Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 82 of 284
Found at i:27460778 original size:33 final size:32
Alignment explanation
Indices: 27460736--27460944 Score: 112
Period size: 33 Copynumber: 5.8 Consensus size: 32
27460726 ATGTGAAAGG
27460736 GGTTGCTAAGTGCTGATTCCCCGAGTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGA-TCATTGGT
*
27460769 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-ATC----AT-TG--GT
* *
27460810 GGCTTGCTAAGTGTTGATTTCCCGAATCATTGGT
1 GG-TTGCTAAGTGCTGATTCCCCG-ATCATTGGT
* * *
27460844 GGTTGCTAAGTGTTGATCCCACCGTATCTTAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-ATC----AT-TG--GT
* *
27460885 GGCTTGCTAAGTGTTGATTTCCCGAATCATTGGT
1 GG-TTGCTAAGTGCTGATTCCCCG-ATCATTGGT
* *
27460919 GGTTGCTAAGTGTTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
27460945 AACGGATACC
Statistics
Matches: 141, Mismatches: 15, Indels: 40
0.72 0.08 0.20
Matches are distributed among these distances:
33 54 0.38
34 20 0.14
35 1 0.01
36 4 0.03
37 4 0.03
38 4 0.03
39 4 0.03
41 18 0.13
42 32 0.23
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCCGATCATTGGT
Found at i:27460780 original size:75 final size:75
Alignment explanation
Indices: 27460657--27460942 Score: 425
Period size: 75 Copynumber: 3.8 Consensus size: 75
27460647 TGATTCCCCC
* * *
27460657 AAGGGG-TTGCTAAGTGCTGATT-CCCTAATTCATTGGTGGTTGCAAAGTGCTGATTCCACAGTA
1 AAGGGGCTTGCTAAGTGCTGATTCCCCGAA-TCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA
27460720 TCTTAAATGTG
65 TCTTAAATGTG
*
27460731 AAAGGGG-TTGCTAAGTGCTGATTCCCCGAGTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA
1 -AAGGGGCTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA
27460795 TCTTAAATGTG
65 TCTTAAATGTG
* * * *
27460806 AAGGGGCTTGCTAAGTGTTGATTTCCCGAATCATTGGTGGTTGCTAAGTGTTGATCCCACCGTAT
1 AAGGGGCTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
27460871 CTTAAATGTG
66 CTTAAATGTG
* * * *
27460881 AAGGGGCTTGCTAAGTGTTGATTTCCCGAATCATTGGTGGTTGCTAAGTGTTGAATCCACCG
1 AAGGGGCTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
27460943 ATAACGGATA
Statistics
Matches: 198, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
74 6 0.03
75 188 0.95
76 4 0.02
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.33
Consensus pattern (75 bp):
AAGGGGCTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
CTTAAATGTG
Found at i:27470335 original size:102 final size:102
Alignment explanation
Indices: 27470159--27470389 Score: 401
Period size: 102 Copynumber: 2.3 Consensus size: 102
27470149 ATTGAATATA
*
27470159 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTTCTCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTTCTCGAATCATTGGT
27470224 GGTTGCTAAGTGCTGATTC-CACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGA-TCGCACCGTATCTTAAATGTG
* **
27470261 AAGGGGGTTGCTAAGTGTTGATTCCCCTGAGGGGTTGCTAAGTGCTGATTTCTCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTTCTCGAATCATTGGT
27470326 GGTTGCTAAGTGCTGATCGCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATCGCACCGTATCTTAAATGTG
*
27470363 AAAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
27470390 AACTCATTGG
Statistics
Matches: 122, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
101 2 0.02
102 120 0.98
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.32
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTTCTCGAATCATTGGT
GGTTGCTAAGTGCTGATCGCACCGTATCTTAAATGTG
Found at i:27471580 original size:38 final size:36
Alignment explanation
Indices: 27471511--27471615 Score: 135
Period size: 38 Copynumber: 2.9 Consensus size: 36
27471501 GGCCTATTTT
*
27471511 TATTTTAAAAAT-TTTTAAAA-ATAAAAA-AAAAAG
1 TATTTTAAAAATATTTTAAAATAAAAAAATAAAAAG
27471544 TATTTTAAAAATATTTTAAAATAAAAAAATTTAAAAAG
1 TATTTTAAAAATATTTTAAAATAAAAAAA--TAAAAAG
* *
27471582 TATGTAAAAAATATTTTAAAATTAAAAAAATAAA
1 TATTTTAAAAATATTTTAAAA-TAAAAAAATAAA
27471616 TATATTTATT
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
33 12 0.19
34 8 0.13
35 6 0.10
37 4 0.06
38 25 0.40
39 8 0.13
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (36 bp):
TATTTTAAAAATATTTTAAAATAAAAAAATAAAAAG
Found at i:27471602 original size:11 final size:11
Alignment explanation
Indices: 27471511--27471564 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
27471501 GGCCTATTTT
27471511 TATTTTAAAAA
1 TATTTTAAAAA
27471522 T-TTTTAAAAA
1 TATTTTAAAAA
****
27471532 TAAAAAAAAAA
1 TATTTTAAAAA
27471543 GTATTTTAAAAA
1 -TATTTTAAAAA
27471555 TATTTTAAAA
1 TATTTTAAAA
27471565 TAAAAAAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
10 10 0.30
11 16 0.48
12 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:27473652 original size:18 final size:17
Alignment explanation
Indices: 27473604--27473653 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
27473594 CACTTAAAAG
27473604 AATTTTATTTTAATAAT
1 AATTTTATTTTAATAAT
* * *
27473621 GATATTAATGTTAATAAT
1 AAT-TTTATTTTAATAAT
27473639 AAATTTTATTTTAAT
1 -AATTTTATTTTAAT
27473654 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
17 2 0.08
18 21 0.84
19 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTTATTTTAATAAT
Found at i:27475034 original size:19 final size:22
Alignment explanation
Indices: 27474985--27475030 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
27474975 AATCTATAAC
27474985 CTCTATAATCATTTTACTTCTT
1 CTCTATAATCATTTTACTTCTT
27475007 CTCTATAATCATTTTACTTCTT
1 CTCTATAATCATTTTACTTCTT
27475029 CT
1 CT
27475031 TAATTCTTGA
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:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (22 bp):
CTCTATAATCATTTTACTTCTT
Found at i:27476980 original size:24 final size:24
Alignment explanation
Indices: 27476944--27476999 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
27476934 AATTTGAGTT
27476944 TTGATTTGAGTGTTGTGATGGCAA
1 TTGATTTGAGTGTTGTGATGGCAA
* *
27476968 TTGGTTTGAGTGTTGTGATGGCAG
1 TTGATTTGAGTGTTGTGATGGCAA
27476992 TTGATTTG
1 TTGATTTG
27477000 GTCCTTGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.16, C:0.04, G:0.36, T:0.45
Consensus pattern (24 bp):
TTGATTTGAGTGTTGTGATGGCAA
Found at i:27481728 original size:18 final size:17
Alignment explanation
Indices: 27481706--27481749 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
27481696 AAAAATTTAT
27481706 AAATTTTTAAAAAATAA
1 AAATTTTTAAAAAATAA
* *
27481723 AGAATTATGAAAAAATAA
1 A-AATTTTTAAAAAATAA
27481741 AAATTTTTA
1 AAATTTTTA
27481750 GAATTCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
AAATTTTTAAAAAATAA
Found at i:27500991 original size:90 final size:90
Alignment explanation
Indices: 27500838--27501002 Score: 321
Period size: 90 Copynumber: 1.8 Consensus size: 90
27500828 ATCAAGATGC
27500838 AGGAGATGTTTGAAATGTCTGATTTAGGGAAAATGTCCTATTTTCTGGGAATGGAGGTGACACAA
1 AGGAGATGTTTGAAATGTCTGATTTAGGGAAAATGTCCTATTTTCTGGGAATGGAGGTGACACAA
27500903 ACACAAGATGGGATATTCCTAAGAT
66 ACACAAGATGGGATATTCCTAAGAT
27500928 AGGAGATGTTTGAAATGTCTGATTTAGGGAAAATGTCCTATTTTCTGGGAATGGAGGTGACACAA
1 AGGAGATGTTTGAAATGTCTGATTTAGGGAAAATGTCCTATTTTCTGGGAATGGAGGTGACACAA
*
27500993 ACACAGGATG
66 ACACAAGATG
27501003 CCTCGAAGAT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (90 bp):
AGGAGATGTTTGAAATGTCTGATTTAGGGAAAATGTCCTATTTTCTGGGAATGGAGGTGACACAA
ACACAAGATGGGATATTCCTAAGAT
Found at i:27509894 original size:120 final size:118
Alignment explanation
Indices: 27509676--27509920 Score: 350
Period size: 120 Copynumber: 2.1 Consensus size: 118
27509666 GGACTAAGAT
*
27509676 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
* ** *
27509741 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGGTTAAGTC
66 ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TAGCTAAATCC-GGTTAAATC
* *
27509795 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA
* * *
27509860 TAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAATT
65 -AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTAAATCCGGTTAAATC
27509914 CCGAAGG
1 CCGAAGG
27509921 TACGTGATTT
Statistics
Matches: 113, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
119 51 0.45
120 60 0.53
121 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (118 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTAAATCCGGTTAAATC
Found at i:27509901 original size:40 final size:40
Alignment explanation
Indices: 27509623--27509887 Score: 367
Period size: 40 Copynumber: 6.7 Consensus size: 40
27509613 TTGAATGATG
* * * * *
27509623 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
27509663 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
27509703 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
27509742 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
27509782 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
27509822 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
27509863 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
27509888 AACGAGTAGC
Statistics
Matches: 207, Mismatches: 13, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
39 35 0.17
40 162 0.78
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:27518731 original size:30 final size:30
Alignment explanation
Indices: 27518689--27518747 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
27518679 TTCTCACTCC
27518689 CAAGCTTCTGAACG-CAATATCGAGTCTTCA
1 CAAGCTTCTGAACGAC-ATATCGAGTCTTCA
*
27518719 CAAGC-TCTTGAACGACATATCTAGTCTTC
1 CAAGCTTC-TGAACGACATATCGAGTCTTC
27518748 TCAATCCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 2 0.08
30 23 0.88
31 1 0.04
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
CAAGCTTCTGAACGACATATCGAGTCTTCA
Found at i:27518780 original size:66 final size:66
Alignment explanation
Indices: 27518653--27518782 Score: 147
Period size: 66 Copynumber: 2.0 Consensus size: 66
27518643 CAAATCTTTT
* * * * *
27518653 CAAGCTCTTAAACAAGATATCATGTATTCTCACTCCCAAGCTTCTGAACGCAATATCGAGTCTTC
1 CAAGCTCTTAAACAACATATCATGTATTCTCAATCCCAAGATCCTAAACGCAATATCGAGTCTTC
27518718 A
66 A
* * * *
27518719 CAAGCTCTTGAACGACATATC-TAGTCTTCTCAATCCCAAGATCCTAAACG-AGATATTGAGTCT
1 CAAGCTCTTAAACAACATATCAT-GTATTCTCAATCCCAAGATCCTAAACGCA-ATATCGAGTCT
27518782 T
64 T
27518783 TCCAAACTCC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
65 2 0.04
66 51 0.96
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (66 bp):
CAAGCTCTTAAACAACATATCATGTATTCTCAATCCCAAGATCCTAAACGCAATATCGAGTCTTC
A
Found at i:27526099 original size:11 final size:10
Alignment explanation
Indices: 27526063--27526090 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
27526053 ATGATGAAGA
27526063 ACAAAAGTTC
1 ACAAAAGTTC
27526073 ACAAAAGTTC
1 ACAAAAGTTC
27526083 ACAAAAGT
1 ACAAAAGT
27526091 ATGACAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.54, C:0.18, G:0.11, T:0.18
Consensus pattern (10 bp):
ACAAAAGTTC
Found at i:27534451 original size:20 final size:21
Alignment explanation
Indices: 27534413--27534451 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27534403 GGTTCAAAGC
*
27534413 AAATAAATTATTGAAAAATAA
1 AAATAAATTATTAAAAAATAA
27534434 AAATAAATTA-TAAAAAAT
1 AAATAAATTATTAAAAAAT
27534452 GATTTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (21 bp):
AAATAAATTATTAAAAAATAA
Found at i:27534648 original size:10 final size:10
Alignment explanation
Indices: 27534633--27534679 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
27534623 TTTAATCTTT
27534633 TATTTTTAAA
1 TATTTTTAAA
27534643 TATTTTT--A
1 TATTTTTAAA
27534651 T-TTTTTAAA
1 TATTTTTAAA
*
27534660 TATTTTTAAT
1 TATTTTTAAA
*
27534670 TTTTTTTAAA
1 TATTTTTAAA
27534680 CTTATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
7 5 0.16
8 2 0.06
9 2 0.06
10 22 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:27534657 original size:17 final size:17
Alignment explanation
Indices: 27534630--27534674 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
27534620 CTTTTTAATC
27534630 TTTTA-TTTTTAAATAT
1 TTTTATTTTTTAAATAT
27534646 TTTTATTTTTTAAATAT
1 TTTTATTTTTTAAATAT
27534663 TTTTAATTTTTT
1 TTTT-ATTTTTT
27534675 TTAAACTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 5 0.19
17 15 0.56
18 7 0.26
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTTAAATAT
Found at i:27548515 original size:155 final size:155
Alignment explanation
Indices: 27548318--27548628 Score: 613
Period size: 155 Copynumber: 2.0 Consensus size: 155
27548308 TTATAATTAA
27548318 TTTAATCATTTTTCTACTAATTTTTTTATTTATTAAAAAATTATACATTTTATAATTAACAAATT
1 TTTAATCATTTTTCTACTAATTTTTTTATTTATTAAAAAATTATACATTTTATAATTAACAAATT
27548383 TTTACTCATTATTATTTATAATTATTAATTTTTATTGGTTAATAAATCGTGGGTGAATCTTATAT
66 TTTACTCATTATTATTTATAATTATTAATTTTTATTGGTTAATAAATCGTGGGTGAATCTTATAT
27548448 ATCATATACATCAATTAACTTATAC
131 ATCATATACATCAATTAACTTATAC
*
27548473 TTTAATCATTTTTGTACTAATTTTTTTATTTATTAAAAAATTATACATTTTATAATTAACAAATT
1 TTTAATCATTTTTCTACTAATTTTTTTATTTATTAAAAAATTATACATTTTATAATTAACAAATT
27548538 TTTACTCATTATTATTTATAATTATTAATTTTTATTGGTTAATAAATCGTGGGTGAATCTTATAT
66 TTTACTCATTATTATTTATAATTATTAATTTTTATTGGTTAATAAATCGTGGGTGAATCTTATAT
27548603 ATCATATACATCAATTAACTTATAC
131 ATCATATACATCAATTAACTTATAC
27548628 T
1 T
27548629 AACAAATGGT
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 155 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (155 bp):
TTTAATCATTTTTCTACTAATTTTTTTATTTATTAAAAAATTATACATTTTATAATTAACAAATT
TTTACTCATTATTATTTATAATTATTAATTTTTATTGGTTAATAAATCGTGGGTGAATCTTATAT
ATCATATACATCAATTAACTTATAC
Found at i:27552184 original size:44 final size:42
Alignment explanation
Indices: 27552146--27552391 Score: 192
Period size: 44 Copynumber: 5.6 Consensus size: 42
27552136 TTTAATCCAT
* * *
27552146 TCCACTGCAACTTCAAGGAGATAGGATTAGTAGCTTTAA-CCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATT-GTAGCTTCAATCC--C
* * * *
27552190 TCCACTGTAACTTCAGGGAGATAAGGTTTGATATCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAA-GATTG-TAGCTTCAATC-CC
* * *
27552235 TCCACTGCAGCTTCAGGGAGATAAGACTTGTAGTTTTAATCTGCC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGTAGCTTCAATC--CC
* * * * *
27552280 -CCACTGCAAATTCAGGGGGATAAGATTTGTATCTTCAGTCTAC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGTAGCTTCAATC-CC
* *
27552323 TCCACTGCAACTTCAAGGAGATAAGACTTGTAACTTCAA-CCTGC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGTAGCTTCAATCC--C
27552367 TCCACTGCAACTTCAGGGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAG
27552392 GTTTGATATG
Statistics
Matches: 160, Mismatches: 33, Indels: 18
0.76 0.16 0.09
Matches are distributed among these distances:
43 2 0.01
44 120 0.75
45 37 0.23
46 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (42 bp):
TCCACTGCAACTTCAGGGAGATAAGATTGTAGCTTCAATCCC
Found at i:27552346 original size:88 final size:89
Alignment explanation
Indices: 27552146--27552400 Score: 361
Period size: 88 Copynumber: 2.9 Consensus size: 89
27552136 TTTAATCCAT
* *
27552146 TCCACTGCAACTTCAAGGAGATAGGA-TTAGTAGCTTTAACCTGCTCCACTGTAACTTCAGGGAG
1 TCCACTGCAACTTCAAGGAGATAAGACTT-GTAGCTTTAACCTGCTCCACTGCAACTTCAGGGAG
*
27552210 ATAAGGTTTGATATCTTCAATCTGC
65 ATAAGGTTTGATATCTTCAATCTAC
* * * * * * *
27552235 TCCACTGCAGCTTCAGGGAGATAAGACTTGTAGTTTTAATCTGCCCCACTGCAAATTCAGGGGGA
1 TCCACTGCAACTTCAAGGAGATAAGACTTGTAGCTTTAACCTGCTCCACTGCAACTTCAGGGAGA
* *
27552300 TAAGATTTG-TATCTTCAGTCTAC
66 TAAGGTTTGATATCTTCAATCTAC
* *
27552323 TCCACTGCAACTTCAAGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGA
1 TCCACTGCAACTTCAAGGAGATAAGACTTGTAGCTTTAACCTGCTCCACTGCAACTTCAGGGAGA
27552388 TAAGGTTTGATAT
66 TAAGGTTTGATAT
27552401 GATCTGCTCT
Statistics
Matches: 142, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
88 76 0.54
89 64 0.45
90 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (89 bp):
TCCACTGCAACTTCAAGGAGATAAGACTTGTAGCTTTAACCTGCTCCACTGCAACTTCAGGGAGA
TAAGGTTTGATATCTTCAATCTAC
Found at i:27552540 original size:181 final size:180
Alignment explanation
Indices: 27552299--27552749 Score: 493
Period size: 182 Copynumber: 2.5 Consensus size: 180
27552289 ATTCAGGGGG
* *
27552299 ATAAGATTTG-TATCTTCAGTCTACTCCACTGCAACTTCAAGGAGATAAGACTTGTAACTTCAAC
1 ATAAGATTTGCTATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAT
* * * * * *
27552363 CTGCTCCACTGCAACTTCA-GGGAGATAAGGTT-TGA-TATGATCTGCTCTACTAAAACTTAAAA
66 CTGC-CCACTGAAACTTCAGGGGA-ATAAGATTGTGACTATAACCTACTCCACTAAAACTTAAAA
* * *
27552425 GATATAAGATCTGTAATTTATAG-CTTCAATCTGTTCCACTGCAACTTTAAGG-AC
129 GAGATAAGATCTATAA-TT-TAGCCTT-AATCTGTTCCACTGCAAC-TTAAGGAAA
* * *
27552479 ATAAGATTTGCTATCTTCAGTCTACTCCTCTGTAACTTCAGGGAGATAAGACTTTTAACTTCAAT
1 ATAAGATTTGCTATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAT
* * * * **
27552544 CTGCCCTACTAAAACTTCAGGGGAATAAGATTGGTGACTTTAACCTACTCCACTACAACTTCAGG
66 CTGCCC-ACTGAAACTTCAGGGGAATAAGATT-GTGACTATAACCTACTCCACTAAAACTTAAAA
* * *
27552609 GAGGTAAGGTCTATAATTTAGCCTTAATCTGTTCCACTGCAACTTCAGGAAA
129 GAGATAAGATCTATAATTTAGCCTTAATCTGTTCCACTGCAACTTAAGGAAA
* * * *
27552661 ATGAGATTTGCTATCTTCAGTCTGCTCCACTGCATCTTCAGGGAGATCAA-ACTTGTAACTGCAA
1 ATAAGATTTGCTATCTTCAGTCTACTCCACTGCAACTTCAGGGAGAT-AAGACTTGTAACTTCAA
* *
27552725 TCTACCCCACTGTAACTTCACGGGG
65 TCT-GCCCACTGAAACTTCA-GGGG
27552750 CAAGATTAGT
Statistics
Matches: 227, Mismatches: 33, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
180 12 0.05
181 75 0.33
182 93 0.41
183 17 0.07
184 30 0.13
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (180 bp):
ATAAGATTTGCTATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAT
CTGCCCACTGAAACTTCAGGGGAATAAGATTGTGACTATAACCTACTCCACTAAAACTTAAAAGA
GATAAGATCTATAATTTAGCCTTAATCTGTTCCACTGCAACTTAAGGAAA
Found at i:27552702 original size:182 final size:179
Alignment explanation
Indices: 27552270--27552727 Score: 487
Period size: 181 Copynumber: 2.5 Consensus size: 179
27552260 ACTTGTAGTT
** * **
27552270 TTAATCTGCCCCACTGCAAATTCAGGGGGATAAGATTTG-TATCTTCAGTCTACTCCACTGCAAC
1 TTAATCTGTTCCACTGCAACTTCA-GGAAATAAGATTTGCTATCTTCAGTCTACTCCACTGCAAC
* * ** *
27552334 TTCAAGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGAT
65 TTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTAAAACTTCAGGGAGATAAGATTTGAT
* * * * * *
27552399 ATGATCTGCTCTACTAAAACTTAAAAGATATAAGATCTGTAATTTATAGC
130 ATAACCTACTCCACTAAAACTTAAAAGAGATAAGATCTATAATTTATAGC
* * * *
27552449 TTCAATCTGTTCCACTGCAACTTTAAGGACATAAGATTTGCTATCTTCAGTCTACTCCTCTGTAA
1 TT-AATCTGTTCCACTGCAAC-TTCAGGAAATAAGATTTGCTATCTTCAGTCTACTCCACTGCAA
*
27552514 CTTCAGGGAGATAAGACTTTTAACTTCAATCTGC-CCTACTAAAACTTCAGGG-GAATAAGATTG
64 CTTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCC-ACTAAAACTTCAGGGAG-ATAAGATT-
* * * ** * *
27552577 GTGACTTTAACCTACTCCACTACAACTTCAGGGAGGTAAGGTCTATAA-TT-TAGCC
126 -TGA-TATAACCTACTCCACTAAAACTTAAAAGAGATAAGATCTATAATTTATAG-C
* * *
27552632 TTAATCTGTTCCACTGCAACTTCAGGAAAATGAGATTTGCTATCTTCAGTCTGCTCCACTGCATC
1 TTAATCTGTTCCACTGCAACTTCAGG-AAATAAGATTTGCTATCTTCAGTCTACTCCACTGCAAC
*
27552697 TTCAGGGAGATCAA-ACTTGTAACTGCAATCT
65 TTCAGGGAGAT-AAGACTTGTAACTTCAATCT
27552728 ACCCCACTGT
Statistics
Matches: 232, Mismatches: 36, Indels: 19
0.81 0.13 0.07
Matches are distributed among these distances:
179 2 0.01
180 30 0.13
181 81 0.35
182 79 0.34
183 10 0.04
184 30 0.13
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (179 bp):
TTAATCTGTTCCACTGCAACTTCAGGAAATAAGATTTGCTATCTTCAGTCTACTCCACTGCAACT
TCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTAAAACTTCAGGGAGATAAGATTTGATA
TAACCTACTCCACTAAAACTTAAAAGAGATAAGATCTATAATTTATAGC
Found at i:27557411 original size:22 final size:21
Alignment explanation
Indices: 27557381--27557438 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
27557371 ATACAATCGT
*
27557381 AGATTTGATATGTAATCTTAG
1 AGATTTGATTTGTAATCTTAG
*
27557402 AAGATATGATTTTGTAATCTTAG
1 -AGATTTGA-TTTGTAATCTTAG
27557425 AGATTTGATTTGTA
1 AGATTTGATTTGTA
27557439 GATACCATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 14 0.44
23 12 0.38
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:27557421 original size:23 final size:22
Alignment explanation
Indices: 27557391--27557435 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
27557381 AGATTTGATA
27557391 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAG-AGATATGATTT
*
27557414 TGTAATCTTAGAGATTTGATTT
1 TGTAATCTTAGAGATATGATTT
27557436 GTAGATACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (22 bp):
TGTAATCTTAGAGATATGATTT
Found at i:27560467 original size:27 final size:27
Alignment explanation
Indices: 27560426--27560478 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
27560416 TCTCGGTGTG
*
27560426 AGAAAGCTTTTGACCAAGTAAAGCAAA
1 AGAAAGCTTTCGACCAAGTAAAGCAAA
27560453 AGAAAGCTTTCGACCAAGTAAAGCAA
1 AGAAAGCTTTCGACCAAGTAAAGCAA
27560479 GCAATGGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (27 bp):
AGAAAGCTTTCGACCAAGTAAAGCAAA
Found at i:27562585 original size:22 final size:22
Alignment explanation
Indices: 27562555--27562656 Score: 91
Period size: 22 Copynumber: 4.6 Consensus size: 22
27562545 ATACAATCGT
*
27562555 AGATTTGATATGTAATCTTAGG
1 AGATTTGATTTGTAATCTTAGG
* ** * *
27562577 AGATATGATTTTGTAA-AATCGT
1 AGATTTGA-TTTGTAATCTTAGG
* *
27562599 AGATTTGATATGTAATCTTAGA
1 AGATTTGATTTGTAATCTTAGG
*
27562621 AGATATGATTTTGTAATCTTA-G
1 AGATTTGA-TTTGTAATCTTAGG
27562643 AGATTTGATTTGTA
1 AGATTTGATTTGTA
27562657 GATACCATTC
Statistics
Matches: 61, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
21 12 0.20
22 32 0.52
23 17 0.28
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (22 bp):
AGATTTGATTTGTAATCTTAGG
Found at i:27562599 original size:44 final size:44
Alignment explanation
Indices: 27562549--27562636 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
27562539 GAGGATATAC
*
27562549 AATCGTAGATTTGATATGTAATCTTAGGAGATATGATTTTGTAA
1 AATCGTAGATTTGATATGTAATCTTAGAAGATATGATTTTGTAA
27562593 AATCGTAGATTTGATATGTAATCTTAGAAGATATGATTTTGTAA
1 AATCGTAGATTTGATATGTAATCTTAGAAGATATGATTTTGTAA
27562637 TCTTAGAGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (44 bp):
AATCGTAGATTTGATATGTAATCTTAGAAGATATGATTTTGTAA
Found at i:27566509 original size:43 final size:43
Alignment explanation
Indices: 27566455--27566618 Score: 224
Period size: 43 Copynumber: 3.8 Consensus size: 43
27566445 CTAATGAGTG
* *
27566455 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAAGACCT
1 TTAGCGACGCTTTTTCCACAAACGCCGCTAAAAACCAGGACCT
*
27566498 TTAGCGACGC-TTTTCCTACAAACGCCGCTAAAGACCAGGACCT
1 TTAGCGACGCTTTTTCC-ACAAACGCCGCTAAAAACCAGGACCT
* * *
27566541 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCAGGACCT
1 TTAGCGACGCTTTTTCCACAAACGCCGCTAAAAACCAGGACCT
* *
27566584 TTAGC-AGTGCTTTTACCACAAACGCCGCTAAAAAC
1 TTAGCGA-CGCTTTTTCCACAAACGCCGCTAAAAAC
27566619 ATGACTTAAA
Statistics
Matches: 108, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
42 6 0.06
43 96 0.89
44 6 0.06
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (43 bp):
TTAGCGACGCTTTTTCCACAAACGCCGCTAAAAACCAGGACCT
Found at i:27566554 original size:86 final size:86
Alignment explanation
Indices: 27566455--27566615 Score: 254
Period size: 86 Copynumber: 1.9 Consensus size: 86
27566445 CTAATGAGTG
27566455 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAAGACCTTTAGC-GACGCTTTT-CCTACA
1 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAAGACCTTTAGCAG-CGCTTTTACC-ACA
27566518 AACGCCGCTAAAGACCAGGACCT
64 AACGCCGCTAAAGACCAGGACCT
* * * *
27566541 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCAGGACCTTTAGCAGTGCTTTTACCACAAA
1 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAAGACCTTTAGCAGCGCTTTTACCACAAA
27566606 CGCCGCTAAA
66 CGCCGCTAAA
27566616 AACATGACTT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
86 66 0.96
87 3 0.04
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (86 bp):
TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAAGACCTTTAGCAGCGCTTTTACCACAAA
CGCCGCTAAAGACCAGGACCT
Found at i:27566837 original size:18 final size:18
Alignment explanation
Indices: 27566814--27566873 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
27566804 TTAAAACAAG
27566814 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
27566832 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
27566849 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
27566867 TTACATT
1 TTACATT
27566874 AGAATTACAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 14 0.48
19 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:27567105 original size:15 final size:15
Alignment explanation
Indices: 27567085--27567115 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27567075 TACGATTGTT
*
27567085 TTCTCAGAAAGGGAA
1 TTCTCACAAAGGGAA
27567100 TTCTCACAAAGGGAA
1 TTCTCACAAAGGGAA
27567115 T
1 T
27567116 ATTGCTGTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (15 bp):
TTCTCACAAAGGGAA
Found at i:27570875 original size:13 final size:13
Alignment explanation
Indices: 27570857--27570881 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27570847 TGTCAATCTA
27570857 TTACATTAATTTG
1 TTACATTAATTTG
27570870 TTACATTAATTT
1 TTACATTAATTT
27570882 ATTTATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TTACATTAATTTG
Found at i:27571378 original size:21 final size:21
Alignment explanation
Indices: 27571344--27571407 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
27571334 TCTCAAATCT
* *
27571344 TTAAACCCTAAATCACTAACTC
1 TTAACCCCT-AATCACTAACCC
*
27571366 TTAACCCCTAATCTCTAACCC
1 TTAACCCCTAATCACTAACCC
*
27571387 CTAACCCCTAA-CTACTAACCC
1 TTAACCCCTAATC-ACTAACCC
27571408 ATAAATCTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 1 0.03
21 27 0.75
22 8 0.22
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (21 bp):
TTAACCCCTAATCACTAACCC
Found at i:27571499 original size:7 final size:7
Alignment explanation
Indices: 27571489--27571518 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
27571479 TAACGCAAAT
27571489 CCCTAAC
1 CCCTAAC
27571496 CCCTAAC
1 CCCTAAC
27571503 CCCTAAC
1 CCCTAAC
27571510 CCCTAAC
1 CCCTAAC
27571517 CC
1 CC
27571519 TTACACCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.60, G:0.00, T:0.13
Consensus pattern (7 bp):
CCCTAAC
Found at i:27572188 original size:41 final size:41
Alignment explanation
Indices: 27572124--27572408 Score: 408
Period size: 41 Copynumber: 7.0 Consensus size: 41
27572114 TCAAAAACGG
* *
27572124 GCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
* * * **
27572165 GCATTAGCGGCACTTCTTCAAAAACACCGCTAAAGGTCTAA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
* * * *
27572206 GCATTAGCGGAGCTTCTTCAAAAACGCCACTAAAGGTCTGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
* *
27572247 GCATTAGTGGCGCTTCTTTAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
27572288 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
* *
27572329 GCATTAGCGGCGCATCTTCAAAAACGCCACTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
* * *
27572370 ACGTTAGCGGCGCTTCTTCAAAAACTCCGCTAAAGGCCC
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
27572409 CAAAAACTCA
Statistics
Matches: 217, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 217 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (41 bp):
GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
Found at i:27572503 original size:39 final size:39
Alignment explanation
Indices: 27572456--27572577 Score: 147
Period size: 40 Copynumber: 3.1 Consensus size: 39
27572446 TTTGCGTCGC
* * *
27572456 TTTTCAAAAAACACCGCTAATGCTT-ATTTTTTGCGGCG
1 TTTTCAAAAAGCGCCGCTAATGCTTGATTTTTAGCGGCG
**
27572494 TTTTCCAAAAAGCGCCGCTAATGCTTGACCTTTAGCGGCG
1 TTTT-CAAAAAGCGCCGCTAATGCTTGATTTTTAGCGGCG
* * *
27572534 TTTTTAGAAAAGCGCCGCTAATGCTTGGTTTTTAGTGGCG
1 TTTTCA-AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCG
27572574 TTTT
1 TTTT
27572578 TTGTCCAAAC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
38 4 0.06
39 20 0.28
40 47 0.66
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (39 bp):
TTTTCAAAAAGCGCCGCTAATGCTTGATTTTTAGCGGCG
Found at i:27573329 original size:20 final size:20
Alignment explanation
Indices: 27573292--27573334 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27573282 AAAATAAACA
* **
27573292 TATAATTATTTATTTAATAT
1 TATAATTATTCAAATAATAT
27573312 TATAATTATTCAAATAATAT
1 TATAATTATTCAAATAATAT
27573332 TAT
1 TAT
27573335 TGAAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATTATTCAAATAATAT
Found at i:27573600 original size:17 final size:18
Alignment explanation
Indices: 27573562--27573600 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
27573552 TTACAATATG
**
27573562 TATTGGAACACTTATAGT
1 TATTGGAACACTTATAAA
27573580 TATTGGAACAC-TATAAA
1 TATTGGAACACTTATAAA
27573597 TATT
1 TATT
27573601 TGAAAACGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (18 bp):
TATTGGAACACTTATAAA
Found at i:27573687 original size:171 final size:171
Alignment explanation
Indices: 27573402--27574019 Score: 1069
Period size: 171 Copynumber: 3.6 Consensus size: 171
27573392 ACCCATTCAT
* * *
27573402 TTATAGTTATTGGAACACTATAAATATTTAAAAATGTTGC-AGTGATTCATTCATTTCCCTAAAC
1 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTT-CTAGTGATTCATTCATTTCCCAAAAC
* *
27573466 AAAGGTCTGAAATCTAAACTT-AGAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATG
65 AAAGGTCCGAAATCCAAACTTCA-AACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATG
*
27573530 ATGAAAATAATATTACGAGAGGTTACAATATGTATTGGAACAC
129 ATGAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
27573573 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
1 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
*
27573638 AAGGTCTGAAATCCAAACTTCAAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGAT
66 AAGGTCCGAAATCCAAACTTCAAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGAT
27573703 GAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
131 GAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
27573744 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
1 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
*
27573809 AAGGTCCGAAATCCAAACTTCAAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGAC
66 AAGGTCCGAAATCCAAACTTCAAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGAT
27573874 GAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
131 GAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
* * ** * * *
27573915 TTATAGTTATTGGAACACTATAAATATTTGAAAATGTTCCAGAAATTTATTTATTTCCCTAAACA
1 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
27573980 AAGGTCCGAAATCCAAACTTCAAACTAAAAATAAATTGTA
66 AAGGTCCGAAATCCAAACTTCAAACTAAAAATAAATTGTA
27574020 CTCCATACCG
Statistics
Matches: 431, Mismatches: 14, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
170 1 0.00
171 429 1.00
172 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (171 bp):
TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
AAGGTCCGAAATCCAAACTTCAAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGAT
GAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
Found at i:27573771 original size:17 final size:18
Alignment explanation
Indices: 27573728--27573771 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
27573718 AGAGGTTACA
*
27573728 ATAAGTATTGGAACACTT
1 ATAAATATTGGAACACTT
**
27573746 ATAGTTATTGGAACAC-T
1 ATAAATATTGGAACACTT
27573763 ATAAATATT
1 ATAAATATT
27573772 TGAAAACGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (18 bp):
ATAAATATTGGAACACTT
Found at i:27573942 original size:17 final size:18
Alignment explanation
Indices: 27573899--27573942 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
27573889 AGAGGTTACA
*
27573899 ATAAGTATTGGAACACTT
1 ATAAATATTGGAACACTT
**
27573917 ATAGTTATTGGAACAC-T
1 ATAAATATTGGAACACTT
27573934 ATAAATATT
1 ATAAATATT
27573943 TGAAAATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (18 bp):
ATAAATATTGGAACACTT
Found at i:27576619 original size:20 final size:20
Alignment explanation
Indices: 27576582--27576624 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27576572 AAAATAAACA
* **
27576582 TATAATTATTTATTTAATAT
1 TATAATTATTCAAATAATAT
27576602 TATAATTATTCAAATAATAT
1 TATAATTATTCAAATAATAT
27576622 TAT
1 TAT
27576625 TGAAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATTATTCAAATAATAT
Found at i:27576890 original size:17 final size:18
Alignment explanation
Indices: 27576847--27576890 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
27576837 AGAGGTTACA
*
27576847 ATAAGTATTGGAACACTT
1 ATAAATATTGGAACACTT
**
27576865 ATAGTTATTGGAACAC-T
1 ATAAATATTGGAACACTT
27576882 ATAAATATT
1 ATAAATATT
27576891 TGAAAACGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (18 bp):
ATAAATATTGGAACACTT
Found at i:27576977 original size:171 final size:170
Alignment explanation
Indices: 27576692--27577139 Score: 738
Period size: 171 Copynumber: 2.6 Consensus size: 170
27576682 ACCCATTCAT
27576692 TTATAGTTATTGGAACACTATAAATATTTGAAAATGTTGCAGTGATTCATTCATTTCCCTAAACA
1 TTATAGTTATTGGAACACTATAAATATTTGAAAATGTT-CAGTGATTCATTCATTTCCCTAAACA
* * *
27576757 AAGGTCTGAAATCTAAACTT-AGAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGA
65 AAGGTCCGAAATCCAAACTTCA-AACTAAAAATAAATTGTACTTGCAAGACTCCATATCGTATGA
* *
27576821 TGAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
129 CGAAAATAATATTAAGAGAGGTTACAATAAGTATTGGAACAC
* *
27576863 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
1 TTATAGTTATTGGAACACTATAAATATTTGAAAATGTTC-AGTGATTCATTCATTTCCCTAAACA
27576928 AAGGTCCGAAATCCAAACTTCAAACTAAAAATAAATTGTACTTGCAAGACTCCATATCGTATGAC
65 AAGGTCCGAAATCCAAACTTCAAACTAAAAATAAATTGTACTTGCAAGACTCCATATCGTATGAC
*
27576993 GCAAATAATATTAAGAGAGGTTACAATAAGTATTGGAACAC
130 GAAAATAATATTAAGAGAGGTTACAATAAGTATTGGAACAC
* * *
27577034 TTATAGTTATTGGAACATTATAAATATTTGAAAATGTTCAGTAATTCATTTATTTCCCTAAACGA
1 TTATAGTTATTGGAACACTATAAATATTTGAAAATGTTCAGTGATTCATTCATTTCCCTAAAC-A
*
27577099 AA-GTCCGAAATCCAAACTTCAAATTAAAAATAAATTGTACT
65 AAGGTCCGAAATCCAAACTTCAAACTAAAAATAAATTGTACT
27577140 CCATACCGTA
Statistics
Matches: 260, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
170 60 0.23
171 199 0.77
172 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (170 bp):
TTATAGTTATTGGAACACTATAAATATTTGAAAATGTTCAGTGATTCATTCATTTCCCTAAACAA
AGGTCCGAAATCCAAACTTCAAACTAAAAATAAATTGTACTTGCAAGACTCCATATCGTATGACG
AAAATAATATTAAGAGAGGTTACAATAAGTATTGGAACAC
Found at i:27577061 original size:17 final size:18
Alignment explanation
Indices: 27577018--27577061 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
27577008 AGAGGTTACA
*
27577018 ATAAGTATTGGAACACTT
1 ATAAATATTGGAACACTT
**
27577036 ATAGTTATTGGAACA-TT
1 ATAAATATTGGAACACTT
27577053 ATAAATATT
1 ATAAATATT
27577062 TGAAAATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.39
Consensus pattern (18 bp):
ATAAATATTGGAACACTT
Found at i:27580335 original size:98 final size:98
Alignment explanation
Indices: 27580164--27580360 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
27580154 GTGCAATAAA
*
27580164 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
27580229 CCTCTAAAATCTCAAACTCGGAATATTTCATTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCATTT
*
27580262 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATATGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
27580327 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCATTT
27580360 A
1 A
27580361 TTATTTTTAA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCATTT
Found at i:27581823 original size:22 final size:21
Alignment explanation
Indices: 27581788--27581845 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
27581778 AAAGGGTATC
* *
27581788 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
27581809 TACAAAATCATATCTTCTAATAT
1 TAC-AAATCATATC-TCTAAGAT
* *
27581832 TGCATATCATATCT
1 TACAAATCATATCT
27581846 AAGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:27581852 original size:19 final size:19
Alignment explanation
Indices: 27581824--27581925 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
27581814 AATCATATCT
*
27581824 TCTAATATTGCATATCATA
1 TCTAAGATTGCATATCATA
27581843 TCTAAGATTGCATATCTGCATATA
1 TCTAAGATTGCATA--T-C--ATA
27581867 TCATATCTAAGATTGCATATCATA
1 TC-----TAAGATTGCATATCATA
*
27581891 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
27581910 CCTAAGATTGCATATC
1 TCTAAGATTGCATATC
27581926 CTCAAAAATT
Statistics
Matches: 69, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
19 43 0.62
21 1 0.01
22 1 0.01
24 10 0.14
26 1 0.01
27 1 0.01
29 12 0.17
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:27581858 original size:14 final size:14
Alignment explanation
Indices: 27581839--27581887 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
27581829 TATTGCATAT
27581839 CATATCTAAGATTG
1 CATATCTAAGATTG
* *
27581853 CATATCTGCATATAT-
1 CATATCT-AAGAT-TG
27581868 CATATCTAAGATTG
1 CATATCTAAGATTG
27581882 CATATC
1 CATATC
27581888 ATATCTAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 1 0.04
14 16 0.57
15 10 0.36
16 1 0.04
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (14 bp):
CATATCTAAGATTG
Found at i:27581966 original size:47 final size:47
Alignment explanation
Indices: 27581897--27581992 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
27581887 CATATCTAGG
27581897 ATTGCATATCATACCTAAGATTGCATATCCTCAAAAATTATGTTTCC
1 ATTGCATATCATACCTAAGATTGCATATCCTCAAAAATTATGTTTCC
27581944 ATTGCATATCATACCTAAGATTGCATATCCTCAAAAATTATGTTTCC
1 ATTGCATATCATACCTAAGATTGCATATCCTCAAAAATTATGTTTCC
27581991 AT
1 AT
27581993 ATGTGAGCCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.36
Consensus pattern (47 bp):
ATTGCATATCATACCTAAGATTGCATATCCTCAAAAATTATGTTTCC
Found at i:27582438 original size:132 final size:132
Alignment explanation
Indices: 27582201--27582985 Score: 1347
Period size: 132 Copynumber: 5.9 Consensus size: 132
27582191 CTGCAACTGC
* *
27582201 AGGGAGATAAGA-CTTAGAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGC
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGC
* * * *
27582265 TTCAATGTACTCCACTGTAACCACAGGGAGGAAAAATCCGCCATCTTCGATCTACTCCACTATTG
65 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
27582330 CTT
130 CTT
* ** * ** * *
27582333 AGGGAGATAAAATCTGAAATCTGAAATCTATTCCACTATTCCCCAGGGAAGTAGAGTTATTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* * *
27582398 TAAATGTACTCCACTATAACCACAAGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
27582463 TT
131 TT
* *
27582465 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACGGTTGTCCAGGGAAGTAGAATTACTGACT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
27582530 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATTCGCCATCTTCAATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
27582595 TT
131 TT
27582597 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
27582662 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
27582727 TT
131 TT
27582729 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
27582794 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
27582859 TT
131 TT
27582861 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
27582926 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCATCTTCGATATGCTCCACT
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACT
27582986 GTCAATGCAG
Statistics
Matches: 618, Mismatches: 34, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
132 615 1.00
133 3 0.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:27582909 original size:44 final size:45
Alignment explanation
Indices: 27582439--27582909 Score: 162
Period size: 44 Copynumber: 10.7 Consensus size: 45
27582429 AAAATCCGCC
* * **
27582439 ATCTTCAATCTGCTCCACTACTG-CTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTATTGTCACAGGGAGATAAGATCTGAA
* **
27582483 ATCTTCAATCTATTCCACGGTTGTC-CAGGGA-AGT-AGAATTACTG--
1 ATCTTCAATCTACTCCACTATTGTCACAGGGAGA-TAAG-A-T-CTGAA
* *** * * **
27582527 A-CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT-TCGCC
1 ATCTTCAATCTACTCCACTATTGTCACAGGGAGATAAGATCT-GAA
* * **
27582571 ATCTTCAATCTGCTCCACTACTG-CTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTATTGTCACAGGGAGATAAGATCTGAA
* *
27582615 ATCTTCAATCTATTCCACTGTTGTC-CAGGGA-AGT-AGAATTACTG--
1 ATCTTCAATCTACTCCACTATTGTCACAGGGAGA-TAAG-A-T-CTGAA
* * *** * * * **
27582659 -GCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCC
1 ATCTTCAATCTACTCCACTATTGTCACAGGGAGATAAGATCTGAA
* * * **
27582703 ATCTTCGATCTGCTCCACTACTG-CTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTATTGTCACAGGGAGATAAGATCTGAA
* *
27582747 ATCTTCAATCTATTCCACTGTTGTC-CAGGGA-AGT-AGAATTACTG--
1 ATCTTCAATCTACTCCACTATTGTCACAGGGAGA-TAAG-A-T-CTGAA
* * *** * * * **
27582791 -GCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCC
1 ATCTTCAATCTACTCCACTATTGTCACAGGGAGATAAGATCTGAA
* * * **
27582835 ATCTTCGATCTGCTCCACTACTG-CTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTATTGTCACAGGGAGATAAGATCTGAA
* *
27582879 ATCTTCAATCTATTCCACTGTTGTC-CAGGGA
1 ATCTTCAATCTACTCCACTATTGTCACAGGGA
27582910 AGTAGAATTA
Statistics
Matches: 300, Mismatches: 91, Indels: 72
0.65 0.20 0.16
Matches are distributed among these distances:
41 1 0.00
42 5 0.02
43 62 0.21
44 166 0.55
45 57 0.19
46 9 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (45 bp):
ATCTTCAATCTACTCCACTATTGTCACAGGGAGATAAGATCTGAA
Found at i:27585560 original size:27 final size:27
Alignment explanation
Indices: 27585522--27585575 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
27585512 AACCCTGTTG
27585522 GTTAGCAATCAATTTTCTGTATGTATT
1 GTTAGCAATCAATTTTCTGTATGTATT
27585549 GTTAGCAATCAATTTTCTGTATGTATT
1 GTTAGCAATCAATTTTCTGTATGTATT
27585576 CACGCTGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (27 bp):
GTTAGCAATCAATTTTCTGTATGTATT
Found at i:27588441 original size:98 final size:98
Alignment explanation
Indices: 27588270--27588466 Score: 376
Period size: 98 Copynumber: 2.0 Consensus size: 98
27588260 GTGCAATAAA
*
27588270 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
27588335 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
27588368 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
27588433 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
27588466 A
1 A
27588467 TTGTTTTTAG
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:27589385 original size:25 final size:25
Alignment explanation
Indices: 27589325--27589385 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
27589315 ATATATAGCT
27589325 AAAA-TAATAATAATTACATATGAA
1 AAAATTAATAATAATTACATATGAA
*
27589349 AATATTAATAATAATTACAT-T-AA
1 AAAATTAATAATAATTACATATGAA
27589372 CAAAATTAACTAAT
1 -AAAATTAA-TAAT
27589386 TTTAAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 2 0.06
24 11 0.34
25 19 0.59
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAATTAATAATAATTACATATGAA
Found at i:27589944 original size:23 final size:22
Alignment explanation
Indices: 27589901--27589958 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
27589891 AAAGGGTATC
* *
27589901 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
27589922 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
27589945 TGCATATCATATCT
1 TACAAATCATATCT
27589959 AAAATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:27595119 original size:44 final size:44
Alignment explanation
Indices: 27594986--27595736 Score: 320
Period size: 44 Copynumber: 16.7 Consensus size: 44
27594976 CTTCAGTTTG
* *
27594986 CTCCACTGCAACTTCAGGGAGATAAGGCTTGCTATGGTAGATTTAATCTGA
1 CTCCACTGCAACTTCAGGGAGATAA-G-AT--T-T-GTAGCTTTAATCT-A
* * * ** * * *
27595037 C-CTACTGTAACTTCAGAGG-TATAAGATTCATCGTTTTAATCCA
1 CTCCACTGCAACTTCAG-GGAGATAAGATTTGTAGCTTTAATCTA
* * * * * *
27595080 TTCCACTGCAACTTCAAGGAGATAGGATTAGTAGCTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTA
* * * * *
27595124 CTCCACTGTAACTTCAGGGAGATAAGGTTTGATATCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTA
* * * *
27595169 CTCCACTGTAGCTTCAGGGAGATAAGACTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTA
* * * * * *
27595213 CCCCACTGCAAATTCAGGGGGATAAGATTTGTATCTTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTA
** * * * * *
27595257 CTCCACTGCAACTTCAAAGAGATAAGACTTGTAACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTA
* * * * *
27595301 CTCCACTGCAAGTTCAGGGAGATAAGGTTTG-A--TATGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTA
* ** ** * * * *
27595342 CTCTACTAAAACTTCAAAGATATAAGATCTGTAATTTATAGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGAT-A-A---G--ATTTGTAGCTTTAATCTA
* * * * *
27595393 TTCCACTGCAACTTTAGGGACATAAGATTTGCTATCTTTAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTA
* * * *
27595438 CTCCTCTGCAACTTCAGGGAGATAAGACTTT-TAACTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-TTTGTAGCTTTAATCTA
** * *
27595482 C-CCTACTAAAACTTCAGGG-GAATAAGATTGGT-GACTTTAACCTA
1 CTCC-ACTGCAACTTCAGGGAG-ATAAGATTTGTAG-CTTTAATCTA
* * * * * *
27595526 CTCCACTACAACTTCAGGGAGGTAAGGTCTGTAATTTAGCCTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAA-G-AT-T--TGTAGCTTTAATCTA
* * * * * * *
27595575 TTCCACTGCAACTTCAGGGAAATGAGATTTGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTA
* * * **
27595620 CTCCACTGCATCTTCAGGGAGATCAA-ACTTGTAACTGCAATCTA
1 CTCCACTGCAACTTCAGGGAGAT-AAGATTTGTAGCTTTAATCTA
* * * * * *
27595664 CCCCACTGTAACTTCACGGG-G-CAAGATTAGTGGCTTTAATCTG
1 CTCCACTGCAACTTCA-GGGAGATAAGATTTGTAGCTTTAATCTA
* * * *
27595707 TTTCACTGTAACTTTAGGGAGATAAGATTT
1 CTCCACTGCAACTTCAGGGAGATAAGATTT
27595737 ACCATAATGA
Statistics
Matches: 515, Mismatches: 151, Indels: 75
0.70 0.20 0.10
Matches are distributed among these distances:
41 21 0.04
42 6 0.01
43 34 0.07
44 254 0.49
45 110 0.21
46 9 0.02
47 2 0.00
48 5 0.01
49 31 0.06
50 19 0.04
51 24 0.05
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTA
Found at i:27595679 original size:182 final size:182
Alignment explanation
Indices: 27595200--27595684 Score: 534
Period size: 182 Copynumber: 2.7 Consensus size: 182
27595190 ATAAGACTTG
* ** * **
27595200 TAGCTTTAATCTGCCCCACTGCAAATTCAGGGGGATAAGATTTG-TATCTTCAGTCTACTCCACT
1 TAGCCTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTACTCCACT
** * * * * *
27595264 GCAACTTCAAAGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAAGTTCA-GGGAGATAAGG
66 GCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCCCCACTGAAACTTCAGGGGAGATAAGA
* * * * *
27595328 TTTGATATGATCTGCTCTACTAAAACTTCAAAGATATAAGATCTGTAATTTA
131 TTTGATATAACCTACTCCACTAAAACTTCAAAGAGATAAGATCTGTAATTTA
* * * *
27595380 TAG-CTTCAATCTGTTCCACTGCAACTTTAGGGACATAAGATTTGCTATCTTTAGTCTACTCCTC
1 TAGCCTT-AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTACTCCAC
* * *
27595444 TGCAACTTCAGGGAGATAAGACTTTTAACTTCAATCTGCCCTACTAAAACTTCAGGGGA-ATAAG
65 TGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCCCCACTGAAACTTCAGGGGAGATAAG
* * ** * *
27595508 ATTGGTGACTTTAACCTACTCCACTACAACTTCAGGGAGGTAAGGTCTGTAA-TT-
130 ATT--TGA-TATAACCTACTCCACTAAAACTTCAAAGAGATAAGATCTGTAATTTA
* *
27595562 TAGCCTTAATCTGTTCCACTGCAACTTCAGGGAAATGAGATTTGCTATCTTCAGTCTGCTCCACT
1 TAGCCTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTACTCCACT
* * * *
27595627 GCATCTTCAGGGAGATCAA-ACTTGTAACTGCAATCTACCCCACTGTAACTTCACGGGG
66 GCAACTTCAGGGAGAT-AAGACTTGTAACTTCAATCTGCCCCACTGAAACTTCA-GGGG
27595685 CAAGATTAGT
Statistics
Matches: 253, Mismatches: 43, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
179 2 0.01
180 34 0.13
181 69 0.27
182 102 0.40
183 14 0.06
184 32 0.13
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (182 bp):
TAGCCTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTACTCCACT
GCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCCCCACTGAAACTTCAGGGGAGATAAGA
TTTGATATAACCTACTCCACTAAAACTTCAAAGAGATAAGATCTGTAATTTA
Found at i:27603510 original size:20 final size:20
Alignment explanation
Indices: 27603473--27603515 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27603463 AAAATAAACA
* **
27603473 TATAATTATTTATTTAATAT
1 TATAATTATTCAAATAATAT
27603493 TATAATTATTCAAATAATAT
1 TATAATTATTCAAATAATAT
27603513 TAT
1 TAT
27603516 TGAAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATTATTCAAATAATAT
Found at i:27603781 original size:17 final size:18
Alignment explanation
Indices: 27603738--27603781 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
27603728 AGAGGTTACA
*
27603738 ATAAGTATTGGAACACTT
1 ATAAATATTGGAACACTT
**
27603756 ATAGTTATTGGAACAC-T
1 ATAAATATTGGAACACTT
27603773 ATAAATATT
1 ATAAATATT
27603782 TGAAAACGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (18 bp):
ATAAATATTGGAACACTT
Found at i:27603868 original size:171 final size:171
Alignment explanation
Indices: 27603583--27604203 Score: 1104
Period size: 171 Copynumber: 3.6 Consensus size: 171
27603573 ACCCATTCAT
* * *
27603583 TTATAGTTATTGGAACACTATAAATATTTAAAAATGTTGC-AGTGATTCATTCATTTCCCTAAAC
1 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTT-CTAGTGATTCATTCATTTCCCAAAAC
* ** *
27603647 AAAGGTCTGAAATCTAAACTTAGAACTAATTATAAATTGTAATTGCAAGACTCCATATCGTAAGA
65 AAAGGTCTGAAATCCAAACTTAGAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGA
27603712 TGAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
130 TGAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
27603754 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
1 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
27603819 AAGGTCTGAAATCCAAACTTCA-AACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGA
66 AAGGTCTGAAATCCAAACTT-AGAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGA
27603883 TGAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
130 TGAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
* *
27603925 TTATAGTTATTGGAACACTATAAATATTTGAAAAAGTTCTAGTGATTCATTCATTTCCCTAAACA
1 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
*
27603990 AAGGTCTGAAATCTAAACTTAGAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGAT
66 AAGGTCTGAAATCCAAACTTAGAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGAT
27604055 GAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
131 GAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
27604096 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
1 TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
27604161 AAGGTCTGAAATCCAAACTTCA-AACTAAAAATAAATTGTAATT
66 AAGGTCTGAAATCCAAACTT-AGAACTAAAAATAAATTGTAATT
27604204 NTTCCTGTGT
Statistics
Matches: 433, Mismatches: 13, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
170 2 0.00
171 429 0.99
172 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (171 bp):
TTATAGTTATTGGAACACTATAAATATTTGAAAACGTTCTAGTGATTCATTCATTTCCCAAAACA
AAGGTCTGAAATCCAAACTTAGAACTAAAAATAAATTGTAATTGCAAGACTCCATATCGTATGAT
GAAAATAATATTACGAGAGGTTACAATAAGTATTGGAACAC
Found at i:27603952 original size:17 final size:18
Alignment explanation
Indices: 27603909--27603952 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
27603899 AGAGGTTACA
*
27603909 ATAAGTATTGGAACACTT
1 ATAAATATTGGAACACTT
**
27603927 ATAGTTATTGGAACAC-T
1 ATAAATATTGGAACACTT
27603944 ATAAATATT
1 ATAAATATT
27603953 TGAAAAAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (18 bp):
ATAAATATTGGAACACTT
Found at i:27604123 original size:17 final size:18
Alignment explanation
Indices: 27604080--27604123 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
27604070 AGAGGTTACA
*
27604080 ATAAGTATTGGAACACTT
1 ATAAATATTGGAACACTT
**
27604098 ATAGTTATTGGAACAC-T
1 ATAAATATTGGAACACTT
27604115 ATAAATATT
1 ATAAATATT
27604124 TGAAAACGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (18 bp):
ATAAATATTGGAACACTT
Found at i:27611603 original size:27 final size:28
Alignment explanation
Indices: 27611551--27611603 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
27611541 GGCTTGTCTC
* *
27611551 TAATTTGGTCACCCCAATTTTATTTTTT
1 TAATTTGGTCACCCAAAATTTATTTTTT
27611579 TAATTTGGTCACCCAAAATTT-TTTT
1 TAATTTGGTCACCCAAAATTTATTTT
27611604 ATCAAATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.51
Consensus pattern (28 bp):
TAATTTGGTCACCCAAAATTTATTTTTT
Found at i:27611611 original size:28 final size:28
Alignment explanation
Indices: 27611552--27611617 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
27611542 GCTTGTCTCT
* * **
27611552 AATTTGGTCACCCCAATTTTATTTTTTT
1 AATTTGGTCACCCAAATTTTATTTATCA
27611580 AATTTGGTCACCCAAAATTTT-TTTATCA
1 AATTTGGTCACCC-AAATTTTATTTATCA
27611608 AATTT-GTCAC
1 AATTTGGTCAC
27611618 TCCACTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 5 0.15
28 22 0.67
29 6 0.18
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (28 bp):
AATTTGGTCACCCAAATTTTATTTATCA
Found at i:27612263 original size:22 final size:22
Alignment explanation
Indices: 27612238--27612314 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
27612228 CCAAAATATT
27612238 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
* * * *
27612260 ATCTCCT-AA-TTAAACCAAAATATT
1 ATCTCCTAAACTT-TAGC---ATCTA
27612284 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
27612306 ATCTCCTAA
1 ATCTCCTAA
27612315 TTAAAAGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 2 0.05
21 4 0.10
22 19 0.46
24 10 0.24
25 4 0.10
26 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (22 bp):
ATCTCCTAAACTTTAGCATCTA
Found at i:27612292 original size:46 final size:46
Alignment explanation
Indices: 27612225--27612319 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
27612215 ACAAAGATAG
27612225 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
27612271 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
27612317 AAA
1 AAA
27612320 AGAAAATAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:27619210 original size:40 final size:40
Alignment explanation
Indices: 27619127--27619269 Score: 173
Period size: 41 Copynumber: 3.5 Consensus size: 40
27619117 TACCCCTTGG
* * *
27619127 GGAATTTGCACTTAGCAACCCCTCTTTTATCAGAGTTTCGA
1 GGAATCTGCACTTAGCAACCCCT-TTTTATCAGTGATTCGA
*
27619168 GGAATTTGCACTTAGCAA-CCCTTTTTGATCAGTGATTCGA
1 GGAATCTGCACTTAGCAACCCCTTTTT-ATCAGTGATTCGA
*
27619208 GGAATCTGCACTTAACAACCCCTTTTTAATCAGTGATTCTG-
1 GGAATCTGCACTTAGCAACCCCTTTTT-ATCAGTGATTC-GA
* *
27619249 GGAATCTACACTTAGAAACCC
1 GGAATCTGCACTTAGCAACCC
27619270 TTACATTCAA
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
39 4 0.04
40 31 0.34
41 55 0.60
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (40 bp):
GGAATCTGCACTTAGCAACCCCTTTTTATCAGTGATTCGA
Found at i:27621085 original size:18 final size:18
Alignment explanation
Indices: 27621047--27621086 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
27621037 TTACGTCCTT
*
27621047 TACAGATACAGATACAGA
1 TACAGATACAGATACAAA
*
27621065 TACAGATACAGATATAAA
1 TACAGATACAGATACAAA
27621083 TACA
1 TACA
27621087 AATATGCAGA
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:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (18 bp):
TACAGATACAGATACAAA
Found at i:27621090 original size:6 final size:6
Alignment explanation
Indices: 27621047--27621078 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
27621037 TTACGTCCTT
27621047 TACAGA TACAGA TACAGA TACAGA TACAGA TA
1 TACAGA TACAGA TACAGA TACAGA TACAGA TA
27621079 TAAATACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
TACAGA
Found at i:27621475 original size:19 final size:18
Alignment explanation
Indices: 27621436--27621472 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
27621426 ATCACATAAA
27621436 CTTTAGGGTTAAATTAGC
1 CTTTAGGGTTAAATTAGC
*
27621454 CTTTAGGGTTTAATTAGC
1 CTTTAGGGTTAAATTAGC
27621472 C
1 C
27621473 CTTACCGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (18 bp):
CTTTAGGGTTAAATTAGC
Found at i:27622782 original size:18 final size:18
Alignment explanation
Indices: 27622741--27622782 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
27622731 GAATAATAGT
27622741 GCACAAAGCACATTCTGGA
1 GCACAAAGCACATTCT-GA
*
27622760 GCACAAAGCGCATATCT-A
1 GCACAAAGCACAT-TCTGA
27622778 GCACA
1 GCACA
27622783 CGAAATGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 12 0.57
20 3 0.14
ACGTcount: A:0.38, C:0.29, G:0.19, T:0.14
Consensus pattern (18 bp):
GCACAAAGCACATTCTGA
Found at i:27625037 original size:23 final size:24
Alignment explanation
Indices: 27625011--27625063 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
27625001 GTGCCGCATT
27625011 TTGGTAC-AGCATGGTGTGTAG-GG
1 TTGGTACGAG-ATGGTGTGTAGAGG
27625034 TTGG-ACGGAGATGGTGTGTAGAGG
1 TTGGTAC-GAGATGGTGTGTAGAGG
27625058 TTGGTA
1 TTGGTA
27625064 GGTAGGATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 2 0.08
23 15 0.58
24 8 0.31
25 1 0.04
ACGTcount: A:0.19, C:0.06, G:0.45, T:0.30
Consensus pattern (24 bp):
TTGGTACGAGATGGTGTGTAGAGG
Found at i:27627276 original size:14 final size:15
Alignment explanation
Indices: 27627257--27627285 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27627247 GCAAAACCTC
27627257 TTTATTTTT-TATTT
1 TTTATTTTTATATTT
27627271 TTTATTTTTATATTT
1 TTTATTTTTATATTT
27627286 CAATCCACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTATTTTTATATTT
Found at i:27643872 original size:66 final size:66
Alignment explanation
Indices: 27643786--27643966 Score: 213
Period size: 66 Copynumber: 2.7 Consensus size: 66
27643776 GAGAAAGATC
* * * * *
27643786 AAATATCG-GATCTTCTCAAGCTCTTAAACGAGATATCATGTCTTCTCAATCCCAAGCTCTTGAA
1 AAATATCGAG-TCTTCCCAAGCTCTTAAACGAGATATCAAGTCTTCTCAATCCAAAGATCCTGAA
27643850 C-
65 CT
* * *
27643851 ACAATATCGAGTCTTCCCAAGCTCCTAAACGATATATCAAGTCTTCTTAATCCAAAGATCCTGAA
1 A-AATATCGAGTCTTCCCAAGCTCTTAAACGAGATATCAAGTCTTCTCAATCCAAAGATCCTGAA
27643916 CT
65 CT
* * * * *
27643918 AAATATCAAGTCTTCCAAAACTCTTGAACGAGATATCAAGCCTTCTCAA
1 AAATATCGAGTCTTCCCAAGCTCTTAAACGAGATATCAAGTCTTCTCAA
27643967 GTTCCTGAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
65 1 0.01
66 94 0.97
67 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (66 bp):
AAATATCGAGTCTTCCCAAGCTCTTAAACGAGATATCAAGTCTTCTCAATCCAAAGATCCTGAAC
T
Found at i:27644807 original size:25 final size:25
Alignment explanation
Indices: 27644777--27644842 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
27644767 ATTATTATTT
27644777 TATATTTACGAGTCAAATATAGTAG
1 TATATTTACGAGTCAAATATAGTAG
27644802 TATATTTACGAGTCAAATATAGTAG
1 TATATTTACGAGTCAAATATAGTAG
*
27644827 TATATTTACAAGTCAA
1 TATATTTACGAGTCAA
27644843 GTGGTTTTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (25 bp):
TATATTTACGAGTCAAATATAGTAG
Found at i:27648892 original size:21 final size:22
Alignment explanation
Indices: 27648866--27648907 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
27648856 GATACTGCTG
27648866 TCACATCGCATCCTCA-AGCTC
1 TCACATCGCATCCTCAGAGCTC
* *
27648887 TCACATGGCCTCCTCAGAGCT
1 TCACATCGCATCCTCAGAGCT
27648908 ATGATTACGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.21, C:0.40, G:0.14, T:0.24
Consensus pattern (22 bp):
TCACATCGCATCCTCAGAGCTC
Found at i:27656566 original size:58 final size:58
Alignment explanation
Indices: 27656495--27656616 Score: 199
Period size: 58 Copynumber: 2.1 Consensus size: 58
27656485 GTATTCTGAT
* * *
27656495 AAAACGTTCATCTCTTTTGGAAACCCAAGTTTTACCAACTTCTAGCAGATATAAACAG
1 AAAACATTCATCTCTTTTGGAAACCCAAGTTTTACCAACTTCTAGCAGAAATAAACAA
* *
27656553 AAAACATTCATCTCTTTTGGAAACCCAAGTTTTACCTACTTCTAGCAGAAATAAATAA
1 AAAACATTCATCTCTTTTGGAAACCCAAGTTTTACCAACTTCTAGCAGAAATAAACAA
27656611 AAAACA
1 AAAACA
27656617 GTATAAAATC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (58 bp):
AAAACATTCATCTCTTTTGGAAACCCAAGTTTTACCAACTTCTAGCAGAAATAAACAA
Found at i:27659161 original size:6 final size:6
Alignment explanation
Indices: 27659152--27659187 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
27659142 ACTTGGGACC
27659152 TCCGAG TCCGAG TCCGAG TCC--G TCCGAG TCCGAG TC
1 TCCGAG TCCGAG TCCGAG TCCGAG TCCGAG TCCGAG TC
27659188 GTGTTAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
6 24 0.86
ACGTcount: A:0.14, C:0.36, G:0.31, T:0.19
Consensus pattern (6 bp):
TCCGAG
Found at i:27659178 original size:16 final size:16
Alignment explanation
Indices: 27659157--27659187 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
27659147 GGACCTCCGA
27659157 GTCCGAGTCCGAGTCC
1 GTCCGAGTCCGAGTCC
27659173 GTCCGAGTCCGAGTC
1 GTCCGAGTCCGAGTC
27659188 GTGTTAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.35, G:0.32, T:0.19
Consensus pattern (16 bp):
GTCCGAGTCCGAGTCC
Found at i:27659829 original size:8 final size:8
Alignment explanation
Indices: 27659816--27659840 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
27659806 TTTTAAATGA
27659816 TATTTTAT
1 TATTTTAT
27659824 TATTTTAT
1 TATTTTAT
27659832 TATTTTAT
1 TATTTTAT
27659840 T
1 T
27659841 TAGTGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:27681312 original size:25 final size:26
Alignment explanation
Indices: 27681266--27681325 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
27681256 TAAACATATG
27681266 AATTATAAAACATGAAAATATA-AAT
1 AATTATAAAACATGAAAATATATAAT
* **
27681291 AATTATAAAATATGAATGTATATAAT
1 AATTATAAAACATGAAAATATATAAT
27681317 -ATATATAAA
1 AAT-TATAAA
27681326 CTATATACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 21 0.70
26 9 0.30
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AATTATAAAACATGAAAATATATAAT
Found at i:27681510 original size:13 final size:14
Alignment explanation
Indices: 27681469--27681510 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
27681459 TAATTAACAG
27681469 AAATAAAC-AATAA
1 AAATAAACTAATAA
*
27681482 AAATAAAATAATAA
1 AAATAAACTAATAA
27681496 AAATAAACTAA-AA
1 AAATAAACTAATAA
27681509 AA
1 AA
27681511 CAAATGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (14 bp):
AAATAAACTAATAA
Found at i:27684049 original size:18 final size:18
Alignment explanation
Indices: 27684026--27684070 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
27684016 CAAATCCAAT
*
27684026 TCTCTCAATTCTTTCTAG
1 TCTCTCAATTCTTTCAAG
*
27684044 TCTCTCTAA-TCTTTCAAT
1 TCTCTC-AATTCTTTCAAG
27684062 TCTCTCAAT
1 TCTCTCAAT
27684071 ATTTTAGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 19 0.83
19 2 0.09
ACGTcount: A:0.20, C:0.29, G:0.02, T:0.49
Consensus pattern (18 bp):
TCTCTCAATTCTTTCAAG
Found at i:27684737 original size:3 final size:3
Alignment explanation
Indices: 27684729--27684768 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
27684719 CTTGGCAATT
*
27684729 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
27684769 CTACTTATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:27688311 original size:9 final size:9
Alignment explanation
Indices: 27688278--27688891 Score: 769
Period size: 9 Copynumber: 68.7 Consensus size: 9
27688268 TGCATACGCC
27688278 AGTTATGT-
1 AGTTATGTA
27688286 A-TTATGT-
1 AGTTATGTA
27688293 A-TTATGTA
1 AGTTATGTA
27688301 AG-TATTGTA
1 AGTTA-TGTA
27688310 AGTTATGTA
1 AGTTATGTA
27688319 AGTTATGTA
1 AGTTATGTA
*
27688328 AGTTATTTA
1 AGTTATGTA
*
27688337 ATTTATGTA
1 AGTTATGTA
27688346 AGTTATGTA
1 AGTTATGTA
27688355 AGTTATGTA
1 AGTTATGTA
*
27688364 AGTTATTTA
1 AGTTATGTA
*
27688373 ATTTATGTA
1 AGTTATGTA
27688382 AGTTATGTA
1 AGTTATGTA
*
27688391 AGTTATGCA
1 AGTTATGTA
27688400 AGTTATGTA
1 AGTTATGTA
*
27688409 AGTTA-CTA
1 AGTTATGTA
*
27688417 CATTTATGTA
1 -AGTTATGTA
27688427 AGTTATGTA
1 AGTTATGTA
* *
27688436 AGATATTTA
1 AGTTATGTA
*
27688445 ATTTATGTA
1 AGTTATGTA
27688454 AGTTATGTA
1 AGTTATGTA
27688463 AGTTATGTA
1 AGTTATGTA
*
27688472 AGTTATTTA
1 AGTTATGTA
*
27688481 ATTTATGTA
1 AGTTATGTA
27688490 AGTTATGTA
1 AGTTATGTA
27688499 AGTTATGTA
1 AGTTATGTA
*
27688508 AGTTATTTA
1 AGTTATGTA
*
27688517 ATTTATGTA
1 AGTTATGTA
27688526 AGTTATGTA
1 AGTTATGTA
27688535 AGTTATGTA
1 AGTTATGTA
*
27688544 AGTTATTTA
1 AGTTATGTA
*
27688553 ATTTATGTA
1 AGTTATGTA
27688562 AGTTATGTA
1 AGTTATGTA
27688571 AGTTATGTA
1 AGTTATGTA
*
27688580 AGTTATTTA
1 AGTTATGTA
*
27688589 ATTTATGTA
1 AGTTATGTA
27688598 AGTTATGTA
1 AGTTATGTA
27688607 AGTTATGTA
1 AGTTATGTA
*
27688616 AGTTATTTA
1 AGTTATGTA
*
27688625 ATTTATGTA
1 AGTTATGTA
27688634 AGTTATGTA
1 AGTTATGTA
27688643 AGTTATGTA
1 AGTTATGTA
*
27688652 AGTTATTTA
1 AGTTATGTA
*
27688661 ATTTATGTA
1 AGTTATGTA
27688670 AGTTATGTA
1 AGTTATGTA
27688679 AGTTATGTA
1 AGTTATGTA
*
27688688 AGTTATTTA
1 AGTTATGTA
*
27688697 ATTTATGTA
1 AGTTATGTA
27688706 AGTTATGTA
1 AGTTATGTA
27688715 AGTTATGTA
1 AGTTATGTA
*
27688724 AGTTATTTA
1 AGTTATGTA
*
27688733 ATTTATGTA
1 AGTTATGTA
27688742 AGTTATGTA
1 AGTTATGTA
*
27688751 AGTTATGCA
1 AGTTATGTA
27688760 AGTTATGTA
1 AGTTATGTA
*
27688769 AGTTA-CTA
1 AGTTATGTA
*
27688777 CATTTATGTA
1 -AGTTATGTA
27688787 AGTTATGTA
1 AGTTATGTA
* *
27688796 AGATATTTA
1 AGTTATGTA
* *
27688805 ATTTTTGTA
1 AGTTATGTA
27688814 AGTTATGTA
1 AGTTATGTA
27688823 AGTTACT-TA
1 AGTTA-TGTA
*
27688832 ATTTATGTA
1 AGTTATGTA
*
27688841 AGTTATGCA
1 AGTTATGTA
*
27688850 AGTTATTTA
1 AGTTATGTA
* *
27688859 ATTTTTGTA
1 AGTTATGTA
*
27688868 AGTTATATA
1 AGTTATGTA
27688877 A-TTAATGTA
1 AGTT-ATGTA
27688886 AGTTAT
1 AGTTAT
27688892 TTAATTTGTG
Statistics
Matches: 516, Mismatches: 78, Indels: 23
0.84 0.13 0.04
Matches are distributed among these distances:
7 13 0.03
8 11 0.02
9 483 0.94
10 9 0.02
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (9 bp):
AGTTATGTA
Found at i:27688898 original size:36 final size:36
Alignment explanation
Indices: 27688306--27688891 Score: 926
Period size: 36 Copynumber: 16.3 Consensus size: 36
27688296 ATGTAAGTAT
27688306 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
27688342 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
* * *
27688378 TGTAAGTTATGTAAGTTATGCAAGTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
* * *
27688414 -CTACATTTATGTAAGTTATGTAAGATATTTAATTTA
1 TGTA-AGTTATGTAAGTTATGTAAGTTATTTAATTTA
27688450 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
27688486 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
27688522 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
27688558 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
27688594 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
27688630 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
27688666 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
27688702 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
* * *
27688738 TGTAAGTTATGTAAGTTATGCAAGTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
* * * *
27688774 -CTACATTTATGTAAGTTATGTAAGATATTTAATTTT
1 TGTA-AGTTATGTAAGTTATGTAAGTTATTTAATTTA
* * *
27688810 TGTAAGTTATGTAAGTTACT-TAATTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTA-TGTAAGTTATTTAATTTA
* * * * * *
27688846 TGCAAGTTATTTAATTTTTGTAAGTTATATAATTAA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
27688882 TGTAAGTTAT
1 TGTAAGTTAT
27688892 TTAATTTGTG
Statistics
Matches: 506, Mismatches: 38, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
35 5 0.01
36 496 0.98
37 5 0.01
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (36 bp):
TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTA
Found at i:27692771 original size:14 final size:15
Alignment explanation
Indices: 27692740--27692774 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
27692730 TCTGACCCCA
*
27692740 AAATCCCTAAACCTT
1 AAATCCCTAAACCCT
27692755 AAATCCC-AAACCCT
1 AAATCCCTAAACCCT
27692769 AAATCC
1 AAATCC
27692775 ATACAAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATCCCTAAACCCT
Found at i:27693570 original size:21 final size:20
Alignment explanation
Indices: 27693546--27693630 Score: 53
Period size: 21 Copynumber: 4.0 Consensus size: 20
27693536 ACTAGTTAAT
27693546 CTAAACTGTAAACCATAAACC
1 CTAAACT-TAAACCATAAACC
* * *
27693567 CTAAAATCATAAACCCTTAACAC
1 CT-AAA-CTTAAACCATAAAC-C
* * *
27693590 ATAACCTTAAACCTTAAACC
1 CTAAACTTAAACCATAAACC
* *
27693610 CCAACCTTTAAACCATAAACC
1 CTAAAC-TTAAACCATAAACC
27693631 ATAGACCAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
20 5 0.10
21 26 0.53
22 15 0.31
23 3 0.06
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (20 bp):
CTAAACTTAAACCATAAACC
Found at i:27693571 original size:14 final size:14
Alignment explanation
Indices: 27693554--27693633 Score: 56
Period size: 14 Copynumber: 5.6 Consensus size: 14
27693544 ATCTAAACTG
27693554 TAAACCATAAACCC
1 TAAACCATAAACCC
*
27693568 TAAAATCATAAACCC
1 T-AAACCATAAACCC
* *
27693583 TTAACACAT-AACCT
1 TAAAC-CATAAACCC
*
27693597 TAAACCTTAAACCC
1 TAAACCATAAACCC
* * *
27693611 -CAACCTTTAAACCA
1 TAAACC-ATAAACCC
27693625 TAAACCATA
1 TAAACCATA
27693634 GACCAAATAC
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
13 6 0.12
14 24 0.48
15 20 0.40
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:27693916 original size:115 final size:115
Alignment explanation
Indices: 27693707--27693916 Score: 253
Period size: 115 Copynumber: 1.8 Consensus size: 115
27693697 AAACTCTGCG
* *
27693707 TTTTGGTTAAGATATTTTCCGGCGCTTCTCAAAAAGCGCCGCTAATACGATGCTTTAGCGGCAAT
1 TTTTGGTTAAGATATTTTCCGGCGCTTCTCAAAAAGCGCCGCAAATAAGATGCTTTAGCGGCAAT
* * * * * *
27693772 TTCTCGTGGACGCCACTAATTCCAGTATACATCAAGACTTAAACGTTGCA
66 TCCCCATAGACGCCACTAAGTCCAATATACATCAAGACTTAAACGTTGCA
* * * * * *
27693822 TTTTTGTTAATATATTTTGCGGCGCTTCTCAGAAAGCGCCGCAAATAATATGCTTTAGCGGC-GT
1 TTTTGGTTAAGATATTTTCCGGCGCTTCTCAAAAAGCGCCGCAAATAAGATGCTTTAGCGGCAAT
*
27693886 TCCCCCATA-AGCGCCACTAAGTCTAATATAC
66 T-CCCCATAGA-CGCCACTAAGTCCAATATAC
27693917 CTCATGAAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
114 3 0.04
115 75 0.96
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (115 bp):
TTTTGGTTAAGATATTTTCCGGCGCTTCTCAAAAAGCGCCGCAAATAAGATGCTTTAGCGGCAAT
TCCCCATAGACGCCACTAAGTCCAATATACATCAAGACTTAAACGTTGCA
Found at i:27694247 original size:189 final size:188
Alignment explanation
Indices: 27693890--27694341 Score: 430
Period size: 189 Copynumber: 2.4 Consensus size: 188
27693880 CGGCGTTCCC
* * ** * *
27693890 CCATAAGCGCCACTAAGTCTAATATACCTCATGAAAAAACTCTGCGTTTTGG-TGAGCATTTTTT
1 CCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAG-ATATTTT
** * * * *** **
27693954 GCGGCGCTTTTTGCCAAGCGCCGCTAATACTATGATTTAGCGGCGTTTTTTGATATGCGCCACTA
65 GCGGCGCTTCCTGCAAAACACCGCTAATACTATGATTTAGCGGCGTTTTCCCATAAACGCCACTA
* * ** *
27694019 ATAACTGTATACATCAAGACAAAAACGTTGCGTTTTGGTTACCAAA-TGTTGCGGCG-TGTA
130 ATAAC--TATACACCAAGACAAAAACGGTGCACTTTGGTTACCAAAGT-TTGCGACGTTGTA
* ** *
27694079 CCCTTTGCGCCACTAATTCTAGTATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATATTTTG
1 CCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATATTTTG
* * *
27694144 CGGCGCTTCCCT-CAAAACACCGCTAATATTATGCTTTAGCGGCGTTTTCCCTTAAACGCCACTA
66 CGGCGCTT-CCTGCAAAACACCGCTAATACTATGATTTAGCGGCGTTTTCCCATAAACGCCACTA
* ** * * * *
27694208 ACTGTAAC-ATACACCAAGACCAAAACGGTGCACTTTGGTTAGGATAGTTTGTGACGTTTTT
130 A---TAACTATACACCAAGACAAAAACGGTGCACTTTGGTTACCAAAGTTTGCGACGTTGTA
* * * *
27694269 CCATAAGCGCCA-TAAATTCTAACATACCTCTAGACCAAACTCTGCGTTTTGGTTAACATATGTT
1 CCATAAGCGCCACT-AATTCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATATTTT
27694333 GCGGCGCTT
65 GCGGCGCTT
27694342 TTGGTAAGCG
Statistics
Matches: 212, Mismatches: 43, Indels: 15
0.79 0.16 0.06
Matches are distributed among these distances:
189 138 0.65
190 70 0.33
192 4 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (188 bp):
CCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATATTTTG
CGGCGCTTCCTGCAAAACACCGCTAATACTATGATTTAGCGGCGTTTTCCCATAAACGCCACTAA
TAACTATACACCAAGACAAAAACGGTGCACTTTGGTTACCAAAGTTTGCGACGTTGTA
Found at i:27694520 original size:112 final size:112
Alignment explanation
Indices: 27694262--27694543 Score: 327
Period size: 112 Copynumber: 2.5 Consensus size: 112
27694252 TAGTTTGTGA
* * * ** *
27694262 CGTTTTTCCATAAGCGCCA-TAAATTCTAACATACCTCTAGACCAAACTCTGCGTTTTGGTTAAC
1 CGTTTTTCCATAAGCGCCACT-AATTCTAACATACATCAAGACAAAACAATGCGTTTTCGTTAAC
* *
27694326 ATATGTTGCGGCGCTTTTGGTAAGCGCCGCTAATACTTCCTTTAGCGG
65 ATATGTTGCGGCGCTTTCGGCAAGCGCCGCTAATACTTCCTTTAGCGG
* * * * * * * * *
27694374 CGGGTTTT-CGTAAGCGCCACTAATGCTAATATACAGCGAGATAAAACGATGCGTTTTCGTTAAG
1 C-GTTTTTCCATAAGCGCCACTAATTCTAACATACATCAAGACAAAACAATGCGTTTTCGTTAAC
*
27694438 AT-TTTTGCGGCGCTTTCGGCAATGCGCCGCTAATACTTCCTTTAGCGG
65 ATATGTTGCGGCGCTTTCGGCAA-GCGCCGCTAATACTTCCTTTAGCGG
* *
27694486 CGTTTTTCCATAAACGCCACTAATTCTAGCATACATCAAGACCAAAACAATGCGTTTT
1 CGTTTTTCCATAAGCGCCACTAATTCTAACATACATCAAGA-CAAAACAATGCGTTTT
27694544 GATCTTCAGA
Statistics
Matches: 139, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
111 22 0.16
112 97 0.70
113 20 0.14
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (112 bp):
CGTTTTTCCATAAGCGCCACTAATTCTAACATACATCAAGACAAAACAATGCGTTTTCGTTAACA
TATGTTGCGGCGCTTTCGGCAAGCGCCGCTAATACTTCCTTTAGCGG
Found at i:27696892 original size:40 final size:40
Alignment explanation
Indices: 27696848--27696923 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
27696838 ACAAAAAATC
*
27696848 GAGCATTAGCGGCGATTTAGCC-AAAGCGCCGCTAAAGGTA
1 GAGCATCAGCGGCGATTT-GCCGAAAGCGCCGCTAAAGGTA
* *
27696888 GAGCATCAGCGGCGATTTTCCGGAAGCGCCGCTAAA
1 GAGCATCAGCGGCGATTTGCCGAAAGCGCCGCTAAA
27696924 AATAGGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 30 0.94
ACGTcount: A:0.28, C:0.25, G:0.30, T:0.17
Consensus pattern (40 bp):
GAGCATCAGCGGCGATTTGCCGAAAGCGCCGCTAAAGGTA
Found at i:27697067 original size:41 final size:41
Alignment explanation
Indices: 27697003--27697281 Score: 244
Period size: 41 Copynumber: 6.8 Consensus size: 41
27696993 TTTTTTAAAC
*
27697003 CTTTAGCGGCGTTTTTATCTAAGCGACGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGAT
* * * *
27697044 CTTTAGCGGCGTTTTTCTATAAGCGCCGCTATTGCTCGGGT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGAT
* * * *
27697085 ATTTAGCGGCGTTGTTATCCT-AGCGCCGCTAATTCTCTGG-C
1 CTTTAGCGGCGTTTTTAT-CTAAGCGCCGCTAATGCTC-GGAT
* * * *
27697126 CTTTGGCGGCGTTTTTATGTAAGCGCCGGTAATGGTCGGAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGAT
* * * * *
27697167 CTTTAGCGGCGTTTTTAACTGAGCGCCACTAATTCTCTTG-T
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTC-GGAT
* * * ** *
27697208 CTTCAGCGGCGTTTGTAGCTAAGCGCCGCTAATGCAT-TTAC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGC-TCGGAT
* *
27697249 CTTTAGCGGCGTTTTT-GCAAAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTATC-TAAGCGCCGCTAAT
27697282 AGTAACAAAA
Statistics
Matches: 190, Mismatches: 40, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
40 6 0.03
41 179 0.94
42 5 0.03
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGAT
Found at i:27697233 original size:123 final size:123
Alignment explanation
Indices: 27697002--27697264 Score: 302
Period size: 123 Copynumber: 2.1 Consensus size: 123
27696992 ATTTTTTAAA
*
27697002 CCTTTAGCGGCGTTTTTATCTAAGCGACGCTAATGCTCGGATCTTTAGCGGCGTTTTTCTATAAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGACGCTAATGCTCGGATCTTTAGCGGCGTTTTTCAATAAG
* *
27697067 CGCCGCTATTGCTCGGGTATTTAGCGGCGTTGTTATCCTAGCGCCGCTAATTCTCTGG
66 CGCCACTATTGCTCGGGTATTCAGCGGCGTTGTTATCCTAGCGCCGCTAATTCTCTGG
* * * * * *
27697125 CCTTTGGCGGCGTTTTTATGTAAGCGCCGGTAATGGTCGGATCTTTAGCGGCGTTTTT-AACTGA
1 CCTTTAGCGGCGTTTTTATCTAAGCGACGCTAATGCTCGGATCTTTAGCGGCGTTTTTCAA-TAA
** * * * **
27697189 GCGCCACTAATT-CTCTTGTCTTCAGCGGCGTT-TGTA-GCTAAGCGCCGCTAATGCAT-TTA
65 GCGCCACT-ATTGCTCGGGTATTCAGCGGCGTTGT-TATCCT-AGCGCCGCTAATTC-TCTGG
27697248 CCTTTAGCGGCGTTTTT
1 CCTTTAGCGGCGTTTTT
27697265 GCAAAAGCGC
Statistics
Matches: 118, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
122 4 0.03
123 110 0.93
124 4 0.03
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (123 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGACGCTAATGCTCGGATCTTTAGCGGCGTTTTTCAATAAG
CGCCACTATTGCTCGGGTATTCAGCGGCGTTGTTATCCTAGCGCCGCTAATTCTCTGG
Found at i:27697796 original size:15 final size:15
Alignment explanation
Indices: 27697775--27697812 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
27697765 TTTAAGGTTA
27697775 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
27697790 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
27697805 ATTTAGGG
1 ATTTAGGG
27697813 TTTCAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:27697815 original size:14 final size:14
Alignment explanation
Indices: 27697748--27697815 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
27697738 TACGGGGTAT
*
27697748 AGATTTAAGGTTTG
1 AGATTTAGGGTTTG
* *
27697762 GGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
27697774 A-ATTTAGGGGTTAG
1 AGATTTA-GGGTTTG
*
27697788 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
27697803 AGATTTAGGGTTT
1 AGATTTAGGGTTT
27697816 CAATTATCGG
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 3 0.07
14 16 0.37
15 17 0.40
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:27698789 original size:13 final size:13
Alignment explanation
Indices: 27698771--27698795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27698761 GTTAGAGATT
27698771 TAGGGGTTAGGAG
1 TAGGGGTTAGGAG
27698784 TAGGGGTTAGGA
1 TAGGGGTTAGGA
27698796 ATTTAGGGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.52, T:0.24
Consensus pattern (13 bp):
TAGGGGTTAGGAG
Found at i:27698792 original size:28 final size:29
Alignment explanation
Indices: 27698749--27698833 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 29
27698739 ATATAAGGTT
* *
27698749 TAGGGGTTAAGGGTTAGAGATTTAGGGGT-
1 TAGGAGTTAGGGGTTAG-GATTTAGGGGTC
27698778 TAGGAG-TAGGGGTTAGGAATTTA-GGGTC
1 TAGGAGTTAGGGGTTAGG-ATTTAGGGGTC
*
27698806 TAGGAGATTTAGGGGTTAGGAGTTAGGG
1 TAGGAG--TTAGGGGTTAGGATTTAGGG
27698834 ATTTAGGGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 5 0.11
28 20 0.43
29 5 0.11
30 4 0.09
31 13 0.28
ACGTcount: A:0.25, C:0.01, G:0.45, T:0.29
Consensus pattern (29 bp):
TAGGAGTTAGGGGTTAGGATTTAGGGGTC
Found at i:27698817 original size:16 final size:14
Alignment explanation
Indices: 27698758--27698826 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 14
27698748 TTAGGGGTTA
27698758 AGGGTTA-GAGATTT
1 AGGGTTAGGA-ATTT
*
27698772 AGGGGTTAGG-A-GT
1 A-GGGTTAGGAATTT
27698785 AGGGGTTAGGAATTT
1 A-GGGTTAGGAATTT
27698800 AGGGTCTAGGAGATTT
1 AGGGT-TAGGA-ATTT
27698816 AGGGGTTAGGA
1 A-GGGTTAGGA
27698827 GTTAGGGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
13 11 0.24
14 7 0.15
15 13 0.28
16 11 0.24
17 4 0.09
ACGTcount: A:0.26, C:0.01, G:0.43, T:0.29
Consensus pattern (14 bp):
AGGGTTAGGAATTT
Found at i:27698846 original size:15 final size:15
Alignment explanation
Indices: 27698727--27698849 Score: 78
Period size: 14 Copynumber: 8.5 Consensus size: 15
27698717 TATATGATTA
27698727 TTAGGGTTT-GGGAT
1 TTAGGGTTTAGGGAT
* * *
27698741 ATAAGGTTTAGGGGT
1 TTAGGGTTTAGGGAT
* *
27698756 TAAGGG-TTAGAGAT
1 TTAGGGTTTAGGGAT
*
27698770 TTAGGGGTTA-GGA-
1 TTAGGGTTTAGGGAT
* * *
27698783 GTAGGGGTTAGGAAT
1 TTAGGGTTTAGGGAT
*
27698798 TTAGGGTCTAGGAGAT
1 TTAGGGTTTAGG-GAT
* *
27698814 TTAGGGGTTA-GGAG
1 TTAGGGTTTAGGGAT
27698828 TTAGGGATTTAGGG-T
1 TTAGGG-TTTAGGGAT
27698843 TTAGGGT
1 TTAGGGT
27698850 GTCAGTTAAT
Statistics
Matches: 81, Mismatches: 21, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
13 9 0.11
14 31 0.38
15 29 0.36
16 12 0.15
ACGTcount: A:0.24, C:0.01, G:0.42, T:0.33
Consensus pattern (15 bp):
TTAGGGTTTAGGGAT
Found at i:27701734 original size:22 final size:22
Alignment explanation
Indices: 27701688--27701766 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
27701678 TTACATTACT
*
27701688 TACATTACTTACTAAAATAT-A-G
1 TACATTACTTA--AATATATAACG
27701710 TACATTACTTAAATATATAACG
1 TACATTACTTAAATATATAACG
* *
27701732 TACA--A---AAATTTATAACT
1 TACATTACTTAAATATATAACG
27701749 TACATTACTTAAATATAT
1 TACATTACTTAAATATAT
27701767 TACATTACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
17 14 0.30
19 1 0.02
20 7 0.15
21 1 0.02
22 23 0.50
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.38
Consensus pattern (22 bp):
TACATTACTTAAATATATAACG
Found at i:27701771 original size:18 final size:18
Alignment explanation
Indices: 27701691--27701779 Score: 74
Period size: 18 Copynumber: 4.8 Consensus size: 18
27701681 CATTACTTAC
*
27701691 ATTAC-TTACTAAAATAT
1 ATTACATTACTTAAATAT
*
27701708 AGTACATTACTTAAATAT
1 ATTACATTACTTAAATAT
* * **
27701726 ATAAC-GTACAAAAATTTAT
1 ATTACATTACTTAAA--TAT
27701745 AACTTACATTACTTAAATAT
1 -A-TTACATTACTTAAATAT
27701765 ATTACATTACTTAAA
1 ATTACATTACTTAAA
27701780 CTTTATATAT
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
17 10 0.18
18 28 0.51
19 4 0.07
20 4 0.07
21 3 0.05
22 6 0.11
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.38
Consensus pattern (18 bp):
ATTACATTACTTAAATAT
Found at i:27701932 original size:121 final size:121
Alignment explanation
Indices: 27701806--27702029 Score: 369
Period size: 121 Copynumber: 1.9 Consensus size: 121
27701796 AAAATTTAGC
* ***
27701806 TATATGGTATGGATATATAACCTATATTCCAATTTTATT-GTCAATAAATTTTATAATTTTGCCA
1 TATATGGTATGGATATATAACCTATATTCCAATTTTATTAG-AAATAAATTTTATAATTTTAAAA
*
27701870 ATAATTGTAAATGTTATTTTTAAATATTAAAACCTATATTTTTAATATATCAGCCCA
65 ATAAATGTAAATGTTATTTTTAAATATTAAAACCTATATTTTTAATATATCAGCCCA
* *
27701927 TATATGGTATGGATATATAACCTATATTTCAATTTTATTAGAAATGAATTTTATAATTTTAAAAA
1 TATATGGTATGGATATATAACCTATATTCCAATTTTATTAGAAATAAATTTTATAATTTTAAAAA
27701992 TAAATGTAAATGTTATTTTTAAATATTAAAACCTATAT
66 TAAATGTAAATGTTATTTTTAAATATTAAAACCTATAT
27702030 GTTATTTTTA
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
121 94 0.99
122 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (121 bp):
TATATGGTATGGATATATAACCTATATTCCAATTTTATTAGAAATAAATTTTATAATTTTAAAAA
TAAATGTAAATGTTATTTTTAAATATTAAAACCTATATTTTTAATATATCAGCCCA
Found at i:27702031 original size:27 final size:27
Alignment explanation
Indices: 27702001--27702056 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
27701991 ATAAATGTAA
27702001 ATGTTATTTTTAAATATTAAAACCTAT
1 ATGTTATTTTTAAATATTAAAACCTAT
27702028 ATGTTATTTTTAAATATTAAAACCTAT
1 ATGTTATTTTTAAATATTAAAACCTAT
27702055 AT
1 AT
27702057 TTTTAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (27 bp):
ATGTTATTTTTAAATATTAAAACCTAT
Found at i:27702041 original size:148 final size:148
Alignment explanation
Indices: 27701880--27702258 Score: 731
Period size: 148 Copynumber: 2.6 Consensus size: 148
27701870 ATAATTGTAA
27701880 ATGTTATTTTTAAATATTAAAACCTATATTTTTAATATATCAGCCCATATATGGTATGGATATAT
1 ATGTTATTTTTAAATATTAAAACCTATATTTTTAATATATCAGCCCATATATGGTATGGATATAT
27701945 AACCTATATTTCAATTTTATTAGAAATGAATTTTATAATTTTAAAAATAAATGTAAATGTTATTT
66 AACCTATATTTCAATTTTATTAGAAATGAATTTTATAATTTTAAAAATAAATGTAAATGTTATTT
27702010 TTAAATATTAAAACCTAT
131 TTAAATATTAAAACCTAT
27702028 ATGTTATTTTTAAATATTAAAACCTATATTTTTAATATATCAGCCCATATATGGTATGGATATAT
1 ATGTTATTTTTAAATATTAAAACCTATATTTTTAATATATCAGCCCATATATGGTATGGATATAT
27702093 AACCTATATTTCAATTTTATTAGAAATGAATTTTATAATTTTAAAAATAAATGTAAATGTTATTT
66 AACCTATATTTCAATTTTATTAGAAATGAATTTTATAATTTTAAAAATAAATGTAAATGTTATTT
27702158 TTAAATATTAAAACCTAT
131 TTAAATATTAAAACCTAT
*
27702176 ATGTTATTTTTAAATATTAAAACCTATATTTTTAATATATCACCCCATATATGGTATGGATATAT
1 ATGTTATTTTTAAATATTAAAACCTATATTTTTAATATATCAGCCCATATATGGTATGGATATAT
* *
27702241 ATCCTACATTTCAATTTT
66 AACCTATATTTCAATTTT
27702259 TAATAACTTA
Statistics
Matches: 228, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 228 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.45
Consensus pattern (148 bp):
ATGTTATTTTTAAATATTAAAACCTATATTTTTAATATATCAGCCCATATATGGTATGGATATAT
AACCTATATTTCAATTTTATTAGAAATGAATTTTATAATTTTAAAAATAAATGTAAATGTTATTT
TTAAATATTAAAACCTAT
Found at i:27702066 original size:121 final size:120
Alignment explanation
Indices: 27701820--27702066 Score: 272
Period size: 121 Copynumber: 2.0 Consensus size: 120
27701810 TGGTATGGAT
* * * *** *
27701820 ATATAACCTATATTCCAATTTTATTGTCAATAAATTTTATAATTTTGCCAATAATTGTAAATGTT
1 ATATAACCTATATTTCAATTTTATTG-AAATGAATTTTATAATTTTAAAAATAAATGTAAATGTT
* ** **
27701885 ATTTTTAAATATTAAAACC--TA---TATTTTT-AATATATCAGCCCATATATGGTATGGA
65 ATTTTTAAATATTAAAACCTATATGTTATTTTTAAATAT-TAAAACC-TATAT--T-TTTA
27701940 TATATAACCTATATTTCAATTTTATTAGAAATGAATTTTATAATTTTAAAAATAAATGTAAATGT
1 -ATATAACCTATATTTCAATTTTATT-GAAATGAATTTTATAATTTTAAAAATAAATGTAAATGT
27702005 TATTTTTAAATATTAAAACCTATATGTTATTTTTAAATATTAAAACCTATATTTTTA
64 TATTTTTAAATATTAAAACCTATATGTTATTTTTAAATATTAAAACCTATATTTTTA
27702062 ATATA
1 ATATA
27702067 TCAGCCCATA
Statistics
Matches: 107, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
121 80 0.75
122 3 0.03
123 3 0.03
125 5 0.05
126 11 0.10
127 5 0.05
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (120 bp):
ATATAACCTATATTTCAATTTTATTGAAATGAATTTTATAATTTTAAAAATAAATGTAAATGTTA
TTTTTAAATATTAAAACCTATATGTTATTTTTAAATATTAAAACCTATATTTTTA
Found at i:27702179 original size:27 final size:27
Alignment explanation
Indices: 27702149--27702204 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
27702139 ATAAATGTAA
27702149 ATGTTATTTTTAAATATTAAAACCTAT
1 ATGTTATTTTTAAATATTAAAACCTAT
27702176 ATGTTATTTTTAAATATTAAAACCTAT
1 ATGTTATTTTTAAATATTAAAACCTAT
27702203 AT
1 AT
27702205 TTTTAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (27 bp):
ATGTTATTTTTAAATATTAAAACCTAT
Found at i:27702284 original size:16 final size:16
Alignment explanation
Indices: 27702263--27702305 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
27702253 AATTTTTAAT
*
27702263 AACTTACATAATATAC
1 AACTTACATAATACAC
27702279 AACTTACATAATACAC
1 AACTTACATAATACAC
*
27702295 AACTTATATAA
1 AACTTACATAA
27702306 CTTAAATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAATACAC
Found at i:27702426 original size:25 final size:25
Alignment explanation
Indices: 27702354--27702688 Score: 325
Period size: 25 Copynumber: 13.4 Consensus size: 25
27702344 CATTATACAC
* **
27702354 AACTTACATAATACATTACTTACTT
1 AACTTACATAATACATAACTTAAAT
* *
27702379 AACATACATAGCCTACATAACTTAAAT
1 AACTTACATA--ATACATAACTTAAAT
* **
27702406 AATTTACATGTTACATAACTTAAAT
1 AACTTACATAATACATAACTTAAAT
***
27702431 AACTTACATAATACATAACTTTGGT
1 AACTTACATAATACATAACTTAAAT
* * * * *
27702456 AACTAACATTATACACATCTTACAT
1 AACTTACATAATACATAACTTAAAT
* **
27702481 AATTTACATGTTACATAACTTAAAT
1 AACTTACATAATACATAACTTAAAT
27702506 AACTTACATAATACATAACTTAAAT
1 AACTTACATAATACATAACTTAAAT
**
27702531 AACTTACATAATACATAACTTTGAT
1 AACTTACATAATACATAACTTAAAT
* * *
27702556 AACTTACATAATACACATCTTACAT
1 AACTTACATAATACATAACTTAAAT
* ** *
27702581 AATTTACA-ACCACTTAACTTAAAT
1 AACTTACATAATACATAACTTAAAT
27702605 AACTTACATAATACATAACTTAAAT
1 AACTTACATAATACATAACTTAAAT
**
27702630 AACTTACATAATACATAACTTTGAT
1 AACTTACATAATACATAACTTAAAT
* * * *
27702655 AACTAACATTATACACAACTTACAT
1 AACTTACATAATACATAACTTAAAT
27702680 AA--TACATAA
1 AACTTACATAA
27702689 CTTACTTAAC
Statistics
Matches: 249, Mismatches: 58, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
23 5 0.02
24 17 0.07
25 209 0.84
27 18 0.07
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (25 bp):
AACTTACATAATACATAACTTAAAT
Found at i:27702479 original size:59 final size:59
Alignment explanation
Indices: 27702279--27702691 Score: 168
Period size: 59 Copynumber: 6.9 Consensus size: 59
27702269 CATAATATAC
* * ***
27702279 AACTTACATAATACACAACTTATATAACTTAAATAGAAACACATAATA-ATAACTTTGAT
1 AACTAACATAATACACAACTTACATAACTTAAATA-ACTTACATAATACATAACTTTGAT
* * * * * * **
27702338 AACTAACATTATACACAACTTACATAA--TACATTACTTACTTAACATACATAGCCTACAT
1 AACTAACATAATACACAACTTACATAACTTAAATAACTTACAT-A-ATACATAACTTTGAT
** ** *
27702397 AACTTAA-ATAATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGGT
1 AAC-TAACATAATACACAACTTACATAACTTAAATAACTTACATAATACATAACTTTGAT
* * * * * * **
27702456 AACTAACATTATACACATCTTACATAATTTACAT--GTTACATAACTTAAATAACTTACAT
1 AACTAACATAATACACAACTTACATAACTTAAATAACTTACATAA--TACATAACTTTGAT
* * * ** ** *
27702515 AA-T-ACATAACTTAAATAACTTACATAA--TACATAACTTTGATAACTTACATAA--TACAC
1 AACTAACATAA--TACACAACTTACATAACTTAAATAACTTACATAA--TACATAACTTTGAT
* * ** * * **
27702572 ATCTTACATAATTTACAAC-CACTTAACTTAAATAACTTACATAATACATAACTTAAAT
1 AACTAACATAATACACAACTTACATAACTTAAATAACTTACATAATACATAACTTTGAT
* * * *
27702630 AACTTACATAATACATAACTTTGATAACTAACATTATACACAACTTACATAATACATAACTT
1 AACTAACATAATACACAAC-TT-A-CA-TAAC-TTA-A-ATAACTTACATAATACATAACTT
27702692 ACTTAACATA
Statistics
Matches: 262, Mismatches: 65, Indels: 47
0.70 0.17 0.13
Matches are distributed among these distances:
56 16 0.06
57 33 0.13
58 39 0.15
59 128 0.49
60 4 0.02
61 12 0.05
63 4 0.02
64 3 0.01
65 1 0.00
66 22 0.08
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.33
Consensus pattern (59 bp):
AACTAACATAATACACAACTTACATAACTTAAATAACTTACATAATACATAACTTTGAT
Found at i:27702487 original size:9 final size:9
Alignment explanation
Indices: 27702474--27702879 Score: 225
Period size: 9 Copynumber: 48.6 Consensus size: 9
27702464 TTATACACAT
27702474 CTTACATAA
1 CTTACATAA
*
27702483 TTTACAT--
1 CTTACATAA
*
27702490 GTTACATAA
1 CTTACATAA
*
27702499 CTTAAATAA
1 CTTACATAA
27702508 CTTACATAA
1 CTTACATAA
27702517 --TACATAA
1 CTTACATAA
*
27702524 CTTAAATAA
1 CTTACATAA
27702533 CTTACATAA
1 CTTACATAA
27702542 --TACATAA
1 CTTACATAA
**
27702549 CTTTGATAA
1 CTTACATAA
27702558 CTTACATAA
1 CTTACATAA
* *
27702567 --TACACAT
1 CTTACATAA
27702574 CTTACATAA
1 CTTACATAA
*
27702583 TTTAC--AA
1 CTTACATAA
* *
27702590 C-CACTTAA
1 CTTACATAA
*
27702598 CTTAAATAA
1 CTTACATAA
27702607 CTTACATAA
1 CTTACATAA
27702616 --TACATAA
1 CTTACATAA
*
27702623 CTTAAATAA
1 CTTACATAA
27702632 CTTACATAA
1 CTTACATAA
27702641 --TACATAA
1 CTTACATAA
**
27702648 CTTTGATAA
1 CTTACATAA
* *
27702657 CTAACATTA
1 CTTACATAA
*
27702666 --TACACAA
1 CTTACATAA
27702673 CTTACATAA
1 CTTACATAA
27702682 --TACATAA
1 CTTACATAA
*
27702689 CTTACTTAA
1 CTTACATAA
* *
27702698 CATACATAG
1 CTTACATAA
* *
27702707 CCTACACAA
1 CTTACATAA
27702716 CTTACATAA
1 CTTACATAA
*
27702725 TTTACAT--
1 CTTACATAA
*
27702732 GTTACATAA
1 CTTACATAA
*
27702741 CTTAAATAA
1 CTTACATAA
27702750 CTTACATAA
1 CTTACATAA
27702759 --TACATAA
1 CTTACATAA
*
27702766 CTTTGC-TAA
1 C-TTACATAA
* *
27702775 CTAACATTA
1 CTTACATAA
*
27702784 --TACACAA
1 CTTACATAA
27702791 CTTACATAA
1 CTTACATAA
*
27702800 --TACATTA
1 CTTACATAA
27702807 CTTACATAA
1 CTTACATAA
27702816 CTTAAAGCATAA
1 CTT--A-CATAA
27702828 --TA-ATAA
1 CTTACATAA
27702834 CTTACATAA
1 CTTACATAA
*
27702843 --TACACAA
1 CTTACATAA
*
27702850 CTTACATAG
1 CTTACATAA
*
27702859 CTTACACAA
1 CTTACATAA
27702868 --TACATAA
1 CTTACATAA
27702875 CTTAC
1 CTTAC
27702880 CCGTGCAATT
Statistics
Matches: 294, Mismatches: 64, Indels: 78
0.67 0.15 0.18
Matches are distributed among these distances:
6 6 0.02
7 87 0.30
8 8 0.03
9 184 0.63
10 3 0.01
11 1 0.00
12 5 0.02
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.33
Consensus pattern (9 bp):
CTTACATAA
Found at i:27702488 original size:50 final size:50
Alignment explanation
Indices: 27702354--27702768 Score: 319
Period size: 50 Copynumber: 8.4 Consensus size: 50
27702344 CATTATACAC
** ** * * **
27702354 AACTTACATAATACATTACTTACTTAACATACATAGCCTACATAACTTAAAT
1 AACTTACATAATACACAACTTAAATAACTTACATA--ATACATAACTTTGAT
* ** * *
27702406 AATTTACATGTTACATAACTTAAATAACTTACATAATACATAACTTTGGT
1 AACTTACATAATACACAACTTAAATAACTTACATAATACATAACTTTGAT
* * * * * ** **
27702456 AACTAACATTATACACATCTTACATAATTTACATGTTACATAACTTAAAT
1 AACTTACATAATACACAACTTAAATAACTTACATAATACATAACTTTGAT
*
27702506 AACTTACATAATACATAACTTAAATAACTTACATAATACATAACTTTGAT
1 AACTTACATAATACACAACTTAAATAACTTACATAATACATAACTTTGAT
* * * ** * **
27702556 AACTTACATAATACACATCTTACATAATTTACA-ACCACTTAACTTAAAT
1 AACTTACATAATACACAACTTAAATAACTTACATAATACATAACTTTGAT
*
27702605 AACTTACATAATACATAACTTAAATAACTTACATAATACATAACTTTGAT
1 AACTTACATAATACACAACTTAAATAACTTACATAATACATAACTTTGAT
* * * *
27702655 AACTAACATTATACACAACTTACATAA--TACAT-A-AC-TTAC--T--T
1 AACTTACATAATACACAACTTAAATAACTTACATAATACATAACTTTGAT
* * * * ** **
27702696 AACATACATAGCCTACACAACTTACATAATTTACATGTTACATAACTTAAAT
1 AACTTACATA--ATACACAACTTAAATAACTTACATAATACATAACTTTGAT
*
27702748 AACTTACATAATACATAACTT
1 AACTTACATAATACACAACTT
27702769 TGCTAACTAA
Statistics
Matches: 284, Mismatches: 67, Indels: 26
0.75 0.18 0.07
Matches are distributed among these distances:
41 8 0.03
43 17 0.06
45 8 0.03
46 2 0.01
47 3 0.01
48 8 0.03
49 40 0.14
50 160 0.56
52 38 0.13
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (50 bp):
AACTTACATAATACACAACTTAAATAACTTACATAATACATAACTTTGAT
Found at i:27702703 original size:25 final size:25
Alignment explanation
Indices: 27702666--27702799 Score: 117
Period size: 25 Copynumber: 5.3 Consensus size: 25
27702656 ACTAACATTA
*
27702666 TACACAACTTACATAATACATAACT
1 TACATAACTTACATAATACATAACT
* * * *
27702691 TACTTAACATACATAGCCTACACAACT
1 TACATAACTTACATA--ATACATAACT
* **
27702718 TACATAATTTACATGTTACATAACT
1 TACATAACTTACATAATACATAACT
*
27702743 TAAATAACTTACATAATACATAACTT
1 TACATAACTTACATAATACATAAC-T
* * * *
27702769 TGC-TAACTAACATTATACACAACT
1 TACATAACTTACATAATACATAACT
27702793 TACATAA
1 TACATAA
27702800 TACATTACTT
Statistics
Matches: 84, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
24 3 0.04
25 60 0.71
26 2 0.02
27 19 0.23
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (25 bp):
TACATAACTTACATAATACATAACT
Found at i:27702776 original size:118 final size:118
Alignment explanation
Indices: 27702556--27702877 Score: 389
Period size: 118 Copynumber: 2.8 Consensus size: 118
27702546 TAACTTTGAT
* * ** **
27702556 AACTTACATAATACACATCTTACATAATTTACA-A-CC-ACTTAACTTAAATAACTTACATAATA
1 AACTTACATAATACATAACTTACATAACATACATAGCCTACACAACTTAAATAACTTACATAATA
27702618 CATAACTTAAATAACTTACATAATACATAACTTTGATAACTAACATTATACAC
66 CATAACTTAAATAACTTACATAATACATAACTTTGATAACTAACATTATACAC
* * * **
27702671 AACTTACATAATACATAACTTACTTAACATACATAGCCTACACAACTTACATAATTTACATGTTA
1 AACTTACATAATACATAACTTACATAACATACATAGCCTACACAACTTAAATAACTTACATAATA
*
27702736 CATAACTTAAATAACTTACATAATACATAACTTTGCTAACTAACATTATACAC
66 CATAACTTAAATAACTTACATAATACATAACTTTGATAACTAACATTATACAC
* * *
27702789 AACTTACATAATACATTACTTACATAACTTA-A-AG----CATAA--T-AATAACTTACATAATA
1 AACTTACATAATACATAACTTACATAACATACATAGCCTACACAACTTAAATAACTTACATAATA
* * * *
27702845 CACAACTTACATAGCTTACACAATACATAACTT
66 CATAACTTAAATAACTTACATAATACATAACTT
27702878 ACCCGTGCAA
Statistics
Matches: 180, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
109 41 0.23
110 1 0.01
112 4 0.02
115 28 0.16
116 3 0.02
117 3 0.02
118 100 0.56
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (118 bp):
AACTTACATAATACATAACTTACATAACATACATAGCCTACACAACTTAAATAACTTACATAATA
CATAACTTAAATAACTTACATAATACATAACTTTGATAACTAACATTATACAC
Found at i:27708422 original size:66 final size:66
Alignment explanation
Indices: 27708279--27708443 Score: 174
Period size: 66 Copynumber: 2.5 Consensus size: 66
27708269 AGCAAATTAC
* * * * *
27708279 ACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGATGTTCAAAGAAGATATGAAGAACTCCAGC
1 ACAACTTAAAGCAGAAGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAGATATGAAGAACTCCAGC
27708344 T
66 T
* * * * *
27708345 ACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAA-AGTATGAAGACCTTCAG
1 ACAACTTAAAGCAGAAGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAGA-TATGAAGAACTCCAG
27708409 C-
65 CT
* *
27708410 AGCAGCTTAAAGCAGAAG-AGACAGCAAGAGAAGC
1 A-CAACTTAAAGCAGAAGCAG-CAGCGAGAGAAGC
27708444 AAAGGCGGCA
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
65 4 0.05
66 79 0.95
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.13
Consensus pattern (66 bp):
ACAACTTAAAGCAGAAGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAGATATGAAGAACTCCAGC
T
Found at i:27708476 original size:42 final size:42
Alignment explanation
Indices: 27708430--27708528 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 42
27708420 AGCAGAAGAG
* * **
27708430 ACAGCAAGAGAAGCAAAGGCGGCAGCGAGAGAAGTACAGGCT
1 ACAGCGAGGGAAGCAAAGGCGAAAGCGAGAGAAGTACAGGCT
* * *
27708472 ACAGCGAGGGAAGCAAAGGCTAAAGCGAGGGAAGTAGAGGCT
1 ACAGCGAGGGAAGCAAAGGCGAAAGCGAGAGAAGTACAGGCT
*
27708514 GCAGCGAGGGAAGCA
1 ACAGCGAGGGAAGCA
27708529 GAGCAGCGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.38, C:0.17, G:0.39, T:0.05
Consensus pattern (42 bp):
ACAGCGAGGGAAGCAAAGGCGAAAGCGAGAGAAGTACAGGCT
Found at i:27708531 original size:21 final size:21
Alignment explanation
Indices: 27708430--27708528 Score: 99
Period size: 21 Copynumber: 4.7 Consensus size: 21
27708420 AGCAGAAGAG
* * *
27708430 ACAGCAAGAGAAGCAAAGGCG
1 ACAGCGAGGGAAGCAAAGGCT
* * * *
27708451 GCAGCGAGAGAAGTACAGGCT
1 ACAGCGAGGGAAGCAAAGGCT
27708472 ACAGCGAGGGAAGCAAAGGCT
1 ACAGCGAGGGAAGCAAAGGCT
* * *
27708493 AAAGCGAGGGAAGTAGAGGCT
1 ACAGCGAGGGAAGCAAAGGCT
*
27708514 GCAGCGAGGGAAGCA
1 ACAGCGAGGGAAGCA
27708529 GAGCAGCGTC
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.38, C:0.17, G:0.39, T:0.05
Consensus pattern (21 bp):
ACAGCGAGGGAAGCAAAGGCT
Done.