Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011830.1 Corchorus olitorius cultivar O-4 contig11863, 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: 40536
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:856 original size:27 final size:27
Alignment explanation
Indices: 825--938 Score: 97
Period size: 27 Copynumber: 4.2 Consensus size: 27
815 ACTTGCCCCA
*
825 CCACCAACATTTTCAGCCACTCTTGGC
1 CCACCAACATTTTCAGCCACACTTGGC
* ** * *
852 CCACCAACATTGTCAGATACCCTTGGA
1 CCACCAACATTTTCAGCCACACTTGGC
* *
879 CCACCAAGATTTTCAGCCCCACTT-GC
1 CCACCAACATTTTCAGCCACACTTGGC
* **
905 ACCACCAAGATTTTCAGACC-CACTAAGC
1 -CCACCAACATTTTCAG-CCACACTTGGC
933 CCACCA
1 CCACCA
939 GCAGTCACCT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
26 1 0.01
27 66 0.93
28 4 0.06
ACGTcount: A:0.28, C:0.39, G:0.11, T:0.21
Consensus pattern (27 bp):
CCACCAACATTTTCAGCCACACTTGGC
Found at i:2596 original size:17 final size:17
Alignment explanation
Indices: 2574--2608 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2564 AGGATTGATT
2574 AACCCTAAATTAGTTTA
1 AACCCTAAATTAGTTTA
* *
2591 AACCCTAGATTATTTTA
1 AACCCTAAATTAGTTTA
2608 A
1 A
2609 TTTAATCAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (17 bp):
AACCCTAAATTAGTTTA
Found at i:5558 original size:16 final size:16
Alignment explanation
Indices: 5537--5569 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5527 AAAACAGAGG
5537 ATTAAGAATAA-CAATT
1 ATTAAGAA-AAGCAATT
5553 ATTAAGAAAAGCAATT
1 ATTAAGAAAAGCAATT
5569 A
1 A
5570 AACTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (16 bp):
ATTAAGAAAAGCAATT
Found at i:8387 original size:28 final size:28
Alignment explanation
Indices: 8320--8441 Score: 185
Period size: 28 Copynumber: 4.4 Consensus size: 28
8310 GTCACCTAAG
* *
8320 GGGGCATTTTGGTCATTTT-TATA-CTA
1 GGGGCATTTTGGTCATTTTGCATATCCA
*
8346 AGGGCATTTTGGTCATTTTGCATATCCA
1 GGGGCATTTTGGTCATTTTGCATATCCA
*
8374 GGGGCATTTTGGTCATTTTGCATGTCCA
1 GGGGCATTTTGGTCATTTTGCATATCCA
*
8402 GGGGCATTTTGGTCATTTTGCACATCCA
1 GGGGCATTTTGGTCATTTTGCATATCCA
8430 GGGGCATTTTGG
1 GGGGCATTTTGG
8442 GTCACTTCAA
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
26 18 0.21
27 3 0.03
28 66 0.76
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.39
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTGCATATCCA
Found at i:9033 original size:25 final size:25
Alignment explanation
Indices: 8998--9052 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
8988 TTTTTTTTTG
*
8998 TGCACTATACATTTGCATTTCTGTT
1 TGCACTATACATTTGCATTCCTGTT
* *
9023 TGCACTCTACATTTGCATTCCTTTT
1 TGCACTATACATTTGCATTCCTGTT
9048 TGCAC
1 TGCAC
9053 CAAATAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.11, T:0.45
Consensus pattern (25 bp):
TGCACTATACATTTGCATTCCTGTT
Found at i:13487 original size:28 final size:28
Alignment explanation
Indices: 13419--13490 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
13409 GGTCACTTAA
*
13419 AGGGGCATTTTGATCATTTTGCATGACC
1 AGGGGCATTTTGGTCATTTTGCATGACC
13447 AGGGGCATTTTGGTCATTTTGCAT-ATCC
1 AGGGGCATTTTGGTCATTTTGCATGA-CC
13475 AGGGGCATTTTGGTCA
1 AGGGGCATTTTGGTCA
13491 CTTCAAGTGC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
27 1 0.02
28 41 0.98
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTGCATGACC
Found at i:25292 original size:15 final size:16
Alignment explanation
Indices: 25262--25295 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
25252 TTACTTTGCT
25262 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
25278 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
25293 TTG
1 TTG
25296 CTGTCTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:30724 original size:15 final size:16
Alignment explanation
Indices: 30694--30733 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
30684 TTACTTTGCT
30694 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
*
30710 TTGTTTT-TTGTTTAA
1 TTGTTTTCTAGTTTAA
*
30725 TTGCTTTCT
1 TTGTTTTCT
30734 TTCAACCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:33490 original size:76 final size:76
Alignment explanation
Indices: 33362--33502 Score: 194
Period size: 76 Copynumber: 1.9 Consensus size: 76
33352 GGACAAGGAC
* * * * *
33362 CCCGACTCCTCCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTTATGACCCAG
1 CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCAACCATGTGATTTGCCTGATCACCCAG
33427 TTGGGCAGTGT
66 TTGGGCAGTGT
* * *
33438 CCCGACTCCACCTGGGTGCCCACATGGTTTGTC-TGAGGAACCATGTGATTTGCCTGATCACCCA
1 CCCGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAGCAACCATGTGATTTGCCTGATCACCCA
33502 G
65 G
33503 GTAGGTTGTG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 52 0.93
77 4 0.07
ACGTcount: A:0.16, C:0.33, G:0.26, T:0.26
Consensus pattern (76 bp):
CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCAACCATGTGATTTGCCTGATCACCCAG
TTGGGCAGTGT
Done.