Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 22 of 34
Found at i:3333756 original size:40 final size:40
Alignment explanation
Indices: 3333675--3333754 Score: 101
Period size: 38 Copynumber: 2.0 Consensus size: 40
3333665 CATCCTTCAT
*
3333675 ACCAAAAAAAAAAACAAAACAAAAAAAAACCAAGAAAAAA
1 ACCAAAAAAAAAAACAAAACAAAAAAAAACCAAAAAAAAA
* * *
3333715 ACCAAAAAAATAAA-AAAA-TAGAAAAAACCAAAAACAAAA
1 ACCAAAAAAAAAAACAAAACAAAAAAAAACCAAAAA-AAAA
3333754 A
1 A
3333755 ACAAGCAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 13 0.37
39 9 0.26
40 13 0.37
ACGTcount: A:0.81, C:0.14, G:0.03, T:0.03
Consensus pattern (40 bp):
ACCAAAAAAAAAAACAAAACAAAAAAAAACCAAAAAAAAA
Found at i:3333768 original size:27 final size:24
Alignment explanation
Indices: 3333695--3333768 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 24
3333685 AAAACAAAAC
*
3333695 AAAAAAAAACCAAGAAAAAAACCA
1 AAAAAAAAAACAAGAAAAAAACCA
* *
3333719 AAAAAATAAAAAAATAGAAAAAACCA
1 AAAAAA-AAAACAAGA-AAAAAACCA
3333745 AAAACAAAAAACAAGCAAACAAAA
1 AAAA-AAAAAACAAG-AAA-AAAA
3333769 AAGGGGTCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 6 0.15
25 6 0.15
26 21 0.52
27 7 0.17
ACGTcount: A:0.80, C:0.14, G:0.04, T:0.03
Consensus pattern (24 bp):
AAAAAAAAAACAAGAAAAAAACCA
Found at i:3335050 original size:28 final size:28
Alignment explanation
Indices: 3335019--3335681 Score: 756
Period size: 28 Copynumber: 23.5 Consensus size: 28
3335009 CGTTCATCTC
* *
3335019 TTCAAAGCCCACAGGTCAGTGACATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
3335047 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
3335075 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
3335103 TTCAAAGCCCACAGGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
3335131 TTCAAAGCCCAGAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
3335159 TTTAAAGCCCATAAGTCAATGACATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
3335187 TTCAAAGCCCACAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
3335214 CTTCAAATGACCATAAGTCAATGGCATCCT
1 -TTCAAA-GCCCACAAGTCAGTGGCATCCT
* * *
3335244 TTCAAAGCCCGCAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
3335272 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
3335300 TTCAAAGCCCATAAGTTAGTGTCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
**
3335328 TTCAAAGCCCACAAGTTGGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
3335356 TTCAAAGGCCACAAGTCAATGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
3335383 CTTCAAAAGACCACAAGTCAATGGCATTCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
* ** *
3335413 TTCAAAACCTGCAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*** * *
3335441 TTCAAAGCGTGCAAGTCAGTAGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
3335469 TTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* * *
3335499 TTCAAAGCCCATAAGTCAATGGCAACCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
3335527 TTAAAAGCCCACAAGTCAGTGACA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* * * *
3335555 TTCAAAGCCCACAAGTCAATGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
3335583 TTCAAAGCCCACAAATCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
3335611 TTCAAAGCCCACAAGTAAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
**
3335641 TTCAAAGCCCACAAGTTGGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
3335669 TTCAAAGCCCACA
1 TTCAAAGCCCACA
3335682 TAAATCGGTG
Statistics
Matches: 547, Mismatches: 76, Indels: 24
0.85 0.12 0.04
Matches are distributed among these distances:
27 6 0.01
28 438 0.80
29 48 0.09
30 55 0.10
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:3335297 original size:169 final size:168
Alignment explanation
Indices: 3335019--3335679 Score: 829
Period size: 169 Copynumber: 3.9 Consensus size: 168
3335009 CGTTCATCTC
* * * *
3335019 TTCAAAGCCCACAGGTCAGTGACATC-CTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGACATCTC-TTCAAAGACCACAAGTCAATGGCATCCTTTCAAAGC
* * * *
3335083 CCACAAGTCAGTGGCATCTTTTCAAAGCCCACAGGTTAGTGGCATCCTTTCAAAGCCCAGAAGTT
65 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTT
* *
3335148 AGTGGCATCCTTTTAAAGCCCATAAGTCAATGACATCCT
130 AGTGGCATCCTTTCAAAGCCCATAAGTCAATGGCATCCT
* *
3335187 TTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAATGACCATAAGTCAATGGCATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGACATCTCTTCAAA-GACCACAAGTCAATGGCATCCTTTCAAAGC
* * *
3335252 CCGCAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTT
65 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTT
* * ***
3335317 AGTGTCATCCTTTCAAAGCCCACAAGTTGGTGGCATCCT
130 AGTGGCATCCTTTCAAAGCCCATAAGTCAATGGCATCCT
* * * * *
3335356 TTCAAAGGCCACAAGTCAATGGCATCTCTTCAAAAGACCACAAGTCAATGGCATTCTTTCAAAAC
1 TTCAAAGCCCACAAGTCAGTGACATCTCTTC-AAAGACCACAAGTCAATGGCATCCTTTCAAAGC
** * * *** * * * *
3335421 CTGCAAGTTAGTGGCATCCTTTCAAAGCGTGCAAGTCAGTAGCACCCTTTCAAAGCCCACAAGTC
65 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTT
*
3335486 AGTGGCATACCCTTTCAAAGCCCATAAGTCAATGGCAACCT
130 AGTGGCAT--CCTTTCAAAGCCCATAAGTCAATGGCATCCT
* * * * * * *
3335527 TTAAAAGCCCACAAGTCAGTGACACCTTTTCAAAGCCCACAAGTCAATGGTACCCCTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGACATCTCTTCAAAGACCACAAGTCAATGGCATCCTTTCAAAGCC
* *
3335592 CACAAATCAGTGGCACCCTTTCAAAGCCCACAAGTAAGTGGCATACCCTTTCAAAGCCCACAAGT
66 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCAT--CCTTTCAAAGCCCACAAGT
*
3335657 TGGTGGCATCCTTTCAAAGCCCA
129 TAGTGGCATCCTTTCAAAGCCCA
3335680 CATAAATCGG
Statistics
Matches: 421, Mismatches: 65, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
168 30 0.07
169 236 0.56
170 78 0.19
171 51 0.12
172 26 0.06
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (168 bp):
TTCAAAGCCCACAAGTCAGTGACATCTCTTCAAAGACCACAAGTCAATGGCATCCTTTCAAAGCC
CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTA
GTGGCATCCTTTCAAAGCCCATAAGTCAATGGCATCCT
Found at i:3336670 original size:30 final size:30
Alignment explanation
Indices: 3336634--3336690 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
3336624 AAAAGTCACA
3336634 TTTTTACCTAGATGTATCGATACATTTATC
1 TTTTTACCTAGATGTATCGATACATTTATC
*
3336664 TTTTTACCTAGATGTATTGATACATTT
1 TTTTTACCTAGATGTATCGATACATTT
3336691 TTCAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (30 bp):
TTTTTACCTAGATGTATCGATACATTTATC
Found at i:3336730 original size:40 final size:40
Alignment explanation
Indices: 3336675--3336807 Score: 160
Period size: 40 Copynumber: 3.5 Consensus size: 40
3336665 TTTTACCTAG
3336675 ATGTATTGATACATTTTTCAATATATCGGTACAAGTATGA
1 ATGTATTGATACATTTTTCAATATATCGGTACAAGTATGA
* *
3336715 ATGTATTGATACATTTTATC--T-T-T--TTAC--CTA-G-
1 ATGTATTGATACATTTT-TCAATATATCGGTACAAGTATGA
3336746 ATGTATTGATACATTTTTCAATATATCGGTACAAGTATGA
1 ATGTATTGATACATTTTTCAATATATCGGTACAAGTATGA
*
3336786 ATGTATCGATACATTTTTCAAT
1 ATGTATTGATACATTTTTCAAT
3336808 GTGTCGATAT
Statistics
Matches: 77, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
30 2 0.03
31 17 0.22
32 2 0.03
33 3 0.04
34 1 0.01
35 3 0.04
36 3 0.04
37 1 0.01
38 3 0.04
39 2 0.03
40 38 0.49
41 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (40 bp):
ATGTATTGATACATTTTTCAATATATCGGTACAAGTATGA
Found at i:3336760 original size:71 final size:71
Alignment explanation
Indices: 3336645--3336802 Score: 300
Period size: 71 Copynumber: 2.2 Consensus size: 71
3336635 TTTTACCTAG
3336645 ATGTATCGATACA-TTTATCTTTTTACCTAGATGTATTGATACATTTTTCAATATATCGGTACAA
1 ATGTATCGATACATTTTATCTTTTTACCTAGATGTATTGATACATTTTTCAATATATCGGTACAA
3336709 GTATGA
66 GTATGA
*
3336715 ATGTATTGATACATTTTATCTTTTTACCTAGATGTATTGATACATTTTTCAATATATCGGTACAA
1 ATGTATCGATACATTTTATCTTTTTACCTAGATGTATTGATACATTTTTCAATATATCGGTACAA
3336780 GTATGA
66 GTATGA
3336786 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
3336803 TCAATGTGTC
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
70 12 0.14
71 73 0.86
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (71 bp):
ATGTATCGATACATTTTATCTTTTTACCTAGATGTATTGATACATTTTTCAATATATCGGTACAA
GTATGA
Found at i:3336808 original size:20 final size:20
Alignment explanation
Indices: 3336746--3336816 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
3336736 TTTTACCTAG
*
3336746 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * ** * *
3336766 ATATATCGGTACAAGTATGA
1 ATGTATCGATACATTTTTCA
3336786 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
3336806 ATGTGTCGATA
1 ATGTATCGATA
3336817 TATTCTGTCT
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3336865 original size:31 final size:31
Alignment explanation
Indices: 3336806--3336882 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
3336796 ACATTTTTCA
* *
3336806 ATGTGTCGATATATTCTGTCTTTATACCCAG
1 ATGTATCGATACATTCTGTCTTTATACCCAG
*
3336837 ATGTATCGATACATTTTGTCCTTT-TACCCAG
1 ATGTATCGATACATTCTGT-CTTTATACCCAG
3336868 ATGTATCGATACATT
1 ATGTATCGATACATT
3336883 GAATAATGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
31 38 0.90
32 4 0.10
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (31 bp):
ATGTATCGATACATTCTGTCTTTATACCCAG
Found at i:3341289 original size:48 final size:48
Alignment explanation
Indices: 3341234--3341341 Score: 130
Period size: 48 Copynumber: 2.2 Consensus size: 48
3341224 TATCAACACA
*
3341234 ATGTATCGATACAAATTGCTTTATATTGATACAGTT-TGGAAAACT-TAG
1 ATGTATCGATACAAATTGCCTTATATTGATACA-TTCT-GAAAACTCTAG
** * *
3341282 ATGTATCGATACATTTTGCCTTGTATTGATACATTCTGAAAATTCTAG
1 ATGTATCGATACAAATTGCCTTATATTGATACATTCTGAAAACTCTAG
*
3341330 AAGTATCGATAC
1 ATGTATCGATAC
3341342 TTTGAGCAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 8 0.15
48 44 0.85
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (48 bp):
ATGTATCGATACAAATTGCCTTATATTGATACATTCTGAAAACTCTAG
Found at i:3346502 original size:41 final size:43
Alignment explanation
Indices: 3346451--3346531 Score: 114
Period size: 41 Copynumber: 1.9 Consensus size: 43
3346441 CCATTGGGCT
3346451 AATTGTATCGATACAATT-CTA-G-ATGTATCGACACATTTTGG
1 AATTGTATCGATA-AATTCCTATGTATGTATCGACACATTTTGG
* *
3346492 AATTGTATCGATAGATTCCTATGTATGTATCGATACATTT
1 AATTGTATCGATAAATTCCTATGTATGTATCGACACATTT
3346532 AAAGGATAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 3 0.09
41 16 0.46
42 1 0.03
43 15 0.43
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (43 bp):
AATTGTATCGATAAATTCCTATGTATGTATCGACACATTTTGG
Found at i:3349456 original size:9 final size:9
Alignment explanation
Indices: 3349438--3349466 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3349428 AAACTCGTTT
3349438 AAAAAT-AA
1 AAAAATCAA
3349446 AAAAATCAA
1 AAAAATCAA
3349455 AAAAATCAA
1 AAAAATCAA
3349464 AAA
1 AAA
3349467 TTAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAATCAA
Found at i:3350971 original size:65 final size:65
Alignment explanation
Indices: 3350862--3351132 Score: 203
Period size: 65 Copynumber: 4.2 Consensus size: 65
3350852 TCGATGGTTG
* * * * *
3350862 GAAACCATACAAACCATCTAAGGGTGACCA-CTGCAAAACTTAAGTCAAAAAAGGGTTGGCTAGG
1 GAAACCATACAAAACAACTAAGGGTGACCAGGTG--GAACCTAAGTCAAAAAAGGGTTGGCTAGG
3350926 AT
64 AT
* * *
3350928 GAAACCGTACAAAACAACCT-A-GGTGACCAGGGTGGAACCTAAGTTGAAAAAA-GGTTGG-TGG
1 GAAACCATACAAAACAA-CTAAGGGTGACCA-GGTGGAACCTAAG-TCAAAAAAGGGTTGGCTAG
3350989 GAT
63 GAT
* * * * * * *
3350992 GAAACCATACGAACCAACTAAGGGTGATCAGGTGGAACCTAAGTTAAAAAGGGGTTGGCTTGGGT
1 GAAACCATACAAAACAACTAAGGGTGACCAGGTGGAACCTAAGTCAAAAAAGGGTTGGCTAGGAT
** * * * ** ** *
3351057 GAAACCATATGAACCAACTAAAGGTGACTAGGGTACAATTTGAGTCAAAAAAGGGTTGG-TCAGG
1 GAAACCATACAAAACAACTAAGGGTGACCA-GGTGGAACCTAAGTCAAAAAAGGGTTGGCT-AGG
3351121 AT
64 AT
*
3351123 AAAACCATAC
1 GAAACCATAC
3351133 GTTGGATAAC
Statistics
Matches: 164, Mismatches: 31, Indels: 20
0.76 0.14 0.09
Matches are distributed among these distances:
63 8 0.05
64 39 0.24
65 59 0.36
66 54 0.33
67 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.19
Consensus pattern (65 bp):
GAAACCATACAAAACAACTAAGGGTGACCAGGTGGAACCTAAGTCAAAAAAGGGTTGGCTAGGAT
Found at i:3351032 original size:64 final size:64
Alignment explanation
Indices: 3350902--3351090 Score: 206
Period size: 65 Copynumber: 2.9 Consensus size: 64
3350892 CTGCAAAACT
* * * * *
3350902 TAAGTCAAAAAAGGGTTGGCTAGGATGAAACCGTACAAAACAACCT-AGGTGACCAGGGTGGAAC
1 TAAGTTAAAAAA-GGTTGGCTGGGATGAAACCATACGAACCAA-CTAAGGTGACCAGGGTGGAAC
3350966 C
64 C
*
3350967 TAAGTTGAAAAAAGGTTGG-TGGGATGAAACCATACGAACCAACTAAGGGTGATCA-GGTGGAAC
1 TAAGTT-AAAAAAGGTTGGCTGGGATGAAACCATACGAACCAACTAA-GGTGACCAGGGTGGAAC
3351030 C
64 C
* * *
3351031 TAAGTTAAAAAGGGGTTGGCTTGGG-TGAAACCATATGAACCAACTAAAGGTGACTAGGGT
1 TAAGTTAAAAA-AGGTTGGC-TGGGATGAAACCATACGAACCAACT-AAGGTGACCAGGGT
3351091 ACAATTTGAG
Statistics
Matches: 106, Mismatches: 10, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
63 7 0.07
64 41 0.39
65 43 0.41
66 15 0.14
ACGTcount: A:0.37, C:0.15, G:0.29, T:0.19
Consensus pattern (64 bp):
TAAGTTAAAAAAGGTTGGCTGGGATGAAACCATACGAACCAACTAAGGTGACCAGGGTGGAACC
Found at i:3351367 original size:65 final size:66
Alignment explanation
Indices: 3351229--3351377 Score: 162
Period size: 66 Copynumber: 2.3 Consensus size: 66
3351219 TTGGTTGAGC
* * * **
3351229 AAACTATATGAACCAACTTTTGGTAACCAAGGTAAAACCTAAGTCAAAATGGGGTTGGTTGTGAC
1 AAACCATATGAACCAACTTTTGGTAACCAAGGTAAAACCTAAGTCAAAAAGGAGTTGGAAGTGAC
3351294 A
66 A
* * * *
3351295 AAACCATATGAACTAAC-TTTGGATGACCAAGGTGAAACTTAAGT-AAAAAGGAGTTGGCAAG-G
1 AAACCATATGAACCAACTTTTGG-TAACCAAGGTAAAACCTAAGTCAAAAAGGAGTTGG-AAGTG
3351357 ACA
64 ACA
3351360 AAACCATACT-AACCAACT
1 AAACCATA-TGAACCAACT
3351378 AAGGGTGACT
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
65 34 0.49
66 35 0.51
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (66 bp):
AAACCATATGAACCAACTTTTGGTAACCAAGGTAAAACCTAAGTCAAAAAGGAGTTGGAAGTGAC
A
Found at i:3351578 original size:30 final size:30
Alignment explanation
Indices: 3351537--3351626 Score: 128
Period size: 31 Copynumber: 3.0 Consensus size: 30
3351527 AACTTGAGTC
*
3351537 AAAAAAAGGTTGGCTAGGATAAAACCATAT
1 AAAAAAGGGTTGGCTAGGATAAAACCATAT
* *
3351567 AAAAAAGGGTTGGCTAGGACAAAA-CTTGAAT
1 AAAAAAGGGTTGGCTAGGATAAAACCAT--AT
3351598 AAAAAAGGGTTGGCTAGGATAAAACCATA
1 AAAAAAGGGTTGGCTAGGATAAAACCATA
3351627 CGAACCAACT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
29 2 0.04
30 23 0.44
31 25 0.48
32 2 0.04
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.19
Consensus pattern (30 bp):
AAAAAAGGGTTGGCTAGGATAAAACCATAT
Found at i:3351600 original size:31 final size:31
Alignment explanation
Indices: 3351526--3351622 Score: 126
Period size: 31 Copynumber: 3.1 Consensus size: 31
3351516 GACCAGGGTG
* *
3351526 AAACTTGAGTCAAAAAAAGGTTGGCTAGGATA
1 AAACTTGAAT-AAAAAAGGGTTGGCTAGGATA
* *
3351558 AAAC--CATATAAAAAAGGGTTGGCTAGGACA
1 AAACTTGA-ATAAAAAAGGGTTGGCTAGGATA
3351588 AAACTTGAATAAAAAAGGGTTGGCTAGGATA
1 AAACTTGAATAAAAAAGGGTTGGCTAGGATA
3351619 AAAC
1 AAAC
3351623 CATACGAACC
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
30 24 0.43
31 27 0.48
32 5 0.09
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.20
Consensus pattern (31 bp):
AAACTTGAATAAAAAAGGGTTGGCTAGGATA
Found at i:3351722 original size:66 final size:65
Alignment explanation
Indices: 3351652--3351792 Score: 160
Period size: 65 Copynumber: 2.2 Consensus size: 65
3351642 TGACTAAGGT
* * * *
3351652 AAAACTTGAGGCAAAATAAGGTTAGCTGAGACAAAACCATGCA-AACCATATT-TGGATGACTAG
1 AAAACTTAAGACAAAATAAGGTTAGCCGAGAC-AAACCAT-AAGAACCA-ATTCTGGATGACTAG
3351715 GAC
63 GAC
* ** * *
3351718 AAAACCTAAGACAAAATGGGGTTGGCCGAGACAAACCATAAGAACCAATTCTGGATGACTAGGGC
1 AAAACTTAAGACAAAATAAGGTTAGCCGAGACAAACCATAAGAACCAATTCTGGATGACTAGGAC
3351783 AAAACTTAAG
1 AAAACTTAAG
3351793 TTGAAAACAG
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
64 4 0.06
65 34 0.54
66 25 0.40
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.18
Consensus pattern (65 bp):
AAAACTTAAGACAAAATAAGGTTAGCCGAGACAAACCATAAGAACCAATTCTGGATGACTAGGAC
Found at i:3351779 original size:65 final size:64
Alignment explanation
Indices: 3351599--3351873 Score: 198
Period size: 66 Copynumber: 4.2 Consensus size: 64
3351589 AACTTGAATA
* * * ** * * * * * * *
3351599 AAAAAGGGTTGGCTAGGATAAAACCATACGAACCAACTTGGGGTGACTAAGGTAAAACTTGAGGC
1 AAAAAGGGTTGGCCAAGACAAAACCATATAAACCAA-TTTGGATGACTAGGGCAAAACCTAAGTC
* * ** ** * *
3351664 AAAATAAGGTTAGCTGAGACAAAACCATGCAAACCATATTTGGATGACTAGGACAAAACCTAAGA
1 AAAA-AGGGTTGGCCAAGACAAAACCATATAAACCA-ATTTGGATGACTAGGGCAAAACCTAAGT
3351729 C
64 C
* * *
3351730 AAAATGGGGTTGGCCGAGAC-AAACCATA-AGAACCAATTCTGGATGACTAGGGCAAAACTTAAG
1 AAAA-AGGGTTGGCCAAGACAAAACCATATA-AACCAATT-TGGATGACTAGGGCAAAACCTAAG
*
3351793 TTG
63 -TC
* *
3351796 AAAACA-GGTTGGCCAAGACAAAACCATATAAACCAATTAAGGGTGACTAGGGC-AAACCTAAGT
1 AAAA-AGGGTTGGCCAAGACAAAACCATATAAACCAATT-TGGATGACTAGGGCAAAACCTAAGT
3351859 C
64 C
3351860 AAAAAAGGGTTGGC
1 -AAAAAGGGTTGGC
3351874 TAGGATGATA
Statistics
Matches: 169, Mismatches: 32, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
64 6 0.04
65 69 0.41
66 92 0.54
67 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (64 bp):
AAAAAGGGTTGGCCAAGACAAAACCATATAAACCAATTTGGATGACTAGGGCAAAACCTAAGTC
Found at i:3351845 original size:66 final size:65
Alignment explanation
Indices: 3351737--3352061 Score: 189
Period size: 66 Copynumber: 5.0 Consensus size: 65
3351727 GACAAAATGG
* ** * **
3351737 GGTTGGCCGAGAC-AAACCATA-AGAACCAATTCTGGATGACTAGGGCAAAACTTAAGTTGAAAA
1 GGTTGGCCAAGACGAAACCATATA-AACCAATTAAGGGTGACTAGGGCAAAACTTAAGTAAAAAA
3351800 C
65 C
* *
3351801 AGGTTGGCCAAGACAAAACCATATAAACCAATTAAGGGTGACTAGGGC-AAACCTAAGTCAAAAA
1 -GGTTGGCCAAGACGAAACCATATAAACCAATTAAGGGTGACTAGGGCAAAACTTAAGT-AAAAA
*
3351865 AG
64 AC
* * * * * * * * * *
3351867 GGTTGGCTAGGATGATACCATACAAACCAACTAAGGGTGAATAGTATG-AAATC-TGAGTAAAAA
1 GGTTGGCCAAGACGAAACCATATAAACCAATTAAGGGTGACTAG--GGCAAAACTTAAGT-AAAA
3351930 AAC
63 AAC
* * *** * * * *
3351933 GATTAGTTGAGATGAAACCATATAAACCAACTTTA-GGTGACTAGGGTAAAACTTGAGTTAAAAG
1 GGTTGGCCAAGACGAAACCATATAAACCAA-TTAAGGGTGACTAGGGCAAAACTTAAG-TAAAA-
*
3351997 GA-
63 AAC
* * * * * *
3351999 GGTTGGCCAGGACTAAACCATATAAACCAACTAAGGGTGAAC-AAGGCAAAACTTGAGTCAAAA
1 GGTTGGCCAAGACGAAACCATATAAACCAATTAAGGGTG-ACTAGGGCAAAACTTAAGTAAAAA
3352062 TGGGTTGGAC
Statistics
Matches: 199, Mismatches: 48, Indels: 27
0.73 0.18 0.10
Matches are distributed among these distances:
64 1 0.01
65 67 0.34
66 120 0.60
67 11 0.06
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.19
Consensus pattern (65 bp):
GGTTGGCCAAGACGAAACCATATAAACCAATTAAGGGTGACTAGGGCAAAACTTAAGTAAAAAAC
Found at i:3351887 original size:131 final size:132
Alignment explanation
Indices: 3351580--3351898 Score: 296
Period size: 131 Copynumber: 2.4 Consensus size: 132
3351570 AAAGGGTTGG
* * * * *
3351580 CTAGGACAAAACTTGA-ATAAAAAAGGGTTGGCTAGGATAAAACCATACGAACCAACTTGGGGTG
1 CTAGGACAAAACCTAAGACAAAAAAGGGTTGGCTAGGATAAAACCATAAGAACCAACTTGGGATG
* * ** * *
3351644 ACTAAGGTAAAACTTGAGGCAAAATAAGGTTAGCTGAGACAAAACCATGCAAACCATATTTGGAT
66 ACTAAGGCAAAACTTAAGGCAAAATAAGGTTAGCCAAGACAAAACCATACAAACCATATTAGGAT
3351709 GA
131 GA
** * * *
3351711 CTAGGACAAAACCTAAGACAAAATGGGGTTGGC-CGAGA-CAAACCATAAGAACCAA-TTCTGGA
1 CTAGGACAAAACCTAAGACAAAAAAGGGTTGGCTAG-GATAAAACCATAAGAACCAACTT-GGGA
* * * *
3351773 TGACTAGGGCAAAACTTAAGTTG-AAAA-CAGGTTGGCCAAGACAAAACCATATAAACCA-ATTA
64 TGACTAAGGCAAAACTTAAG--GCAAAATAAGGTTAGCCAAGACAAAACCATACAAACCATATT-
*
3351835 AGGGTGA
126 AGGATGA
* * * *
3351842 CTAGGGC-AAACCTAAGTCAAAAAAGGGTTGGCTAGGATGATACCATACA-AACCAACT
1 CTAGGACAAAACCTAAGACAAAAAAGGGTTGGCTAGGATAAAACCATA-AGAACCAACT
3351899 AAGGGTGAAT
Statistics
Matches: 150, Mismatches: 28, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
130 29 0.19
131 99 0.66
132 21 0.14
133 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (132 bp):
CTAGGACAAAACCTAAGACAAAAAAGGGTTGGCTAGGATAAAACCATAAGAACCAACTTGGGATG
ACTAAGGCAAAACTTAAGGCAAAATAAGGTTAGCCAAGACAAAACCATACAAACCATATTAGGAT
GA
Found at i:3352056 original size:132 final size:130
Alignment explanation
Indices: 3351816--3352061 Score: 284
Period size: 132 Copynumber: 1.9 Consensus size: 130
3351806 GGCCAAGACA
* *
3351816 AAACCATATAAACCAATTAAGGGTGACTAGGGCAAACCTAAGTCAAAAAAGGGTTGGCTAGGATG
1 AAACCATATAAACCAATTAAGGGTGACTAGGGAAAACCTAAGTCAAAAAAGGGTTGGCCAGGATG
* * * *
3351881 ATACCATACAAACCAACTAAGGGTGAATAGTATGAAATCTGAGTAAAAAAACGATTAGTTGAGAT
66 AAACCATACAAACCAACTAAGGGTGAACAG-AGGAAAACTGAGTAAAAAAACGATTAGTTGAGAT
3351946 G
130 G
* * * * *
3351947 AAACCATATAAACCAACTTTA-GGTGACTAGGGTAAAACTTGAGT-TAAAAGGAGGTTGGCCAGG
1 AAACCATATAAACCAA-TTAAGGGTGACTAGGG-AAAACCTAAGTCAAAAAAG-GGTTGGCCAGG
* *
3352010 ACT-AAACCATATAAACCAACTAAGGGTGAACA-AGGCAAAACTTGAGTCAAAA
63 A-TGAAACCATACAAACCAACTAAGGGTGAACAGAGG-AAAAC-TGAGTAAAAA
3352062 TGGGTTGGAC
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
130 2 0.02
131 36 0.38
132 57 0.59
133 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (130 bp):
AAACCATATAAACCAATTAAGGGTGACTAGGGAAAACCTAAGTCAAAAAAGGGTTGGCCAGGATG
AAACCATACAAACCAACTAAGGGTGAACAGAGGAAAACTGAGTAAAAAAACGATTAGTTGAGATG
Found at i:3352159 original size:197 final size:197
Alignment explanation
Indices: 3351773--3352159 Score: 419
Period size: 197 Copynumber: 2.0 Consensus size: 197
3351763 CAATTCTGGA
*
3351773 TGACTAGGGCAAAACTTAAGTTGAAAACAGGTTGGCCAAGACAAAACCATATAAACCAATTAAGG
1 TGACTAGGGCAAAACTTAAGTTGAAAACAGGTTGGCCAAGACAAAACCATATAAACCAACTAAGG
* ** * *
3351838 GTGACTAGGGCAAACCTAAGTCAAAAAAGGGTTGGCTAGGATGATACCATACAAACCAACTAAGG
66 GTGACTAAGGCAAACCTAAGTCAAAAAAGGGTTGGCTAACATAAAACCATACAAACCAACTAAGG
* * * ** ** *
3351903 GTGAATAGTATGAAATCTGAGTAAAAAAACGATTAGTTGAGATGAAACCATATAAACCAACTTTA
131 GTGAATAGGATGAAACCTAAGTAAAAAAACGATTAGTCAAGACAAAACCATACAAACCAACTTTA
3351968 GG
196 GG
* * * * *
3351970 TGACTAGGGTAAAACTTGAGTT-AAAAGGAGGTTGGCCAGGACTAAACCATATAAACCAACTAAG
1 TGACTAGGGCAAAACTTAAGTTGAAAA-CAGGTTGGCCAAGACAAAACCATATAAACCAACTAAG
* * * * *
3352034 GGTGAAC-AAGGCAAAACTTGAGTC-AAAATGGGTTGGAC-AACATAAAACCTTACGAACCAACT
65 GGTG-ACTAAGGC-AAACCTAAGTCAAAAAAGGGTTGG-CTAACATAAAACCATACAAACCAACT
* * *
3352096 AAGGGTGACA-AGGATGAAACCTAAGTCAAAAAAGA-GTTTA-TCAAGGCAAAACTATACAAACC
127 AAGGGTGA-ATAGGATGAAACCTAAGT-AAAAAA-ACGATTAGTCAAGACAAAACCATACAAACC
3352158 AA
189 AA
3352160 TTAAGGTTGA
Statistics
Matches: 156, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
196 4 0.03
197 128 0.82
198 23 0.15
199 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (197 bp):
TGACTAGGGCAAAACTTAAGTTGAAAACAGGTTGGCCAAGACAAAACCATATAAACCAACTAAGG
GTGACTAAGGCAAACCTAAGTCAAAAAAGGGTTGGCTAACATAAAACCATACAAACCAACTAAGG
GTGAATAGGATGAAACCTAAGTAAAAAAACGATTAGTCAAGACAAAACCATACAAACCAACTTTA
GG
Found at i:3352751 original size:10 final size:10
Alignment explanation
Indices: 3352736--3352768 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3352726 AATGCTTGGA
*
3352736 TTTCTTGATG
1 TTTCTTGTTG
3352746 TTTCTTGTTG
1 TTTCTTGTTG
3352756 TTTCTTGTTG
1 TTTCTTGTTG
3352766 TTT
1 TTT
3352769 TTCAGCTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.03, C:0.09, G:0.18, T:0.70
Consensus pattern (10 bp):
TTTCTTGTTG
Found at i:3353108 original size:33 final size:32
Alignment explanation
Indices: 3353048--3353111 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
3353038 CAATTAAGTG
*
3353048 TGTATCGATACTAAGAACATGTATCGATACAA
1 TGTATCGATACAAAGAACATGTATCGATACAA
* *
3353080 TGTATTGATACAAAGCAATATGTATCGATACA
1 TGTATCGATACAAAG-AACATGTATCGATACA
3353112 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAA
Found at i:3362256 original size:20 final size:20
Alignment explanation
Indices: 3362231--3362280 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
3362221 AATTAGTAAA
3362231 GAGGCAAATGTACTCAAAAC
1 GAGGCAAATGTACTCAAAAC
*
3362251 GAGGCAAATGTACTCAAAAT
1 GAGGCAAATGTACTCAAAAC
3362271 GAGGCAAATG
1 GAGGCAAATG
3362281 CCAATATCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (20 bp):
GAGGCAAATGTACTCAAAAC
Found at i:3364815 original size:21 final size:21
Alignment explanation
Indices: 3364775--3364815 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3364765 AACATGTCAT
*
3364775 AAATGCATGAAGCGTAGCTTA
1 AAATGCATGAAGCATAGCTTA
* *
3364796 AAATGCATGAATCATGGCTT
1 AAATGCATGAAGCATAGCTT
3364816 GTTAACATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (21 bp):
AAATGCATGAAGCATAGCTTA
Found at i:3365727 original size:52 final size:51
Alignment explanation
Indices: 3365649--3365797 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
3365639 CGAAATATGA
3365649 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
3365701 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
3365753 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
3365798 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:3365804 original size:13 final size:13
Alignment explanation
Indices: 3365786--3365810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3365776 CAAAGATCAG
3365786 TGTATCGATACAA
1 TGTATCGATACAA
3365799 TGTATCGATACA
1 TGTATCGATACA
3365811 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3365888 original size:33 final size:33
Alignment explanation
Indices: 3365851--3365917 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3365841 AGTAGCTTAA
3365851 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3365884 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3365917 A
1 A
3365918 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3365891 original size:13 final size:13
Alignment explanation
Indices: 3365873--3365897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3365863 CAAAAAAATA
3365873 TGTATCGATACAT
1 TGTATCGATACAT
3365886 TGTATCGATACA
1 TGTATCGATACA
3365898 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3369776 original size:95 final size:92
Alignment explanation
Indices: 3369668--3369858 Score: 274
Period size: 95 Copynumber: 2.0 Consensus size: 92
3369658 TGAATTTTGA
* * *
3369668 TTTTTATTTGGTTCTAATGTTTGATATTCAATTATATTTCCCATATATAATATTTAATAGAATAA
1 TTTTTATTCGGTTCCAATGTTTGATATTCAATTATATTTCCCATATATAATATTTAAT--AACAA
**
3369733 ATTTATTATTTCGTGGGAGAAAACCAAGTT
64 ATTTATTATTTC-TAAGAGAAAACCAAGTT
* * *
3369763 TTTTTATTCGGTTCCATTGTTTGCTATTCAATTATATTTCTCATATATAATATTTAATAACAAAT
1 TTTTTATTCGGTTCCAATGTTTGATATTCAATTATATTTCCCATATATAATATTTAATAACAAAT
*
3369828 TTATTATTTCTAAGAGAAAATCAAGTT
66 TTATTATTTCTAAGAGAAAACCAAGTT
3369855 TTTT
1 TTTT
3369859 AATATTTTTG
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
92 18 0.21
93 16 0.18
95 53 0.61
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (92 bp):
TTTTTATTCGGTTCCAATGTTTGATATTCAATTATATTTCCCATATATAATATTTAATAACAAAT
TTATTATTTCTAAGAGAAAACCAAGTT
Found at i:3372170 original size:25 final size:24
Alignment explanation
Indices: 3372121--3372170 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
3372111 TAAAAAAATT
* *
3372121 AAAATTGAAATTAATAATTATAAA
1 AAAATTGAAATAAATAATGATAAA
3372145 AAAATTGGAAATGAAATAATGA-AAA
1 AAAATT-GAAAT-AAATAATGATAAA
3372170 A
1 A
3372171 TATCTTGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 6 0.27
25 9 0.41
26 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (24 bp):
AAAATTGAAATAAATAATGATAAA
Found at i:3376509 original size:33 final size:33
Alignment explanation
Indices: 3376467--3376530 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
3376457 AAATTCCCAG
3376467 ATGTATCGATACAAAG-ATCAATGTATCAATAAA
1 ATGTATCGATACAAAGAAT-AATGTATCAATAAA
**
3376500 ATGTATCGATACATTGAATAATGTATCAATA
1 ATGTATCGATACAAAGAATAATGTATCAATA
3376531 CATTTCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCAATAAA
Found at i:3377472 original size:66 final size:66
Alignment explanation
Indices: 3377399--3377525 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
3377389 CGACTGAGGG
** * * * * *
3377399 TGACAAAGGTGAAATCTGAGTCGAAAAAGG-GTTGGCTAAGATGAAACCATATGAAACAACTTTG
1 TGACAAAGGCAAAACCTGAGTAG-AAAAGGAGTTAGCTAAGATCAAACAATATGAAACAACTTTG
3377463 GA
65 GA
* *
3377465 TGACAAAGGCAAAACCTGAGTAGAAAAGGAGTTAGCTAGGATCAAACAATATGAACCAACT
1 TGACAAAGGCAAAACCTGAGTAGAAAAGGAGTTAGCTAAGATCAAACAATATGAAACAACT
3377526 AAGGGTGACC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 6 0.12
66 45 0.88
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (66 bp):
TGACAAAGGCAAAACCTGAGTAGAAAAGGAGTTAGCTAAGATCAAACAATATGAAACAACTTTGG
A
Found at i:3380935 original size:31 final size:31
Alignment explanation
Indices: 3380874--3380974 Score: 166
Period size: 31 Copynumber: 3.2 Consensus size: 31
3380864 AGCTTCATAG
3380874 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATAC-AAACTTATGTAT
* * *
3380906 CGATGCATTATATCGATACAAACTAATGTAT
1 CGATACATTGTATCGATACAAACTTATGTAT
3380937 CGATACATTGTATCGATACAAACTTATGTAT
1 CGATACATTGTATCGATACAAACTTATGTAT
3380968 CGATACA
1 CGATACA
3380975 ATTACGGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
31 46 0.73
32 17 0.27
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.33
Consensus pattern (31 bp):
CGATACATTGTATCGATACAAACTTATGTAT
Found at i:3380950 original size:13 final size:13
Alignment explanation
Indices: 3380932--3380956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3380922 TACAAACTAA
3380932 TGTATCGATACAT
1 TGTATCGATACAT
3380945 TGTATCGATACA
1 TGTATCGATACA
3380957 AACTTATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3380989 original size:21 final size:17
Alignment explanation
Indices: 3380881--3380997 Score: 79
Period size: 18 Copynumber: 6.9 Consensus size: 17
3380871 TAGCGATACA
3380881 TTGTATCGATACAAAACT
1 TTGTATCGATAC-AAACT
*
3380899 TATGTATCGATGC--A--
1 T-TGTATCGATACAAACT
*
3380913 TTATATCGATACAAACT
1 TTGTATCGATACAAACT
*
3380930 AATGTATCGATAC--A--
1 -TTGTATCGATACAAACT
3380944 TTGTATCGATACAAACT
1 TTGTATCGATACAAACT
3380961 TATGTATCGATACAATTACGGT
1 T-TGTATCGATACAA--AC--T
3380983 TTGTATCGATACAAA
1 TTGTATCGATACAAA
3380998 TTGTTGAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 29
0.69 0.05 0.26
Matches are distributed among these distances:
13 20 0.26
14 1 0.01
15 2 0.03
16 2 0.03
17 1 0.01
18 24 0.31
19 11 0.14
20 2 0.03
21 13 0.17
22 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (17 bp):
TTGTATCGATACAAACT
Found at i:3381905 original size:49 final size:49
Alignment explanation
Indices: 3381747--3382373 Score: 517
Period size: 43 Copynumber: 13.6 Consensus size: 49
3381737 GCTAGTGTGT
* * * *
3381747 TGATTCATGGCCAACGACATTGGGTTTTAAGGACAAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCGACATT-GGTCTTAAAGACAAAGGTGCCAATATGC
* * * * * *
3381797 TGATTCAAAGCTAGTGATATTGGACTT------AAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
* * *
3381840 TGATTCAATGCCAGCGACATTGGTTTTAAAGACAAAAGTGCCAATATGC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
* * * * * *
3381889 TGATTCAAGGCTAGCGATATTGGACTT------AAAGGTGTCGATGTGC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
* *
3381932 TGATTCAAGGCCAGCGACATTAGTCTTAAAGACAAAGGTGCCAATATAC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
* * * *
3381981 TGATTCAAGGCCAACGATATTGGACTT------AAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
*
3382024 TAATTCAAGGCCAGCGACATTGGTC-T----ACAAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
* * * * * *
3382068 TGATTTAAGGCCAGCGATATTAGAC-T---G--AAAGGTGCTAATGTGC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
3382111 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
* * ** *
3382160 TGATTCAAGGCCAGCGATATTGGACTT------AAAGGTGCTGATGTGC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
* * *
3382203 TAATTCAAGGCCAGTGACATTGGTCTTAAAGACAAAGGTGCTAATATGC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
* * *
3382252 TGATTCAAGGCCAGCGATATTGGACTT------AAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
* * *
3382295 TAATTCAAGGCCAACGACATTAGTCTTAAAGACAAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
* * *
3382344 TGATTCAAGGCCAACGATATTGGACTTAAA
1 TGATTCAAGGCCAGCGACATTGGTCTTAAA
3382374 AGAAAATGCC
Statistics
Matches: 459, Mismatches: 85, Indels: 67
0.75 0.14 0.11
Matches are distributed among these distances:
42 1 0.00
43 213 0.46
44 37 0.08
47 1 0.00
49 192 0.42
50 15 0.03
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (49 bp):
TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGC
Found at i:3381908 original size:92 final size:92
Alignment explanation
Indices: 3381742--3382373 Score: 941
Period size: 92 Copynumber: 6.9 Consensus size: 92
3381732 AGAATGCTAG
* * * * * *
3381742 TGTGTTGATTCATGGCCAACGACATTGGGTTTTAAGGACAAAGGTGCCAATATGCTGATTCAAAG
1 TGTGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGG
* *
3381807 CTAGTGATATTGGACTTAAAGGTGCCAA
65 CCAGCGATATTGGACTTAAAGGTGCCAA
* * *
3381835 TGTGCTGATTCAATGCCAGCGACATTGGTTTTAAAGACAAAAGTGCCAATATGCTGATTCAAGGC
1 TGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGC
* * *
3381900 TAGCGATATTGGACTTAAAGGTGTCGA
66 CAGCGATATTGGACTTAAAGGTGCCAA
* *
3381927 TGTGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGACAAAGGTGCCAATATACTGATTCAAGGC
1 TGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGC
*
3381992 CAACGATATTGGACTTAAAGGTGCCAA
66 CAGCGATATTGGACTTAAAGGTGCCAA
* *
3382019 TGTGCTAATTCAAGGCCAGCGACATTGGTC-T----ACAAAGGTGCCAATATGCTGATTTAAGGC
1 TGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGC
* * *
3382079 CAGCGATATTAGACTGAAAGGTGCTAA
66 CAGCGATATTGGACTTAAAGGTGCCAA
3382106 TGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGC
1 TGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGC
**
3382171 CAGCGATATTGGACTTAAAGGTGCTGA
66 CAGCGATATTGGACTTAAAGGTGCCAA
* * *
3382198 TGTGCTAATTCAAGGCCAGTGACATTGGTCTTAAAGACAAAGGTGCTAATATGCTGATTCAAGGC
1 TGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGC
3382263 CAGCGATATTGGACTTAAAGGTGCCAA
66 CAGCGATATTGGACTTAAAGGTGCCAA
* * *
3382290 TGTGCTAATTCAAGGCCAACGACATTAGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGC
1 TGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGC
*
3382355 CAACGATATTGGACTTAAA
66 CAGCGATATTGGACTTAAA
3382374 AGAAAATGCC
Statistics
Matches: 492, Mismatches: 42, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
87 79 0.16
88 1 0.00
91 1 0.00
92 389 0.79
93 22 0.04
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (92 bp):
TGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGC
CAGCGATATTGGACTTAAAGGTGCCAA
Found at i:3382262 original size:271 final size:273
Alignment explanation
Indices: 3381779--3382369 Score: 945
Period size: 271 Copynumber: 2.2 Consensus size: 273
3381769 GGTTTTAAGG
* * * *
3381779 ACAAAGGTGCCAATATGCTGATTCAAAGCTAGTGATATTGGACTTAAAGGTGCCAATGTGCTGAT
1 ACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTGAAAGGTGCCAATGTGCTGAT
* * *
3381844 TCAATGCCAGCGACATTGGTTTTAAAGACAAAAGTGCCAATATGCTGATTCAAGGCTAGCGATAT
66 TCAAGGCCAGCGACATTGGTCTTAAAGACAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATAT
*
3381909 TGGACTTAAAGGTGTCGATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGACAAAGGTGCC
131 TGGACTTAAAGGTGTCGATGTGCTAATTCAAGGCCAGCGACATTAGTCTTAAAGACAAAGGTGCC
*
3381974 AATATACTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCAGC
196 AATATACTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCAAC
*
3382039 GACATTGGTC-T-
261 GACATTAGTCTTA
* * *
3382050 ACAAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTAGACTGAAAGGTGCTAATGTGCTGAT
1 ACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTGAAAGGTGCCAATGTGCTGAT
*
3382115 TCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
66 TCAAGGCCAGCGACATTGGTCTTAAAGACAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATAT
* *
3382180 TGGACTTAAAGGTG-CTGATGTGCTAATTCAAGGCCAGTGACATTGGTCTTAAAGACAAAGGTGC
131 TGGACTTAAAGGTGTC-GATGTGCTAATTCAAGGCCAGCGACATTAGTCTTAAAGACAAAGGTGC
* * *
3382244 TAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCAA
195 CAATATACTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCAA
3382309 CGACATTAGTCTTAAA
260 CGACATTAGTCTT--A
*
3382325 GACAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACT
1 -ACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
3382370 TAAAAGAAAA
Statistics
Matches: 292, Mismatches: 22, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
270 1 0.00
271 249 0.85
272 1 0.00
276 41 0.14
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (273 bp):
ACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTGAAAGGTGCCAATGTGCTGAT
TCAAGGCCAGCGACATTGGTCTTAAAGACAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATAT
TGGACTTAAAGGTGTCGATGTGCTAATTCAAGGCCAGCGACATTAGTCTTAAAGACAAAGGTGCC
AATATACTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCAAC
GACATTAGTCTTA
Found at i:3382496 original size:34 final size:34
Alignment explanation
Indices: 3382401--3382508 Score: 103
Period size: 34 Copynumber: 3.2 Consensus size: 34
3382391 TGTGTGGGCT
* * * *
3382401 TTTGAAAAGGAGAAAGATGCCACAGAGTTGTGGAC
1 TTTGAAAA-GAAAAAGGTGCCACAAAGTTATGGAC
* * * *
3382436 -TT-AAAGGGAACAAGGTGTCACGAAGTTATGGAC
1 TTTGAAA-AGAAAAAGGTGCCACAAAGTTATGGAC
*
3382469 TTTGAAAAGAAAAAGGTGCCACAAAGTTATGGGC
1 TTTGAAAAGAAAAAGGTGCCACAAAGTTATGGAC
3382503 TTTGAA
1 TTTGAA
3382509 GAAAAGATGC
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
33 22 0.39
34 32 0.56
35 3 0.05
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.22
Consensus pattern (34 bp):
TTTGAAAAGAAAAAGGTGCCACAAAGTTATGGAC
Found at i:3382589 original size:33 final size:33
Alignment explanation
Indices: 3382459--3382675 Score: 202
Period size: 33 Copynumber: 6.8 Consensus size: 33
3382449 GGTGTCACGA
* * **
3382459 AGTTATGGACTTTGAAAAGAAAA-AGGTGCCACAA
1 AGTTGTGGACTTTG--AAGAAAAGAGATGCCACTG
* * *
3382493 AGTTATGGGCTTTGAAG-AAA-AGATGCAACTG
1 AGTTGTGGACTTTGAAGAAAAGAGATGCCACTG
*
3382524 AGTCGTGGACTTT---GAAAAGAGATTGCCACTG
1 AGTTGTGGACTTTGAAGAAAAGAGA-TGCCACTG
3382555 AGTTGTGGACTTTGAAGAAAAGAGATGCCACTG
1 AGTTGTGGACTTTGAAGAAAAGAGATGCCACTG
* * *
3382588 AGTCGTGGACTTTG-AG-AGA-AGATGCCATTG
1 AGTTGTGGACTTTGAAGAAAAGAGATGCCACTG
** *
3382618 AGTCATGGACTTTGAAGAAAAGAGATGCCATTG
1 AGTTGTGGACTTTGAAGAAAAGAGATGCCACTG
*
3382651 AGTTGTGGACTTTG-AGAAGAGAGAT
1 AGTTGTGGACTTTGAAGAAAAGAGAT
3382676 TTGAAGAATT
Statistics
Matches: 156, Mismatches: 18, Indels: 20
0.80 0.09 0.10
Matches are distributed among these distances:
28 1 0.01
29 3 0.02
30 26 0.17
31 43 0.28
32 17 0.11
33 44 0.28
34 22 0.14
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (33 bp):
AGTTGTGGACTTTGAAGAAAAGAGATGCCACTG
Found at i:3382637 original size:63 final size:65
Alignment explanation
Indices: 3382497--3382676 Score: 244
Period size: 63 Copynumber: 2.8 Consensus size: 65
3382487 CCACAAAGTT
* * *
3382497 ATGGGCTTTGAAG-AAA-AGATGCAACTGAGTCGTGGACTTTGA-AAAGAGATTGCCACTGAGTT
1 ATGGACTTTGAAGAAAAGAGATGCCACTGAGTCGTGGACTTTGAGAAAGAGATTGCCACTGAGTC
* * *
3382559 GTGGACTTTGAAGAAAAGAGATGCCACTGAGTCGTGGACTTTGAGAGA-AGA-TGCCATTGAGTC
1 ATGGACTTTGAAGAAAAGAGATGCCACTGAGTCGTGGACTTTGAGAAAGAGATTGCCACTGAGTC
* *
3382622 ATGGACTTTGAAGAAAAGAGATGCCATTGAGTTGTGGACTTTGAGAAGAGAGATT
1 ATGGACTTTGAAGAAAAGAGATGCCACTGAGTCGTGGACTTTGAGAA-AGAGATT
3382677 TGAAGAATTG
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
62 11 0.11
63 56 0.55
64 29 0.28
65 5 0.05
66 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.31, T:0.26
Consensus pattern (65 bp):
ATGGACTTTGAAGAAAAGAGATGCCACTGAGTCGTGGACTTTGAGAAAGAGATTGCCACTGAGTC
Found at i:3383948 original size:13 final size:13
Alignment explanation
Indices: 3383932--3383971 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
3383922 TGCCTTTGCA
3383932 TTTTTTTTGTGTT
1 TTTTTTTTGTGTT
3383945 TTTTTTTCT-TGTT
1 TTTTTTT-TGTGTT
*
3383958 TTGTTTTTGTGTT
1 TTTTTTTTGTGTT
3383971 T
1 T
3383972 ACTTTTGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (13 bp):
TTTTTTTTGTGTT
Found at i:3384655 original size:15 final size:15
Alignment explanation
Indices: 3384635--3384666 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3384625 CCTACATGCC
3384635 GTCGGGCAAAGGCAA
1 GTCGGGCAAAGGCAA
3384650 GTCGGGCAAAGGCAA
1 GTCGGGCAAAGGCAA
3384665 GT
1 GT
3384667 AGGTTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.41, T:0.09
Consensus pattern (15 bp):
GTCGGGCAAAGGCAA
Found at i:3389228 original size:29 final size:29
Alignment explanation
Indices: 3389186--3389243 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3389176 ACCAACTTGG
**
3389186 GGTGACCAAGGCAAAACTTGAGTCGAAAA
1 GGTGACCAAGGCAAAACTAAAGTCGAAAA
* *
3389215 GGTGACTAGGGCAAAACTAAAGTCGAAAA
1 GGTGACCAAGGCAAAACTAAAGTCGAAAA
3389244 AGGGTTGGCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.28, T:0.14
Consensus pattern (29 bp):
GGTGACCAAGGCAAAACTAAAGTCGAAAA
Found at i:3389345 original size:64 final size:65
Alignment explanation
Indices: 3389215--3389347 Score: 153
Period size: 66 Copynumber: 2.0 Consensus size: 65
3389205 GAGTCGAAAA
* * *
3389215 GGTGACTAGGGCAAAACTAAAGTCGAAAAAGGGTTGGCCAGGATGAAACCATACGAACTAAATTT
1 GGTGACTAGGGCAAAACTAAAGTCAAAAAAGGGTT-GACAGGATGAAACCATACGAACCAAATTT
3389280 G
65 G
** * * * *
3389281 GGTGACTAGGGCAAAACTTGAG-CAAAAAAAGGGTT-ACTGGATGAAACCATGCGAGCCAACTTT
1 GGTGACTAGGGCAAAACTAAAGTC-AAAAAAGGGTTGACAGGATGAAACCATACGAACCAAATTT
3389344 G
65 G
3389345 GGT
1 GGT
3389348 AACCAGGGGA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
64 26 0.46
65 1 0.02
66 30 0.53
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.19
Consensus pattern (65 bp):
GGTGACTAGGGCAAAACTAAAGTCAAAAAAGGGTTGACAGGATGAAACCATACGAACCAAATTTG
Found at i:3389969 original size:60 final size:60
Alignment explanation
Indices: 3389876--3390094 Score: 210
Period size: 60 Copynumber: 3.6 Consensus size: 60
3389866 GGCCGGCATG
* * * * *
3389876 AAACCAAAAACCTAAACAATGGCTTAGGTGAAACCAAGACTCAATGAAATAGCAAGGATA
1 AAACCAGAAACCTAAATAATGACTTAGGTGAAACTAAGACTCAATGAAATAGCATGGATA
* * * * **
3389936 AAACCAGAAACCTAAATAATGACTTGGGTGAAACTAAGACTTAACT-AAATGGCTTGGACG
1 AAACCAGAAACCTAAATAATGACTTAGGTGAAACTAAGACTCAA-TGAAATAGCATGGATA
* * * *
3389996 AAACCA-AAATCCTAAATAATGACTTTGG-CAAAGCTAAGACTCAATGAAATAGCCTTGATA
1 AAACCAGAAA-CCTAAATAATGACTTAGGTGAAA-CTAAGACTCAATGAAATAGCATGGATA
* * * **
3390056 AAACTAGAAACCTAAATAATAACTTCGGCAAAACTAAGA
1 AAACCAGAAACCTAAATAATGACTTAGGTGAAACTAAGA
3390095 ATTGGGAAAA
Statistics
Matches: 130, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
59 7 0.05
60 116 0.89
61 7 0.05
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.20
Consensus pattern (60 bp):
AAACCAGAAACCTAAATAATGACTTAGGTGAAACTAAGACTCAATGAAATAGCATGGATA
Found at i:3390090 original size:120 final size:120
Alignment explanation
Indices: 3389875--3390094 Score: 298
Period size: 120 Copynumber: 1.8 Consensus size: 120
3389865 TGGCCGGCAT
* *
3389875 GAAACCAAAAACCTAAACAATGGCTTAGGTGAAACCAAGACTCAATGAAATAGCAAGGATAAAAC
1 GAAACCAAAAACCTAAACAATGACTTAGGTCAAACCAAGACTCAATGAAATAGCAAGGATAAAAC
* * **
3389940 CAGAAACCTAAATAATGACTTGGGTGAAACTAAGACTTAACTAAATGGCTTGGAC
66 CAGAAACCTAAATAATAACTTCGGCAAAACTAAGACTTAACTAAATGGCTTGGAC
* * * * ***
3389995 GAAACCAAAATCCTAAATAATGACTTTGG-CAAAGCTAAGACTCAATGAAATAGCCTTGATAAAA
1 GAAACCAAAAACCTAAACAATGACTTAGGTCAAA-CCAAGACTCAATGAAATAGCAAGGATAAAA
*
3390059 CTAGAAACCTAAATAATAACTTCGGCAAAACTAAGA
65 CCAGAAACCTAAATAATAACTTCGGCAAAACTAAGA
3390095 ATTGGGAAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
119 3 0.04
120 82 0.96
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.20
Consensus pattern (120 bp):
GAAACCAAAAACCTAAACAATGACTTAGGTCAAACCAAGACTCAATGAAATAGCAAGGATAAAAC
CAGAAACCTAAATAATAACTTCGGCAAAACTAAGACTTAACTAAATGGCTTGGAC
Found at i:3390299 original size:110 final size:110
Alignment explanation
Indices: 3390103--3390300 Score: 267
Period size: 110 Copynumber: 1.8 Consensus size: 110
3390093 GAATTGGGAA
* * * **
3390103 AAACCAAGACTCAACTAAATGGCTTGGATGAAATCGAAAGCCTAAACAATGACTTAGGGGAAACT
1 AAACCAAGACTCAACTAAATGGCTTAGATGAAATAGAAAGCCTAAACAATGACATAGGCAAAACT
3390168 AAGACTCAATAAAATGACCTAGAAATCTAAACAATGACTTTGGAG
66 AAGACTCAATAAAATGACCTAGAAATCTAAACAATGACTTTGGAG
* *
3390213 AAACCAAGACTCAACTAAATGGCTTAGATGAAGCTAGAAA-CCTAGACAATGACATAGGCAAAA-
1 AAACCAAGACTCAACTAAATGGCTTAGATGAA-ATAGAAAGCCTAAACAATGACATAGGCAAAAC
* *
3390276 TCATGACTCAA-AGAAATGGCCTAGA
65 T-AAGACTCAATA-AAATGACCTAGA
3390301 TAAAACCAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
109 2 0.03
110 69 0.91
111 5 0.07
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (110 bp):
AAACCAAGACTCAACTAAATGGCTTAGATGAAATAGAAAGCCTAAACAATGACATAGGCAAAACT
AAGACTCAATAAAATGACCTAGAAATCTAAACAATGACTTTGGAG
Found at i:3390322 original size:60 final size:60
Alignment explanation
Indices: 3390258--3390384 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
3390248 AGAAACCTAG
*
3390258 ACAATGACATAGGCAAAATC-ATGACTCAAAGAAATGGCCTAGATAAAACCAAAAA-CTCAA
1 ACAATGACATAGGCAAAATCGA-AACTCAAAGAAATGGCCTAGATAAAACCAAAAATCT-AA
* * * * * * *
3390318 ACAATAACTTTGGCAAAATCGAAACTCAATGCAATGGCTTGGATAAAACCAAAAATCTAA
1 ACAATGACATAGGCAAAATCGAAACTCAAAGAAATGGCCTAGATAAAACCAAAAATCTAA
3390378 A-AATGAC
1 ACAATGAC
3390385 TATATATGAG
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
59 5 0.09
60 48 0.86
61 3 0.05
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.18
Consensus pattern (60 bp):
ACAATGACATAGGCAAAATCGAAACTCAAAGAAATGGCCTAGATAAAACCAAAAATCTAA
Found at i:3390636 original size:82 final size:82
Alignment explanation
Indices: 3390530--3390724 Score: 318
Period size: 82 Copynumber: 2.4 Consensus size: 82
3390520 AATGGAAAAT
* * *
3390530 TTAGTAAAGAGGCAAATGCACATGAAATGATGAAATATCATCTAATGTTGAAGATGTTCATGAAA
1 TTAGCAAATAGGCAAATGCACATGAAATGATGAAATATCATCTAATGTTAAAGATGTTCATGAAA
*
3390595 TGATTCCAATGCAAGTG
66 TGATTCCAATGCAAGTA
*
3390612 TTAGCAAATAGGCAAATGCACATGAAATGATGAAATATCGTCTAATGTTAAAGATGTTCATGAAA
1 TTAGCAAATAGGCAAATGCACATGAAATGATGAAATATCATCTAATGTTAAAGATGTTCATGAAA
*
3390677 TGTTTCCAATGCAAGTA
66 TGATTCCAATGCAAGTA
**
3390694 TTAGCAAATAGGCAAATGCATTTGAAATGAT
1 TTAGCAAATAGGCAAATGCACATGAAATGAT
3390725 ATGAATGCTA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 105 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (82 bp):
TTAGCAAATAGGCAAATGCACATGAAATGATGAAATATCATCTAATGTTAAAGATGTTCATGAAA
TGATTCCAATGCAAGTA
Found at i:3391540 original size:20 final size:20
Alignment explanation
Indices: 3391515--3391568 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3391505 CTACCATTGT
*
3391515 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
3391535 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
*
3391555 TTGTATTGATACAT
1 TTGTATCGATACAT
3391569 TGCTTCTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:3397901 original size:20 final size:20
Alignment explanation
Indices: 3397864--3397902 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3397854 TTACAAATTT
*
3397864 CTTCATTTTTACTTAAAATA
1 CTTCATTTTTACTCAAAATA
3397884 CTTCATTTTTTA-TCAAAAT
1 CTTCA-TTTTTACTCAAAAT
3397903 CACCAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (20 bp):
CTTCATTTTTACTCAAAATA
Found at i:3400366 original size:20 final size:20
Alignment explanation
Indices: 3400341--3400394 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
3400331 TTACCACTAT
3400341 TTGTATCGATACATGAT-ACA
1 TTGTATCGATACATGATGA-A
*
3400361 TTGTATCAATACATGATGAA
1 TTGTATCGATACATGATGAA
3400381 TTGTATCGATACAT
1 TTGTATCGATACAT
3400395 TGCTTCTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:3428984 original size:21 final size:21
Alignment explanation
Indices: 3428954--3429028 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
3428944 TTCTACAATT
*
3428954 TGTATCGATACAAACAGTAAA
1 TGTATCGATACATACAGTAAA
* * *
3428975 TGTATTGATACATGC-CTAAAA
1 TGTATCGATACATACAGT-AAA
3428996 TGTATCGATACATA-AGTAAA
1 TGTATCGATACATACAGTAAA
3429016 TGTATCGATACAT
1 TGTATCGATACAT
3429029 GCTTACAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.38
21 28 0.62
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
TGTATCGATACATACAGTAAA
Found at i:3429026 original size:41 final size:43
Alignment explanation
Indices: 3428954--3429047 Score: 138
Period size: 42 Copynumber: 2.2 Consensus size: 43
3428944 TTCTACAATT
*
3428954 TGTATCGATACAAACAGTAAATGTATTGATACATGCCTA-AAA
1 TGTATCGATACAAACAGTAAATGTATCGATACATGCCTACAAA
* * *
3428996 TGTATCGATACATA-AGTAAATGTATCGATACATGCTTACAAT
1 TGTATCGATACAAACAGTAAATGTATCGATACATGCCTACAAA
3429038 TGTATCGATA
1 TGTATCGATA
3429048 TATTCTGGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
41 22 0.47
42 25 0.53
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (43 bp):
TGTATCGATACAAACAGTAAATGTATCGATACATGCCTACAAA
Found at i:3431016 original size:13 final size:13
Alignment explanation
Indices: 3430998--3431022 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3430988 ACTGAAGTAA
3430998 TGTATCGATACAT
1 TGTATCGATACAT
3431011 TGTATCGATACA
1 TGTATCGATACA
3431023 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3433015 original size:21 final size:21
Alignment explanation
Indices: 3432991--3433032 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3432981 ATCCATTTCT
*
3432991 TCATTTTCATCAATC-TCTTGA
1 TCATCTTCATC-ATCATCTTGA
3433012 TCATCTTCATCATCATCTTGA
1 TCATCTTCATCATCATCTTGA
3433033 ACGATTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.24, C:0.26, G:0.05, T:0.45
Consensus pattern (21 bp):
TCATCTTCATCATCATCTTGA
Found at i:3434163 original size:34 final size:35
Alignment explanation
Indices: 3434125--3434191 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
3434115 CCTTACAACA
3434125 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
3434159 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
3434192 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:3434688 original size:13 final size:13
Alignment explanation
Indices: 3434670--3434695 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3434660 CTATTTATGA
3434670 TGTATCGATACAC
1 TGTATCGATACAC
3434683 TGTATCGATACAC
1 TGTATCGATACAC
3434696 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:3434825 original size:53 final size:53
Alignment explanation
Indices: 3434758--3434894 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
3434748 CTACTTCCAA
3434758 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
3434811 TGTATCAATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
3434864 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
3434895 TATGCAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:3434927 original size:20 final size:20
Alignment explanation
Indices: 3434864--3434934 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3434854 GCCAATGTCC
**
3434864 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
3434884 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
3434904 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
3434924 TGTATCGATAC
1 TGTATCGATAC
3434935 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:3435000 original size:21 final size:21
Alignment explanation
Indices: 3434974--3435014 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3434964 GTCAACCTTG
3434974 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
3434995 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
3435015 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:3442248 original size:22 final size:20
Alignment explanation
Indices: 3442223--3442263 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
3442213 GGTGAATGAC
3442223 TAAATAAACTAAAAAAATAAAT
1 TAAATAAA-T-AAAAAATAAAT
3442245 TAAATAAATAAAAAATAAA
1 TAAATAAATAAAAAATAAA
3442264 AGGTTGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAATAAATAAAAAATAAAT
Found at i:3442891 original size:13 final size:13
Alignment explanation
Indices: 3442873--3442897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3442863 ATTTCGAAAA
3442873 AAAGAAAAAATTT
1 AAAGAAAAAATTT
3442886 AAAGAAAAAATT
1 AAAGAAAAAATT
3442898 CAAATTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
AAAGAAAAAATTT
Found at i:3442971 original size:166 final size:167
Alignment explanation
Indices: 3442503--3442978 Score: 624
Period size: 164 Copynumber: 2.9 Consensus size: 167
3442493 GATTCCCTTA
* * * * ** *
3442503 AAAAAATTTTATGGAGTAGAAAGCTTTGTATTTCGAAAAAAAAGGGGAAATTTTAAGGAAAAAA-
1 AAAAAA-TTTACGGAATAGAAAACTTCGTATTTCG-AAAAAAA-GAAAAAATTTAAGGAAAAAAT
* * *
3442567 TCAAAACTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATATAAAATAAATAATAATATTT
63 TCAAAATTTATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATAATATTT
*
3442632 GATGAATTTTAAAAATAAAAAAACAAGAAAAATTCTCCCG
128 GATGAATTTTAAAAATAAAAAAACAAGAAAAATTCTCCCC
* * * *
3442672 AAAAAATTTACAGAATAGAAAACTCCATATTT---AAAAAA-AAGAAATTTCAAGGAAAAAATTC
1 AAAAAATTTACGGAATAGAAAACTTCGTATTTCGAAAAAAAGAAAAAATTT-AAGGAAAAAATTC
* * *
3442733 AAAATTTAAGAAAATGAATGAATTTTTGGAAACTAAATTAATATGAAATAAATAATAATATTTGA
65 AAAATTTATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATAATATTTGA
*
3442798 TGAATTTTAAAAATCAAAAAACAAGAAAAA-TC-CCCC
130 TGAATTTTAAAAATAAAAAAACAAGAAAAATTCTCCCC
*
3442834 AAAACAATTTACGGAATAGAAAACTTCGTATTTCGAAAAAAAGAAAAAATTTAAAGAAAAAATTC
1 AAAA-AATTTACGGAATAGAAAACTTCGTATTTCGAAAAAAAGAAAAAATTTAAGGAAAAAATTC
* * * * *
3442899 AAATTTTATGGAAATGAATAAAATTTTAAAAAATAAATTAATATGAAATAAATAATAATATTTGA
65 AAAATTTATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATAATATTTGA
3442964 TGAATTTTCAAAAAT
130 TGAATTTT-AAAAAT
3442979 TTTAAACCCA
Statistics
Matches: 267, Mismatches: 32, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
162 12 0.04
163 37 0.14
164 96 0.36
166 83 0.31
167 14 0.05
168 19 0.07
169 6 0.02
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.29
Consensus pattern (167 bp):
AAAAAATTTACGGAATAGAAAACTTCGTATTTCGAAAAAAAGAAAAAATTTAAGGAAAAAATTCA
AAATTTATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATAATATTTGAT
GAATTTTAAAAATAAAAAAACAAGAAAAATTCTCCCC
Found at i:3444875 original size:20 final size:20
Alignment explanation
Indices: 3444850--3444908 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
3444840 AATTGCTTGC
*
3444850 ATGTATCAATACATTGAAGA
1 ATGTATCAATACATTGAAAA
* *
3444870 ATGTATCAATTCAATGAAAA
1 ATGTATCAATACATTGAAAA
*
3444890 ATGTATCTATACATTGAAA
1 ATGTATCAATACATTGAAA
3444909 GCAGGTATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (20 bp):
ATGTATCAATACATTGAAAA
Found at i:3445024 original size:20 final size:20
Alignment explanation
Indices: 3445001--3445054 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3444991 CATTTCAAGA
* *
3445001 ATGTATTGATACATTCACTT
1 ATGTATCGATACATTAACTT
**
3445021 ATGTATCGATGTATTAACTT
1 ATGTATCGATACATTAACTT
3445041 ATTGTATCGATACA
1 A-TGTATCGATACA
3445055 AATTGTAGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTAACTT
Found at i:3445904 original size:13 final size:13
Alignment explanation
Indices: 3445871--3445903 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3445861 CGACTATTCC
3445871 TATTTTTTCTCTT
1 TATTTTTTCTCTT
3445884 TATTTTTTCT-TT
1 TATTTTTTCTCTT
*
3445896 TCTTTTTT
1 TATTTTTT
3445904 TTGGGTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (13 bp):
TATTTTTTCTCTT
Found at i:3450207 original size:21 final size:20
Alignment explanation
Indices: 3450174--3450213 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3450164 GAGGTGTTGG
3450174 ACATACTAAAAATGCATGAA
1 ACATACTAAAAATGCATGAA
* *
3450194 ACATAGCTCAAAATGTATGA
1 ACATA-CTAAAAATGCATGA
3450214 GCATGGGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.23
Consensus pattern (20 bp):
ACATACTAAAAATGCATGAA
Found at i:3451205 original size:50 final size:51
Alignment explanation
Indices: 3451138--3451257 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 51
3451128 ATCGATACAT
* *
3451138 TGAATAATGTATCGATACATCTGGGTAAAATCC-AGAATGTATCAAGACAA
1 TGAATAATGTATTGATACATCTGGGTAAAAACCAAGAATGTATCAAGACAA
* * * *
3451188 TGAAGAATGTATTGATACATTTGGGTAAAAACCAAGAATGTATCGATACAA
1 TGAATAATGTATTGATACATCTGGGTAAAAACCAAGAATGTATCAAGACAA
3451239 TGAATAATGTATTGATACA
1 TGAATAATGTATTGATACA
3451258 AACAGTAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 29 0.47
51 33 0.53
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.28
Consensus pattern (51 bp):
TGAATAATGTATTGATACATCTGGGTAAAAACCAAGAATGTATCAAGACAA
Found at i:3451248 original size:51 final size:50
Alignment explanation
Indices: 3451127--3451257 Score: 190
Period size: 50 Copynumber: 2.6 Consensus size: 50
3451117 TTACCTGCAT
* * *
3451127 TATCGATACATTGAATAATGTATCGATACATCTGGGTAAAATCCAGAATG
1 TATCGATACAATGAATAATGTATTGATACATCTGGGTAAAAACCAGAATG
* * * *
3451177 TATCAAGACAATGAAGAATGTATTGATACATTTGGGTAAAAACCAAGAATG
1 TATCGATACAATGAATAATGTATTGATACATCTGGGTAAAAACC-AGAATG
3451228 TATCGATACAATGAATAATGTATTGATACA
1 TATCGATACAATGAATAATGTATTGATACA
3451258 AACAGTAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
50 37 0.53
51 33 0.47
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (50 bp):
TATCGATACAATGAATAATGTATTGATACATCTGGGTAAAAACCAGAATG
Found at i:3453276 original size:78 final size:78
Alignment explanation
Indices: 3453129--3453278 Score: 196
Period size: 78 Copynumber: 1.9 Consensus size: 78
3453119 ATGAACGAGG
* * *
3453129 AAAAAGAAGGAGAAGAAGGCAATTCTATTTCAGCTGAAGTTGCTAGCAGCAAAGCTCAACAAATA
1 AAAAAGAAGGAGAAGAAAGCAATTCTATTTCAGCTGAAGTTGCGAGCAGCAAAGCTAAACAAATA
3453194 TAGCAAAGATACA
66 TAGCAAAGATACA
* * * * *
3453207 AAAAAGAAGGAGAAGAAAGTAATTTTGTTTTAGCTGAAGTTGCGAGTAGCAAAGC-AAAGCAAA-
1 AAAAAGAAGGAGAAGAAAGCAATTCTATTTCAGCTGAAGTTGCGAGCAGCAAAGCTAAA-CAAAT
3453270 AGTAGCAAA
65 A-TAGCAAA
3453279 CGAAATAGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 3 0.05
78 59 0.95
ACGTcount: A:0.47, C:0.12, G:0.23, T:0.19
Consensus pattern (78 bp):
AAAAAGAAGGAGAAGAAAGCAATTCTATTTCAGCTGAAGTTGCGAGCAGCAAAGCTAAACAAATA
TAGCAAAGATACA
Found at i:3456833 original size:52 final size:52
Alignment explanation
Indices: 3456763--3456883 Score: 217
Period size: 52 Copynumber: 2.3 Consensus size: 52
3456753 GAAAATTTAT
3456763 CTGCATGTATCGATACA-TTTAAAAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTTAAAA-TGTATCGATACATCTGGGCAAATTTGC
*
3456815 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGCAAATTTGC
3456867 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
3456884 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
52 61 0.91
53 6 0.09
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGCAAATTTGC
Found at i:3456896 original size:52 final size:51
Alignment explanation
Indices: 3456763--3456903 Score: 210
Period size: 52 Copynumber: 2.7 Consensus size: 51
3456753 GAAAATTTAT
*
3456763 CTGCATGTATCGATACATTTAAAAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTT-ATAGTGTATCGATACATCTGGGCAAATTTGC
*
3456815 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTTATAGTGTATCGATACATCTGGGCAAATTTGC
***
3456867 CTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAT-AGTGTATCGATACA
3456904 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 76 0.94
53 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTTATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:3456910 original size:13 final size:13
Alignment explanation
Indices: 3456892--3456916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3456882 CAAAGATCAG
3456892 TGTATCGATACAA
1 TGTATCGATACAA
3456905 TGTATCGATACA
1 TGTATCGATACA
3456917 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3457000 original size:13 final size:13
Alignment explanation
Indices: 3456982--3457006 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3456972 TAAAAAAATA
3456982 TGTATCGATACAT
1 TGTATCGATACAT
3456995 TGTATCGATACA
1 TGTATCGATACA
3457007 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3457415 original size:40 final size:40
Alignment explanation
Indices: 3457342--3457731 Score: 286
Period size: 40 Copynumber: 9.8 Consensus size: 40
3457332 CATGGTCAAC
* ** *
3457342 CCTTCCAATCTATTGGCTCCATC-AGTTTCGCCCTGACCAA
1 CCTTCCAATCTGTTGGCTTTATCGA-TTTTGCCCTGACCAA
* *
3457382 CCTTCCAATCTGTTGGTTTTATCGATTTTGCCCTAACCAA
1 CCTTCCAATCTGTTGGCTTTATCGATTTTGCCCTGACCAA
* * * * **
3457422 CTTTCCAATCGGTTGACTTTATCGGTTTTGCCCT-AGTTAA
1 CCTTCCAATCTGTTGGCTTTATCGATTTTGCCCTGA-CCAA
* * * * *
3457462 CTCTTCCAATTTGTTGGCTTTATCAATTTTACCTTGGCCAA
1 C-CTTCCAATCTGTTGGCTTTATCGATTTTGCCCTGACCAA
* * * * * *
3457503 CCTTCTAATTTGTTGGCTTTATCGGTTTCGCCTTGGCCAA
1 CCTTCCAATCTGTTGGCTTTATCGATTTTGCCCTGACCAA
*
3457543 CCTTCCAATCTGTTGGCTTTATCGATTTCGCCCT-AGCCAA
1 CCTTCCAATCTGTTGGCTTTATCGATTTTGCCCTGA-CCAA
* * * * *
3457583 CCTTCAAATCTATTAGTTTTATCGATTTTACCCTGACCAA
1 CCTTCCAATCTGTTGGCTTTATCGATTTTGCCCTGACCAA
* * * * * * * *
3457623 CTTTTCAATCAGTTGACTTTATTGGTTTTGCCTTGGCCAA
1 CCTTCCAATCTGTTGGCTTTATCGATTTTGCCCTGACCAA
* * * * * *
3457663 CCTTTCAATATGTTGGTTTTATCG-GTTTCCCCTGGCCAA
1 CCTTCCAATCTGTTGGCTTTATCGATTTTGCCCTGACCAA
* **
3457702 CCTTCTAAT-TGATTAACTTTATCGATTTTG
1 CCTTCCAATCTG-TTGGCTTTATCGATTTTG
3457732 TCCTAGTCAT
Statistics
Matches: 273, Mismatches: 69, Indels: 16
0.76 0.19 0.04
Matches are distributed among these distances:
38 2 0.01
39 29 0.11
40 212 0.78
41 30 0.11
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.41
Consensus pattern (40 bp):
CCTTCCAATCTGTTGGCTTTATCGATTTTGCCCTGACCAA
Found at i:3457582 original size:80 final size:80
Alignment explanation
Indices: 3457342--3457795 Score: 365
Period size: 80 Copynumber: 5.7 Consensus size: 80
3457332 CATGGTCAAC
* * ** * * *
3457342 CCTTCCAATCTATTGGCTCCATCAGTTTCGCCCTGACCAACCTTCCAATCTGTTGGTTTTATCGA
1 CCTTCAAATCTGTTGGCTTTATCGGTTTCGCCCTGGCCAACCTTCCAATCTGTTGGCTTTATCGA
*
3457407 TTTTGCCCTAACCAA
66 TTTTGCCCTAGCCAA
* * * * * * ** * *
3457422 CTTTCCAATCGGTTGACTTTATCGGTTTTGCCCTAGTTAACTCTTCCAATTTGTTGGCTTTATCA
1 CCTTCAAATCTGTTGGCTTTATCGGTTTCGCCCTGGCCAAC-CTTCCAATCTGTTGGCTTTATCG
* * *
3457487 ATTTTACCTTGGCCAA
65 ATTTTGCCCTAGCCAA
* * *
3457503 CCTTCTAATTTGTTGGCTTTATCGGTTTCGCCTTGGCCAACCTTCCAATCTGTTGGCTTTATCGA
1 CCTTCAAATCTGTTGGCTTTATCGGTTTCGCCCTGGCCAACCTTCCAATCTGTTGGCTTTATCGA
*
3457568 TTTCGCCCTAGCCAA
66 TTTTGCCCTAGCCAA
* * * * ** * * * * * * *
3457583 CCTTCAAATCTATTAGTTTTATCGATTTTACCCTGACCAACTTTTCAATCAGTTGACTTTATTGG
1 CCTTCAAATCTGTTGGCTTTATCGGTTTCGCCCTGGCCAACCTTCCAATCTGTTGGCTTTATCGA
* *
3457648 TTTTGCCTTGGCCAA
66 TTTTGCCCTAGCCAA
* * * **
3457663 CCTTTC-AATATGTTGGTTTTATCGGTTTC-CCCTGGCCAACCTTCTAAT-TGATTAACTTTATC
1 CC-TTCAAATCTGTTGGCTTTATCGGTTTCGCCCTGGCCAACCTTCCAATCTG-TTGGCTTTATC
* * *
3457725 GATTTTGTCCTAGTCATC
64 GATTTTGCCCTAGCCA-A
* * * * **
3457743 CCTTCAAATCCGTTGGCTTTATTGGTTTCGTCATGGCCAACCTTTTAATCTGT
1 CCTTCAAATCTGTTGGCTTTATCGGTTTCGCCCTGGCCAACCTTCCAATCTGT
3457796 CGACTTGTCA
Statistics
Matches: 288, Mismatches: 79, Indels: 13
0.76 0.21 0.03
Matches are distributed among these distances:
78 1 0.00
79 38 0.13
80 164 0.57
81 83 0.29
82 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.41
Consensus pattern (80 bp):
CCTTCAAATCTGTTGGCTTTATCGGTTTCGCCCTGGCCAACCTTCCAATCTGTTGGCTTTATCGA
TTTTGCCCTAGCCAA
Found at i:3457650 original size:120 final size:119
Alignment explanation
Indices: 3457372--3457730 Score: 344
Period size: 120 Copynumber: 3.0 Consensus size: 119
3457362 ATCAGTTTCG
* * ** * * * ** * *
3457372 CCCTGACCAACCTTCCAATCTGTTGGTTTTATCGATTTTGCCCTAACCAACTTTCCAATCGGTTG
1 CCCTGACCAACCTTCTAATCAGTTGACTTTATCGGTTTCGCCTTGGCCAACCTTCCAATCTGTTG
* * ** * * * *
3457437 ACTTTATCGGTTTTGCCCTAGTTAACTCTTCCAATTTGTTGGCTTTATCAATTTTA
66 GCTTTATCGGTTTCGCCCTAGCCAAC-CTT-CAAATTATTAGCTTTATCGATTTTA
* * ** *
3457493 CCTTGGCCAACCTTCTAATTTGTTGGCTTTATCGGTTTCGCCTTGGCCAACCTTCCAATCTGTTG
1 CCCTGACCAACCTTCTAATCAGTTGACTTTATCGGTTTCGCCTTGGCCAACCTTCCAATCTGTTG
* *
3457558 GCTTTATCGATTTCGCCCTAGCCAACCTTCAAATCTATTAGTTTTATCGATTTTA
66 GCTTTATCGGTTTCGCCCTAGCCAACCTTCAAAT-TATTAGCTTTATCGATTTTA
* * * * *
3457613 CCCTGACCAA-CTTTTCAATCAGTTGACTTTATTGGTTTTGCCTTGGCCAACCTTTCAATATGTT
1 CCCTGACCAACCTTCT-AATCAGTTGACTTTATCGGTTTCGCCTTGGCCAACCTTCCAATCTGTT
* * * *
3457677 GGTTTTATCGGTTTC-CCCTGGCCAACCTTCTAATTGATTAACTTTATCGATTTT
65 GGCTTTATCGGTTTCGCCCTAGCCAACCTTCAAATT-ATTAGCTTTATCGATTTT
3457731 GTCCTAGTCA
Statistics
Matches: 197, Mismatches: 38, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
118 1 0.01
119 41 0.21
120 81 0.41
121 74 0.38
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.41
Consensus pattern (119 bp):
CCCTGACCAACCTTCTAATCAGTTGACTTTATCGGTTTCGCCTTGGCCAACCTTCCAATCTGTTG
GCTTTATCGGTTTCGCCCTAGCCAACCTTCAAATTATTAGCTTTATCGATTTTA
Found at i:3457763 original size:120 final size:120
Alignment explanation
Indices: 3457479--3457787 Score: 329
Period size: 120 Copynumber: 2.6 Consensus size: 120
3457469 AATTTGTTGG
* * * ** *
3457479 CTTTATCAATTTTACCTTGGCCAA-CCTTCTAATTTGTTGGCTTTATCGGTTTCGCCTTGGCCAA
1 CTTTATCGATTTTACCCTGACCAACCCTTC-AATCAGTTGGCTTTATTGGTTTCGCCTTGGCCAA
* * *
3457543 CCTTCCAATCTGTTGGCTTTATCGATTTCGCCCTAGCCAACCTTCAAATCTATTAG
65 CCTTTCAATATGTTGGCTTTATCGATTTCGCCCTAGCCAACCTTCAAATCTATTAA
* ** * *
3457599 TTTTATCGATTTTACCCTGACCAACTTTTCAATCAGTTGACTTTATTGGTTTTGCCTTGGCCAAC
1 CTTTATCGATTTTACCCTGACCAACCCTTCAATCAGTTGGCTTTATTGGTTTCGCCTTGGCCAAC
* * * *
3457664 CTTTCAATATGTTGGTTTTATCGGTTTC-CCCTGGCCAACCTTCTAAT-TGATTAA
66 CTTTCAATATGTTGGCTTTATCGATTTCGCCCTAGCCAACCTTCAAATCT-ATTAA
** * * * * *
3457718 CTTTATCGATTTTGTCCT-AGTCATCCCTTCAAATCCGTTGGCTTTATTGGTTTCGTCATGGCCA
1 CTTTATCGATTTTACCCTGA-CCAACCCTTC-AATCAGTTGGCTTTATTGGTTTCGCCTTGGCCA
3457782 ACCTTT
64 ACCTTT
3457788 TAATCTGTCG
Statistics
Matches: 155, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
118 2 0.01
119 42 0.27
120 108 0.70
121 3 0.02
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (120 bp):
CTTTATCGATTTTACCCTGACCAACCCTTCAATCAGTTGGCTTTATTGGTTTCGCCTTGGCCAAC
CTTTCAATATGTTGGCTTTATCGATTTCGCCCTAGCCAACCTTCAAATCTATTAA
Found at i:3459024 original size:23 final size:20
Alignment explanation
Indices: 3459006--3459049 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3458996 GAAACAGGAG
3459006 CAACAACAGCAAAGAAACAA
1 CAACAACAGCAAAGAAACAA
*
3459026 CAGCAACAGCAAAAGAAACGAA
1 CAACAACAGC-AAAGAAAC-AA
3459048 CA
1 CA
3459050 GCAGTAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.61, C:0.25, G:0.14, T:0.00
Consensus pattern (20 bp):
CAACAACAGCAAAGAAACAA
Found at i:3459034 original size:20 final size:22
Alignment explanation
Indices: 3459009--3459052 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
3458999 ACAGGAGCAA
3459009 CAACAGC-AAAGAAAC-AACAG
1 CAACAGCAAAAGAAACGAACAG
3459029 CAACAGCAAAAGAAACGAACAG
1 CAACAGCAAAAGAAACGAACAG
3459051 CA
1 CA
3459053 GTAGTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 7 0.32
ACGTcount: A:0.59, C:0.25, G:0.16, T:0.00
Consensus pattern (22 bp):
CAACAGCAAAAGAAACGAACAG
Found at i:3460203 original size:6 final size:6
Alignment explanation
Indices: 3460192--3460223 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3460182 TAAAATGGTC
3460192 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
3460224 ACTTACTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:3460649 original size:128 final size:129
Alignment explanation
Indices: 3460417--3460884 Score: 532
Period size: 128 Copynumber: 3.6 Consensus size: 129
3460407 ATCATCATTA
* * * * ** *
3460417 TTTATCTTTTTAAGTCCTTTAGGATTA-CTAGGATACTTTTATGTCGAAGGTAT-CCCCCAAGGG
1 TTTACCTTTTTAAGTCCTTTAGGGTTACCGAGGATACTTTCACATCGAAGGTATACCCCTAAGGG
* * * *
3460480 TATTTTAGTAATTTTCCTAAAATCGAGTCCTAGCAAAGGTGTACGTTTAGGATAAGTTCATCCC
66 CATTTTAGTAATTTTTCTAAAATCGAGTCCTAGCGAAGGTGTACGTTTAGGATAGGTTCATCCC
* * *
3460544 TTTACCTTTTTAAATCCTTTAGGGTTACCGA-GATACTTTCACATCGAAGGTATACTCTTAAGGG
1 TTTACCTTTTTAAGTCCTTTAGGGTTACCGAGGATACTTTCACATCGAAGGTATACCCCTAAGGG
* * *
3460608 CATTTTAATAATTTTTCTAAAACCGAGTCCTAGCGAAGGTGTGCGTTTAGGTAGGATAGGTTCAT
66 CATTTTAGTAATTTTTCTAAAATCGAGTCCTAGCGAAGGTGTACG-TT---TAGGATAGGTTCAT
**
3460673 CAT
127 CCC
* * * * * *
3460676 TTTATCGTTTTAAGTCCTTTAGGGTTATC-AGGATACTTTCACGTCGAAGGTATACCTCTAGGGG
1 TTTACCTTTTTAAGTCCTTTAGGGTTACCGAGGATACTTTCACATCGAAGGTATACCCCTAAGGG
* * * * * *
3460740 AATTTTAGTAATTTTTTTAGAATCGAGTCCTAGCGAAGGTGTATGTTTAGGATAGGTTTATTCC
66 CATTTTAGTAATTTTTCTAAAATCGAGTCCTAGCGAAGGTGTACGTTTAGGATAGGTTCATCCC
* * * * *
3460804 TTTACCTTTTTAAGTCCTTTAAGGTTA-CGGGGATACTTTCACATCAAAAGTATACCCCTAGGGG
1 TTTACCTTTTTAAGTCCTTTAGGGTTACCGAGGATACTTTCACATCGAAGGTATACCCCTAAGGG
3460868 CATTTTAGTAAATTTTT
66 CATTTTAGT-AATTTTT
3460885 TTAGAATCAA
Statistics
Matches: 284, Mismatches: 48, Indels: 16
0.82 0.14 0.05
Matches are distributed among these distances:
127 44 0.15
128 123 0.43
129 9 0.03
131 3 0.01
132 105 0.37
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (129 bp):
TTTACCTTTTTAAGTCCTTTAGGGTTACCGAGGATACTTTCACATCGAAGGTATACCCCTAAGGG
CATTTTAGTAATTTTTCTAAAATCGAGTCCTAGCGAAGGTGTACGTTTAGGATAGGTTCATCCC
Found at i:3461112 original size:152 final size:153
Alignment explanation
Indices: 3460774--3461436 Score: 581
Period size: 152 Copynumber: 4.3 Consensus size: 153
3460764 GAGTCCTAGC
* * * * **
3460774 GAAGGTGTATGTTTAGGATAGGTTTATTCCTTTACCTTTTTAAGTCCTTTAAGG-TTACGGGGAT
1 GAAGGTGTATGTTTAGGATAGGTTCATCCCTTTACATTTTTAAGT-CTTTTAGGATTACCAGGAT
* * * * * * * *
3460838 ACTTTCACATCAAAAGTATACCCCTAGGGGCATTTTAGTAAATTTTTTTAGAATCAAGTTCTAAG
65 ACTTTCACGTCAAAGGTATACCCTTAGGAGCATTTTAGT-AACTTTTTTAAAATCGAGTCCTAAG
* *
3460903 TTATCAC-CGAGTATGCTTCTATGCC
129 TTATCACTAG-GTATGCTTCTATGCT
* * * * *
3460928 GAAGGTGTATGTTTTGGATAAGTTCATCCCTTTTCATTCTTAAGTCTTTTAGGATTACCGGGATA
1 GAAGGTGTATGTTTAGGATAGGTTCATCCCTTTACATTTTTAAGTCTTTTAGGATTACCAGGATA
* * * *
3460993 CTTTCACGTCAAAGGTTTACGCTTAGGAGCATTTTAGTAA-TTTTTTAAAATCGAGTCATAGGTT
66 CTTTCACGTCAAAGGTATACCCTTAGGAGCATTTTAGTAACTTTTTTAAAATCGAGTCCTAAGTT
* *
3461057 ATCACTAGGTCTGCTTCCATGCT
131 ATCACTAGGTATGCTTCTATGCT
* * * * * *
3461080 GAAGGTGTACGTTTAGGATAGGTTCATCCCTTTACCTTTTTAAGTCCTTTAAGATTATCAGAATA
1 GAAGGTGTATGTTTAGGATAGGTTCATCCCTTTACATTTTTAAGTCTTTTAGGATTACCAGGATA
* * * *
3461145 CTTTTACGTCGAAA-GTATTCCCTAAAG-GCATTTTAGTAA-TTTTTTAAAAATCGAGTCCTAAG
66 CTTTCACGTC-AAAGGTATACCCTTAGGAGCATTTTAGTAACTTTTTT-AAAATCGAGTCCTAAG
** ** * *
3461207 TTATCACCGGGTCCGCTTCAATACT
129 TTATCACTAGGTATGCTTCTATGCT
* * ** * * *
3461232 AAAAGTGTACATTTAGGATAGGTTCATCCCTTTACCA-TTTTAAGTTTCTTTA-AAGTTACCAAG
1 GAAGGTGTATGTTTAGGATAGGTTCATCCCTTTA-CATTTTTAAGTCT-TTTAGGA-TTACCAGG
* * * * * ** * *
3461295 ATACTTTTACGTCGAAGGTATACCCATAGAAGCATTTTAATAACTTTCCTAAAACCGAGTCCTAG
63 ATACTTTCACGTCAAAGGTATACCCTTAGGAGCATTTTAGTAACTTTTTTAAAATCGAGTCCTAA
*
3461360 GTTATCA-TCAAGTATGCTTCTATG-T
128 GTTATCACT-AGGTATGCTTCTATGCT
* * * * *
3461385 CGAAAGTGTATGGTTAGGATAGGTTTATCCCTTTTCATTTTTAAGTCCTTTA
1 -GAAGGTGTATGTTTAGGATAGGTTCATCCCTTTACATTTTTAAGTCTTTTA
3461437 AAGTTATCGA
Statistics
Matches: 412, Mismatches: 84, Indels: 27
0.79 0.16 0.05
Matches are distributed among these distances:
151 18 0.04
152 183 0.44
153 51 0.12
154 156 0.38
155 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (153 bp):
GAAGGTGTATGTTTAGGATAGGTTCATCCCTTTACATTTTTAAGTCTTTTAGGATTACCAGGATA
CTTTCACGTCAAAGGTATACCCTTAGGAGCATTTTAGTAACTTTTTTAAAATCGAGTCCTAAGTT
ATCACTAGGTATGCTTCTATGCT
Found at i:3461363 original size:306 final size:305
Alignment explanation
Indices: 3460773--3461456 Score: 763
Period size: 306 Copynumber: 2.2 Consensus size: 305
3460763 CGAGTCCTAG
* * *
3460773 CGAAGGTGTATGTTTAGGATAGGTTTATTCCTTTACCTTTTTAAGTCCTTTAAGGTTA-CGGGGA
1 CGAAGGTGTATGTTTAGGATAGGTTTATCCCTTTACCTTTTTAAGTCCTTTAAGATTATC--GAA
** * * *
3460837 TACTTTCACATCAAAAGTATACCCCTAGGGGCATTTTAGTAAATTTTTTTAGAATCAAGTTCTAA
64 TACTTTCACATCAAAAGTATACCCCTAAAGGCATTTTAGTAAATTTTTTAAAAATCAAGTCCTAA
* * * * * ** * *
3460902 GTTATCACCGAGTATGCTTCTATGCCGAAGGTGTATGTTTTGGATAAGTTCATCCCTTTTCATTC
129 GTTATCACCGAGTACGCTTCAATACCAAAAGTGTACATTTAGGATAAGTTCATCCCTTTCCATTC
* * ** * * * * *
3460967 TTAAGTCTTTTAGGATTACCGGGATACTTTCACGTCAAAGGTTTACGCTTAGGAGCATTTTAGTA
194 TTAAGTCTTTAAAGATTACCAAGATACTTTCACGTCAAAGGTATACCCATAGAAGCATTTTAATA
** * * *
3461032 ATTTTTTAAAATCGAGTCATAGGTTATCA-CTAGGTCTGCTTCCATG-
259 ATTTCCTAAAACCGAGTCATAGGTTATCATC-AAGTATGCTTCCATGT
* *
3461078 CTGAAGGTGTACGTTTAGGATAGGTTCATCCCTTTACCTTTTTAAGTCCTTTAAGATTATCAGAA
1 C-GAAGGTGTATGTTTAGGATAGGTTTATCCCTTTACCTTTTTAAGTCCTTTAAGATTATC-GAA
* * * * *
3461143 TACTTTTACGTCGAAAGTAT-TCCCTAAAGGCATTTTAGT-AATTTTTTAAAAATCGAGTCCTAA
64 TACTTTCACATCAAAAGTATACCCCTAAAGGCATTTTAGTAAATTTTTTAAAAATCAAGTCCTAA
* * * *
3461206 GTTATCACCGGGTCCGCTTCAATACTAAAAGTGTACATTTAGGATAGGTTCATCCCTTTACCATT
129 GTTATCACCGAGTACGCTTCAATACCAAAAGTGTACATTTAGGATAAGTTCATCCCTTT-CCATT
* *
3461271 -TTAAGTTTCTTTAAAG-TTACCAAGATACTTTTACGTCGAAGGTATACCCATAGAAGCATTTTA
193 CTTAAG--TCTTTAAAGATTACCAAGATACTTTCACGTCAAAGGTATACCCATAGAAGCATTTTA
* *
3461334 ATAACTTTCCTAAAACCGAGTCCTAGGTTATCATCAAGTATGCTTCTATGT
256 ATAA-TTTCCTAAAACCGAGTCATAGGTTATCATCAAGTATGCTTCCATGT
* * * *
3461385 CGAAAGTGTATGGTTAGGATAGGTTTATCCCTTTTCATTTTTAAGTCCTTTAA-AGTTATCGAGA
1 CGAAGGTGTATGTTTAGGATAGGTTTATCCCTTTACCTTTTTAAGTCCTTTAAGA-TTATCGA-A
3461449 TACTTTCA
64 TACTTTCA
3461457 ATTGGTAGGT
Statistics
Matches: 315, Mismatches: 54, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
304 72 0.23
305 66 0.21
306 174 0.55
307 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (305 bp):
CGAAGGTGTATGTTTAGGATAGGTTTATCCCTTTACCTTTTTAAGTCCTTTAAGATTATCGAATA
CTTTCACATCAAAAGTATACCCCTAAAGGCATTTTAGTAAATTTTTTAAAAATCAAGTCCTAAGT
TATCACCGAGTACGCTTCAATACCAAAAGTGTACATTTAGGATAAGTTCATCCCTTTCCATTCTT
AAGTCTTTAAAGATTACCAAGATACTTTCACGTCAAAGGTATACCCATAGAAGCATTTTAATAAT
TTCCTAAAACCGAGTCATAGGTTATCATCAAGTATGCTTCCATGT
Found at i:3463542 original size:22 final size:22
Alignment explanation
Indices: 3463515--3463577 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
3463505 AATTAATATT
3463515 TTTAAAATAATATTATATTTAA
1 TTTAAAATAATATTATATTTAA
*
3463537 TTTAAATTTAA-ATTAT-TTTAAA
1 TTTAAA-ATAATATTATATTT-AA
*
3463559 TTT-AAATAAT-TAATATTTA
1 TTTAAAATAATATTATATTTA
3463578 TAATTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 16 0.47
23 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAAAATAATATTATATTTAA
Found at i:3463816 original size:22 final size:22
Alignment explanation
Indices: 3463784--3463860 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
3463774 CGGGTTCTGA
*
3463784 TCAATCGGGTTTAACGCTCGGG
1 TCAATCGGGTTTAATGCTCGGG
* *
3463806 TCAATCAGGTTTAATGCTCAGG
1 TCAATCGGGTTTAATGCTCGGG
*
3463828 TCAATCGGGCTTAATGCTCGGG
1 TCAATCGGGTTTAATGCTCGGG
* *
3463850 TTAATTGGGTT
1 TCAATCGGGTT
3463861 CGGGTTAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (22 bp):
TCAATCGGGTTTAATGCTCGGG
Found at i:3463865 original size:15 final size:15
Alignment explanation
Indices: 3463845--3463886 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
3463835 GGCTTAATGC
3463845 TCGGGTTAATTGGGT
1 TCGGGTTAATTGGGT
3463860 TCGGGTTAATTGGGT
1 TCGGGTTAATTGGGT
3463875 TCGGGTTAATTG
1 TCGGGTTAATTG
3463887 AGTTTAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.14, C:0.07, G:0.38, T:0.40
Consensus pattern (15 bp):
TCGGGTTAATTGGGT
Found at i:3464914 original size:26 final size:29
Alignment explanation
Indices: 3464850--3464914 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
3464840 TAACTTTTTC
3464850 TTTA-TATAAATAAATAATTAATTAAATAA
1 TTTATTATAAATAAATAATTAA-TAAATAA
*
3464879 TTT-TTAATAAATAAATTA-TAA-AAAT-A
1 TTTATT-ATAAATAAATAATTAATAAATAA
3464905 TTTATTATAA
1 TTTATTATAA
3464915 TTTAATTGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
26 8 0.25
27 6 0.19
29 7 0.22
30 11 0.34
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTATTATAAATAAATAATTAATAAATAA
Found at i:3507099 original size:16 final size:16
Alignment explanation
Indices: 3507078--3507113 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
3507068 TCGAATCTAA
3507078 AAATGATTCGAATCCG
1 AAATGATTCGAATCCG
*
3507094 AAATGATTTGAATCCG
1 AAATGATTCGAATCCG
3507110 AAAT
1 AAAT
3507114 AACTTAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (16 bp):
AAATGATTCGAATCCG
Found at i:3511902 original size:78 final size:78
Alignment explanation
Indices: 3511803--3512003 Score: 233
Period size: 79 Copynumber: 2.6 Consensus size: 78
3511793 AATAACGGGG
* * * * * *
3511803 TTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAG
*
3511867 AAAAAAAATCAGGA
65 AAAAAAAACCAGGA
* *
3511881 TTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTAG
* * * * *
3511946 GAATAAAGCCGGGG
65 AAAAAAAACCAGGA
* *
3511960 TTGGAGTATTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
3512004 GAAATAACAA
Statistics
Matches: 104, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
77 1 0.01
78 51 0.49
79 52 0.50
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (78 bp):
TTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAACCAGGA
Found at i:3512011 original size:28 final size:27
Alignment explanation
Indices: 3511955--3512026 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
3511945 GGAATAAAGC
*
3511955 CGGGGTTGGAGTATTCCCTCGGAAGTAA
1 CGGGGTTGGAGTA-TCCCTCGGAAATAA
3511983 CGGGGTTGGAGTATCCC-CGATGAAATAA
1 CGGGGTTGGAGTATCCCTCG--GAAATAA
**
3512011 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
3512027 TCGACTGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 33 0.85
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTCGGAAATAA
Found at i:3512077 original size:52 final size:51
Alignment explanation
Indices: 3512014--3512399 Score: 226
Period size: 52 Copynumber: 7.4 Consensus size: 51
3512004 GAAATAACAA
* * * * * *
3512014 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTGGAAATAAAACCGG
* * * * * *
3512066 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGGAAATAAAACCGG
* * *
3512118 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * * * **
3512170 GATTGGAATATCCCCGAATATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
** * **** * *
3512221 GGTTGGAGTATCCCC---TCGGAAATAACGGGGTTGGAGTATCCCCGATGAT-CAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TT--AGTGTTTTGGA-AATAAAACCGG
* * *
3512276 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATTAGTG--TTTTGGAAATAAAACCGG
* * *
3512330 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAACCGG
* *
3512381 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
3512400 GTGGAGAATT
Statistics
Matches: 256, Mismatches: 58, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
48 5 0.02
49 2 0.01
51 73 0.29
52 92 0.36
53 26 0.10
54 24 0.09
55 18 0.07
56 7 0.03
57 2 0.01
58 6 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:3512227 original size:51 final size:52
Alignment explanation
Indices: 3512106--3512235 Score: 154
Period size: 51 Copynumber: 2.5 Consensus size: 52
3512096 GGTGTTTCGA
* * * * *
3512106 AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG
1 AAATAAAACCGGGGTTGGAGTATCCCCGAATATGGAAAAATCAATATTTTAG
* * * *
3512158 CAATAAAACCGGGATTGGAATATCCCCGAATAT-GAAAAATCAATATTTTGG
1 AAATAAAACCGGGGTTGGAGTATCCCCGAATATGGAAAAATCAATATTTTAG
**
3512209 AAATAAAGTCGGGGTTGGAGTATCCCC
1 AAATAAAACCGGGGTTGGAGTATCCCC
3512236 TCGGAAATAA
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
51 36 0.56
52 28 0.44
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (52 bp):
AAATAAAACCGGGGTTGGAGTATCCCCGAATATGGAAAAATCAATATTTTAG
Found at i:3512282 original size:27 final size:26
Alignment explanation
Indices: 3512218--3512293 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
3512208 GAAATAAAGT
3512218 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
3512246 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
3512273 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
3512294 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:3512395 original size:263 final size:262
Alignment explanation
Indices: 3511904--3512404 Score: 774
Period size: 263 Copynumber: 1.9 Consensus size: 262
3511894 TCGAAAATAA
* * * *
3511904 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* * *
3511969 TCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGACTG
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-AATAACAAGGTTGGAGTATCCCCGACTG
*
3512034 TGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
130 TGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGT
* *
3512099 GTTTCGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
195 GTTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
3512164 AAC
260 AAC
*
3512167 CGGGATTGGAATATCCCCGAA-TATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTA
1 CGGGATTGGAATATCCCC-AATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTA
** *
3512231 TCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATCAACGGGGTTGGAGTATCCCCGATT
65 TCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAT-AACAAGGTTGGAGTATCCCCGACT
* *
3512295 GTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA-GAAAATT
129 GTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATT
* *
3512359 AGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
192 AGTGTTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
3512405 GAATTGAGAA
Statistics
Matches: 216, Mismatches: 18, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
261 2 0.01
262 25 0.12
263 147 0.68
264 42 0.19
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (262 bp):
CGGGATTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAATAACAAGGTTGGAGTATCCCCGACTGT
GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
TTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
AC
Found at i:3514786 original size:13 final size:13
Alignment explanation
Indices: 3514768--3514793 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3514758 ACAAAGATCC
3514768 ATGTATCGATACA
1 ATGTATCGATACA
3514781 ATGTATCGATACA
1 ATGTATCGATACA
3514794 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3514789 original size:33 final size:33
Alignment explanation
Indices: 3514747--3514813 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3514737 AAAATTTCCA
***
3514747 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3514780 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
3514813 A
1 A
3514814 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:3514851 original size:19 final size:18
Alignment explanation
Indices: 3514827--3514926 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
3514817 CCTTGGCTAA
3514827 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3514846 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3514861 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3514878 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3514893 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3514910 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3514927 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3514867 original size:13 final size:13
Alignment explanation
Indices: 3514849--3514905 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
3514839 ACAATACTTA
3514849 TGTATCGATACAT
1 TGTATCGATACAT
3514862 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
3514880 ATGTATCGATACAT
1 -TGTATCGATACAT
3514894 TGTATCGATACA
1 TGTATCGATACA
3514906 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3514871 original size:32 final size:32
Alignment explanation
Indices: 3514830--3514924 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
3514820 TGGCTAATTA
*
3514830 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3514862 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3514894 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3514925 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3515006 original size:21 final size:21
Alignment explanation
Indices: 3514982--3515038 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3514972 CATTTGTAGG
3514982 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
3515003 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
3515024 ATGTATCGATACATT
1 ATGTATCGATACATT
3515039 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:3516081 original size:13 final size:13
Alignment explanation
Indices: 3516063--3516087 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3516053 TACAAAGATC
3516063 AATGTATCAATAT
1 AATGTATCAATAT
3516076 AATGTATCAATA
1 AATGTATCAATA
3516088 CATTGAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
AATGTATCAATAT
Found at i:3516099 original size:20 final size:20
Alignment explanation
Indices: 3516074--3516111 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3516064 ATGTATCAAT
3516074 ATAATGTATCAATACATTGA
1 ATAATGTATCAATACATTGA
*
3516094 ATAATGTATCGATACATT
1 ATAATGTATCAATACATT
3516112 TCCTTGGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (20 bp):
ATAATGTATCAATACATTGA
Found at i:3516154 original size:13 final size:13
Alignment explanation
Indices: 3516136--3516161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3516126 CAGAGTAGCT
3516136 TTGTATCGATACA
1 TTGTATCGATACA
3516149 TTGTATCGATACA
1 TTGTATCGATACA
3516162 ACACTCATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3517886 original size:14 final size:15
Alignment explanation
Indices: 3517859--3517889 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3517849 TTGCTTGAAA
3517859 TTTAAAATTTATTTT
1 TTTAAAATTTATTTT
3517874 TTTAAAA-TTATTTT
1 TTTAAAATTTATTTT
3517888 TT
1 TT
3517890 ATGAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTAAAATTTATTTT
Found at i:3522944 original size:13 final size:13
Alignment explanation
Indices: 3522926--3522952 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3522916 TACAAAACTT
3522926 ATGTATCGATACA
1 ATGTATCGATACA
3522939 ATGTATCGATACA
1 ATGTATCGATACA
3522952 A
1 A
3522953 CACTTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3522949 original size:32 final size:33
Alignment explanation
Indices: 3522908--3522972 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3522898 TAGCTTAAAT
3522908 TGTATCGATACAAAAC-TTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
*
3522940 TGTATCGATACAACACTTTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
3522973 ATCGTTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAACTTTATGTATCGATACAA
Found at i:3523635 original size:5 final size:5
Alignment explanation
Indices: 3523620--3523701 Score: 139
Period size: 5 Copynumber: 16.4 Consensus size: 5
3523610 CATCTAATAC
3523620 ATTTAA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTT-A ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
*
3523671 ATTTA ATTTA ATTTA ATTTA A-TAA ATTTA AT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT
3523702 AATTTTAAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
4 3 0.04
5 66 0.90
6 4 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATTTA
Found at i:3524379 original size:16 final size:17
Alignment explanation
Indices: 3524355--3524395 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
3524345 CGATATGATT
3524355 ATATAAAATAAAAAATA
1 ATATAAAATAAAAAATA
* *
3524372 AT-TAAAATATAATATA
1 ATATAAAATAAAAAATA
3524388 ATATAAAA
1 ATATAAAA
3524396 AATAAAACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATATAAAATAAAAAATA
Found at i:3525111 original size:16 final size:15
Alignment explanation
Indices: 3525080--3525113 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3525070 ATAGTTTTAT
*
3525080 AATTTTAAAATAATA
1 AATTTTAAAAAAATA
3525095 AATTTTAAAAAAGATA
1 AATTTTAAAAAA-ATA
3525111 AAT
1 AAT
3525114 ATTTTTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
AATTTTAAAAAAATA
Found at i:3532409 original size:21 final size:19
Alignment explanation
Indices: 3532385--3532434 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
3532375 TTCAATAATT
*
3532385 TGTATCGATACATTCAGTAAA
1 TGTATCGATACA-TAAGT-AA
*
3532406 TGTATCAATACATAAGTAA
1 TGTATCGATACATAAGTAA
3532425 TGTATCGATA
1 TGTATCGATA
3532435 TAGTGTATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 11 0.42
20 4 0.15
21 11 0.42
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (19 bp):
TGTATCGATACATAAGTAA
Found at i:3532428 original size:19 final size:21
Alignment explanation
Indices: 3532385--3532430 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3532375 TTCAATAATT
* *
3532385 TGTATCGATACATTCAGTAAA
1 TGTATCAATACATTAAGTAAA
3532406 TGTATCAATACA-TAAGT-AA
1 TGTATCAATACATTAAGTAAA
3532425 TGTATC
1 TGTATC
3532431 GATATAGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 4 0.17
21 11 0.48
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTATCAATACATTAAGTAAA
Found at i:3532486 original size:13 final size:13
Alignment explanation
Indices: 3532468--3532506 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3532458 GCCAAGGAAA
*
3532468 TGTATCTATACAT
1 TGTATCGATACAT
3532481 TGTATCGATACAT
1 TGTATCGATACAT
3532494 TGTATCGATACAT
1 TGTATCGATACAT
3532507 CAATCTTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3532569 original size:20 final size:20
Alignment explanation
Indices: 3532544--3532599 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
3532534 GTTTACCCAG
3532544 ATGTATCGATACATTTTACA
1 ATGTATCGATACATTTTACA
* *
3532564 ATGTATCAATACATTCTACA
1 ATGTATCGATACATTTTACA
3532584 ATGTATCGATACATTT
1 ATGTATCGATACATTT
3532600 AGGCATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTACA
Found at i:3534941 original size:51 final size:50
Alignment explanation
Indices: 3534885--3535070 Score: 203
Period size: 51 Copynumber: 3.6 Consensus size: 50
3534875 TTAAGTTTCT
* * *
3534885 CAATTTTTCATAATCGGGGATACTCCAACCCTGGTTTTATTTCTAAAACAC
1 CAATTTTCCACAATCGGGGATACTCCAACCC-GATTTTATTTCTAAAACAC
* *
3534936 TAATTTTCCACAATCGGGGATACTGCAACCCCGATTTTATTT-TCAAAACAC
1 CAATTTTCCACAATCGGGGATACTCCAA-CCCGATTTTATTTCT-AAAACAC
** * *
3534987 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATAC
1 CAATTTTCC-ACAATCGGGGATACTCCAAC-CCGATTTTATTT-CTAAAACAC
* * *
3535040 CAATTTTTCACAATCAGGGATACTCTAACCC
1 CAATTTTCCACAATCGGGGATACTCCAACCC
3535071 CGTTAATCAT
Statistics
Matches: 113, Mismatches: 16, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
50 1 0.01
51 51 0.45
52 47 0.42
53 14 0.12
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (50 bp):
CAATTTTCCACAATCGGGGATACTCCAACCCGATTTTATTTCTAAAACAC
Done.