Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003738.1 Hibiscus syriacus cultivar Beakdansim tig00007997_pilon, 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: 76840
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:472 original size:19 final size:20
Alignment explanation
Indices: 429--476 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
419 TCTAAATCCT
*
429 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
449 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
468 TTTTCAAAA
1 TTTTCAAAA
477 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1363 original size:31 final size:32
Alignment explanation
Indices: 1328--1388 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1318 CCTTTCCAAC
*
1328 TCCCTAG-TTTTTACGGGATAAACTAGAACTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACTT
* *
1359 TCCCTAGCTTTTCACGGGCTAAGCTAGAAC
1 TCCCTAGCTTTTCACGGGATAAACTAGAAC
1389 CAAACCCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (32 bp):
TCCCTAGCTTTTCACGGGATAAACTAGAACTT
Found at i:1866 original size:21 final size:21
Alignment explanation
Indices: 1840--1896 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1830 CTAGTGGAAA
*
1840 GTGCATGGATGCACTGTAAGG
1 GTGCATGGATGCACTGCAAGG
*
1861 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAAGG
1882 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1897 TTGACACCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAAGG
Found at i:5902 original size:21 final size:21
Alignment explanation
Indices: 5863--5902 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5853 GCAACACAGG
*
5863 TTCCAAAATCGCAATGCAATT
1 TTCCAAAATCGCAACGCAATT
* *
5884 TTCCAAATTCGTAACGCAA
1 TTCCAAAATCGCAACGCAA
5903 ATAGTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (21 bp):
TTCCAAAATCGCAACGCAATT
Found at i:5975 original size:20 final size:20
Alignment explanation
Indices: 5952--5997 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
5942 AATAGTTAAA
*
5952 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
5972 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
5992 TCGCAA
1 TCGCAA
5998 AGCGCGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:5976 original size:40 final size:42
Alignment explanation
Indices: 5887--5978 Score: 111
Period size: 40 Copynumber: 2.3 Consensus size: 42
5877 TGCAATTTTC
* *
5887 CAAATTCGTAACGCAAATAGTTAAATCGCAACTATAATATGT
1 CAAATTCGCAACGCAAATAGTTAAATCGCAACTATAATAAGT
* * *
5929 -AAA-TCGCAATGCGAATAGTTAAATCGCAAC-A-CATAAGT
1 CAAATTCGCAACGCAAATAGTTAAATCGCAACTATAATAAGT
5967 CAAATTCGCAAC
1 CAAATTCGCAAC
5979 ACAGAAGTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
38 5 0.12
39 4 0.10
40 30 0.71
41 3 0.07
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (42 bp):
CAAATTCGCAACGCAAATAGTTAAATCGCAACTATAATAAGT
Found at i:6015 original size:19 final size:19
Alignment explanation
Indices: 5991--6032 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5981 AGAAGTCAAA
**
5991 TTCGCAAAGCGCGTTTATT
1 TTCGCAAAGCGAATTTATT
*
6010 TTCGCAACGCGAATTTATT
1 TTCGCAAAGCGAATTTATT
6029 TTCG
1 TTCG
6033 AATTCGAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (19 bp):
TTCGCAAAGCGAATTTATT
Found at i:6580 original size:20 final size:20
Alignment explanation
Indices: 6533--6594 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
6523 AAACTTAAAT
*
6533 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
6553 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
6573 TCGCAACGTTGCGAAAATGAAA
1 TCGCAAC---GCGAAAATGAAA
6595 TTTGTGTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 26 0.68
23 12 0.32
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:6646 original size:20 final size:20
Alignment explanation
Indices: 6600--6669 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
6590 TGAAATTTGT
6600 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGC
*
6619 GTTGCGATTTTCATTTTTGC
1 GTTGCGATTTTCATTTTCGC
*
6639 GTTACGATTTTCATTTTCGC
1 GTTGCGATTTTCATTTTCGC
6659 GTTGCGATTTT
1 GTTGCGATTTT
6670 AAGTTTTAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 13 0.28
20 33 0.72
ACGTcount: A:0.11, C:0.17, G:0.20, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGC
Found at i:8218 original size:21 final size:21
Alignment explanation
Indices: 8189--8249 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
8179 ATACAGCTCT
*
8189 ACAATGAGAGCCATCACCTCC
1 ACAACGAGAGCCATCACCTCC
*
8210 ACAACGAGAGCTATCACCTCC
1 ACAACGAGAGCCATCACCTCC
8231 ACAACGAGAGCCATCACCT
1 ACAACGAGAGCCATCACCT
8250 ATTCCATCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.34, C:0.38, G:0.15, T:0.13
Consensus pattern (21 bp):
ACAACGAGAGCCATCACCTCC
Found at i:8397 original size:21 final size:21
Alignment explanation
Indices: 8364--8413 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
8354 GTTAGGGGAG
*
8364 TTACGTGATGAGGTCAATACT
1 TTACGTGAGGAGGTCAATACT
* **
8385 TTGCGTGAGGAGGTCGGTACT
1 TTACGTGAGGAGGTCAATACT
8406 TTACGTGA
1 TTACGTGA
8414 CGACAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:8875 original size:21 final size:21
Alignment explanation
Indices: 8851--8924 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
8841 CCTATCGTTA
8851 AAGAGGCCCCTATCATCCTTC
1 AAGAGGCCCCTATCATCCTTC
*
8872 AAGAGGCCCCTCTCA-CCGTTC
1 AAGAGGCCCCTATCATCC-TTC
* *
8893 AAGAGGCCCCTGTCATCGTTC
1 AAGAGGCCCCTATCATCCTTC
*
8914 AAGAGGTCCCT
1 AAGAGGCCCCT
8925 TCCACCATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (21 bp):
AAGAGGCCCCTATCATCCTTC
Found at i:8935 original size:21 final size:20
Alignment explanation
Indices: 8869--8939 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
8859 CCTATCATCC
*
8869 TTCAAGAGGCCCCTCTCACCG
1 TTCAAGAGGCCCTTC-CACCG
*
8890 TTCAAGAGGCCCCTGT-CATCG
1 TTCAAGAGG-CCCT-TCCACCG
*
8911 TTCAAGAGGTCCCTTCCACCA
1 TTCAAGAGG-CCCTTCCACCG
8932 TTCAAGAG
1 TTCAAGAG
8940 CCCAATTCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
20 1 0.02
21 37 0.88
22 3 0.07
23 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.23
Consensus pattern (20 bp):
TTCAAGAGGCCCTTCCACCG
Found at i:8936 original size:42 final size:41
Alignment explanation
Indices: 8817--8939 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 41
8807 GCTCGATTCA
* * *
8817 CCTGTCATCTTTCAAGAGG-CCTCTCCTATCGTTAAAGAGGCC
1 CCTGTCATCCTTCAAGAGGCCCT-TCC-ACCGTTCAAGAGGCC
* *
8859 CCTATCATCCTTCAAGAGGCCCCTCTCACCGTTCAAGAGGCC
1 CCTGTCATCCTTCAAGAGGCCCTTC-CACCGTTCAAGAGGCC
* *
8901 CCTGTCATCGTTCAAGAGGTCCCTTCCACCATTCAAGAG
1 CCTGTCATCCTTCAAGAGG-CCCTTCCACCGTTCAAGAG
8940 CCCAATTCAT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
42 61 0.88
43 8 0.12
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (41 bp):
CCTGTCATCCTTCAAGAGGCCCTTCCACCGTTCAAGAGGCC
Found at i:10461 original size:20 final size:20
Alignment explanation
Indices: 10436--10495 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
10426 ACACTATCGT
*
10436 AACGCGAAAATCAAATTCGC
1 AACGCGAAAGTCAAATTCGC
* *
10456 AACGCGAAAGTTAAAATCGC
1 AACGCGAAAGTCAAATTCGC
10476 AACGCGAAAGTCAAATTCGC
1 AACGCGAAAGTCAAATTCGC
10496 GTTGCGATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.15
Consensus pattern (20 bp):
AACGCGAAAGTCAAATTCGC
Found at i:10514 original size:20 final size:20
Alignment explanation
Indices: 10491--10579 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
10481 GAAAGTCAAA
10491 TTCGCGTTGCGATTTTGATT
1 TTCGCGTTGCGATTTTGATT
*
10511 TTCGCGTTGCAATTTTGATT
1 TTCGCGTTGCGATTTTGATT
* *
10531 TTCGCGTTGCGATTTTAACT
1 TTCGCGTTGCGATTTTGATT
*
10551 TTCGCGTTGCGAATTTGATT
1 TTCGCGTTGCGATTTTGATT
10571 TTCGCGTTG
1 TTCGCGTTG
10580 TAAATTCAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.12, C:0.17, G:0.24, T:0.47
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTGATT
Found at i:10747 original size:20 final size:20
Alignment explanation
Indices: 10722--10836 Score: 158
Period size: 20 Copynumber: 5.8 Consensus size: 20
10712 CAGAAGGTAC
*
10722 ACTTTCGCGTTACGATTTTG
1 ACTTTCGCGTTGCGATTTTG
10742 ACTTTCGCGTTGCGATTTTG
1 ACTTTCGCGTTGCGATTTTG
* *
10762 ATTTTCGCGTTGTGATTTTG
1 ACTTTCGCGTTGCGATTTTG
*
10782 ACTTTCACGTTGCGATTTTG
1 ACTTTCGCGTTGCGATTTTG
* * *
10802 TCTTTCGTGTTGCGAATTTG
1 ACTTTCGCGTTGCGATTTTG
*
10822 ATTTTCGCGTTGCGA
1 ACTTTCGCGTTGCGA
10837 AAGTGTACCT
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.47
Consensus pattern (20 bp):
ACTTTCGCGTTGCGATTTTG
Found at i:11153 original size:18 final size:18
Alignment explanation
Indices: 11130--11165 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11120 AAGTCGGTTG
*
11130 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
11148 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
11166 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:13461 original size:24 final size:24
Alignment explanation
Indices: 13434--13493 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
13424 CTGAAACATC
*
13434 ATCAAAATTTGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* *
13458 ATCAAAGTTCGTGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
13482 ATCAAATTTCGA
1 ATCAAAATTCGA
13494 ATACTGACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:13501 original size:24 final size:24
Alignment explanation
Indices: 13450--13501 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
13440 ATTTGAGTAT
** *
13450 TGACCAAGATCAAAGTTCGTGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
13474 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
13498 TGAC
1 TGAC
13502 TAGTACTCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:13634 original size:12 final size:12
Alignment explanation
Indices: 13613--13647 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
13603 GGTTGTGGGT
*
13613 TTTGAGATTGTG
1 TTTGATATTGTG
13625 TTTGATATTGTG
1 TTTGATATTGTG
*
13637 TTTGGTATTGT
1 TTTGATATTGT
13648 AAATGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:14475 original size:20 final size:20
Alignment explanation
Indices: 14451--14519 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
14441 TTAAAATTCA
14451 TGTTGCGAATTCGAAAATCG
1 TGTTGCGAATTCGAAAATCG
* *
14471 AGTTGCGAAATC-AAAATTCG
1 TGTTGCGAATTCGAAAA-TCG
* * *
14491 TGTTGCGATTTAGAAAATCT
1 TGTTGCGAATTCGAAAATCG
14511 TGTTGCGAA
1 TGTTGCGAA
14520 AAGGAAACTT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 4 0.10
20 31 0.79
21 4 0.10
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (20 bp):
TGTTGCGAATTCGAAAATCG
Found at i:14487 original size:40 final size:40
Alignment explanation
Indices: 14432--14520 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
14422 AATAAAAGTT
* * *
14432 GTTGCAAAATTAAAATTCATGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATCAAAATTCATGTTGCGAATTAGAAAATCGA
* * **
14472 GTTGCGAAATCAAAATTCGTGTTGCGATTTAGAAAATCTT
1 GTTGCGAAATCAAAATTCATGTTGCGAATTAGAAAATCGA
14512 GTTGCGAAA
1 GTTGCGAAA
14521 AGGAAACTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (40 bp):
GTTGCGAAATCAAAATTCATGTTGCGAATTAGAAAATCGA
Found at i:15625 original size:18 final size:18
Alignment explanation
Indices: 15602--15636 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
15592 AATCATATAT
*
15602 TTTTGCTGATTTGGTTGA
1 TTTTGCTCATTTGGTTGA
15620 TTTTGCTCATTTGGTTG
1 TTTTGCTCATTTGGTTG
15637 GCGTGGAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.09, G:0.26, T:0.57
Consensus pattern (18 bp):
TTTTGCTCATTTGGTTGA
Found at i:15913 original size:3 final size:3
Alignment explanation
Indices: 15905--15941 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
15895 CTGAAAAGAA
15905 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
15942 TCGGATGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19452 original size:24 final size:26
Alignment explanation
Indices: 19425--19473 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
19415 CACATCTCCA
19425 TTGGTGTC-TT-AAGCTCTATTGCAG
1 TTGGTGTCTTTGAAGCTCTATTGCAG
*
19449 TTGGTGTCTTTGGAGCTCTATTGCA
1 TTGGTGTCTTTGAAGCTCTATTGCA
19474 TCCCTCAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 2 0.09
26 12 0.55
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (26 bp):
TTGGTGTCTTTGAAGCTCTATTGCAG
Found at i:22364 original size:36 final size:36
Alignment explanation
Indices: 22317--22390 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
22307 GAGATTTGGA
22317 TAAATAATTAGACAAAAGCTTTGTCTAAAATACTTG
1 TAAATAATTAGACAAAAGCTTTGTCTAAAATACTTG
22353 TAAATAATTAGACAAAAGCTTTGTCTAAAATACTTG
1 TAAATAATTAGACAAAAGCTTTGTCTAAAATACTTG
22389 TA
1 TA
22391 CTTTATTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (36 bp):
TAAATAATTAGACAAAAGCTTTGTCTAAAATACTTG
Found at i:22412 original size:2 final size:2
Alignment explanation
Indices: 22405--22435 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22395 ATTTGACGAC
22405 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 T
22436 TTTAATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28443 original size:15 final size:15
Alignment explanation
Indices: 28423--28454 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28413 CGTAGCATAA
28423 TCAAATTCACCCTAT
1 TCAAATTCACCCTAT
28438 TCAAATTCACCCTAT
1 TCAAATTCACCCTAT
28453 TC
1 TC
28455 GATTCAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (15 bp):
TCAAATTCACCCTAT
Found at i:29589 original size:6 final size:6
Alignment explanation
Indices: 29578--29606 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29568 AGTAACCCAT
29578 ACTTTA ACTTTA ACTTTA ACTTTA ACTTT
1 ACTTTA ACTTTA ACTTTA ACTTTA ACTTT
29607 GTTTTCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (6 bp):
ACTTTA
Found at i:31903 original size:21 final size:22
Alignment explanation
Indices: 31870--31914 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
31860 TAAGGATTTT
31870 TATTTTTATATTATT-AAAATA
1 TATTTTTATATTATTAAAAATA
31891 TATTCTTTA-ATTATTAAAAATA
1 TATT-TTTATATTATTAAAAATA
31913 TA
1 TA
31915 AAAATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTTATATTATTAAAAATA
Found at i:31932 original size:42 final size:43
Alignment explanation
Indices: 31877--31985 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 43
31867 TTTTATTTTT
*
31877 ATATTAT-TAAAATATATT-CTTTAATTATTAAAAATATAA-AA
1 ATATTATAT-AAATATATTACTTTAATAATTAAAAATATAATAA
* *
31918 ATTATTATATAAATATATTATTTTAATAATTTAAAATATAATAA
1 A-TATTATATAAATATATTACTTTAATAATTAAAAATATAATAA
* *
31962 ATAAT-TATAAATATATTATTTTAA
1 ATATTATATAAATATATTACTTTAA
31986 AATATTAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
41 1 0.02
42 34 0.57
43 22 0.37
44 3 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (43 bp):
ATATTATATAAATATATTACTTTAATAATTAAAAATATAATAA
Found at i:31995 original size:21 final size:22
Alignment explanation
Indices: 31924--31999 Score: 79
Period size: 21 Copynumber: 3.6 Consensus size: 22
31914 AAAAATTATT
31924 ATATAAATATATTATTTTAATA
1 ATATAAATATATTATTTTAATA
* * *
31946 ATTTAAA-ATA-TA-ATAAATA
1 ATATAAATATATTATTTTAATA
31965 ATTATAAATATATTATTTTAA-A
1 A-TATAAATATATTATTTTAATA
*
31987 ATATTAATATATT
1 ATATAAATATATT
32000 CGAGTTAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 6 0.14
20 7 0.16
21 17 0.40
22 10 0.23
23 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATAAATATATTATTTTAATA
Found at i:32269 original size:16 final size:16
Alignment explanation
Indices: 32248--32279 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
32238 AATAAATAAG
32248 CGAACATAAACGAACA
1 CGAACATAAACGAACA
32264 CGAACATAAACGAACA
1 CGAACATAAACGAACA
32280 ATTTTTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:32365 original size:16 final size:16
Alignment explanation
Indices: 32344--32388 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
32334 TAATAAATAA
32344 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
32360 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
32376 ACGAACATAAACG
1 ACGAACATAAACG
32389 TTGGAGACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.56, C:0.22, G:0.13, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:32863 original size:65 final size:63
Alignment explanation
Indices: 32744--32953 Score: 214
Period size: 65 Copynumber: 3.3 Consensus size: 63
32734 TTTTTCAGAG
* *
32744 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGA--AT-TATATTG-AACATCGAATG
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCA-C-TGAGGATCT-T-TTGAAACATCGAATG
32805 CATT
60 CATT
*
32809 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTGAGGATCTTT-TG-AAACATCGAATGCAT
32873 T
63 T
* * ** * *
32874 TGATGCATCGATGCACCAGCCATGCATCGATGCACTTTGGCTCTTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTGAGGATCTTTTGAAACATCGAATGCATT
32938 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
32954 TCTTAGTGCA
Statistics
Matches: 127, Mismatches: 10, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
62 4 0.03
63 5 0.04
64 49 0.39
65 64 0.50
66 5 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTGAGGATCTTTTGAAACATCGAATGCATT
Found at i:32953 original size:17 final size:19
Alignment explanation
Indices: 32925--32973 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
32915 TCTTTTGAAA
32925 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
32943 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
32962 CACCGATGCACT
1 CATCGATGCACT
32974 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:52029 original size:10 final size:9
Alignment explanation
Indices: 51942--52028 Score: 108
Period size: 9 Copynumber: 9.6 Consensus size: 9
51932 CATGAAGATG
51942 AAAAATGAA
1 AAAAATGAA
51951 AAAAATG--
1 AAAAATGAA
51958 AAAAATG-A
1 AAAAATGAA
*
51966 AAAAATAAAA
1 AAAAAT-GAA
51976 AAAAATGAA
1 AAAAATGAA
51985 AAAAATGAAA
1 AAAAATG-AA
51995 AAAAATGAAAA
1 AAAAATG--AA
52006 AAAAATGAA
1 AAAAATGAA
52015 AAAAATGAA
1 AAAAATGAA
52024 AAAAA
1 AAAAA
52029 ACAAAACAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
7 7 0.10
8 6 0.08
9 32 0.45
10 16 0.23
11 10 0.14
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.10
Consensus pattern (9 bp):
AAAAATGAA
Found at i:52029 original size:30 final size:29
Alignment explanation
Indices: 51949--52028 Score: 114
Period size: 30 Copynumber: 2.9 Consensus size: 29
51939 ATGAAAAATG
51949 AAAAAAATG--AAAAATG-AAAAAAT-AA
1 AAAAAAATGAAAAAAATGAAAAAAATAAA
*
51974 AAAAAAATGAAAAAAATGAAAAAAAATGAA
1 AAAAAAATGAAAAAAATG-AAAAAAATAAA
52004 AAAAAAATGAAAAAAATGAAAAAAA
1 AAAAAAATGAAAAAAATGAAAAAAA
52029 ACAAAACAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
25 9 0.18
27 7 0.14
29 14 0.28
30 20 0.40
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.10
Consensus pattern (29 bp):
AAAAAAATGAAAAAAATGAAAAAAATAAA
Found at i:52049 original size:10 final size:10
Alignment explanation
Indices: 51965--52040 Score: 75
Period size: 10 Copynumber: 7.6 Consensus size: 10
51955 ATGAAAAATG
51965 AAAAAATAAA
1 AAAAAATAAA
*
51975 AAAAAAT-GA
1 AAAAAATAAA
*
51984 AAAAAATGAA
1 AAAAAATAAA
51994 AAAAAATGAAA
1 AAAAAAT-AAA
*
52005 AAAAAAT-GA
1 AAAAAATAAA
*
52014 AAAAAATGAA
1 AAAAAATAAA
*
52024 AAAAAACAAA
1 AAAAAATAAA
52034 ACAAAAA
1 A-AAAAA
52041 CAAATAAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
9 16 0.29
10 25 0.45
11 14 0.25
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:53756 original size:160 final size:159
Alignment explanation
Indices: 53378--53989 Score: 950
Period size: 160 Copynumber: 3.8 Consensus size: 159
53368 GCAACAGAAG
*
53378 ATTGTTTGAGTTCTACTCCCTGAAGAAAATAG-G-GCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTCTACTCCCTGAAG-AAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
* *
53441 TCTACTCCCTGAA-AAATAG-G-GTGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTG
65 TCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTC-TACTCCCTG
53503 AAGAAATAGAGAGC-GAGCCCGTAGGAAGATT
129 AAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
*
53534 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
*
53599 TCTTACTCCCTGAAGAAAAATAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTG
65 TC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTG
53664 AAGAAATAGAGAGCGGACCCGTAGGAAGATT
129 AAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
53695 ATTGTTCGAGCTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
53760 CTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTTGAGTTCTACTCCCTGA
66 C-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGA
53825 AGAAATAGAGAGCGGACCCGTAGGAAGATT
130 AGAAATAGAGAGCGGACCCGTAGGAAGATT
* * ** * *
53855 ATTATTCGAGTTCTACTCCCTGAAGGAGGAGAGAGCAGACCCGTAGGAAGATGATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
* ** *
53920 CTACTCCCTGAAGAAAAGAGGGAGC-GAGCCCGTAGGAAGAAGAATGTTCGAGTTCTACTCCCTG
66 CTACTCCCTGAAGAAAA-AGAGAGCGGA-CCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTG
53984 AAGAAA
129 AAGAAA
53990 GAGGAAGTGA
Statistics
Matches: 425, Mismatches: 21, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
156 17 0.04
157 13 0.03
158 32 0.08
159 29 0.07
160 251 0.59
161 50 0.12
162 33 0.08
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (159 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
CTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAA
GAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:54015 original size:53 final size:53
Alignment explanation
Indices: 53378--53989 Score: 934
Period size: 54 Copynumber: 11.5 Consensus size: 53
53368 GCAACAGAAG
*
53378 ATTGTTTGAGTTCTACTCCCTGAAGAAAATAG-G-GCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAG-AAATAGAGAGCGGACCCGTAGGAAGATT
*
53430 ATTGTTCGAGTTCTACTCCCTGAA-AAATAG-G-GTGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
53480 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
*
53534 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
53588 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAATAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
53642 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
53695 ATTGTTCGAGCTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
53748 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
53802 ATTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * ** * *
53855 ATTATTCGAGTTCTACTCCCTGAAGGAGGAGAGAGCAGACCCGTAGGAAGATG
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
**
53908 ATTGTTCGAGTTCTACTCCCTGAAGAAA-AGAGGGAGC-GAGCCCGTAGGAAGAAG
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGA--GAGCGGA-CCCGTAGGAAGATT
*
53962 AATGTTCGAGTTCTACTCCCTGAAGAAA
1 ATTGTTCGAGTTCTACTCCCTGAAGAAA
53990 GAGGAAGTGA
Statistics
Matches: 526, Mismatches: 24, Indels: 18
0.93 0.04 0.03
Matches are distributed among these distances:
50 38 0.07
51 11 0.02
52 32 0.06
53 217 0.41
54 226 0.43
55 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:57104 original size:20 final size:20
Alignment explanation
Indices: 57079--57118 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
57069 TTTTGGTGCA
*
57079 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
*
57099 GAGGGAACCGATTCCCCCTT
1 GAGGGAACCGATCCCCCCTT
57119 TGAAGGGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:63443 original size:2 final size:2
Alignment explanation
Indices: 63436--63470 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
63426 CAGCTTAAGC
*
63436 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63471 TTAATCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:64052 original size:65 final size:64
Alignment explanation
Indices: 63933--64139 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 64
63923 TTTTTCAAAG
* * * *
63933 TGATGCACCGATGCACCAATCCATGCATCAATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCACCAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
63995 ATT
62 ATT
* *
63998 TCATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
64061 TT
63 TT
* * * * *
64063 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
64127 TGATGCATCGATG
1 TGATGCATCGATG
64140 GTGAACCGAT
Statistics
Matches: 121, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 44 0.36
65 69 0.57
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:68938 original size:14 final size:14
Alignment explanation
Indices: 68921--68994 Score: 56
Period size: 14 Copynumber: 5.9 Consensus size: 14
68911 ATTGGGTTAA
68921 ACATAAATGAACGC
1 ACATAAATGAACGC
68935 ACATAAATG-A---
1 ACATAAATGAACGC
*
68945 ACATAATTGAACGC
1 ACATAAATGAACGC
*
68959 ACAT--A--AACGA
1 ACATAAATGAACGC
*
68969 ACATAACTGAACGC
1 ACATAAATGAACGC
*
68983 ACATAAACGAAC
1 ACATAAATGAAC
68995 ATAACCGAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
10 16 0.36
11 1 0.02
13 1 0.02
14 27 0.60
ACGTcount: A:0.51, C:0.22, G:0.12, T:0.15
Consensus pattern (14 bp):
ACATAAATGAACGC
Found at i:68999 original size:24 final size:24
Alignment explanation
Indices: 68920--69005 Score: 136
Period size: 24 Copynumber: 3.6 Consensus size: 24
68910 TATTGGGTTA
* *
68920 AACATAAATGAACGCACATAAATG
1 AACATAACTGAACGCACATAAACG
*
68944 AACATAATTGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
68968 AACATAACTGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
*
68992 AACATAACCGAACG
1 AACATAACTGAACG
69006 TTCATGAACG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.51, C:0.22, G:0.13, T:0.14
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:71219 original size:12 final size:12
Alignment explanation
Indices: 71200--71232 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
71190 TAAACATTAA
71200 AGATTATAATTC
1 AGATTATAATTC
*
71212 ATATTATAATTC
1 AGATTATAATTC
71224 AGATTATAA
1 AGATTATAA
71233 GCCTTTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (12 bp):
AGATTATAATTC
Found at i:75320 original size:21 final size:21
Alignment explanation
Indices: 75296--75354 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
75286 ATTATTCAAT
* *
75296 AAACTTGACATCTATAACAAC
1 AAACTTGAAATCCATAACAAC
75317 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
75338 CAACTTGAACTCCATAA
1 AAACTTGAAATCCATAA
75355 TAATAAACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.47, C:0.25, G:0.05, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Done.