Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013402.1 Corchorus capsularis cultivar CVL-1 contig13423, 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: 54000
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:6139 original size:16 final size:16
Alignment explanation
Indices: 6118--6149 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6108 GGAATGTAGG
6118 TTTATTAGTTTGTTTA
1 TTTATTAGTTTGTTTA
*
6134 TTTATTTGTTTGTTTA
1 TTTATTAGTTTGTTTA
6150 GTTTGTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (16 bp):
TTTATTAGTTTGTTTA
Found at i:24390 original size:19 final size:19
Alignment explanation
Indices: 24366--24404 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
24356 CCTTTGTATG
24366 TGTTTTCTGTGTGGTGCTA
1 TGTTTTCTGTGTGGTGCTA
24385 TGTTTTCTGTGTGGTGCTA
1 TGTTTTCTGTGTGGTGCTA
24404 T
1 T
24405 CAGACTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.10, G:0.31, T:0.54
Consensus pattern (19 bp):
TGTTTTCTGTGTGGTGCTA
Found at i:27236 original size:87 final size:87
Alignment explanation
Indices: 27089--27438 Score: 592
Period size: 87 Copynumber: 4.0 Consensus size: 87
27079 GGTCACCACA
* * *
27089 TCAGTGCCTTTTGGCATCTGAGTGCCCTCAGATGATTCGTGCTCGGTGACTGTATCGGTGGTGGT
1 TCAGTGTCTTTTGGCATCTGAGTACCCTCAGATGATTCGTGCTCGGTGACTGTATTGGTGGTGGT
27154 AGCAGGAATGGCTGCATTATTT
66 AGCAGGAATGGCTGCATTATTT
* *
27176 TCAGTGTCTTTTGGCGTCTGTGTACCCTCAGATGATTCGTGCTCGGTGACTGTATTGGTGGTGGT
1 TCAGTGTCTTTTGGCATCTGAGTACCCTCAGATGATTCGTGCTCGGTGACTGTATTGGTGGTGGT
27241 AGCAGGAATGGCTGCATTATTT
66 AGCAGGAATGGCTGCATTATTT
* *
27263 TCAGTATCTTTTGGCATCTGTGTACCCTCAGATGATTCGTGCTCGGTGACTGTATTGGTGGTGGT
1 TCAGTGTCTTTTGGCATCTGAGTACCCTCAGATGATTCGTGCTCGGTGACTGTATTGGTGGTGGT
27328 AGCAGGAATGGCTGCATTATTT
66 AGCAGGAATGGCTGCATTATTT
* *
27350 TCAGTGTCTTTTGGCATGTGAGTACCCTCAGATGATTCGTGCTCGGTGACTGTATTGGTGGTCGT
1 TCAGTGTCTTTTGGCATCTGAGTACCCTCAGATGATTCGTGCTCGGTGACTGTATTGGTGGTGGT
** *
27415 AGCAGGGGTAGCTGCATTATTT
66 AGCAGGAATGGCTGCATTATTT
27437 TC
1 TC
27439 CTCGAGTTTC
Statistics
Matches: 249, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 249 1.00
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.36
Consensus pattern (87 bp):
TCAGTGTCTTTTGGCATCTGAGTACCCTCAGATGATTCGTGCTCGGTGACTGTATTGGTGGTGGT
AGCAGGAATGGCTGCATTATTT
Found at i:43449 original size:36 final size:36
Alignment explanation
Indices: 43396--43528 Score: 155
Period size: 36 Copynumber: 3.8 Consensus size: 36
43386 AAGGATAGAC
* * *
43396 TGGCTTAGTTTCGAGGAAACTAGGTAAAGAAAAGAT
1 TGGCTTAATTTCAAGGAAACTAAGTAAAGAAAAGAT
* *
43432 TGGCTTAATTTCAAGGAAATTAAGT--A-AAAAGAC
1 TGGCTTAATTTCAAGGAAACTAAGTAAAGAAAAGAT
* * *
43465 TGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAATAT
1 TGGCTTAATTTCAAGGAAACTAAGTAAAGAAAAGAT
* *
43501 TAGCTTAATTTCAAGGAAATTAAGTAAA
1 TGGCTTAATTTCAAGGAAACTAAGTAAA
43529 AAAGACTGAC
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
33 28 0.35
34 1 0.01
35 1 0.01
36 50 0.62
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (36 bp):
TGGCTTAATTTCAAGGAAACTAAGTAAAGAAAAGAT
Found at i:43469 original size:33 final size:34
Alignment explanation
Indices: 43378--43536 Score: 149
Period size: 36 Copynumber: 4.6 Consensus size: 34
43368 AGACTGACTT
* * * *
43378 AATTAAGTAAGGATAGACTGGCTTAGTTTCGAGGA
1 AATTAAGTAA-AAAAGACTGGCTTAATTTCAAGGA
* * *
43413 AACTAGGTAAAGAAAAGATTGGCTTAATTTCAAGGA
1 AATTAAGT-AA-AAAAGACTGGCTTAATTTCAAGGA
*
43449 AATTAAGT-AAAAAGACTGGCTTAGTTTCAAGGA
1 AATTAAGTAAAAAAGACTGGCTTAATTTCAAGGA
* * * * *
43482 AACTAGGTAAAGAAAATATTAGCTTAATTTCAAGGA
1 AATTAAGT-AA-AAAAGACTGGCTTAATTTCAAGGA
43518 AATTAAGTAAAAAAGACTG
1 AATTAAGTAAAAAAGACTG
43537 ACTCAGTTTA
Statistics
Matches: 98, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
33 28 0.29
34 7 0.07
35 9 0.09
36 54 0.55
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.26
Consensus pattern (34 bp):
AATTAAGTAAAAAAGACTGGCTTAATTTCAAGGA
Found at i:43470 original size:69 final size:69
Alignment explanation
Indices: 43378--43552 Score: 262
Period size: 69 Copynumber: 2.5 Consensus size: 69
43368 AGACTGACTT
* * *
43378 AATTAAGTAAGGATAGACTGGCTTAGTTTCGAGGAAACTAGGTAAAGAAAAGATTGGCTTAATTT
1 AATTAAGTAA--AAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGATTAGCTTAATTT
43443 CAAGGA
64 CAAGGA
*
43449 AATTAAGTAAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAATATTAGCTTAATTTCA
1 AATTAAGTAAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGATTAGCTTAATTTCA
43514 AGGA
66 AGGA
* *
43518 AATTAAGTAAAAAAGACTGACTCAGTTT-AAGGAAA
1 AATTAAGT-AAAAAGACTGGCTTAGTTTCAAGGAAA
43553 GAAATTAGGT
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
69 70 0.72
70 17 0.18
71 10 0.10
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (69 bp):
AATTAAGTAAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGATTAGCTTAATTTCA
AGGA
Found at i:43650 original size:35 final size:36
Alignment explanation
Indices: 43570--43706 Score: 222
Period size: 36 Copynumber: 3.8 Consensus size: 36
43560 GGTAAAGACC
*
43570 AGCACAGACTTAATTTCACAAGAATTAAGTAAAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
* **
43606 AGCATAGACTTAATCCCACAAGAATTAAGT-AAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
43641 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
*
43677 AGCAAATACTTAATTTCACAAGAATTAAGT
1 AGCAAAGACTTAATTTCACAAGAATTAAGT
43707 CAGCAAAGGT
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 32 0.34
36 61 0.66
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (36 bp):
AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
Found at i:43662 original size:71 final size:71
Alignment explanation
Indices: 43570--43706 Score: 229
Period size: 71 Copynumber: 1.9 Consensus size: 71
43560 GGTAAAGACC
* *
43570 AGCACAGACTTAATTTCACAAGAATTAAGTAAAATTAGCATAGACTTAATCCCACAAGAATTAAG
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAGACTTAATCCCACAAGAATTAAG
43635 TAAATT
66 TAAATT
* **
43641 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTAGCAAATACTTAATTTCACAAGAATTAAG
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAGACTTAATCCCACAAGAATTAAG
43706 T
66 T
43707 CAGCAAAGGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (71 bp):
AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAGACTTAATCCCACAAGAATTAAG
TAAATT
Found at i:43797 original size:11 final size:11
Alignment explanation
Indices: 43777--44012 Score: 222
Period size: 11 Copynumber: 21.2 Consensus size: 11
43767 AAAATTAGAT
*
43777 TGAAAGAAGAC
1 TGAAATAAGAC
43788 TGAAATAAGAC
1 TGAAATAAGAC
* *
43799 TGAAAGAAGGC
1 TGAAATAAGAC
*
43810 TGAAAAGAAGAC
1 TG-AAATAAGAC
*
43822 TGAATTAAGAC
1 TGAAATAAGAC
*
43833 TGAAATTAGAC
1 TGAAATAAGAC
* *
43844 TGATAGAAGAC
1 TGAAATAAGAC
*
43855 TGAAATTAGAC
1 TGAAATAAGAC
*
43866 TGAAAATTAGAC
1 TG-AAATAAGAC
*
43878 TGAAATTAGAC
1 TGAAATAAGAC
* *
43889 TGAAATCAGGC
1 TGAAATAAGAC
*
43900 TGAAAAAAGAC
1 TGAAATAAGAC
*
43911 TGAAATTAAGAT
1 TGAAA-TAAGAC
*
43923 TGAAATTAGAC
1 TGAAATAAGAC
*
43934 TGAAAGAAGAC
1 TGAAATAAGAC
*
43945 TGAAATTAGAC
1 TGAAATAAGAC
43956 TGAAATTAA-AC
1 TGAAA-TAAGAC
* *
43967 TGAAAGAGGAC
1 TGAAATAAGAC
43978 TGAAATAAGAC
1 TGAAATAAGAC
* *
43989 TGAGAGAAGAC
1 TGAAATAAGAC
*
44000 TGAAAGAAGAC
1 TGAAATAAGAC
44011 TG
1 TG
44013 GCTTAGTTTC
Statistics
Matches: 185, Mismatches: 35, Indels: 10
0.80 0.15 0.04
Matches are distributed among these distances:
10 1 0.01
11 152 0.82
12 32 0.17
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.19
Consensus pattern (11 bp):
TGAAATAAGAC
Found at i:43815 original size:45 final size:45
Alignment explanation
Indices: 43766--44012 Score: 238
Period size: 45 Copynumber: 5.5 Consensus size: 45
43756 TTAACTTCAA
* * * *
43766 GAAAATTAGATTGAAAGAAGACTGAAATAAGACTGAAAGAAGGCT
1 GAAAATTAGACTGAAATAAGACTGAAATTAGACTGAAAGAAGACT
** * *
43811 GAAAAGAAGACTGAATTAAGACTGAAATTAGACTGATAGAAGACT
1 GAAAATTAGACTGAAATAAGACTGAAATTAGACTGAAAGAAGACT
* ** *
43856 G-AAATTAGACTGAAAATTAGACTGAAATTAGACTGAAATCAGGCT
1 GAAAATTAGACTG-AAATAAGACTGAAATTAGACTGAAAGAAGACT
* *
43901 GAAAA-AAGACTGAAATTAAGATTGAAATTAGACTGAAAGAAGACT
1 GAAAATTAGACTGAAA-TAAGACTGAAATTAGACTGAAAGAAGACT
* *
43946 G-AAATTAGACTGAAATTAA-ACTGAAA-GAGGACTGAAATAAGACT
1 GAAAATTAGACTGAAA-TAAGACTGAAATTA-GACTGAAAGAAGACT
* *
43990 GAGAGA--AGACTGAAAGAAGACTG
1 GA-AAATTAGACTGAAATAAGACTG
44013 GCTTAGTTTC
Statistics
Matches: 166, Mismatches: 28, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
43 3 0.02
44 49 0.30
45 109 0.66
46 5 0.03
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.19
Consensus pattern (45 bp):
GAAAATTAGACTGAAATAAGACTGAAATTAGACTGAAAGAAGACT
Found at i:44002 original size:33 final size:33
Alignment explanation
Indices: 43777--44012 Score: 242
Period size: 34 Copynumber: 7.1 Consensus size: 33
43767 AAAATTAGAT
* *
43777 TGAAAGAAGACTGAAATAAGACTGAAAGAAGGC
1 TGAAATAAGACTGAAATAAGACTGAAAGAAGAC
* * **
43810 TGAAAAGAAGACTGAATTAAGACTGAAATTAGAC
1 TG-AAATAAGACTGAAATAAGACTGAAAGAAGAC
* * *
43844 TGATAGAAGACTGAAATTAGACTGAAA-ATTAGAC
1 TGAAATAAGACTGAAATAAGACTGAAAGA--AGAC
* * * *
43878 TGAAATTAGACTGAAATCAGGCTGAAAAAAGAC
1 TGAAATAAGACTGAAATAAGACTGAAAGAAGAC
* *
43911 TGAAATTAAGATTGAAATTAGACTGAAAGAAGAC
1 TGAAA-TAAGACTGAAATAAGACTGAAAGAAGAC
* *
43945 TGAAATTAGACTGAAATTAA-ACTGAAAGAGGAC
1 TGAAATAAGACTGAAA-TAAGACTGAAAGAAGAC
* *
43978 TGAAATAAGACTGAGAGAAGACTGAAAGAAGAC
1 TGAAATAAGACTGAAATAAGACTGAAAGAAGAC
44011 TG
1 TG
44013 GCTTAGTTTC
Statistics
Matches: 170, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
32 2 0.01
33 82 0.48
34 85 0.50
35 1 0.01
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.19
Consensus pattern (33 bp):
TGAAATAAGACTGAAATAAGACTGAAAGAAGAC
Found at i:44054 original size:36 final size:36
Alignment explanation
Indices: 44007--44288 Score: 372
Period size: 36 Copynumber: 7.9 Consensus size: 36
43997 GACTGAAAGA
* *
44007 AGACTGGCTTAGTTTCAAGGAAACTAGGTAAATG-AT
1 AGACTGGCTTAATTTCAAGGAAACTAAGTAAA-GAAT
* *
44043 AGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAT
1 AGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAAT
*
44079 AGACTGGCTTAATTTCAAGGAAATTAAGTAAAG-A-
1 AGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAAT
* *
44113 AGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAT
1 AGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAAT
* *
44149 AGACTGACTTAATTTCAAGGAAACTAGGTAAAGAAT
1 AGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAAT
** *
44185 AGGTTGGCTTAATTTCAAGGAAATTAAGTAAAGAAT
1 AGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAAT
* * * * *
44221 AAACTGCCTTGATTTCAAGGAAATTAAGTAAAGAAA
1 AGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAAT
*
44257 AGACTGGCTTAATTTCAAGGAAATTAAGTAAA
1 AGACTGGCTTAATTTCAAGGAAACTAAGTAAA
44289 AAGACACATG
Statistics
Matches: 221, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
34 30 0.14
35 3 0.01
36 188 0.85
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (36 bp):
AGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAAT
Found at i:44193 original size:106 final size:106
Alignment explanation
Indices: 44002--44288 Score: 425
Period size: 106 Copynumber: 2.7 Consensus size: 106
43992 GAGAAGACTG
*
44002 AAAGAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAATG-ATAGACTGGCTTAGTTTCAAGGAAA
1 AAAGAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAA-GAATAGACTGGCTTAATTTCAAGGAAA
44066 CTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAGT
65 CTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAGT
*
44108 AAAGAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGACTTAATTTCAAGGAAAC
1 AAAGAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAAC
**
44173 TAGGTAAAGAATAGGTTGGCTTAATTTCAAGGAAATTAAGT
66 TAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAGT
* * * * *
44214 AAAGAATAAACTGCCTT-GATTTCAAGGAAATTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGA
1 AAAG-A-AGACTGGCTTAG-TTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGA
* *
44278 AATTAAGTAAA
63 AACTAGGTAAA
44289 AAGACACATG
Statistics
Matches: 165, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
105 1 0.01
106 104 0.63
107 2 0.01
108 58 0.35
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.26
Consensus pattern (106 bp):
AAAGAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAAC
TAGGTAAAGAATAGACTGGCTTAATTTCAAGGAAATTAAGT
Found at i:44339 original size:72 final size:70
Alignment explanation
Indices: 44003--44356 Score: 256
Period size: 72 Copynumber: 4.9 Consensus size: 70
43993 AGAAGACTGA
* * * * * * *
44003 AAGAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAATG-ATAGACTGGCTTAGTTTCAAGGAAAC
1 AAGAA-ACTGCCTTAATTTCAAGGAAATTAAGTAAA-GAAAAGAC--GCTTAATTTCAAGGAAAT
*
44067 TAGGTAAAG
62 TAAGTAAAG
* * * * *
44076 AATAGACTGGCTTAATTTCAAGGAAATTAAGTAAAG--AAGACTGGCTTAGTTTCAAGGAAACTA
1 AAGAAACTGCCTTAATTTCAAGGAAATTAAGTAAAGAAAAGAC--GCTTAATTTCAAGGAAATTA
*
44139 GGTAAAG
64 AGTAAAG
* * * * * * **
44146 AATAGACTGACTTAATTTCAAGGAAACTAGGTAAAGAATAGGTTGGCTTAATTTCAAGGAAATTA
1 AAGAAACTGCCTTAATTTCAAGGAAATTAAGTAAAGAA-AAG-ACGCTTAATTTCAAGGAAATTA
44211 AGTAAAG
64 AGTAAAG
* *
44218 AATAAACTGCCTTGATTTCAAGGAAATTAAGTAAAGAAAAGACTGGCTTAATTTCAAGGAAATTA
1 AAGAAACTGCCTTAATTTCAAGGAAATTAAGTAAAGAAAAGAC--GCTTAATTTCAAGGAAATTA
44283 AGTAAA-
64 AGTAAAG
* * * *
44289 AAGACACATG-CTTAATTTCAGTAAAGGAAATTAAGTATAA-TAAAGA-GCTTAA-TTCAGGGTA
1 AAGAAAC-TGCCTTAATTTC----AAGGAAATTAAGTA-AAGAAAAGACGCTTAATTTCAAGGAA
44350 ATTAAGT
60 ATTAAGT
44357 GAAGTCAATA
Statistics
Matches: 240, Mismatches: 29, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
70 66 0.28
71 30 0.12
72 118 0.49
73 5 0.02
75 19 0.08
76 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.27
Consensus pattern (70 bp):
AAGAAACTGCCTTAATTTCAAGGAAATTAAGTAAAGAAAAGACGCTTAATTTCAAGGAAATTAAG
TAAAG
Found at i:49024 original size:62 final size:62
Alignment explanation
Indices: 48927--49045 Score: 184
Period size: 62 Copynumber: 1.9 Consensus size: 62
48917 TGTACAACAA
** *
48927 TTTTATTTTTAGTATTGTCAACATTATTTGACAATTCATAAATCTTGAAGAGAAAATCCATT
1 TTTTATTTTTAGTACCGCCAACATTATTTGACAATTCATAAATCTTGAAGAGAAAATCCATT
* * *
48989 TTTTATTTTTAGTACCGCCAACATTATTTGACAATTGATAAATCTTGCATAGAAAAT
1 TTTTATTTTTAGTACCGCCAACATTATTTGACAATTCATAAATCTTGAAGAGAAAAT
49046 GGAATGCCAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (62 bp):
TTTTATTTTTAGTACCGCCAACATTATTTGACAATTCATAAATCTTGAAGAGAAAATCCATT
Found at i:50456 original size:2 final size:2
Alignment explanation
Indices: 50449--50481 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
50439 GTTAAAAATA
50449 AT AT AT AT AT AT AT AT AT AT AGT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
50482 TTTACGATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51710 original size:584 final size:575
Alignment explanation
Indices: 50552--51716 Score: 1610
Period size: 584 Copynumber: 2.0 Consensus size: 575
50542 CTCTCAATCA
* * *
50552 TAAATACTAGAACTTCATGGCCGCGCTTCGCGTGCGGCTGTTTTATTTTATAAATTCTTTTAAGA
1 TAAAAACTAGAACTTCACGGCCGCGCTTCGCGAGCGGCTGTTTTATTTTATAAATTCTTTTAAGA
* * *
50617 AAATTCAGTTTAGAAATCAAATTTTATTGTGAAATGATAACAAATCAAAGCAATGGAGTAAAATT
66 AAATTCAGTTAAGAAATCAAATTTTATTGTGAAATGATAACAAAACAAAGCAATGGAATAAAATT
* * * *
50682 GAAGTATGTAAAAGACAAGAGAATAGAGAGATAATAGAATATGGAGAATAAGAAAATATGAAGAA
131 GAAGTATGGAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAGAAAATATGAAAAA
* **
50747 TGAGAGAAATTGTTCTCATTCATTTTATTCCATAACAAAGTAAGTGGCCTAGTTATAGGCATATA
196 GGAGAGAAA---TTCTCATTCATCCTATTCCATAACAAAGTAAGTGGCCTAGTTATAGGCA-ATA
* * * *
50812 GATACATCAATATAAATATAAGAGGAAGAACTTAGCATATAGGTATATGTGTATGAATGAACCAA
257 GACACATCAATATAAATATAAGAGGAAGAACTTAACACATAGGTATATATGTATGAATGAACCAA
50877 GTCATCAATCTTATCCATGCTTTAATTAGATTCATGGACATACACAACATACATGTATATTCATA
322 GTCATCAATCTTATCCATGCTTTAATTAGATTCATGGACATACACAACATACATGTATATTCATA
*
50942 ATAAATTAATTTATAATTATTTGCTAATTTATTTTATATAGGAAAGGGAATGAATGTATTTTAAT
387 ATAAATTAATTTATAATTATTTGCTAATTTATTTTATATAGGAAAGGGAATAAATGTATTTTAAT
*
51007 TTTTCCAAACTAAATGAATACAAATATAATAAACAAAACATTTAGAAAATTAATTATTGACACTT
452 TTTTCCAAACTAAATGAATACAAATATAATAAACAAAACATTTAGAAAATTAACTATTGACACTT
* *
51072 GTCAAAGAAACCAAATACCAAGTGGCACTCAATGAGAGTCTTGTACATAAAATTAATAG
517 GTCAAAAAAACCAAATACCAAGTGGCACTCAATGAAAGTCTTGTACATAAAATTAATAG
* * *
51131 TAAAAACTAGAATTTCCCGGCCGTGCTTCGCGAGCGGCTGTTTTATTTTATAAATTCTTTTAAGA
1 TAAAAACTAGAACTTCACGGCCGCGCTTCGCGAGCGGCTGTTTTATTTTATAAATTCTTTTAAGA
* *
51196 AAATTTCAGTTAAGAAATGAAATTTTGTTGTGAAATGATAACAAAACAAA-CGAA-GAGAATAGA
66 AAA-TTCAGTTAAGAAATCAAATTTTATTGTGAAATGATAACAAAACAAAGC-AATG-GAAT--A
51259 AAATTGAAGTATGGAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAGAAAATATG
126 AAATTGAAGTATGGAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAGAAAATATG
* * ** *
51324 AAAAAGGGGAGAAA-T-T-ATTCATCCTATTTCATAACAAAGTAAGTGGTGTATTTATAGGC-AT
191 AAAAAGGAGAGAAATTCTCATTCATCCTATTCCATAACAAAGTAAGTGGCCTAGTTATAGGCAAT
* *
51385 AGACACATC-ATCATAAATATAAGAGGATGAACTTAATACATAGGTATATATGTATGAATGAACC
256 AGACACATCAAT-ATAAATATAAGAGGAAGAACTTAACACATAGGTATATATGTATGAATGAACC
* * * * *
51449 AAGTTATTAATCTTATCCATGCTTTAATTTTAGATTTATGGACATCCACAATATACATGTATATT
320 AAGTCATCAATCTTATCCATGCTTTAA--TTAGATTCATGGACATACACAACATACATGTATATT
* * **
51514 CATAACAAATTTATAATTAATTTATGATTATTTGATTAATTTATTTTATATAGGAAAAGGGGGTA
383 CAT----AA--TA-AATTAATTTATAATTATTTG-CTAATTTATTTTATATAGG-AAAGGGAATA
* ** *
51579 AATGTCTTTTGTTTTTTCCAATCTAAATGAATACAAATATAATAAACAAAACA-TTAGAAAATTA
439 AATGTATTTTAATTTTTCCAAACTAAATGAATACAAATATAATAAACAAAACATTTAGAAAATTA
* * * * *
51643 ACTATTGACACTTGTCAAAAAAACCTAATGCCATGTGGCACTCAATGAAAGTTTTGCT-TATAAA
504 ACTATTGACACTTGTCAAAAAAACCAAATACCAAGTGGCACTCAATGAAAGTCTTG-TACATAAA
51707 ATTAATAG
568 ATTAATAG
51715 TA
1 TA
51717 GGTTTAATTA
Statistics
Matches: 517, Mismatches: 51, Indels: 31
0.86 0.09 0.05
Matches are distributed among these distances:
573 2 0.00
574 82 0.16
576 73 0.14
577 1 0.00
578 1 0.00
579 64 0.12
580 49 0.09
582 76 0.15
583 19 0.04
584 93 0.18
585 57 0.11
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (575 bp):
TAAAAACTAGAACTTCACGGCCGCGCTTCGCGAGCGGCTGTTTTATTTTATAAATTCTTTTAAGA
AAATTCAGTTAAGAAATCAAATTTTATTGTGAAATGATAACAAAACAAAGCAATGGAATAAAATT
GAAGTATGGAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAGAAAATATGAAAAA
GGAGAGAAATTCTCATTCATCCTATTCCATAACAAAGTAAGTGGCCTAGTTATAGGCAATAGACA
CATCAATATAAATATAAGAGGAAGAACTTAACACATAGGTATATATGTATGAATGAACCAAGTCA
TCAATCTTATCCATGCTTTAATTAGATTCATGGACATACACAACATACATGTATATTCATAATAA
ATTAATTTATAATTATTTGCTAATTTATTTTATATAGGAAAGGGAATAAATGTATTTTAATTTTT
CCAAACTAAATGAATACAAATATAATAAACAAAACATTTAGAAAATTAACTATTGACACTTGTCA
AAAAAACCAAATACCAAGTGGCACTCAATGAAAGTCTTGTACATAAAATTAATAG
Found at i:51727 original size:16 final size:16
Alignment explanation
Indices: 51706--51740 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
51696 TTGCTTATAA
51706 AATTAATAGTAGGTTT
1 AATTAATAGTAGGTTT
51722 AATTAATAGTAGGTTT
1 AATTAATAGTAGGTTT
51738 AAT
1 AAT
51741 AGATACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (16 bp):
AATTAATAGTAGGTTT
Found at i:52112 original size:54 final size:54
Alignment explanation
Indices: 52030--52139 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
52020 ATGACCTGCA
52030 ATTAGAAACCCACATGTTTCATGCTTAGTTTATATGTATTATTATATAATTAGG
1 ATTAGAAACCCACATGTTTCATGCTTAGTTTATATGTATTATTATATAATTAGG
52084 ATTAGAAACCCACATGTTTCATGCTTAGTTTATATGTATTATTATATAATTAGG
1 ATTAGAAACCCACATGTTTCATGCTTAGTTTATATGTATTATTATATAATTAGG
52138 AT
1 AT
52140 CATTACTATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (54 bp):
ATTAGAAACCCACATGTTTCATGCTTAGTTTATATGTATTATTATATAATTAGG
Done.