Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004073.1 Hibiscus syriacus cultivar Beakdansim tig00008918_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: 150804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:6165 original size:24 final size:24
Alignment explanation
Indices: 6138--6194 Score: 105
Period size: 24 Copynumber: 2.3 Consensus size: 24
6128 GATAGATAAA
6138 TGTGAAATAGGTATTTCTGTTCTT
1 TGTGAAATAGGTATTTCTGTTCTT
6162 TGTGAAATAGGTATTTCTGTTCTT
1 TGTGAAATAGGTATTTCTGTTCTT
6186 TGTGTAAAT
1 TGTG-AAAT
6195 GTGAATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.23, C:0.07, G:0.21, T:0.49
Consensus pattern (24 bp):
TGTGAAATAGGTATTTCTGTTCTT
Found at i:18345 original size:27 final size:27
Alignment explanation
Indices: 18288--18351 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
18278 GGAAGACGAC
18288 GAAA-TCGAGAAAGCTGAGACCTCAAA
1 GAAACTCGAGAAAGCTGAGACCTCAAA
* * *
18314 GAAACTTGAGAAAGCTGAGGCCTTGAAA
1 GAAACTCGAGAAAGCTGAGACC-TCAAA
18342 -AAACTCGAGA
1 GAAACTCGAGA
18352 TTAAAGAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.12
27 24 0.75
28 4 0.12
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.14
Consensus pattern (27 bp):
GAAACTCGAGAAAGCTGAGACCTCAAA
Found at i:24861 original size:27 final size:26
Alignment explanation
Indices: 24822--24931 Score: 127
Period size: 25 Copynumber: 4.3 Consensus size: 26
24812 AATACGATAT
* *
24822 ATATATATAATATGTCG-TTTAAAAA
1 ATATATATAATATATAGTTTTAAAAA
* *
24847 ATATATATAATATATAGTTTTGAAAT
1 ATATATATAATATATAGTTTTAAAAA
*
24873 ATATATAT-ATATATAGTTTTTAAAA
1 ATATATATAATATATAGTTTTAAAAA
*
24898 ATATATA-ATGTATATAGGTTTTAAAAA
1 ATATATATA-ATATATA-GTTTTAAAAA
24925 ATATATA
1 ATATATA
24932 ATTTTTGAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
25 37 0.51
26 20 0.27
27 16 0.22
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.44
Consensus pattern (26 bp):
ATATATATAATATATAGTTTTAAAAA
Found at i:24933 original size:27 final size:25
Alignment explanation
Indices: 24818--24931 Score: 129
Period size: 26 Copynumber: 4.3 Consensus size: 25
24808 TTATAATACG
24818 ATATATATATATAATATGTCGTTTAAAAA
1 ATATATATATAT-ATA-GT--TTTAAAAA
* *
24847 ATATATATAATATATAGTTTTGAAAT
1 ATATATAT-ATATATAGTTTTAAAAA
*
24873 ATATATATATATATAGTTTTTAAAA
1 ATATATATATATATAGTTTTAAAAA
*
24898 ATATATAATGTATATAGGTTTTAAAAA
1 ATATAT-ATATATATA-GTTTTAAAAA
24925 ATATATA
1 ATATATA
24932 ATTTTTGAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
25 21 0.28
26 23 0.30
27 15 0.20
28 2 0.03
29 11 0.14
30 4 0.05
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.44
Consensus pattern (25 bp):
ATATATATATATATAGTTTTAAAAA
Found at i:24975 original size:27 final size:27
Alignment explanation
Indices: 24945--25004 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
24935 TTTGAAAACG
*
24945 TATTATATGGTTTTTGAAAATATA-A-TA
1 TATTATATAG-TTTT-AAAATATATATTA
24972 TATTATATAGTTTTAAAATATATATTA
1 TATTATATAGTTTTAAAATATATATTA
24999 TATTAT
1 TATTAT
25005 TATTATTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 8 0.27
26 5 0.17
27 17 0.57
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.52
Consensus pattern (27 bp):
TATTATATAGTTTTAAAATATATATTA
Found at i:25077 original size:5 final size:6
Alignment explanation
Indices: 24999--25076 Score: 61
Period size: 6 Copynumber: 13.0 Consensus size: 6
24989 ATATATATTA
* * * * *
24999 TATTAT TATTAT TACTTTT TA-TTT TA-TTT TATTAT TGTTTT TGTTTT
1 TATTTT TATTTT TA-TTTT TATTTT TATTTT TATTTT TATTTT TATTTT
* *
25046 TATTATT TACTTT CATTTT TATTTT TATTTT
1 TATT-TT TATTTT TATTTT TATTTT TATTTT
25077 AGGTCCAACT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
5 10 0.17
6 40 0.67
7 10 0.17
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.74
Consensus pattern (6 bp):
TATTTT
Found at i:31492 original size:9 final size:8
Alignment explanation
Indices: 31469--31556 Score: 56
Period size: 8 Copynumber: 10.9 Consensus size: 8
31459 TTTCTATATA
*
31469 TTTACTTT
1 TTTATTTT
31477 TTTATTTT
1 TTTATTTT
31485 TCTTATTTT
1 T-TTATTTT
*
31494 ATTT-GTTT
1 -TTTATTTT
*
31502 TTT-TTTC
1 TTTATTTT
*
31509 TTT-TCTT
1 TTTATTTT
*
31516 TTTATTAT
1 TTTATTTT
*
31524 TTTATTAT
1 TTTATTTT
31532 TTTATTTT
1 TTTATTTT
*
31540 TTATATTAGT
1 TT-TATT-TT
31550 TTTATTT
1 TTTATTT
31557 ATATATTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
7 13 0.20
8 30 0.47
9 17 0.27
10 4 0.06
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTATTTT
Found at i:31495 original size:5 final size:5
Alignment explanation
Indices: 31476--31581 Score: 53
Period size: 5 Copynumber: 20.8 Consensus size: 5
31466 ATATTTACTT
* * * *
31476 TTTTA TTTT- TCTTA TTTTA TTTGT- TTTT- TTTTC TTTTC TTTT- TATTA
1 TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA
*
31523 TTTTA --TTA TTTTA TTTTTTA TATTA GTTTTA TTTATA TATTTA TTTTCA
1 TTTTA TTTTA TTTTA --TTTTA TTTTA -TTTTA TTT-TA T-TTTA TTTT-A
31572 TTTGTA TTTT
1 TTT-TA TTTT
31582 CCTCTTATTT
Statistics
Matches: 82, Mismatches: 6, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
3 3 0.04
4 11 0.13
5 41 0.50
6 19 0.23
7 8 0.10
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:31540 original size:33 final size:33
Alignment explanation
Indices: 31476--31540 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
31466 ATATTTACTT
* *
31476 TTTTATTTTTCTTATTTTATTTGTTTTTTTTTC
1 TTTTATTTTTATTATTTTATTTATTTTTTTTTC
*
31509 TTTTCTTTTTATTATTTTA-TTATTTTATTTTT
1 TTTTATTTTTATTATTTTATTTATTTT-TTTTT
31541 TATATTAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.82
Consensus pattern (33 bp):
TTTTATTTTTATTATTTTATTTATTTTTTTTTC
Found at i:31546 original size:14 final size:14
Alignment explanation
Indices: 31476--31569 Score: 56
Period size: 14 Copynumber: 6.6 Consensus size: 14
31466 ATATTTACTT
31476 TTTTATTTTTCT-TA
1 TTTTATTTTT-TATA
31490 TTTTATTTGTTT-T-
1 TTTTATTT-TTTATA
* *
31503 TTTT-TCTTTTCT-
1 TTTTATTTTTTATA
31515 TTTTATTATTTTATTA
1 TTTTATT-TTTTA-TA
31531 TTTTATTTTTTATA
1 TTTTATTTTTTATA
*
31545 TTAGTT-TTATTTATA
1 TT--TTATTTTTTATA
31560 TATTTATTTT
1 T-TTTATTTT
31570 CATTTGTATT
Statistics
Matches: 65, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
11 3 0.05
12 7 0.11
13 5 0.08
14 20 0.31
15 20 0.31
16 10 0.15
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTATTTTTTATA
Found at i:31546 original size:17 final size:17
Alignment explanation
Indices: 31515--31574 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
31505 TTTCTTTTCT
*
31515 TTTTATTATTT-TATTA
1 TTTTATTTTTTATATTA
31531 TTTTATTTTTTATATTA
1 TTTTATTTTTTATATTA
*
31548 GTTTTA-TTTATATATTTA
1 -TTTTATTTTTTATA-TTA
31566 TTTTCATTT
1 TTTT-ATTT
31575 GTATTTTCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
16 10 0.27
17 16 0.43
18 9 0.24
19 2 0.05
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTTATATTA
Found at i:31546 original size:22 final size:20
Alignment explanation
Indices: 31455--31543 Score: 72
Period size: 22 Copynumber: 4.2 Consensus size: 20
31445 ATCCTCATTA
*
31455 TTATTTTCTATATATTTACTTTT
1 TTATTTT-TTTAT-TTTA-TTTT
*
31478 TTATTTTTCTTATTTTATTTG
1 TTATTTTT-TTATTTTATTTT
* *
31499 TT-TTTTTTTCTTTTCTTTTT
1 TTATTTTTTTATTTT-ATTTT
*
31519 ATTATTTTATTATTTTATTTT
1 -TTATTTTTTTATTTTATTTT
31540 TTAT
1 TTAT
31544 ATTAGTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
19 6 0.11
20 12 0.22
21 11 0.20
22 15 0.28
23 10 0.19
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.78
Consensus pattern (20 bp):
TTATTTTTTTATTTTATTTT
Found at i:31742 original size:9 final size:9
Alignment explanation
Indices: 31670--31845 Score: 63
Period size: 9 Copynumber: 19.6 Consensus size: 9
31660 GCTCATTATC
31670 TTTATTTTGA
1 TTTATTTT-A
31680 TTTA-TTTA
1 TTTATTTTA
31688 TTTATTTT-
1 TTTATTTTA
31696 TCTTCA-TTT-
1 T-TT-ATTTTA
31705 TTTATTTCT-
1 TTTATTT-TA
*
31714 TTT-GTTT-
1 TTTATTTTA
* *
31721 TTTATGTTC
1 TTTATTTTA
31730 TTTATTTTA
1 TTTATTTTA
*
31739 TTTAGTTT-
1 TTTATTTTA
31747 TTTATCTTTA
1 TTTAT-TTTA
*
31757 TTTTATTGT-
1 -TTTATTTTA
31766 TTTATGTTT-
1 TTTAT-TTTA
*
31775 TTT-CTTTA
1 TTTATTTTA
31783 TCTTATTTT-
1 T-TTATTTTA
31792 TCTT-TTTTCA
1 T-TTATTTT-A
31802 TTTATTTTTA
1 TTTA-TTTTA
**
31812 TTTCCTTTA
1 TTTATTTTA
31821 TTTTATTTTTA
1 -TTTA-TTTTA
*
31832 TTTAGTTTA
1 TTTATTTTA
31841 TTTAT
1 TTTAT
31846 CTTCGTTGCA
Statistics
Matches: 129, Mismatches: 17, Indels: 41
0.69 0.09 0.22
Matches are distributed among these distances:
7 8 0.06
8 28 0.22
9 58 0.45
10 22 0.17
11 13 0.10
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:31782 original size:13 final size:13
Alignment explanation
Indices: 31665--31830 Score: 51
Period size: 14 Copynumber: 12.1 Consensus size: 13
31655 ATTGTGCTCA
31665 TTATCTTTATTTT
1 TTATCTTTATTTT
*
31678 GATT-TATTTATTTAT
1 --TTATCTTTATTT-T
* *
31693 TTTTCTTCATTTT
1 TTATCTTTATTTT
*
31706 TTATTTCTTTTGTTTT
1 TTA--TC-TTTATTTT
*
31722 TTATGTTCT-TTATT
1 TTATCTT-TATT-TT
31736 TTA--TTTAGTTTT
1 TTATCTTTA-TTTT
31748 TTATCTTTATTTT
1 TTATCTTTATTTT
*
31761 ATTGT-TTTATGTTT
1 -TTATCTTTAT-TTT
31775 TT-TCTTTATCTTAT
1 TTATCTTTAT-TT-T
*
31789 TTTTCTTT-TTTCAT
1 TTATCTTTATTT--T
*
31803 TTATTTTTATTTCCT
1 TTATCTTTATTT--T
31818 TTAT-TTTATTTT
1 TTATCTTTATTTT
31830 T
1 T
31831 ATTTAGTTTA
Statistics
Matches: 121, Mismatches: 12, Indels: 39
0.70 0.07 0.23
Matches are distributed among these distances:
11 1 0.01
12 10 0.08
13 31 0.26
14 51 0.42
15 19 0.16
16 9 0.07
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (13 bp):
TTATCTTTATTTT
Found at i:33401 original size:17 final size:18
Alignment explanation
Indices: 33379--33427 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
33369 GTTTCAGATT
*
33379 CAGATTCCAATTCC-TGA
1 CAGATTCCAATTCCTTCA
33396 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCCTTCA
*
33414 CATATTCCAATTCC
1 CAGATTCCAATTCC
33428 CTCAGAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.29, C:0.33, G:0.06, T:0.33
Consensus pattern (18 bp):
CAGATTCCAATTCCTTCA
Found at i:35026 original size:63 final size:63
Alignment explanation
Indices: 34949--35067 Score: 184
Period size: 63 Copynumber: 1.9 Consensus size: 63
34939 AACAAACAAC
* * * *
34949 AATATTAAAATATCAAATTTTAAGATTCAAACTATAATATTAACTCTAGAATAATAAAATCAT
1 AATATTAAAATATCAAATCTTAAGACTCAAACCATAATATTAACTCTAGAAAAATAAAATCAT
* *
35012 AATATTAAAGTATCAAATCTTAAGACTCAAACCATAATATTAAGTCTAGAAAAATA
1 AATATTAAAATATCAAATCTTAAGACTCAAACCATAATATTAACTCTAGAAAAATA
35068 GTAAACCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 50 1.00
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (63 bp):
AATATTAAAATATCAAATCTTAAGACTCAAACCATAATATTAACTCTAGAAAAATAAAATCAT
Found at i:43698 original size:22 final size:22
Alignment explanation
Indices: 43664--43741 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
43654 TTAGAGATTA
*
43664 TTTTAAAATT-TATGTATTTTCT
1 TTTTAAAATTATA-GTATTTTAT
*
43686 TTTTCAAAATTATATTATTTTAT
1 TTTT-AAAATTATAGTATTTTAT
* ** *
43709 TTTTAAAATTTTA-TATTAAAA
1 TTTTAAAATTATAGTATTTTAT
43730 TTTTAAAATTAT
1 TTTTAAAATTAT
43742 CATATTGTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 16 0.34
22 12 0.26
23 17 0.36
24 2 0.04
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (22 bp):
TTTTAAAATTATAGTATTTTAT
Found at i:43722 original size:24 final size:23
Alignment explanation
Indices: 43664--43726 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
43654 TTAGAGATTA
* *
43664 TTTTAAAATTTAT-GTATTTTCT
1 TTTTAAAATTTATATTATTTTAT
43686 TTTTCAAAA-TTATATTATTTTAT
1 TTTT-AAAATTTATATTATTTTAT
43709 TTTTAAAATTTTATATTA
1 TTTTAAAA-TTTATATTA
43727 AAATTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 12 0.34
23 15 0.43
24 8 0.23
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTAAAATTTATATTATTTTAT
Found at i:49123 original size:19 final size:19
Alignment explanation
Indices: 49079--49125 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
49069 AAACTATTGT
* * *
49079 TAAATTGTTAATAAATTAT
1 TAAATTATTAATAAACTAA
49098 TAAATTATTAATAAACTAA
1 TAAATTATTAATAAACTAA
*
49117 TACATTATT
1 TAAATTATT
49126 TAAATTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (19 bp):
TAAATTATTAATAAACTAA
Found at i:52027 original size:22 final size:22
Alignment explanation
Indices: 52002--52043 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
51992 TAAATCCAAG
52002 TATTATT-TCATTAATTTTTAAA
1 TATTATTCT-ATTAATTTTTAAA
52024 TATTATTCTATTAATTTTTA
1 TATTATTCTATTAATTTTTA
52044 TATTCGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTATTCTATTAATTTTTAAA
Found at i:52602 original size:19 final size:19
Alignment explanation
Indices: 52578--52614 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52568 ATTTAAAAAA
*
52578 TAAAAAATATTTTTTTTAT
1 TAAAAAATAATTTTTTTAT
*
52597 TAAAAAGTAATTTTTTTA
1 TAAAAAATAATTTTTTTA
52615 AAAAAAATCC
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:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TAAAAAATAATTTTTTTAT
Found at i:52620 original size:19 final size:18
Alignment explanation
Indices: 52579--52622 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
52569 TTTAAAAAAT
* *
52579 AAAAAATATTTTTTTTATT
1 AAAAAATAATTTTTTTA-A
*
52598 AAAAAGTAATTTTTTTAA
1 AAAAAATAATTTTTTTAA
52616 AAAAAAT
1 AAAAAAT
52623 CCCCACCCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AAAAAATAATTTTTTTAA
Found at i:54457 original size:19 final size:19
Alignment explanation
Indices: 54433--54471 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
54423 AAAATTCTAC
*
54433 GGCGCACGTAGCATAGTAT
1 GGCGCACATAGCATAGTAT
54452 GGCGCACATAGCATAGTAT
1 GGCGCACATAGCATAGTAT
54471 G
1 G
54472 TGACGTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (19 bp):
GGCGCACATAGCATAGTAT
Found at i:55377 original size:19 final size:19
Alignment explanation
Indices: 55353--55398 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
55343 TTGATATGTA
55353 AATTTTAATATTGAT-CATT
1 AATTTTAATATTGATGC-TT
*
55372 AATTTTAATTTTGATGCTT
1 AATTTTAATATTGATGCTT
55391 AATTTTAA
1 AATTTTAA
55399 CTTGATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (19 bp):
AATTTTAATATTGATGCTT
Found at i:55799 original size:40 final size:40
Alignment explanation
Indices: 55725--55800 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
55715 TTCTAAACAA
* * * *
55725 ATAAATAACTTAATTTAATTGTATTTTTAATAAAATAATC
1 ATAAATAACTTAAATTAATTATAATTCTAATAAAATAATC
* *
55765 ATAAATTACTTAAATTAATTATAATTCTATTAAAAT
1 ATAAATAACTTAAATTAATTATAATTCTAATAAAAT
55801 TAAAAAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (40 bp):
ATAAATAACTTAAATTAATTATAATTCTAATAAAATAATC
Found at i:56614 original size:3 final size:3
Alignment explanation
Indices: 56606--56635 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
56596 TCTTACCAAC
56606 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
56636 ACCTTCCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:58818 original size:31 final size:31
Alignment explanation
Indices: 58777--58850 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
58767 CAAAAGTAAC
* * *
58777 AAATTAGTCACTAATATTATCGATTTGTAAAA
1 AAATT-GTCACTAACATTATCAATTTATAAAA
* * *
58809 AAATTGTCACCAACGTTATCAATTTATAACA
1 AAATTGTCACTAACATTATCAATTTATAAAA
58840 AAATTGTCACT
1 AAATTGTCACT
58851 CTATCTCTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 30 0.86
32 5 0.14
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (31 bp):
AAATTGTCACTAACATTATCAATTTATAAAA
Found at i:61671 original size:13 final size:14
Alignment explanation
Indices: 61647--61676 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
61637 ACTTTCAAAG
61647 TTTCTCTTTTCTTT
1 TTTCTCTTTTCTTT
61661 TTTCT-TTTTCTTT
1 TTTCTCTTTTCTTT
61674 TTT
1 TTT
61677 GAATTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTCTCTTTTCTTT
Found at i:64179 original size:12 final size:12
Alignment explanation
Indices: 64164--64188 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64154 TCTCGGTATT
64164 AAAAGTTAATGG
1 AAAAGTTAATGG
64176 AAAAGTTAATGG
1 AAAAGTTAATGG
64188 A
1 A
64189 TTTCCTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AAAAGTTAATGG
Found at i:75398 original size:3 final size:3
Alignment explanation
Indices: 75390--75415 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
75380 GAATTGGGTT
75390 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
75416 TAGGGCTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:90447 original size:14 final size:15
Alignment explanation
Indices: 90413--90454 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
90403 TAGATCGGGT
* *
90413 AATAATGGAAGATGC
1 AATAATAGAAGGTGC
*
90428 AATAATTGAAGGTG-
1 AATAATAGAAGGTGC
90442 AATAATAGAAGGT
1 AATAATAGAAGGT
90455 TCGCCCCCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.48, C:0.02, G:0.26, T:0.24
Consensus pattern (15 bp):
AATAATAGAAGGTGC
Found at i:98335 original size:11 final size:11
Alignment explanation
Indices: 98319--98345 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
98309 GGAAGATGTT
98319 TGCCTCAAGTC
1 TGCCTCAAGTC
98330 TGCCTCAAGTC
1 TGCCTCAAGTC
98341 TGCCT
1 TGCCT
98346 GTGGGTGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.37, G:0.19, T:0.30
Consensus pattern (11 bp):
TGCCTCAAGTC
Found at i:102905 original size:2 final size:2
Alignment explanation
Indices: 102898--102929 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
102888 ATCAAAATCA
102898 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
102930 GTTGCTCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107757 original size:5 final size:5
Alignment explanation
Indices: 107747--107997 Score: 446
Period size: 5 Copynumber: 51.8 Consensus size: 5
107737 TAAGTCAAAA
107747 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
107797 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
107847 ATATT ATATT ATATT ATATT ATATT ATA-T ATATT ATATT ATATT ATA-T
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
107895 AT-TT ATATT ATATT ATATT ATATT ATATT ATA-T -TATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
107942 ATATT ATATT ATATT ATATT ATATT ATATT ATA-T -TATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
107990 ATA-T ATAT
1 ATATT ATAT
107998 ACAAAGGATT
Statistics
Matches: 238, Mismatches: 0, Indels: 16
0.94 0.00 0.06
Matches are distributed among these distances:
3 4 0.02
4 18 0.08
5 216 0.91
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:109132 original size:28 final size:27
Alignment explanation
Indices: 109072--109132 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
109062 TTTAATTGTG
109072 ATTATATTTTAAAATTTTAAAAACATA
1 ATTATATTTTAAAATTTTAAAAACATA
* * * *
109099 ATTTATATTTTTTATATTTTAAAATCTTA
1 A-TTATA-TTTTAAAATTTTAAAAACATA
109128 ATTAT
1 ATTAT
109133 CAAACAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.04
28 9 0.32
29 18 0.64
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTATATTTTAAAATTTTAAAAACATA
Found at i:109269 original size:19 final size:20
Alignment explanation
Indices: 109247--109299 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
109237 TATTTAAACT
109247 TAAATAAAAATAATTAA-AA
1 TAAATAAAAATAATTAATAA
*
109266 TAAATATAAAAT-TTTAATAA
1 TAAATA-AAAATAATTAATAA
*
109286 TATAT-AAAATAATT
1 TAAATAAAAATAATT
109300 TATATGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 5 0.18
19 12 0.43
20 11 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATAAAAATAATTAATAA
Found at i:109301 original size:20 final size:20
Alignment explanation
Indices: 109253--109314 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
109243 AACTTAAATA
*
109253 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
109273 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
109291 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
109310 AAAAT
1 AAAAT
109315 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:109311 original size:26 final size:25
Alignment explanation
Indices: 109282--109350 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 25
109272 TAAAATTTTA
109282 ATAATATATAAAATAATTTATATGAT
1 ATAATATATAAAATAATTTATAT-AT
* *
109308 ATAA-A-ATTAAAT-ATCTATA-AT
1 ATAATATATAAAATAATTTATATAT
* *
109329 ATAATAT-TAAAAAAATTAATAT
1 ATAATATATAAAATAATTTATAT
109351 TTAATTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
21 6 0.18
22 5 0.15
23 11 0.33
24 6 0.18
25 1 0.03
26 4 0.12
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (25 bp):
ATAATATATAAAATAATTTATATAT
Found at i:109387 original size:65 final size:64
Alignment explanation
Indices: 109317--109473 Score: 225
Period size: 63 Copynumber: 2.5 Consensus size: 64
109307 TATAAAATTA
109317 AATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATTTAAAAAATCAATATTAAAATC
1 AATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATTT-AAAAATCAATATTAAAATC
* *
109382 AATATCTATAATATAATATT--AAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAATT
1 AATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATTTAAAAATCAATATTAAAATC
*
109444 AAAATC-A-AATATAATA-TAATATAAAATTAA
1 AATATCTATAATATAATATTAA-A-AAAATTAA
109474 ATATAAAACC
Statistics
Matches: 85, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
59 1 0.01
60 9 0.11
61 1 0.01
62 23 0.27
63 31 0.36
65 20 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (64 bp):
AATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATTTAAAAATCAATATTAAAATC
Found at i:109413 original size:27 final size:24
Alignment explanation
Indices: 109370--109437 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 24
109360 TTAAAAAATC
*
109370 AATATT-AAAATCAATATCTATAATAT
1 AATATTAAAAATTAATAT-T-TAAT-T
109396 AATATTAAAAATTAATATTTAATT
1 AATATTAAAAATTAATATTTAATT
*
109420 TAT-TTAAAAATTAATATT
1 AATATTAAAAATTAATATT
109438 AAAATTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 15 0.38
24 3 0.08
25 4 0.10
26 7 0.18
27 10 0.26
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (24 bp):
AATATTAAAAATTAATATTTAATT
Found at i:109441 original size:12 final size:12
Alignment explanation
Indices: 109364--109445 Score: 69
Period size: 12 Copynumber: 6.7 Consensus size: 12
109354 ATTTATTTAA
*
109364 AAAATCAATATT
1 AAAATTAATATT
*
109376 AAAATCAATATCT
1 AAAATTAATAT-T
*
109389 ATAATATAATATT
1 AAAAT-TAATATT
109402 AAAAATTAATATT
1 -AAAATTAATATT
* *
109415 -TAATTTAT-TT
1 AAAATTAATATT
109425 AAAAATTAATATT
1 -AAAATTAATATT
109438 AAAATTAA
1 AAAATTAA
109446 AATCAAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
10 2 0.04
11 6 0.11
12 25 0.44
13 15 0.26
14 9 0.16
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:114465 original size:20 final size:20
Alignment explanation
Indices: 114424--114466 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
114414 AAATTATTTA
*
114424 TTTGGTCACCACCTTTATAT
1 TTTGGTCACCAACTTTATAT
114444 TTTGGTCACCAACTATTA-AT
1 TTTGGTCACCAACT-TTATAT
114464 TTT
1 TTT
114467 CTTTTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (20 bp):
TTTGGTCACCAACTTTATAT
Found at i:118830 original size:29 final size:29
Alignment explanation
Indices: 118735--118833 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
118725 GAATATAATG
* * *
118735 AATAGTCGAGTGATCATGTTGTAACTTTT
1 AATAGTCAAGGGATCATATTGTAACTTTT
* * *
118764 AATAGTGAAGGGACTCGATAAAT-CAACTCTTT
1 AATAGTCAAGGGA-TC-AT-ATTGTAACT-TTT
*
118796 -ATAGTCAAGGGATCATTTTGTAACTTTT
1 AATAGTCAAGGGATCATATTGTAACTTTT
118824 AATAGTCAAG
1 AATAGTCAAG
118834 AGACTCAATA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 4 0.07
29 25 0.46
30 4 0.07
31 17 0.31
32 4 0.07
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (29 bp):
AATAGTCAAGGGATCATATTGTAACTTTT
Found at i:119849 original size:20 final size:21
Alignment explanation
Indices: 119824--119864 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
119814 TGCTTTCAGT
*
119824 CCAAAATTT-CGTTTGAAACG
1 CCAAAATTTACGTTTAAAACG
119844 CCAAAATTTACGTTTAAAACG
1 CCAAAATTTACGTTTAAAACG
119865 TGATTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (21 bp):
CCAAAATTTACGTTTAAAACG
Found at i:124989 original size:2 final size:2
Alignment explanation
Indices: 124977--125009 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
124967 AGTATTGGAC
*
124977 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
125010 TAAGTCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:125438 original size:5 final size:5
Alignment explanation
Indices: 125193--125436 Score: 299
Period size: 5 Copynumber: 48.8 Consensus size: 5
125183 AATATTATAT
* * * * * * * * * *
125193 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT
1 TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC
* * * * * * *
125243 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAC TGTAT TGTAC TGTAC
1 TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC
125293 TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC
1 TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC
125343 TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC
1 TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC
* * * *
125393 TGTAC TGTAC TGTAC TGTAT TGTAC TGTAT TGTAT TGTAT TGTA
1 TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTAC TGTA
125437 TTATATATAC
Statistics
Matches: 233, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 233 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (5 bp):
TGTAC
Found at i:126742 original size:20 final size:20
Alignment explanation
Indices: 126694--126755 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
126684 AACTTAAATC
*
126694 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
126714 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
126732 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
126751 AAAAT
1 AAAAT
126756 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:126752 original size:26 final size:25
Alignment explanation
Indices: 126723--126791 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 25
126713 TAAAATTTTA
126723 ATAATATATAAAATAATTTATATGAT
1 ATAATATATAAAATAATTTATAT-AT
* *
126749 ATAA-A-ATTAAAT-ATCTATA-AT
1 ATAATATATAAAATAATTTATATAT
* *
126770 ATAATAT-TAAAAAAATTAATAT
1 ATAATATATAAAATAATTTATAT
126792 TTAATTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
21 6 0.18
22 5 0.15
23 11 0.33
24 6 0.18
25 1 0.03
26 4 0.12
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (25 bp):
ATAATATATAAAATAATTTATATAT
Found at i:131786 original size:20 final size:20
Alignment explanation
Indices: 131745--131787 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
131735 AAATTATTTA
*
131745 TTTGGTCACCACCTTTATAT
1 TTTGGTCACCAACTTTATAT
131765 TTTGGTCACCAACTATTA-AT
1 TTTGGTCACCAACT-TTATAT
131785 TTT
1 TTT
131788 CTTTTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (20 bp):
TTTGGTCACCAACTTTATAT
Found at i:134933 original size:29 final size:29
Alignment explanation
Indices: 134838--134936 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
134828 GAATATAATG
* * *
134838 AATAGTCGAGTGATCATGTTGTAACTTTT
1 AATAGTCAAGGGATCATATTGTAACTTTT
* * *
134867 AATAGTGAAGGGACTCGATAAAT-CAACTCTTT
1 AATAGTCAAGGGA-TC-AT-ATTGTAACT-TTT
*
134899 -ATAGTCAAGGGATCATTTTGTAACTTTT
1 AATAGTCAAGGGATCATATTGTAACTTTT
134927 AATAGTCAAG
1 AATAGTCAAG
134937 AGACTCAATA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 4 0.07
29 25 0.46
30 4 0.07
31 17 0.31
32 4 0.07
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (29 bp):
AATAGTCAAGGGATCATATTGTAACTTTT
Found at i:135396 original size:17 final size:18
Alignment explanation
Indices: 135357--135395 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
135347 AACAAGACCC
135357 AAAATAACATATTTATTA
1 AAAATAACATATTTATTA
135375 AAAATAACATATTTATTA
1 AAAATAACATATTTATTA
135393 AAA
1 AAA
135396 TTATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATAACATATTTATTA
Found at i:137480 original size:27 final size:27
Alignment explanation
Indices: 137248--137469 Score: 225
Period size: 27 Copynumber: 8.2 Consensus size: 27
137238 ACGGCCTCTT
* * *
137248 GGATCAACATGCCTCTGTTGGTCCCTA
1 GGATCAGCATGTCTCTGTTGGTCCCTG
* *
137275 GGATCAGCATGTCTATGTTGG-CCTCTA
1 GGATCAGCATGTCTCTGTTGGTCC-CTG
*
137302 GGATCAGCATGTCTCTGTAGGTCCC-G
1 GGATCAGCATGTCTCTGTTGGTCCCTG
* *** *
137328 TGGATCAGCATGTCTGTGTACATCCCTT
1 -GGATCAGCATGTCTCTGTTGGTCCCTG
* * *
137356 GGATCAACATGTCTCTGTAGGTCCCGG
1 GGATCAGCATGTCTCTGTTGGTCCCTG
137383 GGATCAGCATGTCTCTGTTGGTCCCTG
1 GGATCAGCATGTCTCTGTTGGTCCCTG
*
137410 GGATCAGCATTTCTCTGTTGGTCCCTG
1 GGATCAGCATGTCTCTGTTGGTCCCTG
* ** *
137437 GGGTTTGCAT-TCCTCTGTTGATCCCTG
1 GGATCAGCATGT-CTCTGTTGGTCCCTG
137464 GGATCA
1 GGATCA
137470 ACATACCTCT
Statistics
Matches: 163, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
26 3 0.02
27 158 0.97
28 2 0.01
ACGTcount: A:0.15, C:0.26, G:0.27, T:0.32
Consensus pattern (27 bp):
GGATCAGCATGTCTCTGTTGGTCCCTG
Found at i:141601 original size:158 final size:156
Alignment explanation
Indices: 141218--141611 Score: 590
Period size: 157 Copynumber: 2.5 Consensus size: 156
141208 TTACATAGGT
* * * * * *
141218 ATTCTATTATGGTATATGAGCATGTGGTTTAAATTTGATAAAAAAACGAACTTAAAATAAATGAC
1 ATTCTACTATGGTTTAAGAGCATGTGGTTCAAATTTGGTAAAAAAAAG-ACTTAAAATAAATGAC
* * *
141283 AAATTGAAGAAATAAGGAGAATATTAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTGTTAT
65 GAATTGAAGAAATAAGGAGAATATGAAAAATTGAAGGAATAAATTGAAAAATAAAAAATTGTTAT
*
141348 CAAAAAGAGGAATTGAAAGTACAATGT
130 CAAAAAGAGGAATTGAAAGTACAATGC
* * *
141375 ATTCTACTATGGTTTAGGAGCATGTGGCTCAAATTTGGTAAAAAACAGACTTAAAATAAATGACG
1 ATTCTACTATGGTTTAAGAGCATGTGGTTCAAATTTGGTAAAAAAAAGACTTAAAATAAATGACG
* *
141440 AATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGAATAAATTGAAAAATTAAAAATTTGTTAT
66 AATTGAAGAAATAAGGAGAATATGAAAAATTGAAGGAATAAATTGAAAAA-TAAAAAATTGTTAT
141505 CAAAAAGAGGAATTGAAAGTACACATGC
130 CAAAAAGAGGAATTGAAAGTACA-ATGC
* * * *
141533 ATTCTACTATGGTTTAAGAGCAAGTGGTTCAAATTTGGTAAAAAAAAGACTTAAAATGAAGGAGG
1 ATTCTACTATGGTTTAAGAGCATGTGGTTCAAATTTGGTAAAAAAAAGACTTAAAATAAATGACG
141598 AATTGAAGAAATAA
66 AATTGAAGAAATAA
141612 TGAAATCAGG
Statistics
Matches: 214, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
156 63 0.29
157 76 0.36
158 75 0.35
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (156 bp):
ATTCTACTATGGTTTAAGAGCATGTGGTTCAAATTTGGTAAAAAAAAGACTTAAAATAAATGACG
AATTGAAGAAATAAGGAGAATATGAAAAATTGAAGGAATAAATTGAAAAATAAAAAATTGTTATC
AAAAAGAGGAATTGAAAGTACAATGC
Found at i:144260 original size:52 final size:52
Alignment explanation
Indices: 144179--144284 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
144169 ACTTACATTA
144179 ATTAAATTGAAACAAAAGCGACAAGATTTATAAGAACTAATCAAAATCCAAC
1 ATTAAATTGAAACAAAAGCGACAAGATTTATAAGAACTAATCAAAATCCAAC
*
144231 ATTAAATTGAAACAAAAGCGACAATATTTATAAGAACTAATCAAAATCCAAC
1 ATTAAATTGAAACAAAAGCGACAAGATTTATAAGAACTAATCAAAATCCAAC
144283 AT
1 AT
144285 ACCACAGTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (52 bp):
ATTAAATTGAAACAAAAGCGACAAGATTTATAAGAACTAATCAAAATCCAAC
Found at i:147673 original size:15 final size:15
Alignment explanation
Indices: 147653--147684 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
147643 ATTTTGAGAG
147653 AGACAAAATTACAAT
1 AGACAAAATTACAAT
147668 AGACAAAATTACAAT
1 AGACAAAATTACAAT
147683 AG
1 AG
147685 TTTCAAAAAT
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:0.59, C:0.12, G:0.09, T:0.19
Consensus pattern (15 bp):
AGACAAAATTACAAT
Found at i:147939 original size:25 final size:28
Alignment explanation
Indices: 147911--147993 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 28
147901 AATCATTAAA
*
147911 ATTAACTATT-TTTTTA-TA-AAAGTAT
1 ATTAACTATTGTTTTTATTACAAAATAT
147936 ATTAACTATTGTTTTTATTACAAAATAT
1 ATTAACTATTGTTTTTATTACAAAATAT
* * * *
147964 ATTAATTATTATATTTATTACAAAAAAT
1 ATTAACTATTGTTTTTATTACAAAATAT
147992 AT
1 AT
147994 GTATATATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
25 10 0.20
26 6 0.12
27 2 0.04
28 32 0.64
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.49
Consensus pattern (28 bp):
ATTAACTATTGTTTTTATTACAAAATAT
Done.