Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003548.1 Hibiscus syriacus cultivar Beakdansim tig00007480_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: 58969
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4629 original size:11 final size:11
Alignment explanation
Indices: 4615--4643 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4605 TTTTTGATTA
4615 TATATTATATT
1 TATATTATATT
4626 TATATTATATT
1 TATATTATATT
4637 TA-ATTAT
1 TATATTAT
4644 TTAAACAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTATATT
Found at i:6030 original size:2 final size:2
Alignment explanation
Indices: 6023--6060 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6013 AATGACGATA
6023 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
6061 TTGTATGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8058 original size:16 final size:17
Alignment explanation
Indices: 8031--8063 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
8021 ATCCATGCAC
8031 ATCTGAAATTTTAGGAT
1 ATCTGAAATTTTAGGAT
*
8048 ATCTG-AATTTTCGGAT
1 ATCTGAAATTTTAGGAT
8064 CAAATATACG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.42
Consensus pattern (17 bp):
ATCTGAAATTTTAGGAT
Found at i:8157 original size:2 final size:2
Alignment explanation
Indices: 8150--8190 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
8140 TCTACTAAAT
8150 TA TA 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 TA TA T
8191 GTATGTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18293 original size:2 final size:2
Alignment explanation
Indices: 18288--18312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18278 ACTCAAAAAA
18288 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
18313 AACATACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19410 original size:18 final size:19
Alignment explanation
Indices: 19375--19411 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
19365 CACGGAATGT
19375 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
19395 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
19412 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:20218 original size:15 final size:15
Alignment explanation
Indices: 20200--20230 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20190 TATTCCACTT
20200 ATAATTATTTTTTAA
1 ATAATTATTTTTTAA
*
20215 ATAATTTTTTTTTAA
1 ATAATTATTTTTTAA
20230 A
1 A
20231 AAATACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATAATTATTTTTTAA
Found at i:20755 original size:2 final size:2
Alignment explanation
Indices: 20743--20807 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
20733 ATTGCTGTAC
20743 AT AT A- 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
20784 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
20808 CATGGATTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23322 original size:21 final size:20
Alignment explanation
Indices: 23294--23332 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
23284 TAATCATCAT
23294 TTTATAATAATTTGATAAAA
1 TTTATAATAATTTGATAAAA
* *
23314 TTTATTAATTATTTTATAA
1 TTTA-TAATAATTTGATAA
23333 CAGGTCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTATAATAATTTGATAAAA
Found at i:23329 original size:32 final size:31
Alignment explanation
Indices: 23292--23364 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
23282 TGTAATCATC
* * *
23292 ATTTTATAATAATTTGATAAAATTTATTAATT
1 ATTTTATAATAAGTCGAT-AAATTTAATAATT
* *
23324 ATTTTATAACAGGTCGATAAATTTAATAATT
1 ATTTTATAATAAGTCGATAAATTTAATAATT
*
23355 GTTTTATAAT
1 ATTTTATAAT
23365 TTTAAAAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (31 bp):
ATTTTATAATAAGTCGATAAATTTAATAATT
Found at i:33309 original size:14 final size:14
Alignment explanation
Indices: 33290--33320 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
33280 TGATTTACTA
33290 AATATTTTTTTATT
1 AATATTTTTTTATT
33304 AATATTTTTTTATT
1 AATATTTTTTTATT
33318 AAT
1 AAT
33321 TAAACATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
AATATTTTTTTATT
Found at i:39693 original size:23 final size:23
Alignment explanation
Indices: 39667--39711 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
39657 GTTATTTAAA
39667 CGGGTAATGGGTCGGTATTGGGT
1 CGGGTAATGGGTCGGTATTGGGT
*
39690 CGGGTATTGGGTCGGTATTGGG
1 CGGGTAATGGGTCGGTATTGGG
39712 CCAGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.09, G:0.49, T:0.31
Consensus pattern (23 bp):
CGGGTAATGGGTCGGTATTGGGT
Found at i:39697 original size:12 final size:11
Alignment explanation
Indices: 39669--39711 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
39659 TATTTAAACG
*
39669 GGTAATGGGTC
1 GGTATTGGGTC
39680 GGTATTGGGTC
1 GGTATTGGGTC
39691 GGGTATTGGGTC
1 -GGTATTGGGTC
39703 GGTATTGGG
1 GGTATTGGG
39712 CCAGGAATCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.12, C:0.07, G:0.49, T:0.33
Consensus pattern (11 bp):
GGTATTGGGTC
Found at i:39842 original size:13 final size:13
Alignment explanation
Indices: 39826--39858 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
39816 ATATTTATCA
39826 GGGCGGGTAATCG
1 GGGCGGGTAATCG
39839 GGGCGGGTAATCG
1 GGGCGGGTAATCG
39852 GGGCGGG
1 GGGCGGG
39859 GATTACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.61, T:0.12
Consensus pattern (13 bp):
GGGCGGGTAATCG
Found at i:41761 original size:31 final size:31
Alignment explanation
Indices: 41725--41784 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
41715 AACTTAAAAG
* *
41725 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
41756 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
41785 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:42360 original size:23 final size:26
Alignment explanation
Indices: 42306--42375 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 26
42296 TATATGATAT
42306 AAATTAAATATCTATAATATTATATTAAA
1 AAATT-AATAT-T-TAATATTATATTAAA
42335 AAA-TAATATTTAAT-TTAT-TTAAA
1 AAATTAATATTTAATATTATATTAAA
42358 AAATTAATA-TTAATATTA
1 AAATTAATATTTAATATTA
42376 ATATCTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
23 13 0.33
24 12 0.31
25 4 0.10
26 1 0.03
27 5 0.13
28 1 0.03
29 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATTAATATTTAATATTATATTAAA
Found at i:42471 original size:64 final size:64
Alignment explanation
Indices: 42306--42454 Score: 225
Period size: 63 Copynumber: 2.4 Consensus size: 64
42296 TATATGATAT
* *
42306 AAATTAAATATCTATAATATTATATT-AAAAAATAATATTTAATTTATTTAAAAAATTAATATTA
1 AAATTAAA-ATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAACTAATATTA
* *
42370 ATATTAATATCTATAATATAATATTAAAAAAATAATATTTAATTTA-TTAAAAAACTAATATTA
1 AAATTAAAATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAACTAATATTA
42433 AAATTAAAATC-A-AATATAATAT
1 AAATTAAAATCTATAATATAATAT
42455 AATATAAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
61 10 0.13
62 1 0.01
63 41 0.53
64 26 0.33
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (64 bp):
AAATTAAAATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAACTAATATTA
Found at i:42793 original size:20 final size:20
Alignment explanation
Indices: 42770--42819 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
42760 CGCGATCCCT
42770 AGAATCGCAAATCAGTTTCC
1 AGAATCGCAAATCAGTTTCC
42790 AGAATCGCAAATCAGTTTCC
1 AGAATCGCAAATCAGTTTCC
*
42810 AAAATCGCAA
1 AGAATCGCAA
42820 CGCGATTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.22
Consensus pattern (20 bp):
AGAATCGCAAATCAGTTTCC
Found at i:42836 original size:21 final size:20
Alignment explanation
Indices: 42810--42907 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
42800 ATCAGTTTCC
42810 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * *
42831 AAAATCGCAATGCGATAGTAG
1 AAAATCGCAACGCGAT-TTTG
* ** *
42852 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-G
* * *
42873 ATAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
42893 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
42908 ACACATAAAT
Statistics
Matches: 59, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:42900 original size:20 final size:20
Alignment explanation
Indices: 42875--43068 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
42865 GATTTTCCAT
* *
42875 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
42895 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
42915 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
42935 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
42955 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
42975 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
42995 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
43015 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
43036 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
43056 AATCGCAACGCGA
1 AATCGCAACGCGA
43069 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:42922 original size:40 final size:39
Alignment explanation
Indices: 42871--43068 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
42861 TTGCGATTTT
* ** *
42871 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
42909 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
42950 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
42990 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
43029 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
43069 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:42958 original size:60 final size:60
Alignment explanation
Indices: 42875--43067 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
42865 GATTTTCCAT
* ** * *
42875 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
42935 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
42995 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
43056 AATCGCAACGCG
1 AATCGCAACGCG
43068 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:43487 original size:33 final size:33
Alignment explanation
Indices: 43448--43518 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
43438 TTCACTTAGA
*
43448 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
43481 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
43514 TTTCA
1 TTTCA
43519 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:43657 original size:14 final size:14
Alignment explanation
Indices: 43638--43692 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
43628 AGAATGACTG
43638 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
43652 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
43671 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
43685 TCGCAACG
1 TCGCAACG
43693 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:43675 original size:33 final size:33
Alignment explanation
Indices: 43638--43708 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
43628 AGAATGACTG
**
43638 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
43671 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
43704 TCGCA
1 TCGCA
43709 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:43726 original size:19 final size:19
Alignment explanation
Indices: 43704--43801 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
43694 GAAACCAAAA
*
43704 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
43723 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
43737 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
43756 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
43770 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
43789 TCGCGTTGCGATT
1 TCGCGTTGCGATT
43802 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:43745 original size:14 final size:14
Alignment explanation
Indices: 43726--43815 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
43716 TTTCATTTCG
43726 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
43740 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
43759 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
43773 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
43790 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
43806 CGTTGCGATT
1 CGTTGCGATT
43816 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:43751 original size:33 final size:33
Alignment explanation
Indices: 43709--43823 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
43699 CAAAATCGCA
43709 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
43742 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
43775 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
43808 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
43824 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:45919 original size:93 final size:93
Alignment explanation
Indices: 45516--46076 Score: 1071
Period size: 92 Copynumber: 6.1 Consensus size: 93
45506 TAGATTGCTT
*
45516 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45581 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45609 AGTAAATTTGTTCGGTTGCTGCC-ATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45672 -TTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45698 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45762 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45790 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45855 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45883 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45948 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45975 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46040 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46068 AGTAAATTT
1 AGTAAATTT
46077 ATCCATTCAA
Statistics
Matches: 462, Mismatches: 1, Indels: 10
0.98 0.00 0.02
Matches are distributed among these distances:
89 40 0.09
90 49 0.11
91 11 0.02
92 209 0.45
93 153 0.33
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:45941 original size:185 final size:186
Alignment explanation
Indices: 45516--46076 Score: 1071
Period size: 185 Copynumber: 3.0 Consensus size: 186
45506 TAGATTGCTT
*
45516 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45581 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCC-ATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
45645 GTGTATTCTTTAACACTGTGAAATA-TA-TTGTCTTTG-TTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
45698 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45762 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
45827 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
45883 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45948 TTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
46012 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
46068 AGTAAATTT
1 AGTAAATTT
46077 ATCCATTCAA
Statistics
Matches: 373, Mismatches: 1, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
181 53 0.14
182 99 0.27
183 2 0.01
184 9 0.02
185 191 0.51
186 19 0.05
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:46160 original size:19 final size:19
Alignment explanation
Indices: 46120--46248 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
46110 TAGTTTACTT
* *
46120 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
46140 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
46159 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
46178 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
46192 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
46211 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
46225 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
46244 TCGCA
1 TCGCA
46249 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:46199 original size:33 final size:32
Alignment explanation
Indices: 46156--46248 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
46146 CGCGAAACCA
**
46156 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
46188 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
46221 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
46249 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:46246 original size:52 final size:52
Alignment explanation
Indices: 46120--46248 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
46110 TAGTTTACTT
**
46120 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
46172 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
46225 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
46249 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:46266 original size:19 final size:19
Alignment explanation
Indices: 46244--46378 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
46234 GAAACCAAAA
*
46244 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
46263 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
46279 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
46296 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
46312 T--CGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
46329 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
46348 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
46368 TCGTGTTGCGA
1 TCGCGTTGCGA
46379 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 15 0.16
16 10 0.11
17 11 0.12
19 46 0.49
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:46285 original size:14 final size:14
Alignment explanation
Indices: 46266--46322 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
46256 TTTCATTTCG
46266 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
46280 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
46297 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
46313 CGTTGCGATT
1 CGTTGCGATT
46323 TTAATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:46291 original size:33 final size:33
Alignment explanation
Indices: 46249--46341 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
46239 CAAAATCGCA
*
46249 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
46282 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
46315 TTGCGATTTTAATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
46342 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:46892 original size:21 final size:20
Alignment explanation
Indices: 46838--46898 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
46828 CTCGAGAGTC
46838 CCCTCCCACCATTCAAGAGG
1 CCCTCCCACCATTCAAGAGG
** * *
46858 CCACTGTCATCATTGAAGAGG
1 CC-CTCCCACCATTCAAGAGG
46879 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCATTCAAGAG
46899 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.26, C:0.38, G:0.16, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCATTCAAGAGG
Found at i:48318 original size:14 final size:14
Alignment explanation
Indices: 48299--48334 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
48289 ATTGTTTAAT
48299 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
48313 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
48327 TGATTTGT
1 TGATTTGT
48335 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:48457 original size:19 final size:19
Alignment explanation
Indices: 48441--48542 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
48431 AAAAATGACT
48441 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48460 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
48479 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
48493 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48512 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
48532 ATCGCAATGCG
1 ATCGCAATGCG
48543 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:48595 original size:19 final size:19
Alignment explanation
Indices: 48571--48901 Score: 433
Period size: 19 Copynumber: 18.7 Consensus size: 19
48561 GATTATCTCG
48571 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48590 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
48609 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
48623 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48642 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48661 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
48675 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48694 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48713 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
48732 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
48751 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
48765 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48784 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
48803 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
48817 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
48836 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
48855 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
48869 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
48889 TTGCGATTTTCAT
1 TTGCGATTTTCAT
48902 GTTGGGATTT
Statistics
Matches: 276, Mismatches: 10, Indels: 51
0.82 0.03 0.15
Matches are distributed among these distances:
14 30 0.11
16 36 0.13
17 33 0.12
18 2 0.01
19 162 0.59
20 13 0.05
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:48738 original size:142 final size:140
Alignment explanation
Indices: 48571--48927 Score: 539
Period size: 142 Copynumber: 2.6 Consensus size: 140
48561 GATTATCTCG
48571 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCAT
*
48636 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCG-ATTGCGAT
48701 TTTCATTTCGCA
129 TTTCATTTCGCA
* * *
48713 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCAT
48778 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCG-ATTGCGAT
48843 TTTCATTTCGCA
129 TTTCATTTCGCA
* * *
48855 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
48914 A-TTCGCGTTGCGAT
64 ATTTCGCATTGCGAT
48928 GTATTTTCCG
Statistics
Matches: 203, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
137 26 0.13
138 25 0.12
139 5 0.02
140 3 0.01
142 144 0.71
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (140 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGATTGCGATTT
TCATTTCGCA
Found at i:48863 original size:52 final size:52
Alignment explanation
Indices: 48571--48901 Score: 399
Period size: 52 Copynumber: 6.2 Consensus size: 52
48561 GATTATCTCG
* * * * *
48571 TTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
*
48623 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
*
48675 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
48732 TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
48784 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
48836 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
48889 TTGCGATTTTCAT
1 TTGCGATTTTCAT
48902 GTTGGGATTT
Statistics
Matches: 258, Mismatches: 8, Indels: 25
0.89 0.03 0.09
Matches are distributed among these distances:
52 186 0.72
53 17 0.07
54 11 0.04
55 10 0.04
56 1 0.00
57 28 0.11
58 1 0.00
59 4 0.02
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:51221 original size:12 final size:12
Alignment explanation
Indices: 51204--51228 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51194 TCTTCGGGGA
51204 CTTTTTCTTCTT
1 CTTTTTCTTCTT
51216 CTTTTTCTTCTT
1 CTTTTTCTTCTT
51228 C
1 C
51229 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:51437 original size:24 final size:24
Alignment explanation
Indices: 51403--51449 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
51393 CTGAAACATC
51403 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
51427 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
51450 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:52157 original size:20 final size:20
Alignment explanation
Indices: 52129--52497 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
52119 AAATTTCAGT
* * * *
52129 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
52149 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
52169 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
52189 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
52209 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
52229 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
52249 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
52269 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
52289 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
52309 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
52329 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
52349 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
52369 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
52389 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
52409 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
52429 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
52449 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
52469 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
52489 GTTGCGATT
1 GTTGCGATT
52498 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:55209 original size:15 final size:15
Alignment explanation
Indices: 55186--55215 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55176 TCTGAAAAAC
*
55186 TAAATTAAAATTTTA
1 TAAAGTAAAATTTTA
55201 TAAAGTAAAATTTTA
1 TAAAGTAAAATTTTA
55216 GTTTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TAAAGTAAAATTTTA
Found at i:57849 original size:18 final size:17
Alignment explanation
Indices: 57806--57849 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
57796 AGTACTTTTT
*
57806 AATTACATTGAAATAAA
1 AATTAAATTGAAATAAA
* *
57823 AAATGAATTGAATATAAA
1 AATTAAATTGAA-ATAAA
57841 AATTAAATT
1 AATTAAATT
57850 TTGACCATGG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (17 bp):
AATTAAATTGAAATAAA
Done.