Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 8 of 27
Found at i:1138911 original size:15 final size:15
Alignment explanation
Indices: 1138891--1138924 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1138881 TCCTATATTA
1138891 TTAACAATAAAATTT
1 TTAACAATAAAATTT
1138906 TTAACAATAAAATTT
1 TTAACAATAAAATTT
1138921 TTAA
1 TTAA
1138925 AAGAAATCAT
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:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAACAATAAAATTT
Found at i:1138937 original size:55 final size:55
Alignment explanation
Indices: 1138813--1138969 Score: 193
Period size: 55 Copynumber: 2.9 Consensus size: 55
1138803 TTAGAAATTT
*
1138813 TTTTTAAAAGAAATCATTT-C-ATATTATTAACAATAAAA---TTAACAAT-ATA
1 TTTTTAAAAGAAATCATTTCCTATATTATTAACAATAAAATTTTTAACAATAAAA
* * * **
1138862 -TATAAAAATATATAAAATTTCCTATATTATTAACAATAAAATTTTTAACAATAAAA
1 TTTTTAAAAGA-A-ATCATTTCCTATATTATTAACAATAAAATTTTTAACAATAAAA
1138918 TTTTTAAAAGAAATCATTTCCTATATTATTAACAATAAAATTTTTAACAATA
1 TTTTTAAAAGAAATCATTTCCTATATTATTAACAATAAAATTTTTAACAATA
1138970 TATATAAAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
48 7 0.08
49 1 0.01
50 5 0.06
51 1 0.01
52 18 0.20
55 46 0.52
56 3 0.03
57 7 0.08
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.39
Consensus pattern (55 bp):
TTTTTAAAAGAAATCATTTCCTATATTATTAACAATAAAATTTTTAACAATAAAA
Found at i:1139934 original size:2 final size:2
Alignment explanation
Indices: 1139929--1139960 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1139919 AAAATGTAAA
1139929 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
1139961 TATGTCTGCC
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:1140477 original size:21 final size:22
Alignment explanation
Indices: 1140421--1140484 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
1140411 ATAATCGAAG
* *
1140421 ATAATTTAATATAAATATAAAAT
1 ATAATTTAAAAAAAATAT-AAAT
* **
1140444 ATAAATTTTAAAAAATATAAA-
1 ATAATTTAAAAAAAATATAAAT
1140465 ATAATTTAAAAAAAAT-TAAA
1 ATAATTTAAAAAAAATATAAA
1140485 GATATTAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
20 4 0.12
21 13 0.39
22 3 0.09
23 13 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAATTTAAAAAAAATATAAAT
Found at i:1141666 original size:2 final size:2
Alignment explanation
Indices: 1141659--1141687 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1141649 AAAGCCATCG
1141659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1141688 AATTAAGCCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1144623 original size:15 final size:15
Alignment explanation
Indices: 1144603--1144636 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1144593 CAATAATATA
1144603 ATATATATTACTTTT
1 ATATATATTACTTTT
1144618 ATATATATTACTTTT
1 ATATATATTACTTTT
1144633 ATAT
1 ATAT
1144637 TTTTATATAT
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:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATATATTACTTTT
Found at i:1144705 original size:19 final size:19
Alignment explanation
Indices: 1144683--1144727 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1144673 CATATGTAAT
1144683 ATTAAAACTTAATAAAA-AA
1 ATTAAAACTTAA-AAAATAA
**
1144702 ATTAAATTTTAAAAAATAA
1 ATTAAAACTTAAAAAATAA
1144721 ATTAAAA
1 ATTAAAA
1144728 AATTAATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTAAAACTTAAAAAATAA
Found at i:1145867 original size:2 final size:2
Alignment explanation
Indices: 1145860--1145886 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1145850 GTGTAGCTAT
1145860 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1145887 AGATAACTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1147142 original size:5 final size:6
Alignment explanation
Indices: 1147128--1147152 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1147118 ACTTAGGGCA
1147128 TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT T
1147153 CTTTTTTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:1147884 original size:3 final size:3
Alignment explanation
Indices: 1147876--1147910 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1147866 GTGCCATGAT
1147876 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1147911 GAAACTACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1148681 original size:2 final size:2
Alignment explanation
Indices: 1148676--1148709 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1148666 ACACACTCAA
1148676 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
1148710 GCTACGCGTC
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:1159538 original size:3 final size:3
Alignment explanation
Indices: 1159530--1159564 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1159520 TTTCTGTTTT
1159530 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1159565 GTTACTACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1160312 original size:2 final size:2
Alignment explanation
Indices: 1160305--1160342 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1160295 TAGCTATGTA
1160305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1160343 GAAACATTCC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1160710 original size:2 final size:2
Alignment explanation
Indices: 1160703--1160733 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1160693 ACGGTATCTC
1160703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1160734 GTATTATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1164410 original size:15 final size:15
Alignment explanation
Indices: 1164356--1164413 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
1164346 TATTTAAATT
1164356 TATATAAATATAAAA
1 TATATAAATATAAAA
* * *
1164371 TATTTTAAAAAT-AAT
1 TA-TATAAATATAAAA
1164386 TATA-ATAATATAAAA
1 TATATA-AATATAAAA
1164401 TATATAAATATAA
1 TATATAAATATAA
1164414 TCAATTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 19 0.58
16 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TATATAAATATAAAA
Found at i:1164438 original size:17 final size:18
Alignment explanation
Indices: 1164406--1164439 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1164396 TAAAATATAT
*
1164406 AAATATAATCAATTTAAA
1 AAATATAATAAATTTAAA
1164424 AAATA-AATAAATTTAA
1 AAATATAATAAATTTAA
1164440 TCCGCTGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATATAATAAATTTAAA
Found at i:1164891 original size:3 final size:3
Alignment explanation
Indices: 1164883--1164914 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1164873 TGAGCTAGTG
1164883 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1164915 CAAAGCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1165146 original size:39 final size:39
Alignment explanation
Indices: 1165096--1165171 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
1165086 TAAAAAGTTT
1165096 CCCCAAGTTAAATTCTTTTTACAGGTGAATTTATATTTC
1 CCCCAAGTTAAATTCTTTTTACAGGTGAATTTATATTTC
1165135 CCCCAAGTTAAATTCTTTTTACAGGTGAATTTATATT
1 CCCCAAGTTAAATTCTTTTTACAGGTGAATTTATATT
1165172 AGATAATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (39 bp):
CCCCAAGTTAAATTCTTTTTACAGGTGAATTTATATTTC
Found at i:1166348 original size:16 final size:16
Alignment explanation
Indices: 1166324--1166369 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1166314 ATATCATAAC
1166324 ATTTAATTAAATATAT
1 ATTTAATTAAATATAT
* *
1166340 ATTTTATTAAATATTT
1 ATTTAATTAAATATAT
* *
1166356 ATTAAATTTAATAT
1 ATTTAATTAAATAT
1166370 TAAAATTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTAATTAAATATAT
Found at i:1166393 original size:21 final size:21
Alignment explanation
Indices: 1166344--1166390 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
1166334 ATATATATTT
1166344 TATTAAATATTTATTAAATTTAA
1 TATTAAA-A-TTATTAAATTTAA
*
1166367 TATTAAAATTATTTAA-TTAA
1 TATTAAAATTATTAAATTTAA
1166387 TATT
1 TATT
1166391 TAATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 7 0.30
22 1 0.04
23 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTAAAATTATTAAATTTAA
Found at i:1166599 original size:6 final size:6
Alignment explanation
Indices: 1166584--1166630 Score: 78
Period size: 6 Copynumber: 7.8 Consensus size: 6
1166574 GGATATAATC
1166584 AATA-A AATATA AATATA AATATA AATATA AATATA AATATTA AATAT
1 AATATA AATATA AATATA AATATA AATATA AATATA AATA-TA AATAT
1166631 TATATTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 4 0.10
6 30 0.75
7 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:1166661 original size:27 final size:28
Alignment explanation
Indices: 1166620--1166701 Score: 112
Period size: 29 Copynumber: 2.9 Consensus size: 28
1166610 ATAAATATAA
1166620 ATATTAAATATTATATTTTAAT-TATTTAT
1 ATATTAAA-A-TATATTTTAATATATTTAT
*
1166649 ATATTAAAATATATTTTAATAATTTTTAT
1 ATATTAAAATATATTTTAAT-ATATTTAT
*
1166678 ATATTAAAATATATTTTAAAATAT
1 ATATTAAAATATATTTTAATATAT
1166702 AAAAATTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
27 11 0.23
28 4 0.08
29 33 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATATTAAAATATATTTTAATATATTTAT
Found at i:1166667 original size:12 final size:12
Alignment explanation
Indices: 1166646--1166702 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 12
1166636 TTTAATTATT
1166646 TATATATTAAAA
1 TATATATTAAAA
*
1166658 TATATTTTAATAA
1 TATATATTAA-AA
1166671 TTTTTATATATTAAAA
1 ----TATATATTAAAA
*
1166687 TATATTTTAAAA
1 TATATATTAAAA
1166699 TATA
1 TATA
1166703 AAAATTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 24 0.65
13 2 0.05
16 2 0.05
17 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATATTAAAA
Found at i:1168563 original size:27 final size:27
Alignment explanation
Indices: 1168525--1168587 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
1168515 GAAAATTATC
*
1168525 TTTTTTTAATATTAAATTTAATAA-TAAA
1 TTTTTTT-ATATTAAA-TAAATAATTAAA
*
1168553 TTTTTTTATATTGAATAAATAATTAAA
1 TTTTTTTATATTAAATAAATAATTAAA
*
1168580 TATTTTTA
1 TTTTTTTA
1168588 ATTTATTAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 6 0.19
27 18 0.58
28 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTTTTTATATTAAATAAATAATTAAA
Found at i:1170633 original size:21 final size:21
Alignment explanation
Indices: 1170609--1170669 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
1170599 TCGACATGAA
1170609 AAAATAACATAATATAAATAT
1 AAAATAACATAATATAAATAT
* * **
1170630 AAAA-ATACGTAACATTTATAT
1 AAAATA-ACATAATATAAATAT
*
1170651 AAAACTAATATAATATAAA
1 AAAA-TAACATAATATAAA
1170670 ATTAAGAGTC
Statistics
Matches: 28, Mismatches: 9, Indels: 5
0.67 0.21 0.12
Matches are distributed among these distances:
20 1 0.04
21 19 0.68
22 7 0.25
23 1 0.04
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATAACATAATATAAATAT
Found at i:1170862 original size:22 final size:21
Alignment explanation
Indices: 1170831--1170884 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1170821 TGTCAAAAGT
* * *
1170831 TATACATATATGATACATAAAA
1 TATAAATATAT-ATAAAAAAAA
*
1170853 TATAATTATAATATAAAAAAAA
1 TATAAATAT-ATATAAAAAAAA
1170875 TATAAATATA
1 TATAAATATA
1170885 AATATTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (21 bp):
TATAAATATATATAAAAAAAA
Found at i:1171175 original size:3 final size:3
Alignment explanation
Indices: 1171161--1171217 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
1171151 ATTATTTTTT
* * *
1171161 ATA ATA ACA ATA ATA ATA ATT ATT ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1171209 ATA ATA ATA
1 ATA ATA ATA
1171218 GTGGTGCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1171618 original size:55 final size:54
Alignment explanation
Indices: 1171542--1171652 Score: 163
Period size: 55 Copynumber: 2.0 Consensus size: 54
1171532 TTTGTAATAA
*
1171542 ATATAAAAATAATATGATAAATATAAAAT-ATTATATTT-AATCATAATTAATATG
1 ATATAAAAATAATATAATAAATATAAAATAATT-TATTTAAAT-ATAATTAATATG
*
1171596 ATATAAAAAATAATATAATAAATATAAGATAATTTATTTAAATATAATTAATATG
1 ATAT-AAAAATAATATAATAAATATAAAATAATTTATTTAAATATAATTAATATG
1171651 AT
1 AT
1171653 TTTTTTAGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
54 4 0.08
55 42 0.81
56 6 0.12
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.39
Consensus pattern (54 bp):
ATATAAAAATAATATAATAAATATAAAATAATTTATTTAAATATAATTAATATG
Found at i:1171622 original size:14 final size:14
Alignment explanation
Indices: 1171544--1171628 Score: 66
Period size: 14 Copynumber: 6.1 Consensus size: 14
1171534 TGTAATAAAT
* *
1171544 ATAAAAATAATATG
1 ATAAATATAATATA
*
1171558 ATAAATATAAAATA
1 ATAAATATAATATA
* * *
1171572 TTATATTTAATCATA
1 ATAAATATAAT-ATA
* *
1171587 ATTAATATGATATA
1 ATAAATATAATATA
1171601 A-AAA-ATAATATA
1 ATAAATATAATATA
*
1171613 ATAAATATAAGATA
1 ATAAATATAATATA
1171627 AT
1 AT
1171629 TTATTTAAAT
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
12 8 0.15
13 5 0.09
14 31 0.58
15 9 0.17
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (14 bp):
ATAAATATAATATA
Found at i:1172039 original size:20 final size:19
Alignment explanation
Indices: 1171990--1172046 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1171980 CGGTATATAC
1171990 ATGAAAAAATAAT-TAAAA
1 ATGAAAAAATAATATAAAA
*
1172008 ATGATAGAAAATAATATAAAT
1 ATGA-A-AAAATAATATAAAA
1172029 ATGAAATAAAT-ATATAAA
1 ATGAAA-AAATAATATAAA
1172047 CGTGTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 4 0.12
19 9 0.26
20 13 0.38
21 8 0.24
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (19 bp):
ATGAAAAAATAATATAAAA
Found at i:1173128 original size:19 final size:19
Alignment explanation
Indices: 1173104--1173146 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1173094 TCGGCTTGGT
*
1173104 TTAAAATAGTATTTATTAA
1 TTAAAATAATATTTATTAA
* *
1173123 TTAAAATAATATTTTTTAT
1 TTAAAATAATATTTATTAA
1173142 TTAAA
1 TTAAA
1173147 TTTAATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAAAATAATATTTATTAA
Found at i:1173185 original size:15 final size:16
Alignment explanation
Indices: 1173159--1173190 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1173149 TAATTATAAA
1173159 TAAAAAATATTAATAT
1 TAAAAAATATTAATAT
1173175 TAAAAAA-ATTAATAT
1 TAAAAAATATTAATAT
1173190 T
1 T
1173191 TTATTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAAAATATTAATAT
Found at i:1175914 original size:26 final size:23
Alignment explanation
Indices: 1175857--1175922 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 23
1175847 TAATGAATAG
*
1175857 AATTATATTATT-AAAT-TTAAT
1 AATTAAATTATTAAAATATTAAT
*
1175878 AATTAATTTATTAAAATATTAAT
1 AATTAAATTATTAAAATATTAAT
*
1175901 AATATAAAAATTATAAAAATAT
1 AAT-T--AAATTATTAAAATAT
1175923 ATAAACTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 10 0.28
22 4 0.11
23 8 0.22
24 1 0.03
26 13 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTAAATTATTAAAATATTAAT
Found at i:1176341 original size:2 final size:2
Alignment explanation
Indices: 1176334--1176372 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1176324 TTGTTTGGAG
1176334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1176373 GGTATGTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1182783 original size:12 final size:12
Alignment explanation
Indices: 1182766--1182790 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1182756 AATATAAGAT
1182766 AAATTGAATTTA
1 AAATTGAATTTA
1182778 AAATTGAATTTA
1 AAATTGAATTTA
1182790 A
1 A
1182791 TTTATTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AAATTGAATTTA
Found at i:1183959 original size:12 final size:12
Alignment explanation
Indices: 1183944--1183974 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1183934 TATTATTTTT
1183944 TATTTTATATAA
1 TATTTTATATAA
1183956 TATTTTATATAA
1 TATTTTATATAA
1183968 TATTTTA
1 TATTTTA
1183975 ATTATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTTTATATAA
Found at i:1184002 original size:24 final size:24
Alignment explanation
Indices: 1183958--1184003 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1183948 TTATATAATA
**
1183958 TTTTATATAATATTTTAATTATTT
1 TTTTATATAATATGATAATTATTT
1183982 TTTTATCATAATATGAT-ATTAT
1 TTTTAT-ATAATATGATAATTAT
1184004 ATCCAATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTATATAATATGATAATTATTT
Found at i:1184499 original size:2 final size:2
Alignment explanation
Indices: 1184492--1184518 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1184482 GTATTATAAT
1184492 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 T
1184519 TGTATGCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1185712 original size:2 final size:2
Alignment explanation
Indices: 1185705--1185743 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1185695 CCAGCCTAAT
1185705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1185744 CTTTTTTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1186380 original size:19 final size:21
Alignment explanation
Indices: 1186350--1186390 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1186340 AGTAAAGAAA
1186350 TTAATAATATATATA-AATTT
1 TTAATAATATATATATAATTT
1186370 TTAAT-ATATATATATAATTT
1 TTAATAATATATATATAATTT
1186390 T
1 T
1186391 AGGGTAGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAATAATATATATATAATTT
Found at i:1186653 original size:3 final size:3
Alignment explanation
Indices: 1186645--1186676 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1186635 ACATAAAATA
1186645 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1186677 GTACTAGCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1186867 original size:2 final size:2
Alignment explanation
Indices: 1186860--1186884 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1186850 TTTTAAAAAC
1186860 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1186885 CGAGATAGTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1187887 original size:22 final size:22
Alignment explanation
Indices: 1187855--1187896 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1187845 AATATTATTT
1187855 TTTAAAAAT-AATATTTAATAAA
1 TTTAAAAATAAATA-TTAATAAA
*
1187877 TTTAAATATAAATATTAATA
1 TTTAAAAATAAATATTAATA
1187897 TTTACAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAAAAATAAATATTAATAAA
Found at i:1188120 original size:46 final size:46
Alignment explanation
Indices: 1188065--1188158 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
1188055 AAATATTTAT
1188065 ATATGAACTAAAATTTTAGGTAAAATTCAACCAAGCAATGAGATTA
1 ATATGAACTAAAATTTTAGGTAAAATTCAACCAAGCAATGAGATTA
1188111 ATATGAACTAAAATTTTAGGTAAAATTCAACCAAGCAATGAGATTA
1 ATATGAACTAAAATTTTAGGTAAAATTCAACCAAGCAATGAGATTA
1188157 AT
1 AT
1188159 TATTAATGAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.29
Consensus pattern (46 bp):
ATATGAACTAAAATTTTAGGTAAAATTCAACCAAGCAATGAGATTA
Found at i:1189585 original size:14 final size:13
Alignment explanation
Indices: 1189516--1189611 Score: 66
Period size: 14 Copynumber: 6.9 Consensus size: 13
1189506 AATAATATTG
*
1189516 AAAATAAATTTTTT
1 AAAAT-AATTTTTA
* *
1189530 TAAATATTTTTTA
1 AAAATAATTTTTA
*
1189543 TAAATATAATTTTAA
1 -AAA-ATAATTTTTA
*
1189558 AAAATAATTATTA
1 AAAATAATTTTTA
1189571 AAAATAATATTTTA
1 AAAATAAT-TTTTA
***
1189585 ATTTTAAATTTTTAA
1 AAAAT-AATTTTT-A
1189600 AAAATAATTTTT
1 AAAATAATTTTT
1189612 TATTTTTTAA
Statistics
Matches: 62, Mismatches: 15, Indels: 10
0.71 0.17 0.11
Matches are distributed among these distances:
13 22 0.35
14 26 0.42
15 14 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAAATAATTTTTA
Found at i:1189594 original size:28 final size:29
Alignment explanation
Indices: 1189563--1189618 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1189553 TTTAAAAAAT
1189563 AATTATT-AAAAATAATATTTTAATTTTA
1 AATTATTAAAAAATAATATTTTAATTTTA
* * *
1189591 AATTTTTAAAAAATAATTTTTTATTTTT
1 AATTATTAAAAAATAATATTTTAATTTT
1189619 TAAAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
AATTATTAAAAAATAATATTTTAATTTTA
Found at i:1189618 original size:22 final size:22
Alignment explanation
Indices: 1189583--1189644 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
1189573 AATAATATTT
*
1189583 TAATT-TTAAATTTTTAAAAAA
1 TAATTATTAATTTTTTAAAAAA
* *
1189604 TAATTTTTTATTTTTT-AAAAA
1 TAATTATTAATTTTTTAAAAAA
1189625 TAATTATTAATTATTTTAAA
1 TAATTATTAATT-TTTTAAA
1189645 TTTTATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 20 0.59
22 12 0.35
23 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTATTAATTTTTTAAAAAA
Found at i:1190955 original size:9 final size:9
Alignment explanation
Indices: 1190914--1190975 Score: 53
Period size: 8 Copynumber: 7.2 Consensus size: 9
1190904 GTTTATTTTG
*
1190914 TATTAATTA
1 TATTAAATA
1190923 TA-TAAATA
1 TATTAAATA
1190931 TAATATAAAT-
1 T-AT-TAAATA
1190941 TATTAAATA
1 TATTAAATA
1190950 TATTAAA-A
1 TATTAAATA
*
1190958 TTTTAAATA
1 TATTAAATA
1190967 -A-TAAATA
1 TATTAAATA
1190974 TA
1 TA
1190976 ATATATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
7 6 0.14
8 19 0.43
9 13 0.30
10 1 0.02
11 5 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TATTAAATA
Found at i:1190963 original size:17 final size:19
Alignment explanation
Indices: 1190918--1190976 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
1190908 ATTTTGTATT
1190918 AATTATATAAATATAATATA
1 AATTAT-TAAATATAATATA
*
1190938 AATTATTAAATATATTA-A
1 AATTATTAAATATAATATA
1190956 AATT-TTAAATAATAAATATA
1 AATTATTAAAT-AT-AATATA
1190976 A
1 A
1190977 TATATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 13 0.38
20 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTATTAAATATAATATA
Found at i:1191182 original size:26 final size:27
Alignment explanation
Indices: 1191161--1191213 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1191151 CATTTCATGT
1191161 ATAA-ACGTATTACATTATTTTCATAA
1 ATAATACGTATTACATTATTTTCATAA
**
1191187 ATAATATTTATTACATTATTTTCATAA
1 ATAATACGTATTACATTATTTTCATAA
1191214 TTGTTAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (27 bp):
ATAATACGTATTACATTATTTTCATAA
Found at i:1198997 original size:16 final size:18
Alignment explanation
Indices: 1198960--1198997 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1198950 TTACTAACGT
*
1198960 ATAAAATATTATATAAAT
1 ATAAAATATTATATAAAC
1198978 ATAAAATATT-T-TAAAC
1 ATAAAATATTATATAAAC
1198994 ATAA
1 ATAA
1198998 TTATAATACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAAATATTATATAAAC
Found at i:1200776 original size:18 final size:19
Alignment explanation
Indices: 1200755--1200793 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
1200745 TATAGTAATT
1200755 TTTAAAAATATT-T-ATATA
1 TTTAAAAA-ATTATAATATA
1200773 TTTAAAAAATTATAATATA
1 TTTAAAAAATTATAATATA
1200792 TT
1 TT
1200794 ATATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 9 0.47
19 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAAAAATTATAATATA
Found at i:1201406 original size:24 final size:25
Alignment explanation
Indices: 1201361--1201407 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1201351 TTTGATATAA
*
1201361 AAAAATTAATACTAAGTTAAAATTT
1 AAAAATTAATACTAAATTAAAATTT
1201386 AAAAA-TAATA-TAAATTCAAAAT
1 AAAAATTAATACTAAATT-AAAAT
1201408 AACTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAAATTAATACTAAATTAAAATTT
Found at i:1205388 original size:25 final size:24
Alignment explanation
Indices: 1205354--1205422 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
1205344 TTTTTATTTT
1205354 AAATTAAACTCAAGTTTTAAAAGTA
1 AAATTAAACTCAAGTTTTAAAAG-A
* *
1205379 AAATTTAACT-AAGTTTGAAAAGA
1 AAATTAAACTCAAGTTTTAAAAGA
* *
1205402 ACATTAAATCTCAAATTTTAA
1 AAATTAAA-CTCAAGTTTTAA
1205423 TTTAAGTTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 7 0.19
24 13 0.36
25 16 0.44
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (24 bp):
AAATTAAACTCAAGTTTTAAAAGA
Found at i:1208216 original size:18 final size:17
Alignment explanation
Indices: 1208182--1208236 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
1208172 TCATAATATT
1208182 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
1208199 ATTTTGATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
1208216 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
1208231 ATTTTA
1 ATTTTA
1208237 AAATATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.09
14 2 0.06
15 5 0.15
16 7 0.21
17 7 0.21
18 6 0.18
19 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:1208232 original size:32 final size:33
Alignment explanation
Indices: 1208184--1208246 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
1208174 ATAATATTAT
* *
1208184 TTTATATTTATATAAATTTTGATATATTAATAA
1 TTTATATTTATATAAATTTTAAAATATTAATAA
1208217 TTTATA-TTATATAAATTTTAAAATATTAAT
1 TTTATATTTATATAAATTTTAAAATATTAAT
1208247 GTATTCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (33 bp):
TTTATATTTATATAAATTTTAAAATATTAATAA
Found at i:1211129 original size:12 final size:12
Alignment explanation
Indices: 1211112--1211141 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1211102 ATAATATTAA
1211112 ATATTTAAATTT
1 ATATTTAAATTT
1211124 ATATTTAAATTT
1 ATATTTAAATTT
1211136 AT-TTTA
1 ATATTTA
1211142 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATTTAAATTT
Found at i:1211154 original size:15 final size:16
Alignment explanation
Indices: 1211117--1211166 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
1211107 ATTAAATATT
1211117 TAAATTTATATTTAAA
1 TAAATTTATATTTAAA
**
1211133 TTTATTT-TATTTAAA
1 TAAATTTATATTTAAA
1211148 TAAATTTAAATATTTAAA
1 TAAATTT--ATATTTAAA
1211166 T
1 T
1211167 CTAATATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 13 0.48
16 5 0.19
18 9 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAAATTTATATTTAAA
Found at i:1211155 original size:31 final size:34
Alignment explanation
Indices: 1211117--1211180 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
1211107 ATTAAATATT
*
1211117 TAAATTT-ATATTTAAAT-TTAT-TTTATTTAAA
1 TAAATTTAATATTTAAATCTAATATTTATTTAAA
1211148 TAAATTTAAATATTTAAATCTAATATTTATTTA
1 TAAATTT-AATATTTAAATCTAATATTTATTTA
1211181 TACATTTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 7 0.25
33 10 0.36
34 3 0.11
35 8 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (34 bp):
TAAATTTAATATTTAAATCTAATATTTATTTAAA
Found at i:1211188 original size:33 final size:32
Alignment explanation
Indices: 1211117--1211188 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 32
1211107 ATTAAATATT
*
1211117 TAAATTT--ATATTTAAATTTATTTTATTTAAA
1 TAAATTTAAATATTTAAATTAATTTTATTT-AA
1211148 TAAATTTAAATATTTAAATCTAATATTTATTT-A
1 TAAATTTAAATATTTAAAT-TAAT-TTTATTTAA
*
1211181 TACATTTA
1 TAAATTTA
1211189 CTTCTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 7 0.20
33 18 0.51
34 3 0.09
35 7 0.20
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (32 bp):
TAAATTTAAATATTTAAATTAATTTTATTTAA
Found at i:1216558 original size:19 final size:19
Alignment explanation
Indices: 1216514--1216559 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1216504 TTTAAAATTT
* *
1216514 ATTAA-TTTAAATATCAAA
1 ATTAATTTTAAAAATAAAA
1216532 A-TATATTTTAAAAATAAAA
1 ATTA-ATTTTAAAAATAAAA
1216551 ATTAATTTT
1 ATTAATTTT
1216560 TTACTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 17 0.74
20 2 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTAATTTTAAAAATAAAA
Found at i:1216780 original size:19 final size:19
Alignment explanation
Indices: 1216756--1216792 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1216746 TGTATATATA
*
1216756 TATATATTATTATTTTTAC
1 TATATATTATTACTTTTAC
1216775 TATATATTATTACTTTTA
1 TATATATTATTACTTTTA
1216793 ATTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATATTATTACTTTTAC
Found at i:1223058 original size:78 final size:78
Alignment explanation
Indices: 1222775--1223172 Score: 438
Period size: 79 Copynumber: 5.1 Consensus size: 78
1222765 ATTTATGTTT
* * * * *
1222775 TTATTTTCGAGGAGATACTCCAACTCCAGTTTTATTTTCAAAGCTATCGATTTTTCACAATTGGG
1 TTATTTTCGAGG-GATACTTCAACTCCGGTTTTATTTTCAAAAC-ACCGATTTTTCACAATCGGG
1222840 GATACTCCAACCTCG
64 GATACTCCAACCTCG
* * * *
1222855 TTATTTTCTAGGGGATAC-TCTAAC-CTCGGTTTTATTTCCAAAACACTGA-TTTTCTATAATCG
1 TTATTTTCGA-GGGATACTTC-AACTC-CGGTTTTATTTTCAAAACACCGATTTTTC-ACAATCG
1222917 GGGATACTCCAACC-CTG
62 GGGATACTCCAACCTC-G
* **
1222934 TTATTTTCGAGAGGATACTTCAACTCCGGTTTTA-TTTCTAAAACACCGATTTTTCAAAATCGAT
1 TTATTTTCGAG-GGATACTTCAACTCCGGTTTTATTTTC-AAAACACCGATTTTTCACAATCGGG
*
1222998 TATACTCCAATCC-CG
64 GATACTCCAA-CCTCG
* *
1223013 TTATTTTCAAGGGATACTTCGACTCCGGTTTTATTTTCAAAACACCGA-TTTTCACAATCGGGGA
1 TTATTTTCGAGGGATACTTCAACTCCGGTTTTATTTTCAAAACACCGATTTTTCACAATCGGGGA
1223077 TACTCCAACCTCG
66 TACTCCAACCTCG
* * *
1223090 TTATTTTCGAGGAATAC-TCTAA-TCTCGGTTTTATTTCCAAAACACTGATTTTTCACAATCGGG
1 TTATTTTCGAGGGATACTTC-AACTC-CGGTTTTATTTTCAAAACACCGATTTTTCACAATCGGG
* *
1223153 GATACT-CAACCCCA
64 GATACTCCAACCTCG
1223167 TTATTT
1 TTATTT
1223173 CTGAGGGGAT
Statistics
Matches: 273, Mismatches: 29, Indels: 35
0.81 0.09 0.10
Matches are distributed among these distances:
76 6 0.02
77 71 0.26
78 61 0.22
79 90 0.33
80 43 0.16
81 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (78 bp):
TTATTTTCGAGGGATACTTCAACTCCGGTTTTATTTTCAAAACACCGATTTTTCACAATCGGGGA
TACTCCAACCTCG
Found at i:1223196 original size:105 final size:107
Alignment explanation
Indices: 1223072--1223298 Score: 316
Period size: 106 Copynumber: 2.1 Consensus size: 107
1223062 TTTCACAATC
* * * *
1223072 GGGGATACTCCAACCTCGTTATTTTCGAGGA-ATACTCTAATCTCGGTTTTATTTCCAAAACACT
1 GGGGATACTCCAACCTCGTTATTTTCGAAGAGATACTCCAACCCCGGTTTTATTTCCAAAACACT
*
1223136 GATTTTTCACAATCGGGGATACT-CAACCCCATTA-TTTCTGA
66 GATTTTTCACAATCAGGGATACTCCAACCCCATTATTTTC-GA
* * *
1223177 GGGGATATTCCAACCTCGTTATTTTTGAAGAGATACTCCAACCCCGGTTTTATTTCCAAAATACT
1 GGGGATACTCCAACCTCGTTATTTTCGAAGAGATACTCCAACCCCGGTTTTATTTCCAAAACACT
* * *
1223242 GATTTTTTACAATCAGGGATACTCCAACCTCGTTATTTTCGA
66 GATTTTTCACAATCAGGGATACTCCAACCCCATTATTTTCGA
*
1223284 GGGGATACTCTAACC
1 GGGGATACTCCAACC
1223299 CCGGGTTTTA
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
105 28 0.26
106 50 0.47
107 24 0.23
108 4 0.04
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (107 bp):
GGGGATACTCCAACCTCGTTATTTTCGAAGAGATACTCCAACCCCGGTTTTATTTCCAAAACACT
GATTTTTCACAATCAGGGATACTCCAACCCCATTATTTTCGA
Found at i:1223198 original size:28 final size:28
Alignment explanation
Indices: 1223150--1223221 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
1223140 TTTCACAATC
1223150 GGGGATACT-CAACCCCATTATTTCTGA
1 GGGGATACTCCAACCCCATTATTTCTGA
* * * *
1223177 GGGGATATTCCAACCTCGTTATTTTTGA
1 GGGGATACTCCAACCCCATTATTTCTGA
* *
1223205 AGAGATACTCCAACCCC
1 GGGGATACTCCAACCCC
1223222 GGTTTTATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 8 0.22
28 28 0.78
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTCTGA
Found at i:1223339 original size:79 final size:79
Alignment explanation
Indices: 1223178--1223351 Score: 206
Period size: 79 Copynumber: 2.2 Consensus size: 79
1223168 TATTTCTGAG
* * * *
1223178 GGGATATTCCAACCTCGTTATTTTTGAAGAGATACTCCAACCCCGGTTTTATTTCCAAAATACTG
1 GGGATACTCCAACCTCGTTATTTTCGAAGAGATACTCCAACCCCGGTTTTATCTCCAAAATACTA
**
1223243 ATTTTTTACAATCA
66 AACTTTTACAATCA
* * * *
1223257 GGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCTAACCCCGGGTTTTATCTCCAAAATATT
1 GGGATACTCCAACCTCGTTATTTTCGAAGAGATACTCCAACCCC-GGTTTTATCTCCAAAATACT
* *
1223322 AAACTTTT-CATTGA
65 AAACTTTTACAATCA
1223336 GGGATATACTCCAACC
1 GGG--ATACTCCAACC
1223352 GCGTATCTCG
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
79 46 0.57
80 23 0.29
81 11 0.14
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (79 bp):
GGGATACTCCAACCTCGTTATTTTCGAAGAGATACTCCAACCCCGGTTTTATCTCCAAAATACTA
AACTTTTACAATCA
Found at i:1230874 original size:2 final size:2
Alignment explanation
Indices: 1230867--1230898 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1230857 TAATTTCTGC
1230867 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
1230899 GTATTCCCTG
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:1232552 original size:18 final size:17
Alignment explanation
Indices: 1232529--1232566 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1232519 TAATTAAAAA
*
1232529 ATTAAATATTAAATAAGT
1 ATTAAATA-TAAATAAAT
1232547 ATTAAATATAAATAAAT
1 ATTAAATATAAATAAAT
1232564 ATT
1 ATT
1232567 TTATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTAAATATAAATAAAT
Found at i:1237996 original size:19 final size:20
Alignment explanation
Indices: 1237960--1238007 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1237950 AAATTAATTA
**
1237960 ATTTT-ATAAATTTTTATT-
1 ATTTTAATAAATTGATATTG
1237978 ATTTTAATAAATTGATATTG
1 ATTTTAATAAATTGATATTG
*
1237998 AATTTAATAA
1 ATTTTAATAA
1238008 TATATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 5 0.20
19 11 0.44
20 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
ATTTTAATAAATTGATATTG
Found at i:1240535 original size:16 final size:14
Alignment explanation
Indices: 1240501--1240528 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1240491 AATTAATATT
1240501 TAAAATATATTTAA
1 TAAAATATATTTAA
1240515 TAAAATATATTTAA
1 TAAAATATATTTAA
1240529 AATAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATATATTTAA
Found at i:1241080 original size:20 final size:20
Alignment explanation
Indices: 1241055--1241105 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1241045 TATAAGTATT
1241055 AATATTAAAATTATATTTTA
1 AATATTAAAATTATATTTTA
* *
1241075 AATATTTTAAA-TATTTTTTA
1 AATA-TTAAAATTATATTTTA
*
1241095 AATAATAAAAT
1 AATATTAAAAT
1241106 AGATTCTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.16
20 16 0.64
21 5 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTAAAATTATATTTTA
Found at i:1241080 original size:26 final size:24
Alignment explanation
Indices: 1241030--1241080 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
1241020 AAATATTTTG
* *
1241030 TAATTTAAATTTAATTATAAGTAT
1 TAATTTAAAATTAATTATAAATAT
*
1241054 TAATATTAAAATTATATTTTAAATAT
1 TAAT-TTAAAATTA-ATTATAAATAT
1241080 T
1 T
1241081 TTAAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 4 0.18
25 8 0.36
26 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TAATTTAAAATTAATTATAAATAT
Found at i:1241098 original size:11 final size:9
Alignment explanation
Indices: 1241067--1241091 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1241057 TATTAAAATT
1241067 ATATTTTAA
1 ATATTTTAA
1241076 ATATTTTAA
1 ATATTTTAA
1241085 ATATTTT
1 ATATTTT
1241092 TTAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATATTTTAA
Found at i:1241967 original size:2 final size:2
Alignment explanation
Indices: 1241960--1241987 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1241950 TGTAGAATTC
1241960 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
1241988 CGTTTTGCAT
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:1242779 original size:1 final size:1
Alignment explanation
Indices: 1242768--1242800 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
1242758 AGCCAGCAAT
*
1242768 CCCCTCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1242801 GAGGCTAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:1243618 original size:28 final size:27
Alignment explanation
Indices: 1243575--1243645 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
1243565 ATTTTGTCTC
1243575 TAAAAAATTAATAAATATGATA-ATTTTAGA
1 TAAAAAA-TAA-AAATATGATACA-TTTA-A
*
1243605 TAAAAAATAAAAATATTATACATTTAA
1 TAAAAAATAAAAATATGATACATTTAA
*
1243632 T-AAATATAAAAATA
1 TAAAAAATAAAAATA
1243646 ATATAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 12 0.32
27 2 0.05
28 13 0.34
29 4 0.11
30 7 0.18
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (27 bp):
TAAAAAATAAAAATATGATACATTTAA
Found at i:1243657 original size:24 final size:26
Alignment explanation
Indices: 1243611--1243658 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1243601 TAGATAAAAA
* *
1243611 ATAAAAATATTATACATTTAATAAAT
1 ATAAAAATAATATACATTAAATAAAT
1243637 ATAAAAATAATATA-A-TAAATAA
1 ATAAAAATAATATACATTAAATAA
1243659 TAAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 1 0.05
26 13 0.65
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
ATAAAAATAATATACATTAAATAAAT
Found at i:1244314 original size:17 final size:19
Alignment explanation
Indices: 1244288--1244322 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1244278 AAATTTCAAT
1244288 AAAAATTATTTT-TACTTC
1 AAAAATTATTTTCTACTTC
1244306 AAAAA-TATTTTCTACTT
1 AAAAATTATTTTCTACTT
1244323 TTTTTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAAATTATTTTCTACTTC
Found at i:1244593 original size:22 final size:21
Alignment explanation
Indices: 1244567--1244607 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1244557 AGATTTAAAA
1244567 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1244587 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1244608 TAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1245883 original size:236 final size:236
Alignment explanation
Indices: 1245435--1245886 Score: 537
Period size: 236 Copynumber: 1.9 Consensus size: 236
1245425 AGTATCCTTA
* * * *
1245435 ATATTAATATAAATAATTTTATTGTAGTTATAAATTTTAAATATGTAAGAATTAGTTATTTTTAT
1 ATATTAATATAAATAATTTTATTGTAATTATAAATATTAAACATGTAAGAATTAGTTATTTTCAT
* * *
1245500 TAAAATTTTAAATTATTTTTTATTAAATTGATTACATAATTATACAAGTAAAAATATATAAGTAA
66 TAAAATTTTAAATTATTATTTATTAAATTGATTAAATAATTATACAAATAAAAATATATAAGTAA
* * * *
1245565 TAATTAAAAAGTAAATAAAAAATAAAATAATTTCACTTTTATTTTCTTTTTGTTTTTTTAAACCA
131 TAATTAAAAAGCAAATAAAAAACAAAATAATTTCACTTTTATTTTC-TTATGTTTTTTTAAACAA
* *
1245630 AGCAAATAAAGAAAATGAAGGCCTAATTGGATGACATGTTTC
195 AGAAAATAAAAAAAATGAAGGCCTAATTGGATGACATGTTTC
* *
1245672 ATATTAATA-AAATGATTTTATAT-TAATTATATAA-ATTAAACATGTAAGAATTATTTATTTTC
1 ATATTAATATAAATAATTTTAT-TGTAATTATA-AATATTAAACATGTAAGAATTAGTTATTTTC
** * *
1245734 ATTAATTTTTTTGAATTATTATTTATTAAATTGATTAAATAATTATATAAATAAAATTATATATA
64 ATTAA-AATTTTAAATTATTATTTATTAAATTGATTAAATAATTATACAAATAAAA--ATATATA
* * *
1245799 CA-TAATGATTAAAAA-CAAAT-AAAAACAAAATATTTTC-TTTTTATTTTC-TAT-TTTTTTTA
126 -AGTAATAATTAAAAAGCAAATAAAAAACAAAATAATTTCACTTTTATTTTCTTATGTTTTTTTA
1245858 AA-AAAGAAATATAGCAAAAAAAATGAAGG
190 AACAAAGAAA-AT---AAAAAAAATGAAGG
1245887 TCAAAGACAA
Statistics
Matches: 183, Mismatches: 22, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
232 5 0.03
233 12 0.07
234 2 0.01
236 70 0.38
237 70 0.38
238 4 0.02
239 19 0.10
240 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (236 bp):
ATATTAATATAAATAATTTTATTGTAATTATAAATATTAAACATGTAAGAATTAGTTATTTTCAT
TAAAATTTTAAATTATTATTTATTAAATTGATTAAATAATTATACAAATAAAAATATATAAGTAA
TAATTAAAAAGCAAATAAAAAACAAAATAATTTCACTTTTATTTTCTTATGTTTTTTTAAACAAA
GAAAATAAAAAAAATGAAGGCCTAATTGGATGACATGTTTC
Found at i:1246468 original size:16 final size:17
Alignment explanation
Indices: 1246437--1246469 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1246427 GAGACCAAAC
*
1246437 CCAGGATAAGATAAAAT
1 CCAGGATAAAATAAAAT
1246454 CCAGGA-AAAATAAAAT
1 CCAGGATAAAATAAAAT
1246470 AAAAAAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (17 bp):
CCAGGATAAAATAAAAT
Found at i:1247487 original size:27 final size:27
Alignment explanation
Indices: 1247456--1247511 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1247446 CCGGTGTTAA
* *
1247456 AAGTACCTTTGTCAAAGTGTCTATGCC
1 AAGTACCTGTGTCAAAGTGCCTATGCC
*
1247483 AAGTACCTGTGTCAAAGTGCCTGTGCC
1 AAGTACCTGTGTCAAAGTGCCTATGCC
1247510 AA
1 AA
1247512 AGCACTTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (27 bp):
AAGTACCTGTGTCAAAGTGCCTATGCC
Found at i:1247505 original size:14 final size:14
Alignment explanation
Indices: 1247440--1247513 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
1247430 TACTTGTGCT
* *
1247440 AAAGTACCGGTGTTA
1 AAAGTACCTGTG-TC
*
1247455 AAAGTACCTTTGTC
1 AAAGTACCTGTGTC
** *
1247469 AAAGTGTCTATG-C
1 AAAGTACCTGTGTC
*
1247482 CAAGTACCTGTGTC
1 AAAGTACCTGTGTC
* *
1247496 AAAGTGCCTGTGCC
1 AAAGTACCTGTGTC
1247510 AAAG
1 AAAG
1247514 CACTTGTGCT
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
13 9 0.20
14 26 0.58
15 10 0.22
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (14 bp):
AAAGTACCTGTGTC
Found at i:1247728 original size:5 final size:6
Alignment explanation
Indices: 1247713--1247745 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1247703 CATATTCAAT
1247713 AAATAA AAAT-A AAATAA AAATAAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAAT-AA AAATAA AAA
1247746 AATGTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:1247729 original size:11 final size:11
Alignment explanation
Indices: 1247713--1247737 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1247703 CATATTCAAT
1247713 AAATAAAAATA
1 AAATAAAAATA
1247724 AAATAAAAATA
1 AAATAAAAATA
1247735 AAA
1 AAA
1247738 AATAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:1248935 original size:15 final size:15
Alignment explanation
Indices: 1248917--1248968 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
1248907 TTTTTGGTAT
1248917 AGATACCTTTGACAC
1 AGATACCTTTGACAC
*
1248932 AGATACTTTTGACAC
1 AGATACCTTTGACAC
*
1248947 AGATA-TTTTGACAC
1 AGATACCTTTGACAC
*
1248961 AGGTACCT
1 AGATACCT
1248969 GACATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (15 bp):
AGATACCTTTGACAC
Found at i:1248955 original size:14 final size:15
Alignment explanation
Indices: 1248917--1248962 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
1248907 TTTTTGGTAT
*
1248917 AGATACCTTTGACAC
1 AGATACTTTTGACAC
1248932 AGATACTTTTGACAC
1 AGATACTTTTGACAC
1248947 AGATA-TTTTGACAC
1 AGATACTTTTGACAC
1248961 AG
1 AG
1248963 GTACCTGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (15 bp):
AGATACTTTTGACAC
Found at i:1249237 original size:42 final size:42
Alignment explanation
Indices: 1249174--1249378 Score: 293
Period size: 42 Copynumber: 4.9 Consensus size: 42
1249164 ACATGTTGTG
*
1249174 ATATAATAAGTATCAATCCCTTGTTACCAAAATATTTATATT
1 ATATAATAAGTATCAATCCCTTGTTACCAGAATATTTATATT
* * * * *
1249216 ATATAATAAATATCAACCCCTTGTTATCAGAATATTTTTGTT
1 ATATAATAAGTATCAATCCCTTGTTACCAGAATATTTATATT
1249258 ATATAATAAGTATCAATCCCTTGTTACCAGAATATTTATATT
1 ATATAATAAGTATCAATCCCTTGTTACCAGAATATTTATATT
* ** * *
1249300 ATATAATAAGTATCAACCCCTTGTTATTAGAATATTTTTGTT
1 ATATAATAAGTATCAATCCCTTGTTACCAGAATATTTATATT
* *
1249342 ATATAATAAGTATCAATCCTTTATTACCAGAATATTT
1 ATATAATAAGTATCAATCCCTTGTTACCAGAATATTT
1249379 CTAATAGTAT
Statistics
Matches: 142, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 142 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.42
Consensus pattern (42 bp):
ATATAATAAGTATCAATCCCTTGTTACCAGAATATTTATATT
Found at i:1249315 original size:84 final size:84
Alignment explanation
Indices: 1249169--1249378 Score: 366
Period size: 84 Copynumber: 2.5 Consensus size: 84
1249159 TTTCAACATG
* *
1249169 TTGTGATATAATAAGTATCAATCCCTTGTTACCAAAATATTTATATTATATAATAAATATCAACC
1 TTGTTATATAATAAGTATCAATCCCTTGTTACCAGAATATTTATATTATATAATAAATATCAACC
1249234 CCTTGTTATCAGAATATTT
66 CCTTGTTATCAGAATATTT
*
1249253 TTGTTATATAATAAGTATCAATCCCTTGTTACCAGAATATTTATATTATATAATAAGTATCAACC
1 TTGTTATATAATAAGTATCAATCCCTTGTTACCAGAATATTTATATTATATAATAAATATCAACC
*
1249318 CCTTGTTATTAGAATATTT
66 CCTTGTTATCAGAATATTT
* *
1249337 TTGTTATATAATAAGTATCAATCCTTTATTACCAGAATATTT
1 TTGTTATATAATAAGTATCAATCCCTTGTTACCAGAATATTT
1249379 CTAATAGTAT
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 120 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (84 bp):
TTGTTATATAATAAGTATCAATCCCTTGTTACCAGAATATTTATATTATATAATAAATATCAACC
CCTTGTTATCAGAATATTT
Found at i:1252242 original size:2 final size:2
Alignment explanation
Indices: 1252235--1252272 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1252225 CTTCCTGGAA
1252235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1252273 CCGTTTTGCA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1252581 original size:3 final size:3
Alignment explanation
Indices: 1252573--1252602 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1252563 CTTTTTTAAA
1252573 ATT ATT ATT ATT ATT ATT ATAT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT AT
1252603 ACTTGATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1256608 original size:6 final size:6
Alignment explanation
Indices: 1256599--1256624 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1256589 GCACATACGT
1256599 ATACAC ATACAC ATACAC ATACAC AT
1 ATACAC ATACAC ATACAC ATACAC AT
1256625 CTCAAGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (6 bp):
ATACAC
Found at i:1259565 original size:10 final size:10
Alignment explanation
Indices: 1259550--1259596 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
1259540 CTCCTTCCCC
1259550 TTTTCTTTTT
1 TTTTCTTTTT
*
1259560 TTTTCTTTTG
1 TTTTCTTTTT
1259570 TTTTC-TTTT
1 TTTTCTTTTT
* *
1259579 TCTTCCTTTT
1 TTTTCTTTTT
1259589 TTTTCTTT
1 TTTTCTTT
1259597 AAAAAACCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 7 0.23
10 24 0.77
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:1259575 original size:20 final size:19
Alignment explanation
Indices: 1259550--1259596 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1259540 CTCCTTCCCC
* *
1259550 TTTTCTTTTTTTTTCTTTT
1 TTTTCTTTTTCTTCCTTTT
1259569 GTTTTCTTTTTCTTCCTTTT
1 -TTTTCTTTTTCTTCCTTTT
1259589 TTTTCTTT
1 TTTTCTTT
1259597 AAAAAACCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTCTTTTTCTTCCTTTT
Found at i:1260319 original size:14 final size:15
Alignment explanation
Indices: 1260292--1260338 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1260282 TTTTATAATA
1260292 ATAATTATATATTTTT
1 ATAATTA-ATATTTTT
**
1260308 ATAATTAA-ATTTAA
1 ATAATTAATATTTTT
*
1260322 ATAATAAATATTTTT
1 ATAATTAATATTTTT
1260337 AT
1 AT
1260339 TAAATAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 11 0.44
15 7 0.28
16 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATAATTAATATTTTT
Found at i:1260325 original size:30 final size:30
Alignment explanation
Indices: 1260291--1260347 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1260281 TTTTTATAAT
* *
1260291 AATAATTATATATTTTTA-TAATTAAATTTA
1 AATAA-TAAATATTTTTATTAAATAAATTTA
1260321 AATAATAAATATTTTTATTAAATAAAT
1 AATAATAAATATTTTTATTAAATAAAT
1260348 AATTATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
AATAATAAATATTTTTATTAAATAAATTTA
Found at i:1260337 original size:17 final size:20
Alignment explanation
Indices: 1260316--1260359 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 20
1260306 TTATAATTAA
1260316 ATTTAAAT-AATAAAT-ATT
1 ATTTAAATAAATAAATAATT
*
1260334 -TTT-ATTAAATAAATAATT
1 ATTTAAATAAATAAATAATT
1260352 ATTTAAAT
1 ATTTAAAT
1260360 TAGATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 6
0.71 0.07 0.21
Matches are distributed among these distances:
16 2 0.10
17 10 0.50
18 3 0.15
19 3 0.15
20 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAAATAAATAAATAATT
Found at i:1260361 original size:21 final size:20
Alignment explanation
Indices: 1260312--1260361 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1260302 ATTTTTATAA
1260312 TTAAATTTAAATAATAAATAT
1 TTAAA-TTAAATAATAAATAT
** *
1260333 TTTTATTAAATAAATAATTAT
1 TTAAATTAAAT-AATAAATAT
1260354 TTAAATTA
1 TTAAATTA
1260362 GATTAAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAATTAAATAATAAATAT
Found at i:1261457 original size:15 final size:15
Alignment explanation
Indices: 1261427--1261481 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1261417 TAGTTAAATC
1261427 AATAAATATTTAAAAA
1 AATAAA-ATTTAAAAA
*
1261443 AATAAAATTTTAAAA
1 AATAAAATTTAAAAA
* *
1261458 AGTAAAATATAATAAA
1 AATAAAATTTAA-AAA
1261474 TAATAAAA
1 -AATAAAA
1261482 ATATTATTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 17 0.53
16 9 0.28
17 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AATAAAATTTAAAAA
Found at i:1262972 original size:10 final size:10
Alignment explanation
Indices: 1262957--1263021 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
1262947 TATATTTAGT
1262957 TTTAAATATA
1 TTTAAATATA
*
1262967 TTTAAAAAT-
1 TTTAAATATA
1262976 TTTAAAATATA
1 TTT-AAATATA
*
1262987 TTTAAA-AAA
1 TTTAAATATA
1262996 TTTTAAA-ATA
1 -TTTAAATATA
**
1263006 TTTTTATATA
1 TTTAAATATA
1263016 TTTAAA
1 TTTAAA
1263022 AATTATATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
9 9 0.21
10 31 0.72
11 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TTTAAATATA
Found at i:1262983 original size:20 final size:20
Alignment explanation
Indices: 1262956--1263031 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
1262946 ATATATTTAG
1262956 TTTT-AAATATATTTAAAAA
1 TTTTAAAATATATTTAAAAA
1262975 TTTTAAAATATATTTAAAAAA
1 TTTTAAAATATATTT-AAAAA
* * *
1262996 TTTTAAAATATTTTTATATA
1 TTTTAAAATATATTTAAAAA
*
1263016 TTTAAAAATTATATTT
1 TTTTAAAA-TATATTT
1263032 TTATTTATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 4 0.08
20 20 0.41
21 25 0.51
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAAAATATATTTAAAAA
Found at i:1263177 original size:19 final size:21
Alignment explanation
Indices: 1263153--1263193 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1263143 GTAGTTTTTA
1263153 AAGTGGT-AGTT-TTTGAAAT
1 AAGTGGTCAGTTGTTTGAAAT
*
1263172 AAGTGGTCAGTTGTTTTAAAT
1 AAGTGGTCAGTTGTTTGAAAT
1263193 A
1 A
1263194 CATGTTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.41
Consensus pattern (21 bp):
AAGTGGTCAGTTGTTTGAAAT
Found at i:1263318 original size:33 final size:34
Alignment explanation
Indices: 1263281--1263345 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
1263271 AATTAAAAAA
* * *
1263281 TATAAATATTTTATAATA-TTATTATTATTTAAT
1 TATAAAAATATTAAAATATTTATTATTATTTAAT
*
1263314 TATAAAAATATTAAAATATTTATTATTTTTTA
1 TATAAAAATATTAAAATATTTATTATTATTTA
1263346 TTAAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 15 0.56
34 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
TATAAAAATATTAAAATATTTATTATTATTTAAT
Found at i:1263355 original size:42 final size:41
Alignment explanation
Indices: 1263252--1263355 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 41
1263242 TTTTTAAAAA
*
1263252 AATATATATTATATAAAATAATTAAAAAATATAAATATTTTAT
1 AATAT-TATTAT-TAAATTAATTAAAAAATATAAATATTTTAT
*
1263295 AATATTATTATT-ATTTAATTATAAAAATATTAAA-ATATTTAT
1 AATATTATTATTAAATTAATTA-AAAAATA-TAAATAT-TTTAT
* *
1263337 TAT-TTTTTATTAAATTAAT
1 AATATTATTATTAAATTAAT
1263356 ATCATTTAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
40 7 0.13
41 17 0.33
42 23 0.44
43 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (41 bp):
AATATTATTATTAAATTAATTAAAAAATATAAATATTTTAT
Found at i:1265787 original size:26 final size:26
Alignment explanation
Indices: 1265737--1265787 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1265727 TGTATGTATT
*
1265737 TATATCTTAAAAAAATAATATAAAAA
1 TATATCTTAAAAAAATAATAAAAAAA
*
1265763 TATATCATTAAAAAAA-ATTAAAAAA
1 TATATC-TTAAAAAAATAATAAAAAA
1265788 TAAATATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (26 bp):
TATATCTTAAAAAAATAATAAAAAAA
Found at i:1266875 original size:23 final size:23
Alignment explanation
Indices: 1266849--1266916 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
1266839 GAAATTATTT
*
1266849 ATATTTATTTTTATTTTTTTAAA
1 ATATTTATTTTTATTTTTATAAA
* *
1266872 ATA-TTATGTTTA--TTAATAAA
1 ATATTTATTTTTATTTTTATAAA
*
1266892 ATAATATTATTTTTATTTTTCTAAA
1 AT-AT-TTATTTTTATTTTTATAAA
1266917 TAATAATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
20 8 0.24
21 1 0.03
22 8 0.24
23 11 0.32
25 6 0.18
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (23 bp):
ATATTTATTTTTATTTTTATAAA
Found at i:1267884 original size:93 final size:95
Alignment explanation
Indices: 1267740--1267923 Score: 257
Period size: 93 Copynumber: 2.0 Consensus size: 95
1267730 CAGATTTTTA
* ** * *
1267740 TTAATTAATTTATTTGATGTAATGTTTGATAATAATTATAATTCTCGTATAATTATAATTT-TAA
1 TTAATTAATTTATTTGATGTAATATTTGATAATAATTATAACACTCATATAATTATAATTTAAAA
*
1267804 AAA-AAATAAATTAATCAATTAATGATCGG
66 AAATAAATAAATTAATCAATCAATGATCGG
* *
1267833 TTAATTAATTTATTTGATGTAATATTTGATTATAATCT-TAACACTCATATAATTGTAATTTAAA
1 TTAATTAATTTATTTGATGTAATATTTGATAATAAT-TATAACACTCATATAATTATAATTTAAA
*
1267897 AAAATAAATAAATTGATCAATCAATGA
65 AAAATAAATAAATTAATCAATCAATGA
1267924 AAAATTTACT
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
93 53 0.67
94 6 0.08
95 20 0.25
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (95 bp):
TTAATTAATTTATTTGATGTAATATTTGATAATAATTATAACACTCATATAATTATAATTTAAAA
AAATAAATAAATTAATCAATCAATGATCGG
Found at i:1268390 original size:4 final size:4
Alignment explanation
Indices: 1268381--1268405 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1268371 ATGTATCATC
1268381 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
1268406 AGTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1271492 original size:4 final size:4
Alignment explanation
Indices: 1271483--1271544 Score: 97
Period size: 4 Copynumber: 15.5 Consensus size: 4
1271473 CATGAATTGC
* *
1271483 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TGTG TGTG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
1271531 TGTG TATG TATG TA
1 TATG TATG TATG TA
1271545 GTTCAATATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1277020 original size:2 final size:2
Alignment explanation
Indices: 1277013--1277039 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1277003 AAGATTATAA
1277013 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1277040 AGAACAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1277720 original size:2 final size:2
Alignment explanation
Indices: 1277648--1277700 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
1277638 ATATTTTTAG
* *
1277648 TA TA TA TA TA TA TA T- TA -A AA TCA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
1277689 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1277701 CACACCAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
1 2 0.04
2 42 0.93
3 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1277758 original size:19 final size:18
Alignment explanation
Indices: 1277718--1277759 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1277708 ATATTTTATA
*
1277718 TATATGCTTTAGTATATT
1 TATATGCTTTAGTATATG
1277736 TATATGCATATTA-TATATG
1 TATATGC-T-TTAGTATATG
1277755 TATAT
1 TATAT
1277760 ATGAAAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 11 0.52
20 3 0.14
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (18 bp):
TATATGCTTTAGTATATG
Found at i:1277955 original size:12 final size:12
Alignment explanation
Indices: 1277938--1277966 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1277928 GAATAGAATA
1277938 ATCTCTTTACCT
1 ATCTCTTTACCT
1277950 ATCTCTTTACCT
1 ATCTCTTTACCT
1277962 A-CTCT
1 ATCTCT
1277967 ATTGCTATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.48
Consensus pattern (12 bp):
ATCTCTTTACCT
Found at i:1280112 original size:63 final size:66
Alignment explanation
Indices: 1280031--1280214 Score: 203
Period size: 63 Copynumber: 2.7 Consensus size: 66
1280021 GCTGGTTTTA
*
1280031 ATTTGAATCAAATTTATTAGTTAGGTTAAAGCACTACTAATCCTAATCCTAACAAATAAAT-G-G
1 ATTTGAATGAAATTTATTAGTTAGGTTAAAGCACTACTAATCCTAATCCTAACAAATAAATAGTG
1280094 C
66 C
* * *
1280095 -TTTGAATGGAATTTATTAGTTAGGTTAAAGCATTCCTATTCCTAATCCTAATCCTTACAAATAT
1 ATTTGAATGAAATTTATTAGTTAGGTTAAAGCA---CTA---CTAATCCTAATCCTAACAAATAA
* *
1280159 GTAGTTC
60 ATAGTGC
* *
1280166 TAATTTGAATGAAAATTATTAGTTAGGTTAAAGCACTCCTAATCCTAAT
1 --ATTTGAATGAAATTTATTAGTTAGGTTAAAGCACTACTAATCCTAAT
1280215 ACTAGCCCTT
Statistics
Matches: 100, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
63 30 0.30
66 3 0.03
68 11 0.11
69 22 0.22
70 1 0.01
71 3 0.03
74 30 0.30
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (66 bp):
ATTTGAATGAAATTTATTAGTTAGGTTAAAGCACTACTAATCCTAATCCTAACAAATAAATAGTG
C
Found at i:1280193 original size:74 final size:70
Alignment explanation
Indices: 1280029--1280214 Score: 206
Period size: 74 Copynumber: 2.7 Consensus size: 70
1280019 ATGCTGGTTT
*
1280029 TAATTTGAATCAAATTTATTAGTTAGGTTAAAGCA--CTA--CTAATCCTAATCCTAACAAATAA
1 TAATTTGAATGAAATTTATTAGTTAGGTTAAAGCATCCTATCCTAATCCTAATCCTAACAAATAA
1280090 ATGGC
66 ATGGC
* *
1280095 ---TTTGAATGGAATTTATTAGTTAGGTTAAAGCATTCCTATTCCTAATCCTAATCCTTACAAAT
1 TAATTTGAATGAAATTTATTAGTTAGGTTAAAGCA-TCCTA-TCCTAATCCTAATCCTAACAAAT
** *
1280157 ATGTAGTTC
64 AAAT-G-GC
*
1280166 TAATTTGAATGAAAATTATTAGTTAGGTTAAAGCACTCCTAATCCTAAT
1 TAATTTGAATGAAATTTATTAGTTAGGTTAAAGCA-TCCT-ATCCTAAT
1280215 ACTAGCCCTT
Statistics
Matches: 99, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
63 30 0.30
66 3 0.03
69 22 0.22
70 1 0.01
71 1 0.01
74 41 0.41
75 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (70 bp):
TAATTTGAATGAAATTTATTAGTTAGGTTAAAGCATCCTATCCTAATCCTAATCCTAACAAATAA
ATGGC
Found at i:1280365 original size:3 final size:3
Alignment explanation
Indices: 1280357--1280385 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1280347 TTGTAATAGG
1280357 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1280386 TAGTAGTAGT
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1283465 original size:16 final size:16
Alignment explanation
Indices: 1283444--1283474 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1283434 AAAATAAATG
1283444 GGTGACTACATTTCCA
1 GGTGACTACATTTCCA
*
1283460 GGTGACTGCATTTCC
1 GGTGACTACATTTCC
1283475 TCTAACTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (16 bp):
GGTGACTACATTTCCA
Found at i:1283639 original size:17 final size:16
Alignment explanation
Indices: 1283600--1283662 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
1283590 ATATAAAAAA
*
1283600 TTTATATAATATTAAT
1 TTTATATAATATAAAT
*
1283616 TAT-TATAATATCAAAT
1 TTTATATAATAT-AAAT
1283632 TTTATATAAATATATAAT
1 TTTATAT-AATATA-AAT
1283650 ATTT-TA-AATATAA
1 -TTTATATAATATAA
1283663 TTATAACACA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
15 9 0.23
16 13 0.33
17 4 0.10
18 10 0.26
19 3 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTATATAATATAAAT
Found at i:1283653 original size:20 final size:20
Alignment explanation
Indices: 1283630--1283668 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1283620 ATAATATCAA
*
1283630 ATTTTATATA-AATATATAAT
1 ATTTTAAATATAAT-TATAAT
1283650 ATTTTAAATATAATTATAA
1 ATTTTAAATATAATTATAA
1283669 CACAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTAAATATAATTATAAT
Found at i:1288796 original size:2 final size:2
Alignment explanation
Indices: 1288791--1288831 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1288781 TTGCACCTGT
1288791 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1288832 TGGATGCCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.