Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 63 of 141
Found at i:18664639 original size:105 final size:106
Alignment explanation
Indices: 18664389--18664682 Score: 423
Period size: 105 Copynumber: 2.8 Consensus size: 106
18664379 AAGATATAAG
* *
18664389 AGGATATTTGGCTATTTGGTCCAACGAG--AAATCGAAACTCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
18664452 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAATTTTTTAAA
66 GAATTTCCAAACGC--AA-ATTGCCTTATTTTAAAATTTTTAAA
* * * * * * *
18664496 AGGATATTCGGCTATTTGATTGAACAAGAAAAATCGAAACCCAGCACATTAGAGAATGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
18664561 GAATTTCCAAACGCAAA-TGCCTTATTTTAAAATTTTTAAA
66 GAATTTCCAAACGCAAATTGCCTTATTTTAAAATTTTTAAA
* *
18664601 AGGATATTTGGATATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTT
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
18664666 GAATTTCCAAACGCAAA
66 GAATTTCCAAACGCAAA
18664683 ACATTACCTT
Statistics
Matches: 165, Mismatches: 20, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
105 94 0.57
106 1 0.01
107 25 0.15
109 45 0.27
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (106 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAATTGCCTTATTTTAAAATTTTTAAA
Found at i:18665447 original size:16 final size:16
Alignment explanation
Indices: 18665428--18665458 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18665418 ATGAATAAAC
18665428 AATAACAATAATAATT
1 AATAACAATAATAATT
*
18665444 AATAATAATAATAAT
1 AATAACAATAATAAT
18665459 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAACAATAATAATT
Found at i:18665943 original size:11 final size:12
Alignment explanation
Indices: 18665923--18665947 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18665913 TTTTTCATTC
18665923 AAAAGAAAAAAA
1 AAAAGAAAAAAA
18665935 AAAAGAAAAAAA
1 AAAAGAAAAAAA
18665947 A
1 A
18665948 CTCTCTCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:18668437 original size:64 final size:64
Alignment explanation
Indices: 18668358--18668534 Score: 229
Period size: 64 Copynumber: 2.8 Consensus size: 64
18668348 ATATATATTT
* * *
18668358 AAAGTTCTTGAGCTGAATTTAGTGTATGAATTTTATATACATATGTGGTTTAAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
*
18668422 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
* * *
18668486 -AATTTCTTTGAACTGAATTTTAATGT-TGTAA-ATT--ATACATATGTGGTTC
1 AAAGTTC-TTGAGCTGAA-TTTAATGTATG-AATTTTACATACATATGTGGTTC
18668535 GAATGTTTGT
Statistics
Matches: 103, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
62 15 0.15
63 5 0.05
64 73 0.71
65 10 0.10
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (64 bp):
AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
Found at i:18668708 original size:41 final size:41
Alignment explanation
Indices: 18668644--18668762 Score: 211
Period size: 41 Copynumber: 2.9 Consensus size: 41
18668634 ATCTGAGATT
*
18668644 ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGA
1 ATCAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGA
*
18668685 ATCGGGTTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGA
1 ATCAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGA
*
18668726 ATCAGGTTATAAGCCTAGCAGGCTAAGTGCCAGTGAA
1 ATCAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTGAA
18668763 TTTATTTAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.21
Consensus pattern (41 bp):
ATCAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGA
Found at i:18670151 original size:91 final size:92
Alignment explanation
Indices: 18670055--18670225 Score: 254
Period size: 92 Copynumber: 1.9 Consensus size: 92
18670045 CTTTCTTATA
* * ** **
18670055 TTTTTTCAAAAAAGAGATTCGAGTTCTAAAATTAAAT-AATTAAAAATGTTGAAACGGCCTCAAC
1 TTTTTTAAAAAAAGAGATTCAAGTTCTAAAACCAAATAAATTAAAAATGTTGAAACAACCTCAAC
18670119 AGAAATCTCGAAGCTTTCTTATATTTT
66 AGAAATCTCGAAGCTTTCTTATATTTT
* * *
18670146 TTTTTTAAAAAAAGAGATTCAAGTTTTAAAACCAAATAAATTGAAAATGTTGAAACAACCTCGAC
1 TTTTTTAAAAAAAGAGATTCAAGTTCTAAAACCAAATAAATTAAAAATGTTGAAACAACCTCAAC
18670211 AGAAATCTCGAAGCT
66 AGAAATCTCGAAGCT
18670226 CAACTCATTT
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
91 32 0.46
92 38 0.54
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (92 bp):
TTTTTTAAAAAAAGAGATTCAAGTTCTAAAACCAAATAAATTAAAAATGTTGAAACAACCTCAAC
AGAAATCTCGAAGCTTTCTTATATTTT
Found at i:18670675 original size:33 final size:33
Alignment explanation
Indices: 18670638--18670706 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
18670628 TAAAAATGCT
18670638 AAGCCTTCATAAGTAACCCTCCATTCAAATATA
1 AAGCCTTCATAAGTAACCCTCCATTCAAATATA
18670671 AAGCCTTCATAAGTAACCCTCCATTCAAATATA
1 AAGCCTTCATAAGTAACCCTCCATTCAAATATA
18670704 AAG
1 AAG
18670707 AAGTGTATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (33 bp):
AAGCCTTCATAAGTAACCCTCCATTCAAATATA
Found at i:18673729 original size:22 final size:22
Alignment explanation
Indices: 18673694--18673739 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
18673684 CAAATTTCAA
18673694 TCAAGTTTCAAAAGTCCAAA-AT
1 TCAAGTTTCAAAAGT-CAAATAT
18673716 TCAA-TTTCACAAAGTCAAATAT
1 TCAAGTTTCA-AAAGTCAAATAT
18673738 TC
1 TC
18673740 TAGTCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (22 bp):
TCAAGTTTCAAAAGTCAAATAT
Found at i:18677130 original size:15 final size:15
Alignment explanation
Indices: 18677110--18677140 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18677100 AAAATAAAGC
18677110 AAATAATAGGCTGTT
1 AAATAATAGGCTGTT
18677125 AAATAATAGGCTGTT
1 AAATAATAGGCTGTT
18677140 A
1 A
18677141 TGAAACAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
AAATAATAGGCTGTT
Found at i:18679323 original size:37 final size:36
Alignment explanation
Indices: 18679282--18679359 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
18679272 AATAAGTCAA
*
18679282 AATTTGAGAAAAAAAATCAATGTTTAAATCGGTTTAT
1 AATTT-AGAAAAAAAATCAATGTTTAAATCGGTTTAC
***
18679319 AATTTTTTAAAAAAATCAATGTTTAAATCGGTTTAC
1 AATTTAGAAAAAAAATCAATGTTTAAATCGGTTTAC
18679355 AATTT
1 AATTT
18679360 TTTAGGCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 32 0.86
37 5 0.14
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (36 bp):
AATTTAGAAAAAAAATCAATGTTTAAATCGGTTTAC
Found at i:18679362 original size:37 final size:36
Alignment explanation
Indices: 18679291--18679363 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
18679281 AAATTTGAGA
*
18679291 AAAAAAATCAATGTTTAAATCGGTTTATAATTTTTT
1 AAAAAAATCAATGTTTAAATCGGTTTACAATTTTTT
18679327 AAAAAAATCAATGTTTAAATCGGTTTACAATTTTTT
1 AAAAAAATCAATGTTTAAATCGGTTTACAATTTTTT
18679363 A
1 A
18679364 GGCTTAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (36 bp):
AAAAAAATCAATGTTTAAATCGGTTTACAATTTTTT
Found at i:18680615 original size:18 final size:19
Alignment explanation
Indices: 18680592--18680637 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
18680582 AACTCTCTTT
18680592 ATTCTCTCTAAA-CTC-CAA
1 ATTCTCTC-AAATCTCTCAA
18680610 ATTCTCTCAAATCTCTCAA
1 ATTCTCTCAAATCTCTCAA
18680629 ATT-TCTCAA
1 ATTCTCTCAA
18680638 TTTTTGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 3 0.12
18 17 0.65
19 6 0.23
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTCTCTCAAATCTCTCAA
Found at i:18684394 original size:50 final size:50
Alignment explanation
Indices: 18684291--18684483 Score: 242
Period size: 50 Copynumber: 3.7 Consensus size: 50
18684281 GGGAATGAGA
*
18684291 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
*
18684347 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * **
18684397 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
18684447 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
18684484 ATACAGAAAA
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
50 83 0.67
53 3 0.02
55 1 0.01
56 36 0.29
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:18684517 original size:49 final size:48
Alignment explanation
Indices: 18684347--18684522 Score: 156
Period size: 50 Copynumber: 3.6 Consensus size: 48
18684337 TTATGAGAGG
* * * * * **
18684347 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C-ATAAGAAAAC
** * *
18684397 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C-ATAAGAAAAC
* * *
18684447 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA-ATACAGAAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACATA-AGAAAAC
*
18684495 ATCCCATGTAAGACTATGTCTGGGACAT
1 -TCCCATGTAAGACCATGTCTGGGACAT
18684523 AGCTTTGGCA
Statistics
Matches: 107, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
47 3 0.03
48 5 0.05
49 24 0.22
50 75 0.70
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (48 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACATAAGAAAAC
Found at i:18694796 original size:3 final size:3
Alignment explanation
Indices: 18694788--18694816 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18694778 AGTGTATCTA
18694788 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
18694817 CCATTTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:18697257 original size:23 final size:24
Alignment explanation
Indices: 18697231--18697285 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
18697221 CAATATTAAG
*
18697231 ATTTTTTA-ATAAATTAAATAAAT
1 ATTTTTTATATAAATAAAATAAAT
*
18697254 A-TTTTTATTTAAATAAAATAAAT
1 ATTTTTTATATAAATAAAATAAAT
18697277 ATTTTTTAT
1 ATTTTTTAT
18697286 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 6 0.21
23 15 0.54
24 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTTTTATATAAATAAAATAAAT
Found at i:18703764 original size:21 final size:23
Alignment explanation
Indices: 18703730--18703790 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 23
18703720 CATTCTTATA
18703730 ATTTATATATTATAAAATATAATAAT
1 ATTTATATA-TAT--AATATAATAAT
*
18703756 ATTTATATATATTATATAATAAT
1 ATTTATATATATAATATAATAAT
18703779 ATTTATATATAT
1 ATTTATATATAT
18703791 TTAAATTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 22 0.65
25 3 0.09
26 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTATATATATAATATAATAAT
Found at i:18703767 original size:10 final size:10
Alignment explanation
Indices: 18703754--18703793 Score: 53
Period size: 10 Copynumber: 3.7 Consensus size: 10
18703744 AAATATAATA
18703754 ATATTTATAT
1 ATATTTATAT
18703764 ATATTATATAAT
1 ATATT-TAT-AT
18703776 AATATTTATAT
1 -ATATTTATAT
18703787 ATATTTA
1 ATATTTA
18703794 AATTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 12 0.44
11 5 0.19
12 5 0.19
13 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATATTTATAT
Found at i:18703786 original size:14 final size:13
Alignment explanation
Indices: 18703746--18703787 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
18703736 ATATTATAAA
18703746 ATATAATAATATT
1 ATATAATAATATT
18703759 -TAT-AT-ATATT
1 ATATAATAATATT
18703769 ATATAATAATATTT
1 ATATAATAATA-TT
18703783 ATATA
1 ATATA
18703788 TATTTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 5 0.20
11 5 0.20
12 5 0.20
13 3 0.12
14 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATAATAATATT
Found at i:18703805 original size:21 final size:23
Alignment explanation
Indices: 18703746--18703791 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
18703736 ATATTATAAA
18703746 ATATAATAATATTTATATATATT
1 ATATAATAATATTTATATATATT
18703769 ATATAATAATATTTATATATATT
1 ATATAATAATATTTATATATATT
18703792 TAAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATAATAATATTTATATATATT
Found at i:18707007 original size:30 final size:31
Alignment explanation
Indices: 18706939--18707011 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
18706929 CAAACTGAAA
* *
18706939 AAACTCAAGTACCAAAATAAATATCGAAGCT
1 AAACTCAAGTATCAAAATAAATATCAAAGCT
* *
18706970 AAACTCAAGTATCAAAGTAAATATTAAAGC-
1 AAACTCAAGTATCAAAATAAATATCAAAGCT
*
18707000 CAACTCAAGTAT
1 AAACTCAAGTAT
18707012 TAAATTAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.22
Consensus pattern (31 bp):
AAACTCAAGTATCAAAATAAATATCAAAGCT
Found at i:18709525 original size:17 final size:17
Alignment explanation
Indices: 18709505--18709537 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18709495 TCTTTTTTTT
*
18709505 TTTCTTTTAAATTATTG
1 TTTCATTTAAATTATTG
18709522 TTTCATTTAAATTATT
1 TTTCATTTAAATTATT
18709538 TGTCTCATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTCATTTAAATTATTG
Found at i:18709545 original size:18 final size:17
Alignment explanation
Indices: 18709510--18709545 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18709500 TTTTTTTTCT
*
18709510 TTTAAATTATTGTTTCA
1 TTTAAATTATTGTCTCA
18709527 TTTAAATTATTTGTCTCA
1 TTTAAATTA-TTGTCTCA
18709545 T
1 T
18709546 CTCCACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTAAATTATTGTCTCA
Found at i:18709705 original size:12 final size:14
Alignment explanation
Indices: 18709676--18709704 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
18709666 CATGCATGAG
18709676 AAATATAAAGATAA
1 AAATATAAAGATAA
18709690 AAATA-AAAGATAA
1 AAATATAAAGATAA
18709703 AA
1 AA
18709705 TGGAGAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (14 bp):
AAATATAAAGATAA
Found at i:18718203 original size:13 final size:14
Alignment explanation
Indices: 18718187--18718218 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
18718177 TTTTTGTTTA
18718187 TTATTTA-TTTATT
1 TTATTTACTTTATT
18718200 TTA-TTACTTTATT
1 TTATTTACTTTATT
18718213 TTATTT
1 TTATTT
18718219 TATTATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 12 0.71
14 2 0.12
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTTACTTTATT
Found at i:18718431 original size:22 final size:21
Alignment explanation
Indices: 18718384--18718438 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
18718374 GCCCAGAATG
* *
18718384 CCTGCAGCCAAACTACCCTATT
1 CCTGCAGCC-AACCACCCTATC
*
18718406 CCTGCAGCCAACCACTCTTATC
1 CCTGCAGCCAACCAC-CCTATC
*
18718428 CCTGCACCCAA
1 CCTGCAGCCAA
18718439 GCATCACCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.25, C:0.45, G:0.09, T:0.20
Consensus pattern (21 bp):
CCTGCAGCCAACCACCCTATC
Found at i:18719573 original size:19 final size:18
Alignment explanation
Indices: 18719551--18719592 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
18719541 TTCCTAAAGC
18719551 ATAAAAATATAAATAATAA
1 ATAAAAATATAAA-AATAA
*
18719570 AT--AAATATCAAAATAA
1 ATAAAAATATAAAAATAA
18719586 ATAAAAA
1 ATAAAAA
18719593 AGAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
16 7 0.35
17 8 0.40
18 3 0.15
19 2 0.10
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAAATATAAAAATAA
Found at i:18719586 original size:16 final size:17
Alignment explanation
Indices: 18719555--18719590 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
18719545 TAAAGCATAA
18719555 AAATATAAATAATAAAT
1 AAATATAAATAATAAAT
*
18719572 AAATATCAA-AATAAAT
1 AAATATAAATAATAAAT
18719588 AAA
1 AAA
18719591 AAAGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATATAAATAATAAAT
Found at i:18720196 original size:15 final size:15
Alignment explanation
Indices: 18720171--18720205 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
18720161 GACTCTATTT
*
18720171 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
18720185 TAATTAATATTAAGA
1 TAATTAATATTAAGA
18720200 TAATTA
1 TAATTA
18720206 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:18723573 original size:43 final size:43
Alignment explanation
Indices: 18723524--18723648 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 43
18723514 GGATTCCGAT
* * *
18723524 ATGTGTTTTCCTGTAAGACCACGTCTGGGACATTGGCATCGAC
1 ATGTGTTTACATGTAAGACCACGTCTGGGATATTGGCATCGAC
* * ** * **
18723567 CTGTGTTTACGTGTAAGACCTTGTCTGGGATAGTGGCATCGGT
1 ATGTGTTTACATGTAAGACCACGTCTGGGATATTGGCATCGAC
* * *
18723610 ATGTGATTACATGTAAGACCACGTTTGGGATGTTGGCAT
1 ATGTGTTTACATGTAAGACCACGTCTGGGATATTGGCAT
18723649 TGTACGAGCT
Statistics
Matches: 65, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.33
Consensus pattern (43 bp):
ATGTGTTTACATGTAAGACCACGTCTGGGATATTGGCATCGAC
Found at i:18726657 original size:25 final size:25
Alignment explanation
Indices: 18726599--18726658 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
18726589 TTTTATCAAG
* *
18726599 GGTAAAATCGTCAAAATTTTATGGG
1 GGTAAAATTGTCAAAATTTTATGGA
* *
18726624 GGTAAAATTGTCAAATTTTTATTGA
1 GGTAAAATTGTCAAAATTTTATGGA
18726649 GGTAAAATTG
1 GGTAAAATTG
18726659 GGGTGAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (25 bp):
GGTAAAATTGTCAAAATTTTATGGA
Found at i:18733622 original size:32 final size:32
Alignment explanation
Indices: 18733385--18733633 Score: 172
Period size: 32 Copynumber: 8.0 Consensus size: 32
18733375 TGTTTGTTTT
* * * *
18733385 GAATTGAAATGTATATGT-T-TTATATATTACT
1 GAATTGAATTGTATATGTATACT-TATATTGCC
* * * *
18733416 GAATTGATTTATATATG-ATA-TT-TATAGTC
1 GAATTGAATTGTATATGTATACTTATATTGCC
* * * *
18733445 GAATTGATTTGTATACGAATA--TACATTGCC
1 GAATTGAATTGTATATGTATACTTATATTGCC
* *** *
18733475 GAATTGAATTGTATAGGTATACACCTATTACC
1 GAATTGAATTGTATATGTATACTTATATTGCC
* *
18733507 GAATTGAAATGTATATATATACTTATATTGCC
1 GAATTGAATTGTATATGTATACTTATATTGCC
* * * ***
18733539 GAAATGAATTGTATAGGTATGCACCTATTGCC
1 GAATTGAATTGTATATGTATACTTATATTGCC
*
18733571 GAATTGAATTATATATGTATACTTATATTGCC
1 GAATTGAATTGTATATGTATACTTATATTGCC
* *
18733603 GAATTGAATTTTATTTGTATA-TATATATTGC
1 GAATTGAATTGTATATGTATACT-TATATTGC
18733634 TGATTTGATT
Statistics
Matches: 168, Mismatches: 43, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
29 19 0.11
30 26 0.15
31 17 0.10
32 106 0.63
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (32 bp):
GAATTGAATTGTATATGTATACTTATATTGCC
Found at i:18733633 original size:64 final size:64
Alignment explanation
Indices: 18733469--18733612 Score: 234
Period size: 64 Copynumber: 2.2 Consensus size: 64
18733459 ACGAATATAC
* *
18733469 ATTGCCGAATTGAATTGTATAGGTATACACCTATTACCGAATTGAAATGTATATATATACTTAT
1 ATTGCCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTGAAATATATATATATACTTAT
* * * *
18733533 ATTGCCGAAATGAATTGTATAGGTATGCACCTATTGCCGAATTGAATTATATATGTATACTTAT
1 ATTGCCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTGAAATATATATATATACTTAT
18733597 ATTGCCGAATTGAATT
1 ATTGCCGAATTGAATT
18733613 TTATTTGTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 73 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (64 bp):
ATTGCCGAATTGAATTGTATAGGTATACACCTATTGCCGAATTGAAATATATATATATACTTAT
Found at i:18733820 original size:41 final size:41
Alignment explanation
Indices: 18733772--18733857 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
18733762 TGATTTTGTG
18733772 TAAGACCATATCTGGGACATTAGCATCGTGTATGATTCGTA
1 TAAGACCATATCTGGGACATTAGCATCGTGTATGATTCGTA
*
18733813 TAAGACCATGTCTGGGACATTAGCATCGTGTATGATTCGTA
1 TAAGACCATATCTGGGACATTAGCATCGTGTATGATTCGTA
18733854 TAAG
1 TAAG
18733858 GCCCTGTATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (41 bp):
TAAGACCATATCTGGGACATTAGCATCGTGTATGATTCGTA
Found at i:18733870 original size:41 final size:41
Alignment explanation
Indices: 18733772--18733870 Score: 153
Period size: 41 Copynumber: 2.4 Consensus size: 41
18733762 TGATTTTGTG
* *
18733772 TAAGACCATATCTGGGACATTAGCATCGTGTATGATTCGTA
1 TAAGACCATGTATGGGACATTAGCATCGTGTATGATTCGTA
*
18733813 TAAGACCATGTCTGGGACATTAGCATCGTGTATGATTCGTA
1 TAAGACCATGTATGGGACATTAGCATCGTGTATGATTCGTA
* *
18733854 TAAGGCCCTGTATGGGA
1 TAAGACCATGTATGGGA
18733871 TAGTGGCATC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (41 bp):
TAAGACCATGTATGGGACATTAGCATCGTGTATGATTCGTA
Found at i:18734675 original size:16 final size:17
Alignment explanation
Indices: 18734654--18734686 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18734644 TTGAGCAAGT
*
18734654 AAAATG-TGTTTGGTTA
1 AAAATGTTGTTTAGTTA
18734670 AAAATGTTGTTTAGTTA
1 AAAATGTTGTTTAGTTA
18734687 CGAAATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (17 bp):
AAAATGTTGTTTAGTTA
Found at i:18742103 original size:40 final size:40
Alignment explanation
Indices: 18742042--18742174 Score: 141
Period size: 40 Copynumber: 3.5 Consensus size: 40
18742032 CGAAAGTTGC
* *
18742042 GCCCAGCACTAGTCGGGTAAACCGACAAATATAATGGTGT
1 GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
* **
18742082 GCCCAGCACTAGTCAGATAAACTGACAAAGGT--T-GTG-
1 GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
* *
18742118 G-CCAGCGCTAGTCAGGTAAACCGACAAATATAATGGTGT
1 GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
* * *
18742157 GTCCAACACTAGTTAGAT
1 GCCCAGCACTAGTCAGAT
18742175 GTACCAATGA
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
35 25 0.34
36 1 0.01
37 4 0.05
38 4 0.05
39 1 0.01
40 39 0.53
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (40 bp):
GCCCAGCACTAGTCAGATAAACCGACAAATATAATGGTGT
Found at i:18742123 original size:75 final size:75
Alignment explanation
Indices: 18742003--18742174 Score: 247
Period size: 75 Copynumber: 2.3 Consensus size: 75
18741993 GTATAAAAAA
* * *
18742003 GTGTGCCCAGCACTAGTCAGGTAAATTGACGAAAGTTGCGCCCAGCACTAGTCGGGTAAACCGAC
1 GTGTGCCCAGCACTAGTCAGATAAACTGACGAAAGTTGCGCCCAGCACTAGTCAGGTAAACCGAC
18742068 AAATATAATG
66 AAATATAATG
* * *
18742078 GTGTGCCCAGCACTAGTCAGATAAACTGAC-AAAGGTTGTGGCCAGCGCTAGTCAGGTAAACCGA
1 GTGTGCCCAGCACTAGTCAGATAAACTGACGAAA-GTTGCGCCCAGCACTAGTCAGGTAAACCGA
18742142 CAAATATAATG
65 CAAATATAATG
* * *
18742153 GTGTGTCCAACACTAGTTAGAT
1 GTGTGCCCAGCACTAGTCAGAT
18742175 GTACCAATGA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 3 0.03
75 84 0.97
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (75 bp):
GTGTGCCCAGCACTAGTCAGATAAACTGACGAAAGTTGCGCCCAGCACTAGTCAGGTAAACCGAC
AAATATAATG
Found at i:18742130 original size:35 final size:35
Alignment explanation
Indices: 18742004--18742145 Score: 117
Period size: 35 Copynumber: 3.9 Consensus size: 35
18741994 TATAAAAAAG
* **
18742004 TGTGCCCAGCACTAGTCAGGTAAATTGACGAAA-GT
1 TGTGCCCAGCACTAGTCAGATAAACCGAC-AAAGGT
* * *
18742039 TGCGCCCAGCACTAGTCGGGTAAACCGACAAATATAATGG-
1 TGTGCCCAGCACTAGTCAGATAAACCGAC----A-AA-GGT
*
18742079 TGTGCCCAGCACTAGTCAGATAAACTGACAAAGGT
1 TGTGCCCAGCACTAGTCAGATAAACCGACAAAGGT
* * *
18742114 TGTGGCCAGCGCTAGTCAGGTAAACCGACAAA
1 TGTGCCCAGCACTAGTCAGATAAACCGACAAA
18742146 TATAATGGTG
Statistics
Matches: 87, Mismatches: 13, Indels: 14
0.76 0.11 0.12
Matches are distributed among these distances:
34 2 0.02
35 55 0.63
36 1 0.01
38 1 0.01
39 2 0.02
40 25 0.29
41 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.19
Consensus pattern (35 bp):
TGTGCCCAGCACTAGTCAGATAAACCGACAAAGGT
Found at i:18742223 original size:75 final size:76
Alignment explanation
Indices: 18742003--18742220 Score: 199
Period size: 75 Copynumber: 2.9 Consensus size: 76
18741993 GTATAAAAAA
* * *** * * * *
18742003 GTGTGCCCAGCACTAGTCAGGTAAATTGACGAA-AGTTGCGCCCAGCACTAGTCGGGTAAACCGA
1 GTGTGCCCAACACTAGTCAGATAAACCAACAAAGAGTTGCGCCCAGCGCTAGTTGAGTAAACCGA
18742067 CAAATATAATG
66 CAAATATAATG
* ** * * *
18742078 GTGTGCCCAGCACTAGTCAGATAAACTGACAAAG-GTTGTGGCCAGCGCTAG-TCAGGTAAACCG
1 GTGTGCCCAACACTAGTCAGATAAACCAACAAAGAGTTGCGCCCAGCGCTAGTTGA-GTAAACCG
18742141 ACAAATATAATG
65 ACAAATATAATG
* * ** ** * *
18742153 GTGTGTCCAACACTAGTTAGATGTACCAATGATGAGTTGCGCCCAACGCTAGTTGAGTAAACCGA
1 GTGTGCCCAACACTAGTCAGATAAACCAACAAAGAGTTGCGCCCAGCGCTAGTTGAGTAAACCGA
18742218 CAA
66 CAA
18742221 TATCGATTGC
Statistics
Matches: 116, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
75 88 0.76
76 26 0.22
77 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (76 bp):
GTGTGCCCAACACTAGTCAGATAAACCAACAAAGAGTTGCGCCCAGCGCTAGTTGAGTAAACCGA
CAAATATAATG
Found at i:18742595 original size:35 final size:35
Alignment explanation
Indices: 18742549--18742628 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
18742539 GGCCCGGTCT
18742549 GAAATATGGGAGGGTTCAGGTAAAAATACAGGCCC
1 GAAATATGGGAGGGTTCAGGTAAAAATACAGGCCC
*
18742584 GAAATATGGGAGGGTTCAGGTAAAAATATAGGCCC
1 GAAATATGGGAGGGTTCAGGTAAAAATACAGGCCC
18742619 GAAATATGGG
1 GAAATATGGG
18742629 TTTGGGCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.38, C:0.11, G:0.33, T:0.19
Consensus pattern (35 bp):
GAAATATGGGAGGGTTCAGGTAAAAATACAGGCCC
Found at i:18745354 original size:18 final size:18
Alignment explanation
Indices: 18745331--18745393 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
18745321 AAGGAATATA
18745331 ATAATAATAATCATCATT
1 ATAATAATAATCATCATT
* *
18745349 ATAATAATAA-CATTAAT
1 ATAATAATAATCATCATT
* *
18745366 ATTAATAATCAT-ATCATG
1 A-TAATAATAATCATCATT
*
18745384 GTAATAATAA
1 ATAATAATAA
18745394 ATAAATGATG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (18 bp):
ATAATAATAATCATCATT
Found at i:18745544 original size:29 final size:27
Alignment explanation
Indices: 18745477--18745546 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 27
18745467 AAATATCAAA
*
18745477 AATAATAAAATAAATAATAAAATAAAGAG
1 AATAAT-AAAT-AATAATAAAATAAAAAG
*
18745506 AATAAAAAATAATAATAAAATATAATAACG
1 AATAATAAATAATAATAAAATA-AA-AA-G
18745536 -ATAATAAATAA
1 AATAATAAATAA
18745547 AAAATTGCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 12 0.34
28 6 0.17
29 16 0.46
30 1 0.03
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.23
Consensus pattern (27 bp):
AATAATAAATAATAATAAAATAAAAAG
Found at i:18745648 original size:15 final size:16
Alignment explanation
Indices: 18745628--18745659 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
18745618 ATAAATAGAT
18745628 AAAAATAAAA-AAATA
1 AAAAATAAAACAAATA
18745643 AAAAATAAAACAAATA
1 AAAAATAAAACAAATA
18745659 A
1 A
18745660 GTAAATACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAATAAAACAAATA
Found at i:18745770 original size:18 final size:18
Alignment explanation
Indices: 18745747--18745783 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
18745737 ATAAGTAAAT
18745747 AAATAAATAAAAGAATTA
1 AAATAAATAAAAGAATTA
*
18745765 AAATAAATAAAAGACTTA
1 AAATAAATAAAAGAATTA
18745783 A
1 A
18745784 TCATAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (18 bp):
AAATAAATAAAAGAATTA
Found at i:18747251 original size:26 final size:24
Alignment explanation
Indices: 18747222--18747278 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 24
18747212 CGGTTATAAT
* *
18747222 ATTTTGGTTTTATTTGATTTATCTAA
1 ATTTTGGTTTAATATG-TTT-TCTAA
* *
18747248 ATTTGGGTTTAATATGTTTTGTAA
1 ATTTTGGTTTAATATGTTTTCTAA
18747272 ATTTTGG
1 ATTTTGG
18747279 ACTGTTTTCG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 10 0.38
25 3 0.12
26 13 0.50
ACGTcount: A:0.23, C:0.02, G:0.18, T:0.58
Consensus pattern (24 bp):
ATTTTGGTTTAATATGTTTTCTAA
Found at i:18748091 original size:23 final size:22
Alignment explanation
Indices: 18748049--18748091 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
18748039 TTCAATACTT
*
18748049 AATTTTTAATAACATATCAAAC
1 AATTTTTAATAAAATATCAAAC
18748071 AATTTTATAATATAAAT-TCAA
1 AATTTT-TAATA-AAATATCAA
18748092 TACTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.33
23 9 0.50
24 3 0.17
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTTTTAATAAAATATCAAAC
Found at i:18748615 original size:18 final size:20
Alignment explanation
Indices: 18748578--18748627 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
18748568 TAAAATATAA
*
18748578 ATTTTGGAATTTTCATAAA-T
1 ATTTT-GAATTTTCAAAAATT
18748598 ATTTTGAATTTT-AAAAATT
1 ATTTTGAATTTTCAAAAATT
18748617 ATTTTG-ATTTT
1 ATTTTGAATTTT
18748628 TTTTCGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.32
19 14 0.50
20 5 0.18
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (20 bp):
ATTTTGAATTTTCAAAAATT
Found at i:18755831 original size:31 final size:31
Alignment explanation
Indices: 18755775--18755835 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
18755765 AAAAAATCCT
*
18755775 TATAACTTTTTAGTAATTTTTTAATATTTTC
1 TATAACTTTCTAGTAATTTTTTAATATTTTC
18755806 TATAA-TTTCTAGTAATTTTTATAATATTTT
1 TATAACTTTCTAGTAATTTTT-TAATATTTT
18755836 AAAAATTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (31 bp):
TATAACTTTCTAGTAATTTTTTAATATTTTC
Found at i:18755874 original size:25 final size:26
Alignment explanation
Indices: 18755832--18755890 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
18755822 TTTTATAATA
*
18755832 TTTTAAAAATTACAAATTTCATATTT
1 TTTTAAAAATTACAAATTTCAAATTT
* * *
18755858 TTTTTAAAATTA-GAATTTTAAA-TT
1 TTTTAAAAATTACAAATTTCAAATTT
18755882 TTTTAAAAA
1 TTTTAAAAA
18755891 GAATTTTTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 10 0.36
25 7 0.25
26 11 0.39
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTTAAAAATTACAAATTTCAAATTT
Found at i:18755898 original size:22 final size:23
Alignment explanation
Indices: 18755857--18755908 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
18755847 ATTTCATATT
18755857 TTTTTTAAAATTAGAATTTTA-AA
1 TTTTTTAAAA-TAGAATTTTAGAA
*
18755880 TTTTTTAAAA-AGAATTTTTAGAG
1 TTTTTTAAAATAGAA-TTTTAGAA
18755903 TTTTTT
1 TTTTTT
18755909 GTTAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 4 0.15
22 5 0.19
23 17 0.65
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.56
Consensus pattern (23 bp):
TTTTTTAAAATAGAATTTTAGAA
Found at i:18758803 original size:22 final size:22
Alignment explanation
Indices: 18758741--18758803 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
18758731 TTTTACTTTT
*
18758741 TTGCTGTTGTTTTCTGCGTTTG
1 TTGCTATTGTTTTCTGCGTTTG
* *
18758763 TTGTCTATTGTTGTGTGCGTTGTG
1 TTG-CTATTGTTTTCTGCGTT-TG
18758787 TT-CGT-TTGTTTTCTGCG
1 TTGC-TATTGTTTTCTGCG
18758804 CAGGTACATG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
22 14 0.42
23 15 0.45
24 4 0.12
ACGTcount: A:0.02, C:0.13, G:0.29, T:0.57
Consensus pattern (22 bp):
TTGCTATTGTTTTCTGCGTTTG
Found at i:18759050 original size:21 final size:21
Alignment explanation
Indices: 18759020--18759064 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18759010 CTGAGCCATG
*
18759020 TTTGGCCTAGAATTTTTGTAA
1 TTTGGACTAGAATTTTTGTAA
* *
18759041 TTTGGACTAGACTTTTTTTAA
1 TTTGGACTAGAATTTTTGTAA
18759062 TTT
1 TTT
18759065 TAATTTGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (21 bp):
TTTGGACTAGAATTTTTGTAA
Found at i:18759464 original size:44 final size:44
Alignment explanation
Indices: 18759416--18759529 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
18759406 TTAATCCGCT
* *
18759416 CCACTACAACTTCAGGGAGATAAGATTTGC-CTCTTCAGTCTGCC
1 CCACTGCAACTTCAGGGAGATAAGACTTGCTCTC-TCAGTCTGCC
** * * * * *
18759460 CCACTGTGACTTCAGGGGGATAAAACTTGTTTTCTCAGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTTGCTCTCTCAGTCTGCC
*
18759504 CCACTGCAACTTTAGGGAGATAAGAC
1 CCACTGCAACTTCAGGGAGATAAGAC
18759530 CCGATGCGAT
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
44 53 0.96
45 2 0.04
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGACTTGCTCTCTCAGTCTGCC
Found at i:18759810 original size:87 final size:87
Alignment explanation
Indices: 18759688--18760105 Score: 703
Period size: 87 Copynumber: 4.8 Consensus size: 87
18759678 GCTAGTGCTT
* *
18759688 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTCATTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTCGTTTT
18759753 CGATCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCTGTTAATGC
* * * * *
18759775 AGGAAGGAAAAATATGCTATCTTTAACCAACTCCACTGCAACTGATGGAGGCAAGGCTTCGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTCGTTTT
*
18759840 CGATCTGCTTCGCTGTTAATGT
66 CGATCTGCTTCGCTGTTAATGC
*
18759862 AGGAAGGCAATATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTCGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTCGTTTT
18759927 CGATCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCTGTTAATGC
* *
18759949 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAATCAATGGAGGCAAGGCTTCGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTCGTTTT
*
18760014 CTATCTGCTTCGCTGTTAATGC
66 CGATCTGCTTCGCTGTTAATGC
* *
18760036 AGGAAAGCAAGATCTGCTATCTTTAACCAGC-CCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTCGTTTT
18760100 CGATCT
66 CGATCT
18760106 TCACTAATCT
Statistics
Matches: 308, Mismatches: 23, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
86 35 0.11
87 273 0.89
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTCGTTTT
CGATCTGCTTCGCTGTTAATGC
Found at i:18759958 original size:43 final size:43
Alignment explanation
Indices: 18759910--18760046 Score: 102
Period size: 43 Copynumber: 3.2 Consensus size: 43
18759900 CAACCGATGG
*
18759910 AGGCAAGGCTTCGTTTTCGATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGCTTCGTTTTCAATCTGCTTCGCTGTTAATGCAGGA
* * * * * * * *
18759953 AGGCAAGATCTGC-TATCTTTAACCAGCTCCACTG-CAAT-CAATGG-
1 AGGCAAG-GCTTCGT-T-TTCAATCTGCTTCGCTGTTAATGC-A-GGA
*
18759997 AGGCAAGGCTTCGTTTTCTATCTGCTTCGCTGTTAATGCAGGA
1 AGGCAAGGCTTCGTTTTCAATCTGCTTCGCTGTTAATGCAGGA
*
18760040 AAGCAAG
1 AGGCAAG
18760047 ATCTGCTATC
Statistics
Matches: 66, Mismatches: 19, Indels: 18
0.64 0.18 0.17
Matches are distributed among these distances:
42 13 0.20
43 23 0.35
44 17 0.26
45 13 0.20
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (43 bp):
AGGCAAGGCTTCGTTTTCAATCTGCTTCGCTGTTAATGCAGGA
Found at i:18761345 original size:7 final size:7
Alignment explanation
Indices: 18761333--18761370 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
18761323 ATTTTTACTA
18761333 TTTCATT
1 TTTCATT
18761340 TTTCATTTT
1 TTTCA--TT
18761349 TTTCA-T
1 TTTCATT
18761355 TTTCATT
1 TTTCATT
18761362 TTTCATT
1 TTTCATT
18761369 TT
1 TT
18761371 CTCTCTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.21
7 15 0.54
9 7 0.25
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTCATT
Found at i:18761346 original size:21 final size:22
Alignment explanation
Indices: 18761333--18761375 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
18761323 ATTTTTACTA
*
18761333 TTTCATTTTTCATTTTTTTCAT
1 TTTCATTTTTCATTTTTCTCAT
18761355 TTTCATTTTTCATTTTCTCTC
1 TTTCATTTTTCATTTT-TCTC
18761376 TCTCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTCATTTTTCATTTTTCTCAT
Found at i:18761357 original size:15 final size:16
Alignment explanation
Indices: 18761333--18761364 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
18761323 ATTTTTACTA
18761333 TTTCATTTTTCATTTT
1 TTTCATTTTTCATTTT
18761349 TTTCA-TTTTCATTTT
1 TTTCATTTTTCATTTT
18761364 T
1 T
18761365 CATTTTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTCATTTTTCATTTT
Found at i:18761747 original size:35 final size:35
Alignment explanation
Indices: 18761708--18761820 Score: 135
Period size: 35 Copynumber: 3.3 Consensus size: 35
18761698 TTCTTTTCTT
18761708 TTTCTCTTTTCATATTTTATTTTGACTTTGATTGA
1 TTTCTCTTTTCATATTTTATTTTGACTTTGATTGA
* * * **
18761743 TTTCTCTTTT-TTGCTTTTGATTTT-TCTTTTCTT--
1 TTTCTCTTTTCAT-ATTTT-ATTTTGACTTTGATTGA
18761776 TTTCTCTTTTCATATTTTATTTTGACTTTGATTGA
1 TTTCTCTTTTCATATTTTATTTTGACTTTGATTGA
18761811 TTTCTCTTTT
1 TTTCTCTTTT
18761821 TTGCTTTTGA
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
32 5 0.08
33 20 0.32
34 2 0.03
35 30 0.48
36 5 0.08
ACGTcount: A:0.12, C:0.13, G:0.07, T:0.68
Consensus pattern (35 bp):
TTTCTCTTTTCATATTTTATTTTGACTTTGATTGA
Found at i:18761771 original size:12 final size:12
Alignment explanation
Indices: 18761750--18761883 Score: 53
Period size: 12 Copynumber: 10.8 Consensus size: 12
18761740 TGATTTCTCT
18761750 TTTTTGCTTTTGA
1 TTTTT-CTTTTGA
**
18761763 TTTTTCTTTTCT
1 TTTTTCTTTTGA
*
18761775 TTTTCTCTTTTCA
1 TTTT-TCTTTTGA
*
18761788 TATTTTATTTTGA
1 T-TTTTCTTTTGA
* **
18761801 CTTTGATTGATTTCTCT
1 -TTT--TT-CTTT-TGA
18761818 TTTTTGCTTTTGA
1 TTTTT-CTTTTGA
*
18761831 TTTTTCTTTT-C
1 TTTTTCTTTTGA
*
18761842 TTTTTC----GT
1 TTTTTCTTTTGA
*
18761850 TTTTTATTTTGA
1 TTTTTCTTTTGA
*
18761862 TTTTTATTTTGA
1 TTTTTCTTTTGA
18761874 TTTTTCTTTT
1 TTTTTCTTTT
18761884 TTTTTTTTGA
Statistics
Matches: 94, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
8 5 0.05
11 6 0.06
12 36 0.38
13 27 0.29
14 10 0.11
15 2 0.02
16 7 0.07
17 1 0.01
ACGTcount: A:0.09, C:0.10, G:0.07, T:0.73
Consensus pattern (12 bp):
TTTTTCTTTTGA
Found at i:18761783 original size:13 final size:12
Alignment explanation
Indices: 18761696--18761846 Score: 50
Period size: 13 Copynumber: 11.2 Consensus size: 12
18761686 TGGCCTCTCC
18761696 TTTTCTTTTCTT
1 TTTTCTTTTCTT
*
18761708 TTTCTCTTTTCATA
1 TTT-TCTTTTC-TT
*
18761722 TTTTATTTTGACTT
1 TTTTCTTTT--CTT
**
18761736 TGATTGATTTCTCTT
1 T--TTTCTTT-TCTT
**
18761751 TTTTGCTTTTGAT
1 TTTT-CTTTTCTT
18761764 TTTTCTTTTCTT
1 TTTTCTTTTCTT
*
18761776 TTTCTCTTTTCATA
1 TTT-TCTTTTC-TT
*
18761790 TTTTATTTTGACTT
1 TTTTCTTTT--CTT
**
18761804 TGATTGATTTCTCTT
1 T--TTTCTTT-TCTT
**
18761819 TTTTGCTTTTGAT
1 TTTT-CTTTTCTT
18761832 TTTTCTTTTCTT
1 TTTTCTTTTCTT
18761844 TTT
1 TTT
18761847 CGTTTTTTAT
Statistics
Matches: 103, Mismatches: 20, Indels: 32
0.66 0.13 0.21
Matches are distributed among these distances:
12 21 0.20
13 40 0.39
14 18 0.17
15 10 0.10
16 12 0.12
17 2 0.02
ACGTcount: A:0.09, C:0.13, G:0.07, T:0.71
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:18761805 original size:68 final size:68
Alignment explanation
Indices: 18761696--18761887 Score: 304
Period size: 68 Copynumber: 2.9 Consensus size: 68
18761686 TGGCCTCTCC
18761696 TTTTCTTTTCTTTTTCTCTTTTCATATTTTATTTTGACTTTGATTGATTTCTCTTTTTTGCTTTT
1 TTTTCTTTTCTTTTTCTCTTTTCATATTTTATTTTGACTTTGATTGATTTCTCTTTTTTGCTTTT
18761761 GAT
66 GAT
18761764 TTTTCTTTTCTTTTTCTCTTTTCATATTTTATTTTGACTTTGATTGATTTCTCTTTTTTGCTTTT
1 TTTTCTTTTCTTTTTCTCTTTTCATATTTTATTTTGACTTTGATTGATTTCTCTTTTTTGCTTTT
18761829 GAT
66 GAT
* * *
18761832 TTTTCTTTTCTTTTTCGT-TTTT--TATTTTGATTTTTATTTTGATT--TTTCTTTTTTTT
1 TTTTCTTTTCTTTTTC-TCTTTTCATATTTT-ATTTTGACTTTGATTGATTTCTCTTTTTT
18761888 TTTTGAATCT
Statistics
Matches: 119, Mismatches: 3, Indels: 7
0.92 0.02 0.05
Matches are distributed among these distances:
65 11 0.09
66 6 0.05
67 13 0.11
68 88 0.74
69 1 0.01
ACGTcount: A:0.09, C:0.11, G:0.07, T:0.72
Consensus pattern (68 bp):
TTTTCTTTTCTTTTTCTCTTTTCATATTTTATTTTGACTTTGATTGATTTCTCTTTTTTGCTTTT
GAT
Found at i:18761859 original size:13 final size:12
Alignment explanation
Indices: 18761850--18761883 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
18761840 TCTTTTTCGT
18761850 TTTTTATTTTGA
1 TTTTTATTTTGA
18761862 TTTTTATTTTGA
1 TTTTTATTTTGA
*
18761874 TTTTTCTTTT
1 TTTTTATTTT
18761884 TTTTTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTATTTTGA
Found at i:18761860 original size:31 final size:32
Alignment explanation
Indices: 18761790--18761893 Score: 99
Period size: 32 Copynumber: 3.3 Consensus size: 32
18761780 TCTTTTCATA
* * *
18761790 TTTTATTTTGACTTTGA--TTGATTTCTC-TT
1 TTTTATTTTGATTTTTATTTTGATTTTTCGTT
* * *
18761819 TTTTGCTTTTGATTTTTCTTTT-CTTTTTCGTT
1 TTTT-ATTTTGATTTTTATTTTGATTTTTCGTT
*
18761851 TTTTATTTTGATTTTTATTTTGATTTTTCTTT
1 TTTTATTTTGATTTTTATTTTGATTTTTCGTT
*
18761883 TTTTTTTTTGA
1 TTTTATTTTGA
18761894 ATCTGAACCC
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
29 4 0.07
30 9 0.15
31 20 0.34
32 26 0.44
ACGTcount: A:0.10, C:0.08, G:0.09, T:0.74
Consensus pattern (32 bp):
TTTTATTTTGATTTTTATTTTGATTTTTCGTT
Found at i:18763299 original size:39 final size:37
Alignment explanation
Indices: 18763232--18763324 Score: 89
Period size: 39 Copynumber: 2.5 Consensus size: 37
18763222 ACCAATATGG
* *
18763232 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
18763271 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* * *
18763308 TACCTAGTACCTCATCG
1 CACCCAGTGCCTCATCG
18763325 AATCTATCCG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
37 18 0.40
38 2 0.04
39 22 0.49
40 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:18763537 original size:23 final size:24
Alignment explanation
Indices: 18763493--18763538 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
18763483 TTTCTCACAT
* **
18763493 TTTCAATTCAATCATTTTTCCACC
1 TTTCAATTCAATAATTAATCCACC
18763517 TTTCAA-TCAATAATTAATCCAC
1 TTTCAATTCAATAATTAATCCAC
18763539 AATTCATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTCAATTCAATAATTAATCCACC
Found at i:18763686 original size:3 final size:3
Alignment explanation
Indices: 18763678--18763738 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
18763668 CCACTCATTT
* *
18763678 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18763726 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
18763739 TTTACTAGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18764018 original size:24 final size:23
Alignment explanation
Indices: 18763978--18764024 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
18763968 CTCAATTTAA
18763978 TCCTAACTAAATTCACT-TATTT
1 TCCTAACTAAATTCACTCTATTT
*
18764000 TCCTAACTCAATTCACACTCTATTT
1 TCCTAACTAAATT--CACTCTATTT
18764025 CTATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.57
24 4 0.19
25 5 0.24
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.43
Consensus pattern (23 bp):
TCCTAACTAAATTCACTCTATTT
Found at i:18764442 original size:17 final size:17
Alignment explanation
Indices: 18764422--18764461 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
18764412 TTTCCTATTC
*
18764422 TGTTTCTTTTCTTCTTT
1 TGTTTCTTTTATTCTTT
18764439 TGTTTCTTTTATTCTTT
1 TGTTTCTTTTATTCTTT
18764456 TAGTTT
1 T-GTTT
18764462 ATGTTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.75
Consensus pattern (17 bp):
TGTTTCTTTTATTCTTT
Found at i:18764505 original size:16 final size:17
Alignment explanation
Indices: 18764477--18764508 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
18764467 TTGTTTATTA
18764477 TTTAATAAATATAATAC
1 TTTAATAAATATAATAC
18764494 TTTAAT-AATATAATA
1 TTTAATAAATATAATA
18764509 TAATATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAATAAATATAATAC
Found at i:18764529 original size:25 final size:25
Alignment explanation
Indices: 18764473--18764534 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
18764463 TGTTTTGTTT
*
18764473 ATTATTTAATAAATATAATACTTTA
1 ATTATATAATAAATATAATACTTTA
* *
18764498 ATAATATAATATAATATAATA-TTTT
1 ATTATATAATA-AATATAATACTTTA
*
18764523 CTTATATAATAA
1 ATTATATAATAA
18764535 GTAATTACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.03
25 21 0.68
26 9 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATATAATAAATATAATACTTTA
Found at i:18764675 original size:14 final size:14
Alignment explanation
Indices: 18764631--18764681 Score: 66
Period size: 14 Copynumber: 3.4 Consensus size: 14
18764621 ATTTTATAAT
18764631 ATAATAATAATTATA
1 ATAATAATAATT-TA
*
18764646 ATAATTTAACAATTTA
1 ATAA--TAATAATTTA
18764662 ATAATAATAATTTA
1 ATAATAATAATTTA
18764676 ATAATA
1 ATAATA
18764682 TTTTTTAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 6 0.19
17 7 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:18769695 original size:208 final size:209
Alignment explanation
Indices: 18769440--18769859 Score: 824
Period size: 208 Copynumber: 2.0 Consensus size: 209
18769430 TTAAACTAAA
18769440 TGGTATATAAAAATACATGAAAAAAAAAAGTATTGAGTTTTTAGAATTCTATAAAAATTACAGGA
1 TGGTATATAAAAATACATGAAAAAAAAAAGTATTGAGTTTTTAGAATTCTATAAAAATTACAGGA
18769505 TAACAAATAGCTAAATAAATTAATAAATAAAGCTTAAACAATTTAATTGAGTAAATAGGGATTAA
66 TAACAAATAGCTAAATAAATTAATAAATAAAGCTTAAACAATTTAATTGAGTAAATAGGGATTAA
18769570 ACTGAATTTAAAACAAAGTCAAAAAGACAAAACGAAAATAAAACAGAGTTTAGGCGCAAAATGAA
131 ACTGAATTTAAAACAAAGTCAAAAAGACAAAACGAAAATAAAACAGAGTTTAGGCGCAAAATGAA
18769635 ACGCGTGAATAACG
196 ACGCGTGAATAACG
18769649 TGGTATATAAAAATACATG-AAAAAAAAAGTATTGAGTTTTTAGAATTCTATAAAAATTACAGGA
1 TGGTATATAAAAATACATGAAAAAAAAAAGTATTGAGTTTTTAGAATTCTATAAAAATTACAGGA
18769713 TAACAAATAGCTAAATAAATTAATAAATAAAGCTTAAACAATTTAATTGAGTAAATAGGGATTAA
66 TAACAAATAGCTAAATAAATTAATAAATAAAGCTTAAACAATTTAATTGAGTAAATAGGGATTAA
*
18769778 ACTGAATTTAAAACAAAGTCAAAAAGACAAAACGAAAATAAAACAGAGTTTAGGGGCAAAATGAA
131 ACTGAATTTAAAACAAAGTCAAAAAGACAAAACGAAAATAAAACAGAGTTTAGGCGCAAAATGAA
18769843 ACGCGTGAATAACG
196 ACGCGTGAATAACG
18769857 TGG
1 TGG
18769860 GGGACTAGTT
Statistics
Matches: 210, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
208 191 0.91
209 19 0.09
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (209 bp):
TGGTATATAAAAATACATGAAAAAAAAAAGTATTGAGTTTTTAGAATTCTATAAAAATTACAGGA
TAACAAATAGCTAAATAAATTAATAAATAAAGCTTAAACAATTTAATTGAGTAAATAGGGATTAA
ACTGAATTTAAAACAAAGTCAAAAAGACAAAACGAAAATAAAACAGAGTTTAGGCGCAAAATGAA
ACGCGTGAATAACG
Found at i:18770395 original size:13 final size:13
Alignment explanation
Indices: 18770379--18770419 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
18770369 ACCAAAACCG
*
18770379 AAAAGAAAACTGA
1 AAAAGAAAACGGA
*
18770392 AAAAGAAAAAAGGA
1 AAAAG-AAAACGGA
18770406 AAAAGAAAACGGA
1 AAAAGAAAACGGA
18770419 A
1 A
18770420 GAAGCAAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.73, C:0.05, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAAGAAAACGGA
Found at i:18778500 original size:21 final size:21
Alignment explanation
Indices: 18778474--18778516 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
18778464 CAACGTGGCA
18778474 AGTTAACTGGCCACATCAGCT
1 AGTTAACTGGCCACATCAGCT
*
18778495 AGTTAACTGGCCACGTCAGCT
1 AGTTAACTGGCCACATCAGCT
18778516 A
1 A
18778517 TCCTATTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCT
Found at i:18782020 original size:50 final size:51
Alignment explanation
Indices: 18781934--18782029 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 51
18781924 CGATTTCTTA
* * *
18781934 TCGTAAGCCTCCCCCCATGCGTCTGGGAGTAGGGATATTATTAAACATCGT
1 TCGTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATTATTAAACATCGT
* * *
18781985 TCGTAAGTCT-CCCTCATGCGTCTATGAGCAAGGATATTATTAAAC
1 TCGTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATTATTAAAC
18782030 CCCATTTGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 30 0.77
51 9 0.23
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (51 bp):
TCGTAAGCCTCCCCCCATGCGTCTAGGAGCAAGGATATTATTAAACATCGT
Found at i:18782269 original size:58 final size:58
Alignment explanation
Indices: 18782207--18782339 Score: 178
Period size: 58 Copynumber: 2.3 Consensus size: 58
18782197 GAGCTCTTGG
* * * * *
18782207 CGGAGGTGAGACATATCTTCTATATTTGGGCCCCTCCAG-GAACCCTTTGGGCTCTCAA
1 CGGAGGTGAGGCATATCTTCTACATTCGAGCCCCTCC-GCGAACCCTTTAGGCTCTCAA
* *
18782265 CGGAGGTGAGGCGTATCTTCTACATTCGAGCCCCTCCGCGAACCCTTTAGGCTTTCAA
1 CGGAGGTGAGGCATATCTTCTACATTCGAGCCCCTCCGCGAACCCTTTAGGCTCTCAA
*
18782323 TGGAGGTGAGGCATATC
1 CGGAGGTGAGGCATATC
18782340 ATCTTCATAA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
57 1 0.02
58 64 0.98
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.26
Consensus pattern (58 bp):
CGGAGGTGAGGCATATCTTCTACATTCGAGCCCCTCCGCGAACCCTTTAGGCTCTCAA
Found at i:18784974 original size:24 final size:25
Alignment explanation
Indices: 18784946--18784994 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
18784936 TAACAAGTAA
*
18784946 CTCCGAAGAGCTAT-TATCAGGAAG
1 CTCCGAAGAGCCATATATCAGGAAG
* *
18784970 CTCCGGATAGCCATATATCAGGAAG
1 CTCCGAAGAGCCATATATCAGGAAG
18784995 TTCAAGTGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (25 bp):
CTCCGAAGAGCCATATATCAGGAAG
Found at i:18790420 original size:13 final size:13
Alignment explanation
Indices: 18790402--18790459 Score: 98
Period size: 13 Copynumber: 4.5 Consensus size: 13
18790392 ACTCAATTTT
18790402 TCAAAAGCACTTC
1 TCAAAAGCACTTC
18790415 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
18790428 TGAAAAGCACTTC
1 TCAAAAGCACTTC
*
18790441 TCAGAAGCACTTC
1 TCAAAAGCACTTC
18790454 TCAAAA
1 TCAAAA
18790460 ACAATGAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:18790653 original size:26 final size:26
Alignment explanation
Indices: 18790622--18790705 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
18790612 TGTTCAACCT
18790622 TTATTTAATGTTTGATGGTTTTATTA
1 TTATTTAATGTTTGATGGTTTTATTA
* * * ** *
18790648 TTATTTATTTTTTGTATAGTTAAAGTA
1 TTATTTAATGTTTG-ATGGTTTTATTA
*
18790675 -T-TTTCATGTTTGATGGTTTTATTA
1 TTATTTAATGTTTGATGGTTTTATTA
18790699 TTATTTA
1 TTATTTA
18790706 TTTTTTGTAT
Statistics
Matches: 41, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
24 8 0.20
25 9 0.22
26 16 0.39
27 8 0.20
ACGTcount: A:0.24, C:0.01, G:0.13, T:0.62
Consensus pattern (26 bp):
TTATTTAATGTTTGATGGTTTTATTA
Found at i:18790689 original size:51 final size:51
Alignment explanation
Indices: 18790629--18790735 Score: 214
Period size: 51 Copynumber: 2.1 Consensus size: 51
18790619 CCTTTATTTA
18790629 ATGTTTGATGGTTTTATTATTATTTATTTTTTGTATAGTTAAAGTATTTTC
1 ATGTTTGATGGTTTTATTATTATTTATTTTTTGTATAGTTAAAGTATTTTC
18790680 ATGTTTGATGGTTTTATTATTATTTATTTTTTGTATAGTTAAAGTATTTTC
1 ATGTTTGATGGTTTTATTATTATTTATTTTTTGTATAGTTAAAGTATTTTC
18790731 ATGTT
1 ATGTT
18790736 CGTTTTACGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.61
Consensus pattern (51 bp):
ATGTTTGATGGTTTTATTATTATTTATTTTTTGTATAGTTAAAGTATTTTC
Found at i:18790727 original size:27 final size:27
Alignment explanation
Indices: 18790646--18790727 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 27
18790636 ATGGTTTTAT
18790646 TATTATTTATTTTTTGTATAGTTAAAG
1 TATTATTTATTTTTTGTATAGTTAAAG
* * * ** *
18790673 TATT-TTCA-TGTTTG-ATGGTTTTAT
1 TATTATTTATTTTTTGTATAGTTAAAG
18790697 TATTATTTATTTTTTGTATAGTTAAAG
1 TATTATTTATTTTTTGTATAGTTAAAG
18790724 TATT
1 TATT
18790728 TTCATGTTCG
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
24 10 0.25
25 8 0.20
26 8 0.20
27 14 0.35
ACGTcount: A:0.26, C:0.01, G:0.12, T:0.61
Consensus pattern (27 bp):
TATTATTTATTTTTTGTATAGTTAAAG
Found at i:18796349 original size:39 final size:39
Alignment explanation
Indices: 18796306--18796383 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
18796296 CTAACTCATA
18796306 AATGAGTAAGTCTATCAACATCATATATCTGTTCATGCC
1 AATGAGTAAGTCTATCAACATCATATATCTGTTCATGCC
18796345 AATGAGTAAGTCTATCAACATCATATATCTGTTCATGCC
1 AATGAGTAAGTCTATCAACATCATATATCTGTTCATGCC
18796384 TAACATAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (39 bp):
AATGAGTAAGTCTATCAACATCATATATCTGTTCATGCC
Found at i:18797153 original size:16 final size:16
Alignment explanation
Indices: 18797132--18797173 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
18797122 TCAATATCCA
18797132 ATTATCATATTCACAC
1 ATTATCATATTCACAC
* *
18797148 ATTATCACATTTACAC
1 ATTATCATATTCACAC
18797164 A-TAT-ATATTC
1 ATTATCATATTC
18797174 TTTTCAATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 4 0.18
15 3 0.14
16 15 0.68
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTATCATATTCACAC
Found at i:18802402 original size:14 final size:14
Alignment explanation
Indices: 18802383--18802422 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
18802373 TTGATTGCCA
18802383 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
18802397 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
18802411 GGAAAATGTTTT
1 GTAAAATGTTTT
18802423 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:18802431 original size:20 final size:20
Alignment explanation
Indices: 18802406--18802445 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
18802396 CGTAAAATGA
*
18802406 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
18802426 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
18802446 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:18802435 original size:34 final size:35
Alignment explanation
Indices: 18802391--18802457 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
18802381 CAGTAAAATG
*
18802391 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
18802425 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
18802458 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:18802461 original size:14 final size:15
Alignment explanation
Indices: 18802385--18802461 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
18802375 GATTGCCAGT
* *
18802385 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
18802399 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
18802413 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
18802433 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
18802448 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
18802462 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:18817389 original size:31 final size:31
Alignment explanation
Indices: 18817315--18817390 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
18817305 GGTATTGTCG
*
18817315 TTAAAAACTATTTTCATTTGAGGCAATACCA
1 TTAAAAACTGTTTTCATTTGAGGCAATACCA
** * * * **
18817346 TTAAAATTTGTTTTCATTTTAGGTAGTTTCA
1 TTAAAAACTGTTTTCATTTGAGGCAATACCA
18817377 TTAAAAACTGTTTT
1 TTAAAAACTGTTTT
18817391 TGTAATAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (31 bp):
TTAAAAACTGTTTTCATTTGAGGCAATACCA
Found at i:18820029 original size:14 final size:14
Alignment explanation
Indices: 18820010--18820037 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18820000 TAGTAAATTA
18820010 TTAAAAATATATAT
1 TTAAAAATATATAT
18820024 TTAAAAATATATAT
1 TTAAAAATATATAT
18820038 CATTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATATATAT
Found at i:18822874 original size:12 final size:12
Alignment explanation
Indices: 18822857--18822884 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18822847 GGAGCAACGC
18822857 CGGCACGACGGA
1 CGGCACGACGGA
18822869 CGGCACGACGGA
1 CGGCACGACGGA
18822881 CGGC
1 CGGC
18822885 GACCGAAGCT
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:0.21, C:0.36, G:0.43, T:0.00
Consensus pattern (12 bp):
CGGCACGACGGA
Found at i:18823381 original size:3 final size:3
Alignment explanation
Indices: 18823373--18823417 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
18823363 GTACTTTTGC
18823373 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18823418 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:18825444 original size:19 final size:20
Alignment explanation
Indices: 18825404--18825447 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
18825394 GTCTCTTTAG
* *
18825404 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
18825423 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
18825442 GCATTA
1 GCATTA
18825448 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:18828008 original size:7 final size:8
Alignment explanation
Indices: 18827987--18828015 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
18827977 TCTCATGAAT
18827987 TCAAAAAA
1 TCAAAAAA
18827995 TCAAAAAA
1 TCAAAAAA
18828003 TCAAAAAA
1 TCAAAAAA
18828011 TCAAA
1 TCAAA
18828016 GTCAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (8 bp):
TCAAAAAA
Found at i:18829620 original size:13 final size:13
Alignment explanation
Indices: 18829602--18829630 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
18829592 AACAAAAGGA
18829602 CAAGATGTCGTGT
1 CAAGATGTCGTGT
18829615 CAAGATGTCGTGT
1 CAAGATGTCGTGT
18829628 CAA
1 CAA
18829631 TGTAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (13 bp):
CAAGATGTCGTGT
Found at i:18831498 original size:47 final size:47
Alignment explanation
Indices: 18831422--18831513 Score: 121
Period size: 47 Copynumber: 2.0 Consensus size: 47
18831412 ATTGACCTCT
* ** * *
18831422 TCTTTTATTTTCAATAGTACATCGGGCCTCATGCTTCGAAGTTTCTG
1 TCTTTTATTTTCAACAGTACATCAAGCCTCATCCTTCAAAGTTTCTG
* *
18831469 TCTTTTATTTTGAACAGTACGTCAAGCCTCATCCTTCAAAGTTTC
1 TCTTTTATTTTCAACAGTACATCAAGCCTCATCCTTCAAAGTTTC
18831514 AACTGAACCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (47 bp):
TCTTTTATTTTCAACAGTACATCAAGCCTCATCCTTCAAAGTTTCTG
Found at i:18834079 original size:31 final size:32
Alignment explanation
Indices: 18834035--18834094 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
18834025 AGTTTAGCCA
* *
18834035 TTTATTTTATTACATT-TTATTTTTGCTTTTAG
1 TTTAATTTATTACATTCTAATTTTT-CTTTTAG
18834067 TTTAATTT-TTACATTCTAATTTTTCTTT
1 TTTAATTTATTACATTCTAATTTTTCTTT
18834095 AATTTTGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 11 0.44
32 14 0.56
ACGTcount: A:0.20, C:0.08, G:0.03, T:0.68
Consensus pattern (32 bp):
TTTAATTTATTACATTCTAATTTTTCTTTTAG
Found at i:18834165 original size:26 final size:26
Alignment explanation
Indices: 18834129--18834181 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
18834119 TATTACTAAG
18834129 GAGATGGGTGATAATCAGAATAATCA
1 GAGATGGGTGATAATCAGAATAATCA
18834155 GAGATGGGTGATAATCAGAATAATCA
1 GAGATGGGTGATAATCAGAATAATCA
18834181 G
1 G
18834182 CTTCCTCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.28, T:0.23
Consensus pattern (26 bp):
GAGATGGGTGATAATCAGAATAATCA
Found at i:18834826 original size:37 final size:37
Alignment explanation
Indices: 18834780--18834854 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
18834770 ATTACCCGAA
* *
18834780 TTGAATCACTATATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
* *
18834817 TTGAATCACTACATAATTAAAAGCATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
18834854 T
1 T
18834855 GAAGTTAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.37
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:18835028 original size:38 final size:39
Alignment explanation
Indices: 18834984--18835057 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 39
18834974 ACTTAAGAGT
*
18834984 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
18835022 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATT
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATT
18835058 AGGTTGGGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 27 0.79
39 7 0.21
ACGTcount: A:0.19, C:0.03, G:0.26, T:0.53
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:18835073 original size:17 final size:17
Alignment explanation
Indices: 18835043--18835092 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 17
18835033 TTTAGTTTTA
18835043 TTGGGTTGGGTAATTAGG
1 TTGGGTT-GGTAATTAGG
*
18835061 TTGGGTTGGTAATTGGG
1 TTGGGTTGGTAATTAGG
18835078 TTGGGTTGGATAATT
1 TTGGGTTGG-TAATT
18835093 TTATTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (17 bp):
TTGGGTTGGTAATTAGG
Found at i:18835127 original size:17 final size:18
Alignment explanation
Indices: 18835102--18835138 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
18835092 TTTATTTATT
*
18835102 AATTTTTTTGGTTAACCG
1 AATTTTTTCGGTTAACCG
18835120 AATTTTTTCGGTTAACCG
1 AATTTTTTCGGTTAACCG
18835138 A
1 A
18835139 CCGGTTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (18 bp):
AATTTTTTCGGTTAACCG
Found at i:18847095 original size:39 final size:40
Alignment explanation
Indices: 18847000--18847261 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
18846990 TTGAATGATG
*
18847000 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
18847038 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
18847079 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
18847118 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
18847157 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
18847196 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
18847235 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
18847262 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:18849599 original size:69 final size:69
Alignment explanation
Indices: 18849492--18849828 Score: 453
Period size: 69 Copynumber: 4.9 Consensus size: 69
18849482 AAATGATACA
* * * * *
18849492 TGAACTGGATAGATTCCCTGTAACAACATAATGCGTGAATAGGAGAGATTCCCTGCAAGAAATGA
1 TGAACAGGAAAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGA
18849557 TGTG
66 TGTG
* * * *** *
18849561 TGAATAGGAGAGATTCCCTACAACAAAATAAAATGTGAACAGGAGAGATTCCCTACAAGAAATGA
1 TGAACAGGAAAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGA
18849626 TGTG
66 TGTG
* * * * *
18849630 TGAACAGGAAAGATTCCTTGCAACAAAATAATGCGTGAACAGGAAAGATTCACTGCAACAAAATA
1 TGAACAGGAAAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAA-GAAATG
*
18849695 ATGCG
65 ATGTG
*
18849700 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGA
1 TGAACAGGAAAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGA
18849765 --TG
66 TGTG
* * *
18849767 TGAACAGGAAAGATTCCCTGCAACAGAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAA
1 TGAACAGGAAAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAA
18849829 AGACAAGTGA
Statistics
Matches: 232, Mismatches: 35, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
67 59 0.25
69 111 0.48
70 62 0.27
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (69 bp):
TGAACAGGAAAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGA
TGTG
Found at i:18849605 original size:35 final size:35
Alignment explanation
Indices: 18849492--18849829 Score: 389
Period size: 35 Copynumber: 9.8 Consensus size: 35
18849482 AAATGATACA
* * * *
18849492 TGAACTGGATAGATTCCCTGTAACAACATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
* * * *
18849527 TGAATAGGAGAGATTCCCTGCAA-GAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
* * ***
18849561 TGAATAGGAGAGATTCCCTACAACAAAATAAAATG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
* * * *
18849596 TGAACAGGAGAGATTCCCTACAA-GAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
* *
18849630 TGAACAGGAAAGATTCCTTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
* *
18849665 TGAACAGGAAAGATTCACTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
18849700 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
* *
18849735 TGAACAGGAGAGATTCCCTGCAA-GAAATGAT--G
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
* *
18849767 TGAACAGGAAAGATTCCCTGCAACAGAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
* * *
18849802 TGAACAGGAAATATTCCCTGCAAGAAAA
1 TGAACAGGAGAGATTCCCTGCAACAAAA
18849830 GACAAGTGAA
Statistics
Matches: 261, Mismatches: 37, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
32 23 0.09
33 5 0.02
34 62 0.24
35 171 0.66
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (35 bp):
TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
Found at i:18853898 original size:35 final size:35
Alignment explanation
Indices: 18853811--18853984 Score: 282
Period size: 35 Copynumber: 5.1 Consensus size: 35
18853801 GTCCAAAAAG
* * *
18853811 AAATAATACATGAACAGGAGAGATTCCCTGCAA-G
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
*
18853845 AAATGAT--GTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
18853878 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
18853913 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
*
18853948 AAATAATGCGTGAACAGAAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
18853983 AA
1 AA
18853985 TATTCCCTGC
Statistics
Matches: 132, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
32 23 0.17
33 6 0.05
34 6 0.05
35 97 0.73
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (35 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
Found at i:18854252 original size:29 final size:29
Alignment explanation
Indices: 18854220--18854292 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
18854210 TTCTCAAGAC
* *
18854220 ATTTAAGTTTTCAAAAATTTAGTTTTTAA
1 ATTTAAGTTTTCAAAAATTAAGTTTTCAA
*
18854249 ATTTCCAAATTTTC--AAATTAAGTTTTCAA
1 ATTT--AAGTTTTCAAAAATTAAGTTTTCAA
* *
18854278 ACTTAAGCTTTCAAA
1 ATTTAAGTTTTCAAA
18854293 TTACAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
27 6 0.18
29 21 0.62
31 7 0.21
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTTAAGTTTTCAAAAATTAAGTTTTCAA
Found at i:18854276 original size:13 final size:13
Alignment explanation
Indices: 18854258--18854295 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
18854248 AATTTCCAAA
18854258 TTTTCAAATTAAG
1 TTTTCAAATTAAG
18854271 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
18854285 CTTTCAAATTA
1 TTTTCAAATTA
18854296 CAAATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:18856595 original size:16 final size:16
Alignment explanation
Indices: 18856570--18856603 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18856560 TGTGTTTTGC
* *
18856570 TTTGATTGCATGGCAT
1 TTTGACTGCATAGCAT
18856586 TTTGACTGCATAGCAT
1 TTTGACTGCATAGCAT
18856602 TT
1 TT
18856604 CATCATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (16 bp):
TTTGACTGCATAGCAT
Found at i:18859121 original size:9 final size:9
Alignment explanation
Indices: 18859107--18859131 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18859097 AGAAACATGA
18859107 TGACCCAGT
1 TGACCCAGT
18859116 TGACCCAGT
1 TGACCCAGT
18859125 TGACCCA
1 TGACCCA
18859132 ATTATTGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (9 bp):
TGACCCAGT
Found at i:18867030 original size:24 final size:24
Alignment explanation
Indices: 18866998--18867055 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
18866988 ATGTCCCAAA
18866998 ATTACAGTGGATTAAACCTTGAAG
1 ATTACAGTGGATTAAACCTTGAAG
*
18867022 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAGTGGATTAAACCTTGAAG
18867046 ATTACAGTGG
1 ATTACAGTGG
18867056 GGACAATTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (24 bp):
ATTACAGTGGATTAAACCTTGAAG
Found at i:18867408 original size:46 final size:46
Alignment explanation
Indices: 18867341--18867758 Score: 432
Period size: 46 Copynumber: 9.0 Consensus size: 46
18867331 GCAGTGGAGC
* * *
18867341 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
*
18867387 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGCAGTGGAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGC-----AAT
*
18867438 AGATTAAAGCT-AACGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * *
18867483 AGATTAAAGCTGAAGGCAGCTAATCTT-TTTCCCTAGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * * * **
18867528 AGGTTAAAGCTGAAGGCAACGAATCTTATTTCCTTGACGTTGCCGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* ** * * ** *
18867574 GGA--GCAGCTGAAGGCAGCAAATCTTATTTCTCTGGCGTTATAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * *
18867618 AGATCAAAGCTGAGGGTAGCGAATCTTATTT-CCTCGGCGTTGCAGTGGAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCT-GGCGTTGC-----AAT
* *
18867669 AGATTAAAGCTGAAGGCAGCGAATATTATTTCCCCGGCGTTGCAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * *
18867715 AGATTAAGGCTGAAGGCAGCGAATCTTATTTCTCTGGTGTTGCA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCA
18867759 GTGGAATAGA
Statistics
Matches: 307, Mismatches: 49, Indels: 32
0.79 0.13 0.08
Matches are distributed among these distances:
44 33 0.11
45 56 0.18
46 137 0.45
50 29 0.09
51 50 0.16
52 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (46 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
Found at i:18867627 original size:90 final size:89
Alignment explanation
Indices: 18867490--18867666 Score: 228
Period size: 90 Copynumber: 2.0 Consensus size: 89
18867480 AATAGATTAA
* * * *
18867490 AGCTGAAGGCAGCTAATCTTTTTCCCTAGCGTTGCAGTAGGTTAAAGCTGAAGGCAACGAATCTT
1 AGCTGAAGGCAGCAAATCTTTTTCCCTAGCGTTACAGTAGATCAAAGCTGAAGGCAACGAATCTT
* *
18867555 ATTTCCTTGACGTTGCCGTGGAGC
66 ATTTCCTCGACGTTGCAGTGGAGC
* * * * * *
18867579 AGCTGAAGGCAGCAAATCTTATTTCTCTGGCGTTATAGTAGATCAAAGCTGAGGGTAGCGAATCT
1 AGCTGAAGGCAGCAAATCTT-TTTCCCTAGCGTTACAGTAGATCAAAGCTGAAGGCAACGAATCT
*
18867644 TATTTCCTCGGCGTTGCAGTGGA
65 TATTTCCTCGACGTTGCAGTGGA
18867667 ATAGATTAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
89 19 0.26
90 55 0.74
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (89 bp):
AGCTGAAGGCAGCAAATCTTTTTCCCTAGCGTTACAGTAGATCAAAGCTGAAGGCAACGAATCTT
ATTTCCTCGACGTTGCAGTGGAGC
Found at i:18867676 original size:141 final size:135
Alignment explanation
Indices: 18867341--18867751 Score: 439
Period size: 141 Copynumber: 2.9 Consensus size: 135
18867331 GCAGTGGAGC
* *
18867341 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGTAGATTAAAGCTGAAGGCAG
1 AGATCAAAGCTGAAGGCAGCGAATCTT-TTTCCCTAGCGTTGCAGTAGATTAAAGCTGAAGGCAG
* *
18867406 CGAATCTTATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCT-AACGCAGCGAATCTTATTTCC
65 CGAATCTTATTTCCTTGGCGTTGCAGTGG---AG----AAGCTGAAGGCAGCGAATCTTATTTCT
*
18867470 CTGGCGTTGCAAT
123 CTGGCGTTACAAT
* * * *
18867483 AGATTAAAGCTGAAGGCAGCTAATCTTTTTCCCTAGCGTTGCAGTAGGTTAAAGCTGAAGGCAAC
1 AGATCAAAGCTGAAGGCAGCGAATCTTTTTCCCTAGCGTTGCAGTAGATTAAAGCTGAAGGCAGC
* * * *
18867548 GAATCTTATTTCCTTGACGTTGCCGTGGAGCAGCTGAAGGCAGCAAATCTTATTTCTCTGGCGTT
66 GAATCTTATTTCCTTGGCGTTGCAGTGGAGAAGCTGAAGGCAGCGAATCTTATTTCTCTGGCGTT
* *
18867613 ATAGT
131 ACAAT
* * *
18867618 AGATCAAAGCTGAGGGTAGCGAATCTTATTT-CCTCGGCGTTGCAGTGGAATAGATTAAAGCTGA
1 AGATCAAAGCTGAAGGCAGCGAATCTT-TTTCCCT-AGCGTTGCA---G--TAGATTAAAGCTGA
* ** * * *
18867682 AGGCAGCGAATATTATTTCCCCGGCGTTGCAATAGATTAAGGCTGAAGGCAGCGAATCTTATTTC
59 AGGCAGCGAATCTTATTTCCTTGGCGTTGCAGTGGA-GAA-GCTGAAGGCAGCGAATCTTATTTC
18867747 TCTGG
122 TCTGG
18867752 TGTTGCAGTG
Statistics
Matches: 229, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
134 4 0.02
135 54 0.24
136 11 0.05
138 2 0.01
139 1 0.00
141 102 0.45
142 27 0.12
143 28 0.12
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (135 bp):
AGATCAAAGCTGAAGGCAGCGAATCTTTTTCCCTAGCGTTGCAGTAGATTAAAGCTGAAGGCAGC
GAATCTTATTTCCTTGGCGTTGCAGTGGAGAAGCTGAAGGCAGCGAATCTTATTTCTCTGGCGTT
ACAAT
Found at i:18867727 original size:97 final size:98
Alignment explanation
Indices: 18867341--18867776 Score: 434
Period size: 97 Copynumber: 4.6 Consensus size: 98
18867331 GCAGTGGAGC
* *
18867341 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCC-CTAGCGTT---GT--AGTAGATTAAAGCTGA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
*
18867400 AGGCAGCGAATCTTATTTCCTTGGCGTTGCAGTGGAAT
66 AGGCAGCGAATCTTATTTCCCTGGCGTTGC-----AAT
*
18867438 AGATTAAAGCT-AACGCAGCGAATCTTATTTCC-CTGGCGTTGC-----AATAGATTAAAGCTGA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
* * *
18867496 AGGCAGCTAATCTT-TTTCCCTAGCGTTGCAGT
66 AGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * * * *
18867528 AGGTTAAAGCTGAAGGCAACGAATCTTATTTCCT-TGACGTTGCCGTGG---AG----CAGCTGA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
* * ** *
18867585 AGGCAGCAAATCTTATTTCTCTGGCGTTATAGT
66 AGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * *
18867618 AGATCAAAGCTGAGGGTAGCGAATCTTATTTCCTC-GGCGTTGCAGTGGAATAGATTAAAGCTGA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
* *
18867682 AGGCAGCGAATATTATTTCCCCGGCGTTGCAAT
66 AGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * *
18867715 AGATTAAGGCTGAAGGCAGCGAATCTTATTT-CTCTGGTGTTGCAGTGGAATAGATTGAAGCT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCT
18867777 ACTAATCCTA
Statistics
Matches: 282, Mismatches: 38, Indels: 38
0.79 0.11 0.11
Matches are distributed among these distances:
89 19 0.07
90 66 0.23
91 27 0.10
93 4 0.01
95 13 0.05
96 58 0.21
97 95 0.34
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (98 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
AGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
Found at i:18880972 original size:14 final size:15
Alignment explanation
Indices: 18880950--18881026 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
18880940 CAATCAAACA
18880950 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
18880964 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
* *
18880979 ACAGAAAAGTAAAATATTTT
1 CCAGAAAA-T----CATTTT
18880999 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
18881013 CCGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
18881027 ACTAGCAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 21 0.43
15 15 0.31
16 1 0.02
18 1 0.02
19 3 0.06
20 8 0.16
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:18885894 original size:45 final size:44
Alignment explanation
Indices: 18885817--18885918 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 44
18885807 AATGGTAGCA
* *
18885817 GTAACAGTAACAGTAACAGTATTCAACGCACAAAGTG-CTGAATC
1 GTAATAGTAACAGTAACAGTATTCAACACACAAAGTGTC-GAATC
* *
18885861 TGTAATAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATC
1 -GTAATAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATC
18885906 GATAATAGTAACA
1 G-TAATAGTAACA
18885919 ATAGTCAGCA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 1 0.02
45 48 0.96
46 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23
Consensus pattern (44 bp):
GTAATAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATC
Found at i:18886165 original size:40 final size:40
Alignment explanation
Indices: 18886121--18886207 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
18886111 AGTTCATTAC
* *
18886121 TTTAGTAA-TCTCACAGTTCAATGCAATACACATAACAATA
1 TTTAGTAACT-TCACAATTCAATGCAATACACAAAACAATA
* * *
18886161 TTTAGTAACTTCACAATTCAATTCAGTACTCAAAACAATA
1 TTTAGTAACTTCACAATTCAATGCAATACACAAAACAATA
*
18886201 TTCAGTA
1 TTTAGTA
18886208 TTCCATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 39 0.98
41 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (40 bp):
TTTAGTAACTTCACAATTCAATGCAATACACAAAACAATA
Found at i:18886881 original size:25 final size:23
Alignment explanation
Indices: 18886837--18886897 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
18886827 ATTTTGATTT
*
18886837 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
18886861 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
18886885 ATATAAATTATAT
1 AT-TTAATTATAT
18886898 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Done.