Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold430
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: 405003
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 28743 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:100 original size:14 final size:16
Alignment explanation
Indices: 79--113 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
69 ATGTTTTAGT
*
79 CAATATATTTTTCAAA
1 CAATATATTCTTCAAA
95 CAATATATTCTTCAAA
1 CAATATATTCTTCAAA
111 CAA
1 CAA
114 ATACGATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (16 bp):
CAATATATTCTTCAAA
Found at i:1792 original size:20 final size:20
Alignment explanation
Indices: 1767--1813 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1757 TATAATGCTT
*
1767 CCAACGGCTAGAACCTATCC
1 CCAACGGCTAGAAACTATCC
*
1787 CCAACGGCTAGAAATTATCC
1 CCAACGGCTAGAAACTATCC
1807 CCAACGG
1 CCAACGG
1814 TAGTAAACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.17, T:0.15
Consensus pattern (20 bp):
CCAACGGCTAGAAACTATCC
Found at i:2938 original size:82 final size:83
Alignment explanation
Indices: 2800--2966 Score: 327
Period size: 82 Copynumber: 2.0 Consensus size: 83
2790 TTGGTTAACA
2800 AAAAAATATTTTCTTTTTTTTTTAATTTCTTTTTTTCTAAACCATAAGATTCCCAACCAACCGTA
1 AAAAAATATTTTCTTTTTTTTTTAATTTCTTTTTTTCTAAACCATAAGATTCCCAACCAACCGTA
2865 AGAAAGATTAAAAAGCTG
66 AGAAAGATTAAAAAGCTG
2883 AAAAAATATTTT-TTTTTTTTTTAATTTCTTTTTTTCTAAACCATAAGATTCCCAACCAACCGTA
1 AAAAAATATTTTCTTTTTTTTTTAATTTCTTTTTTTCTAAACCATAAGATTCCCAACCAACCGTA
2947 AGAAAGATTAAAAAGCTG
66 AGAAAGATTAAAAAGCTG
2965 AA
1 AA
2967 CAACAATCAT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 72 0.86
83 12 0.14
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (83 bp):
AAAAAATATTTTCTTTTTTTTTTAATTTCTTTTTTTCTAAACCATAAGATTCCCAACCAACCGTA
AGAAAGATTAAAAAGCTG
Found at i:7288 original size:27 final size:30
Alignment explanation
Indices: 7222--7298 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 30
7212 TAAATTCACT
7222 TTTAAAAATAATTATAATATTTAATTTAGAA
1 TTTAAAAATAATTATAATATTTAA-TTAGAA
* * *
7253 TTAATAAAATAGTTGTAATATTT-A-TA-AA
1 TTTA-AAAATAATTATAATATTTAATTAGAA
7281 TTTAAAAATAATTATAAT
1 TTTAAAAATAATTATAAT
7299 TATTAGTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 12 0.31
28 5 0.13
29 2 0.05
31 4 0.10
32 16 0.41
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (30 bp):
TTTAAAAATAATTATAATATTTAATTAGAA
Found at i:7994 original size:23 final size:20
Alignment explanation
Indices: 7947--7996 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
7937 ATTCATCGTA
7947 TTAATAATAAGTGATATTAG
1 TTAATAATAAGTGATATTAG
7967 TTAATAATAAGTGATATTAG
1 TTAATAATAAGTGATATTAG
7987 TTAATAATAA
1 TTAATAATAA
7997 ATAAAATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (20 bp):
TTAATAATAAGTGATATTAG
Found at i:8403 original size:22 final size:23
Alignment explanation
Indices: 8378--8425 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
8368 TATTCATTGA
*
8378 TTACATGATTAT-TT-AGTTTATT
1 TTACAT-ATTATATTAAATTTATT
8400 TTACATATTATATTAAATTTATT
1 TTACATATTATATTAAATTTATT
8423 TTA
1 TTA
8426 AGCTTAGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 8 0.35
23 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TTACATATTATATTAAATTTATT
Found at i:8706 original size:3 final size:3
Alignment explanation
Indices: 8698--8735 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
8688 ATGATGGATT
8698 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
8736 TGATGATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:8740 original size:3 final size:3
Alignment explanation
Indices: 8734--8772 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
8724 AGAAGAAGAA
8734 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
8773 TGATAGGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:11760 original size:32 final size:33
Alignment explanation
Indices: 11693--11760 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
11683 AAATAAAGAT
* *
11693 AAAAAAATGTATATGTGTATATATTTACAAAATA
1 AAAAAAATGTATA-GAGTATATATATACAAAATA
11727 AAAAAAATGTATA-AGTATATATATA-AAATATA
1 AAAAAAATGTATAGAGTATATATATACAAA-ATA
11759 AA
1 AA
11761 GTATATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 3 0.10
32 15 0.48
34 13 0.42
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.32
Consensus pattern (33 bp):
AAAAAAATGTATAGAGTATATATATACAAAATA
Found at i:11797 original size:18 final size:17
Alignment explanation
Indices: 11745--11797 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
11735 GTATAAGTAT
**
11745 ATATATAAAATATAAAGT
1 ATATA-AAAATATAAAAA
* *
11763 ATATAAAAGTTTTAAAAA
1 ATATAAAA-ATATAAAAA
11781 ATATAAAAATATAAAAA
1 ATATAAAAATATAAAAA
11798 CGTATGAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
ATATAAAAATATAAAAA
Found at i:11882 original size:25 final size:26
Alignment explanation
Indices: 11840--11929 Score: 96
Period size: 25 Copynumber: 3.6 Consensus size: 26
11830 AAGCTTAAAA
*
11840 TATATATATATATTTAAAAAAATGCG
1 TATATATATATATATAAAAAAATGCG
* *
11866 TATATAT-TATATATAAAAATATGTG
1 TATATATATATATATAAAAAAATGCG
* * * *
11891 TGTTTA-ATACATA-AAAAAAATGCA
1 TATATATATATATATAAAAAAATGCG
11915 TATATATATATATAT
1 TATATATATATATAT
11930 TGTAAAAACC
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
24 12 0.24
25 30 0.61
26 7 0.14
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATATATATATATATAAAAAAATGCG
Found at i:15645 original size:25 final size:23
Alignment explanation
Indices: 15599--15647 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
15589 TTTCTATTTT
**
15599 TTTATAATTTTTTAAATTATAAA
1 TTTATAATTTTTTAAAAAATAAA
15622 TTTATTAATTTTTATAAAAAATAAA
1 TTTA-TAATTTTT-TAAAAAATAAA
15647 T
1 T
15648 AATGTTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 8 0.36
25 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTATAATTTTTTAAAAAATAAA
Found at i:16111 original size:10 final size:10
Alignment explanation
Indices: 16096--16121 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
16086 TCATTAAGTG
16096 CTAACAAATA
1 CTAACAAATA
16106 CTAACAAATA
1 CTAACAAATA
16116 CTAACA
1 CTAACA
16122 TATCAGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (10 bp):
CTAACAAATA
Found at i:16547 original size:243 final size:243
Alignment explanation
Indices: 16112--16612 Score: 903
Period size: 243 Copynumber: 2.1 Consensus size: 243
16102 AATACTAACA
* * *
16112 AATACTAACATATCAGTAAGTGCTAACCAGAGAAAGGCACATATGCCAATTCATACATTAATCAT
1 AATACTAACAGATCAATAAGTGCTAACCAGAGAAAGACACATATGCCAATTCATACATTAATCAT
*
16177 ACATTGCTCACTTGACTAACATTAATCATTACTCATCATGTAATTTAGCCAATTAGTCCACATGC
66 ACATTGCTCACTTGACTAACATTAATCATTACTCATCATGTAATTTAGCCAATCAGTCCACATGC
* *
16242 CAATTCCATATGCTATAAATCATGCCAAAATTACCAAAATTCATGACATAGGCACGTATGTATTT
131 CAATTCCATATGCTATAAATCATGCCAAAATTACCAAAATTCATGACATAGCCACATATGTATTT
*
16307 ACCTACCATCAACCAAATATAACAGCTCATCACTGCCATTTCCCAAAT
196 ACCTACCATCAACCAAATAAAACAGCTCATCACTGCCATTTCCCAAAT
* *
16355 AATACTAATAGATCAATAAGTGCTAATCAGAGAAAGACACATATGCCAATTCATACATTAATCAT
1 AATACTAACAGATCAATAAGTGCTAACCAGAGAAAGACACATATGCCAATTCATACATTAATCAT
16420 ACATTGCTCACTTGACTAACATTAATCATTACTCATCATGTAATTTAGCCAATCAGTCCACATGC
66 ACATTGCTCACTTGACTAACATTAATCATTACTCATCATGTAATTTAGCCAATCAGTCCACATGC
16485 CAATTCCATATGCTATAAATCATGCCAAAATTACCAAAATTCATGACATAGCCACATATGTATTT
131 CAATTCCATATGCTATAAATCATGCCAAAATTACCAAAATTCATGACATAGCCACATATGTATTT
*
16550 ACCTACCATCAACCAAATAAAACAGCTCATCATTGCCATTTCCCAAAT
196 ACCTACCATCAACCAAATAAAACAGCTCATCACTGCCATTTCCCAAAT
*
16598 AATACTAACAAATCA
1 AATACTAACAGATCA
16613 GAGTAAAAAT
Statistics
Matches: 246, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
243 246 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (243 bp):
AATACTAACAGATCAATAAGTGCTAACCAGAGAAAGACACATATGCCAATTCATACATTAATCAT
ACATTGCTCACTTGACTAACATTAATCATTACTCATCATGTAATTTAGCCAATCAGTCCACATGC
CAATTCCATATGCTATAAATCATGCCAAAATTACCAAAATTCATGACATAGCCACATATGTATTT
ACCTACCATCAACCAAATAAAACAGCTCATCACTGCCATTTCCCAAAT
Found at i:19780 original size:11 final size:11
Alignment explanation
Indices: 19766--19791 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19756 TTTTATGTGT
19766 TTTTTTAAATA
1 TTTTTTAAATA
19777 TTTTTTAAATA
1 TTTTTTAAATA
19788 TTTT
1 TTTT
19792 ATTATACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:20091 original size:24 final size:24
Alignment explanation
Indices: 20059--20108 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
20049 TGTTAGAATT
20059 ATCTATACTATATTTAAGATTTTG
1 ATCTATACTATATTTAAGATTTTG
*
20083 ATCTTTACTATATTTAAGATTTTG
1 ATCTATACTATATTTAAGATTTTG
20107 AT
1 AT
20109 TGAGTTAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (24 bp):
ATCTATACTATATTTAAGATTTTG
Found at i:21593 original size:3 final size:3
Alignment explanation
Indices: 21580--21645 Score: 62
Period size: 3 Copynumber: 21.0 Consensus size: 3
21570 TGTACATGAA
* *
21580 AAT AAT AAAT AAT AAT AAAT AAT AAT AAG AAT AAT AAAC AAGT AAT AAT
1 AAT AAT -AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AA-T AAT AAT
*
21629 AAA AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
21646 GTAAAAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 2 0.04
3 40 0.77
4 10 0.19
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:21601 original size:17 final size:18
Alignment explanation
Indices: 21579--21645 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 18
21569 ATGTACATGA
21579 AAATAATA-AATAATAAT
1 AAATAATACAATAATAAT
*
21596 AAATAAT--AATAAGAAT
1 AAATAATACAATAATAAT
21612 -AATAA-ACAAGTAATAAT
1 AAATAATACAA-TAATAAT
*
21629 AAA-AATATAATAATAAT
1 AAATAATACAATAATAAT
21646 GTAAAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
15 5 0.12
16 10 0.24
17 22 0.52
18 5 0.12
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (18 bp):
AAATAATACAATAATAAT
Found at i:21605 original size:20 final size:19
Alignment explanation
Indices: 21580--21645 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
21570 TGTACATGAA
21580 AATAATAAATAATAATAAAT
1 AATAAT-AATAATAATAAAT
* *
21600 AATAATAAGAATAATAAAC
1 AATAATAATAATAATAAAT
*
21619 AAGTAATAATAAAAATATAAT
1 AA-TAATAATAATAATA-AAT
21640 AATAAT
1 AATAAT
21646 GTAAAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 13 0.33
20 22 0.56
21 4 0.10
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (19 bp):
AATAATAATAATAATAAAT
Found at i:21625 original size:23 final size:21
Alignment explanation
Indices: 21580--21645 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
21570 TGTACATGAA
21580 AATAAT-AAATAATAATAAAT
1 AATAATAAAATAATAATAAAT
21600 AATAATAAGAATAATAA-ACAAGT
1 AATAATAA-AATAATAATA-AA-T
21623 AATAATAAAA-ATATAAT-AAT
1 AATAATAAAATA-ATAATAAAT
21643 AAT
1 AAT
21646 GTAAAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
20 10 0.25
21 5 0.12
22 16 0.40
23 9 0.22
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (21 bp):
AATAATAAAATAATAATAAAT
Found at i:21628 original size:14 final size:13
Alignment explanation
Indices: 21597--21644 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
21587 AATAATAATA
*
21597 AATAATAATAAG-
1 AATAATAAAAAGT
21609 AATAATAAACAAGT
1 AATAATAAA-AAGT
*
21623 AATAATAAAAATAT
1 AATAATAAAAA-GT
21637 AATAATAA
1 AATAATAA
21645 TGTAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 8 0.26
13 5 0.16
14 18 0.58
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (13 bp):
AATAATAAAAAGT
Found at i:22231 original size:15 final size:14
Alignment explanation
Indices: 22208--22240 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
22198 TTTTAAACAA
22208 AAAATAAAATAAAT
1 AAAATAAAATAAAT
22222 AAAATGAAAATAAAT
1 AAAAT-AAAATAAAT
22237 AAAA
1 AAAA
22241 AACGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:23383 original size:44 final size:44
Alignment explanation
Indices: 23342--24057 Score: 176
Period size: 44 Copynumber: 16.3 Consensus size: 44
23332 ACCATCTTTG
*
23342 ATCTACTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTACTCAGGGAGATAAGATCTGTAATCTTCA
* ** * * * *
23386 ATCTATTCCACTGTTGCCCAGGGAGAT-AGA-AT-TACTGGCTTCA
1 ATCTACTCCACTACTACTCAGGGAGATAAGATCTGTAAT--CTTCA
* * * * * ** **
23429 ATGTACTCCACT-GTAACCTCAGAGAGGTAAAATCTGCCATCTTTG
1 ATCTACTCCACTACT-A-CTCAGGGAGATAAGATCTGTAATCTTCA
* * *
23474 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTACTCAGGGAGATAAGATCTGTAATCTTCA
* ** * * * * *
23518 ATCTATTCCAACTGTTGC-CCGGGAGAT-AGA-AT-TACTGGCTCCA
1 ATCTACTCC-ACTACTACTCAGGGAGATAAGATCTGTAAT--CTTCA
* * * * * * ** **
23561 ATATACTCCGCTGCAACCTCAGGGAGGTAAAATCTGCCATCTTTT
1 ATCTACTCCACTACTA-CTCAGGGAGATAAGATCTGTAATCTTCA
* * * *
23606 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
1 ATCTACTCCACTACTACTCAGGGAGATAAGATCTGTAATCTTCA
* ** * * * *
23650 ATCTATTCCACTGTTGCCCAGGGAGATAGGAGTACTG---GCTTCA
1 ATCTACTCCACTACTACTCAGGGAGATAAGA-T-CTGTAATCTTCA
* * * * * ** **
23693 ATGTACTCCACT-GTAACCTCAGAGAGGTAAAATCTGCCATCTTTG
1 ATCTACTCCACTACT-A-CTCAGGGAGATAAGATCTGTAATCTTCA
* * *
23738 ATCTACTCCACTACTGCTTAGAGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTACTCAGGGAGATAAGATCTGTAATCTTCA
* ** * * * *
23782 ATCTATTCCACTGTTGCCCAGGGAGATAGGAGTACTG---GCTTCA
1 ATCTACTCCACTACTACTCAGGGAGATAAGA-T-CTGTAATCTTCA
* * * * **** **
23825 ATGTACTCCACT-GTAACCTCAGGGAGGTAAAATCCACCATCTTTG
1 ATCTACTCCACTACT-A-CTCAGGGAGATAAGATCTGTAATCTTCA
* * * *
23870 ATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCA
1 ATCTACTCCACTACTACTCAGGGAGATAAGATCTGTAATCTTCA
* ** * * * *
23914 ATCTATTCCACTGTTGCCCAGGGAGAT-AGA-AT-TACTAGCTTCA
1 ATCTACTCCACTACTACTCAGGGAGATAAGATCTGTA--ATCTTCA
* * * * **** *
23957 ATGTACTCCACT-GTAACCTCAGGGAGGTAAAATCCACCATCTTCG
1 ATCTACTCCACTACT-A-CTCAGGGAGATAAGATCTGTAATCTTCA
* * * * *
24002 ATCTGCTCAACTACTTCTTAGGGAGATAAGATCTATAATCTTCA
1 ATCTACTCCACTACTACTCAGGGAGATAAGATCTGTAATCTTCA
*
24046 ATCTATTCCACT
1 ATCTACTCCACT
24058 GTTGCCCAGG
Statistics
Matches: 458, Mismatches: 174, Indels: 80
0.64 0.24 0.11
Matches are distributed among these distances:
41 8 0.02
42 14 0.03
43 83 0.18
44 260 0.57
45 80 0.17
46 11 0.02
47 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTACTCCACTACTACTCAGGGAGATAAGATCTGTAATCTTCA
Found at i:23456 original size:132 final size:132
Alignment explanation
Indices: 23271--24182 Score: 1421
Period size: 132 Copynumber: 6.9 Consensus size: 132
23261 CCACTACCGA
* ** * * * *
23271 CCAGGGAAATAGAATTACTGGCACCAATATACTCCGCTGCAACCCCAGGGAGGTAAAATCTACCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCA
* *
23336 TCTTTGATCTACTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
23401 GC
131 GC
* *
23403 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGAGAGGTAAAATCTGCCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCA
23468 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCAACTGT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCC-ACTGT
23533 TGC
130 TGC
* * * * *
23536 CC-GGGAGATAGAATTACTGGCTCCAATATACTCCGCTGCAACCTCAGGGAGGTAAAATCTGCCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCA
* *
23600 TCTTTTATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
23665 GC
131 GC
* * * *
23667 CCAGGGAGATAGGAGTACTGGCTTCAATGTACTCCACTGTAACCTCAGAGAGGTAAAATCTGCCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCA
* *
23732 TCTTTGATCTACTCCACTACTGCTTAGAGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
23797 GC
131 GC
* * *
23799 CCAGGGAGATAGGAGTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCA
*
23864 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCACTGTT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
23929 GC
131 GC
* *
23931 CCAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCA
* * * *
23996 TCTTCGATCTGCTCAACTACTTCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGTT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
24061 GC
131 GC
* * * *
24063 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTATAACTTCAAGGAGGTAAAATCCACCA
1 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCA
* * * * *
24128 TATTTGATCTGCTCCACTACTACTTAGGCAGATAAGATCTGTTATCTTCGATCTA
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTA
24183 CTTCACGCCA
Statistics
Matches: 723, Mismatches: 55, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
131 10 0.01
132 703 0.97
133 10 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCA
TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTT
GC
Found at i:25519 original size:13 final size:13
Alignment explanation
Indices: 25488--25518 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
25478 TGGCCTCTCC
25488 ATTTTTCTTTTTT
1 ATTTTTCTTTTTT
25501 ATTTTTC-TTTTT
1 ATTTTTCTTTTTT
25513 ATTTTT
1 ATTTTT
25519 TTGGACTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTCTTTTTT
Found at i:28332 original size:19 final size:19
Alignment explanation
Indices: 28308--28353 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
28298 AACTGTGTTT
* *
28308 AATGCATATG-ATGTAATG
1 AATGCAAATGCATGAAATG
28326 AAATGCAAATGCATGAAATG
1 -AATGCAAATGCATGAAATG
28346 AATGCAAA
1 AATGCAAA
28354 AAAGAGACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.24
Consensus pattern (19 bp):
AATGCAAATGCATGAAATG
Found at i:29446 original size:21 final size:21
Alignment explanation
Indices: 29422--29462 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
29412 TATTTTAAAG
29422 AAATAATAAAATATTATTATA
1 AAATAATAAAATATTATTATA
29443 AAATAATAAAATATTATTAT
1 AAATAATAAAATATTATTAT
29463 TTTAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATAATAAAATATTATTATA
Found at i:29463 original size:24 final size:24
Alignment explanation
Indices: 29406--29477 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
29396 CTTAGTGTCG
*
29406 AAAAT-TTATT-TTAAAGAAATAAT
1 AAAATATTATTATTATA-AAATAAT
29429 -AAA-A-TATTATTATAAAATAAT
1 AAAATATTATTATTATAAAATAAT
*
29450 AAAATATTATTATTTTAAAGA-AAT
1 AAAATATTATTATTATAAA-ATAAT
29474 AAAA
1 AAAA
29478 CATCACACCT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
21 11 0.27
22 10 0.24
23 1 0.02
24 18 0.44
25 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (24 bp):
AAAATATTATTATTATAAAATAAT
Found at i:32492 original size:13 final size:13
Alignment explanation
Indices: 32474--32514 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
32464 GAATTTTTGC
*
32474 TTTCTTTTCCCTA
1 TTTCTTTTCCATA
*
32487 TTTCTTCTCCAT-
1 TTTCTTTTCCATA
32499 TTTCTTTTCCATA
1 TTTCTTTTCCATA
32512 TTT
1 TTT
32515 ATCTTTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCTTTTCCATA
Found at i:35727 original size:39 final size:37
Alignment explanation
Indices: 35681--35763 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 37
35671 TTAAATTTAA
35681 TATTAAGATAA-TCATTTTAATATTAAATTAATA-AAATAC
1 TATTAAGATAAGT-A-TTTAAT-TTAAATTAATATAAAT-C
*
35720 TATTAAGATAAGTATTTAATTTAATTTAATATTAAATC
1 TATTAAGATAAGTATTTAATTTAAATTAATA-TAAATC
35758 TATTAA
1 TATTAA
35764 AATATTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
37 10 0.25
38 13 0.32
39 16 0.40
40 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (37 bp):
TATTAAGATAAGTATTTAATTTAAATTAATATAAATC
Found at i:41664 original size:91 final size:91
Alignment explanation
Indices: 41509--41714 Score: 290
Period size: 91 Copynumber: 2.3 Consensus size: 91
41499 AGTTTAAGTA
* * * * *
41509 CAAACACTAGTGGTTTATCCATACACTTACTGACAAATTTTATCTGCAAACCCTTTATGCATTCA
1 CAAACACTGGTGGTTTATCCACAAAATTACTGACAAATTTTATCTGCAAACCCGTTATGCATTCA
* *
41574 CAACCTACTGGCAGCGTATTAACTTG
66 CAACCTACTAGCAACGTATTAACTTG
* *
41600 CAAACACTGGTGGTTTATCCACAAAATTACTGA-AAGCTTTTATCTGCAAACCCGTTGTGCATTC
1 CAAACACTGGTGGTTTATCCACAAAATTACTGACAA-ATTTTATCTGCAAACCCGTTATGCATTC
41664 ACAACCTACTAGCAACGTATTAACTTG
65 ACAACCTACTAGCAACGTATTAACTTG
* *
41691 C-GACACTGGTGGTTCATCCACAAA
1 CAAACACTGGTGGTTTATCCACAAA
41715 CTGGAGTGTC
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
90 23 0.22
91 80 0.78
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (91 bp):
CAAACACTGGTGGTTTATCCACAAAATTACTGACAAATTTTATCTGCAAACCCGTTATGCATTCA
CAACCTACTAGCAACGTATTAACTTG
Found at i:42968 original size:34 final size:34
Alignment explanation
Indices: 42925--43154 Score: 460
Period size: 34 Copynumber: 6.8 Consensus size: 34
42915 TTAATAAATA
42925 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
1 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
42959 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
1 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
42993 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
1 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
43027 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
1 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
43061 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
1 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
43095 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
1 TTTTTTAAATTTAAAAAATATTTTTATATTATTT
43129 TTTTTTAAATTTAAAAAATATTTTTA
1 TTTTTTAAATTTAAAAAATATTTTTA
43155 AAAATAAATT
Statistics
Matches: 196, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 196 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (34 bp):
TTTTTTAAATTTAAAAAATATTTTTATATTATTT
Found at i:47287 original size:19 final size:19
Alignment explanation
Indices: 47263--47301 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
47253 AACAAAATAA
*
47263 ATACATTCTATATTTAATT
1 ATACATTCTATAATTAATT
*
47282 ATACATTTTATAATTAATT
1 ATACATTCTATAATTAATT
47301 A
1 A
47302 AAAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (19 bp):
ATACATTCTATAATTAATT
Found at i:50875 original size:21 final size:21
Alignment explanation
Indices: 50834--50876 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
50824 ATTAATCAAC
*
50834 TATTTCTAATGCATCCAAACA
1 TATTTCTAATGCATCAAAACA
*
50855 TATTT-TAATGCATGAATAACA
1 TATTTCTAATGCATCAA-AACA
50876 T
1 T
50877 GAACGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (21 bp):
TATTTCTAATGCATCAAAACA
Found at i:52837 original size:10 final size:10
Alignment explanation
Indices: 52822--52848 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
52812 GACAATTCTA
52822 AAGACTATAT
1 AAGACTATAT
52832 AAGACTATAT
1 AAGACTATAT
52842 AAGACTA
1 AAGACTA
52849 ATGAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (10 bp):
AAGACTATAT
Found at i:57661 original size:27 final size:27
Alignment explanation
Indices: 57611--57662 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
57601 TGTCGTATAA
**
57611 CATATAATGCGATAAAATTTCCAATAT
1 CATATAATGCGATAAAATCGCCAATAT
57638 CATATAATGCGATAAAATCGCCAAT
1 CATATAATGCGATAAAATCGCCAAT
57663 CCCTTCGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (27 bp):
CATATAATGCGATAAAATCGCCAATAT
Found at i:62140 original size:25 final size:22
Alignment explanation
Indices: 62110--62156 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
62100 TTAAGACTGG
* *
62110 TCGTGGTGGCTTCCTCTAATTC
1 TCGTGGTGGTTTCCTCCAATTC
62132 TCGTGGTGGTTTCCTCCAATTC
1 TCGTGGTGGTTTCCTCCAATTC
62154 TCG
1 TCG
62157 CGGTTTCTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.28, G:0.23, T:0.40
Consensus pattern (22 bp):
TCGTGGTGGTTTCCTCCAATTC
Found at i:66872 original size:20 final size:20
Alignment explanation
Indices: 66847--66886 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
66837 CTTGTACAGG
*
66847 GTTTGCACTTTGGTGCCTCT
1 GTTTGCACTTTGATGCCTCT
66867 GTTTGCACTTTGATGCCTCT
1 GTTTGCACTTTGATGCCTCT
66887 ATTCACACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.45
Consensus pattern (20 bp):
GTTTGCACTTTGATGCCTCT
Found at i:66895 original size:20 final size:20
Alignment explanation
Indices: 66852--66896 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
66842 ACAGGGTTTG
* * **
66852 CACTTTGGTGCCTCTGTTTG
1 CACTTTGATGCCTCTATTCA
66872 CACTTTGATGCCTCTATTCA
1 CACTTTGATGCCTCTATTCA
66892 CACTT
1 CACTT
66897 CGGCACCTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.13, C:0.29, G:0.16, T:0.42
Consensus pattern (20 bp):
CACTTTGATGCCTCTATTCA
Found at i:68908 original size:27 final size:27
Alignment explanation
Indices: 68878--68991 Score: 122
Period size: 27 Copynumber: 4.2 Consensus size: 27
68868 TCAAGACAAC
* * * *
68878 AAACACGGTGTAGTCTGCCAAGACAGT
1 AAACACGGGGTAGTCCGTCGAGACAGT
* * *
68905 AAACATGAGGTAGTCCGTCGAGATAGCT
1 AAACACGGGGTAGTCCGTCGAGACAG-T
*
68933 -AACACGGGGTAGTCCATCGAGACAGT
1 AAACACGGGGTAGTCCGTCGAGACAGT
* *
68959 AAACACGGGGTAGTCTGTCGAGACAGA
1 AAACACGGGGTAGTCCGTCGAGACAGT
68986 AAACAC
1 AAACAC
68992 AAGGAAGCTC
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.01
27 69 0.97
28 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (27 bp):
AAACACGGGGTAGTCCGTCGAGACAGT
Found at i:73911 original size:32 final size:32
Alignment explanation
Indices: 73870--73939 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
73860 CAATATTCCA
73870 ACACGTCTGTGTGATTCAGTCATGTGGGGCCC
1 ACACGTCTGTGTGATTCAGTCATGTGGGGCCC
73902 ACACGTCTGTGTGATTCAGTCATGTGGGGCCC
1 ACACGTCTGTGTGATTCAGTCATGTGGGGCCC
73934 ACACGT
1 ACACGT
73940 TCATCTAACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.17, C:0.26, G:0.30, T:0.27
Consensus pattern (32 bp):
ACACGTCTGTGTGATTCAGTCATGTGGGGCCC
Found at i:86344 original size:16 final size:16
Alignment explanation
Indices: 86323--86374 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
86313 TTTGGTTCGC
86323 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
86339 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
86355 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
86371 TGTA
1 TGTA
86375 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:89002 original size:13 final size:13
Alignment explanation
Indices: 88965--89030 Score: 89
Period size: 13 Copynumber: 4.8 Consensus size: 13
88955 TGCCTACTGG
88965 AGAAAGCAAAGGAGAA
1 AGAAAGCAAA-G-G-A
88981 AGCAAAGCAAAGGA
1 AG-AAAGCAAAGGA
88995 AGAAAGCAAAGGA
1 AGAAAGCAAAGGA
89008 AGAAAGCAAAGG-
1 AGAAAGCAAAGGA
89020 AGAAAGCAAAG
1 AGAAAGCAAAG
89031 AAAACAAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.22
13 23 0.47
14 3 0.06
15 1 0.02
16 3 0.06
17 8 0.16
ACGTcount: A:0.61, C:0.09, G:0.30, T:0.00
Consensus pattern (13 bp):
AGAAAGCAAAGGA
Found at i:89097 original size:19 final size:19
Alignment explanation
Indices: 89073--89192 Score: 86
Period size: 19 Copynumber: 6.1 Consensus size: 19
89063 CAAATCGGGC
89073 GAAACAGAAGAGGCAAAGG
1 GAAACAGAAGAGGCAAAGG
*
89092 GAAACAGAAGAGGCAGAGG
1 GAAACAGAAGAGGCAAAGG
* *
89111 AGAAAGCA-AAGAAAAG-AAA-A
1 -GAAA-CAGAAG--AGGCAAAGG
*
89131 GAAACAG-AGGGAGCAAATCGGG
1 GAAACAGAAGAG-GCAAA---GG
89153 CGAAACAGAAGAGGCAAAGG
1 -GAAACAGAAGAGGCAAAGG
*
89173 GAAACAGAAGAGGCAGAGG
1 GAAACAGAAGAGGCAAAGG
89192 G
1 G
89193 TAAAACAGGG
Statistics
Matches: 79, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
17 1 0.01
18 7 0.09
19 41 0.52
20 9 0.11
21 4 0.05
22 2 0.03
23 12 0.15
24 3 0.04
ACGTcount: A:0.52, C:0.11, G:0.37, T:0.01
Consensus pattern (19 bp):
GAAACAGAAGAGGCAAAGG
Found at i:89097 original size:42 final size:42
Alignment explanation
Indices: 89050--89180 Score: 132
Period size: 42 Copynumber: 3.2 Consensus size: 42
89040 GAAAAGAAAA
89050 GAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGG
1 GAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGG
* * * * *
89092 GAAACAGA-AGAGGCAGA---GGAGAAAGCA-AAGAAAAG-AAA-A
1 GAAACAGAGGGA-GCAAATCGGGCGAAA-CAGAAG--AGGCAAAGG
89131 GAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGG
1 GAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGG
89173 GAAACAGA
1 GAAACAGA
89181 AGAGGCAGAG
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
39 21 0.31
40 9 0.13
41 9 0.13
42 29 0.43
ACGTcount: A:0.51, C:0.12, G:0.35, T:0.02
Consensus pattern (42 bp):
GAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGG
Found at i:89124 original size:81 final size:81
Alignment explanation
Indices: 89037--89191 Score: 310
Period size: 81 Copynumber: 1.9 Consensus size: 81
89027 AAAGAAAACA
89037 AAAGAAAAGAAAAGAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGGGAAACAGAAG
1 AAAGAAAAGAAAAGAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGGGAAACAGAAG
89102 AGGCAGAGGAGAAAGC
66 AGGCAGAGGAGAAAGC
89118 AAAGAAAAGAAAAGAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGGGAAACAGAAG
1 AAAGAAAAGAAAAGAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGGGAAACAGAAG
89183 AGGCAGAGG
66 AGGCAGAGG
89192 GTAAAACAGG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 74 1.00
ACGTcount: A:0.53, C:0.11, G:0.35, T:0.01
Consensus pattern (81 bp):
AAAGAAAAGAAAAGAAACAGAGGGAGCAAATCGGGCGAAACAGAAGAGGCAAAGGGAAACAGAAG
AGGCAGAGGAGAAAGC
Found at i:91327 original size:43 final size:43
Alignment explanation
Indices: 91280--91362 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
91270 CCTAATCATT
** * *
91280 ACAATTAGGGACTCAAATCCAATCTGGGCCCAACCTTTTGTGA
1 ACAATTACAGACTCAAATCCAACCGGGGCCCAACCTTTTGTGA
* *
91323 ACAATTACAGACTCGAATCTAACCGGGGCCCAACCTTTTG
1 ACAATTACAGACTCAAATCCAACCGGGGCCCAACCTTTTG
91363 CGAAGAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (43 bp):
ACAATTACAGACTCAAATCCAACCGGGGCCCAACCTTTTGTGA
Found at i:105161 original size:29 final size:29
Alignment explanation
Indices: 105119--105176 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
105109 ACCACAATAG
105119 AATATGTCTCTTCATAATCAATGTCGAGC
1 AATATGTCTCTTCATAATCAATGTCGAGC
105148 AATATGTCTCTTCATAATCAATGTCGAGC
1 AATATGTCTCTTCATAATCAATGTCGAGC
105177 CTTTGCGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (29 bp):
AATATGTCTCTTCATAATCAATGTCGAGC
Found at i:109675 original size:30 final size:32
Alignment explanation
Indices: 109614--109716 Score: 77
Period size: 32 Copynumber: 3.2 Consensus size: 32
109604 ATTTTTTTAA
*
109614 TTAATTTATATATTTATATATTTTTATTTTTT
1 TTAATTTATATATTTATATATTTTTAATTTTT
*
109646 TTAATTT-T-TATTTGTATA-TTTTAGATTTTT
1 TTAATTTATATATTTATATATTTTTA-ATTTTT
* * * * * * *
109676 AAATAATTTTTATCTTTACAAATGTTTAATTTTG
1 --TTAATTTATATATTTATATATTTTTAATTTTT
109710 TTAATTT
1 TTAATTT
109717 TTTGAAATTA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
29 5 0.09
30 14 0.25
31 1 0.02
32 19 0.35
33 1 0.02
34 11 0.20
35 4 0.07
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (32 bp):
TTAATTTATATATTTATATATTTTTAATTTTT
Found at i:109683 original size:32 final size:31
Alignment explanation
Indices: 109607--109688 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
109597 GAAGACAATT
*
109607 TTTTTAATTAATTTATATATTTATATATTTTTA
1 TTTTTAATTAATTT-T-TATTTATATATTTTGA
* *
109640 TTTTT-TTTAATTTTTATTTGTATATTTTAGA
1 TTTTTAATTAATTTTTATTTATATATTTT-GA
*
109671 TTTTTAAATAATTTTTAT
1 TTTTTAATTAATTTTTAT
109689 CTTTACAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 13 0.31
31 7 0.17
32 17 0.40
33 5 0.12
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (31 bp):
TTTTTAATTAATTTTTATTTATATATTTTGA
Found at i:124031 original size:100 final size:100
Alignment explanation
Indices: 123890--124164 Score: 379
Period size: 100 Copynumber: 2.8 Consensus size: 100
123880 ACAGTGGAGC
* * *
123890 AGATTAAAGCCGCAATGGCGAATCTTACTCCCCTGGCGGTGTAGTAGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* * * *
123955 CGATGAATTTCGTTTCCCCAACATTGCAATTAAAA
66 AGACGAATCTCATTTCCCCAACATTGCAATTAAAA
**
123990 AGATTGAAGCCGCAACGATGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* *
124055 AGGCGAATCTCATTTCCCCAACATTGCAATTTAAA
66 AGACGAATCTCATTTCCCCAACATTGCAATTAAAA
* * * * * * *
124090 AGATTGAAGCCGCAACGGCGAATCTTATTTCCCTGGCGTTGTAGCGGAGCAGATTGAAGCCATGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
*
124155 CGACGAATCT
66 AGACGAATCT
124165 TATCTCCCTG
Statistics
Matches: 153, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 153 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (100 bp):
AGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
AGACGAATCTCATTTCCCCAACATTGCAATTAAAA
Found at i:124044 original size:50 final size:50
Alignment explanation
Indices: 123882--124049 Score: 126
Period size: 50 Copynumber: 3.4 Consensus size: 50
123872 TTAGCATTAC
* * * **
123882 AGTGGAGCAGATTAAAGCCGCAATGGCGAATCTTACTCCCCTGGCGGTGT
1 AGTGGAACAGATTGAAGCCGCAACGATGAATCTTACTCCCCTGGCGGTGT
* ** * ** ** *
123932 AGTAGAACAGATTGAAGCTACGACGATGAAT-TT-CGTTTCCCC-AACATTGC
1 AGTGGAACAGATTGAAGCCGCAACGATGAATCTTAC---TCCCCTGGCGGTGT
* ** *
123982 AATTAAAAAGATTGAAGCCGCAACGATGAATCTTACTCCCCTGGCGGTGT
1 AGTGGAACAGATTGAAGCCGCAACGATGAATCTTACTCCCCTGGCGGTGT
124032 AGTGGAACAGATTGAAGC
1 AGTGGAACAGATTGAAGC
124050 TACGAAGGCG
Statistics
Matches: 82, Mismatches: 30, Indels: 12
0.66 0.24 0.10
Matches are distributed among these distances:
48 1 0.01
49 7 0.09
50 66 0.80
51 7 0.09
52 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.23
Consensus pattern (50 bp):
AGTGGAACAGATTGAAGCCGCAACGATGAATCTTACTCCCCTGGCGGTGT
Found at i:128200 original size:26 final size:27
Alignment explanation
Indices: 128122--128201 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
128112 TTAACAATTA
*
128122 ATAAATTATTTGTAAATTTAAT-TATAC
1 ATAAAATATTT-TAAATTTAATATATAC
128149 ATAAAATATTTTAAAATTTTAA-ATATAC
1 ATAAAATATTTT-AAA-TTTAATATATAC
* *
128177 ATTAAATA-TTTAAATCTAATATATA
1 ATAAAATATTTTAAATTTAATATATA
128202 TTCTATAGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 4 0.09
26 9 0.20
27 16 0.35
28 17 0.37
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (27 bp):
ATAAAATATTTTAAATTTAATATATAC
Found at i:129786 original size:3 final size:3
Alignment explanation
Indices: 129768--129819 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
129758 NNNNNNNNNT
* *
129768 ATA ATA ATG ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
129816 ATA A
1 ATA A
129820 CCAAAATGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:136424 original size:43 final size:44
Alignment explanation
Indices: 136362--137221 Score: 412
Period size: 44 Copynumber: 19.7 Consensus size: 44
136352 TGGTGCGATT
* * * * * *
136362 TGCTCCACTATAACTTCAGGGAGATAGGAT-AGTGTCTTCGATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
* * *
136405 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
* * **
136449 TGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTCGGTC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATC---ACTGGCTTCAATC
* * * * *
136495 TACTCCATTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
* ** * * *** *
136536 TACTCTGCTGTAACTTCAGAGAGATAAGA-C-CTTTATTTTAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCAC-TGGCTTCAATC
* * * * * *
136579 CGCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
* * * *
136623 TACTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
* * * **
136667 TGCTCTACTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTCGGTC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATC---ACTGGCTTCAATC
* * * * *
136713 TACTCCATTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
* ** * * *** *
136754 TACTCTGCTGTAACTTCAGAGAGATAAGA-C-CTTTATTTTAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCAC-TGGCTTCAATC
* * * * *** *
136797 CGCTCCACTGTAACTTCAGAGAGATAAGACTC-TTTAATTTAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGA-TCACTGGCTTCAATC
** * * * * *
136841 CACTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
* * *
136884 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
* * * **
136928 TGCTCTACTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTCGGTC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATC---ACTGGCTTCAATC
* * * * *
136974 TACTCCATTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
* ** * * * *** *
137015 TACTCTGCTGTAACTTCAGAGAGATAAGACTC-TTTAATTTAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGA-TCACTGGCTTCAATC
** * * * *
137059 CACTCCACTGTAACTTCAGGGAGATAGGATTACTAGCTTCAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
* * * * *
137103 TACTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAACC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
* * * * **
137147 TGCTCCACTGTAACTTCAGAGAGATAAGATCTGAAAT-TCTTCGGTC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATC---ACTGGCTTCAATC
* *
137193 TACTCCATTGTAACCTCAGGGAGATAAGA
1 TGCTCCACTGTAACCTCAGGGAGATAAGA
137222 CCTGATGCGA
Statistics
Matches: 624, Mismatches: 166, Indels: 51
0.74 0.20 0.06
Matches are distributed among these distances:
41 94 0.15
42 2 0.00
43 116 0.19
44 276 0.44
45 5 0.01
46 127 0.20
47 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
TGCTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATC
Found at i:136740 original size:218 final size:218
Alignment explanation
Indices: 136363--136915 Score: 857
Period size: 218 Copynumber: 2.5 Consensus size: 218
136353 GGTGCGATTT
* * * * *
136363 GCTCCACTATAACTTCAGGGAGATAGGA-TAGT-GTCTTCGATCTGCTCCGCTGTAATCTCAGGG
1 GCTCCACTGTAACTTCAGAGAGATAGGATTACTAG-CTTCAATCTACTCCGCTGTAATCTCAGGG
136426 AGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTC
65 AGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTC
136491 GGTCTACTCCATTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGA
130 GGTCTACTCCATTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGA
136556 GAGATAAGACCTTTATTTTAATCC
195 GAGATAAGACCTTTATTTTAATCC
136580 GCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGA
1 GCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGA
*
136645 GATAAGATCTCTGGCTTCAATCTGCTCTACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
66 GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
136710 GTCTACTCCATTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
131 GTCTACTCCATTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
136775 AGATAAGACCTTTATTTTAATCC
196 AGATAAGACCTTTATTTTAATCC
* * * * * *
136798 GCTCCACTGTAACTTCAGAGAGATAAGACTCT-TTA-ATTTAATCCACTCCACTGTAA-CTTCAG
1 GCTCCACTGTAACTTCAGAGAGATAGGA-T-TACTAGCTTCAATCTACTCCGCTGTAATC-TCAG
* ** * * * *
136860 GGAGATAGGAT-AGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
63 GGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT
136916 CTGGCTTCAA
Statistics
Matches: 311, Mismatches: 20, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
217 65 0.21
218 241 0.77
219 4 0.01
220 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (218 bp):
GCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGA
GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
GTCTACTCCATTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
AGATAAGACCTTTATTTTAATCC
Found at i:136923 original size:261 final size:262
Alignment explanation
Indices: 136543--137084 Score: 964
Period size: 261 Copynumber: 2.1 Consensus size: 262
136533 ATCTACTCTG
* *
136543 CTGTAACTTCAGAGAGATAAGACCTTTATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGA
1 CTGTAACTTCAGAGAGATAAGACCTTTAATTTAATCCACTCCACTGTAACTTCAGAGAGATAGGA
136608 TTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCT
66 TTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCT
136673 ACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCATTGTAACCTCAGGGAGAT
131 ACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCATTGTAACCTCAGGGAGAT
* *
136738 AAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGAC-CTTTATTTTAATCCGCTC
196 AAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGACTCTTTAATTTAATCCACTC
136802 CA
261 CA
*
136804 CTGTAACTTCAGAGAGATAAGACTCTTTAATTTAATCCACTCCACTGTAACTTCAGGGAGATAGG
1 CTGTAACTTCAGAGAGATAAGAC-CTTTAATTTAATCCACTCCACTGTAACTTCAGAGAGATAGG
* * *
136869 A-TAGT-GTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCT
65 ATTACTAG-CTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCT
136932 CTACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCATTGTAACCTCAGGGAG
129 CTACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCATTGTAACCTCAGGGAG
136997 ATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGACTCTTTAATTTAATCCAC
194 ATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGACTCTTTAATTTAATCCAC
137062 TCCA
259 TCCA
*
137066 CTGTAACTTCAGGGAGATA
1 CTGTAACTTCAGAGAGATA
137085 GGATTACTAG
Statistics
Matches: 269, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
260 1 0.00
261 193 0.72
262 75 0.28
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (262 bp):
CTGTAACTTCAGAGAGATAAGACCTTTAATTTAATCCACTCCACTGTAACTTCAGAGAGATAGGA
TTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCT
ACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCATTGTAACCTCAGGGAGAT
AAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGACTCTTTAATTTAATCCACTC
CA
Found at i:137185 original size:219 final size:218
Alignment explanation
Indices: 136804--137306 Score: 900
Period size: 219 Copynumber: 2.3 Consensus size: 218
136794 ATCCGCTCCA
136804 CTGTAACTTCAGAGAGATAAGACTCTTTAATTTAATCCACTCCACTGTAACTTCAGGGAGATAGG
1 CTGTAACTTCAGAGAGATAAGACTCTTTAATTTAATCCACTCCACTGTAACTTCAGGGAGATAGG
* * * * *
136869 ATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCT
66 ATACTGTCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAACCTGCTCC
*
136934 ACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCATTGTAACCTCAGGGAGAT
131 ACTGTAACCTCAGAGAGATAAGATCTGAAATTCTTCGGTCTACTCCATTGTAACCTCAGGGAGAT
136999 AAGACCTGATGCGATCTACTCTG
196 AAGACCTGATGCGATCTACTCTG
137022 CTGTAACTTCAGAGAGATAAGACTCTTTAATTTAATCCACTCCACTGTAACTTCAGGGAGATAGG
1 CTGTAACTTCAGAGAGATAAGACTCTTTAATTTAATCCACTCCACTGTAACTTCAGGGAGATAGG
137087 ATTACTAG-CTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAACCTGCT
66 A-TACT-GTCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAACCTGCT
*
137151 CCACTGTAACTTCAGAGAGATAAGATCTGAAATTCTTCGGTCTACTCCATTGTAACCTCAGGGAG
129 CCACTGTAACCTCAGAGAGATAAGATCTGAAATTCTTCGGTCTACTCCATTGTAACCTCAGGGAG
137216 ATAAGACCTGATGCGATCTACTCTG
194 ATAAGACCTGATGCGATCTACTCTG
* *
137241 CTGTAACTTCAGAGAGATAAGACCCTTTAATTTAATCCGCTCCACTGTAACTTCAGGGAGATAGG
1 CTGTAACTTCAGAGAGATAAGACTCTTTAATTTAATCCACTCCACTGTAACTTCAGGGAGATAGG
137306 A
66 A
137307 CTTGTAACTT
Statistics
Matches: 274, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
218 66 0.24
219 207 0.76
220 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (218 bp):
CTGTAACTTCAGAGAGATAAGACTCTTTAATTTAATCCACTCCACTGTAACTTCAGGGAGATAGG
ATACTGTCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAACCTGCTCC
ACTGTAACCTCAGAGAGATAAGATCTGAAATTCTTCGGTCTACTCCATTGTAACCTCAGGGAGAT
AAGACCTGATGCGATCTACTCTG
Found at i:137478 original size:25 final size:25
Alignment explanation
Indices: 137434--137483 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
137424 CTTGGGAAGT
* *
137434 AAGATTCGCCGTTGTAGCTTTAATC
1 AAGATTCACCGATGTAGCTTTAATC
*
137459 AAGATTCACCGATGTGGCTTTAATC
1 AAGATTCACCGATGTAGCTTTAATC
137484 TTTTCAACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (25 bp):
AAGATTCACCGATGTAGCTTTAATC
Found at i:137493 original size:125 final size:126
Alignment explanation
Indices: 137345--137583 Score: 327
Period size: 125 Copynumber: 1.9 Consensus size: 126
137335 GATTCGCCAT
* * * *
137345 TGTGGCTTTTAATCTTTTTAACTGCAATGTCGGAGAAACAAGATTCACCAATTTGGCTTTAATCT
1 TGTGGCTTTTAATCTTTTCAACTGCAATGTAGGAGAAACAAGATGCACCAATGTGGCTTTAATCT
* * * *
137410 ATTCCACTGCATCGCTTGGGAAGTAAGATTCGCCGTTGTAGCTTTAATCAAGATTCACCGA
66 ATTCCACTGCACCACCTGGGAAGTAAGATTCGCCGCTGTAGCTTTAATCAAGATTCACCGA
* * * * *
137471 TGTGGC-TTTAATCTTTTCAACTGCAATGTAGGGGAAGCAAGATGCATCGATGTGGTTTTAATCT
1 TGTGGCTTTTAATCTTTTCAACTGCAATGTAGGAGAAACAAGATGCACCAATGTGGCTTTAATCT
* * *
137535 GTTCCACTGCACCACCTGGGAGGTAAGATTCGCTGCTGTAGCTTTAATC
66 ATTCCACTGCACCACCTGGGAAGTAAGATTCGCCGCTGTAGCTTTAATC
137584 TTTTTAATCG
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
125 91 0.94
126 6 0.06
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (126 bp):
TGTGGCTTTTAATCTTTTCAACTGCAATGTAGGAGAAACAAGATGCACCAATGTGGCTTTAATCT
ATTCCACTGCACCACCTGGGAAGTAAGATTCGCCGCTGTAGCTTTAATCAAGATTCACCGA
Found at i:137615 original size:50 final size:50
Alignment explanation
Indices: 137554--137812 Score: 215
Period size: 50 Copynumber: 5.2 Consensus size: 50
137544 CACCACCTGG
* *
137554 GAGGTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATCGCAATGTCAGT
1 GAGGCAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATCGCAATGTCAGA
* * * * * * *
137604 GAGGCAAGATTCACCTTC-GTGGCTTTAATCTTTTTACT-GCACA-GCCTGG
1 GAGGCAAGATTC-GCTGCTGTAGCTTTAATCTTTTTAATCGCA-ATGTCAGA
** * *
137653 GAGATAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACCGCGATGTCAGA
1 GAGGCAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATCGCAATGTCAGA
* * * * * * * * * *
137703 GAGGCAAGATTCACCGTTGTGGCTTTAATC-TATTACT-GCACTGCCTGG
1 GAGGCAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATCGCAATGTCAGA
** *
137751 GAGATAAGATTCGCTG-TAGTAGCTTTAATCTTTTTAACCGCAATGTCAGA
1 GAGGCAAGATTCGCTGCT-GTAGCTTTAATCTTTTTAATCGCAATGTCAGA
137801 GAGGCAAGATTC
1 GAGGCAAGATTC
137813 ATGGTTTTAG
Statistics
Matches: 154, Mismatches: 47, Indels: 16
0.71 0.22 0.07
Matches are distributed among these distances:
47 1 0.01
48 32 0.21
49 42 0.27
50 76 0.49
51 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (50 bp):
GAGGCAAGATTCGCTGCTGTAGCTTTAATCTTTTTAATCGCAATGTCAGA
Found at i:137676 original size:99 final size:99
Alignment explanation
Indices: 137475--137813 Score: 454
Period size: 99 Copynumber: 3.4 Consensus size: 99
137465 CACCGATGTG
* * * * * * * * *
137475 GCTTTAATCTTTTCAACTGCAATGT-AGGGGAAGCAAGATGCATCGATGTGGTTTTAATCTGTTC
1 GCTTTAATCTTTTTAACCGCAATGTCA-GAGAGGCAAGATTCACCGTTGTGGCTTTAATCT-TTT
* *
137539 CACTGCACCA-CCTGGGAGGTAAGATTCGCTGCTGTA
64 TACTGCA-CAGCCTGGGAGATAAGATTCGCTGCTGTA
* *
137575 GCTTTAATCTTTTTAATCGCAATGTCAGTGAGGCAAGATTCACC-TTCGTGGCTTTAATCTTTTT
1 GCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTT-GTGGCTTTAATCTTTTT
137639 ACTGCACAGCCTGGGAGATAAGATTCGCTGCTGTA
65 ACTGCACAGCCTGGGAGATAAGATTCGCTGCTGTA
* *
137674 GCTTTAATCTTTTTAACCGCGATGTCAGAGAGGCAAGATTCACCGTTGTGGCTTTAATC-TATTA
1 GCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTTGTGGCTTTAATCTTTTTA
*
137738 CTGCACTGCCTGGGAGATAAGATTCGCTG-TAGTA
66 CTGCACAGCCTGGGAGATAAGATTCGCTGCT-GTA
137772 GCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCA
1 GCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCA
137814 TGGTTTTAGT
Statistics
Matches: 216, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
97 1 0.00
98 78 0.36
99 87 0.40
100 49 0.23
101 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (99 bp):
GCTTTAATCTTTTTAACCGCAATGTCAGAGAGGCAAGATTCACCGTTGTGGCTTTAATCTTTTTA
CTGCACAGCCTGGGAGATAAGATTCGCTGCTGTA
Found at i:138152 original size:87 final size:87
Alignment explanation
Indices: 138021--138564 Score: 887
Period size: 87 Copynumber: 6.3 Consensus size: 87
138011 TACCGCTTAG
* * * *
138021 GGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTACTATCTT
1 GGAGGCAAGGCTT-TGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTT
138086 TAACCAGCTCCACTGCAACCGAT
65 TAACCAGCTCCACTGCAACCGAT
* * * * *
138109 GGAGGCAAGGCTTTATTTTTGATCTGCTTCGCTATTAACGCAGGAAGGCAAGATTTGCTATCTTC
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
* *
138174 AACCAGCTCCAGTACAACCGAT
66 AACCAGCTCCACTGCAACCGAT
* * *
138196 GGAGGCAATGCTTTATTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
138261 AACCAGCTCCACTGCAACCGAT
66 AACCAGCTCCACTGCAACCGAT
138283 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
*
138347 AACCAGCTCCACTGCAACCTA-
66 AACCAGCTCCACTGCAACCGAT
* *
138368 GAGAGGCAAGGCTTTGTTTTCGATTTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTT
1 G-GAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTT
138433 TAACCAGCTCCACTGCAACCGAT
65 TAACCAGCTCCACTGCAACCGAT
138456 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
*
138520 AACCAGCTCCACTGCAACCTAT
66 AACCAGCTCCACTGCAACCGAT
138542 GGAGGCAAGGCTTTGTTTTCGAT
1 GGAGGCAAGGCTTTGTTTTCGAT
138565 TTTCACTGAT
Statistics
Matches: 424, Mismatches: 29, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
85 1 0.00
86 130 0.31
87 279 0.66
88 14 0.03
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (87 bp):
GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTT
AACCAGCTCCACTGCAACCGAT
Found at i:138501 original size:260 final size:260
Alignment explanation
Indices: 138021--138564 Score: 885
Period size: 260 Copynumber: 2.1 Consensus size: 260
138011 TACCGCTTAG
* *
138021 GGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTACTATCTT
1 GGAGGCAAGGCTT-TGTTTTCGATCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTACTATCTT
*
138086 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATTTTTGATCTGCTTCGCTATTAACGCA
65 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATTTTCGATCTGCTTCGCTATTAACGCA
* * *
138151 GGAAGGCAAGATTTGCTATCTTCAACCAGCTCCAGTACAACCGATGGAGGCAATGCTTTATTTTC
130 GGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTATTTTC
*
138216 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
195 GATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCG
138281 AT
259 AT
* *
138283 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTACTATCTTT
* * * * *
138347 AACCAGCTCCACTGCAACCTA-GAGAGGCAAGGCTTTGTTTTCGATTTGCTTCGCTGTTAATGCA
66 AACCAGCTCCACTGCAACCGATG-GAGGCAAGGCTTTATTTTCGATCTGCTTCGCTATTAACGCA
* * *
138411 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTC
130 GGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTATTTTC
*
138476 GATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTA
195 GATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGA
138541 T
260 T
138542 GGAGGCAAGGCTTTGTTTTCGAT
1 GGAGGCAAGGCTTTGTTTTCGAT
138565 TTTCACTGAT
Statistics
Matches: 263, Mismatches: 18, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
259 50 0.19
260 158 0.60
261 42 0.16
262 13 0.05
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (260 bp):
GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTACTATCTTT
AACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATTTTCGATCTGCTTCGCTATTAACGCAG
GAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTATTTTCG
ATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGAT
Found at i:138566 original size:173 final size:173
Alignment explanation
Indices: 138021--138564 Score: 928
Period size: 173 Copynumber: 3.1 Consensus size: 173
138011 TACCGCTTAG
* * *
138021 GGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTACTATCTT
1 GGAGGCAAGGCTT-TGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTT
* * *
138086 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTATTTTTGATCTGCTTCGCTATTAACGCA
65 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCA
* * * * *
138151 GGAAGGCAAGATTTGCTATCTTCAACCAGCTCCAGTACAACCGAT
130 GGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCTAT
* *
138196 GGAGGCAATGCTTTATTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTT
1 GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTT
138261 AACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
66 AACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
138326 GAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTA-
131 GAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTAT
*
138368 GAGAGGCAAGGCTTTGTTTTCGATTTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTT
1 G-GAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTT
138433 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCA
65 TAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCA
138498 GGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTAT
130 GGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTAT
138542 GGAGGCAAGGCTTTGTTTTCGAT
1 GGAGGCAAGGCTTTGTTTTCGAT
138565 TTTCACTGAT
Statistics
Matches: 351, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
172 1 0.00
173 212 0.60
174 126 0.36
175 12 0.03
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (173 bp):
GGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTT
AACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
GAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCTAT
Found at i:150040 original size:3 final size:3
Alignment explanation
Indices: 150022--150073 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
150012 NNNNNNNNNT
* *
150022 ATA ATA ATG ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
150070 ATA A
1 ATA A
150074 CCAAAATGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:150790 original size:6 final size:7
Alignment explanation
Indices: 150775--150799 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
150765 GAATAAACAG
150775 AAAATAA
1 AAAATAA
150782 AAAATAA
1 AAAATAA
150789 AAAATAA
1 AAAATAA
150796 AAAA
1 AAAA
150800 AGGAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:152051 original size:20 final size:21
Alignment explanation
Indices: 152022--152065 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
152012 ATATATTATG
152022 AAAATAATATACT-TATTTTAA
1 AAAATAATATA-TATATTTTAA
*
152043 AAAAT-ATATATATTTTTTAA
1 AAAATAATATATATATTTTAA
152063 AAA
1 AAA
152066 TCTTAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 15 0.71
21 5 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATAATATATATATTTTAA
Found at i:152056 original size:18 final size:19
Alignment explanation
Indices: 152011--152058 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
152001 GTGTCCATGC
*
152011 TATATATTATGAAAATAATA
1 TATATATT-TTAAAATAATA
152031 TACT-TATTTTAAAA-AATA
1 TA-TATATTTTAAAATAATA
152049 TATATATTTT
1 TATATATTTT
152059 TTAAAAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 1 0.04
18 12 0.48
19 5 0.20
20 6 0.24
21 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TATATATTTTAAAATAATA
Found at i:162175 original size:18 final size:20
Alignment explanation
Indices: 162152--162191 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
162142 ATTGGCCTAT
162152 TACAGTAAC-AATAAT-CAG
1 TACAGTAACAAATAATACAG
162170 TACAGTAACAAATAATACAG
1 TACAGTAACAAATAATACAG
162190 TA
1 TA
162192 TACAGGTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
19 6 0.30
20 5 0.25
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.23
Consensus pattern (20 bp):
TACAGTAACAAATAATACAG
Found at i:166666 original size:28 final size:27
Alignment explanation
Indices: 166610--166675 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
166600 CTATTCAGTA
*
166610 ACAGT-ACAGTGTGGCATTAGCCCAAT
1 ACAGTAACAGTGTAGCATTAGCCCAAT
* * *
166636 ACAGTAACAGTGTAAGCCTTAGTCCATT
1 ACAGTAACAGTGT-AGCATTAGCCCAAT
*
166664 ACAGTATCAGTG
1 ACAGTAACAGTG
166676 CAGTGTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 5 0.15
27 7 0.21
28 21 0.64
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (27 bp):
ACAGTAACAGTGTAGCATTAGCCCAAT
Found at i:166804 original size:26 final size:26
Alignment explanation
Indices: 166774--166850 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 26
166764 GCCAACACAC
166774 CAATATCATAGCAAAGCTGCCAGTAAT
1 CAATATCA-AGCAAAGCTGCCAGTAAT
166801 -AATAATGCAA-CAAAGCTGCCAGT-AT
1 CAAT-AT-CAAGCAAAGCTGCCAGTAAT
* *
166826 CAGTATCGCAGCAAAGCTGCCAGTA
1 CAATATC-AAGCAAAGCTGCCAGTA
166851 CAGTATACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
24 1 0.02
25 5 0.12
26 31 0.74
27 3 0.07
28 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (26 bp):
CAATATCAAGCAAAGCTGCCAGTAAT
Found at i:172561 original size:26 final size:27
Alignment explanation
Indices: 172532--172597 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
172522 AATATTGGAA
* *
172532 CAAAGCTACCAGTAAT-AGCACCGTAG
1 CAAAGCTGCCAGTAATCAGCACCGCAG
* * *
172558 CAAAGTTGCCAGT-ATCAGTATCGCAG
1 CAAAGCTGCCAGTAATCAGCACCGCAG
172584 CAAAGCTGCCAGTA
1 CAAAGCTGCCAGTA
172598 CAGTATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (27 bp):
CAAAGCTGCCAGTAATCAGCACCGCAG
Found at i:175166 original size:41 final size:41
Alignment explanation
Indices: 175031--175195 Score: 222
Period size: 42 Copynumber: 4.0 Consensus size: 41
175021 GAACATGGTC
175031 TTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTCTT
1 TTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTT-TT
* * * * *
175073 CTAAGCACTGCTAAAGAACATGGTCTTTAGTGGCCTTTTTT
1 TTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT
** *
175114 TCTAAGCGCCGCTAAAGAACATTATCTTTAGCAGCGTTTTTT
1 T-TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT
* *
175156 TTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTT
1 TTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
175196 ATACAAAAAC
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
41 37 0.35
42 68 0.65
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (41 bp):
TTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT
Found at i:180923 original size:9 final size:9
Alignment explanation
Indices: 180906--181153 Score: 139
Period size: 9 Copynumber: 27.8 Consensus size: 9
180896 TATGTATTAA
*
180906 GTAAATTAT
1 GTAAGTTAT
180915 GTAAGTTAT
1 GTAAGTTAT
180924 GTACA-TGTA-
1 GTA-AGT-TAT
180933 -TAAGTTAT
1 GTAAGTTAT
180941 GTAAGTTAT
1 GTAAGTTAT
*
180950 GT-A-TTAA
1 GTAAGTTAT
*
180957 GTAAGCTAT
1 GTAAGTTAT
* *
180966 TTAAGTTGT
1 GTAAGTTAT
180975 GT-A-TTAT
1 GTAAGTTAT
180982 GTAAGTTAT
1 GTAAGTTAT
180991 GTAAGTTAT
1 GTAAGTTAT
** *
181000 CAAAGTAAT
1 GTAAGTTAT
*
181009 GTATGTTAT
1 GTAAGTTAT
181018 GTAAG-T-T
1 GTAAGTTAT
181025 GTAAGTTAT
1 GTAAGTTAT
*
181034 -TATGTATTAT
1 GTAAG--TTAT
181044 GTAAGTTAT
1 GTAAGTTAT
181053 GTAAGTTAAAT
1 GTAAGTT--AT
181064 GTATTA-TGTAT
1 GTA--AGT-TAT
181075 GTAAGTTAT
1 GTAAGTTAT
* *
181084 GTATGCTAT
1 GTAAGTTAT
*
181093 GTAAGTAAT
1 GTAAGTTAT
181102 GT-A-TTAT
1 GTAAGTTAT
181109 GTAAGTTTAT
1 GTAAG-TTAT
*
181119 ATAAGTTAATAT
1 GTAAG-T--TAT
*
181131 GTAAGTAAT
1 GTAAGTTAT
181140 GT-A-TTAT
1 GTAAGTTAT
181147 GTAAGTT
1 GTAAGTT
181154 TATATAAAAA
Statistics
Matches: 183, Mismatches: 29, Indels: 54
0.69 0.11 0.20
Matches are distributed among these distances:
7 29 0.16
8 16 0.09
9 96 0.52
10 18 0.10
11 14 0.08
12 8 0.04
13 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:180926 original size:25 final size:25
Alignment explanation
Indices: 180895--180999 Score: 113
Period size: 25 Copynumber: 4.2 Consensus size: 25
180885 TGATATATAT
180895 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* *
180920 TTATGTA-CATGTATAAGTTATGTAAG
1 TTATGTATTAAGTA-AA-TTATGTAAG
** *
180946 TTATGTATTAAGTAAGCTATTTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* * *
180971 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
180996 TTAT
1 TTAT
181000 CAAAGTAATG
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
24 4 0.06
25 40 0.62
26 17 0.26
27 4 0.06
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (25 bp):
TTATGTATTAAGTAAATTATGTAAG
Found at i:180995 original size:34 final size:34
Alignment explanation
Indices: 180910--181153 Score: 137
Period size: 34 Copynumber: 7.4 Consensus size: 34
180900 TATTAAGTAA
180910 ATTATGTAAGTTATGT-A-C-ATGTATAAGTTATGT
1 ATTATGTAAGTTATGTAAGCTAT-T-TAAGTTATGT
* *
180943 AAGTTATGT-A-TTAAGTAAGCTATTTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAGCTATTTAAGTTATGT
* ** *
180977 ATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
1 ATTATGTAAGTTATGTAAGCTATTTAAGTTATGT
181011 ATGTTATGTAAG-T-TGTAAG----TT-A-TTATGT
1 A--TTATGTAAGTTATGTAAGCTATTTAAGTTATGT
*
181039 ATTATGTAAGTTATGTAAG----TTAAATGTAT-T
1 ATTATGTAAGTTATGTAAGCTATTTAAGT-TATGT
* * *
181069 ATGTATGTAAGTTATGTATGCTATGTAAGTAATGT
1 AT-TATGTAAGTTATGTAAGCTATTTAAGTTATGT
* * *
181104 ATTATGTAAGTTTATATAAGTTAATATGTAAGTAATGT
1 ATTATGTAAG-TTATGTAAGCT-AT-T-TAAGTTATGT
181142 ATTATGTAAGTT
1 ATTATGTAAGTT
181154 TATATAAAAA
Statistics
Matches: 168, Mismatches: 19, Indels: 43
0.73 0.08 0.19
Matches are distributed among these distances:
26 9 0.05
27 1 0.01
28 14 0.08
29 2 0.01
30 4 0.02
31 19 0.11
32 6 0.04
33 7 0.04
34 47 0.28
35 24 0.14
36 13 0.08
37 2 0.01
38 20 0.12
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (34 bp):
ATTATGTAAGTTATGTAAGCTATTTAAGTTATGT
Found at i:181023 original size:18 final size:18
Alignment explanation
Indices: 180933--181152 Score: 113
Period size: 16 Copynumber: 12.3 Consensus size: 18
180923 TGTACATGTA
*
180933 TAAGTTATGTAAGTTATG
1 TAAGTAATGTAAGTTATG
* * *
180951 T-ATTAA-GTAAGCTATT
1 TAAGTAATGTAAGTTATG
**
180967 TAAGTTGTGT-A-TTATG
1 TAAGTAATGTAAGTTATG
* *
180983 TAAGTTATGTAAGTTATC
1 TAAGTAATGTAAGTTATG
* *
181001 AAAGTAATGTATGTTATG
1 TAAGTAATGTAAGTTATG
181019 TAAGT--TGTAAGTTAT-
1 TAAGTAATGTAAGTTATG
*
181034 TATGTATTATGTAAGTTATG
1 TAAGTA--ATGTAAGTTATG
181054 TAAGTTAAATGTATTA-TGTATG
1 TAAG-T-AATGTA--AGT-TATG
* * *
181076 TAAGTTATGTATGCTATG
1 TAAGTAATGTAAGTTATG
181094 TAAGTAATGT-A-TTATG
1 TAAGTAATGTAAGTTATG
* *
181110 TAAGTTTATATAAGTTAATATG
1 TAAG-TAATGTAAG-T--TATG
181132 TAAGTAATGT-A-TTATG
1 TAAGTAATGTAAGTTATG
181148 TAAGT
1 TAAGT
181153 TTATATAAAA
Statistics
Matches: 152, Mismatches: 29, Indels: 44
0.68 0.13 0.20
Matches are distributed among these distances:
15 4 0.03
16 47 0.31
17 11 0.07
18 40 0.26
19 10 0.07
20 15 0.10
21 7 0.05
22 18 0.12
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.45
Consensus pattern (18 bp):
TAAGTAATGTAAGTTATG
Found at i:181038 original size:19 final size:19
Alignment explanation
Indices: 181014--181052 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
181004 GTAATGTATG
181014 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
181033 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
181052 T
1 T
181053 GTAAGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:181073 original size:62 final size:61
Alignment explanation
Indices: 180957--181151 Score: 177
Period size: 62 Copynumber: 3.1 Consensus size: 61
180947 TATGTATTAA
* ** *
180957 GTAAGCTATTTAAGTTGTGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTA-T-GTTAT
1 GTAAGCTATGTAAGTAATGTATTATGTAAGTTATGTAAGTTA--AATGTAATGTAGTAGTTAT
181018 GTAAG-T-TGTAAGTTATTATGTATTATGTAAGTTATGTAAGTTAAATGTATTATGTATGTAAGT
1 GTAAGCTATGTAAG-TA--ATGTATTATGTAAGTTATGTAAGTTAAATGTA--ATGTA-GT-AGT
181081 TAT
59 TAT
* *
181084 GTATGCTATGTAAGTAATGTATTATGTAAGTTTATATAAGTTAATATGTAA-GTAATGTA-TTAT
1 GTAAGCTATGTAAGTAATGTATTATGTAAG-TTATGTAAGTTAA-ATGTAATGT-A-GTAGTTAT
181147 GTAAG
1 GTAAG
181152 TTTATATAAA
Statistics
Matches: 113, Mismatches: 7, Indels: 26
0.77 0.05 0.18
Matches are distributed among these distances:
59 5 0.04
60 7 0.06
61 5 0.04
62 30 0.27
63 8 0.07
64 4 0.04
65 19 0.17
66 21 0.19
67 8 0.07
68 6 0.05
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (61 bp):
GTAAGCTATGTAAGTAATGTATTATGTAAGTTATGTAAGTTAAATGTAATGTAGTAGTTAT
Found at i:183949 original size:44 final size:44
Alignment explanation
Indices: 183891--183978 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
183881 TTAAAACATT
*
183891 TTTGCGGCGTTTTAAGCAAAGCGCCACAAACTATAAGTCAAAAC
1 TTTGCGGCGTTTTAAACAAAGCGCCACAAACTATAAGTCAAAAC
* *
183935 TTTGCGGCGTTTTAAACTAAGCGCCACTAACTATAAGTCAAAAC
1 TTTGCGGCGTTTTAAACAAAGCGCCACAAACTATAAGTCAAAAC
183979 GCAGTCGCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (44 bp):
TTTGCGGCGTTTTAAACAAAGCGCCACAAACTATAAGTCAAAAC
Found at i:184228 original size:147 final size:147
Alignment explanation
Indices: 183953--184258 Score: 328
Period size: 147 Copynumber: 2.1 Consensus size: 147
183943 GTTTTAAACT
* * *
183953 AAGCGCCACTAACTATAAGTCAAAACGCAGTCGCTTCATCAACACTTACCTCAAACCCGTGGCAT
1 AAGCGCCACTAACTATAAGTCAAAACGAAGCCGCTTCACCAACACTTACCTCAAACCCGTGGCAT
* ** * * ** *
184018 TTGCGAGAAAACGCCACTAATAACATTTACAAAACGGCAACGTTTCAACAAATGTTAGAACAATT
66 TTCCGAGAAAACGCCACTAATAACATAGACAAAACGACAACATTTCAACAAACATAAGAACAATT
* * *
184083 TTGTGGCGTTTCAAGTA
131 TTGCGGAGTTTCAAGGA
* * * **** *
184100 AAGCGCCACTAACTATAAGTCAAAACGAAGCCGTTTCCCCAACAGTTTACC-CAATGTTGTGGCG
1 AAGCGCCACTAACTATAAGTCAAAACGAAGCCGCTTCACCAACA-CTTACCTCAAACCCGTGGCA
* * **
184164 TTTCCGA-AAAACGCCACTAATACCATAGACAAAAACGACAACATTTCAATAAACATAATTACAA
65 TTTCCGAGAAAACGCCACTAATAACATAGAC-AAAACGACAACATTTCAACAAACATAAGAACAA
*
184228 TTTTGCGGAGTTTCATGGA
129 TTTTGCGGAGTTTCAAGGA
*
184247 ACGCGCCACTAA
1 AAGCGCCACTAA
184259 TAGCAACATA
Statistics
Matches: 129, Mismatches: 28, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
146 20 0.16
147 104 0.81
148 5 0.04
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (147 bp):
AAGCGCCACTAACTATAAGTCAAAACGAAGCCGCTTCACCAACACTTACCTCAAACCCGTGGCAT
TTCCGAGAAAACGCCACTAATAACATAGACAAAACGACAACATTTCAACAAACATAAGAACAATT
TTGCGGAGTTTCAAGGA
Found at i:184733 original size:14 final size:14
Alignment explanation
Indices: 184710--184748 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
184700 TCTAAACCTT
*
184710 AAACCTCAAAAACC
1 AAACCCCAAAAACC
**
184724 AAACCCCAAACCCC
1 AAACCCCAAAAACC
184738 AAACCCCAAAA
1 AAACCCCAAAA
184749 CCCCAAACAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.54, C:0.44, G:0.00, T:0.03
Consensus pattern (14 bp):
AAACCCCAAAAACC
Found at i:184751 original size:8 final size:7
Alignment explanation
Indices: 184722--184756 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
184712 ACCTCAAAAA
184722 CCAAACC
1 CCAAACC
184729 CCAAACC
1 CCAAACC
184736 CCAAACC
1 CCAAACC
184743 CCAAAACC
1 CC-AAACC
184751 CCAAAC
1 CCAAAC
184757 ACTAAAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.46, C:0.54, G:0.00, T:0.00
Consensus pattern (7 bp):
CCAAACC
Found at i:184763 original size:15 final size:15
Alignment explanation
Indices: 184722--184763 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
184712 ACCTCAAAAA
*
184722 CCAAAC-CCCAAACC
1 CCAAACACCAAAACC
*
184736 CCAAACCCCAAAACC
1 CCAAACACCAAAACC
*
184751 CCAAACACTAAAA
1 CCAAACACCAAAA
184764 GTCAAAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (15 bp):
CCAAACACCAAAACC
Found at i:185658 original size:18 final size:18
Alignment explanation
Indices: 185635--185670 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
185625 ATTGAATTTT
185635 AATT-AATATAAATAAACA
1 AATTAAATATAAA-AAACA
185653 AATTAAATATAAAAAACA
1 AATTAAATATAAAAAACA
185671 TATAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AATTAAATATAAAAAACA
Found at i:185678 original size:18 final size:19
Alignment explanation
Indices: 185639--185678 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
185629 AATTTTAATT
*
185639 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
185658 AATATAAA-AAACATATAA
1 AATATAAATAAACAAATAA
185676 AAT
1 AAT
185679 GATTTTGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:186170 original size:114 final size:113
Alignment explanation
Indices: 185884--186176 Score: 369
Period size: 113 Copynumber: 2.6 Consensus size: 113
185874 GTGGCGCTTA
* * * *
185884 CCAA-AAAGCGCCACTAACTCTAATATACGTCAAGGCC-AAACTCTGCGTTTTGGTTAAGATACT
1 CCAATAAA-CGCCACTAATTCTAATATACCTCAAGACCAAAAC-CTGCGTTTTGGTTAAGATATT
* *
185947 TTGCGGCGCTTTCCACAAACGCCGCTACTACTATACTTTAGCGGCGTTTT
64 TTGAGGCGCTTACCACAAACGCCGCTACTACTATACTTTAGCGGCGTTTT
* * *
185997 CCAATAAGCGCCACTAATTCTAATATACCTCAAGACTAAATTCC-GCGTTTTGGTTAAGATATTT
1 CCAATAAACGCCACTAATTCTAATATACCTCAAGACCAAA-ACCTGCGTTTTGGTTAAGATATTT
* * * *
186061 TGAGGCGCTTACCACCAAACGCTGCTATTACTATGCTTTAGTGGCGTTTT
65 TGAGGCGCTTACCA-CAAACGCCGCTACTACTATACTTTAGCGGCGTTTT
* * *
186111 CC-TTAAACGCCACTAATTATAATATACCTCAAGACCAAAACGCTGCGTTTTGGTTAAGATGTTT
1 CCAATAAACGCCACTAATTCTAATATACCTCAAGACCAAAAC-CTGCGTTTTGGTTAAGATATTT
186175 TG
65 TG
186177 CGGCATTTTC
Statistics
Matches: 155, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
112 1 0.01
113 94 0.61
114 59 0.38
115 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (113 bp):
CCAATAAACGCCACTAATTCTAATATACCTCAAGACCAAAACCTGCGTTTTGGTTAAGATATTTT
GAGGCGCTTACCACAAACGCCGCTACTACTATACTTTAGCGGCGTTTT
Found at i:186326 original size:190 final size:190
Alignment explanation
Indices: 186000--186354 Score: 480
Period size: 190 Copynumber: 1.9 Consensus size: 190
185990 GCGTTTTCCA
* * *
186000 ATAAGCGCCACTAATTCTAATATACCTCAAGACTAAATTCCGCGTTTTGGTTAAGATATTTTGAG
1 ATAAGCGCCACTAATTCTAATATACATCAAGACCAAATTCCGCGTTTTGGTTAACATATTTTGAG
* * * ** *
186065 GCGCTTACCACCAAACGCTGCTATTACTATGCTTTAGTGGCGTTTTCCTTAAACGCCACTAATTA
66 GCGCTTACCACCAAACGCCGCTAATACTATGCATTACCGGCGTTTTCCGTAAACGCCACTAATTA
* *
186130 TAATATACCTCAAGACCAAAACGCTGCGTTTTGGTTAAGATGTTTTGCGGCATTTTCTTT
131 TAATATACATCAAGACCAAAACGCTGCGTGTTGGTTAAGATGTTTTGCGGCATTTTCTTT
* * * *
186190 ATAAGCGCCACTAATTGTAATATACATCAAGACCAAACTT-TGCGTTTTGGTTAACATCTTTTGC
1 ATAAGCGCCACTAATTCTAATATACATCAAGACCAAA-TTCCGCGTTTTGGTTAACATATTTTGA
* * * * *
186254 GGCGCTT-CCGCTAAGCGCCGCTAATACTATGCATTACCGGCGTTTGTTCGTAAGCGCCACTAAT
65 GGCGCTTACCACCAAACGCCGCTAATACTATGCATTACCGGCGTTT-TCCGTAAACGCCACTAAT
* *
186318 TCTAATATACATCAAGACCAGAACGCTGCGTGTTGGT
129 TATAATATACATCAAGACCAAAACGCTGCGTGTTGGT
186355 CTTGAGATTT
Statistics
Matches: 141, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
189 30 0.21
190 109 0.77
191 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (190 bp):
ATAAGCGCCACTAATTCTAATATACATCAAGACCAAATTCCGCGTTTTGGTTAACATATTTTGAG
GCGCTTACCACCAAACGCCGCTAATACTATGCATTACCGGCGTTTTCCGTAAACGCCACTAATTA
TAATATACATCAAGACCAAAACGCTGCGTGTTGGTTAAGATGTTTTGCGGCATTTTCTTT
Found at i:186863 original size:21 final size:22
Alignment explanation
Indices: 186818--186864 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
186808 AATAATTAAC
*
186818 TTATACCAAATTTTCAAATAAA
1 TTATACCAAATTTTAAAATAAA
* *
186840 TTATACCGAA-TTTAAAATATA
1 TTATACCAAATTTTAAAATAAA
186861 TTAT
1 TTAT
186865 TTTATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (22 bp):
TTATACCAAATTTTAAAATAAA
Found at i:188125 original size:17 final size:18
Alignment explanation
Indices: 188099--188132 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
188089 TTTTATATTA
*
188099 TTTTTGAAAAGTACAAAC
1 TTTTTGAAAAATACAAAC
188117 TTTTT-AAAAATACAAA
1 TTTTTGAAAAATACAAA
188133 AAATTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (18 bp):
TTTTTGAAAAATACAAAC
Found at i:194861 original size:21 final size:22
Alignment explanation
Indices: 194837--194883 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
194827 TGAAATTTAT
* *
194837 TTTTTTATTTTTATTTTA-AAA
1 TTTTTAATTTTTATATTACAAA
194858 TTTTTAATTTTTATATTACAAA
1 TTTTTAATTTTTATATTACAAA
194880 TTTT
1 TTTT
194884 AAAATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTAATTTTTATATTACAAA
Found at i:197515 original size:25 final size:25
Alignment explanation
Indices: 197487--197553 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
197477 AAATTTATTT
197487 ATATATTATAATAGTTAAAGTTAAA
1 ATATATTATAATAGTTAAAGTTAAA
197512 ATATATTATAATAGTTAAAGTTAAA
1 ATATATTATAATAGTTAAAGTTAAA
*
197537 ATATGTTATAAT-GTTAA
1 ATATATTATAATAGTTAA
197554 GAAATTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
24 5 0.12
25 36 0.88
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (25 bp):
ATATATTATAATAGTTAAAGTTAAA
Found at i:200261 original size:69 final size:69
Alignment explanation
Indices: 200147--200944 Score: 600
Period size: 69 Copynumber: 11.6 Consensus size: 69
200137 GTCACATCAA
* * * * * * * * * *
200147 CTCTCACTAACTATGTTTGAAGCTGCGGCTCTTAGCCAACAAGCCTTAGTATGATAGTTGGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
200212 TTTG
66 TTTG
* * * * **
200216 CTCTCGTTAACTGTGTTAGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATAAAAATTGGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
200281 TTTG
66 TTTG
* * * ** * * * *
200285 CTCTTGCTAATTGTGTTGGAAGCTGCAACTCTTCG-CTGGCAAGCCTCAGTATGACAGCTGGGAG
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCT-ACGAGCCTTAATATGACAGCTGGGAG
*
200349 TTTTG
65 CTTTG
* ** ** *** * *
200354 CTCTCGCTAATTGTGTTGGAGATTGTAGCTCTTCGCCTGTAAACCTTAATATGACAGCTAGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
*
200419 TTTA
66 TTTG
* * * * * *
200423 CTCTCGCTAATTGTGTTGGAGGTTGCGGCTTTTTGCCTACAAGCCTTAATATGACAACTGGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
* *
200488 CTTA
66 TTTG
* * * ** * * ** * * *
200492 CTATTGCTAACTGTGTTAGAAACTGCAGCTCTTC-ACTGGTGAGCATTAGTATGACAGTTGGGAG
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCT-ACGAGCCTTAATATGACAGCTGGGAG
200556 CTTTG
65 CTTTG
** ** ** * * * * *
200561 CTCTTACTAACTACGTTGGAGGCTATGACTTTTTCTG--TACGAGCCATAATATAACAGCTAGGA
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGC-TCTTC-GCCTACGAGCCTTAATATGACAGCTGGGA
200624 GCTTTG
64 GCTTTG
* * *
200630 CTCTCGCTAACTGTGTTGGAGGCTGTGGCTCTTCGCCTACGAGCCTTAATATGATAGCTGGAAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
200695 TTTG
66 TTTG
* * * * ** * * * *
200699 GTCTCGTTAACTGTGGTGGAGGATGTAGCTATTCGCCTTCGAGCCTTAATATGATAACTGGGAGC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
*
200764 TTTA
66 TTTG
* * * * * * * * * **
200768 CTCTCGCTAATTGTATTGGAGGTTGCGGC-CTTCACCTGCAAGTCTTAATATGATAGTTGGGAAT
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
*
200832 TTTT
66 TTTG
* * * *
200836 CTCTCGCTAACTGTGTTGGAGGCTACGACTCTTCGCTTGCGAGCCTTAATATGA-ATGCTGGGAG
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACA-GCTGGGAG
*
200900 TTTTG
65 CTTTG
* *
200905 CTCTCGCTAACTGTGTTGGAGGCTACGACTCTTCGCCTAC
1 CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTAC
200945 AAATCTTAAT
Statistics
Matches: 573, Mismatches: 146, Indels: 20
0.78 0.20 0.03
Matches are distributed among these distances:
67 1 0.00
68 62 0.11
69 503 0.88
70 7 0.01
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (69 bp):
CTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCCTACGAGCCTTAATATGACAGCTGGGAGC
TTTG
Found at i:212290 original size:9 final size:9
Alignment explanation
Indices: 212276--212300 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
212266 AGCAATTCAT
212276 AATTCAACA
1 AATTCAACA
212285 AATTCAACA
1 AATTCAACA
212294 AATTCAA
1 AATTCAA
212301 AATAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (9 bp):
AATTCAACA
Found at i:212341 original size:17 final size:18
Alignment explanation
Indices: 212321--212354 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
212311 AAAAATACAT
212321 AAATAAATTTA-AATTTA
1 AAATAAATTTATAATTTA
*
212338 AAATATATTTATAATTT
1 AAATAAATTTATAATTT
212355 TTTTGGTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAAATTTATAATTTA
Found at i:219517 original size:26 final size:27
Alignment explanation
Indices: 219488--219540 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
219478 ATTTTACATC
* * *
219488 AATAAAATTATCAC-AATTTTTTTTAA
1 AATAAAACTAACACAAATTTTGTTTAA
219514 AATAAAACTAACACAAATTTTGTTTAA
1 AATAAAACTAACACAAATTTTGTTTAA
219541 GTGAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (27 bp):
AATAAAACTAACACAAATTTTGTTTAA
Found at i:219732 original size:44 final size:44
Alignment explanation
Indices: 219683--219772 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
219673 TAATTATAAC
* * * *
219683 TTAAATTCTAATTATTTTTAAATGTGTAATTATCACAACTTTTA
1 TTAAATTCTAATAATTCTTAAATGTATAATTATCACAACTTCTA
* *
219727 TTAAATTGTAATAATTCTTAAATGTATAATTATCATAACTTCTA
1 TTAAATTCTAATAATTCTTAAATGTATAATTATCACAACTTCTA
219771 TT
1 TT
219773 TCATTTCAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (44 bp):
TTAAATTCTAATAATTCTTAAATGTATAATTATCACAACTTCTA
Found at i:220885 original size:16 final size:16
Alignment explanation
Indices: 220864--220898 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
220854 CAAATCGTAT
*
220864 TTGTTTGAAGAATATA
1 TTGTTTGAAAAATATA
220880 TTGTTTGAAAAATATA
1 TTGTTTGAAAAATATA
220896 TTG
1 TTG
220899 ACTAAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (16 bp):
TTGTTTGAAAAATATA
Found at i:228123 original size:97 final size:98
Alignment explanation
Indices: 227999--228193 Score: 383
Period size: 97 Copynumber: 2.0 Consensus size: 98
227989 TACCATTACT
227999 AATTTAAAATTTTATAAATTATAAAAATACCTAAATGGGAAATTTTTCATTTTAATGGGGTTGGG
1 AATTTAAAATTTTATAAATTATAAAAATACCTAAATGGGAAATTTTTCATTTTAATGGGGTTGGG
228064 CCGGGCTTTGTCACTGTCTACCACACTTTGATA
66 CCGGGCTTTGTCACTGTCTACCACACTTTGATA
228097 AATTTAAAA-TTTATAAATTATAAAAATACCTAAATGGGAAATTTTTCATTTTAATGGGGTTGGG
1 AATTTAAAATTTTATAAATTATAAAAATACCTAAATGGGAAATTTTTCATTTTAATGGGGTTGGG
228161 CCGGGCTTTGTCACTGTCTACCACACTTTGATA
66 CCGGGCTTTGTCACTGTCTACCACACTTTGATA
228194 CCTTTGTAGT
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 88 0.91
98 9 0.09
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (98 bp):
AATTTAAAATTTTATAAATTATAAAAATACCTAAATGGGAAATTTTTCATTTTAATGGGGTTGGG
CCGGGCTTTGTCACTGTCTACCACACTTTGATA
Found at i:228310 original size:19 final size:19
Alignment explanation
Indices: 228285--228336 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
228275 AACACATGAC
228285 AAATTTTAATAAAAA-ATAT
1 AAATTTT-ATAAAAATATAT
* *
228304 TAATTTTTTAAAAATATAT
1 AAATTTTATAAAAATATAT
228323 AAA-TTTATAAAAAT
1 AAATTTTATAAAAAT
228337 TATCTTACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTTATAAAAATATAT
Found at i:229703 original size:31 final size:31
Alignment explanation
Indices: 229665--229737 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
229655 CAACAACTAC
*
229665 CGCTGACATGGAGCACCACATCAATAGCTGT
1 CGCTGACATGGAGCACCACATCAATAACTGT
* * *
229696 CGCTGACATGGAGCATCACGTCAATAATTGT
1 CGCTGACATGGAGCACCACATCAATAACTGT
*
229727 CGTTGACATGG
1 CGCTGACATGG
229738 TCAAAGTGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (31 bp):
CGCTGACATGGAGCACCACATCAATAACTGT
Found at i:231103 original size:43 final size:42
Alignment explanation
Indices: 231056--231144 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
231046 GCGTGTGCGT
* *
231056 AGGCTATGTAAACCACACAGGTAGAGGACATGGGTGTGTTTCC
1 AGGCTATGTAAACCACACAGGCA-AGGACATGGGTGTGTGTCC
* * * *
231099 AGGCTGTGTGAGCCACACGGGCAAGGACATGGGTGTGTGTCC
1 AGGCTATGTAAACCACACAGGCAAGGACATGGGTGTGTGTCC
231141 AGGC
1 AGGC
231145 CGTATGGCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 22 0.55
43 18 0.45
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (42 bp):
AGGCTATGTAAACCACACAGGCAAGGACATGGGTGTGTGTCC
Found at i:231686 original size:24 final size:22
Alignment explanation
Indices: 231643--231686 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
231633 GAATAACTGC
* *
231643 ATATGAATCTAATTTGTTCTGT
1 ATATGAAACTAAATTGTTCTGT
231665 ATATGAAACTGAAATTGCTTCT
1 ATATGAAACT-AAATTG-TTCT
231687 ACGTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 5 0.28
24 4 0.22
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAACTAAATTGTTCTGT
Found at i:231771 original size:25 final size:25
Alignment explanation
Indices: 231737--231789 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
231727 CTTCTGTTAT
231737 CTAACCGAATCTTGGGATTCAAAAA
1 CTAACCGAATCTTGGGATTCAAAAA
*
231762 CTAACTGAATCTTGGGATTCAAAAA
1 CTAACCGAATCTTGGGATTCAAAAA
231787 CTA
1 CTA
231790 TATTATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (25 bp):
CTAACCGAATCTTGGGATTCAAAAA
Found at i:232401 original size:27 final size:27
Alignment explanation
Indices: 232379--232431 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
232369 TTTATATTAT
* *
232379 TATTTTGAAAT-TAAAAATATATAAAA
1 TATTTTAAAATATAAAAAAATATAAAA
232405 TATTTTAAAATATAAAAAAATATAAAA
1 TATTTTAAAATATAAAAAAATATAAAA
232432 ATTATTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
TATTTTAAAATATAAAAAAATATAAAA
Found at i:232543 original size:77 final size:78
Alignment explanation
Indices: 232445--232599 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 78
232435 ATTTCACATC
232445 CAAAATGAACTTGGTTGTCTAAATTCTAATCAACTTGGACATTCATTTATCCAAATCCATTCTGG
1 CAAAATGAACTTGGTTGTCTAAATTCTAATCAACTTGGACATTCATTTATCCAAATCCATTCTGG
232510 ACTTGCTTTTTTA
66 ACTTGCTTTTTTA
232523 CAAAATGAAC-TGGTTGTCTAAATTCTAATCAACTTGGACATTCATTTATCCAAATCCATTCTGG
1 CAAAATGAACTTGGTTGTCTAAATTCTAATCAACTTGGACATTCATTTATCCAAATCCATTCTGG
232587 ACTTGCTTTTTTA
66 ACTTGCTTTTTTA
232600 GTAATTTCAT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 67 0.87
78 10 0.13
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (78 bp):
CAAAATGAACTTGGTTGTCTAAATTCTAATCAACTTGGACATTCATTTATCCAAATCCATTCTGG
ACTTGCTTTTTTA
Found at i:233209 original size:19 final size:18
Alignment explanation
Indices: 233184--233229 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
233174 TAAGGTTAAT
233184 ATTTAATATCTAAGTTTGA-
1 ATTTAATATC-AA-TTTGAC
*
233203 TTTTAATATCAATTTGAC
1 ATTTAATATCAATTTGAC
233221 ATTTAATAT
1 ATTTAATAT
233230 TTTTTTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 9 0.38
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (18 bp):
ATTTAATATCAATTTGAC
Found at i:234159 original size:22 final size:22
Alignment explanation
Indices: 234127--234179 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
234117 TAAATGAATG
* *
234127 AAAAT-ATTAAATATTTAAA-TC
1 AAAATAATTAAA-ATATAAATTA
234148 AAAATAATTAAAATATAAATTA
1 AAAATAATTAAAATATAAATTA
234170 AAAATAATTA
1 AAAATAATTA
234180 CAAAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATAATTAAAATATAAATTA
Found at i:242671 original size:27 final size:27
Alignment explanation
Indices: 242633--242687 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
242623 TAGACAAGTC
242633 TTCGTTATCCCTTTCGATCAGAACCAA
1 TTCGTTATCCCTTTCGATCAGAACCAA
242660 TTCGTTATCCCTTTCGATCAGAACCAA
1 TTCGTTATCCCTTTCGATCAGAACCAA
242687 T
1 T
242688 GTAAAATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.35
Consensus pattern (27 bp):
TTCGTTATCCCTTTCGATCAGAACCAA
Found at i:247585 original size:19 final size:19
Alignment explanation
Indices: 247561--247662 Score: 177
Period size: 19 Copynumber: 5.3 Consensus size: 19
247551 GATTACAAAT
247561 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
247580 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
247599 ATATATCATATCTAAGATTGC
1 --ATATCATATCTAAGATTGC
*
247620 ATATCATATCTAGGATTGC
1 ATATCATATCTAAGATTGC
247639 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
247658 ATATC
1 ATATC
247663 CTCAAAAATT
Statistics
Matches: 79, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
19 60 0.76
21 19 0.24
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:247607 original size:40 final size:40
Alignment explanation
Indices: 247559--247662 Score: 185
Period size: 40 Copynumber: 2.6 Consensus size: 40
247549 AAGATTACAA
247559 ATATATCATATCTAAGATTGCATATCATATCTAAGATTGC
1 ATATATCATATCTAAGATTGCATATCATATCTAAGATTGC
*
247599 ATATATCATATCTAAGATTGCATATCATATCTAGGATTGC
1 ATATATCATATCTAAGATTGCATATCATATCTAAGATTGC
247639 --ATATCATATCTAAGATTGCATATC
1 ATATATCATATCTAAGATTGCATATC
247663 CTCAAAAATT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
38 24 0.38
40 39 0.62
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (40 bp):
ATATATCATATCTAAGATTGCATATCATATCTAAGATTGC
Found at i:248807 original size:63 final size:62
Alignment explanation
Indices: 248703--248900 Score: 200
Period size: 63 Copynumber: 3.1 Consensus size: 62
248693 TGGCAGGCCA
* * * * *
248703 TGTGACTCACTGTTTTCCATTAAAGACCACAGGGGCCAGAGACACAGGTGTGTGTCTAGGTCG
1 TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCTAGAGACACAGGTGTGTGTCCAGG-CG
* * ** **
248766 TGTGACTCACTGTTTGCCATTAAGGACCATACAGGCTAGAGAC-TTGAGCATGTGTCCAGGCTG
1 TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCTAGAGACACAG-GTGTGTGTCCAGGC-G
* * * * * *
248829 TGCGACTCACTGTTTGCCATTAGGGACCACATGGGCTAGAGACACGGGTGCGTGTCCAGGCCA
1 TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCTAGAGACACAGGTGTGTGTCCAGG-CG
248892 TGTGACTCA
1 TGTGACTCA
248901 TTATTTGGGA
Statistics
Matches: 108, Mismatches: 23, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
62 2 0.02
63 104 0.96
64 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (62 bp):
TGTGACTCACTGTTTGCCATTAAGGACCACACGGGCTAGAGACACAGGTGTGTGTCCAGGCG
Found at i:251992 original size:145 final size:146
Alignment explanation
Indices: 251728--252017 Score: 573
Period size: 145 Copynumber: 2.0 Consensus size: 146
251718 TGAAAAGCGT
251728 AAGTCATTTTTCAAAAAAGAGCTTGTTTATGAACAATTTTTTAATATAAAAATTAACTTCAACCA
1 AAGTCATTTTTCAAAAAAGAGCTTGTTTATGAACAATTTTTTAATATAAAAATTAACTTCAACCA
251793 AGCCTAATATTATTATTTTAGTACTAATAATAAATTTTAATTTTAATTTTTTTAAAATATTAAAT
66 AGCCTAATATTATTATTTTAGTACTAATAATAAATTTTAATTTTAATTTTTTTAAAATATTAAAT
251858 ATTAAAATATTAAAGA
131 ATTAAAATATTAAAGA
251874 AAGTCATTTTTC-AAAAAGAGCTTGTTTATGAACAATTTTTTAATATAAAAATTAACTTCAACCA
1 AAGTCATTTTTCAAAAAAGAGCTTGTTTATGAACAATTTTTTAATATAAAAATTAACTTCAACCA
251938 AGCCTAATATTATTATTTTAGTACTAATAATAAATTTTAATTTTAATTTTTTTAAAATATTAAAT
66 AGCCTAATATTATTATTTTAGTACTAATAATAAATTTTAATTTTAATTTTTTTAAAATATTAAAT
252003 ATTAAAATATTAAAG
131 ATTAAAATATTAAAG
252018 TCAAATATTA
Statistics
Matches: 144, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
145 132 0.92
146 12 0.08
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.43
Consensus pattern (146 bp):
AAGTCATTTTTCAAAAAAGAGCTTGTTTATGAACAATTTTTTAATATAAAAATTAACTTCAACCA
AGCCTAATATTATTATTTTAGTACTAATAATAAATTTTAATTTTAATTTTTTTAAAATATTAAAT
ATTAAAATATTAAAGA
Found at i:256675 original size:18 final size:17
Alignment explanation
Indices: 256634--256667 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
256624 GTCGTTTGTT
256634 TTTA-AAATATTATTCA
1 TTTACAAATATTATTCA
256650 TTTACAAATAGTTATTCA
1 TTTACAAATA-TTATTCA
256668 ATTTCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTACAAATATTATTCA
Found at i:259133 original size:13 final size:13
Alignment explanation
Indices: 259115--259143 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
259105 CCACAGACAC
259115 CCAAAGCACTTAA
1 CCAAAGCACTTAA
259128 CCAAAGCACTTAA
1 CCAAAGCACTTAA
259141 CCA
1 CCA
259144 TTGAAGCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.34, G:0.07, T:0.14
Consensus pattern (13 bp):
CCAAAGCACTTAA
Found at i:262984 original size:25 final size:25
Alignment explanation
Indices: 262929--262995 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
262919 TTTTAAGTGT
*
262929 TTTCAGTATAGT-CTATCTATAATAG
1 TTTCAGTATA-TACTATCTATAACAG
* *
262954 TCTCAGTATATACTATCTATAGCAG
1 TTTCAGTATATACTATCTATAACAG
*
262979 TTTCAGAATATACTATC
1 TTTCAGTATATACTATC
262996 AAAGACAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 1 0.03
25 35 0.97
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.40
Consensus pattern (25 bp):
TTTCAGTATATACTATCTATAACAG
Found at i:263004 original size:25 final size:25
Alignment explanation
Indices: 262956--263006 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
262946 TATAATAGTC
* *
262956 TCAGTATATACTATCTATAGCAGTT
1 TCAGAATATACTATCTAAAGCAGTT
262981 TCAGAATATACTATC-AAAGACAGTT
1 TCAGAATATACTATCTAAAG-CAGTT
263006 T
1 T
263007 TAGTTTCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (25 bp):
TCAGAATATACTATCTAAAGCAGTT
Found at i:263356 original size:18 final size:18
Alignment explanation
Indices: 263325--263372 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
263315 TGTTGTTCGT
*
263325 TTTCAAAACATTATTC-A
1 TTTCAAAACGTTATTCAA
*
263342 TTTACAAATCGTTATTCAA
1 TTT-CAAAACGTTATTCAA
263361 TTTCAAAACGTT
1 TTTCAAAACGTT
263373 TTTTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (18 bp):
TTTCAAAACGTTATTCAA
Found at i:276414 original size:22 final size:22
Alignment explanation
Indices: 276381--276427 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
276371 ATTTGAATTT
* *
276381 AAAATTTTTTAAA-TATATAAA
1 AAAATTTATTAAACTAAATAAA
276402 AAAACTTTATTAAACTAAATAAA
1 AAAA-TTTATTAAACTAAATAAA
276425 AAA
1 AAA
276428 TTAATGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 10 0.45
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATTTATTAAACTAAATAAA
Done.