Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008554.1 Hibiscus syriacus cultivar Beakdansim tig00111458_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: 3217407
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:307628 original size:16 final size:16
Alignment explanation
Indices: 307593--307647 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
307583 TAATTAGAGT
*
307593 AGTTGAGAGTGTTAAAG
1 AGTTGAGAGT-TTTAAG
307610 AGTTGAGAGTTTTAAG
1 AGTTGAGAGTTTTAAG
307626 AGTTGAGAGTTTTAAG
1 AGTTGAGAGTTTTAAG
307642 AGTTGA
1 AGTTGA
307648 ATTTATTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
16 27 0.73
17 10 0.27
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (16 bp):
AGTTGAGAGTTTTAAG
Found at i:309200 original size:2 final size:2
Alignment explanation
Indices: 309193--309258 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
309183 GATCATAACC
309193 AT AT 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 AT AT
309235 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
309259 CATTTAGACT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:312201 original size:10 final size:8
Alignment explanation
Indices: 312177--312215 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
312167 ATTGTTATTC
312177 TTCATATA
1 TTCATATA
312185 TTCATATA
1 TTCATATA
312193 TTCATATA
1 TTCATATA
*
312201 TTCATGTA
1 TTCATATA
312209 TTCATAT
1 TTCATAT
312216 CATTTCTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.51
Consensus pattern (8 bp):
TTCATATA
Found at i:316670 original size:183 final size:183
Alignment explanation
Indices: 316362--316729 Score: 727
Period size: 183 Copynumber: 2.0 Consensus size: 183
316352 TTCATCTTTC
316362 ACTGAACACTATAACTTCCAATCCATCTGAATTGATTAATGTTACCCTCTTCAATCTACAATCAA
1 ACTGAACACTATAACTTCCAATCCATCTGAATTGATTAATGTTACCCTCTTCAATCTACAATCAA
316427 CATTGGCATGATAGCGATATAACCAGTCTATTCCTAGTATCACCTCGAATTCGTCAAAAGGTAAT
66 CATTGGCATGATAGCGATATAACCAGTCTATTCCTAGTATCACCTCGAATTCGTCAAAAGGTAAT
316492 TCCATCAGATTAGCAGGGAATTCAATTCTCTGAATCCGTATGAGACACCCTCG
131 TCCATCAGATTAGCAGGGAATTCAATTCTCTGAATCCGTATGAGACACCCTCG
316545 ACTGAACACTATAACTTCCAATCCATCTGAATTGATTAATGTTACCCTCTTCAATCTACAATCAA
1 ACTGAACACTATAACTTCCAATCCATCTGAATTGATTAATGTTACCCTCTTCAATCTACAATCAA
*
316610 CATTGGCATGATAGCGATATAACCAGTCTATTCCTAGTATCACCTCGAATTTGTCAAAAGGTAAT
66 CATTGGCATGATAGCGATATAACCAGTCTATTCCTAGTATCACCTCGAATTCGTCAAAAGGTAAT
316675 TCCATCAGATTAGCAGGGAATTCAATTCTCTGAATCCGTATGAGACACCCTCG
131 TCCATCAGATTAGCAGGGAATTCAATTCTCTGAATCCGTATGAGACACCCTCG
316728 AC
1 AC
316730 ATACTCTATT
Statistics
Matches: 184, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 184 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (183 bp):
ACTGAACACTATAACTTCCAATCCATCTGAATTGATTAATGTTACCCTCTTCAATCTACAATCAA
CATTGGCATGATAGCGATATAACCAGTCTATTCCTAGTATCACCTCGAATTCGTCAAAAGGTAAT
TCCATCAGATTAGCAGGGAATTCAATTCTCTGAATCCGTATGAGACACCCTCG
Found at i:323777 original size:49 final size:49
Alignment explanation
Indices: 323720--324010 Score: 505
Period size: 49 Copynumber: 5.9 Consensus size: 49
323710 AATTACCATT
*
323720 ACCTTTTATGTCGAAATGTACCGTTATGCATTTAACTTTCATTAGTGGC
1 ACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGC
323769 ACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGC
1 ACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGC
* *
323818 ACCTTTTATGCCGAAATGTACCGTTATGCATTTAACTTTCATTAGTGGC
1 ACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGC
*
323867 ACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGTC
1 ACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGC
*
323916 ACCTTTTATG-CTGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGT
1 ACCTTTTATGTC-GAAATGCACCGTTATGCATTTAACTTTCATTAGTGGC
323965 ACCTTTTATG-CTGAAATGCACCGTTATGCATTTAACTTTCATTAGT
1 ACCTTTTATGTC-GAAATGCACCGTTATGCATTTAACTTTCATTAGT
324011 TCATTTTAGA
Statistics
Matches: 233, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
48 1 0.00
49 232 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (49 bp):
ACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGC
Found at i:324460 original size:18 final size:18
Alignment explanation
Indices: 324437--324485 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
324427 TACCTTCCTC
324437 TTAGTATCGATACCCACA
1 TTAGTATCGATACCCACA
324455 TTAGTATCGATACCCACA
1 TTAGTATCGATACCCACA
*
324473 TCAGTATCGATAC
1 TTAGTATCGATAC
324486 TAATTGCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (18 bp):
TTAGTATCGATACCCACA
Found at i:325641 original size:18 final size:19
Alignment explanation
Indices: 325618--325657 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
325608 GCAACCAACA
325618 TCAAAACTGG-TGCCGCCG
1 TCAAAACTGGTTGCCGCCG
325636 TCAAAACTGGTTGCCGCCG
1 TCAAAACTGGTTGCCGCCG
325655 TCA
1 TCA
325658 GTTAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (19 bp):
TCAAAACTGGTTGCCGCCG
Found at i:327946 original size:32 final size:32
Alignment explanation
Indices: 327905--327969 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
327895 ATAGCTCCCA
327905 ACACTTCTAGGATATTTAACAGTGGATTCTGT
1 ACACTTCTAGGATATTTAACAGTGGATTCTGT
* *
327937 ACACTTCTAGGATATTTTACTGTGGATTCTGT
1 ACACTTCTAGGATATTTAACAGTGGATTCTGT
327969 A
1 A
327970 GTCCATGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.40
Consensus pattern (32 bp):
ACACTTCTAGGATATTTAACAGTGGATTCTGT
Found at i:329421 original size:86 final size:87
Alignment explanation
Indices: 329220--329393 Score: 305
Period size: 87 Copynumber: 2.0 Consensus size: 87
329210 ACAAGTTGAT
*
329220 AAACGAGCTTGTTTGTGAATATAAACGAATTGAATACACTTATGTTCATGTTCATTTTTTCATTA
1 AAACGAGCTTCTTTGTGAATATAAACGAATTGAATACACTTATGTTCATGTTCATTTTTTCATTA
329285 AATGAACATAAATGTATTTTTC
66 AATGAACATAAATGTATTTTTC
*
329307 AAACGAGCTTGTTTGTGAATATAAACGAATTGAATACACTTATGTTCATGTTCA-TTTTTCATTA
1 AAACGAGCTTCTTTGTGAATATAAACGAATTGAATACACTTATGTTCATGTTCATTTTTTCATTA
* *
329371 AATGAATATAAATGTTTTTTTC
66 AATGAACATAAATGTATTTTTC
329393 A
1 A
329394 TACTCGTTTC
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 31 0.36
87 54 0.64
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (87 bp):
AAACGAGCTTCTTTGTGAATATAAACGAATTGAATACACTTATGTTCATGTTCATTTTTTCATTA
AATGAACATAAATGTATTTTTC
Found at i:335091 original size:24 final size:24
Alignment explanation
Indices: 335064--335175 Score: 145
Period size: 24 Copynumber: 4.7 Consensus size: 24
335054 ATTTGATTTA
*
335064 TGATCTGATACTTGACATGGATTC
1 TGATATGATACTTGACATGGATTC
*
335088 TGATTTGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACATGGATTC
* * *
335112 TGATCTGATACTTGACTTGGATTT
1 TGATATGATACTTGACATGGATTC
* *
335136 TGATATGATACTTGACTTGGATTT
1 TGATATGATACTTGACATGGATTC
335160 TGATATGATACTTGAC
1 TGATATGATACTTGAC
335176 GTGAATTATG
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:335187 original size:24 final size:24
Alignment explanation
Indices: 335061--335192 Score: 140
Period size: 24 Copynumber: 5.5 Consensus size: 24
335051 TCGATTTGAT
*
335061 TTATGATCTGATACTTGACATGGA
1 TTATGATATGATACTTGACATGGA
* *
335085 TTCTGATTTGATA-TCTGACATGGA
1 TTATGATATGATACT-TGACATGGA
* * *
335109 TTCTGATCTGATACTTGACTTGGA
1 TTATGATATGATACTTGACATGGA
* *
335133 TTTTGATATGATACTTGACTTGGA
1 TTATGATATGATACTTGACATGGA
* * *
335157 TTTTGATATGATACTTGACGTGAA
1 TTATGATATGATACTTGACATGGA
*
335181 TTATGATGTGAT
1 TTATGATATGAT
335193 TTTTGATATA
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 94 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (24 bp):
TTATGATATGATACTTGACATGGA
Found at i:339826 original size:48 final size:48
Alignment explanation
Indices: 339772--339903 Score: 176
Period size: 48 Copynumber: 2.8 Consensus size: 48
339762 TCGATTTGAT
339772 TTCTGATCTGATACTTGACATGGATTCTGATTTGATATCTT-ACATGGA
1 TTCTGATCTGATACTTGACATGGATTCTGATTTGATA-CTTGACATGGA
* * *
339820 TTCTGATCTGATACTTGACTTGGATTCTGATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGATTCTGATTTGATACTTGACATGGA
* * * * *
339868 TTTTGATATGATACTTGACGTGAATTATGATTTGAT
1 TTCTGATCTGATACTTGACATGGATTCTGATTTGAT
339904 TTTTGATATA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 3 0.04
48 71 0.96
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (48 bp):
TTCTGATCTGATACTTGACATGGATTCTGATTTGATACTTGACATGGA
Found at i:339903 original size:24 final size:24
Alignment explanation
Indices: 339772--339886 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
339762 TCGATTTGAT
339772 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
339796 TTCTGATTTGATATCTT-ACATGGA
1 TTCTGATCTGATA-CTTGACATGGA
*
339820 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
*
339844 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
339868 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
339887 GTGAATTATG
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 3 0.04
24 77 0.93
25 3 0.04
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:341719 original size:25 final size:24
Alignment explanation
Indices: 341670--341722 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 24
341660 TGAACTAACT
341670 TATAAAATTTTAGAAGAAATGAATA
1 TATAAAATTTTAGAAGAAA-GAATA
341695 TATAAAATTTTAGAAAGCAAA-AATA
1 TATAAAATTTTAG-AAG-AAAGAATA
341720 TAT
1 TAT
341723 TATCAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 20 0.77
26 3 0.12
27 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (24 bp):
TATAAAATTTTAGAAGAAAGAATA
Found at i:346406 original size:20 final size:19
Alignment explanation
Indices: 346349--346415 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
346339 TGCAAAAATG
* *
346349 GTATCGATACCGTAATAG-A
1 GTATCGATACCAT-GTAGAA
346368 GTATCGATACCATGTAGAA
1 GTATCGATACCATGTAGAA
346387 GTATCGATACCATGGTAGAA
1 GTATCGATACCAT-GTAGAA
346407 GTATCGATA
1 GTATCGATA
346416 TAATTGAGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 3 0.07
19 26 0.59
20 15 0.34
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (19 bp):
GTATCGATACCATGTAGAA
Found at i:351383 original size:21 final size:20
Alignment explanation
Indices: 351365--351408 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
351355 CACCGAAGTG
351365 CCATATAGAATGTCTGAAGGA
1 CCATATAG-ATGTCTGAAGGA
*
351386 CCATATAGATGTCCCGAAGGA
1 CCATATAGATGT-CTGAAGGA
351407 CC
1 CC
351409 GCGTAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (20 bp):
CCATATAGATGTCTGAAGGA
Found at i:351429 original size:24 final size:24
Alignment explanation
Indices: 351397--351461 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
351387 CATATAGATG
351397 TCCCGAAGGACCGCGTAGAAATTA
1 TCCCGAAGGACCGCGTAGAAATTA
** *
351421 TCTTGAAGGACCACGTAG-AATTA
1 TCCCGAAGGACCGCGTAGAAATTA
351444 TCCCGAAGG--CGCGTAGAA
1 TCCCGAAGGACCGCGTAGAA
351462 CCCTTGACTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 6 0.18
22 1 0.03
23 12 0.35
24 15 0.44
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.18
Consensus pattern (24 bp):
TCCCGAAGGACCGCGTAGAAATTA
Found at i:355625 original size:12 final size:12
Alignment explanation
Indices: 355608--355634 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
355598 GGACCAAGGG
355608 AATAATTATACC
1 AATAATTATACC
355620 AATAATTATACC
1 AATAATTATACC
355632 AAT
1 AAT
355635 TTTCTTCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAATTATACC
Found at i:356419 original size:21 final size:21
Alignment explanation
Indices: 356369--356419 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
356359 GGTCTAGAAA
*
356369 TATTGATACTCCTTCATTGGG
1 TATTGATACTCCTTCATAGGG
** *
356390 TATCAATACT-CTTCGTAGGAG
1 TATTGATACTCCTTCATAGG-G
356411 TATTGATAC
1 TATTGATAC
356420 CTGGGTCACT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (21 bp):
TATTGATACTCCTTCATAGGG
Found at i:357783 original size:23 final size:23
Alignment explanation
Indices: 357714--357798 Score: 106
Period size: 23 Copynumber: 3.8 Consensus size: 23
357704 CAGCTCGTAA
357714 TTTGCACCAAAGTGCCACATAA-
1 TTTGCACCAAAGTGCCACATAAG
*
357736 -TTGTC-CCAAAG-GACCACATAGG
1 TTTG-CACCAAAGTG-CCACATAAG
*
357758 TTTGCACCGAAGTGCCACATAAG
1 TTTGCACCAAAGTGCCACATAAG
357781 TTTGCACCAAAGTGCCAC
1 TTTGCACCAAAGTGCCAC
357799 CTAATTGTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
20 1 0.02
21 16 0.30
22 2 0.04
23 33 0.62
24 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (23 bp):
TTTGCACCAAAGTGCCACATAAG
Found at i:358070 original size:29 final size:30
Alignment explanation
Indices: 358010--358070 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
358000 TCATATAATC
* * **
358010 ATAAAACATAGCTTATATAATATAAATTGA
1 ATAAAACATAGCTAATATAACATAAAAGGA
*
358040 ATAAAACATTG-TAATATAACATAAAAGGA
1 ATAAAACATAGCTAATATAACATAAAAGGA
358069 AT
1 AT
358071 TATAAAGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.30
Consensus pattern (30 bp):
ATAAAACATAGCTAATATAACATAAAAGGA
Found at i:361799 original size:35 final size:36
Alignment explanation
Indices: 361731--361886 Score: 155
Period size: 35 Copynumber: 4.4 Consensus size: 36
361721 AGCATAGTAT
*
361731 ATATAATATATAGTTTTTTTAAAAAATAGTTTTGAAAAT
1 ATATAATATATAG-TTTTTT--AAAATAGTTTTGAAAAC
* *
361770 GTATAATATAT-GTTTTTTAAAATGGTTTTGAAAAC
1 ATATAATATATAGTTTTTTAAAATAGTTTTGAAAAC
** * *
361805 ATATGGTATATAGGTTTTTAAAATAATTTTGAAAAC
1 ATATAATATATAGTTTTTTAAAATAGTTTTGAAAAC
* *
361841 -----GTATATAG-TTTTTAAAATAGTTTTGAAAAT
1 ATATAATATATAGTTTTTTAAAATAGTTTTGAAAAC
361871 ATATAATATATAGTTT
1 ATATAATATATAGTTT
361887 ATAAAACCTA
Statistics
Matches: 98, Mismatches: 12, Indels: 17
0.77 0.09 0.13
Matches are distributed among these distances:
30 20 0.20
31 8 0.08
35 30 0.31
36 23 0.23
37 6 0.06
38 1 0.01
39 10 0.10
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.46
Consensus pattern (36 bp):
ATATAATATATAGTTTTTTAAAATAGTTTTGAAAAC
Found at i:361854 original size:30 final size:31
Alignment explanation
Indices: 361810--361869 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
361800 AAAACATATG
361810 GTATATAGGTTTTTAAAATAATTTTGAAAAC
1 GTATATAGGTTTTTAAAATAATTTTGAAAAC
*
361841 GTATATA-GTTTTTAAAATAGTTTTGAAAA
1 GTATATAGGTTTTTAAAATAATTTTGAAAA
361870 TATATAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.43
Consensus pattern (31 bp):
GTATATAGGTTTTTAAAATAATTTTGAAAAC
Found at i:361969 original size:30 final size:29
Alignment explanation
Indices: 361935--361998 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
361925 TTTAAAACGA
*
361935 TTTTTGAAAATATATTAAAATATTATATAG
1 TTTTTGAAAATATAAT-AAATATTATATAG
* * *
361965 TTTTTGGAAATATAATATATGTTATATAG
1 TTTTTGAAAATATAATAAATATTATATAG
361994 TTTTT
1 TTTTT
361999 TATTATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (29 bp):
TTTTTGAAAATATAATAAATATTATATAG
Found at i:362010 original size:19 final size:19
Alignment explanation
Indices: 361998--362061 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
361988 ATATAGTTTT
361998 TTATTATTTATATTATTTA
1 TTATTATTTATATTATTTA
362017 TTATTATTT-TAGGTTATATTA
1 TTATTATTTATA--TTAT-TTA
*
362038 TTATTATTATTTATTGATTTA
1 TTATTATT-TATATT-ATTTA
362059 TTA
1 TTA
362062 AATTTTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.05
19 9 0.23
20 4 0.10
21 19 0.49
22 3 0.08
23 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTATTATTTATATTATTTA
Found at i:362011 original size:9 final size:10
Alignment explanation
Indices: 361998--362061 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 10
361988 ATATAGTTTT
361998 TTATTATTTA
1 TTATTATTTA
362008 -TATTATTTA
1 TTATTATTTA
362017 TTATTA-TT-
1 TTATTATTTA
362025 TTAGGTTATATTA
1 TTA--TTAT-TTA
362038 TTATTA-TTA
1 TTATTATTTA
362047 TTTATTGATTTA
1 -TTATT-ATTTA
362059 TTA
1 TTA
362062 AATTTTAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
8 3 0.07
9 14 0.31
10 13 0.29
11 7 0.16
12 5 0.11
13 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (10 bp):
TTATTATTTA
Found at i:387952 original size:37 final size:37
Alignment explanation
Indices: 387911--387985 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
387901 AAAGTTGAAG
* *
387911 ACAACATCAGTTAAAGCCTTGCAGAGTTTGAATTTGT
1 ACAACATCAATTAAAGCCTTACAGAGTTTGAATTTGT
*
387948 ACAACATCAATTAAAGCCTTACAGAGTTTGAGTTTGT
1 ACAACATCAATTAAAGCCTTACAGAGTTTGAATTTGT
387985 A
1 A
387986 TTCCATGTTT
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:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (37 bp):
ACAACATCAATTAAAGCCTTACAGAGTTTGAATTTGT
Found at i:393113 original size:24 final size:23
Alignment explanation
Indices: 393081--393127 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
393071 ATGACATCTC
393081 AATAGTTATGTTATTTTTTTAATT
1 AATAGTTATGTTA-TTTTTTAATT
393105 AATAGTTATGTTATTTTTTAATT
1 AATAGTTATGTTATTTTTTAATT
393128 GTGGGTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.62
Consensus pattern (23 bp):
AATAGTTATGTTATTTTTTAATT
Found at i:394416 original size:20 final size:20
Alignment explanation
Indices: 394393--394438 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
394383 GTTTTCAGAT
*
394393 TCGCAACGCGATTATAACTA
1 TCGCAACACGATTATAACTA
* * *
394413 TCGCAATACGATTTTGACTA
1 TCGCAACACGATTATAACTA
394433 TCGCAA
1 TCGCAA
394439 TACAATTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (20 bp):
TCGCAACACGATTATAACTA
Found at i:394439 original size:20 final size:20
Alignment explanation
Indices: 394409--394447 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
394399 CGCGATTATA
*
394409 ACTATCGCAATACGATTTTG
1 ACTATCGCAATACAATTTTG
394429 ACTATCGCAATACAATTTT
1 ACTATCGCAATACAATTTT
394448 CCAATTTCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (20 bp):
ACTATCGCAATACAATTTTG
Found at i:394484 original size:21 final size:21
Alignment explanation
Indices: 394433--394485 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
394423 ATTTTGACTA
* *
394433 TCGCAATACAATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
394454 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
394475 TCGCAATGCGA
1 TCGCAATGCGA
394486 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:394505 original size:41 final size:41
Alignment explanation
Indices: 394460--394732 Score: 166
Period size: 41 Copynumber: 6.7 Consensus size: 41
394450 AATTTCGCGT
** *
394460 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCGTAAATCGCAATGCGAATAAGTAAATCGCAA
* * * * *
394501 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCGTAAATCGCAATGCGAATAAGT-A-AATCGCAA
* * * * *
394542 TGCGAATTTGGAAAATCGCAATGCG-AT-ATTGACTATCGCAA
1 TGCGATTTTCGTAAATCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * * **
394583 TGCGATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCGTAAATCGCAATGCGA-ATAAGTAAATCGCAA
* *
394624 TGCGATTTTCATAATTCGCAATGCGAATACA-TAAATCGCAA
1 TGCGATTTTCGTAAATCGCAATGCGAATA-AGTAAATCGCAA
* * * *
394665 CGCGA-ATTAGTAAATCGCAATGCGAATTAAGAAAATCGCAA
1 TGCGATTTTCGTAAATCGCAATGCGAA-TAAGTAAATCGCAA
* *
394706 TGCGA-ATACGTAAATCGCAATGCGAAT
1 TGCGATTTTCGTAAATCGCAATGCGAAT
394733 CTTACTATCG
Statistics
Matches: 186, Mismatches: 37, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
39 2 0.01
40 25 0.13
41 157 0.84
43 1 0.01
44 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (41 bp):
TGCGATTTTCGTAAATCGCAATGCGAATAAGTAAATCGCAA
Found at i:394518 original size:21 final size:21
Alignment explanation
Indices: 394475--394567 Score: 102
Period size: 21 Copynumber: 4.5 Consensus size: 21
394465 TTTTCCCAAT
** *
394475 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
394495 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
* **
394516 TCGCAATGCG-ATACT-GACTA
1 TCGCAATGCGAAT-TTGGAAAA
394536 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
394557 TCGCAATGCGA
1 TCGCAATGCGA
394568 TATTGACTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:394546 original size:82 final size:81
Alignment explanation
Indices: 394460--394689 Score: 200
Period size: 82 Copynumber: 2.8 Consensus size: 81
394450 AATTTCGCGT
** * *
394460 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCGCAATGC
1 TGCGATTTTCAAAATTCGCAATGCGAATAA-TAAATCGCAATGCGAATTTAGTAAATCGCAATGC
394525 GATACTGAC-TA-TCGCAA
65 GAT--TGACGTATTCGCAA
** * * * ** * *
394542 TGCGAATTTGGAAAA-TCGCAATGCG-ATATTGACTATCGCAATGCGATTTTCCTAATTCGCATT
1 TGCG-ATTTTCAAAATTCGCAATGCGAATAAT-A-AATCGCAATGCGAATTTAGTAAATCGCAAT
* **
394605 GCGATTTACGTATTCGCGT
63 GCGATTGACGTATTCGCAA
* *
394624 TGCGATTTTCATAATTCGCAATGCGAATACATAAATCGCAACGCGAA-TTAGTAAATCGCAATGC
1 TGCGATTTTCAAAATTCGCAATGCGAATA-ATAAATCGCAATGCGAATTTAGTAAATCGCAATGC
394688 GA
65 GA
394690 ATTAAGAAAA
Statistics
Matches: 114, Mismatches: 26, Indels: 17
0.73 0.17 0.11
Matches are distributed among these distances:
80 4 0.04
81 28 0.25
82 71 0.62
83 10 0.09
84 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (81 bp):
TGCGATTTTCAAAATTCGCAATGCGAATAATAAATCGCAATGCGAATTTAGTAAATCGCAATGCG
ATTGACGTATTCGCAA
Found at i:394607 original size:21 final size:21
Alignment explanation
Indices: 394577--394649 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
394567 ATATTGACTA
*
394577 TCGCAATGCGATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
394598 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
394618 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
394639 TCGCAATGCGA
1 TCGCAATGCGA
394650 ATACATAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:394689 original size:61 final size:60
Alignment explanation
Indices: 394475--394758 Score: 188
Period size: 61 Copynumber: 4.7 Consensus size: 60
394465 TTTTCCCAAT
* ** *
394475 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGA-AAATCGCAATGCG-ATACTGACTA
1 TCGCAATGCGAATTAGTAAATCGCAATGCG-ATTTTCATAAATCGCAATGCGAATACT-A-AA
* * * * * * *
394536 TCGCAATGCGAATTTGGAAAATCGCAATGCGATATTGACT--ATCGCAATGCGATTTTCCTAAT
1 TCGCAATGCGAA-TTAGTAAATCGCAATGCGATTTTCA-TAAATCGCAATGCGA--ATACTAAA
* * * ** *
394598 TCGCATTGCGATTTACGT-ATTCGCGTTGCGATTTTCATAATTCGCAATGCGAATACATAAA
1 TCGCAATGCGAATTA-GTAAATCGCAATGCGATTTTCATAAATCGCAATGCGAATAC-TAAA
* * * *
394659 TCGCAACGCGAATTAGTAAATCGCAATGCGA-ATTAAGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTAGTAAATCGCAATGCGATTTTCA-TAAATCGCAATGCGAATAC-TAAA
* *
394720 TCGCAATGCGAATCT--TACTATCGCAATGCGATTTACATA
1 TCGCAATGCGAAT-TAGTA-AATCGCAATGCGATTTTCATA
394759 GCGCCATTCG
Statistics
Matches: 169, Mismatches: 39, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
60 10 0.06
61 115 0.68
62 40 0.24
63 1 0.01
64 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (60 bp):
TCGCAATGCGAATTAGTAAATCGCAATGCGATTTTCATAAATCGCAATGCGAATACTAAA
Found at i:394742 original size:20 final size:20
Alignment explanation
Indices: 394475--394750 Score: 136
Period size: 20 Copynumber: 13.6 Consensus size: 20
394465 TTTTCCCAAT
*
394475 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
** *
394495 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
394516 TCGCAATGCG-ATAC-TGACTA
1 TCGCAATGCGAATACGT-A-AA
** *
394536 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
394557 TCGCAATGCGATATTGAC-T--A
1 TCGCAATGCGA-A-T-ACGTAAA
* * * *
394577 TCGCAATGCGATTTTCCTAAT
1 TCGCAATGCGA-ATACGTAAA
* * *
394598 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGA-ATACGTAAA
** * * * *
394618 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGA-ATACGTAAA
*
394639 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
*
394659 TCGCAACGCGAATTA-GTAAA
1 TCGCAATGCGAA-TACGTAAA
* *
394679 TCGCAATGCGAATTAAGAAAA
1 TCGCAATGCGAA-TACGTAAA
394700 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
394720 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
394740 TCGCAATGCGA
1 TCGCAATGCGA
394751 TTTACATAGC
Statistics
Matches: 205, Mismatches: 36, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.00
19 7 0.03
20 120 0.59
21 72 0.35
22 5 0.02
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:395300 original size:19 final size:19
Alignment explanation
Indices: 395262--395328 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
395252 TTCGAGAATG
395262 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
395282 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
395301 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
395320 AAAATCGCA
1 AAAATCGCA
395329 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:395346 original size:19 final size:19
Alignment explanation
Indices: 395324--395450 Score: 94
Period size: 19 Copynumber: 7.1 Consensus size: 19
395314 GAAACCAAAA
*
395324 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
395343 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
395362 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
395376 TCTCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
395390 TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
* *
395410 TCACGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
395429 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
395449 TC
1 TC
395451 AACCAAAAGA
Statistics
Matches: 93, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
14 24 0.26
16 2 0.02
17 3 0.03
19 33 0.35
20 31 0.33
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:395384 original size:14 final size:14
Alignment explanation
Indices: 395365--395401 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
395355 TTTCATTTCG
395365 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
395379 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
395393 CGTTGCGAT
1 CGTTGCGAT
395402 AGTCATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.27, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:395442 original size:20 final size:20
Alignment explanation
Indices: 395390--395448 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
395380 GTTGCGATTC
** *
395390 TCTCGTTGCGATAGTCATTT
1 TCTCGTTGCGATTCTCATTA
*
395410 TCACGTTGCGATTCTCATTA
1 TCTCGTTGCGATTCTCATTA
*
395430 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTCTCATT
395449 TCAACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (20 bp):
TCTCGTTGCGATTCTCATTA
Found at i:399005 original size:13 final size:14
Alignment explanation
Indices: 398980--399014 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
398970 ATTGTTTAAT
398980 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
398994 TGATTTGT-AAAGT
1 TGATTTGTAAAAGG
399007 TGATTTGT
1 TGATTTGT
399015 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:399023 original size:13 final size:14
Alignment explanation
Indices: 398967--399015 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
398957 TTGCTTATTT
*
398967 TTGA-TTGTTTAA-
1 TTGATTTGTTAAAG
*
398979 TTGATTTGTAAAAG
1 TTGATTTGTTAAAG
*
398993 GTGATTTG-TAAAG
1 TTGATTTGTTAAAG
399006 TTGATTTGTT
1 TTGATTTGTT
399016 TAATTGATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 4 0.14
13 17 0.59
14 8 0.28
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:399155 original size:33 final size:33
Alignment explanation
Indices: 399117--399206 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
399107 AAAAAGTACT
* *
399117 ATCGCAATGCGAAATGAAGATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
399150 TTCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
399183 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
399207 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:399224 original size:19 final size:19
Alignment explanation
Indices: 399202--399300 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 19
399192 CGAAATTAAA
*
399202 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
399221 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
399237 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
399254 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
399268 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
399287 TTCGTATTGCGATT
1 TTCGCATTGCGATT
399301 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
14 18 0.30
16 6 0.10
17 6 0.10
19 30 0.50
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:399322 original size:33 final size:33
Alignment explanation
Indices: 399206--399313 Score: 164
Period size: 33 Copynumber: 3.3 Consensus size: 33
399196 ATTAAATTCG
*
399206 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
399239 CGTTGCGATTTTCATTTCGCATTGCGAAAT-TCG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
*
399272 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
399305 CGTTGCGAT
1 CGTTGCGAT
399314 AGTAATTTCC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 2 0.03
33 63 0.94
34 2 0.03
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:399322 original size:66 final size:67
Alignment explanation
Indices: 399199--399332 Score: 207
Period size: 66 Copynumber: 2.0 Consensus size: 67
399189 ACGCGAAATT
** *
399199 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTT-CGCATTG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
399263 CG
66 CG
* * *
399265 AAATTCGCGTTGCGATTTTCATTTCGTATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCGTTG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
399330 CG
66 CG
399332 A
1 A
399333 TAGACATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
66 52 0.85
67 9 0.15
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.40
Consensus pattern (67 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
CG
Found at i:401803 original size:24 final size:24
Alignment explanation
Indices: 401769--401822 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
401759 CTGAAACATC
*
401769 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
401793 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
401817 ATCAAA
1 ATCAAA
401823 TTTCGAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:402658 original size:20 final size:20
Alignment explanation
Indices: 402625--402703 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
402615 GAATAAGTAA
* *
402625 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
402645 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
402666 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
402686 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
402704 AAATCGCAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:402710 original size:20 final size:20
Alignment explanation
Indices: 402663--402712 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
402653 GAGATAATAC
402663 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
402683 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
402703 AAAATCGCAA
1 AAAATCGCAA
402713 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:403018 original size:20 final size:20
Alignment explanation
Indices: 402924--403010 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
402914 GCAACGGGAA
402924 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
402944 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
402964 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
402984 ATCGCAACGCG-AAATGGCT
1 ATCGCAACGCGAAAATGGCT
403003 ATCGCAAC
1 ATCGCAAC
403011 TAGAAAATCG
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
19 13 0.23
20 43 0.77
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:403022 original size:33 final size:37
Alignment explanation
Indices: 402944--403032 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 37
402934 GAAAATGGCT
402944 ATCGCAACGCGAAAATGGCTATCGCAATTCGAAATGAAAA
1 ATCGCAACGCG-AAATGGCTATCGCAA-TC-AAATGAAAA
*
402984 ATCGCAACGCGAAATGGCTATCGCAA-C-TA-G-AAA
1 ATCGCAACGCGAAATGGCTATCGCAATCAAATGAAAA
*
403017 ATCGCAATGCGAAATG
1 ATCGCAACGCGAAATG
403033 AAAATCGCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
33 18 0.38
34 1 0.02
35 1 0.02
37 1 0.02
39 15 0.32
40 11 0.23
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (37 bp):
ATCGCAACGCGAAATGGCTATCGCAATCAAATGAAAA
Found at i:403081 original size:19 final size:19
Alignment explanation
Indices: 403059--403104 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
403049 TTTCTCGTTA
403059 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
*
403078 CGATTTTCATTTTGCATTG
1 CGATTTTCATTTCGCATTG
403097 CGATTTTC
1 CGATTTTC
403105 TCGTTGCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:405139 original size:19 final size:20
Alignment explanation
Indices: 405115--405169 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
405105 GAAACTTAAA
405115 ATCGCAACGCGAAAAT-ACT
1 ATCGCAACGCGAAAATGACT
* *
405134 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
405154 ATCGCAATGC-AAAATG
1 ATCGCAACGCGAAAATG
405170 CAAATCACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:405196 original size:33 final size:33
Alignment explanation
Indices: 405154--405247 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
405144 GGAAATGGCT
* * *
405154 ATCGCAATGCAAAATGCAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
405187 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
405220 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
405248 CGAAACACAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:405269 original size:19 final size:19
Alignment explanation
Indices: 405183--405269 Score: 87
Period size: 19 Copynumber: 4.8 Consensus size: 19
405173 ATCACAACGA
405183 CAAAATCGCAATGCGAAAT
1 CAAAATCGCAATGCGAAAT
*
405202 GAAAATCGCAA--CG--A-
1 CAAAATCGCAATGCGAAAT
405216 CAAAATCGCAATGCGAAAT
1 CAAAATCGCAATGCGAAAT
* *
405235 GAAAATCGCAACGCGAAA-
1 CAAAATCGCAATGCGAAAT
*
405253 CACAAATCGCATTGCGA
1 CA-AAATCGCAATGCGA
405270 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 38 0.69
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (19 bp):
CAAAATCGCAATGCGAAAT
Found at i:405284 original size:17 final size:17
Alignment explanation
Indices: 405262--405320 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
405252 ACACAAATCG
405262 CATTGCGATTTTCATTT
1 CATTGCGATTTTCATTT
*
405279 CATTGCGA-TTT--TGT
1 CATTGCGATTTTCATTT
*
405293 CGTTGCGATTTTCATTT
1 CATTGCGATTTTCATTT
405310 CGCATTGCGAT
1 --CATTGCGAT
405321 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 9 0.27
15 3 0.09
16 3 0.09
17 10 0.30
19 8 0.24
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (17 bp):
CATTGCGATTTTCATTT
Found at i:405339 original size:20 final size:19
Alignment explanation
Indices: 405305--405359 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
405295 TTGCGATTTT
*
405305 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
405324 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
405344 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
405360 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:407226 original size:19 final size:20
Alignment explanation
Indices: 407177--407234 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
407167 AGAATAGTTT
** *
407177 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
407197 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
*
407217 G-AATTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
407235 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:407523 original size:22 final size:22
Alignment explanation
Indices: 407496--407539 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
407486 GATGGAGATA
407496 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
407518 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
407540 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:407758 original size:20 final size:20
Alignment explanation
Indices: 407708--407842 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
407698 CGCTTTGAAA
*
407708 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
407729 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
*
407749 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
407769 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
* *
407790 ATCGTATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
407810 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
407830 ATCGCATTGCGAT
1 ATCGCATTGCGAT
407843 TTTCCCAATT
Statistics
Matches: 92, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
19 5 0.05
20 63 0.68
21 22 0.24
22 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:407814 original size:61 final size:61
Alignment explanation
Indices: 407708--407845 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
407698 CGCTTTGAAA
* * *
407708 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
407769 ATCTCGTTGCGATTTTGTATTATCGTATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
407830 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
407846 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:407861 original size:61 final size:61
Alignment explanation
Indices: 407708--407863 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
407698 CGCTTTGAAA
* ** * * *
407708 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * ** * *
407769 ATCTCGTTGCGATTTTGTATTATCGTATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
407830 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
407864 TTACTTATTC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 76 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:409066 original size:13 final size:15
Alignment explanation
Indices: 409043--409079 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
409033 ATTGAATACT
409043 AATATTAATT-AAA-A
1 AATA-TAATTAAAATA
409057 AATATAATTAAAATA
1 AATATAATTAAAATA
409072 AATATAAT
1 AATATAAT
409080 CTTAGATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 7 0.33
15 9 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATAATTAAAATA
Found at i:410537 original size:55 final size:55
Alignment explanation
Indices: 410453--410564 Score: 188
Period size: 55 Copynumber: 2.0 Consensus size: 55
410443 TCCTCCTTTC
* *
410453 TCCCTTTCTTTTCCCCTTTTTTAGTTCCAAAAATCGACACCCATGTTCTTATTCT
1 TCCCTTTCTTTTCCCCTTGTTTAGTTCCAAAAATCAACACCCATGTTCTTATTCT
* *
410508 TCCCTTTCTTTTCCTCTTGTTTAGTTCCAAAAATCAACACCCATGTTCTTGTTCT
1 TCCCTTTCTTTTCCCCTTGTTTAGTTCCAAAAATCAACACCCATGTTCTTATTCT
410563 TC
1 TC
410565 TCCTCAACTG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.18, C:0.30, G:0.06, T:0.46
Consensus pattern (55 bp):
TCCCTTTCTTTTCCCCTTGTTTAGTTCCAAAAATCAACACCCATGTTCTTATTCT
Found at i:412037 original size:20 final size:20
Alignment explanation
Indices: 412014--412101 Score: 57
Period size: 20 Copynumber: 4.6 Consensus size: 20
412004 ATTTTGTCCC
412014 ATATATATATATTTTTAATT
1 ATATATATATATTTTTAATT
*
412034 ATAT-T-T-T-TTATTTATTT
1 ATATATATATATT-TTTAATT
* *
412051 ACTATAT-TCCT-TTTTTATTT
1 A-TATATAT-ATATTTTTAATT
412071 ATAT-TATATTATTTTT-ATT
1 ATATATATA-TATTTTTAATT
412090 ATATATATATAT
1 ATATATATATAT
412102 ATATATATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
16 2 0.04
17 8 0.14
18 5 0.09
19 17 0.30
20 21 0.38
21 3 0.05
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
ATATATATATATTTTTAATT
Found at i:412084 original size:14 final size:14
Alignment explanation
Indices: 412065--412109 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
412055 TATTCCTTTT
412065 TTATTTATATTATA
1 TTATTTATATTATA
*
412079 TTATTTTTATTATA
1 TTATTTATATTATA
*
412093 TATATATATATATATA
1 T-TATTTATAT-TATA
412109 T
1 T
412110 ATATATATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 14 0.54
15 7 0.27
16 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:412096 original size:2 final size:2
Alignment explanation
Indices: 412089--412117 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
412079 TTATTTTTAT
412089 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
412118 GTATGTATTA
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:412269 original size:29 final size:28
Alignment explanation
Indices: 412221--412275 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
412211 TATTTTTGTT
412221 TTTATTTATTTATATATATTATATTTTAC
1 TTTATTTATTTATATATATTAT-TTTTAC
* * *
412250 TTTATTTATTTTTTTCTATTATTTTT
1 TTTATTTATTTATATATATTATTTTT
412276 CTTAATATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTATTTATTTATATATATTATTTTTAC
Found at i:415657 original size:28 final size:25
Alignment explanation
Indices: 415626--415678 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 25
415616 CAAAAAGAGA
415626 AAAAAGAGAAAAAAAGCAAAGAGAAAAT
1 AAAAAGAG-AAAAAA-CAAAG-GAAAAT
415654 AAAAAGAGAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAACAAAGGAAAAT
415679 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 6 0.24
28 8 0.32
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (25 bp):
AAAAAGAGAAAAAACAAAGGAAAAT
Found at i:415659 original size:13 final size:14
Alignment explanation
Indices: 415628--415678 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
415618 AAAAGAGAAA
*
415628 AAAGAGAAAAAAAGC
1 AAAGAGAAAATAA-C
415643 AAAGAGAAAATAA-
1 AAAGAGAAAATAAC
415656 AAAGAGAAAA-AAC
1 AAAGAGAAAATAAC
415669 AAAG-GAAAAT
1 AAAGAGAAAAT
415679 TGAAGAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
15 12 0.36
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAGAAAATAAC
Found at i:415665 original size:26 final size:26
Alignment explanation
Indices: 415619--415678 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
415609 ATCAGAACAA
* *
415619 AAAGAG-AAA-AAAGAGAAAAAAAGC
1 AAAGAGAAAATAAAAAGAAAAAAAAC
*
415643 AAAGAGAAAATAAAAAGAGAAAAAAC
1 AAAGAGAAAATAAAAAGAAAAAAAAC
415669 AAAG-GAAAAT
1 AAAGAGAAAAT
415679 TGAAGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 9 0.29
26 16 0.52
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.03
Consensus pattern (26 bp):
AAAGAGAAAATAAAAAGAAAAAAAAC
Found at i:417375 original size:37 final size:37
Alignment explanation
Indices: 417334--417647 Score: 161
Period size: 37 Copynumber: 9.1 Consensus size: 37
417324 TAAAAAGAAG
*
417334 ATTTTATCTCACTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* * * *
417371 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* *
417408 A----A---CA-TTGAAAACA-TTTCCCTTGAAA-TAA
1 ATTTTATCTCACTTG-AGACAGTTTCCCTTGAAACAAA
** *
417436 ATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* *
417472 ATTTT-TCTCTCTTGAGACAGTTTCCCTCGAAAC-AA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* ***
417507 A--TTAT-T---TT-A-ATATGTTTTATTTGAAAC-AA
1 ATTTTATCTCACTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
417536 ATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
417573 GTTTTGTCACTCTTGAGACAGTTTCTCTTGAAAC-AA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
** * * *
417609 ATTTCGTCTCTCTTGAGATAGTTTCCTTTGAAACAAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
417646 AT
1 AT
417648 CTTTGAATTT
Statistics
Matches: 215, Mismatches: 39, Indels: 46
0.72 0.13 0.15
Matches are distributed among these distances:
28 4 0.02
29 28 0.13
30 7 0.03
31 3 0.01
32 1 0.00
33 3 0.01
34 1 0.00
35 37 0.17
36 63 0.29
37 68 0.32
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (37 bp):
ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
Found at i:417468 original size:36 final size:36
Alignment explanation
Indices: 417421--417645 Score: 198
Period size: 36 Copynumber: 6.4 Consensus size: 36
417411 ATTGAAAACA
*
417421 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
417457 TTTCCCTTGAAACAAATTT-TTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
417492 TTTCCCTCGAAACAAA--T--TAT-T-TT-A-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * *
417521 TTTTATTTGAAACAAATTTCATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * * *
417557 TTTCTTTTGGAACTAAGTTTTGTCACTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
417594 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
417630 TTTCCTTTGAAACAAA
1 TTTCCCTTGAAACAAA
417646 ATCTTTGAAT
Statistics
Matches: 151, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.01
29 14 0.09
30 2 0.01
31 2 0.01
32 2 0.01
33 3 0.02
35 32 0.21
36 63 0.42
37 31 0.21
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:417531 original size:100 final size:101
Alignment explanation
Indices: 417334--417611 Score: 308
Period size: 100 Copynumber: 2.8 Consensus size: 101
417324 TAAAAAGAAG
* * *
417334 ATTTTATCTCACTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTCATCTCACTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
** * *
417399 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
66 TGAAACA-AATTATTGAAAACATTTCACTTGAAACAA
* * *
417436 ATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTT-TCTCTCTTGAGACAGTTTCCCT
1 ATTTCATCTCACTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
* * * ** * *
417499 CGAAACAAATTATTTTAATATGTTTTATTTGAAACAA
66 TGAAACAAATTA-TTGAAAACATTTCACTTGAAACAA
* ** * * * *
417536 ATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCACTCTTGAGACAGTTTCTCT
1 ATTTCATCTCACTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
417601 TGAAACAAATT
66 TGAAACAAATT
417612 TCGTCTCTCT
Statistics
Matches: 147, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
99 3 0.02
100 71 0.48
101 13 0.09
102 60 0.41
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (101 bp):
ATTTCATCTCACTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
TGAAACAAATTATTGAAAACATTTCACTTGAAACAA
Found at i:417692 original size:138 final size:137
Alignment explanation
Indices: 417445--417699 Score: 339
Period size: 138 Copynumber: 1.9 Consensus size: 137
417435 AATTTCGTCT
* *
417445 CTCTTGAGACAGTTTCCCTTGAAACAAATTTTTCTCTCTTGAGACAGTTTCCCTCGAAACAAATT
1 CTCTTGAGACAGTTTCCCTTGAAACAAATTTGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAAT
* * * ** *
417510 ATTTTAATATGTTTTATTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGT
66 ATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGT
417575 TTTGTCA
131 TTTGTCA
* * * *
417582 CTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGATAGTTTCCTTTGAAACAAAA
1 CTCTTGAGACAGTTTCCCTTGAAACAAATTT-GTCTCTCTTGAGACAGTTTCCCTCGAAACAAAA
* * * ** *
417647 TCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACATTTTCT
65 TATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCT
417700 CTTGAAACAC
Statistics
Matches: 99, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
137 30 0.30
138 69 0.70
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (137 bp):
CTCTTGAGACAGTTTCCCTTGAAACAAATTTGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAAT
ATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGT
TTTGTCA
Found at i:417707 original size:65 final size:67
Alignment explanation
Indices: 417603--417765 Score: 197
Period size: 67 Copynumber: 2.4 Consensus size: 67
417593 GTTTCTCTTG
* * * **
417603 AAACAAATTTCGTCTCTCTTGAGATAGTTTCCTTTG-AA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCTTTGAAACACAAAATCTTCAAATTTATTTCCCC
417666 TA
66 TA
*
417668 AAACAAATTTTGTCTCCCTTGAGACA-TTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCT-TTGAAACACAAAATCTTCAAATTTATTTCCC
*
417732 TTA
65 CTA
* * *
417735 ACACAAAATTTTGTTTCCCTTGAGACCGTTT
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTT
417766 TCATGAAACA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 5 0.06
65 26 0.31
66 2 0.02
67 27 0.33
68 20 0.24
69 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCCTTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:417773 original size:67 final size:68
Alignment explanation
Indices: 417603--417786 Score: 191
Period size: 67 Copynumber: 2.8 Consensus size: 68
417593 GTTTCTCTTG
* * * * **
417603 AAACAAATTTCGTCTCTCTTGAGATAGTTTC-CTTTG--A-AACAAAATCTTTGAATTTATTTCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTC-ATGAAACAACAAAATCTTCAAATTTATTTCC
417664 CCTA
65 CCTA
* *
417668 AAACAAATTTTGTCTCCCTTGAGACATTTTCTCTTGAAAC-ACAAAATCTTCAAATTTATTTCCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACAACAAAATCTTCAAATTTATTTCCC
*
417732 TTA
66 CTA
* * *
417735 ACACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACAACAAATATCTT
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACAACAAA-ATCTT
417787 TGAGATCGTT
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
65 30 0.30
66 1 0.01
67 36 0.36
68 28 0.28
69 5 0.05
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (68 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACAACAAAATCTTCAAATTTATTTCCC
CTA
Found at i:420238 original size:2 final size:2
Alignment explanation
Indices: 420231--420280 Score: 50
Period size: 2 Copynumber: 25.5 Consensus size: 2
420221 TTAATTTTAT
* *
420231 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
*
420272 TA GA TA TA T
1 TA TA TA TA T
420281 TAATTTTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
1 2 0.05
2 36 0.90
3 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:420324 original size:17 final size:17
Alignment explanation
Indices: 420304--420363 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
420294 TTTAGTATGT
420304 ATATATATTTTTTCTTA
1 ATATATATTTTTTCTTA
* *
420321 ATATTATATTTTATACGTTTTT
1 ATA-TATATTTT-T---TCTTA
420343 ATATATATTTTTTCTTA
1 ATATATATTTTTTCTTA
420360 ATAT
1 ATAT
420364 TCTATTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 10 0.29
18 8 0.24
19 1 0.03
20 1 0.03
21 8 0.24
22 6 0.18
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (17 bp):
ATATATATTTTTTCTTA
Found at i:420414 original size:17 final size:16
Alignment explanation
Indices: 420376--420428 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
420366 TATTTTTGTT
*
420376 TTTATTTATTTATATATA
1 TTTATTT-TTTCTAT-TA
*
420394 TTATATTTTTACT-TTA
1 TT-TATTTTTTCTATTA
420410 TTTATTTTTTCTATTA
1 TTTATTTTTTCTATTA
420426 TTT
1 TTT
420429 TTCTTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 9 0.30
16 10 0.33
17 1 0.03
18 5 0.17
19 5 0.17
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTATTTTTTCTATTA
Found at i:420646 original size:11 final size:10
Alignment explanation
Indices: 420613--420655 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
420603 TTTTTTAACA
420613 TTTTATTCATT
1 TTTTATT-ATT
420624 TTTT-TTA-T
1 TTTTATTATT
420632 TTTTATTATT
1 TTTTATTATT
420642 ATTTTATTATT
1 -TTTTATTATT
420653 TTT
1 TTT
420656 ACGTGTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 5 0.17
9 4 0.14
10 6 0.21
11 14 0.48
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTATTATT
Found at i:420656 original size:9 final size:9
Alignment explanation
Indices: 420613--420656 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
420603 TTTTTTAACA
420613 TTTTATTCAT
1 TTTTATT-AT
*
420623 TTTTTTTAT
1 TTTTATTAT
420632 TTTTATTATT
1 TTTTATTA-T
420642 ATTTTATTAT
1 -TTTTATTAT
420652 TTTTA
1 TTTTA
420657 CGTGTTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 14 0.47
10 8 0.27
11 8 0.27
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTATTAT
Found at i:420677 original size:25 final size:26
Alignment explanation
Indices: 420640--420689 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
420630 ATTTTTATTA
*
420640 TTATTTTATTATTTTTACGTGTTTTG
1 TTATTTTACTATTTTTACGTGTTTTG
* *
420666 TTATTTT-CTATTTTTTCTTGTTTT
1 TTATTTTACTATTTTTACGTGTTTT
420690 ATTTATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.74
Consensus pattern (26 bp):
TTATTTTACTATTTTTACGTGTTTTG
Found at i:423153 original size:21 final size:20
Alignment explanation
Indices: 423117--423174 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 20
423107 TGTCTAAGGT
423117 ATATTTTA-TTATATT-TTTA
1 ATATTTTATTTA-ATTATTTA
423136 ATATTTTGTATTTAATTTATTTA
1 ATA-TTT-TATTTAA-TTATTTA
423159 ATATTTTATTTAATTA
1 ATATTTTATTTAATTA
423175 ATTTTTTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.09
20 6 0.18
21 10 0.29
22 8 0.24
23 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
ATATTTTATTTAATTATTTA
Found at i:425443 original size:13 final size:13
Alignment explanation
Indices: 425402--425445 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
425392 TATTTAGTAC
*
425402 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
425415 TGTTTATTGGATT
1 TTTTTATTGTAAT
425428 TTTTTATTGTAAT
1 TTTTTATTGTAAT
425441 TTTTT
1 TTTTT
425446 TTATTTATCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:425551 original size:34 final size:32
Alignment explanation
Indices: 425468--425551 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 32
425458 TAATACTTAC
* *
425468 TTTAATTTGTTAATATGGTTGGATTTATTTTAA
1 TTTATTTTGTTAAT-TTGTTGGATTTATTTTAA
*
425501 TTTATTTTGATAAATTTGTTGGACTTT-TTGTTAA
1 TTTATTTTG-TTAATTTGTTGGA-TTTATT-TTAA
425535 TTTATTTTGCTTAATTT
1 TTTATTTTG-TTAATTT
425552 TGTTTATTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 17 0.40
34 26 0.60
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.61
Consensus pattern (32 bp):
TTTATTTTGTTAATTTGTTGGATTTATTTTAA
Found at i:428926 original size:16 final size:16
Alignment explanation
Indices: 428907--428937 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
428897 ATTTTTTTCA
*
428907 AATAATTATAATAAAC
1 AATAAGTATAATAAAC
428923 AATAAGTATAATAAA
1 AATAAGTATAATAAA
428938 AAAATTTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
AATAAGTATAATAAAC
Found at i:430127 original size:3 final size:3
Alignment explanation
Indices: 430119--430164 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
430109 AAAGATAAGC
430119 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
430165 TGATAGGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:430228 original size:27 final size:27
Alignment explanation
Indices: 430190--430249 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
430180 AGCTAAATTA
430190 GGGTTTTGTTGATGATGGGCGAGAATG
1 GGGTTTTGTTGATGATGGGCGAGAATG
430217 GGGTTTTGTTGATGATGGGCGAGAATG
1 GGGTTTTGTTGATGATGGGCGAGAATG
*
430244 GTGTTT
1 GGGTTT
430250 CAATGATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.17, C:0.03, G:0.43, T:0.37
Consensus pattern (27 bp):
GGGTTTTGTTGATGATGGGCGAGAATG
Found at i:430256 original size:27 final size:27
Alignment explanation
Indices: 430199--430256 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
430189 AGGGTTTTGT
***
430199 TGATGATGGGCGAGAATGGGGTTTTGT
1 TGATGATGGGCGAGAATGGGGTTTCAA
*
430226 TGATGATGGGCGAGAATGGTGTTTCAA
1 TGATGATGGGCGAGAATGGGGTTTCAA
430253 TGAT
1 TGAT
430257 AATGATTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.05, G:0.40, T:0.33
Consensus pattern (27 bp):
TGATGATGGGCGAGAATGGGGTTTCAA
Found at i:433737 original size:15 final size:15
Alignment explanation
Indices: 433704--433757 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
433694 GTAAGCACAT
* *
433704 AAATT-TTAGATTTA
1 AAATTATTAAATTAA
433718 AAATTATTAAATTAA
1 AAATTATTAAATTAA
*
433733 AAATTATTTAATTAA
1 AAATTATTAAATTAA
*
433748 TAAATCATTA
1 -AAATTATTA
433758 TATTTCACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
14 5 0.15
15 21 0.64
16 7 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
AAATTATTAAATTAA
Found at i:433898 original size:2 final size:2
Alignment explanation
Indices: 433893--433920 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
433883 AACTGTATTA
433893 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
433921 CAAGATTTTA
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:434689 original size:2 final size:2
Alignment explanation
Indices: 434684--434719 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
434674 AAATGTATTA
434684 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
434720 CAAGATTTTA
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:441797 original size:112 final size:111
Alignment explanation
Indices: 441596--441913 Score: 349
Period size: 112 Copynumber: 2.8 Consensus size: 111
441586 CTCAAAGAAG
* *
441596 ATTGAATCGGGGAAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGT-GA-
1 ATTGAATCGGGGAAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGA-TAGAC
* * * *
441659 TCTATTCC-ATTTCTTCTGAAAGGAATATCAGATATGGAGGAGTTGATCC
65 T-TGTTCCGCTTAC-TCT-AAAGGAATATCAGATATGGAGGAATTGATCC
* * *
441708 ATTGAATCAGGGAAGACTTATTCCGCTGTCACTCAGGGAATATCAAATCTTTGAAAAGATAGACT
1 ATTGAATCGGGGAAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGATAGACT
* *
441773 TGTTCCGCTTACTCTAAAGAGAATATCATATATGGGGGAATTGATCC
66 TGTTCCGCTTACTCTAAAG-GAATATCAGATATGGAGGAATTGATCC
* * * * * *
441820 ATTGAATCGGGGTAGATTTGTTTCGCT-T-ACTCTGAAGGGGATATCAAATCTTGGAAAAGAGAT
1 ATTGAATCGGGGAAGACTTGTTCCGCTGTCACTC---AGGGAATATCAAATCTTGGAAAAGATAG
* *
441883 ACATGTTCCGCTTACTCTGAAGGGAATATCA
63 ACTTGTTCCGCTTACTCT-AAAGGAATATCA
441914 AATCTTGGAA
Statistics
Matches: 176, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
110 4 0.02
111 6 0.03
112 110 0.62
113 53 0.30
114 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (111 bp):
ATTGAATCGGGGAAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGATAGACT
TGTTCCGCTTACTCTAAAGGAATATCAGATATGGAGGAATTGATCC
Found at i:441899 original size:48 final size:48
Alignment explanation
Indices: 441838--441961 Score: 194
Period size: 48 Copynumber: 2.6 Consensus size: 48
441828 GGGGTAGATT
* * *
441838 TGTTTCGCTTACTCTGAAGGGGATATCAAATCTTGGAAAAGAGATACA
1 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACA
* *
441886 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAATAGAGACC
1 TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACA
*
441934 TGTTCCGCTTACTCTGAAGGGTATATCA
1 TGTTCCGCTTACTCTGAAGGGAATATCA
441962 GATATGGAGA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (48 bp):
TGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACA
Found at i:442028 original size:162 final size:161
Alignment explanation
Indices: 441742--442070 Score: 426
Period size: 162 Copynumber: 2.0 Consensus size: 161
441732 GCTGTCACTC
* * * *
441742 AGGGAATATCAAATCTTTGAAAAGATAGACTTGTTCCGCTTACTCTAAAGAGAATATCATATATG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCCGCTTACTCTAAAGAGAATATCAGATATG
* * * * * * * *
441807 GGGGAATTGATCCATTGAATCGGGGTAGATTTGTTTCGCTTACTCTGAAGGGGATATCAAATCTT
66 GGAGAATTGATCCATTGAATCGGGGCAAACTTATTCCACTTACTCTGAAGGGAATATCAAATCTT
* *
441872 GGAAAAGAGATACATGTTCCGCTTACTCTGA
131 GGAAAAGAGAGACATATTCCGCTTACTCTGA
* * * *
441903 AGGGAATATCAAATCTTGGAAAATAGAGACCTGTTCCGCTTACTCTGAAGGGTATATCAGATAT-
1 AGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCCGCTTACTCTAAAGAGAATATCAGATATG
* *
441967 GGAGAAGTTTGATCCATTGAATTGGTGCAAACTTATTCCACTTACTCTGAAGGGAATATCAAATC
66 GGAGAA--TTGATCCATTGAATCGGGGCAAACTTATTCCACTTACTCTGAAGGGAATATCAAATC
* *
442032 TTGGAAACGAGAGGCATATTCCGCTTACTCTGA
129 TTGGAAAAGAGAGACATATTCCGCTTACTCTGA
*
442065 AAGGAA
1 AGGGAA
442071 CATTAGATAT
Statistics
Matches: 143, Mismatches: 23, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
160 5 0.03
161 56 0.39
162 82 0.57
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (161 bp):
AGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCCGCTTACTCTAAAGAGAATATCAGATATG
GGAGAATTGATCCATTGAATCGGGGCAAACTTATTCCACTTACTCTGAAGGGAATATCAAATCTT
GGAAAAGAGAGACATATTCCGCTTACTCTGA
Found at i:442126 original size:275 final size:273
Alignment explanation
Indices: 441630--442193 Score: 712
Period size: 275 Copynumber: 2.1 Consensus size: 273
441620 GCTGTCACTC
* * * *
441630 AGGGAATATCAAATCTTGGAAGAGAGTGATCTATTCCATTTCTTCTGAAAGGAATATCAGATATG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACCTATTCCATTACTTCTGAAAGGAATATCAGATATG
* * *
441695 GAGGAGTTGATCCATTGAATCAGGGAAGACTTATTCCGCTGTCACTCAGGGAATATCAAATCTTT
66 GAGAAGTTGATCCATTGAATCAGGGAAGACTTATTCCACTGTCACTCAGGGAATATCAAATCTTG
* * * * *
441760 GAAAAGATAGACTTGTTCCGCTTACTCTAAAGAGAATATCATATATGGGGGAATTGATCCATTGA
131 GAAAAGAGAGACATATTCCGCTTACTCTAAAGAGAACATCAGATATGGGGGAATTGATCCATTGA
* * * * * *
441825 ATCGGGGTAGATTTGTTTCGCTTACTCTGAAGGGGATATCAAATCTTGGAAAAGA-GATACATGT
196 ATCAGGGCAGACTTGTTTCACTTACTCTGAAGGGAATATCAAATCTTGGAAAA-ATGAGACATGT
441889 TCCGCTTACTCTGA
260 TCCGCTTACTCTGA
* * * * *
441903 AGGGAATATCAAATCTTGGAAAATAGAGACCTGTTCCGCTTAC-TCTGAAGGGTATATCAGATAT
1 AGGGAATATCAAATCTTGGAAAAGAGAGACCTATTCC-ATTACTTCTGAAAGGAATATCAGATAT
*
441967 GGAGAAGTTTGATCCATTGAAT-TGGTGCAA-ACTTATTCCACT-T-ACTCTGAAGGGAATATCA
65 GGAGAAG-TTGATCCATTGAATCAGG-G-AAGACTTATTCCACTGTCACTC---AGGGAATATCA
* * *
442028 AATCTTGGAAACGAGAGGCATATTCCGCTTACTCTGAAAG-GAACATTAGATATGGGGGAATTGA
124 AATCTTGGAAAAGAGAGACATATTCCGCTTACTCT-AAAGAGAACATCAGATATGGGGGAATTGA
*
442092 TCCATTGAATCAGGGCATACTT-TTTCTACTTACTCTGAAGGGAATATCAAATCTTGGAAAAATG
188 TCCATTGAATCAGGGCAGACTTGTTTC-ACTTACTCTGAAGGGAATATCAAATCTTGGAAAAATG
*
442156 AGACATGTTCTGCTTACTCTGA
252 AGACATGTTCCGCTTACTCTGA
*
442178 AGGGAATATCAGATCT
1 AGGGAATATCAAATCT
442194 GTAAATTAAA
Statistics
Matches: 251, Mismatches: 30, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
272 4 0.02
273 60 0.24
274 34 0.14
275 149 0.59
276 4 0.02
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (273 bp):
AGGGAATATCAAATCTTGGAAAAGAGAGACCTATTCCATTACTTCTGAAAGGAATATCAGATATG
GAGAAGTTGATCCATTGAATCAGGGAAGACTTATTCCACTGTCACTCAGGGAATATCAAATCTTG
GAAAAGAGAGACATATTCCGCTTACTCTAAAGAGAACATCAGATATGGGGGAATTGATCCATTGA
ATCAGGGCAGACTTGTTTCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAATGAGACATGTT
CCGCTTACTCTGA
Found at i:442171 original size:113 final size:113
Alignment explanation
Indices: 441888--442191 Score: 391
Period size: 113 Copynumber: 2.7 Consensus size: 113
441878 GAGATACATG
* *
441888 TTCCGCTTACTCTGAAGGGAATATCAAATCTTGG-AAAATAGAGACCTGTTCCGCTTACTCTGAA
1 TTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAAT-GAGACATGTTCCGCTTACTCTGAA
* * *
441952 GGGTATATCAGATATGGAGAAGTTTGATCCATTGAATTGGTGCAAACTTA
65 GGGAACATCAGATATGGAGAAG-TTGATCCATTGAATAGGTGCAAACTTA
* * *
442002 TTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAACGA-GAGGCATATTCCGCTTACTCTGAA
1 TTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAA-AATGAGACATGTTCCGCTTACTCTGAA
* * * * *
442066 AGGAACATTAGATATGGGGGAA-TTGATCCATTGAATCAGG-GCATACTTT
65 GGGAACATCAGATAT-GGAGAAGTTGATCCATTGAAT-AGGTGCAAACTTA
* *
442115 TTCTACTTACTCTGAAGGGAATATCAAATCTTGGAAAAATGAGACATGTTCTGCTTACTCTGAAG
1 TTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAATGAGACATGTTCCGCTTACTCTGAAG
*
442180 GGAATATCAGAT
66 GGAACATCAGAT
442192 CTGTAAATTA
Statistics
Matches: 164, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
112 1 0.01
113 88 0.54
114 67 0.41
115 7 0.04
116 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (113 bp):
TTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAATGAGACATGTTCCGCTTACTCTGAAG
GGAACATCAGATATGGAGAAGTTGATCCATTGAATAGGTGCAAACTTA
Found at i:444442 original size:19 final size:18
Alignment explanation
Indices: 444393--444444 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 18
444383 GTTGGATTTG
*
444393 TTTCATTTATTCTTCTTTT
1 TTTC-TTTATTTTTCTTTT
444412 TATTCTTTATTTTTCTTATT
1 T-TTCTTTATTTTTCTT-TT
444432 TTTCTTTATTTTT
1 TTTCTTTATTTTT
444445 TGTGTGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 24 0.80
20 6 0.20
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCTTTATTTTTCTTTT
Found at i:444456 original size:23 final size:23
Alignment explanation
Indices: 444402--444482 Score: 60
Period size: 23 Copynumber: 3.5 Consensus size: 23
444392 GTTTCATTTA
* *
444402 TTCTTCTTTT-TAT-TCTTTATTT
1 TTCTTTTTTTCTATATCTTT-TTC
* *
444424 TTCTTATTTTTCTTTAT-TTTTTG
1 TTCTT-TTTTTCTATATCTTTTTC
* *
444447 TGTGTTTTTTGCTATATCTTTTTC
1 T-TCTTTTTTTCTATATCTTTTTC
444471 TTCTTTTTTTCT
1 TTCTTTTTTTCT
444483 CCCCATGTTG
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
22 5 0.11
23 25 0.56
24 14 0.31
25 1 0.02
ACGTcount: A:0.07, C:0.12, G:0.05, T:0.75
Consensus pattern (23 bp):
TTCTTTTTTTCTATATCTTTTTC
Found at i:451090 original size:18 final size:18
Alignment explanation
Indices: 451063--451105 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
451053 GGGCACCCAA
*
451063 AATT-AAATTTGTCATTTT
1 AATTAAAATTT-TAATTTT
451081 AA-TAAAATTTTAATTTT
1 AATTAAAATTTTAATTTT
451098 AATTAAAA
1 AATTAAAA
451106 AAGATAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
AATTAAAATTTTAATTTT
Found at i:454067 original size:36 final size:35
Alignment explanation
Indices: 454013--454109 Score: 97
Period size: 36 Copynumber: 2.7 Consensus size: 35
454003 ACCTGGCCCT
**
454013 ATAAATATTAAAAATAATTATTATATATATAATATTA
1 ATAAAT-TTAAATTTAATTA-TATATATATAATATTA
* * *
454050 ATAAATTTAAATTTAATTAAAAAATATATAATATTT
1 ATAAATTTAAATTTAATT-ATATATATATAATATTA
* *
454086 ATATATTT-AATTTAAATATATATA
1 ATAAATTTAAATTTAATTATATATA
454110 CCCGGCCCGA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
34 5 0.10
35 8 0.16
36 30 0.60
37 7 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
ATAAATTTAAATTTAATTATATATATATAATATTA
Found at i:454124 original size:12 final size:12
Alignment explanation
Indices: 454107--454137 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
454097 TTAAATATAT
454107 ATACCCGGCCCG
1 ATACCCGGCCCG
*
454119 ATACCCGGCTCG
1 ATACCCGGCCCG
454131 ATACCCG
1 ATACCCG
454138 TTTATGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (12 bp):
ATACCCGGCCCG
Found at i:454930 original size:21 final size:22
Alignment explanation
Indices: 454895--454935 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
454885 AAACAGAATG
454895 CTCAGAGGGAACCGATTCCCTC
1 CTCAGAGGGAACCGATTCCCTC
*
454917 CTCAG-GGGTACCGATTCCC
1 CTCAGAGGGAACCGATTCCC
454936 CCTGATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.37, G:0.24, T:0.20
Consensus pattern (22 bp):
CTCAGAGGGAACCGATTCCCTC
Found at i:456221 original size:19 final size:20
Alignment explanation
Indices: 456197--456244 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
456187 AATGATTTTC
*
456197 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
456216 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
456236 TTTTGAAAA
1 TTTTGAAAA
456245 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:466438 original size:5 final size:5
Alignment explanation
Indices: 466389--466419 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
466379 TTATTATGCC
466389 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
466420 TATAAGGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:466733 original size:11 final size:11
Alignment explanation
Indices: 466719--466749 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
466709 ACCAAAAATT
466719 ATATAAAATAA
1 ATATAAAATAA
466730 ATATAAAATAA
1 ATATAAAATAA
466741 ATATAAAAT
1 ATATAAAAT
466750 GGAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATATAAAATAA
Found at i:470594 original size:42 final size:41
Alignment explanation
Indices: 470517--470600 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 41
470507 GTATATGTTA
* **
470517 TCATATCATTCATATCATACTATGGTTAGTTTATCATGTTCT
1 TCATATCATTCATATCATACTATGATTAGCATATCAT-TTCT
470559 TCATATCATTCATAT-ATATGCTATGATT-GCATATCATTTCT
1 TCATATCATTCATATCATA--CTATGATTAGCATATCATTTCT
470600 T
1 T
470601 AGGATATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 8 0.22
42 22 0.59
43 7 0.19
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (41 bp):
TCATATCATTCATATCATACTATGATTAGCATATCATTTCT
Found at i:474229 original size:21 final size:20
Alignment explanation
Indices: 474184--474236 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
474174 TGACACTAGG
474184 TACCTAGCTAGCTAACTTAAC
1 TACCTAGCTAGCTAACTT-AC
*
474205 TACCTAGCTAGCTACCTCT-C
1 TACCTAGCTAGCTAACT-TAC
474225 TTACCTAGCTAG
1 -TACCTAGCTAG
474237 ATTCACTACC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.30
Consensus pattern (20 bp):
TACCTAGCTAGCTAACTTAC
Found at i:475574 original size:17 final size:17
Alignment explanation
Indices: 475552--475597 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
475542 CGAATAATTG
475552 AATCAAATATAATTTAA
1 AATCAAATATAATTTAA
**
475569 AATCAAATATAATTTTG
1 AATCAAATATAATTTAA
*
475586 AATCGAATATAA
1 AATCAAATATAA
475598 AATCTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (17 bp):
AATCAAATATAATTTAA
Found at i:477438 original size:20 final size:20
Alignment explanation
Indices: 477413--477704 Score: 184
Period size: 20 Copynumber: 14.5 Consensus size: 20
477403 AATTTTCCAG
* *
477413 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
477433 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
* *
477453 AATCGCAACGTG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
477472 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* * * *
477494 AATTGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
477514 AATTGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
477535 AATCGCAACGTGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
477555 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* *
477575 AATCGCAATGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
* *
477595 AATCGCAAAGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* *
477615 AATCGCAATGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
477635 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
* *
477655 AATCGCAACACGAACACGTA
1 AATCGCAACGCGAATACGTA
*
477675 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
477695 AATCACAACG
1 AATCGCAACG
477705 AGATTCTGAC
Statistics
Matches: 218, Mismatches: 40, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
18 1 0.00
19 5 0.02
20 174 0.80
21 36 0.17
22 2 0.01
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:477590 original size:40 final size:40
Alignment explanation
Indices: 477413--477663 Score: 254
Period size: 40 Copynumber: 6.2 Consensus size: 40
477403 AATTTTCCAG
* * * * * **
477413 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
* * * *
477453 AATCGCAACGTG-ATTCTG-ACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTA-TCTGTA-AATCGCAACGAGAATACGT-A
* * * * *
477494 AATTGCAACGTGTATCCGTAAATTGCAACGACAATACGTAA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGT-A
*
477535 AATCGCAACGTGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
* *
477575 AATCGCAATGCGTATCTGTAAATCGCAAAGAGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
* * *
477615 AATCGCAATGCGTATCTGTAAATCGCAATGCGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
477655 AATCGCAAC
1 AATCGCAAC
477664 ACGAACACGT
Statistics
Matches: 180, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.01
40 110 0.61
41 66 0.37
42 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (40 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
Found at i:477676 original size:40 final size:40
Alignment explanation
Indices: 477413--477704 Score: 232
Period size: 40 Copynumber: 7.2 Consensus size: 40
477403 AATTTTCCAG
* * * * * * **
477413 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCTGTAAATCGCAATGAGAATACGTA
* * * * *
477453 AATCGCAACGTG-ATTCTG-ACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTA-TCTGTA-AATCGCAATGAGAATACGT-A
* * * * * *
477494 AATTGCAACGTGTATCCGTAAATTGCAACGACAATACGTAA
1 AATCGCAACGCGTATCTGTAAATCGCAATGAGAATACGT-A
* *
477535 AATCGCAACGTGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAATGAGAATACGTA
* *
477575 AATCGCAATGCGTATCTGTAAATCGCAAAGAGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAATGAGAATACGTA
* *
477615 AATCGCAATGCGTATCTGTAAATCGCAATGCGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAATGAGAATACGTA
* * * *
477655 AATCGCAACACG-AACACGTAAATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGTATC-TGTAAATCGCAATGAGAATAC-GTA
*
477695 AATCACAACG
1 AATCGCAACG
477705 AGATTCTGAC
Statistics
Matches: 214, Mismatches: 31, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
39 5 0.02
40 141 0.66
41 66 0.31
42 2 0.01
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (40 bp):
AATCGCAACGCGTATCTGTAAATCGCAATGAGAATACGTA
Found at i:481224 original size:34 final size:34
Alignment explanation
Indices: 481133--481233 Score: 132
Period size: 34 Copynumber: 3.0 Consensus size: 34
481123 CTTAATGTCT
* *
481133 ATCGCAACGCGGAAATTACTATCGCAATGAGAGA
1 ATCGCAACGCGGAAATGACTATCGCAATGAGAAA
* ** *
481167 ATCGCAATGC-GAAATGAAAATCGCAATGTGAAA
1 ATCGCAACGCGGAAATGACTATCGCAATGAGAAA
*
481200 ATCGCAACGCGGAAATGACTATCGCAATGCGAAA
1 ATCGCAACGCGGAAATGACTATCGCAATGAGAAA
481234 TGAAAATCGC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.48
34 29 0.52
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (34 bp):
ATCGCAACGCGGAAATGACTATCGCAATGAGAAA
Found at i:481224 original size:53 final size:52
Alignment explanation
Indices: 481166--481383 Score: 186
Period size: 52 Copynumber: 4.3 Consensus size: 52
481156 GCAATGAGAG
* * *
481166 AATCGCAATGCGAAATGAAAATCGCAATGTGAAAATCGCAACGCGGAAATGAC
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGC-GAAATGAA
* * *
481219 TATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAA
** *
481271 AATCGCAA--CG--A-GGGAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAACGCGAAATGAA
** * *
481318 AATCGCAATGCGAAATGAAAATCGCAACGAGGGAATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAA
*
481370 AATCGCAACGCGAA
1 AATCGCAATGCGAA
481384 TTTAGTTTCG
Statistics
Matches: 132, Mismatches: 18, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
47 27 0.20
48 3 0.02
49 6 0.05
50 6 0.05
51 3 0.02
52 48 0.36
53 39 0.30
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAA
Found at i:481225 original size:20 final size:19
Alignment explanation
Indices: 481195--481383 Score: 103
Period size: 19 Copynumber: 10.9 Consensus size: 19
481185 AATCGCAATG
481195 TGAAAATCGCAACGCGGAAA
1 TGAAAATCGCAACGC-GAAA
** *
481215 TGACTATCGCAATGCGAAA
1 TGAAAATCGCAACGCGAAA
481234 TGAAAATCGCAA--CG--A
1 TGAAAATCGCAACGCGAAA
* *
481249 -GAGAATCGCAATGCGAAA
1 TGAAAATCGCAACGCGAAA
481267 TGAAAATCGCAA--CG--A
1 TGAAAATCGCAACGCGAAA
** *
481282 -GGGAATCGCAATGCGAAA
1 TGAAAATCGCAACGCGAAA
481300 TGAAAATCGCAA--CG--A
1 TGAAAATCGCAACGCGAAA
* *
481315 -GAGAATCGCAATGCGAAA
1 TGAAAATCGCAACGCGAAA
481333 TGAAAATCGCAA--CG--A
1 TGAAAATCGCAACGCGAAA
** * *
481348 -GGGAATTGCAATGCGAAA
1 TGAAAATCGCAACGCGAAA
481366 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
481384 TTTAGTTTCG
Statistics
Matches: 129, Mismatches: 20, Indels: 41
0.68 0.11 0.22
Matches are distributed among these distances:
14 37 0.29
15 4 0.03
16 8 0.06
17 8 0.06
18 4 0.03
19 56 0.43
20 12 0.09
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (19 bp):
TGAAAATCGCAACGCGAAA
Found at i:481257 original size:14 final size:14
Alignment explanation
Indices: 481238--481325 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
481228 GCGAAATGAA
481238 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
481252 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
481271 AATCGCAACGAGGG
1 AATCGCAACGAGAG
*
481285 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
481304 AATCGCAACGAGAG
1 AATCGCAACGAGAG
481318 AATCGCAA
1 AATCGCAA
481326 TGCGAAATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 27 0.47
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 19 0.33
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:481261 original size:33 final size:33
Alignment explanation
Indices: 481220--481379 Score: 293
Period size: 33 Copynumber: 4.8 Consensus size: 33
481210 GGAAATGACT
481220 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
481253 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
481286 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
481319 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
481352 ATTGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
481380 CGAATTTAGT
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 123 1.00
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:481289 original size:86 final size:86
Alignment explanation
Indices: 481126--481313 Score: 243
Period size: 86 Copynumber: 2.2 Consensus size: 86
481116 CAATCATCTT
* * ** *
481126 AATGTCTATCGCAACGCGGAAATTACTATCGCAATGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
* *
481191 AATGTGAAAATCGCAACGCGGA
66 AACGAGAAAATCGCAACGC-GA
*
481213 AATGACTATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
** *
481277 AACGAGGGAATCGCAATGCGA
66 AACGAGAAAATCGCAACGCGA
**
481298 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
481314 AGAGAATCGC
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
85 15 0.17
86 57 0.66
87 15 0.17
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.16
Consensus pattern (86 bp):
AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
AACGAGAAAATCGCAACGCGA
Done.