Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008298.1 Hibiscus syriacus cultivar Beakdansim tig00110984_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: 1334650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:357612 original size:15 final size:15
Alignment explanation
Indices: 357584--357665 Score: 105
Period size: 15 Copynumber: 5.3 Consensus size: 15
357574 TATTATTAAT
357584 ATAAT-ATATATATA
1 ATAATAATATATATA
357598 ATAATAACT-TATATA
1 ATAATAA-TATATATA
*
357613 ATAATAACATATATA
1 ATAATAATATATATA
357628 ATTAATATATATATATA
1 A-TAATA-ATATATATA
357645 ATTAATAATATATATA
1 A-TAATAATATATATA
357661 ATAAT
1 ATAAT
357666 GTAAACGGAC
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
14 5 0.08
15 25 0.41
16 16 0.26
17 15 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAATATATATA
Found at i:357628 original size:24 final size:21
Alignment explanation
Indices: 357597--357665 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 21
357587 ATATATATAT
357597 AATAATAACTTATATAATAATA
1 AATAATAA-TTATATAATAATA
357619 ACATATATAATTAATATATATATATA
1 A-ATA-ATAATT-ATATA-ATA-ATA
*
357645 ATTAATAATATATATAATAAT
1 AATAATAAT-TATATAATAAT
357666 GTAAACGGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
22 3 0.08
23 8 0.20
24 19 0.47
25 6 0.15
26 4 0.10
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAATAATTATATAATAATA
Found at i:358441 original size:21 final size:20
Alignment explanation
Indices: 358389--358441 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
358379 AAGTTATGGC
*
358389 CACTTATGTTATTGATTGTTA
1 CACTT-TGTTATTGACTGTTA
358410 CACTTTGGTTATTGAACTGTTA
1 CACTTT-GTTATTG-ACTGTTA
**
358432 TTCTTTGTTA
1 CACTTTGTTA
358442 ATTTGATGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 16 0.59
22 10 0.37
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.53
Consensus pattern (20 bp):
CACTTTGTTATTGACTGTTA
Found at i:358509 original size:25 final size:24
Alignment explanation
Indices: 358481--358527 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
358471 GTTAATTTTT
* *
358481 AATTTGACTTATGATCTTTAAATAG
1 AATTTGAATT-TGATCCTTAAATAG
*
358506 AATTTTAATTTGATCCTTAAAT
1 AATTTGAATTTGATCCTTAAAT
358528 TCTAAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (24 bp):
AATTTGAATTTGATCCTTAAATAG
Found at i:358925 original size:18 final size:19
Alignment explanation
Indices: 358879--358927 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
358869 TAACTATATT
*
358879 TTTTAATATTTATAAATTA
1 TTTTAATATTTATAAAATA
** *
358898 TAGTAGTATTT-TAAAATA
1 TTTTAATATTTATAAAATA
358916 TTTTAATATTTA
1 TTTTAATATTTA
358928 AACTAATAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTTAATATTTATAAAATA
Found at i:359711 original size:35 final size:35
Alignment explanation
Indices: 359649--359725 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
359639 ACTATTCATT
*
359649 TAAAGATTAAAAATTTAAAAATAATATTA-TAATTTA
1 TAAATATTAAAAATTTAAAAATAATATTAGT-A-TTA
*
359685 TAAATATTAAAAA-TTAAAAATTATATTAGTATTA
1 TAAATATTAAAAATTTAAAAATAATATTAGTATTA
359719 TAAATAT
1 TAAATAT
359726 AACGAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 10 0.26
35 15 0.39
36 13 0.34
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (35 bp):
TAAATATTAAAAATTTAAAAATAATATTAGTATTA
Found at i:359734 original size:36 final size:35
Alignment explanation
Indices: 359656--359736 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
359646 ATTTAAAGAT
*
359656 TAAAAATTTAAAAATAATATTATAATTTATAAATA
1 TAAAAAATTAAAAATAATATTATAATTTATAAATA
* *
359691 TTAAAAATTAAAAATTATATTAGT-A-TTATAAATA
1 TAAAAAATTAAAAATAATATTA-TAATTTATAAATA
359725 TAACGAAAATTA
1 TAA--AAAATTA
359737 TATAATTTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
34 11 0.28
35 20 0.51
36 8 0.21
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (35 bp):
TAAAAAATTAAAAATAATATTATAATTTATAAATA
Found at i:360139 original size:13 final size:15
Alignment explanation
Indices: 360119--360158 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
360109 AATATAATTG
360119 ATATTATAAATAA-A
1 ATATTATAAATAACA
360133 A-ATTATAAAATAACA
1 ATATTAT-AAATAACA
360148 ATATTATAAAT
1 ATATTATAAAT
360159 TAAAGAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.22
14 7 0.30
15 6 0.26
16 5 0.22
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATTATAAATAACA
Found at i:360155 original size:16 final size:15
Alignment explanation
Indices: 360119--360162 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
360109 AATATAATTG
360119 ATATTAT-AAATAAA
1 ATATTATAAAATAAA
360133 A-ATTATAAAATAACA
1 ATATTATAAAATAA-A
*
360148 ATATTATAAATTAAA
1 ATATTATAAAATAAA
360163 GAGTATGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.19
14 7 0.27
15 3 0.12
16 11 0.42
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATTATAAAATAAA
Found at i:361307 original size:30 final size:30
Alignment explanation
Indices: 361228--361318 Score: 96
Period size: 29 Copynumber: 3.0 Consensus size: 30
361218 TGACTTTGAT
* *
361228 TTTAAGGGTTAAATTGATCTTTATCTAAAG
1 TTTAAGGGTCAAATTGATATTTATCTAAAG
* * *
361258 TTCATA--GTCAAAATGATATTTATTTAAAG
1 TTTA-AGGGTCAAATTGATATTTATCTAAAG
*
361287 TTTAAGGGTCAAATTAATATTCTATCTAAAG
1 TTTAAGGGTCAAATTGATATT-TATCTAAAG
361318 T
1 T
361319 CCATGTGTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
28 1 0.02
29 22 0.46
30 15 0.31
31 10 0.21
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (30 bp):
TTTAAGGGTCAAATTGATATTTATCTAAAG
Found at i:371021 original size:20 final size:20
Alignment explanation
Indices: 370942--371029 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
370932 AAGGTGTTAC
*
370942 ATCGATACTCA-CATAGAGT
1 ATCGATACTCAGCCTAGAGT
* *
370961 ATCGATACTTAGTCT--AGT
1 ATCGATACTCAGCCTAGAGT
* * *
370979 ATCGATACCTTAACACCAGAGT
1 ATCGATA-CTCAGC-CTAGAGT
371001 ATCGATACTCAGCCTAGAGT
1 ATCGATACTCAGCCTAGAGT
371021 ATCGATACT
1 ATCGATACT
371030 TCCTTAATCA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
18 10 0.18
19 14 0.25
20 17 0.31
21 4 0.07
22 10 0.18
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (20 bp):
ATCGATACTCAGCCTAGAGT
Found at i:371713 original size:15 final size:15
Alignment explanation
Indices: 371693--371722 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
371683 AGATCGTGGG
371693 GAGTTATCATCAGCA
1 GAGTTATCATCAGCA
*
371708 GAGTTATCGTCAGCA
1 GAGTTATCATCAGCA
371723 ATAGACTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (15 bp):
GAGTTATCATCAGCA
Found at i:373534 original size:2 final size:2
Alignment explanation
Indices: 373522--373554 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
373512 TGAGTTCTTT
*
373522 TA TA TA CA 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 TA TA T
373555 TTTAAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:378369 original size:155 final size:156
Alignment explanation
Indices: 378165--378485 Score: 465
Period size: 155 Copynumber: 2.1 Consensus size: 156
378155 TATTGTGGTA
* *
378165 TATGAGCATGTGATTCAAATTTGGTAAAAGACACTTAAAATAAATGATGAATTGAAGAAATAAGG
1 TATGAGCATGTGATTCAAATTTAGTAAAAGACACTTAAAATAAAGGATGAATTGAAGAAATAAGG
* * *
378230 AAAA-ATGAAAAATTAAGGGACTAAATTGAAAAATAAAAAAATTGTTAT-AAAAAAGAGTAATTG
66 AAAATATAAAAAATTAAGGGACTAAATTGAAAAAT-AAAAAATCGTTATAAAAAAAGAGGAATTG
*
378293 AAAGT-ACATATATATTCT-ATGATGATT
130 AAA-TAACATATACATTCTAAT-ATGATT
*
378320 TATGAGCATGTGATTCAAATTTAGTAAAAGACGGAC-TCAAA-AAAGGATGAATTGAAGAAATAA
1 TATGAGCATGTGATTCAAATTTAGTAAAAGAC--ACTTAAAATAAAGGATGAATTGAAGAAATAA
*
378383 GGAAAATATAAAAAATTAAGGGATTAAATTGAAAAATAAAAAATCGTTATAAAAAAAAGAGGAAT
64 GGAAAATATAAAAAATTAAGGGACTAAATTGAAAAATAAAAAATCGTTAT-AAAAAAAGAGGAAT
*
378448 TGAAATAACATATACATTCTAATATGGTT
128 TGAAATAACATATACATTCTAATATGATT
378477 TATGAGCAT
1 TATGAGCAT
378486 TTGGTTTAAA
Statistics
Matches: 150, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
155 70 0.47
156 33 0.22
157 45 0.30
158 2 0.01
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (156 bp):
TATGAGCATGTGATTCAAATTTAGTAAAAGACACTTAAAATAAAGGATGAATTGAAGAAATAAGG
AAAATATAAAAAATTAAGGGACTAAATTGAAAAATAAAAAATCGTTATAAAAAAAGAGGAATTGA
AATAACATATACATTCTAATATGATT
Found at i:393381 original size:27 final size:26
Alignment explanation
Indices: 393339--393392 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
393329 TCATCATTCT
* *
393339 ATTTTAAAATCCTAT-GTCACATAAA
1 ATTTTAAAATCATATGGGCACATAAA
393364 ATTTTATAAATTCATATGGGCACATAAA
1 ATTTTA-AAA-TCATATGGGCACATAAA
393392 A
1 A
393393 ATCTGTCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.25
26 3 0.12
27 5 0.21
28 10 0.42
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (26 bp):
ATTTTAAAATCATATGGGCACATAAA
Found at i:393709 original size:31 final size:31
Alignment explanation
Indices: 393633--393711 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 31
393623 AAATTCTCGC
* *
393633 CCTCGTCTCTTCTCT-TTTTCCTCCTACTTT
1 CCTCTTCTCTTTTCTCTTTTCCTCCTACTTT
* *
393663 CTTCTTCTTCTTTTCTCTTTTCCTCCTATTTT
1 CCTCTTC-TCTTTTCTCTTTTCCTCCTACTTT
393695 CCTCTTCTCTTTTCTCT
1 CCTCTTCTCTTTTCTCT
393712 GTAATTCTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.12
31 17 0.40
32 20 0.48
ACGTcount: A:0.03, C:0.37, G:0.01, T:0.59
Consensus pattern (31 bp):
CCTCTTCTCTTTTCTCTTTTCCTCCTACTTT
Found at i:399338 original size:12 final size:12
Alignment explanation
Indices: 399318--399347 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
399308 AGAAGCGGTT
*
399318 AAAGGAAAAAAA
1 AAAGAAAAAAAA
399330 AAAGAAAAAAAA
1 AAAGAAAAAAAA
399342 AAAGAA
1 AAAGAA
399348 GAGAATTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:399683 original size:40 final size:40
Alignment explanation
Indices: 399599--399694 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
399589 ATTTGACATT
* * * * *
399599 TTAATATCATAGTTTGTTTACGGATTTTATTGTTTTAGAC
1 TTAATATAATGGTTTGTTTACGGATTTTATTATTATAAAC
* * *
399639 TTAATATAATGGTTTGTTTATGTATTTTATTATTATAAAG
1 TTAATATAATGGTTTGTTTACGGATTTTATTATTATAAAC
**
399679 TTAATATTGTGGTTTG
1 TTAATATAATGGTTTG
399695 AAACTTGAGA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.27, C:0.03, G:0.16, T:0.54
Consensus pattern (40 bp):
TTAATATAATGGTTTGTTTACGGATTTTATTATTATAAAC
Found at i:399718 original size:75 final size:75
Alignment explanation
Indices: 399639--399785 Score: 186
Period size: 75 Copynumber: 2.0 Consensus size: 75
399629 TGTTTTAGAC
* * * * *
399639 TTAATATAATGGTTTGTTTATGTATTTTATTATTATAAAGTTAATATTGTGGTTTGAAACTTGAG
1 TTAATATAATGATTTGTTTATGGATTTTATTATTATAAACTTAATATTATGGTATGAAACTTGAG
399704 ATTTGACATT
66 ATTTGACATT
** * * ***
399714 TTAATATTGTGATTTGTTTATGGATTTTATTGTTCTAAACTTAATATTATGGTATGAGTGTTGAG
1 TTAATATAATGATTTGTTTATGGATTTTATTATTATAAACTTAATATTATGGTATGAAACTTGAG
399779 ATTTGAC
66 ATTTGAC
399786 TTTATTTACT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (75 bp):
TTAATATAATGATTTGTTTATGGATTTTATTATTATAAACTTAATATTATGGTATGAAACTTGAG
ATTTGACATT
Found at i:402265 original size:43 final size:43
Alignment explanation
Indices: 402148--402278 Score: 147
Period size: 43 Copynumber: 3.0 Consensus size: 43
402138 ACAATTCCAA
* * **
402148 AATCTAAAGTAATAATCTAGAAATACATCGAACTAAGTTATTA-
1 AATC-AAAGTAATAATCCAGAAATACATCAAACTAACATATTAC
* * * * *
402191 AACCATAGTAACAATCCAGAAGTACACCAAACTAACATATTAC
1 AATCAAAGTAATAATCCAGAAATACATCAAACTAACATATTAC
* *
402234 AATCAAAATAATAATCCACAAATACATCAAACTAACATATTAC
1 AATCAAAGTAATAATCCAGAAATACATCAAACTAACATATTAC
402277 AA
1 AA
402279 CCATTCCTGA
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 30 0.42
43 41 0.58
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (43 bp):
AATCAAAGTAATAATCCAGAAATACATCAAACTAACATATTAC
Found at i:407516 original size:37 final size:39
Alignment explanation
Indices: 407465--407543 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 39
407455 ATTGTAGCAC
* * *
407465 TTTAAGATAAAC-TTTATCATGTAAATGTTCATGT-TAT
1 TTTAAGATAAACTTTTATCATATAAAAGTTCATATATAT
* *
407502 TTTAAGGTACACTTTTATCATATAAAAGTTCATATATAT
1 TTTAAGATAAACTTTTATCATATAAAAGTTCATATATAT
407541 TTT
1 TTT
407544 TGAAGTTACG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 10 0.29
38 19 0.54
39 6 0.17
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (39 bp):
TTTAAGATAAACTTTTATCATATAAAAGTTCATATATAT
Found at i:408141 original size:32 final size:32
Alignment explanation
Indices: 408105--408190 Score: 154
Period size: 32 Copynumber: 2.7 Consensus size: 32
408095 CTTAATATTT
408105 ACTTTTTGTTTCATTTCAGTACTCCGTTGTTA
1 ACTTTTTGTTTCATTTCAGTACTCCGTTGTTA
*
408137 ACTTTTTATTTCATTTCAGTACTCCGTTGTTA
1 ACTTTTTGTTTCATTTCAGTACTCCGTTGTTA
*
408169 ACTTTTTGTTTCATTTTAGTAC
1 ACTTTTTGTTTCATTTCAGTAC
408191 CTAAATTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.55
Consensus pattern (32 bp):
ACTTTTTGTTTCATTTCAGTACTCCGTTGTTA
Found at i:413028 original size:50 final size:50
Alignment explanation
Indices: 412970--413095 Score: 146
Period size: 50 Copynumber: 2.5 Consensus size: 50
412960 AGCAGAAAAA
* * *
412970 CGCGCCCCCTACACCGCGCTATATGCTGATTTGGCGCCACGTGGGTATAG
1 CGCGCCCCCTACACCGCGCTATACGCTGATCTGACGCCACGTGGGTATAG
* * * * * *
413020 CGCGCCCCCTGCCCCGCGATATACGGTGATCTGATGTCACGTGGGTATAG
1 CGCGCCCCCTACACCGCGCTATACGCTGATCTGACGCCACGTGGGTATAG
*
413070 CGCGCCCCCTGA-TCCGCGCTATACGC
1 CGCGCCCCCT-ACACCGCGCTATACGC
413096 CACGTAGAGG
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.15, C:0.37, G:0.28, T:0.21
Consensus pattern (50 bp):
CGCGCCCCCTACACCGCGCTATACGCTGATCTGACGCCACGTGGGTATAG
Found at i:417004 original size:9 final size:9
Alignment explanation
Indices: 416989--417035 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
416979 CCTTTCATCA
*
416989 TCATCGTCA
1 TCATCGTCG
*
416998 TCGTCGTCG
1 TCATCGTCG
* *
417007 TCACCATCG
1 TCATCGTCG
417016 TCATCGTCG
1 TCATCGTCG
417025 TCATCGTCG
1 TCATCGTCG
417034 TC
1 TC
417036 GTCCTGAGCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.13, C:0.36, G:0.19, T:0.32
Consensus pattern (9 bp):
TCATCGTCG
Found at i:417016 original size:15 final size:15
Alignment explanation
Indices: 416996--417038 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
416986 TCATCATCGT
416996 CATCGTCGTCGTCAC
1 CATCGTCGTCGTCAC
* **
417011 CATCGTCATCGTCGT
1 CATCGTCGTCGTCAC
417026 CATCGTCGTCGTC
1 CATCGTCGTCGTC
417039 CTGAGCAGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.12, C:0.37, G:0.21, T:0.30
Consensus pattern (15 bp):
CATCGTCGTCGTCAC
Found at i:417393 original size:18 final size:18
Alignment explanation
Indices: 417370--417428 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
417360 GAAAGGCGAT
417370 TGCGGCATCATATATGGC
1 TGCGGCATCATATATGGC
*
417388 TGCGGCATCATATATGGA
1 TGCGGCATCATATATGGC
*
417406 TGCGACATCATATATGGC
1 TGCGGCATCATATATGGC
417424 TGCGG
1 TGCGG
417429 TGGCTGCTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (18 bp):
TGCGGCATCATATATGGC
Found at i:419071 original size:111 final size:111
Alignment explanation
Indices: 418934--419155 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
418924 ATTACAAAAA
* *
418934 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
418999 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
419045 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
419110 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
419156 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:419293 original size:12 final size:10
Alignment explanation
Indices: 419279--419319 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
419269 ACCTTAAAAA
*
419279 GAGAGTATTT
1 GAGAGAATTT
419289 GAGAGAAATTT
1 GAGAG-AATTT
419300 -AGAGAATTT
1 GAGAGAATTT
419309 GAGAGAATTT
1 GAGAGAATTT
419319 G
1 G
419320 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:421219 original size:27 final size:26
Alignment explanation
Indices: 421183--421235 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 26
421173 ATTAAAGTCT
421183 TATATTGTTCGCTTAGTTTGATTGAA
1 TATATTGTTCGCTTAGTTTGATTGAA
421209 TATATATGTTCGCTTAGTTTGATTGAA
1 TATAT-TGTTCGCTTAGTTTGATTGAA
421236 GCTTAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.49
Consensus pattern (26 bp):
TATATTGTTCGCTTAGTTTGATTGAA
Found at i:426115 original size:21 final size:21
Alignment explanation
Indices: 426077--426116 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
426067 TCTTAATATC
** *
426077 ATTTTATTTTCAACTTTAAAT
1 ATTTTATTAGCAAATTTAAAT
426098 ATTTTATTAGCAAATTTAA
1 ATTTTATTAGCAAATTTAA
426117 GGGTGTGATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
ATTTTATTAGCAAATTTAAAT
Found at i:427199 original size:43 final size:43
Alignment explanation
Indices: 427145--427234 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
427135 TTTACGATCT
427145 TTTAAGTTTCTATTTGTTAAAGAAAATTCATAATAGTTACGAG
1 TTTAAGTTTCTATTTGTTAAAGAAAATTCATAATAGTTACGAG
*
427188 TTTAAGTTTCTATTTGTTAAAGAAAATTCATAATAGTTATGAG
1 TTTAAGTTTCTATTTGTTAAAGAAAATTCATAATAGTTACGAG
427231 TTTA
1 TTTA
427235 TTGAATATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (43 bp):
TTTAAGTTTCTATTTGTTAAAGAAAATTCATAATAGTTACGAG
Found at i:431393 original size:25 final size:23
Alignment explanation
Indices: 431343--431394 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
431333 AGGAAGTTAT
* *
431343 ATTAGAATTTTAAAGGGTGTATA
1 ATTAGAATTTTAAAAGGTGTAAA
*
431366 ATTAGAAATTTTCAAAAGTTGTAAA
1 ATTAG-AATTTT-AAAAGGTGTAAA
431391 ATTA
1 ATTA
431395 TATTATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 6 0.25
25 13 0.54
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.38
Consensus pattern (23 bp):
ATTAGAATTTTAAAAGGTGTAAA
Found at i:431422 original size:17 final size:17
Alignment explanation
Indices: 431387--431419 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
431377 TCAAAAGTTG
*
431387 TAAAATTATATTATAAA
1 TAAAAATATATTATAAA
431404 TAAAAATATA-TATAAA
1 TAAAAATATATTATAAA
431420 ATATACCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATATATTATAAA
Found at i:432262 original size:3 final size:3
Alignment explanation
Indices: 432256--432313 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
432246 GAATAATAAC
432256 GAT GAT GAT GAT GAT -AT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
432303 GGT GAT GAT GA
1 GAT GAT GAT GA
432314 GTCTGCCACG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.33, C:0.00, G:0.34, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:434271 original size:45 final size:46
Alignment explanation
Indices: 434186--434273 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
434176 AAATAGCCTG
* * * *
434186 AGTGCATCGATGCTTGGTCTTGTGCATCGATGTATCAAATGCACAA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACAA
434232 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
434274 TTCGATGTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 21 0.55
46 17 0.45
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACAA
Found at i:437822 original size:21 final size:21
Alignment explanation
Indices: 437798--437880 Score: 78
Period size: 23 Copynumber: 3.9 Consensus size: 21
437788 ACCAAAACCC
* *
437798 CAGGGGGTATCGATTCCCCTA
1 CAGGGGGAATCGATTCCCTTA
*
437819 CAGGGGGAATCGGTTCCCATTCA
1 CAGGGGGAATCGATTCCC-TT-A
* *
437842 AAGGGGGAATCGGTTCCCTTA
1 CAGGGGGAATCGATTCCCTTA
* *
437863 -TGGGGGTATCGATTCCCT
1 CAGGGGGAATCGATTCCCT
437881 CTGCCAAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
20 15 0.28
21 17 0.32
22 3 0.06
23 18 0.34
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.25
Consensus pattern (21 bp):
CAGGGGGAATCGATTCCCTTA
Found at i:446835 original size:15 final size:15
Alignment explanation
Indices: 446815--446849 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
446805 AAGATCATGA
446815 GTTTCCTCATCTTTC
1 GTTTCCTCATCTTTC
446830 GTTTCCTCATCTTTC
1 GTTTCCTCATCTTTC
446845 GTTTC
1 GTTTC
446850 TTCCTTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.06, C:0.31, G:0.09, T:0.54
Consensus pattern (15 bp):
GTTTCCTCATCTTTC
Found at i:448729 original size:22 final size:21
Alignment explanation
Indices: 448687--448726 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
448677 GAGTTTATTT
*
448687 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
448708 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
448727 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:455584 original size:31 final size:31
Alignment explanation
Indices: 455549--455689 Score: 273
Period size: 31 Copynumber: 4.5 Consensus size: 31
455539 GTCATAGATT
*
455549 CCGAAGAACCTAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
455580 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
455611 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
455642 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
455673 CCGAAGAACATAGGTAA
1 CCGAAGAACATAGGTAA
455690 CCCTCGACCC
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 109 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:459869 original size:31 final size:31
Alignment explanation
Indices: 459816--459952 Score: 237
Period size: 31 Copynumber: 4.5 Consensus size: 31
459806 TCCATAGATT
*
459816 CCGAAGAACCTAGGT-AACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
459846 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
459877 CCGAAGAACATAGGT-AA-AGTCCATATGT-
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
459905 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
459936 CCGAAGAACATAGGTAA
1 CCGAAGAACATAGGTAA
459953 CCCTCGACCC
Statistics
Matches: 102, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
28 15 0.15
29 13 0.13
30 27 0.26
31 47 0.46
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:459926 original size:59 final size:61
Alignment explanation
Indices: 459816--459953 Score: 253
Period size: 59 Copynumber: 2.3 Consensus size: 61
459806 TCCATAGATT
*
459816 CCGAAGAACCTAGGTAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTC
459877 CCGAAGAACATAGGTAA-AGTCCATATGT-CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTC
459936 CCGAAGAACATAGGTAAC
1 CCGAAGAACATAGGTAAC
459954 CCTCGACCCT
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
59 48 0.64
60 11 0.15
61 16 0.21
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.19
Consensus pattern (61 bp):
CCGAAGAACATAGGTAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:475226 original size:11 final size:11
Alignment explanation
Indices: 475210--475234 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
475200 TCAAAATGTC
475210 AAAATTATTTG
1 AAAATTATTTG
475221 AAAATTATTTG
1 AAAATTATTTG
475232 AAA
1 AAA
475235 CTTTGTACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAATTATTTG
Found at i:479586 original size:24 final size:24
Alignment explanation
Indices: 479549--479612 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
479539 GGATCGTGCA
* *
479549 ACAATAGTAGAGAAAACGA-GTACC
1 ACAAGAGTAGAGAAAAC-ACATACC
* *
479573 AGAAGAGTAGAGAAAACACATGCC
1 ACAAGAGTAGAGAAAACACATACC
479597 ACAAGAGTAGAGAAAA
1 ACAAGAGTAGAGAAAA
479613 GTGTGTCCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.53, C:0.14, G:0.23, T:0.09
Consensus pattern (24 bp):
ACAAGAGTAGAGAAAACACATACC
Found at i:482208 original size:3 final size:3
Alignment explanation
Indices: 482200--482230 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
482190 CAAGTGAAAA
482200 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
482231 CTGATTGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:485273 original size:3 final size:3
Alignment explanation
Indices: 485265--485289 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
485255 ATGAAATATC
485265 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
485290 TAGTATTAAT
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:485680 original size:33 final size:32
Alignment explanation
Indices: 485643--485706 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
485633 ATAAATCAAA
485643 ATCATTTTAAGAGAATTATACAAACTCCAAAAC
1 ATCATTTTAAGAGAATTATACAAAC-CCAAAAC
* ** *
485676 ATCATTTTAGGAGGGTTATATAAACCCAAAA
1 ATCATTTTAAGAGAATTATACAAACCCAAAA
485707 TGATATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 6 0.22
33 21 0.78
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (32 bp):
ATCATTTTAAGAGAATTATACAAACCCAAAAC
Found at i:487243 original size:41 final size:41
Alignment explanation
Indices: 487198--487501 Score: 296
Period size: 41 Copynumber: 7.4 Consensus size: 41
487188 TCGCGCTGCA
*
487198 TTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCT
1 TTTCGCATTGCGATAGTTGAAAATCGCAACGCGATTTTCCT
* * *** *
487239 TTTCGCATTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTCCA
1 TTTCGCATTGCGATAGT-TGAAAATCG-CAACGCGATTTTCCT
**
487280 TTTCGTGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCT
1 TTTCGCATTGCGATAGTTGAAAATCGCAACGCGATTTTCCT
* * *** *
487321 TTTCGCATTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTCCA
1 TTTCGCATTGCGATAGT-TGAAAATCG-CAACGCGATTTTCCT
*
487362 TTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCT
1 TTTCGCATTGCGATAGTTGAAAATCGCAACGCGATTTTCCT
* * *** *
487403 TTTCGCATTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTCCA
1 TTTCGCATTGCGATAGT-TGAAAATCG-CAACGCGATTTTCCT
**
487444 TTTCGTGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCT
1 TTTCGCATTGCGATAGTTGAAAATCGCAACGCGATTTTCCT
487485 TTTCGCATTGCGATAGT
1 TTTCGCATTGCGATAGT
487502 CTACAGTGTC
Statistics
Matches: 204, Mismatches: 47, Indels: 24
0.74 0.17 0.09
Matches are distributed among these distances:
40 6 0.03
41 192 0.94
42 6 0.03
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (41 bp):
TTTCGCATTGCGATAGTTGAAAATCGCAACGCGATTTTCCT
Found at i:487293 original size:82 final size:82
Alignment explanation
Indices: 487196--487519 Score: 630
Period size: 82 Copynumber: 4.0 Consensus size: 82
487186 ATTCGCGCTG
487196 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCTTTTCGCATTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCTTTTCGCATTGCGATAGTCTACA
487261 GTGTCGTTGCGATTTTC
66 GTGTCGTTGCGATTTTC
*
487278 CATTTCGTGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCTTTTCGCATTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCTTTTCGCATTGCGATAGTCTACA
487343 GTGTCGTTGCGATTTTC
66 GTGTCGTTGCGATTTTC
487360 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCTTTTCGCATTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCTTTTCGCATTGCGATAGTCTACA
487425 GTGTCGTTGCGATTTTC
66 GTGTCGTTGCGATTTTC
*
487442 CATTTCGTGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCTTTTCGCATTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCTTTTCGCATTGCGATAGTCTACA
487507 GTGTCGTTGCGAT
66 GTGTCGTTGCGAT
487520 AGTCTACAGT
Statistics
Matches: 239, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 239 1.00
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (82 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCTTTTCGCATTGCGATAGTCTACA
GTGTCGTTGCGATTTTC
Found at i:488249 original size:21 final size:21
Alignment explanation
Indices: 488223--488332 Score: 79
Period size: 21 Copynumber: 5.3 Consensus size: 21
488213 TTAATGGAAA
*
488223 ATCGCAACGACACTGTACACT
1 ATCGCAACGACAATGTACACT
* *
488244 ATCGCAACG-CGAAATGGA-A-A
1 ATCGCAACGAC--AATGTACACT
*
488264 ATCGCAACGACATTGTACACT
1 ATCGCAACGACAATGTACACT
* *
488285 ATCGCAACG-CGAAATGGA-A-A
1 ATCGCAACGAC--AATGTACACT
*
488305 ATCGCAACGACACTGTACACT
1 ATCGCAACGACAATGTACACT
488326 ATCGCAA
1 ATCGCAA
488333 TGCGAAATGC
Statistics
Matches: 67, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
19 8 0.12
20 22 0.33
21 29 0.43
22 8 0.12
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.16
Consensus pattern (21 bp):
ATCGCAACGACAATGTACACT
Found at i:488269 original size:20 final size:20
Alignment explanation
Indices: 488244--488313 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
488234 ACTGTACACT
488244 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * *
488264 ATCGCAA--CGACATTGTACACT
1 ATCGCAACGCGA-AATGGA-A-A
488285 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
488305 ATCGCAACG
1 ATCGCAACG
488314 ACACTGTACA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 3 0.08
19 4 0.10
20 17 0.44
21 8 0.21
22 4 0.10
23 3 0.08
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:488272 original size:41 final size:41
Alignment explanation
Indices: 488215--488341 Score: 236
Period size: 41 Copynumber: 3.1 Consensus size: 41
488205 ATCTTTTTTT
488215 AATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGA
1 AATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGA
*
488256 AATGGAAAATCGCAACGACATTGTACACTATCGCAACGCGA
1 AATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGA
*
488297 AATGGAAAATCGCAACGACACTGTACACTATCGCAATGCGA
1 AATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGA
488338 AATG
1 AATG
488342 CAGCGCGAAT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 83 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (41 bp):
AATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGA
Found at i:489199 original size:20 final size:20
Alignment explanation
Indices: 489163--489200 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
489153 ATCCTATTCC
**
489163 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
489183 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
489201 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:501128 original size:23 final size:23
Alignment explanation
Indices: 501076--501128 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
501066 CAGCTCATAT
501076 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
** * *
501099 ATTTGCACTGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
501122 AAATGCA
1 AAATGCA
501129 TCGCAATTCC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:501759 original size:18 final size:19
Alignment explanation
Indices: 501736--501773 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
501726 ACTTTTTCTT
501736 CTATGGG-GTATCGATACA
1 CTATGGGTGTATCGATACA
*
501754 CTATGGGTGTATCGGTACA
1 CTATGGGTGTATCGATACA
501773 C
1 C
501774 AAATTAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (19 bp):
CTATGGGTGTATCGATACA
Found at i:511566 original size:110 final size:110
Alignment explanation
Indices: 511368--511584 Score: 319
Period size: 110 Copynumber: 2.0 Consensus size: 110
511358 TGTATGCTTT
*
511368 TTGTCAGCTGATCCGTTAAGGGAACTATTATGCTCATAAATTATCAGTCTTTCTCATAGCACAGT
1 TTGTCAGCTGATCCGTTAAGGGAACTATTATGCTCATAAATGATCAGTCTTTCTCATAGCACAGT
* * *
511433 TCAAAGAAAAGTATACCATTTTAAGCCAACCACCATTTGTCCTAC
66 TCAAAGAAAAGTATACAACTTTAAGCCAACAACCATTTGTCCTAC
* * * * * *
511478 TTGTCAGCTGATCCGTTGAGGGAACTCTTATGCTCATAAATGATCATTCTTTGTCTTAGTACAGT
1 TTGTCAGCTGATCCGTTAAGGGAACTATTATGCTCATAAATGATCAGTCTTTCTCATAGCACAGT
*
511543 TCAAAGAAAA-TGATACAACTTTAAGCCAACAATCATTTGTCC
66 TCAAAGAAAAGT-ATACAACTTTAAGCCAACAACCATTTGTCC
511585 AAAAGCCGGT
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
109 1 0.01
110 94 0.99
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (110 bp):
TTGTCAGCTGATCCGTTAAGGGAACTATTATGCTCATAAATGATCAGTCTTTCTCATAGCACAGT
TCAAAGAAAAGTATACAACTTTAAGCCAACAACCATTTGTCCTAC
Found at i:517681 original size:4 final size:4
Alignment explanation
Indices: 517672--517709 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
517662 TGTTTAACAT
*
517672 CTCC CTCC CTCT CTCC CTCC CTCC CTCC CTCC CTCC CT
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CT
517710 GGTATCTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.00, C:0.71, G:0.00, T:0.29
Consensus pattern (4 bp):
CTCC
Found at i:518847 original size:21 final size:21
Alignment explanation
Indices: 518823--518869 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
518813 ATTTTAGGAG
*
518823 ATTTTCGGGTTGAAAATAGCC
1 ATTTTCGGGTTGAAAATAACC
518844 ATTTTCGGGTTGAAAATAACC
1 ATTTTCGGGTTGAAAATAACC
518865 ATTTT
1 ATTTT
518870 GGGCTTAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (21 bp):
ATTTTCGGGTTGAAAATAACC
Found at i:519712 original size:21 final size:22
Alignment explanation
Indices: 519635--519723 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 22
519625 TTCGGGACAA
* **
519635 ATGTGGTACTTCGGTGCAACCCT
1 ATGTGGCACTTCGGTGCAA-ATT
*
519658 ATGTGGCACTTCGGTGCAATTT
1 ATGTGGCACTTCGGTGCAAATT
*
519680 ATATGGTC-CTTCGG-G-ATAATT
1 ATGTGG-CACTTCGGTGCA-AATT
519701 ATGTGGCACTTCGGTGCAAATT
1 ATGTGGCACTTCGGTGCAAATT
519723 A
1 A
519724 CGAGCTGTGG
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
20 2 0.04
21 15 0.27
22 18 0.33
23 20 0.36
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (22 bp):
ATGTGGCACTTCGGTGCAAATT
Found at i:529210 original size:23 final size:23
Alignment explanation
Indices: 529174--529242 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
529164 CACCACAGCT
* * *
529174 CGTATAAATACACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
529197 CGTA-AAATTGCACCGTAGTGCCG
1 CGTAGAAA-TGCACCGAAGTGCCA
529220 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
529243 TATAAGGTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 3 0.08
23 32 0.84
24 3 0.08
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:529626 original size:2 final size:2
Alignment explanation
Indices: 529619--529649 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
529609 TATCTTATTT
529619 TA 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 TA T
529650 TCACATGTTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:530953 original size:64 final size:63
Alignment explanation
Indices: 530844--531005 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
530834 TTCCCTTGAA
* * *
530844 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGGG
* * ** * **
530908 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTATTGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGGG
*
530972 GTGCATCGATGTACTTCCTATGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
531006 CTGAACAATT
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 2 0.02
64 78 0.94
65 3 0.04
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGGG
Found at i:534547 original size:13 final size:13
Alignment explanation
Indices: 534529--534554 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
534519 TATTTATTTT
534529 ATGTTTTATTTAA
1 ATGTTTTATTTAA
534542 ATGTTTTATTTAA
1 ATGTTTTATTTAA
534555 TTTTCAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
ATGTTTTATTTAA
Found at i:534832 original size:23 final size:21
Alignment explanation
Indices: 534802--534887 Score: 104
Period size: 23 Copynumber: 4.0 Consensus size: 21
534792 TCAGGACAAA
534802 TATGTGGCACTTCGGTGCAACCT
1 TATGTGGCACTTCGGTGCAA--T
*
534825 TATGTGGCACTTCGGTACAATT
1 TATGTGGCACTTCGGTGCAA-T
534847 TATGTGGTC-CTTCGG-GACAAT
1 TATGTGG-CACTTCGGTG-CAAT
534868 TATGTGGCACTTCGGTGCAA
1 TATGTGGCACTTCGGTGCAA
534888 ATTACGAGCT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
20 1 0.02
21 17 0.30
22 18 0.32
23 20 0.36
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.33
Consensus pattern (21 bp):
TATGTGGCACTTCGGTGCAAT
Found at i:540808 original size:15 final size:16
Alignment explanation
Indices: 540774--540808 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
540764 ACTTTGTTAC
540774 ATTTTAATCATTAATGT
1 ATTTTAATCATT-ATGT
540791 ATTTTAATCATT-TGT
1 ATTTTAATCATTATGT
540806 ATT
1 ATT
540809 AGTTAGATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
17 12 0.67
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (16 bp):
ATTTTAATCATTATGT
Found at i:547013 original size:66 final size:66
Alignment explanation
Indices: 546853--547076 Score: 301
Period size: 65 Copynumber: 3.4 Consensus size: 66
546843 AATTGACAAA
* *
546853 CTTTGAGATTGTTTCTCTTGAAACAAATTTGGTCTCCCTTGAA-ACAGTTTCTCTTGAAA-ACCC
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTT-AAGACAGTTTCTCTTGAAACACCC
546916 AT
65 AT
*
546918 CTTTGAGATTGTTTCCCTTGAAACGAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACACCCA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACACCCA
546983 T
66 T
* * * * * * * *
546984 ATTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGCTTCTCTTGAAGCA-TCA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACACCCA
547048 T
66 T
* *
547049 CTTTGAGTTTGTTTCTCTTGAAACAAAT
1 CTTTGAGATTGTTTCCCTTGAAACAAAT
547077 CCCTAAAGAT
Statistics
Matches: 141, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
64 2 0.01
65 80 0.57
66 59 0.42
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (66 bp):
CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACACCCA
T
Found at i:547395 original size:134 final size:131
Alignment explanation
Indices: 547075--547412 Score: 347
Period size: 131 Copynumber: 2.6 Consensus size: 131
547065 CTTGAAACAA
* * * * * * *
547075 ATCCCTAAAGATGGCCAGACGTCCTTATCACTTAGGAACCGTGTCATCCCCCGACCATACTTCCT
1 ATCCCTAAAGATGGTCAGTCATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCT
* * * * * * *
547140 TATCACGTAAGAGCCGTGTCACTCTTATATAACCAGCCGTCCTCATCATGTAGGAATCGTGTTAT
66 CATCACGTAAGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTAT
547205 C
131 C
* * *
547206 ATCCCTAAAGATGGTTTA-TCATCCTCATCATGTAGGAATCC-TTTCATCCCCCGACCAGACCTC
1 ATCCCTAAAGATGG-TCAGTCATCCTCATCACGTAGGAA-CCGTGTCATCCCCCGACCAGACCTC
* * ** * * *
547269 CTCATCATGTAGGATTCGTGTCACCCCTGGATAACCAGCTGTCCTCATCGCGTAGGAACCATGTT
64 CTCATCACGTAAGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTT
547334 ATC
129 ATC
* ** *
547337 ACCCTCTCTAAAGATGGTCAGTCATCCTCATCACGTAGGAACCGTGTCATCCATCGACCAGATCT
1 A---TCCCTAAAGATGGTCAGTCATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCT
**
547402 TTTCATCACGT
63 CCTCATCACGT
547413 GGGAGTTGTG
Statistics
Matches: 166, Mismatches: 34, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
131 103 0.62
132 3 0.02
133 4 0.02
134 56 0.34
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.28
Consensus pattern (131 bp):
ATCCCTAAAGATGGTCAGTCATCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCT
CATCACGTAAGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTAT
C
Found at i:547629 original size:3 final size:3
Alignment explanation
Indices: 547621--547660 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
547611 GTCTTAAAAA
547621 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
547661 TAATTTACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:548109 original size:20 final size:21
Alignment explanation
Indices: 548084--548123 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
548074 AGCAAAGAGG
548084 TATTCTAGATTT-TTTATTAT
1 TATTCTAGATTTATTTATTAT
* *
548104 TATTCTCGGTTTATTTATTA
1 TATTCTAGATTTATTTATTA
548124 AATTTTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.62
Consensus pattern (21 bp):
TATTCTAGATTTATTTATTAT
Found at i:552886 original size:199 final size:197
Alignment explanation
Indices: 552160--552962 Score: 837
Period size: 199 Copynumber: 4.1 Consensus size: 197
552150 TTTTACTATA
* * *
552160 ACTAAATAATTTTTTTACAATTTG-TTATTGTGAAATAATATTATTTGTCACAATTTTTTTATAA
1 ACTAAATAAATTTGTTACAA-TTGATTATTGTGAAAGAATATTATTTGTCACAA-TTTTTTATAA
** * * * *
552224 TGAGAAATTAATATTTGTTATAGTTTGTTATTTTGATTAAATAAATGTGTCACAAATTT-TCATT
64 TGAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGT--CAAATTTGTTATT
* ** * * * **
552288 TTGATAAAATATTAGGACGAAATAAATTTGACATAACTTTTTA-CTATGA-TAAAACTTAACGTG
127 TTGAGAAAATATTTTGACGAAATAAATTTGACATAAATTTTTATCT-TAACT-AAATTTAATATG
552351 TTATTGTG
190 TTATTGTG
* * * * * *
552359 ACTAAATCATTTTGTTACAATTTATTACTGTGAAAGAATATTAATTGTCACGATTTTTTATAATG
1 ACTAAATAAATTTGTTACAATTGATTATTGTGAAAGAATATTATTTGTCACAATTTTTTATAATG
* * * * * * * *
552424 AGAAATTATTATTTTTTATAAATTATTATTTTGATTAAATAAATTTGTTACATTTTTTATTTTGA
66 AGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAATTTGTTATTTTGA
* * * * * *
552489 TAAATTATTGTGACAAAATAAATTTGACA-AAA-TTTTATTTTAACTAAATTTACTATGTTATTG
131 GAAAATATTTTGACGAAATAAATTTGACATAAATTTTTATCTTAACTAAATTTAATATGTTATTG
*
552552 TA
196 TG
* * * **
552554 ACTAAATAAATTTGTTACACTTTG-TTATTGTGAAAGAATAGTATTTGTCATAATTTTTTATTTT
1 ACTAAATAAATTTGTTACA-ATTGATTATTGTGAAAGAATATTATTTGTCACAATTTTTTATAAT
* * *
552618 GAGGAATTAAAATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAGGTTGTTATTTT
65 GAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAA-TTTGTTATTTT
* * *
552683 GAGAAAATATTTTGATGAAATAAATTTAACATAAATTTTTATCTTGACTAAATTTAATATGTTAT
129 GAGAAAATATTTTGACGAAATAAATTTGACATAAATTTTTATCTTAACTAAATTTAATATGTTAT
552748 TGTG
194 TGTG
* * * * * * *
552752 ACTAAATAAACTTGTTATAATTGATTATTGTGAAAAACATATTGTTTGTCATAAATTTTTATATT
1 ACTAAATAAATTTGTTACAATTGATTATTGTGAAAGA-ATATTATTTGTCACAATTTTTTATAAT
* * * * ** * *
552817 GTGAAATTAATATTTATTATAATTTGTTATTATAACTATTTAAATTAGTCCTAATTTGTTATTTT
65 GAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGT-CAAATTTGTTATTTT
* * * *
552882 GAGAAAATATTTTGACTAAATAAATTTGACATAATTTTTTATTTTAACTAAATTTAATTTGTTAT
129 GAGAAAATATTTTGACGAAATAAATTTGACATAAATTTTTATCTTAACTAAATTTAATATGTTAT
*
552947 TTTG
194 TGTG
*
552951 TCTAAATAAATT
1 ACTAAATAAATT
552963 ATCATAATTT
Statistics
Matches: 504, Mismatches: 89, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
195 116 0.23
196 45 0.09
197 39 0.08
198 114 0.23
199 187 0.37
200 3 0.01
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.47
Consensus pattern (197 bp):
ACTAAATAAATTTGTTACAATTGATTATTGTGAAAGAATATTATTTGTCACAATTTTTTATAATG
AGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAATTTGTTATTTTGA
GAAAATATTTTGACGAAATAAATTTGACATAAATTTTTATCTTAACTAAATTTAATATGTTATTG
TG
Found at i:553021 original size:18 final size:19
Alignment explanation
Indices: 553000--553046 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
552990 GAATTTTATT
*
553000 TAAAAATT-TTATTATAAC
1 TAAAAATTGTTATGATAAC
553018 TAAAATAATTGGTTATGATAAC
1 T-AAA-AATT-GTTATGATAAC
553040 TAAAAAT
1 TAAAAAT
553047 ATATTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 3 0.12
20 7 0.29
21 3 0.12
22 10 0.42
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.38
Consensus pattern (19 bp):
TAAAAATTGTTATGATAAC
Found at i:553401 original size:21 final size:21
Alignment explanation
Indices: 553371--553417 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
553361 ATTGATTGTT
*
553371 GCATTCTGATCAAGAATTTTG
1 GCATTATGATCAAGAATTTTG
553392 GCATTATGATCAAGAATTTTG
1 GCATTATGATCAAGAATTTTG
553413 GCATT
1 GCATT
553418 TTGGCTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (21 bp):
GCATTATGATCAAGAATTTTG
Found at i:560849 original size:23 final size:23
Alignment explanation
Indices: 560794--560850 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
560784 CACCACAACT
560794 CATAT-AAATTGCACCGAAGTGC
1 CATATAAAATTGCACCGAAGTGC
* * *
560816 CGTATAGAATTGCACCGTAGTGC
1 CATATAAAATTGCACCGAAGTGC
*
560839 CATTTAAAATTG
1 CATATAAAATTG
560851 TCCATAAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (23 bp):
CATATAAAATTGCACCGAAGTGC
Found at i:562869 original size:13 final size:12
Alignment explanation
Indices: 562818--562891 Score: 61
Period size: 11 Copynumber: 6.6 Consensus size: 12
562808 TTAAAGAAAT
562818 AATATATT-TTA
1 AATATATTATTA
*
562829 AAAATATTAATT-
1 AATATATT-ATTA
*
562841 AGTATATT-TTA
1 AATATATTATTA
562852 AATATATTATTA
1 AATATATTATTA
562864 AA-ATA-TATTA
1 AATATATTATTA
* *
562874 TAT-TAATATTA
1 AATATATTATTA
562885 AATATAT
1 AATATAT
562892 AAATAATATT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
10 10 0.20
11 24 0.49
12 13 0.27
13 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (12 bp):
AATATATTATTA
Found at i:562904 original size:27 final size:27
Alignment explanation
Indices: 562874--562954 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
562864 AAATATATTA
562874 TATTAATATTAAATATATAAATAATAT
1 TATTAATATTAAATATATAAATAATAT
* *
562901 TATTCATTATT-AATA-ATTTAATAATAT
1 TATT-AATATTAAATATA-TAAATAATAT
** *
562928 TATTTCTATGAAAT-TAATAAATAATAT
1 TATTAATATTAAATAT-ATAAATAATAT
562955 AAATTTTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
26 4 0.09
27 33 0.77
28 6 0.14
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTAATATTAAATATATAAATAATAT
Found at i:563080 original size:23 final size:22
Alignment explanation
Indices: 563045--563111 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
563035 ATTATAATAC
*
563045 TAAAAATA-CAATATAATATTAT
1 TAAAAATATTAATATAATATT-T
563067 TAAAAATATTAATA-AATATTT
1 TAAAAATATTAATATAATATTT
*
563088 TAAATAT-TTAATAATTAATATTT
1 TAAAAATATTAAT-A-TAATATTT
563111 T
1 T
563112 GATTAAAATC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 5 0.13
21 8 0.21
22 14 0.36
23 12 0.31
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAAATATTAATATAATATTT
Found at i:567307 original size:29 final size:29
Alignment explanation
Indices: 567140--567300 Score: 166
Period size: 29 Copynumber: 5.6 Consensus size: 29
567130 GACTGTTGAC
*
567140 ATGGTGATATTTTAATAATTATTTTGAAA
1 ATGGTGATATTTTAGTAATTATTTTGAAA
*
567169 ATGGTGATATTTTGGTAATTATTTTGAAA
1 ATGGTGATATTTTAGTAATTATTTTGAAA
* * * *
567198 ATGATGCTATTTTCGTAATT-TTTTTAAA
1 ATGGTGATATTTTAGTAATTATTTTGAAA
** * * *
567226 A--GTGATAAATTCGTAATTTTTTTTAAAA
1 ATGGTGATATTTTAGTAA-TTATTTTGAAA
**
567254 AAAGTGATATTTTAGTAATTATTTTGAAA
1 ATGGTGATATTTTAGTAATTATTTTGAAA
*
567283 ATGGTGATATTTTTGTAA
1 ATGGTGATATTTTAGTAA
567301 ATTTTTTTAA
Statistics
Matches: 109, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
26 11 0.10
27 2 0.02
28 16 0.15
29 68 0.62
30 12 0.11
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (29 bp):
ATGGTGATATTTTAGTAATTATTTTGAAA
Found at i:574386 original size:13 final size:13
Alignment explanation
Indices: 574368--574393 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
574358 GACCGGTTCC
574368 AACCCGACCCGTT
1 AACCCGACCCGTT
574381 AACCCGACCCGTT
1 AACCCGACCCGTT
574394 GACTGTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.46, G:0.15, T:0.15
Consensus pattern (13 bp):
AACCCGACCCGTT
Found at i:574440 original size:29 final size:29
Alignment explanation
Indices: 574407--574474 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
574397 TGTTGATCGA
574407 GTGATATTTTAGTAATTATTTTGAAAATG
1 GTGATATTTTAGTAATTATTTTGAAAATG
*
574436 GTGATATTTTGGTAATTATTTTGAAAATG
1 GTGATATTTTAGTAATTATTTTGAAAATG
*
574465 GTGCTATTTT
1 GTGATATTTT
574475 TTTTAAAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.29, C:0.01, G:0.19, T:0.50
Consensus pattern (29 bp):
GTGATATTTTAGTAATTATTTTGAAAATG
Found at i:574527 original size:27 final size:27
Alignment explanation
Indices: 574470--574572 Score: 91
Period size: 28 Copynumber: 3.7 Consensus size: 27
574460 AAATGGTGCT
** * *
574470 ATTTTTTTTAAAAGTGATAAATTCGTAA
1 ATTTTTTAAAAAAGTGAT-ATTTTGTAA
574498 ATTTTTTAAAAAAGTGATATTTTAGT-A
1 ATTTTTTAAAAAAGTGATATTTT-GTAA
**
574525 ATTATTTTGAAAAGGGTGATATTTTGTAA
1 ATT-TTTT-AAAAAAGTGATATTTTGTAA
* *
574554 ATTTTTTTAAAAGGTGATA
1 ATTTTTTAAAAAAGTGATA
574573 AAGGTGTAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
27 17 0.27
28 28 0.44
29 18 0.29
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.47
Consensus pattern (27 bp):
ATTTTTTAAAAAAGTGATATTTTGTAA
Found at i:579440 original size:2 final size:2
Alignment explanation
Indices: 579433--579464 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
579423 ATGTCATTGA
579433 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
579465 CACAGAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:580422 original size:413 final size:410
Alignment explanation
Indices: 579689--580472 Score: 1080
Period size: 413 Copynumber: 1.9 Consensus size: 410
579679 AATGCTTATG
* * *
579689 ATAGTTTAATTTTACATAATGATTAAATATATAACTACAAAAATAATTGATTACTAAAAATTTGA
1 ATAGTATAATTTTACATAATAATTAAATATATAACTACAAAAATAATTGATTACTAAAAATCTGA
* * *
579754 ATTTTATTTTCTGATGTGATAATTTTTTATAACAATAACTATAAATTATAATTACAAAACTTATG
66 ATTTTATTTTCTGATATGATAATTTTTTATAACAATAACTATAAATTATAATTACAAAAATTATC
* * * * **
579819 AATATAACTTTTTGAAACAAAAAAAGTGGAAAAAACATTTATCACAATATATGTTATCACTATAA
131 AATATAACTTTTTAAAACAAAAAAAGTGAAAAAAACAATTAACACAATATATACTATCACTATAA
* * * *
579884 TTAAAATTTATAACTACAAGTATAATTTGTCACAAAAATGTGAATACCGTTATTTTTTGTGAAAA
196 TTAAAATTTATAACTACAAATATAATTTGTCAAAAAAACGTGAATACCATTATTTTTTGTGAAAA
* * * * *
579949 TATTTTTGTAATAATTATAAACACTTATAGTTATAAAATTTGTTATTATATAATTTTTTTGGCGC
261 TATTTTTATAATAATTATAAACACTTATAATTACAAAATTTGTCACTATATAATTTTTTT-GCGC
* *
580014 AATAAAATATAGAGGAAATTTTTTATGACAATATATTTTGTTACTATATAATATTTTTGACACTA
325 AA-AAAATATAGAGGAAAATTTTTATGACAATATATTTTGTCACTATATAATATTTTTGACACTA
580079 AAAATAGGGATAAATAATTCTA
389 AAAATAGGGATAAATAATTCTA
* **
580101 ATAGTATAATTTTTCATAATAATTAAAATATATAGGTA-AAAAAGTAATTGATTA-TAAAAAATC
1 ATAGTATAATTTTACATAATAATT-AAATATATAACTACAAAAA-TAATTGATTACT-AAAAATC
*
580164 TGAATTTTATTATT-TGATATGATAATTTTTTCTATAACAATAACTATAAATTATAATTATAAAA
63 TGAATTTTATT-TTCTGATATGATAA-TTTTT-TATAACAATAACTATAAATTATAATTACAAAA
* *
580228 ATTATCAATATAAC-TTTTAAAAC-AAAAAAGTGAAGAAAAATAATTAAGACAATATATACTATC
125 ATTATCAATATAACTTTTTAAAACAAAAAAAGTGAA-AAAAACAATTAACACAATATATACTATC
* * *
580291 ACTATAGTT-AATTTTATAACTACAAATATAATTTGTCAAAAAAACGTGAATATCATTATTTTTT
189 ACTATAATTAAAATTTATAACTACAAATATAATTTGTCAAAAAAACGTGAATACCATTATTTTTT
* *
580355 GTGACAATGTTTTCTATAATAATTACTAAA-ACTTATAATTACAAAATTTGTCACTATATAA-TT
254 GTGAAAATATTTT-TATAATAATTA-TAAACACTTATAATTACAAAATTTGTCACTATATAATTT
* * *
580418 TTTTGTGTAAAAAATATAGAGGAAAATTTTTGTGACAATATATTTTGTCACTATA
317 TTTTGCGCAAAAAATATAGAGGAAAATTTTTATGACAATATATTTTGTCACTATA
580473 ATTAAAACAT
Statistics
Matches: 326, Mismatches: 37, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
411 42 0.13
412 31 0.10
413 124 0.38
414 82 0.25
415 47 0.14
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (410 bp):
ATAGTATAATTTTACATAATAATTAAATATATAACTACAAAAATAATTGATTACTAAAAATCTGA
ATTTTATTTTCTGATATGATAATTTTTTATAACAATAACTATAAATTATAATTACAAAAATTATC
AATATAACTTTTTAAAACAAAAAAAGTGAAAAAAACAATTAACACAATATATACTATCACTATAA
TTAAAATTTATAACTACAAATATAATTTGTCAAAAAAACGTGAATACCATTATTTTTTGTGAAAA
TATTTTTATAATAATTATAAACACTTATAATTACAAAATTTGTCACTATATAATTTTTTTGCGCA
AAAAATATAGAGGAAAATTTTTATGACAATATATTTTGTCACTATATAATATTTTTGACACTAAA
AATAGGGATAAATAATTCTA
Found at i:580762 original size:15 final size:16
Alignment explanation
Indices: 580734--580763 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
580724 TTTTCTGTTA
580734 TAGTTACTAAAATTTT
1 TAGTTACTAAAATTTT
580750 TAGTTAC-AAAATTT
1 TAGTTACTAAAATTT
580764 GTCACTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
TAGTTACTAAAATTTT
Found at i:582168 original size:14 final size:14
Alignment explanation
Indices: 582124--582160 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
582114 ACTTTATTTA
* *
582124 TTTAATTTTAGTCC
1 TTTAATTTTATTGC
582138 TTTAATTTTATTGC
1 TTTAATTTTATTGC
582152 TTTAATTTT
1 TTTAATTTT
582161 CTATCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.08, G:0.05, T:0.65
Consensus pattern (14 bp):
TTTAATTTTATTGC
Found at i:584524 original size:21 final size:21
Alignment explanation
Indices: 584498--584540 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
584488 AAACGTAACT
584498 AAAAAAATAAAATTCAAGTCG
1 AAAAAAATAAAATTCAAGTCG
*
584519 AAAAAAATCAAATTCAAGTCG
1 AAAAAAATAAAATTCAAGTCG
584540 A
1 A
584541 GTTATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (21 bp):
AAAAAAATAAAATTCAAGTCG
Found at i:586619 original size:30 final size:30
Alignment explanation
Indices: 586585--586643 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
586575 GAATCAGCGG
* *
586585 TTCACACCGATTTTGTCAGTTTTCAGCCGA
1 TTCACACCGATTTTGCCAGTTCTCAGCCGA
* * *
586615 TTCACCCCGGTTTTGCCGGTTCTCAGCCG
1 TTCACACCGATTTTGCCAGTTCTCAGCCG
586644 GTTCTGTGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.14, C:0.32, G:0.20, T:0.34
Consensus pattern (30 bp):
TTCACACCGATTTTGCCAGTTCTCAGCCGA
Found at i:587407 original size:20 final size:20
Alignment explanation
Indices: 587354--587407 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
587344 TTGTTTTGTT
587354 TTATTTTAATTTAGTCACTG
1 TTATTTTAATTTAGTCACTG
587374 TTAGTTTCTAATTTAG-CTACTG
1 TTA-TTT-TAATTTAGTC-ACTG
587396 TTATTTTAATTT
1 TTATTTTAATTT
587408 TTGCATTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.29
21 7 0.23
22 15 0.48
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.57
Consensus pattern (20 bp):
TTATTTTAATTTAGTCACTG
Found at i:592943 original size:19 final size:18
Alignment explanation
Indices: 592905--593025 Score: 78
Period size: 17 Copynumber: 6.8 Consensus size: 18
592895 TATTTCTCTT
*
592905 TTTTTCA-TTTTTC-TCT
1 TTTTTCATTTTTTCTTCC
592921 TTTTTCATTTTTTCTTCCC
1 TTTTTCATTTTTTCTT-CC
**
592940 TTTTTCATTTTTTCTCATTT
1 TTTTTCATTTTTTCT--TCC
*
592960 TTTTTCTTCTTTTTCTT-C
1 TTTTTCAT-TTTTTCTTCC
*
592978 -TTCTCATTTTTTTCATT--
1 TTTTTCA-TTTTTTC-TTCC
*
592995 TTTTTCATTTTTTCAT--
1 TTTTTCATTTTTTCTTCC
593011 TTTTTCATTTTTTCT
1 TTTTTCATTTTTTCT
593026 CTTTTATTTC
Statistics
Matches: 86, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
16 22 0.26
17 23 0.27
18 9 0.10
19 17 0.20
20 7 0.08
21 8 0.09
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTCATTTTTTCTTCC
Found at i:592962 original size:12 final size:12
Alignment explanation
Indices: 592947--592990 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
592937 CCCTTTTTCA
592947 TTTTTTCTCATT
1 TTTTTTCTCATT
*
592959 TTTTTTCTTCTTT
1 TTTTTTC-TCATT
592972 TTCTTCTTCTCATT
1 TT-TT-TTCTCATT
592986 TTTTT
1 TTTTT
592991 CATTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 8 0.30
13 8 0.30
14 8 0.30
15 3 0.11
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTCTCATT
Found at i:593023 original size:8 final size:8
Alignment explanation
Indices: 592904--593024 Score: 93
Period size: 8 Copynumber: 13.9 Consensus size: 8
592894 TTATTTCTCT
592904 TTTTTTCA
1 TTTTTTCA
592912 TTTTTCTC-
1 TTTTT-TCA
592920 TTTTTTCA
1 TTTTTTCA
*
592928 TTTTTTCT
1 TTTTTTCA
592936 TCCCTTTTTCA
1 T---TTTTTCA
592947 TTTTTTCTCA
1 -TTTTT-TCA
*
592957 TTTTTTTTCT
1 --TTTTTTCA
592967 TCTTTTTC-
1 T-TTTTTCA
*
592975 TTCTTCTCA
1 TT-TTTTCA
592984 TTTTTTTCA
1 -TTTTTTCA
592993 TTTTTTTCA
1 -TTTTTTCA
593002 TTTTTTCA
1 TTTTTTCA
593010 TTTTTTCA
1 TTTTTTCA
593018 TTTTTTC
1 TTTTTTC
593025 TCTTTTATTT
Statistics
Matches: 96, Mismatches: 5, Indels: 24
0.77 0.04 0.19
Matches are distributed among these distances:
7 3 0.03
8 47 0.49
9 26 0.27
10 7 0.07
11 12 0.12
12 1 0.01
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:593037 original size:9 final size:8
Alignment explanation
Indices: 592901--593037 Score: 87
Period size: 9 Copynumber: 15.5 Consensus size: 8
592891 CTTTTATTTC
592901 TCTTTTTT
1 TCTTTTTT
*
592909 TC-ATTTT
1 TCTTTTTT
592916 TCTCTTTTT
1 TCT-TTTTT
*
592925 TCATTTTT
1 TCTTTTTT
592933 TCTTCCCTTTT
1 TCTT---TTTT
592944 TCATTTTTT
1 TC-TTTTTT
592953 CTCATTTTTTT
1 -TC--TTTTTT
592964 TCTTCTTTT
1 TCTT-TTTT
* *
592973 TCTTCTTC
1 TCTTTTTT
592981 TCATTTTTT
1 TC-TTTTTT
592990 TCATTTTTT
1 TC-TTTTTT
*
592999 TCATTTTT
1 TCTTTTTT
*
593007 TCATTTTT
1 TCTTTTTT
593015 TCATTTTTT
1 TC-TTTTTT
593024 CTCTTTTATT
1 -TCTTTT-TT
593034 TCTT
1 TCTT
593038 CTTCAAGCGA
Statistics
Matches: 105, Mismatches: 11, Indels: 25
0.74 0.08 0.18
Matches are distributed among these distances:
7 6 0.06
8 31 0.30
9 46 0.44
10 8 0.08
11 12 0.11
12 2 0.02
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.74
Consensus pattern (8 bp):
TCTTTTTT
Found at i:602791 original size:47 final size:47
Alignment explanation
Indices: 602692--602792 Score: 132
Period size: 47 Copynumber: 2.1 Consensus size: 47
602682 TGTTATCCAC
*
602692 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTCAA
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
* * *
602739 AAAAA-ATAAACCTAACCGCATGATATCTAGTTCGCATGCATTTATTCGA
1 AAAAAGA-AATCCTAACCGCATGATATCTAATTCGCATGC--TTATTCAA
602788 AAAAA
1 AAAAA
602793 CAAAAATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
46 1 0.02
47 35 0.74
49 11 0.23
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.27
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
Found at i:604123 original size:47 final size:47
Alignment explanation
Indices: 604024--604124 Score: 132
Period size: 47 Copynumber: 2.1 Consensus size: 47
604014 TGTTATCCAC
*
604024 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTCAA
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
* * *
604071 AAAAA-ATAAACCTAACCGCATGATATCTAGTTCGCATGCATTTATTCGA
1 AAAAAGA-AATCCTAACCGCATGATATCTAATTCGCATGC--TTATTCAA
604120 AAAAA
1 AAAAA
604125 CAAAAATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
46 1 0.02
47 35 0.74
49 11 0.23
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.27
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
Found at i:607350 original size:51 final size:51
Alignment explanation
Indices: 607180--607437 Score: 345
Period size: 51 Copynumber: 4.9 Consensus size: 51
607170 TCAAATGGTG
* * * * ** *
607180 TGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACG
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACT
* * *
607235 GGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACTAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACT
*
607290 TGTCCGCTCCCTATTCCTTTAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
607341 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
607392 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
607438 AAACGAGTTT
Statistics
Matches: 190, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
51 111 0.58
55 79 0.42
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (51 bp):
TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
Found at i:608014 original size:175 final size:175
Alignment explanation
Indices: 607723--608049 Score: 645
Period size: 175 Copynumber: 1.9 Consensus size: 175
607713 ATCTTCAATC
607723 TTCAACTATCATTGGGAAACCTGCAAATGCTTAAGTCATCATGCAATTATGAGTGCCATGATCCT
1 TTCAACTATCATTGGGAAACCTGCAAATGCTTAAGTCATCATGCAATTATGAGTGCCATGATCCT
607788 ATTCATGCCTAAATGTATGCAAATATGCAATTTGATGCACTTTCTTCTTCGAAGGAACTCTATCT
66 ATTCATGCCTAAATGTATGCAAATATGCAATTTGATGCACTTTCTTCTTCGAAGGAACTCTATCT
607853 CCTTTGATCTCGATGGAACTCGGCTTCATCTTGGGCACAAAACGT
131 CCTTTGATCTCGATGGAACTCGGCTTCATCTTGGGCACAAAACGT
*
607898 TTCAACTATCATTGGGAAACCTGTAAATGCTTAAGTCATCATGCAATTATGAGTGCCATGATCCT
1 TTCAACTATCATTGGGAAACCTGCAAATGCTTAAGTCATCATGCAATTATGAGTGCCATGATCCT
607963 ATTCATGCCTAAATGTATGCAAATATGCAATTTGATGCACTTTCTTCTTCGAAGGAACTCTATCT
66 ATTCATGCCTAAATGTATGCAAATATGCAATTTGATGCACTTTCTTCTTCGAAGGAACTCTATCT
608028 CCTTTGATCTCGATGGAACTCG
131 CCTTTGATCTCGATGGAACTCG
608050 ACTTGTAACA
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 151 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (175 bp):
TTCAACTATCATTGGGAAACCTGCAAATGCTTAAGTCATCATGCAATTATGAGTGCCATGATCCT
ATTCATGCCTAAATGTATGCAAATATGCAATTTGATGCACTTTCTTCTTCGAAGGAACTCTATCT
CCTTTGATCTCGATGGAACTCGGCTTCATCTTGGGCACAAAACGT
Found at i:615587 original size:17 final size:17
Alignment explanation
Indices: 615565--615604 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
615555 TTGAACCGGT
615565 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
615582 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
615599 TTGACC
1 TTGACC
615605 GTTGACCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.45, G:0.23, T:0.15
Consensus pattern (17 bp):
TTGACCCGACCCGACCG
Found at i:615604 original size:7 final size:7
Alignment explanation
Indices: 615594--615644 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
615584 GACCCGACCC
615594 GACCGTT
1 GACCGTT
615601 GACCGTT
1 GACCGTT
615608 GACCGTT
1 GACCGTT
615615 GACCGTT
1 GACCGTT
615622 GACCG-T
1 GACCGTT
615628 GACCGTT
1 GACCGTT
*
615635 GACCATT
1 GACCGTT
615642 GAC
1 GAC
615645 TTTCTTTGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
6 6 0.14
7 36 0.86
ACGTcount: A:0.18, C:0.29, G:0.27, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:624719 original size:11 final size:11
Alignment explanation
Indices: 624703--624734 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
624693 TAAAATTAGA
624703 ATTTAATATTT
1 ATTTAATATTT
624714 ATTTAATATTT
1 ATTTAATATTT
624725 -TTTAA-ATTT
1 ATTTAATATTT
624734 A
1 A
624735 ATATTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 4 0.20
10 5 0.25
11 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTAATATTT
Found at i:631978 original size:22 final size:22
Alignment explanation
Indices: 631930--631989 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
631920 TTTTGGTGCA
* *
631930 GAGGGAATCGATCCCCCCTCAT
1 GAGGGAACCGATTCCCCCTCAT
*
631952 GAGGGAACCGATTCCCCCT-TT
1 GAGGGAACCGATTCCCCCTCAT
631973 GAAGGGGAACCGATTCC
1 G-A-GGGAACCGATTCC
631990 ACCCACAGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.06
22 18 0.55
23 13 0.39
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (22 bp):
GAGGGAACCGATTCCCCCTCAT
Found at i:632416 original size:25 final size:27
Alignment explanation
Indices: 632374--632423 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
632364 AGAATTTTCC
* *
632374 AAAAAATTTTAAATTTTTGAAATTAAA
1 AAAAAATGTTAAATTTTTCAAATTAAA
632401 AAAAAATGTT-AA-TTTTCAAATTA
1 AAAAAATGTTAAATTTTTCAAATTA
632424 TTGTGTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 2 0.10
27 9 0.43
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (27 bp):
AAAAAATGTTAAATTTTTCAAATTAAA
Found at i:637271 original size:3 final size:3
Alignment explanation
Indices: 637253--637299 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
637243 TTCTTCTATG
637253 ATA AT- ATA AT- ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
637298 AT
1 AT
637300 GAAAAATAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.15
3 35 0.85
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:637280 original size:17 final size:17
Alignment explanation
Indices: 637253--637297 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
637243 TTCTTCTATG
637253 ATAAT-ATAATATAATA
1 ATAATAATAATATAATA
637269 ATAATAATAATATAATA
1 ATAATAATAATATAATA
637286 ATAATAATAATA
1 ATAATAATAATA
637298 ATGAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 5 0.18
17 23 0.82
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAATAATAATATAATA
Found at i:641361 original size:2 final size:2
Alignment explanation
Indices: 641354--641392 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
641344 TACGTTGAGA
641354 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
641393 ATTCTTATAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:645758 original size:10 final size:9
Alignment explanation
Indices: 645727--645786 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
645717 CCGATTTTCA
645727 ACCGGTTCTG
1 ACCGGTT-TG
*
645737 ATCGGTTTG
1 ACCGGTTTG
645746 ACCGGTTTCG
1 ACCGGTTT-G
*
645756 ACCGGTTCG
1 ACCGGTTTG
*
645765 AACAGGTTTG
1 -ACCGGTTTG
*
645775 ACCGGTCTG
1 ACCGGTTTG
645784 ACC
1 ACC
645787 CGACCGACCG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
9 20 0.49
10 21 0.51
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:645759 original size:29 final size:29
Alignment explanation
Indices: 645722--645780 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
645712 TTTAACCGAT
*
645722 TTTCAACCGGTTCTGATC-GGTTTGACCGG
1 TTTCAACCGGTTC-GAACAGGTTTGACCGG
*
645751 TTTCGACCGGTTCGAACAGGTTTGACCGG
1 TTTCAACCGGTTCGAACAGGTTTGACCGG
645780 T
1 T
645781 CTGACCCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (29 bp):
TTTCAACCGGTTCGAACAGGTTTGACCGG
Found at i:645761 original size:19 final size:18
Alignment explanation
Indices: 645727--645786 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
645717 CCGATTTTCA
*
645727 ACCGGTTCTGATCGGTTTG
1 ACCGGTT-TGACCGGTTTG
*
645746 ACCGGTTTCGACCGGTTCG
1 ACCGGTTT-GACCGGTTTG
* *
645765 AACAGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTTTG
645784 ACC
1 ACC
645787 CGACCGACCG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 3 0.09
19 23 0.70
20 7 0.21
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (18 bp):
ACCGGTTTGACCGGTTTG
Found at i:653003 original size:20 final size:18
Alignment explanation
Indices: 652978--653022 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
652968 GCTGTTGGAA
652978 ACCGGTTTAACGGTTTTCTG
1 ACCGGTTTAACGG-TTTC-G
*
652998 ACCGGTTTACCGGTTTCG
1 ACCGGTTTAACGGTTTCG
653016 ACCGGTT
1 ACCGGTT
653023 CGAACCGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
19 4 0.17
20 12 0.50
ACGTcount: A:0.13, C:0.24, G:0.27, T:0.36
Consensus pattern (18 bp):
ACCGGTTTAACGGTTTCG
Found at i:653081 original size:22 final size:22
Alignment explanation
Indices: 653056--653098 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
653046 CTGACCGACT
653056 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
653078 GACCCGACCGGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
653099 GTTGACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.47, G:0.26, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:653098 original size:17 final size:17
Alignment explanation
Indices: 653055--653087 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
653045 TCTGACCGAC
653055 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
653072 TGACCCGACCCGACCG
1 TGACCCGACCCGACCG
653088 GACCGTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.48, G:0.24, T:0.09
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:654939 original size:2 final size:2
Alignment explanation
Indices: 654932--654961 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
654922 TTATACATAC
654932 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
654962 CTTGGGATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:656985 original size:25 final size:25
Alignment explanation
Indices: 656955--657003 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
656945 TATCTTTTAA
656955 ATTTTATAAAAAAAAATATATATAC
1 ATTTTATAAAAAAAAATATATATAC
* **
656980 ATTTTATTAAAAAGTATATATATA
1 ATTTTATAAAAAAAAATATATATA
657004 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
ATTTTATAAAAAAAAATATATATAC
Found at i:658464 original size:30 final size:30
Alignment explanation
Indices: 658413--658484 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
658403 TTCGAGGGAT
**
658413 CTCTCGGCGTC-TTCCATGCAAAATAGGAC
1 CTCTCGGCGTCTTTGTATGCAAAATAGGAC
* * * *
658442 CTCTTGGCGTCTTTGTATGCAAACTTGGAG
1 CTCTCGGCGTCTTTGTATGCAAAATAGGAC
658472 CTCTCGGCGTCTT
1 CTCTCGGCGTCTT
658485 CAACACAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 10 0.29
30 25 0.71
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.32
Consensus pattern (30 bp):
CTCTCGGCGTCTTTGTATGCAAAATAGGAC
Found at i:659166 original size:14 final size:15
Alignment explanation
Indices: 659134--659166 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
659124 ACATCCCGAT
659134 AGGTTGGTGGTTGGC
1 AGGTTGGTGGTTGGC
659149 -GGTTGGTGGTT-GC
1 AGGTTGGTGGTTGGC
659162 AGGTT
1 AGGTT
659167 ATTAATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.12
14 15 0.88
ACGTcount: A:0.06, C:0.06, G:0.52, T:0.36
Consensus pattern (15 bp):
AGGTTGGTGGTTGGC
Found at i:662047 original size:21 final size:21
Alignment explanation
Indices: 662021--662064 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
662011 TTTACTACTA
662021 TTGATTTAATAATTTAATGAT
1 TTGATTTAATAATTTAATGAT
**
662042 TTGATTTAATGTTTTAATGAT
1 TTGATTTAATAATTTAATGAT
662063 TT
1 TT
662065 AATAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (21 bp):
TTGATTTAATAATTTAATGAT
Found at i:662160 original size:8 final size:8
Alignment explanation
Indices: 662134--662195 Score: 60
Period size: 8 Copynumber: 8.2 Consensus size: 8
662124 TTTTAACTAC
662134 TAATGATT
1 TAATGATT
**
662142 TAAT-AAA
1 TAATGATT
662149 TAATGATT
1 TAATGATT
662157 TAATGATT
1 TAATGATT
* *
662165 TGAT-A-C
1 TAATGATT
662171 TAATGATT
1 TAATGATT
662179 TAAT-ATT
1 TAATGATT
662186 TAATGATT
1 TAATGATT
662194 TA
1 TA
662196 TTAATTATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
6 3 0.07
7 14 0.33
8 25 0.60
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.47
Consensus pattern (8 bp):
TAATGATT
Found at i:662176 original size:14 final size:15
Alignment explanation
Indices: 662157--662195 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
662147 AATAATGATT
*
662157 TAATGATTTGATA-C
1 TAATGATTTAATATC
*
662171 TAATGATTTAATATT
1 TAATGATTTAATATC
662186 TAATGATTTA
1 TAATGATTTA
662196 TTAATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (15 bp):
TAATGATTTAATATC
Found at i:662177 original size:22 final size:23
Alignment explanation
Indices: 662085--662189 Score: 83
Period size: 22 Copynumber: 4.7 Consensus size: 23
662075 TAATAGTAAA
662085 ATTTAATGATTTAAT-AATAATG
1 ATTTAATGATTTAATAAATAATG
* * * ** *
662107 ATGTAATCA-TTATTAAATTTTA
1 ATTTAATGATTTAATAAATAATG
*
662129 ACTACTAATGATTTAATAAATAATG
1 A-T-TTAATGATTTAATAAATAATG
* *
662154 ATTTAATGATTTGAT-ACTAATG
1 ATTTAATGATTTAATAAATAATG
662176 ATTTAAT-ATTTAAT
1 ATTTAATGATTTAAT
662190 GATTTATTAA
Statistics
Matches: 63, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
21 10 0.16
22 25 0.40
23 12 0.19
24 6 0.10
25 10 0.16
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (23 bp):
ATTTAATGATTTAATAAATAATG
Found at i:662210 original size:52 final size:49
Alignment explanation
Indices: 662154--662270 Score: 121
Period size: 52 Copynumber: 2.3 Consensus size: 49
662144 ATAAATAATG
*
662154 ATTTAATGATTTGATACTAATGATTTAATATT-TAATGATTTATTAATTATAA
1 ATTTAATGATTTGAT--TAATGA-TTAAT-TTATAATAATTTATTAATTATAA
* *
662206 ATTTAACAATGATTT-ATTAATTATTAATTTGATAATAATTTATTAATTATTA
1 ATTT---AATGATTTGATTAATGATTAATTT-ATAATAATTTATTAATTATAA
662258 ATTTAATGATTTG
1 ATTTAATGATTTG
662271 CTATTTAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
49 8 0.14
50 2 0.04
51 5 0.09
52 31 0.55
54 2 0.04
55 8 0.14
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (49 bp):
ATTTAATGATTTGATTAATGATTAATTTATAATAATTTATTAATTATAA
Found at i:662216 original size:26 final size:26
Alignment explanation
Indices: 662187--662263 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
662177 TTTAATATTT
*
662187 AATGATTTATTAATTATAAATTTAAC
1 AATGATTTATTAATTATTAATTTAAC
* *
662213 AATGATTTATTAATTATTAATTTGAT
1 AATGATTTATTAATTATTAATTTAAC
*
662239 AATAATTTATTAATTATTAATTTAA
1 AATGATTTATTAATTATTAATTTAA
662264 TGATTTGCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (26 bp):
AATGATTTATTAATTATTAATTTAAC
Found at i:662275 original size:26 final size:24
Alignment explanation
Indices: 662183--662269 Score: 88
Period size: 26 Copynumber: 3.5 Consensus size: 24
662173 ATGATTTAAT
*
662183 ATTTAATGA-TTTATTAATTATAA
1 ATTTAATGATTTTATTAATTATTA
662206 ATTTAACAATGA-TTTATTAATTATTA
1 ATTT---AATGATTTTATTAATTATTA
* *
662232 ATTTGATAATAATTTATTAATTATTA
1 ATTTAATGAT--TTTATTAATTATTA
662258 ATTTAATGATTT
1 ATTTAATGATTT
662270 GCTATTTAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
23 7 0.13
24 2 0.04
26 44 0.83
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (24 bp):
ATTTAATGATTTTATTAATTATTA
Found at i:662321 original size:24 final size:23
Alignment explanation
Indices: 662294--662412 Score: 80
Period size: 24 Copynumber: 5.0 Consensus size: 23
662284 TAATAATGAT
* *
662294 ATGATTTAGTAATGATTACTACTA
1 ATGATTTA-TAATAATTACTAATA
*
662318 ATGAAATTATAATAATTACTAATA
1 ATG-ATTTATAATAATTACTAATA
* * *
662342 ATGA--TCTAATAATTATTACTA
1 ATGATTTATAATAATTACTAATA
** *
662363 ATGATTTAATAATTGTTTAATAATA
1 ATGATTT-ATAA-TAATTACTAATA
662388 ATGATTATATTTAATAATTACTAAT
1 ATGATT-TA--TAATAATTACTAAT
662413 GATTTGATGT
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
21 18 0.25
23 2 0.03
24 22 0.30
25 19 0.26
26 9 0.12
27 3 0.04
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (23 bp):
ATGATTTATAATAATTACTAATA
Done.