Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 145 of 168
Found at i:42596877 original size:13 final size:13
Alignment explanation
Indices: 42596859--42596883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42596849 TATTTTAATA
42596859 TTATTTTGTGTGT
1 TTATTTTGTGTGT
42596872 TTATTTTGTGTG
1 TTATTTTGTGTG
42596884 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:42597224 original size:28 final size:28
Alignment explanation
Indices: 42597127--42597222 Score: 151
Period size: 28 Copynumber: 3.5 Consensus size: 28
42597117 AAAAATAAAA
42597127 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
*
42597155 ATTTACGAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
* *
42597183 ATTTACCAAAATA-TATATC-TTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
42597209 ATTTACCAAAATAT
1 ATTTACCAAAATAT
42597223 ATCAAAAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
26 20 0.32
27 4 0.06
28 39 0.62
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.49
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:42597316 original size:27 final size:27
Alignment explanation
Indices: 42597286--42597363 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
42597276 CCCCAATGGT
*
42597286 ATTGGCGGCACCAAAGGTGCCAAA-TAA
1 ATTGGCGGCACCAATGGTGCCAAAGT-A
* * *
42597313 ATTGGTGGCACCATTGGTGCCAAAGTC
1 ATTGGCGGCACCAATGGTGCCAAAGTA
42597340 ATTGGCGGCACC-ATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
42597364 GGAAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 11 0.25
27 32 0.73
28 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.19
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGTA
Found at i:42597474 original size:18 final size:19
Alignment explanation
Indices: 42597437--42597475 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42597427 CAACTCATAT
* *
42597437 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACACTA
42597456 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACACTA
42597474 TT
1 TT
42597476 AAGTAATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATTTAATAACACTA
Found at i:42597733 original size:2 final size:2
Alignment explanation
Indices: 42597726--42597783 Score: 50
Period size: 2 Copynumber: 30.0 Consensus size: 2
42597716 GGTATAAAGG
* *
42597726 TA TA TA TA TA TA TA TA TA TA T- TCA AA TA -A T- TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
* *
42597766 TC TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
42597784 CTTGAATTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:42598227 original size:41 final size:41
Alignment explanation
Indices: 42598182--42598283 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
42598172 GCTTAGCGCT
*
42598182 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTAAATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
* * *
42598223 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
42598264 TAGCAGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
42598284 TACTGAATCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
40 3 0.05
41 53 0.95
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
Found at i:42600736 original size:3 final size:3
Alignment explanation
Indices: 42600728--42600753 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42600718 ATTTTATATA
42600728 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
42600754 GAATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:42600796 original size:20 final size:20
Alignment explanation
Indices: 42600757--42600796 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42600747 ATTATTAGAA
*
42600757 TTTTAATTTTTTATATAAAT
1 TTTTAATTTTTTATAGAAAT
42600777 TTTTCAATTTTTT-TAGAAAT
1 TTTT-AATTTTTTATAGAAAT
42600797 AAAGTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTAATTTTTTATAGAAAT
Found at i:42602554 original size:24 final size:24
Alignment explanation
Indices: 42602527--42602604 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
42602517 TTTCTCCTAG
*
42602527 GGGAGCAAGAGGTGGTCCTTCGAT
1 GGGAGCAAGAGGTGGTCCTTCTAT
*
42602551 GGGAGCAAGGGGTGGTCCTTCTAT
1 GGGAGCAAGAGGTGGTCCTTCTAT
*
42602575 GGGAGCAAGAGGTGGTCCTCCTAT
1 GGGAGCAAGAGGTGGTCCTTCTAT
42602599 GGGAGC
1 GGGAGC
42602605 TTCAAATCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.19, C:0.18, G:0.42, T:0.21
Consensus pattern (24 bp):
GGGAGCAAGAGGTGGTCCTTCTAT
Found at i:42604757 original size:89 final size:88
Alignment explanation
Indices: 42604651--42604823 Score: 229
Period size: 89 Copynumber: 2.0 Consensus size: 88
42604641 GCTCTTTTTT
* * * * * *
42604651 TTTTTTTTGCATTCAATTGAGCACTTGAACTTTTAAAATACATCAAAAAGGCCCTCAAACTTCTT
1 TTTTTTTTCCACTCAATTAAGCACTTGAACTTTCAAAATACATCAAAAAGACCCTCAAAATTCTT
42604716 CAAAAGAAGCAATAAAGCCCCTAC
66 C-AAAGAAGCAATAAAGCCCCTAC
* * * *
42604740 TTTTTTTTCCACTCAATTAAGTACTTGAACTTTCAAAATGCCTCAAAAAGACCCTCAAAATTTTT
1 TTTTTTTTCCACTCAATTAAGCACTTGAACTTTCAAAATACATCAAAAAGACCCTCAAAATTCTT
* *
42604805 CAAATAAGCAATTAAGCCC
66 CAAAGAAGCAATAAAGCCC
42604824 ATGGTCTTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
88 16 0.22
89 56 0.78
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.32
Consensus pattern (88 bp):
TTTTTTTTCCACTCAATTAAGCACTTGAACTTTCAAAATACATCAAAAAGACCCTCAAAATTCTT
CAAAGAAGCAATAAAGCCCCTAC
Found at i:42604883 original size:19 final size:18
Alignment explanation
Indices: 42604859--42604918 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
42604849 TAATAAATAA
42604859 TAAATTTTAGAAAAATTAT
1 TAAATTTTA-AAAAATTAT
* *
42604878 TAAATTCTAATAAAATTTT
1 TAAATTTTAA-AAAATTAT
** *
42604897 TAAAAATTAAAAATTTAT
1 TAAATTTTAAAAAATTAT
42604915 TAAA
1 TAAA
42604919 AATTAGAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TAAATTTTAAAAAATTAT
Found at i:42604919 original size:18 final size:17
Alignment explanation
Indices: 42604889--42604938 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
42604879 AAATTCTAAT
42604889 AAAATTTTTAAAAATTA
1 AAAATTTTTAAAAATTA
42604906 AAAATTTATTAAAAATTA
1 AAAATTT-TTAAAAATTA
* *
42604924 GAATTTTTTATAAAA
1 AAAATTTTTA-AAAA
42604939 ATCTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAAATTTTTAAAAATTA
Found at i:42604976 original size:19 final size:18
Alignment explanation
Indices: 42604888--42604977 Score: 69
Period size: 19 Copynumber: 4.9 Consensus size: 18
42604878 TAAATTCTAA
42604888 TAAAATTTT-TAAAAA-T
1 TAAAATTTTATAAAAATT
*
42604904 TAAAAATTTATTAAAAA-T
1 TAAAATTTTA-TAAAAATT
*
42604922 TAGAATTTTTTATAAAAATCT
1 TA-AA-ATTTTATAAAAAT-T
* * *
42604943 TAAAAATATAAAAAAATT
1 TAAAATTTTATAAAAATT
42604961 GTAAAATTTTATAAAAA
1 -TAAAATTTTATAAAAA
42604978 AAAAGCCTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
16 8 0.14
18 10 0.18
19 30 0.53
20 6 0.11
21 3 0.05
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (18 bp):
TAAAATTTTATAAAAATT
Found at i:42605250 original size:19 final size:18
Alignment explanation
Indices: 42605226--42605289 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
42605216 ATTCTATATA
42605226 TTTTATAATTTTTGACAAT
1 TTTTATAATTTTT-ACAAT
*
42605245 TTTTATAAAATTTTACAATT
1 TTTTAT-AATTTTTACAA-T
* *
42605265 TTTTATATTTTTTAACGAT
1 TTTTATAATTTTT-ACAAT
42605284 TTTTAT
1 TTTTAT
42605290 TTTTTTCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTATAATTTTTACAAT
Found at i:42627081 original size:50 final size:50
Alignment explanation
Indices: 42626966--42627158 Score: 305
Period size: 50 Copynumber: 3.8 Consensus size: 50
42626956 GATAATAACA
* ** *
42626966 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
42627017 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
42627067 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
42627117 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
42627159 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 97 0.75
51 33 0.25
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:42627274 original size:13 final size:13
Alignment explanation
Indices: 42627253--42627283 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
42627243 GCTTAGATCA
*
42627253 TCATCAAATAAAT
1 TCATAAAATAAAT
42627266 TCATAAAATAAAT
1 TCATAAAATAAAT
42627279 TCATA
1 TCATA
42627284 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:42628339 original size:23 final size:23
Alignment explanation
Indices: 42628291--42628340 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
42628281 ATTCATGCGA
* *
42628291 TCTATTTCTTTTACTTCATCGTT
1 TCTATTTATTTTACTTCATCGGT
*
42628314 TCTATTTATTTT-CATTCATTGGT
1 TCTATTTATTTTAC-TTCATCGGT
42628337 TCTA
1 TCTA
42628341 CATGCAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.16, C:0.18, G:0.06, T:0.60
Consensus pattern (23 bp):
TCTATTTATTTTACTTCATCGGT
Found at i:42634353 original size:13 final size:13
Alignment explanation
Indices: 42634335--42634363 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42634325 ATGCCAAAGA
42634335 AAACTAATTATGC
1 AAACTAATTATGC
42634348 AAACTAATTATGC
1 AAACTAATTATGC
42634361 AAA
1 AAA
42634364 TCGCTTAAGA
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:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (13 bp):
AAACTAATTATGC
Found at i:42634724 original size:7 final size:7
Alignment explanation
Indices: 42634716--42634745 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
42634706 AACAAAATGG
*
42634716 ACCATGG
1 ACCATGA
42634723 ACCATGA
1 ACCATGA
42634730 ACCATGA
1 ACCATGA
42634737 ACCATGA
1 ACCATGA
42634744 AC
1 AC
42634746 AACTTATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.40, C:0.30, G:0.17, T:0.13
Consensus pattern (7 bp):
ACCATGA
Found at i:42637604 original size:33 final size:34
Alignment explanation
Indices: 42637536--42637608 Score: 103
Period size: 33 Copynumber: 2.1 Consensus size: 34
42637526 ATATAATTTG
*
42637536 ATAATTTTACTAACAATTAATACAATTAACAATTA
1 ATAATTTTACTAACAA-TAATACAAGTAACAATTA
**
42637571 ATAATTTTACTAACAA-AATATTAGTAACAATTA
1 ATAATTTTACTAACAATAATACAAGTAACAATTA
42637604 ATAAT
1 ATAAT
42637609 GAATAATTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 19 0.54
35 16 0.46
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (34 bp):
ATAATTTTACTAACAATAATACAAGTAACAATTA
Found at i:42637731 original size:22 final size:22
Alignment explanation
Indices: 42637706--42637748 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42637696 AAAAAAATAT
*
42637706 AATTTGATATAATTTTAATAAC
1 AATTAGATATAATTTTAATAAC
* *
42637728 AATTAGTTTTAATTTTAATAA
1 AATTAGATATAATTTTAATAA
42637749 AAATATAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (22 bp):
AATTAGATATAATTTTAATAAC
Found at i:42637764 original size:23 final size:22
Alignment explanation
Indices: 42637715--42637775 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
42637705 TAATTTGATA
* *
42637715 TAATTTTAATAACAATTAGTTT
1 TAATTTTAATAAAAATTAATTT
42637737 TAATTTTAATAAAAATATAATTT
1 TAATTTTAATAAAAAT-TAATTT
42637760 TAATTTTAATTAAAAA
1 TAATTTTAA-TAAAAA
42637776 ACGGGCCGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.43
23 14 0.40
24 6 0.17
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TAATTTTAATAAAAATTAATTT
Found at i:42646249 original size:21 final size:21
Alignment explanation
Indices: 42646224--42646269 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
42646214 TAGAAATTCA
42646224 TTATCAGTAATATGTCAAAAT
1 TTATCAGTAATATGTCAAAAT
42646245 TTATCAGTAATATGTCAAAAT
1 TTATCAGTAATATGTCAAAAT
42646266 TTAT
1 TTAT
42646270 GACTATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (21 bp):
TTATCAGTAATATGTCAAAAT
Found at i:42648752 original size:21 final size:23
Alignment explanation
Indices: 42648728--42648770 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
42648718 CATTAAAGTT
42648728 TTCTCA-CG-ACAGTTTTGTTTA
1 TTCTCATCGCACAGTTTTGTTTA
* *
42648749 TTCTTATGGCACAGTTTTGTTT
1 TTCTCATCGCACAGTTTTGTTT
42648771 GCTTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 1 0.06
23 12 0.67
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (23 bp):
TTCTCATCGCACAGTTTTGTTTA
Found at i:42649944 original size:5 final size:5
Alignment explanation
Indices: 42649934--42649960 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
42649924 CCTTTGTTTC
42649934 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
42649961 CACTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:42652789 original size:21 final size:20
Alignment explanation
Indices: 42652760--42652800 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
42652750 GGAGGGCACT
*
42652760 CTGAAAAGTTAATATATATTA
1 CTGAAAAGTTAA-ATACATTA
*
42652781 CTGAGAAGTTAAATACATTA
1 CTGAAAAGTTAAATACATTA
42652801 TCCATGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (20 bp):
CTGAAAAGTTAAATACATTA
Found at i:42658448 original size:12 final size:12
Alignment explanation
Indices: 42658431--42658455 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42658421 CAGCAGAAAG
42658431 GAGTGAAGAGAA
1 GAGTGAAGAGAA
42658443 GAGTGAAGAGAA
1 GAGTGAAGAGAA
42658455 G
1 G
42658456 GCATTTCAAG
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:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGTGAAGAGAA
Found at i:42667213 original size:29 final size:31
Alignment explanation
Indices: 42667171--42667237 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
42667161 GTTTGTAATT
*
42667171 TAATATAAATATATATTTA-TTATT-TAACA
1 TAATATAAATATATAATTACTTATTATAACA
* *
42667200 T-ATATAATTGATATAATTACTTTTTATAACA
1 TAATATAAAT-ATATAATTACTTATTATAACA
42667231 TAATATA
1 TAATATA
42667238 TTCAGGCCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 7 0.23
29 9 0.29
30 4 0.13
31 6 0.19
32 5 0.16
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (31 bp):
TAATATAAATATATAATTACTTATTATAACA
Found at i:42668212 original size:29 final size:30
Alignment explanation
Indices: 42668136--42668213 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
42668126 ATTGACATGG
* *
42668136 AAGACTTAATTGATCTTTAATTATTTTACA
1 AAGATTTAATTGATTTTTAATTATTTTACA
* ** *
42668166 AAGGTTTAATAAATTTTTAATTATTTTA-G
1 AAGATTTAATTGATTTTTAATTATTTTACA
**
42668195 GTGATTTAATTGATTTTTA
1 AAGATTTAATTGATTTTTA
42668214 GAAATTATAT
Statistics
Matches: 37, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
29 14 0.38
30 23 0.62
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (30 bp):
AAGATTTAATTGATTTTTAATTATTTTACA
Found at i:42669047 original size:96 final size:96
Alignment explanation
Indices: 42668932--42669124 Score: 341
Period size: 96 Copynumber: 2.0 Consensus size: 96
42668922 TTCTCGTATC
* *
42668932 ATTACTCCTTAATCAAAACCATTACTTATTATTAACCTTAAACCACCAAACACTAAACTTATTCT
1 ATTACTCCTTAATCAAAACCATTACTTATTATTAACCTTAAACCACCAAACACTAAACTCATTAT
*
42668997 TTTTCAAACCTCATACTCTGAACCCGTTATA
66 TTTTCAAACCTCATACTCAGAACCCGTTATA
* *
42669028 ATTACTCTTTAATCAAAACCATTATTTATTATTAACCTTAAACCACCAAACACTAAACTCATTAT
1 ATTACTCCTTAATCAAAACCATTACTTATTATTAACCTTAAACCACCAAACACTAAACTCATTAT
42669093 TTTTCAAACCTCATACTCAGAACCCGTTATA
66 TTTTCAAACCTCATACTCAGAACCCGTTATA
42669124 A
1 A
42669125 GTTTAATCAC
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 92 1.00
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (96 bp):
ATTACTCCTTAATCAAAACCATTACTTATTATTAACCTTAAACCACCAAACACTAAACTCATTAT
TTTTCAAACCTCATACTCAGAACCCGTTATA
Found at i:42669197 original size:10 final size:10
Alignment explanation
Indices: 42669160--42669259 Score: 69
Period size: 10 Copynumber: 9.5 Consensus size: 10
42669150 ATAACAAAAT
*
42669160 TTTTCTATAAT
1 TTTT-TATAAA
*
42669171 TTTCTTATATA
1 TTT-TTATAAA
*
42669182 TATTTATAAA
1 TTTTTATAAA
42669192 TTTTTA-AAA
1 TTTTTATAAA
* *
42669201 CTTTTAATAAG
1 -TTTTTATAAA
42669212 TTTTTATAAA
1 TTTTTATAAA
*
42669222 TTTTATAAATAATT
1 TTTT-T--ATAA-A
42669236 TTTTTATAAA
1 TTTTTATAAA
42669246 -TTTTATAAA
1 TTTTTATAAA
42669255 TTTTT
1 TTTTT
42669260 CTATAAGGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 17
0.71 0.11 0.17
Matches are distributed among these distances:
9 12 0.17
10 32 0.46
11 16 0.23
12 1 0.01
13 5 0.07
14 4 0.06
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:42669225 original size:9 final size:9
Alignment explanation
Indices: 42669184--42669258 Score: 52
Period size: 9 Copynumber: 8.3 Consensus size: 9
42669174 CTTATATATA
42669184 TTTATAAAT
1 TTTATAAAT
42669193 TTT-TAAAACT
1 TTTAT-AAA-T
*
42669203 TTTAATAAGTT
1 TTT-ATAA-AT
42669214 TTTATAAAT
1 TTTATAAAT
42669223 TTTATAAAT
1 TTTATAAAT
*
42669232 AATT-T---T
1 -TTTATAAAT
42669238 TTTATAAAT
1 TTTATAAAT
42669247 TTTATAAAT
1 TTTATAAAT
42669256 TTT
1 TTT
42669259 TCTATAAGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 20
0.68 0.05 0.26
Matches are distributed among these distances:
5 2 0.04
6 2 0.04
8 1 0.02
9 30 0.58
10 10 0.19
11 6 0.12
12 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (9 bp):
TTTATAAAT
Found at i:42669238 original size:23 final size:24
Alignment explanation
Indices: 42669206--42669255 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
42669196 TAAAACTTTT
42669206 AATAA-GTTTTTATAAATTTTATA
1 AATAATGTTTTTATAAATTTTATA
*
42669229 AATAATTTTTTTATAAATTTTATA
1 AATAATGTTTTTATAAATTTTATA
42669253 AAT
1 AAT
42669256 TTTTCTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
AATAATGTTTTTATAAATTTTATA
Found at i:42679073 original size:31 final size:30
Alignment explanation
Indices: 42678944--42679073 Score: 84
Period size: 31 Copynumber: 4.2 Consensus size: 30
42678934 TTGTTTCAAA
*
42678944 AAAAAATTTAATAGGGATATTTTAGATAATAT
1 AAAAAA-TAAATAGGG-TATTTTAGATAATAT
* * * ***
42678976 AAAAATTAATATA-GATATTTTAGGTGGCAT
1 AAAAAATAA-ATAGGGTATTTTAGATAATAT
* * * *
42679006 AAAAAATCAATAGGGGTAATTTAGACATTA-
1 AAAAAATAAATA-GGGTATTTTAGATAATAT
*
42679036 ACAAAAATAAATAGGTGTATTTTAGGTAATAT
1 A-AAAAATAAATAGG-GTATTTTAGATAATAT
42679068 AAAAAA
1 AAAAAA
42679074 GCAGGGATAA
Statistics
Matches: 71, Mismatches: 21, Indels: 13
0.68 0.20 0.12
Matches are distributed among these distances:
29 3 0.04
30 21 0.30
31 38 0.54
32 9 0.13
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.32
Consensus pattern (30 bp):
AAAAAATAAATAGGGTATTTTAGATAATAT
Found at i:42683621 original size:109 final size:108
Alignment explanation
Indices: 42683431--42683641 Score: 298
Period size: 109 Copynumber: 1.9 Consensus size: 108
42683421 CCAACTCATC
* *
42683431 TTGGTATAAACATCAATGAAAACCATGCAATACTTGCTCTCTTTGAGCGACAAAGTTTTGTGAGA
1 TTGGTATAAACATCAATAAAAACCATGCAATACTTACTCTCTTTGAGCGACAAAGTTTTGTGAGA
* *
42683496 TCTAGCCCAGTCCATGTAGATTAGTTTAAGGTTTTCAGACATT
66 TCTAGACCAGTCCATGTAGATTAATTTAAGGTTTTCAGACATT
* * * * *
42683539 TTGGTGTAATCATCAATAAAAACTATGCAATGCTTACTCTCTTTTGAGTGACAAAGTTTTGTGAG
1 TTGGTATAAACATCAATAAAAACCATGCAATACTTACTCTC-TTTGAGCGACAAAGTTTTGTGAG
* *
42683604 ATCTA-ACCAGGTCCATGTTGATTAATTTAAGTTTTTCA
65 ATCTAGACCA-GTCCATGTAGATTAATTTAAGGTTTTCA
42683642 ATAACTCTCT
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
108 38 0.42
109 52 0.58
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (108 bp):
TTGGTATAAACATCAATAAAAACCATGCAATACTTACTCTCTTTGAGCGACAAAGTTTTGTGAGA
TCTAGACCAGTCCATGTAGATTAATTTAAGGTTTTCAGACATT
Found at i:42694856 original size:32 final size:32
Alignment explanation
Indices: 42694802--42694892 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
42694792 AAAAAAAACT
*
42694802 AAAGTTGAAATTTGTTATCATTTTACAAAATTG
1 AAAGTTGTAATTTGTTATCATTTTACAAAA-TG
* *
42694835 AAA-TTGTAATTTGTTACCATTTCACAAAATG
1 AAAGTTGTAATTTGTTATCATTTTACAAAATG
* **
42694866 AAAGTTGTTATTCATTATCATTTTACA
1 AAAGTTGTAATTTGTTATCATTTTACA
42694893 TATTACAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 5 0.10
32 41 0.84
33 3 0.06
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (32 bp):
AAAGTTGTAATTTGTTATCATTTTACAAAATG
Found at i:42696685 original size:22 final size:22
Alignment explanation
Indices: 42696653--42696750 Score: 64
Period size: 22 Copynumber: 4.6 Consensus size: 22
42696643 TCAATTATTT
*
42696653 TCTCAATTTCCTCTCAATTTGC
1 TCTCAAATTCCTCTCAATTTGC
42696675 TCTCAAATTCCT-TCCAAATTT-C
1 TCTCAAATTCCTCT-C-AATTTGC
* **
42696697 TCTCAAA-TCC-AT--ATTTAA
1 TCTCAAATTCCTCTCAATTTGC
* *
42696715 TCTCAATTTGCTCTCAATTTGC
1 TCTCAAATTCCTCTCAATTTGC
* *
42696737 TCTTAAATTTCTCT
1 TCTCAAATTCCTCT
42696751 TAAACCCCTA
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
17 4 0.07
18 6 0.10
19 2 0.03
20 1 0.02
21 5 0.09
22 35 0.60
23 5 0.09
ACGTcount: A:0.24, C:0.28, G:0.03, T:0.45
Consensus pattern (22 bp):
TCTCAAATTCCTCTCAATTTGC
Found at i:42696703 original size:11 final size:11
Alignment explanation
Indices: 42696639--42696704 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
42696629 AAACTAATCA
42696639 TCTCTCAATTATT
1 TCTCTCAA--ATT
42696652 T-TCTC-AATT
1 TCTCTCAAATT
42696661 TCCTCTC-AATT
1 T-CTCTCAAATT
42696672 TGCTCTCAAATT
1 T-CTCTCAAATT
*
42696684 CCT-TCCAAATT
1 TCTCT-CAAATT
42696695 TCTCTCAAAT
1 TCTCTCAAAT
42696705 CCATATTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 4 0.09
10 1 0.02
11 30 0.67
12 9 0.20
13 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.45
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:42696735 original size:11 final size:11
Alignment explanation
Indices: 42696715--42696739 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42696705 CCATATTTAA
42696715 TCTCAATTTGC
1 TCTCAATTTGC
42696726 TCTCAATTTGC
1 TCTCAATTTGC
42696737 TCT
1 TCT
42696740 TAAATTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (11 bp):
TCTCAATTTGC
Found at i:42696763 original size:51 final size:50
Alignment explanation
Indices: 42696664--42696763 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 50
42696654 CTCAATTTCC
*
42696664 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTT-CAAATTTCTCTCAAACCCATATTTAA
* * *
42696715 TCTCAATTTGCTCTCAATTTGCTCTT-AAATTTCTCTTAAACCCCTATTT
1 TCTCAATTTGCTCTCAAATT-C-CTTCAAATTTCTCTCAAACCCATATTT
42696764 TTAAATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 39 0.91
52 1 0.02
53 3 0.07
ACGTcount: A:0.26, C:0.27, G:0.03, T:0.44
Consensus pattern (50 bp):
TCTCAATTTGCTCTCAAATTCCTTCAAATTTCTCTCAAACCCATATTTAA
Found at i:42698180 original size:19 final size:17
Alignment explanation
Indices: 42698146--42698180 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
42698136 TTAAAATAGT
42698146 AACAAAATTAACAATAA
1 AACAAAATTAACAATAA
42698163 AACAAGAATTATACAATA
1 AACAA-AATTA-ACAATA
42698181 TCCAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (17 bp):
AACAAAATTAACAATAA
Found at i:42732204 original size:33 final size:33
Alignment explanation
Indices: 42732122--42732204 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 33
42732112 TGGTCTAACC
* ** * *
42732122 ATGGTCTTACGTTTAAGGTGCCATAACCCAATT
1 ATGGTCTTACATTTAAAATGACATAACCCAACT
* * *
42732155 ATGGTCTTTTCA-TTAAAATGACATAGCTCAACT
1 ATGGTC-TTACATTTAAAATGACATAACCCAACT
42732188 ATGGTCTTACATTTAAA
1 ATGGTCTTACATTTAAA
42732205 CATTGCCATG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
32 4 0.10
33 32 0.82
34 3 0.08
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (33 bp):
ATGGTCTTACATTTAAAATGACATAACCCAACT
Found at i:42733667 original size:30 final size:29
Alignment explanation
Indices: 42733631--42733691 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
42733621 TTTTTAGAAT
42733631 TAATGATAAATAAAATATTAAAAAATTTAA
1 TAATGATAAATAAAAT-TTAAAAAATTTAA
***
42733661 TAATGATAAATGGTATTTAAAAAATTTAA
1 TAATGATAAATAAAATTTAAAAAATTTAA
42733690 TA
1 TA
42733692 TCACTGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (29 bp):
TAATGATAAATAAAATTTAAAAAATTTAA
Found at i:42744662 original size:18 final size:19
Alignment explanation
Indices: 42744641--42744689 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
42744631 TTAATAAAAA
*
42744641 ATATTAAAATA-TTATTTT
1 ATATTAAAATAGTTATATT
42744659 ATATTTAAAATAAGTTATATT
1 ATA-TTAAAAT-AGTTATATT
42744680 AT-TTAAAATA
1 ATATTAAAATA
42744690 AACCACTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.15
19 14 0.52
20 1 0.04
21 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATTAAAATAGTTATATT
Found at i:42745379 original size:228 final size:227
Alignment explanation
Indices: 42744973--42745635 Score: 767
Period size: 228 Copynumber: 2.9 Consensus size: 227
42744963 CTTTGAAGAA
* * *
42744973 GATGCAGATCTTTGTGAAAACCCTTACCGGCAAGACCATAACACTCGAGGTCGAAAGCTCCGACA
1 GATGCAGATCTTTGTCAAAA-CCTTACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACA
* * * *
42745038 CCATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCCGACCAGCAGCGTCTC
65 CCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCTC
* ** * * ** *
42745103 ATTTTCGCTGGCAAACAGCTCGAAGACGGTCGGACCCTT-GCCGATTATAACATCCAGAAAGAAT
130 ATCTTCGCTGGCAAACAATTGGAAGATGGGAGGA-CCTTGGCTGATTATAACATCCAGAAAGAAT
*
42745167 CCACCCTCCACCTCGTCTT-ACGCCTTCGTGG-GG
194 CCACCCTTCACCTCGTCTTGA-GCCTTCGTGGAGG
* * * *
42745200 GCATGCAAATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGTTCCGAC
1 G-ATGCAGATCTTTGTCAAAACCTT-ACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGAC
* * *
42745265 ACCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGCATCCCACCTGACCAACAGCGTTT
64 ACCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCT
* *
42745330 GATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAATATCCA-AAAGGAA
129 CATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAA-GAA
* * *
42745394 TCCACCCTTCACCTTGTTTTGAGGCTTCGTGGAGG
193 TCCACCCTTCACCTCGTCTTGAGCCTTCGTGGAGG
* * * * * * * * *
42745429 GATGCAGATTTTTGTCAAGACTTTGACCGGCAAAACAATCACCTTGGAGGTTGAAAGCTCCGATA
1 GATGCAGATCTTTGTCAAAACCTT-ACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACA
* * * * * * ** *
42745494 CCATTGACAATGTTAAGGCAAAGATTCAGGATAAGGAAGGAATCCCACCTGATCAGCAAAGGCTC
65 CCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCTC
* * * * *
42745559 ATCTTTGCCGGCAAACAATTGGAAGATGGGAGGACTTTGGCTGATTATAACATTCAGAAAGAGTC
130 ATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAAGAATC
*
42745624 TACCCTTCACCT
195 CACCCTTCACCT
42745636 TGTTCTTCGT
Statistics
Matches: 368, Mismatches: 61, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
227 12 0.03
228 349 0.95
229 7 0.02
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.21
Consensus pattern (227 bp):
GATGCAGATCTTTGTCAAAACCTTACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACAC
CATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCTCA
TCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAAGAATCC
ACCCTTCACCTCGTCTTGAGCCTTCGTGGAGG
Found at i:42747209 original size:245 final size:245
Alignment explanation
Indices: 42746871--42747362 Score: 984
Period size: 245 Copynumber: 2.0 Consensus size: 245
42746861 ACCTATTAAT
42746871 ATTGTATTGTTTGTTTCATCTGGTTTTCTTCTTCTCCACTTTCTGATATATGTCTACTTCCATGA
1 ATTGTATTGTTTGTTTCATCTGGTTTTCTTCTTCTCCACTTTCTGATATATGTCTACTTCCATGA
42746936 TTGCAGACACTATATGCTTCCATGCAGGAAGAAAGTTGAATACAACATCACCATTTTGTCAGCCT
66 TTGCAGACACTATATGCTTCCATGCAGGAAGAAAGTTGAATACAACATCACCATTTTGTCAGCCT
42747001 GTATGATAGTGATAATTCCATGGAAAATAATCCATAGCCAACTGACTGGCTGATGAAGCTGAGGC
131 GTATGATAGTGATAATTCCATGGAAAATAATCCATAGCCAACTGACTGGCTGATGAAGCTGAGGC
42747066 TACTTTTTCTAATCCTTGCACTTCTAAACCATGCAATTGGATACTAAATA
196 TACTTTTTCTAATCCTTGCACTTCTAAACCATGCAATTGGATACTAAATA
42747116 ATTGTATTGTTTGTTTCATCTGGTTTTCTTCTTCTCCACTTTCTGATATATGTCTACTTCCATGA
1 ATTGTATTGTTTGTTTCATCTGGTTTTCTTCTTCTCCACTTTCTGATATATGTCTACTTCCATGA
42747181 TTGCAGACACTATATGCTTCCATGCAGGAAGAAAGTTGAATACAACATCACCATTTTGTCAGCCT
66 TTGCAGACACTATATGCTTCCATGCAGGAAGAAAGTTGAATACAACATCACCATTTTGTCAGCCT
42747246 GTATGATAGTGATAATTCCATGGAAAATAATCCATAGCCAACTGACTGGCTGATGAAGCTGAGGC
131 GTATGATAGTGATAATTCCATGGAAAATAATCCATAGCCAACTGACTGGCTGATGAAGCTGAGGC
42747311 TACTTTTTCTAATCCTTGCACTTCTAAACCATGCAATTGGATACTAAATA
196 TACTTTTTCTAATCCTTGCACTTCTAAACCATGCAATTGGATACTAAATA
42747361 AT
1 AT
42747363 AGTAAATACC
Statistics
Matches: 247, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
245 247 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (245 bp):
ATTGTATTGTTTGTTTCATCTGGTTTTCTTCTTCTCCACTTTCTGATATATGTCTACTTCCATGA
TTGCAGACACTATATGCTTCCATGCAGGAAGAAAGTTGAATACAACATCACCATTTTGTCAGCCT
GTATGATAGTGATAATTCCATGGAAAATAATCCATAGCCAACTGACTGGCTGATGAAGCTGAGGC
TACTTTTTCTAATCCTTGCACTTCTAAACCATGCAATTGGATACTAAATA
Found at i:42763676 original size:58 final size:58
Alignment explanation
Indices: 42763538--42763680 Score: 198
Period size: 59 Copynumber: 2.4 Consensus size: 58
42763528 TGGCTTGCGG
*
42763538 TTGCGGTTGCTTTTAGTGCCCAAACAAATTCAATCCTTGACATGCTGGTTATTGTGAC
1 TTGCGGTTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTTATTGTGAC
* * * * * *
42763596 TTGTGGTTTACTTTTAGTGCCAAAACAAATTTAATTCTTGACATGCTTG-TAGTTGTGGC
1 TTGCGG-TTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTTA-TTGTGAC
42763655 TTGCGGTTGCTTTTAGTGCCAAAACA
1 TTGCGGTTGCTTTTAGTGCCAAAACA
42763681 TAGCAACTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 26 0.35
59 48 0.65
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (58 bp):
TTGCGGTTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTTATTGTGAC
Found at i:42764952 original size:121 final size:121
Alignment explanation
Indices: 42764813--42765041 Score: 422
Period size: 121 Copynumber: 1.9 Consensus size: 121
42764803 GTATTGTAGT
* *
42764813 ATTATATATTATGGTTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTA
1 ATTATATATTATGATTTTAATAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTA
*
42764878 TATATTTTTATTAAATTATATTTAATAGTAATTATGTTAAAATGATATTTTATAGC
66 TATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATGATATTTTATAGC
*
42764934 ATTATATATTATGATTTTAATAAATTCATATAAGAATATTTAATATTAATAATTTTATTAAATTA
1 ATTATATATTATGATTTTAATAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTA
42764999 TATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAAT
66 TATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAAT
42765042 ATGATTAAAT
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
121 104 1.00
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.50
Consensus pattern (121 bp):
ATTATATATTATGATTTTAATAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTA
TATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATGATATTTTATAGC
Found at i:42765007 original size:18 final size:18
Alignment explanation
Indices: 42764973--42765019 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
42764963 ATAAGAATAT
42764973 TTAATATTA-ATAATTTTA
1 TTAA-ATTATATAATTTTA
*
42764991 TTAAATTATATATTTTTA
1 TTAAATTATATAATTTTA
42765009 TTAAATTATAT
1 TTAAATTATAT
42765020 TTAATAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATTATATAATTTTA
Found at i:42765083 original size:44 final size:40
Alignment explanation
Indices: 42764970--42765086 Score: 101
Period size: 41 Copynumber: 2.7 Consensus size: 40
42764960 CATATAAGAA
* *
42764970 TATTTAATATTAATAATTTTATT-AAATTATATATTTTTAT
1 TATTT-ATATTAATAATATTATTAAAATTATAAATTTTTAT
*
42765010 TAAATTATATTTAATAATAATTATGTTAAAATATGATTAAATTATTTAT
1 T-ATTTATA-TTAATAAT-ATTA--TTAAAAT-T-A-TAAATT-TTTAT
*
42765059 TATTTATATTAATAATCTTATTAAAATT
1 TATTTATATTAATAATATTATTAAAATT
42765087 TAATAATAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
40 4 0.06
41 11 0.18
42 3 0.05
43 1 0.02
44 9 0.15
45 4 0.06
46 4 0.06
47 9 0.15
48 11 0.18
49 6 0.10
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (40 bp):
TATTTATATTAATAATATTATTAAAATTATAAATTTTTAT
Found at i:42765204 original size:16 final size:16
Alignment explanation
Indices: 42765183--42765235 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
42765173 CAAGAATACT
*
42765183 ATTACGCCTCTATTAC
1 ATTACGCCTCTATTCC
*
42765199 ATTACGCTTCTATTCC
1 ATTACGCCTCTATTCC
42765215 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
42765231 ATTAC
1 ATTAC
42765236 AGCGAACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:42765851 original size:23 final size:24
Alignment explanation
Indices: 42765806--42765858 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
42765796 GTTCGTTTGA
*
42765806 AACATGTTCATGAATATTAAATT-
1 AACATGTTCATGAACATTAAATTG
42765829 AACATGTTCATGAACA-TATAATTG
1 AACATGTTCATGAACATTA-AATTG
42765853 AACATG
1 AACATG
42765859 CTCACAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 19 0.70
24 6 0.22
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (24 bp):
AACATGTTCATGAACATTAAATTG
Found at i:42768458 original size:6 final size:6
Alignment explanation
Indices: 42768425--42768469 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
42768415 ACACAACACC
* * *
42768425 TAACAG TAATCAG TAACGG TAGCAG TAACAG TAATAG TAACAG TA
1 TAACAG TAA-CAG TAACAG TAACAG TAACAG TAACAG TAACAG TA
42768470 TTCAACACAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.22
Consensus pattern (6 bp):
TAACAG
Found at i:42768546 original size:45 final size:45
Alignment explanation
Indices: 42768449--42768553 Score: 151
Period size: 45 Copynumber: 2.3 Consensus size: 45
42768439 AACGGTAGCA
*
42768449 GTAACAGTAATAGTAACAGTATTCAACACACAAAGTGTTGAATCT
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAATCT
*
42768494 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCT-AATC-
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGT-TGAATCT
*
42768538 GATGACAGTAACAGTA
1 G-TAACAGTAACAGTA
42768554 GTCGGCATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
44 1 0.02
45 52 0.96
46 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAATCT
Found at i:42768813 original size:40 final size:41
Alignment explanation
Indices: 42768753--42768860 Score: 116
Period size: 40 Copynumber: 2.7 Consensus size: 41
42768743 AATTCATTAC
* ** *
42768753 TTCAGTAATTTCACTGTTCAATGT-AGTACAC-ATAACAATA
1 TTCAGTAACTTCACAATTCAAT-TCAGTACACAAAAACAATA
*
42768793 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAAACAATA
1 TTCAGTAACTTCACAATTCAATTCAGTACACAAAAACAATA
*
42768834 TTCAGT-A-TTCAATAATTCAATTCAGTA
1 TTCAGTAACTTC-ACAATTCAATTCAGTA
42768861 TCAGTCTCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 4 0.07
40 41 0.69
41 14 0.24
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (41 bp):
TTCAGTAACTTCACAATTCAATTCAGTACACAAAAACAATA
Found at i:42768856 original size:20 final size:19
Alignment explanation
Indices: 42768792--42768861 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
42768782 ACATAACAAT
*
42768792 ATTCAGTAACTTCACAATTCA
1 ATTCAGT-A-TTCAAAATTCA
* *
42768813 ATTCAGTACTCAAAA-ACAA
1 ATTCAGTATTCAAAATTC-A
42768832 TATTCAGTATTCAATAATTCA
1 -ATTCAGTATTCAA-AATTCA
42768853 ATTCAGTAT
1 ATTCAGTAT
42768862 CAGTCTCAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.03
19 6 0.15
20 22 0.55
21 10 0.25
22 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (19 bp):
ATTCAGTATTCAAAATTCA
Found at i:42770295 original size:101 final size:102
Alignment explanation
Indices: 42770180--42770364 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
42770170 AAAGTGATGG
* * *
42770180 TCACGTGTGTAGTACTATGTGCTGGCTACTACGTGTACC--AGAATGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAATGAT-GGTCACATGTGTAGT
*
42770243 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACAATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
*
42770281 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATAATGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAATGATGGTCACATGTGTAGTA
42770346 CAATGTGCAGGCTACTATG
66 CAATGTGCAGGCTACTATG
42770365 TGAACCGGTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 37 0.48
102 33 0.43
103 7 0.09
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAATGATGGTCACATGTGTAGTA
CAATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:42770301 original size:51 final size:50
Alignment explanation
Indices: 42770174--42770372 Score: 222
Period size: 51 Copynumber: 3.9 Consensus size: 50
42770164 AAAGTGAAAG
* * *
42770174 TGATGGTCACGTGTGTAGTACTATGTGCTGGCTACTACGTGTACCAGA-A
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
* * *
42770223 TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
* * * * *
42770274 -GCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATAA
1 TG-AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-A
* * *
42770326 TGATGGTCACATGTGTAGTACAATGTGCAGGCTACTATGTGAACCGG
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
42770373 TATCATTAAT
Statistics
Matches: 122, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
49 4 0.03
50 39 0.32
51 76 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (50 bp):
TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA
Found at i:42770366 original size:26 final size:26
Alignment explanation
Indices: 42770286--42770366 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
42770276 TTCGATCACG
*
42770286 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACAATGTGCAGGCTACTA
* *
42770312 CGTGTA-T-CGAATAATG-ATGG-TCAC-A
1 TGTGTAGTAC-AAT-GTGCA-GGCT-ACTA
42770337 TGTGTAGTACAATGTGCAGGCTACTA
1 TGTGTAGTACAATGTGCAGGCTACTA
42770363 TGTG
1 TGTG
42770367 AACCGGTATC
Statistics
Matches: 41, Mismatches: 5, Indels: 18
0.64 0.08 0.28
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (26 bp):
TGTGTAGTACAATGTGCAGGCTACTA
Found at i:42770402 original size:101 final size:100
Alignment explanation
Indices: 42770182--42770372 Score: 267
Period size: 102 Copynumber: 1.9 Consensus size: 100
42770172 AGTGATGGTC
* * * *
42770182 ACGTGTGTAGTACTATGTGCTGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTACTA
1 ACGTGTGTA-TACTATGTGCAGGCTACTACGTGTACAAGAATGATAGGTCACATGTGTAGTACAA
* *
42770247 TGTGCAGGCTACTATGCGTACCGGATAGCTTCGATC
65 TGTGCAGGCTACTATGCGAACCGGATAGCTTCGATA
*
42770283 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATAATGAT-GGTCACATGTGTAGTAC
1 ACGTGTGTA-TACTATGTGCAGGCTACTACGTGTA-C-AAGAATGATAGGTCACATGTGTAGTAC
*
42770347 AATGTGCAGGCTACTATGTGAACCGG
63 AATGTGCAGGCTACTATGCGAACCGG
42770373 TATCATTAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 34 0.42
102 40 0.49
103 7 0.09
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (100 bp):
ACGTGTGTATACTATGTGCAGGCTACTACGTGTACAAGAATGATAGGTCACATGTGTAGTACAAT
GTGCAGGCTACTATGCGAACCGGATAGCTTCGATA
Found at i:42770440 original size:46 final size:43
Alignment explanation
Indices: 42770368--42770466 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 43
42770358 TACTATGTGA
*
42770368 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* *
42770411 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
42770457 ACCGTGTATC
1 ACCG-GTATC
42770467 TGTTATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 11 0.23
45 2 0.04
46 27 0.56
47 3 0.06
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:42770610 original size:16 final size:16
Alignment explanation
Indices: 42770589--42770620 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42770579 TGATTGAAAG
*
42770589 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
42770605 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
42770621 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:42772889 original size:17 final size:17
Alignment explanation
Indices: 42772867--42772900 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42772857 GAATGGTCTC
*
42772867 TGTTTCTTTTCTTCTTT
1 TGTTTCTTTTATTCTTT
42772884 TGTTTCTTTTATTCTTT
1 TGTTTCTTTTATTCTTT
42772901 CATTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (17 bp):
TGTTTCTTTTATTCTTT
Found at i:42778580 original size:22 final size:22
Alignment explanation
Indices: 42778550--42778596 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
42778540 GTCGAATTTA
*
42778550 TTTTATTAAAAAATTAAAATAT
1 TTTTATTAAAAAAATAAAATAT
* *
42778572 TTTTTTTAAAAAAATAAGATAT
1 TTTTATTAAAAAAATAAAATAT
42778594 TTT
1 TTT
42778597 CTTTCACCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTATTAAAAAAATAAAATAT
Found at i:42778723 original size:13 final size:13
Alignment explanation
Indices: 42778692--42778716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42778682 TCAAACGAAC
42778692 ATAATTATATTTA
1 ATAATTATATTTA
42778705 ATAATTATATTT
1 ATAATTATATTT
42778717 GTTAATTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATAATTATATTTA
Found at i:42785102 original size:21 final size:21
Alignment explanation
Indices: 42785076--42785117 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42785066 TGACAAGTTC
* *
42785076 AAGTACCGAATCAGTAAAAAA
1 AAGTACCAAATCAGGAAAAAA
*
42785097 AAGTACCAAATTAGGAAAAAA
1 AAGTACCAAATCAGGAAAAAA
42785118 GAGTCAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.14, T:0.14
Consensus pattern (21 bp):
AAGTACCAAATCAGGAAAAAA
Found at i:42786822 original size:25 final size:25
Alignment explanation
Indices: 42786793--42786865 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 25
42786783 ATGCAAAAAC
*
42786793 AGTTTATAATAAATGATAAATAA-G-A
1 AGTTTA-AAAAAAT-ATAAATAAGGAA
42786818 AGTTTAAAACAAATA-ATAATGAAGGAA
1 AGTTTAAAA-AAATATA-AAT-AAGGAA
42786845 AGTTTAAAAAAATATAAATAA
1 AGTTTAAAAAAATATAAATAA
42786866 ATAAATAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
23 1 0.02
24 6 0.15
25 14 0.34
26 9 0.22
27 11 0.27
ACGTcount: A:0.60, C:0.01, G:0.11, T:0.27
Consensus pattern (25 bp):
AGTTTAAAAAAATATAAATAAGGAA
Found at i:42788518 original size:132 final size:131
Alignment explanation
Indices: 42788371--42788804 Score: 672
Period size: 132 Copynumber: 3.3 Consensus size: 131
42788361 AGACTGGATG
* * *** ** * *
42788371 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATATAGT-TTCTTTTGTCTGCTCCACTACTGCT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GTAATCTTCAATCTATTCCACTGCTGCC
* *** *
42788435 TAGGGAGATAAGACTGCCGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCACCAT
65 CAGGGAGAT-AGACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCAT
42788500 CTT
129 CTT
*
42788503 CAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
*
42788568 AGGGAGATAGAGCTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGTCATC
66 AGGGAGATAGA-CTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATC
42788633 TT
130 TT
42788635 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
*
42788700 AGAGAGATAGAACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATC
66 AGGGAGATAG-ACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATC
42788765 TT
130 TT
42788767 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
1 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
42788805 GGTTTTAATC
Statistics
Matches: 280, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
131 5 0.02
132 274 0.98
133 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (131 bp):
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
AGGGAGATAGACTAATGGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCT
T
Found at i:42788547 original size:44 final size:44
Alignment explanation
Indices: 42788336--42788804 Score: 248
Period size: 44 Copynumber: 10.8 Consensus size: 44
42788326 TTCCTTCATT
* * *
42788336 TGCTCCACTACTGCTTAGGGAGATAAGA-CTG-GA--TGCGATC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
* * ***
42788376 TGCTCCACTACTGCTTAGGGAGATAAGATATAGT-TTCTTTTGTC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCT-GTAATCTTCAATC
**** *
42788420 TGCTCCACTACTGCTTAGGGAGATAAGA-CTGCCGGCTTCAATG
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
* * * * * ****
42788463 TACTCCACTGTAAT-CTCAGGGAGGTAAAATCCACCATCTTCAATC
1 TGCTCCAC--TACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
42788508 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
** * ** * *
42788552 TATTCCACTGCTGCCCAGGGAGAT-AGAGC--TAATGGCTTCAATG
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT--CTTCAATC
* * * * * * * *
42788595 TACTCCACTGTAAT-CTCAGGGAGGTAAAATCCGTCATCTTCGATC
1 TGCTCCAC--TACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
42788640 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
** * ** * * *
42788684 TATTCCACTGCTGCCCAGAGAGAT-AGAAC--TAATGGCTTCAATG
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT--CTTCAATC
* * * * * * ** *
42788727 TACTCCACTGTAAT-CTCAGGGAGGTAAAATCCGCCATCTTCGATC
1 TGCTCCAC--TACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
42788772 TGCTCCACTACTGCTTAGGGAGATAAGATCTGT
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGT
42788805 GGTTTTAATC
Statistics
Matches: 318, Mismatches: 85, Indels: 48
0.71 0.19 0.11
Matches are distributed among these distances:
40 28 0.09
41 9 0.03
42 2 0.01
43 57 0.18
44 161 0.51
45 56 0.18
47 5 0.02
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
Found at i:42789199 original size:87 final size:87
Alignment explanation
Indices: 42789068--42789459 Score: 680
Period size: 87 Copynumber: 4.5 Consensus size: 87
42789058 CACCAGTATG
* **
42789068 GGAAGACAAGATCTGC-ATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGAATTTGTTTTC
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
**
42789132 GATCTGCTTTGCTGTTAATGCA
66 GATCTGCTCCGCTGTTAATGCA
*
42789154 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTATTTTC
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
*
42789219 TATCTGCTCCGCTGTTAATGCA
66 GATCTGCTCCGCTGTTAATGCA
* *
42789241 AGAAGGCAAGATCTGCTATATTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTT-
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
42789305 GATCTGCTCCGCTGTTAATGCA
66 GATCTGCTCCGCTGTTAATGCA
42789327 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
42789392 GATCTGCTCCGCTGTTAATGCA
66 GATCTGCTCCGCTGTTAATGCA
*
42789414 GGAAGGCAAGATCTACTATCTTTAACCAGCTCCACTGCAACCGATG
1 GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG
42789460 AAGTAAAAAA
Statistics
Matches: 290, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
86 98 0.34
87 192 0.66
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (87 bp):
GGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTTC
GATCTGCTCCGCTGTTAATGCA
Found at i:42789363 original size:173 final size:174
Alignment explanation
Indices: 42789069--42789459 Score: 678
Period size: 173 Copynumber: 2.3 Consensus size: 174
42789059 ACCAGTATGG
*
42789069 GAAGACAAGATCTGC-ATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGAATTTGTTTTCG
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGAATTTGTTTTCG
**
42789133 ATCTGCTTTGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGA
66 ATCTGCTCCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGA
*
42789198 TGGAGGCAAGGTTTTATTTTCTATCTGCTCCGCTGTTAATGCAA
131 TGGAGGCAAGGTTTTATTTTCGATCTGCTCCGCTGTTAATGCAA
* **
42789242 GAAGGCAAGATCTGCTATATTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTT-G
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGAATTTGTTTTCG
42789306 ATCTGCTCCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGA
66 ATCTGCTCCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGA
* *
42789371 TGGAGGCAAGGTTTTGTTTTCGATCTGCTCCGCTGTTAATGCAG
131 TGGAGGCAAGGTTTTATTTTCGATCTGCTCCGCTGTTAATGCAA
*
42789415 GAAGGCAAGATCTACTATCTTTAACCAGCTCCACTGCAACCGATG
1 GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG
42789460 AAGTAAAAAA
Statistics
Matches: 206, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
173 162 0.79
174 44 0.21
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (174 bp):
GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGAATTTGTTTTCG
ATCTGCTCCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGA
TGGAGGCAAGGTTTTATTTTCGATCTGCTCCGCTGTTAATGCAA
Found at i:42795304 original size:26 final size:25
Alignment explanation
Indices: 42795262--42795344 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
42795252 ATTGGATCCA
* *
42795262 AAACTTTAAACCTTGAACCCTGGACCC
1 AAAC-TTAAACCATGAA-CCTGAACCC
42795289 AAACTTAAACCATGAACCTGAACCC
1 AAACTTAAACCATGAACCTGAACCC
* * * *
42795314 TAACTTCAAACCCTAAACATCGAACCC
1 AAACTT-AAACCATGAACCT-GAACCC
42795341 AAAC
1 AAAC
42795345 CACGAACCGC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
25 13 0.28
26 21 0.45
27 13 0.28
ACGTcount: A:0.41, C:0.34, G:0.07, T:0.18
Consensus pattern (25 bp):
AAACTTAAACCATGAACCTGAACCC
Found at i:42805422 original size:113 final size:112
Alignment explanation
Indices: 42805278--42805869 Score: 497
Period size: 113 Copynumber: 5.3 Consensus size: 112
42805268 AAGAAAAAAA
* * *
42805278 ATTTTAGGTGCTGGCCTGTCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTACATTTTGG
1 ATTTT-GGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTATATTTTGG
* *
42805343 GCTATCATTGGCCAACACCAGTATACGAAAAAATTCAAAAAAATTTTAT
65 GCTGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAAAATTTT-T
* * ****** *
42805392 ATTTTGGTGGTGGCCTGGCAATGGCTGGCACCACCTTTATAT-ATAAAAAATTTTACATTTTGGG
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTATATTTTGGG
** * *
42805456 CCCTCATTTGCCGGCACCAGTATACGAAAAAATTC-----AATTTTT
66 CTGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAAAATTTTT
*
42805498 -TTTT-GTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTATATATTTTGGG
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTATATTTTGGG
* * * *
42805561 TTGTCATTGGCTGGA-ACTAGTATACGAAAAAATT-----TAATTTTT
66 CTGTCATTGGC-CGACACCAGTATACGAAAAAATTCAAAAAAATTTTT
* * * * ** * ***
42805603 TTTTTGCTGGTGGCCTAGCAATGGTCGATACCGCCTTTATGTAAAAAAGAGAAATTTTTTTTATA
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT-----A-A-TTTTTTTTTTTATA
* * * *
42805668 TTTT-GGCTGTTATTGGTCGGCACCAGTATACGAAAAAATTCAAAACAAA-ATTT
59 TTTTGGGCTGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAA-AAATTTTT
** **
42805721 -TTTTGGTGGTGGCCTGGCAATGATCGGCACCATGTTTATGTAAACTTTTTTTATTTTATATTTT
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT-AA-TTTTTTT-TTTTATATTTT
* * **
42805785 GGGTTGTCATTGGCCGACACCAGTATACAAAAAAATT-AAAAAAA---AA
63 GGGCTGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAAAATTTTT
*
42805831 ATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACCTTTA
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTA
42805870 CGGGAAAAAA
Statistics
Matches: 382, Mismatches: 74, Indels: 47
0.76 0.15 0.09
Matches are distributed among these distances:
104 34 0.09
105 50 0.13
106 6 0.02
107 36 0.09
111 33 0.09
112 56 0.15
113 79 0.21
114 50 0.13
117 33 0.09
118 3 0.01
119 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (112 bp):
ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTATATTTTGGG
CTGTCATTGGCCGACACCAGTATACGAAAAAATTCAAAAAAATTTTT
Found at i:42805517 original size:104 final size:108
Alignment explanation
Indices: 42805278--42805535 Score: 299
Period size: 112 Copynumber: 2.4 Consensus size: 108
42805268 AAGAAAAAAA
* * * ******
42805278 ATTTTAGGTGCTGGCCTGTCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTACATTTTGG
1 ATTTT-GGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATAT-ATAAAAAATTTTACATTTTGG
*
42805343 GCTATCATTGGCCAACACCAGTATACGAAAAAATTCAAAAAAATTTTAT
64 GCCATCATTGGCCAACACCAGTATACGAAAAAATTC----AAATTTTAT
*
42805392 ATTTTGGTGGTGGCCTGGCAATGGCTGGCACCACCTTTATATATAAAAAATTTTACATTTTGGGC
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATATATAAAAAATTTTACATTTTGGGC
* * **
42805457 CCTCATTTGCCGGCACCAGTATACGAAAAAATTC-AATTTT-T
66 CATCATTGGCCAACACCAGTATACGAAAAAATTCAAATTTTAT
42805498 -TTTT-GTGGTGGCCTGGCAATGGCCGGCACCACCTTTAT
1 ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTAT
42805536 GTAATTTTTT
Statistics
Matches: 128, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
104 33 0.26
105 4 0.03
106 1 0.01
107 6 0.05
112 46 0.36
113 33 0.26
114 5 0.04
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (108 bp):
ATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATATATAAAAAATTTTACATTTTGGGC
CATCATTGGCCAACACCAGTATACGAAAAAATTCAAATTTTAT
Found at i:42805835 original size:114 final size:109
Alignment explanation
Indices: 42805657--42805863 Score: 279
Period size: 114 Copynumber: 1.9 Consensus size: 109
42805647 AAAAGAGAAA
* * * * **
42805657 TTTTTTTTATATTTTGGCTGTTATTGGTCGGCACCAGTATACGAAAAAATTCAAAACAAAATTTT
1 TTTTTTTTATATTTTGGCTGTCATTGGCCGACACCAGTATACAAAAAAATT-AAAA-AAAA-AAT
* *
42805722 TTTGGTGGTGGCCTGGCAATGATCGGCACCATGTTTATGTAAACTTT
63 TTTGGTGGTGGCCTGCCAATGACCGGCACCATGTTTATGTAAACTTT
*
42805769 TTTTATTTTATATTTTGGGTTGTCATTGGCCGACACCAGTATACAAAAAAATTAAAAAAAAAATT
1 TTTT-TTTTATATTTT-GGCTGTCATTGGCCGACACCAGTATACAAAAAAATTAAAAAAAAAATT
*
42805834 TTGGTGGTGGCCTGCCAATGGCCGGCACCA
64 TTGGTGGTGGCCTGCCAATGACCGGCACCA
42805864 CCTTTACGGG
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
111 29 0.35
112 8 0.10
113 15 0.18
114 31 0.37
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (109 bp):
TTTTTTTTATATTTTGGCTGTCATTGGCCGACACCAGTATACAAAAAAATTAAAAAAAAAATTTT
GGTGGTGGCCTGCCAATGACCGGCACCATGTTTATGTAAACTTT
Found at i:42806954 original size:19 final size:19
Alignment explanation
Indices: 42806897--42806955 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
42806887 ATTTACAGAA
42806897 TAATATTCAAACAAATAAT
1 TAATATTCAAACAAATAAT
* * * *
42806916 T-AT-TTTAGATCCATTAAAT
1 TAATATTCA-AACAAAT-AAT
42806935 TAATATTCAAACAAATAAT
1 TAATATTCAAACAAATAAT
42806954 TA
1 TA
42806956 TTTTAGATCC
Statistics
Matches: 28, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
17 3 0.11
18 6 0.21
19 10 0.36
20 6 0.21
21 3 0.11
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (19 bp):
TAATATTCAAACAAATAAT
Found at i:42807519 original size:109 final size:107
Alignment explanation
Indices: 42806964--42807761 Score: 834
Period size: 108 Copynumber: 7.3 Consensus size: 107
42806954 TATTTTAGAT
* * * *
42806964 CCATTGCTAGGCCACCACC-AAATTTTTTTTTTGAATTTTTTCGTATATTAGTGCCGACCAATGA
1 CCATTGCCAGGCCACCACCAAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAATGA
* * *
42807028 CAGCTCAAAGTGTAAATTTTTTTTACATAAAGGTGGTGCCAG
66 CAGCCCAAAATGTAAATTTTTTTTACATAAAGGTGGTGCCGG
**** * * *
42807070 CCATTGCCAGGCCACCA-CAAAA-AAAATTTTTGAATTTTTTCGTACACTGGTGTCGGCTAATGA
1 CCATTGCCAGGCCACCACCAAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAATGA
* *****
42807133 CAGCCAAAAATGTAAAAAAAAAATTTACATAAAGGTGGTGCCGG
66 CAGCCCAAAATGT--AAATTTTTTTTACATAAAGGTGGTGCCGG
*
42807177 CCATTGCCAGGCCACCACCAAAA-TTTTTTTTTGAATTTTTTCGTATATTGGTGCCGGCCAATGA
1 CCATTGCCAGGCCACCACCAAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAATGA
* *
42807241 TAGCCCAAAATGT-AATTTTTTTTACATAAAGGTGGTGCCAG
66 CAGCCCAAAATGTAAATTTTTTTTACATAAAGGTGGTGCCGG
* * * * * *
42807282 CCATTGCCATGCCACCACCAAAAAAATTTTTTTTTGAATTTTTTTGTATACTGATGTCGGCCAAG
1 CCATTGCCAGGCCACCACC--AAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAAT
* **** * *
42807347 GACAGCTCAAAATGTAAAAAAAAATTCTACATAAAGGTGGTGTCGG
64 GACAGCCCAAAATGT--AAATTTTTTTTACATAAAGGTGGTGCCGG
* * * * *
42807393 CCATTGCCAAGCTACCACCAAAACTTTTTTTTTTTGAATTTTTTTCATATACTGGTGCTGGCAAA
1 CCATTGCCAGGCCACCACCAAAA--TTTTTTTTTTGAA-TTTTTTCGTATACTGGTGCCGGCCAA
*
42807458 TGACAACCCAAAATGT-AATTTTTTTTACATAAAGGTGGTGCCGG
63 TGACAGCCCAAAATGTAAATTTTTTTTACATAAAGGTGGTGCCGG
* *
42807502 CAATTGCCAGGCCACCACCAAATTTTTTTTTCTTTTGAATTTTTTCGTATACTGGTGCCGGCCAA
1 CCATTGCCAGGCCACCACCAAA--ATTTTTT-TTTTGAATTTTTTCGTATACTGGTGCCGGCCAA
* * **** **
42807567 TGATAGCCCAAAATATATAAAAAAAAATTTTACATAAAATTGGTGCCGG
63 TGACAGCCC-AAA-ATGT--AAATTTTTTTTACATAAAGGTGGTGCCGG
* *
42807616 CCATTGCCAGGCCACCACCAAAAAAATATTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCAAA
1 CCATTGCCAGGCCACCACC---AAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAA
*
42807681 TGACAGCCCAAAATGTAAAAATTTTTTTTACATAAAGGTGGTGTCGG
63 TGACAGCCCAAAATGT--AAATTTTTTTTACATAAAGGTGGTGCCGG
* * * *
42807728 CTATTGACAGGTCAGCACCAAAATTTTTTTTTTG
1 CCATTGCCAGGCCACCACCAAAATTTTTTTTTTG
42807762 TTCTTTCTTT
Statistics
Matches: 565, Mismatches: 103, Indels: 45
0.79 0.14 0.06
Matches are distributed among these distances:
105 82 0.15
106 19 0.03
107 44 0.08
108 96 0.17
109 95 0.17
110 10 0.02
111 53 0.09
112 75 0.13
113 3 0.01
114 80 0.14
115 5 0.01
117 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (107 bp):
CCATTGCCAGGCCACCACCAAAATTTTTTTTTTGAATTTTTTCGTATACTGGTGCCGGCCAATGA
CAGCCCAAAATGTAAATTTTTTTTACATAAAGGTGGTGCCGG
Found at i:42810907 original size:9 final size:9
Alignment explanation
Indices: 42810889--42810919 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42810879 TTTGGTTAAA
42810889 AATTAACCG
1 AATTAACCG
*
42810898 AATTACCCG
1 AATTAACCG
42810907 AATTAACCG
1 AATTAACCG
42810916 AATT
1 AATT
42810920 GAATCACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:42815566 original size:15 final size:15
Alignment explanation
Indices: 42815547--42815581 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42815537 TTTTTGGACT
*
42815547 TTTTTATTTTATTTTC
1 TTTTTATTCT-TTTTC
42815563 TTTTTATTCTTTTTC
1 TTTTTATTCTTTTTC
42815578 TTTT
1 TTTT
42815582 GGAGATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTCTTTTTC
Found at i:42843184 original size:4 final size:4
Alignment explanation
Indices: 42843177--42843202 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
42843167 CACACTTTTT
42843177 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
42843203 ATGGTTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:42851511 original size:14 final size:14
Alignment explanation
Indices: 42851483--42851515 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
42851473 AAGGAATGTT
42851483 ATTAGTAGATTAAA
1 ATTAGTAGATTAAA
42851497 ATTAG-AGATTAAA
1 ATTAGTAGATTAAA
*
42851510 AATAGT
1 ATTAGT
42851516 TCTTCTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (14 bp):
ATTAGTAGATTAAA
Found at i:42854482 original size:39 final size:39
Alignment explanation
Indices: 42854428--42854507 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
42854418 AGTTGTTTGT
42854428 AAGTACATTTTCATGATGTGGGCACAATCTATATGAGAC
1 AAGTACATTTTCATGATGTGGGCACAATCTATATGAGAC
42854467 AAGTACATTTTCATGATGTGGGCACAATCTATATGAGAC
1 AAGTACATTTTCATGATGTGGGCACAATCTATATGAGAC
42854506 AA
1 AA
42854508 CCTTCTCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (39 bp):
AAGTACATTTTCATGATGTGGGCACAATCTATATGAGAC
Found at i:42875435 original size:18 final size:18
Alignment explanation
Indices: 42875412--42875447 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
42875402 TAGCGCCAAT
42875412 TTTAAATAGATATTAAAA
1 TTTAAATAGATATTAAAA
42875430 TTTAAATAGATATTAAAA
1 TTTAAATAGATATTAAAA
42875448 AATCTATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (18 bp):
TTTAAATAGATATTAAAA
Found at i:42876270 original size:21 final size:23
Alignment explanation
Indices: 42876246--42876293 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
42876236 GCAGTGATTC
*
42876246 AGAACTTAAAAAG-ATAA-AAGA
1 AGAACTGAAAAAGAATAAGAAGA
*
42876267 AGAACTGAAGAAGAATAAGAAGA
1 AGAACTGAAAAAGAATAAGAAGA
42876290 AGAA
1 AGAA
42876294 GAAAAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 4 0.17
23 8 0.35
ACGTcount: A:0.65, C:0.04, G:0.21, T:0.10
Consensus pattern (23 bp):
AGAACTGAAAAAGAATAAGAAGA
Found at i:42878466 original size:11 final size:11
Alignment explanation
Indices: 42878450--42878491 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
42878440 TTAATAAATT
42878450 TAATTTTTTAA
1 TAATTTTTTAA
42878461 TAATTTTTT-A
1 TAATTTTTTAA
*
42878471 T-ATTGTTTAA
1 TAATTTTTTAA
*
42878481 TAATTATTTAA
1 TAATTTTTTAA
42878492 AAAACCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 6 0.22
10 4 0.15
11 17 0.63
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TAATTTTTTAA
Found at i:42878786 original size:31 final size:30
Alignment explanation
Indices: 42878747--42878809 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
42878737 CAGGGGTTAA
*
42878747 AAAGACAAAATATAATCTAACTCCTAATAT
1 AAAGACAAAATACAATCTAACTCCTAATAT
*
42878777 AAAGAACAAAATACAATCTAACTCTTAATAT
1 AAAG-ACAAAATACAATCTAACTCCTAATAT
42878808 AA
1 AA
42878810 GGACGCATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (30 bp):
AAAGACAAAATACAATCTAACTCCTAATAT
Found at i:42884082 original size:18 final size:17
Alignment explanation
Indices: 42884049--42884087 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
42884039 TTGTATAAAT
42884049 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
42884067 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
42884084 TGTG
1 TGTG
42884088 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:42884205 original size:8 final size:8
Alignment explanation
Indices: 42884192--42884220 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
42884182 CACTAGAGAC
42884192 CAGTGTTA
1 CAGTGTTA
42884200 CAGTGTTA
1 CAGTGTTA
42884208 CAGTGTTA
1 CAGTGTTA
42884216 CAGTG
1 CAGTG
42884221 AGTCCCGGGT
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:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:42884334 original size:23 final size:23
Alignment explanation
Indices: 42884307--42884382 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
42884297 AGTGTTATTG
42884307 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
42884330 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
42884353 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
42884376 ATCAGTG
1 ATCAGTG
42884383 TGCACTATGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:42888028 original size:18 final size:19
Alignment explanation
Indices: 42888007--42888049 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
42887997 AAGGAAAAGC
*
42888007 ATTTTACCTTTTA-AATTT
1 ATTTTACCTTTTAGAATTA
**
42888025 ATTTTATTTTTTAGAATTA
1 ATTTTACCTTTTAGAATTA
42888044 ATTTTA
1 ATTTTA
42888050 ATTTTTCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTACCTTTTAGAATTA
Found at i:42888047 original size:19 final size:19
Alignment explanation
Indices: 42888015--42888055 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42888005 GCATTTTACC
*
42888015 TTTTAAATTTATTTT-ATT
1 TTTTAAATTAATTTTAATT
42888033 TTTTAGAATTAATTTTAATT
1 TTTTA-AATTAATTTTAATT
42888053 TTT
1 TTT
42888056 CTATAGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 9 0.45
20 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTAAATTAATTTTAATT
Found at i:42891740 original size:23 final size:23
Alignment explanation
Indices: 42891712--42891763 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
42891702 TATGTACTAT
42891712 TGTATTAAAT-TATTTAAATATAA
1 TGTATTAAATATATTTAAA-ATAA
* **
42891735 TTTATTATTTATATTTAAAATAA
1 TGTATTAAATATATTTAAAATAA
42891758 TGTATT
1 TGTATT
42891764 TATCACTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TGTATTAAATATATTTAAAATAA
Found at i:42896436 original size:9 final size:9
Alignment explanation
Indices: 42896404--42896435 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
42896394 TTTGGTTAAA
42896404 AATTAACCG
1 AATTAACCG
42896413 AATTAACCG
1 AATTAACCG
*
42896422 AATTACCCG
1 AATTAACCG
42896431 AATTA
1 AATTA
42896436 CGCGAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:42896473 original size:17 final size:17
Alignment explanation
Indices: 42896451--42896513 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
42896441 ATTGAATCAG
42896451 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
42896468 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
42896488 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
42896505 TACATAATT
1 TACATAATT
42896514 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:42896492 original size:37 final size:37
Alignment explanation
Indices: 42896442--42896516 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
42896432 ATTACGCGAA
* *
42896442 TTGAATCAGTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
42896479 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
42896516 T
1 T
42896517 GAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:42896730 original size:39 final size:39
Alignment explanation
Indices: 42896648--42896764 Score: 218
Period size: 39 Copynumber: 3.0 Consensus size: 39
42896638 ACTTAAGAGT
*
42896648 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
42896686 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
42896725 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
42896764 T
1 T
42896765 TGGGTTGGAT
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
38 27 0.35
39 50 0.65
ACGTcount: A:0.18, C:0.03, G:0.29, T:0.50
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:42896763 original size:13 final size:13
Alignment explanation
Indices: 42896745--42896769 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42896735 TTTTAGTTTT
42896745 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
42896758 ATTGGGTTGGGT
1 ATTGGGTTGGGT
42896770 TGGATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:42897202 original size:33 final size:33
Alignment explanation
Indices: 42897160--42897282 Score: 219
Period size: 33 Copynumber: 3.7 Consensus size: 33
42897150 TATATATATG
42897160 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
1 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
42897193 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
1 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
42897226 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
1 TAAGACCATAGTTGGGCTATGGCATTCTGATGA
** *
42897259 TAAGACCATAACTGGGTTATGGCA
1 TAAGACCATAGTTGGGCTATGGCA
42897283 CTACAAATGT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (33 bp):
TAAGACCATAGTTGGGCTATGGCATTCTGATGA
Found at i:42897315 original size:66 final size:65
Alignment explanation
Indices: 42897157--42897300 Score: 216
Period size: 66 Copynumber: 2.2 Consensus size: 65
42897147 CAGTATATAT
** * **
42897157 ATGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAGTTGGGCTATGGCATTCTG
1 ATGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGCTATGGCATACAA
*
42897222 ATGATAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTAC
1 ATG-TAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGCTATGGCA-TAC
42897287 AA
64 AA
42897289 ATGTAAGACCAT
1 ATGTAAGACCAT
42897301 GGCAGGGCCA
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
65 3 0.04
66 63 0.89
67 5 0.07
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (65 bp):
ATGTAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGCTATGGCATACAA
Found at i:42898916 original size:5 final size:5
Alignment explanation
Indices: 42898902--42898940 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
42898892 AAAAGTTATG
42898902 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
42898941 AATAAAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 30 0.88
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:42899949 original size:22 final size:22
Alignment explanation
Indices: 42899899--42899979 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 22
42899889 GAACTTTAGC
* *
42899899 GTGCTCTCTGATTACTAGCACGTCA
1 GTGCTCTCTG-TT--TAGCACTTTA
*
42899924 GTGCTATCTGTTTAGCACATTT-
1 GTGCTCTCTGTTTAGCAC-TTTA
*
42899946 GTGCTCTCTGTATAGCACTTTA
1 GTGCTCTCTGTTTAGCACTTTA
42899968 GTGCTCTCTGTT
1 GTGCTCTCTGTT
42899980 CATTAGTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 3 0.06
22 33 0.69
23 1 0.02
24 2 0.04
25 9 0.19
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACTTTA
Found at i:42905502 original size:4 final size:4
Alignment explanation
Indices: 42905493--42905519 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
42905483 TGGTTTGAGC
42905493 ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACA
42905520 GAAGAAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:42909786 original size:20 final size:20
Alignment explanation
Indices: 42909762--42909819 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
42909752 AATTCTATGA
42909762 AATTTTTATATATTCTTTAT
1 AATTTTTATATATTCTTTAT
* * *
42909782 CATTTTTAT-TTTTATTTTAT
1 AATTTTTATATATT-CTTTAT
42909802 AATTTTTA-A-ATTCTTTAT
1 AATTTTTATATATTCTTTAT
42909820 TCGCATGACA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
18 5 0.17
19 5 0.17
20 20 0.67
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTTATATATTCTTTAT
Found at i:42910906 original size:21 final size:21
Alignment explanation
Indices: 42910881--42910922 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
42910871 ATCTAGTAGA
42910881 GTCCCAGAATGAGTATAATTC
1 GTCCCAGAATGAGTATAATTC
42910902 GTCCCAGAATGAGTATAATTC
1 GTCCCAGAATGAGTATAATTC
42910923 TTCCATTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (21 bp):
GTCCCAGAATGAGTATAATTC
Found at i:42918751 original size:2 final size:2
Alignment explanation
Indices: 42918744--42918779 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42918734 TCTATAGGTA
42918744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42918780 TGAATTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42926758 original size:2 final size:2
Alignment explanation
Indices: 42926751--42926791 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
42926741 GGATTACAAC
42926751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42926792 ACTGTTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42931836 original size:2 final size:2
Alignment explanation
Indices: 42931829--42931867 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
42931819 CATTGCAAAG
42931829 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
42931868 GAGGGGAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42935330 original size:21 final size:22
Alignment explanation
Indices: 42935306--42935346 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42935296 AAATAGGAAG
*
42935306 AAAACAA-TAAAAAATAGCATT
1 AAAACAACAAAAAAATAGCATT
*
42935327 AAAATAACAAAAAAATAGCA
1 AAAACAACAAAAAAATAGCA
42935347 ATTTTTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.15
Consensus pattern (22 bp):
AAAACAACAAAAAAATAGCATT
Found at i:42937238 original size:16 final size:16
Alignment explanation
Indices: 42937217--42937255 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42937207 AATAATGGAA
42937217 ATATATAAAAACATGT
1 ATATATAAAAACATGT
* **
42937233 ATATATGAAAGTATGT
1 ATATATAAAAACATGT
42937249 ATATATA
1 ATATATA
42937256 TAAATTAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:42938676 original size:15 final size:15
Alignment explanation
Indices: 42938643--42938691 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
42938633 TTTTTGAATA
42938643 TTGGGCTATAGGT--T
1 TTGGGCT-TAGGTGAT
42938657 TTGGGCTTAGGTGAT
1 TTGGGCTTAGGTGAT
*
42938672 TTGGGTTTAGGTGA-
1 TTGGGCTTAGGTGAT
42938686 TTGGGC
1 TTGGGC
42938692 ATTGTGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 5 0.16
14 12 0.39
15 14 0.45
ACGTcount: A:0.12, C:0.06, G:0.41, T:0.41
Consensus pattern (15 bp):
TTGGGCTTAGGTGAT
Found at i:42939293 original size:50 final size:50
Alignment explanation
Indices: 42939147--42939480 Score: 147
Period size: 50 Copynumber: 6.7 Consensus size: 50
42939137 TTACCATCTC
* * * *
42939147 CAATCTGTTTAACTGCAATGTCA-GGAAATAAGATTTGTCGTCGTAGCTT
1 CAATCTATTTAACTACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
* * ** * * * * *
42939196 CAATCTATTTCATTACACCGCCAGGGAAGTAAAATTCATTGTTGTAGCTT
1 CAATCTATTTAACTACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
* * *
42939246 CAATCTATTTAACCACAATGTCAGGGAAGCAAGATTCGCCGTCGTAGCTT
1 CAATCTATTTAACTACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
* * * ** * ** * * * *
42939296 TAGTCTGTTCCACTGCACCACCT-A-GGAAGTAAGATTCGCCGTTGTGGCCT
1 CAATCTATTTAACT--ACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
* * * * * * *
42939346 CAATCTTTTTAATTGCAATGTCGGGGAAAG-AAGATTCGCCTTTGTAGCTT
1 CAATCTATTTAACTACAATGTCAGGG-AAGTAAGATTCGTCGTCGTAGCTT
** * ** * * * * * *
42939396 CAATCTATTCCACTGCACCGTC-TGGAAGTACGATTCGCCGTTGTGGCCT
1 CAATCTATTTAACTACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
* * * * *
42939445 CAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATT
1 CAATCTATTTAACTACAATGTCAGGGAAGTAAGATT
42939481 TGCCGTTCTG
Statistics
Matches: 205, Mismatches: 72, Indels: 15
0.70 0.25 0.05
Matches are distributed among these distances:
48 6 0.03
49 50 0.24
50 141 0.69
51 4 0.02
52 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (50 bp):
CAATCTATTTAACTACAATGTCAGGGAAGTAAGATTCGTCGTCGTAGCTT
Found at i:42939486 original size:50 final size:50
Alignment explanation
Indices: 42939320--42939700 Score: 286
Period size: 50 Copynumber: 7.6 Consensus size: 50
42939310 GCACCACCTA
*
42939320 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAATTGCAATGTCGG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
* * * * ** ** *
42939370 GGAAAG-AAGATTCGCCTTTGTAGCTTCAATCTATTCCACTGCACCGTC-T
1 GG-AAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
* *
42939419 GGAAGTACGATTCGCCGTTGTGGCCTCAATCTTTTTAATTGCAATGTCGG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
* * * * * * * * *
42939469 GGAAGCAAGATTTGCCGTTCTGACTTCAATCTGTTCAACTGCACTG-CATAG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTC--GG
* * *
42939520 GAAAGTAAGATTCGCCGTTGTGGCCTCAATC-TTTTAAATGCAATATCGG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
*** * * * * * ** ** *
42939569 GGAAACGAGATTCACCGTTATAGCTTCAATCTGTTCCACTGCACCGCCTGG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTC-GG
* * * *
42939620 GAAAGTAAGATTCACCGTTGTGGCCTCAATC-TTTTAAATGCAATGTTGG
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
** * *
42939669 GGAAGCGAGATTCGCTGTTGTGGCTTCAATCT
1 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCT
42939701 GTTCCACTGT
Statistics
Matches: 241, Mismatches: 81, Indels: 18
0.71 0.24 0.05
Matches are distributed among these distances:
48 3 0.01
49 86 0.36
50 96 0.40
51 56 0.23
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (50 bp):
GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAACTGCAATGTCGG
Found at i:42939504 original size:199 final size:200
Alignment explanation
Indices: 42939190--42939709 Score: 622
Period size: 199 Copynumber: 2.6 Consensus size: 200
42939180 TTTGTCGTCG
* * * * * ** * *
42939190 TAGCTTCAATCTATTTCATTACACCGCCAGGG-AAGTAAAATTCATTGTTGTAGCTTCAATCTAT
1 TAGCTTCAATCTATTCCACTGCACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCT-T
*** * * *
42939254 TTAACCACAATGTCAGGGAAGCAAGATTCGCCG-TC-GTAGCTTTAGTCTGTTCCACTGCACCAC
65 TTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTCTG-A-CTTCAATCTGTTCCACTGCACCAC
* * *
42939317 CTAGG-AAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAATTGCAATGTCGGGGAAA-GAAGA
128 ATAGGAAAGTAAGATTCGCCGTTGTGGCCTCAATC-TTTTAAATGCAATATCGGGGAAACG-AGA
* * *
42939380 TTCGCCTTTG
191 TTCACCGTTA
* * *
42939390 TAGCTTCAATCTATTCCACTGCACCGTCT-GG-AAGTACGATTCGCCGTTGTGGCCTCAATCTTT
1 TAGCTTCAATCTATTCCACTGCACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCTCAATC-TT
* * * **
42939453 TTAATTGCAATGTCGGGGAAGCAAGATTTGCCGTTCTGACTTCAATCTGTTCAACTGCACTGCAT
65 TTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTCTGACTTCAATCTGTTCCACTGCACCACAT
42939518 AGGAAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAAATGCAATATCGGGGAAACGAGATTCA
130 AGGAAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAAATGCAATATCGGGGAAACGAGATTCA
42939583 CCGTTA
195 CCGTTA
*
42939589 TAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTTT
1 TAGCTTCAATCTATTCCACTGCACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTTT
* * * * *
42939654 TAAATGCAATGTTGGGGAAGCGAGATTCGCTGTTGTGGCTTCAATCTGTTCCACTG
66 TAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTCTGACTTCAATCTGTTCCACTG
42939710 TACTGCCTGA
Statistics
Matches: 273, Mismatches: 40, Indels: 14
0.83 0.12 0.04
Matches are distributed among these distances:
199 134 0.49
200 111 0.41
201 28 0.10
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (200 bp):
TAGCTTCAATCTATTCCACTGCACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTTT
TAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTCTGACTTCAATCTGTTCCACTGCACCACATA
GGAAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAAATGCAATATCGGGGAAACGAGATTCAC
CGTTA
Found at i:42939718 original size:100 final size:100
Alignment explanation
Indices: 42939147--42939709 Score: 591
Period size: 100 Copynumber: 5.7 Consensus size: 100
42939137 TTACCATCTC
* * * ** * * * * * * *
42939147 CAATCTGTTTAACTGCAATGTC-AGGAAATAAGATTTGTCGTCGTAGCTTCAATCTATTTCATTA
1 CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTG
* *** * *
42939211 CACCGCC-AGGGAAGTAAAATTCATTGTTGTAGCTT
66 CACCGCCTA-GGAAGTAAGATTCGCCGTTGTGGCCT
* *** * * * *
42939246 CAATCTATTTAACCACAATGTCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAGTCTGTTCCACTG
1 CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTG
*
42939311 CACCACCTAGGAAGTAAGATTCGCCGTTGTGGCCT
66 CACCGCCTAGGAAGTAAGATTCGCCGTTGTGGCCT
* * *
42939346 CAATCTTTTTAATTGCAATGTCGGGGAAAG-AAGATTCGCCTTTGTAGCTTCAATCTATTCCACT
1 CAATCTTTTTAAATGCAATGTCGGGG-AAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACT
* *
42939410 GCACCGTCT-GGAAGTACGATTCGCCGTTGTGGCCT
65 GCACCGCCTAGGAAGTAAGATTCGCCGTTGTGGCCT
* * * *
42939445 CAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTTGCCGTTCT-GACTTCAATCTGTTCAACT
1 CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAG-CTTCAATCTGTTCCACT
* *
42939509 GCACTGCATAGGAAAGTAAGATTCGCCGTTGTGGCCT
65 GCACCGCCTAGG-AAGTAAGATTCGCCGTTGTGGCCT
* * * * *
42939546 CAATC-TTTTAAATGCAATATCGGGGAAACGAGATTCACCGTTATAGCTTCAATCTGTTCCACTG
1 CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTG
* *
42939610 CACCGCCTGGGAAAGTAAGATTCACCGTTGTGGCCT
66 CACCGCCTAGG-AAGTAAGATTCGCCGTTGTGGCCT
* * * *
42939646 CAATC-TTTTAAATGCAATGTTGGGGAAGCGAGATTCGCTGTTGTGGCTTCAATCTGTTCCACTG
1 CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTG
42939710 TACTGCCTGA
Statistics
Matches: 394, Mismatches: 62, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
98 4 0.01
99 103 0.26
100 254 0.64
101 33 0.08
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (100 bp):
CAATCTTTTTAAATGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTG
CACCGCCTAGGAAGTAAGATTCGCCGTTGTGGCCT
Found at i:42939928 original size:88 final size:88
Alignment explanation
Indices: 42939805--42940487 Score: 1105
Period size: 88 Copynumber: 7.8 Consensus size: 88
42939795 ACTACCGCTT
*
42939805 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
42939870 TTTGACCTGCTCCACTACAACCG
66 TTTGACCTGCTCCACTACAACCG
* *
42939893 AGGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCATGAAGGCAAGATCTGCTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
42939958 TTTGACCTGCTCCACTACAACCG
66 TTTGACCTGCTCCACTACAACCG
** *
42939981 AAAGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAAATCTGCTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
*
42940046 TTTGACCTGCTCCACTACAACCA
66 TTTGACCTGCTCCACTACAACCG
* * *
42940069 AGGGAAGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATACAGGAATGCAAGATCTGCTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
42940134 TTTGACCTGCTCCACTACAACCG
66 TTTGACCTGCTCCACTACAACCG
* *
42940157 AGGGAGGCAAGGCTTGTGTATTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
*
42940222 TTTGATCTGCTCCACTACAACCG
66 TTTGACCTGCTCCACTACAACCG
* * *
42940245 AGGGAGGCAAAGCTTGTGTCTTCAATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTGCTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
*
42940310 TTTGACCTACTCCACTACAACCG
66 TTTGACCTGCTCCACTACAACCG
* ** * * * * *
42940333 AGGGAGGTAAGATTTGTGTTTTCGATCTGCTTCGCTGTCAATACAAGAAGGCAAAATCTACTATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
*
42940398 TTTGACCTGCTCCACTACAACTG
66 TTTGACCTGCTCCACTACAACCG
* * *
42940421 AGGGAGGTAAGGCTTGTGTCTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCGATC
1 AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
42940486 TT
66 TT
42940488 CATTGATCTG
Statistics
Matches: 546, Mismatches: 49, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 546 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (88 bp):
AGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATC
TTTGACCTGCTCCACTACAACCG
Found at i:42941157 original size:327 final size:327
Alignment explanation
Indices: 42940563--42941543 Score: 1809
Period size: 327 Copynumber: 3.0 Consensus size: 327
42940553 GGAATGATCA
* * *
42940563 AAATGAATCAAATACTCCTAAATAGACATGTGTGAATAGTGTTTGCATGAATGCAAAATTTTATT
1 AAATGAATCAAATGCTCCTAAATAGACATATGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
*
42940628 TTTCCGAGAATGATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAGGCTTTGTGACTAACGT
66 TTTCTGAGAATGATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAGGCTTTGTGACTAACGT
42940693 GCTACGACGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
131 GCTACGACGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
*
42940758 TGAACCTCAAAGTTTAATCCATTGGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
196 TGAACCTCAAAGTTTAATCTATTGGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
* * *
42940823 GAGTAGAAATATGTAGCCTTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTATGGTC
261 GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
42940888 CT
326 CT
42940890 AAATGAATCAAATGCTCCTAAATAGACATATGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
1 AAATGAATCAAATGCTCCTAAATAGACATATGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
*
42940955 TTTCTGAGAATGATCCCACTTAGGTTGTCATTACTCGAAGTTTATTAAGGCTTTGTGACTAACGT
66 TTTCTGAGAATGATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAGGCTTTGTGACTAACGT
* *
42941020 GCTACGACGCCTTCTTGCTTGACTGGTTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCTCACTG
131 GCTACGACGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
*
42941085 TGAACCTCAAAGTTTAATCTATTAGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
196 TGAACCTCAAAGTTTAATCTATTGGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
42941150 GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
261 GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
42941215 CT
326 CT
*
42941217 AAATGAATCAAATGCTCCTAAATAGACATTTGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
1 AAATGAATCAAATGCTCCTAAATAGACATATGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
* *
42941282 TTTCTGAGAATGATCCCGCTTAGGTTGCCATTACTCGAAGTTTATTAAGGCTTTGTAACTAACGT
66 TTTCTGAGAATGATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAGGCTTTGTGACTAACGT
*
42941347 GCTACGATGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
131 GCTACGACGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
*
42941412 TGAACCTCAAAGTTTAATCTATTGGGGCGCAAAATTTGTATCATCATTCTCCTACTGTAATCCAA
196 TGAACCTCAAAGTTTAATCTATTGGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
42941477 GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
261 GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
42941542 CT
326 CT
42941544 TTATGCCATT
Statistics
Matches: 633, Mismatches: 21, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
327 633 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (327 bp):
AAATGAATCAAATGCTCCTAAATAGACATATGTGAATGGTGTTTGCATGAATGCAAAATTTTATT
TTTCTGAGAATGATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAGGCTTTGTGACTAACGT
GCTACGACGCCTTCTTGCTTGACTGGCTTTTCTGAAGAAACATTTAGCCAGGTTGCCCCCCACTG
TGAACCTCAAAGTTTAATCTATTGGGGCGCAAAATTTGTACCATCATTCTCCTACTGTAATCCAA
GAGTAGAAATATGTGGCATTTCCTCAATCTTCTCCTAAGGATACAGAATGTGAAGCTCTTTGGTC
CT
Found at i:42942383 original size:7 final size:7
Alignment explanation
Indices: 42942370--42942403 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
42942360 TTATCCTCTC
42942370 CATTTTT
1 CATTTTT
*
42942377 TATTTTT
1 CATTTTT
42942384 CATTTTT
1 CATTTTT
42942391 CA-TTTT
1 CATTTTT
42942397 CATTTTT
1 CATTTTT
42942404 TTGACTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (7 bp):
CATTTTT
Found at i:42942396 original size:13 final size:14
Alignment explanation
Indices: 42942370--42942403 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
42942360 TTATCCTCTC
*
42942370 CATTTTTTATTTTT
1 CATTTTTCATTTTT
42942384 CATTTTTCA-TTTT
1 CATTTTTCATTTTT
42942397 CATTTTT
1 CATTTTT
42942404 TTGACTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:42955125 original size:25 final size:24
Alignment explanation
Indices: 42955097--42955144 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
42955087 ATCCAGGCAA
42955097 TATAACGGAAAGCTCACAAAGAGCT
1 TATAACGGAAAGCTC-CAAAGAGCT
* **
42955122 TATAATGGGTAGCTCCAAAGAGC
1 TATAACGGAAAGCTCCAAAGAGC
42955145 AATTAATGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (24 bp):
TATAACGGAAAGCTCCAAAGAGCT
Found at i:42955151 original size:24 final size:24
Alignment explanation
Indices: 42955107--42955174 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
42955097 TATAACGGAA
*
42955107 AGCTCACAAAGAGC-TTATAATGGGT
1 AGCTC-CAAAGAGCAAT-TAATGGGT
42955132 AGCTCCAAAGAGCAATTAATGGGT
1 AGCTCCAAAGAGCAATTAATGGGT
* *
42955156 AGCTCCGAAGAGTAATTAA
1 AGCTCCAAAGAGCAATTAA
42955175 CAAGAAGTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
24 33 0.85
25 6 0.15
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (24 bp):
AGCTCCAAAGAGCAATTAATGGGT
Done.