Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022362.1 Corchorus olitorius cultivar O-4 contig22395, 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: 9090
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Found at i:1158 original size:15 final size:15
Alignment explanation
Indices: 1128--1169 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
1118 TTACTCTGCT
1128 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
1144 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
1159 TTGCTTTCTGT
1 TTGTTTTCTGT
1170 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:1417 original size:39 final size:39
Alignment explanation
Indices: 1359--1472 Score: 174
Period size: 39 Copynumber: 2.9 Consensus size: 39
1349 GATAGTGAAC
* *
1359 TGAAAGATGCATATAGCTAAGTTTTGAGATGCAGTGGAT
1 TGAAAAATGCATATGGCTAAGTTTTGAGATGCAGTGGAT
* *
1398 TGAAAAATGCATATGGCTAAGTTTTGTGATGTAGTGGAT
1 TGAAAAATGCATATGGCTAAGTTTTGAGATGCAGTGGAT
* *
1437 TGAAAAATTCATAAGGCTAAGTTTTGAGATGCAGTG
1 TGAAAAATGCATATGGCTAAGTTTTGAGATGCAGTG
1473 AACTTTCATT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 67 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.32
Consensus pattern (39 bp):
TGAAAAATGCATATGGCTAAGTTTTGAGATGCAGTGGAT
Found at i:3008 original size:28 final size:28
Alignment explanation
Indices: 2972--3040 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
2962 AGTGCACCTG
* *
2972 AAATAACCAAAATACCCCTAGATGTGTA
1 AAATGACCAAAATACCCCTAGATGTGCA
* *
3000 AAATGACCAAAATGCCCCTGGATGTGCA
1 AAATGACCAAAATACCCCTAGATGTGCA
3028 AAATGACCAAAAT
1 AAATGACCAAAAT
3041 GCCCTTGGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.19
Consensus pattern (28 bp):
AAATGACCAAAATACCCCTAGATGTGCA
Found at i:3101 original size:28 final size:28
Alignment explanation
Indices: 2999--3101 Score: 136
Period size: 28 Copynumber: 3.7 Consensus size: 28
2989 CTAGATGTGT
* * *
2999 AAAATGACCAAAATGCCCCTGGAT-GTGC
1 AAAATGATCAAAATGCCCTTGG-TCATGC
*
3027 AAAATGACCAAAATGCCCTTGGTCATGC
1 AAAATGATCAAAATGCCCTTGGTCATGC
*
3055 AAAATTATCAAAATGCCCTTGGTCATGC
1 AAAATGATCAAAATGCCCTTGGTCATGC
*
3083 AAAACGATCAAAATGCCCT
1 AAAATGATCAAAATGCCCT
3102 CTTAAATGAC
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 1 0.01
28 67 0.99
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (28 bp):
AAAATGATCAAAATGCCCTTGGTCATGC
Found at i:3406 original size:35 final size:35
Alignment explanation
Indices: 3356--3596 Score: 297
Period size: 35 Copynumber: 6.9 Consensus size: 35
3346 CGAGTTCATA
* *
3356 TTGAAGATGCTACACCGAGGCAACTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
3391 TTGAAGATGCAACACCGAGTCATCTGAACTT-ATCT
1 TTGAAGATGCTACACCGAGTCATCTGAA-TTCATCT
* * *
3426 TTGAAGATGCTACACCGAGTCATCCGAGA-TCCTTT
1 TTGAAGATGCTACACCGAGTCATCTGA-ATTCATCT
3461 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* * ** *
3496 TTAAAGATGCTACACCGAGTCATCTAAATTTGTCC
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* * * **
3531 TTGGAGATGCTACACCGAGGCATCTAAATTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
3566 TTGAAGATGGTACACCGAGTCATCTGAATTC
1 TTGAAGATGCTACACCGAGTCATCTGAATTC
3597 CTGAGAATTT
Statistics
Matches: 178, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
34 2 0.01
35 173 0.97
36 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
Done.