Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold496
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: 765014
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
File 6 of 7
Found at i:530813 original size:14 final size:14
Alignment explanation
Indices: 530794--530820 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
530784 TATTTTAATT
530794 TCATTGTTAATGTC
1 TCATTGTTAATGTC
530808 TCATTGTTAATGT
1 TCATTGTTAATGT
530821 GGTTTTATAA
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:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (14 bp):
TCATTGTTAATGTC
Found at i:532318 original size:20 final size:20
Alignment explanation
Indices: 532285--532324 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
532275 TATTTTTATT
532285 TAAAATTAATTATAAAAATA
1 TAAAATTAATTATAAAAATA
532305 TAAATATTAA-TATAAAAATA
1 TAAA-ATTAATTATAAAAATA
532325 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAATTAATTATAAAAATA
Found at i:533585 original size:17 final size:18
Alignment explanation
Indices: 533540--533576 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
533530 AAAAAGTAAC
*
533540 ATCCGTTAAATATCTAAA
1 ATCCTTTAAATATCTAAA
533558 ATCCTTTAAATATC-AAA
1 ATCCTTTAAATATCTAAA
533575 AT
1 AT
533577 TTATTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (18 bp):
ATCCTTTAAATATCTAAA
Found at i:536921 original size:21 final size:22
Alignment explanation
Indices: 536895--536943 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
536885 AAATTTATAT
*
536895 AATATTT-TTAATAAAATATTC
1 AATATTTCTAAATAAAATATTC
* *
536916 AATATTTCTAAATTAAATTTTC
1 AATATTTCTAAATAAAATATTC
536938 AATATT
1 AATATT
536944 CATAATCCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (22 bp):
AATATTTCTAAATAAAATATTC
Found at i:537157 original size:10 final size:9
Alignment explanation
Indices: 537144--537304 Score: 57
Period size: 9 Copynumber: 17.6 Consensus size: 9
537134 ATAATATTAC
537144 ATAAAATATT
1 ATAAAATA-T
537154 ATAAAATAT
1 ATAAAATAT
*
537163 AAAAAATA-
1 ATAAAATAT
*
537171 ATATGAATAT
1 ATA-AAATAT
537181 ATATAAATAT
1 ATA-AAATAT
* *
537191 TTTAAAT-T
1 ATAAAATAT
*
537199 -TTAAATAAT
1 ATAAAAT-AT
*
537208 ATAAATTAT
1 ATAAAATAT
*
537217 -TAATATAT
1 ATAAAATAT
*
537225 -TAAAATTT
1 ATAAAATAT
537233 ATATAAA-AT
1 ATA-AAATAT
537242 ATAAAATAT
1 ATAAAATAT
* **
537251 TTTTAATAT
1 ATAAAATAT
*
537260 AATTATAATAT
1 -A-TAAAATAT
*
537271 AATAAATTAT
1 -ATAAAATAT
537281 ATAAAA-AT
1 ATAAAATAT
*
537289 AAAATAAATAT
1 -ATA-AAATAT
537300 ATAAA
1 ATAAA
537305 TTATTATATC
Statistics
Matches: 115, Mismatches: 23, Indels: 27
0.70 0.14 0.16
Matches are distributed among these distances:
7 6 0.05
8 20 0.17
9 42 0.37
10 36 0.31
11 11 0.10
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.40
Consensus pattern (9 bp):
ATAAAATAT
Found at i:537167 original size:40 final size:38
Alignment explanation
Indices: 537123--537312 Score: 122
Period size: 38 Copynumber: 4.8 Consensus size: 38
537113 GACAAGCTAA
537123 AAAAAATAATTATAATATTACATAAAATATTATAAAATAT
1 AAAAAATAATTATAATA-TA-ATAAAATATTATAAAATAT
* * *
537163 AAAAAATAA-TATGAATAT-ATATAAATATTTTAAATTTT
1 AAAAAATAATTAT-AATATAATA-AAATATTATAAAATAT
*
537201 AAATAATATAAATTATTAATATATTAAAAT-TTATATAAA-AT
1 AAA-AA-AT-AATTA-TAATATAATAAAATATTATA-AAATAT
* * * * * *
537242 ATAAAATATTTTTAATATAATTATAATATAATAAATTAT
1 AAAAAATAATTATAATATAA-TAAAATATTATAAAATAT
* *
537281 ATAAAAATAA-AATAA-ATATATAAATTATTATA
1 A-AAAAATAATTATAATATA-ATAAAATATTATA
537313 TCTACCAAAG
Statistics
Matches: 115, Mismatches: 21, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
37 10 0.09
38 38 0.33
39 19 0.17
40 23 0.20
41 9 0.08
42 13 0.11
43 3 0.03
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (38 bp):
AAAAAATAATTATAATATAATAAAATATTATAAAATAT
Found at i:537203 original size:16 final size:17
Alignment explanation
Indices: 537147--537231 Score: 57
Period size: 19 Copynumber: 4.8 Consensus size: 17
537137 ATATTACATA
**
537147 AAATATTATAAAATATAAA
1 AAATATTAT-AAAT-TATT
* *
537166 AAATAATATGAATATATAT
1 AAATATTATAAAT-TAT-T
*
537185 AAATATTTTAAATT-TT
1 AAATATTATAAATTATT
*
537201 AAATAATATAAATTATT
1 AAATATTATAAATTATT
537218 AATATATTA-AAATT
1 AA-ATATTATAAATT
537232 TATATAAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
16 13 0.25
17 10 0.19
18 12 0.23
19 18 0.34
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (17 bp):
AAATATTATAAATTATT
Found at i:537228 original size:32 final size:34
Alignment explanation
Indices: 537166--537251 Score: 88
Period size: 34 Copynumber: 2.5 Consensus size: 34
537156 AAAATATAAA
* *
537166 AAATAATATGAATATATATAA-ATATTTTAAATTT-T
1 AAATAATATAAAT-TAT-TAATATA-TTAAAATTTAT
537201 AAATAATATAAATTATTAATATATTAAAATTTAT
1 AAATAATATAAATTATTAATATATTAAAATTTAT
*
537235 ATAA-AATATAAAATATT
1 A-AATAATATAAATTATT
537252 TTTAATATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
33 11 0.24
34 20 0.44
35 14 0.31
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (34 bp):
AAATAATATAAATTATTAATATATTAAAATTTAT
Found at i:537282 original size:23 final size:22
Alignment explanation
Indices: 537256--537313 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
537246 AATATTTTTA
537256 ATATAATTATAATATAATAAATT
1 ATATAATTATAATATAATAAA-T
*
537279 ATATAA--A-AATAAAATAAAT
1 ATATAATTATAATATAATAAAT
*
537298 ATATAAATTATTATAT
1 ATAT-AATTATAATAT
537314 CTACCAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
19 5 0.18
20 12 0.43
21 1 0.04
22 1 0.04
23 9 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAATTATAATATAATAAAT
Found at i:537284 original size:46 final size:49
Alignment explanation
Indices: 537204--537294 Score: 136
Period size: 46 Copynumber: 1.9 Consensus size: 49
537194 AAATTTTAAA
*
537204 TAATATAAATTATTAATATATTAAAATTTATATAAAATATAAAATATTTT
1 TAATATAAATTATTAATATAATAAAATTTATATAAAA-ATAAAATATTTT
537254 TAATAT-AATTA-TAATATAAT-AAA-TTATATAAAAATAAAATA
1 TAATATAAATTATTAATATAATAAAATTTATATAAAAATAAAATA
537295 AATATATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
45 8 0.20
46 10 0.25
47 3 0.08
48 8 0.20
49 5 0.12
50 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (49 bp):
TAATATAAATTATTAATATAATAAAATTTATATAAAAATAAAATATTTT
Found at i:537302 original size:19 final size:20
Alignment explanation
Indices: 537266--537304 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
537256 ATATAATTAT
*
537266 AATATAATAAATTATATAAA
1 AATAAAATAAATTATATAAA
537286 AATAAAATAAA-TATATAAA
1 AATAAAATAAATTATATAAA
537305 TTATTATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAAAATAAATTATATAAA
Found at i:537311 original size:46 final size:48
Alignment explanation
Indices: 537200--537313 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 48
537190 TTTTAAATTT
*
537200 TAAATAATATAAATTATTA-ATATATTAAAATTTATATAAAATATAAAA
1 TAAAT-ATATAAATTATTATATATATTAAAAATTATATAAAATATAAAA
* * *
537248 T--ATTTTTAATATAATTATA-ATA-TAATAAATTATATAAAA-ATAAAA
1 TAAATATATAA-ATTATTATATATATTAA-AAATTATATAAAATATAAAA
537293 TAAATATATAAATTATTATAT
1 TAAATATATAAATTATTATAT
537314 CTACCAAAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
45 14 0.26
46 31 0.58
47 7 0.13
48 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (48 bp):
TAAATATATAAATTATTATATATATTAAAAATTATATAAAATATAAAA
Found at i:537646 original size:18 final size:19
Alignment explanation
Indices: 537609--537647 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
537599 TATAAATTTA
*
537609 ATAAAATTATTTTATTAAAT
1 ATAAAAATATTTTA-TAAAT
537629 ATAAAAATATTTTA-AAAT
1 ATAAAAATATTTTATAAAT
537647 A
1 A
537648 ATAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
20 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAAATATTTTATAAAT
Found at i:538396 original size:3 final size:3
Alignment explanation
Indices: 538388--538435 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
538378 GATCATAGAG
538388 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
538436 ATTGAATTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:539322 original size:3 final size:3
Alignment explanation
Indices: 539314--539346 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
539304 TACCAAATCC
539314 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
539347 GATTATAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:540209 original size:19 final size:17
Alignment explanation
Indices: 540150--540212 Score: 64
Period size: 13 Copynumber: 3.9 Consensus size: 17
540140 TTTAAAATAA
*
540150 AAAAATTATAAATT-TT
1 AAAATTTATAAATTATT
540166 AAAA-TT-T-AATT-TT
1 AAAATTTATAAATTATT
540179 AAAATTTATAAATTATT
1 AAAATTTATAAATTATT
540196 AATAATTATATAAATTA
1 AA-AATT-TATAAATTA
540213 ATTGAGTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
13 10 0.24
14 3 0.07
15 3 0.07
16 8 0.20
17 4 0.10
18 4 0.10
19 9 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAAATTTATAAATTATT
Found at i:541000 original size:3 final size:3
Alignment explanation
Indices: 540992--541033 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
540982 ATTTTATTGC
540992 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
541034 CTATACTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:541300 original size:3 final size:3
Alignment explanation
Indices: 541292--541358 Score: 98
Period size: 3 Copynumber: 22.3 Consensus size: 3
541282 CTTGCTATCA
*
541292 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
541340 AGT AAT AGT AAT AGT AAT A
1 AAT AAT AAT AAT AAT AAT A
541359 GTAGTAGGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:541577 original size:36 final size:36
Alignment explanation
Indices: 541506--541577 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
541496 ACAATATTAA
*
541506 AAATAAAAAAATTTATTAATATTTATAATTAAATTT
1 AAATAAAAAAATTTATTAATATTTATAATAAAATTT
541542 AAATAAAAAATAATTT-TT-AT-TTTATAATAATAATTT
1 AAAT-AAAAA-AATTTATTAATATTTATAATAA-AATTT
541578 GAATTAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
35 9 0.28
36 11 0.34
37 7 0.22
38 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
AAATAAAAAAATTTATTAATATTTATAATAAAATTT
Found at i:544796 original size:21 final size:21
Alignment explanation
Indices: 544762--544816 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
544752 ACGGTTGTGA
*
544762 TAAAA-TAATTATTATAATTA-
1 TAAAATTAAATATTATAA-TAG
*
544782 TGAAATTAAATATTATAATAG
1 TAAAATTAAATATTATAATAG
544803 TAAAATTAAA-ATTA
1 TAAAATTAAATATTA
544817 ATGGTGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TAAAATTAAATATTATAATAG
Found at i:545654 original size:14 final size:15
Alignment explanation
Indices: 545635--545671 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
545625 ATTTTACCTT
545635 TTAAAAATAT-AATA
1 TTAAAAATATGAATA
*
545649 TTAAAAAT-TGATTA
1 TTAAAAATATGAATA
545663 TTAAAAATA
1 TTAAAAATA
545672 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 19 0.95
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TTAAAAATATGAATA
Found at i:545693 original size:19 final size:20
Alignment explanation
Indices: 545659--545703 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
545649 TTAAAAATTG
*
545659 ATTATTAAAAATAATTTTTA
1 ATTATTAAAAATAATTATTA
*
545679 TTTATTAAAAA-AATTATTA
1 ATTATTAAAAATAATTATTA
545698 ATTATT
1 ATTATT
545704 TTCTATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTATTAAAAATAATTATTA
Found at i:545981 original size:13 final size:13
Alignment explanation
Indices: 545956--546003 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
545946 AGTTTTTTGG
*
545956 TATTTTTGT-TTT
1 TATTTTTTTATTT
545968 TATTTTTTTATTT
1 TATTTTTTTATTT
*
545981 TATTTCTTTATTT
1 TATTTTTTTATTT
* *
545994 AATTTATTTA
1 TATTTTTTTA
546004 GTTAGAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 8 0.26
13 23 0.74
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (13 bp):
TATTTTTTTATTT
Found at i:550056 original size:21 final size:22
Alignment explanation
Indices: 550017--550069 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
550007 AAAAAATTCG
* *
550017 ATTAAACTTATAAGCTACTTA-A
1 ATTAAA-TTTTAAGATACTTAGA
550039 ATTAAATTTTAAGATACTTAGA
1 ATTAAATTTTAAGATACTTAGA
*
550061 ATTCAATTT
1 ATTAAATTT
550070 GTTCAATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (22 bp):
ATTAAATTTTAAGATACTTAGA
Found at i:553307 original size:20 final size:20
Alignment explanation
Indices: 553284--553325 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
553274 AATTAATTAA
553284 TAATAATTTAAAATATATTT
1 TAATAATTTAAAATATATTT
* * *
553304 TAATATTTTAATATTTATTT
1 TAATAATTTAAAATATATTT
553324 TA
1 TA
553326 TTTATTTACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATAATTTAAAATATATTT
Found at i:555339 original size:15 final size:15
Alignment explanation
Indices: 555319--555351 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
555309 ATTAAACGAG
555319 TTAAATTAATTTAAA
1 TTAAATTAATTTAAA
*
555334 TTAAATTATTTTAAA
1 TTAAATTAATTTAAA
555349 TTA
1 TTA
555352 TTAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAAATTAATTTAAA
Found at i:556145 original size:21 final size:22
Alignment explanation
Indices: 556119--556160 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
556109 ACTAATTATA
*
556119 TAAATTAAT-TAAATTAAATTT
1 TAAATTAATAAAAATTAAATTT
556140 TAAATTAATAAAAATTAAATT
1 TAAATTAATAAAAATTAAATT
556161 AATTTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATTAATAAAAATTAAATTT
Found at i:556664 original size:17 final size:16
Alignment explanation
Indices: 556631--556663 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
556621 ATAAATAATT
556631 ATTTTAAAAGATAAAA
1 ATTTTAAAAGATAAAA
*
556647 ATTTTTAAAGATAAAA
1 ATTTTAAAAGATAAAA
556663 A
1 A
556664 AATATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
ATTTTAAAAGATAAAA
Found at i:556784 original size:36 final size:33
Alignment explanation
Indices: 556708--556784 Score: 84
Period size: 36 Copynumber: 2.2 Consensus size: 33
556698 GAAAAGTTTT
* *
556708 AAAATTTATTTTTATTATTATATATTTAAAAAT
1 AAAATTTATTTTTATTATTAAATATTTAAAAAA
*
556741 AATATTTATCTTTAATATTATTAAAT-TTTAATAAAA
1 AAAATTTAT-TTT--TATTATTAAATATTTAA-AAAA
556777 AAAATTTA
1 AAAATTTA
556785 CCCTTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 8 0.22
34 3 0.08
35 5 0.14
36 20 0.56
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (33 bp):
AAAATTTATTTTTATTATTAAATATTTAAAAAA
Found at i:557687 original size:15 final size:17
Alignment explanation
Indices: 557669--557704 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
557659 ATTTAAATTT
557669 TTTATATTTTA-A-ATA
1 TTTATATTTTATATATA
557684 TTTATATTTTATATATA
1 TTTATATTTTATATATA
557701 TTTA
1 TTTA
557705 GATATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 1 0.05
17 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATATTTTATATATA
Found at i:557692 original size:24 final size:25
Alignment explanation
Indices: 557658--557709 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
557648 GACTTTATAT
*
557658 TATTTAAATTTTTTATAT-TTTAAA
1 TATTTAAATTTTATATATATTTAAA
* *
557682 TATTTATATTTTATATATATTTAGA
1 TATTTAAATTTTATATATATTTAAA
557707 TAT
1 TAT
557710 AAATATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TATTTAAATTTTATATATATTTAAA
Found at i:557729 original size:16 final size:18
Alignment explanation
Indices: 557713--557746 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
557703 TAGATATAAA
557713 TATAAA-ATATAAAAAAT
1 TATAAATATATAAAAAAT
*
557730 TTTAAATATATAAAAAA
1 TATAAATATATAAAAAA
557747 ATTAAAATTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TATAAATATATAAAAAAT
Found at i:557740 original size:25 final size:24
Alignment explanation
Indices: 557712--557762 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 24
557702 TTAGATATAA
557712 ATATAAAATATAA-AAAATTTTAAAT
1 ATATAAAA-A-AATAAAATTTTAAAT
557737 ATATAAAAAAATTAAAATTTTAAAT
1 ATATAAAAAAA-TAAAATTTTAAAT
557762 A
1 A
557763 CAATTTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 2 0.08
24 1 0.04
25 21 0.88
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATATAAAAAAATAAAATTTTAAAT
Found at i:557754 original size:18 final size:18
Alignment explanation
Indices: 557719--557754 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
557709 TAAATATAAA
* *
557719 ATATAAAAAATTTTAAAT
1 ATATAAAAAAATTAAAAT
557737 ATATAAAAAAATTAAAAT
1 ATATAAAAAAATTAAAAT
557755 TTTAAATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATAAAAAAATTAAAAT
Found at i:558383 original size:2 final size:2
Alignment explanation
Indices: 558376--558401 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
558366 AGCAATATGC
558376 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
558402 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:558406 original size:2 final size:2
Alignment explanation
Indices: 558401--558429 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
558391 TCTCTCTCTC
558401 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
558430 GGATGCATCA
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:558904 original size:30 final size:29
Alignment explanation
Indices: 558870--558947 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 29
558860 CAAATGAGCA
* *
558870 TTTAATTGTTAATTTGTA-TTCAAATATATT
1 TTTAATT-TTAATTTATACTT-AAATAAATT
558900 TTTAATTTTTAATTTATACTTAAATAAATT
1 TTTAA-TTTTAATTTATACTTAAATAAATT
*
558930 TTTAAATTTTAATATATA
1 TTT-AATTTTAATTTATA
558948 TCGTTAACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 36 0.86
31 6 0.14
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (29 bp):
TTTAATTTTAATTTATACTTAAATAAATT
Found at i:559049 original size:29 final size:30
Alignment explanation
Indices: 558975--559057 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
558965 TCTTTCATTT
558975 TAAAAGATTTA-TTCAAATACAAATTAAAAGA
1 TAAAA-ATTTACTT-AAATACAAATTAAAAGA
*
559006 TAAAAATTTATTTAAATAC-AA-TAAAAGCA
1 TAAAAATTTACTTAAATACAAATTAAAAG-A
* * *
559035 TAGAAGTTTACTTAAATAAAAAT
1 TAAAAATTTACTTAAATACAAAT
559058 AATATAAGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
28 6 0.14
29 18 0.41
30 13 0.30
31 7 0.16
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (30 bp):
TAAAAATTTACTTAAATACAAATTAAAAGA
Found at i:559723 original size:29 final size:27
Alignment explanation
Indices: 559670--559723 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 27
559660 TGATTTTTTA
*
559670 TTTTTTAATTAAAACAAATTTATTCTT
1 TTTTTTAATTAAAACAAATTCATTCTT
559697 TTTTTTAATTTCATAAAC-AATTCATTC
1 TTTTTTAA-TT-A-AAACAAATTCATTC
559724 ATCCAATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 8 0.35
28 2 0.09
29 9 0.39
30 4 0.17
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTTTTAATTAAAACAAATTCATTCTT
Found at i:560522 original size:26 final size:27
Alignment explanation
Indices: 560493--560544 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
560483 ATTTTTATAA
* *
560493 AAATTAAAATATATATATAAT-TTTTC
1 AAATTAAAATAAACATATAATGTTTTC
*
560519 AAATTAAGATAAACATATAATGTTTT
1 AAATTAAAATAAACATATAATGTTTT
560545 TGATAGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
AAATTAAAATAAACATATAATGTTTTC
Found at i:563284 original size:19 final size:21
Alignment explanation
Indices: 563235--563287 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
563225 ATATTTTATT
563235 TAAA-TTTAATAATAAAATATA
1 TAAATTTTAAT-ATAAAATATA
*
563256 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
*
563276 -AATTTTTAATAT
1 TAAATTTTAATAT
563288 GATAAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 10 0.36
22 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:564461 original size:4 final size:4
Alignment explanation
Indices: 564452--564477 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
564442 TAATTTTAAC
564452 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
564478 AAAAAACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:564685 original size:15 final size:16
Alignment explanation
Indices: 564657--564687 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
564647 TATGTTCATC
564657 GAATTTTTTGTAAGAA
1 GAATTTTTTGTAAGAA
564673 GAATTTTTT-TAAGAA
1 GAATTTTTTGTAAGAA
564688 TTTCCAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (16 bp):
GAATTTTTTGTAAGAA
Found at i:565290 original size:16 final size:15
Alignment explanation
Indices: 565269--565321 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
565259 AATTTAAAAA
565269 TATATTTATATCATAT
1 TATATTTATAT-ATAT
565285 TATATTT-TA-ATA-
1 TATATTTATATATAT
565297 -AT-TTTATATATAT
1 TATATTTATATATAT
565310 TATATTTATATA
1 TATATTTATATA
565322 ATCGAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
10 3 0.09
11 4 0.12
12 3 0.09
13 3 0.09
14 2 0.06
15 10 0.31
16 7 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTTATATATAT
Found at i:565300 original size:25 final size:26
Alignment explanation
Indices: 565267--565316 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
565257 AAAATTTAAA
565267 AATATA-TTTATATCATATTATATTTT
1 AATATATTTTATAT-ATATTATATTTT
565293 AATA-ATTTTATATATATTATATTT
1 AATATATTTTATATATATTATATTT
565317 ATATAATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
AATATATTTTATATATATTATATTTT
Found at i:568280 original size:23 final size:22
Alignment explanation
Indices: 568236--568280 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
568226 AATCTTATTA
** *
568236 ATAATAAAAAATATTTATAATG
1 ATAATAAAAAATATAAAGAATG
568258 ATAATATAAAAATATAAAGAATG
1 ATAATA-AAAAATATAAAGAATG
568281 CCTATCGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (22 bp):
ATAATAAAAAATATAAAGAATG
Found at i:568682 original size:89 final size:85
Alignment explanation
Indices: 568501--568682 Score: 183
Period size: 91 Copynumber: 2.1 Consensus size: 85
568491 TTATATCAAA
* * * *
568501 TTATTATAAAATTATTTACTTTTTATATTATTGAAAAATTAATTATAAAGATTAAATAATCAGTA
1 TTATTAAAAAATTATTTACTTTTTATATAAGTGAAAAATTAATTATAAAGATAAAATAATCAGTA
*
568566 TAAAATTTAATTCCTTTTATT
66 TAAAATTTAATT-CTTTTAGT
*
568587 TATATTAAATAAATTAATTTACTTTTTAATATAAGTGAAAAATTAAACTT-TTAAGATAAAATAA
1 T-TATTAAA-AAATT-ATTTACTTTTT-ATATAAGTGAAAAATT-AA-TTATAAAGATAAAATAA
*
568651 CTTTA-TATAAACATTTAATT-TTTT-GT
60 --TCAGTATAAA-ATTTAATTCTTTTAGT
568677 TTATTA
1 TTATTA
568683 CTGAGTTAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
86 1 0.01
87 6 0.08
88 5 0.06
89 16 0.20
90 16 0.20
91 18 0.22
92 8 0.10
93 10 0.12
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (85 bp):
TTATTAAAAAATTATTTACTTTTTATATAAGTGAAAAATTAATTATAAAGATAAAATAATCAGTA
TAAAATTTAATTCTTTTAGT
Found at i:569638 original size:36 final size:35
Alignment explanation
Indices: 569568--569639 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
569558 AAAAGATCCT
* *
569568 TAAAAAAAAAAATAGATAATTACTTATCCAAAAAA
1 TAAAAAAAAAAATAGATAATTAATTATACAAAAAA
569603 TAAATAAAAAAAATAGATAATTGATATTA-ACAAAAAA
1 TAAA-AAAAAAAATAGATAATT-A-ATTATACAAAAAA
569640 AAGTCCTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 4 0.12
36 17 0.53
37 8 0.25
38 3 0.09
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.24
Consensus pattern (35 bp):
TAAAAAAAAAAATAGATAATTAATTATACAAAAAA
Found at i:569776 original size:15 final size:14
Alignment explanation
Indices: 569758--569840 Score: 74
Period size: 14 Copynumber: 6.4 Consensus size: 14
569748 ATATACGATT
569758 ATATAAATATAATA
1 ATATAAATATAATA
569772 CATATAAAT-TAATA
1 -ATATAAATATAATA
*
569786 A-A-AAATAAAATA
1 ATATAAATATAATA
569798 ATATAAATAT-AT-
1 ATATAAATATAATA
*
569810 -T-TAAATTTATATA
1 ATATAAATATA-ATA
569823 ATATAAAT-TAATA
1 ATATAAATATAATA
569836 ATATA
1 ATATA
569841 TTAAAATTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
10 6 0.11
11 5 0.09
12 8 0.14
13 12 0.21
14 13 0.23
15 13 0.23
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATAAATATAATA
Found at i:569801 original size:25 final size:25
Alignment explanation
Indices: 569762--569836 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
569752 ACGATTATAT
*
569762 AAATATAATACATATAAATTAATAAA
1 AAATAAAATA-ATATAAATTAATAAA
**
569788 AAATAAAATAATATAAA-TATATTTA
1 AAATAAAATAATATAAATTA-ATAAA
* * *
569813 AATTTATATAATATAAATTAATAA
1 AAATAAAATAATATAAATTAATAA
569837 TATATTAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
24 2 0.05
25 26 0.67
26 11 0.28
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATAAAATAATATAAATTAATAAA
Found at i:569862 original size:17 final size:16
Alignment explanation
Indices: 569812--569892 Score: 60
Period size: 17 Copynumber: 4.9 Consensus size: 16
569802 AAATATATTT
569812 AAATTTATATAATAT-
1 AAATTTATATAATATA
*
569827 AAATTAATA-ATATATTA
1 AAATTTATATA-ATA-TA
569844 AAATTTATATCAATATA
1 AAATTTATAT-AATATA
*
569861 AAATATTTTA-AATATA
1 AAAT-TTATATAATATA
*
569877 TAATTATAATATAATA
1 AAATT-T-ATATAATA
569893 AAATACACAA
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
14 1 0.02
15 12 0.23
16 11 0.21
17 16 0.31
18 11 0.21
19 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTTATATAATATA
Found at i:569878 original size:38 final size:35
Alignment explanation
Indices: 569768--569878 Score: 88
Period size: 35 Copynumber: 3.2 Consensus size: 35
569758 ATATAAATAT
* * * * *
569768 AATACATA-TAAATTAATAAAAAATAAAATAATATA
1 AATATATATTAAATTTATATAATATAAAAT-ATTTA
* *
569803 AATATAT-TTAAATTTATATAATATAAATTA-AT-
1 AATATATATTAAATTTATATAATATAAAATATTTA
*
569835 AATATAT-TAAAATTTATATCAATATAAAATATTTTA
1 AATATATATTAAATTTATAT-AATATAAAATA-TTTA
569871 AATATATA
1 AATATATA
569879 ATTATAATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
32 18 0.29
33 12 0.19
34 1 0.02
35 24 0.39
36 7 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (35 bp):
AATATATATTAAATTTATATAATATAAAATATTTA
Found at i:569905 original size:57 final size:57
Alignment explanation
Indices: 569797--569905 Score: 127
Period size: 57 Copynumber: 1.9 Consensus size: 57
569787 AAAATAAAAT
* *
569797 AATATAAATATATTTAAATTTATATAATATAAATTAATAATATATTAAAATTTATATC
1 AATATAAATATATTTAAA-TTATATAATATAAATTAATAAAATATCAAAATTTATATC
569855 AATATAAA-ATATTTTAAA-TATATAAT-TATAATATAATAAAATA-CACAAATT
1 AATATAAATATA-TTTAAATTATATAATATA-AAT-TAATAAAATATCA-AAATT
569906 AATTCTTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
55 2 0.04
56 12 0.27
57 17 0.38
58 14 0.31
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (57 bp):
AATATAAATATATTTAAATTATATAATATAAATTAATAAAATATCAAAATTTATATC
Found at i:570632 original size:11 final size:11
Alignment explanation
Indices: 570583--570668 Score: 50
Period size: 14 Copynumber: 7.1 Consensus size: 11
570573 TTTAATATGT
570583 TAATAATTTTA
1 TAATAATTTTA
570594 TTATATAAATTTTAA
1 -TA-AT-AATTTT-A
*
570609 TATATATTTTTA
1 TA-ATAATTTTA
570621 TAATAATTTTATA
1 TAATAA-TTT-TA
570634 TTAAATAATATTTA
1 -T-AATAAT-TTTA
570648 TAA-AATTTT-
1 TAATAATTTTA
*
570657 TAATTATTTTA
1 TAATAATTTTA
570668 T
1 T
570669 TTTATATCCA
Statistics
Matches: 61, Mismatches: 3, Indels: 21
0.72 0.04 0.25
Matches are distributed among these distances:
9 3 0.05
10 8 0.13
11 7 0.11
12 10 0.16
13 10 0.16
14 15 0.25
15 8 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TAATAATTTTA
Found at i:570669 original size:24 final size:23
Alignment explanation
Indices: 570594--570670 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 23
570584 AATAATTTTA
570594 TTATATAAATTTTAATATATATT-T
1 TTATA-AAATTTTAAT-TATATTAT
*
570618 TTATAATAATTTTATATTAAATAATAT
1 TTATAA-AATTTTA-ATT--ATATTAT
*
570645 TTATAAAATTTTTAATTATTTTAT
1 TTATAAAA-TTTTAATTATATTAT
570669 TT
1 TT
570671 TATATCCATA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
23 1 0.02
24 20 0.45
25 2 0.05
26 9 0.20
27 12 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATAAAATTTTAATTATATTAT
Found at i:571701 original size:15 final size:14
Alignment explanation
Indices: 571683--571732 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 14
571673 TTTATATAAA
571683 ATTAATTATTAATAT
1 ATTAA-TATTAATAT
*
571698 ATTAAAATT--TAT
1 ATTAATATTAATAT
571710 ATTAATATTTAATAT
1 ATTAATA-TTAATAT
571725 ATTTAATA
1 A-TTAATA
571733 CGATATGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 9 0.31
13 2 0.07
14 3 0.10
15 9 0.31
16 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTAATATTAATAT
Found at i:571712 original size:12 final size:12
Alignment explanation
Indices: 571663--571720 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
571653 ATGATACGAA
571663 TATATTAAAATT
1 TATATTAAAATT
571675 TATA-TAAAA-T
1 TATATTAAAATT
*
571685 TA-ATTATTAA--
1 TATATTA-AAATT
571695 TATATTAAAATT
1 TATATTAAAATT
*
571707 TATATTAATATT
1 TATATTAAAATT
571719 TA
1 TA
571721 ATATATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
9 1 0.03
10 9 0.24
11 11 0.29
12 17 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATTAAAATT
Found at i:571712 original size:20 final size:21
Alignment explanation
Indices: 571675--571721 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
571665 TATTAAAATT
571675 TATA-TAAAATTAATTATTAA
1 TATATTAAAATTAATTATTAA
*
571695 TATATTAAAATTTA-TATTAA
1 TATATTAAAATTAATTATTAA
571715 TAT-TTAA
1 TATATTAA
571722 TATATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 13 0.52
21 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATTAAAATTAATTATTAA
Found at i:571945 original size:15 final size:15
Alignment explanation
Indices: 571925--571953 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
571915 GTTAATTAAA
571925 ATATTATATTTAATT
1 ATATTATATTTAATT
571940 ATATTATATTTAAT
1 ATATTATATTTAAT
571954 AAAATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTATATTTAATT
Found at i:574059 original size:8 final size:8
Alignment explanation
Indices: 574021--574060 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
574011 ATATTTTAAT
574021 AAAGAAAA
1 AAAGAAAA
*
574029 AAA-AAGA
1 AAAGAAAA
*
574036 AAAGAAAG
1 AAAGAAAA
574044 AAAGAAAA
1 AAAGAAAA
574052 AAAGAAAA
1 AAAGAAAA
574060 A
1 A
574061 CCTTTCTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:574931 original size:2 final size:2
Alignment explanation
Indices: 574924--574961 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
574914 TTCAGGTAAA
574924 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
574962 GTTTTGGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:579997 original size:8 final size:7
Alignment explanation
Indices: 579975--580017 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
579965 TACACCAAAA
*
579975 TTTCCTT
1 TTTCTTT
579982 TTTCTTT
1 TTTCTTT
579989 TTTCTTT
1 TTTCTTT
*
579996 TTTCCTT
1 TTTCTTT
*
580003 TTACTTTT
1 TTTC-TTT
580011 TTTCTTT
1 TTTCTTT
580018 AATTTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 25 0.83
8 5 0.17
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTCTTT
Found at i:579999 original size:21 final size:22
Alignment explanation
Indices: 579975--580017 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
579965 TACACCAAAA
*
579975 TTTCCTTTTTC-TTTTTTCTTT
1 TTTCCTTTTACTTTTTTTCTTT
579996 TTTCCTTTTACTTTTTTTCTTT
1 TTTCCTTTTACTTTTTTTCTTT
580018 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCCTTTTACTTTTTTTCTTT
Found at i:583194 original size:17 final size:18
Alignment explanation
Indices: 583159--583197 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
583149 ATTTCTCAAT
*
583159 CTTTGCTTTGTTGTTCCA
1 CTTTGCTTTGTTCTTCCA
583177 CTTTGCTTTG-TCTTCCA
1 CTTTGCTTTGTTCTTCCA
583194 CTTT
1 CTTT
583198 CTTCCTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.05, C:0.26, G:0.13, T:0.56
Consensus pattern (18 bp):
CTTTGCTTTGTTCTTCCA
Found at i:583324 original size:40 final size:40
Alignment explanation
Indices: 583280--583421 Score: 108
Period size: 40 Copynumber: 3.4 Consensus size: 40
583270 TCTTCCACTT
**
583280 TCTTCATTGTTGCTTTGCTTTTCTGTTCCATGTTGTTTTG
1 TCTTCATCATTGCTTTGCTTTTCTGTTCCATGTTGTTTTG
** * * *
583320 TCTTCATCATTGCTGTTTTTTTTTCACGTTAC-T-TTGTCTTCCACTT
1 TCTTCATCATTGC--TTTGCTTTTC-TGTTCCATGTTGT-TT----TG
** *
583366 TCTTCATTGTTGCTTTGCTTTGCTGTTCCATGTTGTTTTG
1 TCTTCATCATTGCTTTGCTTTTCTGTTCCATGTTGTTTTG
583406 TCTTCATCATTGCTTT
1 TCTTCATCATTGCTTT
583422 TTTTTTAAAA
Statistics
Matches: 75, Mismatches: 17, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
40 26 0.35
41 4 0.05
42 11 0.15
43 8 0.11
44 10 0.13
45 4 0.05
46 12 0.16
ACGTcount: A:0.08, C:0.20, G:0.14, T:0.58
Consensus pattern (40 bp):
TCTTCATCATTGCTTTGCTTTTCTGTTCCATGTTGTTTTG
Found at i:583373 original size:43 final size:43
Alignment explanation
Indices: 583238--583374 Score: 118
Period size: 43 Copynumber: 3.1 Consensus size: 43
583228 TTTGTCTTCA
*
583238 TCATTGCTGTTTTGCTTTTCCACGTTACTTTGTCTTCCACTTTCT
1 TCATTGCTGTTTT--TTTTTCACGTTACTTTGTCTTCCACTTTCT
* ** * * *** *
583283 TCATTGTTGCTTTGCTTTTC-TGTTCCATGTTGT-TTTGTC-TTCA
1 TCATTGCTG-TTTTTTTTTCACGTTAC-T-TTGTCTTCCACTTTCT
583326 TCATTGCTGTTTTTTTTTCACGTTACTTTGTCTTCCACTTTCT
1 TCATTGCTGTTTTTTTTTCACGTTACTTTGTCTTCCACTTTCT
583369 TCATTG
1 TCATTG
583375 TTGCTTTGCT
Statistics
Matches: 67, Mismatches: 19, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
41 4 0.06
42 12 0.18
43 28 0.42
44 8 0.12
45 12 0.18
46 3 0.04
ACGTcount: A:0.09, C:0.23, G:0.12, T:0.56
Consensus pattern (43 bp):
TCATTGCTGTTTTTTTTTCACGTTACTTTGTCTTCCACTTTCT
Found at i:583378 original size:86 final size:86
Alignment explanation
Indices: 583172--583427 Score: 380
Period size: 86 Copynumber: 3.0 Consensus size: 86
583162 TGCTTTGTTG
* * * * * *
583172 TTCCACTTTGCTTTGTCTTCCACTTTCTTCCTTATTGCTTTGCTATTC-G----ACGTTGTTTTG
1 TTCCACGTTACTTTGTCTTCCACTTTCTTCATTGTTGCTTTGCTTTTCTGTTCCATGTTGTTTTG
583232 TCTTCATCATTGCTGTTTTGCTT
66 TCTTCATCATTGCTGTTTT--TT
583255 TTCCACGTTACTTTGTCTTCCACTTTCTTCATTGTTGCTTTGCTTTTCTGTTCCATGTTGTTTTG
1 TTCCACGTTACTTTGTCTTCCACTTTCTTCATTGTTGCTTTGCTTTTCTGTTCCATGTTGTTTTG
583320 TCTTCATCATTGCTGTTTTTT
66 TCTTCATCATTGCTGTTTTTT
* *
583341 TTTCACGTTACTTTGTCTTCCACTTTCTTCATTGTTGCTTTGCTTTGCTGTTCCATGTTGTTTTG
1 TTCCACGTTACTTTGTCTTCCACTTTCTTCATTGTTGCTTTGCTTTTCTGTTCCATGTTGTTTTG
583406 TCTTCATCATTGCT-TTTTTT
66 TCTTCATCATTGCTGTTTTTT
583426 TT
1 TT
583428 AAAAATCATT
Statistics
Matches: 160, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
83 43 0.27
84 1 0.01
85 8 0.05
86 79 0.49
88 29 0.18
ACGTcount: A:0.08, C:0.22, G:0.13, T:0.57
Consensus pattern (86 bp):
TTCCACGTTACTTTGTCTTCCACTTTCTTCATTGTTGCTTTGCTTTTCTGTTCCATGTTGTTTTG
TCTTCATCATTGCTGTTTTTT
Found at i:583416 original size:43 final size:43
Alignment explanation
Indices: 583283--583417 Score: 132
Period size: 43 Copynumber: 3.1 Consensus size: 43
583273 TCCACTTTCT
583283 TCATTGTTGCTTTGCTTTTCTGTTCCATGTTGTTTTGTCTTCA
1 TCATTGTTGCTTTGCTTTTCTGTTCCATGTTGTTTTGTCTTCA
* ** * * *** *
583326 TCATTGCTG-TTTTTTTTTCACGTTAC-T-TTGTCTTCCACTTTCT
1 TCATTGTTGCTTTGCTTTTC-TGTTCCATGTTGT-TTTGTC-TTCA
*
583369 TCATTGTTGCTTTGCTTTGCTGTTCCATGTTGTTTTGTCTTCA
1 TCATTGTTGCTTTGCTTTTCTGTTCCATGTTGTTTTGTCTTCA
583412 TCATTG
1 TCATTG
583418 CTTTTTTTTT
Statistics
Matches: 67, Mismatches: 19, Indels: 12
0.68 0.19 0.12
Matches are distributed among these distances:
41 4 0.06
42 12 0.18
43 36 0.54
44 11 0.16
45 4 0.06
ACGTcount: A:0.08, C:0.20, G:0.15, T:0.57
Consensus pattern (43 bp):
TCATTGTTGCTTTGCTTTTCTGTTCCATGTTGTTTTGTCTTCA
Found at i:583861 original size:9 final size:9
Alignment explanation
Indices: 583849--583910 Score: 67
Period size: 8 Copynumber: 6.8 Consensus size: 9
583839 TATTATTATT
583849 ATTTTTTTG
1 ATTTTTTTG
583858 ATTTTTTTG
1 ATTTTTTTG
583867 A-TTTTTT-
1 ATTTTTTTG
583874 ATTAATTTTTG
1 ATT--TTTTTG
583885 ATTTTTTTTTG
1 A--TTTTTTTG
583896 A-TTTTTTG
1 ATTTTTTTG
583904 ATTTTTT
1 ATTTTTT
583911 ATATTATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
7 1 0.02
8 15 0.33
9 15 0.33
10 5 0.11
11 8 0.17
13 2 0.04
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (9 bp):
ATTTTTTTG
Found at i:583870 original size:18 final size:18
Alignment explanation
Indices: 583849--583910 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 18
583839 TATTATTATT
583849 ATTTTTTTGATTTTTTTG
1 ATTTTTTTGATTTTTTTG
583867 A-TTTTTT-ATTAATTTTTG
1 ATTTTTTTGATT--TTTTTG
583885 ATTTTTTTTTGA-TTTTTTG
1 A--TTTTTTTGATTTTTTTG
583904 ATTTTTT
1 ATTTTTT
583911 ATATTATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.08
17 12 0.32
18 8 0.21
19 7 0.18
21 7 0.18
22 1 0.03
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (18 bp):
ATTTTTTTGATTTTTTTG
Found at i:583882 original size:19 final size:19
Alignment explanation
Indices: 583860--583912 Score: 81
Period size: 18 Copynumber: 2.8 Consensus size: 19
583850 TTTTTTTGAT
583860 TTTTTTGATTTTTTATTAA
1 TTTTTTGATTTTTTATTAA
* *
583879 -TTTTTGATTTTTTTTTGA
1 TTTTTTGATTTTTTATTAA
583897 TTTTTTGATTTTTTAT
1 TTTTTTGATTTTTTAT
583913 ATTATTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (19 bp):
TTTTTTGATTTTTTATTAA
Found at i:583926 original size:18 final size:18
Alignment explanation
Indices: 583835--583926 Score: 50
Period size: 18 Copynumber: 5.2 Consensus size: 18
583825 CTCCCCTCTC
583835 TTTTTATTATTATTA-TTT
1 TTTTTA-TATTATTATTTT
* * *
583853 TTTTGATTTTTTTGATTTT
1 TTTTTATATTATT-ATTTT
* *
583872 TTATTA-ATTTTTGATTTT
1 TTTTTATATTATT-ATTTT
**
583890 TTTTTGAT-TT-TT-TGAT
1 TTTTT-ATATTATTATTTT
583906 TTTTTATATTATTATTTT
1 TTTTTATATTATTATTTT
583924 TTT
1 TTT
583927 ATGTTAAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
15 2 0.04
16 9 0.16
17 7 0.12
18 28 0.50
19 10 0.18
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTTATATTATTATTTT
Found at i:584504 original size:42 final size:42
Alignment explanation
Indices: 584404--585437 Score: 890
Period size: 42 Copynumber: 24.2 Consensus size: 42
584394 TAGATGAGCC
* *
584404 AGTCTCCGGGGTCAAAGCCGACAAGCAGACTGAAGGGTAA-GAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTG-AGGG-AAGGAA
* * *
584447 AGTCTTCAGGATCAAAGCTGACAGGCAGACTGAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * * * *
584489 AGTCTCTAGGGTCAAAGTCGGCAGTCAGACTGAGGGAAGCAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* *
584531 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAGCAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * * *
584573 AGTCTCTAAGGTCAAAGCCTACAGGCAGATTGAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* *
584615 AGTCTCCAAGGTCAAAGTCGACAGGCAGACTGAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * * * *
584657 AGTCTCCAAGGCCAAAGCTGACAGGCAGATTGAGGGAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * ** * * * *
584699 AGTCTCTAGGGCCAAAGCAAACAGGTAGACTTTAGATGAA--AT
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGAC-TGAG-GGAAGGAA
* *
584741 AGTCTCC-GAGGTCAAAGCCGACAGGCAGATTGAAGGGAAGAAA
1 AGTCTCCAG-GGTCAAAGCCGACAGGCAGACTG-AGGGAAGGAA
* *
584784 AGTCTCCAAGGTCAAAGCCGACAGGGAGACTGAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
*
584826 AGTCTCCAGAGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * *
584868 AGTCTCCAAGATTAAAGCCGACAGGCAGACTGAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * * *
584910 AGTCTCCAAGGTCAAAG-CGAACAGGCAGACTTTAGATG-AGG-C
1 AGTCTCCAGGGTCAAAGCCG-ACAGGCAGAC-TGAG-GGAAGGAA
* * *
584952 AGTCTCTAGGGTCAAAGCCGACACGCAGACTGAAGGGTAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTG-AGGGAAGGAA
* * * *
584995 AGTCTCCAAGGTTAAAGCCGACAGACA-ACTGAGGGAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* **
585036 AGTCTCGAGGGTCAAAGTTGACAGGCAGACTGAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * * *
585078 AGTCTCCAAGGTCAAAGCCGACAGGCAGAGCCGA--CAA--AC
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGA-CTGAGGGAAGGAA
* * ** * * * * *
585117 AGACT-GAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACATGCAGACTGATGGAAGGAA
1 AGTCTCCAGGG--TCAAAG---CC---GAC-AGGCAGAC-TG-AG---G--GAAG-GAA
* * * * *
585175 AGTCTCTAGAGTTAAAGCCGACAGGCAGACTAAGGGAAAGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * * * *
585217 AGTCTCCAGAGTTAAAGCCGACAGGCAGTCTAAGGGTAA-AAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGG-AAGGAA
** * *
585259 AGTCTCCAGGGTCAAAGTTGACAGGCAGACTGAAGGGTAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTG-AGGGAAGGAA
* * * *
585302 AGTCTCCAAGGTCAAAGCTGACAGGCAGACTAAGGGAAGAAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* *
585344 AGTCTCCAAGGTCAAAGCCGACAGGCATACTGAGGGAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * * *
585386 AGTCTCCAGGGTCAAAGCCGACTGACAGACTAAGGAAAGGAA
1 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
585428 AGTCTCCAGG
1 AGTCTCCAGG
585438 AGTTTAATGA
Statistics
Matches: 811, Mismatches: 138, Indels: 85
0.78 0.13 0.08
Matches are distributed among these distances:
38 3 0.00
39 5 0.01
40 4 0.00
41 42 0.05
42 581 0.72
43 135 0.17
44 4 0.00
45 1 0.00
46 3 0.00
47 6 0.01
48 3 0.00
49 1 0.00
50 6 0.01
51 2 0.00
54 2 0.00
55 1 0.00
57 4 0.00
58 5 0.01
59 3 0.00
ACGTcount: A:0.36, C:0.20, G:0.31, T:0.13
Consensus pattern (42 bp):
AGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
Found at i:584628 original size:126 final size:125
Alignment explanation
Indices: 584404--585435 Score: 1040
Period size: 126 Copynumber: 8.1 Consensus size: 125
584394 TAGATGAGCC
** * * *
584404 AGTCTCCGGGGTCAAAGCCGACAAGCAGACTGAAGGGTAAGAAAGTCT-TCAGGATCAAAGCTGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTG-AGGG-AAGAAAGTCTCTAAGG-TCAAAGCCGA
* * * * * *
584468 CAGGCAGACTGAGGGAAGGAAAGTCTCTAGGGTCAAAGTCGGCAGTCAGACTGAGGGAAGCAA
63 CAGGCAGACTGAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
*
584531 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAGCAAAGTCTCTAAGGTCAAAGCCTACA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAG-AAAGTCTCTAAGGTCAAAGCCGACA
* *
584596 GGCAGATTGAGGGAAGGAAAGTCTCCAAGGTCAAAGTCGACAGGCAGACTGAGGGAAGGAA
65 GGCAGACTGAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * * * * **
584657 AGTCTCCAAGGCCAAAGCTGACAGGCAGATTGAGGGAAGAAAAGTCTCTAGGGCCAAAGCAAACA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAG-AAAGTCTCTAAGGTCAAAGCCGACA
* * * * * * *
584722 GGTAGACTTTAGATGAA--ATAGTCTCCGAGGTCAAAGCCGACAGGCAGATTGAAGGGAAGAAA
65 GGCAGAC-TGAG-GGAAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG-AGGGAAGGAA
* *
584784 AGTCTCCAAGGTCAAAGCCGACAGGGAGACTGAGGGAAGGAAAGTCTC-CAGAGTCAAAGCCGAC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAA-GAAAGTCTCTAAG-GTCAAAGCCGAC
* *
584848 AGGCAGACTGAGGGAAGGAAAGTCTCCAAGATTAAAGCCGACAGGCAGACTGAGGGAAGGAA
64 AGGCAGACTGAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * ** *
584910 AGTCTCCAAGGTCAAAG-CGAACAGGCAGACTTTAGATG-AGGCAGTCTCTAGGGTCAAAGCCGA
1 AGTCTCCAAGGTCAAAGCCG-ACAGGCAGAC-TGAG-GGAAGAAAGTCTCTAAGGTCAAAGCCGA
* * * * *
584973 CACGCAGACTGAAGGGTAGGAAAGTCTCCAAGGTTAAAGCCGACAGACA-ACTGAGGGAAGAAA
63 CAGGCAGACTG-AGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
* * ** *
585036 AGTCTCGAGGGTCAAAGTTGACAGGCAGACTGAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAA-GAAAGTCTCTAAGGTCAAAGCCG--A
* *
585101 GGCAGAGCCGACAAACAGACTGAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACATGCAGACTGA
63 --C--AG--G-----CAGACTGAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGA
*
585166 TGGAAGGAA
117 GGGAAGGAA
* * * * *
585175 AGTCT-CTAGAGTTAAAGCCGACAGGCAGACTAAGGGAAAGAAAGTCTC-CAGAGTTAAAGCCGA
1 AGTCTCCAAG-GTCAAAGCCGACAGGCAGACTGAGGG-AAGAAAGTCTCTAAG-GTCAAAGCCGA
* * * * ** * *
585238 CAGGCAGTCTAAGGGTAA-AAAAGTCTCCAGGGTCAAAGTTGACAGGCAGACTGAAGGGTAGAAA
63 CAGGCAGACTGAGGG-AAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG-AGGGAAGGAA
* * *
585302 AGTCTCCAAGGTCAAAGCTGACAGGCAGACTAAGGGAAGAAAAGTCTCCAAGGTCAAAGCCGACA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAG-AAAGTCTCTAAGGTCAAAGCCGACA
* * * * * *
585367 GGCATACTGAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACTGACAGACTAAGGAAAGGAA
65 GGCAGACTGAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
585428 AGTCTCCA
1 AGTCTCCA
585436 GGAGTTTAAT
Statistics
Matches: 754, Mismatches: 111, Indels: 81
0.80 0.12 0.09
Matches are distributed among these distances:
124 1 0.00
125 12 0.02
126 352 0.47
127 269 0.36
128 11 0.01
130 1 0.00
131 1 0.00
132 1 0.00
133 2 0.00
134 1 0.00
135 1 0.00
137 1 0.00
138 35 0.05
139 64 0.08
140 2 0.00
ACGTcount: A:0.36, C:0.20, G:0.31, T:0.13
Consensus pattern (125 bp):
AGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAGTCTCTAAGGTCAAAGCCGACAG
GCAGACTGAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAA
Found at i:585171 original size:139 final size:139
Alignment explanation
Indices: 584967--585244 Score: 373
Period size: 139 Copynumber: 2.0 Consensus size: 139
584957 CTAGGGTCAA
** * *
584967 AGCCGACACGCAGACTGAAGGGTAGGAAAGTCTCCAAGGTTAAAGCCGACAGACAACTGAGGGAA
1 AGCCGACAAACAGACTGAAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACAGACAACTGAGGGAA
* ** * *
585032 GAAAAGTCTCGAGGGTCAAAGTTGACAGGCAGACTGAGGGAAGGAAAGTCTCCA-AGGTCAAAGC
66 GAAAAGTCTCGAGAGTCAAAGCCGACAGGCAGACTAAGGGAAAGAAAGTCTCCAGA-GTCAAAGC
585096 CGACAGGCAG
130 CGACAGGCAG
* *
585106 AGCCGACAAACAGACTG-AGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACATG-CAGACTGATGG
1 AGCCGACAAACAGACTGAAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACA-GACA-ACTGAGGG
* * * *
585169 AAGGAAAGTCTCTAGAGTTAAAGCCGACAGGCAGACTAAGGGAAAGAAAGTCTCCAGAGTTAAAG
64 AAGAAAAGTCTCGAGAGTCAAAGCCGACAGGCAGACTAAGGGAAAGAAAGTCTCCAGAGTCAAAG
585234 CCGACAGGCAG
129 CCGACAGGCAG
585245 TCTAAGGGTA
Statistics
Matches: 121, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
138 32 0.26
139 88 0.73
140 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.31, T:0.12
Consensus pattern (139 bp):
AGCCGACAAACAGACTGAAGGGAAGGAAAGTCTCCAAGGTCAAAGCCGACAGACAACTGAGGGAA
GAAAAGTCTCGAGAGTCAAAGCCGACAGGCAGACTAAGGGAAAGAAAGTCTCCAGAGTCAAAGCC
GACAGGCAG
Found at i:585192 original size:97 final size:96
Alignment explanation
Indices: 585010--585370 Score: 295
Period size: 97 Copynumber: 4.0 Consensus size: 96
585000 CCAAGGTTAA
* * **
585010 AGCCGACAGACAACTGAGGGAAGAAAAGTCTCGAGGGTCAAAGTTGACAGGCAGACTGAGGGAAG
1 AGCCGACAAACAACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAG
585075 GAAAGTCTCCAAGGTCAAAGCCGACAGGCAG
66 GAAAGTCTCCAAGGTCAAAGCCGACAGGCAG
* * *
585106 AGCCGACAAACAGACTGAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACATGCAGACTGATGGAA
1 AGCCGACAAACA-ACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAA
* *
585171 GGAAAGTCT-CTAGAGTTAAAGCCGACAGGC--
65 GGAAAGTCTCCAAG-GTCAAAGCCGACAGGCAG
* * * * * *
585201 A---GAC---TAA--G-GGAAAG-AAAGTCTCCAGAGTTAAAGCCGACAGGCAGTCTAAGGGTAA
1 AGCCGACAAACAACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGG-AA
* * **
585256 -AAAAGTCTCCAGGGTCAAAGTTGACAGGCAG
65 GGAAAGTCTCCAAGGTCAAAGCCGACAGGCAG
* * * * *
585287 A-CTG-------A---AGGGTAGAAAAGTCTCCAAGGTCAAAGCTGACAGGCAGACTAAGGGAAG
1 AGCCGACAAACAACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAG
*
585341 AAAAGTCTCCAAGGTCAAAGCCGACAGGCA
66 GAAAGTCTCCAAGGTCAAAGCCGACAGGCA
585371 TACTGAGGGA
Statistics
Matches: 221, Mismatches: 33, Indels: 33
0.77 0.11 0.11
Matches are distributed among these distances:
84 59 0.27
85 69 0.31
86 2 0.01
88 2 0.01
89 1 0.00
92 3 0.01
95 1 0.00
96 14 0.06
97 70 0.32
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.12
Consensus pattern (96 bp):
AGCCGACAAACAACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAG
GAAAGTCTCCAAGGTCAAAGCCGACAGGCAG
Found at i:585263 original size:181 final size:181
Alignment explanation
Indices: 584952--585435 Score: 498
Period size: 169 Copynumber: 2.7 Consensus size: 181
584942 TAGATGAGGC
* *
584952 AGTCTCTAGGGTCAAAGCCGACACGCAGACTGAAGGGTAGGAAAGTCTCCAAGGTTAAAGCCGAC
1 AGTCTCCAGGGTCAAAGCCGACACGCAGACTGAAGGGAAGGAAAGTCTCCAAGGTTAAAGCCGAC
* * * ** * *
585017 AGACAACTGAGGGAAGAAAAGTCTCGAGGGTCAAAGTTGACAGGCAGACTGAGGGAAGGAAAGTC
66 AGACAACTAAGGGAAGAAAAGTCTCCAGAGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAGTC
585082 TCCAAGGTCAAAGCCGACAGGCAGAGCCGACAAACAGACTGAGGGAAGGAA
131 TCCAAGGTCAAAGCCGACAGGCAGAGCCGACAAACAGACTGAGGGAAGGAA
* * *
585133 AGTCTCCAGGGTCAAAGCCGACATGCAGACTG-ATGGAAGGAAAGTCT-CTAGAGTTAAAGCCGA
1 AGTCTCCAGGGTCAAAGCCGACACGCAGACTGAAGGGAAGGAAAGTCTCCAAG-GTTAAAGCCGA
* * *
585196 CAGGCAGACTAAGGGAA-AGAAAGTCTCCAGAGTTAAAGCCGACAGGCAGTCTAAGGGTAA-AAA
65 CAGACA-ACTAAGGGAAGA-AAAGTCTCCAGAGTCAAAGCCGACAGGCAGACTAAGGG-AAGAAA
* ** * * *
585259 AGTCTCCAGGGTCAAAGTTGACAGGC--A---G----ACTGA---AGGGTAGAAA
127 AGTCTCCAAGGTCAAAGCCGACAGGCAGAGCCGACAAACAGACTGAGGGAAGGAA
* * * * *
585302 AGTCTCCAAGGTCAAAGCTGACAGGCAGACT-AAGGGAAGAAAAGTCTCCAAGGTCAAAGCCGAC
1 AGTCTCCAGGGTCAAAGCCGACACGCAGACTGAAGGGAAGGAAAGTCTCCAAGGTTAAAGCCGAC
* * * * * * * *
585366 AGGCATACTGAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACTGACAGACTAAGGAAAGGAAAGT
66 AGACA-ACTAAGGGAAGAAAAGTCTCCAGAGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAGT
585431 CTCCA
130 CTCCA
585436 GGAGTTTAAT
Statistics
Matches: 257, Mismatches: 38, Indels: 28
0.80 0.12 0.09
Matches are distributed among these distances:
168 2 0.01
169 116 0.45
170 3 0.01
172 4 0.02
176 1 0.00
179 4 0.02
180 30 0.12
181 95 0.37
182 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.13
Consensus pattern (181 bp):
AGTCTCCAGGGTCAAAGCCGACACGCAGACTGAAGGGAAGGAAAGTCTCCAAGGTTAAAGCCGAC
AGACAACTAAGGGAAGAAAAGTCTCCAGAGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAGTC
TCCAAGGTCAAAGCCGACAGGCAGAGCCGACAAACAGACTGAGGGAAGGAA
Found at i:585351 original size:127 final size:126
Alignment explanation
Indices: 585123--585433 Score: 371
Period size: 127 Copynumber: 2.5 Consensus size: 126
585113 AAACAGACTG
* * * * * *
585123 AGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACATGCAGACTGATGGAAGGAAAGTCTCTAGAGTT
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCAAGAGTC
*
585188 AAAGCCGACAGGCAGACTAAGGGAAAGAAAGTCTCC-AGAGTTAAAGCCGACAGGCAGT-CTA
66 AAAGCCGACAGGCAGACTAAGGGAAAGAAAGTCTCCAAG-GTCAAAGCCGACAGGCA-TACTA
** *
585249 AGGGTAA-AAAAGTCTCCAGGGTCAAAGTTGACAGGCAGACTGAAGGGTAGAAAAGTCTCCAAG-
1 AGGG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTG-AGGGAAGAAAAGTCT-CAAGA
* *
585312 GTCAAAGCTGACAGGCAGACTAAGGG-AAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCATACTG
63 GTCAAAGCCGACAGGCAGACTAAGGGAAAG-AAAGTCTCCAAGGTCAAAGCCGACAGGCATACTA
* * * * * *
585376 AGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACTGACAGACTAAGGAAAGGAAAGTCTC
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTC
585434 CAGGAGTTTA
Statistics
Matches: 157, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
125 1 0.01
126 53 0.34
127 98 0.62
128 5 0.03
ACGTcount: A:0.37, C:0.19, G:0.30, T:0.14
Consensus pattern (126 bp):
AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCAAGAGTC
AAAGCCGACAGGCAGACTAAGGGAAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCATACTA
Found at i:599374 original size:38 final size:38
Alignment explanation
Indices: 599321--599472 Score: 142
Period size: 38 Copynumber: 3.7 Consensus size: 38
599311 TCCTTATTGC
* * *
599321 TTTGCTATTCGACGTTGCTTTGTCTTCATCATTGCTGT
1 TTTGCTTTTCCACGTTACTTTGTCTTCATCATTGCTGT
* *
599359 TTTGCTTTTCCACGTTACTTTGTCTTCCACTTTTTTCATTGTTGC
1 TTTGCTTTTCCACGTTACTTTGTCTT-CA------TCATTGCTGT
*
599404 TTTGCTTTGTTGTCCATGTTACTTTGTCTTCATCATTGCTGT
1 TTTGC--T-TT-TCCACGTTACTTTGTCTTCATCATTGCTGT
*
599446 TTTGCTTTTCCACATTACTTTGTCTTC
1 TTTGCTTTTCCACGTTACTTTGTCTTC
599473 CACTTTTTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
38 40 0.43
39 4 0.04
40 1 0.01
42 13 0.14
45 13 0.14
47 1 0.01
48 4 0.04
49 17 0.18
ACGTcount: A:0.10, C:0.22, G:0.14, T:0.54
Consensus pattern (38 bp):
TTTGCTTTTCCACGTTACTTTGTCTTCATCATTGCTGT
Found at i:599447 original size:87 final size:88
Alignment explanation
Indices: 599338--599536 Score: 310
Period size: 87 Copynumber: 2.3 Consensus size: 88
599328 TTCGACGTTG
* * *
599338 CTTTGTCTTCATCATTGCTGTTTTGCTTTTCCACGTTACTTTGTCTTCCACTTTTTTCATTGTTG
1 CTTTGTCTTCATCATTGCTGTTTTGCTTTTCCACATTACTTTGTCTTCCACTTTTTTCATTATTA
* *
599403 CTTTGCTTTGTTG-TCCATGTTA
66 CTTTGCATTGCTGTTCCATGTTA
*
599425 CTTTGTCTTCATCATTGCTGTTTTGCTTTTCCACATTACTTTGTCTTCCACTTTTTTTATTATTA
1 CTTTGTCTTCATCATTGCTGTTTTGCTTTTCCACATTACTTTGTCTTCCACTTTTTTCATTATTA
* *
599490 CTTTGCATTGCTGTTTCATGTTG
66 CTTTGCATTGCTGTTCCATGTTA
*
599513 CTTTGTCTTCATCATTGCTTTTTT
1 CTTTGTCTTCATCATTGCTGTTTT
599537 TAAATCATCC
Statistics
Matches: 102, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 72 0.71
88 30 0.29
ACGTcount: A:0.11, C:0.21, G:0.12, T:0.56
Consensus pattern (88 bp):
CTTTGTCTTCATCATTGCTGTTTTGCTTTTCCACATTACTTTGTCTTCCACTTTTTTCATTATTA
CTTTGCATTGCTGTTCCATGTTA
Found at i:599964 original size:7 final size:7
Alignment explanation
Indices: 599952--600020 Score: 59
Period size: 7 Copynumber: 9.3 Consensus size: 7
599942 TTTTTTTTAA
599952 TTATTTT
1 TTATTTT
599959 TTATTTT
1 TTATTTT
*
599966 TTATTAAT
1 TTATT-TT
599974 TTATTATT
1 TTATT-TT
*
599982 ATT-TATTA
1 -TTAT-TTT
599990 TTATTTT
1 TTATTTT
599997 TTATTTT
1 TTATTTT
*
600004 TTATATTA
1 TTAT-TTT
600012 TTATTTT
1 TTATTTT
600019 TT
1 TT
600021 TATGTTAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 31 0.61
8 17 0.33
9 3 0.06
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTATTTT
Found at i:600016 original size:38 final size:36
Alignment explanation
Indices: 599942--600023 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 36
599932 CTCCCTTCTC
*
599942 TTTTTTT-TAATTATTTTTTATTTTTTATTAATTTA
1 TTTTTTTATTATTATTTTTTATTTTTTATTAATTTA
*
599977 TTATTATTTATTATTATTTTTTATTTTTTA-TATTATTA
1 TT-TT-TTTATTATTATTTTTTATTTTTTATTAAT-TTA
600015 TTTTTTTAT
1 TTTTTTTAT
600024 GTTAAAAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 2 0.05
36 7 0.17
37 8 0.20
38 24 0.59
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (36 bp):
TTTTTTTATTATTATTTTTTATTTTTTATTAATTTA
Found at i:600021 original size:16 final size:16
Alignment explanation
Indices: 599975--600023 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
599965 TTTATTAATT
599975 TATTATTATTTATTATTA
1 TATTATTATTT-TT-TTA
*
599993 T-TTTTTA-TTTTTTA
1 TATTATTATTTTTTTA
600007 TATTATTATTTTTTTA
1 TATTATTATTTTTTTA
600023 T
1 T
600024 GTTAAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 4 0.15
15 7 0.26
16 10 0.37
17 5 0.19
18 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTATTATTTTTTTA
Found at i:601473 original size:45 final size:45
Alignment explanation
Indices: 601409--601494 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
601399 GTTTACAAAG
601409 AAAGCTTTTCATACATACTTAGGTAAAATTAAAAAAAAAAAACTT
1 AAAGCTTTTCATACATACTTAGGTAAAATTAAAAAAAAAAAACTT
601454 AAAGCTTTTCATACATACTTAGGTAAAATTAAAAAAAAAAA
1 AAAGCTTTTCATACATACTTAGGTAAAATTAAAAAAAAAAA
601495 CTTTTAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (45 bp):
AAAGCTTTTCATACATACTTAGGTAAAATTAAAAAAAAAAAACTT
Found at i:602223 original size:23 final size:22
Alignment explanation
Indices: 602171--602236 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
602161 AAAGATTTAA
* *
602171 ATTTTATAGTATTTTATTTTATT
1 ATTTTAAATTATTTTA-TTTATT
**
602194 AAATTAAATTATTTTATTTATT
1 ATTTTAAATTATTTTATTTATT
* *
602216 CATTTTAATTTAATTTATTTA
1 -ATTTTAAATTATTTTATTTA
602237 ATTTAATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 6 0.18
23 28 0.82
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTAAATTATTTTATTTATT
Found at i:602231 original size:19 final size:19
Alignment explanation
Indices: 602204--602250 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
602194 AAATTAAATT
*
602204 ATTTTATTTATTCATTTTA
1 ATTTTATTTATTCAATTTA
* *
602223 ATTTAATTTATTTAATTTA
1 ATTTTATTTATTCAATTTA
602242 ATTTTATTT
1 ATTTTATTT
602251 TTATAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTATTTATTCAATTTA
Found at i:602236 original size:14 final size:14
Alignment explanation
Indices: 602183--602250 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
602173 TTTATAGTAT
*
602183 TTTATTTTA-TTAA
1 TTTAATTTATTTAA
* * *
602196 ATTAAATTATTTTA
1 TTTAATTTATTTAA
*
602210 TTT-ATTCATTTTAA
1 TTTAATTTA-TTTAA
602224 TTTAATTTATTTAA
1 TTTAATTTATTTAA
602238 TTTAATTTTATTT
1 TTTAA-TTTATTT
602251 TTATAAAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
13 9 0.21
14 22 0.52
15 11 0.26
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTAATTTATTTAA
Found at i:602393 original size:2 final size:2
Alignment explanation
Indices: 602386--602427 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
602376 AGTATTGCCG
602386 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
602427 T
1 T
602428 GGTCCTACCT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:603227 original size:20 final size:20
Alignment explanation
Indices: 603189--603228 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
603179 AGTGAGTAGC
*
603189 TTTTAAAGAAATTATTAATT
1 TTTTAAAAAAATTATTAATT
603209 TTTTAAAAAATATTA-TAATT
1 TTTTAAAAAA-ATTATTAATT
603229 AAAATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTAAAAAAATTATTAATT
Found at i:604237 original size:2 final size:2
Alignment explanation
Indices: 604230--604257 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
604220 GTTCACACGC
604230 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
604258 GAATGAGCAT
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):
AT
Found at i:604881 original size:2 final size:2
Alignment explanation
Indices: 604874--604905 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
604864 ACAAATATGC
604874 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
604906 TATGCAGAAG
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):
AT
Found at i:606188 original size:20 final size:22
Alignment explanation
Indices: 606163--606209 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
606153 TAATAAAAAT
606163 TTAAAAAATATAT-TTTTAT-A
1 TTAAAAAATATATATTTTATAA
**
606183 TTAAAATTTATATATTTTATAA
1 TTAAAAAATATATATTTTATAA
606205 TTAAA
1 TTAAA
606210 TTTATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 6 0.26
22 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAAAAAATATATATTTTATAA
Found at i:606198 original size:22 final size:21
Alignment explanation
Indices: 606170--606217 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 21
606160 AATTTAAAAA
606170 ATATATTTT-TATATTAAAATTT
1 ATATATTTTATA-ATT-AAATTT
606192 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
606213 ATATA
1 ATATA
606218 AAATTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.44
22 12 0.48
23 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:606202 original size:21 final size:22
Alignment explanation
Indices: 606170--606217 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
606160 AATTTAAAAA
606170 ATATATTTTTAT-ATTAAAATTT
1 ATATATTTTTATAATT-AAATTT
606192 ATATA-TTTTATAATTAAATTT
1 ATATATTTTTATAATTAAATTT
606213 ATATA
1 ATATA
606218 AAATTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATATTTTTATAATTAAATTT
Found at i:606268 original size:20 final size:19
Alignment explanation
Indices: 606243--606300 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
606233 TAAATAATAT
* *
606243 TTTAAATGGAATCAAATAAA
1 TTTAAAT-GAATAAAAAAAA
*
606263 TTTAAATTAATAAAAAAAA
1 TTTAAATGAATAAAAAAAA
*
606282 TTTAAATTCAATAAAAAAA
1 TTTAAA-TGAATAAAAAAA
606301 TTGAATCTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (19 bp):
TTTAAATGAATAAAAAAAA
Found at i:606284 original size:19 final size:20
Alignment explanation
Indices: 606260--606300 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
606250 GGAATCAAAT
606260 AAATTTAAATT-AATAAAAA
1 AAATTTAAATTCAATAAAAA
606279 AAATTTAAATTCAATAAAAA
1 AAATTTAAATTCAATAAAAA
606299 AA
1 AA
606301 TTGAATCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATTTAAATTCAATAAAAA
Found at i:608602 original size:21 final size:20
Alignment explanation
Indices: 608571--608609 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
608561 TTTATTAGTT
*
608571 TTATTTATTTTTAAAATTCA
1 TTATTTATTTTCAAAATTCA
608591 TTATTATATTTTCAAAATT
1 TTATT-TATTTTCAAAATT
608610 AAATAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTTATTTTCAAAATTCA
Found at i:614699 original size:2 final size:2
Alignment explanation
Indices: 614692--614720 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
614682 CAGGTTCATT
614692 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
614721 GAAACAAAAA
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:615971 original size:24 final size:22
Alignment explanation
Indices: 615931--615992 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 22
615921 TTTAATATAA
* **
615931 AATTTTTGATTTTTTTAATTTT
1 AATTTTTAATTTTTTTAAAATT
615953 AACTTATTTAATTTTTTTAAAATT
1 AA-TT-TTTAATTTTTTTAAAATT
615977 AATTTTTAATTTTTTT
1 AATTTTTAATTTTTTT
615993 TTATTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 14 0.40
23 4 0.11
24 17 0.49
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (22 bp):
AATTTTTAATTTTTTTAAAATT
Found at i:616091 original size:23 final size:23
Alignment explanation
Indices: 616065--616169 Score: 67
Period size: 23 Copynumber: 4.5 Consensus size: 23
616055 ATTAATAATA
616065 ATTTATTTTATATATTTTTAAAT
1 ATTTATTTTATATATTTTTAAAT
*
616088 ATTTTATTTT-TAT-TTATTTATAT
1 A-TTTATTTTATATATT-TTTAAAT
* * * *
616111 ATTTGATGTTAAAGAATTTTAAAT
1 ATTT-ATTTTATATATTTTTAAAT
*
616135 ATTAAATATTTATA-A-TTTTAAA-
1 ATT-TAT-TTTATATATTTTTAAAT
616157 ATTTATATTTATA
1 ATTTAT-TTTATA
616170 AATAAACATA
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
21 9 0.14
22 8 0.12
23 22 0.34
24 21 0.32
25 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (23 bp):
ATTTATTTTATATATTTTTAAAT
Found at i:616171 original size:15 final size:16
Alignment explanation
Indices: 616136--616173 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
616126 ATTTTAAATA
616136 TTAAATATTTATAATT
1 TTAAATATTTATAATT
616152 TTAAA-ATTTAT-ATT
1 TTAAATATTTATAATT
616166 TATAAATA
1 T-TAAATA
616174 AACATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.20
15 10 0.50
16 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATATTTATAATT
Found at i:616435 original size:18 final size:18
Alignment explanation
Indices: 616401--616457 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 18
616391 TCAAAATATT
*
616401 TTTAAA-TTAAATTATTTA
1 TTTAAATTTAAA-AATTTA
616419 TTTAAATTTAAAAATTTA
1 TTTAAATTTAAAAATTTA
*
616437 TCTAATATTTTAAAAAATTTA
1 TTTAA-A-TTT-AAAAATTTA
616458 AATACAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 15 0.45
19 6 0.18
20 3 0.09
21 9 0.27
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAATTTAAAAATTTA
Found at i:624342 original size:83 final size:83
Alignment explanation
Indices: 624195--624352 Score: 253
Period size: 83 Copynumber: 1.9 Consensus size: 83
624185 ACTTACTGCA
* * * *
624195 TAGGCTATGTTTGGTCTGGTATGTGAAAGGTAGATCAGCTTTCCAGCCAATCTTTAATACATATC
1 TAGGCTATGTCTGGTATGGTATGTGAAAGGTAGATCAGCTTTCCAACCAATCTTTAATAAATATC
624260 CTTATCCACCTTTGGATC
66 CTTATCCACCTTTGGATC
* * *
624278 TAGGCTATGTCTGGTATGGTATGTGAGAGGTAGATCAGCTTTTCAACCAATCTTTGATAAATATC
1 TAGGCTATGTCTGGTATGGTATGTGAAAGGTAGATCAGCTTTCCAACCAATCTTTAATAAATATC
624343 CTTATCCACC
66 CTTATCCACC
624353 GTTAGTTCCT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (83 bp):
TAGGCTATGTCTGGTATGGTATGTGAAAGGTAGATCAGCTTTCCAACCAATCTTTAATAAATATC
CTTATCCACCTTTGGATC
Found at i:625700 original size:51 final size:50
Alignment explanation
Indices: 625555--625702 Score: 190
Period size: 50 Copynumber: 2.9 Consensus size: 50
625545 TTGCATAGAC
* *
625555 TGTATAGGCTGATTTTGAAGCTGTTGGGTTTCAGGTTAGGACTGTATAAGG
1 TGTATAGGCTGATTTTGAAGCTGCTGGGTTTCAGGTTAGGACTGTA-CAGG
* * * *
625606 TGTTTAGGCTAATTTTGAAGCTGC-GGGTTTTAGGTTATGACTGTACAGG
1 TGTATAGGCTGATTTTGAAGCTGCTGGGTTTCAGGTTAGGACTGTACAGG
* * *
625655 TTGTATAGGTTGATTTTGAAGCTGCTAGGTTTCAGGTTGGGACTGTAC
1 -TGTATAGGCTGATTTTGAAGCTGCTGGGTTTCAGGTTAGGACTGTAC
625703 CTCAAGTTGT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
49 3 0.04
50 40 0.49
51 39 0.48
ACGTcount: A:0.20, C:0.09, G:0.32, T:0.39
Consensus pattern (50 bp):
TGTATAGGCTGATTTTGAAGCTGCTGGGTTTCAGGTTAGGACTGTACAGG
Found at i:634950 original size:2 final size:2
Alignment explanation
Indices: 634945--634988 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
634935 TTTGAAAGCA
*
634945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
634987 AT
1 AT
634989 GGTGCTTGCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:637512 original size:27 final size:28
Alignment explanation
Indices: 637454--637528 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
637444 ATTAAAATTT
*
637454 ATATAAAT-AT-AAATATCTTAAATATA
1 ATATAAATAATAAAATATCATAAATATA
*
637480 ATTATAAATAATAAAATAT-ATAAATATG
1 A-TATAAATAATAAAATATCATAAATATA
*
637508 ATATAAATACATAAATTATCA
1 ATATAAATA-ATAAAATATCA
637529 ATTTTATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 1 0.02
27 15 0.37
28 18 0.44
29 7 0.17
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (28 bp):
ATATAAATAATAAAATATCATAAATATA
Found at i:639325 original size:29 final size:28
Alignment explanation
Indices: 639281--639335 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
639271 TTCTTGATTT
*
639281 TTTGAATAAATTATTAAAATAATATTAA
1 TTTGAATAAATAATTAAAATAATATTAA
*
639309 TTTGAAATAAATAATTAAAATATTATT
1 TTTG-AATAAATAATTAAAATAATATT
639336 GTTTTAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (28 bp):
TTTGAATAAATAATTAAAATAATATTAA
Found at i:639601 original size:16 final size:16
Alignment explanation
Indices: 639565--639617 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
639555 TTTTAAATTA
639565 AATAAAAGATTATATTACT
1 AATAAAAGA-TA-A-TACT
639584 AATAAAAGATAATACT
1 AATAAAAGATAATACT
*
639600 AATATAA-AT-ATACT
1 AATAAAAGATAATACT
639614 AATA
1 AATA
639618 GTTTTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
14 9 0.27
15 2 0.06
16 10 0.30
17 1 0.03
18 2 0.06
19 9 0.27
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (16 bp):
AATAAAAGATAATACT
Found at i:639734 original size:24 final size:25
Alignment explanation
Indices: 639675--639749 Score: 89
Period size: 26 Copynumber: 3.0 Consensus size: 25
639665 TTATTTATTT
* *
639675 AGATTATAATCGTCTAATTATTTTA
1 AGATTATAATCATCTAATTATTTAA
*
639700 ATATTTATAATCATCTAATTA-TTAA
1 AGA-TTATAATCATCTAATTATTTAA
* *
639725 AGATTGTAATCATCTAATTTTTTAA
1 AGATTATAATCATCTAATTATTTAA
639750 CTAAGAGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
24 15 0.36
25 11 0.26
26 16 0.38
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (25 bp):
AGATTATAATCATCTAATTATTTAA
Found at i:639933 original size:22 final size:22
Alignment explanation
Indices: 639899--639944 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
639889 TTAGAATTTA
*
639899 AAAATAATAAAAATTTTAAAAT
1 AAAATAATAAAAATTTAAAAAT
* *
639921 AAAATGATTAAAATTTAAAAAT
1 AAAATAATAAAAATTTAAAAAT
639943 AA
1 AA
639945 TTAGACGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATAATAAAAATTTAAAAAT
Found at i:640087 original size:37 final size:37
Alignment explanation
Indices: 639927--640086 Score: 136
Period size: 37 Copynumber: 4.4 Consensus size: 37
639917 AAATAAAATG
* **
639927 ATTAAAATTTAAAAATAATTAGACGATTACAAGATAA
1 ATTAAAATTTAAATATAATTAGACGATTACAACTTAA
* * *
639964 ATTATAATTTTAATATAATTAGACAATTACAACTTAAA
1 ATTAAAATTTAAATATAATTAGACGATTACAACTT-AA
*
640002 ATT----TTTAAA-ATAATTATG-TGATTACAATCCTT-A
1 ATTAAAATTTAAATATAATTA-GACGATTACAA--CTTAA
* * *
640035 ATTTAAATTTAAAATTTAATTAGATGATTACAACTTAA
1 ATTAAAATTT-AAATATAATTAGACGATTACAACTTAA
640073 ATTAAAATTTAAAT
1 ATTAAAATTTAAAT
640087 TAAACATATC
Statistics
Matches: 100, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
33 18 0.18
34 6 0.06
35 3 0.03
37 39 0.39
38 19 0.19
39 15 0.15
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.39
Consensus pattern (37 bp):
ATTAAAATTTAAATATAATTAGACGATTACAACTTAA
Found at i:640176 original size:26 final size:29
Alignment explanation
Indices: 640124--640176 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
640114 GATTATAATC
*
640124 TAAATGAATAAATTTATTGTTATTAATTG
1 TAAATGAATAAATTTATTGTTAATAATTG
*
640153 TAAATGAA-ATATTT-TT-TTAATAAT
1 TAAATGAATAAATTTATTGTTAATAAT
640177 AAAACTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 2 0.09
28 5 0.23
29 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (29 bp):
TAAATGAATAAATTTATTGTTAATAATTG
Found at i:640217 original size:19 final size:19
Alignment explanation
Indices: 640189--640234 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
640179 AACTATTATA
*
640189 TTTA-TAATAATATTACCT
1 TTTATTAATAATATAACCT
*
640207 TTTATTAATAATATAATCT
1 TTTATTAATAATATAACCT
640226 TTTATTAAT
1 TTTATTAAT
640235 TTTAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATTAATAATATAACCT
Found at i:640664 original size:32 final size:32
Alignment explanation
Indices: 640598--640665 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
640588 ATTTTACGTG
*
640598 AGATTCATTAAAGCATTTAGCAATTTCATGTA
1 AGATTCATTAAAGCATTTAGCAATTTCATATA
* *
640630 AGATTTATTAAAGCATTTAGCGA-TTCTATATA
1 AGATTCATTAAAGCATTTAGCAATTTC-ATATA
640662 AGAT
1 AGAT
640666 CTCTTAACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 3 0.09
32 29 0.91
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (32 bp):
AGATTCATTAAAGCATTTAGCAATTTCATATA
Found at i:648942 original size:2 final size:2
Alignment explanation
Indices: 648937--648980 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
648927 TTTGAAAGCA
*
648937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
648979 AT
1 AT
648981 GGTGCTTGCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:651507 original size:27 final size:28
Alignment explanation
Indices: 651449--651523 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
651439 ATTAAAATTT
*
651449 ATATAAAT-AT-AAATATCTTAAATATA
1 ATATAAATAATAAAATATCATAAATATA
*
651475 ATTATAAATAATAAAATAT-ATAAATATG
1 A-TATAAATAATAAAATATCATAAATATA
*
651503 ATATAAATACATAAATTATCA
1 ATATAAATA-ATAAAATATCA
651524 ATTTTATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 1 0.02
27 15 0.37
28 18 0.44
29 7 0.17
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (28 bp):
ATATAAATAATAAAATATCATAAATATA
Found at i:653325 original size:29 final size:28
Alignment explanation
Indices: 653281--653335 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
653271 GTTCTTGATT
*
653281 TTTGAATAAATTATTAAAATAATATTAA
1 TTTGAATAAATAATTAAAATAATATTAA
*
653309 TTTGAAATAAATAATTAAAATATTATT
1 TTTG-AATAAATAATTAAAATAATATT
653336 GTTTTAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (28 bp):
TTTGAATAAATAATTAAAATAATATTAA
Found at i:653737 original size:24 final size:25
Alignment explanation
Indices: 653678--653746 Score: 86
Period size: 26 Copynumber: 2.8 Consensus size: 25
653668 TTATTTATTT
* *
653678 AGATTATAATCGTCTAATTATTTTA
1 AGATTATAATCATCTAATTATTTAA
*
653703 ATATTTATAATCATCTAATTA-TTAA
1 AGA-TTATAATCATCTAATTATTTAA
*
653728 AGATTGTAATCATCTAATT
1 AGATTATAATCATCTAATT
653747 TTTTTAACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
24 15 0.39
25 7 0.18
26 16 0.42
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (25 bp):
AGATTATAATCATCTAATTATTTAA
Found at i:653953 original size:23 final size:23
Alignment explanation
Indices: 653906--653949 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
653896 TTAGAATTTA
653906 AAAATAATTAAAAATTTTAAAAT
1 AAAATAATTAAAAATTTTAAAAT
*
653929 AAAATGATT-AAAATTTTAAAA
1 AAAATAATTAAAAATTTTAAAA
653950 ATAATTAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAATAATTAAAAATTTTAAAAT
Found at i:654034 original size:32 final size:33
Alignment explanation
Indices: 653988--654081 Score: 84
Period size: 39 Copynumber: 2.7 Consensus size: 33
653978 AATTTTAATA
** *
653988 TAATTAGACAATTACAACTTAAAATTTTAAAA-
1 TAATTAGATGATTACAACTTAAAAATTTAAAAT
654020 TAATTATG-TGATTACAATCCTTAATTTAAATTTAAAATT
1 TAATTA-GATGATTACAA--CTTAA---AAATTTAAAA-T
654059 TAATTAGATGATTACAACTTAAA
1 TAATTAGATGATTACAACTTAAA
654082 TTAAAATTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
32 13 0.26
33 1 0.02
34 6 0.12
37 14 0.28
38 1 0.02
39 15 0.30
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (33 bp):
TAATTAGATGATTACAACTTAAAAATTTAAAAT
Done.