Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005349.1 Hibiscus syriacus cultivar Beakdansim tig00012136_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: 1796274
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 3 of 8
Found at i:523993 original size:18 final size:18
Alignment explanation
Indices: 523937--523993 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 18
523927 ACGAGTCAAC
*
523937 GGTCAACGGGTTAACGGGTCC
1 GGTCAACGGG-T--CGGGTCG
523958 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
523976 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
523994 AGTCGGGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
18 24 0.69
20 1 0.03
21 10 0.29
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:529042 original size:21 final size:21
Alignment explanation
Indices: 529018--529062 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
529008 GTCAAACATA
*
529018 CCCAGCGAGCACCGAAATGTC
1 CCCAGCGAGCACCGAAACGTC
*
529039 CCCAGTGAGCACCGAAACGTC
1 CCCAGCGAGCACCGAAACGTC
529060 CCC
1 CCC
529063 CGTATTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.42, G:0.22, T:0.09
Consensus pattern (21 bp):
CCCAGCGAGCACCGAAACGTC
Found at i:530705 original size:17 final size:17
Alignment explanation
Indices: 530683--530716 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
530673 AGGATTTGGA
530683 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
530700 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
530717 TTTGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (17 bp):
ATTAGAGTTTTCAAAGT
Found at i:533306 original size:29 final size:28
Alignment explanation
Indices: 533259--533371 Score: 109
Period size: 29 Copynumber: 3.9 Consensus size: 28
533249 AAAATCACAT
* *
533259 TTTTAAAAATATTTACCAAAATGTCATTA
1 TTTTAAAAA-AATTCCCAAAATGTCATTA
***
533288 TTTTACAAAAAATTCCCAAAATGTCACCG
1 TTTTA-AAAAAATTCCCAAAATGTCATTA
* * *
533317 TTTTAAAAATAATTACTAAAATGTCATTGT
1 TTTTAAAAA-AATTCCCAAAATGTCATT-A
*
533347 TTTTAAAAAAATTCCTAAAATGTCA
1 TTTTAAAAAAATTCCCAAAATGTCA
533372 CCGGGTCGGG
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
28 4 0.06
29 53 0.76
30 13 0.19
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.37
Consensus pattern (28 bp):
TTTTAAAAAAATTCCCAAAATGTCATTA
Found at i:533338 original size:58 final size:58
Alignment explanation
Indices: 533259--533374 Score: 180
Period size: 58 Copynumber: 2.0 Consensus size: 58
533249 AAAATCACAT
*
533259 TTTTAAAAATATTTACCAAAATGTCATT-ATTTTACAAAAAATTCCCAAAATGTCACCG
1 TTTTAAAAATAATTACCAAAATGTCATTGATTTTA-AAAAAATTCCCAAAATGTCACCG
* * *
533317 TTTTAAAAATAATTACTAAAATGTCATTGTTTTTAAAAAAATTCCTAAAATGTCACCG
1 TTTTAAAAATAATTACCAAAATGTCATTGATTTTAAAAAAATTCCCAAAATGTCACCG
533375 GGTCGGGTCG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 48 0.91
59 5 0.09
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (58 bp):
TTTTAAAAATAATTACCAAAATGTCATTGATTTTAAAAAAATTCCCAAAATGTCACCG
Found at i:533396 original size:13 final size:13
Alignment explanation
Indices: 533378--533403 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
533368 GTCACCGGGT
533378 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
533391 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
533404 ACCAGTCAGA
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:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:540613 original size:27 final size:27
Alignment explanation
Indices: 540575--540630 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
540565 TTTTAAAAAT
* *
540575 AATTACCAAAATGTCATTGTTTTTTAA
1 AATTACCAAAATGTCACTATTTTTTAA
*
540602 AATTCCCAAAATGTCACTATTTTTTAA
1 AATTACCAAAATGTCACTATTTTTTAA
540629 AA
1 AA
540631 AAAAATCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.41
Consensus pattern (27 bp):
AATTACCAAAATGTCACTATTTTTTAA
Found at i:540703 original size:32 final size:29
Alignment explanation
Indices: 540564--540736 Score: 129
Period size: 29 Copynumber: 5.9 Consensus size: 29
540554 AATATCACCC
* **
540564 TTTTTAAAAATAATTACCAAAATGTCATTG
1 TTTTTAAAAA-AATTCCCAAAATGTCAGAG
* * *
540594 TTTTT--TAAAATTCCCAAAATGTCACTAT
1 TTTTTAAAAAAATTCCCAAAATGTCA-GAG
* **
540622 TTTTTAAAAAAAAAT-CCAAAATGTCACCG
1 TTTTT-AAAAAAATTCCCAAAATGTCAGAG
* ** *
540651 -TTTTAAAAATATTTATCAAAATGTTAGAG
1 TTTTTAAAAA-AATTCCCAAAATGTCAGAG
540680 TTTTTAAAAAAAAAATTCCCAAAATGTCAGAG
1 TTTTT---AAAAAAATTCCCAAAATGTCAGAG
*
540712 TTTTTTAAAAAATTCCCAAAATGTC
1 TTTTTAAAAAAATTCCCAAAATGTC
540737 GCCGGGTCGG
Statistics
Matches: 113, Mismatches: 20, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
27 20 0.18
28 14 0.12
29 29 0.26
30 20 0.18
31 5 0.04
32 20 0.18
33 5 0.04
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (29 bp):
TTTTTAAAAAAATTCCCAAAATGTCAGAG
Found at i:540767 original size:18 final size:18
Alignment explanation
Indices: 540744--540791 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
540734 GTCGCCGGGT
*
540744 CGGGTCGGTTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
540762 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
*
540780 CTGGTCGGGTCG
1 CGGGTCGGGTCG
540792 AATCGGTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.08, C:0.23, G:0.48, T:0.21
Consensus pattern (18 bp):
CGGGTCGGGTCGGGTCAA
Found at i:543913 original size:23 final size:23
Alignment explanation
Indices: 543861--543916 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
543851 TTAATAATTT
* *
543861 TGTCTTTATGACATTTCTTCTTC
1 TGTCTTTATGACATTGCTTCTTA
* *
543884 TGCCTTTATGACA-TGCTTTTGTA
1 TGTCTTTATGACATTGCTTCT-TA
543907 TGTCTTTATG
1 TGTCTTTATG
543917 GCACGTTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.14, C:0.18, G:0.14, T:0.54
Consensus pattern (23 bp):
TGTCTTTATGACATTGCTTCTTA
Found at i:546969 original size:24 final size:24
Alignment explanation
Indices: 546942--547032 Score: 130
Period size: 24 Copynumber: 3.8 Consensus size: 24
546932 CATAATTCAA
*
546942 GTCAAGTATCATATCAGAATCTAG
1 GTCAAGTATCATATCAGAATCCAG
* *
546966 GTCATGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
546990 GTCAA-TATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
547013 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAAT
547033 TCAAATCAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 21 0.36
24 38 0.64
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:547015 original size:47 final size:48
Alignment explanation
Indices: 546942--547032 Score: 148
Period size: 47 Copynumber: 1.9 Consensus size: 48
546932 CATAATTCAA
* * *
546942 GTCAAGTATCATATCAGAATCTAGGTCATGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCATAACAGAATCCAT
546990 GTCAA-TATCATATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCATAACAGAAT
547033 TCAAATCAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 35 0.88
48 5 0.12
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAATCCAGGTCAGGTATCATAACAGAATCCAT
Found at i:547041 original size:24 final size:24
Alignment explanation
Indices: 546935--547041 Score: 101
Period size: 24 Copynumber: 4.5 Consensus size: 24
546925 ATCAAAACAT
*
546935 AATTCAAGTCAAGTATCATATCAG
1 AATTCAAGTCAGGTATCATATCAG
* *
546959 AA-TCTAGGTCATGTATCATATCAG
1 AATTC-AAGTCAGGTATCATATCAG
* * *
546983 AATCCATGTCA-ATATCATATCAG
1 AATTCAAGTCAGGTATCATATCAG
* * *
547006 AATCCAGGTCAGGTATCATAACAG
1 AATTCAAGTCAGGTATCATATCAG
*
547030 AATTCAAATCAG
1 AATTCAAGTCAG
547042 AAATCAGATA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
23 23 0.33
24 45 0.65
25 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (24 bp):
AATTCAAGTCAGGTATCATATCAG
Found at i:552084 original size:23 final size:24
Alignment explanation
Indices: 552034--552089 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
552024 CATAATTCAA
* *
552034 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
552058 GTCAA-TATCAGATCAGAATCTAG
1 GTCAAGTATCAGATCAGAATCCAG
*
552081 GTCAGGTAT
1 GTCAAGTAT
552090 AATAACAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:556160 original size:3 final size:3
Alignment explanation
Indices: 556152--556184 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
556142 CTTGGTTAAT
556152 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
556185 ATTGGCTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:556993 original size:48 final size:49
Alignment explanation
Indices: 556896--556993 Score: 135
Period size: 48 Copynumber: 2.0 Consensus size: 49
556886 CAATAAGTTT
* * * *
556896 ACATAAAGACAAAAAAAAGTTTGTTACAACAATAAGCACATGATAAAAAA
1 ACATAAAGAC-AAAAAAAGTTAGCTACAACAATAAGCAAATGAGAAAAAA
*
556946 ACATAAAGAC-AAAAAAGTTAGCTACAACAATAAGCAAATGAGGAAAAA
1 ACATAAAGACAAAAAAAGTTAGCTACAACAATAAGCAAATGAGAAAAAA
556994 CATGTTGATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 33 0.77
50 10 0.23
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.15
Consensus pattern (49 bp):
ACATAAAGACAAAAAAAGTTAGCTACAACAATAAGCAAATGAGAAAAAA
Found at i:563121 original size:121 final size:122
Alignment explanation
Indices: 562901--563139 Score: 408
Period size: 121 Copynumber: 2.0 Consensus size: 122
562891 TTATTATGGT
* ** *
562901 ACATTTGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCTGGCATTCT
1 ACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTAT
*
562966 GTTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCAC
66 GCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCAC
563023 ACATATGGAGATTATGGTACCAAACTACCAATGG-CATACAATGAACGTAGCCCTCCAGCATTAT
1 ACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTAT
* *
563087 GCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGATACTTCCAAGTTGG
66 GCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
563140 ACTCTTTAAG
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
121 77 0.70
122 33 0.30
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (122 bp):
ACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTAT
GCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCAC
Found at i:568230 original size:121 final size:121
Alignment explanation
Indices: 568016--568240 Score: 389
Period size: 121 Copynumber: 1.9 Consensus size: 121
568006 TTTATTATGG
* * *
568016 TACATTTGGAGATTATTGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCGGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
568081 TGCTAAATCCACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
66 TGCTAAATCCACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
*
568137 TACATATGGAGATTATGGTACCAAACTACTAATGG-CATACAATGAACGTAGCCCTCCAGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
*
568201 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGA
66 TGCTAAATCC-ACTCGCGACTTTCACATAGTTCAATCTGA
568241 TTGTGGCTGG
Statistics
Matches: 98, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
120 38 0.39
121 60 0.61
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (121 bp):
TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
TGCTAAATCCACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
Found at i:571283 original size:24 final size:24
Alignment explanation
Indices: 571212--571283 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
571202 TATAAACCCT
571212 AAATTCCAAAGTAATTCAATTT--
1 AAATTCCAAAGTAATTCAATTTCA
* *
571234 -TATTCTAAATAGTAAATTC-ATGTTCA
1 AAATTC-CAA-AGT-AATTCAAT-TTCA
571260 AAATTCCAAAGTAATTCAATTTCA
1 AAATTCCAAAGTAATTCAATTTCA
571284 TTTTAAACCC
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
21 4 0.11
22 2 0.05
23 5 0.13
24 16 0.42
25 5 0.13
26 2 0.05
27 4 0.11
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.38
Consensus pattern (24 bp):
AAATTCCAAAGTAATTCAATTTCA
Found at i:571299 original size:35 final size:35
Alignment explanation
Indices: 571260--571334 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
571250 TTCATGTTCA
* * **
571260 AAATTCCAAAGTAATTCAATTTCATTTTAAACCCT
1 AAATTCCAAAATAATTCAATTACATCCTAAACCCT
* *
571295 AAATTTCAAAATAATTCAATTACATCCTAAACCTT
1 AAATTCCAAAATAATTCAATTACATCCTAAACCCT
571330 AAATT
1 AAATT
571335 GAAGTATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.36
Consensus pattern (35 bp):
AAATTCCAAAATAATTCAATTACATCCTAAACCCT
Found at i:571355 original size:21 final size:21
Alignment explanation
Indices: 571331--571373 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
571321 CTAAACCTTA
571331 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
* *
571352 AATTGAATTATTTTGGAATTT
1 AATTGAAGTATTTTAGAATTT
571373 A
1 A
571374 GGGTTTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:571391 original size:35 final size:35
Alignment explanation
Indices: 571342--571427 Score: 118
Period size: 35 Copynumber: 2.5 Consensus size: 35
571332 ATTGAAGTAT
** * *
571342 TTTAGAATTTAATTGAATTATTTTGGAATTTAGGG
1 TTTAGAATAAAATTGAATTACTTTAGAATTTAGGG
*
571377 TTTAGAATAAAATTGAATTACTTTAGAATTTGGGG
1 TTTAGAATAAAATTGAATTACTTTAGAATTTAGGG
*
571412 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
571428 GGATTGTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.43
Consensus pattern (35 bp):
TTTAGAATAAAATTGAATTACTTTAGAATTTAGGG
Found at i:577577 original size:15 final size:16
Alignment explanation
Indices: 577557--577594 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
577547 TTTGGAATTA
577557 GAGTTTTCAAAG-TAT
1 GAGTTTTCAAAGTTAT
*
577572 GAGTTTTCAAAGTTTT
1 GAGTTTTCAAAGTTAT
577588 GAGTTTT
1 GAGTTTT
577595 TTAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.47
Consensus pattern (16 bp):
GAGTTTTCAAAGTTAT
Found at i:579814 original size:65 final size:65
Alignment explanation
Indices: 579742--579896 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 65
579732 ACACAAGGGG
* * *
579742 TGCATCGGTACACT-AATTACATTTGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTC
1 TGCATCGGTACACTAAAATACATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCATGG-C
579805 TA
64 TA
* * *
579807 TGCATCGGTACA-TAAAATGCATTCGATGTTTCAATAAAATCAGGAGTGCATCGATGCATGGCTG
1 TGCATCGGTACACTAAAATACATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGCTA
*
579871 TGCATCGGTACAC-AAAATGCATTCGA
1 TGCATCGGTACACTAAAATACATTCGA
579897 ATTGGGGTGT
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
64 28 0.35
65 51 0.63
66 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (65 bp):
TGCATCGGTACACTAAAATACATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGCTA
Found at i:580254 original size:13 final size:13
Alignment explanation
Indices: 580236--580269 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
580226 TAAGATTTTC
*
580236 TTTGAAAATCATT
1 TTTGAAAATCAAT
580249 TTTG-AAATCAAT
1 TTTGAAAATCAAT
580261 TTTGAAAAT
1 TTTGAAAAT
580270 TACTCTCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:582627 original size:44 final size:44
Alignment explanation
Indices: 582561--582662 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 44
582551 CGATGCACTG
* *
582561 CATAGTGTATCAATGCACATTCAAGGAATGCATCGGTGCACCTT
1 CATAGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCTT
* * * *
582605 CATAGTGTATCGATTCATATTCAAGGGATGCATCGGTACACTTT
1 CATAGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCTT
582649 C-TAGTGTATCGATG
1 CATAGTGTATCGATG
582663 TACGTTGCAC
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 12 0.24
44 39 0.76
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATTCAAGGAATGCATCGGTACACCTT
Found at i:583330 original size:19 final size:19
Alignment explanation
Indices: 583306--583348 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
583296 TAAAAACCAT
583306 GAAATCAACATATTTCCTA
1 GAAATCAACATATTTCCTA
583325 GAAATCAACATATTTCCTA
1 GAAATCAACATATTTCCTA
583344 GAAAT
1 GAAAT
583349 TGACAAGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (19 bp):
GAAATCAACATATTTCCTA
Found at i:588355 original size:19 final size:19
Alignment explanation
Indices: 588331--588402 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
588321 ATAAGACTTA
588331 GTGCATCGGTACATAAGGG
1 GTGCATCGGTACATAAGGG
****
588350 GTGCATCGGTACATTGACCTA
1 GTGCATCGGTACA-T-AAGGG
* *
588371 GTGCATCGATACACAAGGG
1 GTGCATCGGTACATAAGGG
588390 GTGCATCGGTACA
1 GTGCATCGGTACA
588403 CTAATTACAT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 26 0.65
20 1 0.03
21 13 0.32
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (19 bp):
GTGCATCGGTACATAAGGG
Found at i:588460 original size:65 final size:63
Alignment explanation
Indices: 588390--588544 Score: 170
Period size: 64 Copynumber: 2.4 Consensus size: 63
588380 TACACAAGGG
* * *
588390 GTGCATCGGTACACT-AATTACATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGT
1 GTGCATCGGTACA-TAAAATACATTCGACG-TTCAATAA-AACCAGGAGTGCATCGATGCATGGT
588453 CT
63 -T
* * *
588455 GTGCATCGGTACATAAAATGCATTCGACGTTCAATAAAATCAGGAGTGCATCGATGCATTGTT
1 GTGCATCGGTACATAAAATACATTCGACGTTCAATAAAACCAGGAGTGCATCGATGCATGGTT
** * *
588518 GTGCATTAGTACACAAAATGCATTCGA
1 GTGCATCGGTACATAAAATACATTCGA
588545 ATTAGGGTGT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 25 0.32
64 28 0.35
65 26 0.33
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (63 bp):
GTGCATCGGTACATAAAATACATTCGACGTTCAATAAAACCAGGAGTGCATCGATGCATGGTT
Found at i:590431 original size:23 final size:23
Alignment explanation
Indices: 590404--590461 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
590394 ATAATTCTAT
*
590404 CTTTATGATATGTCTTCT-TATGC
1 CTTTATGACATG-CTTCTGTATGC
* *
590427 CTTTATGACATGCTTGTGTATGT
1 CTTTATGACATGCTTCTGTATGC
*
590450 CTTTATGGCATG
1 CTTTATGACATG
590462 TTTTCGGCCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 4 0.13
23 26 0.87
ACGTcount: A:0.17, C:0.16, G:0.19, T:0.48
Consensus pattern (23 bp):
CTTTATGACATGCTTCTGTATGC
Found at i:591674 original size:2 final size:2
Alignment explanation
Indices: 591667--591713 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
591657 TGTCGTAAAT
591667 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
591709 TA TA T
1 TA TA T
591714 TGTAGATTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:592227 original size:17 final size:17
Alignment explanation
Indices: 592205--592237 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
592195 TAAAGTAGTC
592205 CAAACATTTGTAAAGAG
1 CAAACATTTGTAAAGAG
592222 CAAACATTTGTAAAGA
1 CAAACATTTGTAAAGA
592238 TGGTTAACAA
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:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (17 bp):
CAAACATTTGTAAAGAG
Found at i:597403 original size:3 final size:3
Alignment explanation
Indices: 597395--597423 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
597385 AATTTAATCC
597395 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
597424 ATAATATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:602762 original size:18 final size:18
Alignment explanation
Indices: 602739--602789 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
602729 ACAATTGAGT
602739 CGAGCCACTGAGTCGAGC
1 CGAGCCACTGAGTCGAGC
* * *
602757 CGAGCCGCTGAGCCGTGC
1 CGAGCCACTGAGTCGAGC
*
602775 CAAGCCAACTGAGTC
1 CGAGCC-ACTGAGTC
602790 AACCTGCGCT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.22, C:0.35, G:0.31, T:0.12
Consensus pattern (18 bp):
CGAGCCACTGAGTCGAGC
Found at i:602855 original size:23 final size:24
Alignment explanation
Indices: 602824--602896 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
602814 GAGTCAACTC
* *
602824 ACCGGGTCAACTTGTTGACT-TTG
1 ACCGAGTCAACTCGTTGACTATTG
602847 ACCGAGTCAA-TCCGTTGACTATTG
1 ACCGAGTCAACT-CGTTGACTATTG
* *
602871 ACCGAGTCAACCCGTTGACTGTTG
1 ACCGAGTCAACTCGTTGACTATTG
602895 AC
1 AC
602897 TTTGACCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
22 1 0.02
23 16 0.37
24 26 0.60
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (24 bp):
ACCGAGTCAACTCGTTGACTATTG
Found at i:602876 original size:24 final size:23
Alignment explanation
Indices: 602837--602896 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 23
602827 GGGTCAACTT
*
602837 GTTGACTTTGACCGAGTCAATCC
1 GTTGACTTTGACCGAGTCAACCC
602860 GTTGACTATTGACCGAGTCAACCC
1 GTTGACT-TTGACCGAGTCAACCC
602884 GTTGACTGTTGAC
1 GTTGACT-TTGAC
602897 TTTGACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 7 0.21
24 27 0.79
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (23 bp):
GTTGACTTTGACCGAGTCAACCC
Found at i:603746 original size:104 final size:104
Alignment explanation
Indices: 603566--603775 Score: 420
Period size: 104 Copynumber: 2.0 Consensus size: 104
603556 GAAGTTTGAT
603566 AAGGAATCATTTCAAGTTCAGATATTATCCGGGAAAGCAATTAACCCTAGGATCTTCATATTATC
1 AAGGAATCATTTCAAGTTCAGATATTATCCGGGAAAGCAATTAACCCTAGGATCTTCATATTATC
603631 CTTGTTAAGAGTTTAACACTGAAAATTATCTGGTTACAA
66 CTTGTTAAGAGTTTAACACTGAAAATTATCTGGTTACAA
603670 AAGGAATCATTTCAAGTTCAGATATTATCCGGGAAAGCAATTAACCCTAGGATCTTCATATTATC
1 AAGGAATCATTTCAAGTTCAGATATTATCCGGGAAAGCAATTAACCCTAGGATCTTCATATTATC
603735 CTTGTTAAGAGTTTAACACTGAAAATTATCTGGTTACAA
66 CTTGTTAAGAGTTTAACACTGAAAATTATCTGGTTACAA
603774 AA
1 AA
603776 TTACAAAAAT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 106 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (104 bp):
AAGGAATCATTTCAAGTTCAGATATTATCCGGGAAAGCAATTAACCCTAGGATCTTCATATTATC
CTTGTTAAGAGTTTAACACTGAAAATTATCTGGTTACAA
Found at i:606502 original size:21 final size:21
Alignment explanation
Indices: 606470--606525 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
606460 AGGCCCACCC
*
606470 ATATTATTTTATTTTTAATATA
1 ATATT-TTTTATTTTTAATAAA
606492 ATATTTTTTA-TTTTAATAAA
1 ATATTTTTTATTTTTAATAAA
606512 AGTA-TTTTTATTTT
1 A-TATTTTTTATTTT
606526 GTTATATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 16 0.52
21 10 0.32
22 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATATTTTTTATTTTTAATAAA
Found at i:606666 original size:25 final size:23
Alignment explanation
Indices: 606638--606685 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
606628 CACTTTTAAC
*
606638 ATTTATATTATAATATTATATATAT
1 ATTTA-ATT-TAATATGATATATAT
*
606663 ATTTAATTTTATATGATATATAT
1 ATTTAATTTAATATGATATATAT
606686 TATATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
24 3 0.14
25 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTAATTTAATATGATATATAT
Found at i:606696 original size:21 final size:20
Alignment explanation
Indices: 606641--606697 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
606631 TTTTAACATT
606641 TATATTATAATATTATATATA
1 TATATTAT-ATATTATATATA
*
606662 TAT-TTA-ATTTTATATGATA
1 TATATTATATATTATAT-ATA
*
606681 TATATTATATAATATAT
1 TATATTATATATTATAT
606698 TAAAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 8 0.27
19 6 0.20
20 6 0.20
21 10 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TATATTATATATTATATATA
Found at i:607006 original size:17 final size:17
Alignment explanation
Indices: 606984--607027 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
606974 GACAACCTAA
606984 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
*
607001 ATTAGAATTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
*
607018 -TTTGAGTTTT
1 ATTAGAGTTTT
607028 TTTAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.48
Consensus pattern (17 bp):
ATTAGAGTTTTCAAAGT
Found at i:607873 original size:26 final size:27
Alignment explanation
Indices: 607830--607887 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
607820 GTTAAAATAT
* *
607830 ATTA-TTTAATAGTAAAAATGTAACAA
1 ATTATTTTAATAATAAAAATATAACAA
*
607856 ATTATTTTAATAAT-AAAATATAATAA
1 ATTATTTTAATAATAAAAATATAACAA
607882 ATTATT
1 ATTATT
607888 ATTGATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (27 bp):
ATTATTTTAATAATAAAAATATAACAA
Found at i:610792 original size:42 final size:42
Alignment explanation
Indices: 610733--610839 Score: 200
Period size: 42 Copynumber: 2.6 Consensus size: 42
610723 AAGGGAAGGA
610733 ACTAATAAGTCTTTTGATTTATGGGTTATGAATGGATCATGG
1 ACTAATAAGTCTTTTGATTTATGGGTTATGAATGGATCATGG
610775 ACTAATAAGTCTTTTGATTTATGGGTTATGAATGGATCATGG
1 ACTAATAAGTCTTTTGATTTATGGGTTATGAATGGATCATGG
610817 ACTAATAAGTC--TTGATTTATGGG
1 ACTAATAAGTCTTTTGATTTATGGG
610840 AAGGAACTAG
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
40 12 0.18
42 53 0.82
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.40
Consensus pattern (42 bp):
ACTAATAAGTCTTTTGATTTATGGGTTATGAATGGATCATGG
Found at i:620815 original size:12 final size:12
Alignment explanation
Indices: 620798--620835 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
620788 AATATAACAG
620798 ACTGAAATAGAA
1 ACTGAAATAGAA
620810 ACTGAAATAGAA
1 ACTGAAATAGAA
620822 ACTGAAATAGAA
1 ACTGAAATAGAA
620834 AC
1 AC
620836 AAGTTTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.58, C:0.11, G:0.16, T:0.16
Consensus pattern (12 bp):
ACTGAAATAGAA
Found at i:621138 original size:22 final size:22
Alignment explanation
Indices: 621105--621182 Score: 149
Period size: 22 Copynumber: 3.6 Consensus size: 22
621095 AAAATGGAAG
621105 TTTTGAAA-ATTTAAAGTCTGA
1 TTTTGAAAGATTTAAAGTCTGA
621126 TTTTGAAAGATTTAAAGTCTGA
1 TTTTGAAAGATTTAAAGTCTGA
621148 TTTTGAAAGATTTAAAGTCTGA
1 TTTTGAAAGATTTAAAGTCTGA
621170 TTTTGAAAGATTT
1 TTTTGAAAGATTT
621183 GAAATATTGA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 8 0.14
22 48 0.86
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.44
Consensus pattern (22 bp):
TTTTGAAAGATTTAAAGTCTGA
Found at i:624792 original size:31 final size:31
Alignment explanation
Indices: 624754--624845 Score: 184
Period size: 31 Copynumber: 3.0 Consensus size: 31
624744 ATGTTGTTTT
624754 GAAAAAGGAAAATGATGCAATTATGGGCTTG
1 GAAAAAGGAAAATGATGCAATTATGGGCTTG
624785 GAAAAAGGAAAATGATGCAATTATGGGCTTG
1 GAAAAAGGAAAATGATGCAATTATGGGCTTG
624816 GAAAAAGGAAAATGATGCAATTATGGGCTT
1 GAAAAAGGAAAATGATGCAATTATGGGCTT
624846 TTGTCTTATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.23
Consensus pattern (31 bp):
GAAAAAGGAAAATGATGCAATTATGGGCTTG
Found at i:626327 original size:13 final size:13
Alignment explanation
Indices: 626309--626333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
626299 TCGTGCATTT
626309 TAATTTTGTTTTG
1 TAATTTTGTTTTG
626322 TAATTTTGTTTT
1 TAATTTTGTTTT
626334 ATTTATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (13 bp):
TAATTTTGTTTTG
Found at i:626835 original size:25 final size:24
Alignment explanation
Indices: 626807--626853 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
626797 CGATATTTTT
*
626807 AAATAAATAAATATTGTATTTATAA
1 AAATAAATAAATA-TGTAATTATAA
626832 AAATAAATAAATATGTAATTAT
1 AAATAAATAAATATGTAATTAT
626854 TTTAGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATAAATAAATATGTAATTATAA
Found at i:626882 original size:20 final size:20
Alignment explanation
Indices: 626848--626887 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
626838 ATAAATATGT
*
626848 AATTATTTTAGTTTTATTCA
1 AATTATTATAGTTTTATTCA
* *
626868 AATTATTATATTTTTCTTCA
1 AATTATTATAGTTTTATTCA
626888 TTTTATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (20 bp):
AATTATTATAGTTTTATTCA
Found at i:627088 original size:2 final size:2
Alignment explanation
Indices: 627081--627112 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
627071 ATATCCTGCT
627081 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
627113 CTTCGTTTTT
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):
TA
Found at i:633977 original size:75 final size:75
Alignment explanation
Indices: 633846--634019 Score: 188
Period size: 75 Copynumber: 2.3 Consensus size: 75
633836 CAAGAAGAAG
* * * *
633846 ATGTTGGGGCATGTTGAAAACCCATTTCAATCAGAAATTGGAATATTAACGCATTTTGAATGTTT
1 ATGTTGGGGCATGTTGAAAGCCCATTTCAATCAGAAATAGGAATATTAACGCATTTTGAACGTTC
* * **
633911 GTATTAGTAA
66 ATATCAACAA
* * * * * *
633921 ATGTTGGGGCATGTTGAAAGCCCATTTTAATCCG-AATCAGGAATGTTGATGTATTTTGAACGTT
1 ATGTTGGGGCATGTTGAAAGCCCATTTCAATCAGAAAT-AGGAATATTAACGCATTTTGAACGTT
633985 CATATCAACAA
65 CATATCAACAA
* *
633996 ATGTTGGGGCATGCTGAAGGCCCA
1 ATGTTGGGGCATGTTGAAAGCCCA
634020 CATCATCATG
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
74 3 0.04
75 79 0.96
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (75 bp):
ATGTTGGGGCATGTTGAAAGCCCATTTCAATCAGAAATAGGAATATTAACGCATTTTGAACGTTC
ATATCAACAA
Found at i:634820 original size:53 final size:54
Alignment explanation
Indices: 634722--634920 Score: 256
Period size: 54 Copynumber: 3.7 Consensus size: 54
634712 TAGAAGCCAT
* *
634722 AGGAAATTATGAATGTGTTGTCAAATGTTTTACGAGAAATCTGTGCATAAACCAC
1 AGGAAATGATGAATGTGTTGTCAAATGTTTTACGA-ACATCTGTGCATAAACCAC
* * * *
634777 AGGAAATGATGCATGT-TTGTAAAATATTTTACGAACATCTGTGCATAAGCCAC
1 AGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTGCATAAACCAC
* * * * *
634830 AGGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGTACAGAATCCAC
1 AGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTGCATAAACCAC
* * *
634884 AAGAAATGATGAATTTATTGTCAAATGTTTTACGAAC
1 AGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
634921 CAGTTATGGT
Statistics
Matches: 124, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
53 31 0.25
54 79 0.64
55 14 0.11
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (54 bp):
AGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTGCATAAACCAC
Found at i:636055 original size:45 final size:45
Alignment explanation
Indices: 635991--636356 Score: 536
Period size: 45 Copynumber: 8.1 Consensus size: 45
635981 TTCCCATATT
*
635991 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGTTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
636036 TGTAAGCCCTTCAGTGCATGATGTTTTTAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
** * *
636081 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCTAGTTATT
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * * *
636126 TGTAAGACTTTCAGTGCAGGGTGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* *
636171 TGTAAGACCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* *
636216 TGTAAGCCCTTCAG-GCATGATGTTTTCAAAGCCTTCGGGTTATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * * *
636260 TGTAAGACCTTCAGTGCATGATGTTTTCAAAGCCTTTGAGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
**
636305 TGTACTCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC-GGGTCATC
636351 TGTAAG
1 TGTAAG
636357 ACCTAAAGTG
Statistics
Matches: 286, Mismatches: 33, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
44 42 0.15
45 233 0.81
46 11 0.04
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (45 bp):
TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
Found at i:636797 original size:3 final size:3
Alignment explanation
Indices: 636789--636842 Score: 99
Period size: 3 Copynumber: 17.7 Consensus size: 3
636779 AATTTTTTCA
636789 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
636835 TAT TAT TA
1 TAT TAT TA
636843 AATAAAACCC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:637824 original size:13 final size:13
Alignment explanation
Indices: 637806--637830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
637796 TCGTGTATTT
637806 TAATTTTGTTTTG
1 TAATTTTGTTTTG
637819 TAATTTTGTTTT
1 TAATTTTGTTTT
637831 ATTTATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (13 bp):
TAATTTTGTTTTG
Found at i:638292 original size:18 final size:19
Alignment explanation
Indices: 638269--638305 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
638259 TTTGGCTTTA
638269 TTTAATAAAAATT-TATTT
1 TTTAATAAAAATTGTATTT
*
638287 TTTAATAAATATTGTATTT
1 TTTAATAAAAATTGTATTT
638306 ATAAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTAATAAAAATTGTATTT
Found at i:638360 original size:20 final size:20
Alignment explanation
Indices: 638326--638365 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
638316 ATAAATATAT
*
638326 AATTATTTTAGTTTTATTCA
1 AATTATTATAGTTTTATTCA
* *
638346 AATTATTATATTTTTCTTCA
1 AATTATTATAGTTTTATTCA
638366 TTTTATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (20 bp):
AATTATTATAGTTTTATTCA
Found at i:638572 original size:2 final size:2
Alignment explanation
Indices: 638561--638601 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
638551 ATATCTTGCT
638561 TA TA -A 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
638602 ACTTCGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:639236 original size:2 final size:2
Alignment explanation
Indices: 639229--639309 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
639219 GGGTTTGAAG
639229 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
639271 TA TA TA TA 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 TA T
639310 TAGGATCCAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:642218 original size:18 final size:18
Alignment explanation
Indices: 642190--642271 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
642180 ACCGGTCACA
* *
642190 ACCCTACCCGACCCGTTG
1 ACCCGACCCGACCCATTG
*
642208 ACTCGACCCGACCCATTG
1 ACCCGACCCGACCCATTG
642226 ACCCGACCCGACCCATTG
1 ACCCGACCCGACCCATTG
* *
642244 ACCCGACCCGATCCGTTG
1 ACCCGACCCGACCCATTG
*
642262 ACCTGACCCG
1 ACCCGACCCG
642272 TTGACCGACG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.20, C:0.48, G:0.18, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCATTG
Found at i:645381 original size:40 final size:40
Alignment explanation
Indices: 645322--645443 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
645312 TGCAGGTTTA
*
645322 TAATACACTTCGGTATATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
645362 TAATACACTTCAGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
645402 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
645442 TA
1 TA
645444 GCACTGCGGT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:645655 original size:52 final size:46
Alignment explanation
Indices: 645550--645726 Score: 164
Period size: 48 Copynumber: 3.7 Consensus size: 46
645540 AAGCATACAA
* * *
645550 ATAAGCTTACGAGCTTTTGGAAT-AATGGCAAGTATATGGGTAAAAT
1 ATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGG-AAAAT
645596 -T-AGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGAAAAAAAAT
1 ATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATTGG----AAAAT
* * * *
645646 ATAAGCTTACGAGCTTATGAAATTTTAAACGGTAAGTATTTTGGTAAA-
1 ATAAGCTTACGAGCTTATGGAA---TAAATGGTAAGTATATTGGAAAAT
*
645694 ATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 ATAAGCTTACGAGCTTATGGAATAAATGGTAAG
645727 GGATTTTATG
Statistics
Matches: 111, Mismatches: 11, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
44 18 0.16
45 11 0.10
46 1 0.01
47 15 0.14
48 20 0.18
49 3 0.03
50 5 0.05
51 1 0.01
52 18 0.16
53 19 0.17
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (46 bp):
ATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAAAAT
Found at i:647660 original size:24 final size:24
Alignment explanation
Indices: 647628--647681 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
647618 GAATATTTTA
*
647628 TCTGGTTTCTGATTTGAAATATGT
1 TCTGATTTCTGATTTGAAATATGT
* *
647652 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATTTCTGATTTGAAATATGT
647676 TCTGAT
1 TCTGAT
647682 ATATGATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.52
Consensus pattern (24 bp):
TCTGATTTCTGATTTGAAATATGT
Found at i:647688 original size:24 final size:24
Alignment explanation
Indices: 647637--647688 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
647627 ATCTGGTTTC
* *
647637 TGATTTGAAATATGTTCTGATTTC
1 TGATTTGAAATATGTTCTGATATA
* *
647661 TGATTTGAATTCTGTTCTGATATA
1 TGATTTGAAATATGTTCTGATATA
647685 TGAT
1 TGAT
647689 ATATGATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (24 bp):
TGATTTGAAATATGTTCTGATATA
Found at i:652737 original size:19 final size:19
Alignment explanation
Indices: 652722--652761 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
652712 AACAATATAT
652722 TAAAAACA-ATAAAATAAA
1 TAAAAACATATAAAATAAA
* *
652740 TAAAGACATATAAAATTAA
1 TAAAAACATATAAAATAAA
652759 TAA
1 TAA
652762 CTAAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (19 bp):
TAAAAACATATAAAATAAA
Found at i:654113 original size:3 final size:3
Alignment explanation
Indices: 654105--654208 Score: 138
Period size: 3 Copynumber: 35.0 Consensus size: 3
654095 TTAATATATT
* *
654105 TAA TAA TAA TAA -AA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
654152 TAA TAA TGA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
654200 TGA TAA TAA
1 TAA TAA TAA
654209 AATGGATAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
2 2 0.02
3 85 0.98
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:654216 original size:12 final size:11
Alignment explanation
Indices: 654113--654221 Score: 59
Period size: 12 Copynumber: 9.8 Consensus size: 11
654103 TTTAATAATA
* *
654113 ATAAAAAAATA
1 ATAATAAAATG
*
654124 ATAATAATAATA
1 ATAATAA-AATG
*
654136 ATAATAATAATA
1 ATAATAA-AATG
*
654148 AAAATAATAATG
1 ATAATAA-AATG
*
654160 ATAATAATAT-
1 ATAATAAAATG
654170 -TAAT--AATG
1 ATAATAAAATG
654178 ATAATAATAAT-
1 ATAATAA-AATG
654189 ATTAATAATAATG
1 A-TAATAA-AATG
654202 ATAATAAAATGG
1 ATAATAAAAT-G
654214 ATAA-AAAA
1 ATAATAAAA
654222 AATAGTATCT
Statistics
Matches: 83, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
7 2 0.02
9 8 0.10
11 16 0.19
12 56 0.67
13 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (11 bp):
ATAATAAAATG
Found at i:667515 original size:16 final size:16
Alignment explanation
Indices: 667495--667558 Score: 62
Period size: 16 Copynumber: 4.0 Consensus size: 16
667485 GGAAAAAAAT
*
667495 GAAAAAATG-AAA-AT
1 GAAAAAATGAAAAGAA
667509 GAAAAAATGAAAA-AA
1 GAAAAAATGAAAAGAA
667524 TGAAAAAATGAAAAAAGAA
1 -GAAAAAATG--AAAAGAA
*
667543 GAAAAAAAGAAAAGAA
1 GAAAAAATGAAAAGAA
667559 AATGAGGGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 9 0.21
15 4 0.09
16 16 0.37
18 12 0.28
19 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.08
Consensus pattern (16 bp):
GAAAAAATGAAAAGAA
Found at i:667555 original size:8 final size:8
Alignment explanation
Indices: 667488--667539 Score: 90
Period size: 8 Copynumber: 6.8 Consensus size: 8
667478 GCTTGAAGGA
667488 AAAAAATG
1 AAAAAATG
667496 AAAAAATG
1 AAAAAATG
667504 --AAAATG
1 AAAAAATG
667510 AAAAAATG
1 AAAAAATG
667518 AAAAAATG
1 AAAAAATG
667526 AAAAAATG
1 AAAAAATG
667534 AAAAAA
1 AAAAAA
667540 GAAGAAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.14
8 36 0.86
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:668679 original size:105 final size:105
Alignment explanation
Indices: 668489--668861 Score: 552
Period size: 105 Copynumber: 3.6 Consensus size: 105
668479 AACTATAATT
* * * ** * *
668489 CACCCCAGAAGGAGGTGAATCAACATTTCCATAAGAGTTCATAATGAGAAGAACTTGTCCTAAAT
1 CACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTTAAAG
668554 GAGAAGGTTCGTAATGAGAAGAGTC-TGTTCCTTTCAAATC
66 GAGAAGGTTCGTAATGAGAAGAG-CATGTTCCTTTCAAATC
* **
668594 CACCGCATAAGGAGGTGAACCAACATTTATAGAAGAGTTCATAATGAGAAGAACTCATCTTAAAG
1 CACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTTAAAG
*
668659 GAGAAGTTTCGTAATGAGAAGAGCATGTTCCTTTCAAATC
66 GAGAAGGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATC
* *
668699 CACCGGAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAG
1 CACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTTAAAG
* *
668764 GAGAAGGTTCGTAATTAGAAGAGCATG-TCCTTTCAAATT
66 GAGAAGGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATC
* * * *
668803 CACCCCAGAAGGAGGTGAATCAACATTTCTAAAAGAGTTCATAATGAGAAGAACTCATC
1 CACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATC
668862 CGACAAAAGG
Statistics
Matches: 242, Mismatches: 25, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
104 65 0.27
105 177 0.73
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (105 bp):
CACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTTAAAG
GAGAAGGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATC
Found at i:669333 original size:16 final size:16
Alignment explanation
Indices: 669312--669350 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
669302 GGGGCAGTTG
*
669312 TAACCCCTAAGTCCCA
1 TAACCCCTAAATCCCA
669328 TAA-CCCTAAATCCCA
1 TAACCCCTAAATCCCA
669343 TAATCCCC
1 TAA-CCCC
669351 ATTCAAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 14 0.70
16 3 0.15
17 3 0.15
ACGTcount: A:0.33, C:0.44, G:0.03, T:0.21
Consensus pattern (16 bp):
TAACCCCTAAATCCCA
Found at i:673577 original size:28 final size:26
Alignment explanation
Indices: 673525--673578 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
673515 AGATTTATAT
*
673525 TATAAAGTATATTTTTTATCCAAATA
1 TATAAAGTATATTTTTTATCAAAATA
*
673551 TATAAAGTATTTTTCTTTTATCAAAATA
1 TATAAAGTA-TATT-TTTTATCAAAATA
673579 AATACTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.38
27 3 0.12
28 12 0.50
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (26 bp):
TATAAAGTATATTTTTTATCAAAATA
Found at i:679723 original size:9 final size:9
Alignment explanation
Indices: 679709--679743 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
679699 ATTTGGAATT
679709 AGAGTTTTC
1 AGAGTTTTC
679718 AGAGTTTTC
1 AGAGTTTTC
679727 AGAGTTTTC
1 AGAGTTTTC
*
679736 AAAGTTTT
1 AGAGTTTT
679744 GAGTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.46
Consensus pattern (9 bp):
AGAGTTTTC
Found at i:679749 original size:16 final size:17
Alignment explanation
Indices: 679707--679750 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
679697 GGATTTGGAA
*
679707 TTAGAGTTTTCAGAGTT
1 TTAGAGTTTTCAAAGTT
679724 TTCAGAGTTTTCAAAGTT
1 TT-AGAGTTTTCAAAGTT
679742 TT-GAGTTTT
1 TTAGAGTTTT
679751 TTTTATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 7 0.28
17 2 0.08
18 16 0.64
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.50
Consensus pattern (17 bp):
TTAGAGTTTTCAAAGTT
Found at i:680797 original size:33 final size:32
Alignment explanation
Indices: 680760--680833 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 32
680750 TATTTGCATT
**
680760 AAAAAAATAGCTACAATGATAAGCAAATGACAA
1 AAAAAAATAGCTACAACAATAAGCAAATGA-AA
* * *
680793 AAAAAAGTTGCTACAACAATAAGCCAATGAAA
1 AAAAAAATAGCTACAACAATAAGCAAATGAAA
680825 AAAAAAATA
1 AAAAAAATA
680834 TGATTATTAG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 9 0.26
33 25 0.74
ACGTcount: A:0.62, C:0.12, G:0.11, T:0.15
Consensus pattern (32 bp):
AAAAAAATAGCTACAACAATAAGCAAATGAAA
Found at i:681456 original size:12 final size:12
Alignment explanation
Indices: 681439--681463 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
681429 TATTGGTTGG
681439 TTTTTTAATTTT
1 TTTTTTAATTTT
681451 TTTTTTAATTTT
1 TTTTTTAATTTT
681463 T
1 T
681464 GTGTGTGTAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTAATTTT
Found at i:684157 original size:118 final size:118
Alignment explanation
Indices: 683949--684166 Score: 400
Period size: 118 Copynumber: 1.8 Consensus size: 118
683939 CTGTTACTGT
* *
683949 GTGATTGGTGTGATTGGATGGGAAAGTTATTACCGTAGGCTCCTCAGCTTTGTGCTCAGGGTAAG
1 GTGATTGGTGTGATTGGATGGAAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGTAAG
*
684014 TCCTTACTGGTGTGCAGGTGGGTGTACGGTTCTGGGGAACCTACACATTTTGG
66 TCCTTACTGGTGTGCAGGTAGGTGTACGGTTCTGGGGAACCTACACATTTTGG
684067 GTGATTGGTGTGATTGGATGGAAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGTAAG
1 GTGATTGGTGTGATTGGATGGAAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGTAAG
*
684132 TCCTTACTGGTGTGCAGGTAGGTGTATGGTTCTGG
66 TCCTTACTGGTGTGCAGGTAGGTGTACGGTTCTGG
684167 AAAATATACA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 96 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.33
Consensus pattern (118 bp):
GTGATTGGTGTGATTGGATGGAAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGTAAG
TCCTTACTGGTGTGCAGGTAGGTGTACGGTTCTGGGGAACCTACACATTTTGG
Found at i:690357 original size:29 final size:29
Alignment explanation
Indices: 690288--690456 Score: 241
Period size: 29 Copynumber: 5.8 Consensus size: 29
690278 GATCGTTAAC
* *
690288 TGGTGCTATTTTGGTAAATAATTCAGTTTT
1 TGGTGCTATTCTGGTAAATAATTC-GATTT
*
690318 TTGTGCTATTCTGGTAAATAATTCGATTT
1 TGGTGCTATTCTGGTAAATAATTCGATTT
690347 TGGTGCTATTCTGGTAAATAATTCGATTT
1 TGGTGCTATTCTGGTAAATAATTCGATTT
*
690376 TGGTGCTATTTTGGTAAATAATTCGATTT
1 TGGTGCTATTCTGGTAAATAATTCGATTT
* * *
690405 TGGTTCAATTCTGATAAATAATTC-AGTTT
1 TGGTGCTATTCTGGTAAATAATTCGA-TTT
*
690434 TGGTGCTATTCTGGTAATTAATT
1 TGGTGCTATTCTGGTAAATAATT
690457 TAAAAAGGGT
Statistics
Matches: 125, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
28 1 0.01
29 102 0.82
30 22 0.18
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.47
Consensus pattern (29 bp):
TGGTGCTATTCTGGTAAATAATTCGATTT
Found at i:691377 original size:118 final size:118
Alignment explanation
Indices: 691169--691386 Score: 400
Period size: 118 Copynumber: 1.8 Consensus size: 118
691159 CTGTTACTGT
*
691169 GTGATTGGTGTGATTGGATGGGAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGTAAG
1 GTGATTGGTGTGATTGGATGGAAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGTAAG
*
691234 TCCTTACTGGTGTGCAGGTGGGTGTACGGTTCTGGGGAACCTACACATTTTGG
66 TCCTTACTGGTGTGCAGGTAGGTGTACGGTTCTGGGGAACCTACACATTTTGG
*
691287 GTGATTGGTGTGATTGGATGGAAAAGTTATTACCGCTGGCTCCTCAGCTTTGTGCTCAGGGTAAG
1 GTGATTGGTGTGATTGGATGGAAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGTAAG
*
691352 TCCTTACTGGTGTGCAGGTAGGTGTATGGTTCTGG
66 TCCTTACTGGTGTGCAGGTAGGTGTACGGTTCTGG
691387 AAAATATACA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 96 1.00
ACGTcount: A:0.17, C:0.16, G:0.34, T:0.33
Consensus pattern (118 bp):
GTGATTGGTGTGATTGGATGGAAAAGTTATTACCGCAGGCTCCTCAGCTTTGTGCTCAGGGTAAG
TCCTTACTGGTGTGCAGGTAGGTGTACGGTTCTGGGGAACCTACACATTTTGG
Found at i:693941 original size:20 final size:22
Alignment explanation
Indices: 693902--693957 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
693892 AAGCCTGCCC
693902 ATATTATTTTATTTTCAATATA
1 ATATTATTTTATTTTCAATATA
693924 ATATT-TTTTATTTT-AATA-A
1 ATATTATTTTATTTTCAATATA
*
693943 A-AGTAATTTTATTTT
1 ATA-TTATTTTATTTT
693958 GTTATATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 1 0.03
19 3 0.10
20 13 0.42
21 9 0.29
22 5 0.16
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
ATATTATTTTATTTTCAATATA
Found at i:695346 original size:3 final size:3
Alignment explanation
Indices: 695338--695376 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
695328 TAAAGTACAT
695338 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
695377 GTTCCTATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:700434 original size:17 final size:17
Alignment explanation
Indices: 700412--700446 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
700402 TAATGTTATA
*
700412 AACGTTCTAGCTGAATG
1 AACGTTCTACCTGAATG
700429 AACGTTCTACCTGAATG
1 AACGTTCTACCTGAATG
700446 A
1 A
700447 GAAAACTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (17 bp):
AACGTTCTACCTGAATG
Found at i:703354 original size:13 final size:12
Alignment explanation
Indices: 703321--703356 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
703311 CCTAATGGGA
703321 AATTTTGAAAAC
1 AATTTTGAAAAC
*
703333 TATTTTGAAAAC
1 AATTTTGAAAAC
703345 AATGTTTGAAAA
1 AAT-TTTGAAAA
703357 TTCATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (12 bp):
AATTTTGAAAAC
Found at i:703838 original size:20 final size:20
Alignment explanation
Indices: 703813--703869 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 20
703803 AACCCGATGG
*
703813 GTGTATCGGTACACCTAGGA
1 GTGTATCGGTACACCAAGGA
*
703833 GTGTATCGATACACATCCAAGGA
1 GTGTATCGGT--ACA-CCAAGGA
*
703856 ATGTATCGGTACAC
1 GTGTATCGGTACAC
703870 ATTCATAGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 10 0.33
21 3 0.10
22 3 0.10
23 14 0.47
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (20 bp):
GTGTATCGGTACACCAAGGA
Found at i:709076 original size:23 final size:22
Alignment explanation
Indices: 709031--709107 Score: 79
Period size: 23 Copynumber: 3.6 Consensus size: 22
709021 TCCCTCTCTA
* *
709031 TGTATCGATACACT-ATGAATG
1 TGTACCGATACACTCCTGAATG
*
709052 TGTACCGATACATTCCTTGAATG
1 TGTACCGATACACTCC-TGAATG
* *
709075 TGTATCGATACACTCCT--AGG
1 TGTACCGATACACTCCTGAATG
709095 TGTACCGATACAC
1 TGTACCGATACAC
709108 CCGTCAGGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 14 0.30
21 12 0.26
22 1 0.02
23 20 0.43
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (22 bp):
TGTACCGATACACTCCTGAATG
Found at i:709595 original size:12 final size:12
Alignment explanation
Indices: 709566--709600 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
709556 ATATTTTGAT
*
709566 TTTTCAAACATTG
1 TTTTCAAA-ATAG
709579 TTTTCAAAATAG
1 TTTTCAAAATAG
709591 TTTTCAAAAT
1 TTTTCAAAAT
709601 TACCCATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (12 bp):
TTTTCAAAATAG
Found at i:712525 original size:17 final size:17
Alignment explanation
Indices: 712503--712538 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
712493 AAGTTTTCTC
*
712503 ATTCAGCTAGAACTTTT
1 ATTCAGCTAGAACGTTT
712520 ATTCAGCTAGAACGTTT
1 ATTCAGCTAGAACGTTT
712537 AT
1 AT
712539 AACATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (17 bp):
ATTCAGCTAGAACGTTT
Found at i:712784 original size:11 final size:13
Alignment explanation
Indices: 712766--712795 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
712756 AAAAATTTAC
712766 ATTTTTT-TATTA
1 ATTTTTTGTATTA
712778 ATTTTTTGTATTA
1 ATTTTTTGTATTA
712791 ATTTT
1 ATTTT
712796 ATTTCGATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (13 bp):
ATTTTTTGTATTA
Found at i:713427 original size:20 final size:20
Alignment explanation
Indices: 713402--713440 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
713392 TTCCTATTCC
713402 GGTCAACAACTTTGAACTCT
1 GGTCAACAACTTTGAACTCT
713422 GGTCAACAACTTTGAACTC
1 GGTCAACAACTTTGAACTC
713441 CGATCTACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (20 bp):
GGTCAACAACTTTGAACTCT
Found at i:721031 original size:11 final size:11
Alignment explanation
Indices: 721015--721041 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
721005 ACCAATCTAC
721015 CAATGGCCATA
1 CAATGGCCATA
721026 CAATGGCCATA
1 CAATGGCCATA
721037 CAATG
1 CAATG
721042 AACGTAGCCC
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:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (11 bp):
CAATGGCCATA
Found at i:725330 original size:19 final size:19
Alignment explanation
Indices: 725306--725352 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
725296 GGTTTTCGAA
725306 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
725325 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
725343 TTCGCAACAC
1 TTCGCAACAC
725353 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:726276 original size:24 final size:24
Alignment explanation
Indices: 726243--726302 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
726233 TAGTCAGTAT
*
726243 TCGAAATTTGATCTTGGTCAATAC
1 TCGAACTTTGATCTTGGTCAATAC
*
726267 TCGGACTTTGATCTTGGTCAATAC
1 TCGAACTTTGATCTTGGTCAATAC
*
726291 TCGAATTTTGAT
1 TCGAACTTTGAT
726303 GATGTTTCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (24 bp):
TCGAACTTTGATCTTGGTCAATAC
Found at i:728946 original size:20 final size:20
Alignment explanation
Indices: 728923--728991 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
728913 TAACGTTGCA
728923 AATTTGACTATCGCAATGCG
1 AATTTGACTATCGCAATGCG
* **
728943 AATTTGACTTTCGCGTTGCG
1 AATTTGACTATCGCAATGCG
* *
728963 AATTTGACTATCGCAACGTG
1 AATTTGACTATCGCAATGCG
728983 AATTTGACT
1 AATTTGACT
728992 TTCATGTTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (20 bp):
AATTTGACTATCGCAATGCG
Found at i:728960 original size:40 final size:40
Alignment explanation
Indices: 728899--729000 Score: 141
Period size: 40 Copynumber: 2.5 Consensus size: 40
728889 AAATTCGCGT
* *
728899 TGCGAGTTTGACTTTAACGTTGCAAATTTGACTATCGCAA
1 TGCGAATTTGACTTTCACGTTGCAAATTTGACTATCGCAA
* *
728939 TGCGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCAA
1 TGCGAATTTGACTTTCACGTTGCAAATTTGACTATCGCAA
* * *
728979 CGTGAATTTGACTTTCATGTTG
1 TGCGAATTTGACTTTCACGTTG
729001 TGAAAGTGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (40 bp):
TGCGAATTTGACTTTCACGTTGCAAATTTGACTATCGCAA
Found at i:729196 original size:63 final size:64
Alignment explanation
Indices: 729062--729219 Score: 264
Period size: 63 Copynumber: 2.5 Consensus size: 64
729052 AATTTAAAAC
729062 AACAAATCAACTTTTACAAATCAATTAAAAAAGCAAAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAAAAAGCAAAAAATAATTCTTATTTACACATCAATTA
* * * *
729126 AATAAATCAACTTTTACAAATCAATTAAACAAG-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAAAAAGCAAAAAATAATTCTTATTTACACATCAATTA
729189 AACAAATCAACTTTTACAAATCAATGTAAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAAA
729220 TTCAATTAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
63 52 0.60
64 35 0.40
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAAAAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:730646 original size:35 final size:35
Alignment explanation
Indices: 730596--730670 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
730586 GTTCACGTAC
* *
730596 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCAGAGCACAAAGCCGAGGAGCCTCCA
* *
730631 AGTAAGTCCCAGAGCACAAAGCCGATGAGCCTCCA
1 AGTAAGGCCCAGAGCACAAAGCCGAGGAGCCTCCA
730666 AGTAA
1 AGTAA
730671 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.28, G:0.27, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCAGAGCACAAAGCCGAGGAGCCTCCA
Found at i:730774 original size:24 final size:24
Alignment explanation
Indices: 730747--730837 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
730737 CATAATTCAA
*
730747 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
730771 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
730795 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * * *
730818 GTTAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
730838 TCAAATAAGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 20 0.35
24 37 0.65
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:730817 original size:47 final size:48
Alignment explanation
Indices: 730747--730837 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 48
730737 CATAATTCAA
* * *
730747 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
* *
730795 GTCAA-TATCAGATCAGAATCCAGGTTAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
730838 TCAAATAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 33 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:733334 original size:18 final size:18
Alignment explanation
Indices: 733311--733392 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
733301 CAACGGTCAA
*
733311 CGGGTCGGGTGAACGGGT
1 CGGGTCGGGTGAACAGGT
* *
733329 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTGAACAGGT
*
733347 GGGGTCGGGTGAACAGGT
1 CGGGTCGGGTGAACAGGT
* *
733365 CAGGTCGGGTAAACAGGT
1 CGGGTCGGGTGAACAGGT
*
733383 CAGGTCGGGT
1 CGGGTCGGGT
733393 TGCAACCGGT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.16, C:0.17, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTGAACAGGT
Found at i:733346 original size:13 final size:13
Alignment explanation
Indices: 733305--733334 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
733295 ACCAATCAAC
733305 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
733318 GGTGAACGGGTCG
1 GGTCAACGGGTCG
733331 GGTC
1 GGTC
733335 GGGTCAACGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.50, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:734818 original size:21 final size:21
Alignment explanation
Indices: 734792--734889 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
734782 GTGAATCGGG
* * *
734792 CTCTTGAACGGTGGGAGAGAC
1 CTCTTGAACGATGAGAGAGGC
* *
734813 CTCTTGAACGATGATAGGGGC
1 CTCTTGAACGATGAGAGAGGC
*
734834 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGAGGC
*
734855 CTCTTGAACGAT-AGGAGACGC
1 CTCTTGAACGATGA-GAGAGGC
734876 CTCTTGAACGATGA
1 CTCTTGAACGATGA
734890 CAGGTGAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGAGGC
Found at i:737045 original size:20 final size:20
Alignment explanation
Indices: 737020--737102 Score: 96
Period size: 20 Copynumber: 4.2 Consensus size: 20
737010 AAACTTAAAT
*
737020 TCGCAACGCGAATATGAAAA
1 TCGCAACGCGAAAATGAAAA
* * *
737040 TCGCAACGTGAACATAAAAA
1 TCGCAACGCGAAAATGAAAA
*
737060 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
737080 TCGTAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
737099 TCGC
1 TCGC
737103 GTTGCGATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 7 0.13
20 45 0.87
ACGTcount: A:0.46, C:0.20, G:0.18, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:737098 original size:40 final size:39
Alignment explanation
Indices: 737009--737102 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 39
736999 AGTAGTTTCT
* * *
737009 GAAACTTAAATTCGCAACGCGAATATGAAAATCGCAACGT
1 GAAAC-TAAAATCGCAACGCGAAAATGAAAATCGCAACGC
* *
737049 G-AACATAAAAATCGCAATGCGAAAATGAAAATCGTAACGC
1 GAAAC-T-AAAATCGCAACGCGAAAATGAAAATCGCAACGC
737089 GAAACTAAAATCGC
1 GAAACTAAAATCGC
737103 GTTGCGATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
39 12 0.26
40 31 0.67
41 3 0.07
ACGTcount: A:0.47, C:0.19, G:0.17, T:0.17
Consensus pattern (39 bp):
GAAACTAAAATCGCAACGCGAAAATGAAAATCGCAACGC
Found at i:737493 original size:22 final size:22
Alignment explanation
Indices: 737466--737523 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
737456 GATGGAGATA
737466 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
737488 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
737510 GACAGATGTCGCCG
1 GACGGATTTCGCCG
737524 TAGAGAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.43, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:737699 original size:20 final size:20
Alignment explanation
Indices: 737674--737773 Score: 173
Period size: 20 Copynumber: 5.0 Consensus size: 20
737664 ACGCGCTTTC
*
737674 CGAATTTGACTTATGTGTTG
1 CGAATTTGACTTTTGTGTTG
*
737694 CGAATTTGACTTTTATGTTG
1 CGAATTTGACTTTTGTGTTG
737714 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
737734 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
*
737754 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTTTGTGTTG
737774 TGATTTACAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.17, C:0.11, G:0.24, T:0.48
Consensus pattern (20 bp):
CGAATTTGACTTTTGTGTTG
Found at i:737795 original size:60 final size:60
Alignment explanation
Indices: 737674--737801 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
737664 ACGCGCTTTC
* * * **
737674 CGAATTTGACTTATGTGTTGCGAATTTGACTTTTATGTTGCGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTATGTGTTGCGAATTTGACTTCTATGTTGCGAATTTGACATTCGCATTG
* * *
737734 CGAATTTGACTTTTGTGTTGCGAATTTGACTTCTGTGTTGTG-ATTT-ACAAATTCGCATTG
1 CGAATTTGACTTATGTGTTGCGAATTTGACTTCTATGTTGCGAATTTGAC--ATTCGCATTG
737794 CGAATTTG
1 CGAATTTG
737802 GAAAATGGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 2 0.03
59 4 0.07
60 52 0.90
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.46
Consensus pattern (60 bp):
CGAATTTGACTTATGTGTTGCGAATTTGACTTCTATGTTGCGAATTTGACATTCGCATTG
Found at i:741879 original size:22 final size:21
Alignment explanation
Indices: 741828--741878 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
741818 GGAGGGAACT
741828 GATTCCCCCATAGGGGGTACC
1 GATTCCCCCATAGGGGGTACC
741849 GATTCCCCCATAGGGGGTACC
1 GATTCCCCCATAGGGGGTACC
741870 GATTCCCCC
1 GATTCCCCC
741879 CTGCTCAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.37, G:0.25, T:0.20
Consensus pattern (21 bp):
GATTCCCCCATAGGGGGTACC
Found at i:743913 original size:15 final size:15
Alignment explanation
Indices: 743893--743930 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
743883 ATTGAAAGTA
743893 AAATCAAAGATTTGC
1 AAATCAAAGATTTGC
743908 AAATCAAAGATTTGC
1 AAATCAAAGATTTGC
743923 AAATCAAA
1 AAATCAAA
743931 CTAGAAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.24
Consensus pattern (15 bp):
AAATCAAAGATTTGC
Found at i:755449 original size:10 final size:10
Alignment explanation
Indices: 755420--755470 Score: 63
Period size: 10 Copynumber: 5.3 Consensus size: 10
755410 AGTCGAGTCG
755420 GGTCAG-ACC
1 GGTCAGAACC
755429 GGTCA-AACC
1 GGTCAGAACC
755438 GGTTC-GAACC
1 GG-TCAGAACC
*
755448 GGTCAAAACC
1 GGTCAGAACC
755458 GGTCAGAACC
1 GGTCAGAACC
755468 GGT
1 GGT
755471 TGGAAACTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 12 0.33
10 24 0.67
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.14
Consensus pattern (10 bp):
GGTCAGAACC
Found at i:755450 original size:19 final size:20
Alignment explanation
Indices: 755420--755470 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
755410 AGTCGAGTCG
755420 GGTCAG-ACCGGTC-AAACC
1 GGTCAGAACCGGTCAAAACC
755438 GGTTC-GAACCGGTCAAAACC
1 GG-TCAGAACCGGTCAAAACC
755458 GGTCAGAACCGGT
1 GGTCAGAACCGGT
755471 TGGAAACTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.10
19 11 0.38
20 15 0.52
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.14
Consensus pattern (20 bp):
GGTCAGAACCGGTCAAAACC
Found at i:758697 original size:16 final size:16
Alignment explanation
Indices: 758672--758703 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
758662 ATTTCTGGAA
*
758672 ATTTTTTCTTTTTTTT
1 ATTTTGTCTTTTTTTT
758688 ATTTTGTCTTTTTTTT
1 ATTTTGTCTTTTTTTT
758704 GTGCATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.84
Consensus pattern (16 bp):
ATTTTGTCTTTTTTTT
Found at i:763718 original size:26 final size:26
Alignment explanation
Indices: 763689--763740 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
763679 TTTGATCGGT
* * *
763689 TTGACCGGTCACGACCCGTTTACCCG
1 TTGACCCGACACGACCCGTTGACCCG
*
763715 TTGACCCGACCCGACCCGTTGACCCG
1 TTGACCCGACACGACCCGTTGACCCG
763741 ACCGGACCGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.15, C:0.42, G:0.23, T:0.19
Consensus pattern (26 bp):
TTGACCCGACACGACCCGTTGACCCG
Found at i:763752 original size:17 final size:18
Alignment explanation
Indices: 763710--763755 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
763700 CGACCCGTTT
763710 ACCCGTTGACCCGACCCG
1 ACCCGTTGACCCGACCCG
*
763728 ACCCGTTGACCCGACCGG
1 ACCCGTTGACCCGACCCG
763746 A-CCGTTGACC
1 ACCCGTTGACC
763756 GTTGACTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.17, C:0.46, G:0.24, T:0.13
Consensus pattern (18 bp):
ACCCGTTGACCCGACCCG
Found at i:763808 original size:29 final size:29
Alignment explanation
Indices: 763762--763943 Score: 174
Period size: 29 Copynumber: 6.4 Consensus size: 29
763752 GACCGTTGAC
* **
763762 TGGTGCTATTTTGAGAATTAATTCAATTT
1 TGGTGCTATTTTGGGAATTAATTCAAAAT
763791 TGGTGCTATTTTGGGAATTAATTCAAAAT
1 TGGTGCTATTTTGGGAATTAATTCAAAAT
* * *
763820 GGGTGCTATTTTGGTAATT-TTTCAAAA-
1 TGGTGCTATTTTGGGAATTAATTCAAAAT
* * *
763847 -AGTGATATTCTGGGAATTAATTCAAAAT
1 TGGTGCTATTTTGGGAATTAATTCAAAAT
*
763875 TGGTGCTATTTTGGGAATTAAGTCGAAAA-
1 TGGTGCTATTTTGGGAATTAATTC-AAAAT
* ** * * *
763904 GGGTGCTATTTTGATAATTATTTTAAAAA
1 TGGTGCTATTTTGGGAATTAATTCAAAAT
*
763933 GGGTGCTATTT
1 TGGTGCTATTT
763944 GTGTAAAATG
Statistics
Matches: 127, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
26 14 0.11
27 7 0.06
28 11 0.09
29 91 0.72
30 4 0.03
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.42
Consensus pattern (29 bp):
TGGTGCTATTTTGGGAATTAATTCAAAAT
Found at i:763922 original size:84 final size:85
Alignment explanation
Indices: 763776--763933 Score: 248
Period size: 84 Copynumber: 1.9 Consensus size: 85
763766 GCTATTTTGA
** * *
763776 GAATTAATTCAATTTTGGTGCTATTTTGGGAATTAATTCAAAATGGGTGCTATTTTGGTAATT-T
1 GAATTAATTCAAAATTGGTGCTATTTTGGGAATTAAGTCAAAATGGGTGCTATTTTGATAATTAT
763840 TTCAAAAAGTGATATTCTGG
66 TTCAAAAAGTGATATTCTGG
763860 GAATTAATTCAAAATTGGTGCTATTTTGGGAATTAAGTCGAAAA-GGGTGCTATTTTGATAATTA
1 GAATTAATTCAAAATTGGTGCTATTTTGGGAATTAAGTC-AAAATGGGTGCTATTTTGATAATTA
*
763924 TTTTAAAAAG
65 TTTCAAAAAG
763934 GGTGCTATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
84 54 0.81
85 13 0.19
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (85 bp):
GAATTAATTCAAAATTGGTGCTATTTTGGGAATTAAGTCAAAATGGGTGCTATTTTGATAATTAT
TTCAAAAAGTGATATTCTGG
Found at i:767365 original size:18 final size:18
Alignment explanation
Indices: 767342--767376 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
767332 ACCGACCCGA
767342 CCCGACCCGACCCGTTGG
1 CCCGACCCGACCCGTTGG
*
767360 CCCGACCTGACCCGTTG
1 CCCGACCCGACCCGTTG
767377 ATCGGGTGAC
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:0.11, C:0.49, G:0.26, T:0.14
Consensus pattern (18 bp):
CCCGACCCGACCCGTTGG
Found at i:767422 original size:29 final size:28
Alignment explanation
Indices: 767387--767535 Score: 163
Period size: 29 Copynumber: 5.1 Consensus size: 28
767377 ATCGGGTGAC
767387 ATTTTGGGAATTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTAATTCGAAA-GGGTGCT
* * * *
767416 ATTTTGGAAAATAATTTGGAAAGTGTGCT
1 ATTTTGGGAATTAA-TTCGAAAGGGTGCT
* *
767445 ATTTTGGGAATTTAATTTGAAAAGGTGCT
1 ATTTTGGGAA-TTAATTCGAAAGGGTGCT
767474 ATTTTGGGAATTAATTCGAAAAGGGTGCT
1 ATTTTGGGAATTAATTCG-AAAGGGTGCT
* * **
767503 ATTTTGGTAATTATTTTAAAAAGGGTGCT
1 ATTTTGGGAATTA-ATTCGAAAGGGTGCT
767532 ATTT
1 ATTT
767536 CTGTAAAATG
Statistics
Matches: 101, Mismatches: 15, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
28 7 0.07
29 83 0.82
30 11 0.11
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (28 bp):
ATTTTGGGAATTAATTCGAAAGGGTGCT
Found at i:767477 original size:58 final size:57
Alignment explanation
Indices: 767387--767544 Score: 181
Period size: 58 Copynumber: 2.7 Consensus size: 57
767377 ATCGGGTGAC
* * * * *
767387 ATTTTGGGAATTAATTCGAAATGGGTGCTATTTTGGAAAATAATTTGGAAAGTGTGCT
1 ATTTTGGGAATTAATTTGAAA-AGGTGCTATTTTGGAAAATAATTCGAAAAGGGTGCT
* *
767445 ATTTTGGGAATTTAATTTGAAAAGGTGCTATTTTGGGAATTAATTCGAAAAGGGTGCT
1 ATTTTGGGAA-TTAATTTGAAAAGGTGCTATTTTGGAAAATAATTCGAAAAGGGTGCT
* * * *
767503 ATTTTGGTAATTATTTTAAAAAGGGTGCTATTTCTGTAAAAT
1 ATTTTGGGAATTAATTTGAAAA-GGTGCTATTT-TGGAAAAT
767545 GGTTGACAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
57 10 0.12
58 59 0.70
59 15 0.18
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (57 bp):
ATTTTGGGAATTAATTTGAAAAGGTGCTATTTTGGAAAATAATTCGAAAAGGGTGCT
Found at i:772421 original size:27 final size:27
Alignment explanation
Indices: 772360--772412 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
772350 TACCTTCGTC
772360 GGAGGAGCGTCGGGAAGCCCACGAGTA
1 GGAGGAGCGTCGGGAAGCCCACGAGTA
772387 GGAGGAGCGTCGGGAAGCCCACGAGT
1 GGAGGAGCGTCGGGAAGCCCACGAGT
772413 CATCGGAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.45, T:0.08
Consensus pattern (27 bp):
GGAGGAGCGTCGGGAAGCCCACGAGTA
Found at i:772961 original size:36 final size:36
Alignment explanation
Indices: 772921--772999 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
772911 TAATATTTGA
772921 CATTGGCCACTATATTTGTAAATATATTATTTTAGT
1 CATTGGCCACTATATTTGTAAATATATTATTTTAGT
772957 CATTGGCCACTATATTTGTAAATATATTATTTTAGT
1 CATTGGCCACTATATTTGTAAATATATTATTTTAGT
772993 CATTGGC
1 CATTGGC
773000 TTGTGTATAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.46
Consensus pattern (36 bp):
CATTGGCCACTATATTTGTAAATATATTATTTTAGT
Done.