Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold401
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: 1910012
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 5 of 13
Found at i:580966 original size:2 final size:2
Alignment explanation
Indices: 580959--580992 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
580949 CATGTAACCA
*
580959 AT AT AT AT AT AT AC 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
580993 CCGAAACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:581939 original size:3 final size:3
Alignment explanation
Indices: 581931--581970 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
581921 TTAAAATTTC
581931 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
581971 TGATTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:583429 original size:27 final size:24
Alignment explanation
Indices: 583409--583464 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
583399 TATATAAATT
583409 TTAATATATTAATAATTTATATAA
1 TTAATATATTAATAATTTATATAA
* *
583433 TTAATATATTCATAATATAT-TAA
1 TTAATATATTAATAATTTATATAA
*
583456 -TATTATATT
1 TTAATATATT
583465 TATGTTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 8 0.28
23 3 0.10
24 18 0.62
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAATATATTAATAATTTATATAA
Found at i:583448 original size:11 final size:11
Alignment explanation
Indices: 583410--583464 Score: 65
Period size: 11 Copynumber: 4.8 Consensus size: 11
583400 ATATAAATTT
583410 TAATATATTAA
1 TAATATATTAA
*
583421 TAATTTATATAA
1 TAATATAT-TAA
*
583433 TTAATATATTCA
1 -TAATATATTAA
583445 TAATATATTAA
1 TAATATATTAA
*
583456 TATTATATT
1 TAATATATT
583465 TATGTTAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 25 0.68
12 5 0.14
13 7 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
TAATATATTAA
Found at i:584189 original size:3 final size:3
Alignment explanation
Indices: 584174--584203 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
584164 TTCTAATGAA
*
584174 ATT ATT ATG ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
584204 TTTTTTTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:585283 original size:39 final size:40
Alignment explanation
Indices: 585205--585284 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
585195 GATAAATTTT
* *
585205 TTTTATTATCTTTTCATTTTATTTTTTAAAAAATCTATTA
1 TTTTATAATATTTTCATTTTATTTTTTAAAAAATCTATTA
* * *
585245 TTTTATAATATTTTTATTTTA-TTTTTAAAAGATGTATTA
1 TTTTATAATATTTTCATTTTATTTTTTAAAAAATCTATTA
585284 T
1 T
585285 ATTTTATAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 17 0.49
40 18 0.51
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (40 bp):
TTTTATAATATTTTCATTTTATTTTTTAAAAAATCTATTA
Found at i:585460 original size:15 final size:14
Alignment explanation
Indices: 585440--585470 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
585430 ACTTCGCCTT
585440 TCTTCCGTTAAGAGA
1 TCTTCCGTTAAG-GA
585455 TCTTCCGTTAAGGA
1 TCTTCCGTTAAGGA
585469 TC
1 TC
585471 CACAAGTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (14 bp):
TCTTCCGTTAAGGA
Found at i:585740 original size:113 final size:113
Alignment explanation
Indices: 585612--585840 Score: 281
Period size: 114 Copynumber: 2.0 Consensus size: 113
585602 TATCTGTTCA
* * *
585612 TAAATCAAGTTAAATTTA-TTAAAATATT-TA-T-ATTG-A-TTATATTTTATATGTTTAAAAAT
1 TAAATCAAGTCAAATTTATTTAAAA-ATTATATTCATTGAAGTTAGATTTTATAAG-TTAAAAA-
585671 TTTATTTTATTATTTAAAAAAATTAAATATTATTTTTATATATTTTATTATATT
63 -TT-TTTTATTA-TTAAAAAAATTAAATATTATTTTTATATATTTTATTATATT
* * *
585725 TAAATCAAGTCAAATTTATTTAAAAATTATATTTCTTTGAAGTTGGATTTTATAAGTTCAAAATT
1 TAAATCAAGTCAAATTTATTTAAAAATTATA-TTCATTGAAGTTAGATTTTATAAGTTAAAAATT
* *
585790 TTTTATTATTAAAAAAATTAAATTTTATTTTTATATATTTTATTATGTT
65 TTTTATTATTAAAAAAATTAAATATTATTTTTATATATTTTATTATATT
585839 TA
1 TA
585841 TTAAATAATA
Statistics
Matches: 101, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
113 20 0.20
114 49 0.49
115 8 0.08
116 3 0.03
117 3 0.03
118 7 0.07
119 11 0.11
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (113 bp):
TAAATCAAGTCAAATTTATTTAAAAATTATATTCATTGAAGTTAGATTTTATAAGTTAAAAATTT
TTTATTATTAAAAAAATTAAATATTATTTTTATATATTTTATTATATT
Found at i:586104 original size:18 final size:19
Alignment explanation
Indices: 586071--586107 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
586061 TAGGTAAATC
586071 TTTTAAAAGTGAGAAATTAT
1 TTTTAAAAGT-AGAAATTAT
586091 TTTTAAAAGT-GAAATTA
1 TTTTAAAAGTAGAAATTA
586108 ATTAATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.41
Consensus pattern (19 bp):
TTTTAAAAGTAGAAATTAT
Found at i:590425 original size:19 final size:19
Alignment explanation
Indices: 590379--590434 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 19
590369 AAATAATATA
*
590379 AAAATTATTTTTAA--ATT
1 AAAATTAATTTTAATTATT
590396 AAAA-TATATTTTAATTATT
1 AAAATTA-ATTTTAATTATT
590415 AAAATTAATTTT--TTATT
1 AAAATTAATTTTAATTATT
590432 AAA
1 AAA
590435 TAATTATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 2 0.06
17 18 0.53
19 12 0.35
20 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAAATTAATTTTAATTATT
Found at i:590444 original size:15 final size:17
Alignment explanation
Indices: 590410--590506 Score: 50
Period size: 14 Copynumber: 5.8 Consensus size: 17
590400 TATATTTTAA
*
590410 TTATTAAAATTAATTTT
1 TTATTAAAATTAATTAT
590427 TTATT-AAA-TAATTAT
1 TTATTAAAATTAATTAT
590442 TTAATTTAAATTATTAAAATT-T
1 TT-A-TTAAA--ATT--AATTAT
590464 TTATTCAAAATTTAA-TAT
1 TTATT-AAAA-TTAATTAT
590482 TT-TT-AAATTAA--AT
1 TTATTAAAATTAATTAT
590495 TTATT-AAATTAA
1 TTATTAAAATTAA
590507 ATTAAATTAT
Statistics
Matches: 67, Mismatches: 1, Indels: 27
0.71 0.01 0.28
Matches are distributed among these distances:
13 4 0.06
14 13 0.19
15 11 0.16
16 4 0.06
17 10 0.15
18 7 0.10
19 1 0.01
20 5 0.07
21 5 0.07
22 3 0.04
23 4 0.06
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATTAAAATTAATTAT
Found at i:590492 original size:14 final size:14
Alignment explanation
Indices: 590475--590509 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
590465 TATTCAAAAT
590475 TTAATATTT-TTAAA
1 TTAA-ATTTATTAAA
590489 TTAAATTTATTAAA
1 TTAAATTTATTAAA
590503 TTAAATT
1 TTAAATT
590510 AAATTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTAAATTTATTAAA
Found at i:596246 original size:2 final size:2
Alignment explanation
Indices: 596241--596305 Score: 51
Period size: 2 Copynumber: 31.5 Consensus size: 2
596231 CTCTTGATGA
* * * *
596241 AT AT AT AT AT AT AT AT AT AT AT CT CCT GGT -T GAT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT -AT AT -AT AT AT AT AT
*
596283 AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
596306 GCTCTTGATG
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
1 1 0.02
2 48 0.91
3 4 0.08
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:600784 original size:26 final size:26
Alignment explanation
Indices: 600736--600791 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
600726 TAAAAATAAA
*
600736 AAATTTTATTTTTAATAAAATAT-TT
1 AAATTTAATTTTTAATAAAATATGTT
*
600761 AAATTTAATTTATTAATAATATATGTT
1 AAATTTAATTT-TTAATAAAATATGTT
600788 AAAT
1 AAAT
600792 ATAAATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 10 0.37
26 11 0.41
27 6 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
AAATTTAATTTTTAATAAAATATGTT
Found at i:601448 original size:27 final size:27
Alignment explanation
Indices: 601418--601482 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 27
601408 ATTTTTTATA
601418 AATTTATTAAT-TAAATTAATTTTATTT
1 AATTTATTAATATAAATTAA-TTTATTT
* *
601445 AA-TTAATAATATTAATTAATTTATTT
1 AATTTATTAATATAAATTAATTTATTT
601471 --TTTATTATATAT
1 AATTTATTA-ATAT
601483 GATGCACGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 5 0.16
26 18 0.56
27 9 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
AATTTATTAATATAAATTAATTTATTT
Found at i:601454 original size:17 final size:17
Alignment explanation
Indices: 601415--601465 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
601405 AATATTTTTT
*
601415 ATAAATTTATTAATTAA
1 ATAATTTTATTAATTAA
601432 ATTAATTTTATTTAATT-A
1 A-TAATTTTA-TTAATTAA
*
601450 ATAATATTAATTAATT
1 ATAAT-TTTATTAATT
601466 TATTTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 11 0.38
18 12 0.41
19 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATAATTTTATTAATTAA
Found at i:601458 original size:23 final size:22
Alignment explanation
Indices: 601419--601469 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
601409 TTTTTTATAA
601419 ATTTATTAATTAAATTAATTTT
1 ATTTATTAATTAAATTAATTTT
*
601441 ATTTAATTAA-TAATATTAA-TTA
1 ATTT-ATTAATTAA-ATTAATTTT
601463 ATTTATT
1 ATTTATT
601470 TTTTATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.12
22 13 0.50
23 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTATTAATTAAATTAATTTT
Found at i:601510 original size:2 final size:2
Alignment explanation
Indices: 601503--601527 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
601493 TACATATGTG
601503 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
601528 GTTATGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:603392 original size:2 final size:2
Alignment explanation
Indices: 603385--603415 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
603375 TTGAATATTA
603385 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
603416 ATTCCTTCGG
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:605504 original size:16 final size:16
Alignment explanation
Indices: 605483--605544 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
605473 TATATTTATT
605483 ATATATTTAAATATAA
1 ATATATTTAAATATAA
605499 ATATA--T-AATAT-A
1 ATATATTTAAATATAA
605511 ATAT-TTTAAATATAA
1 ATATATTTAAATATAA
* * *
605526 AAATTTTTAAAAATAA
1 ATATATTTAAATATAA
605542 ATA
1 ATA
605545 AACGAGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
12 5 0.13
13 6 0.16
14 6 0.16
15 4 0.11
16 17 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATTTAAATATAA
Found at i:607015 original size:2 final size:2
Alignment explanation
Indices: 607008--607042 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
606998 ACGATTTTCT
607008 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 T
607043 TCGTAGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:607578 original size:18 final size:19
Alignment explanation
Indices: 607555--607611 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
607545 ATTAATATTT
*
607555 ATATATT-TTTAAAATAAA
1 ATATATTATTTTAAATAAA
*
607573 ATATATTATTTTAATTAAA
1 ATATATTATTTTAAATAAA
*
607592 A-ATATTATTTTAAATTAA
1 ATATATTATTTTAAATAAA
607610 AT
1 AT
607612 CAAATTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 23 0.70
19 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATTATTTTAAATAAA
Found at i:607607 original size:19 final size:20
Alignment explanation
Indices: 607535--607610 Score: 84
Period size: 19 Copynumber: 3.8 Consensus size: 20
607525 AATATTAAAA
* * *
607535 ATTATTTTATATTAATATTT
1 ATTATTTTAAATTAAAATAT
*
607555 ATATATTTTTAAAATAAAATAT
1 AT-TA-TTTTAAATTAAAATAT
607577 ATTATTTT-AATTAAAA-AT
1 ATTATTTTAAATTAAAATAT
607595 ATTATTTTAAATTAAA
1 ATTATTTTAAATTAAA
607611 TCAAATTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
18 10 0.21
19 14 0.29
20 6 0.12
21 4 0.08
22 14 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTATTTTAAATTAAAATAT
Found at i:607902 original size:20 final size:22
Alignment explanation
Indices: 607877--607928 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
607867 TAATTAAAAT
607877 TTAATTTATAAATAA-A-TTTA
1 TTAATTTATAAATAATATTTTA
*
607897 TTAA-TTA-AATTAATATTTTA
1 TTAATTTATAAATAATATTTTA
*
607917 TTAATTTCTAAA
1 TTAATTTATAAA
607929 ATCAACTCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
18 5 0.20
19 4 0.16
20 12 0.48
21 2 0.08
22 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAATTTATAAATAATATTTTA
Found at i:609137 original size:6 final size:6
Alignment explanation
Indices: 609122--609176 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
609112 ATTAATTATA
* * *
609122 TATATT TATATG TATATT TATATT TATA-T TATTTT TA-ATA TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
609168 TAT-TT TATA
1 TATATT TATA
609177 AATTAATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
5 12 0.30
6 28 0.70
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:609186 original size:26 final size:28
Alignment explanation
Indices: 609117--609186 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 28
609107 TACTAATTAA
* *
609117 TTATATATATTTAT-ATGTATATTTATAT
1 TTATATA-ATTAATAATATATATTTATAT
* **
609145 TTATATTATTTTTAATATATATTTAT-T
1 TTATATAATTAATAATATATATTTATAT
609172 TTATA-AATTAATAAT
1 TTATATAATTAATAAT
609187 TAATTTTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 7 0.20
27 11 0.31
28 17 0.49
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (28 bp):
TTATATAATTAATAATATATATTTATAT
Found at i:611072 original size:21 final size:20
Alignment explanation
Indices: 611048--611096 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
611038 TTATACATTG
*
611048 AATTAATTTAATTTTATATTA
1 AATTAATTTAATTATAT-TTA
* *
611069 AATTTATTTAATTATATTTT
1 AATTAATTTAATTATATTTA
611089 AATTAATT
1 AATTAATT
611097 AATAATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AATTAATTTAATTATATTTA
Found at i:611299 original size:21 final size:21
Alignment explanation
Indices: 611274--611316 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
611264 CAACCCTCTC
611274 AAAAGTATAATGACTAAATTA
1 AAAAGTATAATGACTAAATTA
611295 AAAAGTATAATGACTAAATTA
1 AAAAGTATAATGACTAAATTA
611316 A
1 A
611317 TTGTTTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (21 bp):
AAAAGTATAATGACTAAATTA
Found at i:611534 original size:17 final size:17
Alignment explanation
Indices: 611495--611547 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
611485 AAAATTATTA
*
611495 TTTTTAATATAATAGA-T
1 TTTTTAATTTAATA-ATT
*
611512 TATTTAATTTAATAATT
1 TTTTTAATTTAATAATT
611529 TTTTTAATTT--TAATT
1 TTTTTAATTTAATAATT
611544 TTTT
1 TTTT
611548 AAAATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 9 0.28
16 1 0.03
17 22 0.69
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTAATTTAATAATT
Found at i:611544 original size:15 final size:16
Alignment explanation
Indices: 611514--611547 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
611504 TAATAGATTA
611514 TTTAATTTAATAATTTT
1 TTTAATTT-ATAATTTT
611531 TTTAATTT-TAATTTT
1 TTTAATTTATAATTTT
611546 TT
1 TT
611548 AAAATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAATTTATAATTTT
Found at i:611754 original size:15 final size:16
Alignment explanation
Indices: 611711--611756 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
611701 AAAAAATATT
611711 AAATTATATAAAATTAAA
1 AAATTA-ATAAAA-TAAA
611729 AAATTAA-AAAATAAA
1 AAATTAATAAAATAAA
*
611744 ATA-TAATAAAATA
1 AAATTAATAAAATA
611757 TTAAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 12 0.46
16 4 0.15
17 1 0.04
18 6 0.23
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATTAATAAAATAAA
Found at i:618879 original size:24 final size:25
Alignment explanation
Indices: 618852--618929 Score: 70
Period size: 24 Copynumber: 3.1 Consensus size: 25
618842 CCTCCCCCAT
618852 TTTTTA-ATAAAAATTAGCCACCAA
1 TTTTTACATAAAAATTAGCCACCAA
* * * *
618876 TTTTGACA-AACAATAAGCCACCAT
1 TTTTTACATAAAAATTAGCCACCAA
* *
618900 TTTTTACATACAAAAATAACCACCATA
1 TTTTTACATA-AAAATTAGCCACCA-A
618927 TTT
1 TTT
618930 GACAAATACA
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
24 25 0.62
25 2 0.05
26 10 0.25
27 3 0.08
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.32
Consensus pattern (25 bp):
TTTTTACATAAAAATTAGCCACCAA
Found at i:618938 original size:28 final size:29
Alignment explanation
Indices: 618881--618969 Score: 105
Period size: 28 Copynumber: 3.2 Consensus size: 29
618871 ACCAATTTTG
* *
618881 ACAAACAATAAGCCACCATTTTTTAC--AT
1 ACAAACAATAA-CCACCATATTTGACAAAT
618909 ACAAA-AATAACCACCATATTTGACAAAT
1 ACAAACAATAACCACCATATTTGACAAAT
**
618937 ACAAAGGA-AACCACCATATTTGACAAAT
1 ACAAACAATAACCACCATATTTGACAAAT
618965 ACAAA
1 ACAAA
618970 GGGTGGCATT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
26 12 0.22
27 5 0.09
28 37 0.67
29 1 0.02
ACGTcount: A:0.51, C:0.22, G:0.06, T:0.21
Consensus pattern (29 bp):
ACAAACAATAACCACCATATTTGACAAAT
Found at i:618970 original size:28 final size:28
Alignment explanation
Indices: 618917--618971 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
618907 ATACAAAAAT
618917 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
618945 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
618972 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:623453 original size:24 final size:24
Alignment explanation
Indices: 623426--623471 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
623416 AATAAAAATT
623426 AGCCACCAATTTTGACAAACAATA
1 AGCCACCAATTTTGACAAACAATA
* * *
623450 AGCCACCATTTTTTACATACAA
1 AGCCACCAATTTTGACAAACAA
623472 AAATAACCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAATA
Found at i:623497 original size:28 final size:28
Alignment explanation
Indices: 623466--623550 Score: 136
Period size: 28 Copynumber: 3.0 Consensus size: 28
623456 CATTTTTTAC
623466 ATACAAA-AATAACCACCATATTTGACAA
1 ATACAAAGAA-AACCACCATATTTGACAA
*
623494 ATACAAAGGAAACCACCATATTTGACAA
1 ATACAAAGAAAACCACCATATTTGACAA
*
623522 ATACAAAGGAAACCACCATATTTGACAA
1 ATACAAAGAAAACCACCATATTTGACAA
623550 A
1 A
623551 GGGTGGCATT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
28 54 0.98
29 1 0.02
ACGTcount: A:0.52, C:0.21, G:0.08, T:0.19
Consensus pattern (28 bp):
ATACAAAGAAAACCACCATATTTGACAA
Found at i:631072 original size:2 final size:2
Alignment explanation
Indices: 631065--631089 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
631055 AACTGATTTA
631065 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
631090 GACCAAAGAT
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:642151 original size:20 final size:20
Alignment explanation
Indices: 642112--642153 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
642102 AAATAAATAA
*
642112 AATAATTTTGTAATTATTAT
1 AATAATTTTATAATTATTAT
642132 AATATATTTTATAATT-TTAT
1 AATA-ATTTTATAATTATTAT
642152 AA
1 AA
642154 AAATAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AATAATTTTATAATTATTAT
Found at i:648434 original size:16 final size:15
Alignment explanation
Indices: 648413--648455 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
648403 TCAAAAAGCT
648413 TTTC-TTTTTCTTTATC
1 TTTCTTTTTTC-TT-TC
648429 TTTCTTTCTTTCTTTC
1 TTTCTTT-TTTCTTTC
648445 TTTCTTTTTTC
1 TTTCTTTTTTC
648456 CCCCCTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.16
16 13 0.52
17 4 0.16
18 4 0.16
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCTTTTTTCTTTC
Found at i:648436 original size:4 final size:4
Alignment explanation
Indices: 648427--648455 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
648417 TTTTTCTTTA
648427 TCTT TCTT TCTT TCTT TCTT TCTT T-TT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TC
648456 CCCCCTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:653222 original size:2 final size:2
Alignment explanation
Indices: 653215--653259 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
653205 CAAAAAGGCC
*
653215 AT AT AT AT AA AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
653256 AT AT
1 AT AT
653260 GATAAAGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:653452 original size:6 final size:6
Alignment explanation
Indices: 653436--653553 Score: 60
Period size: 6 Copynumber: 20.5 Consensus size: 6
653426 TATTATCGAA
* *
653436 TTAAA- TTAAAT TTAAAT TATATTAAT TTTAAT TTTAAT TT-AAT TT-AAT
1 TTAAAT TTAAAT TTAAAT T-TA--AAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
653484 TT-AAT TTAAAAT TTAAAAT TTAAA- TTATAAT ATAAAA TTAAA- TT--AT
1 TTAAAT TT-AAAT TT-AAAT TTAAAT TTA-AAT TTAAAT TTAAAT TTAAAT
*
653530 TTAAA- TTAAA- TT-ATT TTAAAT TTA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTA
653554 TTTATTTTGA
Statistics
Matches: 94, Mismatches: 6, Indels: 25
0.75 0.05 0.20
Matches are distributed among these distances:
3 1 0.01
4 3 0.03
5 34 0.36
6 35 0.37
7 16 0.17
8 1 0.01
9 4 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:653471 original size:22 final size:21
Alignment explanation
Indices: 653436--653553 Score: 62
Period size: 21 Copynumber: 5.4 Consensus size: 21
653426 TATTATCGAA
* *
653436 TTAAATTAAATTTAAATT-AT
1 TTAATTTAATTTTAAATTAAT
*
653456 ATTAATTTTAATTTTAATTTAAT
1 -TTAA-TTTAATTTTAAATTAAT
*
653479 TTAATTTAATTTAAAATTTAAAAT
1 TTAATTTAATTTTAAA-TT--AAT
* * *
653503 TTAAATTATAATATAAAATTAAA
1 TT-AATT-TAATTTTAAATTAAT
* *
653526 TT-ATTTAA-ATTAAATTATT
1 TTAATTTAATTTTAAATTAAT
653545 TTAAATTTA
1 TT-AATTTA
653554 TTTATTTTGA
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
19 10 0.13
20 3 0.04
21 22 0.28
22 17 0.22
23 6 0.08
24 5 0.06
25 6 0.08
26 9 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAATTTAATTTTAAATTAAT
Found at i:653483 original size:10 final size:10
Alignment explanation
Indices: 653434--653492 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
653424 AATATTATCG
* *
653434 AATTAAATTA
1 AATTTAATTT
*
653444 AATTTAAATT
1 AATTTAATTT
653454 -ATATTAATTTT
1 AAT-TTAA-TTT
653465 AATTTTAATTT
1 AA-TTTAATTT
653476 AATTTAATTT
1 AATTTAATTT
653486 AATTTAA
1 AATTTAA
653493 AATTTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.05
10 26 0.63
11 7 0.17
12 5 0.12
13 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
AATTTAATTT
Found at i:653505 original size:19 final size:19
Alignment explanation
Indices: 653481--653527 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
653471 AATTTAATTT
*
653481 AATTTAATTTAAAATTTAA
1 AATTTAATTTAAAATATAA
* *
653500 AATTTAAATTATAATATAA
1 AATTTAATTTAAAATATAA
*
653519 AATTAAATT
1 AATTTAATT
653528 ATTTAAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTAATTTAAAATATAA
Found at i:653537 original size:14 final size:14
Alignment explanation
Indices: 653501--653551 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
653491 AAAATTTAAA
653501 ATTTAAATTATAA-T
1 ATTTAAATTA-AATT
*
653515 A-TAAAATTAAATT
1 ATTTAAATTAAATT
653528 ATTTAAATTAAATT
1 ATTTAAATTAAATT
653542 ATTTTAAATT
1 A-TTTAAATT
653552 TATTTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 2 0.06
13 9 0.28
14 13 0.41
15 8 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTAAATTAAATT
Found at i:653547 original size:15 final size:15
Alignment explanation
Indices: 653518--653561 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
653508 TTATAATATA
653518 AAATTAAATTA-TTT
1 AAATTAAATTATTTT
653532 AAATTAAATTATTTT
1 AAATTAAATTATTTT
* *
653547 AAATTTATTTATTTT
1 AAATTAAATTATTTT
653562 GATTAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATTAAATTATTTT
Found at i:653592 original size:59 final size:58
Alignment explanation
Indices: 653529--653664 Score: 141
Period size: 59 Copynumber: 2.3 Consensus size: 58
653519 AATTAAATTA
* * * *
653529 TTTAAATTAAATTATTTTAAATTT-A-TTTATTTTGATTAAGTTTAAATTTTATATTCTAT
1 TTTAAATTTAATTATTTTAAATTTAATTTTA-TTT-A-TAAGTTCAAATCTTACATTCTAT
* * * * *
653588 TTTAAATTTATTTACTTAAAATTTAAATTTTATTTATAAGTTCGAATCTTACCTTCTAT
1 TTTAAATTTAATTATTTTAAATTT-AATTTTATTTATAAGTTCAAATCTTACATTCTAT
653647 TTTAAATTTAATTATTTT
1 TTTAAATTTAATTATTTT
653665 TATTAAGTTC
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
59 53 0.85
60 1 0.02
61 4 0.06
62 4 0.06
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (58 bp):
TTTAAATTTAATTATTTTAAATTTAATTTTATTTATAAGTTCAAATCTTACATTCTAT
Found at i:653613 original size:40 final size:43
Alignment explanation
Indices: 653541--653620 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 43
653531 TAAATTAAAT
* *
653541 TATTTTAAATTTATTTATTTTGATTAAGTTTAAATTTTATATTC
1 TATTTTAAATTTATTTATCTTGA-TAAATTTAAATTTTATATTC
653585 TATTTTAAATTTATTTA-CTT-A-AAATTTAAATTTTAT
1 TATTTTAAATTTATTTATCTTGATAAATTTAAATTTTAT
653621 TTATAAGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 14 0.41
42 1 0.03
43 2 0.06
44 17 0.50
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (43 bp):
TATTTTAAATTTATTTATCTTGATAAATTTAAATTTTATATTC
Found at i:655017 original size:2 final size:2
Alignment explanation
Indices: 655012--655054 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
655002 TATATGTTTG
655012 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
655054 T
1 T
655055 GTTTCAGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:655294 original size:17 final size:17
Alignment explanation
Indices: 655272--655308 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
655262 TATTTATGAT
655272 TATTTTTTAAATTTAAA
1 TATTTTTTAAATTTAAA
655289 TA-TTTTTAAATTTAAA
1 TATTTTTTAAATTTAAA
655305 -ATTT
1 TATTT
655309 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.05
16 16 0.84
17 2 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTTTTAAATTTAAA
Found at i:655329 original size:23 final size:24
Alignment explanation
Indices: 655253--655329 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 24
655243 AAAATACGTA
* *
655253 TAAATATAATATTTATGATTATTTTT
1 TAAATTTAATATTT-TTA-TATTTTT
*
655279 TAAATTTAAATATTTTTA-A-ATTT
1 TAAATTT-AATATTTTTATATTTTT
*
655302 AAAATTT-ATATTTTTATATTTTT
1 TAAATTTAATATTTTTATATTTTT
655325 TAAAT
1 TAAAT
655330 ATAGAATCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
21 9 0.21
22 1 0.02
23 16 0.38
24 1 0.02
26 8 0.19
27 7 0.17
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (24 bp):
TAAATTTAATATTTTTATATTTTT
Found at i:655460 original size:3 final size:3
Alignment explanation
Indices: 655452--655478 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
655442 AAAGAAAGAG
655452 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
655479 AGTTAGGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:656978 original size:14 final size:14
Alignment explanation
Indices: 656959--656986 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
656949 TGGAGATCGA
656959 GAGAGTGTTTCTTG
1 GAGAGTGTTTCTTG
656973 GAGAGTGTTTCTTG
1 GAGAGTGTTTCTTG
656987 AAGCTGATCT
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:0.14, C:0.07, G:0.36, T:0.43
Consensus pattern (14 bp):
GAGAGTGTTTCTTG
Found at i:660378 original size:18 final size:20
Alignment explanation
Indices: 660340--660378 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
660330 TTATAAATAT
660340 AAATATAATATAAATTATTA
1 AAATATAATATAAATTATTA
*
660360 AAATATATTA-AAATT-TTA
1 AAATATAATATAAATTATTA
660378 A
1 A
660379 TATGAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATATAATATAAATTATTA
Found at i:660441 original size:14 final size:14
Alignment explanation
Indices: 660424--660472 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
660414 TTTTTTTTAA
660424 ATATATTTTATTAT
1 ATATATTTTATTAT
*
660438 ATATATTATATTAT
1 ATATATTTTATTAT
* *
660452 -TTTATATTTATTAA
1 ATATAT-TTTATTAT
660466 ATATATT
1 ATATATT
660473 ATTTTAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 4 0.14
14 20 0.71
15 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATATATTTTATTAT
Found at i:660446 original size:9 final size:9
Alignment explanation
Indices: 660432--660474 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
660422 AAATATATTT
660432 TATTATATA
1 TATTATATA
660441 TATTATATTA
1 TATTATA-TA
* *
660451 TTTTATATT
1 TATTATATA
*
660460 TATTAAATA
1 TATTATATA
660469 TATTAT
1 TATTAT
660475 TTTAATTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TATTATATA
Found at i:660447 original size:5 final size:5
Alignment explanation
Indices: 660425--660474 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
660415 TTTTTTTAAA
* * *
660425 TATAT TTTAT TATA- TATAT TATAT TATTT TATAT T-TAT TA-AA TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
660472 TAT
1 TAT
660475 TTTAATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
4 11 0.31
5 25 0.69
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:660447 original size:19 final size:19
Alignment explanation
Indices: 660425--660464 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
660415 TTTTTTTAAA
660425 TATATT-TTATTATATATAT
1 TATATTATT-TTATATATAT
*
660444 TATATTATTTTATATTTAT
1 TATATTATTTTATATATAT
660463 TA
1 TA
660465 AATATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATATTATTTTATATATAT
Found at i:660469 original size:28 final size:29
Alignment explanation
Indices: 660425--660483 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
660415 TTTTTTTAAA
* *
660425 TATATTTTATTATATATATTATATTATTT
1 TATATTTTATTAAATATATTATATTAATT
*
660454 TATA-TTTATTAAATATATTATTTTAATT
1 TATATTTTATTAAATATATTATATTAATT
660482 TA
1 TA
660484 ATGTTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TATATTTTATTAAATATATTATATTAATT
Found at i:673081 original size:6 final size:6
Alignment explanation
Indices: 673070--673094 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
673060 GCACACTAAA
673070 ACACGC ACACGC ACACGC ACACGC A
1 ACACGC ACACGC ACACGC ACACGC A
673095 TATTATAATA
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:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACACGC
Found at i:677183 original size:11 final size:11
Alignment explanation
Indices: 677167--677212 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
677157 TATTTAAATT
677167 TATTATTAAAA
1 TATTATTAAAA
677178 TATTA-T--AA
1 TATTATTAAAA
677186 T-TT--TAAAA
1 TATTATTAAAA
677194 TATTATTAAAA
1 TATTATTAAAA
677205 TATTATTA
1 TATTATTA
677213 TTTCATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
6 1 0.03
7 2 0.07
8 6 0.20
9 2 0.07
10 1 0.03
11 18 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:677338 original size:17 final size:18
Alignment explanation
Indices: 677298--677358 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 18
677288 ATAATAATAT
* *
677298 TTTAATAATATATTTAAAA
1 TTTAATATTATATTT-ATA
677317 TTTTAATA-TAT-TTTATTA
1 -TTTAATATTATATTTA-TA
677335 TTT-ATATTATATTTATA
1 TTTAATATTATATTTATA
677352 TTTAATA
1 TTTAATA
677359 ATTAAAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
16 3 0.08
17 12 0.33
18 11 0.31
19 3 0.08
20 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTAATATTATATTTATA
Found at i:677362 original size:19 final size:17
Alignment explanation
Indices: 677302--677360 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
677292 TAATATTTTA
*
677302 ATAATATATTTAAAATTT
1 ATAATATATTT-ATATTT
677320 -TAATATATTTTATTATTT
1 ATAATATA-TTTA-TATTT
*
677338 ATATTATATTTATATTT
1 ATAATATATTTATATTT
677355 AATAAT
1 -ATAAT
677361 TAAAATATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 13 0.38
18 15 0.44
19 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATAATATATTTATATTT
Found at i:677903 original size:22 final size:21
Alignment explanation
Indices: 677851--677904 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
677841 TATTATATTA
677851 TATTATATATTTAAATAAAAT
1 TATTATATATTTAAATAAAAT
* *
677872 TATGTTTATATTGT-ATTGAAAAT
1 TAT-TATATATT-TAAAT-AAAAT
677895 TATTATATAT
1 TATTATATAT
677905 AATTAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.11
22 15 0.56
23 9 0.33
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (21 bp):
TATTATATATTTAAATAAAAT
Found at i:678342 original size:16 final size:16
Alignment explanation
Indices: 678298--678346 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
678288 AAAATTTATT
* *
678298 AATAAAAATAATATTA
1 AATAAAAATATTTTTA
678314 AATATATAAATATTTTTA
1 AATA-A-AAATATTTTTA
678332 AATAAAAATATTTTT
1 AATAAAAATATTTTT
678347 CCAAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 14 0.48
17 2 0.07
18 13 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAAAAATATTTTTA
Found at i:679640 original size:53 final size:53
Alignment explanation
Indices: 679560--679675 Score: 187
Period size: 53 Copynumber: 2.2 Consensus size: 53
679550 TCACGTCATG
* *
679560 ATATGCAAAGCATGTCATGTTCACGTCGTTTGACCATTATTTGTTGACAAGAA
1 ATATGCAAAGCATGTCACGTTCACGTCGTTTGACCATTATTTGTCGACAAGAA
* * *
679613 ATATGCAAAGCATGTCACGTTTACGTCGTTTGATCATTATTTGTCGGCAAGAA
1 ATATGCAAAGCATGTCACGTTCACGTCGTTTGACCATTATTTGTCGACAAGAA
679666 ATATGCAAAG
1 ATATGCAAAG
679676 ATTGATGCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (53 bp):
ATATGCAAAGCATGTCACGTTCACGTCGTTTGACCATTATTTGTCGACAAGAA
Found at i:686185 original size:15 final size:14
Alignment explanation
Indices: 686167--686196 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
686157 AATTTTACAC
686167 ATAT-TTTATTAAA
1 ATATATTTATTAAA
686180 ATATATTTATTAAA
1 ATATATTTATTAAA
686194 ATA
1 ATA
686197 AAAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATTTATTAAA
Found at i:686493 original size:50 final size:47
Alignment explanation
Indices: 686424--686532 Score: 116
Period size: 50 Copynumber: 2.3 Consensus size: 47
686414 CTTTTTTTAA
* *
686424 AAAAAATTAATTTATATT-AAGAGTTTATTT-ATACATAAATTAAAAGT
1 AAAAAATTTATTTATATTAAAGA-TTTATTTGA-ACATAAATTAAAAAT
*
686471 AAAAAATTTATTTGAGTGATTAAAGATTTATTTGAATATAAATTAAAAAT
1 AAAAAATTTATTT-A-T-ATTAAAGATTTATTTGAACATAAATTAAAAAT
*
686521 TAAAAA-TTATTT
1 AAAAAATTTATTT
686533 TAGATGTAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
47 12 0.23
48 1 0.02
49 7 0.13
50 28 0.53
51 5 0.09
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.41
Consensus pattern (47 bp):
AAAAAATTTATTTATATTAAAGATTTATTTGAACATAAATTAAAAAT
Found at i:692619 original size:17 final size:17
Alignment explanation
Indices: 692599--692632 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
692589 ATATTTATTC
692599 TAATATAATAAATAAAT
1 TAATATAATAAATAAAT
*
692616 TAATATACTAAATAAAT
1 TAATATAATAAATAAAT
692633 AATTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATATAATAAATAAAT
Found at i:692646 original size:26 final size:26
Alignment explanation
Indices: 692607--692673 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
692597 TCTAATATAA
*
692607 TAAATAAATTAATATACTAAATAA-ATAAT
1 TAAATAAAAT-ATAT-C-AAATAAGAT-AT
*
692636 TAATTAAAATATATCAAATAAGATAT
1 TAAATAAAATATATCAAATAAGATAT
*
692662 TAAATACAATAT
1 TAAATAAAATAT
692674 TAAAAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 18 0.55
27 3 0.09
28 4 0.12
29 8 0.24
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (26 bp):
TAAATAAAATATATCAAATAAGATAT
Found at i:692789 original size:6 final size:6
Alignment explanation
Indices: 692780--692821 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
692770 CTTAATAATA
* * *
692780 ATTTTT ATTTTT A-TTTT ATTATT ATTTTT AATTTT ATATTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
692822 AATATATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:694857 original size:3 final size:3
Alignment explanation
Indices: 694851--694878 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
694841 ACAACAGTAT
694851 CAG CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG C
694879 TCTGATGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:696049 original size:21 final size:22
Alignment explanation
Indices: 696000--696040 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
695990 TATTAATTTC
*
696000 AAATATTTAAACATATAATAAA
1 AAATAATTAAACATATAATAAA
696022 AAATAATTAAA-ATATAATA
1 AAATAATTAAACATATAATA
696041 CGATATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATAATTAAACATATAATAAA
Found at i:697312 original size:26 final size:27
Alignment explanation
Indices: 697251--697313 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
697241 ATGATATATA
*
697251 AATTTATATATTATTAATAAATTAAAT
1 AATTTATATTTTATTAATAAATTAAAT
*
697278 AATAT-TATTTTATTAA-AAA-TATAAT
1 AATTTATATTTTATTAATAAATTA-AAT
697303 AATTTATATTT
1 AATTTATATTT
697314 CATATTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 2 0.06
25 10 0.32
26 15 0.48
27 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTTATATTTTATTAATAAATTAAAT
Found at i:699938 original size:2 final size:2
Alignment explanation
Indices: 699931--699967 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
699921 TTTACTTAAA
699931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
699968 CATCAACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:700638 original size:2 final size:2
Alignment explanation
Indices: 700631--700664 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
700621 AGGAAAACTG
700631 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
700665 TACCTATGAA
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:700842 original size:3 final size:3
Alignment explanation
Indices: 700834--700864 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
700824 AAGGCCCAGG
700834 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
700865 CCGCTTAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:701300 original size:19 final size:20
Alignment explanation
Indices: 701254--701302 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
701244 AATTTAATTT
701254 TTTATTAAAT-TTTAAATAA
1 TTTATTAAATATTTAAATAA
* *
701273 ATTA-AAAATATTTAAAT-A
1 TTTATTAAATATTTAAATAA
701291 TTTATTAAATAT
1 TTTATTAAATAT
701303 AATAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTATTAAATATTTAAATAA
Found at i:701420 original size:18 final size:18
Alignment explanation
Indices: 701397--701432 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
701387 AATTCATTTA
*
701397 GTAAAATATAAATAATAT
1 GTAAAATATAAAAAATAT
*
701415 GTAAAATTTAAAAAATAT
1 GTAAAATATAAAAAATAT
701433 ATAATACTAA
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:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
GTAAAATATAAAAAATAT
Found at i:705308 original size:2 final size:2
Alignment explanation
Indices: 705301--705327 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
705291 TTTCTTTCTT
705301 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
705328 TGGAATTGGA
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:722411 original size:17 final size:16
Alignment explanation
Indices: 722389--722425 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
722379 TTTTTTTATT
722389 TTAAAATAATATAATAA
1 TTAAAATAATATAAT-A
*
722406 TTAAAATATTATAATA
1 TTAAAATAATATAATA
722422 TTAA
1 TTAA
722426 TATCATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAATAATATAATA
Found at i:730602 original size:116 final size:115
Alignment explanation
Indices: 730384--730613 Score: 406
Period size: 116 Copynumber: 2.0 Consensus size: 115
730374 CAAGTCGCAG
*
730384 AAGAAACAGGTTCAAACCGATGCTTGTTTCTCCTTAAACCTCAACATCAAACCATCTTTGATGTT
1 AAGAAACAGGCTCAAACCGATGCTTGTTTCTCCTTAAACCTCAACATCAAACCATCTTTGATGTT
* *
730449 TTGTCAGATCTTCTTAGCATTTTCCTCCTCCAAAAATCTTGACCCCACGA
66 TCGTCAGATCTTCTTAGCATTTCCCTCCTCCAAAAATCTTGACCCCACGA
*
730499 AAGAAACAAGGCTCGAACCGATGCTTGTTTCTCCTTAAACCTCAACATCAAACCATCTTTGATGT
1 AAGAAAC-AGGCTCAAACCGATGCTTGTTTCTCCTTAAACCTCAACATCAAACCATCTTTGATGT
*
730564 TTCGTCAGATCTTCTTAGCATTTCCCTCCTCCGAAAATCTTGACCCCACG
65 TTCGTCAGATCTTCTTAGCATTTCCCTCCTCCAAAAATCTTGACCCCACG
730614 GCCTCATCCT
Statistics
Matches: 109, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
115 7 0.06
116 102 0.94
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.31
Consensus pattern (115 bp):
AAGAAACAGGCTCAAACCGATGCTTGTTTCTCCTTAAACCTCAACATCAAACCATCTTTGATGTT
TCGTCAGATCTTCTTAGCATTTCCCTCCTCCAAAAATCTTGACCCCACGA
Found at i:730648 original size:2 final size:2
Alignment explanation
Indices: 730643--730677 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
730633 CCCCCCTCCC
730643 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
730678 AATGCCTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:732441 original size:18 final size:18
Alignment explanation
Indices: 732418--732454 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
732408 TATACATGCG
732418 CTTTTTCTGTGTTTTTGC
1 CTTTTTCTGTGTTTTTGC
732436 CTTTTTCTGTGTTTTTGC
1 CTTTTTCTGTGTTTTTGC
732454 C
1 C
732455 CTTATATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.19, G:0.16, T:0.65
Consensus pattern (18 bp):
CTTTTTCTGTGTTTTTGC
Found at i:742111 original size:44 final size:43
Alignment explanation
Indices: 742048--742131 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
742038 ATAAAAAATT
* * *
742048 TAAATTTAACTTAATTATTTATTAAAATTTAAGTTAATAATAAA
1 TAAATTAAACTTAAATATTTATT-AAATTAAAGTTAATAATAAA
* *
742092 TAAATTAAATTTAAATATTTATTAAATTAAATTTAATAAT
1 TAAATTAAACTTAAATATTTATTAAATTAAAGTTAATAAT
742132 TTATGAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 15 0.43
44 20 0.57
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (43 bp):
TAAATTAAACTTAAATATTTATTAAATTAAAGTTAATAATAAA
Found at i:742133 original size:22 final size:22
Alignment explanation
Indices: 742047--742135 Score: 83
Period size: 22 Copynumber: 4.0 Consensus size: 22
742037 AATAAAAAAT
* * *
742047 TTAAATTTAACTTAATTATTTA
1 TTAAATTAAATTTAATAATTTA
* * *
742069 TTAAAATTTAAGTTAATAA-TAA
1 TT-AAATTAAATTTAATAATTTA
*
742091 ATAAATTAAATTTAA-ATATTTA
1 TTAAATTAAATTTAATA-ATTTA
742113 TTAAATTAAATTTAATAATTTA
1 TTAAATTAAATTTAATAATTTA
742135 T
1 T
742136 GAATATTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.02
21 12 0.22
22 27 0.49
23 15 0.27
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (22 bp):
TTAAATTAAATTTAATAATTTA
Found at i:742133 original size:56 final size:53
Alignment explanation
Indices: 742028--742134 Score: 119
Period size: 55 Copynumber: 2.0 Consensus size: 53
742018 ATGAATCAAT
* **
742028 TTAATAATTAATAAAAAATTTAAATTTAACTTAATTATTTATTAAAATTTAAG
1 TTAATAATAAATAAAAAATTTAAATTTAACTTAATTAAATATTAAAATTTAAG
*
742081 TTAATAATAAATAAATTAAATTTAAATATTTA-TTAAATTAAAT-TTAATAATTTA
1 TTAATAATAAATAAA--AAATTTAAAT-TTAACTT-AATTAAATATTAA-AATTTA
742135 TGAATATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
53 14 0.31
55 16 0.36
56 15 0.33
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (53 bp):
TTAATAATAAATAAAAAATTTAAATTTAACTTAATTAAATATTAAAATTTAAG
Found at i:742487 original size:21 final size:23
Alignment explanation
Indices: 742463--742510 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
742453 TTTTAAAATA
* *
742463 AATATAA-ATTATTTTATTT-TT
1 AATATAATAATATTTAATTTATT
742484 AATATAATAATATTTAATTTATT
1 AATATAATAATATTTAATTTATT
742507 AATA
1 AATA
742511 ATATAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 10 0.43
23 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATAATAATATTTAATTTATT
Found at i:743272 original size:25 final size:26
Alignment explanation
Indices: 743226--743293 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 26
743216 ATTTTAAATA
* *
743226 AATAAAAATT-ATTAAAATTATATAT
1 AATAATAATTAATTTAAATTATATAT
*
743251 AATAATAATTAATTTAAA-TATATCT
1 AATAATAATTAATTTAAATTATATAT
743276 ATATGATATAATTAATTT
1 A-AT-A-ATAATTAATTT
743294 TTTTTTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 16 0.44
26 8 0.22
27 1 0.03
28 11 0.31
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
AATAATAATTAATTTAAATTATATAT
Found at i:744279 original size:19 final size:18
Alignment explanation
Indices: 744256--744291 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
744246 TTTTCTTTTT
744256 TTTTTTAATAAACTATTC
1 TTTTTTAATAAACTATTC
*
744274 TTTTTTGATAAACTATTC
1 TTTTTTAATAAACTATTC
744292 ACTTTATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTTTTAATAAACTATTC
Found at i:744575 original size:18 final size:20
Alignment explanation
Indices: 744547--744586 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
744537 TATAATTAAA
744547 TTTAAATTAAAAAT-ATTAT
1 TTTAAATTAAAAATAATTAT
744566 TTTAAA-TAAAAATAATTAT
1 TTTAAATTAAAAATAATTAT
744585 TT
1 TT
744587 AAGTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATTAAAAATAATTAT
Found at i:744587 original size:18 final size:18
Alignment explanation
Indices: 744546--744588 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
744536 TTATAATTAA
744546 ATTTAAATTAAAAATATT
1 ATTTAAATTAAAAATATT
744564 ATTTTAAA-TAAAAATAATT
1 A-TTTAAATTAAAAAT-ATT
744583 ATTTAA
1 ATTTAA
744589 GTTTAATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTAAATTAAAAATATT
Found at i:747718 original size:2 final size:2
Alignment explanation
Indices: 747711--747754 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
747701 GGTTACTTGA
747711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
747753 AT
1 AT
747755 GAATGATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:751817 original size:2 final size:2
Alignment explanation
Indices: 751810--751848 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
751800 CAAAAGGAAA
751810 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 A
751849 ATCAACAAGA
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:753499 original size:28 final size:28
Alignment explanation
Indices: 753467--753521 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
753457 ATTAAAAATT
753467 TAATAAAAAATT-AAAAAATTAAATTTTA
1 TAAT-AAAAATTAAAAAAATTAAATTTTA
* *
753495 TAATAAACATTAAAAAAATTTAATTTT
1 TAATAAAAATTAAAAAAATTAAATTTT
753522 TTCCTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
TAATAAAAATTAAAAAAATTAAATTTTA
Found at i:754203 original size:22 final size:22
Alignment explanation
Indices: 754178--754220 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
754168 TAATTTTATT
754178 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAATT-TAAAAATATA
754200 TAAATATTAATTTAAAAATAT
1 TAAATATTAATTTAAAAATAT
754221 TTTTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATATTAATTTAAAAATATA
Found at i:754647 original size:14 final size:14
Alignment explanation
Indices: 754587--754656 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
754577 TAATTTTATT
754587 TTTAATTTAAATTTAA
1 TTTAA-TTAAATTT-A
* *
754603 TGTTAAATAAAAATTA
1 T-TT-AATTAAATTTA
* *
754619 TATTATTTAAGTTTA
1 T-TTAATTAAATTTA
754634 TTTAATTAAATTTA
1 TTTAATTAAATTTA
*
754648 TTTACTTAA
1 TTTAATTAA
754657 TAAAAATAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
14 19 0.45
15 8 0.19
16 5 0.12
17 8 0.19
18 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (14 bp):
TTTAATTAAATTTA
Found at i:756548 original size:2 final size:2
Alignment explanation
Indices: 756541--756574 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
756531 ACATGCATAC
756541 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
756575 ATATATATAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:763940 original size:18 final size:19
Alignment explanation
Indices: 763890--763940 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
763880 ATTATTAAAA
*
763890 ATATTAAAAAT-TATTTTT
1 ATATTAAATATATATTTTT
*
763908 ATATTAATATTTATATATTTT
1 ATATTAA-ATATATAT-TTTT
763929 ATATTAAATATA
1 ATATTAAATATA
763941 AATAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 7 0.26
19 2 0.07
20 7 0.26
21 11 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTAAATATATATTTTT
Found at i:764128 original size:13 final size:13
Alignment explanation
Indices: 764112--764157 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
764102 CATCCGATGC
764112 ATATACAAAATAT
1 ATATACAAAATAT
*
764125 ATATACAAAATAA
1 ATATACAAAATAT
*
764138 ATGATATAAAATAT
1 AT-ATACAAAATAT
764152 GATATA
1 -ATATA
764158 AAATTATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 14 0.50
14 12 0.43
15 2 0.07
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (13 bp):
ATATACAAAATAT
Found at i:764155 original size:12 final size:13
Alignment explanation
Indices: 764138--764166 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
764128 TACAAAATAA
764138 ATGATATAAAA-T
1 ATGATATAAAATT
764150 ATGATATAAAATT
1 ATGATATAAAATT
764163 ATGA
1 ATGA
764167 ATTATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (13 bp):
ATGATATAAAATT
Found at i:764791 original size:50 final size:50
Alignment explanation
Indices: 764714--765022 Score: 474
Period size: 50 Copynumber: 6.2 Consensus size: 50
764704 TATACTTAGA
* *
764714 GTCAACAATTATGGCCACCTTTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
764764 GTCAACAATAATGGCCACCTCTTTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * * *
764814 GTGAACAATTACGGTCACCTCTCTCTATTATCAAATGTTGGTGAGGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
764864 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
764914 ATCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
764964 GTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
765014 GTCAACAAT
1 GTCAACAAT
765023 GGCAACAACT
Statistics
Matches: 234, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 234 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (50 bp):
GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:769473 original size:50 final size:50
Alignment explanation
Indices: 769414--769672 Score: 392
Period size: 50 Copynumber: 5.2 Consensus size: 50
769404 TATACTTAGA
* * *
769414 GTCAACAATTATGGCCACATTTCTCTATTGTCAAAGGTTGGTGAAAAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
* *
769464 GTCAACAATTACGACCACCTCTCTTTATTGTCAAAGGTTGGTGAAAAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
*
769514 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
* *
769564 GTCAACAATTACGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
*** * * *
769614 GTCAACAATTACGATTACCTCTCTCTATTGTCAAAGGTTAGTGAAAGATA
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
769664 GTCAACAAT
1 GTCAACAAT
769673 GGCAACAACT
Statistics
Matches: 194, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 194 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (50 bp):
GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
Found at i:770094 original size:18 final size:17
Alignment explanation
Indices: 770059--770097 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
770049 TATGTATATT
770059 ATTTTTATTTATTCTAA
1 ATTTTTATTTATTCTAA
770076 ATTTTTATAATTATT-TAA
1 ATTTTTAT--TTATTCTAA
770094 ATTT
1 ATTT
770098 AATTCTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 7 0.35
19 5 0.25
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTATTTATTCTAA
Found at i:770253 original size:3 final size:3
Alignment explanation
Indices: 770245--770286 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
770235 AGAATAAGAT
770245 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
770287 GTGTGTACAA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:770714 original size:123 final size:124
Alignment explanation
Indices: 770579--770817 Score: 444
Period size: 124 Copynumber: 1.9 Consensus size: 124
770569 ATAATGAATA
*
770579 AAATCATCAATTT-CAAATTTTAACATAAAAATTTTAAATTAATAAAGTTAGAATTTAAATTGAA
1 AAATCATCAATTTCCAAATTTTAACATAAAAATTTTAAATTAATAAAGTTAGAATTTAAACTGAA
770643 TTGTTATGAAAAACTATATAAAATATTTACAAGGAACTTATATTTATCAAAACTATATG
66 TTGTTATGAAAAACTATATAAAATATTTACAAGGAACTTATATTTATCAAAACTATATG
*
770702 AAATCATCAATTTCCAAATTTTAACATAAAAATTTTATATTAATAAAGTTAGAATTTAAACTGAA
1 AAATCATCAATTTCCAAATTTTAACATAAAAATTTTAAATTAATAAAGTTAGAATTTAAACTGAA
*
770767 TTGTTATGAAAAACTATATAAAATATTTACAAGGAGCTTATATTTATCAAA
66 TTGTTATGAAAAACTATATAAAATATTTACAAGGAACTTATATTTATCAAA
770818 TTTAATCTAG
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
123 13 0.12
124 99 0.88
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (124 bp):
AAATCATCAATTTCCAAATTTTAACATAAAAATTTTAAATTAATAAAGTTAGAATTTAAACTGAA
TTGTTATGAAAAACTATATAAAATATTTACAAGGAACTTATATTTATCAAAACTATATG
Found at i:771226 original size:32 final size:32
Alignment explanation
Indices: 771173--771251 Score: 106
Period size: 32 Copynumber: 2.4 Consensus size: 32
771163 ACACTATATG
*
771173 AATTACTTGAATATATTAAAATTTATATAAAATT
1 AATTA-TTGAATATATCAAAATTTATATAAAA-T
*
771207 AATTATT-AATATATCAAAATTTATATAATAT
1 AATTATTGAATATATCAAAATTTATATAAAAT
771238 AATATATTGAATAT
1 AAT-TATTGAATAT
771252 TATTACAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
31 4 0.10
32 25 0.61
33 7 0.17
34 5 0.12
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (32 bp):
AATTATTGAATATATCAAAATTTATATAAAAT
Found at i:771985 original size:18 final size:18
Alignment explanation
Indices: 771962--772027 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
771952 AAATATATAT
771962 ATATATATTATAATTTTA
1 ATATATATTATAATTTTA
*
771980 ATATATATTAAATATTTTA
1 ATATATATTATA-ATTTTA
* * *
771999 A-ATTTATTTTCAATTTAA
1 ATATATATTAT-AATTTTA
772017 ATTATATATTA
1 A-TATATATTA
772028 GGTTTAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
18 23 0.62
19 8 0.22
20 6 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATATATTATAATTTTA
Found at i:772002 original size:26 final size:26
Alignment explanation
Indices: 771953--772003 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
771943 GGGTTTGGAA
*
771953 AATATATATATATATATTATAATTTT
1 AATATATATAAATATATTATAATTTT
*
771979 AATATATATTAAATATTTTA-AATTT
1 AATATATA-TAAATATATTATAATTT
772004 ATTTTCAATT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
AATATATATAAATATATTATAATTTT
Found at i:772504 original size:16 final size:18
Alignment explanation
Indices: 772461--772507 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
772451 AATTTGATAG
772461 TAATT-AAAAATAATTTTA
1 TAATTAAAAAAT-ATTTTA
772479 TAATTAAAAAATATTTTA
1 TAATTAAAAAATATTTTA
772497 -AA-TAAAAAATA
1 TAATTAAAAAATA
772508 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.32
17 2 0.07
18 11 0.39
19 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATTAAAAAATATTTTA
Found at i:772527 original size:10 final size:9
Alignment explanation
Indices: 772507--772531 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
772497 AATAAAAAAT
772507 AAAAAATAA
1 AAAAAATAA
772516 AAAAAATAA
1 AAAAAATAA
772525 AAAAAAT
1 AAAAAAT
772532 TATATTTTTA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:772609 original size:48 final size:47
Alignment explanation
Indices: 772520--772611 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 47
772510 AAATAAAAAA
**
772520 AATAAAAAAAATTATATTTTTATTTTTATTTAAAATTAATTTATAAAT
1 AATAAAAAAAATTATATTTTTATTTAAATTTAAAA-TAATTTATAAAT
772568 AATAAAAAATAATTATA-TTTTATATTAAACTTTAAAA-AATTTAT
1 AATAAAAAA-AATTATATTTTTAT-TTAAA-TTTAAAATAATTTAT
772612 CTAAAGAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
48 22 0.56
49 10 0.26
50 7 0.18
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (47 bp):
AATAAAAAAAATTATATTTTTATTTAAATTTAAAATAATTTATAAAT
Found at i:778014 original size:29 final size:31
Alignment explanation
Indices: 777982--778056 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
777972 AAGGGTAAAC
777982 TATTAAATTTTTTTAAAATTTTA-TA-ATTT
1 TATTAAATTTTTTTAAAATTTTATTATATTT
* *
778011 TATTTAAATAAATTTTTAAATTTTTATTATATTT
1 TA-TTAAAT--TTTTTTAAAATTTTATTATATTT
*
778045 AATTAAATTTTT
1 TATTAAATTTTT
778057 ATCAATTGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
29 2 0.05
30 6 0.16
31 3 0.08
32 13 0.35
33 8 0.22
34 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TATTAAATTTTTTTAAAATTTTATTATATTT
Found at i:778036 original size:32 final size:33
Alignment explanation
Indices: 777991--778052 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
777981 CTATTAAATT
*
777991 TTTTTAAAATTTTATAAT-TTTATTTAAATAAA
1 TTTTTAAAATTTTATAATATTTAATTAAATAAA
* *
778023 TTTTTAAATTTTTATTATATTTAATTAAAT
1 TTTTTAAAATTTTATAATATTTAATTAAAT
778053 TTTTATCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TTTTTAAAATTTTATAATATTTAATTAAATAAA
Found at i:778057 original size:29 final size:31
Alignment explanation
Indices: 777991--778057 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
777981 CTATTAAATT
*
777991 TTTTTAAAATTTTATAATTTTATTTAAATAAA
1 TTTTT-AAATTTTATAATTATATTTAAATAAA
*
778023 TTTTTAAATTTT-T-ATTATATTTAATTAAA
1 TTTTTAAATTTTATAATTATATTTAAATAAA
778052 TTTTTA
1 TTTTTA
778058 TCAATTGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 20 0.61
30 1 0.03
31 7 0.21
32 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTTAAATTTTATAATTATATTTAAATAAA
Found at i:778134 original size:18 final size:19
Alignment explanation
Indices: 778094--778134 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
778084 TTTATATCAA
778094 ATAAAATATTAATTTAAAT
1 ATAAAATATTAATTTAAAT
* *
778113 -TAAAA-ATTTATTTAAGT
1 ATAAAATATTAATTTAAAT
778130 ATAAA
1 ATAAA
778135 TTAAAAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATAAAATATTAATTTAAAT
Found at i:778147 original size:29 final size:29
Alignment explanation
Indices: 778109--778174 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 29
778099 ATATTAATTT
* *
778109 AAATTAAAAATTTATTTAAGTATAAATTAA
1 AAATTAAAATTTTATTTAA-TAAAAATTAA
*
778139 AAGTTAAAATTTTATTTAATAAAAATTAA
1 AAATTAAAATTTTATTTAATAAAAATTAA
778168 AAATTAA
1 AAATTAA
778175 TTTAAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
AAATTAAAATTTTATTTAATAAAAATTAA
Found at i:778161 original size:22 final size:23
Alignment explanation
Indices: 778131--778185 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
778121 TATTTAAGTA
* * *
778131 TAAATTAAAAGTTAAAATTTTATT
1 TAAA-TAAAAATTAAAAATTAATT
778155 T-AATAAAAATTAAAAATTAATT
1 TAAATAAAAATTAAAAATTAATT
778177 TAAATAAAA
1 TAAATAAAA
778186 TTATTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.63
23 9 0.33
24 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAATAAAAATTAAAAATTAATT
Found at i:778170 original size:23 final size:22
Alignment explanation
Indices: 778092--778185 Score: 66
Period size: 23 Copynumber: 4.1 Consensus size: 22
778082 TTTTTATATC
*
778092 AAATAAAATATTAATTTAAATTAA
1 AAATTAAA-ATTAATTTAAA-TAA
* * *
778116 AAATT-TATTTAAGTATAAATTAA
1 AAATTAAAATTAA-TTTAAA-TAA
* *
778139 AAGTTAAAATTTTATTT-AATAA
1 AAATTAAAA-TTAATTTAAATAA
778161 AAATTAAAAATTAATTTAAATAA
1 AAATT-AAAATTAATTTAAATAA
778184 AA
1 AA
778186 TTATTAAATT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
22 17 0.31
23 27 0.50
24 7 0.13
25 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATTAAAATTAATTTAAATAA
Done.