Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold82
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: 2626005
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 196346 characters in sequence are not A, C, G, or T
File 4 of 17
Found at i:425143 original size:23 final size:22
Alignment explanation
Indices: 425104--425155 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
425094 ATATTTTATT
* *
425104 TAAATTTAATTATAAAATAATA
1 TAAATTTAATAAGAAAATAATA
425126 TAAATATTAATAAGAAAATAATA
1 TAAAT-TTAATAAGAAAATAATA
425149 TAAATTT
1 TAAATTT
425156 TGAAGGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATTTAATAAGAAAATAATA
Found at i:428173 original size:18 final size:18
Alignment explanation
Indices: 428146--428180 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
428136 ATATTCAACA
428146 ATATAAATGATTATATAT
1 ATATAAATGATTATATAT
*
428164 ATATATATGATTATATA
1 ATATAAATGATTATATA
428181 AAATAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
ATATAAATGATTATATAT
Found at i:429672 original size:2 final size:2
Alignment explanation
Indices: 429665--429711 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
429655 AATGCCTAAA
429665 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
429707 GAT AT
1 -AT AT
429712 GCAAATGTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:430506 original size:2 final size:2
Alignment explanation
Indices: 430499--430535 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
430489 ATAAGAAAGC
430499 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 A
430536 ATTGAATTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:430865 original size:23 final size:24
Alignment explanation
Indices: 430839--430894 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 24
430829 TGAAGTTTGA
* * *
430839 ATTTTAATATTTATAGTTTTTT-T
1 ATTTTAAAAATTATAATTTTTTAT
430862 A-TTTAAAAATTATAATTTTTTAT
1 ATTTTAAAAATTATAATTTTTTAT
430885 A--TTAAAAATT
1 ATTTTAAAAATT
430895 TTAAAAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
ATTTTAAAAATTATAATTTTTTAT
Found at i:432943 original size:2 final size:2
Alignment explanation
Indices: 432936--432982 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
432926 GAATTTCTGC
* * * *
432936 AT AT AT AT AC AT AC AT AC 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 AT AT AT AT
432978 AT AT A
1 AT AT A
432983 AATAAGGGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:434276 original size:12 final size:13
Alignment explanation
Indices: 434251--434275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
434241 GAAATGCGCC
434251 CAATTTTTAAAAA
1 CAATTTTTAAAAA
434264 CAATTTTTAAAA
1 CAATTTTTAAAA
434276 CCCAAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
CAATTTTTAAAAA
Found at i:436543 original size:20 final size:21
Alignment explanation
Indices: 436500--436549 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 21
436490 GATCAATTCA
436500 TTCTTATTATAAATGATATTTT
1 TTCTTATTATAAATGATA-TTT
436522 TTCTATATTATAAAT-ATATTT
1 TTCT-TATTATAAATGATATTT
436543 TT-TTATT
1 TTCTTATT
436550 CAAATATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.15
20 1 0.04
21 5 0.19
22 7 0.26
23 10 0.37
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTCTTATTATAAATGATATTT
Found at i:436546 original size:23 final size:22
Alignment explanation
Indices: 436500--436545 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
436490 GATCAATTCA
436500 TTCTTATTATAAATGATATTTT
1 TTCTTATTATAAATGATATTTT
436522 TTCTATATTATAAAT-ATATTTT
1 TTCT-TATTATAAATGATATTTT
436544 TT
1 TT
436546 TATTCAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (22 bp):
TTCTTATTATAAATGATATTTT
Found at i:442856 original size:15 final size:14
Alignment explanation
Indices: 442820--442859 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
442810 TTTTGGTATA
442820 TTAAAATTT-ATTT
1 TTAAAATTTAATTT
*
442833 TTAAGATTTAATTT
1 TTAAAATTTAATTT
442847 TTAATAATTTAAT
1 TTAA-AATTTAAT
442860 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 8 0.35
14 8 0.35
15 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
TTAAAATTTAATTT
Found at i:442989 original size:25 final size:26
Alignment explanation
Indices: 442950--443004 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
442940 TTTTATGATA
442950 AAAATTACATAATA-TATAAAAATAT
1 AAAATTACATAATATTATAAAAATAT
*
442975 AAAATTA-ATATATATTATAAAATTAT
1 AAAATTACATA-ATATTATAAAAATAT
443001 AAAA
1 AAAA
443005 CAGGCTGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.11
25 10 0.37
26 14 0.52
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAATTACATAATATTATAAAAATAT
Found at i:443776 original size:40 final size:37
Alignment explanation
Indices: 443729--443820 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 37
443719 TGAATTGAAT
* *
443729 TTTAATTTTAATTTTAATTTTTTAATTTAAATAAATTTAA
1 TTTAATTTTAATTTTAATTGTTTAA--TAAAAAAATTT-A
*
443769 TTTAATTTGAA--TT-ATTGTTTAATAAAAAAATTTA
1 TTTAATTTTAATTTTAATTGTTTAATAAAAAAATTTA
* *
443803 TTTAAATTTAATTATAAT
1 TTTAATTTTAATTTTAAT
443821 AATATATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
34 10 0.23
35 10 0.23
36 1 0.02
37 10 0.23
38 2 0.05
40 10 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (37 bp):
TTTAATTTTAATTTTAATTGTTTAATAAAAAAATTTA
Found at i:443840 original size:22 final size:21
Alignment explanation
Indices: 443805--443845 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
443795 AAAATTTATT
443805 TAAATTTAATTATAATAATATA
1 TAAATTTAATTATAA-AATATA
443827 TAAATGTTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
443846 ATTTTTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:444433 original size:23 final size:23
Alignment explanation
Indices: 444393--444437 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
444383 GAAAATAATA
444393 ATTTTATGTTAAAATAATTATAT
1 ATTTTATGTTAAAATAATTATAT
*
444416 ATTTTAT-TTAAATTTAATTATA
1 ATTTTATGTTAAA-ATAATTATA
444438 AAATATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTTATGTTAAAATAATTATAT
Found at i:444511 original size:19 final size:18
Alignment explanation
Indices: 444484--444519 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
444474 AAAATAAACA
*
444484 GTAATTCAAATTTAAATTC
1 GTAAATCAAA-TTAAATTC
444503 GTAAATCAAATTAAATT
1 GTAAATCAAATTAAATT
444520 AAATTCGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (18 bp):
GTAAATCAAATTAAATTC
Found at i:445517 original size:20 final size:21
Alignment explanation
Indices: 445479--445529 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
445469 TTTGACAATT
*
445479 TTTTCATAACTTTCAATATAA
1 TTTTAATAACTTTCAATATAA
* *
445500 TTTTAATAA-TTTCTATATAG
1 TTTTAATAACTTTCAATATAA
*
445520 TTTTGATAAC
1 TTTTAATAAC
445530 AATTGATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTTAATAACTTTCAATATAA
Found at i:445794 original size:21 final size:20
Alignment explanation
Indices: 445743--445798 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
445733 AGCTTTGATG
*
445743 ATTTTGATAATCTTTGATATA
1 ATTTT-ATAATTTTTGATATA
* *
445764 ATTGTCATAATTTTTTATATA
1 ATT-TTATAATTTTTGATATA
445785 AGTTTTATAATTTT
1 A-TTTTATAATTTT
445799 GGTTTTGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.57
Consensus pattern (20 bp):
ATTTTATAATTTTTGATATA
Found at i:445923 original size:42 final size:42
Alignment explanation
Indices: 445862--445960 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
445852 TAACATGTAA
* *
445862 TTTTAATAAACTTAT-ATATAAAATTTGAAAAAATTTTA-ATAG
1 TTTTAAT-AACTTTTAATAT-AAATTTGAAAAAATTTAATATAG
* ** * *
445904 TTTTGATAACTTTTAATATAGTTTTGACAATATTTAATATAG
1 TTTTAATAACTTTTAATATAAATTTGAAAAAATTTAATATAG
445946 TTTTAATAACTTTTA
1 TTTTAATAACTTTTA
445961 TAGCTATTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
41 19 0.40
42 28 0.60
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.48
Consensus pattern (42 bp):
TTTTAATAACTTTTAATATAAATTTGAAAAAATTTAATATAG
Found at i:445926 original size:21 final size:21
Alignment explanation
Indices: 445900--445960 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
445890 AAAAATTTTA
445900 ATAGTTTTGATAACTTTTAAT
1 ATAGTTTTGATAACTTTTAAT
*
445921 ATAGTTTTGACAA-TATTTAAT
1 ATAGTTTTGATAACT-TTTAAT
*
445942 ATAGTTTTAATAACTTTTA
1 ATAGTTTTGATAACTTTTA
445961 TAGCTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (21 bp):
ATAGTTTTGATAACTTTTAAT
Found at i:446228 original size:21 final size:20
Alignment explanation
Indices: 446195--446238 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
446185 ATTCCTTTAT
* *
446195 TTTTGTAATTTTTTATATTA
1 TTTTGTAAATTTTTATATAA
*
446215 TTTTGATAAATTTTTTTATAA
1 TTTTG-TAAATTTTTATATAA
446236 TTT
1 TTT
446239 ATATAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTGTAAATTTTTATATAA
Found at i:446441 original size:21 final size:22
Alignment explanation
Indices: 446409--446464 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
446399 TATAATAAAT
*
446409 TTTG-ATATCATTTGCAATAA-
1 TTTGAATAACATTTGCAATAAC
*
446429 TTTGAATAACATTTGTAATAAC
1 TTTGAATAACATTTGCAATAAC
*
446451 TTT-AATAACTTTTG
1 TTTGAATAACATTTG
446465 ATACTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 24 0.77
22 3 0.10
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (22 bp):
TTTGAATAACATTTGCAATAAC
Found at i:446870 original size:21 final size:21
Alignment explanation
Indices: 446844--446943 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
446834 GAATTTGACC
*
446844 ATTTTTTATATAGTTTTAATA
1 ATTTTTTATATAATTTTAATA
* *
446865 ATTTTTAATATAA--TTGATA
1 ATTTTTTATATAATTTTAATA
** * *
446884 ACATTTAATATAATTTTGATA
1 ATTTTTTATATAATTTTAATA
* * *
446905 ATATTCTATATAAGTTTAATA
1 ATTTTTTATATAATTTTAATA
446926 ATTTTTTTATATAATTTT
1 A-TTTTTTATATAATTTT
446944 TTTTTGTAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
19 16 0.25
21 34 0.54
22 13 0.21
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTTTTTATATAATTTTAATA
Found at i:447020 original size:21 final size:21
Alignment explanation
Indices: 446996--447081 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
446986 TTTTATTTAC
*
446996 TTTTAATACAATTTTGATAAT
1 TTTTAATATAATTTTGATAAT
* *
447017 TTTTGATATACTTTTG-TAAT
1 TTTTAATATAATTTTGATAAT
** *
447037 AATTTTAATAATCGTTTTGTTAAT
1 --TTTTAAT-ATAATTTTGATAAT
* *
447061 TTTTTATATAATTTTAATAAT
1 TTTTAATATAATTTTGATAAT
447082 ATTCATAATA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
20 4 0.08
21 23 0.46
22 12 0.24
23 7 0.14
24 4 0.08
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTTAATATAATTTTGATAAT
Found at i:447096 original size:42 final size:44
Alignment explanation
Indices: 447007--447110 Score: 122
Period size: 42 Copynumber: 2.4 Consensus size: 44
446997 TTTAATACAA
* * * * *
447007 TTTTGATAATTTTTGATATACTTTTGTAATAATTTTAATAATCG
1 TTTTGTTAATTTTTTATATACATTTGTAATAATATTAATAATAG
*
447051 TTTTGTTAATTTTTTATATA-ATTT-TAATAATATTCATAATAG
1 TTTTGTTAATTTTTTATATACATTTGTAATAATATTAATAATAG
*
447093 TTTTATATAATTTTTTAT
1 TTTTGT-TAATTTTTTAT
447111 CAAAAAATGT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 20 0.38
43 14 0.27
44 18 0.35
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.59
Consensus pattern (44 bp):
TTTTGTTAATTTTTTATATACATTTGTAATAATATTAATAATAG
Found at i:450548 original size:29 final size:32
Alignment explanation
Indices: 450502--450624 Score: 134
Period size: 29 Copynumber: 3.9 Consensus size: 32
450492 AGTTACTCTA
*
450502 ATAATATTAAAATTA-TTATA-TATATTTATAT
1 ATAATATT-TAATTATTTATATTATATTTATAT
450533 A-AAT-TTTAATATATTATATATTTATATTTATAT
1 ATAATATTTAAT-TATT-TATA-TTATATTTATAT
*
450566 ATCATATTTAATTATTTATA-T-T-TTTATAT
1 ATAATATTTAATTATTTATATTATATTTATAT
*
450595 ATTATATTTAATTATTTATATTATATTTAT
1 ATAATATTTAATTATTTATATTATATTTAT
450625 GTTATATTTA
Statistics
Matches: 79, Mismatches: 3, Indels: 19
0.78 0.03 0.19
Matches are distributed among these distances:
28 3 0.04
29 30 0.38
30 6 0.08
31 7 0.09
32 5 0.06
33 16 0.20
34 6 0.08
35 6 0.08
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.59
Consensus pattern (32 bp):
ATAATATTTAATTATTTATATTATATTTATAT
Found at i:450564 original size:19 final size:20
Alignment explanation
Indices: 450515--450631 Score: 93
Period size: 19 Copynumber: 6.0 Consensus size: 20
450505 ATATTAAAAT
*
450515 TATTATATATAT-TTATATA
1 TATTATATTTATATTATATA
* * *
450534 AATTTTA-ATATATTATATA
1 TATTATATTTATATTATATA
450553 T-TTATATTTATA-TATCATA
1 TATTATATTTATATTAT-ATA
*
450572 T-TTAATTATTTATATTTTTATA
1 TATT-A-TATTTATA-TTATATA
*
450594 TATTATATTTA-ATTATTTA
1 TATTATATTTATATTATATA
*
450613 TATTATATTTATGTTATAT
1 TATTATATTTATATTATAT
450632 TTAAAATTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
18 11 0.14
19 38 0.48
20 7 0.09
21 14 0.18
22 5 0.06
23 4 0.05
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (20 bp):
TATTATATTTATATTATATA
Found at i:451120 original size:41 final size:41
Alignment explanation
Indices: 451075--451186 Score: 106
Period size: 41 Copynumber: 2.8 Consensus size: 41
451065 AGGTCTTGTC
451075 AATTATTATTTAAATAATAAAAATATTTTTATTTAAATTTA
1 AATTATTATTTAAATAATAAAAATATTTTTATTTAAATTTA
* * ** *
451116 AATTATAAATATT-AAT-ATAAAAATATATTT-TTTATTTTTT
1 AATTAT-TAT-TTAAATAATAAAAATATTTTTATTTAAATTTA
* *
451156 TATTATT-TTTAAATAATAAAATAAATTTTTA
1 AATTATTATTTAAATAATAAAA-ATATTTTTA
451187 AATTTAATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
37 2 0.04
38 4 0.07
39 6 0.11
40 18 0.32
41 19 0.34
42 5 0.09
43 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (41 bp):
AATTATTATTTAAATAATAAAAATATTTTTATTTAAATTTA
Found at i:454163 original size:3 final size:3
Alignment explanation
Indices: 454151--454196 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
454141 ATTACCTAAC
454151 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
454197 TAGTAAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:456150 original size:27 final size:28
Alignment explanation
Indices: 456106--456161 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
456096 AATAAATCTA
** * *
456106 TAATTTTTTTGTTATATATTTAAAGATT
1 TAATTTTTTTCATATATAATTAAACATT
456134 TAATTTTTTTCAT-TATAATTAAACATT
1 TAATTTTTTTCATATATAATTAAACATT
456161 T
1 T
456162 TACATTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (28 bp):
TAATTTTTTTCATATATAATTAAACATT
Found at i:456163 original size:28 final size:28
Alignment explanation
Indices: 456106--456161 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
456096 AATAAATCTA
* *
456106 TAATTTTTTTGTTATATATTTAAAGATT
1 TAATTTTTTTATTATATATTTAAACATT
456134 TAATTTTTTTCATTATA-A-TTAAACATT
1 TAATTTTTTT-ATTATATATTTAAACATT
456161 T
1 T
456162 TACATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.36
28 11 0.44
29 5 0.20
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (28 bp):
TAATTTTTTTATTATATATTTAAACATT
Found at i:459681 original size:19 final size:16
Alignment explanation
Indices: 459637--459683 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
459627 TTTGAAAATG
459637 ATTATAATAATATAAT
1 ATTATAATAATATAAT
459653 ATTA-ATATAATATGAAT
1 ATTATA-ATAATAT-AAT
459670 ATATATACATAATA
1 AT-TATA-ATAATA
459684 AATTATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.04
16 11 0.42
17 5 0.19
18 2 0.08
19 7 0.27
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATTATAATAATATAAT
Found at i:459738 original size:20 final size:18
Alignment explanation
Indices: 459691--459739 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
459681 ATAAATTATT
* *
459691 TAAATTTTAAAATTTATA
1 TAAATTATAAAATTTAAA
459709 TAAATATATAAAATTTTAAA
1 TAAAT-TATAAAA-TTTAAA
459729 TATAATTATAA
1 TA-AATTATAA
459740 TATATGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 6 0.23
20 12 0.46
21 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTATAAAATTTAAA
Found at i:460018 original size:2 final size:2
Alignment explanation
Indices: 459967--459998 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
459957 TTTAATCCTG
459967 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
459999 AAAGGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:460292 original size:9 final size:9
Alignment explanation
Indices: 460265--460329 Score: 53
Period size: 9 Copynumber: 6.9 Consensus size: 9
460255 ATATAAACAC
*
460265 AATATATATG
1 AATATAT-TA
460275 AAT-TATTA
1 AATATATTA
460283 AATATATTA
1 AATATATTA
*
460292 AA-ATTTTA
1 AATATATTA
460300 AATATAAATATA
1 AATAT--AT-TA
460312 ATATATATTA
1 A-ATATATTA
460322 AATATATT
1 AATATATT
460330 GTACTGATTG
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
8 11 0.24
9 19 0.41
10 6 0.13
11 3 0.07
12 3 0.07
13 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (9 bp):
AATATATTA
Found at i:460538 original size:2 final size:2
Alignment explanation
Indices: 460525--460558 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
460515 CCTGAGCATG
*
460525 AT AT AT AC 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
460559 GCATATCCTT
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:460962 original size:16 final size:15
Alignment explanation
Indices: 460941--460989 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
460931 AAGTAAAGCT
460941 TACATATACGTATACA
1 TACATATAC-TATACA
*
460957 TACATATACATATACG
1 TACATATAC-TATACA
*
460973 TATATATA-TATACA
1 TACATATACTATACA
460987 TAC
1 TAC
460990 CCTTTATGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 7 0.25
16 21 0.75
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (15 bp):
TACATATACTATACA
Found at i:460969 original size:22 final size:20
Alignment explanation
Indices: 460941--460988 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 20
460931 AAGTAAAGCT
460941 TACATATACGTATACATACATA
1 TACATATACGTAT--ATACATA
*
460963 TACATATACGTATATATATA
1 TACATATACGTATATACATA
460983 TACATA
1 TACATA
460989 CCCTTTATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.48
22 13 0.52
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (20 bp):
TACATATACGTATATACATA
Found at i:461054 original size:2 final size:2
Alignment explanation
Indices: 461047--461080 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
461037 TCTAATAGTA
461047 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
461081 GGCAACAGAC
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:462398 original size:21 final size:21
Alignment explanation
Indices: 462351--462404 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
462341 CTTTATTTTT
*
462351 ATAAAATTTATAAACATTAAA
1 ATAATATTTATAAACATTAAA
*
462372 ATTAATATTT-TAAACATATTAA
1 A-TAATATTTATAAACAT-TAAA
*
462394 ATAATAATTAT
1 ATAATATTTAT
462405 TATATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATATTTATAAACATTAAA
Found at i:463389 original size:42 final size:42
Alignment explanation
Indices: 463326--463405 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
463316 GAAAAAGACC
*
463326 CATTGTAATGTGTAAGGCTTTAGCCTTATTTTCCTCTTCACT
1 CATTGTAATGTGTAAGGCTTTAGCCCTATTTTCCTCTTCACT
* *
463368 CATTGTAATGTGTTAGTCTTTAGCCCTATTTTCCTCTT
1 CATTGTAATGTGTAAGGCTTTAGCCCTATTTTCCTCTT
463406 TACTGTCTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.47
Consensus pattern (42 bp):
CATTGTAATGTGTAAGGCTTTAGCCCTATTTTCCTCTTCACT
Found at i:467871 original size:2 final size:2
Alignment explanation
Indices: 467864--467897 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
467854 TCTCCCGGTA
467864 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
467898 TTGCTGACGG
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:470992 original size:36 final size:36
Alignment explanation
Indices: 470951--471020 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
470941 TAAAAGGTTG
*
470951 TCTTATTTAATGAGATTTAAATTATTAATAATAATA
1 TCTTATTTAATGAGATTTAAATTACTAATAATAATA
* *
470987 TCTTATTTAATGGGATTTAAATTACTAGTAATAA
1 TCTTATTTAATGAGATTTAAATTACTAATAATAA
471021 CAGTAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (36 bp):
TCTTATTTAATGAGATTTAAATTACTAATAATAATA
Found at i:471315 original size:19 final size:19
Alignment explanation
Indices: 471291--471327 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
471281 ATTGTTCTGC
471291 GAATGACTTGTTTCATGAA
1 GAATGACTTGTTTCATGAA
*
471310 GAATGATTTGTTTCATGA
1 GAATGACTTGTTTCATGA
471328 GAAAATTGTT
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:0.30, C:0.08, G:0.22, T:0.41
Consensus pattern (19 bp):
GAATGACTTGTTTCATGAA
Found at i:471338 original size:16 final size:18
Alignment explanation
Indices: 471298--471338 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
471288 TGCGAATGAC
*
471298 TTGTTTCATGAAGAATGAT
1 TTGTTTCATGAAGAA-GAA
471317 TTGTTTCATG-AGAA-AA
1 TTGTTTCATGAAGAAGAA
471333 TTGTTT
1 TTGTTT
471339 TGAACAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 7 0.33
18 4 0.19
19 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.46
Consensus pattern (18 bp):
TTGTTTCATGAAGAAGAA
Found at i:471394 original size:16 final size:16
Alignment explanation
Indices: 471375--471455 Score: 110
Period size: 16 Copynumber: 5.1 Consensus size: 16
471365 AGTTTTGAAC
*
471375 ATAAATTGTTTTAAAT
1 ATAAATTATTTTAAAT
471391 ATAAATTATTTTAAAT
1 ATAAATTATTTTAAAT
*
471407 A-AAATTTATTTTGAAT
1 ATAAA-TTATTTTAAAT
*
471423 ATAAATTATTTTAATT
1 ATAAATTATTTTAAAT
*
471439 ATAAATTATTTTGAAT
1 ATAAATTATTTTAAAT
471455 A
1 A
471456 GAAACTGTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
15 3 0.05
16 51 0.89
17 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (16 bp):
ATAAATTATTTTAAAT
Found at i:471424 original size:32 final size:31
Alignment explanation
Indices: 471377--471474 Score: 115
Period size: 32 Copynumber: 3.1 Consensus size: 31
471367 TTTTGAACAT
* *
471377 AAATTGTTTTAAATATAAATTATTTTAAATA
1 AAATTATTTTGAATATAAATTATTTTAAATA
*
471408 AAATTTATTTTGAATATAAATTATTTTAATTA
1 AAA-TTATTTTGAATATAAATTATTTTAAATA
* * * *
471440 TAAATTATTTTGAATAGAAACTGTTTTGAATA
1 -AAATTATTTTGAATATAAATTATTTTAAATA
471472 AAA
1 AAA
471475 GTTACTCTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
31 6 0.11
32 48 0.84
33 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (31 bp):
AAATTATTTTGAATATAAATTATTTTAAATA
Found at i:471467 original size:48 final size:48
Alignment explanation
Indices: 471366--471471 Score: 142
Period size: 48 Copynumber: 2.2 Consensus size: 48
471356 CATAATAATA
* * *
471366 GTTTTGAACATAAATTGTTTTAAATATAAATTATTTTAAATAAAATTT
1 GTTTTGAATATAAATTATTTTAAATATAAATTATTTTAAATAAAATCT
* * *
471414 ATTTTGAATATAAATTATTTTAATTATAAATTATTTTGAATAGAAA-CT
1 GTTTTGAATATAAATTATTTTAAATATAAATTATTTTAAATA-AAATCT
471462 GTTTTGAATA
1 GTTTTGAATA
471472 AAAGTTACTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 47 0.94
49 3 0.06
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (48 bp):
GTTTTGAATATAAATTATTTTAAATATAAATTATTTTAAATAAAATCT
Found at i:472168 original size:2 final size:2
Alignment explanation
Indices: 472161--472190 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
472151 ATAATAAGAA
472161 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
472191 CAAAAGAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:472582 original size:22 final size:22
Alignment explanation
Indices: 472556--472597 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
472546 AATTTAAAAT
472556 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
472578 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
472598 CATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:472740 original size:17 final size:17
Alignment explanation
Indices: 472713--472767 Score: 67
Period size: 16 Copynumber: 3.1 Consensus size: 17
472703 TGAAGTCAAT
*
472713 ATTTCATTTAAAATAAAG
1 ATTT-ATTTAAAATAAAA
472731 ATTTATTT-AAATAAAA
1 ATTTATTTAAAATAAAA
472747 ATTTATTTAAATATAATAA
1 ATTTATTTAAA-ATAA-AA
472766 AT
1 AT
472768 ATAAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 15 0.45
17 6 0.18
18 8 0.24
19 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTTATTTAAAATAAAA
Found at i:473233 original size:24 final size:25
Alignment explanation
Indices: 473187--473247 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
473177 TTTAATATAA
**
473187 ATATATTTAAAATTTTAATTTTT-T
1 ATATATTTAAAAAATTAATTTTTAT
473211 ATATATTTAAAAAATTATATTTTATAT
1 ATATATTTAAAAAATTA-ATTTT-TAT
*
473238 TTATATTTAA
1 ATATATTTAA
473248 GTATACGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.48
25 5 0.16
26 1 0.03
27 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATATATTTAAAAAATTAATTTTTAT
Found at i:473292 original size:22 final size:23
Alignment explanation
Indices: 473257--473307 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
473247 AGTATACGAT
473257 AAAAATAAAATAATATAA-ATTAA
1 AAAAATAAAATAATA-AATATTAA
*
473280 AAAAAT-AATTAATAAATATTAA
1 AAAAATAAAATAATAAATATTAA
473302 AAAAAT
1 AAAAAT
473308 TTATATAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 2 0.08
22 18 0.69
23 6 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAAATAAAATAATAAATATTAA
Found at i:473315 original size:21 final size:21
Alignment explanation
Indices: 473267--473316 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
473257 AAAAATAAAA
473267 TAATATAA-ATTAAAAAAATAAT
1 TAATA-AATATTAAAAAAAT-AT
473289 TAATAAATATTAAAAAAAT-T
1 TAATAAATATTAAAAAAATAT
473309 TATATAAA
1 TA-ATAAA
473317 GAATACCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 16 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TAATAAATATTAAAAAAATAT
Found at i:473359 original size:16 final size:15
Alignment explanation
Indices: 473324--473359 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
473314 AAAGAATACC
473324 TAAATTTAAAATTAT
1 TAAATTTAAAATTAT
*
473339 AAAATTTAAAATTTAT
1 TAAATTTAAAA-TTAT
473355 TAAAT
1 TAAAT
473360 ATTATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTTAAAATTAT
Found at i:475013 original size:20 final size:18
Alignment explanation
Indices: 474988--475028 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
474978 ATAAGATTTA
474988 TTTAATTTATAAGTAAAAAT
1 TTTAATTT-T-AGTAAAAAT
*
475008 TTTAATTTTATTAAAAAT
1 TTTAATTTTAGTAAAAAT
475026 TTT
1 TTT
475029 TGTTATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 1 0.05
20 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TTTAATTTTAGTAAAAAT
Found at i:476183 original size:27 final size:28
Alignment explanation
Indices: 476141--476193 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
476131 TTAACATCGT
* *
476141 TAAATTTTAAATTAATATATAATAAAAA
1 TAAAATTTAAATTAATAAATAATAAAAA
*
476169 TAAAATTTAAA-TAATAAATTATAAA
1 TAAAATTTAAATTAATAAATAATAAA
476194 TTTTTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAAATTTAAATTAATAAATAATAAAAA
Found at i:476200 original size:23 final size:23
Alignment explanation
Indices: 476174--476218 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
476164 AAAAATAAAA
476174 TTTAAATAATAAATTATAAATTT
1 TTTAAATAATAAATTATAAATTT
*
476197 TTTAAATATTAAATTATAAATT
1 TTTAAATAATAAATTATAAATT
476219 GAGTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAAATAATAAATTATAAATTT
Found at i:476441 original size:2 final size:2
Alignment explanation
Indices: 476434--476465 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
476424 ACCCTTATAA
476434 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
476466 GCTGTTTCTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:481351 original size:2 final size:2
Alignment explanation
Indices: 481344--481387 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
481334 TTGTTGGGGC
481344 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
481386 TA
1 TA
481388 ATCTTTGTCC
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):
TA
Found at i:481976 original size:32 final size:32
Alignment explanation
Indices: 481938--482024 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
481928 AATTTGATGA
*
481938 ATTAAATATAATTATTCGTAAATTTAATAAAT
1 ATTAAATATAATTATTCATAAATTTAATAAAT
* *
481970 ATTAAATAAAATTATTTATAAATTTAATAAAT
1 ATTAAATATAATTATTCATAAATTTAATAAAT
** *
482002 ATTATGTATAATTACTCATAAAT
1 ATTAAATATAATTATTCATAAAT
482025 ATGGTAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (32 bp):
ATTAAATATAATTATTCATAAATTTAATAAAT
Found at i:482005 original size:22 final size:23
Alignment explanation
Indices: 481959--482012 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
481949 TTATTCGTAA
481959 ATTTAATAAATATTAAATAAAATT
1 ATTT-ATAAATATTAAATAAAATT
481983 ATTTATAAAT-TT-AATAAATATT
1 ATTTATAAATATTAAATAAA-ATT
*
482005 ATGTATAA
1 ATTTATAA
482013 TTACTCATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 6 0.21
22 12 0.43
23 6 0.21
24 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTTATAAATATTAAATAAAATT
Found at i:483137 original size:11 final size:11
Alignment explanation
Indices: 483121--483158 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
483111 TTTAATATAA
483121 AAATATTTTTT
1 AAATATTTTTT
483132 AAATATTTTTT
1 AAATATTTTTT
* *
483143 TAATATATTTT
1 AAATATTTTTT
483154 AAATA
1 AAATA
483159 ATAAAATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AAATATTTTTT
Found at i:483150 original size:13 final size:12
Alignment explanation
Indices: 483121--483153 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
483111 TTTAATATAA
483121 AAATA-TTTTTT
1 AAATATTTTTTT
483132 AAATATTTTTTT
1 AAATATTTTTTT
483144 AATATATTTT
1 AA-ATATTTT
483154 AAATAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 8 0.40
13 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AAATATTTTTTT
Found at i:484103 original size:20 final size:19
Alignment explanation
Indices: 484078--484123 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
484068 TATAAAAGAA
484078 AATTTTTCCAAAAGAATGGT
1 AATTTTTCCAAAA-AATGGT
** *
484098 AATTTTTTTAAAAAGTGGT
1 AATTTTTCCAAAAAATGGT
484117 AATTTTT
1 AATTTTT
484124 TTAAGAGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (19 bp):
AATTTTTCCAAAAAATGGT
Found at i:485249 original size:18 final size:19
Alignment explanation
Indices: 485228--485265 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
485218 ATAGCCATTA
485228 TATT-CAATATATCGATAC
1 TATTACAATATATCGATAC
*
485246 TATTCACAATGTATCGATAC
1 TATT-ACAATATATCGATAC
485266 ATGAACAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (19 bp):
TATTACAATATATCGATAC
Found at i:486035 original size:29 final size:31
Alignment explanation
Indices: 485976--486036 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
485966 ATTTAACGCA
**
485976 ATAATACTAAATATAATTAAAAATTTTATAT
1 ATAATACTAAATATAATTAAAAATAGTATAT
486007 ATAATA-TAAATATAA-T-AAAATAAGTATAT
1 ATAATACTAAATATAATTAAAAAT-AGTATAT
486036 A
1 A
486037 CATTCTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 7 0.26
30 9 0.33
31 6 0.22
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (31 bp):
ATAATACTAAATATAATTAAAAATAGTATAT
Found at i:486720 original size:20 final size:20
Alignment explanation
Indices: 486695--486747 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
486685 AAACCCTTGA
* *
486695 ATGTATCGATATACACCTAG
1 ATGTATCGATACACACCCAG
486715 ATGTATCGATACACACCCAG
1 ATGTATCGATACACACCCAG
*
486735 ATGTATCCATACA
1 ATGTATCGATACA
486748 TGCTGTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (20 bp):
ATGTATCGATACACACCCAG
Found at i:486803 original size:21 final size:19
Alignment explanation
Indices: 486755--486809 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
486745 ACATGCTGTT
**
486755 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGGACA
*
486774 TTATATCGATACATGGACAAA
1 TTGTATCGATACATGGAC--A
486795 TTGTATCGATACATG
1 TTGTATCGATACATG
486810 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATGGACA
Found at i:487703 original size:20 final size:21
Alignment explanation
Indices: 487668--487706 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
487658 TATAAATATT
*
487668 TTTATAATATTATTTATTTAA
1 TTTATAATAATATTTATTTAA
487689 TTTATAA-AATATTTATTT
1 TTTATAATAATATTTATTT
487707 TTTAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATAATAATATTTATTTAA
Found at i:488654 original size:16 final size:16
Alignment explanation
Indices: 488635--488718 Score: 50
Period size: 16 Copynumber: 5.2 Consensus size: 16
488625 AAATATTTTA
488635 AAATTTTATATAATAT
1 AAATTTTATATAATAT
** *
488651 AAATTATTA-ATTTTTT
1 AAATT-TTATATAATAT
*
488667 AAATTTTATGTGAATAT
1 AAATTTTATAT-AATAT
488684 AAAATATTT-T-TAATAT
1 -AAAT-TTTATATAATAT
*
488700 -AATTATAATATAATAT
1 AAATT-TTATATAATAT
488716 AAA
1 AAA
488719 AGGTAATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 17
0.67 0.11 0.22
Matches are distributed among these distances:
13 1 0.02
14 4 0.08
15 4 0.08
16 26 0.51
17 8 0.16
18 5 0.10
19 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
AAATTTTATATAATAT
Found at i:494920 original size:13 final size:13
Alignment explanation
Indices: 494898--494944 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
494888 ATTTTAATTT
*
494898 TTTATCATAAATA
1 TTTATTATAAATA
*
494911 TTTATTATAATTA
1 TTTATTATAAATA
* *
494924 ATTATAAT-AATA
1 TTTATTATAAATA
494936 TTTATTATA
1 TTTATTATA
494945 TTTATAATGT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTATTATAAATA
Found at i:496007 original size:115 final size:120
Alignment explanation
Indices: 495810--496037 Score: 304
Period size: 124 Copynumber: 1.9 Consensus size: 120
495800 TAAATTTTTA
* *
495810 AGTTTGAGTGAATAATATCTTCAAATAAAATTAATCAAAATTAAAAAAATTCTTTACATAATAAA
1 AGTTTGACTAAATAATATCTTCAAATAAAATTAATCAAAATTAAAAAAA----TTACATAATAAA
*
495875 TAATATATGTAAATTATAAATTTTTAAAAAGTCAGA-TTAAAATTTTATTTTATTTTTCG
62 TAATATATGT-AATTATAAATTTTTAAAAAATCAGAGTTAAAATTTTATTTTATTTTTCG
* * * *
495934 AGTTTGACTAAATTATATCTTTAAATAAATTTAATCAAAATTTAAAAAA-TACATAATAAATAAT
1 AGTTTGACTAAATAATATCTTCAAATAAAATTAATCAAAATTAAAAAAATTACATAATAAATAAT
*
495998 AT-T-T-ATTATAAATTTTTAAAAAATCAGAGTTAGAATTTTA
66 ATATGTAATTATAAATTTTTAAAAAATCAGAGTTAAAATTTTA
496038 CTTTGTCAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
115 23 0.24
116 10 0.11
117 1 0.01
118 1 0.01
119 17 0.18
124 43 0.45
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (120 bp):
AGTTTGACTAAATAATATCTTCAAATAAAATTAATCAAAATTAAAAAAATTACATAATAAATAAT
ATATGTAATTATAAATTTTTAAAAAATCAGAGTTAAAATTTTATTTTATTTTTCG
Found at i:501447 original size:15 final size:15
Alignment explanation
Indices: 501394--501452 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
501384 TTTATTAATT
*
501394 TTAAATTTGAATTATA
1 TTAAATTT-AATTAAA
* * *
501410 TCAACTTTAAATAAA
1 TTAAATTTAATTAAA
501425 TT--ATTTAATTAAA
1 TTAAATTTAATTAAA
501438 TTAAATTTAATTAAA
1 TTAAATTTAATTAAA
501453 ATATAAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
13 11 0.32
15 17 0.50
16 6 0.18
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (15 bp):
TTAAATTTAATTAAA
Found at i:502027 original size:13 final size:12
Alignment explanation
Indices: 501994--502033 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
501984 GATAGTCTTA
501994 AATATAAAAAAT
1 AATATAAAAAAT
502006 CAAT-TAAAAAAT
1 -AATATAAAAAAT
502018 AATATAAAAAAT
1 AATATAAAAAAT
502030 AATA
1 AATA
502034 ATTTAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (12 bp):
AATATAAAAAAT
Found at i:502089 original size:16 final size:16
Alignment explanation
Indices: 502068--502106 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
502058 AAAAAATAAT
* *
502068 AAAATCGGTTAAATTA
1 AAAATCAGTTAAACTA
502084 AAAATCAGTTAAACTA
1 AAAATCAGTTAAACTA
502100 AAAATCA
1 AAAATCA
502107 ATAATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (16 bp):
AAAATCAGTTAAACTA
Found at i:502573 original size:2 final size:2
Alignment explanation
Indices: 502566--502616 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
502556 AGGTTTGTAG
502566 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
*
502608 AT AT GT AT A
1 AT AT AT AT A
502617 CATCTTCTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:502758 original size:13 final size:13
Alignment explanation
Indices: 502740--502765 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
502730 TTCCAAGGGA
502740 TTTTTTTTCTTAT
1 TTTTTTTTCTTAT
502753 TTTTTTTTCTTAT
1 TTTTTTTTCTTAT
502766 GGGCATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTCTTAT
Found at i:503939 original size:4 final size:4
Alignment explanation
Indices: 503930--503961 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
503920 GTAAAACCAA
503930 AAAT AAAT AAAT AAAT AAAT AAAT AAAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAA
503962 CAAAATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:504361 original size:24 final size:25
Alignment explanation
Indices: 504329--504379 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
504319 GATATGATAC
*
504329 AAATATAATATGA-AAAAATAAT-TA
1 AAATATAATACGATAAAAA-AATATA
504353 AAATATAATACGATAAAAAAATATA
1 AAATATAATACGATAAAAAAATATA
504378 AA
1 AA
504380 TAATGACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (25 bp):
AAATATAATACGATAAAAAAATATA
Found at i:504873 original size:39 final size:39
Alignment explanation
Indices: 504823--504953 Score: 113
Period size: 39 Copynumber: 3.2 Consensus size: 39
504813 TTATTAATAC
504823 ATAAAATATTTATTAAATTAAATCATAATAATAAATTAA
1 ATAAAATATTTATTAAATTAAATCATAATAATAAATTAA
* * *
504862 ATAAAATATTTA-TAAATTAAGATAAGATAAAAATATGATATGAA
1 ATAAAATATTTATTAAATTAA-AT--CATAATAATA--A-ATTAA
* * * * *
504906 TATAAAAT-TTTTTTAAATAAAATTATAATAATTAATTAT
1 -ATAAAATATTTATTAAATTAAATCATAATAATAAATTAA
504945 ATAAAATAT
1 ATAAAATAT
504954 AAAATAAATT
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
38 15 0.21
39 18 0.25
40 1 0.01
41 8 0.11
42 7 0.10
43 1 0.01
44 9 0.12
45 14 0.19
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (39 bp):
ATAAAATATTTATTAAATTAAATCATAATAATAAATTAA
Found at i:504911 original size:84 final size:84
Alignment explanation
Indices: 504823--504998 Score: 219
Period size: 84 Copynumber: 2.1 Consensus size: 84
504813 TTATTAATAC
* ** *
504823 ATAAAATATTTATTAAATTAAATCATAATAATAAATTAAATAAAATAT-TTATAAATTAAGATAA
1 ATAAAAT-TTTATTAAATAAAATCATAATAATAAATTAAATAAAATATAAAATAAATTAAAATAA
* *
504887 GATAAAAATATGATATGAAT
65 GATAAAAATATAATATAAAT
* * * * *
504907 ATAAAATTTTTTTAAATAAAATTATAATAATTAATTATATAAAATATAAAATAAATTAAAATATG
1 ATAAAATTTTATTAAATAAAATCATAATAATAAATTAAATAAAATATAAAATAAATTAAAATAAG
*
504972 ATATAAATATAATATAAAT
66 ATAAAAATATAATATAAAT
*
504991 AAAAAATT
1 ATAAAATT
504999 AAAATATAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
83 35 0.45
84 43 0.55
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.37
Consensus pattern (84 bp):
ATAAAATTTTATTAAATAAAATCATAATAATAAATTAAATAAAATATAAAATAAATTAAAATAAG
ATAAAAATATAATATAAAT
Found at i:504979 original size:11 final size:11
Alignment explanation
Indices: 504965--505035 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
504955 AAATAAATTA
*
504965 AAATATGATAT
1 AAATATAATAT
504976 AAATATAATAT
1 AAATATAATAT
* *
504987 AAATAAAAAATT
1 AAATATAATA-T
504999 AAAATATAATAT
1 -AAATATAATAT
* *
505011 AAAAAATAAAAT
1 -AAATATAATAT
*
505023 AAATATGATAT
1 AAATATAATAT
505034 AA
1 AA
505036 TTTAACAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
11 28 0.58
12 12 0.25
13 8 0.17
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (11 bp):
AAATATAATAT
Found at i:504982 original size:35 final size:36
Alignment explanation
Indices: 504943--505027 Score: 111
Period size: 35 Copynumber: 2.4 Consensus size: 36
504933 ATAATTAATT
* *
504943 ATATAAAATATAA-AATAAATTAAAATATGATAT-AA
1 ATATAAAATA-AATAAAAAATTAAAATATAATATAAA
*
504978 ATATAATATAAATAAAAAATTAAAATATAATATAAA
1 ATATAAAATAAATAAAAAATTAAAATATAATATAAA
*
505014 AAATAAAATAAATA
1 ATATAAAATAAATA
505028 TGATATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 2 0.05
35 27 0.63
36 14 0.33
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (36 bp):
ATATAAAATAAATAAAAAATTAAAATATAATATAAA
Found at i:504990 original size:22 final size:19
Alignment explanation
Indices: 504943--505028 Score: 67
Period size: 18 Copynumber: 4.5 Consensus size: 19
504933 ATAATTAATT
504943 ATATAAA-ATATAAAATAA
1 ATATAAATATATAAAATAA
504961 AT-TAAAATATGATATAAATATA
1 ATAT-AAATAT-ATA-AAATA-A
504983 ATATAAATA-A-AAAATTAA
1 ATATAAATATATAAAA-TAA
*
505001 A-ATATAATATAAAAAATAA
1 ATATA-AATATATAAAATAA
505020 A-ATAAATAT
1 ATATAAATAT
505029 GATATAATTT
Statistics
Matches: 58, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
17 4 0.07
18 19 0.33
19 13 0.22
20 8 0.14
21 5 0.09
22 8 0.14
23 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (19 bp):
ATATAAATATATAAAATAA
Found at i:505007 original size:24 final size:27
Alignment explanation
Indices: 504975--505040 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 27
504965 AAATATGATA
*
504975 TAAATATAATATAAA-TAAAA-AATTA
1 TAAATATAATATAAATTAAAATAAATA
505000 -AAATATAATAT-AA--AAAATAAA-A
1 TAAATATAATATAAATTAAAATAAATA
* *
505022 TAAATATGATATAATTTAA
1 TAAATATAATATAAATTAA
505041 CAAATCAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 5 0.15
23 14 0.42
24 12 0.36
26 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
TAAATATAATATAAATTAAAATAAATA
Found at i:505025 original size:47 final size:46
Alignment explanation
Indices: 504947--505035 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 46
504937 TTAATTATAT
* * *
504947 AAAATATAAAATAAATTAAAATATGATATAAATATAATATAAATAA
1 AAAATATAAAATAAATTAAAAAATAAAATAAATATAATATAAATAA
*
504993 AAAAT-TAAAATATAATATAAAAAATAAAATAAATATGATATAA
1 AAAATATAAAATA-AAT-TAAAAAATAAAATAAATATAATATAA
505036 TTTAACAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 7 0.19
46 8 0.22
47 22 0.59
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (46 bp):
AAAATATAAAATAAATTAAAAAATAAAATAAATATAATATAAATAA
Found at i:505293 original size:3 final size:3
Alignment explanation
Indices: 505285--505325 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
505275 ATTAAAATGC
505285 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
505326 AATAATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:510074 original size:2 final size:2
Alignment explanation
Indices: 510069--510108 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
510059 CCCTCCATCC
510069 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
510109 ATATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:510113 original size:2 final size:2
Alignment explanation
Indices: 510108--510133 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
510098 TCTCTCTCTC
510108 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
510134 AGAATGTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:520367 original size:17 final size:16
Alignment explanation
Indices: 520299--520378 Score: 65
Period size: 17 Copynumber: 4.9 Consensus size: 16
520289 TTAGTTCAGG
*
520299 TTATTTTT-TATTCAAA
1 TTATTTTTAAATTC-AA
*
520315 TT-TTTTTGAAAATCAA
1 TTATTTTT-AAATTCAA
* **
520331 TTTATTTTGATTTTCAA
1 -TTATTTTTAAATTCAA
520348 TTATTTTTAAATTCAGA
1 TTATTTTTAAATTCA-A
520365 TTATTTTTAAATTC
1 TTATTTTTAAATTC
520379 GAATAAATCA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
15 5 0.10
16 16 0.32
17 25 0.50
18 4 0.08
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (16 bp):
TTATTTTTAAATTCAA
Found at i:521747 original size:12 final size:13
Alignment explanation
Indices: 521721--521752 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
521711 TTAATAATTT
521721 AAAT-TAATATAA
1 AAATATAATATAA
521733 AAATATAATAT-A
1 AAATATAATATAA
521745 AAATATAA
1 AAATATAA
521753 ACATGATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:521795 original size:14 final size:15
Alignment explanation
Indices: 521776--521805 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
521766 TATTTAAATG
521776 TAATTAATATA-ATA
1 TAATTAATATACATA
521790 TAATTAATATACATA
1 TAATTAATATACATA
521805 T
1 T
521806 TATATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATTAATATACATA
Found at i:526295 original size:2 final size:2
Alignment explanation
Indices: 526284--526320 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
526274 AAACGAATAC
526284 AT AT -T AT AT AT AT AT AT AT AT A- 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
526321 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:526309 original size:15 final size:15
Alignment explanation
Indices: 526291--526320 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
526281 TACATATTAT
526291 ATATATATATATATA
1 ATATATATATATATA
526306 ATATATATATATATA
1 ATATATATATATATA
526321 GAGAGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:526309 original size:17 final size:17
Alignment explanation
Indices: 526284--526320 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
526274 AAACGAATAC
*
526284 ATATTATATATATATAT
1 ATATAATATATATATAT
526301 ATATAATATATATATAT
1 ATATAATATATATATAT
526318 ATA
1 ATA
526321 GAGAGAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATAATATATATATAT
Found at i:531286 original size:25 final size:24
Alignment explanation
Indices: 531248--531296 Score: 64
Period size: 27 Copynumber: 2.0 Consensus size: 24
531238 TCTGATTTTA
531248 CTGATTTTTTCAATT-TTTGGTTT
1 CTGATTTTTTCAATTATTTGGTTT
531271 CTGAGTTTTTATCAATTAATTTGGTT
1 CTGA-TTTTT-TCAATT-ATTTGGTT
531297 CGCTAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 5 0.23
25 6 0.27
27 7 0.32
ACGTcount: A:0.18, C:0.08, G:0.14, T:0.59
Consensus pattern (24 bp):
CTGATTTTTTCAATTATTTGGTTT
Found at i:531771 original size:16 final size:16
Alignment explanation
Indices: 531750--531795 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
531740 GCAGGTGCAA
531750 AATTAATTAATTTTTT
1 AATTAATTAATTTTTT
531766 AATTAATTATATTATTTT
1 AATTAATTA-ATT-TTTT
531784 -ATT-ATT-ATTTTT
1 AATTAATTAATTTTT
531796 ATTATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.11
14 3 0.11
16 12 0.43
17 6 0.21
18 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTAATTAATTTTTT
Found at i:531782 original size:20 final size:19
Alignment explanation
Indices: 531750--531809 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 19
531740 GCAGGTGCAA
531750 AATTA-ATTAATTTTTTAATT
1 AATTATATT-ATTTTTT-ATT
531770 AATTATATTATTTTATTATT
1 AATTATATTATTTT-TTATT
* *
531790 ATTTTTATTATTTTTATATT
1 AATTATATTATTTTT-TATT
531810 TTATGAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.03
20 29 0.83
21 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
AATTATATTATTTTTTATT
Found at i:531797 original size:9 final size:9
Alignment explanation
Indices: 531761--531811 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
531751 ATTAATTAAT
531761 TTTTTAATTA
1 TTTTT-ATTA
* *
531771 ATTATATTA
1 TTTTTATTA
531780 TTTTATTATTA
1 -TTT-TTATTA
531791 TTTTTATTA
1 TTTTTATTA
531800 TTTTTA-TA
1 TTTTTATTA
531808 TTTT
1 TTTT
531812 ATGAAAAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 6 0.17
9 16 0.46
10 8 0.23
11 5 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTATTA
Found at i:532530 original size:20 final size:21
Alignment explanation
Indices: 532507--532550 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
532497 AATTATGTAA
*
532507 TAAATATGA-TATAATATATT
1 TAAATATGATTAAAATATATT
*
532527 TAAATATGATTAAAATGTATT
1 TAAATATGATTAAAATATATT
532548 TAA
1 TAA
532551 TATAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
TAAATATGATTAAAATATATT
Found at i:532622 original size:104 final size:103
Alignment explanation
Indices: 532481--532675 Score: 293
Period size: 104 Copynumber: 1.9 Consensus size: 103
532471 ATAGTTAATC
* * *
532481 ATTTAATAAATATAAAAATTATGTAATAAATATGATATAATATATTTAAATATGATTAAAATGTA
1 ATTTAATAAATATAAAAATAATGTAACAAACATGATATAATATATTTAAATATGATTAAAATGTA
*
532546 TTTAATATAAATATTATATTCATATTTAAAATTTTAATGT
66 TCTAATAT--ATATTATATTCATATTTAAAATTTTAATGT
* * *
532586 ATTTGATAAATATAAAAATAATG-AACAAACATGATATAATATATTTAAATATGTTTAAGATGTA
1 ATTTAATAAATATAAAAATAATGTAACAAACATGATATAATATATTTAAATATGATTAAAATGTA
*
532650 TCTAATATATATTATATTTATATTTA
66 TCTAATATATATTATATTCATATTTA
532676 TGATTTTGAC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
102 17 0.21
104 44 0.54
105 21 0.26
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.44
Consensus pattern (103 bp):
ATTTAATAAATATAAAAATAATGTAACAAACATGATATAATATATTTAAATATGATTAAAATGTA
TCTAATATATATTATATTCATATTTAAAATTTTAATGT
Found at i:537502 original size:13 final size:13
Alignment explanation
Indices: 537484--537509 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
537474 AAGTGAAATT
537484 TTAAAAAAAAAAA
1 TTAAAAAAAAAAA
537497 TTAAAAAAAAAAA
1 TTAAAAAAAAAAA
537510 AGAAAGAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TTAAAAAAAAAAA
Found at i:537953 original size:3 final size:3
Alignment explanation
Indices: 537945--537989 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
537935 TTCAGACAAG
* *
537945 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTG TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
537990 ATTTGATGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:540252 original size:17 final size:18
Alignment explanation
Indices: 540230--540263 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
540220 TAATTTAATT
540230 TTTTATTTAAA-ATAAAA
1 TTTTATTTAAATATAAAA
540247 TTTTATTTAAATATAAA
1 TTTTATTTAAATATAAA
540264 TAAAAATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTATTTAAATATAAAA
Found at i:543394 original size:22 final size:20
Alignment explanation
Indices: 543371--543409 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
543361 TTATTTTTTA
543371 AAAAATTTTCATATATTTACT
1 AAAAATTTT-ATATATTTACT
*
543392 AAATATTTTATATATTTA
1 AAAAATTTTATATATTTA
543410 TATCTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAAATTTTATATATTTACT
Found at i:543406 original size:20 final size:18
Alignment explanation
Indices: 543355--543409 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
543345 ATGTTATCTC
*
543355 AATATTTTAT-TTTTTAA
1 AATATTTTATATATTTAA
*
543372 AAAATTTTCATATATTTACTA
1 AATATTTT-ATATATTTA--A
543393 AATATTTTATATATTTA
1 AATATTTTATATATTTA
543410 TATCTATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 7 0.23
18 2 0.06
19 5 0.16
20 9 0.29
21 8 0.26
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (18 bp):
AATATTTTATATATTTAA
Found at i:543643 original size:22 final size:22
Alignment explanation
Indices: 543614--543661 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
543604 ACTCACGATC
543614 AAATTTATTT-ATAAATCATTT
1 AAATTTATTTAATAAATCATTT
*
543635 AAATCTTATTTAATAAATCGTTT
1 AAAT-TTATTTAATAAATCATTT
543658 AAAT
1 AAAT
543662 ATAATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.17
22 6 0.25
23 14 0.58
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (22 bp):
AAATTTATTTAATAAATCATTT
Found at i:545086 original size:15 final size:16
Alignment explanation
Indices: 545057--545087 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
545047 ATAAAAATTT
545057 AAAAATTTATATTTAA
1 AAAAATTTATATTTAA
545073 AAAAATTTAT-TTTAA
1 AAAAATTTATATTTAA
545088 TTAAACCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAAATTTATATTTAA
Found at i:545349 original size:15 final size:15
Alignment explanation
Indices: 545329--545367 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
545319 ATAAAAAATT
545329 ATTAAATTATTAAAA
1 ATTAAATTATTAAAA
545344 ATTAAAATT-TTAAAA
1 ATT-AAATTATTAAAA
*
545359 AATAAATTA
1 ATTAAATTA
545368 AAAATAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 5 0.24
15 11 0.52
16 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAATTATTAAAA
Found at i:545359 original size:16 final size:18
Alignment explanation
Indices: 545320--545361 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
545310 TAAAACTTAA
545320 TAAAAAATTATTAAATTAT
1 TAAAAAATTA-TAAATTAT
545339 T-AAAAATTA-AAATT-T
1 TAAAAAATTATAAATTAT
545354 TAAAAAAT
1 TAAAAAAT
545362 AAATTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 11 0.50
18 8 0.36
19 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAAATTATAAATTAT
Found at i:549652 original size:2 final size:2
Alignment explanation
Indices: 549647--549691 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
549637 CTTTTGAAGC
549647 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
549689 AT A
1 AT A
549692 CTAGTTCTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:553841 original size:2 final size:2
Alignment explanation
Indices: 553834--553872 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
553824 CAACCTAGCT
553834 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
553873 TGGTGCTGCC
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:555435 original size:2 final size:2
Alignment explanation
Indices: 555422--555469 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
555412 TATATTCTTC
* * *
555422 AT AT AG AT AT AT AT AT AT AG AT AT AT AT AG 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 AT AT
555463 AT AT AT A
1 AT AT AT A
555470 ACATGCAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (2 bp):
AT
Found at i:556523 original size:91 final size:90
Alignment explanation
Indices: 556368--556548 Score: 299
Period size: 91 Copynumber: 2.0 Consensus size: 90
556358 TTATCATACT
*
556368 TTTAATTAATTTTCACAACTATGTTTTCAATCTACATACTATCAAATTACACAATCATTGGTGGC
1 TTTAATTAATTTTCACAACTATATTTTCAATCTACATACTATCAAATTACACAATCATTGGTGGC
556433 AAGTTTATGATTAAGATTCATGCACA
66 AAG-TTATGATTAAGATTCATGCACA
* * * * *
556459 TTTAATTAATTTTCATAATTATATTTTCAGTCTACATATTATCAAATTACGCAATCATTGGTGGC
1 TTTAATTAATTTTCACAACTATATTTTCAATCTACATACTATCAAATTACACAATCATTGGTGGC
556524 AAGTTATGATTAAGATTCATGCACA
66 AAGTTATGATTAAGATTCATGCACA
556549 AGAAATCTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 22 0.26
91 62 0.74
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (90 bp):
TTTAATTAATTTTCACAACTATATTTTCAATCTACATACTATCAAATTACACAATCATTGGTGGC
AAGTTATGATTAAGATTCATGCACA
Found at i:556895 original size:20 final size:20
Alignment explanation
Indices: 556860--556926 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
556850 CGAATTATTA
*
556860 ATAATAT-TAAAATTTATAT
1 ATAATATATAAAATTTAAAT
556879 A-AATATATAAAATTTTAAAT
1 ATAATATATAAAA-TTTAAAT
* *
556899 ATAAT-TATAATAATATGAAT
1 ATAATATATAA-AATTTAAAT
556919 ATAATATA
1 ATAATATA
556927 AAATATAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 5 0.12
19 6 0.15
20 22 0.55
21 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
ATAATATATAAAATTTAAAT
Found at i:559550 original size:2 final size:2
Alignment explanation
Indices: 559543--559583 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
559533 GCTCTTCACT
* *
559543 TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC GC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
559584 GTCATGTGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.05, T:0.46
Consensus pattern (2 bp):
TC
Found at i:559901 original size:7 final size:7
Alignment explanation
Indices: 559889--559922 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
559879 CTTAAAGCAA
559889 AAAAAAT
1 AAAAAAT
559896 AAAAAAT
1 AAAAAAT
559903 AAAAAAT
1 AAAAAAT
559910 AAATAAAT
1 AAA-AAAT
559918 AAAAA
1 AAAAA
559923 TGGTGGTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:560753 original size:2 final size:2
Alignment explanation
Indices: 560748--560772 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
560738 TAGAAATAGT
560748 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
560773 TGTCTCTAGT
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:562293 original size:22 final size:19
Alignment explanation
Indices: 562268--562333 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 19
562258 TTACGGAAAA
562268 AAATAAATATAAAGAATATTAT
1 AAATAAA-ATAAA-AATA-TAT
562290 AAATAAAATAAAAATATAT
1 AAATAAAATAAAAATATAT
* *
562309 AAA-AATATTAAAA-AT-T
1 AAATAAAATAAAAATATAT
562325 AAATAAAAT
1 AAATAAAAT
562334 TAATCATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 4 0.10
17 6 0.15
18 8 0.20
19 6 0.15
20 4 0.10
21 5 0.12
22 7 0.17
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAATAAAATAAAAATATAT
Found at i:562312 original size:10 final size:10
Alignment explanation
Indices: 562274--562368 Score: 56
Period size: 10 Copynumber: 9.4 Consensus size: 10
562264 AAAAAAATAA
562274 ATATAAAGAAT
1 ATATAAA-AAT
562285 ATTATAAATAA-
1 A-TATAAA-AAT
562296 A-ATAAAAAT
1 ATATAAAAAT
562305 ATATAAAAAT
1 ATATAAAAAT
562315 AT-TAAAAATT
1 ATATAAAAA-T
* *
562325 AAATAAAATT
1 ATATAAAAAT
*
562335 AATCATTAAAAT
1 -AT-ATAAAAAT
562347 AT-T-AAAAT
1 ATATAAAAAT
* *
562355 TTATATAAAT
1 ATATAAAAAT
562365 ATAT
1 ATAT
562369 CAAATCTTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
8 8 0.12
9 14 0.21
10 20 0.30
11 10 0.15
12 14 0.21
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (10 bp):
ATATAAAAAT
Done.