Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 101 of 173
Found at i:31319447 original size:16 final size:16
Alignment explanation
Indices: 31319428--31319762 Score: 104
Period size: 16 Copynumber: 20.9 Consensus size: 16
31319418 TATTAGGTAA
31319428 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
31319444 ATTATATAAGTTATGT
1 ATTATGTAAGTTATGT
31319460 AAGTTATGT-A-TTATGT
1 -A-TTATGTAAGTTATGT
* * *
31319476 AAGCTATGTAACTTATTT
1 -A-TTATGTAAGTTATGT
* *
31319494 AAGTTACGTAAGTTGTGT
1 -A-TTATGTAAGTTATGT
*
31319512 ATTATGTTAGTTATGT
1 ATTATGTAAGTTATGT
*
31319528 ACTATGTAAGTTATGTGT
1 ATTATGTAAGTTA--TGT
31319546 ATTATGT-A-TTATGT
1 ATTATGTAAGTTATGT
*
31319560 ATGTTATGT-A--TA-AT
1 A--TTATGTAAGTTATGT
*
31319574 ATTAAT-TAAGTTGTGT
1 ATT-ATGTAAGTTATGT
*
31319590 ATTGTGT-A-TTATGT
1 ATTATGTAAGTTATGT
*
31319604 ATGCTATGT-A--TA-AT
1 AT--TATGTAAGTTATGT
*
31319618 ATTAAT-TAAGTTGTGT
1 ATT-ATGTAAGTTATGT
31319634 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
31319650 A-T-T-TAAGTGTATG-
1 ATTATGTAAGT-TATGT
* *
31319663 -TTATGTAACTTGTGT
1 ATTATGTAAGTTATGT
* * **
31319678 ATAATGTTAGTTATCAA
1 ATTATGTAAGTTAT-GT
* *
31319695 AGTTATGT-A-CTATTT
1 A-TTATGTAAGTTATGT
*
31319710 AAGTTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGT
31319728 ATTATGTAAGTTATTATGTT
1 ATTATGTAAG---TTATG-T
31319748 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
31319763 CAAGTTTATA
Statistics
Matches: 241, Mismatches: 41, Indels: 73
0.68 0.12 0.21
Matches are distributed among these distances:
12 5 0.02
13 12 0.05
14 25 0.10
15 15 0.06
16 115 0.48
17 14 0.06
18 40 0.17
19 4 0.02
20 11 0.05
ACGTcount: A:0.30, C:0.02, G:0.18, T:0.49
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:31319570 original size:9 final size:9
Alignment explanation
Indices: 31319384--31319569 Score: 112
Period size: 9 Copynumber: 22.0 Consensus size: 9
31319374 ACTATAAATG
31319384 AGTTATGTA
1 AGTTATGTA
31319393 AGTTATGATA
1 AGTTATG-TA
* * *
31319403 TGATATAT-
1 AGTTATGTA
*
31319411 ATTTATGT-
1 AGTTATGTA
*
31319419 A-TTAGGTA
1 AGTTATGTA
*
31319427 AATTATGTA
1 AGTTATGTA
31319436 AGTTATGT-
1 AGTTATGTA
*
31319444 A-TTATATA
1 AGTTATGTA
31319452 AGTTATGTA
1 AGTTATGTA
31319461 AGTTATGT-
1 AGTTATGTA
31319469 A-TTATGTA
1 AGTTATGTA
*
31319477 AGCTATGTA
1 AGTTATGTA
* *
31319486 ACTTATTTA
1 AGTTATGTA
*
31319495 AGTTACGTA
1 AGTTATGTA
*
31319504 AGTTGTGT-
1 AGTTATGTA
*
31319512 A-TTATGTT
1 AGTTATGTA
31319520 AGTTATGT-
1 AGTTATGTA
*
31319528 A-CTATGTA
1 AGTTATGTA
*
31319536 AGTTATGTGT
1 AGTTATGT-A
31319546 A-TTATGT-
1 AGTTATGTA
31319553 A-TTATGTA
1 AGTTATGTA
*
31319561 TGTTATGTA
1 AGTTATGTA
31319570 TAATATTAAT
Statistics
Matches: 137, Mismatches: 26, Indels: 28
0.72 0.14 0.15
Matches are distributed among these distances:
7 33 0.24
8 14 0.10
9 83 0.61
10 7 0.05
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (9 bp):
AGTTATGTA
Found at i:31319581 original size:25 final size:25
Alignment explanation
Indices: 31319523--31319619 Score: 80
Period size: 25 Copynumber: 4.1 Consensus size: 25
31319513 TTATGTTAGT
* * * *
31319523 TATGTACTATGTAAGTTATGTGTAT
1 TATGTATTATGTATGTTATGTATAA
31319548 TATGTATTATGTATGTTATGTATAA
1 TATGTATTATGTATGTTATGTATAA
* *
31319573 TAT-TA--AT-TAAGTTGTGTAT--
1 TATGTATTATGTATGTTATGTATAA
* *
31319592 TGTGTATTATGTATGCTATGTATAA
1 TATGTATTATGTATGTTATGTATAA
31319617 TAT
1 TAT
31319620 TAATTAAGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
19 2 0.04
20 2 0.04
21 10 0.18
22 4 0.07
23 9 0.16
24 2 0.04
25 26 0.47
ACGTcount: A:0.30, C:0.02, G:0.18, T:0.51
Consensus pattern (25 bp):
TATGTATTATGTATGTTATGTATAA
Found at i:31319600 original size:44 final size:44
Alignment explanation
Indices: 31319541--31319651 Score: 186
Period size: 44 Copynumber: 2.5 Consensus size: 44
31319531 ATGTAAGTTA
*
31319541 TGTGTATTATGTATTATGTATGTTATGTATAATATTAATTAAGT
1 TGTGTATTATGTATTATGTATGCTATGTATAATATTAATTAAGT
*
31319585 TGTGTATTGTGTATTATGTATGCTATGTATAATATTAATTAAGT
1 TGTGTATTATGTATTATGTATGCTATGTATAATATTAATTAAGT
31319629 TGTGTATTATGTAAGTTATGTAT
1 TGTGTATTATGT-A-TTATGTAT
31319652 TTAAGTGTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
44 53 0.85
45 1 0.02
46 8 0.13
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (44 bp):
TGTGTATTATGTATTATGTATGCTATGTATAATATTAATTAAGT
Found at i:31319649 original size:9 final size:9
Alignment explanation
Indices: 31319635--31319788 Score: 54
Period size: 9 Copynumber: 17.1 Consensus size: 9
31319625 AAGTTGTGTA
31319635 TTATGTAAG
1 TTATGTAAG
*
31319644 TTATGT-AT
1 TTATGTAAG
*
31319652 TTAAGTGTATG
1 TT-A-TGTAAG
*
31319663 TTATGTAAC
1 TTATGTAAG
*
31319672 TTGTGT-A-
1 TTATGTAAG
* *
31319679 TAATGTTAG
1 TTATGTAAG
**
31319688 TTATCAAAG
1 TTATGTAAG
31319697 TTATGT-A-
1 TTATGTAAG
* *
31319704 CTATTTAAG
1 TTATGTAAG
31319713 TTATGTAAG
1 TTATGTAAG
*
31319722 TTGTGT-A-
1 TTATGTAAG
31319729 TTATGTAAG
1 TTATGTAAG
*
31319738 TTAT-TATG
1 TTATGTAAG
31319746 TTATTATGTAAG
1 ---TTATGTAAG
*
31319758 TTATGCAAG
1 TTATGTAAG
*
31319767 TTTATATATAAG
1 --T-TATGTAAG
31319779 TTATGTAAG
1 TTATGTAAG
31319788 T
1 T
31319789 ATATCACTTT
Statistics
Matches: 103, Mismatches: 26, Indels: 32
0.64 0.16 0.20
Matches are distributed among these distances:
7 13 0.13
8 12 0.12
9 57 0.55
10 5 0.05
11 7 0.07
12 9 0.09
ACGTcount: A:0.31, C:0.03, G:0.18, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:31319714 original size:25 final size:25
Alignment explanation
Indices: 31319681--31319741 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
31319671 CTTGTGTATA
*
31319681 ATGTTAGTTATCAAAGTTATGTACT
1 ATGTAAGTTATCAAAGTTATGTACT
* ** * *
31319706 ATTTAAGTTATGTAAGTTGTGTATT
1 ATGTAAGTTATCAAAGTTATGTACT
31319731 ATGTAAGTTAT
1 ATGTAAGTTAT
31319742 TATGTTATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.18, T:0.48
Consensus pattern (25 bp):
ATGTAAGTTATCAAAGTTATGTACT
Found at i:31320023 original size:17 final size:17
Alignment explanation
Indices: 31320003--31320036 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31319993 TATCCATACC
31320003 ATATATAAAAATTTTAA
1 ATATATAAAAATTTTAA
*
31320020 ATATATATAAATTTTAA
1 ATATATAAAAATTTTAA
31320037 GTAATGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATAAAAATTTTAA
Found at i:31320055 original size:18 final size:18
Alignment explanation
Indices: 31320032--31320120 Score: 101
Period size: 18 Copynumber: 4.8 Consensus size: 18
31320022 ATATATAAAT
31320032 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
31320050 TTTAAGTAATGTAAATTATAAA
1 TTTAAGTAATGT-AA-TAT--A
*
31320072 TTTTAGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
*
31320089 TTTAAGTAATGTAACATA
1 TTTAAGTAATGTAATATA
*
31320107 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
31320121 GTAAGTAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 13 0.21
18 27 0.44
19 5 0.08
20 5 0.08
21 2 0.03
22 9 0.15
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:31320091 original size:39 final size:41
Alignment explanation
Indices: 31320025--31320102 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 41
31320015 TTTAAATATA
31320025 TATAAATTTTAAGTAATGTAATATATTTAAGTAATGTAAAT
1 TATAAATTTTAAGTAATGTAATATATTTAAGTAATGTAAAT
31320066 TATAAATTTT-AGTAA-GTAATATATTTAAGTAATGTAA
1 TATAAATTTTAAGTAATGTAATATATTTAAGTAATGTAA
31320103 CATATTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 22 0.59
40 5 0.14
41 10 0.27
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (41 bp):
TATAAATTTTAAGTAATGTAATATATTTAAGTAATGTAAAT
Found at i:31320102 original size:22 final size:22
Alignment explanation
Indices: 31320037--31320129 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 22
31320027 TAAATTTTAA
31320037 GTAATGTAATATATTTAAGTAAT
1 GTAA-GTAATATATTTAAGTAAT
* * *
31320060 GTAAATTATAAATTT---T-A-
1 GTAAGTAATATATTTAAGTAAT
31320077 GTAAGTAATATATTTAAGTAAT
1 GTAAGTAATATATTTAAGTAAT
* *
31320099 GTAA--CATATTTTAGTAAGTAAT
1 GTAAGTAATATATT--TAAGTAAT
31320121 GTAAGTAAT
1 GTAAGTAAT
31320130 GTAATATATA
Statistics
Matches: 52, Mismatches: 9, Indels: 17
0.67 0.12 0.22
Matches are distributed among these distances:
17 12 0.23
18 1 0.02
19 1 0.02
20 7 0.13
21 1 0.02
22 24 0.46
23 4 0.08
24 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.13, T:0.42
Consensus pattern (22 bp):
GTAAGTAATATATTTAAGTAAT
Found at i:31320119 original size:39 final size:39
Alignment explanation
Indices: 31320030--31320124 Score: 117
Period size: 39 Copynumber: 2.4 Consensus size: 39
31320020 ATATATATAA
31320030 ATTTTAAGTAATGTAATATATTTAAGTAATGTAAATTAT
1 ATTTTAAGTAATGTAATATATTTAAGTAATGTAAATTAT
31320069 AAATTTT-AGTAA-GTAATATATTTAAGTAATGTAACA-TAT
1 --ATTTTAAGTAATGTAATATATTTAAGTAATGTAA-ATTAT
31320108 -TTTAGTAAGTAATGTAA
1 ATTT--TAAGTAATGTAA
31320125 GTAATGTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
36 3 0.06
38 1 0.02
39 30 0.61
40 10 0.20
41 5 0.10
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.43
Consensus pattern (39 bp):
ATTTTAAGTAATGTAATATATTTAAGTAATGTAAATTAT
Found at i:31320162 original size:47 final size:47
Alignment explanation
Indices: 31320104--31320285 Score: 225
Period size: 47 Copynumber: 4.0 Consensus size: 47
31320094 GTAATGTAAC
* *
31320104 ATATTTTAGTAAGTAATGTAAGTAATGTAATATATACTTAAAAATAT
1 ATATTTCAGTAAGTAATGTAAGTAATGTAATATATACTTAAGAATAT
31320151 ATATTTCAGTAAGTAATGTAAGTAATGTAATATATACTTAAGAATAT
1 ATATTTCAGTAAGTAATGTAAGTAATGTAATATATACTTAAGAATAT
* * * * *
31320198 ATA-TT---TAAGTAATGTAAGTAAAGTAA-ACT-GAGTTATGTA-AT
1 ATATTTCAGTAAGTAATGTAAGTAATGTAATA-TATACTTAAGAATAT
* *
31320239 ATATTTCAGTAAGTAATGTAAGTAATCTAATATATGCTTAAGAATAT
1 ATATTTCAGTAAGTAATGTAAGTAATGTAATATATACTTAAGAATAT
31320286 TGCGTTTTTT
Statistics
Matches: 113, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
41 5 0.04
42 9 0.08
43 21 0.19
45 20 0.18
46 8 0.07
47 50 0.44
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (47 bp):
ATATTTCAGTAAGTAATGTAAGTAATGTAATATATACTTAAGAATAT
Found at i:31320994 original size:17 final size:19
Alignment explanation
Indices: 31320953--31321004 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
31320943 TTAGTAAAGT
31320953 ATATATTCCAGCAACTGGA
1 ATATATTCCAGCAACTGGA
*
31320972 ATATATTCTAGCAACTGGA
1 ATATATTCCAGCAACTGGA
31320991 ATATATTCCAGCAA
1 ATATATTCCAGCAA
31321005 GTATATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (19 bp):
ATATATTCCAGCAACTGGA
Found at i:31323019 original size:38 final size:38
Alignment explanation
Indices: 31322976--31323079 Score: 145
Period size: 38 Copynumber: 2.7 Consensus size: 38
31322966 TAAAGCATAA
*
31322976 CCCCTAACCCCTAAAGCATAACCCCTAAACCCTAAATC
1 CCCCTAACCCATAAAGCATAACCCCTAAACCCTAAATC
** *
31323014 CCCCTAACCTTTAAAGCATAACCCTTAAACCCTAAATC
1 CCCCTAACCCATAAAGCATAACCCCTAAACCCTAAATC
* * *
31323052 CCTCTAGCTCATAAAGCATAACCCCTAA
1 CCCCTAACCCATAAAGCATAACCCCTAA
31323080 CCTTAAACCA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.37, C:0.39, G:0.04, T:0.20
Consensus pattern (38 bp):
CCCCTAACCCATAAAGCATAACCCCTAAACCCTAAATC
Found at i:31323049 original size:21 final size:21
Alignment explanation
Indices: 31322954--31323049 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
31322944 CCCTTAAATC
*
31322954 CCCCTTAACCCTTAAAGCATAA
1 CCCCTAAACCC-TAAAGCATAA
*
31322976 CCCCTAACCCCTAAAGCATAA
1 CCCCTAAACCCTAAAGCATAA
*
31322997 CCCCTAAACCCT-AA--AT-C
1 CCCCTAAACCCTAAAGCATAA
*
31323014 CCCCT-AACCTTTAAAGCATAA
1 CCCCTAAACC-CTAAAGCATAA
*
31323035 CCCTTAAACCCTAAA
1 CCCCTAAACCCTAAA
31323050 TCCCTCTAGC
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
16 4 0.07
17 6 0.10
18 4 0.07
20 4 0.07
21 29 0.48
22 13 0.22
ACGTcount: A:0.38, C:0.40, G:0.03, T:0.20
Consensus pattern (21 bp):
CCCCTAAACCCTAAAGCATAA
Found at i:31323317 original size:14 final size:14
Alignment explanation
Indices: 31323298--31323331 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
31323288 GAAACGGATG
31323298 AAATTTGGTATAAT
1 AAATTTGGTATAAT
31323312 AAATTTGGTATAAT
1 AAATTTGGTATAAT
31323326 AAATTT
1 AAATTT
31323332 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (14 bp):
AAATTTGGTATAAT
Found at i:31323385 original size:36 final size:33
Alignment explanation
Indices: 31323306--31323389 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 33
31323296 TGAAATTTGG
* *
31323306 TATAATAAATTTGGTATAATAAATTTTATTTTTT
1 TATAAT-AATTTGGTATAATAAAATGTATTTTTT
31323340 TATAA-AATTTGGTATAA-AAAATGTATTTTTT
1 TATAATAATTTGGTATAATAAAATGTATTTTTT
31323371 ATCCAATAATAATTTGGTA
1 -T---ATAATAATTTGGTA
31323390 AAGAATGACA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
31 12 0.28
32 13 0.30
34 5 0.12
35 4 0.09
36 9 0.21
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.49
Consensus pattern (33 bp):
TATAATAATTTGGTATAATAAAATGTATTTTTT
Found at i:31324504 original size:13 final size:13
Alignment explanation
Indices: 31324469--31324506 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
31324459 GTTATATTTG
*
31324469 TAATTTGAAAGCT
1 TAATTTGAAAACT
31324482 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
31324496 TAATTTGAAAA
1 TAATTTGAAAA
31324507 TTTGGAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:31324544 original size:29 final size:27
Alignment explanation
Indices: 31324470--31324544 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
31324460 TTATATTTGT
* * * *
31324470 AATTTGAAAGCTTAAGTTTGAAAACTT
1 AATTTGAAAACTTAAATTTAAAAACTA
*
31324497 AATTTGAAAATTTGGAAATTTAAAAACTA
1 AATTTGAAAACTT--AAATTTAAAAACTA
31324526 AATTTTTGAAAACTTAAAT
1 AA--TTTGAAAACTTAAAT
31324545 GTCTTGAGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 11 0.29
29 17 0.45
31 10 0.26
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (27 bp):
AATTTGAAAACTTAAATTTAAAAACTA
Found at i:31325501 original size:14 final size:14
Alignment explanation
Indices: 31325482--31325511 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
31325472 CCAAAATGGT
31325482 TGGAAACTTGAAGG
1 TGGAAACTTGAAGG
31325496 TGGAAACTTGAAGG
1 TGGAAACTTGAAGG
31325510 TG
1 TG
31325512 CTACAGACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.37, T:0.23
Consensus pattern (14 bp):
TGGAAACTTGAAGG
Found at i:31328760 original size:21 final size:21
Alignment explanation
Indices: 31328736--31328791 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
31328726 CTGAACAATT
*
31328736 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
31328757 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
31328777 AAGAAATAGAATCAA
1 AAGAAAAAG-ATCAA
31328792 CGATTTGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:31328777 original size:20 final size:23
Alignment explanation
Indices: 31328747--31328791 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
31328737 AGAAAAAGAG
31328747 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
31328768 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
31328790 AA
1 AA
31328792 CGATTTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:31330915 original size:13 final size:13
Alignment explanation
Indices: 31330897--31330935 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
31330887 AATTTCCAAA
31330897 TTTTCAAATTAAG
1 TTTTCAAATTAAG
31330910 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
31330924 CTTTCAAATTAA
1 TTTTCAAATTAA
31330936 AAATATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:31330928 original size:14 final size:13
Alignment explanation
Indices: 31330898--31330935 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
31330888 ATTTCCAAAT
*
31330898 TTTCAAATTAAGT
1 TTTCAAATTAAGC
31330911 TTTCAAACTTAAGC
1 TTTCAAA-TTAAGC
31330925 TTTCAAATTAA
1 TTTCAAATTAA
31330936 AAATATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.42
Consensus pattern (13 bp):
TTTCAAATTAAGC
Found at i:31332701 original size:115 final size:114
Alignment explanation
Indices: 31332396--31332817 Score: 337
Period size: 114 Copynumber: 3.7 Consensus size: 114
31332386 GAGAGCGCCA
* * * * * **
31332396 CTAAATCCCCCGAAAGCACAGAAAACGACGTCGTTGGGCTTA-GTTTTTCTTGAGGCGCTACCCC
1 CTAAA-CCCCCGAAAGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTT-TTGCGGCGCTTCTTC
* * * *** * * * * * * * * *
31332460 AAAAACGTCGTTAAATCCCCGAGCACTAGCGGCGCTTCTAGAGAAACGCCA
64 AAAAACGCCGCTAAAGCCATAAGCATTAGCAGCACTCCAATAAAAACACCG
* * * * ** * * * *
31332511 CTAGATCCCCAAAATCTCAGAAAACAGCGTCGTTGGGCTTAGGTTATTTTGCAGCACTTCTCCAA
1 CTAAACCCCCGAAAGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTCTTCAA
* * * ** **
31332576 AAACGCCGCTAAAGCTATGAGCATTAGCGGTGCTCCCTTAAAAACACCG
66 AAACGCCGCTAAAGCCATAAGCATTAGCAGCACTCCAATAAAAACACCG
* * *
31332625 CTAAATCCCTGAAAAGCTCAG-AAATGGTGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTCTTC
1 CTAAACCCCCG-AAAGCTCAGAAAATGGCGTCGTTGGGCTTAGG-TTTTTTTGCGGCGCTTCTTC
* * ** *
31332689 AAAAACGCCGCTAAAGCCCTAAGTATTAGCAGCACTTTAATAAAAACGCCG
64 AAAAACGCCGCTAAAGCCATAAGCATTAGCAGCACTCCAATAAAAACACCG
* *
31332740 CTAAACCCCCGAATGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTTTTGCGGTGCATT-TTCA
1 CTAAACCCCCGAAAGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGC-TTCTTCA
31332804 AAAACGCCGCTAAA
65 AAAACGCCGCTAAA
31332818 TCCCCTAAAG
Statistics
Matches: 246, Mismatches: 56, Indels: 11
0.79 0.18 0.04
Matches are distributed among these distances:
114 142 0.58
115 104 0.42
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (114 bp):
CTAAACCCCCGAAAGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTCTTCAA
AAACGCCGCTAAAGCCATAAGCATTAGCAGCACTCCAATAAAAACACCG
Found at i:31332824 original size:115 final size:115
Alignment explanation
Indices: 31332537--31332825 Score: 316
Period size: 115 Copynumber: 2.5 Consensus size: 115
31332527 TCAGAAAACA
* * * * * ** * *
31332537 GCGTCGTTGGGCTTAGG-TTATTTTGCAGCACTTCTCCAAAAACGCCGCTAAAGCTATGAGCATT
1 GCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTCTTCAAAAACGCCGCTAAACCCCTAAGTATT
* ** **** * *
31332601 AGCGGTGCTCCCTTAAAAACACCGCTAAATCCCTGAAAAGCTCAGAAATG
66 AGCAGCACTTTAATAAAAACACCGCTAAACCCCCGAAAAGCTCAGAAATG
* *
31332651 GTGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTAAGTATT
1 GCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTCTTCAAAAACGCCGCTAAACCCCTAAGTATT
* *
31332716 AGCAGCACTTTAATAAAAACGCCGCTAAACCCCCG-AATGCTCAGAAAATG
66 AGCAGCACTTTAATAAAAACACCGCTAAACCCCCGAAAAGCTCAG-AAATG
*
31332766 GCGTCGTTGGGCTTAGG-TTTTTTTGCGGTGCATT-TTCAAAAACGCCGCTAAATCCCCTAA
1 GCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGC-TTCTTCAAAAACGCCGCTAAA-CCCCTAA
31332826 AGTTCGGTAA
Statistics
Matches: 148, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
114 55 0.37
115 93 0.63
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (115 bp):
GCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTCTTCAAAAACGCCGCTAAACCCCTAAGTATT
AGCAGCACTTTAATAAAAACACCGCTAAACCCCCGAAAAGCTCAGAAATG
Found at i:31334494 original size:18 final size:18
Alignment explanation
Indices: 31334452--31334495 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31334442 AAAGGAGGAT
* *
31334452 TAGATGAACCAATTGAAT
1 TAGAAGAACCAATTGAAG
* *
31334470 TAAAAGAACCAATTGGAG
1 TAGAAGAACCAATTGAAG
31334488 TAGAAGAA
1 TAGAAGAA
31334496 ACACTAAAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.20
Consensus pattern (18 bp):
TAGAAGAACCAATTGAAG
Found at i:31335123 original size:41 final size:41
Alignment explanation
Indices: 31335068--31335284 Score: 236
Period size: 41 Copynumber: 5.3 Consensus size: 41
31335058 ATGTTTTTAA
* * * * *
31335068 AAAAAGTGCTGCTAATGCTCAGATCTTTAGCAGCGTTTTTG
1 AAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTTTTC
* * ** * *
31335109 AAAAAGTGTCGCTAATGCTCAGATATTTAGCGGCATTTTTA
1 AAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTTTTC
*
31335150 AAAAAGCGCCGCTAATGCTCAGAGATTTAGCGGCGTTTTTC
1 AAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTTTTC
* * * * * *
31335191 AAGAAGCGCCGCTAATGCTCCGGGCTTTAGTGGTGTTTTCC
1 AAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTTTTC
* * * *
31335232 AAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTG
1 AAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTTTTC
31335273 AAAAAGCGCCGC
1 AAAAAGCGCCGC
31335285 AAAAACATTT
Statistics
Matches: 152, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 152 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.29
Consensus pattern (41 bp):
AAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCGTTTTTC
Found at i:31335429 original size:26 final size:26
Alignment explanation
Indices: 31335381--31335431 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
31335371 AAAATGGATA
** * *
31335381 AATTTGAAATAATGACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
31335407 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
31335432 AATATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:31335719 original size:14 final size:15
Alignment explanation
Indices: 31335691--31335723 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
31335681 AAGGTTTATA
31335691 GATTATGGAATTAGG
1 GATTATGGAATTAGG
31335706 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
31335720 GATT
1 GATT
31335724 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:31335764 original size:7 final size:7
Alignment explanation
Indices: 31335754--31335797 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
31335744 TAAGGTTTAT
31335754 GGGTTAG
1 GGGTTAG
31335761 GGGTTAG
1 GGGTTAG
31335768 GGGTTAG
1 GGGTTAG
31335775 GGGTTAG
1 GGGTTAG
* *
31335782 AGGTTAA
1 GGGTTAG
*
31335789 GAGTTAG
1 GGGTTAG
31335796 GG
1 GG
31335798 ATTTAGGGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.20, C:0.00, G:0.52, T:0.27
Consensus pattern (7 bp):
GGGTTAG
Found at i:31335807 original size:21 final size:20
Alignment explanation
Indices: 31335754--31335807 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
31335744 TAAGGTTTAT
* *
31335754 GGGTTAGGGGTTAGGGGTTAG
1 GGGTTA-GGGTTAAGAGTTAG
31335775 GGGTTAGAGGTTAAGAGTTAG
1 GGGTTAG-GGTTAAGAGTTAG
*
31335796 GGATTTAGGGTT
1 GG-GTTAGGGTT
31335808 TATGGATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.20, C:0.00, G:0.48, T:0.31
Consensus pattern (20 bp):
GGGTTAGGGTTAAGAGTTAG
Found at i:31337033 original size:21 final size:21
Alignment explanation
Indices: 31337007--31337054 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
31336997 TAAATTTCTT
* *
31337007 CCCCCTGAGATCCCCAATTTC
1 CCCCCTAAAATCCCCAATTTC
*
31337028 CCCCCTAAAATCCCTAATTTC
1 CCCCCTAAAATCCCCAATTTC
31337049 CCCCCT
1 CCCCCT
31337055 TGAAACCCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.50, G:0.04, T:0.25
Consensus pattern (21 bp):
CCCCCTAAAATCCCCAATTTC
Found at i:31337343 original size:24 final size:23
Alignment explanation
Indices: 31337316--31337365 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
31337306 GTCGAAAGTT
31337316 ACAACCAAAAAACCTAAAATATGA
1 ACAACC-AAAAACCTAAAATATGA
*
31337340 ACAATCAAAAACCTAAAATATGA
1 ACAACCAAAAACCTAAAATATGA
31337363 ACA
1 ACA
31337366 CTAATCGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.62, C:0.20, G:0.04, T:0.14
Consensus pattern (23 bp):
ACAACCAAAAACCTAAAATATGA
Found at i:31341038 original size:43 final size:43
Alignment explanation
Indices: 31340930--31341068 Score: 126
Period size: 42 Copynumber: 3.3 Consensus size: 43
31340920 AAGTCATGTT
* *
31340930 TTTAACGGCGTTTGTCA-AAAAGC-TCTGCTAAAAGTTATCT-T-
1 TTTAGCGGCGTTTGTGATAAAAGCGTC-GCTAAAAGTTAT-TATC
* * * *
31340971 TATAGTGGCGTTTGTGGTATAAGCGTCGCTAAAAGTTATTATC
1 TTTAGCGGCGTTTGTGATAAAAGCGTCGCTAAAAGTTATTATC
* * * * *
31341014 TTTAGCGGCGTTTGTGATAGAAGCG-CCCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGATAAAAGCGTCGCTAAAAGTTATTATC
31341056 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
31341069 TCCCACATAA
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
41 13 0.16
42 44 0.55
43 23 0.29
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGTCGCTAAAAGTTATTATC
Found at i:31353020 original size:50 final size:50
Alignment explanation
Indices: 31352903--31353088 Score: 139
Period size: 50 Copynumber: 3.8 Consensus size: 50
31352893 ACATTAAGAG
* * *
31352903 GATGAG-A-TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 GATGAGAACTCCCATGTAAGACCATGTCTGAGACATGGCATGGGCACCGA
** ** *
31352951 GATGAGAGGTCCCCGGTAAGACCATGTTTGAGACATGGCATGGGCACCGA
1 GATGAGAACTCCCATGTAAGACCATGTCTGAGACATGGCATGGGCACCGA
* ** * * * * **
31353001 TATGAGAACTTTCATGTAAGACCATATCTGGGATATGACATTTGCA--GTA
1 GATGAGAACTCCCATGTAAGACCATGTCTGAGACATGGCATGGGCACCG-A
* * *
31353050 CAGGA-AACATCCCATGTAAGACCATGTCTGGGACATGGC
1 GATGAGAAC-TCCCATGTAAGACCATGTCTGAGACATGGC
31353089 TTTTGCATGT
Statistics
Matches: 106, Mismatches: 28, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
48 10 0.09
49 29 0.27
50 67 0.63
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
GATGAGAACTCCCATGTAAGACCATGTCTGAGACATGGCATGGGCACCGA
Found at i:31363887 original size:9 final size:9
Alignment explanation
Indices: 31363873--31363938 Score: 59
Period size: 9 Copynumber: 7.4 Consensus size: 9
31363863 ATTTTTTCTA
31363873 TAAAAATAT
1 TAAAAATAT
31363882 TAAAAAT-T
1 TAAAAATAT
*
31363890 AGAAAAATAT
1 -TAAAAATAT
31363900 TAAAAAAATAT
1 T--AAAAATAT
31363911 TAAAAA-A-
1 TAAAAATAT
31363918 T-AAAATAT
1 TAAAAATAT
*
31363926 TTAAAATAT
1 TAAAAATAT
31363935 TAAA
1 TAAA
31363939 TTTGATATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
6 4 0.09
7 2 0.04
8 3 0.06
9 28 0.60
10 1 0.02
11 9 0.19
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
TAAAAATAT
Found at i:31363906 original size:11 final size:11
Alignment explanation
Indices: 31363883--31363917 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
31363873 TAAAAATATT
*
31363883 AAAA-ATTAGA
1 AAAATATTAAA
31363893 AAAATATTAAA
1 AAAATATTAAA
31363904 AAAATATTAAA
1 AAAATATTAAA
31363915 AAA
1 AAA
31363918 TAAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
AAAATATTAAA
Found at i:31363966 original size:19 final size:17
Alignment explanation
Indices: 31363944--31364014 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 17
31363934 TTAAATTTGA
31363944 TATAAACTTATAAAAATAT
1 TATAAA-TTATAAAAAT-T
31363963 TATAAA-TATAATAAATCT
1 TATAAATTATAA-AAAT-T
*
31363981 AATAAATTATAAAAATT
1 TATAAATTATAAAAATT
31363998 TATAAAATTAATAAAAA
1 TAT-AAATT-ATAAAAA
31364015 CATATTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
17 8 0.18
18 19 0.42
19 18 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TATAAATTATAAAAATT
Found at i:31363970 original size:37 final size:34
Alignment explanation
Indices: 31363919--31364008 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 34
31363909 ATTAAAAAAT
*
31363919 AAAATATT-TAAAATATTAAATTTGATATAAACTTATA
1 AAAATATTAT-AAATATTAAATCT-A-ATAAA-TTATA
31363956 AAAATATTATAAATATAATAAATCTAATAAATTATA
1 AAAATATTATAAATAT--TAAATCTAATAAATTATA
31363992 AAAAT-TTATAAA-ATTAA
1 AAAATATTATAAATATTAA
31364009 TAAAAACATA
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
32 3 0.06
34 2 0.04
35 7 0.14
36 10 0.20
37 19 0.39
38 2 0.04
39 6 0.12
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (34 bp):
AAAATATTATAAATATTAAATCTAATAAATTATA
Found at i:31364103 original size:29 final size:29
Alignment explanation
Indices: 31364070--31364145 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
31364060 TAACAACTTA
* *
31364070 TAAAAATTCATAAAATTTTTAAAAAATAT
1 TAAAAATTCATAAAAATATTAAAAAATAT
*
31364099 T-AAAATTGATATAAAATATTAAAAAATAT
1 TAAAAATTCATA-AAAATATTAAAAAATAT
* *
31364128 AAAAAGAATCATAAAAAT
1 TAAAA-ATTCATAAAAAT
31364146 TTGAACTGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 9 0.24
29 16 0.42
30 8 0.21
31 5 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (29 bp):
TAAAAATTCATAAAAATATTAAAAAATAT
Found at i:31364775 original size:27 final size:29
Alignment explanation
Indices: 31364732--31364790 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
31364722 TAATTTTTTA
31364732 ATATTTTAATAATTTA-TTA-GAATATTT
1 ATATTTTAATAATTTATTTATGAATATTT
* *
31364759 ATATTATTTATAA-TTATTTATGAATTTTT
1 ATATT-TTAATAATTTATTTATGAATATTT
31364788 ATA
1 ATA
31364791 AGTTTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 9 0.33
29 10 0.37
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (29 bp):
ATATTTTAATAATTTATTTATGAATATTT
Found at i:31364807 original size:10 final size:9
Alignment explanation
Indices: 31364720--31365096 Score: 103
Period size: 10 Copynumber: 39.6 Consensus size: 9
31364710 ACTATTTCTA
31364720 TATAATTTT
1 TATAATTTT
31364729 T-TAATATTT
1 TATAAT-TTT
31364738 TAATAATTTAT
1 T-ATAATTT-T
* *
31364749 TAGAATATT
1 TATAATTTT
31364758 TAT-ATTATT
1 TATAATT-TT
31364767 TATAATTATT
1 TATAATT-TT
31364777 TATGAATTTT
1 TAT-AATTTT
31364787 TATAAGTTTT
1 TATAA-TTTT
31364797 TATAATATTT
1 TATAAT-TTT
31364807 TA-AATATATCT
1 TATAAT-T-T-T
*
31364818 TATTAA-TTA
1 TA-TAATTTT
31364827 TAT-ATTTT
1 TATAATTTT
31364835 TAATAATTTAT
1 T-ATAATTT-T
*
31364846 TAAAATTTAT
1 TATAATTT-T
* *
31364856 TAGATTTTT
1 TATAATTTT
*
31364865 TATAATCTT
1 TATAATTTT
*
31364874 TACAAGTTTT
1 TATAA-TTTT
*
31364884 TATGATTTT
1 TATAATTTT
31364893 T-TAATATTT
1 TATAAT-TTT
* *
31364902 AATAATTTA
1 TATAATTTT
* *
31364911 TATTATTTC
1 TATAATTTT
31364920 TA-ATATTTT
1 TATA-ATTTT
*
31364929 TTTATATTTT
1 TATA-ATTTT
* **
31364939 TCTGGTTTT
1 TATAATTTT
*
31364948 TATAGGTTTT
1 TATA-ATTTT
* *
31364958 AAAGAATTTT
1 -TATAATTTT
*
31364968 TATATGTTTT
1 TATA-ATTTT
*
31364978 TAATAAAATTT
1 T-AT-AATTTT
31364989 TA-AATATTT
1 TATAAT-TTT
*
31364998 TAAACATGTTT
1 TATA-AT-TTT
*
31365009 TATTACTTTT
1 TA-TAATTTT
*
31365019 GTAAAATTTT
1 -TATAATTTT
31365029 TATAATTTAT
1 TATAATTT-T
*
31365039 TAT-A-GTT
1 TATAATTTT
*
31365046 TAT-ATATT
1 TATAATTTT
*
31365054 T-TAATATT
1 TATAATTTT
31365062 TATAAGTTTT
1 TATAA-TTTT
*
31365072 TATTACTTTT
1 TA-TAATTTT
*
31365082 TTTAATTTTT
1 TATAA-TTTT
31365092 TATAA
1 TATAA
31365097 GTTTATATTG
Statistics
Matches: 277, Mismatches: 52, Indels: 77
0.68 0.13 0.19
Matches are distributed among these distances:
7 7 0.03
8 25 0.09
9 85 0.31
10 120 0.43
11 36 0.13
12 2 0.01
13 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.59
Consensus pattern (9 bp):
TATAATTTT
Found at i:31364836 original size:28 final size:25
Alignment explanation
Indices: 31364796--31364848 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
31364786 TTATAAGTTT
31364796 TTATAATATTTTAAATATATCTTATTAA
1 TTATAATATTTT-AATA-AT-TTATTAA
31364824 TTAT-ATATTTTTAATAATTTATTAA
1 TTATAATA-TTTTAATAATTTATTAA
31364849 AATTTATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.29
26 2 0.08
27 7 0.29
28 8 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TTATAATATTTTAATAATTTATTAA
Found at i:31364845 original size:25 final size:28
Alignment explanation
Indices: 31364796--31364848 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
31364786 TTATAAGTTT
31364796 TTATAATATTTTAAATATATCTTATTAA
1 TTATAATATTTTAAATATATCTTATTAA
*
31364824 TTAT-ATATTTTTAATA-AT-TTATTAA
1 TTATAATATTTTAAATATATCTTATTAA
31364849 AATTTATTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 2 0.08
27 11 0.46
28 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TTATAATATTTTAAATATATCTTATTAA
Found at i:31364855 original size:28 final size:27
Alignment explanation
Indices: 31364795--31364924 Score: 72
Period size: 29 Copynumber: 4.6 Consensus size: 27
31364785 TTTATAAGTT
*
31364795 TTTATAATATTTTAAATATATCTTATTAA
1 TTTAT-ATATTTTTAATA-ATCTTATTAA
31364824 -TTATATATTTTTAATAAT-TTATTAAAA
1 TTTATATATTTTTAATAATCTTATT--AA
* * *
31364851 TTTATTAGATTTTTTATAATCTT-TACAA
1 TTTA-TATATTTTTAATAATCTTAT-TAA
* *
31364879 GTTTTTATGATTTTTTAAT-AT-TTAATAA
1 -TTTATAT-A-TTTTTAATAATCTTATTAA
*
31364907 TTTATATTATTTCTAATA
1 TTTATA-TATTTTTAATA
31364925 TTTTTTTATA
Statistics
Matches: 78, Mismatches: 11, Indels: 26
0.68 0.10 0.23
Matches are distributed among these distances:
25 5 0.06
26 9 0.12
27 19 0.24
28 16 0.21
29 20 0.26
30 9 0.12
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTATATATTTTTAATAATCTTATTAA
Found at i:31364869 original size:29 final size:29
Alignment explanation
Indices: 31364830--31364895 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
31364820 TTAATTATAT
* *
31364830 ATTTTTAATAATTTATTA-AAATTTATTA-G
1 ATTTTTTATAATCT-TTACAAATTT-TTATG
*
31364859 ATTTTTTATAATCTTTACAAGTTTTTATG
1 ATTTTTTATAATCTTTACAAATTTTTATG
31364888 ATTTTTTA
1 ATTTTTTA
31364896 ATATTTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (29 bp):
ATTTTTTATAATCTTTACAAATTTTTATG
Found at i:31368923 original size:25 final size:25
Alignment explanation
Indices: 31368889--31368940 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
31368879 ATAAGAGATG
31368889 AAGTAACTGTGATTGTTGGTTTTGT
1 AAGTAACTGTGATTGTTGGTTTTGT
31368914 AAGTAACTGTGATTGTTGGTTTTGT
1 AAGTAACTGTGATTGTTGGTTTTGT
31368939 AA
1 AA
31368941 TAGTGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.04, G:0.27, T:0.46
Consensus pattern (25 bp):
AAGTAACTGTGATTGTTGGTTTTGT
Found at i:31371278 original size:29 final size:28
Alignment explanation
Indices: 31371248--31371301 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
31371238 AAAGCCCTTT
31371248 TTTTTTAA-ATTTACCGAAATGGGCCGG
1 TTTTTTAATATTTACCGAAATGGGCCGG
*
31371275 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAA-TATTTACCGAAATGGGCC
31371302 ATTTTCCCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 8 0.33
29 16 0.67
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (28 bp):
TTTTTTAATATTTACCGAAATGGGCCGG
Found at i:31371539 original size:22 final size:22
Alignment explanation
Indices: 31371514--31371580 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
31371504 AAACAAATCC
*
31371514 TATCTCAATTTCATTCAAAAAT
1 TATCTCAATTTCCTTCAAAAAT
* *
31371536 TATCTCAAATTCCTTCAAGAAT
1 TATCTCAATTTCCTTCAAAAAT
* *
31371558 TCTCTCAATTTCCTTCCAAAAT
1 TATCTCAATTTCCTTCAAAAAT
31371580 T
1 T
31371581 CTCTTAAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.01, T:0.40
Consensus pattern (22 bp):
TATCTCAATTTCCTTCAAAAAT
Found at i:31371615 original size:22 final size:22
Alignment explanation
Indices: 31371589--31371639 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
31371579 TTCTCTTAAA
*
31371589 CTCTCAAATTCCTTC-CAAAAT
1 CTCTCAAATTCCTTCAAAAAAT
*
31371610 CTTCTCAATTTCCTTCAAAAAAT
1 C-TCTCAAATTCCTTCAAAAAAT
31371633 CTCTCAA
1 CTCTCAA
31371640 CTCCATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.73
23 6 0.23
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.35
Consensus pattern (22 bp):
CTCTCAAATTCCTTCAAAAAAT
Found at i:31371616 original size:52 final size:52
Alignment explanation
Indices: 31371538--31371636 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
31371528 TCAAAAATTA
* *
31371538 TCTCAAATTCCTTCAAGAATTCTCTCAATTTCCTTCCAAAATTCTCTTAAAC
1 TCTCAAATTCCTTCAAGAATTCTCTCAATTTCCTTCAAAAAATCTCTTAAAC
31371590 TCTCAAATTCCTTCCAA-AA-TCTTCTCAATTTCCTTCAAAAAATCTCT
1 TCTCAAATTCCTT-CAAGAATTC-TCTCAATTTCCTTCAAAAAATCTCT
31371637 CAACTCCATA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
51 2 0.05
52 38 0.88
53 3 0.07
ACGTcount: A:0.31, C:0.29, G:0.01, T:0.38
Consensus pattern (52 bp):
TCTCAAATTCCTTCAAGAATTCTCTCAATTTCCTTCAAAAAATCTCTTAAAC
Found at i:31371711 original size:29 final size:28
Alignment explanation
Indices: 31371673--31371730 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
31371663 ATTCAATTTC
31371673 ATTTTTTTAAGAA-AATTTGAAATATTTTT
1 ATTTTTTTAA-AATAATTTGAAA-ATTTTT
*
31371702 ATTTTTTTAAAATAATTTTAAAATTTTT
1 ATTTTTTTAAAATAATTTGAAAATTTTT
31371730 A
1 A
31371731 ATATTTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
ATTTTTTTAAAATAATTTGAAAATTTTT
Found at i:31371737 original size:29 final size:29
Alignment explanation
Indices: 31371676--31371737 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
31371666 CAATTTCATT
*
31371676 TTTTTAAGAAAATTTGAAATATTTTTATT
1 TTTTTAAGAAAATTTGAAATATTTTTATA
*
31371705 TTTTTAA-AATAATTTTAAA-ATTTTTAATA
1 TTTTTAAGAA-AATTTGAAATATTTTT-ATA
31371734 TTTT
1 TTTT
31371738 CAACAATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTTTAAGAAAATTTGAAATATTTTTATA
Found at i:31372831 original size:7 final size:7
Alignment explanation
Indices: 31372819--31372843 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31372809 AGTGGATTGA
31372819 TATTTAG
1 TATTTAG
31372826 TATTTAG
1 TATTTAG
31372833 TATTTAG
1 TATTTAG
31372840 TATT
1 TATT
31372844 ATGTATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:31374041 original size:23 final size:23
Alignment explanation
Indices: 31374011--31374128 Score: 173
Period size: 23 Copynumber: 4.8 Consensus size: 23
31374001 ATATTATTTG
31374011 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
31374034 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
31374057 ATTTAATTAAAAACCCTAAACTTTAACCTA
1 ATTTAATTAAAAA-CC----C--TAACCTA
31374087 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
31374110 ATTTAATTAAAAACCCTAA
1 ATTTAATTAAAAACCCTAA
31374129 ACCCTAACCT
Statistics
Matches: 88, Mismatches: 0, Indels: 14
0.86 0.00 0.14
Matches are distributed among these distances:
23 62 0.70
24 2 0.02
25 1 0.01
28 1 0.01
29 2 0.02
30 20 0.23
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (23 bp):
ATTTAATTAAAAACCCTAACCTA
Found at i:31374085 original size:30 final size:29
Alignment explanation
Indices: 31374022--31374460 Score: 480
Period size: 29 Copynumber: 15.1 Consensus size: 29
31374012 TTTAATTAAA
31374022 AACCCTAACCTAATTTAATT--AAA----
1 AACCCTAACCTAATTTAATTAAAAACCCT
31374045 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
**
31374074 AAACTTTAACCTAATTTAATT--AAA----
1 -AACCCTAACCTAATTTAATTAAAAACCCT
31374098 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
31374127 AAACCCTAACCTAATTTAATTAAAAACCTT
1 -AACCCTAACCTAATTTAATTAAAAACCCT
*
31374157 AACCCTAACCTAATCTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
31374186 AACCCTAACCTAATTT-ATCTAAAAGCCTT
1 AACCCTAACCTAATTTAAT-TAAAAACCCT
31374215 AAACCCTAACCTAATTTAATTAAATTAAAAACCCT
1 -AACCCTAACCTAA--T--TT-AATTAAAAACCCT
*
31374250 AAACCCTAACATAATTTAATTAAATTAAAAACCCT
1 -AACCCTAACCTAA--T--TT-AATTAAAAACCCT
31374285 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
** *
31374314 AA-CCTAATTTAATTAAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
31374342 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
31374371 AA-CCTAA-TTAAATTAAATTAAAAACCCT
1 AACCCTAACCT-AATTTAATTAAAAACCCT
31374399 AAACCCTAACCTAATTTAATTAAAAACCCT
1 -AACCCTAACCTAATTTAATTAAAAACCCT
**
31374429 AA-CCTAATTTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
31374457 AACC
1 AACC
31374461 TAATTTGATA
Statistics
Matches: 362, Mismatches: 26, Indels: 50
0.83 0.06 0.11
Matches are distributed among these distances:
23 38 0.10
25 6 0.02
27 1 0.00
28 78 0.22
29 95 0.26
30 83 0.23
31 1 0.00
32 2 0.01
34 14 0.04
35 42 0.12
36 2 0.01
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:31374220 original size:36 final size:36
Alignment explanation
Indices: 31374179--31374422 Score: 133
Period size: 35 Copynumber: 7.7 Consensus size: 36
31374169 ATCTAATTAA
* * *
31374179 AAACCCTAACCCTAACCTAATT-TATCTAAAAGCCTT
1 AAACCCTAACCCTAACCTAATTAAAT-TAAAAACCCT
**
31374215 AAACCCTAA-CCTAATTTAATTAAATTAAAAACCCT
1 AAACCCTAACCCTAACCTAATTAAATTAAAAACCCT
* **
31374250 AAACCCTAA-CATAATTTAATTAAATTAAAAACCCT
1 AAACCCTAACCCTAACCTAATTAAATTAAAAACCCT
31374285 -AACCCTAA-CCTAA--T--TT-AATTAAAAACCCT
1 AAACCCTAACCCTAACCTAATTAAATTAAAAACCCT
*
31374314 -AA-CCTAA---T---TTAATTAAATTAAAAACCCT
1 AAACCCTAACCCTAACCTAATTAAATTAAAAACCCT
31374342 -AACCCTAA-CCTAA--T--TT-AATTAAAAACCCT
1 AAACCCTAACCCTAACCTAATTAAATTAAAAACCCT
*
31374371 -AA-CCTAA---TTA---AATTAAATTAAAAACCCT
1 AAACCCTAACCCTAACCTAATTAAATTAAAAACCCT
**
31374399 AAACCCTAA-CCTAATTTAATTAAA
1 AAACCCTAACCCTAACCTAATTAAA
31374423 AACCCTAACC
Statistics
Matches: 179, Mismatches: 9, Indels: 41
0.78 0.04 0.18
Matches are distributed among these distances:
25 1 0.01
26 3 0.02
27 4 0.02
28 38 0.21
29 37 0.21
30 9 0.05
31 1 0.01
32 4 0.02
34 12 0.07
35 59 0.33
36 11 0.06
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (36 bp):
AAACCCTAACCCTAACCTAATTAAATTAAAAACCCT
Found at i:31374311 original size:23 final size:23
Alignment explanation
Indices: 31374285--31374466 Score: 112
Period size: 28 Copynumber: 6.7 Consensus size: 23
31374275 TAAAAACCCT
31374285 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
31374308 AACCCTAACCTAATTTAATTAAATTAAA
1 AACCCTAACCTAA--T--TT-AATTAAA
31374336 AACCCTAACCCTAACCTAATTTAATTAAA
1 AA--C----CCTAACCTAATTTAATTAAA
31374365 AACCCTAACCTAATTAAATTAAATTAAA
1 AACCCTAACCTAA-T---TT-AATTAAA
31374393 AACCCTAAACCCTAACCTAATTTAATTAAA
1 AA-------CCCTAACCTAATTTAATTAAA
31374423 AACCCTAACCTAATTTAATTTAATTAAA
1 AACCCTAACC-----TAATTTAATTAAA
31374451 AACCCTAACCTAATTT
1 AACCCTAACCTAATTT
31374467 GATAATCTTA
Statistics
Matches: 131, Mismatches: 0, Indels: 56
0.70 0.00 0.30
Matches are distributed among these distances:
23 37 0.28
24 1 0.01
25 1 0.01
27 5 0.04
28 41 0.31
29 9 0.07
30 12 0.09
31 2 0.02
32 1 0.01
34 11 0.08
35 11 0.08
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:31374311 original size:57 final size:57
Alignment explanation
Indices: 31374250--31374460 Score: 386
Period size: 57 Copynumber: 3.7 Consensus size: 57
31374240 TAAAAACCCT
*
31374250 AAACCCTAACATAATTTAATTAAATTAAAAACCCTAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCCTAACCTAATTTAATTAA
31374307 AAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCCTAACCTAATTTAATTAA
*
31374364 AAACCCTAACCTAATTAAATTAAATTAAAAACCCTAAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAAATTAAAAACCCT-AACCCTAACCTAATTTAATTAA
*
31374422 AAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACC
1 AAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACC
31374461 TAATTTGATA
Statistics
Matches: 149, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
57 94 0.63
58 55 0.37
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (57 bp):
AAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCCTAACCTAATTTAATTAA
Found at i:31377898 original size:126 final size:125
Alignment explanation
Indices: 31377689--31377970 Score: 399
Period size: 126 Copynumber: 2.2 Consensus size: 125
31377679 CAAGAGGGCA
* * *
31377689 CGATTTGACACTATTTGCTCAGAAACGTAAAAAAATAATTATTTCCTACATGACCAACTGTAGCG
1 CGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCG
* * * * **
31377754 AAATCGCGTCCACGAGGGCGCAATTTCACAATTTCTTCTCAT-ATAGCATCCTGGTATCAG
66 AAATCGCGTCCACAAGGGCACAATTTCACAATTTCTTCTC-TGATAGCATCCTAGCAGAAG
*
31377814 CGATTTTATACTATTTGCTCAGAAAACGTCAAAAAATAATTATTTCTTACATGACCAACTGT-GT
1 CGATTTTATACTATTTGCTCAG-AAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAG-
* *
31377878 CGAAATGGCGTCCACAAGGGCACGATTTCACAATTTCTTCTCTGATAGCATCCTAGCAGAAG
64 CGAAATCGCGTCCACAAGGGCACAATTTCACAATTTCTTCTCTGATAGCATCCTAGCAGAAG
31377940 CGATTTTATACTATTTGAC-CAGAAACGTCAA
1 CGATTTTATACTATTTG-CTCAGAAACGTCAA
31377971 CTCGAAATAA
Statistics
Matches: 141, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
125 31 0.22
126 109 0.77
127 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (125 bp):
CGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACAAGGGCACAATTTCACAATTTCTTCTCTGATAGCATCCTAGCAGAAG
Found at i:31379660 original size:12 final size:11
Alignment explanation
Indices: 31379643--31379677 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
31379633 AATACACATG
31379643 AATTTATATATA
1 AATTTATATA-A
31379655 AATTTATA-AA
1 AATTTATATAA
31379665 AATTTATATAA
1 AATTTATATAA
31379676 AA
1 AA
31379678 AAATACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.41
11 5 0.23
12 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AATTTATATAA
Found at i:31379933 original size:20 final size:20
Alignment explanation
Indices: 31379898--31379939 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31379888 TTAGTTTGAA
* *
31379898 AAAAAAATACATATGTACAT
1 AAAAAAATACACATGTAAAT
*
31379918 AAAAAAATATACATGTAAAT
1 AAAAAAATACACATGTAAAT
31379938 AA
1 AA
31379940 TAATTACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (20 bp):
AAAAAAATACACATGTAAAT
Found at i:31379966 original size:21 final size:22
Alignment explanation
Indices: 31379941--31379981 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31379931 TGTAAATAAT
31379941 AATTACA-TATAAAAATTAAAA
1 AATTACATTATAAAAATTAAAA
*
31379962 AATTACATTATTAAAATTAA
1 AATTACATTATAAAAATTAA
31379982 TTAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
AATTACATTATAAAAATTAAAA
Found at i:31379987 original size:22 final size:21
Alignment explanation
Indices: 31379938--31379987 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
31379928 ACATGTAAAT
31379938 AATAATTACATATAAAAATTA
1 AATAATTACATATAAAAATTA
* *
31379959 AAAAATTACATTATTAAAATTA
1 AATAATTACA-TATAAAAATTA
*
31379981 ATTAATT
1 AATAATT
31379988 TTAAGATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAATTACATATAAAAATTA
Found at i:31381720 original size:44 final size:44
Alignment explanation
Indices: 31381672--31381899 Score: 185
Period size: 44 Copynumber: 5.2 Consensus size: 44
31381662 CATCCTCGAT
* *
31381672 CTACTCCACTACTTCTTAGGGAGATAAGATCTGTAATTTTCAAC
1 CTACTCCACTACTGCTTAGGGAGATAAGAGCTGTAATTTTCAAC
* * * ** * * *
31381716 CTACTCTACTACTGCTCAGGGAGACAAG-GCTGGGGA-CTTCGAT
1 CTACTCCACTACTGCTTAGGGAGATAAGAGCT-GTAATTTTCAAC
* *
31381759 CTGCTCCACTACTGCTTAGGGAGATAAGAACTGTAATTTTCAAC
1 CTACTCCACTACTGCTTAGGGAGATAAGAGCTGTAATTTTCAAC
* * * ** * * *
31381803 CTACTCCACTGCTGCTCAGGGAGACAAG-GCTGGGGACTTT-GAT
1 CTACTCCACTACTGCTTAGGGAGATAAGAGCT-GTAATTTTCAAC
* * * **
31381846 CTGCTTCACTACTGCTTAGGTAGATAAGATTTGTAATTTTCAAC
1 CTACTCCACTACTGCTTAGGGAGATAAGAGCTGTAATTTTCAAC
31381890 CTACTCCACT
1 CTACTCCACT
31381900 GCTGTCCAGG
Statistics
Matches: 133, Mismatches: 45, Indels: 12
0.70 0.24 0.06
Matches are distributed among these distances:
43 62 0.47
44 71 0.53
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
CTACTCCACTACTGCTTAGGGAGATAAGAGCTGTAATTTTCAAC
Found at i:31381766 original size:87 final size:87
Alignment explanation
Indices: 31381667--31381942 Score: 455
Period size: 87 Copynumber: 3.2 Consensus size: 87
31381657 TTTACCATCC
* * * *
31381667 TCGATCTACTCCACTACTTCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCTACTACTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
31381732 CAGGGAGACAAGGCTGGGGACT
66 CAGGGAGACAAGGCTGGGGACT
*
31381754 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGAACTGTAATTTTCAACCTACTCCACTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
31381819 CAGGGAGACAAGGCTGGGGACT
66 CAGGGAGACAAGGCTGGGGACT
* * * *
31381841 TTGATCTGCTTCACTACTGCTTAGGTAGATAAGATTTGTAATTTTCAACCTACTCCACTGCTG-T
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
31381905 CCAGGGAGACAAGGCTGGGGACT
66 -CAGGGAGACAAGGCTGGGGACT
31381928 TCGATCTGCTCCACT
1 TCGATCTGCTCCACT
31381943 GTCAGTGCAG
Statistics
Matches: 176, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
86 1 0.01
87 175 0.99
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (87 bp):
TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCT
CAGGGAGACAAGGCTGGGGACT
Found at i:31381772 original size:43 final size:43
Alignment explanation
Indices: 31381723--31381942 Score: 165
Period size: 43 Copynumber: 5.1 Consensus size: 43
31381713 AACCTACTCT
31381723 ACTACTGCTCAGGGAGACAAGGCTGGGGACTTCGATCTGCTCC
1 ACTACTGCTCAGGGAGACAAGGCTGGGGACTTCGATCTGCTCC
* * * ** * * * *
31381766 ACTACTGCTTAGGGAGATAAGAACT-GTAATTTTCAACCTACTCC
1 ACTACTGCTCAGGGAGACAAG-GCTGGGGA-CTTCGATCTGCTCC
* * *
31381810 ACTGCTGCTCAGGGAGACAAGGCTGGGGACTTTGATCTGCTTC
1 ACTACTGCTCAGGGAGACAAGGCTGGGGACTTCGATCTGCTCC
* * * ** * ** * * * *
31381853 ACTACTGCTTAGGTAGATAAGATTTGTAATTTTCAACCTACTCC
1 ACTACTGCTCAGGGAGACAAGGCTGGGGA-CTTCGATCTGCTCC
*
31381897 ACTGCTG-TCCAGGGAGACAAGGCTGGGGACTTCGATCTGCTCC
1 ACTACTGCT-CAGGGAGACAAGGCTGGGGACTTCGATCTGCTCC
31381940 ACT
1 ACT
31381943 GTCAGTGCAG
Statistics
Matches: 123, Mismatches: 49, Indels: 10
0.68 0.27 0.05
Matches are distributed among these distances:
43 65 0.53
44 58 0.47
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.27
Consensus pattern (43 bp):
ACTACTGCTCAGGGAGACAAGGCTGGGGACTTCGATCTGCTCC
Found at i:31382022 original size:88 final size:88
Alignment explanation
Indices: 31381881--31382465 Score: 706
Period size: 88 Copynumber: 6.6 Consensus size: 88
31381871 AAGATTTGTA
* * *** * * * * * * *
31381881 ATTTTCAACCTACTCCACTGCTGTCCAGGGAGACAAGGCTGGGGACTTCGATCTGCTCCACTGTC
1 ATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTC
* * *
31381946 AGTGCAGGAAGGCAAGATCTACT
66 GGCGCAGGAAGGCAAGATCTGCT
** *
31381969 ATTTTTAACCTATTCCGCTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTC
1 ATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTC
* *
31382034 GGCTCAGGAAGGCAAGATCTGGT
66 GGCGCAGGAAGGCAAGATCTGCT
* * *
31382057 ATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGTAAGGCTGGTGT-TTTCGATCTGCTTCGCTGT
1 ATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTT-GATCTGCTTCGCTGT
* * *
31382121 CGGCGTAGGAAGGCAAAATATGCT
65 CGGCGCAGGAAGGCAAGATCTGCT
* * * *
31382145 A-TTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATTTGTTTCGTTGTT
1 ATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTC
*
31382209 GGCGCAGGAAGGCAAGATCTACT
66 GGCGCAGGAAGGCAAGATCTGCT
* * * ** *
31382232 TTTTTTAACCTGCTCCACTACAACCCAGGGAGGCAAGGTTGGTGTCTTCGATCTATTTCACTGTC
1 ATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTC
*
31382297 GGCGCAGGAAAGCAAGATCTGCT
66 GGCGCAGGAAGGCAAGATCTGCT
* * *
31382320 ATTTTTAACCTGCTCCACTGCAACCTAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTATC
1 ATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTC
* *
31382385 GGTGGAGGAAGGCAAGATCTGCT
66 GGCGCAGGAAGGCAAGATCTGCT
* * ** *
31382408 ATTTTTAAACCTGCTTCGCTGCAACTTAGGGAGGCAAGGTTGGTGTCTTTTATCTGCT
1 ATTTTT-AACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCT
31382466 ATTTTTAACC
Statistics
Matches: 430, Mismatches: 63, Indels: 7
0.86 0.13 0.01
Matches are distributed among these distances:
87 74 0.17
88 310 0.72
89 46 0.11
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (88 bp):
ATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTC
GGCGCAGGAAGGCAAGATCTGCT
Found at i:31382113 original size:43 final size:42
Alignment explanation
Indices: 31381982--31382119 Score: 123
Period size: 44 Copynumber: 3.2 Consensus size: 42
31381972 TTTAACCTAT
*
31381982 TCCGCTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGC
1 TCCGCTGCAACCCAGGGAGGCAAGGCTGGTGT-TTTGATCTGC
* ** * * * * * *
31382025 TTCGCTGTCGGCTCAGGAAGGCAAGATCTGGTATTTTTAACCTGC
1 TCCGCTG-CAACCCAGGGAGGCAAG-GCTGGT-GTTTTGATCTGC
*
31382070 TCCGCTGCAACCCAGGGAGGTAAGGCTGGTGTTTTCGATCTGC
1 TCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTTTT-GATCTGC
*
31382113 TTCGCTG
1 TCCGCTG
31382120 TCGGCGTAGG
Statistics
Matches: 70, Mismatches: 21, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
42 4 0.06
43 22 0.31
44 25 0.36
45 18 0.26
46 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (42 bp):
TCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTTTTGATCTGC
Found at i:31382174 original size:175 final size:176
Alignment explanation
Indices: 31381905--31382465 Score: 730
Period size: 175 Copynumber: 3.2 Consensus size: 176
31381895 CCACTGCTGT
* * * * * * * *
31381905 CCAGGGAGACAAGGCTGGGGACTTCGATCTGCTCCACTGTCAGTGCAGGAAGGCAAGATCTACTA
1 CCAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCACTGTCGGCGCAGGAAGGCAAGATCTGCTA
** *
31381970 TTTTTAACCTATTCCGCTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCG
66 TTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCG
*
31382035 GCTCAGGAAGGCAAGATCTGGTATTTTTAACCTGCTCCGCTGCAAC
131 GCTCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* * * * * * *
31382081 CCAGGGAGGTAAGGCTGGTGTTTTCGATCTGCTTCGCTGTCGGCGTAGGAAGGCAAAATATGCTA
1 CCAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCACTGTCGGCGCAGGAAGGCAAGATCTGCTA
* * * *
31382146 -TTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATTTGTTTCGTTGTTG
66 TTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCG
* * * * *
31382210 GCGCAGGAAGGCAAGATCTACTTTTTTTAACCTGCTCCACTACAAC
131 GCTCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
** *
31382256 CCAGGGAGGCAAGGTTGGTGTCTTCGATCTATTTCACTGTCGGCGCAGGAAAGCAAGATCTGCTA
1 CCAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCACTGTCGGCGCAGGAAGGCAAGATCTGCTA
* * *
31382321 TTTTTAACCTGCTCCACTGCAACCTAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTATCG
66 TTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCG
* *
31382386 G-TGGAGGAAGGCAAGATCTGCTATTTTTAAACCTGCTTCGCTGCAAC
131 GCT-CAGGAAGGCAAGATCTGCTATTTTT-AACCTGCTCCGCTGCAAC
** **
31382433 TTAGGGAGGCAAGGTTGGTGTCTTTTATCTGCT
1 CCAGGGAGGCAAGGTTGGTGTCTTCGATCTGCT
31382466 ATTTTTAACC
Statistics
Matches: 326, Mismatches: 56, Indels: 5
0.84 0.14 0.01
Matches are distributed among these distances:
175 152 0.47
176 132 0.40
177 42 0.13
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (176 bp):
CCAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCACTGTCGGCGCAGGAAGGCAAGATCTGCTA
TTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCG
GCTCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
Found at i:31382298 original size:263 final size:265
Alignment explanation
Indices: 31381949--31382457 Score: 770
Period size: 263 Copynumber: 1.9 Consensus size: 265
31381939 CACTGTCAGT
* * *
31381949 GCAGGAAGGCAAGATCTACTATTTTTAACCTATTCCGCTGCAACCCAGGGAGGCAAGGTTGGTGT
1 GCAGGAAGGCAAGATCTACTATTTTTAACCTACTCCACTACAACCCAGGGAGGCAAGGTTGGTGT
* * * * * * *
31382014 CTTTGATCTGCTTCGCTGTCGGCTCAGGAAGGCAAGATCTGGTATTTTTAACCTGCTCCGCTGCA
66 CTTCGATCTACTTCACTGTCGGCGCAGGAAAGCAAGATCTGCTATTTTTAACCTGCTCCACTGCA
* * * *
31382079 ACCCAGGGAGGTAAGGCTGGTGTTTTCGATCTGCTTCGCTGTCGGCGTAGGAAGGCAAAATATGC
131 ACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTATCGGCGGAGGAAGGCAAAATATGC
31382144 TA-TTTT-AACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATTTGTTTCGTTG
196 TATTTTTAAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATTTGTTTCGTTG
31382207 TTGGC
261 TTGGC
* *
31382212 GCAGGAAGGCAAGATCTACTTTTTTTAACCTGCTCCACTACAACCCAGGGAGGCAAGGTTGGTGT
1 GCAGGAAGGCAAGATCTACTATTTTTAACCTACTCCACTACAACCCAGGGAGGCAAGGTTGGTGT
*
31382277 CTTCGATCTATTTCACTGTCGGCGCAGGAAAGCAAGATCTGCTATTTTTAACCTGCTCCACTGCA
66 CTTCGATCTACTTCACTGTCGGCGCAGGAAAGCAAGATCTGCTATTTTTAACCTGCTCCACTGCA
* * * * *
31382342 ACCTAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTATCGGTGGAGGAAGGCAAGATCTGC
131 ACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTATCGGCGGAGGAAGGCAAAATATGC
* * **
31382407 TATTTTTAAACCTGCTTCGCTGCAACTTAGGGAGGCAAGGTTGGTGTCTTT
196 TATTTTTAAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTT
31382458 TATCTGCTAT
Statistics
Matches: 218, Mismatches: 26, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
263 175 0.80
264 4 0.02
265 39 0.18
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.29
Consensus pattern (265 bp):
GCAGGAAGGCAAGATCTACTATTTTTAACCTACTCCACTACAACCCAGGGAGGCAAGGTTGGTGT
CTTCGATCTACTTCACTGTCGGCGCAGGAAAGCAAGATCTGCTATTTTTAACCTGCTCCACTGCA
ACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTATCGGCGGAGGAAGGCAAAATATGC
TATTTTTAAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATTTGTTTCGTTG
TTGGC
Found at i:31382499 original size:57 final size:58
Alignment explanation
Indices: 31382400--31382522 Score: 171
Period size: 57 Copynumber: 2.1 Consensus size: 58
31382390 AGGAAGGCAA
* * *
31382400 GATCTGCTATTTTTAAACCTGCTTCGCTGCAACTTAGGGAGGCAAGGTTGGTGTCTTT
1 GATCTGCTATTTTTAAACCTGCTTCGCTACAACCTAGGGAGGCAAGGTTGGTGTCTTC
*
31382458 TATCTGCTATTTTT-AACCTG-TTC-CATTACAACCTAGGGAGGCAAGGTTGGTGTCTTC
1 GATCTGCTATTTTTAAACCTGCTTCGC--TACAACCTAGGGAGGCAAGGTTGGTGTCTTC
31382515 GATCTGCT
1 GATCTGCT
31382523 TCGTTGTCGG
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
55 1 0.02
56 3 0.05
57 41 0.71
58 13 0.22
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (58 bp):
GATCTGCTATTTTTAAACCTGCTTCGCTACAACCTAGGGAGGCAAGGTTGGTGTCTTC
Found at i:31388658 original size:19 final size:19
Alignment explanation
Indices: 31388634--31388678 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31388624 AACGAGCAAG
* **
31388634 ATAAAAAATTAATGAAAAC
1 ATAAAAAAATAAAAAAAAC
31388653 ATAAAAAAATAAAAAAAAC
1 ATAAAAAAATAAAAAAAAC
31388672 A-AAAAAA
1 ATAAAAAA
31388679 CAAAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (19 bp):
ATAAAAAAATAAAAAAAAC
Found at i:31388664 original size:8 final size:8
Alignment explanation
Indices: 31388634--31388690 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
31388624 AACGAGCAAG
31388634 ATAAAAAA
1 ATAAAAAA
*
31388642 TTAATGAAAA
1 ATAA--AAAA
31388652 CATAAAAAA
1 -ATAAAAAA
31388661 ATAAAAAAA
1 AT-AAAAAA
*
31388670 ACAAAAAA
1 ATAAAAAA
*
31388678 ACAAAAAA
1 ATAAAAAA
31388686 ATAAA
1 ATAAA
31388691 GGTACATGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 23 0.56
9 11 0.27
10 4 0.10
11 3 0.07
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Found at i:31388750 original size:12 final size:11
Alignment explanation
Indices: 31388733--31388766 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
31388723 AATACACATG
31388733 AATTTATATATA
1 AATTTATATA-A
31388745 AATTTATA-AA
1 AATTTATATAA
31388755 AATTTATATAA
1 AATTTATATAA
31388766 A
1 A
31388767 CAAAATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.43
11 4 0.19
12 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTATATAA
Found at i:31388834 original size:18 final size:18
Alignment explanation
Indices: 31388793--31388831 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
31388783 AAAAATAAAG
31388793 AAAA-ATATAGAAATATA
1 AAAATATATAGAAATATA
31388810 AAAATATATAGAAATTATA
1 AAAATATATAGAAA-TATA
31388829 AAA
1 AAA
31388832 TATGTGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAATATATAGAAATATA
Found at i:31389072 original size:17 final size:17
Alignment explanation
Indices: 31389032--31389078 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
31389022 AATACATATG
31389032 TACATA-AAAAAAT-A-
1 TACATATAAAAAATAAT
* *
31389046 TACATGTAAATAATAAT
1 TACATATAAAAAATAAT
31389063 TACATATAAAAAATAA
1 TACATATAAAAAATAA
31389079 AAAATTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 1 0.04
17 14 0.54
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (17 bp):
TACATATAAAAAATAAT
Found at i:31399856 original size:27 final size:26
Alignment explanation
Indices: 31399826--31399891 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
31399816 TATTACAAAA
*
31399826 TATGCCACAAAGACAATTCATATAGAG
1 TATGCCACAAAG-CAATTCATACAGAG
* *
31399853 TATGCCAAAAATGCGATTCATACAGAG
1 TATGCCACAAA-GCAATTCATACAGAG
31399880 TATGCCACAAAG
1 TATGCCACAAAG
31399892 GTTGACAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.03
27 32 0.94
28 1 0.03
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (26 bp):
TATGCCACAAAGCAATTCATACAGAG
Found at i:31406416 original size:67 final size:66
Alignment explanation
Indices: 31406305--31406429 Score: 189
Period size: 67 Copynumber: 1.9 Consensus size: 66
31406295 AAATTTCATT
* * *
31406305 AAATAATTGAAAAGGACCATGAATGATGCGGTTGGAAGGATCCATAAAATAATTTCTCGTTTCGA
1 AAATAATTGAAAAGGACCATAAATGATACGGTGGGAAGGATCCATAAAATAATTTCTCGTTTCGA
31406370 G
66 G
*
31406371 AAATAATTGAAAAGAGACCATAAATGATATGGTGGGAAAGG-TCCATAAAATAATTTCTC
1 AAATAATTGAAAAG-GACCATAAATGATACGGTGGG-AAGGATCCATAAAATAATTTCTC
31406430 TTTAAACAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
66 14 0.26
67 35 0.66
68 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (66 bp):
AAATAATTGAAAAGGACCATAAATGATACGGTGGGAAGGATCCATAAAATAATTTCTCGTTTCGA
G
Found at i:31406462 original size:28 final size:28
Alignment explanation
Indices: 31406430--31406491 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
31406420 ATAATTTCTC
31406430 TTTAAACAATAAAAAATTTAAAAAAT-AT
1 TTTAAACAA-AAAAAATTTAAAAAATAAT
** * *
31406458 TTTAATTAAAAAATATTTAAAGAATAAT
1 TTTAAACAAAAAAAATTTAAAAAATAAT
31406486 TTTAAA
1 TTTAAA
31406492 ATTATTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
TTTAAACAAAAAAAATTTAAAAAATAAT
Found at i:31414784 original size:15 final size:14
Alignment explanation
Indices: 31414736--31414793 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
31414726 AATAAAATGC
31414736 AATAATAAT-AATGAT
1 AATAATAATAAAT--T
*
31414751 AATAATAATAATAAT
1 AATAATAATAA-ATT
31414766 AATAATAATAAATT
1 AATAATAATAAATT
31414780 CAATAATAAATAAA
1 -AATAAT-AATAAA
31414794 ATGACAGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 2 0.05
15 27 0.73
16 7 0.19
17 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (14 bp):
AATAATAATAAATT
Found at i:31414788 original size:3 final size:3
Alignment explanation
Indices: 31414736--31414776 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
31414726 AATAAAATGC
*
31414736 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31414777 ATTCAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31416421 original size:99 final size:97
Alignment explanation
Indices: 31416233--31417010 Score: 867
Period size: 99 Copynumber: 7.9 Consensus size: 97
31416223 AAAATGTCAT
* * * * * * * *
31416233 GGAAGTGAGATTTGCCATTGTAGCTTTAATTTGTTCCACTGTACCTGCTTAGGAA-TAAGATTTA
1 GGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATC-GCTT-GGAAGTAAGA-TTG
*
31416297 CCGTTGTGGCCTCAATCTTTT-AATTGCAATGTCAG
63 CCGTTGTGGCCTCGATCTTTTAAATTGCAATGTC-G
* * * *
31416332 GGAAGTGAGATTCGCCATTGTAGCTTCAATCTGTTACGCTGCATTGCTTGGAAGTAGGATCTGCC
1 GGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGAAGTAAGAT-TGCC
* *
31416397 GTCGTGGCCTCAATCTTTTAAATTGCAATGTCG
65 GTTGTGGCCTCGATCTTTTAAATTGCAATGTCG
* * * * *
31416430 AGGGAGTGAGATCCGCCATTGTAGCTTCAATCTGTTCCTCTAG-ATCGCTTGGAAGTAAGATCCG
1 -GGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCT-GCATCGCTTGGAAGTAAGAT-TG
*
31416494 CCGTTGTGGCCTCAATCTTTTAAATTGCAATGTCGG
63 CCGTTGTGGCCTCGATCTTTTAAATTGCAATGTC-G
* ** * * *
31416530 GGAAGTGAGATTCACCGTTGTAGCTTCAATCTGTTTTGATGCATCGCTAAGTAAGTAAGATCTGC
1 GGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCT-TGGAAGTAAGAT-TGC
**
31416595 CGTCATGGCCTCGATCTTTTAAATTGCAATG--G
64 CGTTGTGGCCTCGATCTTTTAAATTGCAATGTCG
* * * *
31416627 GGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATTGCCTGAAAGTAAGATTTGCC
1 GGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGAAGTAAGA-TTGCC
*
31416692 GTTGTGGCTTCGATCTTTTAAATTGCAATG--G
65 GTTGTGGCCTCGATCTTTTAAATTGCAATGTCG
* * *
31416723 GGAAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCC
1 GGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGAAGTAAGATT-GCC
*
31416788 GTTGTGGCCTCGATCTTTTAAATTGTAATG--G
65 GTTGTGGCCTCGATCTTTTAAATTGCAATGTCG
* * * **
31416819 GGAAGTGAGACTCGCTGTTGTAGCTTCAATCTGTTCCACTGCAAT-GC-CAGAAGGTAAGATTCG
1 GGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCTTGGAA-GTAAGATT-G
* *
31416882 CCGTTGTGGCTTTGATCTTTTAAATTGCAATGTCGG
63 CCGTTGTGGCCTCGATCTTTTAAATTGCAATGTC-G
* *
31416918 GGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCC
1 GGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGAAGTAAGATT-GCC
* * *
31416983 ATCGTGGCTTCGATCTTTTAAATTGCAA
65 GTTGTGGCCTCGATCTTTTAAATTGCAA
31417011 ACTATGGTTT
Statistics
Matches: 597, Mismatches: 65, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
95 5 0.01
96 209 0.35
97 50 0.08
98 33 0.06
99 254 0.43
100 46 0.08
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (97 bp):
GGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGAAGTAAGATTGCCG
TTGTGGCCTCGATCTTTTAAATTGCAATGTCG
Found at i:31429643 original size:15 final size:14
Alignment explanation
Indices: 31429595--31429652 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
31429585 AATAAAATGC
31429595 AATAATAAT-AATGAT
1 AATAATAATAAAT--T
*
31429610 AATAATAATAATAAT
1 AATAATAATAA-ATT
31429625 AATAATAATAAATT
1 AATAATAATAAATT
31429639 CAATAATAAATAAA
1 -AATAAT-AATAAA
31429653 ATGACAGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 2 0.05
15 27 0.73
16 7 0.19
17 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (14 bp):
AATAATAATAAATT
Found at i:31429647 original size:3 final size:3
Alignment explanation
Indices: 31429595--31429635 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
31429585 AATAAAATGC
*
31429595 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31429636 ATTCAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31430901 original size:30 final size:30
Alignment explanation
Indices: 31430856--31430914 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
31430846 TGTTCACTTG
*
31430856 AGTCGCTGTTACTAAATTATTTATATCTTA
1 AGTCACTGTTACTAAATTATTTATATCTTA
*
31430886 AGTCACTGTTCCTAAATTATTTATATCTT
1 AGTCACTGTTACTAAATTATTTATATCTT
31430915 GAGCTACAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (30 bp):
AGTCACTGTTACTAAATTATTTATATCTTA
Found at i:31443105 original size:20 final size:20
Alignment explanation
Indices: 31443082--31443121 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31443072 ATGTGATATA
31443082 CACTATATGAATATGATTTG
1 CACTATATGAATATGATTTG
* *
31443102 CACTATCTGAATATGCTTTG
1 CACTATATGAATATGATTTG
31443122 AATCTATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
CACTATATGAATATGATTTG
Found at i:31448210 original size:24 final size:22
Alignment explanation
Indices: 31448163--31448234 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
31448153 ATATTTATTT
31448163 TTTATTTTTAATCAAATATATA
1 TTTATTTTTAATCAAATATATA
31448185 TTTATTTTTAATCAAACATATATA
1 TTTATTTTTAATC-AA-ATATATA
* * *
31448209 TTT-TATATATATTAAATATATA
1 TTTATTTTTA-ATCAAATATATA
31448231 TTTA
1 TTTA
31448235 ATATGGGCCG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 23 0.53
23 8 0.19
24 12 0.28
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTATTTTTAATCAAATATATA
Found at i:31448218 original size:11 final size:11
Alignment explanation
Indices: 31448202--31448238 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
31448192 TTAATCAAAC
*
31448202 ATATATATTTT
1 ATATATATTTA
*
31448213 ATATATATTAA
1 ATATATATTTA
31448224 ATATATATTTA
1 ATATATATTTA
31448235 ATAT
1 ATAT
31448239 GGGCCGGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATATATTTA
Found at i:31456350 original size:17 final size:17
Alignment explanation
Indices: 31456325--31456357 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31456315 TCCCTAAATA
31456325 AATAATAAATAATATAT
1 AATAATAAATAATATAT
*
31456342 AATAGTAAATAATATA
1 AATAATAAATAATATA
31456358 ATTAAAAAAT
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:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AATAATAAATAATATAT
Found at i:31467315 original size:131 final size:131
Alignment explanation
Indices: 31467076--31467395 Score: 523
Period size: 131 Copynumber: 2.4 Consensus size: 131
31467066 ATGAATATTA
* *
31467076 CAGATCTTATCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCCAAGA
1 CAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAAGA
* * *
31467141 GTAGGGAATCAGATTTAAGCCACAAGTCCTATGTCCCTAACCAGTAGTGGAATAGGTTGGAAATT
66 GTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTAACCAGCAGTGGAATAGGCTGGAAATT
31467206 G
131 G
* * * *
31467207 CAGATCTTGTCTCCCTAAGCAATAGTGGAGTAGATCGAAGATGGCGAATCTTATCTTCCCCAGGA
1 CAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAAGA
* *
31467272 GTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCTCTGACCAGCAGTGGAATAGGCTGGAAATT
66 GTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTAACCAGCAGTGGAATAGGCTGGAAATT
31467337 G
131 G
* *
31467338 CAGATCTTGTCTCCCTAAGTAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTC
1 CAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTC
31467396 AAGTGTAAGG
Statistics
Matches: 173, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 173 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (131 bp):
CAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAAGA
GTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTAACCAGCAGTGGAATAGGCTGGAAATT
G
Found at i:31467640 original size:216 final size:217
Alignment explanation
Indices: 31467374--31467801 Score: 687
Period size: 216 Copynumber: 2.0 Consensus size: 217
31467364 GGAGCAGATC
*
31467374 GAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGATAATCTTATCTCCCTG
1 GAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGATAATCCTATCTCCCTG
* * *
31467439 AAGTTGTAGTTGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTACAGTAGAGTGGATCG
66 AAGTTGTAGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTACAGCAGAATGGATCG
* * ** *
31467504 CATCAGGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGAAAACAAGTCTTATGCCCCTGA
131 CATCAGGTCTTATCTCCCTAAAGTTGCAGCAGAGCAGACTGAGAAAACAAGTCTTATCCCCCTGA
31467569 AGTCACAGTGGGGCAGACTGAA
196 AGTCACAGTGGGGCAGACTGAA
*
31467591 GAAG-CGGCGGATCTTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGATAATCCTATCTCCCTG
1 GAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGATAATCCTATCTCCCTG
* * * * *
31467655 AATTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGCAGAATGGATTG
66 AAGTTGTAGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTACAGCAGAATGGATCG
* *
31467720 CATCAGGTCTTATCTCCCTAAAGTTGCAGCAGAGCAGACTGAGTAAGCAAGTCTTATCCCCCTGA
131 CATCAGGTCTTATCTCCCTAAAGTTGCAGCAGAGCAGACTGAGAAAACAAGTCTTATCCCCCTGA
*
31467785 AGTTACAGTGGGGCAGA
196 AGTCACAGTGGGGCAGA
31467802 TCAAAGATGA
Statistics
Matches: 193, Mismatches: 18, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
216 189 0.98
217 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (217 bp):
GAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGATAATCCTATCTCCCTG
AAGTTGTAGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTACAGCAGAATGGATCG
CATCAGGTCTTATCTCCCTAAAGTTGCAGCAGAGCAGACTGAGAAAACAAGTCTTATCCCCCTGA
AGTCACAGTGGGGCAGACTGAA
Found at i:31467788 original size:44 final size:45
Alignment explanation
Indices: 31467726--31467837 Score: 111
Period size: 44 Copynumber: 2.5 Consensus size: 45
31467716 ATTGCATCAG
* * * **
31467726 GTCTTATCTCCCTAAAGTTGCAGCAGAGCAGA-CTGAGTAAG-CAA
1 GTCTTATCCCCCTGAAGTTACAGCAGAGCAGATCAAAG-AAGACAA
** * *
31467770 GTCTTATCCCCCTGAAGTTACAGTGGGGCAGATCAAAGATGACAA
1 GTCTTATCCCCCTGAAGTTACAGCAGAGCAGATCAAAGAAGACAA
*
31467815 GTCTTATCCCCCTGAAGTCACAG
1 GTCTTATCCCCCTGAAGTTACAG
31467838 TGGGGCAGAC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
44 28 0.50
45 28 0.50
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.23
Consensus pattern (45 bp):
GTCTTATCCCCCTGAAGTTACAGCAGAGCAGATCAAAGAAGACAA
Found at i:31468452 original size:18 final size:16
Alignment explanation
Indices: 31468429--31468485 Score: 71
Period size: 15 Copynumber: 3.5 Consensus size: 16
31468419 TGCCCGGCCC
31468429 AAATTAAATAATAAACAA
1 AAATTAAA-AATAAA-AA
*
31468447 AAATTAAAAATTAAAA
1 AAATTAAAAATAAAAA
*
31468463 AAATT-AAAATTAAAA
1 AAATTAAAAATAAAAA
31468478 AAATTAAA
1 AAATTAAA
31468486 GGCCCAAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
15 15 0.41
16 9 0.24
17 5 0.14
18 8 0.22
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATTAAAAATAAAAA
Found at i:31468471 original size:15 final size:15
Alignment explanation
Indices: 31468445--31468485 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
31468435 AATAATAAAC
31468445 AAAAATTAAAAATTAA
1 AAAAATT-AAAATTAA
31468461 AAAAATTAAAATTAA
1 AAAAATTAAAATTAA
31468476 AAAAATTAAA
1 AAAAATTAAA
31468486 GGCCCAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATTAAAATTAA
Found at i:31490297 original size:195 final size:197
Alignment explanation
Indices: 31489983--31490365 Score: 495
Period size: 195 Copynumber: 2.0 Consensus size: 197
31489973 TCTCTGAAAT
* * * * *
31489983 AAGGAGATTGGATCAAGATTGCATTGAAAACCTATCTGTAAGATCTTCACATTATCTTGGTATTT
1 AAGGAGATTAGACCAAGATTGCATTCAAAACCTATCTCTAAGATATTCACATTATCTTGGTATTT
* * * * *
31490048 ATTATTATATTGTATATATTATTTTAGCTGCAATTTCATATGTGATAGGATTGTAATTGATCTAG
66 ATTATTATATTATATATATTATTTTAGATACAATTTCATATGGGATAGGATTGTAATTGATCTAA
*** * *
31490113 TATGTTAGCAAGTCTTGATCTCTTAGATATTTAGAGAGACTTGTATAGGTTTTGTATAGAAGGTT
131 TATGTTAGCAAGTCGCAATCTCTTAGATATTTAGAGAGACTTGCATAGATTTTGTATAGAAGGTT
31490178 AC
196 AC
* * * * *
31490180 AAGGAGATTAGACCAGGATTGCATTCAAGACTTA-CTCTAAGATATTCACTTTATCTTGGTCTTT
1 AAGGAGATTAGACCAAGATTGCATTCAAAACCTATCTCTAAGATATTCACATTATCTTGGTATTT
* **
31490244 A-TATTATATTATATAT-TCTATTTTAGATACAATTTTATA-GAGGATTTGATTGTAATTGATCT
66 ATTATTATATTATATATAT-TATTTTAGATACAATTTCATATG-GGATAGGATTGTAATTGATCT
* *
31490306 AATATGTTAGCAAGTCGCAATCTCTTATATATTTGGAGAGACTTGCATAGATTTTGTATA
129 AATATGTTAGCAAGTCGCAATCTCTTAGATATTTAGAGAGACTTGCATAGATTTTGTATA
31490366 AGCACTATAT
Statistics
Matches: 159, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
194 2 0.01
195 102 0.64
196 27 0.17
197 28 0.18
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (197 bp):
AAGGAGATTAGACCAAGATTGCATTCAAAACCTATCTCTAAGATATTCACATTATCTTGGTATTT
ATTATTATATTATATATATTATTTTAGATACAATTTCATATGGGATAGGATTGTAATTGATCTAA
TATGTTAGCAAGTCGCAATCTCTTAGATATTTAGAGAGACTTGCATAGATTTTGTATAGAAGGTT
AC
Found at i:31494140 original size:17 final size:17
Alignment explanation
Indices: 31494114--31494146 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31494104 TAATAAGATT
*
31494114 TAATATTAAATTTAATC
1 TAATAGTAAATTTAATC
31494131 TAATAGTAAATTTAAT
1 TAATAGTAAATTTAAT
31494147 TTTAAAGTGA
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:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (17 bp):
TAATAGTAAATTTAATC
Found at i:31494436 original size:110 final size:110
Alignment explanation
Indices: 31494235--31494460 Score: 407
Period size: 110 Copynumber: 2.0 Consensus size: 110
31494225 CACACACTTG
*
31494235 AATTCAAGAAAAAGTTGTAGAGAGAAAATTCACTGAAGAGATTATTTCAGAAAATTTTTAGAGAT
1 AATT-AAGAAAAAGTTGTAGAGAGAAAATTCACTGAAGAGATTATTTCAGAAAATTTTTAAAGAT
31494300 ATTTTTCTGATTTACAACTTGACCCAAAAGTTTAGAGAAATTGCGA
65 ATTTTTCTGATTTACAACTTGACCCAAAAGTTTAGAGAAATTGCGA
* *
31494346 AATTAAGAGAAAGTTGTAGAGAGAAAATTCACTGAAGAGATTATTTCAGAAAATTTTTAAATATA
1 AATTAAGAAAAAGTTGTAGAGAGAAAATTCACTGAAGAGATTATTTCAGAAAATTTTTAAAGATA
*
31494411 TTTTTTTGATTTACAACTTGACCCAAAAGTTTAGAGAAATTGCGA
66 TTTTTCTGATTTACAACTTGACCCAAAAGTTTAGAGAAATTGCGA
31494456 AATTA
1 AATTA
31494461 CTTCACTTGT
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
110 107 0.96
111 4 0.04
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (110 bp):
AATTAAGAAAAAGTTGTAGAGAGAAAATTCACTGAAGAGATTATTTCAGAAAATTTTTAAAGATA
TTTTTCTGATTTACAACTTGACCCAAAAGTTTAGAGAAATTGCGA
Found at i:31496409 original size:820 final size:827
Alignment explanation
Indices: 31495267--31496939 Score: 2946
Period size: 820 Copynumber: 2.0 Consensus size: 827
31495257 GCTTCATAGC
31495267 TGATCGATTTTGCAATTAAGGTAACATTCTAACTTTTCTTGATCAAATGGAGTGTGTTATCATTT
1 TGATCGATTTTGCAATTAAGGTAACATTCTAACTTTTCTTGATCAAATGGAGTGTGTTATCATTT
*
31495332 CAAATTGCTTTTTAATTGATTAAATCAAGATTTCAATAGATCGTTAGATTTTAAGTTGATTTTAA
66 CAAATTGCTTTTTAATTGATTAAATCAAGATTTCAATAGATCGTTAGATTTTAAGCTGATTTTAA
31495397 GCTTGAAAATAGCGAATCTCGTATTATTAAGTTAAAGTATTGTTTCAAAGCTCTTTTAAACTTAT
131 GCTTGAAAATAGCGAATCTCGTATTATTAAGTTAAAGTATTGTTTCAAAGCTCTTTTAAACTTAT
31495462 TTTGATCCTATTAAAAGGTTTTTAACCTTAATTTAACAAGTCTTTAAGTAATTTTGAAGAACTTG
196 TTTGATCCTATTAAAAGGTTTTTAACCTTAATTTAACAAGTCTTTAAGTAATTTTGAAGAACTTG
*
31495527 AATGTTTTCTTCTCTTTAAAGTTTATTTGGCCTGATTTTTCCAGAAAAATGATATTCATGTAATT
261 AATGTTTTCTTCTCTTTAAAGTTTATTTGGCCTGATCTTTCCAGAAAAATGATATTCATGTAATT
*
31495592 GGACAAAAATGAAGGTTTAAATATGTAACTAAATGATGTTTAAGAAGATTAGGATCGAAATTAAG
326 GGACAAAAATGAAGGTTTAAATATGTAACTAAATGATGTTTAAGAAGATTAGGATCAAAATTAAG
31495657 GTTTAGAAACAAAATTTGAGTGGTAAAATCATACTTTCGGCAAAACTAGCTAAGTTTTTAGTATA
391 GTTTAGAAACAAAATTTGAGTGGTAAAATCATACTTTCGGCAAAACTAGCTAAGTTTTTAGTATA
31495722 GAGATATAGAGGCTTTGATCTATAATTTTAGAATAAATTAATCTTGTTTGTTGTGGTTTGTAATG
456 GAGATATAGAGGCTTTGATCTATAATTTTAGAATAAATTAATCTTGTTTGTTGTGGTTTGTAATG
31495787 CCTTTGTATTTTATTTGATGTGTATGTAAAGTGCCAATTCATTTGGGAGCATCCACAAGCAAGTA
521 CCTTTGTATTTTATTTGATGTGTATGTAAAGTGCCAATTCATTTGGGAGCATCCACAAGCAAGTA
*
31495852 CAAAGGCAAGTAAAAGCTTACTTGAGCTTTGTCATTGAAGTAAGTTACTAAGGTGAG-TG-G-T-
586 CAAAGGCAAGTAAAAGCTTACTTGAGCTTTGTCATTGAAGCAAGTTACTAAGGTGAGCTGTGATG
*
31495913 C-T-GTG-GGGGGCTTAGATGATCAATTCATCTAATCTAAGTCCAGGAGTAAGTTTTCTTACTTG
651 CATAGTGAGGGGGCTTAGATGATCAATTCATCTAATCTAAGTCCAGGAGTAAGTGTTCTTACTTG
*
31495975 AGCTTTGTTATTTTGCAAATAAGCTTACATGTGTTGTGATATGTTTAAGTTTGTAATGTGAATAT
716 AGCTTTGTTATTTTGCAAATAAGCTTACATGTGTTGTGATATGTTTAAGTTTATAATGTGAATAT
*
31496040 ATGTGTTGAATATATATCTGAATATGTTTTGTGAACAGTTGGTTTTA
781 ATGTGTTGAATATATATCTGAATATGCTTTGTGAACAGTTGGTTTTA
*
31496087 TGATCGATTTTGCAATTAAGGTAACATTCTAACTTTTCTTGATCAAATGGAGTGTTTTATCATTT
1 TGATCGATTTTGCAATTAAGGTAACATTCTAACTTTTCTTGATCAAATGGAGTGTGTTATCATTT
31496152 CAAATTGCTTTTTAATTGATTAAATCAAGATTTCAATAGATCGTTAGATTTTAAGCTGATTTTAA
66 CAAATTGCTTTTTAATTGATTAAATCAAGATTTCAATAGATCGTTAGATTTTAAGCTGATTTTAA
*
31496217 GCTTGAAAATGGCGAATCTCGTATTATTAAGTTAAAGTATTGTTTCAAAGCTCTTTTAAACTTAT
131 GCTTGAAAATAGCGAATCTCGTATTATTAAGTTAAAGTATTGTTTCAAAGCTCTTTTAAACTTAT
*
31496282 TTTGATCCTATTAAAAGGTTTTTAACCTTAATTTAACAAGTCTTTAAGTAATTTTGAAGAATTTG
196 TTTGATCCTATTAAAAGGTTTTTAACCTTAATTTAACAAGTCTTTAAGTAATTTTGAAGAACTTG
31496347 AATGTTTTCTTCTCTTTAAAGTTTATTTGGCCTGATCTTTCCAGAAAAATGATATTCATGTAATT
261 AATGTTTTCTTCTCTTTAAAGTTTATTTGGCCTGATCTTTCCAGAAAAATGATATTCATGTAATT
*
31496412 GGACAAAAATGAAGGTTTAAATATGTAATTAAATGATGTTTAAGAAGATTAGGATCAAAATTAAG
326 GGACAAAAATGAAGGTTTAAATATGTAACTAAATGATGTTTAAGAAGATTAGGATCAAAATTAAG
*
31496477 GTTTAGAAACAAAATTTGAGTGGTAAAATCATACTTTCGGCAAAATTAGCTAAGTTTTTAGTATA
391 GTTTAGAAACAAAATTTGAGTGGTAAAATCATACTTTCGGCAAAACTAGCTAAGTTTTTAGTATA
*
31496542 GAGATATAGAGGCTTTGATCTATAATTTTAGAATGAATTAATCTTGTTTGTTGTGGTTTGTAATG
456 GAGATATAGAGGCTTTGATCTATAATTTTAGAATAAATTAATCTTGTTTGTTGTGGTTTGTAATG
31496607 CCTTTGTATTTTATTTGATGTGTATGTAAAGTGCCAATTCATTTGGGAGCATCCACAAGCAAGTA
521 CCTTTGTATTTTATTTGATGTGTATGTAAAGTGCCAATTCATTTGGGAGCATCCACAAGCAAGTA
31496672 CAAAGGCAAGTAAAAGCTTACTTGAGCTTTGTCATTGAAGCAAGTTACTAAGGTGAGTCATCTGT
586 CAAAGGCAAGTAAAAGCTTACTTGAGCTTTGTCATTGAAGCAAGTTACTAAGGTGAG----CTGT
*
31496737 GCTATAATTAATGCATAAAACAGTGAATTAAAGGGGGCTTAGGTGATCAATTCATCTAATCTAAG
647 G---------ATGCAT-----AGTG------AGGGGGCTTAGATGATCAATTCATCTAATCTAAG
*
31496802 TCTAGGAGTAAGTGTTCTTACTTGAGCTTTGTTATTTTGCAAATAAGCTTACATGTGTTGTGATA
692 TCCAGGAGTAAGTGTTCTTACTTGAGCTTTGTTATTTTGCAAATAAGCTTACATGTGTTGTGATA
31496867 TGTTTAAGTTTATAATGTGAATATATGTGTTGAATATATATCTGAATATGCTTTGTGAACAGTTG
757 TGTTTAAGTTTATAATGTGAATATATGTGTTGAATATATATCTGAATATGCTTTGTGAACAGTTG
31496932 GTTTTA
822 GTTTTA
31496938 TG
1 TG
31496940 CACACATATC
Statistics
Matches: 807, Mismatches: 15, Indels: 31
0.95 0.02 0.04
Matches are distributed among these distances:
820 632 0.78
825 2 0.00
826 1 0.00
836 1 0.00
837 1 0.00
838 1 0.00
844 3 0.00
851 166 0.21
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (827 bp):
TGATCGATTTTGCAATTAAGGTAACATTCTAACTTTTCTTGATCAAATGGAGTGTGTTATCATTT
CAAATTGCTTTTTAATTGATTAAATCAAGATTTCAATAGATCGTTAGATTTTAAGCTGATTTTAA
GCTTGAAAATAGCGAATCTCGTATTATTAAGTTAAAGTATTGTTTCAAAGCTCTTTTAAACTTAT
TTTGATCCTATTAAAAGGTTTTTAACCTTAATTTAACAAGTCTTTAAGTAATTTTGAAGAACTTG
AATGTTTTCTTCTCTTTAAAGTTTATTTGGCCTGATCTTTCCAGAAAAATGATATTCATGTAATT
GGACAAAAATGAAGGTTTAAATATGTAACTAAATGATGTTTAAGAAGATTAGGATCAAAATTAAG
GTTTAGAAACAAAATTTGAGTGGTAAAATCATACTTTCGGCAAAACTAGCTAAGTTTTTAGTATA
GAGATATAGAGGCTTTGATCTATAATTTTAGAATAAATTAATCTTGTTTGTTGTGGTTTGTAATG
CCTTTGTATTTTATTTGATGTGTATGTAAAGTGCCAATTCATTTGGGAGCATCCACAAGCAAGTA
CAAAGGCAAGTAAAAGCTTACTTGAGCTTTGTCATTGAAGCAAGTTACTAAGGTGAGCTGTGATG
CATAGTGAGGGGGCTTAGATGATCAATTCATCTAATCTAAGTCCAGGAGTAAGTGTTCTTACTTG
AGCTTTGTTATTTTGCAAATAAGCTTACATGTGTTGTGATATGTTTAAGTTTATAATGTGAATAT
ATGTGTTGAATATATATCTGAATATGCTTTGTGAACAGTTGGTTTTA
Found at i:31499528 original size:15 final size:16
Alignment explanation
Indices: 31499508--31499538 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31499498 TGACGGTTGG
31499508 ATTGTT-AAAATATTA
1 ATTGTTGAAAATATTA
31499523 ATTGTTGAAAATATTA
1 ATTGTTGAAAATATTA
31499539 TGAAATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (16 bp):
ATTGTTGAAAATATTA
Found at i:31505919 original size:32 final size:32
Alignment explanation
Indices: 31505865--31505925 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
31505855 CATGTTTAGG
*
31505865 ATGAATCTAGATAAATACTTGTCCAGGTTCAA
1 ATGAATCTAGATAAACACTTGTCCAGGTTCAA
** *
31505897 ATGAATCTAGATAGCCATTTGTCCAGGTT
1 ATGAATCTAGATAAACACTTGTCCAGGTT
31505926 GGTCCTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (32 bp):
ATGAATCTAGATAAACACTTGTCCAGGTTCAA
Found at i:31506016 original size:21 final size:20
Alignment explanation
Indices: 31505983--31506043 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
31505973 AAGATTTTTT
*
31505983 AAATAATTATTAAAAATAAAA
1 AAATAAATATT-AAAATAAAA
* *
31506004 AAATAAATCTTAAATTAAAAA
1 AAATAAATATTAAAAT-AAAA
31506025 ATAACTAAA-ATTAAAATAA
1 A-AA-TAAATATTAAAATAA
31506044 CCGTCACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 4 0.12
21 16 0.50
22 8 0.25
23 4 0.12
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATAAATATTAAAATAAAA
Found at i:31506023 original size:19 final size:17
Alignment explanation
Indices: 31505995--31506040 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
31505985 ATAATTATTA
*
31505995 AAAATAAAAAAATAAATCT
1 AAAATTAAAAAAT-AA-CT
*
31506014 TAAATTAAAAAATAACT
1 AAAATTAAAAAATAACT
31506031 AAAATTAAAA
1 AAAATTAAAA
31506041 TAACCGTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.46
18 2 0.08
19 11 0.46
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATTAAAAAATAACT
Found at i:31506339 original size:13 final size:13
Alignment explanation
Indices: 31506291--31506340 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
31506281 TTTTTACTAG
*
31506291 TTATTATAA-TTT
1 TTATAATAATTTT
31506303 TTA-AATAATTTT
1 TTATAATAATTTT
31506315 TTAT-ATCAATTTT
1 TTATAAT-AATTTT
*
31506328 TTATAATTATTTT
1 TTATAATAATTTT
31506341 AAAAAAACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 4 0.12
12 11 0.34
13 15 0.47
14 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATAATAATTTT
Found at i:31508071 original size:6 final size:6
Alignment explanation
Indices: 31508057--31508089 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
31508047 TCTTTTAATA
*
31508057 TTTAGC TTTACC TTTAGC TTTAGC TTTAGC TTT
1 TTTAGC TTTAGC TTTAGC TTTAGC TTTAGC TTT
31508090 GGCTCTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.15, C:0.18, G:0.12, T:0.55
Consensus pattern (6 bp):
TTTAGC
Found at i:31513019 original size:18 final size:18
Alignment explanation
Indices: 31512996--31513033 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
31512986 TATATTAAAA
31512996 TATAAAT-TTTAGAATTTT
1 TATAAATATTT-GAATTTT
31513014 TATAAATACTTTGAATTTT
1 TATAAATA-TTTGAATTTT
31513033 T
1 T
31513034 TTGTAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 8 0.44
20 3 0.17
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (18 bp):
TATAAATATTTGAATTTT
Found at i:31513696 original size:26 final size:26
Alignment explanation
Indices: 31513639--31513702 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
31513629 AGTATAAATT
* * *
31513639 AAATATCAAATAATAATAAAAGTATC
1 AAATATCAAATAACAATAAAAGCATA
*
31513665 AAATATCAAATAACGATAAAAGCA-A
1 AAATATCAAATAACAATAAAAGCATA
*
31513690 AACATATAAAATA
1 AA-ATATCAAATA
31513703 TTATATAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.64, C:0.09, G:0.05, T:0.22
Consensus pattern (26 bp):
AAATATCAAATAACAATAAAAGCATA
Found at i:31521052 original size:18 final size:17
Alignment explanation
Indices: 31521040--31521072 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31521030 ATAATTATTA
31521040 AGGA-TTATTTAATTTT
1 AGGATTTATTTAATTTT
31521056 AGGATTTTATTTAATTT
1 AGGA-TTTATTTAATTT
31521073 ATCTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
18 11 0.73
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (17 bp):
AGGATTTATTTAATTTT
Found at i:31527301 original size:12 final size:12
Alignment explanation
Indices: 31527263--31527317 Score: 60
Period size: 12 Copynumber: 4.5 Consensus size: 12
31527253 TAACCCAATT
*
31527263 TTTATTT-TTAT
1 TTTATTTATTAC
31527274 TTTATTTTATTTAC
1 TTTA-TTTA-TTAC
31527288 TTTATTTATTAC
1 TTTATTTATTAC
31527300 TTTATTTTATTA-
1 TTTA-TTTATTAC
31527312 TTTATT
1 TTTATT
31527318 ACTTATTTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 15 0.38
13 11 0.28
14 7 0.18
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATTTATTAC
Found at i:31527521 original size:22 final size:21
Alignment explanation
Indices: 31527472--31527531 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
31527462 GTGCAGAATG
* *
31527472 CCTGCAGCCAAACTACCCTATT
1 CCTGCAGCC-AACCACCCTATC
*
31527494 CTTGCAGCCAACCACCCTTATC
1 CCTGCAGCCAACCACCC-TATC
* *
31527516 CCTGCACCCAAGCACC
1 CCTGCAGCCAACCACC
31527532 ACCCCTCAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.25, C:0.47, G:0.10, T:0.18
Consensus pattern (21 bp):
CCTGCAGCCAACCACCCTATC
Found at i:31528630 original size:101 final size:100
Alignment explanation
Indices: 31528440--31528628 Score: 227
Period size: 101 Copynumber: 1.8 Consensus size: 100
31528430 AAGAACATGT
* * * * *
31528440 TGGGCTGAGTAACTGGGGTGTGGTGCTTGGCTATCATCTCTCTTCACGTCAAAAGGTTCGATGTG
1 TGGGCTGAGTAACCGAGGTGGGGTGCTTGGCTATCATCTCTCTTCACGTCAAAAGGTTAGATATG
* *
31528505 TTCTTAAGAAAAAATTATAATAAATTAGAAGTCTGC
66 TCCTAAAGAAAAAA-TATAATAAATTAGAAGTCTGC
* * *
31528541 TGGGCTTAGTAACCGAGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTTAGTATA
1 TGGGCTGAGTAACCGAGGTGGGGTGCTTGGCTATCATCTCTCTTCACGTCAAAAGG-TTAG-ATA
31528606 T-TCCTAAAGCATAAAAAATATAA
64 TGTCCTAAAG---AAAAAATATAA
31528629 ATAATAAATA
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
101 50 0.68
102 9 0.12
103 3 0.04
104 5 0.07
105 6 0.08
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (100 bp):
TGGGCTGAGTAACCGAGGTGGGGTGCTTGGCTATCATCTCTCTTCACGTCAAAAGGTTAGATATG
TCCTAAAGAAAAAATATAATAAATTAGAAGTCTGC
Found at i:31528635 original size:16 final size:14
Alignment explanation
Indices: 31528616--31528688 Score: 65
Period size: 16 Copynumber: 4.8 Consensus size: 14
31528606 TTCCTAAAGC
31528616 ATAAAAAATATAAATA
1 ATAAAAAA-ATAAA-A
*
31528632 ATAAATAAATAAAA
1 ATAAAAAAATAAAA
31528646 ATCAAAATAAATAAAAA
1 AT-AAAA-AAAT-AAAA
*
31528663 ATAAAAAAAGAAAA
1 ATAAAAAAATAAAA
*
31528677 AGAAAAAGAATA
1 ATAAAAA-AATA
31528689 TAATTTAGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
14 13 0.27
15 14 0.29
16 15 0.31
17 6 0.12
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (14 bp):
ATAAAAAAATAAAA
Found at i:31528641 original size:11 final size:11
Alignment explanation
Indices: 31528625--31528667 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
31528615 CATAAAAAAT
31528625 ATAAATAATAA
1 ATAAATAATAA
31528636 ATAAATAA-AA
1 ATAAATAATAA
*
31528646 ATCAA-AATAA
1 ATAAATAATAA
*
31528656 ATAAAAAATAA
1 ATAAATAATAA
31528667 A
1 A
31528668 AAAAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 2 0.07
10 12 0.43
11 14 0.50
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (11 bp):
ATAAATAATAA
Found at i:31528667 original size:7 final size:7
Alignment explanation
Indices: 31528616--31528683 Score: 50
Period size: 7 Copynumber: 9.0 Consensus size: 7
31528606 TTCCTAAAGC
31528616 ATAAAAA
1 ATAAAAA
31528623 ATATAAATA
1 ATA-AAA-A
31528632 ATAAATAA
1 ATAAA-AA
31528640 AT-AAAA
1 ATAAAAA
31528646 ATCAAAATAA
1 AT--AAA-AA
31528656 ATAAAAA
1 ATAAAAA
31528663 ATAAAAA
1 ATAAAAA
31528670 A-AGAAAA
1 ATA-AAAA
*
31528677 AGAAAAA
1 ATAAAAA
31528684 GAATATAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
6 5 0.10
7 24 0.46
8 12 0.23
9 7 0.13
10 4 0.08
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.16
Consensus pattern (7 bp):
ATAAAAA
Found at i:31529265 original size:15 final size:15
Alignment explanation
Indices: 31529240--31529274 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
31529230 AACTCTATTT
*
31529240 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
31529254 TAATTAATATTAAGA
1 TAATTAATATTAAGA
31529269 TAATTA
1 TAATTA
31529275 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:31533205 original size:25 final size:24
Alignment explanation
Indices: 31533169--31533227 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
31533159 TTTGACTAAT
*
31533169 GGAGCCAATAACATCCGTGAATT-AA
1 GGAGCCATTAACAT-C-TGAATTAAA
*
31533194 GGAGCCATTAACGTCTGAATTAAA
1 GGAGCCATTAACATCTGAATTAAA
*
31533218 GGATCCATTA
1 GGAGCCATTA
31533228 GCCTTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.20
24 12 0.40
25 12 0.40
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (24 bp):
GGAGCCATTAACATCTGAATTAAA
Found at i:31535401 original size:51 final size:52
Alignment explanation
Indices: 31535341--31535444 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
31535331 TTTTTTAAAA
*
31535341 AGATGTTTTGTGC-TTTTTTATCTATTTATTCATACAAACAAAATCATAATT
1 AGATGTTTTGTGCTTTTTTTATCTATTTATTCATACAAACAAAATCACAATT
*
31535392 AGATGTTTTGTGCTTTTTTTATCTATTTCTTCATACAAACAAAATCACAATT
1 AGATGTTTTGTGCTTTTTTTATCTATTTATTCATACAAACAAAATCACAATT
31535444 A
1 A
31535445 AGTTTTTGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 13 0.26
52 37 0.74
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (52 bp):
AGATGTTTTGTGCTTTTTTTATCTATTTATTCATACAAACAAAATCACAATT
Found at i:31535465 original size:52 final size:52
Alignment explanation
Indices: 31535341--31535465 Score: 148
Period size: 52 Copynumber: 2.4 Consensus size: 52
31535331 TTTTTTAAAA
** *
31535341 AGATGTTTTGTGC-TTTTTTATCTATTTATTCATACAAACAAAATCATAATT
1 AGATGTTTTGTGCATGATTTATCTATTTATTCATACAAACAAAATCACAATT
* ** *
31535392 AGATGTTTTGTGCTTTTTTTATCTATTTCTTCATACAAACAAAATCACAATT
1 AGATGTTTTGTGCATGATTTATCTATTTATTCATACAAACAAAATCACAATT
31535444 A-A-GTTTTTGTTGCATGATTTAT
1 AGATG-TTTTG-TGCATGATTTAT
31535466 GTGAATGAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
50 1 0.02
51 19 0.29
52 46 0.70
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (52 bp):
AGATGTTTTGTGCATGATTTATCTATTTATTCATACAAACAAAATCACAATT
Found at i:31545582 original size:22 final size:24
Alignment explanation
Indices: 31545532--31545582 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
31545522 TTGCAATGCT
31545532 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
31545557 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
31545578 TTTAT
1 TTTAT
31545583 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Done.