Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 185 of 210
Found at i:54783795 original size:9 final size:9
Alignment explanation
Indices: 54783781--54783847 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
54783771 GTAGTGATTC
54783781 AATTCGGTT
1 AATTCGGTT
54783790 AATTCGGTT
1 AATTCGGTT
54783799 AATTCGAG-T
1 AATTCG-GTT
*
54783808 AATCCGGTT
1 AATTCGGTT
54783817 AATTCGGTT
1 AATTCGGTT
*
54783826 AATTCGGGT
1 AATTCGGTT
*
54783835 AATTCGATT
1 AATTCGGTT
54783844 AATT
1 AATT
54783848 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
8 1 0.02
9 49 0.96
10 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:54788394 original size:46 final size:47
Alignment explanation
Indices: 54788321--54788419 Score: 130
Period size: 46 Copynumber: 2.1 Consensus size: 47
54788311 TACCCTGTTT
* * *
54788321 TGGACAGCATTTATACATCAAATTGGACAACATCGATATGCTC-AAA
1 TGGACAACATTTATACATCAAAGTGGACAACATCAATATGCTCTAAA
* *
54788367 CTGGACAACA-TTATACATTAAAGTGGACAGCATCAATATGCTCTAAA
1 -TGGACAACATTTATACATCAAAGTGGACAACATCAATATGCTCTAAA
54788414 TGGACA
1 TGGACA
54788420 GCATCAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 35 0.76
47 11 0.24
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (47 bp):
TGGACAACATTTATACATCAAAGTGGACAACATCAATATGCTCTAAA
Found at i:54788444 original size:24 final size:24
Alignment explanation
Indices: 54788338--54788447 Score: 109
Period size: 24 Copynumber: 4.7 Consensus size: 24
54788328 CATTTATACA
* * *
54788338 TCAAATTGGACAACATCGATATGC
1 TCAAAATGGACAGCATCAATATGC
* * *
54788362 TCAAACTGGACA--A-CATTATAC
1 TCAAAATGGACAGCATCAATATGC
* *
54788383 ATTAAAGTGGACAGCATCAATATGC
1 -TCAAAATGGACAGCATCAATATGC
*
54788408 TCTAAATGGACAGCATCAATATGC
1 TCAAAATGGACAGCATCAATATGC
54788432 TCAAAATGGACAGCAT
1 TCAAAATGGACAGCAT
54788448 TATACATCTA
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
21 5 0.07
22 11 0.16
24 48 0.69
25 6 0.09
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (24 bp):
TCAAAATGGACAGCATCAATATGC
Found at i:54789265 original size:40 final size:42
Alignment explanation
Indices: 54789139--54789274 Score: 156
Period size: 41 Copynumber: 3.3 Consensus size: 42
54789129 TTGCCATCGT
* * *
54789139 ATAGCCGAAGCTATTAT-AATCTCGCACACTAAGTGCCTTAC
1 ATAGCCGAAGCTATTCTCAATCTCGCACACTAAGTGCCATAA
* * *
54789180 ATAGCCGAAGCTA-TCTCAGTCTCGCACACTAAGTGTCATAT
1 ATAGCCGAAGCTATTCTCAATCTCGCACACTAAGTGCCATAA
*
54789221 ATAGCTGAAGCTATTC-CAAAT-T-GCACACTAAGTGCCATAA
1 ATAGCCGAAGCTATTCTC-AATCTCGCACACTAAGTGCCATAA
*
54789261 ATAGCCCAAGCTAT
1 ATAGCCGAAGCTAT
54789275 CTCGAATTTC
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
40 30 0.37
41 47 0.58
42 4 0.05
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (42 bp):
ATAGCCGAAGCTATTCTCAATCTCGCACACTAAGTGCCATAA
Found at i:54790245 original size:13 final size:14
Alignment explanation
Indices: 54790224--54790252 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54790214 TGTATTTTTA
54790224 TTTC-TTTTTTATT
1 TTTCGTTTTTTATT
54790237 TTTCGTTTTTTATT
1 TTTCGTTTTTTATT
54790251 TT
1 TT
54790253 CAGCCAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTCGTTTTTTATT
Found at i:54791250 original size:3 final size:3
Alignment explanation
Indices: 54791231--54791290 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
54791221 TATTAATTAG
* * * *
54791231 ATT ATT AATT AAT -TT ATT ATT ATT ATT ATT ATC AGT GTT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
54791276 ACT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT
54791291 GATCTTGTTA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
2 1 0.02
3 40 0.91
4 3 0.07
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:54791602 original size:12 final size:12
Alignment explanation
Indices: 54791563--54791603 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
54791553 TATTTCAACT
54791563 TATATA-TA-TA
1 TATATATTATTA
*
54791573 TATATATTATCA
1 TATATATTATTA
54791585 TATATATTATTA
1 TATATATTATTA
*
54791597 TTTATAT
1 TATATAT
54791604 CAAGTTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 6 0.23
11 2 0.08
12 18 0.69
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (12 bp):
TATATATTATTA
Found at i:54791603 original size:14 final size:16
Alignment explanation
Indices: 54791568--54791597 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54791558 CAACTTATAT
54791568 ATATATATATATTATC
1 ATATATATATATTATC
54791584 ATATATAT-TATTAT
1 ATATATATATATTAT
54791598 TTATATCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATATATATTATC
Found at i:54795106 original size:2 final size:2
Alignment explanation
Indices: 54795099--54795128 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
54795089 GCTAAGTAAT
54795099 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54795129 GTGTTGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:54795222 original size:28 final size:28
Alignment explanation
Indices: 54795176--54795247 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
54795166 TATACATATA
*
54795176 TTATATATATATATGTGCATGACTTCATC
1 TTATATA-ATATATATGCATGACTTCATC
* * *
54795205 TTATATAATATATATGCATGTCTTTATT
1 TTATATAATATATATGCATGACTTCATC
**
54795233 TTACCTAATATATAT
1 TTATATAATATATAT
54795248 TAATGGATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 30 0.81
29 7 0.19
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (28 bp):
TTATATAATATATATGCATGACTTCATC
Found at i:54795274 original size:5 final size:5
Alignment explanation
Indices: 54795264--54795303 Score: 71
Period size: 5 Copynumber: 7.8 Consensus size: 5
54795254 ATTTTGGTAT
54795264 TATAA TATAA TATAA TATAA TATAA TATAA TATATA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATA
54795304 TGCATGGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:54795656 original size:36 final size:36
Alignment explanation
Indices: 54795609--54795689 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
54795599 TTGTGAACCA
* * *
54795609 TGTTAACTTGGTGAAT-TATATTATTATGGCGAACTG
1 TGTTAATTTGGT-AATCTATATTAATATGGCAAACTG
*
54795645 TGTTAATTTGGTAATCTGTATTAATATGGCAAACTG
1 TGTTAATTTGGTAATCTATATTAATATGGCAAACTG
**
54795681 CATTAATTT
1 TGTTAATTT
54795690 TTCAAATTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 3 0.08
36 35 0.92
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.43
Consensus pattern (36 bp):
TGTTAATTTGGTAATCTATATTAATATGGCAAACTG
Found at i:54795668 original size:18 final size:18
Alignment explanation
Indices: 54795635--54795689 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
54795625 TATATTATTA
* *
54795635 TGGCGAACTGTGTTAATT
1 TGGCAAACTGTATTAATT
* * *
54795653 TGGTAATCTGTATTAATA
1 TGGCAAACTGTATTAATT
*
54795671 TGGCAAACTGCATTAATT
1 TGGCAAACTGTATTAATT
54795689 T
1 T
54795690 TTCAAATTGT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (18 bp):
TGGCAAACTGTATTAATT
Found at i:54796396 original size:51 final size:51
Alignment explanation
Indices: 54796333--54796440 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 51
54796323 CTGATAGAGC
* * *
54796333 ATGAACTTTTATTTCGCATGAAG-TGTTATTCGGTATGAACTGATATTTCAT
1 ATGAACTATTATTTCGCATG-AGCTGTCATTCGGTAAGAACTGATATTTCAT
* * *
54796384 ATGAACTATTATTTTGCATGAGCTGTCATTTGGTAAGAACTGTTATTTCAT
1 ATGAACTATTATTTCGCATGAGCTGTCATTCGGTAAGAACTGATATTTCAT
54796435 ATGAAC
1 ATGAAC
54796441 AGATGTTTGG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
50 2 0.04
51 48 0.96
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.42
Consensus pattern (51 bp):
ATGAACTATTATTTCGCATGAGCTGTCATTCGGTAAGAACTGATATTTCAT
Found at i:54796440 original size:17 final size:17
Alignment explanation
Indices: 54796333--54796440 Score: 83
Period size: 17 Copynumber: 6.4 Consensus size: 17
54796323 CTGATAGAGC
* *
54796333 ATGAACTTTTATTTCGC
1 ATGAACTGTTATTTCGT
*
54796350 ATGAAGTGTTA-TTCGGT
1 ATGAACTGTTATTTC-GT
* *
54796367 ATGAACTGATATTTCAT
1 ATGAACTGTTATTTCGT
* * *
54796384 ATGAACTATTATTTTGC
1 ATGAACTGTTATTTCGT
* * *
54796401 ATGAGCTGTCATTTGGT
1 ATGAACTGTTATTTCGT
* *
54796418 AAGAACTGTTATTTCAT
1 ATGAACTGTTATTTCGT
54796435 ATGAAC
1 ATGAAC
54796441 AGATGTTTGG
Statistics
Matches: 67, Mismatches: 22, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
16 3 0.04
17 61 0.91
18 3 0.04
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.42
Consensus pattern (17 bp):
ATGAACTGTTATTTCGT
Found at i:54804114 original size:20 final size:20
Alignment explanation
Indices: 54804089--54804126 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
54804079 ACTCCCATCA
54804089 GTAGTAATAGTAAATGAGTT
1 GTAGTAATAGTAAATGAGTT
*
54804109 GTAGTATTAGTAAATGAG
1 GTAGTAATAGTAAATGAG
54804127 CCCAATGCTA
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:0.39, C:0.00, G:0.26, T:0.34
Consensus pattern (20 bp):
GTAGTAATAGTAAATGAGTT
Found at i:54805840 original size:11 final size:13
Alignment explanation
Indices: 54805816--54805847 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54805806 TAGTTTATTA
54805816 ATATTTTAATATG
1 ATATTTTAATATG
54805829 AT-TTTTAA-ATG
1 ATATTTTAATATG
54805840 ATATTTTA
1 ATATTTTA
54805848 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:54809757 original size:19 final size:20
Alignment explanation
Indices: 54809717--54809762 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
54809707 TTTTCATTCT
* *
54809717 ATATTTCTCTTTGTTTTATA
1 ATATTTATCTTTGTTATATA
54809737 ATATTTATCTTT-TTATATA
1 ATATTTATCTTTGTTATATA
*
54809756 ATTTTTA
1 ATATTTA
54809763 AATAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (20 bp):
ATATTTATCTTTGTTATATA
Found at i:54815646 original size:61 final size:61
Alignment explanation
Indices: 54815581--54815709 Score: 213
Period size: 61 Copynumber: 2.1 Consensus size: 61
54815571 GGCCACACGA
* **
54815581 GCATGTGCAAGGCCATGTGGACCACACAGGCCAGCTACCTAGGTCGTGTTAATCCACATGG
1 GCATGTGCAAGGCCACGTGGACCACACAGGCCAGCTACCTAGACCGTGTTAATCCACATGG
*
54815642 GCATGTGTAAGGCCACGTGGACCACACAGGCCAGCTACCTAGACCGTGTTAATCCACATGG
1 GCATGTGCAAGGCCACGTGGACCACACAGGCCAGCTACCTAGACCGTGTTAATCCACATGG
*
54815703 GCGTGTG
1 GCATGTG
54815710 GGCCAAAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.24, C:0.28, G:0.29, T:0.19
Consensus pattern (61 bp):
GCATGTGCAAGGCCACGTGGACCACACAGGCCAGCTACCTAGACCGTGTTAATCCACATGG
Found at i:54837736 original size:7 final size:7
Alignment explanation
Indices: 54837694--54837736 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
54837684 ACACTCCTTT
*
54837694 AAATAAT
1 AAATAAG
54837701 AAATAAG
1 AAATAAG
54837708 AAATAAG
1 AAATAAG
* *
54837715 TAAACAAA
1 -AAATAAG
54837723 AAATAAG
1 AAATAAG
54837730 AAATAAG
1 AAATAAG
54837737 GGGCTCCCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 25 0.83
8 5 0.17
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (7 bp):
AAATAAG
Found at i:54841349 original size:20 final size:20
Alignment explanation
Indices: 54841324--54841375 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
54841314 CCCTCTCTTG
54841324 CGTTCTTATTTTCTGTGGCT
1 CGTTCTTATTTTCTGTGGCT
54841344 CGTTCTTATTTTCTGTGGCT
1 CGTTCTTATTTTCTGTGGCT
*
54841364 TGTTCTTATTTT
1 CGTTCTTATTTT
54841376 GTTCTTCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.06, C:0.17, G:0.17, T:0.60
Consensus pattern (20 bp):
CGTTCTTATTTTCTGTGGCT
Found at i:54841953 original size:2 final size:2
Alignment explanation
Indices: 54841946--54841971 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54841936 TACCTACTTT
54841946 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
54841972 ATTTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54842617 original size:16 final size:16
Alignment explanation
Indices: 54842596--54842632 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
54842586 CCCAAATCAG
* *
54842596 AAAACAATAACAGAAA
1 AAAACAACAAAAGAAA
54842612 AAAACAACAAAAGAAA
1 AAAACAACAAAAGAAA
54842628 AAAAC
1 AAAAC
54842633 CTAGCCCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.78, C:0.14, G:0.05, T:0.03
Consensus pattern (16 bp):
AAAACAACAAAAGAAA
Found at i:54842981 original size:21 final size:20
Alignment explanation
Indices: 54842955--54842993 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54842945 ATAAACTCTA
*
54842955 TTTTCCCTTTTATTTTTTTAT
1 TTTTCCC-TTCATTTTTTTAT
54842976 TTTTCCCTTCATTTTTTT
1 TTTTCCCTTCATTTTTTT
54842994 CTTCCTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCCCTTCATTTTTTTAT
Found at i:54843041 original size:17 final size:16
Alignment explanation
Indices: 54843014--54843045 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
54843004 AAACTGTTTG
54843014 TTTTCTTTATTTTTAT
1 TTTTCTTTATTTTTAT
54843030 TTTTCTTTTATTTTTA
1 TTTTC-TTTATTTTTA
54843046 AAAACTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCTTTATTTTTAT
Found at i:54843969 original size:22 final size:22
Alignment explanation
Indices: 54843944--54844000 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
54843934 TACATATATA
54843944 TATATATATATATATACCTTAT
1 TATATATATATATATACCTTAT
* * * *
54843966 TATAAATATCTTTATATCTTAT
1 TATATATATATATATACCTTAT
*
54843988 TATGTATATATAT
1 TATATATATATAT
54844001 CTATATCTCT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (22 bp):
TATATATATATATATACCTTAT
Found at i:54843995 original size:26 final size:25
Alignment explanation
Indices: 54843962--54844011 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
54843952 TATATATACC
*
54843962 TTATTATAAATATCTTTATATCTTA
1 TTATTATAAATATCTATATATCTTA
* *
54843987 TTATGTATATATATCTATATCTCTT
1 TTAT-TATAAATATCTATATATCTT
54844012 TTTAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTATAAATATCTATATATCTTA
Found at i:54846242 original size:7 final size:7
Alignment explanation
Indices: 54846230--54846273 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
54846220 AAAATTAAAT
54846230 AAATGAA
1 AAATGAA
54846237 AAATG-A
1 AAATGAA
*
54846243 GAATGAA
1 AAATGAA
54846250 AAATGAA
1 AAATGAA
54846257 AAATG-A
1 AAATGAA
54846263 AAATGAA
1 AAATGAA
54846270 AAAT
1 AAAT
54846274 AGAGAGGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 11 0.33
7 22 0.67
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
AAATGAA
Found at i:54846249 original size:13 final size:14
Alignment explanation
Indices: 54846230--54846273 Score: 65
Period size: 13 Copynumber: 3.3 Consensus size: 14
54846220 AAAATTAAAT
54846230 AAATGAAAAATG-A
1 AAATGAAAAATGAA
*
54846243 GAATGAAAAATGAA
1 AAATGAAAAATGAA
54846257 AAATG-AAAATGAA
1 AAATGAAAAATGAA
54846270 AAAT
1 AAAT
54846274 AGAGAGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 23 0.82
14 5 0.18
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (14 bp):
AAATGAAAAATGAA
Found at i:54846253 original size:20 final size:20
Alignment explanation
Indices: 54846230--54846273 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
54846220 AAAATTAAAT
*
54846230 AAATGAAAAATGAGAATGAA
1 AAATGAAAAATGAAAATGAA
54846250 AAATGAAAAATGAAAATGAA
1 AAATGAAAAATGAAAATGAA
54846270 AAAT
1 AAAT
54846274 AGAGAGGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (20 bp):
AAATGAAAAATGAAAATGAA
Found at i:54848039 original size:87 final size:87
Alignment explanation
Indices: 54847768--54848929 Score: 603
Period size: 87 Copynumber: 13.3 Consensus size: 87
54847758 TCGCATCAAG
* * * *
54847768 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAG----TCAGATCTTATCTCCCTGAGGTTA
* * **
54847833 CAGTGGAGCAGATTGAAG-CTAGAGA
62 CAGTGGAGCAGATCGAAGAATTCAGA
* * * * *
54847858 TCTTATCTCCCTG-AGATTACAGTGGAGCAGATCAAAGACACTATCCTATCTCCCTGA-GTTACA
1 TCTTATCTCCCTGAAG-TTACAGCGGAGCAGATCGAAGTCA-GATCTTATCTCCCTGAGGTTACA
* * **
54847921 GTGGAGCGGAT-TAA-AATAAAAGA
64 GTGGAGCAGATCGAAGAAT-TCAGA
* * * * *
54847944 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA-TCAGGTCTTATCTCCCTGAGGTTACAGT
1 TCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGTCAGATCTTATCTCCCTGAGGTTACAGT
* *
54848008 GGAGTAGACCGAAGAATTTCAGA
66 GGAGCAGATCGAAGAA-TTCAGA
* * * * *
54848031 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGTC--AGATCTTATCTCCCTGAGGTTACA
* * *
54848096 GCGGAGCAGATCAAAG-A--CACTA
64 GTGGAGCAGATCGAAGAATTCA-GA
* * * ** * * * * *
54848118 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAAGATCTTCTCTCTCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGT--CAGATCTTATCTCCCTGAGGTTACA
* * * *
54848183 GTAGAGTAGATC---GCATT-AGG
64 GTGGAGCAGATCGAAGAATTCAGA
* * * * * *
54848203 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTTAGATCTTATCTCCTTGAGGTTA
1 TCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAG----TCAGATCTTATCTCCCTGAGGTTA
* * *
54848268 CAGTGGAGCAGATTGAAGCCA--GAGA
62 CAGTGGAGCAGATCGAAG-AATTCAGA
* * * * * *
54848293 TCTTATCTCCCTG-AGATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCTTGAAGTTACA
1 TCTTATCTCCCTGAAG-TTACAGCGGAGCAGATCGAAGTCA-GATCTTATCTCCCTGAGGTTACA
* * * **
54848357 ATGGAGCGGAT-TAA-AATAAAGGA
64 GTGGAGCAGATCGAAGAATTCA-GA
* * * * *
54848380 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA-TCAGGTCTTATCTCCCTGAGGTTACAGT
1 TCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGTCAGATCTTATCTCCCTGAGGTTACAGT
* *
54848444 GGAGTAGACCGAAGAATTTCAGA
66 GGAGCAGATCGAAGAA-TTCAGA
* * ** * * *
54848467 TCTTATCTCCTTGAGGTTACAATGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGTC--AGATCTTATCTCCCTGAGGTTACA
* * *
54848532 GCGGAGCAGATTGAAGATAGT-A-A
64 GTGGAGCAGATCGAAGA-ATTCAGA
* * * ** * * * *
54848555 TCTTAATCTCCCTGATA-TTATAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTA
1 TCTT-ATCTCCCTGA-AGTTACAGCGGAGCAGATCGAAGT-CA-GATCTTATCTCCCTGAGGTTA
** * * *
54848619 CAGTACAGTAGATC---GCA-TCAGG
62 CAGTGGAGCAGATCGAAGAATTCAGA
* * * *
54848641 TCTTATCTCCCTGAGGTTACAGTGGAGTAGA-CTGAAGAATTTCAGATCTTATCTCCCTGAGATT
1 TCTTATCTCCCTGAAGTTACAGCGGAGCAGATC-GAAG----TCAGATCTTATCTCCCTGAGGTT
* * *
54848705 ACAGTGGAGCAGATTGAAGCCA--GAGA
61 ACAGTGGAGCAGATCGAAG-AATTCAGA
* * * * *
54848731 TCTTATCTCCCTG-AGATTACAGCGGAGCAAATCGAAGACACTATCCTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAAG-TTACAGCGGAGCAGATCGAAGTCA-GATCTTATCTCCCTGAGGTTACA
* * **
54848795 GTGGAGCGGAT-TAA-AATAAAGGA
64 GTGGAGCAGATCGAAGAATTCA-GA
* * * * * *
54848818 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCA-TCAGGTCTTATCTCCCTGAGGTTGCAGT
1 TCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGTCAGATCTTATCTCCCTGAGGTTACAGT
* *
54848882 GGACCAGA-CGAAAAATATCA-A
66 GGAGCAGATCGAAGAAT-TCAGA
* * * *
54848903 TCGTGTCTCCCTGAAGTTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTACAGCGGAG
54848930 TGGATGAAAA
Statistics
Matches: 810, Mismatches: 196, Indels: 137
0.71 0.17 0.12
Matches are distributed among these distances:
84 17 0.02
85 150 0.19
86 77 0.10
87 319 0.39
88 16 0.02
89 59 0.07
90 166 0.20
91 6 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (87 bp):
TCTTATCTCCCTGAAGTTACAGCGGAGCAGATCGAAGTCAGATCTTATCTCCCTGAGGTTACAGT
GGAGCAGATCGAAGAATTCAGA
Found at i:54848095 original size:131 final size:129
Alignment explanation
Indices: 54847768--54848893 Score: 612
Period size: 131 Copynumber: 8.6 Consensus size: 129
54847758 TCGCATCAAG
* * * *
54847768 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAA---GAGATCTTATCTCCCTGAGATTA
* * * **
54847833 CAGTGGAGCAGATTGAAGCTAGAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAG-A-
63 CAGTGGAGCAGATCGAATC-AG-G-TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGAAT
*
54847896 -CACTA
125 TCA-GA
* * ** * * *
54847901 TCCTATCTCCCTGA-GTTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGA-AGTTAC
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGA-TCGAAGAAGAGATCTTATCTCCCTGAGA-TTAC
** * * * **
54847964 AGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCA
64 AGTGGAGCAGATCGAATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGAA-TTCA
54848029 GA
128 GA
* *
54848031 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAG-AAGAGATCTTATCTCCCTGAGATTACA
* * * ** * * * **
54848096 GCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATT-AA-AATAAA
65 GTGGAGCAGATCGAA-TCA-GGTCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGAAT-TC
54848159 AGA
127 AGA
* * * * * * ** *
54848162 TCTTCTCTCTCTGAAGTTACAGTAGAGTAGATCGCATTAG-G-TCTTATCTCCCTGAGGTTACAG
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAAGAGATCTTATCTCCCTGAGATTACAG
* * * * * *
54848225 TGGAGTAGACCGAAGAATTTTAGATCTTATCTCCTTGAGGTTACAGTGGAGCAGATTGAAGCCA-
66 TGGAGCAGATC---GAA--TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAG-AAT
*
54848289 -GAGA
125 TCAGA
* * * ** * *
54848293 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACA-CTATCCTATCTCCTTGA-AGTTAC
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGA-AGAGATCTTATCTCCCTGAGA-TTAC
* * ** * * * ** * * *
54848356 AATGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGA-T--CGCA-T
64 AGTGGAGCAGA-TCGAAT-CAGG-TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGAATT
*
54848417 CAGG
126 CAGA
* * * * *
54848421 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCTTGAGGTTA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAA---GAGATCTTATCTCCCTGAGATTA
* * * * *
54848486 CAATGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATA
63 CAGTGGAGCAGATCGAA-TCAG-G-TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGA-A
*
54848551 GT-A-A
124 TTCAGA
** * * * * * *
54848555 TCTTAATCTCCCTGATATTATAGTGGAGCGGAT-TAAAATAAAGGATCTTATCTCTCTGA-AGTT
1 TCTT-ATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGA-AGA-GATCTTATCTCCCTGAGA-TT
** * * * *
54848618 ACAGTACAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAGAATTT
62 ACAGTGGAGCAGATCGAATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGAA-TT
54848683 CAGA
126 CAGA
* * *
54848687 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAG-AAGAGATCTTATCTCCCTGAGATTACA
* * * ** * * * **
54848752 GCGGAGCAAATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATT-AA-AATAAA
65 GTGGAGCAGATCGAA-TCA-GGTCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGAATTCA
54848815 GGA
128 -GA
* * ** * * ** * *
54848818 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG-G-TCTTATCTCCCTGAGGTTGCAG
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAAGAGATCTTATCTCCCTGAGATTACAG
*
54848881 TGGACCAGA-CGAA
66 TGGAGCAGATCGAA
54848894 AAATATCAAT
Statistics
Matches: 757, Mismatches: 184, Indels: 110
0.72 0.18 0.10
Matches are distributed among these distances:
127 40 0.05
128 93 0.12
129 6 0.01
130 100 0.13
131 317 0.42
132 42 0.06
133 124 0.16
134 9 0.01
135 25 0.03
136 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (129 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAAGAGATCTTATCTCCCTGAGATTACAG
TGGAGCAGATCGAATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGAATTCAGA
Found at i:54848282 original size:218 final size:218
Alignment explanation
Indices: 54847702--54848929 Score: 2068
Period size: 218 Copynumber: 5.6 Consensus size: 218
54847692 NNNNNNNNNN
* * *
54847702 CAGTGGAGCGGATTAAAATAAACGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAA
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
54847767 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
66 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
* *
54847832 ACAGTGGAGCAGATTGAAGCTAGAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAC
131 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
54847897 ACTATCCTATCTCCCTG-AGTTA
196 ACTATCCTATCTCCCTGAAGTTA
*
54847919 CAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
54847984 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
66 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
54848049 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
131 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
54848114 ACTATCCTATCTCCCTGAAGTTA
196 ACTATCCTATCTCCCTGAAGTTA
* * * *
54848137 CAGTGGAGCGGATTAAAATAAAAGATCTTCTCTCTCTGAAGTTACAGTAGAGTAGATCGCATTAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
* *
54848202 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTTAGATCTTATCTCCTTGAGGTT
66 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
54848267 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
131 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
*
54848332 ACTATCCTATCTCCTTGAAGTTA
196 ACTATCCTATCTCCCTGAAGTTA
*
54848355 CAATGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
*
54848420 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCTTGAGGTT
66 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
* ** *
54848485 ACAATGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAT
131 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
* *
54848550 AGTAATCTTAATCTCCCTGATA-TTA
196 ACT-ATCCT-ATCTCCCTGA-AGTTA
* * *
54848575 TAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTACAGTAGATCGCATCAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
* *
54848640 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAGAATTTCAGATCTTATCTCCCTGAGATT
66 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
* *
54848705 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAAATCGAAGAC
131 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
54848770 ACTATCCTATCTCCCTGAAGTTA
196 ACTATCCTATCTCCCTGAAGTTA
54848793 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
* ** * * * * *
54848858 GTCTTATCTCCCTGAGGTTGCAGTGGACCAGA-CGAAAAATATCA-ATCGTGTCTCCCTGAAGTT
66 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
*
54848921 GCAGTGGAG
131 ACAGTGGAG
54848930 TGGATGAAAA
Statistics
Matches: 955, Mismatches: 51, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
216 23 0.02
217 217 0.23
218 508 0.53
219 8 0.01
220 198 0.21
221 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (218 bp):
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
ACTATCCTATCTCCCTGAAGTTA
Found at i:54848583 original size:45 final size:44
Alignment explanation
Indices: 54847768--54848806 Score: 582
Period size: 44 Copynumber: 23.8 Consensus size: 44
54847758 TCGCATCAAG
* * ** *
54847768 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA---GAGA
*
54847814 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAG-CTAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGAC-AGAGA
** **
54847858 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAGAGA
* * * * *
54847901 TCCTATCTCCCTGAG-TTACAGTGGAGCGGATT-AAAATAAAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGA-CAGAGA
* ** * * * *
54847944 TCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCA-TCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAGAGA
* * ** *
54847985 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA---GAGA
* *
54848031 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAGAGA
* ** **
54848075 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAGAGA
* * * * *
54848118 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATT-AAAATAAAAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGA-CAGAGA
* * * * * * **
54848162 TCTTCTCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-TTAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAGAGA
* * ** *
54848203 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTTTAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA---GAGA
* * *
54848249 TCTTATCTCCTTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAGAGA
* ** **
54848293 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAGAGA
* * * * * * *
54848336 TCCTATCTCCTTGA-AGTTACAATGGAGCGGATT-AAAATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAGA-GA
* ** * * * *
54848380 TCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCA-TCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAGAGA
* * ** *
54848421 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA---GAGA
* * * *
54848467 TCTTATCTCCTTGAGGTTACAATGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAGAGA
* *
54848511 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG-AGA
* * * * * *
54848555 TCTTAATCTCCCTGATATTATAGTGGAGCGGATT-AAAATAAAGGA
1 TCTT-ATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAGA-GA
* ** * * * *
54848600 TCTTATCTCTCTGA-AGTTACAGTACAGTAGATCGCA-TCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAGAGA
* * * *
54848641 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA---GAGA
*
54848687 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAGAGA
* * * **
54848731 TCTTATCTCCCTGAGATTACAGCGGAGCAAATCGAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAGAGA
* *
54848774 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATT
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATT
54848807 AAAATAAAGG
Statistics
Matches: 764, Mismatches: 174, Indels: 113
0.73 0.17 0.11
Matches are distributed among these distances:
41 122 0.16
42 30 0.04
43 114 0.15
44 286 0.37
45 40 0.05
46 167 0.22
47 5 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAGAGA
Found at i:54848777 original size:438 final size:436
Alignment explanation
Indices: 54847702--54848884 Score: 2091
Period size: 438 Copynumber: 2.7 Consensus size: 436
54847692 NNNNNNNNNN
* *
54847702 CAGTGGAGCGGATTAAAATAAACGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAA
1 CAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
54847767 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
66 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
* *
54847832 ACAGTGGAGCAGATTGAAGCTAGAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAC
131 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
*
54847897 ACTATCCTATCTCCCTG-AGTTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGT
196 ACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
54847961 TACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
261 TACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
*
54848026 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGA
326 TCAGATCTTATCTCCCTGAGGTTACAATGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGA
54848091 TTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTA
391 TTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTA
* *
54848137 CAGTGGAGCGGATTAAAATAAAAGATCTTCTCTCTCTGAAGTTACAGTAGAGTAGATCGCATTAG
1 CAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* *
54848202 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTTAGATCTTATCTCCTTGAGGTT
66 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
54848267 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
131 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
* *
54848332 ACTATCCTATCTCCTTGAAGTTACAATGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
196 ACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
54848397 TACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
261 TACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
*
54848462 TCAGATCTTATCTCCTTGAGGTTACAATGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGA
326 TCAGATCTTATCTCCCTGAGGTTACAATGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGA
** * * *
54848527 TTACAGCGGAGCAGATTGAAGATAGTAATCTTAATCTCCCTGATA-TTA
391 TTACAGCGGAGCAGATCAAAGACACT-ATCCT-ATCTCCCTGA-AGTTA
* * *
54848575 TAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTACAGTAGATCGCATCAG
1 CAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* *
54848640 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAGAATTTCAGATCTTATCTCCCTGAGATT
66 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
* *
54848705 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAAATCGAAGAC
131 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
54848770 ACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
196 ACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
*
54848835 TACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGTGGA
261 TACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGA
54848885 CCAGACGAAA
Statistics
Matches: 712, Mismatches: 32, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
435 203 0.29
436 195 0.27
437 4 0.01
438 309 0.43
439 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (436 bp):
CAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTT
ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAC
ACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
TACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
TCAGATCTTATCTCCCTGAGGTTACAATGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGA
TTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTA
Found at i:54849128 original size:438 final size:433
Alignment explanation
Indices: 54847702--54849073 Score: 1736
Period size: 438 Copynumber: 3.1 Consensus size: 433
54847692 NNNNNNNNNN
* * * *
54847702 CAGTGGAGCGGATTAAAATAAACGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCA-
1 CAGTGGAGCGGATTAAAATAAA-GATCTTATCTCTCTGAAGTTACAGT-GAGCAGATAGAACCAC
*
54847766 AGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGT
64 AGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAGAATTTCAGATCTTATCTCCCTGAGGT
* *
54847831 TACAGTGGAGCAGATTGAAGCTAGAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGA
129 TACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA
*
54847896 CACTATCCTATCTCCCTG-AGTTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAG
194 CACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAG
54847960 TTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAAT
259 TTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAAT
54848025 TTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAG
324 TTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCT---
* * * * *
54848090 ATTACAG-CGGAGCAGATC-AA--AGA-CACTATCC-TATCTCCCTGAAGTTA
386 A--A-AGTTGGAG-AGGTCGAATTGGATCA-TAACCTTATCTCCCTAAAGTTA
* *
54848137 CAGTGGAGCGGATTAAAATAAAAGATCTTCTCTCTCTGAAGTTACAGT-AG-AG-TAGATCGCAT
1 CAGTGGAGCGGATTAAAAT-AAAGATCTTATCTCTCTGAAGTTACAGTGAGCAGATAGAAC-CA-
* * * *
54848199 TAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTTAGATCTTATCTCCTTGAG
63 CA-GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
54848264 GTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAA
127 GTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAA
* *
54848329 GACACTATCCTATCTCCTTGAAGTTACAATGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA
192 GACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA
54848394 AGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
257 AGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
* *
54848459 ATTTCAGATCTTATCTCCTTGAGGTTACAATGGAGCAGATTGAAGCCAGAGATCTTATCTCCCT-
322 ATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTA
* ** * * * *
54848523 GAGATTACAGCGG-AGCAGATTGAAGAT-AGTAATCTTAATCTCCCTGATA-TTA
387 AAG-TTGGAGAGGTCG-A-ATTG--GATCA-TAACCTT-ATCTCCCT-AAAGTTA
* *
54848575 TAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGT-A-CAG-TAGATCGCAT
1 CAGTGGAGCGGATTAAAATAAA-GATCTTATCTCTCTGAAGTTACAGTGAGCAGATAGAAC-CA-
54848637 CAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
63 CA-GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAGAATTTCAGATCTTATCTCCCTGAG
* * *
54848702 ATTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAAATCGAA
127 GTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAA
54848767 GACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA
192 GACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA
* ** *
54848832 AGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGTGGACCAGA-CGAAAA
257 AGTTACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
* * * * * ** ** * *
54848896 ATATCA-ATCGTGTCTCCCTGAAGTTGCAGTGGAGTGGA-TGAAAAC-GATGAATCATATAC-CT
322 ATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGA-G-ATCTTAT-CTCC
*
54848957 CTAAAGTTGGAGTAGGTCGAATTGGATCA-AACCTTATCTCCCTAAAGTCA
384 CTAAAGTTGGAG-AGGTCGAATTGGATCATAACCTTATCTCCCTAAAGTTA
* * * *
54849007 CAGTGGAACAGG-TTGAAGATACAA-ATCTTATCTCCCTGACG-TAGCAGTGGAGCAGACTAGAA
1 CAGTGGAGC-GGATT-AAAATA-AAGATCTTATCTCTCTGAAGTTA-CAGT-GAGCAGA-TAGAA
54849069 CCACA
60 CCACA
54849074 AACATCATCC
Statistics
Matches: 830, Mismatches: 69, Indels: 76
0.85 0.07 0.08
Matches are distributed among these distances:
429 2 0.00
430 1 0.00
431 9 0.01
432 43 0.05
433 14 0.02
434 9 0.01
435 197 0.24
436 221 0.27
437 25 0.03
438 308 0.37
439 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (433 bp):
CAGTGGAGCGGATTAAAATAAAGATCTTATCTCTCTGAAGTTACAGTGAGCAGATAGAACCACAG
TCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACA
CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTT
ACAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTT
CAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTAAAGT
TGGAGAGGTCGAATTGGATCATAACCTTATCTCCCTAAAGTTA
Found at i:54849639 original size:22 final size:23
Alignment explanation
Indices: 54849613--54849661 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
54849603 TTTCGGCTAT
54849613 AAAGCCGAATGTGTTGCATT-TA
1 AAAGCCGAATGTGTTGCATTGTA
54849635 AAAGCCGAATGTGTTGCATTGTA
1 AAAGCCGAATGTGTTGCATTGTA
54849658 AAAG
1 AAAG
54849662 TGGGGGGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (23 bp):
AAAGCCGAATGTGTTGCATTGTA
Found at i:54856819 original size:23 final size:22
Alignment explanation
Indices: 54856762--54856804 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
54856752 TTTAACATTT
54856762 ATTTTGATAAAAATATTAAAGC
1 ATTTTGATAAAAATATTAAAGC
54856784 ATTTTGATAAAAATATTAAAG
1 ATTTTGATAAAAATATTAAAG
54856805 TGATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (22 bp):
ATTTTGATAAAAATATTAAAGC
Found at i:54857921 original size:29 final size:28
Alignment explanation
Indices: 54857879--54857933 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
54857869 TTAATATAAT
* **
54857879 TATTGATATAATATTTTTTATATTTAAA
1 TATTGATACAATATTAATTATATTTAAA
54857907 TATTGCATACAATATTAATTATATTTA
1 TATTG-ATACAATATTAATTATATTTA
54857934 TCTAATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (28 bp):
TATTGATACAATATTAATTATATTTAAA
Found at i:54859148 original size:20 final size:20
Alignment explanation
Indices: 54859120--54859160 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54859110 CAAAAGTAAA
*
54859120 TAAATAATTTTATAAAATTT
1 TAAAGAATTTTATAAAATTT
* *
54859140 TAAAGAATTTTTTAATATTT
1 TAAAGAATTTTATAAAATTT
54859160 T
1 T
54859161 TTTTAGAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TAAAGAATTTTATAAAATTT
Found at i:54862155 original size:8 final size:8
Alignment explanation
Indices: 54862142--54862166 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54862132 AAATTTATGT
54862142 TCAATTTC
1 TCAATTTC
54862150 TCAATTTC
1 TCAATTTC
54862158 TCAATTTC
1 TCAATTTC
54862166 T
1 T
54862167 TTCGCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCAATTTC
Found at i:54863972 original size:14 final size:16
Alignment explanation
Indices: 54863953--54863986 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
54863943 AAGGGTTTAG
54863953 TTTTTA-TCTTCA-TC
1 TTTTTACTCTTCATTC
54863967 TTTTTACTCTTCATTC
1 TTTTTACTCTTCATTC
54863983 TTTT
1 TTTT
54863987 GCCATTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 6 0.33
16 6 0.33
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTACTCTTCATTC
Found at i:54867009 original size:23 final size:23
Alignment explanation
Indices: 54866973--54867173 Score: 264
Period size: 23 Copynumber: 8.8 Consensus size: 23
54866963 CTACCCTGTT
*
54866973 TTGGACAGCTTTTATACATCAAA
1 TTGGACAGCATTTATACATCAAA
* *
54866996 TTGGACAACATTTATACACCAAA
1 TTGGACAGCATTTATACATCAAA
* *
54867019 TTAGACAGTATTTATACATCAAA
1 TTGGACAGCATTTATACATCAAA
* *
54867042 TTGGGCAACATTTATACATCAAA
1 TTGGACAGCATTTATACATCAAA
*
54867065 TTAGG-CAGCA--TATACACCAAA
1 TT-GGACAGCATTTATACATCAAA
* *
54867086 TTGGACAACATTTATACATTAAA
1 TTGGACAGCATTTATACATCAAA
54867109 TTGGACAGCATTTATACATCAAA
1 TTGGACAGCATTTATACATCAAA
* *
54867132 TTGGACAACATTTATACATTAAA
1 TTGGACAGCATTTATACATCAAA
54867155 TTGGACAGCATTTATACAT
1 TTGGACAGCATTTATACAT
54867174 GTAAAAACAG
Statistics
Matches: 153, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
20 2 0.01
21 16 0.10
23 133 0.87
24 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (23 bp):
TTGGACAGCATTTATACATCAAA
Found at i:54867043 original size:46 final size:46
Alignment explanation
Indices: 54866976--54867173 Score: 292
Period size: 46 Copynumber: 4.3 Consensus size: 46
54866966 CCCTGTTTTG
* *
54866976 GACAGCTTTTATACATCAAATTGGACAACATTTATACACCAAATTA
1 GACAGCATTTATACATCAAATTGGACAACATTTATACATCAAATTA
* *
54867022 GACAGTATTTATACATCAAATTGGGCAACATTTATACATCAAATTA
1 GACAGCATTTATACATCAAATTGGACAACATTTATACATCAAATTA
* * * *
54867068 GGCAGCA--TATACACCAAATTGGACAACATTTATACATTAAATTG
1 GACAGCATTTATACATCAAATTGGACAACATTTATACATCAAATTA
* *
54867112 GACAGCATTTATACATCAAATTGGACAACATTTATACATTAAATTG
1 GACAGCATTTATACATCAAATTGGACAACATTTATACATCAAATTA
54867158 GACAGCATTTATACAT
1 GACAGCATTTATACAT
54867174 GTAAAAACAG
Statistics
Matches: 138, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
44 39 0.28
46 99 0.72
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (46 bp):
GACAGCATTTATACATCAAATTGGACAACATTTATACATCAAATTA
Found at i:54867141 original size:90 final size:90
Alignment explanation
Indices: 54866985--54867165 Score: 283
Period size: 90 Copynumber: 2.0 Consensus size: 90
54866975 GGACAGCTTT
* * *
54866985 TATACATCAAATTGGACAACATTTATACACCAAATTAGACAGTATTTATACATCAAATTGGGCAA
1 TATACACCAAATTGGACAACATTTATACACCAAATTAGACAGCATTTATACATCAAATTGGACAA
54867050 CATTTATACATCAAATTAGG-CAGCA
66 CATTTATACATCAAATT-GGACAGCA
** *
54867075 TATACACCAAATTGGACAACATTTATACATTAAATTGGACAGCATTTATACATCAAATTGGACAA
1 TATACACCAAATTGGACAACATTTATACACCAAATTAGACAGCATTTATACATCAAATTGGACAA
*
54867140 CATTTATACATTAAATTGGACAGCA
66 CATTTATACATCAAATTGGACAGCA
54867165 T
1 T
54867166 TTATACATGT
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
89 2 0.02
90 81 0.98
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (90 bp):
TATACACCAAATTGGACAACATTTATACACCAAATTAGACAGCATTTATACATCAAATTGGACAA
CATTTATACATCAAATTGGACAGCA
Found at i:54868045 original size:40 final size:40
Alignment explanation
Indices: 54867915--54868049 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 40
54867905 ATTATAATCC
* * * **
54867915 CGCACACTAAGTGCCTTACATAGCTGAAGCTATCTCAGTTT
1 CGCACACTAAGTGCCATAAATAGCCGAAGCTATCTC-GAAT
* * *
54867956 CGCACACTAAGTGCCATATATAACCGAAGCTAT-TCCCAAT
1 CGCACACTAAGTGCCATAAATAGCCGAAGCTATCT-CGAAT
*
54867996 CGCACACTAAGTGCCATAAATAGCCGAAGCTGTCTCGAAT
1 CGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAAT
* *
54868036 CACATACTAAGTGC
1 CGCACACTAAGTGC
54868050 TAAACATAGT
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
40 48 0.61
41 31 0.39
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (40 bp):
CGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAAT
Found at i:54873253 original size:5 final size:5
Alignment explanation
Indices: 54873243--54873274 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
54873233 GGTTGGAATG
54873243 TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT
54873275 GTTGAGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:54879287 original size:18 final size:19
Alignment explanation
Indices: 54879245--54879288 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
54879235 CTATAATAAT
54879245 AATATATTTTAATTTTAGGA
1 AATATATTTTAATTTTA-GA
* *
54879265 CATATATTTTATTTTTA-A
1 AATATATTTTAATTTTAGA
54879283 AATATA
1 AATATA
54879289 ATTATATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (19 bp):
AATATATTTTAATTTTAGA
Found at i:54881529 original size:14 final size:14
Alignment explanation
Indices: 54881510--54881543 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
54881500 ATTTTTGAAA
54881510 TCGAAATGGAGGTT
1 TCGAAATGGAGGTT
54881524 TCGAAATGGAGGTT
1 TCGAAATGGAGGTT
*
54881538 TAGAAA
1 TCGAAA
54881544 CGAGGTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (14 bp):
TCGAAATGGAGGTT
Found at i:54884342 original size:38 final size:38
Alignment explanation
Indices: 54884300--54884372 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
54884290 AAAAAAATAT
54884300 TTTTAAACAGTTACGATTTGACAA-AATTAGAATCTAGC
1 TTTTAAACAGTTACGATTTGA-AACAATTAGAATCTAGC
*
54884338 TTTTAAACGGTTACGATTTGAAACAATTAGAATCT
1 TTTTAAACAGTTACGATTTGAAACAATTAGAATCT
54884373 GGCTATTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 2 0.06
38 31 0.94
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (38 bp):
TTTTAAACAGTTACGATTTGAAACAATTAGAATCTAGC
Found at i:54889194 original size:20 final size:20
Alignment explanation
Indices: 54889132--54889197 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
54889122 TTTTAATTTT
*
54889132 AAATATTAATTGTATATATAA
1 AAATATTTATTGTATAT-TAA
*
54889153 CAAAT-TTTATTAGTATA-CAA
1 -AAATATTTATT-GTATATTAA
*
54889173 AAATATTTATTTTATATTAA
1 AAATATTTATTGTATATTAA
54889193 AAATA
1 AAATA
54889198 AATTTTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 8 0.22
20 15 0.41
21 5 0.14
22 9 0.24
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
AAATATTTATTGTATATTAA
Found at i:54889720 original size:9 final size:9
Alignment explanation
Indices: 54889664--54889722 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
54889654 ATTTAAAATG
54889664 TTATAAAAA
1 TTATAAAAA
*
54889673 CTAATAAAAA
1 -TTATAAAAA
*
54889683 TCATAAAAA
1 TTATAAAAA
*
54889692 TTATTAAAA
1 TTATAAAAA
*
54889701 TCATAAAAA
1 TTATAAAAA
*
54889710 TTATAACAA
1 TTATAAAAA
54889719 TTAT
1 TTAT
54889723 TAAATAGAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
9 33 0.80
10 8 0.20
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:54893182 original size:24 final size:24
Alignment explanation
Indices: 54893148--54893200 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
54893138 TTTCTAGAAG
* *
54893148 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
54893172 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
54893196 ATTTA
1 ATTTA
54893201 ACTTTGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:54893210 original size:24 final size:24
Alignment explanation
Indices: 54893155--54893211 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
54893145 AAGATTTAGT
* * *
54893155 ATTTATGAGTATAATATATTTAGC
1 ATTTATTAGCATAATATATTTAAC
54893179 ATTTATTAGCATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
54893203 -TTTGATTAG
1 ATTT-ATTAG
54893212 AATTAGGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:54905255 original size:106 final size:106
Alignment explanation
Indices: 54905063--54905484 Score: 702
Period size: 106 Copynumber: 4.0 Consensus size: 106
54905053 TGGATTGAGA
* * * *
54905063 TTTAAGAGGATATTTGGCTATTTAGTTGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTC
* * *
54905128 TCTCGAATTTCTAAACGCAAAATATTGCCTCACTTTGAAAT
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
*
54905169 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTGGGGCACGTTC
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTC
*
54905234 TCTCGAATTTCCAAACACAAAATATTGCCTTACTTTGAAAG
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
*
54905275 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTC
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTC
*
54905340 TCTCGAATTTCCAAATGCAAAATATTGCCTTACTTTGAAAG
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
*
54905381 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTC
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTC
* * *
54905446 TCTCGAATTTCTAAACGCGAAATATTACCTTA-TTTGAAA
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
54905485 ACTTTTTCCT
Statistics
Matches: 299, Mismatches: 17, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
105 7 0.02
106 292 0.98
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (106 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTC
TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAG
Found at i:54916410 original size:41 final size:41
Alignment explanation
Indices: 54916353--54916454 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
54916343 GCATAGCGCT
*
54916353 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
* *
54916394 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
54916435 TAGCAGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
54916455 TACTGAATCA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 3 0.05
41 54 0.95
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
Found at i:54924063 original size:41 final size:41
Alignment explanation
Indices: 54924002--54924100 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 41
54923992 GCATAGCGCT
* * *
54924002 TAGCAGGCTTATTGCTGGTGAAGCACTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
* * *
54924043 TAGCATGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
54924084 TAGCAGGC-TAAGTGCCG
1 TAGCAGGCTTAA-TGCCG
54924101 ATGTATTGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 3 0.06
41 47 0.94
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
Found at i:54928755 original size:105 final size:106
Alignment explanation
Indices: 54928577--54928987 Score: 598
Period size: 106 Copynumber: 3.9 Consensus size: 106
54928567 GATTTAAGAG
* * * *
54928577 GATATTTGGCTATTTAGTTGAACGAGAAATCGAAACTCAGCACGTTAGGGCACGTTTTCTCGAA-
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
* * * *
54928641 TTTCTAAACGCAAAATATTGGCTCACTTTGAAATTTTAAAAG
66 TTTC-AAACGCAAAATATTGCCTTACTTTGAAAGTTTAAAAA
* *
54928683 GATATTTGGCT-TTTGGTCGAACGAGAAATCGGAACCCAGCACGTTAGGGCATGTTCTCTCGAAT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
*
54928747 TTTCAAACGCAAAATATTACCTTACTTTGAAAGTTTAAAAA
66 TTTCAAACGCAAAATATTGCCTTACTTTGAAAGTTTAAAAA
* * * * * *
54928788 GATATTTGGCTATTTGGTCGAATGAGAAATCGAAACCTAGCTCGTTAGAGCACGTTCTCCCAAAT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
54928853 TTTCAAACGCAAAATATTGCCTTACTTTGAAAGTTTAAAAA
66 TTTCAAACGCAAAATATTGCCTTACTTTGAAAGTTTAAAAA
* *
54928894 GATATTTTGC--TTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
*
54928957 TTTCAAACGCGAAATATTGCCTTA-TTTGAAA
66 TTTCAAACGCAAAATATTGCCTTACTTTGAAA
54928988 ACTTTTTCCT
Statistics
Matches: 274, Mismatches: 29, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
103 7 0.03
104 69 0.25
105 89 0.32
106 109 0.40
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (106 bp):
GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
TTTCAAACGCAAAATATTGCCTTACTTTGAAAGTTTAAAAA
Found at i:54932830 original size:18 final size:19
Alignment explanation
Indices: 54932803--54932838 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
54932793 CTTTGATCCA
54932803 TTTCCAATTTT-TTTTCTT
1 TTTCCAATTTTCTTTTCTT
*
54932821 TTTCCCATTTTCTTTTCT
1 TTTCCAATTTTCTTTTCT
54932839 AACCCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTCCAATTTTCTTTTCTT
Found at i:54940716 original size:27 final size:26
Alignment explanation
Indices: 54940686--54940952 Score: 302
Period size: 27 Copynumber: 9.9 Consensus size: 26
54940676 ATAAATGATT
*
54940686 GAAATACCTCCATAGGATAAAATGACC
1 GAAATACC-CCATAGGGTAAAATGACC
*
54940713 GAAATACCCCCATAAGGTAAAATGACC
1 GAAATA-CCCCATAGGGTAAAATGACC
* * * *
54940740 AAAATATGCCCATAGGGTAGAATGACT
1 GAAATA-CCCCATAGGGTAAAATGACC
*
54940767 GAAATACCCCTATAGGGTAAAATGACT
1 GAAATACCCC-ATAGGGTAAAATGACC
*
54940794 GAAATACCCCTATAGGGTAAAATAACC
1 GAAATACCCC-ATAGGGTAAAATGACC
*
54940821 GAAATACCCCCATAGGGTAAAATGACT
1 GAAATA-CCCCATAGGGTAAAATGACC
*
54940848 GAAATACCCTCATAGGGTAGAATGACC
1 GAAATACCC-CATAGGGTAAAATGACC
* * **
54940875 GAAATACCTCCATTGGGTAAAATAATT
1 GAAATACC-CCATAGGGTAAAATGACC
54940902 GAAATACCCCCATA-GGTAAAATGACC
1 GAAATA-CCCCATAGGGTAAAATGACC
*
54940928 GAAATACCCCCATAAGGTAAAATGA
1 GAAATA-CCCCATAGGGTAAAATGA
54940953 TTTTTATACC
Statistics
Matches: 207, Mismatches: 26, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
26 29 0.14
27 169 0.82
28 9 0.04
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.19
Consensus pattern (26 bp):
GAAATACCCCATAGGGTAAAATGACC
Found at i:54940745 original size:54 final size:53
Alignment explanation
Indices: 54940678--54940952 Score: 354
Period size: 54 Copynumber: 5.1 Consensus size: 53
54940668 AGAGGTGGAT
* * *
54940678 AAATGATTGAAATACCTCCATAGGATAAAATGACCGAAATACCCCCATAAGGTA
1 AAATGACTGAAATACC-CCATAGGGTAAAATGACCGAAATACCCCCATAGGGTA
** * * * *
54940732 AAATGACCAAAATATGCCCATAGGGTAGAATGACTGAAATACCCCTATAGGGTA
1 AAATGACTGAAATA-CCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTA
*
54940786 AAATGACTGAAATACCCCTATAGGGTAAAATAACCGAAATACCCCCATAGGGTA
1 AAATGACTGAAATACCCC-ATAGGGTAAAATGACCGAAATACCCCCATAGGGTA
* * *
54940840 AAATGACTGAAATACCCTCATAGGGTAGAATGACCGAAATACCTCCATTGGGTA
1 AAATGACTGAAATACCC-CATAGGGTAAAATGACCGAAATACCCCCATAGGGTA
* * *
54940894 AAATAATTGAAATACCCCCATA-GGTAAAATGACCGAAATACCCCCATAAGGTA
1 AAATGACTGAAATA-CCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTA
54940947 AAATGA
1 AAATGA
54940953 TTTTTATACC
Statistics
Matches: 190, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
53 35 0.18
54 150 0.79
55 5 0.03
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (53 bp):
AAATGACTGAAATACCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTA
Found at i:54940814 original size:81 final size:80
Alignment explanation
Indices: 54940678--54940952 Score: 340
Period size: 81 Copynumber: 3.4 Consensus size: 80
54940668 AGAGGTGGAT
* * * * *
54940678 AAATGATTGAAATACCTCC-ATAGGATAAAATGACCGAAATACCCCCATAAGGTAAAATGACCAA
1 AAATGACTGAAATACC-CCTATAGGGTAAAATGACCGAAATA-CCCCATAGGGTAAAATAACCGA
**
54940742 AATATGCCCATAGGGTA
64 AATACCCCCATAGGGTA
* *
54940759 GAATGACTGAAATACCCCTATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAATAACCGAA
1 AAATGACTGAAATACCCCTATAGGGTAAAATGACCGAAATACCCC-ATAGGGTAAAATAACCGAA
54940824 ATACCCCCATAGGGTA
65 ATACCCCCATAGGGTA
* * **
54940840 AAATGACTGAAATA-CCCTCATAGGGTAGAATGACCGAAATACCTCCATTGGGTAAAATAATTGA
1 AAATGACTGAAATACCCCT-ATAGGGTAAAATGACCGAAATACC-CCATAGGGTAAAATAACCGA
54940904 AATACCCCCATA-GGTA
64 AATACCCCCATAGGGTA
* * *
54940920 AAATGACCGAAATACCCCCATAAGGTAAAATGA
1 AAATGACTGAAATACCCCTATAGGGTAAAATGA
54940953 TTTTTATACC
Statistics
Matches: 170, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
80 39 0.23
81 129 0.76
82 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (80 bp):
AAATGACTGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCATAGGGTAAAATAACCGAAA
TACCCCCATAGGGTA
Found at i:54941178 original size:27 final size:26
Alignment explanation
Indices: 54941148--54941207 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
54941138 CCTACTAGTG
* * *
54941148 GCTTTGCCACATATACTGTTACTGATA
1 GCTTTGCCAC-GATACTATTACTGACA
* *
54941175 GCTTTGCTACGATACTATTACTGGCA
1 GCTTTGCCACGATACTATTACTGACA
54941201 GCTTTGC
1 GCTTTGC
54941208 TGCGATATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 19 0.68
27 9 0.32
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (26 bp):
GCTTTGCCACGATACTATTACTGACA
Found at i:54941196 original size:26 final size:26
Alignment explanation
Indices: 54941160--54941214 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
54941150 TTTGCCACAT
* *
54941160 ATACTGTTACTGATAGCTTTGCTACG
1 ATACTATTACTGACAGCTTTGCTACG
* *
54941186 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGACAGCTTTGCTACG
54941212 ATA
1 ATA
54941215 TTGGTGTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (26 bp):
ATACTATTACTGACAGCTTTGCTACG
Found at i:54941432 original size:28 final size:27
Alignment explanation
Indices: 54941319--54941433 Score: 140
Period size: 28 Copynumber: 4.1 Consensus size: 27
54941309 TGCACTGCAT
*
54941319 TGTTACTGTATTGGGCTAAGGCCTACAC
1 TGTT-CTGTATTGGGCTAAGGCCCACAC
* * *
54941347 TAATTCTCTATTGGGCTAAGGCCCATAC
1 T-GTTCTGTATTGGGCTAAGGCCCACAC
54941375 TGATTCTGTATTGGGCTAAGGCCCACAC
1 TG-TTCTGTATTGGGCTAAGGCCCACAC
* *
54941403 TGTTACTGTAATGGGCCAAGGCCCACAC
1 TGTT-CTGTATTGGGCTAAGGCCCACAC
54941431 TGT
1 TGT
54941434 ATTGATACTG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 71 0.95
29 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (27 bp):
TGTTCTGTATTGGGCTAAGGCCCACAC
Found at i:54945549 original size:3 final size:3
Alignment explanation
Indices: 54945543--54945568 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54945533 TCGAAGAAGT
54945543 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
54945569 TGGGTGCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:54947724 original size:16 final size:17
Alignment explanation
Indices: 54947692--54947724 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54947682 ATAATTTATC
*
54947692 AATTTATATTTTTTAGA
1 AATTTATATTATTTAGA
54947709 AATTTATA-TATTTAGA
1 AATTTATATTATTTAGA
54947725 TGGGTTTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
AATTTATATTATTTAGA
Found at i:54948156 original size:20 final size:21
Alignment explanation
Indices: 54948127--54948186 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
54948117 CTCAAGTATT
*
54948127 AAAAATTATGAGAGAATATC-
1 AAAAAATATGAGAGAATATCA
*
54948147 AAAAAGTATGAGA-AAGTATCA
1 AAAAAATATGAGAGAA-TATCA
*
54948168 AAAAAATATAAGAGAATAT
1 AAAAAATATGAGAGAATAT
54948187 GAAATATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 2 0.06
20 16 0.47
21 14 0.41
22 2 0.06
ACGTcount: A:0.60, C:0.03, G:0.15, T:0.22
Consensus pattern (21 bp):
AAAAAATATGAGAGAATATCA
Found at i:54948666 original size:20 final size:21
Alignment explanation
Indices: 54948627--54948667 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
54948617 AAAAACATTA
54948627 GAAATCATAAAAATTTATAAT
1 GAAATCATAAAAATTTATAAT
54948648 GAAATC-TAACAAA-TTATAAT
1 GAAATCATAA-AAATTTATAAT
54948668 TTTTTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (21 bp):
GAAATCATAAAAATTTATAAT
Found at i:54948748 original size:29 final size:28
Alignment explanation
Indices: 54948716--54948786 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 28
54948706 AATGTTATAA
54948716 AAAATAATAAAAAAATCATAAAAATTATT
1 AAAAT-ATAAAAAAATCATAAAAATTATT
* *
54948745 AAAATCATAAAAAAATTATAACAATTATT
1 AAAAT-ATAAAAAAATCATAAAAATTATT
*
54948774 AAAATTTAAAAAA
1 AAAATATAAAAAA
54948787 TAAAAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
28 7 0.18
29 31 0.82
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAATATAAAAAAATCATAAAAATTATT
Found at i:54948765 original size:11 final size:10
Alignment explanation
Indices: 54948675--54948866 Score: 53
Period size: 9 Copynumber: 19.3 Consensus size: 10
54948665 AATTTTTTAT
54948675 AAAATTAATAA
1 AAAATT-ATAA
54948686 AACATATT-TAA
1 AA-A-ATTATAA
*
54948697 AATATT-TAA
1 AAAATTATAA
**
54948706 AATGTTATAA
1 AAAATTATAA
*
54948716 AAAATAATAAA
1 AAAATTAT-AA
*
54948727 AAAATCAT-A
1 AAAATTATAA
*
54948736 AAAATTAT-T
1 AAAATTATAA
*
54948745 AAAATCATAAA
1 AAAATTAT-AA
54948756 AAAATTAT-A
1 AAAATTATAA
* *
54948765 ACAATTAT-T
1 AAAATTATAA
54948774 AAAATT-TAA
1 AAAATTATAA
54948783 AAAA-TA-AA
1 AAAATTATAA
** *
54948791 AAATAAAATACC
1 AAA-ATTATA-A
* *
54948803 AGAATTGATAT
1 AAAATT-ATAA
*
54948814 AAACTTAT-A
1 AAAATTATAA
54948823 AAAATTATAAA
1 AAAATTAT-AA
* *
54948834 AAAATCACAA
1 AAAATTATAA
*
54948844 AAATTTATAA
1 AAAATTATAA
* *
54948854 AAACTTTTAA
1 AAAATTATAA
54948864 AAA
1 AAA
54948867 CTACCTAACA
Statistics
Matches: 134, Mismatches: 32, Indels: 31
0.68 0.16 0.16
Matches are distributed among these distances:
8 7 0.05
9 51 0.38
10 31 0.23
11 36 0.27
12 6 0.04
13 3 0.02
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAATTATAA
Found at i:54948777 original size:20 final size:20
Alignment explanation
Indices: 54948727--54948763 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54948717 AAATAATAAA
54948727 AAAATCAT--AAAAATTATT
1 AAAATCATAAAAAAATTATT
54948745 AAAATCATAAAAAAATTAT
1 AAAATCATAAAAAAATTAT
54948764 AACAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATCATAAAAAAATTATT
Found at i:54950599 original size:3 final size:3
Alignment explanation
Indices: 54950591--54950640 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
54950581 GTAGGCTTCT
54950591 TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
54950637 TAA T
1 TAA T
54950641 TGTAACACCT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:54953390 original size:16 final size:16
Alignment explanation
Indices: 54953369--54953401 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54953359 TTGATTTTGT
54953369 TTAACGTATGATGTTG
1 TTAACGTATGATGTTG
54953385 TTAACGTATGATGTTG
1 TTAACGTATGATGTTG
54953401 T
1 T
54953402 GTATATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.45
Consensus pattern (16 bp):
TTAACGTATGATGTTG
Found at i:54954469 original size:12 final size:12
Alignment explanation
Indices: 54954431--54954472 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
54954421 ATTGGTCATA
54954431 GAGAGATTTGAG
1 GAGAGATTTGAG
* *
54954443 GAGGGATATT-TG
1 GAGAGAT-TTGAG
54954455 GAGAGATTTGAG
1 GAGAGATTTGAG
54954467 GAGAGA
1 GAGAGA
54954473 ATATTGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:54954479 original size:24 final size:24
Alignment explanation
Indices: 54954431--54954477 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
54954421 ATTGGTCATA
*
54954431 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAGGAGGAATATTTG
54954455 GAGAGATTTGAGGAGAGAATATT
1 GAGAGATTTGAGGAG-GAATATT
54954478 GGGATTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (24 bp):
GAGAGATTTGAGGAGGAATATTTG
Found at i:54955184 original size:27 final size:27
Alignment explanation
Indices: 54955145--54955554 Score: 408
Period size: 27 Copynumber: 15.2 Consensus size: 27
54955135 AGAGGTCGAT
* *
54955145 AAATGACCAAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
54955172 AAATAACCGAAATAGCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
54955199 GAATGACCGAAATACTCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
** * *
54955226 GCATGACAGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * ** * *
54955253 GAATAACTTAAATACCCCTATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
54955280 GAATGACTGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
54955307 GAATGACCGAAATAACCACATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
54955334 GAATGATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
54955361 GAATGACCAAAATACCCCCGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
54955388 AAATCATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* **
54955415 AAATGACTGAAATACCTTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
54955442 AATTGA-CTAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
54955468 GAATGATCGAAATACCCCCATTGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *** *
54955495 AAATAATTAAAATACCCGCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
54955522 AAATGACCAAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
54955549 AAATGA
1 AAATGA
54955555 TTTTTATACC
Statistics
Matches: 320, Mismatches: 62, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 20 0.06
27 300 0.94
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:54955941 original size:28 final size:28
Alignment explanation
Indices: 54955896--54955980 Score: 136
Period size: 28 Copynumber: 3.0 Consensus size: 28
54955886 TGCATTGTAT
54955896 TGTTACTGTATTGGGCTAAGGCCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
54955924 TGATT-CTGTATTGGGCTAAGGCCCACAC
1 TG-TTACTGTATTGGGCTAAGGCCCACAC
* *
54955952 TGTTACTGTAATGGGCCAAGGCCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
54955980 T
1 T
54955981 ATATTGATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.04
28 49 0.92
29 2 0.04
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (28 bp):
TGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:54957027 original size:18 final size:18
Alignment explanation
Indices: 54956983--54957030 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
54956973 ACCTACAAAG
* * *
54956983 AAAGAAATAAAATTAATT
1 AAAGAAATTAAATAAAAT
**
54957001 AAACCAATTAAATAAAAT
1 AAAGAAATTAAATAAAAT
54957019 AAAGAAATTAAA
1 AAAGAAATTAAA
54957031 AGAAAATTAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAGAAATTAAATAAAAT
Found at i:54972599 original size:14 final size:14
Alignment explanation
Indices: 54972579--54972614 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
54972569 AATATTGTAG
54972579 ATAAAAATTTTAAAA
1 ATAAAAA-TTTAAAA
*
54972594 ATAAAAATTTATAA
1 ATAAAAATTTAAAA
54972608 ATAAAAA
1 ATAAAAA
54972615 AGAAGAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAAAATTTAAAA
Found at i:54972814 original size:9 final size:9
Alignment explanation
Indices: 54972795--54972909 Score: 51
Period size: 9 Copynumber: 12.8 Consensus size: 9
54972785 TTCTTTCTAG
54972795 TTTTTAT-A
1 TTTTTATAA
54972803 TTTTTATAA
1 TTTTTATAA
*
54972812 TTTATTAGAAA
1 TTT-TTA-TAA
* *
54972823 ATTTTA-CA
1 TTTTTATAA
* *
54972831 TGATTTATAT
1 T-TTTTATAA
54972841 TTTTTATAA
1 TTTTTATAA
*
54972850 TTTGTATAA
1 TTTTTATAA
*
54972859 CTTTATATCAA
1 -TTTTTAT-AA
*
54972870 TTTTAAT-A
1 TTTTTATAA
*
54972878 -TTTAATAA
1 TTTTTATAA
*
54972886 -TTTAATAA
1 TTTTTATAA
*
54972894 TTTTTATGA
1 TTTTTATAA
54972903 TTTTTAT
1 TTTTTAT
54972910 GATTCTTTAA
Statistics
Matches: 83, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
7 6 0.07
8 18 0.22
9 35 0.42
10 18 0.22
11 6 0.07
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:54976404 original size:20 final size:22
Alignment explanation
Indices: 54976381--54976437 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
54976371 AGGCGTACCC
54976381 AAAATTATGAAGGAATAA-C-A
1 AAAATTATGAAGGAATAACCAA
54976401 AAAATTATG-AGTGAA-AACCAA
1 AAAATTATGAAG-GAATAACCAA
*
54976422 AAAAATATGAAGGAAT
1 AAAATTATGAAGGAAT
54976438 TTGTTTTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 4 0.13
20 13 0.42
21 12 0.39
22 2 0.06
ACGTcount: A:0.60, C:0.05, G:0.16, T:0.19
Consensus pattern (22 bp):
AAAATTATGAAGGAATAACCAA
Found at i:54978195 original size:33 final size:33
Alignment explanation
Indices: 54978143--54978232 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
54978133 TCCCAACAGA
* * *
54978143 TTCTACCCTTTCCAGATCACCTTCACCATCATA-
1 TTCTACCCCTTCAACATCACCTTCACCATCA-AC
* * *
54978176 TTCTACCCCTTCATCATCACCCTCCCCATCAAC
1 TTCTACCCCTTCAACATCACCTTCACCATCAAC
*
54978209 TTCTATCCCTTCAACATCACCTTC
1 TTCTACCCCTTCAACATCACCTTC
54978233 CGCAACAGTC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 1 0.02
33 46 0.98
ACGTcount: A:0.22, C:0.44, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCTACCCCTTCAACATCACCTTCACCATCAAC
Found at i:54979557 original size:6 final size:6
Alignment explanation
Indices: 54979538--54979576 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
54979528 ACAATTCACA
* *
54979538 TTTCAT TTTCCAT TTTCAT TTTCAT TTCCAA TTTCAT TT
1 TTTCAT TTT-CAT TTTCAT TTTCAT TTTCAT TTTCAT TT
54979577 CTTATTACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTCAT
Found at i:54979565 original size:18 final size:19
Alignment explanation
Indices: 54979538--54979576 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
54979528 ACAATTCACA
*
54979538 TTTCATTTTCCATTTTCAT
1 TTTCATTTTCCAATTTCAT
54979557 TTTCA-TTTCCAATTTCAT
1 TTTCATTTTCCAATTTCAT
54979575 TT
1 TT
54979577 CTTATTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTCATTTTCCAATTTCAT
Found at i:54982994 original size:12 final size:12
Alignment explanation
Indices: 54982977--54983004 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
54982967 AGACAGCCTG
54982977 AGGCATCTCACA
1 AGGCATCTCACA
54982989 AGGCATCTCACA
1 AGGCATCTCACA
54983001 AGGC
1 AGGC
54983005 CATGTGCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.14
Consensus pattern (12 bp):
AGGCATCTCACA
Found at i:54985982 original size:15 final size:15
Alignment explanation
Indices: 54985962--54985990 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54985952 GTATTATTGC
54985962 TTGATAACACGATGA
1 TTGATAACACGATGA
54985977 TTGATAACACGATG
1 TTGATAACACGATG
54985991 TGTGAAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (15 bp):
TTGATAACACGATGA
Found at i:54987325 original size:19 final size:19
Alignment explanation
Indices: 54987301--54987337 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54987291 CAACATATCA
54987301 TAATAAAACAAAATTTTAG
1 TAATAAAACAAAATTTTAG
* *
54987320 TAATAATACATAATTTTA
1 TAATAAAACAAAATTTTA
54987338 AAACAAGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
TAATAAAACAAAATTTTAG
Found at i:54987524 original size:15 final size:15
Alignment explanation
Indices: 54987492--54987530 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
54987482 TATAAAAAAT
* *
54987492 ATAAAAATAATAGGA
1 ATAATAATAATAGCA
*
54987507 ATAATAATAATATCA
1 ATAATAATAATAGCA
54987522 ATAATAATA
1 ATAATAATA
54987531 TAAAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (15 bp):
ATAATAATAATAGCA
Found at i:54987602 original size:16 final size:16
Alignment explanation
Indices: 54987558--54987602 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
54987548 TTAAAATAAT
54987558 AATAAAGATAATTTAAA
1 AATAAA-ATAATTTAAA
54987575 AA-AACAACTAATTTAAA
1 AATAA-AA-TAATTTAAA
54987592 AATAAAATAAT
1 AATAAAATAAT
54987603 AGAAAGACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 7 0.28
17 16 0.64
18 2 0.08
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (16 bp):
AATAAAATAATTTAAA
Found at i:54989571 original size:114 final size:114
Alignment explanation
Indices: 54989390--54989817 Score: 610
Period size: 114 Copynumber: 3.8 Consensus size: 114
54989380 AAGTTCGAGC
* * * * *
54989390 ATTAGCGGTGCTTTTCTAAAAACG-TTGCAAAAATG-TAATCAAAACGCATCGTTCTATCTTCAA
1 ATTAGCTGCGCTTTTCTAAAAACGCCT-CAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAG
*
54989453 CTTTAGTGGCACTAGCGGCGCTTATTCAAAAACGCCGCTATATGTCAAGA
65 CTTTAGTGGCATTAGCGGCGCTTATTCAAAAACGCCGCTATATGTCAAGA
* ** * *
54989503 ATTAGCGGCATTTTTCTAAAAATGCCTCAAAAATGTTAATCAAAATGCATCGTTCTATCTTGAGC
1 ATTAGCTGCGCTTTTCTAAAAACGCCTCAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGC
* *** * * *
54989568 TTTAGTGGCATTAGTGGCGCTTACAGAAAAATGCCGCTATAGGTCGAGA
66 TTTAGTGGCATTAGCGGCGCTTATTCAAAAACGCCGCTATATGTCAAGA
* * *
54989617 ATTAGCTGCGCTTTTCTAAAAACACCACAAAAATGTTAATCAAAACGCATCGTTCTGTCTTGAGC
1 ATTAGCTGCGCTTTTCTAAAAACGCCTCAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGC
*
54989682 TTTAGTGGCATTAGCGGCGCTTATTCAAAAACGCCTCTATATGTCAAGA
66 TTTAGTGGCATTAGCGGCGCTTATTCAAAAACGCCGCTATATGTCAAGA
*
54989731 ATTAGCTGCGCTTTTCTAAAAACG-CTGTAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAG
1 ATTAGCTGCGCTTTTCTAAAAACGCCT-CAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAG
54989795 CTTTAGTGGCATTAGCGGCGCTT
65 CTTTAGTGGCATTAGCGGCGCTT
54989818 TCCGGAAAAC
Statistics
Matches: 276, Mismatches: 36, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
113 29 0.11
114 247 0.89
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (114 bp):
ATTAGCTGCGCTTTTCTAAAAACGCCTCAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGC
TTTAGTGGCATTAGCGGCGCTTATTCAAAAACGCCGCTATATGTCAAGA
Found at i:54989748 original size:228 final size:227
Alignment explanation
Indices: 54989384--54989817 Score: 672
Period size: 228 Copynumber: 1.9 Consensus size: 227
54989374 CAGCAAAAGT
* * ****
54989384 TCGAGCATTAGCGGTGCTTTTCTAAAAACGTTGCAAAAATGTAATCAAAACGCATCGTTCTATCT
1 TCGAGAATTAGCGGCGCTTTTCTAAAAACACCACAAAAATGTAATCAAAACGCATCGTTCTATCT
*
54989449 TCAACTTTAGTGGCACTAGCGGCGCTTATTCAAAAACGCCGCTATATGTCAAGAATTAGCGGCAT
66 TCAACTTTAGTGGCACTAGCGGCGCTTATTCAAAAACGCCGCTATATGTCAAGAATTAGCGGCAC
* *
54989514 TTTTCTAAAAATGCCT-CAAAAATGTTAATCAAAATGCATCGTTCTATCTTGAGCTTTAGTGGCA
131 TTTTCTAAAAACG-CTGCAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTTAGTGGCA
*
54989578 TTAGTGGCGCTTACAGAAAAATGCCGCTATAGG
195 TTAGCGGCGCTTACAGAAAAATGCCGCTATAGG
* *
54989611 TCGAGAATTAGCTGCGCTTTTCTAAAAACACCACAAAAATGTTAATCAAAACGCATCGTTCTGTC
1 TCGAGAATTAGCGGCGCTTTTCTAAAAACACCACAAAAATG-TAATCAAAACGCATCGTTCTATC
* * * * * *
54989676 TTGAGCTTTAGTGGCATTAGCGGCGCTTATTCAAAAACGCCTCTATATGTCAAGAATTAGCTGCG
65 TTCAACTTTAGTGGCACTAGCGGCGCTTATTCAAAAACGCCGCTATATGTCAAGAATTAGCGGCA
*
54989741 CTTTTCTAAAAACGCTGTAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTTAGTGGCA
130 CTTTTCTAAAAACGCTGCAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTTAGTGGCA
54989806 TTAGCGGCGCTT
195 TTAGCGGCGCTT
54989818 TCCGGAAAAC
Statistics
Matches: 186, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
227 36 0.19
228 150 0.81
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (227 bp):
TCGAGAATTAGCGGCGCTTTTCTAAAAACACCACAAAAATGTAATCAAAACGCATCGTTCTATCT
TCAACTTTAGTGGCACTAGCGGCGCTTATTCAAAAACGCCGCTATATGTCAAGAATTAGCGGCAC
TTTTCTAAAAACGCTGCAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTTAGTGGCAT
TAGCGGCGCTTACAGAAAAATGCCGCTATAGG
Found at i:54990618 original size:21 final size:20
Alignment explanation
Indices: 54990592--54990632 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
54990582 CTTGTAAAAT
54990592 ATTAACACAATTATTGATTTA
1 ATTAACACAATT-TTGATTTA
* *
54990613 ATTAACATAATTTTTATTTA
1 ATTAACACAATTTTGATTTA
54990633 TATATTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTAACACAATTTTGATTTA
Found at i:54990682 original size:21 final size:20
Alignment explanation
Indices: 54990656--54990704 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
54990646 TAAATATTTA
54990656 TATTTATTCAATATAAATGTG
1 TATTTATTCAATA-AAATGTG
***
54990677 TATTTATTTTTTAAAATGTG
1 TATTTATTCAATAAAATGTG
54990697 TATTTATT
1 TATTTATT
54990705 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (20 bp):
TATTTATTCAATAAAATGTG
Found at i:54990715 original size:21 final size:20
Alignment explanation
Indices: 54990670--54990712 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
54990660 TATTCAATAT
54990670 AAATGTGTATTTATTTTTTA
1 AAATGTGTATTTATTTTTTA
54990690 AAATGTGTATTTATTTTTTA
1 AAATGTGTATTTATTTTTTA
54990710 AAA
1 AAA
54990713 ATGCATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (20 bp):
AAATGTGTATTTATTTTTTA
Found at i:54991408 original size:18 final size:19
Alignment explanation
Indices: 54991371--54991425 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
54991361 TACCCCAATT
54991371 CTAA-ATTTCCCCAAATCC
1 CTAACATTTCCCCAAATCC
54991389 CTAACATTTCCCCAAA-CC
1 CTAACATTTCCCCAAATCC
**
54991407 CTTTCATTTTCCCCAAATC
1 CTAACA-TTTCCCCAAATC
54991426 AAAATCGAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 10 0.31
19 21 0.66
20 1 0.03
ACGTcount: A:0.29, C:0.40, G:0.00, T:0.31
Consensus pattern (19 bp):
CTAACATTTCCCCAAATCC
Found at i:54993403 original size:29 final size:26
Alignment explanation
Indices: 54993351--54993404 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
54993341 TTTAAAATAC
*
54993351 TTTTAAAATATTTTTATTTTTATTAT
1 TTTTAAAATATTTTTATGTTTATTAT
54993377 TTTTAAAATAATTTTTTAATGTTTATTA
1 TTTTAAAAT-A-TTTTT-ATGTTTATTA
54993405 AAAAATAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 1 0.04
28 5 0.21
29 9 0.38
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTAAAATATTTTTATGTTTATTAT
Found at i:54993668 original size:9 final size:9
Alignment explanation
Indices: 54993654--54993690 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
54993644 TATAGTTTGA
54993654 TATTCGAAT
1 TATTCGAAT
54993663 TATTCGAAT
1 TATTCGAAT
*
54993672 TATTCGAGT
1 TATTCGAAT
54993681 TATTCGAAT
1 TATTCGAAT
54993690 T
1 T
54993691 TGACAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54994272 original size:9 final size:9
Alignment explanation
Indices: 54994258--54994426 Score: 88
Period size: 9 Copynumber: 19.0 Consensus size: 9
54994248 TTCCATTAAC
54994258 TTACATAAT
1 TTACATAAT
*
54994267 TTACATAAC
1 TTACATAAT
54994276 TTACATAAT
1 TTACATAAT
* *
54994285 GT--A-AAG
1 TTACATAAT
54994291 TT-CA-AAT
1 TTACATAAT
*
54994298 TT-CATAAC
1 TTACATAAT
54994306 TTACATAATT
1 TTACATAA-T
*
54994316 TTCAGATCAAAT
1 TT-ACAT--AAT
*
54994328 TT-CATAAC
1 TTACATAAT
*
54994336 TTACATACT
1 TTACATAAT
*
54994345 TTACATAAC
1 TTACATAAT
54994354 TTACATAA-
1 TTACATAAT
*
54994362 -TACATAAC
1 TTACATAAT
54994370 TTACATAATT
1 TTACATAA-T
*
54994380 TTAAGATCAAAT
1 TT-ACAT--AAT
*
54994392 TT-CATAAA
1 TTACATAAT
54994400 TTACATAAT
1 TTACATAAT
*
54994409 TTACATAAC
1 TTACATAAT
54994418 TTACATAAT
1 TTACATAAT
54994427 ACATAAATAT
Statistics
Matches: 123, Mismatches: 22, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
6 3 0.02
7 15 0.12
8 12 0.10
9 69 0.56
10 8 0.07
11 6 0.05
12 6 0.05
13 4 0.03
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.38
Consensus pattern (9 bp):
TTACATAAT
Found at i:54994304 original size:30 final size:30
Alignment explanation
Indices: 54994264--54994411 Score: 147
Period size: 30 Copynumber: 4.8 Consensus size: 30
54994254 TAACTTACAT
* *
54994264 AATTTACATAACTTACATAATGTAAAGTTCA
1 AATTT-CATAACTTACATAATTTAAAGATCA
**
54994295 AATTTCATAACTTACATAATTTTCAGATCA
1 AATTTCATAACTTACATAATTTAAAGATCA
*
54994325 AATTTCATAACTTACATACTTTACATA-ACTTACA
1 AATTTCATAACTTACATAATTTA-A-AGA--T-CA
* *
54994359 TAA-TACATAACTTACATAATTTTAAGATCA
1 -AATTTCATAACTTACATAATTTAAAGATCA
*
54994389 AATTTCATAAATTACATAATTTA
1 AATTTCATAACTTACATAATTTA
54994412 CATAACTTAC
Statistics
Matches: 96, Mismatches: 13, Indels: 17
0.76 0.10 0.13
Matches are distributed among these distances:
29 2 0.02
30 61 0.64
31 7 0.07
32 2 0.02
33 3 0.03
34 19 0.20
35 2 0.02
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.39
Consensus pattern (30 bp):
AATTTCATAACTTACATAATTTAAAGATCA
Found at i:54994387 original size:64 final size:64
Alignment explanation
Indices: 54994300--54994432 Score: 239
Period size: 64 Copynumber: 2.1 Consensus size: 64
54994290 GTTCAAATTT
* * *
54994300 CATAACTTACATAATTTTCAGATCAAATTTCATAACTTACATACTTTACATAACTTACATAATA
1 CATAACTTACATAATTTTAAGATCAAATTTCATAAATTACATAATTTACATAACTTACATAATA
54994364 CATAACTTACATAATTTTAAGATCAAATTTCATAAATTACATAATTTACATAACTTACATAATA
1 CATAACTTACATAATTTTAAGATCAAATTTCATAAATTACATAATTTACATAACTTACATAATA
54994428 CATAA
1 CATAA
54994433 ATATATATCA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.37
Consensus pattern (64 bp):
CATAACTTACATAATTTTAAGATCAAATTTCATAAATTACATAATTTACATAACTTACATAATA
Found at i:54994433 original size:34 final size:33
Alignment explanation
Indices: 54994330--54994459 Score: 115
Period size: 34 Copynumber: 3.9 Consensus size: 33
54994320 GATCAAATTT
* *
54994330 CATAACTTACATACTTTACATAACTTACATAATA
1 CATAAATTACATAATTT-CATAACTTACATAATA
* ** *
54994364 CATAACTTACATAATTT--TAAGAT-CA-AATTT
1 CATAAATTACATAATTTCATAACTTACATAA-TA
54994394 CATAAATTACATAATTTACATAACTTACATAATA
1 CATAAATTACATAATTT-CATAACTTACATAATA
* * *
54994428 CATAAATATATATCATATCATAACTTACATAA
1 CATAAAT-TACATAATTTCATAACTTACATAA
54994460 CTTAATTACA
Statistics
Matches: 78, Mismatches: 11, Indels: 14
0.76 0.11 0.14
Matches are distributed among these distances:
29 2 0.03
30 19 0.24
31 4 0.05
33 4 0.05
34 40 0.51
35 9 0.12
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (33 bp):
CATAAATTACATAATTTCATAACTTACATAATA
Found at i:54999129 original size:21 final size:21
Alignment explanation
Indices: 54999091--54999134 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
54999081 CTTAGAGCGG
* *
54999091 AGGCAGCAACGAGGGAGGTAA
1 AGGCAGCAACGAGAGAGGCAA
**
54999112 AGGCAGCAGTGAGAGAGGCAA
1 AGGCAGCAACGAGAGAGGCAA
54999133 AG
1 AG
54999135 CAAAACAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.14, G:0.43, T:0.05
Consensus pattern (21 bp):
AGGCAGCAACGAGAGAGGCAA
Found at i:54999509 original size:43 final size:43
Alignment explanation
Indices: 54999450--54999841 Score: 394
Period size: 43 Copynumber: 9.1 Consensus size: 43
54999440 GCGTTTGTAA
** * *
54999450 AAAAAAGTGCCGCTAAAGACTACGAATTATAGCGGCATTTTAT
1 AAAAAAGCACCGCTAAAGACCACGACTTATAGCGGCATTTTAT
* * * * * *
54999493 AAAAAAACACTGCTAAAGGCCATGGCTTATAGTGGCATTTTAT
1 AAAAAAGCACCGCTAAAGACCACGACTTATAGCGGCATTTTAT
* * * *
54999536 AAAACAGCACCGCTAAAGGCAATGACTTATAGCGGCATTTTAT
1 AAAAAAGCACCGCTAAAGACCACGACTTATAGCGGCATTTTAT
* * * *
54999579 AAAAAAGCGCCGCTAAAGGCCATGACTTATAGCGGCGTTTTAT
1 AAAAAAGCACCGCTAAAGACCACGACTTATAGCGGCATTTTAT
54999622 AAAAAAGCACCGCTAAAGACCACGACTTATAGCGGCATTTTAT
1 AAAAAAGCACCGCTAAAGACCACGACTTATAGCGGCATTTTAT
* * * *
54999665 AAAAAAGCGCCGGTAAAGACCACAACTTATAGCGGCGTTTTAT
1 AAAAAAGCACCGCTAAAGACCACGACTTATAGCGGCATTTTAT
* * * *
54999708 AAAAAAGCGCCGCTAAAGGCCGCGACTTATAGCGGC-TTTTTT
1 AAAAAAGCACCGCTAAAGACCACGACTTATAGCGGCATTTTAT
* * * ** * **
54999750 ATAATAGCGCCGCTAAAGACCACGACCTT-TAGCAACGTTTGCT
1 AAAAAAGCACCGCTAAAGACCACGA-CTTATAGCGGCATTTTAT
* * *
54999793 ATAATAGCACCGCTAAAGACCACGACCTT-TAGCGACATCTTCTAT
1 AAAAAAGCACCGCTAAAGACCACGA-CTTATAGCGGCAT-TT-TAT
54999838 AAAA
1 AAAA
54999842 GCGCCGTTAA
Statistics
Matches: 298, Mismatches: 47, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
42 31 0.10
43 261 0.88
44 2 0.01
45 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (43 bp):
AAAAAAGCACCGCTAAAGACCACGACTTATAGCGGCATTTTAT
Found at i:55000566 original size:48 final size:47
Alignment explanation
Indices: 55000445--55000566 Score: 136
Period size: 48 Copynumber: 2.6 Consensus size: 47
55000435 GGGTGTCACA
* * *
55000445 CGACCAATGGTTTATCCACAACATATTTTAGTCAACAATCATCTACT
1 CGACCAGTGGTTTATCCACAACGTATTCTAGTCAACAATCATCTACT
* * * * ** *
55000492 CGACTAGTGGTTTATCTATAATGTATTCTAGTTGACAGATCATCTGCT
1 CGACCAGTGGTTTATCCACAACGTATTCTAGTCAACA-ATCATCTACT
*
55000540 TGACCAGTGGTTTATCCACAACGTATT
1 CGACCAGTGGTTTATCCACAACGTATT
55000567 AGTAACTTTT
Statistics
Matches: 59, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
47 28 0.47
48 31 0.53
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (47 bp):
CGACCAGTGGTTTATCCACAACGTATTCTAGTCAACAATCATCTACT
Found at i:55002604 original size:30 final size:32
Alignment explanation
Indices: 55002548--55002606 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
55002538 AGTAATAGTT
55002548 ATTATATTAATACTTATAAAACATATTATTTC
1 ATTATATTAATACTTATAAAACATATTATTTC
**
55002580 ATTATA-TAATAC-TATATCACATATTAT
1 ATTATATTAATACTTATAAAACATATTAT
55002607 ATAATAGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 13 0.52
31 6 0.24
32 6 0.24
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (32 bp):
ATTATATTAATACTTATAAAACATATTATTTC
Found at i:55005043 original size:48 final size:48
Alignment explanation
Indices: 55004958--55005053 Score: 122
Period size: 48 Copynumber: 2.0 Consensus size: 48
55004948 TTTCATGTTA
* * *
55004958 TTTCAAGTTTTTTATTTTTAATTGATATTTATGATTAATAAATATTTT
1 TTTCAAGTTTTTTATTTTTAATTCATATTTATAATTAACAAATATTTT
* * *
55005006 TTTCAAG-TTTTTATTTTTAATTCATCTTTTTTAATTAACAAATCTTTT
1 TTTCAAGTTTTTTATTTTTAATTCAT-ATTTATAATTAACAAATATTTT
55005054 ATTTATAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 17 0.41
48 24 0.59
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (48 bp):
TTTCAAGTTTTTTATTTTTAATTCATATTTATAATTAACAAATATTTT
Found at i:55008647 original size:18 final size:19
Alignment explanation
Indices: 55008624--55008659 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
55008614 ACTTTGCTCA
55008624 CAATAATATCAC-CACAAG
1 CAATAATATCACGCACAAG
55008642 CAATAATATCACGCACAA
1 CAATAATATCACGCACAA
55008660 AAAGTTACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.17
Consensus pattern (19 bp):
CAATAATATCACGCACAAG
Found at i:55018509 original size:22 final size:21
Alignment explanation
Indices: 55018479--55018523 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
55018469 CTACACCAAC
*
55018479 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCG-TTTTTT
55018501 AGGCCTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGTTTTTT
55018522 AG
1 AG
55018524 CGCCGCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.42
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGTTTTTT
Found at i:55018660 original size:44 final size:43
Alignment explanation
Indices: 55018594--55018778 Score: 216
Period size: 43 Copynumber: 4.3 Consensus size: 43
55018584 CGTCGCTAAC
* * *
55018594 TTTAGCGGCGCTTTTTCCACAAACGCCTCTGAAGACCAAGACC
1 TTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAAGACA
*
55018637 TTTAGCGGCGCATTTTTCCACAAACGCCGCTAAAGACTAAGACA
1 TTTAGCGGCGC-TTTTTCCACAAACGCCGCTAAAGACCAAGACA
* *
55018681 TTTAGCGACGC-TTTTCTCACAAACGCCGCTAAAGACCATGACA
1 TTTAGCGGCGCTTTTTC-CACAAACGCCGCTAAAGACCAAGACA
* * * *
55018724 TTTAGCAGCGCTTTTTATCACAAA-GCCGCTATAGATCAA-ATC-
1 TTTAGCGGCGCTTTTT-CCACAAACGCCGCTAAAGACCAAGA-CA
55018766 TTTAGCGGCGCTT
1 TTTAGCGGCGCTT
55018779 CTCAAAAAAA
Statistics
Matches: 123, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
42 18 0.15
43 57 0.46
44 48 0.39
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCAAGACA
Found at i:55018693 original size:87 final size:86
Alignment explanation
Indices: 55018594--55018754 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 86
55018584 CGTCGCTAAC
* * * * *
55018594 TTTAGCGGCGCTTTT-TCCACAAACGCCTCTGAAGACCAAGACCTTTAGCGGCGCATTTTT-CCA
1 TTTAGCGACGCTTTTCT-CACAAACGCCGCTAAAGACCAAGACATTTAGCAGCGC-TTTTTACCA
55018657 CAAACGCCGCTAAAGACTAAGACA
64 CAAA-GCCGCTAAAGACTAAGACA
* *
55018681 TTTAGCGACGCTTTTCTCACAAACGCCGCTAAAGACCATGACATTTAGCAGCGCTTTTTATCACA
1 TTTAGCGACGCTTTTCTCACAAACGCCGCTAAAGACCAAGACATTTAGCAGCGCTTTTTACCACA
55018746 AAGCCGCTA
66 AAGCCGCTA
55018755 TAGATCAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
86 12 0.18
87 52 0.80
88 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (86 bp):
TTTAGCGACGCTTTTCTCACAAACGCCGCTAAAGACCAAGACATTTAGCAGCGCTTTTTACCACA
AAGCCGCTAAAGACTAAGACA
Found at i:55023220 original size:41 final size:41
Alignment explanation
Indices: 55023175--55023371 Score: 211
Period size: 41 Copynumber: 4.8 Consensus size: 41
55023165 TGACCTGAGC
*
55023175 ATTAGCGGCGCTTCATT-AAAAACGCCGCTAAAGCCCCGAGT
1 ATTAGCGGCGCTT-TTTCAAAAACGCCGCTAAAGCCCCGAGT
** * *
55023216 ATTAGCGGCGCTTTTTCAAAAATACTGCTAAAGCCTCGAGT
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGT
* * * *
55023257 ATTAGCGGCACTTTTTCAGAAACGCCGCTAAAGACCC-AAT
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGT
* * * *
55023297 CATTAGCGGTGCTTTTT-AAAAAGCGCCGCTAAAACCCTGAGC
1 -ATTAGCGGCGCTTTTTCAAAAA-CGCCGCTAAAGCCCCGAGT
* *
55023339 ATTAGCGGCGCTTTTTAAAAAACGCCACTAAAG
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAG
55023372 TTGTGAAATA
Statistics
Matches: 127, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
40 8 0.06
41 113 0.89
42 6 0.05
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGT
Found at i:55023543 original size:40 final size:40
Alignment explanation
Indices: 55023414--55023545 Score: 140
Period size: 40 Copynumber: 3.3 Consensus size: 40
55023404 TAGGTTTTTT
* * * *
55023414 GCGGCGCTTTTTGAAAATCGCCGCTAATGC-TAATTTTTA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTTAATATTTA
** * * *
55023453 GCGGCGTTTTCCAAAAAGCGCCGCTAATACTCAATCTTTA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTTAATATTTA
* * *
55023493 GTGGCGTTTTTTTAAAAGCGCCCCTAATGCTTAATATTTA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTTAATATTTA
*
55023533 GCGGCATTTTTTA
1 GCGGCGTTTTTTA
55023546 TCCAAACGCC
Statistics
Matches: 73, Mismatches: 19, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
39 24 0.33
40 49 0.67
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (40 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTTAATATTTA
Found at i:55026282 original size:11 final size:11
Alignment explanation
Indices: 55026255--55026298 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
55026245 AGATAAATAT
*
55026255 TATTTAATTAA
1 TATTTTATTAA
55026266 TATTTTATTAA
1 TATTTTATTAA
* *
55026277 GATTTTTAGTAA
1 TA-TTTTATTAA
55026289 TATTTTATTA
1 TATTTTATTA
55026299 TTAAATGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:55028644 original size:17 final size:17
Alignment explanation
Indices: 55028622--55028655 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
55028612 CGTTTTGGGG
55028622 TTTGGT-CTATTTCCTTT
1 TTTGGTCCT-TTTCCTTT
55028639 TTTGGTCCTTTTCCTTT
1 TTTGGTCCTTTTCCTTT
55028656 CACGCGCGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.03, C:0.21, G:0.12, T:0.65
Consensus pattern (17 bp):
TTTGGTCCTTTTCCTTT
Found at i:55029110 original size:2 final size:2
Alignment explanation
Indices: 55029103--55029133 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
55029093 ATGATTGATT
*
55029103 TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55029134 TTGTCTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55034367 original size:88 final size:88
Alignment explanation
Indices: 55034270--55035209 Score: 931
Period size: 88 Copynumber: 10.6 Consensus size: 88
55034260 CTAAAAACAA
* * * *
55034270 TAGATCTTGTCTTCCTGTACCGGCAGTGAAGCAAATCAAAGCCACCAGTCTTATCTCCTTGAGCA
1 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCTATCTCCCTGAGCA
* *
55034335 GTAGCCGAGTAGGTCGAAGATTG
66 GCAGCAGAGTAGGTCGAAGATTG
* * * *
55034358 TAGATCTTGTCTTCATGTACCGGCAGCGAAACAGATCAAAGCCACCAGTCTTATCTCCTTGAGCA
1 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCTATCTCCCTGAGCA
* *
55034423 GTAGCCGAGTAGGTCGAAGATTG
66 GCAGCAGAGTAGGTCGAAGATTG
* * *
55034446 TAGATCTTGTCTTCATGTACCGGCAGCGAAACAGATTAAAGCCACCAGTCCTATCTCCCTGAGCA
1 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCTATCTCCCTGAGCA
**
55034511 GCAGCAGAGTAGGTTAAAGATTG
66 GCAGCAGAGTAGGTCGAAGATTG
*
55034534 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCTATCTCCCTGAGTA
1 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCTATCTCCCTGAGCA
* **
55034599 GCAGCAGAGTAGGTCAAATTTTTG
66 GCAGCAGAGTAGGTCGAA-GATTG
* * *
55034623 TAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAGATTAAAGCCACCAGTCCTATCTCCCTAAGCA
1 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCTATCTCCCTGAGCA
*
55034688 GCAGCGGAGTAGGTCGAAGATTG
66 GCAGCAGAGTAGGTCGAAGATTG
* * * * * * *
55034711 TAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAGCCACTAGTCTTATCTCTCTGAACA
1 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCTATCTCCCTGAGCA
* *
55034776 GCAGCGGAGTAGGTCCAAGATTG
66 GCAGCAGAGTAGGTCGAAGATTG
* * * * * * * * *
55034799 TAGATCTTGTCTTCCTATACCGACAGTGAAGCAGATCGAAGCCA-AATTCCTATATCCCTAAGCG
1 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCTATCTCCCTGAGCA
55034863 GCAGCAGAGTAGGTCGAAGATTG
66 GCAGCAGAGTAGGTCGAAGATTG
* * * ** * * *
55034886 TAGATCTTATCTTCCAGTACTGGCAGTAAAGCAGATCGAAGCCACCAG-CCTCGTCTTCCTGAGT
1 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCT-ATCTCCCTGAG-
** * * * *
55034950 TTGCAGCGGAGCA-GACTGAAGATAG
64 CAGCAGCAGAGTAGGTC-GAAGATTG
* ** * *
55034975 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAGATCGAAGACACCAG-CCTCATCTCCCTGAGT
1 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCT-ATCTCCCTGAG-
** * ** * * * *
55035039 TTGAAGTGGAGCA-GACTAAAGATAG
64 CAGCAGCAGAGTAGGTC-GAAGATTG
** * * * * ** *
55035064 TAGATCTTGTCTTCCTGTATTGGCGGCGAAGTAGATCGAAGACACCAG-CCTCGCCTCTCTGAGT
1 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCT-ATCTCCCTGAG-
** * * *
55035128 TTGTAGCAGAGCA-GACTGAAGATTG
64 CAGCAGCAGAGTAGGTC-GAAGATTG
* * ** *
55035153 TAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATTGAAGACACCAGTCCTATCTC
1 TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCTATCTC
55035210 TTTGACATTA
Statistics
Matches: 750, Mismatches: 96, Indels: 11
0.88 0.11 0.01
Matches are distributed among these distances:
87 74 0.10
88 376 0.50
89 297 0.40
90 3 0.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (88 bp):
TAGATCTTGTCTTCCTGTACCGGCAGCGAAGCAGATCAAAGCCACCAGTCCTATCTCCCTGAGCA
GCAGCAGAGTAGGTCGAAGATTG
Found at i:55034963 original size:44 final size:44
Alignment explanation
Indices: 55034915--55035142 Score: 142
Period size: 45 Copynumber: 5.1 Consensus size: 44
55034905 CTGGCAGTAA
*
55034915 AGCAGATCGAAGCCACCAGCCTCGTCTTCCTGAGTTTGCAGCGG
1 AGCAGATCGAAGACACCAGCCTCGTCTTCCTGAGTTTGCAGCGG
* * * * * *
55034959 AGCAGA-CTGAAGATAGCAGATCTTGTCTTCCTGTA-TTGGCAGCGA
1 AGCAGATC-GAAGACACCAG-CCTCGTCTTCCTG-AGTTTGCAGCGG
* * * *
55035004 AGCAGATCGAAGACACCAGCCTCATCTCCCTGAGTTTGAAGTGG
1 AGCAGATCGAAGACACCAGCCTCGTCTTCCTGAGTTTGCAGCGG
* * ** * * * * *
55035048 AGCAGA-CTAAAGATAGTAGATCTTGTCTTCCTGTA-TTGGCGGCGA
1 AGCAGATC-GAAGACACCAG-CCTCGTCTTCCTG-AGTTTGCAGCGG
* * * *
55035093 AGTAGATCGAAGACACCAGCCTCG-CCTCTCTGAGTTTGTAGCAG
1 AGCAGATCGAAGACACCAGCCTCGTCTTC-CTGAGTTTGCAGCGG
55035137 AGCAGA
1 AGCAGA
55035143 CTGAAGATTG
Statistics
Matches: 129, Mismatches: 44, Indels: 22
0.66 0.23 0.11
Matches are distributed among these distances:
43 7 0.05
44 58 0.45
45 60 0.47
46 4 0.03
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (44 bp):
AGCAGATCGAAGACACCAGCCTCGTCTTCCTGAGTTTGCAGCGG
Found at i:55034988 original size:45 final size:45
Alignment explanation
Indices: 55034938--55035169 Score: 145
Period size: 45 Copynumber: 5.2 Consensus size: 45
55034928 CACCAGCCTC
55034938 GTCTTCCTGAGTTTGCAGCGGAGCAGACTGAAGATAGCAGATCTT
1 GTCTTCCTGAGTTTGCAGCGGAGCAGACTGAAGATAGCAGATCTT
* * * * * *
55034983 GTCTTCCTGTA-TTGGCAGCGAAGCAGA-TCGAAGACACCAG-CCTC
1 GTCTTCCTG-AGTTTGCAGCGGAGCAGACT-GAAGATAGCAGATCTT
* * * * * *
55035027 ATCTCCCTGAGTTTGAAGTGGAGCAGACTAAAGATAGTAGATCTT
1 GTCTTCCTGAGTTTGCAGCGGAGCAGACTGAAGATAGCAGATCTT
* * * * * * * *
55035072 GTCTTCCTGTA-TTGGCGGCGAAGTAGA-TCGAAGACACCAG-CCTC
1 GTCTTCCTG-AGTTTGCAGCGGAGCAGACT-GAAGATAGCAGATCTT
* * * * *
55035116 G-CCTCTCTGAGTTTGTAGCAGAGCAGACTGAAGATTGTAGATCTT
1 GTCTTC-CTGAGTTTGCAGCGGAGCAGACTGAAGATAGCAGATCTT
55035161 GTCTTCCTG
1 GTCTTCCTG
55035170 TACTGGCAGT
Statistics
Matches: 129, Mismatches: 46, Indels: 24
0.65 0.23 0.12
Matches are distributed among these distances:
43 5 0.04
44 53 0.41
45 66 0.51
46 5 0.04
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (45 bp):
GTCTTCCTGAGTTTGCAGCGGAGCAGACTGAAGATAGCAGATCTT
Found at i:55035130 original size:178 final size:178
Alignment explanation
Indices: 55034879--55035209 Score: 477
Period size: 178 Copynumber: 1.9 Consensus size: 178
55034869 GAGTAGGTCG
* * * *
55034879 AAGATTGTAGATCTTATCTTCCAGTACTGGCAGTAAAGCAGATCGAAGCCACCAGCCTCGTCTTC
1 AAGATAGTAGATCTTATCTTCCAGTACTGGCAGCAAAGCAGATCGAAGACACCAGCCTCGCCTTC
* *
55034944 CTGAGTTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGCAG
66 CTGAGTTTGCAGCAGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAG
55035009 ATCGAAGACACCAG-CCTCATCTCCCTGAGTTTGAAGTGGAGCAGACTA
131 ATCGAAGACACCAGTCCT-ATCTCCCTGAGTTTGAAGTGGAGCAGACTA
* * * * * *
55035057 AAGATAGTAGATCTTGTCTTCCTGTATTGGCGGCGAAGTAGATCGAAGACACCAGCCTCGCC-TC
1 AAGATAGTAGATCTTATCTTCCAGTACTGGCAGCAAAGCAGATCGAAGACACCAGCCTCGCCTTC
* * * *
55035121 TCTGAGTTTGTAGCAGAGCAGACTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGCA
66 -CTGAGTTTGCAGCAGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCA
*
55035186 GATTGAAGACACCAGTCCTATCTC
130 GATCGAAGACACCAGTCCTATCTC
55035210 TTTGACATTA
Statistics
Matches: 134, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
177 2 0.01
178 129 0.96
179 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (178 bp):
AAGATAGTAGATCTTATCTTCCAGTACTGGCAGCAAAGCAGATCGAAGACACCAGCCTCGCCTTC
CTGAGTTTGCAGCAGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGCAG
ATCGAAGACACCAGTCCTATCTCCCTGAGTTTGAAGTGGAGCAGACTA
Done.