Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003011.1 Kokia drynarioides strain JFW-HI SEQ_115519, whole genome shotgun sequence
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: 423923
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 46 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:5366 original size:11 final size:11
Alignment explanation
Indices: 5350--5378 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
5340 TGAACATACT
5350 ATAAAATAATC
1 ATAAAATAATC
5361 ATAAAATAATC
1 ATAAAATAATC
5372 ATAAAAT
1 ATAAAAT
5379 TCCTTGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAAATAATC
Found at i:10152 original size:39 final size:40
Alignment explanation
Indices: 9994--10153 Score: 123
Period size: 39 Copynumber: 4.0 Consensus size: 40
9984 GTTATGCTAC
* * * *
9994 GTAATTATCAAGCTGT-GTGCCTAGTAGGCTTTGTGCCGGT
1 GTAATTATCGAGCT-TAGTGCCTAGCAAGCTTCGTGCCGGT
* * **
10034 GTAATTATCG-GTCGT-GTGCCTAGCAAGTTTCGTGTTGGT
1 GTAATTATCGAG-CTTAGTGCCTAGCAAGCTTCGTGCCGGT
* * * * *
10073 GTAATTATC-AGGTTTAGTGCCTAGAAAGCTACATGACGGT
1 GTAATTATCGA-GCTTAGTGCCTAGCAAGCTTCGTGCCGGT
* *
10113 GT-ATTATCGAGCTTAGAGCCTAGCAGGCTTCGTGCCGGT
1 GTAATTATCGAGCTTAGTGCCTAGCAAGCTTCGTGCCGGT
10152 GT
1 GT
10154 GTTGTATTAG
Statistics
Matches: 92, Mismatches: 23, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
39 60 0.65
40 32 0.35
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.33
Consensus pattern (40 bp):
GTAATTATCGAGCTTAGTGCCTAGCAAGCTTCGTGCCGGT
Found at i:11199 original size:21 final size:21
Alignment explanation
Indices: 11175--11222 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
11165 CACACAAGTG
11175 GACACATAG-TCGTGTGGGATA
1 GACACA-AGATCGTGTGGGATA
* *
11196 GACACACGATCGTGTGGGGTA
1 GACACAAGATCGTGTGGGATA
11217 GACACA
1 GACACA
11223 CGACCATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.29, C:0.19, G:0.33, T:0.19
Consensus pattern (21 bp):
GACACAAGATCGTGTGGGATA
Found at i:11223 original size:21 final size:21
Alignment explanation
Indices: 11184--11225 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11174 GGACACATAG
11184 TCGTGTGGGATAGACACACGA
1 TCGTGTGGGATAGACACACGA
*
11205 TCGTGTGGGGTAGACACACGA
1 TCGTGTGGGATAGACACACGA
11226 CCATGTTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (21 bp):
TCGTGTGGGATAGACACACGA
Found at i:31982 original size:52 final size:51
Alignment explanation
Indices: 31902--32192 Score: 300
Period size: 52 Copynumber: 5.6 Consensus size: 51
31892 TAAATGAAAT
* *
31902 AGGTCTGATGACTATGTGTCATCATGAGTATATGAATCTTTTACGAATTATG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACG-ATTATG
*
31954 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTA-CGATTATG
* * * *
32006 AGGT-TCGATGACTATGTGTTATTGTGAGTATAAGAATCCTTTATGTATTATG
1 AGGTCT-GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACG-ATTATG
* *
32058 AGGTC-CAAGAACTATGTGTCATCGTGAGTATATGAATCCTTTACTGATTATG
1 AGGTCTGATG-ACTATGTGTCATCGTGAGTATATGAATCCTTTAC-GATTATG
** * * ** ** *
32110 AGGTCCCATGAATATGTGTCATTGTGAGTATATGGTTCCCAATACGGATTA-A
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAAT-CCTTTAC-GATTATG
* * *
32162 AGGTCCGCTGACTCTGTGTCATCGTGAGTAT
1 AGGTCTGATGACTATGTGTCATCGTGAGTAT
32193 CAAACTCTTG
Statistics
Matches: 204, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
51 4 0.02
52 185 0.91
53 15 0.07
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (51 bp):
AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGATTATG
Found at i:32088 original size:104 final size:104
Alignment explanation
Indices: 31902--32141 Score: 331
Period size: 104 Copynumber: 2.3 Consensus size: 104
31892 TAAATGAAAT
* ** * * * *
31902 AGGTCTGATGACTATGTGTCATCATGAGTATATGAATCTTTTACGAATTATGAGGTCTGATGACT
1 AGGTCCGATGACTATGTGTCATTGTGAGTATAAGAATCCTTTACGAATTATGAGGTCTCAAGACT
31967 ATGTGTCATCGTGAGTATATGAATCCTTTA-TGGATTATG
66 ATGTGTCATCGTGAGTATATGAATCCTTTACT-GATTATG
* * * *
32006 AGGTTCGATGACTATGTGTTATTGTGAGTATAAGAATCCTTTATGTATTATGAGGTC-CAAGAAC
1 AGGTCCGATGACTATGTGTCATTGTGAGTATAAGAATCCTTTACGAATTATGAGGTCTCAAG-AC
32070 TATGTGTCATCGTGAGTATATGAATCCTTTACTGATTATG
65 TATGTGTCATCGTGAGTATATGAATCCTTTACTGATTATG
* *
32110 AGGTCCCATGAATATGTGTCATTGTGAGTATA
1 AGGTCCGATGACTATGTGTCATTGTGAGTATA
32142 TGGTTCCCAA
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
103 2 0.02
104 116 0.97
105 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (104 bp):
AGGTCCGATGACTATGTGTCATTGTGAGTATAAGAATCCTTTACGAATTATGAGGTCTCAAGACT
ATGTGTCATCGTGAGTATATGAATCCTTTACTGATTATG
Found at i:32189 original size:156 final size:156
Alignment explanation
Indices: 31912--32192 Score: 377
Period size: 156 Copynumber: 1.8 Consensus size: 156
31902 AGGTCTGATG
* ** *
31912 ACTATGTGTCATCATGAGTATATGAATCTTTTACGAATTATGAGGTCTGATGACTATGTGTCATC
1 ACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATGAGGTCCCATGAATATGTGTCATC
** * * * * *
31977 GTGAGTATATGAATCCTTTATGGATTATGAGGTTCGATGACTATGTGTTATTGTGAGTATAAGAA
66 GTGAGTATATGAATCCAATACGGATTATAAGGTCCGATGACTATGTGTCATCGTGAGTATAAGAA
32042 TCCTTTATGTATTATGAGGTCCAAGA
131 TCCTTTATGTATTATGAGGTCCAAGA
*
32068 ACTATGTGTCATCGTGAGTATATGAATCCTTTACTG-ATTATGAGGTCCCATGAATATGTGTCAT
1 ACTATGTGTCATCATGAGTATATGAATCCTTTAC-GAATTATGAGGTCCCATGAATATGTGTCAT
* ** * *
32132 TGTGAGTATATGGTTCCCAATACGGATTA-AAGGTCCGCTGACTCTGTGTCATCGTGAGTAT
65 CGTGAGTATATGAAT-CCAATACGGATTATAAGGTCCGATGACTATGTGTCATCGTGAGTAT
32193 CAAACTCTTG
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
156 95 0.90
157 11 0.10
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (156 bp):
ACTATGTGTCATCATGAGTATATGAATCCTTTACGAATTATGAGGTCCCATGAATATGTGTCATC
GTGAGTATATGAATCCAATACGGATTATAAGGTCCGATGACTATGTGTCATCGTGAGTATAAGAA
TCCTTTATGTATTATGAGGTCCAAGA
Found at i:32853 original size:21 final size:21
Alignment explanation
Indices: 32801--32874 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
32791 AGAGTTTTTA
* *
32801 GTATCGGTAGAAGTA-AGACGT
1 GTATCGGTAGAAG-AGACACTT
* * *
32822 GTTTCGATAGAAGAGTCACTT
1 GTATCGGTAGAAGAGACACTT
**
32843 GTATCGGTAGAATTGACACTT
1 GTATCGGTAGAAGAGACACTT
32864 GTATCGGTAGA
1 GTATCGGTAGA
32875 TGTCTGCACT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAGAGACACTT
Found at i:34786 original size:19 final size:18
Alignment explanation
Indices: 34761--34805 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
34751 TATATGTCAG
*
34761 TTTATTTGAGTTATGTTA
1 TTTATTTGAATTATGTTA
* *
34779 TTTGATTTTAATTATGTTC
1 TTT-ATTTGAATTATGTTA
34798 TTTATTTG
1 TTTATTTG
34806 GAAAATCCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.20, C:0.02, G:0.13, T:0.64
Consensus pattern (18 bp):
TTTATTTGAATTATGTTA
Found at i:35238 original size:24 final size:24
Alignment explanation
Indices: 35154--35228 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
35144 AGAAATAATT
* *
35154 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
35178 TTTCAATTAAACTTTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
35202 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
35226 TTT
1 TTT
35229 GAGTCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.11, G:0.08, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:36816 original size:151 final size:152
Alignment explanation
Indices: 36539--36844 Score: 524
Period size: 151 Copynumber: 2.0 Consensus size: 152
36529 TGTGGGCTTA
*
36539 TAATATGAGATCTTAGTTAGTTTGTTCATCCAAGTAATAATGAATTGCAAATGGTTATTTTGAAT
1 TAATATGAGATCTTAGGTAGTTTGTTCATCCAAG--ATAATGAATTGCAAATGGTTATTTTGAAT
*
36604 AGGGTCTATTTGGTTAGGTTTGAAATGATGTGAGTTGAACTTGGTTTGATGCTAGAAGTGTGTTT
64 AGGGTCTATTTGGTTAGGTTTGAAATGATGTGAGTTGAACTTGGTTTCATGCTAGAAGTGTGTTT
*
36669 TGAACCTTAGGAAATTTTCCTCAT
129 TGAACCTTAGGAAATTTGCCTCAT
*
36693 TAATATGAGATCTTAGGTAGTTTGTTCATCTAAG-TAATGAATTGCAAATGGTTATTTTGAATAG
1 TAATATGAGATCTTAGGTAGTTTGTTCATCCAAGATAATGAATTGCAAATGGTTATTTTGAATAG
* * *
36757 GGTCTTTTTGGTTAGGTTTGAAATGATGTGAGTTGAACTTGGTTTCATGCTTGGAGTGTGTTTTG
66 GGTCTATTTGGTTAGGTTTGAAATGATGTGAGTTGAACTTGGTTTCATGCTAGAAGTGTGTTTTG
36822 AACCTTAGGAAATTTGCCTCAT
131 AACCTTAGGAAATTTGCCTCAT
36844 T
1 T
36845 GGTAGAGTAC
Statistics
Matches: 145, Mismatches: 7, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
151 113 0.78
154 32 0.22
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (152 bp):
TAATATGAGATCTTAGGTAGTTTGTTCATCCAAGATAATGAATTGCAAATGGTTATTTTGAATAG
GGTCTATTTGGTTAGGTTTGAAATGATGTGAGTTGAACTTGGTTTCATGCTAGAAGTGTGTTTTG
AACCTTAGGAAATTTGCCTCAT
Found at i:37524 original size:3 final size:3
Alignment explanation
Indices: 37505--37563 Score: 67
Period size: 3 Copynumber: 21.7 Consensus size: 3
37495 TTTAGGGTTT
37505 AAG AAG AA- AA- AAG -AG AAG AA- AAG AAG -AG AAG AAG AAG -AG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
37547 AAG AAG AAG AAT AAG AA
1 AAG AAG AAG AAG AAG AA
37564 AATGGAGATT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
2 12 0.24
3 37 0.76
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:37531 original size:8 final size:8
Alignment explanation
Indices: 37508--37563 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
37498 AGGGTTTAAG
*
37508 AAGAAAAA
1 AAGAAGAA
37516 AGAGAAGAA
1 A-AGAAGAA
*
37525 AAGAAGAG
1 AAGAAGAA
37533 AAGAAGAA
1 AAGAAGAA
*
37541 GAGAAGAA
1 AAGAAGAA
37549 GAAGAAGAA
1 -AAGAAGAA
37558 TAAGAA
1 -AAGAA
37564 AATGGAGATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
8 21 0.52
9 19 0.47
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.02
Consensus pattern (8 bp):
AAGAAGAA
Found at i:37539 original size:11 final size:11
Alignment explanation
Indices: 37515--37563 Score: 62
Period size: 11 Copynumber: 4.2 Consensus size: 11
37505 AAGAAGAAAA
37515 AAGAGAAGAAAAG
1 AAGAGAAG--AAG
37528 AAGAGAAGAAG
1 AAGAGAAGAAG
37539 AAGAGAAGAAG
1 AAGAGAAGAAG
*
37550 AAGAAGAATAAG
1 AAG-AGAAGAAG
37562 AA
1 AA
37564 AATGGAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 17 0.50
12 9 0.26
13 8 0.24
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (11 bp):
AAGAGAAGAAG
Found at i:39473 original size:12 final size:12
Alignment explanation
Indices: 39456--39495 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
39446 TAGGGTATTA
39456 AAAACAACATAC
1 AAAACAACATAC
*
39468 AAAACAAAATA-
1 AAAACAACATAC
39479 AATAACAACATAC
1 AA-AACAACATAC
39492 AAAA
1 AAAA
39496 TAATATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.72, C:0.17, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAACAACATAC
Found at i:39662 original size:15 final size:15
Alignment explanation
Indices: 39642--39672 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39632 TCACAATAAG
39642 CAACATCATCTTGGT
1 CAACATCATCTTGGT
39657 CAACATCATCTTGGT
1 CAACATCATCTTGGT
39672 C
1 C
39673 CTTACTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (15 bp):
CAACATCATCTTGGT
Found at i:41826 original size:46 final size:47
Alignment explanation
Indices: 41770--41873 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 47
41760 AGATAACCAT
*
41770 AAATCAAAATCAAAAATGAAAATC-AATTTAAA-AAACCCTAAATCAA
1 AAATCAAAATCAAAAATG-AAATCAAAATTAAATAAACCCTAAATCAA
* * * * *
41816 AAATGAAAATCAATATTGAAATCAAAATTAAATAAACCCTAAATTAT
1 AAATCAAAATCAAAAATGAAATCAAAATTAAATAAACCCTAAATCAA
*
41863 AAATCACAATC
1 AAATCAAAATC
41874 CCTAAACAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
45 5 0.10
46 22 0.46
47 21 0.44
ACGTcount: A:0.60, C:0.14, G:0.03, T:0.23
Consensus pattern (47 bp):
AAATCAAAATCAAAAATGAAATCAAAATTAAATAAACCCTAAATCAA
Found at i:42879 original size:22 final size:23
Alignment explanation
Indices: 42827--42887 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 23
42817 AAAAAAAATT
* *
42827 AATTTTTAATAATTTTAAAGGAAA
1 AATTTTTAA-ATTTTTAAAGCAAA
*
42851 AA-GTTTAAATTTTTAAA-CAAA
1 AATTTTTAAATTTTTAAAGCAAA
*
42872 AATTTTT-ATTTTTTAA
1 AATTTTTAAATTTTTAA
42888 CTATTTCGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 13 0.42
22 11 0.35
23 5 0.16
24 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (23 bp):
AATTTTTAAATTTTTAAAGCAAA
Found at i:49449 original size:16 final size:16
Alignment explanation
Indices: 49430--49464 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49420 TTTATTCTTA
*
49430 TTTCATCTTTATTTAT
1 TTTCATCTCTATTTAT
*
49446 TTTCATGTCTATTTAT
1 TTTCATCTCTATTTAT
49462 TTT
1 TTT
49465 TATGTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.11, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTCATCTCTATTTAT
Found at i:49476 original size:16 final size:16
Alignment explanation
Indices: 49439--49469 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49429 ATTTCATCTT
49439 TATTTATTTTCATGTC
1 TATTTATTTTCATGTC
*
49455 TATTTATTTTTATGT
1 TATTTATTTTCATGT
49470 TTTTTTACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.68
Consensus pattern (16 bp):
TATTTATTTTCATGTC
Found at i:50459 original size:64 final size:64
Alignment explanation
Indices: 50386--50514 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
50376 AGTTTTAAAT
50386 TAGATAACTTTGGTGAACACATCTTAGTTCAGTTACAAATAAACCAGACACATTTTTTTTAGAG
1 TAGATAACTTTGGTGAACACATCTTAGTTCAGTTACAAATAAACCAGACACATTTTTTTTAGAG
*
50450 TAGATAACTTTGGTGAACACATCTTAGTTCAGTTACAAATAAGCCAGACACATTTTTTTTAGAG
1 TAGATAACTTTGGTGAACACATCTTAGTTCAGTTACAAATAAACCAGACACATTTTTTTTAGAG
50514 T
1 T
50515 TTTTATTTAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (64 bp):
TAGATAACTTTGGTGAACACATCTTAGTTCAGTTACAAATAAACCAGACACATTTTTTTTAGAG
Found at i:53083 original size:29 final size:29
Alignment explanation
Indices: 53051--53135 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
53041 TTATGAAATA
53051 AAATTTTAGCACTAAGCTTTAA-TTTTATT
1 AAATTTTAGCACTAA-CTTTAATTTTTATT
* *
53080 AAATTTT-GTCATTAATTTTAATTTTTTATT
1 AAATTTTAG-CACTAACTTTAA-TTTTTATT
*
53110 AAATTTTATCACTTAA-TATTAATTTT
1 AAATTTTAGCAC-TAACT-TTAATTTT
53136 GATGATTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
28 6 0.13
29 12 0.26
30 21 0.46
31 7 0.15
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (29 bp):
AAATTTTAGCACTAACTTTAATTTTTATT
Found at i:53109 original size:30 final size:31
Alignment explanation
Indices: 53073--53135 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
53063 TAAGCTTTAA
* *
53073 TTTTATTAAATTTTGTCA-TTAATTTTAATT
1 TTTTATTAAATTTTATCACTTAATATTAATT
53103 TTTTATTAAATTTTATCACTTAATATTAATT
1 TTTTATTAAATTTTATCACTTAATATTAATT
53134 TT
1 TT
53136 GATGATTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTATTAAATTTTATCACTTAATATTAATT
Found at i:57114 original size:9 final size:9
Alignment explanation
Indices: 57098--57132 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
57088 TTAAGTGAGA
57098 AATTAATTT
1 AATTAATTT
*
57107 AGTTAATTT
1 AATTAATTT
*
57116 AATTAATTA
1 AATTAATTT
57125 AATTAATT
1 AATTAATT
57133 GATTAAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (9 bp):
AATTAATTT
Found at i:57125 original size:13 final size:13
Alignment explanation
Indices: 57097--57140 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
57087 TTTAAGTGAG
*
57097 AAATTAATTTAGTT
1 AAATTAA-TTAATT
*
57111 AATTTAATTAATT
1 AAATTAATTAATT
*
57124 AAATTAATTGATT
1 AAATTAATTAATT
57137 AAAT
1 AAAT
57141 AGTATTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:63618 original size:18 final size:18
Alignment explanation
Indices: 63595--63649 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
63585 TTACTTAAAC
63595 ATAGAGCTCG-AAAATCAT
1 ATAGAGCTCGCAAAA-CAT
*
63613 ATAGAGTTCGCAAAACAT
1 ATAGAGCTCGCAAAACAT
* *
63631 ACAGGGCTCGCAAAACAT
1 ATAGAGCTCGCAAAACAT
63649 A
1 A
63650 ACACAATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (18 bp):
ATAGAGCTCGCAAAACAT
Found at i:71110 original size:21 final size:20
Alignment explanation
Indices: 71084--71133 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
71074 TCTATGACAG
* *
71084 TTCTACCAATACAAGTGAAGC
1 TTCTACCAA-ACAAATCAAGC
71105 TTCTACCGAAACAAATCAAGC
1 TTCTACC-AAACAAATCAAGC
71126 TTCTACCA
1 TTCTACCA
71134 GTACTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.88
22 2 0.08
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (20 bp):
TTCTACCAAACAAATCAAGC
Found at i:72832 original size:16 final size:16
Alignment explanation
Indices: 72808--72839 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
72798 TCCTTACAAA
*
72808 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
72824 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
72840 AAATATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:85620 original size:24 final size:24
Alignment explanation
Indices: 85588--85644 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
85578 AATCTTTCAG
* *
85588 TTAAACTCTATTTATTTGTTTTAA
1 TTAAACTCTATTTATTTATTTGAA
85612 TTAAACTCTATTTATTTATTTGAA
1 TTAAACTCTATTTATTTATTTGAA
*
85636 TCAAACTCT
1 TTAAACTCT
85645 TATTAGTCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.53
Consensus pattern (24 bp):
TTAAACTCTATTTATTTATTTGAA
Found at i:86549 original size:20 final size:20
Alignment explanation
Indices: 86517--86612 Score: 79
Period size: 20 Copynumber: 4.7 Consensus size: 20
86507 TAAAAATTAC
86517 AAAATAATT-AAAATAATTTT
1 AAAA-AATTCAAAATAATTTT
*
86537 CAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
** * *
86557 GTAAAATTCAAAGT-ATCTAT
1 AAAAAATTCAAAATAAT-TTT
*
86577 AAAAAATTCAAAATTTATATTT
1 AAAAAATTCAAAA-TAAT-TTT
86599 AAAAAATTCTAAAA
1 AAAAAATTC-AAAA
86613 AACATATAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
19 6 0.10
20 37 0.61
21 1 0.02
22 13 0.21
23 4 0.07
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:86619 original size:23 final size:22
Alignment explanation
Indices: 86576--86619 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
86566 AAAGTATCTA
***
86576 TAAAAAATTCAAAATTTATATT
1 TAAAAAATTCAAAAAACATATT
86598 TAAAAAATTCTAAAAAACATAT
1 TAAAAAATTC-AAAAAACATAT
86620 AAAAAGTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAAAAATTCAAAAAACATATT
Found at i:88285 original size:22 final size:27
Alignment explanation
Indices: 88255--88313 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 27
88245 TGCACAACGA
88255 ACGGAGAGCACCAA-A-GTGCT-AAT-
1 ACGGAGAGCACCAATACGTGCTAAATG
88278 A-GGAGAGCA-CAATACGTGCTAAATG
1 ACGGAGAGCACCAATACGTGCTAAATG
88303 ACGGAGAGCAC
1 ACGGAGAGCAC
88314 GCTAGGGTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 3 0.10
22 9 0.30
23 6 0.20
24 3 0.10
25 1 0.03
26 8 0.27
ACGTcount: A:0.39, C:0.20, G:0.29, T:0.12
Consensus pattern (27 bp):
ACGGAGAGCACCAATACGTGCTAAATG
Found at i:101692 original size:21 final size:19
Alignment explanation
Indices: 101642--101684 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
101632 AATGTTCTAC
*
101642 AAATCTATTGGATTTGAGA
1 AAATCTAGTGGATTTGAGA
*
101661 AAATCTAGTGGATTTGGGA
1 AAATCTAGTGGATTTGAGA
101680 AAATC
1 AAATC
101685 CTTAGTGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (19 bp):
AAATCTAGTGGATTTGAGA
Found at i:103303 original size:6 final size:7
Alignment explanation
Indices: 103286--103310 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
103276 AACAGTAATT
103286 TTTTTTC
1 TTTTTTC
103293 TTTTTTC
1 TTTTTTC
103300 TTTTTTC
1 TTTTTTC
103307 TTTT
1 TTTT
103311 GACCAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:108129 original size:44 final size:44
Alignment explanation
Indices: 108063--108154 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
108053 TAATAGCTTC
* * *
108063 AATAAATTTTTTGAGTAATTTAATGATTTAAATAAAAA-TTTTT
1 AATAAATTTTTTGAATAATTTAATAATTTAAATAAAAACTTTTG
* *
108106 AATAAATTTTTTTGAATAGTTTAATAATTTAACTAAAAACTTTTG
1 AATAAA-TTTTTTGAATAATTTAATAATTTAAATAAAAACTTTTG
108151 AATA
1 AATA
108155 GTTCAATGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 6 0.14
44 28 0.67
45 8 0.19
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (44 bp):
AATAAATTTTTTGAATAATTTAATAATTTAAATAAAAACTTTTG
Found at i:110155 original size:24 final size:24
Alignment explanation
Indices: 110123--110170 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
110113 TTTCATTAGT
110123 AAGGATTTTATTTAAAAAGCTAGC
1 AAGGATTTTATTTAAAAAGCTAGC
110147 AAGGATTTTATTTAAAAAGCTAGC
1 AAGGATTTTATTTAAAAAGCTAGC
110171 CAAATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (24 bp):
AAGGATTTTATTTAAAAAGCTAGC
Found at i:120479 original size:3 final size:3
Alignment explanation
Indices: 120473--120499 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
120463 CTTCTTCTTT
120473 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
120500 TTCTTCTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:120904 original size:3 final size:3
Alignment explanation
Indices: 120896--120925 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
120886 GTACAACTAG
*
120896 GAT GAT GAT GAT GAT GAT GAT GGT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
120926 CATCATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:125704 original size:21 final size:20
Alignment explanation
Indices: 125678--125723 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
125668 TACGAAAGGC
*
125678 TTTTAAATGATTCTAAAATGA
1 TTTTAAATGATT-GAAAATGA
* *
125699 TTTTAAGTGCTTGAAAATGA
1 TTTTAAATGATTGAAAATGA
125719 TTTTA
1 TTTTA
125724 GCATATTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (20 bp):
TTTTAAATGATTGAAAATGA
Found at i:128293 original size:26 final size:26
Alignment explanation
Indices: 128264--128393 Score: 136
Period size: 26 Copynumber: 5.0 Consensus size: 26
128254 AAGAGCGTAC
128264 TCTGTCTGGGCTCGTAAGAGCTAAAT
1 TCTGTCTGGGCTCGTAAGAGCTAAAT
*
128290 TCTGTCTGGGCTCATAAGAGC-AATAT
1 TCTGTCTGGGCTCGTAAGAGCTAA-AT
* * * *
128316 TTTTTCTAGGCTCGTAAGAGCTAAAC
1 TCTGTCTGGGCTCGTAAGAGCTAAAT
* *
128342 TCTGTCTTGGCTCGTAAGAGCTAAAAA
1 TCTGTCTGGGCTCGTAAGAGCT-AAAT
* * * *
128369 TATATTTGGGCTCGTATGAGCTAAA
1 TCTGTCTGGGCTCGTAAGAGCTAAA
128394 CTTTTGGAAT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
25 2 0.02
26 62 0.72
27 22 0.26
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (26 bp):
TCTGTCTGGGCTCGTAAGAGCTAAAT
Found at i:131805 original size:26 final size:26
Alignment explanation
Indices: 131763--131896 Score: 171
Period size: 26 Copynumber: 5.1 Consensus size: 26
131753 ATAAAAGCGT
*
131763 ACTCTGTCTGGGCTCGTAAGAGCTAA
1 ACTCTTTCTGGGCTCGTAAGAGCTAA
*
131789 ATTCTTTCTGGGCTCGTAAGAGCTAA
1 ACTCTTTCTGGGCTCGTAAGAGCTAA
*
131815 ACTCTATCTGGGCTCGTAAGAGCTAA
1 ACTCTTTCTGGGCTCGTAAGAGCTAA
* *
131841 ACTCTATT-TGGGCTCGGAAGAGGTAAA
1 ACTCT-TTCTGGGCTCGTAAGAGCT-AA
* * *
131868 AATCTGTCTGGGCTCGTATGAGCTAA
1 ACTCTTTCTGGGCTCGTAAGAGCTAA
131894 ACT
1 ACT
131897 TTTGGAACAG
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
26 72 0.78
27 20 0.22
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (26 bp):
ACTCTTTCTGGGCTCGTAAGAGCTAA
Found at i:131841 original size:52 final size:53
Alignment explanation
Indices: 131763--131896 Score: 191
Period size: 52 Copynumber: 2.5 Consensus size: 53
131753 ATAAAAGCGT
* *
131763 ACTCTGTCTGGGCTCGTAAGAGCTAAATTCT-TTCTGGGCTCGTAAGAGCT-AA
1 ACTCTGTCTGGGCTCGTAAGAGCTAAACTCTATT-TGGGCTCGGAAGAGCTAAA
* *
131815 ACTCTATCTGGGCTCGTAAGAGCTAAACTCTATTTGGGCTCGGAAGAGGTAAA
1 ACTCTGTCTGGGCTCGTAAGAGCTAAACTCTATTTGGGCTCGGAAGAGCTAAA
* *
131868 AATCTGTCTGGGCTCGTATGAGCTAAACT
1 ACTCTGTCTGGGCTCGTAAGAGCTAAACT
131897 TTTGGAACAG
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
52 43 0.59
53 30 0.41
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (53 bp):
ACTCTGTCTGGGCTCGTAAGAGCTAAACTCTATTTGGGCTCGGAAGAGCTAAA
Found at i:134088 original size:24 final size:24
Alignment explanation
Indices: 134054--134144 Score: 137
Period size: 24 Copynumber: 3.8 Consensus size: 24
134044 ACAAAATTAA
*
134054 CTCTTACGAGCCTAAATAGGTTAG
1 CTCTTACGAGCCTAGATAGGTTAG
* *
134078 CTCTTATGAGCCCAGATAGGTTAG
1 CTCTTACGAGCCTAGATAGGTTAG
*
134102 CTCTTACAAGCCTAGATAGGTTAG
1 CTCTTACGAGCCTAGATAGGTTAG
*
134126 CTCTTACGAGCCGAGATAG
1 CTCTTACGAGCCTAGATAG
134145 AGTTTAACCA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
CTCTTACGAGCCTAGATAGGTTAG
Found at i:142166 original size:12 final size:11
Alignment explanation
Indices: 142137--142180 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 11
142127 GCAAAAAAAA
142137 TTTTTCTTCTTT
1 TTTTTC-TCTTT
142149 TCTTTTCTCTTT
1 T-TTTTCTCTTT
142161 CTTTTTCTCATTT
1 -TTTTTCTC-TTT
142174 TTTTTCT
1 TTTTTCT
142181 TTTCAAGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTCTCTTT
Found at i:155500 original size:23 final size:24
Alignment explanation
Indices: 155454--155527 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
155444 AGTTTATCTA
*
155454 AAACAAATAAACTAAATTTAATTG
1 AAACAAATAAACAAAATTTAATTG
* *
155478 AAACAAATAAA-AGAGTTTAATTG
1 AAACAAATAAACAAAATTTAATTG
155501 AAACAAATAAACAAAATTTAATTG
1 AAACAAATAAACAAAATTTAATTG
155525 AAA
1 AAA
155528 GATTATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 20 0.45
24 24 0.55
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.26
Consensus pattern (24 bp):
AAACAAATAAACAAAATTTAATTG
Found at i:163165 original size:60 final size:61
Alignment explanation
Indices: 163040--163167 Score: 179
Period size: 61 Copynumber: 2.1 Consensus size: 61
163030 GGATTCAAAA
* *
163040 TTTTTTTAACTTTTAAAGGCTAAAATAATATTTTACCAACTTTTAAGAGGTTCAAATTTTT
1 TTTTTTTAACTTTTAAAGGCCAAAATAATATTTTACCAACTTTTAAGAGGATCAAATTTTT
* * * *
163101 TTTTTTTAGCTTTTAAGGGCCCAAA-AATAATTTTACCAACTTTTAAG-GGATCTAATTTTT
1 TTTTTTTAACTTTTAAAGGCCAAAATAAT-ATTTTACCAACTTTTAAGAGGATCAAATTTTT
163161 TTTTTTT
1 TTTTTTT
163168 CCAATTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
60 21 0.35
61 39 0.65
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.49
Consensus pattern (61 bp):
TTTTTTTAACTTTTAAAGGCCAAAATAATATTTTACCAACTTTTAAGAGGATCAAATTTTT
Found at i:166167 original size:47 final size:47
Alignment explanation
Indices: 166116--166222 Score: 187
Period size: 47 Copynumber: 2.3 Consensus size: 47
166106 TTTATACATT
* *
166116 TTAATTTTGCCCAGTAATTTATTCGTACTTACAATTTGGTCCTTTAC
1 TTAATTTTGCCCAGTAATTTATCCGCACTTACAATTTGGTCCTTTAC
*
166163 TTAATTTTGCCCAGTAATTTATCCGCACTTACAATTTGGTCCTTTAT
1 TTAATTTTGCCCAGTAATTTATCCGCACTTACAATTTGGTCCTTTAC
166210 TTAATTTTGCCCA
1 TTAATTTTGCCCA
166223 TTTATTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (47 bp):
TTAATTTTGCCCAGTAATTTATCCGCACTTACAATTTGGTCCTTTAC
Found at i:166333 original size:11 final size:12
Alignment explanation
Indices: 166317--166345 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
166307 TTTCTTTTAG
166317 TATTTAA-TTTT
1 TATTTAATTTTT
166328 TATTTAATTTTT
1 TATTTAATTTTT
166340 TATTTA
1 TATTTA
166346 TTGTATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTAATTTTT
Found at i:166519 original size:36 final size:36
Alignment explanation
Indices: 166450--166519 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
166440 TATCTTTGAC
* *
166450 TTTATTTAATTTTATTCGTTCATTATTTTTTTTCTT
1 TTTATTTAATTATATTCGTTCATTATTTATTTTCTT
166486 TTTATTTAATTATATT-GATTCAATTA-TTATTTTC
1 TTTATTTAATTATATTCG-TTC-ATTATTTATTTTC
166520 CATGATTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 1 0.03
36 25 0.83
37 4 0.13
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (36 bp):
TTTATTTAATTATATTCGTTCATTATTTATTTTCTT
Found at i:166662 original size:22 final size:22
Alignment explanation
Indices: 166637--166685 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
166627 TTTTATAGTG
*
166637 TTATT-AATTGTATTCATTTATT
1 TTATTCAATT-TATGCATTTATT
* *
166659 TTATTCTATTTATGCATTTTTT
1 TTATTCAATTTATGCATTTATT
166681 TTATT
1 TTATT
166686 TTTCTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.67
Consensus pattern (22 bp):
TTATTCAATTTATGCATTTATT
Found at i:169834 original size:58 final size:58
Alignment explanation
Indices: 169763--169878 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
169753 AGAATGAACC
169763 TTGGAGACAAGTGATAGGCAACTTCGACACTCTTAGAGGCAAGTCAGAGATCGAGACT
1 TTGGAGACAAGTGATAGGCAACTTCGACACTCTTAGAGGCAAGTCAGAGATCGAGACT
*
169821 TTGGAGACTAGTGATAGGCAACTTCGACACTCTTAGAGGCAAGTCAGAGATCGAGACT
1 TTGGAGACAAGTGATAGGCAACTTCGACACTCTTAGAGGCAAGTCAGAGATCGAGACT
169879 ATGTCATGGG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.22
Consensus pattern (58 bp):
TTGGAGACAAGTGATAGGCAACTTCGACACTCTTAGAGGCAAGTCAGAGATCGAGACT
Found at i:171851 original size:21 final size:21
Alignment explanation
Indices: 171808--171858 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
171798 GCACTAGTTT
**
171808 TACCGATACAAGTAAGATTTC
1 TACCGATACAAGTAAGACATC
* *
171829 TACCGATACAAGTTATACATC
1 TACCGATACAAGTAAGACATC
*
171850 TACTGATAC
1 TACCGATAC
171859 CAAAAACTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (21 bp):
TACCGATACAAGTAAGACATC
Found at i:195940 original size:17 final size:17
Alignment explanation
Indices: 195918--195952 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
195908 ATCCAAGTGC
195918 TTCCATTTGTTAAACAA
1 TTCCATTTGTTAAACAA
195935 TTCCATTTGTTAAACAA
1 TTCCATTTGTTAAACAA
195952 T
1 T
195953 GATAAGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (17 bp):
TTCCATTTGTTAAACAA
Found at i:199418 original size:48 final size:48
Alignment explanation
Indices: 199339--199932 Score: 655
Period size: 48 Copynumber: 12.5 Consensus size: 48
199329 TGAAATGGAG
**
199339 TGAAGCTACCACATATAATCTTATACCCCTAAATCCAGAGGGGCAAAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGGCAAAT
* * * * * *
199387 TAAAGCCACCACATCCAATCATATACACCTAAATCCAGAGAGGCAGAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGGCAAAT
* * ** *
199435 TAAAGCTACCACATCAAATCTTATACTTCTAAATCCAGAGGGGCATAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGGCAAAT
* * * *
199483 TGAAGCTACCACATTCAATCTTATACCACTAAATCCAAAGGGATG-GAA-
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGG--GCAAAT
* * * * * *
199531 TGAAGCTCCCAAATCTAATCTTTTACCCCTAAATCCAGAGGGGTAGAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGGCAAAT
* * * *
199579 TAAAGCTACCACATCCAATCATATACCCCTAAATCTAGAGGGACAAAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGGCAAAT
* * * * * *
199627 TAAAGCTACGACATCCAA-CTTAAACCCCTAAATCCAAAAGGGCAGAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGGCAAAT
* * * *
199674 TGAAGCTACCACATCTAA-CTTATACCCCAAAATCTAG-GGAGGCGAAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGG-GGCAAAT
* * *
199721 TAAAGCTACCACAT-CAATCTTATACCCCTAAATCCAAAGGGGCAGAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGGCAAAT
* * * *
199768 TGAAGCTACCATATCCAATCTTATACCCCCAAATCCAAAGGGGCAGAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGGCAAAT
* **
199816 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCA-AAGCACAAAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGGCAAAT
* * *
199863 TGAAGCTACCACATCCAATCTTCTA-CACTAAATCTAGAGGGGCAAAT
1 TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGGCAAAT
199910 TGAAGCTACCACATCCAATCTTA
1 TGAAGCTACCACATCCAATCTTA
199933 AATCCAAAGA
Statistics
Matches: 454, Mismatches: 83, Indels: 19
0.82 0.15 0.03
Matches are distributed among these distances:
46 13 0.03
47 163 0.36
48 276 0.61
49 1 0.00
50 1 0.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (48 bp):
TGAAGCTACCACATCCAATCTTATACCCCTAAATCCAGAGGGGCAAAT
Found at i:202955 original size:28 final size:27
Alignment explanation
Indices: 202911--202964 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
202901 AGCAAGTAGC
* *
202911 AACGATAGTAAACACAACAACAATAAA
1 AACGATAGTAAAAACAACAAAAATAAA
*
202938 AACGGTAGATAAAAACAACAAAAATAA
1 AACGATAG-TAAAAACAACAAAAATAA
202965 TAAGGAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.65, C:0.15, G:0.09, T:0.11
Consensus pattern (27 bp):
AACGATAGTAAAAACAACAAAAATAAA
Found at i:207895 original size:36 final size:37
Alignment explanation
Indices: 207850--207920 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
207840 TATCTTTGCC
* ** *
207850 TTTATTTAATTTTATTTTTTC-ATTATTTTTTTCCTT
1 TTTATTTAATTATATTGATTCAATTATTATTTTCCTT
207886 TTTATTTAATTATATTGATTCAATTATTATTTTCC
1 TTTATTTAATTATATTGATTCAATTATTATTTTCC
207921 ATTATTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 18 0.60
37 12 0.40
ACGTcount: A:0.23, C:0.08, G:0.01, T:0.68
Consensus pattern (37 bp):
TTTATTTAATTATATTGATTCAATTATTATTTTCCTT
Found at i:213265 original size:21 final size:22
Alignment explanation
Indices: 213230--213272 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
213220 TCTTTGAAGT
213230 TTTTGGTATCGGTAGAAGTAAG
1 TTTTGGTATCGGTAGAAGTAAG
*
213252 TTTT-GTATCTGTAGAAGTAAG
1 TTTTGGTATCGGTAGAAGTAAG
213273 AGTTGTTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.40
Consensus pattern (22 bp):
TTTTGGTATCGGTAGAAGTAAG
Found at i:213278 original size:21 final size:21
Alignment explanation
Indices: 213235--213288 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
213225 GAAGTTTTTG
**
213235 GTATCGGTAGAAGTAAGTTTT
1 GTATCGGTAGAAGTAAGAGTT
*
213256 GTATCTGTAGAAGTAAGAGTT
1 GTATCGGTAGAAGTAAGAGTT
*
213277 GTTTCGGTAGAA
1 GTATCGGTAGAA
213289 CCGTCACATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAGTAAGAGTT
Found at i:216913 original size:137 final size:138
Alignment explanation
Indices: 216603--216918 Score: 456
Period size: 138 Copynumber: 2.3 Consensus size: 138
216593 TGAGAAAATT
* * *
216603 AATATAATTAATATATGTATTTGATTCATACAAAATATTAAGTCTATATATATTACTGAAATTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAAGTCAATATATATTACCGAAATTAT
* * * *
216668 TAATTTAAATAGTTATAACATTTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTT
66 TAATATAAATAGTTATAACAATTAATTTCGATCAAAATATAAAAGAAATAGAAATTAATATTCTT
216733 TTAGAAAG
131 TTAGAAAG
* * * * * *
216741 AATATACTTAATATATGAATTTGATTCACACAAAATATTAATTGAATATA-ATTTACCGAATTTG
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAAGTCAATATATA-TTACCGAAATTA
** *
216805 TTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAA-AAATAGAAATTAATATTCT
65 TTAATATAAATAGTTATAACAATTAATTTCGATCAAAATATAAAAGAAATAGAAATTAATATTCT
*
216869 TTTGGAAAG
130 TTTAGAAAG
216878 AATATAATTAATATATGAATTTGATTCATACAAAATATTAA
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAA
216919 CTGTAAACTG
Statistics
Matches: 158, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
137 65 0.41
138 93 0.59
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (138 bp):
AATATAATTAATATATGAATTTGATTCATACAAAATATTAAGTCAATATATATTACCGAAATTAT
TAATATAAATAGTTATAACAATTAATTTCGATCAAAATATAAAAGAAATAGAAATTAATATTCTT
TTAGAAAG
Found at i:218849 original size:48 final size:48
Alignment explanation
Indices: 218797--218889 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
218787 TTATTGAGCT
** *
218797 TCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGA
1 TCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGATGA
* *
218845 TCGCTTCATTGATTTAATCCACTTCTTTGTATCTCATTAGGAAGA
1 TCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGA
218890 CGGATTTGGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (48 bp):
TCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGATGA
Found at i:218961 original size:85 final size:85
Alignment explanation
Indices: 218807--218966 Score: 241
Period size: 85 Copynumber: 1.9 Consensus size: 85
218797 TCGCTTCATT
* *
218807 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTT
1 GATTTGGGCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTGAATCCACTTCTT
218872 TGTATCTCATTAGGAAGACG
66 TGTATCTCATTAGGAAGACG
* * * * *
218892 GATTTGGGCTATTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTGGATCCTCTT-TT
1 GATTTGGGCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTGAATCCACTTCTT
218956 ATGTATCTCAT
66 -TGTATCTCAT
218967 CACAAAGATG
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
84 2 0.03
85 65 0.97
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.41
Consensus pattern (85 bp):
GATTTGGGCTACTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTGAATCCACTTCTT
TGTATCTCATTAGGAAGACG
Found at i:219066 original size:208 final size:206
Alignment explanation
Indices: 218693--219881 Score: 1323
Period size: 208 Copynumber: 5.7 Consensus size: 206
218683 TTCTTGGTCT
* * * *
218693 ACTTCTCTGTATCTTATCAGGAAGATGATCGCTTTATTACTTCTACCCATTTCTCTGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCC--TTCTCTGTATCTCAT
* * *
218758 TAGGAAGATAGGGGTTTGAAGTCTCATTCTTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCT
64 CAGGAAGAT-GGGGTTTGAAGTCTCACTCATATTGAGCTTCGCTTCATTGATTTGGTCTACTTCT
* * * *
218823 CTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCTTTGTATCTCATTAGGAA
128 CTATATCTCATCAGGAAGATGATCGCCTCATTGTTTTAATCCACTTCTTTGTATCTCATCAGGAA
*
218888 GACGGATTTGGGCT-
193 GACAGATTT-GGCTC
* * * * *
218902 ATTTCTCTGTATCTCATCAGGAAGATGATCGCTTTATTGCTTGGATCCTCTTTTATGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGA-CC-CTTCTCTGTATCTCAT
** * * **
218967 CACAAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCATTTCATTGATTTGGTCTACTTCTC
64 CAGGAAGATGGGGTTTGAAGTCTCACTCATATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTC
* * * * * *
219032 TATATCTCATTAGGAAGATAACCGCCTAATTGATTTAATCCACTTCCTTGTATCTCATCAGGAAG
129 TATATCTCATCAGGAAGATGATCGCCTCATTGTTTTAATCCACTTCTTTGTATCTCATCAGGAAG
* *
219097 GCGGATTTGG-TC
194 ACAGATTTGGCTC
* * * *
219109 TACTTCTCTGTATCTCATCAAGAAGATGACCGTTTTATTACTTTGACCCACTTCTCTGTATCTCA
1 -ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGA-CC-CTTCTCTGTATCTCA
*
219174 TCAGGAAGATGGGGTTTGAAGTTTCACTCATATTGAGCTTCGCTTCATTGATTTGGTCTACTTCT
63 TCAGGAAGATGGGGTTTGAAGTCTCACTCATATTGAGCTTCGCTTCATTGATTTGGTCTACTTCT
* * * * *
219239 -TAGTATCTCATTAGGAAGATAATCACCTCATTGTTTTAATCCACTTCTTTATATCTCATCAGAA
128 CTA-TATCTCATCAGGAAGATGATCGCCTCATTGTTTTAATCCACTTCTTTGTATCTCATCAGGA
*
219303 AGACAGATTTGGTTC
192 AGACAGATTTGGCTC
* * * **
219318 ACTTCTCTATATCTCATCAGGAAGGTGACCGTTTTATTGCTTTAACCCACTTCTC--TATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGA-CC-CTTCTCTGTATCTCAT
* * * * * *
219381 CAGGAAGATAGGGTTTGAAGTTTCACTCACATTAAGCTTTGCTTCATTTATTTGGTCTACTTCTC
64 CAGGAAGATGGGGTTTGAAGTCTCACTCATATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTC
* * *
219446 -AGTATCTCATCAGGAAGATGATCACCTCATTGTTTTAATTCACTTCTCTGTATCTCATCAGGAA
129 TA-TATCTCATCAGGAAGATGATCGCCTCATTGTTTTAATCCACTTCTTTGTATCTCATCAGGAA
* **
219510 GATAGATTTGATTC
193 GACAGATTTGGCTC
* *** * * * * * *
219524 ACTTTTCTACGTCCCGTCAAGAAGATGACCACTTTATTTCTTCAACCCACTTCTCTGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGA-CC-CTTCTCTGTATCTCAT
* * * *
219589 CAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTAATTTGGTCTACTTCTC
64 CAGGAAGATGGGGTTTGAAGTCTCACTCATATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTC
* * * * *
219654 TGTATCTCATCAAGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGTATCTCATCAAGAAG
129 TATATCTCATCAGGAAGATGATCGCCTCATTGTTTTAATCCACTTCTTTGTATCTCATCAGGAAG
*
219719 ACAGATTTGGTTC
194 ACAGATTTGGCTC
** * * * * *
219732 ACTTCTCTGCGTCTCGTCAGGAAGATGACCGTTTTATTGCTTTGACCTACTTCTCTTTATCTTAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACC--CTTCTCTGTATCTCAT
* * * * *
219797 CAGGAAGATGGGGATTGAAGTTTCACTCACATTGAGC-TCTACTTCATTGA-TTGATCTACTTCT
64 CAGGAAGATGGGGTTTGAAGTCTCACTCATATTGAGCTTC-GCTTCATTGATTTGGTCTACTTCT
* *
219860 CTGTATCTCATCAAGAAGATGA
128 CTATATCTCATCAGGAAGATGA
219882 CCACTTCTTT
Statistics
Matches: 854, Mismatches: 114, Indels: 26
0.86 0.11 0.03
Matches are distributed among these distances:
206 182 0.21
207 42 0.05
208 566 0.66
209 61 0.07
210 2 0.00
211 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.39
Consensus pattern (206 bp):
ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCCTTCTCTGTATCTCATCA
GGAAGATGGGGTTTGAAGTCTCACTCATATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTA
TATCTCATCAGGAAGATGATCGCCTCATTGTTTTAATCCACTTCTTTGTATCTCATCAGGAAGAC
AGATTTGGCTC
Found at i:219160 original size:85 final size:85
Alignment explanation
Indices: 219015--219181 Score: 221
Period size: 85 Copynumber: 2.0 Consensus size: 85
219005 TCATTTCATT
* * *
219015 GATTTGGTCTACTTCTCTATATCTCATTAGGAAGATAACCGCCTAATTGATTTAATCCACTTC-C
1 GATTTGGTCTACTTCTCTATATCTCATCAAGAAGATAACCGCCTAATTGATTTAACCCACTTCTC
219079 TTGTATCTCATCAGGAAGGCG
66 -TGTATCTCATCAGGAAGGCG
* * ** * *
219100 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGTTTTATT-ACTTTGACCCACTTCT
1 GATTTGGTCTACTTCTCTATATCTCATCAAGAAGATAACCGCCTAATTGA-TTTAACCCACTTCT
219164 CTGTATCTCATCAGGAAG
65 CTGTATCTCATCAGGAAG
219182 ATGGGGTTTG
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
84 1 0.01
85 69 0.97
86 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (85 bp):
GATTTGGTCTACTTCTCTATATCTCATCAAGAAGATAACCGCCTAATTGATTTAACCCACTTCTC
TGTATCTCATCAGGAAGGCG
Found at i:219784 original size:85 final size:85
Alignment explanation
Indices: 219638--219804 Score: 194
Period size: 85 Copynumber: 2.0 Consensus size: 85
219628 CGCTTCATTA
* *
219638 ATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCT
1 ATTTGGTCTACTTCTCTGCATCTCATCAAGAAGATGACCGCCTCATTGCTTTAATCCACTTCTCT
219703 GTATCTCATCAAGAAGACAG
66 GTATCTCATCAAGAAGACAG
* * * ** * *
219723 ATTTGGT-TCACTTCTCTGCGTCTCGTCAGGAAGATGACCGTTTTATTGCTTTGA-CCTACTTCT
1 ATTTGGTCT-ACTTCTCTGCATCTCATCAAGAAGATGACCGCCTCATTGCTTTAATCC-ACTTCT
* * *
219786 CTTTATCTTATCAGGAAGA
64 CTGTATCTCATCAAGAAGA
219805 TGGGGATTGA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
84 3 0.04
85 65 0.96
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (85 bp):
ATTTGGTCTACTTCTCTGCATCTCATCAAGAAGATGACCGCCTCATTGCTTTAATCCACTTCTCT
GTATCTCATCAAGAAGACAG
Found at i:220154 original size:85 final size:85
Alignment explanation
Indices: 220049--220204 Score: 231
Period size: 85 Copynumber: 1.8 Consensus size: 85
220039 TGATCTACAT
* * * * **
220049 CTCTGTATCTCATCAGGAAGATGATCACTTCATTGTTTTAATTCACTTCTCTGTATCTCATCAGG
1 CTCTGCATCTCATCAGGAAGATGACCACTTCATTATTTCAACCCACTTCTCTGTATCTCATCAGG
220114 AAGATGAATTTGGTTCACTC
66 AAGATGAATTTGGTTCACTC
* * *
220134 CTCTGCATCTCGTCAGGAAGATGACCACTTTATTATTTCGACCCACTTCTCTGTATCTCATCAGG
1 CTCTGCATCTCATCAGGAAGATGACCACTTCATTATTTCAACCCACTTCTCTGTATCTCATCAGG
220199 AAGATG
66 AAGATG
220205 GGGGTTTGAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 62 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (85 bp):
CTCTGCATCTCATCAGGAAGATGACCACTTCATTATTTCAACCCACTTCTCTGTATCTCATCAGG
AAGATGAATTTGGTTCACTC
Found at i:220279 original size:42 final size:43
Alignment explanation
Indices: 220231--220374 Score: 148
Period size: 42 Copynumber: 3.3 Consensus size: 43
220221 CTTTTGACTA
* * *
220231 GGGGTAAAAGATCGAAAT-ATGGCTACAATCTACCTCATGATC
1 GGGGTAAGAGATTGAAATGATGGCTACAATCTACCCCATGATC
* * ** * *
220273 GGGGTAAGAGATTG-GATGGTGGCTGTAATTTGCCCCATGATC
1 GGGGTAAGAGATTGAAATGATGGCTACAATCTACCCCATGATC
*
220315 GGGGTAAGAGATTGAATGATGATGGCTACAATCTACCCCATGATTA
1 GGGGTAAGAGATTGAA--ATGATGGCTACAATCTACCCCATGA-TC
*
220361 AGGGTAAGAGATTG
1 GGGGTAAGAGATTG
220375 GTGTGTCTTA
Statistics
Matches: 80, Mismatches: 17, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
41 2 0.03
42 44 0.55
45 20 0.25
46 14 0.17
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.26
Consensus pattern (43 bp):
GGGGTAAGAGATTGAAATGATGGCTACAATCTACCCCATGATC
Found at i:220757 original size:49 final size:49
Alignment explanation
Indices: 220704--220954 Score: 197
Period size: 49 Copynumber: 5.1 Consensus size: 49
220694 TAAGGTACTA
* * * *
220704 GGTTCGTCTTTACGACCTCAACCTTTTCCTTCAACTCTTCATGGTACCG
1 GGTTCGCCGTTACGGCCTCAACCTTTCCCTTCAACTCTTCATGGTACCG
* * * *
220753 GGTTCACCGTTACGGCCTGAACCTTTCCCATC-ACAT-TTCATGGAACCG
1 GGTTCGCCGTTACGGCCTCAACCTTTCCCTTCAAC-TCTTCATGGTACCG
* * * * * * * **
220801 GATTCGCCATTGCGGTCTCAATCC-TCCCCATC-ACATCTTCTAAGGTACTA
1 GGTTCGCCGTTACGGCCTCAA-CCTTTCCCTTCAAC-TCTTC-ATGGTACCG
* * ** * *
220851 TGTTCGTCGTTGTGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATCG
1 GGTTCGCCGTTACGGCCTCAACCTTTCCCTTCAACTCTTCATGGTACCG
* *
220900 GGTTCGCCGTTACGGCCTCAACCTTTCCCTTCATA-TCTTCATGGTATCA
1 GGTTCGCCGTTACGGCCTCAACCTTTCCCTTCA-ACTCTTCATGGTACCG
220949 GGTTCG
1 GGTTCG
220955 TTTCGCCATT
Statistics
Matches: 158, Mismatches: 37, Indels: 14
0.76 0.18 0.07
Matches are distributed among these distances:
48 39 0.25
49 86 0.54
50 32 0.20
51 1 0.01
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (49 bp):
GGTTCGCCGTTACGGCCTCAACCTTTCCCTTCAACTCTTCATGGTACCG
Found at i:221911 original size:7 final size:7
Alignment explanation
Indices: 221901--221925 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
221891 TTTTTCTATT
221901 TTTTTCC
1 TTTTTCC
221908 TTTTTCC
1 TTTTTCC
221915 TTTTTCC
1 TTTTTCC
221922 TTTT
1 TTTT
221926 CTTCTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCC
Found at i:221937 original size:27 final size:27
Alignment explanation
Indices: 221875--221937 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
221865 TCACCTCAAC
*
221875 CTTTTCTTTTTCCTATTTTTTCTATTTT
1 CTTTTCTTTTTCC-ATTTTTCCTATTTT
* *
221903 -TTTCCTTTTTCC-TTTTTCCTTTTCTT
1 CTTTTCTTTTTCCATTTTTCCTATT-TT
221929 CTTTTCTTT
1 CTTTTCTTT
221938 CTTATTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 9 0.31
26 2 0.07
27 18 0.62
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (27 bp):
CTTTTCTTTTTCCATTTTTCCTATTTT
Found at i:226339 original size:18 final size:18
Alignment explanation
Indices: 226316--226377 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
226306 GACTCGACTT
226316 TTAAAATCATTTAATTTG
1 TTAAAATCATTTAATTTG
* * *
226334 TTAAAACCCTAATATATCTT-
1 TTAAAATCAT-TTA-AT-TTG
226354 TTAAAATCATTTAATTTG
1 TTAAAATCATTTAATTTG
226372 TTAAAA
1 TTAAAA
226378 CCCTAATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 2 0.06
18 16 0.47
19 4 0.12
20 10 0.29
21 2 0.06
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (18 bp):
TTAAAATCATTTAATTTG
Found at i:226356 original size:38 final size:38
Alignment explanation
Indices: 226313--226397 Score: 170
Period size: 38 Copynumber: 2.2 Consensus size: 38
226303 TAAGACTCGA
226313 CTTTTAAAATCATTTAATTTGTTAAAACCCTAATATAT
1 CTTTTAAAATCATTTAATTTGTTAAAACCCTAATATAT
226351 CTTTTAAAATCATTTAATTTGTTAAAACCCTAATATAT
1 CTTTTAAAATCATTTAATTTGTTAAAACCCTAATATAT
226389 CTTTTAAAA
1 CTTTTAAAA
226398 AAAGAATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (38 bp):
CTTTTAAAATCATTTAATTTGTTAAAACCCTAATATAT
Found at i:226359 original size:20 final size:20
Alignment explanation
Indices: 226334--226397 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
226324 ATTTAATTTG
226334 TTAAAACCCTAATATATCTT
1 TTAAAACCCTAATATATCTT
* * *
226354 TTAAAATCAT-TTA-AT-TT
1 TTAAAACCCTAATATATCTT
226371 GTTAAAACCCTAATATATCTT
1 -TTAAAACCCTAATATATCTT
226392 TTAAAA
1 TTAAAA
226398 AAAGAATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 2 0.06
18 10 0.29
19 4 0.12
20 16 0.47
21 2 0.06
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (20 bp):
TTAAAACCCTAATATATCTT
Found at i:228045 original size:22 final size:24
Alignment explanation
Indices: 228002--228051 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
227992 CAAATTATTA
*
228002 CTTTTTGGTTTTTTTTTGCTTG-T
1 CTTTTTGGTTTTTTGTTGCTTGCT
228025 CTTTTT-G-TTTTTGTTGCCTTGCT
1 CTTTTTGGTTTTTTGTTG-CTTGCT
228048 CTTT
1 CTTT
228052 GTCGTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 8 0.33
22 5 0.21
23 11 0.46
ACGTcount: A:0.00, C:0.14, G:0.16, T:0.70
Consensus pattern (24 bp):
CTTTTTGGTTTTTTGTTGCTTGCT
Found at i:228052 original size:21 final size:21
Alignment explanation
Indices: 228011--228053 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
228001 ACTTTTTGGT
* *
228011 TTTTTTTTGCTTGTCTTTTTG
1 TTTTTGTTGCTTGTCTCTTTG
228032 TTTTTGTTGCCTTG-CTCTTTG
1 TTTTTGTTG-CTTGTCTCTTTG
228053 T
1 T
228054 CGTTTTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.00, C:0.14, G:0.16, T:0.70
Consensus pattern (21 bp):
TTTTTGTTGCTTGTCTCTTTG
Found at i:228618 original size:138 final size:137
Alignment explanation
Indices: 228364--228743 Score: 526
Period size: 138 Copynumber: 2.8 Consensus size: 137
228354 GGGCTCCAAC
* * *
228364 ATATATATTTTACCGAATTTGTTAATATAAATAGTTATATTAATTAATTTCGATCAAAATATAAA
1 ATATATATTTTACCGAATTTATTAATATAAAAAGTTATATTAATTAATTTCAATCAAAATATAAA
* * * *
228429 AGACATTGAAAGTAATATTGTTCTAGAAAGAATAAAATTAATATATAAATTTGATTCATAAAAAA
66 AGACA-TGAAATTAATATTCTTTTAGAAAGAATATAATTAATATATAAATTTGATTCATAAAAAA
228494 TATTAATT
130 TATTAATT
* * ** * *
228502 ATATTTATTTTACCAAATTTATTAATATAAAAAAATATACTAATTAATTTCAATCAAAATGTAAA
1 ATATATATTTTACCGAATTTATTAATATAAAAAGTTATATTAATTAATTTCAATCAAAATATAAA
* * * *
228567 AGACATGAAAATTAATATTCTTTTAAAAAGAATATAATTAATATATGAATTTTATTCATACAAAA
66 AGACATG-AAATTAATATTCTTTTAGAAAGAATATAATTAATATATAAATTTGATTCATAAAAAA
228632 TATTAATT
130 TATTAATT
* * * *
228640 GTATATATTTTACCGAATTTATTAATATAGACAGTTATATTAATTAATTTCAATCAAGATATAAA
1 ATATATATTTTACCGAATTTATTAATATAAAAAGTTATATTAATTAATTTCAATCAAAATATAAA
* *
228705 AGACATGGAAATTAATGTTCTTTTGGAAAGAATATAATT
66 AGACAT-GAAATTAATATTCTTTTAGAAAGAATATAATT
228744 CCTTTTTCTA
Statistics
Matches: 210, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
137 2 0.01
138 207 0.99
139 1 0.00
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.39
Consensus pattern (137 bp):
ATATATATTTTACCGAATTTATTAATATAAAAAGTTATATTAATTAATTTCAATCAAAATATAAA
AGACATGAAATTAATATTCTTTTAGAAAGAATATAATTAATATATAAATTTGATTCATAAAAAAT
ATTAATT
Found at i:232237 original size:30 final size:30
Alignment explanation
Indices: 232197--232260 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
232187 AAATTGATTA
* *
232197 TTTTATTTCGTATTATTTATAACTTTTATT
1 TTTTAATTCGTATTATATATAACTTTTATT
* *
232227 TTTTAATTCGTATTGTATCTAACTTTTATT
1 TTTTAATTCGTATTATATATAACTTTTATT
232257 TTTT
1 TTTT
232261 GTTTTTGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.22, C:0.08, G:0.05, T:0.66
Consensus pattern (30 bp):
TTTTAATTCGTATTATATATAACTTTTATT
Found at i:232374 original size:9 final size:9
Alignment explanation
Indices: 232360--232407 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
232350 ACTGTTTGTG
232360 TATGTATGT
1 TATGTATGT
*
232369 TATGTATAT
1 TATGTATGT
232378 TATGTATG-
1 TATGTATGT
*
232386 TA--TA-AT
1 TATGTATGT
232392 TATGTATGT
1 TATGTATGT
232401 TATGTAT
1 TATGTAT
232408 ATATAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
6 4 0.13
8 4 0.13
9 23 0.74
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (9 bp):
TATGTATGT
Found at i:232381 original size:14 final size:14
Alignment explanation
Indices: 232364--232400 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
232354 TTTGTGTATG
232364 TATGTTATGTAT-AT
1 TATG-TATGTATAAT
232378 TATGTATGTATAAT
1 TATGTATGTATAAT
232392 TATGTATGT
1 TATGTATGT
232401 TATGTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (14 bp):
TATGTATGTATAAT
Found at i:232398 original size:23 final size:23
Alignment explanation
Indices: 232358--232421 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
232348 TTACTGTTTG
*
232358 TGTATGTAT-GTTATGTATATTA
1 TGTATGTATAATTATGTATATTA
*
232380 TGTATGTATAATTATGTATGTTA
1 TGTATGTATAATTATGTATATTA
*
232403 TGTATATATAATTATGTAT
1 TGTATGTATAATTATGTAT
232422 GATACGAGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 9 0.24
23 29 0.76
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (23 bp):
TGTATGTATAATTATGTATATTA
Found at i:236859 original size:21 final size:21
Alignment explanation
Indices: 236819--236859 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
236809 CTTTCTCGCT
*
236819 CTCTTTTTCTTTTCCCTTTTA
1 CTCTTTTTCTTTTCCATTTTA
236840 CTCTTTTTCTATTT-CATTTT
1 CTCTTTTTCT-TTTCCATTTT
236860 CCGTTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.68
Consensus pattern (21 bp):
CTCTTTTTCTTTTCCATTTTA
Found at i:244116 original size:28 final size:26
Alignment explanation
Indices: 244085--244137 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
244075 CAAATAAACT
244085 TAAAAACATTAAAACAAACATTAAAAAA
1 TAAAAA-ATTAAAA-AAACATTAAAAAA
* *
244113 TAAAAAATTTAAAATACATTAAAAA
1 TAAAAAATTAAAAAAACATTAAAAA
244138 TTATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 11 0.48
27 6 0.26
28 6 0.26
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.23
Consensus pattern (26 bp):
TAAAAAATTAAAAAAACATTAAAAAA
Found at i:244118 original size:20 final size:20
Alignment explanation
Indices: 244080--244118 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
244070 TATATCAAAT
*
244080 AAACTTAAAAACATTAAAAC
1 AAACTTAAAAACATAAAAAC
244100 AAACATTAAAAA-ATAAAAA
1 AAAC-TTAAAAACATAAAAA
244119 ATTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (20 bp):
AAACTTAAAAACATAAAAAC
Found at i:244300 original size:44 final size:44
Alignment explanation
Indices: 244251--244351 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
244241 AAAAACGAAT
* * * *
244251 AAAAATAACATCCAAACAATC-AAAATAACAACCAAAACAGCAGC
1 AAAAATAACAGCAAAACAA-CAAAAATAACAACAAAAACAGCAAC
* *
244295 AAAAATAACAGCAAAACAACAAAAATAGCAACAAAAACAGTAAC
1 AAAAATAACAGCAAAACAACAAAAATAACAACAAAAACAGCAAC
*
244339 AAAATTAACAGCA
1 AAAAATAACAGCA
244352 TCAAACTAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
43 1 0.02
44 48 0.98
ACGTcount: A:0.64, C:0.21, G:0.06, T:0.09
Consensus pattern (44 bp):
AAAAATAACAGCAAAACAACAAAAATAACAACAAAAACAGCAAC
Found at i:244319 original size:20 final size:21
Alignment explanation
Indices: 244251--244330 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 21
244241 AAAAACGAAT
*
244251 AAAAATAACATCC-AAACAATC
1 AAAAATAACA-CCAAAACAAGC
244272 -AAAATAACAACCAAAACAGCAGC
1 AAAAATAAC-ACCAAAACA--AGC
*
244295 AAAAATAACAGCAAAACAA-C
1 AAAAATAACACCAAAACAAGC
* *
244315 AAAAATAGCAACAAAA
1 AAAAATAACACCAAAA
244331 ACAGTAACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 25 0.50
21 7 0.14
23 10 0.20
24 8 0.16
ACGTcount: A:0.66, C:0.21, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAATAACACCAAAACAAGC
Found at i:244389 original size:12 final size:12
Alignment explanation
Indices: 244372--244411 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
244362 AAAAAAGCAT
*
244372 CAAAACAGTAAC
1 CAAAACAGCAAC
244384 CAAAACAGCAA-
1 CAAAACAGCAAC
244395 -AAAA-AGCAAC
1 CAAAACAGCAAC
244405 CAAAACA
1 CAAAACA
244412 ATAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
9 5 0.21
10 4 0.17
11 4 0.17
12 11 0.46
ACGTcount: A:0.65, C:0.25, G:0.07, T:0.03
Consensus pattern (12 bp):
CAAAACAGCAAC
Found at i:244417 original size:21 final size:21
Alignment explanation
Indices: 244381--244420 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
244371 TCAAAACAGT
*
244381 AACCAAAACAGCAAAAAAAGC
1 AACCAAAACAACAAAAAAAGC
*
244402 AACCAAAACAATAAAAAAA
1 AACCAAAACAACAAAAAAA
244421 ATCAAAATAA
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:0.72, C:0.20, G:0.05, T:0.03
Consensus pattern (21 bp):
AACCAAAACAACAAAAAAAGC
Found at i:249496 original size:3 final size:3
Alignment explanation
Indices: 249488--249528 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
249478 TGATTATGAA
249488 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
249529 ACATTATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:256715 original size:3 final size:3
Alignment explanation
Indices: 256707--256773 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
256697 TGATTATGAA
256707 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
256755 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
256774 CATTATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:258255 original size:461 final size:461
Alignment explanation
Indices: 257393--258775 Score: 2604
Period size: 461 Copynumber: 3.0 Consensus size: 461
257383 CAATGAATTT
257393 GAGTTTGTAGCATATATGTGGATTATATTTGATAAATAGTATTTAATCTTCTTAGCAATGTTATT
1 GAGTTTGTAGCATATATGTGGATTATATTTGATAAATAGTATTTAATCTTCTTAGCAATGTTATT
257458 AAGTGAATTCTCTTGAAGAAATTATGAAGAATAGTATAAAGATTCTTAAAGTGATATGTTATTCT
66 AAGTGAATTCTCTTGAAGAAATTATGAAGAATAGTATAAAGATTCTTAAAGTGATATGTTATTCT
257523 CTGTACACTGACGAGCGAAGACGTTTTGAACGAGCTCTTGCATGTGTTGCAGACTTGGATAAAAG
131 CTGTACACTGACGAGCGAAGACGTTTTGAACGAGCTCTTGCATGTGTTGCAGACTTGGATAAAAG
257588 TGAGACACGGACTTAGCTTAGGGTAGCTATCCATTGTTATTTATTTCAATTCCTATCTCTGGCCA
196 TGAGACACGGACTTAGCTTAGGGTAGCTATCCATTGTTATTTATTTCAATTCCTATCTCTGGCCA
257653 AGCTAGTATTATATGAACGATCAGTGATATAAGTTTGAAAGGAAAGCCTGTCACGTTTCATTTTG
261 AGCTAGTATTATATGAACGATCAGTGATATAAGTTTGAAAGGAAAGCCTGTCACGTTTCATTTTG
* *
257718 ATTTTGAAATAGCTAACGAGCTTAAACGTTCTGTAGATCCATTTGAGATGCTTTTATATAGTTTC
326 ATTTTGAAATAGCTGACGAGCTTAAACGTTCTGTAGAACCATTTGAGATGCTTTTATATAGTTTC
257783 ATCAAGATGATGAATGTTAAGTTCATAAGTAATGAGATTTTTGAGTTATGTGGCATTACCCTAAT
391 ATCAAGATGATGAATGTTAAGTTCATAAGTAATGAGATTTTTGAGTTATGTGGCATTACCCTAAT
257848 AAATGA
456 AAATGA
257854 GAGTTTGTAGCATATATGTGGATTATATTTGATAAATAGTATTTAATCTTCTTAGCAATGTTATT
1 GAGTTTGTAGCATATATGTGGATTATATTTGATAAATAGTATTTAATCTTCTTAGCAATGTTATT
257919 AAGTGAATTCTCTTGAAGAAATTATGAAGAATAGTATAAAGATTCTTAAAGTGATATGTTATTCT
66 AAGTGAATTCTCTTGAAGAAATTATGAAGAATAGTATAAAGATTCTTAAAGTGATATGTTATTCT
* *
257984 TTGTACACTGACGAGCGAAGACGTTTTGAACGAGCTCTTGCATGTGTTGCAGACTCGGATAAAAG
131 CTGTACACTGACGAGCGAAGACGTTTTGAACGAGCTCTTGCATGTGTTGCAGACTTGGATAAAAG
* * *
258049 TGAGACACGGACTTAGCTTAGGGTAGCTATCCATTGTTATTCATTTCAGTTCCTAGCTCTGGCCA
196 TGAGACACGGACTTAGCTTAGGGTAGCTATCCATTGTTATTTATTTCAATTCCTATCTCTGGCCA
258114 AGCTAGTATTATATGAACGATCAGTGATATAAGTTTGAAAGGAAAGCCTGTCACGTTTCATTTTG
261 AGCTAGTATTATATGAACGATCAGTGATATAAGTTTGAAAGGAAAGCCTGTCACGTTTCATTTTG
*
258179 ATTTTGAAATAGCTGACGAGCTTAAACGTTCTGTAGAACCATTTGAGATGCTTTTATATAATTTC
326 ATTTTGAAATAGCTGACGAGCTTAAACGTTCTGTAGAACCATTTGAGATGCTTTTATATAGTTTC
*
258244 ATCAAGATGATGAATCTTAAGTTCATAAGTAATGAGATTTTTGAGTTATGTGGCATTACCCTAAT
391 ATCAAGATGATGAATGTTAAGTTCATAAGTAATGAGATTTTTGAGTTATGTGGCATTACCCTAAT
258309 AAATGA
456 AAATGA
* *
258315 GAGTTTGTAGCATATATGTGGTTTATATTTGATAAATAGTCTTTAATCTTCTTAGCAATGTTATT
1 GAGTTTGTAGCATATATGTGGATTATATTTGATAAATAGTATTTAATCTTCTTAGCAATGTTATT
258380 AAGTGAATTCTCTTGAAGAAATTATGAAGAATAGTATAAAGATTCTTAAAGTGATATGTTATTCT
66 AAGTGAATTCTCTTGAAGAAATTATGAAGAATAGTATAAAGATTCTTAAAGTGATATGTTATTCT
* *
258445 CTGTACACTGACGAGCGAAGACGTTTTGAATGAGCTCTTGCATGTGTTGCAGACTTAGATAAAAG
131 CTGTACACTGACGAGCGAAGACGTTTTGAACGAGCTCTTGCATGTGTTGCAGACTTGGATAAAAG
258510 TGAGACACGGACTTAGCTTAGGGTAGCTATCCATTGTTATTTATTTCAATTCCTATCTCTGGCCA
196 TGAGACACGGACTTAGCTTAGGGTAGCTATCCATTGTTATTTATTTCAATTCCTATCTCTGGCCA
*
258575 AGCTAGTATTATATGAACGATCAGTGATATAAGTTTGAAAGGAAAGCCTGTCACATTTCATTTTG
261 AGCTAGTATTATATGAACGATCAGTGATATAAGTTTGAAAGGAAAGCCTGTCACGTTTCATTTTG
* * *
258640 ATTTTGAACTAGTTGACGAGCTTAAACATTCTGTAGAACCATTTGAGATGCTTTTATATAGTTTC
326 ATTTTGAAATAGCTGACGAGCTTAAACGTTCTGTAGAACCATTTGAGATGCTTTTATATAGTTTC
*
258705 ATCGAGATGATGAATGTTAAGTTCATAAGTAATGAGATTTTTGAGTTATGTGGCATTACCCTAAT
391 ATCAAGATGATGAATGTTAAGTTCATAAGTAATGAGATTTTTGAGTTATGTGGCATTACCCTAAT
258770 AAATGA
456 AAATGA
258776 AACCATCTTT
Statistics
Matches: 897, Mismatches: 25, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
461 897 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (461 bp):
GAGTTTGTAGCATATATGTGGATTATATTTGATAAATAGTATTTAATCTTCTTAGCAATGTTATT
AAGTGAATTCTCTTGAAGAAATTATGAAGAATAGTATAAAGATTCTTAAAGTGATATGTTATTCT
CTGTACACTGACGAGCGAAGACGTTTTGAACGAGCTCTTGCATGTGTTGCAGACTTGGATAAAAG
TGAGACACGGACTTAGCTTAGGGTAGCTATCCATTGTTATTTATTTCAATTCCTATCTCTGGCCA
AGCTAGTATTATATGAACGATCAGTGATATAAGTTTGAAAGGAAAGCCTGTCACGTTTCATTTTG
ATTTTGAAATAGCTGACGAGCTTAAACGTTCTGTAGAACCATTTGAGATGCTTTTATATAGTTTC
ATCAAGATGATGAATGTTAAGTTCATAAGTAATGAGATTTTTGAGTTATGTGGCATTACCCTAAT
AAATGA
Found at i:260871 original size:28 final size:28
Alignment explanation
Indices: 260831--260887 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
260821 AAAGCATAAA
260831 TTAATGCACTATAGTCATTGATTTTAAC
1 TTAATGCACTATAGTCATTGATTTTAAC
260859 TTAATGCACTATAGTCATTGATTTTAAC
1 TTAATGCACTATAGTCATTGATTTTAAC
260887 T
1 T
260888 GTTAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (28 bp):
TTAATGCACTATAGTCATTGATTTTAAC
Found at i:261931 original size:19 final size:19
Alignment explanation
Indices: 261886--261939 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
261876 AAATATTATT
261886 TTATTT-TATATTTTAAAC
1 TTATTTATATATTTTAAAC
** * *
261904 TTAACTATATATTTTTAAG
1 TTATTTATATATTTTAAAC
261923 TTATTTATAT-TTTTAAA
1 TTATTTATATATTTTAAA
261940 ATATTGTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (19 bp):
TTATTTATATATTTTAAAC
Found at i:261944 original size:17 final size:17
Alignment explanation
Indices: 261911--261944 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
261901 AACTTAACTA
**
261911 TATATTTTTAAGTTATT
1 TATATTTTTAAAATATT
261928 TATATTTTTAAAATATT
1 TATATTTTTAAAATATT
261945 GTTTCATCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TATATTTTTAAAATATT
Found at i:263811 original size:81 final size:81
Alignment explanation
Indices: 263720--263886 Score: 291
Period size: 81 Copynumber: 2.1 Consensus size: 81
263710 AAAAATTTAC
*
263720 AAATTAGGTACCACCGTTAACAAAA-TTTAAAAAAAATTTAATTTTTTAGGGGCCCAAAAAAATT
1 AAATTAGGTACCACCGTTAACAAAATTTTAAAAAAAAATTAATTTTTTAGGGGCCC-AAAAAATT
263784 TTAACTTTTAAAGGTCA
65 TTAACTTTTAAAGGTCA
* *
263801 AAATTAGGTACTACCGTTAACAAAATTTTAAAAAAAAATTATTTTTTTAGGGGCCCAAAAAATTT
1 AAATTAGGTACCACCGTTAACAAAATTTTAAAAAAAAATTAATTTTTTAGGGGCCCAAAAAATTT
263866 TAACTTTTAAAGGTCA
66 TAACTTTTAAAGGTCA
263882 AAATT
1 AAATT
263887 TTTTAAAACT
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
81 54 0.66
82 28 0.34
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (81 bp):
AAATTAGGTACCACCGTTAACAAAATTTTAAAAAAAAATTAATTTTTTAGGGGCCCAAAAAATTT
TAACTTTTAAAGGTCA
Found at i:263930 original size:30 final size:30
Alignment explanation
Indices: 263885--263950 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
263875 AAGGTCAAAA
*
263885 TTTTTTAAAACTTTTAAG-CGCCCAAAATT
1 TTTTTTAAAACTTTTAAGACACCCAAAATT
* *
263914 TTTTTTACAAATTTTTAAGACACCTAAAATT
1 TTTTTTA-AAACTTTTAAGACACCCAAAATT
263945 TTTTTT
1 TTTTTT
263951 CTCTAACTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 7 0.22
30 10 0.31
31 15 0.47
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (30 bp):
TTTTTTAAAACTTTTAAGACACCCAAAATT
Found at i:263962 original size:32 final size:30
Alignment explanation
Indices: 263885--263974 Score: 101
Period size: 32 Copynumber: 2.9 Consensus size: 30
263875 AAGGTCAAAA
* *
263885 TTTTTTA-AAACTTTTAAGCGCCCAAAATT
1 TTTTTTACAAACTTTTAAGCACCTAAAATT
*
263914 TTTTTTACAAATTTTTAAGACACCTAAAATT
1 TTTTTTACAAACTTTTAAG-CACCTAAAATT
* *
263945 TTTTTTCTCTAACTTTTAAGCAACCTAAAA
1 TTTTTT-ACAAACTTTTAAGC-ACCTAAAA
263975 CCTCATTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 7 0.14
30 10 0.20
31 16 0.31
32 18 0.35
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (30 bp):
TTTTTTACAAACTTTTAAGCACCTAAAATT
Found at i:264274 original size:31 final size:31
Alignment explanation
Indices: 264218--264291 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
264208 TGTATACATG
*
264218 AATTTTAA-TTTGGTGTAATTATATATGTGA
1 AATTTTAATTTTGGTGTAAATATATATGTGA
* *
264248 AATTTTAATTTTGGT-TCAAATGTATATTTGA
1 AATTTTAATTTTGGTGT-AAATATATATGTGA
* *
264279 CACTTTAATTTTG
1 AATTTTAATTTTG
264292 ATTTAATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 9 0.24
31 28 0.76
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (31 bp):
AATTTTAATTTTGGTGTAAATATATATGTGA
Found at i:264474 original size:29 final size:30
Alignment explanation
Indices: 264442--264512 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
264432 AAATTAAAAT
*
264442 TTCATGTATAAAATCACACA-AAAATATAG
1 TTCATATATAAAATCACACATAAAATATAG
* * *
264471 TTCATATATACAATTACACATTAAACTATAG
1 TTCATATATAAAATCACACA-TAAAATATAG
*
264502 TTCATACATAA
1 TTCATATATAA
264513 TTTTAAGATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.50
31 17 0.50
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.32
Consensus pattern (30 bp):
TTCATATATAAAATCACACATAAAATATAG
Found at i:275172 original size:19 final size:20
Alignment explanation
Indices: 275148--275193 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
275138 TCTTAAACAC
275148 TTTTCA-ATGTACGGACCCT
1 TTTTCATATGTACGGACCCT
*
275167 TTTTCATTTGTACGGACCCT
1 TTTTCATATGTACGGACCCT
275187 TTTTCAT
1 TTTTCAT
275194 TTGCCTCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.46
Consensus pattern (20 bp):
TTTTCATATGTACGGACCCT
Found at i:275180 original size:20 final size:20
Alignment explanation
Indices: 275155--275196 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
275145 CACTTTTCAA
275155 TGTACGGACCCTTTTTCATT
1 TGTACGGACCCTTTTTCATT
275175 TGTACGGACCCTTTTTCATT
1 TGTACGGACCCTTTTTCATT
275195 TG
1 TG
275197 CCTCATCGAA
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:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (20 bp):
TGTACGGACCCTTTTTCATT
Found at i:276326 original size:15 final size:15
Alignment explanation
Indices: 276273--276335 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 15
276263 TTAAAATTAT
* *
276273 TAAAATTATTAATAA
1 TAAAATTAATAGTAA
*
276288 TAAAA-TAA-ACTAA
1 TAAAATTAATAGTAA
*
276301 CAAAA-TAATAGTAA
1 TAAAATTAATAGTAA
276315 TAAAATTAATAGTAA
1 TAAAATTAATAGTAA
*
276330 GAAAAT
1 TAAAAT
276336 AAAAAAAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.28
14 10 0.25
15 19 0.47
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (15 bp):
TAAAATTAATAGTAA
Found at i:277139 original size:23 final size:23
Alignment explanation
Indices: 277111--277236 Score: 207
Period size: 23 Copynumber: 5.5 Consensus size: 23
277101 ACATTATGCC
277111 TTAATATTTAAGCATAAATCACA
1 TTAATATTTAAGCATAAATCACA
*
277134 TTAATATTTAAGCAAAAATCACA
1 TTAATATTTAAGCATAAATCACA
*
277157 TTAATATTTAAGCACAAATCACA
1 TTAATATTTAAGCATAAATCACA
* *
277180 TTAACATTTAAGCATAAATCATA
1 TTAATATTTAAGCATAAATCACA
*
277203 TTAACATTTAAGCATAAATCACA
1 TTAATATTTAAGCATAAATCACA
277226 TTAATATTTAA
1 TTAATATTTAA
277237 CACATTTAAT
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 96 1.00
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.34
Consensus pattern (23 bp):
TTAATATTTAAGCATAAATCACA
Found at i:280257 original size:29 final size:23
Alignment explanation
Indices: 280193--280421 Score: 336
Period size: 23 Copynumber: 10.0 Consensus size: 23
280183 TCCATTTACA
*
280193 CATAAATCGCATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
280216 CATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
280239 CATAAATCATATTAACATTTAAG
1 CATAAATCACATTAATATTTAAG
*
280262 TATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
280285 CACAAATCACATTAATATTTGAG
1 CATAAATCACATTAATATTTAAG
*
280308 AATAAATCA-ATTTAATATTTAAG
1 CATAAATCACA-TTAATATTTAAG
*
280331 CACAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
280354 CATAAATCACATTAACT-TTTAAG
1 CATAAATCACATTAA-TATTTAAG
* *
280377 CATAAATCATATTAACATTTAAG
1 CATAAATCACATTAATATTTAAG
280400 CATAAATCACATTAATATTTAA
1 CATAAATCACATTAATATTTAA
280422 CACATTTAAT
Statistics
Matches: 183, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
22 1 0.01
23 180 0.98
24 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (23 bp):
CATAAATCACATTAATATTTAAG
Found at i:289100 original size:30 final size:30
Alignment explanation
Indices: 289064--289123 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
289054 AGATCAAATA
*
289064 TGAGTAAGAATTTACAGGTAATTCATGGAC
1 TGAGTAAGAATTTACAGGTAACTCATGGAC
289094 TGAGTAAGAATTTACAGGTAACTCATGGAC
1 TGAGTAAGAATTTACAGGTAACTCATGGAC
289124 CACTTTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (30 bp):
TGAGTAAGAATTTACAGGTAACTCATGGAC
Found at i:295121 original size:2 final size:2
Alignment explanation
Indices: 295114--295168 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
295104 ATTAATACCA
* *
295114 AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AT AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
295156 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
295169 TGTTTCTAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.45, G:0.00, T:0.04
Consensus pattern (2 bp):
AC
Found at i:295137 original size:20 final size:20
Alignment explanation
Indices: 295114--295169 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
295104 ATTAATACCA
295114 ACACACACACACACATACAC
1 ACACACACACACACATACAC
295134 ACACACACACACACATACAC
1 ACACACACACACACATACAC
295154 ACACACACACACACAT
1 ACACACACACACACAT
295170 GTTTCTAGCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.50, C:0.45, G:0.00, T:0.05
Consensus pattern (20 bp):
ACACACACACACACATACAC
Found at i:296394 original size:14 final size:14
Alignment explanation
Indices: 296375--296402 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
296365 TATATTAGTG
296375 TTTTCTATTCTATT
1 TTTTCTATTCTATT
296389 TTTTCTATTCTATT
1 TTTTCTATTCTATT
296403 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:299521 original size:29 final size:26
Alignment explanation
Indices: 299457--299537 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 26
299447 AATATTTAAT
299457 AAATTTAGGTACCAAATTGAATAAAA
1 AAATTTAGGTACCAAATTGAATAAAA
* *
299483 AAACTTAGGTACCAAATTGAGTCCAAAAA
1 AAATTTAGGTACCAAATTGAAT---AAAA
299512 AAATTTAGGTACCAAATT-AA-AAAA
1 AAATTTAGGTACCAAATTGAATAAAA
299536 AA
1 AA
299538 TCAAATTCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 6 0.12
26 20 0.42
28 1 0.02
29 21 0.44
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (26 bp):
AAATTTAGGTACCAAATTGAATAAAA
Found at i:299825 original size:24 final size:25
Alignment explanation
Indices: 299797--299845 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
299787 AAAATTATAA
299797 TTTAATT-TTAATTATTTTAAAATT
1 TTTAATTATTAATTATTTTAAAATT
* *
299821 TTTAATTATTATTTTTTTTAAAATT
1 TTTAATTATTAATTATTTTAAAATT
299846 ATAATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTAATTATTAATTATTTTAAAATT
Found at i:299850 original size:24 final size:22
Alignment explanation
Indices: 299795--299856 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 22
299785 TAAAAATTAT
299795 AATTTAATTTTAATTATTTTAA
1 AATTTAATTTTAATTATTTTAA
* *
299817 AATTTTTAATTATTATTTTTTTTAA
1 AA--TTTAATT-TTAATTATTTTAA
299842 AATTATAA-TTTAATT
1 AATT-TAATTTTAATT
299857 TTCACCATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 7 0.21
23 3 0.09
24 10 0.30
25 13 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
AATTTAATTTTAATTATTTTAA
Found at i:300497 original size:14 final size:14
Alignment explanation
Indices: 300434--300500 Score: 55
Period size: 14 Copynumber: 4.5 Consensus size: 14
300424 ATTTTGAGAG
* *
300434 AATTAAAATTTTAA
1 AATTAAAATATAAA
300448 AATTCGAAAATTATAAA
1 AATT--AAAA-TATAAA
*
300465 AACTAAAATGA-ATAA
1 AATTAAAAT-ATA-AA
300480 AATTAAAATATAAA
1 AATTAAAATATAAA
300494 AATTAAA
1 AATTAAA
300501 TTTATAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 16 0.37
15 16 0.37
16 4 0.09
17 7 0.16
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (14 bp):
AATTAAAATATAAA
Found at i:302079 original size:20 final size:20
Alignment explanation
Indices: 302056--302103 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
302046 AATGTAAGTG
302056 ATAAAAATGTAACATTTCAA
1 ATAAAAATGTAACATTTCAA
302076 ATAAAAATGTAACATTTCAA
1 ATAAAAATGTAACATTTCAA
*
302096 ATATAAAT
1 ATAAAAAT
302104 AACTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.31
Consensus pattern (20 bp):
ATAAAAATGTAACATTTCAA
Found at i:302626 original size:9 final size:9
Alignment explanation
Indices: 302606--302638 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
302596 ACCTGTGACG
302606 AAAAATAAT
1 AAAAATAAT
302615 AAAAA-AATT
1 AAAAATAA-T
302624 AAAAATAAT
1 AAAAATAAT
302633 AAAAAT
1 AAAAAT
302639 TATTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:303056 original size:15 final size:15
Alignment explanation
Indices: 303036--303069 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
303026 TGATATTTTT
303036 AAATAAAATAATTAA
1 AAATAAAATAATTAA
**
303051 AAATAAAATTTTTAA
1 AAATAAAATAATTAA
303066 AAAT
1 AAAT
303070 TGAACTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAAAATAATTAA
Found at i:303726 original size:18 final size:18
Alignment explanation
Indices: 303703--303744 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
303693 TTTTCAATTG
303703 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
303721 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
303739 TAATTA
1 TAATTA
303745 GAAATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:312110 original size:13 final size:13
Alignment explanation
Indices: 312075--312113 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
312065 CTCATTTTAT
312075 TTTATTTTGTATTA
1 TTTATTTT-TATTA
**
312089 TTTCCTTTTATTA
1 TTTATTTTTATTA
312102 TTTATTTTTATT
1 TTTATTTTTATT
312114 TTTGCTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTATTTTTATTA
Found at i:312112 original size:10 final size:10
Alignment explanation
Indices: 312099--312162 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 10
312089 TTTCCTTTTA
312099 TTATTTATTT
1 TTATTTATTT
*
312109 TTATTT-TTGC
1 TTATTTATT-T
312119 TTATTTATTT
1 TTATTTATTT
312129 TTATGCTTA-TT
1 TTAT--TTATTT
312140 TTATTTTATTT
1 TTA-TTTATTT
312151 TCTATTATATTT
1 T-TATT-TATTT
312163 GGTTTAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
9 2 0.05
10 19 0.43
11 12 0.27
12 11 0.25
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (10 bp):
TTATTTATTT
Found at i:312147 original size:16 final size:16
Alignment explanation
Indices: 312107--312148 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
312097 TATTATTTAT
312107 TTTTATTTT-TGCTTA
1 TTTTATTTTATGCTTA
312122 -TTTATTTTTATGCTTA
1 TTTTA-TTTTATGCTTA
312138 TTTTATTTTAT
1 TTTTATTTTAT
312149 TTTCTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.17
15 4 0.17
16 12 0.50
17 4 0.17
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (16 bp):
TTTTATTTTATGCTTA
Found at i:312275 original size:15 final size:15
Alignment explanation
Indices: 312255--312285 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
312245 TCATATTTTG
312255 TGTCATTAGTATCAT
1 TGTCATTAGTATCAT
*
312270 TGTCATTATTATCAT
1 TGTCATTAGTATCAT
312285 T
1 T
312286 TTTTACTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.52
Consensus pattern (15 bp):
TGTCATTAGTATCAT
Found at i:315905 original size:17 final size:17
Alignment explanation
Indices: 315885--315921 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
315875 TTGCATTTTT
*
315885 ATTGTCGTTGCATCTAC
1 ATTGTCATTGCATCTAC
315902 ATTGTCATTGCATCTAC
1 ATTGTCATTGCATCTAC
315919 ATT
1 ATT
315922 AATAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (17 bp):
ATTGTCATTGCATCTAC
Found at i:315957 original size:18 final size:18
Alignment explanation
Indices: 315934--315969 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
315924 TAAATATATA
*
315934 TATTAATGCCATTGCATT
1 TATTAATGCCAGTGCATT
*
315952 TATTAATGTCAGTGCATT
1 TATTAATGCCAGTGCATT
315970 GGGGACAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (18 bp):
TATTAATGCCAGTGCATT
Done.