Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 30
Found at i:984118 original size:22 final size:20
Alignment explanation
Indices: 984075--984120 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
984065 TATATATATA
*
984075 TATAGTTTTGAAAAATATAT
1 TATAGTTTTGAAAAATACAT
*
984095 TATAGTTTTTGAAAATGTACAT
1 TATAG-TTTTGAAAA-ATACAT
984117 TATA
1 TATA
984121 TATTATGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (20 bp):
TATAGTTTTGAAAAATACAT
Found at i:994471 original size:19 final size:19
Alignment explanation
Indices: 994384--994471 Score: 72
Period size: 19 Copynumber: 4.6 Consensus size: 19
994374 TGCATTGGGC
*
994384 TATGAATTTGAAAATAA-T
1 TATGAATCTGAAAATAAGT
* *
994402 TAATGAATTTGAAAATAAGA
1 T-ATGAATCTGAAAATAAGT
* *
994422 TATGAATCT-AACAGTAAGC
1 TATGAATCTGAA-AATAAGT
* *
994441 TACGAGTCTGAAAATAAGT
1 TATGAATCTGAAAATAAGT
*
994460 TATGAATATGAA
1 TATGAATCTGAA
994472 TTAAGTTCTA
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
18 3 0.05
19 49 0.89
20 3 0.05
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.31
Consensus pattern (19 bp):
TATGAATCTGAAAATAAGT
Found at i:996096 original size:18 final size:18
Alignment explanation
Indices: 996056--996095 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
996046 GGGTTTTAGT
996056 AAAAATGATTATATAATA
1 AAAAATGATTATATAATA
996074 AAAAATGATT-TA-AAGTA
1 AAAAATGATTATATAA-TA
996091 AAAAA
1 AAAAA
996096 AAAGAATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.10
17 9 0.43
18 10 0.48
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (18 bp):
AAAAATGATTATATAATA
Found at i:996703 original size:19 final size:19
Alignment explanation
Indices: 996674--996711 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
996664 TTAGAATGTT
996674 TAAAAATAAAACTT-AAAA
1 TAAAAATAAAACTTGAAAA
996692 TAAAAATAAAAACTTGAAAA
1 TAAAAAT-AAAACTTGAAAA
996712 GAAAGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (19 bp):
TAAAAATAAAACTTGAAAA
Found at i:1008510 original size:22 final size:22
Alignment explanation
Indices: 1008480--1008532 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1008470 TTCAAAAAGG
*
1008480 ATCGATCCCTCGACCCGAAAAT
1 ATCGGTCCCTCGACCCGAAAAT
*
1008502 ATTGGTCCCTCGACCCGAAAAT
1 ATCGGTCCCTCGACCCGAAAAT
1008524 ATCGGTCCC
1 ATCGGTCCC
1008533 AAAGTTTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21
Consensus pattern (22 bp):
ATCGGTCCCTCGACCCGAAAAT
Found at i:1013718 original size:77 final size:78
Alignment explanation
Indices: 1013624--1013772 Score: 171
Period size: 77 Copynumber: 1.9 Consensus size: 78
1013614 AGTAAGTAAG
* *
1013624 CATTAAAAGAATTTAATTTAGATTACAACTCTTTTAAT-TGATATTTAA-TTCAAATAATTAAAT
1 CATTAAAAGAATTTAATTAAGATTACAACTC-TTTAATAT-ATATTTAATTTCAAATAAATAAAT
1013687 AAGATTTTAAATAAA
64 AAGATTTTAAATAAA
* * * * *
1013702 CATT-AAAG-ATTGTAATTAATATTATAAGTCTTTAATATATATTTAATTTGAATTAAATAAATA
1 CATTAAAAGAATT-TAATTAAGATTACAACTCTTTAATATATATTTAATTTCAAATAAATAAATA
*
1013765 ATATTTTA
65 AGATTTTA
1013773 TTTAATAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
76 17 0.28
77 39 0.65
78 4 0.07
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (78 bp):
CATTAAAAGAATTTAATTAAGATTACAACTCTTTAATATATATTTAATTTCAAATAAATAAATAA
GATTTTAAATAAA
Found at i:1022450 original size:21 final size:20
Alignment explanation
Indices: 1022406--1022468 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
1022396 TGTGTTGTAC
**
1022406 TGTGGCACTTCGGTAATTAT
1 TGTGGCACTTCGGTGCTTAT
1022426 TGTGGCACTTCGGTGCTTAAT
1 TGTGGCACTTCGGTGCTT-AT
* *
1022447 TGTGGCACTTTGGTGCATAT
1 TGTGGCACTTCGGTGCTTAT
1022467 TG
1 TG
1022469 GTTTGCCACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 20 0.53
21 18 0.47
ACGTcount: A:0.16, C:0.16, G:0.29, T:0.40
Consensus pattern (20 bp):
TGTGGCACTTCGGTGCTTAT
Found at i:1026134 original size:21 final size:21
Alignment explanation
Indices: 1026110--1026150 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1026100 GTGTTGTACT
*
1026110 GTGGCACTTCGGTGCTTATTA
1 GTGGCACTTCAGTGCTTATTA
1026131 GTGGCACTTCAGTGCTTATT
1 GTGGCACTTCAGTGCTTATT
1026151 GGTATGGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.20, G:0.27, T:0.39
Consensus pattern (21 bp):
GTGGCACTTCAGTGCTTATTA
Found at i:1026162 original size:23 final size:22
Alignment explanation
Indices: 1026111--1026197 Score: 77
Period size: 23 Copynumber: 3.9 Consensus size: 22
1026101 TGTTGTACTG
* *
1026111 TGGCACTTCGGTGCTTATTAG-
1 TGGCACTTCAGTGCTTATTGGT
1026132 TGGCACTTCAGTGCTTATTGGT
1 TGGCACTTCAGTGCTTATTGGT
** * *
1026154 ATGGCACTTTGGTGTTTACTGGTT
1 -TGGCACTTCAGTGCTTATTGG-T
* *
1026178 TGGCACTTAAGTGTTTATTG
1 TGGCACTTCAGTGCTTATTG
1026198 AGTACCTTGC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 19 0.35
23 34 0.63
24 1 0.02
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.43
Consensus pattern (22 bp):
TGGCACTTCAGTGCTTATTGGT
Found at i:1042896 original size:20 final size:20
Alignment explanation
Indices: 1042873--1042910 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1042863 GAATTGAAAG
*
1042873 TTAGAATATTAAATTTGATC
1 TTAGAATATGAAATTTGATC
*
1042893 TTAGAATGTGAAATTTGA
1 TTAGAATATGAAATTTGA
1042911 CTATTTTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (20 bp):
TTAGAATATGAAATTTGATC
Found at i:1044662 original size:19 final size:19
Alignment explanation
Indices: 1044546--1044660 Score: 140
Period size: 19 Copynumber: 6.1 Consensus size: 19
1044536 TATTCACTGG
*
1044546 GCTATGAATATGAAAATAA
1 GCTATGAATCTGAAAATAA
* *
1044565 GCTATGAATTTAAAAATAA
1 GCTATGAATCTGAAAATAA
*
1044584 GCTATGAATTTGAAAATAA
1 GCTATGAATCTGAAAATAA
* * *
1044603 GATATGAATCTGATAGTAA
1 GCTATGAATCTGAAAATAA
*
1044622 GCTATGAGTCTGAAAATAA
1 GCTATGAATCTGAAAATAA
* *
1044641 GTTATGAATCTGGAAATAA
1 GCTATGAATCTGAAAATAA
1044660 G
1 G
1044661 TTCTAATTCA
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 82 1.00
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:1052434 original size:21 final size:21
Alignment explanation
Indices: 1052408--1052451 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1052398 GTCTACGGGA
1052408 AAGAATGTAATTTACCGATTG
1 AAGAATGTAATTTACCGATTG
1052429 AAGAATGTAATTTACCGATTG
1 AAGAATGTAATTTACCGATTG
1052450 AA
1 AA
1052452 CTTGAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (21 bp):
AAGAATGTAATTTACCGATTG
Found at i:1062881 original size:10 final size:9
Alignment explanation
Indices: 1062860--1062932 Score: 55
Period size: 9 Copynumber: 8.6 Consensus size: 9
1062850 GGTTTTAATT
1062860 TTTTTGGGA
1 TTTTTGGGA
1062869 TTTTTGGGA
1 TTTTTGGGA
* *
1062878 ATTTAGGG-
1 TTTTTGGGA
1062886 TTTTT-GG-
1 TTTTTGGGA
*
1062893 -TTTTAGGA
1 TTTTTGGGA
* *
1062901 ATTTTGAGA
1 TTTTTGGGA
*
1062910 ATTTTGGGA
1 TTTTTGGGA
*
1062919 TTTTTAGGA
1 TTTTTGGGA
1062928 TTTTT
1 TTTTT
1062933 AATTTTTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
6 4 0.08
7 4 0.08
8 3 0.06
9 41 0.79
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (9 bp):
TTTTTGGGA
Found at i:1062930 original size:17 final size:17
Alignment explanation
Indices: 1062861--1062931 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
1062851 GTTTTAATTT
*
1062861 TTTTGGGATTTTTGGGAA
1 TTTTGGGATTTTTAGG-A
*
1062879 TTTAGGG-TTTTT-GG-
1 TTTTGGGATTTTTAGGA
* * *
1062893 TTTTAGGAATTTTGAGAA
1 TTTT-GGGATTTTTAGGA
1062911 TTTTGGGATTTTTAGGA
1 TTTTGGGATTTTTAGGA
1062928 TTTT
1 TTTT
1062932 TAATTTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
14 3 0.07
15 2 0.05
16 6 0.15
17 20 0.49
18 10 0.24
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (17 bp):
TTTTGGGATTTTTAGGA
Found at i:1073965 original size:15 final size:16
Alignment explanation
Indices: 1073945--1073979 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1073935 CATTTATATA
*
1073945 TAAATTAT-ATCAATT
1 TAAATTATAATAAATT
1073960 TAAATTATAATAAATT
1 TAAATTATAATAAATT
1073976 TAAA
1 TAAA
1073980 AAGATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTATAATAAATT
Found at i:1074045 original size:51 final size:51
Alignment explanation
Indices: 1073939--1074045 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
1073929 TATTTACATT
* * * *
1073939 TATATATAAATTATATCAATTTAAATTATAATAAATTTAAAAAGATATTAT
1 TATATATAAATTATATCAATTTAAAATATAATAAATATAAAAAGATATAAA
* *
1073990 TATATATCAATTATATCAATTTAAAATATAATAAAAATATAATAA-ATA-AAA
1 TATATATAAATTATATCAATTTAAAATATAAT--AAATATAAAAAGATATAAA
1074041 TATAT
1 TATAT
1074046 TTTATATAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
51 36 0.75
52 3 0.06
53 9 0.19
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (51 bp):
TATATATAAATTATATCAATTTAAAATATAATAAATATAAAAAGATATAAA
Found at i:1077840 original size:10 final size:10
Alignment explanation
Indices: 1077825--1077849 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1077815 CAAATATGAC
1077825 CTAAATACAA
1 CTAAATACAA
1077835 CTAAATACAA
1 CTAAATACAA
1077845 CTAAA
1 CTAAA
1077850 ATGTTATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (10 bp):
CTAAATACAA
Found at i:1078634 original size:44 final size:44
Alignment explanation
Indices: 1078574--1078657 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
1078564 AAAAGAAAAA
* *
1078574 AGAATATATATTTTAACAAATGCAAGCTTGTGAAGCTTACAAAG
1 AGAATATATATGTTAACAAATGCAAGCTTCTGAAGCTTACAAAG
* *
1078618 AGAATATATATGTTAACAAATGTAAGCTTCTGAAGTTTAC
1 AGAATATATATGTTAACAAATGCAAGCTTCTGAAGCTTAC
1078658 TCACATTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (44 bp):
AGAATATATATGTTAACAAATGCAAGCTTCTGAAGCTTACAAAG
Found at i:1080281 original size:23 final size:23
Alignment explanation
Indices: 1080255--1080299 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1080245 CACCACAGCT
*
1080255 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
1080278 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1080300 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1080537 original size:149 final size:149
Alignment explanation
Indices: 1080278--1080581 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
1080268 CGAAGTGCCC
* *
1080278 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1080343 CATATACATATGCCAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCCAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
1080408 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
1080427 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
* *
1080492 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCCAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
1080557 CATATGTCTCGAAGAACCG
131 CATATGTCCCGAAGAACCG
1080576 CGTAGA
1 CGTAGA
1080582 CCCTCGACTC
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCCAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:1081119 original size:18 final size:18
Alignment explanation
Indices: 1081098--1081132 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1081088 TCCCCTCTAG
1081098 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1081116 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1081133 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1081736 original size:21 final size:21
Alignment explanation
Indices: 1081712--1081756 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1081702 TGTTGTTCGT
* *
1081712 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1081733 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1081754 TTG
1 TTG
1081757 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1084466 original size:45 final size:45
Alignment explanation
Indices: 1084411--1084713 Score: 479
Period size: 45 Copynumber: 6.8 Consensus size: 45
1084401 TATAAAATTT
* *
1084411 CTTATCATTTA-TCCTATAAGATCGTAAGCTTATTTTACCAA-ATTA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATA-TA
*
1084456 CTTACAATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
1084501 CTTACCATTTATTCCATAAGCTCGTAAGATTATTTTACTAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
1084546 CTTAACATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1084591 CTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
1084635 CTTACCATTTATTCTATAAGCTCGTAAGCTTATTTTGCCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
1084680 CTTACCA-TTATTCCATAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1084714 GCATGCTTAC
Statistics
Matches: 241, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
44 69 0.29
45 168 0.70
46 4 0.02
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:1084534 original size:21 final size:21
Alignment explanation
Indices: 1084509--1084579 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1084499 TACTTACCAT
1084509 TTATTCCATAAGCTCGTAAGA
1 TTATTCCATAAGCTCGTAAGA
** ** * *
1084530 TTATTTTACTAATATACTTAACA
1 TTATTCCA-TAAGCT-CGTAAGA
*
1084553 TTTATTCCATAAGCTCGTAAGC
1 -TTATTCCATAAGCTCGTAAGA
1084575 TTATT
1 TTATT
1084580 TTACCAATAT
Statistics
Matches: 34, Mismatches: 13, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
21 11 0.32
22 8 0.24
23 9 0.26
24 6 0.18
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.42
Consensus pattern (21 bp):
TTATTCCATAAGCTCGTAAGA
Found at i:1084648 original size:89 final size:89
Alignment explanation
Indices: 1084426--1084713 Score: 479
Period size: 89 Copynumber: 3.2 Consensus size: 89
1084416 CATTTATCCT
* *
1084426 ATAAGATCGTAAGCTTATTTTACCAA-ATTACTTACAATTTATTCCATAAGCTCGTAAGCTTATT
1 ATAAGCTCGTAAGCTTATTTTACCAATA-TACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1084490 TTACCAATATACTTACCATTTATTCC
65 TTACCAATATACTTACCA-TTATTCC
* * *
1084516 ATAAGCTCGTAAGATTATTTTACTAATATACTTAACATTTATTCCATAAGCTCGTAAGCTTATTT
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1084581 TACCAATATACTTACCATTATTCC
66 TACCAATATACTTACCATTATTCC
*
1084605 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCTATAAGCTCGTAAGCTTATTT
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
*
1084670 TGCCAATATACTTACCATTATTCC
66 TACCAATATACTTACCATTATTCC
*
1084694 ATAAGCTCATAAGCTTATTT
1 ATAAGCTCGTAAGCTTATTT
1084714 GCATGCTTAC
Statistics
Matches: 186, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
89 110 0.59
90 75 0.40
91 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (89 bp):
ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
TACCAATATACTTACCATTATTCC
Found at i:1084657 original size:134 final size:135
Alignment explanation
Indices: 1084411--1084713 Score: 479
Period size: 134 Copynumber: 2.3 Consensus size: 135
1084401 TATAAAATTT
* *
1084411 CTTATCATTTA-TCCTATAAGATCGTAAGCTTATTTTACCAAATTACTTACAATTTATTCCATAA
1 CTTAACATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAAATTACTTACAATTTATTCCATAA
*
1084475 GCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGATTATTTTACT
65 GCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGATTATTTTACC
1084540 AATATA
130 AATATA
*
1084546 CTTAACATTTATTCCATAAGCTCGTAAGCTTATTTTACC-AATATACTTACCA-TTATTCCATAA
1 CTTAACATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAT-TACTTACAATTTATTCCATAA
* * *
1084609 GCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCTATAAGCTCGTAAGCTTATTTTGCC
65 GCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGATTATTTTACC
1084674 AATATA
130 AATATA
* *
1084680 CTTACCA-TTATTCCATAAGCTCATAAGCTTATTT
1 CTTAACATTTATTCCATAAGCTCGTAAGCTTATTT
1084714 GCATGCTTAC
Statistics
Matches: 157, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
133 26 0.17
134 87 0.55
135 41 0.26
136 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (135 bp):
CTTAACATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAATTACTTACAATTTATTCCATAAG
CTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGATTATTTTACCA
ATATA
Found at i:1087127 original size:31 final size:30
Alignment explanation
Indices: 1087089--1087148 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
1087079 TTATATACGC
1087089 TATGTGATAAA-GTGATGGAACATGATATGTT
1 TATGTGATAAAGGT-ATGGAA-ATGATATGTT
*
1087120 TATGTGATAAAGGTATGGAAATTATATGT
1 TATGTGATAAAGGTATGGAAATGATATGT
1087149 CTATACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 17 0.63
32 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATGATATGTT
Found at i:1087407 original size:23 final size:23
Alignment explanation
Indices: 1087371--1087425 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1087361 AATCTTATAT
* *
1087371 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGATGCAATTCTACGC
* *
1087394 GGTACTTCGATGCAATTCTACGT
1 GGCACTTCGATGCAATTCTACGC
1087417 GGCACTTCG
1 GGCACTTCG
1087426 GTGCGTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTTCGATGCAATTCTACGC
Found at i:1095870 original size:14 final size:13
Alignment explanation
Indices: 1095835--1095884 Score: 61
Period size: 12 Copynumber: 4.0 Consensus size: 13
1095825 GCCTGGGTCG
1095835 TTATTATTA-TTA
1 TTATTATTATTTA
1095847 TTATTATTATTTA
1 TTATTATTATTTA
*
1095860 TCTATTTTTATTTA
1 T-TATTATTATTTA
1095874 -TATT-TTATTTA
1 TTATTATTATTTA
1095885 AAGGCTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
11 7 0.20
12 13 0.37
13 4 0.11
14 11 0.31
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:1096443 original size:39 final size:37
Alignment explanation
Indices: 1096369--1096443 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 37
1096359 AATTGATTTT
* *
1096369 AGAGAGAAAAAAAGAGCTTTAAAAGAAAGAAAAAAAC
1 AGAGAGAAAAAAAAAGCTTTAAAAAAAAGAAAAAAAC
*
1096406 AGAGAGAAAAAAGAAAGCCTTTGAAAAAAAAGGAAAAA
1 AGAGAGAAAAAA-AAAG-CTTT-AAAAAAAAGAAAAAA
1096444 TAGAGACTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 12 0.38
38 3 0.09
39 4 0.12
40 13 0.41
ACGTcount: A:0.67, C:0.05, G:0.20, T:0.08
Consensus pattern (37 bp):
AGAGAGAAAAAAAAAGCTTTAAAAAAAAGAAAAAAAC
Found at i:1096449 original size:39 final size:37
Alignment explanation
Indices: 1096368--1096449 Score: 94
Period size: 39 Copynumber: 2.2 Consensus size: 37
1096358 AAATTGATTT
* *
1096368 TAGAGAGAAAAAAAGAGCTTTAAAAGAAAGAAAAAAA
1 TAGAGAGAAAAAAAAAGCTTTAAAAAAAAGAAAAAAA
* *
1096405 CAGAGAGAAAAAAGAAAGCCTTTGAAAAAAAAG-GAAAAA
1 TAGAGAGAAAAAA-AAAG-CTTT-AAAAAAAAGAAAAAAA
1096444 TAGAGA
1 TAGAGA
1096450 CTTTACCACA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
37 12 0.32
38 3 0.08
39 14 0.38
40 8 0.22
ACGTcount: A:0.65, C:0.05, G:0.21, T:0.10
Consensus pattern (37 bp):
TAGAGAGAAAAAAAAAGCTTTAAAAAAAAGAAAAAAA
Found at i:1097978 original size:22 final size:22
Alignment explanation
Indices: 1097924--1097986 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
1097914 ACTCCCCTAT
*
1097924 CAGTATCGATACCTTCTTCAAC
1 CAGTATCGATACATTCTTCAAC
* *
1097946 CAGTTTTGATACATTCTTCAAC
1 CAGTATCGATACATTCTTCAAC
*
1097968 CAGTAGCGATACTATTCTT
1 CAGTATCGATAC-ATTCTT
1097987 TGAATTCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 28 0.82
23 6 0.18
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (22 bp):
CAGTATCGATACATTCTTCAAC
Found at i:1102281 original size:23 final size:23
Alignment explanation
Indices: 1102251--1102303 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1102241 TCCCGAAGGA
*
1102251 CCACATAGGTTTGCACCAAAGTG
1 CCACATAGGTTTGCAACAAAGTG
1102274 CCACATAGGTTTGCAACAAAGTG
1 CCACATAGGTTTGCAACAAAGTG
1102297 CCACATA
1 CCACATA
1102304 ATTGTCCCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (23 bp):
CCACATAGGTTTGCAACAAAGTG
Found at i:1107401 original size:23 final size:22
Alignment explanation
Indices: 1107324--1107403 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 22
1107314 CATAGCAGAG
* * *
1107324 TGCATCGATGTATATTCCAGGAA
1 TGCATCGATGCACATT-CAGGGA
* * *
1107347 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAGGGA
*
1107368 TGTATCGATGCACATTCAAGGGA
1 TGCATCGATGCACATTC-AGGGA
1107391 TGCATCGATGCAC
1 TGCATCGATGCAC
1107404 TGTCTAGTGT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
21 14 0.32
22 6 0.14
23 24 0.55
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACATTCAGGGA
Found at i:1107419 original size:20 final size:20
Alignment explanation
Indices: 1107394--1107442 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1107384 CAAGGGATGC
1107394 ATCGATGCACTGTCTAGTGT
1 ATCGATGCACTGTCTAGTGT
1107414 ATCGATGCACTGTCTAGTGT
1 ATCGATGCACTGTCTAGTGT
1107434 ATCGATGCA
1 ATCGATGCA
1107443 TTATGCACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGATGCACTGTCTAGTGT
Found at i:1107422 original size:43 final size:44
Alignment explanation
Indices: 1107322--1107423 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 44
1107312 TGCATAGCAG
* * * * *
1107322 AGTGCATCGATGTATATTCCAGGAATGCATCGGTGCACCTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGATGCACCTTCAT
* *
1107366 GGTGTATCGATGCACATTCAAGGGATGCATCGATGCA-CTGTC-T
1 AGTGTATCGATGCACATTCAAGGAATGCATCGATGCACCT-TCAT
1107409 AGTGTATCGATGCAC
1 AGTGTATCGATGCAC
1107424 TGTCTAGTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 17 0.35
44 32 0.65
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGATGCACCTTCAT
Found at i:1111914 original size:76 final size:76
Alignment explanation
Indices: 1111819--1111975 Score: 223
Period size: 76 Copynumber: 2.1 Consensus size: 76
1111809 CATAGTTATG
1111819 AGTTAGACAACTAATTTTAGATTCTTTGTCACCTTAT-AT-CTTCAT-GTGACCTGAAGTTTATC
1 AGTTAGACAACTAATTTTAGATTC-TT-T-ACCTTATGATGCTTCATAGTGA-CTGAAGTTTATC
1111881 ACATATCTCCTTGGC
62 ACATATCTCCTTGGC
* *
1111896 AGTTAGA-GACTAATTTTAGATTCTTTACCTTATGTTGCTTCATGAGTGACTGAAGTTTATCACA
1 AGTTAGACAACTAATTTTAGATTCTTTACCTTATGATGCTTCAT-AGTGACTGAAGTTTATCACA
1111960 TATCTCCTTGGC
65 TATCTCCTTGGC
1111972 AGTT
1 AGTT
1111976 GTACAAGATG
Statistics
Matches: 74, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
73 7 0.09
74 2 0.03
75 8 0.11
76 46 0.62
77 11 0.15
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (76 bp):
AGTTAGACAACTAATTTTAGATTCTTTACCTTATGATGCTTCATAGTGACTGAAGTTTATCACAT
ATCTCCTTGGC
Found at i:1114114 original size:134 final size:133
Alignment explanation
Indices: 1113564--1114233 Score: 714
Period size: 133 Copynumber: 5.0 Consensus size: 133
1113554 AATCGTACGT
* * *
1113564 GATTTGCTTCGCT-CTCTTCATGAAGACCAAATCTGAAAGAAGTCAA-AA-CTACTACACTACTC
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAG--AAGAATCTACTCCACTACTC
* * * *
1113626 TTTAGGGGAGATCAGA--C-ATG-TAATTTTGATACACTTTACTACTCTTCAGGGAAGATTAAAT
64 TTTAGGGGAGATCAGACTCGA-GAAAATTTTGATCCACTTTGCTACTCTTCAGGGAAGATTGAAT
1113687 CGGAATC
128 C-GAATC
* * ** **
1113694 GATTTGCTTCACTACTCTTCAGGAAGACCAAATATGAAAGAAGGTGGGTCTACTCCACTACTCTT
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACTCTT
* * * * * * * *
1113759 TAAGGGAGATCAGACACG-TAATATTTTGATCCACTTTGTTTCTCTTCAAGAAAGATTGAATCAG
66 TAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTTGCTACTCTTCAGGGAAGATTGAATC-G
1113823 AATC
130 AATC
* * * * *
1113827 GATTTGCTTCACTGCTCTTAAGGAATACCAAATCTGAAAGAATGCAG-GTCTGCTCCACTACTCT
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAA-GAAGAATCTACTCCACTACTCT
* * * * * *
1113891 TTAGGGGAGATAAGACAT-G-TAATATTTTGATCCACTTGGCTACTCTTCAGCGAAAATTGAATC
65 TTAGGGGAGATCAGAC-TCGAGAAAATTTTGATCCACTTTGCTACTCTTCAGGGAAGATTGAATC
*
1113954 GAAATA
129 G-AATC
* * *
1113960 GATTTGCTTCACTTCCCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTT
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACTCTT
* * * * *
1114025 TAAGGGAGATCAGACTCGAGAAAATTTTGATTCACTTCGCTTCTCTTCAGGGAAGACTGAATCGA
66 TAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTTGCTACTCTTCAGGGAAGATTGAATCGA
*
1114090 ACTT
131 A-TC
* * * *
1114094 GATTTGCTTCACTGCTCTTCAGAAAGACCAAATCTGAAAGAAGAAGAATCTACTCCAATATTATT
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACTCTT
* * * * *
1114159 TAGGGGAGATCAGACTCGAGAAAATTTTGATCCATTTTGCTGCTCTTAAGGGAAGACTAAATCGA
66 TAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTTGCTACTCTTCAGGGAAGATTGAATCGA
1114224 GATC
131 -ATC
1114228 GATTTG
1 GATTTG
1114234 TTTCTCTTAT
Statistics
Matches: 455, Mismatches: 70, Indels: 26
0.83 0.13 0.05
Matches are distributed among these distances:
130 12 0.03
131 55 0.12
132 5 0.01
133 219 0.48
134 163 0.36
135 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (133 bp):
GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACTCTT
TAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTTGCTACTCTTCAGGGAAGATTGAATCGA
ATC
Found at i:1114895 original size:45 final size:44
Alignment explanation
Indices: 1114831--1115309 Score: 324
Period size: 45 Copynumber: 10.7 Consensus size: 44
1114821 AATGACATCT
* *
1114831 CTAAAAGGTTGACTTCTCTTCACTAGAAAGTCAAATAGGACAAAA
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAA-AGGACAAAA
** * * *
1114876 CTAAAAGATCAACTCCTCTTCGCGAGAAAGTCAAGGAA-GACAACA
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAA--AAGGACAAAA
* * *
1114921 CT-AAAGATTGAC-TCATCTTCATGAGAAAGTCAAGAATGACAATA
1 CTAAAAGATTGACTTC-TCTTCACGAGAAAGTCAA-AAGGACAAAA
* * * * ** **
1114965 CTAAAAGGTTAACTTCTCTTTATGAGAAAGTCAAGAACAACACCA
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAA-AAGGACAAAA
* * * * *
1115010 CTAAAAGGTTGACTTCTCTTAAGGAGAAAGTCAAGTAGGACAACA
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAA-AAGGACAAAA
* * * *
1115055 CTAAAAGATCGACTCCTCTTCGCGAGAAAGTCAAGGAA-GATAAAA
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAA--AAGGACAAAA
* * * *
1115100 CTAAAAGATTGACTCCTCTTCACGAGAAAGTGAAACATGACAATA
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAA-AGGACAAAA
* * * * ** *
1115145 CTAAAAGGTTAACTTATCTTCACGAGAAATTCAAGAACAACAATA
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAA-AAGGACAAAA
* * * ** *
1115190 CTGAAATATCGACTTCTCTTCATAAGAAAGTCAAGTAGGA-AAACA
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAA-AAGGACAAA-A
* * *
1115235 CTAAAAGATCGACTTCTCTTCACGAGAAAGTCGAGAATGA-AAATA
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTC-AAAAGGACAAA-A
* *
1115280 CTGAAAGATTGA-TTCCTTTTCACGAGAAAG
1 CTAAAAGATTGACTT-CTCTTCACGAGAAAG
1115310 CCAGGAATAA
Statistics
Matches: 348, Mismatches: 73, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
43 5 0.01
44 37 0.11
45 298 0.86
46 7 0.02
47 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (44 bp):
CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAAAGGACAAAA
Found at i:1115060 original size:90 final size:90
Alignment explanation
Indices: 1114831--1115309 Score: 441
Period size: 90 Copynumber: 5.3 Consensus size: 90
1114821 AATGACATCT
* * * * *
1114831 CTAAAAGGTTGACTTCTCTTCACTAGAAAGTCAAATAGGACAAAACTAAAAGATCAACTCCTCTT
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGTAGGACAACACTAAAAGATCAACTTCTCTT
* *
1114896 CGCGAGAAAGTCAAGGAA-GACAACA
66 CACGAGAAAGTCAA-GAACAACAACA
* * * * * *
1114921 CT-AAAGATTGAC-TCATCTTCATGAGAAAGTCAAGAATGACAATACTAAAAGGTTAACTTCTCT
1 CTAAAAGATTGACTTC-TCTTCACGAGAAAGTCAAGTAGGACAACACTAAAAGATCAACTTCTCT
* * *
1114984 TTATGAGAAAGTCAAGAACAACACCA
65 TCACGAGAAAGTCAAGAACAACAACA
* * * * *
1115010 CTAAAAGGTTGACTTCTCTTAAGGAGAAAGTCAAGTAGGACAACACTAAAAGATCGACTCCTCTT
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGTAGGACAACACTAAAAGATCAACTTCTCTT
* *
1115075 CGCGAGAAAGTCAAGGAAGATA-AA-A
66 CACGAGAAAGTCAA-GAACA-ACAACA
* * ** * * * * *
1115100 CTAAAAGATTGACTCCTCTTCACGAGAAAGTGAAACATGACAATACTAAAAGGTTAACTTATCTT
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGTAGGACAACACTAAAAGATCAACTTCTCTT
* *
1115165 CACGAGAAATTCAAGAACAACAATA
66 CACGAGAAAGTCAAGAACAACAACA
* * * ** * *
1115190 CTGAAATATCGACTTCTCTTCATAAGAAAGTCAAGTAGGAAAACACTAAAAGATCGACTTCTCTT
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGTAGGACAACACTAAAAGATCAACTTCTCTT
* * *
1115255 CACGAGAAAGTCGAGAATGAA-AATA
66 CACGAGAAAGTCAAGAA-CAACAACA
* *
1115280 CTGAAAGATTGA-TTCCTTTTCACGAGAAAG
1 CTAAAAGATTGACTT-CTCTTCACGAGAAAG
1115310 CCAGGAATAA
Statistics
Matches: 308, Mismatches: 71, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
88 6 0.02
89 75 0.24
90 217 0.70
91 9 0.03
92 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (90 bp):
CTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGTAGGACAACACTAAAAGATCAACTTCTCTT
CACGAGAAAGTCAAGAACAACAACA
Found at i:1115128 original size:135 final size:134
Alignment explanation
Indices: 1114831--1115271 Score: 410
Period size: 135 Copynumber: 3.3 Consensus size: 134
1114821 AATGACATCT
* * * * * * **
1114831 CTAAAAGGTTGACTTCTCTTCACTAGAAAGTC-A-AATAGGACAAAACTAAAAGATCAACTCCTC
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCGAGAACA-GACAACACTAAAAGGTTAACTTATC
** * * *
1114894 TTCGCGAGAAAGTCAAGGAAGACAACACTAAAGATTGACTCATCTTCATGAGAAAGTCAA-GAAT
65 TTAACGAGAAAGTCAAGAAAGACAACACTAAAGATCGACTCCTCTTCATGAGAAAGTCAAGGAA-
*
1114958 GACAATA
129 GA-AAAA
* * * * * * * *
1114965 CTAAAAGGTTAACTTCTCTTTATGAGAAAGTCAAGAACA-ACACCACTAAAAGGTTGACTTCTCT
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCGAGAACAGACAACACTAAAAGGTTAACTTATCT
* * * **
1115029 TAAGGAGAAAGTCAAGTAGGACAACACTAAAAGATCGACTCCTCTTCGCGAGAAAGTCAAGGAAG
66 TAACGAGAAAGTCAAGAAAGACAACACT-AAAGATCGACTCCTCTTCATGAGAAAGTCAAGGAAG
1115094 ATAAAA
130 A-AAAA
* *
1115100 CTAAAAGATTGACTCCTCTTCACGAGAAAGT-GA-AACATGACAATACTAAAAGGTTAACTTATC
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCGAGAACA-GACAACACTAAAAGGTTAACTTATC
* * * * * * *
1115163 TTCACGAGAAATTCAAGAACA-ACAATACTGAAATATCGACTTCTCTTCATAAGAAAGTCAAGTA
65 TTAACGAGAAAGTCAAGAA-AGACAACACT-AAAGATCGACTCCTCTTCATGAGAAAGTCAAGGA
*
1115227 GGAAAACA
128 AGAAAA-A
*
1115235 CTAAAAGATCGACTTCTCTTCACGAGAAAGTCGAGAA
1 CTAAAAGATTGACTTCTCTTCACGAGAAAGTCGAGAA
1115272 TGAAAATACT
Statistics
Matches: 249, Mismatches: 48, Indels: 17
0.79 0.15 0.05
Matches are distributed among these distances:
133 4 0.02
134 74 0.30
135 161 0.65
136 8 0.03
137 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (134 bp):
CTAAAAGATTGACTTCTCTTCACGAGAAAGTCGAGAACAGACAACACTAAAAGGTTAACTTATCT
TAACGAGAAAGTCAAGAAAGACAACACTAAAGATCGACTCCTCTTCATGAGAAAGTCAAGGAAGA
AAAA
Found at i:1115208 original size:180 final size:178
Alignment explanation
Indices: 1114831--1115323 Score: 612
Period size: 180 Copynumber: 2.7 Consensus size: 178
1114821 AATGACATCT
* * * * * *
1114831 CTAAAAGGTTGACTTCTCTTCACTAGAAAGTCAAATAGGACAAAACTAAAAGATCAACTCCTCTT
1 CTAAAAGATCGACTTCTCTTCACAAGAAAGTCAAGTAGGACAACACTAAAAGATCGACTCCTCTT
* * *
1114896 CGCGAGAAAGTCAAGGAAGACAACACTAAAGATTGACTCATCTTCATGAGAAAGTCAAGAATGAC
66 CGCGAGAAAGTCAAGGAAGA-AAAACTAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGAC
* * * *
1114961 AATACTAAAAGGTTAACTTCTCTTTATGAGAAAGTCAAGAACAACACCA
130 AATACTAAAAGGTTAACTTATCTTCACGAGAAAGTCAAGAACAACAACA
* * * **
1115010 CTAAAAGGTTGACTTCTCTTAAGGAGAAAGTCAAGTAGGACAACACTAAAAGATCGACTCCTCTT
1 CTAAAAGATCGACTTCTCTTCACAAGAAAGTCAAGTAGGACAACACTAAAAGATCGACTCCTCTT
*
1115075 CGCGAGAAAGTCAAGGAAGATAAAACTAAAAGATTGACTCCTCTTCACGAGAAAGTGAA-ACATG
66 CGCGAGAAAGTCAAGGAAGA-AAAACT-AAAGATTGACTCCTCTTCACGAGAAAGTCAAGA-ATG
* *
1115139 ACAATACTAAAAGGTTAACTTATCTTCACGAGAAATTCAAGAACAACAATA
128 ACAATACTAAAAGGTTAACTTATCTTCACGAGAAAGTCAAGAACAACAACA
* * * * *
1115190 CTGAAATATCGACTTCTCTTCATAAGAAAGTCAAGTAGGAAAACACTAAAAGATCGACTTCTCTT
1 CTAAAAGATCGACTTCTCTTCACAAGAAAGTCAAGTAGGACAACACTAAAAGATCGACTCCTCTT
* * * * * * *
1115255 CACGAGAAAGTCGA-GAATGAAAATACTGAAAGATTGATTCCTTTTCACGAGAAAGCCAGGAATA
66 CGCGAGAAAGTCAAGGAA-GAAAA-ACT-AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATG
1115319 ACAAT
128 ACAAT
1115324 GAAATATTGA
Statistics
Matches: 274, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
179 91 0.33
180 182 0.66
181 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (178 bp):
CTAAAAGATCGACTTCTCTTCACAAGAAAGTCAAGTAGGACAACACTAAAAGATCGACTCCTCTT
CGCGAGAAAGTCAAGGAAGAAAAACTAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACA
ATACTAAAAGGTTAACTTATCTTCACGAGAAAGTCAAGAACAACAACA
Found at i:1115322 original size:135 final size:132
Alignment explanation
Indices: 1115062--1115357 Score: 319
Period size: 135 Copynumber: 2.2 Consensus size: 132
1115052 ACACTAAAAG
*** * *
1115062 ATCGACTCCTCTTCGCGAGAAAGTCAAGGAAGATAAAACTAAAAGATTGACTCCTCTTCACGAGA
1 ATCGACTCCTCTTCATAAGAAAGTCAAGTAAGATAAAACTAAAAGATCGACTCCTCTTCACGAGA
* * **
1115127 AAGTGAAACATGACAATACTAAAAGGTTAACTTATCTTCACGAGAAATTCAAGAACAACAATACT
66 AAGTGAAACATGAAAATACTAAAAGATTAACTTATCTTCACGAGAAAGCCAAGAACAAC-A-A-T
1115192 GAAAT
128 GAAAT
* * *
1115197 ATCGACTTCTCTTCATAAGAAAGTCAAGTAGGA-AAACACTAAAAGATCGACTTCTCTTCACGAG
1 ATCGACTCCTCTTCATAAGAAAGTCAAGTAAGATAAA-ACTAAAAGATCGACTCCTCTTCACGAG
* * * * * * *
1115261 AAAGTCGAGA-ATGAAAATACTGAAAGATTGA-TTCCTTTTCACGAGAAAGCCAGGAATAACAAT
65 AAAGT-GAAACATGAAAATACTAAAAGATTAACTT-ATCTTCACGAGAAAGCCAAGAACAACAAT
1115324 GAAAT
128 GAAAT
* * *
1115329 ATTGACTCCTCTTCATGAGAGAGTCAAGT
1 ATCGACTCCTCTTCATAAGAAAGTCAAGT
1115358 TGAAGCTTTA
Statistics
Matches: 135, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
132 31 0.23
133 1 0.01
134 6 0.04
135 94 0.70
136 3 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (132 bp):
ATCGACTCCTCTTCATAAGAAAGTCAAGTAAGATAAAACTAAAAGATCGACTCCTCTTCACGAGA
AAGTGAAACATGAAAATACTAAAAGATTAACTTATCTTCACGAGAAAGCCAAGAACAACAATGAA
AT
Found at i:1117679 original size:2 final size:2
Alignment explanation
Indices: 1117672--1117699 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1117662 GTTGGCGGTG
1117672 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
1117700 GTGTTATTTT
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:1127639 original size:16 final size:16
Alignment explanation
Indices: 1127618--1127649 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1127608 AAATATAATT
1127618 AAAAGAGGAAGAAAAG
1 AAAAGAGGAAGAAAAG
1127634 AAAAGAGGAAGAAAAG
1 AAAAGAGGAAGAAAAG
1127650 TGCTCAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AAAAGAGGAAGAAAAG
Found at i:1133912 original size:22 final size:22
Alignment explanation
Indices: 1133887--1133932 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1133877 AATGCATGCA
1133887 TGCATGCATGCATGAAAATCAG
1 TGCATGCATGCATGAAAATCAG
1133909 TGCATGCATGCATGAAAATCAG
1 TGCATGCATGCATGAAAATCAG
1133931 TG
1 TG
1133933 GAAATTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (22 bp):
TGCATGCATGCATGAAAATCAG
Found at i:1134728 original size:21 final size:22
Alignment explanation
Indices: 1134684--1134731 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
1134674 CATTGAATTA
*
1134684 TAAATTAGTTAAAATTTTAAAGG
1 TAAATTAGTTAAAA-TTAAAAGG
*
1134707 TAAATTATTTAAAA-TAAAAGG
1 TAAATTAGTTAAAATTAAAAGG
1134728 TAAA
1 TAAA
1134732 ATGTACCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
23 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.35
Consensus pattern (22 bp):
TAAATTAGTTAAAATTAAAAGG
Found at i:1140975 original size:2 final size:2
Alignment explanation
Indices: 1140968--1141059 Score: 175
Period size: 2 Copynumber: 46.0 Consensus size: 2
1140958 GCTCGTTCGA
1140968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1141010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1141052 AT AT AT AT
1 AT AT AT AT
1141060 CTTGTTGTTA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1141536 original size:3 final size:3
Alignment explanation
Indices: 1141528--1141576 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1141518 AATGTATTAA
1141528 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1141576 A
1 A
1141577 TATATATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1141581 original size:2 final size:2
Alignment explanation
Indices: 1141574--1141598 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1141564 AATAATAATA
1141574 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
1141599 GAGAGAGCCA
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:1142013 original size:20 final size:20
Alignment explanation
Indices: 1141988--1142032 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1141978 TACGTGATGA
1141988 GGATGGTAGGACATCTTTAG
1 GGATGGTAGGACATCTTTAG
1142008 GGATGGTAGGACATCTTTAG
1 GGATGGTAGGACATCTTTAG
1142028 GGATG
1 GGATG
1142033 ATAACATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (20 bp):
GGATGGTAGGACATCTTTAG
Found at i:1142194 original size:151 final size:150
Alignment explanation
Indices: 1141891--1142170 Score: 339
Period size: 151 Copynumber: 1.9 Consensus size: 150
1141881 GATAACACGA
* * *
1141891 TTCCTACGCGATGAAGACGGCTGGTTATCTAGGGGTGACATGGCTCCTACGTGTTGAGGAGGTAT
1 TTCCAACGCGATGAAGACGGCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTAT
* ** * **
1141956 GGTCGGGGGATGACACGGTTCCTACGTGATGAGGATGGTAGGACATCTTTAGGGATGGTAGGACA
66 GGTCGGGGGATGACACGGTTCCTACGCGATGAGGATCATAGGACATCTTTAGGGATGATAACACA
*
1142021 TCTTTAGGGATGATAACATGG
131 TCTATAGGGATGA-AACATGG
* * * * *
1142042 TTCCAACGTGATGAGGACGGCTGGTTATCTAGGGTTGACACGGCTCCTACTTGATGAGGAGGTCT
1 TTCCAACGCGATGAAGACGGCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTAT
* * * * *
1142107 GGTCGGTGGATGACATGGTTCTTACGCGATGAGGA-CATCA-TACTATCTTTTGGGATGATAACA
66 GGTCGGGGGATGACACGGTTCCTACGCGATGAGGATCAT-AGGAC-ATCTTTAGGGATGATAACA
1142170 C
129 C
1142171 GATTCCTATG
Statistics
Matches: 108, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
150 3 0.03
151 105 0.97
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.28
Consensus pattern (150 bp):
TTCCAACGCGATGAAGACGGCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTAT
GGTCGGGGGATGACACGGTTCCTACGCGATGAGGATCATAGGACATCTTTAGGGATGATAACACA
TCTATAGGGATGAAACATGG
Found at i:1142259 original size:130 final size:131
Alignment explanation
Indices: 1142020--1142264 Score: 359
Period size: 130 Copynumber: 1.9 Consensus size: 131
1142010 ATGGTAGGAC
* *
1142020 ATCTTTAGGGATGATAACATGGTTCCAACGTGATGAGGACGGCTGGTTATCTAGGGTTGACACGG
1 ATCTTTAGGGATGATAACACGATTCCAACGTGATGAGGACGGCTGGTTATCTAGGGTTGACACGG
* * * *
1142085 CTCCTACTTGATGAGGAGGTCTGGTCGGTGGATGACATGGTTCTTACGCGATGAGGACATCATAC
66 CTCCTACTTGATGAGAAGGTCTGGTCGGTGGATAACACGATTCTTACGCGATGAGGACATCATAC
1142150 T
131 T
* * * * * *
1142151 ATCTTTTGGGATGATAACACGATTCCTATGTGATGAGGATGGTTGGTTATCTAGGG-TGACATGG
1 ATCTTTAGGGATGATAACACGATTCCAACGTGATGAGGACGGCTGGTTATCTAGGGTTGACACGG
1142215 CTCCTA-TGTGATGAGAAGGTCTGGTCGGTGGATAACACGATTCTTACGCG
66 CTCCTACT-TGATGAGAAGGTCTGGTCGGTGGATAACACGATTCTTACGCG
1142265 GTGATGACGG
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
129 1 0.01
130 51 0.50
131 49 0.49
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (131 bp):
ATCTTTAGGGATGATAACACGATTCCAACGTGATGAGGACGGCTGGTTATCTAGGGTTGACACGG
CTCCTACTTGATGAGAAGGTCTGGTCGGTGGATAACACGATTCTTACGCGATGAGGACATCATAC
T
Found at i:1142371 original size:20 final size:20
Alignment explanation
Indices: 1142346--1142385 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1142336 AAGGGGGGCA
1142346 AAATTTGTTTCAAGAGAAAC
1 AAATTTGTTTCAAGAGAAAC
*
1142366 AAATTTGTTTCAAGGGAAAC
1 AAATTTGTTTCAAGAGAAAC
1142386 GATCTCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (20 bp):
AAATTTGTTTCAAGAGAAAC
Found at i:1142624 original size:37 final size:36
Alignment explanation
Indices: 1142536--1142666 Score: 149
Period size: 37 Copynumber: 3.6 Consensus size: 36
1142526 TTTCTTAAAG
* *
1142536 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTT-GA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTAGA
** *
1142571 GAGAAATTAACTCAAGCGAGACAAAATTTGTTATTAGC
1 GA-AAATTGTCTCAAGCGAGACAAAATTTGTT-TTAGA
*
1142609 GAAAATTGTCTCAAGCGAGATAAAATTTGTTTTTA-A
1 GAAAATTGTCTCAAGCGAGACAAAATTTG-TTTTAGA
*
1142645 GAAAACTTGTCTCAGGCGAGAC
1 GAAAA-TTGTCTCAAGCGAGAC
1142667 GACCCTTTGT
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
35 2 0.03
36 30 0.38
37 43 0.54
38 5 0.06
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTAGA
Found at i:1143860 original size:16 final size:15
Alignment explanation
Indices: 1143839--1143885 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 15
1143829 TTTGCATGTG
1143839 TTTCTTATCTTTTTTC
1 TTTCTT-TCTTTTTTC
*
1143855 TTTCTTTGTTTTTTC
1 TTTCTTTCTTTTTTC
*
1143870 -TT-TTGCTTTTTTC
1 TTTCTTTCTTTTTTC
1143883 TTT
1 TTT
1143886 ATTTTTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 9 0.33
14 4 0.15
15 8 0.30
16 6 0.22
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTCTTTCTTTTTTC
Found at i:1143869 original size:11 final size:11
Alignment explanation
Indices: 1143846--1143893 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
1143836 GTGTTTCTTA
1143846 TCTTT-TTTCTT
1 TCTTTGTTT-TT
1143857 TCTTTGTTTTT
1 TCTTTGTTTTT
1143868 TCTTTTGCTTTTT
1 TC-TTTG-TTTTT
*
1143881 TCTTTATTTTT
1 TCTTTGTTTTT
1143892 TC
1 TC
1143894 ATTTCTCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 16 0.48
12 10 0.30
13 7 0.21
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (11 bp):
TCTTTGTTTTT
Found at i:1143908 original size:18 final size:18
Alignment explanation
Indices: 1143887--1143926 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1143877 TTTTTCTTTA
1143887 TTTTTTCATTTCTCATTG
1 TTTTTTCATTTCTCATTG
* *
1143905 TTTTTTCTTTTCTCTTTG
1 TTTTTTCATTTCTCATTG
1143923 TTTT
1 TTTT
1143927 GATTGGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTTTCATTTCTCATTG
Found at i:1145151 original size:23 final size:23
Alignment explanation
Indices: 1145125--1145212 Score: 106
Period size: 23 Copynumber: 3.8 Consensus size: 23
1145115 CACCACAACT
* *
1145125 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCG
* * *
1145148 CGTAGAATTGAACC-ATAGTACCG
1 CGTAGAAATGCACCGA-AGTGCCG
*
1145171 CGTAGAAATGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
1145194 CGTAGAAATGCACCGAAGT
1 CGTAGAAATGCACCGAAGT
1145213 TCCATATAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.02
23 52 0.98
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1146661 original size:22 final size:22
Alignment explanation
Indices: 1146636--1146678 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1146626 TTTTGTTCGT
*
1146636 TTGAAGGGGTATCGGTTCCCCC
1 TTGAAGGGGTATCGATTCCCCC
*
1146658 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
1146679 TAGCCCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (22 bp):
TTGAAGGGGTATCGATTCCCCC
Found at i:1148240 original size:27 final size:26
Alignment explanation
Indices: 1148185--1148251 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
1148175 TTCATGAATG
1148185 ATGCATATG-AAAATGCTTAAAAATAAA
1 ATGCATATGCAAAATG--TAAAAATAAA
1148212 ATGCATATGCAAAATG-AAAAGATACAA
1 ATGCATATGCAAAATGTAAAA-ATA-AA
*
1148239 ATGTA-ATGCAAAA
1 ATGCATATGCAAAA
1148252 ATGTTGATCC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 4 0.11
26 11 0.31
27 15 0.42
28 6 0.17
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.22
Consensus pattern (26 bp):
ATGCATATGCAAAATGTAAAAATAAA
Found at i:1151396 original size:25 final size:25
Alignment explanation
Indices: 1151368--1151418 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1151358 CGCTGGCTTT
* * **
1151368 CGTGTCGTCCACTGCCTGTCGCCGC
1 CGTGCCGTCCACCGCCTACCGCCGC
1151393 CGTGCCGTCCACCGCCTACCGCCGC
1 CGTGCCGTCCACCGCCTACCGCCGC
1151418 C
1 C
1151419 ATACCGTCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.06, C:0.51, G:0.25, T:0.18
Consensus pattern (25 bp):
CGTGCCGTCCACCGCCTACCGCCGC
Found at i:1151425 original size:25 final size:25
Alignment explanation
Indices: 1151373--1151426 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
1151363 GCTTTCGTGT
* ** * *
1151373 CGTCCACTGCCTGTCGCCGCCGTGC
1 CGTCCACCGCCTACCGCCGCCATAC
1151398 CGTCCACCGCCTACCGCCGCCATAC
1 CGTCCACCGCCTACCGCCGCCATAC
1151423 CGTC
1 CGTC
1151427 TATCGCTGTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.09, C:0.52, G:0.22, T:0.17
Consensus pattern (25 bp):
CGTCCACCGCCTACCGCCGCCATAC
Found at i:1155445 original size:11 final size:11
Alignment explanation
Indices: 1155429--1155469 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1155419 GATATGGGAA
1155429 AAATTTAATTT
1 AAATTTAATTT
1155440 AAATTTAAATTT
1 AAATTT-AATTT
1155452 AAA-TTAATTT
1 AAATTTAATTT
*
1155462 AATTTTAA
1 AAATTTAA
1155470 AATAACGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 7 0.26
11 12 0.44
12 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:1155446 original size:6 final size:6
Alignment explanation
Indices: 1155429--1155470 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1155419 GATATGGGAA
*
1155429 AAATTT -AATTT AAATTT AAATTT AAA-TT -AATTT AATTTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA
1155471 ATAACGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 2 0.06
5 9 0.29
6 20 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:1155481 original size:22 final size:22
Alignment explanation
Indices: 1155433--1155474 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1155423 TGGGAAAAAT
*
1155433 TTAATTTAAATTTAAATTTAAA
1 TTAATTTAAATTTAAATATAAA
*
1155455 TTAATTTAATTTTAAA-ATAA
1 TTAATTTAAATTTAAATATAA
1155475 CGTTAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAATTTAAATTTAAATATAAA
Found at i:1155839 original size:21 final size:21
Alignment explanation
Indices: 1155809--1155858 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1155799 ACTATGGAGA
*
1155809 AGGCTGTTCGAGACGGACTAG
1 AGGCTCTTCGAGACGGACTAG
1155830 AGGCTCTTCGAGACGGACTAG
1 AGGCTCTTCGAGACGGACTAG
1155851 AGGCTCTT
1 AGGCTCTT
1155859 TATAAGAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.22
Consensus pattern (21 bp):
AGGCTCTTCGAGACGGACTAG
Found at i:1158339 original size:20 final size:20
Alignment explanation
Indices: 1158314--1158364 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1158304 TCAAGGGATA
1158314 CATCGATACATGGTGTAGTG
1 CATCGATACATGGTGTAGTG
1158334 CATCGATACATGGTGTAGTG
1 CATCGATACATGGTGTAGTG
1158354 CATCGATACAT
1 CATCGATACAT
1158365 ACCTTCATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (20 bp):
CATCGATACATGGTGTAGTG
Found at i:1160334 original size:13 final size:13
Alignment explanation
Indices: 1160316--1160344 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1160306 TTACAACACA
1160316 TCACATTCACATT
1 TCACATTCACATT
1160329 TCACATTCACATT
1 TCACATTCACATT
1160342 TCA
1 TCA
1160345 TATCAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
TCACATTCACATT
Found at i:1163507 original size:17 final size:18
Alignment explanation
Indices: 1163485--1163518 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1163475 TCAACAGGTC
1163485 CGGTT-CGAACGGTTCAG
1 CGGTTCCGAACGGTTCAG
*
1163502 CGGTTCCGACCGGTTCA
1 CGGTTCCGAACGGTTCA
1163519 CTAGTAGCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.29, G:0.32, T:0.24
Consensus pattern (18 bp):
CGGTTCCGAACGGTTCAG
Found at i:1165649 original size:31 final size:33
Alignment explanation
Indices: 1165613--1165693 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 33
1165603 TAAATTTTAT
*
1165613 TTTATTTTTAATTTAA-CTACT-TAACTTTCAAA
1 TTTATTTTTAATTTAATC-ACTCAAACTTTCAAA
** *
1165645 -TTATTCCTAGTTTAATCACTCAAACTTTCAAA
1 TTTATTTTTAATTTAATCACTCAAACTTTCAAA
*
1165677 TTTAATTTTTATTTTAA
1 TTT-ATTTTTAATTTAA
1165694 ATTATATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
31 15 0.39
32 11 0.29
33 2 0.05
34 10 0.26
ACGTcount: A:0.33, C:0.14, G:0.01, T:0.52
Consensus pattern (33 bp):
TTTATTTTTAATTTAATCACTCAAACTTTCAAA
Found at i:1169800 original size:22 final size:22
Alignment explanation
Indices: 1169775--1169830 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1169765 TTCTTCAATA
1169775 TTAATAATATTAATATAATAATT
1 TTAATAATATTAA-ATAATAATT
* * *
1169798 TAAATAAAATTAAATTATAATT
1 TTAATAATATTAAATAATAATT
*
1169820 TTTATAATATT
1 TTAATAATATT
1169831 TAATTTAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAATAATATTAAATAATAATT
Found at i:1170396 original size:156 final size:153
Alignment explanation
Indices: 1170184--1170496 Score: 524
Period size: 156 Copynumber: 2.0 Consensus size: 153
1170174 AATATATAAA
1170184 AATCGAATATCAGATTAAAATAAATTAAAATAAACTCAGGATTAAAATATTATTTATTAAAATTA
1 AATCGAATATCAGATTAAAATAAATT--AATAAACTCAGGATTAAAATATTATTTATTAAAATTA
1170249 AGGGA-TAATATATTATTTATCCTAAATATTTATAAATACGGTTAAGGGTTAAAAATAAAAAAGA
64 AGGGACTAATATA-TATTT-TCCTAAATATTTAT-AATACGGTTAAGGGTTAAAAAT-AAAAAGA
1170313 AAATTTAGAAAACCAAATTAAAAGGATTAT
125 AAATTTAG-AAACCAAATTAAAAGGATTAT
1170343 AATCGAATATCAGATTAAAATTAAA-T-ATAAACTCAGGATTAAAATATTATTTATTAAAATTAA
1 AATCGAATATCAGATTAAAA-TAAATTAATAAACTCAGGATTAAAATATTATTTATTAAAATTAA
*
1170406 GGGACTAATATATATTTTCCTAAATATTTATAATACGGTTAAGGGTTAAATATAAAAAGAAAATT
65 GGGACTAATATATATTTTCCTAAATATTTATAATACGGTTAAGGGTTAAAAATAAAAAGAAAATT
1170471 TAGAAACCAAATTAAAAGGATTAT
130 TAGAAACCAAATTAAAAGGATTAT
1170495 AA
1 AA
1170497 ATTTGATTTA
Statistics
Matches: 151, Mismatches: 1, Indels: 11
0.93 0.01 0.07
Matches are distributed among these distances:
152 23 0.15
153 15 0.10
154 21 0.14
155 14 0.09
156 46 0.30
157 7 0.05
159 21 0.14
160 4 0.03
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (153 bp):
AATCGAATATCAGATTAAAATAAATTAATAAACTCAGGATTAAAATATTATTTATTAAAATTAAG
GGACTAATATATATTTTCCTAAATATTTATAATACGGTTAAGGGTTAAAAATAAAAAGAAAATTT
AGAAACCAAATTAAAAGGATTAT
Found at i:1171510 original size:3 final size:3
Alignment explanation
Indices: 1171502--1171555 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
1171492 AATTATTTTT
* *
1171502 TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
1171547 TAG TAA TAA
1 TAA TAA TAA
1171556 AAAAAATTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1173375 original size:31 final size:32
Alignment explanation
Indices: 1173331--1173406 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
1173321 ATGGTCATTT
* * *
1173331 ATTTTATTGAAATTG-TAAAAAATGATTATTAA
1 ATTTTA-TCAAATTGTTAAAAAATGATCACTAA
*
1173363 ATTTTATCAAATTGTTACAAAATGATCACTAA
1 ATTTTATCAAATTGTTAAAAAATGATCACTAA
1173395 A-TTTATCAAATT
1 ATTTTATCAAATT
1173407 TTTATAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 18 0.46
32 21 0.54
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (32 bp):
ATTTTATCAAATTGTTAAAAAATGATCACTAA
Found at i:1178815 original size:2 final size:2
Alignment explanation
Indices: 1178808--1178842 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
1178798 ATGGATTGCT
1178808 TA TA TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T
1178843 GTTTAGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1178905 original size:2 final size:2
Alignment explanation
Indices: 1178898--1178922 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1178888 TCAATCTACA
1178898 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
1178923 ATTTACGAAA
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:1179984 original size:15 final size:15
Alignment explanation
Indices: 1179964--1180012 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
1179954 ATATTATTCA
1179964 TTTTTTAAATTTTAC
1 TTTTTTAAATTTTAC
1179979 TTTTTT--ATTATTA-
1 TTTTTTAAATT-TTAC
*
1179992 TTTTTTAAATTTGAC
1 TTTTTTAAATTTTAC
1180007 TTTTTT
1 TTTTTT
1180013 CTAATGGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 9 0.31
14 5 0.17
15 15 0.52
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTTTAAATTTTAC
Found at i:1180002 original size:28 final size:29
Alignment explanation
Indices: 1179955--1180012 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
1179945 TCATTTGATA
*
1179955 TATTATTCATTTTTTAAATTTTACTTTTT
1 TATTATTCATTTTTTAAATTTGACTTTTT
1179984 TATTATT-ATTTTTTAAATTTGACTTTTT
1 TATTATTCATTTTTTAAATTTGACTTTTT
1180012 T
1 T
1180013 CTAATGGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (29 bp):
TATTATTCATTTTTTAAATTTGACTTTTT
Found at i:1180296 original size:2 final size:2
Alignment explanation
Indices: 1180289--1180350 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1180279 TATGTTTCTT
1180289 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
1180331 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1180351 ATGGGTATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1184778 original size:20 final size:20
Alignment explanation
Indices: 1184753--1184813 Score: 97
Period size: 19 Copynumber: 3.1 Consensus size: 20
1184743 AAATTGGCAT
* *
1184753 GGGGGTATCGGTACCATCTG
1 GGGGGTACCAGTACCATCTG
1184773 GGGGGTACCAGTACCATCT-
1 GGGGGTACCAGTACCATCTG
1184792 GGGGGTACCAGTACCATCTG
1 GGGGGTACCAGTACCATCTG
1184812 GG
1 GG
1184814 CAATCTGGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.18, C:0.23, G:0.38, T:0.21
Consensus pattern (20 bp):
GGGGGTACCAGTACCATCTG
Found at i:1187401 original size:20 final size:20
Alignment explanation
Indices: 1187376--1187413 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1187366 CCAAATCTCG
1187376 ATGGGGGTATCGGTACCCTC
1 ATGGGGGTATCGGTACCCTC
1187396 ATGGGGGTATCGGTACCC
1 ATGGGGGTATCGGTACCC
1187414 ATTCAAAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.24, G:0.37, T:0.24
Consensus pattern (20 bp):
ATGGGGGTATCGGTACCCTC
Found at i:1187427 original size:22 final size:20
Alignment explanation
Indices: 1187379--1187434 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
1187369 AATCTCGATG
**
1187379 GGGGTATCGGTACCCTCATG
1 GGGGTATCGGTACCCTCAAA
1187399 GGGGTATCGGTACCCATTCAAA
1 GGGGTATCGGTACCC--TCAAA
*
1187421 GGGGTATCGATACC
1 GGGGTATCGGTACC
1187435 TAGCGCGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 15 0.48
22 16 0.52
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (20 bp):
GGGGTATCGGTACCCTCAAA
Found at i:1195617 original size:22 final size:21
Alignment explanation
Indices: 1195577--1195640 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
1195567 AAAAATGGTC
*
1195577 TCGGTACCGTA-T-TAGAGTA
1 TCGGTACCATAGTATAGAGTA
1195596 TCGGTACCATAGTATAGTAGTA
1 TCGGTACCATAGTATAG-AGTA
* * *
1195618 TCGATACCATGGTAT-GGGTA
1 TCGGTACCATAGTATAGAGTA
1195638 TCG
1 TCG
1195641 ATACTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
19 10 0.26
20 7 0.18
21 4 0.11
22 17 0.45
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (21 bp):
TCGGTACCATAGTATAGAGTA
Found at i:1196145 original size:112 final size:108
Alignment explanation
Indices: 1195972--1196513 Score: 827
Period size: 112 Copynumber: 5.0 Consensus size: 108
1195962 CCCAAATAGT
* *
1195972 CACTAAGTGTGCAATTCACGAAATTCATCATTTGTTGATGAATAACCGTTTCGACACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
1196037 CAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGA
66 CAATTCACGGAATTCATC----ATATGTTGATGAATAACCGTTTCGA
* * *
1196084 CACTAAGTGTGCAATTCATGAAATTCATCATATGTTGATGAATAACCGTTTCGACAATAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
* ** *
1196149 CAATTCACGGAATTCACCATATGCCGATGAATAACCGTTTCGG
66 CAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
1196192 CACTAAGTGTGCAATTCAC-AGAATTCATCATATATATGTTGATGAATAACCGTTTCGGCACTAA
1 CACTAAGTGTGCAATTCACGA-AATTCATC----ATATGTTGATGAATAACCGTTTCGGCACTAA
* *
1196256 GTTTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
61 GTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
* *
1196304 CACTAAGTGTGC-ATTCACGTAATTCATCATATGTTGATGAATAACAGTTTCGGCACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
*
1196368 CACTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
66 CAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
* *
1196411 CACTAAGTGTACAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
**
1196476 CAATTCACAAAATTCATCATATGTTGATGAATAACCGT
66 CAATTCACGGAATTCATCATATGTTGATGAATAACCGT
1196514 ATGGGCACTA
Statistics
Matches: 398, Mismatches: 25, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
107 87 0.22
108 133 0.33
111 14 0.04
112 164 0.41
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (108 bp):
CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
CAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
Found at i:1196256 original size:166 final size:166
Alignment explanation
Indices: 1195972--1196523 Score: 889
Period size: 166 Copynumber: 3.4 Consensus size: 166
1195962 CCCAAATAGT
* *
1195972 CACTAAGTGTGCAATTCACGAAATTCATCATTTGTTGATGAATAACCGTTTCGACACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
1196037 CAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAATTCA
66 CAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAATTCA
* * *
1196102 TGAAATTCATCATATGTTGATGAATAACCGTTTCGA
131 CGGAATTCATCATATGTTGATGAATAACCGTTTCGG
* * * **
1196138 CAATAAGTGTGCAATTCACGGAATTCACCATATGCCGATGAATAACCGTTTCGGCACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
* * *
1196203 CAATTCACAGAATTCATCATATATATGTTGATGAATAACCGTTTCGGCACTAAGTTTGCAATTCA
66 CAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAATTCA
1196268 CGGAATTCATCATATGTTGATGAATAACCGTTTCGG
131 CGGAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
1196304 CACTAAGTGTGC-ATTCACGTAATTCATCATATGTTGATGAATAACAGTTTCGGCACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
* *
1196368 CACTTCACGGAATTCATC----ATATGTTGATGAATAACCGTTTCGACACTAAGTGTACAATTCA
66 CAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAATTCA
1196429 CGGAATTCATCATATGTTGATGAATAACCGTTTCGG
131 CGGAATTCATCATATGTTGATGAATAACCGTTTCGG
* * *
1196465 CACTAAGTGTGCAATTCACAAAATTCATCATATGTTGATGAATAACCGTATGGGCACTA
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTA
1196524 TTGGTGCATT
Statistics
Matches: 356, Mismatches: 29, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
161 88 0.25
162 41 0.12
165 63 0.18
166 164 0.46
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (166 bp):
CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
CAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGACACTAAGTGTGCAATTCA
CGGAATTCATCATATGTTGATGAATAACCGTTTCGG
Found at i:1196531 original size:54 final size:54
Alignment explanation
Indices: 1195972--1196523 Score: 827
Period size: 54 Copynumber: 10.1 Consensus size: 54
1195962 CCCAAATAGT
* * *
1195972 CACTAAGTGTGCAATTCACGAAATTCATCATTTGTTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
*
1196026 CACTAAGTGTGCAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAATTCACGGAATTCATC----ATATGTTGATGAATAACCGTTTCGG
* * *
1196084 CACTAAGTGTGCAATTCATGAAATTCATCATATGTTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
* * **
1196138 CAATAAGTGTGCAATTCACGGAATTCACCATATGCCGATGAATAACCGTTTCGG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
*
1196192 CACTAAGTGTGCAATTCACAGAATTCATCATATATATGTTGATGAATAACCGTTTCGG
1 CACTAAGTGTGCAATTCACGGAATTCATC----ATATGTTGATGAATAACCGTTTCGG
*
1196250 CACTAAGTTTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
1196304 CACTAAGTGTGC-ATTCACGTAATTCATCATATGTTGATGAATAACAGTTTCGG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
1196357 CACTAAGTGTGCACTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
*
1196411 CACTAAGTGTACAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
** * *
1196465 CACTAAGTGTGCAATTCACAAAATTCATCATATGTTGATGAATAACCGTATGGG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
1196519 CACTA
1 CACTA
1196524 TTGGTGCATT
Statistics
Matches: 456, Mismatches: 33, Indels: 18
0.90 0.07 0.04
Matches are distributed among these distances:
53 51 0.11
54 304 0.67
58 101 0.22
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (54 bp):
CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
Found at i:1197916 original size:8 final size:8
Alignment explanation
Indices: 1197901--1197956 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
1197891 AATTATTTTT
1197901 TTAT-ATA
1 TTATAATA
1197908 TTATAATA
1 TTATAATA
1197916 TTATAATA
1 TTATAATA
*
1197924 TTA-CATA
1 TTATAATA
1197931 TT-TAATTA
1 TTATAA-TA
1197939 TTAATAAT-
1 TT-ATAATA
1197947 TTAT-ATA
1 TTATAATA
1197954 TTA
1 TTA
1197957 AATTAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
6 2 0.05
7 15 0.37
8 20 0.49
9 1 0.02
10 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (8 bp):
TTATAATA
Found at i:1197931 original size:23 final size:24
Alignment explanation
Indices: 1197900--1197961 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
1197890 TAATTATTTT
*
1197900 TTTATATATTATAA-TATT-ATAA
1 TTTACATATTATAATTATTAATAA
1197922 TATTACATATT-TAATTATTAATAA
1 T-TTACATATTATAATTATTAATAA
*
1197946 TTTATATATTA-AATTA
1 TTTACATATTATAATTA
1197962 AAATAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 4 0.12
23 25 0.74
24 5 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTACATATTATAATTATTAATAA
Found at i:1197957 original size:15 final size:15
Alignment explanation
Indices: 1197900--1197957 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 15
1197890 TAATTATTTT
1197900 TTTATATATT-ATAA
1 TTTATATATTAATAA
1197914 TATTATAATATTACAT-A
1 T-TTAT-ATATTA-ATAA
1197931 TTTA-ATTATTAATAA
1 TTTATA-TATTAATAA
1197946 TTTATATATTAA
1 TTTATATATTAA
1197958 ATTAAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
14 4 0.11
15 20 0.54
16 9 0.24
17 2 0.05
18 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTATATATTAATAA
Found at i:1199947 original size:12 final size:12
Alignment explanation
Indices: 1199919--1199984 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
1199909 ACCCTCTCAG
1199919 CAGCACAATC-A
1 CAGCACAATCAA
1199930 CTAGCACAATCAA
1 C-AGCACAATCAA
**
1199943 CAGCACCCTCAA
1 CAGCACAATCAA
* *
1199955 CAGTACAATCAG
1 CAGCACAATCAA
* *
1199967 CAGCACACTCAT
1 CAGCACAATCAA
1199979 CAGCAC
1 CAGCAC
1199985 CCTCACCAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
11 1 0.02
12 41 0.93
13 2 0.05
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.12
Consensus pattern (12 bp):
CAGCACAATCAA
Found at i:1199947 original size:75 final size:78
Alignment explanation
Indices: 1199798--1199953 Score: 221
Period size: 75 Copynumber: 2.0 Consensus size: 78
1199788 ATCTCCAATA
*
1199798 TCATCAAGACCAACAACATCAACTACATTTTCAACAACCCTCTCAGCAGCACAATCAACAGCACC
1 TCATCAAGACCAACAACATCAACTACATTTTCAACAACCCTCTCAGCAGCACAATCAACAGCACA
* * *
1199863 CTTACCAGCACCC
66 ATCAACAGCACCC
* *
1199876 TCATCAAGACC-ACCA-AT-AACTACATTTTCAGCAACCCTCTCAGCAGCACAATC-ACTAGCAC
1 TCATCAAGACCAACAACATCAACTACATTTTCAACAACCCTCTCAGCAGCACAATCAAC-AGCAC
1199937 AATCAACAGCACCC
65 AATCAACAGCACCC
1199951 TCA
1 TCA
1199954 ACAGTACAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
74 2 0.03
75 53 0.75
76 2 0.03
77 3 0.04
78 11 0.15
ACGTcount: A:0.37, C:0.38, G:0.07, T:0.17
Consensus pattern (78 bp):
TCATCAAGACCAACAACATCAACTACATTTTCAACAACCCTCTCAGCAGCACAATCAACAGCACA
ATCAACAGCACCC
Found at i:1199989 original size:12 final size:12
Alignment explanation
Indices: 1199943--1200025 Score: 76
Period size: 12 Copynumber: 6.9 Consensus size: 12
1199933 GCACAATCAA
*
1199943 CAGCACCCTCAA
1 CAGCACCCTCAC
* ** *
1199955 CAGTACAATCAG
1 CAGCACCCTCAC
* *
1199967 CAGCACACTCAT
1 CAGCACCCTCAC
1199979 CAGCACCCTCAC
1 CAGCACCCTCAC
*
1199991 CAGTACCCTCAC
1 CAGCACCCTCAC
*
1200003 CAGCACCCTCAT
1 CAGCACCCTCAC
*
1200015 GAGCACCCTCA
1 CAGCACCCTCA
1200026 GCGGCAGTTA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 58 1.00
ACGTcount: A:0.30, C:0.46, G:0.11, T:0.13
Consensus pattern (12 bp):
CAGCACCCTCAC
Found at i:1200007 original size:36 final size:36
Alignment explanation
Indices: 1199914--1200025 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 36
1199904 CAGCAACCCT
* * * * *
1199914 CTCAGCAGCACAATCACTAGCACAATCAACAGCACC
1 CTCAACAGTACAATCACCAGCACACTCATCAGCACC
*
1199950 CTCAACAGTACAATCAGCAGCACACTCATCAGCACC
1 CTCAACAGTACAATCACCAGCACACTCATCAGCACC
* ** * *
1199986 CTCACCAGTACCCTCACCAGCACCCTCATGAGCACC
1 CTCAACAGTACAATCACCAGCACACTCATCAGCACC
1200022 CTCA
1 CTCA
1200026 GCGGCAGTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.33, C:0.43, G:0.11, T:0.13
Consensus pattern (36 bp):
CTCAACAGTACAATCACCAGCACACTCATCAGCACC
Found at i:1204519 original size:14 final size:14
Alignment explanation
Indices: 1204500--1204528 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1204490 TCATAACCTG
1204500 AGATAATTAATTCT
1 AGATAATTAATTCT
1204514 AGATAATTAATTCT
1 AGATAATTAATTCT
1204528 A
1 A
1204529 TTATAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
AGATAATTAATTCT
Found at i:1207760 original size:218 final size:218
Alignment explanation
Indices: 1207382--1207825 Score: 852
Period size: 218 Copynumber: 2.0 Consensus size: 218
1207372 GGTAATGAGA
*
1207382 GAAGAGTTGAACTCTTTCCTTTTCTCCCTCTTCTCACCGTAGACATCAGTGGCAAAGGTAAGGAT
1 GAAGAGTTAAACTCTTTCCTTTTCTCCCTCTTCTCACCGTAGACATCAGTGGCAAAGGTAAGGAT
1207447 CTAAATTTTTTATTGTTCCTTTAATTTTTGGTTTAGTAATGGAAGGTTGGGTATTATATAAGCTT
66 CTAAATTTTTTATTGTTCCTTTAATTTTTGGTTTAGTAATGGAAGGTTGGGTATTATATAAGCTT
1207512 AAGGAAAGCTTATATAGCATTAAAACAACAAGATGAGTATTTTAGAGAATGATTTGTAAAATGAG
131 AAGGAAAGCTTATATAGCATTAAAACAACAAGATGAGTATTTTAGAGAATGATTTGTAAAATGAG
1207577 TTTTTAGATGAAATTTTGTTATG
196 TTTTTAGATGAAATTTTGTTATG
* *
1207600 GAAGAGTTAAACTCTTTCCTTTTCTCCCTCTTTTCACCGTGGACATCAGTGGCAAAGGTAAGGAT
1 GAAGAGTTAAACTCTTTCCTTTTCTCCCTCTTCTCACCGTAGACATCAGTGGCAAAGGTAAGGAT
1207665 CTAAATTTTTTATTGTTCCTTTAATTTTTGGTTTAGTAATGGAAGGTTGGGTATTATATAAGCTT
66 CTAAATTTTTTATTGTTCCTTTAATTTTTGGTTTAGTAATGGAAGGTTGGGTATTATATAAGCTT
1207730 AAGGAAAGCTTATATAGCATTAAAACAACAAGATGAGTATTTTAGAGAATGATTTGTAAAATGAG
131 AAGGAAAGCTTATATAGCATTAAAACAACAAGATGAGTATTTTAGAGAATGATTTGTAAAATGAG
1207795 TTTTTAGATGAAATTTTGTTATG
196 TTTTTAGATGAAATTTTGTTATG
*
1207818 GATGAGTT
1 GAAGAGTT
1207826 TTTGAAGTTT
Statistics
Matches: 222, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
218 222 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (218 bp):
GAAGAGTTAAACTCTTTCCTTTTCTCCCTCTTCTCACCGTAGACATCAGTGGCAAAGGTAAGGAT
CTAAATTTTTTATTGTTCCTTTAATTTTTGGTTTAGTAATGGAAGGTTGGGTATTATATAAGCTT
AAGGAAAGCTTATATAGCATTAAAACAACAAGATGAGTATTTTAGAGAATGATTTGTAAAATGAG
TTTTTAGATGAAATTTTGTTATG
Found at i:1208928 original size:22 final size:22
Alignment explanation
Indices: 1208868--1208922 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
1208858 TCCTTCGGAA
1208868 CAAA-TATGTGGCAC-TCGGTG
1 CAAACTATGTGGCACTTCGGTG
*
1208888 CAACCCTATGTGGCACTTCGGTG
1 CAA-ACTATGTGGCACTTCGGTG
1208911 CAAACTATGTGG
1 CAAACTATGTGG
1208923 TCCTTCACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 3 0.10
22 18 0.60
23 9 0.30
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (22 bp):
CAAACTATGTGGCACTTCGGTG
Found at i:1208958 original size:21 final size:21
Alignment explanation
Indices: 1208894--1208959 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
1208884 GGTGCAACCC
* *
1208894 TATGTGGCACTTCGGTGCAAAC
1 TATGTGGCACTTC-GTACAAAT
1208916 TATGTGGTC-CTTC--ACGACAAT
1 TATGTGG-CACTTCGTAC-A-AAT
1208937 TATGTGGCACTTCGTACAAAT
1 TATGTGGCACTTCGTACAAAT
1208958 TA
1 TA
1208960 CGAGATGTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 18 0.50
22 12 0.33
23 3 0.08
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
TATGTGGCACTTCGTACAAAT
Found at i:1209933 original size:20 final size:19
Alignment explanation
Indices: 1209908--1210018 Score: 96
Period size: 20 Copynumber: 5.5 Consensus size: 19
1209898 GGGAAAATCA
1209908 CAATGCGATACTGACTATCG
1 CAATGCGATACT-ACTATCG
1209928 CAATGCGATACTTACTATCG
1 CAATGCGATAC-TACTATCG
* * *
1209948 CAATGCGATAATACAAAATCA
1 CAATGCGATACTAC--TATCG
* * *
1209969 CAACGAGATACTGACTTTCG
1 CAATGCGATACT-ACTATCG
*
1209989 CAATGCGATAATACATAATCG
1 CAATGCGATACTAC-T-ATCG
1210010 CAATGCGAT
1 CAATGCGAT
1210019 TTTCAAAGCA
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
19 5 0.07
20 40 0.56
21 25 0.35
22 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (19 bp):
CAATGCGATACTACTATCG
Found at i:1210214 original size:22 final size:22
Alignment explanation
Indices: 1210186--1210229 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1210176 CACTCTCTCA
*
1210186 CCCATCTCTGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1210208 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1210230 TATCTCCATC
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:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1210546 original size:20 final size:20
Alignment explanation
Indices: 1210492--1210550 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1210482 ACGATTCTCT
**
1210492 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1210512 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1210532 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1210551 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1212717 original size:19 final size:19
Alignment explanation
Indices: 1212693--1212760 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
1212683 ATCGCAACGA
1212693 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1212712 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
1212731 GAAAATCACAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1212745 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1212761 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
19 29 0.66
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1213039 original size:20 final size:20
Alignment explanation
Indices: 1213014--1213105 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
1213004 TTGAAGATGA
1213014 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1213034 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
1213054 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
1213075 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
1213095 TTGCGATTTTC
1 TTGCGATTTTC
1213106 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1213134 original size:20 final size:21
Alignment explanation
Indices: 1213090--1213141 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1213080 ATAGTCAGTA
*
1213090 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1213111 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1213131 TCGCATTGCGA
1 TCGCATTGCGA
1213142 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1214160 original size:12 final size:12
Alignment explanation
Indices: 1214142--1214178 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1214132 ATATAATCCT
1214142 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
1214154 TAAGAAGAAAAA
1 GAAGAAGAAAAA
1214166 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1214178 G
1 G
1214179 TCCCCGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1216470 original size:20 final size:20
Alignment explanation
Indices: 1216440--1216496 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
1216430 CAATCATCTT
*
1216440 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
* *
1216460 AATTACTATCGCAATGC-GA
1 AATGACTATCGCAACGCGGA
**
1216479 AATGAAAATCGCAACGCG
1 AATGACTATCGCAACGCG
1216497 AATTTCGCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:1216489 original size:19 final size:19
Alignment explanation
Indices: 1216467--1216564 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1216457 GGAAATTACT
1216467 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1216486 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
1216500 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1216519 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1216533 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1216552 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1216565 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
15 4 0.07
16 2 0.03
17 2 0.03
18 4 0.07
19 30 0.50
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1216510 original size:33 final size:33
Alignment explanation
Indices: 1216468--1216567 Score: 159
Period size: 33 Copynumber: 3.0 Consensus size: 33
1216458 GAAATTACTA
1216468 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
1216501 TCGCAATGCGAAATGAAAATCGCAACGAGGGAA--
1 TCGCAATGCGAAATGAAAATCGCAAC--GCGAATT
1216534 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1216567 T
1 T
1216568 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
31 4 0.07
33 53 0.87
35 4 0.07
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:1216582 original size:19 final size:19
Alignment explanation
Indices: 1216560--1216601 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1216550 AAATCGCAAC
1216560 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* *
1216579 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
1216598 GCGA
1 GCGA
1216602 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:1216602 original size:19 final size:19
Alignment explanation
Indices: 1216569--1216635 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
1216559 CGCGAATTTA
1216569 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
1216588 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
1216605 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
1216621 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
1216636 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
16 3 0.08
17 3 0.08
19 24 0.60
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:1216761 original size:14 final size:14
Alignment explanation
Indices: 1216742--1216778 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1216732 CATCAATTAA
1216742 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1216756 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1216770 ACAAATCAA
1 ACAAATCAA
1216779 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1218651 original size:91 final size:90
Alignment explanation
Indices: 1218476--1218660 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
1218466 ATTTCAAACT
*
1218476 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
1218541 AGAATTGGCAGCAACCGAATAATTTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
1218569 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
1218633 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
1218660 T
1 T
1218661 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1220371 original size:40 final size:37
Alignment explanation
Indices: 1220327--1220436 Score: 129
Period size: 33 Copynumber: 3.0 Consensus size: 37
1220317 TCTTTTGGTT
**
1220327 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGACTATCGCAACG-GA-AATGAGAATCGCAACGC
1220366 GGAAATGACTATCGCAAC-G--A-GAGAATCGCAACGC
1 -GAAATGACTATCGCAACGGAAATGAGAATCGCAACGC
*
1220400 GAAATGACTATCGCAACGCGAAATGAAAATCGCAACG
1 GAAATGACTATCGCAACG-GAAATGAGAATCGCAACG
1220437 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
33 17 0.27
34 14 0.23
35 2 0.03
37 1 0.02
38 13 0.21
40 15 0.24
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.13
Consensus pattern (37 bp):
GAAATGACTATCGCAACGGAAATGAGAATCGCAACGC
Found at i:1220414 original size:19 final size:19
Alignment explanation
Indices: 1220327--1220463 Score: 105
Period size: 19 Copynumber: 7.6 Consensus size: 19
1220317 TCTTTTGGTT
* *
1220327 GAAATGAAAATCGCAACGA
1 GAAATGACAATCGCAACGC
*
1220346 GATAATGAGAATCGCAACGC
1 GA-AATGACAATCGCAACGC
*
1220366 GGAAATGACTATCGCAA--C
1 -GAAATGACAATCGCAACGC
*
1220384 G--A-GAGAATCGCAACGC
1 GAAATGACAATCGCAACGC
*
1220400 GAAATGACTATCGCAACGC
1 GAAATGACAATCGCAACGC
*
1220419 GAAATGAAAATCGCAA--C
1 GAAATGACAATCGCAACGC
*
1220436 G--A-GAGAATCGCAACGC
1 GAAATGACAATCGCAACGC
*
1220452 GAAATGAAAATC
1 GAAATGACAATC
1220464 ACAATGCGAT
Statistics
Matches: 94, Mismatches: 12, Indels: 24
0.72 0.09 0.18
Matches are distributed among these distances:
14 19 0.20
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 34 0.36
20 27 0.29
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGACAATCGCAACGC
Found at i:1220436 original size:52 final size:53
Alignment explanation
Indices: 1220335--1220463 Score: 188
Period size: 52 Copynumber: 2.4 Consensus size: 53
1220325 TTGAAATGAA
* * **
1220335 AATCGCAACGAGATAATGAGAATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGACAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
*
1220389 AATCGCAACGCGAAATGACTATCGCAACGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGACAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
*
1220441 AATCGCAACGCGAAATGAAAATC
1 AATCGCAACGCGAAATGACAATC
1220464 ACAATGCGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 41 0.60
53 15 0.22
54 12 0.18
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (53 bp):
AATCGCAACGCGAAATGACAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
Found at i:1220490 original size:19 final size:19
Alignment explanation
Indices: 1220468--1220512 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1220458 AAAATCACAA
*
1220468 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1220487 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1220506 TGAGATT
1 TGCGATT
1220513 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.13, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1221097 original size:20 final size:20
Alignment explanation
Indices: 1221067--1221119 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1221057 CGCTATGTAA
*
1221067 ATCGTATTGCGATAGTAAG-
1 ATCGCATTGCGATAGTAAGT
*
1221086 ATTCGCATTGCGATAGTCAGT
1 A-TCGCATTGCGATAGTAAGT
1221107 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1221120 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:1221153 original size:21 final size:20
Alignment explanation
Indices: 1221129--1221181 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
1221119 TTTTCCAAAT
1221129 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
1221150 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
1221171 TCGCATTGCGA
1 TCGCATTGCGA
1221182 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.81
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:1224879 original size:73 final size:73
Alignment explanation
Indices: 1224738--1224909 Score: 256
Period size: 73 Copynumber: 2.4 Consensus size: 73
1224728 CAACATATCT
* * * *
1224738 GGTAGGTAGTTTAATGTAATATGTAGTGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTA
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTA
1224803 AAAAAACC
66 AAAAAACC
*
1224811 GGTAGGTATTTTAATGTAATAGGTAGCGCCTA-TTTTTTTATCGTTTACATTATTAACAACCTTC
1 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTT-
*
1224875 AAAAAAATC
65 AAAAAAACC
* *
1224884 GATAGGTATTTTAATGTAATGGGTAG
1 GGTAGGTATTTTAATGTAATAGGTAG
1224910 TTTAAATTTT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
72 29 0.32
73 61 0.68
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (73 bp):
GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTA
AAAAAACC
Found at i:1225143 original size:23 final size:23
Alignment explanation
Indices: 1225117--1225173 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
1225107 GTAATTAACA
*
1225117 TATTTTATTATATAAGCGCTACC
1 TATTATATTATATAAGCGCTACC
* * *
1225140 TATTATGTTATATAAGTGTTACC
1 TATTATATTATATAAGCGCTACC
* *
1225163 TAATATGTTAT
1 TATTATATTAT
1225174 TGTGCTTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (23 bp):
TATTATATTATATAAGCGCTACC
Done.