Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 189 of 250
Found at i:59416383 original size:14 final size:15
Alignment explanation
Indices: 59416364--59416393 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
59416354 TTGTTGGAAT
59416364 AATTTT-AAATTTAA
1 AATTTTAAAATTTAA
59416378 AATTTTAAAATTTAA
1 AATTTTAAAATTTAA
59416393 A
1 A
59416394 TAAGTTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTTAAAATTTAA
Found at i:59420843 original size:64 final size:64
Alignment explanation
Indices: 59420762--59420945 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
59420752 AGACATTATG
* * *
59420762 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTAAGAGATAA
* * * * * *
59420826 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTAAGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTAAGAGAT
59420891 AA
63 AA
* * * *
59420893 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
59420946 CAAACTATAT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 21 0.22
65 8 0.08
66 16 0.16
67 30 0.31
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTAAGAGATAA
Found at i:59429250 original size:25 final size:25
Alignment explanation
Indices: 59429215--59429262 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
59429205 CTTATATATA
59429215 TTGATACCTATGTATAAAATAAAAT
1 TTGATACCTATGTATAAAATAAAAT
* * *
59429240 TTGATATCTATTTATTAAATAAA
1 TTGATACCTATGTATAAAATAAA
59429263 TTCCAAGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (25 bp):
TTGATACCTATGTATAAAATAAAAT
Found at i:59436070 original size:6 final size:6
Alignment explanation
Indices: 59436061--59436105 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
59436051 CACTGTAAGG
*
59436061 GTAACA GTAACA GTAACA GTAACA ATAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GTA
59436106 GCGGTACACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:59437168 original size:35 final size:35
Alignment explanation
Indices: 59437129--59437201 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
59437119 ATTTTCTAAA
59437129 ATCAGAACAGGGGATTTCAAGGTCATTTTGACTCT
1 ATCAGAACAGGGGATTTCAAGGTCATTTTGACTCT
59437164 ATCAGAACAGGGGATTTCAAGGTCATTTTGACTCT
1 ATCAGAACAGGGGATTTCAAGGTCATTTTGACTCT
59437199 ATC
1 ATC
59437202 TTACGCCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (35 bp):
ATCAGAACAGGGGATTTCAAGGTCATTTTGACTCT
Found at i:59437935 original size:39 final size:39
Alignment explanation
Indices: 59437891--59438011 Score: 206
Period size: 39 Copynumber: 3.1 Consensus size: 39
59437881 AATTATGTTA
*
59437891 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* *
59437930 CCAGCACGAAGCCTGCGAGACTTTAGCCCAGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
59437969 CCAGCACGAAGCCTGCGGGTCTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
59438008 CCAG
1 CCAG
59438012 TGTCTTGCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 76 1.00
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
Found at i:59440619 original size:15 final size:15
Alignment explanation
Indices: 59440583--59440624 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
59440573 TAATATAATA
*
59440583 ATTTAATAAATATCT
1 ATTTAATAAAAATCT
59440598 A-TT-ATAAAAATCT
1 ATTTAATAAAAATCT
59440611 ATTTAATAACAAAT
1 ATTTAATAA-AAAT
59440625 ATTCTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 10 0.43
14 4 0.17
15 5 0.22
16 4 0.17
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAATAAAAATCT
Found at i:59446870 original size:11 final size:11
Alignment explanation
Indices: 59446843--59446885 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
59446833 TGACCTTTCC
59446843 AAGGTATGGG-
1 AAGGTATGGGA
*
59446853 TAGGTATGGGA
1 AAGGTATGGGA
*
59446864 AAGGTATGGGC
1 AAGGTATGGGA
59446875 AAGGTATGGGA
1 AAGGTATGGGA
59446886 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:59446882 original size:22 final size:21
Alignment explanation
Indices: 59446843--59446885 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
59446833 TGACCTTTCC
*
59446843 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
59446864 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
59446886 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:59450953 original size:18 final size:18
Alignment explanation
Indices: 59450930--59451022 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
59450920 CCCAACTACT
*
59450930 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
59450948 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* *
59450966 GTATATGTAAATAGTACC
1 GTATACGTGAATAGTACC
* *
59450984 GTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
59451002 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
59451020 GTA
1 GTA
59451023 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:59451582 original size:11 final size:11
Alignment explanation
Indices: 59451555--59451597 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
59451545 TGACCTTTCC
59451555 AAGGTATGGG-
1 AAGGTATGGGA
*
59451565 TAGGTATGGGA
1 AAGGTATGGGA
*
59451576 AAGGTATGGGC
1 AAGGTATGGGA
59451587 AAGGTATGGGA
1 AAGGTATGGGA
59451598 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:59451594 original size:22 final size:21
Alignment explanation
Indices: 59451555--59451597 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
59451545 TGACCTTTCC
*
59451555 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
59451576 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
59451598 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:59452313 original size:21 final size:20
Alignment explanation
Indices: 59452287--59452325 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
59452277 TTTCCCTTCT
*
59452287 TTTTGTTTTTCTTATTTTTTC
1 TTTTGTTTTT-TAATTTTTTC
59452308 TTTTGTTTTTTAATTTTT
1 TTTTGTTTTTTAATTTTT
59452326 ATCTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTGTTTTTTAATTTTTTC
Found at i:59456474 original size:21 final size:21
Alignment explanation
Indices: 59456448--59456488 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59456438 AGACGAGCAA
* *
59456448 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
59456469 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
59456489 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:59461034 original size:4 final size:4
Alignment explanation
Indices: 59461025--59461122 Score: 196
Period size: 4 Copynumber: 24.5 Consensus size: 4
59461015 AGTACAAGTG
59461025 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
59461073 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
59461121 AT
1 AT
59461123 GCATGCAGAT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 94 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:59463021 original size:28 final size:24
Alignment explanation
Indices: 59462963--59463011 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
59462953 TAAATCATAT
59462963 ATATATACACAATTTGTTTAAATA
1 ATATATACACAATTTGTTTAAATA
*
59462987 ATATATATACAATTTGTTTAAATA
1 ATATATACACAATTTGTTTAAATA
59463011 A
1 A
59463012 GTATGCTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (24 bp):
ATATATACACAATTTGTTTAAATA
Found at i:59464080 original size:15 final size:15
Alignment explanation
Indices: 59464060--59464111 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
59464050 ACTACAAAGC
59464060 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
59464075 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
59464094 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
59464109 ATT
1 ATT
59464112 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:59464172 original size:15 final size:16
Alignment explanation
Indices: 59464143--59464178 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
59464133 AGGTGAAGAA
*
59464143 TATTATTTAATATTAT
1 TATTATTTAAAATTAT
59464159 TATT-TTTAAAATTAT
1 TATTATTTAAAATTAT
59464174 TATTA
1 TATTA
59464179 AAATAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:59464197 original size:19 final size:17
Alignment explanation
Indices: 59464165--59464208 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 17
59464155 TTATTATTTT
59464165 TAAAATTATTATTAAAA
1 TAAAATTATTATTAAAA
59464182 TAAAATTAATTTATTAAAA
1 TAAAATT-A-TTATTAAAA
59464201 TAATAATT
1 TAA-AATT
59464209 TATATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.29
18 1 0.04
19 12 0.50
20 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTATTATTAAAA
Found at i:59465653 original size:44 final size:45
Alignment explanation
Indices: 59465581--59465701 Score: 138
Period size: 44 Copynumber: 2.7 Consensus size: 45
59465571 CAATATCCTG
* * * *
59465581 CCAATGCCATACTT-TGACATGGACTTACATGAATTATTCCTGTCT
1 CCAATGCCATA-TTATAATATGGACTTACATGAATCAATCCTGTCT
**
59465626 CCAATGCCATA-TATAATATGGACTTACATGGCTCAATCCTGTCT
1 CCAATGCCATATTATAATATGGACTTACATGAATCAATCCTGTCT
* *
59465670 CCAAAGCCATATTTCTAATATGGACTTACATG
1 CCAATGCCATA-TTATAATATGGACTTACATG
59465702 GCTCATTTCT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 35 0.54
45 11 0.17
46 18 0.28
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (45 bp):
CCAATGCCATATTATAATATGGACTTACATGAATCAATCCTGTCT
Found at i:59465703 original size:46 final size:44
Alignment explanation
Indices: 59465599--59465706 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
59465589 ATACTTTGAC
** * * *
59465599 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
59465643 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
59465689 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
59465707 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:59468581 original size:20 final size:21
Alignment explanation
Indices: 59468558--59468608 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
59468548 AAATATAAAA
*
59468558 TTTGAATTTTTTATAAA-TAT
1 TTTGAATTTTTTAAAAATTAT
59468578 TTTGAA-TTTTTAAAAATTAT
1 TTTGAATTTTTTAAAAATTAT
59468598 TTT-AATTTTTT
1 TTTGAATTTTTT
59468609 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
TTTGAATTTTTTAAAAATTAT
Found at i:59468587 original size:19 final size:20
Alignment explanation
Indices: 59468558--59468607 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
59468548 AAATATAAAA
*
59468558 TTTGAATTTTTTATAAA-TAT
1 TTTGAA-TTTTTAAAAATTAT
59468578 TTTGAATTTTTAAAAATTAT
1 TTTGAATTTTTAAAAATTAT
59468598 TTT-AATTTTT
1 TTTGAATTTTT
59468608 TTTTGTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTGAATTTTTAAAAATTAT
Found at i:59469631 original size:7 final size:8
Alignment explanation
Indices: 59469612--59469643 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
59469602 CGCACAATAA
59469612 AAAAAATT
1 AAAAAATT
59469620 AAAAAATT
1 AAAAAATT
59469628 AAAAAATT
1 AAAAAATT
59469636 AAAAAATT
1 AAAAAATT
59469644 CTGTTCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAAAATT
Found at i:59473543 original size:11 final size:11
Alignment explanation
Indices: 59473501--59473556 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
59473491 TTATCAATAT
*
59473501 AATAGCAAAAT
1 AATAGCAAAAC
59473512 AATAGCAAAAC
1 AATAGCAAAAC
**
59473523 AGCAGCAAAAC
1 AATAGCAAAAC
*
59473534 AATAGTAAAA-
1 AATAGCAAAAC
* *
59473544 AACAACAAAAC
1 AATAGCAAAAC
59473555 AA
1 AA
59473557 CAAAACAACA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
10 7 0.20
11 28 0.80
ACGTcount: A:0.66, C:0.16, G:0.09, T:0.09
Consensus pattern (11 bp):
AATAGCAAAAC
Found at i:59473555 original size:8 final size:8
Alignment explanation
Indices: 59473542--59473567 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
59473532 ACAATAGTAA
59473542 AAAACAAC
1 AAAACAAC
59473550 AAAACAAC
1 AAAACAAC
59473558 AAAACAAC
1 AAAACAAC
59473566 AA
1 AA
59473568 TAGGGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAACAAC
Found at i:59477299 original size:25 final size:25
Alignment explanation
Indices: 59477271--59477379 Score: 75
Period size: 24 Copynumber: 4.4 Consensus size: 25
59477261 AGCTCTTTCA
59477271 AGCCATATAACAGGAAGCTCATAAG
1 AGCCATATAACAGGAAGCTCATAAG
** *
59477296 AGCC--ATAATTGGAAAGCTCATACG
1 AGCCATATAACAGG-AAGCTCATAAG
* * *
59477320 AGCCAT-TATCGGGTAGCTC-TAGAG
1 AGCCATATAACAGGAAGCTCATA-AG
*
59477344 AGCCAT-TAATCAGGAAGCTCATGAAAA
1 AGCCATATAA-CAGGAAGCTCAT--AAG
59477371 AGCCATATA
1 AGCCATATA
59477380 TTGGGAAGCT
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
23 8 0.13
24 28 0.44
25 16 0.25
26 1 0.02
27 7 0.11
28 3 0.05
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (25 bp):
AGCCATATAACAGGAAGCTCATAAG
Found at i:59477316 original size:24 final size:24
Alignment explanation
Indices: 59477283--59477409 Score: 96
Period size: 24 Copynumber: 5.1 Consensus size: 24
59477273 CCATATAACA
59477283 GGAAGCTCATAAGAGCCATAATTG
1 GGAAGCTCATAAGAGCCATAATTG
* * * *
59477307 GAAAGCTCATACGAGCCATTATCG
1 GGAAGCTCATAAGAGCCATAATTG
* **
59477331 GGTAGCTC-TAGAGAGCCATTAATCA
1 GGAAGCTCATA-AGAGCCA-TAATTG
*
59477356 GGAAGCTCATGAAAAAGCCATATATTG
1 GGAAGCTCAT--AAGAGCCATA-ATTG
*
59477383 GGAAGCTCCAGAA-AGCCATATATTG
1 GGAAGCT-CATAAGAGCCATA-ATTG
59477408 GG
1 GG
59477410 CCGCTTATAA
Statistics
Matches: 82, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
23 2 0.02
24 32 0.39
25 25 0.30
26 5 0.06
27 15 0.18
28 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATTG
Found at i:59477567 original size:24 final size:24
Alignment explanation
Indices: 59477516--59477577 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
59477506 ATATTAGGAA
* * *
59477516 GCTCATGAGAGCCAATATCGAGAT
1 GCTCATGAGAGCTAATAACGAGAC
*
59477540 GCTCATGAGAGCTAATAACGGGAC
1 GCTCATGAGAGCTAATAACGAGAC
* *
59477564 GCTCTTGCGAGCTA
1 GCTCATGAGAGCTA
59477578 TGGTGTGTCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (24 bp):
GCTCATGAGAGCTAATAACGAGAC
Found at i:59479318 original size:6 final size:7
Alignment explanation
Indices: 59479302--59479326 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
59479292 CCGAGCAAAC
59479302 AAAACCA
1 AAAACCA
59479309 AAAACCA
1 AAAACCA
59479316 AAAACCA
1 AAAACCA
59479323 AAAA
1 AAAA
59479327 AACAAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAACCA
Found at i:59482318 original size:132 final size:132
Alignment explanation
Indices: 59481757--59482401 Score: 499
Period size: 131 Copynumber: 4.9 Consensus size: 132
59481747 TCATTCATTC
* * * *
59481757 AAAAATTC-TTCAAAACGAAGACGAGATTTGATGTTTGGCAATTCGCAGAATCGTGCCCTAACGA
1 AAAAATCCTTTCAAAACGAAG-CGATATTCGATGTTTGGCAATTCG-AGAATCGTGCCCTAACGT
* * ** *
59481821 GTTGGGTTGCAATTTCGCG-TTTACTCAAAATAATCGAATA-TCACTTCAAAATTTCACTCATGT
64 GTTGGGTTGCGATTTCTCGTTTTTTTCAAAACAATCGAATATTC-CTTCAAAATTTCACTCATGT
59481884 CTTTT
128 CTTTT
* * * *
59481889 AAAAATCCCTT--AAACGAAGGCGATATGCGATATTTGGCAATTCGTGGAATCGTGCCCTAACGT
1 AAAAATCCTTTCAAAACGAA-GCGATATTCGATGTTTGGCAATTCG-AGAATCGTGCCCTAACGT
* * * * * * * *
59481952 GTTAGGTTGCAATTTCCCATTTGTTT-AAAATAATCAAATATCCCTTCAAAATTTCACTC-TGGT
64 GTTGGGTTGCGATTTCTCGTTTTTTTCAAAACAATCGAATATTCCTTCAAAATTTCACTCAT-GT
*
59482015 CTTCT
128 CTTTT
* * * * ** * * *
59482020 AAAAATCCTTT-AAAGCGAAGGCAATAATCGGTGTTTGATAATTCGAGAATCATGCCCTATCGTA
1 AAAAATCCTTTCAAAACGAA-GCGATATTCGATGTTTGGCAATTCGAGAATCGTGCCCTAACGTG
* * * * *** *
59482084 CTGGGTTGTGATTTCTCG-TTTGTTCAAAACAATCGAATATTCCTTTAGGTTTTCACTCGTGT-T
65 TTGGGTTGCGATTTCTCGTTTTTTTCAAAACAATCGAATATTCCTTCAAAATTTCACTCATGTCT
59482147 TATT
130 T-TT
* * * * ** * *
59482151 AAAAA-CCTTCCAAAACGAAGACAATACTCGGTGTTTGATAATTCGGGAATCGTGCCCGAACGTG
1 AAAAATCCTTTCAAAACGAAG-CGATATTCGATGTTTGGCAATTCGAGAATCGTGCCCTAACGTG
* * * *
59482215 TTGGGTTGTGATTTCTCGTTTTTTTCAAAACAATCGAAGATTCCTTCGAAATTTCACTCACGT-T
65 TTGGGTTGCGATTTCTCGTTTTTTTCAAAACAATCGAATATTCCTTCAAAATTTCACTCATGTCT
59482279 TATT
130 T-TT
* * * * * *
59482283 AAAAA-CCTTTCAAAACGAATGCGATGTTCGATGTTTGGCGATTTGAGAATAGAGCCCTATCGTG
1 AAAAATCCTTTCAAAACGAA-GCGATATTCGATGTTTGGCAATTCGAGAATCGTGCCCTAACGTG
* * * * ** * * *
59482347 CTGGGTTGCGCTTTTTCATTTGCTT-AAAACAATCGAAGATCCCTTCGAAATTTCA
65 TTGGGTTGCGATTTCTCGTTTTTTTCAAAACAATCGAATATTCCTTCAAAATTTCA
59482402 TTCGTATTTT
Statistics
Matches: 414, Mismatches: 86, Indels: 27
0.79 0.16 0.05
Matches are distributed among these distances:
130 12 0.03
131 255 0.62
132 144 0.35
133 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (132 bp):
AAAAATCCTTTCAAAACGAAGCGATATTCGATGTTTGGCAATTCGAGAATCGTGCCCTAACGTGT
TGGGTTGCGATTTCTCGTTTTTTTCAAAACAATCGAATATTCCTTCAAAATTTCACTCATGTCTT
TT
Found at i:59484001 original size:10 final size:10
Alignment explanation
Indices: 59483988--59484018 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
59483978 ATTAAAACAT
*
59483988 AAAAAAATAC
1 AAAAAAATAA
59483998 AAAAAAATAA
1 AAAAAAATAA
59484008 AAAAAAATAA
1 AAAAAAATAA
59484018 A
1 A
59484019 TTTTTACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:59487590 original size:21 final size:22
Alignment explanation
Indices: 59487556--59487600 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
59487546 AGGAAAAAAA
* *
59487556 GATGTACCTAAGGTTAGACGCT
1 GATGTACCAAAGGTCAGACGCT
*
59487578 GATGT-CCAAAGGTCAGAGGCT
1 GATGTACCAAAGGTCAGACGCT
59487599 GA
1 GA
59487601 GAAGTGGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (22 bp):
GATGTACCAAAGGTCAGACGCT
Found at i:59496845 original size:132 final size:132
Alignment explanation
Indices: 59496608--59497779 Score: 1932
Period size: 132 Copynumber: 8.9 Consensus size: 132
59496598 CTACAGATCG
* * * *
59496608 TGTTTCCCTGAAGTTACAGTGAAGCAGATCAAAGACGGAGAATCTTGGCTTCCTGAGGTTGCAGT
1 TGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGTTGCAGT
* * *
59496673 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGAAGTAGGCTAAAATTTTATGT
66 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
59496738 CT
131 CT
59496740 TGTTTCCCT-AGAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGTTGCAG
1 TGTTTCCCTGA-AGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGTTGCAG
* *
59496804 TGAAGCAGATTTAAGCCACAAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATTTTAGG
65 TGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGG
59496869 TCT
130 TCT
* * * * * *
59496872 TGTTTCCCTGAAGTTGCAGTGAAGTAGATCGAAGATGGCGGATCTTGACTTCCTAAAGTTACAGT
1 TGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGTTGCAGT
* *
59496937 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTAGAGCAGGCTGAAATTTTAGGT
66 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
59497002 CT
131 CT
* * ** *
59497004 TGTTTCCCTGAAGTTGTAGTGAAGTAGATCGAAGACGATGAATCTTGGCTTCCTGAAGTTGCGGT
1 TGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGTTGCAGT
* * *
59497069 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATTTCAGAT
66 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
59497134 CT
131 CT
* * *
59497136 TGTTCCCCTGAAGATGCAGTGAAGCAGATCGAAGACGGCAAATCTTGGCTTCCTGAAGTTGCAGT
1 TGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGTTGCAGT
*
59497201 GAAGTAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
66 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
59497266 CT
131 CT
* *
59497268 TGTTTCCCTGGAGTTGCAGTGAAGCAGATCGAAGACGCCGAATCTTGGCTTCCTGAAGTTGCAGT
1 TGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGTTGCAGT
* *
59497333 GAAGCATATTTAAGCTACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
66 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
59497398 CT
131 CT
* *
59497400 TGTTTCCCTGAAGTTGCAGTGACGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGTTGCAGT
1 TGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGTTGCAGT
59497465 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
66 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
59497530 CT
131 CT
* *
59497532 TGTTTCTCTGAAGTTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTTCCTGAAGTTGCAGT
1 TGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGTTGCAGT
59497597 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
66 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
59497662 CT
131 CT
* *
59497664 TGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGACTTCTTGAAGTTGCAGT
1 TGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGTTGCAGT
* * * * *
59497729 GAAGCATATTTAAGCCACTAACCTAGCTCTCTAAAGTTATAGCGGAGTAGG
66 GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGG
59497780 TCGAAGATTA
Statistics
Matches: 970, Mismatches: 68, Indels: 4
0.93 0.07 0.00
Matches are distributed among these distances:
131 1 0.00
132 968 1.00
133 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (132 bp):
TGTTTCCCTGAAGTTGCAGTGAAGCAGATCGAAGACGGCGAATCTTGGCTTCCTGAAGTTGCAGT
GAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAATTTTAGGT
CT
Found at i:59497199 original size:45 final size:45
Alignment explanation
Indices: 59497010--59497605 Score: 134
Period size: 45 Copynumber: 13.5 Consensus size: 45
59497000 GTCTTGTTTC
* * **
59497010 CCTGAAGTTGTAGTGAAGTAGATCGAAGACGATGAATCTTGGCTT
1 CCTGAAGTTGCAGTGAAGCAGATCGAAGACGACAAATCTTGGCTT
* ** * * * * *
59497055 CCTGAAGTTGCGGTGAAGCAGATTTAAG-CCACCAA-CCTAGCTC
1 CCTGAAGTTGCAGTGAAGCAGATCGAAGACGACAAATCTTGGCTT
* * * * * * * *** *
59497098 CCTAAAGTTGTAGTGGAGTAG-GCTAAAATTTCAGATCTT-G-TT
1 CCTGAAGTTGCAGTGAAGCAGATCGAAGACGACAAATCTTGGCTT
* *
59497140 CCCCTGAAGATGCAGTGAAGCAGATCGAAGACGGCAAATCTTGGCTT
1 --CCTGAAGTTGCAGTGAAGCAGATCGAAGACGACAAATCTTGGCTT
* ** * * * * *
59497187 CCTGAAGTTGCAGTGAAGTAGATTTAAG-CCACCAA-CCTAGCTC
1 CCTGAAGTTGCAGTGAAGCAGATCGAAGACGACAAATCTTGGCTT
* * * * * **** ** *
59497230 CCTAAAGTTGTAGTGGAGTAG-GCTGAA-ATTTTAGGTCTT-GTTT
1 CCTGAAGTTGCAGTGAAGCAGATC-GAAGACGACAAATCTTGGCTT
* * *
59497273 CCCTGGAGTTGCAGTGAAGCAGATCGAAGACGCCGAATCTTGGCTT
1 -CCTGAAGTTGCAGTGAAGCAGATCGAAGACGACAAATCTTGGCTT
* ** * * * * *
59497319 CCTGAAGTTGCAGTGAAGCATATTTAAG-CTACCAA-CCTAGCTC
1 CCTGAAGTTGCAGTGAAGCAGATCGAAGACGACAAATCTTGGCTT
* * * * * **** ** *
59497362 CCTAAAGTTGTAGTGGAGTAG-GCTGAA-ATTTTAGGTCTT-GTTT
1 CCTGAAGTTGCAGTGAAGCAGATC-GAAGACGACAAATCTTGGCTT
* ***
59497405 CCCTGAAGTTGCAGTGACGCAGATCGAAGACGGTGAATCTTGGCTT
1 -CCTGAAGTTGCAGTGAAGCAGATCGAAGACGACAAATCTTGGCTT
** * * * * *
59497451 CCTGAAGTTGCAGTGAAGCAGATTTAAG-CCACCAA-CCTAGCTC
1 CCTGAAGTTGCAGTGAAGCAGATCGAAGACGACAAATCTTGGCTT
* * * * * **** ** *
59497494 CCTAAAGTTGTAGTGGAGTAG-GCTGAA-ATTTTAGGTCTT-GTTT
1 CCTGAAGTTGCAGTGAAGCAGATC-GAAGACGACAAATCTTGGCTT
***
59497537 CTCTGAAGTTGCAGTGAAGCAGATCGAAGACGGTGAATCTTGGCTT
1 C-CTGAAGTTGCAGTGAAGCAGATCGAAGACGACAAATCTTGGCTT
59497583 CCTGAAGTTGCAGTGAAGCAGAT
1 CCTGAAGTTGCAGTGAAGCAGAT
59497606 TTAAGCCACC
Statistics
Matches: 366, Mismatches: 157, Indels: 56
0.63 0.27 0.10
Matches are distributed among these distances:
42 4 0.01
43 104 0.28
44 96 0.26
45 149 0.41
46 11 0.03
47 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (45 bp):
CCTGAAGTTGCAGTGAAGCAGATCGAAGACGACAAATCTTGGCTT
Found at i:59498182 original size:25 final size:26
Alignment explanation
Indices: 59498148--59498198 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
59498138 CCGGCCCGAG
*
59498148 CAAACAAAACCA-AAAACCAAAAATA
1 CAAACAAAACAAGAAAACCAAAAATA
*
59498173 CAAACAAAACAAGAAAATCAAAAATA
1 CAAACAAAACAAGAAAACCAAAAATA
59498199 TTATAACAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.73, C:0.20, G:0.02, T:0.06
Consensus pattern (26 bp):
CAAACAAAACAAGAAAACCAAAAATA
Found at i:59500808 original size:131 final size:131
Alignment explanation
Indices: 59500651--59500894 Score: 384
Period size: 131 Copynumber: 1.9 Consensus size: 131
59500641 AGATTTGATG
*
59500651 TTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCGC-GTTTGCTCAAAATAA
1 TTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTC-CTATTTGCTCAAAATAA
* *
59500715 TCGAATATCACTTCAAAATTTCACTCATG-TCTTTTAAAAATCCCTTAAACAAAGGCGATATACG
65 TCAAATATCACTTCAAAATTTCACTCA-GATCTTCTAAAAATCCCTTAAACAAAGGCGATATACG
59500779 ATA
129 ATA
* * *
59500782 TTTGGCAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCCTATTTGTTTAAAATAAT
1 TTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCCTATTTGCTCAAAATAAT
* *
59500847 CAAATATCCCTTCAAAATTTCACTCAGATCTTCTAAAAATCCTTTAAA
66 CAAATATCACTTCAAAATTTCACTCAGATCTTCTAAAAATCCCTTAAA
59500895 ACGAATGCAA
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
130 2 0.02
131 101 0.98
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (131 bp):
TTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCCTATTTGCTCAAAATAAT
CAAATATCACTTCAAAATTTCACTCAGATCTTCTAAAAATCCCTTAAACAAAGGCGATATACGAT
A
Found at i:59501180 original size:132 final size:130
Alignment explanation
Indices: 59500664--59501266 Score: 504
Period size: 132 Copynumber: 4.6 Consensus size: 130
59500654 GGCAATTCGC
* * *
59500664 GGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATA-TCACTT
1 GGAATCGTGCCCTAACGTGTTGGGTTGCGATTTCTCGTTTGTTCAAAATAATCGAATATTC-CTT
* * * * **
59500728 CAAAATTTCACTCATGTCTTTTAAAAATCCCTT-AAACAAAGGCGATA-TACGATATTTGGCAAT
65 CAAAATTTCACTCATGTCTTTTAAAAATCCTTTAAAACGAAGGCAATACT-CGATGTTTGATAAT
59500791 TCGT
129 T--T
* * * * *
59500795 GGAATCGTGCCCTAACGTGTTGGGTTGCAATTTC-CTATTTGTTTAAAATAATCAAATATCCCTT
1 GGAATCGTGCCCTAACGTGTTGGGTTGCGATTTCTC-GTTTGTTCAAAATAATCGAATATTCCTT
* * *
59500859 CAAAATTTCACTCA-GATCTTCTAAAAATCCTTTAAAACGAATGCAATACTCGGTGTTTGATAAT
65 CAAAATTTCACTCATG-TCTTTTAAAAATCCTTTAAAACGAAGGCAATACTCGATGTTTGATAAT
*
59500923 TC
129 TT
* * * * *
59500925 GAGAATCATGCCCTATCGTGCTGGGGTTGTGATTTCTCGTTTGTTCAAAATAATCAAATATTCCT
1 G-GAATCGTGCCCTAACGTG-TTGGGTTGCGATTTCTCGTTTGTTCAAAATAATCGAATATTCCT
* *** * * * *
59500990 TTAGGTTTTCACTCGTGT-TTATTAAAAA-CCTTCCAAAACGAAGACAATACTCGGTGTTTGATA
64 TCAAAATTTCACTCATGTCTT-TTAAAAATCCTT-TAAAACGAAGGCAATACTCGATGTTTGATA
59501053 ATTT
127 ATTT
* * * *
59501057 AGGAATCGTGCCCTAACGTGTTGGGTTGTGATTTCTCGTTTTTTTCAAAACAATCGAAGATTCCT
1 -GGAATCGTGCCCTAACGTGTTGGGTTGCGATTTCTCG-TTTGTTCAAAATAATCGAATATTCCT
* * * ** ** * *
59501122 TCGAAATTTCACTCACGT-TTATTAAAAA-CCTTTCAAAGCGAAGGCGTTGTTCGATGTTTGGTG
64 TCAAAATTTCACTCATGTCTT-TTAAAAATCCTTT-AAAACGAAGGCAATACTCGATGTTTGATA
59501185 ATTT
127 ATTT
* * * * * * * * * *
59501189 GAGAATCGAGCCCTATCGTGCTGGGTTGCGCTTTTTCATTTGCTCAAAACAATCGAAGATCCCTT
1 G-GAATCGTGCCCTAACGTGTTGGGTTGCGATTTCTCGTTTGTTCAAAATAATCGAATATTCCTT
**
59501254 CGGAATTTCACTC
65 CAAAATTTCACTC
59501267 GTATTTTCTA
Statistics
Matches: 389, Mismatches: 68, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
130 3 0.01
131 160 0.41
132 222 0.57
133 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (130 bp):
GGAATCGTGCCCTAACGTGTTGGGTTGCGATTTCTCGTTTGTTCAAAATAATCGAATATTCCTTC
AAAATTTCACTCATGTCTTTTAAAAATCCTTTAAAACGAAGGCAATACTCGATGTTTGATAATTT
Found at i:59501265 original size:263 final size:263
Alignment explanation
Indices: 59500795--59501268 Score: 559
Period size: 264 Copynumber: 1.8 Consensus size: 263
59500785 GGCAATTCGT
* *
59500795 GGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCCTATTTGTTTAAAATAATCAAATATCCCTTC
1 GGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCCTATTTGTTTAAAACAATCAAAGATCCCTTC
* *
59500860 AAAATTTCACTCAGATCTTCTAAAAATCCTTTAAAACGAATGCAATACTCGGTGTTTGATAATTC
66 AAAATTTCACTCAGATCTTCTAAAAATCCTTTAAAACGAAGGCAATACTCGATGTTTGATAATTC
* * * * * *
59500925 GAGAATCATGCCCTATCGTGCTGGGGTTGTGATTTCTCGTTTGTTCAAAATAATCAAATATTCCT
131 GAGAATCATGCCCTATCGTGCTGGGGTTGCGATTTCTCATTTGCTCAAAACAATCAAAGATTCCC
*
59500990 TTAGGTTTTCACTCGTGTTTATTAAAAACCTTCCAAAACGAAGACAATACTCGGTGTTTGATAAT
196 TTAGGATTTCACTCGTGTTTATTAAAAACCTTCCAAAACGAAGACAATACTCGGTGTTTGATAAT
59501055 TTA
261 TTA
** * *
59501058 GGAATCGTGCCCTAACGTGTTGGGTTGTGATTTCTCGT-TTT-TTTCAAAACAATCGAAGATTCC
1 GGAATCGTGCCCTAACGTGTTGGGTTGCAATTTC-C-TATTTGTTT-AAAACAATCAAAGATCCC
* * * ** ** *
59501121 TTCGAAATTTCACTCACG-T-TTATTAAAAA-CCTTTCAAAGCGAAGGCGTTGTTCGATGTTTGG
63 TTCAAAATTTCACTCA-GATCTT-CTAAAAATCCTTT-AAAACGAAGGCAATACTCGATGTTTGA
* * * * *
59501183 TGATTTGAGAATCGA-GCCCTATCGTGCT-GGGTTGCGCTTTTTCATTTGCTCAAAACAATCGAA
125 TAATTCGAGAATC-ATGCCCTATCGTGCTGGGGTTGCGATTTCTCATTTGCTCAAAACAATCAAA
*
59501246 GA-TCCCTTCGGAATTTCACTCGT
189 GATTCCCTTAGG-ATTTCACTCGT
59501269 ATTTTCTAAG
Statistics
Matches: 174, Mismatches: 29, Indels: 16
0.79 0.13 0.07
Matches are distributed among these distances:
262 7 0.04
263 81 0.47
264 83 0.48
265 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (263 bp):
GGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCCTATTTGTTTAAAACAATCAAAGATCCCTTC
AAAATTTCACTCAGATCTTCTAAAAATCCTTTAAAACGAAGGCAATACTCGATGTTTGATAATTC
GAGAATCATGCCCTATCGTGCTGGGGTTGCGATTTCTCATTTGCTCAAAACAATCAAAGATTCCC
TTAGGATTTCACTCGTGTTTATTAAAAACCTTCCAAAACGAAGACAATACTCGGTGTTTGATAAT
TTA
Found at i:59505274 original size:39 final size:39
Alignment explanation
Indices: 59505215--59505391 Score: 295
Period size: 39 Copynumber: 4.5 Consensus size: 39
59505205 ATCATGATCT
** *
59505215 GAAGCCCGAAATCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
59505254 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
59505293 GAAGCCC-AGAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGA-AGGCTAACTGAAGCACATAAGTGCTAAACG
59505332 GAAGCCC-AGAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGA-AGGCTAACTGAAGCACATAAGTGCTAAACG
59505371 GAAGCCCGAAGGCTAACTGAA
1 GAAGCCCGAAGGCTAACTGAA
59505392 ACTCATCAGA
Statistics
Matches: 133, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
38 1 0.01
39 131 0.98
40 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:59518507 original size:101 final size:98
Alignment explanation
Indices: 59518388--59518582 Score: 309
Period size: 101 Copynumber: 2.0 Consensus size: 98
59518378 ATTGAAGAAA
* * *
59518388 GCTTTGGTACTATGTGAAGATTCAAAGATAACAAATATACAAATACACAATGAAACTTAAAACTC
1 GCTTTGGTACCATGTGAAGATTCAAAGATAACAAATATACAAATACACAATGAAACTCAAAACGC
59518453 AAAGGAATACAAACTTAGAATAATAGAAAAAAAAAT
66 AAAGG-A-A-AAACTTAGAATAATAGAAAAAAAAAT
* *
59518489 GCTTTGGTACCATGTGAAGATTCTAAGATAACAAATATACAAATACATAATGAAACTCAAAACGC
1 GCTTTGGTACCATGTGAAGATTCAAAGATAACAAATATACAAATACACAATGAAACTCAAAACGC
*
59518554 AAAGGAAGAACTTAGAATAATAGAAAAAA
66 AAAGGAAAAACTTAGAATAATAGAAAAAA
59518583 TTGGTACATT
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
98 21 0.24
99 1 0.01
100 1 0.01
101 65 0.74
ACGTcount: A:0.52, C:0.12, G:0.13, T:0.22
Consensus pattern (98 bp):
GCTTTGGTACCATGTGAAGATTCAAAGATAACAAATATACAAATACACAATGAAACTCAAAACGC
AAAGGAAAAACTTAGAATAATAGAAAAAAAAAT
Found at i:59525522 original size:23 final size:25
Alignment explanation
Indices: 59525476--59525531 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
59525466 TTTATTACAT
59525476 ATTATTTTAAATTATTTTACATATTAC
1 ATTATTTTAAATTATTTTA-ATA-TAC
*
59525503 -TTATTTTAAGTT-TTTT-ATATAC
1 ATTATTTTAAATTATTTTAATATAC
59525525 ATTATTT
1 ATTATTT
59525532 ATTTTAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.11
23 9 0.33
25 4 0.15
26 11 0.41
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (25 bp):
ATTATTTTAAATTATTTTAATATAC
Found at i:59525534 original size:27 final size:27
Alignment explanation
Indices: 59525465--59525539 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 27
59525455 CCTTAAACGG
59525465 TTTTAT-TACA-TATTATTTTAAATTA
1 TTTTATATACATTATTATTTTAAATTA
* *
59525490 TTTTACAT--ATTACTTATTTTAAGTT-
1 TTTTATATACATTA-TTATTTTAAATTA
59525515 TTTTATATACATTATTTATTTTAAA
1 TTTTATATACATTA-TTATTTTAAA
59525540 CTTTTACATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
24 1 0.03
25 14 0.35
26 12 0.30
27 13 0.32
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTTATATACATTATTATTTTAAATTA
Found at i:59525544 original size:27 final size:25
Alignment explanation
Indices: 59525465--59525545 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 25
59525455 CCTTAAACGG
59525465 TTTTAT-TACA-TATTATTTTAAAT
1 TTTTATATACATTATTATTTTAAAT
* * *
59525488 TATTT-TACATATTACTTATTTTAAGTT
1 T-TTTATATACATTA-TTATTTTAA-AT
*
59525515 TTTTATATACATTATTTATTTTAAAC
1 TTTTATATACATTA-TTATTTTAAAT
59525541 TTTTA
1 TTTTA
59525546 CATATATATA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
23 2 0.05
24 5 0.11
25 2 0.05
26 17 0.39
27 18 0.41
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.60
Consensus pattern (25 bp):
TTTTATATACATTATTATTTTAAAT
Found at i:59525584 original size:46 final size:45
Alignment explanation
Indices: 59525516--59525603 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 45
59525506 TTTTAAGTTT
* * *
59525516 TTTATATACATTATTTATTTTAAACT-TTTACATATATATATTTAAG
1 TTTATATACATAATGTAGTTTAAACTATTT-CATATAT-TATTTAAG
* *
59525562 TTTATGTACATAATGTAGTTTAAACTATTTTATATATTATTT
1 TTTATATACATAATGTAGTTTAAACTATTTCATATATTATTT
59525604 CTTTTAAACC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 5 0.14
46 28 0.78
47 3 0.08
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.55
Consensus pattern (45 bp):
TTTATATACATAATGTAGTTTAAACTATTTCATATATTATTTAAG
Found at i:59525620 original size:25 final size:24
Alignment explanation
Indices: 59525580--59525731 Score: 91
Period size: 24 Copynumber: 6.3 Consensus size: 24
59525570 CATAATGTAG
59525580 TTTAAACTATTTTATATATTATTTCT
1 TTTAAAC-ATTTT-TATATTATTTCT
* * *
59525606 TTTAAAC-CTTTTATATTAGTTAT
1 TTTAAACATTTTTATATTATTTCT
** * * *
59525629 TTTAAACCGTTTTACATTGTTTAT
1 TTTAAACATTTTTATATTATTTCT
*
59525653 TTTAAACATTTTT-TGTTATTT-T
1 TTTAAACATTTTTATATTATTTCT
*
59525675 TTT-AACTATTTTATATATTA-TTCAC
1 TTTAAAC-ATTTT-TATATTATTTC-T
* *
59525700 TTTAAA-TTTTTTATATAATATTCAT
1 TTTAAACATTTTTATATTAT-TTC-T
59525725 TTTAAAC
1 TTTAAAC
59525732 TGTTTTTTAA
Statistics
Matches: 99, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
21 3 0.03
22 9 0.09
23 31 0.31
24 34 0.34
25 13 0.13
26 9 0.09
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.59
Consensus pattern (24 bp):
TTTAAACATTTTTATATTATTTCT
Found at i:59525631 original size:23 final size:23
Alignment explanation
Indices: 59525594--59525664 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
59525584 AACTATTTTA
* *
59525594 TATATTATTTCTTTTAAACCTTT
1 TATATTAGTTATTTTAAACCTTT
59525617 TATATTAGTTATTTTAAACCGTTT
1 TATATTAGTTATTTTAAACC-TTT
* *
59525641 TACATT-GTTTATTTTAAACATTT
1 TATATTAG-TTATTTTAAACCTTT
59525664 T
1 T
59525665 TTGTTATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 23 0.55
24 19 0.45
ACGTcount: A:0.28, C:0.10, G:0.04, T:0.58
Consensus pattern (23 bp):
TATATTAGTTATTTTAAACCTTT
Found at i:59525709 original size:23 final size:24
Alignment explanation
Indices: 59525683--59525730 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
59525673 TTTTTAACTA
*
59525683 TTTTATATATTATTCACTTTAAATT
1 TTTTATATAATATTCACTTTAAA-T
*
59525708 TTTTATATAATATTCATTTTAAA
1 TTTTATATAATATTCACTTTAAA
59525731 CTGTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTATATAATATTCACTTTAAAT
Found at i:59526087 original size:25 final size:24
Alignment explanation
Indices: 59526037--59526096 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
59526027 TTTTAGACTT
59526037 TTTATTTTAAATTGTTTTGTATTA
1 TTTATTTTAAATTGTTTTGTATTA
*
59526061 TTTACTTTAAATTGTTTT-TATGGTA
1 TTTATTTTAAATTGTTTTGTAT--TA
59526086 TTTATTTTAAA
1 TTTATTTTAAA
59526097 CCTTTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 3 0.09
24 17 0.53
25 12 0.38
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (24 bp):
TTTATTTTAAATTGTTTTGTATTA
Found at i:59526111 original size:25 final size:23
Alignment explanation
Indices: 59526037--59526111 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 23
59526027 TTTTAGACTT
*
59526037 TTTATTTTAAATTGTTTTGTAT-TA
1 TTTATTTTAAA-T-TTTTATATGTA
* *
59526061 TTTACTTTAAATTGTTTTTATGGTA
1 TTTATTTTAAATT-TTTATAT-GTA
59526086 TTTATTTTAAACCTTTTTATATGTA
1 TTTATTTTAAA--TTTTTATATGTA
59526111 T
1 T
59526112 ATATATTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
22 1 0.02
23 7 0.17
24 10 0.24
25 16 0.38
26 6 0.14
27 2 0.05
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.63
Consensus pattern (23 bp):
TTTATTTTAAATTTTTATATGTA
Found at i:59529362 original size:57 final size:56
Alignment explanation
Indices: 59529300--59529457 Score: 152
Period size: 57 Copynumber: 2.9 Consensus size: 56
59529290 TTTTTATAGT
* *
59529300 ATTATATATTATGATTT-TT-AATTCATA-TAATAATAATTATATTAAGAATTTTATTAA
1 ATTATATATTAT--TTTATTGAATT-ATATTAATAATAATTATATTAA-AATATGATTAA
* *
59529357 ATTATATATTATTTTATTGAATTATATTTAATAATAATTATGTTAAAATATGGTTAA
1 ATTATATATTATTTTATTGAATTATA-TTAATAATAATTATATTAAAATATGATTAA
* *
59529414 ATTATTTATTATTTAATT--ATT-T-TTAATAATAATCT-TATTAAAAT
1 ATTATATATTATTTTATTGAATTATATTAATAATAAT-TATATTAAAAT
59529458 TTAATAACAA
Statistics
Matches: 89, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
52 19 0.21
53 1 0.01
54 1 0.01
55 6 0.07
56 5 0.06
57 40 0.45
58 17 0.19
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (56 bp):
ATTATATATTATTTTATTGAATTATATTAATAATAATTATATTAAAATATGATTAA
Found at i:59529648 original size:16 final size:16
Alignment explanation
Indices: 59529629--59529673 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
59529619 AATTACAACT
*
59529629 CTATTCCATTATAGCC
1 CTATTCCATTACAGCC
*
59529645 CTATTCAATTACAGCC
1 CTATTCCATTACAGCC
59529661 CTATTCCATTACA
1 CTATTCCATTACA
59529674 ATGAACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.04, T:0.36
Consensus pattern (16 bp):
CTATTCCATTACAGCC
Found at i:59537174 original size:63 final size:63
Alignment explanation
Indices: 59537075--59537201 Score: 218
Period size: 63 Copynumber: 2.0 Consensus size: 63
59537065 GATAGCTTCG
59537075 GCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTAATAGCTTCGGCCACACTTATCT
1 GCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTAATAGCTTCGGCCACACTTATCT
* * * *
59537138 GCTACACTTATCTGATCAAGGACTAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCT
1 GCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTAATAGCTTCGGCCACACTTATCT
59537201 G
1 G
59537202 ATCAAGGACA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (63 bp):
GCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTAATAGCTTCGGCCACACTTATCT
Found at i:59537243 original size:51 final size:50
Alignment explanation
Indices: 59537138--59537243 Score: 158
Period size: 50 Copynumber: 2.1 Consensus size: 50
59537128 ACACTTATCT
* * * *
59537138 GCTACACTTATCTGATCAAGGACTAGTGAAAGTGATAAGTGATAGCTTCG
1 GCTACACTTATCTGATCAAGGACAAATGAAAGTGAAAAGTGATAGCTTCA
*
59537188 GCTACACTTATCTGATCAAGGACAAATGACAAGTGAAAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGGACAAATGA-AAGTGAAAAGTGATAGCTTCA
59537239 GCTAC
1 GCTAC
59537244 CTGATCAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 27 0.54
51 23 0.46
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (50 bp):
GCTACACTTATCTGATCAAGGACAAATGAAAGTGAAAAGTGATAGCTTCA
Found at i:59537259 original size:31 final size:31
Alignment explanation
Indices: 59537219--59537367 Score: 219
Period size: 31 Copynumber: 4.8 Consensus size: 31
59537209 ACAAATGACA
*
59537219 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
59537250 AATGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
59537281 AGTGAAAAGTGGTAGCTTCGGCTACCTAATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
59537312 AGTGCAAAA-TGGTAGCTCCGGCTACCTGATC
1 AGTG-AAAAGTGGTAGCTTCGGCTACCTGATC
* *
59537343 AGTGAATAGTGGTAGCTTCGACTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
59537368 AAGTGACAAG
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
30 3 0.03
31 99 0.93
32 4 0.04
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:59537540 original size:49 final size:48
Alignment explanation
Indices: 59537467--59537572 Score: 149
Period size: 49 Copynumber: 2.2 Consensus size: 48
59537457 GCATCAGTGA
* * *
59537467 GATATGTGATTCGTGTAAGACCATAGCTGGGCTACGGCATCGATATGT
1 GATATGTGATACGTGTAAGACCATAGCTAGGCTACGGCATCGATATAT
* *
59537515 GATATGTGACTACGTGTAAGGCCATAGCTAGGCTATGGCATCGATATAT
1 GATATGTGA-TACGTGTAAGACCATAGCTAGGCTACGGCATCGATATAT
59537564 GAATATGTG
1 G-ATATGTG
59537573 TAAGACCATA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 9 0.18
49 35 0.69
50 7 0.14
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (48 bp):
GATATGTGATACGTGTAAGACCATAGCTAGGCTACGGCATCGATATAT
Found at i:59537574 original size:42 final size:42
Alignment explanation
Indices: 59537528--59537642 Score: 135
Period size: 42 Copynumber: 2.7 Consensus size: 42
59537518 ATGTGACTAC
* *
59537528 GTGTAAGGCCATAGCTAGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAG-TAGGCTATGGCATCGATTATATGAAGAT
* *
59537570 GTGTAAGACCATAGTTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAG-TAGGCTATGGCATCGATTATATGAAGAT
* *
59537612 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGTAG-GCTATGGCATCGA
59537643 GAAAACGAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 3 0.05
42 59 0.94
43 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCATAGTAGGCTATGGCATCGATTATATGAAGAT
Found at i:59537859 original size:29 final size:28
Alignment explanation
Indices: 59537815--59537869 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
59537805 AAAAACCTAA
59537815 CCCAAAAAAAAAAAGAAAAACCTAGCCTC
1 CCCAAAAAAAAAAAG-AAAACCTAGCCTC
** *
59537844 CCCAAAAAAACCAAGAAACCCTAGCC
1 CCCAAAAAAAAAAAGAAAACCTAGCC
59537870 ACCTAGCCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.55, C:0.33, G:0.07, T:0.05
Consensus pattern (28 bp):
CCCAAAAAAAAAAAGAAAACCTAGCCTC
Found at i:59540359 original size:12 final size:12
Alignment explanation
Indices: 59540342--59540377 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
59540332 ATTCATTTGA
59540342 CATTCATGCATT
1 CATTCATGCATT
59540354 CATTCATGCATT
1 CATTCATGCATT
*
59540366 CATTCATACATT
1 CATTCATGCATT
59540378 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:59548799 original size:69 final size:67
Alignment explanation
Indices: 59548636--59548807 Score: 211
Period size: 68 Copynumber: 2.5 Consensus size: 67
59548626 TTTTCAAGGG
* *
59548636 AAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTAATTTTTTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTAATTTTTTT
59548701 TCA
66 T-A
* ** * *
59548704 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTATG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTA-TTTTAATTT-T-
59548769 TTTT-
63 TTTTA
** *
59548773 AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
59548808 TTTAATTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
68 46 0.51
69 39 0.43
70 1 0.01
71 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (67 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTAATTTTTTT
TA
Found at i:59548928 original size:72 final size:72
Alignment explanation
Indices: 59548807--59548965 Score: 241
Period size: 72 Copynumber: 2.2 Consensus size: 72
59548797 GAGTTAAGCC
* *
59548807 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
59548871 TGAGGTA
66 TGAGGTA
** *
59548878 TTTTCAATTTTTGTGTTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACG
1 TTTTCAATTTTTGT-TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
59548942 CTGAGGTA
65 CTGAGGTA
*
59548950 TTTTCAATTTCTGTTT
1 TTTTCAATTTTTGTTT
59548966 CAATTTACGT
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 6 0.08
72 70 0.88
73 4 0.05
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (72 bp):
TTTTCAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
TGAGGTA
Found at i:59549368 original size:140 final size:140
Alignment explanation
Indices: 59548905--59549528 Score: 1168
Period size: 139 Copynumber: 4.5 Consensus size: 140
59548895 TTAATTTCAA
59548905 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTG-TTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
59548969 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
59549034 TCAAAATCAG
131 TCAAAATCAG
59549044 CTCATATTGCGAGA-GTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
59549108 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGA-GTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
59549172 TCAAAATCAG
131 TCAAAATCAG
59549182 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
59549247 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
59549312 TCAAAATCAG
131 TCAAAATCAG
59549322 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
59549387 TTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTAC-TTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
59549451 TCAAAATCAG
131 TCAAAATCAG
59549461 CTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCTGAGGTATTTTCAATTTCTGT-TT
59549525 TCAA
62 TCAA
59549529 AAAAAAAATC
Statistics
Matches: 477, Mismatches: 1, Indels: 11
0.98 0.00 0.02
Matches are distributed among these distances:
138 98 0.21
139 186 0.39
140 164 0.34
141 23 0.05
142 6 0.01
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (140 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
TCAAAATCAG
Found at i:59549385 original size:13 final size:13
Alignment explanation
Indices: 59549367--59549400 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
59549357 CGCTGAGGTA
*
59549367 TTTTCAATTTCTG
1 TTTTCAATTTATG
59549380 TTTTCAATTTATG
1 TTTTCAATTTATG
59549393 TTGTTCAA
1 TT-TTCAA
59549401 GAATCAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:59549458 original size:279 final size:278
Alignment explanation
Indices: 59548905--59549528 Score: 1164
Period size: 279 Copynumber: 2.2 Consensus size: 278
59548895 TTAATTTCAA
59548905 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTG-TTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
59548969 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
59549034 TCAAAATCAGCTCATATTGCGAGAGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTC
131 TCAAAATCAGCTCATATTGCGAGAGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTC
59549099 TGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGTGGGTTGAACCTTTTAATTT
196 TGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGTGGGTTGAACCTTTTAATTT
59549164 CTACTTTTTCAAAATCAG
261 CTACTTTTTCAAAATCAG
59549182 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
59549247 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
59549312 TCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTT
131 TCAAAATCAGCTCATATTGCGAGA-GTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTT
*
59549377 CTGTTTTCAATTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAAT
195 CTGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGA-GTGGGTTGAACCTTTTAAT
59549442 TTCTAC-TTTTCAAAATCAG
259 TTCTACTTTTTCAAAATCAG
59549461 CTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCTGAGGTATTTTCAATTTCTGT-TT
59549525 TCAA
62 TCAA
59549529 AAAAAAAATC
Statistics
Matches: 339, Mismatches: 1, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
277 58 0.17
278 97 0.29
279 130 0.38
280 25 0.07
281 23 0.07
282 6 0.02
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (278 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
TCAAAATCAGCTCATATTGCGAGAGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTC
TGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGTGGGTTGAACCTTTTAATTT
CTACTTTTTCAAAATCAG
Found at i:59549631 original size:49 final size:49
Alignment explanation
Indices: 59549554--59549648 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
59549544 ATATTGCGAG
*
59549554 AATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTCAA
1 AATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTCAA
59549603 AATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTT
1 AATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTT
59549649 TTCAAAATTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (49 bp):
AATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTCAA
Found at i:59549781 original size:197 final size:198
Alignment explanation
Indices: 59549439--59549796 Score: 553
Period size: 197 Copynumber: 1.8 Consensus size: 198
59549429 TGAACCTTTT
* ** *
59549439 AATTTCTACTTTTCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCGGTTCACATGCTGA
1 AATTTCTACTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG-T-ACATGCTGA
59549504 GGTATTTTCAATTTCTGTCTTTCAAAAAAAAAATCAACTCATATTGCGAGAATGAGTTGAGCCTC
64 GGTATTTTCAATTTCTGTCTTTCAAAAAAAAAATCAACTCATATTGCGAGAATGAGTTGAGCCTC
*
59549569 AAGACACGTTGAGGTAATTTCAATTTCTGTTCAAAATGAGTTGAGCCTCAAGACACGCTGAGGTA
129 AAGACACGCTGAGGTAATTTCAATTTCTGTTCAAAATGAGTTGAGCCTCAAGACACGCTGAGGTA
59549634 ATTTC
194 ATTTC
* *
59549639 AATTTCT-GTTTTCAAAATTCAACTCATATTGCGAGAAATTAGTTGAGCCTCAAG-ACATGCTGA
1 AATTTCTACTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGTACATGCTGA
*
59549702 GGTATTTTCAATTT-TGT-TTTCAAAAAAAAAATCAACTCATATTGTGAGAAATGAGTTGAGCCT
64 GGTATTTTCAATTTCTGTCTTTCAAAAAAAAAATCAACTCATATTGCGAG-AATGAGTTGAGCCT
* *
59549765 CAAGACATGCTGAGGTATTTTCAATTTCTGTT
128 CAAGACACGCTGAGGTAATTTCAATTTCTGTT
59549797 TTTCAAAAAA
Statistics
Matches: 145, Mismatches: 10, Indels: 9
0.88 0.06 0.05
Matches are distributed among these distances:
196 30 0.21
197 46 0.32
198 23 0.16
199 9 0.06
200 36 0.25
201 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (198 bp):
AATTTCTACTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGTACATGCTGAGG
TATTTTCAATTTCTGTCTTTCAAAAAAAAAATCAACTCATATTGCGAGAATGAGTTGAGCCTCAA
GACACGCTGAGGTAATTTCAATTTCTGTTCAAAATGAGTTGAGCCTCAAGACACGCTGAGGTAAT
TTC
Found at i:59549851 original size:74 final size:73
Alignment explanation
Indices: 59549602--59549946 Score: 435
Period size: 74 Copynumber: 4.7 Consensus size: 73
59549592 TTTCTGTTCA
* *
59549602 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTC-AAAATTCAACTCAT
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTCAAAAAATCAACTCAT
59549666 ATTGCGAG
66 ATTGCGAG
* *
59549674 AAATTAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTT-TGTTTTCAAAAAAAAAATCAAC
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTC----AAAAAATCAAC
*
59549738 TCATATTGTGAG
62 TCATATTGCGAG
*
59549750 AAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAATCAACTCA
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTG-TTTTCAAAAAATCAACTCA
59549815 TATTGCGAG
65 TATTGCGAG
** * * * *
59549824 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATCAAC-CGT
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTCAAAAAATCAACTCAT
*
59549888 ATTGTGAG
66 ATTGCGAG
*** * * *
59549896 AGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTTTT
1 AAATGAGTTGAGCCTCAAG--ACACGCTGAGGTATTTTCAATTTCTGTTTT
59549947 TCAATTTCTG
Statistics
Matches: 244, Mismatches: 20, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
71 7 0.03
72 66 0.27
73 15 0.06
74 88 0.36
76 61 0.25
77 2 0.01
78 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (73 bp):
AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTCAAAAAATCAACTCAT
ATTGCGAG
Found at i:59550024 original size:92 final size:91
Alignment explanation
Indices: 59549874--59550042 Score: 232
Period size: 92 Copynumber: 1.8 Consensus size: 91
59549864 TTCTGTTGTC
* * *
59549874 AAAAAATCAACCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATT
1 AAAAAATCAACCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGCTATTTTCAATT
*
59549939 TCCGTTTTTCAATTTCTGCCTTTCAA
66 TCCGTCTTTCAATTTCTGCCTTTCAA
* * * *
59549965 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGCGCTGAGCTATTTTCAA
1 AAAAAATCAAC-CATATTGCGAGAGGCGAGTTGAGCCTCAGG-TCACACGCCGAGCTATTTTCAA
*
59550029 TTTCTGTCTTTCAA
64 TTTCCGTCTTTCAA
59550043 AAAAATCAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
91 13 0.19
92 54 0.81
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (91 bp):
AAAAAATCAACCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGCTATTTTCAATT
TCCGTCTTTCAATTTCTGCCTTTCAA
Found at i:59550072 original size:77 final size:77
Alignment explanation
Indices: 59549944--59550444 Score: 419
Period size: 77 Copynumber: 6.2 Consensus size: 77
59549934 CAATTTCCGT
**
59549944 TTTTCAATTTCTGCCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTC
1 TTTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTC
*
59550009 ACGCGCTGAGCTA
65 ACGTGCTGAGCTA
* * *
59550022 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTCAGATC
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGCTC
*** *
59550086 ACACACTGAGGTA
65 ACGTGCTGAGCTA
* * * *
59550099 TTTTTTCAATTT-TATTTTTC-AAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCAGG-
1 --TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGC
* *
59550161 TCACATG-TCGAGGTA
63 TCACGTGCT-GAGCTA
** *
59550176 TTTTCAAAATCTGTTTTTCAGATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
1 TTTTCAATTTCTGTTTTTCA-A----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
59550241 GCCTTGGCTCACGTGCTGAGCTA
55 GCCTTGGCTCACGTGCTGAGCTA
* *
59550264 TTTTCAATTTCTTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA
1 TTTTCAATTTC--TGTTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC---CT-
** * * *
59550329 ATTTCTGCGA-GAGTTGAGTTGAGA
59 -TGGCT-C-ACGTGCTGAGCT---A
59550353 CTTTT-AATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTC
1 -TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTC
59550415 ACGTGCTGAGCTA
65 ACGTGCTGAGCTA
59550428 -TTTCAATTTCTGTTTTT
1 TTTTCAATTTCTGTTTTT
59550445 AATGTCTGTT
Statistics
Matches: 347, Mismatches: 39, Indels: 78
0.75 0.08 0.17
Matches are distributed among these distances:
73 3 0.01
74 13 0.04
75 9 0.03
76 11 0.03
77 94 0.27
78 36 0.10
79 18 0.05
80 29 0.08
81 1 0.00
83 1 0.00
84 30 0.09
85 8 0.02
86 8 0.02
87 10 0.03
88 55 0.16
89 9 0.03
90 12 0.03
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (77 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCA
CGTGCTGAGCTA
Found at i:59550340 original size:30 final size:30
Alignment explanation
Indices: 59550304--59550365 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
59550294 CAACTCATAT
59550304 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGAC-TTTTAATTTC
*
59550334 TGCGAGAGTTGAGTTGAGACTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGACTTTTAATTTC
59550364 TG
1 TG
59550366 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGACTTTTAATTTC
Found at i:59551878 original size:13 final size:13
Alignment explanation
Indices: 59551857--59551886 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
59551847 ATATTATTGT
59551857 TGTAAATTTTTTA
1 TGTAAATTTTTTA
*
59551870 TGTATATTTTTTA
1 TGTAAATTTTTTA
59551883 TGTA
1 TGTA
59551887 CGTTTCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (13 bp):
TGTAAATTTTTTA
Found at i:59555407 original size:28 final size:28
Alignment explanation
Indices: 59555357--59555609 Score: 213
Period size: 28 Copynumber: 9.0 Consensus size: 28
59555347 CACGAAAGTT
* * * * *
59555357 AAGAATAGCTTTTTTGGCAAACTATGAA
1 AAGAATAACCTTTGTGGCGAACTCTGAA
* *
59555385 AAGAATAACCTTTGTGGTGAACTTTGAA
1 AAGAATAACCTTTGTGGCGAACTCTGAA
* * *
59555413 AAGAATAGCTTTTGTGGCGAACTTTGAA
1 AAGAATAACCTTTGTGGCGAACTCTGAA
* * * * *
59555441 AAGAATAGCTTTTATGGCAAACTCTAAA
1 AAGAATAACCTTTGTGGCGAACTCTGAA
* *
59555469 AAGAATAGA-CTGTGTGGCGAACTATGAA
1 AAGAATA-ACCTTTGTGGCGAACTCTGAA
* ** * *
59555497 AATAATAGGCTTTGTGGCAAACTCTAAA
1 AAGAATAACCTTTGTGGCGAACTCTGAA
* *
59555525 AAGAATAACCTTTATGGCGAAATCTGAA
1 AAGAATAACCTTTGTGGCGAACTCTGAA
* * *
59555553 AAGAAT-AGCTTGTGTAGTGAACTCTGAA
1 AAGAATAACCTT-TGTGGCGAACTCTGAA
* *
59555581 AAGAACAGCCTTTGTGGCGAACTCTGAA
1 AAGAATAACCTTTGTGGCGAACTCTGAA
59555609 A
1 A
59555610 GGGATGCCTT
Statistics
Matches: 178, Mismatches: 43, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
27 4 0.02
28 171 0.96
29 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (28 bp):
AAGAATAACCTTTGTGGCGAACTCTGAA
Found at i:59555443 original size:56 final size:56
Alignment explanation
Indices: 59555357--59555628 Score: 242
Period size: 56 Copynumber: 4.9 Consensus size: 56
59555347 CACGAAAGTT
* * * ** * *
59555357 AAGAATAGCTTTTTTGGCAAACTATGAAAAGAATAACCTTTGTGGTGAACTTTGAA
1 AAGAATAGCCTTTGTGGCGAACTATGAAAAGAATAACCTTTGTGGCAAACTCTAAA
* * * * *
59555413 AAGAATAGCTTTTGTGGCGAACTTTGAAAAGAATAGCTTTTATGGCAAACTCTAAA
1 AAGAATAGCCTTTGTGGCGAACTATGAAAAGAATAACCTTTGTGGCAAACTCTAAA
* * * **
59555469 AAGAATAGACTGTGTGGCGAACTATGAAAATAATAGGCTTTGTGGCAAACTCTAAA
1 AAGAATAGCCTTTGTGGCGAACTATGAAAAGAATAACCTTTGTGGCAAACTCTAAA
* * * * * * ** *
59555525 AAGAATAACCTTTATGGCGAAATCTGAAAAGAAT-AGCTTGTGTAGTGAACTCTGAA
1 AAGAATAGCCTTTGTGGCGAACTATGAAAAGAATAACCTT-TGTGGCAAACTCTAAA
* * * * *
59555581 AAGAACAGCCTTTGTGGCGAACTCTGAAAGGGAT-GCCTTTGTGGCAAA
1 AAGAATAGCCTTTGTGGCGAACTATGAAAAGAATAACCTTTGTGGCAAA
59555629 TTTTACATGG
Statistics
Matches: 174, Mismatches: 41, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
55 10 0.06
56 164 0.94
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (56 bp):
AAGAATAGCCTTTGTGGCGAACTATGAAAAGAATAACCTTTGTGGCAAACTCTAAA
Found at i:59555498 original size:84 final size:83
Alignment explanation
Indices: 59555357--59555609 Score: 296
Period size: 84 Copynumber: 3.0 Consensus size: 83
59555347 CACGAAAGTT
* * * *
59555357 AAGAATAGCTTTTTTGGCAAACTATGAAAAGAATA-ACCTTTGTGGTGAACTTTGAAAAGAATAG
1 AAGAATAGCTTTTATGGCAAACTCTGAAAAGAATAGA-CTGTGTGGTGAACTATGAAAAGAATAG
*
59555421 CTTTTGTGGCGAACTTTGAA
65 C-TTTGTGGCGAACTCTGAA
* * *
59555441 AAGAATAGCTTTTATGGCAAACTCTAAAAAGAATAGACTGTGTGGCGAACTATGAAAATAATAGG
1 AAGAATAGCTTTTATGGCAAACTCTGAAAAGAATAGACTGTGTGGTGAACTATGAAAAGAATA-G
* *
59555506 CTTTGTGGCAAACTCTAAA
65 CTTTGTGGCGAACTCTGAA
* * * * *
59555525 AAGAATAACCTTTATGGCGAAA-TCTGAAAAGAATAG-CTTGTGTAGTGAACTCTGAAAAGAACA
1 AAGAATAGCTTTTATGGC-AAACTCTGAAAAGAATAGAC-TGTGTGGTGAACTATGAAAAGAATA
59555588 GCCTTTGTGGCGAACTCTGAA
64 G-CTTTGTGGCGAACTCTGAA
59555609 A
1 A
59555610 GGGATGCCTT
Statistics
Matches: 144, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
83 2 0.01
84 136 0.94
85 6 0.04
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (83 bp):
AAGAATAGCTTTTATGGCAAACTCTGAAAAGAATAGACTGTGTGGTGAACTATGAAAAGAATAGC
TTTGTGGCGAACTCTGAA
Found at i:59555687 original size:27 final size:27
Alignment explanation
Indices: 59555588--59555680 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 27
59555578 GAAAAGAACA
* * * *
59555588 GCCTTTGTGGCGAACTCTGAAAGGGAT-
1 GCCTTTGTGGC-AAATTTTAAATGGATC
* *
59555615 GCCTTTGTGGCAAATTTTACATGGCTC
1 GCCTTTGTGGCAAATTTTAAATGGATC
*
59555642 GGCTTTGTGGCAAATTTTAAATGGATC
1 GCCTTTGTGGCAAATTTTAAATGGATC
59555669 GCCTTTGTGGCA
1 GCCTTTGTGGCA
59555681 TGTTTTATCT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 9 0.16
27 46 0.84
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.33
Consensus pattern (27 bp):
GCCTTTGTGGCAAATTTTAAATGGATC
Found at i:59558377 original size:42 final size:42
Alignment explanation
Indices: 59558318--59558441 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 42
59558308 TGAGTTTCTT
*
59558318 TTTAACCCTAATGGGTTTCCGTTTAGCTCTTTTGAGC-TCCAG
1 TTTAACCCTAATGGGTTTCCGTTTAGCTCTTATGAGCTTCC-G
* * * *
59558360 TTTAACCCTTATGGGTTTCCATTCAGCTCTTATGAGCTTTCG
1 TTTAACCCTAATGGGTTTCCGTTTAGCTCTTATGAGCTTCCG
* * * * *
59558402 TTCAACCCTCACGGGTTTCCGTTTAGCACTTATGTGCTTC
1 TTTAACCCTAATGGGTTTCCGTTTAGCTCTTATGAGCTTC
59558442 TGTGTAGCCT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 66 0.97
43 2 0.03
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (42 bp):
TTTAACCCTAATGGGTTTCCGTTTAGCTCTTATGAGCTTCCG
Found at i:59563505 original size:15 final size:14
Alignment explanation
Indices: 59563473--59563516 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
59563463 TTTTAGTACC
*
59563473 AAATTTTACTATTA
1 AAATATTACTATTA
59563487 AAATATTACTATATA
1 AAATATTACTAT-TA
* *
59563502 AAATAATAATATTA
1 AAATATTACTATTA
59563516 A
1 A
59563517 GACAATAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATTACTATTA
Found at i:59564741 original size:201 final size:198
Alignment explanation
Indices: 59564395--59565169 Score: 718
Period size: 201 Copynumber: 3.9 Consensus size: 198
59564385 GGAGGAAGTT
* * * * * *
59564395 GAGTTCCTAATATCCCTTTCTTTACCACCACAATAATCTGAAACATTTTGTGTTGAAATTAAAGC
1 GAGTTCCTAACATCCATTTCTTTAACACCAGAATAATCTGAAACATTTGGTGTTGAACTTAAAGC
* * * *
59564460 TTCAGAGCTA-CTTGATGCAAGGGTCACCGGACTTGTCATGTTTCTCATATCCAATTCATCTCTC
66 TTCAGAGC-AGCTTGATGCAAGGGTCA-CTGACTAGTCATGTTTCTTATATCCAATTCATCCCTC
* *
59564524 ACAACA-TTGATGGGTTCTGGAGATGGGGAAAAGGAGTTGCCGATATCCATTTCTTTAACAACGT
129 ACAACATTTG-TGGGTTCTGGAGATGAGGAAAAGGAGTT-CCAATATCCATTTCTTTAA-AA-GT
*
59564588 -AGGGCATG
190 GAGCGCATG
* **
59564596 GAGTTCCT-ACAATCCATTTGTTTAACACCAGAATAATCCAAAACATTTGGTGTTGAACTTAAAG
1 GAGTTCCTAAC-ATCCATTTCTTTAACACCAGAATAATCTGAAACATTTGGTGTTGAACTTAAAG
**
59564660 CTTCAGAGCAGCTTGATGCAAGGGTCACTGAACTAGTCATGTTTCTTGCATCCAATTCATCCCTC
65 CTTCAGAGCAGCTTGATGCAAGGGTCACTG-ACTAGTCATGTTTCTTATATCCAATTCATCCCTC
* *
59564725 GCAACATTTGTGGGTTCTGGAGATGAGGAAATGGAGTTCCCAATATCCATTTCTTTAAAAGTGGA
129 ACAACATTTGTGGGTTCTGGAGATGAGGAAAAGGAGTT-CCAATATCCATTTCTTTAAAAGT-GA
*
59564790 GCGCATT
192 GCGCATG
** * * * *
59564797 GAGTTCCTAACATCCACCTCTTTAACACAAGAATAATATGAAGCATTTGATGTTGAACTTAAAGC
1 GAGTTCCTAACATCCATTTCTTTAACACCAGAATAATCTGAAACATTTGGTGTTGAACTTAAAGC
* * * * *
59564862 TTCATAGCAGCTTGCTGCAAGGGTCACTTGACTAATCCTGTTTCTTATATCTAATTCATCCCTCA
66 TTCAGAGCAGCTTGATGCAAGGGTCAC-TGACTAGTCATGTTTCTTATATCCAATTCATCCCTCA
** * * *
59564927 CAACATTCATGGGTTCTGGAGACGAGGAAATA-GAGTTCACAATATCCATTTC-TT--GAG-CA-
130 CAACATTTGTGGGTTCTGGAGATGAGGAAA-AGGAGTTC-CAATATCCATTTCTTTAAAAGTGAG
59564986 C-CA--
193 CGCATG
* **** ** * *
59564989 GAG---GTAATGGACATTTCTTCGACACCAGAATAATCCGAAATATTTGGTGTTGAACTTAAAGC
1 GAGTTCCTAACATCCATTTCTTTAACACCAGAATAATCTGAAACATTTGGTGTTGAACTTAAAGC
* * * * * * ** ** *
59565051 TCCACAGAAACTTAATGTATTGGTCACTGGACTAGTTGTGTTTCTCATATCCAATTCATCCCTCA
66 TTCAGAGCAGCTTGATGCAAGGGTCACT-GACTAGTCATGTTTCTTATATCCAATTCATCCCTCA
* * * ** * * *
59565116 TAACATCTATCAGTTCAGGAGATGAGGAGATGGAGTTCCTAATATCCATTTCTT
130 CAACATTTGTGGGTTCTGGAGATGAGGAAAAGGAGTTCC-AATATCCATTTCTT
59565170 CTACACCAGA
Statistics
Matches: 477, Mismatches: 83, Indels: 39
0.80 0.14 0.07
Matches are distributed among these distances:
188 2 0.00
189 133 0.28
190 1 0.00
192 3 0.01
194 2 0.00
195 1 0.00
196 1 0.00
198 2 0.00
199 2 0.00
200 9 0.02
201 314 0.66
202 7 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (198 bp):
GAGTTCCTAACATCCATTTCTTTAACACCAGAATAATCTGAAACATTTGGTGTTGAACTTAAAGC
TTCAGAGCAGCTTGATGCAAGGGTCACTGACTAGTCATGTTTCTTATATCCAATTCATCCCTCAC
AACATTTGTGGGTTCTGGAGATGAGGAAAAGGAGTTCCAATATCCATTTCTTTAAAAGTGAGCGC
ATG
Found at i:59565322 original size:162 final size:161
Alignment explanation
Indices: 59565000--59565341 Score: 397
Period size: 162 Copynumber: 2.1 Consensus size: 161
59564990 AGGTAATGGA
* * *
59565000 CATTTCTTCGACACCAGAATAATCCGAAATATTTGGTGTTGAACTTAAAGCTCCACAGAAACTTA
1 CATTTCTTCAACACCAGAATAATCCGAAACATTCGGTGTTGAACTTAAAGCTCCACAGAAACTTA
* * *
59565065 ATGTATTGGTCACTGGACTAGTTGTGTTTCTCATATCCAATTCATCCCTCATAACATCTATCAGT
66 ATGTAATGGTCACTGGACTAGTCGTGTTTCTCATATACAATTCATCCCTCATAACATCTATCAGT
* *
59565130 TCAGGAGATGAGGAGATGGAGTTCCTAATATC
131 TCAGGAGATGAGAAGA-GGAGTTACTAATATC
* * * * *
59565162 CATTTCTTCTACACCAGAATAATCTGAAACATTCGGTGTTGAACTTAAAGCTTCAGA-AAATTTT
1 CATTTCTTCAACACCAGAATAATCCGAAACATTCGGTGTTGAACTTAAAGCTCCACAGAAA-CTT
* * * *
59565226 GATGTAATGGTCACTGGACTAGTCGTGTTTCTCATATACAGTTCATCCCTTGC-T-TCATTTA-C
65 AATGTAATGGTCACTGGACTAGTCGTGTTTCTCATATACAATTCATCCC-T-CATAACATCTATC
** *
59565288 GAGTTTTGGGGATGAAGAAGCA-GAGTTACTAATATC
128 -AGTTCAGGAGATG-AGAAG-AGGAGTTACTAATATC
*
59565324 CATTTCTTCAACAGCAGA
1 CATTTCTTCAACACCAGA
59565342 GCAAATAGAG
Statistics
Matches: 153, Mismatches: 21, Indels: 12
0.82 0.11 0.06
Matches are distributed among these distances:
161 4 0.03
162 141 0.92
163 6 0.04
164 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (161 bp):
CATTTCTTCAACACCAGAATAATCCGAAACATTCGGTGTTGAACTTAAAGCTCCACAGAAACTTA
ATGTAATGGTCACTGGACTAGTCGTGTTTCTCATATACAATTCATCCCTCATAACATCTATCAGT
TCAGGAGATGAGAAGAGGAGTTACTAATATC
Found at i:59565556 original size:201 final size:201
Alignment explanation
Indices: 59565145--59565678 Score: 500
Period size: 201 Copynumber: 2.7 Consensus size: 201
59565135 AGATGAGGAG
* * * *
59565145 ATGGAGTTCCTAATATCCATTTCTTCTACACCAGAATAATCTGAAACATTCGGTGTTGAACTTAA
1 ATGGAGTTCCTAACATCCATTTCTCCAACACCAGAATAATCTGAAACATTTGGTGTTGAACTTAA
* * *** * * * * *
59565210 AGCTTCAGA-AAATTTTGATGTAATGGTCACTGGACTAGTCGTGTTTCTCATATACAGTTCATCC
66 AGCTTCAGAGCAA-CTTGACACAAGGGTCACTGGACTAGTCATGGTTCTCATATACAATACATCC
** * * * ** * * * * * *
59565274 CTTGCTTCATTTACGAGTTTTGGGGATGAAGAAGCAGAGTTACTAATATCCATTTCTTCAACAGC
130 CTCACATCATCTACAAGTCCTCGAGATGAAGAAACACAGTCACTAATATCCATTTCTTCAACACC
59565339 AGAGCAA
195 AGAGCAA
* * * *
59565346 ATAGAGTTCCTAACATCCATTTCTCCAACACCAGAATAATCCGAAACATTTGGTGCTGAGCTTAA
1 ATGGAGTTCCTAACATCCATTTCTCCAACACCAGAATAATCTGAAACATTTGGTGTTGAACTTAA
*
59565411 AGCTTCAGAGCAACTTGACACAAGGGTCACTGGGCTAGTCATGGTTCTCATA-ACTAATACATCC
66 AGCTTCAGAGCAACTTGACACAAGGGTCACTGGACTAGTCATGGTTCTCATATAC-AATACATCC
* * * * *
59565475 CTCACATCATCTATAAGTCCTCGAGATGAGGAAACACAG-CACGTAGTATCCGTTTCTTTAACAC
130 CTCACATCATCTACAAGTCCTCGAGATGAAGAAACACAGTCAC-TAATATCCATTTCTTCAACAC
**
59565539 CAGAGGGA
194 CAGAGCAA
* ** * * * *
59565547 ATGGAGTTCCTCACATCCATTTC-CGTGAGACCAGAATAATCTAAAACATTTGATGTTGAACTTG
1 ATGGAGTTCCTAACATCCATTTCTC-CAACACCAGAATAATCTGAAACATTTGGTGTTGAACTTA
* *** * * * * * *
59565611 AAGCTTCAGTGCAACTTGATGTAAGAGTCAGTGAACTAGTCATGTTTCTCATATACAATTCATTC
65 AAGCTTCAGAGCAACTTGACACAAGGGTCACTGGACTAGTCATGGTTCTCATATACAATACATCC
59565676 CTC
130 CTC
59565679 GAAACATTTA
Statistics
Matches: 267, Mismatches: 61, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
200 5 0.02
201 258 0.97
202 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (201 bp):
ATGGAGTTCCTAACATCCATTTCTCCAACACCAGAATAATCTGAAACATTTGGTGTTGAACTTAA
AGCTTCAGAGCAACTTGACACAAGGGTCACTGGACTAGTCATGGTTCTCATATACAATACATCCC
TCACATCATCTACAAGTCCTCGAGATGAAGAAACACAGTCACTAATATCCATTTCTTCAACACCA
GAGCAA
Found at i:59566236 original size:99 final size:100
Alignment explanation
Indices: 59566098--59566310 Score: 340
Period size: 99 Copynumber: 2.1 Consensus size: 100
59566088 CATCATTATT
*
59566098 GCTACTTGGCCTGC-AAACGGGACAATCTTCACCAGCAGTTGGTCCACTTACAGGGGCATTTTCC
1 GCTACTTGGCCTGCTAAACGGGACAATCTTCACCAGCAGTTGGTCCACTTACAGGAGCATTTTCC
*
59566162 CCAATACTTAACCTGCTTATAGGGGCATCAACACT
66 CCAATACTTAACCTGCTTATAGGGGCATCAACACC
* **
59566197 TCTACTTGGCCTGCTAAA-GGGGTAATCTTCACCAGCAGTTGGTCCACTTACAGGAGCATTTTCC
1 GCTACTTGGCCTGCTAAACGGGACAATCTTCACCAGCAGTTGGTCCACTTACAGGAGCATTTTCC
* *
59566261 CCCATACTTAACCTGCTTATAGGGGCATCATCACC
66 CCAATACTTAACCTGCTTATAGGGGCATCAACACC
*
59566296 GCTACTAGGCCTGCT
1 GCTACTTGGCCTGCT
59566311 TATAGGAGCA
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 101 0.97
100 3 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (100 bp):
GCTACTTGGCCTGCTAAACGGGACAATCTTCACCAGCAGTTGGTCCACTTACAGGAGCATTTTCC
CCAATACTTAACCTGCTTATAGGGGCATCAACACC
Found at i:59566314 original size:33 final size:33
Alignment explanation
Indices: 59566272--59566392 Score: 115
Period size: 33 Copynumber: 3.7 Consensus size: 33
59566262 CCATACTTAA
*
59566272 CCTGCTTATAGGGGCATCATCACC-GCTACTAGG
1 CCTGCTTATAGGAGCATCATC-CCAGCTACTAGG
*
59566305 CCTGCTTATAGGAGCATCATCCCAGGTACTTGAGG
1 CCTGCTTATAGGAGCATCATCCCAGCTAC-T-AGG
* * *
59566340 --TGCTCACAGGGGCATCATCCCTA-CTACTAGG
1 CCTGCTTATAGGAGCATCATCCC-AGCTACTAGG
* *
59566371 ACTACTTATAGGAGCATCATCC
1 CCTGCTTATAGGAGCATCATCC
59566393 GTTCTACTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
31 3 0.04
32 3 0.04
33 61 0.85
34 2 0.03
35 3 0.04
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (33 bp):
CCTGCTTATAGGAGCATCATCCCAGCTACTAGG
Found at i:59566335 original size:66 final size:66
Alignment explanation
Indices: 59566265--59566392 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 66
59566255 TTTTCCCCCA
* * * * *
59566265 TACTTAACCTGCTTATAGGGGCATCATCACC-GCTACTAGGCCTGCTTATAGGAGCATCATCCCA
1 TACTTAACCTGCTCACAGGGGCATCATC-CCTACTACTAGGACTACTTATAGGAGCATCATCCCA
59566329 GG
65 GG
* **
59566331 TACTTGAGGTGCTCACAGGGGCATCATCCCTACTACTAGGACTACTTATAGGAGCATCATCC
1 TACTTAACCTGCTCACAGGGGCATCATCCCTACTACTAGGACTACTTATAGGAGCATCATCC
59566393 GTTCTACTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 2 0.04
66 51 0.96
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (66 bp):
TACTTAACCTGCTCACAGGGGCATCATCCCTACTACTAGGACTACTTATAGGAGCATCATCCCAG
G
Found at i:59574899 original size:17 final size:17
Alignment explanation
Indices: 59574877--59574916 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
59574867 TAAATTTAAT
*
59574877 TTTTAATTTACA-TATTA
1 TTTTAATTTA-ATTATGA
59574894 TTTTAATTTAATTATGA
1 TTTTAATTTAATTATGA
59574911 TTTTAA
1 TTTTAA
59574917 AAAATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTAATTTAATTATGA
Found at i:59576901 original size:27 final size:27
Alignment explanation
Indices: 59576870--59576950 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
59576860 ATAGGTGGTG
*
59576870 CCTATCTGGTAGGCGCCACTGGTGACT
1 CCTATCTGATAGGCGCCACTGGTGACT
* * *
59576897 CCTATCTGATAGGTGCCGCTAGTGACT
1 CCTATCTGATAGGCGCCACTGGTGACT
*
59576924 CCTACCTGATAGGCGCCACTGGTGACT
1 CCTATCTGATAGGCGCCACTGGTGACT
59576951 TTTATCTGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.17, C:0.30, G:0.27, T:0.26
Consensus pattern (27 bp):
CCTATCTGATAGGCGCCACTGGTGACT
Found at i:59579697 original size:10 final size:9
Alignment explanation
Indices: 59579680--59579718 Score: 51
Period size: 10 Copynumber: 4.0 Consensus size: 9
59579670 TCTTCTTAAC
59579680 AGAAAGAAA
1 AGAAAGAAA
59579689 AGAAAAGAAA
1 AG-AAAGAAA
59579699 AGGAAAGAGAA
1 A-GAAAGA-AA
59579710 AGAAAGAAA
1 AGAAAGAAA
59579719 TTATTTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 4 0.15
10 19 0.70
11 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (9 bp):
AGAAAGAAA
Found at i:59580137 original size:16 final size:16
Alignment explanation
Indices: 59580086--59580128 Score: 77
Period size: 16 Copynumber: 2.6 Consensus size: 16
59580076 TTATCTCAAC
59580086 TAAAGAAAATTTGAATT
1 TAAA-AAAATTTGAATT
59580103 TAAAAAAATTTGAATT
1 TAAAAAAATTTGAATT
59580119 TAAAAAAATT
1 TAAAAAAATT
59580129 CGAGTTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (16 bp):
TAAAAAAATTTGAATT
Found at i:59580811 original size:17 final size:17
Alignment explanation
Indices: 59580789--59580827 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
59580779 AACTAGTATA
59580789 ATAATAAACAATAATAT
1 ATAATAAACAATAATAT
* *
59580806 ATAATATATAATAATAT
1 ATAATAAACAATAATAT
*
59580823 GTAAT
1 ATAAT
59580828 GTTTAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
ATAATAAACAATAATAT
Found at i:59580842 original size:14 final size:14
Alignment explanation
Indices: 59580817--59580848 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
59580807 TAATATATAA
*
59580817 TAATATGTAATGTT
1 TAATATATAATGTT
59580831 TAATATATAATGTT
1 TAATATATAATGTT
59580845 TAAT
1 TAAT
59580849 CATTGATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (14 bp):
TAATATATAATGTT
Found at i:59583830 original size:21 final size:21
Alignment explanation
Indices: 59583783--59583830 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
59583773 TCCTCACGTC
** *
59583783 CGTGTGTCCACCAGACACGAT
1 CGTGTGTCCAAAACACACGAT
* *
59583804 CATGTGTCCAAAACACACGCT
1 CGTGTGTCCAAAACACACGAT
59583825 CGTGTG
1 CGTGTG
59583831 GAATCCATAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (21 bp):
CGTGTGTCCAAAACACACGAT
Found at i:59586507 original size:28 final size:28
Alignment explanation
Indices: 59586446--59586507 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
59586436 TCAGTGTACG
59586446 AAATATTGAGAATGACACTTAGTGTGCA
1 AAATATTGAGAATGACACTTAGTGTGCA
*
59586474 AGATATTGAGAATGACACTTAGTGTGCA
1 AAATATTGAGAATGACACTTAGTGTGCA
59586502 AAATAT
1 AAATAT
59586508 CGAATGATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (28 bp):
AAATATTGAGAATGACACTTAGTGTGCA
Found at i:59589231 original size:16 final size:16
Alignment explanation
Indices: 59589210--59589243 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
59589200 CTGAAAAAGC
59589210 TTGAGCCCAAGAAAAT
1 TTGAGCCCAAGAAAAT
*
59589226 TTGAGCCCGAGAAAAT
1 TTGAGCCCAAGAAAAT
59589242 TT
1 TT
59589244 AAGTCTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (16 bp):
TTGAGCCCAAGAAAAT
Found at i:59597094 original size:21 final size:20
Alignment explanation
Indices: 59597043--59597104 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
59597033 AATTACTTTG
*
59597043 ATAATTATTTTCAATATTTTT
1 ATAA-TATTTTAAATATTTTT
** *
59597064 ATTACCATTTTTAATAATTTTT
1 A-TAATATTTTAAAT-ATTTTT
59597086 ATAATATTTTAAATCATTT
1 ATAATATTTTAAAT-ATTT
59597105 GAACAAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
21 23 0.72
22 9 0.28
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (20 bp):
ATAATATTTTAAATATTTTT
Found at i:59600110 original size:31 final size:32
Alignment explanation
Indices: 59600067--59600130 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
59600057 TTAGTTTATA
59600067 TGTATTGTTATTTTAAAAGTCGATATAATTTT
1 TGTATTGTTATTTTAAAAGTCGATATAATTTT
*
59600099 TGTA-TGTTATTTTAAAAGTTGATATAATTTT
1 TGTATTGTTATTTTAAAAGTCGATATAATTTT
59600130 T
1 T
59600131 AACTCATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (32 bp):
TGTATTGTTATTTTAAAAGTCGATATAATTTT
Found at i:59612789 original size:18 final size:18
Alignment explanation
Indices: 59612766--59612801 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
59612756 TCCAAACTTG
*
59612766 CACCAATATGATTTTATA
1 CACCAATATGATTATATA
59612784 CACCAATATGATTATATA
1 CACCAATATGATTATATA
59612802 AGTTAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.36
Consensus pattern (18 bp):
CACCAATATGATTATATA
Found at i:59621030 original size:22 final size:22
Alignment explanation
Indices: 59621005--59621046 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
59620995 TCAATACATA
* *
59621005 CAAAAGCGGTGATTCGAACACC
1 CAAAAGCGGAGAATCGAACACC
*
59621027 CAAAATCGGAGAATCGAACA
1 CAAAAGCGGAGAATCGAACA
59621047 AACGAAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.12
Consensus pattern (22 bp):
CAAAAGCGGAGAATCGAACACC
Found at i:59623165 original size:3 final size:3
Alignment explanation
Indices: 59623087--59623149 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
59623077 TTAATTCTGA
* * **
59623087 TAT TAT TAT TAT TA- TAT TCAC TAT TATT TAT TTT TAT TGG TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TA-T TAT TAT TAT TAT TAT TAT
59623133 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
59623150 ATATATGTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.86
4 5 0.10
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:59623271 original size:27 final size:26
Alignment explanation
Indices: 59623202--59623281 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 26
59623192 TACTTTACAT
* * *
59623202 TATTATATTTATTATTTATTTCTAACA
1 TATTATATTTAAT-TTTATTTATATCA
* *
59623229 TATTATTATTTTATTTTCTTTATATCA
1 TATTA-TATTTAATTTTATTTATATCA
*
59623256 TCATTATATTTAATTTGTGTTTATAT
1 T-ATTATATTTAATTT-TATTTATAT
59623282 ATTTTCTCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (26 bp):
TATTATATTTAATTTTATTTATATCA
Found at i:59623870 original size:15 final size:17
Alignment explanation
Indices: 59623850--59623882 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
59623840 CCGTCACCTT
59623850 ACATAT-TAT-TATATA
1 ACATATGTATATATATA
59623865 ACATATGTATATATATA
1 ACATATGTATATATATA
59623882 A
1 A
59623883 TTCATTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
ACATATGTATATATATA
Found at i:59628110 original size:14 final size:14
Alignment explanation
Indices: 59628091--59628122 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
59628081 TATGCCTAAA
*
59628091 AAAAAGAAAGAAAG
1 AAAAAGAAAAAAAG
59628105 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
59628119 AAAA
1 AAAA
59628123 GATCAAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:59629018 original size:73 final size:73
Alignment explanation
Indices: 59628934--59629082 Score: 253
Period size: 73 Copynumber: 2.0 Consensus size: 73
59628924 TTTATTTCTG
* * *
59628934 TTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAA
1 TTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAAGTATGTTCAA
59628999 TTTTTGTT
66 TTTTTGTT
* *
59629007 TTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAAGTATGTTCAG
1 TTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAAGTATGTTCAA
59629072 TTTTTGTT
66 TTTTTGTT
59629080 TTT
1 TTT
59629083 TAATTTATGT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (73 bp):
TTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAAGTATGTTCAA
TTTTTGTT
Found at i:59629173 original size:17 final size:17
Alignment explanation
Indices: 59629151--59629186 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
59629141 CGTTGAGGCA
*
59629151 TTTTCAATTTCTATTTT
1 TTTTCAATTTATATTTT
59629168 TTTTCAATTTATATTTT
1 TTTTCAATTTATATTTT
59629185 TT
1 TT
59629187 AAAAAATCAA
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:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTCAATTTATATTTT
Found at i:59629309 original size:178 final size:177
Alignment explanation
Indices: 59629092--59629604 Score: 558
Period size: 178 Copynumber: 2.9 Consensus size: 177
59629082 TTAATTTATG
59629092 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGTTGAGGCATTTTC
1 TTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCACACGTTGAGGCATTTTC
* **
59629156 AATTTCTATTTTTTTTCAATTTATATTTTTTAAAAAATCAACTCATATTACGAGAAATGAGTTGA
64 AATTTC--TTTTTTTTCAATTTATATTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* * * *
59629221 GCCTCGGGTCATATG-TCGAGGTATTTTCAAACTCTGCTTCTCAAATT-AAGT
127 GCCTCGGCTCACATGCT-GAGCTATTTTCAAACTCT-ATTCTCAAATTCAAGT
* * *
59629272 TTT-AACAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGA-GCTATTTT
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGT--TGAGGC-ATTTT
* * * * *
59629335 CAATTTCTGTTTTTTT-AA-TT-CATGTTTTCAAAAATTAACTCATATTGCTAGAGGTGAGTTGA
63 CAATTTCT-TTTTTTTCAATTTATATTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* * ** * ** *
59629397 GCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTATTTTTTAATTCATGT
127 GCCTCGGCTCACATGCTGAGCTATTTTCAAACTCTATTCTCAAATTCAAGT
* * *
59629448 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTC
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--CACACGTTGAGGCATTTTC
* * * * *
59629513 TATTTC-TGTTTTTCAATTTATATTTTTCAAAAGACCAACTCATATTGCGAGAGGTGAGTTGAGC
64 AATTTCTTTTTTTTCAATTTATATTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
59629577 CTTGGCTCACGTGCTGAGCTATTTTCAA
129 CTCGGCTCACATGCTGAGCTATTTTCAA
59629605 TTTCTGTTTT
Statistics
Matches: 280, Mismatches: 39, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
175 13 0.05
176 68 0.24
177 59 0.21
178 109 0.39
179 13 0.05
180 18 0.06
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (177 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGTTGAGGCATTTTCAA
TTTCTTTTTTTTCAATTTATATTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
CGGCTCACATGCTGAGCTATTTTCAAACTCTATTCTCAAATTCAAGT
Found at i:59629575 original size:267 final size:268
Alignment explanation
Indices: 59628992--59629615 Score: 776
Period size: 267 Copynumber: 2.4 Consensus size: 268
59628982 CGCTGAGGTA
* * * * *
59628992 TTTTT-AATTTTTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-GCA
1 TTTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCA
* * * *
59629055 C--GCTGAAG-TATGTTCAGTTTTTG-TTTTTTAATTTATGTTTCAAAAAATCAACTCATATTGC
65 CGTGCTG-AGCTATTTTCAATTTCTGTTTTTTTAATTCATGTTTCAAAAAATCAACTCATATTGC
*
59629116 GAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGCATTTTCAATTTCTATTTTTTTTCAATTTATA
129 GAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGCATTTTCAATTTCTA-TTTTTTTCAATTTACA
* * *
59629181 TTTTTTAAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCGGGTCATATGTCGAGGTATT
193 TGTTTTAAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCGGCTCACATGTCGAGGTATT
59629246 TTCAAACTCTG
258 TTCAAACTCTG
* * * * *
59629257 CTTCTCAAATTA-AGTTTT-AACAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCAC
1 TTTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCAC
* *
59629320 GTGCTGAGCTATTTTCAATTTCTGTTTTTTTAATTCATGTTTTC-AAAAATTAACTCATATTGCT
66 GTGCTGAGCTATTTTCAATTTCTGTTTTTTTAATTCATG-TTTCAAAAAATCAACTCATATTGCG
* *
59629384 AGAGGTGAGTTGAGCCT-TGGCTCACGTGCTGA-GCTATTTTCAATTTCTA-TTTTTT-AA-TT-
130 AGAGGTGAGTTGAGCCTCAGG-ACACGT--TGAGGC-ATTTTCAATTTCTATTTTTTTCAATTTA
* * **
59629443 CATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATG-CTGAGGT
191 CATGTTTTAAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCGGCTCACATGTC-GAGGT
* **
59629507 ATTTTCTATTTCTG
255 ATTTTCAAACTCTG
*
59629521 TTTTTCAATTTATATTTTTCAAAAGACCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCA
1 TTTTTCAATTTATATTTTTCAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCA
59629586 CGTGCTGAGCTATTTTCAATTTCTGTTTTT
65 CGTGCTGAGCTATTTTCAATTTCTGTTTTT
59629616 AATGTCTGTT
Statistics
Matches: 309, Mismatches: 35, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
263 3 0.01
264 112 0.36
265 16 0.05
266 27 0.09
267 128 0.41
268 6 0.02
269 17 0.06
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.40
Consensus pattern (268 bp):
TTTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCAC
GTGCTGAGCTATTTTCAATTTCTGTTTTTTTAATTCATGTTTCAAAAAATCAACTCATATTGCGA
GAGGTGAGTTGAGCCTCAGGACACGTTGAGGCATTTTCAATTTCTATTTTTTTCAATTTACATGT
TTTAAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCGGCTCACATGTCGAGGTATTTTC
AAACTCTG
Found at i:59629617 original size:177 final size:177
Alignment explanation
Indices: 59628992--59629626 Score: 679
Period size: 177 Copynumber: 3.6 Consensus size: 177
59628982 CGCTGAGGTA
* * * * *
59628992 TTTTT-AATTTTTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-GCA
1 TTTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCA
* * * * *
59629055 C--GCTGAAG-TATGTTCAGTTTTTGTTTTTTAATTTATG-TTTCAAAAAATCAACTCATATTGC
65 CGTGCTG-AGCTATTTTCAATTTCTGCTTTTTAATTCATGTTTTC-AAAAATCAACTCATATTGC
* * * *
59629116 GAGAGGTGAGTTGAGCCTCAGG---ACACGTTGAGGCATTTTCAATTTCTATTT
128 GAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTTTCAATTTC---TG
* * ** * *
59629167 TTTTTCAATTTATATTTTTTAAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCGGGTCA
1 TTTTTCAATTTATA-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCA
** * ** ** * *
59629232 TATG-TCGAGGTATTTTCAAACTCTGCTTCTCAAATT-AAGTTTT-AACAATCAACTCATATTGC
65 CGTGCT-GAGCTATTTTCAATTTCTGCTT-TTTAATTCATGTTTTCAAAAATCAACTCATATTGC
* * *
59629294 GAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTG
128 GAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATTTCTG
* * * * *
59629344 TTTTTTTAATTCAT-GTTTTCAAAAATTAACTCATATTGCTAGAGGTGAGTTGAGCCTTGGCTCA
1 -TTTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCA
**
59629408 CGTGCTGAGCTATTTTCAATTTCTATTTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCGA
65 CGTGCTGAGCTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCGA
*
59629473 GAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCTATTTCTG
130 GAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATTTCTG
*
59629521 TTTTTCAATTTATATTTTTCAAAAGACCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCA
1 TTTTTCAATTTATATTTTTCAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCA
59629586 CGTGCTGAGCTATTTTCAATTTCTG-TTTTTAATGTC-TGTTT
65 CGTGCTGAGCTATTTTCAATTTCTGCTTTTTAAT-TCATGTTT
59629627 AAAGAGTTAA
Statistics
Matches: 381, Mismatches: 60, Indels: 36
0.80 0.13 0.08
Matches are distributed among these distances:
175 10 0.03
176 85 0.22
177 130 0.34
178 113 0.30
179 16 0.04
180 27 0.07
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.40
Consensus pattern (177 bp):
TTTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCAC
GTGCTGAGCTATTTTCAATTTCTGCTTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCGAG
AGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATTTCTG
Found at i:59629788 original size:44 final size:44
Alignment explanation
Indices: 59629724--59629824 Score: 184
Period size: 44 Copynumber: 2.3 Consensus size: 44
59629714 CAGATTTGGC
*
59629724 CTCCCTGAAGTTGCAGTGAAGCAGGTCAAAGTTGCAAGTCTTGT
1 CTCCCTGAAGTTGCAATGAAGCAGGTCAAAGTTGCAAGTCTTGT
*
59629768 CTCCCTAAAGTTGCAATGAAGCAGGTCAAAGTTGCAAGTCTTGT
1 CTCCCTGAAGTTGCAATGAAGCAGGTCAAAGTTGCAAGTCTTGT
59629812 CTCCCTGAAGTTG
1 CTCCCTGAAGTTG
59629825 TAGTAGAGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (44 bp):
CTCCCTGAAGTTGCAATGAAGCAGGTCAAAGTTGCAAGTCTTGT
Found at i:59631466 original size:3 final size:3
Alignment explanation
Indices: 59631396--59631450 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
59631386 TGATATTTTT
* * *
59631396 TTA TTA TTA -TA TTCA TTA TTA TTTA TTG TTA TTG GTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
59631442 TTA TTA TTA
1 TTA TTA TTA
59631451 ATATATGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:59631554 original size:21 final size:21
Alignment explanation
Indices: 59631504--59631554 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
59631494 TACTTTACAT
59631504 TATTATATTTATTATTTATTTC
1 TATTATA-TTATTATTTATTTC
**
59631526 TAACATATTATTATTTATTTTC
1 TATTATATTATTATTTA-TTTC
59631548 T-TTATAT
1 TATTATAT
59631555 CATCATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTATATTATTATTTATTTC
Found at i:59632043 original size:25 final size:25
Alignment explanation
Indices: 59631998--59632053 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
59631988 GTTAGTTTTT
* * *
59631998 ATACTATCTTATGTGTATATTTTGA
1 ATACTATCTTATGTATATATTCTAA
*
59632023 ATACTATGC-TATGTATGTATTCTAA
1 ATACTAT-CTTATGTATATATTCTAA
59632048 ATACTA
1 ATACTA
59632054 CATTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (25 bp):
ATACTATCTTATGTATATATTCTAA
Found at i:59632184 original size:15 final size:17
Alignment explanation
Indices: 59632164--59632196 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
59632154 CCATCACCTT
59632164 ACATAT-TAT-TATATA
1 ACATATGTATATATATA
59632179 ACATATGTATATATATA
1 ACATATGTATATATATA
59632196 A
1 A
59632197 TTCATTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
ACATATGTATATATATA
Found at i:59632994 original size:14 final size:14
Alignment explanation
Indices: 59632975--59633001 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
59632965 ATAGAGATAT
59632975 AAATAGATAAATAC
1 AAATAGATAAATAC
59632989 AAATAGATAAATA
1 AAATAGATAAATA
59633002 ATAGTATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (14 bp):
AAATAGATAAATAC
Found at i:59634655 original size:25 final size:23
Alignment explanation
Indices: 59634624--59634674 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
59634614 CTTACTTTTA
59634624 TATTATATAT-TGTAAGATTATTT
1 TATTATATATAT-TAAGATTATTT
*
59634647 TATTATATATATTAATATTA-TT
1 TATTATATATATTAAGATTATTT
59634669 TATTAT
1 TATTAT
59634675 CTATTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 8 0.31
23 17 0.65
24 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (23 bp):
TATTATATATATTAAGATTATTT
Found at i:59634752 original size:21 final size:21
Alignment explanation
Indices: 59634720--59634786 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
59634710 ATTGTTTTAT
*
59634720 TATTAT-TATATTTTTACTTG
1 TATTATATATATTTTTACTTA
*
59634740 TATTATATATATTTATTAATTA
1 TATTATATATATTT-TTACTTA
* *
59634762 TTTATATATATATTTTTACATA
1 TAT-TATATATATTTTTACTTA
59634784 TAT
1 TAT
59634787 ACTTTCATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 6 0.16
21 7 0.18
22 14 0.37
23 11 0.29
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (21 bp):
TATTATATATATTTTTACTTA
Found at i:59634882 original size:30 final size:29
Alignment explanation
Indices: 59634842--59634916 Score: 71
Period size: 30 Copynumber: 2.6 Consensus size: 29
59634832 TATATTTAAA
*
59634842 TTATATTTTATTATATAAAATTTATTATATT
1 TTAT-TTTTATTATATAAAACTTATTAT-TT
** **
59634873 TTATTTTTATCCTATATTACTTATTATTT
1 TTATTTTTATTATATAAAACTTATTATTT
*
59634902 TTCTTTTT-TTATATA
1 TTATTTTTATTATATA
59634917 TGTTATGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 5 0.14
29 9 0.25
30 18 0.50
31 4 0.11
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATTTTTATTATATAAAACTTATTATTT
Found at i:59634943 original size:12 final size:12
Alignment explanation
Indices: 59634926--59634952 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
59634916 ATGTTATGTA
59634926 TATCATATATAT
1 TATCATATATAT
59634938 TATCATATATAT
1 TATCATATATAT
59634950 TAT
1 TAT
59634953 TTATGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
TATCATATATAT
Found at i:59636274 original size:12 final size:12
Alignment explanation
Indices: 59636257--59636289 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
59636247 ATGACATTAA
59636257 AATAATA-ACAAT
1 AATAATATA-AAT
59636269 AATAATATAAAT
1 AATAATATAAAT
59636281 AATAATATA
1 AATAATATA
59636290 TAAAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.95
13 1 0.05
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (12 bp):
AATAATATAAAT
Found at i:59637581 original size:21 final size:21
Alignment explanation
Indices: 59637520--59637604 Score: 72
Period size: 20 Copynumber: 4.2 Consensus size: 21
59637510 TTAAAATTAT
*
59637520 ATAATAATAA-ATAATGAATA
1 ATAATAATAATATAGTGAATA
*
59637540 ATTATAAT-ATATAGT-AA-A
1 ATAATAATAATATAGTGAATA
*
59637558 ATAACAATAATATAGTGAATA
1 ATAATAATAATATAGTGAATA
* *
59637579 AT-ATATATAATAAAATGATATA
1 ATAATA-ATAATATAGTGA-ATA
59637601 ATAA
1 ATAA
59637605 AATGTATAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
18 7 0.14
19 10 0.20
20 15 0.29
21 13 0.25
22 5 0.10
23 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (21 bp):
ATAATAATAATATAGTGAATA
Found at i:59637590 original size:12 final size:12
Alignment explanation
Indices: 59637517--59637690 Score: 63
Period size: 12 Copynumber: 13.9 Consensus size: 12
59637507 TTTTTAAAAT
59637517 TATATAATAATA
1 TATATAATAATA
59637529 -A-ATAATGAATA
1 TATATAAT-AATA
59637540 -ATTATAATATATA
1 TA-TATAATA-ATA
* *
59637553 GTAAAATAACAATAA
1 -T-ATATAATAAT-A
59637568 TATAGTGAATAATA
1 TATA-T-AATAATA
*
59637582 TATATAATAAAA
1 TATATAATAATA
*
59637594 TGATATAATAAAA
1 T-ATATAATAATA
* *
59637607 TGTATAAATCAAAA
1 TATAT-AAT-AATA
*
59637621 TATATAATAAAA
1 TATATAATAATA
*
59637633 TATA-AATGATA
1 TATATAATAATA
*
59637644 TA-ACAAATAATA
1 TATA-TAATAATA
* * *
59637656 CACA-AATATAAA
1 TATATAATA-ATA
* *
59637668 TAAAAAATAATA
1 TATATAATAATA
59637680 TATATAATAAT
1 TATATAATAAT
59637691 TTTTCATATA
Statistics
Matches: 127, Mismatches: 17, Indels: 36
0.71 0.09 0.20
Matches are distributed among these distances:
10 6 0.05
11 17 0.13
12 41 0.32
13 34 0.27
14 17 0.13
15 11 0.09
16 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (12 bp):
TATATAATAATA
Found at i:59637601 original size:13 final size:13
Alignment explanation
Indices: 59637583--59637633 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
59637573 TGAATAATAT
59637583 ATATAATAAAATG
1 ATATAATAAAATG
59637596 ATATAATAAAATG
1 ATATAATAAAATG
59637609 -TATAAATCAAAAT-
1 ATAT-AAT-AAAATG
59637622 ATATAATAAAAT
1 ATATAATAAAAT
59637634 ATAAATGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.23
13 19 0.54
14 8 0.23
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (13 bp):
ATATAATAAAATG
Found at i:59637630 original size:26 final size:27
Alignment explanation
Indices: 59637582--59637633 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
59637572 GTGAATAATA
59637582 TATATAATAAAATGATATAATAAAATG
1 TATATAATAAAATGATATAATAAAATG
59637609 TATA-AATCAAAAT-ATATAATAAAAT
1 TATATAAT-AAAATGATATAATAAAAT
59637634 ATAAATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (27 bp):
TATATAATAAAATGATATAATAAAATG
Done.