Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001948.1 Hibiscus syriacus cultivar Beakdansim tig00003942_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: 119616
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1105 original size:32 final size:32
Alignment explanation
Indices: 1058--1130 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
1048 CATTTAATTA
*
1058 AATAAAAGGTTGGATTCATAATATTATGGAGGG
1 AATAAAA-TTTGGATTCATAATATTATGGAGGG
* * *
1091 AATAAAATTTGGATTCATAATTTTTTTGAGGG
1 AATAAAATTTGGATTCATAATATTATGGAGGG
*
1123 AATGAAAT
1 AATAAAAT
1131 ATTTTCTGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 28 0.80
33 7 0.20
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.36
Consensus pattern (32 bp):
AATAAAATTTGGATTCATAATATTATGGAGGG
Found at i:3967 original size:34 final size:34
Alignment explanation
Indices: 3929--3994 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
3919 TTATCTTTTA
*
3929 AATAGTCATATTGACACAAATTTAAAAATAGTCT
1 AATAGTCATAATGACACAAATTTAAAAATAGTCT
3963 AATAGTCATAATGACACAAATTTAAAAATAGT
1 AATAGTCATAATGACACAAATTTAAAAATAGT
3995 GAGCATTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (34 bp):
AATAGTCATAATGACACAAATTTAAAAATAGTCT
Found at i:4714 original size:45 final size:45
Alignment explanation
Indices: 4663--4749 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
4653 ACTCACCAAT
*
4663 TCACTCAAACATCTATCAACTCTCTCAAAGCTTTCTAAGCTTATA
1 TCACTCAAACATCTATCAACTCTCTCAAAACTTTCTAAGCTTATA
* *
4708 TCACTCAAACATCTCTCAACTCTCTTAAAACTTTCTAAGCTT
1 TCACTCAAACATCTATCAACTCTCTCAAAACTTTCTAAGCTT
4750 TTGGCTCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.34
Consensus pattern (45 bp):
TCACTCAAACATCTATCAACTCTCTCAAAACTTTCTAAGCTTATA
Found at i:9620 original size:2 final size:2
Alignment explanation
Indices: 9615--9651 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9605 TGTGTGTGTG
9615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9652 CTTGCACATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10363 original size:21 final size:20
Alignment explanation
Indices: 10314--10352 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
10304 TTATTTAACT
*
10314 AGTTACAAGTGTAATTACACC
1 AGTTACAAGAGTAATTACA-C
10335 AGTTACAAGAGTAATTAC
1 AGTTACAAGAGTAATTAC
10353 GAATGTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
AGTTACAAGAGTAATTACAC
Found at i:11442 original size:26 final size:26
Alignment explanation
Indices: 11406--11473 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
11396 CATGATATAG
*
11406 ACGAGTAATATGAACTCGTGTACTAC
1 ACGAGTAATATGAACTCATGTACTAC
11432 ACGAGTAATATGAACTCATGTACTAC
1 ACGAGTAATATGAACTCATGTACTAC
11458 ACGAGTAATATGAACT
1 ACGAGTAATATGAACT
11474 AAAATATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (26 bp):
ACGAGTAATATGAACTCATGTACTAC
Found at i:17590 original size:4 final size:4
Alignment explanation
Indices: 17581--17615 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
17571 CAATGCATGT
17581 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
17616 CATAGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:21626 original size:2 final size:2
Alignment explanation
Indices: 21619--21662 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
21609 AAATTGTTGG
21619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21661 AT
1 AT
21663 GAATAGAACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23855 original size:20 final size:20
Alignment explanation
Indices: 23830--23884 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
23820 ATAGTAATAG
23830 GTAATAGGTAAAACAATGGA
1 GTAATAGGTAAAACAATGGA
23850 GTAATAGGTAAAACAATGGA
1 GTAATAGGTAAAACAATGGA
23870 GTAATAGGTAAAACA
1 GTAATAGGTAAAACA
23885 GAGTTTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (20 bp):
GTAATAGGTAAAACAATGGA
Found at i:24228 original size:29 final size:28
Alignment explanation
Indices: 24210--24349 Score: 183
Period size: 29 Copynumber: 4.9 Consensus size: 28
24200 AAACAAGACA
* *
24210 GAGATATAATCCCATACAGAATGAGGAC
1 GAGATATAATCCCATGCAGAATCAGGAC
*
24238 GGGGATATAATCCCATGCAGAATCAGGAC
1 -GAGATATAATCCCATGCAGAATCAGGAC
24267 GAGAATATAATCCCATGCAGAATCAGGAC
1 GAG-ATATAATCCCATGCAGAATCAGGAC
*
24296 GAGATATAATCTCATGCAGAATCAGGAC
1 GAGATATAATCCCATGCAGAATCAGGAC
**
24324 -ATTGATATAATCTAATGCAGAATCAG
1 GA--GATATAATCCCATGCAGAATCAG
24350 AATAAAGATA
Statistics
Matches: 102, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
27 1 0.01
28 26 0.25
29 75 0.74
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (28 bp):
GAGATATAATCCCATGCAGAATCAGGAC
Found at i:24322 original size:57 final size:57
Alignment explanation
Indices: 24212--24349 Score: 181
Period size: 57 Copynumber: 2.4 Consensus size: 57
24202 ACAAGACAGA
* * *
24212 GATATAATCCCATACAGAATGAGGACGGGGATATAATCCCATGCAGAATCAGGACGA-
1 GATATAATCCCATGCAGAATCAGGACGGAGATATAATCCCATGCAGAATCAGGAC-AT
*
24269 GAATATAATCCCATGCAGAATCAGGAC-GAGATATAATCTCATGCAGAATCAGGACATT
1 G-ATATAATCCCATGCAGAATCAGGACGGAGATATAATCCCATGCAGAATCAGGACA-T
**
24327 GATATAATCTAATGCAGAATCAG
1 GATATAATCCCATGCAGAATCAG
24350 AATAAAGATA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
56 1 0.01
57 47 0.65
58 24 0.33
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (57 bp):
GATATAATCCCATGCAGAATCAGGACGGAGATATAATCCCATGCAGAATCAGGACAT
Found at i:24359 original size:29 final size:28
Alignment explanation
Indices: 24241--24380 Score: 102
Period size: 29 Copynumber: 4.9 Consensus size: 28
24231 TGAGGACGGG
** * **
24241 GATATAATCCCATGCAGAATCAGGACGA
1 GATATAATCTAATGCAGAATCAGAAAAA
** * **
24269 GAATATAATCCCATGCAGAATCAGGACGA
1 G-ATATAATCTAATGCAGAATCAGAAAAA
* * **
24298 GATATAATCTCATGCAGAATCAGGACATT
1 GATATAATCTAATGCAGAATCA-GAAAAA
24327 GATATAATCTAATGCAGAATCAGAATAAA
1 GATATAATCTAATGCAGAATCAGAA-AAA
* *
24356 GATATAATC-AGTGTAGAATCAGAAA
1 GATATAATCTAATGCAGAATCAGAAA
24381 TGCATCAATA
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.01
28 36 0.37
29 60 0.62
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.22
Consensus pattern (28 bp):
GATATAATCTAATGCAGAATCAGAAAAA
Found at i:40894 original size:27 final size:27
Alignment explanation
Indices: 40856--40923 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
40846 CTATCACACA
*
40856 TTTCTCTCTCATTTTTAACTTTTTCTT
1 TTTCTCTCTCATTTGTAACTTTTTCTT
*
40883 TTTCTCTTTCATTTGTAACTTTTTCTT
1 TTTCTCTCTCATTTGTAACTTTTTCTT
40910 TTTCTCTCTCATTT
1 TTTCTCTCTCATTT
40924 CTTCATCTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.10, C:0.22, G:0.01, T:0.66
Consensus pattern (27 bp):
TTTCTCTCTCATTTGTAACTTTTTCTT
Found at i:43475 original size:10 final size:10
Alignment explanation
Indices: 43460--43488 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
43450 TAGGATCATG
43460 TAGTTGCATA
1 TAGTTGCATA
43470 TAGTTGCATA
1 TAGTTGCATA
43480 TAGTTGCAT
1 TAGTTGCAT
43489 TTGTGGTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (10 bp):
TAGTTGCATA
Found at i:47295 original size:20 final size:20
Alignment explanation
Indices: 47272--47321 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
47262 TGGCCCTTCA
47272 GTATCGATACTAACCCT-TTG
1 GTATCGATACTAA-CCTATTG
* * *
47292 GTATTGATATTCACCTATTG
1 GTATCGATACTAACCTATTG
47312 GTATCGATAC
1 GTATCGATAC
47322 CCCAAGCTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (20 bp):
GTATCGATACTAACCTATTG
Found at i:54078 original size:21 final size:21
Alignment explanation
Indices: 54052--54093 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
54042 TTAAAAACTC
* *
54052 AACCCAAGGTATGTTTTTCCT
1 AACCCAAGGTAAGTGTTTCCT
54073 AACCCAAGGTAAGTGTTTCCT
1 AACCCAAGGTAAGTGTTTCCT
54094 TCCCCTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (21 bp):
AACCCAAGGTAAGTGTTTCCT
Found at i:56036 original size:29 final size:30
Alignment explanation
Indices: 56004--56060 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
55994 AAATTTTAAC
*
56004 TAGTGACCAAA-ATGTAAATTTT-GAAAACT
1 TAGTGACCAAAGA-ATAAATTTTGGAAAACT
*
56033 TAGTGGCCAAAGAATAAATTTTGGAAAA
1 TAGTGACCAAAGAATAAATTTTGGAAAA
56061 GTTTAAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.28
Consensus pattern (30 bp):
TAGTGACCAAAGAATAAATTTTGGAAAACT
Found at i:58784 original size:25 final size:25
Alignment explanation
Indices: 58718--58836 Score: 123
Period size: 26 Copynumber: 4.7 Consensus size: 25
58708 TTATACATTC
** *
58718 AGTGATATATGGCACTTTTAAGTGT
1 AGTGATACGTGGCACTTTTGAGTGT
*
58743 AAGTGATACGTGACACTTTTGAGTGT
1 -AGTGATACGTGGCACTTTTGAGTGT
* * *
58769 AGCGATACGTGGCACTTACT-AGTGCA
1 AGTGATACGTGGCACTT-TTGAGTG-T
* *
58795 AGTGATACGTGACACTTTTGAGTGC
1 AGTGATACGTGGCACTTTTGAGTGT
58820 AGTGATACGTGGCACTT
1 AGTGATACGTGGCACTT
58837 ACGAGTGCAA
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
25 36 0.47
26 41 0.53
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (25 bp):
AGTGATACGTGGCACTTTTGAGTGT
Found at i:58803 original size:51 final size:51
Alignment explanation
Indices: 58738--58852 Score: 194
Period size: 51 Copynumber: 2.3 Consensus size: 51
58728 GGCACTTTTA
* * *
58738 AGTGTAAGTGATACGTGACACTTTTGAGTGTAGCGATACGTGGCACTTACT
1 AGTGCAAGTGATACGTGACACTTTTGAGTGCAGCGATACGTGGCACTTACG
*
58789 AGTGCAAGTGATACGTGACACTTTTGAGTGCAGTGATACGTGGCACTTACG
1 AGTGCAAGTGATACGTGACACTTTTGAGTGCAGCGATACGTGGCACTTACG
58840 AGTGCAAGTGATA
1 AGTGCAAGTGATA
58853 TGAGCACTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (51 bp):
AGTGCAAGTGATACGTGACACTTTTGAGTGCAGCGATACGTGGCACTTACG
Found at i:58842 original size:25 final size:26
Alignment explanation
Indices: 58738--58852 Score: 126
Period size: 25 Copynumber: 4.5 Consensus size: 26
58728 GGCACTTTTA
* **
58738 AGTGTAAGTGATACGTGACACTTTTG
1 AGTGCAAGTGATACGTGACACTTACG
* * * *
58764 AGTG-TAGCGATACGTGGCACTTACT
1 AGTGCAAGTGATACGTGACACTTACG
**
58789 AGTGCAAGTGATACGTGACACTTTTG
1 AGTGCAAGTGATACGTGACACTTACG
*
58815 AGTGC-AGTGATACGTGGCACTTACG
1 AGTGCAAGTGATACGTGACACTTACG
58840 AGTGCAAGTGATA
1 AGTGCAAGTGATA
58853 TGAGCACTAA
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
25 41 0.57
26 31 0.43
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
AGTGCAAGTGATACGTGACACTTACG
Found at i:59544 original size:12 final size:12
Alignment explanation
Indices: 59527--59557 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
59517 TGCGGGAAAA
59527 TTAAAATCTATT
1 TTAAAATCTATT
*
59539 TTAAAATTTATT
1 TTAAAATCTATT
59551 TTAAAAT
1 TTAAAAT
59558 ATAGATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:59572 original size:22 final size:21
Alignment explanation
Indices: 59544--59997 Score: 521
Period size: 22 Copynumber: 20.6 Consensus size: 21
59534 CTATTTTAAA
59544 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATAT-GATTG
59566 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAT-GATTG
59588 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATAT-GATTG
***
59610 ATTTATTTTAAAATATGGAAAAA
1 ATTTATTTTAAAATAT-G-ATTG
59633 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATAT-GATTG
***
59655 ATTTATTTTAAAATATGAAAA
1 ATTTATTTTAAAATATGATTG
59676 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATAT-GATTG
***
59699 ATTTATTTTAAAATATGAAAA
1 ATTTATTTTAAAATATGATTG
59720 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATAT-GATTG
59743 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAT-GATTG
* ***
59765 ATATATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATG-ATTG
*
59787 ATTTATTTTAAAATATGAATTT
1 ATTTATTTTAAAATATG-ATTG
***
59809 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATG-ATTG
59831 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAT-GATTG
59853 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAT-GATTG
*
59875 ATTTAGTTTAAAATATGTATTG
1 ATTTATTTTAAAATATG-ATTG
* ***
59897 ATTTATTTTGAAATATGAAAAA
1 ATTTATTTTAAAATATG-ATTG
59919 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATG-ATTG
59941 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAT-GATTG
59963 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATG-ATTG
59985 ATTTATTTTAAAA
1 ATTTATTTTAAAA
59998 AATTTATTAT
Statistics
Matches: 375, Mismatches: 47, Indels: 20
0.85 0.11 0.05
Matches are distributed among these distances:
21 9 0.02
22 340 0.91
23 26 0.07
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (21 bp):
ATTTATTTTAAAATATGATTG
Found at i:59595 original size:44 final size:44
Alignment explanation
Indices: 59544--59997 Score: 579
Period size: 44 Copynumber: 10.3 Consensus size: 44
59534 CTATTTTAAA
*
59544 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
* ***
59588 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGAAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGG-ATTG
* ***
59633 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
***
59676 ATTTTATTTTAAAATATGGATTGATTTATTTTAAAATAT-GAAAA
1 A-TTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
59720 ATTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
* * *** * *
59765 ATATATTTTAAAATATGAAAAAATTTATTTTAAAATATGAATTT
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
* ***
59809 ATTTATTTTAAAATATGAAAAAATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
* *
59853 ATTTATTTTAAAATATGGATTGATTTAGTTTAAAATATGTATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
* * *** *
59897 ATTTATTTTGAAATATGAAAAAATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
*
59941 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
59985 ATTTATTTTAAAA
1 ATTTATTTTAAAA
59998 AATTTATTAT
Statistics
Matches: 372, Mismatches: 35, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
43 5 0.01
44 325 0.87
45 42 0.11
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (44 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
Found at i:60078 original size:31 final size:31
Alignment explanation
Indices: 60021--60079 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
60011 AGTTGTATGG
*
60021 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
60052 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
60080 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:61232 original size:38 final size:39
Alignment explanation
Indices: 61158--61240 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
61148 AATCATACCT
* * *
61158 AAAA-TTTAATTTTTGTTTCATTTTAGTTCCCGCCATTC
1 AAAATTTTAATTTTTGTTTCATTTTAGATACAGCCATTC
* *
61196 AAAATTTTAGTTTTTGTTTCATTTTA-ATACATCCATTC
1 AAAATTTTAATTTTTGTTTCATTTTAGATACAGCCATTC
61234 AAAATTT
1 AAAATTT
61241 AGCGTTATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 19 0.49
39 20 0.51
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (39 bp):
AAAATTTTAATTTTTGTTTCATTTTAGATACAGCCATTC
Found at i:63564 original size:14 final size:14
Alignment explanation
Indices: 63545--63573 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
63535 CACTTAAATC
63545 TATAATTGATTGTG
1 TATAATTGATTGTG
63559 TATAATTGATTGTG
1 TATAATTGATTGTG
63573 T
1 T
63574 CAAGAAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (14 bp):
TATAATTGATTGTG
Found at i:66939 original size:60 final size:60
Alignment explanation
Indices: 66866--66987 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
66856 AAAATTTGTG
66866 CTCAATTATATTCATTTTTTAGCGTTCTTTCTTTGTTCTAGAATTGTGCAAACATCTTAC
1 CTCAATTATATTCATTTTTTAGCGTTCTTTCTTTGTTCTAGAATTGTGCAAACATCTTAC
66926 CTCAATTATATTCATTTTTTAGCGTTCTTTCTTTGTTCTAGAATTGTGCAAACATCTTAC
1 CTCAATTATATTCATTTTTTAGCGTTCTTTCTTTGTTCTAGAATTGTGCAAACATCTTAC
66986 CT
1 CT
66988 TGTGAGGTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (60 bp):
CTCAATTATATTCATTTTTTAGCGTTCTTTCTTTGTTCTAGAATTGTGCAAACATCTTAC
Found at i:74537 original size:17 final size:19
Alignment explanation
Indices: 74501--74541 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
74491 GATTTGGTTA
*
74501 TTTGAATATTTGGTTGTTT
1 TTTGAATACTTGGTTGTTT
74520 TTTGAATACTTGTGTT-TTT
1 TTTGAATACTTG-GTTGTTT
74539 TTT
1 TTT
74542 TATTGATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.15, C:0.02, G:0.17, T:0.66
Consensus pattern (19 bp):
TTTGAATACTTGGTTGTTT
Found at i:74688 original size:26 final size:26
Alignment explanation
Indices: 74659--74716 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
74649 ATTGTTTATG
74659 AATATTGATTATGTGAACTAGTGGCT
1 AATATTGATTATGTGAACTAGTGGCT
** *
74685 AATATTTCTTATGTGGACTAGTGGCT
1 AATATTGATTATGTGAACTAGTGGCT
74711 AATATT
1 AATATT
74717 TCTCTTGGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (26 bp):
AATATTGATTATGTGAACTAGTGGCT
Found at i:74717 original size:26 final size:26
Alignment explanation
Indices: 74667--74719 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
74657 TGAATATTGA
74667 TTATGTGAACTAGTGGCTAATATTTC
1 TTATGTGAACTAGTGGCTAATATTTC
*
74693 TTATGTGGACTAGTGGCTAATATTTC
1 TTATGTGAACTAGTGGCTAATATTTC
74719 T
1 T
74720 CTTGGCTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (26 bp):
TTATGTGAACTAGTGGCTAATATTTC
Found at i:76460 original size:58 final size:56
Alignment explanation
Indices: 76382--76545 Score: 143
Period size: 58 Copynumber: 2.8 Consensus size: 56
76372 TAAATCATTG
*
76382 AATTTATTTTCTTATTAATCTGATATGATTTTGTTTGGTAAAAAGAAATAAAACGTAA
1 AATTTATTTTCTTA-GAATCTGATATGATTTTGTTT-GTAAAAAGAAATAAAACGTAA
* * ** * ** *
76440 AATTTATTTTCTTGGAAATCTTGA-ACGATTTCATCTTGTAAGAAGGAAATAAATTGTTA
1 AATTTATTTTCTTAG-AATC-TGATATGATTTTGT-TTGTAA-AAAGAAATAAAACGTAA
* * *
76499 AATTTATTTTCATAGAATCTTATATGATTCTGTTT-TATAAAAGAAAT
1 AATTTATTTTCTTAGAATCTGATATGATTTTGTTTGTA-AAAAGAAAT
76546 TAAATCATTG
Statistics
Matches: 83, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
56 9 0.11
57 5 0.06
58 38 0.46
59 31 0.37
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (56 bp):
AATTTATTTTCTTAGAATCTGATATGATTTTGTTTGTAAAAAGAAATAAAACGTAA
Found at i:82541 original size:19 final size:19
Alignment explanation
Indices: 82504--82542 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
82494 GACTGGTTCT
*
82504 AACCGGTTTGACCTATCTG
1 AACCGGTTTGACCGATCTG
*
82523 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGATCTG
82542 A
1 A
82543 CCCGACCGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGATCTG
Found at i:82577 original size:22 final size:21
Alignment explanation
Indices: 82548--82590 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
82538 TCTGACCCGA
*
82548 CCGACCGACCCGACCGTTGAC
1 CCGACCGACCCGACCATTGAC
82569 CCGACCCGACCCGACCATTGAC
1 CCGA-CCGACCCGACCATTGAC
82591 AGTTGACCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.21, C:0.49, G:0.21, T:0.09
Consensus pattern (21 bp):
CCGACCGACCCGACCATTGAC
Found at i:89860 original size:14 final size:14
Alignment explanation
Indices: 89827--89857 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
89817 GAACCGGTTT
89827 GACCGATCTGACCC
1 GACCGATCTGACCC
89841 GACCGATC-GACCC
1 GACCGATCTGACCC
89854 GACC
1 GACC
89858 CGACCGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.23, C:0.45, G:0.23, T:0.10
Consensus pattern (14 bp):
GACCGATCTGACCC
Found at i:89873 original size:22 final size:22
Alignment explanation
Indices: 89848--89891 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
89838 CCCGACCGAT
89848 CGACCCGACCCGACCGTTGACC
1 CGACCCGACCCGACCGTTGACC
89870 CGACCCGACCCGACCGTTGACC
1 CGACCCGACCCGACCGTTGACC
89892 GTTGACTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.50, G:0.23, T:0.09
Consensus pattern (22 bp):
CGACCCGACCCGACCGTTGACC
Found at i:89891 original size:17 final size:18
Alignment explanation
Indices: 89836--89879 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
89826 TGACCGATCT
89836 GACCCGACCGATCGACCC
1 GACCCGACCGATCGACCC
*
89854 GACCCGACCG-TTGACCC
1 GACCCGACCGATCGACCC
89871 GACCCGACC
1 GACCCGACC
89880 CGACCGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.20, C:0.50, G:0.23, T:0.07
Consensus pattern (18 bp):
GACCCGACCGATCGACCC
Found at i:91925 original size:10 final size:10
Alignment explanation
Indices: 91910--91943 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
91900 TTTTGAAACA
91910 TTCTTTTTTT
1 TTCTTTTTTT
91920 TTCTTTTTTT
1 TTCTTTTTTT
91930 TCTCTTTTTTT
1 T-TCTTTTTTT
91941 TTC
1 TTC
91944 ATCTACTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:91929 original size:11 final size:11
Alignment explanation
Indices: 91913--91942 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
91903 TGAAACATTC
91913 TTTTTTTTTCT
1 TTTTTTTTTCT
*
91924 TTTTTTTCTCT
1 TTTTTTTTTCT
91935 TTTTTTTT
1 TTTTTTTT
91943 CATCTACTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:94916 original size:14 final size:14
Alignment explanation
Indices: 94897--94923 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
94887 TTTAAAAATA
94897 AATTAAAAGAAAAG
1 AATTAAAAGAAAAG
94911 AATTAAAAGAAAA
1 AATTAAAAGAAAA
94924 CGAAATGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (14 bp):
AATTAAAAGAAAAG
Found at i:96780 original size:16 final size:16
Alignment explanation
Indices: 96759--96791 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
96749 TGTTATCTTC
96759 AAAAAGTCATTGATAA
1 AAAAAGTCATTGATAA
96775 AAAAAGTCATTGATAA
1 AAAAAGTCATTGATAA
96791 A
1 A
96792 CCTCCGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (16 bp):
AAAAAGTCATTGATAA
Found at i:107728 original size:21 final size:21
Alignment explanation
Indices: 107702--107752 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
107692 GTGCGATTCC
107702 ATTGCTTCAAATTCATAAACT
1 ATTGCTTCAAATTCATAAACT
*
107723 ATTGCTTCAAATTCATAAATT
1 ATTGCTTCAAATTCATAAACT
107744 ATTGCTTCA
1 ATTGCTTCA
107753 TCTGTCGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (21 bp):
ATTGCTTCAAATTCATAAACT
Found at i:109890 original size:28 final size:28
Alignment explanation
Indices: 109853--109956 Score: 113
Period size: 28 Copynumber: 3.7 Consensus size: 28
109843 CTAAACATTA
*
109853 AAAATATATTTTATTCTTATCATATATT
1 AAAATATATTTTATTCTTATTATATATT
* *
109881 AAAATATATTTTATTCTTATTTTAAATT
1 AAAATATATTTTATTCTTATTATATATT
*
109909 AAAAATATATTTTAATTTTTATTA-ACT-TT
1 -AAAATATATTTT-ATTCTTATTATA-TATT
* *
109938 AAAACATAATTTATTCTTA
1 AAAATATATTTTATTCTTA
109957 CTTTAATTGA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 6 0.09
28 35 0.55
29 15 0.23
30 8 0.12
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (28 bp):
AAAATATATTTTATTCTTATTATATATT
Found at i:109917 original size:57 final size:57
Alignment explanation
Indices: 109849--109962 Score: 151
Period size: 57 Copynumber: 2.0 Consensus size: 57
109839 ACATCTAAAC
* * *
109849 ATTAAAAATATATTTT-ATTCTTATCATA-TATTAAAATATATTTTATTCTTATTTTAA
1 ATTAAAAATATATTTTAATTCTTATCA-ACT-TTAAAACATAATTTATTCTTACTTTAA
* *
109906 ATTAAAAATATATTTTAATTTTTATTAACTTTAAAACATAATTTATTCTTACTTTAA
1 ATTAAAAATATATTTTAATTCTTATCAACTTTAAAACATAATTTATTCTTACTTTAA
109963 TTGAAATATT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 41 0.82
58 9 0.18
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (57 bp):
ATTAAAAATATATTTTAATTCTTATCAACTTTAAAACATAATTTATTCTTACTTTAA
Found at i:109939 original size:29 final size:27
Alignment explanation
Indices: 109850--109949 Score: 87
Period size: 29 Copynumber: 3.5 Consensus size: 27
109840 CATCTAAACA
* *
109850 TTAAAAATATATTTTATTCTTATCATAT
1 TTAAAAATATATTTTATTTTTATTA-AT
* *
109878 ATT-AAAATATATTTTATTCTTATTTTAAA
1 -TTAAAAATATATTTTATT-TT-TATTAAT
109907 TTAAAAATATATTTTAATTTTTATTAACT
1 TTAAAAATATATTTT-ATTTTTATTAA-T
109936 TTAAAACATA-ATTT
1 TTAAAA-ATATATTT
109950 ATTCTTACTT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
28 22 0.37
29 28 0.47
30 9 0.15
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAAAAATATATTTTATTTTTATTAAT
Found at i:110153 original size:30 final size:28
Alignment explanation
Indices: 110119--110188 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 28
110109 TAACGATTAA
*
110119 TTAATAATTTAAGGTAAGACTAGAATATAT
1 TTAATAATTTAAGGTAAGAATA-AA-ATAT
* *
110149 TTAATAATTTAAGTTAAGAATATAATAT
1 TTAATAATTTAAGGTAAGAATAAAATAT
*
110177 GTAATAATTTAA
1 TTAATAATTTAA
110189 AATTAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 15 0.42
29 1 0.03
30 20 0.56
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.40
Consensus pattern (28 bp):
TTAATAATTTAAGGTAAGAATAAAATAT
Found at i:110198 original size:28 final size:28
Alignment explanation
Indices: 110145--110198 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
110135 AGACTAGAAT
* *
110145 ATATTTAATAATTTAAGTTAAGAATATA
1 ATATGTAATAATTTAAATTAAGAATATA
110173 ATATGTAATAATTTAAAATTAA-AATA
1 ATATGTAATAATTT-AAATTAAGAATA
110199 AACTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (28 bp):
ATATGTAATAATTTAAATTAAGAATATA
Found at i:110229 original size:31 final size:31
Alignment explanation
Indices: 110193--110266 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
110183 ATTTAAAATT
* *
110193 AAAATAAACTATAT-TTTTATAAGTTAAGATA
1 AAAATAAAATATATATTTT-TAAGATAAGATA
110224 AAAATAAAATATATATTTTTAAGATAAGATA
1 AAAATAAAATATATATTTTTAAGATAAGATA
* *
110255 AGATTAAAATAT
1 AAAATAAAATAT
110267 GTTAAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.36
Consensus pattern (31 bp):
AAAATAAAATATATATTTTTAAGATAAGATA
Found at i:110366 original size:29 final size:29
Alignment explanation
Indices: 110341--110414 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
110331 TATAATATAT
110341 ATAAAATATATTTTTAATTTAAAATAAGA
1 ATAAAATATATTTTTAATTTAAAATAAGA
* * *
110370 ATAAAATATATTTTAAAGTTAAGATAAGA
1 ATAAAATATATTTTTAATTTAAAATAAGA
110399 ATAAAATATATATTTT
1 ATAAAATATAT-TTTT
110415 TAATGTTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 37 0.93
30 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (29 bp):
ATAAAATATATTTTTAATTTAAAATAAGA
Found at i:110728 original size:75 final size:75
Alignment explanation
Indices: 110646--110795 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
110636 GATTGGTGCG
110646 AAATAAAATTATTAAATTAAATAAAGTAAACCCTCCAATCGAATGGCGACATGTGGCACGATCTG
1 AAATAAAATTATTAAATTAAATAAAGTAAACCCTCCAATCGAATGGCGACATGTGGCACGATCTG
110711 ATTCGAAGAT
66 ATTCGAAGAT
110721 AAATAAAATTATTAAATTAAATAAAGTAAACCCTCCAATCGAATGGCGACATGTGGCACGATCTG
1 AAATAAAATTATTAAATTAAATAAAGTAAACCCTCCAATCGAATGGCGACATGTGGCACGATCTG
110786 ATTCGAAGAT
66 ATTCGAAGAT
110796 TATATTTATT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (75 bp):
AAATAAAATTATTAAATTAAATAAAGTAAACCCTCCAATCGAATGGCGACATGTGGCACGATCTG
ATTCGAAGAT
Found at i:113876 original size:3 final size:3
Alignment explanation
Indices: 113861--113944 Score: 86
Period size: 3 Copynumber: 29.0 Consensus size: 3
113851 TTATATCATT
* *
113861 TTA TTA GTA TTA TTA TT- TTA TTA TTAA TT- TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
* * *
113905 TTT TTA TTA TTG TTA TTA -TG TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
113945 AATAATAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
2 7 0.11
3 56 0.85
4 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:115215 original size:23 final size:24
Alignment explanation
Indices: 115189--115248 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
115179 ATACTATAGT
* *
115189 TTTAATTATTATTTTAGTCA-CTG
1 TTTAATTATTATTTAAGTCATATG
* * *
115212 TTTAGTTATTATTTAATTTATATG
1 TTTAATTATTATTTAAGTCATATG
115236 TTTAATTATTATT
1 TTTAATTATTATT
115249 ATTATTATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (24 bp):
TTTAATTATTATTTAAGTCATATG
Found at i:115256 original size:24 final size:24
Alignment explanation
Indices: 115189--115256 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
115179 ATACTATAGT
* *
115189 TTTAATTATTATTTTAGTCA-CTG
1 TTTAATTATTATTTTAGTTATATG
* * *
115212 TTTAGTTATTATTTAATTTATATG
1 TTTAATTATTATTTTAGTTATATG
115236 TTTAATTATTATTATTA-TTAT
1 TTTAATTATTATT-TTAGTTAT
115257 TATTATTGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 16 0.44
24 18 0.50
25 2 0.06
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (24 bp):
TTTAATTATTATTTTAGTTATATG
Found at i:116174 original size:2 final size:2
Alignment explanation
Indices: 116167--116199 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
116157 TTTATACTAT
116167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
116200 TCTTTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117536 original size:43 final size:44
Alignment explanation
Indices: 117475--117558 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 44
117465 TGGCTTTAGA
* *
117475 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTATT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTATT
* *
117518 GAAGTTAGGACTGAAAGTTGTCCCCTACATGTAAAAGTTTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTT
117559 GTTTGATGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 28 0.78
44 8 0.22
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTATT
Found at i:117796 original size:19 final size:20
Alignment explanation
Indices: 117764--117801 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
117754 TGCATCTTTT
* *
117764 CATTTTTATGTTTGTATTTA
1 CATTTTCATGTTTGCATTTA
117784 CATTTTCAT-TTTGCATTT
1 CATTTTCATGTTTGCATTT
117802 GCATCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.18, C:0.11, G:0.08, T:0.63
Consensus pattern (20 bp):
CATTTTCATGTTTGCATTTA
Done.