Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016980.1 Corchorus olitorius cultivar O-4 contig17013, 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: 97409
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:2235 original size:20 final size:20
Alignment explanation
Indices: 2207--2250 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2197 TGCATGCAAA
2207 CAAAAAAAAA-GAAAAATATG
1 CAAAAAAAAATGAAAAA-ATG
* *
2227 CAAACAAAAATGCAAAAATG
1 CAAAAAAAAATGAAAAAATG
2247 CAAA
1 CAAA
2251 TTTTTTTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.70, C:0.11, G:0.09, T:0.09
Consensus pattern (20 bp):
CAAAAAAAAATGAAAAAATG
Found at i:4964 original size:19 final size:18
Alignment explanation
Indices: 4931--4966 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4921 TGGAAATAAT
4931 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
4949 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
4967 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:5422 original size:15 final size:15
Alignment explanation
Indices: 5402--5431 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5392 CATCATTTTT
5402 AAGTAGCTATAATCA
1 AAGTAGCTATAATCA
*
5417 AAGTAGCTTTAATCA
1 AAGTAGCTATAATCA
5432 CTTGCCATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (15 bp):
AAGTAGCTATAATCA
Found at i:6222 original size:33 final size:33
Alignment explanation
Indices: 6185--6250 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
6175 AAAATTGGGG
6185 AAATAAGATCAATAAAAAACAATCAAATTCTAT
1 AAATAAGATCAATAAAAAACAATCAAATTCTAT
6218 AAATAAGATCAATAAAAAACAATCAAATTCTAT
1 AAATAAGATCAATAAAAAACAATCAAATTCTAT
6251 CCTAGGTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.61, C:0.12, G:0.03, T:0.24
Consensus pattern (33 bp):
AAATAAGATCAATAAAAAACAATCAAATTCTAT
Found at i:6560 original size:30 final size:30
Alignment explanation
Indices: 6521--6579 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
6511 GTTTATTAAT
6521 GAAACTTGAAAATTAAAGACATAAAATAAAG
1 GAAACTTGAAAATTAAAG-CATAAAATAAAG
*
6552 GAAA-TTGAAAATTAAAGCATAAATTAAA
1 GAAACTTGAAAATTAAAGCATAAAATAAA
6580 TAACTAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 13 0.48
31 4 0.15
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.22
Consensus pattern (30 bp):
GAAACTTGAAAATTAAAGCATAAAATAAAG
Found at i:6908 original size:20 final size:20
Alignment explanation
Indices: 6862--6908 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
6852 AGTTAGAAAC
*
6862 ATACCTGAACTAGGAATTCA
1 ATACCTTAACTAGGAATTCA
6882 ATACCTTAACTAGGAATTCA
1 ATACCTTAACTAGGAATTCA
6902 ATACCTT
1 ATACCTT
6909 GTAGGAGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (20 bp):
ATACCTTAACTAGGAATTCA
Found at i:7435 original size:6 final size:6
Alignment explanation
Indices: 7424--7450 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7414 GATTAGTGTA
7424 AAAATT AAAATT AAAATT AAAATT AAA
1 AAAATT AAAATT AAAATT AAAATT AAA
7451 TATGCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:11755 original size:19 final size:18
Alignment explanation
Indices: 11722--11757 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11712 TGGAAATAAT
11722 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
11740 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
11758 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:12530 original size:30 final size:31
Alignment explanation
Indices: 12450--12530 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 31
12440 ATTTTTCTTT
12450 TCAACTTTT-CAAACCTTACCATCATCTTCC
1 TCAACTTTTACAAACCTTACCATCATCTTCC
* * *
12480 TCAA-TTCTCACAAACC-TACCATTC-TTTTTC
1 TCAACTT-TTACAAACCTTACCA-TCATCTTCC
12510 TCAACTTTTAC-AACCTTACCA
1 TCAACTTTTACAAACCTTACCA
12531 AACTTCTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
29 6 0.14
30 26 0.62
31 10 0.24
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.37
Consensus pattern (31 bp):
TCAACTTTTACAAACCTTACCATCATCTTCC
Found at i:16455 original size:21 final size:21
Alignment explanation
Indices: 16418--16466 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
16408 TAGATCTAGA
* *
16418 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTACATTGCTTTCTT
16439 TTCTAATTTA-ATTGCTTTCTT
1 TT-TAATTTACATTGCTTTCTT
16460 TTTAATT
1 TTTAATT
16467 GTGATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 13 0.52
22 7 0.28
ACGTcount: A:0.18, C:0.10, G:0.06, T:0.65
Consensus pattern (21 bp):
TTTAATTTACATTGCTTTCTT
Found at i:17685 original size:16 final size:16
Alignment explanation
Indices: 17661--17691 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17651 AAACGAAATA
17661 AAATAAAAAATAGAAC
1 AAATAAAAAATAGAAC
*
17677 AAATTAAAAATAGAA
1 AAATAAAAAATAGAA
17692 ATTAAGTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.16
Consensus pattern (16 bp):
AAATAAAAAATAGAAC
Found at i:23880 original size:30 final size:29
Alignment explanation
Indices: 23800--23880 Score: 69
Period size: 30 Copynumber: 2.7 Consensus size: 29
23790 ATTTTTCTTT
23800 TCAACTTTCCAAACCTTACCATCATCTTCC
1 TCAACTTT-CAAACCTTACCATCATCTTCC
* *
23830 TCAA-TTCTCACAAACC-TACCATTC-TTTTTC
1 TCAACTT-T--CAAACCTTACCA-TCATCTTCC
23860 TCAACTTTCATAACCTTACCA
1 TCAACTTTCA-AACCTTACCA
23881 AACTTCTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
28 2 0.05
29 6 0.14
30 24 0.57
31 10 0.24
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (29 bp):
TCAACTTTCAAACCTTACCATCATCTTCC
Found at i:27011 original size:2 final size:2
Alignment explanation
Indices: 27006--27034 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26996 TTTTCCTATG
27006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27035 CTTGCTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31326 original size:11 final size:11
Alignment explanation
Indices: 31310--31334 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31300 ACCTTTTAAT
31310 AAAAGAAAAGA
1 AAAAGAAAAGA
31321 AAAAGAAAAGA
1 AAAAGAAAAGA
31332 AAA
1 AAA
31335 CAAATAAACA
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:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:31489 original size:39 final size:38
Alignment explanation
Indices: 31446--31669 Score: 153
Period size: 39 Copynumber: 5.8 Consensus size: 38
31436 GCCCCCATTC
* * *
31446 AGAATTGCCATTTAAGGAAACCTGTTTAGGTCTATGTTT
1 AGAATT-CCGTTTAAGCAAACCTGCTTAGGTCTATGTTT
* * *
31485 AGAA-TCTCGTTTAATCAAACCTACTTAGGTCTCTGTTT
1 AGAATTC-CGTTTAAGCAAACCTGCTTAGGTCTATGTTT
* * ** *
31523 AGAATTTTCGTTTAAGTAAACCTGCTTAGGTCCCTGTGT
1 AGAA-TTCCGTTTAAGCAAACCTGCTTAGGTCTATGTTT
* * * * *
31562 AGAACTTCCGTCTAGGAAAACTTGCTTAGGTCTACGTTT
1 AGAA-TTCCGTTTAAGCAAACCTGCTTAGGTCTATGTTT
** * ** *
31601 AGGAGCTCCGTTTAATCAAACCTGCTTAGGTCCCTGTGT
1 A-GAATTCCGTTTAAGCAAACCTGCTTAGGTCTATGTTT
* * * *
31640 AAAATTGTCGTTTAAGTAAACCTACTTAGG
1 AGAATT-CCGTTTAAGCAAACCTGCTTAGG
31670 ATCTCTGCTT
Statistics
Matches: 140, Mismatches: 40, Indels: 10
0.74 0.21 0.05
Matches are distributed among these distances:
37 1 0.01
38 32 0.23
39 104 0.74
40 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (38 bp):
AGAATTCCGTTTAAGCAAACCTGCTTAGGTCTATGTTT
Found at i:31668 original size:78 final size:78
Alignment explanation
Indices: 31456--31712 Score: 229
Period size: 78 Copynumber: 3.3 Consensus size: 78
31446 AGAATTGCCA
* * ** * *
31456 TTTAAGGAAACCTGTTTAGGTCTATGTTTAG-AATCTCGTTTAA-TCAAACCTACTTAGGTCTCT
1 TTTAAGTAAACCTGCTTAGGTCCCTGTGTAGAAATTTCGTTTAAGT-AAACCTACTTAGGTCTCT
** *
31519 GTTTAGAATTTTCG
65 GTTTAGAAGCTCCG
* * * * * * *
31533 TTTAAGTAAACCTGCTTAGGTCCCTGTGTAGAACTTCCGTCTAGGAAAACTTGCTTAGGTCTAC-
1 TTTAAGTAAACCTGCTTAGGTCCCTGTGTAGAAATTTCGTTTAAGTAAACCTACTTAGGTCT-CT
*
31597 GTTTAGGAGCTCCG
65 GTTTAGAAGCTCCG
31611 TTTAA-TCAAACCTGCTTAGGTCCCTGTGTA-AAATTGTCGTTTAAGTAAACCTACTTAGGATCT
1 TTTAAGT-AAACCTGCTTAGGTCCCTGTGTAGAAATT-TCGTTTAAGTAAACCTACTTAGG-TCT
* *
31674 CTGCTTAG-AGCTTCG
63 CTGTTTAGAAGCTCCG
* * *
31689 ATCAAGTAAACCTGATTAGGTCCC
1 TTTAAGTAAACCTGCTTAGGTCCC
31713 CATTTTGAAT
Statistics
Matches: 143, Mismatches: 29, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
77 31 0.22
78 102 0.71
79 10 0.07
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (78 bp):
TTTAAGTAAACCTGCTTAGGTCCCTGTGTAGAAATTTCGTTTAAGTAAACCTACTTAGGTCTCTG
TTTAGAAGCTCCG
Found at i:31708 original size:117 final size:116
Alignment explanation
Indices: 31458--31710 Score: 296
Period size: 117 Copynumber: 2.2 Consensus size: 116
31448 AATTGCCATT
* * * * * *
31458 TAAGGAAACCTGTTTAGGTCTATGTTTAGAATCTCGTTTAATCAAACCTACTTAGGTCTCTGTTT
1 TAAGAAAACCTGATTAGGTCTACGTTTAGAAGCTCGTTTAATCAAACCTACTTAGGTCCCTGTGT
* * *
31523 AGAATTTTCGTTTAAGTAAACCTGCTTAGGTCCCTGTGTAGAACTTCCGTC
66 AAAATTGTCGTTTAAGTAAACCTACTTAGGTCCCTGTGTAGAACTTCCGTC
* * * * *
31574 TAGGAAAACTTGCTTAGGTCTACGTTTAGGAGCTCCGTTTAATCAAACCTGCTTAGGTCCCTGTG
1 TAAGAAAACCTGATTAGGTCTACGTTTAGAAGCT-CGTTTAATCAAACCTACTTAGGTCCCTGTG
* *
31639 TAAAATTGTCGTTTAAGTAAACCTACTTAGGATCTCTGCT-TAGAGCTT-CGATC
65 TAAAATTGTCGTTTAAGTAAACCTACTTAGG-TCCCTG-TGTAGAACTTCCG-TC
*
31692 -AAGTAAACCTGATTAGGTC
1 TAAGAAAACCTGATTAGGTC
31711 CCCATTTTGA
Statistics
Matches: 114, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
116 27 0.24
117 72 0.63
118 14 0.12
119 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (116 bp):
TAAGAAAACCTGATTAGGTCTACGTTTAGAAGCTCGTTTAATCAAACCTACTTAGGTCCCTGTGT
AAAATTGTCGTTTAAGTAAACCTACTTAGGTCCCTGTGTAGAACTTCCGTC
Found at i:32449 original size:23 final size:23
Alignment explanation
Indices: 32417--32515 Score: 109
Period size: 23 Copynumber: 4.5 Consensus size: 23
32407 TTAATAACAC
*
32417 CTTGGGCCATTTTATTTTATTTA
1 CTTGGTCCATTTTATTTTATTTA
*
32440 CTTGGTCCATTTTATTTTCTTTA
1 CTTGGTCCATTTTATTTTATTTA
*
32463 CTTGGTCC-----GTTTTATTTA
1 CTTGGTCCATTTTATTTTATTTA
* *
32481 CTTGGTCCGTTTTATTTTCTTTA
1 CTTGGTCCATTTTATTTTATTTA
*
32504 CTCGGTCCATTT
1 CTTGGTCCATTT
32516 CTTTATTTCC
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
18 16 0.25
23 47 0.75
ACGTcount: A:0.12, C:0.18, G:0.13, T:0.57
Consensus pattern (23 bp):
CTTGGTCCATTTTATTTTATTTA
Found at i:32453 original size:18 final size:18
Alignment explanation
Indices: 32430--32497 Score: 73
Period size: 18 Copynumber: 3.5 Consensus size: 18
32420 GGGCCATTTT
32430 ATTTTATTTACTTGGTCC
1 ATTTTATTTACTTGGTCC
32448 ATTTTATTTTCTTTACTTGGTCC
1 ATTTTA-----TTTACTTGGTCC
*
32471 GTTTTATTTACTTGGTCC
1 ATTTTATTTACTTGGTCC
*
32489 GTTTTATTT
1 ATTTTATTT
32498 TCTTTACTCG
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
18 27 0.61
23 17 0.39
ACGTcount: A:0.13, C:0.15, G:0.12, T:0.60
Consensus pattern (18 bp):
ATTTTATTTACTTGGTCC
Found at i:32488 original size:41 final size:41
Alignment explanation
Indices: 32431--32511 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
32421 GGCCATTTTA
*
32431 TTTTATTTACTTGGTCCATTTTATTTTCTTTACTTGGTCCG
1 TTTTATTTACTTGGTCCATTTTATTTTCTTTACTCGGTCCG
*
32472 TTTTATTTACTTGGTCCGTTTTATTTTCTTTACTCGGTCC
1 TTTTATTTACTTGGTCCATTTTATTTTCTTTACTCGGTCC
32512 ATTTCTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.11, C:0.19, G:0.12, T:0.58
Consensus pattern (41 bp):
TTTTATTTACTTGGTCCATTTTATTTTCTTTACTCGGTCCG
Found at i:33716 original size:22 final size:19
Alignment explanation
Indices: 33670--33707 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
33660 AGAACCCAAG
33670 AAAAAACAACAGTTCATAC
1 AAAAAACAACAGTTCATAC
*
33689 AAAAAAGAACAGTTCATAC
1 AAAAAACAACAGTTCATAC
33708 CCAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.58, C:0.18, G:0.08, T:0.16
Consensus pattern (19 bp):
AAAAAACAACAGTTCATAC
Found at i:33768 original size:17 final size:17
Alignment explanation
Indices: 33734--33779 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
33724 AAAACAGAAT
*
33734 CATACA-AT-CCATACA
1 CATACAGATCCCAAACA
33749 CATACAGATCCCAAACA
1 CATACAGATCCCAAACA
33766 CATACAGATCCCAA
1 CATACAGATCCCAA
33780 GAACAACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 6 0.21
16 2 0.07
17 20 0.71
ACGTcount: A:0.46, C:0.35, G:0.04, T:0.15
Consensus pattern (17 bp):
CATACAGATCCCAAACA
Found at i:39262 original size:2 final size:2
Alignment explanation
Indices: 39255--39287 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39245 TAATATGTAG
39255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39288 GGGTTGCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40388 original size:20 final size:19
Alignment explanation
Indices: 40363--40419 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 19
40353 TAATAAGAAT
40363 AATTTATTATATATATCATA
1 AATTTATTATATATAT-ATA
40383 AATTTATTTTATATTATATATA
1 AATTTA--TTATA-TATATATA
* *
40405 TATATATTATATATA
1 AATTTATTATATATA
40420 ATACCATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 4 0.12
20 11 0.34
22 12 0.38
23 5 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTTATTATATATATATA
Found at i:40412 original size:22 final size:23
Alignment explanation
Indices: 40369--40428 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
40359 GAATAATTTA
*
40369 TTATA-TATATCATAAATTTATT
1 TTATATTATATCATAAATATATT
*
40391 TTATATTATAT-ATATATATATT
1 TTATATTATATCATAAATATATT
* * *
40413 ATATATAATACCATAA
1 TTATATTATATCATAA
40429 TCGTGTTGGG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 22 0.73
23 8 0.27
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATATTATATCATAAATATATT
Found at i:46014 original size:24 final size:26
Alignment explanation
Indices: 45962--46014 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
45952 GTCATCTTTC
*
45962 AATCTTGGCCATTGGATGATTTCAATA
1 AATCTTGGCCATTGCAT-ATTTCAATA
*
45989 AATCTTGGCCA-TGCAT-TTTCATTA
1 AATCTTGGCCATTGCATATTTCAATA
46013 AA
1 AA
46015 GCCACATGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
26 4 0.17
27 11 0.46
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (26 bp):
AATCTTGGCCATTGCATATTTCAATA
Found at i:55032 original size:76 final size:76
Alignment explanation
Indices: 54864--55021 Score: 192
Period size: 76 Copynumber: 2.1 Consensus size: 76
54854 GAGTGAGGTT
* * * * *
54864 CGTCTGCGTCGACGCTCTGCCTCACTTGCGGACGAACGGGGGCGCCAGCCTAGGCATTCAGCCGT
1 CGTCAGCGTGGACGCTCTGCCTCACTTGCGGACGAACGGGGGCGCCAGCCTAGACACTCAACCGT
*
54929 TTAGTGAGTGG
66 TGAGTGAGTGG
* * * * *
54940 CGTCTGCGTGGACGCTCTGCCTCATTTGCGG-CGAACGGGGGCGCCAGTCTAGACGCTCAACTGT
1 CGTCAGCGTGGACGCTCTGCCTCACTTGCGGACGAACGGGGGCGCCAGCCTAGACACTCAACCGT
55004 TGAGTGAGGTGG
66 TGAGTGA-GTGG
*
55016 TGTCAG
1 CGTCAG
55022 TCTAGGCGCT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
75 33 0.47
76 37 0.53
ACGTcount: A:0.15, C:0.28, G:0.35, T:0.22
Consensus pattern (76 bp):
CGTCAGCGTGGACGCTCTGCCTCACTTGCGGACGAACGGGGGCGCCAGCCTAGACACTCAACCGT
TGAGTGAGTGG
Found at i:55142 original size:110 final size:110
Alignment explanation
Indices: 54921--55129 Score: 276
Period size: 110 Copynumber: 1.9 Consensus size: 110
54911 GCCTAGGCAT
* * * *
54921 TCAGCCGTTTAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCATTTGCGGCGAACGGGGGCGCCA
1 TCAGCCGTTGAGTGAGTGGCGTCTGCATGGAAGCTCTGCCTCACTTGCGGCGAACGGGGGCGCCA
* * * *
54986 GTCTAGACGCTCAACTGTTGAGTGAGGTGGTGTCAGTCTAGGCGC
66 ATCTAGACGCTCAACCGTTAAGTGAGGTCGTGTCAGTCTAGGCGC
* * *
55031 TCAGCCGTTGAGTGTGTGGCGTCTGCATGGAAGCTCTGCCTCACTTGCGGACGAATGGGGGGGCC
1 TCAGCCGTTGAGTGAGTGGCGTCTGCATGGAAGCTCTGCCTCACTTGCGG-CGAACGGGGGCGCC
* * *
55096 AATCTAGGCGCTTAGCCGTTAAGTGA-GTCGTGTC
65 AATCTAGACGCTCAACCGTTAAGTGAGGTCGTGTC
55130 TGCGTGGACG
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
110 52 0.62
111 32 0.38
ACGTcount: A:0.15, C:0.24, G:0.36, T:0.25
Consensus pattern (110 bp):
TCAGCCGTTGAGTGAGTGGCGTCTGCATGGAAGCTCTGCCTCACTTGCGGCGAACGGGGGCGCCA
ATCTAGACGCTCAACCGTTAAGTGAGGTCGTGTCAGTCTAGGCGC
Found at i:60683 original size:22 final size:22
Alignment explanation
Indices: 60658--60699 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
60648 TAGCACGGGC
60658 ATGGCCGGTGGTGGCATGGTGA
1 ATGGCCGGTGGTGGCATGGTGA
* *
60680 ATGGCCGGTTGTGGCTTGGT
1 ATGGCCGGTGGTGGCATGGT
60700 AGTGGCGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.10, C:0.14, G:0.48, T:0.29
Consensus pattern (22 bp):
ATGGCCGGTGGTGGCATGGTGA
Found at i:69129 original size:11 final size:11
Alignment explanation
Indices: 69113--69138 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
69103 AGATAATTTC
69113 TTTTCTTCTAG
1 TTTTCTTCTAG
69124 TTTTCTTCTAG
1 TTTTCTTCTAG
69135 TTTT
1 TTTT
69139 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:69928 original size:15 final size:16
Alignment explanation
Indices: 69897--69936 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
69887 TTACTCTGCT
69897 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
69913 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTTTAA
69928 TTGTTTTCT
1 TTGTTTTCT
69937 GTCAATCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:75041 original size:15 final size:16
Alignment explanation
Indices: 75011--75045 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
75001 TTAGGTTTAA
75011 TTTAGTTTAACTTTATT
1 TTTAGTTTAAC-TTATT
75028 TTTAGTTTAA-TTATT
1 TTTAGTTTAACTTATT
75043 TTT
1 TTT
75046 CTTTATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
17 10 0.56
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTAGTTTAACTTATT
Found at i:75853 original size:16 final size:16
Alignment explanation
Indices: 75835--75895 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
75825 AATTTTGGGT
*
75835 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAATG
75851 ACCCGAACCCGAAAATG
1 ACCCGAACCCG-AAATG
* *
75868 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
75884 ACCCGAACCCGA
1 ACCCGAACCCGA
75896 TCAACCCGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
16 26 0.67
17 13 0.33
ACGTcount: A:0.41, C:0.39, G:0.13, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:79205 original size:5 final size:5
Alignment explanation
Indices: 79195--79243 Score: 55
Period size: 5 Copynumber: 9.4 Consensus size: 5
79185 CTCAAATTAA
*
79195 TTTCT TTTCT TTTCTT TTCTCT TTTCT TTT-A TTTCT TTTACT TTTCT
1 TTTCT TTTCT TTTC-T TT-TCT TTTCT TTTCT TTTCT TTT-CT TTTCT
79242 TT
1 TT
79244 AAAATTGGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 3 0.08
5 22 0.58
6 11 0.29
7 2 0.05
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:79210 original size:10 final size:10
Alignment explanation
Indices: 79195--79243 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 10
79185 CTCAAATTAA
79195 TTTCTTTTCT
1 TTTCTTTTCT
79205 TTTCTTTTCTCT
1 TTTC-TTT-TCT
*
79217 TTTCTTTT-A
1 TTTCTTTTCT
79226 TTTCTTTTACT
1 TTTCTTTT-CT
79237 TTTCTTT
1 TTTCTTT
79244 AAAATTGGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 8 0.24
10 5 0.15
11 13 0.39
12 7 0.21
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTTTTCT
Found at i:79303 original size:14 final size:14
Alignment explanation
Indices: 79262--79301 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
79252 GCCTAGCCCA
79262 TTCTTTC-TTTC-T
1 TTCTTTCTTTTCTT
79274 TTCTTTCTTTTCTT
1 TTCTTTCTTTTCTT
79288 TTCTTT-TTTT-TT
1 TTCTTTCTTTTCTT
79300 TT
1 TT
79302 TTTTAAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 11 0.42
13 8 0.31
14 7 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (14 bp):
TTCTTTCTTTTCTT
Found at i:80862 original size:16 final size:16
Alignment explanation
Indices: 80822--80869 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
80812 GATGACCTGA
* *
80822 AACCGAAAACGACCC-
1 AACCCAAAATGACCCG
80837 AACCCAAAATTGACCCG
1 AACCCAAAA-TGACCCG
80854 AACCC-AAATGACCCG
1 AACCCAAAATGACCCG
80869 A
1 A
80870 CATTTGAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 16 0.55
16 8 0.28
17 5 0.17
ACGTcount: A:0.44, C:0.38, G:0.12, T:0.06
Consensus pattern (16 bp):
AACCCAAAATGACCCG
Found at i:81888 original size:22 final size:22
Alignment explanation
Indices: 81840--81892 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
81830 GATTTTGTTT
81840 TAAAAA-ATTTTTAATATTTAA
1 TAAAAATATTTTTAATATTTAA
* *
81861 TTAAAATATTTATTATTATTTAA
1 TAAAAATATTT-TTAATATTTAA
81884 -AAAAATATT
1 TAAAAATATT
81893 AAAAAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 12 0.44
23 10 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAAAAATATTTTTAATATTTAA
Found at i:82457 original size:41 final size:41
Alignment explanation
Indices: 82401--82493 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
82391 TCATTATAAT
82401 ATATCCTTCAAAAATAAATCCTTTAAAAAATACAATCTTAA
1 ATATCCTTCAAAAATAAATCCTTTAAAAAATACAATCTTAA
* * * *
82442 ATATCCTTCAAAAATAAATCCTTTTAAAAATATATTTTTAA
1 ATATCCTTCAAAAATAAATCCTTTAAAAAATACAATCTTAA
82483 ATATCCTTCAA
1 ATATCCTTCAA
82494 TGATGGAGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (41 bp):
ATATCCTTCAAAAATAAATCCTTTAAAAAATACAATCTTAA
Found at i:87374 original size:15 final size:15
Alignment explanation
Indices: 87352--87429 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
87342 TACCATAAAT
87352 TTCGGTGCCATCATC
1 TTCGGTGCCATCATC
* *
87367 TTCAGTGCCGTCGAT-
1 TTCGGTGCCATC-ATC
*
87382 TTTGGTGCCATCATC
1 TTCGGTGCCATCATC
*
87397 TTCGGTGCCGTCGAT-
1 TTCGGTGCCATC-ATC
*
87412 TTTGGTGCCATCATC
1 TTCGGTGCCATCATC
87427 TTC
1 TTC
87430 TTCCATGACA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
14 4 0.08
15 41 0.84
16 4 0.08
ACGTcount: A:0.12, C:0.28, G:0.23, T:0.37
Consensus pattern (15 bp):
TTCGGTGCCATCATC
Found at i:87391 original size:30 final size:30
Alignment explanation
Indices: 87350--87429 Score: 142
Period size: 30 Copynumber: 2.7 Consensus size: 30
87340 GGTACCATAA
*
87350 ATTTCGGTGCCATCATCTTCAGTGCCGTCG
1 ATTTTGGTGCCATCATCTTCAGTGCCGTCG
*
87380 ATTTTGGTGCCATCATCTTCGGTGCCGTCG
1 ATTTTGGTGCCATCATCTTCAGTGCCGTCG
87410 ATTTTGGTGCCATCATCTTC
1 ATTTTGGTGCCATCATCTTC
87430 TTCCATGACA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.12, C:0.28, G:0.23, T:0.38
Consensus pattern (30 bp):
ATTTTGGTGCCATCATCTTCAGTGCCGTCG
Found at i:88517 original size:15 final size:15
Alignment explanation
Indices: 88497--88535 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
88487 GCATCCTTCC
* *
88497 GCACCGGGTTTTTCT
1 GCACCGGATGTTTCT
88512 GCACCGGATGTTTCT
1 GCACCGGATGTTTCT
*
88527 GCACTGGAT
1 GCACCGGAT
88536 CTCTTAACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.33
Consensus pattern (15 bp):
GCACCGGATGTTTCT
Found at i:88689 original size:18 final size:18
Alignment explanation
Indices: 88666--88731 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
88656 GAACAAGTGT
88666 GGCAACTTGGTGCGGTGC
1 GGCAACTTGGTGCGGTGC
88684 GGCAACTTGGTGTC-GTGC
1 GGCAACTTGGTG-CGGTGC
* *
88702 AGCCACTTGGTGCGGTGC
1 GGCAACTTGGTGCGGTGC
* *
88720 GACCACTTGGTG
1 GGCAACTTGGTG
88732 TTGTGCGGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.02
18 40 0.95
19 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.39, T:0.24
Consensus pattern (18 bp):
GGCAACTTGGTGCGGTGC
Found at i:88737 original size:18 final size:19
Alignment explanation
Indices: 88670--88738 Score: 67
Period size: 18 Copynumber: 3.8 Consensus size: 19
88660 AAGTGTGGCA
*
88670 ACTTGGTG-CGGTGCG-GCA
1 ACTTGGTGTC-GTGCGAGCC
88688 ACTTGGTGTCGTGC-AGCC
1 ACTTGGTGTCGTGCGAGCC
88706 ACTTGGTG-CGGTGCGA-CC
1 ACTTGGTGTC-GTGCGAGCC
*
88724 ACTTGGTGTTGTGCG
1 ACTTGGTGTCGTGCG
88739 GCTTCTGGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
17 1 0.02
18 41 0.93
19 2 0.05
ACGTcount: A:0.10, C:0.23, G:0.39, T:0.28
Consensus pattern (19 bp):
ACTTGGTGTCGTGCGAGCC
Found at i:89363 original size:48 final size:47
Alignment explanation
Indices: 89288--89418 Score: 147
Period size: 50 Copynumber: 2.7 Consensus size: 47
89278 GAGCGTGCCA
* * * * *
89288 ATCAATTTTGACAAAAAATAGATAAAAAGTGCAA-TGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG
89335 ATCAATTTTGTCTTAAAAATTGAGAAAAAAGGTGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAG-AAAAA-GTGCAAGTAAAAATAAAAG
* *
89385 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCA
89419 GGAAAAGTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
47 11 0.15
48 13 0.18
49 10 0.14
50 37 0.51
51 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Found at i:89383 original size:50 final size:49
Alignment explanation
Indices: 89311--89418 Score: 148
Period size: 50 Copynumber: 2.2 Consensus size: 49
89301 AAAAATAGAT
* **
89311 AAAAAGTGCAATGAAAATTAAAAGATCAATTTTGTCTTAAAAATTGAGA
1 AAAAAGTGCAATGAAAAATAAAAGATCAATTTTGTAGTAAAAATTGAGA
*
89360 AAAAAGGTGCAA-GTAAAAATAAAAGTTCAATTTTGTAGTAAAAATTGAG-
1 AAAAA-GTGCAATG-AAAAATAAAAGATCAATTTTGTAGTAAAAATTGAGA
89409 AAAAAGTGCA
1 AAAAAGTGCA
89419 GGAAAAGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
48 5 0.09
49 11 0.21
50 37 0.70
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.26
Consensus pattern (49 bp):
AAAAAGTGCAATGAAAAATAAAAGATCAATTTTGTAGTAAAAATTGAGA
Done.