Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021937.1 Corchorus olitorius cultivar O-4 contig21970, 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: 59368
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:151 original size:28 final size:29
Alignment explanation
Indices: 111--173 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
101 GAAATCAAAC
111 ATGGAATATGC-AAATGTAACCTCTAAAA
1 ATGGAATATGCAAAATGTAACCTCTAAAA
* * *
139 ATGGAATATGCAAAATGTAACTTCTTAGA
1 ATGGAATATGCAAAATGTAACCTCTAAAA
168 ATGGAA
1 ATGGAA
174 CTTAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.27
Consensus pattern (29 bp):
ATGGAATATGCAAAATGTAACCTCTAAAA
Found at i:1138 original size:41 final size:41
Alignment explanation
Indices: 1081--1164 Score: 143
Period size: 41 Copynumber: 2.0 Consensus size: 41
1071 TTCTACATAG
1081 ATGCAAACTTTGATTATGCAATATGGAGATGGTCCAATTAA
1 ATGCAAACTTTGATTATGCAATATGGAGATGGTCCAATTAA
*
1122 ATGCAAA-TTATGATTATGCAATATGGAGGTGGTCCAATTAA
1 ATGCAAACTT-TGATTATGCAATATGGAGATGGTCCAATTAA
1163 AT
1 AT
1165 CACTATGAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 2 0.05
41 39 0.95
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (41 bp):
ATGCAAACTTTGATTATGCAATATGGAGATGGTCCAATTAA
Found at i:3123 original size:29 final size:30
Alignment explanation
Indices: 3091--3156 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
3081 TGGCACTGAT
3091 TTGAGCAAGTTG-AAAAATTTGATACCAAA
1 TTGAGCAAGTTGCAAAAATTTGATACCAAA
** * *
3120 TTGAGCATTTTGTCAAACATTTGGTACCAAA
1 TTGAGCAAGTTG-CAAAAATTTGATACCAAA
3151 TTGAGC
1 TTGAGC
3157 TTTTAGCCGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 10 0.32
31 21 0.68
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (30 bp):
TTGAGCAAGTTGCAAAAATTTGATACCAAA
Found at i:4180 original size:2 final size:2
Alignment explanation
Indices: 4173--4210 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4163 TTAAGGGGTG
4173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4211 CTTTATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4636 original size:2 final size:2
Alignment explanation
Indices: 4606--4660 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
4596 ATACAAATAC
*
4606 AT AT AT AA AT -T AT -T AT -T AT -T AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4643 AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT A
4661 ACACATTACG
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
1 6 0.13
2 39 0.87
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:10869 original size:39 final size:39
Alignment explanation
Indices: 10814--10894 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
10804 TTTATATACT
*
10814 TGATCAACATACATGTCTTTTCATATAGACATAACTTTA
1 TGATCAACATACATGTCTTTCCATATAGACATAACTTTA
* *
10853 TGATCAATATATATGTCTTTCCATATAGACATAACTTTA
1 TGATCAACATACATGTCTTTCCATATAGACATAACTTTA
10892 TGA
1 TGA
10895 ATAATTATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (39 bp):
TGATCAACATACATGTCTTTCCATATAGACATAACTTTA
Found at i:12967 original size:18 final size:18
Alignment explanation
Indices: 12946--13006 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
12936 ACATACATGT
12946 CTTTTCATATATACATAA
1 CTTTTCATATATACATAA
*
12964 CTTTATGATCA-ATACATATA
1 CTTT-TCAT-ATATACATA-A
* *
12984 TCTTTCCATATAGACATAA
1 -CTTTTCATATATACATAA
13003 CTTT
1 CTTT
13007 ATTATGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
18 8 0.24
19 12 0.35
20 10 0.29
21 4 0.12
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.43
Consensus pattern (18 bp):
CTTTTCATATATACATAA
Found at i:17806 original size:10 final size:8
Alignment explanation
Indices: 17784--17809 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17774 AGCTTTTATG
17784 AATATATC
1 AATATATC
17792 AATATATC
1 AATATATC
17800 AATATATC
1 AATATATC
17808 AA
1 AA
17810 ATGTAGTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (8 bp):
AATATATC
Found at i:23508 original size:19 final size:19
Alignment explanation
Indices: 23468--23504 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23458 AATTTTTAAG
23468 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
23487 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
23505 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:37399 original size:12 final size:13
Alignment explanation
Indices: 37381--37410 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
37371 GTTTTCTTTA
37381 ATTTTCTTGATTG
1 ATTTTCTTGATTG
37394 -TTTTCTTGATTG
1 ATTTTCTTGATTG
37406 ATTTT
1 ATTTT
37411 AATTGCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:37642 original size:16 final size:17
Alignment explanation
Indices: 37621--37652 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
37611 GAAATTGCGT
37621 TTTATTTTTCT-TTTTC
1 TTTATTTTTCTATTTTC
37637 TTTATTTTTCTATTTT
1 TTTATTTTTCTATTTT
37653 AATTTGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Found at i:47453 original size:12 final size:13
Alignment explanation
Indices: 47435--47464 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
47425 GTTTTCATTA
47435 ATTTTCTTGATTG
1 ATTTTCTTGATTG
47448 -TTTTCTTGATTG
1 ATTTTCTTGATTG
47460 ATTTT
1 ATTTT
47465 AATTGCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Done.