Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015284.1 Kokia drynarioides strain JFW-HI SEQ_130329, 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: 395889
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 520 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:466 original size:12 final size:12
Alignment explanation
Indices: 384--469 Score: 63
Period size: 12 Copynumber: 7.1 Consensus size: 12
374 CTCACCAACT
384 ATAACAACATTAA
1 ATAACAA-ATTAA
*
397 ATAACAAATCAA
1 ATAACAAATTAA
*
409 CTAA-AAATTAA
1 ATAACAAATTAA
420 ATTAA-AAA--AA
1 A-TAACAAATTAA
*
430 ATAAAAAACTTAAA
1 ATAACAAA-TT-AA
444 ATAATCAAATTAA
1 ATAA-CAAATTAA
*
457 CTAACAAATTAA
1 ATAACAAATTAA
469 A
1 A
470 ATATTTTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
9 3 0.05
10 6 0.10
11 6 0.10
12 21 0.36
13 12 0.20
14 8 0.14
15 3 0.05
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.23
Consensus pattern (12 bp):
ATAACAAATTAA
Found at i:487 original size:12 final size:12
Alignment explanation
Indices: 472--496 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
462 AAATTAAAAT
472 ATTTTAAAATTA
1 ATTTTAAAATTA
484 ATTTTAAAATTA
1 ATTTTAAAATTA
496 A
1 A
497 CCATACTTAA
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:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:705 original size:4 final size:4
Alignment explanation
Indices: 698--743 Score: 65
Period size: 4 Copynumber: 11.2 Consensus size: 4
688 TTCTTCCTTC
* *
698 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TTTT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT T
744 CAATTTTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 34 0.92
5 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTCT
Found at i:730 original size:25 final size:25
Alignment explanation
Indices: 696--743 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
686 CCTTCTTCCT
696 TCTTCTTTCTTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTTCTTTCTTTC
* *
721 TCTTTTTTCTTTCTTTTTTTCTT
1 TCTTCTTTCTTTCTTTCTTTCTT
744 CAATTTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (25 bp):
TCTTCTTTCTTTCTTTCTTTCTTTC
Found at i:11225 original size:6 final size:6
Alignment explanation
Indices: 11214--11242 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
11204 ATCCAGAATA
11214 ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATA
11243 TATTAGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:13658 original size:27 final size:27
Alignment explanation
Indices: 13622--13691 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 27
13612 AATAAGCGGT
13622 ATATGCTGT-TTTTAATAAATAATTAGAG
1 ATATG-TGTATTTTAA-AAATAATTAGAG
*
13650 ATATGTGTTAATTTTAAAAATAATTAGGG
1 ATATGTG-T-ATTTTAAAAATAATTAGAG
*
13679 ATATATGTATTTT
1 ATATGTGTATTTT
13692 TATATGCTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 7 0.19
28 7 0.19
29 17 0.46
30 6 0.16
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (27 bp):
ATATGTGTATTTTAAAAATAATTAGAG
Found at i:13701 original size:71 final size:71
Alignment explanation
Indices: 13621--13763 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
13611 AAATAAGCGG
13621 TATATGCTGTTTTTAATAAATAATTAGAGATATGTGTTAATTTTAAAAATAATTAGGGATATATG
1 TATATGCTGTTTTTAATAAATAATTAGAGATATGTGTTAATTTTAAAAATAATTAGGGATATATG
13686 TATTTT
66 TATTTT
13692 TATATGCTGTTTTTAATAAATAATTAGAGATATGTGTTAATTTTAAAAATAATTAGGGATATATG
1 TATATGCTGTTTTTAATAAATAATTAGAGATATGTGTTAATTTTAAAAATAATTAGGGATATATG
13757 TATTTT
66 TATTTT
13763 T
1 T
13764 TTGGAAGAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.47
Consensus pattern (71 bp):
TATATGCTGTTTTTAATAAATAATTAGAGATATGTGTTAATTTTAAAAATAATTAGGGATATATG
TATTTT
Found at i:13764 original size:29 final size:30
Alignment explanation
Indices: 13692--13763 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
13682 TATGTATTTT
* *
13692 TATATGCTGTTTTTAATAAATAATTAGAGA
1 TATATGTTATTTTTAATAAATAATTAGAGA
* * *
13722 TATGTGTTAATTTTAA-AAATAATTAGGGA
1 TATATGTTATTTTTAATAAATAATTAGAGA
13751 TATATG-TATTTTT
1 TATATGTTATTTTT
13764 TTGGAAGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
28 6 0.17
29 17 0.49
30 12 0.34
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.47
Consensus pattern (30 bp):
TATATGTTATTTTTAATAAATAATTAGAGA
Found at i:18700 original size:29 final size:29
Alignment explanation
Indices: 18604--18796 Score: 112
Period size: 29 Copynumber: 6.5 Consensus size: 29
18594 ATTTAATAAA
* *
18604 TTTAGGTACCAAATTGAACCTAAAAAAA-
1 TTTAGGTACCAAATTGAGCCAAAAAAAAG
* * * *
18632 CTTAGGTACCAAGTTAAG-AAAAAAATGCCAAG
1 TTTAGGTACCAAATTGAGCCAAAAAA----AAG
*
18664 TTTAGGTACCAAATTGAGCCCAAAAAAAG
1 TTTAGGTACCAAATTGAGCCAAAAAAAAG
*
18693 TTTAGGTACCAAATTGAACCTAAAAAAAA-
1 TTTAGGTACCAAATTGAGCC-AAAAAAAAG
* * *
18722 CTTAGTTACCAAATTAAG--AAAAAATGCCAAG
1 TTTAGGTACCAAATTGAGCCAAAAAA----AAG
* *
18753 TTTAAGTACCAAATTGGGCCCCAAAAAAAA-
1 TTTAGGTACCAAATTGAG--CCAAAAAAAAG
*
18783 -TTAAGTACCAAATT
1 TTTAGGTACCAAATT
18797 AAAAAAAATG
Statistics
Matches: 127, Mismatches: 22, Indels: 31
0.71 0.12 0.17
Matches are distributed among these distances:
26 6 0.05
27 5 0.04
28 14 0.11
29 50 0.39
30 9 0.07
31 17 0.13
32 15 0.12
33 5 0.04
35 6 0.05
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (29 bp):
TTTAGGTACCAAATTGAGCCAAAAAAAAG
Found at i:18755 original size:89 final size:89
Alignment explanation
Indices: 18601--18796 Score: 306
Period size: 89 Copynumber: 2.2 Consensus size: 89
18591 AACATTTAAT
*
18601 AAATTTAGGTACCAAATTGAACCTAAAAAAACTTAGGTACCAAGTTAAGAAAAAAATGCCAAGTT
1 AAATTTAGGTACCAAATTGAACCTAAAAAAACTTAGGTACCAAATTAAGAAAAAAATGCCAAGTT
*
18666 TAGGTACCAAATTGAG-CCCAAAA
66 TAAGTACCAAATTGAGCCCCAAAA
*
18689 AAAGTTTAGGTACCAAATTGAACCTAAAAAAAACTTAGTTACCAAATTAAG-AAAAAATGCCAAG
1 AAA-TTTAGGTACCAAATTGAACCT-AAAAAAACTTAGGTACCAAATTAAGAAAAAAATGCCAAG
*
18753 TTTAAGTACCAAATTGGGCCCCAAAA
64 TTTAAGTACCAAATTGAGCCCCAAAA
* *
18779 AAAATTAAGTACCAAATT
1 AAATTTAGGTACCAAATT
18797 AAAAAAAATG
Statistics
Matches: 99, Mismatches: 6, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
88 3 0.03
89 63 0.64
90 33 0.33
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.22
Consensus pattern (89 bp):
AAATTTAGGTACCAAATTGAACCTAAAAAAACTTAGGTACCAAATTAAGAAAAAAATGCCAAGTT
TAAGTACCAAATTGAGCCCCAAAA
Found at i:18762 original size:60 final size:59
Alignment explanation
Indices: 18690--18860 Score: 199
Period size: 60 Copynumber: 2.9 Consensus size: 59
18680 AGCCCAAAAA
* *
18690 AAGTTTAGGTACCAAATT-GAACCTAAAAAAAACTT-AGTTACCAAATTAAGAAAAAATGCC
1 AAGTTTAAGTACCAAATTGGAACCCAAAAAAAA-TTAAG-TACCAAATTAA-AAAAAATGCC
**
18750 AAGTTTAAGTACCAAATTGGGCCCCAAAAAAAATTAAGTACCAAATTAAAAAAAATGCC
1 AAGTTTAAGTACCAAATTGGAACCCAAAAAAAATTAAGTACCAAATTAAAAAAAATGCC
* ** * *
18809 AAGTTTAAGTACC-AATT-TAA-ATAAAAAAATTTAAGTACTAAATTAAAAAAAA
1 AAGTTTAAGTACCAAATTGGAACCCAAAAAAAATTAAGTACCAAATTAAAAAAAA
18861 AAGTATTAAA
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
56 28 0.29
58 4 0.04
59 23 0.23
60 30 0.31
61 13 0.13
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (59 bp):
AAGTTTAAGTACCAAATTGGAACCCAAAAAAAATTAAGTACCAAATTAAAAAAAATGCC
Found at i:18841 original size:26 final size:25
Alignment explanation
Indices: 18775--18862 Score: 97
Period size: 26 Copynumber: 3.3 Consensus size: 25
18765 ATTGGGCCCC
18775 AAAAAAAA-TTAAGTACCAAATTAA
1 AAAAAAAATTTAAGTACCAAATTAA
*
18799 AAAAAATGCCAAGTTTAAGTACCAATTTAA
1 AAAAAA----AA-TTTAAGTACCAAATTAA
*
18829 ATAAAAAAATTTAAGTACTAAATTAA
1 A-AAAAAAATTTAAGTACCAAATTAA
18855 AAAAAAAA
1 AAAAAAAA
18863 GTATTAAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
24 6 0.11
25 7 0.13
26 16 0.30
27 2 0.04
28 2 0.04
30 16 0.30
31 5 0.09
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.24
Consensus pattern (25 bp):
AAAAAAAATTTAAGTACCAAATTAA
Found at i:20935 original size:30 final size:30
Alignment explanation
Indices: 20880--20941 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
20870 TTGATTTAAT
* *
20880 GTGCAATTGTATACATGAGCTTTAATT-TG
1 GTGCAATTGTACACATGAACTTTAATTATG
*
20909 GTGCAATTGTACACGTGAAACTTTAATTATG
1 GTGCAATTGTACACATG-AACTTTAATTATG
20940 GT
1 GT
20942 TCTGATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.54
30 9 0.32
31 4 0.14
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (30 bp):
GTGCAATTGTACACATGAACTTTAATTATG
Found at i:33055 original size:6 final size:6
Alignment explanation
Indices: 33044--33079 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
33034 GTATATTAGA
*
33044 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTC TCTCTT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT
33080 CACATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
TCTCTT
Found at i:38494 original size:4 final size:4
Alignment explanation
Indices: 38450--38510 Score: 54
Period size: 4 Copynumber: 14.5 Consensus size: 4
38440 CAACCCAAAA
*
38450 TTAT TTAT TCAT TTAACT TT-T TATAT TTCAT TT-T ATTAT TTAT TTAT
1 TTAT TTAT TTAT TT-A-T TTAT T-TAT TT-AT TTAT -TTAT TTAT TTAT
38497 TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TT
38511 CTAGCACCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 3 0.06
4 34 0.71
5 8 0.17
6 3 0.06
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:45817 original size:23 final size:22
Alignment explanation
Indices: 45786--45838 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
45776 ATTATGCATT
*
45786 TTATAAAATTATAAAAAATTATA
1 TTATAAAATCATAAAAAATT-TA
* * *
45809 TTATTAAATCCTAGAAAATTTA
1 TTATAAAATCATAAAAAATTTA
45831 TTATAAAA
1 TTATAAAA
45839 AATTAATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
TTATAAAATCATAAAAAATTTA
Found at i:45892 original size:25 final size:25
Alignment explanation
Indices: 45829--45892 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
45819 CTAGAAAATT
*
45829 TATTATAAAAA-A-T-TAATTTATA
1 TATTATAAAAATATTATAATATATA
*
45851 TATTATAAAAGTATTATAATATATA
1 TATTATAAAAATATTATAATATATA
45876 TATTTATAAAAAT-TTAT
1 TA-TTATAAAAATATTAT
45893 GGCCAAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 10 0.29
23 1 0.03
24 1 0.03
25 14 0.40
26 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TATTATAAAAATATTATAATATATA
Found at i:47003 original size:21 final size:19
Alignment explanation
Indices: 46959--47006 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
46949 GCAACAAAAT
* *
46959 AATAGCAATATAATAGTGA
1 AATAACAATAAAATAGTGA
46978 AATAACAATAAAATAGTGGAA
1 AATAACAATAAAATAGT-G-A
46999 AATAACAA
1 AATAACAA
47007 CAGATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.60
20 1 0.04
21 9 0.36
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.21
Consensus pattern (19 bp):
AATAACAATAAAATAGTGA
Found at i:50598 original size:18 final size:18
Alignment explanation
Indices: 50575--50616 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
50565 GAATAATTTT
*
50575 TTAATTTAATAAATTT-AA
1 TTAATTGAA-AAATTTAAA
*
50593 TTAATTGAAAATTTTAAA
1 TTAATTGAAAAATTTAAA
50611 TTAATT
1 TTAATT
50617 ACAACTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAATTGAAAAATTTAAA
Found at i:52874 original size:24 final size:24
Alignment explanation
Indices: 52841--52891 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
52831 AGAAATAATA
* *
52841 TTTCAGTTAAACTCTGTTTTTTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
52865 TTTCAATTAAGCTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
52889 TTT
1 TTT
52892 GAGTCAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.10, G:0.12, T:0.61
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:61950 original size:5 final size:5
Alignment explanation
Indices: 61940--61975 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
61930 CTTGAAAATG
61940 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT T
1 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT T
61976 TGCTTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TCTCT
Found at i:75480 original size:32 final size:32
Alignment explanation
Indices: 75435--75496 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 32
75425 TTGGGCTTAG
75435 GTCTTGAAAGTTTAAGC-CTGAGCCCGACTCGA
1 GTCTTGAAAGTTTAAGCTC-GAGCCCGACTCGA
75467 GTCTT-AAAGGTTTAAGCTCGAGCCCGACTC
1 GTCTTGAAA-GTTTAAGCTCGAGCCCGACTC
75497 ATATTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 3 0.11
32 24 0.86
33 1 0.04
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (32 bp):
GTCTTGAAAGTTTAAGCTCGAGCCCGACTCGA
Found at i:89409 original size:2 final size:2
Alignment explanation
Indices: 89402--89428 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
89392 TAAACCTGAT
89402 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
89429 TAGTCTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90638 original size:17 final size:19
Alignment explanation
Indices: 90616--90653 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
90606 TTTCAAGGCC
90616 TTAATTT-TTTTCT-TTGT
1 TTAATTTATTTTCTATTGT
90633 TTAATTTAATTTTCTATTGT
1 TTAATTT-ATTTTCTATTGT
90653 T
1 T
90654 ATTAGTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TTAATTTATTTTCTATTGT
Found at i:102355 original size:18 final size:18
Alignment explanation
Indices: 102328--102364 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
102318 TACAGTGAAA
*
102328 AAAGATTCGAATACATGG
1 AAAGACTCGAATACATGG
*
102346 AAAGACTCGAATCCATGG
1 AAAGACTCGAATACATGG
102364 A
1 A
102365 CCAAATGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (18 bp):
AAAGACTCGAATACATGG
Found at i:108235 original size:105 final size:105
Alignment explanation
Indices: 108053--108254 Score: 305
Period size: 105 Copynumber: 1.9 Consensus size: 105
108043 TGAATAAACC
** * * * * * *
108053 TAATCTTATTTGATAAATTAGATTTGGGGTTGTATTATGATTAGTAGTGTACGTTAAAATATGGG
1 TAATCTTATTTGATAAATTAGATTTAAGATTGTATTATAATTAATAATATACGTTAAAATATGAG
* *
108118 GTTTAATTTTATTTGAGTCGTGGTTTTAGATTATTTAATT
66 GTTTAATCTTATTTAAGTCGTGGTTTTAGATTATTTAATT
*
108158 TAATCTTATTTGATAAATTAGATTTAAGATTGTGTTATAATTAATAATATACGTTAAAATATGAG
1 TAATCTTATTTGATAAATTAGATTTAAGATTGTATTATAATTAATAATATACGTTAAAATATGAG
108223 GTTTAATCTTATTTAAGTCGTGGTTTTAGATT
66 GTTTAATCTTATTTAAGTCGTGGTTTTAGATT
108255 TCCATTGTGT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 86 1.00
ACGTcount: A:0.31, C:0.03, G:0.18, T:0.48
Consensus pattern (105 bp):
TAATCTTATTTGATAAATTAGATTTAAGATTGTATTATAATTAATAATATACGTTAAAATATGAG
GTTTAATCTTATTTAAGTCGTGGTTTTAGATTATTTAATT
Found at i:116087 original size:14 final size:14
Alignment explanation
Indices: 116031--116102 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 14
116021 ATAGGCATTA
116031 AAAAATATAAATAT
1 AAAAATATAAATAT
116045 AAAAA-ATCGGAAATAT
1 AAAAATAT---AAATAT
116061 ATATAATATATAAA-AT
1 A-A-AA-ATATAAATAT
116077 AAAACATATAAATTAT
1 AAAA-ATATAAA-TAT
116093 AAAAATATAA
1 AAAAATATAA
116103 TTAGCTTATG
Statistics
Matches: 48, Mismatches: 1, Indels: 17
0.73 0.02 0.26
Matches are distributed among these distances:
13 2 0.04
14 14 0.29
15 7 0.15
16 16 0.33
17 4 0.08
18 2 0.04
19 1 0.02
20 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (14 bp):
AAAAATATAAATAT
Found at i:118364 original size:15 final size:16
Alignment explanation
Indices: 118333--118365 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
118323 ATGAGACTCA
*
118333 TATTTTTTAATAAATT
1 TATTTATTAATAAATT
118349 TATTTATTAA-AAATT
1 TATTTATTAATAAATT
118364 TA
1 TA
118366 ATATAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTATTAATAAATT
Found at i:118516 original size:21 final size:21
Alignment explanation
Indices: 118492--118531 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
118482 AAGACAAAAA
*
118492 TACTTTGATA-ATAATATAACT
1 TACTTT-ATATATAAAATAACT
118513 TACTTTATATATAAAATAA
1 TACTTTATATATAAAATAA
118532 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (21 bp):
TACTTTATATATAAAATAACT
Found at i:119169 original size:9 final size:9
Alignment explanation
Indices: 119133--119225 Score: 61
Period size: 9 Copynumber: 10.6 Consensus size: 9
119123 ATATGACAAA
119133 AAAAATTAT
1 AAAAATTAT
119142 AAAAA--AT
1 AAAAATTAT
*
119149 AAAAATCAAT
1 AAAAAT-TAT
119159 AAAAATTAT
1 AAAAATTAT
119168 AAAAA-TATT
1 AAAAATTA-T
**
119177 AAATTTTAAT
1 AAAAATT-AT
*
119187 AAAAACTA-
1 AAAAATTAT
* *
119195 CAAAATTAC
1 AAAAATTAT
*
119204 AAAAATCAT
1 AAAAATTAT
119213 AAAAA-TAT
1 AAAAATTAT
119221 AAAAA
1 AAAAA
119226 AGTATTTTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
7 7 0.11
8 15 0.23
9 28 0.43
10 14 0.22
11 1 0.02
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAAATTAT
Found at i:119169 original size:19 final size:18
Alignment explanation
Indices: 119133--119225 Score: 72
Period size: 17 Copynumber: 5.3 Consensus size: 18
119123 ATATGACAAA
*
119133 AAAAATTATAAAAA--AT
1 AAAAATCATAAAAATTAT
119149 AAAAATCAATAAAAATTAT
1 AAAAATC-ATAAAAATTAT
**
119168 AAAAAT-ATTAAATTTTAAT
1 AAAAATCA-TAAAAATT-AT
*
119187 AAAAA-C-TACAAAATTAC
1 AAAAATCATA-AAAATTAT
119204 AAAAATCATAAAAA-TAT
1 AAAAATCATAAAAATTAT
119221 AAAAA
1 AAAAA
119226 AGTATTTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
16 6 0.10
17 23 0.38
18 15 0.25
19 17 0.28
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATCATAAAAATTAT
Found at i:119169 original size:26 final size:26
Alignment explanation
Indices: 119133--119226 Score: 84
Period size: 26 Copynumber: 3.6 Consensus size: 26
119123 ATATGACAAA
119133 AAAAATTATAAAAAATAAAAATCAAT
1 AAAAATTATAAAAAATAAAAATCAAT
** *
119159 AAAAATTATAAAAATATTAAATTTTAAT
1 AAAAATTATAAAAA-A-TAAAAATCAAT
* * * *
119187 AAAAACTACAAAATTACAAAAATC-AT
1 AAAAATTATAAAA-AATAAAAATCAAT
119213 AAAAA-TATAAAAAA
1 AAAAATTATAAAAAA
119227 GTATTTTTTA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
24 1 0.02
25 6 0.11
26 21 0.40
27 5 0.09
28 20 0.38
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (26 bp):
AAAAATTATAAAAAATAAAAATCAAT
Found at i:119319 original size:19 final size:19
Alignment explanation
Indices: 119246--119328 Score: 60
Period size: 19 Copynumber: 4.4 Consensus size: 19
119236 ATAAAAACAG
*
119246 TAAAAATTATAAAAAAACTA
1 TAAAAA-TATAAAAAAATTA
* ** * *
119266 TTACTATAGAAAAATATTA
1 TAAAAATATAAAAAAATTA
* * * *
119285 TAACATTGTAAGAAAATTA
1 TAAAAATATAAAAAAATTA
119304 TAAAAATATAAAAAAA-TA
1 TAAAAATATAAAAAAATTA
119322 TAAAAAT
1 TAAAAAT
119329 TATCGTATCA
Statistics
Matches: 46, Mismatches: 17, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
18 9 0.20
19 34 0.74
20 3 0.07
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
TAAAAATATAAAAAAATTA
Found at i:121520 original size:55 final size:56
Alignment explanation
Indices: 121456--121582 Score: 161
Period size: 55 Copynumber: 2.3 Consensus size: 56
121446 GATGTGTTGT
* * *
121456 ATAATAATTGATTTAAAAT-TATAAATAATCGATTTAAAAAAAATATTATT-TCAAC
1 ATAACAATTGATTTAAAATATATAAACAATCGATTCAAAAAAAATATTATTCT-AAC
* *
121511 ATACCAATTGATTT-AAATATATAAACAATCGATTCAAAAGAAATATTATTCTAAC
1 ATAACAATTGATTTAAAATATATAAACAATCGATTCAAAAAAAATATTATTCTAAC
* *
121566 ATAATAATCGATTTAAA
1 ATAACAATTGATTTAAA
121583 CATACTGCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
54 4 0.07
55 54 0.89
56 3 0.05
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (56 bp):
ATAACAATTGATTTAAAATATATAAACAATCGATTCAAAAAAAATATTATTCTAAC
Found at i:123538 original size:17 final size:17
Alignment explanation
Indices: 123516--123578 Score: 92
Period size: 17 Copynumber: 3.7 Consensus size: 17
123506 TTGGAAATTG
*
123516 AATTTAAGTTTATTTGA
1 AATTTAAATTTATTTGA
123533 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTGA
123550 AATTTAAATTTATTAT-A
1 AATTTAAATTTATT-TGA
*
123567 AAATTAAATTTA
1 AATTTAAATTTA
123579 GAAAAGTCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
17 42 0.98
18 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTATTTGA
Found at i:123640 original size:15 final size:15
Alignment explanation
Indices: 123622--123680 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
123612 AGTCCAAATT
123622 ACAAATGGCCCAATA
1 ACAAATGGCCCAATA
* *
123637 ACAAATGGCCCAGTT
1 ACAAATGGCCCAATA
*
123652 ACAGATGGCCCAA-A
1 ACAAATGGCCCAATA
*
123666 TACAAATGGTCCAAT
1 -ACAAATGGCCCAAT
123681 TATAAAGTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (15 bp):
ACAAATGGCCCAATA
Found at i:123640 original size:30 final size:29
Alignment explanation
Indices: 123602--123671 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
123592 ACAAAAAAAT
*
123602 CCAAAACAAAAGTCCAAATTACAAATGGC
1 CCAAAACAAAAGGCCAAATTACAAATGGC
* * * *
123631 CCAATAACAAATGGCCCAGTTACAGATGGC
1 CCAA-AACAAAAGGCCAAATTACAAATGGC
123661 CCAAATACAAA
1 CCAAA-ACAAA
123672 TGGTCCAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.47, C:0.26, G:0.13, T:0.14
Consensus pattern (29 bp):
CCAAAACAAAAGGCCAAATTACAAATGGC
Found at i:125240 original size:12 final size:12
Alignment explanation
Indices: 125223--125247 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
125213 ATTTTATAAC
125223 ATAAATATTGTT
1 ATAAATATTGTT
125235 ATAAATATTGTT
1 ATAAATATTGTT
125247 A
1 A
125248 ATAGCCTCTG
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:126299 original size:12 final size:12
Alignment explanation
Indices: 126282--126306 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
126272 TGACCCGTTT
126282 TCCTATAATCTA
1 TCCTATAATCTA
126294 TCCTATAATCTA
1 TCCTATAATCTA
126306 T
1 T
126307 AATATAGAAA
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:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (12 bp):
TCCTATAATCTA
Found at i:128085 original size:2 final size:2
Alignment explanation
Indices: 128073--128103 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
128063 AATAACGAAT
*
128073 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 T
128104 TATTAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:136908 original size:45 final size:46
Alignment explanation
Indices: 136853--136969 Score: 148
Period size: 45 Copynumber: 2.5 Consensus size: 46
136843 ATAGACCAAT
*
136853 AATATGGTCTTTCCTTATGATGCTATAGCCTAACTAT-TCTTACAC
1 AATATGGTCTTTCCTTATGATGCTATAGCCCAACTATGTCTTACAC
* ** *
136898 AATATTGTCTTTCCTTATGATG-TCATAGCCCAGTTATGGTTTTACAC
1 AATATGGTCTTTCCTTATGATGCT-ATAGCCCAACTAT-GTCTTACAC
*
136945 AATATGGCCTTTCCTTATGATGCTA
1 AATATGGTCTTTCCTTATGATGCTA
136970 ATCGGCCTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
44 1 0.02
45 31 0.51
47 28 0.46
48 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.41
Consensus pattern (46 bp):
AATATGGTCTTTCCTTATGATGCTATAGCCCAACTATGTCTTACAC
Found at i:147167 original size:21 final size:21
Alignment explanation
Indices: 147141--147182 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
147131 GATACCCAAT
*
147141 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACATTTTG
147162 AAAAGGTATCGATACATTTTG
1 AAAAGGTATCGATACATTTTG
147183 TCATTGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (21 bp):
AAAAGGTATCGATACATTTTG
Found at i:152003 original size:26 final size:25
Alignment explanation
Indices: 151932--152003 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
151922 GCCGTTACAG
*
151932 AAATATAGCTCATTCAATGCCAGATA
1 AAATATAGCTCATTCAA-GCCAGAAA
* * * **
151958 GATTATTGCTCATTTGAGCCTAGAAA
1 AAATATAGCTCATTCAAGCC-AGAAA
151984 AAATATAGCTCATTCAAGCC
1 AAATATAGCTCATTCAAGCC
152004 CAAAGCAGAG
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
25 3 0.09
26 31 0.91
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (25 bp):
AAATATAGCTCATTCAAGCCAGAAA
Found at i:162522 original size:15 final size:15
Alignment explanation
Indices: 162502--162548 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
162492 CATTTTCATC
162502 TTTTCTTTTATTTGT
1 TTTTCTTTTATTTGT
162517 TTTTCTTTTATTTGT
1 TTTTCTTTTATTTGT
** *
162532 TTCACTTTTACTTGT
1 TTTTCTTTTATTTGT
162547 TT
1 TT
162549 CGTTTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.09, C:0.11, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTCTTTTATTTGT
Found at i:168789 original size:21 final size:21
Alignment explanation
Indices: 168751--168792 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
168741 TACTGAAGGG
* * *
168751 GAGGAAACACAAGTTGAAGAA
1 GAGGAAAAAAAAGATGAAGAA
168772 GAGGAAAAAAAAGATGAAGAA
1 GAGGAAAAAAAAGATGAAGAA
168793 AAAATGCTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.29, T:0.07
Consensus pattern (21 bp):
GAGGAAAAAAAAGATGAAGAA
Found at i:169246 original size:17 final size:17
Alignment explanation
Indices: 169224--169257 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
169214 TGTTAGTAAG
*
169224 CATTGTCGTTGCATTTT
1 CATTGTCATTGCATTTT
169241 CATTGTCATTGCATTTT
1 CATTGTCATTGCATTTT
169258 AGTGTTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.53
Consensus pattern (17 bp):
CATTGTCATTGCATTTT
Found at i:170389 original size:38 final size:38
Alignment explanation
Indices: 170308--170390 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
170298 TTAGTCTATT
* **
170308 CAGAATTGCGCCCAAAATTGTCACTACATGATGATGTT
1 CAGAATTACGCCCAAAATTGTCACTACATGATGATGCC
* * *
170346 TAGAATTACGGCCAAAATTGTCACTGCATGA-GCATGCC
1 CAGAATTACGCCCAAAATTGTCACTACATGATG-ATGCC
170384 CAGAATT
1 CAGAATT
170391 GTCGCTGTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
37 1 0.03
38 36 0.97
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (38 bp):
CAGAATTACGCCCAAAATTGTCACTACATGATGATGCC
Found at i:173406 original size:53 final size:52
Alignment explanation
Indices: 173112--173407 Score: 357
Period size: 52 Copynumber: 5.7 Consensus size: 52
173102 TACATTTTTT
* * * * * * *
173112 TATACTCACAATGACACAGAGTCATCGGACCATTAATCGGTATTGGGAATCA
1 TATACTCACAATGACACAGAGTCATCGAACCTTTAATCCGAAATAGGATTCA
* * * *
173164 TATACTCACGATGACACATAGTTATCGAACCTTATAATCC-ATAA-AAGATTCA
1 TATACTCACAATGACACAGAGTCATCGAACCTT-TAATCCGA-AATAGGATTCA
* *
173216 TATACTCACGATGACACAGAGTCATCGAACCTGTAATCCGAAATAGGATTCA
1 TATACTCACAATGACACAGAGTCATCGAACCTTTAATCCGAAATAGGATTCA
* *
173268 TATACTCACGATGACACAGAGTCATC-AGACCTGTAATCCGAAATAGGATTCA
1 TATACTCACAATGACACAGAGTCATCGA-ACCTTTAATCCGAAATAGGATTCA
* *
173320 TATAACTCATAATGACACAGAGTCATC-AGACCTTTAATCCAAAATAGGATTCA
1 TAT-ACTCACAATGACACAGAGTCATCGA-ACCTTTAATCCGAAATAGGATTCA
173373 TATAACTCACAATGACACAGAGTCATCGAACCTTT
1 TAT-ACTCACAATGACACAGAGTCATCGAACCTTT
173408 TTGCATTTAC
Statistics
Matches: 217, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
51 9 0.04
52 124 0.57
53 83 0.38
54 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (52 bp):
TATACTCACAATGACACAGAGTCATCGAACCTTTAATCCGAAATAGGATTCA
Found at i:173809 original size:144 final size:144
Alignment explanation
Indices: 173549--173834 Score: 482
Period size: 144 Copynumber: 2.0 Consensus size: 144
173539 AATACGAACT
* *
173549 TACCAGACTAGATTGCAGTTGTTGAATAGATTTCTAGGACTAATCCACAACTTTTCCTTTTCCAT
1 TACCAGACTAGATTACAGTTGTTGAATAGATTTCTAGGACTAATCCACAACTTTTCCTTTTCCAA
* *
173614 GATCTACAACTCGATCGTAATCTAACACAACAATCATCCAATTTCTCACATTAAATCATGTATTA
66 GATATACAACTCGATCGTAATCTAACACAACAATCATCCAATTTCTCACATTAAATAATGTATTA
173679 AATCATCTAAAACA
131 AATCATCTAAAACA
* *
173693 TACCAGACTAGATTACAGTTGTTTAATAGATTTCTAGGACTAATCCGCAACTTTTCCTTTTCCAA
1 TACCAGACTAGATTACAGTTGTTGAATAGATTTCTAGGACTAATCCACAACTTTTCCTTTTCCAA
* **
173758 GATATGCGGCTCGATCGTAATCTAACACAACAATCATCCAATTTCTCACATTAAATAATGTATTA
66 GATATACAACTCGATCGTAATCTAACACAACAATCATCCAATTTCTCACATTAAATAATGTATTA
*
173823 AATCATTTAAAA
131 AATCATCTAAAA
173835 ATTTTAATTT
Statistics
Matches: 132, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 132 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (144 bp):
TACCAGACTAGATTACAGTTGTTGAATAGATTTCTAGGACTAATCCACAACTTTTCCTTTTCCAA
GATATACAACTCGATCGTAATCTAACACAACAATCATCCAATTTCTCACATTAAATAATGTATTA
AATCATCTAAAACA
Found at i:176157 original size:27 final size:25
Alignment explanation
Indices: 176089--176158 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 25
176079 GTCGTTATAG
* *
176089 AAATATAGCTTATTCAAGCCTAGAC
1 AAATATAGCTCATTCGAGCCTAGAC
*
176114 AAATTATTGCTCATTCGAGCCTAGACC
1 AAA-TATAGCTCATTCGAGCCTAGA-C
176141 AGAATATAGCTCATTCGA
1 A-AATATAGCTCATTCGA
176159 ACCCAGAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 3 0.08
26 18 0.47
27 15 0.39
28 2 0.05
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (25 bp):
AAATATAGCTCATTCGAGCCTAGAC
Found at i:176170 original size:27 final size:27
Alignment explanation
Indices: 176122--176242 Score: 125
Period size: 27 Copynumber: 4.5 Consensus size: 27
176112 ACAAATTATT
* * * *
176122 GCTCATTCGAGCCTAGACCAGAATATA
1 GCTCATTCGAGCCCAGAACAGAGTTTA
* *
176149 GCTCATTCGAACCCAGAACAGATTTTA
1 GCTCATTCGAGCCCAGAACAGAGTTTA
* * *
176176 GCTTATTTGAGCCCAGAACATAGTTTA
1 GCTCATTCGAGCCCAGAACAGAGTTTA
* * *
176203 GATCATTTGAGCCCAAAACAGAGTTTA
1 GCTCATTCGAGCCCAGAACAGAGTTTA
*
176230 GCTCATTTGAGCC
1 GCTCATTCGAGCC
176243 TGGAATAGAT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 79 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (27 bp):
GCTCATTCGAGCCCAGAACAGAGTTTA
Found at i:176325 original size:28 final size:28
Alignment explanation
Indices: 176285--176342 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
176275 CTAGAATATT
* * *
176285 GCTCTTGCAAGCT-AGAGTACAGAGTTAC
1 GCTCTTACAAGCTCA-AATACAGAATTAC
*
176313 GCTCTTACGAGCTCAAATACAGAATTAC
1 GCTCTTACAAGCTCAAATACAGAATTAC
176341 GC
1 GC
176343 CTTGAGCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (28 bp):
GCTCTTACAAGCTCAAATACAGAATTAC
Found at i:180795 original size:16 final size:16
Alignment explanation
Indices: 180751--180797 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
180741 GGAGAATGTG
*
180751 TAAAAAAACAT-AAATA
1 TAAATAAACATGAAA-A
*
180767 TAAATAGACATGAAAA
1 TAAATAAACATGAAAA
*
180783 TAAATAAAGATGAAA
1 TAAATAAACATGAAA
180798 TAAGAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 23 0.88
17 3 0.12
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19
Consensus pattern (16 bp):
TAAATAAACATGAAAA
Found at i:184514 original size:21 final size:21
Alignment explanation
Indices: 184452--184505 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
184442 TATTAGAGTT
** *
184452 AAAAACCCTAAA-CCCTAATC
1 AAAAACCCTAAATCCAAAACC
184472 ATAAAACCCTAAATCCAAAACC
1 A-AAAACCCTAAATCCAAAACC
184494 AAAAACCCTAAA
1 AAAAACCCTAAA
184506 CATAAAACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 22 0.76
22 6 0.21
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.13
Consensus pattern (21 bp):
AAAAACCCTAAATCCAAAACC
Found at i:184962 original size:26 final size:26
Alignment explanation
Indices: 184931--185115 Score: 237
Period size: 26 Copynumber: 7.1 Consensus size: 26
184921 ACCCAAAACC
184931 TTAAATACAAACATAAACATAATTAA
1 TTAAATACAAACATAAACATAATTAA
* *
184957 TGAAATACAAAAATAAACATAATTAA
1 TTAAATACAAACATAAACATAATTAA
* * *
184983 -TGAATACAAAAATAAACATTATTAA
1 TTAAATACAAACATAAACATAATTAA
185008 TTAAATACAAACATAAACATAATTAA
1 TTAAATACAAACATAAACATAATTAA
* *
185034 TTAAATATAAACATAAACATTATTAA
1 TTAAATACAAACATAAACATAATTAA
*
185060 TTAAATACAAATATAAACATAATTAA
1 TTAAATACAAACATAAACATAATTAA
* ** *
185086 TTCCAAATTCATTCGTAAACATAATTAA
1 TT--AAATACAAACATAAACATAATTAA
185114 TT
1 TT
185116 CCAAATGAAA
Statistics
Matches: 138, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
25 22 0.16
26 95 0.69
28 21 0.15
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (26 bp):
TTAAATACAAACATAAACATAATTAA
Found at i:185059 original size:77 final size:78
Alignment explanation
Indices: 184931--185115 Score: 246
Period size: 77 Copynumber: 2.4 Consensus size: 78
184921 ACCCAAAACC
* *
184931 TTAAATACAAACATAAACATAATTAATGAAATACAAAAATAAACATAATTAA-TGAATACAAAAA
1 TTAAATACAAACATAAACATAATTAATTAAATACAAAAATAAACATAATTAATTAAATACAAAAA
*
184995 TAAACATTATTAA
66 TAAACATAATTAA
* * * *
185008 TTAAATACAAACATAAACATAATTAATTAAATATAAACATAAACATTATTAATTAAATACAAATA
1 TTAAATACAAACATAAACATAATTAATTAAATACAAAAATAAACATAATTAATTAAATACAAAAA
185073 TAAACATAATTAA
66 TAAACATAATTAA
* ** *
185086 TTCCAAATTCATTCGTAAACATAATTAATT
1 TT--AAATACAAACATAAACATAATTAATT
185116 CCAAATGAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
77 48 0.51
78 24 0.26
80 22 0.23
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (78 bp):
TTAAATACAAACATAAACATAATTAATTAAATACAAAAATAAACATAATTAATTAAATACAAAAA
TAAACATAATTAA
Found at i:185092 original size:22 final size:24
Alignment explanation
Indices: 185057--185121 Score: 62
Period size: 28 Copynumber: 2.6 Consensus size: 24
185047 TAAACATTAT
* *
185057 TAATTAAATACAAAT-A-TAAACA
1 TAATTAATTCCAAATCATTAAACA
185079 TAATTAATTCCAAATTCATTCGTAAACA
1 TAATTAATTCCAAA-TCA-T--TAAACA
185107 TAATTAATTCCAAAT
1 TAATTAATTCCAAAT
185122 GAAAAATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
22 12 0.34
23 1 0.03
24 1 0.03
27 1 0.03
28 20 0.57
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.34
Consensus pattern (24 bp):
TAATTAATTCCAAATCATTAAACA
Found at i:185509 original size:27 final size:27
Alignment explanation
Indices: 185479--185543 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
185469 ATGATACTCG
*
185479 TGGCTTGACCAACCCGTGTAATATCCA
1 TGGCTTGACCAACCCGTATAATATCCA
*
185506 TGGCTTGACCAACCCGTATGATATCCA
1 TGGCTTGACCAACCCGTATAATATCCA
*
185533 TCGCTTGACCA
1 TGGCTTGACCA
185544 CCTCAGATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (27 bp):
TGGCTTGACCAACCCGTATAATATCCA
Found at i:185626 original size:6 final size:6
Alignment explanation
Indices: 185606--185639 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
185596 TCAAGCTCAT
* *
185606 GCTCAG GCTCAG GCTCGG GCTCGG GCTCGG GCTC
1 GCTCGG GCTCGG GCTCGG GCTCGG GCTCGG GCTC
185640 AGGCAGATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.06, C:0.35, G:0.41, T:0.18
Consensus pattern (6 bp):
GCTCGG
Found at i:185626 original size:12 final size:12
Alignment explanation
Indices: 185582--185643 Score: 70
Period size: 12 Copynumber: 5.2 Consensus size: 12
185572 TCGAGCTAAT
*
185582 GCTCGGGCTCAA
1 GCTCGGGCTCAG
** *
185594 GCTCAAGCTCAT
1 GCTCGGGCTCAG
*
185606 GCTCAGGCTCAG
1 GCTCGGGCTCAG
*
185618 GCTCGGGCTCGG
1 GCTCGGGCTCAG
185630 GCTCGGGCTCAG
1 GCTCGGGCTCAG
185642 GC
1 GC
185644 AGATGAAAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.13, C:0.34, G:0.35, T:0.18
Consensus pattern (12 bp):
GCTCGGGCTCAG
Found at i:185632 original size:18 final size:18
Alignment explanation
Indices: 185582--185639 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
185572 TCGAGCTAAT
* *
185582 GCTCGGGCTCAAGCTCAA
1 GCTCGGGCTCAGGCTCAG
**
185600 GCTCATGCTCAGGCTCAG
1 GCTCGGGCTCAGGCTCAG
* *
185618 GCTCGGGCTCGGGCTCGG
1 GCTCGGGCTCAGGCTCAG
185636 GCTC
1 GCTC
185640 AGGCAGATGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.12, C:0.34, G:0.34, T:0.19
Consensus pattern (18 bp):
GCTCGGGCTCAGGCTCAG
Found at i:187645 original size:26 final size:26
Alignment explanation
Indices: 187591--187666 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 26
187581 TTTCATGTAA
* * *
187591 TTTATTGAAAAAAGTAACAAT-T-TTA
1 TTTATTG-AAAAATTAAAAATATCTTG
187616 TTTATTGAAAAATTAAAAATATCTTG
1 TTTATTGAAAAATTAAAAATATCTTG
**
187642 TTTATAAAAAAATT-AAAATATCTTG
1 TTTATTGAAAAATTAAAAATATCTTG
187667 AGAAATAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
24 11 0.25
25 19 0.43
26 14 0.32
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.41
Consensus pattern (26 bp):
TTTATTGAAAAATTAAAAATATCTTG
Found at i:187674 original size:26 final size:26
Alignment explanation
Indices: 187623--187674 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
187613 TTATTTATTG
***
187623 AAAAATTAAAAATATCTTGTTTATAA
1 AAAAATTAAAAATATCTTGGAAATAA
187649 AAAAATT-AAAATATCTTGAGAAATAA
1 AAAAATTAAAAATATCTTG-GAAATAA
187675 TAAATGATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.33
Consensus pattern (26 bp):
AAAAATTAAAAATATCTTGGAAATAA
Found at i:189180 original size:6 final size:7
Alignment explanation
Indices: 189162--189186 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
189152 TAAATATATT
189162 ATTTTTA
1 ATTTTTA
189169 ATTTTTA
1 ATTTTTA
189176 ATTTTTA
1 ATTTTTA
189183 ATTT
1 ATTT
189187 ATCTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:189299 original size:29 final size:29
Alignment explanation
Indices: 189243--189299 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
189233 TAGTAAATAT
* * *
189243 AATTTTTATATGTGTAATATTTATTTTTC
1 AATTTTCATATGTGTAATATTAAATTTTC
189272 AATTTTCATTATGTGT-ATATTAAATTTT
1 AATTTTCA-TATGTGTAATATTAAATTTT
189300 TGTATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.60
Consensus pattern (29 bp):
AATTTTCATATGTGTAATATTAAATTTTC
Found at i:189299 original size:30 final size:29
Alignment explanation
Indices: 189243--189300 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
189233 TAGTAAATAT
* *
189243 AATTTTTATATGTGTAATATTTATTTTTC
1 AATTTTCATATGTGTAATATTAATTTTTC
189272 AATTTTCATTATGTGT-ATATTAAATTTTT
1 AATTTTCA-TATGTGTAATATT-AATTTTT
189301 GTATTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.60
Consensus pattern (29 bp):
AATTTTCATATGTGTAATATTAATTTTTC
Found at i:199680 original size:15 final size:15
Alignment explanation
Indices: 199660--199698 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
199650 TCCTTTTTCC
199660 ATGCTCGCAACATCA
1 ATGCTCGCAACATCA
* *
199675 ATGCTCGTAACATTA
1 ATGCTCGCAACATCA
*
199690 GTGCTCGCA
1 ATGCTCGCA
199699 TCAAAGGTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (15 bp):
ATGCTCGCAACATCA
Found at i:201030 original size:12 final size:12
Alignment explanation
Indices: 200996--201030 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
200986 GTTCACGAAC
200996 AAGCTCGTTTAA
1 AAGCTCGTTTAA
* *
201008 AAACTCATTTAA
1 AAGCTCGTTTAA
201020 AAGCTCGTTTA
1 AAGCTCGTTTA
201031 TTGACTTGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (12 bp):
AAGCTCGTTTAA
Found at i:201041 original size:12 final size:12
Alignment explanation
Indices: 201023--201055 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
201013 CATTTAAAAG
201023 CTCGTTTATTGA
1 CTCGTTTATTGA
*
201035 CTTGTTTA-TGA
1 CTCGTTTATTGA
201046 CTCGTTTATT
1 CTCGTTTATT
201056 TATTAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:218816 original size:22 final size:19
Alignment explanation
Indices: 218787--218826 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 19
218777 TTTTATGTGG
218787 AATTTTGAATTGAAAGATTTT
1 AATTTTGAATT-AAA-ATTTT
218808 AATTATTGAATTAAAATTT
1 AATT-TTGAATTAAAATTT
218827 AGTACAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (19 bp):
AATTTTGAATTAAAATTTT
Found at i:220469 original size:24 final size:24
Alignment explanation
Indices: 220437--220495 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
220427 TTAAACTCTA
220437 TCTGGGCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
220461 TCTGGGCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
*
220485 TTTGGGCTCGT
1 TCTGGGCTCGT
220496 GTGGGTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAACCAT
Found at i:221435 original size:17 final size:16
Alignment explanation
Indices: 221372--221449 Score: 57
Period size: 17 Copynumber: 4.6 Consensus size: 16
221362 GGTGTTACAG
* *
221372 TTGTCATCACATTCCCA
1 TTGTCATTACATT-TCA
* *
221389 TTTTCATTACATTCTAA
1 TTGTCATTACATT-TCA
* *
221406 TTGTCGTTGCATTTGCA
1 TTGTCATTACATTT-CA
221423 TTGTCATTACATTTCTA
1 TTGTCATTACATTTC-A
221440 TTTGTCATTA
1 -TTGTCATTA
221450 TAATTTATTG
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
16 2 0.04
17 37 0.77
18 9 0.19
ACGTcount: A:0.22, C:0.21, G:0.09, T:0.49
Consensus pattern (16 bp):
TTGTCATTACATTTCA
Found at i:240751 original size:21 final size:22
Alignment explanation
Indices: 240727--240771 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
240717 ATCTTTATGC
240727 TTTTTAAA-AT-TTATTTTAAAA
1 TTTTTAAATATATT-TTTTAAAA
240748 -TTTTAAATATATTTTTTAAAA
1 TTTTTAAATATATTTTTTAAAA
240769 TTT
1 TTT
240772 AATTATGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.33
21 10 0.48
22 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTTAAATATATTTTTTAAAA
Found at i:242088 original size:22 final size:22
Alignment explanation
Indices: 242060--242114 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
242050 TTGCAACCGA
242060 GGCTTTTATTTATTA-TCTGCTT
1 GGCTTTTATTTATTACT-TGCTT
*
242082 GGCTTTTATTTATTACTTGTTT
1 GGCTTTTATTTATTACTTGCTT
242104 GGCTTTTATTT
1 GGCTTTTATTT
242115 TTTCTTCGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.13, C:0.11, G:0.15, T:0.62
Consensus pattern (22 bp):
GGCTTTTATTTATTACTTGCTT
Found at i:243406 original size:6 final size:6
Alignment explanation
Indices: 243395--243420 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
243385 GCCTCCTCGG
243395 CTCTCC CTCTCC CTCTCC CTCTCC CT
1 CTCTCC CTCTCC CTCTCC CTCTCC CT
243421 ATCTCTCCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CTCTCC
Found at i:247763 original size:29 final size:28
Alignment explanation
Indices: 247726--248041 Score: 205
Period size: 29 Copynumber: 10.8 Consensus size: 28
247716 GAAAAAAATA
247726 GGGTCAAAAATG-AAGTTTTGGAGAGTTCG
1 GGGT-AAAAATGTAA-TTTTGGAGAGTTCG
* * * * *
247755 GGGTTAAAACGTAATTTTGGAAAATTTTAG
1 GGGTAAAAATGTAATTTTGG-AGA-GTTCG
*
247785 GGGTAAAAATGTAATTTTGAGAGAGTTTG
1 GGGTAAAAATGTAATTTTG-GAGAGTTCG
*
247814 GGGTAAAAATGTGATTTTTGGA-AGTTCGG
1 GGGTAAAAATGT-AATTTTGGAGAGTTC-G
* *
247843 GGGTAAAAATGTGACTTTTGGA-AGTTTG
1 GGGTAAAAATGT-AATTTTGGAGAGTTCG
* ** *
247871 GGAGCAAAAATGTAATTTTTAAGAAGTTTAG
1 GG-GTAAAAATGTAATTTTGGAG-AG-TTCG
*
247902 GGGTAAAAATGTGATTTTTGGA-AGTTCG
1 GGGTAAAAATGT-AATTTTGGAGAGTTCG
* *
247930 AGGGTAAAAATGTGATTTTTGGA-AGTTAGG
1 -GGGTAAAAATGT-AATTTTGGAGAGTT-CG
* *
247960 GGGCAAAAATGTAATTTTTTGGA-AGTTTAG
1 GGGTAAAAATGTAA--TTTTGGAGAG-TTCG
* * *
247990 GGATAAAAATGTGATTTT-TAGAAGTTCG
1 GGGTAAAAATGTAATTTTGGAG-AGTTCG
*
248018 AGGGTAAAAATGTAATTTTTGAGA
1 -GGGTAAAAATGTAATTTTGGAGA
248042 AGTTTGAAGG
Statistics
Matches: 231, Mismatches: 36, Indels: 40
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.00
28 35 0.15
29 118 0.51
30 63 0.27
31 14 0.06
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTGGAGAGTTCG
Found at i:247862 original size:59 final size:57
Alignment explanation
Indices: 247784--248071 Score: 344
Period size: 59 Copynumber: 4.9 Consensus size: 57
247774 GAAAATTTTA
247784 GGGGTAAAAATGTAA-TTTTGAGAGAGTTTGGGGTAAAAATGTGATTTTTGGAAGTTCG
1 GGGGTAAAAATGTAATTTTTG-GA-AGTTTGGGGTAAAAATGTGATTTTTGGAAGTTCG
* * * * * **
247842 GGGGTAAAAATGTGACTTTTGGAAGTTTGGGAGCAAAAATGTAATTTTTAAGAAGTTTA
1 GGGGTAAAAATGTAATTTTTGGAAGTTTGGG-GTAAAAATGTGATTTTT-GGAAGTTCG
* * *
247901 GGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTAG
1 GGGGTAAAAATGTAATTTTTGGAAGTTTG-GGGTAAAAATGTGATTTTTGGAAGTTCG
* * *
247959 GGGGCAAAAATGTAATTTTTTGGAAGTTTAGGGATAAAAATGTGATTTTTAGAAGTTCG
1 GGGGTAAAAATGTAA-TTTTTGGAAGTTT-GGGGTAAAAATGTGATTTTTGGAAGTTCG
* * *
248018 AGGGTAAAAATGTAATTTTTGAGAAGTTTGAAGGTAAAAATATGATTTTTGGAA
1 GGGGTAAAAATGTAATTTTTG-GAAGTTTG-GGGTAAAAATGTGATTTTTGGAA
248072 AGATCAGAGA
Statistics
Matches: 197, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
57 8 0.04
58 57 0.29
59 129 0.65
60 3 0.02
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (57 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTTGGGGTAAAAATGTGATTTTTGGAAGTTCG
Found at i:247921 original size:88 final size:88
Alignment explanation
Indices: 247789--248047 Score: 396
Period size: 88 Copynumber: 2.9 Consensus size: 88
247779 TTTTAGGGGT
* *
247789 AAAAATGTAA-TTTTGAGAGAGTTT-GGGGTAAAAATGTGATTTTTGGAAGTTCGGGGGTAAAAA
1 AAAAATGTAATTTTTAAGA-AGTTTAGGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAA
*
247852 TGTGACTTTTGGAAGTTTGGGAGC
65 TGTGATTTTTGGAAGTTTGGGAGC
247876 AAAAATGTAATTTTTAAGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAAT
1 AAAAATGTAATTTTTAAGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAAT
* *
247941 GTGATTTTTGGAAGTTAGGGGGC
66 GTGATTTTTGGAAGTTTGGGAGC
** * *
247964 AAAAATGTAATTTTTTGGAAGTTTAGGGATAAAAATGTGATTTTTAGAAGTTCGAGGGTAAAAAT
1 AAAAATGTAATTTTTAAGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAAT
*
248029 GTAATTTTTGAGAAGTTTG
66 GTGATTTTTG-GAAGTTTG
248048 AAGGTAAAAA
Statistics
Matches: 158, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
87 15 0.09
88 136 0.86
89 7 0.04
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (88 bp):
AAAAATGTAATTTTTAAGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAAT
GTGATTTTTGGAAGTTTGGGAGC
Found at i:248056 original size:29 final size:29
Alignment explanation
Indices: 247785--248071 Score: 314
Period size: 29 Copynumber: 9.8 Consensus size: 29
247775 AAAATTTTAG
*
247785 GGGTAAAAATGT-AATTTTGAGAGAGTTTG-
1 GGGTAAAAATGTGATTTTTG-GA-AGTTTGA
* *
247814 GGGTAAAAATGTGATTTTTGGAAGTTCGG
1 GGGTAAAAATGTGATTTTTGGAAGTTTGA
*
247843 GGGTAAAAATGTGACTTTTGGAAGTTTG-
1 GGGTAAAAATGTGATTTTTGGAAGTTTGA
* * *
247871 GGAGCAAAAATGTAATTTTTAAGAAGTTT-A
1 GG-GTAAAAATGTGATTTTT-GGAAGTTTGA
*
247901 GGGGTAAAAATGTGATTTTTGGAAGTTCGA
1 -GGGTAAAAATGTGATTTTTGGAAGTTTGA
* *
247931 GGGTAAAAATGTGATTTTTGGAAGTTAGG
1 GGGTAAAAATGTGATTTTTGGAAGTTTGA
* *
247960 GGGCAAAAATGTAATTTTTTGGAAGTTT-A
1 GGGTAAAAATGTGA-TTTTTGGAAGTTTGA
* *
247989 GGGATAAAAATGTGATTTTTAGAAGTTCGA
1 GGG-TAAAAATGTGATTTTTGGAAGTTTGA
*
248019 GGGTAAAAATGTAATTTTTGAGAAGTTTGA
1 GGGTAAAAATGTGATTTTTG-GAAGTTTGA
* *
248049 AGGTAAAAATATGATTTTTGGAA
1 GGGTAAAAATGTGATTTTTGGAA
248072 AGATCAGAGA
Statistics
Matches: 219, Mismatches: 28, Indels: 22
0.81 0.10 0.08
Matches are distributed among these distances:
28 7 0.03
29 131 0.60
30 79 0.36
31 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTGATTTTTGGAAGTTTGA
Found at i:248067 original size:88 final size:86
Alignment explanation
Indices: 247741--248071 Score: 382
Period size: 88 Copynumber: 3.8 Consensus size: 86
247731 AAAAATGAAG
* * * * *
247741 TTTTGGAGAGTTCG-GGGTTAAAACGT-AATTTTGGAAAATTTTAGGGGTAAAAATGTAA-TTTT
1 TTTTGGA-AGTTCGAGGGTAAAAATGTGATTTTTGG--AAGTTT-GGGGCAAAAATGTAATTTTT
247803 GAGAGAGTTT-GGGGTAAAAATGTGAT
62 G-GA-AGTTTAGGGGTAAAAATGTGAT
* * *
247829 TTTTGGAAGTTCGGGGGTAAAAATGTGACTTTTGGAAGTTTGGGAGCAAAAATGTAATTTTTAAG
1 TTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTTGGG-GCAAAAATGTAATTTTT-GG
247894 AAGTTTAGGGGTAAAAATGTGAT
64 AAGTTTAGGGGTAAAAATGTGAT
*
247917 TTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTAGGGGGCAAAAATGTAATTTTTTGG
1 TTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTT-TGGGGCAAAAATGTAA-TTTTTGG
*
247982 AAGTTTAGGGATAAAAATGTGAT
64 AAGTTTAGGGGTAAAAATGTGAT
* * * * * *
248005 TTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTTGAAGGTAAAAATATGATTTTTGG
1 TTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTG-GAAGTTTG-GGGCAAAAATGTAATTTTTGG
248070 AA
64 AA
248072 AGATCAGAGA
Statistics
Matches: 215, Mismatches: 18, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
86 3 0.01
87 27 0.13
88 154 0.72
89 31 0.14
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.35
Consensus pattern (86 bp):
TTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTTGGGGCAAAAATGTAATTTTTGGAA
GTTTAGGGGTAAAAATGTGAT
Found at i:249875 original size:17 final size:17
Alignment explanation
Indices: 249855--249941 Score: 86
Period size: 17 Copynumber: 5.1 Consensus size: 17
249845 AATTAAATTT
249855 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
*
249872 TAAATTTAAACTCATAAA
1 TAAATTTAAATTCA-AAA
* *
249890 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
* *
249907 TAAATATAAACAT-AAAA
1 TAAATTTAAA-TTCAAAA
* *
249924 TAAATTAAAATTTAAAA
1 TAAATTTAAATTCAAAA
249941 T
1 T
249942 TTAAAATTGG
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
16 1 0.02
17 41 0.72
18 15 0.26
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:250518 original size:39 final size:38
Alignment explanation
Indices: 250464--250997 Score: 286
Period size: 39 Copynumber: 13.7 Consensus size: 38
250454 GATGGTTGCA
** * *
250464 ATCTGCCCTTGGCTCGGGGTAAAAGATTAGCTGATAGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATT-GCTGATGGTG
*
250503 ATCTGCCCCAGGCTCGGGGTAAAAGA-T-C-GAATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGCTG-ATGG-TG
* * *
250540 CAATCTGCCCTAGGCTCGAGGTAAAAGATTGGCTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATT-GCTGATGGTG
* * * ** * * ***
250581 ATCTACCCCAAGCTTGAAGTAAAAGATTGAATGACT-ACA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTG-CTGA-TGGTG
* *
250620 ATTTGCCCCAGGCTCGAGGTAAGAGATTGACTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTG-CTGATGGTG
* * * * *
250659 ATTTGCCCCAAGCTCGAGGTAAGCGATTG--AATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGCTGATGG-TG
* * * *
250696 CAATTTGCCTCAGGCTCGAGGTAAAAGATTGACTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTG-CTGATGGTG
* * *
250737 ATCTGCCCTAAGCTCGGGGTAAGAGA-T-C-GAATGGCTACA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGCTG-ATGG-T--G
* *
250776 ATCTGCACCAGGCTCGGGGTAAGAGATTGACTGATAGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTG-CTGATGGTG
* ** * *
250815 ATTTGCCCCAATCTTGGGGTTAGAGA-T-C-GAATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGCTG-ATGG-TG
* *
250852 CAATTTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATT-GCTGATGGTG
* * **
250893 ATCTGTCCCAAGCTCGGGGTAAGAGA-T-CAAATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGCTGATGG-TG
*
250930 CAATCTGCCCCTGGCTCGGGGTAAGAGATTGTCTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTG-CTGATGGTG
* * *
250971 ATCTGCCTCAGGCTCGGGATAAAAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
250998 CGACTGGCTG
Statistics
Matches: 385, Mismatches: 71, Indels: 78
0.72 0.13 0.15
Matches are distributed among these distances:
35 3 0.01
36 22 0.06
37 9 0.02
38 6 0.02
39 305 0.79
40 5 0.01
41 9 0.02
42 23 0.06
43 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (38 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGCTGATGGTG
Found at i:250590 original size:78 final size:78
Alignment explanation
Indices: 250455--251008 Score: 648
Period size: 78 Copynumber: 7.1 Consensus size: 78
250445 TTTTTATTGG
* * * * *
250455 ATGGTTGCAATCTGCCCTTGGCTCGGGGTAAAAGATT-AGCTGATAGTGATCTGCCCCAGGCTCG
1 ATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGA-CTGATGGTGATCTGCCCCAAGCTCG
*
250519 GGGTAAAAGATCGA
65 GGGTAAGAGATCGA
* * * * * *
250533 ATGGCTGCAATCTGCCCTAGGCTCGAGGTAAAAGATTGGCTGATGGTGATCTACCCCAAGCTTGA
1 ATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGG
* * *
250598 AGTAAAAGATTGA
66 GGTAAGAGATCGA
* * * * * * *
250611 ATGACTACAATTTGCCCCAGGCTCGAGGTAAGAGATTGACTGATGGTGATTTGCCCCAAGCTCGA
1 ATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGG
* *
250676 GGTAAGCGATTGA
66 GGTAAGAGATCGA
* * * *
250689 ATGGCTGCAATTTG-CCTCAGGCTCGAGGTAAAAGATTGACTGATGGTGATCTGCCCTAAGCTCG
1 ATGGCTGCAATCTGCCCT-AGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCG
250753 GGGTAAGAGATCGA
65 GGGTAAGAGATCGA
* * * * *
250767 ATGGCTACAATCTGCACC-AGGCTCGGGGTAAGAGATTGACTGATAGTGATTTGCCCCAATCTTG
1 ATGGCTGCAATCTGC-CCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCG
*
250831 GGGTTAGAGATCGA
65 GGGTAAGAGATCGA
* * *
250845 ATGGCTGCAATTTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGTCCCAAGCTCGG
1 ATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGG
*
250910 GGTAAGAGATCAA
66 GGTAAGAGATCGA
* * *
250923 ATGGCTGCAATCTGCCCCT-GGCTCGGGGTAAGAGATTGTCTGATGGTGATCTGCCTCAGGCTCG
1 ATGGCTGCAATCTG-CCCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCG
* *
250987 GGATAAAAGATCGA
65 GGGTAAGAGATCGA
*
251001 CTGGCTGC
1 ATGGCTGC
251009 CCTTCTTGAG
Statistics
Matches: 409, Mismatches: 61, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
77 4 0.01
78 399 0.98
79 4 0.01
80 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (78 bp):
ATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGG
GGTAAGAGATCGA
Found at i:254465 original size:17 final size:17
Alignment explanation
Indices: 254443--254479 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
254433 CCGTCCTTTG
254443 TTGTAAACTTTTAAAAC
1 TTGTAAACTTTTAAAAC
254460 TTGTAAACTTTTAAAAC
1 TTGTAAACTTTTAAAAC
254477 TTG
1 TTG
254480 GAAAAGGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (17 bp):
TTGTAAACTTTTAAAAC
Found at i:254649 original size:97 final size:97
Alignment explanation
Indices: 254483--254676 Score: 264
Period size: 97 Copynumber: 2.0 Consensus size: 97
254473 AAACTTGGAA
* * * **
254483 AAGGGTATTTGATTATCCCGATTTGAAGAAAAGTCGTGCCTAGTAAGTTAAGGCACAAAATTTTA
1 AAGGGTAGTCGATTATCCCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTTA
* *
254548 AAACCAGAGATAAAGAAACATTGCCTCGATTT
66 AAACCAGAAATAAAGAAACATCGCCTCGATTT
* *
254580 AAGGGTAGTCGATTATCTCGGTTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCAC-AAATTTTC
1 AAGGGTAGTCGATTATCCCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTT-
* * *
254644 AAAACCCGAAATAAAGGAATATCGCCTCGATTT
65 AAAACCAGAAATAAAGAAACATCGCCTCGATTT
254677 TAAATATTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 7 0.08
97 77 0.92
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (97 bp):
AAGGGTAGTCGATTATCCCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTTA
AAACCAGAAATAAAGAAACATCGCCTCGATTT
Found at i:255016 original size:28 final size:28
Alignment explanation
Indices: 254979--255211 Score: 144
Period size: 28 Copynumber: 8.1 Consensus size: 28
254969 AAGTTTTAGG
* *
254979 GGTAAAAATATCATTTTAGGAAATTCGA
1 GGTAAAAATATCATTTTTGGAAGTTCGA
*
255007 GGTAAAAATA-CTATTTTTAGAAGTTCGA
1 GGTAAAAATATC-ATTTTTGGAAGTTCGA
** * * ** *
255035 GGGCAAAATGTGATTTTTGGGTGTTCGG
1 GGTAAAAATATCATTTTTGGAAGTTCGA
* *
255063 GGTAAAAATGTGATTTTTGGAAGTTCGA
1 GGTAAAAATATCATTTTTGGAAGTTCGA
* ***
255091 GGGCAAAAATGGAATTTTTGGAAGTTCGA
1 -GGTAAAAATATCATTTTTGGAAGTTCGA
* * * *
255120 GGGTAAAAATATAATTGTTGAGAAGTTTGG
1 -GGTAAAAATATCATTTTTG-GAAGTTCGA
* * *
255150 GCGTTAAAATGTAATTTTTGGAAAGTTCGA
1 G-GTAAAAATATCATTTTTGG-AAGTTCGA
* * * *
255180 GGATTAAAATGTAATTTTTGGAAAGTTTGA
1 GG-TAAAAATATCATTTTTGG-AAGTTCGA
255210 GG
1 GG
255212 GTTAAAATGT
Statistics
Matches: 167, Mismatches: 31, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
27 1 0.01
28 65 0.39
29 44 0.26
30 57 0.34
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (28 bp):
GGTAAAAATATCATTTTTGGAAGTTCGA
Found at i:255067 original size:56 final size:58
Alignment explanation
Indices: 254991--255178 Score: 172
Period size: 56 Copynumber: 3.3 Consensus size: 58
254981 TAAAAATATC
* * *
254991 ATTTTAGGAAATTCGAGGTAAAAATACT-ATTTTTAGAAGTTCGAGGGC-AAAATGTG-
1 ATTTTTGGAAGTTCGGGGTAAAAATACTGATTTTTAGAAGTTCGAGGGCAAAAATG-GA
** * *
255047 ATTTTTGGGTGTTCGGGGTAAAAAT-GTGATTTTTGGAAGTTCGAGGGCAAAAATGGA
1 ATTTTTGGAAGTTCGGGGTAAAAATACTGATTTTTAGAAGTTCGAGGGCAAAAATGGA
* * * ** *
255104 ATTTTTGGAAGTTCGAGGGTAAAAATA-TAATTGTTGAGAAGTTTG-GGCGTTAAAATGTA
1 ATTTTTGGAAGTTCG-GGGTAAAAATACTGATT-TTTAGAAGTTCGAGG-GCAAAAATGGA
255163 ATTTTTGGAAAGTTCG
1 ATTTTTGG-AAGTTCG
255179 AGGATTAAAA
Statistics
Matches: 108, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
55 1 0.01
56 40 0.37
57 19 0.18
58 16 0.15
59 25 0.23
60 7 0.06
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (58 bp):
ATTTTTGGAAGTTCGGGGTAAAAATACTGATTTTTAGAAGTTCGAGGGCAAAAATGGA
Found at i:255159 original size:30 final size:30
Alignment explanation
Indices: 254949--255308 Score: 230
Period size: 30 Copynumber: 12.3 Consensus size: 30
254939 AAGAGTTTAA
* *
254949 GGTTAAAATGCAA-TTTTGGAAAGTTTTAGG
1 GGTTAAAATGTAATTTTTGGAAAGTTTGA-G
* * * * *
254979 GGTAAAAATATCATTTTAGGAAA-TTCGA-
1 GGTTAAAATGTAATTTTTGGAAAGTTTGAG
* * * *
255007 GGTAAAAATACT-ATTTTTAG-AAGTTCGAG
1 GGTTAAAAT-GTAATTTTTGGAAAGTTTGAG
* * ** *
255036 GG-CAAAATGTGATTTTTGG-GTGTTCG-G
1 GGTTAAAATGTAATTTTTGGAAAGTTTGAG
* * *
255063 GGTAAAAATGTGATTTTTGG-AAGTTCGAG
1 GGTTAAAATGTAATTTTTGGAAAGTTTGAG
** * *
255092 GGCAAAAATGGAATTTTTGG-AAGTTCGAG
1 GGTTAAAATGTAATTTTTGGAAAGTTTGAG
* * *
255121 GGTAAAAATATAATTGTT-GAGAAGTTTG-G
1 GGTTAAAATGTAATTTTTGGA-AAGTTTGAG
*
255150 GCGTTAAAATGTAATTTTTGGAAAGTTCGAG
1 G-GTTAAAATGTAATTTTTGGAAAGTTTGAG
*
255181 GATTAAAATGTAATTTTTGGAAAGTTTGAG
1 GGTTAAAATGTAATTTTTGGAAAGTTTGAG
* *
255211 GGTTAAAATGTAATTTTT-AAGAAGTTTAAG
1 GGTTAAAATGTAATTTTTGGA-AAGTTTGAG
* * *
255241 GG-GAAAATGTAATTTTTGAGGAA-TTCGAG
1 GGTTAAAATGTAATTTTTG-GAAAGTTTGAG
* *
255270 GGTTAAAATGCAATTTTTGG-AAGTTTTAAG
1 GGTTAAAATGTAATTTTTGGAAAG-TTTGAG
255300 GGTTAAAAT
1 GGTTAAAAT
255309 ATGATTTCTA
Statistics
Matches: 268, Mismatches: 44, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
27 6 0.02
28 61 0.23
29 68 0.25
30 121 0.45
31 12 0.04
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (30 bp):
GGTTAAAATGTAATTTTTGGAAAGTTTGAG
Found at i:255206 original size:60 final size:59
Alignment explanation
Indices: 254991--255294 Score: 223
Period size: 59 Copynumber: 5.2 Consensus size: 59
254981 TAAAAATATC
* * * * * *
254991 ATTTTAGGAAATTCGAGG-TAAAAATACT-ATT-TTTAGAAGTTCGAGGG-CAAAATGTG
1 ATTTTTGGAAGTTCGAGGATAAAAATA-TAATTGTTGAGAAGTTTGAGGGTTAAAATGTA
** * * * * * ** *
255047 ATTTTTGGGTGTTCG-GGGTAAAAATGTGATTTTTG-GAAGTTCGAGGGCAAAAATGGA
1 ATTTTTGGAAGTTCGAGGATAAAAATATAATTGTTGAGAAGTTTGAGGGTTAAAATGTA
*
255104 ATTTTTGGAAGTTCGAGGGTAAAAATATAATTGTTGAGAAGTTTG-GGCGTTAAAATGTA
1 ATTTTTGGAAGTTCGAGGATAAAAATATAATTGTTGAGAAGTTTGAGG-GTTAAAATGTA
* * *
255163 ATTTTTGGAAAGTTCGAGGATTAAAATGTAATTTTTG-GAAAGTTTGAGGGTTAAAATGTA
1 ATTTTTGG-AAGTTCGAGGATAAAAATATAATTGTTGAG-AAGTTTGAGGGTTAAAATGTA
* ** ** * * * *
255223 ATTTTTAAGAAGTTTAAGG-GGAAAATGTAATTTTTGAGGAA-TTCGAGGGTTAAAATGCA
1 ATTTTT-GGAAGTTCGAGGATAAAAATATAATTGTTGA-GAAGTTTGAGGGTTAAAATGTA
255282 ATTTTTGGAAGTT
1 ATTTTTGGAAGTT
255295 TTAAGGGTTA
Statistics
Matches: 205, Mismatches: 30, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
55 3 0.01
56 33 0.16
57 21 0.10
58 25 0.12
59 61 0.30
60 58 0.28
61 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (59 bp):
ATTTTTGGAAGTTCGAGGATAAAAATATAATTGTTGAGAAGTTTGAGGGTTAAAATGTA
Found at i:255301 original size:59 final size:58
Alignment explanation
Indices: 255026--255294 Score: 235
Period size: 59 Copynumber: 4.6 Consensus size: 58
255016 ACTATTTTTA
* * ** * *
255026 GAAGTTCGAGGG-CAAAATGTGATTTTTGGGTGTTC-GGGGTAAAAATGTGATTTTT-G
1 GAAGTTCGAGGGTTAAAATGTAATTTTTGGAAGTTCAAGGG-AAAAATGTAATTTTTGG
** * * * * *
255082 GAAGTTCGAGGGCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTGTTGA
1 GAAGTTCGAGGGTTAAAATGTAATTTTTGGAAGTTCAAGGG-AAAAATGTAATTTTTGG
* *
255141 GAAGTTTG-GGCGTTAAAATGTAATTTTTGGAAAGTTCGA-GGATTAAAATGTAATTTTTGG
1 GAAGTTCGAGG-GTTAAAATGTAATTTTTGG-AAGTTCAAGGGA--AAAATGTAATTTTTGG
* * * * *
255201 AAAGTTTGAGGGTTAAAATGTAATTTTTAAGAAGTTTAAGGGGAAAATGTAATTTTTGAG
1 GAAGTTCGAGGGTTAAAATGTAATTTTT-GGAAGTTCAAGGGAAAAATGTAATTTTTG-G
*
255261 GAA-TTCGAGGGTTAAAATGCAATTTTTGGAAGTT
1 GAAGTTCGAGGGTTAAAATGTAATTTTTGGAAGTT
255295 TTAAGGGTTA
Statistics
Matches: 176, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
56 12 0.07
57 18 0.10
58 25 0.14
59 62 0.35
60 54 0.31
61 5 0.03
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (58 bp):
GAAGTTCGAGGGTTAAAATGTAATTTTTGGAAGTTCAAGGGAAAAATGTAATTTTTGG
Found at i:255302 original size:89 final size:88
Alignment explanation
Indices: 255067--255310 Score: 289
Period size: 89 Copynumber: 2.8 Consensus size: 88
255057 GTTCGGGGTA
* ** * * *
255067 AAAATGTGATTTTT-GGAAGTTCGAGGGCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATA
1 AAAATGTAATTTTTGGGAAGTTCGAGGGTTAAAATGCAATTTTTGGAAGTTTGAGGGTTAAAATA
*
255131 TAATTGTTGAGAAGTTTGGGCGTT
66 TAATTGTTAAGAAGTTTGGGCG-T
* * *
255155 AAAATGTAATTTTTGGAAAGTTCGAGGATTAAAATGTAATTTTTGGAAAGTTTGAGGGTTAAAAT
1 AAAATGTAATTTTTGGGAAGTTCGAGGGTTAAAATGCAATTTTTGG-AAGTTTGAGGGTTAAAAT
* *
255220 GTAATTTTTAAGAAGTTTAAGGG-G-
65 ATAATTGTTAAGAAGTTT--GGGCGT
*
255244 AAAATGTAATTTTTGAGGAA-TTCGAGGGTTAAAATGCAATTTTTGGAAGTTTTAAGGGTTAAAA
1 AAAATGTAATTTTTG-GGAAGTTCGAGGGTTAAAATGCAATTTTTGGAAG-TTTGAGGGTTAAAA
255308 TAT
64 TAT
255311 GATTTCTAAA
Statistics
Matches: 134, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
88 16 0.12
89 80 0.60
90 34 0.25
91 1 0.01
92 3 0.02
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (88 bp):
AAAATGTAATTTTTGGGAAGTTCGAGGGTTAAAATGCAATTTTTGGAAGTTTGAGGGTTAAAATA
TAATTGTTAAGAAGTTTGGGCGT
Found at i:257165 original size:28 final size:28
Alignment explanation
Indices: 257133--257188 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
257123 TTGGTTTTAT
257133 TAAATTTAAAATTAAAATAAATTTAAAA
1 TAAATTTAAAATTAAAATAAATTTAAAA
**
257161 TAAATTTAATCTTAAAATAAATTTAAAA
1 TAAATTTAAAATTAAAATAAATTTAAAA
257189 GGTTTAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAATTTAAAATTAAAATAAATTTAAAA
Found at i:257188 original size:11 final size:11
Alignment explanation
Indices: 257139--257169 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
257129 TTATTAAATT
*
257139 TAAAATTAAAA
1 TAAATTTAAAA
257150 TAAATTTAAAA
1 TAAATTTAAAA
257161 TAAATTTAA
1 TAAATTTAA
257170 TCTTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:257860 original size:209 final size:208
Alignment explanation
Indices: 257499--258383 Score: 1108
Period size: 209 Copynumber: 4.3 Consensus size: 208
257489 TCACCACAAT
*
257499 CTTTGAGTCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCA
1 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCA
** * * * * * **
257564 CTTGTTTTGATCCACTTCTCTGTGTCTTATTAGGAAGATGGATCTGGTTCACTTCTTTGTATCTC
66 CTTGTTTCAATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTCCACTTCTCAGTATCTC
257629 ATCAAGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTT
131 ATCAAGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTT
257694 TGAAGATTTGCTCG
196 TGAAG-TTTGCTCG
257708 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGA-CGACATC
1 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCG-CATC
** * * * * *
257772 ACTTGTTTTGATCCACTTCTCTGTGTCTTATTAGGAAGACGGATCTGGTTCACTTCTCTGTATCT
65 ACTTGTTTCAATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTCCACTTCTCAGTATCT
* **
257837 CATTAAGAAGGTAACTGCTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGT
130 CATCAAGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGT
*
257902 TCGAAGATTTGCTCG
195 TTGAAG-TTTGCTCG
* *
257917 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCACATCA
1 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCA
* * * * * *
257982 CTTGTTTCAATTCGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTT
66 CTTGTTTCAATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTCCACTTCTCAGTATCTC
* * * * * * *
258047 ATCAAGAAGCTGACCGCTTTATTGCTTCGACTTGCTTCTCAATATCTCATCAGAAAGCTGGGGTT
131 ATCAAGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTT
258112 TGAAG-TT--TCG
196 TGAAGTTTGCTCG
* * * ** *
258122 C-TT-----T-GTTTCATTGAGTTGGTATAATTCTTTGTATCTCATCAGGAAGATGACCGCCTCA
1 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCA
* * * * * * *
258180 CTCGTTTCAATCCGCTTCTCTGTCTCTCATCAGGAAGACAAATTTGGTCCACTCCTCAATATCTC
66 CTTGTTTCAATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTCCACTTCTCAGTATCTC
* * * * **
258245 ATCAGGAAGGTGACCATTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCGGGAAGCTAAGGTT
131 ATCAAGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTT
*
258310 TGAAGTTTCGCTCA
196 TGAAGTTT-GCTCG
** * * *
258324 CAATGAGCTTGGTTTCATTGATCTGGTCCACTTCTCAGTATCTCATCAGGAAGATGACCG
1 CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCG
258384 TCTCGTTGTT
Statistics
Matches: 597, Mismatches: 66, Indels: 26
0.87 0.10 0.04
Matches are distributed among these distances:
198 162 0.27
199 3 0.01
202 3 0.01
203 1 0.00
204 2 0.00
205 4 0.01
207 2 0.00
208 3 0.01
209 416 0.70
210 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (208 bp):
CTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCA
CTTGTTTCAATCCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTCCACTTCTCAGTATCTC
ATCAAGAAGGTAACCACTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTT
TGAAGTTTGCTCG
Found at i:270161 original size:97 final size:97
Alignment explanation
Indices: 269986--270162 Score: 241
Period size: 97 Copynumber: 1.8 Consensus size: 97
269976 AACCTTGGAA
* ** *
269986 AAGGGTATTCGATTATCCCAATTTGAAGAAAAGTCATGCCTAGTAAGTTAAGGCATAAATTTTCA
1 AAGGGTAGTCGATTATCCCAATTTGAAGAAAAACCATGCCTAGTAAGTTAAGGCACAAATTTTCA
*
270051 AAACCAGAGATAAAGAAACATTGCCTAGATTT
66 AAACCAGAAATAAAGAAACATTGCCTAGATTT
*** *
270083 AAGGGTAGTCGATTATCCTGGTTTGAAGAAAAACCGTGCC-AGGTAAGTTAAGGCACAAATTTTC
1 AAGGGTAGTCGATTATCCCAATTTGAAGAAAAACCATGCCTA-GTAAGTTAAGGCACAAATTTTC
270147 AAAACTC-GAAATAAAG
65 AAAAC-CAGAAATAAAG
270163 GAATATCGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
96 1 0.01
97 67 0.97
98 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (97 bp):
AAGGGTAGTCGATTATCCCAATTTGAAGAAAAACCATGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCAGAAATAAAGAAACATTGCCTAGATTT
Found at i:270475 original size:28 final size:30
Alignment explanation
Indices: 270427--270490 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
270417 ACCAAGGTCG
* *
270427 AAAATGAAGTTTAGGAGAG-TTT-GGGGTT
1 AAAATGAAGTTTAGGAAAGTTTTAGGGGTA
*
270455 AAAATGTAA-TTTTGGAAAGTTTTAGGGGTA
1 AAAATG-AAGTTTAGGAAAGTTTTAGGGGTA
270485 AAAATG
1 AAAATG
270491 CCATTTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 14 0.47
29 5 0.17
30 11 0.37
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.33
Consensus pattern (30 bp):
AAAATGAAGTTTAGGAAAGTTTTAGGGGTA
Found at i:270546 original size:58 final size:56
Alignment explanation
Indices: 270464--270680 Score: 209
Period size: 58 Copynumber: 3.7 Consensus size: 56
270454 TAAAATGTAA
* * * * *
270464 TTTTGGAAAGTTTTAGGGGTAAAAATGCCATTTTTGTGAAATTCGAGGTAAAAATACAAC
1 TTTTGG-AAGTTTGA-GGGCAAAAATGCAATTTTTG-GAAATTCGAGGCAAAAATA-AAT
* * * ** * * *
270524 TCTTGGAAGTTCGGGGGCAAAAATGTGATTTTTGGGAGTTCGAGGCAAAAATATGATT
1 TTTTGGAAGTTTGAGGGCAAAAATGCAATTTTTGGAAATTCGAGGCAAAAATA--AAT
* * *
270582 TTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTGGAAGTTCGAGGGCAAAAATGAAAT
1 TTTTGGAAGTTTGAGGGCAAAAATGCAATTTTTGGAAATTCGA-GGCAAAAAT-AAAT
270640 TTTTGAGAAGTTTGAGGGCAAAAATGCAATTTTTGGAAATT
1 TTTTG-GAAGTTTGAGGGCAAAAATGCAATTTTTGGAAATT
270681 TTTGGGGTCA
Statistics
Matches: 129, Mismatches: 24, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
57 16 0.12
58 61 0.47
59 46 0.36
60 6 0.05
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (56 bp):
TTTTGGAAGTTTGAGGGCAAAAATGCAATTTTTGGAAATTCGAGGCAAAAATAAAT
Found at i:270558 original size:29 final size:29
Alignment explanation
Indices: 270526--270677 Score: 182
Period size: 29 Copynumber: 5.2 Consensus size: 29
270516 AATACAACTC
* **
270526 TTGGAAGTTCGGGGGCAAAAATGTGATTT
1 TTGGAAGTTCGAGGGCAAAAATGAAATTT
* *
270555 TTGGGAGTTCGA-GGCAAAAAT-ATGATTTT
1 TTGGAAGTTCGAGGGCAAAAATGA--AATTT
* *
270584 TTGGAAGTTTGAGGGTAAAAATGAAATTT
1 TTGGAAGTTCGAGGGCAAAAATGAAATTT
270613 TTGGAAGTTCGAGGGCAAAAATGAAATTT
1 TTGGAAGTTCGAGGGCAAAAATGAAATTT
* *
270642 TTGAGAAGTTTGAGGGCAAAAATGCAATTT
1 TTG-GAAGTTCGAGGGCAAAAATGAAATTT
270672 TTGGAA
1 TTGGAA
270678 ATTTTTGGGG
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
28 9 0.09
29 60 0.57
30 35 0.33
31 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (29 bp):
TTGGAAGTTCGAGGGCAAAAATGAAATTT
Found at i:272443 original size:17 final size:17
Alignment explanation
Indices: 272421--272564 Score: 139
Period size: 17 Copynumber: 8.4 Consensus size: 17
272411 CTTTATTAAT
272421 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
272438 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAA
** **
272456 TTTAAACATAATTTAAA
1 TTTAAATTTAAAATAAA
*
272473 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
** *
272490 TTTAAAAATAAATTTAAA
1 TTTAAATTTAAA-ATAAA
** *
272508 CAT-AATTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
272525 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
272542 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
272559 TTTAAA
1 TTTAAA
272565 AGGTTTAGTT
Statistics
Matches: 102, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
16 3 0.03
17 70 0.69
18 29 0.28
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:272491 original size:46 final size:46
Alignment explanation
Indices: 272441--272530 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
272431 AAATAAATTT
272441 AAATTTAAAAATAAATTTAAACATAATTTAAATTTAAATTTAAAAC
1 AAATTTAAAAATAAATTTAAACATAATTTAAATTTAAATTTAAAAC
272487 AAATTTAAAAATAAATTTAAACATAATTTAAATTTAAATTTAAA
1 AAATTTAAAAATAAATTTAAACATAATTTAAATTTAAATTTAAA
272531 TTTAAAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (46 bp):
AAATTTAAAAATAAATTTAAACATAATTTAAATTTAAATTTAAAAC
Found at i:272546 original size:23 final size:22
Alignment explanation
Indices: 272425--272530 Score: 114
Period size: 23 Copynumber: 4.9 Consensus size: 22
272415 ATTAATTTTA
272425 AATTTAAAATAAATTT-AA-AT
1 AATTTAAAATAAATTTAAACAT
*
272445 --TTAAAAATAAATTTAAACAT
1 AATTTAAAATAAATTTAAACAT
*
272465 AATTTAAATTTAAATTTAAAACA-
1 AATTTAAA-ATAAATTT-AAACAT
272488 AATTTAAAAATAAATTTAAACAT
1 AATTT-AAAATAAATTTAAACAT
*
272511 AATTTAAATTTAAATTTAAA
1 AATTTAAA-ATAAATTTAAA
272531 TTTAAAATAA
Statistics
Matches: 72, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
18 13 0.18
19 2 0.03
20 2 0.03
22 13 0.18
23 34 0.47
24 8 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTTAAAATAAATTTAAACAT
Found at i:272552 original size:23 final size:23
Alignment explanation
Indices: 272434--272553 Score: 87
Period size: 23 Copynumber: 5.4 Consensus size: 23
272424 AAATTTAAAA
*
272434 TAAATTTAAATTTAAAAATAAATT
1 TAAACTTAAATTT-AAAATAAATT
* *
272458 TAAACAT-AATTTAAATTTAAATT
1 TAAACTTAAATTTAAA-ATAAATT
272481 TAAAAC--AAATTTAAAAATAAATT
1 T-AAACTTAAATTT-AAAATAAATT
*
272504 TAAACAT-AA-TT----TAAATT
1 TAAACTTAAATTTAAAATAAATT
*
272521 TAAATTTAAATTTAAAATAAATT
1 TAAACTTAAATTTAAAATAAATT
*
272544 TAATCTTAAA
1 TAAACTTAAA
272554 ATAAATTTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
17 11 0.14
18 2 0.03
19 2 0.03
22 9 0.12
23 40 0.53
24 12 0.16
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAACTTAAATTTAAAATAAATT
Found at i:272553 original size:46 final size:46
Alignment explanation
Indices: 272421--272564 Score: 161
Period size: 46 Copynumber: 3.1 Consensus size: 46
272411 CTTTATTAAT
* *
272421 TTTAAATTTAAA-ATAAATTTAAATTTAAAAATAAATTTAAACATAA
1 TTTAAATTTAAATTTAAATTTAAATTT-AAAATTAATTTAAACATAA
** *
272467 TTTAAATTTAAATTTAAA-ACAAATTTAAAAATAAATTTAAACATAA
1 TTTAAATTTAAATTTAAATTTAAATTT-AAAATTAATTTAAACATAA
* *
272513 TTTAAATTTAAATTTAAATTTAAA-ATAAATTTAATCTTAAA-ATAAA
1 TTTAAATTTAAATTTAAATTTAAATTTAAAATTAAT-TTAAACAT-AA
272559 TTTAAA
1 TTTAAA
272565 AGGTTTAGTT
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
45 9 0.10
46 70 0.81
47 7 0.08
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (46 bp):
TTTAAATTTAAATTTAAATTTAAATTTAAAATTAATTTAAACATAA
Found at i:280168 original size:14 final size:15
Alignment explanation
Indices: 280149--280184 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
280139 GTAAGCATGT
*
280149 ATAAATATACG-AAA
1 ATAAATATAAGAAAA
280163 ATAAATATAAGAAAA
1 ATAAATATAAGAAAA
280178 ATAAATA
1 ATAAATA
280185 CGAATTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (15 bp):
ATAAATATAAGAAAA
Found at i:280406 original size:58 final size:59
Alignment explanation
Indices: 280339--280504 Score: 176
Period size: 58 Copynumber: 2.8 Consensus size: 59
280329 GAAAATTTTA
* ** * *
280339 GGGGTAAAAATGTCATTTTAAGAGAGTTCGAGGGTAAAAATGTGATTTTTGT-TAAGTT-
1 GGGGAAAAAATGTCATTTTTGGA-AGTTCGAGGGTAAAAATGTAATTTTTGTGGAAGTTC
* * * *
280397 GGGGAAAAAATGTTATTTTTGGAAATTCAAGGGCAAAAATGTAATTTTT-TGGAAGTTC
1 GGGGAAAAAATGTCATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGTGGAAGTTC
* * * * *
280455 GGGGCAAAAATGTGATTTTTGGAAGTTTGGGGGTAAAAATATAATTTTTG
1 GGGGAAAAAATGTCATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTG
280505 AGAAGTTTGG
Statistics
Matches: 88, Mismatches: 17, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
56 1 0.01
57 27 0.31
58 60 0.68
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (59 bp):
GGGGAAAAAATGTCATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGTGGAAGTTC
Found at i:280487 original size:29 final size:29
Alignment explanation
Indices: 280374--280531 Score: 133
Period size: 29 Copynumber: 5.4 Consensus size: 29
280364 GTTCGAGGGT
* *
280374 AAAAATGTGATTTTTGTTAAG-TT-GGGGA
1 AAAAATGTGATTTTTG-GAAGTTTGGGGGC
* * ***
280402 AAAAATGTTATTTTTGGAAATTCAAGGGC
1 AAAAATGTGATTTTTGGAAGTTTGGGGGC
* *
280431 AAAAATGTAATTTTTTGGAAG-TTCGGGGC
1 AAAAATGTGA-TTTTTGGAAGTTTGGGGGC
*
280460 AAAAATGTGATTTTTGGAAGTTTGGGGGT
1 AAAAATGTGATTTTTGGAAGTTTGGGGGC
* * * *
280489 AAAAATATAATTTTTGAGAAGTTTGGAGGT
1 AAAAATGTGATTTTTG-GAAGTTTGGGGGC
*
280519 AAAAATATGATTT
1 AAAAATGTGATTT
280532 CTAGAAAGTT
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
27 2 0.02
28 26 0.24
29 46 0.43
30 33 0.31
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAAATGTGATTTTTGGAAGTTTGGGGGC
Found at i:280510 original size:58 final size:56
Alignment explanation
Indices: 280369--280531 Score: 164
Period size: 58 Copynumber: 2.8 Consensus size: 56
280359 AGAGAGTTCG
* * *
280369 AGGGTAAAAATGTGATTTTTGTTAAGTTGGGGAAAAAATGTTATTTTTGGAAATTCA
1 AGGGTAAAAATGTAATTTTTG-GAAGTTGGGGAAAAAATGTGATTTTTGGAAATTCA
* * * **
280426 AGGGCAAAAATGTAATTTTTTGGAAGTTCGGGGCAAAAATGTGATTTTTGGAAGTTTG
1 AGGGTAAAAATGTAA-TTTTTGGAAGTT-GGGGAAAAAATGTGATTTTTGGAAATTCA
* * * *
280484 GGGGTAAAAATATAATTTTTGAGAAGTTTGGAGGTAAAAATATGATTT
1 AGGGTAAAAATGTAATTTTTG-GAAG-TTGG-GGAAAAAATGTGATTT
280532 CTAGAAAGTT
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
57 24 0.27
58 48 0.55
59 16 0.18
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.36
Consensus pattern (56 bp):
AGGGTAAAAATGTAATTTTTGGAAGTTGGGGAAAAAATGTGATTTTTGGAAATTCA
Found at i:280512 original size:30 final size:29
Alignment explanation
Indices: 280279--280524 Score: 153
Period size: 30 Copynumber: 8.4 Consensus size: 29
280269 AGAAAAAAAA
* * *
280279 TGGGGTTAAAAAT-AAAGTTTTGGAGAGTT
1 TGGGGGTAAAAATGTAATTTTTGGA-AGTT
* * *
280308 T-TGGGTTAAAATGTAA-TTTTGGAAAATTT
1 TGGGGGTAAAAATGTAATTTTTGG--AAGTT
* * **
280337 TAGGGGTAAAAATGTCATTTTAAGAGAGTT
1 TGGGGGTAAAAATGTAATTTTTGGA-AGTT
* * * *
280367 CGAGGGTAAAAATGTGATTTTTGTTAAG-T
1 TGGGGGTAAAAATGTAATTTTTG-GAAGTT
* * *
280396 T-GGGGAAAAAATGTTATTTTTGGAAATT
1 TGGGGGTAAAAATGTAATTTTTGGAAGTT
*** *
280424 CAAGGGCAAAAATGTAATTTTTTGGAAG-T
1 TGGGGGTAAAAATGTAA-TTTTTGGAAGTT
* * *
280453 TCGGGGCAAAAATGTGATTTTTGGAAGTT
1 TGGGGGTAAAAATGTAATTTTTGGAAGTT
*
280482 TGGGGGTAAAAATATAATTTTTGAGAAGTT
1 TGGGGGTAAAAATGTAATTTTTG-GAAGTT
*
280512 TGGAGGTAAAAAT
1 TGGGGGTAAAAAT
280525 ATGATTTCTA
Statistics
Matches: 167, Mismatches: 38, Indels: 23
0.73 0.17 0.10
Matches are distributed among these distances:
27 2 0.01
28 43 0.26
29 55 0.33
30 62 0.37
31 5 0.03
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
TGGGGGTAAAAATGTAATTTTTGGAAGTT
Found at i:280541 original size:30 final size:29
Alignment explanation
Indices: 280442--280542 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 29
280432 AAAATGTAAT
* * * *
280442 TTTTTGGAAGTTCGG-GGCAAAAATGTGA
1 TTTTTGAAAGTTTGGAGGTAAAAATATGA
* * *
280470 TTTTTGGAAGTTTGGGGGTAAAAATATAA
1 TTTTTGAAAGTTTGGAGGTAAAAATATGA
280499 TTTTTGAGAAGTTTGGAGGTAAAAATATGA
1 TTTTTGA-AAGTTTGGAGGTAAAAATATGA
*
280529 TTTCTAGAAAGTTT
1 TTT-TTGAAAGTTT
280543 AGGGATCTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 14 0.23
29 16 0.26
30 29 0.47
31 3 0.05
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.38
Consensus pattern (29 bp):
TTTTTGAAAGTTTGGAGGTAAAAATATGA
Found at i:281591 original size:16 final size:16
Alignment explanation
Indices: 281572--281602 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
281562 ATTTATTACA
281572 TTTTATTAATATTATT
1 TTTTATTAATATTATT
281588 TTTTATTAATATTAT
1 TTTTATTAATATTAT
281603 ACTTATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTATTAATATTATT
Found at i:282339 original size:6 final size:6
Alignment explanation
Indices: 282322--282402 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
282312 GAACTTTTAA
* * * * *
282322 TTAAATT TTAAAT TTAAAC TCAAAA ATAAAT TTAAAT TTAAA- ATAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * *
282370 TTAAAC TTAAA- ATAAAT TAAAAT TTAAAA TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
282403 GTTCAATTTT
Statistics
Matches: 57, Mismatches: 15, Indels: 5
0.74 0.19 0.06
Matches are distributed among these distances:
5 8 0.14
6 44 0.77
7 5 0.09
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:282366 original size:17 final size:17
Alignment explanation
Indices: 282330--282399 Score: 95
Period size: 17 Copynumber: 4.1 Consensus size: 17
282320 AATTAAATTT
**
282330 TAAATTTAAACTCAAAAA
1 TAAATTTAAA-TTTAAAA
282348 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
282365 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
282382 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
282399 T
1 T
282400 TAAGTTCAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 37 0.79
18 10 0.21
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:282387 original size:34 final size:35
Alignment explanation
Indices: 282330--282399 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 35
282320 AATTAAATTT
*
282330 TAAATTTAAACTCAAAAATAAATTTAAATTTAAAA
1 TAAATTTAAACTCAAAAATAAATTAAAATTTAAAA
*
282365 TAAATTTAAACT-TAAAATAAATTAAAATTTAAAA
1 TAAATTTAAACTCAAAAATAAATTAAAATTTAAAA
282399 T
1 T
282400 TAAGTTCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 21 0.64
35 12 0.36
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (35 bp):
TAAATTTAAACTCAAAAATAAATTAAAATTTAAAA
Found at i:292594 original size:55 final size:55
Alignment explanation
Indices: 292527--292640 Score: 228
Period size: 55 Copynumber: 2.1 Consensus size: 55
292517 CCAAGACATT
292527 ACATAGTACTTTGAGTCTATATTCTACCTTACACAATCATACATTTCTACTTACA
1 ACATAGTACTTTGAGTCTATATTCTACCTTACACAATCATACATTTCTACTTACA
292582 ACATAGTACTTTGAGTCTATATTCTACCTTACACAATCATACATTTCTACTTACA
1 ACATAGTACTTTGAGTCTATATTCTACCTTACACAATCATACATTTCTACTTACA
292637 ACAT
1 ACAT
292641 TTCATCAAAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (55 bp):
ACATAGTACTTTGAGTCTATATTCTACCTTACACAATCATACATTTCTACTTACA
Found at i:293146 original size:52 final size:52
Alignment explanation
Indices: 293007--293245 Score: 255
Period size: 52 Copynumber: 4.6 Consensus size: 52
292997 ATTACACTCA
* ** * ** * * * *
293007 ATACTCATGATGACACATAGTCATCAAACCTCTTGTTCCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTTAAGGATTTAC
* * * *
293059 ACACTCACGATGACACATTGTCA-CTGGACCTCATAATTCGTGAAGGATTTAC
1 ATACTCACGATGACACATAGTCATC-GGACCTCATAATCCGTTAAGGATTTAC
* * * *
293111 ATACTCACGATGACACGTAGTCATCAGACCCCATAATCCATTAAGGATTTAC
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTTAAGGATTTAC
** * * *
293163 GGATTCACGATGACACGTAGTCATCGGACCTCATAACCCGTTAAGGATTTAC
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTTAAGGATTTAC
293215 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
293246 TTCTCATTTA
Statistics
Matches: 153, Mismatches: 32, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
51 1 0.01
52 151 0.99
53 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTTAAGGATTTAC
Found at i:293727 original size:17 final size:17
Alignment explanation
Indices: 293705--293742 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
293695 TAATAAGTAC
293705 AACAATATCACCATTTT
1 AACAATATCACCATTTT
293722 AACAATATCACCATTTT
1 AACAATATCACCATTTT
293739 AACA
1 AACA
293743 TTTTAGTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.32
Consensus pattern (17 bp):
AACAATATCACCATTTT
Found at i:296973 original size:21 final size:21
Alignment explanation
Indices: 296949--297010 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
296939 AACCCTTGAA
*
296949 TTGCACTATGGTGCCCCTATC
1 TTGCACTATGATGCCCCTATC
* * * * *
296970 TTGCATTACGATGTCTCTGTC
1 TTGCACTATGATGCCCCTATC
296991 TTGCACTATGATGCCCCTAT
1 TTGCACTATGATGCCCCTAT
297011 GAATGCACTT
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (21 bp):
TTGCACTATGATGCCCCTATC
Found at i:300747 original size:2 final size:2
Alignment explanation
Indices: 300735--300766 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
300725 TAATTTTCTA
300735 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
300767 GCACATAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:301702 original size:15 final size:15
Alignment explanation
Indices: 301682--301711 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
301672 CAATGTTACT
*
301682 TCTCAAAGTTTCAAA
1 TCTCAAAGTTCCAAA
301697 TCTCAAAGTTCCAAA
1 TCTCAAAGTTCCAAA
301712 AGGCTTAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (15 bp):
TCTCAAAGTTCCAAA
Found at i:317187 original size:30 final size:30
Alignment explanation
Indices: 317115--317189 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 30
317105 TAGAATGAAC
*
317115 TAAAATTTTCAAAAATTTTGTAAAAAAATATG
1 TAAAATTTTC--AAATTTTGAAAAAAAATATG
317147 TAGAAA-TTTCAAATTTT-AAATAAAAATA-G
1 TA-AAATTTTCAAATTTTGAAA-AAAAATATG
317176 ATAAAATTTTCAAA
1 -TAAAATTTTCAAA
317190 AATAGATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
29 6 0.16
30 23 0.61
32 6 0.16
33 3 0.08
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (30 bp):
TAAAATTTTCAAATTTTGAAAAAAAATATG
Done.