Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009890.1 Kokia drynarioides strain JFW-HI SEQ_124626, 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: 220235
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 48 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:47 original size:23 final size:23
Alignment explanation
Indices: 21--161 Score: 154
Period size: 23 Copynumber: 6.4 Consensus size: 23
11 AGTGCTGGGC
21 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
44 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
63 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
83 ATA-AGAGAGCACACACAGTGCTA
1 A-ACAGAGAGCACACAAAGTGCTA
* * *
106 ATCAGAGAGCACACGAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
*
129 AACAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
152 AACAGAGAGC
1 AACAGAGAGC
162 GCGCTAGTGT
Statistics
Matches: 98, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.10
18 3 0.03
19 1 0.01
20 1 0.01
21 1 0.01
22 1 0.01
23 81 0.83
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:262 original size:24 final size:26
Alignment explanation
Indices: 224--271 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
214 TCTACATGGG
224 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
250 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
272 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:2014 original size:29 final size:30
Alignment explanation
Indices: 1965--2184 Score: 255
Period size: 30 Copynumber: 7.3 Consensus size: 30
1955 AGGATGTTAC
1965 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
*
1995 AAGTTTGGGGGT-TAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* *
2024 AAATTTGGGGGTTAAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* * *
2054 AAGTTTGAGAGTCAAAATATGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* * *
2084 ATGTTTGGGGGTCAAAATCTAATTTTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGA--TTTTGGAA
* ** * *
2116 AACTTTACGGGTCAAAGTGTAATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* * *
2146 AAGTTT-GGAGTCAAAATCTAATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
2175 AAGTTTGGGG
1 AAGTTTGGGG
2185 ACTTCTTGAG
Statistics
Matches: 161, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
29 52 0.32
30 85 0.53
32 24 0.15
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (30 bp):
AAGTTTGGGGGTCAAAATGTGATTTTGGAA
Found at i:2060 original size:59 final size:59
Alignment explanation
Indices: 1965--2184 Score: 244
Period size: 59 Copynumber: 3.7 Consensus size: 59
1955 AGGATGTTAC
* * *
1965 AAGTTTGGGGGTCAAAATGTGATTTTGGAAAAGTTTGGGGGTTAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGGGTAAAATGTGATTTTGGAA
* * * * * * *
2024 AAATTTGGGGGTTAAAATGTGATTTTGGAAAAGTTTGAGAGTCAAAATATGATTTTGGAA
1 AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGGGT-AAAATGTGATTTTGGAA
* * ** * *
2084 ATGTTTGGGGGTCAAAATCTAATTTTTTGGAAAACTTTACGGGTCAAAGTGTAATTTTGGAA
1 AAGTTTGGGGGTCAAAATCTAA--TTTTGGAAAAGTTTGGGGGT-AAAATGTGATTTTGGAA
*
2146 AAGTTT-GGAGTCAAAATCTAATTTTGGAAAAGTTTGGGG
1 AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGG
2185 ACTTCTTGAG
Statistics
Matches: 135, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
59 53 0.39
60 32 0.24
61 14 0.10
62 36 0.27
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (59 bp):
AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGGGTAAAATGTGATTTTGGAA
Found at i:4310 original size:29 final size:30
Alignment explanation
Indices: 4261--4480 Score: 255
Period size: 30 Copynumber: 7.3 Consensus size: 30
4251 AGGATGTTAC
4261 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
*
4291 AAGTTTGGGGGT-TAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* *
4320 AAATTTGGGGGTTAAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* * *
4350 AAGTTTGAGAGTCAAAATATGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* * *
4380 ATGTTTGGGGGTCAAAATCTAATTTTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGA--TTTTGGAA
* ** * *
4412 AACTTTACGGGTCAAAGTGTAATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* * *
4442 AAGTTT-GGAGTCAAAATCTAATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
4471 AAGTTTGGGG
1 AAGTTTGGGG
4481 ACTTCTTGAG
Statistics
Matches: 161, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
29 52 0.32
30 85 0.53
32 24 0.15
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (30 bp):
AAGTTTGGGGGTCAAAATGTGATTTTGGAA
Found at i:4356 original size:59 final size:59
Alignment explanation
Indices: 4261--4480 Score: 244
Period size: 59 Copynumber: 3.7 Consensus size: 59
4251 AGGATGTTAC
* * *
4261 AAGTTTGGGGGTCAAAATGTGATTTTGGAAAAGTTTGGGGGTTAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGGGTAAAATGTGATTTTGGAA
* * * * * * *
4320 AAATTTGGGGGTTAAAATGTGATTTTGGAAAAGTTTGAGAGTCAAAATATGATTTTGGAA
1 AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGGGT-AAAATGTGATTTTGGAA
* * ** * *
4380 ATGTTTGGGGGTCAAAATCTAATTTTTTGGAAAACTTTACGGGTCAAAGTGTAATTTTGGAA
1 AAGTTTGGGGGTCAAAATCTAA--TTTTGGAAAAGTTTGGGGGT-AAAATGTGATTTTGGAA
*
4442 AAGTTT-GGAGTCAAAATCTAATTTTGGAAAAGTTTGGGG
1 AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGG
4481 ACTTCTTGAG
Statistics
Matches: 135, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
59 53 0.39
60 32 0.24
61 14 0.10
62 36 0.27
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (59 bp):
AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGGGTAAAATGTGATTTTGGAA
Found at i:5543 original size:29 final size:30
Alignment explanation
Indices: 5494--5713 Score: 255
Period size: 30 Copynumber: 7.3 Consensus size: 30
5484 AGGATGTTAC
5494 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
*
5524 AAGTTTGGGGGT-TAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* *
5553 AAATTTGGGGGTTAAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* * *
5583 AAGTTTGAGAGTCAAAATATGATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* * *
5613 ATGTTTGGGGGTCAAAATCTAATTTTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGA--TTTTGGAA
* ** * *
5645 AACTTTACGGGTCAAAGTGTAATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
* * *
5675 AAGTTT-GGAGTCAAAATCTAATTTTGGAA
1 AAGTTTGGGGGTCAAAATGTGATTTTGGAA
5704 AAGTTTGGGG
1 AAGTTTGGGG
5714 ACTTCTTGAG
Statistics
Matches: 161, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
29 52 0.32
30 85 0.53
32 24 0.15
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (30 bp):
AAGTTTGGGGGTCAAAATGTGATTTTGGAA
Found at i:5589 original size:59 final size:59
Alignment explanation
Indices: 5494--5713 Score: 244
Period size: 59 Copynumber: 3.7 Consensus size: 59
5484 AGGATGTTAC
* * *
5494 AAGTTTGGGGGTCAAAATGTGATTTTGGAAAAGTTTGGGGGTTAAATGTGATTTTGGAA
1 AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGGGTAAAATGTGATTTTGGAA
* * * * * * *
5553 AAATTTGGGGGTTAAAATGTGATTTTGGAAAAGTTTGAGAGTCAAAATATGATTTTGGAA
1 AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGGGT-AAAATGTGATTTTGGAA
* * ** * *
5613 ATGTTTGGGGGTCAAAATCTAATTTTTTGGAAAACTTTACGGGTCAAAGTGTAATTTTGGAA
1 AAGTTTGGGGGTCAAAATCTAA--TTTTGGAAAAGTTTGGGGGT-AAAATGTGATTTTGGAA
*
5675 AAGTTT-GGAGTCAAAATCTAATTTTGGAAAAGTTTGGGG
1 AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGG
5714 ACTTCTTGAG
Statistics
Matches: 135, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
59 53 0.39
60 32 0.24
61 14 0.10
62 36 0.27
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (59 bp):
AAGTTTGGGGGTCAAAATCTAATTTTGGAAAAGTTTGGGGGTAAAATGTGATTTTGGAA
Found at i:12548 original size:96 final size:95
Alignment explanation
Indices: 12386--12573 Score: 250
Period size: 96 Copynumber: 2.0 Consensus size: 95
12376 GGAAGAGAGT
* * * * *
12386 GATGAAGTAAACTGCTAATAAAGCCTGTGTACTGACCGCTTGTTTTCAGTTTTGGGCCTGGGGTA
1 GATGAAGTAAACTACTAATAAAACCTGTGTACTGAACGCTTGTTTTCAGTTTTGGGCCTAGAGTA
*
12451 AAGTTCTAGTTTTTGAATTTTTTTAGAGAAC
66 AAGTTCTAATTTTTGAA-TTTTTTAGAGAAC
* * * * * *
12482 GATGAAGTAAGCTATTAATAAAACTTGTGTTCTGAAGGCTTGTTTTCAGTTTTGGGTCTAGAGTA
1 GATGAAGTAAACTACTAATAAAACCTGTGTACTGAACGCTTGTTTTCAGTTTTGGGCCTAGAGTA
*
12547 AAGTTCTAATTTTTGGATTTTTTAGAG
66 AAGTTCTAATTTTTGAATTTTTTAGAG
12574 TTTGGGCCTT
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
95 10 0.13
96 69 0.87
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (95 bp):
GATGAAGTAAACTACTAATAAAACCTGTGTACTGAACGCTTGTTTTCAGTTTTGGGCCTAGAGTA
AAGTTCTAATTTTTGAATTTTTTAGAGAAC
Found at i:18854 original size:16 final size:17
Alignment explanation
Indices: 18829--18862 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18819 AGAGAGAAGA
*
18829 AATTTTATTT-ATTTTT
1 AATTTAATTTAATTTTT
18845 AATTTAATTTAATTTTT
1 AATTTAATTTAATTTTT
18862 A
1 A
18863 CTTAGAGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AATTTAATTTAATTTTT
Found at i:23081 original size:9 final size:9
Alignment explanation
Indices: 23067--23112 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
23057 TATTCATTCT
23067 AAAATTATA
1 AAAATTATA
23076 AAAATTA-A
1 AAAATTATA
*
23084 AAAAAT-TA
1 AAAATTATA
*
23092 AAAATTTTA
1 AAAATTATA
*
23101 AAGATTATA
1 AAAATTATA
23110 AAA
1 AAA
23113 TTACAAGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
8 12 0.40
9 18 0.60
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:24837 original size:83 final size:82
Alignment explanation
Indices: 24734--24962 Score: 235
Period size: 83 Copynumber: 2.8 Consensus size: 82
24724 GTACTCTCAA
* * * * *
24734 AAAGGTGTTTGCTTAAATAATTTGTTAAGTGCCTTAAGAGGGTAGAATCGATTCTTCTATTGACT
1 AAAGGTGTGTGCTCAAATAATTAGCTAAGTGCCTTAAGAGGCTAGAATCGATTCTTCTATTGACT
24799 CGG-GAAGCAATACCCTC
66 CGGCG-AGCAATACCCTC
* * * * * *
24816 GAAAGGTGTGTGCTCAAATAATTCGCTAAGTGCCTTAAGAAGTTAGGATGGATTCTTATATTGAC
1 -AAAGGTGTGTGCTCAAATAATTAGCTAAGTGCCTTAAGAGGCTAGAATCGATTCTTCTATTGAC
*
24881 TTGGCGAGCAATACCCTC
65 TCGGCGAGCAATACCCTC
* * * * * * * *
24899 AACAAGTGTGTGTTCAATTTTATTAGCCAAGTGCCATAAGAGGCTAGAAGCAATTCTTCTATTG
1 AA-AGGTGTGTGCTCAA-ATAATTAGCTAAGTGCCTTAAGAGGCTAGAATCGATTCTTCTATTG
24963 TGTTAGTGGG
Statistics
Matches: 119, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
82 2 0.02
83 82 0.69
84 35 0.29
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (82 bp):
AAAGGTGTGTGCTCAAATAATTAGCTAAGTGCCTTAAGAGGCTAGAATCGATTCTTCTATTGACT
CGGCGAGCAATACCCTC
Found at i:25367 original size:56 final size:56
Alignment explanation
Indices: 25302--25513 Score: 228
Period size: 56 Copynumber: 3.7 Consensus size: 56
25292 ATTTAACTGT
* * * *
25302 TAAGATATTATTATGCGATATTATCTTTTAACAATTTAATTTCTAACAGGATATTA
1 TAAGATATTATTATGAGATATTATCTTTTAACAATTTAATTCCTAATAAGATATTA
* * **
25358 TAAGATATTATTATGTGATATTATATTTTAACAATTTAATTCCTAATTTGATATTA
1 TAAGATATTATTATGAGATATTATCTTTTAACAATTTAATTCCTAATAAGATATTA
* * * *
25414 TAAGATATTATGATGGGATAATATTAT-TTCTTAACAATTTGATTCCTAATAAAATATTA
1 TAAGATATTATTAT--GA-GATATTATCTT-TTAACAATTTAATTCCTAATAAGATATTA
* * * * *
25473 GAGGATATTATTATGATATATTATCTCTTAGCAATTTAATT
1 TAAGATATTATTATGAGATATTATCTTTTAACAATTTAATT
25514 TCTACGTAAC
Statistics
Matches: 131, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
56 82 0.63
57 3 0.02
58 3 0.02
59 43 0.33
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (56 bp):
TAAGATATTATTATGAGATATTATCTTTTAACAATTTAATTCCTAATAAGATATTA
Found at i:25528 original size:115 final size:115
Alignment explanation
Indices: 25319--25529 Score: 248
Period size: 115 Copynumber: 1.8 Consensus size: 115
25309 TTATTATGCG
* ** *
25319 ATATTATCTTTTAACAATTTAATTTCTAACAGGATATTATAAGATATTATTATGTGATATTATAT
1 ATATTATCTTTTAACAATTTAATTCCTAACAAAATATTAGAAGATATTATTATGTGATATTATAT
* ** *
25384 TTTAACAATTTAATTCCTAATTTGATATTATAAGATATTATGATGGGATA
66 CTTAACAATTTAATTCCTAACGTAATATTATAAGATATTATGATGGGATA
* * *
25434 ATATTAT-TTCTTAACAATTTGATTCCTAATAAAATATTAGAGGATATTATTATGAT-ATATTAT
1 ATATTATCTT-TTAACAATTTAATTCCTAACAAAATATTAGAAGATATTATTATG-TGATATTAT
* * *
25497 CTCTTAGCAATTTAATTTCT-ACGTAACTATTAT
64 ATCTTAACAATTTAATTCCTAACGTAA-TATTAT
25530 TGTATAGATA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
114 5 0.06
115 73 0.92
116 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (115 bp):
ATATTATCTTTTAACAATTTAATTCCTAACAAAATATTAGAAGATATTATTATGTGATATTATAT
CTTAACAATTTAATTCCTAACGTAATATTATAAGATATTATGATGGGATA
Found at i:26203 original size:50 final size:51
Alignment explanation
Indices: 26149--26263 Score: 130
Period size: 51 Copynumber: 2.3 Consensus size: 51
26139 ATAAATATAA
* *
26149 ATATTTATCTTAAATATAACAT-TTC-AACAAAAT-A-ATATAAACAAATATTT
1 ATATTTAT-TTAAAAACAACATATTCAAAC-AAATCACAT-TAAACAAATATTT
* * *
26199 ATATTTATATAAAAACAACATATTTAAACAAATCACATTAAATAAATATTT
1 ATATTTATTTAAAAACAACATATTCAAACAAATCACATTAAACAAATATTT
26250 ATATTTATTTAAAA
1 ATATTTATTTAAAA
26264 CATCAGATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
49 10 0.18
50 14 0.25
51 29 0.53
52 2 0.04
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (51 bp):
ATATTTATTTAAAAACAACATATTCAAACAAATCACATTAAACAAATATTT
Found at i:27680 original size:24 final size:24
Alignment explanation
Indices: 27648--27696 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
27638 GATATGGAAT
27648 CAATAGAAAATGAAGATCCAACTC
1 CAATAGAAAATGAAGATCCAACTC
27672 CAATAGAAAATGAAGATCCAACTC
1 CAATAGAAAATGAAGATCCAACTC
27696 C
1 C
27697 GTGTATGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.22, G:0.12, T:0.16
Consensus pattern (24 bp):
CAATAGAAAATGAAGATCCAACTC
Found at i:31298 original size:20 final size:20
Alignment explanation
Indices: 31237--31298 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
31227 TCTGACAATA
*
31237 AATATTAACAAGAGTCAAGT
1 AATATAAACAAGAGTCAAGT
* *
31257 AATAT-AAC-A-TGTCACG-
1 AATATAAACAAGAGTCAAGT
31273 -ATATAAACAAGAGTCAAGT
1 AATATAAACAAGAGTCAAGT
31292 AATATAA
1 AATATAA
31299 TTTAATAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 6 0.18
18 6 0.18
19 3 0.09
20 11 0.33
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.24
Consensus pattern (20 bp):
AATATAAACAAGAGTCAAGT
Found at i:31307 original size:43 final size:43
Alignment explanation
Indices: 31260--31356 Score: 167
Period size: 43 Copynumber: 2.3 Consensus size: 43
31250 GTCAAGTAAT
31260 ATAACATGTCACGATATAAACAAGAGTCAAGTAATATAATTTA
1 ATAACATGTCACGATATAAACAAGAGTCAAGTAATATAATTTA
* * *
31303 ATAACATGTCACGATATTAACACGGGTCAAGTAATATAATTTA
1 ATAACATGTCACGATATAAACAAGAGTCAAGTAATATAATTTA
31346 ATAACATGTCA
1 ATAACATGTCA
31357 ATGAATAACA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.29
Consensus pattern (43 bp):
ATAACATGTCACGATATAAACAAGAGTCAAGTAATATAATTTA
Found at i:32732 original size:28 final size:28
Alignment explanation
Indices: 32700--32762 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
32690 ATTAATTAAT
* * *
32700 ATTACTTACTTATTATTAACAAAATAAA
1 ATTACTTACTAACTACTAACAAAATAAA
32728 ATTACTTACTAACTACTAACAAAATAAA
1 ATTACTTACTAACTACTAACAAAATAAA
32756 ACTTACT
1 A-TTACT
32763 AACAAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (28 bp):
ATTACTTACTAACTACTAACAAAATAAA
Found at i:32888 original size:25 final size:23
Alignment explanation
Indices: 32840--32896 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 23
32830 TTACTCTAAT
*
32840 AAAT-AAA-AAAAATTAAATATC
1 AAATCAAATAAAAATTAAATAAC
32861 AAATCAAATAAAAATTAAATTAAAC
1 AAATCAAATAAAAATTAAA-T-AAC
*
32886 AAAACAAATAA
1 AAATCAAATAA
32897 CTTAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 10 0.33
24 1 0.03
25 12 0.40
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (23 bp):
AAATCAAATAAAAATTAAATAAC
Found at i:33417 original size:12 final size:12
Alignment explanation
Indices: 33400--33425 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33390 TACTTTGTCA
33400 GTGTATTTTATC
1 GTGTATTTTATC
33412 GTGTATTTTATC
1 GTGTATTTTATC
33424 GT
1 GT
33426 ATTTTATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.19, T:0.58
Consensus pattern (12 bp):
GTGTATTTTATC
Found at i:37223 original size:17 final size:18
Alignment explanation
Indices: 37196--37241 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
37186 GAATCATCTC
37196 TATTATAAAAAATATATA
1 TATTATAAAAAATATATA
37214 TATT-TAAAAAATATAT-
1 TATTATAAAAAATATATA
37230 T-TTGATAAAAAA
1 TATT-ATAAAAAA
37242 AAAAAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.08
16 1 0.04
17 19 0.73
18 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
TATTATAAAAAATATATA
Found at i:44841 original size:23 final size:19
Alignment explanation
Indices: 44789--44828 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
44779 TAAAAGAAGT
44789 CTAATTTATTTGGACTGTA
1 CTAATTTATTTGGACTGTA
44808 CTAATTTATTTGGACTGTA
1 CTAATTTATTTGGACTGTA
44827 CT
1 CT
44829 TTTTATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (19 bp):
CTAATTTATTTGGACTGTA
Found at i:47355 original size:14 final size:14
Alignment explanation
Indices: 47336--47366 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
47326 AGAATAGATT
47336 TTTAATTAATTAAA
1 TTTAATTAATTAAA
47350 TTTAATTAATTAAA
1 TTTAATTAATTAAA
47364 TTT
1 TTT
47367 TTTAAACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:48978 original size:16 final size:16
Alignment explanation
Indices: 48957--49010 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
48947 TTTGATTCAT
48957 TGTAATGGAATAAAAC
1 TGTAATGGAATAAAAC
**
48973 TGTAATGGAATAAAGT
1 TGTAATGGAATAAAAC
* *
48989 TGTAATTGAATAGAAC
1 TGTAATGGAATAAAAC
49005 TGTAAT
1 TGTAAT
49011 TAATAATTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAAAAC
Found at i:54099 original size:21 final size:20
Alignment explanation
Indices: 54060--54099 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
54050 TGAATTTTTT
*
54060 AAATTGAGTTGATTAAAATG
1 AAATTGAGTTGAGTAAAATG
*
54080 AAATTCGAGTTGAGTCAAAT
1 AAATT-GAGTTGAGTAAAAT
54100 CGAATCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (20 bp):
AAATTGAGTTGAGTAAAATG
Found at i:54221 original size:16 final size:16
Alignment explanation
Indices: 54200--54230 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54190 CATGTTCGAG
54200 CACATAAATTTGAAAC
1 CACATAAATTTGAAAC
*
54216 CACATATATTTGAAA
1 CACATAAATTTGAAA
54231 AATTTTAAAA
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:0.48, C:0.16, G:0.06, T:0.29
Consensus pattern (16 bp):
CACATAAATTTGAAAC
Found at i:55425 original size:25 final size:25
Alignment explanation
Indices: 55388--55589 Score: 172
Period size: 25 Copynumber: 8.0 Consensus size: 25
55378 AGACAATCAA
* * *
55388 GATATTTTGTCTGGCTCGTAAGTGC
1 GATATTCTATCTGGCTCGTAAGAGC
*
55413 GGTATTCTATCTGGCTCGTAAGAGC
1 GATATTCTATCTGGCTCGTAAGAGC
* * * *
55438 GATATTATGTCTAGCTCATAAGAGC
1 GATATTCTATCTGGCTCGTAAGAGC
* * * * *
55463 GATATTTTTTCTAGCTCGTAAGTGT
1 GATATTCTATCTGGCTCGTAAGAGC
* * * *
55488 GATATTTTGTCTAGCTCGTAAGAGT
1 GATATTCTATCTGGCTCGTAAGAGC
* *
55513 GGTATTCTATTTGGCTCGTAAGAGC
1 GATATTCTATCTGGCTCGTAAGAGC
*
55538 AATACTT-TATCTGGGCTCGTAAGAGC
1 GATA-TTCTATCT-GGCTCGTAAGAGC
* *
55564 GATACTCTATTTGGGCTCGTAAGAGC
1 GATATTCTATCT-GGCTCGTAAGAGC
55590 TAAACTCTAT
Statistics
Matches: 146, Mismatches: 28, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
25 110 0.75
26 36 0.25
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (25 bp):
GATATTCTATCTGGCTCGTAAGAGC
Found at i:55535 original size:75 final size:75
Alignment explanation
Indices: 55388--55589 Score: 197
Period size: 75 Copynumber: 2.7 Consensus size: 75
55378 AGACAATCAA
* * * *
55388 GATATTTTGTCTGGCTCGTAAGTGCGGTATTCTATCTGGCTCGTAAGAGCGATATTATGTCTAGC
1 GATATTTTATCTGGCTCGTAAGTGCGATATTCTATCTAGCTCGTAAGAGCGATATTATATCTAGC
55453 TCATAAGAGC
66 TCATAAGAGC
* * * * * * * * * *
55463 GATATTTTTTCTAGCTCGTAAGTGTGATATTTTGTCTAGCTCGTAAGAGTGGTATTCTATTTGGC
1 GATATTTTATCTGGCTCGTAAGTGCGATATTCTATCTAGCTCGTAAGAGCGATATTATATCTAGC
*
55528 TCGTAAGAGC
66 TCATAAGAGC
* * * * * *
55538 AATACTTTATCTGGGCTCGTAAGAGCGATACTCTATTTGGGCTCGTAAGAGC
1 GATATTTTATCT-GGCTCGTAAGTGCGATATTCTATCT-AGCTCGTAAGAGC
55590 TAAACTCTAT
Statistics
Matches: 99, Mismatches: 26, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
75 70 0.71
76 18 0.18
77 11 0.11
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (75 bp):
GATATTTTATCTGGCTCGTAAGTGCGATATTCTATCTAGCTCGTAAGAGCGATATTATATCTAGC
TCATAAGAGC
Found at i:55561 original size:26 final size:26
Alignment explanation
Indices: 55518--55606 Score: 128
Period size: 26 Copynumber: 3.5 Consensus size: 26
55508 AGAGTGGTAT
55518 TCTATTT-GGCTCGTAAGAGCAATAC
1 TCTATTTGGGCTCGTAAGAGCAATAC
* * *
55543 TTTATCTGGGCTCGTAAGAGCGATAC
1 TCTATTTGGGCTCGTAAGAGCAATAC
55569 TCTATTTGGGCTCGTAAGAGCTAA-AC
1 TCTATTTGGGCTCGTAAGAGC-AATAC
55595 TCTATTTGGGCT
1 TCTATTTGGGCT
55607 TGTTTGAGCT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
25 5 0.09
26 50 0.89
27 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (26 bp):
TCTATTTGGGCTCGTAAGAGCAATAC
Found at i:55605 original size:52 final size:51
Alignment explanation
Indices: 55501--55606 Score: 142
Period size: 52 Copynumber: 2.1 Consensus size: 51
55491 ATTTTGTCTA
* * * *
55501 GCTCGTAAGAGTGGTATTCTATTTGGCTCGTAAGAGCAATACTTTATCTGG
1 GCTCGTAAGAGCGATACTCTATTTGGCTCGTAAGAGCAATACTCTATCTGG
*
55552 GCTCGTAAGAGCGATACTCTATTTGGGCTCGTAAGAGCTAA-ACTCTATTTGG
1 GCTCGTAAGAGCGATACTCTATTT-GGCTCGTAAGAGC-AATACTCTATCTGG
55604 GCT
1 GCT
55607 TGTTTGAGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 21 0.44
52 25 0.52
53 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (51 bp):
GCTCGTAAGAGCGATACTCTATTTGGCTCGTAAGAGCAATACTCTATCTGG
Found at i:56124 original size:43 final size:42
Alignment explanation
Indices: 56030--56423 Score: 428
Period size: 43 Copynumber: 9.2 Consensus size: 42
56020 TGCAAAAAAT
* *
56030 GCCGCTAAAGAAAATGGTCTTTAGCGGCACTTTCCCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCACAAAC
* * *
56072 ACCGCTAAAGAACATGGTCTTTAGTGGTGCTTTCCCCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTT-CCCACAAAC
*
56115 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCACACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCACAAAC
** * *
56158 GCTTCTAAAGAACATGGTCTTTAGCAGCGTTTTCCTCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCC-CACAAAC
* * * *
56201 GTCGCTAAAGAACACGGTCTTTAGCGGCACTTTTCACACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCACAAAC
* * *
56244 GCCGTTAAAAAACACGGTCTTTAGCGGCGCTTTCCCCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTT-CCCACAAAC
* * * * *
56287 ACCGCTAAAGAACATGATATTTAATCGGCACTTTCCCACAAAC
1 GCCGCTAAAGAACATGGTCTTT-AGCGGCGCTTTCCCACAAAC
* * ** *
56330 GCCACTAAAGAACACGGTCTTTAGCGTTGCTTTTCCCACAAAT
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCACAAAC
* * * * *
56373 GTCGCTAAAAAACACGATCTTTAGCGACGCTTTCCCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCACAAAC
*
56415 ACCGCTAAA
1 GCCGCTAAA
56424 TTACCTGATT
Statistics
Matches: 291, Mismatches: 54, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
42 57 0.20
43 218 0.75
44 16 0.05
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (42 bp):
GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCACAAAC
Found at i:56263 original size:129 final size:128
Alignment explanation
Indices: 56031--56423 Score: 500
Period size: 129 Copynumber: 3.1 Consensus size: 128
56021 GCAAAAAATG
* * *
56031 CCGCTAAAGAAAATGGTCTTTAGCGGCACTTTCCCACAAACACCGCTAAAGAACATGGTCTTTAG
1 CCGCTAAAGAACATGGTCTTTAGCGGCACTTTCCCACAAACGCCGCTAAAGAACACGGTCTTTAG
* * * * * *
56096 TGGTGCTTTCCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCACACAAACG
66 CGGTGCTTTTCCCACAAACGCCGCTAAAAAACACGGTCTTTAGCGGCGCTTTTCCCACAAACA
** * ** *
56159 CTTCTAAAGAACATGGTCTTTAGCAGCGTTTTCCTCACAAACGTCGCTAAAGAACACGGTCTTTA
1 CCGCTAAAGAACATGGTCTTTAGCGGCACTTTCC-CACAAACGCCGCTAAAGAACACGGTCTTTA
** * * *
56224 GCGGCACTTTTCACACAAACGCCGTTAAAAAACACGGTCTTTAGCGGCGCTTTCCCCACAAACA
65 GCGGTGCTTTTCCCACAAACGCCGCTAAAAAACACGGTCTTTAGCGGCGCTTTTCCCACAAACA
* * * *
56288 CCGCTAAAGAACATGATATTTAATCGGCACTTTCCCACAAACGCCACTAAAGAACACGGTCTTTA
1 CCGCTAAAGAACATGGTCTTT-AGCGGCACTTTCCCACAAACGCCGCTAAAGAACACGGTCTTTA
* * * * *
56353 GCGTTGCTTTTCCCACAAATGTCGCTAAAAAACACGATCTTTAGCGACGC-TTTCCCACAAACA
65 GCGGTGCTTTTCCCACAAACGCCGCTAAAAAACACGGTCTTTAGCGGCGCTTTTCCCACAAACA
56416 CCGCTAAA
1 CCGCTAAA
56424 TTACCTGATT
Statistics
Matches: 223, Mismatches: 40, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
128 48 0.22
129 166 0.74
130 9 0.04
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (128 bp):
CCGCTAAAGAACATGGTCTTTAGCGGCACTTTCCCACAAACGCCGCTAAAGAACACGGTCTTTAG
CGGTGCTTTTCCCACAAACGCCGCTAAAAAACACGGTCTTTAGCGGCGCTTTTCCCACAAACA
Found at i:56737 original size:21 final size:21
Alignment explanation
Indices: 56708--56748 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
56698 TGCTTCCCTA
* *
56708 GCTTGCCTCGTTACTGCCTCT
1 GCTTCCCTCGCTACTGCCTCT
*
56729 GCTTCCCTCGCTGCTGCCTC
1 GCTTCCCTCGCTACTGCCTC
56749 CACTTTAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.44, G:0.20, T:0.34
Consensus pattern (21 bp):
GCTTCCCTCGCTACTGCCTCT
Found at i:60920 original size:25 final size:25
Alignment explanation
Indices: 60886--60936 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
60876 AATAGCTGCG
**
60886 TTTGTAGGAAAACGCTGCTATTACT
1 TTTGTAGGAAAACGCCACTATTACT
*
60911 TTTGTGGGAAAACGCCACTATTACT
1 TTTGTAGGAAAACGCCACTATTACT
60936 T
1 T
60937 AACCTTTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (25 bp):
TTTGTAGGAAAACGCCACTATTACT
Found at i:61111 original size:42 final size:40
Alignment explanation
Indices: 60984--61115 Score: 138
Period size: 42 Copynumber: 3.2 Consensus size: 40
60974 GGTCAGAGCA
* * * *
60984 TTAGCGGCGCTATCAATAAACGCTGCTAATGCTCTGACCTT
1 TTAGCGGCGCTATGAAAAAACGCCGTTAATGCTCTGACC-T
* * * * *
61025 TTAGCAGCGTTTATGATAAAGCGCCGTTAATGCTCTGACTT
1 TTAGCGGCG-CTATGAAAAAACGCCGTTAATGCTCTGACCT
*
61066 TTAGCGGCGCCTATGAGAAAAACGCCGTTAATGCTCTAACCT
1 TTAGCGGCG-CTATGA-AAAAACGCCGTTAATGCTCTGACCT
61108 TTAGCGGC
1 TTAGCGGC
61116 ATTTACGGGG
Statistics
Matches: 73, Mismatches: 16, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
41 22 0.30
42 51 0.70
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (40 bp):
TTAGCGGCGCTATGAAAAAACGCCGTTAATGCTCTGACCT
Found at i:61155 original size:83 final size:82
Alignment explanation
Indices: 60965--61156 Score: 199
Period size: 83 Copynumber: 2.3 Consensus size: 82
60955 CACCATAAAT
* * *
60965 GCCGCTAAAGGTCAGAGCATTAGCGGCGCTATCAATAAACGCTGCTAATGCTCTGACCTTTTAGC
1 GCCGCTAAAGGTCAGAGCATTAGCGGCGCTATCAAAAAACGCCGCTAATGCTCTAACCTTTTAGC
* * *
61030 AGCGTTTATGATAAAGC
66 AGCATTTACGAGAAAGC
* * * * * * *
61047 GCCGTTAATGCTCTGA-CTTTTAGCGGCGCCTATGAGAAAAACGCCGTTAATGCTCTAACC-TTT
1 GCCGCTAAAGGTCAGAGC-ATTAGCGGCG-CTATCA-AAAAACGCCGCTAATGCTCTAACCTTTT
* * *
61110 AGCGGCATTTACGGGGAAGC
63 AGCAGCATTTACGAGAAAGC
61130 GCCGCTAAAGGTCAGAGCATTAGCGGC
1 GCCGCTAAAGGTCAGAGCATTAGCGGC
61157 ATTTTTCCAT
Statistics
Matches: 85, Mismatches: 21, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
81 1 0.01
82 21 0.25
83 42 0.49
84 21 0.25
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (82 bp):
GCCGCTAAAGGTCAGAGCATTAGCGGCGCTATCAAAAAACGCCGCTAATGCTCTAACCTTTTAGC
AGCATTTACGAGAAAGC
Found at i:63366 original size:41 final size:41
Alignment explanation
Indices: 63303--63677 Score: 380
Period size: 41 Copynumber: 9.1 Consensus size: 41
63293 TAAAATATCG
*
63303 GCGTTTATGAGAAAGCGCCGCTAATGCTTTGACCTTTAGCA
1 GCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTTTAGCA
* *
63344 GTGTTTATGAGAAAGCGTCGCTAATGCTCTGACCTTTAGCA
1 GCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTTTAGCA
* * * * *
63385 GCGTTTGTGGGAAATCGCTGCTAATGCTCTGACCTTTAGTA
1 GCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTTTAGCA
* * * * * *
63426 GCGTTTGA-GGGAAAGCACCGTTAATACTCTGACCTTTAACT
1 GCGTTT-ATGAGAAAGCGCCGCTAATGCTCTGACCTTTAGCA
* * * *
63467 GCATTTGA-GGGAAAGCGTCGCTAATGCTCTGACCTTTAGCG
1 GCGTTT-ATGAGAAAGCGCCGCTAATGCTCTGACCTTTAGCA
* * *
63508 GTGTTT-TAAGGAAAGCGCCGCTAATGCTCTGACCTTTAGCG
1 GCGTTTATGA-GAAAGCGCCGCTAATGCTCTGACCTTTAGCA
* ** * *
63549 GCGTTTATGAGAATGCGCCATTAATGCTCTGATCTTTAGCG
1 GCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTTTAGCA
* *
63590 GGGTTTATGAGAAAGCGTCGCTAATGCTCTGACCTTTAGCA
1 GCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTTTAGCA
* *** * *
63631 ACGTTT-TCCCATAAGCGCCGCTAATGCTCTGACTTTTAGCC
1 GCGTTTATGAGA-AAGCGCCGCTAATGCTCTGACCTTTAGCA
63672 GCGTTT
1 GCGTTT
63678 GTGATAAGGT
Statistics
Matches: 276, Mismatches: 53, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
40 2 0.01
41 272 0.99
42 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (41 bp):
GCGTTTATGAGAAAGCGCCGCTAATGCTCTGACCTTTAGCA
Found at i:64665 original size:21 final size:21
Alignment explanation
Indices: 64636--64684 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
64626 CTTGACTCGA
*
64636 ACTCTAACTCGAAACGAGTTG
1 ACTCGAACTCGAAACGAGTTG
64657 ACTCGAACTCGAAACGAGTTG
1 ACTCGAACTCGAAACGAGTTG
64678 ACTCGAA
1 ACTCGAA
64685 TAATTCGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (21 bp):
ACTCGAACTCGAAACGAGTTG
Found at i:64694 original size:9 final size:9
Alignment explanation
Indices: 64678--64707 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
64668 AAACGAGTTG
64678 ACTCGAATA
1 ACTCGAATA
*
64687 ATTCGAATA
1 ACTCGAATA
64696 ACTCGAATA
1 ACTCGAATA
64705 ACT
1 ACT
64708 TGAAATTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (9 bp):
ACTCGAATA
Found at i:65400 original size:25 final size:25
Alignment explanation
Indices: 65372--65420 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
65362 TCTCTTTCAA
*
65372 TTAATAAAATTCT-TTGAGTTTTTTC
1 TTAA-AAAATTCTCTCGAGTTTTTTC
*
65397 TTAAAAATTTCTCTCGAGTTTTTT
1 TTAAAAAATTCTCTCGAGTTTTTT
65421 TTTTTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (25 bp):
TTAAAAAATTCTCTCGAGTTTTTTC
Found at i:66750 original size:21 final size:21
Alignment explanation
Indices: 66726--66782 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
66716 TCTTTCATTT
* *
66726 TCACTATTGTTTTCTCTCACC
1 TCACCATTGTTTTCCCTCACC
* *
66747 TCACCATCGTTTTCCCTTACC
1 TCACCATTGTTTTCCCTCACC
66768 TCACCATTGTTTTCC
1 TCACCATTGTTTTCC
66783 TTTTTTTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.14, C:0.37, G:0.05, T:0.44
Consensus pattern (21 bp):
TCACCATTGTTTTCCCTCACC
Found at i:67789 original size:23 final size:24
Alignment explanation
Indices: 67740--67794 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
67730 CAAATTAAAT
*
67740 ATCGTATCTAAAAAAAAATCATCC
1 ATCGTATCTAAAAAAAAACCATCC
* *
67764 ATCGTATCT-AAATAAAACCATTC
1 ATCGTATCTAAAAAAAAACCATCC
67787 ATC-TATCT
1 ATCGTATCT
67795 CCATGGCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 5 0.18
23 14 0.50
24 9 0.32
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.31
Consensus pattern (24 bp):
ATCGTATCTAAAAAAAAACCATCC
Found at i:68153 original size:18 final size:18
Alignment explanation
Indices: 68130--68167 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
68120 TTGAAGAGGG
*
68130 TGGCATGGTGGGAGAAGT
1 TGGCATGATGGGAGAAGT
*
68148 TGGCATGATGGGAGGAGT
1 TGGCATGATGGGAGAAGT
68166 TG
1 TG
68168 ATTGTGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.50, T:0.24
Consensus pattern (18 bp):
TGGCATGATGGGAGAAGT
Found at i:68262 original size:24 final size:24
Alignment explanation
Indices: 68223--68268 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
68213 TAACAGTTTG
** *
68223 AGAAGGAGCTGGTGGAGCAGAATC
1 AGAAGGAGCTACTGGAGAAGAATC
68247 AGAAGGAGCTACTGGAGAAGAA
1 AGAAGGAGCTACTGGAGAAGAA
68269 GCTATTGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.39, T:0.11
Consensus pattern (24 bp):
AGAAGGAGCTACTGGAGAAGAATC
Found at i:68396 original size:23 final size:21
Alignment explanation
Indices: 68370--68531 Score: 83
Period size: 21 Copynumber: 7.3 Consensus size: 21
68360 AAACTACATA
68370 ATACATATAACAGTAAACATAAC
1 ATACATATAACA-T-AACATAAC
68393 ATACATAATTATACAT-ACAT-A-
1 ATACAT-A-TA-ACATAACATAAC
68414 ATACATATAACAATACACATAAC
1 ATACATATAAC-ATA-ACATAAC
*
68437 ATACATACAA-ATATACA-AAC
1 ATACATATAACATA-ACATAAC
68457 ATAACAGTA-AACATAACAT-AC
1 AT-ACA-TATAACATAACATAAC
68478 ATA-ATA-ATACATACACAATATAC
1 ATACATATA-ACATA-AC-ATA-AC
68501 ATAACATACATAACAGT-ACATAAC
1 AT-ACAT--ATAACA-TAACATAAC
68525 ATACATA
1 ATACATA
68532 ATTATACATA
Statistics
Matches: 114, Mismatches: 2, Indels: 48
0.70 0.01 0.29
Matches are distributed among these distances:
18 5 0.04
19 10 0.09
20 9 0.08
21 31 0.27
22 7 0.06
23 27 0.24
24 6 0.05
25 8 0.07
26 5 0.04
27 4 0.04
28 2 0.02
ACGTcount: A:0.56, C:0.19, G:0.02, T:0.23
Consensus pattern (21 bp):
ATACATATAACATAACATAAC
Found at i:68419 original size:44 final size:44
Alignment explanation
Indices: 68364--68545 Score: 168
Period size: 44 Copynumber: 4.1 Consensus size: 44
68354 TAAACAAAAC
68364 TACATAATACATATAACAGTAAACATAACATACATAATTATACA
1 TACATAATACATATAACAGTAAACATAACATACATAATTATACA
* * *
68408 TACATAATACATATAACAATACACATAACATACATACA--A-ATA
1 TACATAATACATATAACAGTAAACATAACATACATA-ATTATACA
*
68450 TAC--AA-AC--ATAACAGTAAACATAACATACATAATAATACA
1 TACATAATACATATAACAGTAAACATAACATACATAATTATACA
68489 TACACAATATACATAACATACATAACAGT--ACATAACATACATAATTATACA
1 T--AC---ATA-AT-ACAT--ATAACAGTAAACATAACATACATAATTATACA
68540 TACATA
1 TACATA
68546 CACAAACAGT
Statistics
Matches: 113, Mismatches: 7, Indels: 34
0.73 0.05 0.22
Matches are distributed among these distances:
36 1 0.01
37 22 0.19
38 1 0.01
39 5 0.04
40 2 0.02
41 2 0.02
42 5 0.04
43 1 0.01
44 34 0.30
45 1 0.01
46 4 0.04
47 1 0.01
49 4 0.04
51 22 0.19
53 8 0.07
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (44 bp):
TACATAATACATATAACAGTAAACATAACATACATAATTATACA
Found at i:68491 original size:14 final size:13
Alignment explanation
Indices: 68391--68545 Score: 81
Period size: 12 Copynumber: 12.7 Consensus size: 13
68381 AGTAAACATA
68391 ACATACATAATTAT
1 ACATACATAA-TAT
68405 ACATACAT-A-AT
1 ACATACATAATAT
*
68416 ACAT--ATAACAAT
1 ACATACATAA-TAT
*
68428 AC--ACATAACAT
1 ACATACATAATAT
68439 ACATACA-AATAT
1 ACATACATAATAT
* *
68451 ACAAACATAACAGT
1 ACATACATAATA-T
*
68465 A-A-ACATAACAT
1 ACATACATAATAT
68476 ACATA-AT-A-AT
1 ACATACATAATAT
*
68486 ACATACACAATAT
1 ACATACATAATAT
68499 ACATAACATACATA-
1 ACAT-ACATA-ATAT
*
68513 ACAGTACATAACAT
1 ACA-TACATAATAT
68527 ACATA-AT--TAT
1 ACATACATAATAT
68537 ACATACATA
1 ACATACATA
68546 CACAAACAGT
Statistics
Matches: 113, Mismatches: 8, Indels: 42
0.69 0.05 0.26
Matches are distributed among these distances:
9 2 0.02
10 15 0.13
11 16 0.14
12 32 0.28
13 19 0.17
14 25 0.22
15 4 0.04
ACGTcount: A:0.55, C:0.19, G:0.01, T:0.25
Consensus pattern (13 bp):
ACATACATAATAT
Found at i:68505 original size:32 final size:33
Alignment explanation
Indices: 68393--68547 Score: 125
Period size: 37 Copynumber: 4.4 Consensus size: 33
68383 TAAACATAAC
* *
68393 ATACATAATTATACATACATAATACATATAACAAT
1 ATACATAA-CATACATACATAATACATA-CACAAT
* * * *
68428 ACACATAACATACATACAAATATACAAACATAACAGT
1 ATACATAACATACATACATA-ATACATAC---ACAAT
*
68465 AAACATAACATACATA-ATAATACATACACAAT
1 ATACATAACATACATACATAATACATACACAAT
*
68497 ATACATAACATACATAACAGTACATAACATACATAATT
1 ATACATAACATACAT-ACA-TA-AT-ACATACACAA-T
68535 ATACAT-ACATACA
1 ATACATAACATACA
68548 CAAACAGTAG
Statistics
Matches: 98, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
32 18 0.18
33 1 0.01
34 11 0.11
35 22 0.22
36 4 0.04
37 35 0.36
38 7 0.07
ACGTcount: A:0.55, C:0.19, G:0.01, T:0.25
Consensus pattern (33 bp):
ATACATAACATACATACATAATACATACACAAT
Found at i:68507 original size:37 final size:36
Alignment explanation
Indices: 68338--68547 Score: 121
Period size: 37 Copynumber: 5.9 Consensus size: 36
68328 AATAAACAGT
* *
68338 CATACA-A-ACATA-ACAATAAACAAAAC-TACATA
1 CATACATATACATACACAATATACATAACATACATA
* *
68370 -ATACATATAACAGTAAAC-ATA-ACAT-ACATAATTATA
1 CATACATAT-ACA-TACACAATATACATAACAT-A-CATA
* *
68406 CATACATAATACATATAACAATACACATAACATACATA
1 CATACAT-ATACATA-CACAATATACATAACATACATA
68444 CA-A-ATATACA-A-AC-ATA-ACAGTAAACATAACATA
1 CATACATATACATACACAATATACA-T-AACAT-ACATA
68477 CATA-ATAATACATACACAATATACATAACATACATAA
1 CATACAT-ATACATACACAATATACATAACATACAT-A
*
68514 CAGTACATA-ACATACATAATTATACAT-ACATACA
1 CA-TACATATACATACACAA-TATACATAACATACA
68548 CAAACAGTAG
Statistics
Matches: 147, Mismatches: 4, Indels: 49
0.74 0.02 0.25
Matches are distributed among these distances:
30 3 0.02
31 9 0.06
32 8 0.05
33 9 0.06
34 11 0.07
35 16 0.11
36 14 0.10
37 39 0.27
38 24 0.16
39 10 0.07
40 4 0.03
ACGTcount: A:0.57, C:0.19, G:0.01, T:0.23
Consensus pattern (36 bp):
CATACATATACATACACAATATACATAACATACATA
Found at i:68691 original size:30 final size:30
Alignment explanation
Indices: 68655--68718 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
68645 CAACAAAAAC
*
68655 AAAAAATAAAAGTTAGATATAATACGAATT
1 AAAAAATAAAAGTTAGATATAATACGAAAT
* *
68685 AAAAAATAAAAGTTATATATAATATGAAAT
1 AAAAAATAAAAGTTAGATATAATACGAAAT
68715 AAAA
1 AAAA
68719 CAATCAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.27
Consensus pattern (30 bp):
AAAAAATAAAAGTTAGATATAATACGAAAT
Found at i:69202 original size:19 final size:19
Alignment explanation
Indices: 69164--69202 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
69154 TTGTTGATTT
* * *
69164 AATTTTTTTTTAGTTTTTC
1 AATTTTTATTTAATTCTTC
69183 AATTTTTATTTAATTCTTC
1 AATTTTTATTTAATTCTTC
69202 A
1 A
69203 TTAAATTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (19 bp):
AATTTTTATTTAATTCTTC
Found at i:73536 original size:7 final size:7
Alignment explanation
Indices: 73522--73557 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
73512 TAATAAAAAA
73522 TTTA-AT
1 TTTATAT
73528 TTTATAT
1 TTTATAT
73535 TTTATAT
1 TTTATAT
73542 TTTATAT
1 TTTATAT
73549 TTTA-AT
1 TTTATAT
73555 TTT
1 TTT
73558 CATACCAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 9 0.31
7 20 0.69
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATAT
Found at i:74933 original size:30 final size:31
Alignment explanation
Indices: 74868--74936 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
74858 TGTTAATCAA
74868 TGACTGTTTTGTCACTTTTCAATAATGTTAG
1 TGACTGTTTTGTCACTTTTCAATAATGTTAG
74899 TGACTGTTTTGTCACATTTTC-A-AA-GTTGAG
1 TGACTGTTTTGTCAC-TTTTCAATAATGTT-AG
74929 TGACTGTT
1 TGACTGTT
74937 GTGTTAAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.33
31 16 0.44
32 5 0.14
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (31 bp):
TGACTGTTTTGTCACTTTTCAATAATGTTAG
Found at i:83211 original size:2 final size:2
Alignment explanation
Indices: 83204--83228 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
83194 CTATACATGA
83204 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
83229 AGAATGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:86291 original size:3 final size:3
Alignment explanation
Indices: 86283--86308 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
86273 GACTCGTCTT
86283 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
86309 TTGGTGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:89874 original size:24 final size:24
Alignment explanation
Indices: 89838--89883 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
89828 GAAAAATAAG
*
89838 AAGAAGAACAAAAGAGAAAAGGAT
1 AAGAAGAACAAAAGAAAAAAGGAT
** *
89862 AAGAAGAGGAAAATAAAAAAGG
1 AAGAAGAACAAAAGAAAAAAGG
89884 TAATTTTATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.26, T:0.04
Consensus pattern (24 bp):
AAGAAGAACAAAAGAAAAAAGGAT
Found at i:92723 original size:28 final size:28
Alignment explanation
Indices: 92663--92749 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 28
92653 GGACATTTTT
* *
92663 TATTTGAAATTAATTAAGTTTATAA-ATG
1 TATTTGAAATTAATTATGTTTA-AATTTG
*
92691 AATTTGAAATTAATTATGTTTAAATTTG
1 TATTTGAAATTAATTATGTTTAAATTTG
* * **
92719 TATTT--AATTAATAATTTTTATGTTTG
1 TATTTGAAATTAATTATGTTTAAATTTG
92745 TATTT
1 TATTT
92750 TGGTTTAAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 22 0.44
27 2 0.04
28 26 0.52
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (28 bp):
TATTTGAAATTAATTATGTTTAAATTTG
Found at i:92727 original size:26 final size:26
Alignment explanation
Indices: 92698--92749 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
92688 ATGAATTTGA
*
92698 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
* **
92724 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
92750 TGGTTTAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTGTATTT
Found at i:92948 original size:16 final size:17
Alignment explanation
Indices: 92907--92952 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
92897 CGGTTCATGG
*
92907 TTTAAGGTTTATGATTA
1 TTTAAGGTTTAAGATTA
*
92924 TTTAGGGTTTAAGATT-
1 TTTAAGGTTTAAGATTA
92940 TTTAAGGTTTAAG
1 TTTAAGGTTTAAG
92953 GTATTGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (17 bp):
TTTAAGGTTTAAGATTA
Found at i:94078 original size:43 final size:43
Alignment explanation
Indices: 94014--94109 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
94004 ATTGCACAAT
* * * *
94014 TAATAACATGTCATGATATTAATAAGAGTCAAGTAATATAATT
1 TAATAACATGCCATCATATTAACAAGAGTCAAGTAATATAATG
* *
94057 TAGTAACATGCCATCATATTAACATGAGTCAAGTAATATAATG
1 TAATAACATGCCATCATATTAACAAGAGTCAAGTAATATAATG
94100 TAATAACATG
1 TAATAACATG
94110 TCAATGAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.32
Consensus pattern (43 bp):
TAATAACATGCCATCATATTAACAAGAGTCAAGTAATATAATG
Found at i:95462 original size:24 final size:26
Alignment explanation
Indices: 95435--95483 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
95425 TTATTATTAT
*
95435 TATTATTAT-ATTTAAAT-TTTTAAA
1 TATTATTATAATTAAAATCTTTTAAA
*
95459 TATTATTTTAATTAAAATCTTTTAA
1 TATTATTATAATTAAAATCTTTTAA
95484 CCTAAACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 7 0.33
26 6 0.29
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TATTATTATAATTAAAATCTTTTAAA
Found at i:95462 original size:27 final size:26
Alignment explanation
Indices: 95432--95483 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
95422 TTATTATTAT
*
95432 TATTATTATTATATTTAAAT-TTTTAAA
1 TATTATT-TTA-ATTAAAATCTTTTAAA
95459 TATTATTTTAATTAAAATCTTTTAA
1 TATTATTTTAATTAAAATCTTTTAA
95484 CCTAAACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 9 0.39
27 7 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTATTTTAATTAAAATCTTTTAAA
Found at i:95851 original size:21 final size:21
Alignment explanation
Indices: 95826--95865 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
95816 TACTTACTAC
*
95826 TACTAACAAAATAAAATTACT
1 TACTAAAAAAATAAAATTACT
*
95847 TACTAAAAAAATTAAATTA
1 TACTAAAAAAATAAAATTA
95866 AAAATAATCA
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:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (21 bp):
TACTAAAAAAATAAAATTACT
Found at i:95930 original size:12 final size:12
Alignment explanation
Indices: 95913--95953 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
95903 TTTACTCAAC
95913 TAAATAAAAAAT
1 TAAATAAAAAAT
*
95925 TAAATAACAAAT
1 TAAATAAAAAAT
*
95937 CAAATAAAAAAT
1 TAAATAAAAAAT
95949 TAAAT
1 TAAAT
95954 TAAACAAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAATAAAAAAT
Found at i:95941 original size:24 final size:26
Alignment explanation
Indices: 95914--95969 Score: 89
Period size: 24 Copynumber: 2.2 Consensus size: 26
95904 TTACTCAACT
*
95914 AAATAAAAAATTAAA-T-AACAAATC
1 AAATAAAAAATTAAATTAAACAAAAC
95938 AAATAAAAAATTAAATTAAACAAAAC
1 AAATAAAAAATTAAATTAAACAAAAC
95964 AAATAA
1 AAATAA
95970 CTTAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.52
25 1 0.03
26 13 0.45
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (26 bp):
AAATAAAAAATTAAATTAAACAAAAC
Found at i:98289 original size:16 final size:16
Alignment explanation
Indices: 98249--98293 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
98239 AGTTTAGGGT
*
98249 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
98266 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
98280 TTAAAAATTTATTT
1 TTAAAAATTTATTT
98294 TCATTCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 10 0.40
17 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:99733 original size:2 final size:2
Alignment explanation
Indices: 99726--99756 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
99716 TGCTTTATTT
99726 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
99757 CAGCTAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:108955 original size:59 final size:58
Alignment explanation
Indices: 108887--109075 Score: 188
Period size: 59 Copynumber: 3.2 Consensus size: 58
108877 GGGAAGTTCG
* * * *
108887 GGGTC-AAAAATAGAATTTTTAGACATTCGGGGGT-AATATGTAATGTTTGGAAAAATC
1 GGGTCAAAAAATGGAA-TTTTAGAAATTCGGGGGTAAAAATGTAATTTTTGGAAAAATC
* * *
108944 GTGGTCAAAAAA-GGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAAAATTA
1 G-GGTCAAAAAATGGAATTTTAGAAA-TTCGGGGGTAAAAATGTAATTTTTGG-AAAAA-TC
** * *
109005 GGGT-TTAAAATGGAATTTTAGAAATTTGGGGGTAAAAATGTAATTTTTTGAAAAATC
1 GGGTCAAAAAATGGAATTTTAGAAATTCGGGGGTAAAAATGTAATTTTTGGAAAAATC
*
109062 AAGGTCAAAAAATG
1 -GGGTCAAAAAATG
109076 TAAAAGTTTA
Statistics
Matches: 106, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
57 9 0.08
58 23 0.22
59 52 0.49
60 20 0.19
61 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (58 bp):
GGGTCAAAAAATGGAATTTTAGAAATTCGGGGGTAAAAATGTAATTTTTGGAAAAATC
Found at i:109049 original size:28 final size:29
Alignment explanation
Indices: 108975--109051 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
108965 GAAAGTTCGA
108975 GGGTAAAAATGTAATTTTTGGAAAAAATTAG
1 GGGTAAAAATGTAA-TTTT-GAAAAAATTAG
* * * * * *
109006 GGTTTAAAATGGAATTTT-AGAAATTTGG
1 GGGTAAAAATGTAATTTTGAAAAAATTAG
109034 GGGTAAAAATGTAATTTT
1 GGGTAAAAATGTAATTTT
109052 TTGAAAAATC
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
28 22 0.59
30 4 0.11
31 11 0.30
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTGAAAAAATTAG
Found at i:109944 original size:26 final size:27
Alignment explanation
Indices: 109897--109949 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
109887 ATTTAAAAAA
109897 TTTTAAAACCCTTTTTC-TTTTTCTTT
1 TTTTAAAACCCTTTTTCATTTTTCTTT
*
109923 TTTTAAAAGCC-TTTTCGATTTTTCTTT
1 TTTTAAAACCCTTTTTC-ATTTTTCTTT
109950 GAAAATCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 10 0.42
27 9 0.38
ACGTcount: A:0.17, C:0.17, G:0.04, T:0.62
Consensus pattern (27 bp):
TTTTAAAACCCTTTTTCATTTTTCTTT
Found at i:110261 original size:3 final size:3
Alignment explanation
Indices: 110253--110332 Score: 117
Period size: 3 Copynumber: 26.0 Consensus size: 3
110243 TCGTTTTCTC
110253 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
110301 TTA TTTA TTA CTT- TTG TTA TTA TTA TTTA TTA
1 TTA -TTA TTA -TTA TTA TTA TTA TTA -TTA TTA
110333 AAAGCTTTGA
Statistics
Matches: 72, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
2 2 0.03
3 62 0.86
4 8 0.11
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:111032 original size:6 final size:6
Alignment explanation
Indices: 111005--111074 Score: 76
Period size: 6 Copynumber: 12.2 Consensus size: 6
110995 ACATTTATTT
* *
111005 ATTTAA ATTTATA A--TAA TTTTAA ATTTAA ACTTAA A-TTAA ATTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
111051 ATTTAA A-ATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
111075 AGGGGCCGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
4 1 0.02
5 11 0.20
6 40 0.74
7 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:111034 original size:23 final size:23
Alignment explanation
Indices: 111005--111074 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
110995 ACATTTATTT
* *
111005 ATTTAAATTTATAA-TAATTTTAA
1 ATTTAAACTTA-AATTAAATTTAA
111028 ATTTAAACTTAAATTAAATTTAA
1 ATTTAAACTTAAATTAAATTTAA
*
111051 ATTTAAA-ATAAATTTAAATTTAA
1 ATTTAAACTTAAA-TTAAATTTAA
111074 A
1 A
111075 AGGGGCCGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 6 0.14
23 36 0.86
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAAACTTAAATTAAATTTAA
Found at i:111062 original size:11 final size:12
Alignment explanation
Indices: 111024--111074 Score: 61
Period size: 11 Copynumber: 4.4 Consensus size: 12
111014 TATAATAATT
111024 TTAAATTTAAAC
1 TTAAATTTAAAC
*
111036 TTAAA-TTAAAT
1 TTAAATTTAAAC
111047 TTAAATTTAAA-
1 TTAAATTTAAAC
* *
111058 ATAAATTTAAAT
1 TTAAATTTAAAC
111070 TTAAA
1 TTAAA
111075 AGGGGCCGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 20 0.59
12 14 0.41
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TTAAATTTAAAC
Found at i:111075 original size:17 final size:17
Alignment explanation
Indices: 111025--111075 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
111015 ATAATAATTT
* *
111025 TAAATTTAAACTTAAAT
1 TAAATTTAAATTTAAAA
111042 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
111059 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
111076 GGGGCCGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:111320 original size:59 final size:57
Alignment explanation
Indices: 111228--111343 Score: 187
Period size: 59 Copynumber: 2.0 Consensus size: 57
111218 ACACTTGACT
*
111228 TGTAGTTCATTCTACTCCATTACGACTGCGGGGAGAGTGTGATCTATTATCCCATTTTG
1 TGTAGTTCATTCTACTCCATTACGACTGC-GGG-GAGTGTGATATATTATCCCATTTTG
* *
111287 TGTAGTTCATTCTACTCCATTGCGACTGCGGGGAGTGTGATATGTTATCCCATTTTG
1 TGTAGTTCATTCTACTCCATTACGACTGCGGGGAGTGTGATATATTATCCCATTTTG
111344 CTGCATGCTT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 23 0.43
58 3 0.06
59 28 0.52
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (57 bp):
TGTAGTTCATTCTACTCCATTACGACTGCGGGGAGTGTGATATATTATCCCATTTTG
Found at i:111664 original size:49 final size:48
Alignment explanation
Indices: 111602--112093 Score: 244
Period size: 49 Copynumber: 10.0 Consensus size: 48
111592 TTTCCGCTTG
* *
111602 TGTCTTCGTGGTACAGGATCCGTCGTTGCAGCTTAGATCTTTCCCTTCA
1 TGTCTT-GAGGTACAGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTCA
* * * * * *
111651 TGTCTCTGAGGTACTAGG-TTCGCCATTAC-GACTTAAACCTTTCCCTTTA
1 TGTCT-TGAGGTAC-AGGATCCGCCGTTGCAG-CTTAGATCTTTCCCTTCA
* ** * *
111700 TGTCTTCATGGTATTGGATCCGCCGTTGCGGGTTAGATCTTTCCCTTCA
1 TGTCTTGA-GGTACAGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTCA
* * * * * *
111749 TGTCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCA
1 TGTCTT-GAGGTACAGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTCA
* * * * * * * *
111798 TG-CTTCTGAGGAACTAGG-TTCGCCATTACGGCTTAAACCTTTCCCTTAA
1 TGTC-T-TGAGGTAC-AGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTCA
* * ** *
111847 TGTCTTCATGGTACTGGATCCATCGTTGCAGCTTAGATCTTTCCCTT-G
1 TGTCTTGA-GGTACAGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTCA
* * * *
111895 TGTCTTCATGGTACTGGATCCGCTGTTGCAGCTTAGATCTTTCCCTT-G
1 TGTCTTGA-GGTACAGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTCA
* * * * * *
111943 TGTCTTTGTAGGTACAGGGTTCGCCGTTTC-GACTTAAACCTTTCCCTTTA
1 TGTC-TTG-AGGTACAGGATCCGCCGTTGCAG-CTTAGATCTTTCCCTTCA
* * * * * ** * * **
111993 TTTTGTTGTGGTACTGGATTCGCTATTGC-GACTCAAATCTTTCCCTATTG
1 -TGTCTTGAGGTACAGGATCCGCCGTTGCAG-CTTAGATCTTTCCCT-TCA
* * ** *
112043 TATCTTTGCGGTATTGGATCCACCGTTGCAGCTTAGATCTTTCCCTTCA
1 TGTC-TTGAGGTACAGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTCA
112092 TG
1 TG
112094 CTTCATGGTA
Statistics
Matches: 341, Mismatches: 81, Indels: 42
0.73 0.17 0.09
Matches are distributed among these distances:
48 60 0.18
49 232 0.68
50 46 0.13
51 3 0.01
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.39
Consensus pattern (48 bp):
TGTCTTGAGGTACAGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTCA
Found at i:111712 original size:98 final size:97
Alignment explanation
Indices: 111559--111993 Score: 336
Period size: 98 Copynumber: 4.5 Consensus size: 97
111549 TTTTTGATTA
* * * * *
111559 TGAGGTA-TAAGGCTCGCCATTACAACTTAAACCTTTCCGC-TTGTGTCTTCGTGGTACAGGATC
1 TGAGGTACT-AGGTTCGCCGTTACGACTTAAACCTTTCC-CTTTATGTCTTCATGGTACAGGATC
*
111622 CGTCGTTGCAGCTTAGATCTTTCCCTTCATGTCT
64 CGCCGTTGCAGCTTAGATCTTTCCCTTCATGTCT
* **
111656 CTGAGGTACTAGGTTCGCCATTACGACTTAAACCTTTCCCTTTATGTCTTCATGGTATTGGATCC
1 -TGAGGTACTAGGTTCGCCGTTACGACTTAAACCTTTCCCTTTATGTCTTCATGGTACAGGATCC
* *
111721 GCCGTTGCGGGTTAGATCTTTCCCTTCATGTCT
65 GCCGTTGCAGCTTAGATCTTTCCCTTCATGTCT
* * * * * * *
111754 TCGTGGTACT-GGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTC-TGAGGAACTAGG
1 T-GAGGTACTAGG-TTCGCCGTTACGACTTAAACCTTTCCCTTTATGTCTTCAT--GGTAC-AGG
* * * * * * *
111816 -TTCGCCATTACGGCTTAAACCTTTCCCTTAATGTCT
61 ATCCGCCGTTGCAGCTTAGATCTTTCCCTTCATGTCT
* * * * * * *
111852 TCATGGTACT-GGATC-CATCGTTGC-AGCTTAGATCTTTCCC-TTGTGTCTTCATGGTACTGGA
1 TGA-GGTACTAGGTTCGC--CGTTACGA-CTTAAACCTTTCCCTTTATGTCTTCATGGTACAGGA
* *
111913 TCCGCTGTTGCAGCTTAGATCTTTCCCTT-GTGTCTT
62 TCCGCCGTTGCAGCTTAGATCTTTCCCTTCATGTC-T
*
111949 TGTAGGTAC-AGGGTTCGCCGTTTCGACTTAAACCTTTCCCTTTAT
1 TG-AGGTACTA-GGTTCGCCGTTACGACTTAAACCTTTCCCTTTAT
111994 TTTGTTGTGG
Statistics
Matches: 267, Mismatches: 49, Indels: 42
0.75 0.14 0.12
Matches are distributed among these distances:
96 8 0.03
97 63 0.24
98 191 0.72
99 5 0.02
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (97 bp):
TGAGGTACTAGGTTCGCCGTTACGACTTAAACCTTTCCCTTTATGTCTTCATGGTACAGGATCCG
CCGTTGCAGCTTAGATCTTTCCCTTCATGTCT
Found at i:111814 original size:147 final size:146
Alignment explanation
Indices: 111591--112097 Score: 592
Period size: 147 Copynumber: 3.4 Consensus size: 146
111581 CAACTTAAAC
* **
111591 CTTTCCGCTTGTGTCTTCGTGGTACAGGATCCGTCGTTGCAGCTTAGATCTTTCCCTTCATG-TC
1 CTTTCC-CTTGTGTCTTCGTGGTACTGGATCCACCGTTGCAGCTTAGATCTTTCCCTTCATGCT-
*
111655 TCTGAGGTACTAGGTTCGCCATTACGACTTAAACCTTTCCCTTTATGTCTTCATGGTATTGGATC
64 TCTGAGGTACTAGGTTCGCCATTACGACTTAAACCTTTCCCTTTATGTCTTCATGGTACTGGATC
*
111720 CGCCGTTGCGGGTTAGAT
129 CGCCGTTGCGGCTTAGAT
* * * *
111738 CTTTCCCTTCATGTCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
1 CTTTCCCTT-GTGTCTTCGTGGTACTGGATCCACCGTTGCAGCTTAGATCTTTCCCTTCATGCTT
* * *
111803 CTGAGGAACTAGGTTCGCCATTACGGCTTAAACCTTTCCCTTAATGTCTTCATGGTACTGGATCC
65 CTGAGGTACTAGGTTCGCCATTACGACTTAAACCTTTCCCTTTATGTCTTCATGGTACTGGATCC
** *
111868 ATCGTTGCAGCTTAGAT
130 GCCGTTGCGGCTTAGAT
* * * *
111885 CTTTCCCTTGTGTCTTCATGGTACTGGATCCGCTGTTGCAGCTTAGATCTTTCCCTT-GTGTCTT
1 CTTTCCCTTGTGTCTTCGTGGTACTGGATCCACCGTTGCAGCTTAGATCTTTCCCTTCATG-CTT
* * * **
111949 -TGTAGGTAC-AGGGTTCGCCGTTTCGACTTAAACCTTTCCCTTTAT-TTTGTTGTGGTACTGGA
65 CTG-AGGTACTA-GGTTCGCCATTACGACTTAAACCTTTCCCTTTATGTCT-TCATGGTACTGGA
* ** * * *
112011 TTCGCTATTGCGACTCAAAT
127 TCCGCCGTTGCGGCTTAGAT
* * * *
112031 CTTTCCCTATTGTATCTTTGCGGTATTGGATCCACCGTTGCAGCTTAGATCTTTCCCTTCATGCT
1 CTTTCCC--TTGTGTCTTCGTGGTACTGGATCCACCGTTGCAGCTTAGATCTTTCCCTTCATGCT
112096 TC
64 TC
112098 ATGGTACTGA
Statistics
Matches: 302, Mismatches: 48, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
145 7 0.02
146 111 0.37
147 135 0.45
148 47 0.16
149 2 0.01
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.39
Consensus pattern (146 bp):
CTTTCCCTTGTGTCTTCGTGGTACTGGATCCACCGTTGCAGCTTAGATCTTTCCCTTCATGCTTC
TGAGGTACTAGGTTCGCCATTACGACTTAAACCTTTCCCTTTATGTCTTCATGGTACTGGATCCG
CCGTTGCGGCTTAGAT
Found at i:112103 original size:98 final size:97
Alignment explanation
Indices: 111682--112106 Score: 269
Period size: 98 Copynumber: 4.3 Consensus size: 97
111672 GCCATTACGA
* * * * ** ** *
111682 CTTAAACCTTTCCCTTTATGTCTTCATGGTATTGGATCCGCCGTTGCGGGTTAGATCTTTCCCT-
1 CTTAAATCTTTCCCTTCATG-CTTCATGGTACTGGATTCGCTATTGCGACTTAAATCTTTCCCTA
* * * *
111746 TCATG-TCTTCGTGGTACTGGATTCACCGTTGCGG
65 T--TGTTCTTTGAGGTACTGGATCCACCGTTGCAG
* * * * *
111780 CTTAAATCTTTCCCTTCATGCTTC-TGAGGAACTAGG-TTCGCCATTACGGCTTAAACCTTTCCC
1 CTTAAATCTTTCCCTTCATGCTTCAT--GGTACT-GGATTCGCTATTGCGACTTAAATCTTTCCC
* * *
111843 TTAATG-TC-TTCATGGTACTGGATCCATCGTTGCAG
63 -TATTGTTCTTTGA-GGTACTGGATCCACCGTTGCAG
* * * * *
111878 CTTAGATCTTTCCCTT-GTGTCTTCATGGTACTGGATCCGCTGTTGC-AGCTTAGATCTTTCCC-
1 CTTAAATCTTTCCCTTCATG-CTTCATGGTACTGGATTCGCTATTGCGA-CTTAAATCTTTCCCT
* * * * *
111940 -TTGTGTCTTTGTAGGTACAGGGTTCGCCGTTTC-G
64 ATTGT-TCTTTG-AGGTACTGGATCCACCGTTGCAG
* * ** ** *
111974 ACTTAAACCTTTCCCTTTATTTTGTTGTGGTACTGGATTCGCTATTGCGACTCAAATCTTTCCCT
1 -CTTAAATCTTTCCCTTCATGCT-TCATGGTACTGGATTCGCTATTGCGACTTAAATCTTTCCCT
* *
112039 ATTGTATCTTTGCGGTATTGGATCCACCGTTGCAG
64 ATTGT-TCTTTGAGGTACTGGATCCACCGTTGCAG
*
112074 CTTAGATCTTTCCCTTCATGCTTCATGGTACTG
1 CTTAAATCTTTCCCTTCATGCTTCATGGTACTG
112107 AGACTTGTAA
Statistics
Matches: 245, Mismatches: 61, Indels: 42
0.70 0.18 0.12
Matches are distributed among these distances:
94 2 0.01
96 6 0.02
97 62 0.25
98 128 0.52
99 36 0.15
100 11 0.04
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (97 bp):
CTTAAATCTTTCCCTTCATGCTTCATGGTACTGGATTCGCTATTGCGACTTAAATCTTTCCCTAT
TGTTCTTTGAGGTACTGGATCCACCGTTGCAG
Found at i:122563 original size:14 final size:14
Alignment explanation
Indices: 122544--122570 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
122534 ACATAATATA
122544 ATGTCGCACAAAAG
1 ATGTCGCACAAAAG
122558 ATGTCGCACAAAA
1 ATGTCGCACAAAA
122571 AATCCCCAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (14 bp):
ATGTCGCACAAAAG
Found at i:123521 original size:29 final size:30
Alignment explanation
Indices: 123489--123670 Score: 128
Period size: 29 Copynumber: 6.2 Consensus size: 30
123479 GGTAATATGT
*
123489 AATTTTTGGAAAAATT-AGGGTTAAAATGG
1 AATTTTTGGAAAAATTGAGGGTAAAAATGG
* *
123518 AA-TTTT-GAAAAGTTCGAGGGTAAAAATGT
1 AATTTTTGGAAAAATT-GAGGGTAAAAATGG
* * *
123547 AATTTTTGG-AAAATTGAGGTTTATAATGG
1 AATTTTTGGAAAAATTGAGGGTAAAAATGG
* ** * *
123576 AA-TTTTAGAAAGTTTGGGGGTAAAAATGT
1 AATTTTTGGAAAAATTGAGGGTAAAAATGG
* *
123605 AATTTTTGGAAAAA-TCATGGTCAAAAAATGG
1 AATTTTTGGAAAAATTGAGGGT--AAAAATGG
* * * *
123636 AA-TTTTGG-AAAGTTTAAGGTAAAAATGT
1 AATTTTTGGAAAAATTGAGGGTAAAAATGG
123664 AATTTTT
1 AATTTTT
123671 TAAGAGTTTA
Statistics
Matches: 116, Mismatches: 27, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
27 7 0.06
28 18 0.16
29 53 0.46
30 28 0.24
31 10 0.09
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.36
Consensus pattern (30 bp):
AATTTTTGGAAAAATTGAGGGTAAAAATGG
Found at i:123666 original size:59 final size:56
Alignment explanation
Indices: 123485--123670 Score: 219
Period size: 58 Copynumber: 3.2 Consensus size: 56
123475 CGGGGGTAAT
* * *
123485 ATGTAATTTTTGGAAAAATTAGGGTTAAAATGGAATTTTGAAAAGTTCGAGGGTAAAA
1 ATGTAATTTTTGGAAAAATCA-GGTTAAAATGGAATTTTGGAAAGTT-TAGGGTAAAA
* * * * *
123543 ATGTAATTTTTGGAAAATTGAGGTTTATAATGGAATTTTAGAAAGTTTGGGGGTAAAA
1 ATGTAATTTTTGGAAAAATCAGG-TTAAAATGGAATTTTGGAAAGTTT-AGGGTAAAA
* *
123601 ATGTAATTTTTGGAAAAATCATGGTCAAAAAATGGAATTTTGGAAAGTTTAAGGTAAAA
1 ATGTAATTTTTGGAAAAATCA-GGT--TAAAATGGAATTTTGGAAAGTTTAGGGTAAAA
123660 ATGTAATTTTT
1 ATGTAATTTTT
123671 TAAGAGTTTA
Statistics
Matches: 109, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
57 2 0.02
58 67 0.61
59 20 0.18
60 20 0.18
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.36
Consensus pattern (56 bp):
ATGTAATTTTTGGAAAAATCAGGTTAAAATGGAATTTTGGAAAGTTTAGGGTAAAA
Found at i:124495 original size:26 final size:26
Alignment explanation
Indices: 124447--124500 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
124437 GATCTAAAAA
*
124447 TTTTTAAAACCCTTTTTATTTTTTCT
1 TTTTTAAAACCCTTTTGATTTTTTCT
*
124473 TTTTTAAAAGCCTTTTCGA-TTTTTCT
1 TTTTTAAAACCCTTTT-GATTTTTTCT
124499 TT
1 TT
124501 GAAAATCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.19, C:0.15, G:0.04, T:0.63
Consensus pattern (26 bp):
TTTTTAAAACCCTTTTGATTTTTTCT
Found at i:124820 original size:3 final size:3
Alignment explanation
Indices: 124812--124883 Score: 74
Period size: 3 Copynumber: 23.0 Consensus size: 3
124802 GTTTTCTCTT
* *
124812 TTA TTA TTA TTA TTA TTA TTA TTTA TTA ATA TTA TTTA TTA CTT- TTG
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA -TTA TTA
*
124859 TTA TTA TTA TTA TTA GTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA
124884 AAAGCTTTGA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
2 2 0.03
3 47 0.80
4 10 0.17
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:125581 original size:17 final size:17
Alignment explanation
Indices: 125559--125664 Score: 90
Period size: 17 Copynumber: 6.2 Consensus size: 17
125549 TTATTTATTA
*
125559 AAATTTATAATAATTTT
1 AAATTTATAATAAATTT
*
125576 AAATTTAAAAATAAATTT
1 AAATTT-ATAATAAATTT
* *
125594 AAACTTA-ATTTAAATTT
1 AAATTTATA-ATAAATTT
**
125611 AAATTTATTTTAAATTT
1 AAATTTATAATAAATTT
* *
125628 AAATTTAAAACAAATTT
1 AAATTTATAATAAATTT
*
125645 -AATCTTAAAATAAATTT
1 AAAT-TTATAATAAATTT
125662 AAA
1 AAA
125665 AAGGGCACGG
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
16 4 0.05
17 53 0.73
18 16 0.22
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTATAATAAATTT
Found at i:125584 original size:6 final size:6
Alignment explanation
Indices: 125573--125636 Score: 78
Period size: 6 Copynumber: 11.0 Consensus size: 6
125563 TTATAATAAT
** * *
125573 TTTAAA TTTAAA AATAAA TTTAAA CTT-AA TTTAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
125619 TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
125637 ACAAATTTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 8 0.17
6 40 0.83
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:125626 original size:23 final size:24
Alignment explanation
Indices: 125569--125636 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 24
125559 AAATTTATAA
**
125569 TAATTTTAAATTTAAAAATAAATT
1 TAATTTTAAATTTAAATTTAAATT
**
125593 TAAACTT-AATTTAAATTTAAATT
1 TAATTTTAAATTTAAATTTAAATT
125616 T-ATTTTAAATTTAAATTTAAA
1 TAATTTTAAATTTAAATTTAAA
125637 ACAAATTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 3 0.08
23 29 0.78
24 5 0.14
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATTTTAAATTTAAATTTAAATT
Found at i:132870 original size:23 final size:23
Alignment explanation
Indices: 132844--132925 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
132834 TTATCTGCCT
*
132844 TTGTGGCACACTTTTCTTCTGTC
1 TTGTGGCACGCTTTTCTTCTGTC
* *
132867 TTGTGGTACGCTTTTCGTCTGTC
1 TTGTGGCACGCTTTTCTTCTGTC
** * *
132890 TCATGACACGCTTTT-TGTCTGCC
1 TTGTGGCACGCTTTTCT-TCTGTC
132913 TTGTGGCACGCTT
1 TTGTGGCACGCTT
132926 CTATCTTATG
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.09, C:0.26, G:0.22, T:0.44
Consensus pattern (23 bp):
TTGTGGCACGCTTTTCTTCTGTC
Found at i:135213 original size:21 final size:21
Alignment explanation
Indices: 135171--135214 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
135161 TAATATAAAA
* * * *
135171 TAAAAAGTTACATTTAATTTT
1 TAAAAAGTGAAATTAAAATTT
135192 TAAAAAGTGAAATTAAAATTT
1 TAAAAAGTGAAATTAAAATTT
135213 TA
1 TA
135215 TTAGAAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (21 bp):
TAAAAAGTGAAATTAAAATTT
Found at i:137360 original size:28 final size:28
Alignment explanation
Indices: 137232--137679 Score: 277
Period size: 29 Copynumber: 15.5 Consensus size: 28
137222 TCCTGGGGGC
137232 AAAATGGTAATTTTGGGAAAGTTTGGGGTCA
1 AAAATGG-AATTTT-GGAAAGTTTGGGGT-A
* * *
137263 AAAATGAAATTTTTAGG-CA-TTCGGGGGT-
1 AAAATGGAA-TTTT-GGAAAGTT-TGGGGTA
* ** *
137291 AAAATGATAATTTTGGAAAAATTGGTGTCA
1 AAAATG-GAATTTTGGAAAGTTTGGGGT-A
* *
137321 AAAAAGGAATTTTGGAAAGTTTGGGGAA
1 AAAATGGAATTTTGGAAAGTTTGGGGTA
** * * * *
137349 AAAATATAATTTTCGAAAAGTTCGAGGTT
1 AAAATGGAATTTT-GGAAAGTTTGGGGTA
137378 AAAAT-GACATTTTTGG-AAGTTT--GGTCA
1 AAAATGGA-A-TTTTGGAAAGTTTGGGGT-A
* * * * *
137405 TAAAATGGTAATTTTTAGAAA-ATCGAGGTC
1 -AAAATGG-AA-TTTTGGAAAGTTTGGGGTA
*
137435 AAAATGGAATTTTGGAAAGTTCGGGGATA
1 AAAATGGAATTTTGGAAAGTTTGGGG-TA
** * *
137464 AAAATGGAATTTTGGAAAAATCGGGGCCA
1 AAAATGGAATTTTGGAAAGTTTGGGG-TA
* *
137493 AAAATGGAATTTTGGAAAGTTCGGGGTC
1 AAAATGGAATTTTGGAAAGTTTGGGGTA
137521 AAAATGGAATTTTGGAAAGTTTGGGGGTA
1 AAAATGGAATTTTGGAAAGTTT-GGGGTA
* * * *
137550 AAATTGTAATTTTTGAAGAATTTTGGGGTCA
1 AAAATGGAA-TTTTGGA-AAGTTTGGGGT-A
137581 AAAATGGAATTTTGGAAAGTTTAGGGGT-
1 AAAATGGAATTTTGGAAAGTTT-GGGGTA
* * *
137609 AAAATGTAATTTTTGGAGAA-TTTGGGTTT
1 AAAATGGAA-TTTTGGA-AAGTTTGGGGTA
*
137638 AAAATGGAATTTTGGAAAGTTTGAGGGTT
1 AAAATGGAATTTTGGAAAGTTTG-GGGTA
*
137667 AAAATGTAATTTT
1 AAAATGGAATTTT
137680 TAGACAGTTT
Statistics
Matches: 330, Mismatches: 58, Indels: 60
0.74 0.13 0.13
Matches are distributed among these distances:
26 3 0.01
27 12 0.04
28 88 0.27
29 155 0.47
30 44 0.13
31 28 0.08
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTGGGGTA
Found at i:137390 original size:57 final size:55
Alignment explanation
Indices: 137321--137538 Score: 188
Period size: 57 Copynumber: 3.8 Consensus size: 55
137311 ATTGGTGTCA
* * * *
137321 AAAAAGGAATTTTGGAAAGTTTGGGGAAAAAATATAATTTTCGAAAAGTTCGAGGTT
1 AAAATGGAATTTTGGAAAGTTTGGGGAAAAAATGTAATTTTAGAAAA--TCGAGGTC
** *
137378 AAAAT-GACATTTTTGG-AAGTTTGGTCATAAAATGGTAATTTTTAGAAAATCGAGGTC
1 AAAATGGA-A-TTTTGGAAAGTTTGGGGAAAAAAT-GTAA-TTTTAGAAAATCGAGGTC
* * * * *
137435 AAAATGGAATTTTGGAAAGTTCGGGGATAAAAATGGAATTTTGGAAAAATCGGGGCC
1 AAAATGGAATTTTGGAAAGTTTGGGGA-AAAAATGTAATTTTAG-AAAATCGAGGTC
* ** * *
137492 AAAAATGGAATTTTGGAAAGTTCGGGGTCAAAATGGAATTTTGGAAA
1 -AAAATGGAATTTTGGAAAGTTTGGGGAAAAAATGTAATTTTAGAAA
137539 GTTTGGGGGT
Statistics
Matches: 135, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
56 16 0.12
57 68 0.50
58 42 0.31
59 9 0.07
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (55 bp):
AAAATGGAATTTTGGAAAGTTTGGGGAAAAAATGTAATTTTAGAAAATCGAGGTC
Found at i:137621 original size:59 final size:57
Alignment explanation
Indices: 137493--137680 Score: 252
Period size: 57 Copynumber: 3.2 Consensus size: 57
137483 ATCGGGGCCA
* * * * *
137493 AAAATGGAATTTTGGAA-AGTTCGGGGTCAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGTAATTTTTGAAGAATTTGGGGTCAAAATGGAATTTTGGAAAGTTTAGGGGT
137549 AAAATTGTAATTTTTGAAGAATTTTGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAA-TGTAATTTTTGAAGAA-TTTGGGGTC-AAAATGGAATTTTGGAAAGTTTAGGGGT
* * * *
137609 AAAATGTAATTTTTGGAGAATTTGGGTTTAAAATGGAATTTTGGAAAGTTTGAGGGTT
1 AAAATGTAATTTTTGAAGAATTTGGGGTCAAAATGGAATTTTGGAAAGTTT-AGGGGT
137667 AAAATGTAATTTTT
1 AAAATGTAATTTTT
137681 AGACAGTTTA
Statistics
Matches: 118, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
56 4 0.03
57 33 0.28
58 27 0.23
59 23 0.19
60 31 0.26
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.37
Consensus pattern (57 bp):
AAAATGTAATTTTTGAAGAATTTGGGGTCAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:137649 original size:88 final size:85
Alignment explanation
Indices: 137232--137655 Score: 281
Period size: 86 Copynumber: 4.9 Consensus size: 85
137222 TCCTGGGGGC
* * * *
137232 AAAATGGTAATTTTGGGAAAGTTTGGGGTCAAAAATGAAATTTTTAGG-CA-TTCGGGGGTAAAA
1 AAAATGG-AATTTT-GGAAAGTTAGGGGTC-AAAATGGAA-TTTT-GGAAAGTTTGGGGGTAAAA
* * * *
137295 TGATAATTTTGGAAAAATTGGTGTCA
61 TG-GAATTTTGGAAAAATCGGGGCCA
* * ** ** * * * *
137321 AAAAAGGAATTTTGGAAAGTTTGGGGAAAAAATATAATTTTCGAAAAGTTCGAGGTTAAAAT-GA
1 AAAATGGAATTTTGGAAAGTTAGGGGTCAAAATGGAATTTT-GGAAAGTTTGGGGGTAAAATGGA
* ** *
137385 CATTTTTGG--AAGT-TTGGTCA
65 -A-TTTTGGAAAAATCGGGGCCA
* * * * * *
137405 TAAAATGGTAATTTTTAGAAA-ATCGAGGTCAAAATGGAATTTTGGAAAGTTCGGGGATAAAAAT
1 -AAAATGG-AA-TTTTGGAAAGTTAGGGGTCAAAATGGAATTTTGGAAAGTTTGGGGGT-AAAAT
137469 GGAATTTTGGAAAAATCGGGGCCA
62 GGAATTTTGGAAAAATCGGGGCCA
* *
137493 AAAATGGAATTTTGGAAAGTTCGGGGTCAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATTGTA
1 AAAATGGAATTTTGGAAAGTTAGGGGTCAAAATGGAATTTTGGAAAGTTTGGGGGTAAAA-TGGA
* * * *
137558 ATTTTTGAAGAATTTTGGGGTCA
65 ATTTTGGAA-AA-ATCGGGGCCA
* **
137581 AAAATGGAATTTTGGAAAGTTTAGGGGT-AAAATGTAATTTTTGGAGAA-TTTGGGTTTAAAATG
1 AAAATGGAATTTTGGAAAG-TTAGGGGTCAAAATGGAA-TTTTGGA-AAGTTTGGGGGTAAAATG
137644 GAATTTTGGAAA
63 GAATTTTGGAAA
137656 GTTTGAGGGT
Statistics
Matches: 269, Mismatches: 47, Indels: 40
0.76 0.13 0.11
Matches are distributed among these distances:
84 4 0.01
85 45 0.17
86 78 0.29
87 54 0.20
88 55 0.20
89 31 0.12
90 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (85 bp):
AAAATGGAATTTTGGAAAGTTAGGGGTCAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGAA
TTTTGGAAAAATCGGGGCCA
Found at i:138877 original size:3 final size:3
Alignment explanation
Indices: 138869--138913 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
138859 ATATTTTTAA
* *
138869 TAT TAT TAT TAAT TAT TAT TAA TAT TAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
138914 ATGCTATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:138922 original size:12 final size:12
Alignment explanation
Indices: 138848--138915 Score: 86
Period size: 12 Copynumber: 5.7 Consensus size: 12
138838 ATATCCTTTT
138848 TTATTAATACTATA
1 TTATTAATA-T-TA
*
138862 TTTTTAATATTA
1 TTATTAATATTA
138874 TTATT-A-ATTA
1 TTATTAATATTA
138884 TTATTAATATTA
1 TTATTAATATTA
*
138896 TTATTACTATTA
1 TTATTAATATTA
138908 TTATTAAT
1 TTATTAAT
138916 GCTATTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.19
11 2 0.04
12 28 0.58
13 1 0.02
14 8 0.17
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATTAATATTA
Found at i:139666 original size:17 final size:17
Alignment explanation
Indices: 139646--139709 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
139636 AAATAAATTT
* *
139646 TAAATTTAAATTGATAA
1 TAAATTTAAATTTAAAA
**
139663 TAAATTTAAATTTCCAA
1 TAAATTTAAATTTAAAA
*
139680 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
139697 TTAATTTAAATTT
1 TAAATTTAAATTT
139710 TATTAAACCT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:160586 original size:9 final size:9
Alignment explanation
Indices: 160572--160597 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
160562 CCAATTCGTT
160572 GGCTCTTTC
1 GGCTCTTTC
160581 GGCTCTTTC
1 GGCTCTTTC
160590 GGCTCTTT
1 GGCTCTTT
160598 TCCTAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.31, G:0.23, T:0.46
Consensus pattern (9 bp):
GGCTCTTTC
Found at i:163358 original size:56 final size:56
Alignment explanation
Indices: 163272--163384 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
163262 ACAACAATAA
163272 TAATACCAATGAATTAAGACTCAATCCACCCCATATCAATCAATTATTAATTGGTT
1 TAATACCAATGAATTAAGACTCAATCCACCCCATATCAATCAATTATTAATTGGTT
163328 TAATACCAATGAATTAAGACTCAATCCACCCCATATCAATCAATTATTAATTGGTT
1 TAATACCAATGAATTAAGACTCAATCCACCCCATATCAATCAATTATTAATTGGTT
163384 T
1 T
163385 TGAGTATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (56 bp):
TAATACCAATGAATTAAGACTCAATCCACCCCATATCAATCAATTATTAATTGGTT
Found at i:164695 original size:18 final size:18
Alignment explanation
Indices: 164665--164702 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
164655 TAAATTAAAT
*
164665 TTTTTTATTTTTATG-AA
1 TTTTTAATTTTTATGTAA
164682 TTTTTAATTATTTATGTAA
1 TTTTTAATT-TTTATGTAA
164701 TT
1 TT
164703 ATTCTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 6 0.33
19 4 0.22
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTTAATTTTTATGTAA
Found at i:165471 original size:19 final size:19
Alignment explanation
Indices: 165425--165473 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
165415 ATATATAAGG
*
165425 TTATATATTTTAATTTGTAA
1 TTATATATTTTAA-TTATAA
165445 TTATTATATTTTAA-TATAA
1 TTA-TATATTTTAATTATAA
165464 TTTATATATT
1 -TTATATATT
165474 CAAATTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.38
20 6 0.23
21 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTATATATTTTAATTATAA
Found at i:168259 original size:21 final size:21
Alignment explanation
Indices: 168228--168299 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
168218 GTGCTAGTCT
*
168228 TACCAATACAAGTATAACTTC
1 TACCGATACAAGTATAACTTC
*
168249 TATCGATACAAGTATAACTTC
1 TACCGATACAAGTATAACTTC
*
168270 TACCGATACAAGTCAT-GCTTC
1 TACCGATACAAGT-ATAACTTC
*
168291 TACTGATAC
1 TACCGATAC
168300 TAAAAACTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
21 43 0.96
22 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (21 bp):
TACCGATACAAGTATAACTTC
Found at i:173704 original size:14 final size:15
Alignment explanation
Indices: 173685--173713 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
173675 AAATATAATA
173685 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
173699 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
173714 TTTAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:173704 original size:24 final size:24
Alignment explanation
Indices: 173675--173722 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
173665 TATTTTATAA
173675 AAATA-TAATAAAATATTAAAAAAT
1 AAATATTAA-AAAATATTAAAAAAT
*
173699 AAATATTTAAAAAATTTTAAAAAA
1 AAATA-TTAAAAAATATTAAAAAA
173723 AATTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 13 0.62
26 3 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (24 bp):
AAATATTAAAAAATATTAAAAAAT
Found at i:175309 original size:10 final size:10
Alignment explanation
Indices: 175283--175316 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
175273 ATAATAATAG
*
175283 AAAGAAAGAA
1 AAAGAAAAAA
175293 AAA-AAAAAA
1 AAAGAAAAAA
175302 AAAGAAAAAA
1 AAAGAAAAAA
175312 AAAGA
1 AAAGA
175317 GGAATTTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:176102 original size:24 final size:24
Alignment explanation
Indices: 176075--176132 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
176065 ACCAAATATG
176075 CGAGCATAAACGTATAACGACTGA
1 CGAGCATAAACGTATAACGACTGA
* * *
176099 CGAGTATAAACGTATAGCGATTGA
1 CGAGCATAAACGTATAACGACTGA
176123 CGAGCATAAA
1 CGAGCATAAA
176133 TGTACGTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.19
Consensus pattern (24 bp):
CGAGCATAAACGTATAACGACTGA
Found at i:176646 original size:21 final size:22
Alignment explanation
Indices: 176622--176668 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
176612 CGATCTAAGG
176622 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
*
176643 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAACAGAATT
176665 AAAA
1 AAAA
176669 GAAATAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAGAATT
Found at i:176680 original size:22 final size:22
Alignment explanation
Indices: 176622--176682 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
176612 CGATCTAAGG
*
176622 AAAAATAAAA-GAAACAGAATT
1 AAAAATAAAAGGAAATAGAATT
*
176643 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGGAAATAGAATT
*
176665 AAAAGA-AATAGGAAATAG
1 AAAA-ATAAAAGGAAATAG
176683 GAAAGTCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.29
22 23 0.68
23 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGGAAATAGAATT
Found at i:177506 original size:19 final size:19
Alignment explanation
Indices: 177482--177524 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
177472 AAACATAAAT
177482 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
177501 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
177520 TAAAT
1 TAAAT
177525 CCTAATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:178105 original size:12 final size:12
Alignment explanation
Indices: 178081--178113 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
178071 CTTCCTTTTA
178081 TTTT-TTTAATT
1 TTTTCTTTAATT
*
178092 TTTTCTTTATTT
1 TTTTCTTTAATT
178104 TTTTCTTTAA
1 TTTTCTTTAA
178114 GAATACATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTTAATT
Found at i:179083 original size:18 final size:16
Alignment explanation
Indices: 179049--179106 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 16
179039 TTCCTGGACA
179049 AAAATAAATAAATAAAT
1 AAAATAAATAAA-AAAT
179066 AAAATAAGATAGAAAAAT
1 AAAATAA-ATA-AAAAAT
179084 AAAATAAAATAATAAAAAT
1 AAAAT-AAAT-A-AAAAAT
179103 AAAA
1 AAAA
179107 ATAATTGGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 7 0.19
18 14 0.39
19 15 0.42
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATAAATAAAAAAT
Found at i:184691 original size:21 final size:22
Alignment explanation
Indices: 184667--184724 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
184657 CGTTCTAAGG
*
184667 AAAAAGAAAAGAAACAA-AATT
1 AAAAAGAAAAGAAAAAAGAATT
*
184688 AAAAATAAAAGAAAAAAGAATT
1 AAAAAGAAAAGAAAAAAGAATT
184710 -AAAAGAAATAGAAAA
1 AAAAAGAAA-AGAAAA
184725 TAAGGAAGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 22 0.69
22 10 0.31
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (22 bp):
AAAAAGAAAAGAAAAAAGAATT
Found at i:185556 original size:19 final size:19
Alignment explanation
Indices: 185532--185574 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
185522 AAACGTAAAT
185532 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
185551 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
185570 TAAAT
1 TAAAT
185575 CCTAATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:190593 original size:62 final size:66
Alignment explanation
Indices: 190424--190598 Score: 263
Period size: 67 Copynumber: 2.7 Consensus size: 66
190414 CATTTTTCTT
*
190424 ATTATT-TTTATTTATTTA-TATTTTTATGAATATAAATAAATAAAAATAAAATAATATTAATTT
1 ATTATTATTTATTTATTTATTA-TTTTATGAATATAAATAAATAAATATAAAATAATATTAATTT
190487 TG
65 TG
* *
190489 ATTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATT-ATTT
1 A-TTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTT
190553 TG
65 TG
190555 -TT-TTA-TTATTTATTTATTATTTTATGAATATAAATAAATAAATA
1 ATTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATA
190599 ACAAACTCAA
Statistics
Matches: 102, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
62 37 0.36
63 3 0.03
64 2 0.02
65 1 0.01
66 11 0.11
67 46 0.45
68 2 0.02
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (66 bp):
ATTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTT
G
Found at i:193063 original size:31 final size:31
Alignment explanation
Indices: 193028--193093 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
193018 CTTGCATATC
193028 CATTCATAAAATTTCGCATCGCATTTACATG
1 CATTCATAAAATTTCGCATCGCATTTACATG
* * *
193059 CATTCATAAATTTTTGCATCGCATTTTCATG
1 CATTCATAAAATTTCGCATCGCATTTACATG
193090 CATT
1 CATT
193094 AAAAGTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (31 bp):
CATTCATAAAATTTCGCATCGCATTTACATG
Found at i:196479 original size:111 final size:111
Alignment explanation
Indices: 196285--196507 Score: 356
Period size: 111 Copynumber: 2.0 Consensus size: 111
196275 AGTCAGTTTA
* *
196285 AGATCAAGCACCATAATTCAGCACCGTATCACTCGAAAATGAATGAAGCAGTGGAAGCAGCTAAT
1 AGATCAAGCACCATAATTCAACACCGTATCACTCGAAAATGAATGAAGCAGTGGAAACAGCTAAT
*
196350 AAAAACATCAATAAAATCGTGAGGAAAATAACTGAAACCTACAAAG
66 AAAAACATCAAGAAAATCGTGAGGAAAATAACTGAAACCTACAAAG
* ** *
196396 AGATCAAGCACCATAATTCAACACTGTATTGCTCGAAAATGAATGGAGCAGTGGAAACAGCTAAT
1 AGATCAAGCACCATAATTCAACACCGTATCACTCGAAAATGAATGAAGCAGTGGAAACAGCTAAT
* * *
196461 AAAAATATCAAGAAAATCGTGAGGAAAATGACTGAGACCTACAAAG
66 AAAAACATCAAGAAAATCGTGAGGAAAATAACTGAAACCTACAAAG
196507 A
1 A
196508 TTGGCATGAA
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 102 1.00
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.18
Consensus pattern (111 bp):
AGATCAAGCACCATAATTCAACACCGTATCACTCGAAAATGAATGAAGCAGTGGAAACAGCTAAT
AAAAACATCAAGAAAATCGTGAGGAAAATAACTGAAACCTACAAAG
Found at i:197057 original size:37 final size:39
Alignment explanation
Indices: 197011--197084 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
197001 AAAAAAGAAA
*
197011 AAAAGAAAA-GTTGAGTTGAAAACCCAAAAAGGGCGGTT
1 AAAAGAAAAGGTTGAGCTGAAAACCCAAAAAGGGCGGTT
**
197049 AAAA-AAAAGGTTGAGCTGAAAACCCGTAAAGGGCGG
1 AAAAGAAAAGGTTGAGCTGAAAACCCAAAAAGGGCGG
197085 CTCAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 4 0.12
38 28 0.88
ACGTcount: A:0.46, C:0.12, G:0.28, T:0.14
Consensus pattern (39 bp):
AAAAGAAAAGGTTGAGCTGAAAACCCAAAAAGGGCGGTT
Found at i:198060 original size:50 final size:50
Alignment explanation
Indices: 197985--198113 Score: 152
Period size: 50 Copynumber: 2.6 Consensus size: 50
197975 ATCCTATACC
* * *
197985 CCTAAAGCTGTAGAGGAACAGATTGAAGTCACGATGGCAAATCTCATAT-A
1 CCTAAAGCTGTAGAGGGACAGATTGAAGTCACAATGACAAATCTCAT-TCA
* * * * *
198035 CCTAAAGCTGTAAAGGGACAAATTGAAGCCGCAATGACGAATCTCATTCA
1 CCTAAAGCTGTAGAGGGACAGATTGAAGTCACAATGACAAATCTCATTCA
* *
198085 CTTAAAGCTGTAGAGGGGCAGATTGAAGT
1 CCTAAAGCTGTAGAGGGACAGATTGAAGT
198114 TGCAAGGATG
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
49 1 0.02
50 64 0.98
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGACAGATTGAAGTCACAATGACAAATCTCATTCA
Found at i:198127 original size:50 final size:50
Alignment explanation
Indices: 197985--198161 Score: 139
Period size: 50 Copynumber: 3.6 Consensus size: 50
197975 ATCCTATACC
* * * * *
197985 CCTAAAGCTGTAGAGGAACAGATTGAAGTCACG-ATGG-CAAATCTCATATA
1 CCTAAAGCTGTAAAGGGACAAATTGAAG-C-CGCAAGGACGAATCTCATATA
*
198035 CCTAAAGCTGTAAAGGGACAAATTGAAGCCGCAATGACGAATCTCAT-TCA
1 CCTAAAGCTGTAAAGGGACAAATTGAAGCCGCAAGGACGAATCTCATAT-A
* * * * ** * *
198085 CTTAAAGCTGTAGAGGGGCAGATTGAAGTTGCAAGGATGAATCTTATACT-
1 CCTAAAGCTGTAAAGGGACAAATTGAAGCCGCAAGGACGAATCTCATA-TA
* *
198135 CCTGAAGCTG-AAATGGACAAATTGAAG
1 CCTAAAGCTGTAAAGGGACAAATTGAAG
198162 ACCATCCGAT
Statistics
Matches: 101, Mismatches: 21, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
48 2 0.02
49 17 0.17
50 81 0.80
52 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.23
Consensus pattern (50 bp):
CCTAAAGCTGTAAAGGGACAAATTGAAGCCGCAAGGACGAATCTCATATA
Done.