Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 64 of 145
Found at i:21082976 original size:50 final size:50
Alignment explanation
Indices: 21082743--21083024 Score: 219
Period size: 50 Copynumber: 5.5 Consensus size: 50
21082733 AAAGAGATCT
* * * **
21082743 CATGTAAGACCATGTCTGGGACATGGCATTGACATCATTGAGATTATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCA-C--CGAG---ATGAGAACTCC
* * * ** * *
21082799 TATGTAATACCCTGTCTGGGACATGGTGTGGGAACCGAGATGA-AAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAA-CTCC
* * **
21082849 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCC
** *
21082899 CCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCC
* * * *** * *
21082949 CATGTAAGACCATATCTGGGATATGGCATTGG-AATTACA-GAAAACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC-TCC
*
21082998 CATGTAAGACCATTTCTGGGACATGGC
1 CATGTAAGACCATGTCTGGGACATGGC
21083025 TTTCGCATGT
Statistics
Matches: 187, Mismatches: 36, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
48 5 0.03
49 32 0.17
50 119 0.64
51 1 0.01
53 3 0.02
55 1 0.01
56 26 0.14
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCC
Found at i:21090740 original size:43 final size:41
Alignment explanation
Indices: 21090685--21090828 Score: 146
Period size: 43 Copynumber: 3.4 Consensus size: 41
21090675 ATGCCATATT
* *
21090685 CCAGATATGGTCTTACATGTCAATACATTTCGATGCCACTGTC
1 CCAGACATGGTCTTACATGT-AAT-CATTTCGATGCCAATGTC
* * * *
21090728 CCAGACAGGGTCTTATATG-ACTCATATACGATGCCAATGTC
1 CCAGACATGGTCTTACATGTAATCAT-TTCGATGCCAATGTC
* * *
21090769 CCAGACATGGTCTTACACGTTATCTCACTTCGATGCCAATGTC
1 CCAGACATGGTCTTACATG-TA-ATCATTTCGATGCCAATGTC
*
21090812 TCAGACATGGTCTTACA
1 CCAGACATGGTCTTACA
21090829 CGAAATCACA
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
40 3 0.04
41 31 0.36
43 47 0.55
44 4 0.05
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (41 bp):
CCAGACATGGTCTTACATGTAATCATTTCGATGCCAATGTC
Found at i:21098691 original size:16 final size:16
Alignment explanation
Indices: 21098664--21098706 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
21098654 TTTGTTGAAA
21098664 AATTTTAATTTTTATGG
1 AATTTT-ATTTTTATGG
*
21098681 AA-TTTATTTTTATGT
1 AATTTTATTTTTATGG
21098696 AATTTTATTTT
1 AATTTTATTTT
21098707 ATTTTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 11 0.46
16 11 0.46
17 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (16 bp):
AATTTTATTTTTATGG
Found at i:21100541 original size:15 final size:15
Alignment explanation
Indices: 21100517--21100553 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
21100507 GAACAAAATT
21100517 CTGAGAAAGAAGCTA
1 CTGAGAAAGAAGCTA
* *
21100532 CTGAGGAAGAATCTA
1 CTGAGAAAGAAGCTA
21100547 CTGAGAA
1 CTGAGAA
21100554 CATTGTCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.16
Consensus pattern (15 bp):
CTGAGAAAGAAGCTA
Found at i:21117936 original size:22 final size:22
Alignment explanation
Indices: 21117864--21117943 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
21117854 GGACCTTAGC
21117864 GTGCTCTCTGATTATTAGCACATTA
1 GTGCTCTCTG--TA-TAGCACATTA
* * * **
21117889 GTGCTCTCCGTTTAACACATCC
1 GTGCTCTCTGTATAGCACATTA
*
21117911 GTGCTCTCTGTATAGCACTTTA
1 GTGCTCTCTGTATAGCACATTA
21117933 GTGCTCTCTGT
1 GTGCTCTCTGT
21117944 TCAATAGTGC
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
22 34 0.77
23 1 0.02
25 9 0.20
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.39
Consensus pattern (22 bp):
GTGCTCTCTGTATAGCACATTA
Found at i:21120306 original size:40 final size:40
Alignment explanation
Indices: 21120244--21120483 Score: 270
Period size: 40 Copynumber: 6.0 Consensus size: 40
21120234 ATTGTATGAA
*
21120244 TGCACATACGTGCCCC-AGTTTGTACTTCGGTACCCCTGAT
1 TGCACATACGTGCCCCTA-TTTGTACTTCGATACCCCTGAT
* * *
21120284 TGCACATACGTGCTCCTATTTGTACTTCGATACCCCTAAA
1 TGCACATACGTGCCCCTATTTGTACTTCGATACCCCTGAT
* * * * *
21120324 TGCACATTCATGCCCCTATTTGTATTTCGGTACCGCTGAT
1 TGCACATACGTGCCCCTATTTGTACTTCGATACCCCTGAT
* *
21120364 TGCACATATGTGCCCCTATTTGTACTTCAATACCCCCTGAAT
1 TGCACATACGTGCCCCTATTTGTACTTCGATA-CCCCTG-AT
*
21120406 T-CACATACGTGCCCCTTTTTGTACTTC-AGTACCCCTGAT
1 TGCACATACGTGCCCCTATTTGTACTTCGA-TACCCCTGAT
** ** *
21120445 TGCACATTTGTGCCTATGTTTGTACTTCGATACCCCTGA
1 TGCACATACGTGCCCCTATTTGTACTTCGATACCCCTGA
21120484 ATGTACTCAA
Statistics
Matches: 168, Mismatches: 26, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
39 3 0.02
40 129 0.77
41 33 0.20
42 3 0.02
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (40 bp):
TGCACATACGTGCCCCTATTTGTACTTCGATACCCCTGAT
Found at i:21120382 original size:80 final size:80
Alignment explanation
Indices: 21120240--21120486 Score: 334
Period size: 80 Copynumber: 3.1 Consensus size: 80
21120230 AATTATTGTA
* *
21120240 TGAATGCACATACGTGCCCC-AGTTTGTACTTCGGTACCCCTGATTGCACATACGTGCTCCTATT
1 TGAATGCACATACGTGCCCCTA-TTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATT
21120304 TGTACTTCGATACCCC
65 TGTACTTCGATACCCC
* * * * *
21120320 TAAATGCACATTCATGCCCCTATTTGTATTTCGGTACCGCTGATTGCACATATGTGCCCCTATTT
1 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTT
*
21120385 GTACTTCAATACCCCC
66 GTACTTCGATA-CCCC
* * * * ** *
21120401 TGAATTCACATACGTGCCCCTTTTTGTACTTCAGTACCCCTGATTGCACATTTGTGCCTATGTTT
1 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTT
21120466 GTACTTCGATACCCC
66 GTACTTCGATACCCC
21120481 TGAATG
1 TGAATG
21120487 TACTCAATAC
Statistics
Matches: 143, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
80 75 0.52
81 68 0.48
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (80 bp):
TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTT
GTACTTCGATACCCC
Found at i:21120490 original size:20 final size:20
Alignment explanation
Indices: 21120465--21120510 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
21120455 TGCCTATGTT
*
21120465 TGTACTTCGATACCCCTGAA
1 TGTACTTCAATACCCCTGAA
21120485 TGTAC-TCAATACCCCTGAA
1 TGTACTTCAATACCCCTGAA
*
21120504 TGCACTT
1 TGTACTT
21120511 ACGTGCCCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.30
Consensus pattern (20 bp):
TGTACTTCAATACCCCTGAA
Found at i:21120542 original size:58 final size:60
Alignment explanation
Indices: 21120425--21120543 Score: 145
Period size: 58 Copynumber: 2.0 Consensus size: 60
21120415 TGCCCCTTTT
* * * * *
21120425 TGTACTTCAGTACCCCTGATTGCACATTTGTGCCTATGTTTGTACTTCGATACCCCTGAA
1 TGTACTTCAATACCCCTGAATGCACATTCGTGCCTATGTTTATACTTCGATAACCCTGAA
* *
21120485 TGTAC-TCAATACCCCTGAATGCAC-TTACGTGCC-CTGTTTATACTTCGATAACTCTGAA
1 TGTACTTCAATACCCCTGAATGCACATT-CGTGCCTATGTTTATACTTCGATAACCCTGAA
21120543 T
1 T
21120544 TATATAGTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
58 24 0.47
59 22 0.43
60 5 0.10
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (60 bp):
TGTACTTCAATACCCCTGAATGCACATTCGTGCCTATGTTTATACTTCGATAACCCTGAA
Found at i:21129690 original size:9 final size:9
Alignment explanation
Indices: 21129661--21129690 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
21129651 GAAATTTTAC
21129661 AATTCGAAT
1 AATTCGAAT
*
21129670 AACTCGAAT
1 AATTCGAAT
21129679 AATTCGAAT
1 AATTCGAAT
21129688 AAT
1 AAT
21129691 AGATTGGTGT
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:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:21129792 original size:20 final size:20
Alignment explanation
Indices: 21129769--21129811 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
21129759 AAAAATTAAA
21129769 AAAAAATCAAAATAATTTTT
1 AAAAAATCAAAATAATTTTT
** *
21129789 AAAATTTTAAAATAATTTTT
1 AAAAAATCAAAATAATTTTT
21129809 AAA
1 AAA
21129812 GTTCAAAATA
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:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAAATCAAAATAATTTTT
Found at i:21133356 original size:31 final size:31
Alignment explanation
Indices: 21133320--21133378 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
21133310 AGGCATAAGC
*
21133320 TAAATGTTGAGAACTTATTTGGGTACAATTT
1 TAAATGTTGAGAACTTATTTGAGTACAATTT
21133351 TAAATGTTGAGAACTTATTTGAGTACAA
1 TAAATGTTGAGAACTTATTTGAGTACAA
21133379 GATAAAAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.39
Consensus pattern (31 bp):
TAAATGTTGAGAACTTATTTGAGTACAATTT
Found at i:21138868 original size:25 final size:24
Alignment explanation
Indices: 21138804--21138869 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
21138794 TTAAATATAA
*
21138804 AATATTTTATATTAAA-TTAATTT
1 AATATTTTATATTAAATTTAATAT
**
21138827 AATATTTTATAAAAAATTTGGAA-AT
1 AATATTTTATATTAAATTT--AATAT
21138852 AATATTTTATATTAAATT
1 AATATTTTATATTAAATT
21138870 ATATTAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 14 0.40
24 2 0.06
25 17 0.49
26 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
AATATTTTATATTAAATTTAATAT
Found at i:21146155 original size:11 final size:11
Alignment explanation
Indices: 21146135--21146168 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
21146125 GCATCCAAAT
21146135 CAAG-CATAAA
1 CAAGCCATAAA
21146145 CAAGCCATAAA
1 CAAGCCATAAA
21146156 CAAGCCATAAA
1 CAAGCCATAAA
21146167 CA
1 CA
21146169 TATGGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.56, C:0.26, G:0.09, T:0.09
Consensus pattern (11 bp):
CAAGCCATAAA
Found at i:21147268 original size:25 final size:25
Alignment explanation
Indices: 21147172--21147264 Score: 105
Period size: 25 Copynumber: 3.7 Consensus size: 25
21147162 GCTGTGAATT
* *
21147172 GGTATACTCACTCTAGTTATAGATC
1 GGTATACTCACACGAGTTATAGATC
* *
21147197 GGTATACTCTCACGAGTTATAAATC
1 GGTATACTCACACGAGTTATAGATC
* * *
21147222 AGTATCCTCACACGAGTTGTAGATC
1 GGTATACTCACACGAGTTATAGATC
* *
21147247 GGTATGCTCCCACGAGTT
1 GGTATACTCACACGAGTT
21147265 GTAGGTCGAA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (25 bp):
GGTATACTCACACGAGTTATAGATC
Found at i:21154579 original size:25 final size:25
Alignment explanation
Indices: 21154526--21154640 Score: 104
Period size: 25 Copynumber: 4.6 Consensus size: 25
21154516 TCCTGTACAT
* * * * *
21154526 GTATGCTCATACGATCTGTCAACCA
1 GTATGCTCACACGAGCTGTAAATCG
* ** * *
21154551 GTATGCTCGCTTGAGCTATAGATCG
1 GTATGCTCACACGAGCTGTAAATCG
* *
21154576 GTATGCTCTCACGAGCTGTAAATTG
1 GTATGCTCACACGAGCTGTAAATCG
*
21154601 GTATGCTCACACGAGCTGTATATCG
1 GTATGCTCACACGAGCTGTAAATCG
*
21154626 GTATGCTCTCACGAG
1 GTATGCTCACACGAG
21154641 TTGTGGGTCA
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 70 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATCG
Found at i:21179609 original size:40 final size:38
Alignment explanation
Indices: 21179506--21179700 Score: 124
Period size: 38 Copynumber: 5.0 Consensus size: 38
21179496 TACAATGAAT
* * * * *
21179506 TGACACAAAGACTACTAGGCTCAAAGCCTGATATAACAC
1 TGACACAAAGCCTGCTAGGCACAAAGCATGA-ATATCAC
* * * *
21179545 ATCGGCACGAAGCCTGCTAAGCACAAAGCTTGATATAATACAC
1 -T-GACACAAAGCCTGCTAGGCACAAAGCATGA-AT-AT-CAC
* *
21179588 TGACA-AAAGCCTGGTAGGCACAGAGCATGAATATCAC
1 TGACACAAAGCCTGCTAGGCACAAAGCATGAATATCAC
* * ** **
21179625 TGGCACAAAGCCTGCTAGGGACGGAGCCCGAATATCA-
1 TGACACAAAGCCTGCTAGGCACAAAGCATGAATATCAC
** **
21179662 TCGACACAAAGCCTGCTAAACACAAAGCCCGAATATCAC
1 T-GACACAAAGCCTGCTAGGCACAAAGCATGAATATCAC
21179701 CACTTTTCTA
Statistics
Matches: 123, Mismatches: 26, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
37 8 0.07
38 58 0.47
39 2 0.02
40 21 0.17
41 29 0.24
42 2 0.02
43 3 0.02
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (38 bp):
TGACACAAAGCCTGCTAGGCACAAAGCATGAATATCAC
Found at i:21181707 original size:40 final size:41
Alignment explanation
Indices: 21181646--21181748 Score: 154
Period size: 40 Copynumber: 2.5 Consensus size: 41
21181636 AGAAAAATGA
* *
21181646 TGAATTGCACATATGTTCCCCTATTTGTACTTCGATACCC-
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCT
*
21181686 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCT
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCT
* *
21181727 TGAATTACACACACGTGCCCCT
1 TGAATTGCACATACGTGCCCCT
21181749 GATTAGACTT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 37 0.65
41 20 0.35
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCT
Found at i:21181759 original size:41 final size:40
Alignment explanation
Indices: 21181663--21181759 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 40
21181653 CACATATGTT
* * * *
21181663 CCCCTATTTGTACTTCGATACCCTGAATTGCACATACGTG
1 CCCCTGTTAGTACTTCGATACCCTGAATTACACACACGTG
*
21181703 CCCCTGTTTGTACTTCGATACCCTTGAATTACACACACGTG
1 CCCCTGTTAGTACTTCGATACCC-TGAATTACACACACGTG
21181744 CCCCTGATTAG-ACTTC
1 CCCCTG-TTAGTACTTC
21181760 AAAAATTCTG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 22 0.43
41 26 0.51
42 3 0.06
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.32
Consensus pattern (40 bp):
CCCCTGTTAGTACTTCGATACCCTGAATTACACACACGTG
Found at i:21190461 original size:27 final size:27
Alignment explanation
Indices: 21190425--21190610 Score: 199
Period size: 27 Copynumber: 7.1 Consensus size: 27
21190415 AGAGGTCAAT
*
21190425 AAATGACCAAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCTATAGGGTA
*
21190452 AAATGACC-AAA-A----T-TAAGGTA
1 AAATGACCGAAATACCCCTATAGGGTA
* * *
21190472 AAATGATCGAGATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCTATAGGGTA
* * *
21190499 AACTGA-CTAAGATACCCCCATAGGGTA
1 AAATGACCGAA-ATACCCCTATAGGGTA
*
21190526 AAATGACTGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCTATAGGGTA
*
21190553 AGATGACCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCTATAGGGTA
* *
21190580 AGATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCTATAGGGTA
21190607 AAAT
1 AAAT
21190611 AACTGTTATA
Statistics
Matches: 134, Mismatches: 16, Indels: 18
0.80 0.10 0.11
Matches are distributed among these distances:
20 13 0.10
21 3 0.02
22 1 0.01
25 1 0.01
26 5 0.04
27 109 0.81
28 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCCTATAGGGTA
Found at i:21190770 original size:26 final size:26
Alignment explanation
Indices: 21190740--21190794 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
21190730 TGGAGGACGT
* * *
21190740 ATACTGTTACTGGCAGCTTTGTTGCG
1 ATACTGTTACTGCCAACTTTGCTGCG
21190766 ATACTGTTACTGCCAACTTTGCTGCG
1 ATACTGTTACTGCCAACTTTGCTGCG
21190792 ATA
1 ATA
21190795 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (26 bp):
ATACTGTTACTGCCAACTTTGCTGCG
Found at i:21190941 original size:28 final size:28
Alignment explanation
Indices: 21190897--21190955 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
21190887 ATTGCACTGT
21190897 ACTATTACTATACTGGGCTAAGGCCCAC
1 ACTATTACTATACTGGGCTAAGGCCCAC
* *
21190925 ACTATTACTGTATTGGGCTAAGGCCCAC
1 ACTATTACTATACTGGGCTAAGGCCCAC
21190953 ACT
1 ACT
21190956 GTATAATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (28 bp):
ACTATTACTATACTGGGCTAAGGCCCAC
Found at i:21197634 original size:12 final size:12
Alignment explanation
Indices: 21197604--21197642 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
21197594 ACTCGCTTCT
* *
21197604 TTACTTATTCAC
1 TTACTTGTTTAC
21197616 TTACTTGTTTAC
1 TTACTTGTTTAC
*
21197628 TTACTTGCTTAC
1 TTACTTGTTTAC
21197640 TTA
1 TTA
21197643 AATAACTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.54
Consensus pattern (12 bp):
TTACTTGTTTAC
Found at i:21197959 original size:50 final size:50
Alignment explanation
Indices: 21197891--21198036 Score: 193
Period size: 50 Copynumber: 2.9 Consensus size: 50
21197881 TTTTCTGTAC
* * **
21197891 TGCCAATGCCATATCCCAGATATGGTCTTACATGCGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGCGACCTCTCATATCGG
* ** * *
21197941 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGCGACCTCTCATATCGG
* *
21197991 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGCGACCTCTCATA
21198037 ATCTCAATGA
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGCGACCTCTCATATCGG
Found at i:21207113 original size:2 final size:2
Alignment explanation
Indices: 21207106--21207131 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21207096 AGCATATAAC
21207106 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
21207132 TTACCTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21207302 original size:2 final size:2
Alignment explanation
Indices: 21207295--21207320 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21207285 AACATATAAC
21207295 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
21207321 TTACCTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21207418 original size:189 final size:190
Alignment explanation
Indices: 21207087--21207466 Score: 753
Period size: 189 Copynumber: 2.0 Consensus size: 190
21207077 GGGAAAAAAT
21207087 GATACTTGAAGCATATAACATATATATATATATATATATATATATTTACCTTGACATCTGTAAGA
1 GATACTTGAAGCATATAACATATATATATATATATATATATATATTTACCTTGACATCTGTAAGA
21207152 TCCATGTTGTTCTCCCTTAGAAATGAAATGAAATCATTAAAATTTTGTTCTGTAGGTCGATAATG
66 TCCATGTTGTTCTCCCTTAGAAATGAAATGAAATCATTAAAATTTTGTTCTGTAGGTCGATAATG
21207217 ACCACTGTGAGGCCAAACTGCCTGTTGAACAGAGTAATAGTAAGTGTTGTCAAGAGAGTG
131 ACCACTGTGAGGCCAAACTGCCTGTTGAACAGAGTAATAGTAAGTGTTGTCAAGAGAGTG
21207277 GATACTTGAA-CATATAACATATATATATATATATATATATATATTTACCTTGACATCTGTAAGA
1 GATACTTGAAGCATATAACATATATATATATATATATATATATATTTACCTTGACATCTGTAAGA
21207341 TCCATGTTGTTCTCCCTTAGAAATGAAATGAAATCATTAAAATTTTGTTCTGTAGGTCGATAATG
66 TCCATGTTGTTCTCCCTTAGAAATGAAATGAAATCATTAAAATTTTGTTCTGTAGGTCGATAATG
21207406 ACCACTGTGAGGCCAAACTGCCTGTTGAACAGAGTAATAGTAAGTGTTGTCAAGAGAGTG
131 ACCACTGTGAGGCCAAACTGCCTGTTGAACAGAGTAATAGTAAGTGTTGTCAAGAGAGTG
21207466 G
1 G
21207467 CATAACAAAA
Statistics
Matches: 190, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
189 180 0.95
190 10 0.05
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (190 bp):
GATACTTGAAGCATATAACATATATATATATATATATATATATATTTACCTTGACATCTGTAAGA
TCCATGTTGTTCTCCCTTAGAAATGAAATGAAATCATTAAAATTTTGTTCTGTAGGTCGATAATG
ACCACTGTGAGGCCAAACTGCCTGTTGAACAGAGTAATAGTAAGTGTTGTCAAGAGAGTG
Found at i:21212470 original size:84 final size:85
Alignment explanation
Indices: 21212361--21212529 Score: 331
Period size: 84 Copynumber: 2.0 Consensus size: 85
21212351 TATAGCAAAA
21212361 TCTTAATTAAGTGGAATTAAATTTTTTGTATATTAAAATTTTATGTAAATTGTAAAACACTTTTT
1 TCTTAATTAAGTGGAATTAAATTTTTTGTATATTAAAATTTTATGTAAATTGTAAAACACTTTTT
21212426 ATTATTACGTTTTTGAAATG
66 ATTATTACGTTTTTGAAATG
21212446 TCTTAATTAA-TGGAATTAAATTTTTTGTATATTAAAATTTTATGTAAATTGTAAAACACTTTTT
1 TCTTAATTAAGTGGAATTAAATTTTTTGTATATTAAAATTTTATGTAAATTGTAAAACACTTTTT
21212510 ATTATTACGTTTTTGAAATG
66 ATTATTACGTTTTTGAAATG
21212530 CAACCATAAT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 74 0.88
85 10 0.12
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (85 bp):
TCTTAATTAAGTGGAATTAAATTTTTTGTATATTAAAATTTTATGTAAATTGTAAAACACTTTTT
ATTATTACGTTTTTGAAATG
Found at i:21212613 original size:11 final size:11
Alignment explanation
Indices: 21212597--21212622 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21212587 TACAAAGTTT
21212597 ATTATAATAAA
1 ATTATAATAAA
21212608 ATTATAATAAA
1 ATTATAATAAA
21212619 ATTA
1 ATTA
21212623 ATTATGTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTATAATAAA
Found at i:21212724 original size:14 final size:14
Alignment explanation
Indices: 21212705--21212734 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21212695 TTCACTGTTA
*
21212705 TGTCTTTTATATTT
1 TGTCTTTCATATTT
21212719 TGTCTTTCATATTT
1 TGTCTTTCATATTT
21212733 TG
1 TG
21212735 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:0.13, C:0.10, G:0.10, T:0.67
Consensus pattern (14 bp):
TGTCTTTCATATTT
Found at i:21216906 original size:29 final size:29
Alignment explanation
Indices: 21216873--21216949 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
21216863 ATAGGCGATC
*
21216873 ATCGAATATGAAAAGGGATAGCTTCAGTT
1 ATCGAATATGAAAAGGGATAGCTTCAGCT
* *
21216902 ATCG-ATCATGAAAAGGGATAGTTTCGGCT
1 ATCGAAT-ATGAAAAGGGATAGCTTCAGCT
*
21216931 ATCGATTATGAAAAGGGAT
1 ATCGAATATGAAAAGGGAT
21216950 GGTGACGACC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 2 0.05
29 39 0.93
30 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.27
Consensus pattern (29 bp):
ATCGAATATGAAAAGGGATAGCTTCAGCT
Found at i:21217003 original size:30 final size:29
Alignment explanation
Indices: 21216902--21217108 Score: 207
Period size: 29 Copynumber: 7.1 Consensus size: 29
21216892 AGCTTCAGTT
* * ** * *
21216902 ATCGATCATGAAAAGGGATAGTTTCGGCT
1 ATCGATTATGAAAAGGGATGGTGACGACC
21216931 ATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
* * *
21216960 ATCAAGTATGAAAAGGGATGGTGATGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
**
21216989 ATCGATTAATGAAAAGGGATGGTTTCGACC
1 ATCGATT-ATGAAAAGGGATGGTGACGACC
* *
21217019 ATCAAGTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
** *
21217048 ATCGATTAATGAAAAGGGATGGTTTCAACC
1 ATCGATT-ATGAAAAGGGATGGTGACGACC
* * * * *
21217078 ATGGAATATGAAAATGGATGGTTACAACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
21217107 AT
1 AT
21217109 TGTTTAGCAC
Statistics
Matches: 149, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
29 101 0.68
30 48 0.32
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.24
Consensus pattern (29 bp):
ATCGATTATGAAAAGGGATGGTGACGACC
Found at i:21217018 original size:59 final size:59
Alignment explanation
Indices: 21216931--21217108 Score: 261
Period size: 59 Copynumber: 3.0 Consensus size: 59
21216921 AGTTTCGGCT
** *
21216931 ATCGATT-ATGAAAAGGGATGGTGACGACCATCAAGTATGAAAAGGGATGGTGATGACC
1 ATCGATTAATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACC
21216989 ATCGATTAATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACC
1 ATCGATTAATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACC
* * * * *
21217048 ATCGATTAATGAAAAGGGATGGTTTCAACCATGGAA-TATGAAAATGGATGGTTACAACC
1 ATCGATTAATGAAAAGGGATGGTTTCGACCAT-CAAGTATGAAAAGGGATGGTGACGACC
21217107 AT
1 AT
21217109 TGTTTAGCAC
Statistics
Matches: 110, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
58 7 0.06
59 101 0.92
60 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.23
Consensus pattern (59 bp):
ATCGATTAATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACC
Found at i:21217029 original size:88 final size:89
Alignment explanation
Indices: 21216909--21217070 Score: 254
Period size: 88 Copynumber: 1.8 Consensus size: 89
21216899 GTTATCGATC
* * * *
21216909 ATGAAAAGGGATAGTTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCAAGT-ATGAAA
1 ATGAAAAGGGATAGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACCATCAAGTAATGAAA
21216973 AGGGATGGTGATGACCATCGATTA
66 AGGGATGGTGATGACCATCGATTA
* * *
21216997 ATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACCATCGATTAATGAAA
1 ATGAAAAGGGATAGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACCATCAAGTAATGAAA
21217062 AGGGATGGT
66 AGGGATGGT
21217071 TTCAACCATG
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
88 51 0.77
89 15 0.23
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.23
Consensus pattern (89 bp):
ATGAAAAGGGATAGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACCATCAAGTAATGAAA
AGGGATGGTGATGACCATCGATTA
Found at i:21217089 original size:88 final size:88
Alignment explanation
Indices: 21216909--21217100 Score: 244
Period size: 88 Copynumber: 2.2 Consensus size: 88
21216899 GTTATCGATC
* * * * *
21216909 ATGAAAAGGGATAGTTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATCAAGTATGAAAA
1 ATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACCATCAAGTATGAAAA
* *
21216974 GGGATGGTGATGACCATCGATTA
66 GGGATGGTGATAACCATCGAATA
* *
21216997 ATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACCATCGATTAATGAAA
1 ATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACCATCAAGT-ATGAAA
* *
21217062 AGGGATGGT-TTCAACCATGGAAT-
65 AGGGATGGTGAT-AACCATCGAATA
*
21217085 ATGAAAATGGATGGTT
1 ATGAAAAGGGATGGTT
21217101 ACAACCATTG
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
88 67 0.74
89 23 0.26
ACGTcount: A:0.36, C:0.11, G:0.29, T:0.24
Consensus pattern (88 bp):
ATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACCATCAAGTATGAAAA
GGGATGGTGATAACCATCGAATA
Found at i:21219973 original size:20 final size:19
Alignment explanation
Indices: 21219944--21219994 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
21219934 TAGAAAATGA
*
21219944 TTTCTGGAAAATTACTTAC
1 TTTCTGGAAAATGACTTAC
21219963 TTTCTTGGAAAATGACTTAC
1 TTTC-TGGAAAATGACTTAC
21219983 TTTCCTGGAAAA
1 TTT-CTGGAAAA
21219995 GTTAATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 24 0.83
21 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (19 bp):
TTTCTGGAAAATGACTTAC
Found at i:21220451 original size:15 final size:15
Alignment explanation
Indices: 21220426--21220488 Score: 58
Period size: 17 Copynumber: 4.0 Consensus size: 15
21220416 TTAATATTGA
21220426 TATTA-TAATATATT
1 TATTATTAATATATT
21220440 TATTATTAATATATGT
1 TATTATTAATATAT-T
21220456 ATATT-TGTAATAAATATT
1 -TATTAT-TAAT--ATATT
*
21220474 TATTATTAAAATATT
1 TATTATTAATATATT
21220489 AATATTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
14 5 0.12
15 13 0.32
16 2 0.05
17 15 0.37
18 2 0.05
19 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TATTATTAATATATT
Found at i:21228064 original size:24 final size:25
Alignment explanation
Indices: 21228019--21228069 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
21228009 ATTTTTGGGA
*
21228019 AAATTAATTTTGATTAAGTAAAATT
1 AAATTAATTTAGATTAAGTAAAATT
*
21228044 AAATTAA-TTAGATTAATTAAAATT
1 AAATTAATTTAGATTAAGTAAAATT
21228068 AA
1 AA
21228070 TATGATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (25 bp):
AAATTAATTTAGATTAAGTAAAATT
Found at i:21228579 original size:13 final size:13
Alignment explanation
Indices: 21228544--21228581 Score: 67
Period size: 14 Copynumber: 2.8 Consensus size: 13
21228534 GAGATATTTG
21228544 TAATTTGAAAACT
1 TAATTTGAAAACT
21228557 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
21228571 TAATTTGAAAA
1 TAATTTGAAAA
21228582 TTTGGAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:21228900 original size:34 final size:34
Alignment explanation
Indices: 21228818--21229096 Score: 380
Period size: 34 Copynumber: 8.1 Consensus size: 34
21228808 TGCACTTGTC
* * * *
21228818 TTTCTTACAGGGAATATTTTCTGTTCACGCATTA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACGCATCA
* * * *
21228852 TTTTGTTGCAGGGAATCTCTCATGTTCACACATCA
1 -TTTCTTGCAGGGAATCTTTCCTGTTCACGCATCA
21228887 TTTCTTGCAGGGAATCTTTCCTGTTCACGCATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACGCATCA
21228921 TTTCTTGCAGGGAATCTTTCCTGTTCACGCATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACGCATCA
21228955 TTTCTTGCAGGGAATCTTTCCTGTTCACGCATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACGCATCA
*
21228989 TTTCTTGCAGGGAATCTTTCCTGTTCACGCATTA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACGCATCA
* * *
21229023 TTTTGTTGCAGGGAATCTCT-CTGGTTCACACATCA
1 -TTTCTTGCAGGGAATCTTTCCT-GTTCACGCATCA
* * **
21229058 TTTCTTGCAGGGAATCTCTCCTATTCATACATCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACGCATCA
21229092 TTTCT
1 TTTCT
21229097 GGTATTATTT
Statistics
Matches: 221, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
34 166 0.75
35 55 0.25
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (34 bp):
TTTCTTGCAGGGAATCTTTCCTGTTCACGCATCA
Found at i:21231953 original size:21 final size:21
Alignment explanation
Indices: 21231929--21231968 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
21231919 AATTGCTGAT
21231929 TCTATTTATTTTTTG-ATTTGA
1 TCTA-TTATTTTTTGTATTTGA
*
21231950 TCTATTCTTTTTTGTATTT
1 TCTATTATTTTTTGTATTT
21231969 CTCTTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (21 bp):
TCTATTATTTTTTGTATTTGA
Found at i:21235464 original size:15 final size:15
Alignment explanation
Indices: 21235444--21235475 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21235434 CATTTCACTA
*
21235444 TTATGTCTTTTCTAT
1 TTATGTCTTTTATAT
21235459 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
21235474 TT
1 TT
21235476 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.09, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:21235845 original size:15 final size:15
Alignment explanation
Indices: 21235825--21235856 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21235815 CATTTCACTA
*
21235825 TTATGTCTTTTCTAT
1 TTATGTCTTTTATAT
21235840 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
21235855 TT
1 TT
21235857 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.09, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:21243302 original size:10 final size:9
Alignment explanation
Indices: 21243262--21243299 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
21243252 TCGTAATTAG
21243262 ATAAAATAA
1 ATAAAATAA
*
21243271 TTAAAATAA
1 ATAAAATAA
21243280 ATAGAAATAA
1 ATA-AAATAA
21243290 ATAAAATAA
1 ATAAAATAA
21243299 A
1 A
21243300 ATATTACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (9 bp):
ATAAAATAA
Found at i:21245761 original size:36 final size:36
Alignment explanation
Indices: 21245716--21245794 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
21245706 GCTACAAAAG
*
21245716 AAGTAATATGGCTTTCAAAGTTCCTTACAGATCTAA
1 AAGTCATATGGCTTTCAAAGTTCCTTACAGATCTAA
21245752 AAGTCATATGGCTTTCAAAGTTCCTTACAGATCTAA
1 AAGTCATATGGCTTTCAAAGTTCCTTACAGATCTAA
21245788 AAGTCAT
1 AAGTCAT
21245795 TCCTAGTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (36 bp):
AAGTCATATGGCTTTCAAAGTTCCTTACAGATCTAA
Found at i:21247486 original size:19 final size:19
Alignment explanation
Indices: 21247462--21247498 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21247452 TAATTGGGAC
*
21247462 ATTAATTTAATTTGTTTAA
1 ATTAATTTAATATGTTTAA
21247481 ATTAATTTAATATGTTTA
1 ATTAATTTAATATGTTTA
21247499 TTTTTGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTAATTTAATATGTTTAA
Found at i:21249996 original size:5 final size:5
Alignment explanation
Indices: 21249986--21250011 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21249976 TGAGCATTCG
21249986 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
21250012 AATTTTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:21250936 original size:9 final size:9
Alignment explanation
Indices: 21250919--21250949 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
21250909 TCGAGTTGAT
21250919 TCGAATAAC
1 TCGAATAAC
*
21250928 TCGATTAAC
1 TCGAATAAC
21250937 TCGAATAAC
1 TCGAATAAC
21250946 TCGA
1 TCGA
21250950 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:21257381 original size:522 final size:522
Alignment explanation
Indices: 21256397--21257440 Score: 2079
Period size: 522 Copynumber: 2.0 Consensus size: 522
21256387 GAGATTTAAG
21256397 TGTTCCATTGTTGGGGTCTCTTGTCCGCGCAGTGGCTGGGCTTGCTATCTTAGCAATGGTCTTTT
1 TGTTCCATTGTTGGGGTCTCTTGTCCGCGCAGTGGCTGGGCTTGCTATCTTAGCAATGGTCTTTT
21256462 ATTTTTAGTTGACCTTTTATATGAACCCATAGAGATAGAAGAAAATTCTTGCGCACATTTTTTGA
66 ATTTTTAGTTGACCTTTTATATGAACCCATAGAGATAGAAGAAAATTCTTGCGCACATTTTTTGA
21256527 ATGGCTTAAACATAAAATTAATATTTCAACTTGTCTATTTCGTATTTAAGGTTTTTTTTTTCTTT
131 ATGGCTTAAACATAAAATTAATATTTCAACTTGTCTATTTCGTATTTAAGGTTTTTTTTTTCTTT
21256592 GTCTCATATTAAATATCCTAATTTTTTTGTCAACTAAATTAATATTTTTATATAATACCGCTAAA
196 GTCTCATATTAAATATCCTAATTTTTTTGTCAACTAAATTAATATTTTTATATAATACCGCTAAA
21256657 TTTAAGATAAATGACAAAATAAGATTATGACAAATAGCATATTAAAATATATCCAATATTTGACA
261 TTTAAGATAAATGACAAAATAAGATTATGACAAATAGCATATTAAAATATATCCAATATTTGACA
21256722 AACAAAATATTTCCATATTAAAAAAAAACTTCCTAGCTGAAATCTTAACCTAAAAGAAAACAAGT
326 AACAAAATATTTCCATATTAAAAAAAAACTTCCTAGCTGAAATCTTAACCTAAAAGAAAACAAGT
21256787 ACAGATAATACAAAAGTGATTATTTTTGTAATTTATCCTAATCTAATATATATATATATATATAT
391 ACAGATAATACAAAAGTGATTATTTTTGTAATTTATCCTAATCTAATATATATATATATATATAT
21256852 TAAAAATTAATAAAAATATTTTAAAAATATATTTCCACTTTTTTCCTTTGTTCTTCTTTTAGGTT
456 TAAAAATTAATAAAAATATTTTAAAAATATATTTCCACTTTTTTCCTTTGTTCTTCTTTTAGGTT
21256917 TT
521 TT
21256919 TGTTCCATTGTTGGGGTCTCTTGTCCGCGCAGTGGCTGGGCTTGCTATCTTAGCAATGGTCTTTT
1 TGTTCCATTGTTGGGGTCTCTTGTCCGCGCAGTGGCTGGGCTTGCTATCTTAGCAATGGTCTTTT
21256984 ATTTTTAGTTGACCTTTTATATGAACCCATAGAGATAGAAGAAAATTCTTGCGCACATTTTTTGA
66 ATTTTTAGTTGACCTTTTATATGAACCCATAGAGATAGAAGAAAATTCTTGCGCACATTTTTTGA
21257049 ATGGCTTAAACATAAAATTAATATTTCAACTTGTCTATTTCGTATTTAAGGTTTTTTTTTTCTTT
131 ATGGCTTAAACATAAAATTAATATTTCAACTTGTCTATTTCGTATTTAAGGTTTTTTTTTTCTTT
21257114 GTCTCATATTAAATATCCTAATTTTTTTGTCAACTAAATTAATATTTTTATATAATACCGCTAAA
196 GTCTCATATTAAATATCCTAATTTTTTTGTCAACTAAATTAATATTTTTATATAATACCGCTAAA
21257179 TTTAAGATAAATGACAAAATAAGATTATGACAAATAGCATATTAAAATATATCCAATATTTGACA
261 TTTAAGATAAATGACAAAATAAGATTATGACAAATAGCATATTAAAATATATCCAATATTTGACA
21257244 AACAAAATATTTCCATATTAAAAAAAAACTTCCTAGCTGAAATCTTAACCTAAAAGAAAACAAGT
326 AACAAAATATTTCCATATTAAAAAAAAACTTCCTAGCTGAAATCTTAACCTAAAAGAAAACAAGT
21257309 ACAGATAATACAAAAGTGATTATTTTTGTAATTTATCCTAATCTAATATATATATATATATATAT
391 ACAGATAATACAAAAGTGATTATTTTTGTAATTTATCCTAATCTAATATATATATATATATATAT
*
21257374 TAAAAATTAATAAAAATATTTTAAAAATATATTTCCACTTTTTTCCTTTGTTCTTCTTTTCGGTT
456 TAAAAATTAATAAAAATATTTTAAAAATATATTTCCACTTTTTTCCTTTGTTCTTCTTTTAGGTT
21257439 TT
521 TT
21257441 CCTTTTCTTC
Statistics
Matches: 521, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
522 521 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (522 bp):
TGTTCCATTGTTGGGGTCTCTTGTCCGCGCAGTGGCTGGGCTTGCTATCTTAGCAATGGTCTTTT
ATTTTTAGTTGACCTTTTATATGAACCCATAGAGATAGAAGAAAATTCTTGCGCACATTTTTTGA
ATGGCTTAAACATAAAATTAATATTTCAACTTGTCTATTTCGTATTTAAGGTTTTTTTTTTCTTT
GTCTCATATTAAATATCCTAATTTTTTTGTCAACTAAATTAATATTTTTATATAATACCGCTAAA
TTTAAGATAAATGACAAAATAAGATTATGACAAATAGCATATTAAAATATATCCAATATTTGACA
AACAAAATATTTCCATATTAAAAAAAAACTTCCTAGCTGAAATCTTAACCTAAAAGAAAACAAGT
ACAGATAATACAAAAGTGATTATTTTTGTAATTTATCCTAATCTAATATATATATATATATATAT
TAAAAATTAATAAAAATATTTTAAAAATATATTTCCACTTTTTTCCTTTGTTCTTCTTTTAGGTT
TT
Found at i:21261374 original size:66 final size:66
Alignment explanation
Indices: 21261266--21261395 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 66
21261256 TGAAGCACTA
21261266 TTGGCTACTTTCTATAATGTTTTCACTAAACTGCATGAGATTCCGTCACCTTAATCGCAGGATCT
1 TTGGCTACTTTCTATAATGTTTTCACTAAACTGCATGAGATTCCGTCACCTTAATCGCAGGATCT
21261331 C
66 C
* * * *
21261332 TTGGCTACTTTCTATGATGTTTTCACTAAACTGTATGGGATTCCGTCACCTTAATCGTAGGATC
1 TTGGCTACTTTCTATAATGTTTTCACTAAACTGCATGAGATTCCGTCACCTTAATCGCAGGATC
21261396 ATGCCATTCC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (66 bp):
TTGGCTACTTTCTATAATGTTTTCACTAAACTGCATGAGATTCCGTCACCTTAATCGCAGGATCT
C
Found at i:21280976 original size:67 final size:64
Alignment explanation
Indices: 21280900--21281092 Score: 161
Period size: 67 Copynumber: 3.0 Consensus size: 64
21280890 ATTTTATTAG
*
21280900 ATTTAATATTAAATTTAATTTGATACTTTCTTGATAATATTTTATTAATTTGATATTAAAGTGAT
1 ATTTAATATTAAATTTAATTT-ATACTTTCTTGATAATATTATATTAATTT-ATATTAAAGTGAT
21280965 T
64 T
* * * * * *
21280966 ATCTTAATATTAAATTAAATATT-TACCTTATAGATCAAAATTCTATTAATTTA-A-T--A---A
1 AT-TTAATATTAAATTTAAT-TTATACTTTCTTGAT-AATATTATATTAATTTATATTAAAGTGA
21281023 -T
63 TT
* *
21281024 ATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAAGTG
1 ATTTAATATTAAATTTAAT-TTATACTT-TCTTGATAA-TATTATATTAATTT-ATATTAAAGTG
21281089 ATT
62 ATT
21281092 A
1 A
21281093 AAGTTTAATT
Statistics
Matches: 97, Mismatches: 15, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
57 17 0.18
58 8 0.08
59 18 0.19
60 1 0.01
61 1 0.01
62 2 0.02
64 2 0.02
65 1 0.01
66 12 0.12
67 31 0.32
68 4 0.04
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (64 bp):
ATTTAATATTAAATTTAATTTATACTTTCTTGATAATATTATATTAATTTATATTAAAGTGATT
Found at i:21292615 original size:18 final size:18
Alignment explanation
Indices: 21292588--21292623 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21292578 ATATTTGCCT
*
21292588 GTGTGGGCCTACACGCCC
1 GTGTGAGCCTACACGCCC
21292606 GTGTGAGCCTACACGCCC
1 GTGTGAGCCTACACGCCC
21292624 ATGCAACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.39, G:0.31, T:0.17
Consensus pattern (18 bp):
GTGTGAGCCTACACGCCC
Found at i:21292695 original size:92 final size:93
Alignment explanation
Indices: 21292532--21292716 Score: 266
Period size: 92 Copynumber: 2.0 Consensus size: 93
21292522 GGGCGACCCG
* * * **
21292532 TGCAACCTTAGCCATCAAACAGTGGAAATGGGCCCACAAGCCCAAGATATTTGCCTGTGTGGGCC
1 TGCAACCTTAGCCATCAAACAGTGAAAATGGGCCCACAAGCCCAAGAAATTTACCCATGTGGGCC
*
21292597 TACACGCCCGTGTGAGCCTACAC-GCCCA
66 TACACGCCCGTGT-AGCCCACACAGCCCA
* * *
21292625 TGCAA-CTTAGCCATCAAATAGTGAAAATGGGCCCACAAGCCCATGAAATTTACCCATGTGGGCT
1 TGCAACCTTAGCCATCAAACAGTGAAAATGGGCCCACAAGCCCAAGAAATTTACCCATGTGGGCC
21292689 TACACGCCCGTGTAGCCCACACAGCCCA
66 TACACGCCCGTGTAGCCCACACAGCCCA
21292717 AAAATGGCCT
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
91 8 0.10
92 69 0.84
93 5 0.06
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (93 bp):
TGCAACCTTAGCCATCAAACAGTGAAAATGGGCCCACAAGCCCAAGAAATTTACCCATGTGGGCC
TACACGCCCGTGTAGCCCACACAGCCCA
Found at i:21297351 original size:19 final size:20
Alignment explanation
Indices: 21297313--21297353 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
21297303 CCTCCCCTGC
*
21297313 AAATAATATACATTATTATAT
1 AAATAATATA-ATTACTATAT
21297334 AAATAATAT-ATTACTATAT
1 AAATAATATAATTACTATAT
21297353 A
1 A
21297354 TAAATTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAATATAATTACTATAT
Found at i:21297353 original size:21 final size:20
Alignment explanation
Indices: 21297313--21297358 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
21297303 CCTCCCCTGC
21297313 AAATAATATACATTATTATAT
1 AAATAATATA-ATTATTATAT
21297334 AAATAATAT-ATTACTATATAT
1 AAATAATATAATTA-T-TATAT
21297355 AAAT
1 AAAT
21297359 TGTAACGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.17
20 1 0.04
21 18 0.78
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAATATAATTATTATAT
Found at i:21307218 original size:9 final size:9
Alignment explanation
Indices: 21307204--21307262 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
21307194 AAACCTTGTA
21307204 ATATATAAT
1 ATATATAAT
21307213 ATATATGATAT
1 ATATAT-A-AT
21307224 ATATTATAAT
1 ATA-TATAAT
21307234 ATATATAA-
1 ATATATAAT
21307242 A-ATGATAAT
1 ATAT-ATAAT
21307251 AT-TAT-AT
1 ATATATAAT
21307258 ATATA
1 ATATA
21307263 ACTTTAACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
7 6 0.14
8 9 0.21
9 13 0.30
10 6 0.14
11 6 0.14
12 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
ATATATAAT
Found at i:21307419 original size:23 final size:23
Alignment explanation
Indices: 21307383--21307427 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
21307373 TCATATATTA
*
21307383 TATATATTATTATATATAAATAC
1 TATATATTACTATATATAAATAC
*
21307406 TATATGTTACTATATATAAATA
1 TATATATTACTATATATAAATA
21307428 ATAAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
TATATATTACTATATATAAATAC
Found at i:21307553 original size:43 final size:43
Alignment explanation
Indices: 21307504--21307589 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
21307494 CCTTATAAAT
*
21307504 TGCTTCAAATAAAGAAACTCTAAATAATTTAGATAAATAGTGA
1 TGCTTCAAATAAAGAAACTCCAAATAATTTAGATAAATAGTGA
*
21307547 TGCTTCAAATAAAGAAACTCCAAATAATTTAGGTAAATAGTGA
1 TGCTTCAAATAAAGAAACTCCAAATAATTTAGATAAATAGTGA
21307590 GGAAATTAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (43 bp):
TGCTTCAAATAAAGAAACTCCAAATAATTTAGATAAATAGTGA
Found at i:21308002 original size:21 final size:22
Alignment explanation
Indices: 21307949--21308000 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
21307939 TTACCATATT
21307949 AACATTTTTAAAAAAATCACTC
1 AACATTTTTAAAAAAATCACTC
21307971 AACATTTTTAAAAAAATCACTC
1 AACATTTTTAAAAAAATCACTC
21307993 AACATTTT
1 AACATTTT
21308001 AATCAGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (22 bp):
AACATTTTTAAAAAAATCACTC
Found at i:21309913 original size:22 final size:22
Alignment explanation
Indices: 21309872--21309914 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
21309862 AACAATAGCA
* * *
21309872 ATAAAATAGTAGTAATATAATT
1 ATAAAATAATAGCAAAATAATT
21309894 ATAAAATAATAGCAAAATAAT
1 ATAAAATAATAGCAAAATAAT
21309915 GAGAAAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (22 bp):
ATAAAATAATAGCAAAATAATT
Found at i:21315763 original size:125 final size:125
Alignment explanation
Indices: 21315533--21315954 Score: 585
Period size: 125 Copynumber: 3.4 Consensus size: 125
21315523 ACGTGGACGT
* * * * *
21315533 GAAGAATTTGTGAAATCACGTCCTCCTGGACGCGCTTTTGCTACAGTTGGTCTTGGAAGAAATAA
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
* *
21315598 TTTCGAGTTGACGTTTTTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTCTATGA
66 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTATATGA
* ** * *
21315658 GAAGAATTTGTTAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGCAGGTCCT-GAAAAAATTA
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
* * * * *
21315722 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAGCGCTTCAAGCAGGATGCTATTTGA
66 TTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTCTACCAAGATGCTATATGA
* * *
21315783 GAAGAATTTCTGAAATCGCGCCCTCGTGGACTCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
* ** * *
21315848 TTTCGAGTTGATGTTTCTGAGCAAATAGTATAAAATTACTTCTACCAAGATACTTTATGA
66 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTATATGA
* *
21315908 GAAGAATTTGTGAAATCGCACCTACGTGGACGCGCTTTTGCTACAGT
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
21315955 AACATGTTTG
Statistics
Matches: 255, Mismatches: 40, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
124 38 0.15
125 179 0.70
126 38 0.15
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (125 bp):
GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTATATGA
Found at i:21321491 original size:22 final size:21
Alignment explanation
Indices: 21321466--21321537 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 21
21321456 TATGAATTTA
21321466 AGAGAAATTTTGA-AGGAAATTG
1 AGAGAAA--TTGAGAGGAAATTG
21321488 AGAGCAAATTGAGAGGAAATTG
1 AGAG-AAATTGAGAGGAAATTG
21321510 AGAGGAAATTGAGAGGAAATTTG
1 AGA-GAAATTGAGAGGAAA-TTG
21321533 AGAGA
1 AGAGA
21321538 GGATTAGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.09
22 32 0.70
23 10 0.22
ACGTcount: A:0.46, C:0.01, G:0.32, T:0.21
Consensus pattern (21 bp):
AGAGAAATTGAGAGGAAATTG
Found at i:21321498 original size:11 final size:11
Alignment explanation
Indices: 21321475--21321536 Score: 99
Period size: 11 Copynumber: 5.6 Consensus size: 11
21321465 AAGAGAAATT
21321475 TTGA-AGGAAA
1 TTGAGAGGAAA
*
21321485 TTGAGAGCAAA
1 TTGAGAGGAAA
21321496 TTGAGAGGAAA
1 TTGAGAGGAAA
21321507 TTGAGAGGAAA
1 TTGAGAGGAAA
21321518 TTGAGAGGAAA
1 TTGAGAGGAAA
21321529 TTTGAGAG
1 -TTGAGAG
21321537 AGGATTAGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.08
11 37 0.77
12 7 0.15
ACGTcount: A:0.44, C:0.02, G:0.34, T:0.21
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:21331422 original size:16 final size:16
Alignment explanation
Indices: 21331403--21331436 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
21331393 TAAATTAAAT
21331403 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
21331419 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
21331435 TT
1 TT
21331437 CCAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTTTAATA
Found at i:21332473 original size:45 final size:44
Alignment explanation
Indices: 21332384--21332476 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
21332374 ATTACAACAT
* *
21332384 CATTCCATTCAACCAAACACAAGAATACTATTGCAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
*
21332428 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGCTCTATTC
21332473 CATT
1 CATT
21332477 ACACATCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 21 0.48
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:21332479 original size:16 final size:16
Alignment explanation
Indices: 21332458--21332513 Score: 87
Period size: 16 Copynumber: 3.5 Consensus size: 16
21332448 TTGAATTACT
21332458 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
21332474 ATTACA-CATCTATTCA
1 ATTACAGC-TCTATTCC
21332490 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
21332506 ATTACAGC
1 ATTACAGC
21332514 GAACCAAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
15 1 0.03
16 34 0.94
17 1 0.03
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:21333229 original size:7 final size:6
Alignment explanation
Indices: 21333219--21333272 Score: 65
Period size: 6 Copynumber: 8.7 Consensus size: 6
21333209 AAATTTTTAA
*
21333219 AAAAATT AAAAATT AAAAATT AAAAAT -TAAAT AAAAAT AAAAAT AAAAAT
1 AAAAA-T AAAAA-T AAAAA-T AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
21333269 AAAA
1 AAAA
21333273 TTATTCTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
5 4 0.09
6 21 0.48
7 19 0.43
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:21336761 original size:70 final size:70
Alignment explanation
Indices: 21336648--21336786 Score: 260
Period size: 70 Copynumber: 2.0 Consensus size: 70
21336638 TATTTCAAGC
*
21336648 TCCAAAACCAAAAGAAAATGTTCTATATGTGATATATTTATATTATTTTTACTTTTCAAATATAA
1 TCCAAAACCAAAAGAAAATGTTCTATATGTGATATATTTATATTATTTTTACCTTTCAAATATAA
21336713 AAGTT
66 AAGTT
*
21336718 TCCAAAACCAAAATAAAATGTTCTATATGTGATATATTTATATTATTTTTACCTTTCAAATATAA
1 TCCAAAACCAAAAGAAAATGTTCTATATGTGATATATTTATATTATTTTTACCTTTCAAATATAA
21336783 AAGT
66 AAGT
21336787 GAAGAATTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (70 bp):
TCCAAAACCAAAAGAAAATGTTCTATATGTGATATATTTATATTATTTTTACCTTTCAAATATAA
AAGTT
Found at i:21338589 original size:22 final size:22
Alignment explanation
Indices: 21338555--21338610 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
21338545 TCTGGAAATG
* *
21338555 GGTGGAGCCGTGGAGGACCGGA
1 GGTGGATCGGTGGAGGACCGGA
**
21338577 GGTGGATCGGTGGAGGATTGGA
1 GGTGGATCGGTGGAGGACCGGA
*
21338599 GGTGGATTGGTG
1 GGTGGATCGGTG
21338611 CCGGAGGTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.16, C:0.09, G:0.55, T:0.20
Consensus pattern (22 bp):
GGTGGATCGGTGGAGGACCGGA
Found at i:21341311 original size:19 final size:19
Alignment explanation
Indices: 21341289--21341326 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
21341279 TCAATCACCC
21341289 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
21341308 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
21341327 ACTCTTTTAG
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:21352752 original size:19 final size:19
Alignment explanation
Indices: 21352728--21352764 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21352718 GGATCGCTGG
21352728 TGAGATCTAGGCTCTTTAC
1 TGAGATCTAGGCTCTTTAC
*
21352747 TGAGATCTAGGTTCTTTA
1 TGAGATCTAGGCTCTTTA
21352765 GCTTGTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (19 bp):
TGAGATCTAGGCTCTTTAC
Found at i:21355611 original size:23 final size:23
Alignment explanation
Indices: 21355585--21355630 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
21355575 TGTACAGAAG
21355585 TACAAATGTAAGAACCACAACCA
1 TACAAATGTAAGAACCACAACCA
*
21355608 TACAAATGTGAGAACCACAACCA
1 TACAAATGTAAGAACCACAACCA
21355631 GCATCTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.26, G:0.11, T:0.13
Consensus pattern (23 bp):
TACAAATGTAAGAACCACAACCA
Found at i:21363665 original size:14 final size:14
Alignment explanation
Indices: 21363621--21363668 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
21363611 AGTAAAAAAT
*
21363621 AATATAAATTGTATA
1 AATA-AAATTTTATA
*
21363636 ATATATAATCTTTATA
1 A-ATAAAAT-TTTATA
21363652 AATAAAATTTTATA
1 AATAAAATTTTATA
21363666 AAT
1 AAT
21363669 TGTTGAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 9 0.32
15 10 0.36
16 9 0.32
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
AATAAAATTTTATA
Found at i:21363760 original size:21 final size:21
Alignment explanation
Indices: 21363718--21363775 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
21363708 TTTTATAGAT
*
21363718 AAATTTTGT-TAAAGAAATTATA
1 AAATTTT-TATAAATAAA-TATA
*
21363740 AAATTTTTATTAATAAATATA
1 AAATTTTTATAAATAAATATA
**
21363761 TTATTTTTATAAATA
1 AAATTTTTATAAATA
21363776 TNNNNNNNNN
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (21 bp):
AAATTTTTATAAATAAATATA
Found at i:21366700 original size:27 final size:27
Alignment explanation
Indices: 21366482--21366688 Score: 288
Period size: 27 Copynumber: 7.7 Consensus size: 27
21366472 AATGGGCCTA
**
21366482 TAAAATTACTAAAATACCCTCGATGGG
1 TAAAATTACCGAAATACCCTCGATGGG
* *
21366509 TAAAATGACTGAAATACCCTCGATGGG
1 TAAAATTACCGAAATACCCTCGATGGG
*
21366536 TAAAATGACCGAAATACCCTCGATGGG
1 TAAAATTACCGAAATACCCTCGATGGG
*
21366563 TAAAATGACCGAAATACCCTCGATGGG
1 TAAAATTACCGAAATACCCTCGATGGG
* * *
21366590 TAAAATTATCGAAATACCTTTGATGGG
1 TAAAATTACCGAAATACCCTCGATGGG
* * *
21366617 TAAAATTATCGAAATGCCCCCGATGGG
1 TAAAATTACCGAAATACCCTCGATGGG
* *
21366644 TAAAATTATCGAAATACCCTCGAAGGG
1 TAAAATTACCGAAATACCCTCGATGGG
21366671 TAAAATTACCGAAATACC
1 TAAAATTACCGAAATACC
21366689 TCTGAAGGGT
Statistics
Matches: 165, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 165 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCGATGGG
Found at i:21368498 original size:309 final size:309
Alignment explanation
Indices: 21367939--21368541 Score: 1089
Period size: 309 Copynumber: 2.0 Consensus size: 309
21367929 TATCTAACGA
*
21367939 TACATTGTTACCTCACGTAATCTTATATGTGCTTATGAGATTGAATTAATTATTTGAATTGGCAT
1 TACATTGTTACCTCACGTAATCTTATATGTGCTTATGAGATTAAATTAATTATTTGAATTGGCAT
21368004 AGAGATATGTACAAGAGATTATTTTAATTTCAAAAGTATGTATGTGCATTAACACATTTGCTTCT
66 AGAGATATGTACAAGAGATTATTTTAATTTCAAAAGTATGTATGTGCATTAACACATTTGCTTCT
* *
21368069 TAAAATTTGTTTAATCAGTTGAATTGACATAGAGATATAGTCAAGAGATAAATAGATTTTTGTAG
131 TAAAATTTGTTTAATCAGTTGAATTGACATAGAGAGATAGTCAAGAGATAAATAAATTTTTGTAG
*
21368134 GTGAGTATGTTCATAAGTTAGCAAATTATCGAGTCGCCATGAATTTATTCGTAACAACATGAACA
196 GTGAGTATGTTCATAAGTTAGCAAATTACCGAGTCGCCATGAATTTATTCGTAACAACATGAACA
*
21368199 TGAGTTTAATAATTCTAAGTTAAGAAATTTAATTGTTTGAATTTATTAG
261 TGAGTTTAATAATTCTAAGTTAAGAAATGTAATTGTTTGAATTTATTAG
*
21368248 TACATTGTTACCTCACGTAATCTTATATGTGCTTATGAGATTAAATTAATTGTTTGAATTGGCAT
1 TACATTGTTACCTCACGTAATCTTATATGTGCTTATGAGATTAAATTAATTATTTGAATTGGCAT
* *
21368313 AGAGATATGTACAAGAGATTTTTTTAATTTCATAAGTATGTATGTGCATTAACACATTTGCTTCT
66 AGAGATATGTACAAGAGATTATTTTAATTTCAAAAGTATGTATGTGCATTAACACATTTGCTTCT
* * *
21368378 TAAAATTTGTTTAATCGGTTGAATTGACATAGAGAGATTGTCAAGATATAAATAAATTTTTGTAG
131 TAAAATTTGTTTAATCAGTTGAATTGACATAGAGAGATAGTCAAGAGATAAATAAATTTTTGTAG
* *
21368443 GTGAGTATGTTCATAAGTTAGCAAATTACCGAGTTGCCGTGAATTTATTCGTAACAACATGAACA
196 GTGAGTATGTTCATAAGTTAGCAAATTACCGAGTCGCCATGAATTTATTCGTAACAACATGAACA
21368508 TGAGTTTAATAATTCTAAGTTAAGAAATGTAATT
261 TGAGTTTAATAATTCTAAGTTAAGAAATGTAATT
21368542 AATCTAACAC
Statistics
Matches: 281, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
309 281 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (309 bp):
TACATTGTTACCTCACGTAATCTTATATGTGCTTATGAGATTAAATTAATTATTTGAATTGGCAT
AGAGATATGTACAAGAGATTATTTTAATTTCAAAAGTATGTATGTGCATTAACACATTTGCTTCT
TAAAATTTGTTTAATCAGTTGAATTGACATAGAGAGATAGTCAAGAGATAAATAAATTTTTGTAG
GTGAGTATGTTCATAAGTTAGCAAATTACCGAGTCGCCATGAATTTATTCGTAACAACATGAACA
TGAGTTTAATAATTCTAAGTTAAGAAATGTAATTGTTTGAATTTATTAG
Found at i:21370094 original size:69 final size:69
Alignment explanation
Indices: 21369977--21370524 Score: 376
Period size: 69 Copynumber: 7.9 Consensus size: 69
21369967 AATTTTTTTG
* * * * *
21369977 TCATATTAAGGCTCACGGGTGAAGAG-TAGCAGCCTTTAACACAATTAGCGAGAGAAAAGCTCCC
1 TCATATTAAGGCTCGCGAGCGAAGAGCTA-CAGCCTTCAACACAGTTAGCGAGAGAAAAGCTCCC
21370041 AACTA
65 AACTA
* * * * *
21370046 TCATATTAAGTCTCGCGAGTGAAGAGCCACAGCCTTCAATACAGTTAGCGAGAGTAAAGCTCCCA
1 TCATATTAAGGCTCGCGAGCGAAGAGCTACAGCCTTCAACACAGTTAGCGAGAGAAAAGCTCCCA
21370111 ACTA
66 ACTA
* * * * * * *
21370115 TCATATTAAGGCTCAC-AGGCAAAAAGCCACAGCCTCCAACACATTTAGCGAGAGCAAAA-CCCC
1 TCATATTAAGGCTCGCGA-GCGAAGAGCTACAGCCTTCAACACAGTTAGCGAGAG-AAAAGCTCC
*
21370178 CAACTG
64 CAACTA
* * * * ** * *
21370184 TCACATTAAGGCTTGCGGGCGAAAAGCTGTAGCCTACAACACAGTTAGCGAGAGCAAAGCTCCCA
1 TCATATTAAGGCTCGCGAGCGAAGAGCTACAGCCTTCAACACAGTTAGCGAGAGAAAAGCTCCCA
* *
21370249 GCTG
66 ACTA
* * *
21370253 TCATATTAAGGCTCGCGAGCGAAGAGCTGCAG-CTTCCAACACAGTTAGTGAGAGCAAAGCTCCC
1 TCATATTAAGGCTCGCGAGCGAAGAGCTACAGCCTT-CAACACAGTTAGCGAGAGAAAAGCTCCC
*
21370317 AGCTA
65 AACTA
* * * * * * * * * *
21370322 TCATATTAAAGCTCGTGGGCAAAAAG-T-CGTAGCC-TCTAACATAGTTAGTGAGAGTAAACCTT
1 TCATATTAAGGCTCGCGAGCGAAGAGCTAC--AGCCTTC-AACACAGTTAGCGAGAGAAAAGCTC
*
21370384 CCAACTG
63 CCAACTA
* * * * * *** * * *
21370391 TCTTAATAAGGCTTG-TAGGTGAAGAGCCGGAGCCTCCAACACAATTAGCGAGAGCAAAGCTCCC
1 TCATATTAAGGCTCGCGA-GCGAAGAGCTACAGCCTTCAACACAGTTAGCGAGAGAAAAGCTCCC
*
21370455 ATCTA
65 AACTA
* * * * * ** * *
21370460 TCATGTTAAGGCTCCCAAGCAAAAAGCCGCAGCC-TCTAACACAGTTAGCGAGGGCAAAGCTCCC
1 TCATATTAAGGCTCGCGAGCGAAGAGCTACAGCCTTC-AACACAGTTAGCGAGAGAAAAGCTCCC
21370524 A
65 A
21370525 GATACCAGAT
Statistics
Matches: 379, Mismatches: 84, Indels: 32
0.77 0.17 0.06
Matches are distributed among these distances:
67 1 0.00
68 9 0.02
69 362 0.96
70 7 0.02
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (69 bp):
TCATATTAAGGCTCGCGAGCGAAGAGCTACAGCCTTCAACACAGTTAGCGAGAGAAAAGCTCCCA
ACTA
Found at i:21370228 original size:138 final size:138
Alignment explanation
Indices: 21369975--21370524 Score: 523
Period size: 138 Copynumber: 4.0 Consensus size: 138
21369965 TAAATTTTTT
* * * ** **
21369975 TGTCATATTAAGGCTCACGGGTGAAGAGTAGCAGCCTTTAACACAATTAGCGAGAG-AAAAGCTC
1 TGTCATATTAAGGCTCGCAGGCGAAGAGCCGCAGCCTCCAACACAATTAGCGAGAGCAAAA-CTC
* ** * * * *
21370039 CCAACTATCATATTAAGTCTCGCGAGTGAAGAGCCACAGCCT-TCAATACAGTTAGCGAGAGTAA
65 CCAACTATCATATTAAGGCTCGCGAGCAAAAAGCCGCAGCCTCT-AACACAGTTAGCGAGAGCAA
21370103 AGCTCCCAAC
129 AGCTCCCAAC
* * * * * * *
21370113 TATCATATTAAGGCTCACAGGCAAAAAGCCACAGCCTCCAACACATTTAGCGAGAGCAAAACCCC
1 TGTCATATTAAGGCTCGCAGGCGAAGAGCCGCAGCCTCCAACACAATTAGCGAGAGCAAAACTCC
* * * * * * *
21370178 CAACTGTCACATTAAGGCTTGCGGGCGAAAAGCTGTAGCCTAC-AACACAGTTAGCGAGAGCAAA
66 CAACTATCATATTAAGGCTCGCGAGCAAAAAGCCGCAGCCT-CTAACACAGTTAGCGAGAGCAAA
*
21370242 GCTCCCAGC
130 GCTCCCAAC
* * * * *
21370251 TGTCATATTAAGGCTCGC-GAGCGAAGAGCTGCAGCTTCCAACACAGTTAGTGAGAGCAAAGCTC
1 TGTCATATTAAGGCTCGCAG-GCGAAGAGCCGCAGCCTCCAACACAATTAGCGAGAGCAAAACTC
* * * * * * * * *
21370315 CCAGCTATCATATTAAAGCTCGTGGGCAAAAAGTCGTAGCCTCTAACATAGTTAGTGAGAGTAAA
65 CCAACTATCATATTAAGGCTCGCGAGCAAAAAGCCGCAGCCTCTAACACAGTTAGCGAGAGCAAA
* *
21370380 CCTTCCAAC
130 GCTCCCAAC
* * * * * * *
21370389 TGTCTTAATAAGGCTTGTAGGTGAAGAGCCGGAGCCTCCAACACAATTAGCGAGAGCAAAGCTCC
1 TGTCATATTAAGGCTCGCAGGCGAAGAGCCGCAGCCTCCAACACAATTAGCGAGAGCAAAACTCC
* * * * *
21370454 CATCTATCATGTTAAGGCTCCCAAGCAAAAAGCCGCAGCCTCTAACACAGTTAGCGAGGGCAAAG
66 CAACTATCATATTAAGGCTCGCGAGCAAAAAGCCGCAGCCTCTAACACAGTTAGCGAGAGCAAAG
21370519 CTCCCA
131 CTCCCA
21370525 GATACCAGAT
Statistics
Matches: 330, Mismatches: 76, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
137 2 0.01
138 323 0.98
139 5 0.02
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (138 bp):
TGTCATATTAAGGCTCGCAGGCGAAGAGCCGCAGCCTCCAACACAATTAGCGAGAGCAAAACTCC
CAACTATCATATTAAGGCTCGCGAGCAAAAAGCCGCAGCCTCTAACACAGTTAGCGAGAGCAAAG
CTCCCAAC
Found at i:21370345 original size:207 final size:207
Alignment explanation
Indices: 21370014--21370541 Score: 601
Period size: 207 Copynumber: 2.6 Consensus size: 207
21370004 AGCAGCCTTT
* * * *
21370014 AACACAATTAGCGAGAGAAAAGCTCCCAACTATCATATTAAGTCTCGCGAGTGAAGAGCCACAGC
1 AACACAATTAGCGAGAGCAAAGCTCCCAACTATCATATTAAGGCTCGCGAGCGAAGAGCCGCAG-
* * * *
21370079 CTT-CAATACAGTTAGCGAGAGTAAAGCTCCCAACTATCATATTAAGGCTCACAGGCAAAAAGCC
65 CTTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTATCATATTAAAGCTCACAGGCAAAAAGCC
* * *
21370143 ACAGCCTCCAACACATTTAGCGAGAGCAAAACC-CCCAACTGTCACATTAAGGCTTGCGGGCGAA
130 ACAGCCTCCAACACAGTTAGCGAGAG-AAAACCTCCCAACTGTCACAATAAGGCTTGCAGGCGAA
* *
21370207 AAGCTGTAGCCTAC
194 AAGCCGGAGCCTAC
* * * *
21370221 AACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCATATTAAGGCTCGCGAGCGAAGAGCTGCAGC
1 AACACAATTAGCGAGAGCAAAGCTCCCAACTATCATATTAAGGCTCGCGAGCGAAGAGCCGCAGC
* *** * *
21370286 TTCCAACACAGTTAGTGAGAGCAAAGCTCCCAGCTATCATATTAAAGCTCGTGGGCAAAAAGTCG
66 TTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTATCATATTAAAGCTCACAGGCAAAAAGCCA
* * * * * * ** * * *
21370351 TAGCCTCTAACATAGTTAGTGAGAGTAAACCTTCCAACTGTCTTAATAAGGCTTGTAGGTGAAGA
131 CAGCCTCCAACACAGTTAGCGAGAGAAAACCTCCCAACTGTCACAATAAGGCTTGCAGGCGAAAA
*
21370416 GCCGGAGCCTCC
196 GCCGGAGCCTAC
* * * * * *
21370428 AACACAATTAGCGAGAGCAAAGCTCCCATCTATCATGTTAAGGCTCCCAAGCAAAAAGCCGCAGC
1 AACACAATTAGCGAGAGCAAAGCTCCCAACTATCATATTAAGGCTCGCGAGCGAAGAGCCGCAGC
* * * * * *
21370493 CTCTAACACAGTTAGCGAGGGCAAAGCTCCCAGATACCAGATTAAAGCT
66 TTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTATCATATTAAAGCT
21370542 AGTAGGTGAA
Statistics
Matches: 268, Mismatches: 51, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
206 8 0.03
207 260 0.97
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (207 bp):
AACACAATTAGCGAGAGCAAAGCTCCCAACTATCATATTAAGGCTCGCGAGCGAAGAGCCGCAGC
TTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTATCATATTAAAGCTCACAGGCAAAAAGCCA
CAGCCTCCAACACAGTTAGCGAGAGAAAACCTCCCAACTGTCACAATAAGGCTTGCAGGCGAAAA
GCCGGAGCCTAC
Found at i:21374377 original size:10 final size:10
Alignment explanation
Indices: 21374364--21374405 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
21374354 TTAGAAAATA
21374364 TTTTATAATTT
1 TTTTATAA-TT
* *
21374375 TTTTCTTATT
1 TTTTATAATT
21374385 TTTTAT-ATT
1 TTTTATAATT
21374394 TTTTATAATT
1 TTTTATAATT
21374404 TT
1 TT
21374406 GGATTTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 9 0.33
10 12 0.44
11 6 0.22
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTATAATT
Found at i:21389004 original size:15 final size:16
Alignment explanation
Indices: 21388984--21389017 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21388974 ATCCTACTCC
21388984 TAAAATGAT-AAAAAT
1 TAAAATGATCAAAAAT
*
21388999 TAAAATGATCCAAAAT
1 TAAAATGATCAAAAAT
21389015 TAA
1 TAA
21389018 TCACAATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
TAAAATGATCAAAAAT
Found at i:21390960 original size:50 final size:51
Alignment explanation
Indices: 21390872--21391005 Score: 146
Period size: 50 Copynumber: 2.6 Consensus size: 51
21390862 AAAGTGATGG
* * * * *
21390872 TCACGTGTGTAGTACTATGTGCTGGCTACTACGTGTACCAGAAT-G-ATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACC-GAATAGCATAGA
* * * * *
21390922 TCGCATGTGTAGTACTATGTGCAGGCTATTATGCGTACCGGATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCATAGA
*
21390973 TCACATGTGTAGTACTATGTGTAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
21391006 TGAACCGGTA
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
49 3 0.04
50 34 0.49
51 32 0.46
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCATAGA
Found at i:21401479 original size:22 final size:23
Alignment explanation
Indices: 21401426--21401481 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
21401416 TGATTAACTA
*
21401426 TTTTAATTGTGAAATATAAATTAG
1 TTTTAATT-TGAAATATAAATTAC
* * *
21401450 TTTCAATTTTAAATAT-TATTAC
1 TTTTAATTTGAAATATAAATTAC
21401472 TTTTAATTTG
1 TTTTAATTTG
21401482 GATTAATTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 12 0.46
23 7 0.27
24 7 0.27
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
TTTTAATTTGAAATATAAATTAC
Found at i:21402283 original size:35 final size:34
Alignment explanation
Indices: 21402221--21402291 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 34
21402211 AGTGAACATT
*
21402221 ATAATTATAATTTAAATTACAAATATTAGTTAAAA
1 ATAATTATAATTTAAATTACAAATATTA-TAAAAA
* *
21402256 ATAATTATAATTTAATTTA-ACATTATTATAAAAA
1 ATAATTATAATTTAAATTACA-AATATTATAAAAA
21402290 AT
1 AT
21402292 TACTTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 8 0.25
35 24 0.75
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (34 bp):
ATAATTATAATTTAAATTACAAATATTATAAAAA
Found at i:21405468 original size:25 final size:25
Alignment explanation
Indices: 21405435--21405541 Score: 117
Period size: 25 Copynumber: 4.3 Consensus size: 25
21405425 AGCTTCTTTG
* * * *
21405435 AGCTAAATAACGGTAAGCTCCTCCA
1 AGCTGAATAATGGTAAGCTCATACA
* *
21405460 AGTTGAATAATAGTAAGCTCATACA
1 AGCTGAATAATGGTAAGCTCATACA
*
21405485 AGCTGAATAATGGTAAGCTCATACG
1 AGCTGAATAATGGTAAGCTCATACA
* *
21405510 AGCTGAGTATTGGTAAGCTCATA-A
1 AGCTGAATAATGGTAAGCTCATACA
21405534 GAGCTGAA
1 -AGCTGAA
21405542 ATCGGTAACC
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
25 68 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (25 bp):
AGCTGAATAATGGTAAGCTCATACA
Found at i:21411170 original size:20 final size:19
Alignment explanation
Indices: 21411145--21411189 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
21411135 TGGGACTAAA
* *
21411145 TCAAAAATTTAGAGAATTTT
1 TCAAAAACTTAGA-AAATTT
*
21411165 TCAAAAACTTATAAAATTT
1 TCAAAAACTTAGAAAATTT
21411184 TCAAAA
1 TCAAAA
21411190 CTGCAGGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (19 bp):
TCAAAAACTTAGAAAATTT
Found at i:21412667 original size:25 final size:25
Alignment explanation
Indices: 21412626--21412718 Score: 125
Period size: 25 Copynumber: 3.7 Consensus size: 25
21412616 AACTGTAAAT
*
21412626 GGTAAGCTCCT-CTGAGCTGAATAAC
1 GGTAAGCTCATAC-GAGCTGAATAAC
*
21412651 AGTAAGCTCATACGAGCTGAATAAC
1 GGTAAGCTCATACGAGCTGAATAAC
* *
21412676 GGTAAGCTCATACGAGCTGAGTATC
1 GGTAAGCTCATACGAGCTGAATAAC
*
21412701 GGTAAGCTCATAAGAGCT
1 GGTAAGCTCATACGAGCT
21412719 TAAATCGGTA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
25 60 0.98
26 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (25 bp):
GGTAAGCTCATACGAGCTGAATAAC
Found at i:21415510 original size:15 final size:16
Alignment explanation
Indices: 21415487--21415516 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21415477 TTCTTTTTTA
21415487 AAAATTTTAAAAAATT
1 AAAATTTTAAAAAATT
21415503 AAAA-TTTAAAAAAT
1 AAAATTTTAAAAAAT
21415517 ATTTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTTTAAAAAATT
Found at i:21415528 original size:37 final size:39
Alignment explanation
Indices: 21415480--21415554 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 39
21415470 ATTTAATTTC
*
21415480 TTTTTTAAAAATTTTAAAA-AATTAAAAT-TTAAAAAATA
1 TTTTTTAAAAA-TTAAAAATAATTAAAATATTAAAAAATA
21415518 TTTTTT-AAAATTAAAAATAATTAAAATGATTAAAAAA
1 TTTTTTAAAAATTAAAAATAATTAAAAT-ATTAAAAAA
21415555 GTATAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
36 6 0.18
37 13 0.39
38 6 0.18
39 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (39 bp):
TTTTTTAAAAATTAAAAATAATTAAAATATTAAAAAATA
Found at i:21415847 original size:59 final size:59
Alignment explanation
Indices: 21415775--21415892 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
21415765 TTTTGTAAAG
*
21415775 TTAGAAAGTCAAAAATCATTTTATTTTACTTTAATTCTTAATTTATTTGCCTCTAATAA
1 TTAGAAAGTCAAAAATCATTTTATTTTACTTTAATTCTTAATTGATTTGCCTCTAATAA
*
21415834 TTAGAAGGTCAAAAATCATTTTATTTTACTTTAATTCTTAATTGATTTGCCTCTAATAA
1 TTAGAAAGTCAAAAATCATTTTATTTTACTTTAATTCTTAATTGATTTGCCTCTAATAA
21415893 ATTAAATACA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (59 bp):
TTAGAAAGTCAAAAATCATTTTATTTTACTTTAATTCTTAATTGATTTGCCTCTAATAA
Found at i:21419445 original size:294 final size:289
Alignment explanation
Indices: 21418906--21419480 Score: 902
Period size: 294 Copynumber: 2.0 Consensus size: 289
21418896 TAAAAACCAG
21418906 GCAGCTGCTCTGCAAGTGAACTACAATAATGAACTATTTCTAGTTGTAGACCCCAATTTGCAGCA
1 GCAGCTGCTCTGCAAGTGAACTACAATAATGAACTATTTCTAGTTGTAGACCCCAATTTGCAGCA
* *
21418971 AAAATGAGGCAATGCTGGTTCATTGAGGGGAAATGTAGTTCAAGGGGACTTAATATTAGGATTTA
66 AAAATGAGGCAATGCGGGATCATTGAGGGGAAATGTAGTTCAAGGGGACTTAATATTAGGATTTA
* * * * ** *
21419036 TTTGTTCTTTCTAGTGGTTTATGGAGAATAACTAGGGTATTTCCATTTTTTTTATAAAATGATAT
131 TTTGATCTTTCTAGTGGTTTATGGAGAATAACCAGGATATATCCATTGATTTTAGAAAATGATAT
* *
21419101 AGTACTTGCTATTTTGTCAATAAAACCGTATGGTTGCAGTTTAGAACCAACTATATCCAGATTTG
196 AGTACTTGCTATTTTGTCAATAAAACCGTATGGTTGCAGTTTAGAACCAACTATATCCAGATCTA
21419166 CAAGAATTGAAATATGTAGCTGTAATGCA
261 CAAGAATTGAAATATGTAGCTGTAATGCA
* * *
21419195 GCAGCTGTTCTGCAAGTGAACTACAATAATGAACTGTTTTTAGTTGTAGACCCCAACTTTGCAGC
1 GCAGCTGCTCTGCAAGTGAACTACAATAATGAACTATTTCTAGTTGTAGACCCCAA-TTTGCAGC
*
21419260 AAAAATGAGGCAATTG-GGGATCATTGAGGGGAAATGTAGTTCAAGGGGGCTTATATATTAGGAT
65 AAAAATGAGGCAA-TGCGGGATCATTGAGGGGAAATGTAGTTCAAGGGGACTTA-ATATTAGGAT
*
21419324 TTGTTTGATCTTTCTAGTGGTTTATGGAGGAGAATAACCAGGATATATCCA-TGATTTTAGAAAA
128 TTATTTGATCTTTCTAGTGGTTTAT---GGAGAATAACCAGGATATATCCATTGATTTTAGAAAA
* *
21419388 TGATATGGTACTTTCTATTTTTGTCAATAAAACCGTATGGTTGCAGTTTAGAACCAACTATATCC
190 TGATATAGTACTTGCTA-TTTTGTCAATAAAACCGTATGGTTGCAGTTTAGAACCAACTATATCC
*
21419453 TGATCTACAAGAATTGAAATATGTAGCT
254 AGATCTACAAGAATTGAAATATGTAGCT
21419481 CTGCACTGTC
Statistics
Matches: 260, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
289 53 0.20
290 55 0.21
291 35 0.13
293 25 0.10
294 92 0.35
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (289 bp):
GCAGCTGCTCTGCAAGTGAACTACAATAATGAACTATTTCTAGTTGTAGACCCCAATTTGCAGCA
AAAATGAGGCAATGCGGGATCATTGAGGGGAAATGTAGTTCAAGGGGACTTAATATTAGGATTTA
TTTGATCTTTCTAGTGGTTTATGGAGAATAACCAGGATATATCCATTGATTTTAGAAAATGATAT
AGTACTTGCTATTTTGTCAATAAAACCGTATGGTTGCAGTTTAGAACCAACTATATCCAGATCTA
CAAGAATTGAAATATGTAGCTGTAATGCA
Found at i:21429770 original size:48 final size:49
Alignment explanation
Indices: 21429675--21429776 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 49
21429665 TGTTGAGGTT
* * **
21429675 ATGAGAGGTCCCACCTAAGACCATGTGTGGGACATGGTGTCGGCACCGAG
1 ATGAGAGGTCCCACCTAAGA-CACGTCTGGGACATGGAATCGGCACCGAG
* *
21429725 ATGAGAGGTCCC-CCGTAAGA-ACGTCTGGGACATGGAATGGGCACCGAT
1 ATGAGAGGTCCCACC-TAAGACACGTCTGGGACATGGAATCGGCACCGAG
21429773 ATGA
1 ATGA
21429777 AAACTCCCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 26 0.58
49 2 0.04
50 17 0.38
ACGTcount: A:0.26, C:0.23, G:0.33, T:0.18
Consensus pattern (49 bp):
ATGAGAGGTCCCACCTAAGACACGTCTGGGACATGGAATCGGCACCGAG
Found at i:21430045 original size:20 final size:20
Alignment explanation
Indices: 21430020--21430058 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
21430010 TGAGTTATTT
21430020 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
21430040 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
21430059 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:21435293 original size:45 final size:45
Alignment explanation
Indices: 21435218--21435380 Score: 193
Period size: 45 Copynumber: 3.6 Consensus size: 45
21435208 AGCACATAGG
* * * * * *
21435218 ACCACCCTTATAGTCAATGATACTCAGTGGAATCAGCACATAGCA
1 ACCACCTTTATAATCAATGATACCCGGTGGAATCAGCACACAACA
* * * *
21435263 ACCACCTTCATAATCAAT-AGTACCCGGTGGAATTAGGATACAACA
1 ACCACCTTTATAATCAATGA-TACCCGGTGGAATCAGCACACAACA
* *
21435308 ACCACCTTTATAATTAATGATACCTGGTGGAATCAGCACACAACA
1 ACCACCTTTATAATCAATGATACCCGGTGGAATCAGCACACAACA
*
21435353 ACCACCTTTATAATCAATGGTACCCGGT
1 ACCACCTTTATAATCAATGATACCCGGT
21435381 ACACGTAGTA
Statistics
Matches: 97, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
44 1 0.01
45 95 0.98
46 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (45 bp):
ACCACCTTTATAATCAATGATACCCGGTGGAATCAGCACACAACA
Found at i:21441997 original size:50 final size:49
Alignment explanation
Indices: 21441831--21442121 Score: 181
Period size: 49 Copynumber: 5.8 Consensus size: 49
21441821 GGGAATGAGA
* * **
21441831 TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATTATTGAGGTTATGAGATG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ACTGA---TATGA-AAC
* * * ** * *
21441887 TCCCATGTAAGACCATGTCTTGGACATGGCGTTGACACCCAGATGAAAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGATATGAAA-C
** *
21441937 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACTGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGATATGA-AAC
* * * * * *
21441987 TCCCATGTAAGACCATATCTGGGATATGACATTGGCAGT-ACAGGAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGATATGAAAC
* * * * * * * *
21442035 ATCCCATGTAAGACCATATTTAGGATATGGCATTGACAGT-ACAGGAAAC
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGATATGAAAC
* * * *
21442084 ATCCCATGTAAGACCATATCTAGGAAATGGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
21442122 TGTTATTTTC
Statistics
Matches: 196, Mismatches: 36, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
48 3 0.02
49 83 0.42
50 74 0.38
51 2 0.01
53 2 0.01
56 32 0.16
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGATATGAAAC
Found at i:21442052 original size:49 final size:49
Alignment explanation
Indices: 21441943--21442121 Score: 216
Period size: 49 Copynumber: 3.6 Consensus size: 49
21441933 AAGGTCCCCC
* * * * * *
21441943 GTAAGACCATGTCTGGGACATGGCATGGGCACTGATATGAGAAC-TCCCAT
1 GTAAGACCATATCTGGGATATGGCATTGGCAGT-ACAGGA-AACATCCCAT
*
21441993 GTAAGACCATATCTGGGATATGACATTGGCAGTACAGGAAACATCCCAT
1 GTAAGACCATATCTGGGATATGGCATTGGCAGTACAGGAAACATCCCAT
* * *
21442042 GTAAGACCATATTTAGGATATGGCATTGACAGTACAGGAAACATCCCAT
1 GTAAGACCATATCTGGGATATGGCATTGGCAGTACAGGAAACATCCCAT
* * *
21442091 GTAAGACCATATCTAGGAAATGGCTTTGGCA
1 GTAAGACCATATCTGGGATATGGCATTGGCA
21442122 TGTTATTTTC
Statistics
Matches: 113, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
48 3 0.03
49 82 0.73
50 28 0.25
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (49 bp):
GTAAGACCATATCTGGGATATGGCATTGGCAGTACAGGAAACATCCCAT
Found at i:21442349 original size:20 final size:20
Alignment explanation
Indices: 21442324--21442362 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
21442314 TGAGTTATTT
21442324 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
21442344 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
21442363 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:21445860 original size:14 final size:14
Alignment explanation
Indices: 21445843--21445872 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21445833 CATTTAGTAT
*
21445843 GTATGATCATTTTA
1 GTATAATCATTTTA
21445857 GTATAATCATTTTA
1 GTATAATCATTTTA
21445871 GT
1 GT
21445873 TTAGTTGAAT
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:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (14 bp):
GTATAATCATTTTA
Found at i:21448465 original size:21 final size:21
Alignment explanation
Indices: 21448440--21448481 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
21448430 ATGAGTATGT
*
21448440 GATTGGAATGTGATAAGTTGC
1 GATTGGAACGTGATAAGTTGC
21448461 GATTGGAACGTGATAAGTTGC
1 GATTGGAACGTGATAAGTTGC
21448482 TACGTGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.33, T:0.31
Consensus pattern (21 bp):
GATTGGAACGTGATAAGTTGC
Found at i:21468025 original size:15 final size:16
Alignment explanation
Indices: 21468007--21468036 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21467997 AAAAAGAGAC
21468007 AAAAATG-GAAGAAAG
1 AAAAATGTGAAGAAAG
21468022 AAAAATGTGAAGAAA
1 AAAAATGTGAAGAAA
21468037 CAGTGGCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (16 bp):
AAAAATGTGAAGAAAG
Found at i:21469034 original size:23 final size:21
Alignment explanation
Indices: 21468972--21469036 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
21468962 TTTATTTACC
21468972 TATGTATATGTATATTATT-T
1 TATGTATATGTATATTATTAT
* * * *
21468992 TATATATATATAAATAATTAT
1 TATGTATATGTATATTATTAT
21469013 TATTGGTATATGTATATTATTAT
1 TA-T-GTATATGTATATTATTAT
21469036 T
1 T
21469037 TATATTATTA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
20 15 0.44
21 3 0.09
22 1 0.03
23 15 0.44
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (21 bp):
TATGTATATGTATATTATTAT
Found at i:21472167 original size:12 final size:12
Alignment explanation
Indices: 21472150--21472176 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21472140 ACAAGCCACT
21472150 AAATGGAACAGA
1 AAATGGAACAGA
21472162 AAATGGAACAGA
1 AAATGGAACAGA
21472174 AAA
1 AAA
21472177 CAAGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.07, G:0.22, T:0.07
Consensus pattern (12 bp):
AAATGGAACAGA
Found at i:21497039 original size:19 final size:20
Alignment explanation
Indices: 21497008--21497052 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
21496998 CAATATTTCA
21497008 CTTTTTTCATTTTC-CTACT
1 CTTTTTTCATTTTCTCTACT
*
21497027 CTTTTCTTC-TTTTCTCTTCT
1 CTTTT-TTCATTTTCTCTACT
21497047 CTTTTT
1 CTTTTT
21497053 CATCCTCTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (20 bp):
CTTTTTTCATTTTCTCTACT
Found at i:21500738 original size:17 final size:18
Alignment explanation
Indices: 21500716--21500749 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
21500706 TAAATTGAGT
21500716 TCATCTTAG-TTAATAAC
1 TCATCTTAGATTAATAAC
21500733 TCATCTTAGATTAATAA
1 TCATCTTAGATTAATAA
21500750 ATGAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (18 bp):
TCATCTTAGATTAATAAC
Found at i:21502092 original size:17 final size:17
Alignment explanation
Indices: 21502070--21502113 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
21502060 ATTAAAAAAA
*
21502070 TAAAAATATATGAGTAT
1 TAAAAATATACGAGTAT
*
21502087 TAAAAAAATACGAGTAT
1 TAAAAATATACGAGTAT
21502104 TAAAAATATA
1 TAAAAATATA
21502114 AAAAAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (17 bp):
TAAAAATATACGAGTAT
Found at i:21503074 original size:18 final size:18
Alignment explanation
Indices: 21503053--21503097 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
21503043 GAGAGACGAG
21503053 AGAAAAAGAAATCGAAAA
1 AGAAAAAGAAATCGAAAA
* * *
21503071 AGAAGAAGACATTGAAAA
1 AGAAAAAGAAATCGAAAA
21503089 AGAAAAAGA
1 AGAAAAAGA
21503098 GAGTGAGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.69, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCGAAAA
Found at i:21504968 original size:17 final size:18
Alignment explanation
Indices: 21504946--21504979 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
21504936 TAAATTGAGT
21504946 TCATCTTAG-TTAATAAC
1 TCATCTTAGATTAATAAC
21504963 TCATCTTAGATTAATAA
1 TCATCTTAGATTAATAA
21504980 ATGAGTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (18 bp):
TCATCTTAGATTAATAAC
Found at i:21508806 original size:829 final size:826
Alignment explanation
Indices: 21507649--21510084 Score: 3612
Period size: 829 Copynumber: 2.9 Consensus size: 826
21507639 ATGCTTATAC
* * *
21507649 ATGGTTGATTTCATATATATAAGAATAAGTATGCTAACTTGTGAGTTTTGATGATTTTGTATAGG
1 ATGGTTGATTTCATATATATATGAATAAGTATGATAACTTGTGAGTTTTGATGATTTTTTATAGG
*
21507714 CTTATGCCAAGCTTATGGTTTTTGTTGATATTGTACTTATGCTTTATATTTTGCAAATGAAATAG
66 CTTATGCCAAGCTTATGGTTTTTGTTGATATTATACTTATGCTTTATATTTTGCAAATGAAATAG
* * * * *
21507779 TAACTTAAATTTTGGTTTATACAAGCTTACTAAGCACTTGTTCCTTACGTAGTTATTTTCCTTTG
131 TAAGTTAAGTTTTGGTTTATACAAGCTTACTAAGCACTTGTTGCTTACGTAGTT-GTTTCCCTTG
* *
21507844 TTTTATAGATTTTCGAAAGCTCGATTTGGTTGGAAGCTCGTCAGAGACCTATTACACTATCCAGT
195 TTTTATAGATTTTCGAAAGCTCGATTTGGTTGGAAGCTCGTCAAAGACCTATCACACTATCCAGT
* * ** *
21507909 CGTCAATTCGGTAGTTTTTGAGCATTTTAGCCAAGGTTTATAATGGCATGTATTTGGTGCTTTGT
260 AGTCAATTCGGTAGTTTTTGAGCATTTTGGCCAAGGTTTATAATGGCATGTATAGGGTGTTTTGT
** * *
21507974 AATGGTATTTTGATGAATGTATTGTTGTTGTTTTGGTATGTCTAAGTTTTGAAAGTTATGTTTGT
325 AATGGTATTTTGATGAATGTATTAATGTTGTTTTGGCATGTATAAGTTTTGAAAGTTATGTTTGT
* * * *
21508039 TTGGCACTATTTGATTCCTTGTCAAAATATGTTAATTTGATTACCTTATTATTCATGTTTAGAAG
390 TTGGTACTATTTGATGCCTTGTCAAAATATGTTATTTTGATTACCTTATTATTCATGTTTATAAG
21508104 GCTTTGTTTTATGGTATGTTTTGCATGGTTTGAAAATGATTATAAGTGGTATGTTTTAGTAACTA
455 GCTTTGTTTTATGGTATGTTTTGCATGGTTTGAAAATGATTATAAGTGGTATGTTTTAGTAACTA
*
21508169 GTTGGAATAGGTTATCATGTTTGAAATGGTACAATATTGACATGTTTTGATAGTTGTTGCTTTGG
520 GTTGGAATAGGTTATCATGTGTGAAATGGTACAATATTGACATGTTTTGATAGTTGTTG-TTTGG
** * * *
21508234 AATAATGTGGTGCCACTGAACGGCATATTGGTTATTTGAGATAGGATCTTGAAATGACATTTTGA
584 AATAATGTGGTGCCTTTGAATGGCATATTGGTTAGTTGAAATAGGATCTTGAAATGACATTTTGA
21508299 TGTGTATATAGGTGATGTTTAGGTCCCTTTGAAGTGTGCATGAATGGGTTGAAAAGTTATGCATG
649 TGTGTATATAGGTGATGTTTAGGTCCCTTTGAAGTGTGCATGAATGGGTTGAAAAGTTATGCATG
*
21508364 GAATGGTTTTAGGATGGCTTGATTTTAGGTAATTTTGGGTGCACACGGCCTGAGACACGGGTATG
714 GAATGGTTTTAGGATGGCTTGATTTTAGGTAATTTTGGGTGCACAAGGCCTGAGACACGGGTATG
* * *
21508429 TGAGGCACACGGC-ATGGCGACATGGCCGTGTGACATATGGGGATTTCTT
779 TGACGCACACGGCTAAGGC-ACACGGCCGTGTGACATATGGGGATTT-TT
21508478 ATGGTTGATTTCATATATATATGAATAAGTATGATAACTTGTGAGTTTTGATGATTTTTTATAGG
1 ATGGTTGATTTCATATATATATGAATAAGTATGATAACTTGTGAGTTTTGATGATTTTTTATAGG
21508543 CTTATGCCAAGCTTATGGTTTTTGTTGATATTATACTTATGCTTTATATTTTGCAAATGAAATAG
66 CTTATGCCAAGCTTATGGTTTTTGTTGATATTATACTTATGCTTTATATTTTGCAAATGAAATAG
* * * *
21508608 TAAGTGAAGTTTTCGTTTATACAAGCTTACTAAGTACTTGTTGCTTACGTTGTTGTTATCCCATT
131 TAAGTTAAGTTTTGGTTTATACAAGCTTACTAAGCACTTGTTGCTTACGTAGTTGTT-TCCC-TT
* * *
21508673 -TTTTATAGATTTTCGAAAGCTCAATTTGGTTGGAAGCTTGTCAAAGACCTATCACACTATCTAG
194 GTTTTATAGATTTTCGAAAGCTCGATTTGGTTGGAAGCTCGTCAAAGACCTATCACACTATCCAG
* *
21508737 TAGTCAATTCAGTAGCTTTTGAGCATTTTGGCCAAGGTTTATAATGGCATGTATAGGGT-TTTAT
259 TAGTCAATTCGGTAGTTTTTGAGCATTTTGGCCAAGGTTTATAATGGCATGTATAGGGTGTTT-T
*
21508801 GTAATGGTATTTTGATGAATGTATTAATGTTGTTTTGGCATGTATAAGTTTTGAAAGTTAT-ATT
323 GTAATGGTATTTTGATGAATGTATTAATGTTGTTTTGGCATGTATAAGTTTTGAAAGTTATGTTT
* *
21508865 GATTTGGTACTATTTGATGCCTTGTCAAAATGTGTTATTTTGATTACATTATTATT-ACTGTTTA
388 G-TTTGGTACTATTTGATGCCTTGTCAAAATATGTTATTTTGATTACCTTATTATTCA-TGTTTA
* *
21508929 TAAGGCTTTGTTTTATGGTATGTTTTGCATGGTTTGAAAATGATTATAAGTTGTATGTCTTAGTA
451 TAAGGCTTTGTTTTATGGTATGTTTTGCATGGTTTGAAAATGATTATAAGTGGTATGTTTTAGTA
*
21508994 ACTAGTTGGAATAGGTTATCATATGTGAAATGGTACAATATTGACATGTTTTGATAGTTGTTGTT
516 ACTAGTTGGAATAGGTTATCATGTGTGAAATGGTACAATATTGACATGTTTTGATAGTTGTTGTT
* *
21509059 TCGGAATAATGTGGTGCCTTTGAGTGGCATATTGGTTAGTTCAAATAGGATCTTGAAATGACATT
581 T-GGAATAATGTGGTGCCTTTGAATGGCATATTGGTTAGTTGAAATAGGATCTTGAAATGACATT
* * *
21509124 TTGATGTGTATTTAGGTGATGTTTAGGTCCCTTTGAGGTGTGCATGAATGGGTTG---AG-CATG
645 TTGATGTGTATATAGGTGATGTTTAGGTCCCTTTGAAGTGTGCATGAATGGGTTGAAAAGTTATG
*
21509185 CATGGAATGGTTTTTA-GATGGCTTGATTTTAGGTAA-TTT--GTGCACAAGGCCTGAGACACGA
710 CATGGAATGG-TTTTAGGATGGCTTGATTTTAGGTAATTTTGGGTGCACAAGGCCTGAGACACGG
* * ** * *
21509246 GTGTGTGACTCATTCGTCTAAGGCACACGGCCGTGTGACATCTGGGGATTTTT
774 GTATGTGACGCACACGGCTAAGGCACACGGCCGTGTGACATATGGGGATTTTT
* * *
21509299 ATGGTTGATTTCATATATATATATATATATATGAATAAGTACACTATCTTGTGAGTTTTGATGAT
1 ATGGTTGATTTCATATATATAT-GA-ATA-A-G--T-A-T-GA-TAACTTGTGAGTTTTGATGAT
* * * *
21509364 TTTATT-TACGCTTATGCCAAGCTTATGCTTTTTGTTGATATTATTCTTATGTTTTATATTTTGC
56 TTT-TTATAGGCTTATGCCAAGCTTATGGTTTTTGTTGATATTATACTTATGCTTTATATTTTGC
* * *
21509428 AAATGAAATAGTAGGTTAAGTTTTGGTTTATACGAGCTTACTAAGCACTCGTTGCTTACGTAGTT
120 AAATGAAATAGTAAGTTAAGTTTTGGTTTATACAAGCTTACTAAGCACTTGTTGCTTACGTAGTT
* * * *
21509493 GTTTTCCCTTGTTTTATAGCTTTTTGGAAA-CTCGATTTGGTTGAAAGCTCGTCGAAGACCTATC
185 G-TTTCCCTTGTTTTATAG-ATTTTCGAAAGCTCGATTTGGTTGGAAGCTCGTCAAAGACCTATC
* * *
21509557 ACACTATCCAATAGTCAATTCGGTAGTTTTTGAGCATTTTGGCCAAGGCTTATAATGGCATGTGT
248 ACACTATCCAGTAGTCAATTCGGTAGTTTTTGAGCATTTTGGCCAAGGTTTATAATGGCATGTAT
*
21509622 AGGGTGTTTTGTAATGGTATTTTGATGAATGTATTAAAT-TTGTTTTGGCATGTATACGTTTTGA
313 AGGGTGTTTTGTAATGGTATTTTGATGAATGTATT-AATGTTGTTTTGGCATGTATAAGTTTTGA
* * *
21509686 AAGTTATGTTGGTTTAGTACCATTTGATGCCTTGTCAAAATATGTTATTTTGATTACCTTATTAT
377 AAGTTATGTTTGTTTGGTACTATTTGATGCCTTGTCAAAATATGTTATTTTGATTACCTTATTAT
* *
21509751 GCATGTTTATAAGGATTTGTTTTATGGTATGTTTTGCATGGTTTGAAAATGATTATAAGTGGTAT
442 TCATGTTTATAAGGCTTTGTTTTATGGTATGTTTTGCATGGTTTGAAAATGATTATAAGTGGTAT
21509816 GTTTTAGTAACTAGTTGGAATAGGTTATCATGTGTGAAATGGTACAATATTGACATGTTTTGATA
507 GTTTTAGTAACTAGTTGGAATAGGTTATCATGTGTGAAATGGTACAATATTGACATGTTTTGATA
* *
21509881 GTTTTTGTTTTGGAATAACT-TGGTGCCTTTGAATGGCATATTCGTTAGTTGAAATAGGATCTTG
572 GTTGTTG-TTTGGAATAA-TGTGGTGCCTTTGAATGGCATATTGGTTAGTTGAAATAGGATCTTG
* * ** * *
21509945 AACTGAAATTTTGATGTGTATATAGGTGATGTTTTTGTCCCTTTAAAGTGTGCGTGAATGGGTTG
635 AAATGACATTTTGATGTGTATATAGGTGATGTTTAGGTCCCTTTGAAGTGTGCATGAATGGGTTG
** * * *
21510010 AAAAGTTATTAATGGAATGGTTTT-GTGATGGCTTGCTTTTAGGTAATTTTGGGTTCACATGGCC
700 AAAAGTTATGCATGGAATGGTTTTAG-GATGGCTTGATTTTAGGTAATTTTGGGTGCACAAGGCC
*
21510074 TAAGACACGGG
764 TGAGACACGGG
21510085 CGTGTGACTC
Statistics
Matches: 1451, Mismatches: 119, Indels: 65
0.89 0.07 0.04
Matches are distributed among these distances:
821 24 0.02
822 58 0.04
823 7 0.00
824 4 0.00
825 34 0.02
826 7 0.00
827 1 0.00
828 12 0.01
829 634 0.44
830 5 0.00
831 582 0.40
832 25 0.02
834 6 0.00
835 30 0.02
836 3 0.00
838 19 0.01
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (826 bp):
ATGGTTGATTTCATATATATATGAATAAGTATGATAACTTGTGAGTTTTGATGATTTTTTATAGG
CTTATGCCAAGCTTATGGTTTTTGTTGATATTATACTTATGCTTTATATTTTGCAAATGAAATAG
TAAGTTAAGTTTTGGTTTATACAAGCTTACTAAGCACTTGTTGCTTACGTAGTTGTTTCCCTTGT
TTTATAGATTTTCGAAAGCTCGATTTGGTTGGAAGCTCGTCAAAGACCTATCACACTATCCAGTA
GTCAATTCGGTAGTTTTTGAGCATTTTGGCCAAGGTTTATAATGGCATGTATAGGGTGTTTTGTA
ATGGTATTTTGATGAATGTATTAATGTTGTTTTGGCATGTATAAGTTTTGAAAGTTATGTTTGTT
TGGTACTATTTGATGCCTTGTCAAAATATGTTATTTTGATTACCTTATTATTCATGTTTATAAGG
CTTTGTTTTATGGTATGTTTTGCATGGTTTGAAAATGATTATAAGTGGTATGTTTTAGTAACTAG
TTGGAATAGGTTATCATGTGTGAAATGGTACAATATTGACATGTTTTGATAGTTGTTGTTTGGAA
TAATGTGGTGCCTTTGAATGGCATATTGGTTAGTTGAAATAGGATCTTGAAATGACATTTTGATG
TGTATATAGGTGATGTTTAGGTCCCTTTGAAGTGTGCATGAATGGGTTGAAAAGTTATGCATGGA
ATGGTTTTAGGATGGCTTGATTTTAGGTAATTTTGGGTGCACAAGGCCTGAGACACGGGTATGTG
ACGCACACGGCTAAGGCACACGGCCGTGTGACATATGGGGATTTTT
Found at i:21520436 original size:20 final size:19
Alignment explanation
Indices: 21520406--21520457 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
21520396 TATCAATTCA
21520406 AATATTAAAAAAAATTAAAT
1 AATATT-AAAAAAATTAAAT
* *
21520426 AATAATTAAAAAATTTATAT
1 AAT-ATTAAAAAAATTAAAT
*
21520446 CATATTAAAAAA
1 AATATTAAAAAA
21520458 TCGATATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.32
20 16 0.57
21 3 0.11
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AATATTAAAAAAATTAAAT
Found at i:21520438 original size:19 final size:18
Alignment explanation
Indices: 21520414--21520458 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
21520404 CAAATATTAA
21520414 AAAAAATTAAATAATAATT
1 AAAAAATTAAATAAT-ATT
* *
21520433 AAAAAATTTATATCATATT
1 AAAAAA-TTAAATAATATT
21520452 AAAAAAT
1 AAAAAAT
21520459 CGATATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAATTAAATAATATT
Found at i:21522522 original size:27 final size:26
Alignment explanation
Indices: 21522482--21522532 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
21522472 TCATATTGGT
*
21522482 AAATAGAATGTGTAAGAAAATGTGATG
1 AAATAGAATATGTAAGAAAA-GTGATG
* *
21522509 AAATAGTATATGTATGAAAAGTGA
1 AAATAGAATATGTAAGAAAAGTGA
21522533 AAGAGAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (26 bp):
AAATAGAATATGTAAGAAAAGTGATG
Found at i:21529109 original size:14 final size:14
Alignment explanation
Indices: 21529090--21529116 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21529080 ATTACCACAG
21529090 GTGGATTGGTATTT
1 GTGGATTGGTATTT
21529104 GTGGATTGGTATT
1 GTGGATTGGTATT
21529117 CATTGTTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (14 bp):
GTGGATTGGTATTT
Found at i:21540914 original size:178 final size:178
Alignment explanation
Indices: 21540615--21540972 Score: 608
Period size: 178 Copynumber: 2.0 Consensus size: 178
21540605 TTGCTATAAA
*
21540615 CATCATTTCTTGATTCACCACACATTTTTAGCTATAAAATAGAAACATTTTATAATCAACATCAA
1 CATCATTTCTTGATTCACCACACATTTTCAGCTATAAAATAGAAACATTTTATAATCAACATCAA
* * * * *
21540680 AATCCTGACTCAACTCGAATTAACTTGGCATGTACCTCTAAACTTAATTCTGAACTTGATTTTAG
66 AATCCCGACTCAACTCGAATCAACTTGGCATATACCTCTAAACTCAATTCTGAACTTCATTTTAG
* *
21540745 TCCAAGAATCGGCTAAACCAATAGCTCTGACACCATTAACTGTAACAC
131 TCCAAGAATCAGCTAAACCAATAGCTCTGACACCATTAAATGTAACAC
* *
21540793 CATCATTTCTTGATTCACCACACATTTTCAGCTATACAATAGAAACATTTTATAATCAACATCCA
1 CATCATTTCTTGATTCACCACACATTTTCAGCTATAAAATAGAAACATTTTATAATCAACATCAA
*
21540858 AATCCCGACTCAACTCGAATCAACTTGGCATATACCTCTAGACTCAATTCTGAACTTCATTTTAG
66 AATCCCGACTCAACTCGAATCAACTTGGCATATACCTCTAAACTCAATTCTGAACTTCATTTTAG
*
21540923 TCCAAGAATTAGCTAAACCAATAGCTCTGACACCATTAAATGTAACAC
131 TCCAAGAATCAGCTAAACCAATAGCTCTGACACCATTAAATGTAACAC
21540971 CA
1 CA
21540973 CATACCCGAC
Statistics
Matches: 168, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
178 168 1.00
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (178 bp):
CATCATTTCTTGATTCACCACACATTTTCAGCTATAAAATAGAAACATTTTATAATCAACATCAA
AATCCCGACTCAACTCGAATCAACTTGGCATATACCTCTAAACTCAATTCTGAACTTCATTTTAG
TCCAAGAATCAGCTAAACCAATAGCTCTGACACCATTAAATGTAACAC
Found at i:21541541 original size:21 final size:20
Alignment explanation
Indices: 21541500--21541544 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
21541490 CCTTATCAAT
* *
21541500 CATAACTTAAACAACTAATG
1 CATAACTTAAAAAAATAATG
*
21541520 CATAACATTAAAAAAATTATG
1 CATAAC-TTAAAAAAATAATG
21541541 CATA
1 CATA
21541545 CATACCTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (20 bp):
CATAACTTAAAAAAATAATG
Found at i:21551763 original size:27 final size:27
Alignment explanation
Indices: 21551733--21551811 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
21551723 CTCAATCTTT
21551733 GACTAACGAACCCCAGTTCGCCAA-ACA
1 GACTAACGAACCCCAGTTCG-CAACACA
* * *
21551760 GACTAACAAAACCCCAGGTCGCAACTCA
1 GACTAAC-GAACCCCAGTTCGCAACACA
* *
21551788 -ACTAGCGAACCCTCAGTTCACAAC
1 GACTAACGAACCC-CAGTTCGCAAC
21551812 TTACTTAGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 5 0.12
27 24 0.57
28 13 0.31
ACGTcount: A:0.37, C:0.37, G:0.14, T:0.13
Consensus pattern (27 bp):
GACTAACGAACCCCAGTTCGCAACACA
Found at i:21551964 original size:16 final size:16
Alignment explanation
Indices: 21551943--21551987 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
21551933 CTGATACACT
21551943 TTTGGCGAACTCCCCC
1 TTTGGCGAACTCCCCC
*
21551959 TTTGGCGAACTCCCCT
1 TTTGGCGAACTCCCCC
21551975 TTTGGCGAACTCC
1 TTTGGCGAACTCC
21551988 TCAGTTCGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.13, C:0.38, G:0.20, T:0.29
Consensus pattern (16 bp):
TTTGGCGAACTCCCCC
Found at i:21552380 original size:4 final size:4
Alignment explanation
Indices: 21552371--21552398 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
21552361 TTAACTTATG
21552371 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
21552399 TGAAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:21558671 original size:20 final size:21
Alignment explanation
Indices: 21558636--21558679 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
21558626 TTAAACACAT
21558636 AATTTAATCTATTTTTAAATA
1 AATTTAATCTATTTTTAAATA
*
21558657 AATTTAATTTA-TTTTAAATA
1 AATTTAATCTATTTTTAAATA
21558677 AAT
1 AAT
21558680 AAATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTAATCTATTTTTAAATA
Found at i:21583597 original size:21 final size:23
Alignment explanation
Indices: 21583550--21583598 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
21583540 TAAATTGACT
**
21583550 TTTAATTTTTTATCATAATTATT
1 TTTAATTTTTTATCATAATTACA
*
21583573 TTTAA-TTTTTCT-ATAATTACA
1 TTTAATTTTTTATCATAATTACA
21583594 TTTAA
1 TTTAA
21583599 AATTAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 12 0.52
22 6 0.26
23 5 0.22
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTAATTTTTTATCATAATTACA
Found at i:21590121 original size:3 final size:3
Alignment explanation
Indices: 21590113--21590139 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
21590103 TCTATTTCTC
21590113 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
21590140 TATTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.