Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 21 of 175
Found at i:5562150 original size:56 final size:56
Alignment explanation
Indices: 5562056--5562169 Score: 158
Period size: 56 Copynumber: 2.0 Consensus size: 56
5562046 TATTGAGACA
* *
5562056 AATTTGATCAGATTTTATTTATTTCTTTCTTTAGGATTGAGTCAAT-TCTTGATTAT
1 AATTTGATCAGATCTTATTTATTTCTTTCTTTAAGATTGAGTCAATCT-TTGATTAT
* * * *
5562112 AATTTGATGAGATCTTGTTTCTTTCTTTTTTTAAGATTGAGTCAATCTTTGATTAT
1 AATTTGATCAGATCTTATTTATTTCTTTCTTTAAGATTGAGTCAATCTTTGATTAT
5562168 AA
1 AA
5562170 AGATTCTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
56 50 0.98
57 1 0.02
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.53
Consensus pattern (56 bp):
AATTTGATCAGATCTTATTTATTTCTTTCTTTAAGATTGAGTCAATCTTTGATTAT
Found at i:5562936 original size:21 final size:20
Alignment explanation
Indices: 5562898--5562938 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
5562888 GTGGTAGAGA
*
5562898 AAAGGGAGGGTTGCACTATC
1 AAAGGGAGGGTTACACTATC
*
5562918 AAAGAGGAGGGTTATACTATC
1 AAAG-GGAGGGTTACACTATC
5562939 TGGAAGATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (20 bp):
AAAGGGAGGGTTACACTATC
Found at i:5565283 original size:72 final size:68
Alignment explanation
Indices: 5565183--5565366 Score: 197
Period size: 72 Copynumber: 2.6 Consensus size: 68
5565173 TTGTCAAAAA
* * * *
5565183 AAAAAAAAATAGCAGCAATGAGCAGTTGCAGAGACGTGAAAAGGCATCAATTGAATAGCGAAGTA
1 AAAAAAAAATAGCAGC-A-G-G-GGTTGCAGAGACGTGAAAAGGCAGCAATTGAATAGCAAAGCA
*
5565248 GTTGCTGG
62 GTTG-TCG
* * *
5565256 AAAAAAGATAATTGCAGCAAGGGGTTGCAGAGACGTGAAGAGGTAGCAATTGAATAGCAAAGCAG
1 AAAAAA-A-AATAGCAGC-AGGGGTTGCAGAGACGTGAAAAGGCAGCAATTGAATAGCAAAGCAG
5565321 TTGTCG
63 TTGTCG
* **
5565327 AAAAAAAAGTAGCAGCAGGGGTTGCAGAGATATGAAAAGG
1 AAAAAAAAATAGCAGCAGGGGTTGCAGAGACGTGAAAAGG
5565367 ATATTTTAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
68 21 0.22
69 7 0.07
70 1 0.01
71 8 0.08
72 40 0.42
73 7 0.07
74 2 0.02
75 10 0.10
ACGTcount: A:0.42, C:0.11, G:0.30, T:0.17
Consensus pattern (68 bp):
AAAAAAAAATAGCAGCAGGGGTTGCAGAGACGTGAAAAGGCAGCAATTGAATAGCAAAGCAGTTG
TCG
Found at i:5568460 original size:16 final size:17
Alignment explanation
Indices: 5568439--5568471 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5568429 CACATTGAAG
5568439 TGTTTT-TCGAAAACCA
1 TGTTTTATCGAAAACCA
5568455 TGTTTTCATCGAAAACC
1 TGTTTT-ATCGAAAACC
5568472 CTTCTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (17 bp):
TGTTTTATCGAAAACCA
Found at i:5568787 original size:24 final size:24
Alignment explanation
Indices: 5568725--5568789 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
5568715 TCTAGCAAAT
*
5568725 ATAAATCAGTCATTCAAATCACAG
1 ATAAATCAGTCATTTAAATCACAG
* *
5568749 ATAAATCAGTCATTTACATCACGG
1 ATAAATCAGTCATTTAAATCACAG
*
5568773 ATAAATCAATCATTTAA
1 ATAAATCAGTCATTTAA
5568790 CCTCGCAGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (24 bp):
ATAAATCAGTCATTTAAATCACAG
Found at i:5568864 original size:27 final size:27
Alignment explanation
Indices: 5568836--5568976 Score: 140
Period size: 27 Copynumber: 5.1 Consensus size: 27
5568826 CATTACGCTT
* *
5568836 ATTTTACCTTACAGGGGTATTTTAGTT
1 ATTTTACCTTACAGGGGTATTTTGGTC
* * **
5568863 ATTTTACCCTATAGGGGTATTACGGTC
1 ATTTTACCTTACAGGGGTATTTTGGTC
* * *
5568890 ATTTATCCCCTACAGGGGGTAATTTGGTC
1 ATTT-TACCTTACA-GGGGTATTTTGGTC
*
5568919 ATTTTACCTTTCAGGGGTATTTTGGTC
1 ATTTTACCTTACAGGGGTATTTTGGTC
* *
5568946 ATTTTACCTTTC-GAGGGTAATTTGGTC
1 ATTTTACCTTACAG-GGGTATTTTGGTC
5568973 ATTT
1 ATTT
5568977 AACAACTCTT
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
26 1 0.01
27 66 0.69
28 13 0.14
29 15 0.16
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (27 bp):
ATTTTACCTTACAGGGGTATTTTGGTC
Found at i:5568926 original size:56 final size:55
Alignment explanation
Indices: 5568827--5568976 Score: 144
Period size: 56 Copynumber: 2.7 Consensus size: 55
5568817 CTCCAAGGGC
* * * * * *
5568827 ATTACGCTTATTTTACCTTACA-GGGGTATTTTAGTTATTTTACCCTAT-AGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGGTAATTTGGTCATTTTA-CCTATCAGGGGT
* *
5568881 ATTACGGTCATTTATCCCCTACAGGGGGTAATTTGGTCATTTTACCTTTCAGGGGT
1 ATTACGGTCATTT-TACCCTACAGGGGGTAATTTGGTCATTTTACCTATCAGGGGT
** * * *
5568937 ATTTTGGTCATTTTACCTTTC-GAGGGTAATTTGGTCATTT
1 ATTACGGTCATTTTACCCTACAGGGGGTAATTTGGTCATTT
5568977 AACAACTCTT
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
54 29 0.37
55 16 0.20
56 34 0.43
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (55 bp):
ATTACGGTCATTTTACCCTACAGGGGGTAATTTGGTCATTTTACCTATCAGGGGT
Found at i:5572143 original size:35 final size:35
Alignment explanation
Indices: 5572103--5572172 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
5572093 TTCTTATCAT
*
5572103 CAACACCATTCTCAGCATTTAGCCTTATCCCTTGG
1 CAACACCATTCTCAGCATTCAGCCTTATCCCTTGG
*
5572138 CAACACCATTCTCAGCCTTCAGCCTTATCCCTTGG
1 CAACACCATTCTCAGCATTCAGCCTTATCCCTTGG
5572173 GAACTTAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.21, C:0.37, G:0.11, T:0.30
Consensus pattern (35 bp):
CAACACCATTCTCAGCATTCAGCCTTATCCCTTGG
Found at i:5580830 original size:29 final size:29
Alignment explanation
Indices: 5580791--5580857 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
5580781 TTGACTTTGC
*
5580791 CCGTGTGGCCCACATGGCCTAGCACATGG
1 CCGTGTGGCCCACATGGCCTAGCACACGG
*
5580820 TCGTGTGGCCCACATGGCCTAGCACACGG
1 CCGTGTGGCCCACATGGCCTAGCACACGG
5580849 CCGTGTGGC
1 CCGTGTGGC
5580858 GTCGGCAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.15, C:0.34, G:0.33, T:0.18
Consensus pattern (29 bp):
CCGTGTGGCCCACATGGCCTAGCACACGG
Found at i:5582132 original size:11 final size:11
Alignment explanation
Indices: 5582103--5582132 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
5582093 TATTTTTAAT
5582103 TAATATTAAAA
1 TAATATTAAAA
5582114 TCAATATTAAAA
1 T-AATATTAAAA
5582126 TAATATT
1 TAATATT
5582133 CTTTAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:5582180 original size:17 final size:17
Alignment explanation
Indices: 5582158--5582194 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
5582148 AACTCGCTTA
5582158 ATTTTAAATGTTTAACT
1 ATTTTAAATGTTTAACT
*
5582175 ATTTTAAATGTTTAATT
1 ATTTTAAATGTTTAACT
5582192 ATT
1 ATT
5582195 CAATTCACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTTTAAATGTTTAACT
Found at i:5583902 original size:13 final size:13
Alignment explanation
Indices: 5583880--5583915 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
5583870 AGGAGCTCGA
*
5583880 TTTTACATTTTTG
1 TTTTATATTTTTG
5583893 TTTTATATTTTTG
1 TTTTATATTTTTG
5583906 TTTTATATTT
1 TTTTATATTT
5583916 CCTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.75
Consensus pattern (13 bp):
TTTTATATTTTTG
Found at i:5587940 original size:23 final size:23
Alignment explanation
Indices: 5587896--5587944 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5587886 TGAAGGTAGG
* * *
5587896 ATCTGAATCTGTATTTATTATGC
1 ATCTAAATCTGTATCTACTATGC
*
5587919 ATCTAAATCTGTATCTGCTATGC
1 ATCTAAATCTGTATCTACTATGC
5587942 ATC
1 ATC
5587945 GATGTCTGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (23 bp):
ATCTAAATCTGTATCTACTATGC
Found at i:5588120 original size:13 final size:13
Alignment explanation
Indices: 5588098--5588133 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
5588088 AGGAGCTCGA
*
5588098 TTTTACATTTTTG
1 TTTTATATTTTTG
5588111 TTTTATATTTTTG
1 TTTTATATTTTTG
5588124 TTTTATATTT
1 TTTTATATTT
5588134 CCTAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.75
Consensus pattern (13 bp):
TTTTATATTTTTG
Found at i:5595106 original size:26 final size:26
Alignment explanation
Indices: 5595075--5595126 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
5595065 AAAATTTGTG
5595075 GTTATTTTGTTTTTTATGTTGCCGTC
1 GTTATTTTGTTTTTTATGTTGCCGTC
5595101 GTTATTTTGTTTTTTATGTTGCCGTC
1 GTTATTTTGTTTTTTATGTTGCCGTC
5595127 TTAGTCATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.08, C:0.12, G:0.19, T:0.62
Consensus pattern (26 bp):
GTTATTTTGTTTTTTATGTTGCCGTC
Found at i:5599752 original size:33 final size:33
Alignment explanation
Indices: 5599643--5599820 Score: 121
Period size: 33 Copynumber: 5.3 Consensus size: 33
5599633 AATTGACGGA
* *
5599643 TAAGACCATA-ACTGGGTTATGGCACTATGAACG
1 TAAGACCATAGA-TGGGCTATGGCATTATGAACG
* * * * * * *
5599676 TAAGACCATGGTTGGACCATGCCAGTGT-TTATATG
1 TAAGACCATAGATGGGCTATGGCA-T-TATGA-ACG
5599711 TAAGACCATAGATGGGCTATGGCATTATGAACG
1 TAAGACCATAGATGGGCTATGGCATTATGAACG
* * * * * *
5599744 TAAGACCAT-GGTAGGACCATGCCAGTGT-TTATATG
1 TAAGACCATAGAT-GGGCTATGGCA-T-TATGA-ACG
5599779 TAAGACCATAGATGGGCTATGGCATTATGAACG
1 TAAGACCATAGATGGGCTATGGCATTATGAACG
5599812 TAAGACCAT
1 TAAGACCAT
5599821 GGTTGGTTCA
Statistics
Matches: 106, Mismatches: 28, Indels: 22
0.68 0.18 0.14
Matches are distributed among these distances:
32 2 0.02
33 49 0.46
34 11 0.10
35 42 0.40
36 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (33 bp):
TAAGACCATAGATGGGCTATGGCATTATGAACG
Found at i:5599752 original size:68 final size:68
Alignment explanation
Indices: 5599643--5599888 Score: 361
Period size: 68 Copynumber: 3.6 Consensus size: 68
5599633 AATTGACGGA
* *
5599643 TAAGACCATA-ACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGCCAGTGTTTA
1 TAAGACCATAGA-TGGGCTATGGCATTATGAACGTAAGACCATGGTTGGACCATGCCAGTGTTTA
5599707 TATG
65 TATG
*
5599711 TAAGACCATAGATGGGCTATGGCATTATGAACGTAAGACCATGGTAGGACCATGCCAGTGTTTAT
1 TAAGACCATAGATGGGCTATGGCATTATGAACGTAAGACCATGGTTGGACCATGCCAGTGTTTAT
5599776 ATG
66 ATG
** ** *
5599779 TAAGACCATAGATGGGCTATGGCATTATGAACGTAAGACCATGGTTGGTTCATGGAAATGTTTAT
1 TAAGACCATAGATGGGCTATGGCATTATGAACGTAAGACCATGGTTGGACCATGCCAGTGTTTAT
5599844 ATG
66 ATG
* * *
5599847 TAAGACCATAGCTAGGCTATGGCATTCTG-ACGATAAGACCAT
1 TAAGACCATAGATGGGCTATGGCATTATGAACG-TAAGACCAT
5599889 AACTGGGTTA
Statistics
Matches: 164, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
67 3 0.02
68 160 0.98
69 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (68 bp):
TAAGACCATAGATGGGCTATGGCATTATGAACGTAAGACCATGGTTGGACCATGCCAGTGTTTAT
ATG
Found at i:5599941 original size:24 final size:24
Alignment explanation
Indices: 5599909--5599959 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
5599899 TGGCACTACG
5599909 AATGTAAATGATGAATTGACGGAA
1 AATGTAAATGATGAATTGACGGAA
*
5599933 AATGTAAATGATGAATTGACGGCA
1 AATGTAAATGATGAATTGACGGAA
5599957 AAT
1 AAT
5599960 TACCCAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.25
Consensus pattern (24 bp):
AATGTAAATGATGAATTGACGGAA
Found at i:5603693 original size:42 final size:42
Alignment explanation
Indices: 5603579--5603740 Score: 155
Period size: 43 Copynumber: 3.8 Consensus size: 42
5603569 TCAAAAGTTC
* *
5603579 ATACAATGCCAACGTCCCAGACATGGTCTTTCATGTAATCAA
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAA
* * * * * * *
5603621 ATAACGATGTCACTGTCCCAGATAGGGTCTTACACGTAATCAT
1 AT-ACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAA
* *
5603664 ATACAACGCCAATGTCCTAGACATGGTCTTACATGTAAATCTCAA
1 ATACAATGCCAATGTCCCAGACATGGTCTTACATGT-AA--TCAA
* * *
5603709 AT-CGATGCCAACGTCCCGGACATGGTCTTACA
1 ATACAATGCCAATGTCCCAGACATGGTCTTACA
5603741 CGATATCACA
Statistics
Matches: 93, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
42 28 0.30
43 35 0.38
44 25 0.27
45 5 0.05
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
ATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCAA
Found at i:5607392 original size:33 final size:33
Alignment explanation
Indices: 5607350--5607507 Score: 122
Period size: 33 Copynumber: 4.7 Consensus size: 33
5607340 TGTTTATATG
5607350 TAAGACCATAGCTGGGCTATGGCATTCTGATGA
1 TAAGACCATAGCTGGGCTATGGCATTCTGATGA
* * * * *
5607383 TAAGACCATAACTGGGTTATGGCACTATGAACG-
1 TAAGACCATAGCTGGGCTATGGCATTCTG-ATGA
* * * * * * *
5607416 TAAGATCATGGTTGGACCATGGCAATAT-TTATATA
1 TAAGACCATAGCTGGGCTATGGC-AT-TCTGAT-GA
* *
5607451 TAAGACCATAGTTGGGCTATGACATTCTGATGA
1 TAAGACCATAGCTGGGCTATGGCATTCTGATGA
* *
5607484 TAAGACCATAACTGGGTTATGGCA
1 TAAGACCATAGCTGGGCTATGGCA
5607508 CTATGAATGT
Statistics
Matches: 92, Mismatches: 27, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
33 64 0.70
34 9 0.10
35 19 0.21
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (33 bp):
TAAGACCATAGCTGGGCTATGGCATTCTGATGA
Found at i:5607460 original size:101 final size:101
Alignment explanation
Indices: 5607280--5607519 Score: 381
Period size: 101 Copynumber: 2.4 Consensus size: 101
5607270 TGAATTAACA
* * * * * *
5607280 GATATGACCATAACTGGTTTATGGCACTATGAATGTAAGACCATGGTTGGGCCATGGTAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAATATTT
* *
5607345 ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
66 ATATATAAGACCATAGCTGGGCTATGACATTCTGAT
* *
5607381 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGATCATGGTTGGACCATGGCAATATTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAATATTT
*
5607446 ATATATAAGACCATAGTTGGGCTATGACATTCTGAT
66 ATATATAAGACCATAGCTGGGCTATGACATTCTGAT
5607482 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAA
1 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAA
5607520 AGGATGAATT
Statistics
Matches: 127, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 127 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAATATTT
ATATATAAGACCATAGCTGGGCTATGACATTCTGAT
Found at i:5607545 original size:24 final size:24
Alignment explanation
Indices: 5607513--5607563 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
5607503 TGGCACTATG
5607513 AATGTAAAGGATGAATTGACGGAA
1 AATGTAAAGGATGAATTGACGGAA
*
5607537 AATGTAAAGGATGAATTGACGGCA
1 AATGTAAAGGATGAATTGACGGAA
5607561 AAT
1 AAT
5607564 TTCCCAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.06, G:0.27, T:0.22
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGACGGAA
Found at i:5612960 original size:25 final size:25
Alignment explanation
Indices: 5612925--5613114 Score: 138
Period size: 25 Copynumber: 7.7 Consensus size: 25
5612915 CCGTTATTTA
* *
5612925 GCTCTTATGAGCATCCCGATATATG
1 GCTCTCATGAGCTTCCCGATATATG
* * * *
5612950 GCTCTCTTGAGCTTCCTGCTATTTG
1 GCTCTCATGAGCTTCCCGATATATG
* * *
5612975 GCTTTCACGAGCTTCTCGATA-ATTG
1 GCTCTCATGAGCTTCCCGATATA-TG
*
5613000 GTTCTCATGAGCTTCCCGAT-TAATG
1 GCTCTCATGAGCTTCCCGATAT-ATG
*
5613025 ACTCTC-TGAAGCTTCCCGATAT-TG
1 GCTCTCATG-AGCTTCCCGATATATG
* **
5613049 GCTCGCATGAGCTTCCTAAT-TATG
1 GCTCTCATGAGCTTCCCGATATATG
* * * * *
5613073 GCTTTTATGAGCTTTCCGTTACATG
1 GCTCTCATGAGCTTCCCGATATATG
*
5613098 GCTCACATGAGCTTCCC
1 GCTCTCATGAGCTTCCC
5613115 ATTTCATGGC
Statistics
Matches: 122, Mismatches: 35, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
23 1 0.01
24 32 0.26
25 87 0.71
26 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.36
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATATATG
Found at i:5613122 original size:25 final size:25
Alignment explanation
Indices: 5613047--5613126 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
5613037 TTCCCGATAT
* * *
5613047 TGGCTCGCATGAGCTTCCTAATT-A
1 TGGCTCACATGAGCTTCCCATTTCA
*** * * *
5613071 TGGCTTTTATGAGCTTTCCGTTACA
1 TGGCTCACATGAGCTTCCCATTTCA
5613096 TGGCTCACATGAGCTTCCCATTTCA
1 TGGCTCACATGAGCTTCCCATTTCA
5613121 TGGCTC
1 TGGCTC
5613127 GAAAAAGCTT
Statistics
Matches: 41, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
24 15 0.37
25 26 0.63
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.36
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCCATTTCA
Found at i:5613555 original size:26 final size:26
Alignment explanation
Indices: 5613519--5613571 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
5613509 TTAAATGGTA
5613519 AGTTAAATTTCATGTTATAGGAATTT
1 AGTTAAATTTCATGTTATAGGAATTT
5613545 AGTTAAATTTCATGTTATAGGAATTT
1 AGTTAAATTTCATGTTATAGGAATTT
5613571 A
1 A
5613572 CTAAGCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (26 bp):
AGTTAAATTTCATGTTATAGGAATTT
Found at i:5616339 original size:50 final size:50
Alignment explanation
Indices: 5616234--5616358 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 50
5616224 TTATTGAGGT
* * * *
5616234 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGACGTTGGTACTGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGACATGGGCACCGA
* * * *
5616284 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGACATGGGCACCGA
** * *
5616334 TATGAGAACTCTCATGTAAGACCAT
1 TATGAGAGGTCCCACGTAAGACCAT
5616359 ATTTGGGATA
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGACATGGGCACCGA
Found at i:5616656 original size:20 final size:20
Alignment explanation
Indices: 5616631--5616669 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5616621 TGTGTTGTTT
5616631 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
5616651 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
5616670 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:5616932 original size:17 final size:17
Alignment explanation
Indices: 5616910--5616942 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5616900 ATAGAAAGTC
5616910 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
5616927 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
5616943 AAATCTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:5621552 original size:17 final size:17
Alignment explanation
Indices: 5621503--5621545 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
5621493 ATAGAAAGTC
5621503 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
5621520 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
5621537 AAAGATATG
1 AAAGATATG
5621546 AGAATCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.05, G:0.28, T:0.23
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:5624075 original size:146 final size:146
Alignment explanation
Indices: 5623811--5624090 Score: 551
Period size: 146 Copynumber: 1.9 Consensus size: 146
5623801 CAAGACTCAA
*
5623811 AAACAATTTATCCTTGATTAAAATCATGTTGGTGGAAAGGGATGATCATGATCATTAACTCCCAC
1 AAACAATTTATCCTTGATTAAAATCATGTTAGTGGAAAGGGATGATCATGATCATTAACTCCCAC
5623876 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
66 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
5623941 CCACTAAGTATGTCTT
131 CCACTAAGTATGTCTT
5623957 AAACAATTTATCCTTGATTAAAATCATGTTAGTGGAAAGGGATGATCATGATCATTAACTCCCAC
1 AAACAATTTATCCTTGATTAAAATCATGTTAGTGGAAAGGGATGATCATGATCATTAACTCCCAC
5624022 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
66 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
5624087 CCAC
131 CCAC
5624091 ATGTGTATAT
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 133 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (146 bp):
AAACAATTTATCCTTGATTAAAATCATGTTAGTGGAAAGGGATGATCATGATCATTAACTCCCAC
TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
CCACTAAGTATGTCTT
Found at i:5632302 original size:49 final size:50
Alignment explanation
Indices: 5632152--5632440 Score: 260
Period size: 50 Copynumber: 5.7 Consensus size: 50
5632142 GAATATAACA
* * * ** * * *
5632152 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * * * ** * *
5632201 TGCCAATGTCATATCCTAGATATGGTCTTACATTGGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
5632251 TGCCTATGCCATGTCCCAGACATGGTCTTAC-GGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
5632300 TGCCCACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
5632350 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
*
5632406 TGCCAATGCCATGTCCCAGACATGGTCTTACATGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGG
5632441 TTCCTCTTTA
Statistics
Matches: 196, Mismatches: 35, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
49 74 0.38
50 83 0.42
53 5 0.03
56 34 0.17
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:5632343 original size:99 final size:102
Alignment explanation
Indices: 5632222--5632440 Score: 264
Period size: 99 Copynumber: 2.1 Consensus size: 102
5632212 TATCCTAGAT
* ** * * *
5632222 ATGGTCTTACATTGGAGTTCTCATATAGGTGCCTATGCCATGTCCCAGACATGGTCTTAC-GGGG
1 ATGGTCTTACATGGGACCTCTCATATAGGTGCCAACGCCATGTCCCAAACATGGTCTTACAGGGG
* *
5632286 ACCTCTC-ATCTC-GGTGCCCACACCATGTCCCAGAC
66 ACCTCTCAATCTCAGATGCCAACACCATGTCCCAGAC
* * *
5632321 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAACATGGTCTTACATGGG
1 ATGGTCTTACATGGGACCTCTCATATAGGTGCCAACGCCATGTCCCAAACATGGTCTTACAGGGG
**
5632386 ACCTCTCATAATCTCAATGATGCCAATGCCATGTCCCAGAC
66 ACCTCTC--AATCTC-A-GATGCCAACACCATGTCCCAGAC
5632427 ATGGTCTTACATGG
1 ATGGTCTTACATGG
5632441 TTCCTCTTTA
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
99 52 0.52
100 10 0.10
103 5 0.05
106 33 0.33
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (102 bp):
ATGGTCTTACATGGGACCTCTCATATAGGTGCCAACGCCATGTCCCAAACATGGTCTTACAGGGG
ACCTCTCAATCTCAGATGCCAACACCATGTCCCAGAC
Found at i:5648842 original size:43 final size:43
Alignment explanation
Indices: 5648789--5648875 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
5648779 AACAAGACGA
*
5648789 TCGCCTTCATCTTTAGACAAAGCTGATGACCTAATCATTGGTG
1 TCGCCCTCATCTTTAGACAAAGCTGATGACCTAATCATTGGTG
5648832 TCGCCCTCATCTTTAGACAAAGCTGATGACCTAATCATTGGTG
1 TCGCCCTCATCTTTAGACAAAGCTGATGACCTAATCATTGGTG
5648875 T
1 T
5648876 GTGGACACTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (43 bp):
TCGCCCTCATCTTTAGACAAAGCTGATGACCTAATCATTGGTG
Found at i:5655033 original size:14 final size:12
Alignment explanation
Indices: 5654988--5655058 Score: 54
Period size: 13 Copynumber: 5.4 Consensus size: 12
5654978 CTTAACAAAT
5654988 ATTTTAATTA-A
1 ATTTTAATTATA
*
5654999 ATATTTAATAATAA
1 AT-TTTAATTAT-A
5655013 ATTTTAATTGATA
1 ATTTTAATT-ATA
5655026 ATTCTTAAATTATTA
1 ATT-TT-AATTA-TA
*
5655041 TTTTTAATTTATA
1 ATTTTAA-TTATA
5655054 ATTTT
1 ATTTT
5655059 GATTGGTACA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
11 2 0.04
12 7 0.15
13 18 0.38
14 13 0.27
15 8 0.17
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (12 bp):
ATTTTAATTATA
Found at i:5663238 original size:20 final size:20
Alignment explanation
Indices: 5663181--5663239 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
5663171 TTTTTAAAAA
* * *
5663181 ATTAAAGTTTTAAAAAATATT
1 ATTAAAATTATAAAAAA-AGT
* **
5663202 ATAAAAATTATTTAAAAAGT
1 ATTAAAATTATAAAAAAAGT
5663222 ATTAAAATTATAAAAAAA
1 ATTAAAATTATAAAAAAA
5663240 TATATTTTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
ATTAAAATTATAAAAAAAGT
Found at i:5669069 original size:2 final size:2
Alignment explanation
Indices: 5669064--5669106 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5669054 TGAAACCAAA
5669064 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5669106 A
1 A
5669107 AAGAAACAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5670664 original size:3 final size:3
Alignment explanation
Indices: 5670658--5670691 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5670648 CGTTGTTGCA
5670658 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
5670692 AGTCTTCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:5676276 original size:12 final size:12
Alignment explanation
Indices: 5676261--5676298 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
5676251 TGGTACACGG
*
5676261 CCTAACACATGC
1 CCTAACACAAGC
5676273 CCTAACACAAGC
1 CCTAACACAAGC
5676285 CCTAACACAAGC
1 CCTAACACAAGC
5676297 CC
1 CC
5676299 GTGTGACTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.37, C:0.45, G:0.08, T:0.11
Consensus pattern (12 bp):
CCTAACACAAGC
Found at i:5681311 original size:6 final size:6
Alignment explanation
Indices: 5681292--5681334 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
5681282 TCTAAATGAA
*
5681292 TTCATT TCTCATT TTCATT TTCATT TTCATT TTCATT TCCATT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TTCATT
5681335 GAGAAAACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (6 bp):
TTCATT
Found at i:5684437 original size:6 final size:6
Alignment explanation
Indices: 5684398--5684460 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
5684388 CGCTTTTCAT
* * * * * *
5684398 ATTTTT ATTTTG ACTTTG A--TTG ATTTTC TTTTTG CTTTTG ACTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
5684444 ATTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTT
5684461 TTTCTTCTTC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
4 4 0.09
6 42 0.91
ACGTcount: A:0.14, C:0.06, G:0.13, T:0.67
Consensus pattern (6 bp):
ATTTTG
Found at i:5684484 original size:8 final size:9
Alignment explanation
Indices: 5684458--5684492 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
5684448 TGATTTTGAT
5684458 TTTTTTCTTC
1 TTTTTT-TTC
5684468 TTCTTTTTTC
1 TT-TTTTTTC
5684478 TTTTTTTTC
1 TTTTTTTTC
5684487 TTTTTT
1 TTTTTT
5684493 GAAATTAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 13 0.54
10 7 0.29
11 4 0.17
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:5689733 original size:3 final size:3
Alignment explanation
Indices: 5689727--5689760 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
5689717 AAAAAGAGAC
*
5689727 TAA TAA TAA TAA TAA TAA TAA CTAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
5689761 AAACAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:5692107 original size:22 final size:23
Alignment explanation
Indices: 5692059--5692107 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
5692049 TATTGGTATG
5692059 ATTAATGTGTCCTAATAAGTCGT
1 ATTAATGTGTCCTAATAAGTCGT
* *
5692082 -TTAATGTGTCTTAATAGGT-GT
1 ATTAATGTGTCCTAATAAGTCGT
5692103 ATTAA
1 ATTAA
5692108 AGAAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (23 bp):
ATTAATGTGTCCTAATAAGTCGT
Found at i:5695045 original size:2 final size:2
Alignment explanation
Indices: 5695005--5695037 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5694995 TATGGTTGTA
5695005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5695038 GGATATATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5696556 original size:20 final size:19
Alignment explanation
Indices: 5696531--5696583 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
5696521 CTATTTTTTA
*
5696531 ACTTATTAATTTTTTAGTTG
1 ACTTATTAATTTTGTA-TTG
* *
5696551 ACTTATTATATATTGTATTT
1 ACTTATTA-ATTTTGTATTG
5696571 ACTTATTAATTTT
1 ACTTATTAATTTT
5696584 ATTATGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 18 0.64
21 6 0.21
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (19 bp):
ACTTATTAATTTTGTATTG
Found at i:5699919 original size:13 final size:13
Alignment explanation
Indices: 5699901--5699925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5699891 TAAAACCAAA
5699901 AAATGTTTAGTTG
1 AAATGTTTAGTTG
5699914 AAATGTTTAGTT
1 AAATGTTTAGTT
5699926 TGAATCATAT
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:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
AAATGTTTAGTTG
Found at i:5702955 original size:12 final size:11
Alignment explanation
Indices: 5702920--5702971 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
5702910 ATTTAGCAAG
5702920 TATAAAAAAA-
1 TATAAAAAAAT
*
5702930 TATAAAAATAT
1 TATAAAAAAAT
5702941 TATAAAAAAAGT
1 TATAAAAAAA-T
5702953 TATAGAAAATAA-
1 TATA-AAAA-AAT
5702965 TATAAAA
1 TATAAAA
5702972 TTATTCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 9 0.25
11 12 0.33
12 9 0.25
13 4 0.11
14 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (11 bp):
TATAAAAAAAT
Found at i:5712896 original size:30 final size:28
Alignment explanation
Indices: 5712857--5712918 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 28
5712847 ATGGATTTAA
5712857 ATTACTTATTATTTAAGTAAATAGATATTT
1 ATTACTTATTA-TTAAGTAAA-AGATATTT
*
5712887 ATTATTTATTATTAAGTAAAAGATATTT
1 ATTACTTATTATTAAGTAAAAGATATTT
5712915 ATTA
1 ATTA
5712919 ATTAAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 12 0.39
29 9 0.29
30 10 0.32
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (28 bp):
ATTACTTATTATTAAGTAAAAGATATTT
Found at i:5713581 original size:17 final size:18
Alignment explanation
Indices: 5713559--5713594 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5713549 TAAATGAGTC
5713559 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
5713576 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
5713594 A
1 A
5713595 TAAAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:5722970 original size:22 final size:22
Alignment explanation
Indices: 5722945--5722992 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
5722935 GGAGTATGGC
5722945 ATTTAGTACTCAAAAACTTCAT
1 ATTTAGTACTCAAAAACTTCAT
*
5722967 ATTTGGTACTCAAAAACTTCAT
1 ATTTAGTACTCAAAAACTTCAT
5722989 ATTT
1 ATTT
5722993 CAGATTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (22 bp):
ATTTAGTACTCAAAAACTTCAT
Found at i:5723944 original size:6 final size:6
Alignment explanation
Indices: 5723935--5723959 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5723925 TGATAATTCG
5723935 AATTTA AATTTA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA A
5723960 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:5730304 original size:85 final size:86
Alignment explanation
Indices: 5730145--5730319 Score: 262
Period size: 86 Copynumber: 2.0 Consensus size: 86
5730135 GGGTTTTAAT
* * *
5730145 TTTTTTTGTAGTATTATTTATTTGTATGTTTGTAACTTAATTAGTATAAAAAAAACTAAATAAAT
1 TTTTTTTGAAGTATTATTTATTTGTATGCTTCTAACTTAATTAGTATAAAAAAAACTAAATAAAT
*
5730210 ATTGAAATGGTATATTTGAGA
66 ACTGAAATGGTATATTTGAGA
* * *
5730231 TTTTTTTGAATTATTATTTATTTGTATGCTTCTTACTTAATTAGTAT-AAAAAAACTAATTAAAT
1 TTTTTTTGAAGTATTATTTATTTGTATGCTTCTAACTTAATTAGTATAAAAAAAACTAAATAAAT
* *
5730295 ACTGAAATGGTATGTTTGAGG
66 ACTGAAATGGTATATTTGAGA
5730316 TTTT
1 TTTT
5730320 CAAGGGTTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 38 0.47
86 42 0.52
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (86 bp):
TTTTTTTGAAGTATTATTTATTTGTATGCTTCTAACTTAATTAGTATAAAAAAAACTAAATAAAT
ACTGAAATGGTATATTTGAGA
Found at i:5730338 original size:86 final size:86
Alignment explanation
Indices: 5730156--5730338 Score: 215
Period size: 86 Copynumber: 2.1 Consensus size: 86
5730146 TTTTTTGTAG
* * * *
5730156 TATTATTTATTTGTATGTTTGTAACTTAATTAGTATAAAAAAAACTAAATAAATATTGAAATGGT
1 TATTAATTATTTGTATGCTTCTAACTTAATTAGTATAAAAAAAACTAAATAAATACTGAAATGGT
***
5730221 ATATTTGAGATTTTTTTGAAT
66 ATATTTGAGATTTTAAGGAAT
* * *
5730242 TATTATTTATTTGTATGCTTCTTACTTAATTAGTAT-AAAAAAACTAATTAAATACTGAAATGGT
1 TATTAATTATTTGTATGCTTCTAACTTAATTAGTATAAAAAAAACTAAATAAATACTGAAATGGT
* * **
5730306 ATGTTTGAGGTTTTCAAGGGTT
66 ATATTTGAGATTTT-AAGGAAT
*
5730328 TTTTAATTATT
1 TATTAATTATT
5730339 ATTTGTTTGA
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
85 38 0.46
86 44 0.54
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (86 bp):
TATTAATTATTTGTATGCTTCTAACTTAATTAGTATAAAAAAAACTAAATAAATACTGAAATGGT
ATATTTGAGATTTTAAGGAAT
Found at i:5736997 original size:21 final size:21
Alignment explanation
Indices: 5736971--5737013 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5736961 CAACCACTCT
5736971 CAGAAATGAGTATTCATTTCA
1 CAGAAATGAGTATTCATTTCA
5736992 CAGAAATGAGTATTCATTTCA
1 CAGAAATGAGTATTCATTTCA
5737013 C
1 C
5737014 TATGCATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (21 bp):
CAGAAATGAGTATTCATTTCA
Found at i:5739213 original size:30 final size:30
Alignment explanation
Indices: 5739163--5739220 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5739153 TGCTACAACC
*
5739163 ATTCAATAAAACACAAAAATTACTATAACA
1 ATTCAAGAAAACACAAAAATTACTATAACA
* * *
5739193 ATTCAAGAAAATACACAAATTGCTATAA
1 ATTCAAGAAAACACAAAAATTACTATAA
5739221 TTGTTCAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
ATTCAAGAAAACACAAAAATTACTATAACA
Found at i:5740472 original size:27 final size:27
Alignment explanation
Indices: 5740434--5740516 Score: 157
Period size: 27 Copynumber: 3.1 Consensus size: 27
5740424 ATTAATTTAT
5740434 TTTGTAAAGTAATTATTTATTTTGAAC
1 TTTGTAAAGTAATTATTTATTTTGAAC
*
5740461 TTTGTGAAGTAATTATTTATTTTGAAC
1 TTTGTAAAGTAATTATTTATTTTGAAC
5740488 TTTGTAAAGTAATTATTTATTTTGAAC
1 TTTGTAAAGTAATTATTTATTTTGAAC
5740515 TT
1 TT
5740517 AGCAAATAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (27 bp):
TTTGTAAAGTAATTATTTATTTTGAAC
Found at i:5748216 original size:14 final size:14
Alignment explanation
Indices: 5748197--5748223 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5748187 AACACAAAAT
5748197 ATTAGACATTGGAC
1 ATTAGACATTGGAC
5748211 ATTAGACATTGGA
1 ATTAGACATTGGA
5748224 ATTTTGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (14 bp):
ATTAGACATTGGAC
Found at i:5751083 original size:21 final size:21
Alignment explanation
Indices: 5751014--5751178 Score: 106
Period size: 21 Copynumber: 8.0 Consensus size: 21
5751004 CGGGAGGATC
**
5751014 AGCTCTTACGAGCTTCTGTGA
1 AGCTCTTACGAGCTTCTGTTT
*
5751035 AGCTCTTACGAGCTTCTTTTTT
1 AGCTCTTACGAGCTTC-TGTTT
* **
5751057 AACTCTTTTGAGCTTCTGTTT
1 AGCTCTTACGAGCTTCTGTTT
**
5751078 AGCTCTTATAAGCTTCTG-TT
1 AGCTCTTACGAGCTTCTGTTT
* * * * * * *
5751098 GGCATGATT-TG-G-GT-GGATC
1 AGC-T-CTTACGAGCTTCTGTTT
*
5751117 AGCTCTTACGAGCTTCTGTTC
1 AGCTCTTACGAGCTTCTGTTT
*
5751138 AGCTCTTACGAGCTTCTATTT
1 AGCTCTTACGAGCTTCTGTTT
*
5751159 AGCTCTTATGAGCTTCTGTT
1 AGCTCTTACGAGCTTCTGTT
5751179 GGCGTGTTCG
Statistics
Matches: 110, Mismatches: 26, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
17 2 0.02
18 3 0.03
19 5 0.05
20 6 0.05
21 77 0.70
22 17 0.15
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.42
Consensus pattern (21 bp):
AGCTCTTACGAGCTTCTGTTT
Found at i:5751173 original size:81 final size:80
Alignment explanation
Indices: 5751035--5751216 Score: 229
Period size: 81 Copynumber: 2.2 Consensus size: 80
5751025 GCTTCTGTGA
* * ** *
5751035 AGCTCTTACGAGCTTCTTTTTTAACTCTTTTGAGCTTCTGTTTAGCTCTTATAAGCTTCTGTTGG
1 AGCTCTTACGAGCTTC-TGTTCAACTCTTACGAGCTTCTATTTAGCTCTTATAAGCTTCTGTTGG
* ** *
5751100 CATGATTTGGGTGGATC
65 CATG-TTCGGAAGGACC
* *
5751117 AGCTCTTACGAGCTTCTGTTCAGCTCTTACGAGCTTCTATTTAGCTCTTATGAGCTTCTGTTGGC
1 AGCTCTTACGAGCTTCTGTTCAACTCTTACGAGCTTCTATTTAGCTCTTATAAGCTTCTGTTGGC
*
5751182 GTGTTCGGAAGGACC
66 ATGTTCGGAAGGACC
*
5751197 AGCTCTTATGAGCTTCTGTT
1 AGCTCTTACGAGCTTCTGTT
5751217 GACGATGTAC
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 27 0.31
81 44 0.51
82 16 0.18
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (80 bp):
AGCTCTTACGAGCTTCTGTTCAACTCTTACGAGCTTCTATTTAGCTCTTATAAGCTTCTGTTGGC
ATGTTCGGAAGGACC
Found at i:5756376 original size:25 final size:24
Alignment explanation
Indices: 5756333--5756385 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
5756323 AAGTTCAAGC
*
5756333 GAGCCATATCAGGAAGCTCACAAA
1 GAGCCATATCAAGAAGCTCACAAA
* *
5756357 GAGCCTATATCAAGATGCTCATAAA
1 GAGCC-ATATCAAGAAGCTCACAAA
5756382 GAGC
1 GAGC
5756386 TACAGTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.17
Consensus pattern (24 bp):
GAGCCATATCAAGAAGCTCACAAA
Found at i:5756484 original size:64 final size:64
Alignment explanation
Indices: 5756362--5756489 Score: 139
Period size: 64 Copynumber: 2.0 Consensus size: 64
5756352 ACAAAGAGCC
* * * * ** * * ** *
5756362 TATATCAAGATGCTCATAAAGAGCTACAGTATGTCCACATTATATGCAGGATCCATACCTATCA
1 TATAACAAGACGCTCACAAAGAGCTACAGTATATCCACAACACATGCAGAATAAATACCGATCA
* *
5756426 TATAACAAGACGCTCACAAAGAGCTACGGTATATCCGCAACACATGCAGAATAAATACCGATCA
1 TATAACAAGACGCTCACAAAGAGCTACAGTATATCCACAACACATGCAGAATAAATACCGATCA
5756490 GGATGCTCGC
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (64 bp):
TATAACAAGACGCTCACAAAGAGCTACAGTATATCCACAACACATGCAGAATAAATACCGATCA
Found at i:5764841 original size:16 final size:16
Alignment explanation
Indices: 5764820--5764889 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
5764810 TTTGGTTCGC
*
5764820 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
5764836 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
5764852 TGTAATAGATTAGAGG
1 TGTAATGGATTAGAGG
*
5764868 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
5764884 TGTAAT
1 TGTAAT
5764890 AGCAAATCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:5764973 original size:39 final size:43
Alignment explanation
Indices: 5764868--5764977 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
5764858 AGATTAGAGG
5764868 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
5764913 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
5764953 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
5764978 TAATGAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:5765144 original size:18 final size:17
Alignment explanation
Indices: 5765123--5765157 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5765113 TTATTATTAA
*
5765123 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5765141 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5765158 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5765211 original size:157 final size:157
Alignment explanation
Indices: 5765010--5765326 Score: 607
Period size: 157 Copynumber: 2.0 Consensus size: 157
5765000 TAGAATACCC
*
5765010 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
*
5765075 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
5765140 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
5765167 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
5765232 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
5765297 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
5765324 TTA
1 TTA
5765327 ATATTCTTAT
Statistics
Matches: 157, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 157 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:5765301 original size:18 final size:17
Alignment explanation
Indices: 5765280--5765314 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5765270 TTATTATTAA
*
5765280 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5765298 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5765315 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5765631 original size:75 final size:75
Alignment explanation
Indices: 5765508--5765658 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
5765498 ATCCAATGGA
5765508 AGCAAACTAGACTAAAAGCAGATAATAGCCAAATGTTTCCATTTTTTCTTTTTCATGTTTTTAAG
1 AGCAAACTAGACTAAAAGCAGATAATAGCCAAATGTTTCCATTTTTTCTTTTTCATGTTTTTAAG
5765573 ATACAGGCAT
66 ATACAGGCAT
5765583 AGCAAACTAGACTAAAAGCAGATAATAGCCAAATGTTTCCATTTTTTCTTTTTCATGTTTTTAAG
1 AGCAAACTAGACTAAAAGCAGATAATAGCCAAATGTTTCCATTTTTTCTTTTTCATGTTTTTAAG
5765648 ATACAGGCAT
66 ATACAGGCAT
5765658 A
1 A
5765659 CATTGAAAGC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (75 bp):
AGCAAACTAGACTAAAAGCAGATAATAGCCAAATGTTTCCATTTTTTCTTTTTCATGTTTTTAAG
ATACAGGCAT
Found at i:5787681 original size:17 final size:18
Alignment explanation
Indices: 5787655--5787693 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5787645 GGAGCTGTGG
5787655 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
5787671 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
5787689 AAAAT
1 AAAAT
5787694 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:5791236 original size:15 final size:15
Alignment explanation
Indices: 5791226--5791255 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5791216 TCCCTTCTTG
5791226 ACCACGACCTTTTCC
1 ACCACGACCTTTTCC
*
5791241 ACCACGACCATTTCC
1 ACCACGACCTTTTCC
5791256 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCTTTTCC
Found at i:5792023 original size:17 final size:18
Alignment explanation
Indices: 5791997--5792035 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5791987 CAAATTGTGG
5791997 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
5792013 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
5792031 AAAAT
1 AAAAT
5792036 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:5792212 original size:15 final size:15
Alignment explanation
Indices: 5792192--5792222 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5792182 AAAACAATAT
5792192 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
5792207 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
5792222 A
1 A
5792223 CTTACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:5794111 original size:81 final size:81
Alignment explanation
Indices: 5793990--5794139 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 81
5793980 TAGAGCACTC
* *
5793990 GCAAGGCATGGTATACTTCATCCATCGTTGAGACCTGTAGCAAATCATAGTAATACAATGACCAA
1 GCAAGGCATGGTATACTTCATCCATCGTCGAGACCTGTAGCAAATCATAGTAATACAACGACCAA
5794055 CCTCTACTAAGCATTT
66 CCTCTACTAAGCATTT
* * * * *
5794071 GCAAGGCATGGTATACTTCATTCTTCGTCGAGA-TTAGTAGCAGATCATAGTAATACAACGAGCA
1 GCAAGGCATGGTATACTTCATCCATCGTCGAGACCT-GTAGCAAATCATAGTAATACAACGACCA
5794135 ACCTC
65 ACCTC
5794140 CACCAAGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 1 0.02
81 60 0.98
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (81 bp):
GCAAGGCATGGTATACTTCATCCATCGTCGAGACCTGTAGCAAATCATAGTAATACAACGACCAA
CCTCTACTAAGCATTT
Found at i:5797153 original size:45 final size:45
Alignment explanation
Indices: 5797104--5797189 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
5797094 ATCTTTTTAC
* *
5797104 CATGATGTCATAGCGTCATTCATCCATGGTCTTACTCATTTCCAT
1 CATGATGTCATAGCATCATTCAACCATGGTCTTACTCATTTCCAT
** * *
5797149 CATGATGTCATAGCATTTTTCAACTATGGTCTTACTTATTT
1 CATGATGTCATAGCATCATTCAACCATGGTCTTACTCATTT
5797190 TAGGTATAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (45 bp):
CATGATGTCATAGCATCATTCAACCATGGTCTTACTCATTTCCAT
Found at i:5801110 original size:27 final size:27
Alignment explanation
Indices: 5801072--5801136 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
5801062 TTTATCGAGG
* *
5801072 TTATTAGTTTATCGTTAAATAAATATT
1 TTATTAATTTATCGATAAATAAATATT
*
5801099 TTATTAATTTATCGATAAATTAATATT
1 TTATTAATTTATCGATAAATAAATATT
5801126 TTATTAATTTA
1 TTATTAATTTA
5801137 GAGAATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (27 bp):
TTATTAATTTATCGATAAATAAATATT
Found at i:5804048 original size:34 final size:38
Alignment explanation
Indices: 5804010--5804082 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 38
5804000 TAGATCAAAG
5804010 TTAATTGGTTCATGTA-AC-AAAA-AA-AAAGAGTTAA
1 TTAATTGGTTCATGTAGACAAAAAGAATAAAGAGTTAA
*
5804044 TTAATTGGTTCATGTAGCCAAAAAGAATAAAGAGTTAA
1 TTAATTGGTTCATGTAGACAAAAAGAATAAAGAGTTAA
5804082 T
1 T
5804083 GGTTTCAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
34 16 0.47
35 1 0.03
36 4 0.12
37 2 0.06
38 11 0.32
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (38 bp):
TTAATTGGTTCATGTAGACAAAAAGAATAAAGAGTTAA
Found at i:5806739 original size:20 final size:21
Alignment explanation
Indices: 5806698--5806741 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5806688 GAGTTGAAAT
*
5806698 TAAAGTTATGAATTATATATA
1 TAAAGTTATGAATGATATATA
5806719 TAAAGTT-TGAATGA-ATGATA
1 TAAAGTTATGAATGATAT-ATA
5806739 TAA
1 TAA
5806742 GTTGTTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.57
21 7 0.33
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.39
Consensus pattern (21 bp):
TAAAGTTATGAATGATATATA
Found at i:5806895 original size:64 final size:64
Alignment explanation
Indices: 5806810--5806985 Score: 227
Period size: 64 Copynumber: 2.8 Consensus size: 64
5806800 ATATATATTT
* * *
5806810 AAAGTTCTTGAGTTGTATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTTTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
* *
5806874 AAAGTTTTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAATATAGGTTAC
1 AAAGTTTTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
* * *
5806938 AAA-TCTTTGAGCTAAATTTTAATGT-TGTAA--AT-TATACATATGTGGTTC
1 AAAGTTTTTGAGCTGAA-TTTAATGTATG-AATTTTATATACATATGTGGTTC
5806986 GAATGTTTGT
Statistics
Matches: 101, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
61 15 0.15
62 1 0.01
63 13 0.13
64 72 0.71
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (64 bp):
AAAGTTTTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
Found at i:5807164 original size:41 final size:41
Alignment explanation
Indices: 5807105--5807207 Score: 179
Period size: 41 Copynumber: 2.5 Consensus size: 41
5807095 ATCTGATATT
* * *
5807105 TTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
5807146 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
5807187 TTCAGACTTTATGTCTAGCAG
1 TTCAGACTTTATGTCTAGCAG
5807208 GCTTTGTGCC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
Found at i:5807223 original size:41 final size:41
Alignment explanation
Indices: 5807105--5807223 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
5807095 ATCTGATATT
* * * * *
5807105 TTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGCCAGTGAATTAC
* *
5807146 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGCCAGTGAATTAC
*
5807187 TTCAGACTTTATGTCTAGCAGGCTTTG-TGCCAGTGAA
1 TTCAGACTTTATGTCTAGCAGAC-TTGATGCCAGTGAA
5807224 ATGTATCGGG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
41 68 0.96
42 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGACTTGATGCCAGTGAATTAC
Found at i:5812489 original size:20 final size:19
Alignment explanation
Indices: 5812466--5812521 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
5812456 TTATGAAGTC
5812466 GTAATAAAATTATAAAAAAG
1 GTAA-AAAATTATAAAAAAG
***
5812486 GTAAAGAAA-TATAAAATTT
1 GTAAA-AAATTATAAAAAAG
5812505 GTAAAAAAATTATAAAA
1 GT-AAAAAATTATAAAA
5812522 GTTATCATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (19 bp):
GTAAAAAATTATAAAAAAG
Found at i:5812747 original size:11 final size:11
Alignment explanation
Indices: 5812733--5812766 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5812723 TTTTACAAAA
5812733 TTTACAATTTT
1 TTTACAATTTT
**
5812744 TTTATGATTTT
1 TTTACAATTTT
5812755 TTTACAATTTT
1 TTTACAATTTT
5812766 T
1 T
5812767 ATATTTTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.68
Consensus pattern (11 bp):
TTTACAATTTT
Found at i:5812775 original size:18 final size:20
Alignment explanation
Indices: 5812742--5812785 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
5812732 ATTTACAATT
5812742 TTTTTATGATTTTTTTAC-AA
1 TTTTTATGATTTTTTT-CTAA
5812762 TTTTTAT-A-TTTTTTCTAA
1 TTTTTATGATTTTTTTCTAA
5812780 TTTTTA
1 TTTTTA
5812786 ATAAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 1 0.04
20 7 0.30
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTATGATTTTTTTCTAA
Found at i:5812826 original size:9 final size:9
Alignment explanation
Indices: 5812753--5812842 Score: 67
Period size: 9 Copynumber: 9.9 Consensus size: 9
5812743 TTTTATGATT
*
5812753 TTTTTACAA
1 TTTTTATAA
*
5812762 TTTTTATAT
1 TTTTTATAA
*
5812771 TTTTTCTAA
1 TTTTTATAA
5812780 TTTTTAATAA
1 TTTTT-ATAA
* *
5812790 ATTTTAT-T
1 TTTTTATAA
5812798 TTTATTA-AA
1 TTT-TTATAA
* *
5812807 ATTTCATAA
1 TTTTTATAA
5812816 TTTTTATAA
1 TTTTTATAA
*
5812825 TTTTTATTGA
1 TTTTTA-TAA
5812835 TTTTTATA
1 TTTTTATA
5812843 GTTAATGGTC
Statistics
Matches: 61, Mismatches: 15, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
8 4 0.07
9 42 0.69
10 15 0.25
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:5815583 original size:33 final size:35
Alignment explanation
Indices: 5815544--5815630 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 35
5815534 AACCACTACC
5815544 ATAAATATATTAAATATTTTATTATATTAAA-A-A
1 ATAAATATATTAAATATTTTATTATATTAAATATA
* * * *
5815577 ATAAATAAAATAAATGTTTTATTGTATTAAATATA
1 ATAAATATATTAAATATTTTATTATATTAAATATA
5815612 AT-AATAT-TTAAA-ATTTTAT
1 ATAAATATATTAAATATTTTAT
5815631 ATTTTGGGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 6 0.13
33 31 0.69
34 5 0.11
35 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (35 bp):
ATAAATATATTAAATATTTTATTATATTAAATATA
Found at i:5816111 original size:32 final size:32
Alignment explanation
Indices: 5816070--5816135 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
5816060 AGTAGGAGTT
5816070 GGATTGCATTTTGCTCATCTACTTAAAAAATG
1 GGATTGCATTTTGCTCATCTACTTAAAAAATG
5816102 GGATTGCATTTTGCTCATCTACTTAAAAAATG
1 GGATTGCATTTTGCTCATCTACTTAAAAAATG
5816134 GG
1 GG
5816136 CAATTAGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (32 bp):
GGATTGCATTTTGCTCATCTACTTAAAAAATG
Found at i:5817453 original size:42 final size:42
Alignment explanation
Indices: 5817403--5817545 Score: 153
Period size: 42 Copynumber: 3.4 Consensus size: 42
5817393 CCACACAGCC
5817403 AAGGACATGGGCATGTGCCCAGGCCGTGTGAGTCACACGGGT
1 AAGGACATGGGCATGTGCCCAGGCCGTGTGAGTCACACGGGT
** * *
5817445 AAGGACATGGGTGTGTGCCCAAGCCGTGTGA-TCCTCACGGGT
1 AAGGACATGGGCATGTGCCCAGGCCGTGTGAGT-CACACGGGT
* *** * * * *
5817487 AAGGACATAGATGTGTGCCCAGGCCATGTGAGCCACATGGGC
1 AAGGACATGGGCATGTGCCCAGGCCGTGTGAGTCACACGGGT
*
5817529 AAGGACATGTGCATGTG
1 AAGGACATGGGCATGTG
5817546 TTCAGGTCGT
Statistics
Matches: 82, Mismatches: 17, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
41 1 0.01
42 81 0.99
ACGTcount: A:0.23, C:0.22, G:0.36, T:0.19
Consensus pattern (42 bp):
AAGGACATGGGCATGTGCCCAGGCCGTGTGAGTCACACGGGT
Found at i:5820426 original size:30 final size:29
Alignment explanation
Indices: 5820387--5820447 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
5820377 ATTGAACTTT
5820387 AACTATT-AAATCAAAATAATAGAGAGATTA
1 AACTATTAAAAT-AAAA-AATAGAGAGATTA
* * *
5820417 AACTCTTAAAATTAAAAATAGATAGATTA
1 AACTATTAAAATAAAAAATAGAGAGATTA
5820446 AA
1 AA
5820448 TTTTAAGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 14 0.52
30 9 0.33
31 4 0.15
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (29 bp):
AACTATTAAAATAAAAAATAGAGAGATTA
Found at i:5821832 original size:43 final size:42
Alignment explanation
Indices: 5821704--5821833 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 42
5821694 GATAGGATTT
* * *
5821704 TCGATATGTGTTTTCGTGTAAGACTACGTCTGGGACGTTGCCA
1 TCGATATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCA
* * *
5821747 TCGATTTGTGTGTATGTGTAAGACC-CTGTCTAGGACAG-TGGCA
1 TCGATATGTGT-TACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
*
5821790 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCA
5821833 T
1 T
5821834 TGTACGAGTG
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
42 3 0.04
43 65 0.92
44 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (42 bp):
TCGATATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:5827394 original size:41 final size:41
Alignment explanation
Indices: 5827330--5827606 Score: 358
Period size: 41 Copynumber: 6.8 Consensus size: 41
5827320 CTTTAGGGAT
** * * *
5827330 TTTAGCGGCGTTTTTTAAAAAGCGCTGCTAATGCCCTG-GTC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAG-C
* * *
5827371 TTTAGCGGCGTTTTTGGAGAAGCGCCACTAATGCTCAGAGA
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGC
* * * *
5827412 TTTAGCGGCGTTGTTGAAAAATCGCTGCTAATGCTCAGAGC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGC
* *
5827453 TTTAGCGGCGTTTTTGGAGAAGCGTCGCTAATGCTCAGAGC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGC
* * * *
5827494 TTTAGCGGCGTTTTTGGAAAAGCCCCACTAATGCTAAGATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGC
* *
5827535 TTTAGCGGCGTTTTTGGAAAAGCGCCACTAATGCTCAGATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGC
5827576 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
5827607 AATATTTTAT
Statistics
Matches: 205, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
41 204 1.00
42 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGC
Found at i:5828200 original size:13 final size:13
Alignment explanation
Indices: 5828170--5828211 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5828160 TAAATAAGAT
*
5828170 TTAGGGGTTAGAGG
1 TTAGGGTTTAG-GG
5828184 TTAGGGATTT-GGG
1 TTAGGG-TTTAGGG
5828197 TTAGGGTTTAGGG
1 TTAGGGTTTAGGG
5828210 TT
1 TT
5828212 TAGATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 3 0.12
13 13 0.52
14 7 0.28
15 2 0.08
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (13 bp):
TTAGGGTTTAGGG
Found at i:5828208 original size:81 final size:83
Alignment explanation
Indices: 5828115--5828272 Score: 218
Period size: 83 Copynumber: 1.9 Consensus size: 83
5828105 TTAGTGTCAA
5828115 GTTAGGCTTTAGGGTTTAGACT-AATCAGTATGTTTT-AA-TT-TATATTAAATAAGATTTAGGG
1 GTTAGGCTTTAGGGTTTAGA-TAAATCAGTAT-TTTTAAATTTATATATTAAATAAGATTTAGGG
5828176 GTTAG-AGGTTAGGGATTTGG
64 GTTAGTA-GTTAGGGATTTGG
* * * *
5828196 GTTAGGGTTTAGGGTTTAGATAAATTAGTGTTTTTAAATTTATATATTAAATAAGGTTTAGGGGT
1 GTTAGGCTTTAGGGTTTAGATAAATCAGTATTTTTAAATTTATATATTAAATAAGATTTAGGGGT
5828261 TAGTAGTTAGGG
66 TAGTAGTTAGGG
5828273 TTAGGGGTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
80 5 0.07
81 28 0.41
82 2 0.03
83 32 0.47
84 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.42
Consensus pattern (83 bp):
GTTAGGCTTTAGGGTTTAGATAAATCAGTATTTTTAAATTTATATATTAAATAAGATTTAGGGGT
TAGTAGTTAGGGATTTGG
Found at i:5828412 original size:7 final size:7
Alignment explanation
Indices: 5828400--5828442 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
5828390 ATTGTAAAAG
5828400 AGGGGTT
1 AGGGGTT
5828407 AGGGGTT
1 AGGGGTT
*
5828414 AGAGGTT
1 AGGGGTT
* *
5828421 AAGGATT
1 AGGGGTT
5828428 AGGGGTT
1 AGGGGTT
5828435 AGGGGTT
1 AGGGGTT
5828442 A
1 A
5828443 TGGATAGGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.23, C:0.00, G:0.49, T:0.28
Consensus pattern (7 bp):
AGGGGTT
Found at i:5828431 original size:21 final size:21
Alignment explanation
Indices: 5828405--5828447 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5828395 AAAAGAGGGG
5828405 TTAGGGGTTAGAGGTTAAGGA
1 TTAGGGGTTAGAGGTTAAGGA
* *
5828426 TTAGGGGTTAGGGGTTATGGA
1 TTAGGGGTTAGAGGTTAAGGA
5828447 T
1 T
5828448 AGGTAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.44, T:0.33
Consensus pattern (21 bp):
TTAGGGGTTAGAGGTTAAGGA
Found at i:5833739 original size:43 final size:42
Alignment explanation
Indices: 5833662--5833929 Score: 240
Period size: 43 Copynumber: 6.3 Consensus size: 42
5833652 GATATGTTTT
* * * * *
5833662 TAGCAGCGCTTGTGTGAAAAGCGCCACTAAAGGTCTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTA
* * *
5833704 TAGCAGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCTTTATATA
1 TAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTC-TGATCTA
* *
5833748 TAGCAGCGTTTGT-GGAACAAGCGCCGCTAAAAGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAA-AAGCGCCGCTAAAGGTC-TGATCTA
* **
5833791 TAGCGGCGTTT-TGTGAAAAAGCGTTGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTG-GGAAAAGCGCCGCTAAAGGT-CTGATCTA
** * *
5833834 TAGCGGCGTTTTGTGTGG--TTGCACCGCTAAAGGTCCTAATCTA
1 TAGCGGCG-TTTGTG-GGAAAAGCGCCGCTAAAGGT-CTGATCTA
* *
5833877 TAGCGGCGTTT-TTGGAAAAGCGCCGCTAAAGGTTTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG-TCTGATCTA
5833919 TAGCGGCGTTT
1 TAGCGGCGTTT
5833930 ATTTCAAAAA
Statistics
Matches: 188, Mismatches: 27, Indels: 22
0.79 0.11 0.09
Matches are distributed among these distances:
40 2 0.01
41 1 0.01
42 49 0.26
43 108 0.57
44 24 0.13
45 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (42 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTA
Found at i:5833809 original size:86 final size:85
Alignment explanation
Indices: 5833662--5833929 Score: 283
Period size: 86 Copynumber: 3.1 Consensus size: 85
5833652 GATATGTTTT
* * * * *
5833662 TAGCAGCGCTTGTGTGAAAAGCGCCACTAAAGGTCTGTTCTATAGCAGCGTTTGTGGGAAAAAGC
1 TAGCAGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTGATCTATAGCGGCGTTT-TGTGAAAAAGC
*
5833727 GCCGCTAAAGGTCTTTATATA
65 GCCGCTAAAGGTCTTTATCTA
*
5833748 TAGCAGCGTTTGTG-GAACAAGCGCCGCTAAAAGTCTTGATCTATAGCGGCGTTTTGTGAAAAAG
1 TAGCAGCGTTTGTGTGAA-AAGCGCCGCTAAAGGTC-TGATCTATAGCGGCGTTTTGTGAAAAAG
** * *
5833812 CGTTGCTAAAGGTCCTGATCTA
64 CGCCGCTAAAGGTCTTTATCTA
* *** * * *
5833834 TAGCGGCGTTTTGTGTG-GTTGCACCGCTAAAGGTCCTAATCTATAGCGGCGTTTT-TGGAAAAG
1 TAGCAGCG-TTTGTGTGAAAAGCGCCGCTAAAGGT-CTGATCTATAGCGGCGTTTTGTGAAAAAG
5833897 CGCCGCTAAAGGT-TTTGATCTA
64 CGCCGCTAAAGGTCTTT-ATCTA
*
5833919 TAGCGGCGTTT
1 TAGCAGCGTTT
5833930 ATTTCAAAAA
Statistics
Matches: 153, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
84 4 0.03
85 34 0.22
86 91 0.59
87 23 0.15
88 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (85 bp):
TAGCAGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTGATCTATAGCGGCGTTTTGTGAAAAAGCG
CCGCTAAAGGTCTTTATCTA
Found at i:5836104 original size:19 final size:17
Alignment explanation
Indices: 5836078--5836117 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5836068 AAGAAAGCAT
5836078 TTTGAAATTGAATAATGA
1 TTTGAAA-TGAATAATGA
*
5836096 TTTGTAAATGAATAATGT
1 TTTG-AAATGAATAATGA
5836114 TTTG
1 TTTG
5836118 GAAACGAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (17 bp):
TTTGAAATGAATAATGA
Found at i:5837771 original size:81 final size:81
Alignment explanation
Indices: 5837624--5837780 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 81
5837614 TTCAGTGTCA
* * * *
5837624 GGTTAGGATTTAGGGTTTAGATTAATTAGTGTGTTTCAATTTTTATGAAATAAGGTTTAAGTGTT
1 GGTTAGGATTTAGGGTTTAGATTAATTAATATGTTTCAATTTTTATGAAATAAAGTTTAAGGGTT
*
5837689 AGGGGTTAGGGATTTG
66 AGGAGTTAGGGATTTG
* * *
5837705 GGTTAGGATTTAGGGTTTTGATTAATTAATAT-TTTTAATTTGTATATTAAATAAAGTTT-AGGG
1 GGTTAGGATTTAGGGTTTAGATTAATTAATATGTTTCAATTT-T-TATGAAATAAAGTTTAAGGG
*
5837768 TTAGTAGTTAGGG
64 TTAGGAGTTAGGG
5837781 GTTAGTGGTT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 8 0.12
81 44 0.68
82 13 0.20
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.45
Consensus pattern (81 bp):
GGTTAGGATTTAGGGTTTAGATTAATTAATATGTTTCAATTTTTATGAAATAAAGTTTAAGGGTT
AGGAGTTAGGGATTTG
Found at i:5837804 original size:14 final size:14
Alignment explanation
Indices: 5837760--5837798 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5837750 ATTAAATAAA
* *
5837760 GTTTAGGGTTAGTA
1 GTTTGGGGTTAGTG
*
5837774 GTTAGGGGTTAGTG
1 GTTTGGGGTTAGTG
5837788 GTTTGGGGTTA
1 GTTTGGGGTTA
5837799 AGGGTTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (14 bp):
GTTTGGGGTTAGTG
Found at i:5837830 original size:28 final size:28
Alignment explanation
Indices: 5837799--5837860 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
5837789 TTTGGGGTTA
5837799 AGGGTTAAAAGTTAAGAGTTGGTGATTT
1 AGGGTTAAAAGTTAAGAGTTGGTGATTT
*
5837827 AGGGTTAGAAGTTAAGAGTTGGTGATTT
1 AGGGTTAAAAGTTAAGAGTTGGTGATTT
*
5837855 AAGGTT
1 AGGGTT
5837861 TAGAGATTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.35
Consensus pattern (28 bp):
AGGGTTAAAAGTTAAGAGTTGGTGATTT
Found at i:5838222 original size:13 final size:14
Alignment explanation
Indices: 5838194--5838233 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
5838184 TTGGGATTTA
5838194 GGGTTTAGGGTTTG
1 GGGTTTAGGGTTTG
*
5838208 GGGTTT-GGTTTTG
1 GGGTTTAGGGTTTG
*
5838221 GGGTTTAAGGTTT
1 GGGTTTAGGGTTT
5838234 AGAATTTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.07, C:0.00, G:0.45, T:0.47
Consensus pattern (14 bp):
GGGTTTAGGGTTTG
Found at i:5839313 original size:147 final size:144
Alignment explanation
Indices: 5839162--5839572 Score: 371
Period size: 147 Copynumber: 2.8 Consensus size: 144
5839152 TTATAATTTT
* *
5839162 GTTTATTGAAATGTGGTCGTTTTGTCTATGGTATTAGTGGCGTTTTTATGAAAACGCCACAAGCT
1 GTTTATTGAAACGTGGTCGTTTTGTATAT-GTATTAGTGGCGTTTTTA-GAAAACGCCAC-AGCT
* ** *
5839227 TGAGTTAACTGTTGGGGAAACGACTTCG-TTTGAGCTTATAGTTAGTGGCGCTTTACTCAAAACA
63 TGAGCTAACTGTTGATGAAACGACTTCGTTTTGA-CTTATAGTTAGTGGCGCTTCACTCAAAACA
*
5839291 CCGCAAAATTGTTCTAAC
127 CCGCAAAAATGTTCTAAC
* * * * * * *
5839309 GTTTATAGAAACGCT-GTCGTTTTGTAAATGTTATCAGTGGCATTTTTGCGAAAACGCCACGGGT
1 GTTTATTGAAACG-TGGTCGTTTTGTATATG-TATTAGTGGCGTTTTT-AGAAAACGCCAC-AGC
* * * * * * ** * *
5839373 TTGAGGTAAGTGTTGATGAAGCGACTGCGTTTTGATTTATAGTTTGTGGCGCTTCGGTTAAAACG
62 TTGAGCTAACTGTTGATGAAACGACTTCGTTTTGACTTATAGTTAGTGGCGCTTCACTCAAAACA
*
5839438 CCGCAAAAATGTTTTAAC
127 CCGCAAAAATGTTCTAAC
* * * * * *
5839456 ATTTATTGATACGAGGCCGTTTTGTTGTAT-TATTAGTGGCGTTTATTCA-AAAACGCCACAGGT
1 GTTTATTGAAACGTGGTCGTTTTG-TATATGTATTAGTGGCGTTT-TT-AGAAAACGCCACAGCT
** * *
5839519 GTGAGCTATTTGTTGATGAAACGGCTTCGTTTTGACTTTTAGTTAGTGGCGCTT
63 -TGAGCTAACTGTTGATGAAACGACTTCGTTTTGACTTATAGTTAGTGGCGCTT
5839573 ATTTATAAAC
Statistics
Matches: 209, Mismatches: 47, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
145 2 0.01
146 67 0.32
147 131 0.63
148 9 0.04
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (144 bp):
GTTTATTGAAACGTGGTCGTTTTGTATATGTATTAGTGGCGTTTTTAGAAAACGCCACAGCTTGA
GCTAACTGTTGATGAAACGACTTCGTTTTGACTTATAGTTAGTGGCGCTTCACTCAAAACACCGC
AAAAATGTTCTAAC
Found at i:5840475 original size:7 final size:7
Alignment explanation
Indices: 5840463--5840492 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5840453 CCTTACTGTT
5840463 TATTTGG
1 TATTTGG
5840470 TATTTGG
1 TATTTGG
5840477 TATTTGG
1 TATTTGG
5840484 TATTTGG
1 TATTTGG
5840491 TA
1 TA
5840493 ATCAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.57
Consensus pattern (7 bp):
TATTTGG
Found at i:5840539 original size:15 final size:15
Alignment explanation
Indices: 5840519--5840550 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5840509 AGGGTTGAAG
5840519 TATTTGGTACTAATT
1 TATTTGGTACTAATT
5840534 TATTTGGTACTAATT
1 TATTTGGTACTAATT
5840549 TA
1 TA
5840551 CTGTTATTTC
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:0.28, C:0.06, G:0.12, T:0.53
Consensus pattern (15 bp):
TATTTGGTACTAATT
Found at i:5841533 original size:13 final size:13
Alignment explanation
Indices: 5841517--5841575 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
5841507 TTACTAAAAT
*
5841517 TTACTTTAATATA
1 TTACTTAAATATA
*
5841530 TTACTTGAATATA
1 TTACTTAAATATA
*
5841543 TTACTTAAATAAA
1 TTACTTAAATATA
*
5841556 TTACTTAAATACA
1 TTACTTAAATATA
5841569 TTACTTA
1 TTACTTA
5841576 CTAAAATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:5841800 original size:28 final size:29
Alignment explanation
Indices: 5841767--5841832 Score: 107
Period size: 28 Copynumber: 2.3 Consensus size: 29
5841757 CTATCACAAA
*
5841767 AACTTATATGTAAACTTAC-ATAATACAT
1 AACTTATATATAAACTTACAATAATACAT
5841795 AACTTATATATAAACTTACATATAATACAT
1 AACTTATATATAAACTTACA-ATAATACAT
5841825 AACTTATA
1 AACTTATA
5841833 AATTTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 18 0.51
30 17 0.49
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (29 bp):
AACTTATATATAAACTTACAATAATACAT
Found at i:5841832 original size:14 final size:14
Alignment explanation
Indices: 5841786--5841833 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
5841776 GTAAACTTAC
5841786 ATAATACATAACTT
1 ATAATACATAACTT
* * *
5841800 ATATATAAACTTACAT
1 ATA-ATACA-TAACTT
5841816 ATAATACATAACTT
1 ATAATACATAACTT
5841830 ATAA
1 ATAA
5841834 ATTTTTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 11 0.42
15 8 0.31
16 7 0.27
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATACATAACTT
Found at i:5841873 original size:28 final size:28
Alignment explanation
Indices: 5841842--5841986 Score: 123
Period size: 28 Copynumber: 5.0 Consensus size: 28
5841832 AAATTTTTTT
*
5841842 ATATAAACTTACATAATACATTACTTAC
1 ATATAAACTTACATAATACATAACTTAC
* * **
5841870 ATATTAACTTACATAACTTA-TTAA-TATTT
1 ATATAAACTTACATAA--TACATAACT-TAC
*
5841899 ATATAAACTTACATAACTATCACATAAACTTAT
1 ATATAAACTTACAT-A--AT-ACAT-AACTTAC
*
5841932 ATGTAAACTTACATAATACATAACTTAC
1 ATATAAACTTACATAATACATAACTTAC
* *
5841960 ATGTTAACTTACATAATACATAACTTA
1 ATATAAACTTACATAATACATAACTTA
5841987 TAAAAAAATT
Statistics
Matches: 96, Mismatches: 11, Indels: 20
0.76 0.09 0.16
Matches are distributed among these distances:
28 48 0.50
29 20 0.21
30 6 0.06
31 1 0.01
32 3 0.03
33 17 0.18
34 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.01, T:0.37
Consensus pattern (28 bp):
ATATAAACTTACATAATACATAACTTAC
Found at i:5841907 original size:57 final size:55
Alignment explanation
Indices: 5841808--5841914 Score: 153
Period size: 57 Copynumber: 1.9 Consensus size: 55
5841798 TTATATATAA
*
5841808 ACTTACATATAATACATAACTTATAAATTTTTTTATATAAACTTACATAATACATT
1 ACTTACATATAATACATAACTTATAAA-TTATTTATATAAACTTACATAATACATT
*
5841864 ACTTACATATTAACTTACATAACTTATTAA-TATTTATATAAACTTACATAA
1 ACTTACATA-TAA--TACATAACTTATAAATTATTTATATAAACTTACATAA
5841915 CTATCACATA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
56 9 0.20
57 23 0.50
59 14 0.30
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (55 bp):
ACTTACATATAATACATAACTTATAAATTATTTATATAAACTTACATAATACATT
Found at i:5841909 original size:158 final size:157
Alignment explanation
Indices: 5841717--5842047 Score: 556
Period size: 158 Copynumber: 2.1 Consensus size: 157
5841707 TATGTACAAG
5841717 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACAAAAACTTATATGTAAAC
1 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACAAAAACTTATATGTAAAC
* ***
5841782 TTACATAATACATAACTTATATATAAACTTACATATAATACATAACTTAT-AAATTTTTTTATAT
66 TTACATAATACATAACTTACATATAAACTTAC--ATAATACATAACTTATAAAAAAATTTTATAT
*
5841846 AAACTTACATAATACATTACTTACATATT
129 AAACTTACATAACACATTACTTACATATT
*
5841875 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTTATATGTAAAC
1 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACAAAAACTTATATGTAAAC
* *
5841940 TTACATAATACATAACTTACATGTTAACTTACATAATACATAACTTATAAAAAAATTTTATATAA
66 TTACATAATACATAACTTACATATAAACTTACATAATACATAACTTATAAAAAAATTTTATATAA
5842005 ACTTACATAACACATTACTTACATATT
131 ACTTACATAACACATTACTTACATATT
*
5842032 AACTTACATAAGTTAT
1 AACTTACATAACTTAT
5842048 CTACAAGCTT
Statistics
Matches: 163, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
156 16 0.10
157 54 0.33
158 93 0.57
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (157 bp):
AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACAAAAACTTATATGTAAAC
TTACATAATACATAACTTACATATAAACTTACATAATACATAACTTATAAAAAAATTTTATATAA
ACTTACATAACACATTACTTACATATT
Found at i:5841958 original size:16 final size:16
Alignment explanation
Indices: 5841937--5841986 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
5841927 CTTATATGTA
5841937 AACTTACATAATACAT
1 AACTTACATAATACAT
*
5841953 AACTTACAT-GT---T
1 AACTTACATAATACAT
5841965 AACTTACATAATACAT
1 AACTTACATAATACAT
5841981 AACTTA
1 AACTTA
5841987 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
15 1 0.04
16 16 0.57
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:5842099 original size:20 final size:19
Alignment explanation
Indices: 5842074--5842249 Score: 69
Period size: 18 Copynumber: 9.4 Consensus size: 19
5842064 AAACTTGCAT
*
5842074 AACTTACGTAATAACATAAC
1 AACTTACATAAT-ACATAAC
*
5842094 AACTTACATAATACATAGC
1 AACTTACATAATACATAAC
5842113 -A--TACATAACTTACAT---
1 AACTTACATAA--TACATAAC
5842128 AACTTACATAATAC--AA-
1 AACTTACATAATACATAAC
5842144 AACTTACATAACTTACATAATAC
1 AACTTACATAA--TACAT-A-AC
5842167 AAAACTTACATAACTTACAT-A-
1 --AACTTACATAA--TACATAAC
* **
5842188 ATC-TACATAATACAT-TT
1 AACTTACATAATACATAAC
5842205 AACTTACATAACTTACAT---
1 AACTTACATAA--TACATAAC
*
5842223 AACTTACATAATACATAAT
1 AACTTACATAATACATAAC
5842242 AACTTACA
1 AACTTACA
5842250 ACTTAAATAA
Statistics
Matches: 128, Mismatches: 5, Indels: 47
0.71 0.03 0.26
Matches are distributed among these distances:
16 32 0.25
17 2 0.02
18 41 0.32
19 16 0.12
20 16 0.12
21 1 0.01
22 2 0.02
25 18 0.14
ACGTcount: A:0.49, C:0.20, G:0.01, T:0.30
Consensus pattern (19 bp):
AACTTACATAATACATAAC
Found at i:5842125 original size:25 final size:25
Alignment explanation
Indices: 5842094--5842362 Score: 182
Period size: 25 Copynumber: 10.4 Consensus size: 25
5842084 ATAACATAAC
5842094 AACTTACATAA-TACATAGCATACAT
1 AACTTACATAACTACATA-CATACAT
*
5842119 AACTTACATAACTTACATA-ATACAA
1 AACTTACATAAC-TACATACATACAT
*
5842144 AACTTACATAACTTACATA-ATACAA
1 AACTTACATAAC-TACATACATACAT
5842169 AACTTACATAACTTACATA-ATCTACAT
1 AACTTACATAAC-TACATACA--TACAT
*
5842196 AA--TACATTTAACTTACATAACTTACAT
1 AACTTACA--TAAC-TACAT-ACATACAT
*
5842223 AACTTACATAA-TACATA-ATAACTTAC
1 AACTTACATAACTACATACAT-AC--AT
* * **
5842249 AACTTAAATAACATACATTACTTTGAT
1 AACTTACATAAC-TACA-TACATACAT
*
5842276 AACTTACATAACTTACATA-ATACAC
1 AACTTACATAAC-TACATACATACAT
* *
5842301 AACTTACATAGCTTACTTA-ATACAT
1 AACTTACATAAC-TACATACATACAT
*
5842326 AACTTACATAACT-TATACACGTACAT
1 AACTTACATAACTACATACA--TACAT
5842352 AACTTACATAA
1 AACTTACATAA
5842363 TTTACTTAAT
Statistics
Matches: 202, Mismatches: 22, Indels: 39
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.01
24 5 0.02
25 105 0.52
26 29 0.14
27 48 0.24
28 5 0.02
29 6 0.03
30 1 0.00
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (25 bp):
AACTTACATAACTACATACATACAT
Found at i:5842126 original size:9 final size:9
Alignment explanation
Indices: 5842094--5842367 Score: 233
Period size: 9 Copynumber: 31.8 Consensus size: 9
5842084 ATAACATAAC
5842094 AACTTACAT
1 AACTTACAT
5842103 AA--TACAT
1 AACTTACAT
* *
5842110 AGCATACAT
1 AACTTACAT
5842119 AACTTACAT
1 AACTTACAT
5842128 AACTTACAT
1 AACTTACAT
*
5842137 AA--TACAA
1 AACTTACAT
5842144 AACTTACAT
1 AACTTACAT
5842153 AACTTACAT
1 AACTTACAT
*
5842162 AA--TACAA
1 AACTTACAT
5842169 AACTTACAT
1 AACTTACAT
5842178 AACTTACAT
1 AACTTACAT
5842187 AA-TCTACAT
1 AACT-TACAT
5842196 AA--TACATTT
1 AACTTACA--T
5842205 AACTTACAT
1 AACTTACAT
5842214 AACTTACAT
1 AACTTACAT
5842223 AACTTACAT
1 AACTTACAT
*
5842232 AATACATA-AT
1 -A-ACTTACAT
5842242 AACTTAC--
1 AACTTACAT
*
5842249 AACTTAAAT
1 AACTTACAT
*
5842258 AACATACAT
1 AACTTACAT
* **
5842267 TACTTTGAT
1 AACTTACAT
5842276 AACTTACAT
1 AACTTACAT
5842285 AACTTACAT
1 AACTTACAT
*
5842294 AA--TACAC
1 AACTTACAT
5842301 AACTTACAT
1 AACTTACAT
* *
5842310 AGCTTACTT
1 AACTTACAT
5842319 AA--TACAT
1 AACTTACAT
5842326 AACTTACAT
1 AACTTACAT
5842335 AACTT--AT
1 AACTTACAT
*
5842342 ACACGTACAT
1 A-ACTTACAT
5842352 AACTTACAT
1 AACTTACAT
*
5842361 AATTTAC
1 AACTTAC
5842368 TTAATACATA
Statistics
Matches: 214, Mismatches: 28, Indels: 46
0.74 0.10 0.16
Matches are distributed among these distances:
7 43 0.20
8 8 0.04
9 149 0.70
10 6 0.03
11 8 0.04
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:5842134 original size:34 final size:33
Alignment explanation
Indices: 5842094--5842363 Score: 193
Period size: 34 Copynumber: 8.4 Consensus size: 33
5842084 ATAACATAAC
*
5842094 AACTTACATAATACATAGCATACATAACTTACAT
1 AACTTACATAATACATA-CTTACATAACTTACAT
5842128 AACTTAC---ATA-ATAC--A-A-AACTTACAT
1 AACTTACATAATACATACTTACATAACTTACAT
*
5842153 AACTTACATAATACAAAACTTACATAACTTACAT
1 AACTTACATAATAC-ATACTTACATAACTTACAT
5842187 AA-TCTACATAATACATTTAACTTACATAACTTACAT
1 AACT-TACATAATACA--T-ACTTACATAACTTACAT
5842223 AACTTACATAATAC--A--TA-ATAACTTAC--
1 AACTTACATAATACATACTTACATAACTTACAT
* **
5842249 AACTTAAATAACATACATTACTTTGATAACTTACAT
1 AACTTACAT-A-ATACA-TACTTACATAACTTACAT
* * *
5842285 AACTTACATAATACACAACTTACATAGCTTACTT
1 AACTTACATAATACA-TACTTACATAACTTACAT
*
5842319 AA--TACATAACTTACATAACTT--ATACACGTACAT
1 AACTTACATAA--TACAT-ACTTACATA-ACTTACAT
5842352 AACTTACATAAT
1 AACTTACATAAT
5842364 TTACTTAATA
Statistics
Matches: 191, Mismatches: 15, Indels: 61
0.72 0.06 0.23
Matches are distributed among these distances:
25 16 0.08
26 9 0.05
27 2 0.01
28 16 0.08
29 3 0.02
30 6 0.03
31 5 0.03
32 11 0.06
33 12 0.06
34 65 0.34
35 8 0.04
36 37 0.19
37 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (33 bp):
AACTTACATAATACATACTTACATAACTTACAT
Found at i:5847906 original size:21 final size:21
Alignment explanation
Indices: 5847881--5847945 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
5847871 AACTTAAAAT
5847881 AGAGGCAGCAACGAGAGAAGC
1 AGAGGCAGCAACGAGAGAAGC
* *
5847902 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCAGCAACGAGAGAAGC
*
5847923 AGAGGCTA-CAACGCGAGAAGC
1 AGAGGC-AGCAACGAGAGAAGC
5847944 AG
1 AG
5847946 CGAGAGAAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.38, C:0.20, G:0.38, T:0.03
Consensus pattern (21 bp):
AGAGGCAGCAACGAGAGAAGC
Found at i:5848448 original size:42 final size:42
Alignment explanation
Indices: 5848383--5848516 Score: 153
Period size: 42 Copynumber: 3.1 Consensus size: 42
5848373 TTACAGAAAA
*
5848383 AAACGCCGTTAAAG-ATCATGATCTTTAACGGCGTCTTTTTTT
1 AAACGCCGCTAAAGAAT-ATGATCTTTAACGGCGTCTTTTTTT
* * * * *
5848425 AAGCGCTGCTAAAGAATATGATCTTTAGCGGCATCTCTTTTT
1 AAACGCCGCTAAAGAATATGATCTTTAACGGCGTCTTTTTTT
* * *
5848467 AAATGCCGCTAAAGAACATGATCTTTAACGGCGTTTTTTTCTGT
1 AAACGCCGCTAAAGAATATGATCTTTAACGGCGTCTTTTT-T-T
5848511 AAACGC
1 AAACGC
5848517 TGCAAAAGTT
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
42 65 0.88
43 3 0.04
44 6 0.08
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (42 bp):
AAACGCCGCTAAAGAATATGATCTTTAACGGCGTCTTTTTTT
Found at i:5854689 original size:23 final size:25
Alignment explanation
Indices: 5854645--5854698 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
5854635 CTTATGAACA
** *
5854645 TATATATTTTATATAAATAAATATG
1 TATATATACTATATAAATAAATACG
*
5854670 TATATATACTATAT-AA-AAATGCG
1 TATATATACTATATAAATAAATACG
5854693 TATATA
1 TATATA
5854699 AGTTTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 11 0.44
24 2 0.08
25 12 0.48
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (25 bp):
TATATATACTATATAAATAAATACG
Found at i:5856375 original size:100 final size:100
Alignment explanation
Indices: 5856211--5857267 Score: 1634
Period size: 100 Copynumber: 10.5 Consensus size: 100
5856201 TTTGTTCAAC
* * * * * * *
5856211 TGCAATGTC-GGGAAACCATATCCGCCATCGTAGCTTCAATCTGTTCCACCGTACCG-TCAGGGA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCT-AAGGA
* **
5856274 AGTAAGATCTGCCGTTGTGGCTTCAATCTTTTAAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
* * * * *
5856310 TGCAATGTCA-GGAATACTAGATCCGCCGTCGTAGCTTCAATCTATTCCATTGTACTGCTAAGGA
1 TGCAATATCAGGGAA-ACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGA
*
5856374 AGTAAGATCCGCCGTTGTGGTTTCAATCTTTTTTAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
* *
5856410 TGCAATATCAGGGAAACCAGATCCACCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* *
5856475 GTAAGATCCACCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
*
5856510 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* * * *
5856575 GCAAGATCCACCGTTATGGCTTTAATCTTTTTTAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
*
5856610 TGCAATATCAGGGAAACCAGATCCGCCTTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
*
5856675 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
* *
5856710 TGCAATATCAGGGAAACCAGATCCGTCGTCGTAGCTTTAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
*
5856775 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
* * * **
5856810 TGCAATATCAGGGAAACTAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCGCTGCTAATAAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
*
5856875 GTAAGATCCGCCGTTGTGGCTTTAATCTTTTTTAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
* *
5856910 TGTAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATTTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
5856975 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
* *
5857010 TGCAATATCAGGGAAACCAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAAGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* *
5857075 GTAAGATCCGCCGTTGTGACTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
5857110 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCACTGCTA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTT-C-C---ACTGCACTGCTA
*
5857175 AGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
61 AGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
*
5857215 TGTAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGC
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGC
5857268 TGCCCAGAGA
Statistics
Matches: 883, Mismatches: 66, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
99 13 0.01
100 766 0.87
101 6 0.01
102 1 0.00
103 1 0.00
104 1 0.00
105 95 0.11
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (100 bp):
TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
Found at i:5858754 original size:21 final size:21
Alignment explanation
Indices: 5858730--5858771 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5858720 TTAGCCTCTC
*
5858730 CATTTTTACTTTTTCATTTTT
1 CATTTTCACTTTTTCATTTTT
*
5858751 CATTTTCATTTTTTCATTTTT
1 CATTTTCACTTTTTCATTTTT
5858772 TTCACATCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (21 bp):
CATTTTCACTTTTTCATTTTT
Found at i:5858772 original size:8 final size:7
Alignment explanation
Indices: 5858730--5858771 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
5858720 TTAGCCTCTC
5858730 CATTTTT
1 CATTTTT
5858737 -ACTTTTT
1 CA-TTTTT
5858744 CATTTTT
1 CATTTTT
5858751 CA-TTTT
1 CATTTTT
5858757 CATTTTTT
1 CA-TTTTT
5858765 CATTTTT
1 CATTTTT
5858772 TTCACATCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 7 0.23
7 17 0.55
8 7 0.23
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Done.