Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_pilon, 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: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 18
Found at i:2183317 original size:33 final size:32
Alignment explanation
Indices: 2183265--2183426 Score: 148
Period size: 33 Copynumber: 4.8 Consensus size: 32
2183255 CCATTACATT
2183265 TCGCAATGCGGAAATGAAAATCGCAACGAGATAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGA-AA
* *
2183299 TCGCAATGCGAAATGAAAATCGCAATGCGAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAAA
* * *
2183331 T-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-G-AAA
2183370 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGA-AA
*
2183403 TCGCAATGCGAAATTAAAATCGCA
1 TCGCAATGCGAAATGAAAATCGCA
2183427 TTGCGATTCT
Statistics
Matches: 105, Mismatches: 11, Indels: 25
0.74 0.08 0.18
Matches are distributed among these distances:
31 7 0.07
32 8 0.08
33 53 0.50
34 10 0.10
35 1 0.01
36 2 0.02
38 9 0.09
39 8 0.08
40 7 0.07
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (32 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:2183321 original size:19 final size:19
Alignment explanation
Indices: 2183265--2183432 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
2183255 CCATTACATT
2183265 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
2183285 TCGCAA--CG--A-GATAA
1 TCGCAATGCGAAATGAAAA
2183299 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
2183318 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
2183337 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
2183351 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
2183370 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
2183389 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
2183403 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
2183422 TCGCATTGCGA
1 TCGCAATGCGA
2183433 TTCTCCCATT
Statistics
Matches: 125, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.24
15 3 0.02
16 6 0.05
17 5 0.04
18 4 0.03
19 71 0.57
20 6 0.05
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:2183344 original size:52 final size:52
Alignment explanation
Indices: 2183265--2183432 Score: 300
Period size: 52 Copynumber: 3.2 Consensus size: 52
2183255 CCATTACATT
*
2183265 TCGCAATGCGGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
2183318 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
2183370 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
2183422 TCGCATTGCGA
1 TCGCAATGCGA
2183433 TTCTCCCATT
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
52 103 0.92
53 9 0.08
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:2183483 original size:19 final size:19
Alignment explanation
Indices: 2183439--2183538 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
2183429 GCGATTCTCC
2183439 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
*
2183459 CATTGCGATTTTCATTTCA
1 CATTGCGATTTTCATTTCG
*
2183478 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
2183494 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
2183511 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
2183530 CATTGCGAT
1 CATTGCGAT
2183539 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
14 6 0.08
16 6 0.08
17 7 0.10
19 35 0.49
20 17 0.24
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:2183483 original size:53 final size:52
Alignment explanation
Indices: 2183425--2183538 Score: 192
Period size: 52 Copynumber: 2.2 Consensus size: 52
2183415 ATTAAAATCG
2183425 CATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCA
1 CATTGCGATTCTCCCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCA
* * *
2183478 CATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 CATTGCGATTCTCCCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCA
2183530 CATTGCGAT
1 CATTGCGAT
2183539 AGTCAATTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 29 0.50
53 29 0.50
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.44
Consensus pattern (52 bp):
CATTGCGATTCTCCCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCA
Found at i:2183535 original size:52 final size:53
Alignment explanation
Indices: 2183422--2183538 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
2183412 GAAATTAAAA
2183422 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* * *
2183475 TCACATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
2183527 TCGCATTGCGAT
1 TCGCATTGCGAT
2183539 AGTCAATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 29 0.48
53 31 0.52
ACGTcount: A:0.15, C:0.25, G:0.16, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:2183664 original size:14 final size:14
Alignment explanation
Indices: 2183645--2183681 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2183635 CATCAATTAC
2183645 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2183659 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2183673 ACAAATCAA
1 ACAAATCAA
2183682 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2185079 original size:19 final size:19
Alignment explanation
Indices: 2185057--2185155 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
2185047 TCGATCTTGT
2185057 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
2185076 CGTTGCGATTCT-G--T--
1 CGTTGCGATTTTGGTTTCG
**
2185090 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTGGTTTCG
2185109 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
2185128 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-GGTTTCG
*
2185148 TGTTGCGA
1 CGTTGCGA
2185156 AAGTAAACTA
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 11 0.16
16 1 0.01
17 1 0.01
18 1 0.01
19 40 0.60
20 13 0.19
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTGGTTTCG
Found at i:2185091 original size:33 final size:34
Alignment explanation
Indices: 2185028--2185118 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 34
2185018 CTAAGACAAA
*
2185028 TGCGATTTTGGTTT-GCGTTTCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
2185060 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
**
2185093 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2185119 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 14 0.26
33 38 0.70
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47
Consensus pattern (34 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
Found at i:2185358 original size:93 final size:93
Alignment explanation
Indices: 2185199--2185519 Score: 619
Period size: 93 Copynumber: 3.5 Consensus size: 93
2185189 TTGAATGGAT
2185199 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2185264 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
2185292 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2185357 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2185385 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT--CAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2185448 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2185476 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATT
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATT
2185520 AATAACTTAC
Statistics
Matches: 226, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
91 89 0.39
93 137 0.61
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2187267 original size:14 final size:14
Alignment explanation
Indices: 2187248--2187304 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2187238 TTGAAATGAA
2187248 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2187262 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2187281 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2187295 AATCGCAACG
1 AATCGCAACG
2187305 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2187280 original size:33 final size:33
Alignment explanation
Indices: 2187240--2187321 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
2187230 TCTTTTGGTT
2187240 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2187273 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2187306 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2187322 TGCGATTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2187286 original size:19 final size:19
Alignment explanation
Indices: 2187262--2187326 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
2187252 GCAACGAGAG
2187262 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2187281 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2187295 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2187314 AATCGCAATGCGA
1 AATCGCAACGCGA
2187327 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2187357 original size:14 final size:14
Alignment explanation
Indices: 2187338--2187394 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2187328 TTTGGTTTCG
2187338 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2187352 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2187371 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2187385 CGTTGCGATT
1 CGTTGCGATT
2187395 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2187370 original size:33 final size:33
Alignment explanation
Indices: 2187322--2187402 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2187312 AAAATCGCAA
**
2187322 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2187355 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2187388 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
2187403 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2187405 original size:21 final size:21
Alignment explanation
Indices: 2187379--2187454 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2187369 CGCGTTGCGA
2187379 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2187400 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
2187420 TTCTCTTGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
2187441 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
2187455 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2187435 original size:41 final size:41
Alignment explanation
Indices: 2187378--2187455 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
2187368 TCGCGTTGCG
*
2187378 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
*
2187419 ATTCTCTTGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
2187456 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:2187440 original size:20 final size:20
Alignment explanation
Indices: 2187345--2187454 Score: 99
Period size: 21 Copynumber: 5.8 Consensus size: 20
2187335 TCGCGTTGCG
2187345 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2187365 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
2187378 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
2187398 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
*
2187419 ATTCTCTTGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
2187439 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
2187455 CTCTTCTGCA
Statistics
Matches: 70, Mismatches: 11, Indels: 17
0.71 0.11 0.17
Matches are distributed among these distances:
13 3 0.04
14 9 0.13
19 9 0.13
20 20 0.29
21 29 0.41
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2187581 original size:33 final size:33
Alignment explanation
Indices: 2187534--2187604 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
2187524 AATACTAACT
* *
2187534 TGAAAATCGGAACGAGAGAATAGCAACGCAAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCAAAA
* * *
2187567 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCAAAA
2187600 TGAAA
1 TGAAA
2187605 TCTAAGTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCAAAA
Found at i:2187838 original size:22 final size:22
Alignment explanation
Indices: 2187786--2187840 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2187776 TGGTTGTGAG
**
2187786 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2187808 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2187830 GGATTTCTTCG
1 GGATTTCTTCG
2187841 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2188011 original size:20 final size:20
Alignment explanation
Indices: 2187986--2188179 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
2187976 CTTTAAATAT
2187986 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2188006 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2188028 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2188047 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2188067 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2188087 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2188107 CACATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2188127 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2188147 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2188167 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2188180 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2188175 original size:60 final size:60
Alignment explanation
Indices: 2187986--2188179 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
2187976 CTTTAAATAT
**
2187986 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
2188047 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * * ** *
2188107 CACATTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
2188167 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2188180 TGGAAAATCG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 82 0.75
61 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:2188180 original size:20 final size:20
Alignment explanation
Indices: 2188127--2188221 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
2188117 TTTACGGATA
* *
2188127 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
2188147 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
* * *
2188167 CGCGTTGCGATTTTGGAAAAT
1 CGCGTTGCGATTTT-CATATT
**
2188188 CGCAATGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
2188208 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
2188222 GGAAAATCGC
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
19 1 0.02
20 45 0.74
21 15 0.25
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.41
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:2188196 original size:21 final size:21
Alignment explanation
Indices: 2188172--2188268 Score: 97
Period size: 21 Copynumber: 4.7 Consensus size: 21
2188162 ATATTCGCGT
2188172 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGCAA
* * * **
2188193 TGCGATTTT-CATATTCGCGT
1 TGCGATTTTGGAAAATCGCAA
2188213 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGCAA
* * ** *
2188234 TGCGAATTTGTACTATCGCAT
1 TGCGATTTTGGAAAATCGCAA
2188255 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
2188269 CTGATTTGCG
Statistics
Matches: 56, Mismatches: 19, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
20 15 0.27
21 41 0.73
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (21 bp):
TGCGATTTTGGAAAATCGCAA
Found at i:2188205 original size:41 final size:41
Alignment explanation
Indices: 2188152--2188268 Score: 184
Period size: 41 Copynumber: 2.8 Consensus size: 41
2188142 GTGTTCGCGT
2188152 TGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCAA
1 TGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCAA
2188193 TGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCAA
1 TGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCAA
*
2188234 TGCGAATTTGT-ACTA-TCGCATTGCGATTTTGGAAA
1 TGCG-ATTT-TCA-TATTCGCGTTGCGATTTTGGAAA
2188269 CTGATTTGCG
Statistics
Matches: 72, Mismatches: 1, Indels: 5
0.92 0.01 0.06
Matches are distributed among these distances:
41 45 0.62
42 24 0.33
43 3 0.04
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (41 bp):
TGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCAA
Found at i:2196674 original size:2 final size:2
Alignment explanation
Indices: 2196669--2196734 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
2196659 TTTTTTAATC
2196669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2196711 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
2196735 GGGTAAAGTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2197625 original size:2 final size:2
Alignment explanation
Indices: 2197618--2197655 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2197608 ATTATCAATA
2197618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2197656 TTAAAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2200050 original size:2 final size:2
Alignment explanation
Indices: 2200039--2200068 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2200029 ATACAGTTAC
2200039 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2200069 CGAGGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2203870 original size:20 final size:20
Alignment explanation
Indices: 2203845--2203891 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2203835 CCGATTAACG
2203845 GTTAATTCGGTTCGAAATCA
1 GTTAATTCGGTTCGAAATCA
*
2203865 GTTAATTCGGTTCGAAATCG
1 GTTAATTCGGTTCGAAATCA
2203885 GTTAATT
1 GTTAATT
2203892 AACCGAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
GTTAATTCGGTTCGAAATCA
Found at i:2204614 original size:20 final size:20
Alignment explanation
Indices: 2204589--2204629 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2204579 AAAAACGCCT
2204589 AATTCTTACATTCTTCAGCA
1 AATTCTTACATTCTTCAGCA
2204609 AATTCTTACATTCTTCAGCA
1 AATTCTTACATTCTTCAGCA
2204629 A
1 A
2204630 TTTAAAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (20 bp):
AATTCTTACATTCTTCAGCA
Found at i:2204711 original size:15 final size:15
Alignment explanation
Indices: 2204691--2204721 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2204681 TATTTTGGTT
2204691 GTTGGAATCTAGGAG
1 GTTGGAATCTAGGAG
2204706 GTTGGAATCTAGGAG
1 GTTGGAATCTAGGAG
2204721 G
1 G
2204722 GTGTCATGAT
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:0.06, G:0.42, T:0.26
Consensus pattern (15 bp):
GTTGGAATCTAGGAG
Found at i:2218595 original size:12 final size:12
Alignment explanation
Indices: 2218578--2218604 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2218568 TAAAAACAAA
2218578 ATTTTTAAAATT
1 ATTTTTAAAATT
2218590 ATTTTTAAAATT
1 ATTTTTAAAATT
2218602 ATT
1 ATT
2218605 AGAATAAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTTAAAATT
Found at i:2221474 original size:16 final size:17
Alignment explanation
Indices: 2221443--2221475 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2221433 ACCGATCACT
2221443 GAAAAGAGACAGAGAAA
1 GAAAAGAGACAGAGAAA
*
2221460 GAAAAGATA-AGAGAAA
1 GAAAAGAGACAGAGAAA
2221476 ACAAGGCGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.67, C:0.03, G:0.27, T:0.03
Consensus pattern (17 bp):
GAAAAGAGACAGAGAAA
Found at i:2222134 original size:28 final size:27
Alignment explanation
Indices: 2222103--2222159 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
2222093 TGAAAATAAT
2222103 ATTACATGA-TTTTTAAAATTATTAAAAA
1 ATTA-ATGATTTTTTAAAA-TATTAAAAA
* * *
2222131 ATTATTTATTTTTTAAAATATTATAAA
1 ATTAATGATTTTTTAAAATATTAAAAA
2222158 AT
1 AT
2222160 ACTATCCTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
ATTAATGATTTTTTAAAATATTAAAAA
Found at i:2226554 original size:37 final size:37
Alignment explanation
Indices: 2226509--2226586 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
2226499 AAGTCTCACA
2226509 GATTAGAAGAATCCCAGCTTGCATATACAGCCCCGAT
1 GATTAGAAGAATCCCAGCTTGCATATACAGCCCCGAT
2226546 GATTAGAAGAATCCCAGCTTGCATATACAGCCCCGAT
1 GATTAGAAGAATCCCAGCTTGCATATACAGCCCCGAT
2226583 GATT
1 GATT
2226587 TTATCATGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (37 bp):
GATTAGAAGAATCCCAGCTTGCATATACAGCCCCGAT
Found at i:2232945 original size:67 final size:67
Alignment explanation
Indices: 2232837--2232985 Score: 262
Period size: 67 Copynumber: 2.2 Consensus size: 67
2232827 ACCAAACACG
* * *
2232837 GTAATCTTACATTCCTGCTAAGCCAACCAAACACAAAATATAACATTCCTAGTAATCTTATTCCC
1 GTAATCTTACATTCCTACTAAGCCAACCAAACACAAAATATAACATTCCCAGTAATCCTATTCCC
2232902 TA
66 TA
2232904 GTAATCTTACATTCCTACTAAGCCAACCAAACACAAAATATAACATTCCCAGTAATCCTATTCCC
1 GTAATCTTACATTCCTACTAAGCCAACCAAACACAAAATATAACATTCCCAGTAATCCTATTCCC
*
2232969 TG
66 TA
2232971 GTAATCTTACATTCC
1 GTAATCTTACATTCC
2232986 CACTGGTAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 78 1.00
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.30
Consensus pattern (67 bp):
GTAATCTTACATTCCTACTAAGCCAACCAAACACAAAATATAACATTCCCAGTAATCCTATTCCC
TA
Found at i:2232986 original size:18 final size:19
Alignment explanation
Indices: 2232963--2233004 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
2232953 CAGTAATCCT
2232963 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
2232981 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
2233001 ATTC
1 ATTC
2233005 TGTGAACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 3 0.14
20 16 0.73
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.38
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:2237450 original size:98 final size:98
Alignment explanation
Indices: 2237281--2237477 Score: 394
Period size: 98 Copynumber: 2.0 Consensus size: 98
2237271 AGATTAAAAG
2237281 AATCGTTGTGTTTCTTAGAGGCCACGGTTTCGAGCACTAGTGACTACAAGAGTGATTGAGTGTTT
1 AATCGTTGTGTTTCTTAGAGGCCACGGTTTCGAGCACTAGTGACTACAAGAGTGATTGAGTGTTT
2237346 ATTGTCTAATGGTTGAGAGTACTTAGAACATAT
66 ATTGTCTAATGGTTGAGAGTACTTAGAACATAT
2237379 AATCGTTGTGTTTCTTAGAGGCCACGGTTTCGAGCACTAGTGACTACAAGAGTGATTGAGTGTTT
1 AATCGTTGTGTTTCTTAGAGGCCACGGTTTCGAGCACTAGTGACTACAAGAGTGATTGAGTGTTT
2237444 ATTGTCTAATGGTTGAGAGTACTTAGAACATAT
66 ATTGTCTAATGGTTGAGAGTACTTAGAACATAT
2237477 A
1 A
2237478 TTAGCTTGTA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (98 bp):
AATCGTTGTGTTTCTTAGAGGCCACGGTTTCGAGCACTAGTGACTACAAGAGTGATTGAGTGTTT
ATTGTCTAATGGTTGAGAGTACTTAGAACATAT
Found at i:2241278 original size:24 final size:24
Alignment explanation
Indices: 2241182--2241290 Score: 78
Period size: 24 Copynumber: 4.5 Consensus size: 24
2241172 GAATATTTTA
* * *
2241182 TCTGATTTCTGATTTGAATTCTAT
1 TCTGATATCTGATCTGAATTCTGT
* * *
2241206 TTTGACATCTGATATGAAATT-TGT
1 TCTGATATCTGATCTG-AATTCTGT
* * *
2241230 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
2241254 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
2241278 TTTGATTTCTGAT
1 TCTGATATCTGAT
2241291 ATCTTCGTTT
Statistics
Matches: 64, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
23 4 0.06
24 55 0.86
25 5 0.08
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:2241458 original size:2 final size:2
Alignment explanation
Indices: 2241451--2241477 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2241441 CGGATAGGGG
2241451 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2241478 CTGTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2246055 original size:48 final size:48
Alignment explanation
Indices: 2246003--2246111 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
2245993 GAATATTTAA
* *
2246003 TCTGATTTCTGATTTGAATTCTATTTTGACATCTGATCTGAAATATGT
1 TCTGATTTCTGATCTGAATTCTATTCTGACATCTGATCTGAAATATGT
* * * * * * *
2246051 TCTGATTCCTAACCTGGATTCTGTTCTGATATCTGATCTGAATTATGT
1 TCTGATTTCTGATCTGAATTCTATTCTGACATCTGATCTGAAATATGT
*
2246099 TTTGATTTCTGAT
1 TCTGATTTCTGAT
2246112 ATCTCCGTTT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTATTCTGACATCTGATCTGAAATATGT
Found at i:2246099 original size:24 final size:24
Alignment explanation
Indices: 2246003--2246111 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
2245993 GAATATTTAA
* * * *
2246003 TCTGATTTCTGATTTGAATTCTAT
1 TCTGATATCTGATCTGAATTATGT
* * *
2246027 TTTGACATCTGATCTGAAATATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
2246051 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
2246075 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
2246099 TTTGATTTCTGAT
1 TCTGATATCTGAT
2246112 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:2258705 original size:15 final size:16
Alignment explanation
Indices: 2258673--2258705 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2258663 AAAATCTTTC
2258673 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
2258689 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
2258704 TT
1 TT
2258706 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:2259478 original size:16 final size:16
Alignment explanation
Indices: 2259454--2259487 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2259444 TATCGCCGAC
*
2259454 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2259470 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2259486 CG
1 CG
2259488 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:2263428 original size:2 final size:2
Alignment explanation
Indices: 2263421--2263455 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2263411 TTTAAAATTA
2263421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2263456 ATAAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2265755 original size:2 final size:2
Alignment explanation
Indices: 2265748--2265796 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2265738 TCTATTGGGA
2265748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2265790 AT AT AT A
1 AT AT AT A
2265797 GTTTTACAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2266080 original size:21 final size:21
Alignment explanation
Indices: 2266055--2266140 Score: 109
Period size: 21 Copynumber: 4.1 Consensus size: 21
2266045 AAAACCAGAT
* *
2266055 TACGGGTTGCTGGAATATCCG
1 TACGGGTTGCTGTAATACCCG
*
2266076 TACGGGTTTCTGTAATACCCG
1 TACGGGTTGCTGTAATACCCG
* * *
2266097 GACGGGTTGTTGTAATATCCG
1 TACGGGTTGCTGTAATACCCG
*
2266118 TACGGGTTTCTGTAATACCCG
1 TACGGGTTGCTGTAATACCCG
2266139 TA
1 TA
2266141 GGGATTGTTG
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (21 bp):
TACGGGTTGCTGTAATACCCG
Found at i:2266150 original size:42 final size:42
Alignment explanation
Indices: 2266056--2266138 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
2266046 AAACCAGATT
* *
2266056 ACGGGTTGCTGGAATATCCGTACGGGTTTCTGTAATACCCGG
1 ACGGGTTGTTGTAATATCCGTACGGGTTTCTGTAATACCCGG
2266098 ACGGGTTGTTGTAATATCCGTACGGGTTTCTGTAATACCCG
1 ACGGGTTGTTGTAATATCCGTACGGGTTTCTGTAATACCCG
2266139 TAGGGATTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.31
Consensus pattern (42 bp):
ACGGGTTGTTGTAATATCCGTACGGGTTTCTGTAATACCCGG
Found at i:2266161 original size:42 final size:42
Alignment explanation
Indices: 2266056--2266161 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
2266046 AAACCAGATT
* *
2266056 ACGGGTTGCTGGAATATCCGTACGGGTTTCTGTAATACCCGG
1 ACGGGTTGTTGGAATAGCCGTACGGGTTTCTGTAATACCCGG
* * *
2266098 ACGGGTTGTTGTAATATCCGTACGGGTTTCTGTAATACCCGT
1 ACGGGTTGTTGGAATAGCCGTACGGGTTTCTGTAATACCCGG
*
2266140 A-GGGATTGTTGGGATAGCCGTA
1 ACGGG-TTGTTGGAATAGCCGTA
2266162 GGGATTGACA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 3 0.05
42 54 0.95
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (42 bp):
ACGGGTTGTTGGAATAGCCGTACGGGTTTCTGTAATACCCGG
Found at i:2266984 original size:60 final size:59
Alignment explanation
Indices: 2266885--2267066 Score: 190
Period size: 60 Copynumber: 3.1 Consensus size: 59
2266875 GATGAATTTG
* * *
2266885 GGGATGGAATTGGAATATTCAAAAGTTT--GGAGACCAATTTAAAAAGAGGGTCATAGTTT
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGG-G-CCAATTTAAAATGAGGGTCATAGTTT
* * * * *
2266944 AGGGATGAAATTAGAATGTTCAAAAGTTTAAGGGCTAATTTAGAATG-GAAGTCATAATTT
1 -GGGATGAAATTAGAATATTCAAAAGTTTAAGGGCCAATTTAAAATGAG-GGTCATAGTTT
* * * *
2267004 GATGATGAAATTATAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGGGTTATAGTTT
1 G-GGATGAAATTAGAATATTCAAAAGTTTAAGGGCCAATTTAAAATGAGGGTCATAGTTT
2267064 GGG
1 GGG
2267067 GACATAAAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
59 3 0.03
60 92 0.93
61 2 0.02
62 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.31
Consensus pattern (59 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGGCCAATTTAAAATGAGGGTCATAGTTT
Found at i:2270834 original size:28 final size:28
Alignment explanation
Indices: 2270802--2270858 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2270792 ATAGTTTGAG
2270802 TTATAAAATAATATTATTTTATAATTTA
1 TTATAAAATAATATTATTTTATAATTTA
2270830 TTATAAAATAATATTATTTTATAATTTA
1 TTATAAAATAATATTATTTTATAATTTA
2270858 T
1 T
2270859 CTTAGCTATT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTATAAAATAATATTATTTTATAATTTA
Found at i:2275245 original size:29 final size:29
Alignment explanation
Indices: 2275211--2275269 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2275201 CCTAAATTAA
2275211 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2275240 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2275269 T
1 T
2275270 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:2278977 original size:31 final size:31
Alignment explanation
Indices: 2278791--2278962 Score: 308
Period size: 31 Copynumber: 5.5 Consensus size: 31
2278781 AGGGTCGAGG
*
2278791 GTTTACCTATGTTCTTCGGGACATATGGACC
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2278822 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2278853 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2278884 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2278915 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2278946 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
2278963 AGAATCTATG
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 136 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2279372 original size:19 final size:17
Alignment explanation
Indices: 2279331--2279375 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
2279321 ATAATGATGG
*
2279331 TATATGTTTATGTATAT
1 TATATGTTTATGAATAT
*
2279348 TTTATGTTATATGAAATAT
1 TATATGTT-TATG-AATAT
2279367 TATATGTTT
1 TATATGTTT
2279376 TATATGCCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 7 0.30
18 5 0.22
19 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (17 bp):
TATATGTTTATGAATAT
Found at i:2283306 original size:31 final size:31
Alignment explanation
Indices: 2283151--2283293 Score: 268
Period size: 31 Copynumber: 4.6 Consensus size: 31
2283141 AGGGTCGAGG
2283151 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2283182 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2283213 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2283244 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
2283275 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
2283294 AATCTATAGA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 110 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2286568 original size:29 final size:29
Alignment explanation
Indices: 2286534--2286592 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2286524 CCTAAATTAA
*
2286534 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCACTGCTTACATCAATTTAGT
2286563 TTTGATGTCACTGCTTACATCAATTTAGT
1 TTTGATGTCACTGCTTACATCAATTTAGT
2286592 T
1 T
2286593 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (29 bp):
TTTGATGTCACTGCTTACATCAATTTAGT
Found at i:2303374 original size:29 final size:29
Alignment explanation
Indices: 2303341--2303406 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
2303331 GGTAAGAAAT
*
2303341 TTATTTTATGTTAGTATT-T-TAAATAGTTA
1 TTATTTTATATTA-TATTATGTAAATA-TTA
2303370 TTATTTTATATTATATTATGTAAATATTA
1 TTATTTTATATTATATTATGTAAATATTA
2303399 TT-TTTTAT
1 TTATTTTAT
2303407 TAAAATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 10 0.29
29 18 0.53
30 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (29 bp):
TTATTTTATATTATATTATGTAAATATTA
Found at i:2305196 original size:21 final size:21
Alignment explanation
Indices: 2305172--2305264 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
2305162 TATGCCATCT
* *
2305172 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
2305193 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
2305214 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
2305235 CCGCCA-GGTTACATGCCTAG-
1 CCG-CAGGGTTACATGCCTAGC
2305255 CCGCAGGGTT
1 CCGCAGGGTT
2305265 TTTATACCAT
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
19 2 0.03
20 7 0.10
21 57 0.84
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:2306743 original size:246 final size:252
Alignment explanation
Indices: 2306232--2306967 Score: 1293
Period size: 246 Copynumber: 3.0 Consensus size: 252
2306222 TTACCTTATT
2306232 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2306297 TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGATA-
66 TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
*
2306361 TAATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
131 T--GATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
2306426 CGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
194 CGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2306485 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATG-TAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
2306549 TGACGAAATAA-GGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
66 TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
2306613 TGATATCTAGTGTCCCCGAGGGACATGA-TGACATAA-AGGGCAATGATAAC-TATTCTCTGACG
131 TGATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
2306675 AAATAATGGAAGGCGCG-CCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
196 AAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
2306731 TACTGATATATCTAGTGTCCCCGAAGGACATGAGTGACATAATAGGGCAATGATAACATA-T-TC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2306794 TGACG-AATAATGGAAGGCGCG-ACCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
66 TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
2306857 TGATATATCTA--GTCCCCGAGGGACATGAGTGACATAATAGGGCAA-GATAACATATTCTCTGA
131 TG--ATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
2306919 CGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
194 CGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGT
2306968 ACTCCGATTA
Statistics
Matches: 469, Mismatches: 4, Indels: 25
0.94 0.01 0.05
Matches are distributed among these distances:
244 65 0.14
245 31 0.07
246 134 0.29
247 36 0.08
248 42 0.09
249 8 0.02
250 26 0.06
251 51 0.11
252 24 0.05
253 52 0.11
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (252 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
TGATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
AAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:2306762 original size:123 final size:127
Alignment explanation
Indices: 2306232--2306967 Score: 1315
Period size: 126 Copynumber: 5.9 Consensus size: 127
2306222 TTACCTTATT
2306232 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2306297 TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGA
66 TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
2306359 TA-TAATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
2306423 TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2306485 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATG-TAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
2306549 TGACGAAATAA-GGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2306610 TACTG--ATATCTAGTGTCCCCGAGGGACATGA-TGACATAA-AGGGCAATGATAAC-TATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
2306670 TGACGAAATAATGGAAGGCGCG-CCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
2306731 TACTGATATATCTAGTGTCCCCGAAGGACATGAGTGACATAATAGGGCAATGATAACATA-T-TC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
2306794 TGACG-AATAATGGAAGGCGCG-ACCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
2306854 TACTGATATATCTA--GTCCCCGAGGGACATGAGTGACATAATAGGGCAA-GATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
2306916 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGT
2306968 ACTCCGATTA
Statistics
Matches: 589, Mismatches: 7, Indels: 28
0.94 0.01 0.04
Matches are distributed among these distances:
120 9 0.02
121 105 0.18
122 29 0.05
123 135 0.23
124 15 0.03
125 97 0.16
126 149 0.25
127 50 0.08
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (127 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:2315816 original size:20 final size:20
Alignment explanation
Indices: 2315766--2315816 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
2315756 TAATTATTGA
*
2315766 AATTTTATAATTTAAAAAAT
1 AATTTTAAAATTTAAAAAAT
*
2315786 AATTATT-AAATTTATTAAAAT
1 AATT-TTAAAATTTA-AAAAAT
2315807 -ATTTTAAAAT
1 AATTTTAAAAT
2315817 CATATATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.08
20 17 0.65
21 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTTTAAAATTTAAAAAAT
Found at i:2316606 original size:18 final size:18
Alignment explanation
Indices: 2316583--2316635 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
2316573 ACACTACAAG
2316583 TTGAATTGATATATTAAT
1 TTGAATTGATATATTAAT
2316601 TTGAATTGATATATTAAT
1 TTGAATTGATATATTAAT
* *
2316619 TTGAATTTATTTATTAA
1 TTGAATTGATATATTAA
2316636 GATAAAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TTGAATTGATATATTAAT
Found at i:2324943 original size:33 final size:33
Alignment explanation
Indices: 2324905--2324970 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2324895 TAAACTTTGA
2324905 TAACTTCATATTTAGATGAAGAAGGACTAGAAG
1 TAACTTCATATTTAGATGAAGAAGGACTAGAAG
2324938 TAACTTCATATTTAGATGAAGAAGGACTAGAAG
1 TAACTTCATATTTAGATGAAGAAGGACTAGAAG
2324971 AATTCAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.27
Consensus pattern (33 bp):
TAACTTCATATTTAGATGAAGAAGGACTAGAAG
Found at i:2325626 original size:34 final size:34
Alignment explanation
Indices: 2325579--2325646 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
2325569 TAAAATAAGG
*
2325579 ATAGATGCGTGCACCAAAACTCAAACGTAGAATC
1 ATAGATGCATGCACCAAAACTCAAACGTAGAATC
*
2325613 ATAGATGCATGCACCAAAACTCGAACGTAGAATC
1 ATAGATGCATGCACCAAAACTCAAACGTAGAATC
2325647 CATGAAGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (34 bp):
ATAGATGCATGCACCAAAACTCAAACGTAGAATC
Found at i:2330283 original size:83 final size:83
Alignment explanation
Indices: 2330128--2330284 Score: 253
Period size: 83 Copynumber: 1.9 Consensus size: 83
2330118 TAGGGAGTAA
* *
2330128 ATTAAAAATATGTGCTAATTTGGTATGTAAATTATTTTTTAAAAATATATCATTTATAAATTGCA
1 ATTAAAAATATGTGCTAATTTGGTATGTAAATTATTTCTAAAAAATATATCATTTATAAATTGCA
* *
2330193 TAGAAATTAAATATAATC
66 CAAAAATTAAATATAATC
*
2330211 ATTACAAATATGTGCTAATTTGGTATGTAAATTATTTCTAAAAAATATATCATTTAT-AATTAGC
1 ATTAAAAATATGTGCTAATTTGGTATGTAAATTATTTCTAAAAAATATATCATTTATAAATT-GC
2330275 ACAAAAATTA
65 ACAAAAATTA
2330285 TGATTCAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
82 4 0.06
83 64 0.94
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (83 bp):
ATTAAAAATATGTGCTAATTTGGTATGTAAATTATTTCTAAAAAATATATCATTTATAAATTGCA
CAAAAATTAAATATAATC
Found at i:2346247 original size:5 final size:5
Alignment explanation
Indices: 2346237--2346305 Score: 57
Period size: 5 Copynumber: 12.0 Consensus size: 5
2346227 ACCGGTCACA
2346237 ACCCG ACCCG ACCCGTTG ACCCG ACCCG ACCCG TTTACCCG ACCCG ACCCGTTG
1 ACCCG ACCCG ACCC---G ACCCG ACCCG ACCCG ---ACCCG ACCCG ACCC---G
2346291 ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG
2346306 TTGACCGTTG
Statistics
Matches: 55, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
5 40 0.73
8 15 0.27
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.10
Consensus pattern (5 bp):
ACCCG
Found at i:2346260 original size:18 final size:18
Alignment explanation
Indices: 2346237--2346311 Score: 141
Period size: 18 Copynumber: 4.2 Consensus size: 18
2346227 ACCGGTCACA
2346237 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2346255 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
2346273 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
2346291 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
2346309 ACC
1 ACC
2346312 GTTGACCCGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.17, C:0.51, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2346315 original size:7 final size:7
Alignment explanation
Indices: 2346303--2346349 Score: 76
Period size: 7 Copynumber: 6.4 Consensus size: 7
2346293 CCGACCCGAC
2346303 CCGTTGA
1 CCGTTGA
2346310 CCGTTGA
1 CCGTTGA
2346317 CCCGTTGA
1 -CCGTTGA
2346325 CCGTTGA
1 CCGTTGA
2346332 CCCGTTGA
1 -CCGTTGA
2346340 CCGTTGA
1 CCGTTGA
2346347 CCG
1 CCG
2346350 GAGTTGACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 24 0.63
8 14 0.37
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:2346320 original size:15 final size:15
Alignment explanation
Indices: 2346300--2346348 Score: 98
Period size: 15 Copynumber: 3.3 Consensus size: 15
2346290 GACCCGACCC
2346300 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2346315 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2346330 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2346345 GACC
1 GACC
2346349 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:2346331 original size:22 final size:22
Alignment explanation
Indices: 2346304--2346349 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2346294 CGACCCGACC
2346304 CGTTGACCGTTGACCCGTTGAC
1 CGTTGACCGTTGACCCGTTGAC
2346326 CGTTGACCCGTTGA-CCGTTGAC
1 CGTTGA-CCGTTGACCCGTTGAC
2346348 CG
1 CG
2346350 GAGTTGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.26
Consensus pattern (22 bp):
CGTTGACCGTTGACCCGTTGAC
Found at i:2348836 original size:48 final size:48
Alignment explanation
Indices: 2348784--2348915 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
2348774 AATATTTTAC
*
2348784 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
2348832 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
2348880 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
2348916 CTGATTTATA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:2348922 original size:24 final size:24
Alignment explanation
Indices: 2348801--2348915 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
2348791 TCGATTTGAT
2348801 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
2348825 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
2348849 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
2348873 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
2348896 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
2348916 CTGATTTATA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:2348932 original size:24 final size:24
Alignment explanation
Indices: 2348852--2348924 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
2348842 ACATGGATTC
* * *
2348852 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
2348876 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
2348900 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
2348924 T
1 T
2348925 ATTTTGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:2351114 original size:18 final size:18
Alignment explanation
Indices: 2351091--2351165 Score: 132
Period size: 18 Copynumber: 4.2 Consensus size: 18
2351081 ACCGGTCACA
2351091 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2351109 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
2351127 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2351145 ACCCAACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
2351163 ACC
1 ACC
2351166 GTTGACCCGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.19, C:0.51, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2351169 original size:7 final size:7
Alignment explanation
Indices: 2351157--2351203 Score: 76
Period size: 7 Copynumber: 6.4 Consensus size: 7
2351147 CCAACCCGAC
2351157 CCGTTGA
1 CCGTTGA
2351164 CCGTTGA
1 CCGTTGA
2351171 CCCGTTGA
1 -CCGTTGA
2351179 CCGTTGA
1 CCGTTGA
2351186 CCCGTTGA
1 -CCGTTGA
2351194 CCGTTGA
1 CCGTTGA
2351201 CCG
1 CCG
2351204 GAGTTGACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 24 0.63
8 14 0.37
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:2351174 original size:15 final size:15
Alignment explanation
Indices: 2351154--2351202 Score: 98
Period size: 15 Copynumber: 3.3 Consensus size: 15
2351144 GACCCAACCC
2351154 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2351169 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2351184 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
2351199 GACC
1 GACC
2351203 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:2351185 original size:22 final size:22
Alignment explanation
Indices: 2351158--2351203 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2351148 CAACCCGACC
2351158 CGTTGACCGTTGACCCGTTGAC
1 CGTTGACCGTTGACCCGTTGAC
2351180 CGTTGACCCGTTGA-CCGTTGAC
1 CGTTGA-CCGTTGACCCGTTGAC
2351202 CG
1 CG
2351204 GAGTTGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.26
Consensus pattern (22 bp):
CGTTGACCGTTGACCCGTTGAC
Found at i:2353692 original size:48 final size:48
Alignment explanation
Indices: 2353640--2353771 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
2353630 AATATTTTAC
*
2353640 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
2353688 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
2353736 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
2353772 CTGATTTATA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:2353778 original size:24 final size:24
Alignment explanation
Indices: 2353657--2353771 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
2353647 TCGATTTGAT
2353657 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
2353681 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
2353705 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
2353729 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
2353752 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
2353772 CTGATTTATA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:2353788 original size:24 final size:24
Alignment explanation
Indices: 2353708--2353780 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
2353698 ACATGGATTC
* * *
2353708 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
2353732 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
2353756 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
2353780 T
1 T
2353781 ATTTTGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:2358185 original size:16 final size:16
Alignment explanation
Indices: 2358164--2358194 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2358154 ACTAGAGTTT
2358164 TTTCCCTTTCCTTTCC
1 TTTCCCTTTCCTTTCC
*
2358180 TTTCCCTTTCTTTTC
1 TTTCCCTTTCCTTTC
2358195 TTTTAAAGAT
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:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTCCCTTTCCTTTCC
Found at i:2359577 original size:33 final size:33
Alignment explanation
Indices: 2359535--2359598 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
2359525 TAGATACGCT
*
2359535 ATTTAAATAATGTAGATGATACATATCTCTACG
1 ATTTAAATAACGTAGATGATACATATCTCTACG
2359568 ATTTAAATAACGTAGATGATACATATCTCTA
1 ATTTAAATAACGTAGATGATACATATCTCTA
2359599 ATATCTCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (33 bp):
ATTTAAATAACGTAGATGATACATATCTCTACG
Found at i:2361703 original size:60 final size:60
Alignment explanation
Indices: 2361606--2361730 Score: 205
Period size: 60 Copynumber: 2.1 Consensus size: 60
2361596 ATGCGACATC
* *
2361606 AAATACAAGACCTTTAAATCTTCGCTCTCCCAACTGACGTATCGCAGTCAAATTGTACTG
1 AAATACAAGACCTTTAAATCATCGCTCTCCCAACTGACCTATCGCAGTCAAATTGTACTG
* * *
2361666 AAATACACGACCTTTAAATCATCGCTCTTCCAGCTGACCTATCGCAGTCAAATTGTACTG
1 AAATACAAGACCTTTAAATCATCGCTCTCCCAACTGACCTATCGCAGTCAAATTGTACTG
2361726 AAATA
1 AAATA
2361731 ATTTCATGCT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (60 bp):
AAATACAAGACCTTTAAATCATCGCTCTCCCAACTGACCTATCGCAGTCAAATTGTACTG
Found at i:2378056 original size:7 final size:7
Alignment explanation
Indices: 2378044--2378087 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
2378034 TTGTTGATAA
2378044 AAACCCT
1 AAACCCT
2378051 AAACCCT
1 AAACCCT
*
2378058 AAACCAT
1 AAACCCT
* *
2378065 AATCACT
1 AAACCCT
*
2378072 AAACCTT
1 AAACCCT
2378079 AAACCCT
1 AAACCCT
2378086 AA
1 AA
2378088 CCATTCTCCC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:2378310 original size:283 final size:284
Alignment explanation
Indices: 2377787--2378346 Score: 874
Period size: 283 Copynumber: 2.0 Consensus size: 284
2377777 TTGTTGTTGA
*
2377787 AAACCCTAAACCCTAACCATTCTCCCTCTAATCAATTTCTTCTTATAAAAAACAAATACGTAACC
1 AAACCCTAAACCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAAACAAATACGTAACC
* *
2377852 ATCATCATGGTAGATATCACCATGGCCTCTACCCCTTTCATTGCCCTCAACATACCATGAATTTA
66 ACCATCATGGTAGATATCACCATGGCCTCTACCACTTTCATTGCCCTCAACATACCATGAATTTA
** *
2377917 TAAAGGTTTTGAGCAACAACCAAAATATTTTAGAGTTTAGGGTTTGCAAAATCAATAAACACCAA
131 TAAAGGTTTTGAGCAACAACCAAAATATTTTAGAGTTTAGGGTTCACAAAATCAATAAACAACAA
* * * * * *
2377982 TTAATATAAGTAACTATTGATTTTTTGAACCTTAAACTCTAAAATATTTTAGTTGTTGATAAAAA
196 ATAATACAAGTAACTATTGATCTTGTGAACCCTAAACTCTAAAATATTTTAGTTATTGATAAAAA
2378047 CCCTAAACCCTAAACCATAATCACT
261 CCCTAAACCCT-AACCATAATCACT
* *
2378072 AAACCTTAAACCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAAACAAATATGTAACC
1 AAACCCTAAACCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAAACAAATACGTAACC
*
2378137 ACCATCATGGTAGATATCACCAT-G-TTCTACCACTTTCATTGCCCTCAACATACCATGAATTTA
66 ACCATCATGGTAGATATCACCATGGCCTCTACCACTTTCATTGCCCTCAACATACCATGAATTTA
* * * * *
2378200 TAAAGGTTTTTAGCTATAACCAAAATATTTTAGGGTTTAGGGTTCACAAAATCAATATACAACAA
131 TAAAGGTTTTGAGCAACAACCAAAATATTTTAGAGTTTAGGGTTCACAAAATCAATAAACAACAA
* * *
2378265 ATAATACAAGTAGCTATTGATCTTGTGAACCCTAAAC-CTTAAAATATTTTGGTTATTGCTAAAA
196 ATAATACAAGTAACTATTGATCTTGTGAACCCTAAACTC-TAAAATATTTTAGTTATTGATAAAA
2378329 ACCCTAAACCCTAACCAT
260 ACCCTAAACCCTAACCAT
2378347 TCTCCCTCCA
Statistics
Matches: 251, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
282 7 0.03
283 159 0.63
284 1 0.00
285 84 0.33
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.31
Consensus pattern (284 bp):
AAACCCTAAACCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAAACAAATACGTAACC
ACCATCATGGTAGATATCACCATGGCCTCTACCACTTTCATTGCCCTCAACATACCATGAATTTA
TAAAGGTTTTGAGCAACAACCAAAATATTTTAGAGTTTAGGGTTCACAAAATCAATAAACAACAA
ATAATACAAGTAACTATTGATCTTGTGAACCCTAAACTCTAAAATATTTTAGTTATTGATAAAAA
CCCTAAACCCTAACCATAATCACT
Found at i:2380046 original size:28 final size:29
Alignment explanation
Indices: 2380014--2380072 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
2380004 CTCTAATTTA
*
2380014 AAATCTTAAATTG-ATAA-CCCTAAACCTT
1 AAATCATAAA-TGCATAACCCCTAAACCTT
*
2380042 AAATCATAAATGCATAACCCCTAAACTTT
1 AAATCATAAATGCATAACCCCTAAACCTT
2380071 AA
1 AA
2380073 CCTCTAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 13 0.48
29 12 0.44
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.29
Consensus pattern (29 bp):
AAATCATAAATGCATAACCCCTAAACCTT
Found at i:2382498 original size:31 final size:31
Alignment explanation
Indices: 2382457--2382531 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
2382447 ACAAATAAAA
*
2382457 TTTAAATACTAAAACGAAACAAAATTAATAG
1 TTTAAATACTAAAACAAAACAAAATTAATAG
* *
2382488 TTTAAGTACTAAAATAAAACAAAATTAATAG
1 TTTAAATACTAAAACAAAACAAAATTAATAG
*
2382519 TTTAATTACTAAA
1 TTTAAATACTAAA
2382532 CGTGCAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (31 bp):
TTTAAATACTAAAACAAAACAAAATTAATAG
Found at i:2388138 original size:3 final size:3
Alignment explanation
Indices: 2388130--2388170 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
2388120 AGCAACAGCT
2388130 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA GAAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GA
2388171 TCTGAGATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2390462 original size:17 final size:18
Alignment explanation
Indices: 2390442--2390479 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2390432 TATTAGTATG
*
2390442 TCAAA-AAAGTAAAAAAA
1 TCAAATAAAGAAAAAAAA
*
2390459 TCAAATTAAGAAAAAAAA
1 TCAAATAAAGAAAAAAAA
2390477 TCA
1 TCA
2390480 GTGTGTGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.71, C:0.08, G:0.05, T:0.16
Consensus pattern (18 bp):
TCAAATAAAGAAAAAAAA
Found at i:2393284 original size:24 final size:24
Alignment explanation
Indices: 2393257--2393302 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2393247 AATGGAACAT
2393257 TATACTTATTAAATAAATGATAAC
1 TATACTTATTAAATAAATGATAAC
2393281 TATACTTATTAAATAAATGATA
1 TATACTTATTAAATAAATGATA
2393303 TAAAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACTTATTAAATAAATGATAAC
Found at i:2393591 original size:55 final size:54
Alignment explanation
Indices: 2393481--2393599 Score: 204
Period size: 53 Copynumber: 2.2 Consensus size: 54
2393471 TGTTAAACAA
2393481 ATATATATATATATATGAACAAAAAAAATCAGTTTACAAGACACATTAAATAAAT
1 ATATATATATATATATGAAC-AAAAAAATCAGTTTACAAGACACATTAAATAAAT
* *
2393536 ATATATATATATATATGAAC-AAAAAATCAGTTTCCAAGACACATTAAATAAAA
1 ATATATATATATATATGAACAAAAAAATCAGTTTACAAGACACATTAAATAAAT
2393589 ATATATATATA
1 ATATATATATA
2393600 CGTTTAACAA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
53 42 0.68
55 20 0.32
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.30
Consensus pattern (54 bp):
ATATATATATATATATGAACAAAAAAATCAGTTTACAAGACACATTAAATAAAT
Found at i:2393779 original size:51 final size:49
Alignment explanation
Indices: 2393665--2393882 Score: 325
Period size: 49 Copynumber: 4.4 Consensus size: 49
2393655 CTAAGACACA
* *
2393665 TTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATG
1 TTAAACAAATATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
2393714 TTAAACAAATATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
1 TTAAACAAATATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
*
2393763 TTAAACAAATATATATATATAT-ATATGAAAAAAATCAGTTTCCAAGACATG
1 TTAAACAAATATATATATATATGA-A--CAAAAAATCAGTTTCCAAGACATG
**
2393814 TTAAAC-AA-ATATATATATATGAACAAAAAATCAGTTTCCAAGACACA
1 TTAAACAAATATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
* *
2393861 TTAAATAAATAAATATATATAT
1 TTAAACAAATATATATATATAT
2393883 ATATATACAC
Statistics
Matches: 155, Mismatches: 8, Indels: 12
0.89 0.05 0.07
Matches are distributed among these distances:
47 26 0.17
48 3 0.02
49 94 0.61
50 3 0.02
51 29 0.19
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (49 bp):
TTAAACAAATATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
Found at i:2393788 original size:192 final size:191
Alignment explanation
Indices: 2393423--2393783 Score: 513
Period size: 184 Copynumber: 1.9 Consensus size: 191
2393413 ATATATCCAG
* **
2393423 CTAAGCTATACGTTAAACAAATAAAATATGCCTATTCTTCCTAAGACATGTTAAACAAATATATA
1 CTAAGCTATACATTAAACAAATAAAATATGCCTATTCTTCCTAAGACACATTAAACAAATATATA
2393488 TATATATATGAACAAAAAAAATCAGTTTACAAGACACATTAAATAAATATATATATATATATATG
66 TATATATATGAAC-AAAAAAATCAGTTTACAAGACACATTAAATAAATATATATATATATATATG
2393553 AACAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATACGTTTAACAAATAAA
130 AACAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATACGTTTAACAAATAAA
* *
2393615 CTAAGCTATATATTAAACAAAT-AAATAATGGCTATTCTTCCTAAGACACATTAAAC-AA-ATAT
1 CTAAGCTATACATTAAACAAATAAAAT-ATGCCTATTCTTCCTAAGACACATTAAACAAATATAT
* * * ** *
2393677 ATATGTATATGAAC-AAAGAATCAGTTTCCAAGACATGTT-AA-ACA-A-ATATATATATATATG
65 ATATATATATGAACAAAAAAATCAGTTTACAAGACACATTAAATAAATATATATATATATATATG
** * *
2393737 AACAAAAAATCAGTTTCCAAGACATGTTAAACAAATATATATATATA
130 AACAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATA
2393784 TATATGAAAA
Statistics
Matches: 153, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
184 58 0.38
185 1 0.01
186 2 0.01
187 2 0.01
188 21 0.14
190 17 0.11
191 6 0.04
192 46 0.30
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (191 bp):
CTAAGCTATACATTAAACAAATAAAATATGCCTATTCTTCCTAAGACACATTAAACAAATATATA
TATATATATGAACAAAAAAATCAGTTTACAAGACACATTAAATAAATATATATATATATATATGA
ACAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATACGTTTAACAAATAAA
Found at i:2393888 original size:100 final size:102
Alignment explanation
Indices: 2393652--2393886 Score: 360
Period size: 98 Copynumber: 2.4 Consensus size: 102
2393642 ATGGCTATTC
*
2393652 TTCCTAAGACACATTAAAC--A-A-ATATATATGTATATGAACAAAGAATCAGTTTCCAAGACAT
1 TTCC-AAGACACATTAAACAAATATATATATATATATATGAACAAAGAATCAGTTTCCAAGACAT
2393713 GTTAAACAAATATATATATATATGAACAAAAAATCAGT
65 GTTAAACAAATATATATATATATGAACAAAAAATCAGT
**
2393751 TTCCAAGACATGTTAAACAAATATATATATATATATATGAA-AAA-AATCAGTTTCCAAGACATG
1 TTCCAAGACACATTAAACAAATATATATATATATATATGAACAAAGAATCAGTTTCCAAGACATG
2393814 TTAAAC-AA-ATATATATATATGAACAAAAAATCAGT
66 TTAAACAAATATATATATATATGAACAAAAAATCAGT
* *
2393849 TTCCAAGACACATTAAATAAATAAATATATATATATAT
1 TTCCAAGACACATTAAACAAATATATATATATATATAT
2393887 ATACACGTTT
Statistics
Matches: 125, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
98 73 0.58
99 6 0.05
100 26 0.21
101 4 0.03
102 16 0.13
ACGTcount: A:0.51, C:0.12, G:0.08, T:0.30
Consensus pattern (102 bp):
TTCCAAGACACATTAAACAAATATATATATATATATATGAACAAAGAATCAGTTTCCAAGACATG
TTAAACAAATATATATATATATGAACAAAAAATCAGT
Found at i:2394456 original size:15 final size:15
Alignment explanation
Indices: 2394436--2394468 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2394426 TAGTGTGACT
2394436 AAAATATAAATA-TTA
1 AAAATA-AAATACTTA
2394451 AAAATAAAATACTTA
1 AAAATAAAATACTTA
2394466 AAA
1 AAA
2394469 CAAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAATACTTA
Found at i:2395815 original size:3 final size:3
Alignment explanation
Indices: 2395809--2395851 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
2395799 TAAATACACT
* *
2395809 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2395852 TTTTTTAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2396163 original size:105 final size:105
Alignment explanation
Indices: 2396022--2396256 Score: 445
Period size: 105 Copynumber: 2.2 Consensus size: 105
2396012 TCTCGTGGAT
*
2396022 GAGTTCTTCTCATTATGAACTCTTTTGGAAACGTTGATCCAAATCCTTTTGCGGTGGACTTAGAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAACGTTGATCCAAATCCTTTTGCGGTGGACTTAGAA
2396087 AGAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
66 AGAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
*
2396127 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCAAATCCTTTTGCGGTGGACTTAGAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAACGTTGATCCAAATCCTTTTGCGGTGGACTTAGAA
2396192 AGAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
66 AGAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
2396232 GAGTTCTTCTCATTATGAACT-TTCT
1 GAGTTCTTCTCATTATGAACTCTTCT
2396257 CCTTTAGGAC
Statistics
Matches: 128, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
104 4 0.03
105 124 0.97
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAACGTTGATCCAAATCCTTTTGCGGTGGACTTAGAA
AGAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
Found at i:2396249 original size:35 final size:35
Alignment explanation
Indices: 2396203--2396287 Score: 170
Period size: 35 Copynumber: 2.4 Consensus size: 35
2396193 GAACATGTTT
2396203 TTCTCATTATGAACTTTCTCCTTTAGGACGAGTTC
1 TTCTCATTATGAACTTTCTCCTTTAGGACGAGTTC
2396238 TTCTCATTATGAACTTTCTCCTTTAGGACGAGTTC
1 TTCTCATTATGAACTTTCTCCTTTAGGACGAGTTC
2396273 TTCTCATTATGAACT
1 TTCTCATTATGAACT
2396288 CTTCACTGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (35 bp):
TTCTCATTATGAACTTTCTCCTTTAGGACGAGTTC
Found at i:2396444 original size:136 final size:136
Alignment explanation
Indices: 2396236--2396572 Score: 540
Period size: 136 Copynumber: 2.5 Consensus size: 136
2396226 TAGGACGAGT
* * * *
2396236 TCTTCTCATTATGAAC-T-TTCT-CCT-T-TAGGACGAGTTCTTCTCATTATGAACTCTTCACTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
** * * *
2396296 GAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCAAAATGTTATGAATCGAGTGATAGGTCGA
66 GAAATACTGATCCCTCAAGCAAGCTGTCACTGATTCAAAATGTCATGAATCGAGTGATAGGTCGA
2396361 ACAAGC
131 ACAAGC
2396367 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
* *
2396432 GAAATACTGATCCTTCAAGCAAGCTGTCACTGATTCAAAATGTCGTGAATCGAGTGATAGGTCGA
66 GAAATACTGATCCCTCAAGCAAGCTGTCACTGATTCAAAATGTCATGAATCGAGTGATAGGTCGA
2396497 ACAAGC
131 ACAAGC
2396503 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
2396568 GAAAT
66 GAAAT
2396573 GCTGGTTCAC
Statistics
Matches: 190, Mismatches: 11, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
131 16 0.08
132 1 0.01
133 4 0.02
134 3 0.02
135 1 0.01
136 165 0.87
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (136 bp):
TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTG
GAAATACTGATCCCTCAAGCAAGCTGTCACTGATTCAAAATGTCATGAATCGAGTGATAGGTCGA
ACAAGC
Found at i:2397465 original size:15 final size:14
Alignment explanation
Indices: 2397445--2397539 Score: 61
Period size: 16 Copynumber: 6.5 Consensus size: 14
2397435 CAAACCCTCC
*
2397445 TTTTTCTCTTTTTA
1 TTTTTTTCTTTTTA
*
2397459 -TTTTTTC-ATTT-
1 TTTTTTTCTTTTTA
*
2397470 CTTTTTTCATTTTTCA
1 TTTTTTTC-TTTTT-A
2397486 TTTTTTTCTTTTTCA
1 TTTTTTTCTTTTT-A
2397501 TTTTTTTTCATTTTTCA
1 -TTTTTTTC-TTTTT-A
* *
2397518 TCTTTTTATTTGTTA
1 TTTTTTTCTTT-TTA
2397533 TTTTTTT
1 TTTTTTT
2397540 TTCTTCAAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
12 10 0.15
13 6 0.09
14 3 0.05
15 17 0.26
16 23 0.35
17 7 0.11
ACGTcount: A:0.09, C:0.12, G:0.01, T:0.78
Consensus pattern (14 bp):
TTTTTTTCTTTTTA
Found at i:2397476 original size:20 final size:19
Alignment explanation
Indices: 2397447--2397518 Score: 77
Period size: 16 Copynumber: 4.1 Consensus size: 19
2397437 AACCCTCCTT
2397447 TTTCTCTTTTT-ATTTTTTCA
1 TTTCT-TTTTTCA-TTTTTCA
2397467 TTTCTTTTTTCATTTTTCA
1 TTTCTTTTTTCATTTTTCA
2397486 --T-TTTTTTC-TTTTTCA
1 TTTCTTTTTTCATTTTTCA
2397501 -TT-TTTTTTCATTTTTCA
1 TTTCTTTTTTCATTTTTCA
2397518 T
1 T
2397519 CTTTTTATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.15
16 15 0.31
17 8 0.17
19 12 0.25
20 6 0.12
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTCTTTTTTCATTTTTCA
Found at i:2397491 original size:34 final size:34
Alignment explanation
Indices: 2397445--2397542 Score: 134
Period size: 33 Copynumber: 3.0 Consensus size: 34
2397435 CAAACCCTCC
2397445 TTTTTC-TCTTTTTATTTTTTCATTTCTTTTTTCA
1 TTTTTCATCTTTTTATTTTTTCATTT-TTTTTTCA
2397479 TTTTTCAT-TTTTT-TCTTTTTCA-TTTTTTTTCA
1 TTTTTCATCTTTTTAT-TTTTTCATTTTTTTTTCA
*
2397511 TTTTTCATCTTTTTATTTGTT-ATTTTTTTTTC
1 TTTTTCATCTTTTTATTTTTTCATTTTTTTTTC
2397543 TTCAAGCATA
Statistics
Matches: 58, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
32 17 0.29
33 21 0.36
34 19 0.33
35 1 0.02
ACGTcount: A:0.09, C:0.12, G:0.01, T:0.78
Consensus pattern (34 bp):
TTTTTCATCTTTTTATTTTTTCATTTTTTTTTCA
Found at i:2397512 original size:32 final size:32
Alignment explanation
Indices: 2397445--2397540 Score: 124
Period size: 32 Copynumber: 2.9 Consensus size: 32
2397435 CAAACCCTCC
2397445 TTTTTC-TCTTTTTATTTTTTCATTTCTTTTTTCA
1 TTTTTCATCTTTTTA-TTTTTCA-TT-TTTTTTCA
* *
2397479 TTTTTCATTTTTTTCTTTTTCATTTTTTTTCA
1 TTTTTCATCTTTTTATTTTTCATTTTTTTTCA
2397511 TTTTTCATCTTTTTATTTGTT-ATTTTTTTT
1 TTTTTCATCTTTTTATTT-TTCATTTTTTTT
2397541 TCTTCAAGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
32 33 0.59
33 4 0.07
34 13 0.23
35 6 0.11
ACGTcount: A:0.09, C:0.11, G:0.01, T:0.78
Consensus pattern (32 bp):
TTTTTCATCTTTTTATTTTTCATTTTTTTTCA
Found at i:2409305 original size:24 final size:24
Alignment explanation
Indices: 2409278--2409323 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2409268 AATGGAACAT
2409278 TATACTTATTAAATAAATGATAAC
1 TATACTTATTAAATAAATGATAAC
2409302 TATACTTATTAAATAAATGATA
1 TATACTTATTAAATAAATGATA
2409324 TAAAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACTTATTAAATAAATGATAAC
Found at i:2409597 original size:48 final size:50
Alignment explanation
Indices: 2409506--2409617 Score: 183
Period size: 48 Copynumber: 2.3 Consensus size: 50
2409496 TTAAACAAAT
2409506 ATATATATATATATGAACAAAAAAAATCAGTTTACAAGACACATTAAATAA
1 ATATATATATATATGAAC-AAAAAAATCAGTTTACAAGACACATTAAATAA
*
2409557 ATATATATATATAT-AAC-AAAAAATCAGTTTCCAAGACACATTAAATAA
1 ATATATATATATATGAACAAAAAAATCAGTTTACAAGACACATTAAATAA
*
2409605 AAATATATATATA
1 ATATATATATATA
2409618 CGTTTAACAA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
48 42 0.71
50 3 0.05
51 14 0.24
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.29
Consensus pattern (50 bp):
ATATATATATATATGAACAAAAAAATCAGTTTACAAGACACATTAAATAA
Found at i:2409750 original size:187 final size:183
Alignment explanation
Indices: 2409446--2409801 Score: 468
Period size: 184 Copynumber: 1.9 Consensus size: 183
2409436 ATATATCCAG
* **
2409446 CTAAGCTATACGTTAAACAAATAAAATATGCCTATTCTTCCTAAGACATGTTAAACAAATATATA
1 CTAAGCTATACATTAAACAAATAAAATATGCCTATTCTTCCTAAGACACATTAAACAAATATATA
*
2409511 TATATATATGAACAAAAAAAATCAGTTTACAAGACACATTAAATAAATATATATATATATAACAA
66 TATATATATGAAC-AAAAAAATCAGTTTACAAGACACATT-AA-AAATATATATATAT-GAACAA
*
2409576 AAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATACGTTTAACAAATAAA
127 AAAATCAGTTTCCAAGACACATTAAACAAAAATATATATATACGTTTAACAAATAAA
* *
2409633 CTAAGCTATATATTAAACAAAT-AAATAATGGCTATTCTTCCTAAGACACATTAAAC-AA-ATAT
1 CTAAGCTATACATTAAACAAATAAAAT-ATGCCTATTCTTCCTAAGACACATTAAACAAATATAT
* * * **
2409695 ATATGTATATGAAC-AAAGAATCAGTTTCCAAGACATGTTAAACAAATATATATATATATGAACA
65 ATATATATATGAACAAAAAAATCAGTTTACAAGACACATT--A-AAA-ATATATATATATGAACA
** *
2409759 AAAAATCAGTTTCCAAGACATGTTAAACAAATATATATATATA
126 AAAAATCAGTTTCCAAGACACATTAAACAAAAATATATATATA
2409802 TATATGAAAA
Statistics
Matches: 150, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
183 21 0.14
184 47 0.31
185 30 0.20
186 6 0.04
187 46 0.31
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (183 bp):
CTAAGCTATACATTAAACAAATAAAATATGCCTATTCTTCCTAAGACACATTAAACAAATATATA
TATATATATGAACAAAAAAATCAGTTTACAAGACACATTAAAAATATATATATATGAACAAAAAA
TCAGTTTCCAAGACACATTAAACAAAAATATATATATACGTTTAACAAATAAA
Found at i:2409797 original size:51 final size:49
Alignment explanation
Indices: 2409683--2409901 Score: 327
Period size: 49 Copynumber: 4.4 Consensus size: 49
2409673 CTAAGACACA
* *
2409683 TTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATG
1 TTAAACAAATATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
2409732 TTAAACAAATATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
1 TTAAACAAATATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
*
2409781 TTAAACAAATATATATATATAT-ATATGAAAAAAATCAGTTTCCAAGACATG
1 TTAAACAAATATATATATATATGA-A--CAAAAAATCAGTTTCCAAGACATG
**
2409832 TTAAAC-AA-ATATATATATATGAACAAAAAATCAGTTTCCAAGACACA
1 TTAAACAAATATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
*
2409879 TTAAATAAATAATATATATATAT
1 TTAAACAAAT-ATATATATATAT
2409902 ATATATATAT
Statistics
Matches: 156, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
47 26 0.17
48 3 0.02
49 83 0.53
50 15 0.10
51 29 0.19
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (49 bp):
TTAAACAAATATATATATATATGAACAAAAAATCAGTTTCCAAGACATG
Found at i:2409838 original size:187 final size:185
Alignment explanation
Indices: 2409457--2409842 Score: 458
Period size: 187 Copynumber: 2.1 Consensus size: 185
2409447 TAAGCTATAC
**
2409457 GTTAAACAAATAAAATATGCCTATTCTTCCTAAGACATGTTAAACAAATATATATATATATATGA
1 GTTAAACAAATAAAATATGCCTATTCTTCCTAAGACACATTAAACAAATATATATATATATATGA
*
2409522 ACAAAAAAAATCAGTTTACAAGACACATTAAATAAATATATATATATATAACAAAAAATCAGTTT
66 AC-AAAAAAATCAGTTTACAAGACACATTAAACAAATATATATATATATAACAAAAAATCAGTTT
* * ** * * *
2409587 CCAAGACACATTAAATAAAAATATATATATACGTTTAACAAATAAACTAAGCTATAT
130 CCAAGACACATTAAACAAAAATATATATATACATGAAAAAAATAAACCAAGC-ACAT
* * *
2409644 ATTAAACAAAT-AAATAATGGCTATTCTTCCTAAGACACATTAAAC-AA-ATATATATGTATATG
1 GTTAAACAAATAAAAT-ATGCCTATTCTTCCTAAGACACATTAAACAAATATATATATATATATG
* * **
2409706 AAC-AAAGAATCAGTTTCCAAGACATGTTAAACAAATATATATATATATGAACAAAAAATCAGTT
65 AACAAAAAAATCAGTTTACAAGACACATTAAACAAATATATATATATAT-AACAAAAAATCAGTT
** * **
2409770 TCCAAGACATGTTAAACAAATATATATATATATATATGAAAAAAATCAGTTTCCAAG-ACAT
129 TCCAAGACACATTAAACAAA-A-ATATATATATACATGAAAAAAAT-A--AACCAAGCACAT
2409831 GTTAAACAAATA
1 GTTAAACAAATA
2409843 TATATATATG
Statistics
Matches: 168, Mismatches: 23, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
183 40 0.24
184 32 0.19
185 18 0.11
186 24 0.14
187 50 0.30
189 4 0.02
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (185 bp):
GTTAAACAAATAAAATATGCCTATTCTTCCTAAGACACATTAAACAAATATATATATATATATGA
ACAAAAAAATCAGTTTACAAGACACATTAAACAAATATATATATATATAACAAAAAATCAGTTTC
CAAGACACATTAAACAAAAATATATATATACATGAAAAAAATAAACCAAGCACAT
Found at i:2409897 original size:2 final size:2
Alignment explanation
Indices: 2409890--2409918 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2409880 TAAATAAATA
2409890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2409919 CACGTTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2410483 original size:15 final size:15
Alignment explanation
Indices: 2410463--2410495 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2410453 TAGTGTGACT
2410463 AAAATATAAATA-TTA
1 AAAATA-AAATACTTA
2410478 AAAATAAAATACTTA
1 AAAATAAAATACTTA
2410493 AAA
1 AAA
2410496 CAAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAATACTTA
Found at i:2411844 original size:3 final size:3
Alignment explanation
Indices: 2411838--2411880 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
2411828 TAAATACACT
* *
2411838 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2411881 TTTTTTAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2414671 original size:13 final size:15
Alignment explanation
Indices: 2414642--2414678 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2414632 ATTATGTCTT
2414642 ATCTCTTAAATTTTAA
1 ATCT-TTAAATTTTAA
2414658 AT-TTTAAA-TTTAA
1 ATCTTTAAATTTTAA
2414671 ATCTTTAA
1 ATCTTTAA
2414679 TAATATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.35
14 10 0.50
15 1 0.05
16 2 0.10
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (15 bp):
ATCTTTAAATTTTAA
Found at i:2427241 original size:22 final size:23
Alignment explanation
Indices: 2427199--2427241 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2427189 AAATATCAAA
*
2427199 TTATTATTTTTTCATTTATATGT
1 TTATTATTTTTTCATTAATATGT
*
2427222 TTATT-TTTTTTTATTAATAT
1 TTATTATTTTTTCATTAATAT
2427242 AGATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
TTATTATTTTTTCATTAATATGT
Found at i:2434845 original size:2 final size:2
Alignment explanation
Indices: 2434840--2434873 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
2434830 TCCTTTTTAT
2434840 TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T
2434874 CGAGGAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2448012 original size:2 final size:2
Alignment explanation
Indices: 2448005--2448029 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2447995 TTGGACTTTG
2448005 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
2448030 CACATGCATG
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:2449942 original size:12 final size:12
Alignment explanation
Indices: 2449913--2449950 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2449903 ACGAGAGTAA
2449913 AAATAAAT-TAT
1 AAATAAATATAT
*
2449924 TAATAAATATAT
1 AAATAAATATAT
*
2449936 AAATAAATATTT
1 AAATAAATATAT
2449948 AAA
1 AAA
2449951 ATATATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATAAATATAT
Found at i:2449942 original size:23 final size:21
Alignment explanation
Indices: 2449913--2449958 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2449903 ACGAGAGTAA
2449913 AAATAAATTATTAATAAATATAT
1 AAATAAA-TATTAA-AAATATAT
*
2449936 AAATAAATATTTAAAATATAT
1 AAATAAATATTAAAAATATAT
2449957 AA
1 AA
2449959 TAATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 5 0.23
23 7 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATAAATATTAAAAATATAT
Found at i:2460791 original size:3 final size:3
Alignment explanation
Indices: 2460780--2460814 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
2460770 CCTGAAAAAA
*
2460780 AAT ATT AAT AAT AAT AAT AAT AAT AAAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A
2460815 TTAAACCCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2470973 original size:16 final size:16
Alignment explanation
Indices: 2470948--2470991 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
2470938 AGAGTTTTTT
2470948 TTTTAATTTTATAAAA
1 TTTTAATTTTATAAAA
* *
2470964 TTTTAGTTTTTTAAAAA
1 TTTTAATTTTAT-AAAA
*
2470981 TTATAATTTTA
1 TTTTAATTTTA
2470992 GGTTTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TTTTAATTTTATAAAA
Found at i:2471600 original size:18 final size:18
Alignment explanation
Indices: 2471577--2471617 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2471567 GGAATGTAAA
2471577 ATTACCGACGAGAATAAG
1 ATTACCGACGAGAATAAG
* *
2471595 ATTACCGGCGGGAATAAG
1 ATTACCGACGAGAATAAG
2471613 ATTAC
1 ATTAC
2471618 TGGAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (18 bp):
ATTACCGACGAGAATAAG
Done.