Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 67 of 120
Found at i:19913638 original size:20 final size:21
Alignment explanation
Indices: 19913609--19913665 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
19913599 ATAAACTATG
*
19913609 TACCACTCCATTTACTTT-CT
1 TACCATTCCATTTACTTTACT
*
19913629 TACCATTCCACTTA-TTTACT
1 TACCATTCCATTTACTTTACT
* **
19913649 TTCCATTTAATTTACTT
1 TACCATTCCATTTACTT
19913666 AACATAAGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.10
20 24 0.83
21 2 0.07
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (21 bp):
TACCATTCCATTTACTTTACT
Found at i:19914624 original size:138 final size:137
Alignment explanation
Indices: 19914365--19914627 Score: 319
Period size: 138 Copynumber: 1.9 Consensus size: 137
19914355 TAAATGGGTA
* * * *
19914365 TGCTCACACAAGTTGACGGTTAGAATGTAGCTACACGATGCCGCTTACACAAGATGACGAGTATA
1 TGCTCACACAAGTAGACGGTCAGAATGTAGCTACACAATGCCGCTCACACAAGATGACGAGTATA
* * * *
19914430 TGCAAAAAATGCCGGAACTCAGCCATCAATAGCATATTCAGGACCAACACCCGAAACATGGTAAC
66 CGCAAAAAATGCCGGAACTCAGCCATCAATAGAACATTCAGGACCAACACCAGAAACATGGTAAC
19914495 CTTGGTC
131 CTTGGTC
* * * * **
19914502 TGCTTACACAAGTAGACGGTCGGAATGTAAGCTACACAATGCTGCTCACACAAGCTGGTGAGTAT
1 TGCTCACACAAGTAGACGGTCAGAATGT-AGCTACACAATGCCGCTCACACAAGATGACGAGTAT
* * * * * ** *
19914567 CCGCAACAAATGTCGGACCTCAGCTATCGGTAGAACATTCAGGACCAGCACCAGAAACATG
65 ACGCAAAAAATGCCGGAACTCAGCCATCAATAGAACATTCAGGACCAACACCAGAAACATG
19914628 AAAACCCTAA
Statistics
Matches: 103, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
137 24 0.23
138 79 0.77
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (137 bp):
TGCTCACACAAGTAGACGGTCAGAATGTAGCTACACAATGCCGCTCACACAAGATGACGAGTATA
CGCAAAAAATGCCGGAACTCAGCCATCAATAGAACATTCAGGACCAACACCAGAAACATGGTAAC
CTTGGTC
Found at i:19917703 original size:28 final size:28
Alignment explanation
Indices: 19917649--19917877 Score: 302
Period size: 28 Copynumber: 8.3 Consensus size: 28
19917639 CTATTCAGTA
* **
19917649 ACAGT-ACAGTGT-GGCATTAGCCTGAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
19917675 ACAGTAATAGTGTGGGCCTTAGCCCGAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
**
19917703 ACAGTAGTAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
19917731 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* * *
19917759 ATAGTAACAGTGTGGGCCATAGCCCCAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
19917787 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
19917815 ACAGTAACACTGTGGGCCTTAGCCTAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
19917843 ACTGTAACAGTGTGGGCCTTAACCCAA-
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
19917870 ATAGTAAC
1 ACAGTAAC
19917878 TAGTACAGTG
Statistics
Matches: 180, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
26 5 0.03
27 12 0.07
28 163 0.91
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:19925213 original size:26 final size:26
Alignment explanation
Indices: 19925175--19925281 Score: 151
Period size: 26 Copynumber: 4.1 Consensus size: 26
19925165 AACACACCAC
** * *
19925175 TATCGCAAAAAAGTTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
19925201 TATCGCAGTAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
19925227 TATCGCAGCAAAGCTACCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
19925253 TATCGCAGCAAAGTTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
19925279 TAT
1 TAT
19925282 ATGTGGCAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:19925564 original size:27 final size:27
Alignment explanation
Indices: 19925534--19925872 Score: 369
Period size: 27 Copynumber: 12.6 Consensus size: 27
19925524 TCCTATGGCA
*
19925534 GTATTTCAATCATTTTACCCTTCGAGG
1 GTATTTCGATCATTTTACCCTTCGAGG
* * *
19925561 GTATTCCGATCATTTCACCCTTCGGGG
1 GTATTTCGATCATTTTACCCTTCGAGG
* *
19925588 GTATTTTGATCATTTTACCCTTCGGGG
1 GTATTTCGATCATTTTACCCTTCGAGG
* *
19925615 GTATTTCGATCATTTTACCTTTCGGGG
1 GTATTTCGATCATTTTACCCTTCGAGG
* *
19925642 GTATTTTGATCATTTTACCCTTCGGGG
1 GTATTTCGATCATTTTACCCTTCGAGG
* *
19925669 GTATTTTGGTCATTTTACCCTTCGAGG
1 GTATTTCGATCATTTTACCCTTCGAGG
* **
19925696 GTATTTCGGTCATTTTACCAATCGAGG
1 GTATTTCGATCATTTTACCCTTCGAGG
* *
19925723 GTATTTCGATCATTTTACACTTCTAGG
1 GTATTTCGATCATTTTACCCTTCGAGG
* *
19925750 ATATTTTTG-TCATTTTA-CCTATCGAGG
1 GTA-TTTCGATCATTTTACCCT-TCGAGG
* *
19925777 GTATTTCAATTATTTTA-CCTATCGAGG
1 GTATTTCGATCATTTTACCCT-TCGAGG
* * **
19925804 GTATTTCGGTCATTTTACCCATAAAGG
1 GTATTTCGATCATTTTACCCTTCGAGG
* * *
19925831 GTATTTCGGTCATTTTACCCATCAAGG
1 GTATTTCGATCATTTTACCCTTCGAGG
*
19925858 TTATTTCGATCATTT
1 GTATTTCGATCATTT
19925873 GCCCACAAAT
Statistics
Matches: 270, Mismatches: 38, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
26 5 0.02
27 259 0.96
28 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (27 bp):
GTATTTCGATCATTTTACCCTTCGAGG
Found at i:19925590 original size:81 final size:81
Alignment explanation
Indices: 19925504--19925737 Score: 222
Period size: 81 Copynumber: 2.9 Consensus size: 81
19925494 TCATCTCTTA
*
19925504 GGGGTATAACAG-TCATTTTATCCTAT-GGCAGTATTTCAATCATTTTACCCTTCGAGGGTATTC
1 GGGGTAT-ACAGATCATTTTACCCT-TCGGCAGTATTTCAATCATTTTACCCTTCGAGGGTATTC
19925567 CGATCATTTCACCCTTCG
64 CGATCATTTCACCCTTCG
*** ** * * * **
19925585 GGGGTATTTTGATCATTTTACCCTTCGGGGGTATTTCGATCATTTTACCTTTCGGGGGTATTTTG
1 GGGGTATACAGATCATTTTACCCTTCGGCAGTATTTCAATCATTTTACCCTTCGAGGGTATTCCG
*
19925650 ATCATTTTACCCTTCG
66 ATCATTTCACCCTTCG
*** * * ** ** *
19925666 GGGGTATTTTGGTCATTTTACCCTTCGAG-GGTATTTCGGTCATTTTACCAATCGAGGGTATTTC
1 GGGGTATACAGATCATTTTACCCTTCG-GCAGTATTTCAATCATTTTACCCTTCGAGGGTATTCC
19925730 GATCATTT
65 GATCATTT
19925738 TACACTTCTA
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
80 2 0.02
81 129 0.98
82 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (81 bp):
GGGGTATACAGATCATTTTACCCTTCGGCAGTATTTCAATCATTTTACCCTTCGAGGGTATTCCG
ATCATTTCACCCTTCG
Found at i:19925738 original size:81 final size:81
Alignment explanation
Indices: 19925534--19925872 Score: 412
Period size: 81 Copynumber: 4.2 Consensus size: 81
19925524 TCCTATGGCA
* * * * *
19925534 GTATTTCAATCATTTTACCCT-TCGAGGGTATTCCGATCATTTCACCCTTCGGGGGTATTTTGAT
1 GTATTTCGATCATTTTA-CCTATCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTTGGT
*
19925598 CATTTTACCCTTCGGGG
65 CATTTTACCCTTCGAGG
* * * *
19925615 GTATTTCGATCATTTTACCTTTCGGGGGTATTTTGATCATTTTACCCTTCGGGGGTATTTTGGTC
1 GTATTTCGATCATTTTACCTATCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTTGGTC
19925680 ATTTTACCCTTCGAGG
66 ATTTTACCCTTCGAGG
* * * * * *
19925696 GTATTTCGGTCATTTTACCAATCGAGGGTATTTCGATCATTTTACACTTCTAGGATATTTTTGTC
1 GTATTTCGATCATTTTACCTATCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTTGGTC
19925761 ATTTTA-CCTATCGAGG
66 ATTTTACCCT-TCGAGG
* * * * ** *
19925777 GTATTTCAATTATTTTACCTATCGAGGGTATTTCGGTCATTTTACCCATAAAGGGTATTTCGGTC
1 GTATTTCGATCATTTTACCTATCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTTGGTC
* *
19925842 ATTTTACCCATCAAGG
66 ATTTTACCCTTCGAGG
*
19925858 TTATTTCGATCATTT
1 GTATTTCGATCATTT
19925873 GCCCACAAAT
Statistics
Matches: 221, Mismatches: 34, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
80 6 0.03
81 213 0.96
82 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (81 bp):
GTATTTCGATCATTTTACCTATCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTTGGTC
ATTTTACCCTTCGAGG
Found at i:19934088 original size:12 final size:12
Alignment explanation
Indices: 19934071--19934102 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
19934061 CTTTCCTCGA
19934071 GGAAAACTACAT
1 GGAAAACTACAT
19934083 GGAAAACTACAT
1 GGAAAACTACAT
*
19934095 GGATAACT
1 GGAAAACT
19934103 TTAAGCCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (12 bp):
GGAAAACTACAT
Found at i:19936003 original size:14 final size:14
Alignment explanation
Indices: 19935984--19936013 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19935974 TTCGCTAATA
*
19935984 TGTCTTTTGTATTT
1 TGTCTTTTATATTT
19935998 TGTCTTTTATATTT
1 TGTCTTTTATATTT
19936012 TG
1 TG
19936014 CATGCATAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.07, G:0.13, T:0.70
Consensus pattern (14 bp):
TGTCTTTTATATTT
Found at i:19937797 original size:16 final size:16
Alignment explanation
Indices: 19937769--19937828 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
19937759 AATATTAAAT
19937769 TAATATAATATTTATC
1 TAATATAATATTTATC
*
19937785 TAATATAATATTTCTC
1 TAATATAATATTTATC
*
19937801 TTGATA-AATATTATAT-
1 -TAATATAATATT-TATC
*
19937817 TAATTTAATATT
1 TAATATAATATT
19937829 AAAGTGATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 3 0.08
16 27 0.75
17 6 0.17
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (16 bp):
TAATATAATATTTATC
Found at i:19937829 original size:16 final size:16
Alignment explanation
Indices: 19937755--19937829 Score: 55
Period size: 16 Copynumber: 4.7 Consensus size: 16
19937745 TTTTAATAAG
*
19937755 ATTTAATATTAAATTA
1 ATTTAATATTATATTA
*
19937771 ATATAATATT-TATCTA
1 ATTTAATATTATAT-TA
* * * *
19937787 ATATAATATTTCTCTTG
1 ATTTAATA-TTATATTA
*
19937804 A-TAAATATTATATTA
1 ATTTAATATTATATTA
19937819 ATTTAATATTA
1 ATTTAATATTA
19937830 AAGTGATTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
15 8 0.18
16 31 0.69
17 4 0.09
18 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (16 bp):
ATTTAATATTATATTA
Found at i:19942316 original size:51 final size:51
Alignment explanation
Indices: 19942257--19942594 Score: 362
Period size: 51 Copynumber: 6.7 Consensus size: 51
19942247 TATCAATGAA
* **
19942257 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATCTTGGT
* * * * * * *
19942308 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGA-GAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATC-TTGGT
* *
19942359 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAAT-TATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATCT-TGGT
* * ** * *
19942410 CACATGTGTAGTACTAAGTGAAGGCTACTATATGTACCGA-AAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATC-TTGGT
* * **
19942461 GACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTAAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATCTTGGT
* * * *
19942511 CACGTGTGCAGTACTATGTGAAGGCTACCACGTGAACCG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATCTTGGT
* *
19942561 CACGTGTGTAGTACTATGTGAAGGTTGCTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
19942595 TATCGAATGA
Statistics
Matches: 237, Mismatches: 44, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
50 85 0.36
51 149 0.63
52 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATCTTGGT
Found at i:19942433 original size:102 final size:101
Alignment explanation
Indices: 19942257--19942600 Score: 453
Period size: 102 Copynumber: 3.4 Consensus size: 101
19942247 TATCAATGAA
*
19942257 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATTATGGTCACATGTGTAGTAC
19942322 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGA-AAGCTTTGGT
*
19942359 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATTATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATTATGGTCACATGTGTAGTAC
* *
19942424 TAAGTGAAGGCTACTATATGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCG-AAAGCTTTGGT
* * * * *
19942461 GACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTA--ATCACGTGTGCAGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGAT-AAA-TTATGGTCACATGTGTAGT
* * * * * *
19942523 ACTATGTGAAGGCTACCACGTGAACCGTAAAAC-TTGAT
64 ACTAAGTGAAGGCTACAATGTGTACCG-AAAGCTTTGGT
* * *
19942561 CACGTGTGTAGTACTATGTGAAGGTTGCTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
19942601 ATGATAAAAG
Statistics
Matches: 215, Mismatches: 23, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
100 38 0.18
101 38 0.18
102 135 0.63
103 4 0.02
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATTATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAGCTTTGGT
Found at i:19944592 original size:59 final size:58
Alignment explanation
Indices: 19944521--19944649 Score: 170
Period size: 62 Copynumber: 2.2 Consensus size: 58
19944511 ATCACTTTAA
* * *
19944521 TATTAAATTAATATAATATTTATC-AAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAAATAATATAATATTTATCTAAGATAAACATTAAATTAAATTTAATATTAAA-C
* *
19944579 TTATTAAAATAATATAATGTTTATCTATAAGATGAACATTAAATTAAATTTAATATTAAAC
1 -TATTAAAATAATATAATATTTATC--TAAGATAAACATTAAATTAAATTTAATATTAAAC
19944640 TATTAAAATA
1 TATTAAAATA
19944650 TTATTATTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
59 22 0.35
60 10 0.16
61 1 0.02
62 29 0.47
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (58 bp):
TATTAAAATAATATAATATTTATCTAAGATAAACATTAAATTAAATTTAATATTAAAC
Found at i:19947637 original size:7 final size:7
Alignment explanation
Indices: 19947625--19947650 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19947615 TCTTCTTGCA
19947625 TGTTTTG
1 TGTTTTG
19947632 TGTTTTG
1 TGTTTTG
19947639 TGTTTTG
1 TGTTTTG
19947646 TGTTT
1 TGTTT
19947651 GCTTAAGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.27, T:0.73
Consensus pattern (7 bp):
TGTTTTG
Found at i:19950551 original size:29 final size:29
Alignment explanation
Indices: 19950509--19950580 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
19950499 ATTGTTGCAA
* * *
19950509 TGGAAATCGTCTGCAGTTTTCAAT-GAAAT
1 TGGAAATTGTCTGCAGTTTTC-ATCCAAAC
*
19950538 TGGAAATTGTCTGCTGTTTTCATCCAAAC
1 TGGAAATTGTCTGCAGTTTTCATCCAAAC
19950567 TGGAAATTGT-TGCA
1 TGGAAATTGTCTGCA
19950581 TTTGTTTAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.14
29 32 0.86
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (29 bp):
TGGAAATTGTCTGCAGTTTTCATCCAAAC
Found at i:19951092 original size:13 final size:13
Alignment explanation
Indices: 19951074--19951098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19951064 CTTATTAGTG
19951074 AAAGAGTACATAT
1 AAAGAGTACATAT
19951087 AAAGAGTACATA
1 AAAGAGTACATA
19951099 CAAATTTGAT
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:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (13 bp):
AAAGAGTACATAT
Found at i:19953707 original size:47 final size:47
Alignment explanation
Indices: 19953654--19953751 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
19953644 TTTGAATTGA
19953654 TTTGTTGATGTTACTTTAGGTATCTAGTTTATGAAACTTTGGTGGTG
1 TTTGTTGATGTTACTTTAGGTATCTAGTTTATGAAACTTTGGTGGTG
19953701 TTTGTTGATGTTACTTTAGGTATCTAGTTTATGAAACTTTGGTGGTG
1 TTTGTTGATGTTACTTTAGGTATCTAGTTTATGAAACTTTGGTGGTG
19953748 TTTG
1 TTTG
19953752 ATTAAAATTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.18, C:0.06, G:0.26, T:0.50
Consensus pattern (47 bp):
TTTGTTGATGTTACTTTAGGTATCTAGTTTATGAAACTTTGGTGGTG
Found at i:19953740 original size:23 final size:23
Alignment explanation
Indices: 19953666--19953740 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
19953656 TGTTGATGTT
19953666 ACTTTAGGTATCTAGTTTATGAA
1 ACTTTAGGTATCTAGTTTATGAA
* * * * **
19953689 ACTTT-GGTGGTGTTTGTTGATGTT
1 ACTTTAGGT-AT-CTAGTTTATGAA
19953713 ACTTTAGGTATCTAGTTTATGAA
1 ACTTTAGGTATCTAGTTTATGAA
19953736 ACTTT
1 ACTTT
19953741 GGTGGTGTTT
Statistics
Matches: 37, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
22 3 0.08
23 18 0.49
24 13 0.35
25 3 0.08
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.48
Consensus pattern (23 bp):
ACTTTAGGTATCTAGTTTATGAA
Found at i:19954784 original size:16 final size:16
Alignment explanation
Indices: 19954760--19954824 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
19954750 TTCGCTGTAT
*
19954760 TGGATTAGAGGCGTAA
1 TGGAATAGAGGCGTAA
19954776 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
19954792 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
*
19954808 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
19954824 T
1 T
19954825 AGCAAATCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.35, C:0.03, G:0.37, T:0.25
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:19955087 original size:14 final size:15
Alignment explanation
Indices: 19955048--19955089 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
19955038 TTTTAACATA
*
19955048 ATTATTATTAAATAT
1 ATTATAATTAAATAT
19955063 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
19955077 A-TATAATTTAATA
1 ATTATAATTAAATA
19955090 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:19955351 original size:44 final size:44
Alignment explanation
Indices: 19955227--19955443 Score: 144
Period size: 44 Copynumber: 4.9 Consensus size: 44
19955217 TAATTATAAC
* **
19955227 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATT-A
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATTCTTGA
* * * *
19955270 TTATTAATTATAAT-TTA-AT-AATATAT-TATTTCATAAAATTCTTGA
1 TAATAAATT-T--TCTTATATGAATTTATATAATT--TAAAATTCTTGA
* ** **
19955315 TAACAAATTTTCTTATATGAATTTATATAATTTAAAATAATCAA
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATTCTTGA
* * *
19955359 TATTAAATATAAT-TTA-AT-AATGATATATAATATCATAAAATTCTTGA
1 TAATAAAT-T-TTCTTATATGAAT-TTATATAAT-T--TAAAATTCTTGA
19955406 TAATAAATTTTCTTATATGAATTTATATAATTTAAAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAAT
19955444 AATTAATATT
Statistics
Matches: 128, Mismatches: 27, Indels: 37
0.67 0.14 0.19
Matches are distributed among these distances:
42 5 0.04
43 18 0.14
44 44 0.34
45 22 0.17
46 11 0.09
47 25 0.20
48 3 0.02
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (44 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATTCTTGA
Found at i:19955423 original size:91 final size:89
Alignment explanation
Indices: 19955227--19955472 Score: 413
Period size: 91 Copynumber: 2.8 Consensus size: 89
19955217 TAATTATAAC
* * *
19955227 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAATTATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
19955292 -ATATTATTTCATAAAATTCTTGA
66 GATATTATATCATAAAATTCTTGA
* *
19955315 TAACAAATTTTCTTATATGAATTTATATAATTTAAAATAATCAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
19955380 GATATATAATATCATAAAATTCTTGA
66 GATAT-T-ATATCATAAAATTCTTGA
19955406 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
19955471 GA
66 GA
19955473 ACGATCAATG
Statistics
Matches: 147, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
88 60 0.41
89 4 0.03
90 1 0.01
91 82 0.56
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (89 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
GATATTATATCATAAAATTCTTGA
Found at i:19956936 original size:23 final size:23
Alignment explanation
Indices: 19956906--19956966 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
19956896 TGGACAAATG
19956906 AAGGCCATGTTCCTGTTTTTATT
1 AAGGCCATGTTCCTGTTTTTATT
19956929 AAGGCCATGTTCCTGTTTTTATT
1 AAGGCCATGTTCCTGTTTTTATT
**
19956952 GTGGCCATGTTCCTG
1 AAGGCCATGTTCCTG
19956967 AGTTGAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.44
Consensus pattern (23 bp):
AAGGCCATGTTCCTGTTTTTATT
Found at i:19961009 original size:15 final size:15
Alignment explanation
Indices: 19960974--19961025 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
19960964 TTAAGAATTT
*
19960974 TATTAAATTAT-ATA
1 TATTTAATTATAATA
19960988 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
19961002 TATTTAATAATAAT-
1 TATTTAATTATAATA
19961016 TATTTTAATT
1 TA-TTTAATT
19961026 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 7 0.22
15 17 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:19961051 original size:120 final size:120
Alignment explanation
Indices: 19960849--19961258 Score: 732
Period size: 120 Copynumber: 3.4 Consensus size: 120
19960839 AATTATTTTA
* * * * *
19960849 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTT-TCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTT-TAATTTATATTT
*
19960913 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
19960969 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
19961034 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
19961089 AATTTTATTAAATTATATATTTTAATTATATTATATTTAATAATTATTATTTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
19961154 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
19961209 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
19961259 GTCTAAATAT
Statistics
Matches: 279, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
119 5 0.02
120 274 0.98
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:19961083 original size:66 final size:66
Alignment explanation
Indices: 19961007--19961205 Score: 210
Period size: 66 Copynumber: 3.2 Consensus size: 66
19960997 TAATATATTT
*
19961007 AATAATAATTATTTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
19961072 G
66 G
** * * *
19961073 AATATTAATTATTAAGAATTT-TA--TTA-A--AT--TATA-TAT--TTTAATTATATT-ATAT-
1 AATATTAATTATT-TTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
**
19961125 TT
65 AG
19961127 AATAATT-ATTATTTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AAT-ATTAATTATTTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
19961191 AG
65 AG
19961193 AATATTAATTATT
1 AATATTAATTATT
19961206 AAGAATTTTA
Statistics
Matches: 102, Mismatches: 15, Indels: 32
0.68 0.10 0.21
Matches are distributed among these distances:
53 5 0.05
54 11 0.11
55 7 0.07
56 12 0.12
57 1 0.01
58 3 0.03
59 6 0.06
61 6 0.06
62 3 0.03
63 1 0.01
64 12 0.12
65 7 0.07
66 23 0.23
67 5 0.05
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (66 bp):
AATATTAATTATTTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
G
Found at i:19961117 original size:13 final size:14
Alignment explanation
Indices: 19961099--19961154 Score: 64
Period size: 15 Copynumber: 4.1 Consensus size: 14
19961089 AATTTTATTA
19961099 AATTATA-TATTTT
1 AATTATATTATTTT
19961112 AATTATATTATATTT
1 AATTATATTAT-TTT
*
19961127 AATAATTATTATTTT
1 AATTA-TATTATTTT
19961142 AATT-TA-TATTTT
1 AATTATATTATTTT
19961154 A
1 A
19961155 CAGTATCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 7 0.18
13 9 0.24
14 3 0.08
15 13 0.34
16 6 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
AATTATATTATTTT
Found at i:19961121 original size:18 final size:18
Alignment explanation
Indices: 19961090--19961151 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 18
19961080 ATTATTAAGA
*
19961090 ATTTT-ATTAAATTATAT
1 ATTTTAATTATATTATAT
19961107 ATTTTAATTATA-T-TAT
1 ATTTTAATTATATTATAT
19961123 A-TTTAA-TA-ATTAT-T
1 ATTTTAATTATATTATAT
19961137 ATTTTAATTTATATT
1 ATTTTAA-TTATATT
19961152 TTACAGTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.14
15 11 0.30
16 4 0.11
17 8 0.22
18 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTAATTATATTATAT
Found at i:19961249 original size:15 final size:15
Alignment explanation
Indices: 19961214--19961255 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
19961204 TTAAGAATTT
*
19961214 TATTAAATTAT-ATA
1 TATTTAATTATAATA
19961228 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
19961242 TATTTAATAATAAT
1 TATTTAATTATAAT
19961256 TATGTCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:19980781 original size:48 final size:48
Alignment explanation
Indices: 19980692--19980793 Score: 145
Period size: 48 Copynumber: 2.1 Consensus size: 48
19980682 GGGGTAGCAA
*
19980692 AGGGATAATGGGGAAGAGGGAAAAAATCAGAGTAGGAGGAGGGATGGT
1 AGGGAAAATGGGGAAGAGGGAAAAAATCAGAGTAGGAGGAGGGATGGT
* *
19980740 AGGGAAAAT-GGGAAGAGGGAGAGAGAATTAGAGTAGG-GGAGGGATGGT
1 AGGGAAAATGGGGAAGAGGGA-A-AAAATCAGAGTAGGAGGAGGGATGGT
19980788 AGGGAA
1 AGGGAA
19980794 GACGAAGAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
47 11 0.22
48 26 0.53
49 12 0.24
ACGTcount: A:0.39, C:0.01, G:0.48, T:0.12
Consensus pattern (48 bp):
AGGGAAAATGGGGAAGAGGGAAAAAATCAGAGTAGGAGGAGGGATGGT
Found at i:19980895 original size:30 final size:30
Alignment explanation
Indices: 19980829--19980895 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
19980819 ATAGGGGGAT
*
19980829 GAAAAATGGCAGCTCCGTTAAGTTTGTAAA
1 GAAAAATGGCAGCTCCGTTAAGTCTGTAAA
* * ** * *
19980859 GGAAAATGGTAGCTTTGTTACGTCTGTAAC
1 GAAAAATGGCAGCTCCGTTAAGTCTGTAAA
19980889 GAAAAAT
1 GAAAAAT
19980896 AGTTAGTGGT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (30 bp):
GAAAAATGGCAGCTCCGTTAAGTCTGTAAA
Found at i:19980948 original size:20 final size:20
Alignment explanation
Indices: 19980923--19980960 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19980913 TTGTTATTTT
*
19980923 TTGAAATTTGAGTGACTGAA
1 TTGAAACTTGAGTGACTGAA
19980943 TTGAAACTTGAGTGACTG
1 TTGAAACTTGAGTGACTG
19980961 TTTTGTTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (20 bp):
TTGAAACTTGAGTGACTGAA
Found at i:19982464 original size:39 final size:38
Alignment explanation
Indices: 19982420--19982506 Score: 111
Period size: 39 Copynumber: 2.3 Consensus size: 38
19982410 CCACCAGCCA
* * *
19982420 CCACCATCGTCGTTCACCAGTTAGGTAGTCACCACCTAT
1 CCACCATCATCGTTCACCAGTCAAGTAGTCACCA-CTAT
* * *
19982459 CCACCATCATTGTTCATCAGTCAAGTAGTCACCACTGT
1 CCACCATCATCGTTCACCAGTCAAGTAGTCACCACTAT
19982497 CCACCATCAT
1 CCACCATCAT
19982507 TATTCAACAG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 13 0.31
39 29 0.69
ACGTcount: A:0.25, C:0.36, G:0.13, T:0.26
Consensus pattern (38 bp):
CCACCATCATCGTTCACCAGTCAAGTAGTCACCACTAT
Found at i:19984206 original size:23 final size:23
Alignment explanation
Indices: 19984089--19984206 Score: 209
Period size: 23 Copynumber: 5.1 Consensus size: 23
19984079 GTGCCACACG
19984089 GATATGTAGCCGAAGCTACCACT
1 GATATGTAGCCGAAGCTACCACT
* *
19984112 GAAATGTAGCTGAAGCTACCACT
1 GATATGTAGCCGAAGCTACCACT
19984135 GATATGTAGCCGAAGCTACCACT
1 GATATGTAGCCGAAGCTACCACT
*
19984158 GAAATGTAGCCGAAGCTACCACT
1 GATATGTAGCCGAAGCTACCACT
19984181 GATATGTAGCCGAAGCTACCACT
1 GATATGTAGCCGAAGCTACCACT
19984204 GAT
1 GAT
19984207 CAATAACACT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 89 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (23 bp):
GATATGTAGCCGAAGCTACCACT
Found at i:19984688 original size:30 final size:29
Alignment explanation
Indices: 19984653--19984714 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
19984643 TCCTTGACTC
19984653 AAAC-TTTGACAAAATTACAATTTTGCCCCT
1 AAACTTTTG-CAAAATTACAATTTTG-CCCT
* * *
19984683 AAACTTTTGCATATTTACACTTTTGCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCT
19984712 AAA
1 AAA
19984715 GCTCGTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 7 0.25
30 17 0.61
31 4 0.14
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (29 bp):
AAACTTTTGCAAAATTACAATTTTGCCCT
Found at i:19985660 original size:14 final size:14
Alignment explanation
Indices: 19985641--19985694 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
19985631 ACGTTATCGA
19985641 ATAAATATATAAAT
1 ATAAATATATAAAT
* *
19985655 ATAAATAAACAAAT
1 ATAAATATATAAAT
**
19985669 ATTTATATATAAA-
1 ATAAATATATAAAT
19985682 ATAAA-ATATAAAT
1 ATAAATATATAAAT
19985695 TGAATAATTT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 21 0.68
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAATATATAAAT
Found at i:19985678 original size:22 final size:23
Alignment explanation
Indices: 19985643--19985686 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
19985633 GTTATCGAAT
19985643 AAATATATAAATAT-AAATAAAC
1 AAATATATAAATATAAAATAAAC
* *
19985665 AAATATTTATATATAAAATAAA
1 AAATATATAAATATAAAATAAA
19985687 ATATAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATATATAAATATAAAATAAAC
Found at i:19986178 original size:21 final size:20
Alignment explanation
Indices: 19986144--19986185 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
19986134 TTAAATTCAT
19986144 TTGATTAAAATCAAATCAAA
1 TTGATTAAAATCAAATCAAA
*
19986164 TTGATTTAGAATCAAATCAAA
1 TTGA-TTAAAATCAAATCAAA
19986185 T
1 T
19986186 CAAGATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (20 bp):
TTGATTAAAATCAAATCAAA
Found at i:19989172 original size:58 final size:54
Alignment explanation
Indices: 19989110--19989219 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
19989100 GAAATTATTA
* *
19989110 TGGTTTTCTCCAAAATGAAAATGAAGATGGAGAAAATGGAATCATTTGGAAATGAATG
1 TGGTTTTCT-CAAAATGAAAATAAAAAT-GAG-AAAT-GAATCATTTGGAAATGAATG
*
19989168 TGGTTTTCTCAAAATGAAAATAAAAATGAGAAATGATTCATTTGGAAATGAA
1 TGGTTTTCTCAAAATGAAAATAAAAATGAGAAATGAATCATTTGGAAATGAA
19989220 AAAGGATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
54 17 0.35
55 4 0.08
56 3 0.06
57 16 0.33
58 9 0.18
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (54 bp):
TGGTTTTCTCAAAATGAAAATAAAAATGAGAAATGAATCATTTGGAAATGAATG
Found at i:19989234 original size:54 final size:57
Alignment explanation
Indices: 19989120--19989235 Score: 130
Period size: 54 Copynumber: 2.1 Consensus size: 57
19989110 TGGTTTTCTC
* * *** * **
19989120 CAAAATGAAAATGAAGATGGAGAAAATGGAATCATTTGGAAATGAATGTGGTTTTCT
1 CAAAATGAAAATAAAAATGGAGAAAATGGAATCATTTGGAAATGAAAAAGGATTAAT
*
19989177 CAAAATGAAAATAAAAAT-GAG-AAAT-GATTCATTTGGAAATGAAAAAGGATTAAT
1 CAAAATGAAAATAAAAATGGAGAAAATGGAATCATTTGGAAATGAAAAAGGATTAAT
19989231 CAAAA
1 CAAAA
19989236 ATGATCTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
54 27 0.54
55 4 0.08
56 3 0.06
57 16 0.32
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (57 bp):
CAAAATGAAAATAAAAATGGAGAAAATGGAATCATTTGGAAATGAAAAAGGATTAAT
Found at i:19993959 original size:25 final size:26
Alignment explanation
Indices: 19993931--19993979 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
19993921 GTAAATGAAG
*
19993931 TTATAAGCATA-GTGTTTGTTTGAGT
1 TTATAAACATATGTGTTTGTTTGAGT
*
19993956 TTATAAACATATGTTTTTGTTTGA
1 TTATAAACATATGTGTTTGTTTGA
19993980 AGCCTAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (26 bp):
TTATAAACATATGTGTTTGTTTGAGT
Found at i:19994457 original size:9 final size:10
Alignment explanation
Indices: 19994432--19994458 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
19994422 CCTGTCATAG
19994432 AATTTTTCTA
1 AATTTTTCTA
19994442 AATTTTTCTA
1 AATTTTTCTA
19994452 AATTTTT
1 AATTTTT
19994459 TCAAATGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (10 bp):
AATTTTTCTA
Found at i:20000049 original size:20 final size:20
Alignment explanation
Indices: 20000013--20000050 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20000003 GTGAAATTTG
*
20000013 TATGAAAATATAGAATTAAT
1 TATGAAAATATAAAATTAAT
20000033 TATGAAGAATA-AAAATTA
1 TATGAA-AATATAAAATTA
20000051 GTCTCGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.32
Consensus pattern (20 bp):
TATGAAAATATAAAATTAAT
Found at i:20009970 original size:16 final size:15
Alignment explanation
Indices: 20009930--20009976 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
20009920 AGATGATAAT
20009930 TATTAATATATAATTA
1 TATTAAT-TATAATTA
20009946 TATCT-ATTATAATATA
1 TAT-TAATTATAAT-TA
*
20009962 TATTAATTATTATTA
1 TATTAATTATAATTA
20009977 GCTTTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 9 0.33
16 17 0.63
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:20009975 original size:10 final size:11
Alignment explanation
Indices: 20009928--20009976 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
20009918 AAAGATGATA
20009928 ATTATTAATAT
1 ATTATTAATAT
* *
20009939 ATAATTATATCT
1 ATTATTA-ATAT
20009951 ATTA-TAATAT
1 ATTATTAATAT
20009961 A-TATTAAT-T
1 ATTATTAATAT
20009970 ATTATTA
1 ATTATTA
20009977 GCTTTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
9 4 0.13
10 13 0.42
11 8 0.26
12 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTATTAATAT
Found at i:20009975 original size:22 final size:23
Alignment explanation
Indices: 20009928--20009976 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
20009918 AAAGATGATA
20009928 ATTATTAATATATAATTATATCT
1 ATTATTAATATATAATTATATCT
20009951 ATTA-TAATATAT-ATTA-AT-T
1 ATTATTAATATATAATTATATCT
20009970 ATTATTA
1 ATTATTA
20009977 GCTTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.20
20 4 0.16
21 4 0.16
22 8 0.32
23 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTATTAATATATAATTATATCT
Found at i:20019559 original size:9 final size:9
Alignment explanation
Indices: 20019545--20019574 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
20019535 ATTAAAATAT
20019545 TAATTAAAC
1 TAATTAAAC
*
20019554 TAATTAAAT
1 TAATTAAAC
20019563 TAATTAAAC
1 TAATTAAAC
20019572 TAA
1 TAA
20019575 AATAACCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAC
Found at i:20019603 original size:29 final size:29
Alignment explanation
Indices: 20019562--20019617 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
20019552 ACTAATTAAA
*
20019562 TTAATTAAACTAAAATAACCTAATGGATT
1 TTAACTAAACTAAAATAACCTAATGGATT
* * *
20019591 TTAACTAACCTAAGATATCCTAATGGA
1 TTAACTAAACTAAAATAACCTAATGGA
20019618 ATTTCCTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (29 bp):
TTAACTAAACTAAAATAACCTAATGGATT
Found at i:20021833 original size:50 final size:50
Alignment explanation
Indices: 20021722--20021917 Score: 196
Period size: 50 Copynumber: 3.8 Consensus size: 50
20021712 ATTTGGGTAA
* *
20021722 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
*
20021778 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
20021828 AGAGGTCCCCCGTAAGACCGTATCTGGGACATGGCATGGGCACCGATG-TG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GATG
** * * * *
20021878 AGAACTCCCATGTAAGACCATATTTGGGATATGACATTGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
20021918 AAGTATAAGA
Statistics
Matches: 121, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
50 76 0.63
51 1 0.01
53 3 0.02
55 1 0.01
56 40 0.33
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:20026512 original size:50 final size:50
Alignment explanation
Indices: 20026401--20026640 Score: 171
Period size: 50 Copynumber: 4.7 Consensus size: 50
20026391 ATTTGGGTAA
* * **
20026401 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCA-TGGC--CACCGAG---ATG
** * *
20026457 AGAGGTCCCATGTAAAACTGTGTCTGGGACATGGCGTTGCCACCGAGATG
1 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCATGGCCACCGAGATG
** * * *
20026507 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCATGGCCACCGAGATG
** * * * * *
20026557 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGG-CA--GTACAAG
1 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCA-TGGCCACCG-AGATG
* ** *
20026606 AAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGC
20026641 TTTGGCATGT
Statistics
Matches: 152, Mismatches: 30, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
48 1 0.01
49 33 0.22
50 76 0.50
51 3 0.02
53 5 0.03
55 3 0.02
56 31 0.20
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCATGGCCACCGAGATG
Found at i:20029570 original size:41 final size:41
Alignment explanation
Indices: 20029522--20029987 Score: 752
Period size: 41 Copynumber: 11.4 Consensus size: 41
20029512 ATTCACTGGT
* * *
20029522 ACTTAGCCTGCTAGGCTTATAGCCTAATCCAGTTCACCGGC
1 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
*
20029563 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACCGGC
1 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
*
20029604 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGC
1 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
*
20029645 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGC
1 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
*
20029686 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATGACCGGC
1 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
*
20029727 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACCGGC
1 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
* *
20029768 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACCGAC
1 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
* *
20029809 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGT
1 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
* *
20029850 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACTGGC
1 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
* * * * *
20029891 ACTTAGTCAGCTAGGCTTATAACCTTATTTAGATCACCGGC
1 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
*
20029932 ACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGGC
1 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
20029973 ACTTAGCCTGCTAGG
1 ACTTAGCCTGCTAGG
20029988 TTTTAAAACC
Statistics
Matches: 397, Mismatches: 28, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 397 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (41 bp):
ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGC
Found at i:20036150 original size:50 final size:50
Alignment explanation
Indices: 20036083--20036267 Score: 246
Period size: 50 Copynumber: 3.7 Consensus size: 50
20036073 GTGAATGAGA
20036083 TCCCATGTAAAACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAAACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
20036133 TCCCATGTAAAACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAAACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
20036183 TCCCCCGTAATACCATGTCTAGGACATGGCA-TGAGCACCGATATGAGAAC
1 TCCCATGTAAAACCATGTCTGGGACATGGCATTG-GCACCGAGATGAGAGG
* * *
20036233 TCCCATGTAAGACCATATCTGGGATATGGCATTGG
1 TCCCATGTAAAACCATGTCTGGGACATGGCATTGG
20036268 AAGTACAAGA
Statistics
Matches: 116, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 2 0.02
50 112 0.97
51 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAAACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:20041732 original size:38 final size:38
Alignment explanation
Indices: 20041681--20041760 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
20041671 TTATGAAATT
* *
20041681 TTAAATTGGAGGTCTTTATATTTTAATTAGAACATTGG
1 TTAAATTGGAGGTCTTTATATTGTAATTAGAACATTAG
*
20041719 TTAAATTGGAGGTCTTTATATTGTAATTAGACCATTAG
1 TTAAATTGGAGGTCTTTATATTGTAATTAGAACATTAG
20041757 TTAA
1 TTAA
20041761 GTTATGGACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (38 bp):
TTAAATTGGAGGTCTTTATATTGTAATTAGAACATTAG
Found at i:20042744 original size:50 final size:50
Alignment explanation
Indices: 20042689--20042867 Score: 209
Period size: 50 Copynumber: 3.6 Consensus size: 50
20042679 GGGAATGAGA
*
20042689 TCCCATGTAAAACCATGTCTGGGACATGGTATTAACACCGAGATGAGAGG
1 TCCCATGTAAAACCATGTCTGGGACATGGCATTAACACCGAGATGAGAGG
* * **
20042739 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAAACCATGTCTGGGACATGGCATTAACACCGAGATGAGAGG
* * * **
20042789 TCCC-TCG-AAAGACCATGTCTGGGACATGGCATGAACACCAATATGAGAAC
1 TCCCAT-GTAAA-ACCATGTCTGGGACATGGCATTAACACCGAGATGAGAGG
* * *
20042839 TCCCATGTAAAAACATATCTGGGATATGG
1 TCCCATGTAAAACCATGTCTGGGACATGG
20042868 AATTGGAAGT
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 3 0.03
50 101 0.94
51 4 0.04
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (50 bp):
TCCCATGTAAAACCATGTCTGGGACATGGCATTAACACCGAGATGAGAGG
Found at i:20044862 original size:29 final size:29
Alignment explanation
Indices: 20044830--20044888 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
20044820 CAAAAGCTAT
*
20044830 ATGAATG-CATGAAACAGATGAAAATCAAA
1 ATGAATGACATGAAA-AGATAAAAATCAAA
*
20044859 ATGAATGATCATGAAAATATAAAAATCAAA
1 ATGAATGA-CATGAAAAGATAAAAATCAAA
20044889 GTTTGGAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 7 0.27
30 12 0.46
31 7 0.27
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.20
Consensus pattern (29 bp):
ATGAATGACATGAAAAGATAAAAATCAAA
Found at i:20063204 original size:50 final size:49
Alignment explanation
Indices: 20063076--20063316 Score: 169
Period size: 49 Copynumber: 4.8 Consensus size: 49
20063066 GATAATAACA
* * * * *
20063076 TGCCAAAGCCTTGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATAG
* * * *
20063125 TTCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAG
* * ** ** * *
20063174 TGCCCATGCAATTGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG
1 TGCCAATGCCA-TGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAG
* * * * * * *
20063224 TGCCAACGCCATGTCCTAGACATGGTCTTACGTGTGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GT-TC-T--CAT--ATAG
*
20063280 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
20063317 TCTCATTCCC
Statistics
Matches: 147, Mismatches: 36, Indels: 11
0.76 0.19 0.06
Matches are distributed among these distances:
48 3 0.02
49 67 0.46
50 39 0.27
51 2 0.01
52 1 0.01
54 2 0.01
56 33 0.22
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAG
Found at i:20064049 original size:10 final size:11
Alignment explanation
Indices: 20064026--20064050 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20064016 CGAGGACTCC
20064026 AAAAACATTAA
1 AAAAACATTAA
20064037 AAAAACATTAA
1 AAAAACATTAA
20064048 AAA
1 AAA
20064051 CGGGGCTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAACATTAA
Found at i:20070489 original size:20 final size:20
Alignment explanation
Indices: 20070444--20070489 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
20070434 ATCATAGTCT
20070444 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTCTTTACTTAC
*
20070463 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTCTTTACTTAC
20070483 TTGCTTA
1 TTGCTTA
20070490 ATTAAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.13, C:0.24, G:0.07, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTCTTTACTTAC
Found at i:20074770 original size:21 final size:21
Alignment explanation
Indices: 20074744--20074810 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
20074734 ATCATTCTAG
20074744 CAACTTCCTCTTCTTCAGCAA
1 CAACTTCCTCTTCTTCAGCAA
20074765 CAACTTCCTCTTC-T-A-CAA
1 CAACTTCCTCTTCTTCAGCAA
* * *
20074783 AAACTT-CTACTTCTGCAGCAT
1 CAACTTCCT-CTTCTTCAGCAA
20074804 CAACTTC
1 CAACTTC
20074811 TTTCTCAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
17 2 0.05
18 12 0.32
19 1 0.03
20 2 0.05
21 20 0.54
ACGTcount: A:0.27, C:0.36, G:0.04, T:0.33
Consensus pattern (21 bp):
CAACTTCCTCTTCTTCAGCAA
Found at i:20082120 original size:14 final size:14
Alignment explanation
Indices: 20082103--20082132 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20082093 AAATGAAGTT
*
20082103 AAAGAAATATAAAC
1 AAAGAAAAATAAAC
20082117 AAAGAAAAATAAAC
1 AAAGAAAAATAAAC
20082131 AA
1 AA
20082133 TTAGTGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAGAAAAATAAAC
Found at i:20083305 original size:55 final size:55
Alignment explanation
Indices: 20083227--20083334 Score: 126
Period size: 55 Copynumber: 2.0 Consensus size: 55
20083217 TTCTTATCCG
* * * **
20083227 GACAGCTGTCAAGTGTGATGACAATTTTGAACGCAATCTGGAATTAACACATGTA
1 GACAGCTGTCAAGTGCGACGACAATTCTGAACGCAATCTAAAATTAACACATGTA
* * * * *
20083282 GACATCTGTCAAGTGCGGCGACAATTCTGGATGCAATCTAAAATTAACTCATG
1 GACAGCTGTCAAGTGCGACGACAATTCTGAACGCAATCTAAAATTAACACATG
20083335 CAACGGCATT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (55 bp):
GACAGCTGTCAAGTGCGACGACAATTCTGAACGCAATCTAAAATTAACACATGTA
Found at i:20084400 original size:19 final size:19
Alignment explanation
Indices: 20084378--20084415 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20084368 TCAATCATCC
20084378 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
20084397 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
20084416 ACTCTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:20094085 original size:19 final size:19
Alignment explanation
Indices: 20094063--20094100 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20094053 TCAATCATCC
20094063 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
20094082 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
20094101 ACTCTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:20101176 original size:25 final size:25
Alignment explanation
Indices: 20101147--20101197 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
20101137 CTCTAGCAAC
20101147 GACACAGAATAGAAGAGGCAACCTG
1 GACACAGAATAGAAGAGGCAACCTG
20101172 GACACAGAATAGAAGAGGCAACCTG
1 GACACAGAATAGAAGAGGCAACCTG
20101197 G
1 G
20101198 GAACCTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.29, T:0.08
Consensus pattern (25 bp):
GACACAGAATAGAAGAGGCAACCTG
Found at i:20105209 original size:27 final size:27
Alignment explanation
Indices: 20105179--20105233 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
20105169 TTGTGTAAGT
20105179 AGCCCAAATATCACAACTTGTATGAGC
1 AGCCCAAATATCACAACTTGTATGAGC
* *
20105206 AGCCCAAATATCACAGCTTGTGTGAGC
1 AGCCCAAATATCACAACTTGTATGAGC
20105233 A
1 A
20105234 AATCGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (27 bp):
AGCCCAAATATCACAACTTGTATGAGC
Found at i:20111302 original size:11 final size:11
Alignment explanation
Indices: 20111288--20111363 Score: 89
Period size: 11 Copynumber: 6.6 Consensus size: 11
20111278 ACCACCACTT
*
20111288 CACCACCATAG
1 CACCACCATAC
*
20111299 CACCACCATAA
1 CACCACCATAC
20111310 CACCACCATAC
1 CACCACCATAC
20111321 CACCACCATAACAC
1 CACCACCAT---AC
*
20111335 CACCACCATAG
1 CACCACCATAC
*
20111346 CACCACCGTAC
1 CACCACCATAC
20111357 CACCACC
1 CACCACC
20111364 TTTACACCAC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
11 46 0.81
14 11 0.19
ACGTcount: A:0.37, C:0.51, G:0.04, T:0.08
Consensus pattern (11 bp):
CACCACCATAC
Found at i:20111305 original size:22 final size:22
Alignment explanation
Indices: 20111278--20111339 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
20111268 ATTCGATATT
*
20111278 ACCACCACTTCACCACCATAGC
1 ACCACCACTACACCACCATAGC
*
20111300 ACCACCA-TAACACCACCATACC
1 ACCACCACT-ACACCACCATAGC
20111322 ACCACCA-TAACACCACCA
1 ACCACCACT-ACACCACCA
20111340 CCATAGCACC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.39, C:0.50, G:0.02, T:0.10
Consensus pattern (22 bp):
ACCACCACTACACCACCATAGC
Found at i:20111339 original size:36 final size:36
Alignment explanation
Indices: 20111299--20111374 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
20111289 ACCACCATAG
20111299 CACCACCATAACACCACCATACCACCACCATAACAC
1 CACCACCATAACACCACCATACCACCACCATAACAC
* * * *
20111335 CACCACCATAGCACCACCGTACCACCACCTTTACAC
1 CACCACCATAACACCACCATACCACCACCATAACAC
20111371 CACC
1 CACC
20111375 TTCAAAACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.51, G:0.03, T:0.11
Consensus pattern (36 bp):
CACCACCATAACACCACCATACCACCACCATAACAC
Found at i:20111358 original size:22 final size:22
Alignment explanation
Indices: 20111288--20111363 Score: 98
Period size: 22 Copynumber: 3.3 Consensus size: 22
20111278 ACCACCACTT
*
20111288 CACCACCATAGCACCACCATAA
1 CACCACCATAGCACCACCATAC
*
20111310 CACCACCATACCACCACCATAACAC
1 CACCACCATAGCACCACCAT---AC
*
20111335 CACCACCATAGCACCACCGTAC
1 CACCACCATAGCACCACCATAC
20111357 CACCACC
1 CACCACC
20111364 TTTACACCAC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
22 28 0.60
25 19 0.40
ACGTcount: A:0.37, C:0.51, G:0.04, T:0.08
Consensus pattern (22 bp):
CACCACCATAGCACCACCATAC
Found at i:20113645 original size:26 final size:25
Alignment explanation
Indices: 20113616--20113673 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
20113606 TTACAAAATT
* * *
20113616 AAACAACAAAAATAAAAGTTATTCTA
1 AAACAA-AAAAAGAAAACTTAATCTA
*
20113642 AAACAAAAAGAGAAAACTTAATCTA
1 AAACAAAAAAAGAAAACTTAATCTA
20113667 AAA-AAAA
1 AAACAAAA
20113674 TAGAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 4 0.14
25 18 0.64
26 6 0.21
ACGTcount: A:0.67, C:0.10, G:0.05, T:0.17
Consensus pattern (25 bp):
AAACAAAAAAAGAAAACTTAATCTA
Found at i:20115592 original size:14 final size:14
Alignment explanation
Indices: 20115569--20115615 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
20115559 TAAGTATTTT
*
20115569 TTAAGCTTAATTAA
1 TTAAACTTAATTAA
*
20115583 TTAAATTTAATTAAA
1 TTAAACTTAATT-AA
*
20115598 TTAAACATAATTAA
1 TTAAACTTAATTAA
20115612 TTAA
1 TTAA
20115616 CTAAAACATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (14 bp):
TTAAACTTAATTAA
Found at i:20120492 original size:29 final size:29
Alignment explanation
Indices: 20120459--20120517 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
20120449 TTTTTTATCC
*
20120459 ATTTTTTA-ATAAATGACCTAATATTTTT
1 ATTTTTTATATAAATGACCTAATATGTTT
* *
20120487 ATTTTTTATATAAGTGGCCTAATATGTTT
1 ATTTTTTATATAAATGACCTAATATGTTT
20120516 AT
1 AT
20120518 ACTTCTTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (29 bp):
ATTTTTTATATAAATGACCTAATATGTTT
Found at i:20121359 original size:3 final size:3
Alignment explanation
Indices: 20121351--20121424 Score: 125
Period size: 3 Copynumber: 25.3 Consensus size: 3
20121341 GGAAATTTTC
20121351 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
20121399 TCT TCT T-T TCT TCT TC- TCT GCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
20121425 TTTTTTATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 4 0.06
3 63 0.94
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:20121934 original size:17 final size:17
Alignment explanation
Indices: 20121914--20121963 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
20121904 AGCAATTTAA
20121914 TTTTTTTCTTTTATTTT
1 TTTTTTTCTTTTATTTT
** **
20121931 TTTTTAACTTTCCTTTT
1 TTTTTTTCTTTTATTTT
20121948 TTTTTTTC-TTTATTTT
1 TTTTTTTCTTTTATTTT
20121964 CTATTCTCTC
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTTATTTT
Found at i:20126915 original size:43 final size:42
Alignment explanation
Indices: 20126815--20126960 Score: 145
Period size: 43 Copynumber: 3.5 Consensus size: 42
20126805 GTTACTCGGT
* * *
20126815 GGAATCAGCACTTAGCAACCAAC-TTATATTC-AGTGATACGG
1 GGAATCAGCACTTAGCAACCACCTTTACAATCAAG-GATACGG
* * *
20126856 GGAATCAACACATAGCAACC-CCTTTCACAATCAAGGATACAGT
1 GGAATCAGCACTTAGCAACCACCTTT-ACAATCAAGGATAC-GG
* ** *
20126899 GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGG
1 GGAATCAGCACTTAGCAACCACCTTTACAATCAAGGATACGG
*
20126941 GGAATTAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
20126961 CCTCGAGGAA
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
40 1 0.01
41 20 0.23
42 29 0.34
43 31 0.36
44 5 0.06
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCACCTTTACAATCAAGGATACGG
Found at i:20126955 original size:42 final size:42
Alignment explanation
Indices: 20126815--20126960 Score: 152
Period size: 42 Copynumber: 3.5 Consensus size: 42
20126805 GTTACTCGGT
* * * *
20126815 GGAATCAGCACTTAGCAACCAAC-TTATATTCAGTGATACGG
1 GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
* * * *
20126856 GGAATCAACACATAGCAACC-CCTTTCACAATCAAGGATACAGT
1 GGAATCAGCACTTAGCAACCACCTTT-ACAATCAATGATAC-GG
* * *
20126899 GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGG
1 GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
*
20126941 GGAATTAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
20126961 CCTCGAGGAA
Statistics
Matches: 85, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
40 1 0.01
41 20 0.24
42 30 0.35
43 29 0.34
44 5 0.06
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
Found at i:20127012 original size:41 final size:41
Alignment explanation
Indices: 20126967--20127074 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 41
20126957 AACCCCTCGA
*
20126967 GGAATCTGCACTTAGCAACCCCTTTTTGATTAGTGATTCGG
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGATTCGG
*
20127008 GGAATCTGCACTTCGCAACCCC-TTTTGATCAGTGATTCGG
1 GGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGATTCGG
*
20127048 GGAATCTGCACTTAGCAACCCTTTTTT
1 GGAATCTGCACTTAGCAACCCCTTTTT
20127075 TTTTCAATGA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 37 0.60
41 25 0.40
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.33
Consensus pattern (41 bp):
GGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGATTCGG
Found at i:20127019 original size:67 final size:68
Alignment explanation
Indices: 20126899--20127030 Score: 171
Period size: 67 Copynumber: 2.0 Consensus size: 68
20126889 AGGATACAGT
20126899 GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGGGGAATTAGCACTTAGCAACCCCT
1 GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGGGGAATTAGCACTTAGCAACCCCT
20126964 CGA
66 CGA
* * * * * *
20126967 GGAATCTGCACTTAGCAACC-CCTTTTTG-ATTAGTGATTCGGGGAATCT-GCACTTCGCAACCC
1 GGAATCAGCACTTAGCAACCACC-TTTAGAATCAATAATTCGGGGAAT-TAGCACTTAGCAACCC
20127029 CT
64 CT
20127031 TTTGATCAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
67 32 0.57
68 24 0.43
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (68 bp):
GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGGGGAATTAGCACTTAGCAACCCCT
CGA
Found at i:20127262 original size:38 final size:38
Alignment explanation
Indices: 20127219--20127295 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
20127209 TAAATTCCTA
20127219 GGACAAAATAACAATAATTAGCAATATAGAGCAATAGG
1 GGACAAAATAACAATAATTAGCAATATAGAGCAATAGG
20127257 GGACAAAATAACAATAATTAGCAATATAGAGCAATAGG
1 GGACAAAATAACAATAATTAGCAATATAGAGCAATAGG
20127295 G
1 G
20127296 TCGAATCCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.18
Consensus pattern (38 bp):
GGACAAAATAACAATAATTAGCAATATAGAGCAATAGG
Found at i:20128431 original size:23 final size:23
Alignment explanation
Indices: 20128361--20128437 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
20128351 GCTAGATTTT
* *
20128361 TTCTAAATATTGTAACTAAATAA
1 TTCTAAATATTATCACTAAATAA
* *
20128384 TCCTAAATATTATCATTAAATAA
1 TTCTAAATATTATCACTAAATAA
20128407 TTCTAAATATTATCACTAAATAA
1 TTCTAAATATTATCACTAAATAA
*
20128430 TTCAAAAT
1 TTCTAAAT
20128438 TTTAAAATGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (23 bp):
TTCTAAATATTATCACTAAATAA
Found at i:20137111 original size:27 final size:27
Alignment explanation
Indices: 20137055--20137113 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
20137045 CTTCTAAAGA
* * **
20137055 AATAAAATACTCATAAATAAATCTCCT
1 AATAAAATAATAATAAATAAATCTAAT
20137082 AATAAAATAATAATAAACT-AATCTAAT
1 AATAAAATAATAATAAA-TAAATCTAAT
20137109 AATAA
1 AATAA
20137114 TTAATTGACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (27 bp):
AATAAAATAATAATAAATAAATCTAAT
Found at i:20140424 original size:17 final size:18
Alignment explanation
Indices: 20140380--20140426 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
20140370 AATTTAGTTT
20140380 TAATATATATAATTGAATG
1 TAATATAT-TAATTGAATG
*
20140399 TAATTTATTCAATT-AA-G
1 TAATATATT-AATTGAATG
20140416 TAATATATTAA
1 TAATATATTAA
20140427 ATTTCCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.08
17 9 0.36
18 3 0.12
19 11 0.44
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (18 bp):
TAATATATTAATTGAATG
Found at i:20140429 original size:17 final size:19
Alignment explanation
Indices: 20140380--20140429 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 19
20140370 AATTTAGTTT
20140380 TAATATA-TATAATTGAATG
1 TAATATATTA-AATTGAATG
* *
20140399 TAATTTATTCAATT-AA-G
1 TAATATATTAAATTGAATG
20140416 TAATATATTAAATT
1 TAATATATTAAATT
20140430 TCCTAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 13 0.50
18 2 0.08
19 10 0.38
20 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (19 bp):
TAATATATTAAATTGAATG
Found at i:20141595 original size:11 final size:10
Alignment explanation
Indices: 20141572--20141604 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
20141562 GAATCGAGTC
20141572 TTTTT-TTAT
1 TTTTTATTAT
20141581 TTTTTATTCAT
1 TTTTTATT-AT
20141592 TTTTTATTAT
1 TTTTTATTAT
20141602 TTT
1 TTT
20141605 ATTTTGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 7 0.32
11 10 0.45
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:20142194 original size:3 final size:3
Alignment explanation
Indices: 20142188--20142223 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
20142178 TGTTGTTAAG
20142188 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20142224 CTATATATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20142801 original size:10 final size:10
Alignment explanation
Indices: 20142762--20142794 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20142752 TTAACGCATA
20142762 TTTTATA-AT
1 TTTTATATAT
*
20142771 TTATATATAT
1 TTTTATATAT
20142781 TTTTATATAT
1 TTTTATATAT
20142791 TTTT
1 TTTT
20142795 CTTTATTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTATATAT
Found at i:20149298 original size:19 final size:19
Alignment explanation
Indices: 20149253--20149301 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
20149243 TAAACCACTC
*
20149253 CATTTACTTACTTGCTATT
1 CATTTACTTGCTTGCTATT
20149272 CTATTTACTTGCTTGC-ATTT
1 C-ATTTACTTGCTTGCTA-TT
20149292 CATTTACTTG
1 CATTTACTTG
20149302 GCATAAGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.18, C:0.20, G:0.08, T:0.53
Consensus pattern (19 bp):
CATTTACTTGCTTGCTATT
Found at i:20149371 original size:21 final size:21
Alignment explanation
Indices: 20149346--20149386 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20149336 TTGTGTATTT
*
20149346 ATCCAT-GTCATAGGTAAATTC
1 ATCCATAG-CATAAGTAAATTC
20149367 ATCCATAGCATAAGTAAATT
1 ATCCATAGCATAAGTAAATT
20149387 TCTCACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (21 bp):
ATCCATAGCATAAGTAAATTC
Found at i:20157457 original size:23 final size:22
Alignment explanation
Indices: 20157409--20157453 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
20157399 GACTCTTCGG
20157409 ATTTATCGTTTTACCCCTTTCAA
1 ATTTATCGTTTTA-CCCTTTCAA
*
20157432 ATTTATCGTTTT-GCCTTTCAA
1 ATTTATCGTTTTACCCTTTCAA
20157453 A
1 A
20157454 AATTCTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
23 12 0.57
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.49
Consensus pattern (22 bp):
ATTTATCGTTTTACCCTTTCAA
Found at i:20159189 original size:20 final size:20
Alignment explanation
Indices: 20159166--20159214 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
20159156 AGGCCACTAC
**
20159166 TAATGCAGACAAGCTGCCAG
1 TAATGCAGACAAGCCACCAG
** *
20159186 TAATGTGGTCAAGCCACCAG
1 TAATGCAGACAAGCCACCAG
20159206 TAATGCAGA
1 TAATGCAGA
20159215 TAAACTGTTA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.18
Consensus pattern (20 bp):
TAATGCAGACAAGCCACCAG
Found at i:20162202 original size:55 final size:54
Alignment explanation
Indices: 20162119--20162229 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 54
20162109 CCAGTGTTAC
20162119 AAGAACCTAAGGGTCACACCCTATGGTTAAAGCGAACAAAATCATAATTTCAAT
1 AAGAACCTAAGGGTCACACCCTATGGTTAAAGCGAACAAAATCATAATTTCAAT
* *
20162173 AAGAACCTACAGGGTCGCACCCTATGGTTAAAGCGAACAATATCATAATTTCAAT
1 AAGAACCTA-AGGGTCACACCCTATGGTTAAAGCGAACAAAATCATAATTTCAAT
20162228 AA
1 AA
20162230 TTTGATTACA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
54 9 0.17
55 45 0.83
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (54 bp):
AAGAACCTAAGGGTCACACCCTATGGTTAAAGCGAACAAAATCATAATTTCAAT
Found at i:20163600 original size:20 final size:20
Alignment explanation
Indices: 20163572--20163628 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
20163562 AATATTAAGA
* *
20163572 ACCACTCCATTTACTTTCTT
1 ACCATTCCATTTACTTACTT
20163592 ACCATTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
* *
20163612 TCCATTTCATTTACTTA
1 ACCATTCCATTTACTTA
20163629 ACATAAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:20164336 original size:40 final size:40
Alignment explanation
Indices: 20164278--20164577 Score: 363
Period size: 40 Copynumber: 7.5 Consensus size: 40
20164268 ATCGTCAGAT
* *
20164278 CAACCG-AACATACCAGACAAAAGCTCATAAGAGCTAATC
1 CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTAATC
20164317 CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTAATC
1 CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTAATC
* * * * *
20164357 CAACTGAAACACGCCAAACAAAAGCTCATAATAGCTAATC
1 CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTAATC
* * * *
20164397 CAACTGAAACACGCTAAACAGAAGCTCATAAGAGCTAATC
1 CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTAATC
* * *
20164437 TAACCGAAACA-AGCCAAACAGTAGCTCATAAGAGCTAATC
1 CAACCGAAACACA-CCAGACAGAAGCTCATAAGAGCTAATC
*
20164477 CAACCGAAACACACCAGACAGAATCTCAT-AGAGCTAATC
1 CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTAATC
* ** *
20164516 CAATCGAAACATGCCAGACAGAAGCTCATAAAAGCTAATC
1 CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTAATC
* * * *
20164556 CAATCAAAACACGCCAGTCAGA
1 CAACCGAAACACACCAGACAGA
20164578 GAGTATAACA
Statistics
Matches: 230, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 41 0.18
40 188 0.82
41 1 0.00
ACGTcount: A:0.45, C:0.28, G:0.14, T:0.13
Consensus pattern (40 bp):
CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTAATC
Found at i:20173155 original size:50 final size:49
Alignment explanation
Indices: 20173097--20173288 Score: 165
Period size: 49 Copynumber: 3.9 Consensus size: 49
20173087 TATTGAGGTT
*
20173097 ATGAGAGGTCCCACGTAAGATCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGC-TTGGCACCGAG
* * * *
20173147 ATGAGAGGTCCCCCGTCAGACCATGTCTGGGACATGGCAT-GCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCTTGGCACCGAG
** * * * * * *
20173195 ATGAGAACTCCCATGTAAGACCATATCTAGGATATGGCATTGGTA--GTAC
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGC-TTGGCACCG-AG
* * ** *
20173244 AGGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGC-TTGGCA
20173289 TGTTATTATC
Statistics
Matches: 114, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
48 38 0.33
49 39 0.34
50 37 0.32
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (49 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCTTGGCACCGAG
Found at i:20173216 original size:48 final size:49
Alignment explanation
Indices: 20173096--20173281 Score: 155
Period size: 48 Copynumber: 3.8 Consensus size: 49
20173086 TTATTGAGGT
** * *
20173096 TATGAGAGGTCCCACGTAAGATCATGTCTGGGACATGGCGTTGGCACCGA
1 TATGAGAACTCCCACGTAAGACCATGTCTGGGACATGGC-ATGGCACCGA
* ** * *
20173146 GATGAGAGGTCCCCCGTCAGACCATGTCTGGGACATGGCAT-GCACCGA
1 TATGAGAACTCCCACGTAAGACCATGTCTGGGACATGGCATGGCACCGA
* * * * *
20173194 TATGAGAACTCCCATGTAAGACCATATCTAGGATATGGCATTGGTA--GTA
1 TATGAGAACTCCCACGTAAGACCATGTCTGGGACATGGCA-TGGCACCG-A
* * *
20173243 CAGGA-AACATCCCATGTAAGACCATGTCTGGGACATGGC
1 TATGAGAAC-TCCCACGTAAGACCATGTCTGGGACATGGC
20173282 TTTGGCATGT
Statistics
Matches: 112, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
48 42 0.38
49 33 0.29
50 37 0.33
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (49 bp):
TATGAGAACTCCCACGTAAGACCATGTCTGGGACATGGCATGGCACCGA
Found at i:20177797 original size:21 final size:22
Alignment explanation
Indices: 20177769--20177823 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
20177759 AACAGCGGTG
20177769 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTGTA
*
20177790 GTGGTGAGATT-GGATACTGTA
1 GCGGTGAGATTAGGATACTGTA
*
20177811 GCAGTGAGATTAG
1 GCGGTGAGATTAG
20177824 AAACAGCGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.29
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTGTA
Found at i:20182417 original size:31 final size:31
Alignment explanation
Indices: 20182379--20182442 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
20182369 AGGTACTTAG
20182379 AACAACTCTTGACAATCAAATTGCTTCTTCA
1 AACAACTCTTGACAATCAAATTGCTTCTTCA
20182410 AACAACTCTTGACAATCAAATTGCTTCTTCA
1 AACAACTCTTGACAATCAAATTGCTTCTTCA
20182441 AA
1 AA
20182443 TAAATGTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (31 bp):
AACAACTCTTGACAATCAAATTGCTTCTTCA
Found at i:20184057 original size:147 final size:146
Alignment explanation
Indices: 20183758--20184032 Score: 388
Period size: 147 Copynumber: 1.9 Consensus size: 146
20183748 CTCTCCATCA
*
20183758 ATTTCTAGAATATAACAGGAAAAAATAAAAATTCATTTATCAACAGTTTCAACTCTCAATCAATT
1 ATTTCTAGAATATAACAAGAAAAAATAAAAATTCATTTATCAACAGTTTCAACTCTCAATCAATT
* * **
20183823 TCCATAAGATAACAAAAAAAAACTAAAACTAAAACCCACTTCTCAATAATAGATCTGCAAAATTC
66 TCCAGAAGATAACAAAAAAAAACTAAAACTAAAACCCACTTCTCAATAATAAATCTGCAAAATGA
* * * * *
20183888 TCTTCTACTCTCCATC
131 TCTTCGACACGCAAGC
* *
20183904 AATTTCTAGAATATAACAAGAAAGAATAAAAATTCATTTCTCAACAGTTTCAACTCTCAATCAAT
1 -ATTTCTAGAATATAACAAGAAAAAATAAAAATTCATTTATCAACAGTTTCAACTCTCAATCAAT
* * * *
20183969 TTCCAGAAGATAATAAAAAAAAACCTAAAACTAAAGCCCATTTCTCAATAATAAATCTGTAAAA
65 TTCCAGAAGATAACAAAAAAAAA-CTAAAACTAAAACCCACTTCTCAATAATAAATCTGCAAAA
20184033 CGTGATTTGG
Statistics
Matches: 118, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
147 82 0.69
148 36 0.31
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.28
Consensus pattern (146 bp):
ATTTCTAGAATATAACAAGAAAAAATAAAAATTCATTTATCAACAGTTTCAACTCTCAATCAATT
TCCAGAAGATAACAAAAAAAAACTAAAACTAAAACCCACTTCTCAATAATAAATCTGCAAAATGA
TCTTCGACACGCAAGC
Found at i:20188759 original size:25 final size:26
Alignment explanation
Indices: 20188731--20188792 Score: 81
Period size: 25 Copynumber: 2.3 Consensus size: 26
20188721 TAAACATATG
20188731 AATTATAAAACATGAAAATATA-AAT
1 AATTATAAAACATGAAAATATATAAT
* *
20188756 AATTATAAAATATGAATATATATAAT
1 AATTATAAAACATGAAAATATATAAT
20188782 ATATATATAAA
1 A-AT-TATAAA
20188793 CTATATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 20 0.62
26 4 0.12
27 2 0.06
28 6 0.19
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (26 bp):
AATTATAAAACATGAAAATATATAAT
Found at i:20188767 original size:17 final size:18
Alignment explanation
Indices: 20188745--20188791 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
20188735 ATAAAACATG
20188745 AAAATATAAATAAT-TAT
1 AAAATATAAATAATATAT
*
20188762 AAAATATGAAT-ATATAT
1 AAAATATAAATAATATAT
* *
20188779 AATATATATATAA
1 AAAATATAAATAA
20188792 ACTATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.08
17 21 0.88
18 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATATAAATAATATAT
Found at i:20188782 original size:15 final size:14
Alignment explanation
Indices: 20188719--20188783 Score: 55
Period size: 15 Copynumber: 4.7 Consensus size: 14
20188709 TATAAAAATG
20188719 TATAAACATATGAAT
1 TATAAA-ATATGAAT
*
20188734 TATAAAACATGAA-
1 TATAAAATATGAAT
* *
20188747 AATATAA-AT-AAT
1 TATAAAATATGAAT
20188759 TATAAAATATGAAT
1 TATAAAATATGAAT
*
20188773 ATATATAATAT
1 -TATAAAATAT
20188784 ATATATAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
11 2 0.05
12 7 0.17
13 7 0.17
14 9 0.22
15 15 0.38
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (14 bp):
TATAAAATATGAAT
Found at i:20188785 original size:11 final size:10
Alignment explanation
Indices: 20188765--20188803 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
20188755 TAATTATAAA
*
20188765 ATATGAATAT
1 ATATAAATAT
20188775 ATATAATATAT
1 ATATAA-ATAT
20188786 ATATAAACTAT
1 ATATAAA-TAT
20188797 ATATAAA
1 ATATAAA
20188804 AGAAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (10 bp):
ATATAAATAT
Found at i:20193883 original size:3 final size:3
Alignment explanation
Indices: 20193868--20193926 Score: 50
Period size: 3 Copynumber: 19.3 Consensus size: 3
20193858 GATAAGAAGA
** *
20193868 AAT AAT GAA- AAT AAT AAT AAT ACA- AAT AAT AAT AGG ATT AAT AAAT
1 AAT AAT -AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
20193914 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
20193927 TTATTATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
2 3 0.07
3 37 0.80
4 6 0.13
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:20194183 original size:18 final size:21
Alignment explanation
Indices: 20194148--20194191 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
20194138 CTTTTTTTAA
20194148 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGTAAAAAAT
*
20194169 AATCG-AAA-AAGAAAAAAAAT
1 AATCGTAAATAAG-TAAAAAAT
20194189 AAT
1 AAT
20194192 AAGCCACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 13 0.62
21 5 0.24
ACGTcount: A:0.68, C:0.05, G:0.09, T:0.18
Consensus pattern (21 bp):
AATCGTAAATAAGTAAAAAAT
Found at i:20194406 original size:19 final size:19
Alignment explanation
Indices: 20194382--20194435 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
20194372 AATCACATCT
*
20194382 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
20194401 TCTAAGATTGCATATCATC
1 TCTAAGATTGCATATCATA
*
20194420 CCTAAGATTGCATATC
1 TCTAAGATTGCATATC
20194436 CTCGAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.35
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:20194445 original size:17 final size:18
Alignment explanation
Indices: 20194404--20194445 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
20194394 TATCATATCT
*
20194404 AAGATTGCATATCATCCCT
1 AAGATTGCATATCA-CCCG
*
20194423 AAGATTGCATATC-CTCG
1 AAGATTGCATATCACCCG
20194440 AAGATT
1 AAGATT
20194446 ATGTTTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (18 bp):
AAGATTGCATATCACCCG
Found at i:20194634 original size:15 final size:14
Alignment explanation
Indices: 20194599--20194638 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
20194589 ATTAGGTGGG
20194599 TTTTAAATA-AA--
1 TTTTAAATATAATT
20194610 TTTTAAATATAATT
1 TTTTAAATATAATT
20194624 TTTTAAAATATAATT
1 TTTT-AAATATAATT
20194639 ACATGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.36
12 2 0.08
14 4 0.16
15 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTAAATATAATT
Found at i:20194901 original size:21 final size:22
Alignment explanation
Indices: 20194861--20194919 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
20194851 TTTTAATGAT
20194861 AATTATATTAATAATTTTATTA
1 AATTATATTAATAATTTTATTA
* *
20194883 AATTATA-TATTATTTTTATTA
1 AATTATATTAATAATTTTATTA
*
20194904 AATTGTATTTAATAAT
1 AATTATA-TTAATAAT
20194920 AATTATATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 18 0.60
22 7 0.23
23 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATTATATTAATAATTTTATTA
Found at i:20194959 original size:59 final size:59
Alignment explanation
Indices: 20194852--20194964 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
20194842 TAATTCATAT
* * * *
20194852 TTTAATGATAATTATATTAATAATTTTATTAAATTATATATTATTTTTATTAAATTGTA
1 TTTAATAATAATTATATTAATAATATTATTAAATTATATATTAATTTTAATAAATTGTA
20194911 TTTAATAATAATTATATTAA-AATATTATTAAATTAGT-TATTAAATTTTAATAAA
1 TTTAATAATAATTATATTAATAATATTATTAAATTA-TATATT-AATTTTAATAAA
20194965 ATTAAAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 18 0.38
59 30 0.62
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (59 bp):
TTTAATAATAATTATATTAATAATATTATTAAATTATATATTAATTTTAATAAATTGTA
Found at i:20194966 original size:23 final size:22
Alignment explanation
Indices: 20194911--20194968 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
20194901 TTAAATTGTA
20194911 TTTAATAATAATTATATTAAAAT
1 TTTAATAA-AATTATATTAAAAT
* *
20194934 ATT-ATTAAATTAGTTATT-AAAT
1 TTTAATAAAATTA--TATTAAAAT
20194956 TTTAATAAAATTA
1 TTTAATAAAATTA
20194969 AAATTTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 5 0.18
22 9 0.32
23 14 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTAATAAAATTATATTAAAAT
Found at i:20194970 original size:16 final size:16
Alignment explanation
Indices: 20194949--20194979 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20194939 TAAATTAGTT
*
20194949 ATTAAATTTTAATAAA
1 ATTAAAATTTAATAAA
20194965 ATTAAAATTTAATAA
1 ATTAAAATTTAATAA
20194980 CAATAATTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAAAATTTAATAAA
Found at i:20194978 original size:58 final size:58
Alignment explanation
Indices: 20194859--20194979 Score: 131
Period size: 58 Copynumber: 2.1 Consensus size: 58
20194849 TATTTTAATG
* * * ** *
20194859 ATAATTATATTAATAATTTTATTAAATTATATATTATTTTTATTAAATTGTATTTAATA
1 ATAATTATATTAATAATATTATTAAATTATATATTATTTTAATAAAATTAAAATT-ATA
20194918 ATAATTATATTAA-AATATTATTAAATTAGT-TATTAAATTTTAATAAAATTAAAATT-TA
1 ATAATTATATTAATAATATTATTAAATTA-TATATT--ATTTTAATAAAATTAAAATTATA
20194976 ATAA
1 ATAA
20194980 CAATAATTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
58 24 0.45
59 14 0.26
60 15 0.28
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (58 bp):
ATAATTATATTAATAATATTATTAAATTATATATTATTTTAATAAAATTAAAATTATA
Found at i:20195345 original size:18 final size:18
Alignment explanation
Indices: 20195322--20195356 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20195312 TAATTGTTTT
*
20195322 TAAAAATATATAAAATTA
1 TAAAAAAATATAAAATTA
*
20195340 TAAAAAAATTTAAAATT
1 TAAAAAAATATAAAATT
20195357 TGATTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAAAATATAAAATTA
Found at i:20195413 original size:14 final size:15
Alignment explanation
Indices: 20195394--20195431 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
20195384 TAATATTTTT
*
20195394 TTATAAACTA-AAAA
1 TTATAAAATACAAAA
20195408 TTATAAAATATCAAAA
1 TTATAAAATA-CAAAA
20195424 TTATAAAA
1 TTATAAAA
20195432 AAAACTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
16 12 0.57
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (15 bp):
TTATAAAATACAAAA
Found at i:20208529 original size:20 final size:20
Alignment explanation
Indices: 20208504--20208543 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20208494 CGTAAAATGA
*
20208504 TTTCTGGAAAATGGTTTACT
1 TTTCTGGAAAATGATTTACT
*
20208524 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
20208544 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:20208559 original size:14 final size:15
Alignment explanation
Indices: 20208483--20208559 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
20208473 GATTGCCAGT
* *
20208483 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
20208497 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
20208511 AAAATGGTTTACTTTTCTGT
1 AAAAT-G---A-TTTTCTGG
*
20208531 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
20208546 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
20208560 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
19 1 0.02
20 11 0.22
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:20228864 original size:16 final size:18
Alignment explanation
Indices: 20228836--20228873 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
20228826 CTAAATAATA
20228836 AAATATAATAATTA-TTT
1 AAATATAATAATTACTTT
20228853 AAATAT-ATAATTACTTT
1 AAATATAATAATTACTTT
20228870 AAAT
1 AAAT
20228874 TCTTAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATAATAATTACTTT
Found at i:20229369 original size:33 final size:33
Alignment explanation
Indices: 20229332--20229398 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
20229322 TTTTTAAATT
20229332 TAAATTTAATTATAAAAGTATATAAAATATCAA
1 TAAATTTAATTATAAAAGTATATAAAATATCAA
20229365 TAAATTTAATTATAAAAGTATATAAAATATCAA
1 TAAATTTAATTATAAAAGTATATAAAATATCAA
20229398 T
1 T
20229399 TGCAAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (33 bp):
TAAATTTAATTATAAAAGTATATAAAATATCAA
Found at i:20229659 original size:15 final size:15
Alignment explanation
Indices: 20229639--20229673 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20229629 GTCAGTCTCG
20229639 GGTTCAGATTTTTTA
1 GGTTCAGATTTTTTA
*
20229654 GGTTCAGGTTTTTTA
1 GGTTCAGATTTTTTA
*
20229669 AGTTC
1 GGTTC
20229674 GAGTCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.09, G:0.23, T:0.51
Consensus pattern (15 bp):
GGTTCAGATTTTTTA
Done.