Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003805.1 Hibiscus syriacus cultivar Beakdansim tig00008145_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: 2300233
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1162403 original size:17 final size:16
Alignment explanation
Indices: 1162377--1162415 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
1162367 TAACTCTATT
1162377 ATTTATATTTCTTTTC
1 ATTTATATTTCTTTTC
*
1162393 ATTTCATATTTCTTTTT
1 ATTT-ATATTTCTTTTC
1162410 ATTTAT
1 ATTTAT
1162416 TTATTGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTATATTTCTTTTC
Found at i:1168523 original size:16 final size:16
Alignment explanation
Indices: 1168502--1168534 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1168492 TATTTCATAT
*
1168502 TTTAATTTAAATAAAA
1 TTTAATTTAAAAAAAA
1168518 TTTAATTTAAAAAAAA
1 TTTAATTTAAAAAAAA
1168534 T
1 T
1168535 CCTACCACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAATTTAAAAAAAA
Found at i:1175607 original size:19 final size:23
Alignment explanation
Indices: 1175585--1175639 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 23
1175575 TTTGTAAAAG
1175585 TATTTTTATTTTA-AT-T-G-TT
1 TATTTTTATTTTATATATAGTTT
*
1175604 TATTTTTCTTTTATATATAGTTT
1 TATTTTTATTTTATATATAGTTT
1175627 TACTTTTTATTTT
1 TA-TTTTTATTTT
1175640 CCTTATCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 12 0.41
20 2 0.07
21 1 0.03
22 1 0.03
23 4 0.14
24 9 0.31
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (23 bp):
TATTTTTATTTTATATATAGTTT
Found at i:1182438 original size:20 final size:20
Alignment explanation
Indices: 1182409--1182447 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1182399 AAAGCTCATA
*
1182409 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1182429 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1182448 GTGATGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1185711 original size:88 final size:88
Alignment explanation
Indices: 1185580--1185755 Score: 325
Period size: 88 Copynumber: 2.0 Consensus size: 88
1185570 CATAAAGTTA
* * *
1185580 TCCAAAAATGTTATGCATTTGAAAACATTGATATCAATTGTTAGAGAGATATCATTTGCAATAAA
1 TCCAAAAATGTTATGCATTTAAAAAAATTGATATCAATTGTTAGAGAGATATCATTTACAATAAA
1185645 TCACATGCATAAACATTTAAATT
66 TCACATGCATAAACATTTAAATT
1185668 TCCAAAAATGTTATGCATTTAAAAAAATTGATATCAATTGTTAGAGAGATATCATTTACAATAAA
1 TCCAAAAATGTTATGCATTTAAAAAAATTGATATCAATTGTTAGAGAGATATCATTTACAATAAA
1185733 TCACATGCATAAACATTTAAATT
66 TCACATGCATAAACATTTAAATT
1185756 AAGGTAAAAA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (88 bp):
TCCAAAAATGTTATGCATTTAAAAAAATTGATATCAATTGTTAGAGAGATATCATTTACAATAAA
TCACATGCATAAACATTTAAATT
Found at i:1192155 original size:73 final size:73
Alignment explanation
Indices: 1192024--1192175 Score: 223
Period size: 73 Copynumber: 2.1 Consensus size: 73
1192014 ACCTGACCTG
* * **
1192024 AAAGCAATCCGAATGAAAATTAATCCGAACTGAAAGTAAGAATCTTATTGTAAAATTGAAAACAA
1 AAAGTAATCCAAATGAAAATTAATCCGAACTGAAAGTAAGAATCTTATCATAAAATTGAAAACAA
*
1192089 TAACGAAT
66 TAACAAAT
* ***
1192097 AAAGTAATCCAAATGAAAATTAATTCGAACTGAAAGTAAGAATCTTATCATCGGATTGAAAACAA
1 AAAGTAATCCAAATGAAAATTAATCCGAACTGAAAGTAAGAATCTTATCATAAAATTGAAAACAA
1192162 TAACAAAT
66 TAACAAAT
1192170 AAAGTA
1 AAAGTA
1192176 TACTTATCTT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.24
Consensus pattern (73 bp):
AAAGTAATCCAAATGAAAATTAATCCGAACTGAAAGTAAGAATCTTATCATAAAATTGAAAACAA
TAACAAAT
Found at i:1206806 original size:16 final size:16
Alignment explanation
Indices: 1206768--1206830 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
1206758 GATGGATTTA
* *
1206768 TGTTTTGGATATTTGG
1 TGTTTTGAATATTTTG
1206784 T-TGTTTGAATATTTTG
1 TGT-TTTGAATATTTTG
*
1206800 TGTTTTGAAT-GTTTG
1 TGTTTTGAATATTTTG
*
1206815 -ATTTTGAATGATTTTG
1 TGTTTTGAAT-ATTTTG
1206831 ATCTTTATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
14 8 0.21
15 5 0.13
16 24 0.63
17 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (16 bp):
TGTTTTGAATATTTTG
Found at i:1206832 original size:16 final size:16
Alignment explanation
Indices: 1206787--1206832 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1206777 TATTTGGTTG
*
1206787 TTTGAAT-ATTTTGTGT
1 TTTGAATGATTTTG-AT
1206803 TTTGAATG--TTTGAT
1 TTTGAATGATTTTGAT
1206817 TTTGAATGATTTTGAT
1 TTTGAATGATTTTGAT
1206833 CTTTATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 9 0.35
15 4 0.15
16 13 0.50
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.59
Consensus pattern (16 bp):
TTTGAATGATTTTGAT
Found at i:1207662 original size:21 final size:21
Alignment explanation
Indices: 1207636--1207685 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1207626 CAGGAAGTAT
1207636 CGATACCCCTAAGTGGATTAC
1 CGATACCCCTAAGTGGATTAC
1207657 CGATACCCCTAAGTGGATTAC
1 CGATACCCCTAAGTGGATTAC
1207678 CGATACCC
1 CGATACCC
1207686 ATACGCTCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (21 bp):
CGATACCCCTAAGTGGATTAC
Found at i:1209346 original size:45 final size:45
Alignment explanation
Indices: 1209296--1209385 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
1209286 GTCCAATGTG
*
1209296 ACTTTCGGTCCTGCAATTGCCGTGGGGGCCAATGAATTATCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
* * * * *
1209341 ACTTTCGGTGCTGAAATTGTCGTGGGGTCCAATGCATTTTCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
1209386 GTTGCATTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (45 bp):
ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
Found at i:1213965 original size:28 final size:28
Alignment explanation
Indices: 1213922--1213976 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
1213912 CTTCTCATCT
1213922 TCCTCCTCCATATCTCTCTTCTTCTTCC
1 TCCTCCTCCATATCTCTCTTCTTCTTCC
*
1213950 TCCTCCTCCATGTCTCTCTTCTTCTTC
1 TCCTCCTCCATATCTCTCTTCTTCTTC
1213977 ATCGAATGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.05, C:0.45, G:0.02, T:0.47
Consensus pattern (28 bp):
TCCTCCTCCATATCTCTCTTCTTCTTCC
Found at i:1214701 original size:45 final size:45
Alignment explanation
Indices: 1214651--1214740 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
1214641 GTCCAATGTG
*
1214651 ACTTTCGGTCCTGCAATTGCCGTGGGGGCCAATGAATTATCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
* * * * *
1214696 ACTTTCGGTGCTGAAATTGTCGTGGGGTCCAATGCATTTTCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
1214741 GTTGCATTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (45 bp):
ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
Found at i:1218940 original size:20 final size:20
Alignment explanation
Indices: 1218925--1218964 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1218915 TAGATGAATA
1218925 ATATGGATATTGGATGAACT
1 ATATGGATATTGGATGAACT
1218945 ATATGGATATTGGATGAACT
1 ATATGGATATTGGATGAACT
1218965 GGAATGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (20 bp):
ATATGGATATTGGATGAACT
Found at i:1220257 original size:32 final size:31
Alignment explanation
Indices: 1220221--1220292 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
1220211 TAATATTTAA
* * *
1220221 ATAATGCACAACAATGTCAGTGTTGCATGCAT
1 ATAATGCA-AACAATGTCAGGGTCGCATGCAG
* *
1220253 ATAATGCTAAACAGTGTCAGGGTCGCATTCAG
1 ATAATGC-AAACAATGTCAGGGTCGCATGCAG
1220285 ATAATGCA
1 ATAATGCA
1220293 TAGTAGTTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 1 0.03
32 32 0.94
33 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (31 bp):
ATAATGCAAACAATGTCAGGGTCGCATGCAG
Found at i:1221145 original size:2 final size:2
Alignment explanation
Indices: 1221128--1221185 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
1221118 AATTACAATC
* * *
1221128 AT AT AC AT AC AT AT AT AT AA 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
1221170 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1221186 TATCTACACA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1223809 original size:19 final size:19
Alignment explanation
Indices: 1223785--1223821 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1223775 ATTTCTAATA
1223785 AAAATAATAAAATATAAAT
1 AAAATAATAAAATATAAAT
*
1223804 AAAATAATAAAATCTAAA
1 AAAATAATAAAATATAAA
1223822 GTGTTTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATAATAAAATATAAAT
Found at i:1226081 original size:19 final size:20
Alignment explanation
Indices: 1226057--1226105 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1226047 AAATGATTTT
* *
1226057 ATTTTGAAAGCAAAAATG-G
1 ATTTTGAAAACAAAAATGAA
*
1226076 ATTTTGAAAACCAAAATGAA
1 ATTTTGAAAACAAAAATGAA
1226096 ATTTTGAAAA
1 ATTTTGAAAA
1226106 ATGCAAATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (20 bp):
ATTTTGAAAACAAAAATGAA
Found at i:1228480 original size:32 final size:32
Alignment explanation
Indices: 1228439--1228525 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
1228429 TACTAGTTGT
*
1228439 GTGTTGCATTCAGATAATACACAACAATGTTA
1 GTGTTGCATTCAGATAATGCACAACAATGTTA
1228471 GTGTTGCATTCAGATAATGCACAACAATGTTA
1 GTGTTGCATTCAGATAATGCACAACAATGTTA
** *
1228503 GTGTTATATTAAGATAATGCACA
1 GTGTTGCATTCAGATAATGCACA
1228526 TCAGGGTCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (32 bp):
GTGTTGCATTCAGATAATGCACAACAATGTTA
Found at i:1228538 original size:32 final size:32
Alignment explanation
Indices: 1228450--1228599 Score: 122
Period size: 32 Copynumber: 4.7 Consensus size: 32
1228440 TGTTGCATTC
* ** * ** *
1228450 AGATAATACACAACAATGTTAGTGTTGCATTC
1 AGATAATGCACAACAGGGTCAGTGTTATATTT
** * *
1228482 AGATAATGCACAACAATGTTAGTGTTATATTA
1 AGATAATGCACAACAGGGTCAGTGTTATATTT
* *
1228514 AGATAATGCACATCAGGGTCAGTGTTGTATTT
1 AGATAATGCACAACAGGGTCAGTGTTATATTT
* * *
1228546 AGATAAAGCA-AAAAGGTGTCAGTGTAATATTT
1 AGATAATGCACAACAGG-GTCAGTGTTATATTT
* *
1228578 AGATAATGCACAATAGAGTCAG
1 AGATAATGCACAACAGGGTCAG
1228600 GGTCGCATTC
Statistics
Matches: 98, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
31 4 0.04
32 90 0.92
33 4 0.04
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (32 bp):
AGATAATGCACAACAGGGTCAGTGTTATATTT
Found at i:1228538 original size:64 final size:63
Alignment explanation
Indices: 1228470--1228619 Score: 169
Period size: 64 Copynumber: 2.3 Consensus size: 63
1228460 CAACAATGTT
* * *
1228470 AGTGTTGCATTCAGATAATGCACAACAA-TGTTAGTGTTATATTAAGATAATGCAC-ATCAGGGT
1 AGTGTTGCATTCAGATAATGCA-AA-AAGTGTCAGTGTAATATTAAGATAATGCACAAT-AGAGT
1228533 C
63 C
* * * *
1228534 AGTGTTGTATTTAGATAAAGCAAAAAGGTGTCAGTGTAATATTTAGATAATGCACAATAGAGTC
1 AGTGTTGCATTCAGATAATGCAAAAA-GTGTCAGTGTAATATTAAGATAATGCACAATAGAGTC
* *
1228598 AGGGTCGCATTCAGATAATGCA
1 AGTGTTGCATTCAGATAATGCA
1228620 TAGCGGTTAC
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
62 2 0.03
63 2 0.03
64 65 0.92
65 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (63 bp):
AGTGTTGCATTCAGATAATGCAAAAAGTGTCAGTGTAATATTAAGATAATGCACAATAGAGTC
Found at i:1238727 original size:21 final size:21
Alignment explanation
Indices: 1238703--1238743 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1238693 CATCAAGAAC
*
1238703 TTTGTTGAGGCCATGAATTCT
1 TTTGTTGAGGCCATAAATTCT
1238724 TTTGTTGAGGCCATAAATTC
1 TTTGTTGAGGCCATAAATTC
1238744 CTACAATGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (21 bp):
TTTGTTGAGGCCATAAATTCT
Found at i:1245688 original size:46 final size:46
Alignment explanation
Indices: 1245593--1245680 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
1245583 ACCGTTATGT
* * *
1245593 ATTTTCATTTGTGGCATCCTTTCATGCCAATTATTCACTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTCTTATAC
1245639 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTCTT
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTCTT
1245681 CTTCATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTCTTATAC
Found at i:1246113 original size:54 final size:54
Alignment explanation
Indices: 1246036--1246622 Score: 762
Period size: 54 Copynumber: 10.9 Consensus size: 54
1246026 TAGTGTATAT
* * *
1246036 GGTTGTTCATCAACATATGATGAATTCCATGAATTGCACACATAGTGCCAAAAC
1 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAC
* * * * * * * *
1246090 GATTCTTCATCAACATATGATGAATTCCGTGAGTTGAACACATAGTTTCTGAAAG
1 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAG-TGCCGAAAC
* * * *
1246145 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCAAACATAGTGTCAAAAC
1 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAC
* *
1246199 GGTTGTTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTACCGAAAC
1 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAC
* *
1246253 GGTTGTTCATCAACATATGATGAATTCTGTGAGTTGCACACTTAGTGCCGAAAC
1 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAC
* * * * * *
1246307 GGATGTTCATCAACATATGATGAATTTCGTGAATTACAAACTTAGTGTCGAAAT
1 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAC
* * * *
1246361 AGTTGTTCATCAACATATGATGAATTTCGTAAATTGCACACTTAGTGACGAAAC
1 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAC
* * * *
1246415 GGTTGTTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTTCTGAAGC
1 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAC
* * *
1246469 GGTTGTTCATTAACATATGATGAATTCCGTGAGTTGCACACATAGTGCCGAAAC
1 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAC
* * *
1246523 GGTTGTTCATCAACATATGATGAATTCCCTGAATT-CAACACTTAGTGCCAAAAT
1 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGC-ACACTTAGTGCCGAAAC
* ** *
1246577 GGTTGTGCATCAACATATGATGAATTTTGTGAATTCCACACTTAGT
1 GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGT
1246623 ACCTATTTGG
Statistics
Matches: 465, Mismatches: 65, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
53 1 0.00
54 418 0.90
55 46 0.10
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (54 bp):
GGTTGTTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAAC
Found at i:1251387 original size:54 final size:53
Alignment explanation
Indices: 1251328--1251753 Score: 460
Period size: 54 Copynumber: 7.9 Consensus size: 53
1251318 GTGTGTGTAT
* * * *
1251328 GGTTGTTCATTAATAAATGATGAATTACGTGAATTGCGCACTTAGTGCCGAAAC
1 GGTTGTTCATCAACATATGATGAATT-CGTGAATTGCACACTTAGTGCCGAAAC
* * *
1251382 AGTTGTTCATCGACATATGATGAATTTCGTGAGTTGCACACATT-GTGCCGAAAC
1 GGTTGTTCATCAACATATGATGAA-TTCGTGAATTGCACAC-TTAGTGCCGAAAC
* * * *
1251436 GGTTTTTCATCAACATACGATGAATTCTGTGAATTGTACACTTAGTGTCGAAAC
1 GGTTGTTCATCAACATATGATGAATTC-GTGAATTGCACACTTAGTGCCGAAAC
** * * *
1251490 TATTGTT-ATCAACATATGATGAATTCTGTGGATTTCACACTTAGTACCGAAAC
1 GGTTGTTCATCAACATATGATGAATTC-GTGAATTGCACACTTAGTGCCGAAAC
* * * * * *
1251543 GGTTGTTCATCAGCGTATGATGAATTCCATGAGTTGCACACTTAGTGTCAAAAC
1 GGTTGTTCATCAACATATGATGAATT-CGTGAATTGCACACTTAGTGCCGAAAC
* * *
1251597 GGTTGTTCATCAATATATGATGAATTCCGTGAATTGCACATTTAGTGCTGAAAC
1 GGTTGTTCATCAACATATGATGAATT-CGTGAATTGCACACTTAGTGCCGAAAC
* * * * * * *
1251651 GGTTGTTCATCAGCAGATGATGAATTCCATGAGTTGCACAGTTAGTGCTGAAAT
1 GGTTGTTCATCAACATATGATGAATT-CGTGAATTGCACACTTAGTGCCGAAAC
*
1251705 GGTTGTTGATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCC
1 GGTTGTTCATCAACATATGATGAATTC-GTGAATTGCACACTTAGTGCC
1251754 AAAAGGGTAT
Statistics
Matches: 308, Mismatches: 57, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
53 51 0.17
54 252 0.82
55 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (53 bp):
GGTTGTTCATCAACATATGATGAATTCGTGAATTGCACACTTAGTGCCGAAAC
Found at i:1251771 original size:34 final size:34
Alignment explanation
Indices: 1251728--1251795 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1251718 CATATGATGA
1251728 ATTCTGTGAATTGCACACTTAGTGCCAAAAGGGT
1 ATTCTGTGAATTGCACACTTAGTGCCAAAAGGGT
1251762 ATTCTGTGAATTGCACACTTAGTGCCAAAAGGGT
1 ATTCTGTGAATTGCACACTTAGTGCCAAAAGGGT
1251796 TGTTCATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (34 bp):
ATTCTGTGAATTGCACACTTAGTGCCAAAAGGGT
Found at i:1251851 original size:54 final size:54
Alignment explanation
Indices: 1251767--1252002 Score: 323
Period size: 54 Copynumber: 4.4 Consensus size: 54
1251757 AGGGTATTCT
*
1251767 GTGAATTGCACACTTAGTGCCAAAAGGGTTGTTCATCAACATATGATGAATTTC
1 GTGAATTGCACACTTAGTGCCAAAAAGGTTGTTCATCAACATATGATGAATTTC
* * * *
1251821 GTGAATTGCACACTTAGTGTCGAAATGGTTGTTCTTCAA-ATATGATGAATTAT-
1 GTGAATTGCACACTTAGTGCCAAAAAGGTTGTTCATCAACATATGATGAATT-TC
* * * *
1251874 GTGAGTTGTACACATAGTGCCAAAAAGGTTATTCATCAACATATGATGAATTTC
1 GTGAATTGCACACTTAGTGCCAAAAAGGTTGTTCATCAACATATGATGAATTTC
* * * *
1251928 GTGAATTGCACACTTAGTGCCGAAACGATTCTTCATCAACATATGATGAATTTC
1 GTGAATTGCACACTTAGTGCCAAAAAGGTTGTTCATCAACATATGATGAATTTC
*
1251982 ATGAATTGCACACTTAGTGCC
1 GTGAATTGCACACTTAGTGCC
1252003 TATTTGGTAA
Statistics
Matches: 159, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
53 44 0.28
54 115 0.72
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (54 bp):
GTGAATTGCACACTTAGTGCCAAAAAGGTTGTTCATCAACATATGATGAATTTC
Found at i:1251900 original size:142 final size:142
Alignment explanation
Indices: 1251620--1251907 Score: 382
Period size: 142 Copynumber: 2.0 Consensus size: 142
1251610 TATATGATGA
* ** * *
1251620 ATTCCGTGAATTGCACATTTAGTGCTGAAACGGTTGTTCATCAGCAGATGATGAATTCCATGAGT
1 ATTCCGTGAATTGCACACTTAGTGCCAAAACGGTTGTTCATCAACAGATGATGAATTCCATGAAT
* * * *
1251685 TGCACAGTTAGTGCTGAAATGGTTGTTGATCAACATATGATGAATTCTGTGAATTGCACACTTAG
66 TGCACACTTAGTGCTGAAATGGTTGTTCATCAACATATGATGAATTATGTGAATTGCACACATAG
1251750 TGCCAAAAGGGT
131 TGCCAAAAGGGT
* * * * *
1251762 ATTCTGTGAATTGCACACTTAGTGCCAAAAGGGTTGTTCATCAACATATGATGAATTTCGTGAAT
1 ATTCCGTGAATTGCACACTTAGTGCCAAAACGGTTGTTCATCAACAGATGATGAATTCCATGAAT
* * *
1251827 TGCACACTTAGTG-TCGAAATGGTTGTTCTTCAA-ATATGATGAATTATGTGAGTTGTACACATA
66 TGCACACTTAGTGCT-GAAATGGTTGTTCATCAACATATGATGAATTATGTGAATTGCACACATA
*
1251890 GTGCCAAAAAGGTT
130 GTGCC-AAAAGGGT
1251904 ATTC
1 ATTC
1251908 ATCAACATAT
Statistics
Matches: 126, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
141 32 0.25
142 94 0.75
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (142 bp):
ATTCCGTGAATTGCACACTTAGTGCCAAAACGGTTGTTCATCAACAGATGATGAATTCCATGAAT
TGCACACTTAGTGCTGAAATGGTTGTTCATCAACATATGATGAATTATGTGAATTGCACACATAG
TGCCAAAAGGGT
Found at i:1251952 original size:107 final size:108
Alignment explanation
Indices: 1251766--1252002 Score: 343
Period size: 107 Copynumber: 2.2 Consensus size: 108
1251756 AAGGGTATTC
* * *
1251766 TGTGAATTGCACACTTAGTGCCAAAAGGGTTGTTCATCAACATATGATGAATTTCGTGAATTGCA
1 TGTGAATTGCACACATAGTGCCAAAAAGGTTATTCATCAACATATGATGAATTTCGTGAATTGCA
* * * * *
1251831 CACTTAGTGTCGAAATGGTTGTTCTTCAA-ATATGATGAATTA
66 CACTTAGTGCCGAAACGATTCTTCATCAACATATGATGAATTA
* *
1251873 TGTGAGTTGTACACATAGTGCCAAAAAGGTTATTCATCAACATATGATGAATTTCGTGAATTGCA
1 TGTGAATTGCACACATAGTGCCAAAAAGGTTATTCATCAACATATGATGAATTTCGTGAATTGCA
1251938 CACTTAGTGCCGAAACGATTCTTCATCAACATATGATGAATT-
66 CACTTAGTGCCGAAACGATTCTTCATCAACATATGATGAATTA
* *
1251980 TCATGAATTGCACACTTAGTGCC
1 T-GTGAATTGCACACATAGTGCC
1252003 TATTTGGTAA
Statistics
Matches: 114, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
107 85 0.75
108 29 0.25
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (108 bp):
TGTGAATTGCACACATAGTGCCAAAAAGGTTATTCATCAACATATGATGAATTTCGTGAATTGCA
CACTTAGTGCCGAAACGATTCTTCATCAACATATGATGAATTA
Found at i:1252391 original size:42 final size:41
Alignment explanation
Indices: 1252345--1252437 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 41
1252335 CCCTACCATG
* *** *
1252345 GTATCGATACTTCTATGTTATGGTACCAATACCTTTCTTTCA
1 GTATCGATACTACTACACTATGGTACCAATA-CTTCCTTTCA
* * *
1252387 GTATCGATACTACTACACTATGGTGCCGATACTTCCTTTCG
1 GTATCGATACTACTACACTATGGTACCAATACTTCCTTTCA
1252428 GTATCGATAC
1 GTATCGATAC
1252438 CATTTTGACA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 18 0.42
42 25 0.58
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (41 bp):
GTATCGATACTACTACACTATGGTACCAATACTTCCTTTCA
Found at i:1261674 original size:14 final size:14
Alignment explanation
Indices: 1261657--1261687 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1261647 ACATATATAT
*
1261657 ATATTTATTTTTTC
1 ATATTTATTTCTTC
1261671 ATATTTATTTCTTC
1 ATATTTATTTCTTC
1261685 ATA
1 ATA
1261688 CTTTTCTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (14 bp):
ATATTTATTTCTTC
Found at i:1262634 original size:2 final size:2
Alignment explanation
Indices: 1262623--1262657 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1262613 ATTACTTTAT
1262623 TA TA TA -A 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
1262658 ATTTACTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1262982 original size:12 final size:12
Alignment explanation
Indices: 1262965--1263005 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1262955 GTATAATTAT
1262965 AATTTAGTTGAA
1 AATTTAGTTGAA
* *
1262977 AATTTAATT-AT
1 AATTTAGTTGAA
1262988 AATTTAGTTGAA
1 AATTTAGTTGAA
1263000 AATTTA
1 AATTTA
1263006 ATTGTAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (12 bp):
AATTTAGTTGAA
Found at i:1262988 original size:23 final size:23
Alignment explanation
Indices: 1262958--1263008 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
1262948 ACTCAATGTA
1262958 TAATTATAATTTAGTTGAAAATT
1 TAATTATAATTTAGTTGAAAATT
1262981 TAATTATAATTTAGTTGAAAATT
1 TAATTATAATTTAGTTGAAAATT
1263004 TAATT
1 TAATT
1263009 GTAACTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (23 bp):
TAATTATAATTTAGTTGAAAATT
Found at i:1272708 original size:6 final size:6
Alignment explanation
Indices: 1272691--1272791 Score: 53
Period size: 6 Copynumber: 15.5 Consensus size: 6
1272681 GATCAACATT
* * *
1272691 TTTGCA TATGCA TTTGCA TCTTTGCA TTTTGCA TGTGCA TTTGCA TCTTTGAA
1 TTTGCA TTTGCA TTTGCA --TTTGCA -TTTGCA TTTGCA TTTGCA --TTTGCA
* *
1272744 TTTTGCA TGTT-CA TTTTCA TCTTTGCA TTTTGCA TATGCA TTT-CA TTT
1 -TTTGCA T-TTGCA TTTGCA --TTTGCA -TTTGCA TTTGCA TTTGCA TTT
1272792 TTAAGCATTT
Statistics
Matches: 75, Mismatches: 12, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
5 7 0.09
6 33 0.44
7 19 0.25
8 16 0.21
ACGTcount: A:0.18, C:0.17, G:0.14, T:0.51
Consensus pattern (6 bp):
TTTGCA
Found at i:1272722 original size:27 final size:27
Alignment explanation
Indices: 1272690--1272786 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
1272680 GGATCAACAT
1272690 TTTTGCATATGCATTTGCATCTTTGCA
1 TTTTGCATATGCATTTGCATCTTTGCA
* *
1272717 TTTTGCATGTGCATTTGCATCTTTGAA
1 TTTTGCATATGCATTTGCATCTTTGCA
* * *
1272744 TTTTGCATGTTCATTTTCATCTTTGCA
1 TTTTGCATATGCATTTGCATCTTTGCA
1272771 TTTTGCATATGCATTT
1 TTTTGCATATGCATTT
1272787 CATTTTTAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.52
Consensus pattern (27 bp):
TTTTGCATATGCATTTGCATCTTTGCA
Found at i:1272729 original size:21 final size:20
Alignment explanation
Indices: 1272691--1272730 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1272681 GATCAACATT
*
1272691 TTTGCATATGCATTTGCATC
1 TTTGCATATGCATGTGCATC
*
1272711 TTTGCATTTTGCATGTGCAT
1 TTTGCA-TATGCATGTGCAT
1272731 TTGCATCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.47
Consensus pattern (20 bp):
TTTGCATATGCATGTGCATC
Found at i:1275794 original size:47 final size:48
Alignment explanation
Indices: 1275733--1275842 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 48
1275723 AAAAAAAAGC
* *
1275733 AAAG-AGAAAATAAAAAAAGAGAAATTAGAGCAAAAAGAG-AAAAGAA
1 AAAGAAGAAAATAAAAAAAGAGAAATCAAAGCAAAAAGAGAAAAAGAA
* * * *
1275779 AAATAAGAAACTAAAAAAAGAGTAATCAAAGTAAAAAGAGAAAAAGAA
1 AAAGAAGAAAATAAAAAAAGAGAAATCAAAGCAAAAAGAGAAAAAGAA
1275827 AAAGAAGAAAA-AAAAA
1 AAAGAAGAAAATAAAAA
1275843 GCAAAAAGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
46 3 0.06
47 35 0.65
48 16 0.30
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.07
Consensus pattern (48 bp):
AAAGAAGAAAATAAAAAAAGAGAAATCAAAGCAAAAAGAGAAAAAGAA
Found at i:1275848 original size:7 final size:6
Alignment explanation
Indices: 1275812--1275902 Score: 51
Period size: 6 Copynumber: 14.7 Consensus size: 6
1275802 AATCAAAGTA
* * *
1275812 AAAAGAG AAAAAG AAAAAG AAGAAAA AAAAAG CAAAAAG -AAAAT TAAAA-
1 AAAA-AG AAAAAG AAAAAG AA-AAAG AAAAAG -AAAAAG AAAAAG AAAAAG
* * * * *
1275861 AACAAC AAAGAG CAAAAAG AAAAGG AAAAAA AACAAAG AAAA
1 AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AA-AAAG AAAA
1275903 TGGACGAGAA
Statistics
Matches: 65, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
5 7 0.11
6 33 0.51
7 25 0.38
ACGTcount: A:0.78, C:0.05, G:0.14, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:1275854 original size:14 final size:13
Alignment explanation
Indices: 1275806--1275902 Score: 72
Period size: 13 Copynumber: 7.1 Consensus size: 13
1275796 AAGAGTAATC
1275806 AAAGTAAAAAGAGAA
1 AAAG-AAAAAGA-AA
1275821 AAAGAAAAAGAAGA
1 AAAGAAAAAGAA-A
*
1275835 AAA-AAAAAGCAA
1 AAAGAAAAAGAAA
**
1275847 AAAGAAAATTAAA
1 AAAGAAAAAGAAA
*
1275860 AAACAACAAAGAGCAA
1 AAAGAA-AAAGA--AA
*
1275876 AAAGAAAAGGAAA
1 AAAGAAAAAGAAA
1275889 AAA-AACAAAGAAA
1 AAAGAA-AAAGAAA
1275902 A
1 A
1275903 TGGACGAGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
12 6 0.09
13 31 0.47
14 14 0.21
15 8 0.12
16 7 0.11
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:1276983 original size:32 final size:32
Alignment explanation
Indices: 1276935--1277052 Score: 155
Period size: 32 Copynumber: 3.7 Consensus size: 32
1276925 GAACAATGGG
* * * *
1276935 GCATCTTTAAAGATTCAACAGCAAATGTTGGA
1 GCATCTTTAGAGATTCAACATCGAATATTGGA
* * *
1276967 GCATATTTAGATATTCAACATCGAATATTGGG
1 GCATCTTTAGAGATTCAACATCGAATATTGGA
* *
1276999 GAATCTTTAGAGATTCAACATCGATTATTGGA
1 GCATCTTTAGAGATTCAACATCGAATATTGGA
1277031 GCATCTTTAGAGATTCAACATC
1 GCATCTTTAGAGATTCAACATC
1277053 CTGATGCGAA
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 73 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (32 bp):
GCATCTTTAGAGATTCAACATCGAATATTGGA
Found at i:1277032 original size:64 final size:64
Alignment explanation
Indices: 1276931--1277052 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
1276921 AGAGGAACAA
* * *
1276931 TGGGGCATCTTTAAAGATTCAACAGCAAATGTTGGAGCATATTTAGATATTCAACATCGAATAT
1 TGGGGAATCTTTAAAGATTCAACAGCAAATATTGGAGCATATTTAGAGATTCAACATCGAATAT
* * * * *
1276995 TGGGGAATCTTTAGAGATTCAACATCGATTATTGGAGCATCTTTAGAGATTCAACATC
1 TGGGGAATCTTTAAAGATTCAACAGCAAATATTGGAGCATATTTAGAGATTCAACATC
1277053 CTGATGCGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (64 bp):
TGGGGAATCTTTAAAGATTCAACAGCAAATATTGGAGCATATTTAGAGATTCAACATCGAATAT
Found at i:1277582 original size:86 final size:86
Alignment explanation
Indices: 1277434--1277690 Score: 338
Period size: 86 Copynumber: 3.0 Consensus size: 86
1277424 ATATTCGACT
* * *
1277434 GAGGAATATATCACATGGCTTTCCTGTGAAGGGGAGTCATCTAAAGATCATCTCACTTGGTTCAG
1 GAGGAATATACCACATGGCTTTCCTATGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAG
1277499 ACCCGCTAAGGGGAACCACCC
66 ACCCGCTAAGGGGAACCACCC
* *
1277520 GAGGAATATACCACATGGCTTTCCTATGAAGTGGAGTCATCCAAA-ATTCATCTCACTCGGTTCA
1 GAGGAATATACCACATGGCTTTCCTATGAAGGGGAGTCATCCAAAGA-TCATCTCACTTGGTTCA
* * *
1277584 GACCCACTAAGGGGAATCACCT
65 GACCCGCTAAGGGGAACCACCC
* * * *
1277606 GAGGAATATACCACATGGTTTTCC-AGTGAAGGGGAGTTATACAAAGATCATCTCACTTGGTTTA
1 GAGGAATATACCACATGGCTTTCCTA-TGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCA
** * *
1277670 GACTAGTTAAGAGGAACCACC
65 GACCCGCTAAGGGGAACCACC
1277691 TGAACAATTA
Statistics
Matches: 148, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
85 2 0.01
86 145 0.98
87 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (86 bp):
GAGGAATATACCACATGGCTTTCCTATGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAG
ACCCGCTAAGGGGAACCACCC
Found at i:1278086 original size:85 final size:84
Alignment explanation
Indices: 1277758--1278091 Score: 341
Period size: 85 Copynumber: 3.9 Consensus size: 84
1277748 AACTATTGGT
* * * * * *
1277758 AGCAAAACGCAAGGCGATAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCT
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACT
*
1277823 CAAAGG-CACATCAAATTTAC
66 C--AGGACATATCAAATTTAC
* * ** * * * *
1277843 AGCATAACTCAAGGCAAGAAGAGTTATCTGTCAGTAAGAGACCTTTGAGTTTGATTCCATTTAAC
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAA-AGACCTTCGAGTTCGATTACATTCAAC
*
1277908 TCAAGGACA-ACCAAATTTAC
65 TC-AGGACATATCAAATTTAC
* * * **
1277928 AGCATAGCTCAAGGCGAGAAGGGTCATCTGTCAACGCAA-ACCTTCGAGTTCGATTACATTCAGT
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACATTCAAC
*
1277992 TCCAGGACATGTCAAATTTAC
65 T-CAGGACATATCAAATTTAC
* * * *
1278013 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAACACCTTCAAGTTTGATTTCATTCAACT
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACT
*
1278078 CGGTGACATATCAA
66 CAG-GACATATCAA
1278092 CTATATGGTA
Statistics
Matches: 202, Mismatches: 40, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
84 30 0.15
85 146 0.72
86 26 0.13
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (84 bp):
AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAACT
CAGGACATATCAAATTTAC
Found at i:1278860 original size:129 final size:129
Alignment explanation
Indices: 1278666--1279124 Score: 435
Period size: 129 Copynumber: 3.6 Consensus size: 129
1278656 TGACATGATT
* * * * *
1278666 TCCTCATCACGTAGGAACCGTGTCACCTCTTTGATAACCAACCATCCTCTTCACGTAGGAATCGT
1 TCCTCATCACGTAGGAACCGTGTCA-ATCCTTGATAACCAACCGTCCTCATCACGTAGGAACCGT
* *
1278731 GTTATCATCTTAT-GATGACCAAAAATCTTCATCACGTATGAGCCGTGTCATCACCCGACCAGAT
65 GTTATCA-CTTATAGATGGCCAAAAATCTTCATCACGTATGAGCCATGTCATCACCCGACCAGAT
1278795 C
129 C
* * *
1278796 TCCTCATCACGTAGGAACTGTGTCAA-CCTTTGATAA-CATGCCGTCCTCATCACGTAGGAATCG
1 TCCTCATCACGTAGGAACCGTGTCAATCC-TTGATAACCA-ACCGTCCTCATCACGTAGGAACCG
**** * * * ** *
1278859 TGTTATCACTTATAGATGGCCATTCGTCCTCATCACGTAGGAACCATGTCATCATTCGACCTGAT
64 TGTTATCACTTATAGATGGCCAAAAATCTTCATCACGTATGAGCCATGTCATCACCCGACCAGAT
1278924 C
129 C
* * * * * * * * *
1278925 TCCTCATCACATAGGAGCCGTGTTAATCCTCGATAACCAAAAC-TCTTCATCA-GTATGAGCCGG
1 TCCTCATCACGTAGGAACCGTGTCAATCCTTGATAACC-AACCGTCCTCATCACGTAGGAACCGT
* * * * * * *
1278988 GTTATCACCTT-TAGATGGCCAGAACTCTTCATCACATATAAGACTTGTCATCACCCGACTAGAT
65 GTTATCA-CTTATAGATGGCCAAAAATCTTCATCACGTATGAGCCATGTCATCACCCGACCAGAT
*
1279052 T
129 C
* * * * * *
1279053 TCCTCATTATGTAAGAATCGTGTCAATCCTTGATAACCAGCCGTCCTCATCACGTAGGAACCGAG
1 TCCTCATCACGTAGGAACCGTGTCAATCCTTGATAACCAACCGTCCTCATCACGTAGGAACCGTG
1279118 TTATCAC
66 TTATCAC
1279125 CCTTTCTAAA
Statistics
Matches: 260, Mismatches: 60, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
127 2 0.01
128 99 0.38
129 130 0.50
130 28 0.11
131 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (129 bp):
TCCTCATCACGTAGGAACCGTGTCAATCCTTGATAACCAACCGTCCTCATCACGTAGGAACCGTG
TTATCACTTATAGATGGCCAAAAATCTTCATCACGTATGAGCCATGTCATCACCCGACCAGATC
Found at i:1279088 original size:128 final size:134
Alignment explanation
Indices: 1278943--1279210 Score: 302
Period size: 135 Copynumber: 2.0 Consensus size: 134
1278933 ACATAGGAGC
* * * * *
1278943 CGTGTTAATCCTCGATAACCAAAAC-TCTTCATCA-GTATGAGCCGGGTTATCA-CC-TT-T-AG
1 CGTGTCAATCCTCGATAACC-AAACGTCCTCATCACGTAGGAACCGAGTTATCACCCTTTCTAAG
1279002 ATGGCC-AGAACTCTTCATCACATATAAG-ACTTGTCATCACCCGACTAGATTTCCTCATTATGT
65 ATGGCCAAGAACTCTTCATCACATATAAGTACTT-TCATCACCCGACTAGATTTCCTCATTATGT
1279065 AAGAA-T
129 -AGAAGT
* **
1279071 CGTGTCAATCCTTGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTTCTAAAG
1 CGTGTCAATCCTCGATAACCAAACGTCCTCATCACGTAGGAACCGAGTTATCACCCTTTCT-AAG
** * * * * *
1279136 ATGGCCAAGAACTCTTCATCATGTATGAGTAGTTTCATCACCTGACTAGGTTTTCTCATTATGTA
65 ATGGCCAAGAACTCTTCATCACATATAAGTACTTTCATCACCCGACTAGATTTCCTCATTATGTA
1279201 GAAGT
130 GAAGT
1279206 CGTGT
1 CGTGT
1279211 AAACCCTTAG
Statistics
Matches: 115, Mismatches: 15, Indels: 13
0.80 0.10 0.09
Matches are distributed among these distances:
127 2 0.02
128 26 0.23
129 15 0.13
130 2 0.02
131 2 0.02
132 1 0.01
134 12 0.10
135 52 0.45
136 3 0.03
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (134 bp):
CGTGTCAATCCTCGATAACCAAACGTCCTCATCACGTAGGAACCGAGTTATCACCCTTTCTAAGA
TGGCCAAGAACTCTTCATCACATATAAGTACTTTCATCACCCGACTAGATTTCCTCATTATGTAG
AAGT
Found at i:1284665 original size:23 final size:23
Alignment explanation
Indices: 1284633--1284677 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1284623 AAGTTAGTAT
* *
1284633 GTAACGATTTACTTTTGAATTAC
1 GTAACAATTTAATTTTGAATTAC
1284656 GTAACAATTTAATTTTGAATTA
1 GTAACAATTTAATTTTGAATTA
1284678 ATTACATACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (23 bp):
GTAACAATTTAATTTTGAATTAC
Found at i:1285009 original size:17 final size:17
Alignment explanation
Indices: 1284987--1285022 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1284977 ACAAACGATA
*
1284987 ACACACGTTAATTAATG
1 ACACACGCTAATTAATG
1285004 ACACACGCTAATTAATG
1 ACACACGCTAATTAATG
1285021 AC
1 AC
1285023 TTGCAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (17 bp):
ACACACGCTAATTAATG
Found at i:1285276 original size:16 final size:17
Alignment explanation
Indices: 1285249--1285281 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1285239 CGCCACATGC
1285249 TTCCCTTTTTTCTCTTT
1 TTCCCTTTTTTCTCTTT
1285266 TTCCC-TTTTTCTCTTT
1 TTCCCTTTTTTCTCTTT
1285282 GCAGGACTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCCCTTTTTTCTCTTT
Found at i:1286787 original size:23 final size:24
Alignment explanation
Indices: 1286741--1286787 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1286731 ATATTTTTGC
*
1286741 GTGTTTTAGTGTATTTATAGGGTG
1 GTGTTTTAGTGTATTTATAAGGTG
1286765 GTGTTTT-GTGTATGTTA-AAGGTG
1 GTGTTTTAGTGTAT-TTATAAGGTG
1286788 CAGGGTGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (24 bp):
GTGTTTTAGTGTATTTATAAGGTG
Found at i:1289045 original size:2 final size:2
Alignment explanation
Indices: 1289038--1289068 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1289028 TCAATCTACA
1289038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1289069 ATTTACGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1303934 original size:16 final size:17
Alignment explanation
Indices: 1303902--1303934 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1303892 CAATATTAAT
*
1303902 TTAAAGTAAACGTGAAA
1 TTAAAGTAAACGAGAAA
1303919 TTAAAG-AAACGAGAAA
1 TTAAAGTAAACGAGAAA
1303935 AAATATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (17 bp):
TTAAAGTAAACGAGAAA
Found at i:1307404 original size:3 final size:3
Alignment explanation
Indices: 1307383--1307439 Score: 66
Period size: 3 Copynumber: 19.0 Consensus size: 3
1307373 TCTACAAAAA
1307383 TAT T-T TAT TA- TAT TA- TAT TATT TATT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT
1307428 TAT TAT TAT TAT
1 TAT TAT TAT TAT
1307440 ATTTTTTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.12
3 33 0.66
4 11 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1307415 original size:12 final size:11
Alignment explanation
Indices: 1307386--1307453 Score: 56
Period size: 9 Copynumber: 6.3 Consensus size: 11
1307376 ACAAAAATAT
1307386 TTTATTATATTA
1 TTTATTAT-TTA
1307398 TATTATTTATTTA
1 T-TTA-TTATTTA
1307411 TTTATTA-TTA
1 TTTATTATTTA
1307421 -TTATTA-TTA
1 TTTATTATTTA
1307430 -TTATTATTATA
1 TTTATTATT-TA
*
1307441 TTT-TTTTTTA
1 TTTATTATTTA
1307451 TTT
1 TTT
1307454 TTGTAGGCCC
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
9 15 0.30
10 9 0.18
11 9 0.18
12 6 0.12
13 7 0.14
14 4 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:1307539 original size:33 final size:33
Alignment explanation
Indices: 1307502--1307587 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
1307492 TTCAGAAAAT
*
1307502 AAACCAACGTATTTGAGTCATATTAAAACACTA
1 AAACCAACATATTTGAGTCATATTAAAACACTA
*
1307535 AAACCAACATATTTGAGTCATATTGAAACACTA
1 AAACCAACATATTTGAGTCATATTAAAACACTA
1307568 AAACCGAAGCAT-TTTGAGTC
1 AAACC-AA-CATATTTGAGTC
1307588 CAAGTAGGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
33 36 0.73
34 10 0.20
35 3 0.06
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.27
Consensus pattern (33 bp):
AAACCAACATATTTGAGTCATATTAAAACACTA
Found at i:1311844 original size:110 final size:110
Alignment explanation
Indices: 1311691--1312666 Score: 1469
Period size: 110 Copynumber: 8.9 Consensus size: 110
1311681 GATGGTGGTT
* * *
1311691 GCTCAACTTCATAGCGAAGGGGCGACTGACAGTCAATAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1311756 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1311801 GCTCAAATTCACAGCGAAGGGGTGACTGATTATCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
1311866 AATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* ** * *
1311911 GGTCAACTTCACATTGAAGGGGCGACTGACTATCAACAAACAACTTTTCAGTTTCATTCAAAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * * *
1311976 AATTTTAATTTCACAGCGAATGATATTGGACTCGAGACAACACAT
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
*
1312021 GCTCAACTTCACAGCGAAGGGGCGACTGATTGTCAACAAA-AACCTTTTCAGTTTCATTCAGAGT
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAA-CTTTTCAGTTTCATTCAGAGT
* * *
1312085 TAATTTCAACTTCACAGCGAAGGATATAGGACTTGAGACAACACAA
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
1312131 GCTCAACTTCACAGCGAAGGGGTGACTGACTGTCAGCAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
1312196 AATTTCAACTTCAAAGCGAAGGATATTGGACTCAAGATAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
1312241 GCTCAACTTCACAGCGAAGGGGCGACTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTT
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * * *
1312306 AATTTCAATTTCACAGCGAATGATATTGGACTCGAGATAACATAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1312351 GCTGAACTTCAGAGCGAAGGAGCGACTGATTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
1312416 AATTTCAACTTCACAGCGAAAGATATTAGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
1312461 GCTCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACTAACAACTTTTCAGTTTTATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
1312526 AATTTCAACTTCATAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1312571 GCTCAACTTCACTGCGAAGGGGCGGCTGACTGTCAACAAACAACTTTCCA--AT--TTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
1312632 AATTTCAACTTCAC-GACGAAGGATATTGGCCTCGA
66 AATTTCAACTTCACAG-CGAAGGATATTGGACTCGA
1312667 AACGGCACAA
Statistics
Matches: 785, Mismatches: 78, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
105 1 0.00
106 40 0.05
108 1 0.00
109 2 0.00
110 739 0.94
111 2 0.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:1313023 original size:84 final size:82
Alignment explanation
Indices: 1312785--1313552 Score: 746
Period size: 84 Copynumber: 9.3 Consensus size: 82
1312775 TTATGCCCAT
* * *
1312785 CAAAGACCTTCGAGTTTGACTACGCTCAGCTCAAAGGCACAAT-ATTTGCAGCATAGCTTAAGTC
1 CAAAGACCTTCGAGTTTGATTACGCTCAGCTCCAAGGCAC-ATCATTTGCAGCATAACTTAAGTC
*
1312849 AAGAAGGGTTATCTGCCAAC
65 AAGAAGGGTTATCTG--TAC
** * * * * * * * * * *
1312869 TGAAGACCATCGGGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTTGATTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTC
*
1312934 TAGAAGGGTTATCTGTGAC
65 AAGAAGGGTTATCTGT-AC
* *
1312953 CAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTC
1 C-AAAGACCTTCGAGTTTGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
1313018 GAGAAGGGTTATCTGCCAAC
65 AAGAAGGGTTATCTG--TAC
* * * **
1313038 CAAAGACCTTTGAGTTCGATTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGTTTAAGTCA
1 CAAAGACCTTCGAGTTTGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCA
*
1313103 AGAAGGGCTATC--TAC
66 AGAAGGGTTATCTGTAC
* * * * * * *
1313118 CAAAGACCCTCGAGTTTGATTACACTCAGCTTCAAGGGAACATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTTGATTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTC
*
1313183 TAGAAGGGTTATCTGTGAC
65 AAGAAGGGTTATCTGT-AC
* * * *
1313202 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGTC
1 C-AAAGACCTTCGAGTTTGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
*
1313267 AAGAAGGGTTATCTGCCAAC
65 AAGAAGGGTTATCTG--TAC
* * * * *
1313287 CAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACAACATTTGTAGCATAGCTTAAGTCT
1 CAAAGACCTTCGAGTTTGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCA
*
1313352 AGAAGTGTTATCT-T-C
66 AGAAGGGTTATCTGTAC
* * * * * * *
1313367 CAAAGACCCTCGAGTTTAATTACACTCAGCTTCAAGGGCACATCATTTAC-GACATAACTCAAGG
1 CAAAGACCTTCGAGTTTGATTACGCTCAGCTCCAA-GGCACATCATTTGCAG-CATAACTTAAGT
* *
1313431 CTAGAAGGGTTATCTGTCAA
64 CAAGAAGGGTTATCTGT-AC
* * * *
1313451 CAAAGACCTTCGAGTTTGACTT-CACTCAGCTCAAAGGCACCATCATTTGCAGCATAGCTCAAG-
1 CAAAGACCTTCGAGTTTGA-TTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAACTTAAGT
*
1313514 CTAAGAAGGGCTATC--TAC
64 C-AAGAAGGGTTATCTGTAC
*
1313532 CAAAGACCTTCGAGTTCGATT
1 CAAAGACCTTCGAGTTTGATT
1313553 CCGTTCAGGG
Statistics
Matches: 567, Mismatches: 95, Indels: 48
0.80 0.13 0.07
Matches are distributed among these distances:
80 67 0.12
81 87 0.15
82 2 0.00
83 6 0.01
84 306 0.54
85 99 0.17
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (82 bp):
CAAAGACCTTCGAGTTTGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCA
AGAAGGGTTATCTGTAC
Found at i:1313227 original size:249 final size:249
Alignment explanation
Indices: 1312785--1313552 Score: 1113
Period size: 249 Copynumber: 3.1 Consensus size: 249
1312775 TTATGCCCAT
* *
1312785 CAAAGACCTTCGAGTTTGACTACGCTCAGC-TCAAAGGCACAAT-ATTTGCAGCATAGCTTAAGT
1 CAAAGACCTTCGAGTTCGATTACGCTCAGCTTC-AAGGCAC-ATCATTTGCAGCATAGCTTAAGT
* * * * * *
1312848 CAAGAAGGGTTATCTGCCAACTGAAGACCATCGGGTTCGATTACACTCAGCTTCGAGGGCATATC
64 CAAGAAGGGTTATCTACC-A---AAGACCCTCGAGTTTGATTACACTCAGCTTCAAGGGCACATC
1312913 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGACTACG
125 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGACTACG
*
1312978 CTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC
190 CTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAAC
* *
1313038 CAAAGACCTTTGAGTTCGATTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGTTTAAGTCA
1 CAAAGACCTTCGAGTTCGATTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTCA
* *
1313103 AGAAGGGCTATCTACCAAAGACCCTCGAGTTTGATTACACTCAGCTTCAAGGGAACATCATTTAC
66 AGAAGGGTTATCTACCAAAGACCCTCGAGTTTGATTACACTCAGCTTCAAGGGCACATCATTTAC
*
1313168 AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGC
131 AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGACTACGCTCAGC
*
1313233 TCCAAGGCATATCATTTGTAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAAC
196 TCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAAC
* * * *
1313287 CAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACAACATTTGTAGCATAGCTTAAGTCT
1 CAAAGACCTTCGAGTTCGATTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTCA
* * *
1313352 AGAAGTGTTATCTTCCAAAGACCCTCGAGTTTAATTACACTCAGCTTCAAGGGCACATCATTTAC
66 AGAAGGGTTATCTACCAAAGACCCTCGAGTTTGATTACACTCAGCTTCAAGGGCACATCATTTAC
* * * *
1313417 -GACATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTTGACTTCACTCAG
131 AG-CATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGACTACGCTCAG
* * * * *
1313480 CTCAAAGGCACCATCATTTGCAGCATAGCTCAAG-CTAAGAAGGGCTATCT----AC
195 CTCCAAGGCA-TATCATTTGCAGCATAACTTAAGTC-AAGAAGGGTTATCTGCCAAC
1313532 CAAAGACCTTCGAGTTCGATT
1 CAAAGACCTTCGAGTTCGATT
1313553 CCGTTCAGGG
Statistics
Matches: 473, Mismatches: 37, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
245 23 0.05
248 36 0.08
249 340 0.72
252 3 0.01
253 69 0.15
254 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (249 bp):
CAAAGACCTTCGAGTTCGATTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTCA
AGAAGGGTTATCTACCAAAGACCCTCGAGTTTGATTACACTCAGCTTCAAGGGCACATCATTTAC
AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGACTACGCTCAGC
TCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAAC
Found at i:1313457 original size:333 final size:328
Alignment explanation
Indices: 1312785--1313550 Score: 848
Period size: 333 Copynumber: 2.3 Consensus size: 328
1312775 TTATGCCCAT
* * * * * *
1312785 CAAAGACCTTCGAGTTTGACTACGCTCAGCTCAAAGGCACAAT-ATTTGCAGCATAGCTTAAGTC
1 CAAAGACCTTCGAGTTTGATTACACTCAGCTCAAGGGAAC-ATCATTTGCAGCATAGCTCAAGGC
* * ** * * * * *
1312849 AAGAAGGGTTATCTGCCAACTGAAGACCATCGGGTTCGATTACACTCAGCTTCGAGGGCATATCA
65 TAGAAGGGTTATCTG--TACCAAAGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCATATCA
* ** *
1312914 TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGACTACGC
128 TTTACAGCATAACTCAAGGCAAGAAGGGTTATCTGCAACCAAAAGACCTTCGAGTTCGACTACGC
* *
1312979 TCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA
193 TCAGCTCCAAGGCACAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT--C-ACCAAAGA
* * * * * ** * *
1313044 CCTTTGAGTTCGATTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGTTTAAGTCAAGAAGG
255 CCCTCGAGTTCAATTACACTCAGCTTCAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGG
*
1313109 GCTATCTAC
320 GCTATCTAA
* * *
1313118 CAAAGACCCTCGAGTTTGATTACACTCAGCTTCAAGGGAACATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTTGATTACACTCAGC-TCAAGGGAACATCATTTGCAGCATAGCTCAAGGC
*
1313183 TAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCA
65 TAGAAGGGTTATCTGT-ACC-AAAGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCATATCA
** * * *
1313247 TTTGTAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGATTACG
128 TTTACAGCATAACTCAAGGCAAGAAGGGTTATCTG-CAACCAAAAGACCTTCGAGTTCGACTACG
* * * * *
1313311 CTCAGCTCCAAGGCACAACATTTGTAGCATAGCTTAAGTCTAGAAGTGTTATCT-TCCAAAGACC
192 CTCAGCTCCAAGGCACAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTCACCAAAGACC
* *
1313375 CTCGAGTTTAATTACACTCAGCTTCAAGGGCACATCATTTAC-GACATAACTCAAGGCTAGAAGG
257 CTCGAGTTCAATTACACTCAGCTTCAA-GGCACATCATTTACAG-CATAACTCAAGGCAAGAAGG
*
1313439 GTTATCTGTCAA
320 GCTATC--T-AA
* *
1313451 CAAAGACCTTCGAGTTTGACTT-CACTCAGCTCAAAGGCACCATCATTTGCAGCATAGCTCAA-G
1 CAAAGACCTTCGAGTTTGA-TTACACTCAGCTC-AAGGGAACATCATTTGCAGCATAGCTCAAGG
*
1313514 CTAAGAAGGGCTATC--TACCAAAGACCTTCGAGTTCGA
64 CT-AGAAGGGTTATCTGTACCAAAGACCTTCGAGTTCGA
1313551 TTCCGTTCAG
Statistics
Matches: 366, Mismatches: 54, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
329 50 0.14
330 36 0.10
331 1 0.00
332 6 0.02
333 205 0.56
334 68 0.19
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (328 bp):
CAAAGACCTTCGAGTTTGATTACACTCAGCTCAAGGGAACATCATTTGCAGCATAGCTCAAGGCT
AGAAGGGTTATCTGTACCAAAGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCATATCATTT
ACAGCATAACTCAAGGCAAGAAGGGTTATCTGCAACCAAAAGACCTTCGAGTTCGACTACGCTCA
GCTCCAAGGCACAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTCACCAAAGACCCTCG
AGTTCAATTACACTCAGCTTCAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGGGCTATC
TAA
Found at i:1313916 original size:16 final size:16
Alignment explanation
Indices: 1313891--1313963 Score: 52
Period size: 16 Copynumber: 4.8 Consensus size: 16
1313881 GTCTACAAAA
1313891 ATAT-TTTATTATATT
1 ATATATTTATTATATT
1313906 ATATATTTATT-TATT
1 ATATATTTATTATATT
*
1313921 -TATTGATTTATT-GATT
1 ATA-T-ATTTATTATATT
*
1313937 AT-TA-TTAATATATT
1 ATATATTTATTATATT
1313951 AT-TATTTTATTAT
1 ATATA-TTTATTAT
1313964 TTTTAAAGGC
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
13 4 0.09
14 10 0.21
15 10 0.21
16 22 0.47
17 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
ATATATTTATTATATT
Found at i:1313959 original size:29 final size:32
Alignment explanation
Indices: 1313892--1313962 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 32
1313882 TCTACAAAAA
* * *
1313892 TATTTTATTATATTATATATTTATTTATTTAT
1 TATTTTATTAGATTATATATTAATATATTTAT
1313924 TGA-TTTATT-GATTAT-TATTAATATA-TTAT
1 T-ATTTTATTAGATTATATATTAATATATTTAT
1313953 TATTTTATTA
1 TATTTTATTA
1313963 TTTTTAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
28 1 0.03
29 11 0.33
30 8 0.24
31 5 0.15
32 7 0.21
33 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (32 bp):
TATTTTATTAGATTATATATTAATATATTTAT
Found at i:1314060 original size:33 final size:33
Alignment explanation
Indices: 1314023--1314086 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
1314013 TAAACCAACG
1314023 TATTTGAGTCCTATTAAAACACTAAAACTGACA
1 TATTTGAGTCCTATTAAAACACTAAAACTGACA
* *
1314056 TATTTGAGTCTTATTGAAACACTAAAACTGA
1 TATTTGAGTCCTATTAAAACACTAAAACTGA
1314087 AGCATTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (33 bp):
TATTTGAGTCCTATTAAAACACTAAAACTGACA
Found at i:1314448 original size:32 final size:29
Alignment explanation
Indices: 1314411--1314495 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 29
1314401 TTTAATATTT
*
1314411 TTTATTTCTTTTTACATTGTTTTATATATATA
1 TTTATTTATTTTTACATT-TTTTAT-TA-ATA
*
1314443 TTTATTTATTTTTTCATTTTTTATTAATA
1 TTTATTTATTTTTACATTTTTTATTAATA
* * *
1314472 -TTA-TTATATTAATATTTTTTATTA
1 TTTATTTATTTTTACATTTTTTATTA
1314496 TTCTTTTCTC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
27 17 0.36
28 3 0.06
29 3 0.06
30 2 0.04
31 6 0.13
32 16 0.34
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (29 bp):
TTTATTTATTTTTACATTTTTTATTAATA
Found at i:1316611 original size:16 final size:15
Alignment explanation
Indices: 1316590--1316628 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1316580 TTTTATAGTA
1316590 AATATTTATTAATTTT
1 AATATTTA-TAATTTT
*
1316606 AATATTTATATTTTT
1 AATATTTATAATTTT
1316621 ATATATTT
1 A-ATATTT
1316629 TATCAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
AATATTTATAATTTT
Found at i:1316652 original size:13 final size:13
Alignment explanation
Indices: 1316634--1316660 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1316624 TATTTTATCA
1316634 AATAAATAATAGT
1 AATAAATAATAGT
1316647 AATAAATAATAGT
1 AATAAATAATAGT
1316660 A
1 A
1316661 TTTTTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (13 bp):
AATAAATAATAGT
Found at i:1319543 original size:81 final size:81
Alignment explanation
Indices: 1319449--1321669 Score: 3191
Period size: 81 Copynumber: 27.4 Consensus size: 81
1319439 AATTCCAAAA
* * * * *
1319449 TAAAAGATTAATGGCCTAGCTATGCATTTGACAAAAAGGTGTCAATTATGCCAATTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1319514 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * * *
1319530 TAAAATATTAATGGCCTAGCTGTGCAATTGGTAGAAATGTGTCAATTATGCTAGTTAAATGAAAT
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1319595 GTTAAATAACTTTGAG
66 GTTAAATACCTTTGAG
* * *
1319611 TAACAGATTAATGGCCTAGTTGTGAATTTGGCAGAAAGGTTTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
1319676 GTTAAATACCTTTCAA
66 GTTAAATACCTTTGAG
* * * *
1319692 TAAAAGATTAATGGCCTAGTTGTGCATTTGGAAAAAATGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1319757 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
1319773 TAAAATATTATTAGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATCAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
1319838 GTTAAATATCGTTGAG
66 GTTAAATACCTTTGAG
* * * * * * * *
1319854 TAAAATATTAATGGCCTAGCTGTGCAATTGGTAGAAATGTGTCAATTATGCTAGTTAAATGAAAT
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1319919 GTTAAATAACTTTGAG
66 GTTAAATACCTTTGAG
1319935 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
1320000 GTTAAATACCTTTCAA
66 GTTAAATACCTTTGAG
* *
1320016 TAAAAGATTAATGGCCTAGTTGTGCATTTGGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGG-CAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
*
1320081 GGTTAAATATCTTTGAG
65 GGTTAAATACCTTTGAG
* * *
1320098 TAAAATATTAATTGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATCAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
1320163 GTTAAATATCGTTGAG
66 GTTAAATACCTTTGAG
* * * * * * * * *
1320179 TAAAATATTAATGGCCAAGCTGTGCAATTGGTAGAAATGTGTCAATTATGCTAGTTAAATGAAAT
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1320244 GTTAAATAACTTTGAG
66 GTTAAATACCTTTGAG
* *
1320260 TGAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAATTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
1320325 GTTAAATACCTTTCAA
66 GTTAAATACCTTTGAG
* * *
1320341 TAAAAGATTAATGGCCTAGTTGTGCATTTGGAAAAAAGGTTTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1320406 GTTAAATACCATTGAG
66 GTTAAATACCTTTGAG
* * *
1320422 TAAAATATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATCAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * *
1320487 TTTAAATATCGTTGAG
66 GTTAAATACCTTTGAG
* * * * *
1320503 TAAAATATTAATGGCCTAGTTGTGCATTTCGCAAAAAGATGTCAATTATGCCATTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1320568 GTTAAATACTTTTGAG
66 GTTAAATACCTTTGAG
* * *
1320584 TAAACGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1320649 GTTAAATAACTTTGAG
66 GTTAAATACCTTTGAG
*
1320665 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1320730 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * *
1320746 TAAAAGATTAATGGCATAGTTGTGCATTTGACAAAAAAGTGTCAATTATGCTAGTTAAATGAAAT
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1320811 GTTAAATAACTTTGAG
66 GTTAAATACCTTTGAG
* * **
1320827 TAAAATATTAATGGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
1320892 GTTAAATACCTTTCAA
66 GTTAAATACCTTTGAG
* *
1320908 TAAAAGATTAATGGCCTAGTTGTGCATTTGGAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1320973 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
1320989 TAAAATATTAATGACCTAGTTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATCAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
1321054 GTTAAATATCGTTGAG
66 GTTAAATACCTTTGAG
* * * * *
1321070 TAAAATATTAATGACCTAGCTGTGCATTTCGCAGAAAGGTGTCAATTATGCCATTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
1321135 GTTACATACTTTTGAG
66 GTTAAATACCTTTGAG
* * *
1321151 TAAAATATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1321216 GTTAAATAACTTTGAG
66 GTTAAATACCTTTGAG
* * *
1321232 TAAAGGATTAATGGCCTAGTTGTGTATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1321297 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
1321313 TAAACGATTAATGGCCTAGTTGTGCATTTGGCAAAAAAAGTGTCAATTATACCAGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGC-AGAAAGGTGTCAATTATGCCAGTTAGATGAAA
1321378 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * *
1321395 TAAAATATTAATGGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1321460 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
1321476 TAAAAGATTAATGGCCTAGTTGTACATTTGGCAGAAAGTTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
1321541 GTTAAATACATTTGAG
66 GTTAAATACCTTTGAG
* * *
1321557 TAAAATATTAATGGCCTAGTTGTGCATTTGGCAAAAAGGTGTCAATTATGCCAGTTAGATGGAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1321622 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
1321638 TAAAATATTAATAGCCTAGCTGTGCAATTGGC
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGC
1321670 CTGGTTGCAT
Statistics
Matches: 1902, Mismatches: 236, Indels: 4
0.89 0.11 0.00
Matches are distributed among these distances:
81 1755 0.92
82 147 0.08
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:1328730 original size:83 final size:84
Alignment explanation
Indices: 1328574--1328735 Score: 182
Period size: 83 Copynumber: 1.9 Consensus size: 84
1328564 AGGACTCTTG
* * ** * * * *
1328574 TCTTGTGGTATCGATACTTCCATGAGTATCTGTACCAAAAATGCATTAAATATTTTGGAAATTAT
1 TCTTGTGGTATCGATACTCCCATGAGTACCAATACCAAAAATACATTAAATATTTTGAAAAATAC
*
1328639 CTCAGTATCTATACTCCCC
66 CTCAGTATCGATACTCCCC
* * * * *
1328658 TCTTG-GGTATCGATACTCCCTTGAGTACCAATACCAAAATTACTTTCAATTTTTTGAAAAATAC
1 TCTTGTGGTATCGATACTCCCATGAGTACCAATACCAAAAATACATTAAATATTTTGAAAAATAC
*
1328722 CTCGGTATCGATAC
66 CTCAGTATCGATAC
1328736 CCCTATGGGG
Statistics
Matches: 63, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
83 58 0.92
84 5 0.08
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (84 bp):
TCTTGTGGTATCGATACTCCCATGAGTACCAATACCAAAAATACATTAAATATTTTGAAAAATAC
CTCAGTATCGATACTCCCC
Found at i:1334047 original size:17 final size:17
Alignment explanation
Indices: 1334018--1334050 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1334008 ATCCTAATAT
1334018 GAAAATGAATCTCAACA
1 GAAAATGAATCTCAACA
1334035 GAAAA-GAATTCTCAAC
1 GAAAATGAA-TCTCAAC
1334051 TTAATGCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (17 bp):
GAAAATGAATCTCAACA
Found at i:1349564 original size:16 final size:17
Alignment explanation
Indices: 1349538--1349570 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1349528 AATTTTAGTA
1349538 ATCCGAAAATTTCGGAT
1 ATCCGAAAATTTCGGAT
1349555 ATCC-AAAATTTCGGAT
1 ATCCGAAAATTTCGGAT
1349571 CAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (17 bp):
ATCCGAAAATTTCGGAT
Found at i:1351931 original size:19 final size:20
Alignment explanation
Indices: 1351887--1351931 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1351877 ATTTGTTTTT
*
1351887 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
1351907 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
1351926 AATAAA
1 AATAAA
1351932 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:1377268 original size:98 final size:97
Alignment explanation
Indices: 1377148--1377919 Score: 685
Period size: 98 Copynumber: 7.8 Consensus size: 97
1377138 CTAATATTTA
* * * *
1377148 ATAATATAAATTGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAAAGTTACCTAGTACGT
1 ATAATATAAA-GGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAAAGCTACCTACTACAT
* * *
1377213 TATCATGAGCAACATGTTTGGTCTTACTTTTTC
65 TATCATGAGAAACATGTTTTGTCTTACTTTTGC
* * * ** *
1377246 ATAATATAGCAGGTTTCATACTTATAGCTTAAACTGTTGACATAAAAAAGTGTTACCTACTACAT
1 ATAATATA-AAGGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAAAGCTACCTACTACAT
*
1377311 TAACATGAGAAACATGTTTTGTCTTACTTTTGC
65 TATCATGAGAAACATGTTTTGTCTTACTTTTGC
** ** *
1377344 ATAATATAAACGGTTTCATACTTATAACTTAAATTGTTGACATAATAAAAGGCGCTACCAACTAC
1 ATAATATAAA-GGTTTCATACTTATAACTTAAACGGTTGACATAA-AAAA-AAGCTACCTACTAC
* * * *
1377409 GTTATCATGAAAAACTTGTTTTGTCTTACTTTTGT
63 ATTATCATGAGAAACATGTTTTGTCTTACTTTTGC
* * * *
1377444 ATAATATAAACGATTTCATACTTATCACTTAAACGATTGACATTAAAAAAAAAGACGCTACCTAA
1 ATAATATAAA-GGTTTCATACTTATAACTTAAACGGTTGACA-T--AAAAAAA-A-GCTACCTAC
** * * * *
1377509 TATGTTATCATGAGCAACCTATTTTCTCTTACTTTTGC
60 TACATTATCATGAGAAACATGTTTTGTCTTACTTTTGC
** * *
1377547 ATAATATAAACGGTTTCATACTTATAACTTAAATTGTTGACAT--AAAAACGTTACCTACTACAT
1 ATAATATAAA-GGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAAAGCTACCTACTACAT
* * *
1377610 TATCGTGAAAAACTTGTTTTGTCTTACTTTTGC
65 TATCATGAGAAACATGTTTTGTCTTACTTTTGC
* * ***
1377643 ATAATATAAGCGGTTTCATTA-TTATAATTTAAACAACTGACATTATAAAAAAAGACGCTACCTA
1 ATAATATAA-AGGTTTCA-TACTTATAACTTAAACGGTTGAC---ATAAAAAAA-A-GCTACCTA
* * * *
1377707 GTACATTATCATGAGCAACATGTTTTTTCTTGCTTTTGC
59 CTACATTATCATGAGAAACATGTTTTGTCTTACTTTTGC
* * * * * *
1377746 ATAATATAAACG-ATCATACTTATAATTTAAATGGTTGACAT-AAAAAAGGCGATGTCC-ACTAC
1 ATAATATAAAGGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAAAGC--T-ACCTACTAC
* * * *
1377808 GTTATCATGAGAAACTTGTTTTGTCATAATTTTGC
63 ATTATCATGAGAAACATGTTTTGTCTTACTTTTGC
* * *
1377843 ATCATATAAAAAGTTGT-ATACTTATAACTTAAACGATTGACATTAAAAAAAGATGCTACCTACT
1 ATAATAT-AAAGGTT-TCATACTTATAACTTAAACGGTTGACA-TAAAAAAA-A-GCTACCTACT
*
1377907 ACATTATCGTGAG
61 ACATTATCATGAG
1377920 CATAACAAAA
Statistics
Matches: 547, Mismatches: 97, Indels: 57
0.78 0.14 0.08
Matches are distributed among these distances:
95 2 0.00
96 68 0.12
97 48 0.09
98 137 0.25
99 29 0.05
100 84 0.15
101 46 0.08
102 6 0.01
103 127 0.23
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (97 bp):
ATAATATAAAGGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAAAGCTACCTACTACATT
ATCATGAGAAACATGTTTTGTCTTACTTTTGC
Found at i:1377701 original size:199 final size:201
Alignment explanation
Indices: 1377148--1377921 Score: 878
Period size: 199 Copynumber: 3.9 Consensus size: 201
1377138 CTAATATTTA
** * ** *
1377148 ATAATATAAATTGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAAAGTTACCTAGTACGT
1 ATAATATAAACGGTTTCATACTTATAACTTAAATGGTTGACATAAAAAAGCGTTACCTACTACGT
** * * * *
1377213 TATCATGAGCAACATGTTTGGTCTTACTTTTTCATAATAT-AGCAGGTTTCATACTTATAGCTTA
66 TATCATGAAAAACTTGTTTTGTCTTACTTTTGCATAATATAAGC-GGTTTCATACTTATAACTTA
** * * * * * *
1377277 AACTGTTGAC---AT-AAAAAAG-TGTTACCTACTACATTAACATGAGAAACATGTTTTGTCTTA
130 AACAATTGACATTATAAAAAAAGACGCTACCTAATACATTATCATGAGCAACATGTTTTCTCTTA
1377337 CTTTTGC
195 CTTTTGC
* * *
1377344 ATAATATAAACGGTTTCATACTTATAACTTAAATTGTTGACATAATAAAAGGCGCTACCAACTAC
1 ATAATATAAACGGTTTCATACTTATAACTTAAATGGTTGACATAA-AAAA-GCGTTACCTACTAC
* * * *
1377409 GTTATCATGAAAAACTTGTTTTGTCTTACTTTTGTATAATATAAACGATTTCATACTTATCACTT
64 GTTATCATGAAAAACTTGTTTTGTCTTACTTTTGCATAATATAAGCGGTTTCATACTTATAACTT
* * ** * *
1377474 AAACGATTGACATTAAAAAAAAAGACGCTACCTAATATGTTATCATGAGCAACCTATTTTCTCTT
129 AAACAATTGACATTATAAAAAAAGACGCTACCTAATACATTATCATGAGCAACATGTTTTCTCTT
1377539 ACTTTTGC
194 ACTTTTGC
* *
1377547 ATAATATAAACGGTTTCATACTTATAACTTAAATTGTTGACAT-AAAAA-CGTTACCTACTACAT
1 ATAATATAAACGGTTTCATACTTATAACTTAAATGGTTGACATAAAAAAGCGTTACCTACTACGT
* *
1377610 TATCGTGAAAAACTTGTTTTGTCTTACTTTTGCATAATATAAGCGGTTTCATTA-TTATAATTTA
66 TATCATGAAAAACTTGTTTTGTCTTACTTTTGCATAATATAAGCGGTTTCA-TACTTATAACTTA
* * * *
1377674 AACAACTGACATTATAAAAAAAGACGCTACCTAGTACATTATCATGAGCAACATGTTTTTTCTTG
130 AACAATTGACATTATAAAAAAAGACGCTACCTAATACATTATCATGAGCAACATGTTTTCTCTTA
1377739 CTTTTGC
195 CTTTTGC
* *
1377746 ATAATATAAAC-G-ATCATACTTATAATTTAAATGGTTGACATAAAAAAGGCGATGT-CC-ACTA
1 ATAATATAAACGGTTTCATACTTATAACTTAAATGGTTGACATAAAAAA-GCG-T-TACCTACTA
* * * * ***
1377807 CGTTATCATGAGAAACTTGTTTTGTCATAATTTTGCATCATATAAAAAGTTGT-ATACTTATAAC
63 CGTTATCATGAAAAACTTGTTTTGTCTTACTTTTGCATAATATAAGCGGTT-TCATACTTATAAC
* * * *
1377871 TTAAACGATTGACA-T-TAAAAAAAGATGCTACCTACTACATTATCGTGAGCA
127 TTAAACAATTGACATTATAAAAAAAGACGCTACCTAATACATTATCATGAGCA
1377922 TAACAAAATA
Statistics
Matches: 493, Mismatches: 69, Indels: 30
0.83 0.12 0.05
Matches are distributed among these distances:
196 41 0.08
197 30 0.06
198 109 0.22
199 145 0.29
200 69 0.14
201 9 0.02
202 9 0.02
203 81 0.16
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (201 bp):
ATAATATAAACGGTTTCATACTTATAACTTAAATGGTTGACATAAAAAAGCGTTACCTACTACGT
TATCATGAAAAACTTGTTTTGTCTTACTTTTGCATAATATAAGCGGTTTCATACTTATAACTTAA
ACAATTGACATTATAAAAAAAGACGCTACCTAATACATTATCATGAGCAACATGTTTTCTCTTAC
TTTTGC
Found at i:1377831 original size:399 final size:398
Alignment explanation
Indices: 1377148--1377893 Score: 997
Period size: 399 Copynumber: 1.9 Consensus size: 398
1377138 CTAATATTTA
** * *
1377148 ATAATATAAATTGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAAAGTTACCTAGTACGT
1 ATAATATAAACGGTTTCATACTTATAACTTAAACGGTTGACAT-AAAAAAAGTTACCTACTACAT
** * *
1377213 TATCATGAGCAACATGTTTGGTCTTACTTTTTCATAATATAGCAGGTTTCATACTTATAGCTTAA
65 TATCATGAAAAACATGTTTGGTCTTACTTTTGCATAATATAGCAGGTTTCATACTTATAACTTAA
*** * *
1377278 ACTGTTGACATAAAAAAGTGTTACCTACTACATTAACATGAGAAACATGTTTTGTCTTACTTTTG
130 ACAACTGACATAAAAAAGCGCTACCTACTACATTAACATGAGAAACATGTTTTGTCTTACTTTTG
* * *
1377343 CATAATATAAACGGTTTCATACTTATAACTTAAATTGTTGACATAATAAAAGGCGCTACCAACTA
195 CATAATATAAACGGTATCATACTTATAACTTAAATGGTTGACATAATAAAAGGCGATACCAACTA
* * * * *
1377408 CGTTATCATGAAAAACTTGTTTTGTCTTACTTTTGTATAATAT-AAACGATT-TCATACTTATCA
260 CGTTATCATGAAAAACTTGTTTTGTCATAATTTTGCATAATATAAAAAG-TTGT-ATACTTATAA
1377471 CTTAAACGATTGACATTAAAAAAAAAGACGCTACCTAATATGTTATCATGAGCAACCTATTTTCT
323 CTTAAACGATTGACATTAAAAAAAAAGACGCTACCTAATATGTTATCATGAGCAACCTATTTTCT
1377536 CTTACTTTTGC
388 CTTACTTTTGC
** *
1377547 ATAATATAAACGGTTTCATACTTATAACTTAAATTGTTGACAT-AAAAACGTTACCTACTACATT
1 ATAATATAAACGGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAAGTTACCTACTACATT
* * * *
1377611 ATCGTGAAAAACTTGTTTTGTCTTACTTTTGCATAATATAAGC-GGTTTCATTA-TTATAATTTA
66 ATCATGAAAAACATGTTTGGTCTTACTTTTGCATAATAT-AGCAGGTTTCA-TACTTATAACTTA
* * * * *
1377674 AACAACTGACATTATAAAAAAAGACGCTACCTAGTACATTATCATGAGCAACATGTTTTTTCTTG
129 AACAACTGAC---AT-AAAAAAG-CGCTACCTACTACATTAACATGAGAAACATGTTTTGTCTTA
* *
1377739 CTTTTGCATAATATAAAC-G-ATCATACTTATAATTTAAATGGTTGACATAA-AAAAGGCGATGT
189 CTTTTGCATAATATAAACGGTATCATACTTATAACTTAAATGGTTGACATAATAAAAGGCGAT-A
* *
1377801 CC-ACTACGTTATCATGAGAAACTTGTTTTGTCATAATTTTGCATCATATAAAAAGTTGTATACT
253 CCAACTACGTTATCATGAAAAACTTGTTTTGTCATAATTTTGCATAATATAAAAAGTTGTATACT
1377865 TATAACTTAAACGATTGACATTAAAAAAA
318 TATAACTTAAACGATTGACATTAAAAAAA
1377894 GATGCTACCT
Statistics
Matches: 300, Mismatches: 37, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
397 73 0.24
398 5 0.02
399 125 0.42
400 37 0.12
401 8 0.03
402 52 0.17
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (398 bp):
ATAATATAAACGGTTTCATACTTATAACTTAAACGGTTGACATAAAAAAAGTTACCTACTACATT
ATCATGAAAAACATGTTTGGTCTTACTTTTGCATAATATAGCAGGTTTCATACTTATAACTTAAA
CAACTGACATAAAAAAGCGCTACCTACTACATTAACATGAGAAACATGTTTTGTCTTACTTTTGC
ATAATATAAACGGTATCATACTTATAACTTAAATGGTTGACATAATAAAAGGCGATACCAACTAC
GTTATCATGAAAAACTTGTTTTGTCATAATTTTGCATAATATAAAAAGTTGTATACTTATAACTT
AAACGATTGACATTAAAAAAAAAGACGCTACCTAATATGTTATCATGAGCAACCTATTTTCTCTT
ACTTTTGC
Found at i:1387579 original size:27 final size:27
Alignment explanation
Indices: 1387523--1387579 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
1387513 AATATAATCG
* * *
1387523 TTTTACACTTCAAGGGTATTTTGGTTA
1 TTTTACACTCCAAGGGAATTTTGGTAA
*
1387550 TTTTACACTCCAGGGGCAATTTT-GTAA
1 TTTTACACTCCAAGGG-AATTTTGGTAA
1387577 TTT
1 TTT
1387580 CATAATCAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.46
Consensus pattern (27 bp):
TTTTACACTCCAAGGGAATTTTGGTAA
Found at i:1388218 original size:29 final size:29
Alignment explanation
Indices: 1388128--1388219 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
1388118 TGGCTTCTTT
**
1388128 GTCAAAGTCAAT-GGTCAACAATTAGACCG
1 GTCAAAGTC-ATCGGTCAACGGTTAGACCG
* *
1388157 GTCAAAGTCATCGGTCAACGGTCT-GATCA
1 GTCAAAGTCATCGGTCAACGGT-TAGACCG
*
1388186 GTCAAATTCGA-CGGTCAACGGTTAGACCG
1 GTCAAAGTC-ATCGGTCAACGGTTAGACCG
1388215 GTCAA
1 GTCAA
1388220 CAATAAACGA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
28 3 0.06
29 47 0.90
30 2 0.04
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.22
Consensus pattern (29 bp):
GTCAAAGTCATCGGTCAACGGTTAGACCG
Found at i:1396857 original size:109 final size:104
Alignment explanation
Indices: 1396657--1396871 Score: 340
Period size: 109 Copynumber: 2.0 Consensus size: 104
1396647 GTCAAATAAT
* *
1396657 AACACTCTCTATATTACTATTTTTTTTAATTAGATGTGTATTTTATCAAACTAGGAATTATATAT
1 AACACTCTCTAAATTACTATTATTTTTAATTAGATGTGTATTTTATCAAACTAGGAATTATATAT
* *
1396722 ACATTTGTGTTTGATTGGGTTGAATACAAATTTTATCTC
66 AAATTTGTGTTTGATTGGGTGGAATACAAATTTTATCTC
*
1396761 AACACTCTCTAAATTATTATTATTTTTAATTAGATGTGTATTTTATCAAATACAATTAGGAATTA
1 AACACTCTCTAAATTACTATTATTTTTAATTAGATGTGTATTTTATC-AA-AC---TAGGAATTA
1396826 TATATAAATTTGTGTTTGATTGGGTGGAATACAAATTTTATCTC
61 TATATAAATTTGTGTTTGATTGGGTGGAATACAAATTTTATCTC
1396870 AA
1 AA
1396872 AAGACAATGT
Statistics
Matches: 101, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
104 44 0.44
105 2 0.02
106 2 0.02
109 53 0.52
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (104 bp):
AACACTCTCTAAATTACTATTATTTTTAATTAGATGTGTATTTTATCAAACTAGGAATTATATAT
AAATTTGTGTTTGATTGGGTGGAATACAAATTTTATCTC
Found at i:1402055 original size:37 final size:36
Alignment explanation
Indices: 1401980--1402055 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1401970 TTTTTATATT
*
1401980 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1402016 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1402053 TTT
1 TTT
1402056 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1404146 original size:15 final size:16
Alignment explanation
Indices: 1404114--1404155 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
1404104 GATTTCTTTA
1404114 TTATCTTATTTCATCTT
1 TTAT-TTATTTCATCTT
1404131 TTATTTATTT-ATCTT
1 TTATTTATTTCATCTT
*
1404146 TTGTTTATTT
1 TTATTTATTT
1404156 TATTCTAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 6 0.25
17 4 0.17
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTATTTCATCTT
Found at i:1404526 original size:11 final size:10
Alignment explanation
Indices: 1404510--1404555 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
1404500 TTTTTTTTTC
1404510 AAAAAAACAAA
1 AAAAAAAC-AA
1404521 AAAAAAACAA
1 AAAAAAACAA
**
1404531 AAAAAGGCAA
1 AAAAAAACAA
1404541 AAAAAAACAA
1 AAAAAAACAA
1404551 AAAAA
1 AAAAA
1404556 GAGCCAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 23 0.74
11 8 0.26
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:1404535 original size:20 final size:20
Alignment explanation
Indices: 1404509--1404557 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1404499 ATTTTTTTTT
*
1404509 CAAAAAAACA-AAAAAAAAA
1 CAAAAAAAGACAAAAAAAAA
*
1404528 CAAAAAAAGGCAAAAAAAAA
1 CAAAAAAAGACAAAAAAAAA
1404548 CAAAAAAAGA
1 CAAAAAAAGA
1404558 GCCAAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (20 bp):
CAAAAAAAGACAAAAAAAAA
Found at i:1404544 original size:12 final size:11
Alignment explanation
Indices: 1404510--1404566 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 11
1404500 TTTTTTTTTC
1404510 AAAAAAA-CAA
1 AAAAAAAGCAA
*
1404520 AAAAAAAAC-A
1 AAAAAAAGCAA
*
1404530 AAAAAAGGCAA
1 AAAAAAAGCAA
1404541 AAAAAAA-CAA
1 AAAAAAAGCAA
* *
1404551 AAAAAGAGCCA
1 AAAAAAAGCAA
1404562 AAAAA
1 AAAAA
1404567 GCCAAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 24 0.62
11 15 0.38
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAGCAA
Found at i:1404548 original size:31 final size:31
Alignment explanation
Indices: 1404510--1404573 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
1404500 TTTTTTTTTC
*
1404510 AAAAAAACAAAAAAAAAACAAAAAAAGGCAA
1 AAAAAAACAAAAAAAAAACAAAAAAAGCCAA
* * *
1404541 AAAAAAACAAAAAAAGAGCCAAAAAAGCCAA
1 AAAAAAACAAAAAAAAAACAAAAAAAGCCAA
1404572 AA
1 AA
1404574 TTTCAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.80, C:0.12, G:0.08, T:0.00
Consensus pattern (31 bp):
AAAAAAACAAAAAAAAAACAAAAAAAGCCAA
Found at i:1404564 original size:20 final size:20
Alignment explanation
Indices: 1404519--1404566 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1404509 CAAAAAAACA
1404519 AAAAAAAAACAAAAAAAGGC
1 AAAAAAAAACAAAAAAAGGC
1404539 AAAAAAAAACAAAAAAAGAGC
1 AAAAAAAAACAAAAAAAG-GC
*
1404560 CAAAAAA
1 AAAAAAA
1404567 GCCAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.81, C:0.10, G:0.08, T:0.00
Consensus pattern (20 bp):
AAAAAAAAACAAAAAAAGGC
Found at i:1408876 original size:15 final size:16
Alignment explanation
Indices: 1408844--1408885 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
1408834 GATTTCTTTA
1408844 TTATCTTATTTCATCTT
1 TTAT-TTATTTCATCTT
1408861 TTATTTATTT-ATCTT
1 TTATTTATTTCATCTT
*
1408876 TTGTTTATTT
1 TTATTTATTT
1408886 TATTCTAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 6 0.25
17 4 0.17
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTATTTCATCTT
Found at i:1409157 original size:21 final size:21
Alignment explanation
Indices: 1409116--1409159 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1409106 AATGATAGTT
*
1409116 TGTTGATGTAATAATTCATGA
1 TGTTGATGTAACAATTCATGA
1409137 TGTTGATGTAACAATAT-ATGA
1 TGTTGATGTAACAAT-TCATGA
1409158 TG
1 TG
1409160 AACAATGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (21 bp):
TGTTGATGTAACAATTCATGA
Found at i:1409205 original size:17 final size:17
Alignment explanation
Indices: 1409183--1409219 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1409173 TAGATGAACT
1409183 TAATTATTTTCTTTTAC
1 TAATTATTTTCTTTTAC
1409200 TAATTATTTTCTTTTAC
1 TAATTATTTTCTTTTAC
1409217 TAA
1 TAA
1409220 GTTTGAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTATTTTCTTTTAC
Found at i:1411245 original size:8 final size:8
Alignment explanation
Indices: 1411234--1411262 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1411224 ATAATTTAAG
1411234 TATGTATA
1 TATGTATA
1411242 TATGTATA
1 TATGTATA
1411250 TATGTATA
1 TATGTATA
1411258 TATGT
1 TATGT
1411263 GTGTGTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (8 bp):
TATGTATA
Found at i:1412150 original size:21 final size:19
Alignment explanation
Indices: 1412116--1412158 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
1412106 GAGAATTCAA
1412116 TTTTATTTAATTCATGATTCT
1 TTTTATTTAATTCA--ATTCT
**
1412137 TTTTATTTCTTTCAATTCT
1 TTTTATTTAATTCAATTCT
1412156 TTT
1 TTT
1412159 ATTATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
21 12 0.60
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTATTTAATTCAATTCT
Found at i:1415025 original size:2 final size:2
Alignment explanation
Indices: 1415018--1415044 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1415008 AAGAAATAAA
1415018 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1415045 AAAGAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1416355 original size:20 final size:20
Alignment explanation
Indices: 1416330--1416374 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1416320 AAATGAGACA
1416330 CCCTAAGGGAGTACCTTGGG
1 CCCTAAGGGAGTACCTTGGG
1416350 CCCTAAGGGAGTACCTTGGG
1 CCCTAAGGGAGTACCTTGGG
*
1416370 GCCTA
1 CCCTA
1416375 TGGGCCTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.27, G:0.33, T:0.20
Consensus pattern (20 bp):
CCCTAAGGGAGTACCTTGGG
Found at i:1416384 original size:20 final size:20
Alignment explanation
Indices: 1416330--1416384 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1416320 AAATGAGACA
*
1416330 CCCTAAGGGAGTACCTTGGG
1 CCCTAAGGGACTACCTTGGG
*
1416350 CCCTAAGGGAGTACCTTGGG
1 CCCTAAGGGACTACCTTGGG
* * *
1416370 GCCTATGGGCCTACC
1 CCCTAAGGGACTACC
1416385 CAAGGGTCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.18, C:0.29, G:0.33, T:0.20
Consensus pattern (20 bp):
CCCTAAGGGACTACCTTGGG
Found at i:1418084 original size:28 final size:29
Alignment explanation
Indices: 1418039--1418093 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
1418029 TTATATTTTC
*
1418039 TTCCATTTTTTTTAATTTGAG-ACCTTAG
1 TTCCATTTTATTTAATTTGAGTACCTTAG
1418067 TTCC-TTTTATTTACATTTGAGTACCTT
1 TTCCATTTTATTTA-ATTTGAGTACCTT
1418094 TTATTTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 11 0.46
29 5 0.21
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (29 bp):
TTCCATTTTATTTAATTTGAGTACCTTAG
Found at i:1418404 original size:8 final size:8
Alignment explanation
Indices: 1418391--1418419 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1418381 ATAATTTAAG
1418391 TATGTATA
1 TATGTATA
1418399 TATGTATA
1 TATGTATA
1418407 TATGTATA
1 TATGTATA
1418415 TATGT
1 TATGT
1418420 GTGTTCCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (8 bp):
TATGTATA
Found at i:1426744 original size:22 final size:21
Alignment explanation
Indices: 1426692--1426752 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1426682 TTTGGTGCAG
*
1426692 AGGGAATCGA-TCCCCCCATGA
1 AGGGAA-CGATTCCCCCTATGA
* *
1426713 TGGGAACGATTCCCCCTTTGA
1 AGGGAACGATTCCCCCTATGA
1426734 AGGGAACCGATTCCCCCTA
1 AGGGAA-CGATTCCCCCTA
1426753 CAGGGGAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 3 0.09
21 19 0.58
22 11 0.33
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.20
Consensus pattern (21 bp):
AGGGAACGATTCCCCCTATGA
Found at i:1430965 original size:24 final size:24
Alignment explanation
Indices: 1430933--1430986 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
1430923 CAGAAACTCG
1430933 AAAATTTGACT-CGACTCAACTCAA
1 AAAATTTGACTACG-CTCAACTCAA
* *
1430957 AAAATTTGACTATGCTCAACTCGA
1 AAAATTTGACTACGCTCAACTCAA
1430981 AAAATT
1 AAAATT
1430987 CTACGTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (24 bp):
AAAATTTGACTACGCTCAACTCAA
Found at i:1434976 original size:24 final size:24
Alignment explanation
Indices: 1434931--1434976 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1434921 GTTTAAAGAA
* * *
1434931 ATTTTAAGATTATTTTTAATTCGG
1 ATTTTAAAATTATATTCAATTCGG
*
1434955 ATTTTAAAATTATATTCGATTC
1 ATTTTAAAATTATATTCAATTC
1434977 AACCATTCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (24 bp):
ATTTTAAAATTATATTCAATTCGG
Found at i:1435722 original size:54 final size:53
Alignment explanation
Indices: 1435659--1435765 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
1435649 TCCCCCACTC
1435659 TTTTCGAGCAATGAAACAACAACAAATTTTTTTCTCTAATAATTTTTTTTCACA
1 TTTTCGAGCAATGAAACAACAACAAA-TTTTTTCTCTAATAATTTTTTTTCACA
1435713 TTTTCGAGCAATGAAACAACAACAAATTTTTTCTCTAATAATTTTTTTTCACA
1 TTTTCGAGCAATGAAACAACAACAAATTTTTTCTCTAATAATTTTTTTTCACA
1435766 AATTAAAAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 27 0.51
54 26 0.49
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (53 bp):
TTTTCGAGCAATGAAACAACAACAAATTTTTTCTCTAATAATTTTTTTTCACA
Found at i:1435784 original size:2 final size:2
Alignment explanation
Indices: 1435777--1435815 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1435767 ATTAAAAACC
1435777 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1435816 TTGAATGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1436246 original size:16 final size:16
Alignment explanation
Indices: 1436221--1436255 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1436211 CTAAAAAAAT
* *
1436221 AAAATGAAAAATGAAA
1 AAAATAAAAAAGGAAA
1436237 AAAATAAAAAAGGAAA
1 AAAATAAAAAAGGAAA
1436253 AAA
1 AAA
1436256 GATGATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (16 bp):
AAAATAAAAAAGGAAA
Found at i:1441271 original size:31 final size:31
Alignment explanation
Indices: 1441229--1441287 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1441219 TACATTTATC
*
1441229 TGAGACTCCAAAGTCATACCTTTACCTTTTT
1 TGAGACACCAAAGTCATACCTTTACCTTTTT
* *
1441260 TGAGACACCAAATTCATACTTTTACCTT
1 TGAGACACCAAAGTCATACCTTTACCTT
1441288 CTCGGGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (31 bp):
TGAGACACCAAAGTCATACCTTTACCTTTTT
Found at i:1442059 original size:15 final size:14
Alignment explanation
Indices: 1442038--1442175 Score: 58
Period size: 14 Copynumber: 9.7 Consensus size: 14
1442028 TAAAAAGGAG
1442038 AAAGAAGAAAATAA
1 AAAGAAGAAAATAA
*
1442052 AAACGAAGATGAA-AA
1 AAA-GAAGA-AAATAA
1442067 AAAG-AGAAAATAA
1 AAAGAAGAAAATAA
* *
1442080 AATAGAA-AAGATAG
1 AA-AGAAGAAAATAA
*
1442094 AAA-AAGAAAAGAGA
1 AAAGAAGAAAATA-A
*
1442108 AAATATAGAAGAA-AA
1 AAAGA-AGAA-AATAA
*
1442123 AGAA-AAGAAAAGAA
1 A-AAGAAGAAAATAA
*
1442137 AGAGGAA-AAAATAA
1 A-AAGAAGAAAATAA
*
1442151 AAA-AAGAAAAAAGAA
1 AAAGAAG--AAAATAA
1442166 AAAGAAGAAA
1 AAAGAAGAAA
1442176 GAAAATAAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 34
0.68 0.08 0.24
Matches are distributed among these distances:
12 6 0.06
13 15 0.16
14 35 0.36
15 26 0.27
16 12 0.12
17 2 0.02
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (14 bp):
AAAGAAGAAAATAA
Found at i:1442087 original size:22 final size:21
Alignment explanation
Indices: 1442062--1442179 Score: 77
Period size: 22 Copynumber: 5.4 Consensus size: 21
1442052 AAACGAAGAT
1442062 GAAAA-AAAGAGAAAATAAAATA
1 GAAAAGAAAGAGAAAA-AAAA-A
*
1442084 GAAAAGATAGA-AAAAGAAAAGA
1 GAAAAGAAAGAGAAAA-AAAA-A
* *
1442106 GAAAATATAGAAGAAAAAGAAAA
1 GAAAAGAAAG-AGAAAAA-AAAA
1442129 GAAAAGAAAGAGGAAAAAATAAA
1 GAAAAGAAAGA-GAAAAAA-AAA
1442152 -AAAAGAAA-A-AAGAAAAAGAA
1 GAAAAGAAAGAGAA-AAAAA-AA
1442172 G-AAAGAAA
1 GAAAAGAAA
1442180 ATAAATAAAG
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
19 3 0.04
20 13 0.16
21 1 0.01
22 33 0.41
23 24 0.30
24 7 0.09
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (21 bp):
GAAAAGAAAGAGAAAAAAAAA
Found at i:1442134 original size:35 final size:34
Alignment explanation
Indices: 1442066--1442182 Score: 109
Period size: 35 Copynumber: 3.4 Consensus size: 34
1442056 GAAGATGAAA
*
1442066 AAAAGAGAAAATA-AAATAGAAAAG-ATAGAAAAAG
1 AAAAGAGAAAATATAAA-A-AAAAGAAAAGAAAAAG
1442100 AAAAGAGAAAATATAGAAGAAAAAGAAAAG-AAAAG
1 AAAAGAGAAAATATA-AA-AAAAAGAAAAGAAAAAG
* *
1442135 -AAAGAGGAAAAAATAAAAAAAGAAAAAAGAAAAAG
1 AAAAGA-GAAAATATAAAAAAA-AGAAAAGAAAAAG
1442170 AAGAA-AGAAAATA
1 AA-AAGAGAAAATA
1442183 AATAAAGTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
33 4 0.06
34 26 0.37
35 30 0.43
36 8 0.11
37 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (34 bp):
AAAAGAGAAAATATAAAAAAAAGAAAAGAAAAAG
Found at i:1442147 original size:25 final size:24
Alignment explanation
Indices: 1442064--1442180 Score: 71
Period size: 25 Copynumber: 4.7 Consensus size: 24
1442054 ACGAAGATGA
* *
1442064 AAAAAAGAGAAAATAAAATAGAAAAG
1 AAAAAA-AGAAAAGAAAAGA-AAAAG
* *
1442090 ATAGAAAAAGAAAAGAGAAA-ATATAG
1 A-A-AAAAAGAAAAGA-AAAGAAAAAG
*
1442116 AAGAAAAAGAAAAGAAAAGAAAGAG
1 AA-AAAAAGAAAAGAAAAGAAAAAG
* *
1442141 GAAAAAA-TAAA-AAAAGAAAAAAG
1 AAAAAAAGAAAAGAAAAG-AAAAAG
1442164 AAAAAGAAG-AAAGAAAA
1 AAAAA-AAGAAAAGAAAA
1442181 TAAATAAAGT
Statistics
Matches: 74, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
22 5 0.07
23 12 0.16
24 13 0.18
25 23 0.31
26 5 0.07
27 9 0.12
28 7 0.09
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (24 bp):
AAAAAAAGAAAAGAAAAGAAAAAG
Found at i:1442152 original size:7 final size:7
Alignment explanation
Indices: 1442064--1442180 Score: 64
Period size: 7 Copynumber: 16.6 Consensus size: 7
1442054 ACGAAGATGA
1442064 AAAAAAG
1 AAAAAAG
* *
1442071 AGAAAAT
1 AAAAAAG
*
1442078 AAAATAG
1 AAAAAAG
1442085 AAAAGATAG
1 AAAA-A-AG
1442094 -AAAAAG
1 AAAAAAG
*
1442100 AAAAGAG
1 AAAAAAG
1442107 AAAATATAG
1 AAAA-A-AG
1442116 AAGAAAA-
1 AA-AAAAG
*
1442123 AGAAAAG
1 AAAAAAG
1442130 --AAAAG
1 AAAAAAG
* *
1442135 AAAGAGG
1 AAAAAAG
*
1442142 AAAAAATA
1 AAAAAA-G
1442150 AAAAAAG
1 AAAAAAG
1442157 AAAAAAG
1 AAAAAAG
1442164 -AAAAAG
1 AAAAAAG
*
1442170 AAGAAAG
1 AAAAAAG
1442177 AAAA
1 AAAA
1442181 TAAATAAAGT
Statistics
Matches: 82, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
5 5 0.06
6 12 0.15
7 46 0.56
8 10 0.12
9 7 0.09
10 2 0.02
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:1442189 original size:13 final size:12
Alignment explanation
Indices: 1442092--1442189 Score: 53
Period size: 11 Copynumber: 8.2 Consensus size: 12
1442082 TAGAAAAGAT
*
1442092 AGAAAAAGA-AA
1 AGAAAAAAATAA
*
1442103 AGAGAAAATATAGA
1 AGA-AAAAAATA-A
*
1442117 AGAAAAAGA-AA
1 AGAAAAAAATAA
* *
1442128 AGAAAAGAA-AG
1 AGAAAAAAATAA
*
1442139 AGGAAAAAATAA
1 AGAAAAAAATAA
1442151 A-AAAAGAAA-AA
1 AGAAAA-AAATAA
*
1442162 AGAAAAAGAAGAA
1 AGAAAAA-AATAA
1442175 AGAAAATAAATAA
1 AGAAAA-AAATAA
1442188 AG
1 AG
1442190 TATTTCAAGA
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
11 26 0.38
12 17 0.25
13 20 0.29
14 5 0.07
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (12 bp):
AGAAAAAAATAA
Found at i:1445741 original size:134 final size:135
Alignment explanation
Indices: 1445496--1446284 Score: 703
Period size: 134 Copynumber: 5.8 Consensus size: 135
1445486 AGAACAATGA
* * * *
1445496 AATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAAAAG-TAGAACAAAT-CC-TCTATTT
1 AATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAAAAGCGACAACATATCCCTTCTCTTT
* * *
1445558 TCAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATTCAATCTTTCCTGAGTGA
66 TAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTTCCTGAG-AA
1445623 TAGTGG
130 TAGTGG
* *
1445629 AATGAATCAACTCCCCCAGATATGATTTTCCCTCAAGAAGAAGCGA-AACATAT-CCTTCTCTTT
1 AATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAAAAGCGACAACATATCCCTTCTCTTT
* * * * * *
1445692 TTAGATTTGATATTCCCTGAGTAATAGTGGAATAAGTCTGCCTCGATTCAATCTTCCCTGAGTGA
66 TAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTTCCTGAG-AA
* *
1445757 CAGTTG
130 TAGTGG
* * * * *
1445763 AATGAATCAACTCCCCTATATCTAATTTTCACTCAAGAATAAA-C-ATAACATATCCC-TCTCTT
1 AATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAA-AAAGCGACAACATATCCCTTCTCTT
* * * * * * *
1445825 TTCATATTTGATATTCCCTGTGTGACAGTGGAATAAGTCTGCCTCGATTCAATC-TTCTGTGAAG
65 TTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTTC-CTG-AG
1445889 AATTA-TGG
128 AA-TAGTGG
* * * * * * * *
1445897 AATGAATTAACACCCTCAGATCTGATTTTTCATCAGGAAAAAGTG-GAACATATCCATCTTTTTC
1 AATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAAAAGCGACAACATATCC--C---TTC
* * * * * *
1445961 AATCTTTTTCAGGTTTGATATTCCCTGGGTAACAGTGGAACAAGCCTACCTTGATTCAATCTTCC
61 --TC-TTTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTTC
* *
1446026 CTGAAGAACAGTTG
123 CTG-AGAATAGTGG
* ** * * * * *
1446040 AATAAATCAACAT-TTCCAAATCTAATTTTCCCTCAAGAAGAAGCG-GAACAAATCCCTT-TCTT
1 AATGAATCAAC-TCCCCCAGATCTGATTTTCCCTCAAGAAAAAGCGACAACATATCCCTTCTCTT
* * *
1446102 TCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCTCGATTCAATCTTTCCTAAAGA
65 TTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTTCCT-GAGA
1446167 ATAGTGG
129 ATAGTGG
* * * * * * *
1446174 AATGAATCAACATCCCCC-TATCTGATTTTACCTCAGGAACAAGC-ACAATATGTCCCTTAT-TT
1 AATGAATCAAC-TCCCCCAGATCTGATTTTCCCTCAAGAAAAAGCGACAACATATCCCTTCTCTT
* * *
1446236 TCAAGATTTGATATTTCCTGAGTAACAGTGAAACAAGTCTACCTCGATT
65 TTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATT
1446285 TAATATTCCC
Statistics
Matches: 537, Mismatches: 93, Indels: 51
0.79 0.14 0.07
Matches are distributed among these distances:
133 55 0.10
134 362 0.67
135 12 0.02
136 1 0.00
138 2 0.00
140 2 0.00
141 1 0.00
142 3 0.01
143 97 0.18
144 2 0.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (135 bp):
AATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGAAAAAGCGACAACATATCCCTTCTCTTT
TAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTTCCTGAGAAT
AGTGG
Found at i:1446077 original size:277 final size:266
Alignment explanation
Indices: 1445466--1446314 Score: 840
Period size: 277 Copynumber: 3.1 Consensus size: 266
1445456 ACAAATTGAA
* * * * *
1445466 CTTGATTCAACCTTCCCTAAAGAACA-ATGAAATGAATCAACTCCCCCAGATCTGATTTTCCCTC
1 CTTGATTCAATCTTCCCTGAAGAACAGTTG-AATGAATCAACT-CCCCAAATCTAATTTTCCCTC
* *
1445530 AAGAAAAAGTAGAACAAAT-CCTCTATTTTCAGATTTGATATTCCCTGAGTGACAGTGGAACAAG
64 AAGAAAAA-CAGAACAAATCCCTCTCTTTTCAGATTTGATATTCCCTGAGTGACAGTGGAACAAG
* *
1445594 TCTACCTCGATTCAATCTTTCCTGAGTGATAGTGGAATGAATCAACTCCCCCAGATATGATTTTC
128 TCTACCTCGATTCAATCTTTCCTGAGTAATAGTGGAATGAATCAACACCCCCAGATATGATTTTC
* * *
1445659 CCTCAAGAAGAAGCGAAACATATCCTTCTCTTTTTAGATTTGATATTCCCTGAGTAATAGTGGAA
193 CATCAAGAAAAAGCGAAACATATCCTTCTCTTTTTAGATTTGATATTCCCTGAGTAACAGTGGAA
* * *
1445724 TAAGTCTGC
258 CAAGCCTAC
* * * *
1445733 CTCGATTCAATCTTCCCTG-AGTGACAGTTGAATGAATCAACTCCCCTATATCTAATTTTCACTC
1 CTTGATTCAATCTTCCCTGAAG-AACAGTTGAATGAATCAACTCCCC-AAATCTAATTTTCCCTC
* * * * *
1445797 AAGAATAAACATAACATATCCCTCTCTTTTCATATTTGATATTCCCTGTGTGACAGTGGAATAAG
64 AAGAA-AAACAGAACAAATCCCTCTCTTTTCAGATTTGATATTCCCTGAGTGACAGTGGAACAAG
* * * * *
1445862 TCTGCCTCGATTCAATC-TTCTGTGAAG-AATTA-TGGAATGAATTAACACCCTCAGATCTGATT
128 TCTACCTCGATTCAATCTTTC-CTG-AGTAA-TAGTGGAATGAATCAACACCCCCAGATATGATT
* * * * * *
1445924 TTTCATCAGGAAAAAGTGGAACATATCCATCTTTTTCAATCTTTTTCAGGTTTGATATTCCCTGG
190 TTCCATCAAGAAAAAGCGAAACATAT-C--C---TTC--TCTTTTT-AGATTTGATATTCCCTGA
1445989 GTAACAGTGGAACAAGCCTAC
246 GTAACAGTGGAACAAGCCTAC
* **
1446010 CTTGATTCAATCTTCCCTGAAGAACAGTTGAATAAATCAACATTTCCAAATCTAATTTTCCCTCA
1 CTTGATTCAATCTTCCCTGAAGAACAGTTGAATGAATCAAC-TCCCCAAATCTAATTTTCCCTCA
* * *
1446075 AGAAGAAGCGGAACAAATCCCTTTC-TTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAG
65 AGAA-AAACAGAACAAATCCCTCTCTTTTC-AGATTTGATATTCCCTGAGTGACAGTGGAACAAG
* * *
1446139 TCTACCTCGATTCAATCTTTCCTAAAG-AATAGTGGAATGAATCAACATCCCCC-TATCTGATTT
128 TCTACCTCGATTCAATCTTTCCT-GAGTAATAGTGGAATGAATCAACA-CCCCCAGATATGATTT
* * * * * ** *
1446202 TACC-TCAGGAACAAGC-ACAATATGTCCCTTAT-TTTCAAGATTTGATATTTCCTGAGTAACAG
191 T-CCATCAAGAAAAAGCGA-AACATAT-CCTTCTCTTTTTAGATTTGATATTCCCTGAGTAACAG
* *
1446264 TGAAACAAGTCTAC
253 TGGAACAAGCCTAC
* * * * * *
1446278 CTCGATTTAATATTCCCTAAAGAACAATGGAATGAAT
1 CTTGATTCAATCTTCCCTGAAGAACAGTTGAATGAAT
1446315 AAATGTTCCT
Statistics
Matches: 479, Mismatches: 77, Indels: 51
0.79 0.13 0.08
Matches are distributed among these distances:
266 6 0.01
267 60 0.13
268 175 0.37
269 8 0.02
270 1 0.00
271 1 0.00
272 2 0.00
274 3 0.01
275 1 0.00
276 13 0.03
277 196 0.41
278 13 0.03
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (266 bp):
CTTGATTCAATCTTCCCTGAAGAACAGTTGAATGAATCAACTCCCCAAATCTAATTTTCCCTCAA
GAAAAACAGAACAAATCCCTCTCTTTTCAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCT
ACCTCGATTCAATCTTTCCTGAGTAATAGTGGAATGAATCAACACCCCCAGATATGATTTTCCAT
CAAGAAAAAGCGAAACATATCCTTCTCTTTTTAGATTTGATATTCCCTGAGTAACAGTGGAACAA
GCCTAC
Found at i:1446333 original size:411 final size:411
Alignment explanation
Indices: 1445469--1446317 Score: 949
Period size: 411 Copynumber: 2.1 Consensus size: 411
1445459 AATTGAACTT
** * * * * * * *
1445469 GATTCAACCTTCCCTAAAGAACAATGAAATGAATCAACTCCCCCAGATCTGATTTTCCCTCAAGA
1 GATTCAATATTCCCTAAAGAACAATGGAATGAATAAACACCCTCAGATCTGATTTTTCATCAGGA
* * *
1445534 AAAAGTAGAACAAATCC-TC----T--A---TTTTCAGATTTGATATTCCCTGAGTGACAGTGGA
66 AAAAGTGGAACATATCCATCTTTTTCAATCTTTTTCAGATTTGATATTCCCTGAGTAACAGTGGA
* * * * * * *
1445589 ACAAGTCTACCTCGATTCAATCTTTCCTGAGTGATAGTGGAATGAATCAACTCCCCCAGATATGA
131 ACAAGCCTACCTCGATTCAATCTTCCCTGAGTAACAGTGGAATAAATCAACTCCCCCAAATATAA
* ** *
1445654 TTTTCCCTCAAGAAGAAGCGAAACATATCCTTCTCTTTTTAGATTTGATATTCCCTGAGTAATAG
196 TTTTCCCTCAAGAAGAAGCGAAACAAATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTAACAG
* * * * *
1445719 TGGAATAAGTCTGCCTCGATTCAATCTTCCCTGAGTGACAGTTGAATGAATCAACTCCCCTATAT
261 TGGAACAAGTCTACCTCGATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAACTCCCCTATAT
* * * * * *
1445784 CTAATTTTCACTCAAGAATAAACATAACATATCCCTCTCTTTTCATATTTGATATTCCCTGTGTG
326 CTAATTTTCACTCAAGAACAAACACAACATATCCCTCTATTTTCAGATTTGATATTCCCTGAGTA
* * *
1445849 ACAGTGGAATAAGTCTGCCTC
391 ACAGTGAAACAAGTCTACCTC
* ** * ** *
1445870 GATTCAATCTTCTGTGAAGAATTATGGAATGAATTAACACCCTCAGATCTGATTTTTCATCAGGA
1 GATTCAATATTCCCTAAAGAACAATGGAATGAATAAACACCCTCAGATCTGATTTTTCATCAGGA
* *
1445935 AAAAGTGGAACATATCCATCTTTTTCAATCTTTTTCAGGTTTGATATTCCCTGGGTAACAGTGGA
66 AAAAGTGGAACATATCCATCTTTTTCAATCTTTTTCAGATTTGATATTCCCTGAGTAACAGTGGA
* * ** *
1446000 ACAAGCCTACCTTGATTCAATCTTCCCTGAAG-AACAGTTGAATAAATCAACAT-TTCCAAATCT
131 ACAAGCCTACCTCGATTCAATCTTCCCTG-AGTAACAGTGGAATAAATCAAC-TCCCCCAAATAT
* *
1446063 AATTTTCCCTCAAGAAGAAGCGGAACAAATCCCTT-TCTTTCAAGATTTGATATTCCCTGAGTGA
194 AATTTTCCCTCAAGAAGAAGCGAAACAAAT-CCTTCTCTTTCAAGATTTGATATTCCCTGAGTAA
* *
1446127 CAGTGGAACAAGTCTACCTCGATTCAATCTTTCCTAAAG-AATAGTGGAATGAATCAACATCCCC
258 CAGTGGAACAAGTCTACCTCGATTCAATCTTCCCT-AAGTAACAGTGGAATGAATCAAC-TCCCC
* * * * * * *
1446191 -CTATCTGATTTT-ACCTCAGGAACAAGCACAATATGTCCCT-TATTTTCAAGATTTGATATTTC
321 TATATCTAATTTTCA-CTCAAGAACAAACACAACATATCCCTCTATTTTC-AGATTTGATATTCC
1446253 CTGAGTAACAGTGAAACAAGTCTACCTC
384 CTGAGTAACAGTGAAACAAGTCTACCTC
*
1446281 GATTTAATATTCCCTAAAGAACAATGGAATGAATAAA
1 GATTCAATATTCCCTAAAGAACAATGGAATGAATAAA
1446318 TGTTCCTCTA
Statistics
Matches: 364, Mismatches: 67, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
401 67 0.18
402 2 0.01
406 1 0.00
408 1 0.00
410 7 0.02
411 272 0.75
412 14 0.04
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (411 bp):
GATTCAATATTCCCTAAAGAACAATGGAATGAATAAACACCCTCAGATCTGATTTTTCATCAGGA
AAAAGTGGAACATATCCATCTTTTTCAATCTTTTTCAGATTTGATATTCCCTGAGTAACAGTGGA
ACAAGCCTACCTCGATTCAATCTTCCCTGAGTAACAGTGGAATAAATCAACTCCCCCAAATATAA
TTTTCCCTCAAGAAGAAGCGAAACAAATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTAACAG
TGGAACAAGTCTACCTCGATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAACTCCCCTATAT
CTAATTTTCACTCAAGAACAAACACAACATATCCCTCTATTTTCAGATTTGATATTCCCTGAGTA
ACAGTGAAACAAGTCTACCTC
Found at i:1454485 original size:19 final size:20
Alignment explanation
Indices: 1454446--1454487 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1454436 TTTGACCATT
**
1454446 TTGTTCATTTAGTATCGATA
1 TTGTTCATACAGTATCGATA
1454466 TTGTTCATACAGTA-CGATA
1 TTGTTCATACAGTATCGATA
1454485 TTG
1 TTG
1454488 ATGTTCATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (20 bp):
TTGTTCATACAGTATCGATA
Found at i:1454520 original size:41 final size:43
Alignment explanation
Indices: 1454447--1454526 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 43
1454437 TTGACCATTT
* *
1454447 TGTTCATTTAGTATCGATATTGTTCATACAGTAC-GATATTGA
1 TGTTCATTTAGTATCGATACTGCTCATACAGTACTGATATTGA
* * *
1454489 TGTTCA-TTGGTATCGCTACTGCTCATTCAGTACTGATA
1 TGTTCATTTAGTATCGATACTGCTCATACAGTACTGATA
1454527 CTTTTCTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 22 0.69
42 10 0.31
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (43 bp):
TGTTCATTTAGTATCGATACTGCTCATACAGTACTGATATTGA
Found at i:1456280 original size:226 final size:227
Alignment explanation
Indices: 1455886--1456338 Score: 899
Period size: 226 Copynumber: 2.0 Consensus size: 227
1455876 GTCATAAATA
1455886 ACTTCCAATCTAAGAAATTCGATACAATTGTTTATGGTTGTCTTCTTAGCCATATCTTTCGCAAA
1 ACTTCCAATCTAAGAAATTCGATACAATTGTTTATGGTTGTCTTCTTAGCCATATCTTTCGCAAA
1455951 GTTGGTATCAATGTCTCTCTAGATCCAGCTATTCCCCTATCCTCCTATATTGATATTAAATATCT
66 GTTGGTATCAATGTCTCTCTAGATCCAGCTATTCCCCTATCCTCCTATATTGATATTAAATATCT
1456016 TCATAAATCGAGATGGGAAAAGCTTGGGGCGACGTGGACAAGAAAAGGGAAGCAATTCGTATGCT
131 TCATAAATCGAGATGGGAAAAGCTTGGGGCGACGTGGACAAGAAAAGGGAAGCAATTCGTATGCT
1456081 CTGCCTCTAGTTCACCTCAG-CTCAGGATGAT
196 CTGCCTCTAGTTCACCTCAGCCTCAGGATGAT
1456112 ACTTCCAATCTAAGAAATTCGATACAATTGTTTATGGTTGTCTTCTTAGCCATATCTTTCGCAAA
1 ACTTCCAATCTAAGAAATTCGATACAATTGTTTATGGTTGTCTTCTTAGCCATATCTTTCGCAAA
1456177 GTTGGTATCAATGTCTCTCTAGATCCAGCTATTCCCCTATCCTCCTATATTGATATTAAATATCT
66 GTTGGTATCAATGTCTCTCTAGATCCAGCTATTCCCCTATCCTCCTATATTGATATTAAATATCT
1456242 TCATAAATCGAGATGGGAAAAGCTTGGGGCGACGTGGACAAGAAAAGGGAAGCAATTCGTATGCT
131 TCATAAATCGAGATGGGAAAAGCTTGGGGCGACGTGGACAAGAAAAGGGAAGCAATTCGTATGCT
1456307 CTGCCTCTAGTTCACCTCAGCCTCAGGATGAT
196 CTGCCTCTAGTTCACCTCAGCCTCAGGATGAT
1456339 GATCAGATAC
Statistics
Matches: 226, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
226 215 0.95
227 11 0.05
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (227 bp):
ACTTCCAATCTAAGAAATTCGATACAATTGTTTATGGTTGTCTTCTTAGCCATATCTTTCGCAAA
GTTGGTATCAATGTCTCTCTAGATCCAGCTATTCCCCTATCCTCCTATATTGATATTAAATATCT
TCATAAATCGAGATGGGAAAAGCTTGGGGCGACGTGGACAAGAAAAGGGAAGCAATTCGTATGCT
CTGCCTCTAGTTCACCTCAGCCTCAGGATGAT
Found at i:1458959 original size:18 final size:17
Alignment explanation
Indices: 1458921--1458952 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1458911 ATAAAAAATA
1458921 TTATTAGTTTTAATATC
1 TTATTAGTTTTAATATC
1458938 TTATTA-TTTTAATAT
1 TTATTAGTTTTAATAT
1458953 ATCTTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TTATTAGTTTTAATATC
Found at i:1466093 original size:9 final size:9
Alignment explanation
Indices: 1466074--1466111 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
1466064 TTATTCATAA
1466074 TTTCATTTTT
1 TTTC-TTTTT
1466084 TTTC--TTT
1 TTTCTTTTT
1466091 TTTCTTTTT
1 TTTCTTTTT
1466100 TTTCTTTTT
1 TTTCTTTTT
1466109 TTT
1 TTT
1466112 ACAAAGTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.27
9 15 0.58
10 4 0.15
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:1466110 original size:17 final size:17
Alignment explanation
Indices: 1466074--1466109 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1466064 TTATTCATAA
1466074 TTTCATTTTTTTTCTTT
1 TTTCATTTTTTTTCTTT
1466091 TTTC-TTTTTTTTCTTT
1 TTTCATTTTTTTTCTTT
1466107 TTT
1 TTT
1466110 TTACAAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTCATTTTTTTTCTTT
Found at i:1471277 original size:40 final size:40
Alignment explanation
Indices: 1471217--1471295 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
1471207 GTCACTCTCA
* * *
1471217 TTGTGATTGTTGTGGCATAATAAACATGTTGAATGGGTTG
1 TTGTGATTGTCGTGGAATAATAAACATGCTGAATGGGTTG
1471257 TTGTGATTGTCGTGGAATAATAAACATGCTGAATGGGTT
1 TTGTGATTGTCGTGGAATAATAAACATGCTGAATGGGTT
1471296 ATCTTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.27, C:0.06, G:0.29, T:0.38
Consensus pattern (40 bp):
TTGTGATTGTCGTGGAATAATAAACATGCTGAATGGGTTG
Found at i:1474038 original size:20 final size:20
Alignment explanation
Indices: 1474001--1474039 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1473991 ATTCCACCAC
*
1474001 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
* *
1474021 ATGCATCTATATTATCCTA
1 ATGCAACTATATGATCCTA
1474040 TATGAGCTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1481935 original size:138 final size:139
Alignment explanation
Indices: 1481687--1481964 Score: 549
Period size: 138 Copynumber: 2.0 Consensus size: 139
1481677 TCGAACCTTC
1481687 TTCTTCATCCATTAGTGCAATAGATACTGAAGGGCGATTCAGCAAAATGTTGTTGTGAACCTTTT
1 TTCTTCATCCATTAGTGCAATAGATACTGAAGGGCGATTCAGCAAAATGTTGTTGTGAACCTTTT
1481752 TTGCTTCCGGTTGATTCGACAGAGCGATCGGAGATTCCAGT-GGGGGCACAGTGACGCTAGCCGA
66 TTGCTTCCGGTTGATTCGACAGAGCGATCGGAGATTCCAGTGGGGGGCACAGTGACGCTAGCCGA
1481816 AATCGTCGT
131 AATCGTCGT
1481825 TTCTTCATCCATTAGTGCAATAGATACTGAAGGGCGATTCAGCAAAATGTTGTTGTGAACCTTTT
1 TTCTTCATCCATTAGTGCAATAGATACTGAAGGGCGATTCAGCAAAATGTTGTTGTGAACCTTTT
1481890 TTGCTTCCGGTTGATTCGACAGAGCGATCGGAGATTCCAGTGGGGGGCACAGTGACGCTAGCCGA
66 TTGCTTCCGGTTGATTCGACAGAGCGATCGGAGATTCCAGTGGGGGGCACAGTGACGCTAGCCGA
1481955 AATCGTCGT
131 AATCGTCGT
1481964 T
1 T
1481965 GGATGAATGG
Statistics
Matches: 139, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
138 106 0.76
139 33 0.24
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (139 bp):
TTCTTCATCCATTAGTGCAATAGATACTGAAGGGCGATTCAGCAAAATGTTGTTGTGAACCTTTT
TTGCTTCCGGTTGATTCGACAGAGCGATCGGAGATTCCAGTGGGGGGCACAGTGACGCTAGCCGA
AATCGTCGT
Found at i:1482055 original size:20 final size:18
Alignment explanation
Indices: 1482030--1482069 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1482020 TACGAAATGT
1482030 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG--GGAATAA
*
1482050 AAGATTATCAGGGAATAA
1 AAGATTACCAGGGAATAA
1482068 AA
1 AA
1482070 TTACTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (18 bp):
AAGATTACCAGGGAATAA
Found at i:1482204 original size:18 final size:18
Alignment explanation
Indices: 1482181--1482228 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1482171 AAATTATCCT
* *
1482181 TATTATATATTTGTATAA
1 TATTATATATTTGAAAAA
*
1482199 TATTATA-AGTTGAAAAA
1 TATTATATATTTGAAAAA
1482216 TATTTATATATTT
1 TA-TTATATATTT
1482229 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
TATTATATATTTGAAAAA
Found at i:1482294 original size:39 final size:38
Alignment explanation
Indices: 1482211--1482283 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1482201 TTATAAGTTG
*
1482211 AAAAATATTTATATATTTTCTTTAAAAAATTTAAATTC
1 AAAAATATTTATATATTTTCTTTAAAAAATTAAAATTC
*
1482249 ATAAAAT-TTATATATATTTT-TTTACAAAATTAAAA
1 A-AAAATATT-TATATATTTTCTTTAAAAAATTAAAA
1482284 ATATTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 16 0.52
39 15 0.48
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (38 bp):
AAAAATATTTATATATTTTCTTTAAAAAATTAAAATTC
Done.