Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 46 of 171
Found at i:19581952 original size:29 final size:27
Alignment explanation
Indices: 19581920--19581976 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
19581910 CTTCTTTTTT
*
19581920 TTTCAAACATGGAGTTTTAGCATTTTTAA
1 TTTCAAAC-TCGA-TTTTAGCATTTTTAA
*
19581949 TTTCTAACTCGATTTTAGCATTTTTAA
1 TTTCAAACTCGATTTTAGCATTTTTAA
19581976 T
1 T
19581977 CCATAGTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 16 0.62
28 3 0.12
29 7 0.27
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (27 bp):
TTTCAAACTCGATTTTAGCATTTTTAA
Found at i:19586450 original size:2 final size:2
Alignment explanation
Indices: 19586443--19586476 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19586433 AATCTCAAAC
19586443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19586477 ATCAATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19599046 original size:19 final size:18
Alignment explanation
Indices: 19599013--19599048 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19599003 ATTTTATTTT
19599013 TAAATTAAAAAATATATG
1 TAAATTAAAAAATATATG
*
19599031 TAAATATAAAATATATAT
1 TAAAT-TAAAAAATATAT
19599049 CAAAAAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAATTAAAAAATATATG
Found at i:19601340 original size:2 final size:2
Alignment explanation
Indices: 19601333--19601360 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19601323 GAAAGGTGAA
19601333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19601361 TTTATTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19608074 original size:16 final size:17
Alignment explanation
Indices: 19608053--19608089 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
19608043 TCAAAAATTT
*
19608053 TAATTTA-AATATTTTA
1 TAATTTATAAAATTTTA
19608069 TAATTTATAAAATTTTA
1 TAATTTATAAAATTTTA
19608086 -AATT
1 TAATT
19608090 ATTAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATTTATAAAATTTTA
Found at i:19609624 original size:30 final size:29
Alignment explanation
Indices: 19609588--19609909 Score: 186
Period size: 29 Copynumber: 10.9 Consensus size: 29
19609578 TCCCGAGGGC
*
19609588 AAAAATGTAATTTTAGGAAAATTTAGGGTT
1 AAAAATGTAATTTT-GGAAAGTTTAGGGTT
* *
19609618 AAAAATGGAATTTTGGAAAGTTTAGGGGGGT
1 AAAAATGTAATTTTGGAAAGTTTA--GGGTT
*
19609649 -AAAATGGTAATTATTGGTAAA-ATTAGGGTT
1 AAAAAT-GTAATT-TTGG-AAAGTTTAGGGTT
* **
19609679 AAATA-G-AATTTTGGAAAGTTTAGGGGC
1 AAAAATGTAATTTTGGAAAGTTTAGGGTT
**
19609706 AAAAATGTAATTTTTGGTGAAA-TCGA-GGTT
1 AAAAATGTAA-TTTT-G-GAAAGTTTAGGGTT
19609736 AAAAATAG-AATTTTGGAAAGTTT-GAGG-T
1 AAAAAT-GTAATTTTGGAAAGTTTAG-GGTT
*
19609764 -AAAATGGTAATTTTTAGG-AAGTTTGGGGTT
1 AAAAAT-GTAA-TTTT-GGAAAGTTTAGGGTT
* *
19609794 -AAAATGTAATTTTTAGAAAGTTTTGGG-T
1 AAAAATGTAA-TTTTGGAAAGTTTAGGGTT
* * * ** *
19609822 CAAAATATAATTTTGGGGAAGTTCGGGGGT
1 AAAAATGTAATTTT-GGAAAGTTTAGGGTT
* *
19609852 CAAAATGTAATTTTTAGAAAGTTTTAGGGTT
1 AAAAATGTAA-TTTTGGAAAG-TTTAGGGTT
*
19609883 -AAAATATAATTTTGGAGAAGTTTAGGG
1 AAAAATGTAATTTTGGA-AAGTTTAGGG
19609910 ACCTATAGAG
Statistics
Matches: 231, Mismatches: 33, Indels: 57
0.72 0.10 0.18
Matches are distributed among these distances:
26 3 0.01
27 24 0.10
28 16 0.07
29 78 0.34
30 70 0.30
31 26 0.11
32 11 0.05
33 3 0.01
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAAATGTAATTTTGGAAAGTTTAGGGTT
Found at i:19609700 original size:59 final size:57
Alignment explanation
Indices: 19609589--19609777 Score: 199
Period size: 59 Copynumber: 3.2 Consensus size: 57
19609579 CCCGAGGGCA
*
19609589 AAAATGTAATTTTAGG-AAAATTTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGGGT
1 AAAATGTAATTTT-GGTAAAA-TTAGGGTT-AAAATAGAATTTTGGAAAGTTTA-GGGGGT
**
19609649 AAAATGGTAATTATTGGTAAAATTAGGGTT-AAATAGAATTTTGGAAAGTTTAGGGGCA
1 AAAAT-GTAATT-TTGGTAAAATTAGGGTTAAAATAGAATTTTGGAAAGTTTAGGGGGT
* * *
19609707 AAAATGTAATTTTTGGTGAAA-TCGAGGTTAAAAATAGAATTTTGGAAAGTTT--GAGGT
1 AAAATGTAA-TTTTGGTAAAATTAG-GGTT-AAAATAGAATTTTGGAAAGTTTAGGGGGT
19609764 AAAATGGTAATTTT
1 AAAAT-GTAATTTT
19609778 TAGGAAGTTT
Statistics
Matches: 113, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
56 2 0.02
57 27 0.24
58 15 0.13
59 42 0.37
60 5 0.04
61 16 0.14
62 6 0.05
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.34
Consensus pattern (57 bp):
AAAATGTAATTTTGGTAAAATTAGGGTTAAAATAGAATTTTGGAAAGTTTAGGGGGT
Found at i:19609762 original size:29 final size:28
Alignment explanation
Indices: 19609589--19609905 Score: 150
Period size: 30 Copynumber: 10.8 Consensus size: 28
19609579 CCCGAGGGCA
*
19609589 AAAATGTAATTTTAGGAAAATTT-AGGGTT
1 AAAATGTAATTTT-GGAAAGTTTGA-GGTT
* * *
19609618 AAAAATGGAATTTTGGAAAGTTTAGGGGGGT
1 -AAAATGTAATTTTGGAAAGTTT--GAGGTT
* *
19609649 AAAATGGTAATTATTGGTAAAATTAG-GGTT
1 AAAAT-GTAATT-TTGG-AAAGTTTGAGGTT
* **
19609679 -AAATAG-AATTTTGGAAAGTTTAGGGGCA
1 AAAAT-GTAATTTTGGAAAGTTT-GAGGTT
*
19609707 AAAATGTAATTTTTGGTGAAA--TCGAGGTT
1 AAAATGTAA-TTTT-G-GAAAGTTTGAGGTT
19609736 AAAAATAG-AATTTTGGAAAGTTTGAGG-T
1 -AAAAT-GTAATTTTGGAAAGTTTGAGGTT
*
19609764 AAAATGGTAATTTTTAGG-AAGTTTGGGGTT
1 AAAAT-GTAA-TTTT-GGAAAGTTTGAGGTT
* *
19609794 AAAATGTAATTTTTAGAAAGTTTTG-GGTC
1 AAAATGTAA-TTTTGGAAAG-TTTGAGGTT
* * * * *
19609823 AAAATATAATTTTGGGGAAGTTCGGGGGTC
1 AAAATGTAATTTT-GGAAAGTT-TGAGGTT
* *
19609853 AAAATGTAATTTTTAGAAAGTTTTAGGGTT
1 AAAATGTAA-TTTTGGAAAGTTTGA-GGTT
*
19609883 AAAATATAATTTTGGAGAAGTTT
1 AAAATGTAATTTTGGA-AAGTTT
19609906 AGGGACCTAT
Statistics
Matches: 223, Mismatches: 35, Indels: 58
0.71 0.11 0.18
Matches are distributed among these distances:
26 5 0.02
27 15 0.07
28 18 0.08
29 78 0.35
30 79 0.35
31 15 0.07
32 8 0.04
33 5 0.02
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAGTTTGAGGTT
Found at i:19609861 original size:59 final size:57
Alignment explanation
Indices: 19609746--19609904 Score: 194
Period size: 59 Copynumber: 2.7 Consensus size: 57
19609736 AAAAATAGAA
* * ** * *
19609746 TTTTGGAAAG-TTTGAGGTAAAATGGTAATTTTTAGGAAGTTTGGGGTTAAAATGTAAT
1 TTTTAGAAAGTTTTG-GGTAAAAT-ATAATTTTGGGGAAGTTGGGGGTCAAAATGTAAT
19609804 TTTTAGAAAGTTTTGGGTCAAAATATAATTTTGGGGAAGTTCGGGGGTCAAAATGTAAT
1 TTTTAGAAAGTTTTGGGT-AAAATATAATTTTGGGGAAGTT-GGGGGTCAAAATGTAAT
*
19609863 TTTTAGAAAGTTTTAGGGTTAAAATATAATTTTGGAGAAGTT
1 TTTTAGAAAGTTTT-GGG-TAAAATATAATTTTGGGGAAGTT
19609905 TAGGGACCTA
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
58 26 0.29
59 38 0.43
60 24 0.27
61 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (57 bp):
TTTTAGAAAGTTTTGGGTAAAATATAATTTTGGGGAAGTTGGGGGTCAAAATGTAAT
Found at i:19611596 original size:25 final size:25
Alignment explanation
Indices: 19611568--19611615 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
19611558 TGGCAGAATA
*
19611568 GTTTGGAGCCGGTAGTGGCAGAGCG
1 GTTTAGAGCCGGTAGTGGCAGAGCG
*
19611593 GTTTAGAGCCGGTGGTGGCAGAG
1 GTTTAGAGCCGGTAGTGGCAGAG
19611616 GCAGCTTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.17, C:0.15, G:0.48, T:0.21
Consensus pattern (25 bp):
GTTTAGAGCCGGTAGTGGCAGAGCG
Found at i:19611868 original size:17 final size:17
Alignment explanation
Indices: 19611846--19611910 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
19611836 TTGGACATTT
19611846 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
*
19611863 TAAATTTAAATTT-TATG
1 TAAATTTAAATTTATA-A
* * *
19611880 TAAATTTCAATTCAAAA
1 TAAATTTAAATTTATAA
*
19611897 TAAATTTAATTTTA
1 TAAATTTAAATTTA
19611911 AAAAAAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 2 0.05
17 35 0.92
18 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:19611885 original size:34 final size:33
Alignment explanation
Indices: 19611846--19611910 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
19611836 TTGGACATTT
* *
19611846 TAAATTTAAATTTATAATAAATTTAAATTTTATG
1 TAAATTTAAATTCAAAATAAATTT-AATTTTATG
*
19611880 TAAATTTCAATTCAAAATAAATTTAATTTTA
1 TAAATTTAAATTCAAAATAAATTTAATTTTA
19611911 AAAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (33 bp):
TAAATTTAAATTCAAAATAAATTTAATTTTATG
Found at i:19612731 original size:200 final size:200
Alignment explanation
Indices: 19612270--19612991 Score: 1077
Period size: 200 Copynumber: 3.6 Consensus size: 200
19612260 CGTTGACTTT
* * *
19612270 GACCTGCTTCTCAATGTCTCATCAGGAAGCTGGATTCGAAGATTTGCCCGCATTGAGCTTTAGTT
1 GACCTGCTTCTCAATGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCATTGAGC---A--T
* * * * * *
19612335 TGATTTGGTCTTCTTCTCAGTGTATCATCAAGAAGATGACCGCCTCGATTGTTTTAATTCGCTTC
61 TGAGTTGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTC
* * * *
19612400 TCTGGATCTCCTCAGGAAGACGAATCTGGTTCACTTCTCTATATATCTCATCAGGAAGCTAACCA
126 TCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTC--TGTATCTCATCAGGAAGCTAGCCA
*
19612465 TTTTATTACTTC
189 TTTTATTGCTTC
* * *
19612477 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCTCGTTGAGCATTGAGT
1 GACCTGCTTCTCAATGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCATTGAGCATTGAGT
* *
19612542 TGGTATTCTTCTCTGTATCTAATCAAGAAGATGACCGCCTCGTTTGTTTTAATTCGCTTCTCTGG
66 TGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTGG
*
19612607 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCGTCAGGAAGCTAGCCATTTTATT
131 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAGCCATTTTATT
19612672 GCTTC
196 GCTTC
* * * *
19612677 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCTCGTTGAGCGTTGAGT
1 GACCTGCTTCTCAATGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCATTGAGCATTGAGT
* * *
19612742 TTGTATTCTTCTCTGTACCTCATC-AGAAAGATGATCGCCTCGCTTGTTTTAATTCGCTTCTCTG
66 TGGTATTCTTCTCTGTATCTCATCAAG-AAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTG
*
19612806 GATCTCCTCAGAAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAGCCATTTTAT
130 GATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAGCCATTTTAT
19612871 TGCTTC
195 TGCTTC
* * *
19612877 GACCTGCTTCTCAATGTCTCATCAGGAAACTGGGTTCGAAGATTTGCTCGCATTGAGCGTTGAGT
1 GACCTGCTTCTCAATGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCATTGAGCATTGAGT
*
19612942 TGGTATTCTTCTCTGTATTTCATCAAGAAGATGACCGCCTCGCTTGTTTT
66 TGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCGCTTGTTTT
19612992 GTTGAATTAC
Statistics
Matches: 477, Mismatches: 36, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
199 2 0.00
200 324 0.68
201 2 0.00
202 96 0.20
204 1 0.00
207 52 0.11
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (200 bp):
GACCTGCTTCTCAATGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGCATTGAGCATTGAGT
TGGTATTCTTCTCTGTATCTCATCAAGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTGG
ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAGCCATTTTATT
GCTTC
Found at i:19613401 original size:49 final size:49
Alignment explanation
Indices: 19613299--19613486 Score: 270
Period size: 49 Copynumber: 3.8 Consensus size: 49
19613289 TTGCATCATT
* * * *
19613299 GTGGTACTGGATCCGCCGTCGCGATCTTAGATCTTT-CTCTTCATATCTTC
1 GTGGTACTGGATCCGCCGTTGCG-GCTTAGATCTTTCCT-TTGATGTCTTC
* *
19613349 GTGGTACTGGATCCGCCGTTACGGCTTATATCTTTCCTTTGATGTCTTC
1 GTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCTTTGATGTCTTC
**
19613398 GTGGTACTGGATCTACCGTTGCGGCTTAGATCTTTCCTTTGATGTCTTC
1 GTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCTTTGATGTCTTC
*
19613447 GTGGTACTGGATCCGCCGTTGCAGCTTAGATCTTTCCTTT
1 GTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCTTT
19613487 CTATCTTCTG
Statistics
Matches: 124, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
49 101 0.81
50 23 0.19
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.39
Consensus pattern (49 bp):
GTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCTTTGATGTCTTC
Found at i:19613455 original size:98 final size:99
Alignment explanation
Indices: 19613298--19613532 Score: 289
Period size: 98 Copynumber: 2.4 Consensus size: 99
19613288 TTTGCATCAT
** *
19613298 TGTGGTACTGGATCCGCCGTCGCGATCTTAGATCTTT-CTCTTCATATCTTCGTGGTACTGGATC
1 TGTGGTACTGGATCTACCGTTGCGA-CTTAGATCTTTCCTCTTCATATCTTCGTGGTACTGGATC
* * *
19613362 CGCCGTTACGGCTTATATCTTTCCTTTGATGTCTTC
65 CGCCGTTACAGCTTAGATCTTTCCTTT-ATATCTTC
* * *
19613398 -GTGGTACTGGATCTACCGTTGCGGCTTAGATCTTTCCT-TTGATGTCTTCGTGGTACTGGATCC
1 TGTGGTACTGGATCTACCGTTGCGACTTAGATCTTTCCTCTTCATATCTTCGTGGTACTGGATCC
* *
19613461 GCCGTTGCAGCTTAGATCTTTCCTTTCTATCTTC
66 GCCGTTACAGCTTAGATCTTTCCTTTATATCTTC
* * *
19613495 TGAGGTACACGG-TCTACCGTTGCGACTTAGACCTTTCC
1 TGTGGTAC-TGGATCTACCGTTGCGACTTAGATCTTTCC
19613533 CTTTTGTCTT
Statistics
Matches: 117, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
97 6 0.05
98 87 0.74
99 24 0.21
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (99 bp):
TGTGGTACTGGATCTACCGTTGCGACTTAGATCTTTCCTCTTCATATCTTCGTGGTACTGGATCC
GCCGTTACAGCTTAGATCTTTCCTTTATATCTTC
Found at i:19613515 original size:49 final size:48
Alignment explanation
Indices: 19613324--19613532 Score: 181
Period size: 49 Copynumber: 4.3 Consensus size: 48
19613314 CCGTCGCGAT
* * * ** *
19613324 CTTAGATCTTT-CTCTTCATATCTTCGTGGTACTGGATCCGCCGTTACGG
1 CTTAGATCTTTCCT-TTGATATCTTCGAGGTACCGGATCTACCGTTGC-G
* * * *
19613373 CTTATATCTTTCCTTTGATGTCTTCGTGGTACTGGATCTACCGTTGCGG
1 CTTAGATCTTTCCTTTGATATCTTCGAGGTACCGGATCTACCGTTGC-G
* * * **
19613422 CTTAGATCTTTCCTTTGATGTCTTCGTGGTACTGGATCCGCCGTTGCAG
1 CTTAGATCTTTCCTTTGATATCTTCGAGGTACCGGATCTACCGTTGC-G
*
19613471 CTTAGATCTTTCCTTT-CTATCTTCTGAGGTACACGG-TCTACCGTTGCG
1 CTTAGATCTTTCCTTTGATATCTTC-GAGGTAC-CGGATCTACCGTTGCG
*
19613519 ACTTAGACCTTTCC
1 -CTTAGATCTTTCC
19613533 CTTTTGTCTT
Statistics
Matches: 139, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
48 7 0.05
49 128 0.92
50 4 0.03
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.40
Consensus pattern (48 bp):
CTTAGATCTTTCCTTTGATATCTTCGAGGTACCGGATCTACCGTTGCG
Found at i:19614625 original size:23 final size:22
Alignment explanation
Indices: 19614599--19614678 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
19614589 TCGACCTCTC
*
19614599 TTTTCTTTTCTTTTTTTGTTTAT
1 TTTTCTTTTCTTTTTTTCTTT-T
* *
19614622 TTTT-TTTTGTTTTTTTCATTT
1 TTTTCTTTTCTTTTTTTCTTTT
*
19614643 TTTTCGTTTTGTTTTTCTTCTTCTT
1 TTTTC-TTTTCTTTTT-TTCTT-TT
19614668 TTTTCTTTTCT
1 TTTTCTTTTCT
19614679 ATTTATTCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
21 5 0.10
22 13 0.27
23 14 0.29
24 9 0.19
25 7 0.15
ACGTcount: A:0.03, C:0.11, G:0.05, T:0.81
Consensus pattern (22 bp):
TTTTCTTTTCTTTTTTTCTTTT
Found at i:19614628 original size:14 final size:13
Alignment explanation
Indices: 19614599--19614637 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
19614589 TCGACCTCTC
* *
19614599 TTTTCTTTTCTTT
1 TTTTGTTTTTTTT
19614612 TTTTGTTTATTTTT
1 TTTTGTTT-TTTTT
19614626 TTTTGTTTTTTT
1 TTTTGTTTTTTT
19614638 CATTTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.87
Consensus pattern (13 bp):
TTTTGTTTTTTTT
Found at i:19619020 original size:5 final size:5
Alignment explanation
Indices: 19619010--19619036 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19619000 AAGCTGAGTT
19619010 GGATA GGATA GGATA GGATA GGATA GG
1 GGATA GGATA GGATA GGATA GGATA GG
19619037 TGAATATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.44, T:0.19
Consensus pattern (5 bp):
GGATA
Found at i:19619716 original size:22 final size:22
Alignment explanation
Indices: 19619665--19619710 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
19619655 TACAAACATC
19619665 TAAAAATATATAACAAATAAAA
1 TAAAAATATATAACAAATAAAA
*
19619687 TTAAAATATAT-ACAAA-AAAA
1 TAAAAATATATAACAAATAAAA
19619707 TAAA
1 TAAA
19619711 GAAATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 5 0.23
22 10 0.45
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAAATATATAACAAATAAAA
Found at i:19621333 original size:19 final size:19
Alignment explanation
Indices: 19621289--19621340 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
19621279 TTGATGGAGT
* *
19621289 TAATACAATATACATAATA
1 TAATAAAATATAAATAATA
*
19621308 -AATTAAAATATAAATATTA
1 TAA-TAAAATATAAATAATA
19621327 TAATAAAATA-AAAT
1 TAATAAAATATAAAT
19621341 TTTAGTATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.21
19 20 0.71
20 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAAATATAAATAATA
Found at i:19622187 original size:18 final size:19
Alignment explanation
Indices: 19622164--19622205 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
19622154 ACATACTTTT
*
19622164 TATTTTTAT-TTTTTAAAA
1 TATTTTTATAATTTTAAAA
*
19622182 TATTTTTATAATTTTAAAT
1 TATTTTTATAATTTTAAAA
19622201 TATTT
1 TATTT
19622206 GTTAACGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTTTATAATTTTAAAA
Found at i:19623248 original size:31 final size:31
Alignment explanation
Indices: 19623213--19623339 Score: 97
Period size: 31 Copynumber: 4.2 Consensus size: 31
19623203 CATTTGTATT
*
19623213 TAAACTTGACACTTTTTCTTAATTTGATACC
1 TAAACTTGACACTTTTTCTTAATTTGGTACC
* * *
19623244 TAAACTT-----TTTTTGGTCCAATTTGGTA-T
1 TAAACTTGACACTTTTT-CT-TAATTTGGTACC
* *
19623271 TCAAACTTGACAATTTTTCCTAATTTGGTACC
1 T-AAACTTGACACTTTTTCTTAATTTGGTACC
* **
19623303 TAAACTTGACACTTTTT-TTAAGTTGGTATT
1 TAAACTTGACACTTTTTCTTAATTTGGTACC
19623333 TAAACTT
1 TAAACTT
19623340 TTGGGGGTCC
Statistics
Matches: 74, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
26 5 0.07
27 2 0.03
28 14 0.19
30 16 0.22
31 31 0.42
32 1 0.01
33 5 0.07
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (31 bp):
TAAACTTGACACTTTTTCTTAATTTGGTACC
Found at i:19631634 original size:18 final size:16
Alignment explanation
Indices: 19631613--19631648 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
19631603 TTTAAAAAAT
19631613 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
19631631 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
19631647 TT
1 TT
19631649 CTCATTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:19632127 original size:21 final size:21
Alignment explanation
Indices: 19632094--19632136 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
19632084 ATATATATAT
19632094 AAATAAATAAAT-AATTTCAAA
1 AAATAAATAAATAAATTT-AAA
19632115 AAATACAAT-AATAAATTTAAA
1 AAATA-AATAAATAAATTTAAA
19632136 A
1 A
19632137 TATATAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATAAATAAATAAATTTAAA
Found at i:19633308 original size:30 final size:31
Alignment explanation
Indices: 19633235--19633315 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
19633225 AAATGAATAG
*
19633235 TAAGTAGAG-GACTGTTTTGTCACTTTTCGA
1 TAAGTTGAGTGACTGTTTTGTCACTTTTCGA
* *
19633265 TAACTTTAGTGACTGTTTTGTCACATTTTC-A
1 TAAGTTGAGTGACTGTTTTGTCAC-TTTTCGA
*
19633296 -AAGTTGAGTGACTATTTTGT
1 TAAGTTGAGTGACTGTTTTGT
19633316 TAAATGTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
30 23 0.53
31 15 0.35
32 5 0.12
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.44
Consensus pattern (31 bp):
TAAGTTGAGTGACTGTTTTGTCACTTTTCGA
Found at i:19635295 original size:14 final size:16
Alignment explanation
Indices: 19635266--19635298 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
19635256 TGATTAATAG
19635266 ATTATTATGATTTTTA
1 ATTATTATGATTTTTA
19635282 ATTATT-TG-TTTTTA
1 ATTATTATGATTTTTA
19635296 ATT
1 ATT
19635299 TTTAAATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 2 0.12
16 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
ATTATTATGATTTTTA
Found at i:19636392 original size:16 final size:17
Alignment explanation
Indices: 19636371--19636403 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
19636361 AATATTTTTT
19636371 AAAAATATTT-AATATA
1 AAAAATATTTAAATATA
19636387 AAAAATATTTAAATATA
1 AAAAATATTTAAATATA
19636404 CTAAATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAATATTTAAATATA
Found at i:19647088 original size:15 final size:15
Alignment explanation
Indices: 19647068--19647099 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19647058 AGTATCATAC
19647068 AAATATGTGCTCAAG
1 AAATATGTGCTCAAG
19647083 AAATATGTGCTCAAG
1 AAATATGTGCTCAAG
19647098 AA
1 AA
19647100 GAGTATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (15 bp):
AAATATGTGCTCAAG
Found at i:19650661 original size:29 final size:30
Alignment explanation
Indices: 19650611--19650671 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
19650601 AATTGCGATG
19650611 TTATATATAGATTTTAATTTTG-TTCAATT
1 TTATATATAGATTTTAATTTTGATTCAATT
*
19650640 TTATATAT-GAATTGTTAA-TTTGATTTAATT
1 TTATATATAG-ATT-TTAATTTTGATTCAATT
19650670 TT
1 TT
19650672 CAAAAACAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 1 0.04
29 15 0.54
30 12 0.43
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (30 bp):
TTATATATAGATTTTAATTTTGATTCAATT
Found at i:19650817 original size:26 final size:25
Alignment explanation
Indices: 19650787--19650840 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
19650777 TTTTCTACGA
*
19650787 TAATAACAATACAAT-TTTATCATTTT
1 TAATAAC-ATA-AATCTTTATAATTTT
*
19650813 TAATAACTTAAATCTTTATAATTTT
1 TAATAACATAAATCTTTATAATTTT
19650838 TAA
1 TAA
19650841 AGAATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 15 0.60
26 7 0.28
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (25 bp):
TAATAACATAAATCTTTATAATTTT
Found at i:19650848 original size:25 final size:25
Alignment explanation
Indices: 19650802--19650851 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
19650792 ACAATACAAT
* *
19650802 TTTATCATTTTTAATAACTTAAATC
1 TTTATAATTTTTAATAAATTAAATC
19650827 TTTATAATTTTTAA-AGAATTAAATC
1 TTTATAATTTTTAATA-AATTAAATC
19650852 AAAATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (25 bp):
TTTATAATTTTTAATAAATTAAATC
Found at i:19651506 original size:52 final size:51
Alignment explanation
Indices: 19651382--19651510 Score: 134
Period size: 52 Copynumber: 2.5 Consensus size: 51
19651372 ATTAGAATAA
* * * * *
19651382 TAATAAATTTAGCTCTTTAAAATTTATATATTTTATCAATTTAACTTTAATT
1 TAATAAATTTAACT-TATAATATTTATATATTTTACCAATTTAACTTGAATT
* *
19651434 TAATAATTTTAACTTATAATATTTATATATTTTAACCAATTTAA-TCTGCATT
1 TAATAAATTTAACTTATAATATTTATATATTTT-ACCAATTTAACT-TGAATT
* * *
19651486 TTATAAATTTAATTTGTAATATTTA
1 TAATAAATTTAACTTATAATATTTA
19651511 CATAGAATAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
51 18 0.28
52 46 0.72
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (51 bp):
TAATAAATTTAACTTATAATATTTATATATTTTACCAATTTAACTTGAATT
Found at i:19652201 original size:4 final size:4
Alignment explanation
Indices: 19652192--19652216 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
19652182 TCTTCTGGTA
19652192 CTAT CTAT CTAT CTAT CTAT CTAT C
1 CTAT CTAT CTAT CTAT CTAT CTAT C
19652217 ACGACTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (4 bp):
CTAT
Found at i:19665939 original size:61 final size:61
Alignment explanation
Indices: 19665871--19666130 Score: 237
Period size: 61 Copynumber: 4.2 Consensus size: 61
19665861 TAGCAAATTC
* * *
19665871 AATTTTTTTGGTGTTGGTCATATCATGGCCGACA-CCTCTATTTATCTGATAAAAAAATCA
1 AATTTTTTTGGTGTTGGTCATATCATGGTCGACACCCCCTTTTTATCTGATAAAAAAATCA
* * * * *** * *
19665931 AATTTTTTT-ATATTAGTCAT-GCAATGGTCGACACTTTCTTTTT-TCAGATAAAAAATTTTCA
1 AATTTTTTTGGTGTTGGTCATATC-ATGGTCGACACCCCCTTTTTATCTGATAAAAAA--ATCA
19665992 AATTTCTTTTGGTGTTGG-C-TATTGCATGGTCGACACCCCCTTTTTATCTGAATAAAAAAATCA
1 AATTT-TTTTGGTGTTGGTCATA-T-CATGGTCGACACCCCCTTTTTATCTG-ATAAAAAAATCA
** * * *
19666055 AA-TTTTTTGGTGTTGGTCATGCCATGGTCGACATCCCCTTTTTTATCTGGTAAAAAAATTA
1 AATTTTTTTGGTGTTGGTCATATCATGGTCGACA-CCCCCTTTTTATCTGATAAAAAAATCA
*
19666116 AATTTTTTTTGTGTT
1 AATTTTTTTGGTGTT
19666131 AACCATGTAA
Statistics
Matches: 160, Mismatches: 25, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
58 1 0.01
59 28 0.17
60 15 0.09
61 44 0.28
62 33 0.21
63 27 0.17
64 4 0.03
65 8 0.05
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (61 bp):
AATTTTTTTGGTGTTGGTCATATCATGGTCGACACCCCCTTTTTATCTGATAAAAAAATCA
Found at i:19665987 original size:118 final size:119
Alignment explanation
Indices: 19665757--19666097 Score: 320
Period size: 118 Copynumber: 2.8 Consensus size: 119
19665747 TGATAAAAAA
* * *
19665757 TTTTTAGTGTTGGCCACTA-CATGGCTGACACCTC-ATTTTAATCTGA-CAAAAAATC-AATTTT
1 TTTTTGGTGTTGG-CA-TATCATGGCCGACACCTCTA-TTT-ATCTGATAAAAAAATCAAATTTT
* ** * **
19665818 TTTGCTGTTAGTCATGCAATGACCGGCATCCCTTTTTGTCAAATAGCAAA-TTC-AATT
62 TTT-ATGTTAGTCATGCAATGGTCGACATCCCTTTTTGTCAAATAAAAAATTTCAAATT
19665875 TTTTTGGTGTTGGTCATATCATGGCCGACACCTCTATTTATCTGATAAAAAAATCAAATTTTTTT
1 TTTTTGGTGTTGG-CATATCATGGCCGACACCTCTATTTATCTGATAAAAAAATCAAATTTTTTT
* ** *
19665940 ATATTAGTCATGCAATGGTCGACACTTTCTTTTT-TCAGATAAAAAATTTTCAAATT
65 ATGTTAGTCATGCAATGGTCGACA-TCCCTTTTTGTCAAATAAAAAA-TTTCAAATT
* * *
19665996 TCTTTTGGTGTTGGC-TATTGCATGGTCGACACCCCCTTTTTATCTGAATAAAAAAATCAAATTT
1 T-TTTTGGTGTTGGCATA-T-CATGGCCGACA-CCTCTATTTATCTG-ATAAAAAAATCAAATTT
** * *
19666060 TTTGGTGTTGGTCATGCCATGGTCGACATCCCCTTTTT
61 TTTTATGTTAGTCATGCAATGGTCGACAT-CCCTTTTT
19666098 TATCTGGTAA
Statistics
Matches: 185, Mismatches: 24, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
117 8 0.04
118 67 0.36
119 17 0.09
120 5 0.03
121 7 0.04
122 22 0.12
123 13 0.07
124 46 0.25
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (119 bp):
TTTTTGGTGTTGGCATATCATGGCCGACACCTCTATTTATCTGATAAAAAAATCAAATTTTTTTA
TGTTAGTCATGCAATGGTCGACATCCCTTTTTGTCAAATAAAAAATTTCAAATT
Found at i:19666035 original size:63 final size:60
Alignment explanation
Indices: 19665804--19666098 Score: 199
Period size: 59 Copynumber: 4.9 Consensus size: 60
19665794 TTAATCTGAC
* * * * ** * *
19665804 AAAAAATCAATTTTTTTGCTGTTAGTCATGCAATGACCGGCA-TCCCTTTTTGTCA-AATA
1 AAAAAATCAAATTTTTTGGTGTTGGTCATGCCATGGTCGACACCCCCTTTTT-TCAGAATA
** * * ** * * * *
19665863 GCAAATTCAATTTTTTTGGTGTTGGTCATATCATGGCCGACA-CCTCTATTTATCTG-ATA
1 AAAAAATCAAATTTTTTGGTGTTGGTCATGCCATGGTCGACACCCCCT-TTTTTCAGAATA
** * * * ***
19665922 AAAAAATCAAATTTTTTTATATTAGTCATGCAATGGTCGACACTTTCTTTTTTCAG-ATA
1 AAAAAATCAAATTTTTTGGTGTTGGTCATGCCATGGTCGACACCCCCTTTTTTCAGAATA
* *
19665981 AAAAATTTTCAAATTTCTTTTGGTGTTGG-CTATTG-CATGGTCGACACCCCCTTTTTATCTGAA
1 AAAAA--ATCAAA-TT-TTTTGGTGTTGGTC-A-TGCCATGGTCGACACCCCCTTTTT-TCAGAA
19666044 TA
59 TA
*
19666046 AAAAAATCAAATTTTTTGGTGTTGGTCATGCCATGGTCGACATCCCCTTTTTT
1 AAAAAATCAAATTTTTTGGTGTTGGTCATGCCATGGTCGACACCCCCTTTTTT
19666099 ATCTGGTAAA
Statistics
Matches: 181, Mismatches: 42, Indels: 25
0.73 0.17 0.10
Matches are distributed among these distances:
59 84 0.46
60 9 0.05
61 38 0.21
62 6 0.03
63 31 0.17
64 5 0.03
65 8 0.04
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (60 bp):
AAAAAATCAAATTTTTTGGTGTTGGTCATGCCATGGTCGACACCCCCTTTTTTCAGAATA
Found at i:19666149 original size:62 final size:61
Alignment explanation
Indices: 19666022--19666159 Score: 143
Period size: 62 Copynumber: 2.2 Consensus size: 61
19666012 ATTGCATGGT
* *** * **
19666022 CGACACCCCCTTTTTATCTGAATAAAAAAATCAAATTTTTTGGTGTTGGTCATGCCATGGT
1 CGACACCCCTTTTTTATCTGAATAAAAAAATCAAATTTTTTGGTGTTAACCATGCAATGAC
* * * *
19666083 CGACATCCCCTTTTTTATCTG-GTAAAAAAATTAAATTTTTTTTGTGTTAACCATGTAATGAC
1 CGACA-CCCCTTTTTTATCTGAATAAAAAAATCAAA-TTTTTTGGTGTTAACCATGCAATGAC
19666145 CGACACTCCCTTTTT
1 CGACAC-CCCTTTTT
19666160 GTCAGATGAA
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
61 18 0.29
62 45 0.71
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (61 bp):
CGACACCCCTTTTTTATCTGAATAAAAAAATCAAATTTTTTGGTGTTAACCATGCAATGAC
Found at i:19666159 original size:61 final size:61
Alignment explanation
Indices: 19665804--19666159 Score: 156
Period size: 59 Copynumber: 5.9 Consensus size: 61
19665794 TTAATCTGAC
* * ** * * *
19665804 AAAAAATCAATTTTTTTGCTGTTAGTCATGCAATGACCGGCA-TCCCTTTTTGTC-AAATA
1 AAAAAATCAAATTTTTTGGTGTTAACCATGCAATGACCGACACTCCCTTTTTATCTGAATA
** * * *** * * * *
19665863 GCAAATTCAATTTTTTTGGTGTTGGTCATATC-ATGGCCGACAC-CTCTATTTATCTG-ATA
1 AAAAAATCAAATTTTTTGGTGTTAACCAT-GCAATGACCGACACTCCCTTTTTATCTGAATA
** * ** ** ** *
19665922 AAAAAATCAAATTTTTTTATATTAGTCATGCAATGGTCGACACTTTCTTTTT-TCAG-ATA
1 AAAAAATCAAATTTTTTGGTGTTAACCATGCAATGACCGACACTCCCTTTTTATCTGAATA
* ** * ** *
19665981 AAAAATTTTCAAATTTCTTTTGGTGTTGGCTATTGC-ATGGTCGACACCCCCTTTTTATCTGAAT
1 AAAAA--ATCAAA-TT-TTTTGGTGTTAACCA-TGCAATGACCGACACTCCCTTTTTATCTGAAT
19666045 A
61 A
*** * ** *
19666046 AAAAAATCAAATTTTTTGGTGTTGGTCATGCCATGGTCGACA-TCCCCTTTTTTATCTG-GTA
1 AAAAAATCAAATTTTTTGGTGTTAACCATGCAATGACCGACACT-CCC-TTTTTATCTGAATA
* * *
19666107 AAAAAATTAAATTTTTTTTGTGTTAACCATGTAATGACCGACACTCCCTTTTT
1 AAAAAATCAAA-TTTTTTGGTGTTAACCATGCAATGACCGACACTCCCTTTTT
19666160 GTCAGATGAA
Statistics
Matches: 230, Mismatches: 50, Indels: 32
0.74 0.16 0.10
Matches are distributed among these distances:
58 1 0.00
59 85 0.37
60 10 0.04
61 48 0.21
62 40 0.17
63 32 0.14
64 6 0.03
65 8 0.03
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (61 bp):
AAAAAATCAAATTTTTTGGTGTTAACCATGCAATGACCGACACTCCCTTTTTATCTGAATA
Found at i:19668638 original size:59 final size:57
Alignment explanation
Indices: 19668514--19669016 Score: 402
Period size: 61 Copynumber: 8.5 Consensus size: 57
19668504 AGGGAAAGTT
* * * * *
19668514 GGTGTCGGCCATTGCATGGCCAGCACAAAAAAAATTAATTTTTTTACCAAATAAAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACAC-AAAAAATTTGA-TTTTTTATCAGAT--AAAAAGG
** * *
19668575 GGTGTCGGTTATGGCATGGCCAACATCAAAAAATTTGATTTTTTATTCAGATAAAAAGA
1 GGTGTCGGCCATTGCATGGCCAACA-CAAAAAATTTGATTTTTTA-TCAGATAAAAAGG
* * * * * * *
19668634 GGTGTCGACCATGGAATGACCAACACCAAAAAAATTTAAAATTTTTTATCTGACAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACA-C-AAAAAATTT--GATTTTTTATCAGATAAAAAGG
** * *
19668695 GGTGTTTGCCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTATCTGAAAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACA-C-AAAAAATTTG--ATTTTTTATCAGATAAAAAGG
*
19668756 AGTGTCGGCCATTGCATGGCCAACACAAAAAATTTTGATTTTTTTTATCAG-TAAATAA-G
1 GGTGTCGGCCATTGCATGGCCAACACAAAAAA-TTTGA--TTTTTTATCAGATAAA-AAGG
* * * * *
19668815 GGTGTAGGCTATTGCATGACCAACACAAAAAAGTTTAATTTTTTATCAGATAAATAGG
1 GGTGTCGGCCATTGCATGGCCAACACAAAAAA-TTTGATTTTTTATCAGATAAAAAGG
* * * * * * *
19668873 GGTGTCGACCATTGCATGGCCAACACCAAAAA-TTAAATTTTTCTCTGACAAAAAGGG
1 GGTGTCGGCCATTGCATGGCCAACACAAAAAATTTGATTTTTTATCAGATAAAAA-GG
* * * *
19668930 GGTGTCGGTCATTGCATGGCCAACACCCAAAAATTTGATTTTTTTTATCAGATTAGAAGG
1 GGTGTCGGCCATTGCATGGCCAACA-CAAAAAATTTGA--TTTTTTATCAGATAAAAAGG
* *
19668990 GGATGTCTGCTA-TGCAATGGCCAACAC
1 GG-TGTCGGCCATTGC-ATGGCCAACAC
19669017 CAATTTTTTT
Statistics
Matches: 361, Mismatches: 61, Indels: 41
0.78 0.13 0.09
Matches are distributed among these distances:
56 17 0.05
57 37 0.10
58 40 0.11
59 72 0.20
60 41 0.11
61 145 0.40
62 9 0.02
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (57 bp):
GGTGTCGGCCATTGCATGGCCAACACAAAAAATTTGATTTTTTATCAGATAAAAAGG
Found at i:19668666 original size:120 final size:118
Alignment explanation
Indices: 19668514--19668982 Score: 411
Period size: 120 Copynumber: 3.9 Consensus size: 118
19668504 AGGGAAAGTT
* * *
19668514 GGTGTCGGCCATTGCATGGCCAGCACAAAAAAAATT-AATTTTTTTACCAAATAAAAAAAGGGGT
1 GGTGTCGACCATTGCATGGCCAACACCAAAAAAATTAAATTTTTTTACC-AATAAAAAAAGGGGT
** * *
19668578 GTCGGTTATGGCATGGCCAACATCAAAAAATTTGATTTTTTATTCAGATAAAAAG
65 GTCGGCCATTGCATGGCCAACACCAAAAAATTTGATTTTTTA-TCAGATAAAAAG
* * * * * *
19668633 AGGTGTCGACCATGGAATGACCAACACCAAAAAAATTTAAAATTTTTTATC--TGACAAAAAGGG
1 -GGTGTCGACCATTGCATGGCCAACACCAAAAAAA-TTAAATTTTTTTACCAAT-AAAAAAAGGG
** * *
19668696 GTGTTTGCCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTATCTGAAAAAAAG
63 GTGTCGGCCATTGCATGGCCAACACC-AAAAAATTTG--ATTTTTTATCAGATAAAAAG
* * * * * * *
19668755 GAGTGTCGGCCATTGCATGGCCAACA-CAAAAAATTTTGATTTTTTTTATCAGT-AAATAA-GGG
1 G-GTGTCGACCATTGCATGGCCAACACCAAAAAA-ATTAAATTTTTTTACCAATAAAAAAAGGGG
* * * * *
19668817 TGTAGGCTATTGCATGACCAACA-CAAAAAAGTTTAATTTTTTATCAGATAAATAGG
64 TGTCGGCCATTGCATGGCCAACACCAAAAAA-TTTGATTTTTTATCAGATAAA-AAG
* ** * *
19668873 GGTGTCGACCATTGCATGGCCAACACC--AAAAATTAAATTTTTCT-CTGA-CAAAAAGGGGGTG
1 GGTGTCGACCATTGCATGGCCAACACCAAAAAAATTAAATTTTTTTACCAATAAAAAAAGGGGTG
* *
19668934 TCGGTCATTGCATGGCCAACACCCAAAAATTTGATTTTTTTTATCAGAT
66 TCGGCCATTGCATGGCCAACACCAAAAAATTTGA--TTTTTTATCAGAT
19668983 TAGAAGGGGA
Statistics
Matches: 279, Mismatches: 52, Indels: 39
0.75 0.14 0.11
Matches are distributed among these distances:
114 4 0.01
115 35 0.13
116 10 0.04
117 51 0.18
118 10 0.04
119 5 0.02
120 79 0.28
121 36 0.13
122 40 0.14
123 9 0.03
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (118 bp):
GGTGTCGACCATTGCATGGCCAACACCAAAAAAATTAAATTTTTTTACCAATAAAAAAAGGGGTG
TCGGCCATTGCATGGCCAACACCAAAAAATTTGATTTTTTATCAGATAAAAAG
Found at i:19668991 original size:117 final size:116
Alignment explanation
Indices: 19668568--19669019 Score: 420
Period size: 117 Copynumber: 3.8 Consensus size: 116
19668558 TACCAAATAA
* * *
19668568 AAAAAGGGGTGTCGGTTATGGCATGGCCAACATCAAAAAATTTG--ATTTTTTATTCAGATAAAA
1 AAAAAGGGGTGTCGGTCATTGCATGGCCAACACCAAAAAATTTGATATTTTTTA-TCAGATAAAA
* * * *
19668631 AGAGGTGTCGACCATGGAATGACCAACACCAAAAAAATTTAAAATTTTTTATCTGAC
65 AGGGGTGTCGACCATTGCATGGCCAACACC--AAAAATTT-AAA-TTTTT-TCTGAC
** * * * *
19668688 AAAAAGGGGTGTTTGCCATTGCATGGCCAACACCAAAAAAATTTGAAATTTTTTATCTGAAAAAA
1 AAAAAGGGGTGTCGGTCATTGCATGGCCAACACC-AAAAAATTTGATATTTTTTATCAGATAAAA
* * * ** *
19668753 AGGAGTGTCGGCCATTGCATGGCCAACACAAAAAATTTTGATTTTTT-TTATC
65 AGGGGTGTCGACCATTGCATGGCCAACACCAAAAATTTAAATTTTTTCTGA-C
* * *
19668805 AGTAAATAAGGGTGTAGG-CTATTGCATGACCAACA-CAAAAAAGTTT-A-ATTTTTTATCAGAT
1 A--AAA-AGGGGTGTCGGTC-ATTGCATGGCCAACACCAAAAAA-TTTGATATTTTTTATCAGAT
*
19668866 AAATAGGGGTGTCGACCATTGCATGGCCAACACCAAAAA-TTAAATTTTTCTCTGAC
61 AAAAAGGGGTGTCGACCATTGCATGGCCAACACCAAAAATTTAAATTTTT-TCTGAC
* * * *
19668922 AAAAAGGGGGTGTCGGTCATTGCATGGCCAACACCCAAAAATTTGATTTTTTTTATCAGATTAGA
1 AAAAA-GGGGTGTCGGTCATTGCATGGCCAACACCAAAAAATTTGATATTTTTTATCAGATAAAA
*
19668987 AGGGGATGTCTG-CTA-TGCAATGGCCAACACCAA
65 AGGGG-TGTC-GACCATTGC-ATGGCCAACACCAA
19669020 TTTTTTTTTT
Statistics
Matches: 273, Mismatches: 40, Indels: 40
0.77 0.11 0.11
Matches are distributed among these distances:
114 1 0.00
115 28 0.10
116 18 0.07
117 75 0.27
118 34 0.12
119 10 0.04
120 58 0.21
121 10 0.04
122 31 0.11
123 8 0.03
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (116 bp):
AAAAAGGGGTGTCGGTCATTGCATGGCCAACACCAAAAAATTTGATATTTTTTATCAGATAAAAA
GGGGTGTCGACCATTGCATGGCCAACACCAAAAATTTAAATTTTTTCTGAC
Found at i:19669402 original size:38 final size:38
Alignment explanation
Indices: 19669360--19669438 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
19669350 CTTACCTTAG
19669360 ATGAATATGTGCATAACTACTCATTTTGGTCTGCAAGA
1 ATGAATATGTGCATAACTACTCATTTTGGTCTGCAAGA
19669398 ATGAATATGTGCATAACTACTCATTTTGGTCTGCAAGA
1 ATGAATATGTGCATAACTACTCATTTTGGTCTGCAAGA
19669436 ATG
1 ATG
19669439 TTACTCTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (38 bp):
ATGAATATGTGCATAACTACTCATTTTGGTCTGCAAGA
Found at i:19672553 original size:181 final size:181
Alignment explanation
Indices: 19672164--19672580 Score: 475
Period size: 181 Copynumber: 2.3 Consensus size: 181
19672154 AGTTCAACTT
* * * * * * ** *
19672164 CAACATAACAACAATAATCATAATGAGTCAAAGTAATTCTGAATAAAGAAGCTAAACTGAAAGAC
1 CAACACAACAACAATCATCATAATTAATCAAAGTAATTCAGAAGAAAGAAGCTAAACCAAAAAAC
* * * *
19672229 TAGTGGAAAACAAGATTTAACCTATTACAACACATAGATGATCACAAGATTGTTCCTGGGACAAA
66 TAATGGAAAACAAGATTCAACCTATTACAACACATAGATGATCACAAGATTGTTCCAGGCACAAA
* * ** * **
19672294 GTTCTGGAGTTCGAATTGTGTATAAATAAAGACCTCTTTATGTAAGTAGTG
131 GTTCTGGAGTTCGAATTGGGTATAAATAAAGACCTATAAACGTAACCAGTG
* * *
19672345 CAACACAACAACTA-CTATCACAATTAATCCATAGTAATTCAGAAGAAAGAAGCTAAACCAAAAA
1 CAACACAACAACAATC-ATCATAATTAAT-CAAAGTAATTCAGAAGAAAGAAGCTAAACCAAAAA
* * * * *
19672409 ACTAATTGAAAGCAAGATTCAATCTATTTCAACACATAGATGATCACAA-ATTGTTTCAGGCACA
64 ACTAATGGAAAACAAGATTCAACCTATTACAACACATAGATGATCACAAGATTGTTCCAGGCACA
*
19672473 AAGTTC-GAGAGTTCGAATTGGGTATAAATCAAGACCTATAAACGTAACCAGT-
129 AAGTTCTG-GAGTTCGAATTGGGTATAAATAAAGACCTATAAACGTAACCAGTG
*
19672525 CAAACACAACAACAATCATCATAATTAAT-AACAGATAATTAAGAAGAAAGAAGCTA
1 C-AACACAACAACAATCATCATAATTAATCAA-AG-TAATTCAGAAGAAAGAAGCTA
19672581 GAAGAAAGAA
Statistics
Matches: 196, Mismatches: 33, Indels: 14
0.81 0.14 0.06
Matches are distributed among these distances:
179 1 0.01
180 4 0.02
181 118 0.60
182 73 0.37
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (181 bp):
CAACACAACAACAATCATCATAATTAATCAAAGTAATTCAGAAGAAAGAAGCTAAACCAAAAAAC
TAATGGAAAACAAGATTCAACCTATTACAACACATAGATGATCACAAGATTGTTCCAGGCACAAA
GTTCTGGAGTTCGAATTGGGTATAAATAAAGACCTATAAACGTAACCAGTG
Found at i:19672583 original size:14 final size:14
Alignment explanation
Indices: 19672566--19672594 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19672556 CAGATAATTA
19672566 AGAAGAAAGAAGCT
1 AGAAGAAAGAAGCT
19672580 AGAAGAAAGAAGCT
1 AGAAGAAAGAAGCT
19672594 A
1 A
19672595 AACAACAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.28, T:0.07
Consensus pattern (14 bp):
AGAAGAAAGAAGCT
Found at i:19678950 original size:28 final size:25
Alignment explanation
Indices: 19678904--19678955 Score: 59
Period size: 28 Copynumber: 2.0 Consensus size: 25
19678894 TCTATTTTTT
* *
19678904 TAAAAAAAAAAGAGAAAACCTAATC
1 TAAAAAAAAAAGAAAAAACATAATC
19678929 TAAAAATAAAAAGAAAAGAAACATAAT
1 TAAAAA-AAAAAG-AAA-AAACATAAT
19678956 TGGGAAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 6 0.27
27 2 0.09
28 8 0.36
ACGTcount: A:0.71, C:0.08, G:0.08, T:0.13
Consensus pattern (25 bp):
TAAAAAAAAAAGAAAAAACATAATC
Found at i:19683788 original size:21 final size:21
Alignment explanation
Indices: 19683763--19683805 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
19683753 CACACAAATC
19683763 AAAATCTGAATAAATTGGAGA
1 AAAATCTGAATAAATTGGAGA
*
19683784 AAAATCTGAGTAAATTGGAGA
1 AAAATCTGAATAAATTGGAGA
19683805 A
1 A
19683806 TAATGATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.21, T:0.23
Consensus pattern (21 bp):
AAAATCTGAATAAATTGGAGA
Found at i:19687616 original size:22 final size:22
Alignment explanation
Indices: 19687586--19687629 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19687576 GACAAAGAGC
*
19687586 CATCTACTTTCCAAAAGAAACT
1 CATCCACTTTCCAAAAGAAACT
19687608 CATCCACTTTCCAAAAGAAACT
1 CATCCACTTTCCAAAAGAAACT
19687630 GCTGGCGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.30, G:0.05, T:0.25
Consensus pattern (22 bp):
CATCCACTTTCCAAAAGAAACT
Found at i:19690048 original size:18 final size:18
Alignment explanation
Indices: 19690025--19690064 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
19690015 ATTGATACTC
19690025 AAGTTGCTTTGAATTTGG
1 AAGTTGCTTTGAATTTGG
19690043 AAGTTGCTTTGAATTTGG
1 AAGTTGCTTTGAATTTGG
19690061 AAGT
1 AAGT
19690065 GGATAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.05, G:0.28, T:0.42
Consensus pattern (18 bp):
AAGTTGCTTTGAATTTGG
Found at i:19693798 original size:7 final size:7
Alignment explanation
Indices: 19693764--19693790 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
19693754 AAACATAAGG
19693764 AATAATA
1 AATAATA
19693771 AATAATA
1 AATAATA
19693778 AATAATA
1 AATAATA
19693785 AATAAT
1 AATAAT
19693791 TATAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATAATA
Found at i:19693947 original size:30 final size:30
Alignment explanation
Indices: 19693913--19693970 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
19693903 TTTAACTCTC
19693913 TTAAAAATATAAAAATT-TAATTTAATTTTT
1 TTAAAAATATAAAAATTATAA-TTAATTTTT
*
19693943 TTAAAATTATAAAAATTATAATTAATTT
1 TTAAAAATATAAAAATTATAATTAATTT
19693971 CGACTCCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TTAAAAATATAAAAATTATAATTAATTTTT
Found at i:19699523 original size:40 final size:40
Alignment explanation
Indices: 19699464--19699541 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
19699454 ACCATTTAGA
19699464 CCAAACATGGACAAGGGTTGTTTTTGAATTGAGATTGAGT
1 CCAAACATGGACAAGGGTTGTTTTTGAATTGAGATTGAGT
* * *
19699504 CCAAACATTGCCAATGGTTGTTTTTGAATTGAGATTGA
1 CCAAACATGGACAAGGGTTGTTTTTGAATTGAGATTGA
19699542 ATTAGACTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (40 bp):
CCAAACATGGACAAGGGTTGTTTTTGAATTGAGATTGAGT
Found at i:19721566 original size:28 final size:28
Alignment explanation
Indices: 19721535--19721749 Score: 132
Period size: 28 Copynumber: 7.5 Consensus size: 28
19721525 ATTGGGGTTA
*
19721535 AAAATGGGATTTTGGGAAGTTCGGGGGT
1 AAAATGGAATTTTGGGAAGTTCGGGGGT
* * * *
19721563 AAAATGGTA-TTTGGTGAA-ATAGGGGTT
1 AAAATGGAATTTTGG-GAAGTTCGGGGGT
* *
19721590 AAAAATGGGATTTTAGGAAGTTCGGGGGT
1 -AAAATGGAATTTTGGGAAGTTCGGGGGT
* * *
19721619 AAAATGGTAATTTTTGGTGAAATT-AGGGTT
1 AAAATGG-AA-TTTTGG-GAAGTTCGGGGGT
** *
19721649 AAAATGGAATTTTGAAAAGTTCGGGAGT
1 AAAATGGAATTTTGGGAAGTTCGGGGGT
* * *
19721677 AAAATGGTAATTTTTGGTGAAATT-AGGGTT
1 AAAATGG-AA-TTTTGG-GAAGTTCGGGGGT
** **
19721707 AAAAATGGAATTTTGAAAAGTTTAGGGGT
1 -AAAATGGAATTTTGGGAAGTTCGGGGGT
19721736 AAAATGGTAATTTT
1 AAAATGG-AATTTT
19721750 TGAATAGTTT
Statistics
Matches: 143, Mismatches: 30, Indels: 27
0.71 0.15 0.14
Matches are distributed among these distances:
27 15 0.10
28 55 0.38
29 31 0.22
30 26 0.18
31 16 0.11
ACGTcount: A:0.34, C:0.01, G:0.31, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGGAAGTTCGGGGGT
Found at i:19721679 original size:58 final size:59
Alignment explanation
Indices: 19721495--19721751 Score: 332
Period size: 59 Copynumber: 4.4 Consensus size: 59
19721485 ATTTTTGACT
* * * **
19721495 TTCGGGGGTAAAAAT-GTAATTTTTTGT-AGAATTGGGGTTAAAAATGGGATTTTGGGAAG
1 TTCGGGGGT-AAAATGGTAATTTTTGGTGA-AATTAGGGTTAAAAATGGAATTTTGAAAAG
* *
19721554 TTCGGGGGTAAAATGGT-A--TTTGGTGAAA-TAGGGGTTAAAAATGGGATTTT-AGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTA-GGGTTAAAAATGGAATTTTGA-AAAG
19721610 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTT-AAAATGGAATTTTGAAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGAAAAG
*
19721668 TTCGGGAGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGAAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGAAAAG
**
19721727 TTTAGGGGTAAAATGGTAATTTTTG
1 TTCGGGGGTAAAATGGTAATTTTTG
19721752 AATAGTTTAG
Statistics
Matches: 179, Mismatches: 9, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
55 1 0.01
56 47 0.26
57 2 0.01
58 59 0.33
59 68 0.38
60 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.35
Consensus pattern (59 bp):
TTCGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGAAAAG
Found at i:19721753 original size:30 final size:29
Alignment explanation
Indices: 19721614--19721763 Score: 132
Period size: 30 Copynumber: 5.1 Consensus size: 29
19721604 AGGAAGTTCG
*
19721614 GGGGTAAAATGGTAATTTTTGGTGAAA-TTA
1 GGGGTAAAATGGTAATTTTT-G-AAAAGTTA
* *
19721644 GGGTTAAAATGG-AA-TTTTGAAAAGTTC
1 GGGGTAAAATGGTAATTTTTGAAAAGTTA
*
19721671 GGGAGTAAAATGGTAATTTTTGGTGAAA-TTA
1 GGG-GTAAAATGGTAATTTTT-G-AAAAGTTA
*
19721702 GGGTTAAAAATGG-AA-TTTTGAAAAGTTTA
1 GGGGT-AAAATGGTAATTTTTGAAAAG-TTA
*
19721731 GGGGTAAAATGGTAATTTTTGAATAGTTTA
1 GGGGTAAAATGGTAATTTTTGAAAAG-TTA
19721761 GGG
1 GGG
19721764 ACCTATAAGC
Statistics
Matches: 99, Mismatches: 10, Indels: 22
0.76 0.08 0.17
Matches are distributed among these distances:
26 3 0.03
27 9 0.09
28 20 0.20
29 17 0.17
30 34 0.34
31 13 0.13
32 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGAAAAGTTA
Found at i:19722154 original size:15 final size:15
Alignment explanation
Indices: 19722134--19722174 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
19722124 GGATCCTAGT
19722134 AGCGGGTCGGGTCGG
1 AGCGGGTCGGGTCGG
19722149 AGCGGGTCGGGTCGG
1 AGCGGGTCGGGTCGG
* *
19722164 ATCGGTTCGGG
1 AGCGGGTCGGG
19722175 CATGGTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.07, C:0.20, G:0.56, T:0.17
Consensus pattern (15 bp):
AGCGGGTCGGGTCGG
Found at i:19722660 original size:13 final size:13
Alignment explanation
Indices: 19722642--19722666 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19722632 TTTATTATAA
19722642 TATTAATTATTAT
1 TATTAATTATTAT
19722655 TATTAATTATTA
1 TATTAATTATTA
19722667 GAAAGATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTAATTATTAT
Found at i:19722789 original size:24 final size:24
Alignment explanation
Indices: 19722761--19722808 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
19722751 AAAAGTTATT
19722761 AATACTCATTAATGCATTTAAAAC
1 AATACTCATTAATGCATTTAAAAC
*
19722785 AATACTTATTAATGCATTTAAAAC
1 AATACTCATTAATGCATTTAAAAC
19722809 GATGCAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (24 bp):
AATACTCATTAATGCATTTAAAAC
Found at i:19734520 original size:29 final size:29
Alignment explanation
Indices: 19734488--19734581 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
19734478 AAAATATAAT
19734488 TTTTGGTAAAATTAGGGTTAAAAATGGGA
1 TTTTGGTAAAATTAGGGTTAAAAATGGGA
* * * *
19734517 TTTTGG-AAAGTTCGAGGAT-AAAATGGTAA
1 TTTTGGTAAAATTAG-GGTTAAAAATGG-GA
* *
19734546 TTTTTGGTGAAA-TAGGGGTTAAAGATGGGA
1 -TTTTGGTAAAATTA-GGGTTAAAAATGGGA
19734576 TTTTGG
1 TTTTGG
19734582 AAAGTTTAGA
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 13 0.27
29 16 0.33
30 11 0.22
31 9 0.18
ACGTcount: A:0.33, C:0.01, G:0.31, T:0.35
Consensus pattern (29 bp):
TTTTGGTAAAATTAGGGTTAAAAATGGGA
Found at i:19734520 original size:30 final size:31
Alignment explanation
Indices: 19734472--19734627 Score: 93
Period size: 30 Copynumber: 5.3 Consensus size: 31
19734462 TTAACTTTCG
*
19734472 AGGG-TAAAAAT-ATAATTTTTGGTAAAATT
1 AGGGTTAAAAATGGTAATTTTTGGTAAAATT
* *
19734501 AGGGTTAAAAATGG-GA-TTTTGG-AAAGTT
1 AGGGTTAAAAATGGTAATTTTTGGTAAAATT
* * *
19734529 CGAGGAT-AAAATGGTAATTTTTGGTGAAA-T
1 AG-GGTTAAAAATGGTAATTTTTGGTAAAATT
* * *
19734559 AGGGGTTAAAGATGG-GA-TTTTGG-AAAGTTT
1 A-GGGTTAAAAATGGTAATTTTTGGTAAA-ATT
* *
19734589 AGAGG-T-AAAATGGTAATTTTTGGTGAAATC
1 AG-GGTTAAAAATGGTAATTTTTGGTAAAATT
19734619 AGGGTTAAA
1 AGGGTTAAA
19734628 GATAGAATTT
Statistics
Matches: 92, Mismatches: 19, Indels: 30
0.65 0.13 0.21
Matches are distributed among these distances:
28 21 0.23
29 25 0.27
30 33 0.36
31 13 0.14
ACGTcount: A:0.37, C:0.01, G:0.28, T:0.33
Consensus pattern (31 bp):
AGGGTTAAAAATGGTAATTTTTGGTAAAATT
Found at i:19734531 original size:59 final size:58
Alignment explanation
Indices: 19734468--19734729 Score: 278
Period size: 59 Copynumber: 4.4 Consensus size: 58
19734458 ATTTTTAACT
* *
19734468 TTCGAGGGTAAAAAT-ATAATTTTTGGTAAAATTAGGGTTAAAAATGGGATTTTGGAAAG
1 TTCGAGGGT-AAAATGATAATTTTTGGTGAAA-TAGGGTTAAAAATGGAATTTTGGAAAG
* * * *
19734527 TTCGAGGATAAAATGGTAATTTTTGGTGAAATAGGGGTTAAAGATGGGATTTTGGAAAG
1 TTCGAGGGTAAAATGATAATTTTTGGTGAAATA-GGGTTAAAAATGGAATTTTGGAAAG
* * * * **
19734586 TT-TAGAGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAGATAGAATTTTAAAAAG
1 TTCGAG-GGTAAAATGATAATTTTTGGTGAAAT-AGGGTTAAAAATGGAATTTTGGAAAG
* *
19734645 TTCGAGGGTAAAAT-AGTAATTTTTTGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAG
1 TTCGAGGGTAAAATGA-TAATTTTTGGTGAAATAG-GGTTAAAAATGGAATTTTGGAAAG
* * *
19734704 TTTGGGGGGTAAAATGGTAATTTTTG
1 -TTCGAGGGTAAAATGATAATTTTTG
19734730 AATAGTTTAG
Statistics
Matches: 172, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
58 10 0.06
59 139 0.81
60 23 0.13
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.34
Consensus pattern (58 bp):
TTCGAGGGTAAAATGATAATTTTTGGTGAAATAGGGTTAAAAATGGAATTTTGGAAAG
Found at i:19734623 original size:118 final size:119
Alignment explanation
Indices: 19734484--19734729 Score: 341
Period size: 118 Copynumber: 2.1 Consensus size: 119
19734474 GGTAAAAATA
* * * ** *
19734484 TAATTTTTGGTAAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTCGAGGATAAAATGGTAATTT
1 TAATTTTTGGTAAAATCAGGGTTAAAAATAGAATTTTAAAAAGTTCGAGGATAAAATAGTAATTT
* * *
19734549 TTGGTGAAATAGGGGTTAAAGATGGGATTTTGGAAAGTTT-AGAGGTAAAATGG
66 TTGGTGAAATAGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGAGGTAAAATGG
* * *
19734602 TAATTTTTGGTGAAATCAGGGTTAAAGATAGAATTTTAAAAAGTTCGAGGGTAAAATAGTAATTT
1 TAATTTTTGGTAAAATCAGGGTTAAAAATAGAATTTTAAAAAGTTCGAGGATAAAATAGTAATTT
* * * *
19734667 TTTGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGGTAAAATGG
66 TTGGTGAAATAGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGAGGTAAAATGG
19734721 TAATTTTTG
1 TAATTTTTG
19734730 AATAGTTTAG
Statistics
Matches: 111, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
118 91 0.82
119 20 0.18
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.35
Consensus pattern (119 bp):
TAATTTTTGGTAAAATCAGGGTTAAAAATAGAATTTTAAAAAGTTCGAGGATAAAATAGTAATTT
TTGGTGAAATAGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGAGGTAAAATGG
Found at i:19734680 original size:30 final size:30
Alignment explanation
Indices: 19734592--19734687 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
19734582 AAAGTTTAGA
* *
19734592 GGTAAAATGGTAATTTTTGGTGAAATC-AG
1 GGTAAAATAGTAATTTTTTGTGAAATCGAG
**
19734621 GGTTAAAGATAG-AA--TTTT-AAAAAGTTCGAG
1 GG-TAAA-ATAGTAATTTTTTGTGAAA--TCGAG
19734651 GGTAAAATAGTAATTTTTTGTGAAATCGAG
1 GGTAAAATAGTAATTTTTTGTGAAATCGAG
*
19734681 GTTAAAA
1 GGTAAAA
19734688 ATGGAATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
27 3 0.06
28 7 0.14
29 10 0.20
30 21 0.41
31 7 0.14
32 3 0.06
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (30 bp):
GGTAAAATAGTAATTTTTTGTGAAATCGAG
Found at i:19735489 original size:13 final size:14
Alignment explanation
Indices: 19735463--19735492 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19735453 CTTCTTGCCC
19735463 TTTTCTTTTCTTCT
1 TTTTCTTTTCTTCT
19735477 TTTTCTTTT-TTCT
1 TTTTCTTTTCTTCT
19735490 TTT
1 TTT
19735493 AAAAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTTTCTTCT
Found at i:19736005 original size:24 final size:24
Alignment explanation
Indices: 19735977--19736024 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
19735967 AAAAGTTATT
19735977 AATACTCATTAATGCATTTAAAAC
1 AATACTCATTAATGCATTTAAAAC
*
19736001 AATACTTATTAATGCATTTAAAAC
1 AATACTCATTAATGCATTTAAAAC
19736025 GATGCAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (24 bp):
AATACTCATTAATGCATTTAAAAC
Found at i:19736775 original size:6 final size:6
Alignment explanation
Indices: 19736764--19736822 Score: 59
Period size: 6 Copynumber: 9.8 Consensus size: 6
19736754 TTAAATTTGA
* *
19736764 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT AGGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
19736812 ATAAAT TTAAA
1 TTAAAT TTAAA
19736823 ATCAATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 8 0.19
6 30 0.70
8 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:19736785 original size:17 final size:17
Alignment explanation
Indices: 19736765--19736822 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 17
19736755 TAAATTTGAT
19736765 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
*
19736782 TAAATTTAAA--T-AGG
1 TAAATTTAAATTTAAAG
*
19736796 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAG
19736813 TAAATTTAAA
1 TAAATTTAAA
19736823 ATCAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 12 0.34
15 1 0.03
16 1 0.03
17 21 0.60
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:19736818 original size:11 final size:11
Alignment explanation
Indices: 19736802--19736833 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
19736792 TAGGTAAATT
19736802 TAAATTTAAAA
1 TAAATTTAAAA
19736813 TAAATTTAAAA
1 TAAATTTAAAA
*
19736824 TCAATTTAAA
1 TAAATTTAAA
19736834 CTTTTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:19737090 original size:29 final size:29
Alignment explanation
Indices: 19737033--19737100 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
19737023 GCCATGTAAG
19737033 TATTTAATTAATTTTTTAAATTTATAAAA
1 TATTTAATTAATTTTTTAAATTTATAAAA
* * *
19737062 TATTTTATATAATTTTTTAATTTTAAAAAA
1 TATTTAAT-TAATTTTTTAAATTTATAAAA
*
19737092 AATTATAAT
1 TATT-TAAT
19737101 ATGTTTGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 7 0.22
30 22 0.69
31 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TATTTAATTAATTTTTTAAATTTATAAAA
Found at i:19738814 original size:17 final size:17
Alignment explanation
Indices: 19738792--19738825 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19738782 CTTTAATGAG
19738792 GGTTTAAAGGAGTTAGA
1 GGTTTAAAGGAGTTAGA
*
19738809 GGTTTAAATGAGTTAGA
1 GGTTTAAAGGAGTTAGA
19738826 CATCCACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (17 bp):
GGTTTAAAGGAGTTAGA
Found at i:19746005 original size:42 final size:43
Alignment explanation
Indices: 19745889--19746029 Score: 248
Period size: 43 Copynumber: 3.3 Consensus size: 43
19745879 TTATTTGAAA
*
19745889 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
19745932 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
19745975 AAACGCCGCTAAA-AACATGGTCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
19746017 AAACGCCACTAAA
1 AAACGCCGCTAAA
19746030 ATTAACAAAT
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
42 40 0.42
43 55 0.58
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
Found at i:19747515 original size:34 final size:35
Alignment explanation
Indices: 19747444--19747521 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
19747434 TAAAGATAAT
19747444 GCCGCTAAAAATAGCGGCGTTTATTTGAAAAAAAC
1 GCCGCTAAAAATAGCGGCGTTTATTTGAAAAAAAC
19747479 GCCGCTAAAAATAGCGGCGTTTATTTG-AAAAAAC
1 GCCGCTAAAAATAGCGGCGTTTATTTGAAAAAAAC
19747513 GCCGCTAAA
1 GCCGCTAAA
19747522 GAACATGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 16 0.37
35 27 0.63
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (35 bp):
GCCGCTAAAAATAGCGGCGTTTATTTGAAAAAAAC
Found at i:19747735 original size:42 final size:43
Alignment explanation
Indices: 19747509--19747734 Score: 357
Period size: 43 Copynumber: 5.3 Consensus size: 43
19747499 TTATTTGAAA
*
19747509 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
19747552 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
19747595 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * *
19747638 AAACGCCGCTAAAGACCATGTTCTTTAGCAGTGC-TTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
19747680 AAACGCCGCTAAA-AACATGGTCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
19747722 AAACGCCACTAAA
1 AAACGCCGCTAAA
19747735 ATTAACAAAT
Statistics
Matches: 171, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
41 16 0.09
42 40 0.23
43 115 0.67
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
Found at i:19749398 original size:42 final size:43
Alignment explanation
Indices: 19749172--19749397 Score: 357
Period size: 43 Copynumber: 5.3 Consensus size: 43
19749162 TTATTTGAAA
*
19749172 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
19749215 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * *
19749258 AAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * *
19749301 AAACGCCGCTAAAGACCATGTTCTTTAGCAGCGC-TTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
19749343 AAACGCCGCTAAA-AACATGGTCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
19749385 AAACGCCACTAAA
1 AAACGCCGCTAAA
19749398 ATTAACAAAT
Statistics
Matches: 171, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
41 17 0.10
42 40 0.23
43 114 0.67
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
Found at i:19752434 original size:41 final size:41
Alignment explanation
Indices: 19752389--19752730 Score: 406
Period size: 41 Copynumber: 8.4 Consensus size: 41
19752379 TTGAGCGGGA
19752389 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTATGATC
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTATGATC
*
19752430 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTATGATC
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTATGATC
* * *
19752471 TTTAGCGGCGCTTTCCCATAAGCACCGCTATTGTTATGATC
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTATGATC
* ** * * *
19752512 TTTAGCGGCGCTTATGGAAAAGCGCCGCTATTGCTCTAATC
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTATGATC
* * * *
19752553 TTTAGCGGCGCTTTCCCGTAAGCGTCGCTATTGTTATGATC
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTATGATC
* * ** *
19752594 TTTAGCGGCACTTATGGAAAAGCGCCGCTATTGCTATGATC
1 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTATGATC
* * *
19752635 TTTAGCGGCGCTTATGT-GA-AAGCGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTT-T-TCCATAAGCGCCGCTATTGCTATGATC
*
19752676 TTTAGCGGCG-TTTTCCCATAAGCGCCGCTATTGCT-TTATC
1 TTTAGCGGCGCTTTT-CCATAAGCGCCGCTATTGCTATGATC
*
19752716 TTTTGCGGCG-TTTTC
1 TTTAGCGGCGCTTTTC
19752731 TATCCAAACG
Statistics
Matches: 257, Mismatches: 39, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
38 1 0.00
39 2 0.01
40 19 0.07
41 232 0.90
42 2 0.01
43 1 0.00
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTATGATC
Found at i:19752436 original size:24 final size:24
Alignment explanation
Indices: 19752409--19752482 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 24
19752399 CTTTTCCATA
19752409 AGCGCCGCTATTGCTATGATCTTT
1 AGCGCCGCTATTGCTATGATCTTT
* * *
19752433 AGCGGCGCT-TTCCCAT-A-----
1 AGCGCCGCTATTGCTATGATCTTT
19752450 AGCGCCGCTATTGCTATGATCTTT
1 AGCGCCGCTATTGCTATGATCTTT
*
19752474 AGCGGCGCT
1 AGCGCCGCT
19752483 TTCCCATAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 14
0.63 0.12 0.25
Matches are distributed among these distances:
17 8 0.22
18 5 0.14
19 1 0.03
22 1 0.03
23 5 0.14
24 16 0.44
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.31
Consensus pattern (24 bp):
AGCGCCGCTATTGCTATGATCTTT
Found at i:19752575 original size:123 final size:123
Alignment explanation
Indices: 19752389--19752730 Score: 465
Period size: 123 Copynumber: 2.8 Consensus size: 123
19752379 TTGAGCGGGA
* ** * *
19752389 TTTAGCGGCGCTTTTCCATAAGCGCCGCTATTGCTATGATCTTTAGCGGCGCTTTCCCATAAGCG
1 TTTAGCGGCGCTTATGGAAAAGCGCCGCTATTGCTCTGATCTTTAGCGGCGCTTTCCCATAAGCG
* *
19752454 CCGCTATTGCTATGATCTTTAGCGGCGCTTTCCCATAAGCACCGCTATTGTTATGATC
66 CCGCTATTGCTATGATCTTTAGCGGCGCTTTCCCAAAAGCACCGCTATTGCTATGATC
* *
19752512 TTTAGCGGCGCTTATGGAAAAGCGCCGCTATTGCTCTAATCTTTAGCGGCGCTTTCCCGTAAGCG
1 TTTAGCGGCGCTTATGGAAAAGCGCCGCTATTGCTCTGATCTTTAGCGGCGCTTTCCCATAAGCG
* * * ** *
19752577 TCGCTATTGTTATGATCTTTAGCGGCACTTAT-GGAAAAGCGCCGCTATTGCTATGATC
66 CCGCTATTGCTATGATCTTTAGCGGCGCTT-TCCCAAAAGCACCGCTATTGCTATGATC
* *
19752635 TTTAGCGGCGCTTATGTG-AAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGTTTTCCCATAAGC
1 TTTAGCGGCGCTTATG-GAAAAGCGCCGCTATTGCTCTGATCTTTAGCGGCGCTTTCCCATAAGC
* * *
19752699 GCCGCTATTGCT-TTATCTTTTGCGGCGTTTTC
65 GCCGCTATTGCTATGATCTTTAGCGGCGCTTTC
19752731 TATCCAAACG
Statistics
Matches: 191, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
121 1 0.01
122 14 0.07
123 174 0.91
124 2 0.01
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.34
Consensus pattern (123 bp):
TTTAGCGGCGCTTATGGAAAAGCGCCGCTATTGCTCTGATCTTTAGCGGCGCTTTCCCATAAGCG
CCGCTATTGCTATGATCTTTAGCGGCGCTTTCCCAAAAGCACCGCTATTGCTATGATC
Found at i:19754272 original size:24 final size:23
Alignment explanation
Indices: 19754240--19754301 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
19754230 TGCAACGCAA
19754240 TTTAAAAAAAAAAAAAGTTAAAAC
1 TTTAAAAAAAAAAAAAG-TAAAAC
* ** *
19754264 TTTAAAAAAGAAAACCGTATAAC
1 TTTAAAAAAAAAAAAAGTAAAAC
*
19754287 TTTAAAAAATAAAAA
1 TTTAAAAAAAAAAAA
19754302 CTAAAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.66, C:0.06, G:0.05, T:0.23
Consensus pattern (23 bp):
TTTAAAAAAAAAAAAAGTAAAAC
Found at i:19757130 original size:173 final size:171
Alignment explanation
Indices: 19756838--19757173 Score: 557
Period size: 173 Copynumber: 2.0 Consensus size: 171
19756828 TATATTTACC
19756838 TTTGAAAATACGTAAGCGTTTGATGCTTATGTATCTATTTGTAGTGCTAAATTTTAATTTTAATT
1 TTTGAAAATACGTAAGCGTTTGATGCTTATGTATCTATTTGTAGTGCTAAATTTTAATTTTAATT
* * *
19756903 TATATGTAATTGTAACAATAATTAAGTGATAATTAGTTTAAAATAACAAAGTTAATTGTATTAGA
66 TATATGTAACTGTAACAATAATTAAGTGATAATTAGTTTAAAATAACAAAGTTAATTGCATTAAA
19756968 CATCCCCCAAACTATGATTTTCATTCTAAACTGGTTCCCAAAT
131 CAT--CCCAAACTATGATTTTCATTCTAAACTGGTTCCCAAAT
*
19757011 TTTGAAAATACGTAAGCGTTTGATGCTTATGTATCTATTTGTAGTGCTAAGTTTTAATTTTAATT
1 TTTGAAAATACGTAAGCGTTTGATGCTTATGTATCTATTTGTAGTGCTAAATTTTAATTTTAATT
*
19757076 TATATGTAACTGTAATAATAATTAAGTGATAATTAGTTTAAAATAA-AGAAGTTAATTGCATTAA
66 TATATGTAACTGTAACAATAATTAAGTGATAATTAGTTTAAAATAACA-AAGTTAATTGCATTAA
* * * *
19757140 ACATCTCAAACTATGATTTTTATTTTAAATTGGT
130 ACATCCCAAACTATGATTTTCATTCTAAACTGGT
19757174 CCTCAAACTT
Statistics
Matches: 153, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
171 26 0.17
172 1 0.01
173 126 0.82
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (171 bp):
TTTGAAAATACGTAAGCGTTTGATGCTTATGTATCTATTTGTAGTGCTAAATTTTAATTTTAATT
TATATGTAACTGTAACAATAATTAAGTGATAATTAGTTTAAAATAACAAAGTTAATTGCATTAAA
CATCCCAAACTATGATTTTCATTCTAAACTGGTTCCCAAAT
Found at i:19758349 original size:40 final size:42
Alignment explanation
Indices: 19758265--19758580 Score: 246
Period size: 41 Copynumber: 7.8 Consensus size: 42
19758255 AAAGGTAAAG
** *
19758265 CATTAGCGGCGCTT-CCCCA-AAGAGCCGCTAAAGGT-GGGT
1 CATTAGCGGCGCTTATACCACAAGCGCCGCTAAAGGTCGGGT
* *** *
19758304 TATTAGCGGCGCTTATGGGA-AAGCGCCGCTAAAGGT-TGGT
1 CATTAGCGGCGCTTATACCACAAGCGCCGCTAAAGGTCGGGT
* *
19758344 CATTAGCGGCGGTT-TACCACAAGCGCCGCTAAAGGTGGGGT
1 CATTAGCGGCGCTTATACCACAAGCGCCGCTAAAGGTCGGGT
* * **
19758385 CATTAGCAGCGCTT-CACCACAAGCGCCGCTAGTGGTCGGGT
1 CATTAGCGGCGCTTATACCACAAGCGCCGCTAAAGGTCGGGT
* *
19758426 CATTAG-GG-GCGTATTCCCACAAGCGCCGCTAAAGGTCGGGT
1 CATTAGCGGCGCTTA-TACCACAAGCGCCGCTAAAGGTCGGGT
* * * * *
19758467 CATTAGCGGCACTTATA-TAGGAAGCACCGCTAAAGGTCAGGT
1 CATTAGCGGCGCTTATACCA-CAAGCGCCGCTAAAGGTCGGGT
* * * * *
19758509 CATTAGCGGCGCTT-TTCTAATAAGCGTCGCTAAAGGT-GTG-
1 CATTAGCGGCGCTTATAC-CACAAGCGCCGCTAAAGGTCGGGT
* **
19758549 CATTAGCGGCGCTT-TCCCATGAGCGCCGCTAA
1 CATTAGCGGCGCTTATACCACAAGCGCCGCTAA
19758581 TTTATTTAAA
Statistics
Matches: 223, Mismatches: 44, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
39 30 0.13
40 64 0.29
41 76 0.34
42 49 0.22
43 4 0.02
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.22
Consensus pattern (42 bp):
CATTAGCGGCGCTTATACCACAAGCGCCGCTAAAGGTCGGGT
Found at i:19758404 original size:41 final size:39
Alignment explanation
Indices: 19758203--19758580 Score: 230
Period size: 40 Copynumber: 9.4 Consensus size: 39
19758193 CGTTTGGAAA
* * * **
19758203 CAAAGCGCCGCAAAAGGTGAAG-CATTAGCAGCGCTTTTC
1 CAAAGCGCCGCTAAAGGTG-GGTCATTAGCGGCGCTTCAC
* * ** *
19758242 CTAATGCGCCGCAAAAGGTAAAG-CATTAGCGGCGCTTCCC
1 C-AAAGCGCCGCTAAAGGT-GGGTCATTAGCGGCGCTTCAC
* * *
19758282 CAAAGAGCCGCTAAAGGTGGGTTATTAGCGGCGCTT-ATGG
1 CAAAGCGCCGCTAAAGGTGGGTCATTAGCGGCGCTTCA--C
* * * *
19758322 GAAAGCGCCGCTAAAGGTTGGTCATTAGCGGCGGTTTAC
1 CAAAGCGCCGCTAAAGGTGGGTCATTAGCGGCGCTTCAC
*
19758361 CACAAGCGCCGCTAAAGGTGGGGTCATTAGCAGCGCTTCAC
1 CA-AAGCGCCGCTAAAGGT-GGGTCATTAGCGGCGCTTCAC
** * *
19758402 CACAAGCGCCGCTAGTGGTCGGGTCATTAGGGGCGTATTC-C
1 CA-AAGCGCCGCTAAAGGT-GGGTCATTAGCGGCG-CTTCAC
* *
19758443 CACAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCACTT-ATA
1 CA-AAGCGCCGCTAAAGGT-GGGTCATTAGCGGCGCTTCA-C
* * * **
19758484 TAGGAAGCACCGCTAAAGGTCAGGTCATTAGCGGCGCTTTTC
1 CA--AAGCGCCGCTAAAGGT-GGGTCATTAGCGGCGCTTCAC
* * *
19758526 TAATAAGCGTCGCTAAAGGTGTG-CATTAGCGGCGCTTTC-C
1 -CA-AAGCGCCGCTAAAGGTGGGTCATTAGCGGCGC-TTCAC
*
19758566 CATGAGCGCCGCTAA
1 CA-AAGCGCCGCTAA
19758581 TTTATTTAAA
Statistics
Matches: 271, Mismatches: 53, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
38 1 0.00
39 41 0.15
40 95 0.35
41 84 0.31
42 49 0.18
43 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.21
Consensus pattern (39 bp):
CAAAGCGCCGCTAAAGGTGGGTCATTAGCGGCGCTTCAC
Found at i:19758615 original size:5 final size:5
Alignment explanation
Indices: 19758605--19758644 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
19758595 ATATATCTTA
* *
19758605 AAATT AAATT AATTT AATTT AAAATT AAATT AAATT AAAT
1 AAATT AAATT AAATT AAATT -AAATT AAATT AAATT AAAT
19758645 AAAAACAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AAATT
Found at i:19758621 original size:16 final size:16
Alignment explanation
Indices: 19758605--19758643 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
19758595 ATATATCTTA
*
19758605 AAATT-AAATTAATTT
1 AAATTAAAATTAAATT
*
19758620 AATTTAAAATTAAATT
1 AAATTAAAATTAAATT
19758636 AAATTAAA
1 AAATTAAA
19758644 TAAAAACAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTAAAATTAAATT
Found at i:19758628 original size:21 final size:21
Alignment explanation
Indices: 19758602--19758642 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
19758592 TTTATATATC
*
19758602 TTAAAATTAAATTAATTTAAT
1 TTAAAATTAAATTAAATTAAT
19758623 TTAAAATTAAATTAAATTAA
1 TTAAAATTAAATTAAATTAA
19758643 ATAAAAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAAATTAAATTAAATTAAT
Found at i:19758649 original size:21 final size:21
Alignment explanation
Indices: 19758604--19758649 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
19758594 TATATATCTT
* * *
19758604 AAAATTAAATTAATTTAATTT
1 AAAATTAAATTAAATTAAATA
19758625 AAAATTAAATTAAATTAAATA
1 AAAATTAAATTAAATTAAATA
19758646 AAAA
1 AAAA
19758650 CAGAGTTGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATTAAATTAAATTAAATA
Found at i:19758679 original size:18 final size:18
Alignment explanation
Indices: 19758658--19758693 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19758648 AACAGAGTTG
*
19758658 TCTTCGCCCCCAGAACCC
1 TCTTCACCCCCAGAACCC
*
19758676 TCTTCACCCCTAGAACCC
1 TCTTCACCCCCAGAACCC
19758694 GCAGAACCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.53, G:0.08, T:0.19
Consensus pattern (18 bp):
TCTTCACCCCCAGAACCC
Found at i:19759570 original size:355 final size:358
Alignment explanation
Indices: 19758695--19759760 Score: 2014
Period size: 358 Copynumber: 3.0 Consensus size: 358
19758685 CTAGAACCCG
* * *
19758695 CAGAACCCGCTTCTATTCCCCTCACTCCGTTCCCTCTTCACACCCAGAACTCGCTTCTCGAGCCG
1 CAGAACCCGCTTCTGTTCCCCTTACTCCGTTCCCTCTTCACACCCAGAACCCGCTTCTCGAGCCG
*
19758760 ATCTGAAAGCCGTAAATAAAACCCATTACAATCCACTGTTCCCTATCGGTATTACCTTCTACCCT
66 ATCTGAAAGCCGCAAATAAAACCCATTACAATCCACTGTTCCCTATCGGTATTACCTTCTACCCT
* *
19758825 TTTTCCCCCCTTTTATTCATATATAATTTGGTTTCAACTTTTTTTTTGATTTTGGTTGTGTAAAT
131 TTTTCCCCCTTTTTATTCATATATAATTTGGTTTCAACTTTTATTTTGATTTTGGTTGTGTAAAT
19758890 GTGCTTGCTTGCTTTGTGATTTTTATTCTATTCATTTTACTTTCTCTCATGCATGCTATCATGGT
196 GTGCTTGCTTGCTTTGTGATTTTTATTCTATTCATTTTACTTTCTCTCATGCATGCTATCATGGT
19758955 GAAATGAATGGTAATTTTGGAGGGTTTTCTTTTTCTTTTCATTTTATCTTTTAAATGGATATATA
261 GAAATGAATGGTAATTTTGGAGGGTTTTCTTTTTCTTTTCATTTTATCTTTTAAATGGATATATA
19759020 ATTGGTTGTGTTTCTTGCGTTCTTGCTCACTCC
326 ATTGGTTGTGTTTCTTGCGTTCTTGCTCACTCC
*
19759053 CAGAACCCGCTTCTGTTCCCTTTACTCCGTTCCCTCTTCACACCCAGAACCCGCTTCTCGAGCCG
1 CAGAACCCGCTTCTGTTCCCCTTACTCCGTTCCCTCTTCACACCCAGAACCCGCTTCTCGAGCCG
*
19759118 ATCTGAAAGCCGCAAATAAAACCCATTACAATCCACTGTTCCCTATCGTTATTACCTTCTACCCT
66 ATCTGAAAGCCGCAAATAAAACCCATTACAATCCACTGTTCCCTATCGGTATTACCTTCTACCCT
19759183 TTTT-CCCCTTTTTATTCATATATAATTTTGGTTTCAACTTTTATTTTGATTTTGGTTGTGTAAA
131 TTTTCCCCCTTTTTATTCATATATAA-TTTGGTTTCAACTTTTATTTTGATTTTGGTTGTGTAAA
19759247 TGTGCTTGCTTGCTTTGTGATTTTTATTCTATTCATTTTACTTTCTCTCATGCATGCTATCATGG
195 TGTGCTTGCTTGCTTTGTGATTTTTATTCTATTCATTTTACTTTCTCTCATGCATGCTATCATGG
19759312 TGAAATGAATGGTAATTTTGGAGGG-TTT-TTTTTCTTTTCATTTTATCTTTTAAATGGATATAT
260 TGAAATGAATGGTAATTTTGGAGGGTTTTCTTTTTCTTTTCATTTTATCTTTTAAATGGATATAT
19759375 AATTGGTTGTGTTTCTTGCGTTCTTGCTCACTCC
325 AATTGGTTGTGTTTCTTGCGTTCTTGCTCACTCC
19759409 CAGAACCC-CTTCTGTTCCCCTTACTCCGTTCCCTCTTCACACCCAGAACCCGCTTCTCGAGCCG
1 CAGAACCCGCTTCTGTTCCCCTTACTCCGTTCCCTCTTCACACCCAGAACCCGCTTCTCGAGCCG
19759473 ATCTGAAAGCCGCAAATAAAACCCATTACAATCCACTGTTCCCTATCGGTATTACCTTCTACCCT
66 ATCTGAAAGCCGCAAATAAAACCCATTACAATCCACTGTTCCCTATCGGTATTACCTTCTACCCT
19759538 TTTTCCCCCTTTTTATTCATATATAATTTGGTTTCAACTTTTATTTTGATTTTGGTTGTGTAAAT
131 TTTTCCCCCTTTTTATTCATATATAATTTGGTTTCAACTTTTATTTTGATTTTGGTTGTGTAAAT
19759603 GTGCTTGCTTGCTTTGTGATTTTTATTCTATTCATTTTACTTTCTCTCATGCATGCTATCATGGT
196 GTGCTTGCTTGCTTTGTGATTTTTATTCTATTCATTTTACTTTCTCTCATGCATGCTATCATGGT
*
19759668 GAAATGAATGGTAATTTTGGGGGGTTTTCTTTTTCTTTTCATTTTATCTTTTAAATGGATATATA
261 GAAATGAATGGTAATTTTGGAGGGTTTTCTTTTTCTTTTCATTTTATCTTTTAAATGGATATATA
19759733 ATTGGTTGTGTTTCTTGCGTTCTTGCTC
326 ATTGGTTGTGTTTCTTGCGTTCTTGCTC
19759761 TAAATTGGAA
Statistics
Matches: 693, Mismatches: 11, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
355 250 0.36
356 101 0.15
357 87 0.13
358 255 0.37
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.44
Consensus pattern (358 bp):
CAGAACCCGCTTCTGTTCCCCTTACTCCGTTCCCTCTTCACACCCAGAACCCGCTTCTCGAGCCG
ATCTGAAAGCCGCAAATAAAACCCATTACAATCCACTGTTCCCTATCGGTATTACCTTCTACCCT
TTTTCCCCCTTTTTATTCATATATAATTTGGTTTCAACTTTTATTTTGATTTTGGTTGTGTAAAT
GTGCTTGCTTGCTTTGTGATTTTTATTCTATTCATTTTACTTTCTCTCATGCATGCTATCATGGT
GAAATGAATGGTAATTTTGGAGGGTTTTCTTTTTCTTTTCATTTTATCTTTTAAATGGATATATA
ATTGGTTGTGTTTCTTGCGTTCTTGCTCACTCC
Found at i:19761988 original size:10 final size:9
Alignment explanation
Indices: 19761945--19762104 Score: 52
Period size: 8 Copynumber: 17.6 Consensus size: 9
19761935 GTTTAAAGAT
19761945 TTAATTAT-
1 TTAATTATA
19761953 TTAATTATA
1 TTAATTATA
*
19761962 TTAAAGTA-A
1 TT-AATTATA
*
19761971 ATAATTATA
1 TTAATTATA
19761980 TTAAATTAT-
1 TT-AATTATA
*
19761989 TTAATTATGT
1 TTAATTAT-A
19761999 TTAATTATGTA
1 TTAATTA--TA
19762010 TTTAATTATA
1 -TTAATTATA
* *
19762020 -AACAGTATCGA
1 TTA-ATTAT--A
19762031 TTAATTA-A
1 TTAATTATA
* *
19762039 GTATTTA-A
1 TTAATTATA
*
19762047 GTTAA-TAGA
1 -TTAATTATA
19762056 TTTAATTAT-
1 -TTAATTATA
19762065 TTAATTATA
1 TTAATTATA
*
19762074 TTAAGTA-A
1 TTAATTATA
*
19762082 ATAATTATA
1 TTAATTATA
19762091 TTAAATTAT-
1 TT-AATTATA
19762100 TTAAT
1 TTAAT
19762105 CATCATGTTT
Statistics
Matches: 114, Mismatches: 19, Indels: 38
0.67 0.11 0.22
Matches are distributed among these distances:
8 45 0.39
9 29 0.25
10 27 0.24
11 4 0.04
12 9 0.08
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (9 bp):
TTAATTATA
Found at i:19761993 original size:18 final size:18
Alignment explanation
Indices: 19761947--19762232 Score: 90
Period size: 18 Copynumber: 15.3 Consensus size: 18
19761937 TTAAAGATTT
19761947 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
19761965 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
*
19761983 AATTATTTAATTATGTTTA
1 AATTATTTAATTAT-ATTA
19762002 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* **
19762021 ACAGTA-TCGATTA-ATT-
1 A-ATTATTTAATTATATTA
* *
19762037 AAGTATTTAAGTTAATAGATTT
1 AATTATTTAA-TT-AT--ATTA
19762059 AATTATTTAATTATATT-
1 AATTATTTAATTATATTA
* **
19762076 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
*
19762094 AATTATTTAATCATCATGTTTA
1 AATTATTTAAT--T-AT-ATTA
19762116 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* **
19762135 ACAGTA-TCGATTA-ATTA
1 A-ATTATTTAATTATATTA
* *
19762152 AA-TATTTAAGTTAAAAGATTT
1 AATTATTTAA-TT---ATATTA
19762173 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
19762191 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* * *
19762209 AATTATTTAGTTATGTTT
1 AATTATTTAATTATATTA
19762227 AATTAT
1 AATTAT
19762233 GTATTTAATT
Statistics
Matches: 197, Mismatches: 41, Indels: 60
0.66 0.14 0.20
Matches are distributed among these distances:
15 8 0.04
16 16 0.08
17 24 0.12
18 77 0.39
19 8 0.04
20 4 0.02
21 16 0.08
22 33 0.17
23 1 0.01
24 2 0.01
25 8 0.04
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (18 bp):
AATTATTTAATTATATTA
Found at i:19762077 original size:17 final size:17
Alignment explanation
Indices: 19762057--19762104 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
19762047 GTTAATAGAT
19762057 TTAATTATTTAATTATA
1 TTAATTATTTAATTATA
* **
19762074 TTAAGTAAATAATTATA
1 TTAATTATTTAATTATA
19762091 TTAAATTATTTAAT
1 TT-AATTATTTAAT
19762105 CATCATGTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAATTATTTAATTATA
Found at i:19762150 original size:114 final size:111
Alignment explanation
Indices: 19761888--19762263 Score: 664
Period size: 112 Copynumber: 3.3 Consensus size: 111
19761878 AATAATTAAA
*
19761888 TAATTATGTATTTAATTATAAACAGTATCAATTAATTAAATATTTAAGTTTAAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAG-TTAAAGATTTAATTAT
19761953 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
65 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
*
19762000 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAGTATTTAAGTTAATAGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAA-AGATTTAATTAT
19762065 TTAATTATATT-AAGTAAATAATTATATTAAATTATTTAATCATCATGTT
65 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAAT--T-ATGTT
19762114 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTT-AAAGATTTAATTAT
*
19762179 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAGTTATGTT
65 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
19762226 TAATTATGTATTTAATTATAAACAGTATCGATTAATTA
1 TAATTATGTATTTAATTATAAACAGTATCGATTAATTA
19762264 TTTAATTATA
Statistics
Matches: 254, Mismatches: 4, Indels: 12
0.94 0.01 0.04
Matches are distributed among these distances:
111 33 0.13
112 112 0.44
113 2 0.01
114 77 0.30
115 30 0.12
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (111 bp):
TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAAAGATTTAATTATT
TAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
Found at i:19762277 original size:10 final size:12
Alignment explanation
Indices: 19762256--19762292 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
19762246 AACAGTATCG
*
19762256 ATTAATTATTTA
1 ATTAACTATTTA
19762268 ATT-A-TATTTA
1 ATTAACTATTTA
19762278 ATTAACTATTTA
1 ATTAACTATTTA
19762290 ATT
1 ATT
19762293 TAAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.39
11 2 0.09
12 12 0.52
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTAACTATTTA
Found at i:19762331 original size:18 final size:18
Alignment explanation
Indices: 19762310--19762346 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19762300 TTTTCGTAAA
19762310 TAATTATATATAATTATT
1 TAATTATATATAATTATT
* *
19762328 TAATTTTATTTAATTATT
1 TAATTATATATAATTATT
19762346 T
1 T
19762347 CATTGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TAATTATATATAATTATT
Found at i:19762451 original size:31 final size:33
Alignment explanation
Indices: 19762395--19762461 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
19762385 TCAAATATTT
*
19762395 AAGTAAAATTTTGTCACTAATATATATATTTTA
1 AAGTAAAATATTGTCACTAATATATATATTTTA
19762428 AAGTAAAATATTGTCACTAATATATAT-TTTTA
1 AAGTAAAATATTGTCACTAATATATATATTTTA
19762460 AA
1 AA
19762462 TTTAAATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 7 0.21
33 26 0.79
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (33 bp):
AAGTAAAATATTGTCACTAATATATATATTTTA
Found at i:19768001 original size:21 final size:20
Alignment explanation
Indices: 19767977--19768035 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
19767967 TAAAGCAGAG
19767977 GCAGCAGCAAGGCAAGCGGAA
1 GCAGCAGCAAGGCAAGCGG-A
* *
19767998 GCAGCAACGAGGCAAGCGGA
1 GCAGCAGCAAGGCAAGCGGA
* *
19768018 GACAACAGCAAGGGAAGC
1 G-CAGCAGCAAGGCAAGC
19768036 AGAGGCTACA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.39, C:0.24, G:0.37, T:0.00
Consensus pattern (20 bp):
GCAGCAGCAAGGCAAGCGGA
Found at i:19783339 original size:14 final size:13
Alignment explanation
Indices: 19783320--19783350 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
19783310 TACAGGTATG
19783320 TTTTTCTTTTTCTT
1 TTTTTCTTTTT-TT
19783334 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
19783347 TTTT
1 TTTT
19783351 GGGGGGGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:19786277 original size:26 final size:27
Alignment explanation
Indices: 19786216--19786279 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
19786206 ACTGAGGCAT
*
19786216 AACA-CAAAAGATCAAAACAAATACAA
1 AACATCAAATGATCAAAACAAATACAA
* *
19786242 AACCTCAAATGATCAAAA-AAGTACAA
1 AACATCAAATGATCAAAACAAATACAA
*
19786268 AACATGAAATGA
1 AACATCAAATGA
19786280 ACCACACAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 20 0.62
27 12 0.38
ACGTcount: A:0.62, C:0.17, G:0.08, T:0.12
Consensus pattern (27 bp):
AACATCAAATGATCAAAACAAATACAA
Found at i:19794228 original size:65 final size:66
Alignment explanation
Indices: 19794135--19794263 Score: 179
Period size: 65 Copynumber: 2.0 Consensus size: 66
19794125 TTATATATGA
** * *
19794135 AATTTAAAAATTTCAAGTTATAACTTGTTAATTAGGTGTTCGAAAATTATGAT-TACTGATTGAC
1 AATTTAAAAATCCCAAATTATAACTTGTTAATTAGGTGTTCGAAAATTATAATCTACTGATTGAC
19794199 C
66 C
* * * *
19794200 AATTTAAAAATCCCAAATTATGATTTGTTAATTGGGTGTTCGAAAATTATAATCTATTGATTGA
1 AATTTAAAAATCCCAAATTATAACTTGTTAATTAGGTGTTCGAAAATTATAATCTACTGATTGA
19794264 GTGTTCATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
65 46 0.84
66 9 0.16
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (66 bp):
AATTTAAAAATCCCAAATTATAACTTGTTAATTAGGTGTTCGAAAATTATAATCTACTGATTGAC
C
Found at i:19799670 original size:42 final size:42
Alignment explanation
Indices: 19799612--19799695 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
19799602 CTTTAGTAGG
* *
19799612 CGGTTCCTGGCTACCATCTGCCTCAAAATTCTCAACTTTACC
1 CGGTTCCTGACCACCATCTGCCTCAAAATTCTCAACTTTACC
* * *
19799654 CGGTTCCTGACCACCATCTGCCTCTAATTTCTCATCTTTACC
1 CGGTTCCTGACCACCATCTGCCTCAAAATTCTCAACTTTACC
19799696 TAACTCAGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.19, C:0.37, G:0.11, T:0.33
Consensus pattern (42 bp):
CGGTTCCTGACCACCATCTGCCTCAAAATTCTCAACTTTACC
Found at i:19801724 original size:15 final size:15
Alignment explanation
Indices: 19801685--19801724 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
19801675 TAACAAATCT
*
19801685 TTAAAAATTATTAAG
1 TTAAAAATTATTAAA
19801700 TTACAAAAATTATTAAA
1 TT--AAAAATTATTAAA
19801717 TTAAAAAT
1 TTAAAAAT
19801725 AGTAAACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
17 14 0.64
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (15 bp):
TTAAAAATTATTAAA
Found at i:19802349 original size:28 final size:27
Alignment explanation
Indices: 19802283--19802349 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
19802273 CAAATATATA
**
19802283 ACAATTTTTAATAATTTTTTTACAATTT
1 ACAATTTTT-ATAATTTTTCAACAATTT
*
19802311 -CTAATTATTTATAATTTTTACAATAATTT
1 AC-AATT-TTTATAATTTTT-CAACAATTT
19802340 ACAATTTTTA
1 ACAATTTTTA
19802350 ATGCTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
27 1 0.03
28 17 0.53
29 13 0.41
30 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.55
Consensus pattern (27 bp):
ACAATTTTTATAATTTTTCAACAATTT
Found at i:19804971 original size:11 final size:11
Alignment explanation
Indices: 19804955--19804994 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
19804945 TATTTTAATT
19804955 AATTGTTTAAA
1 AATTGTTTAAA
19804966 AATTGTTTAAA
1 AATTGTTTAAA
19804977 AATAT-TTT-AA
1 AAT-TGTTTAAA
19804987 AATTGTTT
1 AATTGTTT
19804995 TAATAGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.04
10 8 0.30
11 17 0.63
12 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (11 bp):
AATTGTTTAAA
Found at i:19809336 original size:33 final size:32
Alignment explanation
Indices: 19809284--19809379 Score: 99
Period size: 32 Copynumber: 3.0 Consensus size: 32
19809274 TGGAATGTTG
*
19809284 TTTGCATCTGTATGGTATGCTTTTTAAGTTACC
1 TTTG-ATCTGTATGATATGCTTTTTAAGTTACC
* * *
19809317 TTTGGATCTGTCTGTTATGC-TTTTATA-TTATC
1 TTT-GATCTGTATGATATGCTTTTTA-AGTTACC
19809349 TTT-ATTCTGTATGATATGCTTTTTAAGTTAC
1 TTTGA-TCTGTATGATATGCTTTTTAAGTTAC
19809380 ATTGTCACAT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
30 1 0.02
31 13 0.25
32 20 0.38
33 17 0.33
34 1 0.02
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.53
Consensus pattern (32 bp):
TTTGATCTGTATGATATGCTTTTTAAGTTACC
Found at i:19823750 original size:63 final size:63
Alignment explanation
Indices: 19823651--19823778 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
19823641 AATGTGACTT
19823651 CTAAGCCAAGAAACACCTCGATCACCATTAGTCCTAGTTCTCTCCACATTAACTTGTGTTTCA
1 CTAAGCCAAGAAACACCTCGATCACCATTAGTCCTAGTTCTCTCCACATTAACTTGTGTTTCA
19823714 CTAAGCCAAGAAACACCTCGATCACCATTAGTCCTAGTTCTCTCCACATTAACTTGTGTTTCA
1 CTAAGCCAAGAAACACCTCGATCACCATTAGTCCTAGTTCTCTCCACATTAACTTGTGTTTCA
19823777 CT
1 CT
19823779 TCTTTTTTCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.30
Consensus pattern (63 bp):
CTAAGCCAAGAAACACCTCGATCACCATTAGTCCTAGTTCTCTCCACATTAACTTGTGTTTCA
Found at i:19831965 original size:6 final size:6
Alignment explanation
Indices: 19831954--19831980 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19831944 ACCTCAAACC
19831954 CAAGTG CAAGTG CAAGTG CAAGTG CAA
1 CAAGTG CAAGTG CAAGTG CAAGTG CAA
19831981 AGCTTTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.30, T:0.15
Consensus pattern (6 bp):
CAAGTG
Found at i:19836000 original size:4 final size:4
Alignment explanation
Indices: 19835991--19836023 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
19835981 ATTAGATATT
19835991 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
19836024 GGTTAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:19839048 original size:6 final size:6
Alignment explanation
Indices: 19839037--19839066 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
19839027 CGTGTTTACG
19839037 CGTTGC CGTTGC CGTTGC CGTTGC CGTTGC
1 CGTTGC CGTTGC CGTTGC CGTTGC CGTTGC
19839067 GGTACTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (6 bp):
CGTTGC
Found at i:19839948 original size:20 final size:20
Alignment explanation
Indices: 19839912--19839949 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19839902 ATTAAGACTT
* *
19839912 ATTTAAAAATTATAAAAAAC
1 ATTTAAAAATGAAAAAAAAC
19839932 ATTTAAAAATGAAAAAAA
1 ATTTAAAAATGAAAAAAA
19839950 TTTCAAATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
ATTTAAAAATGAAAAAAAAC
Found at i:19846949 original size:6 final size:6
Alignment explanation
Indices: 19846938--19846967 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
19846928 CTGGTTAAAT
19846938 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
19846968 GTAATTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:19849434 original size:6 final size:6
Alignment explanation
Indices: 19849423--19849447 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19849413 AATGTGTATA
19849423 GAATAG GAATAG GAATAG GAATAG G
1 GAATAG GAATAG GAATAG GAATAG G
19849448 CTCTGTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GAATAG
Found at i:19850469 original size:30 final size:28
Alignment explanation
Indices: 19850409--19850470 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
19850399 CCTTCAATTT
**
19850409 TTTTGAATTTACACTTTAACCCTTCAAC
1 TTTTGAATTTACACTTTAACCCCACAAC
* *
19850437 TTTTGAATATTCACACTTTGACCCCACTAC
1 TTTTGAAT-TT-ACACTTTAACCCCACAAC
19850467 TTTT
1 TTTT
19850471 CACTTCTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 8 0.29
29 2 0.07
30 18 0.64
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (28 bp):
TTTTGAATTTACACTTTAACCCCACAAC
Found at i:19857941 original size:20 final size:21
Alignment explanation
Indices: 19857910--19857956 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
19857900 ATTTAACACT
*
19857910 AATTAA-CCTTAATTAA-TTA
1 AATTAATCTTTAATTAATTTA
19857929 AATTAATCTTTAATTAATTTA
1 AATTAATCTTTAATTAATTTA
19857950 AATTAAT
1 AATTAAT
19857957 TACAATTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.24
20 9 0.36
21 10 0.40
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTAATCTTTAATTAATTTA
Found at i:19857963 original size:20 final size:20
Alignment explanation
Indices: 19857920--19857965 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
19857910 AATTAACCTT
**
19857920 AATTAATTAAATTAATCTTT
1 AATTAATTAAATTAATCTAC
19857940 AATTAATTTAAATTAAT-TAC
1 AATTAA-TTAAATTAATCTAC
19857960 AATTAA
1 AATTAA
19857966 CCTATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTAATTAAATTAATCTAC
Found at i:19861038 original size:5 final size:5
Alignment explanation
Indices: 19861030--19861060 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
19861020 GCCTTCGCTT
19861030 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC C
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC C
19861061 ATTACCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
CTCTC
Found at i:19872789 original size:24 final size:24
Alignment explanation
Indices: 19872753--19872880 Score: 175
Period size: 24 Copynumber: 5.3 Consensus size: 24
19872743 CAGAGAACAG
**
19872753 GAAGGTGGCAAGAGTTCGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
*
19872777 GAAGGTGGTAAGAGTAAGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
* *
19872801 GAAGATGGCAAGAGTAGGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
*
19872825 GAAAGTGGCAAGAGTAAGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
* * *
19872849 GAAGGTAGTAAGAGTAGGACACAA
1 GAAGGTGGCAAGAGTAAGACACAA
19872873 GAAGGTGG
1 GAAGGTGG
19872881 AAACAAGACT
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 90 1.00
ACGTcount: A:0.44, C:0.11, G:0.34, T:0.11
Consensus pattern (24 bp):
GAAGGTGGCAAGAGTAAGACACAA
Found at i:19872814 original size:48 final size:48
Alignment explanation
Indices: 19872753--19872880 Score: 193
Period size: 48 Copynumber: 2.7 Consensus size: 48
19872743 CAGAGAACAG
** *
19872753 GAAGGTGGCAAGAGTTCGACACAAGAAGGTGGTAAGAGTAAGACACAA
1 GAAGGTGGCAAGAGTAGGACACAAGAAGGTGGCAAGAGTAAGACACAA
* *
19872801 GAAGATGGCAAGAGTAGGACACAAGAAAGTGGCAAGAGTAAGACACAA
1 GAAGGTGGCAAGAGTAGGACACAAGAAGGTGGCAAGAGTAAGACACAA
* *
19872849 GAAGGTAGTAAGAGTAGGACACAAGAAGGTGG
1 GAAGGTGGCAAGAGTAGGACACAAGAAGGTGG
19872881 AAACAAGACT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.44, C:0.11, G:0.34, T:0.11
Consensus pattern (48 bp):
GAAGGTGGCAAGAGTAGGACACAAGAAGGTGGCAAGAGTAAGACACAA
Found at i:19875884 original size:28 final size:29
Alignment explanation
Indices: 19875852--19875925 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
19875842 TTGGATTTTC
19875852 ATTTTTAAATATAAAAATAAAGAG-TTAA
1 ATTTTTAAATATAAAAATAAAGAGATTAA
* *
19875880 ATTTTCTGAA-ATAAAAATAAATAGATTAA
1 ATTTT-TAAATATAAAAATAAAGAGATTAA
19875909 A-TTTTAAATATACAAAA
1 ATTTTTAAATATA-AAAA
19875926 ATATAAAGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 3 0.08
28 24 0.62
29 12 0.31
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (29 bp):
ATTTTTAAATATAAAAATAAAGAGATTAA
Found at i:19882280 original size:2 final size:2
Alignment explanation
Indices: 19882273--19882305 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
19882263 GAATGCTCAT
*
19882273 AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
19882306 ACCAGAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19887471 original size:30 final size:31
Alignment explanation
Indices: 19887426--19887487 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
19887416 TCAGATTTAT
*
19887426 GAATAGTCCCAGTACTTTACT-CAAGTTGTG
1 GAATAATCCCAGTACTTTACTCCAAGTTGTG
* *
19887456 GAATAATCCCTGTACTTTGCTCCAAGTTGTG
1 GAATAATCCCAGTACTTTACTCCAAGTTGTG
19887487 G
1 G
19887488 CACTACCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (31 bp):
GAATAATCCCAGTACTTTACTCCAAGTTGTG
Found at i:19904785 original size:40 final size:41
Alignment explanation
Indices: 19904727--19904808 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
19904717 AGGATGCTCA
19904727 ACTTAGGTGGTGATTTGTCAT-GTATATATTCAACATTTCT
1 ACTTAGGTGGTGATTTGTCATGGTATATATTCAACATTTCT
* *
19904767 ACTTAGGT-GTGTTATTGTCGTGGTATATATTCAACATTTCT
1 ACTTAGGTGGTGAT-TTGTCATGGTATATATTCAACATTTCT
19904808 A
1 A
19904809 TGTAGCTTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 4 0.11
40 14 0.37
41 20 0.53
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (41 bp):
ACTTAGGTGGTGATTTGTCATGGTATATATTCAACATTTCT
Done.