Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006093.1 Hibiscus syriacus cultivar Beakdansim tig00014444_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: 3172561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:1179169 original size:23 final size:23
Alignment explanation
Indices: 1179116--1179171 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1179106 TAATGTTGAA
* *
1179116 TCATTCAACAATGTTTTGCTGTT
1 TCATTCAGCAATGTTTTACTGTT
*
1179139 TCATTCAGCAATGTTTTATTGTT
1 TCATTCAGCAATGTTTTACTGTT
1179162 TCATTCAGCA
1 TCATTCAGCA
1179172 TAGTCTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.46
Consensus pattern (23 bp):
TCATTCAGCAATGTTTTACTGTT
Found at i:1180487 original size:60 final size:60
Alignment explanation
Indices: 1180375--1180487 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 60
1180365 TAGGGATGAA
* * * * * * * *
1180375 ATTAGAATGTTCAAAAGTTTAAAGATTGATTTAGAATGAGAGTCACAGTTTGGGGATCAT
1 ATTAGAATCTTCAAAAATTTAAAGAATAATTTAAAATAAAAGTCACAATTTGGGGATCAT
* *
1180435 ATTAGAATCTTCAAAAATTTAAAGAATAATTTAAAATAAAAGTTATAATTTGG
1 ATTAGAATCTTCAAAAATTTAAAGAATAATTTAAAATAAAAGTCACAATTTGG
1180488 AAACATATGA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 43 1.00
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (60 bp):
ATTAGAATCTTCAAAAATTTAAAGAATAATTTAAAATAAAAGTCACAATTTGGGGATCAT
Found at i:1180546 original size:24 final size:25
Alignment explanation
Indices: 1180514--1180560 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1180504 TAACTCGAAA
1180514 TAAAAAATTAGGAGATC-TTTTAAC
1 TAAAAAATTAGGAGATCATTTTAAC
*
1180538 TAAAAAATTAGGTGATCATTTTA
1 TAAAAAATTAGGAGATCATTTTA
1180561 CGTAAGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (25 bp):
TAAAAAATTAGGAGATCATTTTAAC
Found at i:1181296 original size:32 final size:32
Alignment explanation
Indices: 1181250--1181321 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
1181240 TATGATAACT
* *
1181250 GAACCCGACTTGCATCTTACTGATATAAACCC
1 GAACCCGACCTGCATCTGACTGATATAAACCC
* *
1181282 GAACCTGACCTGCATCTGACTGATATGAACCC
1 GAACCCGACCTGCATCTGACTGATATAAACCC
1181314 GAACCCGA
1 GAACCCGA
1181322 GATTAACCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.21
Consensus pattern (32 bp):
GAACCCGACCTGCATCTGACTGATATAAACCC
Found at i:1181376 original size:16 final size:16
Alignment explanation
Indices: 1181352--1181387 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1181342 GATATTACCC
*
1181352 ACCTGTTATCAACCTG
1 ACCTCTTATCAACCTG
*
1181368 ACCTCTTATGAACCTG
1 ACCTCTTATCAACCTG
1181384 ACCT
1 ACCT
1181388 GTAATTGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.33, G:0.11, T:0.31
Consensus pattern (16 bp):
ACCTCTTATCAACCTG
Found at i:1186204 original size:24 final size:24
Alignment explanation
Indices: 1186169--1186219 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1186159 TCACTTCAAG
* *
1186169 TTGAAGATTCAAGAAACGTGTCTT
1 TTGAAGAATCAAGAAACGTGACTT
* *
1186193 TTGAAGAATCAATAAATGTGACTT
1 TTGAAGAATCAAGAAACGTGACTT
1186217 TTG
1 TTG
1186220 GTGATCCACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (24 bp):
TTGAAGAATCAAGAAACGTGACTT
Found at i:1186268 original size:24 final size:23
Alignment explanation
Indices: 1186229--1186286 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
1186219 GGTGATCCAC
*
1186229 AAGACATGT-CCTTTGACATTTC-A
1 AAGA-ATGTACCTTTGA-AATTCAA
*
1186252 AAGGATGTACCTCTTGAAATTCAA
1 AAGAATGTACCT-TTGAAATTCAA
1186276 AAGAATGTACC
1 AAGAATGTACC
1186287 AATTGAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 4 0.14
23 10 0.34
24 15 0.52
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (23 bp):
AAGAATGTACCTTTGAAATTCAA
Found at i:1189836 original size:7 final size:7
Alignment explanation
Indices: 1189824--1189881 Score: 75
Period size: 7 Copynumber: 8.4 Consensus size: 7
1189814 ATATATATAC
1189824 ATACTTT
1 ATACTTT
1189831 ATACTTT
1 ATACTTT
1189838 ATACTTT
1 ATACTTT
1189845 ATACTTT
1 ATACTTT
**
1189852 ATA-AAT
1 ATACTTT
1189858 ATACTTT
1 ATACTTT
1189865 ATACTTAT
1 ATACTT-T
1189873 ATA-TTT
1 ATACTTT
1189879 ATA
1 ATA
1189882 TATATGTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
6 8 0.18
7 33 0.73
8 4 0.09
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.53
Consensus pattern (7 bp):
ATACTTT
Found at i:1189860 original size:27 final size:25
Alignment explanation
Indices: 1189830--1189910 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 25
1189820 ATACATACTT
1189830 TATACTTTATACTTTATACTTTATAAA
1 TATACTTTATACTTTATACTTTAT--A
1189857 TATACTTTATACTTATATA-TTTATA
1 TATACTTTATACTT-TATACTTTATA
*
1189882 TATA-TGTATAC-TTATACTTATATTA
1 TATACTTTATACTTTATACTT-TA-TA
1189907 TATA
1 TATA
1189911 TGTTTTTAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
22 4 0.08
23 3 0.06
24 8 0.16
25 11 0.22
27 19 0.39
28 4 0.08
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (25 bp):
TATACTTTATACTTTATACTTTATA
Found at i:1189862 original size:20 final size:21
Alignment explanation
Indices: 1189837--1189875 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1189827 CTTTATACTT
1189837 TATACTTTATACTT-TATAAA
1 TATACTTTATACTTATATAAA
1189857 TATACTTTATACTTATATA
1 TATACTTTATACTTATATA
1189876 TTTATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (21 bp):
TATACTTTATACTTATATAAA
Found at i:1190007 original size:2 final size:2
Alignment explanation
Indices: 1190000--1190046 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1189990 ACATTCATTG
1190000 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
1190042 T- TA TA
1 TA TA TA
1190047 ATTTTTTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1190174 original size:12 final size:14
Alignment explanation
Indices: 1190154--1190186 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1190144 TCTTGTTTAA
1190154 TATATTTAT-ATTT
1 TATATTTATAATTT
1190167 TA-ATTTATAATTT
1 TATATTTATAATTT
1190180 TATATTT
1 TATATTT
1190187 GTTCAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 8 0.44
14 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATATTTATAATTT
Found at i:1190261 original size:134 final size:138
Alignment explanation
Indices: 1190120--1190393 Score: 351
Period size: 141 Copynumber: 2.0 Consensus size: 138
1190110 TCACATTTAC
* *
1190120 AATTATTTCGATTTGAT-C-CAT-C-TG-TCTTGTTTAATATATTTATATTTTAATTTATAATTT
1 AATTATTTCAATTTGATCCTCATCCATGATCTTGTTTAATATATTTAAATTTTAATTTATAATTT
* * * * **
1190180 TATATTTGTTCAATTTAGTCCTTAAAATTATATTTTTTTATCCGAAATTAGCCCATTCTTATTTA
66 CATATTTGTTCAATTTAGTCCGTAAAATTATATTTTTTTAT-CAAAATTAACCCATAATTATTTA
1190245 TATTTTTTT
130 TATTTTTTT
* * ** *
1190254 AATTATTTCAATTTGATCCCTCATCCATGATTGTTGTTTAATTTATTTAAATTTTTGTTTGTAAT
1 AATTATTTCAATTTGAT-CCTCATCCATGA-TCTTGTTTAATATATTTAAATTTTAATTTATAAT
*
1190319 TTCATGTTTGTTCAATTTAGTCCGTAAAATTATATTTTTTTATCAAAATTAACCCATAATTATTT
64 TTCATATTTGTTCAATTTAGTCCGTAAAATTATATTTTTTTATCAAAATTAACCCATAATTATTT
*
1190384 TTATTTTTTT
129 ATATTTTTTT
1190394 GTAATTTGCT
Statistics
Matches: 118, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
134 16 0.14
136 1 0.01
137 3 0.03
138 1 0.01
139 2 0.02
140 27 0.23
141 68 0.58
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.55
Consensus pattern (138 bp):
AATTATTTCAATTTGATCCTCATCCATGATCTTGTTTAATATATTTAAATTTTAATTTATAATTT
CATATTTGTTCAATTTAGTCCGTAAAATTATATTTTTTTATCAAAATTAACCCATAATTATTTAT
ATTTTTTT
Found at i:1192248 original size:95 final size:95
Alignment explanation
Indices: 1192084--1192284 Score: 267
Period size: 95 Copynumber: 2.1 Consensus size: 95
1192074 TATTGATGTG
* * *
1192084 AGTATCGATACTAAGAGAAACGTATCGATACCTTGGAATCCAGAATGTAGAAATGGTATCAATAT
1 AGTATCGATACTAAGAGAAACGTACCGATACCATGGAATCCAGAATGTAGAAATGGTATCAATAC
* *
1192149 TGAAAGGGAGTATCGGTACCATAGCATAAA
66 TGAAAGAGAGTATCGATACCATAGCATAAA
* * * * * * * *
1192179 AGTATCGGTACTAGGAGAAAGGTACCGATTCCATGGATTCCATAATGTCGAAATGGTATCGATAC
1 AGTATCGATACTAAGAGAAACGTACCGATACCATGGAATCCAGAATGTAGAAATGGTATCAATAC
* *
1192244 TGAAAGAGAGTATCGATACCATAGTATAGA
66 TGAAAGAGAGTATCGATACCATAGCATAAA
1192274 AGTATCGATAC
1 AGTATCGATAC
1192285 CATGGTATGG
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (95 bp):
AGTATCGATACTAAGAGAAACGTACCGATACCATGGAATCCAGAATGTAGAAATGGTATCAATAC
TGAAAGAGAGTATCGATACCATAGCATAAA
Found at i:1192970 original size:81 final size:81
Alignment explanation
Indices: 1192728--1193100 Score: 586
Period size: 81 Copynumber: 4.6 Consensus size: 81
1192718 AGTTGTGCCT
* * *
1192728 TATTGCAAGTTAGATGACAGACTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTATGCATTT
1 TATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTT
1192793 GGCAGAAAGGTGCCAA
66 GGCAGAAAGGTGCCAA
* *
1192809 TATTGCAAGTTAGATGAAAGGCTAAATGTGCCTTTGAGTAAAAGATTAATTGCCTAGTTGTGTAT
1 TATTGCAAGTTAGATGAAAGGCTAAA--TGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCAT
* *
1192874 TTGGCATAAATGTGCCAA
64 TTGGCAGAAAGGTGCCAA
*
1192892 TATTACAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTT
1 TATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTT
1192957 GGCAGAAAGGTGCCAA
66 GGCAGAAAGGTGCCAA
* *
1192973 TATTGCAAGTTATATGAAAGGTTAAATGCCTTTGAGTAAAAGATTAATTGCCTAG-TAGTGCATT
1 TATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGCT-GTGCATT
1193037 TGGCAGAAAGGTGCCAA
65 TGGCAGAAAGGTGCCAA
* * * *
1193054 TATTGCAAGTTAGATGAAAGGATAAATGCATTTGATTAAAATATTAA
1 TATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAA
1193101 ATGATTAACA
Statistics
Matches: 269, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
80 1 0.00
81 193 0.72
83 75 0.28
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (81 bp):
TATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTT
GGCAGAAAGGTGCCAA
Found at i:1195165 original size:45 final size:45
Alignment explanation
Indices: 1195101--1195235 Score: 252
Period size: 45 Copynumber: 3.0 Consensus size: 45
1195091 GTTTTCATTA
1195101 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
1195146 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
* *
1195191 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
1195236 TATCGCAACC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.21
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATGC
Found at i:1195775 original size:58 final size:58
Alignment explanation
Indices: 1195657--1195776 Score: 129
Period size: 58 Copynumber: 2.1 Consensus size: 58
1195647 AATAAATAAC
** * *
1195657 ATAAGGAAAACAAATAAAATGATAAAACAAACAAACATCAAATAAAACGAAAAAATGA
1 ATAAGGAAAACAAATAAAATGATAAAACAAACAAACAGAAAACAAAAAGAAAAAATGA
* * *
1195715 ATAAGGAAAA-AAATAAAATTATAAAA-AAACATAAAGAGAAAACAAAAATAAAACAA-GA
1 ATAAGGAAAACAAATAAAATGATAAAACAAAC--AAACAGAAAACAAAAAGAAAA-AATGA
1195773 ATAA
1 ATAA
1195777 AAACAAAGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
56 4 0.08
57 15 0.29
58 31 0.60
59 2 0.04
ACGTcount: A:0.72, C:0.07, G:0.08, T:0.12
Consensus pattern (58 bp):
ATAAGGAAAACAAATAAAATGATAAAACAAACAAACAGAAAACAAAAAGAAAAAATGA
Found at i:1196023 original size:14 final size:14
Alignment explanation
Indices: 1195972--1196032 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
1195962 AGGAAGACAA
1195972 AATAA-AAAATAA-
1 AATAATAAAATAAT
*
1195984 AA-AATATATATATAT
1 AATAATA-AAATA-AT
*
1195999 ACATAAGAAAATAAT
1 A-ATAATAAAATAAT
1196014 AATAATAAAATAAT
1 AATAATAAAATAAT
1196028 AATAA
1 AATAA
1196033 ACATAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
11 2 0.05
12 3 0.08
13 4 0.10
14 18 0.46
15 4 0.10
16 5 0.13
17 3 0.08
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:1196038 original size:17 final size:17
Alignment explanation
Indices: 1195984--1196040 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
1195974 TAAAAAATAA
*
1195984 AAAATATATATATATACAT
1 AAAATA-ATA-ATAAACAT
1196003 AAGAA-AATAATAATA-AT
1 AA-AATAATAATAA-ACAT
1196020 AAAATAATAATAAACAT
1 AAAATAATAATAAACAT
1196037 AAAA
1 AAAA
1196041 AAATTAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 3 0.09
17 21 0.64
18 4 0.12
19 3 0.09
20 2 0.06
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAATAATAATAAACAT
Found at i:1196087 original size:24 final size:24
Alignment explanation
Indices: 1196060--1196164 Score: 74
Period size: 24 Copynumber: 4.4 Consensus size: 24
1196050 AAATGTGTAT
1196060 ATATAATAACGTAAAAATAAATAA
1 ATATAATAACGTAAAAATAAATAA
* *
1196084 ATATAATAA---AAATATATAATAT
1 ATATAATAACGTAAAAATA-AATAA
* * ** * *
1196106 TTATAAAAAAATAAAAA-AATGTGTAT
1 ATATAATAACGTAAAAATAA---ATAA
1196132 ATATAATAACGTAAAAATAAATAA
1 ATATAATAACGTAAAAATAAATAA
1196156 ATATAATAA
1 ATATAATAA
1196165 AAAATATACA
Statistics
Matches: 61, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
21 6 0.10
22 11 0.18
23 1 0.02
24 21 0.34
25 4 0.07
26 16 0.26
27 2 0.03
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
ATATAATAACGTAAAAATAAATAA
Found at i:1196093 original size:19 final size:19
Alignment explanation
Indices: 1196071--1196125 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
1196061 TATAATAACG
1196071 TAAAAATAAATAAATATAA
1 TAAAAATAAATAAATATAA
*
1196090 TAAAAATATATAATATTTATAA
1 TAAAAATAAATAA-A--TATAA
*
1196112 -AAAAATAAAAAAAT
1 TAAAAATAAATAAAT
1196126 GTGTATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 1 0.03
19 12 0.40
20 2 0.07
21 10 0.33
22 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAAATAAATAAATATAA
Found at i:1196116 original size:73 final size:74
Alignment explanation
Indices: 1196035--1196189 Score: 271
Period size: 72 Copynumber: 2.1 Consensus size: 74
1196025 AATAATAAAC
1196035 ATAAAAAAATTAAAAAAATGTGTATATATAATAACGTAAAAATAAATAAATATAAT-AAAAATAT
1 ATAAAAAAATTAAAAAAATGTGTATATATAATAACGTAAAAATAAATAAATATAATAAAAAATAT
*
1196099 ATAATATTT
66 ACAATATTT
1196108 ATAAAAAAA-TAAAAAAATGTGTATATATAATAACGTAAAAATAAATAAATATAATAAAAAATAT
1 ATAAAAAAATTAAAAAAATGTGTATATATAATAACGTAAAAATAAATAAATATAATAAAAAATAT
1196172 ACAATATTT
66 ACAATATTT
*
1196181 A-AATAAAAT
1 ATAAAAAAAT
1196190 GAGAAAATAT
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
72 52 0.67
73 26 0.33
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (74 bp):
ATAAAAAAATTAAAAAAATGTGTATATATAATAACGTAAAAATAAATAAATATAATAAAAAATAT
ACAATATTT
Found at i:1196177 original size:27 final size:28
Alignment explanation
Indices: 1196147--1196200 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
1196137 ATAACGTAAA
*
1196147 AATAAATAAATATAAT-AAAAAATATAC
1 AATAAATAAATAAAATGAAAAAATATAC
** *
1196174 AATATTTAAATAAAATGAGAAAATATA
1 AATAAATAAATAAAATGAAAAAATATA
1196201 TAAAAAATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (28 bp):
AATAAATAAATAAAATGAAAAAATATAC
Found at i:1198048 original size:73 final size:74
Alignment explanation
Indices: 1197928--1198075 Score: 208
Period size: 73 Copynumber: 2.0 Consensus size: 74
1197918 ATTGACTTTG
* * *
1197928 AAACTGGAAAGTTTATTTGTTGACAATCAGCCGTCCCTTCATTGTGAAGTTAAACTTGTGTTGTC
1 AAACTGAAAAGTTTATTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTAAACTTGTGTTGTC
1197993 TCGAGTCCA
66 TCGAGTCCA
* * * * *
1198002 AAACTGAAAAG-TTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
1 AAACTGAAAAGTTTATTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTAAACTTGTGTTGTC
*
1198066 TTGAGTCCA
66 TCGAGTCCA
1198075 A
1 A
1198076 TATCCTTCGC
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 55 0.85
74 10 0.15
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (74 bp):
AAACTGAAAAGTTTATTTGTTGACAATCAGCCGCCCCTTCACTGTGAAGTTAAACTTGTGTTGTC
TCGAGTCCA
Found at i:1198139 original size:106 final size:106
Alignment explanation
Indices: 1198010--1198270 Score: 432
Period size: 106 Copynumber: 2.5 Consensus size: 106
1198000 CAAAACTGAA
* ** *
1198010 AAGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCA
1 AAGTTGTTTGTTGACAACCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCA
*
1198075 ATATCCTTCGCTGTTAAGTTGAAATTGGCTCTGAAACTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGG
* *
1198116 AAGTTGTTTGTTGACAACCAGTCGGCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCA
1 AAGTTGTTTGTTGACAACCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCA
1198181 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGG
* * *
1198222 AAATTGTTTGTTGACAACCAGTCACCCCTTCGCTGTGAAGTTGAACTTG
1 AAGTTGTTTGTTGACAACCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
1198271 ACTATGAAAC
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 143 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (106 bp):
AAGTTGTTTGTTGACAACCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCA
ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGG
Found at i:1198650 original size:110 final size:110
Alignment explanation
Indices: 1198514--1198897 Score: 553
Period size: 110 Copynumber: 3.5 Consensus size: 110
1198504 CTGGGAAATT
* *
1198514 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAATCCAATATC
1 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATC
1198579 CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTG
66 CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTG
* *
1198624 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTAAACTTGTGTTATCTCGAGTCCAATATC
1 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATC
* * **
1198689 CTTCGCTGTGAACTTGAAATTGGCTC----TGAAATTGGGTAA-TG
66 CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATT-GAAAAGTG
* * * * ***
1198730 GTTTATTGACAATCGGCCATCCCTTTACTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATC
1 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATC
* *
1198795 CTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTG
66 CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTG
*
1198840 GTTTGTTGACAACCAGCCGTCCCTTCGATGTGAAGTTGAACTTTGTGTTGTCTCGAGT
1 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC-TTGTGTTGTCTCGAGT
1198898 GGCGCGATAT
Statistics
Matches: 237, Mismatches: 30, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
106 88 0.37
107 3 0.01
109 3 0.01
110 127 0.54
111 16 0.07
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (110 bp):
GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATC
CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTG
Found at i:1198837 original size:216 final size:217
Alignment explanation
Indices: 1198480--1198897 Score: 658
Period size: 216 Copynumber: 1.9 Consensus size: 217
1198470 ACCATTCATC
* * * * * **
1198480 GTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
1 GTGAACTTGAAATTGGCTCTGAAACTGGGAAATGGTTTATTGACAACCAGCCATCCCTTCACTGT
* *
1198545 GAAGTTGAACTTGTGTTGTCTTGAATCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAT
66 GAAGTTGAACTTGTGTTGTCTCGAATCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAT
* *
1198610 GAAATTGAAAAGTGGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTAAAC-TTGTGTTAT
131 GAAACTGAAAAGTGGTTTGTTGACAACCAGCCGTCCCTTCGATGTGAAGTTAAACTTTGTGTTAT
1198674 CTCGAGTCCAATATCCTTCGCT
196 CTCGAGTCCAATATCCTTCGCT
* * * * *
1198696 GTGAACTTGAAATTGGCTCTGAAATTGGGTAATGGTTTATTGACAATCGGCCATCCCTTTACTGT
1 GTGAACTTGAAATTGGCTCTGAAACTGGGAAATGGTTTATTGACAACCAGCCATCCCTTCACTGT
*
1198761 GAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAT
66 GAAGTTGAACTTGTGTTGTCTCGAATCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAT
* *
1198826 GAAACTGAAAAGTGGTTTGTTGACAACCAGCCGTCCCTTCGATGTGAAGTTGAACTTTGTGTTGT
131 GAAACTGAAAAGTGGTTTGTTGACAACCAGCCGTCCCTTCGATGTGAAGTTAAACTTTGTGTTAT
1198891 CTCGAGT
196 CTCGAGT
1198898 GGCGCGATAT
Statistics
Matches: 182, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
216 167 0.92
217 15 0.08
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (217 bp):
GTGAACTTGAAATTGGCTCTGAAACTGGGAAATGGTTTATTGACAACCAGCCATCCCTTCACTGT
GAAGTTGAACTTGTGTTGTCTCGAATCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAT
GAAACTGAAAAGTGGTTTGTTGACAACCAGCCGTCCCTTCGATGTGAAGTTAAACTTTGTGTTAT
CTCGAGTCCAATATCCTTCGCT
Found at i:1199455 original size:36 final size:35
Alignment explanation
Indices: 1199414--1199483 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
1199404 AAGATATCTG
* * *
1199414 TTGTTTCATGAGAAACGGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGAAAAACGG-CTCAAGAGAGACAAAAT
* *
1199450 TTGTTTTAAGAAAAACTGCTCAAGAGAGACAAAA
1 TTGTTTCAAGAAAAACGGCTCAAGAGAGACAAAA
1199484 CTTAGTTCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 15 0.52
36 14 0.48
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.24
Consensus pattern (35 bp):
TTGTTTCAAGAAAAACGGCTCAAGAGAGACAAAAT
Found at i:1199713 original size:36 final size:37
Alignment explanation
Indices: 1199655--1199730 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
1199645 GAAACAATTT
*
1199655 CAAAGGTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTTTTCCAAGAGAAACTGTCTCAAGAGAGA
1199692 CAAA-GTTTGTTT-CAAGAGAAACTGTCTCAAGAGAGA
1 CAAAGGTTT-TTTCCAAGAGAAACTGTCTCAAGAGAGA
1199728 CAA
1 CAA
1199731 TGGTGAGCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 30 0.81
37 7 0.19
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (37 bp):
CAAAGGTTTTTTCCAAGAGAAACTGTCTCAAGAGAGA
Found at i:1200244 original size:18 final size:18
Alignment explanation
Indices: 1200217--1200252 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1200207 TATTGAATTC
*
1200217 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1200235 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1200253 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1201332 original size:21 final size:19
Alignment explanation
Indices: 1201315--1201371 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
1201305 TTCCTTTTGA
1201315 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
* * *
1201334 TTGTT-CTTGTTTT-TTCT
1 TTTTTGCTTCTTTTCTTTT
1201351 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
1201370 TT
1 TT
1201372 GTTCTTGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 7 0.23
18 14 0.47
19 9 0.30
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTTTGCTTCTTTTCTTTT
Found at i:1201340 original size:15 final size:16
Alignment explanation
Indices: 1201315--1201377 Score: 74
Period size: 16 Copynumber: 3.8 Consensus size: 16
1201305 TTCCTTTTGA
1201315 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
*
1201331 TTTTTGTTCTTGTTTTTTCT
1 TTTTTG--C-T-TCTTTTCT
1201351 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
1201367 TTTTTG-TTCTT
1 TTTTTGCTTCTT
1201378 GATTGAATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 5 0.12
16 19 0.46
17 1 0.02
18 2 0.05
19 1 0.02
20 13 0.32
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTTTGCTTCTTTTCT
Found at i:1201377 original size:10 final size:10
Alignment explanation
Indices: 1201327--1201364 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
1201317 TTTGCTTCTT
1201327 TTCTTTTTTG
1 TTCTTTTTTG
1201337 TTCTTGTTTT-
1 TTCTT-TTTTG
1201347 TTCTTTTTTG
1 TTCTTTTTTG
1201357 CTTCTTTT
1 -TTCTTTT
1201365 CTTTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 10 0.40
11 11 0.44
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:1202761 original size:184 final size:184
Alignment explanation
Indices: 1202452--1202818 Score: 689
Period size: 184 Copynumber: 2.0 Consensus size: 184
1202442 ATGTTACAAT
* *
1202452 CTTGCTTCCATGTGGTTAAATCCAGTTCATCGAGTCCTTCATGACTTAATTTCATGTTTGTGAAA
1 CTTGCTTCCATGTGGTTAAATCCACTTCATCGAGTCCTTCATAACTTAATTTCATGTTTGTGAAA
1202517 ATGCTTAAAAATTGTAGATGAAGATGCAAAAAGGCAAAAATGCAAAATGCAAGAATGCATGAAAT
66 ATGCTTAAAAATTGTAGATGAAGATGCAAAAAGGCAAAAATGCAAAATGCAAGAATGCATGAAAT
*
1202582 GTTCGAGGCATTGATCCAGAAAAGTGTCCATTATTATAAATAATCTTTACTTAC
131 GTTCGAAGCATTGATCCAGAAAAGTGTCCATTATTATAAATAATCTTTACTTAC
*
1202636 CTTGCTTCCATGTGGTTAAATCCACTTCATCGAGTTCTTCATAACTTAATTTCATGTTTGTGAAA
1 CTTGCTTCCATGTGGTTAAATCCACTTCATCGAGTCCTTCATAACTTAATTTCATGTTTGTGAAA
*
1202701 ATGCTTAAAAATTGTAGATGAATATGCAAAAAGGCAAAAATGCAAAATGCAAGAATGCATGAAAT
66 ATGCTTAAAAATTGTAGATGAAGATGCAAAAAGGCAAAAATGCAAAATGCAAGAATGCATGAAAT
1202766 GTTCGAAGCATTGATCCAGAAAAGTGTCCATTATTATAAATAATCTTTACTTA
131 GTTCGAAGCATTGATCCAGAAAAGTGTCCATTATTATAAATAATCTTTACTTA
1202819 GACAAAAATG
Statistics
Matches: 178, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 178 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (184 bp):
CTTGCTTCCATGTGGTTAAATCCACTTCATCGAGTCCTTCATAACTTAATTTCATGTTTGTGAAA
ATGCTTAAAAATTGTAGATGAAGATGCAAAAAGGCAAAAATGCAAAATGCAAGAATGCATGAAAT
GTTCGAAGCATTGATCCAGAAAAGTGTCCATTATTATAAATAATCTTTACTTAC
Found at i:1205001 original size:6 final size:6
Alignment explanation
Indices: 1204992--1205042 Score: 68
Period size: 6 Copynumber: 8.3 Consensus size: 6
1204982 AACAGTTAGT
*
1204992 AAAATA AAAATA AATATAA ATAAATA AAAATA AAAAT- AAAATA AAAATA
1 AAAATA AAAATA AAAAT-A A-AAATA AAAATA AAAATA AAAATA AAAATA
1205041 AA
1 AA
1205043 TAAATGGCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 5 0.12
6 28 0.70
7 4 0.10
8 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:1205012 original size:10 final size:10
Alignment explanation
Indices: 1204993--1205047 Score: 65
Period size: 10 Copynumber: 5.4 Consensus size: 10
1204983 ACAGTTAGTA
*
1204993 AAATAAAAAT
1 AAATATAAAT
1205003 AAATATAAAT
1 AAATATAAAT
*
1205013 AAATAAAAAT
1 AAATATAAAT
*
1205023 AAAAATAAAAT
1 AAATAT-AAAT
*
1205034 AAAAATAAAT
1 AAATATAAAT
1205044 AAAT
1 AAAT
1205048 GGCAAGAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
10 29 0.74
11 10 0.26
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
AAATATAAAT
Found at i:1205725 original size:10 final size:8
Alignment explanation
Indices: 1205692--1205722 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
1205682 CTTTTAAGAA
1205692 AATATATT
1 AATATATT
1205700 AATATATT
1 AATATATT
1205708 AATATATT
1 AATATATT
1205716 AATATAT
1 AATATAT
1205723 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATATATT
Found at i:1207632 original size:113 final size:110
Alignment explanation
Indices: 1207395--1207971 Score: 553
Period size: 124 Copynumber: 4.9 Consensus size: 110
1207385 ATAGAGTCAT
* * *
1207395 GCAAAAGGCTGAACAAGTTCTTCTCATTATTAACTTCTTCTTCCTCTTTAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
*
1207460 TTATGAACTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 TTATGAACTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTCAA
* *
1207505 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
* * *
1207570 TTATGAACTTCTACCTGGCAATGCTGATCCATCGAGTGATGAATTGAA
66 TTATGAAC-TCT--CTGGAAAAGCTGATCCATCGAGTGATGAATTCAA
*
1207618 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCCTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CCTCTTCAGATGAGTTCTTCTC
* * ** * * * * *
1207683 ATTATGAATTTTCTCTGGAAAAGTTGATGTTGATCTATATCCTTCTATGATAGAGTCAT
65 ATTATGAA--CTCTCTGGAAAAGCTGA--TCCATC--GA---GT-GATG--A-ATTCAA
* * *
1207742 GCAAAAGGTTGAACAAGTTCTTATCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
* ** * *
1207807 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTTCTTCTGTGAT-AGAGTCAT
65 ATTATGAAC--TCTCTGG-AAA----A-GCTGATC---CATC--GAGTGATGA-ATTCAA
* *
1207866 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
* *
1207931 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATG
65 ATTATGAAC--TCTCTGGAAAAGCTGATCCATCGAGTGATG
1207972 GATTTGAATT
Statistics
Matches: 392, Mismatches: 45, Indels: 56
0.80 0.09 0.11
Matches are distributed among these distances:
110 68 0.17
111 3 0.01
113 84 0.21
114 30 0.08
115 10 0.03
117 1 0.00
118 6 0.02
119 1 0.00
120 1 0.00
121 3 0.01
123 6 0.02
124 164 0.42
125 3 0.01
127 2 0.01
128 2 0.01
129 1 0.00
130 4 0.01
131 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (110 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTCAA
Found at i:1207777 original size:124 final size:124
Alignment explanation
Indices: 1207618--1207958 Score: 583
Period size: 124 Copynumber: 2.8 Consensus size: 124
1207608 ATGAATTGAA
* * *
1207618 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCCTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
* *
1207683 ATTATGAATTTTCTCTGGAAAAGTTGATGTTGATCTATATCCTTCTATGATAGAGTCAT
66 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATATCCTTCTATGATAGAGTCAT
* *
1207742 GCAAAAGGTTGAACAAGTTCTTATCATTACGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
* * *
1207807 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTTCTTCTGTGATAGAGTCAT
66 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATATCCTTCTATGATAGAGTCAT
*
1207866 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1207931 ATTATGAACTTTCTCTGGAAAAGTTGAT
66 ATTATGAACTTTCTCTGGAAAAGTTGAT
1207959 CCATCAAGTG
Statistics
Matches: 204, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 204 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (124 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATATCCTTCTATGATAGAGTCAT
Found at i:1207912 original size:24 final size:23
Alignment explanation
Indices: 1207885--1207930 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1207875 TGAACAAGTT
1207885 CTTC-TCATTATGAACTTCTTCTTC
1 CTTCTTCA-TATG-ACTTCTTCTTC
*
1207909 CTTCTTCATATGAGTTCTTCTT
1 CTTCTTCATATGACTTCTTCTT
1207931 ATTATGAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 8 0.40
25 3 0.15
ACGTcount: A:0.15, C:0.26, G:0.07, T:0.52
Consensus pattern (23 bp):
CTTCTTCATATGACTTCTTCTTC
Found at i:1208360 original size:22 final size:21
Alignment explanation
Indices: 1208332--1208411 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 21
1208322 AATAAAGCTT
1208332 TCATCTTTGAAAAGAGAACCTA
1 TCATCTTT-AAAAGAGAACCTA
*
1208354 TCATCTTT-AAAGAGATATGCTA
1 TCATCTTTAAAAGAGA-A-CCTA
* * *
1208376 TTATCTTTAAAGAAAGAATCTA
1 TCATCTTTAAA-AGAGAACCTA
1208398 TCATCTTTGAAAAG
1 TCATCTTT-AAAAG
1208412 TGTAGATGTA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 7 0.15
21 1 0.02
22 29 0.62
23 6 0.13
24 4 0.09
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (21 bp):
TCATCTTTAAAAGAGAACCTA
Found at i:1208692 original size:54 final size:54
Alignment explanation
Indices: 1208599--1208702 Score: 120
Period size: 54 Copynumber: 1.9 Consensus size: 54
1208589 TCTTGTTGTA
* *
1208599 AAACATTTGACAACACATTCATCATTTCTTATGATTTCTGCACAGATGTTTCGT
1 AAACATTTAACAACACATTCATCATTTCTTATGACTTCTGCACAGATGTTTCGT
* * * * * *
1208653 AAACATTTAATAATACATTCATTATTTCCTT-TGGCTTCTGCCCATATGTT
1 AAACATTTAACAACACATTCATCATTT-CTTATGACTTCTGCACAGATGTT
1208703 CTCAATCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
54 38 0.93
55 3 0.07
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (54 bp):
AAACATTTAACAACACATTCATCATTTCTTATGACTTCTGCACAGATGTTTCGT
Found at i:1213330 original size:2 final size:2
Alignment explanation
Indices: 1213323--1213380 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1213313 ACAACAAGGG
1213323 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
1213365 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1213381 TTGAAAGGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1218424 original size:2 final size:2
Alignment explanation
Indices: 1218411--1218447 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1218401 TTTTAAGAAA
*
1218411 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1218448 AATAAGATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1218700 original size:146 final size:145
Alignment explanation
Indices: 1218433--1218711 Score: 384
Period size: 146 Copynumber: 1.9 Consensus size: 145
1218423 ATATATATAT
* * *
1218433 ATATATATATTTATAAATAAGATATTTATTTACTTAGAAATATCAGAAAGGGAATTCTAGGTGCT
1 ATATATATATATAAAAATAAGATATTTATTTACTTAGAAATATCAGAAAAGGAATTCTAGGTGCT
* *
1218498 TTAAGACAGCTCTTTTCTTCGATGTTAAAAGTAAATAAATATTAATAAAACATTTCTATAAAAAA
66 TTAAGACAGCTCTTTTCTTCGATATTAAAAATAAATAAATATTAATAAAACATTTCT-TAAAAAA
1218563 TAATTAAAATAAAATA
130 TAATTAAAATAAAATA
* * * *
1218579 ATATATATATATAAAAATAGGATATTTATTTATTTA-AGAATATTAGAAAAGGACTTCTAGGTGC
1 ATATATATATATAAAAATAAGATATTTATTTACTTAGA-AATATCAGAAAAGGAATTCTAGGTGC
* **
1218643 TTTAAGACAGCTCTTTTCTTCTATATTAATAAATAAAATAAATATT-A-AAAATGTTTCTTAAAA
65 TTTAAGACAGCTCTTTTCTTCGATATTAA-AAAT-AAATAAATATTAATAAAACATTTCTTAAAA
*
1218706 ATTAAT
128 AATAAT
1218712 ATATATTTTA
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
145 11 0.09
146 91 0.78
147 4 0.03
148 11 0.09
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (145 bp):
ATATATATATATAAAAATAAGATATTTATTTACTTAGAAATATCAGAAAAGGAATTCTAGGTGCT
TTAAGACAGCTCTTTTCTTCGATATTAAAAATAAATAAATATTAATAAAACATTTCTTAAAAAAT
AATTAAAATAAAATA
Found at i:1218904 original size:18 final size:17
Alignment explanation
Indices: 1218878--1218916 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1218868 AATATATTGC
1218878 AAATAAACATATAAAATT
1 AAATAAACATATAAAA-T
* *
1218896 AAATCAACATCTAAAAT
1 AAATAAACATATAAAAT
1218913 AAAT
1 AAAT
1218917 GAGATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAACATATAAAAT
Found at i:1220651 original size:18 final size:17
Alignment explanation
Indices: 1220630--1220677 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1220620 TTGAATAAGG
1220630 AAAAAAAATAAAAAT-A
1 AAAAAAAATAAAAATGA
*
1220646 TAAAAAAACATAAAGATGA
1 -AAAAAAA-ATAAAAATGA
*
1220665 AACAAAAATAAAA
1 AAAAAAAATAAAA
1220678 CAAGAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 12 0.46
18 13 0.50
19 1 0.04
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.12
Consensus pattern (17 bp):
AAAAAAAATAAAAATGA
Found at i:1221018 original size:26 final size:28
Alignment explanation
Indices: 1220989--1221041 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
1220979 ATAACGTAAA
*
1220989 AATAAATAAATATAAT-A-AAAATATAC
1 AATAAATAAATAAAATGAGAAAATATAC
**
1221015 AATATTTAAATAAAATGAGAAAATATA
1 AATAAATAAATAAAATGAGAAAATATA
1221042 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 13 0.59
27 1 0.05
28 8 0.36
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (28 bp):
AATAAATAAATAAAATGAGAAAATATAC
Found at i:1222329 original size:45 final size:45
Alignment explanation
Indices: 1222264--1222504 Score: 313
Period size: 45 Copynumber: 5.4 Consensus size: 45
1222254 GGTGTTTTCA
*
1222264 GATGCCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAG
1 GATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
* * * *
1222309 GATGCTATAAAT-AAAGTGCATAACGATGAACTAAAGGCATGAAAG
1 GATGCCATAAATGAAA-TGCATAACGGTGCATTAAAGGCATGAAAG
* **
1222354 GATGCCATAAATGAAATGCATAACAGTGCATTAAATACATGAAAG
1 GATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
* * * *
1222399 GATTCCATAAATGAAATGTATAACGATGCATTAAAGACATGAAAG
1 GATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
* * **
1222444 GATGCCATAAATGAAATCCACAATTGTGCATTAAAGGCATGAAAG
1 GATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
*
1222489 GATGTCATAAATGAAA
1 GATGCCATAAATGAAA
1222505 ATAATGAATA
Statistics
Matches: 168, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
44 3 0.02
45 162 0.96
46 3 0.02
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (45 bp):
GATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAG
Found at i:1222410 original size:21 final size:21
Alignment explanation
Indices: 1222385--1222455 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
1222375 AACAGTGCAT
1222385 TAAATACATGAAAGGATTCCA
1 TAAATACATGAAAGGATTCCA
* * *
1222406 TAAATGAAATGTATAACGA-TGCA
1 TAAAT-ACATG-A-AAGGATTCCA
* *
1222429 TTAAAGACATGAAAGGATGCCA
1 -TAAATACATGAAAGGATTCCA
1222451 TAAAT
1 TAAAT
1222456 GAAATCCACA
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
21 13 0.36
22 7 0.19
23 8 0.22
24 8 0.22
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (21 bp):
TAAATACATGAAAGGATTCCA
Found at i:1228616 original size:21 final size:19
Alignment explanation
Indices: 1228584--1228624 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1228574 TGAAGAATTT
*
1228584 TGATGAATAGTATTGATAC
1 TGATGAATAGTATCGATAC
1228603 TGATGCAATTAGTATCGATAC
1 TGATG-AA-TAGTATCGATAC
1228624 T
1 T
1228625 ATTGTGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (19 bp):
TGATGAATAGTATCGATAC
Found at i:1229261 original size:45 final size:45
Alignment explanation
Indices: 1229197--1229521 Score: 463
Period size: 45 Copynumber: 7.2 Consensus size: 45
1229187 GTTTTCATTA
* * *
1229197 CATAAATGGAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAATGATGC
* *
1229242 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAATGATGC
* * *
1229287 CATAAATGAAATGCATAATGGTGCATTAAAGGCAGGAAATGATGC
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAATGATGC
* *
1229332 CATAAATGAAATGCATAACGATGCATTAAAGGCACGAAAGGATGC
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAATGATGC
*
1229377 CATAAA-GAAATGCATAACGATGCATTAAAGGCATGAAATGATGT
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAATGATGC
* * *
1229421 CATAAATAAAATGCTTAATGATGCATTAAAGGCATGAAATGATGC
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAATGATGC
* * * * * *
1229466 CAAAAATGAAATGCACAACTATGTAATAAAGGCATTAAATGATGC
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAATGATGC
1229511 CATAAATGAAA
1 CATAAATGAAA
1229522 ATAATGAATA
Statistics
Matches: 254, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
44 41 0.16
45 213 0.84
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.22
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAATGATGC
Found at i:1229440 original size:134 final size:135
Alignment explanation
Indices: 1229197--1229521 Score: 490
Period size: 134 Copynumber: 2.4 Consensus size: 135
1229187 GTTTTCATTA
* *
1229197 CATAAATGGAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACG
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACG
* * *
1229262 GTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCAGGAAAT
66 ATGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAATGATGCATTAAAGGCAGGAAAT
1229327 GATGC
131 GATGC
*
1229332 CATAAATGAAATGCATAACGATGCATTAAAGGCACGAAAGGATGCCATAAA-GAAATGCATAACG
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACG
* * * *
1229396 ATGCATTAAAGGCATGAAATGATGTCATAAATAAAATGCTTAATGATGCATTAAAGGCATGAAAT
66 ATGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAATGATGCATTAAAGGCAGGAAAT
1229461 GATGC
131 GATGC
* * * * * * *
1229466 CAAAAATGAAATGCACAACTATGTAATAAAGGCATTAAATGATGCCATAAATGAAA
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATGAAA
1229522 ATAATGAATA
Statistics
Matches: 171, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
134 119 0.70
135 52 0.30
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.22
Consensus pattern (135 bp):
CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACG
ATGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAATGATGCATTAAAGGCAGGAAAT
GATGC
Found at i:1229541 original size:179 final size:180
Alignment explanation
Indices: 1229197--1229521 Score: 465
Period size: 179 Copynumber: 1.8 Consensus size: 180
1229187 GTTTTCATTA
* * *
1229197 CATAAATGGAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACG
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACG
* * * * *
1229262 GTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCAGGAAAT
66 ATGCATTAAAGGCATGAAAGGATGCCAAAAATGAAATGCACAATGATGCAATAAAGGCAGGAAAT
* *
1229327 GATGCCATAAATGAAATGCATAACGATGCATTAAAGGCACGAAAGGATGC
131 GATGCCATAAATGAAATGAATAACAATGCATTAAAGGCACGAAAGGATGC
* * * *
1229377 CATAAA-GAAATGCATAACGATGCATTAAAGGCATGAAATGATGTCATAAATAAAATGCTTAATG
1 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACG
* * **
1229441 ATGCATTAAAGGCATGAAATGATGCCAAAAATGAAATGCACAACT-ATGTAATAAAGGCATTAAA
66 ATGCATTAAAGGCATGAAAGGATGCCAAAAATGAAATGCACAA-TGATGCAATAAAGGCAGGAAA
1229505 TGATGCCATAAATGAAA
130 TGATGCCATAAATGAAA
1229522 ATAATGAATA
Statistics
Matches: 128, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
179 121 0.95
180 7 0.05
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.22
Consensus pattern (180 bp):
CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACG
ATGCATTAAAGGCATGAAAGGATGCCAAAAATGAAATGCACAATGATGCAATAAAGGCAGGAAAT
GATGCCATAAATGAAATGAATAACAATGCATTAAAGGCACGAAAGGATGC
Found at i:1235885 original size:81 final size:81
Alignment explanation
Indices: 1235773--1236326 Score: 928
Period size: 81 Copynumber: 6.8 Consensus size: 81
1235763 ACTACTTGTT
*
1235773 CATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGCAAAAGAT
1 CATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGAT
*
1235838 TAATTGTCTAGCTGTG
66 TAATTGCCTAGCTGTG
* ** * *
1235854 CATTTGGTAGAAAGGTTTCAATATTGCAAGTTAGATGAAAGGCGAAATGCCTTTAAGTAAAAGAT
1 CATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGAT
1235919 TAATTGCCTAGCTGTG
66 TAATTGCCTAGCTGTG
*
1235935 CATTTGGCAGAAAGGTGCTAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGAT
1 CATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGAT
1236000 TAATTGCCTAGCTGTG
66 TAATTGCCTAGCTGTG
*
1236016 CATTTGGTAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGAT
1 CATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGAT
* *
1236081 AAATTGCCTAGTTGTG
66 TAATTGCCTAGCTGTG
* *
1236097 CATTTGGCAGCAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAGAAGAT
1 CATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGAT
*
1236162 TAATTGCCTAGCTATG
66 TAATTGCCTAGCTGTG
* *
1236178 CATTTGACAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGTCTTTGAGTAAAAGAT
1 CATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGAT
* *
1236243 TAATTTCCTAGTTGTG
66 TAATTGCCTAGCTGTG
* *
1236259 CATTTGGCAGAAAGGTGCCAACATTGCAAGTTAGATGTAAGGCTAAATGCCTTTGAGTAAAAGAT
1 CATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGAT
1236324 TAA
66 TAA
1236327 ATGATTAGCA
Statistics
Matches: 439, Mismatches: 34, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 439 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (81 bp):
CATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTAAAAGAT
TAATTGCCTAGCTGTG
Found at i:1237387 original size:30 final size:30
Alignment explanation
Indices: 1237353--1237423 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
1237343 CTTGTCAACA
1237353 TGAATTCTTTGGTGGTAACAAAATCAAACT
1 TGAATTCTTTGGTGGTAACAAAATCAAACT
* * * * **
1237383 TGAATTTTTTAGTGGTATCAAATTTGAACT
1 TGAATTCTTTGGTGGTAACAAAATCAAACT
*
1237413 TGAACTCTTTG
1 TGAATTCTTTG
1237424 ATGGCTAGCA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (30 bp):
TGAATTCTTTGGTGGTAACAAAATCAAACT
Found at i:1242952 original size:81 final size:81
Alignment explanation
Indices: 1242831--1243393 Score: 910
Period size: 81 Copynumber: 7.0 Consensus size: 81
1242821 GTATACTTGA
* *
1242831 CTAGTTGTGCATTTGGCATAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGA
1 CTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGA
*
1242896 GCAAAAGATTAATTGC
66 GTAAAAGATTAATTGC
* *
1242912 CTAGCTGTGCATTTGGTAGAAAGGTTCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGA
1 CTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGA
1242977 GTAAAAGATTAATTGC
66 GTAAAAGATTAATTGC
** *
1242993 CTAGCTGTGCATTTGGCAGAAAGGTGTTAATATTGCAAATTAGATGAAAGGCTAAATGCCTTTGA
1 CTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGA
* *
1243058 GTTAAAGATTAATTGG
66 GTAAAAGATTAATTGC
* *
1243074 CTAGCTGTGCATTTGGTAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATACCTTTGA
1 CTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGA
*
1243139 GTAAAAGATAAATTGC
66 GTAAAAGATTAATTGC
*
1243155 CTAGTTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGA
1 CTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGA
* *
1243220 GTAGAAGTTTAATTGC
66 GTAAAAGATTAATTGC
* * * *
1243236 CTAGCTATGCATTTGACAGAAAGGTGACAATATTGCAAGTTAGATGAAAGGCTAAATGTCTTTGA
1 CTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGA
* *
1243301 GTAAAATATTAATTTC
66 GTAAAAGATTAATTGC
* *
1243317 CTAGTTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGTAAGGCTAAATGCCTTTGA
1 CTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGA
1243382 GTAAAAGATTAA
66 GTAAAAGATTAA
1243394 ATGATTAACA
Statistics
Matches: 440, Mismatches: 42, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 440 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (81 bp):
CTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAATGCCTTTGA
GTAAAAGATTAATTGC
Found at i:1245263 original size:11 final size:12
Alignment explanation
Indices: 1245241--1245281 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
1245231 ATTTCTTATA
1245241 TATATGTATATTT
1 TATAT-TATATTT
1245254 TAT-TTATATTT
1 TATATTATATTT
*
1245265 TATATTAAATTT
1 TATATTATATTT
1245277 T-TATT
1 TATATT
1245282 CATAATTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 14 0.54
12 9 0.35
13 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
TATATTATATTT
Found at i:1245553 original size:19 final size:20
Alignment explanation
Indices: 1245528--1245568 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1245518 TATATAATTG
* *
1245528 TTTTTAAATAAATAATATAA
1 TTTTAAAATAAAAAATATAA
1245548 TTTTAAAAATAAAAAATATAA
1 TTTT-AAAATAAAAAATATAA
1245569 ATCGGGTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTTAAAATAAAAAATATAA
Found at i:1251780 original size:131 final size:131
Alignment explanation
Indices: 1251565--1251899 Score: 490
Period size: 131 Copynumber: 2.6 Consensus size: 131
1251555 TTTTGGTGGG
* * * *
1251565 AGTAATAAATGATTGCTTTAAGGAATGAGAGGTCATTTATTATCGATTGAAAATAATTAGATATA
1 AGTAATAAATGATTGCTTTAAGGAATGAGATGTCATTTATTCTCGATTGGAAATAATTAGATATT
** * * *
1251630 ATCATTTTCTCTCGGATCAATATTGATTTTTAAGACGAAATGGTGATATCTCTTCATTTCGATTG
66 ATCATTTTCAATCGAATCAATATTGAATTTTAAGACGAAATAGTGATATCTCTTCATTTCGATTG
1251695 A
131 A
* * *
1251696 AGTAATAAATAATTGCTTTAAGGCATGAGATGTCATTTATTCTCGACTGGAAATAATTAGATATT
1 AGTAATAAATGATTGCTTTAAGGAATGAGATGTCATTTATTCTCGATTGGAAATAATTAGATATT
* *
1251761 ATCATTTTCAATTGAATCAATATTGAATTTTAAGATGAAATAGTGATATCTCTTCATTTCGATTG
66 ATCATTTTCAATCGAATCAATATTGAATTTTAAGACGAAATAGTGATATCTCTTCATTTCGATTG
*
1251826 G
131 A
* * * *
1251827 AGTAATAAATGACTACTTTAAGGAATGAGATGTCATTTATTCTTGATTAGAAATAATTAGATATT
1 AGTAATAAATGATTGCTTTAAGGAATGAGATGTCATTTATTCTCGATTGGAAATAATTAGATATT
*
1251892 ATCGTTTT
66 ATCATTTT
1251900 AGTTCTTAAA
Statistics
Matches: 181, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
131 181 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (131 bp):
AGTAATAAATGATTGCTTTAAGGAATGAGATGTCATTTATTCTCGATTGGAAATAATTAGATATT
ATCATTTTCAATCGAATCAATATTGAATTTTAAGACGAAATAGTGATATCTCTTCATTTCGATTG
A
Found at i:1255689 original size:38 final size:38
Alignment explanation
Indices: 1255646--1255729 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 38
1255636 TTTCTTAATT
* * * *
1255646 ATAATTATGTAAATA-ATTTAATCAAGTAAATAATTTGA
1 ATAATTATGTAAA-ACAATTAATAAAGTAAAGAATTTAA
1255684 ATAATTATGTAAAACAATTAATAAAGTAAAGAATTTAA
1 ATAATTATGTAAAACAATTAATAAAGTAAAGAATTTAA
1255722 ATAATTAT
1 ATAATTAT
1255730 AACTATTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 1 0.02
38 40 0.98
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (38 bp):
ATAATTATGTAAAACAATTAATAAAGTAAAGAATTTAA
Found at i:1255721 original size:17 final size:17
Alignment explanation
Indices: 1255654--1255721 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
1255644 TTATAATTAT
*
1255654 GTAAATAATTTAATCAA
1 GTAAATAATTTAATAAA
1255671 GTAAATAATTTGAATAATTA
1 GTAAATAATTT-AATAA--A
*
1255691 TGTAAA-ACAATTAATAAA
1 -GTAAATA-ATTTAATAAA
*
1255709 GTAAAGAATTTAA
1 GTAAATAATTTAA
1255722 ATAATTATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
17 21 0.50
18 6 0.14
20 7 0.17
21 8 0.19
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (17 bp):
GTAAATAATTTAATAAA
Found at i:1256231 original size:31 final size:31
Alignment explanation
Indices: 1256195--1256253 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1256185 AACTTAAAAG
* *
1256195 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1256226 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1256254 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1256304 original size:22 final size:22
Alignment explanation
Indices: 1256278--1256320 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1256268 TAATAAATTA
1256278 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1256300 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1256321 GTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1256329 original size:22 final size:22
Alignment explanation
Indices: 1256280--1256328 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1256270 ATAAATTATT
**
1256280 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1256302 TAAAATAAATCAATCCATAGTAA
1 TAAAATAAATCAATCCATA-TAA
1256325 TAAA
1 TAAA
1256329 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1256332 original size:54 final size:54
Alignment explanation
Indices: 1256268--1256787 Score: 471
Period size: 54 Copynumber: 9.4 Consensus size: 54
1256258 ACAACTACAA
*
1256268 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAG
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
1256322 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--C
* * * * * *
1256382 TAAAATAAATCAATCT-ATACAAATAAAT---TA-TTTAAAATAAATCAATTCATAC
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1256434 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
** *
1256488 TAATAAATTATTTAAAATAAATCAATCCATATAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCATAT---TTTAA-AATAAATCAATCCATA--C
* * * * *
1256548 TAAAATAAATCAATTCATACAAAT--AT--AT-TATTTAAAATAAATCAATCCATAC
1 T--AATAAATTATTTAAAATAAATCAATCCATAT-TTTAAAATAAATCAATCCATAC
1256600 TAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATC----C--AT--A-T-TTTAAAATAAATCAATCCATAC
*
1256664 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1256712 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1256766 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
1256788 TATTTTAAAA
Statistics
Matches: 383, Mismatches: 39, Indels: 88
0.75 0.08 0.17
Matches are distributed among these distances:
48 25 0.07
49 6 0.02
50 34 0.09
52 7 0.02
53 2 0.01
54 175 0.46
55 6 0.02
56 1 0.00
57 8 0.02
58 46 0.12
59 1 0.00
60 7 0.02
62 33 0.09
63 5 0.01
64 27 0.07
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:1256373 original size:80 final size:80
Alignment explanation
Indices: 1256283--1256599 Score: 483
Period size: 80 Copynumber: 3.9 Consensus size: 80
1256273 AATTATTTAA
**
1256283 AATAAATCAATCCATATTTTAAAATAAATCAATCCATAGTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1256348 CCATACAACTACAAT
66 CCATACAACTACAAT
*
1256363 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
* *
1256428 TCATACTAA-TAAATTATTT
66 CCATAC-AACTACA--A--T
*
1256447 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCA
*
1256512 ATCCATATAACTACAAT
64 ATCCATACAACTACAAT
* *
1256529 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACAAATATATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1256594 CCATAC
66 CCATAC
1256600 TAATAAATTA
Statistics
Matches: 215, Mismatches: 14, Indels: 16
0.88 0.06 0.07
Matches are distributed among these distances:
80 137 0.64
81 2 0.01
82 2 0.01
84 2 0.01
85 2 0.01
86 70 0.33
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:1256419 original size:14 final size:14
Alignment explanation
Indices: 1256402--1256455 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1256392 CAATCTATAC
1256402 AAATAAATTATTTA
1 AAATAAATTATTTA
*
1256416 AAATAAATCAATTCATA
1 AAATAAAT-TATT--TA
*
1256433 CTAATAAATTATTTA
1 -AAATAAATTATTTA
1256448 AAATAAAT
1 AAATAAAT
1256456 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 5 0.16
17 5 0.16
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:1256419 original size:32 final size:32
Alignment explanation
Indices: 1256380--1256665 Score: 196
Period size: 32 Copynumber: 8.8 Consensus size: 32
1256370 CAATCCATAT
1256380 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
*
1256412 TTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCT-ATACAAATAAATTA
*
1256444 TTTAAAATAAATCAATCCATATTTTA-AAATAAATCAA
1 TTTAAAATAAATCAAT-C-TA---TACAAATAAAT-TA
* * * *
1256481 TCCATACTAATAAAT-TAT-T-TA-AAATAAATCA
1 T--TTA-AAATAAATCAATCTATACAAATAAATTA
* ** * * * *
1256512 ATCCATATAACTACAA--TA-ATAAATCAATCCATA
1 TTTAAAATAAAT-CAATCTATACAAATAAAT---TA
*
1256545 TTTTAAAATAAATCAAT-TCATACAAATATATTA
1 -TTTAAAATAAATCAATCT-ATACAAATAAATTA
* *
1256578 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
*
1256610 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
*
1256642 TTTAAAATAAATCAATCCATACAA
1 TTTAAAATAAATCAATCTATACAA
1256666 CTACAATAAT
Statistics
Matches: 200, Mismatches: 31, Indels: 46
0.72 0.11 0.17
Matches are distributed among these distances:
28 5 0.03
29 2 0.01
30 8 0.04
31 2 0.01
32 136 0.68
33 6 0.03
34 9 0.05
35 2 0.01
36 15 0.08
37 4 0.02
39 4 0.02
40 7 0.04
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACAAATAAATTA
Found at i:1256459 original size:144 final size:139
Alignment explanation
Indices: 1256300--1256743 Score: 527
Period size: 144 Copynumber: 3.2 Consensus size: 139
1256290 CAATCCATAT
*
1256300 TTTAAAATAAATCAATCCATAGTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA-A-
1 TTTAAAATAAATCAATCCATA-TAATAAATTATTTAAAATAAATCAATCCATACTAA-TAAATAT
** * * * *
1256362 T-AATAAATCAATCCATATTTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATCA
64 TAAATAAATCAATCCATATACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCA
1256426 ATTCATACTAATAAATTA
122 ATTCATACTAATAAATTA
1256444 TTTAAAATAAATCAATCC-----AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATT
1 TTTAAAATAAATCAATCCATATAATAAATTATTTAAAATAAATCAATCCATACTAATAAA-TA-T
1256500 TAAAATAAATCAATCCATATAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCA
64 T-AAATAAATCAATCCATAT-ACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCA
* *
1256565 TACAAATATATTA
127 TACTAATAAATTA
*
1256578 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATA-TAATAAATTATTTAAAATAAATCAATCCATACTAATAAA-TA-
* *
1256643 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
63 TT-AAATAAATCAATCCATA-TACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
1256708 ATACTAATAAATTA
126 ATACTAATAAATTA
1256722 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1256744 TTTAAAATAA
Statistics
Matches: 267, Mismatches: 14, Indels: 39
0.83 0.04 0.12
Matches are distributed among these distances:
134 73 0.27
135 4 0.01
136 3 0.01
138 5 0.02
139 1 0.00
140 28 0.10
141 5 0.02
142 1 0.00
143 2 0.01
144 145 0.54
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (139 bp):
TTTAAAATAAATCAATCCATATAATAAATTATTTAAAATAAATCAATCCATACTAATAAATATTA
AATAAATCAATCCATATACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACT
AATAAATTA
Found at i:1256467 original size:166 final size:166
Alignment explanation
Indices: 1256268--1256626 Score: 666
Period size: 166 Copynumber: 2.2 Consensus size: 166
1256258 ACAACTACAA
*
1256268 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAGTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1256333 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA-TC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
*
1256397 TATACAAATAAATTATTTAAAATAAATCAATTCATAC
131 -ATACAAATAAATTATTTAAAATAAATCAATCCATAC
1256434 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
1256499 TTAAAATAAATCAATCCATATAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
*
1256564 ATACAAATATATTATTTAAAATAAATCAATCCATAC
131 ATACAAATAAATTATTTAAAATAAATCAATCCATAC
1256600 TAATAAATTATTTAAAATAAATCAATC
1 TAATAAATTATTTAAAATAAATCAATC
1256627 TATACTAATA
Statistics
Matches: 188, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
166 186 0.99
167 2 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (166 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
ATACAAATAAATTATTTAAAATAAATCAATCCATAC
Found at i:1256470 original size:22 final size:22
Alignment explanation
Indices: 1256444--1256486 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1256434 TAATAAATTA
1256444 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1256466 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1256487 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1256495 original size:22 final size:22
Alignment explanation
Indices: 1256446--1256494 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1256436 ATAAATTATT
**
1256446 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1256468 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1256491 TAAA
1 TAAA
1256495 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1256554 original size:22 final size:23
Alignment explanation
Indices: 1256496--1256566 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 23
1256486 ACTAATAAAT
1256496 TATTTAAAATAAATCAATCCATA
1 TATTTAAAATAAATCAATCCATA
**
1256519 TAACTACAATAATAAATCAATCCATA
1 T-A-TTTAA-AATAAATCAATCCATA
*
1256545 T-TTTAAAATAAATCAATTCATA
1 TATTTAAAATAAATCAATCCATA
1256567 CAAATATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
22 15 0.38
23 4 0.10
24 1 0.03
25 3 0.08
26 17 0.43
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (23 bp):
TATTTAAAATAAATCAATCCATA
Found at i:1256620 original size:14 final size:14
Alignment explanation
Indices: 1256601--1256653 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1256591 AATCCATACT
1256601 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
1256615 AATAAATCAATCTATACT
1 AATAAAT-TAT-T-TA-A
1256633 AATAAATTATTTAA
1 AATAAATTATTTAA
1256647 AATAAAT
1 AATAAAT
1256654 CAATCCATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 4 0.13
16 2 0.06
17 4 0.13
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:1256719 original size:22 final size:23
Alignment explanation
Indices: 1256644--1256718 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
1256634 ATAAATTATT
1256644 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
1256666 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
1256692 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
1256715 TAAA
1 TAAA
1256719 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:1256729 original size:32 final size:31
Alignment explanation
Indices: 1256690--1256787 Score: 115
Period size: 32 Copynumber: 3.4 Consensus size: 31
1256680 CAATCCATAT
1256690 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAAT-CATACTAATAAATTA
1256722 TTTAAAATAAATCAATC---C--AT--A-T-
1 TTTAAAATAAATCAATCATACTAATAAATTA
1256744 TTTAAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAAT-CATACTAATAAATTA
1256776 TTTAAAATAAAT
1 TTTAAAATAAAT
1256788 TATTTTAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 16 0.29
23 2 0.04
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 2 0.04
32 28 0.50
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (31 bp):
TTTAAAATAAATCAATCATACTAATAAATTA
Found at i:1256748 original size:22 final size:22
Alignment explanation
Indices: 1256722--1256824 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
1256712 TAATAAATTA
*
1256722 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
1256744 TTTAAAATAAATCAATACATACT
1 TTTAAAATAAATCAATACATA-T
** * ** * *
1256767 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATACA-TAT
* *
1256791 TTTAAAATAAAACAATCCATAT
1 TTTAAAATAAATCAATACATAT
*
1256813 TTTATAATAAAT
1 TTTAAAATAAAT
1256825 TATTTTAAAA
Statistics
Matches: 59, Mismatches: 19, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
22 33 0.56
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:1256796 original size:15 final size:15
Alignment explanation
Indices: 1256767--1256893 Score: 124
Period size: 15 Copynumber: 8.5 Consensus size: 15
1256757 AATACATACT
1256767 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1256781 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1256796 AATAAAACAATCCATATTTTAT
1 AAT---A-AAT---TATTTTAA
1256818 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1256833 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1256848 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1256863 AAT--A--A--TTAA
1 AATAAATTATTTTAA
1256872 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1256887 AATAAAT
1 AATAAAT
1256894 AACCTTATTA
Statistics
Matches: 95, Mismatches: 4, Indels: 27
0.75 0.03 0.21
Matches are distributed among these distances:
9 7 0.07
11 2 0.02
13 2 0.02
14 9 0.09
15 57 0.60
18 4 0.04
19 4 0.04
22 10 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1256809 original size:69 final size:67
Alignment explanation
Indices: 1256713--1256895 Score: 210
Period size: 69 Copynumber: 2.7 Consensus size: 67
1256703 AATCCATACT
* *
1256713 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAAACAATCCATATTTTAAAATAAAT-AAT-CATA-AAATAAATTAT
1256776 TTTAA
63 TTTAA
* * **
1256781 AATAAATTATTTTAAAATAAAACAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAAACAATCCATATTTTAAAATAAATAATCATAAAATAAATTATTTT
*
1256846 AT
66 AA
**
1256848 AATAAATTATTTTAAAATAATTAA-AATAAATTATTTTAAAATAAATAA
1 AATAAATTATTTTAAAATAA--AACAATCCA-TATTTTAAAATAAATAA
1256896 CCTTATTAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
66 9 0.09
67 26 0.26
68 15 0.15
69 49 0.49
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAAACAATCCATATTTTAAAATAAATAATCATAAAATAAATTATTTT
AA
Found at i:1256906 original size:67 final size:66
Alignment explanation
Indices: 1256713--1256916 Score: 184
Period size: 69 Copynumber: 3.0 Consensus size: 66
1256703 AATCCATACT
* ** * *
1256713 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAAACAATAAATATTTTAAAATAAAT-AA-CCTTA--AATAAATTAT
1256776 TTTAA
62 TTTAA
** * * **
1256781 AATAAATTATTTTAAAATAAAACAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAAACAATAAATATTTTAAAATAAATAACCTT-AAATAAATTATTTT
*
1256846 AT
65 AA
*
1256848 AATAAATTATTTTAAAATAATTAA-AATAAATTATTTTAAAATAAATAACCTT-ATTAAATTA-T
1 AATAAATTATTTTAAAATAA--AACAATAAA-TATTTTAAAATAAATAACCTTAAATAAATTATT
1256910 TTAA
63 TTAA
1256914 AAT
1 AAT
1256917 TATTTTAATA
Statistics
Matches: 115, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
66 16 0.14
67 33 0.29
68 15 0.13
69 51 0.44
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (66 bp):
AATAAATTATTTTAAAATAAAACAATAAATATTTTAAAATAAATAACCTTAAATAAATTATTTTA
A
Found at i:1258562 original size:32 final size:32
Alignment explanation
Indices: 1258516--1258578 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1258506 TTTGTCACAA
* *
1258516 TATTTTATCGAAATAAAAAATT-ATAACAAATT
1 TATTTAATCAAAAT-AAAAATTCATAACAAATT
*
1258548 TATTTAATCAAAATAATAATTCATAACAAAT
1 TATTTAATCAAAATAAAAATTCATAACAAAT
1258579 AATAATTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (32 bp):
TATTTAATCAAAATAAAAATTCATAACAAATT
Found at i:1258809 original size:33 final size:33
Alignment explanation
Indices: 1258715--1258850 Score: 109
Period size: 33 Copynumber: 4.2 Consensus size: 33
1258705 TTCGTCCCAA
* *
1258715 TATTTTATCAAAATGAAAAATTGTGACAAAT-T
1 TATTTAATCAAAATAAAAAATTGTGACAAATAT
* * *
1258747 TATTTAATCAAAATAACAAATTATAACAAATAT
1 TATTTAATCAAAATAAAAAATTGTGACAAATAT
* ** *
1258780 TAATTT-CTCATTATAAAAAATTGTGACAAATAA
1 T-ATTTAATCAAAATAAAAAATTGTGACAAATAT
* * * *
1258813 TATTCT-TTCACAATAACAAATTGTAACAAA-AT
1 TATT-TAATCAAAATAAAAAATTGTGACAAATAT
1258845 TATTTA
1 TATTTA
1258851 GTCACAGTAA
Statistics
Matches: 82, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
31 1 0.01
32 34 0.41
33 43 0.52
34 4 0.05
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (33 bp):
TATTTAATCAAAATAAAAAATTGTGACAAATAT
Found at i:1260521 original size:29 final size:29
Alignment explanation
Indices: 1260479--1260537 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1260469 CACAGAGGAG
*
1260479 TAGGCAAAAAGGGTCACTAAATTGAAGAA
1 TAGGCAAAAAGGGTCACTAAACTGAAGAA
1260508 TAGGCAAAAAGGGTCACTAAACTGAAGAA
1 TAGGCAAAAAGGGTCACTAAACTGAAGAA
1260537 T
1 T
1260538 GATGATGAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.17
Consensus pattern (29 bp):
TAGGCAAAAAGGGTCACTAAACTGAAGAA
Found at i:1264835 original size:29 final size:29
Alignment explanation
Indices: 1264800--1264990 Score: 276
Period size: 29 Copynumber: 6.6 Consensus size: 29
1264790 CACATTCAAA
* *
1264800 AATTCCTAAAATGTCACCTTTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
*
1264829 AATTCCTAGAATGTCACCTTTTT-AAAAT
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
*
1264857 AATTCCCAGAATGTCACATTTTTTCAAAAT
1 AATTCCCAGAATGTCAC-CTTTTTCAAAAT
* *
1264887 AATTCCCAGAATGTCACATTTTTTAAAAT
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
*
1264916 AATTCCCAGAATGTCACCTATTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
*
1264945 AATTCCCAGAATATCACCTTTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
* *
1264974 AATTCTCAGAATATCAC
1 AATTCCCAGAATGTCAC
1264991 TAGGTCGGGT
Statistics
Matches: 149, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
28 21 0.14
29 106 0.71
30 22 0.15
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (29 bp):
AATTCCCAGAATGTCACCTTTTTCAAAAT
Found at i:1268283 original size:109 final size:109
Alignment explanation
Indices: 1268139--1268429 Score: 456
Period size: 109 Copynumber: 2.7 Consensus size: 109
1268129 TTATGTGTAC
* * *
1268139 TATCGACACTAAGTGTGCAACCCCCGAAATTCATAATATGTTTATGAACGACCGTATCGGAACTA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCGTATCGGCACTA
* * *
1268204 AGTGTGCTAAACCATGGAATTCATAATGTGTTTATGAACGACTG
66 AGTGTGCAAAACCACGGAATTCATAATGTGTTTATGAACGACCG
* *
1268248 TATCGGCACTAAGTGTGTAACCCACGAAATTCATAATATGTTTATGAACGACCGTATCAGCACTA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCGTATCGGCACTA
*
1268313 AGTGTGCAAAACCACGGAATTCATAATGTGTTTATGAACTACCG
66 AGTGTGCAAAACCACGGAATTCATAATGTGTTTATGAACGACCG
* * * *
1268357 TATAGGCACTAAGTGTGCGACCCACGGAATTCATAATATGTTTATGAACGACCATATCGGCACTA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCGTATCGGCACTA
*
1268422 CGTGTGCA
66 AGTGTGCA
1268430 CCTCAGAGAA
Statistics
Matches: 166, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
109 166 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (109 bp):
TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCGTATCGGCACTA
AGTGTGCAAAACCACGGAATTCATAATGTGTTTATGAACGACCG
Found at i:1268447 original size:54 final size:54
Alignment explanation
Indices: 1268139--1268429 Score: 402
Period size: 54 Copynumber: 5.4 Consensus size: 54
1268129 TTATGTGTAC
* * *
1268139 TATCGACACTAAGTGTGCAACCCCCGAAATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCG
* * * * *
1268193 TATCGGAACTAAGTGTGCTAAACCATGGAATTCATAATGTGTTTATGAACGACTG
1 TATCGGCACTAAGTGTGC-AACCCACGGAATTCATAATATGTTTATGAACGACCG
* *
1268248 TATCGGCACTAAGTGTGTAACCCACGAAATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCG
* * * *
1268302 TATCAGCACTAAGTGTGCAAAACCACGGAATTCATAATGTGTTTATGAACTACCG
1 TATCGGCACTAAGTGTGC-AACCCACGGAATTCATAATATGTTTATGAACGACCG
* * *
1268357 TATAGGCACTAAGTGTGCGACCCACGGAATTCATAATATGTTTATGAACGACCA
1 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCG
*
1268411 TATCGGCACTACGTGTGCA
1 TATCGGCACTAAGTGTGCA
1268430 CCTCAGAGAA
Statistics
Matches: 204, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
54 110 0.54
55 94 0.46
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCG
Found at i:1274043 original size:3 final size:3
Alignment explanation
Indices: 1274035--1274094 Score: 97
Period size: 3 Copynumber: 20.3 Consensus size: 3
1274025 GTCGAAACCA
1274035 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CT-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
1274080 T-T TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
1274095 TTACAAGCCA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 3 0.05
3 51 0.93
4 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1275356 original size:3 final size:3
Alignment explanation
Indices: 1275348--1275397 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1275338 TTTCTAGAGA
1275348 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1275396 AT
1 AT
1275398 AAATTAGTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1279688 original size:21 final size:21
Alignment explanation
Indices: 1279653--1279696 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1279643 TAAAGGATTG
*
1279653 AAATTAAACTAAATTAAAAGGC
1 AAATCAAACTAAATT-AAAGGC
1279675 AAATCAAA-TAAATTAAAGGC
1 AAATCAAACTAAATTAAAGGC
1279695 AA
1 AA
1279697 TTAATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 6 0.29
22 7 0.33
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.20
Consensus pattern (21 bp):
AAATCAAACTAAATTAAAGGC
Found at i:1281503 original size:139 final size:139
Alignment explanation
Indices: 1281290--1281747 Score: 583
Period size: 139 Copynumber: 3.3 Consensus size: 139
1281280 CTTCTGTTCG
* * *
1281290 GATGCGTTCTTCTCATTATGAACCCTTTCA-TTGAAATGTTGATCCCTCGAGTGAGGTATTGT-T
1 GATGAGTTCTTCTCATTATGAACTC-TCCATTTGAAATGTTGATCCCTCGAGTGAGGTA-TGTCT
* * * *
1281353 GATTCAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTATTCTCATTATGAACTTTTT
64 GATTCAACTCCATATGTGATGAATCGAGCTAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTT
*
1281418 CTTCCTCATCA
129 CTCCCTCATCA
* * * *
1281429 GATGAGTTTTTCTCATTATGAACTCTCCACTAGAAATGTTGATCCCTCGAGTGAGGTGTGTCTGA
1 GATGAGTTCTTCTCATTATGAACTCTCCATTTGAAATGTTGATCCCTCGAGTGAGGTATGTCTGA
1281494 TTCAACTCCATATGTGATGAATCGAGCTAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCT
66 TTCAACTCCATATGTGATGAATCGAGCTAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCT
* *
1281559 CCCTCTGTCG
131 CCCTC-ATCA
* * * * **
1281569 GATGAGTTATTCTCATTATGAACTGTCCATTTGAAATGTTGATCCCTCAAGTGAGGCATCACTGA
1 GATGAGTTCTTCTCATTATGAACTCTCCATTTGAAATGTTGATCCCTCGAGTGAGGTATGTCTGA
*
1281634 TTCAA----A-ATGTCG-TGAATCGAG-TGATAGGTCGAATAAGCTCTTCTCATTATGAACTTCT
66 TTCAACTCCATATGT-GATGAATCGAGCT-A-AGGTTGAATAAGCTCTTCTCATTATGAACTTCT
*
1281692 TCTCCCTGTATCA
128 TCTCCCT-CATCA
*
1281705 GATGAGTTCTTCTCATTATGAACTCTCCATTTGAAATATTGAT
1 GATGAGTTCTTCTCATTATGAACTCTCCATTTGAAATGTTGAT
1281748 TGGTTCATCT
Statistics
Matches: 283, Mismatches: 29, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
134 1 0.00
135 14 0.05
136 83 0.29
138 6 0.02
139 116 0.41
140 63 0.22
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (139 bp):
GATGAGTTCTTCTCATTATGAACTCTCCATTTGAAATGTTGATCCCTCGAGTGAGGTATGTCTGA
TTCAACTCCATATGTGATGAATCGAGCTAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCT
CCCTCATCA
Found at i:1282211 original size:11 final size:11
Alignment explanation
Indices: 1282195--1282257 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
1282185 TAAATTGCAT
1282195 TATTAAAAATA
1 TATTAAAAATA
1282206 TATTAAAAATA
1 TATTAAAAATA
* ***
1282217 CATTATTGATA
1 TATTAAAAATA
1282228 -ATTATAAAAT-
1 TATTA-AAAATA
1282238 T-TTAAAAATA
1 TATTAAAAATA
1282248 TATTAAAAAT
1 TATTAAAAAT
1282258 TCTATAATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:1282771 original size:7 final size:7
Alignment explanation
Indices: 1282759--1282820 Score: 88
Period size: 7 Copynumber: 8.9 Consensus size: 7
1282749 CTTTGTAATG
1282759 AACCCTA
1 AACCCTA
1282766 AACCCTA
1 AACCCTA
1282773 AACCCTA
1 AACCCTA
*
1282780 AATCCTA
1 AACCCTA
1282787 AACCCTA
1 AACCCTA
*
1282794 AACACTA
1 AACCCTA
**
1282801 AACATTA
1 AACCCTA
1282808 AACCCTA
1 AACCCTA
1282815 AACCCT
1 AACCCT
1282821 TAATCATATG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:1285166 original size:15 final size:15
Alignment explanation
Indices: 1285148--1285177 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1285138 AAAACCATGT
1285148 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1285163 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1285178 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:1285184 original size:15 final size:15
Alignment explanation
Indices: 1285151--1285185 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1285141 ACCATGTTAG
* *
1285151 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
1285166 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
1285181 ATAAA
1 ATAAA
1285186 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:1285258 original size:32 final size:30
Alignment explanation
Indices: 1285200--1285285 Score: 77
Period size: 32 Copynumber: 2.7 Consensus size: 30
1285190 TTAATTAAAT
*
1285200 TAAAATAAAGAGAAAACAAATTAAATAA-AAG
1 TAAAAT-AA-AGAAAACAAATAAAATAATAAG
*
1285231 ATAAGATAAAGAAAACAAAGATAAAATAATAAG
1 -TAAAATAAAGAAAAC-AA-ATAAAATAATAAG
*
1285264 TAAAATAAATATAAA-AAATAAA
1 TAAAATAAAGA-AAACAAATAAA
1285286 GAAAAAGAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
30 12 0.26
31 6 0.13
32 22 0.48
33 6 0.13
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.17
Consensus pattern (30 bp):
TAAAATAAAGAAAACAAATAAAATAATAAG
Found at i:1285268 original size:23 final size:22
Alignment explanation
Indices: 1285227--1285290 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
1285217 AAATTAAATA
*
1285227 AAAGATAAGAT-A-AAGAAAAC
1 AAAGATAAAATAATAAGAAAAC
*
1285247 AAAGATAAAATAATAAGTAAAAT
1 AAAGATAAAATAATAAG-AAAAC
*
1285270 AAATATAAAA-AATAAAGAAAA
1 AAAGATAAAATAAT-AAGAAAA
1285291 AGAAGAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 10 0.27
21 1 0.03
22 10 0.27
23 16 0.43
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (22 bp):
AAAGATAAAATAATAAGAAAAC
Found at i:1285291 original size:23 final size:23
Alignment explanation
Indices: 1285236--1285290 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1285226 AAAAGATAAG
1285236 ATAAAGAAAACAAAGATAAAATA
1 ATAAAGAAAACAAAGATAAAATA
* *
1285259 AT-AAGTAAAATAAATATAAAA-A
1 ATAAAG-AAAACAAAGATAAAATA
1285281 ATAAAGAAAA
1 ATAAAGAAAA
1285291 AGAAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (23 bp):
ATAAAGAAAACAAAGATAAAATA
Found at i:1285356 original size:29 final size:29
Alignment explanation
Indices: 1285324--1285384 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
1285314 GAAATAAAAC
1285324 AAATAA-ATA-AAATAATAATAAAAAAGTAA
1 AAATAATATATAAATAA-AATAAAAAA-TAA
*
1285353 AAATAATATATATATAAAATAAAAAATAA
1 AAATAATATATAAATAAAATAAAAAATAA
1285382 AAA
1 AAA
1285385 AGTAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 12 0.41
30 12 0.41
31 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (29 bp):
AAATAATATATAAATAAAATAAAAAATAA
Found at i:1285376 original size:30 final size:33
Alignment explanation
Indices: 1285315--1285405 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 33
1285305 AAAAATATAG
*
1285315 AAATAAAACAAATAAATA-A-A-ATAATAATAAA
1 AAATAAAA-AAGTAAATATATATATAATAATAAA
1285346 AAAGT-AAAAA-T-AATATATATATAA-AATAAA
1 AAA-TAAAAAAGTAAATATATATATAATAATAAA
1285376 AAATAAAAAAGTAAATATATATATATATAA
1 AAATAAAAAAGTAAATATATATATA-ATAA
1285406 ATTAATAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
28 4 0.08
29 3 0.06
30 17 0.33
31 11 0.22
32 13 0.25
33 1 0.02
34 2 0.04
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.25
Consensus pattern (33 bp):
AAATAAAAAAGTAAATATATATATAATAATAAA
Found at i:1285378 original size:24 final size:22
Alignment explanation
Indices: 1285303--1285381 Score: 63
Period size: 25 Copynumber: 3.5 Consensus size: 22
1285293 AAGAAAAAGG
*
1285303 AAAAAAAT-ATAGAA-ATAAAA
1 AAAAAAATAATATAATATAAAA
* *
1285323 CAAATAAATAAAATAATAATAAAA
1 -AAAAAAATAATATAAT-ATAAAA
1285347 AAGTAAAAATAATATATATATAAAA
1 AA--AAAAATAATATA-ATATAAAA
*
1285372 TAAAAAATAA
1 AAAAAAATAA
1285382 AAAAGTAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
21 7 0.15
22 4 0.09
23 10 0.22
24 6 0.13
25 17 0.37
26 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.22
Consensus pattern (22 bp):
AAAAAAATAATATAATATAAAA
Found at i:1285384 original size:36 final size:37
Alignment explanation
Indices: 1285330--1285415 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 37
1285320 AAACAAATAA
*
1285330 ATAAAAT-AATAATAAAAAAGTAAAAATAATATATAT
1 ATAAAATAAAAAATAAAAAAGTAAAAATAATATATAT
*
1285366 ATAAAATAAAAAATAAAAAAGTAAATAT-ATATATAT
1 ATAAAATAAAAAATAAAAAAGTAAAAATAATATATAT
*
1285402 ATAAATTAATAAAA
1 ATAAAATAA-AAAA
1285416 CTGATAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 23 0.51
37 22 0.49
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (37 bp):
ATAAAATAAAAAATAAAAAAGTAAAAATAATATATAT
Found at i:1285516 original size:22 final size:21
Alignment explanation
Indices: 1285462--1285521 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
1285452 TGAAAAAAAT
1285462 AAAAATATATAC-T-AAAGTAA
1 AAAAATAT-TACATAAAAGTAA
* *
1285482 AAAAGAAAATACATAAAATGTAA
1 AAAA-ATATTACATAAAA-GTAA
1285505 AAAAATATTACATAAAA
1 AAAAATATTACATAAAA
1285522 AAAAGAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 7 0.22
21 3 0.09
22 14 0.44
23 8 0.25
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (21 bp):
AAAAATATTACATAAAAGTAA
Found at i:1285890 original size:34 final size:34
Alignment explanation
Indices: 1285847--1285915 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
1285837 GAATCCTAGC
1285847 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
1285881 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1285915 A
1 A
1285916 GTAGGATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:1286669 original size:98 final size:98
Alignment explanation
Indices: 1286500--1286758 Score: 293
Period size: 98 Copynumber: 2.6 Consensus size: 98
1286490 TGGAACCGGA
* * *
1286500 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCA
1 AAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
* * * * *
1286565 ATATCCTTCGTTGTGAAGTTGAGATTGGCTCTG
66 ATATCCTCCGCTGTGAAGTTGAAATTAGCCCTG
** * * * *
1286598 AAATTGTTTGTTGACAGTCAGCTGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCA
1 AAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
1286663 ATATCCTCCGCTGTGAAGTTGAAATTAGCCCTG
66 ATATCCTCCGCTGTGAAGTTGAAATTAGCCCTG
* * * *
1286696 AAACTGGGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
1 AAA-T-TG----T-TTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTC
1286759 ATAGGTAGCA
Statistics
Matches: 132, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
98 87 0.66
99 1 0.01
100 1 0.01
104 1 0.01
105 42 0.32
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (98 bp):
AAATTGTTTGTTGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
ATATCCTCCGCTGTGAAGTTGAAATTAGCCCTG
Found at i:1286752 original size:105 final size:102
Alignment explanation
Indices: 1286500--1286892 Score: 334
Period size: 105 Copynumber: 3.8 Consensus size: 102
1286490 TGGAACCGGA
* *
1286500 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-CC
1 AAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACC
* * ** * ** ** **
1286564 A-ATATCCTTCGTTGT-GAAGTTGAG-ATTG-GCTCTG
65 AGATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
** * * * * *
1286598 AAATTGTTTGTTGACAGTCAGCTGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-CC
1 AAATTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACC
* *
1286662 A-ATATCCTCCG-CTGTGAAGTTGAAATTAGCCCTGAAACTGGG
65 AGATATCCTCCGTC-GTG--G--AAAATCAGCCCTGAAA-TGGG
* * *
1286704 AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCATAGGTAGCA
1 AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACCA
** *
1286769 TGATATCCTCCGTCGTGGAAAATCAGCTTTGAAATTGG
66 -GATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
* **
1286807 AAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTGG
1 AAA-TTGTT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTAC
*
1286872 CACGATATCCTCCATCGTGGA
64 CA-GATATCCTCCGTCGTGGA
1286893 GTTGAAATCG
Statistics
Matches: 238, Mismatches: 42, Indels: 23
0.79 0.14 0.08
Matches are distributed among these distances:
98 67 0.28
101 1 0.00
103 10 0.04
104 19 0.08
105 116 0.49
106 11 0.05
108 13 0.05
109 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (102 bp):
AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTACCA
GATATCCTCCGTCGTGGAAAATCAGCCCTGAAATGGG
Found at i:1287598 original size:31 final size:31
Alignment explanation
Indices: 1287563--1287690 Score: 73
Period size: 31 Copynumber: 3.9 Consensus size: 31
1287553 AGGAAATAAA
1287563 CTCAAAG-ATTTTGTGTTTCAAGAGAAACTGT
1 CTCAAAGAATTTTGTGTTTCAAGAGAAACT-T
** * *
1287594 CTCAAGGGAGACAAAATT-TGTTTCAAGGGAAACAAT
1 CTCAA---AG--AATTTTGTGTTTCAAGAGAAAC-TT
* *
1287630 CTCAAAG-GTTTTGTGTTTCAAGAGAATCATT
1 CTCAAAGAATTTTGTGTTTCAAGAGAAAC-TT
* **
1287661 TTCAAAGGTTTTTTGTGTTTCAAGAGAAAC
1 CTCAAA-GAATTTTGTGTTTCAAGAGAAAC
1287691 AATTTCAAAG
Statistics
Matches: 74, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
30 2 0.03
31 25 0.34
32 1 0.01
33 21 0.28
34 2 0.03
36 20 0.27
37 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (31 bp):
CTCAAAGAATTTTGTGTTTCAAGAGAAACTT
Found at i:1287650 original size:67 final size:67
Alignment explanation
Indices: 1287465--1287655 Score: 247
Period size: 67 Copynumber: 2.8 Consensus size: 67
1287455 TCTTTAAAAA
* * * * *
1287465 AGACAAAATTCGTTTCAAGGGAAACGATCTTAAAGATATATGTTGTTTCATGAGAAACGGCCTCA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACGGCCTCA
1287530 AGGG
64 AGGG
* * * * * *
1287534 AGACAAAATTTTGTTTTAAAGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA
1 AGACAAAA-TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAA
1287599 GGG
65 GGG
*
1287602 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAA
1287656 TCATTTTCAA
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 41 0.39
68 31 0.30
69 11 0.10
70 22 0.21
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (67 bp):
AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAG
GG
Found at i:1287717 original size:36 final size:33
Alignment explanation
Indices: 1287612--1287726 Score: 153
Period size: 33 Copynumber: 3.5 Consensus size: 33
1287602 AGACAAAATT
* *
1287612 TGTTTCAAGGGAAACAATCTCAAAGG--TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
* *
1287643 TGTTTCAAGAGAATCATTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
1287676 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG--T-TTTTTG
1287712 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
1287727 TGTATCAAGG
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
31 22 0.30
33 29 0.40
35 1 0.01
36 21 0.29
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.38
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
Found at i:1287877 original size:36 final size:36
Alignment explanation
Indices: 1287768--1288207 Score: 193
Period size: 37 Copynumber: 12.9 Consensus size: 36
1287758 CAAGGATTGA
*
1287768 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
1287805 TGTTTTAAGAAAAACATGTCTTAAGATAGACAAAATT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
*
1287842 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1287878 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATT
* * *
1287907 TGTTTCAAGGGAAACTGTTTTC-A-A-AG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
1287936 ATGTTTCAATAGAAACTGTCTCAA-AGGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGA-GAGACAAAATT
* *
1287973 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
1288009 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
* *
1288037 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
1288075 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
1288109 TATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
* *
1288137 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
1288175 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
1288208 GTGATGTACT
Statistics
Matches: 309, Mismatches: 52, Indels: 84
0.69 0.12 0.19
Matches are distributed among these distances:
28 5 0.02
29 49 0.16
30 31 0.10
31 1 0.00
32 5 0.02
33 5 0.02
34 20 0.06
35 7 0.02
36 76 0.25
37 90 0.29
38 20 0.06
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1287932 original size:30 final size:30
Alignment explanation
Indices: 1287896--1287954 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1287886 GTAAAACATA
*
1287896 TTCAAAGATTT-TGTTTCAAGGGAAACTGTT
1 TTCAAAG-TTTATGTTTCAAGAGAAACTGTT
*
1287926 TTCAAAGTTTATGTTTCAATAGAAACTGT
1 TTCAAAGTTTATGTTTCAAGAGAAACTGT
1287955 CTCAAAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
TTCAAAGTTTATGTTTCAAGAGAAACTGTT
Found at i:1288057 original size:101 final size:102
Alignment explanation
Indices: 1287909--1288207 Score: 505
Period size: 100 Copynumber: 3.0 Consensus size: 102
1287899 AAAGATTTTG
* * *
1287909 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAATAGAAACTGTCTCAAAGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1287973 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
1288011 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
1288076 GTTTCAAGGGAAACTATCTCAAGAGAGAC--AATTTA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
1288111 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
1288176 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAA
1288208 GTGATGTACT
Statistics
Matches: 186, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
100 96 0.52
101 45 0.24
102 45 0.24
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:1289468 original size:22 final size:20
Alignment explanation
Indices: 1289443--1289482 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1289433 ATGTTTGTTT
1289443 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
1289465 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
1289483 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:1289715 original size:15 final size:15
Alignment explanation
Indices: 1289692--1289727 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1289682 ACTAATATTC
* *
1289692 TTATCATAATATATA
1 TTATAATAACATATA
1289707 TTATAATAACATATA
1 TTATAATAACATATA
1289722 TTATAA
1 TTATAA
1289728 AGCTAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:1293748 original size:22 final size:20
Alignment explanation
Indices: 1293723--1293762 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1293713 ATGTTTGTTT
1293723 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
1293745 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
1293763 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:1293995 original size:15 final size:15
Alignment explanation
Indices: 1293972--1294007 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1293962 ACTAATATTC
* *
1293972 TTATCATAATATATA
1 TTATAATAACATATA
1293987 TTATAATAACATATA
1 TTATAATAACATATA
1294002 TTATAA
1 TTATAA
1294008 AGCTAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:1295005 original size:22 final size:22
Alignment explanation
Indices: 1294980--1295030 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1294970 TTGTGTTTGG
1294980 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1295002 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1295024 TCAAAGG
1 TCAAAGG
1295031 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1295689 original size:8 final size:7
Alignment explanation
Indices: 1295665--1295757 Score: 64
Period size: 7 Copynumber: 12.7 Consensus size: 7
1295655 TTTTTGTCCC
1295665 TTTTTCT
1 TTTTTCT
**
1295672 TTTTGAT
1 TTTTTCT
*
1295679 TTTTGCTT
1 TTTTTC-T
1295687 TTTTTCCT
1 TTTTT-CT
1295695 TTTGTTCT
1 TTT-TTCT
*
1295703 TGTTTCT
1 TTTTTCT
1295710 CTTTTTCT
1 -TTTTTCT
*
1295718 TTGTT-T
1 TTTTTCT
1295724 TTTTT-T
1 TTTTTCT
*
1295730 TTTTGCT
1 TTTTTCT
1295737 TTTTTGCT
1 TTTTT-CT
1295745 TCTTTTCT
1 T-TTTTCT
1295753 TTTTT
1 TTTTT
1295758 GTTCTTGATT
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
6 10 0.14
7 27 0.39
8 25 0.36
9 7 0.10
ACGTcount: A:0.01, C:0.13, G:0.08, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:1295734 original size:14 final size:15
Alignment explanation
Indices: 1295711--1295763 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
1295701 CTTGTTTCTC
1295711 TTTTTCTTTG-TTTT
1 TTTTTCTTTGCTTTT
*
1295725 TTTTTTTTTGCTTTT
1 TTTTTCTTTGCTTTT
* *
1295740 TTGCTTCTTTTCTTTT
1 TT-TTTCTTTGCTTTT
*
1295756 TTGTTCTT
1 TTTTTCTT
1295764 GATTGGATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 9 0.28
15 11 0.34
16 12 0.38
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (15 bp):
TTTTTCTTTGCTTTT
Found at i:1295754 original size:16 final size:16
Alignment explanation
Indices: 1295717--1295763 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
1295707 TCTCTTTTTC
*
1295717 TTTG-TTTTTT-TTTT
1 TTTGCTTTTTTGTTCT
1295731 TTTGCTTTTTTGCTTCT
1 TTTGCTTTTTTG-TTCT
1295748 TTT-CTTTTTTGTTCT
1 TTTGCTTTTTTGTTCT
1295763 T
1 T
1295764 GATTGGATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.14
15 11 0.38
16 8 0.28
17 6 0.21
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.81
Consensus pattern (16 bp):
TTTGCTTTTTTGTTCT
Done.