Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 141 of 182
Found at i:43813025 original size:9 final size:8
Alignment explanation
Indices: 43813006--43813047 Score: 57
Period size: 9 Copynumber: 4.9 Consensus size: 8
43812996 ATTCTAGAAA
43813006 TTTTTAAT
1 TTTTTAAT
43813014 TTTTTAACT
1 TTTTTAA-T
43813023 TTTTTATAT
1 TTTTTA-AT
43813032 TTTTTAGAT
1 TTTTTA-AT
43813041 TTTTTAA
1 TTTTTAA
43813048 AAAATTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 8 0.26
9 22 0.71
10 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (8 bp):
TTTTTAAT
Found at i:43813104 original size:19 final size:19
Alignment explanation
Indices: 43813080--43813137 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 19
43813070 ATAAATTTAA
43813080 GAATTTTTATAAA-TATTTT
1 GAATTTTTA-AAATTATTTT
43813099 GAA-TTTTAAAATTTATTTT
1 GAATTTTTAAAA-TTATTTT
43813118 GAATTTTTGAAAATTATTTT
1 GAATTTTT-AAAATTATTTT
43813138 TTTTTGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.09
18 5 0.14
19 12 0.34
20 11 0.31
21 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
GAATTTTTAAAATTATTTT
Found at i:43813623 original size:20 final size:20
Alignment explanation
Indices: 43813595--43813634 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43813585 GATTCGTTCG
*
43813595 TATAAAAAAATTATTTTTTA
1 TATAAAAAAATAATTTTTTA
*
43813615 TATATAAAAATAATTTTTTA
1 TATAAAAAAATAATTTTTTA
43813635 ACAAGAATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAAAAAAATAATTTTTTA
Found at i:43821479 original size:18 final size:18
Alignment explanation
Indices: 43821456--43821644 Score: 154
Period size: 18 Copynumber: 10.7 Consensus size: 18
43821446 GAGTCCACGC
* *
43821456 TGTGCTCTAAGTTAGCAT
1 TGTGCTCCAAGTTTGCAT
* ***
43821474 TATGCTCCAAGTTCATAT
1 TGTGCTCCAAGTTTGCAT
* *
43821492 TGTGCTCCAAGTTAGCAA
1 TGTGCTCCAAGTTTGCAT
*
43821510 TGTGCTCTAAGTTTGCAT
1 TGTGCTCCAAGTTTGCAT
*
43821528 TGTGCTCCAAGTTTGCAA
1 TGTGCTCCAAGTTTGCAT
* ** * *
43821546 TCTGCTGTAAGTTCGCAA
1 TGTGCTCCAAGTTTGCAT
*
43821564 TATGCTCCAA-TTTGCCA-
1 TGTGCTCCAAGTTTG-CAT
*
43821581 TGTGCT-CAAGTTTGCAA
1 TGTGCTCCAAGTTTGCAT
* *
43821598 TATGCTCCAAGTTCGCAT
1 TGTGCTCCAAGTTTGCAT
*
43821616 T-TGTTCCAAG-TTGCAT
1 TGTGCTCCAAGTTTGCAT
43821632 TGTGCTCCAAGTT
1 TGTGCTCCAAGTT
43821645 CAAATCATGC
Statistics
Matches: 135, Mismatches: 30, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
16 11 0.08
17 33 0.24
18 91 0.67
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (18 bp):
TGTGCTCCAAGTTTGCAT
Found at i:43821480 original size:36 final size:36
Alignment explanation
Indices: 43821440--43821540 Score: 85
Period size: 36 Copynumber: 2.8 Consensus size: 36
43821430 GTTTAAGTTC
* * *
43821440 TGCTCCGAGTCCACGCTGTGCTCTAAGTTAGCATTA
1 TGCTCCAAGTCCACACTGTGCTCCAAGTTAGCATTA
* * * * *
43821476 TGCTCCAAGTTCATATTGTGCTCCAAGTTAGCAATG
1 TGCTCCAAGTCCACACTGTGCTCCAAGTTAGCATTA
* *** *
43821512 TGCTCTAAGTTTGCATTGTGCTCCAAGTT
1 TGCTCCAAGTCCACACTGTGCTCCAAGTT
43821541 TGCAATCTGC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.35
Consensus pattern (36 bp):
TGCTCCAAGTCCACACTGTGCTCCAAGTTAGCATTA
Found at i:43821546 original size:36 final size:36
Alignment explanation
Indices: 43821490--43821644 Score: 165
Period size: 34 Copynumber: 4.4 Consensus size: 36
43821480 CCAAGTTCAT
*
43821490 ATTGTGCTCCAAGTTAGCAATGTGCTCTAAGTTTGC
1 ATTGTGCTCCAAGTTTGCAATGTGCTCTAAGTTTGC
* * *
43821526 ATTGTGCTCCAAGTTTGCAATCTGCTGTAAGTTCGC
1 ATTGTGCTCCAAGTTTGCAATGTGCTCTAAGTTTGC
* * *
43821562 AATATGCTCCAA-TTTGCCATGTGCTC-AAGTTTGC
1 ATTGTGCTCCAAGTTTGCAATGTGCTCTAAGTTTGC
* * * * * *
43821596 AATATGCTCCAAGTTCGC-ATTTGTTCCAAG-TTGC
1 ATTGTGCTCCAAGTTTGCAATGTGCTCTAAGTTTGC
43821630 ATTGTGCTCCAAGTT
1 ATTGTGCTCCAAGTT
43821645 CAAATCATGC
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
34 42 0.41
35 18 0.18
36 42 0.41
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (36 bp):
ATTGTGCTCCAAGTTTGCAATGTGCTCTAAGTTTGC
Found at i:43821558 original size:54 final size:54
Alignment explanation
Indices: 43821456--43821644 Score: 194
Period size: 54 Copynumber: 3.6 Consensus size: 54
43821446 GAGTCCACGC
* * * * *
43821456 TGTGCTCTAAGTTAGCATTATGCTCCAAG-TT-CATATTGTGCTCCAAGTTAGCAA
1 TGTGCTCCAAGTTTGCATTGTGCTCCAAGTTTGCA-A-TATGCTCCAAGTTCGCAA
* * **
43821510 TGTGCTCTAAGTTTGCATTGTGCTCCAAGTTTGCAATCTGCTGTAAGTTCGCAA
1 TGTGCTCCAAGTTTGCATTGTGCTCCAAGTTTGCAATATGCTCCAAGTTCGCAA
*
43821564 TATGCTCCAA-TTTGCCA-TGTGCT-CAAGTTTGCAATATGCTCCAAGTTCGC-A
1 TGTGCTCCAAGTTTG-CATTGTGCTCCAAGTTTGCAATATGCTCCAAGTTCGCAA
* *
43821615 TTTGTTCCAAG-TTGCATTGTGCTCCAAGTT
1 TGTGCTCCAAGTTTGCATTGTGCTCCAAGTT
43821645 CAAATCATGC
Statistics
Matches: 116, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
50 2 0.02
51 18 0.16
52 30 0.26
53 10 0.09
54 51 0.44
55 3 0.03
56 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (54 bp):
TGTGCTCCAAGTTTGCATTGTGCTCCAAGTTTGCAATATGCTCCAAGTTCGCAA
Found at i:43825453 original size:26 final size:26
Alignment explanation
Indices: 43825418--43825470 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
43825408 CCAAACCAAA
43825418 AAAACAAATCATTATGCAAGAAATAT
1 AAAACAAATCATTATGCAAGAAATAT
43825444 AAAACAAATCATTATGCAAGAAATAT
1 AAAACAAATCATTATGCAAGAAATAT
43825470 A
1 A
43825471 TCAAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.23
Consensus pattern (26 bp):
AAAACAAATCATTATGCAAGAAATAT
Found at i:43826441 original size:2 final size:2
Alignment explanation
Indices: 43826436--43826473 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
43826426 ACTTTATATA
43826436 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
43826474 CAGAAATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:43828272 original size:32 final size:33
Alignment explanation
Indices: 43828213--43828276 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
43828203 TTTTTATTAC
*
43828213 ATTATTTAGTGTTGTAACTTTACCATATATAAT
1 ATTATTTAATGTTGTAACTTTACCATATATAAT
*
43828246 ATTATTTAATGTTGT-ATTTTACCATATATAA
1 ATTATTTAATGTTGTAACTTTACCATATATAA
43828277 ATTGATAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (33 bp):
ATTATTTAATGTTGTAACTTTACCATATATAAT
Found at i:43830923 original size:42 final size:42
Alignment explanation
Indices: 43830864--43830951 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
43830854 AAAAAGTACA
* *
43830864 TCCAGTGGAGCATGCTTTCTGCATAA-TTGGCA-GAAAAGCTCG
1 TCCAGTGGAGCATGCTTTCAGCA-AAGTTGGCAGGAAAA-CACG
*
43830906 TCCAGTTGAGCGA-GCTTTCAGCAAAGTTGGCAGGAAAACACG
1 TCCAGTGGAGC-ATGCTTTCAGCAAAGTTGGCAGGAAAACACG
43830948 TCCA
1 TCCA
43830952 ACTGAACGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 2 0.05
42 32 0.80
43 6 0.15
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (42 bp):
TCCAGTGGAGCATGCTTTCAGCAAAGTTGGCAGGAAAACACG
Found at i:43832330 original size:20 final size:18
Alignment explanation
Indices: 43832280--43832331 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
43832270 TATCAAGATA
43832280 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
43832297 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
43832317 AATATTAAATTAATA
1 AATATTAAATTAATA
43832332 AAATAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:43832372 original size:17 final size:17
Alignment explanation
Indices: 43832350--43832383 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
43832340 ATTAAATAAA
43832350 TTTTTATAA-ATGTTTAT
1 TTTTTA-AATATGTTTAT
43832367 TTTTTAAATATGTTTAT
1 TTTTTAAATATGTTTAT
43832384 CATAGTATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTTAAATATGTTTAT
Found at i:43841351 original size:2 final size:2
Alignment explanation
Indices: 43841344--43841380 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43841334 TCTTTTTCAT
43841344 TA TA TA TA 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 TA TA TA TA T
43841381 GAGATTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43843826 original size:62 final size:63
Alignment explanation
Indices: 43843759--43843895 Score: 251
Period size: 62 Copynumber: 2.2 Consensus size: 63
43843749 AAATAGGAGC
43843759 AAAACAAATAAAATGACGAAAGGATTATGTTTTAAAAAGATTTGATGATAAAATAAAAAA-TA
1 AAAACAAATAAAATGACGAAAGGATTATGTTTTAAAAAGATTTGATGATAAAATAAAAAATTA
43843821 AAAACAAATAAAATGACGAAAGGATTATGTTTTAAAAAGATTTGATGATAAAATAAAAAATTA
1 AAAACAAATAAAATGACGAAAGGATTATGTTTTAAAAAGATTTGATGATAAAATAAAAAATTA
*
43843884 AAAA-AATTAAAA
1 AAAACAAATAAAA
43843896 ACAACATAAA
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
62 67 0.92
63 6 0.08
ACGTcount: A:0.60, C:0.03, G:0.12, T:0.26
Consensus pattern (63 bp):
AAAACAAATAAAATGACGAAAGGATTATGTTTTAAAAAGATTTGATGATAAAATAAAAAATTA
Found at i:43847136 original size:12 final size:12
Alignment explanation
Indices: 43847101--43847143 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
43847091 AAGGGTTATC
* *
43847101 AAAATCATTTTT
1 AAAATTATTTTA
*
43847113 AAAATGAGTTTTA
1 AAAATTA-TTTTA
43847126 AAAATTATTTTA
1 AAAATTATTTTA
43847138 AAAATT
1 AAAATT
43847144 TTGGAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (12 bp):
AAAATTATTTTA
Found at i:43848451 original size:30 final size:29
Alignment explanation
Indices: 43848296--43848453 Score: 92
Period size: 30 Copynumber: 5.4 Consensus size: 29
43848286 GAAACATCTG
* *
43848296 GGGGT-AAAATGGTAATTTT-GGAAGTATC
1 GGGGTCAAAAT-GTAATTTTGGGAAGTTTT
* * * * **
43848324 AGGATCAAAAATGGAATTTTTGGAAGTTCG
1 GGGGTC-AAAATGTAATTTTGGGAAGTTTT
***
43848354 GGGGT-AAAAGTGTAATTTTCAAAAGTTTT
1 GGGGTCAAAA-TGTAATTTTGGGAAGTTTT
* *
43848383 GAGGGT-AAAACTATAATTTTTGGAAGTTTT
1 G-GGGTCAAAA-TGTAATTTTGGGAAGTTTT
*
43848413 GTGGTCAAAATGTAATTTTGGAGAAG-TTT
1 GGGGTCAAAATGTAATTTTGG-GAAGTTTT
43848442 GGGGATCAAAAT
1 GGGG-TCAAAAT
43848454 TCAATTTATG
Statistics
Matches: 99, Mismatches: 23, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
28 7 0.07
29 39 0.39
30 53 0.54
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTGGGAAGTTTT
Found at i:43849068 original size:5 final size:5
Alignment explanation
Indices: 43849058--43849088 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
43849048 AAATTTACTC
43849058 CTTTT CTTTT CTTTT CTTTT CTTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT C-TTTT CTTTT
43849089 TCTCTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
CTTTT
Found at i:43849078 original size:15 final size:16
Alignment explanation
Indices: 43849058--43849088 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43849048 AAATTTACTC
43849058 CTTTTC-TTTTCTTTT
1 CTTTTCTTTTTCTTTT
43849073 CTTTTCTTTTTCTTTT
1 CTTTTCTTTTTCTTTT
43849089 TCTCTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
CTTTTCTTTTTCTTTT
Found at i:43849477 original size:13 final size:13
Alignment explanation
Indices: 43849455--43849488 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
43849445 CTTCTTTTTT
*
43849455 TTAATTAATAATA
1 TTAATAAATAATA
*
43849468 TTAATAAATATTA
1 TTAATAAATAATA
43849481 TTAATAAA
1 TTAATAAA
43849489 ATCTTCATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAATAAATAATA
Found at i:43850381 original size:17 final size:17
Alignment explanation
Indices: 43850346--43850393 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
43850336 TTTAAAAATT
*
43850346 ATTTCAAATTCAAACTAA
1 ATTT-AAATTTAAACTAA
*
43850364 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAACTAA
*
43850381 ATTTAATTTTAAA
1 ATTTAAATTTAAA
43850394 AATAAATCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAACTAA
Found at i:43851191 original size:205 final size:206
Alignment explanation
Indices: 43850766--43851577 Score: 1115
Period size: 205 Copynumber: 3.9 Consensus size: 206
43850756 TTTCATTAAC
* * * * ** * *
43850766 TTGGCCTTCTTCTCAGTATTTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATCCACTTCTCTG
1 TTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTG
* * * * * * *
43850831 GGTTTCCACAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTAT
66 GATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * * **
43850896 TGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGTTCGCATTGAAA
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGC
*
43850961 CTGAGTTTGAT
196 CTGGGTTTGAT
* *
43850972 TTGGTCTTCTTCTTAGTGTCTCATCAGGAAGATGACTGCATCACTTGTTTTAATTCGCTTCTCTG
1 TTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTG
* * *
43851037 GATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATTAAGAAGCTAACCA-TTTAT
66 GATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * *
43851101 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGAAAGCTGGGGTTCAAAGATTTGCTAGCATTGAGC
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGC
43851166 CTGGGTTTGAT
196 CTGGGTTTGAT
* * * * *
43851177 TTTGTATTCTTCTTAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTTTTTG
1 TTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTG
* * * *
43851242 GATCTCTTCAAGAAGACTAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCA-TTCAT
66 GATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * * *
43851306 GGCTTCGACCTACTTCTCAGTATCTCATCAGAAAGCTGGGATTCGAAGATTTGCTCCCATTGAGC
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGC
* *
43851371 TTGGGTTTAAT
196 CTGGGTTTGAT
* *
43851382 TTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCGTATCACTTGTTTTAATTCGCTTCTCTG
1 TTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTG
* *
43851447 GATCTCCTCAAGAAGACGAATTTAGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTAT
66 GATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * * * * *
43851512 TGCTTCAACCTGCTTCTTAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTACTCGTATTTGAG
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCGCA-TTGAG
43851577 C
195 C
43851578 GTTGAGTTAG
Statistics
Matches: 533, Mismatches: 71, Indels: 3
0.88 0.12 0.00
Matches are distributed among these distances:
205 370 0.69
206 157 0.29
207 6 0.01
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (206 bp):
TTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTG
GATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
TGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGC
CTGGGTTTGAT
Found at i:43853146 original size:6 final size:6
Alignment explanation
Indices: 43853135--43853215 Score: 51
Period size: 6 Copynumber: 13.5 Consensus size: 6
43853125 CGACCTCTTC
* * * * *
43853135 TTTTCT TTTTCT TTTTCT TTTTGT TGTTGT TTTTGT TATTT-T TTGTT-A
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TT-TTCT
* *
43853183 TTTTGT TTTTCT TCTTCT TTTT-T CTTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT -TTTTCT TTT
43853216 ATTCATTTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
5 4 0.06
6 54 0.87
7 4 0.06
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:43858328 original size:57 final size:59
Alignment explanation
Indices: 43858252--43858385 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 59
43858242 CTTGGGGGCA
** * * * *
43858252 AAAATGGTAATTTTGG-AAAAATTTGGATTTAAAAATGACA-TTT-TAATATCCGAGGGT
1 AAAATGGTAATTTTGGAAAAAATCGGGA-TAAAAAATGAAACTTTGAAACATCCGAGGGT
* *
43858309 AAAACGGTAATTTTTGAAAAAATCGGGATAAAAAATGAAACTTTGAAACATCCGAGGGT
1 AAAATGGTAATTTTGGAAAAAATCGGGATAAAAAATGAAACTTTGAAACATCCGAGGGT
43858368 AAAATGGTAATTTTGGAA
1 AAAATGGTAATTTTGGAA
43858386 GTATCAGGGT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 24 0.38
58 12 0.19
59 28 0.44
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (59 bp):
AAAATGGTAATTTTGGAAAAAATCGGGATAAAAAATGAAACTTTGAAACATCCGAGGGT
Found at i:43858382 original size:29 final size:30
Alignment explanation
Indices: 43858299--43858382 Score: 68
Period size: 29 Copynumber: 2.8 Consensus size: 30
43858289 ACATTTTAAT
*
43858299 ATCCGAGGGTAAAACGGTAATTTTTGAAAAA
1 ATCCGAGGGTAAAATGGTAA-TTTTGAAAAA
* * * *
43858330 AT-CG-GGATAAAAAAT-GAAACTTTG-AAAC
1 ATCCGAGGGT--AAAATGGTAATTTTGAAAAA
43858358 ATCCGAGGGTAAAATGGTAATTTTG
1 ATCCGAGGGTAAAATGGTAATTTTG
43858383 GAAGTATCAG
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
28 10 0.25
29 16 0.40
30 8 0.20
31 6 0.15
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.26
Consensus pattern (30 bp):
ATCCGAGGGTAAAATGGTAATTTTGAAAAA
Found at i:43858404 original size:30 final size:29
Alignment explanation
Indices: 43858363--43858505 Score: 141
Period size: 30 Copynumber: 4.9 Consensus size: 29
43858353 GAAACATCCG
*
43858363 AGGGT-AAAATGGTAA-TTTTGGAAGTATC
1 AGGGTAAAAAT-GTAATTTTTGGAAGTTTC
* *
43858391 AGGGTCAAAAATGGAATTTTTGGAAATTT-
1 AGGGT-AAAAATGTAATTTTTGGAAGTTTC
*
43858420 AGGG-GAAAATGTAATTTTTGGAAGTTTC
1 AGGGTAAAAATGTAATTTTTGGAAGTTTC
* * *
43858448 GAGGGTAAAAGTGTAATTTTTGAAAGTTTT
1 -AGGGTAAAAATGTAATTTTTGGAAGTTTC
* *
43858478 AGGGTTAAAATGTAATTTTGGAGAAGTT
1 AGGGTAAAAATGTAATTTTTG-GAAGTT
43858506 CAAGGATCAA
Statistics
Matches: 94, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
27 20 0.21
28 5 0.05
29 29 0.31
30 40 0.43
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
AGGGTAAAAATGTAATTTTTGGAAGTTTC
Found at i:43858423 original size:29 final size:28
Alignment explanation
Indices: 43858363--43858496 Score: 114
Period size: 29 Copynumber: 4.7 Consensus size: 28
43858353 GAAACATCCG
* *
43858363 AGGGT-AAAATGGTAA-TTTTGGAAGTATC
1 AGGGTAAAAAT-GTAATTTTTGGAAAT-TT
*
43858391 AGGGTCAAAAATGGAATTTTTGGAAATTT
1 AGGGT-AAAAATGTAATTTTTGGAAATTT
* *
43858420 AGGG-GAAAATGTAATTTTTGGAAGTTT
1 AGGGTAAAAATGTAATTTTTGGAAATTT
*
43858447 CGAGGGTAAAAGTGTAATTTTT-GAAAGTTTT
1 --AGGGTAAAAATGTAATTTTTGGAAA--TTT
*
43858478 AGGGTTAAAATGTAATTTT
1 AGGGTAAAAATGTAATTTT
43858497 GGAGAAGTTC
Statistics
Matches: 87, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
27 20 0.23
28 5 0.06
29 32 0.37
30 27 0.31
31 3 0.03
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (28 bp):
AGGGTAAAAATGTAATTTTTGGAAATTT
Found at i:43858440 original size:57 final size:57
Alignment explanation
Indices: 43858363--43858496 Score: 166
Period size: 57 Copynumber: 2.3 Consensus size: 57
43858353 GAAACATCCG
43858363 AGGGTAAAATGGTAA-TTTTGGAAGTATC-AGGGTCAAAAATGGAATTTTTGGAAA-TTT
1 AGGGTAAAAT-GTAATTTTTGGAAGTATCGAGGGT-AAAAATGGAATTTTT-GAAAGTTT
* * * *
43858420 AGGGGAAAATGTAATTTTTGGAAGTTTCGAGGGTAAAAGTGTAATTTTTGAAAGTTTT
1 AGGGTAAAATGTAATTTTTGGAAGTATCGAGGGTAAAAATGGAATTTTTGAAAG-TTT
43858478 AGGGTTAAAATGTAATTTT
1 AGGG-TAAAATGTAATTTT
43858497 GGAGAAGTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
56 8 0.12
57 34 0.51
58 12 0.18
59 13 0.19
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (57 bp):
AGGGTAAAATGTAATTTTTGGAAGTATCGAGGGTAAAAATGGAATTTTTGAAAGTTT
Found at i:43858525 original size:59 final size:57
Alignment explanation
Indices: 43858363--43858512 Score: 137
Period size: 57 Copynumber: 2.6 Consensus size: 57
43858353 GAAACATCCG
* * * * *
43858363 AGGGTAAAATGGTAATTTT-GGAAGTATC-AGGGTCAAAAATGGAATTTTTGGAAATTT
1 AGGGGAAAAT-GTAATTTTGGGAAGTTTCAAGGAT-AAAAGTGTAATTTTTGGAAATTT
* * *
43858420 AGGGGAAAATGTAATTTTTGGAAGTTTCGAGGGTAAAAGTGTAATTTTT-GAAAGTTTT
1 AGGGGAAAATGTAATTTTGGGAAGTTTCAAGGATAAAAGTGTAATTTTTGGAAA--TTT
*
43858478 AGGGTTAAAATGTAATTTTGGAGAAG-TTCAAGGAT
1 AGGG-GAAAATGTAATTTTGG-GAAGTTTCAAGGAT
43858513 CAAATTTTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
56 12 0.15
57 30 0.38
58 12 0.15
59 21 0.27
60 4 0.05
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (57 bp):
AGGGGAAAATGTAATTTTGGGAAGTTTCAAGGATAAAAGTGTAATTTTTGGAAATTT
Found at i:43865356 original size:3 final size:3
Alignment explanation
Indices: 43865348--43865397 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
43865338 AAAATTAAGG
43865348 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43865396 AT
1 AT
43865398 CTTATGGATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:43873644 original size:5 final size:5
Alignment explanation
Indices: 43873634--43873663 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
43873624 GAAATCAATG
43873634 AATAA AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA
43873664 TGTAAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:43880267 original size:19 final size:19
Alignment explanation
Indices: 43880245--43880302 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
43880235 TAATAATTCT
43880245 AATAATTTTTAATTTTAAA
1 AATAATTTTTAATTTTAAA
* ***
43880264 AATAATTTTAATATTTTTTT
1 AATAATTTTTA-ATTTTAAA
43880284 AAT--TTTTTAATTTTAAA
1 AATAATTTTTAATTTTAAA
43880301 AA
1 AA
43880303 ATTAATTAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
17 7 0.23
18 5 0.17
19 10 0.33
20 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATAATTTTTAATTTTAAA
Found at i:43880273 original size:37 final size:37
Alignment explanation
Indices: 43880232--43880302 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
43880222 ATTTTTATTC
43880232 TTTTAATAATTCTAATAA-TTTTTAATTTTAAAAATAA
1 TTTTAAT-ATTCTAATAATTTTTTAATTTTAAAAATAA
* **
43880269 TTTTAATATTTTTTTAATTTTTTAATTTTAAAAA
1 TTTTAATATTCTAATAATTTTTTAATTTTAAAAA
43880303 ATTAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (37 bp):
TTTTAATATTCTAATAATTTTTTAATTTTAAAAATAA
Found at i:43880439 original size:29 final size:31
Alignment explanation
Indices: 43880389--43880446 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
43880379 AGATGATTTG
*
43880389 ATAAAGAAATATAAATTTAAAGACTAAAAAA
1 ATAAAAAAATATAAATTTAAAGACTAAAAAA
43880420 ATAAAAAAAT-TAAA-TTAAAGACTAAAA
1 ATAAAAAAATATAAATTTAAAGACTAAAA
43880447 TGATTTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
30 4 0.15
31 9 0.35
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (31 bp):
ATAAAAAAATATAAATTTAAAGACTAAAAAA
Found at i:43885732 original size:191 final size:188
Alignment explanation
Indices: 43885261--43886039 Score: 581
Period size: 191 Copynumber: 4.0 Consensus size: 188
43885251 TATTGTAGTG
* * * *
43885261 CAAAATTTATCCGTTCGTATTTTATTTTTAATCTTTTTTCAAAATTTATTTGTTC-GTATT-TTT
1 CAAAATTTAT-CTTTCATATTTTAGTTTTAATCTTTTTTCAAAATTTATTT-TTCTATATTATTT
* * * * ** *
43885324 TAA-CTTTTTTTCAAAATATATTTGTTCATATTTTATTTTTAA-TCTTTTATGCAAATTTATTTG
64 TAATCATTTTTT-AAAATTTATCTGTTCGTATTTTATTTTTAACTCTTTT-TTAAAATTTATCTG
* *
43885387 TTCGTATTTTATTTTTAATCTTTTTTTCAAAATTTATCTATTTGTATTTTATTTTTAAACTTTTT
127 TTCGTATTTTATTTTTAATC----TTGCAAAATTTATCTATTCGTATTTTATTTTTAAAC-TTTT
43885452 TT
187 TT
* * * ** *
43885454 CAAAATTTATCTTTCGTATTTTATTTTTAATCTCTTTTCAAAATTTATATGTTGGTATTTTATTT
1 CAAAATTTATCTTTCATATTTTAGTTTTAATCTTTTTTCAAAATTTAT-T-TTTCTATATTA-TT
* * * * * * *
43885519 TTAATCCTTTTTCAATATTTATCTGTTCGTATTTAATTTTTAACACTTTTTTAAAAATTATCTAT
63 TTAATCATTTTTTAAAATTTATCTGTTCGTATTTTATTTTTAACTCTTTTTTAAAATTTATCTGT
* * *
43885584 TGGTATTTTATTTTTAATCTTGCAAAATTTATTTGTTCGTATTTTATTTTTAATAC-TTTTT
128 TCGTATTTTATTTTTAATCTTGCAAAATTTATCTATTCGTATTTTATTTTTAA-ACTTTTTT
*
43885645 CAAAATTTATTTTTTCATATTTT-GTTTTAATCTTTTTTCAAAATTTATCTTTTCATATATTATT
1 CAAAATTTA-TCTTTCATATTTTAGTTTTAATCTTTTTTCAAAATTTAT-TTTTC-TATATTATT
*
43885709 ATTAATCATTTTTTAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTTTTTTAAAATTTAT
63 -TTAATCATTTTTTAAAATTTATCTGTTCGTATTTTATTTTTAA-C--TCTTTTTTAAAATTTAT
* **
43885774 CTGTTTGTATTTTATTTTTAATCTTTTATGCAAATTTTTTCAAAAATTTATCTGCTCGTATTTTA
124 CTGTTCGTATTTTATTTTTAATC---T-TG----------C-AAAATTTATCTATTCGTATTTTA
*
43885839 TTTTTAATCTTTTTTT
174 TTTTTAAAC-TTTTTT
* * * * * * *
43885855 CAAAATTTATTTGTTCGTATTTTATTTTTAATGC-TTTTTCAATATTTATCTGTTCAAATTTTAT
1 CAAAATTTATCT-TTCATATTTTAGTTTTAAT-CTTTTTTCAAAATTTAT-TTTTC-TATATTA-
* * * *
43885919 TTTTAAT-ACTTTTTCAAAATTATCTCTGTT-GATATTTTATTTTAAATCTTTTTTTTAAAATTT
61 TTTTAATCA-TTTTTTAAAATT-TATCTGTTCG-TATTTTATTTTTAA-CTCTTTTTTAAAATTT
* ** * * * * *
43885982 ATCTGTTTGTATTTT-TTAAATATTTTTTCAAAATTTATCTGTTTGTA-TTTATTTTTAA
122 ATCTGTTCGTATTTTATT-TTTAATCTTGCAAAATTTATCTATTCGTATTTTATTTTTAA
43886040 TTTTAATCTT
Statistics
Matches: 487, Mismatches: 60, Indels: 77
0.78 0.10 0.12
Matches are distributed among these distances:
190 4 0.01
191 83 0.17
192 78 0.16
193 14 0.03
194 50 0.10
195 16 0.03
196 60 0.12
197 12 0.02
198 2 0.00
206 1 0.00
207 1 0.00
208 2 0.00
209 33 0.07
210 57 0.12
211 49 0.10
212 25 0.05
ACGTcount: A:0.26, C:0.09, G:0.05, T:0.61
Consensus pattern (188 bp):
CAAAATTTATCTTTCATATTTTAGTTTTAATCTTTTTTCAAAATTTATTTTTCTATATTATTTTA
ATCATTTTTTAAAATTTATCTGTTCGTATTTTATTTTTAACTCTTTTTTAAAATTTATCTGTTCG
TATTTTATTTTTAATCTTGCAAAATTTATCTATTCGTATTTTATTTTTAAACTTTTTT
Found at i:43885755 original size:22 final size:21
Alignment explanation
Indices: 43885730--43885797 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
43885720 TTTAAAATTT
43885730 ATCTGTTCGTATTTTATTTTTA
1 ATCTGTT-GTATTTTATTTTTA
* * **
43885752 ATCT-TTTTTTTTTAAAATTT-
1 ATCTGTTGTATTTT-ATTTTTA
43885772 ATCTGTTTGTATTTTATTTTTA
1 ATCTG-TTGTATTTTATTTTTA
43885794 ATCT
1 ATCT
43885798 TTTATGCAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
20 9 0.26
21 10 0.29
22 15 0.44
ACGTcount: A:0.21, C:0.07, G:0.06, T:0.66
Consensus pattern (21 bp):
ATCTGTTGTATTTTATTTTTA
Found at i:43885758 original size:14 final size:14
Alignment explanation
Indices: 43885739--43885802 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
43885729 TATCTGTTCG
43885739 TATTTTATTTTTAA
1 TATTTTATTTTTAA
* *
43885753 TCTTTTTTTTTTAA
1 TATTTTATTTTTAA
* *
43885767 -AATTTATCTGTTT-G
1 TATTTTAT-T-TTTAA
43885781 TATTTTATTTTTAA
1 TATTTTATTTTTAA
*
43885795 TCTTTTAT
1 TATTTTAT
43885803 GCAAATTTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
13 7 0.19
14 21 0.57
15 9 0.24
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (14 bp):
TATTTTATTTTTAA
Found at i:43885853 original size:40 final size:39
Alignment explanation
Indices: 43885261--43886040 Score: 765
Period size: 39 Copynumber: 19.8 Consensus size: 39
43885251 TATTGTAGTG
*
43885261 CAAAATTTATCCGTTCGTATTTTATTTTTAATCTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
*
43885300 CAAAATTTATTTGTTCGTA---T-TTTTTAA-CTTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATC-TTTTTT
* * * *
43885335 CAAAATATATTTGTTCATATTTTATTTTTAATCTTTTATG
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTT-TT
*
43885375 C-AAATTTATTTGTTCGTATTTTATTTTTAATCTTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATC-TTTTTT
* * *
43885414 CAAAATTTATCTATTTGTATTTTATTTTTAAACTTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATC-TTTTTT
*
43885454 CAAAATTTATCT-TTCGTATTTTATTTTTAATCTCTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
* * *
43885492 CAAAATTTATATGTTGGTATTTTATTTTTAATCCTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
* * *
43885531 CAATATTTATCTGTTCGTATTTAATTTTTAACACTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAA-TCTTTTTT
* * * *
43885571 -AAAAATTATCTATTGGTATTTTATTTTTAATC---TTG
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
*
43885606 CAAAATTTATTTGTTCGTATTTTATTTTTAATAC-TTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAAT-CTTTTTT
* * * *
43885645 CAAAATTTATTTTTTCATATTTT-GTTTTAATCTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
* * * *
43885683 CAAAATTTATCTTTTCATATATTATTATTAATCATTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATC-TTTTTT
43885723 -AAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATC---TTTTTT
* *
43885764 TAAAATTTATCTGTTTGTATTTTATTTTTAATCTTTTATGCAAATTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTT-A------AT-C---TTTTTT
*
43885814 CAAAAATTTATCTGCTCGTATTTTATTTTTAATCTTTTTTT
1 C-AAAATTTATCTGTTCGTATTTTATTTTTAATC-TTTTTT
*
43885855 CAAAATTTATTTGTTCGTATTTTATTTTTAATGC-TTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAAT-CTTTTTT
* **
43885894 CAATATTTATCTGTTCAAATTTTATTTTTAATAC-TTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAAT-CTTTTTT
* *
43885933 CAAAATTATCTCTGTT-GATATTTTATTTTAAATCTTTTTTT
1 CAAAATT-TATCTGTTCG-TATTTTATTTTTAATC-TTTTTT
* * * *
43885974 TAAAATTTATCTGTTTGTA--TT-TTTTAAATATTTTTT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
*
43886010 CAAAATTTATCTGTTTGTA-TTTATTTTTAAT
1 CAAAATTTATCTGTTCGTATTTTATTTTTAAT
43886041 TTTAATCTTT
Statistics
Matches: 629, Mismatches: 74, Indels: 77
0.81 0.09 0.10
Matches are distributed among these distances:
34 1 0.00
35 32 0.05
36 52 0.08
37 12 0.02
38 60 0.10
39 256 0.41
40 123 0.20
41 26 0.04
42 27 0.04
43 2 0.00
44 2 0.00
49 2 0.00
50 8 0.01
51 26 0.04
ACGTcount: A:0.26, C:0.09, G:0.05, T:0.61
Consensus pattern (39 bp):
CAAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTT
Found at i:43885915 original size:93 final size:91
Alignment explanation
Indices: 43885716--43885892 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 91
43885706 ATTATTAATC
* * *
43885716 ATTTTTT-AAAATTTATCTGTTCGTATTTTATTTTTAATCTTTTTTTTTTAAAATTTATCTGTTT
1 ATTTTTTCAAAATTTATCTGCTCGTATTTTATTTTTAATC-TTTTTTTTCAAAATTTATCTGTTC
43885780 GTATTTTATTTTTAATCTTTTATGCAA
65 GTATTTTATTTTTAATCTTTTATGCAA
*
43885807 ATTTTTTCAAAAATTTATCTGCTCGTATTTTATTTTTAATC-TTTTTTTCAAAATTTATTTGTTC
1 ATTTTTTC-AAAATTTATCTGCTCGTATTTTATTTTTAATCTTTTTTTTCAAAATTTATCTGTTC
43885871 GTATTTTATTTTTAATGCTTTT
65 GTATTTTATTTTTAAT-CTTTT
43885893 TCAATATTTA
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
91 43 0.54
92 5 0.06
93 31 0.39
ACGTcount: A:0.24, C:0.08, G:0.06, T:0.63
Consensus pattern (91 bp):
ATTTTTTCAAAATTTATCTGCTCGTATTTTATTTTTAATCTTTTTTTTCAAAATTTATCTGTTCG
TATTTTATTTTTAATCTTTTATGCAA
Found at i:43885983 original size:210 final size:208
Alignment explanation
Indices: 43885607--43885996 Score: 556
Period size: 210 Copynumber: 1.9 Consensus size: 208
43885597 TTAATCTTGC
* * *
43885607 AAAATTTATTTGTTCGTATTTTATTTTTAATACTTTTTCAAAATTTATTTTTTCATATTTTGTTT
1 AAAATTTATCTGCTCGTATTTTATTTTTAATACTTTTTCAAAATTTATTTGTTCATATTTTGTTT
* * *
43885672 TAATCTTTTTTCAAAATTTATCTTTTCATATATTATTATTAATCATTTTTTAAAATTTATCTGTT
66 TAATCTTTTTTCAAAATTTATCTGTTCAAATATTATTATTAATCATTTTTCAAAATTTATCTGTT
*
43885737 CGTATTTTATTTTTAATCTTTTTTTTTTAAAATTTATCTGTTTGTATTTTATTTTTAATCTTTTA
131 CGTATTTTATTTTAAATC-TTTTTTTTTAAAATTTATCTGTTTGTATTTTATTTTTAATCTTTTA
43885802 TGCAAATTTTTTCA
195 TGCAAATTTTTTCA
* *
43885816 AAAATTTATCTGCTCGTATTTTATTTTTAAT-CTTTTTTTCAAAATTTATTTGTTCGTATTTTAT
1 AAAATTTATCTGCTCGTATTTTATTTTTAATAC--TTTTTCAAAATTTATTTGTTCATATTTT-G
* * * *
43885880 TTTTAATGC-TTTTTCAATATTTATCTGTTCAAATTTTATTTTTAAT-ACTTTTTCAAAATTATC
63 TTTTAAT-CTTTTTTCAAAATTTATCTGTTCAAATATTATTATTAATCA-TTTTTCAAAATT-TA
43885943 TCTGTT-GATATTTTATTTTAAATC-TTTTTTTTAAAATTTATCTGTTTGTATTTT
125 TCTGTTCG-TATTTTATTTTAAATCTTTTTTTTTAAAATTTATCTGTTTGTATTTT
43885997 TTAAATATTT
Statistics
Matches: 161, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
208 1 0.01
209 29 0.18
210 57 0.35
211 51 0.32
212 23 0.14
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (208 bp):
AAAATTTATCTGCTCGTATTTTATTTTTAATACTTTTTCAAAATTTATTTGTTCATATTTTGTTT
TAATCTTTTTTCAAAATTTATCTGTTCAAATATTATTATTAATCATTTTTCAAAATTTATCTGTT
CGTATTTTATTTTAAATCTTTTTTTTTAAAATTTATCTGTTTGTATTTTATTTTTAATCTTTTAT
GCAAATTTTTTCA
Found at i:43886008 original size:37 final size:36
Alignment explanation
Indices: 43885807--43886031 Score: 128
Period size: 40 Copynumber: 5.8 Consensus size: 36
43885797 TTTTATGCAA
* * *
43885807 ATTTTTTCAAAAATTTATCTGCTCGTATTTTATTTTTAAT
1 ATTTTTTC-AAAATTTATCTGTTTGTA--TT-TTTTAAAT
* * * *
43885847 CTTTTTTTCAAAATTTATTTGTTCGTATTTTATTTTTAAT
1 -ATTTTTTCAAAATTTATCTGTTTGTA--TT-TTTTAAAT
** * ** * *
43885887 GCTTTTTCAATATTTATCTGTTCAAATTTTATTTTTAAT
1 ATTTTTTCAAAATTTATCTGTT--TGTATT-TTTTAAAT
* *
43885926 ACTTTTTCAAAA-TTATCTCTGTTGATATTTTATTTTAAAT
1 ATTTTTTCAAAATTTATCTGT-TTG-TA--TT-TTTTAAAT
* *
43885966 CTTTTTTTTAAAATTTATCTGTTTGTATTTTTTAAAT
1 -ATTTTTTCAAAATTTATCTGTTTGTATTTTTTAAAT
43886003 ATTTTTTCAAAATTTATCTGTTTGTATTT
1 ATTTTTTCAAAATTTATCTGTTTGTATTT
43886032 ATTTTTAATT
Statistics
Matches: 153, Mismatches: 23, Indels: 21
0.78 0.12 0.11
Matches are distributed among these distances:
36 27 0.18
37 8 0.05
38 10 0.07
39 40 0.26
40 41 0.27
41 20 0.13
42 7 0.05
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.60
Consensus pattern (36 bp):
ATTTTTTCAAAATTTATCTGTTTGTATTTTTTAAAT
Found at i:43886239 original size:27 final size:28
Alignment explanation
Indices: 43886209--43886319 Score: 147
Period size: 27 Copynumber: 4.1 Consensus size: 28
43886199 ACACATAAGG
*
43886209 AAGTTTGTCGAGACAGTAAACACG-GGA
1 AAGTTCGTCGAGACAGTAAACACGAGGA
* * *
43886236 AAGTTTGTTGAGACAATAAACACG-GGA
1 AAGTTCGTCGAGACAGTAAACACGAGGA
43886263 AAGTTCGTCGAGACAGTAAACACGAGG-
1 AAGTTCGTCGAGACAGTAAACACGAGGA
* *
43886290 AAGTTCGCCGAGATAGTAAACACGAGGA
1 AAGTTCGTCGAGACAGTAAACACGAGGA
43886318 AA
1 AA
43886320 TCCTCCGGGA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 71 0.95
28 4 0.05
ACGTcount: A:0.40, C:0.15, G:0.28, T:0.17
Consensus pattern (28 bp):
AAGTTCGTCGAGACAGTAAACACGAGGA
Found at i:43886336 original size:27 final size:27
Alignment explanation
Indices: 43886252--43886345 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 27
43886242 GTTGAGACAA
* * *
43886252 TAAACACG-GGAAAGTTCGTCGAGACAG
1 TAAACACGAGGAAA-TCCGCCGAGATAG
* *
43886279 TAAACACGAGGAAGTTCGCCGAGATAG
1 TAAACACGAGGAAATCCGCCGAGATAG
* *
43886306 TAAACACGAGGAAATCCTCCGGGAT-G
1 TAAACACGAGGAAATCCGCCGAGATAG
43886332 ATAAACACGAGGAA
1 -TAAACACGAGGAA
43886346 GTCCACTAGG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.02
27 53 0.91
28 4 0.07
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (27 bp):
TAAACACGAGGAAATCCGCCGAGATAG
Found at i:43886357 original size:27 final size:27
Alignment explanation
Indices: 43886306--43886365 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
43886296 GCCGAGATAG
* *
43886306 TAAACACGAGGAAATCCTCCGGGATGA
1 TAAACACGAGGAAATCCACCAGGATGA
* * *
43886333 TAAACACGAGGAAGTCCACTAGGATGT
1 TAAACACGAGGAAATCCACCAGGATGA
43886360 TAAACA
1 TAAACA
43886366 TGATTTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (27 bp):
TAAACACGAGGAAATCCACCAGGATGA
Found at i:43891728 original size:16 final size:18
Alignment explanation
Indices: 43891707--43891743 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
43891697 GGTAACCATA
*
43891707 AATTTTTGAAA-GAAT-T
1 AATTTTTAAAATGAATAT
43891723 AATTTTTAAAATGAATAT
1 AATTTTTAAAATGAATAT
43891741 AAT
1 AAT
43891744 AAAAACCTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 4 0.22
18 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (18 bp):
AATTTTTAAAATGAATAT
Found at i:43904521 original size:17 final size:17
Alignment explanation
Indices: 43904499--43904536 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
43904489 AAGGATGAGG
43904499 TTGAGAAAATAATTTAA
1 TTGAGAAAATAATTTAA
*
43904516 TTGAGAAACTAATTTAA
1 TTGAGAAAATAATTTAA
43904533 TTGA
1 TTGA
43904537 TTTAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (17 bp):
TTGAGAAAATAATTTAA
Found at i:43907563 original size:26 final size:26
Alignment explanation
Indices: 43907503--43907566 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
43907493 TTTAGCATTG
* * *
43907503 CTTTTGAGAAA-TATTTTTAAAAAGTG
1 CTTTTGA-AAAGTAATTTTAAAAAATA
* *
43907529 CGTTAGAAAAGTAATTTTAAAAAATA
1 CTTTTGAAAAGTAATTTTAAAAAATA
43907555 CTTTTGAAAAGT
1 CTTTTGAAAAGT
43907567 TTGGTTTAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.38
Consensus pattern (26 bp):
CTTTTGAAAAGTAATTTTAAAAAATA
Found at i:43918215 original size:22 final size:24
Alignment explanation
Indices: 43918182--43918238 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
43918172 AAAAACTATC
43918182 TACA-AATCATATC-TCCAAGA-T
1 TACATAATCATATCTTCCAAGATT
* *
43918203 TACATAATTATATCTTCTAAGATT
1 TACATAATCATATCTTCCAAGATT
43918227 TACAT-ATCATAT
1 TACATAATCATAT
43918239 ATAAGATTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.13
22 8 0.27
23 12 0.40
24 6 0.20
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.39
Consensus pattern (24 bp):
TACATAATCATATCTTCCAAGATT
Found at i:43922879 original size:17 final size:17
Alignment explanation
Indices: 43922859--43922897 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
43922849 CATATTTTAC
43922859 TAAAATAATGAAGAGAA-
1 TAAAA-AATGAAGAGAAT
*
43922876 TAAAAGATGAAGAGAAT
1 TAAAAAATGAAGAGAAT
43922893 TAAAA
1 TAAAA
43922898 GAAAAACCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (17 bp):
TAAAAAATGAAGAGAAT
Found at i:43922887 original size:16 final size:17
Alignment explanation
Indices: 43922866--43922899 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
43922856 TACTAAAATA
43922866 ATGAAGAGAA-TAAAAG
1 ATGAAGAGAATTAAAAG
43922882 ATGAAGAGAATTAAAAG
1 ATGAAGAGAATTAAAAG
43922899 A
1 A
43922900 AAAACCCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (17 bp):
ATGAAGAGAATTAAAAG
Found at i:43925018 original size:245 final size:245
Alignment explanation
Indices: 43924581--43925032 Score: 600
Period size: 245 Copynumber: 1.8 Consensus size: 245
43924571 ATTTCTTGCC
* * * *
43924581 TTTTCCTATCAGAAGCCAACTTATAATTAGTTAACTAAGATGGTGAGGGTACTTGATGGTCGAAT
1 TTTTCCTATCAGAAGCCAACTTATAATTACTTAACTAAGATGGTGAGGATACCTGAGGGTCGAAT
* * * * * * *
43924646 GGAGCCCCAAACAGATCCGAAACAAATTCAAGCATGCAAGAATTAGAATTTTTTCATGTTGTCGC
66 GAAACCCCAAACAAATCCAAAACAAATTCAAGCATGCAAAAATTAGAATTTTGTCATGTTGTCAC
* * **
43924711 GACGTCGTGTGACTTTTCATTGGGACAAGACCTCTGTTTGTCACGTCGTTACGATGTTGAGCATT
131 GACATCGTGTGACTCTTCATTGGGACAAGACCTCTGTTTGTCACGTCGTTACGACATTGAGCATT
43924776 TACTCGTCAAGACGTCGCCCTTTTTTCAGCTTTTAACTTCACTTCTCATA
196 TACTCGTCAAGACGTCGCCCTTTTTTCAGCTTTTAACTTCACTTCTCATA
* * *
43924826 TTTTCCTATCACG-AGCCAACTTATAATTACTTAACTAAGATTGTGAGGATACCTGAGGGTTGGA
1 TTTTCCTATCA-GAAGCCAACTTATAATTACTTAACTAAGATGGTGAGGATACCTGAGGGTCGAA
* * ** *
43924890 TGAAACCTCAAACAAATCCAAAATAGTTTCAAGCATGCAAAAATTAGAATTTTGTCGTGTTGTCA
65 TGAAACCCCAAACAAATCCAAAACAAATTCAAGCATGCAAAAATTAGAATTTTGTCATGTTGTCA
* * * * * * **
43924955 CGATATCGTGTGACTCTTCGTTGGGATAAGAGCTCTGTTTGTCATGTTGTTGTGACATTGAGCAT
130 CGACATCGTGTGACTCTTCATTGGGACAAGACCTCTGTTTGTCACGTCGTTACGACATTGAGCAT
*
43925020 TTGCTCGTCAAGA
195 TTACTCGTCAAGA
43925033 AGCATCTCTG
Statistics
Matches: 174, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
245 173 0.99
246 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (245 bp):
TTTTCCTATCAGAAGCCAACTTATAATTACTTAACTAAGATGGTGAGGATACCTGAGGGTCGAAT
GAAACCCCAAACAAATCCAAAACAAATTCAAGCATGCAAAAATTAGAATTTTGTCATGTTGTCAC
GACATCGTGTGACTCTTCATTGGGACAAGACCTCTGTTTGTCACGTCGTTACGACATTGAGCATT
TACTCGTCAAGACGTCGCCCTTTTTTCAGCTTTTAACTTCACTTCTCATA
Found at i:43928641 original size:2 final size:2
Alignment explanation
Indices: 43928634--43928670 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43928624 AGTAACTAAG
43928634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43928671 ATTTAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43931165 original size:16 final size:16
Alignment explanation
Indices: 43931144--43931197 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
43931134 TTTGGTTCGC
43931144 TGTAATGGAATAGAAG
1 TGTAATGGAATAGAAG
43931160 TGTAATGGAATAG-AG
1 TGTAATGGAATAGAAG
*
43931175 CTGTAATGGAATAGAAC
1 -TGTAATGGAATAGAAG
43931192 TGTAAT
1 TGTAAT
43931198 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
15 2 0.06
16 32 0.91
17 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.28, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAGAAG
Found at i:43932465 original size:14 final size:14
Alignment explanation
Indices: 43932446--43932475 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43932436 TGTTTTACAC
*
43932446 AAATCAATTTCAGA
1 AAATCAAATTCAGA
43932460 AAATCAAATTCAGA
1 AAATCAAATTCAGA
43932474 AA
1 AA
43932476 TATTCTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (14 bp):
AAATCAAATTCAGA
Found at i:43933428 original size:43 final size:43
Alignment explanation
Indices: 43933358--43933478 Score: 179
Period size: 43 Copynumber: 2.8 Consensus size: 43
43933348 GTTTATAACG
* *
43933358 ACAAACGCCGCTAAAGAATATGATCTTTAGCGGCGCTTTCCTC
1 ACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTC
* *
43933401 ACAAACACCGCTAAAGAACATGGTCTTTAGCGGTGCTTTCCTC
1 ACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTC
* * *
43933444 ACAAACGCCACTAAAGAACATAGTCTTTAGTGGCG
1 ACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCG
43933479 TTTTTCCCAC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTC
Found at i:43933567 original size:14 final size:14
Alignment explanation
Indices: 43933550--43933585 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
43933540 TTCTACACAC
43933550 ACATATATAAATAT
1 ACATATATAAATAT
*
43933564 ACATATATACATAT
1 ACATATATAAATAT
43933578 AC-TATATA
1 ACATATATA
43933586 CCACCTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (14 bp):
ACATATATAAATAT
Found at i:43942148 original size:24 final size:25
Alignment explanation
Indices: 43942116--43942166 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
43942106 AGTATAAACT
*
43942116 AAAATCAAAATC-CCAAAAATCTTA
1 AAAAACAAAATCACCAAAAATCTTA
* * *
43942140 AAAAACAAATTCACCATAAATTTTA
1 AAAAACAAAATCACCAAAAATCTTA
43942165 AA
1 AA
43942167 TTTGCCAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAACAAAATCACCAAAAATCTTA
Found at i:43955408 original size:22 final size:22
Alignment explanation
Indices: 43955367--43955412 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
43955357 TTCGAAAAGC
*
43955367 TAAAAAAATATTTTTGAAAATA
1 TAAAAAAATATTGTTGAAAATA
*
43955389 TAAAAAAATATATGTTAAAAATA
1 TAAAAAAATAT-TGTTGAAAATA
43955412 T
1 T
43955413 TTCGAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (22 bp):
TAAAAAAATATTGTTGAAAATA
Found at i:43956830 original size:51 final size:50
Alignment explanation
Indices: 43956705--43956886 Score: 204
Period size: 51 Copynumber: 3.5 Consensus size: 50
43956695 TTTCATTTAA
* * * ** *
43956705 TACTCACGATGACATATAGTCATCAGACCTCTTGTTCCGTATAGGAATTCATA
1 TACTCACGATGACACATAGTCATCGGA-CTTTTAATCCGTAT-GG-ATTCATT
* *
43956758 TACTCACGATAACAC-TGAGTCATCGGACTTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACAT-AGTCATCGGACTTTTAATCCGT-ATGGATTCATT
* *
43956809 TACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACATAGTCATCGGACTTTTAATCCGT-ATGGATTCATT
*
43956860 TACTCACGATGACACTTAGTCATCGGA
1 TACTCACGATGACACATAGTCATCGGA
43956887 TCCTTTCGTT
Statistics
Matches: 112, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
51 76 0.68
52 12 0.11
53 24 0.21
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (50 bp):
TACTCACGATGACACATAGTCATCGGACTTTTAATCCGTATGGATTCATT
Found at i:43964033 original size:51 final size:51
Alignment explanation
Indices: 43963877--43964114 Score: 291
Period size: 51 Copynumber: 4.6 Consensus size: 51
43963867 TTTTATTTAA
* ** ** * * *
43963877 TACTCATGATGACATATAGTCATCGGACCTCTTGTTCCTTATAGGAATTCATA
1 TACTCACGATGACACCTAGTCATCGGACCT-TTAATCCGTAAAGG-ATTCATT
* * * *
43963930 TACTCACGATAACA-CTAAGTCATCGGA-CTTTAATCCATTATGGATTCATT
1 TACTCACGATGACACCT-AGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
43963980 TACTCACGATGACACCTAGTCATCGGACCTTTAATCTGTAAAGGATTCATT
1 TACTCACGATGACACCTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
43964031 TACTCACGATGACACCTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACCTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
43964082 TACTCAAGATGACACTTAGTCATCGGATCCTTT
1 TACTCACGATGACACCTAGTCATCGGA-CCTTT
43964115 CATTTATAGC
Statistics
Matches: 163, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
50 29 0.18
51 104 0.64
52 8 0.05
53 22 0.13
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACCTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:43967751 original size:19 final size:19
Alignment explanation
Indices: 43967708--43967745 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
43967698 ATTTTAATGT
*
43967708 TAATTTCAAATTTAAACTA
1 TAATTTCAAATTCAAACTA
43967727 TAATTTCAAATTCAAACTA
1 TAATTTCAAATTCAAACTA
43967746 GTATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATTTCAAATTCAAACTA
Found at i:43967786 original size:36 final size:38
Alignment explanation
Indices: 43967728--43967808 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 38
43967718 TTTAAACTAT
*
43967728 AATTTCAAATTCAAACTAGTATTTT-ATTTTGAAGTTA
1 AATTTCAAATTCAAACTAGTATTTTAATTTTGAAATTA
*
43967765 AATTT-AAATTTAAAC-ATGTATTTTAATTTTGAAATT-
1 AATTTCAAATTCAAACTA-GTATTTTAATTTTGAAATTA
43967801 AATTTCAA
1 AATTTCAA
43967809 CTTAATTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 1 0.03
36 21 0.54
37 17 0.44
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (38 bp):
AATTTCAAATTCAAACTAGTATTTTAATTTTGAAATTA
Found at i:43967868 original size:18 final size:18
Alignment explanation
Indices: 43967847--43967922 Score: 77
Period size: 18 Copynumber: 4.3 Consensus size: 18
43967837 TTTAAAGTAT
*
43967847 AATTTAATTTTAATTTCA
1 AATTTAATTTCAATTTCA
43967865 AATTTAATTTTC-ATTTCA
1 AATTTAA-TTTCAATTTCA
* **
43967883 ACTTTAATTTCAAACTC-
1 AATTTAATTTCAATTTCA
*
43967900 TA-TTAATTTCAATTTCA
1 AATTTAATTTCAATTTCA
43967917 AATTTA
1 AATTTA
43967923 CTTTGTATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
16 12 0.27
17 5 0.11
18 25 0.56
19 3 0.07
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTAATTTCAATTTCA
Found at i:43974204 original size:16 final size:16
Alignment explanation
Indices: 43974176--43974217 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
43974166 TTTTACAATA
*
43974176 GTAAAAA-TGCAATTT
1 GTAAAAATTACAATTT
43974191 GTAAAAATTACAATTT
1 GTAAAAATTACAATTT
*
43974207 TTAAAAGATTA
1 GTAAAA-ATTA
43974218 AATCAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 7 0.30
16 12 0.52
17 4 0.17
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (16 bp):
GTAAAAATTACAATTT
Found at i:43974816 original size:21 final size:21
Alignment explanation
Indices: 43974775--43974818 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43974765 CCTTTTTTAA
*
43974775 TTTAAAATTTTAATTATAATT
1 TTTAAAATTTTAATCATAATT
43974796 TTTAAAATTTTTAATCA-AATT
1 TTTAAAA-TTTTAATCATAATT
43974817 TT
1 TT
43974819 AGAATTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAAAATTTTAATCATAATT
Found at i:43975298 original size:14 final size:14
Alignment explanation
Indices: 43975279--43975307 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43975269 AAAGGCTAAC
43975279 TTTAACTTTATGTT
1 TTTAACTTTATGTT
43975293 TTTAACTTTATGTT
1 TTTAACTTTATGTT
43975307 T
1 T
43975308 GTGCCATATT
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:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTAACTTTATGTT
Found at i:43975815 original size:32 final size:32
Alignment explanation
Indices: 43975779--43975841 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
43975769 TAACATCTAA
43975779 ACAACA-AAAATAACAATC-AAAATAGCAACAAG
1 ACAACATAAAA-AACAA-CAAAAATAGCAACAAG
*
43975811 ACAACATTAAAAACAACAAAAATAGCAACAA
1 ACAACATAAAAAACAACAAAAATAGCAACAA
43975842 AAATAACAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 1 0.04
32 24 0.86
33 3 0.11
ACGTcount: A:0.67, C:0.19, G:0.05, T:0.10
Consensus pattern (32 bp):
ACAACATAAAAAACAACAAAAATAGCAACAAG
Found at i:43975839 original size:12 final size:12
Alignment explanation
Indices: 43975822--43975861 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
43975812 CAACATTAAA
43975822 AACAACAAAAAT
1 AACAACAAAAAT
*
43975834 AGCAACAAAAAT
1 AACAACAAAAAT
*
43975846 AACAGCAAAAAT
1 AACAACAAAAAT
43975858 AACA
1 AACA
43975862 TGAAAACAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.70, C:0.17, G:0.05, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:43975867 original size:24 final size:24
Alignment explanation
Indices: 43975778--43975861 Score: 63
Period size: 24 Copynumber: 3.7 Consensus size: 24
43975768 ATAACATCTA
43975778 AACAACAAAAATAACAATC-AAAAT
1 AACAACAAAAATAACAA-CAAAAAT
* * *
43975802 AGCAAC---AA-GACAACATTAAA-
1 AACAACAAAAATAACAACA-AAAAT
*
43975822 AACAACAAAAATAGCAACAAAAAT
1 AACAACAAAAATAACAACAAAAAT
*
43975846 AACAGCAAAAATAACA
1 AACAACAAAAATAACA
43975862 TGAAAACAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
19 1 0.02
20 9 0.20
21 5 0.11
23 5 0.11
24 24 0.55
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.10
Consensus pattern (24 bp):
AACAACAAAAATAACAACAAAAAT
Found at i:43975868 original size:44 final size:44
Alignment explanation
Indices: 43975764--43975873 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
43975754 AAAACGCATA
** *
43975764 AAAAATAACATCTAAACAACAAAAATAACAATCAAAATAGCAAC
1 AAAAATAACATAAAAACAACAAAAATAACAATCAAAATAACAAC
* * * *
43975808 -AAGACAACATTAAAAACAACAAAAATAGCAA-CAAAAATAACAGC
1 AAAAATAACA-TAAAAACAACAAAAATAACAATC-AAAATAACAAC
*
43975852 AAAAATAACATGAAAACAACAA
1 AAAAATAACATAAAAACAACAA
43975874 TTAAAACAGT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
43 8 0.15
44 38 0.72
45 7 0.13
ACGTcount: A:0.67, C:0.17, G:0.05, T:0.11
Consensus pattern (44 bp):
AAAAATAACATAAAAACAACAAAAATAACAATCAAAATAACAAC
Found at i:43975952 original size:22 final size:21
Alignment explanation
Indices: 43975876--43975961 Score: 88
Period size: 22 Copynumber: 4.1 Consensus size: 21
43975866 AACAACAATT
43975876 AAAACAGT-AAAAA-A-CACC
1 AAAACAGTAAAAAATAGCACC
* *
43975894 AAAACAGTAAAAAAATAACACA
1 AAAACAGT-AAAAAATAGCACC
**
43975916 AAAACACCAAAAAATAGCAACC
1 AAAACAGTAAAAAATAGC-ACC
*
43975938 AAAACAGTAAAAAATAGCAAC
1 AAAACAGTAAAAAATAGCACC
43975959 AAA
1 AAA
43975962 TCAACAATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
18 8 0.15
20 5 0.09
21 15 0.27
22 27 0.49
ACGTcount: A:0.69, C:0.19, G:0.06, T:0.07
Consensus pattern (21 bp):
AAAACAGTAAAAAATAGCACC
Found at i:43981759 original size:31 final size:31
Alignment explanation
Indices: 43981721--43981794 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
43981711 AACTACATAG
* *
43981721 TTGGTCACTCAATTTTTAGGGTACTTTTATT
1 TTGGTCACCCAATTTTTAGGGTACTTTCATT
*
43981752 TTGGTCACCCAATTTTTAGGTTACTTTCATT
1 TTGGTCACCCAATTTTTAGGGTACTTTCATT
43981783 TTGGTCACCCAA
1 TTGGTCACCCAA
43981795 AAAGTATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (31 bp):
TTGGTCACCCAATTTTTAGGGTACTTTCATT
Found at i:43983174 original size:29 final size:29
Alignment explanation
Indices: 43983127--43983428 Score: 147
Period size: 29 Copynumber: 10.1 Consensus size: 29
43983117 CTCAATGGTG
* *
43983127 AAAATGTAATTTCGGGAAAATTCGGGGTTA
1 AAAATGGAATTT-TGGAAAATTCGGGGTTA
* * *
43983157 AAAATGGAATTTTGGAAAGTTTGAGGGTAA
1 AAAATGGAATTTTGGAAAATTCG-GGGTTA
* *
43983187 AATGGTAATTTGGTAA-TTTGGTAAAATT-AGGGTCA
1 AA----AA--TGG-AATTTTGG-AAAATTCGGGGTTA
* *
43983222 AAAATGGAATTTTGGAAAGTTCGGGGGT-
1 AAAATGGAATTTTGGAAAATTCGGGGTTA
** *
43983250 AAAATGGTAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGG-AA-TTTTGGAAAATTCGGGGTTA
* * *
43983281 AAAATGAAATTTTGGAAAGTTTAGGGG-T-
1 AAAATGGAATTTTGGAAA-ATTCGGGGTTA
*
43983309 AAAATGGTAATTTGGGTAAAATT-GGGGTT-
1 AAAATGG-AATTTTGG-AAAATTCGGGGTTA
* *
43983338 AAAATGGAATTTTGGAAAGTTTGAGGG-T-
1 AAAATGGAATTTTGGAAAATTCG-GGGTTA
* *
43983366 AAAATGGTAATTTTGGGTGAAA-TCGGGGTAA
1 AAAATGG-AATTTT-GG-AAAATTCGGGGTTA
* ** *
43983397 AAAATAGAATTTTGGAAGGTTCGGGGGTA
1 AAAATGGAATTTTGGAAAATTCGGGGTTA
43983426 AAA
1 AAA
43983429 TGGTGATTTT
Statistics
Matches: 211, Mismatches: 35, Indels: 53
0.71 0.12 0.18
Matches are distributed among these distances:
27 5 0.02
28 41 0.19
29 71 0.34
30 54 0.26
31 16 0.08
34 2 0.01
35 7 0.03
36 8 0.04
37 7 0.03
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTGGAAAATTCGGGGTTA
Found at i:43983195 original size:59 final size:60
Alignment explanation
Indices: 43983127--43983460 Score: 346
Period size: 59 Copynumber: 5.6 Consensus size: 60
43983117 CTCAATGGTG
*
43983127 AAAAT-GTAATTTCGGG-AAAATTCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
1 AAAATGGTAATTTTGGGTAAAATTCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
* * * * *
43983185 AAAATGGTAATTTGGTAATTTGGTAAAATT-AGGGTCAAAAATGGAATTTTGGAAAGTTCGGGGG
1 AAAATGGTAA--T--T--TTGGGTAAAATTCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGG
43983249 T
60 T
* ** * *
43983250 AAAATGGTAATTTTTGG-AAGTTTCGAGGTTAAAAATGAAATTTTGGAAAGTTT-AGGGGT
1 AAAATGGTAATTTTGGGTAAAATTCGGGGTTAAAAATGGAATTTTGGAAAGTTTGA-GGGT
43983309 AAAATGGTAA-TTTGGGTAAAATT-GGGGTT-AAAATGGAATTTTGGAAAGTTTGAGGGT
1 AAAATGGTAATTTTGGGTAAAATTCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
* * * * * *
43983366 AAAATGGTAATTTTGGGTGAAA-TCGGGGTAAAAAATAGAATTTTGGAAGGTTCGGGGGT
1 AAAATGGTAATTTTGGGTAAAATTCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
* * * *
43983425 AAAATGGTGATTTTTGGTGAAA-TCGGGGTCAAAAAT
1 AAAATGGTAATTTTGGGTAAAATTCGGGGTTAAAAAT
43983461 ATAATTTATG
Statistics
Matches: 233, Mismatches: 28, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
57 36 0.15
58 35 0.15
59 108 0.46
61 2 0.01
63 2 0.01
65 44 0.19
66 6 0.03
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (60 bp):
AAAATGGTAATTTTGGGTAAAATTCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
Found at i:43983400 original size:116 final size:115
Alignment explanation
Indices: 43983197--43983460 Score: 309
Period size: 116 Copynumber: 2.3 Consensus size: 115
43983187 AATGGTAATT
*
43983197 TGGTAATTTGGTAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
1 TGGTAATTTGGTAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATT
* * * *
43983262 TTTGGAAGTTTCGAGGTTAAAAAT-GAAATTTTGGAAAGTTTAGGGGTAAAA
66 TTGGGAAG-ATCGAGGTAAAAAATAG-AATTTTGGAAAGTTCAGGGGTAAAA
* * *
43983313 TGGTAATTTGGGTAAAATTGGGGT-TAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGGTAAT
1 TGGTAATTT-GGTAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAAT
* * *
43983377 TTTGGGTGAA-ATCGGGGTAAAAAATAGAATTTTGGAAGGTTCGGGGGTAAAA
65 TTT-GG-GAAGATCGAGGTAAAAAATAGAATTTTGGAAAGTTCAGGGGTAAAA
* * **
43983429 TGGTGATTTTTGGTGAAATCGGGGTCAAAAAT
1 TGGT-A-ATTTGGTAAAATTAGGGTCAAAAAT
43983461 ATAATTTATG
Statistics
Matches: 126, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
116 87 0.69
117 28 0.22
118 11 0.09
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (115 bp):
TGGTAATTTGGTAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATT
TTGGGAAGATCGAGGTAAAAAATAGAATTTTGGAAAGTTCAGGGGTAAAA
Found at i:43983437 original size:29 final size:29
Alignment explanation
Indices: 43983222--43983438 Score: 173
Period size: 29 Copynumber: 7.5 Consensus size: 29
43983212 ATTAGGGTCA
43983222 AAAATGG-AATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTGGAAAGTTCGGGGGT
* *
43983250 AAAATGGTAATTTTTGG-AAGTTTCGAGGTT
1 AAAATGGTAA-TTTTGGAAAG-TTCGGGGGT
* **
43983280 AAAAAT-GAAATTTTGGAAAGTTTAGGGGT
1 -AAAATGGTAATTTTGGAAAGTTCGGGGGT
* * *
43983309 AAAATGGTAATTTGGGTAAAATT-GGGGTT
1 AAAATGGTAATTTTGG-AAAGTTCGGGGGT
* *
43983338 AAAATGG-AATTTTGGAAAGTTTGAGGGT
1 AAAATGGTAATTTTGGAAAGTTCGGGGGT
43983366 AAAATGGTAATTTTGGGTGAAA--TC-GGGGT
1 AAAATGGTAATTTT--G-GAAAGTTCGGGGGT
* *
43983395 AAAAAATAG-AATTTTGGAAGGTTCGGGGGT
1 --AAAATGGTAATTTTGGAAAGTTCGGGGGT
*
43983425 AAAATGGTGATTTT
1 AAAATGGTAATTTT
43983439 TGGTGAAATC
Statistics
Matches: 149, Mismatches: 22, Indels: 35
0.72 0.11 0.17
Matches are distributed among these distances:
27 8 0.05
28 37 0.25
29 52 0.35
30 36 0.24
31 12 0.08
32 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTTCGGGGGT
Found at i:43983452 original size:29 final size:29
Alignment explanation
Indices: 43983362--43983458 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 29
43983352 GAAAGTTTGA
* *
43983362 GGGTAAAATGGTAATTTTGGGTGAAATCG
1 GGGTAAAATGGTGATTTTTGGTGAAATCG
** * *
43983391 GGGTAAAA-AATAGAATTTT-G-GAAGGTTCGG
1 GGGTAAAATGGT-GATTTTTGGTGAA--ATC-G
43983421 GGGTAAAATGGTGATTTTTGGTGAAATCG
1 GGGTAAAATGGTGATTTTTGGTGAAATCG
43983450 GGGTCAAAA
1 GGGT-AAAA
43983459 ATATAATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 15
0.67 0.13 0.20
Matches are distributed among these distances:
27 3 0.06
28 2 0.04
29 19 0.38
30 21 0.42
31 2 0.04
32 3 0.06
ACGTcount: A:0.33, C:0.04, G:0.34, T:0.29
Consensus pattern (29 bp):
GGGTAAAATGGTGATTTTTGGTGAAATCG
Found at i:43986179 original size:200 final size:200
Alignment explanation
Indices: 43985828--43986318 Score: 766
Period size: 200 Copynumber: 2.5 Consensus size: 200
43985818 ATTTGGTCCA
* * *
43985828 CTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCGTTGAGCGTTGAGTTGGTAT
1 CTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGTTCGTGTTGAGCGTTGAGTTGGTAT
* * *
43985893 TCTTCTATGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTCC
66 TCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTAGATCTCC
* *
43985958 TCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTTATCAAGAAGCTAACCATTTTATTGTTTCG
131 TCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCG
43986023 ACCCG
196 ACCCG
** * *
43986028 CTTCTCAGTGTCTCATCAGGAAATTGGGTTTGAAGATTTGTTCGTGTTGTGCGTTGAGTTGGTAT
1 CTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGTTCGTGTTGAGCGTTGAGTTGGTAT
* * *
43986093 TCTTCTCTATATCTTATCAGGAAGATGACCGCCTCGGTTGTTTTAATTCGCTTCTCTAGATCTCC
66 TCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTAGATCTCC
* * * * *
43986158 TCAGGAAGGCGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCG
131 TCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCG
*
43986223 ACCTG
196 ACCCG
* *
43986228 CTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGTTCGTGTTGAGCGCTGAGTTGGTGT
1 CTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGTTCGTGTTGAGCGTTGAGTTGGTAT
*
43986293 TCTTCTCTGTATCTCATCAAGAAGAT
66 TCTTCTCTGTATCTCATCAGGAAGAT
43986319 TGCCACCTTA
Statistics
Matches: 261, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
200 261 1.00
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.37
Consensus pattern (200 bp):
CTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGTTCGTGTTGAGCGTTGAGTTGGTAT
TCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTAGATCTCC
TCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCG
ACCCG
Found at i:44001250 original size:21 final size:20
Alignment explanation
Indices: 44001218--44001256 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
44001208 ACGCCTACGA
44001218 AAAGATCACTTGGATTTAAG
1 AAAGATCACTTGGATTTAAG
*
44001238 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCACTTGGATTTA
44001257 TCCATGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (20 bp):
AAAGATCACTTGGATTTAAG
Found at i:44001412 original size:18 final size:15
Alignment explanation
Indices: 44001374--44001407 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
44001364 TTTGGTTTGC
44001374 TTATTTTATTATTTT
1 TTATTTTATTATTTT
*
44001389 TTATTTTATTATTAT
1 TTATTTTATTATTTT
44001404 TTAT
1 TTAT
44001408 CATTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTATTATTTT
Found at i:44001448 original size:32 final size:30
Alignment explanation
Indices: 44001412--44001510 Score: 92
Period size: 32 Copynumber: 3.1 Consensus size: 30
44001402 ATTTATCATT
44001412 TAAATATATATATTTAATATATATAAATTAAA
1 TAAATATA-ATATTTAATATATATAAA-TAAA
* *
44001444 TAAATTAAAATATTTTAATA-ATATAGATAGAA
1 TAAA-TATAATA-TTTAATATATATAAATA-AA
*
44001476 TATATATAATAATATTAATAATATATAAATAAA
1 TAAATATAAT-AT-TTAAT-ATATATAAATAAA
44001509 TA
1 TA
44001511 TATAAAGAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
31 8 0.15
32 24 0.44
33 15 0.27
34 8 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
TAAATATAATATTTAATATATATAAATAAA
Found at i:44001494 original size:9 final size:10
Alignment explanation
Indices: 44001477--44001515 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
44001467 TAGATAGAAT
44001477 ATATATAATA
1 ATATATAATA
44001487 ATAT-TAATA
1 ATATATAATA
44001496 ATATATAAATAA
1 ATATAT-AAT-A
44001508 ATATATAA
1 ATATATAA
44001516 AGAAAATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.35
10 5 0.19
11 5 0.19
12 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATATATAATA
Found at i:44001510 original size:12 final size:11
Alignment explanation
Indices: 44001412--44001516 Score: 56
Period size: 11 Copynumber: 9.4 Consensus size: 11
44001402 ATTTATCATT
44001412 TAAATATATATA
1 TAAATA-ATATA
*
44001424 TTTAAT-ATATA
1 -TAAATAATATA
*
44001435 TAAATTAAATAAA
1 TAAA-T-AATATA
* *
44001448 TTAA-AATATT
1 TAAATAATATA
*
44001458 TTAATAATATA
1 TAAATAATATA
* * *
44001469 GATAGAATATA
1 TAAATAATATA
44001480 TATAATAATAT-
1 TA-AATAATATA
44001491 T-AATAATATA
1 TAAATAATATA
44001501 TAAATAAATATA
1 TAAAT-AATATA
44001513 TAAA
1 TAAA
44001517 GAAAATATGC
Statistics
Matches: 70, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
9 8 0.11
10 12 0.17
11 23 0.33
12 16 0.23
13 11 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TAAATAATATA
Found at i:44001513 original size:23 final size:23
Alignment explanation
Indices: 44001412--44001513 Score: 65
Period size: 23 Copynumber: 4.6 Consensus size: 23
44001402 ATTTATCATT
*
44001412 TAAATATATATATTTAAT-ATATA
1 TAAATAAATATA-TTAATAATATA
* *
44001435 TAAATTAAATAAATTAA-AATATT
1 TAAA-TAAATATATTAATAATATA
* *
44001458 TTAAT-AATATA--GATAGA-ATA
1 TAAATAAATATATTAATA-ATATA
*
44001478 TATAT-AATAATATTAATAATATA
1 TAAATAAAT-ATATTAATAATATA
44001501 TAAATAAATATAT
1 TAAATAAATATAT
44001514 AAAGAAAATA
Statistics
Matches: 59, Mismatches: 11, Indels: 18
0.67 0.12 0.20
Matches are distributed among these distances:
19 1 0.02
20 9 0.15
21 9 0.15
22 2 0.03
23 29 0.49
24 9 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAATAAATATATTAATAATATA
Found at i:44001981 original size:13 final size:13
Alignment explanation
Indices: 44001963--44001987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44001953 TTCGTTGTTG
44001963 AAATCAATATAGT
1 AAATCAATATAGT
44001976 AAATCAATATAG
1 AAATCAATATAG
44001988 ATTTATAGTA
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:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
AAATCAATATAGT
Found at i:44012519 original size:28 final size:27
Alignment explanation
Indices: 44012487--44012590 Score: 127
Period size: 28 Copynumber: 3.7 Consensus size: 27
44012477 GCTATTAAAG
*
44012487 AACAAAGAGCACATAAAGTGTTAATCA
1 AACAAAGAGCACACAAAGTGTTAATCA
**
44012514 CAACAAAGAGCACACAAAGTACTAATCA
1 -AACAAAGAGCACACAAAGTGTTAATCA
* *
44012542 AACTAGAGAACACACAAAGTGTTAATCA
1 AAC-AAAGAGCACACAAAGTGTTAATCA
*
44012570 GAACAAAGAGCACATAAAGTG
1 -AACAAAGAGCACACAAAGTG
44012591 CTAAATATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
27 3 0.05
28 58 0.91
29 3 0.05
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.14
Consensus pattern (27 bp):
AACAAAGAGCACACAAAGTGTTAATCA
Found at i:44012714 original size:3 final size:3
Alignment explanation
Indices: 44012706--44012737 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
44012696 TCTAAAGCTA
44012706 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
44012738 TAATAATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:44012755 original size:12 final size:12
Alignment explanation
Indices: 44012740--44012766 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
44012730 AACAACAATA
44012740 ATAATAGTAATG
1 ATAATAGTAATG
44012752 ATAATAGTAATG
1 ATAATAGTAATG
44012764 ATA
1 ATA
44012767 GTAACAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (12 bp):
ATAATAGTAATG
Found at i:44015172 original size:23 final size:23
Alignment explanation
Indices: 44015146--44015277 Score: 178
Period size: 23 Copynumber: 5.8 Consensus size: 23
44015136 AGCGTGCTTT
44015146 TGTTCAGCACTGTGTGTGCATAC
1 TGTTCAGCACTGTGTGTGCATAC
*
44015169 TGTTCAGCACTGTGTGTGCACAC
1 TGTTCAGCACTGTGTGTGCATAC
*
44015192 TGTTCAGCACTGTGTGTGC-TTC
1 TGTTCAGCACTGTGTGTGCATAC
*
44015214 TGTTCAGCACTGTGTGTGCCTAC
1 TGTTCAGCACTGTGTGTGCATAC
* *
44015237 TGTTCAGCATTGTGTGTGCCT-C
1 TGTTCAGCACTGTGTGTGCATAC
* * *
44015259 TATTTAGCATTGTGTGTGC
1 TGTTCAGCACTGTGTGTGC
44015278 TTCTGTTTCC
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
22 38 0.38
23 63 0.62
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.38
Consensus pattern (23 bp):
TGTTCAGCACTGTGTGTGCATAC
Found at i:44015231 original size:45 final size:45
Alignment explanation
Indices: 44015146--44015277 Score: 185
Period size: 45 Copynumber: 2.9 Consensus size: 45
44015136 AGCGTGCTTT
*
44015146 TGTTCAGCACTGTGTGTGCATACTGTTCAGCACTGTGTGTGCAC-AC
1 TGTTCAGCACTGTGTGTGC-TTCTGTTCAGCACTGTGTGTGC-CTAC
44015192 TGTTCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCCTAC
1 TGTTCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCCTAC
* * * * *
44015237 TGTTCAGCATTGTGTGTGCCTCTATTTAGCATTGTGTGTGC
1 TGTTCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGC
44015278 TTCTGTTTCC
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
44 1 0.01
45 59 0.75
46 19 0.24
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.38
Consensus pattern (45 bp):
TGTTCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCCTAC
Found at i:44015251 original size:68 final size:67
Alignment explanation
Indices: 44015139--44015284 Score: 220
Period size: 68 Copynumber: 2.2 Consensus size: 67
44015129 GAACGCTAGC
* *
44015139 GTGCTTTTGTTCAGCACTGTGTGTGCATACTGTTCAGCACTGTGTGTGCACACTGTTCAGCACTG
1 GTGCTTCTGTTCAGCACTGTGTGTGCATACTGTTCAGCACTGTGTGTGC-CACTATTCAGCACTG
44015204 TGT
65 TGT
* * * * *
44015207 GTGCTTCTGTTCAGCACTGTGTGTGCCTACTGTTCAGCATTGTGTGTGCCTCTATTTAGCATTGT
1 GTGCTTCTGTTCAGCACTGTGTGTGCATACTGTTCAGCACTGTGTGTGCCACTATTCAGCACTGT
44015272 GT
66 GT
44015274 GTGCTTCTGTT
1 GTGCTTCTGTT
44015285 TCCCCAACAG
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 25 0.35
68 46 0.65
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.40
Consensus pattern (67 bp):
GTGCTTCTGTTCAGCACTGTGTGTGCATACTGTTCAGCACTGTGTGTGCCACTATTCAGCACTGT
GT
Found at i:44015325 original size:21 final size:21
Alignment explanation
Indices: 44015299--44015346 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
44015289 CAACAGTTAT
*
44015299 GTACTTCTATTAAGTACTTTG
1 GTACTTCTAGTAAGTACTTTG
44015320 GTACTTCTAGTAAGTACTTTG
1 GTACTTCTAGTAAGTACTTTG
44015341 GTACTT
1 GTACTT
44015347 TCTGTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.46
Consensus pattern (21 bp):
GTACTTCTAGTAAGTACTTTG
Found at i:44023155 original size:73 final size:72
Alignment explanation
Indices: 44023036--44023173 Score: 267
Period size: 73 Copynumber: 1.9 Consensus size: 72
44023026 TAGTTATTAT
44023036 TATTAACGGTGAAAAACTTGGTTTCAACAAAAAATATTGTTTTAATTTTTTAATAAGTTGGATTT
1 TATTAACGGTGAAAAACTTGGTTTCAACAAAAAATATTGTTTTAA-TTTTTAATAAGTTGGATTT
44023101 TTTATAAC
65 TTTATAAC
44023109 TATTAACGGTGAAAAACTTGGTTTCAACAAAAAATATTGTTTTAATTTTTAATAAGTTGGATTTT
1 TATTAACGGTGAAAAACTTGGTTTCAACAAAAAATATTGTTTTAATTTTTAATAAGTTGGATTTT
44023174 ATAAAAAAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
72 20 0.31
73 45 0.69
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (72 bp):
TATTAACGGTGAAAAACTTGGTTTCAACAAAAAATATTGTTTTAATTTTTAATAAGTTGGATTTT
TTATAAC
Found at i:44027945 original size:29 final size:29
Alignment explanation
Indices: 44027902--44028029 Score: 79
Period size: 27 Copynumber: 4.4 Consensus size: 29
44027892 TCGGAGTTGG
* *
44027902 AAATGAGACATTTTGGATACTCGGGGGGCA
1 AAATGATA-ATTTTGGATACTCGGGGGGAA
*
44027932 AAATGATAATTTTGGACT-CTC--GGGGTA
1 AAATGATAATTTTGGA-TACTCGGGGGGAA
* * * * *
44027959 AAATGGTAATTTTGGGAAAATTGGGGGTTAA
1 AAATGATAATTTT-GGATACTCGGGGG-GAA
*
44027990 AAATGAT-ATTTTGGATATTC--GGGGATA
1 AAATGATAATTTTGGATACTCGGGGGGA-A
*
44028017 AAATGGTAATTTT
1 AAATGATAATTTT
44028030 TAGAAAAATC
Statistics
Matches: 76, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
26 1 0.01
27 27 0.36
28 9 0.12
29 16 0.21
30 16 0.21
31 7 0.09
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (29 bp):
AAATGATAATTTTGGATACTCGGGGGGAA
Found at i:44028352 original size:6 final size:6
Alignment explanation
Indices: 44028327--44028396 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
44028317 AAATTCTTTT
* * *
44028327 TTTAAA TTTGAAA -ATAAA TTTAAA TTTAAA TTCAAA TTTAAA -ATAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
44028374 TCTAAA GTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
44028397 AGGGCCCGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
5 11 0.22
6 36 0.72
7 3 0.06
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (6 bp):
TTTAAA
Found at i:44028384 original size:17 final size:17
Alignment explanation
Indices: 44028364--44028396 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44028354 AAATTCAAAT
44028364 TTAAAATAAATCTAAAG
1 TTAAAATAAATCTAAAG
*
44028381 TTAAAATAAATTTAAA
1 TTAAAATAAATCTAAA
44028397 AGGGCCCGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAAAATAAATCTAAAG
Found at i:44029101 original size:206 final size:205
Alignment explanation
Indices: 44028724--44029247 Score: 647
Period size: 206 Copynumber: 2.6 Consensus size: 205
44028714 TCACTTGACA
* * * ** ** * *
44028724 TTCTCCTCAATATCTCATTAGAAAGATGACCGCATCACTTGTTTTGATCCAATTCTCTGTGTTTC
1 TTCTTCTCAGTATCTCATCAGAAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
* * *
44028789 ATTAGGAAGACGGATTTGGT-TCACTTCTCCGTATCTCATCAGGAAGCTAACCACCTTATTGCTT
66 ATCAGGAAGACGAATTTGGTCT-ACTTCTCAGTATCTCATCAGGAAGCTAACCACCTTATTGCTT
* * * * * * * * * *
44028853 CGACCTGCTTCTCAGTATCTCATCAGAAAGTTGGGGTTCGAAGATTTGCTCATATCGAGCGTGGG
130 CAACCCGCTTCTCAATATCTCATAAGAAAGCTGAGATTCGAAGA-TTACTCACATCGAGCATGGG
44028918 TTTGATCTGATC
194 TTTGATCTGATC
* *
44028930 TTCTTCTCAGTATCTCATCAGAAAGATGACCACATCACTTATTTCAATCCGCTTCTCTGTATCTC
1 TTCTTCTCAGTATCTCATCAGAAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
* * ** *
44028995 ATCAAGAAGACGAATTTGGTCTACTTCTCAATATCTCATCAGGAAGCTAACCATTTTATTGTTTC
66 ATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCACCTTATTGCTTC
44029060 AACCCGCTTCTCAATATCTCATTAAG-AAGCTGAGATTCGAAGATTACTCACATCGAGCATGGGT
131 AACCCGCTTCTCAATATCTCA-TAAGAAAGCTGAGATTCGAAGATTACTCACATCGAGCATGGGT
* *
44029124 TTGATTTGGTC
195 TTGATCTGATC
* * * * * * *
44029135 TTCTTTTCAGTATCTCATCAGGAAGATGACTGCGTCATTTGTTTCAATACGCTTCTTTGTATCTC
1 TTCTTCTCAGTATCTCATCAGAAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
* *
44029200 ATCAGGAAGACGAATTTGGTCCACTGCTCAGTATCTCATCAGGAAGCT
66 ATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCT
44029248 GGGGTTCGAA
Statistics
Matches: 272, Mismatches: 44, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
205 127 0.47
206 141 0.52
207 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (205 bp):
TTCTTCTCAGTATCTCATCAGAAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
ATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCACCTTATTGCTTC
AACCCGCTTCTCAATATCTCATAAGAAAGCTGAGATTCGAAGATTACTCACATCGAGCATGGGTT
TGATCTGATC
Found at i:44029367 original size:157 final size:156
Alignment explanation
Indices: 44029069--44029403 Score: 512
Period size: 157 Copynumber: 2.1 Consensus size: 156
44029059 CAACCCGCTT
* *
44029069 CTCAATATCTCATTAAGAAGCTGAGATTCGAAGATTACTCACATCGAGCATGGGTTTGATTTGGT
1 CTCAGTATCTCA-TCAGAAGCTGAGATTCGAAGATTACTCACATCGAGCATGGGTTTGATTTGGT
* * *
44029134 CTTCTTTTCAGTATCTCATCAGGAAGATGACTGCGTCATTTGTTTCAATACGCTTCTTTGTATCT
65 CTTCTTTTCAATATCTCATCAAGAAGATGACTGCGTCATTTGTTTCAATACGCTTCTCTGTATCT
44029199 CATCAGGAAGACGAATTTGGTCCACTG
130 CATCAGGAAGACGAATTTGGTCCACTG
* * *
44029226 CTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCATGGGTTTGATTTGG
1 CTCAGTATCTCATCA-GAAGCTGAGATTCGAAGA-TTACTCACATCGAGCATGGGTTTGATTTGG
* **
44029291 TCTTCTTTTCAATATCTCATCAAGAAGATGACCT-CGTCGTTT-TTTCAATTTGCTTCTCTGTAT
64 TCTTCTTTTCAATATCTCATCAAGAAGATGA-CTGCGTCATTTGTTTCAATACGCTTCTCTGTAT
*
44029354 CTCATCAGGAAGACGAATTTGGTCCACTT
128 CTCATCAGGAAGACGAATTTGGTCCACTG
44029383 CTCAGTATCTCATCAGAAGCT
1 CTCAGTATCTCATCAGAAGCT
44029404 AACCATTTTA
Statistics
Matches: 163, Mismatches: 12, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
156 8 0.05
157 88 0.54
158 65 0.40
159 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (156 bp):
CTCAGTATCTCATCAGAAGCTGAGATTCGAAGATTACTCACATCGAGCATGGGTTTGATTTGGTC
TTCTTTTCAATATCTCATCAAGAAGATGACTGCGTCATTTGTTTCAATACGCTTCTCTGTATCTC
ATCAGGAAGACGAATTTGGTCCACTG
Found at i:44029892 original size:94 final size:93
Alignment explanation
Indices: 44029726--44029997 Score: 399
Period size: 92 Copynumber: 3.0 Consensus size: 93
44029716 GTAGTTTTAT
** * * * **
44029726 TCCAACTTCGCTGCAACTTCAAGAAGATAGGACTTG--GTGTCGAAGCTTCATCTTGCTCTTACT
1 TCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTTAAAGCTTCATCTTGCTCTTACT
* *
44029789 GCAACTTCAGAGAGATAAAGACTTGCCTA
66 ACAACTTCAGAGAGATAAAGACTT-ACTA
*
44029818 TCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTTAAAGCTTTATCTTGCTCTTACT
1 TCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTTAAAGCTTCATCTTGCTCTTACT
44029883 ACAACTTCAGAGAGATAAAGACTTACTA
66 ACAACTTCAGAGAGATAAAGACTTACTA
*
44029911 T-CAACTTTACTGTAACTTCAAGAGGATAGGAATTGATG-TTTAAAGCTTCATCTTGCTCTTACT
1 TCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTTAAAGCTTCATCTTGCTCTTACT
*
44029974 ACAACTTCAGAGAGATAAAAACTT
66 ACAACTTCAGAGAGATAAAGACTT
44029998 TTCCCTTTGT
Statistics
Matches: 165, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
91 47 0.28
92 68 0.41
93 4 0.02
94 46 0.28
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (93 bp):
TCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTTAAAGCTTCATCTTGCTCTTACT
ACAACTTCAGAGAGATAAAGACTTACTA
Found at i:44030242 original size:50 final size:50
Alignment explanation
Indices: 44030014--44030312 Score: 250
Period size: 49 Copynumber: 6.0 Consensus size: 50
44030004 TTGTCATTTT
*
44030014 ACGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCGTGTCTTC
1 ACGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTC
* * * * ** * * ** *
44030064 TAAGGTACACGG-TCCGTCGTTAC-AACTTAGACCTTTCTC-TTTTGTCTTTTT
1 -ACGGTAC-TGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTC--TTC
* * * * * *
44030115 GCGGTACTGGATCTGCCATTGCAGTTTTAGATCTTTCCC-TTATGTCTTC
1 ACGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTC
* * * * * * * *
44030164 ACGATACTAGATCTGCCGTTGTGATCTTAGATCTTTCCTGTCGTGTTTTC
1 ACGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTC
** *
44030214 GTGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCCT-ATGTCTTC
1 ACGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTC
*
44030263 ACGGTACTGGATCCGTCGTTGCGGTCTTAGATCTTTCCCGTCATGT-TTC
1 ACGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTC
44030312 A
1 A
44030313 TGGTGTTAAG
Statistics
Matches: 189, Mismatches: 52, Indels: 16
0.74 0.20 0.06
Matches are distributed among these distances:
49 86 0.46
50 67 0.35
51 34 0.18
52 2 0.01
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.39
Consensus pattern (50 bp):
ACGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCATGTCTTC
Found at i:44030246 original size:99 final size:99
Alignment explanation
Indices: 44030015--44030310 Score: 308
Period size: 99 Copynumber: 3.0 Consensus size: 99
44030005 TGTCATTTTA
** * *
44030015 CGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCGTCGTGTCTTCTAAGGTAC-ACGGTCC
1 CGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCC-TTATGTCTTC-ACGGTACTA-GATCC
* * * * * * *
44030079 GTCGTT-ACAACTTAGACCTTTCTCTTTTGTCTTTTTG
63 GTCGTTGAGATCTTAGATCTTTC-CTGTCGTGTTTTCG
* * * * * * *
44030116 CGGTACTGGATCTGCCATTGCAGTTTTAGATCTTTCCCTTATGTCTTCACGATACTAGATCTGCC
1 CGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTATGTCTTCACGGTACTAGATCCGTC
*
44030181 GTTGTGATCTTAGATCTTTCCTGTCGTGTTTTCG
66 GTTGAGATCTTAGATCTTTCCTGTCGTGTTTTCG
* * *
44030215 TGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCCTATGTCTTCACGGTACTGGATCCGTC
1 CGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTATGTCTTCACGGTACTAGATCCGTC
* * * *
44030280 GTTGCGGTCTTAGATCTTTCCCGTCATGTTT
66 GTTGAGATCTTAGATCTTTCCTGTCGTGTTT
44030311 CATGGTGTTA
Statistics
Matches: 160, Mismatches: 33, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
99 105 0.66
100 21 0.13
101 34 0.21
ACGTcount: A:0.13, C:0.26, G:0.22, T:0.39
Consensus pattern (99 bp):
CGGTACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTATGTCTTCACGGTACTAGATCCGTC
GTTGAGATCTTAGATCTTTCCTGTCGTGTTTTCG
Found at i:44031579 original size:29 final size:27
Alignment explanation
Indices: 44031539--44031599 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
44031529 CGACCTCTCC
*
44031539 TTTTCTTTTCTCTTTTTTGTTTTTTGAT
1 TTTTCTTTTCTCTTTTTT-TCTTTTGAT
*
44031567 TTTTGCTTTTCTCTTTTTTTCTTTTGCT
1 TTTT-CTTTTCTCTTTTTTTCTTTTGAT
44031595 TTTTC
1 TTTTC
44031600 CATTAAATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 1 0.03
28 15 0.50
29 14 0.47
ACGTcount: A:0.02, C:0.15, G:0.07, T:0.77
Consensus pattern (27 bp):
TTTTCTTTTCTCTTTTTTTCTTTTGAT
Found at i:44031590 original size:15 final size:15
Alignment explanation
Indices: 44031539--44031591 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
44031529 CGACCTCTCC
44031539 TTTTCTTTTCTCTTT
1 TTTTCTTTTCTCTTT
**
44031554 TTTGT-TTTT-TGATT
1 TTT-TCTTTTCTCTTT
*
44031568 TTTGCTTTTCTCTTT
1 TTTTCTTTTCTCTTT
44031583 TTTTCTTTT
1 TTTTCTTTT
44031592 GCTTTTTCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
14 10 0.34
15 18 0.62
16 1 0.03
ACGTcount: A:0.02, C:0.13, G:0.06, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTCTCTTT
Found at i:44031598 original size:15 final size:15
Alignment explanation
Indices: 44031539--44031591 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 15
44031529 CGACCTCTCC
44031539 TTTT-CTTTTCTCTT
1 TTTTGCTTTTCTCTT
* **
44031553 TTTTG-TTTTTTGAT
1 TTTTGCTTTTCTCTT
44031567 TTTTGCTTTTCTCTT
1 TTTTGCTTTTCTCTT
*
44031582 TTTTTCTTTT
1 TTTTGCTTTT
44031592 GCTTTTTCCA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 15 0.50
15 15 0.50
ACGTcount: A:0.02, C:0.13, G:0.06, T:0.79
Consensus pattern (15 bp):
TTTTGCTTTTCTCTT
Found at i:44032437 original size:16 final size:17
Alignment explanation
Indices: 44032392--44032437 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
44032382 CGGGTTTTCA
44032392 TCTTAACTTTTCTTCCTTT
1 TCTT-ACTTTT-TTCCTTT
*
44032411 TCTT-CCTTTTTCCTTT
1 TCTTACTTTTTTCCTTT
44032427 T-TTACTTTTTT
1 TCTTACTTTTTT
44032438 ATTGGGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 2 0.08
16 14 0.58
17 4 0.17
19 4 0.17
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.70
Consensus pattern (17 bp):
TCTTACTTTTTTCCTTT
Found at i:44032490 original size:12 final size:12
Alignment explanation
Indices: 44032475--44032506 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
44032465 TTTCGACCCA
44032475 TTTTTCTTCTTT
1 TTTTTCTTCTTT
44032487 TTTTTCTTCTTT
1 TTTTTCTTCTTT
*
44032499 TCTTTCTT
1 TTTTTCTT
44032507 TCTCTCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTCTTCTTT
Found at i:44033935 original size:19 final size:19
Alignment explanation
Indices: 44033911--44033948 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
44033901 CCCGACACTT
44033911 TAAGGAAAACGACTAACTC
1 TAAGGAAAACGACTAACTC
44033930 TAAGGAAAACGACTAACTC
1 TAAGGAAAACGACTAACTC
44033949 AATCATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (19 bp):
TAAGGAAAACGACTAACTC
Found at i:44037229 original size:58 final size:58
Alignment explanation
Indices: 44037109--44037351 Score: 212
Period size: 59 Copynumber: 4.2 Consensus size: 58
44037099 GGAATCCGAG
* *
44037109 GGGT-AAAATGGTAA-TTTTTGAAAGTTTT-GGGTT-AAATTGTAATTTTTAGAAGTTTTA
1 GGGTAAAAAT-GTAATTTTTTG-AAGTTTTGGGGTTAAAATT-AAATTTTTAGAAGTTTGA
* * *
44037166 AGGT-AAAATGTAATTTTTTGTAGTTTTGGGGTTAAAATTAAGATTTTTGGAAGTTTGA
1 GGGTAAAAATGTAATTTTTTGAAGTTTTGGGGTTAAAATTAA-ATTTTTAGAAGTTTGA
* ** * ** *
44037224 GGGTAAAAATATAATTTTGGGAAGTTTCGGGGTTAAAATGGAATTTTTAGAAATTTGA
1 GGGTAAAAATGTAATTTTTTGAAGTTTTGGGGTTAAAATTAAATTTTTAGAAGTTTGA
* * * ** *
44037282 GGGTCAAAAATGAAATTTTTGGAGGTTTAAGGGTAAAAATGT-AATTTTTAGAAGTTT-A
1 GGGT-AAAAATGTAATTTTTTGAAGTTTTGGGGTTAAAAT-TAAATTTTTAGAAGTTTGA
44037340 GGGGTAAAAATG
1 -GGGTAAAAATG
44037352 GTATTTTCAA
Statistics
Matches: 154, Mismatches: 24, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
56 10 0.06
57 20 0.13
58 48 0.31
59 76 0.49
ACGTcount: A:0.35, C:0.01, G:0.25, T:0.40
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTTGAAGTTTTGGGGTTAAAATTAAATTTTTAGAAGTTTGA
Found at i:44037357 original size:29 final size:30
Alignment explanation
Indices: 44037107--44037367 Score: 158
Period size: 29 Copynumber: 9.0 Consensus size: 30
44037097 TTGGAATCCG
44037107 AGGGGT-AAAATGGTAATTTTT-GAAAGTTT
1 AGGGGTAAAAATGGTAATTTTTAG-AAGTTT
* * *
44037136 -TGGGT-TAAATTGTAATTTTTAGAAGTTTT
1 AGGGGTAAAAATGGTAATTTTTAGAAG-TTT
* * *
44037165 A-AGGT-AAAAT-GTAATTTTTTGTAGTTT
1 AGGGGTAAAAATGGTAATTTTTAGAAGTTT
* * *
44037192 TGGGGTTAAAAT--TAAGATTTTTGGAAGTTT
1 AGGGGTAAAAATGGT-A-ATTTTTAGAAGTTT
* **
44037222 -GAGGGTAAAAAT-ATAATTTTGGGAAGTTT
1 AG-GGGTAAAAATGGTAATTTTTAGAAGTTT
* * *
44037251 CGGGGTTAAAATGG-AATTTTTAGAAATTT
1 AGGGGTAAAAATGGTAATTTTTAGAAGTTT
* * *
44037280 -GAGGGTCAAAAAT-GAAATTTTTGGAGGTTT
1 AG-GGGT-AAAAATGGTAATTTTTAGAAGTTT
*
44037310 AAGGGTAAAAAT-GTAATTTTTAGAAGTTT
1 AGGGGTAAAAATGGTAATTTTTAGAAGTTT
* *
44037339 AGGGGTAAAAATGGT-ATTTTCAAAAGTTT
1 AGGGGTAAAAATGGTAATTTTTAGAAGTTT
44037368 TAAGGTCAAA
Statistics
Matches: 187, Mismatches: 29, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
27 3 0.02
28 37 0.20
29 100 0.53
30 46 0.25
31 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.25, T:0.40
Consensus pattern (30 bp):
AGGGGTAAAAATGGTAATTTTTAGAAGTTT
Found at i:44037375 original size:88 final size:89
Alignment explanation
Indices: 44037199--44037377 Score: 227
Period size: 88 Copynumber: 2.0 Consensus size: 89
44037189 TTTTGGGGTT
* * * * *
44037199 AAAATTAAGATTTTTGGAAGTTTGAGGGTAAAAATATAATTTTGGGAAGTTTCGGGGTTAAAATG
1 AAAATGAAGATTTTTGGAAGTTTAAGGGTAAAAATATAATTTTGAGAAGTTTAGGGGTAAAAATG
* *
44037264 GAATTTTTAGAAATTTGAGGGTCA
66 GAATTTTCAGAAATTTGAAGGTCA
* * *
44037288 AAAATGAA-ATTTTTGGAGGTTTAAGGGTAAAAATGTAATTTTTAGAAGTTTAGGGGTAAAAATG
1 AAAATGAAGATTTTTGGAAGTTTAAGGGTAAAAATATAATTTTGAGAAGTTTAGGGGTAAAAATG
* *
44037352 GTATTTTCA-AAAGTTTTAAGGTCA
66 GAATTTTCAGAAA-TTTGAAGGTCA
44037376 AA
1 AA
44037378 TTTTAATTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
87 3 0.04
88 67 0.87
89 7 0.09
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (89 bp):
AAAATGAAGATTTTTGGAAGTTTAAGGGTAAAAATATAATTTTGAGAAGTTTAGGGGTAAAAATG
GAATTTTCAGAAATTTGAAGGTCA
Found at i:44037398 original size:88 final size:89
Alignment explanation
Indices: 44037199--44037418 Score: 220
Period size: 88 Copynumber: 2.5 Consensus size: 89
44037189 TTTTGGGGTT
* ** * *
44037199 AAAATTAAGATTTTT-G-GAAGTTTGAGGGTAAAAATATAATTTTGGGAAGTTTCGGGGTTAAAA
1 AAAATGAA-ATTTTTGGAGAAGTTT-AGGGTAAAAATATAATTTTTAGAAGTTTAGGGGTAAAAA
* *
44037262 TGGAATTTTTAGAAATTTGAGGGTCA
64 TGGAATTTTCAGAAATTTGAAGGTCA
*
44037288 AAAATGAAATTTTTGGAG--GTTTAAGGGTAAAAATGTAATTTTTAGAAGTTTAGGGGTAAAAAT
1 AAAATGAAATTTTTGGAGAAGTTT-AGGGTAAAAATATAATTTTTAGAAGTTTAGGGGTAAAAAT
* *
44037351 GGTATTTTCA-AAAGTTTTAAGGTC-
65 GGAATTTTCAGAAA-TTTGAAGGTCA
* ** *
44037375 AAATTTTAA-TTTTGGAGAAGTTTAGAGGTCAAAATATAATTTTT
1 AAAATGAAATTTTTGGAGAAGTTTAG-GGTAAAAATATAATTTTT
44037419 GGATAGCTTA
Statistics
Matches: 109, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
86 8 0.07
87 11 0.10
88 81 0.74
89 8 0.07
90 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (89 bp):
AAAATGAAATTTTTGGAGAAGTTTAGGGTAAAAATATAATTTTTAGAAGTTTAGGGGTAAAAATG
GAATTTTCAGAAATTTGAAGGTCA
Found at i:44037813 original size:5 final size:5
Alignment explanation
Indices: 44037803--44037827 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
44037793 CGGATCCTGA
44037803 GGTCG GGTCG GGTCG GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTCG
44037828 ATCCATGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:44038526 original size:18 final size:18
Alignment explanation
Indices: 44038503--44038539 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
44038493 AATATTACCA
44038503 AAAATATCTATTATTATT
1 AAAATATCTATTATTATT
*
44038521 AAAATATTTATTATTATT
1 AAAATATCTATTATTATT
44038539 A
1 A
44038540 TTACTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATATCTATTATTATT
Found at i:44039415 original size:11 final size:11
Alignment explanation
Indices: 44039387--44039456 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 11
44039377 TTTGAAAATA
*
44039387 AATTTAATTTT
1 AATTTAAATTT
44039398 AATTTTAAATTT
1 AA-TTTAAATTT
*
44039410 AATTTAAATTCA
1 AATTTAAATT-T
* *
44039422 AATTTAAAATA
1 AATTTAAATTT
*
44039433 AATCTAAATTT
1 AATTTAAATTT
**
44039444 AAAATAAATTT
1 AATTTAAATTT
44039455 AA
1 AA
44039457 AAGGGTCCAG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 30 0.61
12 19 0.39
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:44039434 original size:17 final size:18
Alignment explanation
Indices: 44039398--44039457 Score: 72
Period size: 17 Copynumber: 3.5 Consensus size: 18
44039388 ATTTAATTTT
* **
44039398 AATTTTAAATTTAATTTA
1 AATTCTAAATTTAAAATA
44039416 AATTC-AAATTTAAAATA
1 AATTCTAAATTTAAAATA
44039433 AA-TCTAAATTTAAAATA
1 AATTCTAAATTTAAAATA
44039450 AATT-TAAA
1 AATTCTAAA
44039458 AGGGTCCAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 2 0.05
17 30 0.81
18 5 0.14
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTCTAAATTTAAAATA
Found at i:44039457 original size:6 final size:6
Alignment explanation
Indices: 44039371--44039457 Score: 74
Period size: 6 Copynumber: 15.0 Consensus size: 6
44039361 AAATTCCTTT
* * *
44039371 TTTAAA TTTGAAA -ATAAA TTTAAT TTTAAT TTTAAA TTT-AA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
44039418 TTCAAA TTTAAA -ATAAA TCTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
44039458 AGGGTCCAGT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
5 16 0.25
6 46 0.71
7 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:44041226 original size:21 final size:22
Alignment explanation
Indices: 44041202--44041243 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
44041192 ATTTTCTGAG
44041202 AAAATT-AATAAGAAA-ATAAAT
1 AAAATTAAATAA-AAATATAAAT
44041223 AAAATTAAATAAAAATATAAA
1 AAAATTAAATAAAAATATAAA
44041244 ATATAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATTAAATAAAAATATAAAT
Found at i:44041324 original size:17 final size:17
Alignment explanation
Indices: 44041293--44041337 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
44041283 TATAATACAT
44041293 AATAAATAAAA-ATAAA
1 AATAAATAAAATATAAA
44041309 AATAAATAAAATATAAA
1 AATAAATAAAATATAAA
* *
44041326 ACTAAATGAAAT
1 AATAAATAAAAT
44041338 CACTTTGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (17 bp):
AATAAATAAAATATAAA
Found at i:44041635 original size:22 final size:23
Alignment explanation
Indices: 44041586--44041637 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
44041576 AGATGGCATT
*
44041586 ATAAATATATATATTATTAAAATG
1 ATAAA-ATATATATTATTAAAATC
* *
44041610 ATAAAAT-TATATTTTTATAATC
1 ATAAAATATATATTATTAAAATC
44041632 ATAAAA
1 ATAAAA
44041638 ATTAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 18 0.72
23 2 0.08
24 5 0.20
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAATATATATTATTAAAATC
Found at i:44048046 original size:29 final size:29
Alignment explanation
Indices: 44048014--44048092 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 29
44048004 GAAGTCGAAC
* *
44048014 TTTTGGAAAATTGAGGGTAAAATGGTAAT
1 TTTTGGAAGATTGGGGGTAAAATGGTAAT
* * *
44048043 TTTTGGATGCTTGGGGGT-AAATGGTGAT
1 TTTTGGAAGATTGGGGGTAAAATGGTAAT
*
44048071 TTTTGGAAGTTTGGGGGTAAAA
1 TTTTGGAAGATTGGGGGTAAAA
44048093 ATATGATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 25 0.60
29 17 0.40
ACGTcount: A:0.28, C:0.01, G:0.34, T:0.37
Consensus pattern (29 bp):
TTTTGGAAGATTGGGGGTAAAATGGTAAT
Done.