Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019377.1 Corchorus olitorius cultivar O-4 contig19410, 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: 36431
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4719 original size:29 final size:28
Alignment explanation
Indices: 4678--4732 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
4668 AAAAAAGAAG
*
4678 ATTTTGACGTTTTGCCCCATAAACTTTA
1 ATTTTGACGTTTTACCCCATAAACTTTA
4706 ATTTTGGACGTTTTACCCCATAAACTT
1 ATTTT-GACGTTTTACCCCATAAACTT
4733 GCAATTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (28 bp):
ATTTTGACGTTTTACCCCATAAACTTTA
Found at i:4740 original size:29 final size:28
Alignment explanation
Indices: 4678--4742 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
4668 AAAAAAGAAG
* * *
4678 ATTTTGACGTTTTGCCCCATAAACTTTA
1 ATTTGGACGTTTTACCCCATAAACTTCA
4706 ATTTTGGACGTTTTACCCCATAAACTTGCA
1 A-TTTGGACGTTTTACCCCATAAACTT-CA
4736 ATTTGGA
1 ATTTGGA
4743 ACTATTTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 29 0.91
30 2 0.06
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (28 bp):
ATTTGGACGTTTTACCCCATAAACTTCA
Found at i:4912 original size:29 final size:28
Alignment explanation
Indices: 4878--4961 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 28
4868 AAATGACTTC
* *
4878 AAATTACAAATTTAGGGGTAAAATATCCA
1 AAATTACAAATTTAGGGGCAAAACAT-CA
4907 AAATTA-AAATTTATGGGAGCAAAACATCA
1 AAATTACAAATTTA-GGG-GCAAAACATCA
*
4936 AAATCATACAAGTTTAGGGGACAAAA
1 AAAT--TACAAATTTAGGGG-CAAAA
4962 AAGCATCAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
28 7 0.15
29 15 0.33
30 8 0.17
31 10 0.22
32 6 0.13
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (28 bp):
AAATTACAAATTTAGGGGCAAAACATCA
Found at i:23600 original size:28 final size:26
Alignment explanation
Indices: 23537--23611 Score: 105
Period size: 28 Copynumber: 2.8 Consensus size: 26
23527 GGTCATTTAG
*
23537 GGGGCATTTTGGTCACTTTTAGATTCA
1 GGGGCATTTTGGTCA-TTTTACATTCA
*
23564 GAGGCATTTTGGTCATTTTACACGTTCA
1 GGGGCATTTTGGTCATTTTACA--TTCA
23592 GGGGCATTTTGGTCATTTTA
1 GGGGCATTTTGGTCATTTTA
23612 AGTTCACATT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 6 0.14
27 14 0.33
28 23 0.53
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (26 bp):
GGGGCATTTTGGTCATTTTACATTCA
Found at i:25005 original size:80 final size:81
Alignment explanation
Indices: 24912--25073 Score: 281
Period size: 80 Copynumber: 2.0 Consensus size: 81
24902 CAACACAATC
* *
24912 ACACTCATCTTCTCTCTCTCACTCCCATCTTCCCCCTCCTCTCCATACACACCCGAATCCT-TAC
1 ACACTCATCTTCTCTCTCTCACTCCCATCTTCCCCATCCTCTCCATACACACCCGAATCCTCCAC
* *
24976 ACTCTCATACACACAA
66 ACACTCAAACACACAA
24992 ACACTCATCTTCTCTCTCTCACTCCCATCTTCCCCATCCTCTCCATACACACCCGAATCCTCCAC
1 ACACTCATCTTCTCTCTCTCACTCCCATCTTCCCCATCCTCTCCATACACACCCGAATCCTCCAC
25057 ACACTCAAACACACAA
66 ACACTCAAACACACAA
25073 A
1 A
25074 AATCACACAG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
80 60 0.78
81 17 0.22
ACGTcount: A:0.26, C:0.48, G:0.01, T:0.25
Consensus pattern (81 bp):
ACACTCATCTTCTCTCTCTCACTCCCATCTTCCCCATCCTCTCCATACACACCCGAATCCTCCAC
ACACTCAAACACACAA
Found at i:27895 original size:12 final size:13
Alignment explanation
Indices: 27868--27892 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27858 TATCATAAAA
27868 AAATTATTATTTT
1 AAATTATTATTTT
27881 AAATTATTATTT
1 AAATTATTATTT
27893 AAAAAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AAATTATTATTTT
Found at i:29197 original size:31 final size:29
Alignment explanation
Indices: 29155--29230 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
29145 GGCTAAATAA
* *
29155 TCAATTCAGGATATAAGGTTTGCCACAAAATG
1 TCAATTAAGGATATAAGGTTT--CA-AAAACG
*
29187 -CAATTAAGGATATAATGTTTCAAAAACG
1 TCAATTAAGGATATAAGGTTTCAAAAACG
*
29215 TTAATTAAGGATATAA
1 TCAATTAAGGATATAA
29231 CGTTACCGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 5 0.13
29 16 0.41
31 18 0.46
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (29 bp):
TCAATTAAGGATATAAGGTTTCAAAAACG
Found at i:29376 original size:19 final size:19
Alignment explanation
Indices: 29358--29394 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29348 ATAAAAAATA
29358 AAAAAATTAA-TAATTAAT
1 AAAAAATTAATTAATTAAT
*
29376 AAATAATTAATTAATTAAT
1 AAAAAATTAATTAATTAAT
29395 TACTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATTAATTAATTAAT
Found at i:29386 original size:4 final size:4
Alignment explanation
Indices: 29362--29406 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
29352 AAAATAAAAA
* *
29362 AATT AA-T AATT AA-T AAAT AATT AATT AATT AATT ACTT AATT AAT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AAT
29407 AAAAGAAGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
3 6 0.17
4 30 0.83
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (4 bp):
AATT
Found at i:30527 original size:33 final size:33
Alignment explanation
Indices: 30477--30543 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
30467 TGAAAATAGA
30477 TTTTTTTATTTTAAAAGGGTTGGGCTTAGGGTT
1 TTTTTTTATTTTAAAAGGGTTGGGCTTAGGGTT
* * *
30510 TTTTTTTTTTTTCAAAGGGTTGGGTTTAGGGTT
1 TTTTTTTATTTTAAAAGGGTTGGGCTTAGGGTT
30543 T
1 T
30544 AGACATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.15, C:0.03, G:0.27, T:0.55
Consensus pattern (33 bp):
TTTTTTTATTTTAAAAGGGTTGGGCTTAGGGTT
Found at i:36143 original size:27 final size:27
Alignment explanation
Indices: 36112--36169 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
36102 TTTTTTAAAC
*
36112 ATATTTCTAAAT-TGACATTATTAAAAT
1 ATATTT-TAAATATGACACTATTAAAAT
* *
36139 ATATTTTAATTATGTCACTATTAAAAT
1 ATATTTTAAATATGACACTATTAAAAT
36166 ATAT
1 ATAT
36170 AAAATTACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (27 bp):
ATATTTTAAATATGACACTATTAAAAT
Done.