Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018335.1 Corchorus olitorius cultivar O-4 contig18368, 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: 10985
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:374 original size:2 final size:2
Alignment explanation
Indices: 367--393 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
357 ACATACATAC
367 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
394 CTAGTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2275 original size:21 final size:21
Alignment explanation
Indices: 2225--2318 Score: 100
Period size: 22 Copynumber: 4.3 Consensus size: 21
2215 CTCCAATGTA
*
2225 GAAATATTGATAACCACACTGT
1 GAAAT-TTGATAACCACACTAT
* *
2247 GAAAATTTGATAACCTCATTAT
1 G-AAATTTGATAACCACACTAT
* *
2269 GAAATTTCAATAACCTC-CTAT
1 GAAATTT-GATAACCACACTAT
2290 GAAAATTTGATAACCACACTAT
1 G-AAATTTGATAACCACACTAT
2312 GAAATTT
1 GAAATTT
2319 CGACTTATTG
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
21 23 0.38
22 34 0.56
23 4 0.07
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (21 bp):
GAAATTTGATAACCACACTAT
Found at i:2374 original size:22 final size:22
Alignment explanation
Indices: 2331--2431 Score: 82
Period size: 22 Copynumber: 4.6 Consensus size: 22
2321 ACTTATTGTG
* *
2331 AAATTTTGATAATCTCTA-TATA
1 AAATTTTGATAACCAC-ACTATA
*
2353 AAATTTTGATAATCACACTATA
1 AAATTTTGATAACCACACTATA
* * *
2375 TAA--TTGGTAACCGCACTATGA
1 AAATTTTGATAACCACACTAT-A
* *
2396 AAATTTTAATAACCACACCATA
1 AAATTTTGATAACCACACTATA
*
2418 AAAATTTGATAACC
1 AAATTTTGATAACC
2432 TCCCAATGAG
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
20 13 0.21
21 4 0.06
22 34 0.54
23 12 0.19
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.34
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:2600 original size:22 final size:21
Alignment explanation
Indices: 2572--2720 Score: 68
Period size: 22 Copynumber: 6.8 Consensus size: 21
2562 ATTCCCTCCC
2572 TATGAAATTTTATTAACCTTCT
1 TATGAAATTTTA-TAACCTTCT
**
2594 TATGAAATTTTGATAACCAAAC-
1 TATGAAATTTT-ATAACC-TTCT
* * * *
2616 TATAAAATTTCGATAACTTTCG
1 TATGAAATTT-TATAACCTTCT
* * *
2638 TATAAAATTTTTTTAACCTTCC
1 TATGAAA-TTTTATAACCTTCT
* * *
2660 TAGGAAATTTTAATAATCTTTT
1 TATGAAATTTT-ATAACCTTCT
***
2682 TATGAAAATTCGGTAACCTT-T
1 TATG-AAATTTTATAACCTTCT
2703 GTATGAAATTTTGATAAC
1 -TATGAAATTTT-ATAAC
2721 TACACAATGA
Statistics
Matches: 93, Mismatches: 25, Indels: 18
0.68 0.18 0.13
Matches are distributed among these distances:
21 11 0.12
22 72 0.77
23 10 0.11
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (21 bp):
TATGAAATTTTATAACCTTCT
Found at i:2730 original size:22 final size:22
Alignment explanation
Indices: 2704--2786 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
2694 GTAACCTTTG
2704 TATGAAATTTTGATAACTACAC
1 TATGAAATTTTGATAACTACAC
* * * *
2726 AATGAAGTTTTGATAATTTTCA-
1 TATGAAATTTTGATAA-CTACAC
* * *
2748 TATGAAATTTTGGTGACCACAC
1 TATGAAATTTTGATAACTACAC
2770 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
2787 CTTCCCATGT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
21 2 0.04
22 41 0.89
23 3 0.07
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACAC
Found at i:3358 original size:69 final size:70
Alignment explanation
Indices: 3220--3358 Score: 244
Period size: 69 Copynumber: 2.0 Consensus size: 70
3210 TATTTTTATG
3220 AAATTTTTCCTTTTGCTTACGTGGAATTTTTAGCCACATATCGCGATGATGTGACACTGTTTGAT
1 AAATTTTTCCTTTTGCTTACGTGGAATTTTTAGCCACATATCGCGATGATGTGACACTGTTTGAT
3285 GACGT
66 GACGT
* * *
3290 AAATTTTTCCTTTTGCTTACGTGGAATTTTT-GCCACGTGTCGTGATGATGTGACACTGTTTGAT
1 AAATTTTTCCTTTTGCTTACGTGGAATTTTTAGCCACATATCGCGATGATGTGACACTGTTTGAT
3354 GACGT
66 GACGT
3359 CATTAGGGAA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
69 35 0.53
70 31 0.47
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.41
Consensus pattern (70 bp):
AAATTTTTCCTTTTGCTTACGTGGAATTTTTAGCCACATATCGCGATGATGTGACACTGTTTGAT
GACGT
Found at i:4346 original size:15 final size:17
Alignment explanation
Indices: 4316--4355 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
4306 AACGGATTAA
4316 TTAAATAAATATAAATT
1 TTAAATAAATATAAATT
4333 TTAAATAAA-A-AAATT
1 TTAAATAAATATAAATT
*
4348 TCAAATAA
1 TTAAATAA
4356 TTTTGGGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.55
16 1 0.05
17 9 0.41
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAATAAATATAAATT
Found at i:8154 original size:24 final size:25
Alignment explanation
Indices: 8126--8172 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
8116 TTTCTTAGTC
8126 TCTGCATTTTCTCTA-AAAAAAATT
1 TCTGCATTTTCTCTAGAAAAAAATT
* *
8150 TCTGCGTTTTTTCTAGAAAAAAA
1 TCTGCATTTTCTCTAGAAAAAAA
8173 AATTTCTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (25 bp):
TCTGCATTTTCTCTAGAAAAAAATT
Done.