Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000234.1 Hibiscus syriacus cultivar Beakdansim tig00000404_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: 64718
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5818 original size:65 final size:63
Alignment explanation
Indices: 5749--5928 Score: 213
Period size: 65 Copynumber: 2.8 Consensus size: 63
5739 GAATAAATTG
* * *
5749 AACATCGAATACATTTCATGCATCGATGCACATACTATGCATCGATGCACTC-AGAGT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACAT-CTATGCATCGATGCACTCTAG-CTATTT-TG
5812 AA
63 -A
* *
5814 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTAGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CATCTATGCATCGATGCACTCTAGCTATTTTGA
* *
5878 AACATCGAATGCACTTGATGCATCGATTCAC-TCTTAGTGCATCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACATC-TA-TGCATCGATGCACT
5929 AAGGTTCCAA
Statistics
Matches: 101, Mismatches: 9, Indels: 11
0.83 0.07 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 43 0.43
65 48 0.48
66 7 0.07
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACATCTATGCATCGATGCACTCTAGCTATTTTGA
Found at i:11788 original size:23 final size:23
Alignment explanation
Indices: 11719--11799 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
11709 ACACCTAACA
*
11719 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* * *
11741 GTGCATTGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
11762 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
11785 GTGCATCGATGCACA
1 GTGCATCGATGCACA
11800 AGGCCATGCA
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.02
21 14 0.31
22 9 0.20
23 21 0.47
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:11811 original size:20 final size:20
Alignment explanation
Indices: 11786--11837 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
11776 GCCTTGAATG
*
11786 TGCATCGATGCACAAGGCCA
1 TGCATCGATGCAAAAGGCCA
11806 TGCATCGATGCAAAAGGCCA
1 TGCATCGATGCAAAAGGCCA
11826 TGCATCGATGCA
1 TGCATCGATGCA
11838 TCCGTCGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (20 bp):
TGCATCGATGCAAAAGGCCA
Found at i:11815 original size:43 final size:42
Alignment explanation
Indices: 11718--11817 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 42
11708 TACACCTAAC
* * * *
11718 AGTGCATCGATGCATCCTTGAATGTGCATTGATACACCATGA
1 AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
* * *
11760 AGGTGCACCGATGCACGCCTTGAATGTGCATCGATGCACAAGGCC
1 A-GTGCATCGATGCA-GCCTTGAATGTGCATCGATACACAAGG-A
11805 A-TGCATCGATGCA
1 AGTGCATCGATGCA
11818 AAAGGCCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
42 1 0.02
43 23 0.49
44 22 0.47
45 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (42 bp):
AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
Found at i:13408 original size:21 final size:21
Alignment explanation
Indices: 13368--13409 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13358 TCCGGGAGCG
*
13368 AGCTCTTCACGAGCTGCTCCT
1 AGCTCTTCACGAGCTCCTCCT
* *
13389 AGCTCTTCTCGTGCTCCTCCT
1 AGCTCTTCACGAGCTCCTCCT
13410 CCGGCACCGG
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:0.10, C:0.40, G:0.17, T:0.33
Consensus pattern (21 bp):
AGCTCTTCACGAGCTCCTCCT
Found at i:14585 original size:56 final size:56
Alignment explanation
Indices: 14524--14630 Score: 148
Period size: 56 Copynumber: 1.9 Consensus size: 56
14514 GAATGCATTT
14524 CATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCA-TCGATGCACCAGC
1 CATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCACTCGATGCACCAGC
* *
14580 CATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCA
1 CATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTCGATGCA
14631 TCGATGAACT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
55 15 0.33
56 28 0.61
57 3 0.07
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (56 bp):
CATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTCGATGCACCAGC
Found at i:17123 original size:18 final size:19
Alignment explanation
Indices: 17100--17147 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
17090 TACAATTTTG
* *
17100 GTATCGATACCCATGG-GA
1 GTATCGATACCAAGGGAGA
17118 GTATCGATACCAAGGGTAGA
1 GTATCGATACCAAGGG-AGA
17138 GTATCGATAC
1 GTATCGATAC
17148 TTCCTATAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 14 0.54
20 12 0.46
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (19 bp):
GTATCGATACCAAGGGAGA
Found at i:17494 original size:15 final size:15
Alignment explanation
Indices: 17474--17505 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
17464 GGTGAAATCT
17474 CTGGATATTATTCGA
1 CTGGATATTATTCGA
17489 CTGGATATTATTCGA
1 CTGGATATTATTCGA
17504 CT
1 CT
17506 TGGTAAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (15 bp):
CTGGATATTATTCGA
Found at i:18633 original size:32 final size:32
Alignment explanation
Indices: 18597--18729 Score: 131
Period size: 32 Copynumber: 3.9 Consensus size: 32
18587 GTTTAATTAC
*
18597 TGACATGGCACATGTCACGTCATCATTATGGA
1 TGACATGACACATGTCACGTCATCATTATGGA
* *
18629 TGACATGATACATGGCACGTCATCACTATGAGTGGCCA
1 TGACATGACACATGTCACGTCATCA-T-T-A-TGG--A
* *
18667 CTGACATGGCACATGTCATGTCATCATTATGGA
1 -TGACATGACACATGTCACGTCATCATTATGGA
* * *
18700 TGACATGATACATGACACGTCATCACTATG
1 TGACATGACACATGTCACGTCATCATTATG
18730 AGTGGCCTTA
Statistics
Matches: 82, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
32 47 0.57
33 2 0.02
34 1 0.01
35 4 0.05
36 4 0.05
37 1 0.01
38 2 0.02
39 21 0.26
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (32 bp):
TGACATGACACATGTCACGTCATCATTATGGA
Found at i:18642 original size:39 final size:38
Alignment explanation
Indices: 18599--18713 Score: 113
Period size: 39 Copynumber: 3.1 Consensus size: 38
18589 TTAATTACTG
18599 ACATGGCACATGTCACGTCATCATTATGGATGACATGAT
1 ACATGGCACATGTCA-GTCATCATTATGGATGACATGAT
*
18638 ACATGGCAC--GTCA-TCA-C--TAT-GAGTGGCCACTG--
1 ACATGGCACATGTCAGTCATCATTATGGA-T-GACA-TGAT
18670 ACATGGCACATGTCATGTCATCATTATGGATGACATGAT
1 ACATGGCACATGTCA-GTCATCATTATGGATGACATGAT
18709 ACATG
1 ACATG
18714 ACACGTCATC
Statistics
Matches: 61, Mismatches: 2, Indels: 26
0.69 0.02 0.29
Matches are distributed among these distances:
31 2 0.03
32 13 0.21
33 3 0.05
34 7 0.11
35 3 0.05
36 3 0.05
37 7 0.11
38 3 0.05
39 18 0.30
40 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (38 bp):
ACATGGCACATGTCAGTCATCATTATGGATGACATGAT
Found at i:18711 original size:71 final size:71
Alignment explanation
Indices: 18595--18736 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
18585 GTGTTTAATT
*
18595 ACTGACATGGCACATGTCACGTCATCATTATGGATGACATGATACATGGCACGTCATCACTATGA
1 ACTGACATGGCACATGTCACGTCATCATTATGGATGACATGATACATGACACGTCATCACTATGA
18660 GTGGCC
66 GTGGCC
*
18666 ACTGACATGGCACATGTCATGTCATCATTATGGATGACATGATACATGACACGTCATCACTATGA
1 ACTGACATGGCACATGTCACGTCATCATTATGGATGACATGATACATGACACGTCATCACTATGA
18731 GTGGCC
66 GTGGCC
18737 TTACGCATGC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (71 bp):
ACTGACATGGCACATGTCACGTCATCATTATGGATGACATGATACATGACACGTCATCACTATGA
GTGGCC
Found at i:18872 original size:32 final size:32
Alignment explanation
Indices: 18797--18903 Score: 88
Period size: 32 Copynumber: 3.3 Consensus size: 32
18787 ATTGTAGGTA
* * * *
18797 ACATGACACATCTCATAGCATCACTTTGGATG
1 ACATGGCACATGTCACATCATCACTTTGGATG
** ** * * * *
18829 ATGTGATACATGTTACGTCATTATTTTGGATG
1 ACATGGCACATGTCACATCATCACTTTGGATG
*
18861 ACATGGCACATGTCACATCATCACTTTGGGTG
1 ACATGGCACATGTCACATCATCACTTTGGATG
*
18893 ATATGGCACAT
1 ACATGGCACAT
18904 ATCATGTCAG
Statistics
Matches: 55, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (32 bp):
ACATGGCACATGTCACATCATCACTTTGGATG
Found at i:21352 original size:17 final size:18
Alignment explanation
Indices: 21317--21354 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
21307 CTTTTTGCAA
* *
21317 TTTTATAAAATTTTAAAT
1 TTTTAAAAAATTATAAAT
21335 TTTTAAAAAATTAT-AAT
1 TTTTAAAAAATTATAAAT
21352 TTT
1 TTT
21355 AAGTTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTAAAAAATTATAAAT
Found at i:24760 original size:2 final size:2
Alignment explanation
Indices: 24753--24780 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24743 TAAAATTTTA
24753 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
24781 CAATATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25101 original size:24 final size:24
Alignment explanation
Indices: 25074--25124 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
25064 ACATTTTACG
25074 ATTTACAAGAAACCTACATTTAAA
1 ATTTACAAGAAACCTACATTTAAA
25098 ATTTACAAGAAACCTACATTTAAA
1 ATTTACAAGAAACCTACATTTAAA
25122 ATT
1 ATT
25125 GTTCTGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (24 bp):
ATTTACAAGAAACCTACATTTAAA
Found at i:25494 original size:21 final size:22
Alignment explanation
Indices: 25470--25526 Score: 80
Period size: 23 Copynumber: 2.6 Consensus size: 22
25460 CACCAAAGTG
*
25470 CCACATA-TTTGTCCCGAATGA
1 CCACATAGTTTGTCCCGAAGGA
*
25491 CCACATAGTTTTGTCTCGAAGGA
1 CCACATAG-TTTGTCCCGAAGGA
25514 CCACATAGTTTGT
1 CCACATAGTTTGT
25527 TTCCCGATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 7 0.22
22 5 0.16
23 20 0.62
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (22 bp):
CCACATAGTTTGTCCCGAAGGA
Found at i:25510 original size:23 final size:23
Alignment explanation
Indices: 25470--25533 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
25460 CACCAAAGTG
*
25470 CCACATA--TTTGTCCCGAATGA
1 CCACATAGTTTTGTCCCGAAGGA
*
25491 CCACATAGTTTTGTCTCGAAGGA
1 CCACATAGTTTTGTCCCGAAGGA
*
25514 CCACATAGTTTGTTTCCCGA
1 CCACATAGTTT-TGTCCCGA
25534 TGAACCACGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 7 0.19
23 23 0.64
24 6 0.17
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (23 bp):
CCACATAGTTTTGTCCCGAAGGA
Found at i:32299 original size:23 final size:23
Alignment explanation
Indices: 32273--32317 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
32263 GTGCCATATA
*
32273 TTTGTCCCAAATGACCACATAGT
1 TTTGTCCCAAAGGACCACATAGT
* *
32296 TTTGTCTCGAAGGACCACATAG
1 TTTGTCCCAAAGGACCACATAG
32318 AACCCTCGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (23 bp):
TTTGTCCCAAAGGACCACATAGT
Found at i:33130 original size:11 final size:11
Alignment explanation
Indices: 33114--33150 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
33104 ATTTTTATTT
33114 CAAAATTTAAC
1 CAAAATTTAAC
33125 CAAAATTTAAC
1 CAAAATTTAAC
* *
33136 CAAAACTTACC
1 CAAAATTTAAC
33147 CAAA
1 CAAA
33151 TCTCCTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (11 bp):
CAAAATTTAAC
Found at i:34847 original size:21 final size:21
Alignment explanation
Indices: 34791--34858 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
34781 ATTCTGACTA
* *
34791 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTTCCTAAT
*
34812 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
*
34833 TCGCATTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCCTAAT
34854 TCGCA
1 TCGCA
34859 ACGCGAATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:34864 original size:21 final size:21
Alignment explanation
Indices: 34819--34886 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
34809 AATTCGCGTT
* **
34819 GCGATTTTCCTAATTCGCATT
1 GCGATTTTCATAATTCGCAAC
34840 GCGATTTTCATAATTCGCAAC
1 GCGATTTTCATAATTCGCAAC
* * * *
34861 GCGA-ATACGTAAATCGCAAC
1 GCGATTTTCATAATTCGCAAC
34881 GCGATT
1 GCGATT
34887 AAGTAAATCG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (21 bp):
GCGATTTTCATAATTCGCAAC
Found at i:34941 original size:20 final size:20
Alignment explanation
Indices: 34854--34947 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
34844 TTTTCATAAT
*
34854 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
34874 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
*
34894 TCGCAATGCGAATTA-GGAAA
1 TCGCAATGCGAA-TACGTAAA
34914 TTCGCAATGCGAATACGTAAA
1 -TCGCAATGCGAATACGTAAA
*
34935 TCGCAATGTGAAT
1 TCGCAATGCGAAT
34948 CTGACTATCG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:35551 original size:19 final size:19
Alignment explanation
Indices: 35487--35574 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
35477 TAGTTTCGAG
35487 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
**
35507 AATGACTATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
*
35523 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
35540 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
*
35559 AATGAAAATCACAACG
1 AATGAAAATCGCAACG
35575 AGAGAATGGC
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
14 9 0.16
15 1 0.02
16 2 0.04
17 1 0.02
18 2 0.04
19 30 0.53
20 12 0.21
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:35574 original size:52 final size:53
Alignment explanation
Indices: 35487--35604 Score: 175
Period size: 52 Copynumber: 2.2 Consensus size: 53
35477 TAGTTTCGAG
** *
35487 AATGAAAATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGGAAATGAAAATCACAACGAGAGAATCGCAACGCGA
*
35540 AATGAAAATCGCAACGC-GAAATGAAAATCACAACGAGAGAATGGCAACGCGA
1 AATGAAAATCGCAACGCGGAAATGAAAATCACAACGAGAGAATCGCAACGCGA
**
35592 AACCAAAATCGCA
1 AATGAAAATCGCA
35605 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 42 0.71
53 17 0.29
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (53 bp):
AATGAAAATCGCAACGCGGAAATGAAAATCACAACGAGAGAATCGCAACGCGA
Found at i:35622 original size:19 final size:19
Alignment explanation
Indices: 35600--35745 Score: 141
Period size: 19 Copynumber: 8.1 Consensus size: 19
35590 GAAACCAAAA
*
35600 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
35619 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
35633 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
35652 TCACGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
35666 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
35685 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
35704 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
35724 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
35744 TC
1 TC
35746 AACCAAAAGA
Statistics
Matches: 105, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
14 20 0.19
16 6 0.06
17 6 0.06
19 39 0.37
20 33 0.31
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:35641 original size:14 final size:14
Alignment explanation
Indices: 35622--35678 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35612 TTTCATTTCG
35622 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
35636 CGTTGCGATTTTCATTTCA
1 CGTTGCGA--TTC---TCT
35655 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
35669 CGTTGCGATT
1 CGTTGCGATT
35679 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:35647 original size:33 final size:33
Alignment explanation
Indices: 35605--35737 Score: 176
Period size: 33 Copynumber: 3.8 Consensus size: 33
35595 CAAAATCGCA
35605 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
35638 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
35671 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCGCGTTGCGAT--TC---T-CTCG
*
35710 TTGCGATTTTCATTCTCTCGTTGCGATT
1 TTGCGATTTTCATT-TCGCGTTGCGATT
35738 TTCATTTCAA
Statistics
Matches: 89, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
33 57 0.64
35 2 0.02
38 2 0.02
39 17 0.19
40 11 0.12
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:35711 original size:20 final size:19
Alignment explanation
Indices: 35669--35736 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
35659 GCGATTCTCT
**
35669 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
35688 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
** *
35708 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATAGTCATT-TCG
35728 CGTTGCGAT
1 CGTTGCGAT
35737 TTTCATTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 15 0.36
20 26 0.62
21 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:37569 original size:94 final size:93
Alignment explanation
Indices: 37379--37754 Score: 589
Period size: 94 Copynumber: 4.1 Consensus size: 93
37369 TAGATTGCTT
* * *
37379 AGTAAATTTATTCGGTTACTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
37440 ATTTGTCTTTTGTTTTGTCTTTTGATTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
37469 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
37534 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
37563 AGTAAATTTGTTCGGTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
37628 ATCTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
37657 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
37722 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
37750 AGTAA
1 AGTAA
37755 TGCAATCCAT
Statistics
Matches: 268, Mismatches: 13, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
90 34 0.13
92 3 0.01
93 27 0.10
94 204 0.76
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:37617 original size:17 final size:17
Alignment explanation
Indices: 37587--37619 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
37577 GTTGCTGCCA
37587 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
37604 ATTCT-TTAACACTGTG
1 ATTCTGTTAA-ACTGTG
37620 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:37868 original size:20 final size:20
Alignment explanation
Indices: 37843--37924 Score: 123
Period size: 20 Copynumber: 4.2 Consensus size: 20
37833 TTTTGGTTGA
*
37843 AATGAAAATCGCAATGAGAG
1 AATGAAAATCGCAACGAGAG
37863 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
37883 AATGAAAATCGCAAC-ACGA-
1 AATGAAAATCGCAACGA-GAG
*
37902 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
37922 AAT
1 AAT
37925 TGCAACGCGA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.30
20 39 0.70
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:37918 original size:39 final size:40
Alignment explanation
Indices: 37843--37924 Score: 123
Period size: 39 Copynumber: 2.1 Consensus size: 40
37833 TTTTGGTTGA
* *
37843 AATGAAAATCGCAATGAGAGAATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAATCAGAGAACGAAAATCGCAACGAGAG
37883 AATGAAAATCGCAA-CACGA-AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAATCA-GAGAACGAAAATCGCAACGAGAG
37922 AAT
1 AAT
37925 TGCAACGCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
39 23 0.59
40 16 0.41
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (40 bp):
AATGAAAATCGCAATCAGAGAACGAAAATCGCAACGAGAG
Found at i:37936 original size:33 final size:33
Alignment explanation
Indices: 37866--37984 Score: 112
Period size: 33 Copynumber: 3.4 Consensus size: 33
37856 ATGAGAGAAT
*
37866 GAAAATCGCAACGAGAGAATGAAAATCGCAACACGAAAC
1 GAAAATCGCAACGAGAGAAT-----T-GCAACGCGAAAC
*
37905 GAAAATCGCAACGAGAGAATTGCAACGCGAAAT
1 GAAAATCGCAACGAGAGAATTGCAACGCGAAAC
* * *
37938 GAAAATCGCAACGACAAAATCGCAACGCGAAACC
1 GAAAATCGCAACGAGAGAATTGCAACGCGAAA-C
* *
37972 AAAAATTGCAACG
1 GAAAATCGCAACG
37985 CGAAACTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
33 39 0.55
34 12 0.17
39 20 0.28
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.09
Consensus pattern (33 bp):
GAAAATCGCAACGAGAGAATTGCAACGCGAAAC
Found at i:37976 original size:20 final size:20
Alignment explanation
Indices: 37953--37990 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
37943 TCGCAACGAC
37953 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
*
37973 AAAATTGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
37991 TATAATCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:38056 original size:33 final size:33
Alignment explanation
Indices: 37999--38093 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
37989 ACTATAATCG
** * *
37999 CGTTGCGATTTTTGGTTTCGCGTTGCGATTTTGT
1 CGTTGCGA-TTTTCATTTCGCGTTGCGATTCTCT
*
38033 TGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
38066 CGTTACGATTTTCTTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
38094 AGTCATTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 46 0.87
34 7 0.13
ACGTcount: A:0.08, C:0.19, G:0.24, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:38058 original size:19 final size:18
Alignment explanation
Indices: 37996--38093 Score: 68
Period size: 19 Copynumber: 5.7 Consensus size: 18
37986 GAAACTATAA
*
37996 TCGCGTTGCGATTTTTGGTT
1 TCGCGTTGCGA-TTTT-CTT
*
38016 TCGCGTTGCGATTTT-GT
1 TCGCGTTGCGATTTTCTT
38033 T---GTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
38049 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCTT
* *
38063 TCTCGTTACGATTTTCTTT
1 TCGCGTTGCGATTTTC-TT
38082 TCGCGTTGCGAT
1 TCGCGTTGCGAT
38094 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 21
0.70 0.07 0.24
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 5 0.08
19 21 0.34
20 11 0.18
ACGTcount: A:0.08, C:0.19, G:0.24, T:0.48
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:39985 original size:13 final size:13
Alignment explanation
Indices: 39943--39985 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
39933 TTGCTTATTT
39943 TTGA-TTGTTTAA
1 TTGATTTGTTTAA
**
39955 TTGATTTGTAAAA
1 TTGATTTGTTTAA
*
39968 GTGATTTGTTTAA
1 TTGATTTGTTTAA
39981 TTGAT
1 TTGAT
39986 GGAACGTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (13 bp):
TTGATTTGTTTAA
Found at i:40523 original size:65 final size:65
Alignment explanation
Indices: 40419--40549 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
40409 ATGATTTTGA
40419 TGGCATTGGTGATTCATATGTCAACCTTGTATGGCCACTTTCCTTGCACCGACTACATGTCGATC
1 TGGCATTGGTGATTCATATGTCAACCTTGTATGGCCACTTTCCTTGCACCGACTACATGTCGATC
40484 TGGCATTGGTGATTCATATGTCAACCTTGTATGGCCACTTTCCTTGCACCGACTACATGTCGATC
1 TGGCATTGGTGATTCATATGTCAACCTTGTATGGCCACTTTCCTTGCACCGACTACATGTCGATC
40549 T
1 T
40550 CTTCTTCTCT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (65 bp):
TGGCATTGGTGATTCATATGTCAACCTTGTATGGCCACTTTCCTTGCACCGACTACATGTCGATC
Found at i:42668 original size:24 final size:24
Alignment explanation
Indices: 42634--42687 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
42624 AAAAAAAATC
42634 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
42658 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
42682 ATCAAA
1 ATCAAA
42688 TTCGAATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:43569 original size:61 final size:63
Alignment explanation
Indices: 43504--43693 Score: 221
Period size: 61 Copynumber: 3.1 Consensus size: 63
43494 AGAATCTCGT
* * *
43504 TGCGATTTA-TTAAATCGCAATGCG-ATTACGTAAATCG-AAGTGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA-TGCGAATTAGGAAAATCGCAA
* * *
43565 TGCGA-TTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCG-GTTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATTAGGAAAATCGCAA
* * * * * *
43626 TGCG-GTTACGAAAATCGCAACGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATTAGGAAAATCGCAA
43688 TGCGAT
1 TGCGAT
43694 AGTCAGAATC
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
60 3 0.03
61 73 0.67
62 31 0.28
63 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (63 bp):
TGCGATTTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATTAGGAAAATCGCAA
Found at i:43664 original size:21 final size:21
Alignment explanation
Indices: 43515--43692 Score: 195
Period size: 21 Copynumber: 8.7 Consensus size: 21
43505 GCGATTTATT
*
43515 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTACGA
*
43535 AAATCG-AAGTGCGAATTAGGA
1 AAATCGCAA-TGCGAATTACGA
*
43556 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTACGA
*
43576 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTACGA
* *
43597 AAATCGCAATGCG-GTTACGT
1 AAATCGCAATGCGAATTACGA
*
43617 AAATCGCAATGCG-GTTACGA
1 AAATCGCAATGCGAATTACGA
* *
43637 AAATCGCAACGCGAATTAGGA
1 AAATCGCAATGCGAATTACGA
* ** *
43658 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTACGA
43679 AAATCGCAATGCGA
1 AAATCGCAATGCGA
43693 TAGTCAGAAT
Statistics
Matches: 137, Mismatches: 16, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
19 2 0.01
20 63 0.46
21 70 0.51
22 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (21 bp):
AAATCGCAATGCGAATTACGA
Found at i:43705 original size:41 final size:41
Alignment explanation
Indices: 43515--43693 Score: 245
Period size: 41 Copynumber: 4.4 Consensus size: 41
43505 GCGATTTATT
43515 AAATCGCAATGCGATTACGTAAATCG-AAGTGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAA-TGCGAATTAGGA
43556 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
* * *
43597 AAATCGCAATGCGGTTACGTAAATCGCAATGCG-GTTACGA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
* * * * * *
43637 AAATCGCAACGCGAATTAGGAAAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCG-ATTACGTAAATCGCAATGCGAATTAGGA
43679 AAATCGCAATGCGAT
1 AAATCGCAATGCGAT
43694 AGTCAGAATC
Statistics
Matches: 122, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
40 17 0.14
41 88 0.72
42 17 0.14
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (41 bp):
AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
Found at i:43713 original size:41 final size:41
Alignment explanation
Indices: 43515--43714 Score: 210
Period size: 41 Copynumber: 4.9 Consensus size: 41
43505 GCGATTTATT
*
43515 AAATCGCAATGCGATTACGTAAATCG-AAGTGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCGA-TGCGAATTAGGA
*
43556 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCGATGCGAATTAGGA
* * * *
43597 AAATCGCAATGCGGTTACGTAAATCGCAATGCG-GTTACGA
1 AAATCGCAATGCGATTACGTAAATCGCGATGCGAATTAGGA
* * * * * * *
43637 AAATCGCAACGCGAATTAGGAAAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCG-ATTACGTAAATCGCGATGCGAATTAGGA
*
43679 AAATCGCAATGCGA-TA-GTCAGAATCGCGTTGCGAAT
1 AAATCGCAATGCGATTACGT-A-AATCGCGATGCGAAT
43715 CTGGAAACTG
Statistics
Matches: 137, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 20 0.15
41 99 0.72
42 17 0.12
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.21
Consensus pattern (41 bp):
AAATCGCAATGCGATTACGTAAATCGCGATGCGAATTAGGA
Found at i:49080 original size:27 final size:27
Alignment explanation
Indices: 49050--49111 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
49040 ATATATGGAG
49050 GTGGTGGTATAATCTAATTTTGGACAT
1 GTGGTGGTATAATCTAATTTTGGACAT
49077 GTGGTGGTATAATCTAATTTTGGACAT
1 GTGGTGGTATAATCTAATTTTGGACAT
49104 GTGGTGGT
1 GTGGTGGT
49112 GGTGGTAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.23, C:0.06, G:0.31, T:0.40
Consensus pattern (27 bp):
GTGGTGGTATAATCTAATTTTGGACAT
Found at i:56791 original size:28 final size:28
Alignment explanation
Indices: 56760--56855 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 28
56750 CATTTGTAAA
*
56760 AGCACAGAGGTGCTTGATTTTAGATTGT
1 AGCACAGAGGTGCTAGATTTTAGATTGT
56788 AGCACAGAGGTGCTCA-ATCCTTCTA-A---T
1 AGCACAGAGGTGCT-AGAT--TT-TAGATTGT
* *
56815 -GCACAGAGGTGCCAGATTTTAGATTGA
1 AGCACAGAGGTGCTAGATTTTAGATTGT
56842 AGCACAGAGGTGCT
1 AGCACAGAGGTGCT
56856 CAGTCATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
23 2 0.04
24 3 0.06
25 1 0.02
26 14 0.26
27 1 0.02
28 28 0.52
30 3 0.06
31 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (28 bp):
AGCACAGAGGTGCTAGATTTTAGATTGT
Found at i:56833 original size:54 final size:55
Alignment explanation
Indices: 56761--57081 Score: 204
Period size: 54 Copynumber: 5.8 Consensus size: 55
56751 ATTTGTAAAA
** * *
56761 GCACAGAGGTGCTTGATTTTAGATTGTAGCACAGAGGTGCTCAATCCTTCT-AAT
1 GCACAGAGGTGCCAGATTTTAGATTGAAGCACAGAGGTGCTCAATCATTCTGAAT
* * **
56815 GCACAGAGGTGCCAGATTTTAGATTGAAGCACAGAGGTGCTCAGTCATTTTGGCT
1 GCACAGAGGTGCCAGATTTTAGATTGAAGCACAGAGGTGCTCAATCATTCTGAAT
* ** * * * *
56870 GCACAGAGGTGTCAG-TCCTCGATTGAAGCACAGAGGTGCTCAATC-GTCTTAGCT
1 GCACAGAGGTGCCAGATTTTAGATTGAAGCACAGAGGTGCTCAATCATTCTGA-AT
* * * *** ** * * *
56924 ACACAGAGGTGTCAG-CTCCCGGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACT
1 GCACAGAGGTGCCAGATTTTAGATTGAAGCACAGAGGTGCTCAATCA---TTCTGAA-T
* * * * **
56982 GCACAGAGGTGTCAG-TTCTCGATTGAAGCACAGAGGTGCTCAATCACTTTTGGCT
1 GCACAGAGGTGCCAGATTTTAGATTGAAGCACAGAGGTGCTCAATCA-TTCTGAAT
* ** * * *
57037 ACACAGAGGTATCAG-CTCTCGATTGAAGCACAGAGGTGCTCAATC
1 GCACAGAGGTGCCAGATTTTAGATTGAAGCACAGAGGTGCTCAATC
57082 GTTAATTCTA
Statistics
Matches: 220, Mismatches: 40, Indels: 13
0.81 0.15 0.05
Matches are distributed among these distances:
53 2 0.01
54 111 0.50
55 58 0.26
56 4 0.02
58 45 0.20
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (55 bp):
GCACAGAGGTGCCAGATTTTAGATTGAAGCACAGAGGTGCTCAATCATTCTGAAT
Found at i:56900 original size:27 final size:28
Alignment explanation
Indices: 56782--57078 Score: 119
Period size: 27 Copynumber: 10.8 Consensus size: 28
56772 CTTGATTTTA
* *
56782 GATTGTAGCACAGAGGTGCTCAATCCT-
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
** *
56809 --TCT-AATGCACAGAGGTGC-CAGATTTTA
1 GAT-TGAA-GCACAGAGGTGCTCAG-TCCTC
*
56836 GATTGAAGCACAGAGGTGCTCAGTCAT-
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
* **
56863 -TTTGGCTGCACAGAGGTG-TCAGTCCTC
1 GATT-GAAGCACAGAGGTGCTCAGTCCTC
* *
56890 GATTGAAGCACAGAGGTGCTCAATCGTC
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
*
56918 --TTAGCTA-CACAGAGGTG-TCAGCTCC-C
1 GATT-G-AAGCACAGAGGTGCTCAG-TCCTC
** * *
56944 GGCTGAAGCACAGAGGTGCTCAGTCATTT
1 GATTGAAGCACAGAGGTGCTCAGTC-CTC
** * *
56973 TTTTTAACTGCACAGAGGTG-TCAGTTCTC
1 GATTGAA--GCACAGAGGTGCTCAGTCCTC
*
57002 GATTGAAGCACAGAGGTGCTCAATCACT-
1 GATTGAAGCACAGAGGTGCTCAGTC-CTC
* * *
57030 -TTTGGCTA-CACAGAGGT-ATCAG-CTCTC
1 GATT-G-AAGCACAGAGGTGCTCAGTC-CTC
57057 GATTGAAGCACAGAGGTGCTCA
1 GATTGAAGCACAGAGGTGCTCA
57079 ATCGTTAATT
Statistics
Matches: 197, Mismatches: 42, Indels: 61
0.66 0.14 0.20
Matches are distributed among these distances:
25 4 0.02
26 35 0.18
27 76 0.39
28 49 0.25
29 17 0.09
30 5 0.03
31 11 0.06
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (28 bp):
GATTGAAGCACAGAGGTGCTCAGTCCTC
Found at i:62352 original size:31 final size:31
Alignment explanation
Indices: 62274--62354 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
62264 ATTTAAGTCG
*
62274 AAAC-TAAAGTTCAATGATAAAATTAATTCA
1 AAACTTAAAGTTCAATGATAAAATCAATTCA
* * * * *
62304 AATCTCAAATTTTAATGATAAAATCAATTTA
1 AAACTTAAAGTTCAATGATAAAATCAATTCA
62335 AAACTTTAAA-TTCAATGATA
1 AAAC-TTAAAGTTCAATGATA
62355 TTTAATATTA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
30 3 0.08
31 33 0.82
32 4 0.10
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.35
Consensus pattern (31 bp):
AAACTTAAAGTTCAATGATAAAATCAATTCA
Done.