Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 49 of 54
Found at i:19452995 original size:20 final size:20
Alignment explanation
Indices: 19452970--19453010 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
19452960 TAATTAGTCA
*
19452970 ATAACAATTTACCATTATAT
1 ATAACAATATACCATTATAT
*
19452990 ATAACAATATACTATTATAT
1 ATAACAATATACCATTATAT
19453010 A
1 A
19453011 GTGTATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAACAATATACCATTATAT
Found at i:19453949 original size:19 final size:19
Alignment explanation
Indices: 19453909--19453950 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
19453899 TTTTATATTA
* *
19453909 ATATTTTAATATTGTAAAT
1 ATATTTTAAAATTGAAAAT
19453928 ATATTTTAAAATT-AAAATT
1 ATATTTTAAAATTGAAAA-T
19453947 ATAT
1 ATAT
19453951 AAAAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATTTTAAAATTGAAAAT
Found at i:19455787 original size:415 final size:415
Alignment explanation
Indices: 19455016--19456264 Score: 1961
Period size: 415 Copynumber: 3.0 Consensus size: 415
19455006 GAAGGGTCAA
* *
19455016 TTCATCAAAAGCACTTAAAAACTCGAGATTTAGAGAGAAATTCACATGGTAGATCTGAAGGGATC
1 TTCATCAAAAGCACTTAAAAACTCGAGATTTAGAGAGAAATTCACATAGTAGATCTGAATGGATC
* *
19455081 GAATTTGCCCCAATTAGGTCGGATTTGACGTAGCTAGAGGTTGAAAAAGGCATTAGATAACTGGG
66 GAATTTGCCCCAATTAGGTCGGATTTGACGTAGCTAGAGGTTGAAAAAGGCATTAGATAGCTAGG
** * *
19455146 CAATGAT-TCTAAAATTTAAATTATTTGAATTAATAAATCATTATTTACCATTTTTATATTATGT
131 CAACAATGT-TAATATTTAAATTATTTGAATTAATAAATCATTATTTACCATTTTTATATTATTT
* *
19455210 TATTATCTGATGCATTAATCCAATTAAACATAAATTAATTCATATACTAACATAAAATAAACACA
195 TATTATTTTATGCATTAATCCAATTAAACATAAATTAATTCATATACTAACATAAAATAAACACA
* * *
19455275 AACAAAGAGCAAGCCCAAGACAATCTTACTTTGATTCGTCCCAGACACAAACCCTACTCTTCTTG
260 AACAAATAGCAAGCCCAAGACAATCTTACTTTGATTGGTCCCAGACACAAACCCTACTTTTCTTG
* *
19455340 AACACCAATAGTACACCTCCACCAACAAGGACCCGTTTCCACCTTCTTTCTTTGTTTCTTTCTTT
325 AACACCAATAGTACGCCTCCACCAACAAGGACCCATTTCCACCTTCTTTCTTTGTTTCTTTCTTT
19455405 TCTTTGTTCTCTCTAGTTAGGCTTCCT
390 TCTTT-TTCTCTCTAGTTAGGCTTCCT
* *
19455432 TTCATCAAAAGCACTTAAAAACTCGAGATTTAGAGAGAAATTTACATAGTAGATCTGAATGGATT
1 TTCATCAAAAGCACTTAAAAACTCGAGATTTAGAGAGAAATTCACATAGTAGATCTGAATGGATC
* * * * *
19455497 GCATTTGCCCCGATTAAGTC-TATTTGACGTAGCTAAAGGTTGAAAAAGGCATTAGATAGCTAGG
66 GAATTTGCCCCAATTAGGTCGGATTTGACGTAGCTAGAGGTTGAAAAAGGCATTAGATAGCTAGG
19455561 CAACAATGTTAATATTTAAATTATTTGAATTAATAAATCATTATTTACCATTTTTATATTATTTT
131 CAACAATGTTAATATTTAAATTATTTGAATTAATAAATCATTATTTACCATTTTTATATTATTTT
19455626 ATTATTTTATGCATTAATCCAATTAAACATAAATTAATTCATATACTAACATAAAATAAACACAA
196 ATTATTTTATGCATTAATCCAATTAAACATAAATTAATTCATATACTAACATAAAATAAACACAA
** * *
19455691 ACAAATAGCAAGAACAGGACAATCTTACTTTGATTGGTCCCAGACACAAACCCTACTTTTCTTGG
261 ACAAATAGCAAGCCCAAGACAATCTTACTTTGATTGGTCCCAGACACAAACCCTACTTTTCTTGA
* *
19455756 ACACCAATAGTAGGCCTCCACCAACAAGGACCCATTTCCACCTTCTTT-TTTCGTTTCTTTCTTC
326 ACACCAATAGTACGCCTCCACCAACAAGGACCCATTTCCACCTTCTTTCTTT-GTTTCTTTCTTT
*
19455820 TCTTTCT-TCTCTAGTTAGGCTTCCT
390 TCTTTTTCTCTCTAGTTAGGCTTCCT
* * * * * **
19455845 TTCATCAAAATCACTTAAAAAACTTGAGATTTAGAGACAAATTCACGTAGTACATCCAAATGGAT
1 TTCATCAAAAGCACTT-AAAAACTCGAGATTTAGAGAGAAATTCACATAGTAGATCTGAATGGAT
*
19455910 CGAATTTGCCCCAATTAGGTCGGATTTGACCTAGCTAGAGGTTGAAAAAGGCATTAGATAGCTAG
65 CGAATTTGCCCCAATTAGGTCGGATTTGACGTAGCTAGAGGTTGAAAAAGGCATTAGATAGCTAG
* *
19455975 GCAACAATGCTCATATTTAAATTATTTGAATTAATAAATCATTATTTACCATTTTTATATTATTT
130 GCAACAATGTTAATATTTAAATTATTTGAATTAATAAATCATTATTTACCATTTTTATATTATTT
* *
19456040 TCTTATTTTATGCATCAATCCAATTAAACATAAATTAATTCATATACTAACATAAAATAAACACA
195 TATTATTTTATGCATTAATCCAATTAAACATAAATTAATTCATATACTAACATAAAATAAACACA
* * * *
19456105 AACAAATAGCATGCCCAAGACAATCTTACTTTGATTGGCCCCAAACACAAACCTTA-TTATTCTT
260 AACAAATAGCAAGCCCAAGACAATCTTACTTTGATTGGTCCCAGACACAAACCCTACTT-TTCTT
* *
19456169 GAACACCAATAGTATGCCTCCACCAACAAGGACCCATTTCTACCTTCTTTGC-TTGTTTCTTTCT
324 GAACACCAATAGTACGCCTCCACCAACAAGGACCCATTTCCACCTTCTTT-CTTTGTTTCTTTCT
*
19456233 TTTCTTTCTTCTCTCTAGTTAGGCTTACT
388 TTTCTTT-TTCTCTCTAGTTAGGCTTCCT
19456262 TTC
1 TTC
19456265 TAGGGTGTGC
Statistics
Matches: 763, Mismatches: 61, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
413 33 0.04
414 64 0.08
415 564 0.74
416 82 0.11
417 20 0.03
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (415 bp):
TTCATCAAAAGCACTTAAAAACTCGAGATTTAGAGAGAAATTCACATAGTAGATCTGAATGGATC
GAATTTGCCCCAATTAGGTCGGATTTGACGTAGCTAGAGGTTGAAAAAGGCATTAGATAGCTAGG
CAACAATGTTAATATTTAAATTATTTGAATTAATAAATCATTATTTACCATTTTTATATTATTTT
ATTATTTTATGCATTAATCCAATTAAACATAAATTAATTCATATACTAACATAAAATAAACACAA
ACAAATAGCAAGCCCAAGACAATCTTACTTTGATTGGTCCCAGACACAAACCCTACTTTTCTTGA
ACACCAATAGTACGCCTCCACCAACAAGGACCCATTTCCACCTTCTTTCTTTGTTTCTTTCTTTT
CTTTTTCTCTCTAGTTAGGCTTCCT
Found at i:19463390 original size:18 final size:19
Alignment explanation
Indices: 19463361--19463396 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19463351 ATCAAACCTT
19463361 ACATGCTACATCATATCAA
1 ACATGCTACATCATATCAA
*
19463380 ACATG-TACATCTTATCA
1 ACATGCTACATCATATCA
19463397 TTTTTCTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.31
Consensus pattern (19 bp):
ACATGCTACATCATATCAA
Found at i:19465219 original size:40 final size:42
Alignment explanation
Indices: 19465170--19465254 Score: 124
Period size: 40 Copynumber: 2.1 Consensus size: 42
19465160 TTTCTGTTTC
19465170 TATCTTTCTTCGTTATG-CTTT-TCA-TGGTTG-TTCTTTTAT
1 TATCTTTCTTCGTTATGTCTTTCT-ATTGGTTGTTTCTTTTAT
19465209 TANTCTTTCTTCGTTATGTCTTTCTATTGGTTGTTTCTTTTAT
1 TA-TCTTTCTTCGTTATGTCTTTCTATTGGTTGTTTCTTTTAT
19465252 TAT
1 TAT
19465255 TATTATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
39 2 0.05
40 15 0.37
41 5 0.12
42 8 0.20
43 11 0.27
ACGTcount: A:0.11, C:0.14, G:0.12, T:0.62
Consensus pattern (42 bp):
TATCTTTCTTCGTTATGTCTTTCTATTGGTTGTTTCTTTTAT
Found at i:19465256 original size:3 final size:3
Alignment explanation
Indices: 19465248--19465276 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19465238 GTTGTTTCTT
19465248 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19465277 TCACTTTTTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19467594 original size:25 final size:26
Alignment explanation
Indices: 19467539--19467605 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
19467529 AAACACCTTA
* * *
19467539 AACATGGCATGTAATAACTTTTTTTTT
1 AACATGACATGTAACAAC-TTTTTTTC
19467566 AACATGACATGTAACAA-TTTTTTTC
1 AACATGACATGTAACAACTTTTTTTC
*
19467591 AACATGACCTGTAAC
1 AACATGACATGTAAC
19467606 TTGGTCTCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
25 21 0.58
27 15 0.42
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (26 bp):
AACATGACATGTAACAACTTTTTTTC
Found at i:19467653 original size:123 final size:124
Alignment explanation
Indices: 19467352--19467851 Score: 521
Period size: 123 Copynumber: 4.0 Consensus size: 124
19467342 AAACATAGCA
* * * *
19467352 TGTAACTTGATCTCTATCTTTGTATTTCACTT-GGATATAAACTCTTAGAGTTAAACACCTTAAA
1 TGTAACTTGGTCTCTATCTTTGTATTTCA-TTAAGACATAAACTCTTAAAGTTAAACACCTTAAA
* * * *
19467416 CATGGTATCTAACAACTTTTTTTTCAACATGGA-GTGTAATAAATTTTTTTTCAATAT-ATCG
65 CATGGCATGTAACAACTTTTTTTTCAACAT-GACGTGTAA-CAATTTTTTTTCAACATGA-CG
* *
19467477 TGTAACTTGGTCTCTATCTTTGT-TTTCCATTAAGACATAAACT-GTAAGTGTTAAACACCTTAA
1 TGTAACTTGGTCTCTATCTTTGTATTT-CATTAAGACATAAACTCTTAA-AGTTAAACACCTTAA
* * * *
19467540 ACATGGCATGTAATAACTTTTTTTTTAACATGACATGTAACAA-TTTTTTTCAACATGACC
64 ACATGGCATGTAACAACTTTTTTTTCAACATGACGTGTAACAATTTTTTTTCAACATGACG
* *
19467600 TGTAACTTGGTCTCTATGTTTGTATTTCATTAAGATATAAACTCTTAAAGTTAAACACCTTAAAC
1 TGTAACTTGGTCTCTATCTTTGTATTTCATTAAGACATAAACTCTTAAAGTTAAACACCTTAAAC
** * * ** * * **
19467665 ATGGTGTGTAATAACTTCTTTTTCAACATGGTGCGTAACAACGTTTATTTTTTCAGCATGGTG
66 ATGGCATGTAACAACTTTTTTTTCAACATGACGTGTAACAA---TT-TTTTTTCAACATGACG
** * *
19467728 TGTAACTTGGTCTCTATCTTTGTATTTCA-CCAGAACATAAACTCTTAGAGTTAAGCACCTTAAA
1 TGTAACTTGGTCTCTATCTTTGTATTTCATTAAG-ACATAAACTCTTAAAGTTAAACACCTTAAA
* * *
19467792 TATGGCATGTAACAACATTTTTTTTCAACAT-AGCGTGTAACAACATTTTTTTGAACATGA
65 CATGGCATGTAACAAC-TTTTTTTTCAACATGA-CGTGTAACAA-TTTTTTTTCAACATGA
19467852 TGTGCAATAA
Statistics
Matches: 311, Mismatches: 49, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
123 99 0.32
124 18 0.06
125 79 0.25
126 11 0.04
127 4 0.01
128 79 0.25
129 21 0.07
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (124 bp):
TGTAACTTGGTCTCTATCTTTGTATTTCATTAAGACATAAACTCTTAAAGTTAAACACCTTAAAC
ATGGCATGTAACAACTTTTTTTTCAACATGACGTGTAACAATTTTTTTTCAACATGACG
Found at i:19467945 original size:155 final size:154
Alignment explanation
Indices: 19467709--19467997 Score: 400
Period size: 155 Copynumber: 1.9 Consensus size: 154
19467699 GTAACAACGT
* * * *
19467709 TTATTTTTTCAGCATGGTGTGTAACTTGGTCTCTATCTTTGTATTTCACCAGAACATAAACTCTT
1 TTATTTTTTAAACATAGTGTGTAACTTGGTCTCTATCTTTCTATTTCACCAGAACATAAACTCTT
* * * *
19467774 AGAGTTAAGCACCTTAAATATGGCATGTAACAACATTTTTTTTCAACATAGCGTGTAACAACATT
66 AGAGTTAAACACCTTAAACATGACATATAA-AACATTTTTTTTCAACATAGCGTGTAACAACATT
19467839 TTTTTGAACATGATGTGCAATAATA
130 TTTTTGAACATGATGTGCAATAATA
* *
19467864 TTATTTTTTAAACATAGTGTGTAACTTGGTCTCTATCTTTCTATTTCACTAGGACATAAAC-CTT
1 TTATTTTTTAAACATAGTGTGTAACTTGGTCTCTATCTTTCTATTTCACCAGAACATAAACTC-T
* * * ** * *
19467928 TGGAGTTAAACACCTTAAACATGACGTATAATAGTTTTTTTTTCAACATGGCGTGTATCAACATT
65 TAGAGTTAAACACCTTAAACATGACATATAAAACATTTTTTTTCAACATAGCGTGTAACAACATT
19467993 TTTTT
130 TTTTT
19467998 CTGAGGTTTT
Statistics
Matches: 116, Mismatches: 17, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
154 35 0.30
155 81 0.70
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (154 bp):
TTATTTTTTAAACATAGTGTGTAACTTGGTCTCTATCTTTCTATTTCACCAGAACATAAACTCTT
AGAGTTAAACACCTTAAACATGACATATAAAACATTTTTTTTCAACATAGCGTGTAACAACATTT
TTTTGAACATGATGTGCAATAATA
Found at i:19468720 original size:20 final size:19
Alignment explanation
Indices: 19468499--19468716 Score: 80
Period size: 20 Copynumber: 11.2 Consensus size: 19
19468489 TTTTTAAAAA
*
19468499 TTAATATTTTATTTATACT
1 TTAATATTTTATTTATAAT
** *
19468518 TTAATCATTAACATTATAAAAT
1 TTAAT-ATT-TTATT-TATAAT
*
19468540 ATTAATATATTATTTATAAT
1 -TTAATATTTTATTTATAAT
* *
19468560 TTAA-ATGTTATTATGATTAT
1 TTAATATTTTATT-T-ATAAT
*
19468580 TT-AT-TTTTATTT-TATT
1 TTAATATTTTATTTATAAT
**
19468596 TTAA-A---TATAAATAAT
1 TTAATATTTTATTTATAAT
*
19468611 TT-ATAATTTATTTA-AATT
1 TTAATATTTTATTTATAA-T
19468629 ATTAATATTTGATCATTTA-AAT
1 -TTAATATTT--T-ATTTATAAT
*
19468651 ATTACTATTTTATTTATAAT
1 -TTAATATTTTATTTATAAT
** *
19468671 TTAATCATTGAAATTTTAAAAT
1 TTAAT-ATT-TTA-TTTATAAT
19468693 ATTAATATTTTATTTATAAT
1 -TTAATATTTTATTTATAAT
19468713 TTAA
1 TTAA
19468717 ATATAATTAT
Statistics
Matches: 147, Mismatches: 27, Indels: 50
0.66 0.12 0.22
Matches are distributed among these distances:
14 4 0.03
15 6 0.04
16 4 0.03
17 3 0.02
18 13 0.09
19 32 0.22
20 33 0.22
21 8 0.05
22 27 0.18
23 17 0.12
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (19 bp):
TTAATATTTTATTTATAAT
Found at i:19469016 original size:14 final size:14
Alignment explanation
Indices: 19468978--19469025 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
19468968 ATTAGGATAA
*
19468978 TTTTTAATTTTTTT
1 TTTTTAATTTTTAT
19468992 CTCTTTGTAATTTTTAT
1 -T-TTT-TAATTTTTAT
*
19469009 TTTTTAATTTATAT
1 TTTTTAATTTTTAT
19469023 TTT
1 TTT
19469026 CACTTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 12 0.41
15 4 0.14
16 4 0.14
17 9 0.31
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTTAATTTTTAT
Found at i:19483011 original size:27 final size:27
Alignment explanation
Indices: 19482960--19483011 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
19482950 ATGCCCTGGT
*
19482960 GGTGGAAAATTACAATTTTGCCCCTAG
1 GGTGGAAAATTACAATTTTGACCCTAG
*
19482987 GGTGGCAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
19483012 TTTTCTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAG
Found at i:19483082 original size:20 final size:20
Alignment explanation
Indices: 19483065--19483102 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
19483055 CCTCAAATCT
19483065 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
19483085 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
19483103 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:19484194 original size:119 final size:119
Alignment explanation
Indices: 19483983--19484201 Score: 332
Period size: 119 Copynumber: 1.8 Consensus size: 119
19483973 ATTCTATGAC
* *
19483983 GAAAATCATATAGCTATTTTGTCTTACCATTACTTGATACATGTTGATCTAGAACTTCCTAAAAA
1 GAAAATCATATAGCTATTATGTCTTACCATTACTTGATACATGATGATCTAGAACTTCCTAAAAA
19484048 TATCCATTCCATTACAGCTGTTTTATTGCTATTTGCTAATGAACACTTTATACT
66 TATCCATTCCATTACAGCTGTTTTATTGCTATTTGCTAATGAACACTTTATACT
* * * * *
19484102 GAAAATCATA-AGGCTATTATGTCTTAGCATTAGTTGATATATGATGTTCTAGAACTTCTTAAAA
1 GAAAATCATATA-GCTATTATGTCTTACCATTACTTGATACATGATGATCTAGAACTTCCTAAAA
* * *
19484166 ATTTCCTTTCCATTACAGTTGTTTTATTGCTATTTG
65 ATATCCATTCCATTACAGCTGTTTTATTGCTATTTG
19484202 GTCATCATCA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
118 1 0.01
119 88 0.99
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (119 bp):
GAAAATCATATAGCTATTATGTCTTACCATTACTTGATACATGATGATCTAGAACTTCCTAAAAA
TATCCATTCCATTACAGCTGTTTTATTGCTATTTGCTAATGAACACTTTATACT
Found at i:19486384 original size:20 final size:20
Alignment explanation
Indices: 19486341--19486384 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
19486331 CTATTCTTTT
*
19486341 TTTTTTATCTTCATTTTCAG
1 TTTTTTATCTTCATTTTCAA
* *
19486361 TTTTTTATCTTGATTTTTAA
1 TTTTTTATCTTCATTTTCAA
19486381 TTTT
1 TTTT
19486385 CTATTTTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTTTATCTTCATTTTCAA
Found at i:19486536 original size:17 final size:16
Alignment explanation
Indices: 19486504--19486540 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
19486494 TGTTTCATTC
19486504 TTTT-GTTATTTATTA
1 TTTTAGTTATTTATTA
19486519 TTTTAGTTATTATATTA
1 TTTTAGTTATT-TATTA
19486536 TTTTA
1 TTTTA
19486541 AATTTGGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 10 0.50
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTTAGTTATTTATTA
Found at i:19488839 original size:25 final size:24
Alignment explanation
Indices: 19488789--19488833 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
19488779 CTCATAATTT
*
19488789 TTAAAAAAAATATAATTAATGATA
1 TTAAAAAAAATATAATTAATAATA
*
19488813 TTAAAAATAA-ATAATTAATAA
1 TTAAAAAAAATATAATTAATAA
19488834 AATATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
TTAAAAAAAATATAATTAATAATA
Found at i:19491295 original size:54 final size:55
Alignment explanation
Indices: 19491237--19491340 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 55
19491227 ATAAATTAAG
* * *
19491237 ATAAAGT-CGAAATAAAAATTAATATTAGA-TTTCAGATTAGGCATCGTAATGAAC
1 ATAAAGTACG-AAGAAAAATTAACATTAGATTTTCACATTAGGCATCGTAATGAAC
*
19491291 ATAAAGTACGAAGAAAAATTAACATTAGATTTTCACATTAGGTATCGTAA
1 ATAAAGTACGAAGAAAAATTAACATTAGATTTTCACATTAGGCATCGTAA
19491341 GTTGTTTTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
54 24 0.55
55 20 0.45
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (55 bp):
ATAAAGTACGAAGAAAAATTAACATTAGATTTTCACATTAGGCATCGTAATGAAC
Found at i:19491466 original size:15 final size:15
Alignment explanation
Indices: 19491445--19491473 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19491435 ATATAAAGAA
19491445 AATAAAAATAAAAGG
1 AATAAAAATAAAAGG
19491460 AA-AAAAATAAAAGG
1 AATAAAAATAAAAGG
19491474 GTTTAGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 12 0.86
15 2 0.14
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (15 bp):
AATAAAAATAAAAGG
Found at i:19491507 original size:36 final size:36
Alignment explanation
Indices: 19491460--19491571 Score: 109
Period size: 36 Copynumber: 3.1 Consensus size: 36
19491450 AAATAAAAGG
*
19491460 AAAAAAATAAAAGGGTTTAGTATACTTATAAAGGAA
1 AAAAAAATAAAAGGGTTTAGTATACTTAAAAAGGAA
** ** * * **
19491496 AAAAAAATAAAAATGACTA-AATCCAAAAAAAAGGAA
1 AAAAAAATAAAAGGGTTTAGTATAC-TTAAAAAGGAA
*
19491532 AAAAAGAATAAAAGGGTTTAGTTTACTTAAAAAGGAA
1 AAAAA-AATAAAAGGGTTTAGTATACTTAAAAAGGAA
19491569 AAA
1 AAA
19491572 CAAAGTGAAA
Statistics
Matches: 55, Mismatches: 18, Indels: 5
0.71 0.23 0.06
Matches are distributed among these distances:
35 3 0.05
36 28 0.51
37 22 0.40
38 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.14, T:0.20
Consensus pattern (36 bp):
AAAAAAATAAAAGGGTTTAGTATACTTAAAAAGGAA
Found at i:19491591 original size:28 final size:27
Alignment explanation
Indices: 19491560--19491628 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 27
19491550 TAGTTTACTT
19491560 AAAAAGGAAAAACAAAGTGAAA-AGAAG-A
1 AAAAAGGAAAAA-AAAG-GAAACA-AAGAA
*
19491588 AAAACGTGAATAAAAAAGGAAACAAAGAA
1 AAAAAG-GAA-AAAAAAGGAAACAAAGAA
19491617 AAAAAGGAAAAA
1 AAAAAGGAAAAA
19491629 TAAAAAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 3 0.09
28 15 0.43
29 14 0.40
30 3 0.09
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.04
Consensus pattern (27 bp):
AAAAAGGAAAAAAAAGGAAACAAAGAA
Found at i:19491782 original size:9 final size:9
Alignment explanation
Indices: 19491757--19491823 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
19491747 AAGGAAACAC
19491757 AAAGAGAAA
1 AAAGAGAAA
19491766 AAA-AGAAA
1 AAAGAGAAA
*
19491774 AAAGTGAAA
1 AAAGAGAAA
19491783 AAAGAAGGAAA
1 AAAG-A-GAAA
19491794 AATAGA-AAA
1 AA-AGAGAAA
19491803 AAAG-GAAA
1 AAAGAGAAA
*
19491811 ATAAAAGAAA
1 A-AAGAGAAA
19491821 AAA
1 AAA
19491824 ATAAAAGGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
8 14 0.29
9 20 0.42
10 5 0.10
11 7 0.15
12 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (9 bp):
AAAGAGAAA
Found at i:19491793 original size:28 final size:26
Alignment explanation
Indices: 19491746--19491829 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 26
19491736 GTTTACTTAT
*
19491746 AAAGGAAACACAAAGAGAAAAAAAGAAA
1 AAAGGAAA-ATAAA-AGAAAAAAAGAAA
*
19491774 AAAGTGAAAA-AAGAAGGAAAAATAGAAAA
1 AAAG-GAAAATAA-AA-GAAAAAAAG-AAA
*
19491803 AAAGGAAAATAAAAGAAAAAAATAAA
1 AAAGGAAAATAAAAGAAAAAAAGAAA
19491829 A
1 A
19491830 GGGTTTAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
26 4 0.08
27 10 0.21
28 21 0.44
29 13 0.27
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (26 bp):
AAAGGAAAATAAAAGAAAAAAAGAAA
Found at i:19491794 original size:19 final size:18
Alignment explanation
Indices: 19491763--19491824 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
19491753 ACACAAAGAG
19491763 AAAAAAAGAAAAAAGT-GA
1 AAAAAAAGAAAAAA-TAGA
*
19491781 AAAAAGAAGGAAAAATAGA
1 AAAAA-AAGAAAAAATAGA
* *
19491800 AAAAAAGGAAAATAAAAGA
1 AAAAAAAGAAAA-AATAGA
19491819 AAAAAA
1 AAAAAA
19491825 TAAAAGGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 11 0.30
19 26 0.70
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (18 bp):
AAAAAAAGAAAAAATAGA
Found at i:19491821 original size:17 final size:17
Alignment explanation
Indices: 19491763--19491822 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
19491753 ACACAAAGAG
*
19491763 AAAAAAAGAAAAAAGTGAA
1 AAAAAAAGGAAAAA-T-AA
* *
19491782 AAAAGAAGGAAAAATAG
1 AAAAAAAGGAAAAATAA
19491799 AAAAAAAGG-AAAATAA
1 AAAAAAAGGAAAAATAA
19491815 AAGAAAAA
1 AA-AAAAA
19491823 AATAAAAGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 8 0.23
17 14 0.40
18 1 0.03
19 12 0.34
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAAAAGGAAAAATAA
Found at i:19491855 original size:91 final size:81
Alignment explanation
Indices: 19491798--19491948 Score: 207
Period size: 80 Copynumber: 1.9 Consensus size: 81
19491788 AGGAAAAATA
* * * *
19491798 GAAAAAAAGGAAAATAAAAGAAAA-AAATAAAAGGGTTTAGTATACTTACAAAGGAGAAAAAAAG
1 GAAAAAAAAGAAAAAAAAATAAAAGAAA-AAAAGGGTTTACTATACTTACAAAGGAGAAAAAAAG
19491862 -AAAAAGAAAAAAGAAG
65 AAAAAAGAAAAAAGAAG
* * *
19491878 GAAAAAAAAGAGAAAAAAATAAAAGGAAAAAAGGGTTTACTATACTTATAAAGGAGAAAAAAAGG
1 GAAAAAAAAGAAAAAAAAATAAAAGAAAAAAAGGGTTTACTATACTTACAAAGGAGAAAAAAA-G
19491943 AAAAAA
65 AAAAAA
19491949 AAATAAAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
80 53 0.87
81 3 0.05
82 5 0.08
ACGTcount: A:0.67, C:0.03, G:0.19, T:0.12
Consensus pattern (81 bp):
GAAAAAAAAGAAAAAAAAATAAAAGAAAAAAAGGGTTTACTATACTTACAAAGGAGAAAAAAAGA
AAAAAGAAAAAAGAAG
Found at i:19491858 original size:182 final size:182
Alignment explanation
Indices: 19491530--19491874 Score: 529
Period size: 184 Copynumber: 1.9 Consensus size: 182
19491520 AAAAAAAAGG
* * *
19491530 AAAAAAAGAATAAAAGGGTTTAGTTTACTTAAAAAGGAAAAACAAAGTGAAAAGAAGAAAAACGT
1 AAAAAAAGAATAAAAGGGTTTAGTTTACTTAAAAAGGAAAAACAAAGAGAAAAAAAGAAAAAAGT
19491595 GAATAAAAAAGGAAACAAAGAAAAAAAGGAAAAATAAAAAGAAAAAAATAAAAGAGTTTAGTATA
66 GAATAAAAAAGGAAACAAAGAAAAAAAGGAAAAATAAAAAGAAAAAAATAAAAGAGTTTAGTATA
* *
19491660 CTTATAAAGGAGAAAAAACGGAAAAAGGAAAAAAGTAAAAATGACTAAATTCAA
131 CTTACAAAGGAGAAAAAA-AGAAAAA-GAAAAAAGTAAAAATGACTAAATTCAA
* * *
19491714 AAAAAAATGAA-AAAATGGTTTAGTTTACTTATAAAGGAAACACAAAGAGAAAAAAAGAAAAAAG
1 AAAAAAA-GAATAAAAGGGTTTAGTTTACTTAAAAAGGAAAAACAAAGAGAAAAAAAGAAAAAAG
*
19491778 TGAA-AAAAGAAGGAAA-AATAGAAAAAAAGG-AAAAT-AAAAGAAAAAAATAAAAGGGTTTAGT
65 TGAATAAAA-AAGGAAACAA-AGAAAAAAAGGAAAAATAAAAAGAAAAAAATAAAAGAGTTTAGT
19491839 ATACTTACAAAGGAGAAAAAAAGAAAAAGAAAAAAG
128 ATACTTACAAAGGAGAAAAAAAGAAAAAGAAAAAAG
19491875 AAGGAAAAAA
Statistics
Matches: 149, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
180 8 0.05
181 6 0.04
182 45 0.30
183 11 0.07
184 76 0.51
185 3 0.02
ACGTcount: A:0.65, C:0.04, G:0.17, T:0.14
Consensus pattern (182 bp):
AAAAAAAGAATAAAAGGGTTTAGTTTACTTAAAAAGGAAAAACAAAGAGAAAAAAAGAAAAAAGT
GAATAAAAAAGGAAACAAAGAAAAAAAGGAAAAATAAAAAGAAAAAAATAAAAGAGTTTAGTATA
CTTACAAAGGAGAAAAAAAGAAAAAGAAAAAAGTAAAAATGACTAAATTCAA
Found at i:19491873 original size:13 final size:12
Alignment explanation
Indices: 19491854--19491909 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 12
19491844 TACAAAGGAG
19491854 AAAAAAAGAAAA
1 AAAAAAAGAAAA
19491866 AGAAAAAAGAAGGAA
1 A-AAAAAAGAA--AA
19491881 AAAAAAGAGAAAA
1 AAAAAA-AGAAAA
19491894 AAATAAAAGGAAAA
1 AAA-AAAA-GAAAA
19491908 AA
1 AA
19491910 GGGTTTACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.03
13 15 0.39
14 15 0.39
15 7 0.18
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:19491896 original size:25 final size:26
Alignment explanation
Indices: 19491847--19491909 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 26
19491837 GTATACTTAC
19491847 AAAGGAGAAAAAAAGAAAAAGAAAA-A
1 AAAGGA-AAAAAAAGAAAAAGAAAATA
*
19491873 AGAAGGAAAAAAAAGAGAAA-AAAATA
1 A-AAGGAAAAAAAAGAAAAAGAAAATA
19491899 AAAGGAAAAAA
1 AAAGGAAAAAA
19491910 GGGTTTACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 14 0.41
26 15 0.44
27 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (26 bp):
AAAGGAAAAAAAAGAAAAAGAAAATA
Found at i:19491951 original size:182 final size:181
Alignment explanation
Indices: 19491530--19491950 Score: 500
Period size: 184 Copynumber: 2.3 Consensus size: 181
19491520 AAAAAAAAGG
* * *
19491530 AAAAAAAGAATAAAAGGGTTTAGTTTACTTAAAAAGGAAAAACAAAGTG-AAAAGAAGAAAAACG
1 AAAAAAAGAA-AAAAGGGTTTAGTTTACTTATAAAGGAAAAA-AAAG-GAAAAAAAAGAAAAAAG
19491594 TGAATAAAAAAGGAAACAAAGAAAAAAAGGAAAAATAAAAAGAAAAAAATAAAAGAGTTTAGTAT
63 TGAATAAAAAAGGAAACAAAGAAAAAAAGGAAAAATAAAAAGAAAAAAATAAAAGAGTTTAGTAT
* * * * * *
19491659 ACTTATAAAGGAGAAAAAACGGAAAAAGGAAAAAAGTAAAAATGACTAAATTCAAA
128 ACTTACAAAGGAGAAAAAACAGAAAAAGAAAAAAAGAAAAAAAGACGAAA-T-AAA
* * *
19491715 AAAAAATGAAAAAATGGTTTAGTTTACTTATAAAGGAAACACAAA-GAGAAAAAAAGAAAAAAGT
1 AAAAAAAGAAAAAAGGGTTTAGTTTACTTATAAAGGAAA-AAAAAGGA-AAAAAAAGAAAAAAGT
*
19491779 GAA-AAAAGAAGGAAA-AATAGAAAAAAAGG-AAAAT-AAAAGAAAAAAATAAAAGGGTTTAGTA
64 GAATAAAA-AAGGAAACAA-AGAAAAAAAGGAAAAATAAAAAGAAAAAAATAAAAGAGTTTAGTA
19491840 TACTTACAAAGGAGAAAAAA-AGAAAAAGAAAAAAGAAGGAAAAAAAAGA-GAAA-AAA
127 TACTTACAAAGGAGAAAAAACAGAAAAAG-AAAAA-AA-G-AAAAAAAGACGAAATAAA
* * * *
19491896 ATAAAAGGAAAAAAGGGTTTACTATACTTATAAAGGAGAAAAAAAGGAAAAAAAA
1 AAAAAAAGAAAAAAGGGTTTAGTTTACTTATAAAGGA-AAAAAAAGGAAAAAAAA
19491951 ATAAAAATGA
Statistics
Matches: 206, Mismatches: 19, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
181 53 0.26
182 54 0.26
183 13 0.06
184 69 0.33
185 17 0.08
ACGTcount: A:0.65, C:0.04, G:0.17, T:0.14
Consensus pattern (181 bp):
AAAAAAAGAAAAAAGGGTTTAGTTTACTTATAAAGGAAAAAAAAGGAAAAAAAAGAAAAAAGTGA
ATAAAAAAGGAAACAAAGAAAAAAAGGAAAAATAAAAAGAAAAAAATAAAAGAGTTTAGTATACT
TACAAAGGAGAAAAAACAGAAAAAGAAAAAAAGAAAAAAAGACGAAATAAA
Found at i:19491991 original size:26 final size:26
Alignment explanation
Indices: 19491943--19491999 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
19491933 GAAAAAAAGG
* *
19491943 AAAAAAAAATAAAAATGACTAAATTCA
1 AAAAAAAAAGAAAAATGACTAAAGT-A
19491970 AAAAAAAAAGAAAAA-GTA-TAAAGTA
1 AAAAAAAAAGAAAAATG-ACTAAAGTA
19491995 AAAAA
1 AAAAA
19492000 GAATAAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.22
26 6 0.22
27 15 0.56
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (26 bp):
AAAAAAAAAGAAAAATGACTAAAGTA
Found at i:19492570 original size:9 final size:9
Alignment explanation
Indices: 19492553--19492610 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
19492543 NNNNNNNNNN
19492553 AAAAA-AAA
1 AAAAAGAAA
19492561 AAAAAGAAA
1 AAAAAGAAA
*
19492570 AAATGGAGAAA
1 AAA--AAGAAA
*
19492581 AATAGAGAAA
1 AA-AAAGAAA
19492591 AAAAAGAAA
1 AAAAAGAAA
*
19492600 AAAAATAAA
1 AAAAAGAAA
19492609 AA
1 AA
19492611 GTTACTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
8 5 0.12
9 22 0.51
10 8 0.19
11 7 0.16
12 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:19492687 original size:20 final size:21
Alignment explanation
Indices: 19492664--19492710 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
19492654 GTAGACTTAT
*
19492664 AAAGGAGAAA-AA-AAGAGAAA
1 AAAGAAGAAAGAAGAAGA-AAA
19492684 AAAGAAGAAAGAAGAAGAAAA
1 AAAGAAGAAAGAAGAAGAAAA
19492705 AAAGAA
1 AAAGAA
19492711 AATAAAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 11 0.46
22 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
AAAGAAGAAAGAAGAAGAAAA
Found at i:19492739 original size:70 final size:67
Alignment explanation
Indices: 19492626--19492777 Score: 193
Period size: 70 Copynumber: 2.2 Consensus size: 67
19492616 TAAATTTGAG
* *
19492626 AAAAAG-GGAAAAAGAATAAAAGGGTTTAGTAGACTTATAAAGGAGAAAAAAAGAGAAAAAAGAA
1 AAAAAGAGAAAAAAGAAAAAAAGGGTTTAGTAGACTTATAAAGGAG-AAAAAAGA-AAAAAAGAA
19492690 -GAA
64 GGAA
* * *
19492693 AGAAGAAGA-AAAAAAGAAAATAAAGGGTTTAGTATATTTATAAAGGAGGAAAAAGAAAAAAAGA
1 A-AA-AAGAGAAAAAAGAAAA-AAAGGGTTTAGTAGACTTATAAAGGAGAAAAAAGAAAAAAAGA
19492757 AGGAA
63 AGGAA
19492762 AAAAAGAGAAAAAAGA
1 AAAAAGAGAAAAAAGA
19492778 GGGAAAAGCA
Statistics
Matches: 74, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
67 5 0.07
68 21 0.28
69 23 0.31
70 25 0.34
ACGTcount: A:0.64, C:0.01, G:0.23, T:0.12
Consensus pattern (67 bp):
AAAAAGAGAAAAAAGAAAAAAAGGGTTTAGTAGACTTATAAAGGAGAAAAAAGAAAAAAAGAAGG
AA
Found at i:19492759 original size:21 final size:21
Alignment explanation
Indices: 19492742--19492818 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
19492732 ATAAAGGAGG
19492742 AAAAAGA-AAAAAAGAAGGAA
1 AAAAAGAGAAAAAAGAAGGAA
*
19492762 AAAAAGAGAAAAAAGAGGGAA
1 AAAAAGAGAAAAAAGAAGGAA
* *
19492783 AAGCAAAAATG-AAAAATAAGGAA
1 AA--AAAGA-GAAAAAAGAAGGAA
*
19492806 AAAAGGA-AAAAAA
1 AAAAAGAGAAAAAA
19492819 TTAAAAAGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
20 12 0.26
21 17 0.37
23 16 0.35
24 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.21, T:0.03
Consensus pattern (21 bp):
AAAAAGAGAAAAAAGAAGGAA
Found at i:19492760 original size:18 final size:19
Alignment explanation
Indices: 19492734--19492784 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
19492724 GTATATTTAT
*
19492734 AAAGGAGGAAAAAGA-AAA
1 AAAGAAGGAAAAAGAGAAA
19492752 AAAGAAGGAAAAAAAGAGAAA
1 AAAGAAGG--AAAAAGAGAAA
*
19492773 AAAGAGGGAAAA
1 AAAGAAGGAAAA
19492785 GCAAAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 7 0.25
19 4 0.14
20 7 0.25
21 10 0.36
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (19 bp):
AAAGAAGGAAAAAGAGAAA
Found at i:19492815 original size:7 final size:8
Alignment explanation
Indices: 19492751--19492840 Score: 54
Period size: 9 Copynumber: 10.5 Consensus size: 8
19492741 GAAAAAGAAA
19492751 AAAAGAAGG
1 AAAA-AAGG
19492760 AAAAAAAGAG
1 -AAAAAAG-G
19492770 AAAAAAGAG
1 AAAAAAG-G
** *
19492779 GGAAAAGC
1 AAAAAAGG
* *
19492787 AAAAATGA
1 AAAAAAGG
19492795 AAAATAAGG
1 AAAA-AAGG
19492804 AAAAAAGG
1 AAAAAAGG
**
19492812 AAAAAAAT
1 AAAAAAGG
*
19492820 TAAAAAGAG
1 AAAAAAG-G
19492829 AAAAAAGG
1 AAAAAAGG
19492837 AAAA
1 AAAA
19492841 TAAAAGGATT
Statistics
Matches: 62, Mismatches: 15, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
8 28 0.45
9 29 0.47
10 5 0.08
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.04
Consensus pattern (8 bp):
AAAAAAGG
Found at i:19492833 original size:9 final size:9
Alignment explanation
Indices: 19492742--19492840 Score: 59
Period size: 8 Copynumber: 11.3 Consensus size: 9
19492732 ATAAAGGAGG
19492742 AAAAAGA-A
1 AAAAAGAGA
19492750 AAAAAGAAGGAA
1 AAAAAG-A-G-A
19492762 AAAAAGAGA
1 AAAAAGAGA
*
19492771 AAAAAGAGG
1 AAAAAGAGA
* *
19492780 GAAAAG-CA
1 AAAAAGAGA
*
19492788 AAAATGA-A
1 AAAAAGAGA
19492796 AAATAAG-GA
1 AAA-AAGAGA
19492805 AAAAAG-GA
1 AAAAAGAGA
**
19492813 AAAAA-ATT
1 AAAAAGAGA
19492821 AAAAAGAGA
1 AAAAAGAGA
19492830 AAAAAG-GA
1 AAAAAGAGA
19492838 AAA
1 AAA
19492841 TAAAAGGATT
Statistics
Matches: 71, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
8 34 0.48
9 28 0.39
10 1 0.01
11 1 0.01
12 7 0.10
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.04
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:19493026 original size:9 final size:9
Alignment explanation
Indices: 19493012--19493080 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 9
19493002 TATGAAAGAC
19493012 AAAAAAAGG
1 AAAAAAAGG
19493021 AAAAAAA--
1 AAAAAAAGG
* *
19493028 ATAAAAAGA
1 AAAAAAAGG
19493037 AAAAAGAAGG
1 AAAAA-AAGG
*
19493047 AAAAAGA-G
1 AAAAAAAGG
*
19493055 AAAAAAGGG
1 AAAAAAAGG
19493064 AAAATAAAAGG
1 -AAA-AAAAGG
19493075 AAAAAA
1 AAAAAA
19493081 TTAAAAAGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
7 6 0.13
8 6 0.13
9 16 0.34
10 14 0.30
11 5 0.11
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:19493059 original size:26 final size:25
Alignment explanation
Indices: 19493006--19493088 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 25
19492996 TATACTTATG
19493006 AAAGACAAAAAAAGGAAAAAAAATAA
1 AAAGA-AAAAAAAGGAAAAAAAATAA
19493032 AAAGAAAAAAGAAGGAAAAAGAGAA-AA
1 AAAGAAAAAA-AAGGAAAAA-A-AATAA
* *
19493059 AAGGGAAAATAAAAGG-AAAAAATTAA
1 AA-AGAAAA-AAAAGGAAAAAAAATAA
19493085 AAAG
1 AAAG
19493089 GTTTAGTATA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
25 7 0.15
26 19 0.40
27 9 0.19
28 11 0.23
29 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (25 bp):
AAAGAAAAAAAAGGAAAAAAAATAA
Found at i:19493065 original size:17 final size:17
Alignment explanation
Indices: 19493030--19493072 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
19493020 GAAAAAAAAT
19493030 AAAAAGAAAAAAGAAGG
1 AAAAAGAAAAAAGAAGG
*
19493047 AAAAAGAGAAAA-AAGG
1 AAAAAGAAAAAAGAAGG
* *
19493063 GAAAATAAAA
1 AAAAAGAAAA
19493073 GGAAAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAAGAAGG
Found at i:19493108 original size:88 final size:83
Alignment explanation
Indices: 19493016--19493233 Score: 213
Period size: 88 Copynumber: 2.5 Consensus size: 83
19493006 AAAGACAAAA
* * * *
19493016 AAAGGAAAAAAAATAAAAAGAAAAAAGAAGGAAAAAGAGAAAA-AAGGGAAAATAAAAGGAAAAA
1 AAAGGAGAAAAAAGAAAAAGAAAAAAGAA-GAAAAAAAGAAAATAAAGG-AAA-AAAAGG--AAA
*
19493080 ATTAAAAAGGTTTAGTATACTTAT
61 A-TAAAAAGGTTTAGTACACTTAT
** * *
19493104 AAAGGAGGCAAAAGAAAAAGAAGGAAAAGTAAAAAAAATAAAAAAATTAAAGGAAAAAAAGGAAA
1 AAAGGAGAAAAAAGAAAAAGAA--AAAAG-AAGAAAAA-AAGAAAA-TAAAGGAAAAAAAGGAAA
*
19493169 ATAAAAGGGTTTAGTACACTTAT
61 ATAAAAAGGTTTAGTACACTTAT
* *
19493192 AAAGGAGGAAAAAAGAAAAATAAAAAAAAAGAAAAAAAGAAA
1 AAAGGA-GAAAAAAGAAAAAGAAAAAAGAAGAAAAAAAGAAA
19493234 CAAAAAAGGA
Statistics
Matches: 107, Mismatches: 16, Indels: 17
0.76 0.11 0.12
Matches are distributed among these distances:
85 5 0.05
86 7 0.07
87 4 0.04
88 44 0.41
89 17 0.16
90 10 0.09
91 13 0.12
92 3 0.03
93 4 0.04
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.11
Consensus pattern (83 bp):
AAAGGAGAAAAAAGAAAAAGAAAAAAGAAGAAAAAAAGAAAATAAAGGAAAAAAAGGAAAATAAA
AAGGTTTAGTACACTTAT
Found at i:19493206 original size:329 final size:331
Alignment explanation
Indices: 19492812--19493418 Score: 811
Period size: 329 Copynumber: 1.8 Consensus size: 331
19492802 GGAAAAAAGG
* *
19492812 AAAAAAATTAAAAAGAGAAAAAAGGAAAATAAAAGGATTTAGTATACTTATGAAGGAGAAAAAAA
1 AAAAAAATTAAAAAGAGAAAAAAGGAAAATAAAAGGATTTAGTACACTTATAAAGGAGAAAAAAA
* * * * *
19492877 GAAAAATAAATAATAAGGAAAAAAAGAGAA-ATAAAAGGAAAAAAATTACTAAAT-C-GAAAAAA
66 GAAAAATAAA-AAAAAAGAAAAAAAGA-AACAAAAAAGGAAAAAAATGACTAAATCCAAAAAAAA
** * * * *
19492939 AAA-GCATAAATGAATAAAAGGGTTTAGTA-TAAAGTAAAAAATATAAATGGGGTTTAGTATACT
129 AAATAAATAAATGAATAAAAGGGTTTAATACAAAAG-AAAAAACATAAA-AGGGTTTAGTATACT
*
19493002 TATGAAA-GACAAAAAAAGGAAAAAAAATAA-AAAGAAAAAAGAAGGAAAAAGAGAAAAAAGGGA
192 T-TGAAAGGACAAAAAAAGGAAAAAAAATAAGAAAGAAAAAAGAA--AAAAAGAGAAAAAAAGGA
*
19493065 A-AATAAAAGGAAAAAATTAAAAAGGTTTAGTATACTTATAAAGGAGGCAAAAGAAAAAGAAGGA
254 AGAA-AAAAGGAAAAAAATAAAAAGGTTTAGTATACTTATAAAGGAGGCAAAAGAAAAAGAAGGA
19493129 AAAGTAAAAAAAAT
318 AAAGTAAAAAAAAT
* * *
19493143 AAAAAAATT-AAAGGA-AAAAAAGGAAAATAAAAGGGTTTAGTACACTTATAAAGGAGGAAAAAA
1 AAAAAAATTAAAAAGAGAAAAAAGGAAAATAAAAGGATTTAGTACACTTATAAAGGAGAAAAAAA
* *
19493206 GAAAAATAAAAAAAAAGAAAAAAAGAAACAAAAAAGGAAAAGAATGATTAAATCCAAAAAAAAAA
66 GAAAAATAAAAAAAAAGAAAAAAAGAAACAAAAAAGGAAAAAAATGACTAAATCCAAAAAAAAAA
*
19493271 ATAAATAAATGAATAAAAGGGTTTAATACAAAAGAAAAAACATAAAAGGGTTTAGTATACTTTTA
131 ATAAATAAATGAATAAAAGGGTTTAATACAAAAGAAAAAACATAAAAGGGTTTAGTATACTTTGA
* * * * * * *
19493336 AAGGAGAAAAAAAGGGAAACAATTAAGAAAGAAGAAGGAAAAAAAGGGAAAAAAAGGAATGAAAA
196 AAGGACAAAAAAAGGAAAAAAAATAAGAAAGAAAAAAGAAAAAAAGAGAAAAAAAGGAA-GAAAA
19493401 AAGGAAAAAAATAAAAAG
260 AAGGAAAAAAATAAAAAG
19493419 AGAAAATAAA
Statistics
Matches: 239, Mismatches: 28, Indels: 19
0.84 0.10 0.07
Matches are distributed among these distances:
327 2 0.01
328 34 0.14
329 76 0.32
330 67 0.28
331 56 0.23
332 4 0.02
ACGTcount: A:0.65, C:0.03, G:0.17, T:0.15
Consensus pattern (331 bp):
AAAAAAATTAAAAAGAGAAAAAAGGAAAATAAAAGGATTTAGTACACTTATAAAGGAGAAAAAAA
GAAAAATAAAAAAAAAGAAAAAAAGAAACAAAAAAGGAAAAAAATGACTAAATCCAAAAAAAAAA
ATAAATAAATGAATAAAAGGGTTTAATACAAAAGAAAAAACATAAAAGGGTTTAGTATACTTTGA
AAGGACAAAAAAAGGAAAAAAAATAAGAAAGAAAAAAGAAAAAAAGAGAAAAAAAGGAAGAAAAA
AGGAAAAAAATAAAAAGGTTTAGTATACTTATAAAGGAGGCAAAAGAAAAAGAAGGAAAAGTAAA
AAAAAT
Found at i:19493238 original size:19 final size:19
Alignment explanation
Indices: 19493207--19493246 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
19493197 AGGAAAAAAG
*
19493207 AAAAATAAAAAAAAA-GAA
1 AAAAAGAAAAAAAAAGGAA
19493225 AAAAAGAAACAAAAAAGGAA
1 AAAAAGAAA-AAAAAAGGAA
19493245 AA
1 AA
19493247 GAATGATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAAAAAAAGGAA
Found at i:19493387 original size:10 final size:9
Alignment explanation
Indices: 19493370--19493449 Score: 65
Period size: 10 Copynumber: 8.3 Consensus size: 9
19493360 AAGAAAGAAG
19493370 AAGGAAAAA
1 AAGGAAAAA
19493379 AAGGGAAAAA
1 AA-GGAAAAA
19493389 AAGGAATGAAAA
1 AAGG-A--AAAA
19493401 AAGGAAAAA
1 AAGGAAAAA
*
19493410 AA-TAAAAA
1 AAGGAAAAA
*
19493418 GA-GAAAATA
1 AAGGAAAA-A
19493427 AAGGAAAATA
1 AAGGAAAA-A
19493437 AAGAGAAAAA
1 AAG-GAAAAA
19493447 AAG
1 AAG
19493450 ATTTAGTATA
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
8 10 0.17
9 12 0.20
10 24 0.40
11 6 0.10
12 8 0.13
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (9 bp):
AAGGAAAAA
Found at i:19493410 original size:32 final size:32
Alignment explanation
Indices: 19493335--19493411 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 32
19493325 GTATACTTTT
19493335 AAAGGAGAAAAAAAGGGAAACAATTAAGAAAGAA
1 AAAGGA-AAAAAAAGGGAAACAA-TAAGAAAGAA
* *
19493369 GAAGG-AAAAAAAGGGAAA-AA-AAGGAATGAAA
1 AAAGGAAAAAAAAGGGAAACAATAA-GAAAG-AA
19493400 AAAGGAAAAAAA
1 AAAGGAAAAAAA
19493412 TAAAAAGAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
29 2 0.05
30 4 0.11
31 8 0.22
32 19 0.51
34 4 0.11
ACGTcount: A:0.70, C:0.01, G:0.25, T:0.04
Consensus pattern (32 bp):
AAAGGAAAAAAAAGGGAAACAATAAGAAAGAA
Found at i:19493495 original size:80 final size:79
Alignment explanation
Indices: 19493397--19493569 Score: 201
Period size: 79 Copynumber: 2.2 Consensus size: 79
19493387 AAAAGGAATG
*
19493397 AAAAAAGGAAAAAAATAAAAAGA-GAAA-ATAAAGGAAAATAAAGAGAA-AAAAAGATTTAGTAT
1 AAAAAAGGAAAAAAATAAAAAGACGAAATATAAA--AAAA-AAA-AGAATAAAAAGACTTAGTAT
19493459 ACTTATAAAGGAGA-AGA
62 ACTTATAAAGGAGAGAGA
* * * * * *
19493476 AAAAGAAGGAAAATAATAAAATGACTAAATCTAAAAAAAAAAAGAATAAAAGGGCTTAGTATACT
1 AAAA-AAGGAAAAAAATAAAAAGACGAAATATAAAAAAAAAAAGAATAAAAAGACTTAGTATACT
19493541 TATAAAGGAGAGAGA
65 TATAAAGGAGAGAGA
19493556 AAAAAAGAGAAAAA
1 AAAAAAG-GAAAAA
19493570 TAGGAAAATA
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
78 4 0.05
79 36 0.45
80 33 0.41
81 3 0.04
82 4 0.05
ACGTcount: A:0.65, C:0.03, G:0.17, T:0.14
Consensus pattern (79 bp):
AAAAAAGGAAAAAAATAAAAAGACGAAATATAAAAAAAAAAAGAATAAAAAGACTTAGTATACTT
ATAAAGGAGAGAGA
Found at i:19493665 original size:15 final size:16
Alignment explanation
Indices: 19493634--19493674 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
19493624 AAAGAAAATG
*
19493634 AAAA-AGGAAAGATAA
1 AAAAGAGGAAAGAGAA
19493649 AAAAGAGGAAAG-GAA
1 AAAAGAGGAAAGAGAA
*
19493664 AAAAGAAGAAA
1 AAAAGAGGAAA
19493675 AAAAAAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (16 bp):
AAAAGAGGAAAGAGAA
Found at i:19493672 original size:27 final size:27
Alignment explanation
Indices: 19493619--19493681 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
19493609 TTATAAAGGG
* *
19493619 TAAAAAAAGAAAATGAAAAAGGAAAGA
1 TAAAAAAAGAAAAGGAAAAAAGAAAGA
*
19493646 TAAAAAAGAGGAAAGGAAAAAAG-AAGA
1 TAAAAAA-AGAAAAGGAAAAAAGAAAGA
*
19493673 AAAAAAAAG
1 TAAAAAAAG
19493682 GGTTTAGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 2 0.06
27 17 0.55
28 12 0.39
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.05
Consensus pattern (27 bp):
TAAAAAAAGAAAAGGAAAAAAGAAAGA
Found at i:19494514 original size:52 final size:51
Alignment explanation
Indices: 19494409--19494531 Score: 158
Period size: 52 Copynumber: 2.4 Consensus size: 51
19494399 TAAGTCTTTG
19494409 TATCGTTCGTTCAAGACCAAGTCATCATTAGACCCTTAAGGCGAAGTCCCCA
1 TATCGTT-GTTCAAGACCAAGTCATCATTAGACCCTTAAGGCGAAGTCCCCA
* * * *
19494461 TATCAGTTGTTCAAGACTAAGTCATCATTAGACCCTTGAA-GTGAGGTCTCCA
1 TATC-GTTGTTCAAGACCAAGTCATCATTAGACCCTT-AAGGCGAAGTCCCCA
*
19494513 TATTGTTTGTTCAAGACCA
1 TATCG-TTGTTCAAGACCA
19494532 TGTTGGTCCC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
51 1 0.02
52 56 0.90
53 5 0.08
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (51 bp):
TATCGTTGTTCAAGACCAAGTCATCATTAGACCCTTAAGGCGAAGTCCCCA
Found at i:19495407 original size:74 final size:73
Alignment explanation
Indices: 19495304--19495492 Score: 207
Period size: 74 Copynumber: 2.6 Consensus size: 73
19495294 CAGAGTGCTT
* * * * * *
19495304 TTAGTTGACTAACATACTACTTAGTCGATTAAGTCGTCTCTGTCTTCTAATCTCAGTTTTTGGCA
1 TTAGTTGACTAACATGCTTCTTAGTCGATTAAGTCATCTCTGTCTTCTAATCTAAGTTTCTGACA
19495369 GTGAGCTC
66 GTGAGCTC
* * *
19495377 TTAGTTGACTAACAATGCTTCTTAGTCGATTAAGTTATTTCTGTCTTTTAATCTAAGTTTCTGAC
1 TTAGTTGACTAAC-ATGCTTCTTAGTCGATTAAGTCATCTCTGTCTTCTAATCTAAGTTTCTGAC
*
19495442 AGTGGGCTC
65 AGTGAGCTC
* * * * * * *
19495451 GTAGTTGATTAGCCATGCTTCTTGGTTGACTAAGTCTTCTCT
1 TTAGTTGACTA-ACATGCTTCTTAGTCGATTAAGTCATCTCT
19495493 ATCTCTGAAC
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
73 13 0.14
74 81 0.85
75 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (73 bp):
TTAGTTGACTAACATGCTTCTTAGTCGATTAAGTCATCTCTGTCTTCTAATCTAAGTTTCTGACA
GTGAGCTC
Found at i:19495814 original size:52 final size:52
Alignment explanation
Indices: 19495733--19495873 Score: 167
Period size: 52 Copynumber: 2.7 Consensus size: 52
19495723 AAAGCCAACA
* * *
19495733 AAGTCATCATCAGACCCTT-AAAGCAAAGTCTCCATATCATTTACTCAAAACC
1 AAGTCATCATCAGACCTTTGAAA-CGAAGTCTCCAAATCATTTACTCAAAACC
* * ** * *
19495785 AAGTCATCATCAGACCTTTGAAACGAAGTCTCTAAATTATTTGTTCAAGATC
1 AAGTCATCATCAGACCTTTGAAACGAAGTCTCCAAATCATTTACTCAAAACC
* *
19495837 AAGTCATCATCAAACCTATGAAACGAAGTCTCCAAAT
1 AAGTCATCATCAGACCTTTGAAACGAAGTCTCCAAAT
19495874 TGTTCGTTCA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
52 73 0.96
53 3 0.04
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (52 bp):
AAGTCATCATCAGACCTTTGAAACGAAGTCTCCAAATCATTTACTCAAAACC
Found at i:19495874 original size:52 final size:51
Alignment explanation
Indices: 19495784--19495944 Score: 207
Period size: 52 Copynumber: 3.1 Consensus size: 51
19495774 TACTCAAAAC
* * * *
19495784 CAAGTCATCATCAGACCTTTGAAACGAAGTCTCTAAATTATTTGTTCAAGAT
1 CAAGTCATCATCAAACC-TTGAAACGAAGTCTCCAAATTGTTCGTTCAAGAT
19495836 CAAGTCATCATCAAACCTATGAAACGAAGTCTCCAAATTGTTCGTTCAAGAT
1 CAAGTCATCATCAAACCT-TGAAACGAAGTCTCCAAATTGTTCGTTCAAGAT
* * * *
19495888 CAAGTCATCAT-AAGACCCTTGAAATGAAATCTTCAAATCGTTCGTTCAAGAT
1 CAAGTCATCATCAA-A-CCTTGAAACGAAGTCTCCAAATTGTTCGTTCAAGAT
19495940 CAAGT
1 CAAGT
19495945 TGGAAACCCT
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
51 3 0.03
52 92 0.94
53 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (51 bp):
CAAGTCATCATCAAACCTTGAAACGAAGTCTCCAAATTGTTCGTTCAAGAT
Found at i:19496059 original size:41 final size:40
Alignment explanation
Indices: 19495931--19496064 Score: 171
Period size: 39 Copynumber: 3.4 Consensus size: 40
19495921 CAAATCGTTC
*
19495931 GTTCAAGATCAAGTTGGAAACCCTTGAATCAAAATACGAA
1 GTTCAAGATCAAGTTGAAAACCCTTGAATCAAAATACGAA
* * * *
19495971 GTTCAAAATCAAGTCGTAAACCC-TGAATCAAAATACTAA
1 GTTCAAGATCAAGTTGAAAACCCTTGAATCAAAATACGAA
* **
19496010 GTTCAAGATCAAGTTGCAAAACCCTTGAAACAATGTACGAA
1 GTTCAAGATCAAGTTG-AAAACCCTTGAATCAAAATACGAA
*
19496051 GTTTAAGATCAAGT
1 GTTCAAGATCAAGT
19496065 CATCATGACC
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 29 0.36
40 26 0.32
41 25 0.31
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (40 bp):
GTTCAAGATCAAGTTGAAAACCCTTGAATCAAAATACGAA
Found at i:19496946 original size:29 final size:29
Alignment explanation
Indices: 19496904--19496991 Score: 142
Period size: 29 Copynumber: 3.0 Consensus size: 29
19496894 AATGCATTGG
*
19496904 TTGAGTTTTATGGATTGAAAATTG-TTCAC
1 TTGAGTTTTATGGATTGAAAAATGATT-AC
19496933 TTGAGTTTTATGGATTGAAAAATGATTAC
1 TTGAGTTTTATGGATTGAAAAATGATTAC
*
19496962 TTGAGTTATATGGATTGAAAAATGATTAC
1 TTGAGTTTTATGGATTGAAAAATGATTAC
19496991 T
1 T
19496992 AAATGTTATA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
29 54 0.96
30 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (29 bp):
TTGAGTTTTATGGATTGAAAAATGATTAC
Found at i:19497006 original size:29 final size:29
Alignment explanation
Indices: 19496907--19497009 Score: 111
Period size: 29 Copynumber: 3.6 Consensus size: 29
19496897 GCATTGGTTG
* * **
19496907 AGTTTTATGGATTGAAAATTG-TTCACTTG
1 AGTTATATGGATTGAAAAATGATT-ACTAA
* **
19496936 AGTTTTATGGATTGAAAAATGATTACTTG
1 AGTTATATGGATTGAAAAATGATTACTAA
19496965 AGTTATATGGATTGAAAAATGATTACTAA
1 AGTTATATGGATTGAAAAATGATTACTAA
19496994 ATGTTATAT-GATTGAA
1 A-GTTATATGGATTGAA
19497010 TCTTATTGGA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
29 59 0.87
30 9 0.13
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (29 bp):
AGTTATATGGATTGAAAAATGATTACTAA
Found at i:19506434 original size:24 final size:24
Alignment explanation
Indices: 19506406--19506451 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
19506396 GACTCATTAT
19506406 GAGAA-AAGCTTGATTATAGGAATA
1 GAGAAGAA-CTTGATTATAGGAATA
*
19506430 GAGAAGAACTTGATTGTAGGAA
1 GAGAAGAACTTGATTATAGGAA
19506452 CAGTAGCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.43, C:0.04, G:0.28, T:0.24
Consensus pattern (24 bp):
GAGAAGAACTTGATTATAGGAATA
Found at i:19513458 original size:38 final size:39
Alignment explanation
Indices: 19513372--19513474 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 39
19513362 ACCCGGCTCA
*
19513372 TGTACATCCCCCCACATCGTGCA-GATAGTCGACACCATCG
1 TGTACATCCCCCCACATCGTGCACAATAGTCG--ACCATCG
* *
19513412 TGTGCATCCCCCCACATCGTGCACAATCAGT-G-TCATCG
1 TGTACATCCCCCCACATCGTGCACAAT-AGTCGACCATCG
19513450 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
19513475 CGGGCACTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
38 29 0.51
40 22 0.39
41 3 0.05
42 3 0.05
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACAATAGTCGACCATCG
Found at i:19515091 original size:31 final size:32
Alignment explanation
Indices: 19515055--19515114 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
19515045 TTTTTCTTAT
* *
19515055 TTGGGCTAAGCCCATTTATTTT-TATTTCCTA
1 TTGGGCCAAGCCCACTTATTTTCTATTTCCTA
*
19515086 TTGGGCCATGCCCACTTATTTTCTATTTC
1 TTGGGCCAAGCCCACTTATTTTCTATTTC
19515115 TTTTCTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (32 bp):
TTGGGCCAAGCCCACTTATTTTCTATTTCCTA
Found at i:19515141 original size:16 final size:16
Alignment explanation
Indices: 19515104--19515138 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19515094 TGCCCACTTA
19515104 TTTTCTATTTCTTTTC
1 TTTTCTATTTCTTTTC
*
19515120 TTTTCTTTTTC-TTTC
1 TTTTCTATTTCTTTTC
19515135 TTTT
1 TTTT
19515139 TCTCTCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTATTTCTTTTC
Found at i:19515847 original size:20 final size:20
Alignment explanation
Indices: 19515824--19515863 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19515814 GTATTCTTTG
*
19515824 CTTTTTTTTTATCTTTCTTC
1 CTTTCTTTTTATCTTTCTTC
* *
19515844 CTTTCTTTNTATTTTTCTTC
1 CTTTCTTTTTATCTTTCTTC
19515864 TCCCACTCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.72
Consensus pattern (20 bp):
CTTTCTTTTTATCTTTCTTC
Found at i:19515887 original size:154 final size:153
Alignment explanation
Indices: 19515691--19516005 Score: 612
Period size: 154 Copynumber: 2.1 Consensus size: 153
19515681 GCTTTTGGTT
*
19515691 CTTTCCTTTATTTTTCTTCTCCCACTCTCAACCGACTTCCTCTCCTTTCTCTCTTTTATCTCTTT
1 CTTTCTTTTATTTTTCTTCTCCCACTCTCAACCGACTTCCTCTCCTTTCTCTCTTTTATCTCTTT
19515756 TTCATTTCTTTCATCTCACATGGCCAGCCCCACCATCATTTCTACATTCTTCTCTTTTGTATTCT
66 TTCATTTCTTTCATCTCACATGGCCAGCCCCACCATCATTTCTACATTCTTCTCTTTTGTATTCT
19515821 TTGCTTTTTTTTTATCTTTCTTC
131 TTGCTTTTTTTTTATCTTTCTTC
19515844 CTTTCTTTNTATTTTTCTTCTCCCACTCTCAACCGACTTCCTCTCCTTTCTCTCTTTTATCTCTT
1 CTTTCTTT-TATTTTTCTTCTCCCACTCTCAACCGACTTCCTCTCCTTTCTCTCTTTTATCTCTT
19515909 TTTCATTTCTTTCATCTCACATGGCCAGCCCCACCATCATTTCTACATTCTTCTCTTTTGTATTC
65 TTTCATTTCTTTCATCTCACATGGCCAGCCCCACCATCATTTCTACATTCTTCTCTTTTGTATTC
19515974 TTTGCTTTTTTTTTATCTTTCTTC
130 TTTGCTTTTTTTTTATCTTTCTTC
19515998 CTTTCTTT
1 CTTTCTTT
19516006 CTTTTATTCT
Statistics
Matches: 160, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
153 7 0.04
154 153 0.96
ACGTcount: A:0.11, C:0.31, G:0.04, T:0.53
Consensus pattern (153 bp):
CTTTCTTTTATTTTTCTTCTCCCACTCTCAACCGACTTCCTCTCCTTTCTCTCTTTTATCTCTTT
TTCATTTCTTTCATCTCACATGGCCAGCCCCACCATCATTTCTACATTCTTCTCTTTTGTATTCT
TTGCTTTTTTTTTATCTTTCTTC
Found at i:19531736 original size:2 final size:2
Alignment explanation
Indices: 19531729--19531770 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19531719 GCTTCCATAA
19531729 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19531771 AGCTTCAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:19539205 original size:20 final size:20
Alignment explanation
Indices: 19539180--19539219 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19539170 CTATAAATAT
19539180 CTCATTTCTCT-AGCAGCTTC
1 CTCATTT-TCTGAGCAGCTTC
*
19539200 CTCATTTTTTGAGCAGCTTC
1 CTCATTTTCTGAGCAGCTTC
19539220 TTGCTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.15, C:0.30, G:0.12, T:0.42
Consensus pattern (20 bp):
CTCATTTTCTGAGCAGCTTC
Found at i:19539923 original size:2 final size:2
Alignment explanation
Indices: 19539916--19539954 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
19539906 TGTAATGTTG
* *
19539916 AT AT AT AT AT AT AT AT AT AT AT CT AA AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
19539955 GTATTGATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:19543201 original size:43 final size:45
Alignment explanation
Indices: 19543149--19543250 Score: 116
Period size: 47 Copynumber: 2.2 Consensus size: 45
19543139 TCATATAAAA
* *
19543149 AAATAATAATACAAAGTAAAGATA-TTTCCTAAATCAAGTAATGAAC
1 AAATAATAA-ATAAA-TAAAAATACTTTCCTAAATCAAGTAATGAAC
**
19543195 AAATAATAAATTGAAATAAAAATACTTTCCTATGTCAAGTAATGAAC
1 AAATAATAAA-T-AAATAAAAATACTTTCCTAAATCAAGTAATGAAC
*
19543242 GAATAATAA
1 AAATAATAA
19543251 CTTAGAGTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
45 1 0.02
46 16 0.33
47 31 0.65
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (45 bp):
AAATAATAAATAAATAAAAATACTTTCCTAAATCAAGTAATGAAC
Found at i:19543338 original size:36 final size:36
Alignment explanation
Indices: 19543286--19543356 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
19543276 AAAAGCGCAG
*
19543286 GCAAAAATAATGAATCAAGATAAAATATTTTCCTAA
1 GCAAAAATAATAAATCAAGATAAAATATTTTCCTAA
*
19543322 GCAAAAATAATAAATCAAGGTAAAATATTTTCCTA
1 GCAAAAATAATAAATCAAGATAAAATATTTTCCTA
19543357 TGCTAAATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.28
Consensus pattern (36 bp):
GCAAAAATAATAAATCAAGATAAAATATTTTCCTAA
Found at i:19543560 original size:34 final size:34
Alignment explanation
Indices: 19543497--19543563 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
19543487 AAATGAGTGT
*
19543497 GAAACCCTCACAATAGCTTTTTACGAGATCAAGC
1 GAAACCCTCACAATAGCTTTTTACAAGATCAAGC
* *
19543531 GAAACCCTCAGAAT-GCTTTTTCATAAGATCAAG
1 GAAACCCTCACAATAGCTTTTT-ACAAGATCAAG
19543564 TGGAACCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (34 bp):
GAAACCCTCACAATAGCTTTTTACAAGATCAAGC
Found at i:19544861 original size:28 final size:28
Alignment explanation
Indices: 19544821--19544897 Score: 127
Period size: 28 Copynumber: 2.8 Consensus size: 28
19544811 TTCAATACAA
*
19544821 TGCCTTTTAAAGGTTCAAGCATAACCAT
1 TGCCTTTTCAAGGTTCAAGCATAACCAT
* *
19544849 TGCCTTTTCAAGGATGAAGCATAACCAT
1 TGCCTTTTCAAGGTTCAAGCATAACCAT
19544877 TGCCTTTTCAAGGTTCAAGCA
1 TGCCTTTTCAAGGTTCAAGCA
19544898 CAACTTGTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (28 bp):
TGCCTTTTCAAGGTTCAAGCATAACCAT
Found at i:19544990 original size:64 final size:65
Alignment explanation
Indices: 19544877--19545004 Score: 161
Period size: 64 Copynumber: 2.0 Consensus size: 65
19544867 GCATAACCAT
* * * * *
19544877 TGCCTTTTCAAGGTTCAAGCACAACTTGTACACACTACCTTTTGAAGGCTAAGGTATAACCTTTA
1 TGCCTTTTCAAGGATCAAGCACAACCTCTAAACACTACCTTTTGAAGGCTAAGGTAAAACCTTTA
* * *
19544942 TGCC-TTTCAAGGATCAAGCACAACCTCTAAATATTACGTTATTG-AGGCTAAGGTAAAACCTTT
1 TGCCTTTTCAAGGATCAAGCACAACCTCTAAACACTACCTT-TTGAAGGCTAAGGTAAAACCTTT
19545005 TTCTCCCTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
64 47 0.87
65 7 0.13
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (65 bp):
TGCCTTTTCAAGGATCAAGCACAACCTCTAAACACTACCTTTTGAAGGCTAAGGTAAAACCTTTA
Found at i:19548588 original size:23 final size:22
Alignment explanation
Indices: 19548561--19548605 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
19548551 GACAATTGGT
19548561 AGCCTCCAATTACTCAATTTCA
1 AGCCTCCAATTACTCAATTTCA
19548583 NAGCCTCCAATTACTCAATTTCA
1 -AGCCTCCAATTACTCAATTTCA
19548606 TGATACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.31
Consensus pattern (22 bp):
AGCCTCCAATTACTCAATTTCA
Found at i:19552058 original size:21 final size:20
Alignment explanation
Indices: 19552034--19552083 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
19552024 TGCAAGGGAG
*
19552034 GTTTAAAACTAATTTAAGCAA
1 GTTTAAAACT-ATTTAAACAA
19552055 GTTTTAAAACTATTTAAACAA
1 G-TTTAAAACTATTTAAACAA
*
19552076 GTTCAAAA
1 GTTTAAAA
19552084 ATCATTCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 11 0.42
22 9 0.35
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (20 bp):
GTTTAAAACTATTTAAACAA
Found at i:19552060 original size:22 final size:21
Alignment explanation
Indices: 19552035--19552078 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
19552025 GCAAGGGAGG
*
19552035 TTTAAAACTAATTTAAGCAAGT
1 TTTAAAACT-ATTTAAACAAGT
19552057 TTTAAAACTATTTAAACAAGT
1 TTTAAAACTATTTAAACAAGT
19552078 T
1 T
19552079 CAAAAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTAAAACTATTTAAACAAGT
Found at i:19552127 original size:21 final size:21
Alignment explanation
Indices: 19552077--19552120 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
19552067 TTTAAACAAG
* *
19552077 TTCAAAAATCATTCAAGTAAT
1 TTCAAAACTCATCCAAGTAAT
19552098 TTCAAAACTCATCCAAGTAAT
1 TTCAAAACTCATCCAAGTAAT
19552119 TT
1 TT
19552121 TGAAACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (21 bp):
TTCAAAACTCATCCAAGTAAT
Found at i:19555012 original size:21 final size:21
Alignment explanation
Indices: 19554976--19555028 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
19554966 GGTTGTGACA
* *
19554976 TTCAAAGATTATTCAAACAAG
1 TTCAAAGATCACTCAAACAAG
*
19554997 TTCAAGGATCACTCAAACAAG
1 TTCAAAGATCACTCAAACAAG
19555018 TTCAAAGATCA
1 TTCAAAGATCA
19555029 TTGGAGCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (21 bp):
TTCAAAGATCACTCAAACAAG
Found at i:19562632 original size:34 final size:34
Alignment explanation
Indices: 19562572--19562655 Score: 116
Period size: 34 Copynumber: 2.5 Consensus size: 34
19562562 TCTCATATTC
*
19562572 TTGGTGTGATTCTAG-TTTTTTCTTTTTCGAAAT
1 TTGGTGTGATCCTAGTTTTTTTCTTTTTCGAAAT
* * **
19562605 TTGGTGTCATCCTAGTTTTTTTTTTTTTTTAAAT
1 TTGGTGTGATCCTAGTTTTTTTCTTTTTCGAAAT
19562639 TTGGTGTGATCCTAGTT
1 TTGGTGTGATCCTAGTT
19562656 AATTGTATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 13 0.30
34 31 0.70
ACGTcount: A:0.14, C:0.10, G:0.18, T:0.58
Consensus pattern (34 bp):
TTGGTGTGATCCTAGTTTTTTTCTTTTTCGAAAT
Found at i:19567156 original size:19 final size:19
Alignment explanation
Indices: 19567097--19567156 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
19567087 CTTTTCCTTT
* *
19567097 TTTTTTATTTTGGTTTTTA
1 TTTTTTAATTTGGTTGTTA
*
19567116 TTTTTTAATTCT--TAGTTAA
1 TTTTTTAATT-TGGTTGTT-A
*
19567135 TTTTTTACTTTGGTTGTTA
1 TTTTTTAATTTGGTTGTTA
19567154 TTT
1 TTT
19567157 CATTTTTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
18 4 0.12
19 23 0.72
20 5 0.16
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (19 bp):
TTTTTTAATTTGGTTGTTA
Found at i:19567802 original size:18 final size:18
Alignment explanation
Indices: 19567775--19567809 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19567765 ACAAAAAGTT
*
19567775 TAACAAATAATTTATAAG
1 TAACAAATAATTCATAAG
*
19567793 TAACACATAATTCATAA
1 TAACAAATAATTCATAA
19567810 ATTAACGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.31
Consensus pattern (18 bp):
TAACAAATAATTCATAAG
Found at i:19571127 original size:20 final size:20
Alignment explanation
Indices: 19571102--19571147 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
19571092 CTTCTAAACC
19571102 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
19571122 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
19571142 TCAAAT
1 TCAAAT
19571148 GGGGCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:19588644 original size:20 final size:20
Alignment explanation
Indices: 19588619--19588659 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
19588609 ATAAGCCTTG
*
19588619 TTGATTTTTACGAAATGAAA
1 TTGATTTATACGAAATGAAA
*
19588639 TTGATTTATATGAAATGAAA
1 TTGATTTATACGAAATGAAA
19588659 T
1 T
19588660 GAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.41
Consensus pattern (20 bp):
TTGATTTATACGAAATGAAA
Found at i:19588675 original size:25 final size:25
Alignment explanation
Indices: 19588630--19588677 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
19588620 TGATTTTTAC
*
19588630 GAAATGAAATTGATTTATATGAAAT
1 GAAATGAAATTGATGTATATGAAAT
*
19588655 GAAATGAGATTTGATGT-TATGAA
1 GAAATGA-AATTGATGTATATGAA
19588678 TCATATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (25 bp):
GAAATGAAATTGATGTATATGAAAT
Found at i:19596559 original size:68 final size:68
Alignment explanation
Indices: 19596378--19596706 Score: 356
Period size: 68 Copynumber: 4.9 Consensus size: 68
19596368 CACATACATG
*
19596378 CTTACTCATCTCATA-AGGTATAT-GAATTTACATCATATACATGA-TCTCATGGCATT--T-AT
1 CTTAATCATCTCATATA-GTATATGGAATTTACATCATATACAT-ATTCTCATGGCATTAATCAT
19596437 GC-TA
64 GCATA
* * * *
19596441 GCTCAATCATCTCATGTAGTATATGGAA-ATACATCATATATATATTCTCATGGCATTAATCATG
1 -CTTAATCATCTCATATAGTATATGGAATTTACATCATATACATATTCTCATGGCATTAATCATG
19596505 CATA
65 CATA
* * * *
19596509 CTTAATCATTTCATGTAGTATGTGGAATATACATCATATACATATTCTCATGGCATTAATCATGC
1 CTTAATCATCTCATATAGTATATGGAATTTACATCATATACATATTCTCATGGCATTAATCATGC
19596574 ATA
66 ATA
* * * * *
19596577 CTTAATCACCTCATATGGTATATGGAATTTACATCATATACACCATCCT-A-GAGTA-TACATCA
1 CTTAATCATCTCATATAGTATATGGAATTTACATCATATACA-TATTCTCATG-GCATTA-ATCA
19596639 TGCATA
63 TGCATA
* * * * *
19596645 CTTGATCATCTCATATGGTATATGGAATTTACATCATATACATAATCTTATGGCATTCATCA
1 CTTAATCATCTCATATAGTATATGGAATTTACATCATATACATATTCTCATGGCATTAATCA
19596707 CACCAACATG
Statistics
Matches: 226, Mismatches: 25, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
63 1 0.00
64 43 0.19
65 4 0.02
66 1 0.00
67 34 0.15
68 137 0.61
69 6 0.03
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (68 bp):
CTTAATCATCTCATATAGTATATGGAATTTACATCATATACATATTCTCATGGCATTAATCATGC
ATA
Found at i:19597893 original size:16 final size:16
Alignment explanation
Indices: 19597872--19597910 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
19597862 TTTGGATTCG
*
19597872 ATAAAAATATCAAAA-A
1 ATAAAAAT-CCAAAAGA
19597888 ATAAAAATCCAAAAGA
1 ATAAAAATCCAAAAGA
19597904 ATAAAAA
1 ATAAAAA
19597911 ATCTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (16 bp):
ATAAAAATCCAAAAGA
Found at i:19599399 original size:12 final size:12
Alignment explanation
Indices: 19599382--19599412 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
19599372 CCCAGTGAGT
19599382 GAACAAGGAAGG
1 GAACAAGGAAGG
19599394 GAACAAGGAAGG
1 GAACAAGGAAGG
19599406 GAACAAG
1 GAACAAG
19599413 CAACCATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.10, G:0.39, T:0.00
Consensus pattern (12 bp):
GAACAAGGAAGG
Found at i:19600286 original size:43 final size:43
Alignment explanation
Indices: 19600238--19600347 Score: 150
Period size: 43 Copynumber: 2.6 Consensus size: 43
19600228 TCACCAGCTC
** * **
19600238 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGACTT
*
19600281 ATGCGCACTCCTTACTCGCACATAACCGGGTCATCCTCGACTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGACTT
19600324 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
19600348 GCCNCAATCA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 1 0.02
43 58 0.98
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGACTT
Found at i:19600446 original size:42 final size:42
Alignment explanation
Indices: 19600399--19600518 Score: 168
Period size: 42 Copynumber: 2.9 Consensus size: 42
19600389 TATTCAACAA
* * *
19600399 CTTATGTGCACTCCCACTCACACATAGTCGGGTCAGCAACGG
1 CTTATGTGCACTCCCACTCACACATAGCCAGGTCAACAACGG
*
19600441 CTTATGTGCACTCCCACTCGCACATAGCCAGGTCAACAACGG
1 CTTATGTGCACTCCCACTCACACATAGCCAGGTCAACAACGG
* ** *
19600483 CTTATGTGCACTCCTACTCGTATATAGCCAGGTCAA
1 CTTATGTGCACTCCCACTCACACATAGCCAGGTCAA
19600519 TATCTTTACA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (42 bp):
CTTATGTGCACTCCCACTCACACATAGCCAGGTCAACAACGG
Found at i:19627968 original size:26 final size:26
Alignment explanation
Indices: 19627908--19627969 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
19627898 ACCATATACC
*
19627908 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
19627934 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
19627960 CATCATCATC
1 CATCATCATC
19627970 TCATATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.40, G:0.03, T:0.24
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:19628262 original size:42 final size:42
Alignment explanation
Indices: 19628204--19628284 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
19628194 ATGGAGGCAA
19628204 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
* *
19628246 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGT
19628285 TCAAATCAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.21
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
Found at i:19642570 original size:23 final size:22
Alignment explanation
Indices: 19642544--19642587 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19642534 ATATAAAAAA
19642544 GTAATTTTCAAAATTGATAAACG
1 GTAATTTT-AAAATTGATAAACG
**
19642567 GTAATTTTGTAATTGATAAAC
1 GTAATTTTAAAATTGATAAAC
19642588 AAAATAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.39
Consensus pattern (22 bp):
GTAATTTTAAAATTGATAAACG
Found at i:19642844 original size:46 final size:44
Alignment explanation
Indices: 19642790--19642946 Score: 137
Period size: 46 Copynumber: 3.5 Consensus size: 44
19642780 TGTTAAAAGA
19642790 TAAA-AATATTCTAAGTAATAAAATCAAAATACCTTTTATTATAAT
1 TAAATAATATT-TAA-TAATAAAATCAAAATACCTTTTATTATAAT
* *
19642835 TAAATAATATTT--TCATCAAAATACAAACATA-TTTTTATTATAAT
1 TAAATAATATTTAATAAT-AAAAT-CAAA-ATACCTTTTATTATAAT
* * *
19642879 TTAATAATATTTTATATTAAAAGAT-AATTAA-ACCTTTTATTATAAT
1 TAAATAATATTTAATAAT-AAA-ATCAA--AATACCTTTTATTATAAT
*
19642925 TAAATAATATTTAATACTAAAA
1 TAAATAATATTTAATAATAAAA
19642947 GATAAAATAT
Statistics
Matches: 92, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
42 3 0.03
43 5 0.05
44 28 0.30
45 14 0.15
46 39 0.42
47 3 0.03
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (44 bp):
TAAATAATATTTAATAATAAAATCAAAATACCTTTTATTATAAT
Found at i:19642876 original size:44 final size:46
Alignment explanation
Indices: 19642820--19642936 Score: 139
Period size: 44 Copynumber: 2.6 Consensus size: 46
19642810 AAATCAAAAT
* *
19642820 ACCTTTTATTATAATTAAATAATATTTT-CATCAAAATACAAACAT
1 ACCTTTTATTATAATTAAATAATATTTTACATCAAAAGACAAACAA
* * * * * **
19642865 A-TTTTTATTATAATTTAATAATATTTTATATTAAAAGATAATTAA
1 ACCTTTTATTATAATTAAATAATATTTTACATCAAAAGACAAACAA
19642910 ACCTTTTATTATAATTAAATAATATTT
1 ACCTTTTATTATAATTAAATAATATTT
19642937 AATACTAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 24 0.41
45 12 0.20
46 23 0.39
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.47
Consensus pattern (46 bp):
ACCTTTTATTATAATTAAATAATATTTTACATCAAAAGACAAACAA
Found at i:19642947 original size:46 final size:46
Alignment explanation
Indices: 19642820--19642952 Score: 146
Period size: 46 Copynumber: 2.9 Consensus size: 46
19642810 AAATCAAAAT
* * * *
19642820 ACCTTTTATTATAATTAAATAATATTTTCAT-C-AAAATACAAACAT
1 ACCTTTTATTATAATTAAATAATA-TTTAATACTAAAAGATAAACAA
* * * * **
19642865 A-TTTTTATTATAATTTAATAATATTTTATATTAAAAGATAATTAA
1 ACCTTTTATTATAATTAAATAATATTTAATACTAAAAGATAAACAA
19642910 ACCTTTTATTATAATTAAATAATATTTAATACTAAAAGATAAA
1 ACCTTTTATTATAATTAAATAATATTTAATACTAAAAGATAAA
19642953 ATATATTCTT
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
43 5 0.07
44 20 0.28
45 10 0.14
46 36 0.51
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.44
Consensus pattern (46 bp):
ACCTTTTATTATAATTAAATAATATTTAATACTAAAAGATAAACAA
Found at i:19646283 original size:15 final size:15
Alignment explanation
Indices: 19646260--19646322 Score: 69
Period size: 15 Copynumber: 4.3 Consensus size: 15
19646250 TAATTGAGAT
*
19646260 ATTTTTTAATTAATA
1 ATTTATTAATTAATA
19646275 ATTTATTAATT--T-
1 ATTTATTAATTAATA
*
19646287 ATTCATTAATTAATA
1 ATTTATTAATTAATA
19646302 ATTTATTAATTGATATA
1 ATTTATTAATT-A-ATA
19646319 ATTT
1 ATTT
19646323 TCATTTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 10 0.25
13 1 0.03
14 1 0.03
15 20 0.50
16 1 0.03
17 7 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
ATTTATTAATTAATA
Found at i:19646652 original size:33 final size:33
Alignment explanation
Indices: 19646574--19646662 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 33
19646564 GAGAGAGGAA
* *
19646574 GAAGATCGATTGAGAGAGGACGA--AAGATAGGG
1 GAAGATCGACTGAGAGAGGA-GATGAAGACAGGG
*
19646606 GAAGATCGGCTGAGAGAGGAGATGAAGACAGGG
1 GAAGATCGACTGAGAGAGGAGATGAAGACAGGG
*
19646639 GAAGGTCGACTGAGAGAGGAGATG
1 GAAGATCGACTGAGAGAGGAGATG
19646663 CTTTTCTGGA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 2 0.04
32 18 0.36
33 30 0.60
ACGTcount: A:0.37, C:0.08, G:0.44, T:0.11
Consensus pattern (33 bp):
GAAGATCGACTGAGAGAGGAGATGAAGACAGGG
Found at i:19648198 original size:44 final size:44
Alignment explanation
Indices: 19648150--19648236 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
19648140 AGCATTTGAA
* *
19648150 CATTCCACTTATCATGAAAAGAT-TTTTCAATGTAAGCACATGAT
1 CATTCC-CTTATCAAGAAAAGATATTATCAATGTAAGCACATGAT
* * * *
19648194 CATTCCGTTTTCAAGAAATGATATTATCTATGTAAGCACATGA
1 CATTCCCTTATCAAGAAAAGATATTATCAATGTAAGCACATGA
19648237 AGATTTAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
43 12 0.33
44 24 0.67
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (44 bp):
CATTCCCTTATCAAGAAAAGATATTATCAATGTAAGCACATGAT
Found at i:19649110 original size:16 final size:17
Alignment explanation
Indices: 19649089--19649121 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
19649079 TCGTAAACGA
19649089 TTAATT-AAAACTAAAT
1 TTAATTAAAAACTAAAT
19649105 TTAATTAGAAAACTAAA
1 TTAATTA-AAAACTAAA
19649122 CTAATAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAATTAAAAACTAAAT
Found at i:19650914 original size:55 final size:53
Alignment explanation
Indices: 19650830--19651011 Score: 221
Period size: 55 Copynumber: 3.4 Consensus size: 53
19650820 CCATTAGTTT
* * *
19650830 ATGTGCGCTCCCACACCACACATAACTGGAATCATCACCCTCCGGTCATCAGCTC
1 ATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCCTCC--TCATCAGCTC
*
19650885 ATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCCACCAATCATCAGCTC
1 ATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCCTCC--TCATCAGCTC
* * *
19650940 ATGTGCACTCCCATACCGCACATAGCTGGAAT-A--ACCCT--TCATCACCGGC
1 ATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCCTCCTCATCAGC-TC
19650989 ATGTGCACTCCCACACCGCACAT
1 ATGTGCACTCCCACACCGCACAT
19651012 GCGCGTTACA
Statistics
Matches: 115, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
48 7 0.06
49 23 0.20
52 4 0.03
54 1 0.01
55 80 0.70
ACGTcount: A:0.27, C:0.40, G:0.14, T:0.19
Consensus pattern (53 bp):
ATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCCTCCTCATCAGCTC
Found at i:19653052 original size:21 final size:20
Alignment explanation
Indices: 19653028--19653073 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
19653018 TTAAAGTAAT
19653028 TTAAACTAAAATAACATAAAA
1 TTAAACTAAAATAAC-TAAAA
*
19653049 TTAAACTAAAATAACTTAAA
1 TTAAACTAAAATAACTAAAA
19653069 TTAAA
1 TTAAA
19653074 GAAGAGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (20 bp):
TTAAACTAAAATAACTAAAA
Found at i:19668848 original size:28 final size:28
Alignment explanation
Indices: 19668814--19668879 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
19668804 GTCTTTTCAT
19668814 TATTCATCCATTTCTAGTGGGTTGAAAG
1 TATTCATCCATTTCTAGTGGGTTGAAAG
19668842 TATTCATCCATTTCTAGTGGGTTGAAAG
1 TATTCATCCATTTCTAGTGGGTTGAAAG
19668870 TATTCATCCA
1 TATTCATCCA
19668880 CTTTTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (28 bp):
TATTCATCCATTTCTAGTGGGTTGAAAG
Found at i:19669018 original size:51 final size:51
Alignment explanation
Indices: 19668942--19669038 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
19668932 CATCCACTTT
* * *
19668942 TGATGGTAAAATTATCCATCCACTTCTGGTGGCAAAATTATTATTAGATTC
1 TGATGATAAAATTATACATCCACTTCTGGTGGCAAAATTATAATTAGATTC
* *
19668993 TGATGATAAAATTATATATCCACTTCTGGTGGTAAAATTATAATTA
1 TGATGATAAAATTATACATCCACTTCTGGTGGCAAAATTATAATTA
19669039 AAATAGTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38
Consensus pattern (51 bp):
TGATGATAAAATTATACATCCACTTCTGGTGGCAAAATTATAATTAGATTC
Found at i:19669028 original size:26 final size:26
Alignment explanation
Indices: 19668933--19669034 Score: 100
Period size: 26 Copynumber: 4.0 Consensus size: 26
19668923 TTCAACATTC
* **
19668933 ATCCACTTTTGATGGTAAAATTATCC
1 ATCCACTTCTGATGGTAAAATTATAT
* *
19668959 ATCCACTTCTGGTGGCAAAATTAT-T
1 ATCCACTTCTGATGGTAAAATTATAT
* * *
19668984 AT-TAGATTCTGATGATAAAATTATAT
1 ATCCA-CTTCTGATGGTAAAATTATAT
*
19669010 ATCCACTTCTGGTGGTAAAATTATA
1 ATCCACTTCTGATGGTAAAATTATA
19669035 ATTAAAATAG
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
24 1 0.02
25 17 0.28
26 41 0.68
27 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (26 bp):
ATCCACTTCTGATGGTAAAATTATAT
Found at i:19669566 original size:18 final size:18
Alignment explanation
Indices: 19669543--19669591 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
19669533 ACATAAGAAC
19669543 AAGTATTTAGAAGAAAGA
1 AAGTATTTAGAAGAAAGA
*
19669561 AAGTATTTA-AAGGGAAGA
1 AAGTATTTAGAA-GAAAGA
19669579 AAGTATTTAGAAG
1 AAGTATTTAGAAG
19669592 GAGCAAGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 2 0.07
18 24 0.86
19 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
AAGTATTTAGAAGAAAGA
Found at i:19675501 original size:19 final size:17
Alignment explanation
Indices: 19675461--19675509 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
19675451 AAAAAAGAAG
*
19675461 AAAAAATGGAAAAATTT
1 AAAAAATGAAAAAATTT
19675478 AAAAAATGAAAAAATAATT
1 AAAAAATGAAAAAAT--TT
*
19675497 GAAAAATGAAAAA
1 AAAAAATGAAAAA
19675510 TGTACAACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 14 0.50
19 14 0.50
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAAAATGAAAAAATTT
Found at i:19675509 original size:28 final size:27
Alignment explanation
Indices: 19675451--19675509 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
19675441 AAATGAAAAG
*
19675451 AAAAAAGAAGAAAAAATGGAAAAATTTA
1 AAAAAAGAAGAAAAAATGGAAAAA-TGA
* *
19675479 AAAAATGAA-AAAATAATTGAAAAATGA
1 AAAAAAGAAGAAAA-AATGGAAAAATGA
19675506 AAAA
1 AAAA
19675510 TGTACAACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (27 bp):
AAAAAAGAAGAAAAAATGGAAAAATGA
Found at i:19677063 original size:24 final size:23
Alignment explanation
Indices: 19677036--19677081 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
19677026 AAAATAGTAT
*
19677036 ATAAATAATGATAATAAATAAAAA
1 ATAAATAATAATAAT-AATAAAAA
19677060 ATAAATAATAATAATAATAAAA
1 ATAAATAATAATAATAATAAAA
19677082 TTCATCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (23 bp):
ATAAATAATAATAATAATAAAAA
Found at i:19680394 original size:3 final size:3
Alignment explanation
Indices: 19680386--19680451 Score: 59
Period size: 3 Copynumber: 22.7 Consensus size: 3
19680376 GAACTAAAAG
*
19680386 TAA TAA TAA TAA -AA AAA TAA TAAA TAA TCAA T-A TAA -AA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA TAA TAA
* *
19680429 TAA TAA TAA TAA AAA AAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
19680452 GTAAACTTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
2 8 0.15
3 40 0.74
4 6 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:19680411 original size:18 final size:19
Alignment explanation
Indices: 19680380--19680449 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 19
19680370 ATAGGAGAAC
*
19680380 TAAAAGTAAT-AATAATAA
1 TAAAAATAATAAATAATAA
19680398 -AAAAATAATAAATAATCAA
1 TAAAAATAATAAATAAT-AA
*
19680417 TATAAAATAAAATAATAATAA
1 TA-AAAATAATA-AATAATAA
*
19680438 TAAAAAAAATAA
1 TAAAAATAATAA
19680450 TAGTAAACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 8 0.19
18 6 0.14
19 3 0.07
20 8 0.19
21 12 0.28
22 6 0.14
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (19 bp):
TAAAAATAATAAATAATAA
Found at i:19680450 original size:18 final size:18
Alignment explanation
Indices: 19680381--19680451 Score: 70
Period size: 18 Copynumber: 3.6 Consensus size: 18
19680371 TAGGAGAACT
*
19680381 AAAAGTAATAATAATAAAA
1 AAAAATAATAATAAT-AAA
19680400 AAATAATAAATAATCAATATAAA
1 AAA-AAT-AATAAT--A-ATAAA
19680423 ATAAAATAATAATAATAAA
1 A-AAAATAATAATAATAAA
19680442 AAAAATAATA
1 AAAAATAATA
19680452 GTAAACTTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
18 9 0.20
19 9 0.20
20 3 0.07
21 6 0.13
22 6 0.13
23 8 0.18
24 4 0.09
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (18 bp):
AAAAATAATAATAATAAA
Found at i:19680456 original size:15 final size:15
Alignment explanation
Indices: 19680387--19680456 Score: 65
Period size: 15 Copynumber: 4.8 Consensus size: 15
19680377 AACTAAAAGT
19680387 AATAATAAT-AAAAA
1 AATAATAATAAAAAA
**
19680401 AATAATAAATAATCAA
1 AATAAT-AATAAAAAA
* *
19680417 TATAA-AAT-AAAAT
1 AATAATAATAAAAAA
19680430 AATAATAATAAAAAA
1 AATAATAATAAAAAA
*
19680445 AATAATAGTAAA
1 AATAATAATAAA
19680457 CTTCACAAAC
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
13 6 0.14
14 12 0.28
15 18 0.42
16 7 0.16
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (15 bp):
AATAATAATAAAAAA
Found at i:19682184 original size:22 final size:24
Alignment explanation
Indices: 19682130--19682189 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
19682120 TTTTGTTCTT
19682130 TAAAAATTATGAAAATAAAAAGAAA
1 TAAAAATTATGAAAAT-AAAAGAAA
* *
19682155 GAAAAATTATGAAAAT-AAA-TAA
1 TAAAAATTATGAAAATAAAAGAAA
*
19682177 TAAAAATTTTGAA
1 TAAAAATTATGAA
19682190 TAGAGCTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 13 0.42
23 3 0.10
25 15 0.48
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (24 bp):
TAAAAATTATGAAAATAAAAGAAA
Found at i:19686221 original size:20 final size:20
Alignment explanation
Indices: 19686192--19686245 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
19686182 ATTAGGTTAC
19686192 TTTTAGGTTAGTT-ATTTTAA
1 TTTTAGGTTA-TTCATTTTAA
* *
19686212 TTTTATGTTATTCCTTTTAA
1 TTTTAGGTTATTCATTTTAA
19686232 -TTT-GGTTATT-ATTT
1 TTTTAGGTTATTCATTT
19686246 ATTAATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 3 0.10
18 6 0.21
19 5 0.17
20 15 0.52
ACGTcount: A:0.20, C:0.04, G:0.11, T:0.65
Consensus pattern (20 bp):
TTTTAGGTTATTCATTTTAA
Found at i:19691485 original size:20 final size:20
Alignment explanation
Indices: 19691460--19691505 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
19691450 TTTTGACCCC
19691460 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
19691480 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
19691500 ATTTGA
1 ATTTGA
19691506 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:19696045 original size:18 final size:19
Alignment explanation
Indices: 19696018--19696056 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
19696008 CTCGTTTTTA
*
19696018 TTTTATTTTATT-TCATTT
1 TTTTACTTTATTATCATTT
19696036 TTTTACTTTATTATCATTT
1 TTTTACTTTATTATCATTT
19696055 TT
1 TT
19696057 ATTAGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTACTTTATTATCATTT
Found at i:19699761 original size:20 final size:20
Alignment explanation
Indices: 19699732--19699774 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
19699722 ATTAGGTTAC
19699732 TTTTAAGTTAGTT-ATTTTAA
1 TTTTAAGTTA-TTCATTTTAA
* *
19699752 TTTTATGTTATTCCTTTTAA
1 TTTTAAGTTATTCATTTTAA
19699772 TTT
1 TTT
19699775 GGTTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTAAGTTATTCATTTTAA
Found at i:19701542 original size:9 final size:8
Alignment explanation
Indices: 19701519--19701566 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 8
19701509 TTTCTAGAAA
19701519 AAAAAAACC
1 AAAAAAA-C
19701528 ATAAAAAAC
1 A-AAAAAAC
*
19701537 AGAAAAAC
1 AAAAAAAC
19701545 AACAAAAAC
1 AA-AAAAAC
19701554 AACAAAAAC
1 AA-AAAAAC
19701563 AAAA
1 AAAA
19701567 TGATGATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 9 0.26
9 20 0.57
10 6 0.17
ACGTcount: A:0.79, C:0.17, G:0.02, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:19701551 original size:8 final size:9
Alignment explanation
Indices: 19701539--19701564 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19701529 TAAAAAACAG
19701539 AAAAACAAC
1 AAAAACAAC
19701548 AAAAACAAC
1 AAAAACAAC
19701557 AAAAACAA
1 AAAAACAA
19701565 AATGATGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAACAAC
Found at i:19703992 original size:23 final size:23
Alignment explanation
Indices: 19703935--19704008 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
19703925 TAAATTACAA
* * *
19703935 ATAAAATATTAATACTTAAATA-
1 ATAAATTATTAATATTTAAAAAT
* *
19703957 ATCAACTATTAATATTTAAAAAT
1 ATAAATTATTAATATTTAAAAAT
19703980 ATAAATTATTAATATTTAAAAGAT
1 ATAAATTATTAATATTTAAAA-AT
19704004 A-AAAT
1 ATAAAT
19704009 AAAATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.41
23 23 0.52
24 3 0.07
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (23 bp):
ATAAATTATTAATATTTAAAAAT
Found at i:19704005 original size:22 final size:21
Alignment explanation
Indices: 19703835--19704009 Score: 96
Period size: 22 Copynumber: 8.4 Consensus size: 21
19703825 ATTTAAATTT
*
19703835 ATAAATTATTAATATTTAAAAA
1 ATAAAATATTAATATTT-AAAA
* * *
19703857 ATAAAATA--AATA-ATCATA
1 ATAAAATATTAATATTTAAAA
* *
19703875 ATAACAT-TTAA-A-TTATAA
1 ATAAAATATTAATATTTAAAA
* * * *
19703893 ATAAAATAGTAGTATTTTATA
1 ATAAAATATTAATATTTAAAA
* *
19703914 ATATTAATGATTAA-A-TTACAA
1 ATA-AAAT-ATTAATATTTAAAA
*
19703935 ATAAAATATTAATACTTAAATA
1 ATAAAATATTAATATTTAAA-A
* *
19703957 ATCAACTATTAATATTTAAAA
1 ATAAAATATTAATATTTAAAA
19703978 ATATAAATTATTAATATTTAAAA
1 ATA-AAA-TATTAATATTTAAAA
19704001 GATAAAATA
1 -ATAAAATA
19704010 AAATAAAAAT
Statistics
Matches: 112, Mismatches: 28, Indels: 26
0.67 0.17 0.16
Matches are distributed among these distances:
18 17 0.15
19 10 0.09
20 9 0.08
21 19 0.17
22 33 0.29
23 21 0.19
24 3 0.03
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAAAATATTAATATTTAAAA
Found at i:19705814 original size:3 final size:3
Alignment explanation
Indices: 19705806--19705858 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
19705796 GGAGAACTAA
*
19705806 AAT AAT AAT AA- AA- AAT AAT AAAT AAT CAAT -AT AA- AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT
19705849 AAT AAT AAT A
1 AAT AAT AAT A
19705859 GTAAACTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
2 8 0.19
3 29 0.67
4 6 0.14
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:19705852 original size:23 final size:22
Alignment explanation
Indices: 19705806--19705863 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
19705796 GGAGAACTAA
*
19705806 AATAATAATAAAAAATAATAAAT
1 AATAAT-ATAAAAAAAAATAAAT
19705829 AATCAATATAAAATAAAAAT-AAT
1 AAT-AATATAAAA-AAAAATAAAT
19705852 AATAATAGTAAA
1 AATAATA-TAAA
19705864 CTTCATAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 4 0.13
23 19 0.61
24 8 0.26
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
AATAATATAAAAAAAAATAAAT
Done.