Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 88 of 240
Found at i:27734120 original size:112 final size:115
Alignment explanation
Indices: 27733964--27734174 Score: 347
Period size: 112 Copynumber: 1.9 Consensus size: 115
27733954 TACTTTAATA
*
27733964 TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATT-AAAAAAT-AAAAAAAATC-CCCAAT
1 TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTAAAAAAATCAAAAAAAATCACACAAT
27734026 TTCTTATGAACCCTAAAAAAAATCAGCTAAATATGCTTACTCGAATACAT
66 TTCTTATGAACCCTAAAAAAAATCAGCTAAATATGCTTACTCGAATACAT
*
27734076 TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTTAAAAAATCAAAAAAAATCACACAAT
1 TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTAAAAAAATCAAAAAAAATCACACAAT
* * * *
27734141 TTTTTATGAACCTTAAAACAAATCGGCTAAATAT
66 TTCTTATGAACCCTAAAAAAAATCAGCTAAATAT
27734175 ACAGTGCCTA
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
112 39 0.43
113 7 0.08
114 10 0.11
115 35 0.38
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (115 bp):
TTCACACATGGGAAAGAAATGTTTCATCAATATCCAATTAAAAAAATCAAAAAAAATCACACAAT
TTCTTATGAACCCTAAAAAAAATCAGCTAAATATGCTTACTCGAATACAT
Found at i:27734678 original size:16 final size:16
Alignment explanation
Indices: 27734648--27734677 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27734638 TTAGTTAGGG
27734648 ATTTTAATTTATTTTA
1 ATTTTAATTTATTTTA
27734664 ATTTTAA-TTATTTT
1 ATTTTAATTTATTTT
27734678 TTAAGTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTAATTTATTTTA
Found at i:27738860 original size:30 final size:30
Alignment explanation
Indices: 27738821--27738877 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
27738811 TTTTATAAAT
27738821 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
27738851 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
27738878 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:27739073 original size:13 final size:13
Alignment explanation
Indices: 27739054--27739101 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
27739044 TAAACCAAAT
27739054 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
27739067 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
27739080 TTTTCTATAGCAC
1 TTTTCAAAAGCAC
27739093 TTTTCAAAA
1 TTTTCAAAA
27739102 ACAATGAAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:27742472 original size:14 final size:14
Alignment explanation
Indices: 27742453--27742497 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
27742443 ATTCATCAAC
27742453 ATCTCATCTCACAT
1 ATCTCATCTCACAT
27742467 ATCTCA-CATCACAT
1 ATCTCATC-TCACAT
* *
27742481 ATCACATATCACAT
1 ATCTCATCTCACAT
27742495 ATC
1 ATC
27742498 GATGGTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 26 0.96
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (14 bp):
ATCTCATCTCACAT
Found at i:27742485 original size:21 final size:21
Alignment explanation
Indices: 27742451--27742490 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27742441 CCATTCATCA
* *
27742451 ACATCTCATCTCACATATCTC
1 ACATCACATATCACATATCTC
27742472 ACATCACATATCACATATC
1 ACATCACATATCACATATC
27742491 ACATATCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30
Consensus pattern (21 bp):
ACATCACATATCACATATCTC
Found at i:27742486 original size:7 final size:7
Alignment explanation
Indices: 27742461--27742497 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
27742451 ACATCTCATC
27742461 TCACATA
1 TCACATA
* *
27742468 TCTCACA
1 TCACATA
27742475 TCACATA
1 TCACATA
27742482 TCACATA
1 TCACATA
27742489 TCACATA
1 TCACATA
27742496 TC
1 TC
27742498 GATGGTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.30
Consensus pattern (7 bp):
TCACATA
Found at i:27747295 original size:41 final size:42
Alignment explanation
Indices: 27747242--27747377 Score: 130
Period size: 42 Copynumber: 3.2 Consensus size: 42
27747232 TGCTTCCACA
*
27747242 TTGCTTCCTTTTTAGTCTAAACCTT-GAGGTTGCTTTCCCAAG
1 TTGCCTCCTTTTTAGTCTAAA-CTTGGAGGTTGCTTTCCCAAG
* * * *
27747284 TTGCCTCTTTTTTTGTCTGAACTTGGATGTTGCTTTCCCAAG
1 TTGCCTCCTTTTTAGTCTAAACTTGGAGGTTGCTTTCCCAAG
* * * * * * * *
27747326 TTGCTTCCTTTTTTGTTTAGACATGGATGTTGCTTTTCCATG
1 TTGCCTCCTTTTTAGTCTAAACTTGGAGGTTGCTTTCCCAAG
*
27747368 TTGCTTCCTT
1 TTGCCTCCTT
27747378 GATATTTTTC
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 3 0.04
42 77 0.96
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.49
Consensus pattern (42 bp):
TTGCCTCCTTTTTAGTCTAAACTTGGAGGTTGCTTTCCCAAG
Found at i:27747316 original size:42 final size:42
Alignment explanation
Indices: 27747270--27747377 Score: 137
Period size: 42 Copynumber: 2.6 Consensus size: 42
27747260 AAACCTTGAG
* *
27747270 GTTGCTTTCCCAAGTTGCCTCTTTTTTTGTCTGA-ACTTGGAT
1 GTTGCTTTCCCAAGTTGCCTCCTTTTTTGT-TGAGACATGGAT
* *
27747312 GTTGCTTTCCCAAGTTGCTTCCTTTTTTGTTTAGACATGGAT
1 GTTGCTTTCCCAAGTTGCCTCCTTTTTTGTTGAGACATGGAT
* * *
27747354 GTTGCTTTTCCATGTTGCTTCCTT
1 GTTGCTTTCCCAAGTTGCCTCCTT
27747378 GATATTTTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 2 0.03
42 57 0.97
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.49
Consensus pattern (42 bp):
GTTGCTTTCCCAAGTTGCCTCCTTTTTTGTTGAGACATGGAT
Found at i:27750433 original size:9 final size:9
Alignment explanation
Indices: 27750419--27750458 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
27750409 TTTTGTTAAA
27750419 AATTAACCG
1 AATTAACCG
27750428 AATTAACCG
1 AATTAACCG
*
27750437 AATTACCCG
1 AATTAACCG
*
27750446 AATTACCCG
1 AATTAACCG
27750455 AATT
1 AATT
27750459 GAATCACTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:27750525 original size:17 final size:17
Alignment explanation
Indices: 27750466--27750528 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
27750456 ATTGAATCAC
*
27750466 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
** * *
27750483 TACATAAGGCTTTGAATCAC
1 TACATAA---TTAAAAACAT
27750503 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
27750520 TACATAATT
1 TACATAATT
27750529 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 22 0.65
20 12 0.35
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:27750705 original size:38 final size:39
Alignment explanation
Indices: 27750661--27750753 Score: 161
Period size: 38 Copynumber: 2.4 Consensus size: 39
27750651 ACTTAAGAGT
* *
27750661 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTTGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
27750699 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
27750738 TAGACTTTAGTTTTAG
1 TAGACTTTAGTTTTAG
27750754 GGCCAGTTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
38 27 0.52
39 25 0.48
ACGTcount: A:0.19, C:0.03, G:0.26, T:0.52
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:27752927 original size:72 final size:72
Alignment explanation
Indices: 27752802--27752968 Score: 248
Period size: 72 Copynumber: 2.3 Consensus size: 72
27752792 AAAATCATAT
* * *
27752802 ATAAACAACTATTGATAAAACTA-ATTTAATAAAAATAAGTAGAACATAAATTCAATATCTAAAG
1 ATAAACAACTATTGATAAAACTAGATTTAACAAAAATAAGTAGAACATAAATTCAATATCCAAAA
*
27752866 ACCAAAC
66 ACAAAAC
* *
27752873 ATAAACAACTATTAATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGATTTA-ACAAAAATAAGTAGAACATAAATTCAATATCCAAA
27752937 AACAAAAC
65 AACAAAAC
*
27752945 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTGATAAAACTAG
27752969 TTAGCATTGT
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
71 25 0.29
72 61 0.71
ACGTcount: A:0.57, C:0.13, G:0.05, T:0.25
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTTAACAAAAATAAGTAGAACATAAATTCAATATCCAAAA
ACAAAAC
Found at i:27753421 original size:18 final size:18
Alignment explanation
Indices: 27753398--27753463 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
27753388 TTCATCAATT
*
27753398 TGAACATCATTTGAGATG
1 TGAACATCATTTGAAATG
27753416 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
27753434 TGAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
*
27753452 TGAACATTATTT
1 TGAACATCATTT
27753464 CTCATATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:27755507 original size:14 final size:14
Alignment explanation
Indices: 27755472--27755515 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
27755462 GAACACCAGC
* *
27755472 ACCAGCAAAAAAGA
1 ACCAGCAGAGAAGA
27755486 ACCAGCAGAGAAGA
1 ACCAGCAGAGAAGA
27755500 ACCAGCAGAGAAGA
1 ACCAGCAGAGAAGA
27755514 AC
1 AC
27755516 AAACGTGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.55, C:0.23, G:0.23, T:0.00
Consensus pattern (14 bp):
ACCAGCAGAGAAGA
Found at i:27755764 original size:17 final size:18
Alignment explanation
Indices: 27755731--27755765 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27755721 GCTTAGTTTT
27755731 ATTGAGTTGGATAATTGG
1 ATTGAGTTGGATAATTGG
27755749 ATTGAGTTGG-TAATTGG
1 ATTGAGTTGGATAATTGG
27755766 GTTGGGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (18 bp):
ATTGAGTTGGATAATTGG
Found at i:27755769 original size:12 final size:13
Alignment explanation
Indices: 27755749--27755781 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
27755739 GGATAATTGG
27755749 ATTGAGTT-GGTA
1 ATTGAGTTGGGTA
*
27755761 ATTGGGTTGGGTA
1 ATTGAGTTGGGTA
27755774 ATTGAGTT
1 ATTGAGTT
27755782 TGGTTGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.42
Consensus pattern (13 bp):
ATTGAGTTGGGTA
Found at i:27755770 original size:30 final size:31
Alignment explanation
Indices: 27755731--27755794 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
27755721 GCTTAGTTTT
27755731 ATTGAGTTGGATAATTG-GATTGAGTTGG-TA
1 ATTGAGTTGGATAATTGAGATTG-GTTGGATA
* * *
27755761 ATTGGGTTGGGTAATTGAGTTTGGTTGGATA
1 ATTGAGTTGGATAATTGAGATTGGTTGGATA
27755792 ATT
1 ATT
27755795 TTATTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.42
Consensus pattern (31 bp):
ATTGAGTTGGATAATTGAGATTGGTTGGATA
Found at i:27755844 original size:17 final size:16
Alignment explanation
Indices: 27755824--27755876 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
27755814 GTTAACCGAA
27755824 TAATTGGGTTAGGTTGG
1 TAATTGGGTT-GGTTGG
27755841 TAATTGGGTT-G--GG
1 TAATTGGGTTGGTTGG
27755854 TAATTGGGTTTGGTTGG
1 TAATTGGG-TTGGTTGG
27755871 ATAATT
1 -TAATT
27755877 TTATTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
13 10 0.32
14 2 0.06
15 2 0.06
17 12 0.39
18 5 0.16
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (16 bp):
TAATTGGGTTGGTTGG
Found at i:27755852 original size:12 final size:13
Alignment explanation
Indices: 27755835--27755863 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
27755825 AATTGGGTTA
27755835 GGTT-GGTAATTG
1 GGTTGGGTAATTG
27755847 GGTTGGGTAATTG
1 GGTTGGGTAATTG
27755860 GGTT
1 GGTT
27755864 TGGTTGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (13 bp):
GGTTGGGTAATTG
Found at i:27755878 original size:82 final size:82
Alignment explanation
Indices: 27755741--27755905 Score: 287
Period size: 82 Copynumber: 2.0 Consensus size: 82
27755731 ATTGAGTTGG
27755741 ATAATTGGATTGAGTTGGTAATTGGGTTGGGTAATTGAGTTTGGTTGGATAATTTTATTTATTAA
1 ATAATTGGATTGAGTTGGTAATTGGGTTGGGTAATTGAGTTTGGTTGGATAATTTTATTTATTAA
27755806 TCTTTTCGGTTAACCGA
66 TCTTTTCGGTTAACCGA
* *
27755823 ATAATTGGGTT-AGGTTGGTAATTGGGTTGGGTAATTGGGTTTGGTTGGATAATTTTATTTATTA
1 ATAATTGGATTGA-GTTGGTAATTGGGTTGGGTAATTGAGTTTGGTTGGATAATTTTATTTATTA
*
27755887 ATTTTTTCGGTTAACCGA
65 ATCTTTTCGGTTAACCGA
27755905 A
1 A
27755906 AAAATTTAGT
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
81 1 0.01
82 78 0.99
ACGTcount: A:0.24, C:0.04, G:0.27, T:0.45
Consensus pattern (82 bp):
ATAATTGGATTGAGTTGGTAATTGGGTTGGGTAATTGAGTTTGGTTGGATAATTTTATTTATTAA
TCTTTTCGGTTAACCGA
Found at i:27773165 original size:6 final size:6
Alignment explanation
Indices: 27773154--27773187 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
27773144 ATAAATAAAT
27773154 AAATAG AAATAG AAATAG AAATAG AAATAG AAAT
1 AAATAG AAATAG AAATAG AAATAG AAATAG AAAT
27773188 GCAAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.18
Consensus pattern (6 bp):
AAATAG
Found at i:27774109 original size:44 final size:45
Alignment explanation
Indices: 27773998--27774439 Score: 296
Period size: 45 Copynumber: 9.7 Consensus size: 45
27773988 TTACATTCGT
* * * * * *
27773998 TCCACTGCAATTTCAAGGAAATAAGACTTGCTATCTTCAGTCTGT
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
* * * * * *
27774043 TCCACTGCAATTTC-AGAAAGATAAGACTCGTAAT-TTCAACCTGC
1 TCCACTGCAACTTCAAG-GAGATAAGATTTGTTATCTTCAATCTGC
* *
27774087 TCCACTGCAACTTCAAGGAGATAAGGTTTG-TATATTCAATCTGC
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
* * *
27774131 CCCACTGCAACTTCAAGGGGATAAGGTTTGTTA-CTTCAACCTGCTTTGC
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAA--T-C--TGC
* * * * *
27774180 TGCGAC-GTAACTTC-A-GAGGTAAGATTTGTTATCTTCAGTCTAC
1 T-CCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
* * ** *
27774223 TCCATTGCAACTTCAAGGAGATAAGACTCGTTATGGTAGATTTAAT-TCGAC
1 TCCACTGCAACTTCAAGGAGATAAGA----TT-TGTTATCTTCAATCT-G-C
* * * *
27774274 -CTACTGCAACTTC--GGAGGTATAAGAATAG-TAGCTTCAATCTGC
1 TCCACTGCAACTTCAAGGA-G-ATAAGATTTGTTATCTTCAATCTGC
* * * * *
27774317 TCCACTGCAACTTCAGGGAGATAGGATTGGTTATCTTCAACCTAC
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
* *
27774362 TCCACTGCAACTTCAAGAAGATAAGATTTGTTATCTTCAGTCTGC
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
* *
27774407 TCCACTGCAACTTTAAGGAGATAAGACTTGTTA
1 TCCACTGCAACTTCAAGGAGATAAGATTTGTTA
27774440 CGAAGTGATC
Statistics
Matches: 310, Mismatches: 59, Indels: 56
0.73 0.14 0.13
Matches are distributed among these distances:
42 2 0.01
43 13 0.04
44 102 0.33
45 121 0.39
46 6 0.02
47 14 0.05
48 9 0.03
49 14 0.05
50 28 0.09
51 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (45 bp):
TCCACTGCAACTTCAAGGAGATAAGATTTGTTATCTTCAATCTGC
Found at i:27774699 original size:44 final size:42
Alignment explanation
Indices: 27774599--27775187 Score: 388
Period size: 44 Copynumber: 13.7 Consensus size: 42
27774589 GTCTGATGCG
* * * **
27774599 ATCTGCTCTATTGCAACTTCAGAGAGATAAGATCCATCATTTT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT---TGGTTTTCA
* * * *
27774643 ATCCGCTTCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TT-TTCA
* * * *
27774687 ATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGG-ATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTCA
* * * *
27774728 ATTTGCTCTACTGTAACTTCAGAGAGATAAGATCTCTGGTTTT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-TGGTTTTCA
* * * *
27774772 ATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGCTTCTTCT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TT-TTCA
* * * * *
27774816 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGT-G
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTCA
* *
27774857 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGGTTTT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-TGGTTTTCA
* * * *
27774901 ATCCGCTCCACTGCAACTTCAGGAAGATAGGATTGGCTTCTTCT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TT-TTCA
* * ** *
27774945 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACT-GAATGCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTCA
* *
27774986 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGGTTTT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-TGGTTTTCA
* * * * * *
27775030 ATCCGCTCCATTGTAACTTTAGGGAGATAGGATTGGCTTCTTCT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-TT-TTCA
* * * * * * *
27775074 GTCTGCTCCACTGCAACTTTAGGGAGATAAGACTAG-ATGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTCA
* **
27775115 ATCTGCTCTACTGCAACTTCAGAAAGAT-AGCATCTGTAGTTTT-A
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAG-AT-TG--GTTTTCA
*
27775159 ATCCGCTCCACTGCAACTTCAGGGAGATA
1 ATCTGCTCCACTGCAACTTCAGGGAGATA
27775188 GGACTGGTGT
Statistics
Matches: 414, Mismatches: 102, Indels: 57
0.72 0.18 0.10
Matches are distributed among these distances:
40 2 0.00
41 126 0.30
42 13 0.03
43 11 0.03
44 258 0.62
45 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (42 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTCA
Found at i:27774786 original size:85 final size:83
Alignment explanation
Indices: 27774651--27775105 Score: 319
Period size: 85 Copynumber: 5.3 Consensus size: 83
27774641 TAATCCGCTT
*
27774651 CACTGCAACTTCAG-GAAGATAGGAT-TGGTTTCTTCAATCTGCTCCACTGCAACTTTAGGGAGA
1 CACTGCAACTTCAGAG-AGATAAGATCTGG-TT-TT-AATCTGCTCCACTGCAACTTTAGGGAGA
*
27774714 TAAGATTGGATGCGATTTGCTC
62 TAAGATTGGATGCGATCTGCTC
* * *
27774736 TACTGTAACTTCAGAGAGATAAGATCTCTGGTTTTAATCCGCTCCACTGCAACTTTAGGGAGATA
1 CACTGCAACTTCAGAGAGATAAGA--TCTGGTTTTAATCTGCTCCACTGCAACTTTAGGGAGATA
* * * *
27774801 GGATTGGCTTCTTCTATCTGCTC
64 AGATTGG---ATGCGATCTGCTC
* * * * * * * *
27774824 CACTGCAACTTCAGGGAGATAAGA-CTAGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAG
1 CACTGCAACTTCAGAGAGATAAGATCTGGTTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAG
* *** *
27774888 ATTTGTGGTTTTAATCCGCTC
66 A--T-TGGATGCGATCTGCTC
* ** *
27774909 CACTGCAACTTCAG-GAAGATAGGAT-TGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGA
1 CACTGCAACTTCAGAG-AGATAAGATCTGG-TT-TT-AATCTGCTCCACTGCAACTTTAGGGAGA
* * *
27774972 TAAGACTGAATGCAATCTGCTC
62 TAAGATTGGATGCGATCTGCTC
* * * * *
27774994 TACTGCAACTTCAGAGAGATAAGATTTGTGGTTTTAATCCGCTCCATTGTAACTTTAGGGAGATA
1 CACTGCAACTTCAGAGAGATAAGA--TCTGGTTTTAATCTGCTCCACTGCAACTTTAGGGAGATA
* * *
27775059 GGATTGGCTTCTTCTG-TCTGCTC
64 AGATTGG---ATGC-GATCTGCTC
* *
27775082 CACTGCAACTTTAGGGAGATAAGA
1 CACTGCAACTTCAGAGAGATAAGA
27775106 CTAGATGCGA
Statistics
Matches: 291, Mismatches: 56, Indels: 43
0.75 0.14 0.11
Matches are distributed among these distances:
84 1 0.00
85 177 0.61
86 7 0.02
87 8 0.03
88 98 0.34
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (83 bp):
CACTGCAACTTCAGAGAGATAAGATCTGGTTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAG
ATTGGATGCGATCTGCTC
Found at i:27775209 original size:129 final size:129
Alignment explanation
Indices: 27774593--27775190 Score: 903
Period size: 129 Copynumber: 4.6 Consensus size: 129
27774583 AATAAAGTCT
* ** ** *
27774593 GATGCGATCTGCTCTATTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTTCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
* * * * * *
27774658 ACTTCAGGAAGATAGGATTGGTTTCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTG
66 ACTTCAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* * *
27774722 GATGCGATTTGCTCTACTGTAACTTCAGAGAGATAAGATCTCTGGTTTTAATCCGCTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
*
27774787 ACTTTAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
66 ACTTCAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* *
27774851 GATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGGTTTTAATCCGCTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
* *
27774916 ACTTCAGGAAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT-
66 ACTTCAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* * * *
27774979 GAATGCAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGGTTTTAATCCGCTCCATTGT
1 G-ATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGC
* * *
27775044 AACTTTAGGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTA
65 AACTTCAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* *
27775109 GATGCGATCTGCTCTACTGCAACTTCAGAAAGAT-AGCATCTGTAGTTTTAATCCGCTCCACTGC
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAG-ATCTGTGGTTTTAATCCGCTCCACTGC
27775173 AACTTCAGGGAGATAGGA
65 AACTTCAGGGAGATAGGA
27775191 CTGGTGTTTT
Statistics
Matches: 429, Mismatches: 37, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
128 3 0.01
129 425 0.99
130 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
ACTTCAGGGAGATAGGATTGGCTTCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
Found at i:27775660 original size:24 final size:23
Alignment explanation
Indices: 27775628--27775684 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
27775618 CAGATTGCCC
27775628 CCACTGTAATCTTCAAGGTCCAAT
1 CCACTGTAAT-TTCAAGGTCCAAT
* * *
27775652 CCACTGTAA-TTCTATGTTCAAT
1 CCACTGTAATTTCAAGGTCCAAT
27775674 CCACTGTAATT
1 CCACTGTAATT
27775685 CTTGGACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 19 0.66
23 1 0.03
24 9 0.31
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (23 bp):
CCACTGTAATTTCAAGGTCCAAT
Found at i:27776402 original size:18 final size:18
Alignment explanation
Indices: 27776379--27776414 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27776369 CCTTTCTGAG
27776379 TTTGACATGTGTTTAGGA
1 TTTGACATGTGTTTAGGA
27776397 TTTGACATGTGTTTAGGA
1 TTTGACATGTGTTTAGGA
27776415 GATCTACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (18 bp):
TTTGACATGTGTTTAGGA
Found at i:27776654 original size:11 final size:10
Alignment explanation
Indices: 27776638--27776698 Score: 70
Period size: 11 Copynumber: 5.8 Consensus size: 10
27776628 GGCCTCTCTT
27776638 TTTTCTTTTTC
1 TTTT-TTTTTC
*
27776649 TTTTCTTCTTC
1 TTTT-TTTTTC
27776660 TTTTTTTTTC
1 TTTTTTTTTC
27776670 TTTTTTTTCTC
1 TTTTTTTT-TC
27776681 TTTTTTTTT-
1 TTTTTTTTTC
27776690 TATTTTTTT
1 T-TTTTTTT
27776699 AAATATTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
9 1 0.02
10 21 0.46
11 24 0.52
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:27776689 original size:21 final size:20
Alignment explanation
Indices: 27776632--27776698 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 20
27776622 CACATTGGCC
27776632 TCTCTTTTTTCTTTTTCTTTTCT
1 TCTCTTTTTT-TTTTT-TTTT-T
27776655 TCTTCTTTTTTTTTCTTTTTTT
1 TC-TCTTTTTTTTT-TTTTTTT
27776677 TCTCTTTTTTTTTTATTTTTT
1 TCTCTTTTTTTTTT-TTTTTT
27776698 T
1 T
27776699 AAATATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.02
21 18 0.44
22 3 0.07
23 9 0.22
24 10 0.24
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (20 bp):
TCTCTTTTTTTTTTTTTTTT
Found at i:27780591 original size:107 final size:106
Alignment explanation
Indices: 27780414--27780608 Score: 300
Period size: 107 Copynumber: 1.8 Consensus size: 106
27780404 GATTTAAGAG
* * * * * *
27780414 GATATTTGGCTATTTGGTCAAACGAGAAGTCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAAT
1 GATATTTGACTATTTGGTCAAACGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCAAAT
27780479 TTCCAAACGCAAAATATTGTCTTATTTTGAAATTTTAAAAA
66 TTCCAAACGCAAAATATTGTCTTATTTTGAAATTTTAAAAA
* *
27780520 GATATTTGACTATTTGGTCGAATGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCAAA
1 GATATTTGACTATTTGGTCAAACG-AAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCAAA
*
27780585 TTTCCAAATGCAAAATATTGTCTT
65 TTTCCAAACGCAAAATATTGTCTT
27780609 TATTATTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
106 21 0.27
107 58 0.73
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (106 bp):
GATATTTGACTATTTGGTCAAACGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCAAAT
TTCCAAACGCAAAATATTGTCTTATTTTGAAATTTTAAAAA
Found at i:27780840 original size:73 final size:73
Alignment explanation
Indices: 27780753--27780888 Score: 245
Period size: 73 Copynumber: 1.9 Consensus size: 73
27780743 TCAGGTTTAG
* *
27780753 AAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAAAT
1 AAAAGGGATAATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAAAT
27780818 TTGAGGAA
66 TTGAGGAA
*
27780826 AAAAGGGATAATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTTCCGAGATCGTTTAAAA
1 AAAAGGGATAATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
27780889 CTTGAATTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (73 bp):
AAAAGGGATAATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAAAT
TTGAGGAA
Found at i:27781333 original size:47 final size:47
Alignment explanation
Indices: 27781241--27781333 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
27781231 GAAAATGAAT
*
27781241 AAAATTATAGAAATATAAAAAGATATATATGAATATATATGTATATA
1 AAAATTATAGAAATATAAAAAGATATATATGAATATATATATATATA
* *
27781288 AAAATTATA-AAATATAAAAA-ATATATATATAAGTATGTATATATAT
1 AAAATTATAGAAATATAAAAAGATATATAT-GAA-TATATATATATAT
27781334 TCGTGAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
45 8 0.20
46 13 0.32
47 20 0.49
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (47 bp):
AAAATTATAGAAATATAAAAAGATATATATGAATATATATATATATA
Found at i:27782437 original size:20 final size:20
Alignment explanation
Indices: 27782412--27782453 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
27782402 AAATCCCAAA
27782412 TTGCTACTTTTGATTTTGTC
1 TTGCTACTTTTGATTTTGTC
27782432 TTGCTACTTTTGATTTTGTC
1 TTGCTACTTTTGATTTTGTC
27782452 TT
1 TT
27782454 TCTTTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.62
Consensus pattern (20 bp):
TTGCTACTTTTGATTTTGTC
Found at i:27785067 original size:3 final size:3
Alignment explanation
Indices: 27785059--27785093 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
27785049 GCAAATTTGT
27785059 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27785094 TCATGTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:27785546 original size:48 final size:47
Alignment explanation
Indices: 27785485--27785595 Score: 138
Period size: 45 Copynumber: 2.4 Consensus size: 47
27785475 TATTATAAAA
27785485 TCAAATAATTATTTCAAACACAAAT-ATTATTTTTATATGTAAAATATT
1 TCAAATAATTATTTCAAA-A-AAATCATTATTTTTATATGTAAAATATT
* * * * *
27785533 TTAAATAACTATTTC--AAATATCATTATTTTTATATGTGAAGTATT
1 TCAAATAATTATTTCAAAAAAATCATTATTTTTATATGTAAAATATT
27785578 TCAAATAATTATTTCAAA
1 TCAAATAATTATTTCAAA
27785596 TACACATACA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
44 3 0.06
45 35 0.66
46 1 0.02
47 1 0.02
48 13 0.25
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (47 bp):
TCAAATAATTATTTCAAAAAAATCATTATTTTTATATGTAAAATATT
Found at i:27785569 original size:45 final size:45
Alignment explanation
Indices: 27785510--27785597 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
27785500 AAACACAAAT
*
27785510 ATTATTTTTATATGTAAAATATTTTAAATAACTATTTCAAATATC
1 ATTATTTTTATATGTAAAATATTTCAAATAACTATTTCAAATATC
* * *
27785555 ATTATTTTTATATGTGAAGTATTTCAAATAATTATTTCAAATA
1 ATTATTTTTATATGTAAAATATTTCAAATAACTATTTCAAATA
27785598 CACATACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.49
Consensus pattern (45 bp):
ATTATTTTTATATGTAAAATATTTCAAATAACTATTTCAAATATC
Found at i:27785762 original size:109 final size:105
Alignment explanation
Indices: 27785611--27785839 Score: 227
Period size: 107 Copynumber: 2.1 Consensus size: 105
27785601 ATACAAAATA
* *
27785611 TATAATACTAAAATTTACCACACCAATGGTACGGAATGAAAAATAA-ATATTTCACATATAAGAA
1 TATAATACTAGAATTTACCACACCAATGGTAC-GAATGAAAAATAAGACATTTCA-A-AT-A-AA
*
27785675 TTATA-TTAACTAAA-AATAATGATATTTGAAATAATTGA-TTGATTT
61 TTACATTTAA--AAATAATAATGATATTTGAAATAATT-ATTTGATTT
* * * **
27785720 TATAATACTAGAATTTACCATACCCATATTGTA-G-ATGAAAAAATAATGACATTTGAAATATTT
1 TATAATACTAGAATTTACCACA-CCA-ATGGTACGAATG-AAAAATAA-GACATTTCAAATAAAT
27785783 TACATTTAAAAATAATAATGATATTTGAAATAATTATTTGATTT
62 TACATTTAAAAATAATAATGATATTTGAAATAATTATTTGATTT
*
27785827 TATAATATTAGAA
1 TATAATACTAGAA
27785840 ATCCCTATAC
Statistics
Matches: 103, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
106 4 0.04
107 45 0.44
108 8 0.08
109 31 0.30
110 4 0.04
111 11 0.11
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.37
Consensus pattern (105 bp):
TATAATACTAGAATTTACCACACCAATGGTACGAATGAAAAATAAGACATTTCAAATAAATTACA
TTTAAAAATAATAATGATATTTGAAATAATTATTTGATTT
Found at i:27800210 original size:26 final size:26
Alignment explanation
Indices: 27800155--27800210 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
27800145 ATTACATTGG
* *
27800155 TAATCACTCAACTATAAATAATTTTT
1 TAATCACTCAACTATAAATAATTATA
* *
27800181 TAATTACTCAATTATGAAA-AATTATA
1 TAATCACTCAACTAT-AAATAATTATA
27800207 TAAT
1 TAAT
27800211 AGTTGCTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (26 bp):
TAATCACTCAACTATAAATAATTATA
Found at i:27805660 original size:22 final size:21
Alignment explanation
Indices: 27805620--27805666 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
27805610 ATCACGTATA
* *
27805620 AATCATGTTTAAATTTATTCT
1 AATCATGTCTAAATATATTCT
*
27805641 AATCATGATCTAAATATATTTT
1 AATCATG-TCTAAATATATTCT
27805663 AATC
1 AATC
27805667 TAGAGATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (21 bp):
AATCATGTCTAAATATATTCT
Found at i:27806934 original size:18 final size:18
Alignment explanation
Indices: 27806911--27806954 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
27806901 TCCTCTCTTA
27806911 TCCCTCTCATCGCATCCT
1 TCCCTCTCATCGCATCCT
27806929 TCCCTCTCATCGCATCCT
1 TCCCTCTCATCGCATCCT
27806947 TCCCTCTC
1 TCCCTCTC
27806955 CATTATCCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.09, C:0.52, G:0.05, T:0.34
Consensus pattern (18 bp):
TCCCTCTCATCGCATCCT
Found at i:27807233 original size:16 final size:15
Alignment explanation
Indices: 27807172--27807221 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
27807162 TTTGTTATTA
*
27807172 TTATTATTATTAT-T
1 TTATTGTTATTATAT
*
27807186 TTATT-TTCATTTTTAT
1 TTATTGTT-A-TTATAT
27807202 TTATTGTTATTATAT
1 TTATTGTTATTATAT
27807217 TTATT
1 TTATT
27807222 TGTTTTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 2 0.07
14 6 0.20
15 13 0.43
16 7 0.23
17 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (15 bp):
TTATTGTTATTATAT
Found at i:27808800 original size:18 final size:17
Alignment explanation
Indices: 27808777--27808818 Score: 61
Period size: 15 Copynumber: 2.5 Consensus size: 17
27808767 GGACCTCTCC
27808777 GAGCGGTTCACTCATTTT
1 GAGCGGTTCACT-ATTTT
27808795 GAGCGG--CACTATTTT
1 GAGCGGTTCACTATTTT
27808810 GAGCGGTTC
1 GAGCGGTTC
27808819 GACAGTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.50
16 4 0.18
17 1 0.05
18 6 0.27
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (17 bp):
GAGCGGTTCACTATTTT
Found at i:27808957 original size:6 final size:6
Alignment explanation
Indices: 27808924--27808999 Score: 57
Period size: 6 Copynumber: 12.3 Consensus size: 6
27808914 AGATCATTGA
* * * *
27808924 TTTTAT TTCTCT TTTT-T TTTTCAA TTTTAT TTTTAT CTTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTT-AT TTTTAT TTTTAT TTTTAT TTTTAT
*
27808971 TTTTGT TTTTAGT TGTTTCAT TTTTAT TT
1 TTTTAT TTTTA-T T-TTT-AT TTTTAT TT
27809000 CTTAGACTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
5 9 0.16
6 31 0.56
7 9 0.16
8 5 0.09
9 1 0.02
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:27825584 original size:51 final size:51
Alignment explanation
Indices: 27825508--27825689 Score: 328
Period size: 51 Copynumber: 3.6 Consensus size: 51
27825498 TTTGAGTATT
* *
27825508 TCTGATCAGTGTCAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
27825559 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
27825610 TCTGATCAGTGACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
27825661 TCTGATCAGGGACAAGTGACAAGTGATAA
1 TCTGATCAGTGACAAGTGACAAGTGATAA
27825690 ATGTGATCCG
Statistics
Matches: 126, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 126 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (51 bp):
TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:27830194 original size:31 final size:29
Alignment explanation
Indices: 27830156--27830232 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
27830146 TTAACGGCTC
* *
27830156 AGTGACTAAAATGTTACATCATGATAACATA
1 AGTGACTAAAATGTAACAT-ATCA-AACATA
* *
27830187 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACATATCAAACATA
*
27830216 AGTGACTAAAATATAAC
1 AGTGACTAAAATGTAAC
27830233 CTGAACCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 21 0.52
30 2 0.05
31 17 0.43
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (29 bp):
AGTGACTAAAATGTAACATATCAAACATA
Found at i:27831699 original size:15 final size:15
Alignment explanation
Indices: 27831674--27831708 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27831664 GACTCTATTT
*
27831674 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
27831688 TAATTAATATTAAGA
1 TAATTAATATTAAGA
27831703 TAATTA
1 TAATTA
27831709 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:27835672 original size:12 final size:11
Alignment explanation
Indices: 27835620--27835675 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
27835610 AGGCAACCCA
27835620 ATTTTTATTTT
1 ATTTTTATTTT
* *
27835631 TTTCTTTACTTT
1 ATT-TTTATTTT
*
27835643 ATTTATTACTTT
1 ATTT-TTATTTT
27835655 A-TTTTATTTT
1 ATTTTTATTTT
27835665 ATTATTTATTT
1 ATT-TTTATTT
27835676 GGATATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
10 7 0.19
11 6 0.16
12 24 0.65
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:27835672 original size:17 final size:17
Alignment explanation
Indices: 27835622--27835675 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
27835612 GCAACCCAAT
* *
27835622 TTTTATTTTTTTCTTTA
1 TTTTATTTTATTATTTA
*
27835639 CTTTA-TTTATTACTTTA
1 TTTTATTTTATTA-TTTA
27835656 TTTTATTTTATTATTTA
1 TTTTATTTTATTATTTA
27835673 TTT
1 TTT
27835676 GGATATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 5 0.16
17 19 0.61
18 7 0.23
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTTATTATTTA
Found at i:27837311 original size:15 final size:15
Alignment explanation
Indices: 27837286--27837320 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27837276 CAGACTATTT
*
27837286 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
27837300 TAATTAATATTAAGA
1 TAATTAATATTAAGA
27837315 TAATTA
1 TAATTA
27837321 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:27841174 original size:26 final size:25
Alignment explanation
Indices: 27841132--27841182 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
27841122 GGCCATGGGA
*
27841132 TTGTCTGTATGTGGGAGTTGGGATT
1 TTGTCTGTATGTGGGAGTGGGGATT
27841157 TTGTCATGTAATGT-GGAGTGGGGATT
1 TTGTC-TGT-ATGTGGGAGTGGGGATT
27841183 ATAAGCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 14 0.61
27 4 0.17
ACGTcount: A:0.16, C:0.04, G:0.39, T:0.41
Consensus pattern (25 bp):
TTGTCTGTATGTGGGAGTGGGGATT
Found at i:27847498 original size:14 final size:14
Alignment explanation
Indices: 27847481--27847509 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27847471 TTTTTATTAC
27847481 ATTATCTTTCCTGG
1 ATTATCTTTCCTGG
27847495 ATTATCTTTCCTGG
1 ATTATCTTTCCTGG
27847509 A
1 A
27847510 CATATAATTA
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:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (14 bp):
ATTATCTTTCCTGG
Found at i:27850681 original size:12 final size:12
Alignment explanation
Indices: 27850664--27850688 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27850654 TACTGATAAC
27850664 GTATTATAAAAT
1 GTATTATAAAAT
27850676 GTATTATAAAAT
1 GTATTATAAAAT
27850688 G
1 G
27850689 ATAATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (12 bp):
GTATTATAAAAT
Found at i:27850770 original size:36 final size:36
Alignment explanation
Indices: 27850694--27850770 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
27850684 AAATGATAAT
** *
27850694 AATAATAATGCAAAAAACACAAGAATGTTATAAAAT
1 AATAATAATGCAAAAAACACAAGAATAATATAAAAG
* * **
27850730 AATAATAATGCAAAGAACATAAGAATAATATATCAG
1 AATAATAATGCAAAAAACACAAGAATAATATAAAAG
27850766 AATAA
1 AATAA
27850771 AAAGGGATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.61, C:0.08, G:0.09, T:0.22
Consensus pattern (36 bp):
AATAATAATGCAAAAAACACAAGAATAATATAAAAG
Found at i:27852460 original size:13 final size:14
Alignment explanation
Indices: 27852436--27852464 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
27852426 GATATCATAT
27852436 TAATTATTAATTTA
1 TAATTATTAATTTA
27852450 TAATT-TTAATTTA
1 TAATTATTAATTTA
27852463 TA
1 TA
27852465 TGTAATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATTAATTTA
Found at i:27853235 original size:29 final size:29
Alignment explanation
Indices: 27853187--27853244 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
27853177 ACTGCTCTGC
*
27853187 GTCACACGACCGTGTAGTAGGCTGTGTGG
1 GTCACACGACCATGTAGTAGGCTGTGTGG
* * *
27853216 GTCACATGACCATGTGGTAGGTTGTGTGG
1 GTCACACGACCATGTAGTAGGCTGTGTGG
27853245 TAAACCGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.28
Consensus pattern (29 bp):
GTCACACGACCATGTAGTAGGCTGTGTGG
Found at i:27854427 original size:25 final size:24
Alignment explanation
Indices: 27854380--27854426 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
27854370 TAATTATATA
27854380 GTTTCTTTTAAAAAGAAAAAAAAC
1 GTTTCTTTTAAAAAGAAAAAAAAC
27854404 GTTTCTTTTAAAAAGAAAAAAAA
1 GTTTCTTTTAAAAAGAAAAAAAA
27854427 AATTTGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (24 bp):
GTTTCTTTTAAAAAGAAAAAAAAC
Found at i:27859124 original size:13 final size:13
Alignment explanation
Indices: 27859099--27859188 Score: 51
Period size: 13 Copynumber: 6.5 Consensus size: 13
27859089 AACAAAACTA
27859099 AAATAAAGT-AAAT
1 AAATAAA-TAAAAT
27859112 AAATAAATAAAATT
1 AAATAAATAAAA-T
27859126 CAAA-ATAATAAAAAT
1 -AAATA-AAT-AAAAT
*
27859141 TAATATAATAATAA-
1 AAATA-AATAA-AAT
*
27859155 AAATAATATATAAT
1 AAATAA-ATAAAAT
* *
27859169 AAATATATATAAT
1 AAATAAATAAAAT
27859182 AAATAAA
1 AAATAAA
27859189 AGGAACAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
12 1 0.02
13 26 0.41
14 18 0.29
15 14 0.22
16 4 0.06
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:27859165 original size:19 final size:18
Alignment explanation
Indices: 27859129--27859189 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
27859119 TAAAATTCAA
*
27859129 AATAATAAAAATTAATAT
1 AATAATAAAAATAAATAT
27859147 AATAATAAAAAT-AATAT
1 AATAATAAAAATAAATAT
*
27859164 -ATAAT--AAATATATAT
1 AATAATAAAAATAAATAT
27859179 AATAAATAAAA
1 AAT-AATAAAA
27859190 GGAACAAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
14 4 0.11
15 4 0.11
16 7 0.19
17 8 0.22
18 12 0.32
19 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAATAAAAATAAATAT
Found at i:27859187 original size:27 final size:27
Alignment explanation
Indices: 27859127--27859184 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
27859117 AATAAAATTC
*
27859127 AAAATAATAAAAATTAATATAATAATA
1 AAAATAATAAAAATAAATATAATAATA
*
27859154 AAAATAATATATAATAAATATATATAATA
1 AAAATAATA-AAAATAAATATA-ATAATA
27859183 AA
1 AA
27859185 TAAAAGGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 9 0.33
28 10 0.37
29 8 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAATAATAAAAATAAATATAATAATA
Found at i:27859728 original size:6 final size:7
Alignment explanation
Indices: 27859698--27859736 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
27859688 AGAAGGAAGG
27859698 AAAATAA
1 AAAATAA
27859705 TAAAATAA
1 -AAAATAA
27859713 AAGAA-AA
1 AA-AATAA
27859720 AAAATAA
1 AAAATAA
27859727 AAAATAA
1 AAAATAA
27859734 AAA
1 AAA
27859737 GAAAGAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 2 0.07
7 18 0.62
8 9 0.31
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:27859730 original size:21 final size:23
Alignment explanation
Indices: 27859698--27859740 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
27859688 AGAAGGAAGG
27859698 AAAATAATAAAAT-AAAAGAAAA
1 AAAATAATAAAATAAAAAGAAAA
27859720 AAAATAA-AAAATAAAAAGAAA
1 AAAATAATAAAATAAAAAGAAA
27859741 GAAACCCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.12
Consensus pattern (23 bp):
AAAATAATAAAATAAAAAGAAAA
Found at i:27861774 original size:6 final size:6
Alignment explanation
Indices: 27861763--27861809 Score: 76
Period size: 6 Copynumber: 7.5 Consensus size: 6
27861753 TGTAAAAATT
27861763 AAATAA AAATAA AAATAA AAATAA AAATAA AAATATTA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATA--A AAATAA AAA
27861810 ATGGATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 33 0.85
8 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:27861784 original size:18 final size:19
Alignment explanation
Indices: 27861755--27861809 Score: 80
Period size: 18 Copynumber: 3.0 Consensus size: 19
27861745 AATTAGAATG
27861755 TAAAAAT-T-AAATAAAAA
1 TAAAAATATAAAATAAAAA
27861772 TAAAAATA-AAAATAAAAA
1 TAAAAATATAAAATAAAAA
27861790 TAAAAATATTAAAATAAAAA
1 TAAAAATA-TAAAATAAAAA
27861810 ATGGATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.21
18 17 0.50
20 10 0.29
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAAAATATAAAATAAAAA
Found at i:27868855 original size:16 final size:17
Alignment explanation
Indices: 27868834--27868869 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
27868824 ACGAGAAAAT
*
27868834 TTTAATTATA-ATTTTC
1 TTTAATTATATAGTTTC
27868850 TTTAATTATATAGTTTC
1 TTTAATTATATAGTTTC
27868867 TTT
1 TTT
27868870 TAAAAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTAATTATATAGTTTC
Found at i:27870367 original size:21 final size:23
Alignment explanation
Indices: 27870304--27870367 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
27870294 GGTAGGAAAA
27870304 TACATCTG-ATTCTGAT-CTGTTC
1 TACATCTGTATT-TGATACTGTTC
27870326 TACATCTGTATTTGATA-TGTTC
1 TACATCTGTATTTGATACTGTTC
27870348 TTA-ATCT-TATTTGA-ACTGTT
1 -TACATCTGTATTTGATACTGTT
27870368 ACAACATTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
20 1 0.03
21 11 0.29
22 21 0.55
23 5 0.13
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (23 bp):
TACATCTGTATTTGATACTGTTC
Found at i:27871828 original size:46 final size:46
Alignment explanation
Indices: 27871761--27871899 Score: 233
Period size: 46 Copynumber: 3.0 Consensus size: 46
27871751 AAATTGCTAT
* *
27871761 AACTCAGTATGGTTTTTTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
* *
27871807 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
*
27871853 AACTCAGTATGGTTTTATTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
27871899 A
1 A
27871900 CTTTGCCATG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
Found at i:27872668 original size:17 final size:17
Alignment explanation
Indices: 27872646--27872678 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
27872636 AAATTCTTTT
27872646 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
27872663 TAAATCACAAAATTCA
1 TAAATCACAAAATTCA
27872679 CTAATTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:27875283 original size:23 final size:24
Alignment explanation
Indices: 27875238--27875284 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
27875228 TTTATAAAAA
* *
27875238 AATATTTTAATTTTCTATCTTTTT
1 AATATTTTAAATTTATATCTTTTT
27875262 AATA-TTTAAATTTATAT-TTTTT
1 AATATTTTAAATTTATATCTTTTT
27875284 A
1 A
27875285 TCAAACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 11 0.52
24 4 0.19
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (24 bp):
AATATTTTAAATTTATATCTTTTT
Found at i:27875406 original size:31 final size:29
Alignment explanation
Indices: 27875371--27875432 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
27875361 AATTAATTTT
*
27875371 TTTTTAAAATTTTAAAATATTATAAAAATTA
1 TTTTTAAAAATTT-AAA-ATTATAAAAATTA
* *
27875402 TTTTTAAAAATTTAGAATTATTAAAATTA
1 TTTTTAAAAATTTAAAATTATAAAAATTA
27875431 TT
1 TT
27875433 AAAAGGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 14 0.50
30 2 0.07
31 12 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TTTTTAAAAATTTAAAATTATAAAAATTA
Found at i:27879851 original size:21 final size:21
Alignment explanation
Indices: 27879821--27879862 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27879811 TTTTCCAAAG
* *
27879821 ATGTGTATTGGATTGAATTGA
1 ATGTGAATTGGATTAAATTGA
*
27879842 ATGTGAATTGTATTAAATTGA
1 ATGTGAATTGGATTAAATTGA
27879863 GTTAAATTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (21 bp):
ATGTGAATTGGATTAAATTGA
Found at i:27880421 original size:594 final size:594
Alignment explanation
Indices: 27879288--27880471 Score: 2359
Period size: 594 Copynumber: 2.0 Consensus size: 594
27879278 GAAAGATGAA
27879288 AAATAAAGATGATAAATGAATTAAAAATAAAAATATTATCATTTTATCATCTTTCCTAAATAAAT
1 AAATAAAGATGATAAATGAATTAAAAATAAAAATATTATCATTTTATCATCTTTCCTAAATAAAT
27879353 AATAATAATGGAAACCCTAGTTTGAAGCTTGAAGATAGACAAGCTTATTTAGATTAATTAGGTAT
66 AATAATAATGGAAACCCTAGTTTGAAGCTTGAAGATAGACAAGCTTATTTAGATTAATTAGGTAT
27879418 GTATTCATGTCCCATTTTAATGATTTTTATGTTTCTGAGATCGTAATAGCTTAATCTAGCTATCT
131 GTATTCATGTCCCATTTTAATGATTTTTATGTTTCTGAGATCGTAATAGCTTAATCTAGCTATCT
27879483 CGAGGATTAATTTGTAAAACTATTGAAGTACTAGAGTTTTTTCATGGATGAGTATGTATGAATTA
196 CGAGGATTAATTTGTAAAACTATTGAAGTACTAGAGTTTTTTCATGGATGAGTATGTATGAATTA
27879548 TGAAGTTTTATGGTGGAAAATGAAAGGTTTTTGATAGATAAACAACTTTTGTAAAGTGAATTTTT
261 TGAAGTTTTATGGTGGAAAATGAAAGGTTTTTGATAGATAAACAACTTTTGTAAAGTGAATTTTT
27879613 ACGAAATTGTGATTTAGGGACTAAATTGAAAAGATGAAAAATTCATGGAAAAATTTTGAATTTTA
326 ACGAAATTGTGATTTAGGGACTAAATTGAAAAGATGAAAAATTCATGGAAAAATTTTGAATTTTA
27879678 TGAAATAAATGGACTGCTATTGTTATATATAAAAATTTTATAGGCTTGGAATAAGGATTAAATTG
391 TGAAATAAATGGACTGCTATTGTTATATATAAAAATTTTATAGGCTTGGAATAAGGATTAAATTG
27879743 TATGAATTTCATTTTCCGAGTCTAGGGATTAAATCGTAATTAATCAAAAGTATAGGGGCAATAAT
456 TATGAATTTCATTTTCCGAGTCTAGGGATTAAATCGTAATTAATCAAAAGTATAGGGGCAATAAT
27879808 AAATTTTCCAAAGATGTGTATTGGATTGAATTGAATGTGAATTGTATTAAATTGAGTTAAATTTG
521 AAATTTTCCAAAGATGTGTATTGGATTGAATTGAATGTGAATTGTATTAAATTGAGTTAAATTTG
27879873 CTCATTGGT
586 CTCATTGGT
*
27879882 AAATTAAGATGATAAATGAATTAAAAATAAAAATATTATCATTTTATCATCTTTCCTAAATAAAT
1 AAATAAAGATGATAAATGAATTAAAAATAAAAATATTATCATTTTATCATCTTTCCTAAATAAAT
27879947 AATAATAATGGAAACCCTAGTTTGAAGCTTGAAGATAGACAAGCTTATTTAGATTAATTAGGTAT
66 AATAATAATGGAAACCCTAGTTTGAAGCTTGAAGATAGACAAGCTTATTTAGATTAATTAGGTAT
27880012 GTATTCATGTCCCATTTTAATGATTTTTATGTTTCTGAGATCGTAATAGCTTAATCTAGCTATCT
131 GTATTCATGTCCCATTTTAATGATTTTTATGTTTCTGAGATCGTAATAGCTTAATCTAGCTATCT
27880077 CGAGGATTAATTTGTAAAACTATTGAAGTACTAGAGTTTTTTCATGGATGAGTATGTATGAATTA
196 CGAGGATTAATTTGTAAAACTATTGAAGTACTAGAGTTTTTTCATGGATGAGTATGTATGAATTA
27880142 TGAAGTTTTATGGTGGAAAATGAAAGGTTTTTGATAGATAAACAACTTTTGTAAAGTGAATTTTT
261 TGAAGTTTTATGGTGGAAAATGAAAGGTTTTTGATAGATAAACAACTTTTGTAAAGTGAATTTTT
27880207 ACGAAATTGTGATTTAGGGACTAAATTGAAAAGATGAAAAATTCATGGAAAAATTTTGAATTTTA
326 ACGAAATTGTGATTTAGGGACTAAATTGAAAAGATGAAAAATTCATGGAAAAATTTTGAATTTTA
27880272 TGAAATAAATGGACTGCTATTGTTATATATAAAAATTTTATAGGCTTGGAATAAGGATTAAATTG
391 TGAAATAAATGGACTGCTATTGTTATATATAAAAATTTTATAGGCTTGGAATAAGGATTAAATTG
27880337 TATGAATTTCATTTTCCGAGTCTAGGGATTAAATCGTAATTAATCAAAAGTATAGGGGCAATAAT
456 TATGAATTTCATTTTCCGAGTCTAGGGATTAAATCGTAATTAATCAAAAGTATAGGGGCAATAAT
27880402 AAATTTTCCAAAGATGTGTATTGGATTGAATTGAATGTGAATTGTATTAAATTGAGTTAAATTTG
521 AAATTTTCCAAAGATGTGTATTGGATTGAATTGAATGTGAATTGTATTAAATTGAGTTAAATTTG
27880467 CTCAT
586 CTCAT
27880472 ATAGATCTGG
Statistics
Matches: 589, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
594 589 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (594 bp):
AAATAAAGATGATAAATGAATTAAAAATAAAAATATTATCATTTTATCATCTTTCCTAAATAAAT
AATAATAATGGAAACCCTAGTTTGAAGCTTGAAGATAGACAAGCTTATTTAGATTAATTAGGTAT
GTATTCATGTCCCATTTTAATGATTTTTATGTTTCTGAGATCGTAATAGCTTAATCTAGCTATCT
CGAGGATTAATTTGTAAAACTATTGAAGTACTAGAGTTTTTTCATGGATGAGTATGTATGAATTA
TGAAGTTTTATGGTGGAAAATGAAAGGTTTTTGATAGATAAACAACTTTTGTAAAGTGAATTTTT
ACGAAATTGTGATTTAGGGACTAAATTGAAAAGATGAAAAATTCATGGAAAAATTTTGAATTTTA
TGAAATAAATGGACTGCTATTGTTATATATAAAAATTTTATAGGCTTGGAATAAGGATTAAATTG
TATGAATTTCATTTTCCGAGTCTAGGGATTAAATCGTAATTAATCAAAAGTATAGGGGCAATAAT
AAATTTTCCAAAGATGTGTATTGGATTGAATTGAATGTGAATTGTATTAAATTGAGTTAAATTTG
CTCATTGGT
Found at i:27880445 original size:21 final size:21
Alignment explanation
Indices: 27880415--27880456 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27880405 TTTTCCAAAG
* *
27880415 ATGTGTATTGGATTGAATTGA
1 ATGTGAATTGGATTAAATTGA
*
27880436 ATGTGAATTGTATTAAATTGA
1 ATGTGAATTGGATTAAATTGA
27880457 GTTAAATTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (21 bp):
ATGTGAATTGGATTAAATTGA
Found at i:27880917 original size:27 final size:26
Alignment explanation
Indices: 27880821--27880919 Score: 105
Period size: 27 Copynumber: 3.9 Consensus size: 26
27880811 GGATCTCACG
*
27880821 AGCTTCCCAATTAATGGCTCTCT-TA
1 AGCTTCCCGATTAATGGCTCTCTATA
* * *
27880846 AGCTTCCCG-TTTATGGCT-TGTATG
1 AGCTTCCCGATTAATGGCTCTCTATA
* * *
27880870 AGCTTCCCGATAAAAGACTCTCTCATA
1 AGCTTCCCGATTAATGGCTCTCT-ATA
27880897 AGCTTCCCGATTAATGGCTCTCT
1 AGCTTCCCGATTAATGGCTCTCT
27880920 GGAGCTACGC
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
23 2 0.04
24 18 0.32
25 13 0.23
26 2 0.04
27 22 0.39
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.34
Consensus pattern (26 bp):
AGCTTCCCGATTAATGGCTCTCTATA
Found at i:27880966 original size:25 final size:25
Alignment explanation
Indices: 27880937--27880990 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
27880927 CGCGATATTA
27880937 GCTCACATGAGCTTCCCGTTACATG
1 GCTCACATGAGCTTCCCGTTACATG
* *
27880962 GCTCACATGAGCTTCCTGTTATATG
1 GCTCACATGAGCTTCCCGTTACATG
27880987 GCTC
1 GCTC
27880991 GAAAGAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.31
Consensus pattern (25 bp):
GCTCACATGAGCTTCCCGTTACATG
Found at i:27880998 original size:25 final size:25
Alignment explanation
Indices: 27880937--27880999 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
27880927 CGCGATATTA
*
27880937 GCTCACATGAGCTTCCCGTTACATG
1 GCTCACAAGAGCTTCCCGTTACATG
* * *
27880962 GCTCACATGAGCTTCCTGTTATATG
1 GCTCACAAGAGCTTCCCGTTACATG
27880987 GCTCGA-AAGAGCT
1 GCTC-ACAAGAGCT
27881000 ATTCGTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 33 0.97
26 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (25 bp):
GCTCACAAGAGCTTCCCGTTACATG
Found at i:27881023 original size:25 final size:24
Alignment explanation
Indices: 27880937--27881023 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 24
27880927 CGCGATATTA
*
27880937 GCTCACATGAGCTTCCCG-TTACATG
1 GCTCACATGAGCTT--CGTTTATATG
*
27880962 GCTCACATGAGCTTCCTGTTATATG
1 GCTCACATGAGCTTCGT-TTATATG
*
27880987 GCTCGA-AAGAGCTATTCGTTTATAT-
1 GCTC-ACATGAGC--TTCGTTTATATG
27881012 GCTCACATGAGC
1 GCTCACATGAGC
27881024 ATTCCTGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 38 0.75
26 7 0.14
27 4 0.08
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (24 bp):
GCTCACATGAGCTTCGTTTATATG
Found at i:27887462 original size:29 final size:30
Alignment explanation
Indices: 27887416--27887477 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
27887406 ATTATTCATC
27887416 ATTGAAAAATTAAGAAAAGAAA-ATGATTAA
1 ATTGAAAAATTAAGAAAAGAAAGATGA-TAA
*
27887446 ATTGAAAAGA-TAA-AAAATAAAGATGATAA
1 ATTGAAAA-ATTAAGAAAAGAAAGATGATAA
27887475 ATT
1 ATT
27887478 AATTAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 13 0.45
30 15 0.52
31 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (30 bp):
ATTGAAAAATTAAGAAAAGAAAGATGATAA
Found at i:27888469 original size:25 final size:25
Alignment explanation
Indices: 27888427--27888474 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
27888417 CTCGTATGAG
*
27888427 CTTCCCGATAATTAGCTCTCTGAAA
1 CTTCCCGATAATAAGCTCTCTGAAA
27888452 CTTCCCGATAA-AAGGCTCTCTGA
1 CTTCCCGATAATAA-GCTCTCTGA
27888475 TGAGTTTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (25 bp):
CTTCCCGATAATAAGCTCTCTGAAA
Found at i:27888542 original size:25 final size:25
Alignment explanation
Indices: 27888487--27888578 Score: 71
Period size: 25 Copynumber: 3.7 Consensus size: 25
27888477 AGTTTCCCGA
** **
27888487 ATATGGCTCTTATGAGCTTCCCATT
1 ATATGGCTCACATGAGCTTCCTGTT
**
27888512 CCATGGCTCACATGAGCTTCCTGTT
1 ATATGGCTCACATGAGCTTCCTGTT
* *
27888537 ATATGGCTCGA-AAGAGCTACCTGTT
1 ATATGGCTC-ACATGAGCTTCCTGTT
*
27888562 -TATACGCTCACATGAGC
1 ATAT-GGCTCACATGAGC
27888579 ATTCTGGAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
24 4 0.08
25 47 0.90
26 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (25 bp):
ATATGGCTCACATGAGCTTCCTGTT
Found at i:27900761 original size:35 final size:33
Alignment explanation
Indices: 27900707--27900771 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 33
27900697 TCTAATACAT
*
27900707 ATTTCATTTCATGTCATTTGCTATTTCAATAGC
1 ATTTCATTTCATGTCATTTGCCATTTCAATAGC
*
27900740 ATTTCATCTTCAATTTCATTTGCCATTTCAAT
1 ATTTCAT-TTC-ATGTCATTTGCCATTTCAAT
27900772 TTCAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 7 0.25
34 3 0.11
35 18 0.64
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (33 bp):
ATTTCATTTCATGTCATTTGCCATTTCAATAGC
Found at i:27900771 original size:18 final size:18
Alignment explanation
Indices: 27900711--27900775 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
27900701 ATACATATTT
*
27900711 CATTTC-ATGTCATTTGC
1 CATTTCAATTTCATTTGC
* **
27900728 TATTTCAATAGCATTT--
1 CATTTCAATTTCATTTGC
27900744 CATCTTCAATTTCATTTGC
1 CAT-TTCAATTTCATTTGC
27900763 CATTTCAATTTCA
1 CATTTCAATTTCA
27900776 ATAATACAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
16 2 0.05
17 16 0.42
18 17 0.45
19 3 0.08
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.48
Consensus pattern (18 bp):
CATTTCAATTTCATTTGC
Found at i:27910416 original size:27 final size:27
Alignment explanation
Indices: 27910385--27910629 Score: 312
Period size: 27 Copynumber: 9.1 Consensus size: 27
27910375 TTACACTATT
*
27910385 ATGACCGAATTACCCCCATAGGATAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
27910412 ATGACCGAATTACCCCCATAGGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
* *
27910439 ATAACCGAATTACCCCCATAAGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
* **
27910466 ATGACCGAATTAACCTTATAGGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
** *
27910493 ATGATTGAATTA-CCTCATAGGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
* *
27910519 ATGACCGAATTACCCCATATAGGGTAAG
1 ATGACCGAATTACCCC-CATAGGGTAAA
* *
27910547 ACGACTGAATTACCCCCATAGGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
*
27910574 ATGACCAAATTACCCCCATAGGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
* * **
27910601 ATGATCGAAATACCCCCATATTGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
27910628 AT
1 AT
27910630 AACTGCTATA
Statistics
Matches: 188, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 23 0.12
27 142 0.76
28 23 0.12
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (27 bp):
ATGACCGAATTACCCCCATAGGGTAAA
Found at i:27911035 original size:28 final size:28
Alignment explanation
Indices: 27910995--27911057 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
27910985 GCACTGTACC
* *
27910995 GTTATTGTATTGGGCTAAGGCCCACATT
1 GTTACTGTATTGGGCTAAGGCCCACACT
27911023 GTTACTGTATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
27911051 G-TACTGT
1 GTTACTGT
27911058 TACTAAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 6 0.18
28 27 0.82
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (28 bp):
GTTACTGTATTGGGCTAAGGCCCACACT
Found at i:27911059 original size:33 final size:33
Alignment explanation
Indices: 27910986--27911090 Score: 103
Period size: 33 Copynumber: 3.3 Consensus size: 33
27910976 TGCATTATTG
* *
27910986 CACTGTACCGTTATTGTATTGGGCTAAGGCCCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
27911019 CA---T--TGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
** * *
27911047 CACTGTACTGTTACTAAATAGGGCTCAGGCCCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
*
27911080 GACTGTCACTG
1 CACTGT-ACTG
27911091 CTTGTTGTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
28 25 0.42
30 1 0.02
31 1 0.02
33 28 0.47
34 4 0.07
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.29
Consensus pattern (33 bp):
CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:27914219 original size:42 final size:42
Alignment explanation
Indices: 27914128--27914224 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
27914118 GTTTCAAGTT
** ** *
27914128 AGTGAGTTACACGGCCTGGCACACGACTGTGTGTGGCAACTT
1 AGTGAGTTACACGGCCTGGCACACGACCATGTGTACCAACTC
*
27914170 AGAGAGTTACACGGCCT-GCGACACGACCATGTG-ACCTAACTC
1 AGTGAGTTACACGGCCTGGC-ACACGACCATGTGTACC-AACTC
27914212 AGTGAGTTACACG
1 AGTGAGTTACACG
27914225 AGTGAGGACA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.07
42 43 0.93
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (42 bp):
AGTGAGTTACACGGCCTGGCACACGACCATGTGTACCAACTC
Found at i:27918285 original size:23 final size:23
Alignment explanation
Indices: 27918258--27918308 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
27918248 ATGAATAAAG
*
27918258 ATGAATAGGAAATATTCTTTGGC
1 ATGAATAGGAAATATTCTCTGGC
27918281 ATGAATAGGAAATATTCTCTGGC
1 ATGAATAGGAAATATTCTCTGGC
27918304 ATGAA
1 ATGAA
27918309 CAGTAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (23 bp):
ATGAATAGGAAATATTCTCTGGC
Found at i:27921349 original size:11 final size:11
Alignment explanation
Indices: 27921322--27921356 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
27921312 CATATTGTAC
27921322 TTGAAAAAAAA
1 TTGAAAAAAAA
*
27921333 GT-AAAAAAAA
1 TTGAAAAAAAA
27921343 TTGAAAAAAAA
1 TTGAAAAAAAA
27921354 TTG
1 TTG
27921357 CATAAAGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (11 bp):
TTGAAAAAAAA
Found at i:27923547 original size:28 final size:27
Alignment explanation
Indices: 27923508--27923572 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
27923498 GTCTGTGGAA
* *
27923508 AAATTGAGAGAAACGAACAATGAAAAAG
1 AAATTGAAAGAAACGAA-AAAGAAAAAG
*
27923536 AAATTGAAAGAAATGAAAAAGAAAAAG
1 AAATTGAAAGAAACGAAAAAGAAAAAG
*
27923563 AAAGTGAAAG
1 AAATTGAAAG
27923573 TAAAAAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 18 0.55
28 15 0.45
ACGTcount: A:0.65, C:0.03, G:0.22, T:0.11
Consensus pattern (27 bp):
AAATTGAAAGAAACGAAAAAGAAAAAG
Found at i:27923565 original size:21 final size:21
Alignment explanation
Indices: 27923526--27923566 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27923516 AGAAACGAAC
**
27923526 AATGAAAAAGAAATTGAAAGA
1 AATGAAAAAGAAAAAGAAAGA
27923547 AATGAAAAAGAAAAAGAAAG
1 AATGAAAAAGAAAAAGAAAG
27923567 TGAAAGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.10
Consensus pattern (21 bp):
AATGAAAAAGAAAAAGAAAGA
Found at i:27927165 original size:37 final size:37
Alignment explanation
Indices: 27927115--27927189 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
27927105 TTCTTGGAAA
27927115 TAGAATATTGTGGTGAAGAAGCAACTCTACTCTAAGT
1 TAGAATATTGTGGTGAAGAAGCAACTCTACTCTAAGT
27927152 TAGAATATTGTGGTGAAGAAGCAACTCTACTCTAAGT
1 TAGAATATTGTGGTGAAGAAGCAACTCTACTCTAAGT
27927189 T
1 T
27927190 TCTGTACTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (37 bp):
TAGAATATTGTGGTGAAGAAGCAACTCTACTCTAAGT
Found at i:27942125 original size:26 final size:26
Alignment explanation
Indices: 27942096--27942264 Score: 81
Period size: 26 Copynumber: 6.8 Consensus size: 26
27942086 TCCTCTCTCA
*
27942096 AGCCATATAAT-AGGAGGCTCACAAAG
1 AGCCAT-TAATCAGGAAGCTCACAAAG
*
27942122 AGCCATTAATCGGGAAGCTCACAAAG
1 AGCCATTAATCAGGAAGCTCACAAAG
* * * *
27942148 AGCC--T-ATCAAGAAGGTTATC--TG
1 AGCCATTAATCAGGAAGCTCA-CAAAG
* * *
27942170 GGCTATATAA-CAGGAAGCTCA-TAAG
1 AGCCAT-TAATCAGGAAGCTCACAAAG
* *
27942195 AGCCA-TAATAAGGAAGTTCACAAAG
1 AGCCATTAATCAGGAAGCTCACAAAG
* * *
27942220 A-ACTTTCAATCAGGAAGCTCACGAAG
1 AGCCATT-AATCAGGAAGCTCACAAAG
* *
27942246 AGCCTTTAACCAGG-AGCTC
1 AGCCATTAATCAGGAAGCTC
27942265 CGGATAGCCA
Statistics
Matches: 105, Mismatches: 25, Indels: 27
0.67 0.16 0.17
Matches are distributed among these distances:
22 3 0.03
23 12 0.11
24 12 0.11
25 27 0.26
26 47 0.45
27 4 0.04
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (26 bp):
AGCCATTAATCAGGAAGCTCACAAAG
Found at i:27943014 original size:20 final size:20
Alignment explanation
Indices: 27942973--27943014 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
27942963 AGCCTATGTA
*
27942973 TTTCATAAAATTTAGAATTT
1 TTTCATAAAATTTACAATTT
*
27942993 TTTCATAAATTTTACATATTT
1 TTTCATAAAATTTACA-ATTT
27943014 T
1 T
27943015 CAATATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTCATAAAATTTACAATTT
Found at i:27943247 original size:14 final size:15
Alignment explanation
Indices: 27943228--27943257 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27943218 GTTGGCTTGA
27943228 GGTTA-GGTTTCCAT
1 GGTTAGGGTTTCCAT
27943242 GGTTAGGGTTTCCAT
1 GGTTAGGGTTTCCAT
27943257 G
1 G
27943258 CTTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.13, C:0.13, G:0.33, T:0.40
Consensus pattern (15 bp):
GGTTAGGGTTTCCAT
Found at i:27948994 original size:25 final size:25
Alignment explanation
Indices: 27948965--27949059 Score: 86
Period size: 26 Copynumber: 3.8 Consensus size: 25
27948955 GGAAACTCAT
*
27948965 AAGAGCCATAATTAGGAAGTTCACA
1 AAGAGCCATAATTAGGAAGCTCACA
* * *
27948990 AAGAGCTCTTAATCAAGAAGCTCACA
1 AAGAGC-CATAATTAGGAAGCTCACA
*
27949016 AAGAGCCTTTAATTAGG-AGCTC-CA
1 AAGAGCC-ATAATTAGGAAGCTCACA
* *
27949040 GATAGCCATATATTAGGAAG
1 AAGAGCCATA-ATTAGGAAG
27949060 TTCAAGCGAG
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
23 2 0.04
24 13 0.23
25 14 0.25
26 28 0.49
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (25 bp):
AAGAGCCATAATTAGGAAGCTCACA
Found at i:27950950 original size:4 final size:4
Alignment explanation
Indices: 27950941--27951015 Score: 150
Period size: 4 Copynumber: 18.8 Consensus size: 4
27950931 TTTGAGAAGT
27950941 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
27950989 TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGT
27951016 GCTCTCTGTG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 71 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:27951641 original size:50 final size:50
Alignment explanation
Indices: 27951579--27951776 Score: 209
Period size: 50 Copynumber: 4.0 Consensus size: 50
27951569 CCTTTGTAGT
* * * *
27951579 AAATTGTTTGGGAAGCCTTTGTGACGAGTCATCTGGGAAGCCCTTATGGC
1 AAATTGTTTGGGAAACCTTTGTGGCGAGTCATCTGGAAAGCCCTTGTGGC
* * * * *
27951629 AAATTGTTTGGGAAATCTTTATGGTGAGTCATTTGTAAAGCCCTTGTGGC
1 AAATTGTTTGGGAAACCTTTGTGGCGAGTCATCTGGAAAGCCCTTGTGGC
* * * * * * *
27951679 AAATTATTTAGGAAACATTTGT-GCGATTCATCTGTAAAGCCTTTGTGGT
1 AAATTGTTTGGGAAACCTTTGTGGCGAGTCATCTGGAAAGCCCTTGTGGC
* * * *
27951728 GAATTGTTTGGGAAATCTTTGTGGCAAGTCATCTGGAAAGCCTTTGTGG
1 AAATTGTTTGGGAAACCTTTGTGGCGAGTCATCTGGAAAGCCCTTGTGG
27951777 GGAGTCATTT
Statistics
Matches: 120, Mismatches: 27, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
49 39 0.32
50 81 0.68
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (50 bp):
AAATTGTTTGGGAAACCTTTGTGGCGAGTCATCTGGAAAGCCCTTGTGGC
Found at i:27951788 original size:50 final size:50
Alignment explanation
Indices: 27951566--27951791 Score: 186
Period size: 50 Copynumber: 4.5 Consensus size: 50
27951556 AAACCAAACT
* ** * ** * **
27951566 AAGCCTTTGTAGTAAATTGTTTGGGAAGCCTTTGTGACGAGTCATCTGGG
1 AAGCCTTTGTGGCGAATTATTTGGGAAATCTTTGTGGCGAGTCATCTGTA
* * * * * * *
27951616 AAGCCCTTATGGCAAATTGTTTGGGAAATCTTTATGGTGAGTCATTTGTA
1 AAGCCTTTGTGGCGAATTATTTGGGAAATCTTTGTGGCGAGTCATCTGTA
* * * *
27951666 AAGCCCTTGTGGCAAATTATTTAGGAAA-CATTTGT-GCGATTCATCTGTA
1 AAGCCTTTGTGGCGAATTATTTGGGAAATC-TTTGTGGCGAGTCATCTGTA
* * * *
27951715 AAGCCTTTGTGGTGAATTGTTTGGGAAATCTTTGTGGCAAGTCATCTGGA
1 AAGCCTTTGTGGCGAATTATTTGGGAAATCTTTGTGGCGAGTCATCTGTA
* * *
27951765 AAGCCTTTGTGGGGAGTCATTTGGGAA
1 AAGCCTTTGTGGCGAATTATTTGGGAA
27951792 GTTTGTAAGG
Statistics
Matches: 142, Mismatches: 31, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
49 40 0.28
50 102 0.72
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.35
Consensus pattern (50 bp):
AAGCCTTTGTGGCGAATTATTTGGGAAATCTTTGTGGCGAGTCATCTGTA
Found at i:27953524 original size:39 final size:39
Alignment explanation
Indices: 27953365--27953541 Score: 183
Period size: 39 Copynumber: 4.5 Consensus size: 39
27953355 ATTCACTTTT
** * * * **
27953365 AAGCATATATCATATTACACATATAATCACATAAAATTT
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
* * *
27953404 AAGCATATATCACAATACTCATATAATTACATAACTTCC
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
* * * * * * *
27953443 AAGCACATATCGCAATAATGACATAATAACATAGCATTC
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
27953482 AAGCATATATCGCAATACTCATATAATCACATAACATCC
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
* *
27953521 AAGCATATGTTGCAATACTCA
1 AAGCATATATCGCAATACTCA
27953542 AAAACATGTT
Statistics
Matches: 112, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 112 1.00
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (39 bp):
AAGCATATATCGCAATACTCATATAATCACATAACATCC
Found at i:27959612 original size:50 final size:50
Alignment explanation
Indices: 27959537--27959634 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 50
27959527 GTAAACTCTG
*
27959537 CCATTTACTTTAAGTATAAATACCCCACTCATTCCCCATAACAAACATTT
1 CCATTTACTTCAAGTATAAATACCCCACTCATTCCCCATAACAAACATTT
*
27959587 CCATTTACTTCAAGTATAGATACCCCACTCATTCCCCATAACAAACAT
1 CCATTTACTTCAAGTATAAATACCCCACTCATTCCCCATAACAAACAT
27959635 CCTTCATCCC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.36, C:0.32, G:0.03, T:0.30
Consensus pattern (50 bp):
CCATTTACTTCAAGTATAAATACCCCACTCATTCCCCATAACAAACATTT
Found at i:27965192 original size:18 final size:18
Alignment explanation
Indices: 27965169--27965205 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27965159 AAAAATAGAA
27965169 AGACCATTTCCTACTGCT
1 AGACCATTTCCTACTGCT
27965187 AGACCATTTCCTACTGCT
1 AGACCATTTCCTACTGCT
27965205 A
1 A
27965206 TTCTTTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.11, T:0.32
Consensus pattern (18 bp):
AGACCATTTCCTACTGCT
Found at i:27965623 original size:11 final size:11
Alignment explanation
Indices: 27965560--27965623 Score: 51
Period size: 12 Copynumber: 5.7 Consensus size: 11
27965550 GTAAAACAAA
27965560 TTTAATTT--T
1 TTTAATTTCAT
*
27965569 TTTAATTTTAAT
1 TTTAA-TTTCAT
*
27965581 TTTAATTTTAAT
1 TTTAA-TTTCAT
*
27965593 TTTAATTTTAAT
1 TTTAA-TTTCAT
27965605 TTTAATTTCAT
1 TTTAATTTCAT
*
27965616 TTTTATTT
1 TTTAATTT
27965624 TTTCAATAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
9 5 0.10
10 3 0.06
11 12 0.24
12 30 0.60
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTAATTTCAT
Found at i:27965625 original size:6 final size:6
Alignment explanation
Indices: 27965568--27965612 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
27965558 AATTTAATTT
27965568 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT
27965613 CATTTTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:27967829 original size:25 final size:25
Alignment explanation
Indices: 27967795--27967853 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
27967785 GTCATTAGGG
* *
27967795 TTACCGATTCTCAACTCGTCTGAGC
1 TTACCGATTCTCAACTCATATGAGC
* *
27967820 TTACCGATTCTTAGCTCATATGAGC
1 TTACCGATTCTCAACTCATATGAGC
*
27967845 TTATCGATT
1 TTACCGATT
27967854 TACAATTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.37
Consensus pattern (25 bp):
TTACCGATTCTCAACTCATATGAGC
Found at i:27977187 original size:19 final size:19
Alignment explanation
Indices: 27977163--27977199 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
27977153 TAGGTCAAAG
27977163 TGTAATAGTTAATTTAATA
1 TGTAATAGTTAATTTAATA
27977182 TGTAATAGTTAATTTAAT
1 TGTAATAGTTAATTTAAT
27977200 TTGATGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (19 bp):
TGTAATAGTTAATTTAATA
Found at i:27979062 original size:30 final size:30
Alignment explanation
Indices: 27979024--27979139 Score: 94
Period size: 31 Copynumber: 4.2 Consensus size: 30
27979014 TAAAATTTTT
* *
27979024 TATTTTTTTT--ATTTTTTTACTTTTAAAA
1 TATTTTTTTTAAAATTTTTTAATTTTAAAA
27979052 TACTTTTTTTTAAAATTTTTTAATTTTAAAA
1 TA-TTTTTTTTAAAATTTTTTAATTTTAAAA
*
27979083 TA---TTTTTAAAA-----TATTTTTAAAA
1 TATTTTTTTTAAAATTTTTTAATTTTAAAA
* *
27979105 TA-CTTTTTT-AATTTTTTTAATTTTAAAA
1 TATTTTTTTTAAAATTTTTTAATTTTAAAA
27979133 TATTTTT
1 TATTTTT
27979140 AAAATACTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 21
0.72 0.06 0.21
Matches are distributed among these distances:
22 12 0.17
23 2 0.03
24 5 0.07
27 9 0.13
28 14 0.20
29 11 0.15
31 18 0.25
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (30 bp):
TATTTTTTTTAAAATTTTTTAATTTTAAAA
Found at i:27979080 original size:16 final size:17
Alignment explanation
Indices: 27979037--27979091 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
27979027 TTTTTTTATT
*
27979037 TTTTTACTTTTAAAATA
1 TTTTTAATTTTAAAATA
*
27979054 CTTTT--TTTTAAAAT-
1 TTTTTAATTTTAAAATA
27979068 TTTTTAATTTTAAAATA
1 TTTTTAATTTTAAAATA
27979085 TTTTTAA
1 TTTTTAA
27979092 AATATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 4 0.12
15 9 0.27
16 9 0.27
17 11 0.33
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTAATTTTAAAATA
Found at i:27979140 original size:39 final size:39
Alignment explanation
Indices: 27979027--27979160 Score: 146
Period size: 39 Copynumber: 3.4 Consensus size: 39
27979017 AATTTTTTAT
* * *
27979027 TTTTTTTATTTTTTTACTTTTAAAATACTTTTTTTTAAA-A-
1 TTTTTTAATTTTTTTAATTTTAAAATA---TTTTTAAAATAC
** *
27979067 TTTTTTAATTTTAAAATATTTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTT--TTTAATTTTAAAATATTTTTAAAATAC
27979108 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
*
27979147 TTTTTTAAATTTTT
1 TTTTTTAATTTTTT
27979161 AAAATAAATT
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
39 45 0.56
40 12 0.15
41 12 0.15
42 12 0.15
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:27979172 original size:21 final size:21
Alignment explanation
Indices: 27979134--27979173 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27979124 ATTTTAAAAT
**
27979134 ATTTTTAAAATACTTTTTTAA
1 ATTTTTAAAATAAATTTTTAA
27979155 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
27979174 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTAA
Found at i:27980016 original size:22 final size:22
Alignment explanation
Indices: 27979986--27980029 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
27979976 GAAAGTTTCA
* *
27979986 CCTTTGAAGAAAGTATTTTGGT
1 CCTTGGAAGAAAGTACTTTGGT
27980008 CCTTGGAAGAAAGTACTTTGGT
1 CCTTGGAAGAAAGTACTTTGGT
27980030 TTGACAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.36
Consensus pattern (22 bp):
CCTTGGAAGAAAGTACTTTGGT
Found at i:27982154 original size:50 final size:50
Alignment explanation
Indices: 27982099--27982198 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
27982089 ATTTGACCTG
27982099 ATAAGCTTTATCGTTTAATCGACGAATTTACTAAGCTTTATGTAAGCTTA
1 ATAAGCTTTATCGTTTAATCGACGAATTTACTAAGCTTTATGTAAGCTTA
27982149 ATAAGCTTTATCGTTTAATCGACGAATTTACTAAGCTTTATGTAAGCTTA
1 ATAAGCTTTATCGTTTAATCGACGAATTTACTAAGCTTTATGTAAGCTTA
27982199 CTTGTGTTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (50 bp):
ATAAGCTTTATCGTTTAATCGACGAATTTACTAAGCTTTATGTAAGCTTA
Found at i:27992892 original size:20 final size:21
Alignment explanation
Indices: 27992856--27992904 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
27992846 ATTATATTAA
**
27992856 TAAAT-TTAATAATTAAATTG
1 TAAATATTAATAATTAAAAAG
*
27992876 TAAATATTAATCA-TAAAAAG
1 TAAATATTAATAATTAAAAAG
27992896 TAAATATTA
1 TAAATATTA
27992905 TATTAATGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (21 bp):
TAAATATTAATAATTAAAAAG
Found at i:27995240 original size:27 final size:29
Alignment explanation
Indices: 27995209--27995268 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 29
27995199 GCAGGTTTTG
27995209 AATTTTGA-ATTTTGAATTTCGAGTTT-A
1 AATTTTGAGATTTTGAATTTCGAGTTTCA
**
27995236 AA-TTTGAGATTTTGGGTTTCGAGTTTCA
1 AATTTTGAGATTTTGAATTTCGAGTTTCA
27995264 AATTT
1 AATTT
27995269 CGAGTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 5 0.18
27 18 0.64
28 3 0.11
29 2 0.07
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (29 bp):
AATTTTGAGATTTTGAATTTCGAGTTTCA
Found at i:27999205 original size:21 final size:22
Alignment explanation
Indices: 27999169--27999216 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
27999159 TAAAAATAGT
27999169 TTAATTAAAGAATAAATTAAGG-
1 TTAATTAAAGAATAAA-TAAGGA
*
27999191 TTAATT-AAGATTAAATAAGGA
1 TTAATTAAAGAATAAATAAGGA
27999212 TTAAT
1 TTAAT
27999217 ATTAGTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 13 0.54
22 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.35
Consensus pattern (22 bp):
TTAATTAAAGAATAAATAAGGA
Found at i:28000620 original size:20 final size:20
Alignment explanation
Indices: 28000580--28000621 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28000570 TATTTAAATT
*
28000580 TTTTTGAAAATTATTTAGAA
1 TTTTTGAAAATAATTTAGAA
28000600 TTTTTGAAAATCAATTT-GAA
1 TTTTTGAAAAT-AATTTAGAA
28000620 TT
1 TT
28000622 ATTTTGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTTTGAAAATAATTTAGAA
Found at i:28001251 original size:288 final size:287
Alignment explanation
Indices: 28000697--28001265 Score: 766
Period size: 288 Copynumber: 2.0 Consensus size: 287
28000687 TATTTACACT
* * * *
28000697 AATCTGTTATTCGAATTATTCAAGTTAATCAAATTATAAAATTTAACTTGACTCAAACTCAAAAC
1 AATCCGTTATTCAAATTATTCAAGTTAATCAAATTACAAAATTTAACTCGACTCAAACTCAAAAC
** *
28000762 TTGAATTACTTATTCGAGTTTACTCAAATAACTCGATTGGATGAACTCAAAATTCGATTTTTTTT
66 TCAAATTACTTATCCGAGTTTACTCAAATAACTCGATTGGATGAACTCAAAATTCGATTTTTTTT
* **
28000827 CACTTTTTTTTAATCGAATTGAGTTTTTCTCACCCTAGTTGGCATGCCATAGGGTCAAGATATTG
131 CAATTTTTTCGAATCGAATTGAGTTTTTCTCACCCTAGTTGGCATGCCATAGGGTCAAGATATTG
* * * ** * * *
28000892 ATTAGAAATCATCATTTCTCAGGAACTCCGGGTGGTAGATTGTGCATATAAAGTCATCGTTGCTG
196 ATTAGAAACCATCATTTCTCAGGAACCCCAGGTAATAGATTGTACATATAAAGTCATCGTTACTA
*
28000957 TAACACCCCATACATGACCCGGTCGCC
261 TAACACCCCATACACGACCCGGTCGCC
* * * * * * *
28000984 AATCCGTTATTCAAATTA-TCGAGTTATTCGAATTACAAATTTTAACTCGACTCGAATTCGAAAC
1 AATCCGTTATTCAAATTATTCAAGTTAATCAAATTACAAAATTTAACTCGACTCAAACTCAAAAC
* ** * *
28001048 TCAAATTACTTATCCGAGTTTACTTAAATAACTTTATTGGATGAACTCAAATTTTGATTTTTTTT
66 TCAAATTACTTATCCGAGTTTACTCAAATAACTCGATTGGATGAACTCAAAATTCGATTTTTTTT
* * *
28001113 CTAATTTTTTCGAATTGAATTGAGTTTTTCTCACCCCTATTTGGCATGCCATATGGTCAAGATAT
131 C-AATTTTTTCGAATCGAATTGAGTTTTTCTCA-CCCTAGTTGGCATGCCATAGGGTCAAGATAT
*
28001178 TGATTAGAAACCATCAATTT-T-GGGCAACCCCAGGTAATAGATTGTACATATAAAGTCATCGTT
194 TGATTAGAAACCATC-ATTTCTCAGG-AACCCCAGGTAATAGATTGTACATATAAAGTCATCGTT
28001241 ACTATAACACCCCATACACGACCCG
257 ACTATAACACCCCATACACGACCCG
28001266 ATTGTTGGGT
Statistics
Matches: 243, Mismatches: 35, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
286 95 0.39
287 45 0.19
288 99 0.41
289 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (287 bp):
AATCCGTTATTCAAATTATTCAAGTTAATCAAATTACAAAATTTAACTCGACTCAAACTCAAAAC
TCAAATTACTTATCCGAGTTTACTCAAATAACTCGATTGGATGAACTCAAAATTCGATTTTTTTT
CAATTTTTTCGAATCGAATTGAGTTTTTCTCACCCTAGTTGGCATGCCATAGGGTCAAGATATTG
ATTAGAAACCATCATTTCTCAGGAACCCCAGGTAATAGATTGTACATATAAAGTCATCGTTACTA
TAACACCCCATACACGACCCGGTCGCC
Found at i:28002329 original size:14 final size:14
Alignment explanation
Indices: 28002285--28002332 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
28002275 TAGTTATTTG
28002285 TTTATTTTATTGTTTA
1 TTTATTTT-TTG-TTA
*
28002301 TTTA-TTTTAGTTA
1 TTTATTTTTTGTTA
*
28002314 TTTATTTTTTGATA
1 TTTATTTTTTGTTA
28002328 TTTAT
1 TTTAT
28002333 CTCTTTTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 7 0.25
14 14 0.50
15 3 0.11
16 4 0.14
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (14 bp):
TTTATTTTTTGTTA
Found at i:28005624 original size:44 final size:43
Alignment explanation
Indices: 28005552--28005634 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
28005542 AAAATTTTTA
*
28005552 TTTAATCTTTTAAAAAATATAAACTCTTA-AAATGATATTACAT
1 TTTAATCTTATAAAAAATATAAACTCTTATAAAT-ATATTACAT
* **
28005595 TTTAATTCTTATAACAAATATAATTTCTTATAAATATATT
1 TTTAA-TCTTATAAAAAATATAAACTCTTATAAATATATT
28005635 CAAATAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 5 0.15
44 25 0.74
45 4 0.12
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (43 bp):
TTTAATCTTATAAAAAATATAAACTCTTATAAATATATTACAT
Found at i:28006160 original size:20 final size:19
Alignment explanation
Indices: 28006135--28006174 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28006125 TATTAATTTC
28006135 ATTAATAATATAATTGTAAA
1 ATTAATAATA-AATTGTAAA
* *
28006155 ATTAATACTAAATTTTAAA
1 ATTAATAATAAATTGTAAA
28006174 A
1 A
28006175 ACATGAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
ATTAATAATAAATTGTAAA
Found at i:28010638 original size:27 final size:27
Alignment explanation
Indices: 28010601--28010656 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
28010591 TGATACATTC
*
28010601 ATATAACTAAAATAAAAATT-AAATTAT
1 ATATAAATAAAATAAAAATTGAAA-TAT
* *
28010628 ATATAAATAAATTAATAATTGAAATAT
1 ATATAAATAAAATAAAAATTGAAATAT
28010655 AT
1 AT
28010657 TTGAATAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
ATATAAATAAAATAAAAATTGAAATAT
Done.