Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold41
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: 2798036
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 10448 characters in sequence are not A, C, G, or T
File 4 of 21
Found at i:317609 original size:22 final size:20
Alignment explanation
Indices: 317558--317611 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
317548 AATTACGAAC
*
317558 ATATTA-AAATTTATTAAAT
1 ATATTATAAATTTTTTAAAT
*
317577 ATATAAT-AATTTTTTAAAAT
1 ATATTATAAATTTTTT-AAAT
317597 ATGATTATAAATTTT
1 AT-ATTATAAATTTT
317612 AAAAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 12 0.43
20 6 0.21
21 4 0.14
22 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATTATAAATTTTTTAAAT
Found at i:317611 original size:21 final size:20
Alignment explanation
Indices: 317558--317618 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
317548 AATTACGAAC
317558 ATATTA-AAATTTATT-AAAT
1 ATATTATAAATTT-TTAAAAT
* *
317577 ATATAATAATTTTTTAAAAT
1 ATATTATAAATTTTTAAAAT
*
317597 ATGATTATAAATTTTAAAAAT
1 AT-ATTATAAATTTTTAAAAT
317618 A
1 A
317619 ATATGAATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.21
20 11 0.32
21 16 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATATTATAAATTTTTAAAAT
Found at i:317776 original size:22 final size:22
Alignment explanation
Indices: 317749--317807 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
317739 ATTTAATTTT
317749 TTTATTTAATTTAACATAAATTA
1 TTTATTTAATTTAACA-AAATTA
*
317772 -TTATTT-ATTTAATAAAATTA
1 TTTATTTAATTTAACAAAATTA
317792 TTTTATTTAAATTTAA
1 -TTTATTT-AATTTAA
317808 TTATAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 6 0.19
21 7 0.23
22 12 0.39
24 6 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTATTTAATTTAACAAAATTA
Found at i:318611 original size:2 final size:2
Alignment explanation
Indices: 318604--318636 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
318594 AAAGGTTAAG
318604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
318637 TGTATGCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:320339 original size:21 final size:22
Alignment explanation
Indices: 320313--320355 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
320303 ATAATATAAT
320313 ATATG-ATAAGATATAAAAATA
1 ATATGAATAAGATATAAAAATA
**
320334 ATATGAATATTATATAAAAATA
1 ATATGAATAAGATATAAAAATA
320356 TGAATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (22 bp):
ATATGAATAAGATATAAAAATA
Found at i:320461 original size:11 final size:11
Alignment explanation
Indices: 320422--320463 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
320412 TATAATATTT
*
320422 TATAATTATGA
1 TATAAATATGA
* *
320433 TATAAAAATAA
1 TATAAATATGA
320444 TATAAATATGA
1 TATAAATATGA
320455 TATAAATAT
1 TATAAATAT
320464 ACGAAACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (11 bp):
TATAAATATGA
Found at i:321879 original size:37 final size:35
Alignment explanation
Indices: 321807--321875 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
321797 GTTTTGTATA
321807 AAATGATTTTTAAAAAATAAATTTATTTTTTTATTT
1 AAATGATTTTTAAAAAAT-AATTTATTTTTTTATTT
* *
321843 AAATGATTTTATGAAAAAT-ATTT-TTTTATTATT
1 AAATGATTTT-TAAAAAATAATTTATTTTTTTATT
321876 ATTTTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 9 0.30
35 4 0.13
36 10 0.33
37 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (35 bp):
AAATGATTTTTAAAAAATAATTTATTTTTTTATTT
Found at i:321990 original size:22 final size:22
Alignment explanation
Indices: 321941--321997 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
321931 TTCCTATGGT
** *
321941 GACATTTGAATGTTAAAATCAG
1 GACATTTGAATGCCAAAATCAA
* *
321963 GGCATTTGAATGCCAAAATGAA
1 GACATTTGAATGCCAAAATCAA
*
321985 GACATTCGAATGC
1 GACATTTGAATGC
321998 TTTTGTTTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (22 bp):
GACATTTGAATGCCAAAATCAA
Found at i:324678 original size:29 final size:30
Alignment explanation
Indices: 324624--324683 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
324614 TATTCTTAGG
*
324624 AGTTTGGAGTGCATTAAAACAATAATTTTA
1 AGTTTGGAGTACATTAAAACAATAATTTTA
324654 AGTTTGGAGTACA-TAAAA-AGATAATTTTA
1 AGTTTGGAGTACATTAAAACA-ATAATTTTA
324683 A
1 A
324684 TTTATTATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 1 0.04
29 15 0.54
30 12 0.43
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.35
Consensus pattern (30 bp):
AGTTTGGAGTACATTAAAACAATAATTTTA
Found at i:324697 original size:19 final size:18
Alignment explanation
Indices: 324673--324709 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
324663 TACATAAAAA
324673 GATAATTTTAATTTATTAT
1 GATAATTTTAATTT-TTAT
*
324692 GATAATTTTTATTTTTAT
1 GATAATTTTAATTTTTAT
324710 TAATTAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
GATAATTTTAATTTTTAT
Found at i:326246 original size:32 final size:33
Alignment explanation
Indices: 326191--326260 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 33
326181 TTTTATATAT
* *
326191 TTATATAAATTTTGATACGTTTA-TAATTCATA
1 TTATAAAAATTTTGATACATTTATTAATTCATA
* * *
326223 TTATAAAAATTTTGATATATTTATTTATTTATA
1 TTATAAAAATTTTGATACATTTATTAATTCATA
326256 TTATA
1 TTATA
326261 TTCATGTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 20 0.62
33 12 0.38
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (33 bp):
TTATAAAAATTTTGATACATTTATTAATTCATA
Found at i:326594 original size:2 final size:2
Alignment explanation
Indices: 326587--326629 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
326577 CACACTAATA
326587 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
326628 AT
1 AT
326630 TAAACATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:326767 original size:31 final size:31
Alignment explanation
Indices: 326729--326791 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
326719 GTAAAGATAA
326729 CCATATTCTTCCCCTATACCCCATTAGTTGC
1 CCATATTCTTCCCCTATACCCCATTAGTTGC
326760 CCATATTCTTCCCCTATACCCCATTAGTTGC
1 CCATATTCTTCCCCTATACCCCATTAGTTGC
326791 C
1 C
326792 TTTTCTTCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.40, G:0.06, T:0.35
Consensus pattern (31 bp):
CCATATTCTTCCCCTATACCCCATTAGTTGC
Found at i:327476 original size:2 final size:2
Alignment explanation
Indices: 327469--327500 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
327459 AGAAGGCTTC
327469 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
327501 ACTCTTGAAT
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:328027 original size:23 final size:22
Alignment explanation
Indices: 327971--328033 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
327961 TTTAAGATAT
*
327971 TATATATTTATATAAATTTTAA
1 TATATATTTATATAAATTCTAA
* *
327993 TATAGTAATTATTTAAATTCTAA
1 TATA-TATTTATATAAATTCTAA
328016 TCATATATTTATA-AAATT
1 T-ATATATTTATATAAATT
328034 TTTAAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.26
23 22 0.65
24 3 0.09
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATATTTATATAAATTCTAA
Found at i:332058 original size:6 final size:6
Alignment explanation
Indices: 332035--332074 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
332025 TATATTTTGG
*
332035 TATTTA TA-TTA TTTTTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA -TATTTA TATTTA TATTTA TATTTA TATT
332075 GTTTATCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 3 0.10
6 24 0.80
7 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TATTTA
Found at i:332305 original size:17 final size:17
Alignment explanation
Indices: 332283--332328 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
332273 AATAAATATA
332283 TATTTTTTATTAATTAT
1 TATTTTTTATTAATTAT
**
332300 TATTTTTTATTTTTTAT
1 TATTTTTTATTAATTAT
*
332317 TA-ATTTTATTAA
1 TATTTTTTATTAA
332329 AAATATTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTTTTTATTAATTAT
Found at i:332580 original size:16 final size:16
Alignment explanation
Indices: 332559--332596 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
332549 TTAGTTAAAG
332559 AAAATAATAAA-AAATA
1 AAAATAA-AAATAAATA
*
332575 AAAATAAAAATATATA
1 AAAATAAAAATAAATA
332591 AAAATA
1 AAAATA
332597 TATTTTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAAAAATAAATA
Found at i:332736 original size:24 final size:27
Alignment explanation
Indices: 332695--332747 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 27
332685 AACTTTAAAC
**
332695 TTTTTAAAATAATGATAA-ATAAT-TA
1 TTTTTAAAATAAAAATAACATAATATA
332720 TTTTT-AAATAAAAATAACATAATATA
1 TTTTTAAAATAAAAATAACATAATATA
332746 TT
1 TT
332748 AATATCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.42
25 10 0.42
26 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (27 bp):
TTTTTAAAATAAAAATAACATAATATA
Found at i:333767 original size:19 final size:22
Alignment explanation
Indices: 333743--333783 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
333733 TTTTATTGAA
333743 AAATATTT-TT-ATA-AAAAAT
1 AAATATTTATTAATAGAAAAAT
333762 AAATATTTATTAATAGAAAAAT
1 AAATATTTATTAATAGAAAAAT
333784 TATTTTCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 3 0.16
22 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATATTTATTAATAGAAAAAT
Found at i:334360 original size:29 final size:28
Alignment explanation
Indices: 334328--334431 Score: 98
Period size: 29 Copynumber: 3.9 Consensus size: 28
334318 AAAAATTTAT
*
334328 ATATTTTATAT-AATTAAATTTAAATAAAA
1 ATATTTTATTTAAATT-AA-TTAAATAAAA
334357 ATA-TTT-TTT--ATTAATTAAAT---A
1 ATATTTTATTTAAATTAATTAAATAAAA
334378 ATATTTTATTTAAATTAATCTAAATAAAA
1 ATATTTTATTTAAATTAAT-TAAATAAAA
*
334407 ATATTATATTTAAATTAAATTAAAT
1 ATATTTTATTTAAATT-AATTAAAT
334432 TCAAATTAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
21 4 0.06
22 3 0.05
23 3 0.05
24 6 0.09
25 8 0.12
26 8 0.12
27 2 0.03
28 3 0.05
29 24 0.38
30 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (28 bp):
ATATTTTATTTAAATTAATTAAATAAAA
Found at i:334393 original size:21 final size:20
Alignment explanation
Indices: 334345--334395 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
334335 ATATAATTAA
334345 ATTTAAA-TAAAAATATTTT
1 ATTTAAATTAAAAATATTTT
*
334364 -TTATTAATTAAATAATATTTT
1 ATT-TAAATTAAA-AATATTTT
334385 ATTTAAATTAA
1 ATTTAAATTAA
334396 TCTAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 4 0.15
21 15 0.58
22 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAAATTAAAAATATTTT
Found at i:334423 original size:50 final size:49
Alignment explanation
Indices: 334328--334426 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 49
334318 AAAAATTTAT
*
334328 ATATTTTATATAATTAAATTTAAATAAAAATATTTTTTATTAATTAAATA
1 ATATTTTATATAATTAAATCTAAATAAAAATATTTTTTA-TAATTAAATA
*
334378 ATATTTTATTTAAATT-AATCTAAATAAAAATATTATATTTA-AATTAAAT
1 ATATTTTATAT-AATTAAATCTAAATAAAAATATT-T-TTTATAATTAAAT
334427 TAAATTCAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
50 35 0.80
51 5 0.11
52 4 0.09
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (49 bp):
ATATTTTATATAATTAAATCTAAATAAAAATATTTTTTATAATTAAATA
Found at i:334424 original size:5 final size:5
Alignment explanation
Indices: 334416--334456 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
334406 AATATTATAT
*
334416 TTAAA TTAAA TTAAA TTCAAA TTAAA TT-TA TTAAA TTAAA T
1 TTAAA TTAAA TTAAA TT-AAA TTAAA TTAAA TTAAA TTAAA T
334457 AAAAAACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 3 0.09
5 24 0.75
6 5 0.16
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:334437 original size:11 final size:10
Alignment explanation
Indices: 334416--334456 Score: 57
Period size: 11 Copynumber: 4.1 Consensus size: 10
334406 AATATTATAT
334416 TTAAATTAAA
1 TTAAATTAAA
334426 TTAAATTCAAA
1 TTAAATT-AAA
*
334437 TTAAATT-TA
1 TTAAATTAAA
334446 TTAAATTAAA
1 TTAAATTAAA
334456 T
1 T
334457 AAAAAACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.30
10 9 0.33
11 10 0.37
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
TTAAATTAAA
Found at i:334437 original size:29 final size:28
Alignment explanation
Indices: 334339--334460 Score: 95
Period size: 25 Copynumber: 4.6 Consensus size: 28
334329 TATTTTATAT
334339 AATTAAATTTAAATAAAAATATT-T-TTT-
1 AATTAAA-TTAAAT-AAAATATTATATTTA
*
334366 -ATT-AATTAAAT--AATATTTTATTTA
1 AATTAAATTAAATAAAATATTATATTTA
334390 AATT-AATCTAAATAAAAATATTATATTTA
1 AATTAAAT-TAAAT-AAAATATTATATTTA
** *
334419 AATTAAATTAAATTCAA-ATTAAATTT-
1 AATTAAATTAAATAAAATATTATATTTA
334445 -ATTAAATTAAATAAAA
1 AATTAAATTAAATAAAA
334461 AACTTAATTT
Statistics
Matches: 80, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
21 6 0.08
22 1 0.01
23 3 0.04
24 6 0.08
25 22 0.28
26 8 0.10
27 8 0.10
28 2 0.03
29 21 0.26
30 3 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
AATTAAATTAAATAAAATATTATATTTA
Found at i:334441 original size:50 final size:48
Alignment explanation
Indices: 334347--334451 Score: 115
Period size: 50 Copynumber: 2.1 Consensus size: 48
334337 ATAATTAAAT
** *
334347 TTAAATAAAAATATTTTTTATTAATTAAATAATATTTTATTTAAATTAA
1 TTAAATAAAAATATTTTTTA-TAATTAAATAATATTCAAATTAAATTAA
*
334396 TCTAAATAAAAATATTATATTTA-AATTAAATTAA-ATTCAAATTAAATTTA
1 T-TAAATAAAAATATT-T-TTTATAATTAAA-TAATATTCAAATTAAATTAA
334446 TTAAAT
1 TTAAAT
334452 TAAATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
49 6 0.12
50 34 0.71
51 4 0.08
52 4 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (48 bp):
TTAAATAAAAATATTTTTTATAATTAAATAATATTCAAATTAAATTAA
Found at i:335271 original size:3 final size:3
Alignment explanation
Indices: 335263--335298 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
335253 TAAAACATTA
335263 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
335299 CTACACAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:337343 original size:2 final size:2
Alignment explanation
Indices: 337336--337370 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
337326 AGGATTCAAA
337336 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 A
337371 ATTATGAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:338728 original size:16 final size:16
Alignment explanation
Indices: 338709--338766 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
338699 ATTATTTCGA
338709 GTTTGAATCATTTTAG
1 GTTTGAATCATTTTAG
* ** *
338725 GTTTGGATTGTTTTGG
1 GTTTGAATCATTTTAG
338741 GTTTGAATCATTTTAG
1 GTTTGAATCATTTTAG
* *
338757 ATTTGGATCA
1 GTTTGAATCA
338767 ATCAGGTTTA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.21, C:0.05, G:0.24, T:0.50
Consensus pattern (16 bp):
GTTTGAATCATTTTAG
Found at i:339763 original size:13 final size:13
Alignment explanation
Indices: 339741--339770 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
339731 CTATTCATAG
*
339741 ATAAAGGAAAAAA
1 ATAAAAGAAAAAA
339754 ATAAAAGAAAAAA
1 ATAAAAGAAAAAA
339767 ATAA
1 ATAA
339771 GAAAAAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (13 bp):
ATAAAAGAAAAAA
Found at i:340708 original size:13 final size:15
Alignment explanation
Indices: 340692--340743 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
340682 AAATCTGAAT
340692 AATTTAAAT-A-TCA
1 AATTTAAATGATTCA
340705 AATTTAAATGATTCA
1 AATTTAAATGATTCA
* * *
340720 AACTTAAAACGATTTA
1 AA-TTTAAATGATTCA
340736 AATTTAAA
1 AATTTAAA
340744 ATTACTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.28
14 1 0.03
15 10 0.31
16 12 0.38
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (15 bp):
AATTTAAATGATTCA
Found at i:340915 original size:16 final size:17
Alignment explanation
Indices: 340891--340922 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
340881 ATTTTTTATT
340891 TTTTAAAAAATTATATA
1 TTTTAAAAAATTATATA
340908 TTTT-AAAAATTATAT
1 TTTTAAAAAATTATAT
340923 TTATATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAAAAAATTATATA
Found at i:341588 original size:21 final size:19
Alignment explanation
Indices: 341564--341616 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
341554 GATTGATAAA
341564 ATAATTTATTTAAAATTTAAT
1 ATAATTTA-TT-AAATTTAAT
*
341585 ATAATTTATTAAATTTAAA
1 ATAATTTATTAAATTTAAT
341604 ACTAAATTTATTA
1 A-T-AATTTATTA
341617 TCTAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 9 0.31
20 3 0.10
21 17 0.59
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAATTTATTAAATTTAAT
Found at i:341869 original size:20 final size:19
Alignment explanation
Indices: 341821--341877 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 19
341811 ATTCGAATAA
341821 TAAAATAATTTATTTAAAATT
1 TAAAATAATTTA-TT-AAATT
*
341842 TAATATAATTTATTAAATT
1 TAAAATAATTTATTAAATT
341861 TAAAAATAAGTTTATTA
1 T-AAAATAA-TTTATTA
341878 TCTAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.19
20 8 0.25
21 18 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TAAAATAATTTATTAAATT
Found at i:341921 original size:261 final size:257
Alignment explanation
Indices: 341457--341975 Score: 858
Period size: 261 Copynumber: 2.0 Consensus size: 257
341447 ATTAATTTCT
*
341457 ATTTATATTTTATAATCTTACAATTATTGTTGAAACCAAGTAGCAAATGAGAATAAGAGGAGCTT
1 ATTTATATTTTATAATCTTACAATTATTGTTGAAACCAAGAAGCAAATGAGAATAAGAGGAGCTT
* * * * *
341522 TTCAATGGTAGGAGTAAAATTAGATTAAATTTGATTGATAAAATAATTTATTTAAAATTTAATAT
66 TTCAATGGTAGGAGTAAAATCAAATTAAATTCGAATAATAAAATAATTTATTTAAAATTTAATAT
* *
341587 AATTTATTAAATTTAAAACTAAATTTATTATCTAAAATATACTAAAAATAATTTAAAAACCTTGT
131 AATTTATTAAATTTAAAAATAAATTTATTATCTAAAAAATACTAAAAATAATTTAAAAACCTTGT
*
341652 TAGATATATATATATATATATATATCAAATAATTACAGCATAAAATTTTTATACAAATACCATGC
196 TAG--ATATATATATATATAT-TA-CAAACAATTACAGCATAAAATTTTTATACAAATACCATGC
341717 G
257 G
* * *
341718 ATTTATATTTTATAATCTTACAATTATTGTTTAAACCAAGAAGTAAATGGGAATAAGAGGAGCTT
1 ATTTATATTTTATAATCTTACAATTATTGTTGAAACCAAGAAGCAAATGAGAATAAGAGGAGCTT
*
341783 TTCAATGGTTGGAGTAAAATCAAATTAAATTCGAATAATAAAATAATTTATTTAAAATTTAATAT
66 TTCAATGGTAGGAGTAAAATCAAATTAAATTCGAATAATAAAATAATTTATTTAAAATTTAATAT
* *
341848 AATTTATTAAATTTAAAAATAAGTTTATTATCTAAAAAATATTAAAAATAATTTAAAAACCTTGT
131 AATTTATTAAATTTAAAAATAAATTTATTATCTAAAAAATACTAAAAATAATTTAAAAACCTTGT
*
341913 TAGATATATATATATATATTACATACAATTACAGCATAAAATTTTTATACAAATACCATGCG
196 TAGATATATATATATATATTACAAACAATTACAGCATAAAATTTTTATACAAATACCATGCG
341975 A
1 A
341976 ATATGAACAG
Statistics
Matches: 242, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
257 40 0.17
258 2 0.01
259 16 0.07
261 184 0.76
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (257 bp):
ATTTATATTTTATAATCTTACAATTATTGTTGAAACCAAGAAGCAAATGAGAATAAGAGGAGCTT
TTCAATGGTAGGAGTAAAATCAAATTAAATTCGAATAATAAAATAATTTATTTAAAATTTAATAT
AATTTATTAAATTTAAAAATAAATTTATTATCTAAAAAATACTAAAAATAATTTAAAAACCTTGT
TAGATATATATATATATATTACAAACAATTACAGCATAAAATTTTTATACAAATACCATGCG
Found at i:342785 original size:30 final size:30
Alignment explanation
Indices: 342751--342809 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
342741 GTTAATAGAT
* *
342751 TATTTAGATATCAATTAAAGATTAAAAATA
1 TATTTAAATATAAATTAAAGATTAAAAATA
* *
342781 TATTTAAATGTAAATTAAATATTAAAAAT
1 TATTTAAATATAAATTAAAGATTAAAAAT
342810 TTTATTTGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (30 bp):
TATTTAAATATAAATTAAAGATTAAAAATA
Found at i:343015 original size:31 final size:31
Alignment explanation
Indices: 343003--343063 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
342993 AATTTAAAAT
343003 ATATATTTTAAATTAAATTAAATTTAAATAA
1 ATATATTTTAAATTAAATTAAATTTAAATAA
* *
343034 ATATA-TATAATATTAATATTATATTTAAAT
1 ATATATTTTAA-ATTAA-ATTAAATTTAAAT
343064 TTGATTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.15
31 10 0.38
32 12 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATATATTTTAAATTAAATTAAATTTAAATAA
Found at i:343024 original size:35 final size:35
Alignment explanation
Indices: 342976--343042 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
342966 TTTAAAAATA
*
342976 TAAATAAATTTAAATATAATTTAAA-ATATATATTT
1 TAAATAAATTTAAATATAA-ATAAATATATATATTT
*
343011 TAAATTAAA-TTAAATTTAAATAAATATATATA
1 TAAA-TAAATTTAAATATAAATAAATATATATA
343043 ATATTAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 4 0.14
35 20 0.71
36 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (35 bp):
TAAATAAATTTAAATATAAATAAATATATATATTT
Found at i:343031 original size:41 final size:43
Alignment explanation
Indices: 342945--343032 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 43
342935 ATTAATTAAC
* *
342945 AAAT-TAAGTTTAAATTATTTATTTAAAAATATAAATAAATTT
1 AAATATAAGTTTAAAATATATATTTAAAAATATAAATAAATTT
*
342987 AAATATAA-TTTAAAATATATATTT-TAAAT-TAAATTAAATTT
1 AAATATAAGTTTAAAATATATATTTAAAAATATAAA-TAAATTT
343028 AAATA
1 AAATA
343033 AATATATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
40 4 0.10
41 16 0.39
42 18 0.44
43 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (43 bp):
AAATATAAGTTTAAAATATATATTTAAAAATATAAATAAATTT
Found at i:343302 original size:2 final size:2
Alignment explanation
Indices: 343295--343330 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
343285 AAATGAAGGA
*
343295 AG AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
343331 TCGAAACACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:343516 original size:14 final size:14
Alignment explanation
Indices: 343481--343518 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
343471 AATTTAAATA
343481 ATATTATAA-TATG
1 ATATTATAATTATG
*
343494 ATATTATAATTATT
1 ATATTATAATTATG
*
343508 ATTTTATAATT
1 ATATTATAATT
343519 TTAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
ATATTATAATTATG
Found at i:344846 original size:3 final size:3
Alignment explanation
Indices: 344838--344881 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
344828 TCTAAACCTG
344838 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
344882 TTACAAGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:348723 original size:3 final size:3
Alignment explanation
Indices: 348715--348742 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
348705 GATCTCAAAT
348715 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
348743 ATATATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:349372 original size:9 final size:9
Alignment explanation
Indices: 349308--349375 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
349298 ATATAAAAAT
349308 TATA-TAAA
1 TATATTAAA
349316 T-TATTAAA
1 TATATTAAA
*
349324 TATGTTAAA
1 TATATTAAA
*
349333 -ATTTTAAA
1 TATATTAAA
349341 TATA-TACGAA
1 TATATTA--AA
349351 TATGA-TAAA
1 TAT-ATTAAA
349360 TATATTAAA
1 TATATTAAA
349369 TATATTA
1 TATATTA
349376 TATTAATTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
7 2 0.04
8 16 0.32
9 24 0.48
10 5 0.10
11 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (9 bp):
TATATTAAA
Found at i:349379 original size:14 final size:14
Alignment explanation
Indices: 349360--349398 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 14
349350 ATATGATAAA
349360 TATATTAAATATAT
1 TATATTAAATATAT
349374 TATATT-AAT-TA-
1 TATATTAAATATAT
349385 TAT-TTAAATATAT
1 TATATTAAATATAT
349398 T
1 T
349399 GTATCATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
10 2 0.09
11 6 0.27
12 4 0.18
13 4 0.18
14 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATATTAAATATAT
Found at i:349412 original size:24 final size:24
Alignment explanation
Indices: 349359--349412 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
349349 AATATGATAA
*
349359 ATATATTAAATATATTATATTAATT
1 ATAT-TTAAATATATTATATCAATT
*
349384 ATATTTAAATATATTGTATCATATT
1 ATATTTAAATATATTATATCA-ATT
349409 -TATT
1 ATATT
349413 ATACAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
ATATTTAAATATATTATATCAATT
Found at i:350770 original size:13 final size:13
Alignment explanation
Indices: 350754--350778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
350744 ATTTATTAAA
350754 TATATAATATTTT
1 TATATAATATTTT
350767 TATATAATATTT
1 TATATAATATTT
350779 AAAATTATTA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATAATATTTT
Found at i:351033 original size:12 final size:12
Alignment explanation
Indices: 351004--351039 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
350994 CGACATGTTT
*
351004 ATTTGTTTATTC
1 ATTTATTTATTC
351016 ATTTTATTTATTC
1 A-TTTATTTATTC
351029 ATTTATTTATT
1 ATTTATTTATT
351040 GTCAGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (12 bp):
ATTTATTTATTC
Found at i:353153 original size:26 final size:26
Alignment explanation
Indices: 353088--353153 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
353078 AGCCCAAATT
353088 AAAAAAAATCAAAAGATTTAATTAAA
1 AAAAAAAATCAAAAGATTTAATTAAA
** *
353114 AAATGAAATCAAAAGATTTGATTAAA
1 AAAAAAAATCAAAAGATTTAATTAAA
353140 ACAAAAAAAT-AAAA
1 A-AAAAAAATCAAAA
353154 CAAAGTTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 28 0.82
27 6 0.18
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (26 bp):
AAAAAAAATCAAAAGATTTAATTAAA
Found at i:356060 original size:15 final size:16
Alignment explanation
Indices: 356036--356065 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
356026 TTTAATTTTT
356036 AAATTAAAAAATTATA
1 AAATTAAAAAATTATA
356052 AAATT-AAAAATTAT
1 AAATTAAAAAATTAT
356066 TTTTAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTAAAAAATTATA
Found at i:356722 original size:17 final size:18
Alignment explanation
Indices: 356702--356739 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
356692 TATTTATTGT
356702 ATAA-TTAAATTTAAA-TA
1 ATAATTTAAA-TTAAATTA
356719 ATAATTTAAATTAAATTA
1 ATAATTTAAATTAAATTA
356737 ATA
1 ATA
356740 TAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTTAAATTAAATTA
Found at i:356727 original size:18 final size:17
Alignment explanation
Indices: 356702--356752 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
356692 TATTTATTGT
356702 ATAATTAAATTTAAA-TA
1 ATAATTAAA-TTAAATTA
356719 ATAATTTAAATTAAATTA
1 ATAA-TTAAATTAAATTA
356737 AT-A-TAAA-TAAATTA
1 ATAATTAAATTAAATTA
356751 AT
1 AT
356753 TTTTAGAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 9 0.28
15 4 0.12
17 10 0.31
18 9 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTAAATTAAATTA
Found at i:356742 original size:23 final size:24
Alignment explanation
Indices: 356704--356751 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
356694 TTTATTGTAT
*
356704 AATTAAATTTAAAT-AATAATTTA
1 AATTAAATTTAAATAAATAAATTA
356727 AATTAAA-TTAATATAAATAAATTA
1 AATTAAATTTAA-ATAAATAAATTA
356751 A
1 A
356752 TTTTTAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 9 0.41
24 9 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AATTAAATTTAAATAAATAAATTA
Found at i:356752 original size:14 final size:15
Alignment explanation
Indices: 356720--356752 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
356710 ATTTAAATAA
*
356720 TAATTTAAATTAAAT
1 TAATATAAATTAAAT
356735 TAATATAAA-TAAAT
1 TAATATAAATTAAAT
356749 TAAT
1 TAAT
356753 TTTTAGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATATAAATTAAAT
Found at i:358594 original size:16 final size:16
Alignment explanation
Indices: 358560--358621 Score: 83
Period size: 16 Copynumber: 3.9 Consensus size: 16
358550 AATTTAAATA
* *
358560 TTAAAATT-AACTGAT
1 TTAAAATTAAAATAAT
358575 TTAAAATTAAAATAAT
1 TTAAAATTAAAATAAT
358591 TTAAAATTAAAATAAT
1 TTAAAATTAAAATAAT
358607 TT-AAATATAAAATAA
1 TTAAAAT-TAAAATAA
358622 ACCTAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
15 12 0.28
16 31 0.72
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (16 bp):
TTAAAATTAAAATAAT
Found at i:363910 original size:16 final size:16
Alignment explanation
Indices: 363884--363924 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
363874 TAATTTATGC
363884 ATTTATATTATATT-TA
1 ATTT-TATTATATTATA
363900 TATTTTATTATATTATA
1 -ATTTTATTATATTATA
363917 ATTTTATT
1 ATTTTATT
363925 TAAGTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTATTATATTATA
Found at i:364014 original size:20 final size:19
Alignment explanation
Indices: 363991--364031 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
363981 TTTTAAAATA
363991 TTTATATCGTATTCATATTT
1 TTTATATCGTATT-ATATTT
**
364011 TTTATATTTTATTATATTT
1 TTTATATCGTATTATATTT
364030 TT
1 TT
364032 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTATATCGTATTATATTT
Found at i:364027 original size:10 final size:10
Alignment explanation
Indices: 364000--364051 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
363990 ATTTATATCG
364000 TATTCATATTT
1 TATT-ATATTT
364011 T-TTATATTT
1 TATTATATTT
364020 TATTATATTTT
1 TATTATA-TTT
*
364031 TATTTTATTT
1 TATTATATTT
364041 TAATTAT-TTT
1 T-ATTATATTT
364051 T
1 T
364052 TGTGTTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 7 0.19
10 15 0.42
11 14 0.39
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (10 bp):
TATTATATTT
Found at i:364033 original size:11 final size:11
Alignment explanation
Indices: 364008--364052 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
363998 CGTATTCATA
364008 TTTT-TTATA-
1 TTTTATTATAT
364017 TTTTATTATAT
1 TTTTATTATAT
*
364028 TTTTATTTTAT
1 TTTTATTATAT
*
364039 TTTAATTAT-T
1 TTTTATTATAT
364049 TTTT
1 TTTT
364053 GTGTTATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 4 0.13
10 9 0.30
11 17 0.57
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTATTATAT
Found at i:364059 original size:21 final size:21
Alignment explanation
Indices: 364015--364059 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
364005 ATATTTTTTA
*
364015 TATTTTATTATATTTTTATTT
1 TATTTTATTATATTTTTATGT
*
364036 TATTTTAATTAT-TTTTTGTGT
1 TATTTT-ATTATATTTTTATGT
364057 TAT
1 TAT
364060 GTAATGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (21 bp):
TATTTTATTATATTTTTATGT
Found at i:364133 original size:2 final size:2
Alignment explanation
Indices: 364126--364174 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
364116 TAAGAACATC
364126 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
364168 AT AT AT A
1 AT AT AT A
364175 AGCTGAAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:364536 original size:11 final size:10
Alignment explanation
Indices: 364520--364562 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
364510 ATAAAATTTT
364520 AATATTAAATA
1 AATATT-AATA
364531 AATATTAATA
1 AATATTAATA
*
364541 ATTA-TAATA
1 AATATTAATA
364550 AATATTTAATA
1 AATA-TTAATA
364561 AA
1 AA
364563 ATTCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.29
10 7 0.25
11 13 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATATTAATA
Found at i:364542 original size:20 final size:21
Alignment explanation
Indices: 364523--364562 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
364513 AAATTTTAAT
364523 ATTA-AATAAATA-TTAAT-A
1 ATTATAATAAATATTTAATAA
364541 ATTATAATAAATATTTAATAA
1 ATTATAATAAATATTTAATAA
364562 A
1 A
364563 ATTCTACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 8 0.42
20 5 0.26
21 2 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATAATAAATATTTAATAA
Found at i:364608 original size:48 final size:48
Alignment explanation
Indices: 364500--364608 Score: 120
Period size: 48 Copynumber: 2.3 Consensus size: 48
364490 AAAGAATTTA
*
364500 AATATAAA-AT-ATAAAATTTTAATATTAAATAAATATTAATAATTAT
1 AATATAAATATAATAAAATTCTAATATTAAATAAATATTAATAATTAT
* * *
364546 AATA-AATATTTAATAAAATTCTACAT-TTAATTAAATATT-ATAATTTTT
1 AATATAA-ATATAATAAAATTCTA-ATATTAAATAAATATTAATAA-TTAT
364594 AATATAAATATAATA
1 AATATAAATATAATA
364609 TAAACAAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
45 2 0.04
46 5 0.10
47 5 0.10
48 36 0.69
49 4 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (48 bp):
AATATAAATATAATAAAATTCTAATATTAAATAAATATTAATAATTAT
Found at i:364730 original size:4 final size:4
Alignment explanation
Indices: 364721--364747 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
364711 CACATATTTA
364721 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
364748 AGTTAAGCAC
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:365968 original size:24 final size:24
Alignment explanation
Indices: 365924--365969 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
365914 TATTGTGTTC
* *
365924 ATTTTTTTGTATTGTGTTTTAAAT
1 ATTTTTTTATATTGTGATTTAAAT
365948 ATTTTTCTTATATTGT-ATTTAA
1 ATTTTT-TTATATTGTGATTTAA
365970 GTCGAGCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.09, T:0.65
Consensus pattern (24 bp):
ATTTTTTTATATTGTGATTTAAAT
Found at i:366752 original size:23 final size:23
Alignment explanation
Indices: 366720--366765 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
366710 TATCTTATGT
* *
366720 AAGTTCAAAAATGTTAAAAAAAA
1 AAGTTAAAAAATCTTAAAAAAAA
366743 AAGTTAAAAAATCTTAAAAAAAA
1 AAGTTAAAAAATCTTAAAAAAAA
366766 TAATTTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (23 bp):
AAGTTAAAAAATCTTAAAAAAAA
Found at i:367683 original size:13 final size:14
Alignment explanation
Indices: 367653--367690 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
367643 AAAAATTTAA
367653 TAAAAATAATATAG
1 TAAAAATAATATAG
**
367667 TAAAAATAAT-TTT
1 TAAAAATAATATAG
367680 TAAAAATAATA
1 TAAAAATAATA
367691 ATTAGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
TAAAAATAATATAG
Found at i:369003 original size:36 final size:36
Alignment explanation
Indices: 368961--369046 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
368951 TTATTTATCA
** *
368961 TTTAAATAATAA-ACAATTAT-TTTTATTTAAATTAT
1 TTTAAATAATAATACAAAAATATTTT-TTAAAATTAT
* *
368996 TTATAAATATTAATATAAAAATATTTTTTAAAATTAT
1 TT-TAAATAATAATACAAAAATATTTTTTAAAATTAT
369033 TTTAAATAATAATA
1 TTTAAATAATAATA
369047 TGAGTTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
35 2 0.05
36 20 0.48
37 16 0.38
38 4 0.10
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (36 bp):
TTTAAATAATAATACAAAAATATTTTTTAAAATTAT
Found at i:369206 original size:32 final size:31
Alignment explanation
Indices: 369154--369214 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
369144 TTCGTTATAT
**
369154 TAATTAAATTAATATTTTAAAAAATAAAAATA
1 TAATTAAATTAATACATT-AAAAATAAAAATA
* *
369186 TAATTAACTTAATACATTAAATATAAAAA
1 TAATTAAATTAATACATTAAAAATAAAAA
369215 GTTTTAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (31 bp):
TAATTAAATTAATACATTAAAAATAAAAATA
Found at i:370003 original size:13 final size:13
Alignment explanation
Indices: 369985--370014 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
369975 AAATTTTAAA
369985 AATATTTATATTT
1 AATATTTATATTT
*
369998 AATATTTATTTTT
1 AATATTTATATTT
370011 AATA
1 AATA
370015 AAAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:370059 original size:10 final size:10
Alignment explanation
Indices: 370037--370124 Score: 54
Period size: 10 Copynumber: 8.4 Consensus size: 10
370027 AAATTAATTA
370037 TTTATATTATT
1 TTTATA-TATT
370048 TTTATATATT
1 TTTATATATT
370058 TTTATATATCT
1 TTTATATAT-T
**
370069 TAAAATATAATT
1 T-TTATAT-ATT
* *
370081 ATATT-TAAAAT
1 -T-TTATATATT
*
370092 ATTATATATT
1 TTTATATATT
*
370102 TATATA-ATT
1 TTTATATATT
370111 TTTATATATT
1 TTTATATATT
370121 TTTA
1 TTTA
370125 AATCATATTA
Statistics
Matches: 59, Mismatches: 12, Indels: 13
0.70 0.14 0.15
Matches are distributed among these distances:
9 10 0.17
10 28 0.47
11 10 0.17
12 7 0.12
13 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTATATATT
Found at i:370101 original size:16 final size:16
Alignment explanation
Indices: 370059--370103 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
370049 TTATATATTT
370059 TTATATATCTTAAAATA
1 TTATATAT-TTAAAATA
*
370076 TAATTATATTTAAAATA
1 TTA-TATATTTAAAATA
370093 TTATATATTTA
1 TTATATATTTA
370104 TATAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.32
17 12 0.48
18 5 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATATATTTAAAATA
Found at i:370206 original size:25 final size:24
Alignment explanation
Indices: 370178--370228 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
370168 ATCTTATTAA
* * *
370178 AATTATCAAATTTAATAAAAAATAT
1 AATTATAAAATAT-ATAAAAAAAAT
*
370203 AATTTTAAAATATATAAAAAAAAT
1 AATTATAAAATATATAAAAAAAAT
370227 AA
1 AA
370229 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTATAAAATATATAAAAAAAAT
Found at i:373817 original size:26 final size:26
Alignment explanation
Indices: 373764--373817 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
373754 GTTTTTTTTG
* * *
373764 ATAAAATATATATTATATATGTTTAT
1 ATAAAATATAAAATATATATGTTAAT
373790 ATAAAATATAAAATATAATAT-TTAAT
1 ATAAAATATAAAATAT-ATATGTTAAT
373816 AT
1 AT
373818 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
ATAAAATATAAAATATATATGTTAAT
Found at i:375664 original size:2 final size:2
Alignment explanation
Indices: 375657--375681 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
375647 AATCGCATTC
375657 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
375682 GAAAGTTGAG
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:381497 original size:186 final size:187
Alignment explanation
Indices: 381172--381523 Score: 548
Period size: 186 Copynumber: 1.9 Consensus size: 187
381162 ACTGCAATAC
381172 TATGTTATAATTACTATTTAAATCTTAAAAAAATACCATAACCTAACAAATGACACGATAGTACC
1 TATGTTATAATTACTATTTAAATCTTAAAAAAATACCATAACCTAACAAATGACACGATAGTACC
* *
381237 AAGCTTGACGCGTATGATCTTCTAACTTCTAAGACATATATAAACATTACAATTGTTTTTTGTGG
66 AAGCTTGACGCGTATGATCTTCCAACTTCTAAGACATATATAAACATTACAATTGTTTTTCGTGG
* *
381302 GATCAAAGTTTTAGTACCAAAATACTGGTTATTTTGATACTAAAGTTTTGATAACAA
131 GACCAAAGTTTTAGTACCAAAATACTGGTCATTTTGATACTAAAGTTTTGATAACAA
* * *
381359 TATGTTACT-ATTACTATTTAAATCTT-AAAAAATATCATAACCTAACAAATGATAC-ATGCGTA
1 TATGTTA-TAATTACTATTTAAATCTTAAAAAAATACCATAACCTAACAAATGACACGAT-AGTA
* * *
381421 TCAAGCTTGATGCGTATGATCTTCCAACTTCTAGGACATATATAAACATTACAATTGTTTTTCGT
64 CCAAGCTTGACGCGTATGATCTTCCAACTTCTAAGACATATATAAACATTACAATTGTTTTTCGT
* * *
381486 GGGACCAAAGTTTTGGTACCAAATTGCTGGTCATTTTG
129 GGGACCAAAGTTTTAGTACCAAAATACTGGTCATTTTG
381524 TGAACGAGAG
Statistics
Matches: 150, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
185 2 0.01
186 123 0.82
187 24 0.16
188 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (187 bp):
TATGTTATAATTACTATTTAAATCTTAAAAAAATACCATAACCTAACAAATGACACGATAGTACC
AAGCTTGACGCGTATGATCTTCCAACTTCTAAGACATATATAAACATTACAATTGTTTTTCGTGG
GACCAAAGTTTTAGTACCAAAATACTGGTCATTTTGATACTAAAGTTTTGATAACAA
Found at i:383141 original size:17 final size:17
Alignment explanation
Indices: 383119--383151 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
383109 TCTATGAAAC
383119 TATCAAATATATATATT
1 TATCAAATATATATATT
383136 TATCAAATATATATAT
1 TATCAAATATATATAT
383152 ATATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TATCAAATATATATATT
Found at i:383663 original size:27 final size:26
Alignment explanation
Indices: 383620--383672 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
383610 TGTAACGATG
*
383620 AATAAAATATAATAT-AATATTAAAAA
1 AATAAAATATAACATAAATA-TAAAAA
383646 AATATAAATATAACATAAATATAAAAA
1 AATA-AAATATAACATAAATATAAAAA
383673 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (26 bp):
AATAAAATATAACATAAATATAAAAA
Found at i:383771 original size:14 final size:15
Alignment explanation
Indices: 383752--383781 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
383742 ATAATTATAA
383752 ATAATA-AAATATGT
1 ATAATATAAATATGT
383766 ATAATATAAATATGT
1 ATAATATAAATATGT
383781 A
1 A
383782 AATTATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
ATAATATAAATATGT
Found at i:383771 original size:29 final size:28
Alignment explanation
Indices: 383719--383774 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
383709 TTAAAATTTA
*
383719 TATAAATATAAAATATTTTAAATATAAT
1 TATAAATATAAAATATTATAAATATAAT
383747 TATAAATAATAAAATATGTAT-AATATAA
1 TATAAAT-ATAAAATAT-TATAAATATAA
383775 ATATGTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 7 0.28
29 16 0.64
30 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
TATAAATATAAAATATTATAAATATAAT
Found at i:384958 original size:13 final size:14
Alignment explanation
Indices: 384931--384959 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
384921 TTTTATGAAT
384931 TAAATTATATAATA
1 TAAATTATATAATA
384945 TAAATTAT-TAATA
1 TAAATTATATAATA
384958 TA
1 TA
384960 TCAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAATTATATAATA
Found at i:384984 original size:17 final size:18
Alignment explanation
Indices: 384937--384988 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
384927 GAATTAAATT
*
384937 ATATAATATAAATTA-TTA
1 ATAT-ATATAATTTATTTA
*
384955 ATATATCAAAATTTATTTA
1 ATATAT-ATAATTTATTTA
384974 A-ATATATAATTTATT
1 ATATATATAATTTATT
384989 ATGATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 11 0.38
18 14 0.48
19 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATATATAATTTATTTA
Found at i:385063 original size:3 final size:3
Alignment explanation
Indices: 385055--385083 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
385045 AAGCCACTTA
385055 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
385084 GACATGAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:385567 original size:29 final size:30
Alignment explanation
Indices: 385525--385599 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
385515 TTTATTTTTA
** *
385525 ATTTTTATCCATTTAAGC-CCCAAACATTT
1 ATTTTTATTAATTTAAACACCCAAACATTT
* *
385554 ATTTTTATTAATTTAAACACTCGAACATTT
1 ATTTTTATTAATTTAAACACCCAAACATTT
385584 ATTTTTATTAAATTTA
1 ATTTTTATT-AATTTA
385600 GTCTTCTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 15 0.38
30 18 0.46
31 6 0.15
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.48
Consensus pattern (30 bp):
ATTTTTATTAATTTAAACACCCAAACATTT
Found at i:385748 original size:22 final size:23
Alignment explanation
Indices: 385720--385766 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
385710 ATAAAATTTT
*
385720 AAATAATTATTTA-ATTTTAATC
1 AAATAATTATTTATATTTAAATC
*
385742 AAATAATTTTTTATATTTAAATC
1 AAATAATTATTTATATTTAAATC
385765 AA
1 AA
385767 TTTTATATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATAATTATTTATATTTAAATC
Found at i:388784 original size:13 final size:14
Alignment explanation
Indices: 388758--388786 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
388748 TAAAAATCAA
388758 AATAAAATTAAAAT
1 AATAAAATTAAAAT
388772 AATAAAA-TAAAAT
1 AATAAAATTAAAAT
388785 AA
1 AA
388787 ATTAAGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAAAATTAAAAT
Found at i:389702 original size:24 final size:24
Alignment explanation
Indices: 389618--389702 Score: 72
Period size: 24 Copynumber: 3.8 Consensus size: 24
389608 TAAATTATAT
*
389618 ATTAATATAATATATTTAATAATT
1 ATTAATATAATATATTTAATAATA
*
389642 A-TAA-A-AATA-ATATAATAA-A
1 ATTAATATAATATATTTAATAATA
* * * * *
389661 ATCAGTATGATATTTTTACTAATA
1 ATTAATATAATATATTTAATAATA
389685 ATTAATATAATATATTTA
1 ATTAATATAATATATTTA
389703 TGCATGTATA
Statistics
Matches: 44, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
19 1 0.02
20 9 0.20
21 5 0.11
22 4 0.09
23 9 0.20
24 16 0.36
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
ATTAATATAATATATTTAATAATA
Found at i:391544 original size:20 final size:20
Alignment explanation
Indices: 391519--391565 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
391509 TTATTTAATC
**
391519 TTTATATCAATCCGTATTAA
1 TTTATATCAATCAATATTAA
391539 TTTATATCAATCAATATTAA
1 TTTATATCAATCAATATTAA
*
391559 TATATAT
1 TTTATAT
391566 TAGTCTATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (20 bp):
TTTATATCAATCAATATTAA
Found at i:391841 original size:25 final size:27
Alignment explanation
Indices: 391790--391841 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
391780 AACATATATA
*
391790 TATATATAATTAAAGTATTTTTGTAAG
1 TATATATAATTAAAGTATTTATGTAAG
391817 TATATATAA-TAAA-TACTTTAT-TAAG
1 TATATATAATTAAAGTA-TTTATGTAAG
391842 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 6 0.26
26 8 0.35
27 9 0.39
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (27 bp):
TATATATAATTAAAGTATTTATGTAAG
Found at i:392184 original size:2 final size:2
Alignment explanation
Indices: 392177--392203 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
392167 CATACATGTG
392177 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
392204 GATGCACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:393872 original size:20 final size:20
Alignment explanation
Indices: 393849--393887 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
393839 TAAAATAACT
*
393849 TAATACGATTTAAAAATTAA
1 TAATAAGATTTAAAAATTAA
*
393869 TAATAATATTTAAAAATTA
1 TAATAAGATTTAAAAATTA
393888 TTTACTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
TAATAAGATTTAAAAATTAA
Found at i:394715 original size:14 final size:14
Alignment explanation
Indices: 394682--394725 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
394672 TTTTAATTTT
394682 TTTATATATTTAAAA
1 TTTATAT-TTTAAAA
* *
394697 GTTATATTTTAATA
1 TTTATATTTTAAAA
*
394711 TTTATATTTAAAAA
1 TTTATATTTTAAAA
394725 T
1 T
394726 ATATTCAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
TTTATATTTTAAAA
Found at i:395605 original size:13 final size:13
Alignment explanation
Indices: 395587--395612 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
395577 TAAAAATTAA
395587 AAATATAAAATAT
1 AAATATAAAATAT
395600 AAATATAAAATAT
1 AAATATAAAATAT
395613 TAAGAATAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATATAAAATAT
Found at i:398437 original size:2 final size:2
Alignment explanation
Indices: 398430--398465 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
398420 GGATTTTGGA
398430 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
398466 GTTAATGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:399491 original size:2 final size:2
Alignment explanation
Indices: 399486--399517 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
399476 AAGTTAGTCC
399486 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
399518 CCATTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:400050 original size:154 final size:155
Alignment explanation
Indices: 399866--400328 Score: 860
Period size: 154 Copynumber: 3.0 Consensus size: 155
399856 TTACTAAACT
*
399866 TCTATTATTTATAAATTAAGCTATTTAAGTTGATTTTATTAAATAATTTTAATAAAAAAATTGAC
1 TCTATTATTTATAAATTAAGCTATTTAAGTTGATTTTGTTAAATAATTTTAATAAAAAAATTGAC
*
399931 TCAATATACATATACAATTTATTTTTTACATCTTATAAGATAATATCTAATAAAAATATGCTATG
66 TCAATATACATATACAATTTATTTTTTACATCTTATAAGATAATATCTAATAGAAATATGCTATG
399996 TATGTATATTTTAATAAAGTTAACG
131 TATGTATATTTTAATAAAGTTAACG
*
400021 T-TATTATTTATAAATTAAGCTATTTAAGTTGATTCTGTTAAATAATTTTAATAAAAAAATTGAC
1 TCTATTATTTATAAATTAAGCTATTTAAGTTGATTTTGTTAAATAATTTTAATAAAAAAATTGAC
*
400085 TCAATATACATATATAATTTATTTTTTACATCTTATAAGATAATATCTAATAGAAATATGCTATG
66 TCAATATACATATACAATTTATTTTTTACATCTTATAAGATAATATCTAATAGAAATATGCTATG
400150 TATGTATATTTTAATAAAGTTAACG
131 TATGTATATTTTAATAAAGTTAACG
*
400175 TCTATTATTTATAAATTAATCTATTTAAGTTGA-TTTGTTAAATAATTTTAAT-AAAAAATTGAC
1 TCTATTATTTATAAATTAAGCTATTTAAGTTGATTTTGTTAAATAATTTTAATAAAAAAATTGAC
400238 TCAATATACATATACAATTTATTTTTTACATCTTATAAGATAATATCTAATAGAAATATGCTATG
66 TCAATATACATATACAATTTATTTTTTACATCTTATAAGATAATATCTAATAGAAATATGCTATG
400303 TATGTATATTTTAATAAAGTTAACG
131 TATGTATATTTTAATAAAGTTAACG
400328 T
1 T
400329 AAAATATTTA
Statistics
Matches: 300, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
153 101 0.34
154 168 0.56
155 31 0.10
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (155 bp):
TCTATTATTTATAAATTAAGCTATTTAAGTTGATTTTGTTAAATAATTTTAATAAAAAAATTGAC
TCAATATACATATACAATTTATTTTTTACATCTTATAAGATAATATCTAATAGAAATATGCTATG
TATGTATATTTTAATAAAGTTAACG
Found at i:402435 original size:16 final size:16
Alignment explanation
Indices: 402414--402445 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
402404 AAAGCTTTTG
402414 AATATTTTGATATAAT
1 AATATTTTGATATAAT
402430 AATATTTTGATATAAT
1 AATATTTTGATATAAT
402446 CTGGCCAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
AATATTTTGATATAAT
Found at i:402591 original size:20 final size:19
Alignment explanation
Indices: 402529--402609 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
402519 CTTAATAATT
402529 TTAAATAT-A-AT-AAAAA
1 TTAAATATAACATAAAAAA
* *
402545 TTAAAATAAAACATAAAATA
1 TT-AAATATAACATAAAAAA
402565 -TATAATATAACATTAAAAAA
1 TTA-AATATAACA-TAAAAAA
*
402585 TTAAATATAATA-AAAAATA
1 TTAAATATAACATAAAAA-A
402604 TTAAAT
1 TTAAAT
402610 TTATATAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.04
17 5 0.10
18 7 0.13
19 18 0.35
20 18 0.35
21 2 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TTAAATATAACATAAAAAA
Found at i:402606 original size:19 final size:19
Alignment explanation
Indices: 402529--402628 Score: 64
Period size: 20 Copynumber: 5.3 Consensus size: 19
402519 CTTAATAATT
402529 TTAAATATAAT-AAAAAT-
1 TTAAATATAATAAAAAATA
* * * *
402546 TAAAATAAAACATAAAATA
1 TTAAATATAATAAAAAATA
*
402565 -TATAATATAACATTAAAAA-A
1 TTA-AATAT-A-ATAAAAAATA
402585 TTAAATATAATAAAAAATA
1 TTAAATATAATAAAAAATA
* * *
402604 TTAAATTTATATAATAATTA
1 TTAAATATA-ATAAAAAATA
402624 TTAAA
1 TTAAA
402629 ATTTATATAA
Statistics
Matches: 62, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
17 8 0.13
18 13 0.21
19 14 0.23
20 20 0.32
21 7 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAATATAATAAAAAATA
Found at i:404493 original size:12 final size:11
Alignment explanation
Indices: 404463--404495 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
404453 AGGTACATAC
404463 ATATATA-TAT
1 ATATATATTAT
404473 ATATATATTAT
1 ATATATATTAT
404484 AATATATATTAT
1 -ATATATATTAT
404496 CAAATCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 3 0.14
12 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATATTAT
Found at i:406478 original size:32 final size:36
Alignment explanation
Indices: 406442--406524 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 36
406432 TCAAAATAAG
*
406442 TATATTTAATATATATATATT-TATTT-T-TTT-AA
1 TATATTTAAAATATATATATTATATTTATATTTAAA
*
406474 TATA-TTAAAAAATCATATATTATATTTATATTTAAA
1 TATATTTAAAATAT-ATATATTATATTTATATTTAAA
*
406510 TATATCTAAAATATA
1 TATATTTAAAATATA
406525 AGACATTAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
31 7 0.17
32 11 0.27
33 5 0.12
34 1 0.02
35 3 0.07
36 7 0.17
37 7 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (36 bp):
TATATTTAAAATATATATATTATATTTATATTTAAA
Found at i:407128 original size:24 final size:24
Alignment explanation
Indices: 407078--407125 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
407068 TTTTATATTT
* *
407078 ATATTTAAATATATATAAATCTAA
1 ATATTTAAATAAATAAAAATCTAA
*
407102 ATATTTAAA-AAATAAAAATTTAA
1 ATATTTAAATAAATAAAAATCTAA
407125 A
1 A
407126 ATAACTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATTTAAATAAATAAAAATCTAA
Found at i:408352 original size:23 final size:24
Alignment explanation
Indices: 408298--408352 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
408288 ACTATTGTTT
* *
408298 AATAATAATAAAATTAATTTTAAA
1 AATAATATTAAAATTAATTCTAAA
* *
408322 AAT-TTATTAATATTAA-TCTAAA
1 AATAATATTAAAATTAATTCTAAA
408344 AATAATATT
1 AATAATATT
408353 TTAATATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 8 0.32
23 14 0.56
24 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AATAATATTAAAATTAATTCTAAA
Found at i:408576 original size:17 final size:17
Alignment explanation
Indices: 408556--408588 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
408546 AATTTTAATA
408556 TTTATAATTTTT-TTATT
1 TTTA-AATTTTTGTTATT
408573 TTTAAATTTTTGTTAT
1 TTTAAATTTTTGTTAT
408589 GAAAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTAAATTTTTGTTATT
Found at i:410062 original size:15 final size:16
Alignment explanation
Indices: 410044--410084 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
410034 ATATAAAATA
410044 ATTAAATAT-ATTTAT
1 ATTAAATATAATTTAT
410059 ATTAAATATAAATTTAT
1 ATTAAATAT-AATTTAT
*
410076 ATTTAATAT
1 ATTAAATAT
410085 TCAATTCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTAAATATAATTTAT
Found at i:412290 original size:33 final size:35
Alignment explanation
Indices: 412239--412304 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
412229 TTATTTATAA
412239 TATAATATATATATAAAGCACAAATATAAAAAAAT
1 TATAATATATATATAAAGCACAAATATAAAAAAAT
**
412274 TATAATATAT-TA-AAAGCATGAATATAAAAAA
1 TATAATATATATATAAAGCACAAATATAAAAAA
412305 TTTTAAACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 17 0.59
34 2 0.07
35 10 0.34
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (35 bp):
TATAATATATATATAAAGCACAAATATAAAAAAAT
Found at i:413721 original size:20 final size:22
Alignment explanation
Indices: 413693--413734 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
413683 TAATAATTTT
413693 TTAAAAAATA-TT-ATATATAA
1 TTAAAAAATATTTAATATATAA
*
413713 TTAATAAATATTTAATATATAA
1 TTAAAAAATATTTAATATATAA
413735 AATTTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAAAAATATTTAATATATAA
Found at i:413727 original size:31 final size:30
Alignment explanation
Indices: 413669--413727 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
413659 AATTAATATT
* * * *
413669 AATATTTTTATATTTAATAATTTTTTAAAA
1 AATATTTATATAATTAATAAATATTTAAAA
413699 AATATTATATATAATTAATAAATATTTAA
1 AATATT-TATATAATTAATAAATATTTAA
413728 TATATAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
AATATTTATATAATTAATAAATATTTAAAA
Found at i:413746 original size:22 final size:22
Alignment explanation
Indices: 413721--413783 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
413711 AATTAATAAA
*
413721 TATTTAATATATAAAATTTATT
1 TATTTAATATATAAAATATATT
* *
413743 TATTTTATATTTAAAA-ATATT
1 TATTTAATATATAAAATATATT
413764 T-TTTATATATACTAAAATAT
1 TATTTA-ATATA-TAAAATAT
413784 TTAAAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 3 0.09
21 9 0.27
22 19 0.58
23 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTAATATATAAAATATATT
Found at i:413769 original size:19 final size:20
Alignment explanation
Indices: 413745--413785 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
413735 AATTTATTTA
*
413745 TTTTATATTTA-AAAATATT
1 TTTTATATATACAAAATATT
413764 TTTTATATATACTAAAATATT
1 TTTTATATATAC-AAAATATT
413785 T
1 T
413786 AAAATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTATATATACAAAATATT
Found at i:413788 original size:9 final size:9
Alignment explanation
Indices: 413776--413809 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
413766 TTATATATAC
413776 TAAAATATT
1 TAAAATATT
413785 TAAAATATT
1 TAAAATATT
413794 TATAAATATAT
1 TA-AAATAT-T
413805 TAAAA
1 TAAAA
413810 CATATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 11 0.48
10 9 0.39
11 3 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TAAAATATT
Found at i:413792 original size:21 final size:20
Alignment explanation
Indices: 413768--413814 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
413758 AATATTTTTT
413768 ATATATACTAAA-ATATTTAAA
1 ATATATA-TAAATATA-TTAAA
*
413789 ATATTTATAAATATATTAAA
1 ATATATATAAATATATTAAA
*
413809 ACATAT
1 ATATAT
413815 TAATATTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATATATAAATATATTAAA
Found at i:413815 original size:31 final size:31
Alignment explanation
Indices: 413749--413809 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
413739 TATTTATTTT
* *
413749 ATATTTAAAAATATTTTTTATATATACTAAA
1 ATATTTAAAAATATTTTATAAATATACTAAA
*
413780 ATATTT-AAAATA-TTTATAAATATATTAAA
1 ATATTTAAAAATATTTTATAAATATACTAAA
413809 A
1 A
413810 CATATTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 15 0.56
30 6 0.22
31 6 0.22
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (31 bp):
ATATTTAAAAATATTTTATAAATATACTAAA
Found at i:414451 original size:29 final size:29
Alignment explanation
Indices: 414419--414481 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
414409 AAATTATTTT
*
414419 TAATTTCAAT-TAAAATAATACATTAAAT-A
1 TAATTT-AATCTAAAATAATA-ATAAAATAA
*
414448 TAATTTTATCTAAAATAATAATAAAATAA
1 TAATTTAATCTAAAATAATAATAAAATAA
414477 TAATT
1 TAATT
414482 AACCAGCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (29 bp):
TAATTTAATCTAAAATAATAATAAAATAA
Found at i:415374 original size:35 final size:34
Alignment explanation
Indices: 415326--415397 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 34
415316 ATCGTCGAGC
*
415326 TAAATTAGGTCGATCTTAGGTTTGAGCTAAAAGGT
1 TAAATTAGATCGATCTTAGGTTTGAGCTAAAA-GT
415361 TAAATTAGATCGATCTTAGGTTTGAGCTAAAAGT
1 TAAATTAGATCGATCTTAGGTTTGAGCTAAAAGT
415395 TAA
1 TAA
415398 GTGAGCTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 5 0.14
35 31 0.86
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (34 bp):
TAAATTAGATCGATCTTAGGTTTGAGCTAAAAGT
Found at i:416380 original size:18 final size:18
Alignment explanation
Indices: 416357--416393 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
416347 TTCTCAAGAT
416357 TACCATATATGTGGAGGA
1 TACCATATATGTGGAGGA
416375 TACCATATATGTGGAGGA
1 TACCATATATGTGGAGGA
416393 T
1 T
416394 TTTTTGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (18 bp):
TACCATATATGTGGAGGA
Found at i:423692 original size:2 final size:2
Alignment explanation
Indices: 423687--423715 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
423677 GAACCATATA
423687 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
423716 TTGAGTTGAA
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:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:426602 original size:2 final size:2
Alignment explanation
Indices: 426595--426643 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
426585 TTTATCTTCC
426595 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
426637 TA TA TA T
1 TA TA TA T
426644 CGGATAAGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.