Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007011.1 Corchorus capsularis cultivar CVL-1 contig07032, 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: 46115
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Found at i:1829 original size:19 final size:18
Alignment explanation
Indices: 1796--1831 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1786 TTGAAATAAT
1796 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
1814 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
1832 GAAATCTTCA
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:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:10060 original size:16 final size:16
Alignment explanation
Indices: 10039--10070 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10029 CTACAGCAAA
10039 CAAGCAATGCCGCACC
1 CAAGCAATGCCGCACC
*
10055 CAAGCAATGTCGCACC
1 CAAGCAATGCCGCACC
10071 TTAGTAAATG
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:0.31, C:0.41, G:0.19, T:0.09
Consensus pattern (16 bp):
CAAGCAATGCCGCACC
Found at i:10295 original size:51 final size:50
Alignment explanation
Indices: 10171--10526 Score: 425
Period size: 51 Copynumber: 7.1 Consensus size: 50
10161 CAACAATGAA
* *
10171 GAGATGCGGCGTCAAATATCATGGCATAAGAAGTCTATTGGCATTAAGACAT
1 GAGATGCGGCGTCAAACATTATGGCATAAGAAGTCTA-TGGCA-TAAGACAT
* * * *
10223 GAGATGCGACGTCAAATATTATGGCATAAGAAGTCTATGGCGTATTGACAT
1 GAGATGCGGCGTCAAACATTATGGCATAAGAAGTCTATGGCATA-AGACAT
* * * *
10274 GAGACGCGGCGTCAAACATTATGGCAT--CATGTCTATGGCGTAATGACAT
1 GAGATGCGGCGTCAAACATTATGGCATAAGAAGTCTATGGCATAA-GACAT
* * *
10323 GAAATGCAGCGTCAAACATTATGGCAT--CAAGTCTATGGCATAAGACAT
1 GAGATGCGGCGTCAAACATTATGGCATAAGAAGTCTATGGCATAAGACAT
* *
10371 GAGATGCGGCGTCAAACATTACGGCATCAA-AAGTCTATGGCATAAGGCAT
1 GAGATGCGGCGTCAAACATTATGGCAT-AAGAAGTCTATGGCATAAGACAT
* *
10421 GAGATGCTGCGTCAAACATTATGGCATAAGAAGTCTATGGCAAAAAGACAT
1 GAGATGCGGCGTCAAACATTATGGCATAAGAAGTCTATGGC-ATAAGACAT
* * * * *
10472 GAGATGCGGCGTCAAACGTTACGGCTTCAGAAGTCTATGGCATAAGACAA
1 GAGATGCGGCGTCAAACATTATGGCATAAGAAGTCTATGGCATAAGACAT
10522 GAGAT
1 GAGAT
10527 ACGGAGTAAG
Statistics
Matches: 267, Mismatches: 30, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
48 29 0.11
49 58 0.22
50 69 0.26
51 76 0.28
52 35 0.13
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23
Consensus pattern (50 bp):
GAGATGCGGCGTCAAACATTATGGCATAAGAAGTCTATGGCATAAGACAT
Found at i:10574 original size:35 final size:37
Alignment explanation
Indices: 10534--10624 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 37
10524 GATACGGAGT
*
10534 AAGACATGAGATGCGACATCAGACAATTATGGC-AC-
1 AAGACATGAGATGCGACATAAGACAATTATGGCTACA
*
10569 AAGACATGAGACATG-G-CATAAGACATTTATGGCTACA
1 AAGACATGAG--ATGCGACATAAGACAATTATGGCTACA
*
10606 AACACAATGAGATGCGACA
1 AAGAC-ATGAGATGCGACA
10625 CAACAACAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
35 25 0.54
36 6 0.13
37 8 0.17
38 7 0.15
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.18
Consensus pattern (37 bp):
AAGACATGAGATGCGACATAAGACAATTATGGCTACA
Found at i:10717 original size:15 final size:15
Alignment explanation
Indices: 10697--10726 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10687 AACCGCGAGA
*
10697 GCTACGGTATAAGTC
1 GCTACGGCATAAGTC
10712 GCTACGGCATAAGTC
1 GCTACGGCATAAGTC
10727 CCAACCGCGG
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:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (15 bp):
GCTACGGCATAAGTC
Found at i:13540 original size:24 final size:24
Alignment explanation
Indices: 13488--13574 Score: 129
Period size: 24 Copynumber: 3.5 Consensus size: 24
13478 TGTACCGTAA
*
13488 TCATGGCTACCAAGTCCCCACATGGC
1 TCATGGCAACCAAGT-CCC-CATGGC
*
13514 TCACGGCAACCAAGTCCCCATGGC
1 TCATGGCAACCAAGTCCCCATGGC
13538 TCATGGCAACCAAGTCCCCATGGC
1 TCATGGCAACCAAGTCCCCATGGC
*
13562 TTATGGCAACCAA
1 TCATGGCAACCAA
13575 AAATAGGTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
24 41 0.72
25 3 0.05
26 13 0.23
ACGTcount: A:0.26, C:0.37, G:0.20, T:0.17
Consensus pattern (24 bp):
TCATGGCAACCAAGTCCCCATGGC
Found at i:28347 original size:21 final size:22
Alignment explanation
Indices: 28323--28369 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28313 CAATTCCCCT
28323 TTTCTTT-CTT-TAATTTTTCGA
1 TTTCTTTGCTTGTAATTTTT-GA
28344 TTTCTTTGCTTGTAATTTTTGA
1 TTTCTTTGCTTGTAATTTTTGA
28366 TTTC
1 TTTC
28370 AATTGTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.29
22 9 0.38
23 8 0.33
ACGTcount: A:0.13, C:0.13, G:0.09, T:0.66
Consensus pattern (22 bp):
TTTCTTTGCTTGTAATTTTTGA
Found at i:29367 original size:30 final size:30
Alignment explanation
Indices: 29331--29389 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
29321 ATCCATTGGC
29331 CGGTTGTGGCCGGTTGCTCCATGCGATGGG
1 CGGTTGTGGCCGGTTGCTCCATGCGATGGG
*
29361 CGGTTGTGGCCGGTTGCTTCATGCGATGG
1 CGGTTGTGGCCGGTTGCTCCATGCGATGG
29390 CGCATGCGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.07, C:0.22, G:0.42, T:0.29
Consensus pattern (30 bp):
CGGTTGTGGCCGGTTGCTCCATGCGATGGG
Found at i:37802 original size:20 final size:20
Alignment explanation
Indices: 37777--37817 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
37767 TGGTCGGTTG
37777 TGGCCGGTTGCCCCATGCGA
1 TGGCCGGTTGCCCCATGCGA
*
37797 TGGCCGGTTGCTCCATGCGA
1 TGGCCGGTTGCCCCATGCGA
37817 T
1 T
37818 AGCCCTTGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGCCGGTTGCCCCATGCGA
Found at i:38843 original size:33 final size:33
Alignment explanation
Indices: 38776--38843 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
38766 ATTGTTTGCA
* * *
38776 ATGATACTAAATCTGTTTTAGGTGTTATTGGTG
1 ATGACACTAAATCTATTTTAGGTGTAATTGGTG
38809 ATGACACTAAATCTATTTT-GGATGCTAATT-GTG
1 ATGACACTAAATCTATTTTAGG-TG-TAATTGGTG
38842 AT
1 AT
38844 TAAAACAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 2 0.07
33 24 0.80
34 4 0.13
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.43
Consensus pattern (33 bp):
ATGACACTAAATCTATTTTAGGTGTAATTGGTG
Found at i:38890 original size:33 final size:33
Alignment explanation
Indices: 38853--38961 Score: 182
Period size: 33 Copynumber: 3.3 Consensus size: 33
38843 TTAAAACAAA
*
38853 TCTGTTTTGGTTGATCATAGCATTGCAAATCAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
**
38886 TCTGTTTTATTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
38919 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
*
38952 TTTGTTTTGG
1 TCTGTTTTGG
38962 GTGAAAAGAA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 70 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:39346 original size:30 final size:30
Alignment explanation
Indices: 39300--39362 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
39290 TCTTCAAGGG
39300 GGAGAGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGAGAATGATGCG-CCAAGGACTTATCAT
* * *
39330 GGAGGGAATTATGCGCCAAGGACTTATTAT
1 GGAGAGAATGATGCGCCAAGGACTTATCAT
39360 GGA
1 GGA
39363 CTTGAAGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (30 bp):
GGAGAGAATGATGCGCCAAGGACTTATCAT
Found at i:42636 original size:22 final size:21
Alignment explanation
Indices: 42560--42828 Score: 210
Period size: 22 Copynumber: 12.5 Consensus size: 21
42550 ACCATCATTA
*
42560 TTTTACTCATTA-TTCTTTACT
1 TTTTACTGATTACTT-TTTACT
*
42581 TTGTACTGATTACTATTTTACT
1 TTTTACTGATTACT-TTTTACT
* *
42603 CTTGT--TGATTACCTTCTTACT
1 -TTTTACTGATTA-CTTTTTACT
*
42624 TTTTACTAATTACTATTTTACT
1 TTTTACTGATTACT-TTTTACT
* *
42646 TCTTGCTGATTAGCTTTTTACT
1 TTTTACTGATTA-CTTTTTACT
* *
42668 CTTTACTGATCACCTTTTTAC-
1 TTTTACTGATTA-CTTTTTACT
* *
42689 TCTTACTGATTACTATTTACT
1 TTTTACTGATTACTTTTTACT
*
42710 TTTTACTGACTACTATTTTACT
1 TTTTACTGATTACT-TTTTACT
*
42732 CTTGT--TGATTACCTTTTTACT
1 -TTTTACTGATTA-CTTTTTACT
42753 TTTTACTGATTACTATTTTACT
1 TTTTACTGATTACT-TTTTACT
* *
42775 TCTTGCTGATTAGCTTTTTACT
1 TTTTACTGATTA-CTTTTTACT
* *
42797 CTTTACTGATCACCTTTTTAC-
1 TTTTACTGATTA-CTTTTTACT
*
42818 TCTTACTGATT
1 TTTTACTGATT
42829 TCCGTCTACT
Statistics
Matches: 198, Mismatches: 34, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
20 13 0.07
21 67 0.34
22 106 0.54
23 12 0.06
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTACTGATTACTTTTTACT
Found at i:42636 original size:43 final size:43
Alignment explanation
Indices: 42575--42828 Score: 316
Period size: 43 Copynumber: 5.9 Consensus size: 43
42565 CTCATTATTC
* *
42575 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCTT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCTT
* * *
42618 CTTACTTTTTACTAATTACTATTTTACTTCTTGCTGATTAGCTT
1 TTTACTTTTTACTGATTACTATTTTAC-TCTTGCTGATTACCTT
* * * *
42662 TTTACTCTTTACTGATCACCT-TTTTACTCTTACTGATTA-CTA
1 TTTACTTTTTACTGATTA-CTATTTTACTCTTGCTGATTACCTT
* *
42704 TTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCTT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCTT
*
42747 TTTACTTTTTACTGATTACTATTTTACTTCTTGCTGATTAGCTT
1 TTTACTTTTTACTGATTACTATTTTAC-TCTTGCTGATTACCTT
* * *
42791 TTTACTCTTTACTGATCACCT-TTTTACTCTTACTGATT
1 TTTACTTTTTACTGATTA-CTATTTTACTCTTGCTGATT
42829 TCCGTCTACT
Statistics
Matches: 182, Mismatches: 23, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
41 2 0.01
42 33 0.18
43 73 0.40
44 70 0.38
45 4 0.02
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.54
Consensus pattern (43 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTGCTGATTACCTT
Found at i:42674 original size:129 final size:129
Alignment explanation
Indices: 42541--42824 Score: 435
Period size: 129 Copynumber: 2.2 Consensus size: 129
42531 TTTTACTGAA
* * * * *
42541 TTACTGATTACCATCATTA-TTTTACTCATTATTCTTTACTTTGTACTGATTACTATTTTACTCT
1 TTACTGATCACC-TCATTACTCTTACTCATTACTATTTACTTTGTACTGACTACTATTTTACTCT
42605 TGTTGATTACCTTCTTACTTTTTACTAATTACTATTTTACTTCTTGCTGATTAGCTTTTTACTCT
65 TGTTGATTACCTTCTTACTTTTTACTAATTACTATTTTACTTCTTGCTGATTAGCTTTTTACTCT
** * *
42670 TTACTGATCACCTTTTTACTCTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACTCTT
1 TTACTGATCACCTCATTACTCTTACTCATTACTATTTACTTTGTACTGACTACTATTTTACTCTT
* *
42735 GTTGATTACCTTTTTACTTTTTACTGATTACTATTTTACTTCTTGCTGATTAGCTTTTTACTCT
66 GTTGATTACCTTCTTACTTTTTACTAATTACTATTTTACTTCTTGCTGATTAGCTTTTTACTCT
**
42799 TTACTGATCACCTTTTTACTCTTACT
1 TTACTGATCACCTCATTACTCTTACT
42825 GATTTCCGTC
Statistics
Matches: 143, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
128 4 0.03
129 139 0.97
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (129 bp):
TTACTGATCACCTCATTACTCTTACTCATTACTATTTACTTTGTACTGACTACTATTTTACTCTT
GTTGATTACCTTCTTACTTTTTACTAATTACTATTTTACTTCTTGCTGATTAGCTTTTTACTCT
Found at i:42825 original size:129 final size:129
Alignment explanation
Indices: 42575--42828 Score: 472
Period size: 129 Copynumber: 2.0 Consensus size: 129
42565 CTCATTATTC
*
42575 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCTTCTTACTTTTTACTAATTACTAT
1 TTTACTTTGTACTGACTACTATTTTACTCTTGTTGATTACCTTCTTACTTTTTACTAATTACTAT
42640 TTTACTTCTTGCTGATTAGCTTTTTACTCTTTACTGATCACCTTTTTACTCTTACTGATTACTA
66 TTTACTTCTTGCTGATTAGCTTTTTACTCTTTACTGATCACCTTTTTACTCTTACTGATTACTA
* * *
42704 TTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTTTTACTTTTTACTGATTACTAT
1 TTTACTTTGTACTGACTACTATTTTACTCTTGTTGATTACCTTCTTACTTTTTACTAATTACTAT
42769 TTTACTTCTTGCTGATTAGCTTTTTACTCTTTACTGATCACCTTTTTACTCTTACTGATT
66 TTTACTTCTTGCTGATTAGCTTTTTACTCTTTACTGATCACCTTTTTACTCTTACTGATT
42829 TCCGTCTACT
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 121 1.00
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.54
Consensus pattern (129 bp):
TTTACTTTGTACTGACTACTATTTTACTCTTGTTGATTACCTTCTTACTTTTTACTAATTACTAT
TTTACTTCTTGCTGATTAGCTTTTTACTCTTTACTGATCACCTTTTTACTCTTACTGATTACTA
Found at i:42874 original size:35 final size:35
Alignment explanation
Indices: 42812--42880 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
42802 CTGATCACCT
* * *
42812 TTTTACTCTTACTGATTTCCGTCTACTTATTACTA
1 TTTTACCCTTACTGATTACCATCTACTTATTACTA
* * *
42847 TTTTACCCTTACTGATTACTATTTACTTTTTACT
1 TTTTACCCTTACTGATTACCATCTACTTATTACT
42881 GATTGCATGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.54
Consensus pattern (35 bp):
TTTTACCCTTACTGATTACCATCTACTTATTACTA
Found at i:43143 original size:72 final size:72
Alignment explanation
Indices: 43067--43233 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 72
43057 CACTTTAACC
* ** * * *
43067 CTTAATTATCGATTTTTTGATTACTATTTTTACCTTGACTCCTTAATTAATGATTAATTTCTTAC
1 CTTAATTATCAATTTACTGATTACTATATTTACCTAGACTCCTTAATTAATGATTAATCTCTTAC
43132 CTTGACT
66 CTTGACT
* * *
43139 CTTAATTATCAATTTACTGATTACTATATTTACCTAGACTCTTTAATTACTGTTTAATCTCTTAC
1 CTTAATTATCAATTTACTGATTACTATATTTACCTAGACTCCTTAATTAATGATTAATCTCTTAC
43204 CTTGACT
66 CTTGACT
*
43211 CTTAATTATCAGTTTACTGATTA
1 CTTAATTATCAATTTACTGATTA
43234 ATCTCTTTTA
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 85 1.00
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (72 bp):
CTTAATTATCAATTTACTGATTACTATATTTACCTAGACTCCTTAATTAATGATTAATCTCTTAC
CTTGACT
Found at i:43173 original size:40 final size:39
Alignment explanation
Indices: 43117--43240 Score: 120
Period size: 39 Copynumber: 3.3 Consensus size: 39
43107 CCTTAATTAA
*
43117 TGATTAATTTCTTACCTTGACTCTTAATTATCAATTTAC
1 TGATTAATATCTTACCTTGACTCTTAATTATCAATTTAC
*
43156 TGATTACTATAT-TTACCTAGACTC----TT-T-AA-TTAC
1 TGATTA--ATATCTTACCTTGACTCTTAATTATCAATTTAC
* * *
43189 TGTTTAATCTCTTACCTTGACTCTTAATTATCAGTTTAC
1 TGATTAATATCTTACCTTGACTCTTAATTATCAATTTAC
*
43228 TGATTAATCTCTT
1 TGATTAATATCTT
43241 TTACCTAATT
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
31 3 0.04
32 11 0.16
33 9 0.13
34 2 0.03
35 1 0.01
36 4 0.06
37 1 0.01
38 1 0.01
39 22 0.32
40 11 0.16
41 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (39 bp):
TGATTAATATCTTACCTTGACTCTTAATTATCAATTTAC
Found at i:43440 original size:55 final size:55
Alignment explanation
Indices: 43379--43516 Score: 213
Period size: 55 Copynumber: 2.5 Consensus size: 55
43369 CTTTTTACCT
* * * *
43379 ATTTACTTATTACCATTACCTTGATTCTGATTAATCTCTTTTCACTTAATTACTG
1 ATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTG
* * *
43434 ATTTACTGATTACTATTTCCTTAACTCTGATTAATCTCTTTTTACTTATTTACTG
1 ATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTG
43489 ATTTACTGATTACTATTACCTTAACTCT
1 ATTTACTGATTACTATTACCTTAACTCT
43517 TGATCATCAA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 75 1.00
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (55 bp):
ATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTG
Found at i:44297 original size:51 final size:50
Alignment explanation
Indices: 44199--44559 Score: 368
Period size: 51 Copynumber: 7.2 Consensus size: 50
44189 TAAACTTCTA
* * * *
44199 ATTCAAAGGTGACAT-TTTATTTACTATTTACTTAAAAATTCAATCTTTC
1 ATTCAAAGATGAAATCTTTATTTACTAATTACTTAAAAATTCAATCTTTT
* * * *
44248 ATTCAAAGATTAAAGCTTTATTTACTAATCACTCTAAAGATTCAATCTTTT
1 ATTCAAAGATGAAATCTTTATTTACTAATTACT-TAAAAATTCAATCTTTT
** * * * * *
44299 ACCCAAAGACGACATTTTTATTTACCAATTACTTAAAAATCCAAATCTTTT
1 ATTCAAAGATGAAATCTTTATTTACTAATTACTTAAAAATTC-AATCTTTT
* * *
44350 ATTCAAAGGTTAAATCTTTATTTACTAATTACTCTAAAGATTCAATCTTTT
1 ATTCAAAGATGAAATCTTTATTTACTAATTACT-TAAAAATTCAATCTTTT
* * * * * *
44401 ACTCAAAGATGACAT-TTTGTTTACCAATTACTTAACAATTCAATCTCTT
1 ATTCAAAGATGAAATCTTTATTTACTAATTACTTAAAAATTCAATCTTTT
* * *
44450 ATTCAAAGGTTAAATCTTTATTTACTAATTACTCTAAAAATTCAACCTTTT
1 ATTCAAAGATGAAATCTTTATTTACTAATTACT-TAAAAATTCAATCTTTT
* * * *
44501 -TCCCAAAGATGATATTTTTATTTACCAATTTACTTAAAAATTCAATCTTTT
1 AT-TCAAAGATGAAATCTTTATTTACTAA-TTACTTAAAAATTCAATCTTTT
44552 ATTCAAAG
1 ATTCAAAG
44560 GTTACATCTT
Statistics
Matches: 248, Mismatches: 55, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
49 36 0.15
50 53 0.21
51 146 0.59
52 13 0.05
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.42
Consensus pattern (50 bp):
ATTCAAAGATGAAATCTTTATTTACTAATTACTTAAAAATTCAATCTTTT
Found at i:44373 original size:102 final size:100
Alignment explanation
Indices: 44202--44570 Score: 540
Period size: 102 Copynumber: 3.6 Consensus size: 100
44192 ACTTCTAATT
* * * * * *
44202 CAAAGGTGACATTTTATTTACTATTTACTTAAAAATTCAATCTTTCATTCAAAGATTAAAGCTTT
1 CAAAGATGACATTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTT
*
44267 ATTTACTAATCACTCTAAAGATTCAATCTTTTACC
66 ATTTACTAATTACTCTAAAGATTCAATCTTTTACC
* *
44302 CAAAGACGACATTTTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCT
1 CAAAGATGACA-TTTTATTTACCAATTACTTAAAAATTC-AATCTTTTATTCAAAGGTTAAATCT
*
44367 TTATTTACTAATTACTCTAAAGATTCAATCTTTTACT
64 TTATTTACTAATTACTCTAAAGATTCAATCTTTTACC
* * *
44404 CAAAGATGACATTTTGTTTACCAATTACTTAACAATTCAATCTCTTATTCAAAGGTTAAATCTTT
1 CAAAGATGACATTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTT
* * *
44469 ATTTACTAATTACTCTAAAAATTCAACCTTTTTCC
66 ATTTACTAATTACTCTAAAGATTCAATCTTTTACC
* *
44504 CAAAGATGATATTTTTATTTACCAATTTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
1 CAAAGATGACA-TTTTATTTACCAA-TTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCT
44569 TT
64 TT
44571 TAGCAAAAGA
Statistics
Matches: 241, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
100 76 0.32
101 60 0.25
102 105 0.44
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (100 bp):
CAAAGATGACATTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTT
ATTTACTAATTACTCTAAAGATTCAATCTTTTACC
Found at i:44550 original size:202 final size:202
Alignment explanation
Indices: 44201--44570 Score: 573
Period size: 202 Copynumber: 1.8 Consensus size: 202
44191 AACTTCTAAT
* * *
44201 TCAAAGGTGACATTTTATTTACTATTTACTTAAAAATTCAATCTTTCATTCAAAGATTAAAGCTT
1 TCAAAGATGACATTTTATTTACCAATTACTTAAAAATTCAATCTTTCATTCAAAGATTAAAGCTT
* *
44266 TATTTACTAATCACTCTAAAGATTCAATCTTTTACCCAAAGACGACATTTTTATTTACCAATTAC
66 TATTTACTAATCACTCTAAAAATTCAACCTTTTACCCAAAGACGACATTTTTATTTACCAATTAC
44331 TTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATTACTCTAAAGATTCAAT
131 TTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATTACTCTAAAGATTCAAT
44396 CTTTTAC
196 CTTTTAC
* * * *
44403 TCAAAGATGACATTTTGTTTACCAATTACTTAACAATTCAATCTCTT-ATTCAAAGGTTAAATCT
1 TCAAAGATGACATTTTATTTACCAATTACTTAAAAATTCAATCT-TTCATTCAAAGATTAAAGCT
* * * *
44467 TTATTTACTAATTACTCTAAAAATTCAACCTTTTTCCCAAAGATGATATTTTTATTTACCAATTT
65 TTATTTACTAATCACTCTAAAAATTCAACCTTTTACCCAAAGACGACATTTTTATTTACCAA-TT
* *
44532 ACTTAAAAATTC-AATCTTTTATTCAAAGGTTACATCTTT
129 ACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCTTT
44571 TAGCAAAAGA
Statistics
Matches: 151, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
202 136 0.90
203 15 0.10
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (202 bp):
TCAAAGATGACATTTTATTTACCAATTACTTAAAAATTCAATCTTTCATTCAAAGATTAAAGCTT
TATTTACTAATCACTCTAAAAATTCAACCTTTTACCCAAAGACGACATTTTTATTTACCAATTAC
TTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATTACTCTAAAGATTCAAT
CTTTTAC
Found at i:44568 original size:20 final size:20
Alignment explanation
Indices: 44556--44594 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
44546 TCTTTTATTC
*
44556 AAAGGTTACATCTTTTAGCA
1 AAAGATTACATCTTTTAGCA
44576 AAAGATTACATCTTTTAGC
1 AAAGATTACATCTTTTAGC
44595 CAAATATCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
AAAGATTACATCTTTTAGCA
Done.