Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold112
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: 1714866
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 134939 characters in sequence are not A, C, G, or T
File 4 of 11
Found at i:407011 original size:12 final size:12
Alignment explanation
Indices: 406994--407023 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
406984 TAATAATTTT
406994 TTATATGTTATA
1 TTATATGTTATA
*
407006 TTATATTTTATA
1 TTATATGTTATA
407018 TTATAT
1 TTATAT
407024 AATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (12 bp):
TTATATGTTATA
Found at i:407023 original size:17 final size:17
Alignment explanation
Indices: 406931--407054 Score: 68
Period size: 17 Copynumber: 7.5 Consensus size: 17
406921 TCGTACGTAA
*
406931 TTATATT-TAAAATATT
1 TTATATTATATAATATT
*
406947 ATATAATTATATAA-ATT
1 TTAT-ATTATATAATATT
*
406964 TTA-ATT-TATTAATA-A
1 TTATATTATA-TAATATT
*
406979 TT-TATTA-ATAATTTT
1 TTATATTATATAATATT
*
406994 TTATATGTTATATTATATT
1 TTATA--TTATATAATATT
*
407013 TTATATTATATAATAAT
1 TTATATTATATAATATT
*
407030 TTA-ATT-TATGATATAT
1 TTATATTATATAATAT-T
*
407046 TTATGTTAT
1 TTATATTAT
407055 GTTTAAAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 26
0.68 0.11 0.22
Matches are distributed among these distances:
14 6 0.07
15 20 0.25
16 13 0.16
17 23 0.28
18 8 0.10
19 11 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTATATTATATAATATT
Found at i:407045 original size:39 final size:37
Alignment explanation
Indices: 406980--407054 Score: 89
Period size: 39 Copynumber: 2.0 Consensus size: 37
406970 TATTAATAAT
* * *
406980 TTATTAATAATTTTTTATATGTTATATTATATTTTATA
1 TTATTAATAATTTATTATATGATATATT-TATGTTATA
407018 TTATATAATAATTTAATT-TATGATATATTTATGTTAT
1 TTAT-TAATAATTT-ATTATATGATATATTTATGTTAT
407055 GTTTAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 11 0.34
39 19 0.59
40 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (37 bp):
TTATTAATAATTTATTATATGATATATTTATGTTATA
Found at i:407840 original size:17 final size:19
Alignment explanation
Indices: 407810--407844 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
407800 AAAACCCATT
407810 TATTTATTTATTATTTTTA
1 TATTTATTTATTATTTTTA
407829 TATTT-TTT-TTATTTTT
1 TATTTATTTATTATTTTT
407845 TTTCTAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (19 bp):
TATTTATTTATTATTTTTA
Found at i:408185 original size:17 final size:17
Alignment explanation
Indices: 408159--408193 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
408149 TTAACTGATA
*
408159 ATTTTTTTTTATTTTTT
1 ATTTTCTTTTATTTTTT
*
408176 ATTTTCTTTTTTTTTTT
1 ATTTTCTTTTATTTTTT
408193 A
1 A
408194 AAAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (17 bp):
ATTTTCTTTTATTTTTT
Found at i:408740 original size:17 final size:17
Alignment explanation
Indices: 408712--408753 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
408702 ATTATGCATT
*
408712 TTATATTATATA-AAAA
1 TTATAATATATATAAAA
408728 TTA-AATATATATAAAA
1 TTATAATATATATAAAA
408744 TTATAATATA
1 TTATAATATA
408754 AACATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTATAATATATATAAAA
Found at i:408802 original size:60 final size:60
Alignment explanation
Indices: 408724--408850 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
408714 ATATTATATA
* *
408724 AAAATTAAATATATATAAAATTA-T-AATATAAACATTAAAA-AAATATATTATTTATATTTT
1 AAAATTAAATAAAAATAAAATTATTAAATATAAA-A-TAAAATAAATAT-TTATTTATATTTT
* * * * *
408784 AAAATTTAATAAAAATAAAATTATTAAATATTAAATAAAATACATATTTTTTTATTTTTT
1 AAAATTAAATAAAAATAAAATTATTAAATATAAAATAAAATAAATATTTATTTATATTTT
408844 AAAATTA
1 AAAATTA
408851 TAAATAAGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
60 42 0.75
61 7 0.12
62 7 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (60 bp):
AAAATTAAATAAAAATAAAATTATTAAATATAAAATAAAATAAATATTTATTTATATTTT
Found at i:408818 original size:32 final size:32
Alignment explanation
Indices: 408719--408818 Score: 77
Period size: 32 Copynumber: 3.2 Consensus size: 32
408709 ATTTTATATT
* * * *
408719 ATATAAAAATTAAATATATATAAAATTA-T-A
1 ATATTAAAATTTAATAAAAATAAAATTATTAA
* *
408749 ATA-TAAACA-TTAA-AAAAAT-ATATTATTTAT
1 ATATTAAA-ATTTAATAAAAATAAAATTA-TTAA
*
408779 ATTTTAAAATTTAATAAAAATAAAATTATTAA
1 ATATTAAAATTTAATAAAAATAAAATTATTAA
408811 ATATTAAA
1 ATATTAAA
408819 TAAAATACAT
Statistics
Matches: 52, Mismatches: 10, Indels: 14
0.68 0.13 0.18
Matches are distributed among these distances:
27 5 0.10
28 4 0.08
29 7 0.13
30 7 0.13
31 8 0.15
32 16 0.31
33 5 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
ATATTAAAATTTAATAAAAATAAAATTATTAA
Found at i:409761 original size:2 final size:2
Alignment explanation
Indices: 409754--409782 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
409744 CTTTATTTGT
409754 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
409783 GCAATAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:412725 original size:14 final size:14
Alignment explanation
Indices: 412706--412733 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
412696 TATATTTTAA
412706 AATATTTTTATATT
1 AATATTTTTATATT
412720 AATATTTTTATATT
1 AATATTTTTATATT
412734 TTTAGATTTA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:413098 original size:32 final size:31
Alignment explanation
Indices: 413062--413121 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
413052 ATAATGTATT
* *
413062 TAATAAATATATTATATTTTTATTTAAAATCG
1 TAATAAATATATTACATTTATA-TTAAAATCG
* *
413094 TAATATATTTATTACATTTATATTAAAA
1 TAATAAATATATTACATTTATATTAAAA
413122 CAACTGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 6 0.25
32 18 0.75
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (31 bp):
TAATAAATATATTACATTTATATTAAAATCG
Found at i:415876 original size:13 final size:13
Alignment explanation
Indices: 415811--415876 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
415801 AAATTTAATA
415811 ATTTTATATATT-T
1 ATTTT-TATATTAT
415824 ATTTTTATA-T-T
1 ATTTTTATATTAT
*
415835 -TTTTAATATTAT
1 ATTTTTATATTAT
415847 A-TTTTA-ATTAT
1 ATTTTTATATTAT
*
415858 TTTTTTATATTAT
1 ATTTTTATATTAT
415871 ATTTTT
1 ATTTTT
415877 GTGCTCAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
10 7 0.16
11 8 0.18
12 14 0.32
13 15 0.34
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTTATATTAT
Found at i:416167 original size:28 final size:27
Alignment explanation
Indices: 416110--416174 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
416100 TTAGACTATA
* *
416110 AATTT-ATTTATTTATATTATATTAAT
1 AATTTAATTTATATATATTATATTAAG
* *
416136 AATTTAATTTATATATTATTTTTTTAAG
1 AATTTAATTTATATA-TATTATATTAAG
416164 AATTTAATTTA
1 AATTTAATTTA
416175 CTTATAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 5 0.15
27 8 0.24
28 20 0.61
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
AATTTAATTTATATATATTATATTAAG
Found at i:416347 original size:17 final size:17
Alignment explanation
Indices: 416307--416350 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
416297 TGTTAAGGAT
416307 TAATTTTTTTAAAAAAA
1 TAATTTTTTTAAAAAAA
* * * *
416324 TACTTTTTTTATAGAAG
1 TAATTTTTTTAAAAAAA
416341 TAATTTTTTT
1 TAATTTTTTT
416351 CCAACGATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (17 bp):
TAATTTTTTTAAAAAAA
Found at i:418649 original size:16 final size:16
Alignment explanation
Indices: 418628--418660 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
418618 TGTGTTTATT
418628 AATTATATGTAAAGAG
1 AATTATATGTAAAGAG
418644 AATTATATGTAAAGAG
1 AATTATATGTAAAGAG
418660 A
1 A
418661 TATGATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (16 bp):
AATTATATGTAAAGAG
Found at i:420970 original size:13 final size:13
Alignment explanation
Indices: 420952--420982 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
420942 ATTAATTGTG
420952 ATAAATATTAATA
1 ATAAATATTAATA
420965 ATAAATATTAATA
1 ATAAATATTAATA
420978 ATAAA
1 ATAAA
420983 AAAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAAATATTAATA
Found at i:423304 original size:24 final size:25
Alignment explanation
Indices: 423271--423321 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
423261 TTCGTATCAT
423271 TTTTATATTATT-TTTTAATATTATA
1 TTTTATATTATTATTTT-ATATTATA
423296 TTTTA-ATTATTATTTTATATTATA
1 TTTTATATTATTATTTTATATTATA
423320 TT
1 TT
423322 ATCGTGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATATTATTATTTTATATTATA
Found at i:423317 original size:13 final size:13
Alignment explanation
Indices: 423271--423318 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
423261 TTCGTATCAT
423271 TTTTATATTATT-
1 TTTTATATTATTA
423283 TTTTAATATTA-TA
1 TTTT-ATATTATTA
423296 TTTTA-ATTATTA
1 TTTTATATTATTA
423308 TTTTATATTAT
1 TTTTATATTAT
423319 ATTATCGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.12
12 13 0.41
13 15 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTATATTATTA
Found at i:424309 original size:16 final size:16
Alignment explanation
Indices: 424261--424309 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
424251 TATTGTATTA
*
424261 ATAATTTAATTTACAT
1 ATAATTTAATTTACTT
424277 ATAATTT--TTT--TT
1 ATAATTTAATTTACTT
424289 A-AATTTAATTTACTT
1 ATAATTTAATTTACTT
424304 ATAATT
1 ATAATT
424310 AAGTGGATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
11 5 0.19
12 2 0.07
13 3 0.11
14 3 0.11
15 3 0.11
16 11 0.41
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (16 bp):
ATAATTTAATTTACTT
Found at i:426450 original size:2 final size:2
Alignment explanation
Indices: 426443--426471 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
426433 AATATAAACC
426443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
426472 GAAAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:428688 original size:2 final size:2
Alignment explanation
Indices: 428681--428728 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
428671 TTAAAAGGAA
428681 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
428723 AT AT AT
1 AT AT AT
428729 GGCTCCTCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435433 original size:22 final size:21
Alignment explanation
Indices: 435374--435433 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
435364 ATAACATCAT
* * * *
435374 TATAACTATTAACTAATATTG
1 TATAAATATAAACTATTAATG
* *
435395 TATAAATATATATTATTAATG
1 TATAAATATAAACTATTAATG
435416 TATTAAATATAAACTATT
1 TA-TAAATATAAACTATT
435434 TTTTCCCCCC
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (21 bp):
TATAAATATAAACTATTAATG
Found at i:436838 original size:18 final size:19
Alignment explanation
Indices: 436817--436859 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
436807 TTTCTTTTTC
*
436817 TTTAATTTTTTAAA-TATT
1 TTTAATTTTTAAAATTATT
436835 TTTAA-TTTTAAAATTATT
1 TTTAATTTTTAAAATTATT
436853 TTTAATT
1 TTTAATT
436860 ACTATCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 14 0.64
19 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTAATTTTTAAAATTATT
Found at i:437929 original size:11 final size:10
Alignment explanation
Indices: 437890--437940 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 10
437880 ATAATTCGTA
*
437890 TTATATAAAT
1 TTATATATAT
437900 TT-TATAT-T
1 TTATATATAT
437908 TT-TATATAT
1 TTATATATAT
437917 TTATATCATAT
1 TTATAT-ATAT
437928 TTATATTATAT
1 TTATA-TATAT
437939 TT
1 TT
437941 TAATTATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
8 8 0.22
9 7 0.19
10 5 0.14
11 15 0.42
12 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (10 bp):
TTATATATAT
Found at i:438230 original size:2 final size:2
Alignment explanation
Indices: 438225--438249 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
438215 TAAATTTTGG
438225 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
438250 TCATGTTATG
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:441568 original size:15 final size:15
Alignment explanation
Indices: 441539--441567 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
441529 TAATAAGAAA
441539 AAAATTATAAATTTT
1 AAAATTATAAATTTT
441554 AAAATT-TAAATTTT
1 AAAATTATAAATTTT
441568 TTAGATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATTATAAATTTT
Found at i:441717 original size:17 final size:17
Alignment explanation
Indices: 441690--441731 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
441680 TAATCACTTT
441690 TTATT-TTATTTTGTTA
1 TTATTATTATTTTGTTA
*
441706 TTATTATTATTTTTTTA
1 TTATTATTATTTTGTTA
*
441723 TTATAATTA
1 TTATTATTA
441732 GTATCAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTATTATTTTGTTA
Found at i:441844 original size:3 final size:3
Alignment explanation
Indices: 441836--441867 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
441826 AATTATGAGT
*
441836 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
441868 GCCAAATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:442726 original size:2 final size:2
Alignment explanation
Indices: 442705--442747 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
442695 ACTTGACGTC
* * *
442705 AT AT AC AT AC AT AC 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
442747 A
1 A
442748 ATTAAAGAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:448382 original size:2 final size:2
Alignment explanation
Indices: 448375--448400 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
448365 AAAATTTGAA
448375 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
448401 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:448405 original size:2 final size:2
Alignment explanation
Indices: 448400--448433 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
448390 TCTCTCTCTC
448400 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
448434 GTATTAACTA
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):
TA
Found at i:448962 original size:27 final size:28
Alignment explanation
Indices: 448902--448962 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
448892 ATTTTTATAT
*
448902 TAAT-ATTTATATATTTTTATAATTAAA
1 TAATAATTTAAATATTTTTATAATTAAA
**
448929 TTTTAATTTAAATATTTTT-TAATT-AA
1 TAATAATTTAAATATTTTTATAATTAAA
448955 TAAATAAT
1 T-AATAAT
448963 CTATAATTCG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
26 3 0.11
27 11 0.41
28 13 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TAATAATTTAAATATTTTTATAATTAAA
Found at i:449659 original size:24 final size:23
Alignment explanation
Indices: 449630--449695 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 23
449620 TAAAATTATA
*
449630 TTAATATTAATAATTAATTTAAT
1 TTAATATAAATAATTAATTTAAT
*
449653 TTAAATAAAAATAATT-ATTT-A-
1 TT-AATATAAATAATTAATTTAAT
449674 TT-ATATAAATAA-TAATTTAAT
1 TTAATATAAATAATTAATTTAAT
449695 T
1 T
449696 CAAACTAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 1 0.03
19 13 0.36
20 1 0.03
21 3 0.08
22 1 0.03
23 6 0.17
24 11 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAATATAAATAATTAATTTAAT
Found at i:450127 original size:13 final size:13
Alignment explanation
Indices: 450109--450133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
450099 AACCCTGAAA
450109 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
450122 TTTCTTTCTTTC
1 TTTCTTTCTTTC
450134 AACGCCAGAA
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTCTTTCT
Found at i:450157 original size:2 final size:2
Alignment explanation
Indices: 450150--450176 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
450140 AGAACCAGAA
450150 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
450177 TACACCAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:452443 original size:2 final size:2
Alignment explanation
Indices: 452436--452485 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
452426 ATAAAAGTGC
452436 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
452478 AT AT AT AT
1 AT AT AT AT
452486 CAATGCATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:453693 original size:18 final size:16
Alignment explanation
Indices: 453652--453706 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
453642 ATATATATTT
*
453652 TAAAATTTATATAATA
1 TAAAATTTATAAAATA
453668 T-AAA-TTATAAATATA
1 TAAAATTTATAAA-ATA
453683 TCAAAATTTATAAAAATA
1 T-AAAATTTAT-AAAATA
453701 TAAAAT
1 TAAAAT
453707 ACTTTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 6 0.18
15 7 0.21
16 1 0.03
17 8 0.24
18 8 0.24
19 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAATTTATAAAATA
Found at i:453712 original size:20 final size:18
Alignment explanation
Indices: 453653--453705 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
453643 TATATATTTT
*
453653 AAAATTTAT-ATAATAT-
1 AAAATTTATAAAAATATA
* *
453669 -AAA-TTATAAATATATC
1 AAAATTTATAAAAATATA
453685 AAAATTTATAAAAATATA
1 AAAATTTATAAAAATATA
453703 AAA
1 AAA
453706 TACTTTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 4 0.14
15 8 0.28
17 3 0.10
18 14 0.48
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTTATAAAAATATA
Found at i:454679 original size:21 final size:21
Alignment explanation
Indices: 454640--454678 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
454630 CCTTATAGCC
*
454640 TGAATTTGATGCTGTTTTTCA
1 TGAATTGGATGCTGTTTTTCA
454661 TGAATTGGA-GCTGTTTTT
1 TGAATTGGATGCTGTTTTT
454679 TTGGTTTTCA
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:0.18, C:0.08, G:0.23, T:0.51
Consensus pattern (21 bp):
TGAATTGGATGCTGTTTTTCA
Found at i:455628 original size:136 final size:136
Alignment explanation
Indices: 455384--455656 Score: 537
Period size: 136 Copynumber: 2.0 Consensus size: 136
455374 ATAGCTATTG
455384 TCGATATTGCCTAGTTATGGCTTCGTTTAAGTGAGGTCTTGGAAGGGATAATTAGAAAAAGTCTC
1 TCGATATTGCCTAGTTATGGCTTCGTTTAAGTGAGGTCTTGGAAGGGATAATTAGAAAAAGTCTC
*
455449 ACTCTTTTGTACTTTATCCTAGATCCTTCCAAGCAGATGCTTATTCTGAGTTGGGGAACCTAGGT
66 ACTCTTTTGTACTTTATCCTAGATACTTCCAAGCAGATGCTTATTCTGAGTTGGGGAACCTAGGT
455514 TGTAAT
131 TGTAAT
455520 TCGATATTGCCTAGTTATGGCTTCGTTTAAGTGAGGTCTTGGAAGGGATAATTAGAAAAAGTCTC
1 TCGATATTGCCTAGTTATGGCTTCGTTTAAGTGAGGTCTTGGAAGGGATAATTAGAAAAAGTCTC
455585 ACTCTTTTGTACTTTATCCTAGATACTTCCAAGCAGATGCTTATTCTGAGTTGGGGAACCTAGGT
66 ACTCTTTTGTACTTTATCCTAGATACTTCCAAGCAGATGCTTATTCTGAGTTGGGGAACCTAGGT
455650 TGTAAT
131 TGTAAT
455656 T
1 T
455657 GGAAGGAATT
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 136 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (136 bp):
TCGATATTGCCTAGTTATGGCTTCGTTTAAGTGAGGTCTTGGAAGGGATAATTAGAAAAAGTCTC
ACTCTTTTGTACTTTATCCTAGATACTTCCAAGCAGATGCTTATTCTGAGTTGGGGAACCTAGGT
TGTAAT
Found at i:459827 original size:36 final size:33
Alignment explanation
Indices: 459769--459848 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 33
459759 TATTAAGTTA
* *
459769 AATTTATT-TTTAATAATTAAAATTAATTTAATTT
1 AATTTATTATTTAATAA-TAAAAATAAATT-ATTT
459803 AATTTATTATTTATATAATAAAAATAAATTATTT
1 AATTTATTATTTA-ATAATAAAAATAAATTATTT
459837 ATATTTAATTAT
1 A-ATTT-ATTAT
459849 AAAATTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
34 13 0.32
35 18 0.45
36 9 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AATTTATTATTTAATAATAAAAATAAATTATTT
Found at i:460717 original size:17 final size:15
Alignment explanation
Indices: 460697--460733 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
460687 ATAAATATCG
460697 AATATAAATATATATTT
1 AATATAAATATA-A-TT
460714 AATATAAATATAATT
1 AATATAAATATAATT
460729 AATAT
1 AATAT
460734 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
16 1 0.05
17 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATAAATATAATT
Found at i:460805 original size:13 final size:13
Alignment explanation
Indices: 460789--460820 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
460779 ACTTAAATAT
460789 ATATTTAATATAA
1 ATATTTAATATAA
*
460802 ATATTAAATATAA
1 ATATTTAATATAA
460815 ATATTT
1 ATATTT
460821 TTAAAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATTTAATATAA
Found at i:461099 original size:2 final size:2
Alignment explanation
Indices: 461092--461120 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
461082 ATTATACATA
461092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
461121 GTAACATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:461387 original size:14 final size:15
Alignment explanation
Indices: 461356--461406 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
461346 AGAGATATAA
* * *
461356 AAATAAAAAAATAAT
1 AAATATAAATATATT
461371 AAATATAAATAT-TT
1 AAATATAAATATATT
*
461385 AAATATTAAATTTATT
1 AAATA-TAAATATATT
461401 AAATAT
1 AAATAT
461407 CATTAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 6 0.20
15 17 0.57
16 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATATAAATATATT
Found at i:461812 original size:4 final size:4
Alignment explanation
Indices: 461803--461827 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
461793 TTGATTTGAT
461803 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
461828 GAGAGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:461927 original size:3 final size:3
Alignment explanation
Indices: 461919--461957 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
461909 TTAAGAATCC
461919 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
461958 TTAGTTAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:462222 original size:39 final size:39
Alignment explanation
Indices: 462155--462253 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
462145 ATTTAATAGA
462155 TTTAAATTAAATTAAATTACATGTAATTTAAATAAAAAT
1 TTTAAATTAAATTAAATTACATGTAATTTAAATAAAAAT
* * *
462194 TTTATAATTTAATTAATTTAGAT-TAATTTAAATAAATATAT
1 TTTA-AATTAAATTAAATTACATGTAATTTAAATAAA-A-AT
* * *
462235 TTTTATTTAAATTTAATTA
1 TTTAAATTAAATTAAATTA
462254 TAAAAATATT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
39 17 0.35
40 27 0.55
41 5 0.10
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (39 bp):
TTTAAATTAAATTAAATTACATGTAATTTAAATAAAAAT
Found at i:462529 original size:15 final size:16
Alignment explanation
Indices: 462511--462543 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
462501 TATTTTAATA
462511 TAAAATAT-TATTTTT
1 TAAAATATATATTTTT
462526 TAAAATATATATTTTT
1 TAAAATATATATTTTT
462542 TA
1 TA
462544 CTATAACTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAAAATATATATTTTT
Found at i:463296 original size:22 final size:22
Alignment explanation
Indices: 463271--463312 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
463261 TTTTTAAATT
463271 TAAAT-TTAAATATAAAAATATA
1 TAAATATTAAA-ATAAAAATATA
463293 TAAATATTAAAATAAAAATA
1 TAAATATTAAAATAAAAATA
463313 ATATTTTAAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATATTAAAATAAAAATATA
Found at i:463768 original size:4 final size:4
Alignment explanation
Indices: 463759--463785 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
463749 AAAAAATACC
463759 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
463786 AAGCCTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:463978 original size:18 final size:19
Alignment explanation
Indices: 463939--463988 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
463929 AATATAAAAA
*
463939 TATTTATAATTTAGATTATT
1 TATTTA-AATTTAGAATATT
463959 TATTTAAATTTA-AATATT
1 TATTTAAATTTAGAATATT
463977 TATTTAATATTT
1 TATTTAA-ATTT
463989 GAGTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 12 0.43
19 10 0.36
20 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTTAAATTTAGAATATT
Found at i:464223 original size:21 final size:20
Alignment explanation
Indices: 464190--464232 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
464180 GATATTTATT
464190 TAAAATTTAAAATTTAATAAA
1 TAAAATTTAAAA-TTAATAAA
*
464211 TAAAATATT-AAATTATTAAA
1 TAAAAT-TTAAAATTAATAAA
464231 TA
1 TA
464233 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 9 0.45
22 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAATTTAAAATTAATAAA
Found at i:464239 original size:8 final size:8
Alignment explanation
Indices: 464189--464246 Score: 54
Period size: 7 Copynumber: 7.8 Consensus size: 8
464179 TGATATTTAT
464189 TTAAAAT-
1 TTAAAATA
464196 TTAAAAT-
1 TTAAAATA
464203 TTAATAA-A
1 TTAA-AATA
464211 -TAAAATA
1 TTAAAATA
*
464218 TTAAATTA
1 TTAAAATA
464226 TT-AAATA
1 TTAAAATA
*
464233 TTAAAATT
1 TTAAAATA
464241 TTAAAA
1 TTAAAA
464247 AATATTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
6 2 0.05
7 21 0.49
8 20 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTAAAATA
Found at i:464907 original size:10 final size:10
Alignment explanation
Indices: 464879--464926 Score: 55
Period size: 10 Copynumber: 4.7 Consensus size: 10
464869 GATATTAAAA
464879 AAAT-AAATAT
1 AAATAAAAT-T
464889 AATATAAAATT
1 AA-ATAAAATT
464900 AAATAAAA-T
1 AAATAAAATT
464909 AATATAAAATT
1 AA-ATAAAATT
464920 AAATAAA
1 AAATAAA
464927 TTATCTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
9 3 0.09
10 19 0.56
11 8 0.24
12 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATAAAATT
Found at i:464910 original size:20 final size:21
Alignment explanation
Indices: 464879--464927 Score: 91
Period size: 20 Copynumber: 2.4 Consensus size: 21
464869 GATATTAAAA
464879 AAATAAATATAATATAAAATT
1 AAATAAATATAATATAAAATT
464900 AAATAAA-ATAATATAAAATT
1 AAATAAATATAATATAAAATT
464920 AAATAAAT
1 AAATAAAT
464928 TATCTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAATATAATATAAAATT
Found at i:464923 original size:25 final size:26
Alignment explanation
Indices: 464872--464927 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
464862 ATCACCTGAT
*
464872 ATTAAA-AAAATAAATATAATATAAA
1 ATTAAATAAAATAAATATAAAATAAA
*
464897 ATTAAATAAAAT-AATATAAAATTAA
1 ATTAAATAAAATAAATATAAAATAAA
464922 A-TAAAT
1 ATTAAAT
464928 TATCTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 5 0.18
25 18 0.64
26 5 0.18
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (26 bp):
ATTAAATAAAATAAATATAAAATAAA
Found at i:465081 original size:2 final size:2
Alignment explanation
Indices: 465074--465102 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
465064 CCCTCCCCTT
465074 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
465103 TCCAAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:467795 original size:28 final size:28
Alignment explanation
Indices: 467763--467819 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
467753 TAATAAATTT
* *
467763 TATTTTTAAATTTTT-TTAATATTATTAA
1 TATTTATAAATTTTTATAAAT-TTATTAA
*
467791 TATTTATATATTTTTATAAATTTATTAA
1 TATTTATAAATTTTTATAAATTTATTAA
467819 T
1 T
467820 TCTCATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TATTTATAAATTTTTATAAATTTATTAA
Found at i:467903 original size:8 final size:8
Alignment explanation
Indices: 467881--467927 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
467871 TTATAAATAT
467881 ATTTTAAA
1 ATTTTAAA
* *
467889 ATATTAAT
1 ATTTTAAA
467897 ATTTTAAA
1 ATTTTAAA
467905 ACTTTTTAAA
1 A--TTTTAAA
467915 ATTTTAAA
1 ATTTTAAA
467923 ATTTT
1 ATTTT
467928 TCATCCTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 25 0.76
10 8 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (8 bp):
ATTTTAAA
Found at i:467913 original size:18 final size:17
Alignment explanation
Indices: 467879--467928 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
467869 GATTATAAAT
*
467879 ATATTTTAAAA-TATTA
1 ATATTTTAAAATTTTTA
467895 ATATTTTAAAACTTTTTA
1 ATATTTTAAAA-TTTTTA
*
467913 AAATTTTAAAATTTTT
1 ATATTTTAAAATTTTT
467929 CATCCTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 11 0.37
17 5 0.17
18 14 0.47
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTTTAAAATTTTTA
Found at i:468080 original size:21 final size:22
Alignment explanation
Indices: 468056--468096 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
468046 ATCGGTTGAG
*
468056 ATAAGA-TTTTATTTATTTTTT
1 ATAAGATTTTTACTTATTTTTT
*
468077 ATAATATTTTTACTTATTTT
1 ATAAGATTTTTACTTATTTT
468097 ATCTTTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
ATAAGATTTTTACTTATTTTTT
Found at i:468591 original size:12 final size:12
Alignment explanation
Indices: 468576--468614 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
468566 TTATAAAATA
468576 TAAAAAATATTT
1 TAAAAAATATTT
*
468588 TAAAAATATTTTT
1 TAAAAA-ATATTT
468601 TAAAATAATATTT
1 TAAAA-AATATTT
468614 T
1 T
468615 GTTAAAGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 16 0.70
14 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TAAAAAATATTT
Found at i:473295 original size:30 final size:30
Alignment explanation
Indices: 473261--473330 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
473251 TTATGTAAAA
*
473261 TAAAAATAT-AATATAAATAATTAAATATTT
1 TAAAAATATAAATATAAAT-ATTAAATATAT
* * *
473291 TAAAATTTTAAATATGAATATTAAATATAT
1 TAAAAATATAAATATAAATATTAAATATAT
473321 TAAATAATAT
1 TAAA-AATAT
473331 TTATTATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 21 0.66
31 11 0.34
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (30 bp):
TAAAAATATAAATATAAATATTAAATATAT
Found at i:473331 original size:19 final size:19
Alignment explanation
Indices: 473268--473342 Score: 59
Period size: 19 Copynumber: 4.0 Consensus size: 19
473258 AAATAAAAAT
473268 ATAATA-TAAATA-ATTAA
1 ATAATATTAAATATATTAA
* *
473285 AT-ATTTTAAA-ATTTTAAA
1 ATAATATTAAATATATT-AA
473303 TATGAATATTAAATATATTAA
1 -AT-AATATTAAATATATTAA
* *
473324 ATAATATTTATTATATTAA
1 ATAATATTAAATATATTAA
473343 TTTTTTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
16 3 0.07
17 8 0.18
18 2 0.04
19 17 0.38
20 2 0.04
21 9 0.20
22 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (19 bp):
ATAATATTAAATATATTAA
Found at i:473801 original size:53 final size:53
Alignment explanation
Indices: 473742--473843 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
473732 AATAGATCCG
473742 ATATTTAAATCCATTATCTATAAAAATAATACT-AATTTAAATAATAAATTCAA
1 ATATTTAAATCCATTATCTATAAAAATAATA-TAAATTTAAATAATAAATTCAA
** *
473795 ATATTTAAATTTATTATCTGTAAAAATAATATAAATTTAAATAATAAAT
1 ATATTTAAATCCATTATCTATAAAAATAATATAAATTTAAATAATAAAT
473844 ATTTAAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.02
53 44 0.98
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (53 bp):
ATATTTAAATCCATTATCTATAAAAATAATATAAATTTAAATAATAAATTCAA
Found at i:473836 original size:15 final size:15
Alignment explanation
Indices: 473818--473852 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
473808 TTATCTGTAA
473818 AAATAATATAA-ATTT
1 AAATAATA-AATATTT
473833 AAATAATAAATATTT
1 AAATAATAAATATTT
473848 AAATA
1 AAATA
473853 TTTATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATAATAAATATTT
Found at i:473987 original size:72 final size:71
Alignment explanation
Indices: 473832--473981 Score: 182
Period size: 72 Copynumber: 2.1 Consensus size: 71
473822 AATATAAATT
* *
473832 TAAATAATAAATATTTAAATATTTATATTTATATCTTTTTTAAATCTACTATAAATAATAATTAT
1 TAAAT-ATAAATATTTAAAAATTCATATTTATATCTTTTTTAAATCTACTAT-AATAATAATTAT
*
473897 ATTATTCA
64 AATATTCA
* *
473905 TAAATATAAATATTTAAAAATTCATATTTTTACTTTTTTTTTAAAT-TA-TAT-ATAATAATTAT
1 TAAATATAAATATTTAAAAATTCATATTTATA--TCTTTTTTAAATCTACTATAATAATAATTAT
473967 AAATATT-A
64 -AATATTCA
473975 TAAATAT
1 TAAATAT
473982 TTAAATTAGT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
70 19 0.28
71 5 0.07
72 27 0.39
73 7 0.10
74 11 0.16
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (71 bp):
TAAATATAAATATTTAAAAATTCATATTTATATCTTTTTTAAATCTACTATAATAATAATTATAA
TATTCA
Found at i:474396 original size:17 final size:19
Alignment explanation
Indices: 474362--474457 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
474352 TTATTAGATT
474362 AAAAAATTATTAATATATA
1 AAAAAATTATTAATATATA
474381 AAAAAATT-TTAAATATATA
1 AAAAAATTATT-AATATATA
*
474400 TAATATAAATTATTAATTTATTA
1 -AA-A-AAATTATTAATATA-TA
**
474423 AATTAA-TA-TAA-ATATA
1 AAAAAATTATTAATATATA
*
474439 AAATAATT-TTAA-ATATA
1 AAAAAATTATTAATATATA
474456 AA
1 AA
474458 TTATAATATA
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
16 7 0.11
17 13 0.20
18 5 0.08
19 18 0.28
20 4 0.06
21 1 0.02
22 12 0.19
23 4 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAAATTATTAATATATA
Found at i:474407 original size:26 final size:27
Alignment explanation
Indices: 474376--474455 Score: 74
Period size: 31 Copynumber: 2.8 Consensus size: 27
474366 AATTATTAAT
474376 ATATAAAAAAATTTTAAATATATAT-A
1 ATATAAAAAAATTTTAAATATATATAA
*
474402 ATATAAATTATTAATTTATTAAAT-TAATATAA
1 ATATAAA--A--AAATT-TTAAATAT-ATATAA
*
474434 ATATAAAATAATTTTAAATATA
1 ATATAAAAAAATTTTAAATATA
474456 AATTATAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
26 7 0.16
27 7 0.16
28 5 0.12
30 6 0.14
31 10 0.23
32 8 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATAAAAAAATTTTAAATATATATAA
Found at i:474423 original size:49 final size:49
Alignment explanation
Indices: 474368--474482 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 49
474358 GATTAAAAAA
* *
474368 TTATTAATATATAAAAAAATTTTAAAT-A-TATATAATATAAATTATTAAT
1 TTATTAATATATAAAAAAATATAAAATAATTATA-AATATAAATTA-TAAT
* *
474417 TTATTAA-AT-TAATATAAATATAAAATAATTTTAAATATAAATTATAAT
1 TTATTAATATATAA-AAAAATATAAAATAATTATAAATATAAATTATAAT
* *
474465 ATAATAATATGATAAAAA
1 TTATTAATAT-ATAAAAA
474483 TTTACGAAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
47 3 0.06
48 21 0.40
49 21 0.40
50 5 0.09
51 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (49 bp):
TTATTAATATATAAAAAAATATAAAATAATTATAAATATAAATTATAAT
Found at i:474470 original size:17 final size:16
Alignment explanation
Indices: 474390--474470 Score: 55
Period size: 17 Copynumber: 5.0 Consensus size: 16
474380 AAAAAAATTT
474390 TAAATAT-ATATAATA
1 TAAATATAATATAATA
*
474405 TAAATTATTAAT-TTAT-
1 TAAA-TA-TAATATAATA
474421 TAAAT-TAATATAAATA
1 TAAATATAATAT-AATA
*
474437 TAAA-ATAATTTTAAATA
1 TAAATATAA-TAT-AATA
474454 TAAATTATAATATAATA
1 TAAA-TATAATATAATA
474471 ATATGATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
13 4 0.08
14 1 0.02
15 7 0.13
16 13 0.25
17 19 0.37
18 4 0.08
19 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATATAATATAATA
Found at i:474484 original size:58 final size:58
Alignment explanation
Indices: 474363--474484 Score: 128
Period size: 58 Copynumber: 2.1 Consensus size: 58
474353 TATTAGATTA
* *
474363 AAAAATTATTAATATATAAAAAAATTTTAAATATATATAATATAAATTATTAATTTAT
1 AAAAATTATTAATATATAAAAAAATTTTAAATATATATAATATAAATTAATAATTGAT
* * *
474421 -TAAATTAATATAA-ATATAAAATAATTTTAAATATA-A-ATTAT-AATATAATAATATGAT
1 AAAAATT-AT-TAATATATAAAAAAATTTTAAATATATATAATATAAAT-TAATAAT-TGAT
474478 AAAAATT
1 AAAAATT
474485 TACGAAAGAC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
55 3 0.06
56 10 0.19
57 9 0.17
58 28 0.53
59 3 0.06
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (58 bp):
AAAAATTATTAATATATAAAAAAATTTTAAATATATATAATATAAATTAATAATTGAT
Found at i:475919 original size:13 final size:12
Alignment explanation
Indices: 475900--475942 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
475890 AAAATCTGTA
475900 TTTATTTTAATT
1 TTTATTTTAATT
*
475912 TGTTATTTTTATT
1 T-TTATTTTAATT
* *
475925 TATAATTTAATT
1 TTTATTTTAATT
475937 TTTATT
1 TTTATT
475943 GATTATAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTATTTTAATT
Found at i:476279 original size:17 final size:17
Alignment explanation
Indices: 476257--476289 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
476247 TTTTGTGTTA
476257 TTTTAAATTTAAATTAT
1 TTTTAAATTTAAATTAT
*
476274 TTTTAAGTTTAAATTA
1 TTTTAAATTTAAATTA
476290 ATTAGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTTAAATTTAAATTAT
Found at i:481596 original size:11 final size:11
Alignment explanation
Indices: 481563--481597 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
481553 ATATAATTTT
481563 TTAAATATATA
1 TTAAATATATA
**
481574 AAAAATATATA
1 TTAAATATATA
481585 TTAAATATATA
1 TTAAATATATA
481596 TT
1 TT
481598 CATATTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAAATATATA
Found at i:482016 original size:17 final size:17
Alignment explanation
Indices: 481970--482018 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
481960 GATTTCGATA
481970 TATTTGATATAAAT-TAT
1 TATTT-ATATAAATATAT
481987 TATTTA-ATAAAATAATAT
1 TATTTATAT-AAAT-ATAT
482005 T-TTTATATAAATAT
1 TATTTATATAAATAT
482019 TTAATAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.07
16 7 0.25
17 13 0.46
18 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TATTTATATAAATATAT
Found at i:482023 original size:21 final size:20
Alignment explanation
Indices: 481999--482062 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 20
481989 TTTAATAAAA
481999 TAATATTTTTATATAAATATT
1 TAATATTTTTATAT-AATATT
*
482020 TAATAATTTTT-TTTAATATTT
1 TAAT-ATTTTTATATAATA-TT
482041 TAAT-TTTTTA-ATAATAATT
1 TAATATTTTTATATAAT-ATT
482060 TAA
1 TAA
482063 GTTTACATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 14 0.38
20 5 0.14
21 12 0.32
22 6 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATATTTTTATATAATATT
Found at i:491645 original size:21 final size:20
Alignment explanation
Indices: 491612--491663 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
491602 AAATTTGAAC
*
491612 AATATTTTTTATTTTATATAAA
1 AATATTATTTATTTT-T-TAAA
491634 AATA-TATTTA-TTTTTAAA
1 AATATTATTTATTTTTTAAA
491652 AATATTATTTAT
1 AATATTATTTAT
491664 AAATTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.30
19 7 0.26
20 3 0.11
21 5 0.19
22 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTATTTATTTTTTAAA
Found at i:491724 original size:15 final size:15
Alignment explanation
Indices: 491693--491737 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
491683 ATAAATATAT
*
491693 TTTTTATTTATTATTA
1 TTTTTATATATT-TTA
491709 TTTTTATATATTTTA
1 TTTTTATATATTTTA
* *
491724 TTTTAAAATATTTT
1 TTTTTATATATTTT
491738 TAATTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTATATATTTTA
Found at i:491724 original size:18 final size:17
Alignment explanation
Indices: 491690--491727 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
491680 AAAATAAATA
491690 TATTTTTTATTTATTAT
1 TATTTTTTATTTATTAT
*
491707 TA-TTTTTATATATT-T
1 TATTTTTTATTTATTAT
491722 TATTTT
1 TATTTT
491728 AAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.16
16 14 0.74
17 2 0.11
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTTTATTTATTAT
Found at i:491747 original size:17 final size:17
Alignment explanation
Indices: 491714--491762 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
491704 TATTATTTTT
*
491714 ATATATTTT-ATTTTAAA
1 ATAT-TTTTAATTATAAA
491731 ATATTTTTAATTATAAA
1 ATATTTTTAATTATAAA
*
491748 ATTATCTTTAATTAT
1 A-TATTTTTAATTAT
491763 TATCAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 4 0.14
17 12 0.43
18 12 0.43
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTTTTAATTATAAA
Found at i:491759 original size:18 final size:17
Alignment explanation
Indices: 491727--491762 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
491717 TATTTTATTT
*
491727 TAAAATATTTTTAATTA
1 TAAAATATCTTTAATTA
491744 TAAAATTATCTTTAATTA
1 TAAAA-TATCTTTAATTA
491762 T
1 T
491763 TATCAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAAATATCTTTAATTA
Found at i:491992 original size:25 final size:25
Alignment explanation
Indices: 491964--492019 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
491954 ATTAGATATT
*
491964 AATATATTATTTTATT-TTATTTAAA
1 AATATATTA-ATTATTATTATTTAAA
*
491989 AATAAATTAATTATTATTATTTAAA
1 AATATATTAATTATTATTATTTAAA
492014 AATATA
1 AATATA
492020 AAAATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AATATATTAATTATTATTATTTAAA
Found at i:492057 original size:20 final size:19
Alignment explanation
Indices: 492011--492057 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
492001 ATTATTATTT
*
492011 AAAAATATA--AAAATAAA
1 AAAAATATATTAAAACAAA
492028 AAAAAT-TATTAAAACAAA
1 AAAAATATATTAAAACAAA
492046 AAAATATATATT
1 AAAA-ATATATT
492058 TTTAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 6 0.24
18 11 0.44
19 2 0.08
20 4 0.16
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATATATTAAAACAAA
Found at i:492184 original size:21 final size:21
Alignment explanation
Indices: 492143--492185 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
492133 AAAAAATATA
*
492143 TTTTATATATTTTATTCATTT
1 TTTTATATATTTTATTAATTT
*
492164 TTTTAT-TTTTTTAATTAATTT
1 TTTTATATATTTT-ATTAATTT
492185 T
1 T
492186 ATTTTCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTATATATTTTATTAATTT
Found at i:492723 original size:16 final size:16
Alignment explanation
Indices: 492681--492726 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
492671 ATATGAAAAC
* *
492681 ATAAAAATTTAAAATT
1 ATAAATATTTAATATT
492697 ATAAATATTTAATATT
1 ATAAATATTTAATATT
492713 -TAAATATTTTAATA
1 ATAAATA-TTTAATA
492727 ATAAATAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAAATATTTAATATT
Found at i:492731 original size:15 final size:15
Alignment explanation
Indices: 492681--492733 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
492671 ATATGAAAAC
* *
492681 ATAAAAATTTAAAATT
1 ATAAATATTTAATA-T
492697 ATAAATATTTAATAT
1 ATAAATATTTAATAT
*
492712 TTAAATATTTTAATA-
1 ATAAATA-TTTAATAT
492727 ATAAATA
1 ATAAATA
492734 GATAAAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 13 0.41
16 19 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATATTTAATAT
Found at i:492761 original size:20 final size:20
Alignment explanation
Indices: 492744--492788 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
492734 GATAAAATGA
492744 ATATAAAAATATTTAAATAT
1 ATATAAAAATATTTAAATAT
* *
492764 ATATATAAATATTTAAAAAT
1 ATATAAAAATATTTAAATAT
492784 ATATA
1 ATATA
492789 GTAAAGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAAAAATATTTAAATAT
Found at i:492765 original size:10 final size:10
Alignment explanation
Indices: 492747--492785 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
492737 AAAATGAATA
492747 TAAAAATATT
1 TAAAAATATT
* *
492757 TAAATATATA
1 TAAAAATATT
*
492767 TATAAATATT
1 TAAAAATATT
492777 TAAAAATAT
1 TAAAAATAT
492786 ATAGTAAAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAAAATATT
Found at i:492909 original size:93 final size:90
Alignment explanation
Indices: 492790--492956 Score: 244
Period size: 93 Copynumber: 1.8 Consensus size: 90
492780 AAATATATAG
* *
492790 TAAAGTATTATTAATAAGATTCAATTATGAAAAATATTTTTTAATTATTTAATTTAATAAATATA
1 TAAAGTATTATTAATAAGATCCAATTATGAAAAATATTTTTTAA--ATCTAATTTAATAAATATA
492855 TTTTATTTTTAAAAAATATTAAATACAA
64 -TTTATTTTTAAAAAATATTAAATACAA
* * * * *
492883 TAAATTATTATTAATTAGATCCAATTATTAAAAATGTTTTTTAAGTCTAATTTAATAAATATATT
1 TAAAGTATTATTAATAAGATCCAATTATGAAAAATATTTTTTAAATCTAATTTAATAAATATATT
492948 TATTTTTAA
66 TATTTTTAA
492957 TGAAATTATG
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
90 11 0.16
91 17 0.25
93 39 0.58
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (90 bp):
TAAAGTATTATTAATAAGATCCAATTATGAAAAATATTTTTTAAATCTAATTTAATAAATATATT
TATTTTTAAAAAATATTAAATACAA
Found at i:493645 original size:15 final size:15
Alignment explanation
Indices: 493625--493668 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 15
493615 TTTTTGCGAT
493625 TAAAATTAAAGTATA
1 TAAAATTAAAGTATA
493640 TAAAATAAATTAAAGTATA
1 T---A-AAATTAAAGTATA
493659 TAAAATTAAA
1 TAAAATTAAA
493669 CAACACAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 9 0.36
16 1 0.04
18 1 0.04
19 14 0.56
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
TAAAATTAAAGTATA
Found at i:493651 original size:19 final size:19
Alignment explanation
Indices: 493627--493664 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
493617 TTTGCGATTA
493627 AAATTAAAGTATATAAAAT
1 AAATTAAAGTATATAAAAT
493646 AAATTAAAGTATATAAAAT
1 AAATTAAAGTATATAAAAT
493665 TAAACAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AAATTAAAGTATATAAAAT
Found at i:493992 original size:16 final size:17
Alignment explanation
Indices: 493955--493992 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
493945 ATCAAATTCG
*
493955 GATTTTTTTTAATATTA
1 GATTTTATTTAATATTA
*
493972 GATTTTATTTATTATTA
1 GATTTTATTTAATATTA
493989 -ATTT
1 GATTT
493993 AGATAGAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (17 bp):
GATTTTATTTAATATTA
Found at i:494565 original size:50 final size:50
Alignment explanation
Indices: 494467--494565 Score: 114
Period size: 50 Copynumber: 2.0 Consensus size: 50
494457 AACATGATGC
* ** *
494467 ATAAATTATATAATATATAACATAAATATTTATATTAAAATTTATTTAAT
1 ATAAATTATATAATATATAAAATAAATAAATATATTAAAATATATTTAAT
494517 ATAAATTAT-TAATATATCAAAATTTAAATAAATATA-TAAAATAT-TTTAA
1 ATAAATTATATAATATAT-AAAA--TAAATAAATATATTAAAATATATTTAA
494566 ACACAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
49 8 0.19
50 17 0.40
51 7 0.17
52 10 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (50 bp):
ATAAATTATATAATATATAAAATAAATAAATATATTAAAATATATTTAAT
Found at i:494702 original size:14 final size:14
Alignment explanation
Indices: 494654--494704 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
494644 TTTATTATAT
494654 AATAAAATATTTTA
1 AATAAAATATTTTA
*
494668 AA-AATATA-TTTA
1 AATAAAATATTTTA
*
494680 TAATTAAATATTTTA
1 -AATAAAATATTTTA
494695 AATAAAATAT
1 AATAAAATAT
494705 ATTTTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 4 0.13
13 7 0.23
14 15 0.50
15 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAAAATATTTTA
Found at i:494704 original size:28 final size:28
Alignment explanation
Indices: 494646--494704 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
494636 TGATCTATTT
*
494646 TATTATATAATAAAATATTTTAAAAATA
1 TATTATATAATAAAATATTTTAAAAAAA
*
494674 TATT-TATAATTAAATATTTTAAATAAAA
1 TATTATATAATAAAATATTTTAAA-AAAA
494702 TAT
1 TAT
494705 ATTTTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TATTATATAATAAAATATTTTAAAAAAA
Found at i:495462 original size:30 final size:30
Alignment explanation
Indices: 495422--495493 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
495412 ATGGTGGACT
*
495422 TGGTGGCTTGTAAGGGGGTGTTGGAGTTGG
1 TGGTGGCTTGTAAGGGGGTGCTGGAGTTGG
* * *
495452 TGGTGCCTTGTAAGGGGGTGCTGGTGTTGT
1 TGGTGGCTTGTAAGGGGGTGCTGGAGTTGG
495482 TGGTGGCTTGTA
1 TGGTGGCTTGTA
495494 TGGAGGTGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.08, C:0.07, G:0.49, T:0.36
Consensus pattern (30 bp):
TGGTGGCTTGTAAGGGGGTGCTGGAGTTGG
Found at i:495634 original size:48 final size:48
Alignment explanation
Indices: 495524--495634 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 48
495514 GTGCTGTTGG
* * * * *
495524 CTTGGTTGGTGGTGCTGGAGTTGGGGGCTTATATGGGGGTGTAGGGGC
1 CTTGGTTGGAGGTGCAGGAGTTGGGAGCTTATATGGGGGAGTAGGAGC
*** * * * *
495572 CTTCACTGGGGGTGCAGGAGTTGGTAGTTTATATGGGGGAGTCGGAGC
1 CTTGGTTGGAGGTGCAGGAGTTGGGAGCTTATATGGGGGAGTAGGAGC
495620 CTTGGTTGGAGGTGC
1 CTTGGTTGGAGGTGC
495635 TGGTGCCTTA
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.12, C:0.11, G:0.48, T:0.30
Consensus pattern (48 bp):
CTTGGTTGGAGGTGCAGGAGTTGGGAGCTTATATGGGGGAGTAGGAGC
Found at i:495739 original size:48 final size:48
Alignment explanation
Indices: 495655--495750 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
495645 GTTAGTGGTG
* * * ** *
495655 CAGGAGTTGGGGGTTTATATGGGGGAGTGGGGGCCTTGATTGGCGGTA
1 CAGGAGCTGGGGGCTTATATGGAGGAGAAGGAGCCTTGATTGGCGGTA
495703 CAGGAGCTGGGGGCTTATATGGAGGAGAAGGAGCCTTGATTGGCGGTA
1 CAGGAGCTGGGGGCTTATATGGAGGAGAAGGAGCCTTGATTGGCGGTA
495751 TTGGGGCCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.19, C:0.10, G:0.47, T:0.24
Consensus pattern (48 bp):
CAGGAGCTGGGGGCTTATATGGAGGAGAAGGAGCCTTGATTGGCGGTA
Found at i:495760 original size:117 final size:117
Alignment explanation
Indices: 495532--495778 Score: 289
Period size: 117 Copynumber: 2.1 Consensus size: 117
495522 GGCTTGGTTG
* * * * *
495532 GTGGTGCTGGAGTTGGGGGCTTATATGGGGGTGTAGGGGCCTTCACTGGGGGTGCAGGAGTTGGT
1 GTGGTGCTGGAGTTGGGGGCTTATATGGGGGAGTAGGGGCCTTCACTGGCGGTACAGGAGCTGGG
* * ** * * *
495597 AGTTTATATGGGGGAGTCGGAGCCTTGGTTGGAGGTGCTGGTGCCTTAGT-TA
66 AGCTTATATGGAGGAGAAGGAGCCTTGATTGGAGGTACTGGGGCCTT-GTATA
* * * * *
495649 GTGGTGCAGGAGTTGGGGGTTTATATGGGGGAGTGGGGGCCTTGATTGGCGGTACAGGAGCTGGG
1 GTGGTGCTGGAGTTGGGGGCTTATATGGGGGAGTAGGGGCCTTCACTGGCGGTACAGGAGCTGGG
* * * *
495714 GGCTTATATGGAGGAGAAGGAGCCTTGATTGGCGGTATTGGGGCCTTGTATG
66 AGCTTATATGGAGGAGAAGGAGCCTTGATTGGAGGTACTGGGGCCTTGTATA
495766 GTGGTGCTGGAGT
1 GTGGTGCTGGAGT
495779 GGTGGGAGTC
Statistics
Matches: 107, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
116 2 0.02
117 105 0.98
ACGTcount: A:0.14, C:0.11, G:0.47, T:0.28
Consensus pattern (117 bp):
GTGGTGCTGGAGTTGGGGGCTTATATGGGGGAGTAGGGGCCTTCACTGGCGGTACAGGAGCTGGG
AGCTTATATGGAGGAGAAGGAGCCTTGATTGGAGGTACTGGGGCCTTGTATA
Found at i:497048 original size:27 final size:27
Alignment explanation
Indices: 497003--497055 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
496993 TAAAATTTAC
*
497003 ATTATATAAATTATTAATATGTTAAAA
1 ATTATATAAATTATAAATATGTTAAAA
*
497030 ATTATATAAA-TATAAAATATTTTAAA
1 ATTATATAAATTAT-AAATATGTTAAA
497056 TATAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTATATAAATTATAAATATGTTAAAA
Found at i:497192 original size:183 final size:183
Alignment explanation
Indices: 496879--497255 Score: 709
Period size: 183 Copynumber: 2.1 Consensus size: 183
496869 ACCAAATTTG
496879 ATAAGTCTAATTTTTGAATATTAATTTGGATTAAATCTTTCAAATTTTTTAACATTCTAAACAAA
1 ATAA-TCTAATTTTTGAATATTAATTTGGATTAAATCTTTCAAATTTTTTAACATTCTAAACAAA
496944 TGTATATAACTATAATTATATGAATATGAGATAAAATAAATGTATATTTTAAAATTTACATTATA
65 TGTATATAACTATAATTATATGAATATGAGATAAAATAAATGTATATTTTAAAATTTACATTATA
*
497009 TAAATTATTAATATGTTAAAAATTATATAAATATAAAATATTTTAAATATAATT
130 TAAATTATTAATATATTAAAAATTATATAAATATAAAATATTTTAAATATAATT
*
497063 ATAATCTAATTTTTTAATATTAATTTGGATTAAATCTTTCAAATTTTTTAACATTCTAAACAAAT
1 ATAATCTAATTTTTGAATATTAATTTGGATTAAATCTTTCAAATTTTTTAACATTCTAAACAAAT
*
497128 GTATATAACTATAATTATATGAATATGAGATAAAATAAATGTATATTTTAAAATTTATATTATAT
66 GTATATAACTATAATTATATGAATATGAGATAAAATAAATGTATATTTTAAAATTTACATTATAT
*
497193 AAATTATTAATATATTAAAATTTATATAAATATAAAATATTTTAAATATAATT
131 AAATTATTAATATATTAAAAATTATATAAATATAAAATATTTTAAATATAATT
497246 ATAATCTAAT
1 ATAATCTAAT
497256 AAAATATAAA
Statistics
Matches: 189, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
183 185 0.98
184 4 0.02
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (183 bp):
ATAATCTAATTTTTGAATATTAATTTGGATTAAATCTTTCAAATTTTTTAACATTCTAAACAAAT
GTATATAACTATAATTATATGAATATGAGATAAAATAAATGTATATTTTAAAATTTACATTATAT
AAATTATTAATATATTAAAAATTATATAAATATAAAATATTTTAAATATAATT
Found at i:497216 original size:32 final size:33
Alignment explanation
Indices: 497170--497233 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
497160 AAATAAATGT
* * *
497170 ATATTTTAAAATTTATAT-TATATAAATTATTA
1 ATATATTAAAATTTATATAAATATAAAATATTA
497202 ATATATTAAAATTTATATAAATATAAAATATT
1 ATATATTAAAATTTATATAAATATAAAATATT
497234 TTAAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
ATATATTAAAATTTATATAAATATAAAATATTA
Found at i:497217 original size:18 final size:17
Alignment explanation
Indices: 497176--497243 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 17
497166 ATGTATATTT
*
497176 TAAAATTTA-TATTATA
1 TAAAATTTATTAATATA
497192 T-AAA-TTATTAATATA
1 TAAAATTTATTAATATA
497207 TTAAAATTTATATAA-ATA
1 -TAAAATTTAT-TAATATA
497225 TAAAATATT-TTAA-ATA
1 TAAAAT-TTATTAATATA
497241 TAA
1 TAA
497244 TTATAATCTA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
14 3 0.07
15 9 0.20
16 11 0.24
17 10 0.22
18 9 0.20
19 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATTTATTAATATA
Found at i:497738 original size:13 final size:13
Alignment explanation
Indices: 497720--497745 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
497710 AATTTTGACC
497720 TTTTTTTTAATTT
1 TTTTTTTTAATTT
497733 TTTTTTTTAATTT
1 TTTTTTTTAATTT
497746 ATTTGATAGC
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTAATTT
Found at i:497933 original size:15 final size:16
Alignment explanation
Indices: 497900--497962 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 16
497890 AAATTTAAAT
*
497900 TTAAATTTTAAATTTA
1 TTAAATTTTAAATTAA
497916 TTAAATTTT-AATTAA
1 TTAAATTTTAAATTAA
* ** *
497931 TTATATAAATCAATTAGA
1 TTAAAT-TTTAAATTA-A
497949 TTAAATTTTAAATT
1 TTAAATTTTAAATT
497963 TAAATTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 10 0.28
16 10 0.28
17 10 0.28
18 6 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
TTAAATTTTAAATTAA
Found at i:499628 original size:53 final size:53
Alignment explanation
Indices: 499506--499628 Score: 135
Period size: 53 Copynumber: 2.4 Consensus size: 53
499496 ATATTTTATA
* * *
499506 ATAAA-TT-GATAATAGATTCAGATATATAAATTTATTATCCACAAAAATAAT
1 ATAAATTTAGATAATAAATTCAAACATATAAATTTATTATCCACAAAAATAAT
* * * ** *
499557 ATAGATTTAGATAGTAAATTCAAACATCTAAATTTATTATTTATAAAAATAAT
1 ATAAATTTAGATAATAAATTCAAACATATAAATTTATTATCCACAAAAATAAT
499610 ATAAATTTTA-ATAATAAAT
1 ATAAA-TTTAGATAATAAAT
499629 ATTTAAAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
51 4 0.07
52 2 0.03
53 48 0.83
54 4 0.07
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (53 bp):
ATAAATTTAGATAATAAATTCAAACATATAAATTTATTATCCACAAAAATAAT
Found at i:500041 original size:13 final size:13
Alignment explanation
Indices: 500023--500047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
500013 GATTTAATTC
500023 ATTAAATTTTTTT
1 ATTAAATTTTTTT
500036 ATTAAATTTTTT
1 ATTAAATTTTTT
500048 ATAATATTTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTAAATTTTTTT
Found at i:502129 original size:2 final size:2
Alignment explanation
Indices: 502122--502161 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
502112 TACGTTAATA
502122 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
502162 GCACACACAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:503142 original size:59 final size:59
Alignment explanation
Indices: 503076--503192 Score: 225
Period size: 59 Copynumber: 2.0 Consensus size: 59
503066 TATTGTAAGT
*
503076 TCTCTTGCTAGAAGTACACAAAAATTGAAATAAACAGAATGTAGAAAGCTCGTGAAAGA
1 TCTCTTGCTAGAAATACACAAAAATTGAAATAAACAGAATGTAGAAAGCTCGTGAAAGA
503135 TCTCTTGCTAGAAATACACAAAAATTGAAATAAACAGAATGTAGAAAGCTCGTGAAAG
1 TCTCTTGCTAGAAATACACAAAAATTGAAATAAACAGAATGTAGAAAGCTCGTGAAAG
503193 TATCATGGGC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.22
Consensus pattern (59 bp):
TCTCTTGCTAGAAATACACAAAAATTGAAATAAACAGAATGTAGAAAGCTCGTGAAAGA
Found at i:504509 original size:28 final size:28
Alignment explanation
Indices: 504469--504524 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
504459 ACTCAAAGCT
504469 AAAAGCAAGATATCCCATAGGCTCTGAC
1 AAAAGCAAGATATCCCATAGGCTCTGAC
504497 AAAAGCAAGATATCCCATAGGCTCTGAC
1 AAAAGCAAGATATCCCATAGGCTCTGAC
504525 TCATACTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (28 bp):
AAAAGCAAGATATCCCATAGGCTCTGAC
Found at i:505444 original size:2 final size:2
Alignment explanation
Indices: 505437--505481 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
505427 AAAACTAGCC
505437 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
505479 TA T
1 TA T
505482 GGAACTTTTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:511420 original size:19 final size:19
Alignment explanation
Indices: 511336--511426 Score: 60
Period size: 19 Copynumber: 5.3 Consensus size: 19
511326 TGAATTGAAT
511336 TATTTAAT-TAA-AATA-A
1 TATTTAATATAATAATATA
*
511352 T-TTTAATATTA-AATA-A
1 TATTTAATATAATAATATA
*
511368 GTA-TTAA-AT-ATAATAAA
1 -TATTTAATATAATAATATA
*
511385 TATTTAATATAAAAATATA
1 TATTTAATATAATAATATA
511404 TATTTAAGTA-AATAATATA
1 TATTTAA-TATAATAATATA
511423 -ATTT
1 TATTT
511427 TAAATTAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
15 7 0.11
16 16 0.26
17 10 0.16
18 6 0.10
19 21 0.34
20 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TATTTAATATAATAATATA
Found at i:511421 original size:17 final size:18
Alignment explanation
Indices: 511353--511422 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 18
511343 TTAAAATAAT
*
511353 TTTAATATTAAATAA-GTA
1 TTTAATA-TAAATAATATA
*
511371 TTAAATAT-AATAA-ATA
1 TTTAATATAAATAATATA
*
511387 TTTAATATAAAAATATATA
1 TTTAATATAAATA-ATATA
*
511406 TTTAA-GTAAATAATATA
1 TTTAATATAAATAATATA
511423 ATTTTAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
16 14 0.33
17 9 0.21
18 12 0.28
19 8 0.19
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TTTAATATAAATAATATA
Found at i:511569 original size:2 final size:2
Alignment explanation
Indices: 511558--511589 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
511548 CTTTCCATTC
511558 TA TA -A 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 T
511590 TAGATATCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:512234 original size:6 final size:6
Alignment explanation
Indices: 512223--512257 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
512213 TGTTTTGGCT
*
512223 CTGAGC CTGAGC CTGAGC CTGCGC CTGAGC CTGAG
1 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAG
512258 GAAGCGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.14, C:0.34, G:0.34, T:0.17
Consensus pattern (6 bp):
CTGAGC
Found at i:513199 original size:19 final size:19
Alignment explanation
Indices: 513139--513205 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 19
513129 TTTCGATCCT
513139 ATTTTAAGTAATTTATATAATT-
1 ATTTTAA-T-ATTTATAT--TTA
513161 ATTTATAATATTTA-ATTTTA
1 ATTT-TAATATTTATA-TTTA
513181 ATTTTAATATTTATATTTA
1 ATTTTAATATTTATATTTA
513200 TATTTT
1 -ATTTT
513206 TTTCTTACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
19 15 0.38
20 11 0.28
21 6 0.15
22 5 0.12
23 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (19 bp):
ATTTTAATATTTATATTTA
Found at i:513403 original size:26 final size:27
Alignment explanation
Indices: 513374--513435 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
513364 TGTTGAATAA
*
513374 ATTTTTTTAAAATTTATA-TTAATT-T
1 ATTTTTTTAAAATTAATATTTAATTAT
*
513399 GATTTAATTT-AAATTAATATTTAATTAT
1 -ATTT-TTTTAAAATTAATATTTAATTAT
513427 ATTTTTTTA
1 ATTTTTTTA
513436 TTTAAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
26 15 0.52
27 13 0.45
28 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
ATTTTTTTAAAATTAATATTTAATTAT
Found at i:513463 original size:30 final size:29
Alignment explanation
Indices: 513405--513467 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
513395 ATTTGATTTA
** *
513405 ATTTAAATTAATATTTAATTATATTTTTTT
1 ATTTAAATTAATATTTAAAAATA-ATTTTT
513435 ATTTAAATTAA-ATTATAAAAATAATTTTT
1 ATTTAAATTAATATT-TAAAAATAATTTTT
513464 ATTT
1 ATTT
513468 TATTTCAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTTAAATTAATATTTAAAAATAATTTTT
Done.