Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003018.1 Hibiscus syriacus cultivar Beakdansim tig00006265_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: 175702
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5959 original size:53 final size:54
Alignment explanation
Indices: 5878--5988 Score: 206
Period size: 53 Copynumber: 2.1 Consensus size: 54
5868 TAATGAAACG
*
5878 AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAATATAATTCATAA
1 AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAAATAATTCATAA
5932 AAATAT-GGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAAATAATTCATAA
1 AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAAATAATTCATAA
5985 AAAT
1 AAAT
5989 TGAAACTTTC
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
53 50 0.89
54 6 0.11
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.32
Consensus pattern (54 bp):
AAATATGGGTAATTGTAATTTGTAAGAATCTCAATGCGAGAAAATAATTCATAA
Found at i:6716 original size:20 final size:20
Alignment explanation
Indices: 6693--6766 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
6683 GAATATGTAA
* *
6693 ATCGCAATGCGATTATAACT
1 ATCGCAATGCGATTCTGACT
*
6713 ATCGCAATACGATTCTGACT
1 ATCGCAATGCGATTCTGACT
*
6733 ATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATTCTGACT
*
6753 GTCGCAATGCGATT
1 ATCGCAATGCGATT
6767 TTCAAATTCG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGATTCTGACT
Found at i:6780 original size:40 final size:39
Alignment explanation
Indices: 6609--6779 Score: 128
Period size: 40 Copynumber: 4.2 Consensus size: 39
6599 CAGTTTCCAG
* * *
6609 ATTCGCAATGCGATTCTGACTATCACATTGCGATTTTTCAA
1 ATTCGCAATGCGATTCTGACTATCGCAATACGA-TTTT-AA
** * *
6650 ATTCGCGTTGCGATTTTCCGACTATCGCAATACGAATATGTAA
1 ATTCGCAATGCGA--TTCTGACTATCGCAATACG-AT-TTTAA
* * * *
6693 A-TCGCAATGCGATTATAACTATCGCAATACGATTCTGA
1 ATTCGCAATGCGATTCTGACTATCGCAATACGATTTTAA
* * * *
6731 CTATCGCAACGCGATTCTGACTGTCGCAATGCGATTTTCAA
1 AT-TCGCAATGCGATTCTGACTATCGCAATACGATTTT-AA
6772 ATTCGCAA
1 ATTCGCAA
6780 CAGGTTTTAG
Statistics
Matches: 100, Mismatches: 23, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
38 3 0.03
39 2 0.02
40 51 0.51
41 13 0.13
42 9 0.09
43 19 0.19
44 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (39 bp):
ATTCGCAATGCGATTCTGACTATCGCAATACGATTTTAA
Found at i:7630 original size:24 final size:24
Alignment explanation
Indices: 7573--7632 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
7563 TAGTCGGTAT
7573 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
7597 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
7621 TCGAATTTTGAT
1 TCGAAATTTGAT
7633 GATGTTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:10274 original size:34 final size:34
Alignment explanation
Indices: 10231--10326 Score: 165
Period size: 34 Copynumber: 2.8 Consensus size: 34
10221 TCATTTGAAT
10231 ATCGCAACGCGAATTTGATTATCACAACTCAAAA
1 ATCGCAACGCGAATTTGATTATCACAACTCAAAA
10265 ATCGCAACGCGAATTTGATTATCACAACTCAAAA
1 ATCGCAACGCGAATTTGATTATCACAACTCAAAA
* * *
10299 ATCGCAACGCAAATTTGACTATCGCAAC
1 ATCGCAACGCGAATTTGATTATCACAAC
10327 ACGAATATGA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGATTATCACAACTCAAAA
Found at i:10324 original size:20 final size:20
Alignment explanation
Indices: 10299--10559 Score: 220
Period size: 20 Copynumber: 14.0 Consensus size: 20
10289 CAACTCAAAA
*
10299 ATCGCAACGCAAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
10319 ATCGCAACACGAATATGACT
1 ATCGCAACGCGAATTTGACT
* *
10339 ATCACAACGC-AA----A-A
1 ATCGCAACGCGAATTTGACT
*
10353 ATCGCAACGCGAATTTGTCT
1 ATCGCAACGCGAATTTGACT
10373 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
10393 ATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACT
* *
10413 ATCGCAATG-GCTATTTGACT
1 ATCGCAACGCG-AATTTGACT
*
10433 ATCGCAACGAGAA----A--
1 ATCGCAACGCGAATTTGACT
10447 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
10467 ATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACT
* *
10487 ATCGCAACGAGTATTTGACT
1 ATCGCAACGCGAATTTGACT
*
10507 ATCGCAACGAGAA----A--
1 ATCGCAACGCGAATTTGACT
* * *
10521 ATCGCAAAGCGTATTAGACT
1 ATCGCAACGCGAATTTGACT
10541 ATCGCAACGCGAA-TTGACT
1 ATCGCAACGCGAATTTGACT
10560 TTCGTGTTGC
Statistics
Matches: 193, Mismatches: 28, Indels: 41
0.74 0.11 0.16
Matches are distributed among these distances:
14 31 0.16
15 3 0.02
16 2 0.01
18 2 0.01
19 8 0.04
20 146 0.76
21 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:10332 original size:54 final size:54
Alignment explanation
Indices: 10265--10402 Score: 213
Period size: 54 Copynumber: 2.6 Consensus size: 54
10255 CAACTCAAAA
* *
10265 ATCGCAACGCGAATTTGATTATCACAACTCAAAAATCGCAACGCAAATTTGACT
1 ATCGCAACGCGAATTTGACTATCACAACGCAAAAATCGCAACGCAAATTTGACT
* * * *
10319 ATCGCAACACGAATATGACTATCACAACGCAAAAATCGCAACGCGAATTTGTCT
1 ATCGCAACGCGAATTTGACTATCACAACGCAAAAATCGCAACGCAAATTTGACT
*
10373 ATCGCAACGCGAATTTGACTATCGCAACGC
1 ATCGCAACGCGAATTTGACTATCACAACGC
10403 GAATTTGATT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCACAACGCAAAAATCGCAACGCAAATTTGACT
Found at i:10451 original size:74 final size:74
Alignment explanation
Indices: 10373--10555 Score: 314
Period size: 74 Copynumber: 2.5 Consensus size: 74
10363 GAATTTGTCT
*
10373 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAATG-GCTATTTGACTATCG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGAG-TATTTGACTATCG
10437 CAACGAGAAA
65 CAACGAGAAA
10447 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGAGTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGAGTATTTGACTATCGC
10512 AACGAGAAA
66 AACGAGAAA
* * *
10521 ATCGCAAAGCGTATTAGACTATCGCAACGCGAATT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATT
10556 GACTTTCGTG
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
74 103 0.99
75 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGAGTATTTGACTATCGC
AACGAGAAA
Found at i:10525 original size:54 final size:54
Alignment explanation
Indices: 10265--10559 Score: 199
Period size: 54 Copynumber: 5.4 Consensus size: 54
10255 CAACTCAAAA
* * * * *
10265 ATCGCAACGCGAATTTGATTATCACAACTCA-AAAATCGCAACGCAAATTTGACT
1 ATCGCAACGAGAATTTGACTATCGCAAC-GAGAAAATCGCAACGCGAATTTGACT
* * *
10319 ATCGCAAC-ACGAATATGACTATCACAACGCA-AAAATCGCAACGCGAATTTGTCT
1 ATCGCAACGA-GAATTTGACTATCGCAACG-AGAAAATCGCAACGCGAATTTGACT
* * * *
10373 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAATG-GCTATTTGACT
1 ATCGCAACGAGAATTTGACTATCGCAACGAGAA----A--ATCGCAACGCG-AATTTGACT
* * * *** ** *
10433 ATCGCAACGAGAAAATCG-C-AACGCGAATTTGACTATCGCAACGCGAATTTGATT
1 ATCGCAACGAG-AATTTGACTATCGC-AACGAGAAAATCGCAACGCGAATTTGACT
* * * *
10487 ATCGCAACGAGTATTTGACTATCGCAACGAGAAAATCGCAAAGCGTATTAGACT
1 ATCGCAACGAGAATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACT
*
10541 ATCGCAACGCGAA-TTGACT
1 ATCGCAACGAGAATTTGACT
10560 TTCGTGTTGC
Statistics
Matches: 185, Mismatches: 40, Indels: 33
0.72 0.16 0.13
Matches are distributed among these distances:
53 9 0.05
54 131 0.71
55 5 0.03
58 1 0.01
59 5 0.03
60 30 0.16
61 4 0.02
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (54 bp):
ATCGCAACGAGAATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACT
Found at i:10609 original size:20 final size:20
Alignment explanation
Indices: 10554--10611 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
10544 GCAACGCGAA
* *
10554 TTGACTTTCGTGTTGCGATT
1 TTGACTTTAGCGTTGCGATT
* * *
10574 TTGTCTTTCGCATTGCGATT
1 TTGACTTTAGCGTTGCGATT
*
10594 TTGAGTTTAGCGTTGCGA
1 TTGACTTTAGCGTTGCGA
10612 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (20 bp):
TTGACTTTAGCGTTGCGATT
Found at i:10770 original size:14 final size:14
Alignment explanation
Indices: 10710--10771 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
10700 CACAAATAAG
*
10710 AATTATTTACACATC
1 AATT-TTTACAAATC
**
10725 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
10740 AACTTTTACAAATC
1 AATTTTTACAAATC
*
10754 AATTTTTATAAATC
1 AATTTTTACAAATC
10768 AATT
1 AATT
10772 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:12794 original size:20 final size:20
Alignment explanation
Indices: 12769--12824 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
12759 TTGCAACACG
12769 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
12789 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
12809 AATGACTATCGCAACG
1 AATGACTATCGCAACG
12825 AGAGAATCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:13064 original size:18 final size:18
Alignment explanation
Indices: 13041--13091 Score: 102
Period size: 18 Copynumber: 2.8 Consensus size: 18
13031 ATTTACTAAG
13041 TAATCTAAGTGAAATGGT
1 TAATCTAAGTGAAATGGT
13059 TAATCTAAGTGAAATGGT
1 TAATCTAAGTGAAATGGT
13077 TAATCTAAGTGAAAT
1 TAATCTAAGTGAAAT
13092 TACGAGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (18 bp):
TAATCTAAGTGAAATGGT
Found at i:14829 original size:20 final size:20
Alignment explanation
Indices: 14806--14861 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
14796 TCTGAAACTT
14806 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
* *
14826 AAAATCACAACACAAAAATG
1 AAAATCGCAACACGAAAATG
** *
14846 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
14862 TTTGACTATC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:15288 original size:22 final size:22
Alignment explanation
Indices: 15257--15313 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
15247 GATGGAGATA
15257 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
15279 GACTGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
15301 GACGGATGTCGCC
1 GACGGATTTCGCC
15314 TTAGAGAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.19, G:0.42, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:15502 original size:20 final size:20
Alignment explanation
Indices: 15477--15529 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
15467 ACGCTTTGAA
15477 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
15497 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
15517 AATCACGTTGCGA
1 AATCGCGTTGCGA
15530 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:19380 original size:31 final size:33
Alignment explanation
Indices: 19332--19410 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
19322 TTTAAATAGT
*
19332 TATTATATTTTATATT-AAT-ATAATTATATAAA
1 TATTAT-TTTTTTATTAAATAATAATTATATAAA
* *
19364 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATAATTATATAAA
*
19398 TATTATTTATTTA
1 TATTATTTTTTTA
19411 AATTTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.20
32 6 0.15
33 3 0.08
34 23 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATAATTATATAAA
Found at i:19402 original size:34 final size:31
Alignment explanation
Indices: 19322--19433 Score: 88
Period size: 34 Copynumber: 3.6 Consensus size: 31
19312 CAGTTATTTT
* * *
19322 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
19354 ATTATATAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
* *
19388 TTTATATAATTATTATTTATTTA--AATTTA
1 TTTATATAATTATTATTTTTTTATTAATATA
*
19417 TTAAT-TAATTATT-TTTT
1 TTTATATAATTATTATTTT
19434 GTGCTAATTA
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
27 3 0.05
28 8 0.12
29 6 0.09
30 3 0.05
31 8 0.12
32 12 0.18
33 3 0.05
34 23 0.35
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:21240 original size:21 final size:21
Alignment explanation
Indices: 21214--21286 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
21204 TATGTCATCT
*
21214 CCGCAGGGTTACATTTCTAGC
1 CCGCAGGGTTACATTCCTAGC
21235 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
21256 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
21277 CCGCAGGGTT
1 CCGCAGGGTT
21287 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.23
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:21842 original size:34 final size:34
Alignment explanation
Indices: 21799--21905 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
21789 ATAAATGTTT
**
21799 TTAAAATACAAATTATAGTATTTGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
* * *
21833 TTAAAATACAAATAATATTATTCAAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
* *
21867 TTAAAATATAAATTATAGTATTCAAAATTTAACA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
21901 TTAAA
1 TTAAA
21906 TTCAAGTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCAAAATTTAAAA
Found at i:22032 original size:14 final size:14
Alignment explanation
Indices: 22013--22042 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22003 TTTTATCATT
*
22013 AACATATATATTAA
1 AACATATACATTAA
22027 AACATATACATTAA
1 AACATATACATTAA
22041 AA
1 AA
22043 TCAACTTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:31232 original size:2 final size:2
Alignment explanation
Indices: 31225--31283 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
31215 ATTCAAGAGC
31225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31267 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
31284 CAAGGTCAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33105 original size:22 final size:22
Alignment explanation
Indices: 33051--33098 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
33041 GATTTATGTA
* *
33051 GAGATAGTTTTGTAGGGATATT
1 GAGATAGTTTTGAAGGCATATT
33073 GAGATAGTTTTGAAGGCATATT
1 GAGATAGTTTTGAAGGCATATT
33095 GAGA
1 GAGA
33099 GTTTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.35
Consensus pattern (22 bp):
GAGATAGTTTTGAAGGCATATT
Found at i:36495 original size:84 final size:83
Alignment explanation
Indices: 36289--37742 Score: 1619
Period size: 84 Copynumber: 17.6 Consensus size: 83
36279 GAGCAGACAA
* * * * * * * *
36289 TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATAATGTGCCCTCGGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCT-TGAGCTGAG
* * * **
36354 TGGAATCGAACTCGGGGGTC
64 CGTAGTCGAACTCGAAGGTC
* * *
36374 --TT-TT-GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGC
*
36435 GTAGTCGAACTCAAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * *
36454 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGC
36519 GTAGTCGAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
*
36538 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGC
*
36603 GTAGTCGAACTCAAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * **
36622 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGC
36687 GTAGTCGAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * *
36706 TTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAG
** * **
36771 TATAATCGAACTCGGGGGTC
64 CGTAGTCGAACTCGAAGGTC
* * * *
36791 ---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCC----GTTGAGCG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAGCTGAGCG
* *
36848 TAGTAGAACTCAAAGGTC
66 TAGTCGAACTCGAAGGTC
* * * **
36866 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGC
*
36931 GTAGTCAAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
* *
36950 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAG
* * **
37015 TGTAATCGAACTCGGGGGTC
64 CGTAGTCGAACTCGAAGGTC
** *
37035 ---T-TTGGCAGATGGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGC
*
37096 GTAGTCGAACTCAAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * ** *
37115 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGAAACTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTG-AGCTGAGC
37180 GTAGTCGAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
* *
37199 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAG
* * **
37264 TGTAATCGAACTCGGGGGTC
64 CGTAGTCGAACTCGAAGGTC
* *
37284 ---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGC
*
37345 GTAGTCGAACTCAAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * **
37364 -TTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGC
37428 GTAGTCGAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * *
37447 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATAATGTGCCCTCGAAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAG
* * * **
37512 TGTAATCAAACTCGGGGGTC
64 CGTAGTCGAACTCGAAGGTC
* *
37532 ---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGC
* *
37593 GTAGTCAAACTCAAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * **
37612 TTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGC
37677 GTAGTCGAACTCGAAGGTC
65 GTAGTCGAACTCGAAGGTC
* * * * * *
37696 -TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCCGCAAATGAT
1 TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
37743 TTGTTTAAAA
Statistics
Matches: 1152, Mismatches: 175, Indels: 86
0.82 0.12 0.06
Matches are distributed among these distances:
75 18 0.02
78 1 0.00
79 40 0.03
80 98 0.09
81 215 0.19
82 7 0.01
83 122 0.11
84 547 0.47
85 104 0.09
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (83 bp):
TTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAGCTGAGCG
TAGTCGAACTCGAAGGTC
Found at i:37223 original size:249 final size:249
Alignment explanation
Indices: 36298--37742 Score: 2286
Period size: 249 Copynumber: 5.8 Consensus size: 249
36288 ATTTTGTTGA
* * * * * * * * *
36298 CAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATAATGTGCCCTCGGAGCTGAGTGGAATCGA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGT-TGAGCTGAGCGTAGTCGA
*** * * * * * * **
36363 ACTCGGGGGTC--TT-TT-GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCG
65 ACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCC-
* * * *
36424 TT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
129 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTT
* * * * * * **
36488 GTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
194 ATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGG
* *
36547 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
36612 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
66 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
*
36677 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTAT
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
*
36742 GCTGCAAATGATGTGCCCTCGAAGCTGAGTATAATCGAACTCGGGGGTCTTTGG
196 GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* *
36796 CAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCG-T----TGAGCGTAGTAGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
36856 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
66 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
*
36921 GGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
36986 GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
196 GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
*
37040 CAGATGGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
37105 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
66 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
* *
37170 GAAACTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
37235 GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
196 GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
37289 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
37354 CTCAAAGGTC-TTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
66 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
37418 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* * *
37483 GCTACAAATAATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGG
196 GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
*
37537 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCAAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
37602 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
66 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
* * * *
37667 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTAT
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
*
37731 GCCGCAAATGAT
196 GCTGCAAATGAT
37743 TTGTTTAAAA
Statistics
Matches: 1121, Mismatches: 63, Indels: 25
0.93 0.05 0.02
Matches are distributed among these distances:
244 237 0.21
245 1 0.00
248 300 0.27
249 441 0.39
250 2 0.00
251 5 0.00
252 109 0.10
253 26 0.02
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.29
Consensus pattern (249 bp):
CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
Found at i:37644 original size:497 final size:497
Alignment explanation
Indices: 36298--37742 Score: 2291
Period size: 497 Copynumber: 2.9 Consensus size: 497
36288 ATTTTGTTGA
* * * * * * * * *
36298 CAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATAATGTGCCCTCGGAGCTGAGTGGAATCGA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGT-TGAGCTGAGCGTAGTCGA
*** * * * * * * **
36363 ACTCGGGGGTC-TT-TT-GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGT
65 ACTCAAAGGTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCC-T
* * * * *
36425 T-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
129 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTA
* * * * * **
36489 TGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATA
194 TGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAGATA
* *
36553 ACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAA
255 GCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAA
36618 GGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCT
320 GGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCT
*
36683 GAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCA
385 GAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
36748 AATGATGTGCCCTCGAAGCTGAGTATAATCGAACTCGGGGGTCTTTGG
450 AATGATGTGCCCTCGAAGCTGAGTATAATCGAACTCGGGGGTCTTTGG
* *
36796 CAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCG-T----TGAGCGTAGTAGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
36856 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
66 CTCAAAGGTC-TTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTT
*
36921 GGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
*
36986 GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATGGCCCT
195 GCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCT
37051 TCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCT
260 TCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCT
* *
37116 TTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGAAACTGAGCG
325 TTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGCG
37181 TAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
390 TAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
*
37246 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
455 TGTGCCCTCGAAGCTGAGTATAATCGAACTCGGGGGTCTTTGG
37289 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
37354 CTCAAAGGTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTG
66 CTCAAAGGTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTG
37419 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
131 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
37484 CTACAAATAATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGCAGATAGCCCTT
196 CTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTT
*
37549 CTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTT
261 CTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
37614 TTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGCGT
326 TTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGCGT
* * * * *
37679 AGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCCGCAAATGAT
391 AGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
37743 TTGTTTAAAA
Statistics
Matches: 879, Mismatches: 57, Indels: 24
0.92 0.06 0.03
Matches are distributed among these distances:
492 17 0.02
493 290 0.33
494 3 0.00
495 5 0.01
496 146 0.17
497 356 0.41
498 62 0.07
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.29
Consensus pattern (497 bp):
CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTG
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTT
CTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
TTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGCGT
AGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
GTGCCCTCGAAGCTGAGTATAATCGAACTCGGGGGTCTTTGG
Found at i:40596 original size:17 final size:17
Alignment explanation
Indices: 40570--40602 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40560 TGCAAACGAT
*
40570 GAACACAAAATAAAAGA
1 GAACAAAAAATAAAAGA
40587 GAACAAAAAATAAAAG
1 GAACAAAAAATAAAAG
40603 GGTTAGTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACAAAAAATAAAAGA
Found at i:42906 original size:2 final size:2
Alignment explanation
Indices: 42894--42945 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
42884 TAAAATGTAA
* *
42894 AT AT AT GT AT AT AT AT AT AT AT GT AT AT A- AT -T AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42933 AT A- AT AT -T AT AT A
1 AT AT AT AT AT AT AT A
42946 AATAACGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
1 5 0.12
2 36 0.88
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43991 original size:72 final size:72
Alignment explanation
Indices: 43905--44046 Score: 180
Period size: 73 Copynumber: 2.0 Consensus size: 72
43895 TAAACTCAAG
* * *
43905 TTTAGGATAATATTTTAAATATTATAT-TTTATCTTT-GTATTTTAGTTTAAATAGGTTTTAGTA
1 TTTAGGATAATATTTT-AATATTATATCTCTAT-TTTAATATTTTAGTTGAAATAGGTTTTAGTA
43968 TTTTAAGTT
64 TTTTAAGTT
* * * *
43977 TTTAGGATATTATTTTTATATTTTATCTCTGTTTTAAATATTTTAGTTGAAATAGGTTTTAGTAT
1 TTTAGGATAATATTTTAATATTATATCTCTATTTT-AATATTTTAGTTGAAATAGGTTTTAGTAT
44042 TTTAA
65 TTTAA
44047 TTAGGATTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
71 11 0.18
72 18 0.30
73 31 0.52
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (72 bp):
TTTAGGATAATATTTTAATATTATATCTCTATTTTAATATTTTAGTTGAAATAGGTTTTAGTATT
TTAAGTT
Found at i:44736 original size:19 final size:17
Alignment explanation
Indices: 44712--44754 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
44702 CTTTAATTTG
44712 TTTATTTAATTAATTTTCT
1 TTTATTTAATT-ATTTT-T
*
44731 TTTATTTAATTCTTTTT
1 TTTATTTAATTATTTTT
44748 TTTATTT
1 TTTATTT
44755 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.35
18 4 0.17
19 11 0.48
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTAATTATTTTT
Found at i:44835 original size:17 final size:17
Alignment explanation
Indices: 44813--44851 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
44803 TTATTATTCA
*
44813 ATTATTT-TTCTTTCTTT
1 ATTATTTATTCTAT-TTT
44830 ATTATTTATTCTATTTT
1 ATTATTTATTCTATTTT
44847 ATTAT
1 ATTAT
44852 ACATTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTATTTATTCTATTTT
Found at i:45198 original size:33 final size:33
Alignment explanation
Indices: 45159--45235 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
45149 AATAAAATGA
* *
45159 AGAGAGGGTTCTTTGTACCCTTT-AGGATTTATC
1 AGAGAGGGTTCCTCGTA-CCTTTCAGGATTTATC
*
45192 AGAGAGGGTTCCTCGTACCTTTCAGGGTTTATC
1 AGAGAGGGTTCCTCGTACCTTTCAGGATTTATC
* *
45225 AAAAAGGGTTC
1 AGAGAGGGTTC
45236 GTGGCAACCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
32 5 0.13
33 33 0.87
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (33 bp):
AGAGAGGGTTCCTCGTACCTTTCAGGATTTATC
Found at i:53149 original size:45 final size:45
Alignment explanation
Indices: 53082--53187 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
53072 TGCACTACTT
* * *
53082 GTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATT-AATGG
1 GTGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TTAAAAGA
*
53126 GATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAGA
1 G-TGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAGA
53172 GTGCATCGATGCACTA
1 GTGCATCGATGCACTA
53188 CCTGTGCATC
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
44 1 0.02
45 41 0.76
46 12 0.22
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (45 bp):
GTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAGA
Found at i:59378 original size:15 final size:15
Alignment explanation
Indices: 59360--59388 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59350 GACCACTACA
59360 TCCCGAAGGACTATG
1 TCCCGAAGGACTATG
59375 TCCCGAAGGACTAT
1 TCCCGAAGGACTAT
59389 TATACCCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.21
Consensus pattern (15 bp):
TCCCGAAGGACTATG
Found at i:59977 original size:63 final size:63
Alignment explanation
Indices: 59899--60064 Score: 176
Period size: 63 Copynumber: 2.6 Consensus size: 63
59889 CAATTTCCTC
* * * *
59899 TTTTAGAAGTATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTA
1 TTTTAAAAG-ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCAATCAATGTTTTTA
** * * *
59962 TTATTAATGGATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCAATCAATGTTTTTA
1 TT-TTAAAAGATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCAATCAATGTTTTTA
*
60026 TTTTAAAAGAGTGCATCGATGCACTACCTGTGCATCGAT
1 TTTTAAAAGA-TGCATCGATGCACTACTTGTGCATCGAT
60065 ACACCTTCAA
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 46 0.55
64 35 0.42
65 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (63 bp):
TTTTAAAAGATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCAATCAATGTTTTTA
Found at i:67275 original size:19 final size:19
Alignment explanation
Indices: 67253--67302 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
67243 GTTATTTTTA
67253 AAATAAAAAAATAAGAATT
1 AAATAAAAAAATAAGAATT
*
67272 AAATAAAATAAA-AATAATT
1 AAATAAAA-AAATAAGAATT
*
67291 AAATAAATAAAT
1 AAATAAAAAAAT
67303 TAAAGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAATAAAAAAATAAGAATT
Found at i:67890 original size:21 final size:21
Alignment explanation
Indices: 67864--67912 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
67854 GCCTTCAAAT
67864 TCTTAAAAAC-AAGCTAAAACA
1 TCTTAAAAACTAA-CTAAAACA
* *
67885 TCTTAAATACTAATTAAAACA
1 TCTTAAAAACTAACTAAAACA
67906 -CTTAAAA
1 TCTTAAAA
67913 CTATTTAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 16 0.67
22 2 0.08
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (21 bp):
TCTTAAAAACTAACTAAAACA
Found at i:67985 original size:62 final size:63
Alignment explanation
Indices: 67888--68007 Score: 172
Period size: 62 Copynumber: 1.9 Consensus size: 63
67878 TAAAACATCT
* * *
67888 TAAATACTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAA-AAATATAATATTC
1 TAAATACTAATTAAAACACTAAAAACTATTTAAACTAAAATACATAAAACAAAGATAATATTC
* *
67950 TAAATCCTAATTAAAATAC-AAAAACCTATTTAAACTAAAATACATAAAACAAAGATAA
1 TAAATACTAATTAAAACACTAAAAA-CTATTTAAACTAAAATACATAAAACAAAGATAA
68008 AATATAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
61 4 0.08
62 40 0.78
63 7 0.14
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.28
Consensus pattern (63 bp):
TAAATACTAATTAAAACACTAAAAACTATTTAAACTAAAATACATAAAACAAAGATAATATTC
Found at i:70108 original size:15 final size:14
Alignment explanation
Indices: 70079--70113 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
70069 TAAGCATCTG
70079 ATAAAAAAAATAAA
1 ATAAAAAAAATAAA
*
70093 ATAAATAAAATGAAA
1 ATAAAAAAAAT-AAA
70108 ATAAAA
1 ATAAAA
70114 CGAAATGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (14 bp):
ATAAAAAAAATAAA
Found at i:75735 original size:19 final size:18
Alignment explanation
Indices: 75716--75764 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
75706 GTTGCTTTTA
75716 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
75734 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
75753 AAATAAATAAAT
1 AAATAAA-AAAT
75765 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:77066 original size:17 final size:17
Alignment explanation
Indices: 77044--77077 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
77034 ATCAATTGAG
77044 GACATTTTCTCACATGT
1 GACATTTTCTCACATGT
77061 GACATTTTCTCACATGT
1 GACATTTTCTCACATGT
77078 CACTATATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (17 bp):
GACATTTTCTCACATGT
Found at i:91305 original size:22 final size:23
Alignment explanation
Indices: 91271--91314 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
91261 AGGGTTTCAT
91271 AGGTCATTCGGGACATA-CTCAC
1 AGGTCATTCGGGACATATCTCAC
* *
91293 AGGTCCTTTGGGACATATCTCA
1 AGGTCATTCGGGACATATCTCA
91315 TATGCCACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (23 bp):
AGGTCATTCGGGACATATCTCAC
Found at i:91875 original size:21 final size:21
Alignment explanation
Indices: 91849--91896 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
91839 TGGCCAATAT
91849 CACTGTAGCAGTGCATCGATA
1 CACTGTAGCAGTGCATCGATA
* *
91870 CACTGTAGCAGTGTATCGGTA
1 CACTGTAGCAGTGCATCGATA
91891 CACTGT
1 CACTGT
91897 TCATTATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (21 bp):
CACTGTAGCAGTGCATCGATA
Found at i:92300 original size:2 final size:2
Alignment explanation
Indices: 92293--92348 Score: 80
Period size: 2 Copynumber: 28.5 Consensus size: 2
92283 TCTTATAAAG
*
92293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
92336 A- AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT A
92349 AATTAAAGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93389 original size:23 final size:22
Alignment explanation
Indices: 93347--93404 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
93337 TGGATTATCG
*
93347 ATATTTATTATTTATTATTTTT
1 ATATTTATTATTTATAATTTTT
93369 ATATTATATTATATT-TAATTTTT
1 ATATT-TATTAT-TTATAATTTTT
93392 ATATTTATT-TTTA
1 ATATTTATTATTTA
93405 GTTTTCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.06
21 1 0.03
22 9 0.28
23 18 0.56
24 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
ATATTTATTATTTATAATTTTT
Found at i:93409 original size:18 final size:16
Alignment explanation
Indices: 93350--93409 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 16
93340 ATTATCGATA
93350 TTTATTATT-TATTATT
1 TTTATT-TTATATTATT
*
93366 TTTATATTATATTATAT
1 TTTATTTTATATTAT-T
*
93383 TTAATTTTTATATTTATT
1 TTTA-TTTTATA-TTATT
93401 TTTAGTTTT
1 TTTA-TTTT
93410 CAATAATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 2 0.06
16 11 0.31
17 4 0.11
18 14 0.40
19 4 0.11
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTATTTTATATTATT
Found at i:93470 original size:15 final size:15
Alignment explanation
Indices: 93450--93480 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
93440 CTTTTTTCGG
93450 TTTGTTTGATTTTTT
1 TTTGTTTGATTTTTT
*
93465 TTTGTTTTATTTTTT
1 TTTGTTTGATTTTTT
93480 T
1 T
93481 CTCGTGATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.00, G:0.10, T:0.84
Consensus pattern (15 bp):
TTTGTTTGATTTTTT
Found at i:98487 original size:2 final size:2
Alignment explanation
Indices: 98446--98471 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
98436 ATAATTATTC
98446 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
98472 TTTAAAAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99482 original size:7 final size:7
Alignment explanation
Indices: 99470--99508 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
99460 ATATGTATTG
*
99470 TTTTTTC
1 TTTTATC
*
99477 TTTTTTC
1 TTTTATC
99484 TTTTATC
1 TTTTATC
99491 TTTTATC
1 TTTTATC
99498 TTTTATC
1 TTTTATC
99505 TTTT
1 TTTT
99509 TTTGGTTCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTATC
Found at i:119904 original size:21 final size:21
Alignment explanation
Indices: 119878--119920 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
119868 TTTTCGGGCT
* *
119878 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
119899 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
119920 A
1 A
119921 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:119979 original size:65 final size:67
Alignment explanation
Indices: 119900--120049 Score: 214
Period size: 66 Copynumber: 2.3 Consensus size: 67
119890 ACCCATTCAA
* *
119900 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
119964 -G
66 GG
* * * *
119965 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
120030 GGG
66 -GG
*
120033 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
120050 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
65 26 0.35
66 32 0.43
68 17 0.23
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.18
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
GG
Found at i:120784 original size:23 final size:22
Alignment explanation
Indices: 120696--120776 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
120686 ATCATTATAT
*
120696 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
*
120718 GGTACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
120740 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
120763 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
120777 TTTATACGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 40 0.73
23 15 0.27
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:126849 original size:21 final size:21
Alignment explanation
Indices: 126823--126865 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
126813 TTTTCGGGCT
* *
126823 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
126844 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
126865 A
1 A
126866 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:126919 original size:65 final size:67
Alignment explanation
Indices: 126845--126994 Score: 223
Period size: 66 Copynumber: 2.3 Consensus size: 67
126835 ACCCATTCAA
* *
126845 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
126909 -G
66 GG
* * *
126910 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
126975 GGG
66 -GG
*
126978 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
126995 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
65 26 0.34
66 33 0.43
68 17 0.22
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:127663 original size:13 final size:13
Alignment explanation
Indices: 127645--127707 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
127635 TTATATGGCA
127645 CTACGGTGCAATT
1 CTACGGTGCAATT
127658 CTACGG-GC-A--
1 CTACGGTGCAATT
*
127667 CTTCGGTGCAATT
1 CTACGGTGCAATT
127680 CTACGG-GC-A--
1 CTACGGTGCAATT
*
127689 CTTCGGTGCAATT
1 CTACGGTGCAATT
127702 CTACGG
1 CTACGG
127708 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:127673 original size:22 final size:22
Alignment explanation
Indices: 127641--127721 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
127631 ATCATTATAT
*
127641 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
127663 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
127685 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
127708 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
127722 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:135426 original size:19 final size:19
Alignment explanation
Indices: 135399--135435 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
135389 ACCTTTTTTT
135399 TATTATTATTATTATATTA
1 TATTATTATTATTATATTA
* *
135418 TATTTTTATTATTCTATT
1 TATTATTATTATTATATT
135436 TTTTCTACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTATTATTATTATATTA
Found at i:135470 original size:20 final size:21
Alignment explanation
Indices: 135432--135470 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
135422 TTTATTATTC
*
135432 TATTTTTTCTACTATTATTAA
1 TATTTTTTCTACTAATATTAA
*
135453 TATTTTTTC-CCTAATATT
1 TATTTTTTCTACTAATATT
135471 TGATTATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTTCTACTAATATTAA
Found at i:135792 original size:19 final size:21
Alignment explanation
Indices: 135768--135806 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
135758 ATACGCTATA
135768 ATTATTATT-TA-ATTTTTCT
1 ATTATTATTATATATTTTTCT
135787 ATTATTATTATATATTTTTC
1 ATTATTATTATATATTTTTC
135807 CCTCTCTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTATTATTATATATTTTTCT
Found at i:135793 original size:22 final size:21
Alignment explanation
Indices: 135763--135806 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
135753 ACTTTATACG
*
135763 CTATAATTATTATTTAATTTTT
1 CTATAATTATTATAT-ATTTTT
*
135785 CTATTATTATTATATATTTTT
1 CTATAATTATTATATATTTTT
135806 C
1 C
135807 CCTCTCTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (21 bp):
CTATAATTATTATATATTTTT
Found at i:146568 original size:53 final size:54
Alignment explanation
Indices: 146471--146574 Score: 122
Period size: 53 Copynumber: 1.9 Consensus size: 54
146461 AATACTTCGC
* ** * **
146471 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGGGGAAAAAAAAA-AGAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGGAAAAAAAAAAAGAGAACGT
*
146524 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATT-GAAAAAGAAAAAAGAGAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGGAAAAA-AAAAAAGAGAA
146575 GAAAAAGAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
52 4 0.10
53 34 0.81
54 4 0.10
ACGTcount: A:0.46, C:0.13, G:0.27, T:0.13
Consensus pattern (54 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGGAAAAAAAAAAAGAGAACGT
Found at i:147521 original size:105 final size:105
Alignment explanation
Indices: 147339--148343 Score: 1613
Period size: 105 Copynumber: 9.7 Consensus size: 105
147329 AGGTTTTACC
*
147339 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
147404 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
147444 CAGAGCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
147509 ACGAAGGGACCGCTAGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
147549 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
147614 ACGAAGGGACCGTTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
147654 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
147719 ACGAAGGGACCGTTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
147759 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
147824 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCGAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
147864 CCGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
147929 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
147969 CCGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
148034 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* * *
148075 CAAAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
148140 GCGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* * * *
148181 CAGAGTCAATTTCAACTTCACAGCGAAGAATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
148246 ACGAAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
148279 C----CCAATTTCAACTTCACAACGAAGGATGTTGGACTCAAGACAGTAC-C-AGTTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA--ACGCAAGTTCAACTTCA
148338 CGACGA
64 CGACGA
148344 GGATGTCATT
Statistics
Matches: 857, Mismatches: 40, Indels: 17
0.94 0.04 0.02
Matches are distributed among these distances:
94 54 0.06
95 1 0.00
96 2 0.00
98 7 0.01
103 1 0.00
105 602 0.70
106 190 0.22
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:150127 original size:19 final size:19
Alignment explanation
Indices: 150103--150139 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
150093 ATACGCTATA
150103 ATTATTATT-TAATTTTTCT
1 ATTATTATTAT-ATTTTTCT
150122 ATTATTATTATATTTTTC
1 ATTATTATTATATTTTTC
150140 CCTCTCTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTATTATTATATTTTTCT
Found at i:155832 original size:22 final size:22
Alignment explanation
Indices: 155794--155836 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
155784 GACTATCTGT
155794 AAGATAAAGCAGAATTATCTAG
1 AAGATAAAGCAGAATTATCTAG
*
155816 AAGATAAATCATG-ATTATCTA
1 AAGATAAAGCA-GAATTATCTA
155837 TGTATTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (22 bp):
AAGATAAAGCAGAATTATCTAG
Found at i:156082 original size:17 final size:17
Alignment explanation
Indices: 156060--156095 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
156050 CTAAGCATAT
156060 TCTAAACTCTTATTTAG
1 TCTAAACTCTTATTTAG
156077 TCTAAACTCTTATTTAG
1 TCTAAACTCTTATTTAG
156094 TC
1 TC
156096 AAAAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (17 bp):
TCTAAACTCTTATTTAG
Found at i:162075 original size:3 final size:3
Alignment explanation
Indices: 162067--162152 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
162057 TTTTTATCCA
* *
162067 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
162115 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
162153 AATATATATT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:174862 original size:1 final size:1
Alignment explanation
Indices: 174856--174899 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
174846 TAGCTTGAAG
* * * *
174856 AAAAAAAAAAGAAAAAAAAAAGAAAAAAAAGAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
174900 GGAGGTTCAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:174869 original size:11 final size:11
Alignment explanation
Indices: 174853--174900 Score: 71
Period size: 11 Copynumber: 4.3 Consensus size: 11
174843 TATTAGCTTG
174853 AAGAAAAAAAA
1 AAGAAAAAAAA
174864 AAGAAAAAAAA
1 AAGAAAAAAAA
174875 AAGAAAAAAAA
1 AAGAAAAAAAA
174886 GAA-AAAAAAGAA
1 -AAGAAAAAA-AA
174898 AAG
1 AAG
174901 GAGGTTCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 30 0.88
12 4 0.12
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:174872 original size:9 final size:9
Alignment explanation
Indices: 174858--174899 Score: 66
Period size: 9 Copynumber: 4.4 Consensus size: 9
174848 GCTTGAAGAA
174858 AAAAAAAAG
1 AAAAAAAAG
174867 AAAAAAAAAAG
1 --AAAAAAAAG
174878 AAAAAAAAG
1 AAAAAAAAG
174887 AAAAAAAAG
1 AAAAAAAAG
174896 AAAA
1 AAAA
174900 GGAGGTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 22 0.71
11 9 0.29
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:175234 original size:36 final size:33
Alignment explanation
Indices: 175194--175265 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 33
175184 GCTTGCCAAA
175194 ATTTGA-ATACAATTCTATTTATTGCAAGTTCAATTT
1 ATTTGAGAT-CAATT-TATTT-TTGCAA-TTCAATTT
*
175230 ATTTGAGATCAATTTATTTTTGGAATTCAATTT
1 ATTTGAGATCAATTTATTTTTGCAATTCAATTT
175263 ATT
1 ATT
175266 CTTTCTATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
33 11 0.32
34 5 0.15
35 5 0.15
36 11 0.32
37 2 0.06
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (33 bp):
ATTTGAGATCAATTTATTTTTGCAATTCAATTT
Done.