Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009576.1 Hibiscus syriacus cultivar Beakdansim tig00116944_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: 1684752
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1141697 original size:25 final size:24
Alignment explanation
Indices: 1141643--1141697 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1141633 TGTTTATTAT
* *
1141643 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1141667 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1141693 TGTTT
1 TGTTT
1141698 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1142847 original size:18 final size:18
Alignment explanation
Indices: 1142826--1142870 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1142816 TCCACTTCGG
*
1142826 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1142844 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1142862 GAGCCATCA
1 GAGCCATCA
1142871 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1143406 original size:19 final size:20
Alignment explanation
Indices: 1143352--1143418 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1143342 TAGTTTACTT
* *
1143352 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1143372 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1143392 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1143411 TCGCAACG
1 TCGCAACG
1143419 ACAAAACCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1143435 original size:33 final size:33
Alignment explanation
Indices: 1143393--1143482 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
1143383 AAATGGCTAT
1143393 CGCAATGCGAAATGAAAATCGCAACGACAAAAC
1 CGCAATGCGAAATGAAAATCGCAACGACAAAAC
*
1143426 CGCAATGCGAAATGAAAATCGCAACGACAAAAT
1 CGCAATGCGAAATGAAAATCGCAACGACAAAAC
* *
1143459 CGTAACGCGAAATGAAAATCGCAA
1 CGCAATGCGAAATGAAAATCGCAA
1143483 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
CGCAATGCGAAATGAAAATCGCAACGACAAAAC
Found at i:1143448 original size:19 final size:19
Alignment explanation
Indices: 1143391--1143487 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
1143381 GGAAATGGCT
1143391 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1143410 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1143424 ACCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1143443 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
1143457 ATCGTAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1143476 ATCGCAATGCGA
1 ATCGCAATGCGA
1143488 TTTGTGTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 18 0.31
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 29 0.49
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1143516 original size:14 final size:13
Alignment explanation
Indices: 1143494--1143524 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1143484 GCGATTTGTG
1143494 TTTTGCGTTGCGA
1 TTTTGCGTTGCGA
1143507 TTTTGTCGTTGCGA
1 TTTTG-CGTTGCGA
1143521 TTTT
1 TTTT
1143525 CATTTCGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.06, C:0.13, G:0.26, T:0.55
Consensus pattern (13 bp):
TTTTGCGTTGCGA
Found at i:1143559 original size:20 final size:19
Alignment explanation
Indices: 1143525--1143580 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1143515 TTGCGATTTT
*
1143525 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1143544 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1143564 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
1143581 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1144043 original size:41 final size:41
Alignment explanation
Indices: 1143947--1144034 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
1143937 GACTCACCTG
* *
1143947 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGT-CCCTCCAACCGTTCAAGAGGCCACTA
* * *
1143989 TCCTCCCTCAAGAGTCCCTCCTACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCTCCAACCGTTCAAGAGGCCACTA
1144030 TCATC
1 TCATC
1144035 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 26 0.65
42 14 0.35
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.23
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:1145467 original size:14 final size:14
Alignment explanation
Indices: 1145448--1145483 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1145438 ATTGTTTAAT
1145448 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1145462 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1145476 TGATTTGT
1 TGATTTGT
1145484 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1145647 original size:19 final size:19
Alignment explanation
Indices: 1145623--1145704 Score: 137
Period size: 19 Copynumber: 4.3 Consensus size: 19
1145613 GCAACGAGAG
*
1145623 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1145642 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1145661 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
1145680 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1145699 AATCGC
1 AATCGC
1145705 CATTTTCGCG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 58 1.00
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1145728 original size:20 final size:20
Alignment explanation
Indices: 1145703--1145743 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1145693 AATGAAAATC
1145703 GCCATTTTCGCGTTGCGATA
1 GCCATTTTCGCGTTGCGATA
1145723 GCCATTTTCGCGTTGCGATA
1 GCCATTTTCGCGTTGCGATA
1145743 G
1 G
1145744 TCAAATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (20 bp):
GCCATTTTCGCGTTGCGATA
Found at i:1146095 original size:20 final size:20
Alignment explanation
Indices: 1146067--1146119 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1146057 GATTCTGTAT
*
1146067 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1146087 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1146107 TATCGCATTGCGA
1 TATCGCGTTGCGA
1146120 TTTTACCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1146151 original size:20 final size:21
Alignment explanation
Indices: 1146109--1146158 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1146099 ATAGTCAGTA
1146109 TCGCATTGCGATTTTACCAAT
1 TCGCATTGCGATTTTACCAAT
* **
1146130 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
1146150 TCGCATTGC
1 TCGCATTGC
1146159 AAATTGGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:1146601 original size:19 final size:19
Alignment explanation
Indices: 1146577--1146677 Score: 166
Period size: 19 Copynumber: 5.3 Consensus size: 19
1146567 GCAACGAGAG
*
1146577 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1146596 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1146615 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
*
1146634 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
1146653 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1146672 AATCGC
1 AATCGC
1146678 CATTTTCGCG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 77 1.00
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1146701 original size:20 final size:20
Alignment explanation
Indices: 1146676--1146716 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1146666 AATGAAAATC
1146676 GCCATTTTCGCGTTGCGATA
1 GCCATTTTCGCGTTGCGATA
1146696 GCCATTTTCGCGTTGCGATA
1 GCCATTTTCGCGTTGCGATA
1146716 G
1 G
1146717 TCAAATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (20 bp):
GCCATTTTCGCGTTGCGATA
Found at i:1147068 original size:20 final size:20
Alignment explanation
Indices: 1147040--1147092 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1147030 GATTCTGTAT
*
1147040 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1147060 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1147080 TATCGCATTGCGA
1 TATCGCGTTGCGA
1147093 TTTTACCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1147124 original size:20 final size:21
Alignment explanation
Indices: 1147082--1147131 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1147072 ATAGTCAGTA
1147082 TCGCATTGCGATTTTACCAAT
1 TCGCATTGCGATTTTACCAAT
* **
1147103 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
1147123 TCGCATTGC
1 TCGCATTGC
1147132 AAATTGGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:1147509 original size:973 final size:973
Alignment explanation
Indices: 1145623--1147525 Score: 3770
Period size: 973 Copynumber: 2.0 Consensus size: 973
1145613 GCAACGAGAG
**
1145623 AATCGCAATACGAAATGAAAATCGCAATGTGAAATGAAAATCGCAATGCAAAATGAAAATCGCAA
1 AATCGCAATACGAAATGAAAATCGCAATGCAAAATGAAAATCGCAATGCAAAATGAAAATCGCAA
1145688 TGCGAAATGAAAATCGCCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAA
66 TGCGAAATGAAAATCGCCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAA
1145753 TGTCTAACACCATGAACATTCTCTCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAAC
131 TGTCTAACACCATGAACATTCTCTCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAAC
1145818 ATTAGATGATTTCATGGTTGTAAATTAATTTACTAAACAAACGAGCTGCGAAACTAAGACCTGTT
196 ATTAGATGATTTCATGGTTGTAAATTAATTTACTAAACAAACGAGCTGCGAAACTAAGACCTGTT
1145883 GCCGGATGGGGAAGGATGTAGGAATGGATGTCGCCAGAGAGAGTGAAAGATGGAGATGGAATGAG
261 GCCGGATGGGGAAGGATGTAGGAATGGATGTCGCCAGAGAGAGTGAAAGATGGAGATGGAATGAG
1145948 TTACGATTTAGGGATTTAGGTTATGAGTTGTTGCTGCTGCGTAGATATATACCCAAAAAATTTGT
326 TTACGATTTAGGGATTTAGGTTATGAGTTGTTGCTGCTGCGTAGATATATACCCAAAAAATTTGT
1146013 GTTGCGAAACTAAAACCTGTTGCGAACTTTGAAAATCGCATTGCGATTCTGTATTATCTCGTTGC
391 GTTGCGAAACTAAAACCTGTTGCGAACTTTGAAAATCGCATTGCGATTCTGTATTATCTCGTTGC
1146078 GAAAGTCAGTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTACCAATTCGCGTTGCGATT
456 GAAAGTCAGTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTACCAATTCGCGTTGCGATT
1146143 TACTTATTCGCATTGCAAATTGGGAAAATCGCAACAACACTGTAGACCATCGCAACGCGATTTCC
521 TACTTATTCGCATTGCAAATTGGGAAAATCGCAACAACACTGTAGACCATCGCAACGCGATTTCC
1146208 AACTATCGCAACGCGAATTTGCGATAATGGAGATCGCGTTGCGAATTAGCGATCGCATTGCGATT
586 AACTATCGCAACGCGAATTTGCGATAATGGAGATCGCGTTGCGAATTAGCGATCGCATTGCGATT
1146273 TTGTTGGTCATTTTGGCAAATCCGGAAAAAGTTGGTTAAAATCGTATATTATAAGGCATTTTTGG
651 TTGTTGGTCATTTTGGCAAATCCGGAAAAAGTTGGTTAAAATCGTATATTATAAGGCATTTTTGG
1146338 TCACTAAGGCGATTTTCTCATTAAAGATCTTTCGACTTCAATTCCGACTTTTGTCTTCAATATAT
716 TCACTAAGGCGATTTTCTCATTAAAGATCTTTCGACTTCAATTCCGACTTTTGTCTTCAATATAT
1146403 CTTCTCTAAAGACTATTGTTTTATCCAATATTCGTTTATCAAATAGTTTGCCTGATGATCTATGT
781 CTTCTCTAAAGACTATTGTTTTATCCAATATTCGTTTATCAAATAGTTTGCCTGATGATCTATGT
1146468 CATCATCTTCCCAAACTTGAAGGGCTTTATTTGGGCTTAAATGAATTATCCGGTCATATTCCACC
846 CATCATCTTCCCAAACTTGAAGGGCTTTATTTGGGCTTAAATGAATTATCCGGTCATATTCCACC
1146533 AAGTATAGGCAAATGCAGCACGAAACTGACTATCGCAACGAGAGAATCGCAATACGAAATGAA
911 AAGTATAGGCAAATGCAGCACGAAACTGACTATCGCAACGAGAGAATCGCAATACGAAATGAA
**
1146596 AATCGCAATGTGAAATGAAAATCGCAATGCAAAATGAAAATCGCAATGCAAAATGAAAATCGCAA
1 AATCGCAATACGAAATGAAAATCGCAATGCAAAATGAAAATCGCAATGCAAAATGAAAATCGCAA
1146661 TGCGAAATGAAAATCGCCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAA
66 TGCGAAATGAAAATCGCCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAA
1146726 TGTCTAACACCATGAACATTCTCTCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAAC
131 TGTCTAACACCATGAACATTCTCTCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAAC
1146791 ATTAGATGATTTCATGGTTGTAAATTAATTTACTAAACAAACGAGCTGCGAAACTAAGACCTGTT
196 ATTAGATGATTTCATGGTTGTAAATTAATTTACTAAACAAACGAGCTGCGAAACTAAGACCTGTT
1146856 GCCGGATGGGGAAGGATGTAGGAATGGATGTCGCCAGAGAGAGTGAAAGATGGAGATGGAATGAG
261 GCCGGATGGGGAAGGATGTAGGAATGGATGTCGCCAGAGAGAGTGAAAGATGGAGATGGAATGAG
1146921 TTACGATTTAGGGATTTAGGTTATGAGTTGTTGCTGCTGCGTAGATATATACCCAAAAAATTTGT
326 TTACGATTTAGGGATTTAGGTTATGAGTTGTTGCTGCTGCGTAGATATATACCCAAAAAATTTGT
1146986 GTTGCGAAACTAAAACCTGTTGCGAACTTTGAAAATCGCATTGCGATTCTGTATTATCTCGTTGC
391 GTTGCGAAACTAAAACCTGTTGCGAACTTTGAAAATCGCATTGCGATTCTGTATTATCTCGTTGC
1147051 GAAAGTCAGTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTACCAATTCGCGTTGCGATT
456 GAAAGTCAGTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTACCAATTCGCGTTGCGATT
1147116 TACTTATTCGCATTGCAAATTGGGAAAATCGCAACAACACTGTAGACCATCGCAACGCGATTTCC
521 TACTTATTCGCATTGCAAATTGGGAAAATCGCAACAACACTGTAGACCATCGCAACGCGATTTCC
1147181 AACTATCGCAACGCGAATTTGCGATAATGGAGATCGCGTTGCGAATTAGCGATCGCATTGCGATT
586 AACTATCGCAACGCGAATTTGCGATAATGGAGATCGCGTTGCGAATTAGCGATCGCATTGCGATT
1147246 TTGTTGGTCATTTTGGCAAATCCGGAAAAAGTTGGTTAAAATCGTATATTATAAGGCATTTTTGG
651 TTGTTGGTCATTTTGGCAAATCCGGAAAAAGTTGGTTAAAATCGTATATTATAAGGCATTTTTGG
1147311 TCACTAAGGCGATTTTCTCATTAAAGATCTTTCGACTTCAATTCCGACTTTTGTCTTCAATATAT
716 TCACTAAGGCGATTTTCTCATTAAAGATCTTTCGACTTCAATTCCGACTTTTGTCTTCAATATAT
1147376 CTTCTCTAAAGACTATTGTTTTATCCAATATTCGTTTATCAAATAGTTTGCCTGATGATCTATGT
781 CTTCTCTAAAGACTATTGTTTTATCCAATATTCGTTTATCAAATAGTTTGCCTGATGATCTATGT
1147441 CATCATCTTCCCAAACTTGAAGGGCTTTATTTGGGCTTAAATGAATTATCCGGTCATATTCCACC
846 CATCATCTTCCCAAACTTGAAGGGCTTTATTTGGGCTTAAATGAATTATCCGGTCATATTCCACC
1147506 AAGTATAGGCAAATGCAGCA
911 AAGTATAGGCAAATGCAGCA
1147526 ACCTTCAAAT
Statistics
Matches: 926, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
973 926 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (973 bp):
AATCGCAATACGAAATGAAAATCGCAATGCAAAATGAAAATCGCAATGCAAAATGAAAATCGCAA
TGCGAAATGAAAATCGCCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAA
TGTCTAACACCATGAACATTCTCTCATGACCCTCCAAAACACAAATCTATCCAAACATGATCAAC
ATTAGATGATTTCATGGTTGTAAATTAATTTACTAAACAAACGAGCTGCGAAACTAAGACCTGTT
GCCGGATGGGGAAGGATGTAGGAATGGATGTCGCCAGAGAGAGTGAAAGATGGAGATGGAATGAG
TTACGATTTAGGGATTTAGGTTATGAGTTGTTGCTGCTGCGTAGATATATACCCAAAAAATTTGT
GTTGCGAAACTAAAACCTGTTGCGAACTTTGAAAATCGCATTGCGATTCTGTATTATCTCGTTGC
GAAAGTCAGTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTACCAATTCGCGTTGCGATT
TACTTATTCGCATTGCAAATTGGGAAAATCGCAACAACACTGTAGACCATCGCAACGCGATTTCC
AACTATCGCAACGCGAATTTGCGATAATGGAGATCGCGTTGCGAATTAGCGATCGCATTGCGATT
TTGTTGGTCATTTTGGCAAATCCGGAAAAAGTTGGTTAAAATCGTATATTATAAGGCATTTTTGG
TCACTAAGGCGATTTTCTCATTAAAGATCTTTCGACTTCAATTCCGACTTTTGTCTTCAATATAT
CTTCTCTAAAGACTATTGTTTTATCCAATATTCGTTTATCAAATAGTTTGCCTGATGATCTATGT
CATCATCTTCCCAAACTTGAAGGGCTTTATTTGGGCTTAAATGAATTATCCGGTCATATTCCACC
AAGTATAGGCAAATGCAGCACGAAACTGACTATCGCAACGAGAGAATCGCAATACGAAATGAA
Found at i:1149976 original size:29 final size:30
Alignment explanation
Indices: 1149944--1150010 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
1149934 AATCAATGTA
*
1149944 ACCACCGAACT-TTCAATTGAATCAATCAG
1 ACCACCGAACTATTCAATTGAACCAATCAG
* *
1149973 ACCACCCAACTATTTAATTGAACCAATCAG
1 ACCACCGAACTATTCAATTGAACCAATCAG
1150003 ACCACCGA
1 ACCACCGA
1150011 CCATTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.39, C:0.31, G:0.09, T:0.21
Consensus pattern (30 bp):
ACCACCGAACTATTCAATTGAACCAATCAG
Found at i:1150442 original size:16 final size:17
Alignment explanation
Indices: 1150405--1150442 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1150395 TGACAAAAAA
*
1150405 TTAAACAAATTATTTGT
1 TTAAACAAATTATTTAT
1150422 TTAAACAAATTA-TTAT
1 TTAAACAAATTATTTAT
1150438 TTAAA
1 TTAAA
1150443 TTAATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAACAAATTATTTAT
Found at i:1150655 original size:28 final size:29
Alignment explanation
Indices: 1150594--1150649 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
1150584 AAAATCCATT
*
1150594 TAATTCGATTCGGTTAATAATTTTTAAAA
1 TAATTCGATTCGGTTAATAATTTTCAAAA
*
1150623 TAATTCGGTT-GGTTAATAATTTTCAAA
1 TAATTCGATTCGGTTAATAATTTTCAAA
1150650 TAAATTTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (29 bp):
TAATTCGATTCGGTTAATAATTTTCAAAA
Found at i:1150659 original size:25 final size:26
Alignment explanation
Indices: 1150605--1150661 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
1150595 AATTCGATTC
*
1150605 GGTTAATAATTTTTAAAATAATTCGGTT
1 GGTTAATAATTTTCAAAATAATT--GTT
1150633 GGTTAATAATTTTC-AAATAAATT-TT
1 GGTTAATAATTTTCAAAAT-AATTGTT
1150658 GGTT
1 GGTT
1150662 CGATTAACCG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.22
27 4 0.15
28 17 0.63
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (26 bp):
GGTTAATAATTTTCAAAATAATTGTT
Found at i:1150753 original size:96 final size:94
Alignment explanation
Indices: 1150623--1150859 Score: 286
Period size: 96 Copynumber: 2.5 Consensus size: 94
1150613 ATTTTTAAAA
*
1150623 TAATTCGGTT-GGTTAATAATTTTCAAATAAATTTTGGTTCGATTAA-C-C-GAATTTTTGCTTC
1 TAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCACTGAAATTTTGCTTC
* *
1150684 GATTAATTCGGTTAATAATTTTAAAAAAATCATT
66 GATTAATTCAGTTAAT-A----AAAAAAATCAGT
1150718 TAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCAAACTGAAATTTTGCT
1 TAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACC--ACTGAAATTTTGCT
**
1150783 TCGATTAATTCAGTTAATAAAAAAAATTGGT
64 TCGATTAATTCAGTTAATAAAAAAAATCAGT
* * * * *
1150814 TAATTCGATTCGATTAATAATTTTTAAATTAA-TTTGGTTCGGTTAA
1 TAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAA
1150860 TAATTTTCGA
Statistics
Matches: 126, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
95 23 0.18
96 73 0.58
97 1 0.01
100 2 0.02
101 27 0.21
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (94 bp):
TAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCACTGAAATTTTGCTTC
GATTAATTCAGTTAATAAAAAAAATCAGT
Found at i:1150962 original size:117 final size:117
Alignment explanation
Indices: 1150807--1151094 Score: 382
Period size: 117 Copynumber: 2.5 Consensus size: 117
1150797 TAATAAAAAA
* * * * *
1150807 AATT-GGTTAATTCGATTCGATTAATAATTTTTAAATTAATTTGGTTCGGTTAATAATTTTCGAA
1 AATTCGGTTAATTTGGTTCGGTTAATAATTTTCAAATTAATTTGGTTCGGTTAATAATTTTCAAA
* * * **
1150871 TAACTTTTAGTTCGATTAACCGAAATGAATTAAC-CAAATTTTTGCTTCAATT
66 TAAATTTTAGTTCGATTAACCGAAACGAATTAACAAAAAAATTT-CTTCAATT
* * *
1150923 AATTCGGTTAATTTGGTTTGGTTAATAATTTTCAAATTAATTCGGTTTGGTTAATAATTTTCAAA
1 AATTCGGTTAATTTGGTTCGGTTAATAATTTTCAAATTAATTTGGTTCGGTTAATAATTTTCAAA
* * *
1150988 TAAATTTTGGTTCGATTAACCGAACCGAATTAACAAAAAAATTTCTTCGATT
66 TAAATTTTAGTTCGATTAACCGAAACGAATTAACAAAAAAATTTCTTCAATT
* *
1151040 AATTCGGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAA
1 AATTCGGTTAATTTGGTTCGGTTAATAATTTTCAAATTAA-TTTGGTTCGGTTAA
1151095 CCGAACCGTA
Statistics
Matches: 148, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
116 4 0.03
117 127 0.86
118 17 0.11
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (117 bp):
AATTCGGTTAATTTGGTTCGGTTAATAATTTTCAAATTAATTTGGTTCGGTTAATAATTTTCAAA
TAAATTTTAGTTCGATTAACCGAAACGAATTAACAAAAAAATTTCTTCAATT
Found at i:1150963 original size:29 final size:29
Alignment explanation
Indices: 1150930--1150999 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
1150920 ATTAATTCGG
1150930 TTAATTTGGTTTGGTTAATAATTTTCAAA
1 TTAATTTGGTTTGGTTAATAATTTTCAAA
*
1150959 TTAATTCGGTTTGGTTAATAATTTTCAAA
1 TTAATTTGGTTTGGTTAATAATTTTCAAA
*
1150988 TAAATTTTGGTT
1 TTAA-TTTGGTT
1151000 CGATTAACCG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 31 0.84
30 6 0.16
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.51
Consensus pattern (29 bp):
TTAATTTGGTTTGGTTAATAATTTTCAAA
Found at i:1151066 original size:88 final size:89
Alignment explanation
Indices: 1150959--1151120 Score: 290
Period size: 88 Copynumber: 1.8 Consensus size: 89
1150949 AATTTTCAAA
*
1150959 TTAATTCGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAA-CA
1 TTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCA
1151023 AAAAAATTTCTTCGATTAATTCGG
66 AAAAAATTTCTTCGATTAATTCGG
* *
1151047 TTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGTATTAACCA
1 TTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCA
1151112 AAAAAATTT
66 AAAAAATTT
1151121 ATTTAACTGT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
88 59 0.84
89 11 0.16
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (89 bp):
TTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCA
AAAAAATTTCTTCGATTAATTCGG
Found at i:1151416 original size:268 final size:272
Alignment explanation
Indices: 1150898--1151455 Score: 1061
Period size: 268 Copynumber: 2.1 Consensus size: 272
1150888 AACCGAAATG
*
1150898 AATTAACCAAATTTTTGCTTCAATTAATTCGGTTAATTTGGTTTGGTTAATAATTTTCAAATTAA
1 AATTAACCGAATTTTTGCTTCAATTAATTCGGTTAATTTGGTTTGGTTAATAATTTTCAAATTAA
1150963 TTCGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACAAAAAA
66 TTCGGTTTGGTTAATAATTTTCAAATAAA-TTT-GTTCGATTAACCGAACCGAATTAACAAAAAA
1151028 ATTTCTTCGATTAATTCGGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATT
129 ATTTCTTCGATTAATTCGGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATT
1151093 AACCGAACCGTATTAACCAAAAAAATTTATTTAACTGTTAATCGAACCAAAATAAATTTGAAAAT
194 AACCGAACCGTATTAACCAAAAAAATTTATTTAACTGTTAATCGAACCAAAATAAATTTGAAAAT
1151158 TACTAACCGAATCA
259 TACTAACCGAATCA
1151172 AATTAACCGAATTTTTGCTTCAATTAATTCGGTTAATTTGGTTTGGTTAATAATTTTCAAATTAA
1 AATTAACCGAATTTTTGCTTCAATTAATTCGGTTAATTTGGTTTGGTTAATAATTTTCAAATTAA
1151237 -TCGGTTTGGTTAATAATTTTCAAATAAA-TT-TTCGATTAACCGAACCGAATTAACAAAAAAAT
66 TTCGGTTTGGTTAATAATTTTCAAATAAATTTGTTCGATTAACCGAACCGAATTAACAAAAAAAT
1151299 TTCTTCGATTAATTCGGTTAATTTGGTTCGGTTAATAA-TTTCAAATAAATTTTGGTTCGATTAA
131 TTCTTCGATTAATTCGGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAA
1151363 CCGAACCGTATTAACCAAAAAAATTTATTTAACTGTTAATCGAACCAAAATAAATTTGAAAATTA
196 CCGAACCGTATTAACCAAAAAAATTTATTTAACTGTTAATCGAACCAAAATAAATTTGAAAATTA
1151428 CTAACCGAATCA
261 CTAACCGAATCA
1151440 AATTAACCGAATTTTT
1 AATTAACCGAATTTTT
1151456 TTCTTTAACC
Statistics
Matches: 283, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
268 119 0.42
269 70 0.25
271 2 0.01
273 28 0.10
274 64 0.23
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (272 bp):
AATTAACCGAATTTTTGCTTCAATTAATTCGGTTAATTTGGTTTGGTTAATAATTTTCAAATTAA
TTCGGTTTGGTTAATAATTTTCAAATAAATTTGTTCGATTAACCGAACCGAATTAACAAAAAAAT
TTCTTCGATTAATTCGGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAA
CCGAACCGTATTAACCAAAAAAATTTATTTAACTGTTAATCGAACCAAAATAAATTTGAAAATTA
CTAACCGAATCA
Found at i:1151433 original size:69 final size:69
Alignment explanation
Indices: 1151360--1151510 Score: 158
Period size: 69 Copynumber: 2.2 Consensus size: 69
1151350 TTGGTTCGAT
* ** *
1151360 TAACCGAACCGTATTAACCAAAAAAATTTATTTAACTGTTAATCGAACCAAAATAAATTTGAAAA
1 TAACCGAACCGAATTAACCAAAAAAATTTATTTAACCATTAATCAAACCAAAATAAATTTGAAAA
1151425 TTAC
66 TTAC
* * * **** * * **
1151429 TAACCGAATCAAATTAACCGAATTTTTTTCTTTAACCATTAATCAAACCGAAATTTATTTGAAAA
1 TAACCGAACCGAATTAACCAAAAAAATTTATTTAACCATTAATCAAACCAAAATAAATTTGAAAA
*
1151494 TTAT
66 TTAC
1151498 TAACCGAACCGAA
1 TAACCGAACCGAA
1151511 AAAAATTCGG
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.31
Consensus pattern (69 bp):
TAACCGAACCGAATTAACCAAAAAAATTTATTTAACCATTAATCAAACCAAAATAAATTTGAAAA
TTAC
Found at i:1152011 original size:30 final size:29
Alignment explanation
Indices: 1151976--1152041 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 29
1151966 ATTAATGACA
*
1151976 GGTGGTCTGATTGATTCAATTAAATAGTTG
1 GGTGGTCTGATTGATTCAATTAAA-AGTTC
*
1152006 GGTGGTCTGATTGATTCAATTGAAAGTTC
1 GGTGGTCTGATTGATTCAATTAAAAGTTC
1152035 GGTGGTC
1 GGTGGTC
1152042 ACATTAACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 11 0.32
30 23 0.68
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.38
Consensus pattern (29 bp):
GGTGGTCTGATTGATTCAATTAAAAGTTC
Found at i:1152692 original size:23 final size:23
Alignment explanation
Indices: 1152666--1152777 Score: 161
Period size: 23 Copynumber: 4.9 Consensus size: 23
1152656 TCGAAATTCA
* * * *
1152666 AGCTTGATTGAAACTTGATTTTG
1 AGCTCGATTCAAACTCGATTGTG
* *
1152689 AGCTCAATTCAAACTCGATTTTG
1 AGCTCGATTCAAACTCGATTGTG
1152712 AGCTCGATTCAAACTCGATTGTG
1 AGCTCGATTCAAACTCGATTGTG
1152735 AGCTCGATTCAAACTCGATTGTG
1 AGCTCGATTCAAACTCGATTGTG
*
1152758 AGCTCGATTCAAGCTCGATT
1 AGCTCGATTCAAACTCGATT
1152778 TGGAAATAGT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 82 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (23 bp):
AGCTCGATTCAAACTCGATTGTG
Found at i:1152730 original size:11 final size:11
Alignment explanation
Indices: 1152689--1152777 Score: 61
Period size: 11 Copynumber: 7.8 Consensus size: 11
1152679 CTTGATTTTG
*
1152689 AGCTCAATTCA
1 AGCTCGATTCA
* **
1152700 AACTCGATTTTG
1 AGCTCGA-TTCA
1152712 AGCTCGATTCA
1 AGCTCGATTCA
* **
1152723 AACTCGATTGTG
1 AGCTCGATT-CA
1152735 AGCTCGATTCA
1 AGCTCGATTCA
* **
1152746 AACTCGATTGTG
1 AGCTCGATT-CA
1152758 AGCTCGATTCA
1 AGCTCGATTCA
1152769 AGCTCGATT
1 AGCTCGATT
1152778 TGGAAATAGT
Statistics
Matches: 56, Mismatches: 19, Indels: 6
0.69 0.23 0.07
Matches are distributed among these distances:
11 32 0.57
12 24 0.43
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:1153635 original size:7 final size:7
Alignment explanation
Indices: 1153521--1153642 Score: 75
Period size: 7 Copynumber: 17.1 Consensus size: 7
1153511 TTTTTAATAA
1153521 TTAAGGGT
1 TTAA-GGT
*
1153529 TTAGGGT
1 TTAAGGT
1153536 TTAAGG-
1 TTAAGGT
*
1153542 GTAAGGT
1 TTAAGGT
*
1153549 TTAAGGG
1 TTAAGGT
*
1153556 TTAGGGT
1 TTAAGGT
*
1153563 TTAATGT
1 TTAAGGT
*
1153570 TTAATGT
1 TTAAGGT
*
1153577 TTAGGGT
1 TTAAGGT
*
1153584 TTAAGAT
1 TTAAGGT
*
1153591 TTATGGT
1 TTAAGGT
*
1153598 TTATATAGT
1 TTA-A-GGT
*
1153607 TTAAGGC
1 TTAAGGT
*
1153614 TTAAAGT
1 TTAAGGT
**
1153621 TTGTGGT
1 TTAAGGT
1153628 TTAAGGT
1 TTAAGGT
*
1153635 TTAGGGT
1 TTAAGGT
1153642 T
1 T
1153643 CATTGCAAAG
Statistics
Matches: 84, Mismatches: 27, Indels: 7
0.71 0.23 0.06
Matches are distributed among these distances:
6 5 0.06
7 70 0.83
8 4 0.05
9 5 0.06
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.44
Consensus pattern (7 bp):
TTAAGGT
Found at i:1153807 original size:17 final size:16
Alignment explanation
Indices: 1153787--1153828 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1153777 ACAACAATTT
*
1153787 AAATAATTAGTTATTAA
1 AAATAATTA-TCATTAA
1153804 AAAT-ATTATCATTAA
1 AAATAATTATCATTAA
1153819 AAATATATTA
1 AAATA-ATTA
1153829 AATATTTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 10 0.45
16 4 0.18
17 8 0.36
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
AAATAATTATCATTAA
Found at i:1154139 original size:12 final size:11
Alignment explanation
Indices: 1154073--1154135 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
1154063 GTATTATAGA
1154073 ATTTTTAATAT
1 ATTTTTAATAT
1154084 ATTTTTAA-A-
1 ATTTTTAATAT
1154093 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
1154104 ATCAATAGTGT
1 ATTTTTAATAT
1154115 ATTTTTAATAT
1 ATTTTTAATAT
1154126 ATTTTTAATA
1 ATTTTTAATA
1154136 ATATAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:1154747 original size:47 final size:46
Alignment explanation
Indices: 1154650--1154749 Score: 114
Period size: 47 Copynumber: 2.1 Consensus size: 46
1154640 CCACGTAGGG
* * *
1154650 ATATAGCGCGGGGCAGGGGCCGCGCCTTACCTTTAATTCTGATTTAT
1 ATATAACGCGGGGCAGGGGCCGCGCCATACCTTTAA-TCTGATTAAT
*
1154697 ATATAACGCGGGGCAGGGGCTG-GACCATACCTTTAA-CTGATATAATT
1 ATATAACGCGGGGCAGGGGCCGCG-CCATACCTTTAATCTGAT-TAA-T
1154744 ATATAA
1 ATATAA
1154750 GGCGCGGTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
45 5 0.11
46 3 0.07
47 38 0.83
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (46 bp):
ATATAACGCGGGGCAGGGGCCGCGCCATACCTTTAATCTGATTAAT
Found at i:1158436 original size:35 final size:34
Alignment explanation
Indices: 1158351--1158437 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
1158341 AAAATAATTT
* *
1158351 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGA
* *
1158385 TAAATGATAACCAAATTACAATAACTGATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGA
1158423 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1158438 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGA
Found at i:1161738 original size:27 final size:28
Alignment explanation
Indices: 1161680--1161748 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
1161670 AGGTGATGGT
1161680 GGCGGCGGCGGCATCGGGTAAGGGAATA
1 GGCGGCGGCGGCATCGGGTAAGGGAATA
* * **
1161708 -GCGGCGGCGACATCTGGTAATTGAA-A
1 GGCGGCGGCGGCATCGGGTAAGGGAATA
*
1161734 GGCGGTGGCGGCATC
1 GGCGGCGGCGGCATC
1161749 ATATATGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.20, C:0.20, G:0.45, T:0.14
Consensus pattern (28 bp):
GGCGGCGGCGGCATCGGGTAAGGGAATA
Found at i:1163890 original size:2 final size:2
Alignment explanation
Indices: 1163885--1163912 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1163875 TTTTTTTTGG
1163885 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
1163913 CTTCGCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1165176 original size:12 final size:12
Alignment explanation
Indices: 1165159--1165183 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1165149 GTACTTATAC
1165159 TAGGGCTCGATT
1 TAGGGCTCGATT
1165171 TAGGGCTCGATT
1 TAGGGCTCGATT
1165183 T
1 T
1165184 GTTTTACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (12 bp):
TAGGGCTCGATT
Found at i:1166887 original size:12 final size:12
Alignment explanation
Indices: 1166870--1166896 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1166860 GATGTGGCAA
1166870 AGCTCAACAATC
1 AGCTCAACAATC
1166882 AGCTCAACAATC
1 AGCTCAACAATC
1166894 AGC
1 AGC
1166897 CCAAGGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.33, G:0.11, T:0.15
Consensus pattern (12 bp):
AGCTCAACAATC
Found at i:1169112 original size:14 final size:14
Alignment explanation
Indices: 1169086--1169135 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
1169076 ATTTTGTTCT
*
1169086 CTTTCAATCTAATC
1 CTTTCATTCTAATC
*
1169100 CTTACATTCTAATC
1 CTTTCATTCTAATC
1169114 CTTTCATTCTAATC
1 CTTTCATTCTAATC
1169128 CTTTCATT
1 CTTTCATT
1169136 GTTTTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (14 bp):
CTTTCATTCTAATC
Found at i:1169167 original size:3 final size:3
Alignment explanation
Indices: 1169159--1169188 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1169149 AGTTTTACCG
1169159 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1169189 TTGATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1173876 original size:2 final size:2
Alignment explanation
Indices: 1173869--1173903 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1173859 GTGCCTTTAT
1173869 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1173904 TTGGTGTAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1177787 original size:22 final size:21
Alignment explanation
Indices: 1177745--1177797 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1177735 ATTCTGACTA
1177745 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
1177766 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGA-TTTCCCAAAT
*
1177787 TCGCAATGCGA
1 TCGCATTGCGA
1177798 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1177808 original size:20 final size:20
Alignment explanation
Indices: 1177783--1177891 Score: 116
Period size: 20 Copynumber: 5.5 Consensus size: 20
1177773 GCGATTTTCC
*
1177783 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGATTACG
1177803 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
*
1177823 TAAATCGCAATGTGAATTA-G
1 TAAATCGCAATGCG-ATTACG
* *
1177843 GAAACTCGTAATGCGATTACG
1 TAAA-TCGCAATGCGATTACG
* *
1177864 T-ATTCGCATTGCGATTTACG
1 TAAATCGCAATGCGA-TTACG
1177884 T-AATCGCA
1 TAAATCGCA
1177892 TTGCAAATCT
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
19 9 0.12
20 53 0.71
21 13 0.17
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (20 bp):
TAAATCGCAATGCGATTACG
Found at i:1177878 original size:19 final size:20
Alignment explanation
Indices: 1177744--1177922 Score: 89
Period size: 20 Copynumber: 8.8 Consensus size: 20
1177734 GATTCTGACT
* **
1177744 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTACGTA
* * *
1177764 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGATTTACGT-A
* *
1177786 ATCGCAATGCGA-ATACGTAA
1 ATCGCATTGCGATTTACGT-A
*
1177806 ATCGCAATGCGA-TTACGTAA
1 ATCGCATTGCGATTTACGT-A
* * * * *
1177826 ATCGCAATGTGAATTAGGAA
1 ATCGCATTGCGATTTACGTA
* *
1177846 ACTCGTAATGCGA-TTACGTA
1 A-TCGCATTGCGATTTACGTA
*
1177866 TTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
*
1177886 ATCGCATTGCAAATCTTAC-T-
1 ATCGCATTGC-GAT-TTACGTA
*
1177906 ATCGCAATGCGATTTAC
1 ATCGCATTGCGATTTAC
1177923 ATAGCGCCAT
Statistics
Matches: 129, Mismatches: 23, Indels: 16
0.77 0.14 0.10
Matches are distributed among these distances:
18 4 0.03
19 11 0.09
20 68 0.53
21 40 0.31
22 6 0.05
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (20 bp):
ATCGCATTGCGATTTACGTA
Found at i:1177892 original size:20 final size:20
Alignment explanation
Indices: 1177785--1177922 Score: 106
Period size: 20 Copynumber: 6.9 Consensus size: 20
1177775 GATTTTCCTA
*
1177785 AATCGCAATGCGA-ATACGT
1 AATCGCAATGCGATTTACGT
1177804 AAATCGCAATGCGA-TTACGT
1 -AATCGCAATGCGATTTACGT
* * * *
1177824 AAATCGCAATGTGAATTAGGA
1 -AATCGCAATGCGATTTACGT
*
1177845 AACTCGTAATGCGA-TTACGT
1 AA-TCGCAATGCGATTTACGT
* *
1177865 ATTCGCATTGCGATTTACGT
1 AATCGCAATGCGATTTACGT
* *
1177885 AATCGCATTGCAAATCTTAC-T
1 AATCGCAATGC-GAT-TTACGT
1177906 -ATCGCAATGCGATTTAC
1 AATCGCAATGCGATTTAC
1177923 ATAGCGCCAT
Statistics
Matches: 98, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
18 4 0.04
19 11 0.11
20 63 0.64
21 16 0.16
22 4 0.04
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (20 bp):
AATCGCAATGCGATTTACGT
Found at i:1178512 original size:21 final size:21
Alignment explanation
Indices: 1178451--1178529 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
1178441 TTCTAAACTT
1178451 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
1178471 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
1178491 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
1178512 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
1178530 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:1178533 original size:14 final size:14
Alignment explanation
Indices: 1178511--1178575 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
1178501 CGAGAGAAAT
1178511 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
1178525 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
1178543 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
1178558 GATAATCGCAACGC
1 GAAAATCGCAACGA
1178572 GAAA
1 GAAA
1178576 CCAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1178547 original size:33 final size:33
Alignment explanation
Indices: 1178506--1178586 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1178496 CGCAACGAGA
1178506 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1178539 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1178572 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1178587 TTGCAATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1178618 original size:19 final size:19
Alignment explanation
Indices: 1178587--1178693 Score: 98
Period size: 20 Copynumber: 5.8 Consensus size: 19
1178577 CAAAATCGCA
*
1178587 TTGCAATTTTCATTTCTCG
1 TTGCGATTTTCATTTCTCG
* *
1178606 TTGCGATTCTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
1178625 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
** *
1178639 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CTCG
*
1178659 TTGCAATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCTCG
1178679 TTGCGATTTTCATTT
1 TTGCGATTTTCATTT
1178694 TAACCAAAAG
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
14 10 0.14
16 2 0.03
17 2 0.03
19 24 0.35
20 30 0.43
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:1180586 original size:94 final size:93
Alignment explanation
Indices: 1180385--1180663 Score: 390
Period size: 94 Copynumber: 3.0 Consensus size: 93
1180375 TAGATTGCTT
* *
1180385 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACAC-TGAAGTTAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTTGAAGTTAGTA
1180445 TTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTC-TTTGTTTTGTCTTTTGGTTGAA
1180473 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACT-TGAAGTTAGT
1180538 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
1180567 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACT-TGAAGTTAGT
* **
1180632 ATTTAGCAACACTGTTTTGTCTTTTGGTTGAA
65 ATTT-G--TCTTTGTTTTGTCTTTTGGTTGAA
1180664 GTGAAAATCG
Statistics
Matches: 172, Mismatches: 9, Indels: 11
0.90 0.05 0.06
Matches are distributed among these distances:
88 35 0.20
90 3 0.02
91 2 0.01
92 7 0.04
93 20 0.12
94 83 0.48
95 1 0.01
97 21 0.12
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTTGAAGTTAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1180710 original size:19 final size:19
Alignment explanation
Indices: 1180666--1180775 Score: 131
Period size: 19 Copynumber: 6.0 Consensus size: 19
1180656 TGGTTGAAGT
* *
1180666 GAAAATCGCAACGAGAGAAT
1 GAAAATCGCAACGCGA-AAC
*
1180686 GAAAATCGCAATGCGAAAC
1 GAAAATCGCAACGCGAAAC
*
1180705 GAAAATCGCAATGCGAAAC
1 GAAAATCGCAACGCGAAAC
*
1180724 GAAAATCGCAACGCGAAAT
1 GAAAATCGCAACGCGAAAC
1180743 GAAAATCGCAA--CG--AC
1 GAAAATCGCAACGCGAAAC
1180758 -AAAATCGCAACGCGAAAC
1 GAAAATCGCAACGCGAAAC
1180776 TATAATTGCG
Statistics
Matches: 80, Mismatches: 6, Indels: 10
0.83 0.06 0.10
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 49 0.61
20 14 0.17
ACGTcount: A:0.48, C:0.22, G:0.21, T:0.09
Consensus pattern (19 bp):
GAAAATCGCAACGCGAAAC
Found at i:1180826 original size:33 final size:33
Alignment explanation
Indices: 1180784--1180878 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
1180774 ACTATAATTG
* *
1180784 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1180817 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
1180850 CGTTGTGATTTTCGTTTCGCGTTGCGATT
1 CGTTGCGATTTTCATTTCGCGTTGCGATT
1180879 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1180841 original size:19 final size:19
Alignment explanation
Indices: 1180783--1180896 Score: 104
Period size: 19 Copynumber: 6.5 Consensus size: 19
1180773 AACTATAATT
1180783 GCGTTGCGATTTTCATTTC
1 GCGTTGCGATTTTCATTTC
* *
1180802 GCATTGTGA--TTC---TC
1 GCGTTGCGATTTTCATTTC
*
1180816 TCGTTGCGATTTTCATTTC
1 GCGTTGCGATTTTCATTTC
1180835 GCGTTGCGA--TTC---TC
1 GCGTTGCGATTTTCATTTC
* * *
1180849 TCGTTGTGATTTTCGTTTC
1 GCGTTGCGATTTTCATTTC
1180868 GCGTTGCGATTTTCATTTC
1 GCGTTGCGATTTTCATTTC
1180887 GCGTTGCGAT
1 GCGTTGCGAT
1180897 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 20
0.70 0.10 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 45 0.61
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (19 bp):
GCGTTGCGATTTTCATTTC
Found at i:1180902 original size:19 final size:19
Alignment explanation
Indices: 1180864--1180904 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1180854 GTGATTTTCG
**
1180864 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATAGTCA
1180883 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
1180902 TTT
1 TTT
1180905 TTCACTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:1181394 original size:42 final size:42
Alignment explanation
Indices: 1181318--1181398 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
1181308 GACTCGCCTG
* * *
1181318 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
1181360 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCC
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCC
1181399 TGTCATCGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.22
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:1181433 original size:20 final size:20
Alignment explanation
Indices: 1181376--1181434 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1181366 CTCGAGAGTC
1181376 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
1181396 CCCTGTCATCGTTGAAGAGG
1 CCCTCCCACCGTTCAAGAGG
* *
1181416 TCCTCCCACCATTCAAGAG
1 CCCTCCCACCGTTCAAGAG
1181435 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:1182857 original size:19 final size:19
Alignment explanation
Indices: 1182833--1182898 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
1182823 AAAAGTGACT
*
1182833 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1182852 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1182866 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
1182885 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1182899 CTAAATTCGC
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1182915 original size:19 final size:19
Alignment explanation
Indices: 1182865--1182908 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1182855 GCAACGAGAG
1182865 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
1182884 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
1182903 ATTCGC
1 AATCGC
1182909 GTTGCGATTT
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:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:1182950 original size:33 final size:33
Alignment explanation
Indices: 1182908--1183067 Score: 248
Period size: 33 Copynumber: 4.8 Consensus size: 33
1182898 ACTAAATTCG
* * *
1182908 CGTTGCGATTTTTATTTCTCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1182941 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1182974 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* * *
1183007 CATTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1183040 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1183068 AGTCATTTCC
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 119 1.00
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1182967 original size:19 final size:19
Alignment explanation
Indices: 1182943--1183087 Score: 95
Period size: 19 Copynumber: 8.4 Consensus size: 19
1182933 GATTCCCTCG
*
1182943 TTGCGATTTTCATTTCGCT
1 TTGCGATTTTCATTTCGCA
**
1182962 TTGCGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
1182976 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1182995 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
1183009 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1183028 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1183042 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
1183061 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
1183081 TTGCGAT
1 TTGCGAT
1183088 AGACATTAAG
Statistics
Matches: 97, Mismatches: 13, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
14 21 0.22
16 16 0.16
17 16 0.16
19 34 0.35
20 10 0.10
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1183086 original size:20 final size:19
Alignment explanation
Indices: 1183040--1183094 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1183030 GTGATTCTCT
**
1183040 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
1183059 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
1183079 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
1183095 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1185592 original size:23 final size:23
Alignment explanation
Indices: 1185555--1185607 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
1185545 CTGAAAAATC
1185555 ATCAAATCCGAGTA-TGACCAAG
1 ATCAAATCCGAGTATTGACCAAG
*
1185577 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAA-TCCGAGTATTGACCAAG
1185601 ATCAAAT
1 ATCAAAT
1185608 TCGAATACTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 6 0.21
23 8 0.29
24 14 0.50
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (23 bp):
ATCAAATCCGAGTATTGACCAAG
Found at i:1186475 original size:20 final size:21
Alignment explanation
Indices: 1186451--1186608 Score: 147
Period size: 20 Copynumber: 8.0 Consensus size: 21
1186441 CAGAATCTCG
1186451 TTGCGATTTAC-TAAATCGCA
1 TTGCGATTTACGTAAATCGCA
*
1186471 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGTAAATCGCA
* *
1186491 ATGCGA-ATACGT-AATCGCA
1 TTGCGATTTACGTAAATCGCA
* * *
1186510 TTGCGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAAATCGCA
* * *
1186531 TTGCGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAAATCGCA
1186552 TTGCGATTTACGT-AATCGCA
1 TTGCGATTTACGTAAATCGCA
*
1186572 TT--G-TTTACGT-ATTCGCA
1 TTGCGATTTACGTAAATCGCA
*
1186589 TTGCGATTTA-GGAAATCGCA
1 TTGCGATTTACGTAAATCGCA
1186609 ACGCGAATTT
Statistics
Matches: 118, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
17 15 0.13
18 1 0.01
19 18 0.15
20 46 0.39
21 38 0.32
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (21 bp):
TTGCGATTTACGTAAATCGCA
Found at i:1186551 original size:81 final size:78
Alignment explanation
Indices: 1186451--1186597 Score: 188
Period size: 81 Copynumber: 1.8 Consensus size: 78
1186441 CAGAATCTCG
1186451 TTGCGATTTACTAAATCGCAATGCGA-TTACGTAAATCGCAATGCGAATACGTAATCGCATTGCG
1 TTGCGATTTACTAAATCGCAATGCGATTTACGT-AATCGC-AT-CGAATACGTAATCGCATTGCG
1186515 ATTTTCCTAATTCGCA
63 ATTTTCCTAATTCGCA
* * * * ** *
1186531 TTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGTTTACGTATTCGCATTGCGAT
1 TTGCGA-TTTACTAAATCGCAATGCGATTTACGTAATCGCATCGAATACGTAATCGCATTGCGAT
1186596 TT
65 TT
1186598 AGGAAATCGC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
79 21 0.36
80 8 0.14
81 23 0.40
82 6 0.10
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (78 bp):
TTGCGATTTACTAAATCGCAATGCGATTTACGTAATCGCATCGAATACGTAATCGCATTGCGATT
TTCCTAATTCGCA
Found at i:1186580 original size:17 final size:17
Alignment explanation
Indices: 1186558--1186591 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1186548 CGCATTGCGA
1186558 TTTACGTAATCGCATTG
1 TTTACGTAATCGCATTG
*
1186575 TTTACGTATTCGCATTG
1 TTTACGTAATCGCATTG
1186592 CGATTTAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (17 bp):
TTTACGTAATCGCATTG
Found at i:1186589 original size:37 final size:39
Alignment explanation
Indices: 1186466--1186608 Score: 123
Period size: 37 Copynumber: 3.6 Consensus size: 39
1186456 ATTTACTAAA
* * * *
1186466 TCGCAATGCGA-TTACGTAAATCGCAATGCGA-ATACGTAA
1 TCGCATTGCGATTTACGT-AATCGC-ATTCGATTTACGTAT
* * * *
1186505 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAA-TCGCATT-CGATTTACGT-AT
1186547 TCGCATTGCGATTTACGTAATCGCATT-G-TTTACGTAT
1 TCGCATTGCGATTTACGTAATCGCATTCGATTTACGTAT
* *
1186584 TCGCATTGCGATTTAGGAAATCGCA
1 TCGCATTGCGATTTACGTAATCGCA
1186609 ACGCGAATTT
Statistics
Matches: 85, Mismatches: 14, Indels: 12
0.77 0.13 0.11
Matches are distributed among these distances:
37 25 0.29
38 5 0.06
39 15 0.18
40 11 0.13
41 10 0.12
42 19 0.22
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (39 bp):
TCGCATTGCGATTTACGTAATCGCATTCGATTTACGTAT
Found at i:1189105 original size:72 final size:72
Alignment explanation
Indices: 1188988--1189133 Score: 292
Period size: 72 Copynumber: 2.0 Consensus size: 72
1188978 CCAGCTTTCT
1188988 TGTTATGATCATACCCCGGACGTTTCTCTCGTGACATGTAAACAAACATTGGCAACCTTATGTCT
1 TGTTATGATCATACCCCGGACGTTTCTCTCGTGACATGTAAACAAACATTGGCAACCTTATGTCT
1189053 ACATCGG
66 ACATCGG
1189060 TGTTATGATCATACCCCGGACGTTTCTCTCGTGACATGTAAACAAACATTGGCAACCTTATGTCT
1 TGTTATGATCATACCCCGGACGTTTCTCTCGTGACATGTAAACAAACATTGGCAACCTTATGTCT
1189125 ACATCGG
66 ACATCGG
1189132 TG
1 TG
1189134 AAACTAATGA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (72 bp):
TGTTATGATCATACCCCGGACGTTTCTCTCGTGACATGTAAACAAACATTGGCAACCTTATGTCT
ACATCGG
Found at i:1196619 original size:17 final size:17
Alignment explanation
Indices: 1196590--1196639 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
1196580 TATTTTTTAG
1196590 TAATTTATTTAATTATTT
1 TAATTTATTTAA-TATTT
1196608 TAATTT-TTTAATATTT
1 TAATTTATTTAATATTT
*
1196624 T-ATTTAATTAAT-TTT
1 TAATTTATTTAATATTT
1196639 T
1 T
1196640 TTTTGCAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.27
16 11 0.37
17 5 0.17
18 6 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TAATTTATTTAATATTT
Found at i:1196643 original size:29 final size:29
Alignment explanation
Indices: 1196563--1196638 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
1196553 TATTAAGGTA
* *
1196563 TATTTTATTATATTTAGTATTTTTTAGTAATT
1 TATTTAATTAT-TTTA--ATTTTTTAATAATT
*
1196595 TATTTAATTATTTTAATTTTTTAATATTT
1 TATTTAATTATTTTAATTTTTTAATAATT
1196624 TATTTAATTAATTTT
1 TATTTAATT-ATTTT
1196639 TTTTTGCAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 21 0.52
30 5 0.12
31 4 0.10
32 10 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (29 bp):
TATTTAATTATTTTAATTTTTTAATAATT
Found at i:1201917 original size:18 final size:18
Alignment explanation
Indices: 1201890--1201931 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1201880 CGTACTTATT
* *
1201890 CAATTGGAAGTATTGATC
1 CAATTCGAAGAATTGATC
1201908 CAATTCGAAGAATTGATC
1 CAATTCGAAGAATTGATC
1201926 CAATTC
1 CAATTC
1201932 AAAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (18 bp):
CAATTCGAAGAATTGATC
Found at i:1202258 original size:18 final size:18
Alignment explanation
Indices: 1202231--1202272 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1202221 CGTACTTATT
* *
1202231 CAATTGGAAGTATTGATC
1 CAATTCGAAGAATTGATC
1202249 CAATTCGAAGAATTGATC
1 CAATTCGAAGAATTGATC
1202267 CAATTC
1 CAATTC
1202273 AAAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (18 bp):
CAATTCGAAGAATTGATC
Found at i:1202260 original size:341 final size:345
Alignment explanation
Indices: 1201634--1202319 Score: 1335
Period size: 341 Copynumber: 2.0 Consensus size: 345
1201624 ATAAGGCGCG
1201634 TCGCAAGGGGCACGTCTTACCCCACGTGGCTCCAAATCAGCGTATAGCGCGCTGCAGGGGGCGCG
1 TCGCAAGGGGCACGTCTTACCCCACGTGGCTCCAAATCA-CGTATAGCGCGCTGCAGGGGGCGCG
1201699 TCTTACTGAAAAAGGTGTTAGATCGGGAAATATAGTATGATCGGTGTTAGATCAGTAAATATATC
65 TCTTACTGAAAAAGGTGTTAGATCGGGAAATATAGTATGATCGGTGTTAGATCAGTAAATATATC
1201764 GGTCACCGGTGATTTTTTGAGAAAAACGCCTGAATCTATCCTATCCAAAAATTTTTTTGAAGATT
130 GGTCACCGGTGATTTTTTGAGAAAAACGCCTGAATCTATCCTATCCAAAAATTTTTTTGAAGATT
1201829 TAGTTATGATTATGAATGCACTTTTCTATCTTTATCCATGGATCTTTTCCTCGTACTTATTCAAT
195 TAGTTATGATTATGAATGCACTTTTCTATCTTTATCCATGGATCTTTTCCTCGTACTTATTCAAT
1201894 TGGAAGTATTGATCCAATTCGAAGAATTGATCCAATTC-AAAAAAATTATG-TTCGTAATTTGTT
260 TGGAAGTATTGATCCAATTCGAAGAATTGATCCAATTCAAAAAAAATTATGTTTCGTAATTTGTT
1201957 AGGTGTTAAATTTTCTTTTTC
325 AGGTGTTAAATTTTCTTTTTC
1201978 TCGCAAGGGGCACGTCTTACCCCACGTGGCTCCAAATCA-GTATAGCGCGCTGCAGGGGGCGCGT
1 TCGCAAGGGGCACGTCTTACCCCACGTGGCTCCAAATCACGTATAGCGCGCTGCAGGGGGCGCGT
1202042 CTTACTG-AAAAGGTGTTAGATCGGGAAATATAGTATGATCGGTGTTAGATCAGTAAATATATCG
66 CTTACTGAAAAAGGTGTTAGATCGGGAAATATAGTATGATCGGTGTTAGATCAGTAAATATATCG
1202106 GTCACCGGTGATTTTTTGAGAAAAACGCCTGAATCTATCCTATCCAAAAATTTTTTTGAAGATTT
131 GTCACCGGTGATTTTTTGAGAAAAACGCCTGAATCTATCCTATCCAAAAATTTTTTTGAAGATTT
1202171 AGTTATGATTATGAATGCACTTTTCTATCTTTATCCATGGATCTTTTCCTCGTACTTATTCAATT
196 AGTTATGATTATGAATGCACTTTTCTATCTTTATCCATGGATCTTTTCCTCGTACTTATTCAATT
1202236 GGAAGTATTGATCCAATTCGAAGAATTGATCCAATTCAAAAAAAATTATGTTTCGTAATTTGTTA
261 GGAAGTATTGATCCAATTCGAAGAATTGATCCAATTCAAAAAAAATTATGTTTCGTAATTTGTTA
1202301 GGTGTTAAATTTTCTTTTT
326 GGTGTTAAATTTTCTTTTT
1202320 TCTTCCTTTC
Statistics
Matches: 340, Mismatches: 0, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
341 224 0.66
342 44 0.13
343 33 0.10
344 39 0.11
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (345 bp):
TCGCAAGGGGCACGTCTTACCCCACGTGGCTCCAAATCACGTATAGCGCGCTGCAGGGGGCGCGT
CTTACTGAAAAAGGTGTTAGATCGGGAAATATAGTATGATCGGTGTTAGATCAGTAAATATATCG
GTCACCGGTGATTTTTTGAGAAAAACGCCTGAATCTATCCTATCCAAAAATTTTTTTGAAGATTT
AGTTATGATTATGAATGCACTTTTCTATCTTTATCCATGGATCTTTTCCTCGTACTTATTCAATT
GGAAGTATTGATCCAATTCGAAGAATTGATCCAATTCAAAAAAAATTATGTTTCGTAATTTGTTA
GGTGTTAAATTTTCTTTTTC
Found at i:1203315 original size:43 final size:43
Alignment explanation
Indices: 1203241--1203325 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 43
1203231 TTTTTTATTC
1203241 TTTATTCTTTAAGTGACTAGTTTATGGTTTTTTACAATTTGAA
1 TTTATTCTTTAAGTGACTAGTTTATGGTTTTTTACAATTTGAA
1203284 TTTATTC-TTAAGTGACTAGTTTATGGTTTTTTACAATTTGAA
1 TTTATTCTTTAAGTGACTAGTTTATGGTTTTTTACAATTTGAA
1203326 AGAACATGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 35 0.83
43 7 0.17
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.53
Consensus pattern (43 bp):
TTTATTCTTTAAGTGACTAGTTTATGGTTTTTTACAATTTGAA
Found at i:1203955 original size:60 final size:60
Alignment explanation
Indices: 1203830--1203955 Score: 180
Period size: 60 Copynumber: 2.1 Consensus size: 60
1203820 ATAGTCTCCT
* * * *
1203830 AATTATAAGGTATTATTTTATTAAGTTCATCGATTATTAAAAATTATAAAATAGTCATTC
1 AATTATAAGGTATTACTTTATTAAGTTCATCGACTATTAAAAATTATAAAATAATCACTC
* * *
1203890 AATTATAAGGTATTACTTTATTGAGTTTATCGACTATTAAAAGTTATAAAATAATCACTC
1 AATTATAAGGTATTACTTTATTAAGTTCATCGACTATTAAAAATTATAAAATAATCACTC
*
1203950 GATTAT
1 AATTAT
1203956 TTATATATAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (60 bp):
AATTATAAGGTATTACTTTATTAAGTTCATCGACTATTAAAAATTATAAAATAATCACTC
Found at i:1205131 original size:17 final size:14
Alignment explanation
Indices: 1205094--1205141 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
1205084 AAAAACTGAT
1205094 AAACCGAACCGAAA
1 AAACCGAACCGAAA
*
1205108 AACCCGAACCGTTAAAA
1 AAACCGAACCG---AAA
1205125 AAACCGAACCGAAA
1 AAACCGAACCGAAA
1205139 AAA
1 AAA
1205142 TCGGTTTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 16 0.55
17 13 0.45
ACGTcount: A:0.56, C:0.27, G:0.12, T:0.04
Consensus pattern (14 bp):
AAACCGAACCGAAA
Found at i:1205381 original size:27 final size:27
Alignment explanation
Indices: 1205351--1205430 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 27
1205341 GGTGATTTAT
1205351 TTTATCTTATGGTTATTTATAATAATC
1 TTTATCTTATGGTTATTTATAATAATC
* ** ** * *
1205378 TTTAACTGGT-GAAAATT-TGAT-AT-
1 TTTATCTTATGGTTATTTATAATAATC
1205401 -TTATCTTATGGTTATTTATAATAATC
1 TTTATCTTATGGTTATTTATAATAATC
1205427 TTTA
1 TTTA
1205431 ACTGGTGAAA
Statistics
Matches: 34, Mismatches: 14, Indels: 10
0.59 0.24 0.17
Matches are distributed among these distances:
22 6 0.18
23 4 0.12
24 5 0.15
25 5 0.15
26 4 0.12
27 10 0.29
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (27 bp):
TTTATCTTATGGTTATTTATAATAATC
Found at i:1205410 original size:49 final size:50
Alignment explanation
Indices: 1205351--1205457 Score: 200
Period size: 49 Copynumber: 2.2 Consensus size: 50
1205341 GGTGATTTAT
1205351 TTTATCTTATGGTTATTTATAATAATCTTTAACTGGTGAAAATTTGATA-
1 TTTATCTTATGGTTATTTATAATAATCTTTAACTGGTGAAAATTTGATAG
1205400 TTTATCTTATGGTTATTTATAATAATCTTTAACTGGTGAAAATTTGATAG
1 TTTATCTTATGGTTATTTATAATAATCTTTAACTGGTGAAAATTTGATAG
1205450 TTT-TCTTA
1 TTTATCTTA
1205458 AAATATATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
49 54 0.95
50 3 0.05
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (50 bp):
TTTATCTTATGGTTATTTATAATAATCTTTAACTGGTGAAAATTTGATAG
Found at i:1205444 original size:27 final size:27
Alignment explanation
Indices: 1205365--1205444 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
1205355 TCTTATGGTT
1205365 ATTTATAATAATCTTTAACTGGTGAAA
1 ATTTATAATAATCTTTAACTGGTGAAA
* * *
1205392 ATTTGATATTTATC-TT-A-TGGT---T
1 ATTT-ATAATAATCTTTAACTGGTGAAA
1205414 ATTTATAATAATCTTTAACTGGTGAAA
1 ATTTATAATAATCTTTAACTGGTGAAA
1205441 ATTT
1 ATTT
1205445 GATAGTTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
21 7 0.17
22 6 0.15
23 1 0.03
24 4 0.10
25 4 0.10
26 1 0.03
27 10 0.25
28 7 0.17
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.47
Consensus pattern (27 bp):
ATTTATAATAATCTTTAACTGGTGAAA
Found at i:1206364 original size:2 final size:2
Alignment explanation
Indices: 1206357--1206411 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
1206347 TAAAATGAAT
1206357 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1206397 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1206412 GTTGCAAGAG
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1206377 original size:17 final size:17
Alignment explanation
Indices: 1206355--1206411 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
1206345 TTTAAAATGA
1206355 ATTATATATATATATAT
1 ATTATATATATATATAT
1206372 ATTATATATATATATAT
1 ATTATATATATATATAT
*
1206389 AATATATATATATATAT
1 ATTATATATATATATAT
1206406 A-TATAT
1 ATTATAT
1206412 GTTGCAAGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
16 5 0.13
17 34 0.87
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATATATATATATAT
Found at i:1207542 original size:18 final size:19
Alignment explanation
Indices: 1207519--1207561 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1207509 CAGTAATCCT
1207519 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
*
1207537 ATTCCCACTGGTAATCTTAT
1 ATT-CCACTGGTAATCTTAC
1207557 ATTCC
1 ATTCC
1207562 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:1207549 original size:20 final size:20
Alignment explanation
Indices: 1207524--1207561 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1207514 ATCCTATTCC
1207524 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
1207544 CTGGTAATCTTATATTCC
1 CTGGTAATCTTACATTCC
1207562 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1212613 original size:20 final size:20
Alignment explanation
Indices: 1212588--1212627 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1212578 CATCATGTCA
1212588 CATTCAGAACTAATTCATAC
1 CATTCAGAACTAATTCATAC
1212608 CATTCAGAACTAATTCATAC
1 CATTCAGAACTAATTCATAC
1212628 ATAGCCTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (20 bp):
CATTCAGAACTAATTCATAC
Found at i:1212741 original size:21 final size:20
Alignment explanation
Indices: 1212725--1212772 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1212715 ATTTAATCTC
1212725 TAAATCCTAAATTTTAAATCA
1 TAAATCCTAAATTTT-AATCA
*
1212746 TAAATTCTAAATTTTAAATCA
1 TAAATCCTAAATTTT-AATCA
*
1212767 TGAATC
1 TAAATC
1212773 TTGAACTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAATCCTAAATTTTAATCA
Found at i:1212764 original size:14 final size:14
Alignment explanation
Indices: 1212723--1212757 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1212713 TGATTTAATC
*
1212723 TCTAAATCCTAAAT
1 TCTAAATCATAAAT
*
1212737 TTTAAATCATAAAT
1 TCTAAATCATAAAT
1212751 TCTAAAT
1 TCTAAAT
1212758 TTTAAATCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (14 bp):
TCTAAATCATAAAT
Found at i:1224668 original size:79 final size:76
Alignment explanation
Indices: 1224515--1224672 Score: 205
Period size: 78 Copynumber: 2.0 Consensus size: 76
1224505 TTAATATATT
*
1224515 TTTAATATTTTTATAAAATGTTATTTAAAATATTATTTTTTTACAAAAAATGTTAATTTTAGGTG
1 TTTAATATTTTTATAAAATGTTATTTAAAATATTATTTTTTTACAAAAAATGTTAATTTGAGGT-
*
1224580 CTATTTAAAATA
65 CTACTTAAAATA
*
1224592 TTTAATATTTTTGATAAAAT-TCTATTTAAAATATTATTTTTTCTATC-AGAAATGTTAATATTG
1 TTTAATATTTTT-ATAAAATGT-TATTTAAAATATTATTTTTT-TA-CAAAAAATGTTAAT-TTG
1224655 AGCGT-TACTTAAAATA
61 AG-GTCTACTTAAAATA
1224671 TT
1 TT
1224673 ATTTTTTATC
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
77 13 0.18
78 27 0.38
79 25 0.35
80 5 0.07
81 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (76 bp):
TTTAATATTTTTATAAAATGTTATTTAAAATATTATTTTTTTACAAAAAATGTTAATTTGAGGTC
TACTTAAAATA
Found at i:1224737 original size:21 final size:21
Alignment explanation
Indices: 1224688--1224737 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1224678 TTATCAAAAA
* *
1224688 TTAAATAATAAAATTAACATT
1 TTAAATAAAAAAAATAACATT
** *
1224709 TTTTATAAAAAAAATAATATT
1 TTAAATAAAAAAAATAACATT
1224730 TTAAATAA
1 TTAAATAA
1224738 CACTTTATTA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAATAAAAAAAATAACATT
Found at i:1224750 original size:32 final size:31
Alignment explanation
Indices: 1224710--1224774 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 31
1224700 ATTAACATTT
*
1224710 TTTATAAAAAAAATAATATTTTAAATAACAC
1 TTTATAAAAAAAATAATACTTTAAATAACAC
*** *
1224741 TTTATTAAAAATCTTAATACTTTCAATAACAC
1 TTTA-TAAAAAAAATAATACTTTAAATAACAC
1224773 TT
1 TT
1224775 CCTTAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTATAAAAAAAATAATACTTTAAATAACAC
Found at i:1226278 original size:18 final size:18
Alignment explanation
Indices: 1226252--1226292 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1226242 AACCCGACCC
*
1226252 GACCAGACCCGTTTACCA
1 GACCCGACCCGTTTACCA
*
1226270 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTTACCA
1226288 GACCC
1 GACCC
1226293 ATTGACCCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.46, G:0.17, T:0.15
Consensus pattern (18 bp):
GACCCGACCCGTTTACCA
Found at i:1228902 original size:48 final size:48
Alignment explanation
Indices: 1228850--1228975 Score: 200
Period size: 48 Copynumber: 2.6 Consensus size: 48
1228840 TTTGATTTGA
* *
1228850 ATTCTGATCTGATACTTGACATGGATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGGATTATGATCTGATACTTGACATGG
*
1228898 ATTCTGATATGATA-TCTGACATGGATTATGATCTGATACTTGACTTGG
1 ATTCTGATATGATACT-TGACATGGATTATGATCTGATACTTGACATGG
*
1228946 ATTCTGATATGATACTTGACATGAATTATG
1 ATTCTGATATGATACTTGACATGGATTATG
1228976 TTTTGATTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
47 1 0.01
48 70 0.97
49 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (48 bp):
ATTCTGATATGATACTTGACATGGATTATGATCTGATACTTGACATGG
Found at i:1228982 original size:24 final size:24
Alignment explanation
Indices: 1228850--1228968 Score: 177
Period size: 24 Copynumber: 5.0 Consensus size: 24
1228840 TTTGATTTGA
*
1228850 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
1228874 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
1228898 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* * *
1228922 ATTATGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
1228946 ATTCTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
1228969 AATTATGTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.01
24 84 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:1229160 original size:42 final size:43
Alignment explanation
Indices: 1229084--1229177 Score: 163
Period size: 42 Copynumber: 2.2 Consensus size: 43
1229074 AGGCCTTACT
*
1229084 TGGTGTGTTGGTGGGTGTATGGTTATGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTATGGGAAACCTACACATTA
*
1229127 TGGTGTGTTGGT-GGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTATGGGAAACCTACACATTA
1229169 TGGTGTGTT
1 TGGTGTGTT
1229178 CGGTTGGAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 37 0.76
43 12 0.24
ACGTcount: A:0.17, C:0.10, G:0.36, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTATGGGAAACCTACACATTA
Found at i:1231556 original size:20 final size:20
Alignment explanation
Indices: 1231510--1231556 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1231500 TTTGGTTCAC
*
1231510 GAAAATGTAAGATTACCAGT
1 GAAAATGTAAGATTACCAGG
* *
1231530 GAGAATGTAAGATTATCAGG
1 GAAAATGTAAGATTACCAGG
1231550 GAAAATG
1 GAAAATG
1231557 ATTACTTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (20 bp):
GAAAATGTAAGATTACCAGG
Found at i:1233296 original size:19 final size:19
Alignment explanation
Indices: 1233272--1233335 Score: 92
Period size: 19 Copynumber: 3.4 Consensus size: 19
1233262 GCAACGAGAG
*
1233272 AATCGCAACGTGAAATAAA
1 AATCGCAACGCGAAATAAA
*
1233291 AATCGCAACGCAAAATAAA
1 AATCGCAACGCGAAATAAA
**
1233310 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
1233329 AATCGCA
1 AATCGCA
1233336 TTGTGATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:1233353 original size:19 final size:19
Alignment explanation
Indices: 1233331--1233462 Score: 85
Period size: 19 Copynumber: 7.1 Consensus size: 19
1233321 GAAACCAAAA
*
1233331 TCGCATTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1233350 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1233369 TCGCGTTGCGATTCTC--T
1 TCGCATTGCGATTTTCATT
* **
1233386 T-G--TCGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
* **
1233402 TCGCGTTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
* *
1233421 TCCGCGTTGCGATTCTCATT
1 T-CGCATTGCGATTTTCATT
* *
1233441 ATCTCGTTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
1233461 TC
1 TC
1233463 AACCAAAAGA
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
14 8 0.08
16 3 0.03
17 3 0.03
19 48 0.51
20 32 0.34
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1233428 original size:20 final size:19
Alignment explanation
Indices: 1233345--1233453 Score: 95
Period size: 19 Copynumber: 5.9 Consensus size: 19
1233335 ATTGTGATTT
**
1233345 TCATTTCGCGTTGCGATTT
1 TCATTTCGCGTTGCGATAG
1233364 TCATTTCGCGTTGCGAT--
1 TCATTTCGCGTTGCGATAG
*
1233381 TC-TCTT---GTCGCGATAG
1 TCAT-TTCGCGTTGCGATAG
1233397 TCATTTCGCGTTGCGATAG
1 TCATTTCGCGTTGCGATAG
**
1233416 TCATTTCCGCGTTGCGATTC
1 TCATTT-CGCGTTGCGATAG
*
1233436 TCATTATCTCGTTGCGAT
1 TCATT-TCGCGTTGCGAT
1233454 TTTCATTTCA
Statistics
Matches: 76, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
14 7 0.09
16 5 0.07
17 5 0.07
19 32 0.42
20 26 0.34
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:1235620 original size:42 final size:41
Alignment explanation
Indices: 1235544--1235708 Score: 152
Period size: 42 Copynumber: 3.9 Consensus size: 41
1235534 GACTCGCCTG
* * * * * *
1235544 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCC-ACCGTTCAAGAGGCCACTA
*
1235586 TCATTCCTCGAGAGTCCCCTCTCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTC-CACCGTTCAAGAGGCCACTA
* * * * * *
1235628 CCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCTA-TA
1 TCATTCCTCGAGAGTCCCCTCC-ACCGTTCAAGAGGCC-ACTA
*
1235670 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAAGCCA
1 TCATTCCTCGAGAGTCCCCT-CCACCGTTCAAGAGGCCA
1235709 TTGTCATCGT
Statistics
Matches: 98, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
41 2 0.02
42 92 0.94
43 4 0.04
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (41 bp):
TCATTCCTCGAGAGTCCCCTCCACCGTTCAAGAGGCCACTA
Found at i:1235725 original size:84 final size:84
Alignment explanation
Indices: 1235545--1235708 Score: 292
Period size: 84 Copynumber: 2.0 Consensus size: 84
1235535 ACTCGCCTGT
* *
1235545 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCTCA
1 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCA
*
1235610 CCGTTCAAGAGGCCACTGC
66 CCGTTCAAGAAGCCACTGC
*
1235629 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCTATATCATTCCTCGAGAGTCCCCTCCCA
1 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCA
1235694 CCGTTCAAGAAGCCA
66 CCGTTCAAGAAGCCA
1235709 TTGTCATCGT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (84 bp):
CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCA
CCGTTCAAGAAGCCACTGC
Found at i:1235746 original size:84 final size:84
Alignment explanation
Indices: 1235545--1235746 Score: 226
Period size: 84 Copynumber: 2.4 Consensus size: 84
1235535 ACTCGCCTGT
* * * * * *
1235545 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCTCA
1 CATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCA
*
1235610 CCGTTCAAGAGGCCACTGC
66 CCGTTCAAGAAGCCACTGC
* * * * *
1235629 CATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCTATATCATTCCTCGAGAGTCCCCTCCCA
1 CATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCA
* *
1235694 CCGTTCAAGAAGCCATTGT
66 CCGTTCAAGAAGCCACTGC
** * *
1235713 CATCGTTGAAGAGGT-CTCTCCCACCATTCAAGAG
1 CATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
1235747 CCCGATTCAC
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
84 101 0.98
85 2 0.02
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (84 bp):
CATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCATATCATTCCTCGAGAGTCCCCTCCCA
CCGTTCAAGAAGCCACTGC
Found at i:1237062 original size:14 final size:14
Alignment explanation
Indices: 1237043--1237078 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1237033 ATTGTTTAAT
1237043 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1237057 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1237071 TGATTTGT
1 TGATTTGT
1237079 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1237209 original size:19 final size:19
Alignment explanation
Indices: 1237185--1237231 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1237175 AAAAAGTACT
* *
1237185 ATCGCAATGCGAAATGAGA
1 ATCGCAACGCGAAATGAAA
1237204 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1237223 ATCGCAACG
1 ATCGCAACG
1237232 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1237304 original size:33 final size:32
Alignment explanation
Indices: 1237260--1237386 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
1237250 ATTAAATTTG
1237260 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* * **
1237293 CATTGCGATTTTCATTTCGTATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1237326 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1237359 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1237387 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.04
33 76 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1237338 original size:66 final size:66
Alignment explanation
Indices: 1237253--1237385 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1237243 ACGCGAAATT
* *
1237253 AAATTTGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGTATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
1237318 G
66 G
* *
1237319 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
1237384 G
66 G
1237385 A
1 A
1237386 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
G
Found at i:1239696 original size:12 final size:12
Alignment explanation
Indices: 1239679--1239715 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1239669 TCTTCGGGGA
1239679 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1239691 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1239703 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1239715 C
1 C
1239716 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1239928 original size:25 final size:24
Alignment explanation
Indices: 1239890--1239944 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
1239880 CTGAAACATC
*
1239890 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
*
1239914 ATCAAAGTCCCGAGTATTGACCAAG
1 ATCAAAAT-CCGAGTATTGACCAAG
1239939 ATCAAA
1 ATCAAA
1239945 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1241147 original size:20 final size:20
Alignment explanation
Indices: 1241052--1241139 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
1241042 CAACGGGGAA
1241052 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1241072 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
1241092 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
1241112 ATCACAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1241132 ATCGCAAC
1 ATCGCAAC
1241140 TAGAAAATCG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 5 0.09
20 44 0.81
21 5 0.09
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1241190 original size:14 final size:16
Alignment explanation
Indices: 1241170--1241243 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
1241160 TGAAAATCGC
1241170 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
1241185 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
1241202 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
1241221 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
1241237 -TTGCGAT
1 ATTGCGAT
1241244 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:1241207 original size:19 final size:19
Alignment explanation
Indices: 1241166--1241233 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1241156 GAAATGAAAA
1241166 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1241182 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1241199 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1241218 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1241234 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1243273 original size:20 final size:20
Alignment explanation
Indices: 1243258--1243328 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
1243248 CACGAAACTT
1243258 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
**
1243278 ACTATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
*** *
1243298 GCTATCGCAATGCG-AAATG
1 AAAATCGCAACGCGAAAATG
1243317 AAAATCGCAACG
1 AAAATCGCAACG
1243329 ACAAAATCGC
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 13 0.30
20 30 0.70
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:1243336 original size:14 final size:14
Alignment explanation
Indices: 1243317--1243374 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1243307 ATGCGAAATG
1243317 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1243331 AAAATCGCAATACGAA
1 AAAATCGC-A-ACGAC
1243347 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1243363 AAAATCGCAACG
1 AAAATCGCAACG
1243375 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 19 0.50
15 1 0.03
16 10 0.26
17 1 0.03
18 7 0.18
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1243379 original size:32 final size:33
Alignment explanation
Indices: 1243301--1243379 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1243291 GAAAATGGCT
1243301 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1243334 ATCGCAATACGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1243366 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1243380 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 28 0.65
33 15 0.35
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1243408 original size:19 final size:18
Alignment explanation
Indices: 1243386--1243448 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
1243376 GAAACACAAA
1243386 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
1243405 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
1243421 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
1243437 TCGCATTGCGAT
1 TCGCATTGCGAT
1243449 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
16 8 0.22
18 10 0.27
19 10 0.27
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:1243467 original size:20 final size:19
Alignment explanation
Indices: 1243433--1243487 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1243423 GTTGCGATTT
*
1243433 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1243452 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1243472 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1243488 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1243995 original size:18 final size:18
Alignment explanation
Indices: 1243969--1244013 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1243959 TTCGATCAGA
*
1243969 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1243987 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1244005 TGATGGCTC
1 TGATGGCTC
1244014 CCTAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1245358 original size:20 final size:20
Alignment explanation
Indices: 1245333--1245406 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1245323 AATAGTTTCT
*
1245333 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
1245353 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
1245373 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
1245393 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
1245407 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:1245667 original size:22 final size:22
Alignment explanation
Indices: 1245640--1245683 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1245630 GATGGAGATA
*
1245640 GATGGATTTTGCCGGAGATGGG
1 GATGGATTTCGCCGGAGATGGG
*
1245662 GATGGATTTCGTCGGAGATGGG
1 GATGGATTTCGCCGGAGATGGG
1245684 CGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.09, G:0.45, T:0.27
Consensus pattern (22 bp):
GATGGATTTCGCCGGAGATGGG
Found at i:1245957 original size:20 final size:20
Alignment explanation
Indices: 1245851--1246005 Score: 134
Period size: 20 Copynumber: 7.7 Consensus size: 20
1245841 CGCTTTGAAA
*
1245851 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
** * *
1245872 ATCGTGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* * *
1245892 ATCGCGTTGCAAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1245912 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1245933 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
*
1245953 ATCGCATTGTGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1245973 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1245993 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1246006 TTTCCCAATT
Statistics
Matches: 110, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
19 5 0.05
20 81 0.74
21 22 0.20
22 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1245957 original size:61 final size:61
Alignment explanation
Indices: 1245851--1246004 Score: 168
Period size: 61 Copynumber: 2.5 Consensus size: 61
1245841 CGCTTTGAAA
** * *
1245851 ATCGCATTGCGATTATGTATTATCGTGTTGCGAAAGTCAGAATCGCGTTGCAAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCAAAAGTCAGT
* * * * * ** *
1245912 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGTGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCAAAAGTCAGT
*
1245973 ATCGCATTGCGA-TA-GTCAGTATCGCATTGCGA
1 ATCGCATTGCGATTATGT-ATTATCGCATTGCGA
1246005 TTTTCCCAAT
Statistics
Matches: 76, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
59 2 0.03
60 15 0.20
61 59 0.78
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCAAAAGTCAGT
Done.