Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 50
Found at i:6409528 original size:20 final size:20
Alignment explanation
Indices: 6409503--6409622 Score: 132
Period size: 20 Copynumber: 5.7 Consensus size: 20
6409493 TAAATGAAAT
6409503 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
6409523 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
6409543 GCATGAAAGGATACATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
6409563 GAATGAAAAGATGCCATAAAATAAAT
1 GCATGAAAGGATG-CAT----T-AAG
6409589 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
6409609 GCATTAAAGGATGC
1 GCATGAAAGGATGC
6409623 CATAAATGAA
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
20 62 0.75
21 4 0.05
25 4 0.05
26 13 0.16
ACGTcount: A:0.44, C:0.10, G:0.25, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:6409657 original size:86 final size:87
Alignment explanation
Indices: 6409494--6409657 Score: 190
Period size: 86 Copynumber: 1.9 Consensus size: 87
6409484 ATGAATACAT
* * ** *
6409494 AAATGAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCATTAAGGCATGAAAGGATACAT
1 AAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATAAAGAAATGAAAGAATACAT
* *
6409559 TAAGGAATGAAAAGATGCCATA
66 TAACGAAAGAAAAGATGCCATA
* * *
6409581 AAAT-AAATGCATGAAAGGATGCATTAAGGCATTAAAGGATGCCATAAATGAAATTAACGAATA-
1 AAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-CATAAA-GAAATGAAAGAATAC
*
6409644 ATT-ACTAAAGAAAA
64 ATTAACGAAAGAAAA
6409658 ATGAAAGGAA
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
86 43 0.67
87 12 0.19
88 9 0.14
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (87 bp):
AAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATAAAGAAATGAAAGAATACAT
TAACGAAAGAAAAGATGCCATA
Found at i:6413708 original size:18 final size:18
Alignment explanation
Indices: 6413663--6413709 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
6413653 CATTTTGCAT
6413663 TTGCATTTTACTTTTCGCAC
1 TTGCATTTTACTTTTCG--C
6413683 TT-CATTTTACTTTTTCG-
1 TTGCATTTTAC-TTTTCGC
6413700 TTGCATTTTA
1 TTGCATTTTA
6413710 TCCATTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 7 0.28
19 8 0.32
20 8 0.32
ACGTcount: A:0.15, C:0.19, G:0.09, T:0.57
Consensus pattern (18 bp):
TTGCATTTTACTTTTCGC
Found at i:6414896 original size:18 final size:19
Alignment explanation
Indices: 6414847--6414901 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
6414837 ACACCTGACA
* *
6414847 TTTTGCATTTACATTTTAGT
1 TTTTGCA-TTGCATTTTAGC
* *
6414867 TTTTACACTGCATTTTA-C
1 TTTTGCATTGCATTTTAGC
6414885 TTTTGCATTGCATTTTA
1 TTTTGCATTGCATTTTA
6414902 TCTATTCATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 15 0.52
19 8 0.28
20 6 0.21
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.56
Consensus pattern (19 bp):
TTTTGCATTGCATTTTAGC
Found at i:6428168 original size:19 final size:19
Alignment explanation
Indices: 6428144--6428187 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
6428134 GAGATAAATT
6428144 TGCTCCTCACATTCTCATC
1 TGCTCCTCACATTCTCATC
*
6428163 TGCTCCTCACGTTCTCATC
1 TGCTCCTCACATTCTCATC
6428182 TGCTCC
1 TGCTCC
6428188 ATTGGCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.11, C:0.43, G:0.09, T:0.36
Consensus pattern (19 bp):
TGCTCCTCACATTCTCATC
Found at i:6436616 original size:133 final size:133
Alignment explanation
Indices: 6436470--6437037 Score: 472
Period size: 133 Copynumber: 4.3 Consensus size: 133
6436460 TCCTGAAGAA
* * * * ** *
6436470 CAGTGAACCAAATCGATTCTAATTCAATCTTCCATAAACAGTACCGAAGTATATCAAAATATTAT
1 CAGTGAAGCAAATCAATTCTAATTCAATCTTCCCTAAAGAGTACCGAAGTGGATCAAAATATTAC
* * * *
6436535 GTCTTTGATCTCCCCTAATGAGTAGTGAAGCAGGCCCACCTTCTCTT-AGATGTGGTCTTCCTAG
66 GTCTCTGATCTCCCCTAAAGAGTAGTGGAGCAGACCCACCTTCT-TTCAGATGTGGTCTTCCTAG
6436599 AGAG
130 AGAG
* * ** * * *
6436603 CAGTGAAGTAAATCGATT-TCGCTTCAATCTTCCCT-GA-AGTACAACGAAGTGGATTAAAATAA
1 CAGTGAAGCAAATCAATTCT-AATTCAATCTTCCCTAAAGAGTAC--CGAAGTGGATCAAAATAT
* * * ** *
6436665 TACATATCTGATCTCCCCTAAAGAGTAATGGAGCAGACCCATATTCTTTCAGATGTGGTCTTCCC
63 TACGTCTCTGATCTCCCCTAAAGAGTAGTGGAGCAGACCCACCTTCTTTCAGATGTGGTCTTCCT
*
6436730 ATAGAG
128 AGAGAG
* * * * ** *
6436736 CAGCT-AAGCAAAT-AATGTCTGATTTAATCTTCCCTGAAGAGCATTGAAGTGGATCAAAACATT
1 CAG-TGAAGCAAATCAAT-TCTAATTCAATCTTCCCTAAAGAGTACCGAAGTGGATCAAAATATT
* * * *
6436799 ACGTGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGACGCATCTTC-TTCTAGATTTGGTCTTCCT
64 ACGTCTCTGATCTCCCCTAAAGAGTAGTGGAGCAGACCCACCTTCTTTC-AGATGTGGTCTTCCT
* *
6436863 GGAGAA
128 AGAGAG
** ** * * * *
6436869 CAGCAAAGCAAATCACGTCTAATTCAATCTTCCCTAAAGAGAAGCAAAGTGGATTAAAAT-TTA-
1 CAGTGAAGCAAATCAATTCTAATTCAATCTTCCCTAAAGAGTACCGAAGTGGATCAAAATATTAC
** * * ** * *
6436932 GAGTCTGATCTCTCCTAAAGAGTAGTGGAGCATACCTGCCTTCTTTCAGATTTGGTCTTCCTAAA
66 GTCTCTGATCTCCCCTAAAGAGTAGTGGAGCAGACCCACCTTCTTTCAGATGTGGTCTTCCTAGA
6436997 GAG
131 GAG
* * * *
6437000 AAGTGAAGAAAATCAAGTT-TCATTCAATCTTCCTTAAA
1 CAGTGAAGCAAATCAA-TTCTAATTCAATCTTCCCTAAA
6437038 AAACGGTGAA
Statistics
Matches: 348, Mismatches: 73, Indels: 30
0.77 0.16 0.07
Matches are distributed among these distances:
131 87 0.25
132 16 0.05
133 238 0.68
134 4 0.01
135 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (133 bp):
CAGTGAAGCAAATCAATTCTAATTCAATCTTCCCTAAAGAGTACCGAAGTGGATCAAAATATTAC
GTCTCTGATCTCCCCTAAAGAGTAGTGGAGCAGACCCACCTTCTTTCAGATGTGGTCTTCCTAGA
GAG
Found at i:6464583 original size:15 final size:16
Alignment explanation
Indices: 6464563--6464603 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
6464553 GTTTACTTCA
*
6464563 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
6464578 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
6464594 GAATGATTCA
1 GAATGATTCA
6464604 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:6468155 original size:19 final size:19
Alignment explanation
Indices: 6468112--6468152 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
6468102 AAATTATACC
**
6468112 CTTAAATTATATCTAAATT
1 CTTAAATTATATCTAAACA
6468131 CTTAAATTATATCCTAAACA
1 CTTAAATTATAT-CTAAACA
6468151 CT
1 CT
6468153 AAACCTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (19 bp):
CTTAAATTATATCTAAACA
Found at i:6476438 original size:89 final size:88
Alignment explanation
Indices: 6476275--6476549 Score: 406
Period size: 89 Copynumber: 3.1 Consensus size: 88
6476265 CCAGGACTAC
* * * * *
6476275 GTCCGTAGGGCTTACCCTAAGCACATAGCAAAAGGGAGCTAACCTAAAGATATTCCTTGGGGCCT
1 GTCCGTAGGG-TTACCCTAAGCACACAGC-AAAGGGAACCAACCTAAGGATATGCCTTGGGGCCT
6476340 ATTGGCCTACCCAAGGGTATCCTTAG
64 A-TGGCCTACCCAAGGGTATCCTTAG
* * *
6476366 ATCCGTAGGGTTACCCTAAGTACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGAGGCCTAT
1 GTCCGTAGGGTTACCCTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT
6476431 GGGCCTACCCAAGGGTATCCTTAG
66 -GGCCTACCCAAGGGTATCCTTAG
*
6476455 GTCCATAGGGTTACCCTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT
1 GTCCGTAGGGTTACCCTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT
* * *
6476520 GGCCTACCAAAGGGTAACATTAG
66 GGCCTACCCAAGGGTATCCTTAG
6476543 GTCCGTA
1 GTCCGTA
6476550 AGGTCTTACC
Statistics
Matches: 167, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
88 27 0.16
89 115 0.69
90 16 0.10
91 9 0.05
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (88 bp):
GTCCGTAGGGTTACCCTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT
GGCCTACCCAAGGGTATCCTTAG
Found at i:6478474 original size:19 final size:20
Alignment explanation
Indices: 6478432--6478474 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
6478422 TTACCCAGAT
* *
6478432 TTTCTATGTAAAACTAGTAT
1 TTTCTATGCAAAACTAGTAG
*
6478452 TTTCTATGCAAATC-AGTAG
1 TTTCTATGCAAAACTAGTAG
6478471 TTTC
1 TTTC
6478475 GTCAGATCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (20 bp):
TTTCTATGCAAAACTAGTAG
Found at i:6479152 original size:23 final size:23
Alignment explanation
Indices: 6479125--6479192 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
6479115 TGACATTTTA
6479125 GTCAAAGTTAACGGGTTGACTCG
1 GTCAAAGTTAACGGGTTGACTCG
* *
6479148 GTCAAAGTCAACGGGTTGACTCT
1 GTCAAAGTTAACGGGTTGACTCG
*
6479171 GTCAAAGTTAACGAGTTGACTC
1 GTCAAAGTTAACGGGTTGACTC
6479193 ATTGAGTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (23 bp):
GTCAAAGTTAACGGGTTGACTCG
Found at i:6479266 original size:18 final size:18
Alignment explanation
Indices: 6479243--6479302 Score: 111
Period size: 18 Copynumber: 3.3 Consensus size: 18
6479233 TCAGTCAACT
6479243 TGGCTCGGCTTGGCTCAA
1 TGGCTCGGCTTGGCTCAA
6479261 TGGCTCGGCTTGGCTCAA
1 TGGCTCGGCTTGGCTCAA
*
6479279 TGGCTCGGCTTGGCTCAG
1 TGGCTCGGCTTGGCTCAA
6479297 TGGCTC
1 TGGCTC
6479303 TGCTCAACTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.08, C:0.28, G:0.35, T:0.28
Consensus pattern (18 bp):
TGGCTCGGCTTGGCTCAA
Found at i:6481415 original size:89 final size:89
Alignment explanation
Indices: 6481251--6481602 Score: 562
Period size: 89 Copynumber: 3.9 Consensus size: 89
6481241 CCGAAATTCC
* * * * *
6481251 ATCCGTAGAGCTTACCCTAAGCACATAGCAAAAGGGAGCCAACCTAAGGATATTCCTTGGGGCCT
1 ATCCGTAG-GGTTACCCTAAGCACACAAC-AAAGGGAACCAACCTAAGGATATGCCTTGGGGCCT
* * *
6481316 ATTGGCCTACCCTATGGTATCCTTAG
64 ATGGGCCTACCCAAGGGTATCCTTAG
*
6481342 ATCCGTAGGGTTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAC
1 ATCCGTAGGGTTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT
*
6481407 GGGTCTACCCAAGGGTATCCTTAG
66 GGGCCTACCCAAGGGTATCCTTAG
* *
6481431 GTCCTTAGGGTTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT
1 ATCCGTAGGGTTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT
6481496 -GGCCTACCCAAGGGTATCCTTAG
66 GGGCCTACCCAAGGGTATCCTTAG
*
6481519 ATCCGTAGGGTTACCCTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT
1 ATCCGTAGGGTTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT
6481584 GGGCCTACCCAAGGGTATC
66 GGGCCTACCCAAGGGTATC
6481603 ATTCGGTCCG
Statistics
Matches: 243, Mismatches: 17, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
88 84 0.35
89 134 0.55
90 17 0.07
91 8 0.03
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.20
Consensus pattern (89 bp):
ATCCGTAGGGTTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAT
GGGCCTACCCAAGGGTATCCTTAG
Found at i:6481578 original size:177 final size:179
Alignment explanation
Indices: 6481262--6481611 Score: 587
Period size: 177 Copynumber: 2.0 Consensus size: 179
6481252 TCCGTAGAGC
* * * *
6481262 TTACCCTAAGCACATAGCAAAAGGGAGCCAACCTAAGGATATTCCTTGGGGCCTATTGGCCTACC
1 TTACCCTAAGCACACAACAAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTATTGGCCTACC
* *
6481327 CTATGGTATCCTTAGATCCGTAGGGTTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATA
66 CAAGGGTATCCTTAGATCCGTAGGGTTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATA
* *
6481392 TGCCTTGGGGCCTACGGGTCTACCCAAGGGTATCCTTAGGTCCTTAGGG
131 TGCCTTGGGGCCTACGGGCCTACCCAAGGGTATCATTAGGTCCTTAGGG
6481441 TTACCCTAAGCACACAAC-AAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTA-TGGCCTACC
1 TTACCCTAAGCACACAACAAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTATTGGCCTACC
*
6481504 CAAGGGTATCCTTAGATCCGTAGGGTTACCCTAAGCACACAGCAAAGGGAACCAACCTAAGGATA
66 CAAGGGTATCCTTAGATCCGTAGGGTTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATA
* *
6481569 TGCCTTGGGGCCTATGGGCCTACCCAAGGGTATCATTCGGTCC
131 TGCCTTGGGGCCTACGGGCCTACCCAAGGGTATCATTAGGTCC
6481612 GTAAGGTCTT
Statistics
Matches: 160, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
177 110 0.69
178 34 0.21
179 16 0.10
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (179 bp):
TTACCCTAAGCACACAACAAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTATTGGCCTACC
CAAGGGTATCCTTAGATCCGTAGGGTTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATA
TGCCTTGGGGCCTACGGGCCTACCCAAGGGTATCATTAGGTCCTTAGGG
Found at i:6483763 original size:193 final size:193
Alignment explanation
Indices: 6483434--6483820 Score: 738
Period size: 193 Copynumber: 2.0 Consensus size: 193
6483424 ATTTCGTTAT
6483434 TAAAACTCTTAACAAAGATAATAATAATTTAGAGATTCTAGGGTTAATCGCTTACCCGAATAATA
1 TAAAACTCTTAACAAAGATAATAATAATTTAGAGATTCTAGGGTTAATCGCTTACCCGAATAATA
*
6483499 TCTGAACTTAAAATTATTCCTTATCAACTTCTAGTAACTTGTACAAGCCATCTTATGTTTAGAAA
66 TCTGAACTTAAAATTATTCCTTATCAACTTCTAGTAACTTGTACAAGCCATCTTAGGTTTAGAAA
6483564 TCAGTTACCCAGATTTTCTATGCAAAACTAGCATTTTCTATGCACATCAGTAGTTTTCTCAGA
131 TCAGTTACCCAGATTTTCTATGCAAAACTAGCATTTTCTATGCACATCAGTAGTTTTCTCAGA
*
6483627 TAAAACTCTTAACAAAGATAATTATAATTTAGAGATTCTAGGGTTAATCGCTTACCCGAATAATA
1 TAAAACTCTTAACAAAGATAATAATAATTTAGAGATTCTAGGGTTAATCGCTTACCCGAATAATA
* *
6483692 TCTGAACTTGAAATTATTCCTTATCAACTTCTAGTATCTTGTACAAGCCATCTTAGGTTTAGAAA
66 TCTGAACTTAAAATTATTCCTTATCAACTTCTAGTAACTTGTACAAGCCATCTTAGGTTTAGAAA
6483757 TCAGTTACCCAGATTTTCTATGCAAAACTAGCATTTTCTATGCACATCAGTAGTTTTCTCAGA
131 TCAGTTACCCAGATTTTCTATGCAAAACTAGCATTTTCTATGCACATCAGTAGTTTTCTCAGA
6483820 T
1 T
6483821 CAATATGTCT
Statistics
Matches: 190, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 190 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (193 bp):
TAAAACTCTTAACAAAGATAATAATAATTTAGAGATTCTAGGGTTAATCGCTTACCCGAATAATA
TCTGAACTTAAAATTATTCCTTATCAACTTCTAGTAACTTGTACAAGCCATCTTAGGTTTAGAAA
TCAGTTACCCAGATTTTCTATGCAAAACTAGCATTTTCTATGCACATCAGTAGTTTTCTCAGA
Found at i:6484410 original size:30 final size:29
Alignment explanation
Indices: 6484367--6484425 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
6484357 TTTGGTCAAA
* * * *
6484367 GTCAACGGGTTGACTCAGTTAAAGTTAACG
1 GTCAACAGATTGACTC-GTCAAAGTCAACG
6484397 GTCAACAGATTGACTCGTCAAAGTCAACG
1 GTCAACAGATTGACTCGTCAAAGTCAACG
6484426 AGTTGACCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (29 bp):
GTCAACAGATTGACTCGTCAAAGTCAACG
Found at i:6484464 original size:27 final size:28
Alignment explanation
Indices: 6484420--6484477 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
6484410 CTCGTCAAAG
*
6484420 TCAACGAGTTGACCCAGTG-AA-TTGAC
1 TCAACGAGTTAACCCAGTGTAAGTTGAC
*
6484446 TCAACCGAGTTAACTCAGTGTAAGTTGAC
1 TCAA-CGAGTTAACCCAGTGTAAGTTGAC
6484475 TCA
1 TCA
6484478 GTCAGCTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 4 0.15
27 13 0.48
28 2 0.07
29 8 0.30
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (28 bp):
TCAACGAGTTAACCCAGTGTAAGTTGAC
Found at i:6487284 original size:20 final size:20
Alignment explanation
Indices: 6487255--6487294 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6487245 AGTCTAGACA
*
6487255 ATATTGTTATAAATTAAATC
1 ATATTGTTATAAATGAAATC
*
6487275 ATATTTTTATAAATGAAATC
1 ATATTGTTATAAATGAAATC
6487295 TTTTATTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
ATATTGTTATAAATGAAATC
Found at i:6499425 original size:31 final size:31
Alignment explanation
Indices: 6499387--6499445 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
6499377 ATGAAGATAG
6499387 GATATCCTTGTCTTTAGTAGCAATGAGTTAT
1 GATATCCTTGTCTTTAGTAGCAATGAGTTAT
6499418 GATATCCTTGTCTTTAGTAGCAATGAGT
1 GATATCCTTGTCTTTAGTAGCAATGAGT
6499446 CCTTTTGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (31 bp):
GATATCCTTGTCTTTAGTAGCAATGAGTTAT
Found at i:6500268 original size:30 final size:30
Alignment explanation
Indices: 6500233--6500302 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
6500223 AACATCCTTT
6500233 TTCTTCTTTTTCTTTTCTTATTTGTATTCC
1 TTCTTCTTTTTCTTTTCTTATTTGTATTCC
6500263 TTCTTCTTTTTCTTTTCTTATTTGTATTCC
1 TTCTTCTTTTTCTTTTCTTATTTGTATTCC
6500293 TTCTTCTTTT
1 TTCTTCTTTT
6500303 GGAGTTTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.06, C:0.20, G:0.03, T:0.71
Consensus pattern (30 bp):
TTCTTCTTTTTCTTTTCTTATTTGTATTCC
Found at i:6504853 original size:54 final size:54
Alignment explanation
Indices: 6504769--6505087 Score: 381
Period size: 54 Copynumber: 5.9 Consensus size: 54
6504759 TACAATTATA
* * ** *
6504769 TTTTGACACTATGTGTGAAACCCATGGAATTCATCATAAGTTGATGAAGAATCG
1 TTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAATCG
*
6504823 TTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTAATGAACAATCG
1 TTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAATCG
* * * *
6504877 TTCTGGCACTATGTGTGCAACCCACAAAATTCATCATAAGTTTATGAACAA-CTA
1 TTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAATC-G
* * *
6504931 TTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAATTGATGAATAACCG
1 TTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAATCG
* * *
6504985 TTTTGGCACTATGTGTACAACCC-CACGAAATTCATCATATGTTGATGAACAACCG
1 TTTTGGCACTATGTGTGCAACCCACA-G-AATTCATCATAAGTTGATGAACAATCG
* * *** * * *
6505040 TTTAGGCACTATGTGTACAAATTACAGAATTCATAATATGTTTATGAA
1 TTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAA
6505088 TGATCATATT
Statistics
Matches: 234, Mismatches: 26, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
53 3 0.01
54 184 0.79
55 45 0.19
56 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (54 bp):
TTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAATCG
Found at i:6511919 original size:55 final size:54
Alignment explanation
Indices: 6511761--6511997 Score: 296
Period size: 54 Copynumber: 4.4 Consensus size: 54
6511751 TTACAATTGT
*
6511761 GTTTTGGCACTATGTCTGCAACCCACAGAATTCATCATAAGTTGATGAACAACC
1 GTTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACC
* * *
6511815 GTTTTGGCTCTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACATCC
1 GTTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACC
*
6511869 GTTTTGGCACTATGTGTGCAACCC-CACGAAATTCATCATATGTTGATGAACAACC
1 GTTTTGGCACTATGTGTGCAACCCACA-G-AATTCATCATAAGTTGATGAACAACC
* * * * * * * **
6511924 GTCTAGGCACTATGTGTGTAACTCACAGAATTCATAATATGTTTATGAATGACC
1 GTTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACC
* * *
6511978 ATATTGGCACTAAGTGTGCA
1 GTTTTGGCACTATGTGTGCA
6511998 TCTCAACGAA
Statistics
Matches: 159, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 111 0.70
55 45 0.28
56 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (54 bp):
GTTTTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACC
Found at i:6511955 original size:109 final size:108
Alignment explanation
Indices: 6511761--6511972 Score: 300
Period size: 109 Copynumber: 2.0 Consensus size: 108
6511751 TTACAATTGT
* * *
6511761 GTTTTGGCACTATGTCTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGGCTCT
1 GTTTTGGCACTATGTCTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTCTAGGCACT
* *
6511826 ATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACATCC
66 ATGTGTGCAACCCACAGAATTCATAATAAGTTGATGAACATCC
* *
6511869 GTTTTGGCACTATGTGTGCAACCC-CACGAAATTCATCATATGTTGATGAACAACCGTCTAGGCA
1 GTTTTGGCACTATGTCTGCAACCCACA-G-AATTCATCATAAGTTGATGAACAACCGTCTAGGCA
* * * *
6511933 CTATGTGTGTAACTCACAGAATTCATAATATGTTTATGAA
64 CTATGTGTGCAACCCACAGAATTCATAATAAGTTGATGAA
6511973 TGACCATATT
Statistics
Matches: 91, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
107 2 0.02
108 24 0.26
109 65 0.71
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (108 bp):
GTTTTGGCACTATGTCTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTCTAGGCACT
ATGTGTGCAACCCACAGAATTCATAATAAGTTGATGAACATCC
Found at i:6511985 original size:109 final size:108
Alignment explanation
Indices: 6511764--6511997 Score: 292
Period size: 109 Copynumber: 2.2 Consensus size: 108
6511754 CAATTGTGTT
* * * *
6511764 TTGGCACTATGTCTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGGCTCTATG
1 TTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTCTAGGCACTATG
* * * *
6511829 TGTGCAACCCACGGAATTCATCATAAGTTGATGAACATCCGTT
66 TGTGCAACCCACAGAATTCATAATAAGTTGATGAACATCCATA
*
6511872 TTGGCACTATGTGTGCAACCC-CACGAAATTCATCATATGTTGATGAACAACCGTCTAGGCACTA
1 TTGGCACTATGTGTGCAACCCACA-G-AATTCATCATAAGTTGATGAACAACCGTCTAGGCACTA
* * * * *
6511936 TGTGTGTAACTCACAGAATTCATAATATGTTTATGAATGA-CCATA
64 TGTGTGCAACCCACAGAATTCATAATAAGTTGATGAA-CATCCATA
*
6511981 TTGGCACTAAGTGTGCA
1 TTGGCACTATGTGTGCA
6511998 TCTCAACGAA
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
107 2 0.02
108 21 0.19
109 84 0.78
110 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (108 bp):
TTGGCACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTCTAGGCACTATG
TGTGCAACCCACAGAATTCATAATAAGTTGATGAACATCCATA
Found at i:6515137 original size:521 final size:521
Alignment explanation
Indices: 6514156--6515200 Score: 2090
Period size: 521 Copynumber: 2.0 Consensus size: 521
6514146 TACAAGTATT
6514156 TTGGATGTTTAAGATGTACGTAAAGAGTACCTAATTAATTATCAGGGATTTAACACATTTTTTAT
1 TTGGATGTTTAAGATGTACGTAAAGAGTACCTAATTAATTATCAGGGATTTAACACATTTTTTAT
6514221 ACGTTATTAGGCTTTTTATATTACTTATTATAACAAAGGGTATTTTGGTTATTTTACCTATTCAA
66 ACGTTATTAGGCTTTTTATATTACTTATTATAACAAAGGGTATTTTGGTTATTTTACCTATTCAA
6514286 GGGTATTTCAAGGTTCTTCTCATGTTTTAAAAGTAATCACTAATGAATTACATCAGTTCTTAAAG
131 GGGTATTTCAAGGTTCTTCTCATGTTTTAAAAGTAATCACTAATGAATTACATCAGTTCTTAAAG
6514351 TCTTATGATTTTAGAGGTATTTTTATATCAATATAAGCCATTATTCACAAATAGGGGCAATTTGG
196 TCTTATGATTTTAGAGGTATTTTTATATCAATATAAGCCATTATTCACAAATAGGGGCAATTTGG
6514416 TAATTTAGTCCTCTGAAGGCATTTTAGTAATTTCTCACATTCTCAAGTTATATGCTCGATCTAAA
261 TAATTTAGTCCTCTGAAGGCATTTTAGTAATTTCTCACATTCTCAAGTTATATGCTCGATCTAAA
6514481 TTGTTATTAAAATCCTCTATTCAATATCACAAATCCCATTAAATAATCATCATTAATGGTATTAG
326 TTGTTATTAAAATCCTCTATTCAATATCACAAATCCCATTAAATAATCATCATTAATGGTATTAG
6514546 TACCTTTACATGGGTATCGATACTTACCCTAGGGTATCAGTACTCCCCCTGAGTATCGATACCAA
391 TACCTTTACATGGGTATCGATACTTACCCTAGGGTATCAGTACTCCCCCTGAGTATCGATACCAA
6514611 AACTAACCTTGAAAGTCTCATAAAATACCCTTAGTATCTATATCATGAATGTATTATTATAATCT
456 AACTAACCTTGAAAGTCTCATAAAATACCCTTAGTATCTATATCATGAATGTATTATTATAATCT
6514676 C
521 C
6514677 TTGGATGTTTAAGATGTACGTAAAGAGTACCTAATTAATTATCAGGGATTTAACACATTTTTTAT
1 TTGGATGTTTAAGATGTACGTAAAGAGTACCTAATTAATTATCAGGGATTTAACACATTTTTTAT
6514742 ACGTTATTAGGCTTTTTATATTACTTATTATAACAAAGGGTATTTTGGTTATTTTACCTATTCAA
66 ACGTTATTAGGCTTTTTATATTACTTATTATAACAAAGGGTATTTTGGTTATTTTACCTATTCAA
6514807 GGGTATTTCAAGGTTCTTCTCATGTTTTAAAAGTAATCACTAATGAATTACATCAGTTCTTAAAG
131 GGGTATTTCAAGGTTCTTCTCATGTTTTAAAAGTAATCACTAATGAATTACATCAGTTCTTAAAG
6514872 TCTTATGATTTTAGAGGTATTTTTATATCAATATAAGCCATTATTCACAAATAGGGGCAATTTGG
196 TCTTATGATTTTAGAGGTATTTTTATATCAATATAAGCCATTATTCACAAATAGGGGCAATTTGG
6514937 TAATTTAGTCCTCTGAAGGCATTTTAGTAATTTCTCACATTCTCAAGTTATATGCTCGATCTAAA
261 TAATTTAGTCCTCTGAAGGCATTTTAGTAATTTCTCACATTCTCAAGTTATATGCTCGATCTAAA
6515002 TTGTTATTAAAATCCTCTATTCAATATCACAAATCCCATTAAATAATCATCATTAATGGTATTAG
326 TTGTTATTAAAATCCTCTATTCAATATCACAAATCCCATTAAATAATCATCATTAATGGTATTAG
6515067 TACCTTTACATGGGTATCGATACTTACCCTAGGGTATCAGTACTCCCCCTGAGTATCGATACCAA
391 TACCTTTACATGGGTATCGATACTTACCCTAGGGTATCAGTACTCCCCCTGAGTATCGATACCAA
6515132 AACTAACCTTGAAAGTCTCATAAAATACCCTTAGTATCTATATCATGAATGTATTATTATAATCT
456 AACTAACCTTGAAAGTCTCATAAAATACCCTTAGTATCTATATCATGAATGTATTATTATAATCT
6515197 C
521 C
6515198 TTG
1 TTG
6515201 AGTATCAGTA
Statistics
Matches: 524, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
521 524 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (521 bp):
TTGGATGTTTAAGATGTACGTAAAGAGTACCTAATTAATTATCAGGGATTTAACACATTTTTTAT
ACGTTATTAGGCTTTTTATATTACTTATTATAACAAAGGGTATTTTGGTTATTTTACCTATTCAA
GGGTATTTCAAGGTTCTTCTCATGTTTTAAAAGTAATCACTAATGAATTACATCAGTTCTTAAAG
TCTTATGATTTTAGAGGTATTTTTATATCAATATAAGCCATTATTCACAAATAGGGGCAATTTGG
TAATTTAGTCCTCTGAAGGCATTTTAGTAATTTCTCACATTCTCAAGTTATATGCTCGATCTAAA
TTGTTATTAAAATCCTCTATTCAATATCACAAATCCCATTAAATAATCATCATTAATGGTATTAG
TACCTTTACATGGGTATCGATACTTACCCTAGGGTATCAGTACTCCCCCTGAGTATCGATACCAA
AACTAACCTTGAAAGTCTCATAAAATACCCTTAGTATCTATATCATGAATGTATTATTATAATCT
C
Found at i:6516071 original size:17 final size:17
Alignment explanation
Indices: 6516049--6516082 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6516039 ATTTTTTATT
*
6516049 TATATAAATTATATAAA
1 TATATAAATAATATAAA
*
6516066 TATATATATAATATAAA
1 TATATAAATAATATAAA
6516083 AGAAAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATATAAATAATATAAA
Found at i:6518376 original size:20 final size:20
Alignment explanation
Indices: 6518351--6518393 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6518341 TCTAAGAGCT
*
6518351 CATTTAGGACCATGTAGATG
1 CATTTAGGACCATATAGATG
* *
6518371 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
6518391 CAT
1 CAT
6518394 GTGATGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:6529849 original size:17 final size:17
Alignment explanation
Indices: 6529829--6529869 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
6529819 ACCAAATTCT
*
6529829 CAAACCCTCTCAAAGCC
1 CAAACCCTCTAAAAGCC
*
6529846 CAAACCCTCTAAAAGCT
1 CAAACCCTCTAAAAGCC
6529863 CAAACCC
1 CAAACCC
6529870 GATCAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.39, C:0.44, G:0.05, T:0.12
Consensus pattern (17 bp):
CAAACCCTCTAAAAGCC
Found at i:6530096 original size:18 final size:18
Alignment explanation
Indices: 6530073--6530134 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
6530063 TTTAATTTTA
6530073 ATTTTAATTATTGTTAAT
1 ATTTTAATTATTGTTAAT
* *
6530091 ATTTTATTTATT-TAAAT
1 ATTTTAATTATTGTTAAT
* * *
6530108 -TTTTTAGTATTAGTTTAT
1 ATTTTAATTATT-GTTAAT
6530126 ATTTTAATT
1 ATTTTAATT
6530135 TCTATAATAT
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
16 8 0.25
17 4 0.12
18 14 0.44
19 6 0.19
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
ATTTTAATTATTGTTAAT
Found at i:6530113 original size:35 final size:38
Alignment explanation
Indices: 6530074--6530151 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 38
6530064 TTAATTTTAA
* *
6530074 TTTTAATTATT-GTTAATATTTT-ATTTATTTAA-ATT
1 TTTTAAGTATTAGTTAATATTTTAATTTATATAATATT
* *
6530109 TTTT-AGTATTAGTTTATATTTTAATTTCTATAATATT
1 TTTTAAGTATTAGTTAATATTTTAATTTATATAATATT
6530146 TTTTAA
1 TTTTAA
6530152 ATTAGGAGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 5 0.14
35 14 0.40
36 8 0.23
37 7 0.20
38 1 0.03
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (38 bp):
TTTTAAGTATTAGTTAATATTTTAATTTATATAATATT
Found at i:6530156 original size:36 final size:35
Alignment explanation
Indices: 6530089--6530156 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
6530079 ATTATTGTTA
* *
6530089 ATATTTTATTTATTTAAATTTTTTAGTATTAGTTT
1 ATATTTTATTTATATAAATTTTTTAGAATTAGTTT
*
6530124 ATATTTTAATTTCTATAATATTTTTTA-AATTAG
1 ATATTTT-ATTTATATAA-ATTTTTTAGAATTAG
6530157 GAGAGAGATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 7 0.25
36 13 0.46
37 8 0.29
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (35 bp):
ATATTTTATTTATATAAATTTTTTAGAATTAGTTT
Found at i:6535124 original size:13 final size:13
Alignment explanation
Indices: 6535106--6535140 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
6535096 GTTAGATTTA
*
6535106 CTTTTCTTTTCTT
1 CTTTTCCTTTCTT
6535119 CTTTTCCTTTCTT
1 CTTTTCCTTTCTT
6535132 CTTTTCCTT
1 CTTTTCCTT
6535141 GAATTGGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
CTTTTCCTTTCTT
Found at i:6535527 original size:48 final size:48
Alignment explanation
Indices: 6535461--6535554 Score: 179
Period size: 48 Copynumber: 2.0 Consensus size: 48
6535451 GATTAGTGAA
6535461 AGTATTATTCTCTTTAAGTGTTAGGTTCGAACCATTAACAAAAATTAG
1 AGTATTATTCTCTTTAAGTGTTAGGTTCGAACCATTAACAAAAATTAG
*
6535509 AGTATTATTGTCTTTAAGTGTTAGGTTCGAACCATTAACAAAAATT
1 AGTATTATTCTCTTTAAGTGTTAGGTTCGAACCATTAACAAAAATT
6535555 GTGTCTTATC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (48 bp):
AGTATTATTCTCTTTAAGTGTTAGGTTCGAACCATTAACAAAAATTAG
Found at i:6535574 original size:48 final size:48
Alignment explanation
Indices: 6535474--6535574 Score: 132
Period size: 48 Copynumber: 2.1 Consensus size: 48
6535464 ATTATTCTCT
*** *
6535474 TTAAGTGTTAGGTTCGAACCATTAACAAAAATTAGAGTATTATTGTCT
1 TTAAGTGTTAGGTTCGAACCATTAACAAAAATTAGAGTATTATCAACA
* *
6535522 TTAAGTGTTAGGTTCGAACCATTAACAAAAATT-GTGTCTTATCAACGA
1 TTAAGTGTTAGGTTCGAACCATTAACAAAAATTAGAGTATTATCAAC-A
6535570 TTAAG
1 TTAAG
6535575 AAAAATTAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 8 0.17
48 38 0.83
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (48 bp):
TTAAGTGTTAGGTTCGAACCATTAACAAAAATTAGAGTATTATCAACA
Found at i:6537261 original size:25 final size:26
Alignment explanation
Indices: 6537233--6537285 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
6537223 GTTTGAGGAC
* *
6537233 TTATTTAATTTTAAAA-ATAAAAAAA
1 TTATTTAAATTAAAAATATAAAAAAA
6537258 TTATTTAAATTAAAAATATAAAAAAA
1 TTATTTAAATTAAAAATATAAAAAAA
6537284 TT
1 TT
6537286 TATTAAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TTATTTAAATTAAAAATATAAAAAAA
Found at i:6537275 original size:24 final size:26
Alignment explanation
Indices: 6537233--6537300 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 26
6537223 GTTTGAGGAC
*
6537233 TTATTTAATTTTAAAAATA-AAAAAA
1 TTATTTAATATTAAAAATATAAAAAA
6537258 TTATTTAA-ATTAAAAATATAAAAAAA
1 TTATTTAATATTAAAAATAT-AAAAAA
*
6537284 TTTATTAAGATATTAAA
1 -TTATTTA-ATATTAAA
6537301 TACATTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
24 9 0.25
25 8 0.22
26 6 0.17
27 6 0.17
28 1 0.03
29 6 0.17
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (26 bp):
TTATTTAATATTAAAAATATAAAAAA
Found at i:6538718 original size:15 final size:14
Alignment explanation
Indices: 6538667--6538737 Score: 56
Period size: 14 Copynumber: 4.9 Consensus size: 14
6538657 GTTAGATAAG
*
6538667 AAAAAAAATAAAGA
1 AAAAAAAATAAATA
6538681 AAATGAAATAATGAAAT-
1 AAA--AAA-AAT-AAATA
*
6538698 -AAAAAAATAAGTA
1 AAAAAAAATAAATA
*
6538711 AGAAAAAATAAATA
1 AAAAAAAATAAATA
6538725 AAAATAAAATAAA
1 AAAA-AAAATAAA
6538738 GATAAAGATA
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
12 3 0.07
13 3 0.07
14 20 0.44
15 8 0.18
16 5 0.11
17 3 0.07
18 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAAAAATAAATA
Found at i:6538754 original size:15 final size:16
Alignment explanation
Indices: 6538680--6538754 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 16
6538670 AAAAATAAAG
*
6538680 AAAATGAAATAATGA-A
1 AAAATAAAATAA-GATA
6538696 ATAAA-AAAATAAG-TA
1 A-AAATAAAATAAGATA
*
6538711 AGAA-AAAATAA-ATA
1 AAAATAAAATAAGATA
6538725 AAAATAAAATAAAGATA
1 AAAATAAAAT-AAGATA
*
6538742 AAGAT-AAATAAGA
1 AAAATAAAATAAGA
6538755 AGAATACTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
14 14 0.29
15 12 0.24
16 13 0.27
17 10 0.20
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.17
Consensus pattern (16 bp):
AAAATAAAATAAGATA
Found at i:6538816 original size:80 final size:78
Alignment explanation
Indices: 6538694--6538884 Score: 194
Period size: 80 Copynumber: 2.4 Consensus size: 78
6538684 TGAAATAATG
* * *
6538694 AAATAAAAAAAT-AAG-TAAGAAAAAATAAATAAAAATAAAATAAAGATAAAGAT-AAA-TAAGA
1 AAATAAATAAATAAAGATAA-AGAAAATAAA-AAAAATAAAATAAAGATAAA-ATAAAATTAAAA
*
6538755 AGAATACTATA-AAGAT
63 AGAATA-TATATAAAAT
* * * *
6538771 AAATATATATATATATATATAAAGAAAATAAAAACAAATATAATAAAGATAAAATAAAAATTAAA
1 AAATA-A-ATAAATAAAGATAAAGAAAATAAAAA-AAATAAAATAAAGATAAAAT-AAAATTAAA
*
6538836 AATAATATATATAAAAT
62 AAGAATATATATAAAAT
6538853 AAATAAATAAATAAAGATAAAGAAAATAAAAA
1 AAATAAATAAATAAAGATAAAGAAAATAAAAA
6538885 TAAAAATGAA
Statistics
Matches: 93, Mismatches: 12, Indels: 15
0.77 0.10 0.12
Matches are distributed among these distances:
77 5 0.05
78 1 0.01
79 8 0.09
80 50 0.54
81 11 0.12
82 18 0.19
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (78 bp):
AAATAAATAAATAAAGATAAAGAAAATAAAAAAAATAAAATAAAGATAAAATAAAATTAAAAAGA
ATATATATAAAAT
Found at i:6538881 original size:65 final size:64
Alignment explanation
Indices: 6538715--6538889 Score: 149
Period size: 65 Copynumber: 2.7 Consensus size: 64
6538705 TAAGTAAGAA
* ** *
6538715 AAAATAAATAAAAATAAAATAAAGATAAAGATAAAT-AAGA-AGAATACTATAAAGATAAATATA
1 AAAATAAAT--AAAT-AAATAAAGATAAAGA-AAATAAAGATAAAATAAAATAAAAATAAATATA
6538778 TAT
62 TAT
* * * * * * *
6538781 ATATATATATAAAGAAAATAAAAACAAATATAATAAAGATAAAATAAAAATTAAAAAT-AATATA
1 A-AAATAAATAAA-TAAATAAAGATAAAGAAAATAAAGATAAAAT-AAAA-TAAAAATAAATATA
6538845 TAT
62 TAT
*
6538848 AAAATAAATAAATAAATAAAGATAAAGAAAATAAAAATAAAA
1 AAAATAAATAAATAAATAAAGATAAAGAAAATAAAGATAAAA
6538890 ATGAAAATGA
Statistics
Matches: 84, Mismatches: 19, Indels: 13
0.72 0.16 0.11
Matches are distributed among these distances:
64 3 0.04
65 43 0.51
66 14 0.17
67 18 0.21
68 6 0.07
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (64 bp):
AAAATAAATAAATAAATAAAGATAAAGAAAATAAAGATAAAATAAAATAAAAATAAATATATAT
Found at i:6539128 original size:7 final size:7
Alignment explanation
Indices: 6539103--6539221 Score: 50
Period size: 7 Copynumber: 16.4 Consensus size: 7
6539093 AGAAACTAGA
*
6539103 AAATGAT
1 AAATAAT
6539110 AAATAA-
1 AAATAAT
6539116 AAATAAT
1 AAATAAT
6539123 AAATAA-
1 AAATAAT
6539129 AAA-AAGT
1 AAATAA-T
* *
6539136 CCAA-AAG
1 -AAATAAT
6539143 AAATAAT
1 AAATAAT
6539150 AAATATAT
1 AAATA-AT
6539158 ATATATAAT
1 A-A-ATAAT
*
6539167 AAAAAAT
1 AAATAAT
*
6539174 AAAAAAT
1 AAATAAT
*
6539181 AAAAAAT
1 AAATAAT
*
6539188 AAAAAAAT
1 -AAATAAT
6539196 ATGAA-AAT
1 A--AATAAT
6539204 ATAATAAT
1 A-AATAAT
*
6539212 AATTAAT
1 AAATAAT
6539219 AAA
1 AAA
6539222 AGGGTTAATT
Statistics
Matches: 91, Mismatches: 9, Indels: 24
0.73 0.07 0.19
Matches are distributed among these distances:
5 2 0.02
6 11 0.12
7 46 0.51
8 23 0.25
9 6 0.07
10 3 0.03
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:6539212 original size:8 final size:7
Alignment explanation
Indices: 6539071--6539193 Score: 61
Period size: 7 Copynumber: 17.0 Consensus size: 7
6539061 ATAAAATACC
6539071 TAAAAAA
1 TAAAAAA
6539078 TAAAATAA
1 TAAAA-AA
*
6539086 -AATAAA
1 TAAAAAA
* *
6539092 TAGAAAC
1 TAAAAAA
*
6539099 TAGAAAA
1 TAAAAAA
* *
6539106 TGATAAA
1 TAAAAAA
6539113 T-AAAAA
1 TAAAAAA
*
6539119 TAATAAA
1 TAAAAAA
6539126 TAAAAAAA
1 T-AAAAAA
**
6539134 GTCCAAAA
1 -TAAAAAA
* *
6539142 GAAATAA
1 TAAAAAA
6539149 TAAATATATA
1 TAAA-A-A-A
* *
6539159 TATATAA
1 TAAAAAA
6539166 TAAAAAA
1 TAAAAAA
6539173 TAAAAAA
1 TAAAAAA
6539180 TAAAAAA
1 TAAAAAA
6539187 TAAAAAA
1 TAAAAAA
6539194 ATATGAAAAT
Statistics
Matches: 85, Mismatches: 23, Indels: 16
0.69 0.19 0.13
Matches are distributed among these distances:
6 7 0.08
7 60 0.71
8 12 0.14
9 2 0.02
10 4 0.05
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (7 bp):
TAAAAAA
Found at i:6540263 original size:2 final size:2
Alignment explanation
Indices: 6540228--6540252 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6540218 TTTAAGTAGA
6540228 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
6540253 ATGTTATATA
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:6541121 original size:85 final size:85
Alignment explanation
Indices: 6541020--6541966 Score: 1125
Period size: 85 Copynumber: 11.1 Consensus size: 85
6541010 TCTCTACTTA
* * * *
6541020 AGTTATGTTGTGAATTTGACATGCCCTTGAGCTGAATAG-AATCGAACTCGAAGGTATTTGTTGA
1 AGTTATGCTGTAAATTTGATATGCCCTTGAGCTGAAT-GTAATCGAACTCGAAGGTCTTTGTTGA
*
6541084 TAGATAGCCCTTCTCGCCTTG
65 CAGATAGCCCTTCTCGCCTTG
* * * * *
6541105 AGCTATGCTGTAAATTTAATATG-CCTCTGAGCTGAATGTAATTGAACCCGAAGGTCTTGGTTGA
1 AGTTATGCTGTAAATTTGATATGCCCT-TGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGA
* * *
6541169 CAGATAACCCTTTTCTCCTTG
65 CAGATAGCCCTTCTCGCCTTG
* * * *
6541190 AGTTATGCTGTAAATTTGATATGCCTTTGAGTTGAGTGTAATCAAACTCGAAGGTCTTTGTTGAC
1 AGTTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
6541255 AGATAGCCCTTCTCGCCTTG
66 AGATAGCCCTTCTCGCCTTG
* * * * * *
6541275 AGCTATGCTGGAAATTTAATGTG-CCTCTGAGCTTAATGTAATCGAACTCGAAGGTCTTGGTTGA
1 AGTTATGCTGTAAATTTGATATGCCCT-TGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGA
*
6541339 CATATAGCCCTTCTCGCCTTG
65 CAGATAGCCCTTCTCGCCTTG
* * * * * *
6541360 AGTTTTGCCGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTATTTGTTGAC
1 AGTTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
*
6541425 AGATAGCCCTTCTTGCCTTG
66 AGATAGCCCTTCTCGCCTTG
* * *
6541445 AGTTATGTCTGTAAATTTGATGTG-CCTCTGAGCGGAATGTAATCGAACTCGAAGGTCTTGGTTG
1 AGTTATG-CTGTAAATTTGATATGCCCT-TGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTG
* * *
6541509 ACAAATAACCCTTTTCGCCTTG
64 ACAGATAGCCCTTCTCGCCTTG
* * * *
6541531 AGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGAC
1 AGTTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
* *
6541596 ATATAGCCTTTCTCGCCTTG
66 AGATAGCCCTTCTCGCCTTG
* * * * *
6541616 AGCTATGCTGTAAATTTGATGTG-CCTCTGAGCTAAATGTAATCGAACTCAAAGGTCTTGGTTGA
1 AGTTATGCTGTAAATTTGATATGCCCT-TGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGA
* *
6541680 CAGATAACCCTTCTTGCCTTG
65 CAGATAGCCCTTCTCGCCTTG
* * * * *
6541701 ATTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTCTTTGTTGAC
1 AGTTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
* *
6541766 ATATAGCCTTTCTCGCCTTG
66 AGATAGCCCTTCTCGCCTTG
** * * * * *
6541786 AACTATGATGTAAATTTGATGTG-CGTCTGAGCTGAATGTAATAGAACTCGAAGGTCTTGGTTGA
1 AGTTATGCTGTAAATTTGATATGCCCT-TGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGA
*
6541850 CAGATAACCCTTCTCGCCTTG
65 CAGATAGCCCTTCTCGCCTTG
* * * * * *
6541871 AGTTATGTTGTAAATATT-ATATGTCTTTGAGCTGAGTGTAAACGAACTCGAAGGACTTTGTTGA
1 AGTTATGCTGTAAAT-TTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGA
*
6541935 CAGATGGCCCTTCTCGCCTTG
65 CAGATAGCCCTTCTCGCCTTG
6541956 AGTTATGCTGT
1 AGTTATGCTGT
6541967 CAATAGTTCC
Statistics
Matches: 724, Mismatches: 125, Indels: 26
0.83 0.14 0.03
Matches are distributed among these distances:
84 10 0.01
85 632 0.87
86 82 0.11
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (85 bp):
AGTTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
AGATAGCCCTTCTCGCCTTG
Found at i:6541261 original size:170 final size:170
Alignment explanation
Indices: 6541020--6541966 Score: 1405
Period size: 170 Copynumber: 5.6 Consensus size: 170
6541010 TCTCTACTTA
* * * * * * *
6541020 AGTTATGTTGTGAATTTGACATGCCCTTGAGCTGAATAG-AATCGAACTCGAAGGTATTTGTTGA
1 AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGT-GTAATCAAACTCGAAGGTCTTTGTTGA
* * * *
6541084 TAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTAATATGCCTCTGAGCTGAATGTAATTG
65 CAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTCTGAGCTGAATGTAATCG
* *
6541149 AACCCGAAGGTCTTGGTTGACAGATAACCCTTTTCTCCTTG
130 AACTCGAAGGTCTTGGTTGACAGATAACCCTTTTCGCCTTG
*
6541190 AGTTATGCTGTAAATTTGATATGCCTTTGAGTTGAGTGTAATCAAACTCGAAGGTCTTTGTTGAC
1 AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGAC
* * *
6541255 AGATAGCCCTTCTCGCCTTGAGCTATGCTGGAAATTTAATGTGCCTCTGAGCTTAATGTAATCGA
66 AGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTCTGAGCTGAATGTAATCGA
* * *
6541320 ACTCGAAGGTCTTGGTTGACATATAGCCCTTCTCGCCTTG
131 ACTCGAAGGTCTTGGTTGACAGATAACCCTTTTCGCCTTG
* * *
6541360 AGTTTTGCCGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTATTTGTTGAC
1 AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGAC
* * *
6541425 AGATAGCCCTTCTTGCCTTGAGTTATGTCTGTAAATTTGATGTGCCTCTGAGCGGAATGTAATCG
66 AGATAGCCCTTCTCGCCTTGAGCTATG-CTGTAAATTTGATGTGCCTCTGAGCTGAATGTAATCG
*
6541490 AACTCGAAGGTCTTGGTTGACAAATAACCCTTTTCGCCTTG
130 AACTCGAAGGTCTTGGTTGACAGATAACCCTTTTCGCCTTG
*
6541531 AGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGAC
1 AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGAC
* * *
6541596 ATATAGCCTTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTCTGAGCTAAATGTAATCGA
66 AGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTCTGAGCTGAATGTAATCGA
*
6541661 ACTCAAAGGTCTTGGTTGACAGATAACCCTTCTT-GCCTTG
131 ACTCGAAGGTCTTGGTTGACAGATAACCCTT-TTCGCCTTG
* *
6541701 ATTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTCTTTGTTGAC
1 AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGAC
* * * * * *
6541766 ATATAGCCTTTCTCGCCTTGAACTATGATGTAAATTTGATGTGCGTCTGAGCTGAATGTAATAGA
66 AGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTCTGAGCTGAATGTAATCGA
*
6541831 ACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTG
131 ACTCGAAGGTCTTGGTTGACAGATAACCCTTTTCGCCTTG
* * * * *
6541871 AGTTATGTTGTAAATATT-ATATGTCTTTGAGCTGAGTGTAAACGAACTCGAAGGACTTTGTTGA
1 AGTTATGCTGTAAAT-TTGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGA
* *
6541935 CAGATGGCCCTTCTCGCCTTGAGTTATGCTGT
65 CAGATAGCCCTTCTCGCCTTGAGCTATGCTGT
6541967 CAATAGTTCC
Statistics
Matches: 706, Mismatches: 66, Indels: 10
0.90 0.08 0.01
Matches are distributed among these distances:
169 2 0.00
170 545 0.77
171 159 0.23
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (170 bp):
AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGAC
AGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTCTGAGCTGAATGTAATCGA
ACTCGAAGGTCTTGGTTGACAGATAACCCTTTTCGCCTTG
Found at i:6541939 original size:511 final size:510
Alignment explanation
Indices: 6541020--6541966 Score: 1479
Period size: 511 Copynumber: 1.9 Consensus size: 510
6541010 TCTCTACTTA
* * *
6541020 AGTTATGTTGTGAATTTGACATGCCCTTGAGCTGAATAGAATCGAACTCGAAGGTATTTGTTGAT
1 AGTTATGTTGTAAATTTGACATGCCCTTGAGCTGAATAGAATCAAACTCGAAGGTATTTGTTGAC
* *
6541085 AGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTAATATGCCTCTGAGCTGAATGTAATTGA
66 AGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTAATATGCCTCTGAGCTAAATGTAATCGA
* *
6541150 ACCCGAAGGTCTTGGTTGACAGATAACCCTTTTCTCCTTGAGTTATGCTGTAAATTTGATATGCC
131 ACCCAAAGGTCTTGGTTGACAGATAACCCTTTTCGCCTTGAGTTATGCTGTAAATTTGATATGCC
* * *
6541215 TTTGAGTTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTA
196 TTTGAGCTGAGTGTAATCAAACTCAAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAACTA
* * * *
6541280 TGCTGGAAATTTAATGTGCCTCTGAGCTTAATGTAATCGAACTCGAAGGTCTTGGTTGACATATA
261 TGATGGAAATTTAATGTGCCTCTGAGCTGAATGTAATAGAACTCGAAGGTCTTGGTTGACAGATA
* * *
6541345 GCCCTTCTCGCCTTGAGTTTTGCCGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCAAACTCG
326 ACCCTTCTCGCCTTGAGTTATGCCGTAAATTTGATATGCCTTTGAGCTGAGTGTAAACAAACTCG
*
6541410 AAGGTATTTGTTGACAGATAGCCCTTCTTGCCTTGAGTTATGTCTGTAAATTTGATGTGCCTCTG
391 AAGGTATTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATG-CTGTAAATTTGATGTGCCTCTG
6541475 AGCGGAATGTAATCGAACTCGAAGGTCTTGGTTGACAAATAACCCTTTTCGCCTTG
455 AGCGGAATGTAATCGAACTCGAAGGTCTTGGTTGACAAATAACCCTTTTCGCCTTG
* * * *
6541531 AGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAGT-GTAATCAAACTCGAAGGTCTTTGTTGA
1 AGTTATGTTGTAAATTTGACATGCCCTTGAGCTGAATAG-AATCAAACTCGAAGGTATTTGTTGA
* * * *
6541595 CATATAGCCTTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTCTGAGCTAAATGTAATCG
65 CAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTAATATGCCTCTGAGCTAAATGTAATCG
* *
6541660 AACTCAAAGGTCTTGGTTGACAGATAACCCTTCTT-GCCTTGATTTATGCTGTAAATTTGATATG
130 AACCCAAAGGTCTTGGTTGACAGATAACCCTT-TTCGCCTTGAGTTATGCTGTAAATTTGATATG
* *
6541724 CCTTTGAGCTGAGTGTAATCAAACTCAAAGGTCTTTGTTGACATATAGCCTTTCTCGCCTTGAAC
194 CCTTTGAGCTGAGTGTAATCAAACTCAAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAAC
* * *
6541789 TATGATGTAAATTTGATGTGCGTCTGAGCTGAATGTAATAGAACTCGAAGGTCTTGGTTGACAGA
259 TATGATGGAAATTTAATGTGCCTCTGAGCTGAATGTAATAGAACTCGAAGGTCTTGGTTGACAGA
** * *
6541854 TAACCCTTCTCGCCTTGAGTTATGTTGTAAATATT-ATATGTCTTTGAGCTGAGTGTAAACGAAC
324 TAACCCTTCTCGCCTTGAGTTATGCCGTAAAT-TTGATATGCCTTTGAGCTGAGTGTAAACAAAC
*
6541918 TCGAAGG-ACTTTGTTGACAGATGGCCCTTCTCGCCTTGAGTTATGCTGT
388 TCGAAGGTA-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGT
6541967 CAATAGTTCC
Statistics
Matches: 394, Mismatches: 38, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
510 6 0.02
511 384 0.97
512 4 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (510 bp):
AGTTATGTTGTAAATTTGACATGCCCTTGAGCTGAATAGAATCAAACTCGAAGGTATTTGTTGAC
AGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTAATATGCCTCTGAGCTAAATGTAATCGA
ACCCAAAGGTCTTGGTTGACAGATAACCCTTTTCGCCTTGAGTTATGCTGTAAATTTGATATGCC
TTTGAGCTGAGTGTAATCAAACTCAAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAACTA
TGATGGAAATTTAATGTGCCTCTGAGCTGAATGTAATAGAACTCGAAGGTCTTGGTTGACAGATA
ACCCTTCTCGCCTTGAGTTATGCCGTAAATTTGATATGCCTTTGAGCTGAGTGTAAACAAACTCG
AAGGTATTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATGTGCCTCTGA
GCGGAATGTAATCGAACTCGAAGGTCTTGGTTGACAAATAACCCTTTTCGCCTTG
Found at i:6542518 original size:11 final size:11
Alignment explanation
Indices: 6542504--6542530 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6542494 TTCTCTCTTG
6542504 TTTCTCTATGA
1 TTTCTCTATGA
6542515 TTTCTCTATGA
1 TTTCTCTATGA
6542526 TTTCT
1 TTTCT
6542531 TGTTGATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.19, G:0.07, T:0.59
Consensus pattern (11 bp):
TTTCTCTATGA
Found at i:6545500 original size:22 final size:23
Alignment explanation
Indices: 6545461--6545522 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
6545451 TTCCCCTGTG
6545461 GGGGGAATCGGTTCCCCTTCA-AA
1 GGGGGAATCGGTT-CCCTTCATAA
*
6545484 GGGGGAATCGGTTCCC-TCATGA
1 GGGGGAATCGGTTCCCTTCATAA
* *
6545506 GGGGGGATCGATTCCCT
1 GGGGGAATCGGTTCCCT
6545523 CTGCACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.09
22 18 0.53
23 13 0.38
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.23
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCTTCATAA
Found at i:6545523 original size:22 final size:23
Alignment explanation
Indices: 6545438--6545523 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 23
6545428 ACAGAACCCT
*
6545438 AGGGGGGTATCGATTCCC-C-TG
1 AGGGGGGAATCGATTCCCTCATG
* *
6545459 TGGGGGGAATCGGTTCCCCTTCA--
1 AGGGGGGAATCGATT-CCC-TCATG
* *
6545482 AAGGGGGAATCGGTTCCCTCATG
1 AGGGGGGAATCGATTCCCTCATG
6545505 AGGGGGG-ATCGATTCCCTC
1 AGGGGGGAATCGATTCCCTC
6545524 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
21 15 0.29
22 17 0.33
23 19 0.37
24 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.23
Consensus pattern (23 bp):
AGGGGGGAATCGATTCCCTCATG
Found at i:6553091 original size:99 final size:99
Alignment explanation
Indices: 6552920--6553122 Score: 309
Period size: 99 Copynumber: 2.1 Consensus size: 99
6552910 GGGACAGCTC
* * *
6552920 GATATTATAATCACCTTTATTAGGCTAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAAT
1 GATATTATAATCACCTTTATTAGGCTAGCTAAATCTTATCCATAAAGCCAGGGCATTTAACCAAT
* *
6552985 TGATTTAGAGGGACAGCTCAAGCTTTATTGTATA
66 TGATTTAGAGGGACAACTCAAGCTTTACTGTATA
* *
6553019 GATATTATAATCACCTTTATCTA-GTTAGCTAAATCTTATCCATAAAGCCGGGGCATTTAACCAA
1 GATATTATAATCACCTTTAT-TAGGCTAGCTAAATCTTATCCATAAAGCCAGGGCATTTAACCAA
*
6553083 TTGCTTTAGAGGGACAACTCAAGCTTTACTGTATA
65 TTGATTTAGAGGGACAACTCAAGCTTTACTGTATA
*
6553118 TATAT
1 GATAT
6553123 AATATTATAA
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
99 92 0.98
100 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (99 bp):
GATATTATAATCACCTTTATTAGGCTAGCTAAATCTTATCCATAAAGCCAGGGCATTTAACCAAT
TGATTTAGAGGGACAACTCAAGCTTTACTGTATA
Found at i:6556845 original size:9 final size:9
Alignment explanation
Indices: 6556818--6556981 Score: 68
Period size: 9 Copynumber: 18.6 Consensus size: 9
6556808 TAGATAGGAA
6556818 AAAATAAAG
1 AAAATAAAG
6556827 AAAAT---G
1 AAAATAAAG
6556833 -AAATAAAG
1 AAAATAAAG
*
6556841 AAAATAAAT
1 AAAATAAAG
*
6556850 AAGAT--A-
1 AAAATAAAG
6556856 AAAATAAAG
1 AAAATAAAG
6556865 AAAATAAAG
1 AAAATAAAG
6556874 ATAAATAAGACG
1 A-AAATAA-A-G
6556886 AATACTATAAAG
1 AA-A--ATAAAG
* *
6556898 ATAAAAAAAT
1 A-AAATAAAG
*
6556908 AAATATATATAT
1 AAA-ATA-A-AG
*
6556920 ATATATAAAG
1 A-AAATAAAG
6556930 AAAAT--A-
1 AAAATAAAG
6556936 AAAATAAAG
1 AAAATAAAG
6556945 AAAAT--A-
1 AAAATAAAG
6556951 AAAATAAAG
1 AAAATAAAG
6556960 AAAATAAAG
1 AAAATAAAG
*
6556969 AAAA-AAAT
1 AAAATAAAG
6556977 AAAAT
1 AAAAT
6556982 GGGAAAATGG
Statistics
Matches: 120, Mismatches: 10, Indels: 50
0.67 0.06 0.28
Matches are distributed among these distances:
5 4 0.03
6 15 0.12
7 3 0.03
8 11 0.09
9 49 0.41
10 15 0.12
11 4 0.03
12 12 0.10
13 3 0.03
14 4 0.03
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (9 bp):
AAAATAAAG
Found at i:6557093 original size:15 final size:14
Alignment explanation
Indices: 6556818--6557113 Score: 105
Period size: 15 Copynumber: 20.3 Consensus size: 14
6556808 TAGATAGGAA
6556818 AAAATAAAGAAAAT
1 AAAATAAAGAAAAT
*
6556832 GAAATAAAGAAAAT
1 AAAATAAAGAAAAT
*
6556846 -AAAT-AAG-ATA-
1 AAAATAAAGAAAAT
6556856 AAAATAAAGAAAAT
1 AAAATAAAGAAAAT
*
6556870 AAAGATAAATAAGACGAAT
1 AAA-AT--A-AAGA-AAAT
**
6556889 ACTATAAAGATAAA-
1 AAAATAAAGA-AAAT
*
6556903 AAAATAAATATATATAT
1 AAAATAAAGA-A-A-AT
*
6556920 ATATATAAAGAAAAT
1 A-AAATAAAGAAAAT
6556935 AAAAATAAAGAAAAT
1 -AAAATAAAGAAAAT
6556950 AAAAATAAAGAAAAT
1 -AAAATAAAGAAAAT
*
6556965 -AAAGAAA-AAAAT
1 AAAATAAAGAAAAT
**
6556977 AAAAT-GGGAAAAT
1 AAAATAAAGAAAAT
6556990 GGAAAATGGAAA-AAAAGT
1 --AAAAT--AAAGAAAA-T
* *
6557008 AAAAATAATA-TATAT
1 -AAAATAA-AGAAAAT
*
6557023 AAAATAAATAAAAT
1 AAAATAAAGAAAAT
*
6557037 AAAGATAAAGATAAT
1 AAA-ATAAAGAAAAT
*
6557052 AAAAATGAAAGAAAGCT
1 -AAAAT-AAAGAAA-AT
*
6557069 -AAA-CAAGATAAAT
1 AAAATAAAGA-AAAT
*
6557082 AAAATAAAGATAA-
1 AAAATAAAGAAAAT
* *
6557095 AAATTAAAAAAAATT
1 AAAATAAAGAAAA-T
6557110 AAAA
1 AAAA
6557114 AAAAATAAAA
Statistics
Matches: 212, Mismatches: 37, Indels: 65
0.68 0.12 0.21
Matches are distributed among these distances:
11 6 0.03
12 11 0.05
13 36 0.17
14 45 0.21
15 67 0.32
16 16 0.08
17 13 0.06
18 14 0.07
19 4 0.02
ACGTcount: A:0.71, C:0.01, G:0.09, T:0.18
Consensus pattern (14 bp):
AAAATAAAGAAAAT
Found at i:6557108 original size:10 final size:10
Alignment explanation
Indices: 6557093--6557127 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
6557083 AAATAAAGAT
6557093 AAAAATTAAA
1 AAAAATTAAA
6557103 AAAAATTAAA
1 AAAAATTAAA
*
6557113 AAAAAATAAA
1 AAAAATTAAA
6557123 AAAAA
1 AAAAA
6557128 AAAGTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:6557127 original size:9 final size:9
Alignment explanation
Indices: 6556999--6557127 Score: 51
Period size: 9 Copynumber: 12.9 Consensus size: 9
6556989 TGGAAAATGG
*
6556999 AAAAAAAGT
1 AAAAAAAAT
6557008 AAAAATAATAT
1 AAAAA-AA-AT
* *
6557019 ATATAAAAT
1 AAAAAAAAT
*
6557028 AAATAAAAT
1 AAAAAAAAT
6557037 AAAGATAAAGAT
1 AAA-A-AAA-AT
*
6557049 AATAAAAAT
1 AAAAAAAAT
**
6557058 GAAAGAAAGCT
1 -AAA-AAAAAT
* *
6557069 AAACAAGAT
1 AAAAAAAAT
*
6557078 AAATAAAAT
1 AAAAAAAAT
6557087 AAAGATAAAAATT
1 -AA-A-AAAAA-T
6557100 AAAAAAAATT
1 AAAAAAAA-T
6557110 AAAAAAAAAT
1 -AAAAAAAAT
6557120 AAAAAAAA
1 AAAAAAAA
6557128 AAAGTATATT
Statistics
Matches: 94, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
9 39 0.41
10 22 0.23
11 22 0.23
12 10 0.11
13 1 0.01
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:6557128 original size:10 final size:10
Alignment explanation
Indices: 6557082--6557128 Score: 58
Period size: 10 Copynumber: 4.4 Consensus size: 10
6557072 CAAGATAAAT
6557082 AAAATAAAGATA
1 AAAATAAA-A-A
6557094 AAAATTAAAAA
1 AAAA-TAAAAA
*
6557105 AAATTAAAAA
1 AAAATAAAAA
6557115 AAAATAAAAA
1 AAAATAAAAA
6557125 AAAA
1 AAAA
6557129 AAGTATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 19 0.59
11 4 0.12
12 5 0.16
13 4 0.12
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:6557129 original size:11 final size:11
Alignment explanation
Indices: 6557082--6557129 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
6557072 CAAGATAAAT
*
6557082 AAAATAAAGATA
1 AAAATAAA-AAA
*
6557094 AAAAT-TAAAA
1 AAAATAAAAAA
*
6557104 AAAATTAAAAA
1 AAAATAAAAAA
6557115 AAAATAAAAAA
1 AAAATAAAAAA
6557126 AAAA
1 AAAA
6557130 AGTATATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 7 0.23
11 19 0.61
12 5 0.16
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:6557306 original size:62 final size:58
Alignment explanation
Indices: 6557240--6557415 Score: 133
Period size: 62 Copynumber: 2.9 Consensus size: 58
6557230 AATAATATAT
**
6557240 ATATATATATACATAAATAAAATACTTTAAAATAAAATAAAATAAATAAAAACCAGAAAATG
1 ATATATATATA-ATAAATAAAATA-TCAAAAATAAAATAAAATAAATAAAAA-CA-AAAATG
* * * *
6557302 ATATATAAAAATAATAAATAAAAAAGTCCAAAAGAAAA-AAAATAATATAAAATA-AAAATTATA
1 ATATAT--ATATAATAAATAAAATA-TCAAAAATAAAATAAAATAA-ATAAAA-ACAAAA--AT-
*
6557365 T
58 G
* *
6557366 ATATATATATAATAAA-AAAATATGAAAAATATAATAATAATAAATAAAAA
1 ATATATATATAATAAATAAAATATCAAAAATAAAATAA-AATAAATAAAAA
6557416 AAAGGGCTAA
Statistics
Matches: 92, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
60 9 0.10
61 16 0.17
62 28 0.30
63 28 0.30
64 11 0.12
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (58 bp):
ATATATATATAATAAATAAAATATCAAAAATAAAATAAAATAAATAAAAACAAAAATG
Found at i:6557415 original size:22 final size:21
Alignment explanation
Indices: 6557372--6557417 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
6557362 ATATATATAT
6557372 ATATAATAAAAAAATATGAAAA
1 ATATAATAAAAAAATA-GAAAA
*
6557394 ATATAATAATAATAAATAAAAAA
1 ATATAATAA-AA-AAATAGAAAA
6557417 A
1 A
6557418 AGGGCTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 7 0.33
24 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
ATATAATAAAAAAATAGAAAA
Found at i:6558238 original size:33 final size:33
Alignment explanation
Indices: 6558200--6558277 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
6558190 GGTCGTTGGT
6558200 TGCGTGAGGAATCGGTGAG-GGCACTTGAGGAGA
1 TGCGTGAGGAATCGGTG-GCGGCACTTGAGGAGA
*
6558233 TGCGTGAGGAATCGGTGGCGGCATTTGAGGAGA
1 TGCGTGAGGAATCGGTGGCGGCACTTGAGGAGA
*
6558266 TGGGTGAGGAAT
1 TGCGTGAGGAAT
6558278 GGTTGGAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 1 0.02
33 41 0.98
ACGTcount: A:0.23, C:0.10, G:0.46, T:0.21
Consensus pattern (33 bp):
TGCGTGAGGAATCGGTGGCGGCACTTGAGGAGA
Found at i:6558470 original size:2 final size:2
Alignment explanation
Indices: 6558463--6558507 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
6558453 TTTAAGTAGA
*
6558463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6558504 AT AT
1 AT AT
6558508 GGACGAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6566442 original size:24 final size:26
Alignment explanation
Indices: 6566396--6566447 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
6566386 CGTTCGTGAA
*
6566396 CGTTCGATTATATGTTCGCTTATGTT
1 CGTTCGATTATATGTTCACTTATGTT
*
6566422 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCACTTATGTT
6566446 CG
1 CG
6566448 AACATATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 3 0.12
26 5 0.21
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.52
Consensus pattern (26 bp):
CGTTCGATTATATGTTCACTTATGTT
Found at i:6566772 original size:20 final size:20
Alignment explanation
Indices: 6566749--6566788 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6566739 CGTTTATGTT
* *
6566749 CGTTCGTTTGTGTTTGTTTA
1 CGTTCGTTTATGTTCGTTTA
*
6566769 CGTTTGTTTATGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
6566789 TCATTTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.07, C:0.10, G:0.23, T:0.60
Consensus pattern (20 bp):
CGTTCGTTTATGTTCGTTTA
Found at i:6566879 original size:16 final size:16
Alignment explanation
Indices: 6566854--6566894 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
6566844 AATAAAATTT
6566854 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
6566870 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
6566886 T-TT-ATTTAT
1 TGTTCATTTAT
6566895 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:6569938 original size:19 final size:18
Alignment explanation
Indices: 6569890--6569946 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 18
6569880 CTTGGAGCGT
6569890 TGGGGGTATCGGTACCCC
1 TGGGGGTATCGGTACCCC
*
6569908 TGCATAGGGTATCGGTACCTCC
1 TG---GGGGTATCGGTACC-CC
6569930 TGGGGGTATCGGTACCC
1 TGGGGGTATCGGTACCC
6569947 TCCGAGCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 3 0.09
19 13 0.39
21 13 0.39
22 4 0.12
ACGTcount: A:0.14, C:0.26, G:0.35, T:0.25
Consensus pattern (18 bp):
TGGGGGTATCGGTACCCC
Found at i:6570413 original size:21 final size:21
Alignment explanation
Indices: 6570387--6570426 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6570377 AATTATTCCC
6570387 CCTTACTCTAATACTTTGATA
1 CCTTACTCTAATACTTTGATA
6570408 CCTTACTCTAATACTTTGA
1 CCTTACTCTAATACTTTGA
6570427 AAATAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.25, G:0.05, T:0.42
Consensus pattern (21 bp):
CCTTACTCTAATACTTTGATA
Found at i:6571820 original size:23 final size:23
Alignment explanation
Indices: 6571786--6571838 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
6571776 CCTTAGGGGA
* *
6571786 GGGTATCGGTACCCATTCAAAGG
1 GGGTATCAGTACCCAATCAAAGG
6571809 GGGTATCAGTACCCAATCAAAGG
1 GGGTATCAGTACCCAATCAAAGG
6571832 GGGTATC
1 GGGTATC
6571839 GATACCTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (23 bp):
GGGTATCAGTACCCAATCAAAGG
Found at i:6571844 original size:23 final size:23
Alignment explanation
Indices: 6571786--6571844 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
6571776 CCTTAGGGGA
* *
6571786 GGGTATCGGTACCCATTCAAAGG
1 GGGTATCGATACCCAATCAAAGG
6571809 GGGTATC-AGTACCCAATCAAAGG
1 GGGTATCGA-TACCCAATCAAAGG
6571832 GGGTATCGATACC
1 GGGTATCGATACC
6571845 TCATATGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (23 bp):
GGGTATCGATACCCAATCAAAGG
Found at i:6575686 original size:21 final size:21
Alignment explanation
Indices: 6575660--6575701 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6575650 GAGATTATTT
*
6575660 TCATTTTTCA-ATTTTGAAATA
1 TCATTTTT-ATATTTAGAAATA
6575681 TCATTTTTATATTTAGAAATA
1 TCATTTTTATATTTAGAAATA
6575702 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (21 bp):
TCATTTTTATATTTAGAAATA
Found at i:6579292 original size:3 final size:3
Alignment explanation
Indices: 6579286--6579320 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
6579276 ATCTTTTTTT
6579286 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6579321 ATTACATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:6581404 original size:4 final size:4
Alignment explanation
Indices: 6581389--6581504 Score: 88
Period size: 4 Copynumber: 29.0 Consensus size: 4
6581379 AATTTCATGC
* * * * *
6581389 GTGT GCGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GCGC GCGC
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * * * * ** * * *
6581437 GTGC GTGC GTGC GTGC GTGA GTGC GTAC GTGC GTGC GTGC GTGT GTGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
6581485 GTGT GTGT GTGT GTGT GTGT
1 GTGT GTGT GTGT GTGT GTGT
6581505 ACATGGAATT
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 102 1.00
ACGTcount: A:0.02, C:0.12, G:0.49, T:0.37
Consensus pattern (4 bp):
GTGT
Found at i:6586064 original size:33 final size:33
Alignment explanation
Indices: 6586000--6586068 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
6585990 AGAATCAGTG
* *
6586000 TTGAAGCAATCAACATCAACTATTGAGGCATCT
1 TTGAAGCAATCAACATCAACTATTCAAGCATCT
*
6586033 TTGAAGCAATCAACATCGAA-TGTTCAAGCATCT
1 TTGAAGCAATCAACATC-AACTATTCAAGCATCT
6586066 TTG
1 TTG
6586069 GGGATTCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (33 bp):
TTGAAGCAATCAACATCAACTATTCAAGCATCT
Found at i:6586290 original size:66 final size:63
Alignment explanation
Indices: 6586150--6586494 Score: 252
Period size: 62 Copynumber: 5.4 Consensus size: 63
6586140 TTACCAGTAT
* * *
6586150 CCTTT-AGT-TGTTTCTCTTGAAACAAATTTTG--TCTCTTGAAAC-AGTTTCTTTTAAAAAAA
1 CCTTTGAGTCTGTTTCTCTGGAAACAAATTTTGTCTCTCTTGAGACAATTTTC-TTTAAAAAAA
*
6586209 TTCTTTGAGTCTGTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTCTTTAAGGAAA
1 -CCTTTGAGTCTGTTTCTCTGGAAACAAA-TTTTGTCTCTCTTGAGACAATTTTCTTTAA--AAA
6586274 AA
62 AA
* * * * *
6586276 CCTTTGAAAT-TGTTTC-CATTGAAACAAATTTTATCTCTC--GAGACAGTTCCTT-TTGAAAAA
1 CCTTTG-AGTCTGTTTCTC-TGGAAACAAATTTTGTCTCTCTTGAGACAATT--TTCTTTAAAAA
6586336 AA
62 AA
** * *
6586338 TATTTGAGTCTGTTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCCTTTGAGAAAAA
1 CCTTTGAGTCTGTTTCTCTGGAAACAAA-TTTTGTCTCTCTTGAGACAATTTTCTTT---AAAAA
6586403 AA
62 AA
** * * *
6586405 CCTTTGAGATCT-TTTC-CATTAAAACAAATTTTG--TCTCTTGAGCCAGTTTCTTTTTAGAAAA
1 CCTTTGAG-TCTGTTTCTC-TGGAAACAAATTTTGTCTCTCTTGAGACAATTT-TCTTTA-AAAA
*
6586466 AT
62 AA
*
6586468 CC-TTGAGTCTGTTTCTTTGGAAACAAA
1 CCTTTGAGTCTGTTTCTCTGGAAACAAA
6586495 ATTTACCATC
Statistics
Matches: 226, Mismatches: 32, Indels: 52
0.73 0.10 0.17
Matches are distributed among these distances:
60 4 0.02
61 8 0.04
62 59 0.26
63 31 0.14
64 20 0.09
65 39 0.17
66 30 0.13
67 32 0.14
68 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (63 bp):
CCTTTGAGTCTGTTTCTCTGGAAACAAATTTTGTCTCTCTTGAGACAATTTTCTTTAAAAAAA
Found at i:6586385 original size:128 final size:128
Alignment explanation
Indices: 6586157--6586494 Score: 484
Period size: 128 Copynumber: 2.6 Consensus size: 128
6586147 TATCCTTTAG
*
6586157 TTGTTTCTC-TTGAAACAAATTTTGTCTCTTGAAACAGTTTCTTTTAAAAAAATTCTTTGAGTCT
1 TTGTTTC-CATTGAAACAAATTTTGTCTCTTGAGACAGTTTCTTTTAAAAAAA-TCTTTGAGTCT
* * *
6586221 GTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTCTTTAAG-GAAAAACCTTTGAAA
64 GTTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCCTTTAAGAAAAAAACCTTTGAAA
* * * *
6586285 TTGTTTCCATTGAAACAAATTTTATCTCTCGAGACAGTTCCTTTTGAAAAAAATATTTGAGTCTG
1 TTGTTTCCATTGAAACAAATTTTGTCTCTTGAGACAGTTTCTTTT-AAAAAAATCTTTGAGTCTG
* *
6586350 TTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCCTTTGAGAAAAAAACCTTTGAGA
65 TTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCCTTTAAGAAAAAAACCTTTGAAA
* * * *
6586414 TCT-TTTCCATTAAAACAAATTTTGTCTCTTGAGCCAGTTTCTTTTTAGAAAAATCCTTGAGTCT
1 T-TGTTTCCATTGAAACAAATTTTGTCTCTTGAGACAGTTTC-TTTTAAAAAAATCTTTGAGTCT
6586478 GTTTCTTTGGAAACAAA
64 GTTTCTTTGGAAACAAA
6586495 ATTTACCATC
Statistics
Matches: 187, Mismatches: 18, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
127 1 0.01
128 95 0.51
129 86 0.46
130 5 0.03
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (128 bp):
TTGTTTCCATTGAAACAAATTTTGTCTCTTGAGACAGTTTCTTTTAAAAAAATCTTTGAGTCTGT
TTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCCTTTAAGAAAAAAACCTTTGAAA
Found at i:6586458 original size:129 final size:127
Alignment explanation
Indices: 6586169--6586494 Score: 474
Period size: 129 Copynumber: 2.5 Consensus size: 127
6586159 GTTTCTCTTG
* *
6586169 AAACAAATTTTGTCTCTTGAAACAGTTTCTTTTAAAAAAATTCTTTGAGTCTGTTTCTCTGGAAA
1 AAACAAATTTTGTCTCTTGAGACAGTTTCTTTTAAAAAAA-TCTTTGAGTCTGTTTCTTTGGAAA
* * *
6586234 CAAAGTTTTGTCTCTCTTGAGACAATTTTCTTTAAGGAAAAACCTTTGAAATTGTTTCCATTG
65 CAAAGTTTTGTCTCTCTTGAGACAATTTCCTTTAAGAAAAAACCTTTGAAATTGTTTCCATTA
* * * *
6586297 AAACAAATTTTATCTCTCGAGACAGTTCCTTTTGAAAAAAATATTTGAGTCTGTTTCTTTGGAAA
1 AAACAAATTTTGTCTCTTGAGACAGTTTCTTTT-AAAAAAATCTTTGAGTCTGTTTCTTTGGAAA
* *
6586362 CAAAGTTTTGTCTCTCTTGAGACAATTTCCTTTGAGAAAAAAACCTTTGAGATCT-TTTCCATTA
65 CAAAGTTTTGTCTCTCTTGAGACAATTTCCTTTAAG-AAAAAACCTTTGAAAT-TGTTTCCATTA
* * *
6586426 AAACAAATTTTGTCTCTTGAGCCAGTTTCTTTTTAGAAAAATCCTTGAGTCTGTTTCTTTGGAAA
1 AAACAAATTTTGTCTCTTGAGACAGTTTC-TTTTAAAAAAATCTTTGAGTCTGTTTCTTTGGAAA
6586491 CAAA
65 CAAA
6586495 ATTTACCATC
Statistics
Matches: 176, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
128 85 0.48
129 86 0.49
130 5 0.03
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (127 bp):
AAACAAATTTTGTCTCTTGAGACAGTTTCTTTTAAAAAAATCTTTGAGTCTGTTTCTTTGGAAAC
AAAGTTTTGTCTCTCTTGAGACAATTTCCTTTAAGAAAAAACCTTTGAAATTGTTTCCATTA
Found at i:6587059 original size:3 final size:3
Alignment explanation
Indices: 6587046--6587079 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
6587036 GGTCTTTTTT
*
6587046 TTA TTA ATA TTA TTA TTGA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
6587080 ATATATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:6587072 original size:16 final size:16
Alignment explanation
Indices: 6587048--6587078 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6587038 TCTTTTTTTT
6587048 ATTAATATTATTATTG
1 ATTAATATTATTATTG
*
6587064 ATTATTATTATTATT
1 ATTAATATTATTATT
6587079 AATATATTAA
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:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTAATATTATTATTG
Found at i:6589000 original size:30 final size:29
Alignment explanation
Indices: 6588931--6589018 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 29
6588921 TTTATGTATA
* * *
6588931 TTTA-TATTTTAGTCCTTAACTTTTTGAT
1 TTTATTATTTTAGTCTTTAAATTTTTGTT
*
6588959 TTTATTATTTTAGTCATTTAAGTTTTTGTT
1 TTTATTATTTTAGTC-TTTAAATTTTTGTT
* *
6588989 TTTGTTGTTTTAGTCCTTTAAATTTTTGTT
1 TTTATTATTTTAGT-CTTTAAATTTTTGTT
6589019 AATACTATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
28 4 0.08
29 10 0.20
30 36 0.71
31 1 0.02
ACGTcount: A:0.18, C:0.07, G:0.10, T:0.65
Consensus pattern (29 bp):
TTTATTATTTTAGTCTTTAAATTTTTGTT
Found at i:6589332 original size:5 final size:5
Alignment explanation
Indices: 6589319--6589354 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
6589309 ATCTTTTCAT
*
6589319 TTTTA TTTTG TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
6589355 CTTTGCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:6589339 original size:15 final size:15
Alignment explanation
Indices: 6589319--6589359 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
6589309 ATCTTTTCAT
6589319 TTTTATTTTGTTTTA
1 TTTTATTTTGTTTTA
*
6589334 TTTTATTTTATTTTA
1 TTTTATTTTGTTTTA
6589349 TTTTATCTTTG
1 TTTTAT-TTTG
6589360 CAAAAATTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (15 bp):
TTTTATTTTGTTTTA
Found at i:6594506 original size:31 final size:31
Alignment explanation
Indices: 6594471--6594578 Score: 135
Period size: 31 Copynumber: 3.4 Consensus size: 31
6594461 TCCAAAACCA
*
6594471 TACCCAATTTTTACTTTTTATTTCATTTTAG
1 TACCCAATTTTTACTTTTTGTTTCATTTTAG
* * *
6594502 TACCCGATATTTACTTTTTGTTTCATTTTAT
1 TACCCAATTTTTACTTTTTGTTTCATTTTAG
* *
6594533 TACCCCATTGTTAACTTTTTGTTTCATTTTAG
1 TACCCAATT-TTTACTTTTTGTTTCATTTTAG
*
6594565 TACCTAAATTTTTA
1 TACC-CAATTTTTA
6594579 ACAGCAGGGT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
31 34 0.53
32 27 0.42
33 3 0.05
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (31 bp):
TACCCAATTTTTACTTTTTGTTTCATTTTAG
Found at i:6596322 original size:17 final size:17
Alignment explanation
Indices: 6596302--6596337 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
6596292 TATCATCTTA
6596302 AGACATTAACCATCAGT
1 AGACATTAACCATCAGT
*
6596319 AGACATTAACCATCGGT
1 AGACATTAACCATCAGT
6596336 AG
1 AG
6596338 GGCTGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (17 bp):
AGACATTAACCATCAGT
Found at i:6596664 original size:16 final size:16
Alignment explanation
Indices: 6596617--6596667 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
6596607 TTACCCGACT
* * *
6596617 TGTTTTCAATCTGACT
1 TGTTTTTAACCTGACC
6596633 TGTTTTTAACCTGACC
1 TGTTTTTAACCTGACC
6596649 TGTTTTTAACCTGACC
1 TGTTTTTAACCTGACC
6596665 TGT
1 TGT
6596668 AAATGATTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.18, C:0.22, G:0.14, T:0.47
Consensus pattern (16 bp):
TGTTTTTAACCTGACC
Found at i:6597458 original size:19 final size:20
Alignment explanation
Indices: 6597419--6597461 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
6597409 AAATTTTCTA
**
6597419 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAATTTCAAAAT
6597439 TTCCCTCT-AATTTCAAAAT
1 TTCCCTCTAAATTTCAAAAT
6597458 TTCC
1 TTCC
6597462 TAATTTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCCCTCTAAATTTCAAAAT
Found at i:6597460 original size:27 final size:29
Alignment explanation
Indices: 6597427--6597484 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 29
6597417 TATTCCCTCT
6597427 AAATTTCCCAATTTCCCTCT-AATT-TCA
1 AAATTTCCCAATTTCCCTCTAAATTCTCA
* *
6597454 AAATTTCCTAATTTCTCTCTAAATTCTCA
1 AAATTTCCCAATTTCCCTCTAAATTCTCA
6597483 AA
1 AA
6597485 TAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 18 0.67
28 4 0.15
29 5 0.19
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (29 bp):
AAATTTCCCAATTTCCCTCTAAATTCTCA
Found at i:6598014 original size:2 final size:2
Alignment explanation
Indices: 6598007--6598069 Score: 83
Period size: 2 Copynumber: 31.5 Consensus size: 2
6597997 TATGTTTAAT
* *
6598007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
6598049 TA TA CT- TT TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA T
6598070 TATTCAAAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
1 1 0.02
2 52 0.96
3 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:6598589 original size:2 final size:2
Alignment explanation
Indices: 6598582--6598651 Score: 51
Period size: 2 Copynumber: 36.0 Consensus size: 2
6598572 TAATGCATAC
* * *
6598582 AT AT AT AT ACT AT AT -T A- AT AT AA AT -T AT A- AC AT AT AA ACT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
6598622 AT AT -T AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
6598652 TAATATAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
1 5 0.09
2 45 0.82
3 5 0.09
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6598624 original size:29 final size:28
Alignment explanation
Indices: 6598584--6598661 Score: 106
Period size: 26 Copynumber: 2.8 Consensus size: 28
6598574 ATGCATACAT
6598584 ATATATACTATATTAATATAAATTATAAC
1 ATATATACTATATTAATATAAATTAT-AC
* * *
6598613 ATATAAACTATATT-ATATATA-TATAT
1 ATATATACTATATTAATATAAATTATAC
6598639 ATATATACTATATTAATATAAAT
1 ATATATACTATATTAATATAAAT
6598662 AATATTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
26 14 0.33
27 9 0.21
28 6 0.14
29 13 0.31
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (28 bp):
ATATATACTATATTAATATAAATTATAC
Found at i:6598657 original size:19 final size:19
Alignment explanation
Indices: 6598582--6598658 Score: 74
Period size: 19 Copynumber: 4.2 Consensus size: 19
6598572 TAATGCATAC
6598582 ATATATATACTATATTAAT
1 ATATATATACTATATTAAT
* *
6598601 ATAAATTATAAC-ATATAAACT
1 ATATA-TAT-ACTATATTAA-T
6598622 ATAT-TATA-TATA-T-AT
1 ATATATATACTATATTAAT
6598637 ATATATATACTATATTAAT
1 ATATATATACTATATTAAT
6598656 ATA
1 ATA
6598659 AATAATATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
15 5 0.11
16 5 0.11
17 4 0.09
18 5 0.11
19 12 0.26
20 9 0.20
21 6 0.13
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATATACTATATTAAT
Found at i:6598719 original size:13 final size:13
Alignment explanation
Indices: 6598703--6598766 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
6598693 TTAAACATAT
6598703 ATAGTTTATATAC
1 ATAGTTTATATAC
*
6598716 ATAGTTTATATAT
1 ATAGTTTATATAC
* *
6598729 ATAGTTCACATAAAC
1 ATAGTT--TATATAC
* *
6598744 ATAATTTATATAT
1 ATAGTTTATATAC
*
6598757 ATAGCTTATA
1 ATAGTTTATA
6598767 ATAATTATAT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
13 30 0.77
15 9 0.23
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:6598728 original size:26 final size:26
Alignment explanation
Indices: 6598699--6598865 Score: 120
Period size: 28 Copynumber: 6.6 Consensus size: 26
6598689 TAGTTTAAAC
* *
6598699 ATATATAGTTTATATACATAGTTTAT
1 ATATATAGTTTATAAACATAATTTAT
*
6598725 ATATATAGTTCACATAAACATAATTTAT
1 ATATATAGTT--TATAAACATAATTTAT
*
6598753 ATATATAGCTTAT--A-ATAA-TTAT
1 ATATATAGTTTATAAACATAATTTAT
* * *
6598775 ATAGTTTA-TAATATAAATATAA-TT-T
1 ATA-TATAGT-TTATAAACATAATTTAT
*
6598800 ATA-AT--TTTATAAACATAGTTTAT
1 ATATATAGTTTATAAACATAATTTAT
* *
6598823 ATATATAGTTCACATAAATATAATTTAT
1 ATATATAGTT--TATAAACATAATTTAT
6598851 ATATATAGTTTATAA
1 ATATATAGTTTATAA
6598866 TAATTATATA
Statistics
Matches: 111, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
21 9 0.08
22 10 0.09
23 15 0.14
24 3 0.03
25 5 0.05
26 24 0.22
28 45 0.41
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (26 bp):
ATATATAGTTTATAAACATAATTTAT
Found at i:6598730 original size:28 final size:28
Alignment explanation
Indices: 6598687--6598922 Score: 95
Period size: 28 Copynumber: 8.5 Consensus size: 28
6598677 ATATACTTTT
* *
6598687 TATAGTTTAAACATATATAGTTTATATA
1 TATAGTTTATATATATATAGTTTATATA
* * *
6598715 CATAG-TT-TATATATATAGTTCACATAAA
1 TATAGTTTATATATATATAGTT--TATATA
* *
6598743 CATA-ATT-TATATATATAGCTTATAATAATTA
1 TATAGTTTATATATATATAG-TT-T-AT-A-TA
* * *
6598774 TATAGTTTATA-ATATA-AATATA-ATT
1 TATAGTTTATATATATATAGTTTATATA
* * *
6598799 TATAATTT-TATAAACATAGTTTATATA
1 TATAGTTTATATATATATAGTTTATATA
* * * *
6598826 TATAGTTCACATAAATATAATTTATATA
1 TATAGTTTATATATATATAGTTTATATA
6598854 TATAGTTTATAATAATTATATAGTTTATA-A
1 TATAGTTTAT-AT-A-TATATAGTTTATATA
* * *
6598884 TA-A--TTATATA-ATTTA-TAATATAAA
1 TATAGTTTATATATATATAGT-TTATATA
6598908 TATAGTTTATATATA
1 TATAGTTTATATATA
6598923 ATTTTATATT
Statistics
Matches: 157, Mismatches: 29, Indels: 44
0.68 0.13 0.19
Matches are distributed among these distances:
22 1 0.01
23 8 0.05
24 5 0.03
25 13 0.08
26 18 0.11
27 21 0.13
28 52 0.33
29 8 0.05
30 6 0.04
31 16 0.10
32 7 0.04
33 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (28 bp):
TATAGTTTATATATATATAGTTTATATA
Found at i:6598794 original size:18 final size:18
Alignment explanation
Indices: 6598750--6598922 Score: 113
Period size: 18 Copynumber: 9.2 Consensus size: 18
6598740 AAACATAATT
*
6598750 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
6598768 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
* *
6598786 TATAAATATAATTTATAA
1 TATATATATAGTTTATAA
* *
6598804 TTTTATAAACATAGTTTATATA
1 ---TATATATATAGTTTATA-A
* **
6598826 TATAGTTCACATA-AATATAA
1 TATA--T-ATATAGTTTATAA
6598846 TTTATATATATAGTTTATAA
1 --TATATATATAGTTTATAA
6598866 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
6598884 TA-ATTATATAATTTATAA
1 TATA-TATATAGTTTATAA
*
6598902 TATAAATATAGTTTAT-A
1 TATATATATAGTTTATAA
6598919 TATA
1 TATA
6598923 ATTTTATATT
Statistics
Matches: 127, Mismatches: 14, Indels: 29
0.75 0.08 0.17
Matches are distributed among these distances:
17 7 0.06
18 74 0.58
19 10 0.08
20 7 0.06
21 19 0.15
22 10 0.08
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:6598819 original size:98 final size:97
Alignment explanation
Indices: 6598702--6598922 Score: 349
Period size: 98 Copynumber: 2.3 Consensus size: 97
6598692 TTTAAACATA
* *
6598702 TATAGTTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATA
1 TATAATTTATAAACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATA
6598767 ATAATTATATAGTTTATAAT-ATAAATATAATT
66 ATAATTATATAGTTTATAATAAT-AATATAATT
* *
6598799 TATAATTTTATAAACATAGTTTATATATATAGTTCACATAAATATAATTTATATATATAGTTTAT
1 TATAA-TTTATAAACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTAT
*
6598864 AATAATTATATAGTTTATAATAATTATATAATT
65 AATAATTATATAGTTTATAATAATAATATAATT
*
6598897 TATAA--TATAAATATAGTTTATATATA
1 TATAATTTATAAACATAGTTTATATATA
6598923 ATTTTATATT
Statistics
Matches: 116, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
95 20 0.17
97 4 0.03
98 90 0.78
99 2 0.02
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (97 bp):
TATAATTTATAAACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATA
ATAATTATATAGTTTATAATAATAATATAATT
Found at i:6598821 original size:13 final size:13
Alignment explanation
Indices: 6598805--6598865 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
6598795 AATTTATAAT
*
6598805 TTTATAAACATAG
1 TTTATAAATATAG
*
6598818 TTTATATATATAG
1 TTTATAAATATAG
* *
6598831 TTCACATAAATATAA
1 TT--TATAAATATAG
*
6598846 TTTATATATATAG
1 TTTATAAATATAG
6598859 TTTATAA
1 TTTATAA
6598866 TAATTATATA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
13 27 0.73
15 10 0.27
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (13 bp):
TTTATAAATATAG
Found at i:6609829 original size:58 final size:58
Alignment explanation
Indices: 6609765--6609886 Score: 131
Period size: 57 Copynumber: 2.1 Consensus size: 58
6609755 TAATGGTCAT
* * * * *
6609765 GATTAT-ATGGGTTGATTTGTTGAGTATTCTGACTATTAAAAGTTATAAAATAAT-ATCC
1 GATTATAAAGGGTTGATTTGTTAAGT-GTC-AACTATTAAAAGTTATAAAATAATCACCC
* * * *
6609823 GATTATAAAGTGTTGCTTTTTTAAGTGTCAACTATTAAAAGTTATAAAATTATCACCC
1 GATTATAAAGGGTTGATTTGTTAAGTGTCAACTATTAAAAGTTATAAAATAATCACCC
6609881 GATTAT
1 GATTAT
6609887 TTGTATGTTC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
57 22 0.42
58 17 0.32
59 14 0.26
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (58 bp):
GATTATAAAGGGTTGATTTGTTAAGTGTCAACTATTAAAAGTTATAAAATAATCACCC
Found at i:6613402 original size:20 final size:20
Alignment explanation
Indices: 6613347--6613402 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
6613337 AGGGTGTCAA
* * *
6613347 AGTGTATGCATACACCCTGC
1 AGTGTATCCATACACTCTAC
*
6613367 AGTGTATCCATGCACTCTAC
1 AGTGTATCCATACACTCTAC
6613387 AGTGTATCCATACACT
1 AGTGTATCCATACACT
6613403 GTGCATCGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
AGTGTATCCATACACTCTAC
Found at i:6614963 original size:3 final size:3
Alignment explanation
Indices: 6614957--6614983 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6614947 AGAAGGTGAA
6614957 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
6614984 GAGGTAGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6616636 original size:20 final size:19
Alignment explanation
Indices: 6616600--6616656 Score: 98
Period size: 20 Copynumber: 3.0 Consensus size: 19
6616590 CAACAATTTA
6616600 TAACAATTGATAT-TTTTT
1 TAACAATTGATATCTTTTT
6616618 TAACAATTGATATCATTTTT
1 TAACAATTGATATC-TTTTT
6616638 TAACAATTGATATCTTTTT
1 TAACAATTGATATCTTTTT
6616657 CATTAAACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
18 13 0.35
19 5 0.14
20 19 0.51
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (19 bp):
TAACAATTGATATCTTTTT
Found at i:6616938 original size:20 final size:20
Alignment explanation
Indices: 6616883--6616943 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
6616873 AGGGTGTCAA
* *
6616883 AGTGTATCCATGCACCCTAC
1 AGTGTATCCATGCACTCTGC
6616903 AGTGTATCCATGCACTCTGC
1 AGTGTATCCATGCACTCTGC
* *
6616923 AGTGTATCCATACACTGTGC
1 AGTGTATCCATGCACTCTGC
6616943 A
1 A
6616944 TCGATGCACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (20 bp):
AGTGTATCCATGCACTCTGC
Found at i:6617719 original size:300 final size:300
Alignment explanation
Indices: 6617311--6617863 Score: 1061
Period size: 300 Copynumber: 1.8 Consensus size: 300
6617301 CAAGAGAAGA
6617311 AGTTTTTCATTCTTATTTCATATTTCTCTTGTAAATATTTGTTCTTGTGAGCTTAATTCTTGTAA
1 AGTTTTTCATTCTTATTTCATATTTCTCTTGTAAATATTTGTTCTTGTGAGCTTAATTCTTGTAA
6617376 ACACATACCTTTTAGAGGTTTATTTGTTTACTTCTTTTATCCTTTTGTAAAGAGGAAAGGTTATA
66 ACACATACCTTTTAGAGGTTTATTTGTTTACTTCTTTTATCCTTTTGTAAAGAGGAAAGGTTATA
* * *
6617441 GCTTAGCCCATGTAAAATCTAGAGAAAGGTTCTAGTTTATCCCTTGAAAACCTAGGGAGTTGTAA
131 GATTAGCCCATATAAAAGCTAGAGAAAGGTTCTAGTTTATCCCTTGAAAACCTAGGGAGTTGTAA
6617506 AGGTTATCTCTTTGTCCTTAAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAAATCCAACCAAC
196 AGGTTATCTCTTTGTCCTTAAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAAATCCAACCAAC
6617571 TCCTGAAAGAAAACAAGAGCTTCTCCGTCCGGCAAACAAG
261 TCCTGAAAGAAAACAAGAGCTTCTCCGTCCGGCAAACAAG
*
6617611 AGTTTTTCATTCTTATTTCATCTTTCTCTTGTAAATATTTGTTCTTGTGAGCTTAATTCTTGTAA
1 AGTTTTTCATTCTTATTTCATATTTCTCTTGTAAATATTTGTTCTTGTGAGCTTAATTCTTGTAA
6617676 ACACATACCTTTTAGAGGTTTATTTGTTTACTTCTTTTATCCTTTTGTAAAGAGGAAAGGTTATA
66 ACACATACCTTTTAGAGGTTTATTTGTTTACTTCTTTTATCCTTTTGTAAAGAGGAAAGGTTATA
6617741 GATTAGCCCATATAAAAGCTAGAGAAAGGTTCTAGTTTATCCCTTGAAAACCTAGGGAGTTGTAA
131 GATTAGCCCATATAAAAGCTAGAGAAAGGTTCTAGTTTATCCCTTGAAAACCTAGGGAGTTGTAA
*
6617806 AGGTTATCTCTTTGTCCTTAAAAAGAAAGGACAAATTAGTGAATTTGTTGGAAAATCC
196 AGGTTATCTCTTTGTCCTTAAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAAATCC
6617864 TTGGTGAGGA
Statistics
Matches: 248, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
300 248 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (300 bp):
AGTTTTTCATTCTTATTTCATATTTCTCTTGTAAATATTTGTTCTTGTGAGCTTAATTCTTGTAA
ACACATACCTTTTAGAGGTTTATTTGTTTACTTCTTTTATCCTTTTGTAAAGAGGAAAGGTTATA
GATTAGCCCATATAAAAGCTAGAGAAAGGTTCTAGTTTATCCCTTGAAAACCTAGGGAGTTGTAA
AGGTTATCTCTTTGTCCTTAAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAAATCCAACCAAC
TCCTGAAAGAAAACAAGAGCTTCTCCGTCCGGCAAACAAG
Found at i:6618915 original size:2 final size:2
Alignment explanation
Indices: 6618908--6618941 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6618898 ATCATCAATA
6618908 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
6618942 AATTATCAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:6622468 original size:29 final size:29
Alignment explanation
Indices: 6622400--6622711 Score: 119
Period size: 29 Copynumber: 10.8 Consensus size: 29
6622390 TTTTAGATAC
* *
6622400 TTTAAAAACATATTTTACTTTT-ATCTTAA
1 TTTAAAAATATATTTTATTTTTAAT-TTAA
* * *
6622429 CTTATTAAATATATTTTATTTTTAAATTAA
1 TTTA-AAAATATATTTTATTTTTAATTTAA
* * *
6622459 TTT-AAAA-ATATTTTATTATCATTTTAA
1 TTTAAAAATATATTTTATTTTTAATTTAA
* *
6622486 TTTAGAAATATATATTTTATTCTTATTTTAA
1 TTTA-AAA-ATATATTTTATTTTTAATTTAA
* * *
6622517 CTTAAAAATAT-TTTTA---ATAAGTTAA
1 TTTAAAAATATATTTTATTTTTAATTTAA
** * * * * * *
6622542 GATACCAAATAAAATATATGTTTAAACTTAAA
1 TTTA-AAAATATATTTTAT-TTTTAA-TTTAA
* * *
6622574 CTT-AAAATATATTTTATTATTAACTTAA
1 TTTAAAAATATATTTTATTTTTAATTTAA
* *
6622602 TTT-AAGA-ATATTTTATTATT-ATTTCAA
1 TTTAAAAATATATTTTATTTTTAATTT-AA
* *
6622629 TTTAAAAATATATATTTTATTCTT-ATCTTAG
1 TTT-AAAA-ATATATTTTATTTTTAAT-TTAA
** * * *
6622660 CCTAAATATATATTTTATTCTTATTTTAA
1 TTTAAAAATATATTTTATTTTTAATTTAA
* *
6622689 TTTAAAAATA-AATATATTTTTAA
1 TTTAAAAATATATTTTATTTTTAA
6622712 AGATATATAA
Statistics
Matches: 208, Mismatches: 55, Indels: 41
0.68 0.18 0.13
Matches are distributed among these distances:
25 8 0.04
26 8 0.04
27 40 0.19
28 25 0.12
29 41 0.20
30 40 0.19
31 40 0.19
32 6 0.03
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (29 bp):
TTTAAAAATATATTTTATTTTTAATTTAA
Found at i:6622471 original size:27 final size:27
Alignment explanation
Indices: 6622433--6622698 Score: 108
Period size: 27 Copynumber: 9.3 Consensus size: 27
6622423 TCTTAACTTA
* * **
6622433 TTAAATATATTTTATTTTTAAATTAAT
1 TTAAAAATATTTTATTATTATTTTAAT
*
6622460 TTAAAAATATTTTATTATCATTTTAAT
1 TTAAAAATATTTTATTATTATTTTAAT
* *
6622487 TTAGAAATATATATTTTATTCTTATTTTAAC
1 TT--AAA-A-ATATTTTATTATTATTTTAAT
* *** *
6622518 TTAAAAATATTTTTAATAAGTTAAGATACCAA
1 TTAAAAATA-TTTT-ATTA-TTATTTTA--AT
* * * *
6622550 ATAAAATATATGTTTA--A--ACTTAAAC
1 TTAAAA-ATAT-TTTATTATTATTTTAAT
**
6622575 TTAAAATATATTTTATTATTAACTTAAT
1 TTAAAA-ATATTTTATTATTATTTTAAT
* *
6622603 TTAAGAATATTTTATTATTATTTCAAT
1 TTAAAAATATTTTATTATTATTTTAAT
* * **
6622630 TTAAAAATATATATTTTATTCTTATCTTAGC
1 TT--AAA-A-ATATTTTATTATTATTTTAAT
* *
6622661 CTAAATATATATTTTATTCTTATTTTAAT
1 TTAAA-A-ATATTTTATTATTATTTTAAT
6622690 TTAAAAATA
1 TTAAAAATA
6622699 AATATATTTT
Statistics
Matches: 180, Mismatches: 40, Indels: 38
0.70 0.16 0.15
Matches are distributed among these distances:
24 4 0.02
25 11 0.06
26 1 0.01
27 52 0.29
28 15 0.08
29 38 0.21
30 8 0.04
31 37 0.21
32 8 0.04
33 6 0.03
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAAAAATATTTTATTATTATTTTAAT
Found at i:6622504 original size:31 final size:31
Alignment explanation
Indices: 6622466--6622527 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
6622456 TAATTTAAAA
* *
6622466 ATATTTTATTATCATTTTAATTTAGAAATAT
1 ATATTTTATTATCATTTTAACTTAAAAATAT
* *
6622497 ATATTTTATTCTTATTTTAACTTAAAAATAT
1 ATATTTTATTATCATTTTAACTTAAAAATAT
6622528 TTTTAATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (31 bp):
ATATTTTATTATCATTTTAACTTAAAAATAT
Found at i:6623688 original size:30 final size:30
Alignment explanation
Indices: 6623654--6623726 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
6623644 CTCGAAGGAC
6623654 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
6623684 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
6623714 CTGTCCATAGGTC
1 CTATCCAGAGGTC
6623727 CTGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:6623743 original size:30 final size:30
Alignment explanation
Indices: 6623657--6623753 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
6623647 GAAGGACCTA
* *
6623657 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCATAGGTCATAAAGATCCTCGGTAACTG
*
6623687 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCATAAAGATCCTCGGTAACTG
* * * * *
6623717 TCCATAGGTCCTGAAGAACCTAGGTAAATTG
1 TCCATAGGTCATAAAGATCCTCGGT-AACTG
6623748 TCCATA
1 TCCATA
6623754 TGTTCCTTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 49 0.83
31 10 0.17
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (30 bp):
TCCATAGGTCATAAAGATCCTCGGTAACTG
Found at i:6623753 original size:31 final size:31
Alignment explanation
Indices: 6623715--6623775 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
6623705 CCTCGGTAAC
*
6623715 TGTCCATA-GGTCCTGAAGAACCTAGGTAAAT
1 TGTCCATATGGTCCT-AAGAACATAGGTAAAT
* *
6623746 TGTCCATATGTTCCTTAGAACATAGGTAAA
1 TGTCCATATGGTCCTAAGAACATAGGTAAA
6623776 CCCTCGAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (31 bp):
TGTCCATATGGTCCTAAGAACATAGGTAAAT
Found at i:6626461 original size:2 final size:2
Alignment explanation
Indices: 6626454--6626489 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6626444 CTGATCACAA
6626454 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
6626490 TCCCCAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6628840 original size:2 final size:2
Alignment explanation
Indices: 6628833--6628868 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6628823 ACCATATAAC
6628833 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
6628869 CATGGCATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6629220 original size:30 final size:30
Alignment explanation
Indices: 6629186--6629248 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
6629176 CTATATAGAT
6629186 GTCATAAAGATCCTCGGTAACTATCCAGAG
1 GTCATAAAGATCCTCGGTAACTATCCAGAG
* *
6629216 GTCATAAAGATCCTCGGTAACTGTCCATAG
1 GTCATAAAGATCCTCGGTAACTATCCAGAG
6629246 GTC
1 GTC
6629249 CCGAAGAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (30 bp):
GTCATAAAGATCCTCGGTAACTATCCAGAG
Found at i:6632993 original size:2 final size:2
Alignment explanation
Indices: 6632988--6633025 Score: 51
Period size: 2 Copynumber: 18.5 Consensus size: 2
6632978 AAAAAACAAA
6632988 AG AG AG TAG AG TAG AG A- AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG -AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG A
6633026 TGGCGGCTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 28 0.85
3 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (2 bp):
AG
Found at i:6636779 original size:31 final size:30
Alignment explanation
Indices: 6636735--6636844 Score: 98
Period size: 30 Copynumber: 3.6 Consensus size: 30
6636725 ACTTTGGTTT
* *
6636735 AATTTAGGAATCAAATTGATTTTTTATCTA
1 AATTTAGGGATCAAATTGATATTTTATCTA
* * *
6636765 AAGTTTAGGGATCAAAATGATATATTGTCTA
1 AA-TTTAGGGATCAAATTGATATTTTATCTA
* * *
6636796 CATTTCAAGG-TCAAATTAATATTTTATCTA
1 AATTT-AGGGATCAAATTGATATTTTATCTA
*
6636826 AAATTAGGAGA-CAAATTGA
1 AATTTAGG-GATCAAATTGA
6636845 AACTAATGTT
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
29 2 0.03
30 32 0.52
31 27 0.44
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (30 bp):
AATTTAGGGATCAAATTGATATTTTATCTA
Found at i:6637619 original size:31 final size:31
Alignment explanation
Indices: 6637583--6637641 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
6637573 AACTTAAAAG
* *
6637583 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
6637614 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
6637642 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:6637726 original size:32 final size:32
Alignment explanation
Indices: 6637688--6638215 Score: 359
Period size: 32 Copynumber: 17.7 Consensus size: 32
6637678 CAATCTATAT
*
6637688 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* * * *
6637720 TTTAAAATAAATAAATCAAT-C-CATACAACTA
1 TTTAAAATAAATCAATCCATACTAATA-AATTA
*
6637751 --CAATAATAAATCAAT-C---C--AT--ATT-
1 TTTAA-AATAAATCAATCCATACTAATAAATTA
* *
6637773 T-TAAAATAAACCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
6637804 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
6637836 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
6637868 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
6637890 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
6637922 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
6637952 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
6637970 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
6638002 TTTAAAATAAATCAATTCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* *
6638032 --T--AATAAATCAATCCATATTTTAAAATAAATCAA
1 TTTAAAATAAATCAATCCATA--CT--AATAAAT-TA
* ** **
6638065 TTCATACAACTACAAT-AATAAAT-C-AATCCA-TA
1 TT--TA-AAATA-AATCAATCCATACTAATAAATTA
* *
6638097 TTTTAAAATAAATTAATCCATACAAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
* *
6638130 TTTAAAATAAACCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
6638162 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
6638194 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
6638216 AACTACAATA
Statistics
Matches: 398, Mismatches: 37, Indels: 122
0.71 0.07 0.22
Matches are distributed among these distances:
20 1 0.00
22 40 0.10
23 8 0.02
24 3 0.01
25 1 0.00
26 36 0.09
27 1 0.00
28 7 0.02
29 5 0.01
30 31 0.08
31 17 0.04
32 227 0.57
33 5 0.01
34 4 0.01
37 1 0.00
40 8 0.02
41 3 0.01
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.32
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:6637813 original size:14 final size:14
Alignment explanation
Indices: 6637794--6637879 Score: 55
Period size: 14 Copynumber: 5.6 Consensus size: 14
6637784 CAATCCATAC
6637794 AAATAAATTATTTA
1 AAATAAATTATTTA
* *
6637808 AAATAAATCAATCCATA
1 AAATAAAT-TAT--TTA
6637825 CAAATAAATTATTTA
1 -AAATAAATTATTTA
* *
6637840 AAATAAATCAATCCATA
1 AAATAAAT-TAT--TTA
*
6637857 CTAATAAATTATTTA
1 -AAATAAATTATTTA
6637872 AAATAAAT
1 AAATAAAT
6637880 CAATCCATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
14 23 0.43
15 8 0.15
17 8 0.15
18 15 0.28
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:6637894 original size:22 final size:22
Alignment explanation
Indices: 6637868--6637910 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
6637858 TAATAAATTA
6637868 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
6637890 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
6637911 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:6637919 original size:22 final size:22
Alignment explanation
Indices: 6637870--6637918 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
6637860 ATAAATTATT
**
6637870 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
6637892 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
6637915 TAAA
1 TAAA
6637919 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:6637997 original size:80 final size:81
Alignment explanation
Indices: 6637804--6638214 Score: 441
Period size: 80 Copynumber: 5.0 Consensus size: 81
6637794 AAATAAATTA
*
6637804 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAA-TAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTAAA--A
6637868 TTTAAAATAAATCAATCCATAT
63 --T-AAATAAATCAATCCATAT
*
6637890 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-A
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
6637954 ATAAATCAATCCATAT
66 ATAAATCAATCCATAT
* *
6637970 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAAT-A
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
6638034 ATAAATCAATCCATAT
66 ATAAATCAATCCATAT
* * ***
6638050 TTTAAAATAAATCAATTCATAC-AACTACA--A--T--AATAAATCAATCCATA-TTTTAAAATA
1 TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATACAACTAAAATA
* * *
6638107 AATTAATCCATACAAATAAATT
65 AATAAATCAAT-C-CAT--A-T
* *
6638129 ATTTAAAATAAACCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACTAA-TAAATT
1 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTAAA--
6638193 ATTTAAAATAAATCAATCCATA
62 A--T-AAATAAATCAATCCATA
6638215 CAACTACAAT
Statistics
Matches: 282, Mismatches: 20, Indels: 44
0.82 0.06 0.13
Matches are distributed among these distances:
73 5 0.02
74 24 0.09
75 1 0.00
76 3 0.01
78 2 0.01
79 3 0.01
80 144 0.51
81 2 0.01
82 2 0.01
84 2 0.01
85 2 0.01
86 72 0.26
87 4 0.01
88 1 0.00
89 1 0.00
90 2 0.01
91 2 0.01
92 10 0.04
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (81 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
ATAAATCAATCCATAT
Found at i:6637999 original size:22 final size:23
Alignment explanation
Indices: 6637924--6637998 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
6637914 ATAAATTATT
6637924 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
6637946 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
6637972 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
6637995 TAAA
1 TAAA
6637999 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:6638061 original size:22 final size:22
Alignment explanation
Indices: 6638033--6638118 Score: 91
Period size: 22 Copynumber: 3.7 Consensus size: 22
6638023 CAACTACAAT
6638033 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
* * **
6638055 AATAAATCAATTCATACAACTACAA
1 AATAAATCAATCCAT---ATTTTAA
6638080 TAATAAATCAATCCATATTTTAA
1 -AATAAATCAATCCATATTTTAA
*
6638103 AATAAATTAATCCATA
1 AATAAATCAATCCATA
6638119 CAAATAAATT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
22 29 0.57
23 4 0.08
25 4 0.08
26 14 0.27
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Done.