Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001497.1 Hibiscus syriacus cultivar Beakdansim tig00002919_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: 1780709
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1199808 original size:76 final size:76
Alignment explanation
Indices: 1199703--1200164 Score: 843
Period size: 76 Copynumber: 6.1 Consensus size: 76
1199693 CACTGAAGGG
*
1199703 CAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCAC
1 CAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
1199768 TGTAGGACTTA
66 TGTAGGACTTA
* * *
1199779 CAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCTTCCGAAGGCTTTTTGAAAACATCATGCAC
1 CAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
1199844 TGTAGGACTTA
66 TGTAGGACTTA
1199855 CAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
1 CAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
1199920 TGTAGGACTTA
66 TGTAGGACTTA
* *
1199931 CAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCTTCCGAAGGCTTTTTGGAAACATCATGCAC
1 CAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
1199996 TGTAGGACTTA
66 TGTAGGACTTA
1200007 CAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
1 CAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
1200072 TGTAGGACTTA
66 TGTAGGACTTA
* *
1200083 CATATGACCCTAAGGCTTTGAAAACATCGAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
1 CAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
1200148 TGTAGGACTTA
66 TGTAGGACTTA
*
1200159 TAGATG
1 CAGATG
1200165 TGGGAAATAG
Statistics
Matches: 371, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 371 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (76 bp):
CAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCAC
TGTAGGACTTA
Found at i:1200888 original size:22 final size:22
Alignment explanation
Indices: 1200809--1200885 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
1200799 AATAAAGCTT
* *
1200809 TCATCTTCGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATATA
* *
1200831 TCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATATA
*
1200853 TCATCTTTGAAGAGAGAATATA
1 TCATCTTTGAAAAGAGAATATA
1200875 TCATCTTTGAA
1 TCATCTTTGAA
1200886 GAGTGTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:1205365 original size:18 final size:18
Alignment explanation
Indices: 1205342--1205380 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1205332 CCCCTTTTTA
* *
1205342 TTTTTCCCTTTTTTTCTT
1 TTTTTCCCATTTTTCCTT
*
1205360 TTTTTCTCATTTTTCCTT
1 TTTTTCCCATTTTTCCTT
1205378 TTT
1 TTT
1205381 CATCTTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTCCCATTTTTCCTT
Found at i:1205485 original size:1 final size:1
Alignment explanation
Indices: 1205401--1205469 Score: 57
Period size: 1 Copynumber: 69.0 Consensus size: 1
1205391 CTTTTTCATC
* * * * * * * * *
1205401 TTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1205466 TTTT
1 TTTT
1205470 CTCATTTTTC
Statistics
Matches: 50, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:1205516 original size:7 final size:7
Alignment explanation
Indices: 1205351--1205513 Score: 191
Period size: 7 Copynumber: 21.4 Consensus size: 7
1205341 ATTTTTCCCT
1205351 TTTTTTC
1 TTTTTTC
1205358 TTTTTTTC
1 -TTTTTTC
1205366 TCATTTTTCC
1 T--TTTTT-C
1205376 TTTTTCATC
1 TTTTT--TC
*
1205385 TTTTTCC
1 TTTTTTC
1205392 TTTTTCATC
1 TTTTT--TC
1205401 TTTTTTC
1 TTTTTTC
1205408 TTTTTTC
1 TTTTTTC
1205415 TTTTTTC
1 TTTTTTC
1205422 TTTTTTC
1 TTTTTTC
1205429 TTTTTTC
1 TTTTTTC
1205436 TTTTTTC
1 TTTTTTC
1205443 TTTTTTC
1 TTTTTTC
1205450 TTTTTTC
1 TTTTTTC
1205457 TTTTTTC
1 TTTTTTC
1205464 TTTTTTC
1 TTTTTTC
1205471 TCATTTTTCC
1 T--TTTTT-C
1205481 TTTTTCATC
1 TTTTT--TC
1205490 TTTTTTC
1 TTTTTTC
1205497 TTTTTTC
1 TTTTTTC
*
1205504 TTTCTTC
1 TTTTTTC
1205511 TTT
1 TTT
1205514 CTTTACTGGA
Statistics
Matches: 140, Mismatches: 3, Indels: 25
0.83 0.02 0.15
Matches are distributed among these distances:
7 91 0.65
8 15 0.11
9 28 0.20
10 6 0.04
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:1209985 original size:14 final size:13
Alignment explanation
Indices: 1209960--1210015 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 13
1209950 ATACTTGAAT
1209960 AAAATA-AATAAA
1 AAAATATAATAAA
1209972 AAAATATTAATAAA
1 AAAATA-TAATAAA
*
1209986 ATAATATAA-AAA
1 AAAATATAATAAA
*
1209998 ATAATAAGTAATAAA
1 AAAAT-A-TAATAAA
1210013 AAA
1 AAA
1210016 TTTTGAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
12 14 0.38
13 4 0.11
14 14 0.38
15 5 0.14
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (13 bp):
AAAATATAATAAA
Found at i:1209986 original size:11 final size:11
Alignment explanation
Indices: 1209957--1210016 Score: 56
Period size: 10 Copynumber: 5.7 Consensus size: 11
1209947 TTAATACTTG
1209957 AATAAAATAAAT
1 AATAAAAT-AAT
* *
1209969 AAAAAAATATT
1 AATAAAATAAT
1209980 AATAAAATAAT
1 AATAAAATAAT
1209991 -ATAAAA-AAT
1 AATAAAATAAT
*
1210000 AAT-AAGTAAT
1 AATAAAATAAT
1210010 AA-AAAAT
1 AATAAAAT
1210017 TTTGAAAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 5 0.13
10 16 0.41
11 11 0.28
12 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:1210687 original size:16 final size:18
Alignment explanation
Indices: 1210654--1210693 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
1210644 ATAATATAAT
1210654 AATATATTTATATATTAA
1 AATATATTTATATATTAA
*
1210672 AATAT-TTTTTAT-TTAA
1 AATATATTTATATATTAA
1210688 AA-ATAT
1 AATATAT
1210694 CAGAAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 2 0.10
16 7 0.35
17 6 0.30
18 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATATTTATATATTAA
Found at i:1210865 original size:2 final size:2
Alignment explanation
Indices: 1210854--1210884 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1210844 ACTTAGATAA
1210854 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1210885 TGACATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1212415 original size:3 final size:3
Alignment explanation
Indices: 1212407--1212475 Score: 95
Period size: 3 Copynumber: 22.7 Consensus size: 3
1212397 ATATTTATTA
1212407 AAT AAT AAT AAT -AT ATAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
**
1212453 AAT TTT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
1212476 AACGAAATGA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 51 0.86
4 6 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:1214429 original size:19 final size:19
Alignment explanation
Indices: 1214405--1214444 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1214395 CGTAGGGAAA
*
1214405 ACATAGAAGAAAAAAGTTG
1 ACATAGAAGAAAAAAGATG
1214424 ACATAGAAGAAAAAAGATG
1 ACATAGAAGAAAAAAGATG
1214443 AC
1 AC
1214445 TTTACTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.07, G:0.20, T:0.12
Consensus pattern (19 bp):
ACATAGAAGAAAAAAGATG
Found at i:1231310 original size:22 final size:22
Alignment explanation
Indices: 1231268--1231310 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1231258 AATTAATTTT
*
1231268 TTTAATTTAAGAAAAATATATA
1 TTTAATGTAAGAAAAATATATA
1231290 TTTAATGTAA-AAAAATCATAT
1 TTTAATGTAAGAAAAAT-ATAT
1231311 GATATTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
TTTAATGTAAGAAAAATATATA
Found at i:1234062 original size:66 final size:66
Alignment explanation
Indices: 1233956--1234088 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
1233946 ACCCAGCTCT
1233956 AATATAAACTACATGATCTGTTGACCTATAGACCCAGTTAAAAAATATCAAATATTTATAATGAA
1 AATATAAACTACATGATCTGTTGACCTATAGACCCAGTTAAAAAATATCAAATATTTATAATGAA
1234021 A
66 A
1234022 AATATAAACTACATGATCTGTTGACCTATAGACCCAGTTAAAAAATATCAAATATTTATAATGAA
1 AATATAAACTACATGATCTGTTGACCTATAGACCCAGTTAAAAAATATCAAATATTTATAATGAA
1234087 A
66 A
1234088 A
1 A
1234089 TACATGGTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (66 bp):
AATATAAACTACATGATCTGTTGACCTATAGACCCAGTTAAAAAATATCAAATATTTATAATGAA
A
Found at i:1234185 original size:2 final size:2
Alignment explanation
Indices: 1234178--1234227 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1234168 TTAACCGAGC
1234178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1234220 AT AT AT AT
1 AT AT AT AT
1234228 TATTTTTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1234310 original size:39 final size:39
Alignment explanation
Indices: 1234249--1234355 Score: 146
Period size: 39 Copynumber: 2.8 Consensus size: 39
1234239 TAGATTTTTT
1234249 ATTCATAA-TTCTTAAATTATTTCACTCTAACATTTCAA
1 ATTCATAATTTCTTAAATTATTTCACTCTAACATTTCAA
* * * *
1234287 ATTCCTAATTTCTTAAATCATTTCACTATAACATTTTAA
1 ATTCATAATTTCTTAAATTATTTCACTCTAACATTTCAA
*
1234326 ATT-ATTAATTTTTTAAATTATTTCACTCTA
1 ATTCA-TAATTTCTTAAATTATTTCACTCTA
1234356 CCGATCTAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
38 7 0.12
39 52 0.88
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.49
Consensus pattern (39 bp):
ATTCATAATTTCTTAAATTATTTCACTCTAACATTTCAA
Found at i:1234366 original size:39 final size:38
Alignment explanation
Indices: 1234257--1234370 Score: 138
Period size: 39 Copynumber: 2.9 Consensus size: 38
1234247 TTATTCATAA
**
1234257 TTCTTAAATTATTTCACTCTAACATTTCAAATTCCTAAT
1 TTCTTAAATTATTTCACTCTAACATTT-AAATTATTAAT
* *
1234296 TTCTTAAATCATTTCACTATAACATTTTAAATTATTAAT
1 TTCTTAAATTATTTCACTCTAACA-TTTAAATTATTAAT
* * *
1234335 TTTTTAAATTATTTCACTCTACCGATCTAAATTATT
1 TTCTTAAATTATTTCACTCTAAC-ATTTAAATTATT
1234371 TCTTTTAACT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 60 0.94
40 4 0.06
ACGTcount: A:0.34, C:0.17, G:0.01, T:0.48
Consensus pattern (38 bp):
TTCTTAAATTATTTCACTCTAACATTTAAATTATTAAT
Found at i:1236127 original size:29 final size:29
Alignment explanation
Indices: 1236085--1236173 Score: 169
Period size: 29 Copynumber: 3.1 Consensus size: 29
1236075 CAACAGTGGT
1236085 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
*
1236114 CTTGGAGGTCGCCATGGCATCCGAGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1236143 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1236172 CT
1 CT
1236174 GTGTGTATTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.15, C:0.31, G:0.36, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:1236218 original size:18 final size:18
Alignment explanation
Indices: 1236195--1236231 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1236185 AGAATAGGGC
1236195 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
1236213 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
1236231 C
1 C
1236232 GTGGGAATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (18 bp):
CATGCAATCAACATGGGA
Found at i:1236261 original size:44 final size:44
Alignment explanation
Indices: 1236213--1236304 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
1236203 CAACATGGGA
1236213 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
1236257 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
1236301 CATG
1 CATG
1236305 GGGTGGGAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.27, C:0.14, G:0.42, T:0.16
Consensus pattern (44 bp):
CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
Found at i:1236316 original size:15 final size:15
Alignment explanation
Indices: 1236276--1236407 Score: 86
Period size: 15 Copynumber: 8.1 Consensus size: 15
1236266 AACATGGGAC
1236276 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
1236292 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
1236307 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* *
1236322 G-GAGGGATCAACATGGG
1 GTG-GGAAT--GCATGGG
1236339 ATGTGGGAATGCATGGGG
1 --GTGGGAATGCAT-GGG
* * *
1236357 GAGGGGATGGTGCATTGGAC
1 G-TGGGA--ATGCA-TGG-G
1236377 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
1236392 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
1236407 G
1 G
1236408 GAGGGGATGG
Statistics
Matches: 90, Mismatches: 14, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
14 1 0.01
15 37 0.41
16 14 0.16
17 17 0.19
18 3 0.03
19 15 0.17
20 3 0.03
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:1236337 original size:65 final size:68
Alignment explanation
Indices: 1236263--1236392 Score: 203
Period size: 65 Copynumber: 1.9 Consensus size: 68
1236253 GATGCATGCA
*
1236263 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGA-TGCA-TGG-GGTGGGAATGCATGGGGGA
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGAGTGCATTGGACGTGGGAATGCATGGGGGA
1236325 GGG
66 GGG
*
1236328 ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGA--GTGCATTGGACGTGGGAATGCATGGGG
1236393 TGGGAATGCA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
65 35 0.60
68 4 0.07
69 3 0.05
70 16 0.28
ACGTcount: A:0.23, C:0.09, G:0.50, T:0.18
Consensus pattern (68 bp):
ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGAGTGCATTGGACGTGGGAATGCATGGGGGA
GGG
Found at i:1236350 original size:34 final size:33
Alignment explanation
Indices: 1236263--1236361 Score: 141
Period size: 34 Copynumber: 3.0 Consensus size: 33
1236253 GATGCATGCA
1236263 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGG
1 ATCAACATGGGA-GTGGGAATGCATGGGGGA-GGG
*
1236298 AT--GCATGGG-GTGGGAATGCATGGGGGAGGG
1 ATCAACATGGGAGTGGGAATGCATGGGGGAGGG
1236328 ATCAACATGGGATGTGGGAATGCATGGGGGAGGG
1 ATCAACATGGGA-GTGGGAATGCATGGGGGAGGG
1236362 GATGGTGCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
30 5 0.09
31 18 0.31
32 6 0.10
33 6 0.10
34 21 0.36
35 2 0.03
ACGTcount: A:0.24, C:0.09, G:0.51, T:0.16
Consensus pattern (33 bp):
ATCAACATGGGAGTGGGAATGCATGGGGGAGGG
Found at i:1236922 original size:21 final size:21
Alignment explanation
Indices: 1236874--1236922 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1236864 ACTAAAATCT
*
1236874 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTAAGTATA
* *
1236896 AATTATTAGTTTGTAAGTTTA
1 AGTTATTAGTTTGTAAGTATA
1236917 AGTTAT
1 AGTTAT
1236923 ATATTAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGTAAGTATA
Found at i:1236931 original size:25 final size:25
Alignment explanation
Indices: 1236899--1236949 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1236889 TAGTATAAAT
*
1236899 TATTAGTTTGTAAGTTTAAGTTATA
1 TATTAGTTTATAAGTTTAAGTTATA
*
1236924 TATTAGTTTATTAGTTTAAGTTATA
1 TATTAGTTTATAAGTTTAAGTTATA
1236949 T
1 T
1236950 TATATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (25 bp):
TATTAGTTTATAAGTTTAAGTTATA
Found at i:1237787 original size:26 final size:25
Alignment explanation
Indices: 1237758--1237816 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1237748 AAATCATATT
*
1237758 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
1237784 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
1237810 ATTATTA
1 ATTATTA
1237817 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:1240720 original size:26 final size:26
Alignment explanation
Indices: 1240691--1241286 Score: 461
Period size: 26 Copynumber: 24.2 Consensus size: 26
1240681 TTTGATGATT
1240691 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1240717 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
1240743 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* *
1240765 TA--AAT-ATTTAATGAACAAAT-ATT-
1 TAGTAATGATTTGAT-AA-TAATCATTA
1240788 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1240814 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1240840 TAATAATGATTT-ATTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1240866 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1240888 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1240912 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1240938 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
1240964 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1240986 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1241010 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1241036 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
1241062 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1241084 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1241108 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1241134 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1241160 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1241186 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1241208 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1241232 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
1241258 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
1241283 TAGT
1 TAGT
1241287 TATTATTTAG
Statistics
Matches: 479, Mismatches: 43, Indels: 97
0.77 0.07 0.16
Matches are distributed among these distances:
19 5 0.01
20 25 0.05
22 15 0.03
23 61 0.13
24 42 0.09
25 47 0.10
26 260 0.54
27 24 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:1240828 original size:97 final size:98
Alignment explanation
Indices: 1240636--1241151 Score: 400
Period size: 98 Copynumber: 5.3 Consensus size: 98
1240626 ATGTATTTAT
* ****
1240636 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
1240701 TTGATAATAATCATTATAGTAATGATTTGATAA
66 TTGATAATAATCATTATAGTAATGATTTGATAA
1240734 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAAT-ATTTAGTAATGAT
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
1240798 TTGATAATAATCATTATAGTAATGATTTGATAA
66 TTGATAATAATCATTATAGTAATGATTTGATAA
* * * * * *
1240831 TAATCATTATAATAATGATTTATTAATAATCATTATAAA-AATGATTTAA-TAATGATTTA--AA
1 TAATCATTATAATAATGA--T-TTAATAATGATT-TAAATATTTAATGAACAAATGATTTAGTAA
* * * *
1240892 T-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAA
62 TGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAA
* * * * * * * *
1240929 TAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAA-TAATGATTTA--AAT
1 TAATCATTATAATAATGATTTAATAATGAT--TTA-AATATTTAATGAACAAATGATTTAGTAAT
* * * *
1240991 -ATTTAATGATTTGATGATT-TAGTAATGATTTGATAA
63 GATTTGAT-A-ATAATCATTATAGTAATGATTTGATAA
* * * * * * * *
1241027 TAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAA-TAATGATTTA--AAT
1 TAATCATTATAATAATGATTTAATAATGAT--TTA-AATATTTAATGAACAAATGATTTAGTAAT
* * * *
1241089 -ATTTAATGATTTGATGATT-TAGTAATGATTTGATAA
63 GATTTGAT-A-ATAATCATTATAGTAATGATTTGATAA
* *
1241125 TAATCATTATAGTAATGATTTGATAAT
1 TAATCATTATAATAATGATTTAATAAT
1241152 AATCATTATA
Statistics
Matches: 389, Mismatches: 18, Indels: 22
0.91 0.04 0.05
Matches are distributed among these distances:
95 9 0.02
96 3 0.01
97 73 0.19
98 268 0.69
99 10 0.03
100 22 0.06
101 4 0.01
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (98 bp):
TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAA
Found at i:1240949 original size:98 final size:98
Alignment explanation
Indices: 1240814--1241275 Score: 692
Period size: 98 Copynumber: 4.7 Consensus size: 98
1240804 ATAATCATTA
* *
1240814 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATTAATAATCATTATAAAAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAATAATGATTT
1240878 AATAATGATTTAAATATTTAATGATTTGATGATT
65 AATAATGATTTAAATATTTAATGATTTGATGATT
1240912 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1240977 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGATTTAAATATTTAATGATTTGATGATT
1241010 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1241075 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGATTTAAATATTTAATGATTTGATGATT
1241108 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGA-TT-
*
1241173 GTAATAATCATTATAAAAATGATTTAAT-A----ATGATT
64 -TAATAATGATT-T--AAAT-ATTTAATGATTTGATGATT
* * * *
1241208 TA--AAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAATCATTATAATAATGATT
1 TAGTAATGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATT
*
1241269 TTATAAT
64 TAATAAT
1241276 AATTATTTAG
Statistics
Matches: 346, Mismatches: 8, Indels: 23
0.92 0.02 0.06
Matches are distributed among these distances:
95 6 0.02
97 8 0.02
98 292 0.84
99 9 0.03
100 8 0.02
101 10 0.03
102 1 0.00
104 5 0.01
105 7 0.02
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (98 bp):
TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
ATAATGATTTAAATATTTAATGATTTGATGATT
Found at i:1241040 original size:124 final size:120
Alignment explanation
Indices: 1240964--1241203 Score: 129
Period size: 124 Copynumber: 1.9 Consensus size: 120
1240954 ATAATCATTA
* *
1240964 TAATAATGATTTAATAATGATTTAAAT-ATTTAATGATTTGATGATTTAGTAATGATTTGAT-AA
1 TAATAATGATTTAATAATGATTTAAATGATTTAAT-A-TTAATGATTTA--AAT-ATTTAATGAA
* * *
1241027 TAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGAT--TTAAA
61 TAATCATT-TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATT--A
* * * * * *
1241088 TATTTAATGA-TT--TGATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGAT-
1 TA-ATAATGATTTAATAATGATTTA--AATGATTTAATATTAATGATT-TA--AAT-ATTTAATG
* ** *
1241149 AATAATCATTATAATAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAAT
59 AATAATCATT-TAGTAATGATTTGA-TAATAATCATTATAGTAATGATTTGATAAT
1241204 GATTTAAATA
Statistics
Matches: 102, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
122 9 0.09
123 7 0.07
124 74 0.73
125 12 0.12
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (120 bp):
TAATAATGATTTAATAATGATTTAAATGATTTAATATTAATGATTTAAATATTTAATGAATAATC
ATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTA
Found at i:1241204 original size:124 final size:124
Alignment explanation
Indices: 1241010--1241278 Score: 486
Period size: 124 Copynumber: 2.2 Consensus size: 124
1241000 TTTGATGATT
* *
1241010 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAAAAATGATTTA
1241075 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
66 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
1241134 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-AGTAATAATCATTATAAAAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGA-TAATAATCATTATAAAAATGATTT
1241198 AATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
65 AATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
* *
1241258 TAATAATGATTTTATAATAAT
1 TAGTAATGATTTGATAATAAT
1241279 TATTTAGTTA
Statistics
Matches: 140, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
123 1 0.01
124 139 0.99
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (124 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAAAAATGATTTA
ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
Found at i:1241278 original size:98 final size:94
Alignment explanation
Indices: 1240721--1241275 Score: 608
Period size: 98 Copynumber: 5.7 Consensus size: 94
1240711 TCATTATAGT
* * * * * * * *
1240721 AATGATTTGATAATAATCATTATAATAATGATTTAATAATGAT--TTA-AATATTTAATGAACAA
1 AATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAA-TA
* * *
1240783 AT-ATTTAGTAATGATTTGATAATAATCATTATAG
65 ATGATTTA--AAT-ATTTAATGAT-ATGATT-TAG
* *
1240817 TAATGATTTGATAATAATCATTATAATAATGATTT-ATTAATAATCATTATAAAAATGATTTAAT
1 -AATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAATAATGATTTAAT
1240881 AATGATTTAAATATTTAATGATTTGATGATTTAG
64 AATGATTTAAATATTTAATGA--T-ATGATTTAG
1240915 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATA
1 -AATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATA
1240980 ATGATTTAAATATTTAATGATTTGATGATTTAG
65 ATGATTTAAATATTTAATGA--T-ATGATTTAG
1241013 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATA
1 -AATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATA
1241078 ATGATTTAAATATTTAATGATTTGATGATTTAG
65 ATGATTTAAATATTTAATGA--T-ATGATTTAG
1241111 TAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTA
1 -AATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGA-TT--TA
*
1241176 ATAATCATTATAAAAATGATTTAAT-A-ATGATTTA-
62 ATAATGATT-T--AAAT-ATTTAATGATATGATTTAG
* * * * *
1241210 AAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAATCATTATAATAATGATTTTAT
1 AATGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAAT
1241273 AAT
64 AAT
1241276 AATTATTTAG
Statistics
Matches: 422, Mismatches: 19, Indels: 36
0.88 0.04 0.08
Matches are distributed among these distances:
95 6 0.01
96 1 0.00
97 55 0.13
98 295 0.70
99 21 0.05
100 21 0.05
101 10 0.02
102 1 0.00
104 5 0.01
105 7 0.02
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (94 bp):
AATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAA
TGATTTAAATATTTAATGATATGATTTAG
Found at i:1241511 original size:17 final size:17
Alignment explanation
Indices: 1241486--1241518 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1241476 ACTAAATATC
*
1241486 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
1241503 TAATGATTTGATACTA
1 TAATGATTTGATACTA
1241519 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:1243983 original size:47 final size:47
Alignment explanation
Indices: 1243880--1243970 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
1243870 CAACAAACAA
1243880 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
1 ATATAAC-TAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
* *
1243928 ATATAACTAACTA-TTAAC-AATACAAACTAATT-AATTATTTTTT
1 ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1243971 AACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 10 0.24
45 13 0.32
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (47 bp):
ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
Found at i:1244039 original size:41 final size:40
Alignment explanation
Indices: 1243901--1244039 Score: 93
Period size: 41 Copynumber: 3.3 Consensus size: 40
1243891 CTATTTAACT
* * * *
1243901 AACACAAACTAATTAAATAATTTTTTTA-TATAACTAACTATT
1 AACATAAACTAATAAAAT-ATTTTTTAACTAT-A-TAACTATA
* *
1243943 AACAATACAAACTAATTAATTATTTTTTAACTATATAACTATCA
1 AAC-AT--AAACTAATAAAATATTTTTTAACTATATAACTAT-A
* * *
1243987 AACATATACTAATAAAATATTTTTTAATTTATGTATACTAT-
1 AACATAAACTAATAAAATATTTTTTAA-CTATATA-ACTATA
*
1244028 AACTTAAACTAA
1 AACATAAACTAA
1244040 CAATCATATA
Statistics
Matches: 79, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
41 29 0.37
42 8 0.10
43 15 0.19
44 12 0.15
45 15 0.19
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (40 bp):
AACATAAACTAATAAAATATTTTTTAACTATATAACTATA
Found at i:1244202 original size:17 final size:16
Alignment explanation
Indices: 1244203--1244234 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1244193 CCCTTTCTTT
1244203 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
1244220 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
1244235 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:1244204 original size:4 final size:4
Alignment explanation
Indices: 1244176--1244233 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
1244166 TTTCGAATTC
* ** **
1244176 TTCT TACT TTCCT TTCT CCCT TTCT TTCT TTCT TTCCT TTCT CCCT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT
1244226 TTCT TTCT
1 TTCT TTCT
1244234 CGGCTGCAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (4 bp):
TTCT
Found at i:1244210 original size:25 final size:25
Alignment explanation
Indices: 1244176--1244233 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
1244166 TTTCGAATTC
*
1244176 TTCTTACTTTCCTTTCTCCCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
1244201 TTCTTTCTTTCCTTTCTCCCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
1244226 TTCTTTCT
1 TTCTTTCT
1244234 CGGCTGCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (25 bp):
TTCTTTCTTTCCTTTCTCCCTTTCT
Found at i:1244323 original size:25 final size:25
Alignment explanation
Indices: 1244295--1244346 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1244285 TTTCTTTTAT
*
1244295 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
1244320 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
1244345 AA
1 AA
1244347 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:1244494 original size:23 final size:23
Alignment explanation
Indices: 1244467--1244513 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1244457 GAATCTATAT
1244467 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
1244490 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
1244513 G
1 G
1244514 AATGGACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.09, G:0.45, T:0.26
Consensus pattern (23 bp):
GGCTGCATGTGAATGGATGATGG
Found at i:1244518 original size:13 final size:13
Alignment explanation
Indices: 1244500--1244531 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1244490 GGCTGCATGT
*
1244500 GAATGGATGATGG
1 GAATGGACGATGG
1244513 GAATGGACGATGG
1 GAATGGACGATGG
1244526 GAATGG
1 GAATGG
1244532 CGCCGGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.47, T:0.19
Consensus pattern (13 bp):
GAATGGACGATGG
Found at i:1244565 original size:29 final size:29
Alignment explanation
Indices: 1244532--1244640 Score: 166
Period size: 29 Copynumber: 3.8 Consensus size: 29
1244522 ATGGGAATGG
*
1244532 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
*
1244561 CGCCGGGAGTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
1244590 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
1244619 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
1244641 CTCTATTCCA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
29 72 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.30, G:0.32, T:0.16
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:1244696 original size:43 final size:43
Alignment explanation
Indices: 1244635--1244798 Score: 178
Period size: 43 Copynumber: 3.9 Consensus size: 43
1244625 GGCTGCATGG
1244635 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
* ***
1244678 CGACCTCTCTATTCCACTGTATGGCCACCTCGCATGGCTCG--
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
* * **
1244719 C-A-CTC-GTATGGCTCGTA-TGCATGGGGACCTCGCATGGGGAGAA
1 CGACCTCTCTAT---TC-CACTGCATGGCCACCTCGCATGGGGAGAA
1244762 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGG
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGG
1244799 CTCGCACTCG
Statistics
Matches: 95, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
38 3 0.03
39 3 0.03
40 1 0.01
41 21 0.22
42 2 0.02
43 58 0.61
44 1 0.01
45 3 0.03
46 3 0.03
ACGTcount: A:0.18, C:0.34, G:0.24, T:0.23
Consensus pattern (43 bp):
CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
Found at i:1244793 original size:84 final size:84
Alignment explanation
Indices: 1244652--1244829 Score: 329
Period size: 84 Copynumber: 2.1 Consensus size: 84
1244642 TCTATTCCAC
** *
1244652 TGCATGGCCACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGTATGGCCACCTCGCATGGCT
1 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
1244717 CGCACTCGTATGGCTCGTA
66 CGCACTCGTATGGCTCGTA
1244736 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
1 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
1244801 CGCACTCGTATGGCTCGTA
66 CGCACTCGTATGGCTCGTA
1244820 TGCATGGGGA
1 TGCATGGGGA
1244830 GAACCATTGG
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.23
Consensus pattern (84 bp):
TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
CGCACTCGTATGGCTCGTA
Found at i:1244851 original size:35 final size:35
Alignment explanation
Indices: 1244805--1244917 Score: 226
Period size: 35 Copynumber: 3.2 Consensus size: 35
1244795 ATGGCTCGCA
1244805 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1244840 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1244875 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1244910 CTCGTATG
1 CTCGTATG
1244918 TTCCCGTATG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.27
Consensus pattern (35 bp):
CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
Found at i:1246074 original size:18 final size:18
Alignment explanation
Indices: 1246039--1246082 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1246029 AATGACAATC
*
1246039 ATTATTTTATTCTGAAAA
1 ATTATTTTAATCTGAAAA
1246057 ATCTATTTTAAT-TGAAAA
1 AT-TATTTTAATCTGAAAA
1246075 ATTATTTT
1 ATTATTTT
1246083 TAAAATGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 10 0.42
19 8 0.33
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (18 bp):
ATTATTTTAATCTGAAAA
Found at i:1246796 original size:29 final size:29
Alignment explanation
Indices: 1246763--1246851 Score: 160
Period size: 29 Copynumber: 3.1 Consensus size: 29
1246753 TCTACAGTGG
1246763 CCTTGGAGGTCGCCATGGCATCCGGGCGA
1 CCTTGGAGGTCGCCATGGCATCCGGGCGA
*
1246792 CCTTGGAGGTCGCCATGGCATCCAGGCGA
1 CCTTGGAGGTCGCCATGGCATCCGGGCGA
*
1246821 CCTTGGAGGTCGCCATGGCATCCGAGCGA
1 CCTTGGAGGTCGCCATGGCATCCGGGCGA
1246850 CC
1 CC
1246852 GACCTGTGTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.16, C:0.33, G:0.35, T:0.17
Consensus pattern (29 bp):
CCTTGGAGGTCGCCATGGCATCCGGGCGA
Found at i:1246935 original size:81 final size:81
Alignment explanation
Indices: 1246844--1247007 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
1246834 CATGGCATCC
1246844 GAGCGACCGACCTGTGTGTATTTTGCAAAGGAATAGGTCGCCATGCAATCAACATGGGACGTGGG
1 GAGCGACCGACCTGTGTGTATTTTGCAAAGGAATAGGTCGCCATGCAATCAACATGGGACGTGGG
1246909 AATGCATGGGGGAGGG
66 AATGCATGGGGGAGGG
1246925 GAGCGACCGACCTGTGTGTATTTTGCAAAGGAATAGGTCGCCATGCAATCAACATGGGACGTGGG
1 GAGCGACCGACCTGTGTGTATTTTGCAAAGGAATAGGTCGCCATGCAATCAACATGGGACGTGGG
1246990 AATGCATGGGGGAGGG
66 AATGCATGGGGGAGGG
1247006 GA
1 GA
1247008 TGCATGCTGT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.26, C:0.17, G:0.37, T:0.20
Consensus pattern (81 bp):
GAGCGACCGACCTGTGTGTATTTTGCAAAGGAATAGGTCGCCATGCAATCAACATGGGACGTGGG
AATGCATGGGGGAGGG
Found at i:1247551 original size:21 final size:21
Alignment explanation
Indices: 1247526--1247569 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1247516 AATCTAGTTA
1247526 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1247547 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1247568 AT
1 AT
1247570 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1247579 original size:28 final size:28
Alignment explanation
Indices: 1247546--1247599 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1247536 TAGTATAAAT
*
1247546 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTATTAGTTTAAGTTATATTA
1247574 TATTAGTTTATTAGTTTAAGTTATAT
1 TATTAGTTTATTAGTTTAAGTTATAT
1247600 ATTATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAGTTTATTAGTTTAAGTTATATTA
Found at i:1247667 original size:43 final size:47
Alignment explanation
Indices: 1247570--1247668 Score: 134
Period size: 48 Copynumber: 2.1 Consensus size: 47
1247560 TTTAAGTTAT
1247570 ATTATATTAGTTTATTAGTTTAAGTTATATATTATATATATAAAAATTA
1 ATTA-ATTAGTTTATTAGTTTAAGTTATATA-TATATATATAAAAATTA
* *
1247619 GTTAATTAGTTTCTTAGTTTAAGTTAT-TA-A-ATATA-AAAAATTA
1 ATTAATTAGTTTATTAGTTTAAGTTATATATATATATATAAAAATTA
1247662 ATTAATT
1 ATTAATT
1247669 TGTTAGTGTC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
43 14 0.30
44 5 0.11
45 1 0.02
47 2 0.04
48 22 0.47
49 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (47 bp):
ATTAATTAGTTTATTAGTTTAAGTTATATATATATATATAAAAATTA
Found at i:1248070 original size:20 final size:21
Alignment explanation
Indices: 1248026--1248070 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1248016 AAATATTGTG
**
1248026 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
1248047 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
1248067 TTTA
1 TTTA
1248071 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:1248360 original size:26 final size:25
Alignment explanation
Indices: 1248331--1248389 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1248321 AAATCATATT
*
1248331 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
1248357 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
1248383 ATTATTA
1 ATTATTA
1248390 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:1251302 original size:26 final size:26
Alignment explanation
Indices: 1251273--1251699 Score: 334
Period size: 26 Copynumber: 17.2 Consensus size: 26
1251263 TTTGATGATT
*
1251273 TAGTAATGATTTGATAATAACCATTA
1 TAGTAATGATTTGATAATAATCATTA
1251299 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
1251325 TAATAATGATTT-AGTAATAATTATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1251351 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * *
1251373 TA--AAT-ATTTAATAATTTGATGATT-
1 TAGTAATGATTTGATAA--TAATCATTA
1251397 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1251423 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1251449 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1251475 TAAAAATGA-TT--TAATAATGA-T-
1 TAGTAATGATTTGATAATAATCATTA
* * * * *
1251496 T-GAAAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1251521 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1251547 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1251573 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1251599 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1251621 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1251645 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1251671 TAGTAATGATTTGATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
1251696 TAGT
1 TAGT
1251700 TATTATTTAG
Statistics
Matches: 341, Mismatches: 30, Indels: 61
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.01
20 16 0.05
21 1 0.00
22 10 0.03
23 30 0.09
24 23 0.07
25 33 0.10
26 205 0.60
27 20 0.06
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:1251443 original size:124 final size:124
Alignment explanation
Indices: 1251218--1251735 Score: 925
Period size: 124 Copynumber: 4.2 Consensus size: 124
1251208 ATGTATTTAT
1251218 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
*
1251283 TTGATAATAACCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* *
1251342 TAATTATTATAAAAATGATTTAATAATGATTTAAATATTTAATAATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1251407 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
1251466 TAATCATTATAAAAATGATTTAATAATGATTGAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1251531 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1251590 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * *
1251655 TTGATAATAATCATTATAGTAATGATTTGATAATAATTATT-TAGTTATTATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* *
1251713 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAAAAATGATTTAATA
1251736 CTAATGATTT
Statistics
Matches: 381, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
121 18 0.05
123 17 0.04
124 346 0.91
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:1251456 original size:150 final size:148
Alignment explanation
Indices: 1251273--1251616 Score: 421
Period size: 150 Copynumber: 2.3 Consensus size: 148
1251263 TTTGATGATT
* * *
1251273 TAGTAATGATTTGATAATAACCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATAATAATCATTATAAAAATGATTTA
* * * *
1251338 GTAATAATT--ATTATAAAAATGATTTAATAATGATTTA-AAT-ATTTAATAATTTGATGATT-T
65 ATAATAATTGAAATAT-AAAATGA-TT--TAATGATTTAGAATGATTTAATAA--TAATCATTAT
1251398 AGTAATGATTTGATAATAATCATTA
124 AGTAATGATTTGATAATAATCATTA
1251423 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTA-TAATAATCATTATAAAAATGATTTA
* ** * *
1251488 ATAATGATTGAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
65 ATAATAATTGAAATATAAAATGATTTAATGATTTAG-AATGATTTAATAATAATCATTATAGTAA
1251553 TGATTTGATAATAATCATTA
129 TGATTTGATAATAATCATTA
* *
1251573 TAATAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAAT
1 TAGTAATGATTTGA-TAATAATCATTATAATAATGATTT-ATAAT
1251617 GATTTAAATA
Statistics
Matches: 171, Mismatches: 14, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
148 9 0.05
149 8 0.05
150 136 0.80
151 14 0.08
152 4 0.02
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (148 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTATAATAATCATTATAAAAATGATTTAA
TAATAATTGAAATATAAAATGATTTAATGATTTAGAATGATTTAATAATAATCATTATAGTAATG
ATTTGATAATAATCATTA
Found at i:1251774 original size:38 final size:38
Alignment explanation
Indices: 1251704--1251777 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1251694 TTTAGTTATT
* **
1251704 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
1251742 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
1251778 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:1251984 original size:17 final size:17
Alignment explanation
Indices: 1251959--1251991 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1251949 ACTAAATATT
*
1251959 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
1251976 TAATGATTTGATACTA
1 TAATGATTTGATACTA
1251992 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:1251984 original size:25 final size:23
Alignment explanation
Indices: 1251905--1251984 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
1251895 GATTTATTGT
1251905 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
1251926 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
1251953 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
1251975 GTAATGATTT
1 -TAAT-ATTT
1251985 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:1254158 original size:15 final size:14
Alignment explanation
Indices: 1254135--1254165 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1254125 TACAACACTA
1254135 AACTTTAATATAAT
1 AACTTTAATATAAT
1254149 AACTTATAATATAAT
1 AACTT-TAATATAAT
1254164 AA
1 AA
1254166 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:1254173 original size:16 final size:16
Alignment explanation
Indices: 1254140--1254186 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1254130 CACTAAACTT
*
1254140 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
1254155 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
1254171 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
1254187 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:1254452 original size:43 final size:46
Alignment explanation
Indices: 1254347--1254439 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 46
1254337 CAACAAACAA
*
1254347 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATATTTTTT
1 ATATAAC-TAACTA-TTAACTAAAACAAACTAATTAAAT-ATATTTTTT
1254396 ATATAACTAACTATTAAC-AAAACAAACTAATT-AAT-TATTTTTT
1 ATATAACTAACTATTAACTAAAACAAACTAATTAAATATATTTTTT
1254439 A
1 A
1254440 ACTATATAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
43 9 0.21
45 3 0.07
46 13 0.30
47 5 0.12
48 6 0.14
49 7 0.16
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (46 bp):
ATATAACTAACTATTAACTAAAACAAACTAATTAAATATATTTTTT
Found at i:1254507 original size:41 final size:40
Alignment explanation
Indices: 1254419--1254507 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
1254409 TTAACAAAAC
* *
1254419 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
1254460 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
1254501 AAACTAA
1 AAACTAA
1254508 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:1254672 original size:21 final size:21
Alignment explanation
Indices: 1254642--1254694 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1254632 CCCTTTCTTC
*
1254642 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
1254663 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
1254684 TTCTTTCTTTC
1 TTCTTTCTTTC
1254695 TCGGCTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:1254685 original size:17 final size:16
Alignment explanation
Indices: 1254665--1254696 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1254655 TTCTCCCTTT
1254665 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
1254682 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
1254697 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:1254728 original size:23 final size:23
Alignment explanation
Indices: 1254698--1254743 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1254688 TTCTTTCTCG
1254698 GCTGCAATCTCTTCTCCCTTTCT
1 GCTGCAATCTCTTCTCCCTTTCT
1254721 GCTGCAATCTCTTCTCCCTTTCT
1 GCTGCAATCTCTTCTCCCTTTCT
1254744 TTCTTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.09, T:0.43
Consensus pattern (23 bp):
GCTGCAATCTCTTCTCCCTTTCT
Found at i:1254891 original size:27 final size:27
Alignment explanation
Indices: 1254861--1254916 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1254851 AATAATTCAC
1254861 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAATGGTTCACATGCATGCATT
1254888 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAATGGTTCACATGCATGCATT
1254915 GG
1 GG
1254917 GAGCTGTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (27 bp):
GGCTCAAATGGTTCACATGCATGCATT
Found at i:1255021 original size:29 final size:29
Alignment explanation
Indices: 1254989--1255097 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
1254979 ATGGGAATGG
1254989 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
1255018 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
1255047 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
1255076 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
1255098 CTCTATTCCT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.32, G:0.31, T:0.15
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:1255158 original size:13 final size:13
Alignment explanation
Indices: 1255140--1255174 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1255130 TCGTATATGG
1255140 CTCGTATGTCACC
1 CTCGTATGTCACC
*
1255153 CTCGTAGGTCACC
1 CTCGTATGTCACC
1255166 C-CGTATGTC
1 CTCGTATGTC
1255175 GCATGGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.14, C:0.37, G:0.20, T:0.29
Consensus pattern (13 bp):
CTCGTATGTCACC
Found at i:1258388 original size:85 final size:83
Alignment explanation
Indices: 1258240--1258398 Score: 196
Period size: 85 Copynumber: 1.9 Consensus size: 83
1258230 AGCATCACGT
* * * * *
1258240 AAGTTGTAATTTGCATGCAGTACACACTGGTTTTGAACTGGTCTCCACTCCCAGTGATGACAAAA
1 AAGTTCTAATTTACATGCAGCACACACTGGTTTTGAACTGGTCTCCACTCCCACTGATCAC-AAA
1258305 CCTTTGAATTCTTACTTTGA
65 CC-TTGAATTCTTACTTTGA
* **
1258325 AAGTTCTAATTTACTTGCAGCACACTGTGGTTTTGAA-TCGGTCTCCACTCCCACT-ATCCACAA
1 AAGTTCTAATTTACATGCAGCACACACTGGTTTTGAACT-GGTCTCCACTCCCACTGAT-CACAA
1258388 ACCTTGAATTC
64 ACCTTGAATTC
1258399 CAACTTGAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
83 8 0.12
84 8 0.12
85 48 0.75
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (83 bp):
AAGTTCTAATTTACATGCAGCACACACTGGTTTTGAACTGGTCTCCACTCCCACTGATCACAAAC
CTTGAATTCTTACTTTGA
Found at i:1270959 original size:62 final size:60
Alignment explanation
Indices: 1270842--1270984 Score: 187
Period size: 62 Copynumber: 2.4 Consensus size: 60
1270832 GACATTGATT
* * * *
1270842 AAAAAATACTTTAGGTACCTAGATGAAAATGGTGGTATACCTTAATTACCCACTTTGACC
1 AAAAAATATTTTAGGTACCTAAATGAAAAAGGTGGAATACCTTAATTACCCACTTTGACC
* * * *
1270902 AAATAAAATATTTTAGGTACCTAAATGAAAAAGGTGGAATATCTTAGTTATCTACTTTGACC
1 -AA-AAAATATTTTAGGTACCTAAATGAAAAAGGTGGAATACCTTAATTACCCACTTTGACC
*
1270964 AAAAAATATTTTAGCTACCTA
1 AAAAAATATTTTAGGTACCTA
1270985 GATGGAAAGT
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
60 18 0.25
61 4 0.06
62 50 0.69
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (60 bp):
AAAAAATATTTTAGGTACCTAAATGAAAAAGGTGGAATACCTTAATTACCCACTTTGACC
Found at i:1280574 original size:2 final size:2
Alignment explanation
Indices: 1280567--1280612 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1280557 ACATAACATA
1280567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1280609 AT AT
1 AT AT
1280613 TTAATAGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1281205 original size:2 final size:2
Alignment explanation
Indices: 1281194--1281233 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1281184 ATTAATCGGT
*
1281194 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1281234 TATCATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1281713 original size:171 final size:171
Alignment explanation
Indices: 1281428--1281783 Score: 687
Period size: 171 Copynumber: 2.1 Consensus size: 171
1281418 TCCAAACCCT
1281428 AAACTCATTATCTATATATGTATCATATCATATCTTATATTTAAAAATATTATAACGTCGATCGA
1 AAACTCATTATCTATATATGTATCATATCATATCTTATATTTAAAAATATTATAACGTCGATCGA
1281493 ATTCTAATCTTATTTAACAACTCTATATTAAAATTAGATCAATTCAATAAAATCAAGTACCCCTA
66 ATTCTAATCTTATTTAACAACTCTATATTAAAATTAGATCAATTCAATAAAATCAAGTACCCCTA
1281558 AAATTTTCTTCAAATATATAATGCATAAATAATAAAATATA
131 AAATTTTCTTCAAATATATAATGCATAAATAATAAAATATA
*
1281599 AAACTCATTATCTATATATGTATCATATCATATCTTATATTTTAAAATATTATAACGTCGATCGA
1 AAACTCATTATCTATATATGTATCATATCATATCTTATATTTAAAAATATTATAACGTCGATCGA
1281664 ATTCTAATCTTATTTAACAACTCTATATTAAAATTAGATCAATTCAATAAAATCAAGTACCCCTA
66 ATTCTAATCTTATTTAACAACTCTATATTAAAATTAGATCAATTCAATAAAATCAAGTACCCCTA
1281729 AAATTTTCTTCAAATATATAATGCATAAATAATAAAATATA
131 AAATTTTCTTCAAATATATAATGCATAAATAATAAAATATA
1281770 AAACTC-TTACTCTA
1 AAACTCATTA-TCTA
1281784 ACCGAGATAT
Statistics
Matches: 183, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
170 3 0.02
171 180 0.98
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (171 bp):
AAACTCATTATCTATATATGTATCATATCATATCTTATATTTAAAAATATTATAACGTCGATCGA
ATTCTAATCTTATTTAACAACTCTATATTAAAATTAGATCAATTCAATAAAATCAAGTACCCCTA
AAATTTTCTTCAAATATATAATGCATAAATAATAAAATATA
Found at i:1282675 original size:22 final size:22
Alignment explanation
Indices: 1282650--1282691 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1282640 GGTTTGTAAT
*
1282650 TAATTTGTAA-TTATACGTTTAA
1 TAATTTATAACTTA-ACGTTTAA
1282672 TAATTTATAACTTAACGTTT
1 TAATTTATAACTTAACGTTT
1282692 TATCAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (22 bp):
TAATTTATAACTTAACGTTTAA
Found at i:1293289 original size:38 final size:38
Alignment explanation
Indices: 1293247--1293322 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1293237 TCTTGGAAGG
1293247 GCGGTTTATTCCTTGCTACTTGTTTCGATATTTTCTCT
1 GCGGTTTATTCCTTGCTACTTGTTTCGATATTTTCTCT
1293285 GCGGTTTATTCCTTGCTACTTGTTTCGATATTTTCTCT
1 GCGGTTTATTCCTTGCTACTTGTTTCGATATTTTCTCT
1293323 TAGTGGTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.11, C:0.21, G:0.16, T:0.53
Consensus pattern (38 bp):
GCGGTTTATTCCTTGCTACTTGTTTCGATATTTTCTCT
Found at i:1298109 original size:60 final size:61
Alignment explanation
Indices: 1297985--1298115 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 61
1297975 ATTATCATTT
* * * * *
1297985 CATCCTC-AAACTATGACTCATATTCTAAATTGGTCCCAAAACTTTTTAACACTCCAAATT
1 CATCCTCTAAACTATAACACACATTCTAAATCGGTCCCAAAACTTTTTAACACTCCAAATA
* * * *
1298045 CATCC-CTAAACTATAACACACATTCTAAATCGGTCCCCATATTTTTTAACATTCC-AATAA
1 CATCCTCTAAACTATAACACACATTCTAAATCGGTCCCAAAACTTTTTAACACTCCAAAT-A
1298105 CATCCTCTAAA
1 CATCCTCTAAA
1298116 ATCATTCAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 4 0.07
60 50 0.85
61 5 0.08
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (61 bp):
CATCCTCTAAACTATAACACACATTCTAAATCGGTCCCAAAACTTTTTAACACTCCAAATA
Found at i:1298783 original size:8 final size:8
Alignment explanation
Indices: 1298770--1298796 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1298760 ATTATAAAAT
1298770 AATTATAA
1 AATTATAA
1298778 AATTATAA
1 AATTATAA
1298786 AATTATAA
1 AATTATAA
1298794 AAT
1 AAT
1298797 AATCATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AATTATAA
Found at i:1304329 original size:31 final size:31
Alignment explanation
Indices: 1304278--1304350 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
1304268 ATTTAGATCA
* *
1304278 TTAAGATTTATTAAAATATTATAAAATAATCT
1 TTAA-ATTTATCAAAATATTATAAAATAATCC
* *
1304310 TTAAATTTATCAAACTATTATAAAATGATCC
1 TTAAATTTATCAAAATATTATAAAATAATCC
1304341 TTAAATTTAT
1 TTAAATTTAT
1304351 TAGAACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 33 0.89
32 4 0.11
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.44
Consensus pattern (31 bp):
TTAAATTTATCAAAATATTATAAAATAATCC
Found at i:1308121 original size:20 final size:20
Alignment explanation
Indices: 1308075--1308120 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
1308065 CTTGAATTTT
1308075 AAAAAAATCAGAAAAATTAC
1 AAAAAAATCAGAAAAATTAC
1308095 AAAAAAAT-AGAAAAATTAC
1 AAAAAAATCAGAAAAATTAC
1308114 AAAAAAA
1 AAAAAAA
1308121 AATTACTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAAAAATCAGAAAAATTAC
Found at i:1308121 original size:116 final size:117
Alignment explanation
Indices: 1308001--1308218 Score: 384
Period size: 116 Copynumber: 1.9 Consensus size: 117
1307991 TTTATGTTTC
* * *
1308001 AAAAAATTAGTATGTTTATTTATCTAATTTTAATGTATTTTTATCTATCTTACAATTTAATCTAC
1 AAAAAATTACTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTACAAATTAATCTAC
*
1308066 TTGAATTTTAAAAAAATCAGAAAAATTACAAA-AAAATAGAAAAATTACAAA
66 TTGAATTTTAAAAAAATCAAAAAAATTACAAACAAAATAGAAAAATTACAAA
*
1308117 AAAAAATTACTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAAATTAATCTAC
1 AAAAAATTACTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTACAAATTAATCTAC
1308182 TTGAATTTTAAAAAAATCAAAAAAATTACAAACAAAA
66 TTGAATTTTAAAAAAATCAAAAAAATTACAAACAAAA
1308219 AAATTAGTAT
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
116 92 0.96
117 4 0.04
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (117 bp):
AAAAAATTACTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTACAAATTAATCTAC
TTGAATTTTAAAAAAATCAAAAAAATTACAAACAAAATAGAAAAATTACAAA
Found at i:1308145 original size:21 final size:21
Alignment explanation
Indices: 1308121--1308163 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1308111 TACAAAAAAA
*
1308121 AATTACTATGT-TTATTTATCT
1 AATTACAATGTATT-TTTATCT
*
1308142 AATTTCAATGTATTTTTATCT
1 AATTACAATGTATTTTTATCT
1308163 A
1 A
1308164 TCTTGCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (21 bp):
AATTACAATGTATTTTTATCT
Found at i:1308234 original size:99 final size:97
Alignment explanation
Indices: 1308095--1308306 Score: 345
Period size: 99 Copynumber: 2.2 Consensus size: 97
1308085 GAAAAATTAC
*
1308095 AAAAAAAT-AGAAAAATTACAAAAAAAAATTACTATGTTTATTTATCTAATTTCAATGTATTTTT
1 AAAAAAATCAAAAAAATTACAAAAAAAAATTACTATGTTTATTTATCTAATTTCAATGTATTTTT
* *
1308159 ATCTATCTTGCAAATTAATCTACTTGAATTTT
66 ATCTATATTGCAAATTAATCTACTTGAATTTA
*
1308191 AAAAAAATCAAAAAAATTACAAACAAAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTT
1 AAAAAAATCAAAAAAATTAC-AA-AAAAAAATTACTATGTTTATTTATCTAATTTCAATGTATTT
* *
1308256 TTATCTATATTGTAATTTAATCTACTTGAATTTA
64 TTATCTATATTGCAAATTAATCTACTTGAATTTA
1308290 AAAAAAATCAAAAAAAT
1 AAAAAAATCAAAAAAAT
1308307 CAATAAAAAA
Statistics
Matches: 107, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
96 8 0.07
97 10 0.09
98 2 0.02
99 87 0.81
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (97 bp):
AAAAAAATCAAAAAAATTACAAAAAAAAATTACTATGTTTATTTATCTAATTTCAATGTATTTTT
ATCTATATTGCAAATTAATCTACTTGAATTTA
Found at i:1314963 original size:38 final size:37
Alignment explanation
Indices: 1314926--1314999 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 37
1314916 GTTGGAAAAT
*
1314926 ATTTATAT--ATTTTCTTTA-AAAATTTAAATTCATAAA
1 ATTTATATAAATTTT-TTTACAAAATTTAAAAT-ATAAA
1314962 ATTTATATAAATTTTTTTACAAAATTTAAAATATAAA
1 ATTTATATAAATTTTTTTACAAAATTTAAAATATAAA
1314999 A
1 A
1315000 AGGTTTAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 8 0.24
37 10 0.29
38 16 0.47
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATAAATTTTTTTACAAAATTTAAAATATAAA
Found at i:1317692 original size:12 final size:12
Alignment explanation
Indices: 1317675--1317699 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1317665 AGTCTCTTCT
1317675 TCTTTTTTTTTC
1 TCTTTTTTTTTC
1317687 TCTTTTTTTTTC
1 TCTTTTTTTTTC
1317699 T
1 T
1317700 TCTGGTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCTTTTTTTTTC
Found at i:1318267 original size:9 final size:9
Alignment explanation
Indices: 1318253--1318303 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
1318243 ATTATTATTT
1318253 TTTAATATA
1 TTTAATATA
1318262 TTTAATA-A
1 TTTAATATA
1318270 --TAATAATA
1 TTTAAT-ATA
*
1318278 TTTATATGTA
1 TTTA-ATATA
1318288 TTTAATATA
1 TTTAATATA
1318297 TTTAATA
1 TTTAATA
1318304 ATAATAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
6 4 0.11
7 1 0.03
8 2 0.06
9 18 0.51
10 8 0.23
11 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (9 bp):
TTTAATATA
Found at i:1318307 original size:3 final size:3
Alignment explanation
Indices: 1318299--1318446 Score: 226
Period size: 3 Copynumber: 49.7 Consensus size: 3
1318289 TTAATATATT
* *
1318299 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1318347 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1318395 TAA T-A TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1318442 TAA TA
1 TAA TA
1318447 TGGATAAAAA
Statistics
Matches: 131, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
2 2 0.02
3 129 0.98
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1318968 original size:113 final size:113
Alignment explanation
Indices: 1318779--1319662 Score: 1572
Period size: 113 Copynumber: 7.8 Consensus size: 113
1318769 GTTGAACAAG
* * *
1318779 TTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CT
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCT
* * * * * *
1318843 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTC
62 GGAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
1318895 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
*
1318960 AAGCTGATCCATCAAATAATGGATTCAGGTAAAAGGTTGAACAAATTC
66 AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
1319008 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1319073 AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
66 AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
1319121 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1319186 AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
66 AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
1319234 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1319299 AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
66 AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
1319347 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1319412 AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
66 AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
*
1319460 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1319525 AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
66 AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
* * *
1319573 TTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAATTCTTCTCATTATGAACCTTCTCTGGAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
* * *
1319638 AAGATAATCCATCAAATGATAGATT
66 AAGCTGATCCATCAAATGATGGATT
1319663 TGAATCTTTG
Statistics
Matches: 748, Mismatches: 19, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
112 2 0.00
113 714 0.95
116 32 0.04
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
AAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
Found at i:1320599 original size:83 final size:83
Alignment explanation
Indices: 1320396--1321026 Score: 1151
Period size: 83 Copynumber: 7.6 Consensus size: 83
1320386 CCTACTGAAT
* ** *
1320396 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTTTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
*
1320460 ATGATT-GTTTTGTCAAAT
65 ATGATTGGTTTTGTCAAAC
*
1320478 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1320543 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
1320561 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1320626 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
1320644 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1320709 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
1320727 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1320792 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
* *
1320810 CAGATCAGATAACTCAAATAACACTTCCAGAAGATGCTATTGGCATATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1320875 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
1320893 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1320958 TGATT-GTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
*
1320975 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCAT
1321027 TTGTTCTATT
Statistics
Matches: 535, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
82 125 0.23
83 410 0.77
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
TGATTGGTTTTGTCAAAC
Found at i:1322194 original size:12 final size:11
Alignment explanation
Indices: 1322164--1322238 Score: 80
Period size: 11 Copynumber: 6.5 Consensus size: 11
1322154 TTGACCCCCT
1322164 TTTTCTTTTTTCC
1 TTTT-TTTTTT-C
*
1322177 TTTTTTTCTTC
1 TTTTTTTTTTC
1322188 TTTTTTTTTTC
1 TTTTTTTTTTC
*
1322199 TTTTTCATTTTC
1 TTTTT-TTTTTC
1322211 TATTTTTTTTTC
1 T-TTTTTTTTTC
*
1322223 -TTTTTTCTTC
1 TTTTTTTTTTC
1322233 TTTTTT
1 TTTTTT
1322239 CTCTTCAAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
10 9 0.17
11 21 0.39
12 16 0.30
13 8 0.15
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:1322240 original size:7 final size:7
Alignment explanation
Indices: 1322163--1322236 Score: 59
Period size: 6 Copynumber: 10.7 Consensus size: 7
1322153 CTTGACCCCC
1322163 TTTTTCT
1 TTTTTCT
1322170 TTTTTCCTT
1 TTTTT-C-T
1322179 TTTTTCT
1 TTTTTCT
1322186 TCTTTT-T
1 T-TTTTCT
1322193 TTTTTC-
1 TTTTTCT
1322199 TTTTTC-
1 TTTTTCT
*
1322205 ATTTTC-
1 TTTTTCT
*
1322211 TATTT-T
1 TTTTTCT
1322217 TTTTTCT
1 TTTTTCT
1322224 TTTTTCT
1 TTTTTCT
1322231 TCTTTT
1 T-TTTT
1322237 TTCTCTTCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
6 22 0.39
7 18 0.32
8 10 0.18
9 6 0.11
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:1332859 original size:13 final size:15
Alignment explanation
Indices: 1332837--1332873 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1332827 TTTGACAGAA
1332837 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
1332849 AAATAAAATACTTGC
1 AAATAAAATACTTGC
1332864 AAATAAAATA
1 AAATAAAATA
1332874 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:1332928 original size:13 final size:13
Alignment explanation
Indices: 1332910--1332934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1332900 AAATAAATAA
1332910 AAAGAATTAAAAG
1 AAAGAATTAAAAG
1332923 AAAGAATTAAAA
1 AAAGAATTAAAA
1332935 ATTAAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AAAGAATTAAAAG
Found at i:1334990 original size:9 final size:9
Alignment explanation
Indices: 1334976--1335026 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
1334966 ATTATTATTT
1334976 TTTAATATA
1 TTTAATATA
1334985 TTTAATA-A
1 TTTAATATA
1334993 --TAATAATA
1 TTTAAT-ATA
*
1335001 TTTATATGTA
1 TTTA-ATATA
1335011 TTTAATATA
1 TTTAATATA
1335020 TTTAATA
1 TTTAATA
1335027 ATAATAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
6 4 0.11
7 1 0.03
8 2 0.06
9 18 0.51
10 8 0.23
11 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (9 bp):
TTTAATATA
Found at i:1335030 original size:3 final size:3
Alignment explanation
Indices: 1335022--1335154 Score: 214
Period size: 3 Copynumber: 44.7 Consensus size: 3
1335012 TTAATATATT
* *
1335022 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1335070 TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1335117 TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1335155 TGGATAAAAA
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
2 2 0.02
3 118 0.98
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1339900 original size:12 final size:12
Alignment explanation
Indices: 1339883--1339907 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1339873 ATAAAACCAT
1339883 AATTATGAGCAA
1 AATTATGAGCAA
1339895 AATTATGAGCAA
1 AATTATGAGCAA
1339907 A
1 A
1339908 GGCAAATCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
AATTATGAGCAA
Found at i:1342703 original size:27 final size:27
Alignment explanation
Indices: 1342673--1342738 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
1342663 GATAAAAAGC
1342673 AAAATTATAATTTTCTTTGAAATAGGA
1 AAAATTATAATTTTCTTTGAAATAGGA
1342700 AAAATTATAATTTTCTTTGAAATAGGA
1 AAAATTATAATTTTCTTTGAAATAGGA
1342727 AAAATTATAATT
1 AAAATTATAATT
1342739 AGATATATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (27 bp):
AAAATTATAATTTTCTTTGAAATAGGA
Found at i:1344070 original size:29 final size:29
Alignment explanation
Indices: 1344037--1344121 Score: 161
Period size: 29 Copynumber: 2.9 Consensus size: 29
1344027 TCCCAACACA
1344037 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1344066 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
1344095 TAGGTCGCCATGCGCTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
1344122 ACCCTCACTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.11, C:0.38, G:0.32, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:1344177 original size:33 final size:33
Alignment explanation
Indices: 1344125--1344193 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1344115 GCGACCTACC
* *
1344125 CTCACTCGGCTTCCCTCGGATTCCCTCGCATAG
1 CTCACTCGGCTTCCATCGGATGCCCTCGCATAG
1344158 CTCACTCGG-TTGCCATCGGATGCCCTCGCATAG
1 CTCACTCGGCTT-CCATCGGATGCCCTCGCATAG
1344191 CTC
1 CTC
1344194 GTTCGGATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.13, C:0.41, G:0.20, T:0.26
Consensus pattern (33 bp):
CTCACTCGGCTTCCATCGGATGCCCTCGCATAG
Found at i:1344213 original size:14 final size:14
Alignment explanation
Indices: 1344191--1344223 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1344181 CCTCGCATAG
*
1344191 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
1344205 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1344219 CTCGG
1 CTCGG
1344224 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:1344223 original size:10 final size:10
Alignment explanation
Indices: 1344210--1344246 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
1344200 ATGGCCTCGG
1344210 TCGGATGGCC
1 TCGGATGGCC
1344220 TCGGAT-GCTC
1 TCGGATGGC-C
1344230 TCGGATGGCC
1 TCGGATGGCC
1344240 TCGGATG
1 TCGGATG
1344247 CCCAGCGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.11, C:0.27, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:1344235 original size:20 final size:20
Alignment explanation
Indices: 1344210--1344247 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1344200 ATGGCCTCGG
1344210 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
1344230 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGGATGC
1344248 CCAGCGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.37, T:0.24
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:1351406 original size:22 final size:22
Alignment explanation
Indices: 1351374--1351418 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1351364 TATAAAACTG
*
1351374 TAAAAGATAAAATATTGATTAA
1 TAAAAGATAAAATATAGATTAA
* *
1351396 TAAAAGTTAAAATGTAGATTAA
1 TAAAAGATAAAATATAGATTAA
1351418 T
1 T
1351419 TTGGTCGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (22 bp):
TAAAAGATAAAATATAGATTAA
Found at i:1351880 original size:8 final size:8
Alignment explanation
Indices: 1351867--1351900 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1351857 TTTTGTATTA
1351867 ATTATTTT
1 ATTATTTT
*
1351875 ATTATTTA
1 ATTATTTT
1351883 ATT-TTTT
1 ATTATTTT
1351890 ATTATTTT
1 ATTATTTT
1351898 ATT
1 ATT
1351901 TAATTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTATTTT
Found at i:1351889 original size:15 final size:15
Alignment explanation
Indices: 1351864--1351901 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1351854 ATATTTTGTA
1351864 TTAATTATTTTATTAT
1 TTAATT-TTTTATTAT
1351880 TTAATTTTTTATTAT
1 TTAATTTTTTATTAT
*
1351895 TTTATTT
1 TTAATTT
1351902 AATTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTAATTTTTTATTAT
Found at i:1351899 original size:20 final size:20
Alignment explanation
Indices: 1351868--1351917 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1351858 TTTGTATTAA
1351868 TTATTTTATTATTTAATT-TT
1 TTATTTT-TTATTTAATTATT
1351888 TTATTATTTTATTTAATTATT
1 TTATT-TTTTATTTAATTATT
1351909 TTATTTTTT
1 TTATTTTTT
1351918 TTACAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTATTTTTTATTTAATTATT
Found at i:1351909 original size:23 final size:23
Alignment explanation
Indices: 1351867--1351910 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1351857 TTTTGTATTA
*
1351867 ATTATTTTATTATTTAATTTTTT
1 ATTATTTTATTAATTAATTTTTT
1351890 ATTATTTTATTTAATT-ATTTT
1 ATTATTTTA-TTAATTAATTTT
1351911 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTATTTTATTAATTAATTTTTT
Found at i:1351927 original size:28 final size:28
Alignment explanation
Indices: 1351856--1351927 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
1351846 ATTTAATCAT
* *
1351856 ATTTTGTATT-AATTATTTTATTATTTA
1 ATTTTTTATTAAATTATTTAATTATTTA
** *
1351883 ATTTTTTATTATTTTATTTAATTATTTT
1 ATTTTTTATTAAATTATTTAATTATTTA
1351911 ATTTTTT-TTACAATTAT
1 ATTTTTTATTA-AATTAT
1351928 AAATTGGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 12 0.33
28 24 0.67
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (28 bp):
ATTTTTTATTAAATTATTTAATTATTTA
Found at i:1352189 original size:8 final size:8
Alignment explanation
Indices: 1352178--1352228 Score: 63
Period size: 8 Copynumber: 6.8 Consensus size: 8
1352168 AAAAAAAATA
1352178 AAATAATT
1 AAATAATT
1352186 AAAT-A--
1 AAATAATT
*
1352191 AAATAATA
1 AAATAATT
*
1352199 AAAAAATT
1 AAATAATT
1352207 AAATAATT
1 AAATAATT
1352215 AAATAATT
1 AAATAATT
1352223 AAATAA
1 AAATAA
1352229 AATACTAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 4 0.11
6 1 0.03
7 1 0.03
8 31 0.84
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AAATAATT
Found at i:1352191 original size:13 final size:13
Alignment explanation
Indices: 1352173--1352232 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
1352163 ACTGTAAAAA
1352173 AAATAAAATAATT
1 AAATAAAATAATT
1352186 AAATAAAATAA-T
1 AAATAAAATAATT
*
1352198 AAA-AAAATTAAAT
1 AAATAAAA-TAATT
*
1352211 -AATTAAATAATT
1 AAATAAAATAATT
1352223 AAATAAAATA
1 AAATAAAATA
1352233 CTAACAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 4 0.10
12 13 0.32
13 23 0.57
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:1352198 original size:21 final size:21
Alignment explanation
Indices: 1352169--1352232 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
1352159 TATAACTGTA
*
1352169 AAAAAAATAAAATAATTAAAT
1 AAAATAATAAAATAATTAAAT
*
1352190 AAAATAATAAAAAAATTAAAT
1 AAAATAATAAAATAATTAAAT
1352211 --AAT--T-AAATAATTAAAT
1 AAAATAATAAAATAATTAAAT
1352227 AAAATA
1 AAAATA
1352233 CTAACAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 11 0.30
17 1 0.03
18 3 0.08
19 3 0.08
21 19 0.51
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAATAATAAAATAATTAAAT
Found at i:1352205 original size:16 final size:16
Alignment explanation
Indices: 1352169--1352228 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
1352159 TATAACTGTA
1352169 AAAAAAATAAAATAAT
1 AAAAAAATAAAATAAT
*
1352185 ---TAAATAAAATAAT
1 AAAAAAATAAAATAAT
*
1352198 AAAAAAATTAAATAAT
1 AAAAAAATAAAATAAT
* * *
1352214 TAAATAATTAAATAA
1 AAAAAAATAAAATAA
1352229 AATACTAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
13 12 0.33
16 24 0.67
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAAAATAAAATAAT
Found at i:1356404 original size:2 final size:2
Alignment explanation
Indices: 1356397--1356427 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1356387 ATAAGCGAGC
1356397 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1356428 GGGAAAGAGA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1375348 original size:2 final size:2
Alignment explanation
Indices: 1375341--1375370 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1375331 AACTCTGGGA
1375341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1375371 CCACCAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1375630 original size:2 final size:2
Alignment explanation
Indices: 1375623--1375655 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1375613 TAATAAAATA
1375623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1375656 AATTAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1383226 original size:19 final size:18
Alignment explanation
Indices: 1383191--1383231 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1383181 TATAAAATAA
1383191 ATTTTAATTTCTGAATTT
1 ATTTTAATTTCTGAATTT
* *
1383209 GATTTTAATTTTTTAATTT
1 -ATTTTAATTTCTGAATTT
1383228 ATTT
1 ATTT
1383232 AAGTTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (18 bp):
ATTTTAATTTCTGAATTT
Found at i:1386972 original size:2 final size:2
Alignment explanation
Indices: 1386965--1386996 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1386955 ATTTTATAAT
1386965 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1386997 CTCCCGGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1405221 original size:35 final size:34
Alignment explanation
Indices: 1405136--1405222 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
1405126 ATTTGGTATT
* *
1405136 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATAG
* *
1405170 TAAATGATAACCAAATTACAATAACTGATATTAAATAG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATAG
1405208 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1405223 ACTGAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATAG
Found at i:1407024 original size:111 final size:112
Alignment explanation
Indices: 1406877--1407209 Score: 593
Period size: 111 Copynumber: 3.0 Consensus size: 112
1406867 ATTACAAAAA
*
1406877 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1406942 AATTAAAACGTTAAAATGTTA-CAGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCAGTATCAGCAAAGTGTCGAGATAT
1406988 TTAATTCTTAAT-TAAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATT
1 TTAATTCTTAATCT-AATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATT
*
1407052 AAATTAAAACGTTAAAATGTTATC-GTATCAGCAAAGTGTCGAGATAT
65 AAATTAAAACGTTAAAATGTTACCAGTATCAGCAAAGTGTCGAGATAT
*
1407099 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
1407164 AATTAAAACGTTAAAATGTTACCA-TATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCAGTATCAGCAAAGTGTCGAGATAT
1407210 ATGATTTCCA
Statistics
Matches: 214, Mismatches: 4, Indels: 8
0.95 0.02 0.04
Matches are distributed among these distances:
110 1 0.00
111 211 0.99
112 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (112 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCAGTATCAGCAAAGTGTCGAGATAT
Found at i:1407360 original size:10 final size:11
Alignment explanation
Indices: 1407335--1407374 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
1407325 TTAAAAAGAT
1407335 AGAATATTTGAG
1 AGAA-ATTTGAG
1407347 AGAAATTT-AG
1 AGAAATTTGAG
1407357 AG-AATTTGAG
1 AGAAATTTGAG
1407367 AG-AATTTG
1 AGAAATTTG
1407375 GTATGATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.19
10 14 0.52
11 4 0.15
12 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (11 bp):
AGAAATTTGAG
Found at i:1407613 original size:48 final size:47
Alignment explanation
Indices: 1407497--1407613 Score: 117
Period size: 48 Copynumber: 2.4 Consensus size: 47
1407487 AGATACCCAG
* * *
1407497 GTATAGCGCGGATCAGGGGGCGCTATACCCACGTGGCATCAAATCACC
1 GTATAACGCGG-TCAGGGGGCGCTATACCCACGTGACACCAAATCACC
* * * * **
1407545 GTATATCGAGGGCAGGGGGGCGCTATACCCACGTGACGCCAAATCAGT
1 GTATAACGCGGTCA-GGGGGCGCTATACCCACGTGACACCAAATCACC
*
1407593 GTATAACGCGGTTCAAGGGGC
1 GTATAACGCGG-TCAGGGGGC
1407614 ATACTTTACT
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
47 2 0.04
48 51 0.93
49 2 0.04
ACGTcount: A:0.25, C:0.26, G:0.32, T:0.17
Consensus pattern (47 bp):
GTATAACGCGGTCAGGGGGCGCTATACCCACGTGACACCAAATCACC
Done.