA TTTGA TTTGA TTTGA
2341 -TTGA CTTTGA TTTGA TTT
1 TTTGA -TTTGA TTTGA TTT
2359 TTGACTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
4 7 0.14
5 25 0.49
6 15 0.29
7 4 0.08
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.67
Consensus pattern (5 bp):
TTTGA
Found at i:2321 original size:12 final size:13
Alignment explanation
Indices: 2293--2329 Score: 53
Period size: 11 Copynumber: 3.1 Consensus size: 13
2283 TCCATTCTCC
2293 TTTGATTTTGA--
1 TTTGATTTTGATT
2304 TTTGATTTT-ATT
1 TTTGATTTTGATT
2316 TTTGATTTTGATT
1 TTTGATTTTGATT
2329 T
1 T
2330 GATTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.04
11 9 0.39
12 9 0.39
13 4 0.17
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (13 bp):
TTTGATTTTGATT
Found at i:2327 original size:18 final size:17
Alignment explanation
Indices: 2293--2336 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
2283 TCCATTCTCC
2293 TTTGA-TTTTGATTTGA
1 TTTGATTTTTGATTTGA
*
2309 TTTTATTTTTGATTTTGA
1 TTTGATTTTTGA-TTTGA
2327 TTTGATTTTT
1 TTTGATTTTT
2337 TTGATTGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 6 0.25
18 14 0.58
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (17 bp):
TTTGATTTTTGATTTGA
Found at i:2344 original size:18 final size:19
Alignment explanation
Indices: 2298--2353 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 19
2288 TCTCCTTTGA
*
2298 TTTTGATTTGATTT--TAT
1 TTTTGATTTGATTTGATTT
2315 TTTTGATTTTGATTTGATTT
1 TTTTGA-TTTGATTTGATTT
2335 TTTTGA-TTGACTTTGATTT
1 TTTTGATTTGA-TTTGATTT
2354 GATTTTTGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 6 0.18
18 12 0.35
19 8 0.24
20 8 0.24
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (19 bp):
TTTTGATTTGATTTGATTT
Found at i:2344 original size:24 final size:22
Alignment explanation
Indices: 2293--2360 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 22
2283 TCCATTCTCC
2293 TTTGATTTTGATTTGATTTTATT
1 TTTGATTTTGATTTGATTTT-TT
2316 TTTGATTTTGATTTGATTTTTT
1 TTTGATTTTGATTTGATTTTTT
*
2338 TGATTGACTTTGATTTGATTTTT
1 T--TTGATTTTGATTTGATTTTT
2361 GACTTTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 3 0.07
23 20 0.48
24 19 0.45
ACGTcount: A:0.16, C:0.01, G:0.15, T:0.68
Consensus pattern (22 bp):
TTTGATTTTGATTTGATTTTTT
Found at i:2362 original size:18 final size:18
Alignment explanation
Indices: 2293--2366 Score: 62
Period size: 18 Copynumber: 3.9 Consensus size: 18
2283 TCCATTCTCC
2293 TTTGA-TTTTGA-TTTGA
1 TTTGATTTTTGACTTTGA
* *
2309 TTTTATTTTTGATTTTGA
1 TTTGATTTTTGACTTTGA
2327 TTTGATTTTTTTGATTGACTTTGA
1 TTTGA----TTT--TTGACTTTGA
2351 TTTGATTTTTGACTTT
1 TTTGATTTTTGACTTT
2367 TTTTTTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
16 4 0.09
17 6 0.13
18 17 0.36
20 3 0.06
22 3 0.06
24 14 0.30
ACGTcount: A:0.16, C:0.03, G:0.15, T:0.66
Consensus pattern (18 bp):
TTTGATTTTTGACTTTGA
Found at i:3298 original size:76 final size:76
Alignment explanation
Indices: 3158--3306 Score: 185
Period size: 76 Copynumber: 2.0 Consensus size: 76
3148 CACTCACCTT
* * *
3158 GAAATCATCGCTTTGACCAAAACTGATTTTGAAACATCTTTTGATTAAAACACCGTCAATCCTTT
1 GAAATCATAGCTTTGACCAAAACTGATTTTGAAAAATCTTTTGATTAAAACACCATCAATCCTTT
*
3223 GCTTACAGCTC
66 GCTCACAGCTC
* * * * *
3234 GAAATCATAGTTTTGACTAAAACTGATTTTGAAAAATCTTTTTGTTTGAAAC-TCATC-ATCCCT
1 GAAATCATAGCTTTGACCAAAACTGATTTTGAAAAATC-TTTTGATTAAAACACCATCAAT-CCT
3297 TTGCTCACAG
64 TTGCTCACAG
3307 TCTAGATTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
75 2 0.03
76 49 0.79
77 11 0.18
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.36
Consensus pattern (76 bp):
GAAATCATAGCTTTGACCAAAACTGATTTTGAAAAATCTTTTGATTAAAACACCATCAATCCTTT
GCTCACAGCTC
Found at i:4850 original size:21 final size:22
Alignment explanation
Indices: 4817--4858 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
4807 CGAAGGTTTA
4817 ATGGGATGCATGAATGAATGCC
1 ATGGGATGCATGAATGAATGCC
*
4839 ATGGTATG-ATGAATGAATGC
1 ATGGGATGCATGAATGAATGC
4859 ATGAGGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (22 bp):
ATGGGATGCATGAATGAATGCC
Done.