Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009185.1 Hibiscus syriacus cultivar Beakdansim tig00112758_pilon, whole genome shotgun sequence
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: 682201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:306554 original size:27 final size:27
Alignment explanation
Indices: 306518--306570 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
306508 AATTTTATGT
*
306518 TTTTTAAAAAATATATATATAATTTTA
1 TTTTTAAAAAATATATATAAAATTTTA
* * *
306545 TTTTTGAAAATTTTATATAAAATTTT
1 TTTTTAAAAAATATATATAAAATTTT
306571 CAAAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTTTAAAAAATATATATAAAATTTTA
Found at i:308266 original size:25 final size:25
Alignment explanation
Indices: 308232--308287 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
308222 TCTCGCAATT
308232 AGGGATGGCAAACGGGTACAGTTTC
1 AGGGATGGCAAACGGGTACAGTTTC
308257 AGGGATGGCAAACGGGTACAGTTTC
1 AGGGATGGCAAACGGGTACAGTTTC
*
308282 ATGGAT
1 AGGGAT
308288 TCCGCACCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.21
Consensus pattern (25 bp):
AGGGATGGCAAACGGGTACAGTTTC
Found at i:308432 original size:15 final size:15
Alignment explanation
Indices: 308412--308448 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
308402 TGAGACATTA
*
308412 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
308427 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
308442 CCCGCCC
1 CCCGCCC
308449 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:310240 original size:30 final size:29
Alignment explanation
Indices: 310178--310240 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
310168 GTTAGGGAAT
* *
310178 TGAATTTAAATTTATAAAGCTTTAAGAGA
1 TGAATTTAAATTTATAAAGATTTAAAAGA
310207 TGAATTTAAATTTATAAA-ATTCTAATAAGA
1 TGAATTTAAATTTATAAAGATT-TAA-AAGA
310237 TGAA
1 TGAA
310241 AATAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 21 0.70
30 7 0.23
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.38
Consensus pattern (29 bp):
TGAATTTAAATTTATAAAGATTTAAAAGA
Found at i:313141 original size:25 final size:25
Alignment explanation
Indices: 313112--313163 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
313102 GATCATATTT
313112 TGGGAGATGTACATACTTACACCTA
1 TGGGAGATGTACATACTTACACCTA
313137 TGGGAGATGTACATACTTACACCTA
1 TGGGAGATGTACATACTTACACCTA
313162 TG
1 TG
313164 TAAGAATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (25 bp):
TGGGAGATGTACATACTTACACCTA
Found at i:317167 original size:32 final size:34
Alignment explanation
Indices: 317126--317197 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 34
317116 ACATACATAT
317126 ATGTATATT-G-GGAAGAACATTTCCTCGTATCC
1 ATGTATATTGGTGGAAGAACATTTCCTCGTATCC
*
317158 ATGTATATTGGGTTGGAAGATCATTTCCTCGTATCC
1 ATGTATATT-GG-TGGAAGAACATTTCCTCGTATCC
317194 ATGT
1 ATGT
317198 GTCGGACATG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
32 9 0.26
34 1 0.03
36 25 0.71
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (34 bp):
ATGTATATTGGTGGAAGAACATTTCCTCGTATCC
Found at i:321014 original size:20 final size:20
Alignment explanation
Indices: 320961--321043 Score: 102
Period size: 18 Copynumber: 4.3 Consensus size: 20
320951 CACTGAATAT
320961 TTGTCCCGAAGGACCACT-A
1 TTGTCCCGAAGGACCACTGA
320980 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* * *
320999 TTGTTCTGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
321018 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
*
321037 TTATCCC
1 TTGTCCC
321044 TCGACTCTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
18 31 0.58
19 3 0.06
20 19 0.36
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:321699 original size:19 final size:19
Alignment explanation
Indices: 321675--321761 Score: 156
Period size: 19 Copynumber: 4.6 Consensus size: 19
321665 TTTAAGCAGG
*
321675 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCGTA
*
321694 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCGTA
321713 TGCATCGATGCACTCCGTA
1 TGCATCGATGCACTCCGTA
321732 TGCATCGATGCACTCCGTA
1 TGCATCGATGCACTCCGTA
321751 TGCATCGATGC
1 TGCATCGATGC
321762 CCTAATTGCA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.29
Consensus pattern (19 bp):
TGCATCGATGCACTCCGTA
Found at i:321734 original size:11 final size:11
Alignment explanation
Indices: 321682--321754 Score: 65
Period size: 11 Copynumber: 7.5 Consensus size: 11
321672 AGGTGCATCG
*
321682 ATGCACTCCTT
1 ATGCACTCCGT
321693 ATGCA-T-CG-
1 ATGCACTCCGT
*
321701 ATGCACTCCTT
1 ATGCACTCCGT
321712 ATGCA-T-CG-
1 ATGCACTCCGT
321720 ATGCACTCCGT
1 ATGCACTCCGT
321731 ATGCA-T-CG-
1 ATGCACTCCGT
321739 ATGCACTCCGT
1 ATGCACTCCGT
321750 ATGCA
1 ATGCA
321755 TCGATGCCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 18
0.70 0.04 0.25
Matches are distributed among these distances:
8 15 0.30
9 7 0.14
10 8 0.16
11 20 0.40
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.29
Consensus pattern (11 bp):
ATGCACTCCGT
Found at i:327751 original size:18 final size:18
Alignment explanation
Indices: 327725--327797 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
327715 ACTGAATATT
*
327725 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
327743 TGTCCCGAAGGACCATTGA
1 TGTCCCGAAGGACCACT-A
* *
327762 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
327781 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
327798 GATTACCTCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 30 0.65
19 2 0.04
20 14 0.30
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:329747 original size:20 final size:20
Alignment explanation
Indices: 329722--329772 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
329712 ATCCTATTCT
329722 CTGGTAATCTTTTATTTCCA
1 CTGGTAATCTTTTATTTCCA
*
329742 CTGGTAATCTTTTATTTCTA
1 CTGGTAATCTTTTATTTCCA
*
329762 ATGGTAATCTT
1 CTGGTAATCTT
329773 ACATTCCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.51
Consensus pattern (20 bp):
CTGGTAATCTTTTATTTCCA
Found at i:331062 original size:18 final size:17
Alignment explanation
Indices: 330993--331063 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 17
330983 TAATATCTCT
330993 ATATATTATTTTTAATTAA
1 ATATATT-TTTTTAA-TAA
331012 ATCTATATTTTTATTAAATAAA
1 A--TATATTTTT-TT-AAT-AA
*
331034 AAATATTTTTTTAATAA
1 ATATATTTTTTTAATAA
*
331051 ATATATTATTTTA
1 ATATATTTTTTTA
331064 GATTGGGTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
17 13 0.30
18 3 0.07
19 3 0.07
20 11 0.25
21 9 0.20
22 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATTTTTTTAATAA
Found at i:334704 original size:14 final size:14
Alignment explanation
Indices: 334685--334714 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
334675 TTTAGATTTT
*
334685 TTAAAATTACATTA
1 TTAAAAATACATTA
334699 TTAAAAATACATTA
1 TTAAAAATACATTA
334713 TT
1 TT
334715 GATGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:334997 original size:14 final size:14
Alignment explanation
Indices: 334978--335120 Score: 84
Period size: 14 Copynumber: 10.3 Consensus size: 14
334968 TGTGATAAGC
334978 TTTAGGATTTAGGG
1 TTTAGGATTTAGGG
*
334992 TTTAGGATTTAGAG
1 TTTAGGATTTAGGG
* *
335006 TTTATGTGA-TGA-GA
1 TTTA-G-GATTTAGGG
*
335020 TTTAAGG-TTTAAGG
1 TTT-AGGATTTAGGG
*
335034 TTTAAGG-TTTAAGG
1 TTT-AGGATTTAGGG
* *
335048 TTTAGGATTTATGT
1 TTTAGGATTTAGGG
*
335062 TTTAGAATTTAGGG
1 TTTAGGATTTAGGG
* *
335076 TTTAGGTTTTAGGA
1 TTTAGGATTTAGGG
*
335090 TTTA-TATGTTAGGG
1 TTTAGGAT-TTAGGG
335104 -TTA-GAGTTTAGGG
1 TTTAGGA-TTTAGGG
335117 TTTA
1 TTTA
335121 AGTTATACAC
Statistics
Matches: 102, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
13 17 0.17
14 79 0.77
15 4 0.04
16 2 0.02
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (14 bp):
TTTAGGATTTAGGG
Found at i:335009 original size:21 final size:20
Alignment explanation
Indices: 334985--335120 Score: 64
Period size: 21 Copynumber: 6.5 Consensus size: 20
334975 AGCTTTAGGA
334985 TTTAGGGTTTAGGATTTAGAG
1 TTTAGGGTTTAGG-TTTAGAG
* * * *
335006 TTTATGTGATGAGATTTA-AGG
1 TTTA-GGGTTTAGGTTTAGA-G
*
335027 TTTAAGGTTTAAGGTTTA-AGG
1 TTTAGGGTTT-AGGTTTAGA-G
* * *
335048 TTTAGGATTTATGTTTTAGAA
1 TTTAGGGTTTA-GGTTTAGAG
335069 TTTAGGGTTTAGGTTTTAG-G
1 TTTAGGGTTTAGG-TTTAGAG
** *
335089 ATTTA-TATGTTAGGGTTAGAG
1 -TTTAGGGT-TTAGGTTTAGAG
335110 TTTAGGGTTTA
1 TTTAGGGTTTA
335121 AGTTATACAC
Statistics
Matches: 84, Mismatches: 21, Indels: 21
0.67 0.17 0.17
Matches are distributed among these distances:
20 17 0.20
21 61 0.73
22 6 0.07
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (20 bp):
TTTAGGGTTTAGGTTTAGAG
Found at i:335119 original size:7 final size:7
Alignment explanation
Indices: 334978--335120 Score: 58
Period size: 7 Copynumber: 20.6 Consensus size: 7
334968 TGTGATAAGC
*
334978 TTTAGGA
1 TTTAGGG
334985 TTTAGGG
1 TTTAGGG
*
334992 TTTAGGA
1 TTTAGGG
*
334999 TTTAGAG
1 TTTAGGG
*
335006 TTTATGTG
1 TTTA-GGG
* * *
335014 ATGA-GA
1 TTTAGGG
*
335020 TTTAAGG
1 TTTAGGG
*
335027 TTTAAGG
1 TTTAGGG
*
335034 TTTAAGG
1 TTTAGGG
*
335041 TTTAAGG
1 TTTAGGG
*
335048 TTTAGGA
1 TTTAGGG
* *
335055 TTTATGT
1 TTTAGGG
**
335062 TTTAGAA
1 TTTAGGG
335069 TTTAGGG
1 TTTAGGG
*
335076 TTTAGGT
1 TTTAGGG
*
335083 TTTAGGA
1 TTTAGGG
**
335090 TTTA-TA
1 TTTAGGG
335096 TGTTAGGG
1 T-TTAGGG
*
335104 -TTAGAG
1 TTTAGGG
335110 TTTAGGG
1 TTTAGGG
335117 TTTA
1 TTTA
335121 AGTTATACAC
Statistics
Matches: 103, Mismatches: 28, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
6 9 0.09
7 90 0.87
8 4 0.04
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:336521 original size:11 final size:11
Alignment explanation
Indices: 336482--336524 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
336472 ATTTTTAATT
336482 GAGCTTGAATC
1 GAGCTTGAATC
** *
336493 GAGCTCAAAATT
1 GAGCT-TGAATC
336505 GAGCTTGAATC
1 GAGCTTGAATC
336516 GAGCTTGAA
1 GAGCTTGAA
336525 ATTTAGCTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (11 bp):
GAGCTTGAATC
Found at i:336559 original size:23 final size:23
Alignment explanation
Indices: 336529--336647 Score: 177
Period size: 23 Copynumber: 5.2 Consensus size: 23
336519 CTTGAAATTT
336529 AGCTTAGTTTCGAGTTTTAATCTG
1 AGCTTAGTTTCGAGTTTTAATC-G
*
336553 -GTTTAGTTTCGAGTTTTAATCG
1 AGCTTAGTTTCGAGTTTTAATCG
*
336575 AGCTTAGTTTTGAGTTTTAATCG
1 AGCTTAGTTTCGAGTTTTAATCG
* *
336598 AGCTTAGTTTTGAGTTTTAATTG
1 AGCTTAGTTTCGAGTTTTAATCG
*
336621 AGTTTAGTTTCGAGTTTTAATCG
1 AGCTTAGTTTCGAGTTTTAATCG
336644 AGCT
1 AGCT
336648 CTTGAATTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
22 1 0.01
23 85 0.99
ACGTcount: A:0.21, C:0.09, G:0.22, T:0.48
Consensus pattern (23 bp):
AGCTTAGTTTCGAGTTTTAATCG
Found at i:336579 original size:69 final size:69
Alignment explanation
Indices: 336505--336647 Score: 182
Period size: 69 Copynumber: 2.1 Consensus size: 69
336495 GCTCAAAATT
**
336505 GAGCTT-GAATCGAGCTTGAAATTTAGCTTAGTTTCGAGTTTTAATCTG-GTTTAGTTTCGAGTT
1 GAGCTTAGAATCGAG-TTGAAATCGAGCTTAGTTTCGAGTTTTAAT-TGAGTTTAGTTTCGAGTT
336568 TTAATC
64 TTAATC
** * ** *
336574 GAGCTTAGTTTTGAGTTTTAATCGAGCTTAGTTTTGAGTTTTAATTGAGTTTAGTTTCGAGTTTT
1 GAGCTTAGAATCGAGTTGAAATCGAGCTTAGTTTCGAGTTTTAATTGAGTTTAGTTTCGAGTTTT
336639 AATC
66 AATC
336643 GAGCT
1 GAGCT
336648 CTTGAATTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
68 2 0.03
69 57 0.89
70 5 0.08
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.45
Consensus pattern (69 bp):
GAGCTTAGAATCGAGTTGAAATCGAGCTTAGTTTCGAGTTTTAATTGAGTTTAGTTTCGAGTTTT
AATC
Found at i:336680 original size:16 final size:16
Alignment explanation
Indices: 336656--336687 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
336646 CTCTTGAATT
*
336656 TTTTTGAGTTCGAGTC
1 TTTTCGAGTTCGAGTC
336672 TTTTCGAGTTCGAGTC
1 TTTTCGAGTTCGAGTC
336688 GAGTTACAAT
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:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (16 bp):
TTTTCGAGTTCGAGTC
Found at i:340256 original size:23 final size:23
Alignment explanation
Indices: 340230--340274 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
340220 CACCACAGCT
*
340230 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
340253 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
340275 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:340492 original size:149 final size:149
Alignment explanation
Indices: 340242--340556 Score: 553
Period size: 149 Copynumber: 2.1 Consensus size: 149
340232 TATAATTGCA
340242 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
* *
340306 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACATATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTATTTCAAGACTTCACACATGTT
*
340371 CCACAA-AATATATATATATC
130 CCA-AAGAATATACATATATC
*
340391 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTTCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
340456 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTATTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTATTTCAAGACTTCACACATGTTC
*
340521 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
340540 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
340557 CCCTTGACTC
Statistics
Matches: 159, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
148 3 0.02
149 156 0.98
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTATTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:342082 original size:63 final size:63
Alignment explanation
Indices: 341953--342111 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 63
341943 TAATGGAGGC
* * * * **
341953 ATGCATCGATGCACTCCTGATGCATCGATGCACTGAGGGCATTCGATGTTCATTTTATTAGAA
1 ATGCATCGATGCACTCCTAATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
* ** **
342016 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTAAAATTA
1 ATGCATCGATGCACTCCTAATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
*
342079 ATGCATCGATGCACTTCATAAT-CATCGATGCAC
1 ATGCATCGATGCAC-TCCTAATGCATCGATGCAC
342112 CTTCAACAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 78 0.94
64 5 0.06
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTAATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
Found at i:342106 original size:19 final size:21
Alignment explanation
Indices: 342077--342116 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
342067 GTATTAAAAT
342077 TAATGCATCGATGCA-CTTCA
1 TAATGCATCGATGCACCTTCA
342097 TAAT-CATCGATGCACCTTCA
1 TAATGCATCGATGCACCTTCA
342117 ACAAATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (21 bp):
TAATGCATCGATGCACCTTCA
Found at i:349263 original size:34 final size:33
Alignment explanation
Indices: 349225--349306 Score: 146
Period size: 34 Copynumber: 2.4 Consensus size: 33
349215 CAAAAAAGGG
349225 GGAGAAGTGTTAAATGTGTTTTAAATGATAAAT
1 GGAGAAGTGTTAAATGTGTTTTAAATGATAAAT
349258 AGGAGAAGTGTTAAATGTGTTTTAAATGATAAAT
1 -GGAGAAGTGTTAAATGTGTTTTAAATGATAAAT
349292 GAGAGAAGTGTTAAA
1 G-GAGAAGTGTTAAA
349307 GTAAGGGGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
33 1 0.02
34 46 0.98
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.33
Consensus pattern (33 bp):
GGAGAAGTGTTAAATGTGTTTTAAATGATAAAT
Found at i:349292 original size:18 final size:18
Alignment explanation
Indices: 349235--349292 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
349225 GGAGAAGTGT
349235 TAAATGTGTTTTAAATGA
1 TAAATGTGTTTTAAATGA
** * *
349253 TAAATAG-G--AGAAGTGT
1 TAAAT-GTGTTTTAAATGA
349269 TAAATGTGTTTTAAATGA
1 TAAATGTGTTTTAAATGA
349287 TAAATG
1 TAAATG
349293 AGAGAAGTGT
Statistics
Matches: 28, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
15 1 0.04
16 10 0.36
18 16 0.57
19 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (18 bp):
TAAATGTGTTTTAAATGA
Found at i:354771 original size:23 final size:23
Alignment explanation
Indices: 354722--354795 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
354712 TGTTCGTGTT
* * **
354722 TGTTTATTTATTGTTCACGAACA
1 TGTTTATTTAATGTTCATGAATG
354745 TGTTTATTTAATGTTCATGAATG
1 TGTTTATTTAATGTTCATGAATG
** *
354768 TGTTCGTTTATATGTTCATAAATG
1 TGTTTATTTA-ATGTTCATGAATG
354792 TGTT
1 TGTT
354796 CATGAACATT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 27 0.63
24 16 0.37
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.51
Consensus pattern (23 bp):
TGTTTATTTAATGTTCATGAATG
Found at i:354786 original size:24 final size:23
Alignment explanation
Indices: 354751--354796 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
354741 AACATGTTTA
*
354751 TTTAATGTTCATGAATGTGTTCG
1 TTTAATGTTCATAAATGTGTTCG
354774 TTTATATGTTCATAAATGTGTTC
1 TTTA-ATGTTCATAAATGTGTTC
354797 ATGAACATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (23 bp):
TTTAATGTTCATAAATGTGTTCG
Found at i:354881 original size:22 final size:22
Alignment explanation
Indices: 354855--354903 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
354845 GACCATATTC
*
354855 GTTTAACATTCA-TTTAGTGTTT
1 GTTTAACATT-ATTTTAATGTTT
* *
354877 GTTTAGCGTTATTTTAATGTTT
1 GTTTAACATTATTTTAATGTTT
354899 GTTTA
1 GTTTA
354904 CCGTTCGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.20, C:0.06, G:0.16, T:0.57
Consensus pattern (22 bp):
GTTTAACATTATTTTAATGTTT
Found at i:354908 original size:22 final size:22
Alignment explanation
Indices: 354867--354908 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
354857 TTAACATTCA
* *
354867 TTTAGTGTTTGTTTAGCGTTAT
1 TTTAATGTTTGTTTACCGTTAT
354889 TTTAATGTTTGTTTACCGTT
1 TTTAATGTTTGTTTACCGTT
354909 CGATTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.07, G:0.19, T:0.60
Consensus pattern (22 bp):
TTTAATGTTTGTTTACCGTTAT
Found at i:355153 original size:22 final size:22
Alignment explanation
Indices: 355126--355181 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
355116 ATAACGAACT
*
355126 CATAAACGAGCTTGTTCGTGAA
1 CATAAACGAACTTGTTCGTGAA
355148 CATAAACGAACTTGTTCGTGAA
1 CATAAACGAACTTGTTCGTGAA
355170 CATAAACGAACT
1 CATAAACGAACT
355182 GAACACACCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (22 bp):
CATAAACGAACTTGTTCGTGAA
Found at i:369763 original size:227 final size:228
Alignment explanation
Indices: 369368--369825 Score: 900
Period size: 227 Copynumber: 2.0 Consensus size: 228
369358 TTATGCGTGC
369368 TTCAATACATGATGCTGGGCATAAAGATGCAGTTATATTGTTGAAAGCAAAAGCCAGGGCATCGA
1 TTCAATACATGATGCTGGGCATAAAGATGCAGTTATATTGTTGAAAGCAAAAGCCAGGGCATCGA
369433 TTTCCTTGAATGGAGAGGATGTTGGAGTAAGCTTAATTACATTATTTTCTTTGTTTGAATATCGA
66 TTTCCTTGAATGGAGAGGATGTTGGAGTAAGCTTAATTACATTATTTTCTTTGTTTGAATATCGA
369498 ATACTCGTGTTCTATTTTTTTTCCGCTTGTCTGTTTCATTTTTTTCCCTTCTTTGTAGCATCCTT
131 ATACTCGTGTTCTATTTTTTTTCCGCTTGTCTGTTTCATTTTTTTCCCTTCTTTGTAGCATCCTT
369563 AAATC-TTACATTCTGAGTTCATTATTGAAAAT
196 AAATCATTACATTCTGAGTTCATTATTGAAAAT
369595 TTCAATACATGATGCTGGGCATAAAGATGCAGTTATATTGTTGAAAGCAAAAGCCAGGGCATCGA
1 TTCAATACATGATGCTGGGCATAAAGATGCAGTTATATTGTTGAAAGCAAAAGCCAGGGCATCGA
369660 TTTCCTTGAATGGAGAGGATGTTGGAGTAAGCTTAATTACATTATTTTCTTTGTTTGAATATCGA
66 TTTCCTTGAATGGAGAGGATGTTGGAGTAAGCTTAATTACATTATTTTCTTTGTTTGAATATCGA
369725 ATACTCGTGTTCTATTTTTTTTCCGCTTGTCTGTTTCATTTTTTTCCCTTCTTTGTAGCATCCTT
131 ATACTCGTGTTCTATTTTTTTTCCGCTTGTCTGTTTCATTTTTTTCCCTTCTTTGTAGCATCCTT
369790 AAATCTATTACATTCTGAGTTCATTATTGAAAAT
196 AAATC-ATTACATTCTGAGTTCATTATTGAAAAT
369824 TT
1 TT
369826 TTATGTTGCT
Statistics
Matches: 229, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
227 200 0.87
229 29 0.13
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (228 bp):
TTCAATACATGATGCTGGGCATAAAGATGCAGTTATATTGTTGAAAGCAAAAGCCAGGGCATCGA
TTTCCTTGAATGGAGAGGATGTTGGAGTAAGCTTAATTACATTATTTTCTTTGTTTGAATATCGA
ATACTCGTGTTCTATTTTTTTTCCGCTTGTCTGTTTCATTTTTTTCCCTTCTTTGTAGCATCCTT
AAATCATTACATTCTGAGTTCATTATTGAAAAT
Found at i:379300 original size:17 final size:18
Alignment explanation
Indices: 379267--379319 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 18
379257 TTAAATTTTC
*
379267 ATTTTTAATAA-AATAAT
1 ATTTTTAATAATATTAAT
379284 -TTTTTAATAATATTAAT
1 ATTTTTAATAATATTAAT
*
379301 ATTTCTATAATAATTTTAA
1 ATTT-T-TAATAATATTAA
379320 AAAATTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 10 0.33
17 5 0.17
18 3 0.10
19 1 0.03
20 11 0.37
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTTAATAATATTAAT
Found at i:379838 original size:17 final size:17
Alignment explanation
Indices: 379816--379849 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
379806 AAATTGCTAC
379816 ATACAGTAACGAATTCA
1 ATACAGTAACGAATTCA
379833 ATACAGTAACGAATTCA
1 ATACAGTAACGAATTCA
379850 GAAATTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24
Consensus pattern (17 bp):
ATACAGTAACGAATTCA
Found at i:389759 original size:31 final size:31
Alignment explanation
Indices: 389695--389765 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
389685 ATAACTTTTA
* *
389695 ATAGTC-GGGGACTCAACAAATTAGTATTCT
1 ATAGTCGGGGGACTCAACAAAATAGTAGTCT
*
389725 ATAGTCGGGGGACTCTACAAAATAGT-GTCAT
1 ATAGTCGGGGGACTCAACAAAATAGTAGTC-T
*
389756 ATAGTTGGGG
1 ATAGTCGGGG
389766 TCCATTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.23
31 27 0.77
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (31 bp):
ATAGTCGGGGGACTCAACAAAATAGTAGTCT
Found at i:393174 original size:18 final size:18
Alignment explanation
Indices: 393109--393166 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
393099 TTCTACGTGG
*
393109 TCCTTTGGGACATAGT-A
1 TCCTTCGGGACATAGTGA
* *
393126 GTCCTTCGGGACACAGTGG
1 -TCCTTCGGGACATAGTGA
*
393145 TCCTTCGAGACATAGTGA
1 TCCTTCGGGACATAGTGA
393163 TCCT
1 TCCT
393167 ATGGGACAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (18 bp):
TCCTTCGGGACATAGTGA
Found at i:393671 original size:17 final size:17
Alignment explanation
Indices: 393646--393696 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
393636 TATAATATTT
* *
393646 CATATAACATAAAGCATG
1 CATA-AACATAAACCATA
*
393664 CATAAACATATACCATA
1 CATAAACATAAACCATA
*
393681 CATAAACATATACCAT
1 CATAAACATAAACCAT
393697 CATTATCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 26 0.87
18 4 0.13
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.24
Consensus pattern (17 bp):
CATAAACATAAACCATA
Found at i:393980 original size:31 final size:31
Alignment explanation
Indices: 393956--394097 Score: 212
Period size: 31 Copynumber: 4.6 Consensus size: 31
393946 CCATAGATTT
* *
393956 CGAAAAACCTAGGTAATCAGTCCATATGTCC
1 CGAAAAACATAGGTAAACAGTCCATATGTCC
*
393987 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAAAACATAGGTAAACAGTCCATATGTCC
* *
394018 CGAAGAACATAGGTAAATAGTCCATATGTCC
1 CGAAAAACATAGGTAAACAGTCCATATGTCC
* *
394049 CGAAGAACATAGGTAAACAGTCCATATATCC
1 CGAAAAACATAGGTAAACAGTCCATATGTCC
*
394080 CGAAGAACATAGGTAAAC
1 CGAAAAACATAGGTAAAC
394098 CCTCGACCCT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (31 bp):
CGAAAAACATAGGTAAACAGTCCATATGTCC
Found at i:394040 original size:62 final size:63
Alignment explanation
Indices: 393942--394096 Score: 242
Period size: 62 Copynumber: 2.5 Consensus size: 63
393932 CCCGAAGGAC
* ** * *
393942 CAGTCCATAGATTTCGAAAAACCTAGGT-AATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
*
394004 CAGTCCATATGTCCCGAAGAACATAGGTAAAT-AGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
394066 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
394097 CCCTCGACCC
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
62 82 0.96
63 3 0.04
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (63 bp):
CAGTCCATATATCCCGAAGAACATAGGTAAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:398469 original size:31 final size:31
Alignment explanation
Indices: 398434--398589 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
398424 CCCGAAGGAC
* * *
398434 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
398465 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
398496 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
398527 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
398558 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
398589 C
1 C
398590 CCTCGACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:400998 original size:51 final size:51
Alignment explanation
Indices: 400937--401042 Score: 185
Period size: 51 Copynumber: 2.1 Consensus size: 51
400927 AAAAGAATTA
* * *
400937 CTTTATAGAATAGAAGTTTTAAATTTTCTATGGTTTTTATAAAATTATATG
1 CTTTACAGAATAGAAGTTTTAAATTTTCTATGGATTTTATAAAAGTATATG
400988 CTTTACAGAATAGAAGTTTTAAATTTTCTATGGATTTTATAAAAGTATATG
1 CTTTACAGAATAGAAGTTTTAAATTTTCTATGGATTTTATAAAAGTATATG
401039 CTTT
1 CTTT
401043 GACTGATCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (51 bp):
CTTTACAGAATAGAAGTTTTAAATTTTCTATGGATTTTATAAAAGTATATG
Found at i:404099 original size:19 final size:19
Alignment explanation
Indices: 404077--404124 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
404067 ATATAATAAT
* *
404077 AATAATAATTGATAAATTC
1 AATAATAATTAAAAAATTC
*
404096 AATAATATTTAAAAAATTC
1 AATAATAATTAAAAAATTC
404115 AA-AA-AATTAA
1 AATAATAATTAA
404125 TAATAGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 5 0.20
18 2 0.08
19 18 0.72
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (19 bp):
AATAATAATTAAAAAATTC
Found at i:407349 original size:20 final size:21
Alignment explanation
Indices: 407315--407354 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
407305 AAATAATCTA
407315 AAATAAATAATTTTAATTTTT
1 AAATAAATAATTTTAATTTTT
*
407336 AAATTAATAA-TTTAATTTT
1 AAATAAATAATTTTAATTTT
407355 GATTTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATAAATAATTTTAATTTTT
Found at i:411525 original size:2 final size:2
Alignment explanation
Indices: 411518--411556 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
411508 GTGTTCTTAC
411518 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
411557 CACCTACCGT
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:416753 original size:19 final size:18
Alignment explanation
Indices: 416731--416766 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
416721 AAATTTTGGC
416731 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGC-CTTTTTTTG
*
416750 TTTTTTTGCCTTTTTTT
1 TTTTTTGGCCTTTTTTT
416767 TTTGGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTG
Found at i:416768 original size:20 final size:20
Alignment explanation
Indices: 416731--416767 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
416721 AAATTTTGGC
*
416731 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGCCTCTTTTTTTGT
416751 TTTTTTGCCT-TTTTTTT
1 TTTTTTGCCTCTTTTTTT
416768 TTGGAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (20 bp):
TTTTTTGCCTCTTTTTTTGT
Found at i:419822 original size:28 final size:29
Alignment explanation
Indices: 419767--419834 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
419757 ATATAAGAAA
419767 GGTGTCTAACATATGTTTTCGATTTCAGTTT
1 GGTGTCT-A-ATATGTTTTCGATTTCAGTTT
*
419798 GGTGTCTAATATTTTTTCG-TTTCAGTTT
1 GGTGTCTAATATGTTTTCGATTTCAGTTT
*
419826 GGTATCTAA
1 GGTGTCTAA
419835 CGTTTCATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 17 0.49
29 10 0.29
30 1 0.03
31 7 0.20
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (29 bp):
GGTGTCTAATATGTTTTCGATTTCAGTTT
Found at i:425969 original size:20 final size:20
Alignment explanation
Indices: 425946--425995 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
425936 ATGGTTGTGG
*
425946 GTATCGATACTGACCCTTCA
1 GTATCGATACTGAACCTTCA
* **
425966 GTATTGATACTGAACCTTTG
1 GTATCGATACTGAACCTTCA
425986 GTATCGATAC
1 GTATCGATAC
425996 CCACCTGCTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (20 bp):
GTATCGATACTGAACCTTCA
Found at i:437323 original size:86 final size:84
Alignment explanation
Indices: 437120--437345 Score: 268
Period size: 86 Copynumber: 2.7 Consensus size: 84
437110 CCATACAGTA
**
437120 TTATCGAAGAAGAAGAGTGATAAATCAGCCATAC-ACATA-TTCTC-AATT-T-AT-CATGCTTG
1 TTATCGAAGAAGAAGAGTGATAAATCAGCCACCCTACATATTTCTCAAATTATCATGCATGCTTG
* *
437179 CATGCATAAGTTCATATTG
66 CATGCATAAATTCATAGTG
* * * *
437198 TTATTGGAGAAGAAGAGTGATAAATCAGTCACCCATACATATTTCTCAAATTATCATGCTTGCAT
1 TTATCGAAGAAGAAGAGTGATAAATCAGCCACCC-TACATATTTCTCAAATTATCATGCATGC-T
437263 TGCATGCATAAATTCATAGTG
64 TGCATGCATAAATTCATAGTG
* *
437284 TTATCGAAGTAG-AGAGTGATAAATCAGCCACCCCGTACATATATTCTCAATTTATCATGCAT
1 TTATCGAAGAAGAAGAGTGATAAATCAGCCA-CCC-TACATAT-TTCTCAAATTATCATGCAT
437346 ACATACATAC
Statistics
Matches: 123, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
78 29 0.24
80 5 0.04
81 5 0.04
82 4 0.03
83 1 0.01
84 2 0.02
85 21 0.17
86 39 0.32
87 17 0.14
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (84 bp):
TTATCGAAGAAGAAGAGTGATAAATCAGCCACCCTACATATTTCTCAAATTATCATGCATGCTTG
CATGCATAAATTCATAGTG
Found at i:437467 original size:76 final size:76
Alignment explanation
Indices: 437280--437460 Score: 272
Period size: 76 Copynumber: 2.4 Consensus size: 76
437270 ATAAATTCAT
* * * *
437280 AGTGTTATCGAAGTAGAGAGTGATAAATCAGCCACCCCGTACATATATTCTCAATTTATCATGCA
1 AGTGTTATCGAAGAAGAGAGTGACAAATCAGTCACCCCATACATATATTCTCAATTTATCATGCA
*
437345 TACATACATAC
66 TACACACATAC
*
437356 AGTGTTATCAAAGAAGAGAGTGACAAATCAGTCACCCCATACATATATTCTCAATTTATCATGCA
1 AGTGTTATCGAAGAAGAGAGTGACAAATCAGTCACCCCATACATATATTCTCAATTTATCATGCA
*
437421 TACACACATGC
66 TACACACATAC
* * *
437432 AGTGTTGTCGAAGAAAAGAGTGAGAAATC
1 AGTGTTATCGAAGAAGAGAGTGACAAATC
437461 GATCACCTCG
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 94 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (76 bp):
AGTGTTATCGAAGAAGAGAGTGACAAATCAGTCACCCCATACATATATTCTCAATTTATCATGCA
TACACACATAC
Found at i:437950 original size:10 final size:10
Alignment explanation
Indices: 437937--437962 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
437927 AATATTATTT
437937 AATAATTTTA
1 AATAATTTTA
437947 AATAATTTTA
1 AATAATTTTA
437957 AATAAT
1 AATAAT
437963 AAATTTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
AATAATTTTA
Found at i:441841 original size:18 final size:18
Alignment explanation
Indices: 441818--441856 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
441808 ACAATTACTT
441818 GACCAAATAAAGTGATAA
1 GACCAAATAAAGTGATAA
441836 GACCAAATAAAGTGATAA
1 GACCAAATAAAGTGATAA
441854 GAC
1 GAC
441857 AAAAGTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.13, G:0.18, T:0.15
Consensus pattern (18 bp):
GACCAAATAAAGTGATAA
Found at i:451134 original size:149 final size:149
Alignment explanation
Indices: 450872--451168 Score: 576
Period size: 149 Copynumber: 2.0 Consensus size: 149
450862 GGTCTACGCG
*
450872 GTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATC
1 GTCCTTCGGGACATATGTATATTCTTTGGAACAGGTGTGAAGTCTTGAAAGACACATACTTGATC
*
450937 CCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGCAC
66 CCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCAC
451002 TACGGTGCAATTCTACGTT
131 TACGGTGCAATTCTACGTT
451021 GTCCTTCGGGACATATGTATATTCTTTGGAACAGGTGTGAAGTCTTGAAAGACACATACTTGATC
1 GTCCTTCGGGACATATGTATATTCTTTGGAACAGGTGTGAAGTCTTGAAAGACACATACTTGATC
451086 CCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCAC
66 CCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCAC
451151 TACGGTGCAATTCTACGT
131 TACGGTGCAATTCTACGT
451169 GGCACTTCGG
Statistics
Matches: 146, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 146 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (149 bp):
GTCCTTCGGGACATATGTATATTCTTTGGAACAGGTGTGAAGTCTTGAAAGACACATACTTGATC
CCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCAC
TACGGTGCAATTCTACGTT
Found at i:451179 original size:23 final size:23
Alignment explanation
Indices: 451145--451190 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
451135 CATCATTATA
*
451145 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
451168 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
451191 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:451241 original size:16 final size:17
Alignment explanation
Indices: 451220--451253 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
451210 GTGCACAACC
451220 TCGATAG-ACTCACATA
1 TCGATAGTACTCACATA
*
451236 TCGATAGTTCTCACATA
1 TCGATAGTACTCACATA
451253 T
1 T
451254 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (17 bp):
TCGATAGTACTCACATA
Found at i:456227 original size:149 final size:149
Alignment explanation
Indices: 455957--456271 Score: 605
Period size: 149 Copynumber: 2.1 Consensus size: 149
455947 GAGTCGAGGG
455957 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACAGGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACAGGTGTGAAGTCTTGAAAGACACAT
*
456022 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
456087 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
456106 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACAGGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACAGGTGTGAAGTCTTGAAAGACACAT
456171 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
456236 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
456255 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
456272 TGCAATTATA
Statistics
Matches: 164, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 163 0.99
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACAGGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:456272 original size:23 final size:23
Alignment explanation
Indices: 456239--456283 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
456229 ATCATTATAT
*
456239 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
456262 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
456284 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:456334 original size:16 final size:17
Alignment explanation
Indices: 456313--456346 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
456303 GTGCACAACC
456313 TCGATAG-ACTCACATA
1 TCGATAGTACTCACATA
*
456329 TCGATAGTTCTCACATA
1 TCGATAGTACTCACATA
456346 T
1 T
456347 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (17 bp):
TCGATAGTACTCACATA
Found at i:464061 original size:41 final size:41
Alignment explanation
Indices: 464004--464086 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
463994 CTCACCCTAC
464004 TTTTAATCACACGGTATATGTTGTATGTATTATTGCATGTA
1 TTTTAATCACACGGTATATGTTGTATGTATTATTGCATGTA
464045 TTTTAATCACACGGTATATGTTGTATGTATTATTGCATGTA
1 TTTTAATCACACGGTATATGTTGTATGTATTATTGCATGTA
464086 T
1 T
464087 GTAAGCATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (41 bp):
TTTTAATCACACGGTATATGTTGTATGTATTATTGCATGTA
Found at i:466807 original size:32 final size:32
Alignment explanation
Indices: 466771--466837 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
466761 TATTTTGCCT
*
466771 CCTCATTTTCTATGGTTAATTATACTTTGTCC
1 CCTCATTTTCTATGATTAATTATACTTTGTCC
466803 CCTCATTTTCTATGATTAATTATACTTTGTCC
1 CCTCATTTTCTATGATTAATTATACTTTGTCC
466835 CCT
1 CCT
466838 TAAGTTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.19, C:0.24, G:0.07, T:0.49
Consensus pattern (32 bp):
CCTCATTTTCTATGATTAATTATACTTTGTCC
Found at i:469666 original size:20 final size:20
Alignment explanation
Indices: 469622--469662 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
469612 ATTAAAATAA
* *
469622 TATATTTTATAATTATTTAT
1 TATATTTTATAATGATTAAT
469642 TATATTTTA-AATGATTAAT
1 TATATTTTATAATGATTAAT
469661 TA
1 TA
469663 ATATATTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TATATTTTATAATGATTAAT
Found at i:470433 original size:9 final size:9
Alignment explanation
Indices: 470419--470447 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
470409 GAAATCGGTT
470419 AATTAACCG
1 AATTAACCG
470428 AATTAACCG
1 AATTAACCG
470437 AATTAACCG
1 AATTAACCG
470446 AA
1 AA
470448 ATAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (9 bp):
AATTAACCG
Found at i:470823 original size:187 final size:187
Alignment explanation
Indices: 470458--470851 Score: 650
Period size: 187 Copynumber: 2.1 Consensus size: 187
470448 ATAAAATTTT
* * *
470458 AAATTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAATCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGACTCAACCCAAACCATTTAAAACCCAATTAATAA
*
470523 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTTTATATAAAATTT
66 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
* *
470588 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTTTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTAGTTTTTTTGAATTAAA
*
470645 AAATATTAAATATATTATATATAACATATGGACTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGACTCAACCCAAACCATTTAAAACCCAATTAATAA
*
470710 TTTAAGAT-TCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAATTT
66 TTTAAGATCT-AATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAA-AT
*
470774 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-GTTTTTTTGAATTATA
129 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTAGTTTTTTTGAATTAAA
* *
470832 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
470852 AATTATAAAA
Statistics
Matches: 194, Mismatches: 11, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
186 9 0.05
187 143 0.74
188 42 0.22
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (187 bp):
AAATATTAAATATATTATATATAACATATGGACTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTAGTTTTTTTGAATTAAA
Found at i:472666 original size:2 final size:2
Alignment explanation
Indices: 472661--472689 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
472651 AGCGTGTGTG
472661 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
472690 GCATACTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:476788 original size:24 final size:24
Alignment explanation
Indices: 476733--476778 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
476723 AAAGTTGATA
* * *
476733 AAATGCTTTTAGTTCATTTAATTG
1 AAATGATTTTAATTCACTTAATTG
476757 AAATGATTTTAATTCACTTAAT
1 AAATGATTTTAATTCACTTAAT
476779 CTGACAGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (24 bp):
AAATGATTTTAATTCACTTAATTG
Found at i:483028 original size:2 final size:2
Alignment explanation
Indices: 483023--483047 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
483013 TAAAAAAAAC
483023 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 A
483048 AATCGATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:483147 original size:2 final size:2
Alignment explanation
Indices: 483140--483170 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
483130 AACATAATTA
483140 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 A
483171 GATAAAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:484105 original size:30 final size:30
Alignment explanation
Indices: 484062--484136 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
484052 GAAAAAAACG
* *
484062 AAAATACAAATA-AAGAAAAAGA-AGAAAAT
1 AAAATA-AAATATAAAAAAAAGACACAAAAT
* * *
484091 ATAATAAAATATAAAAAAAATACACATAAT
1 AAAATAAAATATAAAAAAAAGACACAAAAT
484121 AAAATAAAATATAAAA
1 AAAATAAAATATAAAA
484137 CAATGAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 5 0.13
29 13 0.34
30 20 0.53
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (30 bp):
AAAATAAAATATAAAAAAAAGACACAAAAT
Found at i:484791 original size:18 final size:18
Alignment explanation
Indices: 484748--484816 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 18
484738 ATAATTACAT
484748 GAATAAATAAAAA-AAT-A
1 GAAT-AATAAAAATAATAA
* *
484765 GTAACAATAGAAATAATAA
1 G-AATAATAAAAATAATAA
* * *
484784 GGATAATATAAAGAATAA
1 GAATAATAAAAATAATAA
*
484802 TAATAATAAAAATAA
1 GAATAATAAAAATAA
484817 AAATGGTAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
17 8 0.21
18 29 0.74
19 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.09, T:0.22
Consensus pattern (18 bp):
GAATAATAAAAATAATAA
Found at i:484903 original size:23 final size:22
Alignment explanation
Indices: 484866--484915 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
484856 ATATATATAC
484866 ATATAATAATAATAATAACAATA
1 ATATAATAATAATAATAAC-ATA
*
484889 ATATAAT-ATATATAATAACGTA
1 ATATAATAATA-ATAATAACATA
484911 ATATA
1 ATATA
484916 TAAAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (22 bp):
ATATAATAATAATAATAACATA
Found at i:486375 original size:20 final size:20
Alignment explanation
Indices: 486352--486393 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
486342 GAATCCTTCG
486352 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
*
486372 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
486392 TC
1 TC
486394 AGAGTTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:486816 original size:106 final size:105
Alignment explanation
Indices: 486453--487388 Score: 1675
Period size: 105 Copynumber: 8.9 Consensus size: 105
486443 TTGTGAAGCT
* * * *
486453 GAAATTGTTTATTGACAACCAGTGGTCCCTTCGTCATGAAGCTGAACTTGCGTTGTCTGGAGTCC
1 GAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
486518 AATATCCTTCGTTGTGAGGTTGAAATTGGCTCTGAATTTGA
65 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
*
486559 GAAATGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
486624 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
486664 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
486729 ATATCCTTCGTTGTGAAGTTGAAATTTGACTCTGAATTTGA
66 ATATCCTTCGTTGTGAAGTTGAAA-TTGGCTCTGAATTTGA
486770 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
486835 ATATCCTTCGTTGTGAAGTTGAAATTTGACTCTGAATTTGA
66 ATATCCTTCGTTGTGAAGTTGAAA-TTGGCTCTGAATTTGA
486876 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
486941 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
*
486981 GAAATGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC-
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
487045 ATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAATTTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
487084 GAAATGTTTGTTGACAACCAGC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
487148 ATATCCTTCTTTGTGAAGTTGAAATTGGCTCTGAATTTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
487188 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
487253 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
* *
487293 GAAATGCTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCC-
1 GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
487357 A-ATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
487389 GGTAAAACCT
Statistics
Matches: 807, Mismatches: 19, Indels: 11
0.96 0.02 0.01
Matches are distributed among these distances:
102 40 0.05
103 88 0.11
104 62 0.08
105 403 0.50
106 214 0.27
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGA
Found at i:492819 original size:50 final size:50
Alignment explanation
Indices: 492744--492843 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
492734 TTATCGATTA
492744 AGACACTTGGTAAAGCGTGCCCCTTACAGTAGGTAGTAATATGTAACGCC
1 AGACACTTGGTAAAGCGTGCCCCTTACAGTAGGTAGTAATATGTAACGCC
492794 AGACACTTGGTAAAGCGTGCCCCTTACAGTAGGTAGTAATATGTAACGCC
1 AGACACTTGGTAAAGCGTGCCCCTTACAGTAGGTAGTAATATGTAACGCC
492844 TTTGTTCGGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (50 bp):
AGACACTTGGTAAAGCGTGCCCCTTACAGTAGGTAGTAATATGTAACGCC
Found at i:492845 original size:27 final size:27
Alignment explanation
Indices: 492765--492845 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 27
492755 AAAGCGTGCC
492765 CCTTACAGTAGGTAGTAATATGTAACG
1 CCTTACAGTAGGTAGTAATATGTAACG
** * * ** * *
492792 CCAGACACTTGGTA--AA-GCGT-GCC
1 CCTTACAGTAGGTAGTAATATGTAACG
492815 CCTTACAGTAGGTAGTAATATGTAACG
1 CCTTACAGTAGGTAGTAATATGTAACG
492842 CCTT
1 CCTT
492846 TGTTCGGCCT
Statistics
Matches: 34, Mismatches: 16, Indels: 8
0.59 0.28 0.14
Matches are distributed among these distances:
23 11 0.32
24 2 0.06
25 4 0.12
26 2 0.06
27 15 0.44
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (27 bp):
CCTTACAGTAGGTAGTAATATGTAACG
Found at i:498796 original size:2 final size:2
Alignment explanation
Indices: 498789--498816 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
498779 AATAAATAAA
498789 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
498817 GTAGAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:499350 original size:18 final size:18
Alignment explanation
Indices: 499307--499375 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 18
499297 ATAATTACAT
499307 GAATAAATAAAAA-AAT-A
1 GAAT-AATAAAAATAATAA
* *
499324 GTAACAATAGAAATAATAA
1 G-AATAATAAAAATAATAA
* * *
499343 GGATAATATAAAGAATAA
1 GAATAATAAAAATAATAA
*
499361 TAATAATAAAAATAA
1 GAATAATAAAAATAA
499376 AAATGGTAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
17 8 0.21
18 29 0.74
19 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.09, T:0.22
Consensus pattern (18 bp):
GAATAATAAAAATAATAA
Found at i:499437 original size:3 final size:3
Alignment explanation
Indices: 499429--499471 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
499419 ATATATACAT
*
499429 ATA ATA ATA ATA ATA ACA ATA ATA ATA TATA TATA TATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA -ATA ATA A
499472 AACGTAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 26 0.70
4 11 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:499468 original size:18 final size:17
Alignment explanation
Indices: 499408--499485 Score: 63
Period size: 18 Copynumber: 4.5 Consensus size: 17
499398 GAAATAAGTA
499408 AATATATACAT-ATATAT
1 AATATATA-ATAATATAT
499425 ACATATAATAATAATA-AT
1 A-ATAT-ATAATAATATAT
*
499443 AACA-ATAATAATATAT
1 AATATATAATAATATAT
* **
499459 ATATATATAATAAAACGT
1 A-ATATATAATAATATAT
499477 AATATATAA
1 AATATATAA
499486 AAAAGATTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
15 9 0.18
16 3 0.06
17 13 0.26
18 19 0.38
19 6 0.12
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (17 bp):
AATATATAATAATATAT
Found at i:501717 original size:19 final size:20
Alignment explanation
Indices: 501681--501720 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
501671 TCGTGTCACG
* *
501681 TTAAAAATTGTATTTTTTAT
1 TTAAAAATTATATATTTTAT
501701 TTAAAAA-TATATATTTTAT
1 TTAAAAATTATATATTTTAT
501720 T
1 T
501721 GTTATCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTAAAAATTATATATTTTAT
Found at i:501770 original size:27 final size:29
Alignment explanation
Indices: 501705--501774 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
501695 TTTTATTTAA
*
501705 AAATATATATTTTATTGTTATCTAAATTTTT
1 AAATATATATTTCATTGTTATCT--ATTTTT
*
501736 AAAAATATATTTCATTGTTAT-T-TTTTT
1 AAATATATATTTCATTGTTATCTATTTTT
*
501763 AAGTATATATTT
1 AAATATATATTT
501775 TATCTTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 15 0.43
30 1 0.03
31 19 0.54
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (29 bp):
AAATATATATTTCATTGTTATCTATTTTT
Found at i:514045 original size:22 final size:22
Alignment explanation
Indices: 514020--514080 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
514010 CAACACATGG
514020 AAGTGCCTTAGCACTGGCACAA
1 AAGTGCCTTAGCACTGGCACAA
* * ***
514042 AAGTGCATTCGCACTAATACAA
1 AAGTGCCTTAGCACTGGCACAA
*
514064 AAGTGCCTTAACACTGG
1 AAGTGCCTTAGCACTGG
514081 GGAGAGAATC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (22 bp):
AAGTGCCTTAGCACTGGCACAA
Found at i:528724 original size:30 final size:30
Alignment explanation
Indices: 528665--528767 Score: 145
Period size: 30 Copynumber: 3.4 Consensus size: 30
528655 CTCGAAGGAC
* *
528665 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
528694 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
528724 CTGTCCAGAGGTCATAAAGATCCTCGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
* *
528755 CTGTCCATAGGTC
1 CTATCCAGAGGTC
528768 CCGAAGAACC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 19 0.28
30 35 0.51
31 14 0.21
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:528760 original size:31 final size:30
Alignment explanation
Indices: 528668--528792 Score: 144
Period size: 30 Copynumber: 4.1 Consensus size: 30
528658 GAAGGACCTA
* *
528668 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
*
528697 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
*
528727 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCACAAAGATCCTCGGT-AACTG
* * * * *
528758 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGATCCTCGGT-AACTG
528789 TCCA
1 TCCA
528793 TATGTCTCAA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
29 16 0.19
30 35 0.41
31 34 0.40
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGATCCTCGGTAACTG
Found at i:528793 original size:31 final size:31
Alignment explanation
Indices: 528668--528817 Score: 110
Period size: 31 Copynumber: 4.9 Consensus size: 31
528658 GAAGGACCTA
* ** *
528668 TCCAGAGGTCACAAAG-ACCCCGGT-AACTA
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* * * *
528697 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* * * *
528727 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* *
528758 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* * *
528789 TCCATATGTCTCAAA-AGACATAGGTAAAC
1 TCCATAGGTCACAAAGA-ACCTAGGTAAAC
528818 CCTCGACTCT
Statistics
Matches: 104, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
29 15 0.14
30 36 0.35
31 53 0.51
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:529388 original size:19 final size:21
Alignment explanation
Indices: 529346--529388 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
529336 TTCATAATCA
529346 CATATTCATATAGTTTATTAT
1 CATATTCATATAGTTTATTAT
*
529367 CATA-TCATATGGTTTA-TAT
1 CATATTCATATAGTTTATTAT
529386 CAT
1 CAT
529389 CATAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (21 bp):
CATATTCATATAGTTTATTAT
Found at i:529397 original size:22 final size:20
Alignment explanation
Indices: 529352--529398 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
529342 ATCACATATT
*
529352 CATATAGTTTATTATCATAT
1 CATATAGTTTATTATCATAA
*
529372 CATATGGTTTATATCATCATAA
1 CATATAGTTTAT-T-ATCATAA
529394 CATAT
1 CATAT
529399 CATATTCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 11 0.48
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (20 bp):
CATATAGTTTATTATCATAA
Found at i:529859 original size:21 final size:21
Alignment explanation
Indices: 529816--529860 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
529806 ATTCTATCGT
* *
529816 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
529837 TTGAATGGGTACCGATTCTCC
1 TTGAAGGGGTACCGATTCCCC
529858 TTG
1 TTG
529861 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:532698 original size:19 final size:21
Alignment explanation
Indices: 532656--532707 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
532646 TTCATAATCA
532656 CATATTCATATAGTTTATTAT
1 CATATTCATATAGTTTATTAT
*
532677 CATA-TCATATGGTTTA-TAT
1 CATATTCATATAGTTTATTAT
*
532696 CATCATACATAT
1 CAT-ATTCATAT
532708 CACATATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 6 0.22
20 12 0.44
21 9 0.33
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATATTCATATAGTTTATTAT
Found at i:533165 original size:21 final size:21
Alignment explanation
Indices: 533122--533166 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
533112 ATTCTGTCAT
* *
533122 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
533143 TTGAATGGGTACCGATTCTCC
1 TTGAAGGGGTACCGATTCCCC
533164 TTG
1 TTG
533167 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:549630 original size:78 final size:79
Alignment explanation
Indices: 549500--549656 Score: 307
Period size: 78 Copynumber: 2.0 Consensus size: 79
549490 CACCTCTCAA
549500 ATCAGAATCAGATAGAGATTTTCCAGATAATTCAGTAGAATTTAGATCAGATTTCAGCAAATTAA
1 ATCAGAATCAGATAGAGATTTTCCAGATAATTCAGTAGAATTTAGATCAGATTTCAGCAAATTAA
549565 ATCTCTTCAAAGCT
66 ATCTCTTCAAAGCT
549579 ATCAGAATCAGATAGAGA-TTTCCAGATAATTCAGTAGAATTTAGATCAGATTTCAGCAAATTAA
1 ATCAGAATCAGATAGAGATTTTCCAGATAATTCAGTAGAATTTAGATCAGATTTCAGCAAATTAA
549643 ATCTCTTCAAAGCT
66 ATCTCTTCAAAGCT
549657 TGATCTCTTC
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 60 0.77
79 18 0.23
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (79 bp):
ATCAGAATCAGATAGAGATTTTCCAGATAATTCAGTAGAATTTAGATCAGATTTCAGCAAATTAA
ATCTCTTCAAAGCT
Found at i:555430 original size:47 final size:48
Alignment explanation
Indices: 555397--555513 Score: 161
Period size: 46 Copynumber: 2.5 Consensus size: 48
555387 TCAATTTAGA
*
555397 GCGCCCTTTCGGG-TTTCACCCTAAA-TTTTTTTTACTTCAACTTAAG
1 GCGCCCTTTCGGGTTTTCACCCTAAACATTTTTTTACTTCAACTTAAG
* *
555443 GCGCCCTTTCGGGTTTTCACCCTAAACATTTTTTTGCTTTAACTT-AG
1 GCGCCCTTTCGGGTTTTCACCCTAAACATTTTTTTACTTCAACTTAAG
* *
555490 G-GCACTTTCAGGTTTTCACCCTAA
1 GCGCCCTTTCGGGTTTTCACCCTAA
555514 GCAAAGTATT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
46 34 0.53
47 15 0.23
48 15 0.23
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (48 bp):
GCGCCCTTTCGGGTTTTCACCCTAAACATTTTTTTACTTCAACTTAAG
Found at i:555447 original size:46 final size:46
Alignment explanation
Indices: 555377--555513 Score: 152
Period size: 46 Copynumber: 2.9 Consensus size: 46
555367 TTTTCTTCCC
* * *
555377 TTTTTTATTTTCAATTTAGAGCGCCCTTTCGGGTTTCACCCTAAA-TT
1 TTTTTTA-CTTCAACTTAG-GCGCCCTTTCGGGTTTCACCCTAAACAT
555424 TTTTTTACTTCAACTTAAGGCGCCCTTTCGGGTTTTCACCCTAAACAT
1 TTTTTTACTTCAACTT-AGGCGCCCTTTCGGG-TTTCACCCTAAACAT
* * * *
555472 TTTTTTGCTTTAACTTAGG-GCACTTTCAGGTTTTCACCCTAA
1 TTTTTTACTTCAACTTAGGCGCCCTTTC-GGGTTTCACCCTAA
555514 GCAAAGTATT
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
46 38 0.48
47 26 0.33
48 15 0.19
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (46 bp):
TTTTTTACTTCAACTTAGGCGCCCTTTCGGGTTTCACCCTAAACAT
Found at i:558289 original size:19 final size:19
Alignment explanation
Indices: 558265--558302 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
558255 TCCCTTACTA
558265 GAGATAGCGTAGGGCACCT
1 GAGATAGCGTAGGGCACCT
*
558284 GAGATAGTGTAGGGCACCT
1 GAGATAGCGTAGGGCACCT
558303 TAGTAGACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.37, T:0.18
Consensus pattern (19 bp):
GAGATAGCGTAGGGCACCT
Found at i:561778 original size:9 final size:9
Alignment explanation
Indices: 561764--561789 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
561754 CACTTTGTAA
561764 AAAAAAAAG
1 AAAAAAAAG
561773 AAAAAAAAG
1 AAAAAAAAG
561782 AAAAAAAA
1 AAAAAAAA
561790 TGAAGTTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:567645 original size:19 final size:22
Alignment explanation
Indices: 567596--567648 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 22
567586 TACAGGCACA
567596 GTATCGATACCTCTACTATAGG
1 GTATCGATACCTCTACTATAGG
* *
567618 GTATTGATACC-CTTCT-TA-G
1 GTATCGATACCTCTACTATAGG
567637 GTATCGATACCT
1 GTATCGATACCT
567649 AAATTTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 11 0.41
20 2 0.07
21 4 0.15
22 10 0.37
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.36
Consensus pattern (22 bp):
GTATCGATACCTCTACTATAGG
Found at i:583578 original size:32 final size:30
Alignment explanation
Indices: 583511--583600 Score: 99
Period size: 32 Copynumber: 2.9 Consensus size: 30
583501 AAAGTACATA
* * * *
583511 TCCATATGTTCGGAAGAACATAGGTAACTG
1 TCCATATGTCCCGAAGGACATAGATAACTG
583541 TCCATATGTCCCGAAGGACATAGATAATACTG
1 TCCATATGTCCCGAAGGACATAGAT-A-ACTG
* * *
583573 TCCATATGTCTCGAATGACATAGGTAAC
1 TCCATATGTCCCGAAGGACATAGATAAC
583601 CCTCAACTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
30 23 0.45
31 2 0.04
32 26 0.51
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (30 bp):
TCCATATGTCCCGAAGGACATAGATAACTG
Found at i:590473 original size:16 final size:17
Alignment explanation
Indices: 590448--590480 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
590438 AAGTTAATAT
590448 AATAAGAATAAT-AAAA
1 AATAAGAATAATGAAAA
*
590464 AATAATAATAATGAAAA
1 AATAAGAATAATGAAAA
590481 TAAAAAGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AATAAGAATAATGAAAA
Found at i:591513 original size:14 final size:14
Alignment explanation
Indices: 591496--591526 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
591486 TAAAATTGAA
591496 AAATAAAAAATATT
1 AAATAAAAAATATT
591510 AAATAAAAAATATT
1 AAATAAAAAATATT
591524 AAA
1 AAA
591527 GAAATTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAAAAATATT
Found at i:592800 original size:15 final size:14
Alignment explanation
Indices: 592764--592805 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
592754 ATTAATAACA
592764 ATATAATAAATAA-
1 ATATAATAAATAAT
592777 A-ATAA-AAATAAT
1 ATATAATAAATAAT
592789 ATATATATAAATAAT
1 ATATA-ATAAATAAT
592804 AT
1 AT
592806 GTATATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.24
12 5 0.20
13 4 0.16
14 1 0.04
15 9 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATAATAAATAAT
Found at i:592810 original size:15 final size:15
Alignment explanation
Indices: 592764--592811 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
592754 ATTAATAACA
592764 ATATA-ATAAATAA-
1 ATATATATAAATAAT
592777 A-ATA-A-AAATAAT
1 ATATATATAAATAAT
592789 ATATATATAAATAAT
1 ATATATATAAATAAT
*
592804 ATGTATAT
1 ATATATAT
592812 GATATTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 6 0.20
12 5 0.17
13 4 0.13
14 1 0.03
15 14 0.47
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
ATATATATAAATAAT
Found at i:592926 original size:73 final size:72
Alignment explanation
Indices: 592844--593056 Score: 257
Period size: 73 Copynumber: 2.9 Consensus size: 72
592834 AAAAACCATT
* * *
592844 AAAAACTATATACTATATGTTTTGAAAAAATATTTTAAAAACTATATACTATACGTTTTCAAAAA
1 AAAAACTATATATTATAAGTTTT-CAAAAATATTTTAAAAACTATATACTATACGTTTTCAAAAA
**
592909 TATTTTTA
65 TATTTAAA
* * * * * *
592917 AAAAACTATATATTATACGTTTTCAAAAGTATTTCTAAAAATTATACATTATATGTTTTCAAAAA
1 AAAAACTATATATTATAAGTTTTCAAAAATATTT-TAAAAACTATATACTATACGTTTTCAAAAA
592982 TATTTAAA
65 TATTTAAA
* **
592990 AAAAACTATATATTATAAGTTTTCAAAAATACTTTTTCAAAAC-ATATACTATACACTTTCAAAA
1 AAAAACTATATATTATAAGTTTTCAAAAATA--TTTTAAAAACTATATACTATACGTTTTCAAAA
593054 ATA
64 ATA
593057 ACGTTTGAAA
Statistics
Matches: 118, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
72 9 0.08
73 101 0.86
74 5 0.04
75 3 0.03
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.39
Consensus pattern (72 bp):
AAAAACTATATATTATAAGTTTTCAAAAATATTTTAAAAACTATATACTATACGTTTTCAAAAAT
ATTTAAA
Found at i:592934 original size:37 final size:36
Alignment explanation
Indices: 592842--593056 Score: 236
Period size: 36 Copynumber: 5.9 Consensus size: 36
592832 ATAAAAACCA
* *
592842 TTAAAAACTATATACTATATGTTTTGAAAAA-ATATT
1 TTAAAAACTATATACTATACGTTTTCAAAAATAT-TT
592878 TTAAAAACTATATACTATACGTTTTCAAAAATATTT
1 TTAAAAACTATATACTATACGTTTTCAAAAATATTT
* *
592914 TTAAAAAACTATATATTATACGTTTTCAAAAGTATTT
1 TT-AAAAACTATATACTATACGTTTTCAAAAATATTT
* * * * *
592951 CTAAAAATTATACATTATATGTTTTCAAAAATATTT
1 TTAAAAACTATATACTATACGTTTTCAAAAATATTT
** * *
592987 AAAAAAAACTATATATTATAAGTTTTCAAAAATACTTT
1 -TTAAAAACTATATACTATACGTTTTCAAAAATA-TTT
* **
593025 TTCAAAAC-ATATACTATACACTTTCAAAAATA
1 TTAAAAACTATATACTATACGTTTTCAAAAATA
593057 ACGTTTGAAA
Statistics
Matches: 154, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
36 83 0.54
37 68 0.44
38 3 0.02
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (36 bp):
TTAAAAACTATATACTATACGTTTTCAAAAATATTT
Found at i:601196 original size:20 final size:22
Alignment explanation
Indices: 601173--601216 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
601163 CACCCGCAGC
601173 ATCCATCCACCCAT-TA-ATAT
1 ATCCATCCACCCATATATATAT
*
601193 ATCCATCCATCCATATATATAT
1 ATCCATCCACCCATATATATAT
601215 AT
1 AT
601217 ATATATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (22 bp):
ATCCATCCACCCATATATATAT
Found at i:602604 original size:35 final size:35
Alignment explanation
Indices: 602500--602585 Score: 154
Period size: 35 Copynumber: 2.5 Consensus size: 35
602490 CTTCAAAAAG
602500 AGAAAAATCAACATGTCTAAGTCTGTAATAATAAA
1 AGAAAAATCAACATGTCTAAGTCTGTAATAATAAA
* *
602535 AGAAAAATCAACATATCTAAGTCTGTAATGATAAA
1 AGAAAAATCAACATGTCTAAGTCTGTAATAATAAA
602570 AGAAAAATCAACATGT
1 AGAAAAATCAACATGT
602586 TTAAAATTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (35 bp):
AGAAAAATCAACATGTCTAAGTCTGTAATAATAAA
Found at i:607222 original size:29 final size:29
Alignment explanation
Indices: 607177--607240 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
607167 TATTTATTTG
* * *
607177 TTATTATAGTCTAATTTTTTCATTACTTT
1 TTATTAAAGTCTAATTTTTTAAATACTTT
*
607206 TTATTAAATGTCT-ATTTTTTAAATATTTT
1 TTATTAAA-GTCTAATTTTTTAAATACTTT
607235 TTATTA
1 TTATTA
607241 CGAGCAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (29 bp):
TTATTAAAGTCTAATTTTTTAAATACTTT
Found at i:610368 original size:2 final size:2
Alignment explanation
Indices: 610361--610398 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
610351 AATGTATGTA
610361 AT 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 AT
610399 GATGTGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:616173 original size:16 final size:17
Alignment explanation
Indices: 616152--616184 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
616142 TACTATTCAC
616152 ATGAATAGT-AAATTTT
1 ATGAATAGTGAAATTTT
616168 ATGAATAGTGAAATTTT
1 ATGAATAGTGAAATTTT
616185 TTCGGCGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (17 bp):
ATGAATAGTGAAATTTT
Found at i:617552 original size:17 final size:17
Alignment explanation
Indices: 617530--617565 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
617520 GCCAAGTCAT
617530 CCAAGGTGATGGATGAG
1 CCAAGGTGATGGATGAG
617547 CCAAGGTGATGGATGAG
1 CCAAGGTGATGGATGAG
617564 CC
1 CC
617566 CAGGATCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.39, T:0.17
Consensus pattern (17 bp):
CCAAGGTGATGGATGAG
Found at i:621946 original size:31 final size:31
Alignment explanation
Indices: 621911--621970 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
621901 AACTTAAAAG
621911 AGTTTTACAATACTGAAAGTTAAATAATTTT
1 AGTTTTACAATACTGAAAGTTAAATAATTTT
* *
621942 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAAGTTAAATAATT
621971 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAAGTTAAATAATTTT
Found at i:622018 original size:22 final size:22
Alignment explanation
Indices: 621993--622422 Score: 655
Period size: 22 Copynumber: 19.6 Consensus size: 22
621983 ATAATAAATT
**
621993 TTTTAAAATAAATCAATTAATA
1 TTTTAAAATAAATCAATCCATA
622015 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
622037 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
622059 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
622081 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
622103 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
622125 TTTTAAAATAACTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
622147 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *
622169 TTTTAATATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
622191 TTTTAAAATAAATCAAT-CATA
1 TTTTAAAATAAATCAATCCATA
622212 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
622234 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
622256 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
622278 ATTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
622300 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
622322 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
622344 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
622366 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
622388 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
**
622410 TTAAAAAATAAAT
1 TTTTAAAATAAAT
622423 TTTAAAATAA
Statistics
Matches: 369, Mismatches: 38, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
21 21 0.06
22 348 0.94
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:626128 original size:17 final size:17
Alignment explanation
Indices: 626092--626127 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
626082 AATTAATGAA
626092 TTTATATAAAAAATATT
1 TTTATATAAAAAATATT
626109 TTTATAT-AAAAATATT
1 TTTATATAAAAAATATT
626125 TTT
1 TTT
626128 TTACTCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATATAAAAAATATT
Found at i:626326 original size:20 final size:18
Alignment explanation
Indices: 626292--626331 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
626282 GACAAGTTCC
626292 TATAAAAATATTTTTTAT
1 TATAAAAATATTTTTTAT
626310 TATAAAATATAATTTTTTAT
1 TATAAAA-AT-ATTTTTTAT
626330 TA
1 TA
626332 AATTTTACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 2 0.10
20 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATAAAAATATTTTTTAT
Found at i:627803 original size:3 final size:3
Alignment explanation
Indices: 627795--627819 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
627785 TTTTCAGTCA
627795 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
627820 TAAAAAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:628062 original size:21 final size:21
Alignment explanation
Indices: 628011--628063 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
628001 ATTATGACTA
628011 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
628032 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
628053 TCGCAATGCGA
1 TCGCAATGCGA
628064 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:628078 original size:20 final size:21
Alignment explanation
Indices: 628053--628104 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
628043 TTTTCCCAAT
*
628053 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
628073 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
628094 TCGCAATGCGA
1 TCGCAATGCGA
628105 TACTGGCTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:628118 original size:20 final size:20
Alignment explanation
Indices: 628094--628225 Score: 158
Period size: 20 Copynumber: 6.7 Consensus size: 20
628084 ATTTGGAAAA
* * *
628094 TCGCAATGCGATACTGGCTA
1 TCGCAACGCGATACTGACTT
628114 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
628134 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATACTGACTT
628154 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
628174 TCGCAACTCGAT-TTGACTT
1 TCGCAACGCGATACTGACTT
* * *
628193 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATACTGACTT
* *
628213 TCTCAACGAGATA
1 TCGCAACGCGATA
628226 ATACAGAATC
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
19 16 0.16
20 82 0.84
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:628220 original size:59 final size:60
Alignment explanation
Indices: 628093--628225 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 60
628083 AATTTGGAAA
* * * *
628093 ATCGCAATGCGATACTGGCTATCGCAACGCGATACTGACTTTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACTATCGCAACGCGATACTGACTTTCGCAACGAGATACTGACT
* * * * *
628153 TTCGCAACGCGATACTGACTTTCGCAACTCGAT-TTGACTTTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACTATCGCAACGCGATACTGACTTTCGCAACGAGATACTGACT
* *
628212 ATCTCAACGAGATA
1 ATCGCAACGCGATA
628226 ATACAGAATC
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
59 33 0.54
60 28 0.46
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (60 bp):
ATCGCAACGCGATACTGACTATCGCAACGCGATACTGACTTTCGCAACGAGATACTGACT
Found at i:628993 original size:24 final size:24
Alignment explanation
Indices: 628966--629019 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
628956 GTATTCGAAA
*
628966 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
628990 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
629014 TTTGAT
1 TTTGAT
629020 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:629211 original size:12 final size:12
Alignment explanation
Indices: 629194--629218 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
629184 ATATAATCCT
629194 GAAGAAGAAAAA
1 GAAGAAGAAAAA
629206 GAAGAAGAAAAA
1 GAAGAAGAAAAA
629218 G
1 G
629219 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:631639 original size:20 final size:20
Alignment explanation
Indices: 631500--631659 Score: 185
Period size: 20 Copynumber: 8.0 Consensus size: 20
631490 CGCAATGGGG
* * *
631500 CTATCGCAACGCGAAAATGG
1 CTATCGCAATGCGGAAATGA
* *
631520 CTATCGCAACGCGGAAATGG
1 CTATCGCAATGCGGAAATGA
* *
631540 CTATCGCAACGCGGAAATGG
1 CTATCGCAATGCGGAAATGA
***
631560 CTATCGCAACATGGAAATGA
1 CTATCGCAATGCGGAAATGA
631580 CTATCGCAATGCGGAAATGA
1 CTATCGCAATGCGGAAATGA
631600 CTATCGCAATGCGGAAATGA
1 CTATCGCAATGCGGAAATGA
**
631620 AAATCGCAATGCGGAAATGA
1 CTATCGCAATGCGGAAATGA
** *
631640 AAATCGCAATGCGAAAATGA
1 CTATCGCAATGCGGAAATGA
631660 AAATCGCATT
Statistics
Matches: 130, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 130 1.00
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.17
Consensus pattern (20 bp):
CTATCGCAATGCGGAAATGA
Done.