Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 2 of 97
Found at i:88367 original size:4 final size:4
Alignment explanation
Indices: 88358--88385 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
88348 TCAAGTTCCA
88358 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
88386 TTATAGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:100694 original size:6 final size:6
Alignment explanation
Indices: 100683--100724 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
100673 CCTCATTCGG
* *
100683 TTGGCA TTGGCA -GGGCA ATGGCA TTGGCA TTGGCA TTGGCA T
1 TTGGCA TTGGCA TTGGCA TTGGCA TTGGCA TTGGCA TTGGCA T
100725 GTAGCACCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.19, C:0.17, G:0.36, T:0.29
Consensus pattern (6 bp):
TTGGCA
Found at i:109256 original size:6 final size:6
Alignment explanation
Indices: 109247--109271 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
109237 AAAATAAAAT
109247 GAGAAA GAGAAA GAGAAA GAGAAA G
1 GAGAAA GAGAAA GAGAAA GAGAAA G
109272 CTGCCAGAGA
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (6 bp):
GAGAAA
Found at i:110063 original size:3 final size:3
Alignment explanation
Indices: 110057--110092 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
110047 TCCCTCCTCC
* *
110057 CTT CTT CTT CCT CGT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
110093 GTTGCTGCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:111038 original size:19 final size:19
Alignment explanation
Indices: 111014--111051 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
111004 ATAAACATAA
111014 TATTTAA-AAAATTTCAAAT
1 TATTTAAGAAAA-TTCAAAT
111033 TATTTAAGAAAATTCAAAT
1 TATTTAAGAAAATTCAAAT
111052 CATCACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (19 bp):
TATTTAAGAAAATTCAAAT
Found at i:117154 original size:2 final size:2
Alignment explanation
Indices: 117147--117228 Score: 103
Period size: 2 Copynumber: 41.0 Consensus size: 2
117137 CATTATGATG
117147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
117189 AT GT GT AT AT -T NT GAT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
117229 TGTGCATGAT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
1 1 0.01
2 69 0.97
3 1 0.01
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117400 original size:38 final size:40
Alignment explanation
Indices: 117344--117446 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 40
117334 ATAGTGCCCG
* *
117344 TGTGCGCGATGTAAGGGGATGTACACGATGGCACTGA-T-
1 TGTGCACGATGTGAGGGGATGTACACGATGGCACTGACTA
* * *
117382 TGTGCACGATGTGGGGGGATGCACATGATGGCACTGACTA
1 TGTGCACGATGTGAGGGGATGTACACGATGGCACTGACTA
*
117422 TGTGCACAATGTGAGGGGATGTACA
1 TGTGCACGATGTGAGGGGATGTACA
117447 TAAGTCGGGT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 32 0.58
39 1 0.02
40 22 0.40
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGAGGGGATGTACACGATGGCACTGACTA
Found at i:119303 original size:20 final size:20
Alignment explanation
Indices: 119266--119303 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
119256 TTTCAGAAGC
*
119266 TTTTCTTCTTGAAGAATCAT
1 TTTTCTTCTTCAAGAATCAT
*
119286 TTTTCTTCTTCAATAATC
1 TTTTCTTCTTCAAGAATC
119304 GACATTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTCTTCTTCAAGAATCAT
Found at i:121160 original size:33 final size:33
Alignment explanation
Indices: 121123--121190 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
121113 GGTACATAGT
121123 GGCAATTATGCTTAGAGACTTGCAGGAGACTAC
1 GGCAATTATGCTTAGAGACTTGCAGGAGACTAC
121156 GGCAATTATGCTTAGAGACTTGCAGGAGACTAC
1 GGCAATTATGCTTAGAGACTTGCAGGAGACTAC
121189 GG
1 GG
121191 TCCTAAACCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (33 bp):
GGCAATTATGCTTAGAGACTTGCAGGAGACTAC
Found at i:125086 original size:30 final size:29
Alignment explanation
Indices: 125010--125101 Score: 94
Period size: 30 Copynumber: 3.1 Consensus size: 29
125000 TATTTAAGTG
* * * *
125010 TAACAAAATGTTTTTGAATATGACGTGTAA
1 TAACAATAT-TTTTTTAACATGACGTATAA
* *
125040 TAATAATATTTTTTTAACATGATGTATAA
1 TAACAATATTTTTTTAACATGACGTATAA
* *
125069 TAACAATATTATTTTTAACGTGACGTGTAA
1 TAACAATATT-TTTTTAACATGACGTATAA
125099 TAA
1 TAA
125102 TATTTTTTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 25 0.49
30 26 0.51
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (29 bp):
TAACAATATTTTTTTAACATGACGTATAA
Found at i:125148 original size:15 final size:16
Alignment explanation
Indices: 125128--125157 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
125118 TGCATAGTAT
125128 ATAATTTTAT-TAATG
1 ATAATTTTATCTAATG
125143 ATAATTTTATCTAAT
1 ATAATTTTATCTAAT
125158 TTAATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
ATAATTTTATCTAATG
Found at i:131752 original size:2 final size:2
Alignment explanation
Indices: 131745--131831 Score: 131
Period size: 2 Copynumber: 43.0 Consensus size: 2
131735 ACTTTAAAGA
*
131745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT NACT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -A-T AT
*
131789 AA AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
131830 AT
1 AT
131832 CTTTAGATGA
Statistics
Matches: 78, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
1 1 0.01
2 75 0.96
3 1 0.01
4 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:144236 original size:2 final size:2
Alignment explanation
Indices: 144229--144254 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
144219 TACTCATGAA
144229 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
144255 TGTATTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:157412 original size:32 final size:32
Alignment explanation
Indices: 157375--157440 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
157365 TTACTGGCCT
* * *
157375 TCTGCTCTTGTTAAAGAGAACAATCAGAAATC
1 TCTGCTCTCGTTAAAGAGAACAATAAAAAATC
* *
157407 TCTGCTCTCGTTAGAGAGCACAATAAAAAATC
1 TCTGCTCTCGTTAAAGAGAACAATAAAAAATC
157439 TC
1 TC
157441 CTCCTCCGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (32 bp):
TCTGCTCTCGTTAAAGAGAACAATAAAAAATC
Found at i:161452 original size:29 final size:31
Alignment explanation
Indices: 161392--161453 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 31
161382 AAGAGCAAAG
*
161392 AAGTTTGCATTTCAACTTACTTTTCAAAAAAAC
1 AAGTTTGCATTTCAACTTA-TTAT-AAAAAAAC
*
161425 AAGTTTGCATTTCAACTT-TTATAGAAAAA
1 AAGTTTGCATTTCAACTTATTATAAAAAAA
161454 GATAATGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 6 0.22
31 3 0.11
33 18 0.67
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (31 bp):
AAGTTTGCATTTCAACTTATTATAAAAAAAC
Found at i:180856 original size:33 final size:31
Alignment explanation
Indices: 180797--180874 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 31
180787 TTAATAAAAT
180797 TTTAAATAATAATATAATATTATAATTTATA
1 TTTAAATAATAATATAATATTATAATTTATA
* *
180828 TTTAAA-AATTATATAATAATT-T-ATTAAT-
1 TTTAAATAATAATATAAT-ATTATAATTTATA
*
180856 TTTAAATAATAAAATAATA
1 TTTAAATAATAATATAATA
180875 AAAAATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 7 0.17
29 14 0.34
30 11 0.27
31 9 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTAAATAATAATATAATATTATAATTTATA
Found at i:182119 original size:3 final size:3
Alignment explanation
Indices: 182111--182141 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
182101 AAGACAATTA
182111 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
182142 TTGTTGTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:185482 original size:2 final size:2
Alignment explanation
Indices: 185475--185511 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
185465 GTTTTAAATA
185475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
185512 ATTTTAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:201535 original size:31 final size:29
Alignment explanation
Indices: 201468--201537 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
201458 TATTTTATAT
* * *
201468 AAAAATTTAATAAATTAAAAGTATTATGA
1 AAAAATTTAAGAAAATAAAAATATTATGA
201497 AAAAATTTAAGAAAATAAAAATATATAAT-A
1 AAAAATTTAAGAAAATAAAAATAT-T-ATGA
201527 ATAAAATTTAA
1 A-AAAATTTAA
201538 CAATTATCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 21 0.60
30 3 0.09
31 11 0.31
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAAATTTAAGAAAATAAAAATATTATGA
Found at i:202801 original size:6 final size:6
Alignment explanation
Indices: 202790--202818 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
202780 CATCAAACAG
202790 TGCTGT TGCTGT TGCTGT TGCTGT TGCTG
1 TGCTGT TGCTGT TGCTGT TGCTGT TGCTG
202819 CTGCCACAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.34, T:0.48
Consensus pattern (6 bp):
TGCTGT
Found at i:214728 original size:2 final size:2
Alignment explanation
Indices: 214721--214749 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
214711 AAACAACAAC
214721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
214750 TGTCTCTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:217456 original size:3 final size:3
Alignment explanation
Indices: 217448--217474 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
217438 ACACACATAT
217448 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
217475 TGGTAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:219226 original size:2 final size:2
Alignment explanation
Indices: 219219--219245 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
219209 GATAAAAGAC
219219 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
219246 ATAAAGTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:219291 original size:2 final size:2
Alignment explanation
Indices: 219284--219325 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
219274 TAATAATTAC
* *
219284 TA TA TA TA TA TN CA 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
219326 AAAGTGGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:219369 original size:45 final size:44
Alignment explanation
Indices: 219316--219400 Score: 152
Period size: 45 Copynumber: 1.9 Consensus size: 44
219306 TATATATATA
219316 TATATATATAAAAGTGGGAAATGACTCAAAACCAATATAAATTTC
1 TATATATATAAAAGTGGGAAATGACTCAAAACCAAT-TAAATTTC
*
219361 TATATATATATAAGTGGGAAATGACTCAAAACCAATTAAA
1 TATATATATAAAAGTGGGAAATGACTCAAAACCAATTAAA
219401 ATCTCTCTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 4 0.10
45 35 0.90
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (44 bp):
TATATATATAAAAGTGGGAAATGACTCAAAACCAATTAAATTTC
Found at i:223699 original size:21 final size:21
Alignment explanation
Indices: 223673--223719 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
223663 TGAGACCTTC
*
223673 AGGGCCATGTTTTTGTGTCTA
1 AGGGCCATGTTTTTGTATCTA
223694 AGGGCCATGTTTTTGTATCTA
1 AGGGCCATGTTTTTGTATCTA
223715 AGGGC
1 AGGGC
223720 TGTCCATGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (21 bp):
AGGGCCATGTTTTTGTATCTA
Found at i:224971 original size:2 final size:2
Alignment explanation
Indices: 224964--225016 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
224954 CTCCTGCATC
224964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
225006 AT AT AT AT AT A
1 AT AT AT AT AT A
225017 AACTCCTATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:249759 original size:2 final size:2
Alignment explanation
Indices: 249752--249785 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
249742 AAAAATCATA
249752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
249786 GCTTCGAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:251764 original size:2 final size:2
Alignment explanation
Indices: 251757--251796 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
251747 ATGTATAAAC
*
251757 AT AT AT AT AT -T AT AT AT AT AT AT -T AT A- AA 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
251796 A
1 A
251797 ATAGAGAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:251775 original size:13 final size:13
Alignment explanation
Indices: 251757--251796 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
251747 ATGTATAAAC
251757 ATATATATATTAT
1 ATATATATATTAT
251770 ATATATATATTAT
1 ATATATATATTAT
*
251783 A-AAATATA-TAT
1 ATATATATATTAT
251794 ATA
1 ATA
251797 ATAGAGAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 4 0.16
12 7 0.28
13 14 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:251797 original size:13 final size:13
Alignment explanation
Indices: 251750--251797 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 13
251740 TGATGCTATG
251750 TATAAACATATATA
1 TATAAA-ATATATA
*
251764 TATTATATATATATA
1 TA-TA-AAATATATA
251779 TTATAAAATATATA
1 -TATAAAATATATA
251793 TATAA
1 TATAA
251798 TAGAGAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 5 0.17
14 10 0.34
15 11 0.38
16 3 0.10
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
TATAAAATATATA
Found at i:251799 original size:11 final size:11
Alignment explanation
Indices: 251757--251799 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
251747 ATGTATAAAC
*
251757 ATATATATATT
1 ATATATATAAT
251768 ATATATAT-AT
1 ATATATATAAT
*
251778 AT-TATAAAAT
1 ATATATATAAT
251788 ATATATATAAT
1 ATATATATAAT
251799 A
1 A
251800 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 4 0.15
10 7 0.26
11 16 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATATATAAT
Found at i:274223 original size:402 final size:402
Alignment explanation
Indices: 273513--275011 Score: 1598
Period size: 402 Copynumber: 3.7 Consensus size: 402
273503 TCAACAATGC
* ** * * * ** * * ** *
273513 ATGCATAAGTATGTTACAAGTAACTCTATTTGGCCTAATAGAACAGCTGGCCATAGCAGAGAAAA
1 ATGCACAAGTATACTACATGTAACACTATTTGGCCTGATACCACGGCTAGCCATAGTGGAGAACA
* * * * * * * *
273578 GATATAGAGCTTTATCCATATCATCT-ATAAGACAGTAGCCCTTGATAAAAGTGTTGTAAGTCAC
66 TATAAAGGGCTTTATCCACATCATTTGA-AAGGCAGCATCCCTTGATAAAAGTGTTGTAAGTCAC
* ** * * * * *
273642 ATGGTTTGGAGGTGGACCCTTTTCTATCATCTCACGAAAAAGCCAATCTGCTTTCTTCATGTCA-
130 ATGGTTGGGAGGTGGACCAATTTCTAGCATCTCCCTAAAAAGCCAATCTGCCTTCTCCATGTCAC
* * * *
273706 CCTATTTTGCAGAGGCCATTTAGAAGATAATTGTGTGCAAGTACATCAGGAATAATACCTTTCTG
195 CCT-TTTTGCACAAGCCATTTAGAAGATAATTGTGTGCAAGCACATCAGGAATAACACCTTTCTG
*
273771 TATCATCTTCCTCCGCAACATTAGAGCTGATCCCAACTTCCCGTCCAAACATAAAACCTGAATTA
259 TATCATCTCCCTCCGCAACATTAGAGCTGATCCCAACTTCCCGTCCAAACATAAAACCTGAATTA
* *
273836 TGGCTTCACCATGGTCCTCCCTTAACATCTTCCCAAGAAGCCTTGTAGCATCTCTCAGAAGATGT
324 TGGCTTCACCATTGTCCTCCCTTAACATCTTCCCAAGAAGCCTTGTAGCATCTCTCAAAAGATGT
273901 CTCTTGCACAATTT
389 CTCTTGCACAATTT
* * * * *
273915 ATGCACAAGCATACTACATGTAACCCTATTTGGCCCGATACCATGGCTAGTCATAGTGGAGAACA
1 ATGCACAAGTATACTACATGTAACACTATTTGGCCTGATACCACGGCTAGCCATAGTGGAGAACA
* * *
273980 TATAAAGGGCTTTATCCACATCATTTGAAAGGCAGCATCCCTTGACAAAGGTGTTGTAGGTCACA
66 TATAAAGGGCTTTATCCACATCATTTGAAAGGCAGCATCCCTTGATAAAAGTGTTGTAAGTCACA
* *
274045 TGGTTGGGAGGTGGGCCAATTTCTAGCATGTCCCTAAAAAGCCAATCTGCCTTCTCCATGTCACC
131 TGGTTGGGAGGTGGACCAATTTCTAGCATCTCCCTAAAAAGCCAATCTGCCTTCTCCATGTCACC
* *
274110 CTTTTTGCACAAGCCATTTAGAAGATAATTGTGTGTAAGCACATCAGGAATAACACCTTTCTTTA
196 CTTTTTGCACAAGCCATTTAGAAGATAATTGTGTGCAAGCACATCAGGAATAACACCTTTCTGTA
* * * * * * * *
274175 TCATCTCCCTCCGTAACCA-TAGAGCTGCTCCCAACTT-CTGCTCCAAACACAAATCTTTAATCA
261 TCATCTCCCTCCGCAA-CATTAGAGCTGATCCCAACTTCCCG-TCCAAACATAAAACCTGAATTA
* * * * * * * * *
274238 TGGCTATCTGTCCAGCATTATCATCACTTAAAATC-TCTCCGAGAA-ACTTCATAGCATCTCTTA
324 TGG----CT-T-CACCATTGTCCTCCCTTAACATCTTC-CCAAGAAGCCTT-GTAGCATCTCTCA
** ** **
274301 CTAGACCTCTCTT-CAACAATGC
381 AAAGATGTCTCTTGC-ACAATTT
* ** * * * * * * *
274323 ATGCATAAGTATGTTACAAGTAACTCTATTTGGCCTAATACAACAGCTGGCCATAGCT-GAGAAA
1 ATGCACAAGTATACTACATGTAACACTATTTGGCCTGATACCACGGCTAGCCATAG-TGGAGAAC
* * * * ** * * * *
274387 AGATAGAGAGCTTTATCCATATCA-TCCATAAGACAGTAGCCCTTGATAAAAGTGTGGTAAGTCA
65 ATATAAAGGGCTTTATCCACATCATTTGA-AAGGCAGCATCCCTTGATAAAAGTGTTGTAAGTCA
* * * * ** * * * *
274451 AACGGTTTGGAGGTGGGCCTTTTTCTATCATCT-CATGAAAAAGCCAATCTGCTTTCTTCATGTC
129 CATGGTTGGGAGGTGGACCAATTTCTAGCATCTCCCT-AAAAAGCCAATCTGCCTTCTCCATGTC
** * * ** *
274515 ACCGATTTTGCACAGGCCATTTAGAAGATAATTGTGTGCAAGTATGTCAGGAATAATACCTTTCT
193 ACCCTTTTTGCACAAGCCATTTAGAAGATAATTGTGTGCAAGCACATCAGGAATAACACCTTTCT
* * ** *
274580 GTATCAGCTTCCTCCGCAACATTAGAGCTGATCCCAACTTCCCGTCTGAACATAAAAACTGAATT
258 GTATCATCTCCCTCCGCAACATTAGAGCTGATCCCAACTTCCCGTCCAAACATAAAACCTGAATT
* * *
274645 ATGGCTACACCATTGTCCTTCCTTAACATCTTCCCAAGAAGCTTTGTAGCATCTCTCAAAAGATG
323 ATGGCTTCACCATTGTCCTCCCTTAACATCTTCCCAAGAAGCCTTGTAGCATCTCTCAAAAGATG
*
274710 TCCCTTGCACAATTT
388 TCTCTTGCACAATTT
*
274725 ATGCACAAGTATACTACATGTAACACTATTTGGCCTGATACCACGGGTAGCCATAGTGGAGAACA
1 ATGCACAAGTATACTACATGTAACACTATTTGGCCTGATACCACGGCTAGCCATAGTGGAGAACA
* * * * * *
274790 TATAAAGGGCTCTATCCGCATCATTTGAAAGGCAACATCCCTTAATAAAGGTGTTGTAGGTCACA
66 TATAAAGGGCTTTATCCACATCATTTGAAAGGCAGCATCCCTTGATAAAAGTGTTGTAAGTCACA
*
274855 TGGTTGGGAGGTGGACCAATTTCTAGCATCTCCCTAATAAGCCAATCTGCCTTCTCCATGTCACC
131 TGGTTGGGAGGTGGACCAATTTCTAGCATCTCCCTAAAAAGCCAATCTGCCTTCTCCATGTCACC
* * * * *
274920 TTTTTTGCACAAGCCATTTAGAAGATAATTGTGTGTAGGCACATCAGGAACAACACCTTTCTTTA
196 CTTTTTGCACAAGCCATTTAGAAGATAATTGTGTGCAAGCACATCAGGAATAACACCTTTCTGTA
274985 TCATCTCCCTCCGCAACCA-TAGAGCTG
261 TCATCTCCCTCCGCAA-CATTAGAGCTG
275012 CTTCTAACTT
Statistics
Matches: 874, Mismatches: 198, Indels: 50
0.78 0.18 0.04
Matches are distributed among these distances:
401 3 0.00
402 533 0.61
403 17 0.02
404 2 0.00
406 2 0.00
407 13 0.01
408 301 0.34
409 3 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (402 bp):
ATGCACAAGTATACTACATGTAACACTATTTGGCCTGATACCACGGCTAGCCATAGTGGAGAACA
TATAAAGGGCTTTATCCACATCATTTGAAAGGCAGCATCCCTTGATAAAAGTGTTGTAAGTCACA
TGGTTGGGAGGTGGACCAATTTCTAGCATCTCCCTAAAAAGCCAATCTGCCTTCTCCATGTCACC
CTTTTTGCACAAGCCATTTAGAAGATAATTGTGTGCAAGCACATCAGGAATAACACCTTTCTGTA
TCATCTCCCTCCGCAACATTAGAGCTGATCCCAACTTCCCGTCCAAACATAAAACCTGAATTATG
GCTTCACCATTGTCCTCCCTTAACATCTTCCCAAGAAGCCTTGTAGCATCTCTCAAAAGATGTCT
CTTGCACAATTT
Found at i:275013 original size:810 final size:810
Alignment explanation
Indices: 273448--275070 Score: 2814
Period size: 810 Copynumber: 2.0 Consensus size: 810
273438 TTTCGAATTG
* * *
273448 TCATCGCTTAAAATCTCTCTGAGAAGCTTCATAGCATCTCTTAATAGACCTCTCTTCAACAATGC
1 TCATCACTTAAAATCTCTCCGAGAAACTTCATAGCATCTCTTAATAGACCTCTCTTCAACAATGC
*
273513 ATGCATAAGTATGTTACAAGTAACTCTATTTGGCCTAATAGAACAGCTGGCCATAGCAGAGAAAA
66 ATGCATAAGTATGTTACAAGTAACTCTATTTGGCCTAATACAACAGCTGGCCATAGCAGAGAAAA
* * * *
273578 GATATAGAGCTTTATCCATATCATCTATAAGACAGTAGCCCTTGATAAAAGTGTTGTAAGTCACA
131 GATAGAGAGCTTTATCCATATCATCCATAAGACAGTAGCCCTTGATAAAAGTGTGGTAAGTCAAA
*
273643 TGGTTTGGAGGTGGACCCTTTTCTATCATCTCACGAAAAAGCCAATCTGCTTTCTTCATGTCACC
196 CGGTTTGGAGGTGGACCCTTTTCTATCATCTCACGAAAAAGCCAATCTGCTTTCTTCATGTCACC
* *
273708 TATTTTGCAGAGGCCATTTAGAAGATAATTGTGTGCAAGTACATCAGGAATAATACCTTTCTGTA
261 GATTTTGCACAGGCCATTTAGAAGATAATTGTGTGCAAGTACATCAGGAATAATACCTTTCTGTA
* *
273773 TCATCTTCCTCCGCAACATTAGAGCTGATCCCAACTTCCCGTCCAAACATAAAACCTGAATTATG
326 TCAGCTTCCTCCGCAACATTAGAGCTGATCCCAACTTCCCGTCCAAACATAAAAACTGAATTATG
* * *
273838 GCTTCACCATGGTCCTCCCTTAACATCTTCCCAAGAAGCCTTGTAGCATCTCTCAGAAGATGTCT
391 GCTACACCATGGTCCTCCCTTAACATCTTCCCAAGAAGCCTTGTAGCATCTCTCAAAAGATGTCC
* * *
273903 CTTGCACAATTTATGCACAAGCATACTACATGTAACCCTATTTGGCCCGATACCATGGCTAGTCA
456 CTTGCACAATTTATGCACAAGCATACTACATGTAACACTATTTGGCCCGATACCACGGCTAGCCA
* * *
273968 TAGTGGAGAACATATAAAGGGCTTTATCCACATCATTTGAAAGGCAGCATCCCTTGACAAAGGTG
521 TAGTGGAGAACATATAAAGGGCTCTATCCACATCATTTGAAAGGCAACATCCCTTAACAAAGGTG
* *
274033 TTGTAGGTCACATGGTTGGGAGGTGGGCCAATTTCTAGCATGTCCCTAAAAAGCCAATCTGCCTT
586 TTGTAGGTCACATGGTTGGGAGGTGGACCAATTTCTAGCATCTCCCTAAAAAGCCAATCTGCCTT
*
274098 CTCCATGTCACCCTTTTTGCACAAGCCATTTAGAAGATAATTGTGTGTAAGCACATCAGGAATAA
651 CTCCATGTCACCCTTTTTGCACAAGCCATTTAGAAGATAATTGTGTGTAAGCACATCAGGAACAA
*
274163 CACCTTTCTTTATCATCTCCCTCCGTAACCATAGAGCTGCTCCCAACTTCTGCTCCAAACACAAA
716 CACCTTTCTTTATCATCTCCCTCCGCAACCATAGAGCTGCTCCCAACTTCTGCTCCAAACACAAA
274228 TCTTTAATCATGGCTATCTGTCCAGCATTA
781 TCTTTAATCATGGCTATCTGTCCAGCATTA
*
274258 TCATCACTTAAAATCTCTCCGAGAAACTTCATAGCATCTCTTACTAGACCTCTCTTCAACAATGC
1 TCATCACTTAAAATCTCTCCGAGAAACTTCATAGCATCTCTTAATAGACCTCTCTTCAACAATGC
*
274323 ATGCATAAGTATGTTACAAGTAACTCTATTTGGCCTAATACAACAGCTGGCCATAGCTGAGAAAA
66 ATGCATAAGTATGTTACAAGTAACTCTATTTGGCCTAATACAACAGCTGGCCATAGCAGAGAAAA
274388 GATAGAGAGCTTTATCCATATCATCCATAAGACAGTAGCCCTTGATAAAAGTGTGGTAAGTCAAA
131 GATAGAGAGCTTTATCCATATCATCCATAAGACAGTAGCCCTTGATAAAAGTGTGGTAAGTCAAA
* * *
274453 CGGTTTGGAGGTGGGCCTTTTTCTATCATCTCATGAAAAAGCCAATCTGCTTTCTTCATGTCACC
196 CGGTTTGGAGGTGGACCCTTTTCTATCATCTCACGAAAAAGCCAATCTGCTTTCTTCATGTCACC
**
274518 GATTTTGCACAGGCCATTTAGAAGATAATTGTGTGCAAGTATGTCAGGAATAATACCTTTCTGTA
261 GATTTTGCACAGGCCATTTAGAAGATAATTGTGTGCAAGTACATCAGGAATAATACCTTTCTGTA
**
274583 TCAGCTTCCTCCGCAACATTAGAGCTGATCCCAACTTCCCGTCTGAACATAAAAACTGAATTATG
326 TCAGCTTCCTCCGCAACATTAGAGCTGATCCCAACTTCCCGTCCAAACATAAAAACTGAATTATG
* * *
274648 GCTACACCATTGTCCTTCCTTAACATCTTCCCAAGAAGCTTTGTAGCATCTCTCAAAAGATGTCC
391 GCTACACCATGGTCCTCCCTTAACATCTTCCCAAGAAGCCTTGTAGCATCTCTCAAAAGATGTCC
* * *
274713 CTTGCACAATTTATGCACAAGTATACTACATGTAACACTATTTGGCCTGATACCACGGGTAGCCA
456 CTTGCACAATTTATGCACAAGCATACTACATGTAACACTATTTGGCCCGATACCACGGCTAGCCA
* *
274778 TAGTGGAGAACATATAAAGGGCTCTATCCGCATCATTTGAAAGGCAACATCCCTTAATAAAGGTG
521 TAGTGGAGAACATATAAAGGGCTCTATCCACATCATTTGAAAGGCAACATCCCTTAACAAAGGTG
*
274843 TTGTAGGTCACATGGTTGGGAGGTGGACCAATTTCTAGCATCTCCCTAATAAGCCAATCTGCCTT
586 TTGTAGGTCACATGGTTGGGAGGTGGACCAATTTCTAGCATCTCCCTAAAAAGCCAATCTGCCTT
* *
274908 CTCCATGTCACCTTTTTTGCACAAGCCATTTAGAAGATAATTGTGTGTAGGCACATCAGGAACAA
651 CTCCATGTCACCCTTTTTGCACAAGCCATTTAGAAGATAATTGTGTGTAAGCACATCAGGAACAA
* *
274973 CACCTTTCTTTATCATCTCCCTCCGCAACCATAGAGCTGCTTCTAACTTCTGCTCCAAACACAAA
716 CACCTTTCTTTATCATCTCCCTCCGCAACCATAGAGCTGCTCCCAACTTCTGCTCCAAACACAAA
275038 TCTTTAATCATGGCTATCTGTCCAGCATTA
781 TCTTTAATCATGGCTATCTGTCCAGCATTA
275068 TCA
1 TCA
275071 GCTTTCAAAG
Statistics
Matches: 765, Mismatches: 48, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
810 765 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (810 bp):
TCATCACTTAAAATCTCTCCGAGAAACTTCATAGCATCTCTTAATAGACCTCTCTTCAACAATGC
ATGCATAAGTATGTTACAAGTAACTCTATTTGGCCTAATACAACAGCTGGCCATAGCAGAGAAAA
GATAGAGAGCTTTATCCATATCATCCATAAGACAGTAGCCCTTGATAAAAGTGTGGTAAGTCAAA
CGGTTTGGAGGTGGACCCTTTTCTATCATCTCACGAAAAAGCCAATCTGCTTTCTTCATGTCACC
GATTTTGCACAGGCCATTTAGAAGATAATTGTGTGCAAGTACATCAGGAATAATACCTTTCTGTA
TCAGCTTCCTCCGCAACATTAGAGCTGATCCCAACTTCCCGTCCAAACATAAAAACTGAATTATG
GCTACACCATGGTCCTCCCTTAACATCTTCCCAAGAAGCCTTGTAGCATCTCTCAAAAGATGTCC
CTTGCACAATTTATGCACAAGCATACTACATGTAACACTATTTGGCCCGATACCACGGCTAGCCA
TAGTGGAGAACATATAAAGGGCTCTATCCACATCATTTGAAAGGCAACATCCCTTAACAAAGGTG
TTGTAGGTCACATGGTTGGGAGGTGGACCAATTTCTAGCATCTCCCTAAAAAGCCAATCTGCCTT
CTCCATGTCACCCTTTTTGCACAAGCCATTTAGAAGATAATTGTGTGTAAGCACATCAGGAACAA
CACCTTTCTTTATCATCTCCCTCCGCAACCATAGAGCTGCTCCCAACTTCTGCTCCAAACACAAA
TCTTTAATCATGGCTATCTGTCCAGCATTA
Found at i:279384 original size:24 final size:23
Alignment explanation
Indices: 279348--279392 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
279338 CACCTGGATC
*
279348 ACAAGTGTTAGAGGAAATTCTAAA
1 ACAAGTGTGAGA-GAAATTCTAAA
* *
279372 ACAATTGTGAGAGCAATTCTA
1 ACAAGTGTGAGAGAAATTCTA
279393 CCAGTTTGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (23 bp):
ACAAGTGTGAGAGAAATTCTAAA
Found at i:279665 original size:86 final size:86
Alignment explanation
Indices: 279520--279692 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
279510 GCAAAATCTC
279520 TATCATATCATTTTGTGACTGATATTGTCACGATGCAATAGGTACATAACTTTATGGAGCACAGA
1 TATCATATCATTTTGTGACTGATATTGTCACGATGCAATAGGTACATAACTTTATGGAGCACAGA
279585 TATGAAGTTCTTTTATTTTCT
66 TATGAAGTTCTTTTATTTTCT
279606 TATCATATCATTTTGTGACTGATATTGTCACGATGCAATAGGTACATAACTTTATGGAGCACAGA
1 TATCATATCATTTTGTGACTGATATTGTCACGATGCAATAGGTACATAACTTTATGGAGCACAGA
279671 TATGAAGTTCTTTTATTTTCT
66 TATGAAGTTCTTTTATTTTCT
279692 T
1 T
279693 TAAATGAGAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (86 bp):
TATCATATCATTTTGTGACTGATATTGTCACGATGCAATAGGTACATAACTTTATGGAGCACAGA
TATGAAGTTCTTTTATTTTCT
Found at i:311291 original size:2 final size:2
Alignment explanation
Indices: 311286--311317 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
311276 GTTATATATA
*
311286 TG TG TG TG TG TG TG TG TG TG TG TG AG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
311318 ATATGAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:316269 original size:19 final size:20
Alignment explanation
Indices: 316218--316269 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
316208 CTAATATTCT
* *
316218 TTTTTATAATATATATTTTA
1 TTTTTATATTAAATATTTTA
316238 TTTTT-TATATAAAT-TTTTA
1 TTTTTATAT-TAAATATTTTA
316257 TTTTTATATTAAA
1 TTTTTATATTAAA
316270 ATTATTAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTATATTAAATATTTTA
Found at i:316272 original size:20 final size:19
Alignment explanation
Indices: 316217--316265 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
316207 CCTAATATTC
*
316217 TTTTTTATAATATATATTTTA
1 TTTTTTAT-ATAAAT-TTTTA
316238 TTTTTTATATAAATTTTTA
1 TTTTTTATATAAATTTTTA
316257 -TTTTTATAT
1 TTTTTTATAT
316266 TAAAATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
19 5 0.19
20 5 0.19
21 8 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTATATAAATTTTTA
Found at i:322937 original size:2 final size:2
Alignment explanation
Indices: 322930--322955 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
322920 CAAAATGTGG
322930 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
322956 TTTGAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:339869 original size:16 final size:16
Alignment explanation
Indices: 339850--339880 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
339840 TTATTTTGAT
339850 TTATGAATATATGTAA
1 TTATGAATATATGTAA
*
339866 TTATGCATATATGTA
1 TTATGAATATATGTA
339881 TTTTATGGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (16 bp):
TTATGAATATATGTAA
Found at i:364569 original size:25 final size:25
Alignment explanation
Indices: 364540--364589 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
364530 GTTCCCCTAC
364540 AAAATTACAGAAACAAGAATTGTAA
1 AAAATTACAGAAACAAGAATTGTAA
364565 AAAATTACAGAAACAAGAATTGTAA
1 AAAATTACAGAAACAAGAATTGTAA
364590 GAGTAACTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (25 bp):
AAAATTACAGAAACAAGAATTGTAA
Found at i:367404 original size:3 final size:3
Alignment explanation
Indices: 367390--367422 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
367380 TATAAAAAAT
*
367390 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
367423 TTCGAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:367939 original size:23 final size:23
Alignment explanation
Indices: 367864--367945 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 23
367854 TATCATTTTT
* *
367864 TATTAATAATATAATATTAATTTTA
1 TATTAATAAT-TAACA-TAATATTA
367889 TATTAATAA-TAACAT-ATATTGA
1 TATTAATAATTAACATAATATT-A
367911 TAATTAATAAGTTAA-ATAATATTA
1 T-ATTAATAA-TTAACATAATATTA
*
367935 TATTAAAAATT
1 TATTAATAATT
367946 TTAATACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
21 4 0.08
22 5 0.10
23 19 0.39
24 4 0.08
25 17 0.35
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTAATAATTAACATAATATTA
Found at i:368600 original size:20 final size:20
Alignment explanation
Indices: 368575--368664 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 20
368565 ATTTAACACG
368575 ATTAAATAAAAATATTTATA
1 ATTAAATAAAAATATTTATA
*
368595 ATTAAAT-ATAAT-TTTATTA
1 ATTAAATAAAAATATTTA-TA
* ** *
368614 TTTAAATTTAAA-ATCTATA
1 ATTAAATAAAAATATTTATA
*
368633 ATT--ATAAAAATAATTATA
1 ATTAAATAAAAATATTTATA
* *
368651 ATAAAACAAAAATA
1 ATTAAATAAAAATA
368665 ATAATAACAT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
17 5 0.10
18 11 0.21
19 16 0.31
20 20 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAAATAAAAATATTTATA
Found at i:368868 original size:18 final size:18
Alignment explanation
Indices: 368847--368903 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
368837 GTATATATGT
*
368847 TTAAACACGATAACACGA
1 TTAAATACGATAACACGA
* **
368865 TTAAATACAATAACATAA
1 TTAAATACGATAACACGA
368883 TTAAATACGATAACACGA
1 TTAAATACGATAACACGA
368901 TTA
1 TTA
368904 TATAAACGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.25
Consensus pattern (18 bp):
TTAAATACGATAACACGA
Found at i:373473 original size:2 final size:2
Alignment explanation
Indices: 373468--373492 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
373458 AATATATACA
373468 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
373493 ACATTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:380205 original size:2 final size:2
Alignment explanation
Indices: 380198--380222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
380188 GGAAAGAGGA
380198 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
380223 AGCAAAAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:387170 original size:13 final size:13
Alignment explanation
Indices: 387152--387181 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
387142 CGTTCGAGTT
*
387152 TCATTTGATAACG
1 TCATTTGAAAACG
387165 TCATTTGAAAACG
1 TCATTTGAAAACG
387178 TCAT
1 TCAT
387182 CATCTAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
TCATTTGAAAACG
Found at i:414426 original size:6 final size:6
Alignment explanation
Indices: 414415--414446 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
414405 CCCACTTCAC
414415 CACCAT CACCAT CACCAT CACCAT CACCAT CA
1 CACCAT CACCAT CACCAT CACCAT CACCAT CA
414447 GCCTTTTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (6 bp):
CACCAT
Found at i:415445 original size:3 final size:3
Alignment explanation
Indices: 415437--415464 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
415427 GTTTATCATT
415437 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
415465 ATTGATGGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:416301 original size:3 final size:3
Alignment explanation
Indices: 416295--416324 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
416285 AAGCGGCGGC
416295 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
416325 AATCTTCTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:417318 original size:81 final size:81
Alignment explanation
Indices: 417223--417403 Score: 213
Period size: 81 Copynumber: 2.2 Consensus size: 81
417213 AACAATAATT
* * * *
417223 AAATCGATTTAATTATATTTTAAAATTAAAATAATC-TAAACAAAATTATATTCCATCTGTTAAT
1 AAATCGATTGAATTATATTTTAAAATAAAAATAATCAT-AACAAAATTACATT-CATCTATTAAT
417287 TTTTAT-AAAAAACAATC
64 TTTTATCAAAAAACAATC
* ** * * *
417304 AAATCGATTGAATTATACTTTAAAATAAAAATAATCATAATTAATTTACATTCATTTATTGATTT
1 AAATCGATTGAATTATATTTTAAAATAAAAATAATCATAACAAAATTACATTCATCTATTAATTT
* *
417369 TTATCAAATAATAATC
66 TTATCAAAAAACAATC
*
417385 AAATCGACTGAATTATATT
1 AAATCGATTGAATTATATT
417404 ACTAATAAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 14 0.17
81 69 0.82
82 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.40
Consensus pattern (81 bp):
AAATCGATTGAATTATATTTTAAAATAAAAATAATCATAACAAAATTACATTCATCTATTAATTT
TTATCAAAAAACAATC
Found at i:450407 original size:12 final size:13
Alignment explanation
Indices: 450384--450412 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
450374 AGCCTCAGGA
450384 TTTCCAATGTCAG
1 TTTCCAATGTCAG
450397 TTTCC-ATGTCAG
1 TTTCCAATGTCAG
450409 TTTC
1 TTTC
450413 TCCATAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.45
Consensus pattern (13 bp):
TTTCCAATGTCAG
Found at i:456227 original size:15 final size:16
Alignment explanation
Indices: 456202--456231 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
456192 TTTTAATTTT
456202 TTTTATAATATATGTG
1 TTTTATAATATATGTG
456218 TTTT-TAATATATGT
1 TTTTATAATATATGT
456232 ATATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (16 bp):
TTTTATAATATATGTG
Found at i:474094 original size:13 final size:14
Alignment explanation
Indices: 474076--474110 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
474066 CACTACCCAG
474076 AAACAAAAAC-AAA
1 AAACAAAAACAAAA
*
474089 AAACAAATACAAAA
1 AAACAAAAACAAAA
474103 AAACAAAA
1 AAACAAAA
474111 TCCCAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.03
Consensus pattern (14 bp):
AAACAAAAACAAAA
Found at i:483183 original size:28 final size:27
Alignment explanation
Indices: 483121--483183 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
483111 TGATAATTCG
483121 ATAATTTTGAATCTATCATTTCAAATTA
1 ATAATTTTGAATCTAT-ATTTCAAATTA
* *
483149 ATTATTTTGAATCTAT-TTTTAAATTTGA
1 ATAATTTTGAATCTATATTTCAAA-TT-A
483177 ATAATTT
1 ATAATTT
483184 AAATTGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 6 0.20
27 2 0.07
28 22 0.73
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (27 bp):
ATAATTTTGAATCTATATTTCAAATTA
Found at i:498402 original size:96 final size:96
Alignment explanation
Indices: 498178--498467 Score: 553
Period size: 99 Copynumber: 3.0 Consensus size: 96
498168 GCAATTTGTG
498178 TTAGATTATTAATACATTGAAATTGAAAAAAAAAAGAAAATTCAGTTGGGGGTCATTTTCCTTTT
1 TTAGATTATTAATACATTGAAATTGAAAAAAAAAAGAAAATTCAGTTGGGGGTCATTTTCCTTTT
498243 ATTTATTTTATTGTAACTAATCATAAATTGA
66 ATTTATTTTATTGTAACTAATCATAAATTGA
498274 TTAGATTATTAATACATTGAAATTGAAAAAAAAAAAGGAAAAATTCAGTTGGGGGTCATTTTCCT
1 TTAGATTATTAATACATTGAAATTG-AAAAAAAAAA-G-AAAATTCAGTTGGGGGTCATTTTCCT
498339 TTTATTTATTTTATTGTAACTAATCATAAATTGA
63 TTTATTTATTTTATTGTAACTAATCATAAATTGA
498373 TTAGATTATTAATACATTGAAATTGAAAAAAAAAAGAAAATTCAGTTGGGGGTCATTTTCCTTTT
1 TTAGATTATTAATACATTGAAATTGAAAAAAAAAAGAAAATTCAGTTGGGGGTCATTTTCCTTTT
498438 ATTTATTTTATTGTAACTAATCATAAATTG
66 ATTTATTTTATTGTAACTAATCATAAATTG
498468 GTTATAAATT
Statistics
Matches: 191, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
96 84 0.44
97 11 0.06
98 11 0.06
99 85 0.45
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (96 bp):
TTAGATTATTAATACATTGAAATTGAAAAAAAAAAGAAAATTCAGTTGGGGGTCATTTTCCTTTT
ATTTATTTTATTGTAACTAATCATAAATTGA
Found at i:499102 original size:12 final size:12
Alignment explanation
Indices: 499085--499118 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
499075 CCGAGTACAA
499085 AAAGAAGAAAAG
1 AAAGAAGAAAAG
499097 AAAGAA-AGAAAG
1 AAAGAAGA-AAAG
499109 AAAGAAGAAA
1 AAAGAAGAAA
499119 TGCAATGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 18 0.90
13 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAGAAGAAAAG
Found at i:499474 original size:2 final size:2
Alignment explanation
Indices: 499467--499505 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
499457 GCCATGAATA
499467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
499506 TCAATTCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:516476 original size:32 final size:32
Alignment explanation
Indices: 516440--516511 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
516430 AATCCTAGAT
516440 TATATATGCTCTGACTACTCGTTAACTAAATC
1 TATATATGCTCTGACTACTCGTTAACTAAATC
516472 TATATATGCTCTGACTACTCGTTAACTAAATC
1 TATATATGCTCTGACTACTCGTTAACTAAATC
*
516504 TACATATG
1 TATATATG
516512 TCTCATGCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.38
Consensus pattern (32 bp):
TATATATGCTCTGACTACTCGTTAACTAAATC
Found at i:517249 original size:31 final size:32
Alignment explanation
Indices: 517180--517266 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 32
517170 ATGTCAATGT
* ** *
517180 CACATCAACATATTAGTGCCATGTGGTACTAC
1 CACATCATCATATTAGTGCCACATGGCACTAC
*
517212 CACATCATCATATTAGTGCCACATGGCA-TGC
1 CACATCATCATATTAGTGCCACATGGCACTAC
**
517243 CACATCATCATATGGGTGCCACAT
1 CACATCATCATATTAGTGCCACAT
517267 CATCATTGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 24 0.50
32 24 0.50
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (32 bp):
CACATCATCATATTAGTGCCACATGGCACTAC
Found at i:519865 original size:2 final size:2
Alignment explanation
Indices: 519860--519891 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
519850 AAAAAAATTC
519860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
519892 TACCCTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:533239 original size:16 final size:16
Alignment explanation
Indices: 533187--533239 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
533177 AGTCCATAGT
*
533187 CAAATGTTTATTAGTA
1 CAAATGTTTATTATTA
* * *
533203 CAAATTTTTCTTATAA
1 CAAATGTTTATTATTA
*
533219 AAAATGTTTATTATTA
1 CAAATGTTTATTATTA
533235 CAAAT
1 CAAAT
533240 TGAAGGCAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (16 bp):
CAAATGTTTATTATTA
Found at i:540066 original size:16 final size:16
Alignment explanation
Indices: 540014--540066 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
540004 AGTTCATAGT
* *
540014 CAAATGTCTATTAGTA
1 CAAATGTTTATTATTA
* * *
540030 CAAATTTTTCTTATAA
1 CAAATGTTTATTATTA
*
540046 AAAATGTTTATTATTA
1 CAAATGTTTATTATTA
540062 CAAAT
1 CAAAT
540067 TGAAGGCAAA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (16 bp):
CAAATGTTTATTATTA
Found at i:544591 original size:3 final size:3
Alignment explanation
Indices: 544583--544672 Score: 57
Period size: 3 Copynumber: 30.7 Consensus size: 3
544573 ACTCCAATAT
* *
544583 TTA TTA TTA TTA TTT TTA -CA TTTA TTA TTTA TT- TT- TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA
* * *
544626 TTA TCA TTA TTT TTA TATA TT- TTT TTA TATA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
544671 TT
1 TT
544673 TTTTTTCTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
2 11 0.16
3 48 0.70
4 10 0.14
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:544685 original size:36 final size:36
Alignment explanation
Indices: 544582--544689 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 36
544572 TACTCCAATA
*
544582 TTTATTATTATTATTTTTACATTTATTATTTATTT-TTTAT
1 TTTATTATTATTATTTTT--ATTT-TT-TTT-TTTATATAT
* * *
544622 TTTATTATCATTATTTTTATATATTTTTTTATATAT
1 TTTATTATTATTATTTTTATTTTTTTTTTTATATAT
544658 TTTATTATTATTATTTTT-TTTCTTTTTTTTAT
1 TTTATTATTATTATTTTTATTT-TTTTTTTTAT
544690 CTAAAAATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
35 5 0.08
36 33 0.56
37 1 0.02
38 3 0.05
40 17 0.29
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (36 bp):
TTTATTATTATTATTTTTATTTTTTTTTTTATATAT
Found at i:553099 original size:15 final size:15
Alignment explanation
Indices: 553053--553104 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
553043 AAACATGGAG
*
553053 TAGTTTTGATTTATT
1 TAGTTTTGAGTTATT
*
553068 TAGATTTTAAAAGTTATT
1 TAG-TTTT--GAGTTATT
553086 TAGTTTTGAGTTATT
1 TAGTTTTGAGTTATT
553101 TAGT
1 TAGT
553105 AGTCTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 14 0.45
16 4 0.13
17 4 0.13
18 9 0.29
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (15 bp):
TAGTTTTGAGTTATT
Found at i:559557 original size:55 final size:54
Alignment explanation
Indices: 559465--559650 Score: 219
Period size: 55 Copynumber: 3.4 Consensus size: 54
559455 ATTAGAGTTA
* * * *
559465 TTTTAGCGTGTCACAGCTTTTCGTGGCGTGTTGTGGGTTAACTAGTTTTTTGGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACT-GTTTTTTGGGT
* * * * *
559520 TGTTAGCGTGTCACGGCTGTTCCTGGCGTGTCATGGGTTAACTGAATTTATGGAT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACTG-TTTTTTGGGT
* * *
559575 TTTTTGCGTGTCACGGTTGTTCCTGACGTGTCGTGGGTTAACTGGTTTTTTGGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACT-GTTTTTTGGGT
* *
559630 TTTTAACATGTCACGGCTGTT
1 TTTTAGCGTGTCACGGCTGTT
559651 GGTGTAACGG
Statistics
Matches: 108, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
54 1 0.01
55 106 0.98
56 1 0.01
ACGTcount: A:0.12, C:0.15, G:0.30, T:0.42
Consensus pattern (54 bp):
TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAACTGTTTTTTGGGT
Found at i:563132 original size:156 final size:156
Alignment explanation
Indices: 562810--563104 Score: 455
Period size: 156 Copynumber: 1.9 Consensus size: 156
562800 TTTGAAAATT
* *
562810 AACTGCAATAACATATATAACTATGTTATTCAATAATCATATATGGAATTGTTGAACATTAATCG
1 AACTGCAATTACATATATAACTATGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCG
* * * *
562875 TTACAACTTTAATATCCTAACCGACGGCTCGTTAGCAATCTGCGGTGGAGCCGGACCTGTCGGTG
66 TTACAACTTTAATATCCTAACCGACGGCTCGTTAGCAATATGCGGTGGAGCCAGACCTATCGGTC
562940 CTTGAGGACCAATTGTCTCTTCCATA
131 CTTGAGGACCAATTGTCTCTTCCATA
* * *
562966 AACTGCAATTACATATATAATTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
1 AACTGCAATTACATATATAACTATGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCG
* * * ** *
563031 TTACAACTTTAATATCCTTACCGTCGGCTTGTTAGCTGTATGCGGTTGAGCCAGACCTATCGGTC
66 TTACAACTTTAATATCCTAACCGACGGCTCGTTAGCAATATGCGGTGGAGCCAGACCTATCGGTC
563096 CTTGAGGAC
131 CTTGAGGAC
563105 TTGTTGTCAT
Statistics
Matches: 124, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
156 124 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (156 bp):
AACTGCAATTACATATATAACTATGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCG
TTACAACTTTAATATCCTAACCGACGGCTCGTTAGCAATATGCGGTGGAGCCAGACCTATCGGTC
CTTGAGGACCAATTGTCTCTTCCATA
Found at i:563149 original size:156 final size:156
Alignment explanation
Indices: 562810--563149 Score: 421
Period size: 156 Copynumber: 2.2 Consensus size: 156
562800 TTTGAAAATT
* * * *
562810 AACTGCAATAACATATATAACTATGTTATTCAATAATCATATATGGAATTGTTGAACATTAATCG
1 AACTGCAATTACAGAAATAACTATGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCG
* * * *
562875 TTACAACTTTAATATCCTAACCGACGGCTCGTTAGCAATCTGCGGTGGAGCCGGACCTGTCGGTG
66 TTACAACTTTAATATCCTAACCGACGGCTCGTTAGCAATATGCGGTGGAGCCAGACCTATCGGTC
562940 CTTGAGGACCAATTGTCTCTTCCATA
131 CTTGAGGACCAATTGTCTCTTCCATA
* * * * *
562966 AACTGCAATTACATATATAATTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
1 AACTGCAATTACAGAAATAACTATGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCG
* * * ** *
563031 TTACAACTTTAATATCCTTACCGTCGGCTTGTTAGCTGTATGCGGTTGAGCCAGACCTATCGGTC
66 TTACAACTTTAATATCCTAACCGACGGCTCGTTAGCAATATGCGGTGGAGCCAGACCTATCGGTC
*** ***
563096 CTTGAGGACTTGTTGTCAT-TTTTGTA
131 CTTGAGGACCAATTGTC-TCTTCCATA
* *
563122 AACTGCAATTATAGAAATTACTATGTTA
1 AACTGCAATTACAGAAATAACTATGTTA
563150 CTCGAGAAAC
Statistics
Matches: 156, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
156 155 0.99
157 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (156 bp):
AACTGCAATTACAGAAATAACTATGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCG
TTACAACTTTAATATCCTAACCGACGGCTCGTTAGCAATATGCGGTGGAGCCAGACCTATCGGTC
CTTGAGGACCAATTGTCTCTTCCATA
Found at i:565132 original size:31 final size:31
Alignment explanation
Indices: 564799--565141 Score: 384
Period size: 31 Copynumber: 11.1 Consensus size: 31
564789 ATAAGGAATG
* *
564799 AATGTTGTGACACGCCATTCATAGCAAG-CAA
1 AATGTTGTGACACGCCATGCATAACAAGTC-A
* * *
564830 AATGTTATGACACGCCATGCATAACAACTTA
1 AATGTTGTGACACGCCATGCATAACAAGTCA
* * *
564861 AATGTTGTGGCACGCCATGCATAACAACTTA
1 AATGTTGTGACACGCCATGCATAACAAGTCA
*
564892 AATGTTGTGACACGCCATGCATAACAAGTTA
1 AATGTTGTGACACGCCATGCATAACAAGTCA
**
564923 AACATTGTGACACGCCATGCATAACAAGTCA
1 AATGTTGTGACACGCCATGCATAACAAGTCA
* * * *
564954 AATGTTGTGACACGTCATGTATATCAAGTAA
1 AATGTTGTGACACGCCATGCATAACAAGTCA
* * *
564985 AATGCTGTCACACGCCATGCATAGCAAGT-A
1 AATGTTGTGACACGCCATGCATAACAAGTCA
* * *
565015 AATTGTTGTGACACGTCATGCATATCAAGTAA
1 AA-TGTTGTGACACGCCATGCATAACAAGTCA
* * * *
565047 AATGCTATCACACGCCATGCATAACAAGTAA
1 AATGTTGTGACACGCCATGCATAACAAGTCA
*
565078 AATGTTGTGACACGCCATGCATATCAAGTCA
1 AATGTTGTGACACGCCATGCATAACAAGTCA
* * * *
565109 AATGTTCTCACACGCCATGCATATCAAATCA
1 AATGTTGTGACACGCCATGCATAACAAGTCA
565140 AA
1 AA
565142 CCATATAAAG
Statistics
Matches: 269, Mismatches: 40, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
30 3 0.01
31 263 0.98
32 3 0.01
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (31 bp):
AATGTTGTGACACGCCATGCATAACAAGTCA
Found at i:565725 original size:53 final size:53
Alignment explanation
Indices: 565668--565768 Score: 166
Period size: 53 Copynumber: 1.9 Consensus size: 53
565658 TAGTAGCTGC
* *
565668 TCAAGCATTGACGTGTCACACACTCTAAGCCATGACCATGGCGTGTCAGCTTT
1 TCAAGCAATGACGTGTCACACACTCTAAACCATGACCATGGCGTGTCAGCTTT
* *
565721 TCAAGCAATGCCGTGTCACACACTCTAAACCATGACCATGTCGTGTCA
1 TCAAGCAATGACGTGTCACACACTCTAAACCATGACCATGGCGTGTCA
565769 CCAACTCTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (53 bp):
TCAAGCAATGACGTGTCACACACTCTAAACCATGACCATGGCGTGTCAGCTTT
Found at i:565841 original size:47 final size:47
Alignment explanation
Indices: 565756--566255 Score: 500
Period size: 47 Copynumber: 10.4 Consensus size: 47
565746 TAAACCATGA
* * * * *
565756 CCATGTCGTGTCACCAACTCTGAACTTTAGAGTGTCACA-ACTTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGA-TTCCCT
* * *
565803 CCATGGCATGTCACCAACTCTTAACTCTGGTGTCTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * *
565850 CCATGGCGTCTTACCAACT-TTGAACACCGGCGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTT-AACTCTGGCGTGTCACAGATTCCCT
** * *
565897 CCATACCATGTCACCAACTCTTAACTCTGACGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * *
565944 CCATGGTGTGTCACCAACTCTTAACTCTAGCGTGTCACACATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * *
565991 TCATGGCGTCTCACCAACTCTAAACGCTGACGTGTCTGACGTCTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAA--CT--C-TG---G-CGTGTCACAGATTCCCT
* * * * *
566047 CCATGGCATCTCACCAACTCTGAACACTGGAGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* ** * *
566094 CCATGTCGTGTCATAAACTCCTAACTCTGGCGTGTTACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * * *
566141 CCATGGCATCTCACCAAATCTGAACGCTGGCGTGTCACAAATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* *
566188 CCATGGCGTGTCGCCAACTCTTAACTCTGGCGTCTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* *
566235 CCATGACGTCTCACCAACTCT
1 CCATGGCGTGTCACCAACTCT
566256 AACCAGTGTC
Statistics
Matches: 367, Mismatches: 74, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
46 2 0.01
47 316 0.86
48 4 0.01
49 2 0.01
51 3 0.01
52 2 0.01
54 1 0.00
55 1 0.00
56 36 0.10
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.27
Consensus pattern (47 bp):
CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
Found at i:566089 original size:197 final size:188
Alignment explanation
Indices: 565766--566255 Score: 584
Period size: 197 Copynumber: 2.6 Consensus size: 188
565756 CCATGTCGTG
* ** * * * * *
565766 TCACCAACTCTGAACTTTAGAGTGTCACAACTTCCCTCCATGGCATGTCACCAACTCTTAACTCT
1 TCACCAAATCTGAACGCTAGCGTGTCACAAATTCCCTCCATGGCGTCTCACCAACTCTAAACTCT
* * * *
565831 GGTGTCTCACAGATTCCCTCCATGGCGTCTTACCAACTTTGAACACCGGCGTGTCACAGATTCCC
66 GGCGTCTCACAGATTCCCTCCATGGCGTCTCACCAACTCTGAACACCGGAGTGTCACAGATTCCC
* * ** *
565896 TCCATACCATGTCACCAACTCTTAACTCTGACGTGTCACAGATTCCCTCCATGGTGTG
131 TCCATACCATGTCACAAACTCCTAACTCTGACGTGTCACAGATTCCCTCCATGGCATC
* * * * *
565954 TCACCAACTCTTAACTCTAGCGTGTCACACATTCCCTTCATGGCGTCTCACCAACTCTAAACGCT
1 TCACCAAATCTGAACGCTAGCGTGTCACAAATTCCCTCCATGGCGTCTCACCAACTCTAAA--CT
* *
566019 GACGTGTCTGACGTCTCACAGATTCCCTCCATGGCATCTCACCAACTCTGAACACTGGAGTGTCA
64 --C-TG---G-CGTCTCACAGATTCCCTCCATGGCGTCTCACCAACTCTGAACACCGGAGTGTCA
** * * * *
566084 CAGATTCCCTCCATGTCGTGTCATAAACTCCTAACTCTGGCGTGTTACAGATTCCCTCCATGGCA
122 CAGATTCCCTCCATACCATGTCACAAACTCCTAACTCTGACGTGTCACAGATTCCCTCCATGGCA
566149 TC
187 TC
* * * *
566151 TCACCAAATCTGAACGCTGGCGTGTCACAAATTCCCTCCATGGCGTGTCGCCAACTCTTAACTCT
1 TCACCAAATCTGAACGCTAGCGTGTCACAAATTCCCTCCATGGCGTCTCACCAACTCTAAACTCT
*
566216 GGCGTCTCACAGATTCCCTCCATGACGTCTCACCAACTCT
66 GGCGTCTCACAGATTCCCTCCATGGCGTCTCACCAACTCT
566256 AACCAGTGTC
Statistics
Matches: 256, Mismatches: 37, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
188 88 0.34
189 1 0.00
190 2 0.01
192 3 0.01
193 3 0.01
195 2 0.01
196 1 0.00
197 156 0.61
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (188 bp):
TCACCAAATCTGAACGCTAGCGTGTCACAAATTCCCTCCATGGCGTCTCACCAACTCTAAACTCT
GGCGTCTCACAGATTCCCTCCATGGCGTCTCACCAACTCTGAACACCGGAGTGTCACAGATTCCC
TCCATACCATGTCACAAACTCCTAACTCTGACGTGTCACAGATTCCCTCCATGGCATC
Found at i:566234 original size:244 final size:244
Alignment explanation
Indices: 565797--566257 Score: 645
Period size: 244 Copynumber: 1.9 Consensus size: 244
565787 GTGTCACAAC
* * * * *
565797 TTCCCTCCATGGCATGTCACCAACTCTTAACTCTGGTGTCTCACAGATTCCCTCCATGGCGTCTT
1 TTCCCTCCATGGCATCTCACCAACTCTGAACACTGGAGTCTCACAGATTCCCTCCATGGCGTCTC
* * * * * *
565862 ACCAACTTTGAACACCGGCGTGTCACAGATTCCCTCCATACCATGTCACCAACTCTTAACTCTGA
66 ACAAACTCTGAACACCGGCGTGTCACAGATTCCCTCCATACCATCTCACCAAATCTGAACGCTGA
* * * *
565927 CGTGTCACAGATTCCCTCCATGGTGTGTCACCAACTCTTAACTCTAGCGTGTCACACATTCCCTT
131 CGTGTCACAAATTCCCTCCATGGCGTGTCACCAACTCTTAACTCTAGCGTCTCACACATTCCCTC
*
565992 CATGGCGTCTCACCAACTCTAAACGCTGACGTGTCTGACGTCTCACAGA
196 CATGACGTCTCACCAACTCTAAACGCTGACGTGTCTGACGTCTCACAGA
* * *
566041 TTCCCTCCATGGCATCTCACCAACTCTGAACACTGGAGTGTCACAGATTCCCTCCATGTCGTGTC
1 TTCCCTCCATGGCATCTCACCAACTCTGAACACTGGAGTCTCACAGATTCCCTCCATGGCGTCTC
* * * * **
566106 ATAAACTCCT-AACTCTGGCGTGTTACAGATTCCCTCCATGGCATCTCACCAAATCTGAACGCTG
66 ACAAACT-CTGAACACCGGCGTGTCACAGATTCCCTCCATACCATCTCACCAAATCTGAACGCTG
* * * *
566170 GCGTGTCACAAATTCCCTCCATGGCGTGTCGCCAACTCTTAACTCTGGCGTCTCACAGATTCCCT
130 ACGTGTCACAAATTCCCTCCATGGCGTGTCACCAACTCTTAACTCTAGCGTCTCACACATTCCCT
566235 CCATGACGTCTCACCAACTCTAA
195 CCATGACGTCTCACCAACTCTAA
566258 CCAGTGTCGT
Statistics
Matches: 187, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
244 186 0.99
245 1 0.01
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.27
Consensus pattern (244 bp):
TTCCCTCCATGGCATCTCACCAACTCTGAACACTGGAGTCTCACAGATTCCCTCCATGGCGTCTC
ACAAACTCTGAACACCGGCGTGTCACAGATTCCCTCCATACCATCTCACCAAATCTGAACGCTGA
CGTGTCACAAATTCCCTCCATGGCGTGTCACCAACTCTTAACTCTAGCGTCTCACACATTCCCTC
CATGACGTCTCACCAACTCTAAACGCTGACGTGTCTGACGTCTCACAGA
Found at i:568376 original size:16 final size:16
Alignment explanation
Indices: 568339--568376 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
568329 CAATGTTTTT
568339 TAATAT-AAAAATAAA
1 TAATATGAAAAATAAA
568354 -AACTATGAAAAATAAA
1 TAA-TATGAAAAATAAA
568370 TAATATG
1 TAATATG
568377 GCATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.10
15 3 0.15
16 13 0.65
17 2 0.10
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (16 bp):
TAATATGAAAAATAAA
Found at i:568554 original size:8 final size:7
Alignment explanation
Indices: 568518--568550 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
568508 CATATTACCC
568518 TTTTTCT
1 TTTTTCT
568525 TTTTTCT
1 TTTTTCT
568532 TTTTTCT
1 TTTTTCT
568539 TTTTTCT
1 TTTTTCT
568546 TTTTT
1 TTTTT
568551 TCTTCATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:571670 original size:2 final size:2
Alignment explanation
Indices: 571663--571690 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
571653 ATCTGTCCCA
571663 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
571691 GTTCAACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:582512 original size:10 final size:9
Alignment explanation
Indices: 582475--582512 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
582465 ATTAAATATT
582475 TAATT-AAA
1 TAATTAAAA
582483 TAATTAAAA
1 TAATTAAAA
582492 TAATTAAAAA
1 TAATT-AAAA
582502 TAATATAAAA
1 TAAT-TAAAA
582512 T
1 T
582513 TTAATTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 5 0.19
9 8 0.30
10 13 0.48
11 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TAATTAAAA
Found at i:588243 original size:40 final size:40
Alignment explanation
Indices: 588186--588263 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
588176 TTGACTATTT
* *
588186 TTCACTTTAGTGAGGTTTTCAACCTTGCCA-AGATTGGTGA
1 TTCACCTTAGTGAGGTTTTCAACCTCGCCACA-ATTGGTGA
*
588226 TTCACCTTAGTGGGGTTTTCAACCTCGCCACAATTGGT
1 TTCACCTTAGTGAGGTTTTCAACCTCGCCACAATTGGT
588264 ATTTTTCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (40 bp):
TTCACCTTAGTGAGGTTTTCAACCTCGCCACAATTGGTGA
Found at i:598521 original size:19 final size:21
Alignment explanation
Indices: 598477--598549 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
598467 AAATCGAATT
*
598477 TATTTTTTAATATAAAAAATA
1 TATTTATTAATATAAAAAATA
598498 TATTTATTAA-ATAAATAAATA
1 TATTTATTAATATAAA-AAATA
* * * *
598519 TTTTTATTTATAAAATTAAAATT
1 TATTTATTAATATAA--AAAATA
598542 TATTTATT
1 TATTTATT
598550 TTTTATTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.12
21 22 0.52
22 3 0.07
23 11 0.26
24 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTATTAATATAAAAAATA
Found at i:606360 original size:8 final size:8
Alignment explanation
Indices: 606349--606410 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
606339 AATTAAAAAG
606349 TTAATATA
1 TTAATATA
606357 TTAATA-A
1 TTAATATA
606364 TTAATA-A
1 TTAATATA
*
606371 ATAA-AGTA
1 TTAATA-TA
*
606379 TTAATATT
1 TTAATATA
*
606387 TTAATATT
1 TTAATATA
606395 TTAATTATA
1 TTAA-TATA
606404 TTAATAT
1 TTAATAT
606411 TAATAATGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 1 0.02
7 11 0.24
8 26 0.57
9 8 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (8 bp):
TTAATATA
Found at i:606369 original size:15 final size:14
Alignment explanation
Indices: 606349--606415 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 14
606339 AATTAAAAAG
606349 TTAATATATTAATAA
1 TTAATATATTAAT-A
* *
606364 TTAATAAATAAAGTA
1 TTAATATATTAA-TA
*
606379 TTAATATTTTAATA
1 TTAATATATTAATA
606393 TTTTAATTATATTAATA
1 --TTAA-TATATTAATA
606410 TTAATA
1 TTAATA
606416 ATGTTTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
14 4 0.10
15 24 0.57
16 5 0.12
17 9 0.21
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (14 bp):
TTAATATATTAATA
Found at i:606426 original size:26 final size:26
Alignment explanation
Indices: 606377--606443 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
606367 ATAAATAAAG
*
606377 TATTAATATT-TTAATATTTTAATTA
1 TATTAATATTATTAATATTTAAATTA
* *
606402 TATTAATATTAATAATGTTTAAATTA
1 TATTAATATTATTAATATTTAAATTA
606428 TATATAA-ATTATTAAT
1 TAT-TAATATTATTAAT
606444 TTTTTATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 10 0.28
26 23 0.64
27 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (26 bp):
TATTAATATTATTAATATTTAAATTA
Found at i:606480 original size:11 final size:10
Alignment explanation
Indices: 606465--606506 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
606455 TATGAATAAA
606465 TTTTTCTTTT
1 TTTTTCTTTT
*
606475 TATTTT-ATTT
1 T-TTTTCTTTT
606485 TTTTTCTTTT
1 TTTTTCTTTT
606495 TTCTTTCTTTT
1 TT-TTTCTTTT
606506 T
1 T
606507 CTCTATGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 4 0.15
10 10 0.37
11 13 0.48
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:622557 original size:3 final size:3
Alignment explanation
Indices: 622549--622585 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
622539 TCCCAACAAG
622549 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
622586 GAATCATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:626562 original size:21 final size:21
Alignment explanation
Indices: 626536--626600 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
626526 ATTAAACGAA
626536 TATATATTTATTAAATATATT
1 TATATATTTATTAAATATATT
*
626557 TATATATATATTTAAA-AT-TT
1 TATATATTTA-TTAAATATATT
* *
626577 TAATATGATTAATTAATTATATT
1 T-ATAT-ATTTATTAAATATATT
626600 T
1 T
626601 TATTTATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 3 0.09
21 19 0.54
22 10 0.29
23 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATATATTTATTAAATATATT
Found at i:626621 original size:23 final size:23
Alignment explanation
Indices: 626536--626623 Score: 60
Period size: 23 Copynumber: 3.8 Consensus size: 23
626526 ATTAAACGAA
* *
626536 TATATATTTATTAA-A-TATATT
1 TATATAATTATTAATATTTTATT
* *
626557 TATAT-ATATATTTAAAATTTTA-A
1 TATATAAT-TA-TTAATATTTTATT
626580 TATGATTAATTAATT-ATATTTTATT
1 TAT-A-TAATT-ATTAATATTTTATT
626605 TATATAATTATTAATATTT
1 TATATAATTATTAATATTT
626624 AATGTTTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
20 1 0.02
21 7 0.13
22 7 0.13
23 15 0.29
24 12 0.23
25 7 0.13
26 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (23 bp):
TATATAATTATTAATATTTTATT
Found at i:645243 original size:2 final size:2
Alignment explanation
Indices: 645236--645263 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
645226 GGTTTGCTTT
645236 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
645264 AGGGGGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:645310 original size:2 final size:2
Alignment explanation
Indices: 645303--645328 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
645293 GGGNCTTTGT
645303 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
645329 AGGGGGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:645516 original size:3 final size:3
Alignment explanation
Indices: 645508--645537 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
645498 CTTAAGGGAT
645508 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
645538 TTAGAAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:661534 original size:10 final size:10
Alignment explanation
Indices: 661501--661539 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
661491 TTTAAAAATT
661501 AAATTAATCA
1 AAATTAATCA
* *
661511 AATTGTAATAA
1 AAAT-TAATCA
661522 AAATTAATCA
1 AAATTAATCA
661532 AAATTAAT
1 AAATTAAT
661540 TGAATTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (10 bp):
AAATTAATCA
Found at i:674926 original size:2 final size:2
Alignment explanation
Indices: 674919--674965 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
674909 TACAAAACAG
674919 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
674961 TA TA T
1 TA TA T
674966 TAAAGTCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:677082 original size:3 final size:3
Alignment explanation
Indices: 677074--677104 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
677064 TACTACATAG
677074 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
677105 TTGCCTGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:687236 original size:40 final size:40
Alignment explanation
Indices: 687191--687270 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
687181 TTAATTTATT
*
687191 ATTATTACTATT-A-TTATAATATTTTTTAAATTTAAAATTA
1 ATTATTA-TATTCATTTATAATA-TTATTAAATTTAAAATTA
* *
687231 ATTATTATTTTCATTTATAATATTATTAAATTTAACATTA
1 ATTATTATATTCATTTATAATATTATTAAATTTAAAATTA
687271 TTTTTAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 3 0.09
40 24 0.69
41 8 0.23
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (40 bp):
ATTATTATATTCATTTATAATATTATTAAATTTAAAATTA
Found at i:692927 original size:99 final size:101
Alignment explanation
Indices: 692810--693018 Score: 278
Period size: 108 Copynumber: 2.0 Consensus size: 101
692800 TGAATTTTTC
*
692810 TGCTTTGGTCTTTTAATTCCATTTG-AT-ATTTAGTCCTTTATTCTTGTGTTTCTCATAGAAAGC
1 TGCTTTGGTCTTTTAATTCCATTTGAATAATTTAGTCCTTTATTCTTGTGTGTCTCATAGAAAGC
*
692873 AACTGTTCCTTGGTTGATCAACAAGTTTAACTAGTT
66 AACTGTGCCTTGGTTGATCAACAAGTTTAACTAGTT
* *
692909 TGCTTTGGTCTTTTAATTCCATTTGATATGAAAGCAATTTAGTCCTTTATTTTTTTGTGTCTCAT
1 TGCTTTGGTCTTTTAATTCCATTTGA-AT------AATTTAGTCCTTTATTCTTGTGTGTCTCAT
* * *
692974 AGAAAGGAACTGTGCCTTGGTTGGTCAACAAGTTTGACTAGTT
59 AGAAAGCAACTGTGCCTTGGTTGATCAACAAGTTTAACTAGTT
693017 TG
1 TG
693019 GCATGCTGAA
Statistics
Matches: 94, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
99 25 0.27
101 2 0.02
108 67 0.71
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (101 bp):
TGCTTTGGTCTTTTAATTCCATTTGAATAATTTAGTCCTTTATTCTTGTGTGTCTCATAGAAAGC
AACTGTGCCTTGGTTGATCAACAAGTTTAACTAGTT
Found at i:697188 original size:95 final size:94
Alignment explanation
Indices: 697025--697210 Score: 248
Period size: 95 Copynumber: 2.0 Consensus size: 94
697015 ATTAGCTGCC
** *
697025 AGTAGGGTGATTGATGCATCCCATGAACGATGGCTTATTCCTGGTTTACAGAGCTTCATAAATTA
1 AGTAGGGTGATCAATGCATCCCATGAACGATGGCTTATTCCTCGTTTACAGAGCTTCATAAATTA
*
697090 AAGTGAAATTTGGCTCATTAGGTTTGCACG
66 AAGTGAAATTT-GCTAATTAGGTTTGCACG
* * * * * *
697120 AGTAGGGTGATCAATGTATCCCGTTAATGATGGCTTATTCCTCGTTTAC-GAAGTTTCATACATT
1 AGTAGGGTGATCAATGCATCCCATGAACGATGGCTTATTCCTCGTTTACAG-AGCTTCATAAATT
*
697184 AAAGTGAACTTTGCTAATTAGGTTTGC
65 AAAGTGAAATTTGCTAATTAGGTTTGC
697211 TATTTTGATA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 15 0.19
95 64 0.81
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (94 bp):
AGTAGGGTGATCAATGCATCCCATGAACGATGGCTTATTCCTCGTTTACAGAGCTTCATAAATTA
AAGTGAAATTTGCTAATTAGGTTTGCACG
Found at i:703786 original size:42 final size:42
Alignment explanation
Indices: 703739--703826 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
703729 CAGCACTTGT
* * *
703739 TTCTCCAATGAAGAGGTTTTCACTATTGCTAAGGCTGGTG-AA
1 TTCTCCAATGAAGAGGTTTT-ACTAGTGCTAAGACTGATGAAA
703781 TTCTCCAATGAAGAGGTTTTACTAGTGCTAAGACTGATGAAA
1 TTCTCCAATGAAGAGGTTTTACTAGTGCTAAGACTGATGAAA
703823 TTCT
1 TTCT
703827 ACTCATTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
41 16 0.38
42 26 0.62
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (42 bp):
TTCTCCAATGAAGAGGTTTTACTAGTGCTAAGACTGATGAAA
Found at i:725998 original size:281 final size:281
Alignment explanation
Indices: 725481--726047 Score: 983
Period size: 281 Copynumber: 2.0 Consensus size: 281
725471 AACTATGCAT
* **
725481 CACAACAATCAGGTTCTAATAAATCATAGATTACCAACAACATCATAAAATGATAAAAATGTAGG
1 CACAACAATCAGGTTCTAATAAATCATAAATTACCAACAACATCATAAAATGATAAAAACATAGG
725546 ACATTTTGGCATTTACTAAACCTTGGAAATTAGACATCAGAATTTACAAATTTTTCACATAGCAT
66 ACATTTTGGCATTTACTAAACCTTGGAAATTAGACATCAGAATTTACAAATTTTTCACATAGCAT
* * * **
725611 TATACTAGTATAAAAAAGGAATCAAGAAATTTATTAAAGAATTTTACTTTAGGTAAAGAATGTAA
131 TATACTAGTACAAAAAAGGAATCAAGAAAGTAATTAAAGAATTTTACTTTAGGTAAAGAACATAA
* *
725676 CAACATTGCTATTATCAAACATCTTAGTTAGAAACAAAAAGACTGGTTGAGAGTTATCAGGTTGC
196 CAACATTGCTATTATCAAACATCTTAATTAGAAACAAAAAGACTGCTTGAGAGTTATCAGGTTGC
*
725741 ACTCTTTTAATAGATTAATGA
261 ACTCTCTTAATAGATTAATGA
*
725762 CACAACAATCAGGTTCTAATAAATCATAAATTACCAATAACATCATAAAATGATAAAAACATAGG
1 CACAACAATCAGGTTCTAATAAATCATAAATTACCAACAACATCATAAAATGATAAAAACATAGG
*
725827 ACATTTTGGCATTTATTAAACCTTGGAAATTAGACATCAGAATTTACAAATTTTTCACATAGCAT
66 ACATTTTGGCATTTACTAAACCTTGGAAATTAGACATCAGAATTTACAAATTTTTCACATAGCAT
*
725892 TATACTAGTACAAAAAAGGCATCAAGAAAGTAATTAAAGAATTTTACTTTAGGTAAAGAACATAA
131 TATACTAGTACAAAAAAGGAATCAAGAAAGTAATTAAAGAATTTTACTTTAGGTAAAGAACATAA
*
725957 CAACATTGCTATTATCAAGCATCTTAATTAG-AACAAAAAAGACTGCTTGAGAGTTATCAGGTTG
196 CAACATTGCTATTATCAAACATCTTAATTAGAAAC-AAAAAGACTGCTTGAGAGTTATCAGGTTG
726021 CACTCTCTTAATAGATTAATGA
260 CACTCTCTTAATAGATTAATGA
726043 CACAA
1 CACAA
726048 TATCTACAAT
Statistics
Matches: 270, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
280 3 0.01
281 267 0.99
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (281 bp):
CACAACAATCAGGTTCTAATAAATCATAAATTACCAACAACATCATAAAATGATAAAAACATAGG
ACATTTTGGCATTTACTAAACCTTGGAAATTAGACATCAGAATTTACAAATTTTTCACATAGCAT
TATACTAGTACAAAAAAGGAATCAAGAAAGTAATTAAAGAATTTTACTTTAGGTAAAGAACATAA
CAACATTGCTATTATCAAACATCTTAATTAGAAACAAAAAGACTGCTTGAGAGTTATCAGGTTGC
ACTCTCTTAATAGATTAATGA
Found at i:744548 original size:54 final size:54
Alignment explanation
Indices: 744484--744593 Score: 195
Period size: 54 Copynumber: 2.0 Consensus size: 54
744474 ATCAGCAGCA
744484 GCTGCAGTCAGTTCTCCTGAGAAG-ACTGTGGGTAATGCAACAAAATCAAATCCT
1 GCTGCAGTCAGTTCTCCTGAGAAGCA-TGTGGGTAATGCAACAAAATCAAATCCT
*
744538 GCTGCAGTCAGTTCTCCTGAGAAGCATGTGGGTAATGCAACAAAATCGAATCCT
1 GCTGCAGTCAGTTCTCCTGAGAAGCATGTGGGTAATGCAACAAAATCAAATCCT
744592 GC
1 GC
744594 AGATCTTCAG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
54 53 0.98
55 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (54 bp):
GCTGCAGTCAGTTCTCCTGAGAAGCATGTGGGTAATGCAACAAAATCAAATCCT
Found at i:761482 original size:23 final size:23
Alignment explanation
Indices: 761435--761483 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
761425 ATAAAATATT
* * **
761435 AAATATCTAAAAATTTATTTTAA
1 AAATAACTAAAAACTTATTAAAA
761458 AAATAACTAAAAACTTATTAAAA
1 AAATAACTAAAAACTTATTAAAA
761481 AAA
1 AAA
761484 ATGAAAAGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATAACTAAAAACTTATTAAAA
Found at i:765258 original size:13 final size:14
Alignment explanation
Indices: 765240--765268 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
765230 AATTAAAAAA
765240 TAAAAAAAT-ATTT
1 TAAAAAAATAATTT
765253 TAAAAAAATAATTT
1 TAAAAAAATAATTT
765267 TA
1 TA
765269 TGTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAAAATAATTT
Found at i:775127 original size:3 final size:3
Alignment explanation
Indices: 775119--775145 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
775109 ACAATTCACG
775119 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
775146 TTAGTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:777113 original size:79 final size:74
Alignment explanation
Indices: 776987--777139 Score: 245
Period size: 79 Copynumber: 2.0 Consensus size: 74
776977 ACATTAAAAA
776987 GTTTAAAGTTAAAACTATTGTTTTTGCTTGTCTAATTTTAACTTTACATTCCTTCTGTC-ACGTT
1 GTTTAAAGTTAAAACTATTGTTTTTGCTTGTCTAATTTTAACTTTACATTCCTTCTGTCTACGTT
777051 TTTTTTTTT
66 TTTTTTTTT
777060 NGTTTAAAAGTTAAAACTTATTTGTTTTTGTCTTGTCTTAATTTTAACTTTACATTCCTTCTGTC
1 -GTTT-AAAGTTAAAAC-TA-TTGTTTTTG-CTTGTC-TAATTTTAACTTTACATTCCTTCTGTC
777125 TACGTTTTTTTTTTT
60 TACGTTTTTTTTTTT
777140 TTTGGTTTCT
Statistics
Matches: 73, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
74 4 0.05
75 11 0.15
76 2 0.03
77 9 0.12
78 6 0.08
79 27 0.37
80 14 0.19
ACGTcount: A:0.20, C:0.13, G:0.09, T:0.57
Consensus pattern (74 bp):
GTTTAAAGTTAAAACTATTGTTTTTGCTTGTCTAATTTTAACTTTACATTCCTTCTGTCTACGTT
TTTTTTTTT
Found at i:777521 original size:31 final size:30
Alignment explanation
Indices: 777486--777549 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
777476 GGCGTAAAAA
* *
777486 AAAAAAGA-ACAAAGACAAGGAGCTTCGCGTC
1 AAAAAAGACA-AAAGACAAAG-GCTACGCGTC
*
777517 AAAAAAGTCAAAAGACAAAGGCTACGCGTC
1 AAAAAAGACAAAAGACAAAGGCTACGCGTC
777547 AAA
1 AAA
777550 CAGGGAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 12 0.41
31 16 0.55
32 1 0.03
ACGTcount: A:0.52, C:0.19, G:0.20, T:0.09
Consensus pattern (30 bp):
AAAAAAGACAAAAGACAAAGGCTACGCGTC
Found at i:778709 original size:2 final size:2
Alignment explanation
Indices: 778702--778730 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
778692 ATTCAGCTAT
778702 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
778731 CTTTGTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:785142 original size:129 final size:128
Alignment explanation
Indices: 784904--785163 Score: 432
Period size: 129 Copynumber: 2.0 Consensus size: 128
784894 CAAACGCGGA
784904 TTTCAACATGTTCCTTTCATTAGAATCTCCCTGGACAGGGAGGTTCCCGTTGTTGGTGGCCGAAA
1 TTTCAACATGTTCCTTTCATTAGAATCTCCCTGGACAGGGAGGTTCCCGTTGTTGGTGGCCGAAA
*
784969 CTGGACAGGCTTCTGACTTCTTATTCAATGAACAAAACATCCTGGAAACAACACTGGTGACAG
66 CTGGACAGGCTTCTGACTTCTTATTCAATGAACAAAACATCCTGGAAACAACACTGGAGACAG
* * *
785032 TTTCAACCTTGTTCCTTTCATTAGAATCTGCCC-GGACAGGGAGGTTCCTGTTGTTGGTGGCGGA
1 TTTCAA-CATGTTCCTTTCATTAGAATCT-CCCTGGACAGGGAGGTTCCCGTTGTTGGTGGCCGA
* * *
785096 AACTGGAGAGGCTTCTGACTTCTTGTTCAATGAACAAAACATCCTGGAAACACCACTGGAGACAG
64 AACTGGACAGGCTTCTGACTTCTTATTCAATGAACAAAACATCCTGGAAACAACACTGGAGACAG
785161 TTT
1 TTT
785164 TGACTTCACT
Statistics
Matches: 123, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
128 6 0.05
129 114 0.93
130 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (128 bp):
TTTCAACATGTTCCTTTCATTAGAATCTCCCTGGACAGGGAGGTTCCCGTTGTTGGTGGCCGAAA
CTGGACAGGCTTCTGACTTCTTATTCAATGAACAAAACATCCTGGAAACAACACTGGAGACAG
Found at i:825706 original size:2 final size:2
Alignment explanation
Indices: 825699--825724 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
825689 ATCCAATTAA
825699 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
825725 TTTATATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:834509 original size:164 final size:162
Alignment explanation
Indices: 834315--834719 Score: 433
Period size: 164 Copynumber: 2.5 Consensus size: 162
834305 AATAACAAAT
* * * *
834315 TCTGAGTTTTGTTTCGATTAGGCAAATGTTTGTTAGAATACTTTATCGTACACTAGTCCATCTAG
1 TCTGAGTTTTGTTTAGATTATGAAAATGTTTGTTAGAATACTTTATCCTACACTA-TCCATCTAG
* ** * * * * *
834380 ACTCTAGAGTCTTGTTGTTTCTTTCCTCGTATTTGGATTTCGGACCCTACAACAACTGCTTTATA
65 ACTCTAGAGTCTTCTTGTTTCCATCCTCATAGTTAGATTT-GGAACCTACAACAACTACTTTATA
* *
834445 CTTCTGTA-TACTTTCACCA-TGATTAAA-ATAAGAA
129 CTT-TGTATTACTTTCA-CAGAGATTAAACA-AAAAA
* * * *
834479 TCTGAGTTTTGTTTAGACTATGAAAATGTTTATTGGAATA-TCTTATCCTACATGTATCCATCTA
1 TCTGAGTTTTGTTTAGATTATGAAAATGTTTGTTAGAATACT-TTATCCTACA-CTATCCATCTA
* * * * *
834543 GACTTTAGAGTCTTCTTGTTTCCATCCTTATAGTTAGATTTTGAACCTGCAAGAACTACTTTATA
64 GACTCTAGAGTCTTCTTGTTTCCATCCTCATAGTTAGATTTGGAACCTACAACAACTACTTTATA
834608 CTTTGTATTTACTTTCACAGAGATTAAACAAAAAA
129 CTTTGTA-TTACTTTCACAGAGATTAAACAAAAAA
* * * * *
834643 TTTGGGTTTTGTTTAGATTATGAAAATGTTTGTTAAAATACTTT-GCCTTACACGTATCCATCTT
1 TCTGAGTTTTGTTTAGATTATGAAAATGTTTGTTAGAATACTTTATCC-TACAC-TATCCATCTA
834707 GACTCTAGAGTCT
64 GACTCTAGAGTCT
834720 CGCTATTATC
Statistics
Matches: 199, Mismatches: 33, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
162 4 0.02
163 27 0.14
164 164 0.82
165 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (162 bp):
TCTGAGTTTTGTTTAGATTATGAAAATGTTTGTTAGAATACTTTATCCTACACTATCCATCTAGA
CTCTAGAGTCTTCTTGTTTCCATCCTCATAGTTAGATTTGGAACCTACAACAACTACTTTATACT
TTGTATTACTTTCACAGAGATTAAACAAAAAA
Found at i:834737 original size:164 final size:159
Alignment explanation
Indices: 834302--834871 Score: 400
Period size: 164 Copynumber: 3.5 Consensus size: 159
834292 GGTAGGAAAA
* * * *
834302 TAAAATAACAAATTCTGAGTTTTGTTTCGATTAGGCAAATGTTTGTTAGAATACTTTATCGTACA
1 TAAAATAA-AAATT-TGAGTTTTGTTTAGATTATGAAAATGTTTGTTAGAATAC-TT-TCCTACA
* ** * * *
834367 C-TAGTCCATCTAGACTCTAGAGTCTTGTTGTTTCTTTCCTCGTATTTGGATTTCGGACCCTACA
62 CGTA-TCCATCTAGACTCTAGAGTC-TGCT-TTTC-TTCCTTATAGTTAGATTTCGGAACCTACA
* *
834431 ACAACTGCTTTATACTTCTGTATACTTTCACCATGAT
123 ACAACTACTTTATACTTCTGTATACTTTCACCAAGAT
* * * * * *
834468 TAAAATAAGAATCTGAGTTTTGTTTAGACTATGAAAATGTTTATTGGAATATCTTATCCTACATG
1 TAAAATAAAAATTTGAGTTTTGTTTAGATTATGAAAATGTTTGTTAGAATA-CTT-TCCTACACG
* * * * * *
834533 TATCCATCTAGACTTTAGAGTCTTCTTGTTTCCATCCTTATAGTTAGATTT-TGAACCTGCAAGA
64 TATCCATCTAGACTCTAGAGTCTGC-T-TTT-CTTCCTTATAGTTAGATTTCGGAACCTACAACA
834597 ACTACTTTATACTT-TGTATTTACTTTCA-CAGAGAT
126 ACTACTTTATACTTCTGTA--TACTTTCACCA-AGAT
* *
834632 TAAACA-AAAAATTTGGGTTTTGTTTAGATTATGAAAATGTTTGTTAAAATACTTTGCCTTACAC
1 TAAA-ATAAAAATTTGAGTTTTGTTTAGATTATGAAAATGTTTGTTAGAATACTTT-CC-TACAC
* * *
834696 GTATCCATCTTGACTCTAGAGTCTCGCTATTATCTTCCTTATA-TGTGGATTTCGG-ACACTGCA
63 GTATCCATCTAGACTCTAGAGTCT-GCT-TT-TCTTCCTTATAGT-TAGATTTCGGAAC-CTACA
* *
834759 ACAA--A----ATACTTTCTGTTTACATTT-A-GAGAGAT
123 ACAACTACTTTATAC-TTCTGTATAC-TTTCACCA-AGAT
* * * * * *
834791 TAAAACAAAAATTTGAGTTTTGTTTACATCAT-AATATGTTAGTTAGATTACCTTAT-CTCACAC
1 TAAAATAAAAATTTGAGTTTTGTTTAGATTATGAAAATGTTTGTTAGAATA-CTT-TCCT-ACAC
* *
834854 GTATCCATTTAAACTCTA
63 GTATCCATCTAGACTCTA
834872 AAACTTGTTG
Statistics
Matches: 330, Mismatches: 52, Indels: 52
0.76 0.12 0.12
Matches are distributed among these distances:
157 1 0.00
158 35 0.11
159 44 0.13
160 6 0.02
161 3 0.01
162 5 0.02
163 32 0.10
164 177 0.54
165 19 0.06
166 8 0.02
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.40
Consensus pattern (159 bp):
TAAAATAAAAATTTGAGTTTTGTTTAGATTATGAAAATGTTTGTTAGAATACTTTCCTACACGTA
TCCATCTAGACTCTAGAGTCTGCTTTTCTTCCTTATAGTTAGATTTCGGAACCTACAACAACTAC
TTTATACTTCTGTATACTTTCACCAAGAT
Found at i:834928 original size:150 final size:154
Alignment explanation
Indices: 834756--835365 Score: 740
Period size: 155 Copynumber: 4.0 Consensus size: 154
834746 TTCGGACACT
* *
834756 GCAACAAAATACTTTCTGTTTACATTTAGAGAGATTAAAACAAAAATTTGAGTTTTGTTTACATC
1 GCAACAAAATACTTTCTGTTTACATTTACAGAGATTAAAACAAAAATTTGAGTTTTGTTTAAATC
* * **
834821 AT-A-ATAT-GTTAGTTAGATTACCTTATCTCACACGTATCCATTTAAACTCTA-AAACTTGTTG
66 ATAAGATATAGTTAGTTAGATTACCCTATCTCACACGTATCCATCTAAACTCTAGAATTTTGTTG
834882 TTTCTTTCTTTGTATTTGGATTTC
131 TTTCTTTCTTTGTATTTGGATTTC
*
834906 GCAACAAAATACTTTCTGTTTACATTTACAGAGATTAAAACAAAAATTTGAGTTTTGTTTAAATT
1 GCAACAAAATACTTTCTGTTTACATTTACAGAGATTAAAACAAAAATTTGAGTTTTGTTTAAATC
* * *
834971 ATAAGATATACATTAGTTAGATTACCCTATCTTACACGTATTCATCTAAACTCTAGAATTTTGTT
66 ATAAGATATA-GTTAGTTAGATTACCCTATCTCACACGTATCCATCTAAACTCTAGAATTTTGTT
* *
835036 GTTTCCTTCTTTGTATATGGATTTC
130 GTTTCTTTCTTTGTATTTGGATTTC
* * *
835061 GCAACAAAATACTTTCTGTTTACATTTACAGCGATTAAAACAAAAATATGAGTTTTGTTTAGATC
1 GCAACAAAATACTTTCTGTTTACATTTACAGAGATTAAAACAAAAATTTGAGTTTTGTTTAAATC
* * * *
835126 ATAAGATATACGTTAGTTAAATTACCCTATCTTACACGCATCCATCTAAATTCTAGAATTTTGTT
66 ATAAGATATA-GTTAGTTAGATTACCCTATCTCACACGTATCCATCTAAACTCTAGAATTTTGTT
*
835191 GTTTCCTTTC-TTGTAGTTGGACTTT-
130 GTTT-CTTTCTTTGTATTTGGA-TTTC
* * * * * * *
835216 --AACAAAATACTTTTTGTTTACATTCACGGAGATTAAAATAAAAATGTGAGTTTTGTTTATATT
1 GCAACAAAATACTTTCTGTTTACATTTACAGAGATTAAAACAAAAATTTGAGTTTTGTTTAAATC
* * * * * * * * *
835279 AT-A-ATAT-GTTAATTAGATTACCTTACCTCACACGTATTCATTTAAGCTCTATAATATTGTTC
66 ATAAGATATAGTTAGTTAGATTACCCTATCTCACACGTATCCATCTAAACTCTAGAATTTTGTTG
* * *
835341 TTACCTTCCTTG-ACTTTGGATTTC
131 TTTCTTTCTTTGTA-TTTGGATTTC
835365 G
1 G
835366 GACCTTGCAA
Statistics
Matches: 401, Mismatches: 48, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
148 8 0.02
149 52 0.13
150 64 0.16
151 5 0.01
152 5 0.01
153 57 0.14
154 39 0.10
155 164 0.41
156 7 0.02
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (154 bp):
GCAACAAAATACTTTCTGTTTACATTTACAGAGATTAAAACAAAAATTTGAGTTTTGTTTAAATC
ATAAGATATAGTTAGTTAGATTACCCTATCTCACACGTATCCATCTAAACTCTAGAATTTTGTTG
TTTCTTTCTTTGTATTTGGATTTC
Found at i:847133 original size:21 final size:23
Alignment explanation
Indices: 847107--847148 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
847097 TAAATTTTAG
847107 TTTTATAAATTA-TT-TTATTTT
1 TTTTATAAATTACTTATTATTTT
847128 TTTTATAAATTACTTATTATT
1 TTTTATAAATTACTTATTATT
847149 ATTAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATAAATTACTTATTATTTT
Found at i:848510 original size:3 final size:3
Alignment explanation
Indices: 848502--848532 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
848492 CAAGCTAACA
848502 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
848533 TCCTAGCTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:849804 original size:2 final size:2
Alignment explanation
Indices: 849797--849830 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
849787 AAAACCTCCA
849797 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
849831 TATATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:852752 original size:55 final size:56
Alignment explanation
Indices: 852664--852769 Score: 146
Period size: 55 Copynumber: 1.9 Consensus size: 56
852654 TTTTTTAATA
*
852664 TAATTTTTATATTATATAGTTTATTTTAATTTCT-TTTACCTATATTATATAAATTT
1 TAATTTTTATATTATATAGTTTATTTTAATTTCTAATT-CCTATATTATATAAATTT
* *
852720 TAATTTCTTATATT-T-TATTTTATTTTAATTTCTAATTCTTATATTATATA
1 TAATTT-TTATATTATATAGTTTATTTTAATTTCTAATTCCTATATTATATA
852770 TTTTATTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
55 29 0.64
56 9 0.20
57 7 0.16
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (56 bp):
TAATTTTTATATTATATAGTTTATTTTAATTTCTAATTCCTATATTATATAAATTT
Found at i:855428 original size:2 final size:2
Alignment explanation
Indices: 855421--855454 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
855411 CGTTCTGCAT
*
855421 GA GA GA GA GA GA GA GA GC GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
855455 CATGGAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:855547 original size:6 final size:6
Alignment explanation
Indices: 855538--855566 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
855528 TCTTGTTCTT
855538 GTTTTC GTTTTC GTTTTC GTTTTC GTTTT
1 GTTTTC GTTTTC GTTTTC GTTTTC GTTTT
855567 GGGGGCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.17, T:0.69
Consensus pattern (6 bp):
GTTTTC
Found at i:862762 original size:53 final size:53
Alignment explanation
Indices: 862682--862787 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
862672 GCACAAAGAA
*
862682 AGACTAAAATTGCTATCTCGATCATGTCTTCCTCAAGGCGAGGCACGGCAATC
1 AGACTAAAATTGCTATCTCGATCATGTCTTCCTCAAGGCAAGGCACGGCAATC
862735 AGACTAAAATTGCTATCTCGATCATGTCTTCCTCAAGGCAAGGCACGGCAATC
1 AGACTAAAATTGCTATCTCGATCATGTCTTCCTCAAGGCAAGGCACGGCAATC
862788 TGTTGGCATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (53 bp):
AGACTAAAATTGCTATCTCGATCATGTCTTCCTCAAGGCAAGGCACGGCAATC
Found at i:868643 original size:15 final size:15
Alignment explanation
Indices: 868625--868692 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 15
868615 TATTAAATTT
868625 TTTAAATATTAATAA
1 TTTAAATATTAATAA
868640 TTTAAA-ATTTAATTAAAA
1 TTTAAATA-TTAA-T--AA
868658 TATT-AATAATTAATAA
1 T-TTAAAT-ATTAATAA
868674 TTTAAATATTAAT-A
1 TTTAAATATTAATAA
868688 TTTAA
1 TTTAA
868693 TTTAATTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
14 7 0.16
15 18 0.40
16 7 0.16
18 6 0.13
19 6 0.13
20 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAATATTAATAA
Done.