Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 133 of 325
Found at i:40246340 original size:40 final size:40
Alignment explanation
Indices: 40246281--40246449 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
40246271 CGGGACTTTA
* * *
40246281 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
40246321 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
40246361 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
40246401 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
40246441 CCCGGATAT
1 CCCGGATAT
40246450 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:40250564 original size:24 final size:24
Alignment explanation
Indices: 40250537--40250719 Score: 285
Period size: 24 Copynumber: 7.6 Consensus size: 24
40250527 CTTATTATGT
* * *
40250537 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
* *
40250561 TCGCACACATAGTGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
*
40250585 TCGCACACATAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
40250609 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
* *
40250633 TCGCACACATAGTACCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
40250657 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
40250681 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
40250705 TCGCACACATAGTGC
1 TCGCACACATAGTGC
40250720 ATTTGAGATA
Statistics
Matches: 151, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 151 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:40250634 original size:72 final size:72
Alignment explanation
Indices: 40250515--40250719 Score: 286
Period size: 72 Copynumber: 2.8 Consensus size: 72
40250505 ACCGAATGTG
* ** * * * *
40250515 GCACACATAGTGCT-TATTATGTTCGCACACATAGAGCTATAGCAAATCGCACACATAGTGCTAT
1 GCACACATAGTGCTATAGTA-AATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCAT
40250579 AGCAAATC
65 AGCAAATC
*
40250587 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTACCATA
1 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATA
**
40250652 GTGAATC
66 GCAAATC
* *
40250659 GCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTGAATCGCACACATAGTGC
1 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGC
40250720 ATTTGAGATA
Statistics
Matches: 119, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
72 115 0.97
73 4 0.03
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (72 bp):
GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATA
GCAAATC
Found at i:40254292 original size:13 final size:13
Alignment explanation
Indices: 40254274--40254302 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40254264 TTTAGTTTAA
40254274 TTAGTTAATTAGT
1 TTAGTTAATTAGT
40254287 TTAGTTAATTAGT
1 TTAGTTAATTAGT
40254300 TTA
1 TTA
40254303 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:40254639 original size:17 final size:18
Alignment explanation
Indices: 40254619--40254652 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40254609 AAGTGAATTG
40254619 AAATTACA-AAATTAAAT
1 AAATTACAGAAATTAAAT
*
40254636 AAATTGCAGAAATTAAA
1 AAATTACAGAAATTAAA
40254653 ATGAGGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (18 bp):
AAATTACAGAAATTAAAT
Found at i:40255368 original size:20 final size:20
Alignment explanation
Indices: 40255330--40255377 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
40255320 TAAATTCTAA
* **
40255330 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
40255350 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
40255370 AAA-ATAAA
1 AAAGATAAA
40255378 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:40255402 original size:27 final size:26
Alignment explanation
Indices: 40255372--40255434 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
40255362 AGATAATTAA
40255372 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
40255399 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
40255426 AATATAAAT
1 AATA-AAAT
40255435 AAAATAGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:40255421 original size:15 final size:15
Alignment explanation
Indices: 40255401--40255430 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40255391 ATAATCCTAA
*
40255401 TAATTATCTTAATAT
1 TAATTATCCTAATAT
40255416 TAATTATCCTAATAT
1 TAATTATCCTAATAT
40255431 AAATAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:40268169 original size:49 final size:49
Alignment explanation
Indices: 40268092--40268336 Score: 310
Period size: 49 Copynumber: 4.9 Consensus size: 49
40268082 TAGCCGAAGC
* * * *
40268092 TATCTGGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* * * *
40268141 TATCCGGTACACGTAGTAACCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-AAT
* * *
40268191 CATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-T
** * *
40268242 TATCAAGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
40268291 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTATACACGTGACC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
40268337 TCACAATAGC
Statistics
Matches: 165, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
49 80 0.48
50 46 0.28
51 39 0.24
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:40272563 original size:42 final size:44
Alignment explanation
Indices: 40272461--40272566 Score: 155
Period size: 44 Copynumber: 2.5 Consensus size: 44
40272451 ATGTGTTTTT
40272461 GTGTAAGACCACGTCTGGGATGTTAGCATCGACTTATGATTTAC
1 GTGTAAGACCACGTCTGGGATGTTAGCATCGACTTATGATTTAC
*
40272505 GTGTAAGACCACGTCTGGGATGTTGGCATCGTA-TT-TGATTT-C
1 GTGTAAGACCACGTCTGGGATGTTAGCATCG-ACTTATGATTTAC
**
40272547 GTGTAAGACCTTGTCTGGGA
1 GTGTAAGACCACGTCTGGGA
40272567 CAGTGGCATC
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
42 19 0.33
43 6 0.10
44 32 0.55
45 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (44 bp):
GTGTAAGACCACGTCTGGGATGTTAGCATCGACTTATGATTTAC
Found at i:40272574 original size:42 final size:42
Alignment explanation
Indices: 40272461--40272618 Score: 149
Period size: 42 Copynumber: 3.7 Consensus size: 42
40272451 ATGTGTTTTT
* *
40272461 GTGTAAGACCACGTCTGGGATGTTAGCATCGACTTATGATTTAC
1 GTGTAAGACCACGTCTGGGAAGTTGGCATCGA-TT-TGATTTAC
*
40272505 GTGTAAGACCACGTCTGGGATGTTGGCATCGTATTTGATTT-C
1 GTGTAAGACCACGTCTGGGAAGTTGGCATCG-ATTTGATTTAC
** * *
40272547 GTGTAAGACCTTGTCTGGGACAG-TGGCATCGATTTTTAATTAC
1 GTGTAAGACCACGTCTGGGA-AGTTGGCATCGA-TTTGATTTAC
* * * * *
40272590 ATGTAAGACGACATTTGGGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGAAGTTGGCAT
40272619 TGTACGAGCT
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.01
42 34 0.35
43 28 0.29
44 32 0.33
45 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.33
Consensus pattern (42 bp):
GTGTAAGACCACGTCTGGGAAGTTGGCATCGATTTGATTTAC
Found at i:40278870 original size:15 final size:15
Alignment explanation
Indices: 40278850--40278901 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
40278840 ACTACAAAAC
40278850 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
40278865 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
40278884 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
40278899 ATT
1 ATT
40278902 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:40278965 original size:16 final size:16
Alignment explanation
Indices: 40278934--40278970 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
40278924 ATGTGAATAA
40278934 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
40278950 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
40278966 TATTA
1 TATTA
40278971 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:40279022 original size:22 final size:22
Alignment explanation
Indices: 40278980--40279037 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
40278970 AAAATAAAAA
*
40278980 TAAAATATTAAA-TA-ATTTAT
1 TAAAATAATAAATTATATTTAT
40279000 TAAAATAATAAATTATATTTAT
1 TAAAATAATAAATTATATTTAT
* * *
40279022 TATATTAATAATTTAT
1 TAAAATAATAAATTAT
40279038 TATATGACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.34
21 2 0.06
22 19 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAATAATAAATTATATTTAT
Found at i:40280773 original size:25 final size:24
Alignment explanation
Indices: 40280723--40280775 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 24
40280713 TATAATGTTC
*
40280723 AAACTTGTTTTATGAAAAAAAAAA
1 AAACTTGTTGTATGAAAAAAAAAA
40280747 AAACTTGATTGTA-GAAGAAAAAGAAA
1 AAACTTG-TTGTATGAA-AAAAA-AAA
40280773 AAA
1 AAA
40280776 GTACTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 10 0.40
25 9 0.36
26 6 0.24
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.23
Consensus pattern (24 bp):
AAACTTGTTGTATGAAAAAAAAAA
Found at i:40280859 original size:22 final size:22
Alignment explanation
Indices: 40280834--40280875 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40280824 TAACAACCCA
*
40280834 AAGACTTAAATGAA-AATTTTTG
1 AAGAATTAAAT-AATAATTTTTG
40280856 AAGAATTAAATAATAATTTT
1 AAGAATTAAATAATAATTTT
40280876 ATGACATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (22 bp):
AAGAATTAAATAATAATTTTTG
Found at i:40285618 original size:20 final size:21
Alignment explanation
Indices: 40285589--40285634 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
40285579 ATTAAAACTT
* * *
40285589 AAAATCAATATAAACTTATAA
1 AAAATCAATAAAAAATAATAA
40285610 AAAAT-AATAAAAAATAATAA
1 AAAATCAATAAAAAATAATAA
40285630 AAAAT
1 AAAAT
40285635 TGTAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATCAATAAAAAATAATAA
Found at i:40285640 original size:10 final size:10
Alignment explanation
Indices: 40285606--40285634 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
40285596 ATATAAACTT
40285606 ATAAAAAATA
1 ATAAAAAATA
40285616 ATAAAAAATA
1 ATAAAAAATA
40285626 ATAAAAAAT
1 ATAAAAAAT
40285635 TGTAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:40285788 original size:19 final size:18
Alignment explanation
Indices: 40285761--40285817 Score: 73
Period size: 17 Copynumber: 3.2 Consensus size: 18
40285751 AAAAAAGAGA
40285761 AAAAT-ATAAAAATTATT
1 AAAATAATAAAAATTATT
40285778 AGAAATAATAAAAATTATT
1 A-AAATAATAAAAATTATT
* *
40285797 -AAATATTAAAAAATATT
1 AAAATAATAAAAATTATT
40285814 AAAA
1 AAAA
40285818 AAATCATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 16 0.46
18 7 0.20
19 12 0.34
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATAATAAAAATTATT
Found at i:40285939 original size:20 final size:21
Alignment explanation
Indices: 40285902--40285950 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
40285892 AGATATATTT
40285902 AAAATATTACAAAAACTTATA
1 AAAATATTACAAAAACTTATA
* *
40285923 AAAAT-TTATAAATACTTATA
1 AAAATATTACAAAAACTTATA
40285943 AATAATAT
1 AA-AATAT
40285951 AAAAATTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 15 0.62
21 8 0.33
22 1 0.04
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATATTACAAAAACTTATA
Found at i:40285975 original size:48 final size:47
Alignment explanation
Indices: 40285833--40285987 Score: 129
Period size: 48 Copynumber: 3.2 Consensus size: 47
40285823 ATAAACCTTG
* * * * *
40285833 TAAAGATTATAAAAAATCTAATAAATTTTAATAAATTATTAAAATATA
1 TAAATATTATAAATAATATAA-AAATTCTAATAAATTATTAAAATTTA
* * *
40285881 TATAAT-TAATAAGATATATTTAAAATATTAC-AA-AAACTTATAAAAATTTA
1 TA-AATATTATAA-ATA-ATATAAAA-ATT-CTAATAAA-TTATTAAAATTTA
40285931 TAAATACTTATAAATAATATAAAAATTCTAATAAATTATTAAAATATTA
1 TAAATA-TTATAAATAATATAAAAATTCTAATAAATTATTAAAAT-TTA
40285980 -AAATATTA
1 TAAATATTA
40285988 AAAAAATTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
47 4 0.05
48 26 0.30
49 25 0.29
50 26 0.30
51 5 0.06
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (47 bp):
TAAATATTATAAATAATATAAAAATTCTAATAAATTATTAAAATTTA
Found at i:40285993 original size:38 final size:37
Alignment explanation
Indices: 40285900--40285998 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 37
40285890 TAAGATATAT
*
40285900 TTAAAATATTACAAAAACTTATAAAAATTTATAAATAC
1 TTAAAATATTA-AAAAAATTATAAAAATTTATAAATAC
* * *
40285938 TTATAAATAATATAAAAATTCTAATAAA-TTATTAAAATA-
1 TTA-AAATATTAAAAAAATTATAA-AAATTTA-T-AAATAC
40285977 TTAAAATATTAAAAAAATTATA
1 TTAAAATATTAAAAAAATTATA
40285999 TAGACATAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
38 31 0.62
39 14 0.28
40 5 0.10
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (37 bp):
TTAAAATATTAAAAAAATTATAAAAATTTATAAATAC
Found at i:40286587 original size:10 final size:9
Alignment explanation
Indices: 40286572--40286645 Score: 69
Period size: 10 Copynumber: 7.9 Consensus size: 9
40286562 CTAGTTCAAA
40286572 TTTTTATGAT
1 TTTTTAT-AT
40286582 TTTTTATAT
1 TTTTTATAT
40286591 TTTTTAATAT
1 TTTTT-ATAT
* *
40286601 TTTATATCAA
1 TTTTTAT-AT
*
40286611 TTTTAATAT
1 TTTTTATAT
40286620 TTTTTA-AT
1 TTTTTATAT
*
40286628 TTTTTATGAA
1 TTTTTAT-AT
40286638 TTTTTATA
1 TTTTTATA
40286646 AGTTCTTAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
8 8 0.15
9 16 0.30
10 29 0.55
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (9 bp):
TTTTTATAT
Found at i:40286596 original size:19 final size:18
Alignment explanation
Indices: 40286572--40286645 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 18
40286562 CTAGTTCAAA
40286572 TTTTTATGATTTTTTATAT
1 TTTTTAT-ATTTTTTATAT
* *
40286591 TTTTTAATATTTTATATCAA
1 TTTTT-ATATTTTTTAT-AT
*
40286611 TTTTAATATTTTTTA-AT
1 TTTTTATATTTTTTATAT
*
40286628 TTTTTATGAATTTTTATA
1 TTTTTAT-ATTTTTTATA
40286646 AGTTCTTAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
17 7 0.16
18 7 0.16
19 23 0.52
20 7 0.16
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTTATATTTTTTATAT
Found at i:40286621 original size:29 final size:27
Alignment explanation
Indices: 40286572--40286641 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 27
40286562 CTAGTTCAAA
* * *
40286572 TTTTTATGATTTTTTATATTTTTTAAT
1 TTTTTATCAATTTTAATATTTTTTAAT
40286599 ATTTTATATCAATTTTAATATTTTTTAAT
1 -TTTT-TATCAATTTTAATATTTTTTAAT
*
40286628 TTTTTATGAATTTT
1 TTTTTATCAATTTT
40286642 TATAAGTTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 9 0.24
28 8 0.22
29 20 0.54
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (27 bp):
TTTTTATCAATTTTAATATTTTTTAAT
Found at i:40286642 original size:20 final size:19
Alignment explanation
Indices: 40286618--40286681 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
40286608 CAATTTTAAT
*
40286618 ATTTTT-TAATTTTTTATGA
1 ATTTTTATAAGTTTTTA-GA
*
40286637 ATTTTTATAAGTTCTTAAGA
1 ATTTTTATAAGTT-TTTAGA
* * *
40286657 AATTTTATACGTTTTTAAA
1 ATTTTTATAAGTTTTTAGA
40286676 ATTTTT
1 ATTTTT
40286682 TTAATATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
19 15 0.42
20 18 0.50
21 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.59
Consensus pattern (19 bp):
ATTTTTATAAGTTTTTAGA
Found at i:40286690 original size:29 final size:28
Alignment explanation
Indices: 40286580--40286692 Score: 84
Period size: 29 Copynumber: 3.9 Consensus size: 28
40286570 AATTTTTATG
* *
40286580 ATTTTTTATATTTTTTAATATTTTATATC
1 ATTTTTAAAATTTTTTAATATTTTATA-C
* * *
40286609 AATTTTAATATTTTTTAATTTTTTATGA-
1 ATTTTTAAAATTTTTTAATATTTTAT-AC
* * * *
40286637 ATTTTTATAAGTTCTTAAGAAATTTTATAC
1 ATTTTTA-AAATTTTTTA-ATATTTTATAC
*
40286667 GTTTTTAAAATTTTTTTAATATTTTA
1 ATTTTTAAAA-TTTTTTAATATTTTA
40286693 AATATGTTTT
Statistics
Matches: 64, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
28 6 0.09
29 39 0.61
30 19 0.30
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.62
Consensus pattern (28 bp):
ATTTTTAAAATTTTTTAATATTTTATAC
Found at i:40286952 original size:17 final size:18
Alignment explanation
Indices: 40286930--40286963 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
40286920 AGTTGAATTG
40286930 AAATTGCG-AAATTAAAT
1 AAATTGCGAAAATTAAAT
40286947 AAATTGCGAAAATTAAA
1 AAATTGCGAAAATTAAA
40286964 ATGGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCGAAAATTAAAT
Found at i:40288363 original size:10 final size:10
Alignment explanation
Indices: 40288344--40288393 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
40288334 TTAAATTCTA
40288344 AAAGATAAAT
1 AAAGATAAAT
40288354 ACAA-ATAAAT
1 A-AAGATAAAT
*
40288364 AAAGATAATT
1 AAAGATAAAT
40288374 AAAGATAAAT
1 AAAGATAAAT
*
40288384 AAAAATAAAT
1 AAAGATAAAT
40288394 CCTAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40288425 original size:13 final size:13
Alignment explanation
Indices: 40288407--40288443 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
40288397 AAATTTAAAT
40288407 TAAATAATTATCC
1 TAAATAATTATCC
*
40288420 TTAATAATTATCC
1 TAAATAATTATCC
40288433 TAATATAATTA
1 TAA-ATAATTA
40288444 AACATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (13 bp):
TAAATAATTATCC
Found at i:40289231 original size:96 final size:97
Alignment explanation
Indices: 40289066--40289247 Score: 276
Period size: 96 Copynumber: 1.9 Consensus size: 97
40289056 ATTTAATTTA
* * * * *
40289066 TTTATTTTTACTTAGGAATATATTGAACCTTTTGACGCGAAGAGAGGTGATAGCCAAGAACCCCA
1 TTTATTTTTACTTAAGAACATATTGAACCTTTTGACGCGAAGAGAGATAACAGCCAAGAACCCCA
*
40289131 CCCCGATTACTCAGCCCAACATACTCCTAATT
66 CCCCGATTACTCAACCCAACATACTCCTAATT
* *
40289163 TTTATTTTT-CTTAAGAACATATTGAACCTTTTGACGCGAAGAGAGATAACAGCCAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATTGAACCTTTTGACGCGAAGAGAGATAACAGCCAAGAACCCCA
*
40289227 CCCCGGTTACTCAACCCAACA
66 CCCCGATTACTCAACCCAACA
40289248 CATTCTTAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
96 67 0.88
97 9 0.12
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATTGAACCTTTTGACGCGAAGAGAGATAACAGCCAAGAACCCCA
CCCCGATTACTCAACCCAACATACTCCTAATT
Found at i:40290319 original size:12 final size:12
Alignment explanation
Indices: 40290302--40290345 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
40290292 ATTAATATCC
40290302 AAATAAAGTAAT
1 AAATAAAGTAAT
*
40290314 AAATAATA-AAAT
1 AAATAA-AGTAAT
40290326 AAAATAAAGTAAT
1 -AAATAAAGTAAT
40290339 AAATAAA
1 AAATAAA
40290346 AAAAATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (12 bp):
AAATAAAGTAAT
Found at i:40290328 original size:5 final size:5
Alignment explanation
Indices: 40290318--40290383 Score: 55
Period size: 5 Copynumber: 12.4 Consensus size: 5
40290308 AGTAATAAAT
*
40290318 AATAA AATAA AATAA AGTAATA AATAA AA-AA AATAGTA AATAA AAT-A
1 AATAA AATAA AATAA AAT-A-A AATAA AATAA AATA--A AATAA AATAA
40290365 AATAAA AATAAA AATAA AA
1 AAT-AA AAT-AA AATAA AA
40290384 ATTGGGTTGC
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
4 8 0.15
5 24 0.46
6 12 0.23
7 8 0.15
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:40290334 original size:25 final size:25
Alignment explanation
Indices: 40290302--40290383 Score: 94
Period size: 25 Copynumber: 3.1 Consensus size: 25
40290292 ATTAATATCC
40290302 AAATAAAGTAATAAATAATAAAATA
1 AAATAAAGTAATAAATAATAAAATA
*
40290327 AAATAAAGTAATAAATAAAAAAAATA
1 AAATAAAGTAATAAAT-AATAAAATA
*
40290353 GTAAATAAAATAAATAAA-AATAAAAATA
1 --AAATAAAGT-AATAAATAAT-AAAATA
40290381 AAA
1 AAA
40290384 ATTGGGTTGC
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
25 16 0.33
26 11 0.22
27 2 0.04
28 14 0.29
29 6 0.12
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.21
Consensus pattern (25 bp):
AAATAAAGTAATAAATAATAAAATA
Found at i:40290379 original size:12 final size:12
Alignment explanation
Indices: 40290311--40290385 Score: 52
Period size: 12 Copynumber: 6.2 Consensus size: 12
40290301 CAAATAAAGT
40290311 AATAAATAAT-AA
1 AATAAA-AATAAA
40290323 AAT-AAAAT-AA
1 AATAAAAATAAA
*
40290333 AGTAATAAATAAA
1 AATAA-AAATAAA
*
40290346 AA-AAATAGTAAA
1 AATAAA-AATAAA
40290358 TAA-AATAAATAAA
1 -AATAA-AAATAAA
40290371 AATAAAAATAAA
1 AATAAAAATAAA
40290383 AAT
1 AAT
40290386 TGGGTTGCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
10 7 0.13
11 4 0.08
12 26 0.50
13 14 0.27
14 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (12 bp):
AATAAAAATAAA
Found at i:40290379 original size:16 final size:17
Alignment explanation
Indices: 40290311--40290382 Score: 89
Period size: 16 Copynumber: 4.4 Consensus size: 17
40290301 CAAATAAAGT
40290311 AATAAATAATAAA-ATAA
1 AATAAATAATAAATA-AA
40290328 AATAAAGTAATAAATAAA
1 AATAAA-TAATAAATAAA
*
40290346 AA-AAATAGTAAAT-AA
1 AATAAATAATAAATAAA
40290361 AATAAATAA-AAATAAA
1 AATAAATAATAAATAAA
40290377 AATAAA
1 AATAAA
40290383 AATTGGGTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
15 8 0.16
16 20 0.41
17 9 0.18
18 11 0.22
19 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AATAAATAATAAATAAA
Found at i:40294064 original size:10 final size:10
Alignment explanation
Indices: 40294019--40294078 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
40294009 TTAAATTCTA
40294019 AAAGATAAAT
1 AAAGATAAAT
40294029 ACAA-ATAAAT
1 A-AAGATAAAT
* *
40294039 AAAGACAATT
1 AAAGATAAAT
*
40294049 AAAGATAATT
1 AAAGATAAAT
40294059 AAAGATAAAT
1 AAAGATAAAT
*
40294069 AAAAATAAAT
1 AAAGATAAAT
40294079 CCTAAATTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
9 2 0.05
10 39 0.91
11 2 0.05
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40294128 original size:14 final size:13
Alignment explanation
Indices: 40294092--40294129 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
40294082 AAATTTAAAT
40294092 CTAAATAATTATC
1 CTAAATAATTATC
*
40294105 CTTAATAATTATC
1 CTAAATAATTATC
40294118 CTAATATAATTA
1 CTAA-ATAATTA
40294130 AACATTAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (13 bp):
CTAAATAATTATC
Found at i:40294471 original size:19 final size:18
Alignment explanation
Indices: 40294402--40294471 Score: 56
Period size: 19 Copynumber: 3.9 Consensus size: 18
40294392 GTATTATTAG
*
40294402 TTTTTATTAATTTTATAAA
1 TTTTTA-TAAGTTTATAAA
* *
40294421 TTTTTATAAATTT-TAGA
1 TTTTTATAAGTTTATAAA
*
40294438 --TTTATTAGATTTATAATA
1 TTTTTATAAG-TTTATAA-A
40294456 TTTTTATAAGTTTATA
1 TTTTTATAAGTTTATA
40294472 TCAAATTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
15 6 0.15
16 3 0.08
17 5 0.12
18 7 0.17
19 12 0.30
20 7 0.17
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTTATAAGTTTATAAA
Found at i:40295107 original size:20 final size:20
Alignment explanation
Indices: 40295049--40295121 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
40295039 TTTGGCATAT
40295049 CAAAATTTCTAATG-GATAC
1 CAAAATTTCTAATGCGATAC
* * *
40295068 CAAAATTTCTCA-CCAAATAC
1 CAAAATTTCTAATGC-GATAC
*
40295088 CAAAATTTTTAATGCGATAC
1 CAAAATTTCTAATGCGATAC
* *
40295108 CAATATTTCAAATG
1 CAAAATTTCTAATG
40295122 AAAATCGTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
19 11 0.27
20 29 0.71
21 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (20 bp):
CAAAATTTCTAATGCGATAC
Found at i:40304648 original size:42 final size:42
Alignment explanation
Indices: 40304571--40304673 Score: 102
Period size: 42 Copynumber: 2.4 Consensus size: 42
40304561 CCTTGATTGA
* **
40304571 GATTTACGTATAAGACCATGTCTGGAACATCGGCATCG-TATCT
1 GATTT-CGTGTAAGACCATGTCTGGAACAGAGGCATCGATAT-T
*
40304614 GATTTCGTGTAAGACCCTGTCTAGG-ACAGAGGCATCGATATT
1 GATTTCGTGTAAGACCATGTCT-GGAACAGAGGCATCGATATT
* *
40304656 GAATTACATGTAAGACCA
1 G-ATTTCGTGTAAGACCA
40304674 CGTCCAGGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
42 27 0.54
43 23 0.46
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (42 bp):
GATTTCGTGTAAGACCATGTCTGGAACAGAGGCATCGATATT
Found at i:40306680 original size:98 final size:95
Alignment explanation
Indices: 40306513--40306687 Score: 253
Period size: 98 Copynumber: 1.8 Consensus size: 95
40306503 TAATGCTGAT
*
40306513 GCCATGTCCCAAACATGGTCTTACACTGGCTCATCTATCAAGTCGATGCCATGTCCCAGACATGG
1 GCCATGTCCCAAACATGGTCTTACACTGGCTCATCTATCAAGTCGATGCCATGTCCCAGACATGA
*
40306578 TCTTACATTGACTATCGAAATCGAGGTCGA
66 TCTTACACTGACTATCGAAATCGAGGTCGA
* * * *
40306608 GCCATGTCCTAGACATGGTCTTACACTAGCTC-TCACATATCCATGTCGATGCCATGTCCCAGAC
1 GCCATGTCCCAAACATGGTCTTACACTGGCTCAT--C-TAT-CAAGTCGATGCCATGTCCCAGAC
40306672 ATGATCTTACACTGAC
62 ATGATCTTACACTGAC
40306688 ACATCTCGTA
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
94 1 0.01
95 29 0.41
96 1 0.01
97 3 0.04
98 36 0.51
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (95 bp):
GCCATGTCCCAAACATGGTCTTACACTGGCTCATCTATCAAGTCGATGCCATGTCCCAGACATGA
TCTTACACTGACTATCGAAATCGAGGTCGA
Found at i:40306740 original size:46 final size:47
Alignment explanation
Indices: 40306610--40306868 Score: 241
Period size: 46 Copynumber: 5.5 Consensus size: 47
40306600 GAGGTCGAGC
* * * *
40306610 CATGTCCTAGACATGGTCTTACACTAGCTCTCACATATC-CATGTCGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTCT-ACATCTCGTA-GCCGATG
*
40306659 CCATGTCCCAGACATGATCTTACACT-G-AC-ACATCTCGTAGCCGATG
1 -CATGTCCCAGACATG-TCTTACACTAGCTCTACATCTCGTAGCCGATG
40306705 CATGTCCCAGACATGTCTTACACTAGCT-TACATCTCG-AGACCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTACATCTCGTAG-CCGATG
* * *
40306751 CATGTCCTAGACATGTCTTACACTAGCTCT-CATCTCAATA-CTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTACATCTC-GTAGCCGATG
* * * *
40306797 CCATGTCCCAAACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCTCTACAT-CTCGTAGCCGATG
*
40306845 CATGTCCTAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
40306869 GGCACACAAA
Statistics
Matches: 178, Mismatches: 18, Indels: 30
0.79 0.08 0.13
Matches are distributed among these distances:
44 9 0.05
45 18 0.10
46 74 0.42
47 27 0.15
48 25 0.14
49 3 0.02
50 22 0.12
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTACATCTCGTAGCCGATG
Found at i:40306817 original size:94 final size:92
Alignment explanation
Indices: 40306510--40306874 Score: 300
Period size: 94 Copynumber: 3.9 Consensus size: 92
40306500 GTATAATGCT
* * * * *
40306510 GATGCCATGTCCCAAACATGGTCTTACACTGGCTC-ATC-TATCAAGTCGATGCCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTA-CATATCGAGCCGATG-CATGTCCTAGA
* ** * *
40306573 CATGGTCTTACATTGACTATCGAAATCGA-GGTC
64 CAT-GTCTTACACTGAC-A-C-ATCTC-ATAGCC
* * * *
40306606 GA-GCCATGTCCTAGACATGGTCTTACACTAGCTCTCACATATCCATGTCGATGCCATGTCCCAG
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-ACATATCGA-GCCGATG-CATGTCCTAG
*
40306670 ACATGATCTTACACTGACACATCTCGTAGCC
63 ACATG-TCTTACACTGACACATCTCATAGCC
*
40306701 GATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TACATCTCGAGACCGATGCATGTCCTAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTACATATCGAG-CCGATGCATGTCCTAGAC
* * *
40306763 ATGTCTTACACTAGCTCTCATCTCAATA-CT
65 ATGTCTTACACT-G-ACACATCTC-ATAGCC
* * *
40306793 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATGTCCTAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTACAT-ATCG-AGCCGATGCATGTCCTAGA
*
40306856 CATGTCTTACACTGGCACA
64 CATGTCTTACACTGACACA
40306875 CAAATAACCC
Statistics
Matches: 228, Mismatches: 25, Indels: 36
0.79 0.09 0.12
Matches are distributed among these distances:
90 9 0.04
91 16 0.07
92 27 0.12
93 17 0.07
94 61 0.27
95 52 0.23
96 5 0.02
97 8 0.04
98 33 0.14
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (92 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTACATATCGAGCCGATGCATGTCCTAGACA
TGTCTTACACTGACACATCTCATAGCC
Found at i:40306828 original size:48 final size:47
Alignment explanation
Indices: 40306508--40306832 Score: 235
Period size: 46 Copynumber: 6.9 Consensus size: 47
40306498 GGGTATAATG
* *
40306508 CTGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATC-TATCAAGT
1 CTGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TCATATCAA-T
* * * *
40306556 C-GATGCCATGTCCCAGACATGGTCTTACA-TTGACTATCGAAATCGAGGT
1 CTGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTC-ATATC-A-AT
* *
40306605 C-GA-GCCATGTCCTAGACATGGTCTTACACTAGCTCTCACATATCCAT
1 CTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT--CATATCAAT
* * * * * * *
40306652 GTCGATGCCATGTCCCAGACATGATCTTACACT-G-ACACATCTCGTAG
1 CT-GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC-AAT
* *
40306699 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TACATCTCGAGA-
1 CTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATATC-A-AT
* * *
40306745 CCGATG-CATGTCCTAGACAT-GTCTTACACTAGCTCTCATCTCAAT
1 CTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAAT
* *
40306790 ACTGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATA
1 -CTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATA
40306833 ATGTGGCCGA
Statistics
Matches: 225, Mismatches: 31, Indels: 42
0.76 0.10 0.14
Matches are distributed among these distances:
44 10 0.04
45 16 0.07
46 64 0.28
47 45 0.20
48 50 0.22
49 14 0.06
50 26 0.12
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (47 bp):
CTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAAT
Found at i:40316543 original size:51 final size:51
Alignment explanation
Indices: 40316465--40316564 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 51
40316455 TGGATGCGAG
* * *
40316465 CATCCGAGCCCGTTGAGTGGTCGGAGTTCATAATGGATGCGATACATGTAA
1 CATCCGAGCCCATTGAGAGGTCCGAGTTCATAATGGATGCGATACATGTAA
* * * *
40316516 CATCCGAGCTCATTGAGAGGTCCGAGTTCATTATGGATGTGTTACATGT
1 CATCCGAGCCCATTGAGAGGTCCGAGTTCATAATGGATGCGATACATGT
40316565 TATAAGGTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (51 bp):
CATCCGAGCCCATTGAGAGGTCCGAGTTCATAATGGATGCGATACATGTAA
Found at i:40319959 original size:33 final size:32
Alignment explanation
Indices: 40319886--40319963 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
40319876 CAGTATTTGT
* *
40319886 ATGTAAGACCATAGCTGGGCTATGACATTCAA
1 ATGTAAGACCATAACTGGGCTATGACATACAA
* * *
40319918 ATGATAAGACCATAACTGGGTTATGGCACTACGA
1 ATG-TAAGACCATAACTGGGCTATGACA-TACAA
*
40319952 GTGTAAGACCAT
1 ATGTAAGACCAT
40319964 GGCAAAGCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.08
33 30 0.79
34 5 0.13
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (32 bp):
ATGTAAGACCATAACTGGGCTATGACATACAA
Found at i:40321323 original size:38 final size:38
Alignment explanation
Indices: 40321272--40321347 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
40321262 AAAGTTAGGG
*
40321272 GCAAAATGGTAATTTTTCCTAGGTTGTAAATTGAGTCC
1 GCAAAATGGTAATTTTGCCTAGGTTGTAAATTGAGTCC
40321310 GCAAAATGGTAATTTTGCCTAGGTTGTAAATTGAGTCC
1 GCAAAATGGTAATTTTGCCTAGGTTGTAAATTGAGTCC
40321348 ACTTGAATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (38 bp):
GCAAAATGGTAATTTTGCCTAGGTTGTAAATTGAGTCC
Found at i:40322749 original size:16 final size:16
Alignment explanation
Indices: 40322728--40322765 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
40322718 TAGTAAATTG
40322728 GAAGCTCGTTGGATTA
1 GAAGCTCGTTGGATTA
*
40322744 GAAGCTCGTTGGATTG
1 GAAGCTCGTTGGATTA
40322760 GAAGCT
1 GAAGCT
40322766 TGGCGAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.34, T:0.29
Consensus pattern (16 bp):
GAAGCTCGTTGGATTA
Found at i:40323584 original size:46 final size:46
Alignment explanation
Indices: 40323521--40323749 Score: 291
Period size: 46 Copynumber: 5.0 Consensus size: 46
40323511 TTCGACATGA
* * * * * *
40323521 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGT
* * ** * * *
40323567 TGCCATGGTATCATTCAACCAAGGTCTTATTCATTTCCCCATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT-TCTATCAGGT
*
40323614 TGCCATGGTATCTTTCAACCATGGTCTTAAACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TATCAGGT
40323660 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TATCAGGT
40323706 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAG
40323750 AGAGCACACT
Statistics
Matches: 162, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
45 1 0.01
46 122 0.75
47 39 0.24
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGT
Found at i:40323680 original size:93 final size:92
Alignment explanation
Indices: 40323521--40323749 Score: 307
Period size: 93 Copynumber: 2.5 Consensus size: 92
40323511 TTCGACATGA
* * * * * *
40323521 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCATTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCATTCAAC
** *
40323586 CAAGGTCTTATTCATTTCCCCATCACGT
66 CAAGGTCTTACACATTT-CACATCACGT
* *
40323614 TGCCATGGTATCTTTCAACCATGGTCTTAAACA-TTTCATATCAGGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TATCAGGTTGCCATGGTATCATTCAA
* * *
40323678 CCATGGTCTTACACATTTCATATCAGGT
65 CCAAGGTCTTACACATTTCACATCACGT
40323706 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAG
40323750 AGAGCACACT
Statistics
Matches: 119, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
92 49 0.41
93 70 0.59
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCATTCAAC
CAAGGTCTTACACATTTCACATCACGT
Found at i:40327200 original size:40 final size:40
Alignment explanation
Indices: 40327155--40327321 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
40327145 CGGAATATAA
40327155 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40327195 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
40327235 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40327275 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40327314 CCGGATAT
1 CCGGATAT
40327322 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40327305 original size:80 final size:79
Alignment explanation
Indices: 40327171--40327321 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
40327161 ATAATCACGT
*
40327171 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
40327236 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
40327251 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
40327314 CCGGATAT
64 CCGGATAT
40327322 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:40328169 original size:17 final size:19
Alignment explanation
Indices: 40328146--40328191 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40328136 AAGAAGCATG
40328146 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40328164 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40328182 AATCATGCTC
1 AATCATGCTC
40328192 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40335202 original size:40 final size:39
Alignment explanation
Indices: 40335157--40335322 Score: 172
Period size: 40 Copynumber: 4.2 Consensus size: 39
40335147 CGGAATATAA
40335157 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGG-CTTAGC
* * * *
40335197 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
** * *
40335236 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-CTTAGC
** * * * *
40335276 CCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
40335315 CCGGATAT
1 CCGGATAT
40335323 CATTCAATTT
Statistics
Matches: 105, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 46 0.44
40 59 0.56
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC
Found at i:40335279 original size:79 final size:79
Alignment explanation
Indices: 40335173--40335322 Score: 205
Period size: 79 Copynumber: 1.9 Consensus size: 79
40335163 ATAATCACGT
*
40335173 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAAC-CAGCA-GAATTGCCTTCGGGCTTAGC
40335236 CCGGATATAGCCACTA
64 CCGGATATAGCCACTA
* * ** * *
40335252 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGCCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC
40335317 GGATAT
66 GGATAT
40335323 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 3 0.05
79 59 0.95
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:40336170 original size:17 final size:19
Alignment explanation
Indices: 40336147--40336192 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40336137 AAGAAGCATG
40336147 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40336165 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40336183 AATCATGCTC
1 AATCATGCTC
40336193 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40338907 original size:40 final size:40
Alignment explanation
Indices: 40338705--40338912 Score: 233
Period size: 40 Copynumber: 5.2 Consensus size: 40
40338695 TGAATGATAC
* * *
40338705 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAATATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
40338745 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * *
40338785 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TCATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* ** *
40338825 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGAT-ACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * * *
40338865 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
40338905 CC-GGCTAA
1 CCGGGCTAA
40338913 ATTCCGAAGA
Statistics
Matches: 145, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 6 0.04
40 137 0.94
41 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:40346940 original size:40 final size:40
Alignment explanation
Indices: 40346738--40346945 Score: 233
Period size: 40 Copynumber: 5.2 Consensus size: 40
40346728 TGAATGATAC
* * *
40346738 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAATATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
40346778 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * *
40346818 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TCATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* ** *
40346858 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGAT-ACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * * *
40346898 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
40346938 CC-GGCTAA
1 CCGGGCTAA
40346946 ATTCCGAAGA
Statistics
Matches: 145, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 6 0.04
40 137 0.94
41 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:40352285 original size:40 final size:40
Alignment explanation
Indices: 40352206--40352407 Score: 311
Period size: 40 Copynumber: 5.1 Consensus size: 40
40352196 AACCCAAGTA
* * * *
40352206 CCTTCGGAATTTAG-CCGGATATAG-CAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
40352245 CCTTCGGGACTTAGCCCGGACATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40352285 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
40352325 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
40352365 CCTTCGGGACTTAGCCC-GATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40352404 CCTT
1 CCTT
40352408 GGATCTTAGT
Statistics
Matches: 154, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
39 38 0.25
40 115 0.75
41 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:40367225 original size:30 final size:30
Alignment explanation
Indices: 40367189--40367257 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
40367179 TGGGGACTGA
40367189 CCGTGTGTCACACACGACCTAGAAACATAC
1 CCGTGTGTCACACACGACCTAGAAACATAC
* * *
40367219 CCGTGTGTCACACACGGCCTAGACACATGC
1 CCGTGTGTCACACACGACCTAGAAACATAC
40367249 CCGTGTGTC
1 CCGTGTGTC
40367258 TACCCGTGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.25, C:0.35, G:0.22, T:0.19
Consensus pattern (30 bp):
CCGTGTGTCACACACGACCTAGAAACATAC
Found at i:40370053 original size:40 final size:40
Alignment explanation
Indices: 40370008--40370174 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
40369998 CGGAATATAA
40370008 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40370048 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
40370088 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40370128 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40370167 CCGGATAT
1 CCGGATAT
40370175 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40370158 original size:80 final size:79
Alignment explanation
Indices: 40370008--40370174 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
40369998 CGGAATATAA
* *
40370008 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
40370073 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
40370088 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
40370150 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
40370167 CCGGATAT
1 CCGGATAT
40370175 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:40371022 original size:17 final size:19
Alignment explanation
Indices: 40370999--40371044 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40370989 AAGAAGCATG
40370999 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40371017 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40371035 AATCATGCTC
1 AATCATGCTC
40371045 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40378061 original size:40 final size:40
Alignment explanation
Indices: 40378016--40378182 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
40378006 CGGAATATAA
40378016 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40378056 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
40378096 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40378136 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40378175 CCGGATAT
1 CCGGATAT
40378183 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40378166 original size:80 final size:79
Alignment explanation
Indices: 40378016--40378182 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
40378006 CGGAATATAA
* *
40378016 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
40378081 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
40378096 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
40378158 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
40378175 CCGGATAT
1 CCGGATAT
40378183 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:40379029 original size:17 final size:19
Alignment explanation
Indices: 40379006--40379051 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40378996 AAGAAGCATG
40379006 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40379024 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40379042 AATCATGCTC
1 AATCATGCTC
40379052 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40382290 original size:21 final size:21
Alignment explanation
Indices: 40382256--40382295 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40382246 TCAAGCTGAT
40382256 AGGGCCACAAGCCCATGTGAA
1 AGGGCCACAAGCCCATGTGAA
* * *
40382277 AGGGCGACACGCCCGTGTG
1 AGGGCCACAAGCCCATGTG
40382296 TCTTCCTAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.30, G:0.35, T:0.10
Consensus pattern (21 bp):
AGGGCCACAAGCCCATGTGAA
Found at i:40383239 original size:2 final size:2
Alignment explanation
Indices: 40383232--40383258 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40383222 ACTACATGCT
40383232 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40383259 CACAGCATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40383561 original size:48 final size:48
Alignment explanation
Indices: 40383506--40383741 Score: 226
Period size: 48 Copynumber: 4.9 Consensus size: 48
40383496 GGTGAATTGT
*
40383506 CGATGCCATGTTCCAAACATGGTCTTACACTGGCT-TACATGTCGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCT-CATATCGAGGC
* * * * *
40383554 CGATGCCA-GGTCCAAACATGGTCTTACACTAGCTCTCATCTCAATGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGAGGC
* * * * * * * **
40383601 CTATGCATATGTCCCAGACATGGTTTTTACACTGGCTCTCACAAC-ATCAC
1 CGATGC-CATGTTCCAAACATGG-TCTTACACTGGCTCTCATATCGA-GGC
* *
40383651 CAATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGAGGC
* * * *
40383699 CGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATC
1 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATC
40383742 ACCCAAATGG
Statistics
Matches: 150, Mismatches: 32, Indels: 12
0.77 0.16 0.06
Matches are distributed among these distances:
47 37 0.25
48 67 0.45
49 24 0.16
50 22 0.15
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGAGGC
Found at i:40383716 original size:97 final size:96
Alignment explanation
Indices: 40383506--40383732 Score: 250
Period size: 98 Copynumber: 2.4 Consensus size: 96
40383496 GGTGAATTGT
* * ** *
40383506 CGATGC-CATGTTCCAAACATGGTCTTACACTGGCT-T-AC-ATGTCGAGGCCGATGCCAGGTCC
1 CGATGCACATGTCCCAGACATGGTCTTACACTGGCTCTCACAACATC-A--CCAATGCCAGGTCC
*
40383567 AAACATGGTCTTACACTAGCTCTCATCTCAATGC
63 AAACATGGTCTTACACTAGCTCTCATATCAATGC
* * * *
40383601 CTATGCATATGTCCCAGACATGGTTTTTACACTGGCTCTCACAACATCACCAATGCCATGTTCCA
1 CGATGCACATGTCCCAGACATGG-TCTTACACTGGCTCTCACAACATCACCAATGCCA-GGTCCA
* *
40383666 AACATGGTCTTACACTGGCTCTCATATC-GTGGC
64 AACATGGTCTTACACTAGCTCTCATATCAAT-GC
40383699 CGATGC-CATGTCCCAGACATGGTCTTACACTGGC
1 CGATGCACATGTCCCAGACATGGTCTTACACTGGC
40383733 ACACATATCA
Statistics
Matches: 110, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
95 5 0.05
96 24 0.22
97 36 0.33
98 39 0.35
99 3 0.03
100 3 0.03
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (96 bp):
CGATGCACATGTCCCAGACATGGTCTTACACTGGCTCTCACAACATCACCAATGCCAGGTCCAAA
CATGGTCTTACACTAGCTCTCATATCAATGC
Found at i:40387104 original size:42 final size:42
Alignment explanation
Indices: 40387035--40387166 Score: 122
Period size: 44 Copynumber: 3.0 Consensus size: 42
40387025 CCTTACATGT
* *
40387035 AATCAAATATCGATGTCATTGTCCCAGATAGGGTCTTACAC-AA
1 AATCAAATA-CGATGCCAATGTCCCAGA-AGGGTCTTACACGAA
* * *
40387078 AATCAAATACGATGCCAATGTCCCAGACATGGTATTACACGTA
1 AATCAAATACGATGCCAATGTCCCAGA-AGGGTCTTACACGAA
** * * *
40387121 AATCATAATTTGATGCCAACGTCCTAGACGTGGTCTTACACGAA
1 AATCA-AATACGATGCCAATGTCCCAGAAG-GGTCTTACACGAA
40387165 AA
1 AA
40387167 CACATATCGG
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
42 26 0.36
43 15 0.21
44 31 0.43
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.26
Consensus pattern (42 bp):
AATCAAATACGATGCCAATGTCCCAGAAGGGTCTTACACGAA
Found at i:40387124 original size:43 final size:43
Alignment explanation
Indices: 40387004--40387162 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 43
40386994 AGCTCGTACA
* * * *
40387004 ATGCCAACATCCCAGACGTGGCCTTACATGT-AATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCAAATA-CG
* ** * * *
40387047 ATGTCATTGTCCCAGATAGGGTCTTACAC-AAAATCAAATACG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCAAATACG
* * **
40387089 ATGCCAATGTCCCAGACATGGTATTACACGTAAATCATAATTTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCA-AATACG
* *
40387133 ATGCCAACGTCCTAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACATGGTCTTACACG
40387163 AAAACACATA
Statistics
Matches: 91, Mismatches: 22, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
42 26 0.29
43 35 0.38
44 30 0.33
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCAAATACG
Found at i:40393403 original size:27 final size:27
Alignment explanation
Indices: 40393355--40393513 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
40393345 CCGAGGCTGC
* *
40393355 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
40393382 CAGATATTGTGGTAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
40393408 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
40393435 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
40393462 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
40393489 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
40393514 GACGCTTCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
26 10 0.09
27 100 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:40393455 original size:54 final size:54
Alignment explanation
Indices: 40393373--40393513 Score: 239
Period size: 54 Copynumber: 2.6 Consensus size: 54
40393363 GTGACGAAGT
* *
40393373 CACCAGATACAGAT-ATTGTGGTAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
40393427 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
40393481 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
40393514 GACGCTTCCT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 5 0.06
54 77 0.94
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:40395156 original size:26 final size:26
Alignment explanation
Indices: 40395125--40395232 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
40395115 TGAAATTCCC
*
40395125 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
40395151 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
40395177 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
40395203 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40395229 ATCA
1 ATCA
40395233 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40400519 original size:27 final size:27
Alignment explanation
Indices: 40400471--40400629 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
40400461 GTGAAGCTAC
* *
40400471 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
40400498 CAGATATTGTGGTAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
40400524 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
40400551 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
40400578 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
40400605 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
40400630 GACGCTTCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
26 10 0.09
27 100 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:40400571 original size:54 final size:54
Alignment explanation
Indices: 40400489--40400629 Score: 239
Period size: 54 Copynumber: 2.6 Consensus size: 54
40400479 GTGACGAAGT
* *
40400489 CACCAGATACAGAT-ATTGTGGTAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
40400543 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
40400597 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
40400630 GACGCTTCCT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 5 0.06
54 77 0.94
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:40402283 original size:26 final size:26
Alignment explanation
Indices: 40402252--40402359 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
40402242 TGAAATTCCC
*
40402252 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
40402278 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
40402304 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
40402330 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40402356 ATCA
1 ATCA
40402360 ATTTATACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40405757 original size:31 final size:31
Alignment explanation
Indices: 40405696--40405757 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
40405686 ATTTAAAACA
*
40405696 AAACCAAATCCAAAATTGAAAACCAAACAGT
1 AAACCAAATCCAAAATTGAAAACAAAACAGT
40405727 AAACCAAATCCAAAATTGAAAACAAAACAGT
1 AAACCAAATCCAAAATTGAAAACAAAACAGT
40405758 CTAGAAAGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.60, C:0.21, G:0.06, T:0.13
Consensus pattern (31 bp):
AAACCAAATCCAAAATTGAAAACAAAACAGT
Found at i:40411440 original size:25 final size:25
Alignment explanation
Indices: 40411412--40411463 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40411402 TATAACTATG
40411412 GATAGAGGACACACTCATGAAGAAC
1 GATAGAGGACACACTCATGAAGAAC
40411437 GATAGAGGACACACTCATGAAGAAC
1 GATAGAGGACACACTCATGAAGAAC
40411462 GA
1 GA
40411464 AGGCTATGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (25 bp):
GATAGAGGACACACTCATGAAGAAC
Found at i:40416364 original size:24 final size:24
Alignment explanation
Indices: 40416337--40416543 Score: 342
Period size: 24 Copynumber: 8.6 Consensus size: 24
40416327 CTTATTATGT
* * *
40416337 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
* *
40416361 TCGCACACATAGTGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
*
40416385 TCGCACACATAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
40416409 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
40416433 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
40416457 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
40416481 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
40416505 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
40416529 TCGCACACATAGTGC
1 TCGCACACATAGTGC
40416544 ATTTGAGATA
Statistics
Matches: 177, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 177 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:40423183 original size:40 final size:40
Alignment explanation
Indices: 40423124--40423292 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
40423114 CGGGACTTTA
* * *
40423124 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
40423164 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
40423204 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
40423244 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
40423284 CCCGGATAT
1 CCCGGATAT
40423293 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:40431549 original size:46 final size:48
Alignment explanation
Indices: 40431427--40431556 Score: 171
Period size: 46 Copynumber: 2.8 Consensus size: 48
40431417 TGTAACCCGC
*
40431427 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCCTAG-T-CAT
* * *
40431477 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG-CAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCCTAGTCAT
40431520 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40431557 TGCCCAAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
43 3 0.04
44 1 0.01
45 2 0.03
46 32 0.45
47 30 0.42
48 2 0.03
49 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (48 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCCTAGTCAT
Found at i:40431575 original size:46 final size:45
Alignment explanation
Indices: 40431432--40431575 Score: 148
Period size: 46 Copynumber: 3.1 Consensus size: 45
40431422 CCCGCCCATA
* *
40431432 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---ACATCCC
* * * * *
40431480 A-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTC-GCATCCATA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAACATCC--C
*
40431525 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AACATCCC
40431571 AGTGA
1 AGTGA
40431576 CATGTCACTT
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
43 4 0.05
45 1 0.01
46 37 0.47
47 31 0.40
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAACATCCC
Found at i:40433979 original size:29 final size:29
Alignment explanation
Indices: 40433940--40434027 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
40433930 CAAAGATAAC
*
40433940 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
40433969 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
40433998 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
40434028 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:40433998 original size:15 final size:15
Alignment explanation
Indices: 40433940--40434018 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
40433930 CAAAGATAAC
*
40433940 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
40433954 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
40433969 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
40433983 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
40433998 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
40434013 AAGAAA
1 AAGAAA
40434019 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:40434027 original size:15 final size:15
Alignment explanation
Indices: 40433951--40434027 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
40433941 AGAAAACCGA
40433951 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
40433966 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
40433980 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
40433994 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
40434010 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
40434025 ATA
1 ATA
40434028 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:40437047 original size:93 final size:93
Alignment explanation
Indices: 40436935--40437106 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40436925 GCCCATAAGT
* *
40436935 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40437000 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
40437028 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40437093 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
40437107 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40437102 original size:46 final size:46
Alignment explanation
Indices: 40436927--40437102 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
40436917 TGTAACCCGC
* * *
40436927 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
40436973 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
40437023 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
40437066 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40437103 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:40438971 original size:28 final size:29
Alignment explanation
Indices: 40438931--40438985 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
40438921 CACAGGGGAT
40438931 GACACGGGCGTGT-CTAGGCCGTGTGAGG
1 GACACGGGCGTGTGCTAGGCCGTGTGAGG
*
40438959 GACACGGGCGTGTGCTTGGCCGTGTGA
1 GACACGGGCGTGTGCTAGGCCGTGTGA
40438986 AAATCCCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.13, C:0.22, G:0.45, T:0.20
Consensus pattern (29 bp):
GACACGGGCGTGTGCTAGGCCGTGTGAGG
Found at i:40441259 original size:81 final size:81
Alignment explanation
Indices: 40441124--40441285 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
40441114 GTGTAGAGCC
40441124 GAATAATTTAGTGGTAAAATGAGTAATGATTCGGCCAGAGCTAATTACTAGTTAGAAAATACATC
1 GAATAATTTAGTGGTAAAATGAGTAATGATTCGGCCAGAGCTAATTACTAGTTAGAAAATACATC
40441189 GAGAGTTTTAGACGAA
66 GAGAGTTTTAGACGAA
40441205 GAATAATTTAGTGGTAAAATGAGTAATGATTCGGCCAGAGCTAATTACTAGTTAGAAAATACATC
1 GAATAATTTAGTGGTAAAATGAGTAATGATTCGGCCAGAGCTAATTACTAGTTAGAAAATACATC
40441270 GAGAGTTTTAGACGAA
66 GAGAGTTTTAGACGAA
40441286 ATGTTATGTC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (81 bp):
GAATAATTTAGTGGTAAAATGAGTAATGATTCGGCCAGAGCTAATTACTAGTTAGAAAATACATC
GAGAGTTTTAGACGAA
Found at i:40443706 original size:44 final size:42
Alignment explanation
Indices: 40443656--40443783 Score: 132
Period size: 42 Copynumber: 3.0 Consensus size: 42
40443646 TTCGAGCCTC
*
40443656 GGCCTAGCAAGCTTTAA-ACTAGTGAATAATATTATCGGGCTTCG
1 GGCCTAGCAAGCTATAATACTAGTGAAT-A-A-TATCGGGCTTCG
* * *
40443700 GGCCTAGCAGGCTATAATGCTGGTGAATAATATCGGGCTTCG
1 GGCCTAGCAAGCTATAATACTAGTGAATAATATCGGGCTTCG
* * ** *
40443742 GGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTC
1 GGCCTAGCAAGCTATAATACTAGTG-AATAATATCGGGCTTC
40443784 AAGCCTAATA
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
42 36 0.47
43 16 0.21
44 16 0.21
45 8 0.11
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (42 bp):
GGCCTAGCAAGCTATAATACTAGTGAATAATATCGGGCTTCG
Found at i:40443740 original size:42 final size:43
Alignment explanation
Indices: 40443683--40443783 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 43
40443673 ACTAGTGAAT
* *
40443683 AATATTATCGGGCTTCGGGCCTAGCAGGCTATAATGCTGGTG-
1 AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
40443725 AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
1 AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
*
40443768 AATGATATCGGGCTTC
1 AATAATATCGGGCTTC
40443784 AAGCCTAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 40 0.73
43 15 0.27
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.27
Consensus pattern (43 bp):
AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGA
Found at i:40448248 original size:14 final size:15
Alignment explanation
Indices: 40448229--40448258 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40448219 GTTTATTATA
40448229 TGTG-AAGTATCATG
1 TGTGAAAGTATCATG
40448243 TGTGAAAGTATCATG
1 TGTGAAAGTATCATG
40448258 T
1 T
40448259 CTAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (15 bp):
TGTGAAAGTATCATG
Found at i:40450010 original size:43 final size:43
Alignment explanation
Indices: 40449922--40450086 Score: 183
Period size: 43 Copynumber: 3.9 Consensus size: 43
40449912 AATGTGATAT
* * * *
40449922 TCGGGCCTC-GGCCTAGCAAGCTTTAA-GCTGGTGAATAATATTA
1 TCGGGCTTCAGGCCTAGCAGGCTATAATGCTGGTG-A-AATAATA
* * *
40449965 TCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAGATAATA
1 TCGGGCTTCAGGCCTAGCAGGCTATAATGCTGGTGAAATAATA
* *
40450008 TCGGGCTCCAGGCCTAGCAGGCTATAATGCTGGTGAAATGATA
1 TCGGGCTTCAGGCCTAGCAGGCTATAATGCTGGTGAAATAATA
* * *
40450051 TCGGGCTTCAAGCCTAGTAGGCGA-AATGCTGGTGAA
1 TCGGGCTTCAGGCCTAGCAGGCTATAATGCTGGTGAA
40450087 TGAGTTCAGA
Statistics
Matches: 105, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
42 12 0.11
43 71 0.68
44 16 0.15
45 6 0.06
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (43 bp):
TCGGGCTTCAGGCCTAGCAGGCTATAATGCTGGTGAAATAATA
Found at i:40456854 original size:29 final size:29
Alignment explanation
Indices: 40456812--40456891 Score: 124
Period size: 29 Copynumber: 2.8 Consensus size: 29
40456802 CACACAACCA
40456812 AGCACACGGGTGTGTGGCATGGTCAGCCT
1 AGCACACGGGTGTGTGGCATGGTCAGCCT
*
40456841 AGCACACGGGTGTGTGGCATGGTCGGCCT
1 AGCACACGGGTGTGTGGCATGGTCAGCCT
** *
40456870 AGCACACAAGCGTGTGGCATGG
1 AGCACACGGGTGTGTGGCATGG
40456892 CTCTGTGTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.19, C:0.24, G:0.39, T:0.19
Consensus pattern (29 bp):
AGCACACGGGTGTGTGGCATGGTCAGCCT
Found at i:40483494 original size:68 final size:68
Alignment explanation
Indices: 40483344--40483501 Score: 167
Period size: 68 Copynumber: 2.3 Consensus size: 68
40483334 CTAGCCAATT
** * * *
40483344 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGCATACATCAC-TCGAATCACACATGCGACCTAGCTACA
**
40483409 TTTA
65 CATA
* * *
40483413 TCCTCTCCGTAGCTCTCTTGTCTACATGGCATACATC-C-CGTATCACACATGTGACCTAGCTAC
1 T-ATCT-CGTAGCTCTCTTGTCTACATGGCATACATCACTCGAATCACACATGCGACCTAGCTAC
40483476 TACATA
64 -ACATA
40483482 GTATCTCGTAGCTCTCTTGT
1 -TATCTCGTAGCTCTCTTGT
40483502 ACACATGATG
Statistics
Matches: 74, Mismatches: 11, Indels: 9
0.79 0.12 0.10
Matches are distributed among these distances:
68 36 0.49
69 7 0.09
70 5 0.07
71 26 0.35
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGCATACATCACTCGAATCACACATGCGACCTAGCTACAC
ATA
Found at i:40502147 original size:25 final size:24
Alignment explanation
Indices: 40502105--40502177 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 24
40502095 CTCTTTCAAG
* *
40502105 TTGTAAATCAGTATGCTCTCACGAA
1 TTGT-AATCGGTAAGCTCTCACGAA
* *
40502130 TTGTAAGTCGGTAAGCTCAT-ATGAG
1 TTGTAA-TCGGTAAGCTC-TCACGAA
*
40502155 TTGTAATCGGTAAGCTCACACGA
1 TTGTAATCGGTAAGCTCTCACGA
40502178 GCTGTGGAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
24 16 0.41
25 22 0.56
26 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (24 bp):
TTGTAATCGGTAAGCTCTCACGAA
Found at i:40507075 original size:23 final size:23
Alignment explanation
Indices: 40507045--40507094 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
40507035 CTCAAGGTTA
40507045 GGACGCAAGCACAATATCCGAAG
1 GGACGCAAGCACAATATCCGAAG
40507068 GGACGCAAGCACAATATCCGAAG
1 GGACGCAAGCACAATATCCGAAG
40507091 GGAC
1 GGAC
40507095 TCAGATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.26, G:0.28, T:0.08
Consensus pattern (23 bp):
GGACGCAAGCACAATATCCGAAG
Found at i:40511470 original size:21 final size:22
Alignment explanation
Indices: 40511403--40511473 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 22
40511393 ATAAGGTGTG
* * *
40511403 GATAAACCACT-TAATGGTGTA
1 GATAAACCACTCAAACGATGTA
* * *
40511424 GGTAAACTACTCAAACGATGTG
1 GATAAACCACTCAAACGATGTA
40511446 GATAAACCACT-AAAC-ACTGTA
1 GATAAACCACTCAAACGA-TGTA
40511467 GATAAAC
1 GATAAAC
40511474 TTCTCACACT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.03
21 23 0.59
22 15 0.38
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (22 bp):
GATAAACCACTCAAACGATGTA
Found at i:40511897 original size:27 final size:28
Alignment explanation
Indices: 40511849--40511957 Score: 87
Period size: 28 Copynumber: 3.9 Consensus size: 28
40511839 AATCCTAGAT
* * *
40511849 CAAAACTATAAAATTTGTAAAATAGAGG
1 CAAAACTGTAAAATCTGAAAAATAGAGG
* ** *
40511877 -AAAATTGTAAAATCTGAAAAACCGTGG
1 CAAAACTGTAAAATCTGAAAAATAGAGG
* *
40511904 CAAAACTGTAAAATCTAAAAAATTA-TGG
1 CAAAACTGTAAAATCTGAAAAA-TAGAGG
* *
40511932 CAAAACTGAAAAATTTTGAAAAATAG
1 CAAAACTGTAAAA-TCTGAAAAATAG
40511958 TGGTAAAATT
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
27 20 0.32
28 36 0.57
29 7 0.11
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.24
Consensus pattern (28 bp):
CAAAACTGTAAAATCTGAAAAATAGAGG
Found at i:40513387 original size:22 final size:21
Alignment explanation
Indices: 40513352--40513393 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
40513342 ACATTCACTA
* *
40513352 TTTTAATTATAAAATATTTAT
1 TTTTAATCATAAAAAATTTAT
40513373 TTTTACATCATAAAAAATTTA
1 TTTTA-ATCATAAAAAATTTA
40513394 AACTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTAATCATAAAAAATTTAT
Found at i:40516865 original size:22 final size:22
Alignment explanation
Indices: 40516840--40516883 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40516830 AATTATTAAC
40516840 ATAATGAATTTTAATTAATTTT
1 ATAATGAATTTTAATTAATTTT
* * *
40516862 ATAATTAATTTTGATTATTTTT
1 ATAATGAATTTTAATTAATTTT
40516884 TATTATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
ATAATGAATTTTAATTAATTTT
Found at i:40521952 original size:22 final size:22
Alignment explanation
Indices: 40521924--40521969 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
40521914 GGGATGTTAC
40521924 ACTCTCTCTTTCAGAAAAACTA
1 ACTCTCTCTTTCAGAAAAACTA
40521946 ACTCTCTCTTTCAGAAAAACTA
1 ACTCTCTCTTTCAGAAAAACTA
40521968 AC
1 AC
40521970 GTCTATTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.30
Consensus pattern (22 bp):
ACTCTCTCTTTCAGAAAAACTA
Found at i:40522575 original size:21 final size:21
Alignment explanation
Indices: 40522551--40522590 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40522541 GGTGTGTGTG
40522551 GCCTTCACACGGGCATGTACA
1 GCCTTCACACGGGCATGTACA
*
40522572 GCCTTCACATGGGCATGTA
1 GCCTTCACACGGGCATGTA
40522591 AACCCCCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (21 bp):
GCCTTCACACGGGCATGTACA
Found at i:40526132 original size:18 final size:18
Alignment explanation
Indices: 40526098--40526135 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
40526088 AACATTACAA
40526098 AAAAATTCAAAGTATTTAT
1 AAAAATTCAAAG-ATTTAT
40526117 AAAAATTCTAAA-ATTTAT
1 AAAAATTC-AAAGATTTAT
40526135 A
1 A
40526136 TTTTAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 8 0.44
20 3 0.17
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAAATTCAAAGATTTAT
Found at i:40526156 original size:7 final size:7
Alignment explanation
Indices: 40526118--40526167 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
40526108 AGTATTTATA
40526118 AAAATTCT
1 AAAATT-T
40526126 AAAATTT
1 AAAATTT
* *
40526133 ATATTTT
1 AAAATTT
* *
40526140 AATATAT
1 AAAATTT
40526147 AAAATTT
1 AAAATTT
40526154 AAAATTT
1 AAAATTT
40526161 AAAATTT
1 AAAATTT
40526168 CTAAAGAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (7 bp):
AAAATTT
Found at i:40526315 original size:2 final size:2
Alignment explanation
Indices: 40526308--40526345 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
40526298 AAAAAGTTTC
40526308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40526346 GGTTTTAAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40527174 original size:13 final size:13
Alignment explanation
Indices: 40527158--40527199 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
40527148 TTATTATTAA
40527158 TAAATATTTAAAT
1 TAAATATTTAAAT
*
40527171 TAAAT-TTTTAAT
1 TAAATATTTAAAT
*
40527183 AAAAATATTTAAAT
1 -TAAATATTTAAAT
40527197 TAA
1 TAA
40527200 TCCACAAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 6 0.26
13 11 0.48
14 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATATTTAAAT
Found at i:40535522 original size:16 final size:16
Alignment explanation
Indices: 40535498--40535532 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
40535488 CCATGTCAAC
40535498 AAATATTAAAAATAAA
1 AAATATTAAAAATAAA
*
40535514 AAATCTTAAAAATAAA
1 AAATATTAAAAATAAA
40535530 AAA
1 AAA
40535533 AGCTTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATATTAAAAATAAA
Found at i:40536222 original size:22 final size:21
Alignment explanation
Indices: 40536183--40536223 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
40536173 TTTATTGGTA
**
40536183 ATTTTGTTATTATTTTAGAGG
1 ATTTTGTTATTAAGTTAGAGG
40536204 ATTTTGCTTATTAAGTTAGA
1 ATTTTG-TTATTAAGTTAGA
40536224 TCTACCTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.54
Consensus pattern (21 bp):
ATTTTGTTATTAAGTTAGAGG
Found at i:40542863 original size:30 final size:30
Alignment explanation
Indices: 40542829--40542891 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
40542819 AAAAAAAGAA
40542829 GAAAAAGTTATCATGTTGTTGAACTTGGCC
1 GAAAAAGTTATCATGTTGTTGAACTTGGCC
40542859 GAAAAAGTTATCATGTTGTTGAACTTGGCC
1 GAAAAAGTTATCATGTTGTTGAACTTGGCC
40542889 GAA
1 GAA
40542892 TAGAAGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (30 bp):
GAAAAAGTTATCATGTTGTTGAACTTGGCC
Found at i:40544256 original size:80 final size:80
Alignment explanation
Indices: 40544123--40544378 Score: 358
Period size: 80 Copynumber: 3.2 Consensus size: 80
40544113 GATGATAACG
* *
40544123 GGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
40544188 CGAGTTACTA-ATTCC
66 CGAGTTACTATA-TCC
* ** *
40544203 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCAAGGCTAAGTCCCGAAGGCATTTGTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
40544268 CGAGTTACTATATCC
66 CGAGTTACTATATCC
* * *
40544283 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT-ATATCCGGGCTAAGTCTCGAAGGCATTTGA
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGT
40544347 GCGAG-TAGCTATATCC
65 GCGAGTTA-CTATATCC
* *
40544363 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
40544379 TACTTGGTTT
Statistics
Matches: 158, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
79 18 0.11
80 139 0.88
81 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (80 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
CGAGTTACTATATCC
Found at i:40544364 original size:40 final size:40
Alignment explanation
Indices: 40544123--40544352 Score: 338
Period size: 40 Copynumber: 5.8 Consensus size: 40
40544113 GATGATAACG
* **
40544123 GGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
40544163 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
*
40544203 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCA
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* *
40544243 AGGCTAAGTCCCGAAGGCATTTGTCCGAGTTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
**
40544283 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
* *
40544323 GGGCTAAGTCTCGAAGGCATTTGAGCGAGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT
40544353 AGCTATATCC
Statistics
Matches: 174, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 2 0.01
40 172 0.99
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:40548380 original size:43 final size:43
Alignment explanation
Indices: 40548314--40548511 Score: 351
Period size: 43 Copynumber: 4.6 Consensus size: 43
40548304 TCGGCATTAC
* *
40548314 GCCTACTAGGCACGAAGGCCCGAATACACATCACTGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
40548357 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
40548400 GCCTGCTAGGCACGAAGGCCCAAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
40548443 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
40548486 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
40548512 TAATACCAGC
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 150 1.00
ACGTcount: A:0.31, C:0.34, G:0.24, T:0.11
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:40548569 original size:38 final size:38
Alignment explanation
Indices: 40548504--40548587 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
40548494 GGCACGAAGG
* * *
40548504 CCCGAATATAATACCAGCACTAGGCCTGTGAGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGAGATTTAT
* * *
40548542 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCGAGATTTAT
*
40548580 CCAGAATA
1 CCCGAATA
40548588 CACATCAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGAGATTTAT
Found at i:40552444 original size:45 final size:44
Alignment explanation
Indices: 40552337--40552462 Score: 127
Period size: 45 Copynumber: 2.9 Consensus size: 44
40552327 TTTTCTCAAA
* *
40552337 TCACCGGCATT-TCGCCTGTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACC-GCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
40552379 TCACCGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
40552422 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAATA
1 -TCACC-GCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
40552463 ATCAAGTCAA
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
41 5 0.07
42 19 0.26
43 8 0.11
44 9 0.12
45 31 0.43
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.25
Consensus pattern (44 bp):
TCACCGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:40552981 original size:42 final size:43
Alignment explanation
Indices: 40552779--40552983 Score: 314
Period size: 41 Copynumber: 4.9 Consensus size: 43
40552769 ACATATCATT
* *
40552779 TCACCGGCATTACGCCTGCTAGGCACGAAGG-CCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
40552821 TCACCGGCA-GAAGCCTGCTAGGCACGAAGG-CCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
40552862 TCACCGGCACGAAGCCTGCTAGGCA--AAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
40552903 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACATA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
40552946 TCACCGGCACTAAGCCTG-TAGGCATGAAGGCCCGAATA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATA
40552984 TAATACCAGC
Statistics
Matches: 154, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
40 4 0.03
41 74 0.48
42 43 0.28
43 33 0.21
ACGTcount: A:0.30, C:0.32, G:0.25, T:0.13
Consensus pattern (43 bp):
TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
Found at i:40552997 original size:83 final size:84
Alignment explanation
Indices: 40552779--40552983 Score: 310
Period size: 83 Copynumber: 2.5 Consensus size: 84
40552769 ACATATCATT
* * *
40552779 TCACCGGCATTACGCCTGCTAGGCACGAAGG-CCGAATACACATCACCGGCA-GAAGCCTGCTAG
1 TCACCGGCACTAAGCCTGCTAGGCA-GAAGGCCCGAATACACATCACCGGCACTAAGCCTGCTAG
40552842 GCACGAAGGCCGAATACACA
65 GCACGAAGGCCGAATACACA
*
40552862 TCACCGGCACGAAGCCTGCTAGGCA-AAGGCCCGAATACACATCACCGGCACTAAGCCTGCTAGG
1 TCACCGGCACTAAGCCTGCTAGGCAGAAGGCCCGAATACACATCACCGGCACTAAGCCTGCTAGG
*
40552926 CACGAAGGCCCGAATACATA
66 CACGAAGG-CCGAATACACA
40552946 TCACCGGCACTAAGCCTG-TAGGCATGAAGGCCCGAATA
1 TCACCGGCACTAAGCCTGCTAGGCA-GAAGGCCCGAATA
40552984 TAATACCAGC
Statistics
Matches: 111, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
81 4 0.04
82 20 0.18
83 48 0.43
84 27 0.24
85 12 0.11
ACGTcount: A:0.30, C:0.32, G:0.25, T:0.13
Consensus pattern (84 bp):
TCACCGGCACTAAGCCTGCTAGGCAGAAGGCCCGAATACACATCACCGGCACTAAGCCTGCTAGG
CACGAAGGCCGAATACACA
Done.