Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017041.1 Corchorus olitorius cultivar O-4 contig17074, 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: 43454
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:9611 original size:67 final size:67
Alignment explanation
Indices: 9503--9636 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
9493 ACAGATTTTT
9503 ATTGTAGACACCGAAATTTAGTTTAGGTCAAGTCTAAGTTTAGTTTTGGTTTAAACTCAGTGATG
1 ATTGTAGACACCGAAATTTAGTTTAGGTCAAGTCTAAGTTTAGTTTTGGTTTAAACTCAGTGATG
9568 TG
66 TG
9570 ATTGTAGACACCGAAATTTAGTTTAGGTCAAGTCTAAGTTTAGTTTTGGTTTAAACTCAGTGATG
1 ATTGTAGACACCGAAATTTAGTTTAGGTCAAGTCTAAGTTTAGTTTTGGTTTAAACTCAGTGATG
9635 TG
66 TG
9637 GCCTGGTTAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.39
Consensus pattern (67 bp):
ATTGTAGACACCGAAATTTAGTTTAGGTCAAGTCTAAGTTTAGTTTTGGTTTAAACTCAGTGATG
TG
Found at i:10193 original size:19 final size:18
Alignment explanation
Indices: 10169--10208 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
10159 TTGAAGATTT
*
10169 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
10188 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
10206 ATT
1 ATT
10209 ATCTCAAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:10790 original size:19 final size:18
Alignment explanation
Indices: 10766--10808 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
10756 TACATCACAA
**
10766 TTCTAGATCTCTTTTTCTC
1 TTCTAGATCTAGTTTT-TC
*
10785 TTCTAGTTCTAGTTTTTC
1 TTCTAGATCTAGTTTTTC
10803 TTCTAG
1 TTCTAG
10809 TTTTTCCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.12, C:0.21, G:0.09, T:0.58
Consensus pattern (18 bp):
TTCTAGATCTAGTTTTTC
Found at i:22981 original size:18 final size:17
Alignment explanation
Indices: 22949--22984 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
22939 AGGAAAGAAG
*
22949 ATTATTGTAATTATATT
1 ATTATTATAATTATATT
22966 ATTATTATATATTATATT
1 ATTATTATA-ATTATATT
22984 A
1 A
22985 CTACAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTATTATAATTATATT
Found at i:23260 original size:14 final size:14
Alignment explanation
Indices: 23241--23279 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
23231 AGCCAATAAA
23241 TTATATAATATTTT
1 TTATATAATATTTT
**
23255 TTATATTTTATTTT
1 TTATATAATATTTT
*
23269 ATATATAATAT
1 TTATATAATAT
23280 ATCTAAAGAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATATAATATTTT
Found at i:24201 original size:11 final size:11
Alignment explanation
Indices: 24187--24211 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24177 AAAAAGGAAA
24187 AAAAAAAAATG
1 AAAAAAAAATG
24198 AAAAAAAAATG
1 AAAAAAAAATG
24209 AAA
1 AAA
24212 GAAAGAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:24215 original size:15 final size:14
Alignment explanation
Indices: 24177--24206 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
24167 TCCTCTCAAC
*
24177 AAAAAGGAAAAAAA
1 AAAAATGAAAAAAA
24191 AAAAATGAAAAAAA
1 AAAAATGAAAAAAA
24205 AA
1 AA
24207 TGAAAGAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (14 bp):
AAAAATGAAAAAAA
Found at i:26296 original size:33 final size:34
Alignment explanation
Indices: 26258--26323 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
26248 AGTTCTTTTG
26258 GGTGG-TTGAATATATCTTACCTCCACTTTCTTT
1 GGTGGTTTGAATATATCTTACCTCCACTTTCTTT
* *
26291 GGTGGTTTGAATATATCTTATCTCCATTTTCTT
1 GGTGGTTTGAATATATCTTACCTCCACTTTCTT
26324 GATGAGGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (34 bp):
GGTGGTTTGAATATATCTTACCTCCACTTTCTTT
Found at i:28606 original size:30 final size:30
Alignment explanation
Indices: 28570--28633 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
28560 AATTGTTGAG
*
28570 GGATGAGAAATCTGTTCGTCTTGATCGGCC
1 GGATGAGAAATCTGGTCGTCTTGATCGGCC
28600 GGATGAGAAATCTGGTCGTCTTGATCGGCC
1 GGATGAGAAATCTGGTCGTCTTGATCGGCC
28630 GGAT
1 GGAT
28634 TCCAAGGAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (30 bp):
GGATGAGAAATCTGGTCGTCTTGATCGGCC
Found at i:32446 original size:18 final size:18
Alignment explanation
Indices: 32425--32495 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
32415 CCCACCTTTA
*
32425 CCACCTTCACCACCACCC
1 CCACCTCCACCACCACCC
32443 CCACCTCCACCACCACCTC
1 CCACCTCCACCACCACC-C
* * *
32462 CATCATCTCCATCACCACCT
1 C--CACCTCCACCACCACCC
*
32482 CCACCTCCTCCACC
1 CCACCTCCACCACC
32496 TCTACCAGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
18 26 0.60
19 2 0.05
20 1 0.02
21 14 0.33
ACGTcount: A:0.21, C:0.63, G:0.00, T:0.15
Consensus pattern (18 bp):
CCACCTCCACCACCACCC
Done.