Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007846.1 Hibiscus syriacus cultivar Beakdansim tig00110202_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: 846497
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 4
Found at i:286030 original size:21 final size:21
Alignment explanation
Indices: 286005--286078 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
285995 GTTGCGATTC
286005 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
286026 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
286047 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
286068 TCTCGTTGCGA
1 TCTCGTTGCGA
286079 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:286200 original size:33 final size:33
Alignment explanation
Indices: 286158--286228 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
286148 AATACTAACT
*
286158 TGAAAATCGCAATGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
286191 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
286224 TGAAA
1 TGAAA
286229 TCTAAGTGAA
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:0.48, C:0.15, G:0.24, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:286633 original size:20 final size:20
Alignment explanation
Indices: 286608--286780 Score: 206
Period size: 20 Copynumber: 8.6 Consensus size: 20
286598 CTTTAAAAAT
286608 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
286628 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
286648 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
286669 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
286689 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
286709 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
286729 CACGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
286749 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
286769 CGCGTTGCGATT
1 CGCGTTGCGATT
286781 CTGGAAAATC
Statistics
Matches: 132, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 114 0.86
21 18 0.14
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:287023 original size:2 final size:2
Alignment explanation
Indices: 287007--287197 Score: 55
Period size: 2 Copynumber: 110.5 Consensus size: 2
286997 TAATATAAAA
* *
287007 AT AT -T AT AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
287044 AT A- AT AT AT A- AT -T A- AT AT AA AG AA AT AT A- AA AT CT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
287080 AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
287116 AT AT AT A- AT -T A- AT AT A- AA AT AT -T AT A- AA AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
287151 AT AT -T TT AT AT AT AT A- AT -T A- AT AT A- AA AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
287187 AT AT AT AT AT A
1 AT AT AT AT AT A
287198 AATAGGGGTG
Statistics
Matches: 145, Mismatches: 14, Indels: 60
0.66 0.06 0.27
Matches are distributed among these distances:
1 30 0.21
2 115 0.79
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:287057 original size:59 final size:60
Alignment explanation
Indices: 286989--287199 Score: 192
Period size: 61 Copynumber: 3.3 Consensus size: 60
286979 GATTTTCTCT
*
286989 TATATAATTAATATAAAAATATTATATATTATATATATAATTAATATAAAA-ATATATAA
1 TATATAATTAATATAAAAATATTATATATTATATATATAATTAATATAAAATATATAAAA
* * *
287048 TATATAATTAATATAAAGAAATATAAAATCTTATATATATAATTAATATAAAATATATAAAA
1 TATATAATTAATAT-AA-AAATATTATATATTATATATATAATTAATATAAAATATATAAAA
* * * *
287110 TATTATATATATAATTAATATAAAATATTATAAAATAT-TATATATTTTATATATATAATTAATA
1 TA-TATA-AT-TAA-T-ATA-AAAATATTATATATTATATATATA-ATTA-ATATA-AAAT-ATA
287174 TAAAA
56 TAAAA
287179 TATTATATATATATATATAAA
1 TA-TATA-AT-TA-ATATAAA
287200 TAGGGGTGGG
Statistics
Matches: 127, Mismatches: 11, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
59 14 0.11
60 2 0.02
61 32 0.25
62 9 0.07
63 4 0.03
64 2 0.02
65 9 0.07
66 16 0.13
67 10 0.08
68 6 0.05
69 22 0.17
70 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.43
Consensus pattern (60 bp):
TATATAATTAATATAAAAATATTATATATTATATATATAATTAATATAAAATATATAAAA
Found at i:287123 original size:69 final size:68
Alignment explanation
Indices: 286997--287191 Score: 240
Period size: 69 Copynumber: 2.8 Consensus size: 68
286987 CTTATATAAT
286997 TAATATAAAAATATTATATATTA-TATATATAATTAATATA-AAAATA-TATAATATATAATTAA
1 TAATAT-AAAATATTATATATTATTATATATAA--AATATATAAAATATTAT-ATATATAATTAA
287059 TATAAAGA
62 TATAAA-A
*
287067 -AATATAAAATCTTATATATATAATTA-ATATAAAATATATAAAATATTATATATATAATTAATA
1 TAATATAAAATATTATATAT-T-ATTATATATAAAATATATAAAATATTATATATATAATTAATA
287130 TAAAA
64 TAAAA
* *
287135 TATTATAAAATATTATATATT-TTATATATATAATTAATATAAAATATTATATATATA
1 TAATATAAAATATTATATATTATTATATATA-AAAT-ATATAAAATATTATATATATA
287192 TATATAAATA
Statistics
Matches: 112, Mismatches: 4, Indels: 19
0.83 0.03 0.14
Matches are distributed among these distances:
66 3 0.03
67 5 0.04
68 24 0.21
69 68 0.61
70 10 0.09
71 2 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.43
Consensus pattern (68 bp):
TAATATAAAATATTATATATTATTATATATAAAATATATAAAATATTATATATATAATTAATATA
AAA
Found at i:287142 original size:44 final size:45
Alignment explanation
Indices: 286989--287201 Score: 173
Period size: 44 Copynumber: 4.9 Consensus size: 45
286979 GATTTTCTCT
* * *
286989 TATATAATTAATATAAAAATATTATATATTATATATATA-ATTA-A
1 TATATAATTAATAT-AAAATATTATAAAATATATATAAATATTATA
* * *
287033 TATA-AA--AATATATAATA-TATAATTAATATAAAGAAATA-TA-A
1 TATATAATTAATATAAAATATTATAA--AATATATATAAATATTATA
* * *
287074 -A-AT-CTTATATATATAATTAATATAAAATATATA-AAATATTATA
1 TATATAATTA-ATATA-AAATATTATAAAATATATATAAATATTATA
* *
287117 TATATAATTAATATAAAATATTATAAAATAT-TATATATTTTATA
1 TATATAATTAATATAAAATATTATAAAATATATATAAATATTATA
*
287161 TATATAATTAATATAAAATATTATATATATATATATAAATA
1 TATATAATTAATATAAAATATTATA-AAATATATATAAATA
287202 GGGGTGGGGC
Statistics
Matches: 134, Mismatches: 18, Indels: 32
0.73 0.10 0.17
Matches are distributed among these distances:
39 5 0.04
40 6 0.04
41 22 0.16
42 15 0.11
43 8 0.06
44 57 0.43
45 12 0.09
46 9 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.43
Consensus pattern (45 bp):
TATATAATTAATATAAAATATTATAAAATATATATAAATATTATA
Found at i:290613 original size:25 final size:26
Alignment explanation
Indices: 290564--290613 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
290554 CGAAGTAGGC
*
290564 AGGCACTATACTTTTTCAAAAAAAAGT
1 AGGCACTATAC-TCTTCAAAAAAAAGT
*
290591 AGGCACTATAC-CTTCAAACAAAA
1 AGGCACTATACTCTTCAAAAAAAA
290614 TAAAAAGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
27 11 0.52
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (26 bp):
AGGCACTATACTCTTCAAAAAAAAGT
Found at i:292330 original size:3 final size:3
Alignment explanation
Indices: 292322--292364 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
292312 TAATTTTAAT
*
292322 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
292365 CAAATTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:293771 original size:30 final size:29
Alignment explanation
Indices: 293700--293848 Score: 95
Period size: 30 Copynumber: 5.0 Consensus size: 29
293690 TTTGTAACTT
* * *
293700 CTATTTTAGTCCTTTAAGTTTCTGTATTTG
1 CTATTTTAGTCC-TTAAATTTATGTTTTTG
* *
293730 -TATTTTGGTCCTTAAATTTATATTTTTTG
1 CTATTTTAGTCCTTAAATTTAT-GTTTTTG
** * *
293759 CTATTTTAGTCCTTTAGGTTTATGTCTTTA
1 CTATTTTAGTCC-TTAAATTTATGTTTTTG
* *
293789 CTGTTTTAGTCCATAAGA-TTATGTTTTTTG
1 CTATTTTAGTCCTTAA-ATTTATG-TTTTTG
* * *
293819 CCATTTTAGGTCCTTTAAGTTTCTGTTTTT
1 CTATTTTA-GTCC-TTAAATTTATGTTTTT
293849 ATTCTAGTCC
Statistics
Matches: 89, Mismatches: 22, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
28 8 0.09
29 22 0.25
30 35 0.39
31 17 0.19
32 7 0.08
ACGTcount: A:0.17, C:0.12, G:0.13, T:0.57
Consensus pattern (29 bp):
CTATTTTAGTCCTTAAATTTATGTTTTTG
Found at i:293816 original size:59 final size:61
Alignment explanation
Indices: 293700--293849 Score: 173
Period size: 60 Copynumber: 2.5 Consensus size: 61
293690 TTTGTAACTT
* * *
293700 CTATTTTAGTCCTTTAAGTTTCTGTATTT-GTATTTTGGTCCTTAAATTTATA-TTTTTTG
1 CTATTTTAGTCCTTTAAGTTTCTGTATTTACTATTTTAGTCCATAAATTTATAGTTTTTTG
* * * *
293759 CTATTTTAGTCCTTTAGGTTTATGTCTTTACTGTTTTAGTCCATAAGA-TTAT-GTTTTTTG
1 CTATTTTAGTCCTTTAAGTTTCTGTATTTACTATTTTAGTCCATAA-ATTTATAGTTTTTTG
* *
293819 CCATTTTAGGTCCTTTAAGTTTCTGTTTTTA
1 CTATTTTA-GTCCTTTAAGTTTCTGTATTTA
293850 TTCTAGTCCC
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 26 0.34
60 30 0.39
61 20 0.26
ACGTcount: A:0.18, C:0.12, G:0.13, T:0.57
Consensus pattern (61 bp):
CTATTTTAGTCCTTTAAGTTTCTGTATTTACTATTTTAGTCCATAAATTTATAGTTTTTTG
Found at i:296064 original size:57 final size:57
Alignment explanation
Indices: 296001--296114 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
295991 GAGAGATAAA
296001 AATAAAGTTAGATGGGAATATTTGAGAAGAAGGTGGGCGCTGTTTCCATGTTCAAAT
1 AATAAAGTTAGATGGGAATATTTGAGAAGAAGGTGGGCGCTGTTTCCATGTTCAAAT
* * *
296058 AATAAAGTTAGATGGGAGTATTTGAGAAGTAGGTGGGCGCTGTTTCCATTTTCAAAT
1 AATAAAGTTAGATGGGAATATTTGAGAAGAAGGTGGGCGCTGTTTCCATGTTCAAAT
296115 GGTTGAATAG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.32, C:0.09, G:0.28, T:0.32
Consensus pattern (57 bp):
AATAAAGTTAGATGGGAATATTTGAGAAGAAGGTGGGCGCTGTTTCCATGTTCAAAT
Found at i:303538 original size:23 final size:24
Alignment explanation
Indices: 303512--303562 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
303502 TAATAATTGT
*
303512 ATTTTAATTAAATTATATTTA-AA
1 ATTTTAATTAAATTATAATTATAA
*
303535 ATTTTAATTAATTTATAATTATAA
1 ATTTTAATTAAATTATAATTATAA
303559 ATTT
1 ATTT
303563 AATACTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTAATTAAATTATAATTATAA
Found at i:303561 original size:18 final size:18
Alignment explanation
Indices: 303519--303561 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
303509 TGTATTTTAA
303519 TTAAATTATATTTAAAAT
1 TTAAATTATATTTAAAAT
* *
303537 TTTAATTA-ATTTATAAT
1 TTAAATTATATTTAAAAT
303554 TATAAATT
1 T-TAAATT
303562 TAATACTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAATTATATTTAAAAT
Found at i:309931 original size:23 final size:23
Alignment explanation
Indices: 309857--309931 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
309847 CATCTTATAT
* *
309857 GGCACTTCAGTGCATTTCTACGC
1 GGCACTACAGTGCAATTCTACGC
*
309880 AGCACTACAGTGCAATTCTACGC
1 GGCACTACAGTGCAATTCTACGC
* *
309903 GACACTACAGTGCAATTCTACGT
1 GGCACTACAGTGCAATTCTACGC
309926 GGCACT
1 GGCACT
309932 TTGGTGCAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (23 bp):
GGCACTACAGTGCAATTCTACGC
Found at i:319088 original size:2 final size:2
Alignment explanation
Indices: 319056--319108 Score: 61
Period size: 2 Copynumber: 26.0 Consensus size: 2
319046 TTCCAATTAA
* * * *
319056 AT AT AGT AT AT TT AT TT AT TT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
319099 AT AT AT AT AT
1 AT AT AT AT AT
319109 TCAGCAGAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:328620 original size:13 final size:13
Alignment explanation
Indices: 328602--328645 Score: 88
Period size: 13 Copynumber: 3.4 Consensus size: 13
328592 TGGATTTCCT
328602 GAGAGAAAAGTTA
1 GAGAGAAAAGTTA
328615 GAGAGAAAAGTTA
1 GAGAGAAAAGTTA
328628 GAGAGAAAAGTTA
1 GAGAGAAAAGTTA
328641 GAGAG
1 GAGAG
328646 TTAACAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.34, T:0.14
Consensus pattern (13 bp):
GAGAGAAAAGTTA
Found at i:328724 original size:6 final size:6
Alignment explanation
Indices: 328713--328737 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
328703 CGCCCACCCA
328713 CTGTCT CTGTCT CTGTCT CTGTCT C
1 CTGTCT CTGTCT CTGTCT CTGTCT C
328738 GTATACTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.16, T:0.48
Consensus pattern (6 bp):
CTGTCT
Found at i:339190 original size:18 final size:18
Alignment explanation
Indices: 339128--339190 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
339118 ACAAACATTA
* *
339128 ATAAATTATTTATGAGTT
1 ATAAATTATTTTTTAGTT
*
339146 AT-AATATAGTTTTTTATTT
1 ATAAAT-TA-TTTTTTAGTT
*
339165 AATTAATTATTTTTTAGTT
1 -ATAAATTATTTTTTAGTT
339184 ATAAATT
1 ATAAATT
339191 GATTAATCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 16 0.44
20 4 0.11
21 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
ATAAATTATTTTTTAGTT
Found at i:340615 original size:30 final size:29
Alignment explanation
Indices: 340581--340677 Score: 83
Period size: 32 Copynumber: 3.2 Consensus size: 29
340571 TTTAATCTTT
340581 ATAATTTTATTAATTTAATTATAATTTAAA
1 ATAATTTTATTAATTT-ATTATAATTTAAA
*
340611 ATAA-TTTAATAATTT-TTA-ATATTTAAAA
1 ATAATTTTATTAATTTATTATA-ATTT-AAA
* * *
340639 ATATTATTTATTTTAATTTATTTTAGTTTAAA
1 ATA--ATTT-TATTAATTTATTATAATTTAAA
340671 ATAATTT
1 ATAATTT
340678 AATCATTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
26 1 0.02
27 7 0.13
28 6 0.11
29 10 0.19
30 9 0.17
31 2 0.04
32 13 0.24
33 5 0.09
34 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
ATAATTTTATTAATTTATTATAATTTAAA
Found at i:340616 original size:10 final size:11
Alignment explanation
Indices: 340591--340623 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
340581 ATAATTTTAT
*
340591 TAATTTAATTA
1 TAATTTAATAA
340602 TAATTTAA-AA
1 TAATTTAATAA
340612 TAATTTAATAA
1 TAATTTAATAA
340623 T
1 T
340624 TTTTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAATTTAATAA
Found at i:340697 original size:17 final size:16
Alignment explanation
Indices: 340670--340706 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
340660 TTTAGTTTAA
340670 AATAATTTAATCATTC
1 AATAATTTAATCATTC
*
340686 AATAATTTTAATCATTG
1 AATAA-TTTAATCATTC
340703 AATA
1 AATA
340707 GGGAAACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (16 bp):
AATAATTTAATCATTC
Found at i:341602 original size:23 final size:23
Alignment explanation
Indices: 341521--341602 Score: 87
Period size: 22 Copynumber: 3.7 Consensus size: 23
341511 ACGATAAACA
*
341521 AACAATAAA-GAACATGTTCGTG
1 AACAATAAATGAACATGTTCGCG
**
341543 AACTCTAAATGAACA-GTTCGCG
1 AACAATAAATGAACATGTTCGCG
* * *
341565 AACATTAAACGAACATGTTTGCG
1 AACAATAAATGAACATGTTCGCG
*
341588 AACAATAAATAAACA
1 AACAATAAATGAACA
341603 AACATGAACA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 25 0.52
23 23 0.48
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (23 bp):
AACAATAAATGAACATGTTCGCG
Found at i:342566 original size:256 final size:261
Alignment explanation
Indices: 342072--342592 Score: 1007
Period size: 256 Copynumber: 2.0 Consensus size: 261
342062 TTCAAATCAC
342072 TTAAAGTTCGTTTTATTTCTTTTTTTTTTTTTAATTTTCAATAAGATGCTGACATATATTGTCGT
1 TTAAAGTTCGTTTTATTTCTTTTTTTTTTTTTAATTTTCAATAAGATGCTGACATATATTGTCGT
342137 ATTATATAGGTGCTAAACTTTTTAAAATTATTTTAAATTAAAATGAAAATTAATTGACATTATTT
66 ATTATATAGGTGCTAAACTTTTTAAAATTATTTTAAATTAAAATGAAAATTAATTGACATTATTT
342202 TTAAATATTTAAAAAATTAATAAGTTATTTTAAATTAGAATCAAATTTATAAAATGTATAAGTTT
131 TTAAATATTTAAAAAATTAATAAGTTATTTTAAATTAGAATCAAATTTATAAAATGTATAAGTTT
342267 TAGGCATTAAATTATTATTATACCGTACAACGATATCACGCATGTTAGATAAAAAAATTAAAGTT
196 TAGGCATTAAATTATTATTATACCGTACAACGATATCACGCATGTTAGATAAAAAAATTAAAGTT
342332 A
261 A
342333 TTAAAGTTCG-TTTATTTCTTTTTTTTTTTTTAATTTTCAATAAGATGCTGACATATATTGTCGT
1 TTAAAGTTCGTTTTATTTCTTTTTTTTTTTTTAATTTTCAATAAGATGCTGACATATATTGTCGT
342397 ATTATATAGGTGCTAAACTTTTT-AAATTATTTTAAATTAAAATGAAAATTAATTGACATTATTT
66 ATTATATAGGTGCTAAACTTTTTAAAATTATTTTAAATTAAAATGAAAATTAATTGACATTATTT
342461 TTAAATATTT-AAAAATTAATAAGTTA-TTTAAATTAG-ATCAAATTTATAAAATGTATAAGTTT
131 TTAAATATTTAAAAAATTAATAAGTTATTTTAAATTAGAATCAAATTTATAAAATGTATAAGTTT
342523 TAGGCATTAAATTATTATTATACCGTACAACGATATCACGCATGTTAGATAAAAAAATTAAAGTT
196 TAGGCATTAAATTATTATTATACCGTACAACGATATCACGCATGTTAGATAAAAAAATTAAAGTT
342588 A
261 A
342589 TTAA
1 TTAA
342593 TGATTACCCC
Statistics
Matches: 260, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
256 96 0.37
257 10 0.04
258 16 0.06
259 51 0.20
260 77 0.30
261 10 0.04
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (261 bp):
TTAAAGTTCGTTTTATTTCTTTTTTTTTTTTTAATTTTCAATAAGATGCTGACATATATTGTCGT
ATTATATAGGTGCTAAACTTTTTAAAATTATTTTAAATTAAAATGAAAATTAATTGACATTATTT
TTAAATATTTAAAAAATTAATAAGTTATTTTAAATTAGAATCAAATTTATAAAATGTATAAGTTT
TAGGCATTAAATTATTATTATACCGTACAACGATATCACGCATGTTAGATAAAAAAATTAAAGTT
A
Found at i:344508 original size:81 final size:81
Alignment explanation
Indices: 344452--344723 Score: 386
Period size: 81 Copynumber: 3.4 Consensus size: 81
344442 TCCATGATTG
* * * * *
344452 ACACTTTTCTGCGAAATGCACAGTTAGGCCATTTATCTTTAACTT-AACGGTCTTTAATCGTTTA
1 ACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTA-TTCAATGGTCTTTAATCGTTTA
*
344516 TCTAACTGGCATAACCA
65 TCTAACTGGCATAATCA
344533 ACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTATTCAATGGTCTTTAATCGTTTAT
1 ACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTATTCAATGGTCTTTAATCGTTTAT
344598 CTAACTGGCATAATCA
66 CTAACTGGCATAATCA
* * *
344614 ACACCTTTATGCCAAATGCACAGCTAGGCCATTTATCTTTTATTCAATGGTCTTTAACCGTTCAT
1 ACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTATTCAATGGTCTTTAATCGTTTAT
* *
344679 TTAACTGGCATAATTA
66 CTAACTGGCATAATCA
* * * *
344695 ACATCTTTCTGTC-AATACACAGTTAGGCC
1 ACACCTTTCTGCCAAATGCACAGCTAGGCC
344724 TCTAAGGCAC
Statistics
Matches: 174, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
80 16 0.09
81 158 0.91
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (81 bp):
ACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTATTCAATGGTCTTTAATCGTTTAT
CTAACTGGCATAATCA
Found at i:344840 original size:67 final size:67
Alignment explanation
Indices: 344665--344868 Score: 266
Period size: 67 Copynumber: 3.0 Consensus size: 67
344655 ATTCAATGGT
* * * * * * * * *
344665 CTTTAACCGTTCATTTAACTGGCATAATTAACATCTTTCTGTCAATACACAGTTAGGCCTCTAAG
1 CTTT-ACCTTTCATCTAACTAGCACAATTGACACCTTTCTATCAATGCACAGTTAGGCCTCAAAG
344730 GCA
65 GCA
* * *
344733 C-TTAACTTTCATCTAACTAGCACAATTGACACATTTCTATCAATGCACATTTAGGCCTCAAAGG
1 CTTTACCTTTCATCTAACTAGCACAATTGACACCTTTCTATCAATGCACAGTTAGGCCTCAAAGG
344797 CA
66 CA
* *
344799 CTTTACCTTTCATCTAACTCGCACAATTGACACCTTCCTATCAATGCACAGTTAGGCCTCAAAGG
1 CTTTACCTTTCATCTAACTAGCACAATTGACACCTTTCTATCAATGCACAGTTAGGCCTCAAAGG
344864 CA
66 CA
344866 CTT
1 CTT
344869 AGGCTTTTGA
Statistics
Matches: 118, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
66 52 0.44
67 65 0.55
68 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (67 bp):
CTTTACCTTTCATCTAACTAGCACAATTGACACCTTTCTATCAATGCACAGTTAGGCCTCAAAGG
CA
Found at i:345136 original size:54 final size:55
Alignment explanation
Indices: 345065--345216 Score: 175
Period size: 55 Copynumber: 2.8 Consensus size: 55
345055 AAATATATTT
* * *
345065 CCCATACAGAAATTCATACACTTAGTATGGATTTTTTAG-TTCGCACA-AATAGTG
1 CCCATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTCACACACAA-AGTA
* * *
345119 CCCATAC-GAAAATTCATACACTTGGTATGAATTTCTTAGTTTTACACACAAAGTA
1 CCCATACAG-AAATTCATACACTTAGTATGGATTTCTTAGTTTCACACACAAAGTA
* * *
345174 CTCATATAGAAATTCATACACCTAGTATGGATTTCTTAAGTTT
1 CCCATACAGAAATTCATACACTTAGTATGGATTTCTT-AGTTT
345217 TTGCACACTT
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
53 1 0.01
54 34 0.41
55 39 0.48
56 8 0.10
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (55 bp):
CCCATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTCACACACAAAGTA
Found at i:345616 original size:19 final size:21
Alignment explanation
Indices: 345573--345626 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
345563 TACCCCCACC
345573 ATGGTATCGATACTACTATACT
1 ATGGTATCGATACTACTATA-T
345595 ATGGTATCGATACT-CTAT-T
1 ATGGTATCGATACTACTATAT
*
345614 ATGGTACCGATAC
1 ATGGTATCGATAC
345627 CATTTTTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 13 0.42
21 4 0.13
22 14 0.45
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (21 bp):
ATGGTATCGATACTACTATAT
Found at i:350834 original size:25 final size:25
Alignment explanation
Indices: 350806--350855 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
350796 AGTCAAGACA
*
350806 GGTGGCCAACCATTGTTGAAATTTG
1 GGTGGCCAACAATTGTTGAAATTTG
*
350831 GGTGGTCAACAATTGTTGAAATTTG
1 GGTGGCCAACAATTGTTGAAATTTG
350856 AAGCATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (25 bp):
GGTGGCCAACAATTGTTGAAATTTG
Found at i:351622 original size:42 final size:42
Alignment explanation
Indices: 351563--351647 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
351553 ATCTGGGTGG
351563 AAGCTAGTTGTCGGGGATGTTTTTCTTTCCCCATCCAATCCA
1 AAGCTAGTTGTCGGGGATGTTTTTCTTTCCCCATCCAATCCA
*
351605 AAGCTAGTTTTCGGGGATGTTTTTCTTTCCCCATCCAATCCA
1 AAGCTAGTTGTCGGGGATGTTTTTCTTTCCCCATCCAATCCA
351647 A
1 A
351648 CTCTTTCTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (42 bp):
AAGCTAGTTGTCGGGGATGTTTTTCTTTCCCCATCCAATCCA
Found at i:353033 original size:20 final size:20
Alignment explanation
Indices: 353008--353050 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
352998 GATGATTGCG
*
353008 CCGATAACGGGACGCAATCA
1 CCGATAACAGGACGCAATCA
353028 CCGATAACAGGACGCAATCA
1 CCGATAACAGGACGCAATCA
353048 CCG
1 CCG
353051 TTTTTCAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.33, G:0.23, T:0.09
Consensus pattern (20 bp):
CCGATAACAGGACGCAATCA
Found at i:358571 original size:18 final size:18
Alignment explanation
Indices: 358548--358591 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
358538 ATCAGCCTCA
358548 AATGTATCCTCCGCTACC
1 AATGTATCCTCCGCTACC
358566 AATGTATCCTCCGCTACC
1 AATGTATCCTCCGCTACC
*
358584 AATATATC
1 AATGTATC
358592 ACCCACCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.34, G:0.09, T:0.30
Consensus pattern (18 bp):
AATGTATCCTCCGCTACC
Found at i:364357 original size:20 final size:20
Alignment explanation
Indices: 364318--364357 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
364308 ATTATTGAGC
* *
364318 TGGTTTTTATGTTCTGTGTT
1 TGGTTTTTAAGTTCTATGTT
*
364338 TGGTTTTTAAGTTTTATGTT
1 TGGTTTTTAAGTTCTATGTT
364358 GTAACAGAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.23, T:0.65
Consensus pattern (20 bp):
TGGTTTTTAAGTTCTATGTT
Found at i:367217 original size:2 final size:2
Alignment explanation
Indices: 367198--367251 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
367188 TAATAAAATA
* *
367198 AT AT AC AT AT AC 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
367240 AT AT AT AT AT AT
1 AT AT AT AT AT AT
367252 TAAAATAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:368241 original size:16 final size:17
Alignment explanation
Indices: 368220--368253 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
368210 ATATTATCCG
368220 ATCCG-AAATTTCAGAT
1 ATCCGAAAATTTCAGAT
*
368236 ATCCGAAAATTTCGGAT
1 ATCCGAAAATTTCAGAT
368253 A
1 A
368254 CTTAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (17 bp):
ATCCGAAAATTTCAGAT
Found at i:368308 original size:16 final size:16
Alignment explanation
Indices: 368277--368325 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
368267 TCCGTATCCG
*
368277 ATCCGAAAAATTCGGAT
1 ATCCG-AAATTTCGGAT
368294 ATCCGAAATTTCGGAT
1 ATCCGAAATTTCGGAT
* *
368310 ATCCTAAATTTTGGAT
1 ATCCGAAATTTCGGAT
368326 CGGATATCCG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 24 0.83
17 5 0.17
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (16 bp):
ATCCGAAATTTCGGAT
Found at i:372592 original size:20 final size:20
Alignment explanation
Indices: 372542--372773 Score: 198
Period size: 20 Copynumber: 11.5 Consensus size: 20
372532 GCACACCCCT
* * *
372542 AATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACGT-A
* * *
372563 AATTGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
372583 AATCGTAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
** * *
372604 AATCATAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
* *
372624 AATCGTAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
372644 AATCGCAACTCGTATATGTA
1 AATCGCAACGCGAATACGTA
*
372664 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * * *
372684 AATCTCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
372704 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
372724 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
372744 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
372764 AATCGCAACG
1 AATCGCAACG
372774 AGATTCTGAC
Statistics
Matches: 176, Mismatches: 31, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
19 1 0.01
20 142 0.81
21 33 0.19
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:372658 original size:40 final size:40
Alignment explanation
Indices: 372542--372772 Score: 225
Period size: 40 Copynumber: 5.7 Consensus size: 40
372532 GCACACCCCT
* * * *
372542 AATCGCAACGAGTATCCGTAAAATTGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGT-AAATCGCAACTCGTATCCGTA
* * ** *
372583 AATCGTAACGACAATACGTAAAATCATAACGCGTATCCGTA
1 AATCGCAACGAGAATACGT-AAATCGCAACTCGTATCCGTA
* **
372624 AATCGTAACGAGAATACGTAAATCGCAACTCGTATATGTA
1 AATCGCAACGAGAATACGTAAATCGCAACTCGTATCCGTA
*
372664 AATCGCAACGAGAATACGTAAATCTCAA-TGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAATCGCAACT-CGTATCCGTA
* * * *
372704 AATCGCAATGCGAATACGTAAATCGCAA-TGCGAATACGTA
1 AATCGCAACGAGAATACGTAAATCGCAACT-CGTATCCGTA
* *
372744 AATCGCAATGCGAAT-CTGTAAATCGCAAC
1 AATCGCAACGAGAATAC-GTAAATCGCAAC
372773 GAGATTCTGA
Statistics
Matches: 165, Mismatches: 22, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
39 2 0.01
40 111 0.67
41 52 0.32
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (40 bp):
AATCGCAACGAGAATACGTAAATCGCAACTCGTATCCGTA
Found at i:373680 original size:24 final size:24
Alignment explanation
Indices: 373623--373682 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
373613 TAGTCAGTAT
373623 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
373647 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
373671 TCGAATTTTGAT
1 TCGAAATTTGAT
373683 GATTTTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:376120 original size:20 final size:20
Alignment explanation
Indices: 376095--376149 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
376085 AGACATTCAT
*
376095 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
376115 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
*
376135 ATGACTATCGCAACG
1 TTGACTATCGCAACG
376150 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:376171 original size:33 final size:36
Alignment explanation
Indices: 376121--376283 Score: 170
Period size: 38 Copynumber: 4.4 Consensus size: 36
376111 GGAATTGACT
* ** *
376121 ATCGCAACGCGGAAATGACTATCGCAA-CG-A-GAGA
1 ATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAA
376155 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
376193 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
* * *
376231 ATCGTAATGTGAAATGAAAATCGCAATGCGAAATGAAT
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
*
376269 ATCGCAATACGAAAT
1 ATCGCAATGCGAAAT
376284 TAGTTTCGCG
Statistics
Matches: 114, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
33 14 0.12
34 9 0.08
35 2 0.02
37 1 0.01
38 88 0.77
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:376178 original size:19 final size:19
Alignment explanation
Indices: 376154--376283 Score: 224
Period size: 19 Copynumber: 6.8 Consensus size: 19
376144 GCAACGAGAG
376154 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
376173 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
376192 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
376211 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
376230 AATCGTAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
376249 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
376268 TATCGCAATACGAAAT
1 AATCGCAATGCGAAAT
376284 TAGTTTCGCG
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 105 1.00
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:376312 original size:20 final size:19
Alignment explanation
Indices: 376287--376373 Score: 94
Period size: 20 Copynumber: 4.7 Consensus size: 19
376277 ACGAAATTAG
376287 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
376306 TTTTCGCATTGCGA--TTCA
1 -TTTCGCGTTGCGATTTTCA
*
376324 ---CTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
376340 TTTCGCATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
376359 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
376374 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
14 8 0.15
16 4 0.07
18 4 0.07
19 17 0.31
20 22 0.40
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:376494 original size:14 final size:14
Alignment explanation
Indices: 376475--376511 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
376465 CATCAATTAA
376475 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
376489 ACAAATCATCTTTT
1 ACAAATCAACATTT
376503 ACAAATCAA
1 ACAAATCAA
376512 TTAAACAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:379966 original size:19 final size:19
Alignment explanation
Indices: 379927--379966 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
379917 TCTTTTGGTT
*
379927 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCACAACGC
*
379946 GAAATGAAAATCACAATGC
1 GAAATGAAAATCACAACGC
379965 GA
1 GA
379967 TTTTGGTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCACAACGC
Found at i:380010 original size:33 final size:33
Alignment explanation
Indices: 379962--380042 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
379952 AAAATCACAA
**
379962 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
379995 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
380028 TACGATTTTCATTTC
1 TGCGATTTTCATTTC
380043 TCTCGTTGCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:380016 original size:19 final size:19
Alignment explanation
Indices: 379992--380096 Score: 60
Period size: 19 Copynumber: 5.6 Consensus size: 19
379982 GCGATTATCT
379992 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
380011 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
* *
380025 CGTTACGATTTTCATTTCTCT
1 CGTTGCGATTTTCA-TT-TCG
**
380046 CGTTGCGATAGTCAATTTCG
1 CGTTGCGATTTTC-ATTTCG
* *
380066 TGTTGCGA-TTTCATTTTCA
1 CGTTGCGATTTTCA-TTTCG
*
380085 TGTTGCGATTTT
1 CGTTGCGATTTT
380097 AAGTTTAGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
14 9 0.14
16 3 0.05
17 3 0.05
18 1 0.02
19 22 0.33
20 12 0.18
21 15 0.23
22 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:380686 original size:20 final size:20
Alignment explanation
Indices: 380661--380871 Score: 217
Period size: 20 Copynumber: 10.4 Consensus size: 20
380651 TAAAAATCGT
380661 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
380681 GTTGCGATTTTACGTATTCGC
1 GTTGCGA-TTTACGGATACGC
* * *
380702 ATTGAGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
* * * *
380722 ATTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
*
380742 GTTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATACGC
* * *
380762 GTTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
* *
380782 ATTGTGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
380802 GTTGCGATTTTACGTAT-TGTC
1 GTTGCGA-TTTACGGATACG-C
380823 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
380843 GTTGCGATTTTACGGATACTC
1 GTTGCGA-TTTACGGATACGC
380864 GTTGCGAT
1 GTTGCGAT
380872 AGTCAGAATC
Statistics
Matches: 154, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
20 102 0.66
21 52 0.34
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:380814 original size:81 final size:80
Alignment explanation
Indices: 380661--380852 Score: 312
Period size: 81 Copynumber: 2.4 Consensus size: 80
380651 TAAAAATCGT
380661 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCGCATTGAGATTTACGGATACACATTG
1 GTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCGCATTGAGATTTACGGATACACATTG
380726 CGATTTACGTATTCTC
65 CGATTTACGTATTCTC
* * * * *
380742 GTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCATTGTGATTTACGGATACGCGTTGC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCGCATTGAGATTTACGGATACACATTGC
*
380807 GATTTTACGTATTGTC
66 GA-TTTACGTATTCTC
380823 GTTGCGATTTACGGATACGCGTTGCGATTT
1 GTTGCGATTTACGGATACGCGTTGCGATTT
380853 TACGGATACT
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 36 0.35
81 67 0.65
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (80 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCGCATTGAGATTTACGGATACACATTGC
GATTTACGTATTCTC
Found at i:380866 original size:41 final size:41
Alignment explanation
Indices: 380661--380871 Score: 309
Period size: 41 Copynumber: 5.2 Consensus size: 41
380651 TAAAAATCGT
*
380661 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCGC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* * * *
380702 ATTGAGATTTACGGATACACATTGCGA-TTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
*
380742 GTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* * *
380782 ATTGTGATTTACGGATACGCGTTGCGATTTTACGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* *
380823 GTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
380864 GTTGCGAT
1 GTTGCGAT
380872 AGTCAGAATC
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 71 0.47
41 79 0.53
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (41 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
Found at i:380907 original size:81 final size:81
Alignment explanation
Indices: 380661--380911 Score: 285
Period size: 81 Copynumber: 3.1 Consensus size: 81
380651 TAAAAATCGT
* * *
380661 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCGCATTGAGATTTACGGATACACATTG
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCATTGAGATTTACGGATACGCGTTG
** * *
380726 CGATTTACGTATTCTC
66 CGATTTATATGTTCGC
* *
380742 GTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCATTGTGATTTACGGATACGCGTTG
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCATTGAGATTTACGGATACGCGTTG
* *
380806 CGATTT-TACGTATTGTC
66 CGATTTATATGT-TCG-C
* * * * * *
380823 GTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCGCGT
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCATTGAGAT-TTACGGATA-CGCGT
380886 TGCGATTTATATGTTCGC
64 TGCGATTTATATGTTCGC
380904 GTTGCGAT
1 GTTGCGAT
380912 ACGCGATTAT
Statistics
Matches: 144, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
79 1 0.01
80 40 0.28
81 63 0.44
82 35 0.24
83 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (81 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCATTGAGATTTACGGATACGCGTTG
CGATTTATATGTTCGC
Found at i:397507 original size:6 final size:6
Alignment explanation
Indices: 397493--397545 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
397483 CATTCCCTTT
* * * * *
397493 TCCTGC TCCTAC TCCTAC TCCTGC TCCTAT TCCTAC TCCTGC TCCTAT
1 TCCTAC TCCTAC TCCTAC TCCTAC TCCTAC TCCTAC TCCTAC TCCTAC
397541 TCCTA
1 TCCTA
397546 TACAGCTTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.11, C:0.45, G:0.06, T:0.38
Consensus pattern (6 bp):
TCCTAC
Found at i:397516 original size:18 final size:18
Alignment explanation
Indices: 397493--397545 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
397483 CATTCCCTTT
*
397493 TCCTGCTCCTACTCCTAC
1 TCCTGCTCCTATTCCTAC
397511 TCCTGCTCCTATTCCTAC
1 TCCTGCTCCTATTCCTAC
397529 TCCTGCTCCTATTCCTA
1 TCCTGCTCCTATTCCTA
397546 TACAGCTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.11, C:0.45, G:0.06, T:0.38
Consensus pattern (18 bp):
TCCTGCTCCTATTCCTAC
Found at i:407215 original size:34 final size:34
Alignment explanation
Indices: 407177--407242 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
407167 TATTATCGAG
* * *
407177 GGTTAGAGTGTTATGTCTATCTTATGTTATTCAA
1 GGTTAGAATGTAATGTCTATCTTATGTAATTCAA
*
407211 GGTTAGAATGTAATGTGTATCTTATGTAATTC
1 GGTTAGAATGTAATGTCTATCTTATGTAATTC
407243 TGGTCTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (34 bp):
GGTTAGAATGTAATGTCTATCTTATGTAATTCAA
Found at i:409304 original size:17 final size:18
Alignment explanation
Indices: 409271--409304 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
409261 CCGCTATTAG
409271 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
409289 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
409305 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:415143 original size:38 final size:38
Alignment explanation
Indices: 415090--415166 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
415080 AATTTTGTTT
415090 TATCACTTCCGAATGGTTTCATCTCTTTCTCTTAGGCC
1 TATCACTTCCGAATGGTTTCATCTCTTTCTCTTAGGCC
*
415128 TATCACTTCCTAATGGTTTCATCTCTTTCTCTTAGGCC
1 TATCACTTCCGAATGGTTTCATCTCTTTCTCTTAGGCC
415166 T
1 T
415167 CCATAGTTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.16, C:0.29, G:0.12, T:0.44
Consensus pattern (38 bp):
TATCACTTCCGAATGGTTTCATCTCTTTCTCTTAGGCC
Found at i:424511 original size:51 final size:51
Alignment explanation
Indices: 424425--424729 Score: 371
Period size: 51 Copynumber: 6.2 Consensus size: 51
424415 CATTAAGAGA
* * * *
424425 TGTTATGGTAGCTGAGTATATGTTTGGGAACCAATGTTTCTACCTTGCTGT
1 TGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTGC
* * *
424476 TGTTGTGGTAGTTGAGTAAATGTTTGGGAAT-CAATGTTTCCACCTTGTTGC
1 TGTTGTGGTAGCTGAGTATATGTTTGGG-ATCCAATGTTTCCACCTTGCTGC
* * *
424527 TGTTGTGGTAGTTGAGTAAATGTTTGGGATCCAATGTTTCCACCTAGCTGC
1 TGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTGC
*
424578 TGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTGA
1 TGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTGC
424629 TG-T-T-G-A--T---TATATGTTTGGGATCCAATGTTTCCACCTTGCTGC
1 TGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTGC
* * ** *
424671 TGTTGTGGCAGCTGATTATATGTTTGGGA-CTCTGTGTTTCCACCTTGTTGC
1 TGTTGTGGTAGCTGAGTATATGTTTGGGATC-CAATGTTTCCACCTTGCTGC
424722 TGTTGTGG
1 TGTTGTGG
424730 GAGCCGAGAA
Statistics
Matches: 225, Mismatches: 17, Indels: 24
0.85 0.06 0.09
Matches are distributed among these distances:
42 36 0.16
43 1 0.00
44 1 0.00
45 2 0.01
46 1 0.00
47 1 0.00
48 2 0.01
49 1 0.00
50 4 0.02
51 175 0.78
52 1 0.00
ACGTcount: A:0.17, C:0.15, G:0.27, T:0.41
Consensus pattern (51 bp):
TGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTGC
Found at i:424653 original size:42 final size:42
Alignment explanation
Indices: 424594--424675 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
424584 GGTAGCTGAG
424594 TATATGTTTGGGATCCAATGTTTCCACCTTGCTGATGTTGAT
1 TATATGTTTGGGATCCAATGTTTCCACCTTGCTGATGTTGAT
*
424636 TATATGTTTGGGATCCAATGTTTCCACCTTGCTGCTGTTG
1 TATATGTTTGGGATCCAATGTTTCCACCTTGCTGATGTTG
424676 TGGCAGCTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (42 bp):
TATATGTTTGGGATCCAATGTTTCCACCTTGCTGATGTTGAT
Found at i:424696 original size:93 final size:93
Alignment explanation
Indices: 424537--424726 Score: 283
Period size: 93 Copynumber: 2.0 Consensus size: 93
424527 TGTTGTGGTA
*
424537 GTTGAGTAAATGTTTGGGATCCAATGTTTCCACCTAGCTGCTGTTGTGGTAGCTGAGTATATGTT
1 GTTGAGTAAATGTTTGGGATCCAATGTTTCCACCTAGCTGCTGTTGTGGCAGCTGAGTATATGTT
424602 TGGGA-TCCAATGTTTCCACCTTGCTGAT
66 TGGGACT-CAATGTTTCCACCTTGCTGAT
* * * *
424630 GTTGATTATATGTTTGGGATCCAATGTTTCCACCTTGCTGCTGTTGTGGCAGCTGATTATATGTT
1 GTTGAGTAAATGTTTGGGATCCAATGTTTCCACCTAGCTGCTGTTGTGGCAGCTGAGTATATGTT
** * *
424695 TGGGACTCTGTGTTTCCACCTTGTTGCT
66 TGGGACTCAATGTTTCCACCTTGCTGAT
424723 GTTG
1 GTTG
424727 TGGGAGCCGA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 86 0.99
94 1 0.01
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (93 bp):
GTTGAGTAAATGTTTGGGATCCAATGTTTCCACCTAGCTGCTGTTGTGGCAGCTGAGTATATGTT
TGGGACTCAATGTTTCCACCTTGCTGAT
Found at i:424751 original size:51 final size:51
Alignment explanation
Indices: 424654--424771 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
424644 TGGGATCCAA
* ** * * **
424654 TGTTTCCACCTTGCTGCTGTTGTGGCAGCTGATTATATGTTTGGGACTCTG
1 TGTTTCCACCTTGCTGCTGTTGTGGCAGCCGAGAAAATATCAGGGACTCTG
* * *
424705 TGTTTCCACCTTGTTGCTGTTGTGGGAGCCGAGAAAATATCAGGGACTTTG
1 TGTTTCCACCTTGCTGCTGTTGTGGCAGCCGAGAAAATATCAGGGACTCTG
424756 TGTTTCCACCTTGCTG
1 TGTTTCCACCTTGCTG
424772 AGTTGGTACC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.38
Consensus pattern (51 bp):
TGTTTCCACCTTGCTGCTGTTGTGGCAGCCGAGAAAATATCAGGGACTCTG
Found at i:424760 original size:144 final size:143
Alignment explanation
Indices: 424485--424776 Score: 338
Period size: 144 Copynumber: 2.0 Consensus size: 143
424475 TTGTTGTGGT
* * *
424485 AGTTGAGTAAATGTTTGGGAATCAATGTTTCCACCTTGTTGCTGTTGTGGTAGTTGAGTAAATGT
1 AGTTGAGTAAATGTTTGGGAATCAATGTTTCCACCTTGCTGCTGTTGTGGCAGCTGAGTAAATGT
* * * * * **
424550 TTGGGATCCAATGTTTCCACCTAGCTGCTGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGT
66 TTGGGATCCAATGTTTCCACCTAGCTGCTGTTGTGGGAGCCGAGAAAATATCAGGGATCCAATGT
424615 TTCCACCTTGCTG
131 TTCCACCTTGCTG
* * * *
424628 ATGTTGATTATATGTTTGGG-ATCCAATGTTTCCACCTTGCTGCTGTTGTGGCAGCTGATTATAT
1 A-GTTGAGTAAATGTTTGGGAAT-CAATGTTTCCACCTTGCTGCTGTTGTGGCAGCTGAGTAAAT
** * * **
424692 GTTTGGGA-CTCTGTGTTTCCACCTTGTTGCTGTTGTGGGAGCCGAGAAAATATCAGGGA-CTTT
64 GTTTGGGATC-CAATGTTTCCACCTAGCTGCTGTTGTGGGAGCCGAGAAAATATCAGGGATC-CA
*
424755 GTGTTTCCACCTTGCTG
127 ATGTTTCCACCTTGCTG
424772 AGTTG
1 AGTTG
424777 GTACCAAGGA
Statistics
Matches: 124, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
143 9 0.07
144 115 0.93
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (143 bp):
AGTTGAGTAAATGTTTGGGAATCAATGTTTCCACCTTGCTGCTGTTGTGGCAGCTGAGTAAATGT
TTGGGATCCAATGTTTCCACCTAGCTGCTGTTGTGGGAGCCGAGAAAATATCAGGGATCCAATGT
TTCCACCTTGCTG
Found at i:426835 original size:12 final size:13
Alignment explanation
Indices: 426808--426833 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
426798 GGGTCGGATA
426808 TCGAGGATTTTTT
1 TCGAGGATTTTTT
426821 TCGAGGATTTTTT
1 TCGAGGATTTTTT
426834 CGGGTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.23, T:0.54
Consensus pattern (13 bp):
TCGAGGATTTTTT
Found at i:426883 original size:2 final size:2
Alignment explanation
Indices: 426876--426972 Score: 90
Period size: 2 Copynumber: 54.0 Consensus size: 2
426866 CCGCCCCGAT
426876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
426918 -A TA T- TT TA TA T- TA -A T- TA TA TA TA -A TA T- TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
426953 T- TT TA TA T- TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
426973 AAATATTTTC
Statistics
Matches: 81, Mismatches: 3, Indels: 22
0.76 0.03 0.21
Matches are distributed among these distances:
1 11 0.14
2 70 0.86
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:426973 original size:32 final size:34
Alignment explanation
Indices: 426898--426978 Score: 121
Period size: 32 Copynumber: 2.4 Consensus size: 34
426888 TATATATATA
426898 TATATATATATATATATATAATATTTTATATTAAT
1 TATATATA-ATATATATATAATATTTTATATTAAT
*
426933 TATATATAATAT-TTTAT-ATATTTTATATTAAT
1 TATATATAATATATATATAATATTTTATATTAAT
*
426965 TATATATAAAATAT
1 TATATATAATATAT
426979 TTTCGGGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 26 0.60
33 5 0.12
34 4 0.09
35 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
TATATATAATATATATATAATATTTTATATTAAT
Found at i:432941 original size:36 final size:31
Alignment explanation
Indices: 432866--432948 Score: 130
Period size: 31 Copynumber: 2.7 Consensus size: 31
432856 GAGTATTATT
* * *
432866 GAGTTCGATTCGATTTGAAAATTTTGAAATA
1 GAGTTCGACTCGACTTGAAAATTCTGAAATA
432897 GAGTTCGACTCGACTTGAAAATTCTGAAATA
1 GAGTTCGACTCGACTTGAAAATTCTGAAATA
*
432928 GAGTTTGACTCGACTTGAAAA
1 GAGTTCGACTCGACTTGAAAA
432949 CTCGCGAGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (31 bp):
GAGTTCGACTCGACTTGAAAATTCTGAAATA
Found at i:435017 original size:26 final size:23
Alignment explanation
Indices: 434987--435040 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
434977 TAATCTTGGG
434987 TTTTTAGACTAGTTTCTCTTCATTCT
1 TTTTTAG-CT-GTTTCTCTTC-TTCT
*
435013 TTTTT-GCTGTTTTTCTTCTTCT
1 TTTTTAGCTGTTTCTCTTCTTCT
435035 TTTTTA
1 TTTTTA
435041 ATGTGAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 9 0.35
23 9 0.35
24 2 0.08
25 1 0.04
26 5 0.19
ACGTcount: A:0.09, C:0.17, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTTTAGCTGTTTCTCTTCTTCT
Found at i:440389 original size:134 final size:134
Alignment explanation
Indices: 440181--440447 Score: 525
Period size: 134 Copynumber: 2.0 Consensus size: 134
440171 TTTTAATAAG
*
440181 TATTAAACTCATAATTTAAGGTAGAGAAGAAATGTTAACTGAAAATTTTTAATCACTTACTATAA
1 TATTAAACTCATAATTTAAGGTAGAGAAGAAATGTCAACTGAAAATTTTTAATCACTTACTATAA
440246 AGATTATTGATAATTTATGTTGAAGACTTTAATTTGATATATCTGAATAACCAATATAAAATACT
66 AGATTATTGATAATTTATGTTGAAGACTTTAATTTGATATATCTGAATAACCAATATAAAATACT
440311 AATT
131 AATT
440315 TATTAAACTCATAATTTAAGGTAGAGAAGAAATGTCAACTGAAAATTTTTAATCACTTACTATAA
1 TATTAAACTCATAATTTAAGGTAGAGAAGAAATGTCAACTGAAAATTTTTAATCACTTACTATAA
440380 AGATTATTGATAATTTATGTTGAAGACTTTAATTTGATATATCTGAATAACCAATATAAAATACT
66 AGATTATTGATAATTTATGTTGAAGACTTTAATTTGATATATCTGAATAACCAATATAAAATACT
440445 AAT
131 AAT
440448 AATGATGGGA
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 132 1.00
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.37
Consensus pattern (134 bp):
TATTAAACTCATAATTTAAGGTAGAGAAGAAATGTCAACTGAAAATTTTTAATCACTTACTATAA
AGATTATTGATAATTTATGTTGAAGACTTTAATTTGATATATCTGAATAACCAATATAAAATACT
AATT
Found at i:440855 original size:31 final size:29
Alignment explanation
Indices: 440783--440859 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 29
440773 ATTAAAGTTT
*
440783 ATTTTTTAATTTAATTACTTAAATTTCAA
1 ATTTTTTAATTTAATCACTTAAATTTCAA
* * *
440812 ATTACTTCTAATTTAATCACTCTAACTTTTAA
1 ATT--TTTTAATTTAATCACT-TAAATTTCAA
440844 ACTTTTTTAATTTAAT
1 A-TTTTTTAATTTAAT
440860 TATATATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 3 0.08
31 25 0.64
32 9 0.23
33 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTTTTTAATTTAATCACTTAAATTTCAA
Found at i:465735 original size:24 final size:24
Alignment explanation
Indices: 465703--465753 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
465693 TGTTCAAGTA
465703 ATCCAATTTCACTATTTAAATTAT
1 ATCCAATTTCACTATTTAAATTAT
465727 ATCCAATTTCACTATTTAAATTAT
1 ATCCAATTTCACTATTTAAATTAT
465751 ATC
1 ATC
465754 TATGCGTTAT
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:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (24 bp):
ATCCAATTTCACTATTTAAATTAT
Found at i:467213 original size:16 final size:17
Alignment explanation
Indices: 467192--467223 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
467182 TCCTTTCCCA
467192 TTCATTA-ATTCAATAT
1 TTCATTAGATTCAATAT
467208 TTCATTAGATTCAATA
1 TTCATTAGATTCAATA
467224 GGAATATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (17 bp):
TTCATTAGATTCAATAT
Found at i:470963 original size:25 final size:26
Alignment explanation
Indices: 470935--470995 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 26
470925 AGATTAGTTT
470935 TAAAAAACAAAT-AAATAAA-TAAGAA
1 TAAAAAACAAATGAAATAAAGTAA-AA
470960 TAAAAAA-AAATGAAATAAAGTAAAA
1 TAAAAAACAAATGAAATAAAGTAAAA
*
470985 TAGAAAACAAA
1 TAAAAAACAAA
470996 ATTAAAAGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 4 0.12
25 22 0.69
26 6 0.19
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (26 bp):
TAAAAAACAAATGAAATAAAGTAAAA
Found at i:472274 original size:2 final size:2
Alignment explanation
Indices: 472269--472308 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
472259 AATATTTAAA
472269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
472309 GGTTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:472368 original size:35 final size:34
Alignment explanation
Indices: 472329--472625 Score: 114
Period size: 38 Copynumber: 7.9 Consensus size: 34
472319 AAAAAAAAAA
*
472329 TTAAAATCATATAATACATATTTTCAAATAATGTT
1 TTAAAATCATATAATATATATTTTCAAA-AATGTT
* *
472364 TTAAAATTATATATTATATATATACTTTCTAAAAAAGGTT
1 TTAAAATCATATA--ATATATAT--TTTC--AAAAATGTT
*
472404 TTCAAAATCATATACTATATAGTTTTC-AAAATGATT
1 TT-AAAATCATATAATATATA-TTTTCAAAAATG-TT
* * * *
472440 TTAAAAACTATATATTATAAATATTTTTCAAACTGATTTT
1 TTAAAATC-ATATA--ATATATA-TTTTCAAA--AATGTT
* **
472480 TTCAAAATTATATATTATATATATATTTTTAAAATGTT
1 TT-AAAATCATATA--ATATATAT-TTTCAAAAATGTT
* *
472518 TTCGAAAATTATATTATATATA-TTTC-AAAATGTTTTT
1 TT--AAAATCATATAATATATATTTTCAAAAATG---TT
* * *
472555 TTCAAAAACTATATAATATATATGTTTTCACAAATATT
1 TT-AAAATC-ATATAATATATA--TTTTCAAAAATGTT
* *
472593 TTCAAAAACTATATGATATATATGTTTTCAAAA
1 TT-AAAATC-ATAT-A-ATATATATTTTCAAAA
472626 TCCATATATT
Statistics
Matches: 204, Mismatches: 30, Indels: 53
0.71 0.10 0.18
Matches are distributed among these distances:
34 6 0.03
35 25 0.12
36 13 0.06
37 29 0.14
38 44 0.22
39 24 0.12
40 40 0.20
41 23 0.11
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (34 bp):
TTAAAATCATATAATATATATTTTCAAAAATGTT
Found at i:472468 original size:38 final size:38
Alignment explanation
Indices: 472366--472626 Score: 177
Period size: 38 Copynumber: 6.8 Consensus size: 38
472356 ATAATGTTTT
* * * *
472366 AAAATTATATATTATATATATACTTTCTAAAAAAGGTTTTCA
1 AAAACTATATATTATA-ATAT--TTT-TCAAAATGATTTTCA
* * *
472408 AAATC-ATATACTAT-ATAGTTTTCAAAATGATTTT-A
1 AAAACTATATATTATAATATTTTTCAAAATGATTTTCA
*
472443 AAAACTATATATTATAAATATTTTTCAAACTGATTTTTTC-
1 AAAACTATATATTAT-AATATTTTTCAAAATGA--TTTTCA
* * *
472483 AAAATTATATATTATATATATATTTTTAAAATG-TTTTCG
1 AAAACTATATATTATA-ATAT-TTTTCAAAATGATTTTCA
* *
472522 AAAA-T-TATATTAT-ATATATTTCAAAATGTTTTTTTCA
1 AAAACTATATATTATAATATTTTTCAAAATG--ATTTTCA
*
472559 AAAACTATATAATAT-ATATGTTTTCACAAAT-ATTTTCA
1 AAAACTATATATTATAATAT-TTTTCA-AAATGATTTTCA
472597 AAAACTATATGA-TAT-ATATGTTTTCAAAAT
1 AAAACTATAT-ATTATAATAT-TTTTCAAAAT
472627 CCATATATTA
Statistics
Matches: 182, Mismatches: 20, Indels: 39
0.76 0.08 0.16
Matches are distributed among these distances:
34 9 0.05
35 9 0.05
36 18 0.10
37 24 0.13
38 51 0.28
39 20 0.11
40 27 0.15
41 21 0.12
42 3 0.02
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (38 bp):
AAAACTATATATTATAATATTTTTCAAAATGATTTTCA
Found at i:472482 original size:76 final size:76
Alignment explanation
Indices: 472331--472626 Score: 240
Period size: 76 Copynumber: 3.9 Consensus size: 76
472321 AAAAAAAATT
* *
472331 AAAATCATATAATACATA--TTTTCAAATAATG-TTTT--AAAATTATATATTATATATATACTT
1 AAAATCATATAATATATATGTTTTC-AA-AATGATTTTCAAAAACTATATA-T-TATATATA-TT
* **
472391 TCTAAAA-AAGGTTTTC
61 TC-AAAATGATTTTTTC
* *
472407 AAAATCATATACTATATA-GTTTTCAAAATGATTTT-AAAAACTATATATTATAAATATTTTTCA
1 AAAATCATATAATATATATGTTTTCAAAATGATTTTCAAAAACTATATATTAT--ATATATTTCA
*
472470 AACTGATTTTTTC
64 AAATGATTTTTTC
* * * *
472483 AAAATTATATATTATATATATATTTTTAAAATG-TTTTCGAAAA-T-TATATTATATATATTTCA
1 AAAATCATATA--ATATATATGTTTTCAAAATGATTTTCAAAAACTATATATTATATATATTTCA
*
472545 AAATGTTTTTTTC
64 AAATGATTTTTTC
* *
472558 AAAAACTATATAATATATATGTTTTCACAAAT-ATTTTCAAAAACTATATGA-TATATATGTTTT
1 AAAATC-ATATAATATATATGTTTTCA-AAATGATTTTCAAAAACTATAT-ATTATATAT-ATTT
472621 CAAAAT
62 CAAAAT
472627 CCATATATTA
Statistics
Matches: 181, Mismatches: 22, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
74 13 0.07
75 47 0.26
76 49 0.27
77 37 0.20
78 21 0.12
79 14 0.08
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (76 bp):
AAAATCATATAATATATATGTTTTCAAAATGATTTTCAAAAACTATATATTATATATATTTCAAA
ATGATTTTTTC
Found at i:472595 original size:75 final size:74
Alignment explanation
Indices: 472402--472615 Score: 220
Period size: 75 Copynumber: 2.8 Consensus size: 74
472392 CTAAAAAAGG
* *
472402 TTTTCAAAATC-ATATACTATATA-GTTTTCAAAATGATTTT-AAAAACTATATATTATAAATAT
1 TTTTCAAAAACTATATAATATATATGTTTTCAAAAT-ATTTTCAAAAA-T-TATATTAT--ATAT
* *
472464 TTTTCAAACTGATT
61 ATTTCAAAATGATT
* * * * *
472478 TTTTCAAAATTA-TATATTATATATATATTTTTAAAATGTTTTCGAAAATTATATTATATATATT
1 TTTTCAAAA--ACTATATAATATATATGTTTTCAAAATATTTTCAAAAATTATATTATATATATT
*
472542 TCAAAATGTTT
64 TCAAAATGATT
* *
472553 TTTTCAAAAACTATATAATATATATGTTTTCACAAATATTTTCAAAAACTATATGATATATAT
1 TTTTCAAAAACTATATAATATATATGTTTTCA-AAATATTTTCAAAAATTATATTATATATAT
472616 GTTTTCAAAA
Statistics
Matches: 114, Mismatches: 17, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
73 1 0.01
74 18 0.16
75 50 0.44
76 9 0.08
77 8 0.07
78 15 0.13
79 13 0.11
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (74 bp):
TTTTCAAAAACTATATAATATATATGTTTTCAAAATATTTTCAAAAATTATATTATATATATTTC
AAAATGATT
Found at i:472618 original size:101 final size:99
Alignment explanation
Indices: 472513--472716 Score: 249
Period size: 101 Copynumber: 2.0 Consensus size: 99
472503 TATTTTTAAA
*
472513 ATGTTTTCGAAAAT-TATATTATATATATTTCAAAATG-TTT-TTTTCA-AAAACTATATAATAT
1 ATGTTTTC-AAAATCTATATTATATAT-TTTCAAAATGTTTTCTTTTCAGAAAACCATATAATAT
472574 ATATGTTTTCACAAAT-ATTTTCAAAAACTAT-ATGATATAT
64 ATA-GTTTTCA-AAATGA-TTTC--AAACTATAAT-ATATAT
* *
472614 ATGTTTTCAAAATCCATATATTATATATTTTCAAAATGTTTTCTTTTTAGAAAACCATATATTAT
1 ATGTTTTCAAAAT-C-TATATTATATATTTTCAAAATGTTTTCTTTTCAGAAAACCATATAATAT
472679 ATAGTTTTCAAAATGATTTCAAACTATAATATATAT
64 ATAGTTTTCAAAATGATTTCAAACTATAATATATAT
472715 AT
1 AT
472717 ATATATAATA
Statistics
Matches: 92, Mismatches: 3, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
100 5 0.05
101 23 0.25
102 12 0.13
103 23 0.25
104 13 0.14
105 16 0.17
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.46
Consensus pattern (99 bp):
ATGTTTTCAAAATCTATATTATATATTTTCAAAATGTTTTCTTTTCAGAAAACCATATAATATAT
AGTTTTCAAAATGATTTCAAACTATAATATATAT
Found at i:472622 original size:26 final size:24
Alignment explanation
Indices: 472588--472649 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 24
472578 GTTTTCACAA
*
472588 ATATTTTCAAAAACTATATGATATAT
1 ATATTTTCAAAAACCATAT-AT-TAT
* *
472614 ATGTTTTCAAAATCCATATATTAT
1 ATATTTTCAAAAACCATATATTAT
472638 ATATTTTCAAAA
1 ATATTTTCAAAA
472650 TGTTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 14 0.44
25 2 0.06
26 16 0.50
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (24 bp):
ATATTTTCAAAAACCATATATTAT
Found at i:473538 original size:84 final size:83
Alignment explanation
Indices: 473317--474134 Score: 754
Period size: 84 Copynumber: 9.9 Consensus size: 83
473307 GTTTGCCTCT
* * * * *
473317 GAGCTGAGTGTAATCGAACTCGTAGGTCTTTG--G-CAGATAGCCCTTCTCGACTTAAGTTATAC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGC
* *
473379 TACAAATGATGTGCCCTCG
66 TGCAAATGATGTG-CCTTG
* * * * *
473398 AAGCTGAGTGTAATCGAACTCG-AGAGTCTTTG--G-CAGATAGCCCTTATCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAG-GTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATG
*
473459 CTGCAAATTATGTGCCTTG
65 CTGCAAATGATGTGCCTTG
* * * * * *
473478 GAGTTGAACGTAGTCAAACTCAAAGGTATTTGATTGACATATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG-TTGACAGATAACCCTTCTCGACTTAAGTTATG
* *
473543 TTGCAAATGATGTGCCCTCG
65 CTGCAAATGATGTG-CCTTG
* * * * * ** *
473563 AAGCTGTGTGTAATCGAACTCG-AGAGTCTTTG--G-CATATAGTCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAG-GTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATG
*
473624 CTGCAAATGATGTGTCTTG
65 CTGCAAATGATGTGCCTTG
* * * *
473643 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGACTTAAGTTATG
* *
473708 TTGCAAATGATATGCCTTG
65 CTGCAAATGATGTGCCTTG
* * *
473727 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTT-ACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATG
* ** * *
473791 ATGTGAATGATATACCCTTG
65 CTGCAAATGATGT-GCCTTG
* * * * ** * * *
473811 AAGCTGAGTGTAATCAAACTCGGGGGTCTTTG--G-CAGATAGCCATTCTCGACTTAAGCTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGC
*
473873 TACAAATGATGTGCCTTG
66 TGCAAATGATGTGCCTTG
* *
473891 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTATTGGA-AGATAACCCTTCTTGACTTAAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTT-GACAGATAACCCTTCTCGACTTAAGTTAT
*
473955 GCTGCAAATGATGTGCCCTCG
64 GCTGCAAATGATGTG-CCTTG
* * * * ** * * * *
473976 AAGCTGAGTGTAATCAAACTCGGGGGT-ATT-TTGTCAGATAACCCTTCTCGACTTAAGCTATGT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGC
*
474039 TGCAAATGATGTGTCTTG
66 TGCAAATGATGTGCCTTG
* * * *
474057 GAGCTGAGCGTAGTCGAACTCGAAGGTATTTTATTGGCAGATAACCCTTCTTGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGT-CTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATG
474122 CTGCAAATGATGT
65 CTGCAAATGATGT
474135 CTTAAAAAAT
Statistics
Matches: 598, Mismatches: 113, Indels: 49
0.79 0.15 0.06
Matches are distributed among these distances:
80 78 0.13
81 171 0.29
82 41 0.07
83 44 0.07
84 215 0.36
85 49 0.08
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (83 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGC
TGCAAATGATGTGCCTTG
Found at i:473557 original size:165 final size:162
Alignment explanation
Indices: 473310--474134 Score: 777
Period size: 165 Copynumber: 5.0 Consensus size: 162
473300 AAATTTGGTT
* * * * *
473310 TGCCTCTG-AGCTGAGTGTAATCGAACTCGTAGGTCTTTG--GCAGATAGCCCTTCTCGACTTAA
1 TGCCT-TGAAGCTGAGCGTAATCAAACTCGAAGGTATTTGTTGCAGATAACCCTTCTCGACTTAA
** * * * * *
473372 GTTATACTACAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGAGTCTTTGGCAGATA
65 GTTATGTTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAGAGTCTTTGGCAGATA
* * *
473437 GCCCTTATCGACTTAAGTTATGCTGCAAATTATG
129 ACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * * * * *
473471 TGCCTTGGAGTTGAACGTAGTCAAACTCAAAGGTATTTGATTGACATATAACCCTTCTCGACTTA
1 TGCCTTGAAGCTGAGCGTAATCAAACTCGAAGGTATTTG-TTG-CAGATAACCCTTCTCGACTTA
* * * * * *
473536 AGTTATGTTGCAAATGATGTGCCCTCGAAGCTGTGTGTAATCGAACTCGAGAGTCTTTGGCATAT
64 AGTTATGTTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAGAGTCTTTGGCAGAT
** *
473601 AGTCCTTCTCGACTTAAGCTATGCTGCAAATGATG
128 AACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * * * * * *
473636 TGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTA
1 TGCCTTGAAGCTGAGCGTAATCAAACTCGAAGGT-ATTTGTT-GCAGATAACCCTTCTCGACTTA
* *
473701 AGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGA-AGGTCTTTGGTTACA
64 AGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAGA-GTCTTTGG---CA
* * * * ** *
473765 GATAACCCTTCTAGCCTTGAGTTATGATGTGAATGATA
125 GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * ** * * *
473803 TACCCTTGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTG--GCAGATAGCCATTCTCGACTTAA
1 T-GCCTTGAAGCTGAGCGTAATCAAACTCGAAGGTATTTGTTGCAGATAACCCTTCTCGACTTAA
* * * *
473866 GCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGA-AGGTCTTTTATTGGAA
65 GTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAGA-GTC---T-TTGGCA
*
473930 GATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATG
125 GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * **
473968 TGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTA-TT-TTGTCAGATAACCCTTCTCGACTTA
1 TG-CCTTGAAGCTGAGCGTAATCAAACTCGAAGGTATTTGTTG-CAGATAACCCTTCTCGACTTA
* * * *
474031 AGCTATGTTGCAAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTATTGGCA
64 AGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCG-A-G-AGTCT-TTGGCA
*
474096 GATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATG
125 GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
474134 T
1 T
474135 CTTAAAAAAT
Statistics
Matches: 557, Mismatches: 83, Indels: 43
0.82 0.12 0.06
Matches are distributed among these distances:
160 2 0.00
161 28 0.05
163 1 0.00
164 101 0.18
165 243 0.44
166 115 0.21
167 36 0.06
168 29 0.05
169 1 0.00
170 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (162 bp):
TGCCTTGAAGCTGAGCGTAATCAAACTCGAAGGTATTTGTTGCAGATAACCCTTCTCGACTTAAG
TTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAGAGTCTTTGGCAGATAAC
CCTTCTCGACTTAAGTTATGCTGCAAATGATG
Found at i:473844 original size:248 final size:246
Alignment explanation
Indices: 473318--474134 Score: 885
Period size: 248 Copynumber: 3.3 Consensus size: 246
473308 TTTGCCTCTG
* *
473318 AGCTGAGTGTAATCGAACTCGTA-GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATACTAC
1 AGCTGAGTGTAATCGAACTCG-AGGGTCTTTGGCAGATAG-CCTTCTCGACTTAAGCTATGCTAC
* * * * *
473382 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG-AGAGTC---TTTGGCAGATAGCCCTT
64 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAG-GTCTTTTTTGGCAGATAACCCTT
* * * * * *
473443 ATCGACTTAAGTTATGCTGCAAATTATGTGCCTTGGAGTTGAACGTAGTCAAACTCAAAGGTATT
127 CTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTATT
* * * * * *
473508 TGATTGACATATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGA
192 TGGTT-ACAGATAACCCTTCTAGACTTAAGTTATGATGCAAATGATATACCCTCGA
* * * *
473564 AGCTGTGTGTAATCGAACTCGAGAGTCTTTGGCATATAGTCCTTCTCGACTTAAGCTATGCTGCA
1 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAG-CCTTCTCGACTTAAGCTATGCTACA
* *
473629 AATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCT
65 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT-TTGGCAGATAACCCTTCT
* * * * *
473694 AGACTTAAGTTGTGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
129 AGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTATTTG
* * ** *
473759 GTTACAGATAACCCTTCTAGCCTTGAGTTATGATGTGAATGATATACCCTTGA
194 GTTACAGATAACCCTTCTAGACTTAAGTTATGATGCAAATGATATACCCTCGA
* *
473812 AGCTGAGTGTAATCAAACTCGGGGGTCTTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTACA
1 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCC-TTCTCGACTTAAGCTATGCTACA
*
473877 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTATTGGAAGATAACCCTTCT
65 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT-TTGGCAGATAACCCTTCT
* * * * * **
473942 TGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTATTT
129 AGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTATTT
* * * * * ** * *
474007 TG-T-CAGATAACCCTTCTCGACTTAAGCTATGTTGCAAATGATGT-GTCTTGG
193 GGTTACAGATAACCCTTCTAGACTTAAGTTATGATGCAAATGATATACCCTCGA
* * * * * * *
474058 AGCTGAGCGTAGTCGAACTCGAAGGTATTTTATTGGCAGATAACCCTTCTTGACTTAAGTTATGC
1 AGCTGAGTGTAATCGAACTCG-AGG--GTCT-TTGGCAGAT-AGCCTTCTCGACTTAAGCTATGC
*
474123 TGCAAATGATGT
61 TACAAATGATGT
474135 CTTAAAAAAT
Statistics
Matches: 478, Mismatches: 80, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
245 26 0.05
246 89 0.19
247 37 0.08
248 183 0.38
249 103 0.22
250 37 0.08
251 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (246 bp):
AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCTTCTCGACTTAAGCTATGCTACAA
ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTTTGGCAGATAACCCTTCTAG
ACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTATTTGGT
TACAGATAACCCTTCTAGACTTAAGTTATGATGCAAATGATATACCCTCGA
Found at i:473887 original size:413 final size:411
Alignment explanation
Indices: 473317--474132 Score: 1152
Period size: 413 Copynumber: 2.0 Consensus size: 411
473307 GTTTGCCTCT
* * * *
473317 GAGCTGAGTGTAATCGAACTCGTAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATACTAC
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATACTAC
* * * *
473382 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGAGTCTTTGGCAGATAGCCCTTATCG
66 AAATGATATACCCTCGAAGCTGAGTGTAATCAAACTCGAGAGTCTTTGGCAGATAGCCATTATCG
* * * *
473447 ACTTAAGTTATGCTGCAAATTATGTGCCTTGGAGTTGAACGTAGTCAAACTCAAAGGTATTTGAT
131 ACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAACGTAGTCAAACTCAAAGGTATTTGAT
* * *
473512 T-GACATATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGAAGCTGTGTGTAA
196 TGGA-AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* * **
473576 TCGAACTCGAGAGT-CTTTGGCATATAGTCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTC
260 TCAAACTCGAGAGTACTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTC
* *
473640 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
325 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTATTGGCAGACAACCCTTCTAGACTTAAGTT
* *
473705 GTGTTGCAAATGATATGCCTTG
390 ATGCTGCAAATGATATGCCTTG
* * *
473727 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGA
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGG---CAGATAACCCTTCTAGACTTAAGTTAT-A
*** * * *
473792 -TGTGAATGATATACCCTTGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGCAGATAGCCATT
62 CTACAAATGATATACCCTCGAAGCTGAGTGTAATCAAACTCGAGAGTCTTTGGCAGATAGCCATT
* * * * *
473856 CTCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
127 ATCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAACGTAGTCAAACTCAAAGGTATT
* *
473921 TTATTGGAAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
192 TGATTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
* * * * *
473986 TAATCAAACTCGGGGGTATTTTGTCAGATAACCCTTCTCGACTTAAGCTATGTTGCAAATGATGT
257 TAATCAAACTCGAGAGTACTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* *
474051 GTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTATTGGCAGATAACCCTTCTTGACTTAA
322 GTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTATTGGCAGACAACCCTTCTAGACTTAA
474116 GTTATGCTGCAAATGAT
387 GTTATGCTGCAAATGAT
474133 GTCTTAAAAA
Statistics
Matches: 354, Mismatches: 46, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
410 30 0.08
413 204 0.58
414 120 0.34
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (411 bp):
GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATACTAC
AAATGATATACCCTCGAAGCTGAGTGTAATCAAACTCGAGAGTCTTTGGCAGATAGCCATTATCG
ACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAACGTAGTCAAACTCAAAGGTATTTGAT
TGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
CAAACTCGAGAGTACTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCT
TGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTATTGGCAGACAACCCTTCTAGACTTAAGTTA
TGCTGCAAATGATATGCCTTG
Found at i:480639 original size:9 final size:10
Alignment explanation
Indices: 480616--480643 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
480606 TAATGAATTA
480616 AAAAAATAAT
1 AAAAAATAAT
480626 AAAAAATAAT
1 AAAAAATAAT
480636 AAAAAATA
1 AAAAAATA
480644 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:480727 original size:35 final size:34
Alignment explanation
Indices: 480688--481020 Score: 122
Period size: 40 Copynumber: 9.0 Consensus size: 34
480678 TTTAAAAAAA
*
480688 TAAAATCATATAATACATATTTTCAAATAATGTTT
1 TAAAATCATATAATATATATTTTCAAA-AATGTTT
* *
480723 TAAAATTATATATTATATATATACTTTCTAAAAAAGTTT
1 TAAAATCATATA--ATATATAT--TTTC-AAAAATGTTT
*
480762 TCAAAATCATATACTATATAGTTTTC-AAAATGATTT
1 T-AAAATCATATAATATATA-TTTTCAAAAATG-TTT
* * * * *
480798 TAAAAACTATATATTATAAATATTTTTGAAACTGATTTTT
1 TAAAATC-ATATA--ATATATA-TTTTCAAA--AATGTTT
* ** *
480838 TCAAAATTATATATTATATATATTTTTTAAAATATTT
1 T-AAAATCATATA--ATATATATTTTCAAAAATGTTT
*
480875 TCAAAA--ATTATAATATATATATTTCAAAATATTTTT
1 T-AAAATCA-TATAATATATAT-TTTCAAAA-ATGTTT
* * * *
480911 TAAAATAAATTATATAATATATATGTTTTTACAAATATTT
1 T---A-AAATCATATAATATATA--TTTTCAAAAATGTTT
* *
480951 TCAAAAAC-TATATATATATGTTTTCAAAAAATGTTT
1 T-AAAATCATATA-ATATATATTTTC-AAAAATGTTT
* *
480987 TCAAAAACCACAT-AT-TATATTTTC-AAAATGTTT
1 T--AAAATCATATAATATATATTTTCAAAAATGTTT
481020 T
1 T
481021 CATTTTAAAA
Statistics
Matches: 231, Mismatches: 38, Indels: 60
0.70 0.12 0.18
Matches are distributed among these distances:
33 10 0.04
34 8 0.03
35 40 0.17
36 34 0.15
37 36 0.16
38 19 0.08
39 23 0.10
40 47 0.20
41 13 0.06
42 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (34 bp):
TAAAATCATATAATATATATTTTCAAAAATGTTT
Found at i:480861 original size:40 final size:37
Alignment explanation
Indices: 480720--480969 Score: 158
Period size: 40 Copynumber: 6.6 Consensus size: 37
480710 TCAAATAATG
*
480720 TTTT-AAAATTATATATTATATATATACTTTCT-AAAAAA
1 TTTTCAAAATTATATATTATATATAT--TTT-TGAAAATA
* * * *
480758 GTTTTCAAAATCATATA--CTATATAGTTTTCAAAATGA
1 -TTTTCAAAATTATATATTATATATATTTTTGAAAAT-A
* * * *
480795 TTTTAAAAACTATATATTATAAATATTTTTGAAACTGATT
1 TTTTCAAAATTATATATTATATATATTTTTGAAA---ATA
*
480835 TTTTCAAAATTATATATTATATATATTTTTTAAAATA
1 TTTTCAAAATTATATATTATATATATTTTTGAAAATA
*
480872 TTTTCAAAAATTATA-A-TATATATA--TTTCAAAATA
1 TTTTC-AAAATTATATATTATATATATTTTTGAAAATA
* * * *
480906 TTTTTTAAAATAAATTATATAATATATATGTTTTTACAAATA
1 -TTTTCAAAAT-TA-TATATTATATATAT-TTTTGA-AAATA
*
480948 TTTTCAAAAACTATATA-TATAT
1 TTTTC-AAAATTATATATTATAT
480970 GTTTTCAAAA
Statistics
Matches: 166, Mismatches: 26, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
34 14 0.08
35 6 0.04
36 30 0.18
37 10 0.06
38 34 0.20
39 8 0.05
40 44 0.27
41 11 0.07
42 9 0.05
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (37 bp):
TTTTCAAAATTATATATTATATATATTTTTGAAAATA
Found at i:480897 original size:76 final size:74
Alignment explanation
Indices: 480835--480993 Score: 66
Period size: 76 Copynumber: 2.1 Consensus size: 74
480825 GAAACTGATT
* *
480835 TTTTC-AAAATTATATATTATATATATTTTTTAAAATA--TTTTCAAAA-ATTATA-ATATATAT
1 TTTTCAAAAATTATA-A-TATATATATTTTTCAAAATATTTTTTCAAAATAATATATATATATAT
* *
480895 ATTTCAAAATA
64 TTTTTAAAATA
* * *
480906 TTTTTTAAAATAAATTAT-ATAATATATATGTTTTTACAAATA--TTTTCAAAA-ACTATATATA
1 --TTTT-CAA-AAATTATAAT-ATATATAT-TTTTCA-AAATATTTTTTCAAAATAATATATATA
* ** *
480967 TATGTTTTCAAAAAATG
59 TATATTTT-TTAAAATA
480984 TTTTCAAAAA
1 TTTTCAAAAA
480994 CCACATATTA
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
73 5 0.07
74 12 0.17
75 9 0.13
76 30 0.43
77 9 0.13
78 5 0.07
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (74 bp):
TTTTCAAAAATTATAATATATATATTTTTCAAAATATTTTTTCAAAATAATATATATATATATTT
TTTAAAATA
Found at i:480986 original size:13 final size:13
Alignment explanation
Indices: 480968--480993 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
480958 CTATATATAT
480968 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
480981 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
480994 CCACATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATGTTTTCAAAAA
Found at i:481175 original size:22 final size:21
Alignment explanation
Indices: 481147--481280 Score: 98
Period size: 22 Copynumber: 6.4 Consensus size: 21
481137 CGCAAATTCG
*
481147 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATT-T
** *
481169 CGTTGCGATTTTCCA-AATTT
1 CGTTGCGATAGTCTACAATTT
* *
481189 -GTTGCGACT-TTCCA-AATTT
1 CGTTGCGA-TAGTCTACAATTT
*
481208 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATT-T
* * *
481229 TGTTGCGATAGTTTACAAATT
1 CGTTGCGATAGTCTACAATTT
*
481250 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATT-T
481272 CGTTGCGAT
1 CGTTGCGAT
481281 TTTCCAAATT
Statistics
Matches: 92, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
18 1 0.01
19 27 0.29
20 5 0.05
21 21 0.23
22 38 0.41
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAATTT
Found at i:481194 original size:19 final size:19
Alignment explanation
Indices: 481170--481215 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
481160 TACAGTTGTC
481170 GTTGCGATTTTCCAAATTT
1 GTTGCGATTTTCCAAATTT
*
481189 GTTGCGACTTTCCAAATTT
1 GTTGCGATTTTCCAAATTT
481208 GTTGCGAT
1 GTTGCGAT
481216 AGTCTACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (19 bp):
GTTGCGATTTTCCAAATTT
Found at i:481255 original size:43 final size:41
Alignment explanation
Indices: 481189--481298 Score: 157
Period size: 43 Copynumber: 2.6 Consensus size: 41
481179 TTCCAAATTT
* * * *
481189 GTTGCGACTTTCCAAATTTGTTGCGATAGTCTACAGTTGTT
1 GTTGCGATTTTACAAATTCGTTGCGATAGTCTACAGTTGTC
481230 GTTGCGATAGTTTACAAATTCGTTGCGATAGTCTACAGTTGTC
1 GTTGCGAT--TTTACAAATTCGTTGCGATAGTCTACAGTTGTC
*
481273 GTTGCGATTTTCCAAATTCGTTGCGA
1 GTTGCGATTTTACAAATTCGTTGCGA
481299 AAATTCGTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
41 24 0.39
43 38 0.61
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (41 bp):
GTTGCGATTTTACAAATTCGTTGCGATAGTCTACAGTTGTC
Found at i:482458 original size:41 final size:41
Alignment explanation
Indices: 482401--482494 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
482391 CTTTTTTTTT
* *
482401 ACTATCGCAACGAATTTGGAAA-ATCACAACGATAACTGTAG
1 ACTATCGCAACAAATTTGGAAACATCACAACGACAACT-TAG
* *
482442 ACTATCGCAACAAATTTGGAAACTATCGCAACGACAACTTGG
1 ACTATCGCAACAAATTTGGAAAC-ATCACAACGACAACTTAG
*
482484 ACTATCACAAC
1 ACTATCGCAAC
482495 GCGAAATGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 21 0.46
42 12 0.26
43 13 0.28
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACAAATTTGGAAACATCACAACGACAACTTAG
Found at i:482487 original size:21 final size:20
Alignment explanation
Indices: 482401--482495 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 20
482391 CTTTTTTTTT
*
482401 ACTATCGCAACG-AATTTGG
1 ACTATCGCAACGAAACTTGG
** * *
482420 AAAATCACAACGATAACTGTAG
1 ACTATCGCAACGA-AACT-TGG
*
482442 ACTATCGCAAC-AAATTTGG
1 ACTATCGCAACGAAACTTGG
482461 AAACTATCGCAACGACAACTTGG
1 --ACTATCGCAACGA-AACTTGG
*
482484 ACTATCACAACG
1 ACTATCGCAACG
482496 CGAAATGGAA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
19 11 0.19
20 3 0.05
21 26 0.46
22 11 0.19
23 6 0.11
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (20 bp):
ACTATCGCAACGAAACTTGG
Found at i:498322 original size:24 final size:24
Alignment explanation
Indices: 498295--498399 Score: 173
Period size: 24 Copynumber: 4.5 Consensus size: 24
498285 GCATGGGTAG
498295 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
498319 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
498343 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
498367 TGCATCGATGCAC-TG-T--AGAA
1 TGCATCGATGCACATGTTAAAGAA
*
498387 TGTATCGATGCAC
1 TGCATCGATGCAC
498400 TTCAAGGGAA
Statistics
Matches: 80, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
20 16 0.20
22 1 0.01
23 2 0.03
24 61 0.76
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAAGAA
Found at i:499482 original size:32 final size:31
Alignment explanation
Indices: 499424--499510 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 31
499414 AGTCGAGGGT
499424 TTACCTATGTTTACGGAACATATGGACAGAA
1 TTACCTATGTTTACGGAACATATGGACAGAA
*
499455 TTACCTATGTCTTTC-GAGACATATGGACAG--
1 TTACCTATGT-TTACGGA-ACATATGGACAGAA
*
499485 TGTACCTATGTTCTAAGGAACATATG
1 T-TACCTATGTT-TACGGAACATATG
499511 AATTGTTTAC
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
30 2 0.04
31 29 0.60
32 17 0.35
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (31 bp):
TTACCTATGTTTACGGAACATATGGACAGAA
Found at i:501553 original size:19 final size:20
Alignment explanation
Indices: 501513--501564 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
501503 TCTTTGAGTA
501513 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGCTTAAGG-AAGC
501534 TTATATAAGCTTAAGG-AGC
1 TTATATAAGCTTAAGGAAGC
501553 TTATATAAGCTT
1 TTATATAAGCTT
501565 TAAACATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (20 bp):
TTATATAAGCTTAAGGAAGC
Found at i:502398 original size:19 final size:19
Alignment explanation
Indices: 502349--502400 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
502339 GAATGCAATT
*
502349 AGTGCATCGATCCATAAGG
1 AGTGCATCGATGCATAAGG
502368 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
502387 AGTGCATCGATGCA
1 AGTGCATCGATGCA
502401 CCCCCTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:502498 original size:20 final size:22
Alignment explanation
Indices: 502453--502510 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
502443 GTATGGGTAG
502453 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
502477 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
502497 TGTATCGATGCACT
1 TGCATCGATGCACT
502511 TCAAGGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:503612 original size:31 final size:31
Alignment explanation
Indices: 503527--503644 Score: 134
Period size: 31 Copynumber: 3.8 Consensus size: 31
503517 GTCGAGGGTT
* *
503527 TACCTATGTTCTACGGAACATATGGACAGAA
1 TACCTATGTTCTAAGGAACATATGGACAGTA
***
503558 TTACC--TG-TCTTTCGAGACATATGGACAGTA
1 -TACCTATGTTCTAAGGA-ACATATGGACAGTA
*
503588 TACCTATGTTCTAAGGAACATATGGACAATA
1 TACCTATGTTCTAAGGAACATATGGACAGTA
*
503619 TACGTATGTTCTAAGGAACATATGGA
1 TACCTATGTTCTAAGGAACATATGGA
503645 TAGTTTAGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
29 9 0.12
30 15 0.21
31 40 0.55
32 9 0.12
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:504553 original size:71 final size:71
Alignment explanation
Indices: 504437--504574 Score: 276
Period size: 71 Copynumber: 1.9 Consensus size: 71
504427 GTTTTGAAAA
504437 GTCAATGTGACACCTCGAACTCGGATTTGGGTCGGATACGAGTTGGGGGTGTTACACTATTTACC
1 GTCAATGTGACACCTCGAACTCGGATTTGGGTCGGATACGAGTTGGGGGTGTTACACTATTTACC
504502 TCAATG
66 TCAATG
504508 GTCAATGTGACACCTCGAACTCGGATTTGGGTCGGATACGAGTTGGGGGTGTTACACTATTTACC
1 GTCAATGTGACACCTCGAACTCGGATTTGGGTCGGATACGAGTTGGGGGTGTTACACTATTTACC
504573 TC
66 TC
504575 GGTAACTAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (71 bp):
GTCAATGTGACACCTCGAACTCGGATTTGGGTCGGATACGAGTTGGGGGTGTTACACTATTTACC
TCAATG
Found at i:506814 original size:23 final size:23
Alignment explanation
Indices: 506788--506835 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
506778 ATAAAGTACA
*
506788 ATAACATACTAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
** *
506811 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
506834 AT
1 AT
506836 TTACTTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:506957 original size:22 final size:21
Alignment explanation
Indices: 506913--506957 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
506903 TAATATGTTG
*
506913 AAAATGTCCATACTTTTTATA
1 AAAATGTCCATACTTTATATA
* *
506934 AAAATGATCGATACTTTATCTA
1 AAAATG-TCCATACTTTATATA
506956 AA
1 AA
506958 GTTATGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (21 bp):
AAAATGTCCATACTTTATATA
Found at i:507290 original size:23 final size:23
Alignment explanation
Indices: 507264--507326 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
507254 ATATAACCAC
507264 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
*
507287 TACCTATTACATTATATAAACGC
1 TACCTATTACATTATATAAACGA
*
507310 TACCTATTACATCATAT
1 TACCTATTACATTATAT
507327 TTTTACCTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:507718 original size:429 final size:429
Alignment explanation
Indices: 506910--508385 Score: 2715
Period size: 429 Copynumber: 3.4 Consensus size: 429
506900 TTATAATATG
* * *
506910 TTGAAAATGTCCATACTTTTTATAAAAATGATCGATACTTTATCTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
* * *
506975 TCAATTTTTTTTAATAGTGTTTCATGTTTTACACCTACAATATGAATTTAATAATTTCATTTGCA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
* *
507040 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAAAATTTTTAATTTAATAATA
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTTAATAATA
507105 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
194 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
**
507170 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGCAAAACAAGTATAGACACTTTTATAA
259 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAACAAGTATAGACACTTTTATAA
507235 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
324 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
*
507300 ATATAAACGCTACCTATTACATCATATTTTTACCTATTATA
389 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
507341 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
507406 TCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
*
507470 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAA
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTTAATAATAA
507535 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
195 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
*
507600 TCACTCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAACAAGTATAGACACTTTTATAAA
260 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAACAAGTATAGACACTTTTATAAA
507665 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
325 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
507730 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
390 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
*
507770 TTGAAAGTATCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
*
507835 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
*
507900 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAATAATAAT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATAAT
507965 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
196 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
*
508030 CACTCAAAAGATAACCTTAAATTAATGTTTT-CACAGTGAAA-AAATATAGACACTTTTATAAAA
261 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAACAAGTATAGACACTTTTATAAAA
508093 AGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTAT
326 AGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTAT
*
508158 ATAAGCGCTACCTATTACATCATATTTGTACCTATTATA
391 ATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
508197 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
*
508262 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACTTACAATATTAATTTAATAATTTCATTTACA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
*
508327 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAA
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAA
508386 CAACATTAAC
Statistics
Matches: 1022, Mismatches: 21, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
427 192 0.19
428 127 0.12
429 532 0.52
430 105 0.10
431 66 0.06
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (429 bp):
TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATAAT
ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAACAAGTATAGACACTTTTATAAAA
AGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTAT
ATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:507719 original size:23 final size:23
Alignment explanation
Indices: 507693--507755 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
507683 ATATAACCAC
507693 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
507716 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
507739 TACCTATTACATCATAT
1 TACCTATTACATTATAT
507756 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:508146 original size:23 final size:23
Alignment explanation
Indices: 508120--508182 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
508110 ATATAACCAC
508120 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
508143 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
508166 TACCTATTACATCATAT
1 TACCTATTACATTATAT
508183 TTGTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:511513 original size:183 final size:183
Alignment explanation
Indices: 510988--511480 Score: 898
Period size: 183 Copynumber: 2.7 Consensus size: 183
510978 TTAAAATTAC
510988 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
511053 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
* *
511118 ATATTATAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
511171 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATTAAGTACCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
511236 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGATCATAAAACCGGTATATTTATACCGGTT
66 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
*
511301 ATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAACTGT
131 ATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* *
511354 CGACACGTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
511418 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCG
65 TATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCG
511481 ATAGCATTGC
Statistics
Matches: 299, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
183 296 0.99
184 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
Found at i:513445 original size:3 final size:3
Alignment explanation
Indices: 513437--513508 Score: 63
Period size: 3 Copynumber: 24.0 Consensus size: 3
513427 ACTTGTTTGG
* * * * * *
513437 ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATT GTC AGC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
513485 GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
513509 GTCAGCTTCA
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.24, C:0.32, G:0.07, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:513491 original size:36 final size:36
Alignment explanation
Indices: 513444--513525 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 36
513434 TGGATCATCA
* *
513444 TCATCATCATCATCGTCATCATCTTCATTGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
* *
513480 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
*
513516 TCATCTTCAT
1 TCATCATCAT
513526 TGACCGCTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.21, C:0.32, G:0.09, T:0.39
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGTCAGCT
Found at i:513509 original size:12 final size:12
Alignment explanation
Indices: 513438--513525 Score: 86
Period size: 12 Copynumber: 7.3 Consensus size: 12
513428 CTTGTTTGGA
* *
513438 TCATCATCATCA
1 TCATCTTCATCG
* * *
513450 TCATCATCGTCA
1 TCATCTTCATCG
*
513462 TCATCTTCATTG
1 TCATCTTCATCG
*
513474 TCAGCTTCATCG
1 TCATCTTCATCG
*
513486 TCATCATCATCG
1 TCATCTTCATCG
513498 TCATCTTCATCG
1 TCATCTTCATCG
* *
513510 TCAGCTTCATCT
1 TCATCTTCATCG
513522 TCAT
1 TCAT
513526 TGACCGCTTG
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.22, C:0.32, G:0.08, T:0.39
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:513519 original size:18 final size:18
Alignment explanation
Indices: 513462--513525 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
513452 ATCATCGTCA
*
513462 TCATCTTCATTGTCAGCT
1 TCATCTTCATCGTCAGCT
* * * *
513480 TCATCGTCATCATCATCG
1 TCATCTTCATCGTCAGCT
513498 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCT
513516 TCATCTTCAT
1 TCATCTTCAT
513526 TGACCGCTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.19, C:0.31, G:0.09, T:0.41
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:513523 original size:6 final size:6
Alignment explanation
Indices: 513438--513525 Score: 61
Period size: 6 Copynumber: 14.7 Consensus size: 6
513428 CTTGTTTGGA
* * * * * * *
513438 TCATCA TCATCA TCATCA TCGTCA TCATCT TCAT-T GTCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT -TCATCT TCATCT
* * * *
513486 TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
513526 TGACCGCTTG
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
5 1 0.01
6 65 0.97
7 1 0.01
ACGTcount: A:0.22, C:0.32, G:0.08, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:515451 original size:200 final size:200
Alignment explanation
Indices: 514963--515938 Score: 1846
Period size: 200 Copynumber: 4.9 Consensus size: 200
514953 TTTAAATTAG
514963 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
515028 CATGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCTATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
515093 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTG-TTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
515157 AAAAA
196 AAAAA
* *
515162 TATCGACACAAACTAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
515227 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
*
515292 TTGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
*
515357 AAAAC
196 AAAAA
*
515362 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
515427 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
515492 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
*
515557 AAAAC
196 AAAAA
515562 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
515627 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
515692 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
515757 AAAAA
196 AAAAA
515762 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
515827 CTTGTACCAGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
* *
515892 TCGACACTTTTTATATATGGTTCGACACTTTATTGTTGCACCCTGTT
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
515939 GGCCATATTG
Statistics
Matches: 761, Mismatches: 15, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
199 170 0.22
200 591 0.78
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
AAAAA
Found at i:516103 original size:19 final size:19
Alignment explanation
Indices: 516057--516105 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
516047 TTATATTCAC
*
516057 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
516076 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
516095 ATACAAAATTA
1 ATACAAAATTA
516106 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:517931 original size:33 final size:33
Alignment explanation
Indices: 517894--517959 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
517884 CATCTTAATA
*
517894 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
517927 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
517960 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:518018 original size:21 final size:21
Alignment explanation
Indices: 517993--518057 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
517983 CCCCTTATGC
* *
517993 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
518014 CTCTCAAGTTTCTATTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
518035 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
518056 CT
1 CT
518058 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:520116 original size:24 final size:24
Alignment explanation
Indices: 520079--520131 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
520069 CCGTTCTATC
520079 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
520103 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
520127 TATTT
1 TATTT
520132 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:520293 original size:17 final size:18
Alignment explanation
Indices: 520271--520313 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
520261 ATATATCCGG
520271 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
520288 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
520308 TATCAT
1 TATCAT
520314 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:520322 original size:20 final size:19
Alignment explanation
Indices: 520276--520336 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
520266 TCCGGTATCA
520276 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
520295 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
* * *
520316 TTTTACCTGTTATATCGTT
1 TTTTACCGGTTTTATCATT
520335 TT
1 TT
520337 GGATCGATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.14
20 27 0.77
21 3 0.09
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:520482 original size:20 final size:20
Alignment explanation
Indices: 520455--520501 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
520445 TCCGGTAACG
520455 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
520474 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
520495 TTTTACC
1 TTTTACC
520502 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:520695 original size:182 final size:181
Alignment explanation
Indices: 520243--520713 Score: 716
Period size: 182 Copynumber: 2.6 Consensus size: 181
520233 CGTACTTACG
* *
520243 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
520308 TATCATATTTTTACCTGTTATATCGTTTTGGATCGAT--ATTTTTTTAAAGTATCAACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCAACACATTAT
*
520371 AGGTGCTAAAACTGCTTCTCTTTTAAATTTACAAAGTGTCGATCCTTATAT
131 AGGTGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
*
520422 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
520487 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCAACACATTAT
* *
520552 AGGAT-TTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGG-TGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * *
520604 AAAGTACCGACACTTTAAATGTATCTGGTAGCGCTTTACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
520668 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
520714 AATTTGGATC
Statistics
Matches: 266, Mismatches: 21, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
179 98 0.37
181 68 0.26
182 99 0.37
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCAACACATTAT
AGGTGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Done.