Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 50
Found at i:5641240 original size:25 final size:24
Alignment explanation
Indices: 5641180--5641244 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 24
5641170 TATAAATAAT
* * *
5641180 ATTTTAATATAAATAATTATTTTA
1 ATTTTTATATAAATAATAATATTA
*
5641204 ATATTTA-A-AAATAATAATATTA
1 ATTTTTATATAAATAATAATATTA
5641226 ATTTTTATGATAAATAATA
1 ATTTTTAT-ATAAATAATA
5641245 TGTTCAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
22 18 0.55
23 1 0.03
24 6 0.18
25 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTTTTATATAAATAATAATATTA
Found at i:5654169 original size:15 final size:15
Alignment explanation
Indices: 5654149--5654178 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5654139 ATAATTATTA
5654149 ATCAATGATTAAAAT
1 ATCAATGATTAAAAT
*
5654164 ATCAATTATTAAAAT
1 ATCAATGATTAAAAT
5654179 TAAGAAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (15 bp):
ATCAATGATTAAAAT
Found at i:5655358 original size:2 final size:2
Alignment explanation
Indices: 5655351--5655383 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5655341 TTATTTAATA
5655351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5655384 TTAATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5655388 original size:7 final size:7
Alignment explanation
Indices: 5655348--5655401 Score: 60
Period size: 6 Copynumber: 7.9 Consensus size: 7
5655338 TAATTATTTA
5655348 ATAATAT
1 ATAATAT
5655355 AT-ATAT
1 ATAATAT
5655361 ATATATAT
1 ATA-ATAT
5655369 ATATATAT
1 ATA-ATAT
5655377 ATAATAT
1 ATAATAT
*
5655384 TTAATA-
1 ATAATAT
5655390 ATAATA-
1 ATAATAT
5655396 ATAATA
1 ATAATA
5655402 ATTTTAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
6 17 0.40
7 11 0.26
8 15 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATAATAT
Found at i:5655396 original size:16 final size:17
Alignment explanation
Indices: 5655333--5655413 Score: 65
Period size: 21 Copynumber: 4.2 Consensus size: 17
5655323 CCTGTTTGTA
5655333 AATA-ATAATTATTTAAT
1 AATATATAA-TATTTAAT
5655350 AATATATATATATATATATAT
1 AATATATA-ATAT-T-TA-AT
5655371 ATATATATAATATTTAAT
1 A-ATATATAATATTTAAT
5655389 AATAATAATAATAATTTTAAT
1 AAT-AT-ATAAT-A-TTTAAT
5655410 AATA
1 AATA
5655414 ATTTAAGTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 17
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.11
18 11 0.20
19 9 0.17
20 5 0.09
21 16 0.30
22 7 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATATAATATTTAAT
Found at i:5655416 original size:12 final size:12
Alignment explanation
Indices: 5655377--5655417 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5655367 ATATATATAT
5655377 ATAATATTTAATA
1 ATAAT-TTTAATA
5655390 ATAA---TAATA
1 ATAATTTTAATA
5655399 ATAATTTTAATA
1 ATAATTTTAATA
5655411 ATAATTT
1 ATAATTT
5655418 AAGTAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
9 9 0.36
12 12 0.48
13 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATTTTAATA
Found at i:5655664 original size:76 final size:76
Alignment explanation
Indices: 5655568--5656281 Score: 1293
Period size: 76 Copynumber: 9.4 Consensus size: 76
5655558 AAAGGTCTTA
* * *
5655568 AAACATCATGCATTGTAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
5655633 AGGCTTTTTGG
66 AGGCTTTTTGG
5655644 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
5655709 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
5655720 AAACATCATGCATTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
5655785 AGGCTTTTTGG
66 AGGCTTTTTGG
*
5655796 AAACATCATGCACTGCAGGACTTACAGATGATCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
5655861 AGGCTTTTTGG
66 AGGCTTTTTGG
*
5655872 AAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
5655937 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
5655948 AAACATCATGCACTGCAGGACTTATAGATGGCCATAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
5656013 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
5656024 AAACATCATGCACTACAGGACTTACAAATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
5656089 AGGCTTTTTGG
66 AGGCTTTTTGG
5656100 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
5656165 AGGCTTTTTGG
66 AGGCTTTTTGG
*
5656176 AAACATCATGCACTGCAGGACTTACATATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
5656241 AGGCTTTTAGG
66 AGGCTTTTTGG
*
5656252 AAACATTATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
5656282 TGGGAAATAG
Statistics
Matches: 613, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 613 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:5656817 original size:18 final size:18
Alignment explanation
Indices: 5656794--5656832 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
5656784 AAATCATCTG
5656794 ATCAACTTGTATCTTTGT
1 ATCAACTTGTATCTTTGT
5656812 ATCAACTTGTATCTTTGT
1 ATCAACTTGTATCTTTGT
5656830 ATC
1 ATC
5656833 TTCTTTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (18 bp):
ATCAACTTGTATCTTTGT
Found at i:5657002 original size:22 final size:22
Alignment explanation
Indices: 5656977--5657031 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
5656967 CATAAAGCTT
5656977 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
5656999 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
5657021 TCATCATTGAA
1 TCATCTTTGAA
5657032 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:5657456 original size:50 final size:54
Alignment explanation
Indices: 5657397--5657550 Score: 190
Period size: 54 Copynumber: 2.9 Consensus size: 54
5657387 TCATTGGTTC
* * *
5657397 GTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTG-TC-GA-G-AT
1 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTAT
* * * * *
5657447 GTAAAACATTTGAAAACACATTCTTCCTTTCTTGTAGCTTCTGCTCAGATGTTT
1 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTAT
* *
5657501 GTAAAGCATTTGACAACACATTCATCCTTTCCTGTGGCTTCTTCTCAGAT
1 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
5657551 TTCTCAATTA
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
50 36 0.42
51 2 0.02
52 2 0.02
53 1 0.01
54 45 0.52
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTAT
Found at i:5659745 original size:115 final size:114
Alignment explanation
Indices: 5659542--5659774 Score: 360
Period size: 115 Copynumber: 2.0 Consensus size: 114
5659532 ATGCAGTTCT
* * * * *
5659542 TCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACAC
1 TCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACAA
5659607 TTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAA-ATTCA
66 TTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAG-AACATTCA
* *
5659656 TCTTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACA
1 TCTTTCAAATCCAATGATTGG-TTCTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACA
* *
5659721 ATTCCAGAAGATGCTATTGTGGCTCCTTATTTCTGCTATGAGAACATTCA
65 ATTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGAACATTCA
5659771 TCTT
1 TCTT
5659775 GCTCCAGTTA
Statistics
Matches: 108, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
114 21 0.19
115 87 0.81
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGAACAA
TTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGAACATTCA
Found at i:5663917 original size:36 final size:36
Alignment explanation
Indices: 5663840--5663929 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
5663830 GTAAATGCAT
* *
5663840 AAATGCATAA-ATGCAAAAATAAGAATACAAACTGTG
1 AAATGCA-AAGATGCAAAAATAAGAATACAAAATGTA
* *
5663876 TAATGCAAAGATGTAAAAAGTAAGAATACAAAATG-A
1 AAATGCAAAGATGCAAAAA-TAAGAATACAAAATGTA
* *
5663912 AAATGCACAGATACAAAA
1 AAATGCAAAGATGCAAAA
5663930 TGTAAATGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 2 0.05
36 28 0.64
37 14 0.32
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.18
Consensus pattern (36 bp):
AAATGCAAAGATGCAAAAATAAGAATACAAAATGTA
Found at i:5667149 original size:15 final size:15
Alignment explanation
Indices: 5667129--5667158 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5667119 ATAATTATTA
5667129 ATCAATGATTAAAAT
1 ATCAATGATTAAAAT
*
5667144 ATCAATTATTAAAAT
1 ATCAATGATTAAAAT
5667159 TAAGAAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (15 bp):
ATCAATGATTAAAAT
Found at i:5668322 original size:3 final size:3
Alignment explanation
Indices: 5668314--5668382 Score: 63
Period size: 3 Copynumber: 23.0 Consensus size: 3
5668304 CCTGTTTGTA
* *
5668314 AAT AAT AAT TAT -TT AAT AAT AAT -AT AAT -AT ATAT ATAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT
*
5668358 AAT ATTT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT
5668383 TTAAGTAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
2 5 0.09
3 42 0.75
4 9 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
AAT
Found at i:5668358 original size:16 final size:16
Alignment explanation
Indices: 5668327--5668382 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
5668317 AATAATTATT
5668327 TAATA-ATAAT-ATAA
1 TAATATATAATAATAA
5668341 T-ATATATATATAATAA
1 TAATATATA-ATAATAA
*
5668357 TAATATTTAATAATAA
1 TAATATATAATAATAA
5668373 TAATA-ATAAT
1 TAATATATAAT
5668383 TTAAGTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
13 3 0.08
14 4 0.11
15 6 0.17
16 17 0.47
17 6 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATATATAATAATAA
Found at i:5668359 original size:19 final size:19
Alignment explanation
Indices: 5668314--5668380 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
5668304 CCTGTTTGTA
*
5668314 AATAATAAT-TATTTA-AT
1 AATAATAATATATATATAT
5668331 AATAATATAATATATATATAT
1 AAT-A-ATAATATATATATAT
*
5668352 AATAATAATATTTA-ATAAT
1 AATAATAATATATATAT-AT
5668371 AATAATAATA
1 AATAATAATA
5668381 ATTTAAGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.07
18 3 0.07
19 26 0.60
20 6 0.14
21 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAATAATATATATATAT
Found at i:5670279 original size:9 final size:9
Alignment explanation
Indices: 5670265--5670290 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5670255 CGAGGTACAT
5670265 GGTAATTTA
1 GGTAATTTA
5670274 GGTAATTTA
1 GGTAATTTA
5670283 GGTAATTT
1 GGTAATTT
5670291 GGATGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (9 bp):
GGTAATTTA
Found at i:5689841 original size:24 final size:24
Alignment explanation
Indices: 5689809--5689857 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5689799 GTTTGGAAGA
5689809 TAAGTTAGGAAAATTGTCAAAAAC
1 TAAGTTAGGAAAATTGTCAAAAAC
5689833 TAAGTTAGGAAAATTGTCAAAAAC
1 TAAGTTAGGAAAATTGTCAAAAAC
5689857 T
1 T
5689858 CTATAGGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (24 bp):
TAAGTTAGGAAAATTGTCAAAAAC
Found at i:5694266 original size:31 final size:30
Alignment explanation
Indices: 5694188--5694268 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
5694178 CTAGTGATTG
*
5694188 AAATG-AAAATTTTAGAAA-TTTAGGGACTA
1 AAATGTAAAATTTTA-AAAGTTTAGGAACTA
* **
5694217 AAGTGTAAAATTGAAAAAGTTTAGGAACTAA
1 AAATGTAAAATTTTAAAAGTTTAGGAACT-A
*
5694248 AAATGTAAATTTTTAAAAGTT
1 AAATGTAAAATTTTAAAAGTT
5694269 ATATTTTGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 7 0.17
30 16 0.39
31 18 0.44
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.32
Consensus pattern (30 bp):
AAATGTAAAATTTTAAAAGTTTAGGAACTA
Found at i:5697949 original size:28 final size:27
Alignment explanation
Indices: 5697918--5697972 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
5697908 AAATTTTAAT
5697918 TTTATATTTAA-TATGTATAAATAAATAA
1 TTTATATTTAACTAT-TA-AAATAAATAA
* *
5697946 TTTATTTTTAACTATTAAAATTAATAA
1 TTTATATTTAACTATTAAAATAAATAA
5697973 GAAAATAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.38
28 12 0.50
29 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTATATTTAACTATTAAAATAAATAA
Found at i:5698223 original size:16 final size:15
Alignment explanation
Indices: 5698202--5698232 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5698192 AGATGAACAT
5698202 AATTAATAATATAAAA
1 AATTAATAA-ATAAAA
5698218 AATTAATAAATAAAA
1 AATTAATAAATAAAA
5698233 TTAAGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATTAATAAATAAAA
Found at i:5703193 original size:35 final size:33
Alignment explanation
Indices: 5703154--5703251 Score: 96
Period size: 35 Copynumber: 3.0 Consensus size: 33
5703144 TTTTAATATT
5703154 AAAAATATATTTTATTATTATCTTAACTAAAATAA
1 AAAAATATATTTTATTATTATCTTAACT-AAAT-A
* * *
5703189 AAAAATAGATTTTAATCTTATCTTAACT---T-
1 AAAAATATATTTTATTATTATCTTAACTAAATA
* *
5703218 AAAAATATATTTTATTTTTACCTTAACTTAAATA
1 AAAAATATATTTTATTATTATCTTAAC-TAAATA
5703252 TTTATATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
29 23 0.45
30 1 0.02
31 1 0.02
33 1 0.02
35 25 0.49
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.45
Consensus pattern (33 bp):
AAAAATATATTTTATTATTATCTTAACTAAATA
Found at i:5703229 original size:29 final size:29
Alignment explanation
Indices: 5703152--5703269 Score: 110
Period size: 29 Copynumber: 3.8 Consensus size: 29
5703142 CATTTTAATA
*
5703152 TTAAAAATATATTTTATTATTATCTTAAC
1 TTAAAAATATATTTTATTCTTATCTTAAC
* *
5703181 TAAAATAAAAAAATAGATTTTAATCTTATCTTAAC
1 T----T--AAAAATATATTTTATTCTTATCTTAAC
* *
5703216 TTAAAAATATATTTTATTTTTACCTTAAC
1 TTAAAAATATATTTTATTCTTATCTTAAC
*
5703245 TTAAATATTTATATTTTATTCTTAT
1 TTAAA-A-ATATATTTTATTCTTAT
5703270 TATATTTTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
29 29 0.41
30 1 0.01
31 15 0.21
33 1 0.01
35 25 0.35
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.50
Consensus pattern (29 bp):
TTAAAAATATATTTTATTCTTATCTTAAC
Found at i:5703308 original size:31 final size:30
Alignment explanation
Indices: 5703270--5703562 Score: 137
Period size: 30 Copynumber: 9.5 Consensus size: 30
5703260 TTATTCTTAT
*
5703270 TATATTTTAAAATTAAGGTAAAAATAAAATA
1 TATATTTT-AAATTAAGATAAAAATAAAATA
* * * *
5703301 TACATTTTTAGTTAAGATAAAAATAAAATG
1 TATATTTTAAATTAAGATAAAAATAAAATA
* * *
5703331 TATATTTCAAATTTAGAATTAAAATAAAATA
1 TATATTTTAAATTAAG-ATAAAAATAAAATA
* * * *
5703362 TATATTTTTTAATTTAAAATAATAATAATATA
1 TATA--TTTTAAATTAAGATAAAAATAAAATA
* * ** *
5703394 TAATAATTTAATAATTTAAGGTAATGAT-AGA-A
1 T-AT-ATTT--TAAATTAAGATAAAAATAAAATA
* * * *
5703426 TATATTTAATAATTATAGTTAAGAATATAATA
1 TATATTTTA-AATTA-AGATAAAAATAAAATA
* ** * *
5703458 TATGTAATAAGTCAAGATAAAAATAAAATA
1 TATATTTTAAATTAAGATAAAAATAAAATA
*
5703488 TAT-TTTTAAAATTTAAGATAAGAATAAAA-A
1 TATATTTT-AAA-TTAAGATAAAAATAAAATA
* * * * *
5703518 -AAAATTTAAGTTAAGATAATATTAAAATA
1 TATATTTTAAATTAAGATAAAAATAAAATA
*
5703547 TATTTTTTAATATTAA
1 TATATTTTAA-ATTAA
5703563 TACGTGAATT
Statistics
Matches: 192, Mismatches: 53, Indels: 34
0.69 0.19 0.12
Matches are distributed among these distances:
28 16 0.08
29 10 0.05
30 68 0.35
31 48 0.25
32 23 0.12
33 12 0.06
34 15 0.08
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.39
Consensus pattern (30 bp):
TATATTTTAAATTAAGATAAAAATAAAATA
Found at i:5703400 original size:26 final size:26
Alignment explanation
Indices: 5703349--5703404 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5703339 AAATTTAGAA
* **
5703349 TTAAAATAAAATATATATTTTTTAAT
1 TTAAAATAAAATATATATATAATAAT
5703375 TTAAAATAATAATA-ATATATAATAAT
1 TTAAAATAA-AATATATATATAATAAT
5703401 TTAA
1 TTAA
5703405 TAATTTAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAAAATAAAATATATATATAATAAT
Found at i:5703544 original size:23 final size:23
Alignment explanation
Indices: 5703493--5703545 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5703483 AAATATATTT
5703493 TTAAAATTTAAGATAAGAATAAA
1 TTAAAATTTAAGATAAGAATAAA
** *
5703516 AAAAAATTTAAGTTAAG-ATAATA
1 TTAAAATTTAAGATAAGAATAA-A
5703539 TTAAAAT
1 TTAAAAT
5703546 ATATTTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (23 bp):
TTAAAATTTAAGATAAGAATAAA
Found at i:5703580 original size:18 final size:19
Alignment explanation
Indices: 5703559--5703596 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5703549 TTTTTTAATA
*
5703559 TTAATACGTGAA-TTAAAT
1 TTAACACGTGAATTTAAAT
*
5703577 TTAACATGTGAATTTAAAT
1 TTAACACGTGAATTTAAAT
5703596 T
1 T
5703597 ATATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
TTAACACGTGAATTTAAAT
Found at i:5708765 original size:2 final size:2
Alignment explanation
Indices: 5708684--5708746 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
5708674 CTATCACACT
5708684 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
5708726 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
5708747 TCAACCTATT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5708971 original size:24 final size:24
Alignment explanation
Indices: 5708939--5708999 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
5708929 TTGTTCTTGT
5708939 AGTATCGATACTCAAGGAAAGAGA
1 AGTATCGATACTCAAGGAAAGAGA
5708963 AGTATCGATACTCAAGGAAAGAGA
1 AGTATCGATACTCAAGGAAAGAGA
*
5708987 AATATCGATACTC
1 AGTATCGATACTC
5709000 TCATGGTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (24 bp):
AGTATCGATACTCAAGGAAAGAGA
Found at i:5710494 original size:14 final size:14
Alignment explanation
Indices: 5710475--5710503 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5710465 ACCCACCCAC
5710475 ACATATATATATAT
1 ACATATATATATAT
5710489 ACATATATATATAT
1 ACATATATATATAT
5710503 A
1 A
5710504 TTAGCCCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ACATATATATATAT
Found at i:5716619 original size:20 final size:20
Alignment explanation
Indices: 5716485--5716618 Score: 144
Period size: 20 Copynumber: 6.7 Consensus size: 20
5716475 AATTGGGAAA
5716485 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
5716505 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
5716525 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
5716545 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
5716566 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* ** *
5716586 TTCGCAACACGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
5716606 TTCGCAACGCGAT
1 ATCGCAATGCGAT
5716619 TTACATAGCG
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 82 0.83
21 13 0.13
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:5717181 original size:19 final size:19
Alignment explanation
Indices: 5717157--5717200 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
5717147 GCAACGAGAG
*
5717157 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
5717176 AATCGC-ACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
5717194 AATCGCA
1 AATCGCA
5717201 TTGCGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:5717218 original size:19 final size:19
Alignment explanation
Indices: 5717196--5717379 Score: 172
Period size: 19 Copynumber: 10.1 Consensus size: 19
5717186 GAAACCAAAA
*
5717196 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5717215 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5717234 TCGCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5717253 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5717272 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * * **
5717286 TCTCATCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
5717305 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
5717319 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
5717338 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
5717358 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
5717378 TC
1 TC
5717380 AACCAAAACA
Statistics
Matches: 135, Mismatches: 18, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
14 18 0.13
16 4 0.03
17 5 0.04
19 76 0.56
20 31 0.23
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5717304 original size:33 final size:33
Alignment explanation
Indices: 5717267--5717354 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
5717257 GTTGCGATTT
5717267 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
* *
5717300 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
5717333 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
5717355 ATTATCTCGT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
33 37 0.71
34 15 0.29
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:5717356 original size:20 final size:20
Alignment explanation
Indices: 5717322--5717379 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
5717312 GCGATTCTCT
**
5717322 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
5717342 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
5717362 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
5717380 AACCAAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:5719181 original size:87 final size:82
Alignment explanation
Indices: 5719044--5719207 Score: 224
Period size: 87 Copynumber: 1.9 Consensus size: 82
5719034 TTAGTAAATT
5719044 TTTCGGTTGCTGCCAATACTGCTAATTGTTTATTAACACTGTGAAGTTAGTA-TTGTCTTTGTTT
1 TTTCGGTTGCTGCCAATACTGCTAATTGTTTATTAACACTGTGAAGTTAGTATTTGTC-TT-TTT
5719108 TGTCTTTTGGTTGAAGTAAA
64 TGTC-TTTGGTTGAAGTAAA
* * *
5719128 TTTCGGTTGCTGCC-ATTCTGCTAAACTGTGTATTCTTTACACTGTGAAGTTAGTATTTGTCTTT
1 TTTCGGTTGCTGCCAATACTGCT-AA-T-TGT-TTATTAACACTGTGAAGTTAGTATTTGTCTTT
5719192 TTTGTCTTTGGTTGAA
62 TTTGTCTTTGGTTGAA
5719208 AGTTTGAAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
83 7 0.10
84 16 0.22
85 11 0.15
86 10 0.14
87 23 0.32
88 5 0.07
ACGTcount: A:0.19, C:0.13, G:0.20, T:0.48
Consensus pattern (82 bp):
TTTCGGTTGCTGCCAATACTGCTAATTGTTTATTAACACTGTGAAGTTAGTATTTGTCTTTTTTG
TCTTTGGTTGAAGTAAA
Found at i:5719483 original size:21 final size:21
Alignment explanation
Indices: 5719454--5719566 Score: 58
Period size: 21 Copynumber: 5.5 Consensus size: 21
5719444 CTATCGTTGA
5719454 AGAGGCCCCTATCATTCCTCG
1 AGAGGCCCCTATCATTCCTCG
* ** *
5719475 AGAGTCCCCTCCCA--CCGTTCA
1 AGAGGCCCCTATCATTCC--TCG
* * * *
5719496 AGAGGCCACTGTCATCCCTCA
1 AGAGGCCCCTATCATTCCTCG
*
5719517 AGAGTCCTCCTATCA-T--T-G
1 AGAGGCC-CCTATCATTCCTCG
5719535 AAGAGGCCCCTATCATTCCTCG
1 -AGAGGCCCCTATCATTCCTCG
*
5719557 AGAGTCCCCT
1 AGAGGCCCCT
5719567 CCACCGTTCA
Statistics
Matches: 67, Mismatches: 15, Indels: 20
0.66 0.15 0.20
Matches are distributed among these distances:
18 7 0.10
19 10 0.15
21 42 0.63
22 6 0.09
23 2 0.03
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (21 bp):
AGAGGCCCCTATCATTCCTCG
Found at i:5719499 original size:42 final size:42
Alignment explanation
Indices: 5719423--5719592 Score: 175
Period size: 42 Copynumber: 4.1 Consensus size: 42
5719413 GACTCGCCTG
* * * *
5719423 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTA
* * * *
5719465 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTA
* * * *
5719507 TCATCCCTCAAGAGT--CCTCCTATCATTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTA
* * * *
5719547 TCATTCCTCGAGAGTCCCCT-CCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTA
5719588 TCATC
1 TCATC
5719593 GTTGAAGAGG
Statistics
Matches: 101, Mismatches: 25, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
40 32 0.32
41 19 0.19
42 50 0.50
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTA
Found at i:5719559 original size:82 final size:83
Alignment explanation
Indices: 5719420--5719592 Score: 314
Period size: 82 Copynumber: 2.1 Consensus size: 83
5719410 CCCGACTCGC
*
5719420 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
5719485 CCCACCGTTCAAGAGGCCA
66 -CCACCGTTCAAGAGGCCA
5719504 CTGTCATCCCTCAAGAGT-C-CTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
5719567 CCACCGTTCAAGAGGCCA
66 CCACCGTTCAAGAGGCCA
5719585 CTGTCATC
1 CTGTCATC
5719593 GTTGAAGAGG
Statistics
Matches: 88, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
81 26 0.30
82 43 0.49
83 1 0.01
84 18 0.20
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (83 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCACCGTTCAAGAGGCCA
Found at i:5719612 original size:41 final size:40
Alignment explanation
Indices: 5719482--5719621 Score: 138
Period size: 41 Copynumber: 3.5 Consensus size: 40
5719472 TCGAGAGTCC
* * *
5719482 CCTCCCACCGTTCAAGAGGCCACTGTCATCCCTCAAGAGT
1 CCTCCCACCATTCAAGAGGCCACTGTCATCCTTGAAGAGT
* * * * * *
5719522 CCTCCTATCATTGAAGAGGCCCCTATCATTCCTCG-AGAGT
1 CCTCCCACCATTCAAGAGGCCACTGTCA-TCCTTGAAGAGT
* * *
5719562 CCCCTCCACCGTTCAAGAGGCCACTGTCATCGTTGAAGAGGT
1 CCTC-CCACCATTCAAGAGGCCACTGTCATCCTTGAAGA-GT
5719604 CCTCCCACCATTCAAGAG
1 CCTCCCACCATTCAAGAG
5719622 CCCGATTCAC
Statistics
Matches: 76, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
40 34 0.45
41 37 0.49
42 5 0.07
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (40 bp):
CCTCCCACCATTCAAGAGGCCACTGTCATCCTTGAAGAGT
Found at i:5719621 original size:82 final size:82
Alignment explanation
Indices: 5719420--5719621 Score: 280
Period size: 82 Copynumber: 2.4 Consensus size: 82
5719410 CCCGACTCGC
* * * *
5719420 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGT-C-CTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
5719485 CCCACCGTTCAAGAGGCCA
64 CCCACCGTTCAAGAGGCCA
* * *
5719504 CTGTCATCCCTCAAGAGTCCTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT-C
1 CTGTCATCCCTCAAGAGTCCTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
5719568 CACCGTTCAAGAGGCCA
66 CACCGTTCAAGAGGCCA
** *
5719585 CTGTCATCGTTGAAGAGGTCCTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCTCCCACCATTCAAGAG
5719622 CCCGATTCAC
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
81 31 0.28
82 60 0.55
83 1 0.01
84 18 0.16
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (82 bp):
CTGTCATCCCTCAAGAGTCCTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
CACCGTTCAAGAGGCCA
Found at i:5720977 original size:13 final size:14
Alignment explanation
Indices: 5720952--5720986 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5720942 ATTGTTTAAT
5720952 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
5720966 TGATTTGT-AAAGT
1 TGATTTGTAAAAGG
5720979 TGATTTGT
1 TGATTTGT
5720987 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:5720995 original size:13 final size:14
Alignment explanation
Indices: 5720939--5720987 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
5720929 GGCTTATTTT
*
5720939 TTGA-TTGTTTAA-
1 TTGATTTGTTAAAG
*
5720951 TTGATTTGTAAAAG
1 TTGATTTGTTAAAG
*
5720965 GTGATTTG-TAAAG
1 TTGATTTGTTAAAG
5720978 TTGATTTGTT
1 TTGATTTGTT
5720988 TAATTGATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 4 0.14
13 17 0.59
14 8 0.28
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:5721129 original size:14 final size:14
Alignment explanation
Indices: 5721110--5721165 Score: 67
Period size: 14 Copynumber: 3.6 Consensus size: 14
5721100 GCGAAATGAA
5721110 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5721124 AATCGCAACGCGAAATGAG
1 AATCGCAA--CG--A-GAG
5721143 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5721157 AATCGCAAC
1 AATCGCAAC
5721166 ACAAAATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 20 0.54
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 11 0.30
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5721137 original size:33 final size:33
Alignment explanation
Indices: 5721092--5721165 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
5721082 AAAAAGTACT
*
5721092 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
5721125 ATCGCAACGCGAAATGAGAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
5721158 ATCGCAAC
1 ATCGCAAC
5721166 ACAAAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:5721151 original size:19 final size:19
Alignment explanation
Indices: 5721092--5721152 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
5721082 AAAAAGTACT
* *
5721092 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAGA
5721111 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAGA
5721125 ATCGCAACGCGAAATGAGA
1 ATCGCAACGCGAAATGAGA
5721144 ATCGCAACG
1 ATCGCAACG
5721153 AGAGAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.56
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAGA
Found at i:5721223 original size:33 final size:32
Alignment explanation
Indices: 5721181--5721306 Score: 166
Period size: 33 Copynumber: 3.9 Consensus size: 32
5721171 ATTAAATTCG
5721181 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
5721214 CGTTGCGATTTTCATTTTGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
5721247 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
5721280 CGTTGCGATTTTCATTTCACA-TGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
5721307 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
31 3 0.04
32 6 0.07
33 70 0.85
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:5721271 original size:19 final size:19
Alignment explanation
Indices: 5721249--5721306 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 19
5721239 GAAATTAGCG
5721249 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5721268 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
5721282 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
5721301 -TGCGAT
1 TTGCGAT
5721307 AGTAATTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 11
0.69 0.07 0.24
Matches are distributed among these distances:
14 6 0.19
16 7 0.23
17 6 0.19
18 6 0.19
19 6 0.19
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5723804 original size:24 final size:24
Alignment explanation
Indices: 5723770--5723823 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5723760 CTGAAACATC
*
5723770 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
5723794 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
5723818 ATCAAA
1 ATCAAA
5723824 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:5724658 original size:20 final size:20
Alignment explanation
Indices: 5724625--5724702 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
5724615 AATTTGGAAA
* *
5724625 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
5724645 ATCGCAACGAGATAAT-ACAA
1 ATCGCAACGAGATACTGAC-T
*
5724665 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
5724685 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
5724703 AAATCGCAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.04
20 44 0.92
21 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:5724707 original size:40 final size:40
Alignment explanation
Indices: 5724621--5724711 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 40
5724611 TGCGAATTTG
* *
5724621 GAAAATCGCAATGCGATACTGACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACTGACTATCGCAACGAGATAAT
* * **
5724661 -ACAAATCGCAACGAGATTCTGACTTTCGCAACGAGATTCT
1 GA-AAATCGCAACGAGATACTGACTATCGCAACGAGATAAT
5724701 GAAAATCGCAA
1 GAAAATCGCAA
5724712 TCATCTTCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
39 1 0.02
40 41 0.95
41 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (40 bp):
GAAAATCGCAACGAGATACTGACTATCGCAACGAGATAAT
Found at i:5724709 original size:20 final size:20
Alignment explanation
Indices: 5724621--5724711 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
5724611 TGCGAATTTG
* *
5724621 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
5724641 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
*
5724661 -ACAAATCGCAACGAGATTCT
1 GA-AAATCGCAACGAGATACT
*** *
5724681 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
5724701 GAAAATCGCAA
1 GAAAATCGCAA
5724712 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
19 1 0.02
20 52 0.96
21 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:5724997 original size:20 final size:20
Alignment explanation
Indices: 5724923--5724989 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
5724913 CAACGGGGAA
5724923 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
5724943 ATCGCAATTCG-AAATGAAA
1 ATCGCAACGCGAAAATGGCT
5724962 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
5724982 ATCGCAAC
1 ATCGCAAC
5724990 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 14 0.39
20 22 0.61
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:5726502 original size:38 final size:38
Alignment explanation
Indices: 5726460--5726532 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
5726450 CGATGACAGT
* * *
5726460 GGCCTCTTGAACG-GTGGGGGGGATTCTTGAGGGATAGG
1 GGCCTCTT-AACGAGTGGAGGGGACTCTTAAGGGATAGG
*
5726498 GGCCTCTTAACGATTGGAGGGGACTCTTAAGGGAT
1 GGCCTCTTAACGAGTGGAGGGGACTCTTAAGGGAT
5726533 GACAGGTGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 4 0.13
38 26 0.87
ACGTcount: A:0.19, C:0.15, G:0.41, T:0.25
Consensus pattern (38 bp):
GGCCTCTTAACGAGTGGAGGGGACTCTTAAGGGATAGG
Found at i:5726936 original size:19 final size:19
Alignment explanation
Indices: 5726885--5726937 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
5726875 ACTTAAAATT
5726885 GCAACGCGAAAATGACTATC
1 GCAACGCG-AAATGACTATC
* *
5726905 GCAACGCGGAATGGCTATC
1 GCAACGCGAAATGACTATC
*
5726924 GCAATGCGAAATGA
1 GCAACGCGAAATGA
5726938 AATCACAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.36, C:0.23, G:0.26, T:0.15
Consensus pattern (19 bp):
GCAACGCGAAATGACTATC
Found at i:5726991 original size:32 final size:32
Alignment explanation
Indices: 5726921--5727029 Score: 193
Period size: 32 Copynumber: 3.4 Consensus size: 32
5726911 CGGAATGGCT
*
5726921 ATCGCAATGCGAAATGAAATCACAACGAC-AA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
5726952 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
5726984 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
5727016 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
5727030 ACACAAATCG
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
31 28 0.37
32 47 0.63
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:5727030 original size:14 final size:14
Alignment explanation
Indices: 5726937--5727024 Score: 70
Period size: 14 Copynumber: 5.8 Consensus size: 14
5726927 ATGCGAAATG
*
5726937 AAATCACAACGAC-
1 AAATCGCAACGACA
*
5726950 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
5726966 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
*
5726982 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
5726998 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
5727014 AAATCGCAACG
1 AAATCGCAACG
5727025 CGAAAACACA
Statistics
Matches: 61, Mismatches: 5, Indels: 17
0.73 0.06 0.20
Matches are distributed among these distances:
13 8 0.13
14 20 0.33
15 3 0.05
16 12 0.20
18 18 0.30
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:5727064 original size:19 final size:19
Alignment explanation
Indices: 5727037--5727204 Score: 89
Period size: 19 Copynumber: 9.6 Consensus size: 19
5727027 AAAACACAAA
*
5727037 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5727056 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
5727072 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
* *
5727088 TCGCATTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
5727104 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
5727121 TCGCATTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
5727137 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
5727154 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
5727173 TCCGCGTTGCGATAGTCATTT
1 T-CGCGTTGCGATTTTCA-TT
*
5727194 TCGTGTTGCGA
1 TCGCGTTGCGA
5727205 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 18, Indels: 31
0.70 0.11 0.19
Matches are distributed among these distances:
14 25 0.22
15 6 0.05
16 8 0.07
17 4 0.03
18 16 0.14
19 30 0.26
20 23 0.20
21 3 0.03
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5727078 original size:14 final size:14
Alignment explanation
Indices: 5727059--5727149 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
5727049 TTTCATTTCG
5727059 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
5727073 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
5727089 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
5727105 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
5727122 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
5727138 CGTTGCGATTTT
1 CGTTGCGATTTT
5727150 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 27 0.42
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.09
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:5727123 original size:33 final size:33
Alignment explanation
Indices: 5727042--5727165 Score: 232
Period size: 33 Copynumber: 3.8 Consensus size: 33
5727032 ACAAATCGCA
*
5727042 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
5727075 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
5727107 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
5727140 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
5727166 AGCCATTTCC
Statistics
Matches: 89, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
32 31 0.35
33 58 0.65
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:5727146 original size:65 final size:66
Alignment explanation
Indices: 5727042--5727165 Score: 232
Period size: 65 Copynumber: 1.9 Consensus size: 66
5727032 ACAAATCGCA
*
5727042 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCATTTCGCATTGCGATTTTGTC
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTGTC
5727106 G
66 G
5727107 TTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
5727166 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
65 38 0.67
66 19 0.33
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.48
Consensus pattern (66 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTGTC
G
Found at i:5727184 original size:20 final size:19
Alignment explanation
Indices: 5727150--5727204 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5727140 TTGCGATTTT
*
5727150 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
5727169 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
5727189 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
5727205 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:5727707 original size:18 final size:18
Alignment explanation
Indices: 5727681--5727725 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5727671 GTCGATCAGA
*
5727681 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
5727699 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
5727717 TGATGGCTC
1 TGATGGCTC
5727726 CCGAAGTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:5729052 original size:19 final size:19
Alignment explanation
Indices: 5729028--5729067 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5729018 TAGTTTCTGA
5729028 AAATGAAAATCGCAACACG
1 AAATGAAAATCGCAACACG
** *
5729047 AAATGACTATCGCAACGCG
1 AAATGAAAATCGCAACACG
5729066 AA
1 AA
5729068 TTTGACTATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCGCAACACG
Found at i:5729075 original size:20 final size:19
Alignment explanation
Indices: 5729036--5729087 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
5729026 GAAAATGAAA
*
5729036 ATCGCAACACGAAATGACT
1 ATCGCAACGCGAAATGACT
*
5729055 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
5729075 ATCGCAACGCGAA
1 ATCGCAACGCGAA
5729088 CTAAAATCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:5729572 original size:21 final size:21
Alignment explanation
Indices: 5729542--5729608 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
5729532 CGCTTTGAAA
*
5729542 ATCGCATTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
* *
5729563 ATCGCGTTGCGA--AAGTCAGT
1 ATCGCGTTGCGATTATGT-ATT
* *
5729583 ATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTATGTATT
5729604 ATCGC
1 ATCGC
5729609 AATGCGATAG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
19 3 0.09
20 13 0.37
21 17 0.49
22 2 0.06
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:5729629 original size:27 final size:27
Alignment explanation
Indices: 5729591--5729645 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
5729581 GTATCTCGTT
5729591 GCGATTTTGTATTATCGCAATGCGATA
1 GCGATTTTGTATTATCGCAATGCGATA
*
5729618 GCGATTTTGTATTATCGCATTGCGATA
1 GCGATTTTGTATTATCGCAATGCGATA
5729645 G
1 G
5729646 TAAGTATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.38
Consensus pattern (27 bp):
GCGATTTTGTATTATCGCAATGCGATA
Found at i:5729655 original size:20 final size:20
Alignment explanation
Indices: 5729630--5729683 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
5729620 GATTTTGTAT
5729630 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
5729650 TATCGCATTGTGATAGTCAG
1 TATCGCATTGCGATAGTAAG
5729670 TATCGCATTGCGAT
1 TATCGCATTGCGAT
5729684 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:5729794 original size:21 final size:21
Alignment explanation
Indices: 5729754--5729794 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5729744 ATTGTAGACC
** *
5729754 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
5729775 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
5729795 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:5731474 original size:86 final size:86
Alignment explanation
Indices: 5731354--5731566 Score: 291
Period size: 86 Copynumber: 2.5 Consensus size: 86
5731344 CGACAATTTT
* * * * *
5731354 GTTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATTTGGTTTGCCTCTGAGCTAAATAT
1 GTTGACAGATAGCCCTTCTCGACTTAAGCCATGCTGCAAATTTGGTTTGCCTCTGAGCTAAATAT
5731419 AATCGAACTCGAAGGTCCTCG
66 AATCGAACTCGAAGGTCCTCG
* * * * *
5731440 GTTGGCAGATAGCCCTTCTCGACTTAAGCCATGCTGCAAATTTGTTTTGCCTTTGAGCTGAATGT
1 GTTGACAGATAGCCCTTCTCGACTTAAGCCATGCTGCAAATTTGGTTTGCCTCTGAGCTAAATAT
*
5731505 AATCGAACTCGAAGGTCTTCG
66 AATCGAACTCGAAGGTCCTCG
* * **
5731526 GTTGACAGATAACCCTTCTCGACCTAAGTTATGCTGCAAAT
1 GTTGACAGATAGCCCTTCTCGACTTAAGCCATGCTGCAAAT
5731567 GATATGCCTT
Statistics
Matches: 111, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 111 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (86 bp):
GTTGACAGATAGCCCTTCTCGACTTAAGCCATGCTGCAAATTTGGTTTGCCTCTGAGCTAAATAT
AATCGAACTCGAAGGTCCTCG
Found at i:5731616 original size:84 final size:85
Alignment explanation
Indices: 5731418--5731628 Score: 228
Period size: 86 Copynumber: 2.5 Consensus size: 85
5731408 GAGCTAAATA
* * * * * *
5731418 TAATCGAACTCGAAGGTCCTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCCATGCTGCAAATTT
1 TAATCGAACTCAAAGGTCTTCAGTTGACAGATAACCCTTCTCGACCTAAGCCATGCTGCAAA-TT
* * * *
5731483 GTTTTGCCTTTGAGCTGAATG
65 GATATGCCTTAGAGCTGAACG
* * **
5731504 TAATCGAACTCGAAGGTCTTCGGTTGACAGATAACCCTTCTCGACCTAAGTTATGCTGCAAA-TG
1 TAATCGAACTCAAAGGTCTTCAGTTGACAGATAACCCTTCTCGACCTAAGCCATGCTGCAAATTG
*
5731568 ATATGCCTTAGAGCTGAGCG
66 ATATGCCTTAGAGCTGAACG
* * *
5731588 TAGTCGAACTTAAAGGTCTTTTAG-TGACAGATAACCCTTCT
1 TAATCGAACTCAAAGGTC-TTCAGTTGACAGATAACCCTTCT
5731629 TTGAGTTGGA
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
84 49 0.45
85 3 0.03
86 56 0.52
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (85 bp):
TAATCGAACTCAAAGGTCTTCAGTTGACAGATAACCCTTCTCGACCTAAGCCATGCTGCAAATTG
ATATGCCTTAGAGCTGAACG
Found at i:5731969 original size:106 final size:106
Alignment explanation
Indices: 5731776--5734850 Score: 4988
Period size: 106 Copynumber: 29.4 Consensus size: 106
5731766 GCATTGTTCC
* * * ** *
5731776 GAGTCCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCAGGAAATTGTTTGTTGACA
1 GAGT-CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
5731841 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5731883 GAGTCCAATAACCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5731948 CCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5731989 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
5732054 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5732095 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5732160 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5732201 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCAGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
5732266 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTATCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5732307 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
5732372 CCAGCGGTCTCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
5732413 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGCCTCTAAAATTGGGAAGTTGCTTGTTGAAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5732478 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5732519 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
5732584 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5732625 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
5732690 CCAGCGGTCTCTTCGTCGTGAAGTTTAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5732731 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5732796 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5732837 GAGTCCAATATCCTTCGTTGTAAAGATGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
5732902 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5732943 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AGTTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
5733007 CCAGCGGTCTCTTCGTC--G-AGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5733045 GAGTCC-A-ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGCTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5733108 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5733149 GAGTCCAATATCGTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5733214 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5733255 GAGTCCAATATACTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGGGAAG-T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5733318 CCAGCGGTCCC--CGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5733357 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5733422 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5733463 GAGTCCAATATCCTTCG-T-T---G-CG-AA---G-T-TGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5733516 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
5733557 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGGAATTTTTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5733622 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5733663 GAGTCC-A-ATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5733726 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
5733767 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTCGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5733832 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
5733873 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAGTTATTTTTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5733938 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
5733979 GTGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5734044 CCAGCGGTCCCTTCGTCGTGATGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5734085 GAGTCCAATATCCTTCGTTGTGAAGTTGAATTTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5734150 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5734191 GAGTCCAATATCCTTCGTTG-CAAGTTGAAA-----T-T---A---GGAAG-TGTTT-ATGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5734241 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
5734282 GAGTCCAATATCCTTCGTTGTGAAGTTTGAAATTGGCTCTAAAATTAAGAAGTT-TGTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAG-TTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
5734346 ACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5734388 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5734453 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5734494 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5734559 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5734600 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5734665 CCAGCGGTCCCTTCGTCGTGATGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5734706 GAGTCCAATATCCTTCGTTGTGAAATTAAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5734771 CCAGCGGTCCCTTCGTCGAGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5734812 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
5734851 CGAGAAAAAT
Statistics
Matches: 2766, Mismatches: 161, Indels: 83
0.92 0.05 0.03
Matches are distributed among these distances:
91 67 0.02
92 8 0.00
93 10 0.00
94 81 0.03
95 2 0.00
96 3 0.00
98 1 0.00
99 5 0.00
100 41 0.01
101 34 0.01
102 102 0.04
103 3 0.00
104 169 0.06
105 75 0.03
106 2161 0.78
107 4 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:5744413 original size:42 final size:42
Alignment explanation
Indices: 5744366--5744491 Score: 189
Period size: 42 Copynumber: 3.0 Consensus size: 42
5744356 AATTTTTTTT
*
5744366 AAGAAAATTACCATTATGGTCCCTAAATATTTCTAAATTTAG
1 AAGAAAATTACCATTCTGGTCCCTAAATATTTCTAAATTTAG
* * * *
5744408 AAGAAAATTACCATTCTAGTCCCTGAATATTTCTAACTTTTG
1 AAGAAAATTACCATTCTGGTCCCTAAATATTTCTAAATTTAG
*
5744450 AAGAAAATTACCATTCTGGTCTCTAAATATTTCTAAAATTTA
1 AAGAAAATTACCATTCTGGTCCCTAAATATTTCT-AAATTTA
5744492 TACTTTACCA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 68 0.93
43 5 0.07
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (42 bp):
AAGAAAATTACCATTCTGGTCCCTAAATATTTCTAAATTTAG
Found at i:5751539 original size:14 final size:14
Alignment explanation
Indices: 5751519--5751580 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 14
5751509 GATTGAGCTA
5751519 AACATAAATGAACG
1 AACATAAATGAACG
*
5751533 TACAT--A--AACG
1 AACATAAATGAACG
5751543 AACATAAATGAACG
1 AACATAAATGAACG
*
5751557 CACAT--A--AACG
1 AACATAAATGAACG
5751567 AACATAAATGAACG
1 AACATAAATGAACG
5751581 TACAAAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
10 16 0.44
12 4 0.11
14 16 0.44
ACGTcount: A:0.55, C:0.18, G:0.13, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:5751551 original size:24 final size:24
Alignment explanation
Indices: 5751519--5751596 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
5751509 GATTGAGCTA
5751519 AACATAAATGAACGTACATAAACG
1 AACATAAATGAACGTACATAAACG
*
5751543 AACATAAATGAACGCACATAAACG
1 AACATAAATGAACGTACATAAACG
* *
5751567 AACATAAATGAACGTACAAAAACA
1 AACATAAATGAACGTACATAAACG
5751591 AACATA
1 AACATA
5751597 TTACCGAACG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.58, C:0.18, G:0.10, T:0.14
Consensus pattern (24 bp):
AACATAAATGAACGTACATAAACG
Found at i:5753217 original size:11 final size:11
Alignment explanation
Indices: 5753203--5753236 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5753193 ACATCATAAA
5753203 ATCATCCTTAC
1 ATCATCCTTAC
* *
5753214 ATCATCATAAC
1 ATCATCCTTAC
5753225 ATCATCCTTAC
1 ATCATCCTTAC
5753236 A
1 A
5753237 CTTAATAGTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (11 bp):
ATCATCCTTAC
Found at i:5753219 original size:22 final size:22
Alignment explanation
Indices: 5753189--5753236 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
5753179 ATTACCATAA
5753189 TACAACATCATAAAATCATCCT
1 TACAACATCATAAAATCATCCT
* *
5753211 TACATCATCATAACATCATCCT
1 TACAACATCATAAAATCATCCT
5753233 TACA
1 TACA
5753237 CTTAATAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (22 bp):
TACAACATCATAAAATCATCCT
Found at i:5754081 original size:16 final size:15
Alignment explanation
Indices: 5754055--5754086 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
5754045 TAATAAATAA
5754055 ACGAAATAAACAAAC
1 ACGAAATAAACAAAC
5754070 ACGAACATAAACAAAC
1 ACGAA-ATAAACAAAC
5754086 A
1 A
5754087 ATTTTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.66, C:0.22, G:0.06, T:0.06
Consensus pattern (15 bp):
ACGAAATAAACAAAC
Found at i:5754167 original size:20 final size:20
Alignment explanation
Indices: 5754142--5754181 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5754132 ATTTAAATGA
*
5754142 TAAACGAACATAAACGAACG
1 TAAACGAACACAAACGAACG
5754162 TAAACGAACACAAACGAACG
1 TAAACGAACACAAACGAACG
5754182 AACATAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.23, G:0.15, T:0.07
Consensus pattern (20 bp):
TAAACGAACACAAACGAACG
Found at i:5754183 original size:14 final size:14
Alignment explanation
Indices: 5754164--5754194 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5754154 AACGAACGTA
5754164 AACGAACACAAACG
1 AACGAACACAAACG
*
5754178 AACGAACATAAACG
1 AACGAACACAAACG
5754192 AAC
1 AAC
5754195 ATAATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:5754198 original size:10 final size:10
Alignment explanation
Indices: 5754141--5754180 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
5754131 CATTTAAATG
5754141 ATAAACGAAC
1 ATAAACGAAC
5754151 ATAAACGAAC
1 ATAAACGAAC
*
5754161 GTAAACGAAC
1 ATAAACGAAC
*
5754171 ACAAACGAAC
1 ATAAACGAAC
5754181 GAACATAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:5754211 original size:23 final size:22
Alignment explanation
Indices: 5754151--5754243 Score: 98
Period size: 23 Copynumber: 4.0 Consensus size: 22
5754141 ATAAACGAAC
*
5754151 ATAAACGAACGTAAACGAACACA
1 ATAAACGAACATAAAC-AACACA
*
5754174 A-ACGAACGAACATAAACGAACATA
1 ATA--AACGAACATAAAC-AACACA
*
5754198 ATAAATGAACATAAACAAACACA
1 ATAAACGAACATAAAC-AACACA
*
5754221 ATAAACAAACATAAACAACACA
1 ATAAACGAACATAAACAACACA
5754243 A
1 A
5754244 ACACAAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
22 8 0.13
23 32 0.53
24 19 0.32
25 1 0.02
ACGTcount: A:0.62, C:0.20, G:0.08, T:0.10
Consensus pattern (22 bp):
ATAAACGAACATAAACAACACA
Found at i:5754245 original size:15 final size:13
Alignment explanation
Indices: 5754210--5754258 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
5754200 AAATGAACAT
*
5754210 AAACAAACACAAT
1 AAACAAACACAAA
*
5754223 AAACAAACATAAA
1 AAACAAACACAAA
5754236 CAACACAAACACAAA
1 -AA-ACAAACACAAA
5754251 AAACAAAC
1 AAACAAAC
5754259 TTATTCGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 17 0.55
14 4 0.13
15 10 0.32
ACGTcount: A:0.71, C:0.24, G:0.00, T:0.04
Consensus pattern (13 bp):
AAACAAACACAAA
Found at i:5754276 original size:32 final size:28
Alignment explanation
Indices: 5754202--5754276 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 28
5754192 AACATAATAA
*
5754202 ATGAACATAAACAAACACAATAAACAAAC
1 ATGAACAT-AACAAACACAAAAAACAAAC
*
5754231 ATAAACA-ACACAAACACAAAAAACAAAC
1 ATGAACATA-ACAAACACAAAAAACAAAC
5754259 TTATTCGAACATAACAAA
1 --A-T-GAACATAACAAA
5754277 TGAATGTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 1 0.03
28 18 0.49
29 6 0.16
30 1 0.03
31 1 0.03
32 9 0.24
33 1 0.03
ACGTcount: A:0.64, C:0.21, G:0.03, T:0.12
Consensus pattern (28 bp):
ATGAACATAACAAACACAAAAAACAAAC
Found at i:5754520 original size:14 final size:14
Alignment explanation
Indices: 5754502--5754557 Score: 85
Period size: 14 Copynumber: 4.0 Consensus size: 14
5754492 CCCTCTGTTT
*
5754502 GAACATAAATGAAT
1 GAACATAAATGAAC
5754516 GAACATAAATGAAC
1 GAACATAAATGAAC
5754530 GAACATAAATGAAC
1 GAACATAAATGAAC
* *
5754544 AAACATAAACGAAC
1 GAACATAAATGAAC
5754558 ATATAATCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.14
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:5754540 original size:24 final size:25
Alignment explanation
Indices: 5754513--5754569 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
5754503 AACATAAATG
*
5754513 AATGAACATAA-ATGAACGAACATA-
1 AATGAACA-AACATAAACGAACATAT
5754537 AATGAACAAACATAAACGAACATAT
1 AATGAACAAACATAAACGAACATAT
5754562 AATCGAAC
1 AAT-GAAC
5754570 GTTCACGAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 2 0.07
24 20 0.69
25 3 0.10
26 4 0.14
ACGTcount: A:0.58, C:0.16, G:0.11, T:0.16
Consensus pattern (25 bp):
AATGAACAAACATAAACGAACATAT
Found at i:5759526 original size:287 final size:284
Alignment explanation
Indices: 5759010--5759577 Score: 1084
Period size: 288 Copynumber: 2.0 Consensus size: 284
5759000 TAAAAGTAAC
5759010 ATACTTAGATCCACCCAAGACGATGTCGTGGAAGGCCCCCATACATCAGAATGCACATAATCAAG
1 ATACTTAGATCCACCCAAGACGATGTCGTGGAAGGCCCCCATACATCAGAATGCACATAATCAAG
5759075 AATCTCTTCAGTTGTGTGCTTCCCAGTCTTGAAACGAACTTTAGTCTGTTTACCAAGAACACAAT
66 AATCTCTTCAGTTGTGTGCTTCCCAGTCTTGAAACGAACTTTAGTCTGTTTACCAAGAACACAAT
5759140 ACTTGCAAAAATCGAGCTTACAACTTTTAACACCATGCAACATAATACTTTTATGTAATTAAGCC
131 ACTTGCAAAAATCGAGCTTACAACTTTTAACACCATGCAACATAATACTTTTATGTAATTAAGCC
5759205 ATACCACGTTCACTAAGATGAGCAAGACGCATATGCCACAGTTTGGTAGTATCATCACAGAACTC
196 ATACCACGTTCACTAAGATGAGCAAGACGCATATGCCACAGTTTGGTAG--T-ATCACAGAACTC
5759270 AACATAATGAACTCCACATACAACATA
258 AACATAATGAACTCCACATACAACATA
5759297 ATACTTAGATCCACCCAAAGACGATGTCGTGGAAGGCCCCCATACATCAGAATGCACATAATCAA
1 ATACTTAGATCCACCC-AAGACGATGTCGTGGAAGGCCCCCATACATCAGAATGCACATAATCAA
5759362 GAATCTCTTCAGTTGTGTGCTTCCCAGTCTTGAAACGAACTTTAGTCTGTTTACCAAGAACACAA
65 GAATCTCTTCAGTTGTGTGCTTCCCAGTCTTGAAACGAACTTTAGTCTGTTTACCAAGAACACAA
5759427 TACTTGCAAAAATCGAGCTTACAAC-TTTAACACCATGCAACATAATACTTTTATGTAATTAAGC
130 TACTTGCAAAAATCGAGCTTACAACTTTTAACACCATGCAACATAATACTTTTATGTAATTAAGC
5759491 CATACCACGTTCACTAAGATGAGCAAGACGCATATGCCACAGTTTGGTAGTATCACAGAACTCAA
195 CATACCACGTTCACTAAGATGAGCAAGACGCATATGCCACAGTTTGGTAGTATCACAGAACTCAA
*
5759556 CATAATGAACTCCACCTACAAC
260 CATAATGAACTCCACATACAAC
5759578 GGTACTACCT
Statistics
Matches: 279, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
284 35 0.13
285 1 0.00
287 105 0.38
288 138 0.49
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (284 bp):
ATACTTAGATCCACCCAAGACGATGTCGTGGAAGGCCCCCATACATCAGAATGCACATAATCAAG
AATCTCTTCAGTTGTGTGCTTCCCAGTCTTGAAACGAACTTTAGTCTGTTTACCAAGAACACAAT
ACTTGCAAAAATCGAGCTTACAACTTTTAACACCATGCAACATAATACTTTTATGTAATTAAGCC
ATACCACGTTCACTAAGATGAGCAAGACGCATATGCCACAGTTTGGTAGTATCACAGAACTCAAC
ATAATGAACTCCACATACAACATA
Found at i:5761360 original size:13 final size:15
Alignment explanation
Indices: 5761332--5761364 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
5761322 GACACAAATA
5761332 TATTTAGTCTTTATT
1 TATTTAGTCTTTATT
5761347 TATTTA-TC-TTATT
1 TATTTAGTCTTTATT
5761360 TATTT
1 TATTT
5761365 CACCAGTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 2 0.11
15 6 0.33
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (15 bp):
TATTTAGTCTTTATT
Found at i:5762906 original size:26 final size:27
Alignment explanation
Indices: 5762875--5762936 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
5762865 GAAAGTCAAT
5762875 ATTCAAACCTC-TATCTTAGTTAAAGA
1 ATTCAAACCTCTTATCTTAGTTAAAGA
5762901 ATTCAAACCTCTTATCTTAGTTAAAGA
1 ATTCAAACCTCTTATCTTAGTTAAAGA
*
5762928 ATTCGAACC
1 ATTCAAACC
5762937 CAATTTCCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (27 bp):
ATTCAAACCTCTTATCTTAGTTAAAGA
Found at i:5764844 original size:16 final size:16
Alignment explanation
Indices: 5764823--5764856 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5764813 GTAGATGAAA
5764823 ATAAATTAT-TTTATTT
1 ATAAATTATATTT-TTT
5764839 ATAAATTATATTTTTT
1 ATAAATTATATTTTTT
5764855 AT
1 AT
5764857 TAAAACCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAAATTATATTTTTT
Found at i:5778471 original size:14 final size:14
Alignment explanation
Indices: 5778452--5778478 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5778442 TAGACATTAC
5778452 GAGGTGGTCAATAT
1 GAGGTGGTCAATAT
5778466 GAGGTGGTCAATA
1 GAGGTGGTCAATA
5778479 GGGTTGGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.37, T:0.26
Consensus pattern (14 bp):
GAGGTGGTCAATAT
Found at i:5781347 original size:19 final size:19
Alignment explanation
Indices: 5781307--5781348 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5781297 TATTATTTCA
* *
5781307 AAATTTTATTTAACATACT
1 AAATTTTATTTAACAAAAT
5781326 AAATTTATATTTAA-AAAAT
1 AAATTT-TATTTAACAAAAT
5781345 AAAT
1 AAAT
5781349 GTTCAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATTTTATTTAACAAAAT
Found at i:5782942 original size:29 final size:28
Alignment explanation
Indices: 5782883--5782947 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 28
5782873 GATCTTTTGA
*
5782883 ATTACTATTTTGATTACTATGAATTATT
1 ATTACTATTTTGATGACTATGAATTATT
5782911 ATTACTATTTTCGTATGA-TATGACATT-TT
1 ATTACTATTTT-G-ATGACTATGA-ATTATT
5782940 ATTA-TATT
1 ATTACTATT
5782948 AATATAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 15 0.45
29 12 0.36
30 6 0.18
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (28 bp):
ATTACTATTTTGATGACTATGAATTATT
Found at i:5783808 original size:2 final size:2
Alignment explanation
Indices: 5783797--5783842 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
5783787 ATTCAAAGCA
5783797 AT AT -T 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
5783838 AT AT A
1 AT AT A
5783843 ACACTCTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5784176 original size:27 final size:27
Alignment explanation
Indices: 5784122--5784177 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
5784112 CCGCCATCAC
* *
5784122 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCACAACAT
*
5784149 CACTTTGAACTTGAAAGTCCACAACAT
1 CACTTTGAACTTGAAACTCCACAACAT
5784176 CA
1 CA
5784178 AGATCTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.27
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAACAT
Found at i:5784410 original size:19 final size:20
Alignment explanation
Indices: 5784386--5784430 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
5784376 ACATAACCGG
* *
5784386 CGGTTCAC-ACCGGTTTTGC
1 CGGTTCACAACCGGTTCTAC
*
5784405 CGGTTCCCAACCGGTTCTAC
1 CGGTTCACAACCGGTTCTAC
5784425 CGGTTC
1 CGGTTC
5784431 TTTAGCGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.11, C:0.36, G:0.24, T:0.29
Consensus pattern (20 bp):
CGGTTCACAACCGGTTCTAC
Found at i:5796606 original size:2 final size:2
Alignment explanation
Indices: 5796599--5796663 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
5796589 TTTCCTTTTA
5796599 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
5796641 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
5796664 ATTTTTAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5812884 original size:20 final size:21
Alignment explanation
Indices: 5812859--5812901 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
5812849 AGTCTAGTAA
5812859 AAAAATAGAATTTCTTT-TTT
1 AAAAATAGAATTTCTTTATTT
**
5812879 AAAAATAGGTTTTCTTTATTT
1 AAAAATAGAATTTCTTTATTT
5812900 AA
1 AA
5812902 GTCTTGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (21 bp):
AAAAATAGAATTTCTTTATTT
Found at i:5813933 original size:187 final size:187
Alignment explanation
Indices: 5813671--5814012 Score: 510
Period size: 187 Copynumber: 1.8 Consensus size: 187
5813661 GCACTAGACA
* * *
5813671 TTCCCAGGATAAGAAAATAAGTTTAAAGTTGAAATTGTTATGAATATATATAATAAATACGAGTT
1 TTCCCAGGATAAGAAAATAAGTTTAAAGCTGAAAATGTTATGAATATATATAATAAATACAAGTT
** * * *
5813736 TTCTCAATAATGTCATGGTACACTAAGAAATAGGTTGTGATATGTAATGTTAATATTTTTATTAA
66 CACCCAATAATGTCATGGTACACTAAGAAATAAGTTGTGATATGTAATGTTAATACTTTTATTAA
* *
5813801 TAAAATAGGTTTCGCCTAA-AATGTTATTAGAGTTTAAGCTGACGGAGCCTTAGATT
131 TAAAATAGGTTGCGCCCAAGAATGTTATTAGAGTTTAAGCTGACGGAGCCTTAGATT
* *
5813857 TTCCCATGATAAGAAAATAA-TTTAAAAGCTGAAAAATGTTATGCATATATATAATAAATA-AAG
1 TTCCCAGGATAAGAAAATAAGTTT-AAAGCTG-AAAATGTTATGAATATATATAATAAATACAAG
* *
5813920 TTGCACCCAATAATGTCATGGTTCACTAAGAAATAAGTTGTGATTTGTAATGTTAATACTTTTAT
64 TT-CACCCAATAATGTCATGGTACACTAAGAAATAAGTTGTGATATGTAATGTTAATACTTTTAT
5813985 TAATAAAATAGGTTGCGCCCAAGAATGT
128 TAATAAAATAGGTTGCGCCCAAGAATGT
5814013 GATTGTTCAC
Statistics
Matches: 138, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
185 3 0.02
186 29 0.21
187 101 0.73
188 5 0.04
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (187 bp):
TTCCCAGGATAAGAAAATAAGTTTAAAGCTGAAAATGTTATGAATATATATAATAAATACAAGTT
CACCCAATAATGTCATGGTACACTAAGAAATAAGTTGTGATATGTAATGTTAATACTTTTATTAA
TAAAATAGGTTGCGCCCAAGAATGTTATTAGAGTTTAAGCTGACGGAGCCTTAGATT
Found at i:5814000 original size:77 final size:73
Alignment explanation
Indices: 5813919--5814153 Score: 196
Period size: 77 Copynumber: 3.1 Consensus size: 73
5813909 AATAAATAAA
5813919 GTTGCACCCAATAATGTCATGGTTCACTAAGAAATAAGTTGTGATTTGTAATGTTAATACTTTTA
1 GTTGCACCCAA-AATGT-AT-GTTCACTAAGAAATAAGTTGTGATTTGTAATGTTAATA-TTTTA
5813984 TTAATAAAATAG
62 TTAATAAAATAG
* * * *
5813996 GTTGCGCCCAAGAATGTGATTGTTCACTAAGAAAGTAGGTTATGACCTCTAATGTAATGCTAATA
1 GTTGCACCCAA-AATGT-A-TGTTCACTAAGAAA-TAAGTTGTGA--T-T--TGTAATGTTAATA
*
5814061 TGTTT-TTAATAAAATAT
57 T-TTTATTAATAAAATAG
** * *
5814078 GTTGCGTCCAAAA---ATG-TCACTAA-AAAT-AGTTTGTGATATGTTATGTTAATATTTTTATT
1 GTTGCACCCAAAATGTATGTTCACTAAGAAATAAG-TTGTGATTTGTAATGTTAATA-TTTTATT
5814137 AATAAAATAG
64 AATAAAATAG
5814147 GTTGCAC
1 GTTGCAC
5814154 AAAAAAAAAC
Statistics
Matches: 131, Mismatches: 16, Indels: 30
0.74 0.09 0.17
Matches are distributed among these distances:
68 14 0.11
69 17 0.13
71 1 0.01
72 1 0.01
73 6 0.05
74 3 0.02
75 7 0.05
76 2 0.02
77 30 0.23
78 9 0.07
80 1 0.01
81 3 0.02
82 22 0.17
83 15 0.11
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (73 bp):
GTTGCACCCAAAATGTATGTTCACTAAGAAATAAGTTGTGATTTGTAATGTTAATATTTTATTAA
TAAAATAG
Found at i:5814891 original size:18 final size:18
Alignment explanation
Indices: 5814868--5814910 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
5814858 GTTGTTTTTA
*
5814868 AAATAAAAGATAACAATT
1 AAATAAAAGAAAACAATT
5814886 AAATAAAAGAAAACAATT
1 AAATAAAAGAAAACAATT
5814904 AAATAAA
1 AAATAAA
5814911 TAAATTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.19
Consensus pattern (18 bp):
AAATAAAAGAAAACAATT
Found at i:5816796 original size:65 final size:63
Alignment explanation
Indices: 5816672--5816826 Score: 172
Period size: 65 Copynumber: 2.4 Consensus size: 63
5816662 ACACCCTAAT
* * * *
5816672 TCGAATGCATTTT-TGTACCGATGCACAATCATGCATCGATGGACTCTTGATTTTATTGAAACA
1 TCGAAT-CATTTTATGTACCGATGCACAACCATGCATCGATAGACTCTGGATCTTATTGAAACA
* *
5816735 TCGAATCCATTTTATGTACCGATGCACATACCATGCATCGATATACTCCTGGCTCTT-TTGAAAC
1 TCGAAT-CATTTTATGTACCGATGCACA-ACCATGCATCGATAGACT-CTGGATCTTATTGAAAC
5816799 A
63 A
*
5816800 TCGAAT-ATAATTAGTGTACCGATGCAC
1 TCGAATCAT-TTTA-TGTACCGATGCAC
5816827 CCCAAGTGTA
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
63 14 0.18
64 17 0.22
65 42 0.53
66 6 0.08
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (63 bp):
TCGAATCATTTTATGTACCGATGCACAACCATGCATCGATAGACTCTGGATCTTATTGAAACA
Found at i:5822421 original size:32 final size:33
Alignment explanation
Indices: 5822344--5822462 Score: 159
Period size: 33 Copynumber: 3.6 Consensus size: 33
5822334 AAGGAATATA
5822344 TCGATGAGTTGTTGGCTGATTGCTCGAGATTTT
1 TCGATGAGTTGTTGGCTGATTGCTCGAGATTTT
* *
5822377 TTGATGAGTTGTTGGCTGATTGGTCGAGA-TTT
1 TCGATGAGTTGTTGGCTGATTGCTCGAGATTTT
* * * *
5822409 TCAATGAGTTGTTGGTTGCTTGCTCAAGATTTT
1 TCGATGAGTTGTTGGCTGATTGCTCGAGATTTT
* *
5822442 TCGATTAGTTGTTGGTTGATT
1 TCGATGAGTTGTTGGCTGATT
5822463 ACTCCATATT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
32 26 0.35
33 48 0.65
ACGTcount: A:0.16, C:0.09, G:0.29, T:0.45
Consensus pattern (33 bp):
TCGATGAGTTGTTGGCTGATTGCTCGAGATTTT
Found at i:5823212 original size:12 final size:12
Alignment explanation
Indices: 5823195--5823219 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5823185 CTGGTCCTAG
5823195 AAAGAGTTAAAC
1 AAAGAGTTAAAC
5823207 AAAGAGTTAAAC
1 AAAGAGTTAAAC
5823219 A
1 A
5823220 CTATTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (12 bp):
AAAGAGTTAAAC
Found at i:5825357 original size:36 final size:36
Alignment explanation
Indices: 5825314--5825393 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
5825304 GAATTAAACG
*
5825314 GGGATGGGGAAAAACCTTTTATGCTAAACGGGGACC
1 GGGATGGGGAAAAACCGTTTATGCTAAACGGGGACC
* *
5825350 GGGATGGGGAAAAACCGTTTATGTTAAACGGGGACG
1 GGGATGGGGAAAAACCGTTTATGCTAAACGGGGACC
5825386 GGGATGGG
1 GGGATGGG
5825394 AACGGGTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.29, C:0.12, G:0.40, T:0.19
Consensus pattern (36 bp):
GGGATGGGGAAAAACCGTTTATGCTAAACGGGGACC
Found at i:5825671 original size:23 final size:24
Alignment explanation
Indices: 5825633--5825680 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5825623 TAAATCCCTA
*
5825633 GTTTTTTAAGCGGGAAC-GGTACGG
1 GTTTTTTAAACGGGAACAGG-ACGG
5825657 GTTTTTTAAAC-GGAACAGGACGG
1 GTTTTTTAAACGGGAACAGGACGG
5825680 G
1 G
5825681 GGGACCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.27
Consensus pattern (24 bp):
GTTTTTTAAACGGGAACAGGACGG
Found at i:5836515 original size:20 final size:21
Alignment explanation
Indices: 5836469--5836516 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
5836459 GATTCTCACC
*
5836469 TCTTTCTTTTTCTTTTACTTG
1 TCTTTCTTCTTCTTTTACTTG
5836490 TC-TTCTTCTTCTTCTT-CTT-
1 TCTTTCTTCTTCTT-TTACTTG
5836509 TCTTTCTT
1 TCTTTCTT
5836517 TGAAGCTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 18 0.75
21 4 0.17
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (21 bp):
TCTTTCTTCTTCTTTTACTTG
Found at i:5839356 original size:21 final size:21
Alignment explanation
Indices: 5839313--5839358 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5839303 AGTCAACCAG
* *
5839313 TATCAATATTGTTCATTATAA
1 TATCAATATTGTTCATCAAAA
*
5839334 TATCAATATTGTTTATCAAAA
1 TATCAATATTGTTCATCAAAA
5839355 TATC
1 TATC
5839359 GATACTCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (21 bp):
TATCAATATTGTTCATCAAAA
Found at i:5841216 original size:66 final size:66
Alignment explanation
Indices: 5841109--5841254 Score: 184
Period size: 66 Copynumber: 2.2 Consensus size: 66
5841099 ACAAGAGTTA
* * * * * * * **
5841109 GTGATGCACTAGGTTGAGTGATAATTGAATATTGTACAGATCACTCGATGAGATTTTTGTACCTT
1 GTGATGCACGAGGTAGAGTGATAAATGAATACTATACAGATCACTCGATAAGACTCGTGTACCTT
5841174 T
66 T
*
5841175 GTGATGCACGAGGTAGAGTGATAAATGAATACTATATAGATCACTCGATAAGACTCGTGTACCTT
1 GTGATGCACGAGGTAGAGTGATAAATGAATACTATACAGATCACTCGATAAGACTCGTGTACCTT
5841240 T
66 T
* *
5841241 GTGGTGCATGAGGT
1 GTGATGCACGAGGT
5841255 TGATTAACTA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (66 bp):
GTGATGCACGAGGTAGAGTGATAAATGAATACTATACAGATCACTCGATAAGACTCGTGTACCTT
T
Found at i:5841329 original size:25 final size:25
Alignment explanation
Indices: 5841296--5841353 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
5841286 ACCTACGGTT
*
5841296 CAATTCTACGAGGCACTTACAAGTG
1 CAATACTACGAGGCACTTACAAGTG
* *
5841321 CAATACTACGAGGTACTTTCAAGTG
1 CAATACTACGAGGCACTTACAAGTG
5841346 CAATACTA
1 CAATACTA
5841354 AATATAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (25 bp):
CAATACTACGAGGCACTTACAAGTG
Found at i:5848219 original size:8 final size:8
Alignment explanation
Indices: 5848196--5848246 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
5848186 TTACTTTTTT
*
5848196 TATTTAAT
1 TATTTAAA
5848204 TATTTAAA
1 TATTTAAA
5848212 TATTTAAA
1 TATTTAAA
* *
5848220 TTTTTATA
1 TATTTAAA
5848228 TATTTAAA
1 TATTTAAA
5848236 -ATTTAAA
1 TATTTAAA
5848243 -ATTT
1 TATTT
5848247 TCAAAATCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
7 11 0.29
8 27 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATTTAAA
Found at i:5850086 original size:17 final size:17
Alignment explanation
Indices: 5850064--5850097 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5850054 TTAGAGTATT
*
5850064 CTAATATGTTGTTAAAA
1 CTAATATATTGTTAAAA
5850081 CTAATATATTGTTAAAA
1 CTAATATATTGTTAAAA
5850098 ATGCTTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (17 bp):
CTAATATATTGTTAAAA
Found at i:5852494 original size:41 final size:41
Alignment explanation
Indices: 5852415--5852505 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
5852405 AATGCTCTAC
*
5852415 TAAGCAGTATAGGTACTACAACAATATTGATAATGGTATCGA
1 TAAG-AGTATAGGTACTACAACAATATTAATAATGGTATCGA
* * * *
5852457 TAAGAGTATTGGTACTACAATAGTATTAAT-ATCGGTATTGA
1 TAAGAGTATAGGTACTACAACAATATTAATAAT-GGTATCGA
*
5852498 TATGAGTA
1 TAAGAGTA
5852506 GACAATAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 2 0.05
41 36 0.86
42 4 0.10
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (41 bp):
TAAGAGTATAGGTACTACAACAATATTAATAATGGTATCGA
Found at i:5855946 original size:12 final size:12
Alignment explanation
Indices: 5855929--5855953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5855919 TTCACTTTTC
5855929 TTTTTATTTGTT
1 TTTTTATTTGTT
5855941 TTTTTATTTGTT
1 TTTTTATTTGTT
5855953 T
1 T
5855954 CAAAACCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (12 bp):
TTTTTATTTGTT
Found at i:5863719 original size:27 final size:25
Alignment explanation
Indices: 5863689--5863753 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 25
5863679 TGAAAATAAA
5863689 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATTTTT-AA-TAAGTTAAT
* *
5863716 AATAAAATATATTTAATAAGTTGAT
1 AATAAAATATTTTTAATAAGTTAAT
5863741 -ATAAAAATATTTT
1 AAT-AAAATATTTT
5863754 AAGTTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.06
25 17 0.50
26 2 0.06
27 13 0.38
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (25 bp):
AATAAAATATTTTTAATAAGTTAAT
Found at i:5863758 original size:21 final size:22
Alignment explanation
Indices: 5863706--5863764 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
5863696 TATTTTTAAA
5863706 TTAAGTTAATAATAAAATATATT
1 TTAAGTTAAT-ATAAAATATATT
*
5863729 TAATAAGTTGATATAAAA-ATATT
1 T--TAAGTTAATATAAAATATATT
5863752 TTAAGTTAATATA
1 TTAAGTTAATATA
5863765 TATAAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 11 0.34
23 7 0.22
24 6 0.19
25 8 0.25
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (22 bp):
TTAAGTTAATATAAAATATATT
Found at i:5866481 original size:38 final size:39
Alignment explanation
Indices: 5866438--5866512 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
5866428 TAAAATAAAT
5866438 AATTTAAAACATTAAT-ATG-AAAATTTTAAGAAATTAAG
1 AATTTAAAACATT-ATGATGTAAAATTTTAAGAAATTAAG
* * * *
5866476 AATTTAGAATATTATGGTGTCAAATTTTAAGAAATTA
1 AATTTAAAACATTATGATGTAAAATTTTAAGAAATTA
5866513 GGATTTTCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
37 2 0.06
38 13 0.42
39 16 0.52
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (39 bp):
AATTTAAAACATTATGATGTAAAATTTTAAGAAATTAAG
Found at i:5867271 original size:3 final size:3
Alignment explanation
Indices: 5867263--5867293 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5867253 AATTTAGAAT
5867263 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5867294 TCATGCTTAA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5867698 original size:16 final size:16
Alignment explanation
Indices: 5867681--5867767 Score: 120
Period size: 16 Copynumber: 5.4 Consensus size: 16
5867671 GGTATTACCC
*
5867681 GACCTGTTTTCAACCC
1 GACCTGTTTTCAACCT
*
5867697 GACTTGTTTTCAACCT
1 GACCTGTTTTCAACCT
5867713 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
5867729 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
* * *
5867745 GGCCTGTTTTTAACCG
1 GACCTGTTTTCAACCT
5867761 GACCTGT
1 GACCTGT
5867768 AAATGATCCG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 64 1.00
ACGTcount: A:0.17, C:0.29, G:0.16, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:5868041 original size:14 final size:14
Alignment explanation
Indices: 5868019--5868065 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
5868009 TGTGAAGGAA
*
5868019 AATTAATATAGTTT
1 AATTTATATAGTTT
5868033 AATTTATATA----
1 AATTTATATAGTTT
5868043 AA-TTATATAGTTT
1 AATTTATATAGTTT
5868056 AATTTATATA
1 AATTTATATA
5868066 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Done.