Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 9 of 25
Found at i:1436844 original size:21 final size:19
Alignment explanation
Indices: 1436801--1436840 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1436791 ATGAATATAT
1436801 TAATATATTAA-ATTTTACA
1 TAATATA-TAATATTTTACA
1436820 TAATATATAATATTTTACA
1 TAATATATAATATTTTACA
1436839 TA
1 TA
1436841 TAATTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATATATAATATTTTACA
Found at i:1436967 original size:16 final size:16
Alignment explanation
Indices: 1436946--1436980 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1436936 GTTAAAGAGC
1436946 ATACATACATAAATAT
1 ATACATACATAAATAT
*
1436962 ATACATACATACATAT
1 ATACATACATAAATAT
1436978 ATA
1 ATA
1436981 TAAATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (16 bp):
ATACATACATAAATAT
Found at i:1436970 original size:20 final size:20
Alignment explanation
Indices: 1436945--1436982 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1436935 CGTTAAAGAG
1436945 CATACATACATAAATATATA
1 CATACATACATAAATATATA
*
1436965 CATACATACATATATATA
1 CATACATACATAAATATA
1436983 AATATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (20 bp):
CATACATACATAAATATATA
Found at i:1438173 original size:2 final size:2
Alignment explanation
Indices: 1438168--1438196 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1438158 TTTAAAAGTT
1438168 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1438197 GAAAGGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1441223 original size:18 final size:17
Alignment explanation
Indices: 1441200--1441233 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1441190 ATTGTTTAAT
1441200 AATATAAAAATATAATTA
1 AATATAAAAAT-TAATTA
*
1441218 AATATAATAATTAATT
1 AATATAAAAATTAATT
1441234 CATTATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATAAAAATTAATTA
Found at i:1443292 original size:15 final size:16
Alignment explanation
Indices: 1443269--1443302 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1443259 ATTTAATTTA
*
1443269 TAATTAATTTAT-ATT
1 TAATAAATTTATAATT
1443284 TAATAAATTTATAATT
1 TAATAAATTTATAATT
1443300 TAA
1 TAA
1443303 ATTTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATAAATTTATAATT
Found at i:1447702 original size:2 final size:2
Alignment explanation
Indices: 1447695--1447744 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1447685 ATATTTACGA
1447695 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1447737 AG AG AG AG
1 AG AG AG AG
1447745 CATTGCTTGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1453038 original size:50 final size:47
Alignment explanation
Indices: 1452984--1453087 Score: 127
Period size: 47 Copynumber: 2.1 Consensus size: 47
1452974 AAATTTAACA
*
1452984 ATTAAATAAATATTTAAAAAAATAATATTTTTAATAAATATGATAATAAT
1 ATTAAATAAATA--T-AAAAAATAATATTTTTAATAAATATAATAATAAT
* ** * *
1453034 ATTAAATTAATATAAAATTTAATATTTTTAATAAATATAATTATATT
1 ATTAAATAAATATAAAAAATAATATTTTTAATAAATATAATAATAAT
1453081 ATTAAAT
1 ATTAAAT
1453088 TTAACTATCA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
47 36 0.75
48 1 0.02
50 11 0.23
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (47 bp):
ATTAAATAAATATAAAAAATAATATTTTTAATAAATATAATAATAAT
Found at i:1453079 original size:21 final size:21
Alignment explanation
Indices: 1453008--1453085 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 21
1452998 TAAAAAAATA
* *
1453008 ATATTTTTAATAAATATGATA
1 ATATTTTTAATAAATATAATT
* * *
1453029 ATAATATTAAATTAATATAAAATTT
1 AT-ATTTTTAA-TAA-ATATAA-TT
1453054 AATATTTTTAATAAATATAATT
1 -ATATTTTTAATAAATATAATT
*
1453076 ATATTATTAA
1 ATATTTTTAA
1453086 ATTTAACTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
21 11 0.26
22 8 0.19
23 8 0.19
24 7 0.16
25 7 0.16
26 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (21 bp):
ATATTTTTAATAAATATAATT
Found at i:1453203 original size:25 final size:26
Alignment explanation
Indices: 1453171--1453246 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 26
1453161 CAAAGGTCTC
*
1453171 AATTTTAATAAATATAAATTTTAATT
1 AATTTTAATATATATAAATTTTAATT
*
1453197 AA-TTTAATTTATATAATTATTTTAA--
1 AATTTTAATATATATAA--ATTTTAATT
*
1453222 AATTTTAATATA-ATAAATCTTAATT
1 AATTTTAATATATATAAATTTTAATT
1453247 TTAATATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
23 6 0.15
25 18 0.44
26 10 0.24
27 7 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
AATTTTAATATATATAAATTTTAATT
Found at i:1453251 original size:16 final size:15
Alignment explanation
Indices: 1453171--1453252 Score: 59
Period size: 16 Copynumber: 5.7 Consensus size: 15
1453161 CAAAGGTCTC
*
1453171 AATTTTAATAAATATA
1 AATTTTAATAAAT-TT
*
1453187 AATTTTAATTAATTT
1 AATTTTAATAAATTT
1453202 AA-TTT-ATATAA-TT
1 AATTTTAATA-AATTT
*
1453215 -ATTTTAA-AATTTT
1 AATTTTAATAAATTT
*
1453228 AA-TATAATAAATCTT
1 AATTTTAATAAAT-TT
1453243 AATTTTAATA
1 AATTTTAATA
1453253 TTTTTTTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
12 2 0.04
13 14 0.27
14 10 0.20
15 7 0.14
16 18 0.35
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTTAATAAATTT
Found at i:1453639 original size:17 final size:17
Alignment explanation
Indices: 1453619--1453653 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1453609 TGATTTTCAT
1453619 ATTTT-TATTTATATTAA
1 ATTTTATATTT-TATTAA
1453636 ATTTTATATTTTATTAA
1 ATTTTATATTTTATTAA
1453653 A
1 A
1453654 AAAAAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTATATTTTATTAA
Found at i:1457765 original size:2 final size:2
Alignment explanation
Indices: 1457758--1457791 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1457748 GAATACACAA
1457758 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
1457792 TTCATCTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1459928 original size:59 final size:59
Alignment explanation
Indices: 1459834--1459951 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
1459824 ATGCATTGGA
* *
1459834 ATAAAGAGCAATTAACTCCAGTATATCTACTCGAAATAAACCTAATGTTTATTCTTATT
1 ATAAAGAGAAATTAACTCCAGTATATCTACACGAAATAAACCTAATGTTTATTCTTATT
*
1459893 ATAAAGAGAAATTAACTCCAGTATATCTACACGAAATAAACCTAATGTTTGTTCTTATT
1 ATAAAGAGAAATTAACTCCAGTATATCTACACGAAATAAACCTAATGTTTATTCTTATT
1459952 CTATGATTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (59 bp):
ATAAAGAGAAATTAACTCCAGTATATCTACACGAAATAAACCTAATGTTTATTCTTATT
Found at i:1466119 original size:50 final size:47
Alignment explanation
Indices: 1466065--1466168 Score: 127
Period size: 47 Copynumber: 2.1 Consensus size: 47
1466055 AAATTTAACA
*
1466065 ATTAAATAAATATTTAAAAAAATAATATTTTTAATAAATATGATAATAAT
1 ATTAAATAAATA--T-AAAAAATAATATTTTTAATAAATATAATAATAAT
* ** * *
1466115 ATTAAATTAATATAAAATTTAATATTTTTAATAAATATAATTATATT
1 ATTAAATAAATATAAAAAATAATATTTTTAATAAATATAATAATAAT
1466162 ATTAAAT
1 ATTAAAT
1466169 TTAACTATCA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
47 36 0.75
48 1 0.02
50 11 0.23
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (47 bp):
ATTAAATAAATATAAAAAATAATATTTTTAATAAATATAATAATAAT
Found at i:1466160 original size:21 final size:21
Alignment explanation
Indices: 1466089--1466166 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 21
1466079 TAAAAAAATA
* *
1466089 ATATTTTTAATAAATATGATA
1 ATATTTTTAATAAATATAATT
* * *
1466110 ATAATATTAAATTAATATAAAATTT
1 AT-ATTTTTAA-TAA-ATATAA-TT
1466135 AATATTTTTAATAAATATAATT
1 -ATATTTTTAATAAATATAATT
*
1466157 ATATTATTAA
1 ATATTTTTAA
1466167 ATTTAACTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
21 11 0.26
22 8 0.19
23 8 0.19
24 7 0.16
25 7 0.16
26 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (21 bp):
ATATTTTTAATAAATATAATT
Found at i:1466284 original size:25 final size:26
Alignment explanation
Indices: 1466252--1466327 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 26
1466242 CAAAGGTCTC
*
1466252 AATTTTAATAAATATAAATTTTAATT
1 AATTTTAATATATATAAATTTTAATT
*
1466278 AA-TTTAATTTATATAATTATTTTAA--
1 AATTTTAATATATATAA--ATTTTAATT
*
1466303 AATTTTAATATA-ATAAATCTTAATT
1 AATTTTAATATATATAAATTTTAATT
1466328 TTAATATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
23 6 0.15
25 18 0.44
26 10 0.24
27 7 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
AATTTTAATATATATAAATTTTAATT
Found at i:1466332 original size:16 final size:15
Alignment explanation
Indices: 1466252--1466333 Score: 59
Period size: 16 Copynumber: 5.7 Consensus size: 15
1466242 CAAAGGTCTC
*
1466252 AATTTTAATAAATATA
1 AATTTTAATAAAT-TT
*
1466268 AATTTTAATTAATTT
1 AATTTTAATAAATTT
1466283 AA-TTT-ATATAA-TT
1 AATTTTAATA-AATTT
*
1466296 -ATTTTAA-AATTTT
1 AATTTTAATAAATTT
*
1466309 AA-TATAATAAATCTT
1 AATTTTAATAAAT-TT
1466324 AATTTTAATA
1 AATTTTAATA
1466334 TTTTTTTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
12 2 0.04
13 14 0.27
14 10 0.20
15 7 0.14
16 18 0.35
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTTAATAAATTT
Found at i:1466720 original size:17 final size:17
Alignment explanation
Indices: 1466700--1466734 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1466690 TGATTTTCAT
1466700 ATTTT-TATTTATATTAA
1 ATTTTATATTT-TATTAA
1466717 ATTTTATATTTTATTAA
1 ATTTTATATTTTATTAA
1466734 A
1 A
1466735 AAAAAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTATATTTTATTAA
Found at i:1472996 original size:59 final size:59
Alignment explanation
Indices: 1472902--1473019 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
1472892 ATGCATTGGA
*
1472902 ATAAAGAGCAATTAACTCCAGTATATCTACTCGAAATAAACCTAATGTTTATTCTTATT
1 ATAAAGAGCAATTAACTCCAGTATATCTACACGAAATAAACCTAATGTTTATTCTTATT
*
1472961 ATAAAGAGCAATTAACTCCAGTATATCTACACGAAATAAACCTAATGTTTGTTCTTATT
1 ATAAAGAGCAATTAACTCCAGTATATCTACACGAAATAAACCTAATGTTTATTCTTATT
1473020 CTATGATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (59 bp):
ATAAAGAGCAATTAACTCCAGTATATCTACACGAAATAAACCTAATGTTTATTCTTATT
Found at i:1476512 original size:19 final size:18
Alignment explanation
Indices: 1476488--1476529 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1476478 CAAAGTAAAT
*
1476488 TTAAAATACTATTTATTAA
1 TTAAAATAATATTT-TTAA
*
1476507 TTAAAATAATATTTTTAT
1 TTAAAATAATATTTTTAA
1476525 TTAAA
1 TTAAA
1476530 TTTAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAAATAATATTTTTAA
Found at i:1478133 original size:12 final size:11
Alignment explanation
Indices: 1478118--1478150 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
1478108 AAAAAGTACT
1478118 TAAATATTATTA
1 TAAATA-TATTA
1478130 TAAATAT-TTA
1 TAAATATATTA
1478140 TAAATATATTA
1 TAAATATATTA
1478151 AAGTCAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 4 0.20
12 6 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAAATATATTA
Found at i:1478306 original size:16 final size:16
Alignment explanation
Indices: 1478277--1478321 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1478267 TTAGATTCGG
* *
1478277 GTCATTTTGGGTTTGA
1 GTCATTTCGAGTTTGA
*
1478293 GTTATTTCGAGTTTGA
1 GTCATTTCGAGTTTGA
*
1478309 GTCATTTGGAGTT
1 GTCATTTCGAGTT
1478322 CGGGTCAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.16, C:0.07, G:0.29, T:0.49
Consensus pattern (16 bp):
GTCATTTCGAGTTTGA
Found at i:1478313 original size:32 final size:33
Alignment explanation
Indices: 1478233--1478315 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 33
1478223 TTTAGATTAT
*
1478233 TTTCGAGTTTGGGTCATTTAAGGTTCGGGTTAC
1 TTTCGAGTTTGGGTCATTTAAGGTTCGAGTTAC
* * ** *
1478266 TTTAGA-TTCGGGTCATTTTGGGTTTGAGTTA-
1 TTTCGAGTTTGGGTCATTTAAGGTTCGAGTTAC
*
1478297 TTTCGAGTTTGAGTCATTT
1 TTTCGAGTTTGGGTCATTT
1478316 GGAGTTCGGG
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
31 5 0.12
32 30 0.75
33 5 0.12
ACGTcount: A:0.16, C:0.10, G:0.28, T:0.47
Consensus pattern (33 bp):
TTTCGAGTTTGGGTCATTTAAGGTTCGAGTTAC
Found at i:1479360 original size:16 final size:16
Alignment explanation
Indices: 1479339--1479426 Score: 67
Period size: 16 Copynumber: 5.5 Consensus size: 16
1479329 ATTTAAGTTT
1479339 GGATCATTTCAGGTTC
1 GGATCATTTCAGGTTC
* **
1479355 GGATCATTTTATATTC
1 GGATCATTTCAGGTTC
1479371 AGG-TCATTTC-GAGTTC
1 -GGATCATTTCAG-GTTC
*
1479387 AGATCATTTC-GGATTC
1 GGATCATTTCAGG-TTC
*
1479403 -AAGTCATTTCAGGTTC
1 GGA-TCATTTCAGGTTC
1479419 GGATCATT
1 GGATCATT
1479427 CTGAATTCAG
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
15 3 0.05
16 48 0.86
17 5 0.09
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (16 bp):
GGATCATTTCAGGTTC
Found at i:1479392 original size:32 final size:31
Alignment explanation
Indices: 1479342--1479444 Score: 118
Period size: 32 Copynumber: 3.2 Consensus size: 31
1479332 TAAGTTTGGA
*
1479342 TCATTTCAGGTTCGGATCATTTTATATTCAGG
1 TCATTTCAGGTTCGGATCATTTCA-ATTCAGG
* * *
1479374 TCATTTC-GAGTTCAGATCATTTCGGATTCAAG
1 TCATTTCAG-GTTCGGATCATTTC-AATTCAGG
*
1479406 TCATTTCAGGTTCGGATCATTCTGAATTCAGG
1 TCATTTCAGGTTCGGATCATT-TCAATTCAGG
1479438 TCATTTC
1 TCATTTC
1479445 GGATTCGAGT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
31 1 0.02
32 56 0.95
33 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (31 bp):
TCATTTCAGGTTCGGATCATTTCAATTCAGG
Found at i:1479410 original size:48 final size:48
Alignment explanation
Indices: 1479358--1479472 Score: 128
Period size: 48 Copynumber: 2.4 Consensus size: 48
1479348 CAGGTTCGGA
* *
1479358 TCATTTTATATTCAGG-TCATT-TCGAGTTCAGATCATTTCGGATTCAAG
1 TCATTTTAGATTC-GGATCATTCT-GAATTCAGATCATTTCGGATTCAAG
* * * *
1479406 TCATTTCAGGTTCGGATCATTCTGAATTCAGGTCATTTCGGATTCGAG
1 TCATTTTAGATTCGGATCATTCTGAATTCAGATCATTTCGGATTCAAG
1479454 TCATTTT-GAGTTCGGATCA
1 TCATTTTAGA-TTCGGATCA
1479473 ATTCAGATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
47 3 0.05
48 52 0.93
49 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (48 bp):
TCATTTTAGATTCGGATCATTCTGAATTCAGATCATTTCGGATTCAAG
Found at i:1479450 original size:16 final size:16
Alignment explanation
Indices: 1479367--1479459 Score: 79
Period size: 16 Copynumber: 5.8 Consensus size: 16
1479357 ATCATTTTAT
1479367 ATTCAGGTCATTTC-G
1 ATTCAGGTCATTTCGG
*
1479382 AGTTCAGATCATTTCGG
1 A-TTCAGGTCATTTCGG
*
1479399 ATTCAAGTCATTTCAGG
1 ATTCAGGTCATTTC-GG
*
1479416 -TTC-GGATCA-TTCTGA
1 ATTCAGG-TCATTTC-GG
1479431 ATTCAGGTCATTTCGG
1 ATTCAGGTCATTTCGG
1479447 ATTC-GAGTCATTT
1 ATTCAG-GTCATTT
1479460 TGAGTTCGGA
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
15 7 0.11
16 47 0.75
17 9 0.14
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (16 bp):
ATTCAGGTCATTTCGG
Found at i:1479458 original size:32 final size:33
Alignment explanation
Indices: 1479342--1479459 Score: 101
Period size: 32 Copynumber: 3.7 Consensus size: 33
1479332 TAAGTTTGGA
*
1479342 TCATTTCAGG-TTCG-GATCATTT-TATATTCAGG
1 TCATTTC-GGATTCGAGATCATTTCGA-ATTCAGG
* *
1479374 TCATTTC-GAGTTC-AGATCATTTCGGATTCAAG
1 TCATTTCGGA-TTCGAGATCATTTCGAATTCAGG
1479406 TCATTTCAGG-TTCG-GATCA-TTCTGAATTCAGG
1 TCATTTC-GGATTCGAGATCATTTC-GAATTCAGG
1479438 TCATTTCGGATTCGAG-TCATTT
1 TCATTTCGGATTCGAGATCATTT
1479460 TGAGTTCGGA
Statistics
Matches: 70, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
30 1 0.01
31 5 0.07
32 60 0.86
33 3 0.04
34 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (33 bp):
TCATTTCGGATTCGAGATCATTTCGAATTCAGG
Found at i:1480758 original size:22 final size:22
Alignment explanation
Indices: 1480715--1480781 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
1480705 TTAATATTTA
* *
1480715 AAATTTTATATCAT-ATTAAAAT
1 AAATTTTATATTATAAAT-AAAT
1480737 AAATTTTATATTATAAATAAAT
1 AAATTTTATATTATAAATAAAT
*
1480759 AAATAATTTATATT-TATATAAAT
1 AAAT--TTTATATTATAAATAAAT
1480782 TTATATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
22 21 0.54
23 10 0.26
24 8 0.21
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATTTTATATTATAAATAAAT
Found at i:1480784 original size:16 final size:16
Alignment explanation
Indices: 1480763--1480811 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
1480753 ATAAATAAAT
1480763 AATTTATATTTATATA
1 AATTTATATTTATATA
*
1480779 AATTTATATTTTTA-A
1 AATTTATATTTATATA
1480794 AATATTAATAATTTATAT
1 AAT-TT-AT-ATTTATAT
1480812 TATATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 2 0.07
18 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTTATATTTATATA
Found at i:1481174 original size:2 final size:2
Alignment explanation
Indices: 1481169--1481193 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1481159 AAAAAAAGTT
1481169 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 T
1481194 TTATCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1481505 original size:15 final size:16
Alignment explanation
Indices: 1481485--1481525 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1481475 CAGACGAAAG
1481485 TATTTAATATAT-ATT
1 TATTTAATATATAATT
*
1481500 TATTTAAT-TTTAATT
1 TATTTAATATATAATT
1481515 TAATTTAATAT
1 T-ATTTAATAT
1481526 TTTAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 12 0.55
16 7 0.32
17 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTAATATATAATT
Found at i:1482051 original size:21 final size:22
Alignment explanation
Indices: 1482030--1482075 Score: 56
Period size: 25 Copynumber: 2.0 Consensus size: 22
1482020 AGTAAATTTA
1482030 TAAATCATCTCTAATTAATTATTTT
1 TAAATCATCTCTAATTAATTA---T
*
1482055 TTAATCATCTCTAATTAATTA
1 TAAATCATCTCTAATTAATTA
1482076 GTTGGAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAATCATCTCTAATTAATTAT
Found at i:1482686 original size:6 final size:6
Alignment explanation
Indices: 1482665--1482759 Score: 53
Period size: 5 Copynumber: 16.8 Consensus size: 6
1482655 AAATAATTTA
* * *
1482665 TATATT TATA-T AATATT TATA-T TATTATT TTTATAT TATAAT TATATT
1 TATATT TATATT TATATT TATATT TA-TATT TATAT-T TATATT TATATT
* * *
1482713 TACA-T TAT-TA TATATT TAT-GT TATATT T-TATT T-TATT T-TATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
*
1482755 CATAT
1 TATAT
1482760 AAATATCTTA
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
5 31 0.46
6 31 0.46
7 6 0.09
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (6 bp):
TATATT
Found at i:1482700 original size:31 final size:31
Alignment explanation
Indices: 1482660--1482723 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1482650 AGATTAAATA
*
1482660 ATTTATATATT-TATATAATATTTATATTATT
1 ATTTATATATTATA-ATAATATTTACATTATT
* *
1482691 ATTTTTATATTATAATTATATTTACATTATT
1 ATTTATATATTATAATAATATTTACATTATT
1482722 AT
1 AT
1482724 ATATTTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (31 bp):
ATTTATATATTATAATAATATTTACATTATT
Found at i:1482701 original size:11 final size:11
Alignment explanation
Indices: 1482663--1482760 Score: 52
Period size: 11 Copynumber: 9.4 Consensus size: 11
1482653 TTAAATAATT
1482663 TATA-TATTTA
1 TATATTATTTA
*
1482673 TATAATATTTA
1 TATATTATTTA
1482684 TATTATTATTT-
1 TA-TATTATTTA
1482695 T-TA-TA-TTA
1 TATATTATTTA
1482703 TA-ATTATATT-
1 TATATTAT-TTA
*
1482713 TACATTA-TTA
1 TATATTATTTA
1482723 TATATTTATGTTA
1 TATA-TTAT-TTA
*
1482736 TATTTTATTT-
1 TATATTATTTA
* *
1482746 TATTTTATTCA
1 TATATTATTTA
1482757 TATA
1 TATA
1482761 AATATCTTAA
Statistics
Matches: 70, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 6 0.09
10 18 0.26
11 23 0.33
12 11 0.16
13 6 0.09
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (11 bp):
TATATTATTTA
Found at i:1482722 original size:14 final size:14
Alignment explanation
Indices: 1482665--1482753 Score: 59
Period size: 14 Copynumber: 6.6 Consensus size: 14
1482655 AAATAATTTA
1482665 TATATTTATA-TA-
1 TATATTTATATTAT
1482677 -ATATTTATATTAT
1 TATATTTATATTAT
*
1482690 TATTTTTATATTATAAT
1 TATATTTATA-T-T-AT
*
1482707 TATATTTACATTAT
1 TATATTTATATTAT
*
1482721 TATATATT-TA-TGT
1 TATAT-TTATATTAT
1482734 TATATTT-TATT-T
1 TATATTTATATTAT
1482746 TAT-TTTAT
1 TATATTTAT
1482754 TCATATAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
11 12 0.19
12 11 0.17
13 8 0.13
14 16 0.25
15 4 0.06
16 2 0.03
17 10 0.16
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (14 bp):
TATATTTATATTAT
Found at i:1482748 original size:25 final size:24
Alignment explanation
Indices: 1482660--1482748 Score: 76
Period size: 25 Copynumber: 3.5 Consensus size: 24
1482650 AGATTAAATA
*
1482660 ATTTATATATTTATATAATATTTAT
1 ATTTATAT-TTTATATATTATTTAT
1482685 A-TTATTATTTT-TATATTATAATTAT
1 ATTTA-TATTTTATATATTAT--TTAT
*
1482710 ATTTACATTATTATATATTTATGTTAT
1 ATTTATATT-TTATATA-TTAT-TTAT
1482737 ATTT-TATTTTAT
1 ATTTATATTTTAT
1482749 TTTATTCATA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
23 7 0.13
24 6 0.11
25 16 0.30
26 8 0.15
27 12 0.23
28 4 0.08
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (24 bp):
ATTTATATTTTATATATTATTTAT
Found at i:1483536 original size:2 final size:2
Alignment explanation
Indices: 1483529--1483561 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1483519 CTCGCTTTGG
*
1483529 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1483562 ATCTTGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1483901 original size:14 final size:15
Alignment explanation
Indices: 1483874--1483915 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
1483864 AAAAGTGATA
1483874 AAAATTATAAATTTT
1 AAAATTATAAATTTT
1483889 AAAATTA-AAATTTT
1 AAAATTATAAATTTT
*
1483903 AAATTTATTAAAT
1 AAAATTA-TAAAT
1483916 AATATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 13 0.54
15 7 0.29
16 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTATAAATTTT
Found at i:1483930 original size:16 final size:16
Alignment explanation
Indices: 1483906--1483938 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1483896 AAATTTTAAA
1483906 TTTATTAAATAATATTT
1 TTTATTAAATAAT-TTT
1483923 TTTA-TAAATAATTTT
1 TTTATTAAATAATTTT
1483938 T
1 T
1483939 ACGAACTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATTAAATAATTTT
Found at i:1484207 original size:2 final size:2
Alignment explanation
Indices: 1484200--1484227 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1484190 TTTGTTATTT
1484200 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
1484228 AAATAATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1484935 original size:2 final size:2
Alignment explanation
Indices: 1484928--1484956 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1484918 CTTGTCGTGG
1484928 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1484957 GCGCTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1485305 original size:36 final size:36
Alignment explanation
Indices: 1485253--1485338 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
1485243 AATTAATAAA
* * *
1485253 ATAATAATATTAAAATTAATTATATATTTTTATATTT
1 ATAAAAATA-TAAAATTAATTATATATTTCTATAATT
*
1485290 ATAAAAATATAAAATTAATTATGTATTTCTATAATT
1 ATAAAAATATAAAATTAATTATATATTTCTATAATT
* *
1485326 AAAAAAAAATAAA
1 ATAAAAATATAAA
1485339 CACGTCTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 35 0.81
37 8 0.19
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (36 bp):
ATAAAAATATAAAATTAATTATATATTTCTATAATT
Found at i:1486001 original size:21 final size:21
Alignment explanation
Indices: 1485962--1486001 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1485952 ATATTTTTTG
*
1485962 TATTATAATTATATTTAAAGT
1 TATTATAATTATATATAAAGT
1485983 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
1486002 TTTTAGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TATTATAATTATATATAAAGT
Found at i:1486029 original size:32 final size:33
Alignment explanation
Indices: 1485993--1486054 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
1485983 TATTATATAT
*
1485993 TTATATAAATTTTAG-TATGTAAATA-ATTTTTA
1 TTATAT-AATTTTAGATATATAAATATATTTTTA
*
1486025 TTATATAATTTTTGATATATAAATATATTT
1 TTATATAATTTTAGATATATAAATATATTT
1486055 GTATCGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 7 0.27
32 15 0.58
33 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (33 bp):
TTATATAATTTTAGATATATAAATATATTTTTA
Found at i:1486103 original size:26 final size:28
Alignment explanation
Indices: 1486061--1486115 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
1486051 ATTTGTATCG
*
1486061 TATTTTTATTTTATTATA-TT-AAATTA
1 TATTTTAATTTTATTATATTTAAAATTA
1486087 TATTTTAATTATT-TTATATTTAAAATTA
1 TATTTTAATT-TTATTATATTTAAAATTA
1486115 T
1 T
1486116 TAAATCTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 14 0.56
27 4 0.16
28 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TATTTTAATTTTATTATATTTAAAATTA
Found at i:1486894 original size:28 final size:25
Alignment explanation
Indices: 1486862--1486940 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 25
1486852 ATATTTTTAT
1486862 TTAAATTTAATTATAAATATATAATAA
1 TTAAATTTAATT-TAAATATA-AATAA
* *
1486889 TATAAAATAAATTTTTAAATATAAATAA
1 T-TAAATTTAA--TTTAAATATAAATAA
1486917 TTAAAATATT-ATTTAAATATAAAT
1 TT-AAAT-TTAATTTAAATATAAAT
1486941 TCAATTTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
26 13 0.30
27 2 0.05
28 17 0.40
29 9 0.21
30 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAAATTTAATTTAAATATAAATAA
Found at i:1486936 original size:45 final size:42
Alignment explanation
Indices: 1486828--1486939 Score: 104
Period size: 45 Copynumber: 2.5 Consensus size: 42
1486818 TTGATTTGAT
* *
1486828 TTAAATTATTATTTAAATAATAAAATATTTTTATTTAAATTTAA
1 TTAAAATATTATTTAAAT-ATAAAATATTTTTATATAAA-TTAA
*
1486872 TTATAAATA-TA-TAATAATATAAAATAAATTTTTAAATATAAA-TAA
1 TTA-AAATATTATTTA-AATATAAAAT--ATTTTT--ATATAAATTAA
1486917 TTAAAATATTATTTAAATATAAA
1 TTAAAATATTATTTAAATATAAA
1486940 TTCAATTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
43 9 0.16
44 13 0.23
45 26 0.46
46 2 0.04
47 6 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (42 bp):
TTAAAATATTATTTAAATATAAAATATTTTTATATAAATTAA
Found at i:1486938 original size:26 final size:27
Alignment explanation
Indices: 1486875--1486940 Score: 91
Period size: 26 Copynumber: 2.4 Consensus size: 27
1486865 AATTTAATTA
1486875 TAAATATATAATAATATAAAATAAATTTT
1 TAAATATA-AATAATATAAAAT-AATTTT
1486904 TAAATATAAATAAT-TAAAAT-ATTATT
1 TAAATATAAATAATATAAAATAATT-TT
1486930 TAAATATAAAT
1 TAAATATAAAT
1486941 TCAATTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 3 0.08
26 13 0.36
27 6 0.17
28 6 0.17
29 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAATATAAATAATATAAAATAATTTT
Found at i:1487177 original size:6 final size:7
Alignment explanation
Indices: 1487145--1487175 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1487135 AGCGCAAAGT
1487145 AAAAGGG
1 AAAAGGG
*
1487152 GAAAGGG
1 AAAAGGG
1487159 AAAAGGG
1 AAAAGGG
1487166 AAAAGGG
1 AAAAGGG
1487173 AAA
1 AAA
1487176 GGAACCAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (7 bp):
AAAAGGG
Found at i:1488307 original size:6 final size:6
Alignment explanation
Indices: 1488296--1488350 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
1488286 AACGAATAAG
* *
1488296 TTTATA TTTATA TTTATA TATT-TA TTTTTAA ATT-TA TTTATA TTTA-A
1 TTTATA TTTATA TTTATA T-TTATA TTTAT-A TTTATA TTTATA TTTATA
1488343 TTTATA TT
1 TTTATA TT
1488351 AATTAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
5 10 0.24
6 27 0.64
7 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:1488325 original size:20 final size:21
Alignment explanation
Indices: 1488296--1488355 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
1488286 AACGAATAAG
1488296 TTTATATTTATATTTA-TATA
1 TTTATATTTATATTTATTATA
* *
1488316 TTTATTTTTAAATTTATTTATA
1 TTTATATTTATATTTA-TTATA
*
1488338 TTTA-ATTTATATTAATTA
1 TTTATATTTATATTTATTA
1488356 AAATTTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 17 0.52
21 8 0.24
22 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTATATTTATATTTATTATA
Found at i:1488335 original size:16 final size:16
Alignment explanation
Indices: 1488300--1488366 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
1488290 AATAAGTTTA
*
1488300 TATTTATATTT--ATA
1 TATTTATATTTAAATT
*
1488314 TATTTATTTTTAAATT
1 TATTTATATTTAAATT
1488330 TATTTATATTT-AATT
1 TATTTATATTTAAATT
*
1488345 TATATTA-ATTAAAATT
1 TAT-TTATATTTAAATT
1488361 TATTTA
1 TATTTA
1488367 AATTATGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
14 10 0.22
15 13 0.29
16 22 0.49
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTATATTTAAATT
Found at i:1488369 original size:10 final size:10
Alignment explanation
Indices: 1488322--1488370 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
1488312 TATATTTATT
1488322 TTTAAATTTA
1 TTTAAATTTA
*
1488332 TTTATATTTAA
1 TTTAAATTT-A
* *
1488343 TTTATATTAA
1 TTTAAATTTA
*
1488353 TTAAAATTTA
1 TTTAAATTTA
1488363 TTTAAATT
1 TTTAAATT
1488371 ATGTTTGAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:1488370 original size:16 final size:16
Alignment explanation
Indices: 1488325--1488371 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1488315 ATTTATTTTT
*
1488325 AAATTTATTTATATT-
1 AAATTTATTTAAATTA
*
1488340 TAATTTATATT-AATTA
1 AAATTTAT-TTAAATTA
1488356 AAATTTATTTAAATTA
1 AAATTTATTTAAATTA
1488372 TGTTTGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATTTATTTAAATTA
Found at i:1488492 original size:22 final size:22
Alignment explanation
Indices: 1488467--1488515 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1488457 ACCTAAAATC
*
1488467 AAATATATTTA-AGAATAATTAA
1 AAATATATTTATA-AATAATAAA
1488489 AAATATATTTATAAATAATAAA
1 AAATATATTTATAAATAATAAA
1488511 AAATA
1 AAATA
1488516 AAGCTTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAATATATTTATAAATAATAAA
Found at i:1488634 original size:24 final size:21
Alignment explanation
Indices: 1488581--1488634 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
1488571 TATAAAGTAA
*
1488581 AAATCAAATATTATTATAAAT
1 AAATCAAATAATATTATAAAT
*
1488602 AAATAAAATAATATTATTAAATT
1 AAATCAAATAATATTA-TAAA-T
1488625 CAAATCAAAT
1 -AAATCAAAT
1488635 CATAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.52
22 4 0.15
23 1 0.04
24 8 0.30
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATCAAATAATATTATAAAT
Found at i:1488645 original size:11 final size:11
Alignment explanation
Indices: 1488593--1488662 Score: 53
Period size: 11 Copynumber: 6.7 Consensus size: 11
1488583 ATCAAATATT
1488593 ATTATAAATAA
1 ATTATAAATAA
1488604 A-TA-AAATAA
1 ATTATAAATAA
1488613 TATTAT---TAA
1 -ATTATAAATAA
*
1488622 ATT-CAAATCAA
1 ATTATAAAT-AA
*
1488633 ATCATAAATAA
1 ATTATAAATAA
*
1488644 ATTTTAAATAA
1 ATTATAAATAA
1488655 ATTATAAA
1 ATTATAAA
1488663 CAAACTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
8 3 0.07
9 9 0.20
10 4 0.09
11 25 0.56
12 4 0.09
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (11 bp):
ATTATAAATAA
Found at i:1490294 original size:27 final size:28
Alignment explanation
Indices: 1490264--1490317 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1490254 TAGATATATA
1490264 TATTATTTTAATT-AATTTAATT-TAAAT
1 TATTA-TTTAATTAAATTTAATTATAAAT
*
1490291 TATTATTTATTTAAATTTAATTATAAA
1 TATTATTTAATTAAATTTAATTATAAA
1490318 AATGAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 6 0.25
27 14 0.58
28 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TATTATTTAATTAAATTTAATTATAAAT
Found at i:1490944 original size:29 final size:28
Alignment explanation
Indices: 1490886--1490947 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
1490876 AATTCGTATT
**
1490886 AAATTAAATTATGATTAAAAAAATTTTA
1 AAATTAAATTATGATTAAAAAAATAATA
* * *
1490914 AAATTAAAATTATTATTTAAAATATAATA
1 AAATT-AAATTATGATTAAAAAAATAATA
1490943 AAATT
1 AAATT
1490948 TTTATATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
AAATTAAATTATGATTAAAAAAATAATA
Found at i:1491042 original size:22 final size:21
Alignment explanation
Indices: 1490984--1491035 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
1490974 TTATAATAAA
*
1490984 ATTTAAATAAAAATATTATTTT
1 ATTTAAA-AAAAATATTATATT
*
1491006 AATTAATAAAAAATATTATATT
1 ATTTAA-AAAAAATATTATATT
1491028 ATTTAAAA
1 ATTTAAAA
1491036 TCAAATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.08
22 23 0.88
23 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTAAAAAAAATATTATATT
Found at i:1491472 original size:20 final size:20
Alignment explanation
Indices: 1491447--1491498 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1491437 ATAATAAAAT
*
1491447 TTAAAATAATTTATT-TTATA
1 TTAAAA-AATTTATTATTAAA
1491467 TT-AAAAATTATATTATTAAA
1 TTAAAAAATT-TATTATTAAA
1491487 TTAAAAAATTTA
1 TTAAAAAATTTA
1491499 GATATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 4 0.14
19 7 0.25
20 10 0.36
21 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAAAAATTTATTATTAAA
Found at i:1498937 original size:70 final size:70
Alignment explanation
Indices: 1498847--1498997 Score: 259
Period size: 70 Copynumber: 2.2 Consensus size: 70
1498837 TTTGGTTTTG
*
1498847 AATTTTGAATTGAGAGTTAATTAAGTAGATTTATATAATTA-TTTTAAAAAAGTAATAATAAATA
1 AATTTTGAATTGAAAGTTAATTAAGTAGATTTATATAATTATTTTTAAAAAA-TAATAATAAATA
1498911 TGTTTA
65 TGTTTA
*
1498917 AATTTTGAATTGAAATTTAATTAAGTAGATTTATATAATTATTTTTAAAAAATAATAATAAATAT
1 AATTTTGAATTGAAAGTTAATTAAGTAGATTTATATAATTATTTTTAAAAAATAATAATAAATAT
1498982 GTTTA
66 GTTTA
*
1498987 AAATTTGAATT
1 AATTTTGAATT
1498998 TCGTAATCTC
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
70 67 0.87
71 10 0.13
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.44
Consensus pattern (70 bp):
AATTTTGAATTGAAAGTTAATTAAGTAGATTTATATAATTATTTTTAAAAAATAATAATAAATAT
GTTTA
Found at i:1501412 original size:22 final size:22
Alignment explanation
Indices: 1501373--1501417 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1501363 TATATTATTA
*
1501373 ATATTTTTATATTAAAATTAAT
1 ATATTTTTATATTAAAATAAAT
1501395 ATATTTTTATGATT-AAATAAAT
1 ATATTTTTAT-ATTAAAATAAAT
1501417 A
1 A
1501418 AAAATAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATTTTTATATTAAAATAAAT
Found at i:1505911 original size:2 final size:2
Alignment explanation
Indices: 1505899--1505929 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1505889 GAAATATAAA
*
1505899 AT AT AT TT 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
1505930 ACAAAATGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1506639 original size:19 final size:21
Alignment explanation
Indices: 1506604--1506643 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
1506594 GAACCGTCGT
1506604 TAATATATATATATTATTTTA
1 TAATATATATATATTATTTTA
1506625 TAATA-ATAT-TATTATTTTA
1 TAATATATATATATTATTTTA
1506644 AATGTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 4 0.21
21 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATATATATATTATTTTA
Found at i:1506881 original size:23 final size:24
Alignment explanation
Indices: 1506846--1506893 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
1506836 ATAAAAATAA
1506846 AAAATAATTTATA-TTTAAT-TAT
1 AAAATAATTTATATTTTAATATAT
*
1506868 AAAATATTTATATATTTTAATATAT
1 AAAATAATT-TATATTTTAATATAT
1506893 A
1 A
1506894 TCTTTCCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 4 0.18
24 6 0.27
25 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AAAATAATTTATATTTTAATATAT
Found at i:1509563 original size:2 final size:2
Alignment explanation
Indices: 1509552--1509584 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1509542 AATCAATAAA
1509552 AT AT -T 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
1509585 CTGAGTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1529475 original size:2 final size:2
Alignment explanation
Indices: 1529468--1529498 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1529458 ATTCAAAGCA
1529468 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1529499 ACAAATGGTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1530673 original size:14 final size:14
Alignment explanation
Indices: 1530654--1530680 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1530644 TAGCTATATA
1530654 TGTCTGTGTGTGTG
1 TGTCTGTGTGTGTG
1530668 TGTCTGTGTGTGT
1 TGTCTGTGTGTGT
1530681 ATATACACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.41, T:0.52
Consensus pattern (14 bp):
TGTCTGTGTGTGTG
Found at i:1531484 original size:3 final size:3
Alignment explanation
Indices: 1531476--1531504 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1531466 AAATTGAAAA
1531476 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1531505 AATGTTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:1533372 original size:2 final size:2
Alignment explanation
Indices: 1533365--1533404 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1533355 TGTAGACATG
1533365 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1533405 AAATTGATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1534383 original size:13 final size:13
Alignment explanation
Indices: 1534365--1534394 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1534355 AGTGCTGCTG
1534365 TTTTTTTTCTCTT
1 TTTTTTTTCTCTT
*
1534378 TTTTTTTTTTCTT
1 TTTTTTTTCTCTT
1534391 TTTT
1 TTTT
1534395 GTAGTGCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTCTCTT
Found at i:1534385 original size:15 final size:14
Alignment explanation
Indices: 1534365--1534394 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1534355 AGTGCTGCTG
1534365 TTTTTTTTCTCTTTT
1 TTTTTTTTCT-TTTT
1534380 TTTTTTTTCTTTTT
1 TTTTTTTTCTTTTT
1534394 T
1 T
1534395 GTAGTGCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTCTTTTT
Found at i:1535769 original size:24 final size:22
Alignment explanation
Indices: 1535742--1535795 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
1535732 AAATTTGATA
*
1535742 TTTAAATTTTAATATTTATAATTT
1 TTTAAATTTTAA-A-TTACAATTT
*
1535766 TTTATTATTTTTAAATTACAATTT
1 TTTA--AATTTTAAATTACAATTT
1535790 TTTAAA
1 TTTAAA
1535796 AAAAACACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
22 1 0.04
24 16 0.64
25 1 0.04
26 7 0.28
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTAAATTTTAAATTACAATTT
Found at i:1536085 original size:17 final size:16
Alignment explanation
Indices: 1536055--1536129 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 16
1536045 TTAAATATGT
**
1536055 TATAATATAAATAATAA
1 TATAATATTTATAA-AA
1536072 TATAATATTTATAAATA
1 TATAATATTTATAAA-A
*
1536089 TATTAAAATTATATAAAATA
1 TA-TAATATT-TAT-AAA-A
1536109 TATAATATTT-T-AAA
1 TATAATATTTATAAAA
1536123 TATAATA
1 TATAATA
1536130 ATAATAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
14 8 0.16
15 2 0.04
16 1 0.02
17 16 0.32
18 7 0.14
19 9 0.18
20 7 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAATATTTATAAAA
Found at i:1536112 original size:37 final size:36
Alignment explanation
Indices: 1536042--1536145 Score: 115
Period size: 37 Copynumber: 2.8 Consensus size: 36
1536032 ATATTAAAAA
* *
1536042 ATTTTAAATATGTTATAATATAAATAATAATATAAT
1 ATTTTAAATATATTAAAATATAAATAATAATATAAT
1536078 ATTTATAAATATATTAAAATTATATAA-AAT-ATATAAT
1 ATTT-TAAATATATTAAAA-TATA-AATAATAATATAAT
*
1536115 ATTTTAAATATAATAATAATA-ATAATAATAA
1 ATTTTAAATATATTAA-AATATA-AATAATAA
1536146 ACAAAACACT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
35 4 0.07
36 20 0.34
37 26 0.44
38 7 0.12
39 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (36 bp):
ATTTTAAATATATTAAAATATAAATAATAATATAAT
Found at i:1536130 original size:17 final size:18
Alignment explanation
Indices: 1536073--1536132 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
1536063 AAATAATAAT
1536073 ATAATATTTATAAATATA
1 ATAATATTTATAAATATA
* *
1536091 TTAAAATTATATAAA-ATA
1 ATAATATT-TATAAATATA
1536109 TATAATATTT-TAAATATA
1 -ATAATATTTATAAATATA
1536127 ATAATA
1 ATAATA
1536133 ATAATAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
17 10 0.29
18 13 0.37
19 12 0.34
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATATTTATAAATATA
Found at i:1537628 original size:25 final size:25
Alignment explanation
Indices: 1537595--1537643 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1537585 TATTTTATAT
1537595 TAATATTTA-TAATTTAAATAATAAA
1 TAATATTTATTAATTT-AATAATAAA
*
1537620 TAATTTTTATTAATTTAATAATAA
1 TAATATTTATTAATTTAATAATAA
1537644 TTTAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATATTTATTAATTTAATAATAAA
Found at i:1537657 original size:15 final size:16
Alignment explanation
Indices: 1537629--1537662 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1537619 ATAATTTTTA
*
1537629 TTAATTTAATAATAAT
1 TTAAATTAATAATAAT
1537645 TTAAATTAA-AATAAT
1 TTAAATTAATAATAAT
1537660 TTA
1 TTA
1537663 TTTAAATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTAATAATAAT
Found at i:1537659 original size:21 final size:21
Alignment explanation
Indices: 1537595--1537659 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
1537585 TATTTTATAT
*
1537595 TAAT-ATTTATAATTTAAATAA
1 TAATAATTTA-AATTAAAATAA
** **
1537616 TAAATAATTTTTATTAATTTAA
1 T-AATAATTTAAATTAAAATAA
1537638 TAATAATTTAAATTAAAATAA
1 TAATAATTTAAATTAAAATAA
1537659 T
1 T
1537660 TTATTTAAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
21 18 0.55
22 11 0.33
23 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATAATTTAAATTAAAATAA
Found at i:1537963 original size:7 final size:7
Alignment explanation
Indices: 1537951--1537976 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1537941 TAATTACTTC
1537951 AATAATA
1 AATAATA
1537958 AATAATA
1 AATAATA
1537965 AATAATA
1 AATAATA
1537972 AATAA
1 AATAA
1537977 AAAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AATAATA
Found at i:1538304 original size:20 final size:20
Alignment explanation
Indices: 1538257--1538313 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1538247 ATTTAAAATA
*
1538257 TTATATATTTTATAATA-TAT
1 TTATAT-TTTTATATTATTAT
* *
1538277 TAATATTTTTATATTATTTT
1 TTATATTTTTATATTATTAT
1538297 TTATATTTTTATATTAT
1 TTATATTTTTATATTAT
1538314 ATTCATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.28
20 23 0.72
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTTTTATATTATTAT
Found at i:1539300 original size:18 final size:19
Alignment explanation
Indices: 1539254--1539301 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1539244 TTTAATTATA
* **
1539254 AATATTAATTTAAAATTTT
1 AATATTAATTTTAAATAAT
1539273 AATATT-ATTTTAAATAAT
1 AATATTAATTTTAAATAAT
1539291 AA-ATTAATTTT
1 AATATTAATTTT
1539302 TAAACTACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 16 0.64
19 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATTAATTTTAAATAAT
Found at i:1540704 original size:14 final size:15
Alignment explanation
Indices: 1540685--1540721 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1540675 AATATAATAT
1540685 TAATATTTATT-TAA
1 TAATATTTATTATAA
1540699 TAATA-TTATTATAA
1 TAATATTTATTATAA
1540713 -AATATTTAT
1 TAATATTTAT
1540722 GTATTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATATTTATTATAA
Found at i:1541230 original size:2 final size:2
Alignment explanation
Indices: 1541223--1541266 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1541213 TTCATGTCCC
* *
1541223 CT CT CT CT CT CT CT CT CT CT CT CT CT GT GT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1541265 CT
1 CT
1541267 AAATTAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.45, G:0.05, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1541583 original size:2 final size:2
Alignment explanation
Indices: 1541576--1541606 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1541566 CTATAATTAC
*
1541576 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1541607 ATTATGACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1544954 original size:20 final size:20
Alignment explanation
Indices: 1544929--1544966 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1544919 AGATTTAACA
1544929 ATTAT-AATTATATATAAAAT
1 ATTATAAATT-TATATAAAAT
1544949 ATTATAAATTTATATAAA
1 ATTATAAATTTATATAAA
1544967 TTTTAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTATAAATTTATATAAAAT
Found at i:1545029 original size:17 final size:19
Alignment explanation
Indices: 1545004--1545055 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1544994 TTTGTCATTT
1545004 TTATTATATTAT-ATTTTA
1 TTATTATATTATAATTTTA
* *
1545022 TT-TTATATTTTAATTTTT
1 TTATTATATTATAATTTTA
*
1545040 TTATTATATTAAAATT
1 TTATTATATTATAATT
1545056 ATGTTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 8 0.29
18 9 0.32
19 11 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTATATTATAATTTTA
Found at i:1546540 original size:2 final size:2
Alignment explanation
Indices: 1546533--1546558 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1546523 TTGATATTGA
1546533 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
1546559 CTTCATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1547268 original size:22 final size:23
Alignment explanation
Indices: 1547236--1547282 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1547226 TTAAAAAATT
* *
1547236 AAAATAAAATT-TAATATTATTA
1 AAAATAAAATTAAAATATGATTA
*
1547258 AAAATATAATTAAAATATGATTA
1 AAAATAAAATTAAAATATGATTA
1547281 AA
1 AA
1547283 TATGTTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAATAAAATTAAAATATGATTA
Found at i:1548292 original size:2 final size:2
Alignment explanation
Indices: 1548287--1548311 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1548277 TCTCTCTCTC
1548287 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 T
1548312 TAAGTGAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1548772 original size:32 final size:31
Alignment explanation
Indices: 1548731--1548791 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
1548721 TAAGATTTAT
*
1548731 TTTTTATTTAAGTTTATTTTTTAA-ATTTAATA
1 TTTTTATTTAA-TTT-TTTTTAAATATTTAATA
1548763 TTTTTATTTAATTTTTTTTAAATATTTAA
1 TTTTTATTTAATTTTTTTTAAATATTTAA
1548792 CAAATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.26
31 9 0.33
32 11 0.41
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (31 bp):
TTTTTATTTAATTTTTTTTAAATATTTAATA
Found at i:1550861 original size:26 final size:26
Alignment explanation
Indices: 1550830--1550918 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 26
1550820 TGTATTTTAT
1550830 TATTTTATAATTATATATATTTAAAA
1 TATTTTATAATTATATATATTTAAAA
* * * *
1550856 TATTTTATATTTATTTAAATTT-TAA
1 TATTTTATAATTATATATATTTAAAA
*
1550881 TATATTAATAATT-TATAT-TTTATAAA
1 TAT-TTTATAATTATATATATTTA-AAA
1550907 -ATTTTA-AATTAT
1 TATTTTATAATTAT
1550919 TTAATATATT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
23 4 0.08
24 7 0.14
25 10 0.20
26 28 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TATTTTATAATTATATATATTTAAAA
Found at i:1550879 original size:17 final size:16
Alignment explanation
Indices: 1550857--1550922 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
1550847 TATTTAAAAT
1550857 ATTTTATATTTATTTAA
1 ATTTTA-ATTTATTTAA
* *
1550874 ATTTTAATATATTAATA
1 ATTTTAATTTATTTA-A
* *
1550891 ATTTATATTTTA-TAAA
1 ATTT-TAATTTATTTAA
*
1550907 ATTTTAAATTATTTAA
1 ATTTTAATTTATTTAA
1550923 TATATTTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
15 5 0.13
16 15 0.38
17 14 0.36
18 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTAATTTATTTAA
Found at i:1550883 original size:18 final size:20
Alignment explanation
Indices: 1550842--1550885 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1550832 TTTTATAATT
*
1550842 ATATATATTTAAAATATTTT
1 ATATATATTTAAAATATTTA
*
1550862 ATATTTATTT-AAAT-TTTA
1 ATATATATTTAAAATATTTA
1550880 ATATAT
1 ATATAT
1550886 TAATAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 8 0.38
19 4 0.19
20 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATATTTAAAATATTTA
Found at i:1550909 original size:33 final size:34
Alignment explanation
Indices: 1550854--1550931 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 34
1550844 ATATATTTAA
* *
1550854 AATATTTTATATTTATTTAAATTTT-AA-TATATT
1 AATAATTTATATTTATTAAAATTTTAAATTAT-TT
1550887 AATAATTTATATTT-TATAAAATTTTAAATTATTT
1 AATAATTTATATTTAT-TAAAATTTTAAATTATTT
1550921 AATATATTTAT
1 AATA-ATTTAT
1550932 GTTATACATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 1 0.03
33 21 0.54
34 8 0.21
35 9 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
AATAATTTATATTTATTAAAATTTTAAATTATTT
Found at i:1550953 original size:52 final size:51
Alignment explanation
Indices: 1550843--1550989 Score: 137
Period size: 51 Copynumber: 2.9 Consensus size: 51
1550833 TTTATAATTA
* *
1550843 TATATATTTAAAATATTTTATATTTATTTAA--AT-TTTA-ATATATTA-ATAATT
1 TATAT-TTTAAAA-ATTTTATA-ATATTTAATTATATTTATAT-TA-TACATATTT
*
1550894 TATATTTTATAAAATTTTA-AATTATTTAA-TATATTTATGTTATACATATTT
1 TATATTTTA-AAAATTTTATAA-TATTTAATTATATTTATATTATACATATTT
*
1550945 TATCATTTTAAAAATTTTATAATATTTAATTATTTTTATATTATA
1 TAT-ATTTTAAAAATTTTATAATATTTAATTATATTTATATTATA
1550990 TTTATGTTGT
Statistics
Matches: 82, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
49 8 0.10
50 14 0.17
51 38 0.46
52 22 0.27
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (51 bp):
TATATTTTAAAAATTTTATAATATTTAATTATATTTATATTATACATATTT
Found at i:1550960 original size:51 final size:52
Alignment explanation
Indices: 1550892--1550989 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 52
1550882 ATATTAATAA
*
1550892 TTTATATTTTATAAAATTTTA-AATTATTTAA-TATATTTATGTTATACATAT
1 TTTATATTTTATAAAATTTTATAA-TATTTAATTATATTTATATTATACATAT
*
1550943 TTTATCATTTTA-AAAATTTTATAATATTTAATTATTTTTATATTATA
1 TTTAT-ATTTTATAAAATTTTATAATATTTAATTATATTTATATTATA
1550990 TTTATGTTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
51 21 0.50
52 21 0.50
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (52 bp):
TTTATATTTTATAAAATTTTATAATATTTAATTATATTTATATTATACATAT
Found at i:1551363 original size:22 final size:21
Alignment explanation
Indices: 1551330--1551370 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1551320 ATTTATATTT
* *
1551330 AAATATTTTTTATTTTAAATA
1 AAATATTATTTATATTAAATA
1551351 AAATATTAATTTATATTAAA
1 AAATATT-ATTTATATTAAA
1551371 AGATTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATATTATTTATATTAAATA
Found at i:1551420 original size:29 final size:29
Alignment explanation
Indices: 1551373--1551439 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1551363 ATATTAAAAG
*
1551373 ATTATAAATTAAACGTTAAGAACATATTTA
1 ATTAT-AATTAAACGTTAAAAACATATTTA
**
1551403 ATTATAATTAAA-GCTTAAAAATTTATTTA
1 ATTATAATTAAACG-TTAAAAACATATTTA
*
1551432 AATATAAT
1 ATTATAAT
1551440 AAAATTACAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 26 0.81
30 5 0.16
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (29 bp):
ATTATAATTAAACGTTAAAAACATATTTA
Found at i:1551799 original size:20 final size:21
Alignment explanation
Indices: 1551774--1551820 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
1551764 TTATTTTATT
1551774 AATTATTTATTTAATA-TTAA
1 AATTATTTATTTAATATTTAA
*
1551794 AATTATTTTTTTAATATTTAA
1 AATTATTTATTTAATATTTAA
1551815 AATTAT
1 AATTAT
1551821 CATAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTATTTATTTAATATTTAA
Found at i:1552147 original size:8 final size:8
Alignment explanation
Indices: 1552128--1552161 Score: 54
Period size: 7 Copynumber: 4.5 Consensus size: 8
1552118 AAAATTTATT
1552128 TTAAAAAA
1 TTAAAAAA
1552136 -TAAAAAA
1 TTAAAAAA
1552143 TTAAAAAA
1 TTAAAAAA
1552151 -TAAAAAA
1 TTAAAAAA
1552158 TTAA
1 TTAA
1552162 TAATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 14 0.58
8 10 0.42
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
TTAAAAAA
Found at i:1552148 original size:15 final size:15
Alignment explanation
Indices: 1552128--1552161 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1552118 AAAATTTATT
1552128 TTAAAAAATAAAAAA
1 TTAAAAAATAAAAAA
1552143 TTAAAAAATAAAAAA
1 TTAAAAAATAAAAAA
1552158 TTAA
1 TTAA
1552162 TAATTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TTAAAAAATAAAAAA
Found at i:1556253 original size:65 final size:66
Alignment explanation
Indices: 1556162--1556290 Score: 206
Period size: 65 Copynumber: 2.0 Consensus size: 66
1556152 TTTTTTTTTT
* * *
1556162 TTTTTTTTGAAATATATATGTTTAATGTTCTAAATATATGATAAAATTTATAAAAAATAAATATA
1 TTTTTTTTGAAATATATATATCTAATGCTCTAAATATATGATAAAATTTATAAAAAATAAATATA
1556227 A
66 A
* *
1556228 TTTTTTTT-AAGTATATATATCTAATGCTCTAAATATATGATAAAGTTTATAAAAAATAAATAT
1 TTTTTTTTGAAATATATATATCTAATGCTCTAAATATATGATAAAATTTATAAAAAATAAATAT
1556291 GAGATATGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
65 50 0.86
66 8 0.14
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (66 bp):
TTTTTTTTGAAATATATATATCTAATGCTCTAAATATATGATAAAATTTATAAAAAATAAATATA
A
Found at i:1557650 original size:24 final size:24
Alignment explanation
Indices: 1557589--1557656 Score: 61
Period size: 26 Copynumber: 2.8 Consensus size: 24
1557579 TTATTATCTA
1557589 ATTT-TATATA-AATATATAAAATT
1 ATTTATATATATAATA-ATAAAATT
*
1557612 -TTAACTATAATTATAATAATAAAATT
1 ATTTA-TAT-A-TATAATAATAAAATT
*
1557638 ATTTATATATATAAAAATA
1 ATTTATATATATAATAATA
1557657 TGTATGCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
22 2 0.06
24 12 0.33
25 2 0.06
26 13 0.36
27 7 0.19
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTATATATATAATAATAAAATT
Found at i:1558900 original size:12 final size:12
Alignment explanation
Indices: 1558883--1558911 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1558873 TATTTAAAAA
1558883 ATATTAAAATTT
1 ATATTAAAATTT
1558895 ATATTAAAATTT
1 ATATTAAAATTT
1558907 ATATT
1 ATATT
1558912 TTATAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATTAAAATTT
Found at i:1558904 original size:20 final size:20
Alignment explanation
Indices: 1558880--1558928 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1558870 AATTATTTAA
1558880 AAAATATTAAAATTTAT-ATT
1 AAAAT-TTAAAATTTATAATT
* *
1558900 AAAATTTATATTTTATAATT
1 AAAATTTAAAATTTATAATT
1558920 -AAATTTAAA
1 AAAATTTAAA
1558929 TAAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATTTAAAATTTATAATT
Found at i:1558926 original size:48 final size:49
Alignment explanation
Indices: 1558843--1558937 Score: 115
Period size: 48 Copynumber: 1.9 Consensus size: 49
1558833 TGATTTTTTT
* *
1558843 ATTTATATTTAATTTTATAATTTATTTAATTATTT-AA-AAAATATTAAA
1 ATTTATATTAAAATTTATAATTTATTTAA-TATTTAAATAAAATATTAAA
*
1558891 ATTTATATTAAAATTTATATTTTATAATTAA-ATTTAAATAAAATATT
1 ATTTATATTAAAATTTATAATTTAT--TTAATATTTAAATAAAATATT
1558938 TTTTATTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
48 26 0.65
49 2 0.05
50 12 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (49 bp):
ATTTATATTAAAATTTATAATTTATTTAATATTTAAATAAAATATTAAA
Found at i:1560602 original size:5 final size:5
Alignment explanation
Indices: 1560584--1560660 Score: 63
Period size: 5 Copynumber: 15.6 Consensus size: 5
1560574 TTTAATTATG
* *
1560584 ATATA AT-T- ATATA ATATAA AAATA ATATA ATATA ATATA ATATA A-AAA
1 ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA ATATA ATATA ATATA
* *
1560632 ATTATA ATATT TTA-A ATATA ATTATA ATA
1 A-TATA ATATA ATATA ATATA A-TATA ATA
1560661 GGTGAATTAC
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
3 2 0.04
4 7 0.12
5 36 0.63
6 12 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:1561608 original size:23 final size:23
Alignment explanation
Indices: 1561558--1561608 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
1561548 TTATTTAATT
*
1561558 CTTAATAATATATAAATATAAGTA
1 CTTATTAATATATAAATATAAG-A
1561582 -TTATTAATATATTAAATATAA-A
1 CTTATTAATATA-TAAATATAAGA
1561604 CTTAT
1 CTTAT
1561609 AATCGTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 1 0.04
23 14 0.58
24 9 0.38
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
CTTATTAATATATAAATATAAGA
Found at i:1562364 original size:15 final size:16
Alignment explanation
Indices: 1562346--1562384 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1562336 ATTTAAATAG
1562346 ATCAAAATTAAACT-A
1 ATCAAAATTAAACTCA
*
1562361 ATCACAATTAAACTCA
1 ATCAAAATTAAACTCA
*
1562377 ATCCAAAT
1 ATCAAAAT
1562385 AATTATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.26
Consensus pattern (16 bp):
ATCAAAATTAAACTCA
Found at i:1562931 original size:5 final size:5
Alignment explanation
Indices: 1562909--1562944 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1562899 ATAAAATCAA
* *
1562909 TTGAT TTAAT TCGAT TTGAT TTGAT TTGAT TTGAT T
1 TTGAT TTGAT TTGAT TTGAT TTGAT TTGAT TTGAT T
1562945 CGGTTCAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.58
Consensus pattern (5 bp):
TTGAT
Found at i:1565142 original size:2 final size:2
Alignment explanation
Indices: 1565135--1565164 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1565125 GCAATTAGTG
1565135 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
1565165 CTGCAGTAAT
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:1565502 original size:26 final size:25
Alignment explanation
Indices: 1565473--1565522 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
1565463 TCAAAACTTC
*
1565473 TTGTTTTGTTTTTGTTTTTTGTTTGT
1 TTGTTTGGTTTTT-TTTTTTGTTTGT
*
1565499 TTGTTTGGTTTTTTTTTTTTTTTG
1 TTGTTTGGTTTTTTTTTTTGTTTG
1565523 GTCTTTTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (25 bp):
TTGTTTGGTTTTTTTTTTTGTTTGT
Found at i:1565524 original size:17 final size:17
Alignment explanation
Indices: 1565476--1565529 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 17
1565466 AAACTTCTTG
*
1565476 TTTTGTTTTT-GTTTTT
1 TTTTTTTTTTGGTTTTT
1565492 TGTTTGTTTGTTTGGTTTTT
1 T-TTT-TTT-TTTGGTTTTT
1565512 TTTTTTTTTTGGTCTTTT
1 TTTTTTTTTTGGT-TTTT
1565530 CCTTGCTGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 1 0.03
17 9 0.28
18 9 0.28
19 6 0.19
20 7 0.22
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (17 bp):
TTTTTTTTTTGGTTTTT
Found at i:1569318 original size:21 final size:21
Alignment explanation
Indices: 1569292--1569340 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1569282 TTAAAGTCTC
* *
1569292 AAAATCAGCTCTCAAACAGCA
1 AAAATCAACTCTAAAACAGCA
*
1569313 AAAATCAACTCTAAAACATC-
1 AAAATCAACTCTAAAACAGCA
1569333 AAAATCAA
1 AAAATCAA
1569341 GATTGCTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.55, C:0.24, G:0.04, T:0.16
Consensus pattern (21 bp):
AAAATCAACTCTAAAACAGCA
Found at i:1574128 original size:24 final size:23
Alignment explanation
Indices: 1574092--1574149 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 23
1574082 TTATCCTAAT
* * *
1574092 TAATTGTACCATACATTATAATAA
1 TAATTTTATCATACAATAT-ATAA
*
1574116 TAATTTTATCATATAATATATAA
1 TAATTTTATCATACAATATATAA
*
1574139 TAA-ATTATCAT
1 TAATTTTATCAT
1574150 TATACGTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 7 0.24
23 7 0.24
24 15 0.52
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (23 bp):
TAATTTTATCATACAATATATAA
Done.