Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008281.1 Hibiscus syriacus cultivar Beakdansim tig00110943_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: 2054746
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 10
Found at i:582001 original size:69 final size:67
Alignment explanation
Indices: 581885--582123 Score: 214
Period size: 69 Copynumber: 3.5 Consensus size: 67
581875 TACCCAGAAC
* * * * * *
581885 AATTATGGTTAGGTGC-TCTCGTGC-AATCACTCTAATCTTTAGGGGCTCTCATGAGAGTCACCT
1 AATTATGATTAGGTGCTTC-CGTACGAGTCACTCTAATCCTCA-GGGCTCCCATGAGAGTCACCT
581948 GAAAT
64 -AAAT
* *
581953 AATTATGATTAGGTGCTTCCGTACGAGCCACTCTAATCCTCCAGGGCTCCCGTGAGAGTCACCCT
1 AATTATGATTAGGTGCTTCCGTACGAGTCACTCTAATCCT-CAGGGCTCCCATGAGAGTCA-CCT
*
582018 TAAT
64 AAAT
* * ** * *
582022 AATTATGATTAGGTG-TTCCCGTACAATTCACTCTAATCCTTTGGATCTCCCATGTGAGTCACCC
1 AATTATGATTAGGTGCTT-CCGTACGAGTCACTCTAATCCTCAGG-GCTCCCATGAGAGTCA-CC
*
582086 AAAAT
63 TAAAT
* * *
582091 AGTTATGATTAGGTGCTCCCTTACGAGTCACTC
1 AATTATGATTAGGTGCTTCCGTACGAGTCACTC
582124 ACATACTTCG
Statistics
Matches: 140, Mismatches: 24, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
68 23 0.16
69 112 0.80
70 5 0.04
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (67 bp):
AATTATGATTAGGTGCTTCCGTACGAGTCACTCTAATCCTCAGGGCTCCCATGAGAGTCACCTAA
AT
Found at i:582116 original size:138 final size:137
Alignment explanation
Indices: 581861--582123 Score: 330
Period size: 138 Copynumber: 1.9 Consensus size: 137
581851 ACGATTAGGT
* * * * *
581861 GCTCCCGTGCGAGTTACCCAGAACAATTATGGTTAGGTGCTCTCGTGCAATCACTCTAATCTTTA
1 GCTCCCGTGAGAGTCACCCAGAACAATTATGATTAGGTGCTCCCGTACAATCACTCTAATCTTTA
* * ** *
581926 GGGGCTCTCATGAGAGTCACCTGAAATAATTATGATTAGGTGCTTCCGTACGAGCCACTCTAATC
66 GGAGCTCCCATGAGAGTCACCCAAAATAATTATGATTAGGTGCTCCCGTACGAGCCACTCTAATC
581991 CTCCAGG
131 CTCCAGG
** * *
581998 GCTCCCGTGAGAGTCACCCTTAATAATTATGATTAGGTGTTCCCGTACAATTCACTCTAATCCTT
1 GCTCCCGTGAGAGTCACCCAGAACAATTATGATTAGGTGCTCCCGTACAA-TCACTCTAAT-CTT
* * * * *
582063 T-GGATCTCCCATGTGAGTCACCCAAAATAGTTATGATTAGGTGCTCCCTTACGAGTCACTC
64 TAGGAGCTCCCATGAGAGTCACCCAAAATAATTATGATTAGGTGCTCCCGTACGAGCCACTC
582124 ACATACTTCG
Statistics
Matches: 105, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
137 41 0.39
138 60 0.57
139 4 0.04
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (137 bp):
GCTCCCGTGAGAGTCACCCAGAACAATTATGATTAGGTGCTCCCGTACAATCACTCTAATCTTTA
GGAGCTCCCATGAGAGTCACCCAAAATAATTATGATTAGGTGCTCCCGTACGAGCCACTCTAATC
CTCCAGG
Found at i:582167 original size:20 final size:19
Alignment explanation
Indices: 582137--582199 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
582127 TACTTCGTAG
* *
582137 AATCTGGTTTCCAATCCCAA
1 AATCAGGTTTCCAA-ACCAA
* *
582157 AGTCAGGTTTCCAAAGCAA
1 AATCAGGTTTCCAAACCAA
582176 AATCAGGTTTCC-AACCTAA
1 AATCAGGTTTCCAAACC-AA
582195 AATCA
1 AATCA
582200 ATTTTCTAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 3 0.08
19 21 0.58
20 12 0.33
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (19 bp):
AATCAGGTTTCCAAACCAA
Found at i:582275 original size:76 final size:77
Alignment explanation
Indices: 582149--582291 Score: 200
Period size: 76 Copynumber: 1.9 Consensus size: 77
582139 TCTGGTTTCC
* * * *
582149 AATCCCAAAGTCAGGTTTCCAAAGCAAAATCAGGTTTCCAACCTAAAATCAA-TTTTCTAAGCTA
1 AATCCCAAACTCAAGTTTCCAAAGCAAAATCAGGTTTCCAAACTAAAATCAAGTTTTCTAACCTA
582213 AAACCTATTTTT
66 AAACCTATTTTT
** *
582225 AATCCCAAACTCAAGTTTCCAACTCAAAATCAGGTTT-CAAACTAAAAATCAAGTTTTTTAACCT
1 AATCCCAAACTCAAGTTTCCAAAGCAAAATCAGGTTTCCAAACT-AAAATCAAGTTTTCTAACCT
582289 AAA
65 AAA
582292 TTTATTTTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
75 5 0.09
76 41 0.71
77 12 0.21
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (77 bp):
AATCCCAAACTCAAGTTTCCAAAGCAAAATCAGGTTTCCAAACTAAAATCAAGTTTTCTAACCTA
AAACCTATTTTT
Found at i:591580 original size:28 final size:28
Alignment explanation
Indices: 591540--591596 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
591530 GAACAAAGAA
591540 AGAACACTCAAGAATAATAAAATTGAGC
1 AGAACACTCAAGAATAATAAAATTGAGC
*
591568 AGAACACTCAAGAATAATACAATTGAGC
1 AGAACACTCAAGAATAATAAAATTGAGC
591596 A
1 A
591597 CAATAAGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.53, C:0.16, G:0.14, T:0.18
Consensus pattern (28 bp):
AGAACACTCAAGAATAATAAAATTGAGC
Found at i:591941 original size:19 final size:19
Alignment explanation
Indices: 591917--591965 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
591907 GCTTAATGCA
591917 TCGGTACACTAGGGGTGGG
1 TCGGTACACTAGGGGTGGG
591936 TCGGTACACTAGGGGTGGG
1 TCGGTACACTAGGGGTGGG
591955 TCGGTACACTA
1 TCGGTACACTA
591966 ATTACATTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.18, C:0.18, G:0.41, T:0.22
Consensus pattern (19 bp):
TCGGTACACTAGGGGTGGG
Found at i:592044 original size:65 final size:65
Alignment explanation
Indices: 591970--592106 Score: 168
Period size: 65 Copynumber: 2.1 Consensus size: 65
591960 ACACTAATTA
* * * * * *
591970 CATTCGATGTTTCAAAAGAGCCAGGGGTGCATTGATGCATG-GTCTATGCATCAGTACATAAAAT
1 CATTCGATGTTTCAAAAGAGCCAAGAGTACATCGATGCATGACT-TATGCATCAGTACACAAAAT
592034 G
65 G
* ** *
592035 CATTCGATGTTTCAAAATATTCAAGAGTACATCGATGCATGACTTGTGCATCAGTACACAAAATG
1 CATTCGATGTTTCAAAAGAGCCAAGAGTACATCGATGCATGACTTATGCATCAGTACACAAAATG
592100 CATTCGA
1 CATTCGA
592107 AATGGGTGTG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
65 60 0.98
66 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (65 bp):
CATTCGATGTTTCAAAAGAGCCAAGAGTACATCGATGCATGACTTATGCATCAGTACACAAAATG
Found at i:593242 original size:27 final size:27
Alignment explanation
Indices: 593188--593243 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
593178 CCGTCATCAC
*
593188 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCATAACAT
*
593215 CACTTTGAACTTGAAAGTCCA-ACACAT
1 CACTTTGAACTTGAAACTCCATA-ACAT
593242 CA
1 CA
593244 AGATCTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.27
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCATAACAT
Found at i:608702 original size:20 final size:20
Alignment explanation
Indices: 608647--608702 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
608637 GGAATTTCCT
* * *
608647 TTAAAAAAGTAAAAAGAATA
1 TTAAAAGAGAAAAAAAAATA
*
608667 ATAAAAGA-AAAGAAAAAATA
1 TTAAAAGAGAAA-AAAAAATA
608687 TTAAAAGAGAAAAAAA
1 TTAAAAGAGAAAAAAA
608703 GAAAAAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (20 bp):
TTAAAAGAGAAAAAAAAATA
Found at i:610031 original size:23 final size:23
Alignment explanation
Indices: 610004--610058 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
609994 AGAATTTGTT
610004 CCGAAGGACCGCGTAGAAATGGC
1 CCGAAGGACCGCGTAGAAATGGC
*
610027 CCGAAGGACCGCGTAGAAATGTC
1 CCGAAGGACCGCGTAGAAATGGC
*
610050 CTGAAGGAC
1 CCGAAGGAC
610059 AACATATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.25, G:0.33, T:0.11
Consensus pattern (23 bp):
CCGAAGGACCGCGTAGAAATGGC
Found at i:610101 original size:21 final size:21
Alignment explanation
Indices: 610026--610103 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
610016 GTAGAAATGG
* *
610026 CCCGAAGGACCGCGTAGAAATGT
1 CCCGAAGGACCACATAG--ATGT
* * *
610049 CCTGAAGGACAACATATATGT
1 CCCGAAGGACCACATAGATGT
610070 CCCGAAGGACCACATAGATGT
1 CCCGAAGGACCACATAGATGT
*
610091 CCCGAATGACCAC
1 CCCGAAGGACCAC
610104 TCCTTAAGGA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
21 34 0.74
23 12 0.26
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.15
Consensus pattern (21 bp):
CCCGAAGGACCACATAGATGT
Found at i:612413 original size:5 final size:5
Alignment explanation
Indices: 612391--612469 Score: 89
Period size: 5 Copynumber: 16.6 Consensus size: 5
612381 TGGACCTAAA
*
612391 ATAAT AATAAT A-AAT ATAAT ATAA- AAAAT ATAAT A-AA- A-AAT ATAA-
1 ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
612436 ATAAT ATTAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATA
612470 TAATGTAATG
Statistics
Matches: 65, Mismatches: 2, Indels: 13
0.81 0.03 0.16
Matches are distributed among these distances:
3 3 0.05
4 14 0.22
5 38 0.58
6 10 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:612439 original size:39 final size:41
Alignment explanation
Indices: 612388--612467 Score: 112
Period size: 39 Copynumber: 2.0 Consensus size: 41
612378 CTTTGGACCT
612388 AAAATAATAATAATA-AATATAATATAA-AAAATATAATAA
1 AAAATAATAATAATATAATATAATATAATAAAATATAATAA
*
612427 AAAAT-ATAAATAATATTAATATAATATAATATAATATAATA
1 AAAATAAT-AATAATA-TAATATAATATAATAAAATATAATA
612468 TATAATGTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
38 2 0.06
39 12 0.33
41 12 0.33
42 10 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (41 bp):
AAAATAATAATAATATAATATAATATAATAAAATATAATAA
Found at i:612478 original size:12 final size:12
Alignment explanation
Indices: 612391--612501 Score: 72
Period size: 12 Copynumber: 9.2 Consensus size: 12
612381 TGGACCTAAA
612391 ATAATA-ATAAT
1 ATAATATATAAT
612402 A-AATATA-ATAT
1 ATAATATATA-AT
* *
612413 AAAAAATATAAT
1 ATAATATATAAT
* *
612425 AAAAAATATAA-
1 ATAATATATAAT
612436 ATAATAT-TAAT
1 ATAATATATAAT
612447 ATAATATAATATAAT
1 AT-A-AT-ATATAAT
612462 ATAATATATAAT
1 ATAATATATAAT
* *
612474 GTAATGAAAT-AT
1 ATAAT-ATATAAT
612486 ATAACTATATAAT
1 ATAA-TATATAAT
612499 ATA
1 ATA
612502 TACTATGTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
10 8 0.10
11 12 0.15
12 38 0.47
13 14 0.17
14 3 0.04
15 6 0.07
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:612485 original size:32 final size:31
Alignment explanation
Indices: 612394--612516 Score: 94
Period size: 32 Copynumber: 3.9 Consensus size: 31
612384 ACCTAAAATA
*
612394 ATAATAATAA-ATATAATATAAAAAATATAAT
1 ATAAT-ATAATATATAATATAATAAATATAAT
* * *
612425 AAAAAAT-ATAAATAATATTAATATAATATAAT
1 ATAATATAATATATAATA-TAATA-AATATAAT
*
612457 ATAATATAATATATAATGTAATGAAATAT-AT
1 ATAATATAATATATAATATAAT-AAATATAAT
* *
612488 A-ACTATATAATATATACTAT-GTAAATATA
1 ATA--ATATAATATATAATATAATAAATATA
612517 TAACTATATA
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
29 1 0.01
30 16 0.22
31 11 0.15
32 36 0.49
33 9 0.12
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (31 bp):
ATAATATAATATATAATATAATAAATATAAT
Found at i:612496 original size:8 final size:8
Alignment explanation
Indices: 612483--612526 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
612473 TGTAATGAAA
612483 TATATAAC
1 TATATAAC
612491 TATATAA-
1 TATATAAC
612498 TATAT-AC
1 TATATAAC
* *
612505 TATGTAAA
1 TATATAAC
612513 TATATAAC
1 TATATAAC
612521 TATATA
1 TATATA
612527 GTATATATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
6 1 0.03
7 9 0.30
8 20 0.67
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (8 bp):
TATATAAC
Found at i:612499 original size:15 final size:15
Alignment explanation
Indices: 612481--612533 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
612471 AATGTAATGA
612481 AATATATAACTATAT
1 AATATATAACTATAT
*
612496 AATATAT-ACTATGT
1 AATATATAACTATAT
612510 AAATATATAACTATAT
1 -AATATATAACTATAT
*
612526 AGTATATA
1 AATATATA
612534 TTATGTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 6 0.18
15 21 0.64
16 6 0.18
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (15 bp):
AATATATAACTATAT
Found at i:612514 original size:30 final size:30
Alignment explanation
Indices: 612480--612539 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
612470 TAATGTAATG
612480 AAATATATAACTATATAATATATACTATGT
1 AAATATATAACTATATAATATATACTATGT
* *
612510 AAATATATAACTATATAGTATATATTATGT
1 AAATATATAACTATATAATATATACTATGT
612540 TTTCAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (30 bp):
AAATATATAACTATATAATATATACTATGT
Found at i:612515 original size:13 final size:14
Alignment explanation
Indices: 612445--612533 Score: 63
Period size: 15 Copynumber: 5.9 Consensus size: 14
612435 AATAATATTA
612445 ATATAATATAATA-T
1 ATATAATAT-ATACT
*
612459 AATATAATATATAAT
1 -ATATAATATATACT
*
612474 GTAATGAAATATATAACT
1 AT-AT--AATATAT-ACT
612492 ATATAATATATACT
1 ATATAATATATACT
*
612506 ATGTAAATATATAACT
1 ATAT-AATATAT-ACT
*
612522 ATATAGTATATA
1 ATATAATATATA
612534 TTATGTTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 15
0.74 0.07 0.18
Matches are distributed among these distances:
14 11 0.18
15 32 0.52
16 6 0.10
17 9 0.15
18 3 0.05
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.39
Consensus pattern (14 bp):
ATATAATATATACT
Found at i:612518 original size:32 final size:30
Alignment explanation
Indices: 612460--612539 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 30
612450 ATATAATATA
612460 ATATAATATATA-ATGTAATGAAATATATAACT
1 ATATAATATATATATGT-A-G-AATATATAACT
612492 ATATAATATATACTATGTA-AATATATAACT
1 ATATAATATATA-TATGTAGAATATATAACT
*
612522 ATATAGTATATATTATGT
1 ATATAATATATA-TATGT
612540 TTTCAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
30 27 0.61
32 12 0.27
33 1 0.02
34 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (30 bp):
ATATAATATATATATGTAGAATATATAACT
Found at i:612570 original size:2 final size:2
Alignment explanation
Indices: 612565--612596 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
612555 TAAAAAACAA
612565 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
612597 TTTTTTTTTT
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:612750 original size:72 final size:73
Alignment explanation
Indices: 612627--612893 Score: 321
Period size: 72 Copynumber: 3.7 Consensus size: 73
612617 TTTCAAAACA
* * * *
612627 TTTTAAAAACCATATATTATAAGTTTTCAAAAATGTTTTCAAAACTATATATTATATACATTTTT
1 TTTTCAAAACAATATATTATACGTTTTCAAAAATGTTTTCAAAACTATATATTATATACGTTTTT
612692 TAAAATCG
66 TAAAATCG
* *
612700 TTTTCAAAACAATATATTATACGTTTT-AAAAATGTTTTCAAAACCATATA-T-TATACGTTTTC
1 TTTTCAAAACAATATATTATACGTTTTCAAAAATGTTTTCAAAACTATATATTATATACGTTTTT
*
612762 AAAAAT-G
66 TAAAATCG
* * *
612769 TTTTCAAAACTATATATTATATACGTTTTCAGAAATGTTTTTAAAACTATATATTATATACGTTT
1 TTTTCAAAACAATATA-T-TATACGTTTTCAAAAATGTTTTCAAAACTATATATTATATACGTTT
*
612834 TTTTAAA-CG
64 TTTAAAATCG
* * *
612843 TTTTTAAAA-ATATATATTATATGTTTTCAAAAATGTATTTTCAAAAGTATA
1 TTTTCAAAACA-ATATATTATACGTTTTCAAAAATG--TTTTCAAAACTATA
612894 CAATATATGT
Statistics
Matches: 165, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
69 16 0.10
70 15 0.09
71 11 0.07
72 58 0.35
73 26 0.16
74 39 0.24
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.45
Consensus pattern (73 bp):
TTTTCAAAACAATATATTATACGTTTTCAAAAATGTTTTCAAAACTATATATTATATACGTTTTT
TAAAATCG
Found at i:612906 original size:72 final size:71
Alignment explanation
Indices: 612616--613010 Score: 315
Period size: 72 Copynumber: 5.5 Consensus size: 71
612606 TCAAAATATG
* * * *
612616 TTTTCAAAACATTTT-AAAAACCATATATTATAAGTTTTCAAAAATGTTTTCAAAACTATATATT
1 TTTTTAAAACGTTTTCAAAAA-TATATATTATATGTTTTCAAAAATGTTTTCAAAACTATATA-T
*
612680 ATATACAT
64 ATATACGT
* *
612688 TTTTTAAAATCGTTTTCAAAACA-ATATATTATACGTTTT-AAAAATGTTTTCAAAACCATATAT
1 TTTTTAAAA-CGTTTTCAAAA-ATATATATTATATGTTTTCAAAAATGTTTTCAAAACTATATAT
612751 -TATACGT
64 ATATACGT
** * * * *
612758 TTTCAAAAATGTTTTCAAAACTATATATTATATACGTTTTCAGAAATGTTTTTAAAACTATATAT
1 TTTTTAAAACGTTTTCAAAAATATATATTATAT--GTTTTCAAAAATGTTTTCAAAACTATATA-
612823 TATATACGT
63 TATATACGT
* * * *
612832 TTTTTTAAACGTTTTTAAAAATATATATTATATGTTTTCAAAAATGTATTTTCAAAAGTATACA-
1 TTTTTAAAACGTTTTCAAAAATATATATTATATGTTTTCAAAAATG--TTTTCAAAACTATATAT
*
612896 ATATATG-
64 ATATACGT
*** * *
612903 TTTTTAAAGACGTATTTTCAAACCCATACTA-TATA--TTTTCAAAAATCGATTTTTAAAAACCA
1 TTTTTAAA-ACG--TTTTCAAAAATATA-TATTATATGTTTTCAAAAAT-G--TTTTCAAAACTA
* *
612965 TATAT-TATATGC
59 TATATATATACGT
**
612977 TTTAAAAAACGTTTTCTAAAAACTATATATTATA
1 TTTTTAAAACGTTTTC-AAAAA-TATATATTATA
613011 AATGTAACAC
Statistics
Matches: 262, Mismatches: 40, Indels: 41
0.76 0.12 0.12
Matches are distributed among these distances:
69 20 0.08
70 13 0.05
71 18 0.07
72 87 0.33
73 50 0.19
74 71 0.27
75 3 0.01
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.43
Consensus pattern (71 bp):
TTTTTAAAACGTTTTCAAAAATATATATTATATGTTTTCAAAAATGTTTTCAAAACTATATATAT
ATACGT
Found at i:612997 original size:37 final size:35
Alignment explanation
Indices: 612611--613010 Score: 302
Period size: 37 Copynumber: 11.1 Consensus size: 35
612601 TTTTTTCAAA
* * *
612611 ATATGTTTTC-AAAACATTTTAAAAACCATATATT
1 ATATGTTTTCAAAAACGTTTTTAAAACTATATATT
* * *
612645 ATAAGTTTTCAAAAATGTTTTCAAAACTATATATT
1 ATATGTTTTCAAAAACGTTTTTAAAACTATATATT
* * * * *
612680 ATATACATTTTTTAAAATCGTTTTCAAAACAATATATT
1 ATAT---GTTTTCAAAAACGTTTTTAAAACTATATATT
* * * *
612718 ATACGTTTT-AAAAATGTTTTCAAAACCATATATT
1 ATATGTTTTCAAAAACGTTTTTAAAACTATATATT
* * *
612752 ATACGTTTTCAAAAATGTTTTCAAAACTATATATT
1 ATATGTTTTCAAAAACGTTTTTAAAACTATATATT
* *
612787 ATATACGTTTTCAGAAATGTTTTTAAAACTATATATT
1 ATAT--GTTTTCAAAAACGTTTTTAAAACTATATATT
*** *
612824 ATATACGTTTTTTTAAACGTTTTTAAAAATATATATT
1 ATAT--GTTTTCAAAAACGTTTTTAAAACTATATATT
* * * *
612861 ATATGTTTTCAAAAATGTATTTTCAAAAGTATACAAT
1 ATATGTTTTCAAAAACGT-TTTT-AAAACTATATATT
* * * ** *
612898 ATATGTTTTTAAAGACGTATTTTCAAAC-CCATACT
1 ATATGTTTTCAAAAACGT-TTTTAAAACTATATATT
* *
612933 ATATATTTTCAAAAATCGATTTTTAAAAACCATATATT
1 ATATGTTTTCAAAAA-CG-TTTTT-AAAACTATATATT
* *
612971 ATATGCTTTAAAAAACGTTTTCTAAAAACTATATATT
1 ATATGTTTTCAAAAACGTTTT-T-AAAACTATATATT
613008 ATA
1 ATA
613011 AATGTAACAC
Statistics
Matches: 300, Mismatches: 52, Indels: 25
0.80 0.14 0.07
Matches are distributed among these distances:
34 40 0.13
35 79 0.26
36 17 0.06
37 119 0.40
38 45 0.15
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (35 bp):
ATATGTTTTCAAAAACGTTTTTAAAACTATATATT
Found at i:613656 original size:26 final size:25
Alignment explanation
Indices: 613622--613804 Score: 117
Period size: 26 Copynumber: 7.8 Consensus size: 25
613612 CTTTCATGCC
*
613622 TTAATGCATCCTTTCATGCATTTCGT
1 TTAAGGCATCCTTTCATGCATTTC-T
*
613648 TTACGGCATCCTTTCATGC----C-
1 TTAAGGCATCCTTTCATGCATTTCT
* *
613668 TTAATGCATCTTTTCATGCATTTCAT
1 TTAAGGCATCCTTTCATGCATTTC-T
* *
613694 TTATGGCATCATTTCATGC----C-
1 TTAAGGCATCCTTTCATGCATTTCT
* *
613714 TTAATGCATCATTTCATGCATTTCAT
1 TTAAGGCATCCTTTCATGCATTTC-T
* *
613740 TTATGGCATCCTTTCAT-C----CC
1 TTAAGGCATCCTTTCATGCATTTCT
*
613760 TTAATGCATCCTTTCATGCATTTCAT
1 TTAAGGCATCCTTTCATGCATTTC-T
*
613786 TTATGGCATCCTTTCATGC
1 TTAAGGCATCCTTTCATGC
613805 CTTAATTCAT
Statistics
Matches: 120, Mismatches: 19, Indels: 36
0.69 0.11 0.21
Matches are distributed among these distances:
20 48 0.40
21 2 0.02
22 2 0.02
24 2 0.02
25 2 0.02
26 64 0.53
ACGTcount: A:0.20, C:0.25, G:0.11, T:0.44
Consensus pattern (25 bp):
TTAAGGCATCCTTTCATGCATTTCT
Found at i:613661 original size:46 final size:46
Alignment explanation
Indices: 613595--613917 Score: 493
Period size: 46 Copynumber: 7.0 Consensus size: 46
613585 TTATTTGTTA
* *
613595 ATTTCATTTATGGCACCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* * *
613641 ATTTCGTTTACGGCATCCTTTCATGCCTTAATGCATCTTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
*
613687 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
613733 ATTTCATTTATGGCATCCTTTCATCCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
613779 ATTTCATTTATGGCATCCTTTCATGCCTTAATTCATCATTTCATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
613825 ATTTCATTTATGGAATCCTTTCATGCCTTAATGCATCATTTCATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* * * *
613871 ATTTTAATTTATGGAATCCTTTTATGCCTTAATGCATCCTTTCATGC
1 A-TTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
613918 CTTAATGCAT
Statistics
Matches: 255, Mismatches: 21, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
46 214 0.84
47 41 0.16
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:623280 original size:29 final size:29
Alignment explanation
Indices: 623242--623301 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
623232 AAAAATGTTT
*
623242 AAATTAAGAAAAGAAAAAGTTAAATAAAAA
1 AAATTAAGAAAAGAAAAA-TAAAATAAAAA
* *
623272 AAATT-AGAAGAGACAAATAAAATAAAAA
1 AAATTAAGAAAAGAAAAATAAAATAAAAA
623300 AA
1 AA
623302 TGAAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 10 0.37
30 5 0.19
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (29 bp):
AAATTAAGAAAAGAAAAATAAAATAAAAA
Found at i:623531 original size:18 final size:18
Alignment explanation
Indices: 623505--623544 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
623495 AAAATATGTT
* *
623505 AAAATTAAAAGAGAAATA
1 AAAAATAAAAAAGAAATA
*
623523 AAAAATAAAAAATAAATA
1 AAAAATAAAAAAGAAATA
623541 AAAA
1 AAAA
623545 TTTTAAGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAAAAAAGAAATA
Found at i:624531 original size:15 final size:16
Alignment explanation
Indices: 624511--624578 Score: 65
Period size: 15 Copynumber: 4.5 Consensus size: 16
624501 TTGGACCTGA
624511 ATAATAATAATA-AAT
1 ATAATAATAATATAAT
*
624526 ATAAT-ATACA-AAAAT
1 ATAATAATA-ATATAAT
*
624541 ATAATAAAAATATAA-
1 ATAATAATAATATAAT
*
624556 ATAATATTAATATAAT
1 ATAATAATAATATAAT
624572 AT-ATAAT
1 ATAATAAT
624579 GTAATGAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
14 4 0.09
15 32 0.74
16 7 0.16
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATAATAATATAAT
Found at i:624733 original size:35 final size:35
Alignment explanation
Indices: 624689--625058 Score: 261
Period size: 37 Copynumber: 10.1 Consensus size: 35
624679 GTGTGTTTTT
* *
624689 AAAACGTTTTCAAAACCATATATTATACGTTTTCA
1 AAAATGTTTTCAAAACTATATATTATACGTTTTCA
* *
624724 AAAATGTTTTTAAAACTATATATTATATACGTTTTTTA
1 AAAATGTTTTCAAAACTATATA-T-TATACG-TTTTCA
** * * *
624762 AAAGCGTTTTCAAAACCATATATTATATGTTTTTA
1 AAAATGTTTTCAAAACTATATATTATACGTTTTCA
624797 AAAATGTTTTCAAAACTATATATTATATACGTTTTCA
1 AAAATGTTTTCAAAACTATATA-T-TATACGTTTTCA
* *
624834 GAAATGTTTTCAAAACTATATATTATATACGTTTTTTTA
1 AAAATGTTTTCAAAACTATATA-T-TATACG--TTTTCA
624873 AAACAT-TTTT-AAAACTATATATATTATACGTTTTCA
1 AAA-ATGTTTTCAAAAC--TATATATTATACGTTTTCA
* * **
624909 AAAATGTGTTT-TAAACTATATAATATTTGTTCTT-A
1 AAAATGT-TTTCAAAACTATATATTATACGTT-TTCA
* *
624944 AAAACGTATTTTCAAAACCATACTA-TATA--TTTTCA
1 AAAA--TGTTTTCAAAACTATA-TATTATACGTTTTCA
* * *
624979 AACACCGAT-TTTTAAAAAGCCATATATTATATGTTTTCA
1 AA-A---ATGTTTTCAAAA-CTATATATTATACGTTTTCA
* * *
625018 GAAATATTTTCTAAAAACTATATATTATATGTTTTCA
1 AAAATGTTTTC--AAAACTATATATTATACGTTTTCA
625055 AAAA
1 AAAA
625059 CTATATTATA
Statistics
Matches: 275, Mismatches: 31, Indels: 56
0.76 0.09 0.15
Matches are distributed among these distances:
34 2 0.01
35 70 0.25
36 36 0.13
37 98 0.36
38 41 0.15
39 20 0.07
40 8 0.03
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (35 bp):
AAAATGTTTTCAAAACTATATATTATACGTTTTCA
Found at i:624770 original size:73 final size:72
Alignment explanation
Indices: 624684--624906 Score: 297
Period size: 73 Copynumber: 3.0 Consensus size: 72
624674 TGTGTGTGTG
*
624684 TTTTTAAAACGTTTTCAAAACCATATATTATACGTTTTCAAAAATGTTTTTAAAACTATATATTA
1 TTTTTAAAACGTTTTCAAAACCATATATTATACGTTTTTAAAAATGTTTTTAAAACTATATATTA
624749 TATACGT
66 TATACGT
* *
624756 TTTTTAAAAGCGTTTTCAAAACCATATATTATATGTTTTTAAAAATGTTTTCAAAACTATATATT
1 TTTTTAAAA-CGTTTTCAAAACCATATATTATACGTTTTTAAAAATGTTTTTAAAACTATATATT
624821 ATATACG-
65 ATATACGT
* * * * **
624828 TTTTCAGAAATGTTTTCAAAACTATATATTATATACGTTTTTTTAAAACATTTTTAAAACTATAT
1 TTTTTA-AAACGTTTTCAAAACCATATA-T-TATACG-TTTTTAAAAATGTTTTTAAAACTATAT
624893 A-TATTATACGT
62 ATTA-TATACGT
624904 TTT
1 TTT
624907 CAAAAATGTG
Statistics
Matches: 133, Mismatches: 11, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
72 30 0.23
73 63 0.47
74 7 0.05
75 30 0.23
76 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (72 bp):
TTTTTAAAACGTTTTCAAAACCATATATTATACGTTTTTAAAAATGTTTTTAAAACTATATATTA
TATACGT
Found at i:624831 original size:37 final size:37
Alignment explanation
Indices: 624683--624930 Score: 280
Period size: 37 Copynumber: 6.8 Consensus size: 37
624673 ATGTGTGTGT
* *
624683 GTTTTT-AAAACGTTTTCAAAACCATATA-T-TATAC
1 GTTTTTAAAAATGTTTTCAAAACTATATATTATATAC
* *
624717 GTTTTCAAAAATGTTTTTAAAACTATATATTATATAC
1 GTTTTTAAAAATGTTTTCAAAACTATATATTATATAC
** *
624754 GTTTTTTAAAAGCGTTTTCAAAACCATATATTATAT--
1 G-TTTTTAAAAATGTTTTCAAAACTATATATTATATAC
624790 GTTTTTAAAAATGTTTTCAAAACTATATATTATATAC
1 GTTTTTAAAAATGTTTTCAAAACTATATATTATATAC
* *
624827 GTTTTCAGAAATGTTTTCAAAACTATATATTATATAC
1 GTTTTTAAAAATGTTTTCAAAACTATATATTATATAC
624864 GTTTTTTTAAAACAT-TTTT-AAAACTATATA-TATTATAC
1 G--TTTTTAAAA-ATGTTTTCAAAACTATATATTA-TATAC
* *
624902 GTTTTCAAAAATGTGTTT-TAAACTATATA
1 GTTTTTAAAAATGT-TTTCAAAACTATATA
624931 ATATTTGTTC
Statistics
Matches: 184, Mismatches: 18, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
34 5 0.03
35 52 0.28
36 11 0.06
37 57 0.31
38 46 0.25
39 11 0.06
40 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (37 bp):
GTTTTTAAAAATGTTTTCAAAACTATATATTATATAC
Found at i:624870 original size:110 final size:109
Alignment explanation
Indices: 624682--625058 Score: 337
Period size: 110 Copynumber: 3.4 Consensus size: 109
624672 TATGTGTGTG
* * *
624682 TGTTTTT-AAAACGTTTTCAAAACCATATATTATACGTTTTCAAAAATGTTTTTAAAACTATATA
1 TGTTTTTAAAAATGTTTTCAAAACTATATATTATACGTTTTCAAAAATGTTTTCAAAACTATATA
*
624746 TTATATACG-TTTTTTAAAAGCGTTTTCAAAAC-CATATATTATA
66 TTATATACGTTTTTTTAAAA-CATTTTCAAAACACATATATTATA
*
624789 TGTTTTTAAAAATGTTTTCAAAACTATATATTATATACGTTTTCAGAAATGTTTTCAAAACTATA
1 TGTTTTTAAAAATGTTTTCAAAACTATATA-T-TATACGTTTTCAAAAATGTTTTCAAAACTATA
* *
624854 TATTATATACGTTTTTTTAAAACATTTTTAAAACTATATATATTATA
64 TATTATATACGTTTTTTTAAAACATTTTCAAAAC-ACATATATTATA
* * * * ** *
624901 CGTTTTCAAAAATGTGTTT-TAAACTATATAATATTTGTTCTT-AAAAACGTATTTTCAAAAC--
1 TGTTTTTAAAAATGT-TTTCAAAACTATATATTATACGTT-TTCAAAAA--TGTTTTCAAAACTA
* * * *
624962 CATACTATATA----TTTTCAAACACCGATTTTTAAAA-AGCCATATATTATA
62 TATATTATATACGTTTTTTTAAA-A-C-ATTTTCAAAACA--CATATATTATA
* * * *
625010 TGTTTTCAGAAATATTTTCTAAAAACTATATATTATATGTTTTCAAAAA
1 TGTTTTTAAAAATGTTTTC--AAAACTATATATTATACGTTTTCAAAAA
625059 CTATATTATA
Statistics
Matches: 226, Mismatches: 25, Indels: 34
0.79 0.09 0.12
Matches are distributed among these distances:
106 7 0.03
107 9 0.04
108 24 0.11
109 33 0.15
110 72 0.32
111 34 0.15
112 44 0.19
113 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (109 bp):
TGTTTTTAAAAATGTTTTCAAAACTATATATTATACGTTTTCAAAAATGTTTTCAAAACTATATA
TTATATACGTTTTTTTAAAACATTTTCAAAACACATATATTATA
Found at i:624971 original size:75 final size:75
Alignment explanation
Indices: 624689--624973 Score: 257
Period size: 73 Copynumber: 3.9 Consensus size: 75
624679 GTGTGTTTTT
* * * ** *
624689 AAAACGTTTTCAAAACCATATAT-TATACGTTT-TCAAAAATGTTTTTAAAACTATATAT-TATA
1 AAAATGTTTTCAAAACTATATATATATACGTTTCTTAAAAACATTTTCAAAACTATATATATATA
*
624751 TACGTTTTTTA
66 TACG-TTTTCA
** * * **
624762 AAAGCGTTTTCAAAACCATATAT-TATATGTTT-TTAAAAATGTTTTCAAAACTATATAT-TATA
1 AAAATGTTTTCAAAACTATATATATATACGTTTCTTAAAAACATTTTCAAAACTATATATATATA
624824 TACGTTTTCA
66 TACGTTTTCA
* * * *
624834 GAAATGTTTTCAAAACTATATATTATATACGTTTTTTTAAAACATTTTTAAAACTATATATAT-T
1 AAAATGTTTTCAAAACTATATA-TATATACGTTTCTTAAAAACATTTTCAAAACTATATATATAT
624898 ATACGTTTTCA
65 ATACGTTTTCA
* ** *
624909 AAAATGTGTTT-TAAACTATATA-ATATTTG-TTCTTAAAAACGTATTTTCAAAACCATACTATA
1 AAAATGT-TTTCAAAACTATATATATATACGTTTCTTAAAAAC--ATTTTCAAAACTATA-TATA
624971 TAT
62 TAT
624974 TTTCAAACAC
Statistics
Matches: 181, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
72 32 0.18
73 68 0.38
74 21 0.12
75 55 0.30
76 5 0.03
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.44
Consensus pattern (75 bp):
AAAATGTTTTCAAAACTATATATATATACGTTTCTTAAAAACATTTTCAAAACTATATATATATA
TACGTTTTCA
Found at i:625066 original size:22 final size:24
Alignment explanation
Indices: 625024--625069 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
625014 TTCAGAAATA
625024 TTTTCTAAAAACTATATATTATATG
1 TTTTCTAAAAAC-ATATATTATATG
625049 TTTTC-AAAAAC-TATATTATAT
1 TTTTCTAAAAACATATATTATAT
625070 TATTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
24 6 0.29
25 5 0.24
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTTCTAAAAACATATATTATATG
Found at i:649371 original size:19 final size:19
Alignment explanation
Indices: 649347--649390 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
649337 TATGGTACTT
*
649347 AGAAAGATTTTGCCAATTC
1 AGAAAGATTTTGCCAACTC
649366 AGAAAGATTTTGCCAACTC
1 AGAAAGATTTTGCCAACTC
649385 AGAAAG
1 AGAAAG
649391 TCTTTTCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (19 bp):
AGAAAGATTTTGCCAACTC
Found at i:649507 original size:14 final size:14
Alignment explanation
Indices: 649488--649549 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 14
649478 TCGTCTGAAT
649488 AATGAAAAATAAAA
1 AATGAAAAATAAAA
649502 AATGAAAAGA-AAAA
1 AATGAAAA-ATAAAA
*
649516 AA-G-AAAATGAAA
1 AATGAAAAATAAAA
*
649528 AA--AAAAAGAAAA
1 AATGAAAAATAAAA
649540 AATGGAAAAA
1 AAT-GAAAAA
649550 GAGAAAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
11 1 0.03
12 17 0.44
13 1 0.03
14 14 0.36
15 6 0.15
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (14 bp):
AATGAAAAATAAAA
Found at i:649515 original size:19 final size:18
Alignment explanation
Indices: 649491--649566 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 18
649481 TCTGAATAAT
649491 GAAAAATAAAAAATGAAAA
1 GAAAAA-AAAAAATGAAAA
649510 GAAAAAAAGAAAATGAAAA
1 GAAAAAAA-AAAATGAAAA
*
649529 AAAAAAGAAAAAATGGAAAAA
1 GAAAAA-AAAAAAT-G-AAAA
* *
649550 GAGAAAAAGAAA-GAAAA
1 GAAAAAAAAAAATGAAAA
649567 AAGAATAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.08
18 3 0.06
19 26 0.53
20 8 0.16
21 8 0.16
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (18 bp):
GAAAAAAAAAAATGAAAA
Found at i:649517 original size:8 final size:8
Alignment explanation
Indices: 649506--649568 Score: 56
Period size: 8 Copynumber: 7.4 Consensus size: 8
649496 ATAAAAAATG
649506 AAAAGAAA
1 AAAAGAAA
649514 AAAAGAAA
1 AAAAGAAA
649522 ATGAAA-AAA
1 A--AAAGAAA
649531 AAAAGAAA
1 AAAAGAAA
*
649539 AAATGGAAA
1 AAA-AGAAA
*
649548 AAGAGAAAA
1 AAAAG-AAA
649557 AGAAAGAAA
1 A-AAAGAAA
649566 AAA
1 AAA
649569 GAATAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
7 3 0.07
8 18 0.40
9 18 0.40
10 6 0.13
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (8 bp):
AAAAGAAA
Found at i:649548 original size:34 final size:34
Alignment explanation
Indices: 649510--649576 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
649500 AAAATGAAAA
*
649510 GAAAAAAAGAAAATGAAAAAAAAAAGAAAAAATG
1 GAAAAAAAGAAAAAGAAAAAAAAAAGAAAAAATG
* * *
649544 GAAAAAGAGAAAAAGAAAGAAAAAAGAATAAAT
1 GAAAAAAAGAAAAAGAAAAAAAAAAGAAAAAAT
649577 AAAAAGGGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (34 bp):
GAAAAAAAGAAAAAGAAAAAAAAAAGAAAAAATG
Found at i:651006 original size:134 final size:134
Alignment explanation
Indices: 650778--651343 Score: 575
Period size: 134 Copynumber: 4.2 Consensus size: 134
650768 ACAAACCGAA
* *
650778 CTCGATTTAATCTTCCCT-AAGTAATAGTGGAATGAATCAACA-TCCCCATATCTAATTTT-CCT
1 CTCGATTCAATCTTCCCTGAAG-AATAGTGGAATGAATCAA-AGTCCCCAGATCTAATTTTCCCT
** ** * * **
650840 CAAGAAGAAGCATAATAGATTCTTTTTCTTTCAAGATTTGATGTTCTTTGAGTAACAGTGAAACA
64 CAAGAAGAAGCGGAATAGA-TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGAAACA
* *
650905 AAT-TAAA
128 AGTCT-AC
* * * * *
650912 CTCGATTCAATCTTCCCTGAAGAACAGTGAAATGAATTAAAGTCCCTAGATCTAATTTTCCCTTA
1 CTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAAAGTCCCCAGATCTAATTTTCCCTCA
* * * ** *
650977 AGAAGAAGCGGAATATATCCCTATCTTTCAATATTTGATATTCATTGAGTAATAGTGAAACAAGT
66 AGAAGAAGCGGAATAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGAAACAAGT
*
651042 CTTC
131 CTAC
* * * * *
651046 CACGATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACGTCCCGAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAAAGTCCCCAGATCTAATTTTCCCTCA
* * * * * * *
651111 AGAAGAAGC-GAACCATATACATCTCTTTTCAGGATTTGATATTCCCTGAGTAAAAGTGGAACAA
66 AGAAGAAGCGGAA-TAGATCCCTCTC-TTTCAAGATTTGATATTCCCTGAGTAACAGTGAAACAA
*
651175 GTCTGC
129 GTCTAC
* * * * * * * * *
651181 CTCGATTCAATCTTTCATTAAGAACAGTGGAATAAATCAACGTCCCCATATATGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAAAGTCCCCAGATCTAATTTTCCCTCA
* * * *
651246 AGAAGAAGTGAAATAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAATAACAGTGGAACAAGT
66 AGAAGAAGCGGAATAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGAAACAAGT
651311 CTAC
131 CTAC
* *
651315 CTTGATTCAATCTTCACTGAAGAATAGTG
1 CTCGATTCAATCTTCCCTGAAGAATAGTG
651344 TAATTAGTCA
Statistics
Matches: 360, Mismatches: 65, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
133 4 0.01
134 223 0.62
135 131 0.36
136 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAAAGTCCCCAGATCTAATTTTCCCTCA
AGAAGAAGCGGAATAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGAAACAAGT
CTAC
Found at i:651275 original size:269 final size:267
Alignment explanation
Indices: 650780--651343 Score: 630
Period size: 269 Copynumber: 2.1 Consensus size: 267
650770 AAACCGAACT
* *
650780 CGATTTAATCTTCCCTAAGTAATAGTGGAATGAATCAACATCCCCATATCTAATTTTCCTCAAGA
1 CGATTCAATCTTCCCTAAG-AATAGTGGAATGAATCAACATCCCCAGATCTAATTTTCCTCAAGA
* * * * * ** *
650845 AGAAGCATAATAGATTCTTTTTCTTTCAAGATTTGATGTTCTTTGAGTAACAGTGAAACAAATTA
65 AGAAGCATAACAGATACTCTCTCTTTCAAGATTTGATATTCCCTGAGTAAAAGTGAAACAAATTA
* * * * *
650910 AACTCGATTCAATCTTCCCTGAAGAACAGTGAAATGAATTAAAGTCCCTAGATCTAATTTTCCCT
130 AACTCGATTCAATCTTCCATGAAGAACAGTGAAATAAATCAAAGTCCCCAGATATAATTTTCCCT
* * * * * * *
650975 TAAGAAGAAGCGGAATATATCCCTATCTTTCAATATTTGATATTCATTGAGTAATAGTGAAACAA
195 CAAGAAGAAGCGAAATAGATCCCTATCTTTCAAGATTTGATATTCACTGAATAACAGTGAAACAA
*
651040 GTCTTCCA
260 GTCTACCA
* * *
651048 CGATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACGTCCCGAGATCTGATTTTCCCTCAAG
1 CGATTCAATCTTCCCT-AAGAATAGTGGAATGAATCAACATCCCCAGATCTAATTTT-CCTCAAG
* * * * *
651113 AAGAAGCGA-ACCATATACATCTCT-TTTCAGGATTTGATATTCCCTGAGTAAAAGTGGAACAAG
64 AAGAAGC-ATAACAGATAC-TCTCTCTTTCAAGATTTGATATTCCCTGAGTAAAAGTGAAACAAA
** * * * * * *
651176 TCT-GCCTCGATTCAATCTTTCATTAAGAACAGTGGAATAAATCAACGTCCCCATATATGATTTT
127 T-TAAACTCGATTCAATCTTCCATGAAGAACAGTGAAATAAATCAAAGTCCCCAGATATAATTTT
* * * *
651240 CCCTCAAGAAGAAGTGAAATAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAATAACAGTGGA
191 CCCTCAAGAAGAAGCGAAATAGATCCCTATCTTTCAAGATTTGATATTCACTGAATAACAGTGAA
*
651305 ACAAGTCTACCT
256 ACAAGTCTACCA
* *
651317 TGATTCAATCTTCACTGAAGAATAGTG
1 CGATTCAATCTTCCCT-AAGAATAGTG
651344 TAATTAGTCA
Statistics
Matches: 244, Mismatches: 47, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
268 48 0.20
269 191 0.78
270 5 0.02
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (267 bp):
CGATTCAATCTTCCCTAAGAATAGTGGAATGAATCAACATCCCCAGATCTAATTTTCCTCAAGAA
GAAGCATAACAGATACTCTCTCTTTCAAGATTTGATATTCCCTGAGTAAAAGTGAAACAAATTAA
ACTCGATTCAATCTTCCATGAAGAACAGTGAAATAAATCAAAGTCCCCAGATATAATTTTCCCTC
AAGAAGAAGCGAAATAGATCCCTATCTTTCAAGATTTGATATTCACTGAATAACAGTGAAACAAG
TCTACCA
Found at i:653617 original size:12 final size:11
Alignment explanation
Indices: 653584--653641 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
653574 ATATATTAAT
*
653584 AATAATAGTAA
1 AATAATAATAA
653595 AATAATAATAA
1 AATAATAATAA
*
653606 AGATAATGATAAA
1 A-ATAATAAT-AA
*
653619 AATAATAGTAA
1 AATAATAATAA
653630 AA-AATAATAA
1 AATAATAATAA
653640 AA
1 AA
653642 CTATAGATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 9 0.22
11 15 0.38
12 13 0.32
13 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (11 bp):
AATAATAATAA
Found at i:659270 original size:40 final size:41
Alignment explanation
Indices: 659191--659395 Score: 202
Period size: 42 Copynumber: 5.0 Consensus size: 41
659181 GGTGATTCAT
*
659191 CGAGAATCGAAAGTGCTATGCTTCCCTTCGTTTACTTTAGC
1 CGAGAATCGAAAGTGCTATGCTTCCCTTCGTTTACTTTAGA
*
659232 CGAGAATCGAAAGTGCTATGCTT-CCTTCATTATA-TTTAGA
1 CGAGAATCGAAAGTGCTATGCTTCCCTTCGTT-TACTTTAGA
* *
659272 CGAGAATTGAAAGTG-TGATGTTTCCCTTCGTTCTACTTTAGA
1 CGAGAATCGAAAGTGCT-ATGCTTCCCTTCGTT-TACTTTAGA
* * * * *
659314 CGAGAATCAAAAGTG-TGATTCTTCCTTTTGTTTAGCTTTTGA
1 CGAGAATCGAAAGTGCT-ATGCTTCCCTTCGTTTA-CTTTAGA
* * ** *
659356 AGAGAATCAAAAGTTTTATGCTTCCCTTTGTTCTACTTTA
1 CGAGAATCGAAAGTGCTATGCTTCCCTTCGTT-TACTTTA
659396 TTCACCTTTA
Statistics
Matches: 139, Mismatches: 18, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
39 1 0.01
40 31 0.22
41 36 0.26
42 68 0.49
43 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (41 bp):
CGAGAATCGAAAGTGCTATGCTTCCCTTCGTTTACTTTAGA
Found at i:659394 original size:84 final size:82
Alignment explanation
Indices: 659192--659395 Score: 225
Period size: 84 Copynumber: 2.5 Consensus size: 82
659182 GTGATTCATC
* * *
659192 GAGAATCGAAAGTGCTATGCTTCCCTTCGTT-TACTTTAGCCGAGAATCGAAAGTGCTATGCTTC
1 GAGAATCGAAAGTGTTATGCTTCCCTTCGTTCTACTTTAGACGAGAATCAAAAGTGCTATGCTTC
*
659256 CTTCATTATATTTAGAC
66 CTTCATTATATTTAGAA
* * * *
659273 GAGAATTGAAAGTGTGATGTTTCCCTTCGTTCTACTTTAGACGAGAATCAAAAGTG-TGATTCTT
1 GAGAATCGAAAGTGTTATGCTTCCCTTCGTTCTACTTTAGACGAGAATCAAAAGTGCT-ATGCTT
* * *
659337 CCTT-TTGTTTAGCTTTTGAA
65 CCTTCAT-TATA--TTTAGAA
* * *
659357 GAGAATCAAAAGTTTTATGCTTCCCTTTGTTCTACTTTA
1 GAGAATCGAAAGTGTTATGCTTCCCTTCGTTCTACTTTA
659396 TTCACCTTTA
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
81 29 0.29
82 34 0.34
84 38 0.38
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (82 bp):
GAGAATCGAAAGTGTTATGCTTCCCTTCGTTCTACTTTAGACGAGAATCAAAAGTGCTATGCTTC
CTTCATTATATTTAGAA
Found at i:661524 original size:13 final size:14
Alignment explanation
Indices: 661506--661535 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
661496 ATTAGTTTTT
661506 TAAAATTTTA-TCA
1 TAAAATTTTATTCA
661519 TAAAATTTTATTCA
1 TAAAATTTTATTCA
661533 TAA
1 TAA
661536 TTTTTTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAAATTTTATTCA
Found at i:661652 original size:12 final size:12
Alignment explanation
Indices: 661635--661668 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
661625 ATCTTATTCC
661635 AAATAAAATTTA
1 AAATAAAATTTA
*
661647 AAATAAAAATTA
1 AAATAAAATTTA
*
661659 AATTAAAATT
1 AAATAAAATT
661669 ATTAAATTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATAAAATTTA
Found at i:661823 original size:11 final size:11
Alignment explanation
Indices: 661807--661833 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
661797 CCAATATCAT
661807 ATGAAAATATA
1 ATGAAAATATA
661818 ATGAAAATATA
1 ATGAAAATATA
661829 ATGAA
1 ATGAA
661834 GAGAAAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (11 bp):
ATGAAAATATA
Found at i:664495 original size:12 final size:12
Alignment explanation
Indices: 664478--664502 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
664468 ATTAGATAAA
664478 TTTGGGTTTGAG
1 TTTGGGTTTGAG
664490 TTTGGGTTTGAG
1 TTTGGGTTTGAG
664502 T
1 T
664503 CAGACCCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.40, T:0.52
Consensus pattern (12 bp):
TTTGGGTTTGAG
Found at i:665346 original size:20 final size:22
Alignment explanation
Indices: 665306--665356 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
665296 ACTCAAGGGA
665306 GTATCGATA-CTATGGTGAA-G
1 GTATCGATACCTATGGTGAAGG
665326 GTATCGATACCCTA-GGT-AAGG
1 GTATCGATA-CCTATGGTGAAGG
*
665347 GTATCTATAC
1 GTATCGATAC
665357 TAAGCTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 12 0.44
21 12 0.44
22 3 0.11
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (22 bp):
GTATCGATACCTATGGTGAAGG
Found at i:670344 original size:37 final size:37
Alignment explanation
Indices: 670294--670375 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
670284 GAATTTGCTA
* *
670294 AACCTGTAGGACTGATACTATTATATGTAACACCCTT
1 AACCTGCAGGACTGATACTATTAAATGTAACACCCTT
670331 AACCTGCAGGACTGATACTATTAAATGTAACACCCTT
1 AACCTGCAGGACTGATACTATTAAATGTAACACCCTT
670368 AACCTGCA
1 AACCTGCA
670376 TTCGTACCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.28
Consensus pattern (37 bp):
AACCTGCAGGACTGATACTATTAAATGTAACACCCTT
Found at i:672125 original size:146 final size:147
Alignment explanation
Indices: 671861--672154 Score: 554
Period size: 146 Copynumber: 2.0 Consensus size: 147
671851 ATATATTTCC
671861 AAATCACCTTCAAATAATACTTTAATATCAGAGTCGTCATTCTATTAATTACTACTCAAGTACTT
1 AAATCACCTTCAAATAATACTTTAATATCAGAGTCGTCATTCTATTAATTACTACTCAAGTACTT
671926 TAATTATTCATATTTATTCTTTAACCTTTAAGCCTACCATTTTAGCATTTTATATTTTGGTTCCC
66 TAATTATTCATATTTATTCTTTAACCTTTAAGCCTACCATTTTAGCATTTTATATTTTGGTTCCC
671991 AAA-CTAACAAACTAGT
131 AAACCTAACAAACTAGT
*
672007 AAATCACCTTCAAATAATACTTTAATATCAGAGTCGTCATTCTATTATTTACTACTCAAGTACTT
1 AAATCACCTTCAAATAATACTTTAATATCAGAGTCGTCATTCTATTAATTACTACTCAAGTACTT
*
672072 TAATTATTCATATTTATTCTTTAACCTTTAAGCTTACCATTTTAGCATTTTATATTTTGGTTCCC
66 TAATTATTCATATTTATTCTTTAACCTTTAAGCCTACCATTTTAGCATTTTATATTTTGGTTCCC
672137 AAACTCTAACAAACTAGT
131 AAAC-CTAACAAACTAGT
672155 CCAAAATCAA
Statistics
Matches: 144, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
146 131 0.91
148 13 0.09
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (147 bp):
AAATCACCTTCAAATAATACTTTAATATCAGAGTCGTCATTCTATTAATTACTACTCAAGTACTT
TAATTATTCATATTTATTCTTTAACCTTTAAGCCTACCATTTTAGCATTTTATATTTTGGTTCCC
AAACCTAACAAACTAGT
Found at i:672180 original size:19 final size:19
Alignment explanation
Indices: 672158--672195 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
672148 AACTAGTCCA
672158 AAATCAACATTTCAATATT
1 AAATCAACATTTCAATATT
* *
672177 AAATCAATATTTTAATATT
1 AAATCAACATTTCAATATT
672196 CAATTCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATCAACATTTCAATATT
Found at i:678652 original size:18 final size:18
Alignment explanation
Indices: 678631--678665 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
678621 GATTATCAAT
*
678631 GGGAATAGGATTACTGGC
1 GGGAATAAGATTACTGGC
678649 GGGAATAAGATTACTGG
1 GGGAATAAGATTACTGG
678666 GAATGTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.37, T:0.23
Consensus pattern (18 bp):
GGGAATAAGATTACTGGC
Found at i:680100 original size:15 final size:15
Alignment explanation
Indices: 680080--680122 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
680070 GCTTGACCCG
680080 ACTGAGTCAACCCAT
1 ACTGAGTCAACCCAT
*
680095 ACTGAGTCAACTC--
1 ACTGAGTCAACCCAT
*
680108 ACTGGGTCAACCCAT
1 ACTGAGTCAACCCAT
680123 TGACTTTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 11 0.48
15 12 0.52
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (15 bp):
ACTGAGTCAACCCAT
Found at i:680139 original size:23 final size:23
Alignment explanation
Indices: 680108--680156 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
680098 GAGTCAACTC
*
680108 ACTGGGTCAACCCATTGACTTTG
1 ACTGAGTCAACCCATTGACTTTG
* *
680131 ACTGAGTCAACCCGTTGATTTTG
1 ACTGAGTCAACCCATTGACTTTG
680154 ACT
1 ACT
680157 TTGACCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (23 bp):
ACTGAGTCAACCCATTGACTTTG
Found at i:682385 original size:24 final size:24
Alignment explanation
Indices: 682358--682461 Score: 100
Period size: 24 Copynumber: 4.3 Consensus size: 24
682348 TTCGATTTGA
*
682358 ATTCTGTTATGATACCTGACATGG
1 ATTCTGTTATGATATCTGACATGG
* * *
682382 ATTCTGTTCTGATATCTGACCTAG
1 ATTCTGTTATGATATCTGACATGG
** * * * *
682406 ATTAAGTTCTGATAACTGACCTGC
1 ATTCTGTTATGATATCTGACATGG
*
682430 ATTCTGTTATGATATCTGACATGA
1 ATTCTGTTATGATATCTGACATGG
*
682454 ATTATGTT
1 ATTCTGTT
682462 TTGGTTTTTG
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.40
Consensus pattern (24 bp):
ATTCTGTTATGATATCTGACATGG
Found at i:684708 original size:13 final size:14
Alignment explanation
Indices: 684656--684713 Score: 66
Period size: 13 Copynumber: 4.1 Consensus size: 14
684646 CCGCTTGACC
*
684656 CGACTGACTCAACT
1 CGACTGAGTCAACT
684670 CG-CGTTGAGTCAACT
1 CGAC--TGAGTCAACT
684685 CGACTGAGTCAACT
1 CGACTGAGTCAACT
*
684699 C-ACTGGGTCAACT
1 CGACTGAGTCAACT
684712 CG
1 CG
684714 TTGACTTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 13 0.34
14 13 0.34
15 11 0.29
16 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (14 bp):
CGACTGAGTCAACT
Found at i:685446 original size:17 final size:17
Alignment explanation
Indices: 685420--685460 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
685410 AAGGTGAAAC
685420 AAATAAATAAAAT-ATCA
1 AAATAAATAAAATCAT-A
*
685437 AAATATATAAAATCATA
1 AAATAAATAAAATCATA
685454 AAATAAA
1 AAATAAA
685461 ACAGACTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAATAAAATCATA
Found at i:693681 original size:18 final size:17
Alignment explanation
Indices: 693648--693681 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
693638 GAACATATAA
693648 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
693665 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
693682 AAATAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:694662 original size:34 final size:34
Alignment explanation
Indices: 694624--694745 Score: 123
Period size: 34 Copynumber: 3.7 Consensus size: 34
694614 TTCATCCTAC
694624 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
694658 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
694693 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
694722 TATGATTTAAACTCCTAAAGATAG
1 TAGGATTCAAACTCCTAAAAATAG
694746 AATCCACAAG
Statistics
Matches: 71, Mismatches: 7, Indels: 20
0.72 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.06
30 13 0.18
34 36 0.51
35 4 0.06
37 8 0.11
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:695166 original size:2 final size:2
Alignment explanation
Indices: 695161--695185 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
695151 TTAGTGTTAT
695161 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 T
695186 TTCCTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:698564 original size:23 final size:21
Alignment explanation
Indices: 698524--698566 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
698514 GAAACAAGAA
698524 CAAAAAAAAAAGAGCAAAAAT
1 CAAAAAAAAAAGAGCAAAAAT
*
698545 CAAAAAGAAAAAGGGACAAAAA
1 CAAAAA-AAAAAGAG-CAAAAA
698567 GCACATGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.02
Consensus pattern (21 bp):
CAAAAAAAAAAGAGCAAAAAT
Found at i:699217 original size:22 final size:22
Alignment explanation
Indices: 699192--699240 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
699182 CCATCAATCT
* *
699192 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
699214 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
699236 TTTGA
1 TTTGA
699241 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:699677 original size:18 final size:18
Alignment explanation
Indices: 699654--699689 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
699644 TCAACATCAA
* *
699654 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
699672 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
699690 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:700210 original size:71 final size:73
Alignment explanation
Indices: 700127--700438 Score: 251
Period size: 72 Copynumber: 4.4 Consensus size: 73
700117 GTTTTTCTTA
* * * * * *
700127 AAACAAGA-TTTGTCTCGCTTGAGACCATTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACCAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
700189 TTTCCCTTG
65 TTTCCCTTG
* *
700198 AAACAAATTTTGTCTCTCTTGAGA-CAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACCAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
700262 TTCCCTTG
66 TTCCCTTG
* * * * *
700270 AAATAAATTTTGTCTCTCTTGAGA-CAGTTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACCAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
700326 TTTTCTTTG
65 TTTCCCTTG
* ** * * * * *
700335 AAACAAATTTTGTCTCCCTTGAGA-CAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACCAGTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
700399 TTTCTCTTG
65 TTTCCCTTG
*
700408 AAAC-AATTTTCGTCTATCTTGAGA-CAGTTTC
1 AAACAAATTTT-GTCTCTCTTGAGACCAGTTTC
700439 CCTTGTAACA
Statistics
Matches: 199, Mismatches: 28, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
64 2 0.01
65 47 0.24
66 5 0.03
70 10 0.05
71 23 0.12
72 77 0.39
73 33 0.17
74 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACCAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:700212 original size:36 final size:36
Alignment explanation
Indices: 700169--700450 Score: 321
Period size: 36 Copynumber: 8.0 Consensus size: 36
700159 ACTAGAAGAG
700169 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
700205 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
700241 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
700277 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
700313 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* ** * *
700342 TTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
700379 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
700414 TTTTCGTCTATCTTGAGACAGTTTCCCTTGTAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
700451 ATCTTTGAAT
Statistics
Matches: 206, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 141 0.68
37 36 0.17
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:700349 original size:65 final size:65
Alignment explanation
Indices: 700267--700571 Score: 202
Period size: 65 Copynumber: 4.5 Consensus size: 65
700257 ACAGTTTCCC
* * *
700267 TTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
1 TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCT
** * ** *
700332 TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC-AA------AATCT-TTGA-AT
700397 A-G-TTTCT
57 ATGTTTTCT
** * * * *
700404 CTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGTAACAAAATCTTTGAATTTATTTC
1 -TTGAAACAAATTTT-GTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTT
*
700468 CC
64 CT
* * * * ** * * *
700470 CTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTC
1 TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATATGTTTT
*
700535 CC
64 CT
* * *
700537 TTAAAACATAATTTTGTTTCCCTTGAGACCGTTTC
1 TTGAAACA-AATTTTGTCTCCCTTGAGACAGTTTC
700572 TCATGAACAA
Statistics
Matches: 189, Mismatches: 34, Indels: 31
0.74 0.13 0.12
Matches are distributed among these distances:
64 1 0.01
65 68 0.36
66 15 0.08
67 29 0.15
68 23 0.12
72 15 0.08
73 36 0.19
74 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (65 bp):
TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTCT
Found at i:700410 original size:102 final size:102
Alignment explanation
Indices: 700225--700413 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 102
700215 CTTGAGACAG
*
700225 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
700290 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* * ** * *
700327 TTTCT-TTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
*
700391 TGAGACAGTTTCTCTTGAAACAA
65 TGAGACAGTTTCCCTTGAAACAA
700414 TTTTCGTCTA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 33 0.42
102 45 0.58
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:700442 original size:138 final size:137
Alignment explanation
Indices: 700189--700513 Score: 463
Period size: 138 Copynumber: 2.4 Consensus size: 137
700179 CTTGAGACAG
*
700189 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
*
700254 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
*
700319 GAATATG
131 GAATATA
* * * * * * *
700326 TTTTCTTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * * *
700391 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGTAACAAAATCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAATAT
*
700455 TTGAATTTA
129 TTGAATATA
* * *
700464 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
700514 CAAAATCTTC
Statistics
Matches: 164, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
137 51 0.31
138 113 0.69
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
GAATATA
Found at i:700513 original size:174 final size:168
Alignment explanation
Indices: 700169--700479 Score: 398
Period size: 174 Copynumber: 1.8 Consensus size: 168
700159 ACTAGAAGAG
*
700169 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
**
700234 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTT
66 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTG-CAATCTT---A-AGTT
* * * *
700299 TCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAACAAA
126 TCCCCTAAAACAAAATATTTGAACATGTTCTCTTTGAAACAAA
** * *
700342 TTTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
700407 GAAACAATTTTCGTCTATCTTGAGACAGTTTCCCTTGTAACA-AAATCTTTG-AAT-TT-A-TTT
65 GAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ATAAAT-TTTGCAATCTTAAGTTT
700467 CCCCTAAAACAAA
127 CCCCTAAAACAAA
700480 TTTTGTCTCC
Statistics
Matches: 124, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
167 14 0.11
168 1 0.01
173 31 0.25
174 67 0.54
175 6 0.05
176 5 0.04
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (168 bp):
TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGCAATCTTAAGTTTCCCC
TAAAACAAAATATTTGAACATGTTCTCTTTGAAACAAA
Found at i:700532 original size:67 final size:65
Alignment explanation
Indices: 700408--700565 Score: 192
Period size: 67 Copynumber: 2.4 Consensus size: 65
700398 GTTTCTCTTG
** * * **
700408 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGTAACAAAATCTTTGAATTTATTTCCCCT
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTACCCTTGAAACAAAATCTTCAAATTTATTTCCCCT
700472 A
65 A
* *
700473 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
700538 TA
64 TA
*
700540 AAACATAATTTTGTTTCCCTTGAGAC
1 AAACA-AATTTTGTCTCCCTTGAGAC
700566 CGTTTCTCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 25 0.31
66 7 0.09
67 29 0.36
68 19 0.24
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.38
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:701354 original size:105 final size:102
Alignment explanation
Indices: 701184--701526 Score: 419
Period size: 98 Copynumber: 3.3 Consensus size: 102
701174 GCCATCTGCG
*
701184 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACGACGGAGGATAT--TGG-ACTCGAGACAACACAAGTTCAACTTCACAACGAA
*
701249 GGGACGGCTGGTTGTCAAC-AACAATTTCCCAGTTTCAGGGCCA
63 GGGACGGCTGGTTGTCAACAAACAATTT--C-G-TTCAGAGCCA
* * * * *
701292 ATTTCAACTTCAC-AGCGGAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGG
1 ATTTCAACTTCACGA-CGGAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
**
701356 GACGGCTGACTGTCAACAAACAATTTCG----GAGCCA
65 GACGGCTGGTTGTCAACAAACAATTTCGTTCAGAGCCA
* * *
701390 ATCTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACGACGGAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
*
701455 ACGGCTGGTTGTCAACAAATAATTTTTCGGTTCCAGAGCCA
66 ACGGCTGGTTGTCAACAAACAA--TTTC-GTT-CAGAGCCA
701496 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACGACGGAGGATATTGGACT
701527 TGGAACAATG
Statistics
Matches: 202, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
98 80 0.40
99 1 0.00
100 4 0.02
101 1 0.00
103 1 0.00
104 1 0.00
105 46 0.23
106 45 0.22
107 1 0.00
108 22 0.11
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (102 bp):
ATTTCAACTTCACGACGGAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAAACAATTTCGTTCAGAGCCA
Found at i:702118 original size:34 final size:34
Alignment explanation
Indices: 702075--702199 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
702065 TTCGTCCTAC
702075 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
702109 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
702144 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
702173 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
702200 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:702617 original size:2 final size:2
Alignment explanation
Indices: 702612--702689 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
702602 TTAGTGTTAT
702612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
702654 TA TA T- 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 TA TA TA T
702690 TTCCTATTTT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:702774 original size:20 final size:20
Alignment explanation
Indices: 702749--702786 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
702739 ATTATTATTA
702749 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
702769 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
702787 TTTACTCATT
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:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:702818 original size:16 final size:18
Alignment explanation
Indices: 702797--702831 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
702787 TTTACTCATT
702797 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
702813 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
702831 T
1 T
702832 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:707262 original size:24 final size:24
Alignment explanation
Indices: 707235--707299 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
707225 TCCGATTTGA
*
707235 ATTCTGTTATGATATCTAACATGG
1 ATTCTGTTCTGATATCTAACATGG
*
707259 ATTCTGTTCTGATATCTAACCTGG
1 ATTCTGTTCTGATATCTAACATGG
* *
707283 TTTCTGTTCTAATATCT
1 ATTCTGTTCTGATATCT
707300 GAACTGAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (24 bp):
ATTCTGTTCTGATATCTAACATGG
Found at i:707635 original size:155 final size:155
Alignment explanation
Indices: 707346--707650 Score: 486
Period size: 155 Copynumber: 2.0 Consensus size: 155
707336 TACGAACGAA
707346 AAATGTTTTATTTGGAGGGTAATGTTGAAGGAAGAATACTTGTAGGCTCCTCGACTTTGTGCTCA
1 AAATGTTTTATTTGGAGGGTAATGTTGAAGGAAGAATACTTGTAGGCTCCTCGACTTTGTGCTCA
* * *
707411 GGGCCTTACTCGATATGAAGGTGGGTGTATGGTTCTGGGAACCTACACATTATGATGTGTTCGGT
66 GGGCCTTACTCGATATGAAGGTGGGTGTATGGTTCTAGGAACCTACACATTATGATGTATTCGGC
707476 TGGAGGGATTACTATGGTTTTTGAT
131 TGGAGGGATTACTATGGTTTTTGAT
* * * * * *
707501 AAATGTTTTATTTGGGGGGTATTGTTGGAGGAAGTATACTTGTAGGTTCCTCGGCTTTGTGCTCA
1 AAATGTTTTATTTGGAGGGTAATGTTGAAGGAAGAATACTTGTAGGCTCCTCGACTTTGTGCTCA
* * *
707566 GGGCCTTACTTGATGTGACA-GTGGGTGTATGGTTCTAGGAACCTACACATTATGATGTATTGGG
66 GGGCCTTACTCGATATGA-AGGTGGGTGTATGGTTCTAGGAACCTACACATTATGATGTATTCGG
707630 CTGGAGGGATTACTATGGTTT
130 CTGGAGGGATTACTATGGTTT
707651 ATGAATTTTA
Statistics
Matches: 137, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
155 136 0.99
156 1 0.01
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.36
Consensus pattern (155 bp):
AAATGTTTTATTTGGAGGGTAATGTTGAAGGAAGAATACTTGTAGGCTCCTCGACTTTGTGCTCA
GGGCCTTACTCGATATGAAGGTGGGTGTATGGTTCTAGGAACCTACACATTATGATGTATTCGGC
TGGAGGGATTACTATGGTTTTTGAT
Found at i:709608 original size:14 final size:14
Alignment explanation
Indices: 709566--709608 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
709556 GACCCGGCTG
709566 CTCGACTGAGTCAA
1 CTCGACTGAGTCAA
* *
709580 CCCGCACTGAATCAA
1 CTCG-ACTGAGTCAA
*
709595 CTCGGCTGAGTCAA
1 CTCGACTGAGTCAA
709609 GTCATTGGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.19
Consensus pattern (14 bp):
CTCGACTGAGTCAA
Found at i:711952 original size:24 final size:24
Alignment explanation
Indices: 711873--711956 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
711863 GTGTTCCAAT
* * * *
711873 TTGAATTCTGTTATGATACCTGAC
1 TTGAATTATGTTCTAATATCTGAC
* * * * *
711897 ATGGATTTTGTTCTTATATCTAAC
1 TTGAATTATGTTCTAATATCTGAC
* *
711921 CTGGATTATGTTCTAATATCTGAC
1 TTGAATTATGTTCTAATATCTGAC
711945 TTGAATTATGTT
1 TTGAATTATGTT
711957 TTGATTTTTG
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (24 bp):
TTGAATTATGTTCTAATATCTGAC
Found at i:713960 original size:43 final size:43
Alignment explanation
Indices: 713898--713982 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
713888 CCACTTGACC
*
713898 CGACTGAGTCATCCCGCGCTGAGTCAACTCGACTAAGTCAACG
1 CGACTGAGTCAACCCGCGCTGAGTCAACTCGACTAAGTCAACG
* *
713941 CGACTGAGTCAACCTGCGCTGAGTCAACTCGACTGAGTCAAC
1 CGACTGAGTCAACCCGCGCTGAGTCAACTCGACTAAGTCAAC
713983 TCATTGGGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.19
Consensus pattern (43 bp):
CGACTGAGTCAACCCGCGCTGAGTCAACTCGACTAAGTCAACG
Found at i:713965 original size:29 final size:29
Alignment explanation
Indices: 713912--713982 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
713902 TGAGTCATCC
713912 CGCG-CTGAGTCAA-CTCGACTAAGTCAA
1 CGCGACTGAGTCAACCTCGACTAAGTCAA
*
713939 CGCGACTGAGTCAACCTGCG-CTGAGTCAA
1 CGCGACTGAGTCAACCT-CGACTAAGTCAA
*
713968 CTCGACTGAGTCAAC
1 CGCGACTGAGTCAAC
713983 TCATTGGGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 4 0.10
28 9 0.23
29 24 0.62
30 2 0.05
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (29 bp):
CGCGACTGAGTCAACCTCGACTAAGTCAA
Found at i:713995 original size:13 final size:14
Alignment explanation
Indices: 713916--713998 Score: 98
Period size: 14 Copynumber: 5.9 Consensus size: 14
713906 TCATCCCGCG
713916 CTGAGTCAACTCGA
1 CTGAGTCAACTCGA
* *
713930 CTAAGTCAACGCGA
1 CTGAGTCAACTCGA
713944 CTGAGTCAACCTGCG-
1 CTGAGTCAA-CT-CGA
713959 CTGAGTCAACTCGA
1 CTGAGTCAACTCGA
713973 CTGAGTCAACTC-A
1 CTGAGTCAACTCGA
* *
713986 TTGGGTCAACTCG
1 CTGAGTCAACTCG
713999 TTGACTTTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
13 13 0.22
14 34 0.58
15 10 0.17
16 2 0.03
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.22
Consensus pattern (14 bp):
CTGAGTCAACTCGA
Found at i:714033 original size:30 final size:30
Alignment explanation
Indices: 713997--714062 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
713987 TGGGTCAACT
* *
713997 CGTTGACTTTGATAGAGTCAACCCATTGAC
1 CGTTGACTTTGACACAGTCAACCCATTGAC
*
714027 CGTTGACTTTGACCCAGTCAACCCATTGAC
1 CGTTGACTTTGACACAGTCAACCCATTGAC
714057 C-TTGAC
1 CGTTGAC
714063 CCAGTAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (30 bp):
CGTTGACTTTGACACAGTCAACCCATTGAC
Found at i:714056 original size:23 final size:23
Alignment explanation
Indices: 714029--714078 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
714019 CCATTGACCG
* *
714029 TTGACTTTGACCCAGTCAACCCA
1 TTGACCTTGACCCAGTAAACCCA
714052 TTGACCTTGACCCAGTAAACCCA
1 TTGACCTTGACCCAGTAAACCCA
714075 TTGA
1 TTGA
714079 TCGTTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.14, T:0.26
Consensus pattern (23 bp):
TTGACCTTGACCCAGTAAACCCA
Found at i:716223 original size:24 final size:23
Alignment explanation
Indices: 716136--716223 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 23
716126 TGTTCCGATT
* * *
716136 TGAATTCTTTTATGATACCTGACAT
1 TGAATT-TGTTATGATATCTGAC-C
716161 TG-ATTCTGTTATGATATCTGACC
1 TGAATT-TGTTATGATATCTGACC
* *
716184 TGAATTTCGTTCTGATATTTGACC
1 TGAATTT-GTTATGATATCTGACC
*
716208 TGAATTATGTTTTGAT
1 TGAATT-TGTTATGAT
716224 TTTTTATACA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
23 3 0.06
24 48 0.89
25 3 0.06
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.47
Consensus pattern (23 bp):
TGAATTTGTTATGATATCTGACC
Found at i:716547 original size:156 final size:155
Alignment explanation
Indices: 716250--716547 Score: 488
Period size: 156 Copynumber: 1.9 Consensus size: 155
716240 TACGGATGTA
*
716250 AAATGTTTTATTTGGGGGTATTGTTGGAGGAAGAATACTTGTAGGCTCCTCGGCTTTATGCTCAG
1 AAATATTTTATTTGGGGGTATTGTTGGAGGAAGAATACTTGTAGGCTCCTCGGCTTTATGCTCAG
* * * * *
716315 GGCCTTACTCGATGTGAAGGTGGGTGTATGGTTCTGGGGAACCTATACATTATGATTTTTTCAGT
66 GGCCTTACTCGATGTGAAGGTGGGTGTATGGTTCTGGGGAACCTACAAATTATGATGTGTTCAGC
716380 TGGAGGGATTACAATAGTTTTTGAT
131 TGGAGGGATTACAATAGTTTTTGAT
* *
716405 AAATATTTTATTTGGGGGGTATTGTTGGAGGAAGTATACTTGTAGGCTCCTCGGCTTTGTGCTCA
1 AAATATTTTATTT-GGGGGTATTGTTGGAGGAAGAATACTTGTAGGCTCCTCGGCTTTATGCTCA
* *
716470 GGGCCTTACTCGATGTGACGGTGGGTGTATGGTTCTGGGGAACCTACAAATTATGATGTGTTGAG
65 GGGCCTTACTCGATGTGAAGGTGGGTGTATGGTTCTGGGGAACCTACAAATTATGATGTGTTCAG
*
716535 CTGGATGGATTAC
130 CTGGAGGGATTAC
716548 TATGGTTTCT
Statistics
Matches: 131, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
155 12 0.09
156 119 0.91
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.36
Consensus pattern (155 bp):
AAATATTTTATTTGGGGGTATTGTTGGAGGAAGAATACTTGTAGGCTCCTCGGCTTTATGCTCAG
GGCCTTACTCGATGTGAAGGTGGGTGTATGGTTCTGGGGAACCTACAAATTATGATGTGTTCAGC
TGGAGGGATTACAATAGTTTTTGAT
Found at i:718723 original size:180 final size:184
Alignment explanation
Indices: 718486--718850 Score: 693
Period size: 180 Copynumber: 2.0 Consensus size: 184
718476 ATAAAATGAA
718486 AACGTAATTTTAGATATGACTGAAAAAAATTTGGGTTACCAAACTATGAGAAAATTATGTTTCAA
1 AACGTAATTTTAGATATGACTGAAAAAAATTTGGGTTACCAAACTATGAGAAAATTATGTTTCAA
718551 TCTTATTTATCTTGATAAGAAATGCTTTTA-TTTTT-TA-CATCAAATCATTGAACTTATGATG-
66 TCTTATTTATCTTGATAAGAAATGCTTTTATTTTTTATACCATCAAATCATTGAACTTATGATGA
718612 TTAAACTGTACTGTGCTATGCATGAGTTTAAAATATTAAATATTAGATTTTGTT
131 TTAAACTGTACTGTGCTATGCATGAGTTTAAAATATTAAATATTAGATTTTGTT
718666 AACGTAATTTTAGATATGACTGAAAAAAATTTGGGTTACCAAACTATGAGAAAATTATGTTTCAA
1 AACGTAATTTTAGATATGACTGAAAAAAATTTGGGTTACCAAACTATGAGAAAATTATGTTTCAA
718731 TCTTATTTATCTTGATAAGAAATGCTTTTATTTTTTAATACCATCAAATCATTGAACTTATGATG
66 TCTTATTTATCTTGATAAGAAATGCTTTTATTTTTT-ATACCATCAAATCATTGAACTTATGATG
718796 ATTAAACTGTACTGTGCTATGCATGAGTTTAAAATATTAAATATTAGATTTTGTT
130 ATTAAACTGTACTGTGCTATGCATGAGTTTAAAATATTAAATATTAGATTTTGTT
718851 GCACTTAAGA
Statistics
Matches: 180, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
180 95 0.53
181 5 0.03
183 2 0.01
184 24 0.13
185 54 0.30
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (184 bp):
AACGTAATTTTAGATATGACTGAAAAAAATTTGGGTTACCAAACTATGAGAAAATTATGTTTCAA
TCTTATTTATCTTGATAAGAAATGCTTTTATTTTTTATACCATCAAATCATTGAACTTATGATGA
TTAAACTGTACTGTGCTATGCATGAGTTTAAAATATTAAATATTAGATTTTGTT
Found at i:719106 original size:31 final size:31
Alignment explanation
Indices: 719063--719170 Score: 180
Period size: 31 Copynumber: 3.5 Consensus size: 31
719053 AAACTACGCA
* *
719063 TTTAGTATCTAAACGATCAGTTGTGATTCGT
1 TTTAGTACCTAAACTATCAGTTGTGATTCGT
719094 TTTAGTACCTAAACTATCAGTTGTGATTCGT
1 TTTAGTACCTAAACTATCAGTTGTGATTCGT
*
719125 TTTAGTACATAAACTATCAGTTGTGATTCGT
1 TTTAGTACCTAAACTATCAGTTGTGATTCGT
*
719156 TTTAATACCTAAACT
1 TTTAGTACCTAAACT
719171 TTTAAATCTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (31 bp):
TTTAGTACCTAAACTATCAGTTGTGATTCGT
Found at i:721810 original size:32 final size:32
Alignment explanation
Indices: 721774--721851 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
721764 ATTCGAACCC
721774 GATGGGGAAAATCGAAAACCGCATTAAACGGG
1 GATGGGGAAAATCGAAAACCGCATTAAACGGG
721806 GATGGGGAAAATCGAAAACCGCATTAAACGGG
1 GATGGGGAAAATCGAAAACCGCATTAAACGGG
721838 GATGGGGAAAATCG
1 GATGGGGAAAATCG
721852 TTTATGCTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.40, C:0.14, G:0.33, T:0.13
Consensus pattern (32 bp):
GATGGGGAAAATCGAAAACCGCATTAAACGGG
Found at i:725493 original size:2 final size:2
Alignment explanation
Indices: 725481--725561 Score: 126
Period size: 2 Copynumber: 40.0 Consensus size: 2
725471 ACAATTACTA
725481 AT AT CAT 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
* * *
725524 AT AT AT GT AT GT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
725562 GTATGTATAA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
2 70 0.97
3 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:726202 original size:21 final size:21
Alignment explanation
Indices: 726151--726203 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
726141 ATTATTACTA
726151 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
726172 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
726193 TCGCAATGCGA
1 TCGCAATGCGA
726204 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:726218 original size:20 final size:21
Alignment explanation
Indices: 726193--726244 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
726183 TTTTCCCAAT
*
726193 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
726213 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
726234 TCGCAATGCGA
1 TCGCAATGCGA
726245 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:726258 original size:20 final size:20
Alignment explanation
Indices: 726233--726367 Score: 146
Period size: 20 Copynumber: 6.7 Consensus size: 20
726223 AATTTGGAAA
*
726233 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
726253 ATCGCAATGCGACACTGACT
1 ATCGCAACGCGATACTGACT
* *
726273 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
726294 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
726314 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
726334 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
726354 TTCGCAACGAGATA
1 ATCGCAACGCGATA
726368 ATACATAATC
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 81 0.82
21 14 0.14
22 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:726298 original size:41 final size:40
Alignment explanation
Indices: 726253--726387 Score: 173
Period size: 41 Copynumber: 3.3 Consensus size: 40
726243 GATACTGACT
* *
726253 ATCGCAATGCGACACTGACTATCGCAACGCGATAATACAAA
1 ATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC-AA
* *
726294 ATCGCAATGCGATACTGACTTTCGCAACGCGATACTTAC-T
1 ATCGCAATGCGATACTGACTTTCGCAACGCGATA-ATACAA
* * *
726334 TTCGCAACGCGATACTGACTTTCGCAACGAGATAATACATA
1 ATCGCAATGCGATACTGACTTTCGCAACGCGATAATACA-A
726375 ATCGCAATGCGAT
1 ATCGCAATGCGAT
726388 TTTCAAAGGG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.39
41 43 0.54
42 3 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (40 bp):
ATCGCAATGCGATACTGACTTTCGCAACGCGATAATACAA
Found at i:726328 original size:81 final size:81
Alignment explanation
Indices: 726234--726387 Score: 236
Period size: 81 Copynumber: 1.9 Consensus size: 81
726224 ATTTGGAAAA
* * *
726234 TCGCAATGCGATACTGACTATCGCAATGCGACACTGACTATCGCAACGCGATAATACAAAATCGC
1 TCGCAACGCGATACTGACTATCGCAACGCGACACTGACTATCGCAACGAGATAATACAAAATCGC
726299 AATGCGATACTGACTT
66 AATGCGATACTGACTT
* * * * *
726315 TCGCAACGCGATACTTACTTTCGCAACGCGATACTGACTTTCGCAACGAGATAATACATAATCGC
1 TCGCAACGCGATACTGACTATCGCAACGCGACACTGACTATCGCAACGAGATAATACAAAATCGC
726380 AATGCGAT
66 AATGCGAT
726388 TTTCAAAGGG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (81 bp):
TCGCAACGCGATACTGACTATCGCAACGCGACACTGACTATCGCAACGAGATAATACAAAATCGC
AATGCGATACTGACTT
Found at i:726346 original size:61 final size:61
Alignment explanation
Indices: 726230--726347 Score: 191
Period size: 61 Copynumber: 1.9 Consensus size: 61
726220 GCGAATTTGG
*
726230 AAAATCGCAATGCGATACTGACTATCGCAATGCGACACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGACACTGACTATCGCAACGCGATAATAC
* * * *
726291 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGACACTGACTATCGCAACGCGATA
726348 CTGACTTTCG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGACACTGACTATCGCAACGCGATAATAC
Found at i:726582 original size:22 final size:22
Alignment explanation
Indices: 726554--726595 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
726544 CACTCTCTCA
726554 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
726576 CCCATCTCTGGCGAAATCCG
1 CCCATCTCCGACGAAATCCG
726596 GCGGCTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.43, G:0.17, T:0.19
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:727515 original size:14 final size:14
Alignment explanation
Indices: 727481--727519 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
727471 TTGATTGTTT
727481 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
727495 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
727509 TGTTGATTTGT
1 AATTGATTTGT
727520 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:727683 original size:19 final size:19
Alignment explanation
Indices: 727659--727749 Score: 173
Period size: 19 Copynumber: 4.8 Consensus size: 19
727649 GCAACGAGAG
727659 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
727678 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
727697 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
727716 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
727735 AATCGCAATGAGAAA
1 AATCGCAATGCGAAA
727750 ATCGCAATGC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
19 71 1.00
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:727750 original size:33 final size:36
Alignment explanation
Indices: 727659--727761 Score: 149
Period size: 38 Copynumber: 2.8 Consensus size: 36
727649 GCAACGAGAG
727659 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAAT-CG-AATGAAAATCGCAATGCGAAATGAA
727697 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAAT-CG-AATGAAAATCGCAATGCGAAATGAA
727735 AATCGCAAT-G-A-GAAAATCGCAATGCGA
1 AATCGCAATCGAATGAAAATCGCAATGCGA
727762 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
33 16 0.25
34 1 0.02
36 1 0.02
38 47 0.72
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (36 bp):
AATCGCAATCGAATGAAAATCGCAATGCGAAATGAA
Found at i:727847 original size:21 final size:20
Alignment explanation
Indices: 727780--727856 Score: 118
Period size: 20 Copynumber: 3.8 Consensus size: 20
727770 TCGCATTGCG
*
727780 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
727800 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
727820 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
*
727840 ATTTTTCGCATTGCGAT
1 A-TTTTCGCGTTGCGAT
727857 TTCCCCGTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 39 0.74
21 14 0.26
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:728428 original size:20 final size:20
Alignment explanation
Indices: 728403--728495 Score: 123
Period size: 20 Copynumber: 4.7 Consensus size: 20
728393 ATTCTGTATT
*
728403 ATCTCGTTGCGATAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
728423 ATCTCGTTGCGAAAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
*
728443 ATCTCGTTGCGAAAGTCAGT
1 ATCTCGTTGCGAAAGTCAGA
* * * *
728463 ATCGCATTGCGATAGTCATA
1 ATCTCGTTGCGAAAGTCAGA
*
728483 ATCGCGTTGCGAA
1 ATCTCGTTGCGAA
728496 TCTGGAAACT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (20 bp):
ATCTCGTTGCGAAAGTCAGA
Found at i:729737 original size:44 final size:44
Alignment explanation
Indices: 729688--729782 Score: 172
Period size: 44 Copynumber: 2.2 Consensus size: 44
729678 TATTAATGTG
729688 GTACATACATTTATATTTACATTATATAATATATACATTGTACC
1 GTACATACATTTATATTTACATTATATAATATATACATTGTACC
*
729732 GTACATACATTTATATTTACATTATATAATGTATACATTGTACC
1 GTACATACATTTATATTTACATTATATAATATATACATTGTACC
*
729776 TTACATA
1 GTACATA
729783 TTCATATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (44 bp):
GTACATACATTTATATTTACATTATATAATATATACATTGTACC
Found at i:731077 original size:9 final size:9
Alignment explanation
Indices: 731065--731128 Score: 56
Period size: 9 Copynumber: 6.6 Consensus size: 9
731055 GTTTTTTTAC
731065 TTTTTATTT
1 TTTTTATTT
731074 TTTTATATTT
1 TTTT-TATTT
*
731084 TCTTTATTT
1 TTTTTATTT
*
731093 CTTTTATTT
1 TTTTTATTT
731102 TACATTTTATTT
1 T---TTTTATTT
*
731114 ATTTTATTT
1 TTTTTATTT
731123 TATTTT
1 T-TTTT
731129 TTAATTTCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 24 0.55
10 12 0.27
12 8 0.18
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTATTT
Found at i:731084 original size:16 final size:16
Alignment explanation
Indices: 731041--731084 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
731031 AAATCCGCCA
*
731041 TTTTTTATTATTATGT
1 TTTTTTATTTTTATGT
731057 TTTTTTACTTTTTAT-T
1 TTTTTTA-TTTTTATGT
731073 TTTTTATATTTT
1 TTTTT-TATTTT
731085 CTTTATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTTTATTTTTATGT
Found at i:731102 original size:25 final size:25
Alignment explanation
Indices: 731041--731138 Score: 83
Period size: 25 Copynumber: 3.8 Consensus size: 25
731031 AAATCCGCCA
*
731041 TTTTTTATTATTATGTTTT-TTTACT
1 TTTTTTATT-TTATATTTTCTTTACT
*
731066 TTTTATTTTTTTATATTTTCTTTA-T
1 TTTT-TTATTTTATATTTTCTTTACT
* * *
731091 TTCTTTTATTTTACATTTTATTTATT
1 TT-TTTTATTTTATATTTTCTTTACT
* *
731117 TTATTTTATTTTTTAATTTCTT
1 TT-TTTTATTTTATATTTTCTT
731139 ACTAACTCTT
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
25 31 0.53
26 28 0.47
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (25 bp):
TTTTTTATTTTATATTTTCTTTACT
Found at i:731110 original size:21 final size:21
Alignment explanation
Indices: 731059--731138 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
731049 TATTATGTTT
731059 TTTTACTTTTTATTT-TTTTA
1 TTTTACTTTTTATTTCTTTTA
*
731079 TATTT--TCTTTATTTCTTTTA
1 T-TTTACTTTTTATTTCTTTTA
* *
731099 TTTTACATTTTATTTATTTTA
1 TTTTACTTTTTATTTCTTTTA
*
731120 TTTTATTTTTTAATTTCTT
1 TTTTACTTTTT-ATTTCTT
731139 ACTAACTCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 11 0.23
20 7 0.15
21 24 0.50
22 6 0.12
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTACTTTTTATTTCTTTTA
Found at i:731113 original size:5 final size:5
Alignment explanation
Indices: 731043--731128 Score: 56
Period size: 5 Copynumber: 16.8 Consensus size: 5
731033 ATCCGCCATT
*
731043 TTTTA TTATTA TGTTT- TTTTA CTTTTTA TTTT- TTTATA TTTT- CTTTA
1 TTTTA TT-TTA T-TTTA TTTTA --TTTTA TTTTA TTT-TA TTTTA TTTTA
*
731090 -TTTC TTTTA TTTTACA TTTTA -TTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTT--A TTTTA TTTTA TTTTA TTTTA TTTT
731129 TTAATTTCTT
Statistics
Matches: 66, Mismatches: 3, Indels: 24
0.71 0.03 0.26
Matches are distributed among these distances:
4 16 0.24
5 30 0.45
6 9 0.14
7 11 0.17
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:731288 original size:15 final size:16
Alignment explanation
Indices: 731263--731292 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
731253 TTACTTTTAT
731263 TTTTGTTTTTATTTTG
1 TTTTGTTTTTATTTTG
731279 TTTT-TTTTTATTTT
1 TTTTGTTTTTATTTT
731293 TCTTTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.87
Consensus pattern (16 bp):
TTTTGTTTTTATTTTG
Found at i:731418 original size:20 final size:20
Alignment explanation
Indices: 731393--731430 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
731383 TATTATTTGT
*
731393 TATGTGCTATGTGTTTTTAA
1 TATGTGCAATGTGTTTTTAA
*
731413 TATGTGCAATTTGTTTTT
1 TATGTGCAATGTGTTTTT
731431 TTTTATTTCT
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:0.18, C:0.05, G:0.18, T:0.58
Consensus pattern (20 bp):
TATGTGCAATGTGTTTTTAA
Found at i:734656 original size:20 final size:19
Alignment explanation
Indices: 734627--734666 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
734617 TAATACTTTG
734627 TATTTTTATTTTCCATGTT
1 TATTTTTATTTTCCATGTT
734646 TATTTTCTATTTTCCATGTT
1 TATTTT-TATTTTCCATGTT
734666 T
1 T
734667 TTACATTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.15, C:0.12, G:0.05, T:0.68
Consensus pattern (19 bp):
TATTTTTATTTTCCATGTT
Found at i:744854 original size:21 final size:21
Alignment explanation
Indices: 744806--744899 Score: 84
Period size: 21 Copynumber: 4.3 Consensus size: 21
744796 TTTATTATTA
744806 TTTTATTATTTCTTTTCTTTT-
1 TTTT-TTATTTCTTTTCTTTTC
*
744827 TCATTTTATTTCTTTTCTTTTC
1 T-TTTTTATTTCTTTTCTTTTC
**
744849 TTTTTTATTT-TTTTACTAACTC
1 TTTTTTATTTCTTTT-CT-TTTC
**
744871 TTTTTTGGGTTCTTTTCTTTTC
1 TTTTTT-ATTTCTTTTCTTTTC
744893 TTTTTTA
1 TTTTTTA
744900 ATTTAACCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
20 4 0.07
21 27 0.47
22 19 0.33
23 4 0.07
24 4 0.07
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (21 bp):
TTTTTTATTTCTTTTCTTTTC
Found at i:745684 original size:14 final size:14
Alignment explanation
Indices: 745665--745706 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
745655 ATCAAGTTCG
745665 AACGAGTTGACTCA
1 AACGAGTTGACTCA
**
745679 AACGAGTTGACTTG
1 AACGAGTTGACTCA
*
745693 AATGAGTTGACTCA
1 AACGAGTTGACTCA
745707 GTTCGAGTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (14 bp):
AACGAGTTGACTCA
Found at i:747390 original size:20 final size:21
Alignment explanation
Indices: 747351--747391 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
747341 CCGAAGTCAT
*
747351 AAAAATTCAAATGACGAAATA
1 AAAAATTCAAATGACCAAATA
*
747372 AAAAATTCAAGT-ACCAAATA
1 AAAAATTCAAATGACCAAATA
747392 CCAAGTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.61, C:0.12, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAAATTCAAATGACCAAATA
Found at i:751004 original size:21 final size:21
Alignment explanation
Indices: 750980--751019 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
750970 ATTTTATAAA
750980 ATGTTTTAATAATTGTTTTGT
1 ATGTTTTAATAATTGTTTTGT
751001 ATGTTTTAATAATTGTTTT
1 ATGTTTTAATAATTGTTTT
751020 TTTATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (21 bp):
ATGTTTTAATAATTGTTTTGT
Found at i:751029 original size:22 final size:21
Alignment explanation
Indices: 750983--751030 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
750973 TTATAAAATG
*
750983 TTTTAATAATTGTTTTGTATG
1 TTTTAATAATTGTTTTGTATA
*
751004 TTTTAATAATTGTTTTTTTATA
1 TTTTAATAATTG-TTTTGTATA
751026 TTTTA
1 TTTTA
751031 TGATGCCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTTAATAATTGTTTTGTATA
Found at i:758782 original size:22 final size:21
Alignment explanation
Indices: 758740--758789 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
758730 AAGGAAGTAA
758740 AATAG-TTTGAAAATTAATTT
1 AATAGTTTTGAAAATTAATTT
* *
758760 AATAGTTTTGGAAAGTTATTTT
1 AATAGTTTT-GAAAATTAATTT
*
758782 ATTAGTTT
1 AATAGTTT
758790 CAAAGTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.20
21 3 0.12
22 17 0.68
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (21 bp):
AATAGTTTTGAAAATTAATTT
Found at i:758929 original size:31 final size:30
Alignment explanation
Indices: 758894--758993 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 30
758884 TCTAATTTCA
758894 TCCTTAAACTATGACTCTCATTCTAAATTAG
1 TCCTTAAACTATGA-TCTCATTCTAAATTAG
* *
758925 TCCTTAAACTTTTGA--ACATTC-AAATTTTA-
1 TCCTTAAAC-TATGATCTCATTCTAAA--TTAG
*
758954 TCC-CAAACTATGAATCTCATTCTAAATTAG
1 TCCTTAAACTATG-ATCTCATTCTAAATTAG
*
758984 TCCCTAAACT
1 TCCTTAAACT
758994 TTTAGATCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
27 3 0.06
28 8 0.15
29 11 0.20
30 11 0.20
31 17 0.31
32 4 0.07
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (30 bp):
TCCTTAAACTATGATCTCATTCTAAATTAG
Done.