Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004721.1 Hibiscus syriacus cultivar Beakdansim tig00010647_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: 66646
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:4083 original size:23 final size:23
Alignment explanation
Indices: 4053--4097 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4043 ATTTGAGATA
* *
4053 CAACATCACCACCATCTTCCATT
1 CAACATCAACAACATCTTCCATT
4076 CAACATCAACAACATCTTCCAT
1 CAACATCAACAACATCTTCCAT
4098 CAAGGCCACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (23 bp):
CAACATCAACAACATCTTCCATT
Found at i:11407 original size:16 final size:16
Alignment explanation
Indices: 11366--11401 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
11356 ATTTAAAGGC
11366 AAAAATTAAAATAATAG
1 AAAAATT-AAATAATAG
11383 AAAAATTAAATAATA-
1 AAAAATTAAATAATAG
11398 AAAA
1 AAAA
11402 TTTTAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 8 0.42
17 7 0.37
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (16 bp):
AAAAATTAAATAATAG
Found at i:12138 original size:20 final size:20
Alignment explanation
Indices: 12113--12163 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
12103 CTTCACAAAG
12113 TAGTATCGATACCATGAGCA
1 TAGTATCGATACCATGAGCA
12133 TAGTATCGATACCATGAGCA
1 TAGTATCGATACCATGAGCA
12153 TAGTATCGATA
1 TAGTATCGATA
12164 TTGGTCAGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (20 bp):
TAGTATCGATACCATGAGCA
Found at i:15872 original size:21 final size:21
Alignment explanation
Indices: 15855--15895 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
15845 ATTGTGTATC
* *
15855 GATGTACTGCTACAGTGTACT
1 GATGCACTACTACAGTGTACT
15876 GATGCACTACTACAGTGTAC
1 GATGCACTACTACAGTGTAC
15896 CAATACACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (21 bp):
GATGCACTACTACAGTGTACT
Found at i:15904 original size:21 final size:21
Alignment explanation
Indices: 15864--15904 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15854 CGATGTACTG
** *
15864 CTACAGTGTACTGATGCACTA
1 CTACAGTGTACCAATACACTA
15885 CTACAGTGTACCAATACACT
1 CTACAGTGTACCAATACACT
15905 GTTGCAGTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.27
Consensus pattern (21 bp):
CTACAGTGTACCAATACACTA
Found at i:16406 original size:44 final size:45
Alignment explanation
Indices: 16314--16481 Score: 252
Period size: 44 Copynumber: 3.8 Consensus size: 45
16304 TATAAAATTT
**
16314 CTTACCATTTA-TCTCATAAGCTCGTAAGCTTATTTTATTAATATA
1 CTTACCATTTATTC-CATAAGCTCGTAAGCTTATTTTACCAATATA
*
16359 CTTACCATTTATTTCATAAGCTCGTAAG-TTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
16403 CTTACCATTTATTCCATAAGCTCGTAAGTTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
16448 CTTGCCA-TTATTCCATAAGCTCTTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
16482 ACATGTTTAC
Statistics
Matches: 114, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
44 66 0.58
45 47 0.41
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:16425 original size:89 final size:89
Alignment explanation
Indices: 16314--16481 Score: 250
Period size: 89 Copynumber: 1.9 Consensus size: 89
16304 TATAAAATTT
** *
16314 CTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTATTAATATACTTACCATTTATTTCATAAG
1 CTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA-TTATTCCATAAG
16379 CTCGTAAG-TTATTTTACCAATATA
65 CTCGTAAGCTTATTTTACCAATATA
* *
16403 CTTACCATTTAT-TCCATAAGCTCGTAAGTTTATTTTACCAATATACTTGCCATTATTCCATAAG
1 CTTACCATTTATCT-CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTCCATAAG
*
16467 CTCTTAAGCTTATTT
65 CTCGTAAGCTTATTT
16482 ACATGTTTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
88 19 0.27
89 52 0.73
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (89 bp):
CTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTCCATAAGC
TCGTAAGCTTATTTTACCAATATA
Found at i:17962 original size:17 final size:17
Alignment explanation
Indices: 17940--17978 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
17930 AAATGTTAGG
*
17940 TACATTTCATCTTAA-TT
1 TACATTTAATC-TAACTT
17957 TACATTTAATCTAACTT
1 TACATTTAATCTAACTT
17974 TACAT
1 TACAT
17979 GAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (17 bp):
TACATTTAATCTAACTT
Found at i:22913 original size:19 final size:20
Alignment explanation
Indices: 22891--22941 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
22881 ATTATTTTTA
22891 TTTTTATTATTTTAAA-TTT
1 TTTTTATTATTTTAAAGTTT
*
22910 TTTTAATT-TATTTAAAGTTT
1 TTTTTATTAT-TTTAAAGTTT
*
22930 TATTTTTTTATT
1 T-TTTTATTATT
22942 GTTTTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
18 1 0.04
19 13 0.52
20 4 0.16
21 6 0.24
22 1 0.04
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTATTATTTTAAAGTTT
Found at i:22939 original size:20 final size:19
Alignment explanation
Indices: 22886--22941 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
22876 AATTAATTAT
22886 TTTTATTTTTATTATTTTAAA
1 TTTTATTTTT-TTA-TTTAAA
*
22907 TTTT-TTTAATTTATTTAAA
1 TTTTATTT-TTTTATTTAAA
22926 GTTTTATTTTTTTATT
1 -TTTTATTTTTTTATT
22942 GTTTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 6 0.20
20 16 0.53
21 8 0.27
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTATTTTTTTATTTAAA
Found at i:24407 original size:20 final size:19
Alignment explanation
Indices: 24368--24421 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
24358 AATTCGCAAC
*
24368 GCGATTTTAGTTTCGTGTT
1 GCGATTTTAGTTTCGCGTT
*
24387 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
24407 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
24422 AGAAACTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:27807 original size:61 final size:62
Alignment explanation
Indices: 27707--27846 Score: 194
Period size: 66 Copynumber: 2.2 Consensus size: 62
27697 TTTTACATTG
*
27707 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
* * *
27767 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA--TTTTT-CTTGATTAATTGATTTGT
27832 A
62 A
27833 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
27847 ATTTCTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
60 17 0.24
61 18 0.26
64 4 0.06
66 31 0.44
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:27931 original size:20 final size:20
Alignment explanation
Indices: 27906--27992 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 20
27896 GTTGAAGGTA
27906 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
27926 CAAATTCACAACGCGAAA-T
1 CAAATTCGCAACGCGAAAGT
*** *
27945 --AA---GCTTTGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
27960 CAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
27980 CAAATTCGCAACG
1 CAAATTCGCAACG
27993 TAATTTTTGG
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
14 6 0.12
15 1 0.02
17 4 0.08
19 1 0.02
20 39 0.76
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:28271 original size:38 final size:39
Alignment explanation
Indices: 28201--28286 Score: 147
Period size: 38 Copynumber: 2.2 Consensus size: 39
28191 TCAAGTTGTA
*
28201 GATTTTGATTTCTTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
28240 GATTTTGATTTCCTTTTG-TTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
28278 GATTTTGAT
1 GATTTTGAT
28287 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 28 0.62
39 17 0.38
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.49
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:28620 original size:18 final size:18
Alignment explanation
Indices: 28597--28633 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28587 CAAAATTTAT
28597 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
28615 ATTGAAATTGAAATTCAA
1 ATTGAAATTCAAACTCAA
28633 A
1 A
28634 CTCCAATTAC
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:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:29456 original size:18 final size:18
Alignment explanation
Indices: 29433--29468 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29423 AAGCCGGTTG
*
29433 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
29451 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
29469 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:29530 original size:19 final size:19
Alignment explanation
Indices: 29506--29548 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
29496 GGATTTTGAT
29506 GAGGATCCATTTTTTGGTA
1 GAGGATCCATTTTTTGGTA
29525 GAGGATCCATTTTTTGGTA
1 GAGGATCCATTTTTTGGTA
29544 GAGGA
1 GAGGA
29549 AAAGATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.37
Consensus pattern (19 bp):
GAGGATCCATTTTTTGGTA
Found at i:30567 original size:20 final size:20
Alignment explanation
Indices: 30529--30570 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
30519 GTTGTCAATT
* * *
30529 GAATTTGACTTTTGTGTTGC
1 GAATTTGACTATCGCGTTGC
30549 GAATTTGACTATCGCGTTGC
1 GAATTTGACTATCGCGTTGC
30569 GA
1 GA
30571 TTTACAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.40
Consensus pattern (20 bp):
GAATTTGACTATCGCGTTGC
Found at i:30583 original size:20 final size:20
Alignment explanation
Indices: 30560--30610 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
30550 AATTTGACTA
30560 TCGCGTTGCGATTTACAAAT
1 TCGCGTTGCGATTTACAAAT
* *
30580 TCGCGTAGCGATTTACAGAT
1 TCGCGTTGCGATTTACAAAT
*
30600 TCGCATTGCGA
1 TCGCGTTGCGA
30611 ATTTGGAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (20 bp):
TCGCGTTGCGATTTACAAAT
Found at i:33804 original size:17 final size:16
Alignment explanation
Indices: 33753--33812 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 16
33743 AATTAGGTCA
33753 TTATTTTATTTTTATTCT
1 TTATTTTATTTTTA-T-T
*
33771 TTTTTTACTATTTTTATT
1 TTATTT--TATTTTTATT
33789 TTATTTTATTTGTTATT
1 TTATTTTATTT-TTATT
*
33806 TAATTTT
1 TTATTTT
33813 TTAATTATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 5 0.14
17 11 0.31
18 11 0.31
19 1 0.03
20 8 0.22
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (16 bp):
TTATTTTATTTTTATT
Found at i:35977 original size:22 final size:23
Alignment explanation
Indices: 35952--36005 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
35942 AAACATACCA
*
35952 AAAACATAGAAAAA-CGTATTAT
1 AAAACATAGAAAAATCGTATCAT
*
35974 AAAACATA-AAAAATCGTGTCAT
1 AAAACATAGAAAAATCGTATCAT
35996 AAAGACATAG
1 AAA-ACATAG
36006 TTATTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.19
22 17 0.63
23 5 0.19
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (23 bp):
AAAACATAGAAAAATCGTATCAT
Found at i:37263 original size:21 final size:22
Alignment explanation
Indices: 37239--37287 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
37229 ATATGATTAA
37239 AATTATCG-TAATTATACATTT
1 AATTATCGATAATTATACATTT
* * *
37260 AATTCTCGATATTTATATATTT
1 AATTATCGATAATTATACATTT
*
37282 TATTAT
1 AATTAT
37288 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (22 bp):
AATTATCGATAATTATACATTT
Found at i:38752 original size:46 final size:46
Alignment explanation
Indices: 38685--38772 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
38675 ACCGCTACGT
* *
38685 ATTTTCATTTGTAGCATCCTTTCATGCCAATTATGCATTGTTATAC
1 ATTTTCATTTATAGCATCCTTTCATGCCAATTATGCACTGTTATAC
38731 ATTTTCATTTAT-GACATCCTTTCATGCCAATTATGCACTGTT
1 ATTTTCATTTATAG-CATCCTTTCATGCCAATTATGCACTGTT
38773 CTTCATCTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 1 0.03
46 38 0.97
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.45
Consensus pattern (46 bp):
ATTTTCATTTATAGCATCCTTTCATGCCAATTATGCACTGTTATAC
Found at i:39109 original size:55 final size:55
Alignment explanation
Indices: 39070--39555 Score: 755
Period size: 55 Copynumber: 8.9 Consensus size: 55
39060 TAACAATATA
* * *
39070 GAAATTCATAAATTTATAATGAATTTCTTAGTTTTGCACACAAAGTGTCCATACG
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACG
* * *
39125 GAAATTCATAAACTTATTATGAATTTCTTAGCTTTGCACAAAAAGTGCTCATACG
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACG
*
39180 GAAATTCATAAACTTATTATGAATTTCTTAGCTTTT-CACACAAAGTGCACATACG
1 GAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCCATACG
* *
39235 GAAATTCAT-AACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCTATA-A
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACG
* * * *
39288 AAAATTCATAAACTTATTATGAATTTTTTAGTTTTGCACACAAATTGCCCATATG
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACG
*
39343 TAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACG
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACG
* * *
39398 AAAATTCATAAACTTATTAT-AATTTCTTAGTTTTGCACACAAAGTGCCTATACA
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACG
*
39452 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGACCATACG
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACG
* *
39507 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACGCATAGTGCC
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCC
39556 ATTTGGTAAT
Statistics
Matches: 395, Mismatches: 31, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
53 12 0.03
54 127 0.32
55 253 0.64
56 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (55 bp):
GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACG
Found at i:39359 original size:109 final size:110
Alignment explanation
Indices: 39071--39555 Score: 739
Period size: 109 Copynumber: 4.4 Consensus size: 110
39061 AACAATATAG
* * *
39071 AAATTCATAAATTTATAATGAATTTCTTAGTTTTGCACACAAAGTGTCCATACGGAAATTCATAA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGGAAATTCATAA
* * *
39136 ACTTATTATGAATTTCTTAGCTTTGCACAAAAAGTG-CTCATACGG
66 ACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCT-ATACGA
*
39181 AAATTCATAAACTTATTATGAATTTCTTAGCTTTT-CACACAAAGTGCACATACGGAAATTCAT-
1 AAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCCATACGGAAATTCATA
*
39244 AACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCTATA-AA
65 AACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCTATACGA
* * * *
39289 AAATTCATAAACTTATTATGAATTTTTTAGTTTTGCACACAAATTGCCCATATGTAAATTCATAA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGGAAATTCATAA
*
39354 ACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGA
66 ACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCTATACGA
* *
39399 AAATTCATAAACTTATTAT-AATTTCTTAGTTTTGCACACAAAGTGCCTATACAGAAATTCATAA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGGAAATTCATAA
*
39463 ACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGACC-ATACGG
66 ACTTATTATGAATTTCTTAGTTTTGCACACAAAGTG-CCTATACGA
* *
39508 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACGCATAGTGCC
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCC
39556 ATTTGGTAAT
Statistics
Matches: 344, Mismatches: 24, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
107 4 0.01
108 53 0.15
109 179 0.52
110 104 0.30
111 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (110 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGGAAATTCATAA
ACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCTATACGA
Found at i:44544 original size:12 final size:12
Alignment explanation
Indices: 44527--44552 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44517 CTTATCCTAT
44527 AATAATAATAAA
1 AATAATAATAAA
44539 AATAATAATAAA
1 AATAATAATAAA
44551 AA
1 AA
44553 AATGTTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:44545 original size:15 final size:14
Alignment explanation
Indices: 44525--44555 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
44515 TACTTATCCT
44525 ATAATAATAATAAAA
1 ATAATAATAA-AAAA
44540 ATAATAATAAAAAA
1 ATAATAATAAAAAA
44554 AT
1 AT
44556 GTTCTCTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAATAATAAAAAA
Found at i:44979 original size:30 final size:29
Alignment explanation
Indices: 44945--45006 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
44935 TCTTATATGT
*
44945 TCAAAGTGCT-ATCATAACGAGTCATATATA
1 TCAAAGTACTGAT-ATAACGAGTCATAT-TA
* *
44975 TCAAAGTACTGATATAACTAGTCTTATTA
1 TCAAAGTACTGATATAACGAGTCATATTA
45004 TCA
1 TCA
45007 TCGTATGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.18
30 21 0.75
31 2 0.07
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (29 bp):
TCAAAGTACTGATATAACGAGTCATATTA
Found at i:51041 original size:45 final size:45
Alignment explanation
Indices: 50971--51810 Score: 340
Period size: 45 Copynumber: 18.9 Consensus size: 45
50961 GATACTACTG
* * * *
50971 AAAAG-TTGACTCAT-TTCTGCAAGAAAATCAAGAATAACACCACT
1 AAAAGATTGACTCATCTTC-GCGAGAAAGTCAAGAAGAACAACACT
* * * * *
51015 AAAAGGTTGACTCTTCTTCGTGAGAAAGTCAATAAGGACAACACT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGAACAACACT
* **
51060 AAAAGATTGACTCATCTTTGCGAGAAAGTCAAGAAGGCCAACACT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGAACAACACT
* * * * * * *
51105 AAGATATTGACTCATCTCCACTAGAAAATCAAGGAAG-ATAACACT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAA-GAAGAACAACACT
* * * *
51150 GAAAGATTGACTTC-TCTTCACTAGAAAGTCAAGAATG-ACAATACT
1 AAAAGATTGAC-TCATCTTCGCGAGAAAGTCAAGAA-GAACAACACT
* * ** * *
51195 GAGAGATTGACTTC-TCTTCATGAAAAAGTCAAGAAAGAA-AATACT
1 AAAAGATTGAC-TCATCTTCGCGAGAAAGTCAAG-AAGAACAACACT
* ** * * *
51240 GAAAGATTGACTTTTCTTCACGAGAAAATCAAGAATG-ACAATACT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAA-GAACAACACT
** * * *
51285 TGAAGATTGAATTC-TCTTCGCGAGAAAGTCAAGAATAACAATACT
1 AAAAGATTG-ACTCATCTTCGCGAGAAAGTCAAGAAGAACAACACT
* ** * * *
51330 GAAAGATTGACTTC-TCTTCAAGAGAAAGTTAAGAATG-CCAATACT
1 AAAAGATTGAC-TCATCTTCGCGAGAAAGTCAAGAA-GAACAACACT
* ** * *
51375 GAAAGATTGACTTC-TCTTCATGAGAAAGTC---AAGAATAACATT
1 AAAAGATTGAC-TCATCTTCGCGAGAAAGTCAAGAAGAACAACACT
* * * * * * *
51417 GAAAGATTGACTCCTCTTCACGAGAGAG-C--CAAGAATAACATT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGAACAACACT
* * * *** **
51459 GAAATATTAACTCATCTTCATAAGGGAGTCAAGAATGAA-AGA-ACT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAA-GAACA-ACACT
* * * *
51504 GAAAGATTGACTTC-TCTTCACGAGAAAGTCAAGAA-AGACAATATT
1 AAAAGATTGAC-TCATCTTCGCGAGAAAGTCAAGAAGA-ACAACACT
* * * * *
51549 GAAAGATTGAATTC-TCTTCACGAGAAAGCCAAGAATG-ACAATACT
1 AAAAGATTG-ACTCATCTTCGCGAGAAAGTCAAGAA-GAACAACACT
* ** * *
51594 GAAAGATTGACTTC-TCTTCATGAGAAAGTCAAGAATAACAATACT
1 AAAAGATTGAC-TCATCTTCGCGAGAAAGTCAAGAAGAACAACACT
* * * * *
51639 GAAAGATTAACTTC-TCTTCACGAGAAATTCAAGAAAGAA-AATACT
1 AAAAGATTGAC-TCATCTTCGCGAGAAAGTCAAG-AAGAACAACACT
* ** * *
51684 GAAAGATTGACTTC-TCTTCATGAGAAAGTCAAGAATG-ACAATATT
1 AAAAGATTGAC-TCATCTTCGCGAGAAAGTCAAGAA-GAACAACACT
* * * * * * *
51729 GAAAGATTGACTTATCTTCACAAGAAAGTC---AATAATAACATT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGAACAACACT
* * * * *
51771 GAAAGATTGACTCCTCTTCACGAGAGAGTCAAGAATAACA
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGAACA
51811 TTGAAAGAAT
Statistics
Matches: 654, Mismatches: 103, Indels: 77
0.78 0.12 0.09
Matches are distributed among these distances:
41 4 0.01
42 97 0.15
43 2 0.00
44 20 0.03
45 506 0.77
46 25 0.04
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (45 bp):
AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGAACAACACT
Found at i:51105 original size:90 final size:88
Alignment explanation
Indices: 50992--51806 Score: 691
Period size: 90 Copynumber: 9.2 Consensus size: 88
50982 CATTTCTGCA
* * ** * * *
50992 AGAAAATCAAGAATAACACCACTAAAAGGTTGAC-TCTTCTTCGTGAGAAAGTCAATAAGGACAA
1 AGAAAGTCAAGAATGACAATACTAAAAGATTGACTTC-TCTTCATGAGAAAGTCAAGAA-GACAA
* **
51056 CACTAAAAGATTGACTCATCTTTGCG
64 CACTGAAAGATTGACTC-TCTTCACG
* * * * * * * *
51082 AGAAAGTCAAGAAGGCCAACACTAAGATATTGAC-TCATCTCCACT-AGAAAATCAAGGAAGATA
1 AGAAAGTCAAGAATGACAATACTAAAAGATTGACTTC-TCTTCA-TGAGAAAGTCAA-GAAGACA
*
51145 ACACTGAAAGATTGACTTCTCTTCACT
63 ACACTGAAAGATTGAC-TCTCTTCACG
* * * * *
51172 AGAAAGTCAAGAATGACAATACTGAGAGATTGACTTCTCTTCATGAAAAAGTCAAGAAAGAAAAT
1 AGAAAGTCAAGAATGACAATACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAG-AAGACAAC
*
51237 ACTGAAAGATTGACTTTTCTTCACG
65 ACTGAAAGATTGAC-TCTCTTCACG
* ** * ** * *
51262 AGAAAATCAAGAATGACAATACTTGAAGATTGAATTCTCTTCGCGAGAAAGTCAAGAATAACAAT
1 AGAAAGTCAAGAATGACAATACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAA-GACAAC
*
51327 ACTGAAAGATTGACTTCTCTTCAAG
65 ACTGAAAGATTGAC-TCTCTTCACG
* * * *
51352 AGAAAGTTAAGAATGCCAATACTGAAAGATTGACTTCTCTTCATGAGAAAGTCAAG-A-ATAACA
1 AGAAAGTCAAGAATGACAATACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAAGACAACA
*
51415 TTGAAAGATTGACTCCTCTTCACG
66 CTGAAAGATTGACT-CTCTTCACG
* * * * * * * **
51439 AGAGAGCCAAGAATAAC-AT--TGAAATATTAAC-TCATCTTCATAAGGGAGTCAAGAATGA-AA
1 AGAAAGTCAAGAATGACAATACTAAAAGATTGACTTC-TCTTCATGAGAAAGTCAAGAA-GACAA
*
51499 GAACTGAAAGATTGACTTCTCTTCACG
64 -CACTGAAAGATTGAC-TCTCTTCACG
* * * * * * *
51526 AGAAAGTCAAGAAAGACAATATTGAAAGATTGAATTCTCTTCACGAGAAAGCCAAGAATGACAAT
1 AGAAAGTCAAGAATGACAATACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAA-GACAAC
*
51591 ACTGAAAGATTGACTTCTCTTCATG
65 ACTGAAAGATTGAC-TCTCTTCACG
* * * * * * *
51616 AGAAAGTCAAGAATAACAATACTGAAAGATTAACTTCTCTTCACGAGAAATTCAAGAAAGAAAAT
1 AGAAAGTCAAGAATGACAATACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAG-AAGACAAC
*
51681 ACTGAAAGATTGACTTCTCTTCATG
65 ACTGAAAGATTGAC-TCTCTTCACG
* * * ** * *
51706 AGAAAGTCAAGAATGACAATATTGAAAGATTGACTTATCTTCACAAGAAAGTCAA-TA-ATAACA
1 AGAAAGTCAAGAATGACAATACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAAGACAACA
*
51769 TTGAAAGATTGACTCCTCTTCACG
66 CTGAAAGATTGACT-CTCTTCACG
*
51793 AGAGAGTCAAGAAT
1 AGAAAGTCAAGAAT
51807 AACATTGAAA
Statistics
Matches: 604, Mismatches: 100, Indels: 45
0.81 0.13 0.06
Matches are distributed among these distances:
83 2 0.00
84 26 0.04
85 1 0.00
86 6 0.01
87 109 0.18
88 4 0.01
89 5 0.01
90 438 0.73
91 13 0.02
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (88 bp):
AGAAAGTCAAGAATGACAATACTAAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAAGACAACA
CTGAAAGATTGACTCTCTTCACG
Found at i:51168 original size:135 final size:133
Alignment explanation
Indices: 50992--51824 Score: 659
Period size: 135 Copynumber: 6.3 Consensus size: 133
50982 CATTTCTGCA
* * * * *
50992 AGAAAATCAAGAATA-ACACCACTAAAAGGTTGAC-TCTTCTTCGTGAGAAAGTCAATAAGGACA
1 AGAAAATCAAGAAGATA-A-CACTGAAAGATTGACTTC-TCTTCGTGAGAAAGTCAAGAATGACA
* * *** * * *
51055 ACACTAAAAGATTGAC-TCATCTTTGCGAGAAAGTCAAGAAGGCCAACACT-AAGATATTGACTC
63 ATACTGAAAGATTGACTTC-TCTTCAAGAGAAAGTCAAGAAAGCCAATACTGAA-AGATTGACTC
*
51118 ATCTCCACT
126 -TCTTCACT
*
51127 AGAAAATCAAGGAAGATAACACTGAAAGATTGACTTCTCTTCACT-AGAAAGTCAAGAATGACAA
1 AGAAAATCAA-GAAGATAACACTGAAAGATTGACTTCTCTTC-GTGAGAAAGTCAAGAATGACAA
* * * ** *
51191 TACTGAGAGATTGACTTCTCTTCATGAAAAAGTCAAGAAAGAAAATACTGAAAGATTGACTTTTC
64 TACTGAAAGATTGACTTCTCTTCAAGAGAAAGTCAAGAAAGCCAATACTGAAAGATTGAC-TCTC
*
51256 TTCACG
128 TTCACT
* * * * *
51262 AGAAAATCAAGAATGACAATACTTG-AAGATTGAATTCTCTTCGCGAGAAAGTCAAGAATAACAA
1 AGAAAATCAAGAA-GATAACAC-TGAAAGATTGACTTCTCTTCGTGAGAAAGTCAAGAATGACAA
* *
51326 TACTGAAAGATTGACTTCTCTTCAAGAGAAAGTTAAGAATGCCAATACTGAAAGATTGACTTCTC
64 TACTGAAAGATTGACTTCTCTTCAAGAGAAAGTCAAGAAAGCCAATACTGAAAGATTGAC-TCTC
51391 TTCA-T
128 TTCACT
* * * ** * * *
51396 GAGAAAGTCAAG-A-ATAACATTGAAAGATTGACTCCTCTTCACGAGAGAGCCAAGAATAAC-AT
1 -AGAAAATCAAGAAGATAACACTGAAAGATTGACTTCTCTTCGTGAGAAAGTCAAGAATGACAAT
* * ** * * *
51458 --TGAAATATTAAC-TCATCTTCATA-AGGGAGTCAAGAATG-AAAGAACTGAAAGATTGACTTC
65 ACTGAAAGATTGACTTC-TCTTCA-AGAGAAAGTCAAGAAAGCCAA-TACTGAAAGATTGAC-TC
*
51518 TCTTCACG
126 TCTTCACT
* * * * * ** *
51526 AGAAAGTCAAGAAAGACAATATTGAAAGATTGAATTCTCTTCACGAGAAAGCCAAGAATGACAAT
1 AGAAAATCAAG-AAGATAACACTGAAAGATTGACTTCTCTTCGTGAGAAAGTCAAGAATGACAAT
* * *
51591 ACTGAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAATA-ACAATACTGAAAGATTAACTTCTC
65 ACTGAAAGATTGACTTCTCTTCAAGAGAAAGTCAAGAA-AGCCAATACTGAAAGATTGAC-TCTC
*
51655 TTCACG
128 TTCACT
* * * *
51661 AGAAATTCAAGAAAGAAAATACTGAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAATGACAAT
1 AGAAAATCAAG-AAGATAACACTGAAAGATTGACTTCTCTTCGTGAGAAAGTCAAGAATGACAAT
* * * *
51726 ATTGAAAGATTGACTTATCTTCACA-AGAAAGTCAATAATA-AC-AT--TGAAAGATTGACTCCT
65 ACTGAAAGATTGACTTCTCTTCA-AGAGAAAGTCAAGAA-AGCCAATACTGAAAGATTGACT-CT
*
51786 CTTCACG
127 CTTCACT
* * * *
51793 AGAGAGTCAAG-A-ATAACATTGAAAGAATGACT
1 AGAAAATCAAGAAGATAACACTGAAAGATTGACT
51825 CTTCTTCACA
Statistics
Matches: 585, Mismatches: 85, Indels: 62
0.80 0.12 0.08
Matches are distributed among these distances:
128 4 0.01
129 78 0.13
130 2 0.00
131 6 0.01
132 106 0.18
133 2 0.00
134 6 0.01
135 361 0.62
136 19 0.03
137 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (133 bp):
AGAAAATCAAGAAGATAACACTGAAAGATTGACTTCTCTTCGTGAGAAAGTCAAGAATGACAATA
CTGAAAGATTGACTTCTCTTCAAGAGAAAGTCAAGAAAGCCAATACTGAAAGATTGACTCTCTTC
ACT
Found at i:51768 original size:354 final size:351
Alignment explanation
Indices: 51142--51878 Score: 1075
Period size: 354 Copynumber: 2.1 Consensus size: 351
51132 ATCAAGGAAG
* * * * *
51142 ATAACACTGAAAGATTGACTTCTCTTCACTAGAAAGTCAAGAATGACAATACTGAGAGATTGACT
1 ATAAAACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAAGACAATACTGAAAGATTGAAT
* * *
51207 TCTCTTCATGAAAAAGTCAAGAAAGAAAATACTGAAAGATTGACTTTTCTTCACGAGAAAATCAA
66 TCTCTTCACGAAAAAGCCAAGAAAGAAAATACTGAAAGATTGACTTCTCTTCACGAGAAAATCAA
* * *
51272 GAATGACAATACTTGAAGATTGAATTCTCTTCGCGAGAAAGTCAAGAATAACAATACTGAAAGAT
131 GAATAACAATACTTGAAGATTGAATTCTCTTCACGAGAAAGTCAAGAATAAAAATACTGAAAGAT
* * * **
51337 TGACTTCTCTTCAAGAGAAAGTTAAGAATGCCAATACTGAAAGATTGACTTCTCTTCATGAGAAA
196 TGACTTCTCTTCAAGAGAAAGTCAAGAATGACAATACTGAAAGATTGACTTATCTTCACAAGAAA
* *
51402 GTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGAGAGCCAAGAATAACATTGAAATATT
261 GTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGAGAGCCAAGAATAACATTGAAAGAAT
*
51467 AACTCATCTTCATAAGGGAGTCAAGA
326 AACTCATCTTCACAAGGGAGTCAAGA
*
51493 ATGAAAGAACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAAGACAATATTGAAAGATTG
1 AT--AA-AACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAAGACAATACTGAAAGATTG
* * * * *
51558 AATTCTCTTCACGAGAAAGCCAAGAATGACAATACTGAAAGATTGACTTCTCTTCATGAGAAAGT
63 AATTCTCTTCACGAAAAAGCCAAGAAAGAAAATACTGAAAGATTGACTTCTCTTCACGAGAAAAT
*
51623 CAAGAATAACAATAC-TGAAAGATT-AACTTCTCTTCACGAGAAATTCAAGAA-AGAAAATACTG
128 CAAGAATAACAATACTTG-AAGATTGAA-TTCTCTTCACGAGAAAGTCAAGAATA-AAAATACTG
* *
51685 AAAGATTGACTTCTCTTCATGAGAAAGTCAAGAATGACAATATTGAAAGATTGACTTATCTTCAC
190 AAAGATTGACTTCTCTTCAAGAGAAAGTCAAGAATGACAATACTGAAAGATTGACTTATCTTCAC
* *
51750 AAGAAAGTCAATAATAACATTGAAAGATTGACTCCTCTTCACGAGAGAGTCAAGAATAACATTGA
255 AAGAAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGAGAGCCAAGAATAACATTGA
* *
51815 AAGAATGACTCTTCTTCACAAGGGAGTCAAGA
320 AAGAATAACTCATCTTCACAAGGGAGTCAAGA
* * * *
51847 ATAATATTGAAAGATCGACTCCTCTTCACGAG
1 ATAAAACTGAAAGATTGACTTCTCTTCACGAG
51879 GTCGTCAAGT
Statistics
Matches: 344, Mismatches: 36, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
351 26 0.08
352 2 0.01
353 7 0.02
354 309 0.90
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (351 bp):
ATAAAACTGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAAGACAATACTGAAAGATTGAAT
TCTCTTCACGAAAAAGCCAAGAAAGAAAATACTGAAAGATTGACTTCTCTTCACGAGAAAATCAA
GAATAACAATACTTGAAGATTGAATTCTCTTCACGAGAAAGTCAAGAATAAAAATACTGAAAGAT
TGACTTCTCTTCAAGAGAAAGTCAAGAATGACAATACTGAAAGATTGACTTATCTTCACAAGAAA
GTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGAGAGCCAAGAATAACATTGAAAGAAT
AACTCATCTTCACAAGGGAGTCAAGA
Found at i:51887 original size:42 final size:42
Alignment explanation
Indices: 51149--51878 Score: 638
Period size: 45 Copynumber: 16.6 Consensus size: 42
51139 AAGATAACAC
* *
51149 TGAAAGATTGACTTCTCTTCACTAGAAAGTCAAGAATGACAATAC
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAT---AATAT
* * * * *
51194 TGAGAGATTGACTTCTCTTCATGAAAAAGTCAAGAAAGAAAATAC
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAG--A-ATAATAT
* *
51239 TGAAAGATTGACTTTTCTTCACGAGAAAATCAAGAATGACAATACT
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAT---AATA-T
* * *
51285 TG-AAGATTGAATTCTCTTCGCGAGAAAGTCAAGAATAACAATAC
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAT---AATAT
* * *
51329 TGAAAGATTGACTTCTCTTCAAGAGAAAGTTAAGAATGCCAATAC
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAT---AATAT
* *
51374 TGAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAATAACAT
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAATAT
* * * *
51416 TGAAAGATTGACTCCTCTTCACGAGAGAGCCAAGAATAACAT
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAATAT
* * ** ** * *
51458 TGAAATATTAAC-TCATCTTCATAAGGGAGTCAAGAATGAAAGAAC
1 TGAAAGATTGACTTC-TCTTCACGAGAAAGTCAAGAAT--AA-TAT
*
51503 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAAGACAATAT
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAG--A-ATAATAT
* * *
51548 TGAAAGATTGAATTCTCTTCACGAGAAAGCCAAGAATGACAATAC
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAT---AATAT
* *
51593 TGAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAATAACAATAC
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAT---AATAT
* * * *
51638 TGAAAGATTAACTTCTCTTCACGAGAAATTCAAGAAAGAAAATAC
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAG--A-ATAATAT
*
51683 TGAAAGATTGACTTCTCTTCATGAGAAAGTCAAGAATGACAATAT
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAT---AATAT
* * * *
51728 TGAAAGATTGACTTATCTTCACAAGAAAGTCAATAATAACAT
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAATAT
* * *
51770 TGAAAGATTGACTCCTCTTCACGAGAGAGTCAAGAATAACAT
1 TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAATAT
* * **
51812 TGAAAGAATGAC-TCTTCTTCACAAGGGAGTCAAGAATAATAT
1 TGAAAGATTGACTTC-TCTTCACGAGAAAGTCAAGAATAATAT
* *
51854 TGAAAGATCGACTCCTCTTCACGAG
1 TGAAAGATTGACTTCTCTTCACGAG
51879 GTCGTCAAGT
Statistics
Matches: 572, Mismatches: 86, Indels: 57
0.80 0.12 0.08
Matches are distributed among these distances:
41 2 0.00
42 167 0.29
43 4 0.01
44 4 0.01
45 383 0.67
46 6 0.01
47 3 0.01
48 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (42 bp):
TGAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAATAT
Found at i:54420 original size:3 final size:3
Alignment explanation
Indices: 54400--54452 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
54390 GCTTTATTGT
54400 ATA AT- ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54445 ATA ATA AT
1 ATA ATA AT
54453 TTATTAACCT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:57258 original size:19 final size:19
Alignment explanation
Indices: 57236--57274 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
57226 TACGATATTG
*
57236 TAATAGAGTATCGATACCA
1 TAATAGAGTATCAATACCA
*
57255 TAATATAGTATCAATACCA
1 TAATAGAGTATCAATACCA
57274 T
1 T
57275 GGTAGGGGTA
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:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (19 bp):
TAATAGAGTATCAATACCA
Found at i:57793 original size:57 final size:57
Alignment explanation
Indices: 57723--58026 Score: 491
Period size: 57 Copynumber: 5.3 Consensus size: 57
57713 AATTTCCGTA
*
57723 TGCAAGAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTTTGTG
1 TGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
57780 TGCAAAAAGTTAAGAAATTCATAATTGGTTTATGAATTTTCGTATGGGCACTTTGTG
1 TGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTTTGTG
*
57837 TGTAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTTTGTG
1 TGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
57894 TGAAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
1 TGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * *
57951 TACAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGGCACTTTATG
1 TGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTTTGTG
* **
58008 TGAAAAAAACTAAGAAATT
1 TGCAAAAAGTTAAGAAATT
58027 ATATGAATTT
Statistics
Matches: 231, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 231 1.00
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (57 bp):
TGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTTTGTG
Found at i:61817 original size:43 final size:43
Alignment explanation
Indices: 61770--62026 Score: 314
Period size: 43 Copynumber: 6.1 Consensus size: 43
61760 TTTAGTGCGT
* *
61770 CGTTTTTGGAACAAACACCGCAAAAGGTCGATATCTATAGCGG
1 CGTTTTTGGAACAAACGCCGCAAAAGGTCAATATCTATAGCGG
* * *
61813 CGTTTTTAGATCAAATGCCGCAAAAGGTCAATATCTATAGCGG
1 CGTTTTTGGAACAAACGCCGCAAAAGGTCAATATCTATAGCGG
*
61856 CGTTTTTGGAACAAACGCCGCAAAAGGT-AAGA-CTTATAGCGG
1 CGTTTTTGGAACAAACGCCGCAAAAGGTCAATATC-TATAGCGG
* * * * *
61898 CATTTTTGGATACAAACGCCGCGAAA-G-AAAGATCTATAGCTG
1 CGTTTTTGGA-ACAAACGCCGCAAAAGGTCAATATCTATAGCGG
*
61940 CGTTTTTGGAACAAACGCCTCAAAA-GTC-A-ATCTATAGCGG
1 CGTTTTTGGAACAAACGCCGCAAAAGGTCAATATCTATAGCGG
* *
61980 CG-TTTTGGAACAAATGCCACAAAAGGTCAATATCTATAGCGG
1 CGTTTTTGGAACAAACGCCGCAAAAGGTCAATATCTATAGCGG
62022 CGTTT
1 CGTTT
62027 GTATCCACAA
Statistics
Matches: 186, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
39 20 0.11
40 15 0.08
41 17 0.09
42 54 0.29
43 80 0.43
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (43 bp):
CGTTTTTGGAACAAACGCCGCAAAAGGTCAATATCTATAGCGG
Found at i:62037 original size:124 final size:126
Alignment explanation
Indices: 61802--62041 Score: 303
Period size: 124 Copynumber: 1.9 Consensus size: 126
61792 AAAGGTCGAT
* *
61802 ATCTATAGCGGCGTTTTTAGATCAAATGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGAA
1 ATCTATAGCGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGAA
* *
61867 CAAACGCCGCAAAAGGTAAGACTTATAGCGGCATTTTTGGATACAAACGCCGCGAAAGAAAG
66 CAAACGCCACAAAAGGTAAGACTTATAGCGGCA-GTTTGGATACAAACGCCGCGAAAGAAAG
* * *
61929 ATCTATAGCTGCGTTTTTGGAACAAACGCCTCAAAA-GTC-A-ATCTATAGCGGCG-TTTTGGAA
1 ATCTATAGCGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGAA
* * *
61990 CAAATGCCACAAAAGGTCAATA-TCTATAGCGGC-GTTTGTATCCACAAACGCC
66 CAAACGCCACAAAAGGT-AAGACT-TATAGCGGCAGTTTGGAT--ACAAACGCC
62042 ACTAATTACC
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
122 6 0.06
123 24 0.24
124 34 0.34
125 1 0.01
126 3 0.03
127 31 0.31
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (126 bp):
ATCTATAGCGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAATATCTATAGCGGCGTTTTTGGAA
CAAACGCCACAAAAGGTAAGACTTATAGCGGCAGTTTGGATACAAACGCCGCGAAAGAAAG
Found at i:65081 original size:41 final size:41
Alignment explanation
Indices: 65032--65449 Score: 388
Period size: 41 Copynumber: 10.3 Consensus size: 41
65022 TTGTGTTTAC
* *
65032 AAACGCCACTAAAGTACAAGTCTTTAGTGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
65073 AAACGCCACTGAAGTACGAGTCTTAAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
65114 AAACGCCACTGAAGTATGACTCTATAGCGGC-ATT-TATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * *
65153 AAACGCCACTGAATTACGAGTCTTTAGCAGCGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A
* *
65195 AAACGCCACTAAAATACGAGTCATTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* *
65236 AAACGCCACTAAA-TAACTAGAT-TTTAGCAGCGTTTGT-TCAA
1 AAACGCCACTAAAGT-ACGAG-TCTTTAGCGGCGTTTGTAT-AA
* * * * * *
65277 AAATGCCACTAATGAACTCA-TTTTTAGCGGCGTTTGTACAAAA
1 AAACGCCACTAAAGTAC-GAGTCTTTAGCGGCGTTTGT--ATAA
*
65320 AAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
65361 AACCCCCACTAAATTAC-AATCTTTAGCGG-GTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
65400 AAACACCACTAAAATATGAGTATTTAGCGGCG-TT-TAAAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
65439 AAACGCCACTA
1 AAACGCCACTA
65450 TAGCACATGT
Statistics
Matches: 311, Mismatches: 51, Indels: 32
0.79 0.13 0.08
Matches are distributed among these distances:
39 67 0.22
40 30 0.10
41 142 0.46
42 39 0.13
43 33 0.11
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:65162 original size:80 final size:83
Alignment explanation
Indices: 65032--65449 Score: 251
Period size: 80 Copynumber: 5.1 Consensus size: 83
65022 TTGTGTTTAC
* * * * * *
65032 AAACGCCACTAAAGTACAAGTCTTTAGTGGCGTTTGTATAAAAACGCCACTGAAGTACGAGTCTT
1 AAACGCCACTAAAATACGACTCATTAGCGGCGATTGTATAAAAACGCCACTGAAGTACGAGTCTT
*
65097 AAGC-GACGTTTGTATA-A
66 AAGCAG-CGTTTGTAAACA
* * * *
65114 AAACGCCACTGAAGTATGACTC-TATAGCGGC-ATT-TATAAAAACGCCACTGAATTACGAGTCT
1 AAACGCCACTAAAATACGACTCAT-TAGCGGCGATTGTATAAAAACGCCACTGAAGTACGAGTCT
*
65176 TTAGCAGCGTTTGTAAACA
65 TAAGCAGCGTTTGTAAACA
* * * *
65195 AAACGCCACTAAAATACGAGTCATTAGCGGCGTTTGTATAAAAACGCCACT-AAATAACTAGAT-
1 AAACGCCACTAAAATACGACTCATTAGCGGCGATTGTATAAAAACGCCACTGAAGT-ACGAG-TC
* **
65258 TTTAGCAGCGTTTGTTCA-A
64 TTAAGCAGCGTTTGTAAACA
* * * * *
65277 AAATGCCACT--AAT--GAACTCATTTTTAGCGGCGTTTGTACAAAAAAATGCCACTAAAGTACG
1 AAACGCCACTAAAATACG-ACTCA---TTAGCGGCGATTGT--ATAAAAACGCCACTGAAGTACG
* * *
65338 AGTCTTTAGCGGCGTTTGTATA-A
60 AGTCTTAAGCAGCGTTTGTAAACA
* * * * * * * * * * * *
65361 AACCCCCACTAAATTAC-AATCTTTAGCGG-GTTTATATAAAAACACCACTAAAATATGAGTATT
1 AAACGCCACTAAAATACGACTCATTAGCGGCGATTGTATAAAAACGCCACTGAAGTACGAGTCTT
* *
65424 TAGCGGCG-TT-TAAA-A
66 AAGCAGCGTTTGTAAACA
65439 AAACGCCACTA
1 AAACGCCACTA
65450 TAGCACATGT
Statistics
Matches: 273, Mismatches: 43, Indels: 44
0.76 0.12 0.12
Matches are distributed among these distances:
78 14 0.05
79 6 0.02
80 73 0.27
81 30 0.11
82 59 0.22
83 43 0.16
84 40 0.15
85 3 0.01
86 5 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (83 bp):
AAACGCCACTAAAATACGACTCATTAGCGGCGATTGTATAAAAACGCCACTGAAGTACGAGTCTT
AAGCAGCGTTTGTAAACA
Found at i:65307 original size:163 final size:163
Alignment explanation
Indices: 65032--65448 Score: 388
Period size: 163 Copynumber: 2.6 Consensus size: 163
65022 TTGTGTTTAC
* * *
65032 AAACGCCACTAAAGTACAAGTCTTTAGTGGCGTTTGTATAAAAACGCCACTGAAGTACGAGTCTT
1 AAACGCCACTAAAATAC-AGTCTTTAGCGGCGTTTGTATAAAAACGCCACT-AAATACGAGTCTT
* * *
65097 AAGCGACGTTTGTATAAAAACGCCACTGAAGTATGACTCTATAGCGGC-ATT-T-ATAAAAACGC
64 AAGCGACGTTTGTATAAAAACGCCACTGAAGAATCACTCTATAGCGGCGATTGTAAAAAAAACGC
* *
65159 CACTGAATTACGAGTCTTTAGCAGCGTTTGTAAACA
129 CACTAAAGTACGAGTCTTTAGCAGCGTTTGTAAA-A
* *
65195 AAACGCCACTAAAATACGAGTCATTAGCGGCGTTTGTATAAAAACGCCACTAAATAACTAGAT-T
1 AAACGCCACTAAAATAC-AGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAT-ACGAG-TCT
* * * * *
65259 TTAGC-AGCGTTTGT-TCAAAAATGCCACT-AATGAACTCA-TTTTTAGCGGCGTTTGTACAAAA
63 TAAGCGA-CGTTTGTAT-AAAAACGCCACTGAA-GAA-TCACTCTATAGCGGCGATTGTA-AAAA
* * *
65320 AAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
123 AAACGCCACTAAAGTACGAGTCTTTAGCAGCGTTTGTAAAA
* * * * * * * * *
65361 AACCCCCACTAAATTACAATCTTTAGCGG-GTTTATATAAAAACACCACTAAAATATGAGTATTT
1 AAACGCCACTAAAATACAGTCTTTAGCGGCGTTTGTATAAAAACGCCACT-AAATACGAGTCTTA
* *
65425 AGCGGCG-TT-TAAAAAAACGCCACT
65 AGCGACGTTTGTATAAAAACGCCACT
65449 ATAGCACATG
Statistics
Matches: 209, Mismatches: 31, Indels: 29
0.78 0.12 0.11
Matches are distributed among these distances:
162 19 0.09
163 88 0.42
164 34 0.16
165 15 0.07
166 15 0.07
167 38 0.18
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (163 bp):
AAACGCCACTAAAATACAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATACGAGTCTTAA
GCGACGTTTGTATAAAAACGCCACTGAAGAATCACTCTATAGCGGCGATTGTAAAAAAAACGCCA
CTAAAGTACGAGTCTTTAGCAGCGTTTGTAAAA
Done.