Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020488.1 Corchorus olitorius cultivar O-4 contig20521, 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: 33794
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:4287 original size:29 final size:29
Alignment explanation
Indices: 4254--4323 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
4244 ATGCATAAAT
* *
4254 AATTTTTTAATTTGGTCCTTACATTTTTC
1 AATTTTTCAATTTGATCCTTACATTTTTC
4283 AATTTTTCAATTTGATCCTTACATTTTTC
1 AATTTTTCAATTTGATCCTTACATTTTTC
4312 AATTTTTCAATT
1 AATTTTTCAATT
4324 CCATCCCCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.24, C:0.14, G:0.04, T:0.57
Consensus pattern (29 bp):
AATTTTTCAATTTGATCCTTACATTTTTC
Found at i:4509 original size:2 final size:2
Alignment explanation
Indices: 4502--4533 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4492 TTTTGCAAAA
4502 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4534 AAAGAATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8608 original size:14 final size:14
Alignment explanation
Indices: 8589--8615 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8579 TACCTACTAC
8589 ATTATTATTTAATT
1 ATTATTATTTAATT
8603 ATTATTATTTAAT
1 ATTATTATTTAAT
8616 AAGTAGTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATTATTTAATT
Found at i:9309 original size:22 final size:19
Alignment explanation
Indices: 9283--9322 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
9273 AAATAAAAGC
9283 ATATAATATAGTAAAATATAGT
1 ATATAAT-TA-TAAAA-ATAGT
9305 ATATAATTATAAAAATAG
1 ATATAATTATAAAAATAG
9323 ATGTGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 2 0.11
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (19 bp):
ATATAATTATAAAAATAGT
Found at i:9704 original size:27 final size:27
Alignment explanation
Indices: 9674--9729 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
9664 CCGTAAGGAG
9674 CGGAAGGAGCGCCATATGGTGCGGCGC
1 CGGAAGGAGCGCCATATGGTGCGGCGC
*
9701 CGGAAGGAGCGCCATATGGTGTGGCGC
1 CGGAAGGAGCGCCATATGGTGCGGCGC
9728 CG
1 CG
9730 TACTGGGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.25, G:0.45, T:0.12
Consensus pattern (27 bp):
CGGAAGGAGCGCCATATGGTGCGGCGC
Found at i:14028 original size:76 final size:76
Alignment explanation
Indices: 13902--14047 Score: 231
Period size: 76 Copynumber: 1.9 Consensus size: 76
13892 CGGATTTGTT
* * * *
13902 GATTTATACTTGTGTTTTTATGTTGAATTTTTTGGGTGATAATTGATTTTGGGTTAACTGTTTCT
1 GATTTATACTTGTATTTTTATGTTGAATTTTTTGGGTAATAATCGATTTTGGGTTAACCGTTTCT
13967 GGAAACCTATC
66 GGAAACCTATC
*
13978 GATTTATGCTTAGTATTTTTATGTTG-ATTTTTTGGGTAATAATCGATTTTGGGTTAACCGTTTC
1 GATTTATACTT-GTATTTTTATGTTGAATTTTTTGGGTAATAATCGATTTTGGGTTAACCGTTTC
14042 TGGAAA
65 TGGAAA
14048 AAAAAATGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
76 51 0.80
77 13 0.20
ACGTcount: A:0.22, C:0.08, G:0.21, T:0.49
Consensus pattern (76 bp):
GATTTATACTTGTATTTTTATGTTGAATTTTTTGGGTAATAATCGATTTTGGGTTAACCGTTTCT
GGAAACCTATC
Found at i:14492 original size:16 final size:15
Alignment explanation
Indices: 14462--14502 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
14452 TTTTAAAGCC
*
14462 TTTTTTTTCTTTTTCT
1 TTTTTTTTC-GTTTCT
14478 TTTTATTTTCGTTTCT
1 TTTT-TTTTCGTTTCT
14494 TTTTTTTTC
1 TTTTTTTTC
14503 AATTTTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 13 0.57
17 5 0.22
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (15 bp):
TTTTTTTTCGTTTCT
Found at i:14507 original size:22 final size:22
Alignment explanation
Indices: 14467--14508 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
14457 AAGCCTTTTT
*
14467 TTTCTTTTTCTTTTTATTTTCG
1 TTTCTTTTTCTTTTAATTTTCG
14489 TTTCTTTTT-TTTTCAATTTT
1 TTTCTTTTTCTTTT-AATTTT
14509 TAAGTAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTCTTTTAATTTTCG
Found at i:20954 original size:72 final size:72
Alignment explanation
Indices: 20833--20976 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 72
20823 AGGGTTCTGC
*
20833 CCCAAAATTAGGTTGACCATGAAACTTTTTTCCCTTAATTGAGCAATTAGTCATATTTATTTGTT
1 CCCAAAATTAGGCTGACCATGAAACTTTTTTCCCTTAATTGAGCAATTAGTCATATTTATTTGTT
20898 ATGTATG
66 ATGTATG
* **
20905 CCCAAAATTAGGCTGACCGTGAAACTTTTTTCCCTTAATTGAGGGATTAGTCATATTTATTTGTT
1 CCCAAAATTAGGCTGACCATGAAACTTTTTTCCCTTAATTGAGCAATTAGTCATATTTATTTGTT
*
20970 CTGTATG
66 ATGTATG
20977 TCTTGACTCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (72 bp):
CCCAAAATTAGGCTGACCATGAAACTTTTTTCCCTTAATTGAGCAATTAGTCATATTTATTTGTT
ATGTATG
Found at i:33239 original size:16 final size:15
Alignment explanation
Indices: 33201--33242 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
33191 ACAGAGATTG
*
33201 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
33216 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
33231 ACTAGAAAACAA
1 AC-AGAAAACAA
33243 AACAAAGTAA
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:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.