Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold58
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: 1582273
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 125418 characters in sequence are not A, C, G, or T
File 9 of 10
Found at i:1346718 original size:15 final size:15
Alignment explanation
Indices: 1346619--1346718 Score: 50
Period size: 15 Copynumber: 6.6 Consensus size: 15
1346609 TGTCTTATAC
1346619 TTAAATATTATTTTTAT
1 TTAAATATTA--TTTAT
1346636 TTAAATA-T-TTTAT
1 TTAAATATTATTTAT
*
1346649 ATAAA-ATATATTTATATT
1 TTAAATAT-TA-TT-TA-T
*
1346667 TTAAATAATA-TTAT
1 TTAAATATTATTTAT
**
1346681 TCTAAATAACA-TT-T
1 T-TAAATATTATTTAT
*
1346695 TTAAGTATTATTTAT
1 TTAAATATTATTTAT
1346710 TTAAATATT
1 TTAAATATT
1346719 TATAAATATT
Statistics
Matches: 65, Mismatches: 8, Indels: 22
0.68 0.08 0.23
Matches are distributed among these distances:
12 1 0.02
13 15 0.23
14 7 0.11
15 21 0.32
16 4 0.06
17 9 0.14
18 7 0.11
19 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (15 bp):
TTAAATATTATTTAT
Found at i:1348017 original size:19 final size:17
Alignment explanation
Indices: 1347985--1348039 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 17
1347975 TTTTTACTTA
1347985 TTTTATTAAATTTTTAT
1 TTTTATTAAATTTTTAT
*
1348002 TTTTATATAAAGTTTTTGT
1 TTTTAT-TAAA-TTTTTAT
1348021 TTTTGATTAAAATTTTTAT
1 TTTT-ATT-AAATTTTTAT
1348040 ATAAAGTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 6 0.19
18 4 0.12
19 17 0.53
20 5 0.16
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (17 bp):
TTTTATTAAATTTTTAT
Found at i:1348610 original size:23 final size:22
Alignment explanation
Indices: 1348570--1348646 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 22
1348560 TAAGATTTAT
* *
1348570 ATTTAATACATTAATAATATATAA
1 ATTT-ATAAATTATTAATA-ATAA
1348594 ATTTATAAATTATTAATAAATAAA
1 ATTTATAAATTATTAAT-AAT-AA
*
1348618 ATTATATCAATTTATTAA-AATAA
1 ATT-TAT-AAATTATTAATAATAA
1348641 ATTTAT
1 ATTTAT
1348647 CTATATTTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
22 3 0.07
23 18 0.39
24 13 0.28
25 3 0.07
26 9 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTATAAATTATTAATAATAA
Found at i:1352308 original size:46 final size:48
Alignment explanation
Indices: 1352238--1352327 Score: 148
Period size: 46 Copynumber: 1.9 Consensus size: 48
1352228 ATAGTAAAAA
* *
1352238 ATTATTTTTTTTTATGGATTTGTATATAGCATATTTAAATAATTCGAT
1 ATTATTTTTTTTTATGGATATGTATATAGCATATTCAAATAATTCGAT
1352286 ATTA-TTTTTTTT-TGGATATGTATATAGCATATTCAAATAATT
1 ATTATTTTTTTTTATGGATATGTATATAGCATATTCAAATAATT
1352328 ATGGATTCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
46 28 0.70
47 8 0.20
48 4 0.10
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.53
Consensus pattern (48 bp):
ATTATTTTTTTTTATGGATATGTATATAGCATATTCAAATAATTCGAT
Found at i:1352503 original size:11 final size:11
Alignment explanation
Indices: 1352474--1352514 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
1352464 ATGTATTTAC
1352474 ATATTTAATTATT
1 ATATTT-ATT-TT
1352487 AT-TTTATTTT
1 ATATTTATTTT
1352497 ATATTTATTTT
1 ATATTTATTTT
1352508 ATATTTA
1 ATATTTA
1352515 GCAAATTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 18 0.67
12 3 0.11
13 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATATTTATTTT
Found at i:1352757 original size:22 final size:23
Alignment explanation
Indices: 1352717--1352763 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1352707 AAAAATTCTA
** *
1352717 TTTGAAAAATAATGTTTTTAGTT
1 TTTGAAAAATAATAATTTTAATT
1352740 TTTGAAAAATAA-AATTTTAATT
1 TTTGAAAAATAATAATTTTAATT
1352762 TT
1 TT
1352764 ATTTATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (23 bp):
TTTGAAAAATAATAATTTTAATT
Found at i:1353417 original size:2 final size:2
Alignment explanation
Indices: 1353410--1353437 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1353400 TTTGAAATTC
1353410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1353438 TGTCTTGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1356226 original size:22 final size:22
Alignment explanation
Indices: 1356186--1356227 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1356176 ATTTAAAAAA
1356186 TTTTATATATTCATATATTAAT
1 TTTTATATATTCATATATTAAT
*
1356208 TTTTA-ATATTACATGTATTA
1 TTTTATATATT-CATATATTA
1356228 TGTGTGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTATATATTCATATATTAAT
Found at i:1356756 original size:16 final size:15
Alignment explanation
Indices: 1356713--1356766 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
1356703 CCCTTAAATT
1356713 TAAAAACTAAATTATTA
1 TAAAAA-TAAATT-TTA
*
1356730 AAAAAAT-AATTTTGA
1 TAAAAATAAATTTT-A
1356745 TAAAAATAAA-TTTA
1 TAAAAATAAATTTTA
1356759 -AAAAATAA
1 TAAAAATAA
1356767 TTGAAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 8 0.24
14 3 0.09
15 14 0.42
16 3 0.09
17 5 0.15
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
TAAAAATAAATTTTA
Found at i:1357436 original size:19 final size:19
Alignment explanation
Indices: 1357389--1357441 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
1357379 TATATTAACT
* *
1357389 TTTAAATTAATTACTATTA
1 TTTAAAGTATTTACTATTA
*
1357408 TTTAAAGTATTTACTATTG
1 TTTAAAGTATTTACTATTA
*
1357427 TTTAAAGTATATACT
1 TTTAAAGTATTTACT
1357442 TTAAACTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.51
Consensus pattern (19 bp):
TTTAAAGTATTTACTATTA
Found at i:1359608 original size:12 final size:12
Alignment explanation
Indices: 1359593--1359673 Score: 51
Period size: 12 Copynumber: 6.8 Consensus size: 12
1359583 GATTCGATCT
1359593 ATTTTTAAATAA
1 ATTTTTAAATAA
* *
1359605 ATTTTAAAATTTA
1 ATTTTTAAA-TAA
* * *
1359618 TTTTTTAATTTA
1 ATTTTTAAATAA
*
1359630 ATATTTTATATAA
1 AT-TTTTAAATAA
*
1359643 ATTTTT--GTAA
1 ATTTTTAAATAA
*
1359653 A-TATTAAATAA
1 ATTTTTAAATAA
1359664 ATTTTTAAAT
1 ATTTTTAAAT
1359674 TTAAATAATC
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
9 3 0.06
10 4 0.08
11 4 0.08
12 23 0.45
13 17 0.33
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (12 bp):
ATTTTTAAATAA
Found at i:1359679 original size:18 final size:20
Alignment explanation
Indices: 1359634--1359681 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
1359624 AATTTAATAT
*
1359634 TTTATATAAATTTTTGTAAA
1 TTTAAATAAATTTTTGTAAA
1359654 TATTAAATAAA-TTTT-TAAA
1 T-TTAAATAAATTTTTGTAAA
1359673 TTTAAATAA
1 TTTAAATAA
1359682 TCTGATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 5 0.19
20 5 0.19
21 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTAAATAAATTTTTGTAAA
Found at i:1362135 original size:17 final size:19
Alignment explanation
Indices: 1362077--1362158 Score: 64
Period size: 18 Copynumber: 4.3 Consensus size: 19
1362067 ACATTTAATT
*
1362077 ATAA-TTAATATAATATATTT
1 ATAATTTAATATAA-AT-TTA
* *
1362097 ATATATTTATATTTATATTTA
1 ATA-ATTTA-ATATAAATTTA
*
1362118 A-AATTTTA-ATAAATTTA
1 ATAATTTAATATAAATTTA
1362135 ATAATTTAATATAAA-TTA
1 ATAATTTAATATAAATTTA
1362153 ATAATT
1 ATAATT
1362159 ACTCTACTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
17 8 0.16
18 16 0.32
19 9 0.18
20 4 0.08
21 4 0.08
22 5 0.10
23 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAATTTAATATAAATTTA
Found at i:1362220 original size:2 final size:2
Alignment explanation
Indices: 1362213--1362238 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1362203 TTAAATTATC
1362213 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1362239 CACATCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1362808 original size:17 final size:17
Alignment explanation
Indices: 1362786--1362827 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1362776 ATAATATTAT
**
1362786 TTATAAATTTTTAAAAA
1 TTATAAATTTAAAAAAA
1362803 TTATAAATTTAAAAAAA
1 TTATAAATTTAAAAAAA
1362820 TTA-AAATT
1 TTATAAATT
1362828 ATAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTATAAATTTAAAAAAA
Found at i:1369451 original size:22 final size:22
Alignment explanation
Indices: 1369426--1369471 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1369416 ACGATCGAAT
**
1369426 TTAAAATTTAATATTTTTAAAA
1 TTAAAATTTAATAAATTTAAAA
*
1369448 TTAATATTTAATAAATTTAAAA
1 TTAAAATTTAATAAATTTAAAA
1369470 TT
1 TT
1369472 TAATTAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAAATTTAATAAATTTAAAA
Found at i:1369453 original size:15 final size:16
Alignment explanation
Indices: 1369425--1369456 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1369415 AACGATCGAA
1369425 TTTAAAATTTAATATT
1 TTTAAAATTTAATATT
1369441 TTTAAAA-TTAATATT
1 TTTAAAATTTAATATT
1369456 T
1 T
1369457 AATAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAAAATTTAATATT
Found at i:1369462 original size:16 final size:16
Alignment explanation
Indices: 1369427--1369475 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1369417 CGATCGAATT
*
1369427 TAAAATTTAATATTT-T
1 TAAAA-TTAATATTTAA
1369443 TAAAATTAATATTTAA
1 TAAAATTAATATTTAA
* *
1369459 TAAATTTAAAATTTAA
1 TAAAATTAATATTTAA
1369475 T
1 T
1369476 TAATAACTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 9 0.31
16 20 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAAATTAATATTTAA
Found at i:1370509 original size:18 final size:20
Alignment explanation
Indices: 1370476--1370518 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1370466 TAAACATATA
*
1370476 TTTTTATTATATTTTTA-TT
1 TTTTTATTACATTTTTACTT
1370495 TTTTTATTACA-TTTTACTT
1 TTTTTATTACATTTTTACTT
1370514 TTTTT
1 TTTTT
1370519 CATGTTAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTATTACATTTTTACTT
Found at i:1371612 original size:23 final size:23
Alignment explanation
Indices: 1371586--1371631 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1371576 TATTATCTAA
1371586 TTTTAAAT-TATTATATAAAATAT
1 TTTTAAATATA-TATATAAAATAT
*
1371609 TTTTATATATATATATAAAATAT
1 TTTTAAATATATATATAAAATAT
1371632 AATTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTAAATATATATATAAAATAT
Found at i:1371747 original size:16 final size:16
Alignment explanation
Indices: 1371726--1371757 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1371716 GTAAATTGAT
1371726 TTTAAAAATCGATTAA
1 TTTAAAAATCGATTAA
*
1371742 TTTAAAAATTGATTAA
1 TTTAAAAATCGATTAA
1371758 ACTAAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (16 bp):
TTTAAAAATCGATTAA
Found at i:1371766 original size:14 final size:14
Alignment explanation
Indices: 1371747--1371784 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1371737 ATTAATTTAA
1371747 AAATTG-ATTAAACT
1 AAATTGAATT-AACT
1371761 AAATTGAATTAACT
1 AAATTGAATTAACT
*
1371775 AAATTTAATT
1 AAATTGAATT
1371785 GATTCAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATTGAATTAACT
Found at i:1372725 original size:14 final size:14
Alignment explanation
Indices: 1372706--1372734 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1372696 TGTGAAAATT
1372706 AATAAGAAGTGTTA
1 AATAAGAAGTGTTA
1372720 AATAAGAAGTGTTA
1 AATAAGAAGTGTTA
1372734 A
1 A
1372735 TTACGCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.28
Consensus pattern (14 bp):
AATAAGAAGTGTTA
Found at i:1373392 original size:22 final size:21
Alignment explanation
Indices: 1373367--1373426 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 21
1373357 CATAATATAA
1373367 ATATATAAATATATTAAAA-TT
1 ATATATAAATATA-TAAAACTT
*
1373388 -TATATAAATATATAATATCTT
1 ATATATAAATATATAA-AACTT
* *
1373409 AAATATAATTATAATAAA
1 ATATATAAATAT-ATAAA
1373427 TATTACATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 3 0.09
20 13 0.41
21 2 0.06
22 10 0.31
23 4 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATATAAATATATAAAACTT
Found at i:1373392 original size:28 final size:29
Alignment explanation
Indices: 1373361--1373429 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 29
1373351 TATAAACATA
1373361 ATATAAATATATAAATATATTAAA-AT-TT
1 ATATAAATATAT-AATATATTAAATATATT
*
1373389 ATATAAATATATAATATCTTAAATATAATT
1 ATATAAATATATAATATATTAAATAT-ATT
1373419 ATAATAAATAT
1 AT-ATAAATAT
1373430 TACATAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 10 0.28
28 14 0.39
30 4 0.11
31 8 0.22
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATAAATATATAATATATTAAATATATT
Found at i:1374947 original size:27 final size:27
Alignment explanation
Indices: 1374907--1374977 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
1374897 GGCGTCTTTC
*
1374907 CCTTCCTTTGCATCTTTCCCAT-TCTT
1 CCTTCCTTTCCATCTTTCCCATCTCTT
* *
1374933 GCCTTCCTTTCCATCCTTGCCATCTCTT
1 -CCTTCCTTTCCATCTTTCCCATCTCTT
*
1374961 CCAT-CTTTGCCATCTTT
1 CCTTCCTTT-CCATCTTT
1374978 GGGTGGAGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.11
27 29 0.78
28 4 0.11
ACGTcount: A:0.08, C:0.39, G:0.06, T:0.46
Consensus pattern (27 bp):
CCTTCCTTTCCATCTTTCCCATCTCTT
Found at i:1374951 original size:18 final size:17
Alignment explanation
Indices: 1374917--1374977 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
1374907 CCTTCCTTTG
*
1374917 CATCTTTCCCATTCTTGC
1 CATCTTT-CCATCCTTGC
*
1374935 CTTCCTTTCCATCCTTGC
1 CAT-CTTTCCATCCTTGC
*
1374953 CATCTCTTCCATCTTTGC
1 CATCT-TTCCATCCTTGC
1374971 CATCTTT
1 CATCTTT
1374978 GGGTGGAGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 29 0.78
19 4 0.11
ACGTcount: A:0.10, C:0.39, G:0.05, T:0.46
Consensus pattern (17 bp):
CATCTTTCCATCCTTGC
Found at i:1374975 original size:9 final size:9
Alignment explanation
Indices: 1374912--1374978 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
1374902 CTTTCCCTTC
1374912 CTTTG-CAT
1 CTTTGCCAT
*
1374920 CTTTCCCAT
1 CTTTGCCAT
*
1374929 -TCTTGCCTT
1 CT-TTGCCAT
1374938 CCTTT-CCAT
1 -CTTTGCCAT
*
1374947 CCTTGCCAT
1 CTTTGCCAT
1374956 CTCTT-CCAT
1 CT-TTGCCAT
1374965 CTTTGCCAT
1 CTTTGCCAT
1374974 CTTTG
1 CTTTG
1374979 GGTGGAGGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
8 10 0.22
9 31 0.67
10 4 0.09
11 1 0.02
ACGTcount: A:0.09, C:0.37, G:0.07, T:0.46
Consensus pattern (9 bp):
CTTTGCCAT
Found at i:1377723 original size:32 final size:32
Alignment explanation
Indices: 1377656--1377724 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 32
1377646 TAGATTTTCA
*
1377656 TTTTATTTAGTTATTTCTTTTTCTTTTTTGAT
1 TTTTATTTAGTTATTTCTTTTTCTTCTTTGAT
*
1377688 TTTTATCTTA-TTATTT-TTTTCTCTCTCTTTGTT
1 TTTTAT-TTAGTTATTTCTTTT-TCT-TCTTTGAT
1377721 TTTT
1 TTTT
1377725 TCCTTCCATC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 4 0.12
32 15 0.47
33 13 0.41
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.75
Consensus pattern (32 bp):
TTTTATTTAGTTATTTCTTTTTCTTCTTTGAT
Found at i:1382840 original size:12 final size:12
Alignment explanation
Indices: 1382823--1382847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1382813 GAAAACAAAG
1382823 GCTGCCAACTGT
1 GCTGCCAACTGT
1382835 GCTGCCAACTGT
1 GCTGCCAACTGT
1382847 G
1 G
1382848 TCGTCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:1382873 original size:12 final size:12
Alignment explanation
Indices: 1382851--1382901 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
1382841 AACTGTGTCG
1382851 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
1382864 TCAATTTGAAAT
1 TCAATTTGAAAT
*
1382876 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
1382891 TCAATTTGAAA
1 TCAATTTGAAA
1382902 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:1382913 original size:27 final size:27
Alignment explanation
Indices: 1382857--1382913 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1382847 GTCGTCAATT
* *
1382857 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
1382884 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
1382911 TTG
1 TTG
1382914 CATAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:1387590 original size:12 final size:12
Alignment explanation
Indices: 1387573--1387597 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1387563 GAAAACAAAG
1387573 GCTGCCAACTGT
1 GCTGCCAACTGT
1387585 GCTGCCAACTGT
1 GCTGCCAACTGT
1387597 G
1 G
1387598 TCGTCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:1387623 original size:12 final size:12
Alignment explanation
Indices: 1387601--1387651 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
1387591 AACTGTGTCG
1387601 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
1387614 TCAATTTGAAAT
1 TCAATTTGAAAT
*
1387626 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
1387641 TCAATTTGAAA
1 TCAATTTGAAA
1387652 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:1387663 original size:27 final size:27
Alignment explanation
Indices: 1387607--1387663 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1387597 GTCGTCAATT
* *
1387607 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
1387634 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
1387661 TTG
1 TTG
1387664 CATAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:1392354 original size:2 final size:2
Alignment explanation
Indices: 1392347--1392378 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1392337 ATATGTGCAA
1392347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1392379 TATTAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1395020 original size:15 final size:15
Alignment explanation
Indices: 1395000--1395030 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1394990 TAAAAATTTG
1395000 TAATTTGTAATTTTT
1 TAATTTGTAATTTTT
*
1395015 TAATTTTTAATTTTT
1 TAATTTGTAATTTTT
1395030 T
1 T
1395031 TAAATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TAATTTGTAATTTTT
Found at i:1396476 original size:19 final size:20
Alignment explanation
Indices: 1396452--1396493 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1396442 AAATAATTTT
1396452 ATTATTTT-AAT-TGTTATTA
1 ATTATTTTAAATAT-TTATTA
1396471 ATTATTTTAAATATTTATTA
1 ATTATTTTAAATATTTATTA
1396491 ATT
1 ATT
1396494 TACCTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 12 0.57
21 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTATTTTAAATATTTATTA
Found at i:1396575 original size:26 final size:26
Alignment explanation
Indices: 1396541--1396618 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
1396531 TTAAAAAACT
1396541 AATATCTAATTTTTAAAAAATATAAA
1 AATATCTAATTTTTAAAAAATATAAA
* *
1396567 AATATCTAAATTTTAAAAACTA-AAA
1 AATATCTAATTTTTAAAAAATATAAA
** *
1396592 AATAAATAATTATTTTAAAAAT-TAAA
1 AATATCTAATT-TTTAAAAAATATAAA
1396618 A
1 A
1396619 GTAAAACATT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 11 0.26
26 32 0.74
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (26 bp):
AATATCTAATTTTTAAAAAATATAAA
Found at i:1396606 original size:27 final size:25
Alignment explanation
Indices: 1396551--1396618 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
1396541 AATATCTAAT
**
1396551 TTTTAAAAAATATAAAAATATCTAAA
1 TTTTAAAAAATA-AAAAATAAATAAA
*
1396577 TTTTAAAAACTAAAAAATAAATAATTA
1 TTTTAAAAAATAAAAAATAAATAA--A
*
1396604 TTTTAAAAATTAAAA
1 TTTTAAAAAATAAAA
1396619 GTAAAACATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 10 0.28
26 11 0.31
27 15 0.42
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (25 bp):
TTTTAAAAAATAAAAAATAAATAAA
Found at i:1404416 original size:9 final size:8
Alignment explanation
Indices: 1404381--1404412 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
1404371 CATTATCAAG
1404381 TTTATGAT
1 TTTATGAT
1404389 TTTATTGAT
1 TTTA-TGAT
1404398 TTTATGAT
1 TTTATGAT
1404406 TTTATGA
1 TTTATGA
1404413 ATTTCTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (8 bp):
TTTATGAT
Found at i:1405593 original size:16 final size:16
Alignment explanation
Indices: 1405574--1405604 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1405564 AATGTATTTG
*
1405574 TTATATAAATATATAT
1 TTATATAAAAATATAT
1405590 TTATATAAAAATATA
1 TTATATAAAAATATA
1405605 AATTTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATATAAAAATATAT
Found at i:1405614 original size:14 final size:14
Alignment explanation
Indices: 1405597--1405677 Score: 60
Period size: 14 Copynumber: 5.8 Consensus size: 14
1405587 TATTTATATA
1405597 AAAATATAAATTTT
1 AAAATATAAATTTT
1405611 AAAATTATAAATATTT
1 AAAA-TATAAAT-TTT
* *
1405627 -ATATTTAATATTTT
1 AAAATATAA-ATTTT
**
1405641 AAAATATAAATAAT
1 AAAATATAAATTTT
* *
1405655 -AAA-ATAAATATA
1 AAAATATAAATTTT
1405667 AAAATATAAAT
1 AAAATATAAAT
1405678 CAATAAATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
12 7 0.13
13 6 0.11
14 20 0.38
15 17 0.32
16 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATATAAATTTT
Found at i:1405619 original size:15 final size:15
Alignment explanation
Indices: 1405595--1405651 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
1405585 TATATTTATA
*
1405595 TAAAAATATAAATTT
1 TAAAATTATAAATTT
1405610 TAAAATTATAAATATT
1 TAAAATTATAAAT-TT
*
1405626 T-ATATT-TAATATTT
1 TAAAATTATAA-ATTT
1405640 TAAAA-TATAAAT
1 TAAAATTATAAAT
1405652 AATAAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 9 0.26
15 23 0.66
16 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAAATTATAAATTT
Found at i:1405665 original size:18 final size:18
Alignment explanation
Indices: 1405642--1405682 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1405632 TAATATTTTA
1405642 AAATATAAATAATA-AAAT
1 AAATATAAA-AATATAAAT
1405660 AAATATAAAAATATAAAT
1 AAATATAAAAATATAAAT
*
1405678 CAATA
1 AAATA
1405683 AATATTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATATAAAAATATAAAT
Found at i:1405685 original size:14 final size:13
Alignment explanation
Indices: 1405642--1405692 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
1405632 TAATATTTTA
1405642 AAATATAAATAAT
1 AAATATAAATAAT
*
1405655 AAA-ATAAATATAA
1 AAATATAAATA-AT
1405668 AAATATAAATCAAT
1 AAATATAAAT-AAT
*
1405682 AAATATTAATA
1 AAATATAAATA
1405693 CAGATCATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 7 0.22
13 8 0.25
14 16 0.50
15 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATATAAATAAT
Found at i:1407275 original size:50 final size:50
Alignment explanation
Indices: 1407215--1407374 Score: 277
Period size: 50 Copynumber: 3.2 Consensus size: 50
1407205 ATATACTTAG
1407215 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
* *
1407265 TGTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
*
1407315 CGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAATG-AT
1 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAAT
1407365 AGTCAACAAT
1 AGTCAACAAT
1407375 GACAACAACT
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
50 103 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (50 bp):
AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:1411827 original size:50 final size:50
Alignment explanation
Indices: 1411767--1411926 Score: 277
Period size: 50 Copynumber: 3.2 Consensus size: 50
1411757 ATATACTTAG
1411767 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
* *
1411817 TGTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
*
1411867 CGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAATG-AT
1 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAAT
1411917 AGTCAACAAT
1 AGTCAACAAT
1411927 GACAACAACT
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
50 103 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (50 bp):
AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:1414527 original size:3 final size:3
Alignment explanation
Indices: 1414519--1414560 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
1414509 TTTAATTAAA
1414519 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
1414561 TACTTAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1417873 original size:24 final size:24
Alignment explanation
Indices: 1417845--1417894 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1417835 AAAAAGAGAA
1417845 TAATATGAGTTAAATGAGTATATT
1 TAATATGAGTTAAATGAGTATATT
1417869 TAATATGAGTTAAATGAGTATATT
1 TAATATGAGTTAAATGAGTATATT
1417893 TA
1 TA
1417895 TAAATTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (24 bp):
TAATATGAGTTAAATGAGTATATT
Found at i:1419026 original size:2 final size:2
Alignment explanation
Indices: 1419019--1419051 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1419009 ACAATTTTGC
1419019 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1419052 TAATTATCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1420111 original size:25 final size:25
Alignment explanation
Indices: 1420036--1420112 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
1420026 TAAGATGAGA
*
1420036 TAATTGTGATGGCAAAATTAGGTGG
1 TAATTGTGACGGCAAAATTAGGTGG
* * * * *
1420061 TAATTAG-GAC-G-ATAA-GATGAGA
1 TAATT-GTGACGGCAAAATTAGGTGG
1420083 TAATTGTGACGGCAAAATTAGGTGG
1 TAATTGTGACGGCAAAATTAGGTGG
1420108 TAATT
1 TAATT
1420113 AAGATGAGTT
Statistics
Matches: 36, Mismatches: 11, Indels: 10
0.63 0.19 0.18
Matches are distributed among these distances:
21 1 0.03
22 11 0.31
23 4 0.11
24 4 0.11
25 15 0.42
26 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (25 bp):
TAATTGTGACGGCAAAATTAGGTGG
Found at i:1420596 original size:17 final size:18
Alignment explanation
Indices: 1420576--1420613 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1420566 AAATATATTT
*
1420576 AAAAGTAAAT-TTTTTTA
1 AAAAGTAAATGTGTTTTA
*
1420593 AAAAGTTAATGTGTTTTA
1 AAAAGTAAATGTGTTTTA
1420611 AAA
1 AAA
1420614 TTAAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (18 bp):
AAAAGTAAATGTGTTTTA
Found at i:1420948 original size:22 final size:22
Alignment explanation
Indices: 1420908--1420949 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1420898 CGATGCTTTG
*
1420908 ATTTTTTTTTTTTTAATTTTAA
1 ATTTTTTTTTGTTTAATTTTAA
1420930 ATTTTTTTATTGTTT-ATTTT
1 ATTTTTTT-TTGTTTAATTTT
1420950 GTATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (22 bp):
ATTTTTTTTTGTTTAATTTTAA
Found at i:1422103 original size:17 final size:18
Alignment explanation
Indices: 1422060--1422097 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1422050 TTTAATAAAT
* *
1422060 TTAAGATAATATAATTAC
1 TTAAGTTAAGATAATTAC
1422078 TTAAGTTAAGATAA-TAC
1 TTAAGTTAAGATAATTAC
1422095 TTA
1 TTA
1422098 GATTAATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (18 bp):
TTAAGTTAAGATAATTAC
Found at i:1425868 original size:16 final size:16
Alignment explanation
Indices: 1425826--1425869 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1425816 TTTATTTAAT
1425826 AATATTTAATAATTTTA
1 AATATTTAAT-ATTTTA
*
1425843 AAT-TTTAATATTTTC
1 AATATTTAATATTTTA
*
1425858 AATATTAAATAT
1 AATATTTAATAT
1425870 CATGGTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 13 0.54
17 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTTAATATTTTA
Found at i:1426881 original size:16 final size:15
Alignment explanation
Indices: 1426845--1426873 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1426835 TAATCTAATT
1426845 AAATTTAAAAGAAAA
1 AAATTTAAAAGAAAA
1426860 AAATTTAAAA-AAAA
1 AAATTTAAAAGAAAA
1426874 TAACATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATTTAAAAGAAAA
Found at i:1427906 original size:3 final size:3
Alignment explanation
Indices: 1427900--1427940 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1427890 TACTACAACC
1427900 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1427941 ATTGTGCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1428881 original size:47 final size:46
Alignment explanation
Indices: 1428814--1428906 Score: 102
Period size: 47 Copynumber: 2.0 Consensus size: 46
1428804 TTATCAATTA
1428814 ATTTTATTTTTTATAAAATT-ATTAAAAATATAATTTTTTATT-TTAAT
1 ATTTTATTTTTTAT-AAATTAATTAAAAAT-T-ATTTTTTATTATTAAT
**
1428861 ATTTATATATTTTTAT-AATTAATTTTAAATTATTTTTTATTATTAA
1 ATTT-TAT-TTTTTATAAATTAATTAAAAATTATTTTTTATTATTAA
1428907 AAAATAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
46 10 0.25
47 13 0.32
48 10 0.25
49 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (46 bp):
ATTTTATTTTTTATAAATTAATTAAAAATTATTTTTTATTATTAAT
Found at i:1428897 original size:24 final size:23
Alignment explanation
Indices: 1428846--1428906 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 23
1428836 TAAAAATATA
* *
1428846 ATTTTTTATTTTAATATTTATAT
1 ATTTTTTATATTAATATTTAAAT
1428869 A-TTTTTATAATTAAT-TTTAAATT
1 ATTTTTTAT-ATTAATATTTAAA-T
1428892 ATTTTTTATTATTAA
1 ATTTTTTA-TATTAA
1428907 AAAATAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 12 0.38
23 8 0.25
24 11 0.34
25 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTTTTATATTAATATTTAAAT
Found at i:1430974 original size:21 final size:20
Alignment explanation
Indices: 1430950--1431011 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
1430940 TATTTAAGTT
*
1430950 TGATTCATTTAAAATTAAATA
1 TGATTAATTT-AAATTAAATA
* *
1430971 TGATTAAATTTAATTTAAATT
1 TGATT-AATTTAAATTAAATA
* *
1430992 TAATTTATTTAAATTAAATA
1 TGATTAATTTAAATTAAATA
1431012 AATTTATTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 12 0.36
21 17 0.52
22 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (20 bp):
TGATTAATTTAAATTAAATA
Found at i:1430990 original size:11 final size:11
Alignment explanation
Indices: 1430974--1431010 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1430964 TTAAATATGA
1430974 TTAAATTTAAT
1 TTAAATTTAAT
1430985 TTAAATTTAAT
1 TTAAATTTAAT
*
1430996 TT--ATTTAAA
1 TTAAATTTAAT
1431005 TTAAAT
1 TTAAAT
1431011 AAATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:1431001 original size:20 final size:19
Alignment explanation
Indices: 1430978--1431021 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1430968 ATATGATTAA
* *
1430978 ATTTAATTTAAATTTAATTT
1 ATTTAAATTAAA-TAAATTT
1430998 ATTTAAATTAAATAAATTT
1 ATTTAAATTAAATAAATTT
1431017 ATTTA
1 ATTTA
1431022 TAAACAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAAATTAAATAAATTT
Found at i:1431003 original size:15 final size:16
Alignment explanation
Indices: 1430977--1431006 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1430967 AATATGATTA
1430977 AATTTAATTTAAATTT
1 AATTTAATTTAAATTT
1430993 AATTT-ATTTAAATT
1 AATTTAATTTAAATT
1431007 AAATAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTAATTTAAATTT
Found at i:1431193 original size:18 final size:19
Alignment explanation
Indices: 1431153--1431201 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1431143 ATTATATTGA
*
1431153 TAAATATATGAAATAATATT
1 TAAATATAT-TAATAATATT
*
1431173 TAAATATATTAATATTA-T
1 TAAATATATTAATAATATT
*
1431191 TAATTATATTA
1 TAAATATATTA
1431202 TTTTCTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 6 0.23
20 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TAAATATATTAATAATATT
Found at i:1433926 original size:2 final size:2
Alignment explanation
Indices: 1433919--1433949 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1433909 TATTCTGTGC
1433919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1433950 AAACTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1435539 original size:12 final size:13
Alignment explanation
Indices: 1435512--1435544 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1435502 AGACTTATTT
1435512 AAAGAAAAAGAAG
1 AAAGAAAAAGAAG
*
1435525 AAAGAAAGA-AAG
1 AAAGAAAAAGAAG
1435537 AAAGAAAA
1 AAAGAAAA
1435545 GATTTACCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAG
Found at i:1437152 original size:17 final size:17
Alignment explanation
Indices: 1437132--1437165 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1437122 TAATTTCATC
1437132 TTAT-TATTATTTTAATT
1 TTATATATT-TTTTAATT
1437149 TTATATATTTTTTAATT
1 TTATATATTTTTTAATT
1437166 AAATTGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATATATTTTTTAATT
Found at i:1437997 original size:14 final size:14
Alignment explanation
Indices: 1437961--1437998 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1437951 ATTAAATTTT
1437961 TTATTTATAA-AAA
1 TTATTTATAATAAA
* *
1437974 GTATTAATAATAAA
1 TTATTTATAATAAA
1437988 TTATTTATAAT
1 TTATTTATAAT
1437999 GATAATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TTATTTATAATAAA
Found at i:1439899 original size:30 final size:30
Alignment explanation
Indices: 1439855--1439911 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
1439845 ATTGTAATTT
1439855 AATTTTTAAATTTATATTTAAATAAATTATG
1 AATTTTTAAATTTATA-TTAAATAAATTATG
1439886 AATTTTT-AATTTATATTAAATAAATT
1 AATTTTTAAATTTATATTAAATAAATT
1439912 GTCAGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.42
30 8 0.31
31 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
AATTTTTAAATTTATATTAAATAAATTATG
Found at i:1439921 original size:30 final size:29
Alignment explanation
Indices: 1439855--1439941 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 29
1439845 ATTGTAATTT
*
1439855 AATTTTTAAATTTATATTTAAATAAATTATG
1 AATTTTT-AATTTATA-TTAAATAAATTATC
*
1439886 AATTTTTAATTTATATTAAATAAATTGTC
1 AATTTTTAATTTATATTAAATAAATTATC
* *
1439915 AGA-TTTTAACTTACATCTAAATAAATT
1 A-ATTTTTAATTTATAT-TAAATAAATT
1439942 TTTAATATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
29 24 0.48
30 19 0.38
31 7 0.14
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (29 bp):
AATTTTTAATTTATATTAAATAAATTATC
Found at i:1446230 original size:11 final size:11
Alignment explanation
Indices: 1446214--1446238 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1446204 CTCATTTGTA
1446214 TTATTAAAAAC
1 TTATTAAAAAC
1446225 TTATTAAAAAC
1 TTATTAAAAAC
1446236 TTA
1 TTA
1446239 AGTAATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
TTATTAAAAAC
Found at i:1447545 original size:3 final size:3
Alignment explanation
Indices: 1447537--1447566 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1447527 ACAAATACTC
1447537 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1447567 CTATAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1447656 original size:4 final size:4
Alignment explanation
Indices: 1447649--1447708 Score: 79
Period size: 4 Copynumber: 15.5 Consensus size: 4
1447639 TGGGCAGCTG
*
1447649 AGAA AGAA AGAA AGAA AGAA AGAA AAAA AGAA AGAA AG-A A-AA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
* *
1447695 AAAA AGAG AGAA AG
1 AGAA AGAA AGAA AG
1447709 GGAAATAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 4 0.08
4 44 0.92
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1447718 original size:22 final size:22
Alignment explanation
Indices: 1447651--1447718 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
1447641 GGCAGCTGAG
1447651 AAAGAAAGAAAGAAAGAAAGAAAA
1 AAAGAAAGAAAG--AGAAAGAAAA
*
1447675 AAAGAAAGAAAGAAAAAGAAAA
1 AAAGAAAGAAAGAGAAAGAAAA
* * *
1447697 AAAGAGAGAAAGGGAAATAAAA
1 AAAGAAAGAAAGAGAAAGAAAA
1447719 GAAAAAGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 27 0.69
24 12 0.31
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (22 bp):
AAAGAAAGAAAGAGAAAGAAAA
Found at i:1447749 original size:6 final size:6
Alignment explanation
Indices: 1447738--1447762 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1447728 AAGAAATTTA
1447738 TGTATT TGTATT TGTATT TGTATT T
1 TGTATT TGTATT TGTATT TGTATT T
1447763 TTTATGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TGTATT
Found at i:1449006 original size:15 final size:16
Alignment explanation
Indices: 1448986--1449021 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1448976 TTTTAAATAC
*
1448986 ATTTTA-TTAATTATA
1 ATTTTATTTAATTAAA
1449001 ATTTTATTTAATTAAA
1 ATTTTATTTAATTAAA
1449017 ATTTT
1 ATTTT
1449022 TATAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTATTTAATTAAA
Found at i:1452112 original size:10 final size:10
Alignment explanation
Indices: 1452086--1452142 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 10
1452076 ATATTTTAAT
*
1452086 ATTTATATTG
1 ATTTATATTA
1452096 A-TTATATTA
1 ATTTATATTA
1452105 ATTTATATTA
1 ATTTATATTA
**
1452115 ATCAATATTA
1 ATTTATATTA
**
1452125 ATCGATATTA
1 ATTTATATTA
*
1452135 TTTTATAT
1 ATTTATAT
1452143 AGATTAGTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
9 8 0.21
10 31 0.79
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (10 bp):
ATTTATATTA
Found at i:1452124 original size:20 final size:19
Alignment explanation
Indices: 1452086--1452126 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1452076 ATATTTTAAT
* *
1452086 ATTTATATTGATTATATTA
1 ATTTATATTAATAATATTA
1452105 ATTTATATTAATCAATATTA
1 ATTTATATTAAT-AATATTA
1452125 AT
1 AT
1452127 CGATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTTATATTAATAATATTA
Found at i:1452460 original size:11 final size:10
Alignment explanation
Indices: 1452432--1452482 Score: 54
Period size: 9 Copynumber: 5.3 Consensus size: 10
1452422 ATATATATTT
1452432 TATTAAAATA
1 TATTAAAATA
1452442 T-TTAAAATA
1 TATTAAAATA
1452451 TATTATAAATA
1 TATTA-AAATA
*
1452462 TA-TATAATA
1 TATTAAAATA
*
1452471 T-TTAAAAAA
1 TATTAAAATA
1452480 TAT
1 TAT
1452483 AACACATGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
9 20 0.59
10 7 0.21
11 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATTAAAATA
Found at i:1453004 original size:29 final size:28
Alignment explanation
Indices: 1452960--1453031 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
1452950 TTACTAGAAC
*
1452960 TAAAATTAT-TAGATTTATAAATAAAATAA
1 TAAAATTATATATATTTATAAA-AAAA-AA
*
1452989 T-AAATTATATATATTTATAAAAATAAA
1 TAAAATTATATATATTTATAAAAAAAAA
1453016 TAAAATTATGATATAT
1 TAAAATTAT-ATATAT
1453032 GATTTTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 3 0.08
28 17 0.45
29 18 0.47
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
TAAAATTATATATATTTATAAAAAAAAA
Found at i:1453057 original size:3 final size:3
Alignment explanation
Indices: 1453043--1453072 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1453033 ATTTTTTAAT
*
1453043 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1453073 AAATTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1455021 original size:16 final size:16
Alignment explanation
Indices: 1455000--1455064 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
1454990 TTTTATTTAT
1455000 AATTTAAATTAAATTA
1 AATTTAAATTAAATTA
*
1455016 AATTTAAA-TAAAATA
1 AATTTAAATTAAATTA
* *
1455031 AATATT-ATTTAATTTAA
1 AAT-TTAAATTAAATT-A
*
1455048 AATTTAAATTAATTTA
1 AATTTAAATTAAATTA
1455064 A
1 A
1455065 TTAAACTCGA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
15 10 0.25
16 18 0.45
17 12 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAAATTAAATTA
Found at i:1455479 original size:14 final size:14
Alignment explanation
Indices: 1455460--1455486 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1455450 TTTATGAAGG
1455460 AAAATATAATTATA
1 AAAATATAATTATA
1455474 AAAATATAATTAT
1 AAAATATAATTAT
1455487 TTTTGAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATATAATTATA
Found at i:1455801 original size:18 final size:18
Alignment explanation
Indices: 1455778--1455815 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1455768 CAAAACTCAA
*
1455778 AATTTTTTTAAATATTAT
1 AATTTTTTAAAATATTAT
*
1455796 AATTTTTTAAAATTTTAT
1 AATTTTTTAAAATATTAT
1455814 AA
1 AA
1455816 AAATAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTTTTAAAATATTAT
Found at i:1459503 original size:20 final size:19
Alignment explanation
Indices: 1459474--1459548 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
1459464 AAAAAGAGAT
1459474 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
1459493 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
1459514 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
1459534 AATGTATCGATACAT
1 AATGTATCGATACAT
1459549 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:1462084 original size:16 final size:16
Alignment explanation
Indices: 1462065--1462106 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1462055 GATTTGAATT
*
1462065 ATTTTGAGTTTAAATC
1 ATTTTGAGTTTAAATA
1462081 ATTTTG-GATTTAAATA
1 ATTTTGAG-TTTAAATA
*
1462097 ATTTCGAGTT
1 ATTTTGAGTT
1462107 CATGTCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (16 bp):
ATTTTGAGTTTAAATA
Found at i:1462106 original size:32 final size:32
Alignment explanation
Indices: 1462050--1462124 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1462040 AGTTTGATTT
* * * *
1462050 TTTTAGATTTGAATTATTTTGAGTTTAAATCA
1 TTTTAGATTTAAATAATTTCGAGTTCAAATCA
* **
1462082 TTTTGGATTTAAATAATTTCGAGTTCATGTCA
1 TTTTAGATTTAAATAATTTCGAGTTCAAATCA
1462114 TTTTAGATTTA
1 TTTTAGATTTA
1462125 GTTTAATTTC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.52
Consensus pattern (32 bp):
TTTTAGATTTAAATAATTTCGAGTTCAAATCA
Found at i:1463176 original size:12 final size:12
Alignment explanation
Indices: 1463145--1463169 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1463135 GAAAACAAAG
1463145 GCTGCCAACTGT
1 GCTGCCAACTGT
1463157 GCTGCCAACTGT
1 GCTGCCAACTGT
1463169 G
1 G
1463170 TCGCCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:1463213 original size:27 final size:27
Alignment explanation
Indices: 1463175--1463227 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1463165 CTGTGTCGCC
*
1463175 AATTTTGAAATTCAATTTGAAACAGTA
1 AATTATGAAATTCAATTTGAAACAGTA
*
1463202 AATTATGAAATTTAATTTGAAACAGT
1 AATTATGAAATTCAATTTGAAACAGT
1463228 GAAGGTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (27 bp):
AATTATGAAATTCAATTTGAAACAGTA
Found at i:1466021 original size:18 final size:18
Alignment explanation
Indices: 1466000--1466040 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1465990 AATGGAGATT
1466000 GAAGAGCCAGTTATCGAA
1 GAAGAGCCAGTTATCGAA
1466018 GAAGAGCCAGTTATCGAA
1 GAAGAGCCAGTTATCGAA
1466036 GAAGA
1 GAAGA
1466041 AGAAATTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.15
Consensus pattern (18 bp):
GAAGAGCCAGTTATCGAA
Found at i:1469069 original size:22 final size:22
Alignment explanation
Indices: 1469022--1469075 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1469012 AGTTTAGAGT
1469022 ATTTTAAATT--AATTATTTAA
1 ATTTTAAATTAAAATTATTTAA
*
1469042 ATTTTAACTTAAAATTATTTTAA
1 ATTTTAAATTAAAATTA-TTTAA
1469065 A-TTTAAATTAA
1 ATTTTAAATTAA
1469076 TTTGAGTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 9 0.31
22 14 0.48
23 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTTAAATTAAAATTATTTAA
Found at i:1469078 original size:17 final size:17
Alignment explanation
Indices: 1469022--1469078 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 17
1469012 AGTTTAGAGT
*
1469022 ATTTTAAATTAATTATTTAA
1 ATTTTAAATTAA--AATT-A
*
1469042 ATTTTAACTTAAAATT-
1 ATTTTAAATTAAAATTA
*
1469058 ATTTTAAATTTAAATTA
1 ATTTTAAATTAAAATTA
1469075 ATTT
1 ATTT
1469079 GAGTTCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 14 0.44
17 4 0.12
18 3 0.09
20 11 0.34
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTAAATTAAAATTA
Found at i:1470757 original size:22 final size:21
Alignment explanation
Indices: 1470715--1470755 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1470705 GAATTTGTAA
1470715 TATTTATTAAATATTTAAAAT
1 TATTTATTAAATATTTAAAAT
*
1470736 TATTATATT-AATTTTTAAAA
1 TATT-TATTAAATATTTAAAA
1470756 ATAAACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTTATTAAATATTTAAAAT
Found at i:1471082 original size:2 final size:2
Alignment explanation
Indices: 1471075--1471117 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1471065 TACATTAGTT
1471075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1471117 T
1 T
1471118 TGAGGTGAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1473444 original size:149 final size:150
Alignment explanation
Indices: 1473232--1473521 Score: 399
Period size: 149 Copynumber: 1.9 Consensus size: 150
1473222 TTAACAGATC
**
1473232 GATTGTCATGAGATATTGTAACGATAAACTTAGAAAGTGATACAATGACCTAACCTAAAACCTAA
1 GATTGTCATGAGATATTACAACGATAAACTTAGAAAGTGATACAATGACCTAACCTAAAACCTAA
* * *
1473297 ATTCTAAG-TTCTACTTAAATCAGGTAATCAAGTGGTCTTAATTTTT-TAAATAAATTAAAATTC
66 ATTCT-AGCTTCTACTTAAATCAAGTAATCAAGTGGCCTTAATTTTTAAAAATAAATTAAAATTC
1473360 ATCTTACTTCCTCGTTAAATA
130 ATCTTACTTCCTCGTTAAATA
* ** * *
1473381 GATTGTCATGAGATATTACAACGATAAA-TCTAGAAGGT-AGTGTAATGGCTTAACCTAAAACCT
1 GATTGTCATGAGATATTACAACGATAAACT-TAGAAAGTGA-TACAATGACCTAACCTAAAACCT
* * *
1473444 AAGTTCTAGCTTCTACTTAAATCAAGTAATTAAGTGGCCTTAATTTTTAAAAAATAGATTAAAAT
64 AAATTCTAGCTTCTACTTAAATCAAGTAATCAAGTGGCCTTAATTTTT-AAAAATAAATTAAAAT
1473509 TCATCTTACTTCC
128 TCATCTTACTTCC
1473522 CCTTTAAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
148 4 0.03
149 93 0.76
151 26 0.21
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (150 bp):
GATTGTCATGAGATATTACAACGATAAACTTAGAAAGTGATACAATGACCTAACCTAAAACCTAA
ATTCTAGCTTCTACTTAAATCAAGTAATCAAGTGGCCTTAATTTTTAAAAATAAATTAAAATTCA
TCTTACTTCCTCGTTAAATA
Found at i:1474047 original size:17 final size:17
Alignment explanation
Indices: 1474006--1474049 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1473996 TATCTTGTTT
*
1474006 TAAATAAATATTTACTC
1 TAAATAAATATATACTC
*
1474023 -AAATTAAATATATATTC
1 TAAA-TAAATATATACTC
1474040 TAAATAAATA
1 TAAATAAATA
1474050 ACATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAAATATATACTC
Found at i:1474194 original size:23 final size:23
Alignment explanation
Indices: 1474164--1474210 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1474154 AATAATCCGA
1474164 TGGATAACTATCCATTACAGAAT
1 TGGATAACTATCCATTACAGAAT
1474187 TGGATAACTATCCATTACAGAAT
1 TGGATAACTATCCATTACAGAAT
1474210 T
1 T
1474211 ATGTTGAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (23 bp):
TGGATAACTATCCATTACAGAAT
Found at i:1475212 original size:25 final size:26
Alignment explanation
Indices: 1475165--1475215 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1475155 AATAAAAAAC
* *
1475165 TTCAAATATATAAATATGAACAATCAA
1 TTCAAATATAAAAAAAT-AACAATCAA
1475192 TTCAAATATAAAAAAAT-ACAATCA
1 TTCAAATATAAAAAAATAACAATCA
1475216 TAATATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
27 15 0.68
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (26 bp):
TTCAAATATAAAAAAATAACAATCAA
Found at i:1476794 original size:17 final size:16
Alignment explanation
Indices: 1476754--1476800 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1476744 TAGTAATCCA
1476754 TATATTAATATTGTA-GT
1 TATATTAAT-TT-TATGT
1476771 TATATTAATTTTATGT
1 TATATTAATTTTATGT
*
1476787 TATAATTATTTTTA
1 TAT-ATTAATTTTA
1476801 AATAATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 7 0.26
17 18 0.67
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
TATATTAATTTTATGT
Found at i:1476837 original size:15 final size:14
Alignment explanation
Indices: 1476819--1476901 Score: 54
Period size: 15 Copynumber: 6.2 Consensus size: 14
1476809 TTTATTTATG
1476819 TAATTTTTAATATAA
1 TAATTTTTAATAT-A
* *
1476834 TAATTTTTTATATT
1 TAATTTTTAATATA
1476848 TAATTTATT-ATATA
1 TAATTT-TTAATATA
*
1476862 -AA-TTTTGATATAA
1 TAATTTTTAATAT-A
*
1476875 TAAATTTT-A-ATA
1 TAATTTTTAATATA
1476887 -AATTTTTAATA-A
1 TAATTTTTAATATA
1476899 TAA
1 TAA
1476902 ACATCGATCA
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
11 8 0.14
12 9 0.16
13 8 0.14
14 13 0.23
15 18 0.32
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (14 bp):
TAATTTTTAATATA
Found at i:1476840 original size:42 final size:42
Alignment explanation
Indices: 1476787--1476884 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 42
1476777 AATTTTATGT
* * *
1476787 TATAATTATTTTTAAATAATT-ATTTATTTATGTAATTTTTAA
1 TATAATAATTTTTAAATAATTAATTTA-TTATATAAATTTTAA
* * *
1476829 TATAATAATTTTT-TATATTTAATTTATTATATAAATTTTGA
1 TATAATAATTTTTAAATAATTAATTTATTATATAAATTTTAA
*
1476870 TATAATAAATTTTAA
1 TATAATAATTTTTAA
1476885 TAAATTTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
41 29 0.63
42 17 0.37
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (42 bp):
TATAATAATTTTTAAATAATTAATTTATTATATAAATTTTAA
Found at i:1476851 original size:14 final size:15
Alignment explanation
Indices: 1476788--1476882 Score: 58
Period size: 14 Copynumber: 6.5 Consensus size: 15
1476778 ATTTTATGTT
1476788 ATAATTATTTT-TA-A
1 ATAATT-TTTTATATA
* *
1476802 ATAATTATTTATTTA
1 ATAATTTTTTATATA
* *
1476817 TGTAATTTTTAATATA
1 -ATAATTTTTTATATA
1476833 ATAATTTTTTATAT-
1 ATAATTTTTTATATA
* *
1476847 TTAATTTATTATAT-
1 ATAATTTTTTATATA
*
1476861 A-AA-TTTTGATATA
1 ATAATTTTTTATATA
1476874 ATAAATTTT
1 AT-AATTTT
1476883 AATAAATTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
12 7 0.11
13 6 0.10
14 19 0.31
15 15 0.25
16 14 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
ATAATTTTTTATATA
Found at i:1476861 original size:29 final size:31
Alignment explanation
Indices: 1476801--1476862 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
1476791 ATTATTTTTA
*
1476801 AATAATTATTTATTTATGTAATTTTTAATAT
1 AATAATTATTTATATATGTAATTTTTAATAT
*
1476832 AATAATT-TTT-TATATTTAATTTATT-ATAT
1 AATAATTATTTATATATGTAATTT-TTAATAT
1476861 AA
1 AA
1476863 ATTTTGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 16 0.57
30 5 0.18
31 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
AATAATTATTTATATATGTAATTTTTAATAT
Found at i:1477046 original size:50 final size:50
Alignment explanation
Indices: 1476992--1477280 Score: 375
Period size: 50 Copynumber: 5.8 Consensus size: 50
1476982 AAGTATTGTC
* **
1476992 ATTGTTGACTATTCTTCACTAACCTTTGACAATCGAGAGAGGTAACTATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCTATA
* * ** **
1477042 ATTGTTGACTATTCTTCACCAACATTTGACAATTGAGAGAGGTAACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCTATA
* *
1477092 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTTATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCTATA
* * * * *
1477142 ATTATTGACTATTCTTCACCTACCTTTAACAATTGAGAGAGGTGGCTGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCTATA
* *
1477192 ATTGTTGA-TGATT-TTCATCAACCTTTGACAATCGAGAGAGGTGGCCATA
1 ATTGTTGACT-ATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCTATA
* *
1477241 ATTGTTGACTATTCTTCCCCAACCTTTGACAATCAAGAGA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGA
1477281 AGTGACCGTA
Statistics
Matches: 206, Mismatches: 30, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
49 42 0.20
50 164 0.80
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCTATA
Found at i:1477174 original size:100 final size:100
Alignment explanation
Indices: 1476992--1477299 Score: 429
Period size: 100 Copynumber: 3.1 Consensus size: 100
1476982 AAGTATTGTC
* * **
1476992 ATTGTTGACTATTCTTCACTAACCTTTGACAATCGAGAGAGGTAACTATAATTGTTGACTATTCT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCTATAATTGTTGACTATTCT
* *
1477057 TCACCAACATTTGACAATTGAGAGAGGTAACCGTA
66 TCACCAACCTTTGACAATTGAGAGAGGTGACCGTA
* *
1477092 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTTATAATTATTGACTATTCT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCTATAATTGTTGACTATTCT
* * * *
1477157 TCACCTACCTTTAACAATTGAGAGAGGTGGCTGTA
66 TCACCAACCTTTGACAATTGAGAGAGGTGACCGTA
* * *
1477192 ATTGTTGATGATT-TTCATCAACCTTTGACAATCGAGAGAGGTGGCCATAATTGTTGACTATTCT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCTATAATTGTTGACTATTCT
* ** *
1477256 TCCCCAACCTTTGACAATCAAGAGAAGTGACCGTA
66 TCACCAACCTTTGACAATTGAGAGAGGTGACCGTA
*
1477291 ATGGTTGAC
1 ATTGTTGAC
1477300 TTTAAGCAAC
Statistics
Matches: 181, Mismatches: 27, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
99 81 0.45
100 100 0.55
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (100 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCTATAATTGTTGACTATTCT
TCACCAACCTTTGACAATTGAGAGAGGTGACCGTA
Found at i:1483715 original size:16 final size:16
Alignment explanation
Indices: 1483694--1483748 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
1483684 CATTTCATAT
1483694 TTTTTCTTTTTTTTTC
1 TTTTTCTTTTTTTTTC
*
1483710 TTTTTCTTTCTTTCTTC
1 TTTTTCTTT-TTTTTTC
* *
1483727 TTTATCTTCTTTCTTTC
1 TTTTTCTT-TTTTTTTC
1483744 TTTTT
1 TTTTT
1483749 TACCTAACTC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 9 0.28
17 22 0.69
18 1 0.03
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTC
Found at i:1483719 original size:20 final size:22
Alignment explanation
Indices: 1483696--1483749 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 22
1483686 TTTCATATTT
1483696 TTTCTTTTTTTT-TCTT-TTTC
1 TTTCTTTTTTTTATCTTCTTTC
1483716 TTTCTTTCTTCTTTATCTTCTTTC
1 TTTCTTT-TT-TTTATCTTCTTTC
1483740 TTTCTTTTTT
1 TTTCTTTTTT
1483750 ACCTAACTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.23
21 2 0.07
22 4 0.13
23 6 0.20
24 11 0.37
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTCTTTTTTTTATCTTCTTTC
Found at i:1483750 original size:20 final size:20
Alignment explanation
Indices: 1483713--1483750 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1483703 TTTTTTCTTT
1483713 TTCTTTCTTTCTTCTTTATC
1 TTCTTTCTTTCTTCTTTATC
*
1483733 TTCTTTCTTTCTTTTTTA
1 TTCTTTCTTTCTTCTTTA
1483751 CCTAACTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (20 bp):
TTCTTTCTTTCTTCTTTATC
Found at i:1485289 original size:50 final size:50
Alignment explanation
Indices: 1485226--1485685 Score: 546
Period size: 50 Copynumber: 9.2 Consensus size: 50
1485216 AGATGTTGTC
*
1485226 ATTGTTGACTATTCTTCACCAATCTTTGACAATCGAGAGAGGTGATCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGATCATA
* * *
1485276 ATTGTTAATTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGATCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGATCATA
* * *
1485326 ATTGTTGACTATTTTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGATCATA
* * * *
1485376 ATTGTTGACGATTCTTCACCGACCTTTGACAATTGAGAGAGGT-AGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGA-TCATA
* * * *
1485426 ATTGTTGACTATTCTTCACAAACTTTTGACAATCGAGAGAGGTGGTCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGATCATA
* * * * * * *
1485476 ATTGTTGACAATTTTTTATCAACCTTTGACAATTGAGAAAGGTGACCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGATCATA
* * * *
1485526 ATTGTTGACTATTCTTCTCCAACCTTTGATAATCGAGATAGGTGGTCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGATCATA
* * * * * * *
1485576 ATTGTT-AATAATTTTTTATCAACCTTTGACAATTGAGAAAGGTGACCATA
1 ATTGTTGACT-ATTCTTCACCAACCTTTGACAATCGAGAGAGGTGATCATA
* * * *
1485626 ATTGTTGACTATTCTTCATCAACTTTTGATAATCGAGAGAGGTGATCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGATCATA
*
1485676 ATTATTGACT
1 ATTGTTGACT
1485686 CTAAGCAACT
Statistics
Matches: 344, Mismatches: 62, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
49 3 0.01
50 339 0.99
51 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGATCATA
Found at i:1487908 original size:84 final size:84
Alignment explanation
Indices: 1487775--1487937 Score: 245
Period size: 84 Copynumber: 1.9 Consensus size: 84
1487765 TTTTAAAAGC
** * *
1487775 ATTAAATTTTAAATTCAAATTTCAAAACGTAACCTAATTTCAGTCCATCAATTAATTACATATAC
1 ATTAAATTTTAAATTCAAATTAAAAAACGTAACCTAATTTCAATCCATCAATTAATCACATATAC
1487840 ATAATTAAGTTTTACATTT
66 ATAATTAAGTTTTACATTT
* ** * *
1487859 ATTAAATTTTAAGTTTGAATTAAAAAACGTAGCCTAATTTCAATTCATCAATTAATCACATATAC
1 ATTAAATTTTAAATTCAAATTAAAAAACGTAACCTAATTTCAATCCATCAATTAATCACATATAC
1487924 ATAATTAAGTTTTA
66 ATAATTAAGTTTTA
1487938 AAGTTAGAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (84 bp):
ATTAAATTTTAAATTCAAATTAAAAAACGTAACCTAATTTCAATCCATCAATTAATCACATATAC
ATAATTAAGTTTTACATTT
Found at i:1488738 original size:21 final size:21
Alignment explanation
Indices: 1488704--1488743 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1488694 ATATTTTATT
1488704 TAAATTTAATTATAAAATACA
1 TAAATTTAATTATAAAATACA
1488725 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
1488744 TTTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAATTATAAAATACA
Found at i:1490683 original size:20 final size:21
Alignment explanation
Indices: 1490640--1490687 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1490630 TTATATAATA
1490640 ATATTTATTAAAAAATTATTT
1 ATATTTATTAAAAAATTATTT
**
1490661 ATATTTATTTTAAAATT-TTT
1 ATATTTATTAAAAAATTATTT
1490681 ATATTTA
1 ATATTTA
1490688 CTTATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTTATTAAAAAATTATTT
Found at i:1492402 original size:23 final size:23
Alignment explanation
Indices: 1492372--1492419 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1492362 CAATCTTACC
1492372 AAGAGATAAGATGCTTAGCGTGG
1 AAGAGATAAGATGCTTAGCGTGG
1492395 AAGAGATAAGATGCTTAGCGTGG
1 AAGAGATAAGATGCTTAGCGTGG
1492418 AA
1 AA
1492420 CTATCATGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (23 bp):
AAGAGATAAGATGCTTAGCGTGG
Found at i:1498111 original size:80 final size:79
Alignment explanation
Indices: 1497993--1498200 Score: 238
Period size: 80 Copynumber: 2.6 Consensus size: 79
1497983 GAGATAATAA
* * * * * * *
1497993 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
1498058 -TTAGAAAAAAAAAAT
65 TTTAG-AAAAAAAAAC
* *
1498073 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* ** * *
1498138 TTTGGGAATAAAGC
66 TTAGAAAAAAAAAC
* *
1498152 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1498201 GAAATAACAA
Statistics
Matches: 108, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
79 51 0.47
80 57 0.53
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:1498208 original size:28 final size:28
Alignment explanation
Indices: 1498152--1498223 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1498142 GGAATAAAGC
** *
1498152 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1498180 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
1498208 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1498224 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1498343 original size:52 final size:52
Alignment explanation
Indices: 1498212--1498550 Score: 162
Period size: 52 Copynumber: 6.4 Consensus size: 52
1498202 AAATAACAAG
* * * * *
1498212 GTTGGAGTATCCTCGACTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGG-AGTTTTGAAAATAAAACCGGA
* ** *
1498264 GTTGGACTATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGGAAAAATTGGAGTTTTGAAAATAAAACC-GGA
* * **
1498317 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGA-AAATAAAACCGGA
* * ** ** * *
1498368 GTTGGAGTATCCCC---T-CGAAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGGAAA-AA-----TTGGAGT-T--TTGAAAATAAAACCGGA
* * * *
1498423 GTTTGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAA-AAATTGGAG--TTTTGAAAATAAAACCGGA
* * * * * *
1498477 GTTAGAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGAAAATAAAACCGGA
*
1498528 GTTGGAATATCCCCGATTGTGGA
1 GTTGGAGTATCCCCGATTGTGGA
1498551 GAATTGATAA
Statistics
Matches: 216, Mismatches: 44, Indels: 54
0.69 0.14 0.17
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
51 42 0.19
52 81 0.38
53 26 0.12
54 29 0.13
55 19 0.09
56 2 0.01
57 3 0.01
58 6 0.03
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGAAAATAAAACCGGA
Found at i:1498400 original size:28 final size:28
Alignment explanation
Indices: 1498355--1498436 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 28
1498345 AGTGTTTTAG
* *
1498355 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
1498382 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* * *
1498409 CGATGATTAACGGGGTTTGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
1498437 GATTGTGAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
26 3 0.07
27 23 0.50
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:1498504 original size:212 final size:212
Alignment explanation
Indices: 1498145--1498550 Score: 602
Period size: 212 Copynumber: 1.9 Consensus size: 212
1498135 TATTTTGGGA
* * * *
1498145 ATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACA
1 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACA
* *
1498210 AGGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGACTATC
66 AGGTTGGAGTATCCCCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGACTATC
* *
1498275 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGA
131 CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGA
1498339 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
* *
1498357 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACA
* * * * *
1498421 GGGTTTGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATCCCCGACTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGACTA
* * *
1498486 TCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGG
129 TCCCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGG
1498550 A
194 A
1498551 GAATTGATAA
Statistics
Matches: 173, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
211 29 0.17
212 106 0.61
213 38 0.22
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACA
AGGTTGGAGTATCCCCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGACTATC
CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:1498523 original size:51 final size:53
Alignment explanation
Indices: 1498427--1498545 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
1498417 AACGGGGTTT
* * *
1498427 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
1498481 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
1498532 GAATATCCCCGATT
1 GAGTATCCCCGATT
1498546 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Done.