Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold78
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: 2238306
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 23262 characters in sequence are not A, C, G, or T
File 10 of 15
Found at i:1356258 original size:16 final size:17
Alignment explanation
Indices: 1356239--1356280 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1356229 TGAAAAACTA
*
1356239 AATAAAAGAAAAT-AAT
1 AATAAAAAAAAATAAAT
1356255 AATAAACTAAAAAATAAAT
1 AATAAA--AAAAAATAAAT
1356274 AATAAAA
1 AATAAAA
1356281 TATTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 6 0.27
17 1 0.05
18 6 0.27
19 9 0.41
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (17 bp):
AATAAAAAAAAATAAAT
Found at i:1356277 original size:25 final size:24
Alignment explanation
Indices: 1356233--1356282 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
1356223 TATAAATGAA
1356233 AAACTAAATAAAAGAAAATAATAAT
1 AAACTAAATAAAAGAAAATAA-AAT
1356258 AAACTAAA-AAATA-AATAATAAAAT
1 AAACTAAATAAA-AGAA-AATAAAAT
1356282 A
1 A
1356283 TTAAAATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (24 bp):
AAACTAAATAAAAGAAAATAAAAT
Found at i:1356415 original size:22 final size:21
Alignment explanation
Indices: 1356375--1356415 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1356365 GAGTTTTAAT
* *
1356375 TTATTTATAAATATTTTTCGA
1 TTATTTATAAAAATATTTCGA
1356396 TTATCTTATAAAAATATTTC
1 TTAT-TTATAAAAATATTTC
1356416 TCTTAATCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (21 bp):
TTATTTATAAAAATATTTCGA
Found at i:1357258 original size:21 final size:21
Alignment explanation
Indices: 1357234--1357274 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1357224 TAAAAATTAT
1357234 TAAAAATAAATAAAATTTAAA
1 TAAAAATAAATAAAATTTAAA
**
1357255 TAAAAATATTTAAAATTTAA
1 TAAAAATAAATAAAATTTAA
1357275 TTATTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAAATAAATAAAATTTAAA
Found at i:1357265 original size:41 final size:41
Alignment explanation
Indices: 1357171--1357269 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 41
1357161 AAAAAATACG
1357171 AAAAATATTTAAATAATTATATAATTTAAATATAATAAATAAAT
1 AAAAATATTTAAA-AATTATATAA--TAAATATAATAAATAAAT
*
1357215 AAAATTATTTAAAAATTAT-TAA-AAATA-AATAAAATTTAAAT
1 AAAAATATTTAAAAATTATATAATAAATATAAT-AAA--TAAAT
1357256 AAAAATATTTAAAA
1 AAAAATATTTAAAA
1357270 TTTAATTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
38 3 0.06
39 8 0.16
41 18 0.36
42 3 0.06
43 6 0.12
44 12 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (41 bp):
AAAAATATTTAAAAATTATATAATAAATATAATAAATAAAT
Found at i:1357270 original size:30 final size:30
Alignment explanation
Indices: 1357207--1357270 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
1357197 TAAATATAAT
**
1357207 AAATAAATAAAATTATTTAAAAATTATTAA
1 AAATAAATAAAATTAAATAAAAATTATTAA
*
1357237 AAATAAATAAAATTTAAATAAAAA-TATTTA
1 AAATAAATAAAA-TTAAATAAAAATTATTAA
1357267 AAAT
1 AAAT
1357271 TTAATTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 21 0.70
31 9 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (30 bp):
AAATAAATAAAATTAAATAAAAATTATTAA
Found at i:1358494 original size:30 final size:30
Alignment explanation
Indices: 1358458--1358520 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
1358448 TGTTATAATT
1358458 CAATTTTTTATGGAGAACCATAATGGAATG
1 CAATTTTTTATGGAGAACCATAATGGAATG
1358488 CAATTTTTTATGGAGAACCATAATGGAATG
1 CAATTTTTTATGGAGAACCATAATGGAATG
1358518 CAA
1 CAA
1358521 AGTTACAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (30 bp):
CAATTTTTTATGGAGAACCATAATGGAATG
Found at i:1359011 original size:10 final size:10
Alignment explanation
Indices: 1358996--1359056 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
1358986 TAATTTAAAT
1358996 ATAAAAATAA
1 ATAAAAATAA
*
1359006 ATAAAACTAA
1 ATAAAAATAA
*
1359016 TTTAAAAACT-A
1 -ATAAAAA-TAA
*
1359027 TTAAAAATAA
1 ATAAAAATAA
*
1359037 ATAAAATCTAA
1 ATAAAA-ATAA
1359048 ATAAAAATA
1 ATAAAAATA
1359057 TTTATATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
9 1 0.02
10 24 0.59
11 15 0.37
12 1 0.02
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:1359053 original size:31 final size:30
Alignment explanation
Indices: 1358992--1359058 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
1358982 TATATAATTT
*
1358992 AAATA-TAAAAATAAATAAAACTAATTTAA
1 AAATATTAAAAATAAATAAAACTAATATAA
1359021 AAACTATTAAAAATAAATAAAATCTAA-ATAA
1 AAA-TATTAAAAATAAATAAAA-CTAATATAA
1359052 AAATATT
1 AAATATT
1359059 TATATTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 3 0.09
30 6 0.18
31 21 0.62
32 4 0.12
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (30 bp):
AAATATTAAAAATAAATAAAACTAATATAA
Found at i:1359338 original size:16 final size:16
Alignment explanation
Indices: 1359295--1359341 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1359285 CTGATTGACT
1359295 CAAACTTGAAAATGATC
1 CAAACTTG-AAATGATC
**
1359312 CAAACCCGAAATGATC
1 CAAACTTGAAATGATC
1359328 CAAACTTGAAATGA
1 CAAACTTGAAATGA
1359342 CCTGAACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (16 bp):
CAAACTTGAAATGATC
Found at i:1360829 original size:13 final size:12
Alignment explanation
Indices: 1360802--1360833 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
1360792 CTCTCTCTAG
1360802 AAAATAAAAAAT
1 AAAATAAAAAAT
1360814 AAAATAAAATAAT
1 AAAATAAAA-AAT
1360827 AAAATAA
1 AAAATAA
1360834 TGTTTTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:1362365 original size:24 final size:25
Alignment explanation
Indices: 1362324--1362370 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1362314 TTGACAAAAT
1362324 AAAAATTTAAATATC-AAATTGAGA
1 AAAAATTTAAATATCAAAATTGAGA
1362348 AAAAGATTTAAATA-CAAAATTGA
1 AAAA-ATTTAAATATCAAAATTGA
1362371 AAATCTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.28
Consensus pattern (25 bp):
AAAAATTTAAATATCAAAATTGAGA
Found at i:1363818 original size:2 final size:2
Alignment explanation
Indices: 1363811--1363850 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1363801 AATTTTGGTC
1363811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1363851 TAATTTTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1364256 original size:12 final size:14
Alignment explanation
Indices: 1364209--1364257 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
1364199 GGCCACAACA
* *
1364209 TAAAATTAAAAGA-
1 TAAAATTTAAATAT
1364222 TAAAATTATAAATAT
1 TAAAATT-TAAATAT
1364237 TAAAATTTAAAT-T
1 TAAAATTTAAATAT
1364250 T-AAATTTA
1 TAAAATTTA
1364258 TTAAATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 7 0.22
13 9 0.28
14 9 0.28
15 7 0.22
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
TAAAATTTAAATAT
Found at i:1367233 original size:2 final size:2
Alignment explanation
Indices: 1367228--1367270 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1367218 ATATATATAT
* *
1367228 AC AC AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC GC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1367270 A
1 A
1367271 TAAATACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.47, G:0.02, T:0.02
Consensus pattern (2 bp):
AC
Found at i:1367871 original size:18 final size:20
Alignment explanation
Indices: 1367825--1367863 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1367815 ATAATTAAAA
* *
1367825 ATAAAATATAAATATATTAT
1 ATAAATTATTAATATATTAT
1367845 ATAAATTATTAATATATTA
1 ATAAATTATTAATATATTA
1367864 AAATTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAATTATTAATATATTAT
Found at i:1369756 original size:21 final size:20
Alignment explanation
Indices: 1369722--1369762 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1369712 AAAATTTATT
*
1369722 TTTATATAAAATTTATATAA
1 TTTATATAAAATTTAAATAA
*
1369742 TTTATAATTAAATTTAAATAA
1 TTTAT-ATAAAATTTAAATAA
1369763 AAATATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTATATAAAATTTAAATAA
Found at i:1370487 original size:22 final size:22
Alignment explanation
Indices: 1370453--1370513 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
1370443 AAAATATTAA
* *
1370453 AAATTATTTTATATTAATATTT
1 AAATAATTTTATATTAATAATT
* *
1370475 ATATATTTTTATAATT-ATAATT
1 AAATAATTTTAT-ATTAATAATT
1370497 AAATAATTTT-TATTAAT
1 AAATAATTTTATATTAAT
1370514 TAGATAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 3 0.10
21 3 0.10
22 22 0.71
23 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AAATAATTTTATATTAATAATT
Found at i:1371175 original size:18 final size:17
Alignment explanation
Indices: 1371117--1371177 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
1371107 AATTAATTAA
1371117 TATTTA-TAAATATTTTT
1 TATTTATTAAATA-TTTT
*
1371134 TAATTATTAAAT-TTTT
1 TATTTATTAAATATTTT
1371150 TATTTTTATGTAAATATTTT
1 TA--TTTAT-TAAATATTTT
1371170 TATTTATT
1 TATTTATT
1371178 TTTATGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 6 0.16
17 6 0.16
18 14 0.38
19 5 0.14
20 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TATTTATTAAATATTTT
Found at i:1371570 original size:17 final size:17
Alignment explanation
Indices: 1371548--1371595 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1371538 CATAAAAAAA
1371548 TAAAATTTAAATCAAAT
1 TAAAATTTAAATCAAAT
* * *
1371565 TAAAATTAAAATTTAATT
1 TAAAATTTAAA-TCAAAT
1371583 TAAAAATTTAAAT
1 T-AAAATTTAAAT
1371596 TTAAATCCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 10 0.40
18 6 0.24
19 9 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATTTAAATCAAAT
Found at i:1371588 original size:13 final size:14
Alignment explanation
Indices: 1371550--1371600 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
1371540 TAAAAAAATA
*
1371550 AAATTTAAATCAAATT
1 AAATTTAAA--AATTT
*
1371566 AAAATT-AAAATTT
1 AAATTTAAAAATTT
1371579 -AATTTAAAAATTT
1 AAATTTAAAAATTT
1371592 AAATTTAAA
1 AAATTTAAA
1371601 TCCCAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 4 0.13
13 11 0.37
14 8 0.27
15 2 0.07
16 5 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATTTAAAAATTT
Found at i:1372599 original size:2 final size:2
Alignment explanation
Indices: 1372588--1372630 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1372578 TATGTAGTTG
1372588 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1372629 AT
1 AT
1372631 GCACACACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1373157 original size:18 final size:18
Alignment explanation
Indices: 1373123--1373162 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1373113 CGACATTAAT
1373123 TATTATTTAAATAATAAA
1 TATTATTTAAATAATAAA
*
1373141 TATTAATTT-AATTATAAA
1 TATT-ATTTAAATAATAAA
1373159 TATT
1 TATT
1373163 TATATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTATTTAAATAATAAA
Found at i:1374071 original size:15 final size:15
Alignment explanation
Indices: 1374053--1374107 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
1374043 ATATTTTACG
1374053 AATAAAAAAAATATA
1 AATAAAAAAAATATA
*
1374068 AATAAAATAAAATTAAA
1 AATAAAA-AAAA-TATA
*
1374085 AATAATAAAAAT-TAA
1 AATAAAAAAAATAT-A
1374100 AATAAAAA
1 AATAAAAA
1374108 TCTTTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 16 0.48
16 8 0.24
17 9 0.27
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AATAAAAAAAATATA
Found at i:1374095 original size:16 final size:16
Alignment explanation
Indices: 1374053--1374101 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1374043 ATATTTTACG
*
1374053 AATAAAAAAAATATAAA
1 AATAATAAAAAT-TAAA
1374070 TAA-AAT-AAAATTAAA
1 -AATAATAAAAATTAAA
1374085 AATAATAAAAATTAAA
1 AATAATAAAAATTAAA
1374101 A
1 A
1374102 TAAAAATCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.07
15 7 0.25
16 15 0.54
17 2 0.07
18 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAATAAAAATTAAA
Found at i:1374116 original size:21 final size:22
Alignment explanation
Indices: 1374060--1374118 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
1374050 ACGAATAAAA
*
1374060 AAAATATAAATAAAA-TAAAATT
1 AAAA-ATAATTAAAATTAAAATT
*
1374082 AAAAATAATAAAAATTAAAA-T
1 AAAAATAATTAAAATTAAAATT
**
1374103 AAAAATCTTTAAAATT
1 AAAAATAATTAAAATT
1374119 TAGTTGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATAATTAAAATTAAAATT
Found at i:1375018 original size:16 final size:16
Alignment explanation
Indices: 1374994--1375031 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1374984 GTTTAAATTG
1374994 TTTTAAATTTGAATCA
1 TTTTAAATTTGAATCA
*
1375010 TTTTGAATTTGAATCA
1 TTTTAAATTTGAATCA
1375026 TTTTAA
1 TTTTAA
1375032 GTTTATCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (16 bp):
TTTTAAATTTGAATCA
Found at i:1375967 original size:17 final size:19
Alignment explanation
Indices: 1375933--1375967 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1375923 TATGTATTAT
1375933 ATTCATATCAAGTATTTTG
1 ATTCATATCAAGTATTTTG
1375952 ATTCATAT-AA-TATTTT
1 ATTCATATCAAGTATTTT
1375968 CTAGGAGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (19 bp):
ATTCATATCAAGTATTTTG
Found at i:1378352 original size:21 final size:23
Alignment explanation
Indices: 1378328--1378391 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 23
1378318 ATAAAATTAC
*
1378328 ATATTTTTAATAATTATGA-A-A
1 ATATTTTTAATAAATATGATATA
*
1378349 ATATTGTTAA-AAATATGATATA
1 ATATTTTTAATAAATATGATATA
*
1378371 ATATGTTTAATTTAAATATGA
1 ATATTTTTAA--TAAATATGA
1378392 GTAATATGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 7 0.21
21 10 0.29
22 9 0.26
25 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (23 bp):
ATATTTTTAATAAATATGATATA
Found at i:1378473 original size:17 final size:19
Alignment explanation
Indices: 1378443--1378477 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1378433 AAATTTTAAG
1378443 ATATTTAATAATTTATATC
1 ATATTTAATAATTTATATC
1378462 ATATTT-AT-ATTTATAT
1 ATATTTAATAATTTATAT
1378478 AATTGATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTAATAATTTATATC
Found at i:1378682 original size:22 final size:21
Alignment explanation
Indices: 1378638--1378683 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
1378628 AATATTTTTA
*
1378638 TTTAAATTTAATTATAAAAAT
1 TTTAAATTTAATTAAAAAAAT
1378659 TTTAAATATTAA-TAAAAAATAT
1 TTTAAAT-TTAATTAAAAAA-AT
1378681 TTT
1 TTT
1378684 TTAATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAAATTTAATTAAAAAAAT
Found at i:1384106 original size:2 final size:2
Alignment explanation
Indices: 1384099--1384141 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1384089 TAGTTGAACC
1384099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1384141 A
1 A
1384142 AGTTGAAGGG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1384813 original size:29 final size:30
Alignment explanation
Indices: 1384780--1384837 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
1384770 GTGAACTCAT
1384780 AAAATTTAATTCATGTTG-AAAATGATATC
1 AAAATTTAATTCATGTTGAAAAATGATATC
1384809 AAAATTTAATTCATGTTGAAAAATGATAT
1 AAAATTTAATTCATGTTGAAAAATGATAT
1384838 AAATTCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (30 bp):
AAAATTTAATTCATGTTGAAAAATGATATC
Found at i:1387727 original size:24 final size:24
Alignment explanation
Indices: 1387668--1387727 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
1387658 ATATATATTT
* *
1387668 AAATATAAATATATAATTTTTTAA
1 AAATATATATATATAACTTTTTAA
* *
1387692 ATATTTAAATATATATAACTTTTTAA
1 A-A-ATATATATATATAACTTTTTAA
1387718 AAATATATAT
1 AAATATATAT
1387728 CCATAATATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
24 7 0.25
25 2 0.07
26 19 0.68
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATATATATATATAACTTTTTAA
Found at i:1391136 original size:149 final size:151
Alignment explanation
Indices: 1390916--1391217 Score: 457
Period size: 149 Copynumber: 2.0 Consensus size: 151
1390906 ATAACCAAAG
*
1390916 GAAATTATGAATCCTGATCAATTCATAAAAATTGAATTCATTTGCCGCTTGTAAATATCACTCCA
1 GAAATTATGAATCCTGATCAATTC-----AATTGAATTCATTTGCCGCTTGTAAATACCACTCCA
* * *
1390981 ATGTTCAAAAAATCAAACTTACAAATTAAAATTAAAATAAATATTATTATAAATAAAATTTTATT
61 ACGTTCAAAAAATCAAACGTACAAATTAAAATCAAAATAAATATTATTATAAATAAAATTTTATT
*
1391046 AACTCTTTATGATTGTAAAACTAAAA
126 AACTCTCTATGATTGTAAAACTAAAA
*
1391072 GAAATTATGAATCCTGATCAATTC-A-TGAATTCATTTGTCGCTTGTAAATACCA-TCCCAACGT
1 GAAATTATGAATCCTGATCAATTCAATTGAATTCATTTGCCGCTTGTAAATACCACT-CCAACGT
* *
1391134 TCAAAAAATCAAACGTACAAATTAATATCAAAATAAATATTATTATAAATGAAATTTTATTAACT
65 TCAAAAAATCAAACGTACAAATTAAAATCAAAATAAATATTATTATAAATAAAATTTTATTAACT
1391199 CTCTATGATTGTAAAACTA
130 CTCTATGATTGTAAAACTA
1391218 TTATTAAAGG
Statistics
Matches: 137, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
148 1 0.01
149 111 0.81
150 1 0.01
156 24 0.18
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (151 bp):
GAAATTATGAATCCTGATCAATTCAATTGAATTCATTTGCCGCTTGTAAATACCACTCCAACGTT
CAAAAAATCAAACGTACAAATTAAAATCAAAATAAATATTATTATAAATAAAATTTTATTAACTC
TCTATGATTGTAAAACTAAAA
Found at i:1391371 original size:14 final size:15
Alignment explanation
Indices: 1391354--1391382 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1391344 AATAAAAAAT
1391354 GATATATA-ATTAAA
1 GATATATATATTAAA
1391368 GATATATATATTAAA
1 GATATATATATTAAA
1391383 TTATGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
GATATATATATTAAA
Found at i:1393144 original size:18 final size:17
Alignment explanation
Indices: 1393121--1393161 Score: 73
Period size: 18 Copynumber: 2.4 Consensus size: 17
1393111 AAATTATTTG
1393121 AAAAATTAATTTTATAT
1 AAAAATTAATTTTATAT
1393138 AACAAATTAATTTTATAT
1 AA-AAATTAATTTTATAT
1393156 AAAAAT
1 AAAAAT
1393162 ATAGATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAAATTAATTTTATAT
Found at i:1393384 original size:31 final size:32
Alignment explanation
Indices: 1393346--1393411 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
1393336 CTGACCCGAA
*
1393346 CTCAAACCCAAAAAAGCCCAACCT-AAAAAAG
1 CTCAAACCCAAAAAAGCCCAAACTCAAAAAAG
* * *
1393377 CTCAAACCCGAATAAGCCCAAACTCGAAAAAG
1 CTCAAACCCAAAAAAGCCCAAACTCAAAAAAG
1393409 CTC
1 CTC
1393412 GAACTCGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.48, C:0.33, G:0.09, T:0.09
Consensus pattern (32 bp):
CTCAAACCCAAAAAAGCCCAAACTCAAAAAAG
Found at i:1393393 original size:16 final size:16
Alignment explanation
Indices: 1393374--1393456 Score: 76
Period size: 16 Copynumber: 5.2 Consensus size: 16
1393364 CAACCTAAAA
1393374 AAGCTCAAACCCGAAT
1 AAGCTCAAACCCGAAT
* * *
1393390 AAGCCCAAACTCGAAA
1 AAGCTCAAACCCGAAT
* *
1393406 AAGCTCGAACTCGAAT
1 AAGCTCAAACCCGAAT
* * * *
1393422 AAGCTAAAATCTGAAA
1 AAGCTCAAACCCGAAT
*
1393438 AAACTCAAACCCGAAT
1 AAGCTCAAACCCGAAT
1393454 AAG
1 AAG
1393457 TCCGAACCCG
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.48, C:0.25, G:0.13, T:0.13
Consensus pattern (16 bp):
AAGCTCAAACCCGAAT
Found at i:1393421 original size:32 final size:33
Alignment explanation
Indices: 1393346--1393516 Score: 129
Period size: 32 Copynumber: 5.4 Consensus size: 33
1393336 CTGACCCGAA
* * * *
1393346 CTCAAACCCAAAAAAG-CCCAAC-CTAAAAAAG
1 CTCAAACCCGAATAAGTCCAAACTCTGAAAAAG
*
1393377 CTCAAACCCGAATAAGCCCAAACTC-GAAAAAG
1 CTCAAACCCGAATAAGTCCAAACTCTGAAAAAG
* * * * *
1393409 CTCGAACTCGAATAAG-CTAAAATCTGAAAAAA
1 CTCAAACCCGAATAAGTCCAAACTCTGAAAAAG
* * **
1393441 CTCAAACCCGAATAAGTCCGAAC-CCGAACGAG
1 CTCAAACCCGAATAAGTCCAAACTCTGAAAAAG
** * * *
1393473 CTTGAACTCAAATAAGTCCAAA-TCTGAAAAAA
1 CTCAAACCCGAATAAGTCCAAACTCTGAAAAAG
1393505 CTCAAACCCGAA
1 CTCAAACCCGAA
1393517 CGAATTTAAA
Statistics
Matches: 104, Mismatches: 31, Indels: 9
0.72 0.22 0.06
Matches are distributed among these distances:
31 20 0.19
32 80 0.77
33 4 0.04
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.13
Consensus pattern (33 bp):
CTCAAACCCGAATAAGTCCAAACTCTGAAAAAG
Found at i:1393439 original size:64 final size:64
Alignment explanation
Indices: 1393370--1393516 Score: 197
Period size: 64 Copynumber: 2.3 Consensus size: 64
1393360 AGCCCAACCT
* *
1393370 AAAAAAGCTCAAACCCGAATAAGCCCAAACTCGAAAAAGCTCGAACTCGAATAAG-CTAAAATCT
1 AAAAAA-CTCAAACCCGAATAAGCCCAAACCCGAAAAAGCTCGAACTCAAATAAGTC-AAAATCT
1393434 G
64 G
* * ** * *
1393435 AAAAAACTCAAACCCGAATAAGTCCGAACCCGAACGAGCTTGAACTCAAATAAGTCCAAATCTG
1 AAAAAACTCAAACCCGAATAAGCCCAAACCCGAAAAAGCTCGAACTCAAATAAGTCAAAATCTG
1393499 AAAAAACTCAAACCCGAA
1 AAAAAACTCAAACCCGAA
1393517 CGAATTTAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
64 66 0.90
65 7 0.10
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.14
Consensus pattern (64 bp):
AAAAAACTCAAACCCGAATAAGCCCAAACCCGAAAAAGCTCGAACTCAAATAAGTCAAAATCTG
Found at i:1393842 original size:23 final size:23
Alignment explanation
Indices: 1393812--1393857 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1393802 AAGACGTAAG
1393812 AATGTTCAATTTAGAAA-AAATTT
1 AATGTTCAATTTA-AAAGAAATTT
1393835 AATGTTCAATTTAAAAGAAATTT
1 AATGTTCAATTTAAAAGAAATTT
1393858 CATATTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (23 bp):
AATGTTCAATTTAAAAGAAATTT
Found at i:1393938 original size:34 final size:33
Alignment explanation
Indices: 1393880--1393950 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 33
1393870 ATATTTGTGT
*
1393880 TATTTTTATATTAAAATATTATAAATTTATATA
1 TATTTTTATATTAAAATATTATAAATTTATACA
* *
1393913 TATTTTTACATATTAATA-ATTATAAATTTTTACA
1 TATTTTT--ATATTAAAATATTATAAATTTATACA
1393947 TATT
1 TATT
1393951 AAAAATTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 18 0.55
35 8 0.24
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (33 bp):
TATTTTTATATTAAAATATTATAAATTTATACA
Found at i:1394261 original size:9 final size:9
Alignment explanation
Indices: 1394223--1394280 Score: 50
Period size: 9 Copynumber: 6.7 Consensus size: 9
1394213 TTTATTTTAA
1394223 AATTAAT-T
1 AATTAATAT
1394231 -ATTACATAT
1 AATTA-ATAT
* *
1394240 ATTTTATAT
1 AATTAATAT
1394249 -ATTAATAT
1 AATTAATAT
1394257 AATTAATAT
1 AATTAATAT
*
1394266 AAATAATAT
1 AATTAATAT
*
1394275 ATTTAA
1 AATTAA
1394281 AATTTTAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
7 4 0.10
8 8 0.21
9 25 0.64
10 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTAATAT
Found at i:1394518 original size:19 final size:19
Alignment explanation
Indices: 1394496--1394535 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1394486 TATTAATATA
* *
1394496 TATTTTTTTTATTTTTAAT
1 TATTTTATTAATTTTTAAT
1394515 TATTTTATTAATTTTTAAT
1 TATTTTATTAATTTTTAAT
1394534 TA
1 TA
1394536 AATTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTATTAATTTTTAAT
Found at i:1398432 original size:16 final size:16
Alignment explanation
Indices: 1398411--1398444 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1398401 GCTGTAAGGT
1398411 AGAGAATAACCAAAGA
1 AGAGAATAACCAAAGA
1398427 AGAGAATAACCAAAGA
1 AGAGAATAACCAAAGA
1398443 AG
1 AG
1398445 GTACAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.21, T:0.06
Consensus pattern (16 bp):
AGAGAATAACCAAAGA
Found at i:1398928 original size:15 final size:16
Alignment explanation
Indices: 1398889--1398969 Score: 62
Period size: 16 Copynumber: 5.0 Consensus size: 16
1398879 AATTTTAATA
1398889 TTTATATAATATAAAT
1 TTTATATAATATAAAT
*
1398905 TATTAATATATTA-AAAT
1 T-TT-ATATAATATAAAT
*
1398922 TTTATATAAATATAAAAAA
1 TTTATAT-AATAT--AAAT
1398941 TTT-TA-AATATAAAT
1 TTTATATAATATAAAT
*
1398955 ATTATATAATA-AAAT
1 TTTATATAATATAAAT
1398970 AAATAAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
14 5 0.10
15 10 0.19
16 15 0.29
17 7 0.13
18 9 0.17
19 6 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTATATAATATAAAT
Found at i:1398942 original size:20 final size:21
Alignment explanation
Indices: 1398917--1398956 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1398907 TTAATATATT
1398917 AAAATTTT-ATATAAATATAA
1 AAAATTTTAATATAAATATAA
1398937 AAAATTTTAAATATAAATAT
1 AAAATTTT-AATATAAATAT
1398957 TATATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATTTTAATATAAATATAA
Found at i:1398960 original size:33 final size:36
Alignment explanation
Indices: 1398872--1398963 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 36
1398862 TATAATATAC
**
1398872 AAATATAAATTTTAATATTTATATAATATAAATTATT
1 AAATATAAATTTT-ATATAAATATAATATAAATTATT
1398909 AATATATTAAAATTTTATATAAATATAA-A-AAATT-TT
1 AA-ATA-T-AAATTTTATATAAATATAATATAAATTATT
*
1398945 AAATATAAATATTATATAA
1 AAATATAAATTTTATATAA
1398964 TAAAATAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
33 12 0.24
34 1 0.02
35 3 0.06
36 4 0.08
37 7 0.14
38 4 0.08
39 11 0.22
40 7 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
AAATATAAATTTTATATAAATATAATATAAATTATT
Found at i:1399367 original size:11 final size:11
Alignment explanation
Indices: 1399351--1399422 Score: 74
Period size: 11 Copynumber: 6.5 Consensus size: 11
1399341 AAGATTATAT
*
1399351 AAATATGATAA
1 AAATATAATAA
*
1399362 AAATATAATTA
1 AAATATAATAA
*
1399373 AAATATAATAT
1 AAATATAATAA
1399384 AAATGATAATATA
1 AAAT-ATAATA-A
*
1399397 AAA-ATAATAT
1 AAATATAATAA
*
1399407 AAATATAATAT
1 AAATATAATAA
1399418 AAATA
1 AAATA
1399423 AAAATATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
10 3 0.06
11 40 0.77
12 6 0.12
13 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
AAATATAATAA
Found at i:1399396 original size:17 final size:16
Alignment explanation
Indices: 1399347--1399477 Score: 70
Period size: 17 Copynumber: 8.0 Consensus size: 16
1399337 AATCAAGATT
* *
1399347 ATATAAATATGATAAAA
1 ATATAAATATAAT-ATA
* *
1399364 ATATAATTAAAATATA
1 ATATAAATATAATATA
1399380 ATATAAATGATAATATA
1 ATATAAAT-ATAATATA
*
1399397 A-AAATAATATAAATATA
1 ATATA-AATAT-AATATA
*
1399414 ATATAAATA-AAAATA
1 ATATAAATATAATATA
* *
1399429 TATATTAAATTTTATATA
1 -ATA-TAAATATAATATA
* * * *
1399447 ATATGAACATGATAAA
1 ATATAAATATAATATA
*
1399463 ATTTAAATA-AATATA
1 ATATAAATATAATATA
1399478 TAATAATAAT
Statistics
Matches: 85, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
15 9 0.11
16 30 0.35
17 40 0.47
18 6 0.07
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (16 bp):
ATATAAATATAATATA
Found at i:1399421 original size:34 final size:34
Alignment explanation
Indices: 1399347--1399422 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
1399337 AATCAAGATT
*
1399347 ATATAAATATGATA-AAAATATAATTAAAATATA
1 ATATAAATATAATATAAAATATAATTAAAATATA
1399380 ATATAAATGATAATATAAAA-ATAA-TATAAATATA
1 ATATAAAT-ATAATATAAAATATAATTA-AAATATA
1399414 ATATAAATA
1 ATATAAATA
1399423 AAAATATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
33 11 0.28
34 24 0.62
35 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (34 bp):
ATATAAATATAATATAAAATATAATTAAAATATA
Found at i:1399438 original size:28 final size:27
Alignment explanation
Indices: 1399347--1399450 Score: 88
Period size: 28 Copynumber: 3.7 Consensus size: 27
1399337 AATCAAGATT
* * *
1399347 ATATAAATATGATAAAAATATAATTAA-A
1 ATATAAATATAAT-ATAATATAA-AAATA
1399375 ATAT-AATATAAATGATAATATAAAAATA
1 ATATAAATAT-AAT-ATAATATAAAAATA
1399403 ATATAAATATAATATAA-ATAAAAATA
1 ATATAAATATAATATAATATAAAAATA
* *
1399429 TATATTAAATTTTATATAATAT
1 -ATA-TAAATATAATATAATAT
1399451 GAACATGATA
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
26 9 0.14
27 14 0.22
28 34 0.53
29 7 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
ATATAAATATAATATAATATAAAAATA
Found at i:1399924 original size:12 final size:12
Alignment explanation
Indices: 1399896--1399947 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
1399886 TGTATTTGTG
1399896 TATTTATATATTTA
1 TATTT-TATA-TTA
1399910 TATTTTATATTA
1 TATTTTATATTA
1399922 TATTTTATATTA
1 TATTTTATATTA
**
1399934 CGTTTTA-ATTA
1 TATTTTATATTA
1399945 TAT
1 TAT
1399948 CATATTGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
11 5 0.15
12 20 0.59
13 4 0.12
14 5 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTTTATATTA
Found at i:1400329 original size:13 final size:13
Alignment explanation
Indices: 1400287--1400330 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1400277 AAGTTTAGAA
1400287 TTTAAATTATAAT
1 TTTAAATTATAAT
* *
1400300 ATTTATAATTCTCAT
1 -TTTA-AATTATAAT
1400315 TTTAAATTATAAT
1 TTTAAATTATAAT
1400328 TTT
1 TTT
1400331 TTATATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 10 0.40
14 8 0.32
15 7 0.28
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTAAATTATAAT
Found at i:1400426 original size:17 final size:17
Alignment explanation
Indices: 1400386--1400426 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1400376 TAATATAATA
*
1400386 TTTTTATTTTTTATATT
1 TTTTTATTTTTTAAATT
* *
1400403 ATATTATTTTTTAAATT
1 TTTTTATTTTTTAAATT
1400420 TTTTTAT
1 TTTTTAT
1400427 ATCATTTTAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATTTTTTAAATT
Found at i:1401316 original size:13 final size:12
Alignment explanation
Indices: 1401287--1401335 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
1401277 TTTTTTAAAA
*
1401287 AAATTAAAATATA
1 AAATT-AAATATT
1401300 AAATTAAATATGT
1 AAATTAAATAT-T
1401313 AAA-TAAATATT
1 AAATTAAATATT
1401324 AAATTTAAATAT
1 AAA-TTAAATAT
1401336 CTAATTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 4 0.12
12 13 0.41
13 15 0.47
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
AAATTAAATATT
Found at i:1401342 original size:37 final size:35
Alignment explanation
Indices: 1401282--1401370 Score: 90
Period size: 37 Copynumber: 2.5 Consensus size: 35
1401272 TTAATTTTTT
* *
1401282 TAAAA-AAATTAAAATATAAAATTAAATATGTAAA
1 TAAAATAAATTTAAATATAAAATTAAATATATAAA
** **
1401316 TAAATATTAAATTTAAATATCTAATTATTTATATAAA
1 TAAA-A-TAAATTTAAATATAAAATTAAATATATAAA
*
1401353 TAAAATAAATTTGAATAT
1 TAAAATAAATTTAAATAT
1401371 TCAATACTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
34 4 0.09
35 13 0.29
36 1 0.02
37 27 0.60
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (35 bp):
TAAAATAAATTTAAATATAAAATTAAATATATAAA
Found at i:1401406 original size:16 final size:16
Alignment explanation
Indices: 1401381--1401412 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1401371 TCAATACTAT
*
1401381 TCTAATCAAAATTAAA
1 TCTAAGCAAAATTAAA
1401397 TCTAAGCAAAATTAAA
1 TCTAAGCAAAATTAAA
1401413 ACAAATTTAG
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:0.56, C:0.12, G:0.03, T:0.28
Consensus pattern (16 bp):
TCTAAGCAAAATTAAA
Found at i:1402075 original size:2 final size:2
Alignment explanation
Indices: 1402068--1402096 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1402058 CCTTTATACC
1402068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1402097 GTATCATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1404647 original size:19 final size:20
Alignment explanation
Indices: 1404625--1404665 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1404615 AATTTATATA
* *
1404625 ATTA-TATAATATTTTAAAT
1 ATTATTATAACATTTAAAAT
1404644 ATTATTATAACATTTAAAAT
1 ATTATTATAACATTTAAAAT
1404664 AT
1 AT
1404666 CTAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTATTATAACATTTAAAAT
Found at i:1405053 original size:24 final size:24
Alignment explanation
Indices: 1405001--1405053 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1404991 ATTATAGACG
*
1405001 TAATT-AATATTTATATTTTAAAT
1 TAATTAAATATTTATATTTTAAAA
*
1405024 TTATTAAATA-TTATTATTTTAAAA
1 TAATTAAATATTTA-TATTTTAAAA
1405048 TAATTA
1 TAATTA
1405054 TATAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAATTAAATATTTATATTTTAAAA
Found at i:1406619 original size:2 final size:2
Alignment explanation
Indices: 1406614--1406638 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1406604 TTTTTACGGC
1406614 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 A
1406639 AACCCCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1408639 original size:93 final size:94
Alignment explanation
Indices: 1408523--1409235 Score: 706
Period size: 93 Copynumber: 7.6 Consensus size: 94
1408513 TTATAACCAC
* * * * *
1408523 GCTTCT-CTTCAGGCTTTGGCTTGTAA-A-TGCCTGGCTTTGCAACATAATTGGGCTTGTGTCCT
1 GCTTCTCCTTCTGGCTTTGGCTTGTAACAGTGCCTGGTTTTGCACCATAGTTGGGCTT-TCTCCT
* * *
1408585 CCTTCTGGCGTTGAACCGTACTCAGTCTTT
65 CCTTCTGGCTTTGAACCATACTCAGGCTTT
* * * * *
1408615 TCTTCTCCTGCTGGCTTTGGCTTGTAATTAGTGCCTGGTTTTTCACCATGGTTGGGCTTGTCTCC
1 GCTTCTCCTTCTGGCTTTGGCTTGTAA-CAGTGCCTGGTTTTGCACCATAGTTGGGCTT-TCTCC
*
1408680 -CGC-T-T-GCTCTGAACCATACTCAGGCTTT
64 TC-CTTCTGGCTTTGAACCATACTCAGGCTTT
* * * ****
1408708 GCTTCTCCTTCCGGCTTCGGCTTGTAACCAGTGCCTGGTTCTGCACCATAGTT-GG-TTTCAGGG
1 GCTTCTCCTTCTGGCTTTGGCTTGTAA-CAGTGCCTGGTTTTGCACCATAGTTGGGCTTTCTCCT
*
1408771 CCTTCAGGCTTTGAACCATACTCAGGCTTT
65 CCTTCTGGCTTTGAACCATACTCAGGCTTT
* * ****
1408801 GCTTCTCCTTCTGGCTTCGGCTTGTAACCAGTGCCTGGTTCTGCACCATAGTT-GG-TTTCAGGG
1 GCTTCTCCTTCTGGCTTTGGCTTGTAA-CAGTGCCTGGTTTTGCACCATAGTTGGGCTTTCTCCT
* *
1408864 CCTTCAGGCTTTGAACCACACTCAGGCTTT
65 CCTTCTGGCTTTGAACCATACTCAGGCTTT
* *
1408894 GCTTCTCCTTCTGGCTTTGGCTTGTAACCAGTTCCTGGTTTTGCACCATAGTTAGGCTTGTCTCC
1 GCTTCTCCTTCTGGCTTTGGCTTGTAA-CAGTGCCTGGTTTTGCACCATAGTTGGGCTT-TCTCC
1408959 TCCTTCTGGCTTTGAACCATACTCAGGCTTT
64 TCCTTCTGGCTTTGAACCATACTCAGGCTTT
* * *
1408990 GCTTCTGCTTCTGGCTTTGGCTTGTAA-A-T-CCATGGTTTTTCACCATAGCTGGGCTTGTCT--
1 GCTTCTCCTTCTGGCTTTGGCTTGTAACAGTGCC-TGGTTTTGCACCATAGTTGGGCTT-TCTCC
* * * *
1409050 T-CTCCTGGATTGGAACCATACTCAAGCTTT
64 TCCTTCTGGCTTTGAACCATACTCAGGCTTT
* * *
1409080 GCTTGTCCTCCTGGCTTTGGCTTGTAACCAGTGCCTGGTTTTTCACCATA-TCTGGGCTTATCTC
1 GCTTCTCCTTCTGGCTTTGGCTTGTAA-CAGTGCCTGGTTTTGCACCATAGT-TGGGCTT-TCTC
* * *
1409144 CTCCTTCTGGCTTTGAACCGTAGTCATGCTTT
63 CTCCTTCTGGCTTTGAACCATACTCAGGCTTT
* * * * * **
1409176 ACGTCTTCTTCTGGTTTTGGTTTGTAATTGGTGCCTGGTTTTGCACCATAGTTGGGCTTT
1 GCTTCTCCTTCTGGCTTTGGCTTGTAA-CAGTGCCTGGTTTTGCACCATAGTTGGGCTTT
1409236 ACTTCACCTT
Statistics
Matches: 531, Mismatches: 68, Indels: 41
0.83 0.11 0.06
Matches are distributed among these distances:
90 52 0.10
91 5 0.01
92 10 0.02
93 296 0.56
94 6 0.01
95 7 0.01
96 154 0.29
97 1 0.00
ACGTcount: A:0.13, C:0.26, G:0.22, T:0.38
Consensus pattern (94 bp):
GCTTCTCCTTCTGGCTTTGGCTTGTAACAGTGCCTGGTTTTGCACCATAGTTGGGCTTTCTCCTC
CTTCTGGCTTTGAACCATACTCAGGCTTT
Found at i:1408978 original size:36 final size:36
Alignment explanation
Indices: 1408928--1409008 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
1408918 TAACCAGTTC
* * * *
1408928 CTGGTTTTGCACCATAGTTAGGC-TTGTCTCCTCCTT
1 CTGGCTTTGAACCATACTCAGGCTTTG-CTCCTCCTT
* *
1408964 CTGGCTTTGAACCATACTCAGGCTTTGCTTCTGCTT
1 CTGGCTTTGAACCATACTCAGGCTTTGCTCCTCCTT
1409000 CTGGCTTTG
1 CTGGCTTTG
1409009 GCTTGTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 35 0.92
37 3 0.08
ACGTcount: A:0.11, C:0.27, G:0.21, T:0.41
Consensus pattern (36 bp):
CTGGCTTTGAACCATACTCAGGCTTTGCTCCTCCTT
Found at i:1410471 original size:16 final size:16
Alignment explanation
Indices: 1410452--1410505 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
1410442 ATTTTTAAAT
1410452 TTTTAAATTTAAATTA
1 TTTTAAATTTAAATTA
* *
1410468 TTTTGATTTTAAATTA
1 TTTTAAATTTAAATTA
* *
1410484 TTTTAAGTTTTAATTA
1 TTTTAAATTTAAATTA
1410500 TTTTAA
1 TTTTAA
1410506 TTAAATTTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:1410488 original size:32 final size:30
Alignment explanation
Indices: 1410444--1410503 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
1410434 TAAATTAAAT
1410444 TTTTAAATTTTTAAATTTAAATTATTTTGA
1 TTTTAAATTTTTAAATTTAAATTATTTTGA
* *
1410474 TTTTAAATTATTTTAAGTTTTAATTATTTT
1 TTTTAAA-T-TTTTAAATTTAAATTATTTT
1410504 AATTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 7 0.27
31 1 0.04
32 18 0.69
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTTTAAATTTAAATTATTTTGA
Found at i:1410682 original size:5 final size:5
Alignment explanation
Indices: 1410672--1410710 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
1410662 TATAATCATT
1410672 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA
1410711 TCAAATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TTAAA
Found at i:1410950 original size:21 final size:21
Alignment explanation
Indices: 1410924--1410963 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1410914 TTTGAAAATT
*
1410924 ATTTTATATT-TATATTTTAAA
1 ATTTTAAATTATA-ATTTTAAA
1410945 ATTTTAAATTATAATTTTA
1 ATTTTAAATTATAATTTTA
1410964 TTAATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTAAATTATAATTTTAAA
Found at i:1412181 original size:13 final size:14
Alignment explanation
Indices: 1412156--1412229 Score: 80
Period size: 14 Copynumber: 5.4 Consensus size: 14
1412146 TGTTTCGTAA
1412156 ATAAATTATTAAAAT
1 ATAAATTA-TAAAAT
1412171 ATAAA-TATAAAAT
1 ATAAATTATAAAAT
**
1412184 AT-AATTATATTAT
1 ATAAATTATAAAAT
* *
1412197 TTAAATTATAAATT
1 ATAAATTATAAAAT
1412211 ATAAATTATAAAAT
1 ATAAATTATAAAAT
*
1412225 TTAAA
1 ATAAA
1412230 ATTAATTATT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
12 2 0.04
13 15 0.31
14 26 0.54
15 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAAATTATAAAAT
Found at i:1414185 original size:2 final size:2
Alignment explanation
Indices: 1414178--1414221 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1414168 TATTCCACTG
*
1414178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1414220 AT
1 AT
1414222 TTTTTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1416218 original size:23 final size:24
Alignment explanation
Indices: 1416164--1416219 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1416154 ATACCTAAAT
*
1416164 TCAGGAAGCTGCAATGACCCAAAA
1 TCAGGCAGCTGCAATGACCCAAAA
**
1416188 TCCA-GCAGCTGCAATGTTCC-AAA
1 T-CAGGCAGCTGCAATGACCCAAAA
1416211 TCAGGCAGC
1 TCAGGCAGC
1416220 AAAATTATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 2 0.07
23 9 0.33
24 14 0.52
25 2 0.07
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (24 bp):
TCAGGCAGCTGCAATGACCCAAAA
Found at i:1416486 original size:20 final size:21
Alignment explanation
Indices: 1416448--1416491 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1416438 AGTTCAAAAG
1416448 TTTGAATTTAAATATAAA-TA
1 TTTGAATTTAAATATAAATTA
*
1416468 TTTGAGTTTAAAT-TAAAATTA
1 TTTGAATTTAAATAT-AAATTA
1416489 TTT
1 TTT
1416492 TTTTTAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 15 0.71
21 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTGAATTTAAATATAAATTA
Found at i:1417920 original size:6 final size:6
Alignment explanation
Indices: 1417909--1417967 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
1417899 TGTGCCAAAC
* * * * * *
1417909 AAAATA AAAATA ATAATA ATAATA ATAATA ATAATA ATAATA AAAAGA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
1417957 AAAATGA AAAA
1 AAAAT-A AAAA
1417968 ATGAAATTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
6 43 0.90
7 5 0.10
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:1417925 original size:3 final size:3
Alignment explanation
Indices: 1417911--1417951 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1417901 TGCCAAACAA
*
1417911 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1417952 AAAGAAAAAT
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1419463 original size:16 final size:16
Alignment explanation
Indices: 1419442--1419484 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1419432 ATATATTATC
1419442 ATATTAATATTTA-AA
1 ATATTAATATTTATAA
1419457 ATAATTAAT-TTTATAA
1 AT-ATTAATATTTATAA
*
1419473 ATTTTAATATTT
1 ATATTAATATTT
1419485 CATATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTAATATTTATAA
Found at i:1420375 original size:18 final size:16
Alignment explanation
Indices: 1420312--1420373 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
1420302 TATATTTTTA
*
1420312 TTATATTTAAATAAAT
1 TTATATATAAATAAAT
* * *
1420328 TT-TA-ATCATTTAAT
1 TTATATATAAATAAAT
1420342 TTATATATAAATAAAT
1 TTATATATAAATAAAT
*
1420358 TTTTATATCAAATAAA
1 TTATATAT-AAATAAA
1420374 ATAATAATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
14 8 0.23
15 4 0.11
16 16 0.46
17 7 0.20
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATATATAAATAAAT
Found at i:1420444 original size:30 final size:30
Alignment explanation
Indices: 1420386--1420452 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
1420376 AATAATTTAA
* * **
1420386 TTTAAGAGCTTGTTTAGATATATTTTAAAAG
1 TTTAAGAGCTTATTTAGATAAAAATT-AAAG
*
1420417 -TTAAGAGTTTATTTAGATAAAAATTAAAG
1 TTTAAGAGCTTATTTAGATAAAAATTAAAG
1420446 TTTAAGA
1 TTTAAGA
1420453 TTTGTTCGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.42
Consensus pattern (30 bp):
TTTAAGAGCTTATTTAGATAAAAATTAAAG
Found at i:1428495 original size:17 final size:17
Alignment explanation
Indices: 1428452--1428495 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1428442 TATAAATACG
* *
1428452 AAAATATAAACTTTTAG
1 AAAATATAAAATTTTAA
*
1428469 AATATATAAAATTTTAA
1 AAAATATAAAATTTTAA
*
1428486 AAAATTTAAA
1 AAAATATAAA
1428496 TATACTCATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
AAAATATAAAATTTTAA
Found at i:1429560 original size:13 final size:13
Alignment explanation
Indices: 1429544--1429568 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1429534 ATTTTAATTT
1429544 TTAATTTAATTAA
1 TTAATTTAATTAA
1429557 TTAATTTAATTA
1 TTAATTTAATTA
1429569 TTTTTAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:1429571 original size:28 final size:28
Alignment explanation
Indices: 1429540--1429594 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1429530 TCAGATTTTA
*
1429540 ATTTTTAATTTAATTAATTAA-TTTAATT
1 ATTTTTAATTTAAAT-ATTAAGTTTAATT
1429568 ATTTTTAATTTAAATATTAAGTTTAAT
1 ATTTTTAATTTAAATATTAAGTTTAAT
1429595 ATTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTTTAATTTAAATATTAAGTTTAATT
Found at i:1431490 original size:7 final size:7
Alignment explanation
Indices: 1431480--1431508 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1431470 ATTATTTAAT
1431480 AATTTTA
1 AATTTTA
1431487 AATTTTA
1 AATTTTA
1431494 AATTTTA
1 AATTTTA
1431501 AATTTTA
1 AATTTTA
1431508 A
1 A
1431509 CATCAGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATTTTA
Found at i:1431869 original size:17 final size:17
Alignment explanation
Indices: 1431849--1431886 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1431839 TTTAAAAATT
1431849 AAATAT-TTTCATATTAA
1 AAATATATTT-ATATTAA
*
1431866 AAATATATTTATATTTA
1 AAATATATTTATATTAA
1431883 AAAT
1 AAAT
1431887 TCACTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATATTTATATTAA
Found at i:1434070 original size:29 final size:31
Alignment explanation
Indices: 1434033--1434093 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
1434023 TTTGTGTTTG
*
1434033 AACTGATTTAAATTTATATTTTAATT-TAAA
1 AACTGATTTAAATTTAAATTTTAATTATAAA
**
1434063 AACT-ATTTTTATTTAAATTTTAATTATAAA
1 AACTGATTTAAATTTAAATTTTAATTATAAA
1434093 A
1 A
1434094 TAATTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (31 bp):
AACTGATTTAAATTTAAATTTTAATTATAAA
Found at i:1434098 original size:17 final size:18
Alignment explanation
Indices: 1434078--1434121 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1434068 TTTTTATTTA
*
1434078 AATTTTAATTAT-AAAAT
1 AATTTTAAATATAAAAAT
*
1434095 AATTTAAAATATAAAAAT
1 AATTTTAAATATAAAAAT
*
1434113 AATATTAAA
1 AATTTTAAA
1434122 AAATTTGTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTTTAAATATAAAAAT
Found at i:1434863 original size:2 final size:2
Alignment explanation
Indices: 1434858--1434886 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1434848 CTTCTTATCG
1434858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1434887 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1436458 original size:17 final size:17
Alignment explanation
Indices: 1436436--1436494 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
1436426 TGTTAAATAT
1436436 ATTTTATATTATTAAAA
1 ATTTTATATTATTAAAA
*
1436453 ATTTTA-ATATATTAATA
1 ATTTTATAT-TATTAAAA
* *
1436470 A-TTTGTATTA-TATAA
1 ATTTTATATTATTAAAA
1436485 ATTTTGATAT
1 ATTTT-ATAT
1436495 ATTTATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 4 0.12
16 10 0.30
17 19 0.58
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTATATTATTAAAA
Found at i:1436488 original size:32 final size:34
Alignment explanation
Indices: 1436442--1436506 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 34
1436432 ATATATTTTA
1436442 TATTATTAAAAATTTTAATATA-TTAATAATTTG
1 TATTATTAAAAATTTTAATATATTTAATAATTTG
* * *
1436475 TATTA-TATAAATTTTGATATATTTATTAATTT
1 TATTATTAAAAATTTTAATATATTTAATAATTT
1436507 ATATCGTGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (34 bp):
TATTATTAAAAATTTTAATATATTTAATAATTTG
Found at i:1436545 original size:11 final size:11
Alignment explanation
Indices: 1436529--1436567 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1436519 TTTTAATTTT
1436529 TTTATATTATA
1 TTTATATTATA
1436540 TTTATATCATATA
1 TTTATAT--TATA
*
1436553 ATTATATTATA
1 TTTATATTATA
1436564 TTTA
1 TTTA
1436568 ATGTTACCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 14 0.58
13 10 0.42
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTATATTATA
Found at i:1437337 original size:37 final size:37
Alignment explanation
Indices: 1437293--1437369 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
1437283 ATAAATCAAA
*
1437293 TTACTTATTTAATTTAATAGATTTAATCTGAATTTAT
1 TTACTTATTTAATTTAATAGATTTAATATGAATTTAT
*
1437330 TTACTTATTTAATTTAATAGATTTGATATGAATTTAT
1 TTACTTATTTAATTTAATAGATTTAATATGAATTTAT
1437367 TTA
1 TTA
1437370 AGTCTTCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (37 bp):
TTACTTATTTAATTTAATAGATTTAATATGAATTTAT
Found at i:1438430 original size:18 final size:19
Alignment explanation
Indices: 1438393--1438435 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1438383 ACTTTTATTT
*
1438393 AATTAAATTTTATAATTAA
1 AATTTAATTTTATAATTAA
1438412 AATTTAATTTTAT-ATTAA
1 AATTTAATTTTATAATTAA
1438430 AATTTA
1 AATTTA
1438436 CTCCCCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTAATTTTATAATTAA
Found at i:1439474 original size:15 final size:15
Alignment explanation
Indices: 1439454--1439494 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1439444 TATTTACGTT
**
1439454 AATTTTAATTTTTTA
1 AATTTTAATTTAATA
1439469 AATTTTAATTTAATA
1 AATTTTAATTTAATA
*
1439484 AATTTTTATTT
1 AATTTTAATTT
1439495 CAAATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTTAATTTAATA
Found at i:1439632 original size:29 final size:28
Alignment explanation
Indices: 1439569--1439632 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
1439559 TAATTACAAG
* **
1439569 ATAAAATTTTAAGATTTTTTATGTATAA
1 ATAAAAATTTAAGATTTTTTAAATATAA
*
1439597 ATTAAAATTTAAGAATTTATTTAAATAT-A
1 ATAAAAATTTAAG-ATTT-TTTAAATATAA
1439626 ATAAAAA
1 ATAAAAA
1439633 ATAAAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 11 0.38
29 11 0.38
30 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (28 bp):
ATAAAAATTTAAGATTTTTTAAATATAA
Found at i:1439642 original size:24 final size:24
Alignment explanation
Indices: 1439615--1439661 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1439605 TTAAGAATTT
1439615 ATTTAAATATAATA-AAAAATAAAA
1 ATTTAAATA-AATAGAAAAATAAAA
* *
1439639 ATTTACATAAATAGAAACATAAA
1 ATTTAAATAAATAGAAAAATAAA
1439662 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (24 bp):
ATTTAAATAAATAGAAAAATAAAA
Found at i:1439680 original size:3 final size:3
Alignment explanation
Indices: 1439672--1439705 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1439662 TTTTAAAAAT
1439672 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1439706 AGTCTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1440048 original size:21 final size:21
Alignment explanation
Indices: 1440022--1440066 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1440012 CAATAATACC
*
1440022 AATT-AAATAATTTAAATGTCA
1 AATTAAAAT-ATTGAAATGTCA
*
1440043 AATTAAAATATTGAAATTTCA
1 AATTAAAATATTGAAATGTCA
1440064 AAT
1 AAT
1440067 AACATGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (21 bp):
AATTAAAATATTGAAATGTCA
Found at i:1442160 original size:5 final size:5
Alignment explanation
Indices: 1442154--1442190 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
1442144 TTTTATGAAA
*
1442154 AATAA AATAT AATAT AATAT AATAT AATAT -ATAT AAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT
1442191 TAAATTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:1442252 original size:11 final size:11
Alignment explanation
Indices: 1442154--1442244 Score: 52
Period size: 10 Copynumber: 8.8 Consensus size: 11
1442144 TTTTATGAAA
1442154 AATA-AAATAT
1 AATATAAATAT
1442164 AATAT-AATAT
1 AATATAAATAT
1442174 AATAT-AATAT
1 AATATAAATAT
*
1442184 -ATATAATTA-
1 AATATAAATAT
* *
1442193 AAT-TATTATTT
1 AATATA-AATAT
* * * *
1442204 ATTTTATATTT
1 AATATAAATAT
*
1442215 AAT-TAAAAAT
1 AATATAAATAT
1442225 AATATAAATAT
1 AATATAAATAT
1442236 AATATAAAT
1 AATATAAAT
1442245 CATATATAGA
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
9 6 0.09
10 32 0.50
11 24 0.38
12 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATATAAATAT
Found at i:1442983 original size:22 final size:22
Alignment explanation
Indices: 1442955--1443024 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 22
1442945 GGATGCGGAT
1442955 AATATTATATAAAAATAATTAA
1 AATATTATATAAAAATAATTAA
* *
1442977 AATATTATAT-AATATAATAAA
1 AATATTATATAAAAATAATTAA
* *
1442998 AATATAAATATATAAATATATTAA
1 AATAT-TATATAAAAATA-ATTAA
1443022 AAT
1 AAT
1443025 TTTAAATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 14 0.36
22 14 0.36
23 4 0.10
24 7 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATTATATAAAAATAATTAA
Found at i:1442988 original size:16 final size:16
Alignment explanation
Indices: 1442969--1443090 Score: 53
Period size: 17 Copynumber: 7.6 Consensus size: 16
1442959 TTATATAAAA
1442969 ATAATTAAAATATTAT
1 ATAATTAAAATATTAT
* *
1442985 ATAATATAATAAAAATAT
1 ATAAT-TAA-AATATTAT
1443003 A-AATATATAAATA-TATT
1 ATAAT-TA-AAATATTA-T
* *
1443020 AAAATTTTAAATTATT-T
1 ATAA--TTAAAATATTAT
*
1443037 ATTATTAAAAT-TTAT
1 ATAATTAAAATATTAT
1443052 ATAATATAAAATATT-T
1 ATAAT-TAAAATATTAT
*
1443068 TTAA-T-AAA-ATTAT
1 ATAATTAAAATATTAT
*
1443081 ATAAATAAAA
1 ATAATTAAAA
1443091 ATATATTATT
Statistics
Matches: 82, Mismatches: 10, Indels: 29
0.68 0.08 0.24
Matches are distributed among these distances:
12 3 0.04
13 7 0.09
14 4 0.05
15 14 0.17
16 17 0.21
17 19 0.23
18 14 0.17
19 3 0.04
20 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAATTAAAATATTAT
Found at i:1443067 original size:31 final size:29
Alignment explanation
Indices: 1443027--1443119 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 29
1443017 ATTAAAATTT
*
1443027 TAAATTATTTATTATTAAAATTTATATAATA
1 TAAAATATTTATTATTAAAA-TTATATAA-A
*
1443058 TAAAATATTT-TTAATAAAATTATATAAA
1 TAAAATATTTATTATTAAAATTATATAAA
*
1443086 TAAAAATATATTATTATTATATAAATATATAAA
1 T-AAAATAT-TTATTATTA-A-AATTATATAAA
1443119 T
1 T
1443120 TTAATTTGTG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.04
29 15 0.28
30 10 0.19
31 14 0.26
32 1 0.02
33 11 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAAATATTTATTATTAAAATTATATAAA
Found at i:1443291 original size:14 final size:14
Alignment explanation
Indices: 1443263--1443296 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1443253 GATCATAAAT
1443263 TTATT-AAATTATA
1 TTATTAAAATTATA
*
1443276 TTATTAAAATTTTA
1 TTATTAAAATTATA
1443290 TTATTAA
1 TTATTAA
1443297 TAAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATTAAAATTATA
Found at i:1443295 original size:22 final size:21
Alignment explanation
Indices: 1443270--1443324 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
1443260 AATTTATTAA
1443270 ATTATATTATTAAAAT-TTTATT
1 ATTA-ATTATTAAAATATTTA-T
*
1443292 ATTAATAAATTAAAATATTTAT
1 ATTAAT-TATTAAAATATTTAT
1443314 ATTAATT-TTAA
1 ATTAATTATTAA
1443325 TAAAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 4 0.14
21 2 0.07
22 19 0.66
23 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTAATTATTAAAATATTTAT
Found at i:1443471 original size:23 final size:22
Alignment explanation
Indices: 1443431--1443494 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
1443421 AATTATTTTT
* * *
1443431 TTAAAAAAAATTACTTAATAAAA
1 TTAATAAAAATAATTTAAT-AAA
**
1443454 TTAATAAAAATAATTTAATTTA
1 TTAATAAAAATAATTTAATAAA
1443476 TTAATAATAAA-AATTTAAT
1 TTAATAA-AAATAATTTAAT
1443495 GATATAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAATAAAAATAATTTAATAAA
Found at i:1443478 original size:22 final size:22
Alignment explanation
Indices: 1443453--1443494 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1443443 ACTTAATAAA
1443453 ATTAATAA-AAATAATTTAATTT
1 ATTAATAATAAA-AATTTAATTT
1443475 ATTAATAATAAAAATTTAAT
1 ATTAATAATAAAAATTTAAT
1443495 GATATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAATAATAAAAATTTAATTT
Found at i:1443502 original size:22 final size:22
Alignment explanation
Indices: 1443453--1443499 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1443443 ACTTAATAAA
*
1443453 ATTAATAA-AAATAATTTAATTT
1 ATTAATAATAAA-AATTTAATAT
1443475 ATTAATAATAAAAATTTAATGAT
1 ATTAATAATAAAAATTTAAT-AT
1443498 AT
1 AT
1443500 AATTTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTAATAATAAAAATTTAATAT
Found at i:1443507 original size:24 final size:25
Alignment explanation
Indices: 1443480--1443539 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
1443470 AATTTATTAA
*
1443480 TAATAAAAATT-TAATGATATAATT
1 TAATAAAAATTAAAATGATATAATT
**
1443504 TAAT-AAAATTAAAATTTTATAATT
1 TAATAAAAATTAAAATGATATAATT
1443528 TATATAAAAATT
1 TA-ATAAAAATT
1443540 GATATTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 6 0.20
24 16 0.53
25 2 0.07
26 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TAATAAAAATTAAAATGATATAATT
Found at i:1443941 original size:22 final size:22
Alignment explanation
Indices: 1443913--1443954 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1443903 TTGAACCCAT
1443913 AAAAATTAAATTAAATTAATAA
1 AAAAATTAAATTAAATTAATAA
* *
1443935 AAAAATTAATTTAATTTAAT
1 AAAAATTAAATTAAATTAAT
1443955 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAATTAAATTAAATTAATAA
Found at i:1444170 original size:178 final size:177
Alignment explanation
Indices: 1443871--1444208 Score: 590
Period size: 178 Copynumber: 1.9 Consensus size: 177
1443861 ATATATATTA
**
1443871 AAATAAAGTAGTTTGTGAATAAATAGGAACTATTGAACCCATAAAAATTAAATTAAATTAATAAA
1 AAATAAAGTAGTTTGTGAATAAATAAAAACTATTGAACCCATAAAAATTAAATTAAATTAATAAA
1443936 AAAATTAATTTAATTTAATTTTTATTTTTAAAAAAATTATTTTATTAAGTGATGTGATACAAATA
66 AAAATTAATTTAATTTAATTTTTATTTTTAAAAAAATTATTTTATTAAGTGATGTGATACAAATA
1444001 TTTAATCTTTTAGTTTTATATTAAAAGATTAATGTTGAAAACACATCT
131 TTTAATCTTTTAGTTTTATATTAAAA-ATTAATGTTGAAAACACATCT
*
1444049 AAATAAAGTAGTTTGTGAATAAATAAAAACTATTGAACCGATAAAAATTAAATTAAATTAAT-AA
1 AAATAAAGTAGTTTGTGAATAAATAAAAACTATTGAACCCATAAAAATTAAATTAAATTAATAAA
* *
1444113 AAAATTAAATTTAAGTTT-ATTTTTATTTTTTAAAAATTTATTTTATTAAGTGATGTGATACAAA
66 AAAATT-AATTTAA-TTTAATTTTTATTTTTAAAAAAATTATTTTATTAAGTGATGTGATACAAA
1444177 TATTTAATCTTTTAGTTTTATATTAAAAATTA
129 TATTTAATCTTTTAGTTTTATATTAAAAATTA
1444209 TACTATATAA
Statistics
Matches: 153, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
177 12 0.08
178 138 0.90
179 3 0.02
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (177 bp):
AAATAAAGTAGTTTGTGAATAAATAAAAACTATTGAACCCATAAAAATTAAATTAAATTAATAAA
AAAATTAATTTAATTTAATTTTTATTTTTAAAAAAATTATTTTATTAAGTGATGTGATACAAATA
TTTAATCTTTTAGTTTTATATTAAAAATTAATGTTGAAAACACATCT
Found at i:1444871 original size:2 final size:2
Alignment explanation
Indices: 1444864--1444895 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1444854 TATCTATAAA
1444864 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
1444896 TACGTTTGTA
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:1446065 original size:17 final size:16
Alignment explanation
Indices: 1446041--1446079 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1446031 ACAAAAACAT
1446041 TCAAATTATAAAAAAA
1 TCAAATTATAAAAAAA
*
1446057 TCAATATTATTAAAAAA
1 TCAA-ATTATAAAAAAA
1446074 T-AAATT
1 TCAAATT
1446080 TATTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 6 0.29
17 12 0.57
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
TCAAATTATAAAAAAA
Found at i:1446082 original size:16 final size:17
Alignment explanation
Indices: 1446045--1446083 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1446035 AAACATTCAA
* *
1446045 ATTATAAAAAAATCAAT
1 ATTATTAAAAAATAAAT
1446062 ATTATTAAAAAATAAAT
1 ATTATTAAAAAATAAAT
1446079 -TTATT
1 ATTATT
1446084 TTTTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTATTAAAAAATAAAT
Found at i:1447065 original size:21 final size:21
Alignment explanation
Indices: 1447041--1447080 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1447031 ATTAAAAATA
1447041 ATTATAATAATAAAATTAATT
1 ATTATAATAATAAAATTAATT
* *
1447062 ATTATAGTAGTAAAATTAA
1 ATTATAATAATAAAATTAA
1447081 AATTGATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTATAATAATAAAATTAATT
Found at i:1447665 original size:21 final size:23
Alignment explanation
Indices: 1447641--1447686 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
1447631 TGTATTAATT
*
1447641 TTATTTTAT-ATTTA-ATAAATA
1 TTATTTGATAATTTATATAAATA
*
1447662 TTATTTGATAATTTATTTAAATA
1 TTATTTGATAATTTATATAAATA
1447685 TT
1 TT
1447687 TTTATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 5 0.24
23 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTATTTGATAATTTATATAAATA
Found at i:1447771 original size:25 final size:26
Alignment explanation
Indices: 1447732--1447791 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
1447722 ATTTTAATAG
* *
1447732 AAAAAACAAATTATAAAATTATAAA-
1 AAAAAATAATTTATAAAATTATAAAT
* *
1447757 AATAAATAATTTATAAAATTTTAAAT
1 AAAAAATAATTTATAAAATTATAAAT
1447783 AAAAAATAA
1 AAAAAATAA
1447792 ATTAATAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 21 0.72
26 8 0.28
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (26 bp):
AAAAAATAATTTATAAAATTATAAAT
Found at i:1447811 original size:52 final size:52
Alignment explanation
Indices: 1447704--1447809 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 52
1447694 ATTATTATTT
*
1447704 AAATAAACAATTTAAAATATTTTAATAGAAAAAACAAATTATAAAATTATAA
1 AAATAAACAATTTAAAATATTTTAATAGAAAAAACAAATTATAAAATTAAAA
* * * *
1447756 AAATAAATAATTTATAAA-ATTTTAA-ATAAAAAATAAATTA-ATAATGTAAAA
1 AAATAAACAATTTA-AAATATTTTAATAGAAAAAACAAATTATAAAAT-TAAAA
1447807 AAA
1 AAA
1447810 ATTGAATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
50 4 0.09
51 20 0.43
52 20 0.43
53 3 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (52 bp):
AAATAAACAATTTAAAATATTTTAATAGAAAAAACAAATTATAAAATTAAAA
Found at i:1448227 original size:2 final size:2
Alignment explanation
Indices: 1448220--1448289 Score: 51
Period size: 2 Copynumber: 37.0 Consensus size: 2
1448210 TTTTAAATTT
* *
1448220 TA TA TA TA TA TA TA TA TA TA TA TT TGA TA TA -A T- TT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
* * *
1448260 TA TA TT TT TG TA -A T- 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
1448290 ATCAATTTGA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
1 5 0.09
2 50 0.89
3 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1450604 original size:2 final size:2
Alignment explanation
Indices: 1450556--1450591 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1450546 AAGAAATACA
1450556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1450592 TCGTATGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1451605 original size:15 final size:15
Alignment explanation
Indices: 1451585--1451614 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1451575 ATTTTAAAAA
*
1451585 TAAATATATTTTTAT
1 TAAATATATATTTAT
1451600 TAAATATATATTTAT
1 TAAATATATATTTAT
1451615 ATTTCACGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAATATATATTTAT
Found at i:1460938 original size:22 final size:24
Alignment explanation
Indices: 1460895--1460951 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
1460885 ACTAAAAATT
1460895 TTAAATTTATTTAACTGATAATCAAA
1 TTAAATTT-TTTAACT-ATAATCAAA
1460921 TTAAATTTTTTAA-T-TAATCAAA
1 TTAAATTTTTTAACTATAATCAAA
* *
1460943 CTGAATTTT
1 TTAAATTTT
1460952 ATTTCAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 15 0.52
24 1 0.03
25 5 0.17
26 8 0.28
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (24 bp):
TTAAATTTTTTAACTATAATCAAA
Done.