Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007744.1 Hibiscus syriacus cultivar Beakdansim tig00110007_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4276731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 16
Found at i:2515703 original size:35 final size:35
Alignment explanation
Indices: 2515652--2515722 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
2515642 AATTTTCTTA
* * *
2515652 TTTCTTTTAAACTCAATTTTCTTTCATTCAGTACT
1 TTTCTTTTAAACTCAATCTTCTTTCATACAATACT
* *
2515687 TTTCTTTTGAATTCAATCTTCTTTCATACAATACT
1 TTTCTTTTAAACTCAATCTTCTTTCATACAATACT
2515722 T
1 T
2515723 CATTTTATCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.24, C:0.20, G:0.03, T:0.54
Consensus pattern (35 bp):
TTTCTTTTAAACTCAATCTTCTTTCATACAATACT
Found at i:2520565 original size:22 final size:22
Alignment explanation
Indices: 2520540--2520593 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
2520530 AAAAATGGGA
*
2520540 GAAATGGTCAGCCATTAGAGAG
1 GAAATGGACAGCCATTAGAGAG
2520562 GAAATGGACAGCCATTAGAGAG
1 GAAATGGACAGCCATTAGAGAG
2520584 GAAATGGACA
1 GAAATGGACA
2520594 TGAAGAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.31, T:0.15
Consensus pattern (22 bp):
GAAATGGACAGCCATTAGAGAG
Found at i:2523362 original size:20 final size:20
Alignment explanation
Indices: 2523337--2523375 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2523327 CAACACGATT
2523337 TTTCTCATTATACAATGATG
1 TTTCTCATTATACAATGATG
*
2523357 TTTCTCATTATAGAATGAT
1 TTTCTCATTATACAATGAT
2523376 TTGTGTTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTCTCATTATACAATGATG
Found at i:2526426 original size:27 final size:29
Alignment explanation
Indices: 2526359--2526426 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 29
2526349 AAAGAAAAAG
*
2526359 AAAATCAGAAAAGAAATTGAAGCACTCCA
1 AAAATAAGAAAAGAAATTGAAGCACTCCA
* * *
2526388 AAAAAAAG-AAAGAAATT-CAGCA-TTCA
1 AAAATAAGAAAAGAAATTGAAGCACTCCA
2526414 AAAATAAGAAAAG
1 AAAATAAGAAAAG
2526427 CAAAGAAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 10 0.30
27 8 0.24
28 9 0.27
29 6 0.18
ACGTcount: A:0.62, C:0.12, G:0.13, T:0.13
Consensus pattern (29 bp):
AAAATAAGAAAAGAAATTGAAGCACTCCA
Found at i:2526430 original size:15 final size:15
Alignment explanation
Indices: 2526419--2526448 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2526409 ATTCAAAAAT
2526419 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
2526434 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
2526448 A
1 A
2526449 GTTGAAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:2527695 original size:24 final size:21
Alignment explanation
Indices: 2527661--2527703 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2527651 TGCACAAGAT
*
2527661 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
2527683 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
2527704 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:2533159 original size:16 final size:16
Alignment explanation
Indices: 2533138--2533168 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2533128 CTCGACAAAT
2533138 TTATATATTTAATATG
1 TTATATATTTAATATG
*
2533154 TTATATATTTTATAT
1 TTATATATTTAATAT
2533169 TCAATGGTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TTATATATTTAATATG
Found at i:2535191 original size:34 final size:33
Alignment explanation
Indices: 2535153--2535228 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 33
2535143 GGTAAGAAAT
* * * * *
2535153 TTATTTTTATGTTAGTATTTTTTTTAAATAGTTA
1 TTATTTTTATATTAATATATTATGTAAATA-TTA
2535187 TTATTTTTATATTAATATATTATGTAAATATTA
1 TTATTTTTATATTAATATATTATGTAAATATTA
2535220 TT-TTTTTAT
1 TTATTTTTAT
2535229 TAAAATAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.19
33 5 0.14
34 25 0.68
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (33 bp):
TTATTTTTATATTAATATATTATGTAAATATTA
Found at i:2535256 original size:34 final size:31
Alignment explanation
Indices: 2535175--2535256 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 31
2535165 TAGTATTTTT
* *
2535175 TTTAAATAGTTATTATTTTTATATTAATATA
1 TTTATATAATTATTATTTTTATATTAATATA
* * *
2535206 -TTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTATATT--AAT-ATA
2535239 TTTATATAATTATTATTT
1 TTTATATAATTATTATTT
2535257 ATTAGAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 19 0.47
32 3 0.08
33 3 0.08
34 15 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTATATTAATATA
Found at i:2535267 original size:16 final size:15
Alignment explanation
Indices: 2535184--2535269 Score: 50
Period size: 15 Copynumber: 5.4 Consensus size: 15
2535174 TTTTAAATAG
*
2535184 TTATTATTT-TTATA
1 TTATTATTTATTAAA
*
2535198 TTAATATATTATGTAAATA
1 TTATTAT-TTAT-T-AA-A
*
2535217 TTATTTTTTTATTAAA
1 TTA-TTATTTATTAAA
* *
2535233 ATAATATTTA-TATAA
1 TTATTATTTATTA-AA
2535248 TTATTATTTATTAGAA
1 TTATTATTTATTA-AA
2535264 TTATTA
1 TTATTA
2535270 ATTTTTTTGC
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
14 8 0.15
15 17 0.31
16 14 0.26
17 3 0.06
18 2 0.04
19 8 0.15
20 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTATTATTTATTAAA
Found at i:2536993 original size:21 final size:21
Alignment explanation
Indices: 2536963--2537010 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2536953 GCAGGGGTAC
* *
2536963 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
2536984 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
2537005 ATGCCA
1 ATGCCA
2537011 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:2537040 original size:21 final size:21
Alignment explanation
Indices: 2537014--2537106 Score: 111
Period size: 21 Copynumber: 4.5 Consensus size: 21
2537004 TATGCCATCT
* *
2537014 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
2537035 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
2537056 CCGCCA-GGTTACATGCCTAG-
1 CCG-CAGGGTTACATGCCTAGC
2537076 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
*
2537097 CCGTAGGGTT
1 CCGCAGGGTT
2537107 TTATACCATA
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.32
21 43 0.65
22 2 0.03
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:2537081 original size:20 final size:20
Alignment explanation
Indices: 2537041--2537097 Score: 96
Period size: 20 Copynumber: 2.8 Consensus size: 20
2537031 GAGCCCGCAG
*
2537041 GGTTACATTCCTAGCCCGCCA
1 GGTTACATGCCTAG-CCGCCA
2537062 GGTTACATGCCTAGCCGCCA
1 GGTTACATGCCTAGCCGCCA
2537082 GGTTACATGCCTAGCC
1 GGTTACATGCCTAGCC
2537098 CGTAGGGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.19, C:0.35, G:0.23, T:0.23
Consensus pattern (20 bp):
GGTTACATGCCTAGCCGCCA
Found at i:2537672 original size:32 final size:34
Alignment explanation
Indices: 2537636--2537708 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 34
2537626 ATTTATTTCA
*
2537636 AAATTTAAAATAAAAATA-AAATAATATTATTC-
1 AAATTTAAAATAAAAATATAAATAATAGTATTCG
* * *
2537668 AAA-TTAAATTTAAAATATAAATTATAGTATTCG
1 AAATTTAAAATAAAAATATAAATAATAGTATTCG
2537701 AAATTTAA
1 AAATTTAA
2537709 CATTAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 12 0.35
32 15 0.44
33 3 0.09
34 4 0.12
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (34 bp):
AAATTTAAAATAAAAATATAAATAATAGTATTCG
Found at i:2538374 original size:124 final size:124
Alignment explanation
Indices: 2538088--2538434 Score: 637
Period size: 124 Copynumber: 2.8 Consensus size: 124
2538078 TAAGTTATTC
2538088 CCCGA-GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
1 CCCGAGGGACATGAGTGACATAATAGGGCAATGAT-A-ATATTCTCTGACGAAATAATGGAAGGC
2538152 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGT
64 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTG-AATAATAGGTACTGATATATCTAGTGT
2538214 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGC
1 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGC
*
2538279 GCCCCCGGGAACGCGCCTTCATGTGAATAGTGAATAATAGGTACTGATATATCTATTGT
66 GCCCCCGGGAACGCGCCTTCATGTGAATAGTGAATAATAGGTACTGATATATCTAGTGT
2538338 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGC
1 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGC
2538403 GCCCCCGGGAA--CGCCTTCATGTGAATAGTGAA
66 GCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
2538435 CCGATTATAG
Statistics
Matches: 219, Mismatches: 1, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
122 21 0.10
124 102 0.47
125 61 0.28
126 6 0.03
127 29 0.13
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.22
Consensus pattern (124 bp):
CCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGC
GCCCCCGGGAACGCGCCTTCATGTGAATAGTGAATAATAGGTACTGATATATCTAGTGT
Found at i:2539778 original size:195 final size:194
Alignment explanation
Indices: 2539447--2539836 Score: 771
Period size: 195 Copynumber: 2.0 Consensus size: 194
2539437 TGAATTTCCA
2539447 GATCTTCCTGATGTTGGCAACTATGACTTCAATCATCAGTCAATGACGGTAATTTACATATTGGA
1 GATCTTCCTGATGTTGGCAACTATGACTTCAATCATCAGTCAATGACGGTAATTTACATATTGGA
2539512 ATGGAGTTCGCATCGAAGGAGGAAGCAATGATGGCAATAAAGAGTTACAATATTCGTAACTTAGT
66 ATGGAGTTCGCATCGAAGGAGGAAGCAATGATGGCAATAAAGAGTTACAATATTCGTAACTTAGT
2539577 TCAGTCCCGAGTTGATCGATCTAACACGGAGAAATATGTCTGCTACTGCGTCCAACGTCACAAC
131 TCAGTCCCGAGTTGATCGATCTAACACGGAGAAATATGTCTGCTACTGCGTCCAACGTCACAAC
2539641 GATCTTCCTGATGTTGGCAACTATGGACTTCAATCATCAGTCAATGACGGTAATTTACATATTGG
1 GATCTTCCTGATGTTGGCAACTAT-GACTTCAATCATCAGTCAATGACGGTAATTTACATATTGG
2539706 AATGGAGTTCGCATCGAAGGAGGAAGCAATGATGGCAATAAAGAGTTACAATATTCGTAACTTAG
65 AATGGAGTTCGCATCGAAGGAGGAAGCAATGATGGCAATAAAGAGTTACAATATTCGTAACTTAG
2539771 TTCAGTCCCGAGTTGATCGATCTAACACGGAGAAATATGTCTGCTACTGCGTCCAACGTCACAAC
130 TTCAGTCCCGAGTTGATCGATCTAACACGGAGAAATATGTCTGCTACTGCGTCCAACGTCACAAC
2539836 G
1 G
2539837 GATGTCAATG
Statistics
Matches: 195, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
194 24 0.12
195 171 0.88
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (194 bp):
GATCTTCCTGATGTTGGCAACTATGACTTCAATCATCAGTCAATGACGGTAATTTACATATTGGA
ATGGAGTTCGCATCGAAGGAGGAAGCAATGATGGCAATAAAGAGTTACAATATTCGTAACTTAGT
TCAGTCCCGAGTTGATCGATCTAACACGGAGAAATATGTCTGCTACTGCGTCCAACGTCACAAC
Found at i:2541733 original size:12 final size:13
Alignment explanation
Indices: 2541700--2541737 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2541690 AAATACATAA
2541700 ATATATTTAATAT
1 ATATATTTAATAT
*
2541713 ATTTATTTAATAT
1 ATATATTTAATAT
2541726 A-ATATTTAATAT
1 ATATATTTAATAT
2541738 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:2543001 original size:31 final size:31
Alignment explanation
Indices: 2542918--2543002 Score: 111
Period size: 31 Copynumber: 2.7 Consensus size: 31
2542908 TCTATCAATG
* * *
2542918 TTATAAATATTTTAATTTTGTTTTATTAATC
1 TTATAAATATTTTATTTTTATTTTATTAAAC
2542949 TTATAAATATTTTATTTTTATTTTATTAGAAC
1 TTATAAATATTTTATTTTTATTTTATTA-AAC
2542981 -TATAAATATTTT-TTTATTATTT
1 TTATAAATATTTTATTT-TTATTT
2543003 ATCCTTTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 3 0.06
31 44 0.90
32 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (31 bp):
TTATAAATATTTTATTTTTATTTTATTAAAC
Found at i:2549891 original size:25 final size:23
Alignment explanation
Indices: 2549863--2549909 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2549853 ATATAAAATT
*
2549863 ATTTTATTATTAATAATATATCTCA
1 ATTTT-TTATCAA-AATATATCTCA
*
2549888 ATTTTTTATCCAAATATATCTC
1 ATTTTTTATCAAAATATATCTC
2549910 GTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 5 0.25
25 5 0.25
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTTTATCAAAATATATCTCA
Found at i:2551226 original size:31 final size:31
Alignment explanation
Indices: 2551172--2551299 Score: 116
Period size: 31 Copynumber: 4.1 Consensus size: 31
2551162 GAACCTCGAC
* * *
2551172 AACTGTCCATAGGTCCCGA-AGAACCTAGGTA
1 AACTGTCCATATGTTCC-ATAGAACATAGGTA
* *
2551203 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* * * *
2551234 TATTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGT-TCCATAGAACATAGGTA
* *
2551265 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCATAGAACATAGGTA
2551297 AAC
1 AAC
2551300 CCTCGACTAT
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
31 50 0.67
32 25 0.33
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:2552447 original size:21 final size:21
Alignment explanation
Indices: 2552415--2552457 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2552405 TGCTTCTTTA
2552415 ATTGAGAGTGCATCGATACAC
1 ATTGAGAGTGCATCGATACAC
*
2552436 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATACAC
2552457 A
1 A
2552458 AAACCCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATACAC
Found at i:2552630 original size:46 final size:47
Alignment explanation
Indices: 2552563--2552660 Score: 189
Period size: 46 Copynumber: 2.1 Consensus size: 47
2552553 TATGTAAACC
2552563 TTCTTATAACACTATAACTCTTCACCATCTCTCATAATTCACCAT-A
1 TTCTTATAACACTATAACTCTTCACCATCTCTCATAATTCACCATAA
2552609 TTCTTATAACACTATAACTCTTCACCATCTCTCATAATTCACCATAA
1 TTCTTATAACACTATAACTCTTCACCATCTCTCATAATTCACCATAA
2552656 TTCTT
1 TTCTT
2552661 GAATCAAGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 45 0.88
47 6 0.12
ACGTcount: A:0.32, C:0.30, G:0.00, T:0.39
Consensus pattern (47 bp):
TTCTTATAACACTATAACTCTTCACCATCTCTCATAATTCACCATAA
Found at i:2557438 original size:16 final size:16
Alignment explanation
Indices: 2557417--2557447 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2557407 AAAGTCAAAT
2557417 GTTTACACAAAGTAAG
1 GTTTACACAAAGTAAG
*
2557433 GTTTACCCAAAGTAA
1 GTTTACACAAAGTAA
2557448 AATTGGATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (16 bp):
GTTTACACAAAGTAAG
Found at i:2558527 original size:18 final size:18
Alignment explanation
Indices: 2558501--2558535 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2558491 GTGAACCAAA
*
2558501 GTTGGTAAGTGTCTCAAG
1 GTTGATAAGTGTCTCAAG
2558519 GTTGATAAGTGTCTCAA
1 GTTGATAAGTGTCTCAA
2558536 AACCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (18 bp):
GTTGATAAGTGTCTCAAG
Found at i:2567232 original size:45 final size:45
Alignment explanation
Indices: 2567178--2567448 Score: 344
Period size: 45 Copynumber: 6.0 Consensus size: 45
2567168 ATACCATAAG
* *
2567178 TGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACATTTTATGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * * *
2567223 TGACACCTTTTATGCTAATAATGCACCATAATGCATTTTCATTTA
1 TGGCACATTTTATGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
2567268 TGGCATATTTTCTGCCAATAATGCACCGTTATCCATTTTCATTTA
1 TGGCACATTTTATGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
2567313 TGACACATTTTCTGACAATAATGCATCGTTATGCATTTTCATTTA
1 TGGCACATTTTATGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * * * *
2567358 TGGCGCCTTTTATGCCGATGATGCACCATTATTCATTTTCATTTA
1 TGGCACATTTTATGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
2567403 TGGCACATTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
1 TGGCACATTTTATGCCAATAATGCACCGTTATGCATTTTCATTTA
2567448 T
1 T
2567449 TTTGTTAACA
Statistics
Matches: 190, Mismatches: 36, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 190 1.00
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.42
Consensus pattern (45 bp):
TGGCACATTTTATGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:2567440 original size:135 final size:135
Alignment explanation
Indices: 2567195--2567448 Score: 409
Period size: 135 Copynumber: 1.9 Consensus size: 135
2567185 TTTTATGCCG
*
2567195 ATAATGCACCGTTATGCATTTTCATTTATGACACCTTTTATGCTAATAATGCACCATAATGCATT
1 ATAATGCACCGTTATGCATTTTCATTTATGACACCTTTTATGCCAATAATGCACCATAATGCATT
*
2567260 TTCATTTATGGCATATTTTCTGCCAATAATGCACCGTTATCCATTTTCATTTATGACACATTTTC
66 TTCATTTATGGCACATTTTCTGCCAATAATGCACCGTTATCCATTTTCATTTATGACACATTTTC
2567325 TGACA
131 TGACA
* * * * * * *
2567330 ATAATGCATCGTTATGCATTTTCATTTATGGCGCCTTTTATGCCGATGATGCACCATTATTCATT
1 ATAATGCACCGTTATGCATTTTCATTTATGACACCTTTTATGCCAATAATGCACCATAATGCATT
* *
2567395 TTCATTTATGGCACATTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTAT
66 TTCATTTATGGCACATTTTCTGCCAATAATGCACCGTTATCCATTTTCATTTAT
2567449 TTTGTTAACA
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
135 108 1.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (135 bp):
ATAATGCACCGTTATGCATTTTCATTTATGACACCTTTTATGCCAATAATGCACCATAATGCATT
TTCATTTATGGCACATTTTCTGCCAATAATGCACCGTTATCCATTTTCATTTATGACACATTTTC
TGACA
Found at i:2567924 original size:20 final size:20
Alignment explanation
Indices: 2567896--2567949 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
2567886 GGCTCAATAC
*
2567896 TATCAATACTCCTACCATGG
1 TATCGATACTCCTACCATGG
* *
2567916 TATCGATACTTCTATACTATGG
1 TATCGATAC-TC-CTACCATGG
*
2567938 TACCGATACTCC
1 TATCGATACTCC
2567950 CTTTCAGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 8 0.30
21 4 0.15
22 15 0.56
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (20 bp):
TATCGATACTCCTACCATGG
Found at i:2570896 original size:2 final size:2
Alignment explanation
Indices: 2570889--2571170 Score: 124
Period size: 2 Copynumber: 151.0 Consensus size: 2
2570879 CAGAACCTTA
* * * * *
2570889 AG AG AG AG AA AG AG ATG GG GG AG AG AG AG AG GG AG GG AG AG AG
1 AG AG AG AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * *
2570932 GG AG A- AG -G AG AG GG AG AG GG AG GG AG AG GG AG AG AA ATG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG
* * *
2570972 AG AG AG GG AG AG AG AG AG AG AG GG GG AG AG AG AG A- ATG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG
* * * *
2571014 AG TG A- AG -G AG GG AG AG A- AG -G AG GG AG AG GG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
2571052 AG GG AG AG A- AG -G AG AG AG AG GG GG AG GG GG AG -G AG -G AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
2571090 -G AG -G AG -G AG GG AG GG A- AA AG GG AG AG -G A- AG AG -G GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2571125 AG AG AG -G AG AG AG -G AG AG AG -G AG AG AG -G AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2571163 AG AG AG AG
1 AG AG AG AG
2571171 CTTTAAAACC
Statistics
Matches: 208, Mismatches: 46, Indels: 52
0.68 0.15 0.17
Matches are distributed among these distances:
1 23 0.11
2 183 0.88
3 2 0.01
ACGTcount: A:0.40, C:0.00, G:0.59, T:0.01
Consensus pattern (2 bp):
AG
Found at i:2570949 original size:30 final size:29
Alignment explanation
Indices: 2570908--2571168 Score: 140
Period size: 28 Copynumber: 9.0 Consensus size: 29
2570898 AAGAGATGGG
* *
2570908 GGAGAGAGAGAGGGAGGGAGAGAGGGAGAA
1 GGAGAGGGAGAGAGAGGGAGAGAGGGAG-A
*
2570938 GGAGAGGGAGAGGGA-GG-GAGAGGGAGA
1 GGAGAGGGAGAGAGAGGGAGAGAGGGAGA
* * *
2570965 -GAAATGGAGAGAG-GGAGAGAGAGAGAGA
1 GGAGAGGGAGAGAGAGG-GAGAGAGGGAGA
** *
2570993 GG-G-GGAGAGAGAGAATGAGAGAGTGA-A
1 GGAGAGG-GAGAGAGAGGGAGAGAGGGAGA
*
2571020 -G-GAGGGAGAGA-AGGAGGGAGAGGGAGA
1 GGAGAGGGAGAGAGAGG-GAGAGAGGGAGA
*
2571047 GAGAGAGGGAGAGA-AGGAGAGAGAGGGGGA
1 G-GAGAGGGAGAGAGAGG-GAGAGAGGGAGA
*
2571077 GG-GGGAGGAG-GAG-GAGGAG-GAGGGAG-
1 GGAGAG-GGAGAGAGAG-GGAGAGAGGGAGA
*
2571103 GGAAAAGGGAGAGGAAGAGGGGAGAGAGGAGAGA
1 GG-AGAGGGAGA-G-AGA-GGGAGAGAGG-GAGA
* *
2571137 GGAGAGAGGAGAGAGGAGAGAGAGAGAGAGA
1 GGAGAG-GGAGAGA-GAGGGAGAGAGGGAGA
2571168 G
1 G
2571169 AGCTTTAAAA
Statistics
Matches: 181, Mismatches: 23, Indels: 53
0.70 0.09 0.21
Matches are distributed among these distances:
25 1 0.01
26 29 0.16
27 17 0.09
28 43 0.24
29 11 0.06
30 41 0.23
31 9 0.05
32 14 0.08
33 9 0.05
34 7 0.04
ACGTcount: A:0.39, C:0.00, G:0.59, T:0.01
Consensus pattern (29 bp):
GGAGAGGGAGAGAGAGGGAGAGAGGGAGA
Found at i:2571092 original size:9 final size:9
Alignment explanation
Indices: 2571069--2571154 Score: 50
Period size: 9 Copynumber: 9.0 Consensus size: 9
2571059 GAAGGAGAGA
*
2571069 GAGGGGGAG
1 GAGGAGGAG
*
2571078 GGGGAGGAG
1 GAGGAGGAG
2571087 GAGGAGGAG
1 GAGGAGGAG
*
2571096 GAGGGAGGGAA
1 GA-GGA-GGAG
*
2571107 AAGG-GAGAG
1 GAGGAG-GAG
*
2571116 GAAGAGG-G
1 GAGGAGGAG
2571124 GAGAGAGGAG
1 GAG-GAGGAG
2571134 AGAGGAGAGAG
1 -GAGGAG-GAG
2571145 GAGAGAGGAG
1 GAG-GAGGAG
2571155 AGAGAGAGAG
Statistics
Matches: 59, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
8 4 0.07
9 26 0.44
10 16 0.27
11 13 0.22
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (9 bp):
GAGGAGGAG
Found at i:2584934 original size:149 final size:149
Alignment explanation
Indices: 2584657--2584955 Score: 582
Period size: 149 Copynumber: 2.0 Consensus size: 149
2584647 ACTAGCTGAA
2584657 GTGCTAGGAGAAATATCATCGTGTGAGCAGCTTCTTGGGAAGAAACTGGATTATGCTGCAATGAA
1 GTGCTAGGAGAAATATCATCGTGTGAGCAGCTTCTTGGGAAGAAACTGGATTATGCTGCAATGAA
2584722 AGTGTTTGGTTGCAAGTTTTTTTCTCATTTAAGGTCATTTCAAAACACATAAGCTTGAGTTTGAT
66 AGTGTTTGGTTGCAAGTTTTTTTCTCATTTAAGGTCATTTCAAAACACATAAGCTTGAGTTTGAT
2584787 CTCAAGTGTGCATGTTTCT
131 CTCAAGTGTGCATGTTTCT
2584806 GTGCTAGGAGAAATATCATCGTGTGAGCAGCTTCTTGGGAAGAAACTGGATTATGCTGCAATGAA
1 GTGCTAGGAGAAATATCATCGTGTGAGCAGCTTCTTGGGAAGAAACTGGATTATGCTGCAATGAA
2584871 AGTGTTTGGTTGCAAGTTTTTTTCTCATTTAAGGTCATTTC-AAACACATAAGCTTGAGTTTTGA
66 AGTGTTTGGTTGCAAGTTTTTTTCTCATTTAAGGTCATTTCAAAACACATAAGCTTGAG-TTTGA
2584935 TCTCAAGTGTGCATGTTTCT
130 TCTCAAGTGTGCATGTTTCT
2584955 G
1 G
2584956 GGTTATAGCC
Statistics
Matches: 149, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
148 17 0.11
149 132 0.89
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (149 bp):
GTGCTAGGAGAAATATCATCGTGTGAGCAGCTTCTTGGGAAGAAACTGGATTATGCTGCAATGAA
AGTGTTTGGTTGCAAGTTTTTTTCTCATTTAAGGTCATTTCAAAACACATAAGCTTGAGTTTGAT
CTCAAGTGTGCATGTTTCT
Found at i:2586677 original size:17 final size:17
Alignment explanation
Indices: 2586651--2586684 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2586641 AACAAACCCC
*
2586651 TCATATCTTGAGGCAAT
1 TCATACCTTGAGGCAAT
2586668 TCATACCTTGAGGCAAT
1 TCATACCTTGAGGCAAT
2586685 CAATTCACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (17 bp):
TCATACCTTGAGGCAAT
Found at i:2589587 original size:82 final size:82
Alignment explanation
Indices: 2589430--2589764 Score: 369
Period size: 82 Copynumber: 4.1 Consensus size: 82
2589420 CTGCAACTTC
* * * *
2589430 AGGGGAAATTAGACTTGATATGTGCCTCTTTTAT-GGGTAGACAAATCTATTTTGGAAGGCATGC
1 AGGGGAAATCAGACTTGATATGTGCCTCTTTT-TCAGGTAGACAAATCTATTTTGGAAGACATGT
2589494 CTGCTCCACTATTTATTT
65 CTGCTCCACTATTTATTT
* * * *
2589512 AGGGGAAATCAGACTTGATATGTGCCTCGTTTTCAGGTAGACAAATCTATTTTGTAAGAAATATC
1 AGGGGAAATCAGACTTGATATGTGCCTCTTTTTCAGGTAGACAAATCTATTTTGGAAGACATGTC
* *
2589577 TACTCTACTATTTA-TT
66 TGCTCCACTATTTATTT
* * * * ** * * *
2589593 ----CAAATCAGACTTGATTTGTACCACTTTTTTGGGTAGACATATCTATTTTGAAAGACGTGTC
1 AGGGGAAATCAGACTTGATATGTGCCTCTTTTTCAGGTAGACAAATCTATTTTGGAAGACATGTC
* *
2589654 TGCTCCACTATTCATTC
66 TGCTCCACTATTTATTT
* * **
2589671 AAGGGAAATCAGACTTGATATGTGCCTCTTTTTCAGGTAGA-AATATCTATTCTGGAAGATGTGT
1 AGGGGAAATCAGACTTGATATGTGCCTCTTTTTCAGGTAGACAA-ATCTATTTTGGAAGACATGT
*
2589735 CTTCTCCACTATTTATTT
65 CTGCTCCACTATTTATTT
2589753 AGGGGAAATCAG
1 AGGGGAAATCAG
2589765 GCTCGAAAAA
Statistics
Matches: 206, Mismatches: 40, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
77 60 0.29
78 1 0.00
81 4 0.02
82 141 0.68
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (82 bp):
AGGGGAAATCAGACTTGATATGTGCCTCTTTTTCAGGTAGACAAATCTATTTTGGAAGACATGTC
TGCTCCACTATTTATTT
Found at i:2589705 original size:159 final size:159
Alignment explanation
Indices: 2589435--2589721 Score: 432
Period size: 159 Copynumber: 1.8 Consensus size: 159
2589425 ACTTCAGGGG
* * * * *
2589435 AAATTAGACTTGATATGTGCCTCTTTTATGGGTAGACAAATCTATTTTGGAAGGCATGCCTGCTC
1 AAATCAGACTTGATATGTACCACTTTTATGGGTAGACAAATCTATTTTGAAAGACATGCCTGCTC
* * *
2589500 CACTATTTATTTAGGGGAAATCAGACTTGATATGTGCCTCGTTTTCAGGTAGACAA-ATCTATTT
66 CACTATTCATTCAAGGGAAATCAGACTTGATATGTGCCTCGTTTTCAGGTAGA-AATATCTATTT
2589564 TGTAAGAAATATCTACTCTACTATTTATTC
130 TGTAAGAAATATCTACTCTACTATTTATTC
* * * * *
2589594 AAATCAGACTTGATTTGTACCACTTTTTTGGGTAGACATATCTATTTTGAAAGACGTGTCTGCTC
1 AAATCAGACTTGATATGTACCACTTTTATGGGTAGACAAATCTATTTTGAAAGACATGCCTGCTC
*
2589659 CACTATTCATTCAAGGGAAATCAGACTTGATATGTGCCTCTTTTTCAGGTAGAAATATCTATT
66 CACTATTCATTCAAGGGAAATCAGACTTGATATGTGCCTCGTTTTCAGGTAGAAATATCTATT
2589722 CTGGAAGATG
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
158 2 0.02
159 111 0.98
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (159 bp):
AAATCAGACTTGATATGTACCACTTTTATGGGTAGACAAATCTATTTTGAAAGACATGCCTGCTC
CACTATTCATTCAAGGGAAATCAGACTTGATATGTGCCTCGTTTTCAGGTAGAAATATCTATTTT
GTAAGAAATATCTACTCTACTATTTATTC
Found at i:2591039 original size:7 final size:7
Alignment explanation
Indices: 2591029--2591116 Score: 65
Period size: 7 Copynumber: 11.9 Consensus size: 7
2591019 CCTTTTACTT
2591029 TTTTTTC
1 TTTTTTC
2591036 TTTTAATT-
1 TTTT--TTC
2591044 TTCTTTTC
1 TT-TTTTC
2591052 TTTTTTC
1 TTTTTTC
*
2591059 -TCTTTC
1 TTTTTTC
*
2591065 TCTTTCTC
1 T-TTTTTC
2591073 TTTTCCTT-
1 TTTT--TTC
2591081 TTTTTTC
1 TTTTTTC
2591088 TTTTTTC
1 TTTTTTC
2591095 TTTTTTTC
1 -TTTTTTC
2591103 TTTTTTC
1 TTTTTTC
2591110 TTCTTTT
1 TT-TTTT
2591117 TCATCTTCAA
Statistics
Matches: 66, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
6 7 0.11
7 30 0.45
8 24 0.36
9 5 0.08
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:2591040 original size:15 final size:15
Alignment explanation
Indices: 2591020--2591106 Score: 59
Period size: 15 Copynumber: 5.3 Consensus size: 15
2591010 CTTGAACACC
2591020 CTTTTACTTTTTTTT
1 CTTTTACTTTTTTTT
*
2591035 CTTTTAATTTTCTTTT
1 CTTTTACTTTT-TTTT
*
2591051 CTTTTTTCTCTTTCTCTTTCT
1 C--TTTT-ACTTT-T-TTT-T
*
2591072 CTTTTCCTTTTTTTT
1 CTTTTACTTTTTTTT
*
2591087 CTTTT-TTCTTTTTTT
1 CTTTTACT-TTTTTTT
2591102 CTTTT
1 CTTTT
2591107 TTCTTCTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
14 1 0.02
15 28 0.47
16 8 0.13
17 1 0.02
18 8 0.13
19 7 0.12
20 5 0.08
21 2 0.03
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.78
Consensus pattern (15 bp):
CTTTTACTTTTTTTT
Found at i:2592387 original size:3 final size:3
Alignment explanation
Indices: 2592379--2592408 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2592369 CAGGGGTTTC
*
2592379 CTT CTT CTT CTT CTT CTT CTT CTT ATT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2592409 AAATATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:2596322 original size:19 final size:19
Alignment explanation
Indices: 2596300--2596337 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2596290 AGCTGAAGTT
2596300 GGTGCTGAAAGCTTGTGAA
1 GGTGCTGAAAGCTTGTGAA
* *
2596319 GGTGTTGGAAGCTTGTGAA
1 GGTGCTGAAAGCTTGTGAA
2596338 ATTTGTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.39, T:0.29
Consensus pattern (19 bp):
GGTGCTGAAAGCTTGTGAA
Found at i:2598803 original size:8 final size:8
Alignment explanation
Indices: 2598792--2598910 Score: 62
Period size: 8 Copynumber: 15.1 Consensus size: 8
2598782 ATTCTCAAGT
2598792 TCTCTATC
1 TCTCTATC
* *
2598800 TCTCTCTA
1 TCTCTATC
*
2598808 TATCTATC
1 TCTCTATC
*
2598816 TGTCTATC
1 TCTCTATC
* *
2598824 TGTCTGTC
1 TCTCTATC
* *
2598832 TGTCTGTC
1 TCTCTATC
*
2598840 TGTCTATC
1 TCTCTATC
* *
2598848 TATCTGTC
1 TCTCTATC
*
2598856 TCTCTCTC
1 TCTCTATC
2598864 TCTCTATC
1 TCTCTATC
* *
2598872 TGTCTGTC
1 TCTCTATC
* *
2598880 TGTCTGTC
1 TCTCTATC
* *
2598888 TATCTGTC
1 TCTCTATC
2598896 TCTC--TC
1 TCTCTATC
2598902 TCTCTATC
1 TCTCTATC
2598910 T
1 T
2598911 GTCTGTCTGT
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
6 6 0.07
8 86 0.93
ACGTcount: A:0.08, C:0.31, G:0.10, T:0.50
Consensus pattern (8 bp):
TCTCTATC
Found at i:2598815 original size:4 final size:4
Alignment explanation
Indices: 2598814--2599009 Score: 164
Period size: 4 Copynumber: 49.8 Consensus size: 4
2598804 TCTATATCTA
* * * * *
2598814 TCTG TCTA TCTG TCTG TCTG TCTG TCTG TCTA TCTA TCTG TCTC TCTC
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
* * * * * *
2598862 TCTC TCTA TCTG TCTG TCTG TCTG TCTA TCTG TC-- TCTC TCTC TCTA
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
* * *
2598908 TCTG TCTG TCTG TCTG TCTG ACTG TCTG TCTG ACTG TTTG TCTG TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
* * * * * * * * *
2598956 TCTG T-AG TCGG TCTA TCTG TCTC TCTG TCTA TCTG ACTA TCTA TCTA
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
2599003 TCTG TCT
1 TCTG TCT
2599010 ATATACAATT
Statistics
Matches: 159, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.01
3 2 0.01
4 155 0.97
ACGTcount: A:0.08, C:0.28, G:0.16, T:0.48
Consensus pattern (4 bp):
TCTG
Found at i:2598823 original size:12 final size:12
Alignment explanation
Indices: 2598794--2599011 Score: 142
Period size: 12 Copynumber: 18.4 Consensus size: 12
2598784 TCTCAAGTTC
* *
2598794 TCTATCTCTCTC
1 TCTATCTGTCTG
* *
2598806 TATATCTATCTG
1 TCTATCTGTCTG
2598818 TCTATCTGTCTG
1 TCTATCTGTCTG
*
2598830 TCTGTCTGTCTG
1 TCTATCTGTCTG
*
2598842 TCTATCTATCTG
1 TCTATCTGTCTG
* * *
2598854 TCTCTCTCTCTC
1 TCTATCTGTCTG
2598866 TCTATCTGTCTG
1 TCTATCTGTCTG
* *
2598878 TCTGTCTGTCTA
1 TCTATCTGTCTG
* *
2598890 TCTGTC--TCTC
1 TCTATCTGTCTG
* *
2598900 TCTCTCTATCTG
1 TCTATCTGTCTG
*
2598912 TCTGTCTGTCTG
1 TCTATCTGTCTG
2598924 TCTGA-CTGTCTG
1 TCT-ATCTGTCTG
*
2598936 TCTGA-CTGTTTG
1 TCT-ATCTGTCTG
*
2598948 TCTGTCTGTCTG
1 TCTATCTGTCTG
* *
2598960 --TAGTCGGTCTA
1 TCTA-TCTGTCTG
* *
2598971 TCTGTCTCTCTG
1 TCTATCTGTCTG
* *
2598983 TCTATCTGACTA
1 TCTATCTGTCTG
*
2598995 TCTATCTATCTG
1 TCTATCTGTCTG
2599007 TCTAT
1 TCTAT
2599012 ATACAATTAT
Statistics
Matches: 160, Mismatches: 39, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
10 9 0.06
11 6 0.04
12 144 0.90
13 1 0.01
ACGTcount: A:0.09, C:0.28, G:0.15, T:0.49
Consensus pattern (12 bp):
TCTATCTGTCTG
Found at i:2600376 original size:59 final size:59
Alignment explanation
Indices: 2600284--2600402 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
2600274 CATTTGTTTA
2600284 TAATTTCTCAAAACTCTTCAACCTGTTGATGATGGCGGTAAATCGATCGAACATGGCTT
1 TAATTTCTCAAAACTCTTCAACCTGTTGATGATGGCGGTAAATCGATCGAACATGGCTT
2600343 TAATTTCTCAAAACTCTTCAACCTGTTGATGATGGCGGTAAATCGATCGAACATGGCTT
1 TAATTTCTCAAAACTCTTCAACCTGTTGATGATGGCGGTAAATCGATCGAACATGGCTT
2600402 T
1 T
2600403 GATATCTTGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (59 bp):
TAATTTCTCAAAACTCTTCAACCTGTTGATGATGGCGGTAAATCGATCGAACATGGCTT
Found at i:2601136 original size:10 final size:10
Alignment explanation
Indices: 2601114--2601146 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2601104 GCAAGGACTT
2601114 ATAAATT-AA
1 ATAAATTAAA
2601123 ATAAATTAAA
1 ATAAATTAAA
*
2601133 ATAAATAAAA
1 ATAAATTAAA
2601143 ATAA
1 ATAA
2601147 GAAAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAATTAAA
Found at i:2603676 original size:51 final size:51
Alignment explanation
Indices: 2603621--2603721 Score: 202
Period size: 51 Copynumber: 2.0 Consensus size: 51
2603611 TAAAAACTTA
2603621 TTATACACGAATAAGGAATTCAAGTAAAATTAATATATGTATTTGATAAGC
1 TTATACACGAATAAGGAATTCAAGTAAAATTAATATATGTATTTGATAAGC
2603672 TTATACACGAATAAGGAATTCAAGTAAAATTAATATATGTATTTGATAAG
1 TTATACACGAATAAGGAATTCAAGTAAAATTAATATATGTATTTGATAAG
2603722 TACATAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.34
Consensus pattern (51 bp):
TTATACACGAATAAGGAATTCAAGTAAAATTAATATATGTATTTGATAAGC
Found at i:2611163 original size:20 final size:21
Alignment explanation
Indices: 2611138--2611177 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2611128 ATGAATGTCC
2611138 TATACAT-TCTATC-TAGCTTA
1 TATACATGT-TATCTTAGCTTA
2611158 TATACATGTTATCTTAGCTT
1 TATACATGTTATCTTAGCTT
2611178 CTAGACGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.47
Consensus pattern (21 bp):
TATACATGTTATCTTAGCTTA
Found at i:2611906 original size:19 final size:19
Alignment explanation
Indices: 2611879--2611920 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2611869 CCATTCGGCC
*
2611879 AAAAGCATGTACTTTCATT
1 AAAAGCATGTAATTTCATT
* *
2611898 AAAATCATGTAATTTCTTT
1 AAAAGCATGTAATTTCATT
2611917 AAAA
1 AAAA
2611921 AAATCATGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (19 bp):
AAAAGCATGTAATTTCATT
Found at i:2613167 original size:19 final size:19
Alignment explanation
Indices: 2613143--2613180 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2613133 TTCTACAACC
2613143 CTTTATGAA-TTTTGATAAT
1 CTTTATGAACTTTTG-TAAT
2613162 CTTTATGAACTTTTGTAAT
1 CTTTATGAACTTTTGTAAT
2613181 TTTCTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.53
Consensus pattern (19 bp):
CTTTATGAACTTTTGTAAT
Found at i:2613417 original size:28 final size:27
Alignment explanation
Indices: 2613373--2613435 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
2613363 TATTGCTATA
* **
2613373 TAAAATATTATATATTAGATTAAATTAT
1 TAAAATATTATAGATTAGA-TAAAACAT
*
2613401 TAAAATA-TATTAGATTATATAAAACAT
1 TAAAATATTA-TAGATTAGATAAAACAT
2613428 TAAAATAT
1 TAAAATAT
2613436 CATGAATGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (27 bp):
TAAAATATTATAGATTAGATAAAACAT
Found at i:2616041 original size:59 final size:58
Alignment explanation
Indices: 2615978--2616100 Score: 133
Period size: 59 Copynumber: 2.1 Consensus size: 58
2615968 CTTAAAGTAA
* * *
2615978 ATAAATGA-TCTTACGATTATA-TAATATTACTTTATTAAATCTATCGACTATTAAAAGTT
1 ATAAATGATTCTTA--ATTATAGTAA-ATTACTTTATTAAATCCATCAACAATTAAAAGTT
* * * *
2616037 ATAAAATTATTCTTAATTATAGTGAGTTACTTTATTAAGTCCATCAACAATTAAAAGTT
1 AT-AAATGATTCTTAATTATAGTAAATTACTTTATTAAATCCATCAACAATTAAAAGTT
2616096 ATAAA
1 ATAAA
2616101 ATAATCACCC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
58 3 0.06
59 39 0.72
60 7 0.13
61 5 0.09
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (58 bp):
ATAAATGATTCTTAATTATAGTAAATTACTTTATTAAATCCATCAACAATTAAAAGTT
Found at i:2617803 original size:138 final size:137
Alignment explanation
Indices: 2617485--2617867 Score: 366
Period size: 138 Copynumber: 2.8 Consensus size: 137
2617475 CTTAGGGGAT
* * *
2617485 TAAACCTAAAAATGTAGGCTCT-AATAT-TAACTTAAATC-ATTTTAAATGAATTATTG-TGTCG
1 TAAACCT-AAAATGAAGGCTCTAAATATAT-ACCT-AATCAATTTT-AATCAATTATTGAT-TCG
* * *
2617546 AATAGTTAAAATGGAACCTCGAGCAAAAGCGAGGACCAAATCTAAAATTATCTTAATTTAAAGGA
61 AATAATTAAAATGAAACCTCGAGCAAAAGCGAGGACCAAAT-TAAAATTATCTTAAATTAAAGGA
*
2617611 CTGAGTTTGAAAC
125 CTAAGTTTGAAAC
* * * * * *
2617624 TAAACCTAAAATGGAGGCTCTAAATATTTACGTAGTCAATTTTAATTAATTATTGATTTGAATAA
1 TAAACCTAAAATGAAGGCTCTAAATATATACCTAATCAATTTTAATCAATTATTGATTCGAATAA
* * *
2617689 TTAAAATGAAACCTCGAGCATAAGCGAGGACCAAATTAAAATTTTCTTAAATTAATGGACTAAGT
66 TTAAAATGAAACCTCGAGCAAAAGCGAGGACCAAATTAAAATTATCTTAAATTAAAGGACTAAGT
*
2617754 TTGAAAATT
131 TTG-AAA-C
*** * * * * * *
2617763 TGAGGTCTAAAGTGAAGGCTCTAAGTA-AT-CCTAATTAATTTTAATCGATTTTTGAATCGAATA
1 T-AAACCTAAAATGAAGGCTCTAAATATATACCTAATCAATTTTAATCAATTATTGATTCGAATA
* **
2617826 ATTAAAAT-AGAACCTCAAGCAAAAATGAGGACCAAATTAAAA
65 ATTAAAATGA-AACCTCGAGCAAAAGCGAGGACCAAATTAAAA
2617868 ACTCTCCAAA
Statistics
Matches: 204, Mismatches: 32, Indels: 17
0.81 0.13 0.07
Matches are distributed among these distances:
137 29 0.14
138 132 0.65
139 23 0.11
140 20 0.10
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (137 bp):
TAAACCTAAAATGAAGGCTCTAAATATATACCTAATCAATTTTAATCAATTATTGATTCGAATAA
TTAAAATGAAACCTCGAGCAAAAGCGAGGACCAAATTAAAATTATCTTAAATTAAAGGACTAAGT
TTGAAAC
Found at i:2619701 original size:54 final size:54
Alignment explanation
Indices: 2619596--2620009 Score: 501
Period size: 54 Copynumber: 7.7 Consensus size: 54
2619586 TTGATATTTC
* * * * * *
2619596 AACTCATTATAAATTTCGTT-GTTTTACACACGTAGTGCCGATACGGTAATTCATA
1 AACTCATTATGAATTTC-TTAG-GTTGCACACATAGTGCCAATACGGAAATTCATA
* * * * * *
2619651 AACTCATTATGAATTACATGGGTTGTACATATAGTGCCAGA-ACGAAAATTCATA
1 AACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCA-ATACGGAAATTCATA
* *
2619705 AACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGTAATTCAAA
1 AACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGAAATTCATA
* * *
2619759 AACTCATTATGAATTACGTGGGTTGCACACATAGTGCCAATACGGAAATTCATA
1 AACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGAAATTCATA
* * * *
2619813 AGCTCATTATGAATTTCTTAGGTTGCACACATAGTTCCAATATGAAAATTCATA
1 AACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGAAATTCATA
* * * * * *
2619867 AACTCATTAAGAATTTCTTAGTTTACACACATAATGCCAATATGGATATTCATA
1 AACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGAAATTCATA
* * *
2619921 AACTCATTTTGAATTTCTTAGGTTGTACACATAGTTCCAATACGG-AATTCATA
1 AACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGAAATTCATA
*
2619974 AACTCATTATGAATTTCTTAGGTTGCACACAAAGTG
1 AACTCATTATGAATTTCTTAGGTTGCACACATAGTG
2620010 TCCATTCGTT
Statistics
Matches: 304, Mismatches: 52, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
53 40 0.13
54 247 0.81
55 17 0.06
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (54 bp):
AACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGAAATTCATA
Found at i:2623251 original size:19 final size:18
Alignment explanation
Indices: 2623223--2623258 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2623213 ACTTTCTTTC
*
2623223 TTTTTGTTTTTTGCTTTTA
1 TTTTTCTTTTTT-CTTTTA
2623242 TTTTTCTTTTTTCTTTT
1 TTTTTCTTTTTTCTTTT
2623259 TCTTTTCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.03, C:0.08, G:0.06, T:0.83
Consensus pattern (18 bp):
TTTTTCTTTTTTCTTTTA
Found at i:2626683 original size:14 final size:15
Alignment explanation
Indices: 2626657--2626685 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2626647 GAATAAATAT
2626657 AATGTATAATGTAAA
1 AATGTATAATGTAAA
2626672 AATGTA-AATGTAAA
1 AATGTATAATGTAAA
2626686 TGCAAACGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (15 bp):
AATGTATAATGTAAA
Found at i:2629773 original size:44 final size:43
Alignment explanation
Indices: 2629700--2629796 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 43
2629690 CAACTCAATG
* * *
2629700 GTATCGATACCCTTAAGGTGTATCGATACTACTATATATAGTA
1 GTATCGATACCCTCAAGGAGTATCGATACTACTATACATAGTA
* * *
2629743 GTATCGATACCGTCCAAGGAGTATCGATACTATTATGCATAGTA
1 GTATCGATACCCT-CAAGGAGTATCGATACTACTATACATAGTA
*
2629787 GTATTGATAC
1 GTATCGATAC
2629797 TGAACATGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 12 0.26
44 34 0.74
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (43 bp):
GTATCGATACCCTCAAGGAGTATCGATACTACTATACATAGTA
Found at i:2630112 original size:18 final size:19
Alignment explanation
Indices: 2630086--2630124 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2630076 GTAATATTTG
*
2630086 AATAATTG-AATTGAATAT
1 AATAATTGAAATCGAATAT
*
2630104 AATATTTGAAATCGAATAT
1 AATAATTGAAATCGAATAT
2630123 AA
1 AA
2630125 AATCTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (19 bp):
AATAATTGAAATCGAATAT
Found at i:2632569 original size:20 final size:19
Alignment explanation
Indices: 2632546--2632619 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 19
2632536 ACTTCATGAC
2632546 TAGTATCGATACTAGGCTAG
1 TAGTATCGATACTA-GCTAG
*
2632566 TAGTATCGATACCTAGCAAGAG
1 TAGTATCGATA-CTAGC--TAG
*
2632588 TAGTATGGATACTATG-TGAG
1 TAGTATCGATACTA-GCT-AG
2632608 TAGTATCGATAC
1 TAGTATCGATAC
2632620 CACGTGCACA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
20 26 0.58
21 6 0.13
22 13 0.29
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (19 bp):
TAGTATCGATACTAGCTAG
Found at i:2638380 original size:44 final size:44
Alignment explanation
Indices: 2638329--2638427 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 44
2638319 CAACTCAACG
* *
2638329 GTATCGATACCCTTCAAGGAGTATCGATACTACTATATATAGTA
1 GTATCGATACCCTCCAAGGAGTATCGATACTACTATACATAGTA
* * * *
2638373 TTATCGATATCGTCCAAGGAGTATCGATACTACTATGCATAGTA
1 GTATCGATACCCTCCAAGGAGTATCGATACTACTATACATAGTA
2638417 GTATCGATACC
1 GTATCGATACC
2638428 GAACATGGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (44 bp):
GTATCGATACCCTCCAAGGAGTATCGATACTACTATACATAGTA
Found at i:2638421 original size:24 final size:24
Alignment explanation
Indices: 2638348--2638426 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 24
2638338 CCCTTCAAGG
*
2638348 AGTATCGATACTACTATATATAGT
1 AGTATCGATACTACTATACATAGT
* * * *
2638372 ATTATCGATA-T-C-GTCCA-AGG
1 AGTATCGATACTACTATACATAGT
*
2638392 AGTATCGATACTACTATGCATAGT
1 AGTATCGATACTACTATACATAGT
2638416 AGTATCGATAC
1 AGTATCGATAC
2638427 CGAACATGGT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
20 11 0.26
21 3 0.07
22 2 0.05
23 4 0.10
24 22 0.52
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (24 bp):
AGTATCGATACTACTATACATAGT
Found at i:2638759 original size:19 final size:19
Alignment explanation
Indices: 2638721--2638760 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2638711 CGAATAATTG
* *
2638721 AATCGAATATAATATTTTA
1 AATCGAATATAAAATCTTA
2638740 AATCGAATATAAAATCTTA
1 AATCGAATATAAAATCTTA
2638759 AA
1 AA
2638761 ATTAATTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (19 bp):
AATCGAATATAAAATCTTA
Found at i:2640699 original size:27 final size:27
Alignment explanation
Indices: 2640662--2640715 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2640652 GTTTATCAAG
2640662 GCAGCAAATGGCAAGATAACAGTCATA
1 GCAGCAAATGGCAAGATAACAGTCATA
2640689 GCAGCAAATGGCAAGATAACAGTCATA
1 GCAGCAAATGGCAAGATAACAGTCATA
2640716 AGTGATAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (27 bp):
GCAGCAAATGGCAAGATAACAGTCATA
Found at i:2642829 original size:14 final size:15
Alignment explanation
Indices: 2642789--2642830 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2642779 AGCCAAGCCG
*
2642789 ACTGAGTCAACTTGC
1 ACTGAGTCAACTCGC
* *
2642804 ACTGAGTTAACTCGG
1 ACTGAGTCAACTCGC
2642819 A-TGAGTCAACTC
1 ACTGAGTCAACTC
2642831 ACGGGGTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (15 bp):
ACTGAGTCAACTCGC
Found at i:2644681 original size:24 final size:24
Alignment explanation
Indices: 2644646--2644712 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
2644636 TTTGTCTGAT
* *
2644646 TTCTATTATGATTTCTGATCCGGA
1 TTCTATTATGATATCTGATACGGA
2644670 TTCTACTT-TGATATCTGATACGGA
1 TTCTA-TTATGATATCTGATACGGA
*
2644694 TTCTGTTATGATATCTGAT
1 TTCTATTATGATATCTGAT
2644713 CTGAATTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 2 0.05
24 34 0.89
25 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.46
Consensus pattern (24 bp):
TTCTATTATGATATCTGATACGGA
Found at i:2644724 original size:24 final size:24
Alignment explanation
Indices: 2644646--2644729 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 24
2644636 TTTGTCTGAT
* * * *
2644646 TTCTATTATGATTTCTGATCCGGA
1 TTCTGTTATGATATCTGATACGAA
* *
2644670 TTCTACTT-TGATATCTGATACGGA
1 TTCT-GTTATGATATCTGATACGAA
2644694 TTCTGTTATGATATCTGAT-CTGAA
1 TTCTGTTATGATATCTGATAC-GAA
* *
2644718 TTTTGTTCTGAT
1 TTCTGTTATGAT
2644730 TTTTAATTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
23 3 0.06
24 45 0.90
25 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (24 bp):
TTCTGTTATGATATCTGATACGAA
Found at i:2647936 original size:21 final size:21
Alignment explanation
Indices: 2647910--2647956 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2647900 TATGAAGAAT
*
2647910 ATTTTTAGA-TATTGAAATATG
1 ATTTTTAGATTATT-AAATATA
*
2647931 ATTTTTGGATTATTAAATATA
1 ATTTTTAGATTATTAAATATA
2647952 ATTTT
1 ATTTT
2647957 AATAAAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (21 bp):
ATTTTTAGATTATTAAATATA
Found at i:2653808 original size:66 final size:69
Alignment explanation
Indices: 2653654--2653842 Score: 224
Period size: 66 Copynumber: 2.8 Consensus size: 69
2653644 CTTTCGGGCT
* * * * * * ** * *
2653654 CCCGTACGATTCACCCAAAATTAATTATGATTTGATAATCCTGTACGAGTAACTCTTATCCTTCA
1 CCCGTACGAGTCACCTAGAATTAACTATGATTAGGTGCTCCTGTACGAGTCACTCTAATCCTTCA
2653719 GGGA
66 GGGA
*
2653723 TCCCGTATGAGTCACCTAGAATTAACTATGATTAGGTGCT-CTGTACGAGTCACTCTAATCCTTC
1 -CCCGTACGAGTCACCTAGAATTAACTATGATTAGGTGCTCCTGTACGAGTCACTCTAATCCTTC
2653787 -GGG-
65 AGGGA
*
2653790 GCCGTACGAGTCACCTAGAATTAACTATGATTAGGTGCTCCCT-TACGAGTCAC
1 CCCGTACGAGTCACCTAGAATTAACTATGATTAGGTGCT-CCTGTACGAGTCAC
2653843 CTATAATTAA
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
66 37 0.36
67 10 0.10
68 5 0.05
69 22 0.21
70 30 0.29
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (69 bp):
CCCGTACGAGTCACCTAGAATTAACTATGATTAGGTGCTCCTGTACGAGTCACTCTAATCCTTCA
GGGA
Found at i:2653935 original size:109 final size:105
Alignment explanation
Indices: 2653721--2653951 Score: 284
Period size: 109 Copynumber: 2.2 Consensus size: 105
2653711 ATCCTTCAGG
* * *
2653721 GATCCCGTATGAGTCACCTAGAATTAACTATGATTAGGTGCTCTGTACGAGTCACTCTAATCCTT
1 GATCCCGTACGAGTCACCTAGAATTAAATATGATTAGGTGCTCTGTACGACTCACTCTAATCCTT
** *
2653786 CGGGGCCGTACGAGTCACCTAGAATTAACTATGATTAGGT
66 CAAGGCCGTACGAGTCACCGAGAATTAACTATGATTAGGT
* * * * **
2653826 GCTCCCTTACGAGTCACCTATAATTAAATATGATTAGGTGCTTTCGTATTACTCACTCTAATCCT
1 GATCCCGTACGAGTCACCTAGAATTAAATATGATTAGGTGCTCT-GTACGACTCACTCTAATCCT
*
2653891 TCAAGGCTCTTGTACGAGTCACCCGA-AATTAACTATTATTAGGT
65 TCAAGGC-C--GTACGAGTCA-CCGAGAATTAACTATGATTAGGT
*
2653935 GATCTCGTACGAGTCAC
1 GATCCCGTACGAGTCAC
2653952 TCTAATCCTT
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
105 38 0.36
106 22 0.21
107 1 0.01
109 41 0.39
110 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (105 bp):
GATCCCGTACGAGTCACCTAGAATTAAATATGATTAGGTGCTCTGTACGACTCACTCTAATCCTT
CAAGGCCGTACGAGTCACCGAGAATTAACTATGATTAGGT
Found at i:2654044 original size:69 final size:70
Alignment explanation
Indices: 2653836--2654100 Score: 304
Period size: 70 Copynumber: 3.8 Consensus size: 70
2653826 GCTCCCTTAC
* * * ** * **
2653836 GAGTCACCTATAATTAAATATGATTAGGTGCTTTCGTATTACTCACTCTAATCCTTCAAGGCTCT
1 GAGTCACCCATAATTAACTATGATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTCGGGGCTCT
2653901 --TGT
66 CATGT
* *
2653904 ACGAGTCACCCGA-AATTAACTATTATTAGGTGATCTCGTACGAGTCACTCTAATCCTTCGGGGC
1 --GAGTCACCC-ATAATTAACTATGATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTCGGGGC
*
2653968 TCCCATGT
63 TCTCATGT
*
2653976 GAGTCACCCATAATTAACTATGATTAGGTTCTCTC-TACGAGTCACTCTAATCCTTCGGGGCTCT
1 GAGTCACCCATAATTAACTATGATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTCGGGGCTCT
2654040 CATGT
66 CATGT
* * * * * * *
2654045 GGGTCACCTAAAATTAACTATGATTAGGTCCTCCCGTATGAGTCATTCTAATCCTT
1 GAGTCACCCATAATTAACTATGATTAGGTGCTCTCGTACGAGTCACTCTAATCCTT
2654101 TAAGGCTCCC
Statistics
Matches: 168, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
69 64 0.38
70 100 0.60
71 1 0.01
72 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (70 bp):
GAGTCACCCATAATTAACTATGATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTCGGGGCTCT
CATGT
Found at i:2654088 original size:139 final size:139
Alignment explanation
Indices: 2653836--2654100 Score: 327
Period size: 139 Copynumber: 1.9 Consensus size: 139
2653826 GCTCCCTTAC
* * **
2653836 GAGTCACCTATAATTAAATATGATTAGGTGCTTTCGTATTACTCACTCTAATCCTTCAAGGCTCT
1 GAGTCACCCATAATTAAATATGATTAGGTGCTCTCGTACGACTCACTCTAATCCTTCAAGGCTCT
* * * *
2653901 TGTACGAGTCACCCGAAATTAACTATTATTAGGTGATCTCGTACGAGTCACTCTAATCCTTCGGG
66 TGTA-GAGTCACCCAAAATTAACTATGATTAGGTCATCCCGTACGAGTCACTCTAATCCTTCGGG
2653966 GCTCCCATGT
130 GCTCCCATGT
* * * **
2653976 GAGTCACCCATAATTAACTATGATTAGGTTCTCTC-TACGAGTCACTCTAATCCTTCGGGGCTCT
1 GAGTCACCCATAATTAAATATGATTAGGTGCTCTCGTACGACTCACTCTAATCCTTCAAGGCTCT
* * * * *
2654040 CATGT-GGGTCACCTAAAATTAACTATGATTAGGTCCTCCCGTATGAGTCATTCTAATCCTT
66 --TGTAGAGTCACCCAAAATTAACTATGATTAGGTCATCCCGTACGAGTCACTCTAATCCTT
2654101 TAAGGCTCCC
Statistics
Matches: 105, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
139 71 0.68
140 31 0.30
141 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (139 bp):
GAGTCACCCATAATTAAATATGATTAGGTGCTCTCGTACGACTCACTCTAATCCTTCAAGGCTCT
TGTAGAGTCACCCAAAATTAACTATGATTAGGTCATCCCGTACGAGTCACTCTAATCCTTCGGGG
CTCCCATGT
Found at i:2654119 original size:139 final size:139
Alignment explanation
Indices: 2653826--2654120 Score: 324
Period size: 139 Copynumber: 2.1 Consensus size: 139
2653816 ATGATTAGGT
* * * **
2653826 GCTCCCTTACGAGTCACCTATAATTAAATATGATTAGGTGCTTTCGTATTACTCACTCTAATCCT
1 GCTCCCATACGAGTCACCCATAATTAAATATGATTAGGTGCTCTCGTACGACTCACTCTAATCCT
* * * *
2653891 TCAAGGCTCTTGTACGAGTCACCCGAAATTAACTATTATTAGGTGATCTCGTACGAGTCACTCTA
66 TCAAGGCTCTTGTA-GAGTCACCCAAAATTAACTATGATTAGGTCATCCCGTACGAGTCACTCTA
**
2653956 ATCCTTCGGG
130 ATCCTTCAAG
** * * *
2653966 GCTCCCATGTGAGTCACCCATAATTAACTATGATTAGGTTCTCTC-TACGAGTCACTCTAATCCT
1 GCTCCCATACGAGTCACCCATAATTAAATATGATTAGGTGCTCTCGTACGACTCACTCTAATCCT
** * * * * *
2654030 TCGGGGCTCTCATGT-GGGTCACCTAAAATTAACTATGATTAGGTCCTCCCGTATGAGTCATTCT
66 TCAAGGCTCT--TGTAGAGTCACCCAAAATTAACTATGATTAGGTCATCCCGTACGAGTCACTCT
*
2654094 AATCCTTTAAG
129 AATCCTTCAAG
*
2654105 GCTCCCGTACGAGTCA
1 GCTCCCATACGAGTCA
2654121 TCTGAAATAA
Statistics
Matches: 126, Mismatches: 27, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
139 85 0.67
140 38 0.30
141 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (139 bp):
GCTCCCATACGAGTCACCCATAATTAAATATGATTAGGTGCTCTCGTACGACTCACTCTAATCCT
TCAAGGCTCTTGTAGAGTCACCCAAAATTAACTATGATTAGGTCATCCCGTACGAGTCACTCTAA
TCCTTCAAG
Found at i:2655895 original size:26 final size:26
Alignment explanation
Indices: 2655866--2656092 Score: 139
Period size: 25 Copynumber: 8.9 Consensus size: 26
2655856 TTTTCTATAG
*
2655866 TGAAACTTAACATAAACTTACACCGA
1 TGAAACTTAACATAAACTTACACCAA
* * * *
2655892 TGAAA-TGAACACTTAA-TTTCAACAA
1 TGAAACTTAACA-TAAACTTACACCAA
* *
2655917 TGAAACTTAACATAAACTTATACCAG
1 TGAAACTTAACATAAACTTACACCAA
* * * *
2655943 TGAAA-TCAACACTTAA-TTTCAACAA
1 TGAAACTTAACA-TAAACTTACACCAA
*
2655968 TGAAACTTAACATAAACTTACACCAG
1 TGAAACTTAACATAAACTTACACCAA
* * * *
2655994 TGAAA-TCAACACTTAA-TTCCAGCAA
1 TGAAACTTAACA-TAAACTTACACCAA
* * *
2656019 TGAAACTTAACATAGACTTACACTAG
1 TGAAACTTAACATAAACTTACACCAA
* * *
2656045 T-ATAA-TTAACACTTAA-TTCCAGCAA
1 TGA-AACTTAACA-TAAACTTACACCAA
*
2656070 TGAAACTTAACATAGACTTACAC
1 TGAAACTTAACATAAACTTACAC
2656093 TGGAAAATCA
Statistics
Matches: 143, Mismatches: 44, Indels: 28
0.67 0.20 0.13
Matches are distributed among these distances:
25 72 0.50
26 71 0.50
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.26
Consensus pattern (26 bp):
TGAAACTTAACATAAACTTACACCAA
Found at i:2656216 original size:203 final size:203
Alignment explanation
Indices: 2655866--2656266 Score: 536
Period size: 203 Copynumber: 2.0 Consensus size: 203
2655856 TTTTCTATAG
* *
2655866 TGAAACTTAACATAAACTTACACCGATGAAATGAACACTTAATTTCAACAATGAAACTTAACATA
1 TGAAACTTAACATAAACTTACACCGA-GAAATCAACACTTAATTCCAACAATGAAACTTAACATA
* * * *
2655931 AACTTATACCAGTGAAATCAACACTTAATTTCAACAATGAAACTTAACATAAACTTACACCAGTG
65 AACTTACACCAGTAAAATCAACACTTAATTCCAACAATGAAACTTAACATAAACTTACACCAGTA
* * ** * *
2655996 AAATCAACACTTAATTCCAGCAATGAAACTTAACATAGACTTACACTAG-TATAATTAACACTTA
130 AAATCAACACATAATTCCAACAATGAAACCAAACATAGACTTACAC-AGATAAAATCAACACTTA
2656060 ATTCCAGCAA
194 ATTCCAGCAA
* * * *
2656070 TGAAACTTAACATAGACTTACACTG-GAAAATCAACATTTAATTCCAACAATGAAGCTTAACATA
1 TGAAACTTAACATAAACTTACACCGAG-AAATCAACACTTAATTCCAACAATGAAACTTAACATA
* * ** * *
2656134 GACTTACACCGGTAAAATCAACACTTAATTCCAACAATGACGCTTAACATAGACTTACACCGGTA
65 AACTTACACCAGTAAAATCAACACTTAATTCCAACAATGAAACTTAACATAAACTTACACCAGTA
* * *
2656199 AAATCAACACATAATTCCAACCATGAAACCAAACATATACTTACACCGATAAAATCAACACTTAA
130 AAATCAACACATAATTCCAACAATGAAACCAAACATAGACTTACACAGATAAAATCAACACTTAA
2656264 TTC
195 TTC
2656267 TAGTACTGAA
Statistics
Matches: 170, Mismatches: 25, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
202 2 0.01
203 145 0.85
204 23 0.14
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (203 bp):
TGAAACTTAACATAAACTTACACCGAGAAATCAACACTTAATTCCAACAATGAAACTTAACATAA
ACTTACACCAGTAAAATCAACACTTAATTCCAACAATGAAACTTAACATAAACTTACACCAGTAA
AATCAACACATAATTCCAACAATGAAACCAAACATAGACTTACACAGATAAAATCAACACTTAAT
TCCAGCAA
Found at i:2656266 original size:51 final size:51
Alignment explanation
Indices: 2655866--2656266 Score: 495
Period size: 51 Copynumber: 7.9 Consensus size: 51
2655856 TTTTCTATAG
* * * *
2655866 TGAAACTTAACATAAACTTACACCGATGAAATGAACACTTAATTTCAACAA
1 TGAAACTTAACATAGACTTACACCGATAAAATCAACACTTAATTCCAACAA
* * * *
2655917 TGAAACTTAACATAAACTTATACC-AGTGAAATCAACACTTAATTTCAACAA
1 TGAAACTTAACATAGACTTACACCGA-TAAAATCAACACTTAATTCCAACAA
* * *
2655968 TGAAACTTAACATAAACTTACACC-AGTGAAATCAACACTTAATTCCAGCAA
1 TGAAACTTAACATAGACTTACACCGA-TAAAATCAACACTTAATTCCAACAA
* * * *
2656019 TGAAACTTAACATAGACTTACA-CTAGTATAATTAACACTTAATTCCAGCAA
1 TGAAACTTAACATAGACTTACACCGA-TAAAATCAACACTTAATTCCAACAA
* * *
2656070 TGAAACTTAACATAGACTTACACTG-GAAAATCAACATTTAATTCCAACAA
1 TGAAACTTAACATAGACTTACACCGATAAAATCAACACTTAATTCCAACAA
* *
2656120 TGAAGCTTAACATAGACTTACACCGGTAAAATCAACACTTAATTCCAACAA
1 TGAAACTTAACATAGACTTACACCGATAAAATCAACACTTAATTCCAACAA
** * * *
2656171 TGACGCTTAACATAGACTTACACCGGTAAAATCAACACATAATTCCAACCA
1 TGAAACTTAACATAGACTTACACCGATAAAATCAACACTTAATTCCAACAA
** *
2656222 TGAAACCAAACATATACTTACACCGATAAAATCAACACTTAATTC
1 TGAAACTTAACATAGACTTACACCGATAAAATCAACACTTAATTC
2656267 TAGTACTGAA
Statistics
Matches: 316, Mismatches: 30, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
50 45 0.14
51 271 0.86
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (51 bp):
TGAAACTTAACATAGACTTACACCGATAAAATCAACACTTAATTCCAACAA
Found at i:2657835 original size:3 final size:3
Alignment explanation
Indices: 2657827--2657878 Score: 63
Period size: 3 Copynumber: 17.0 Consensus size: 3
2657817 TTTTGTCTGG
2657827 ATT ATT ATT ATT -TAT ATTT ATT ATT ATCT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT AT-T A-TT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
2657873 ATT ATT
1 ATT ATT
2657879 TAATATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 3 0.07
3 36 0.82
4 4 0.09
5 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2657849 original size:16 final size:15
Alignment explanation
Indices: 2657827--2657878 Score: 70
Period size: 15 Copynumber: 3.4 Consensus size: 15
2657817 TTTTGTCTGG
2657827 ATTATTATTATTTAT
1 ATTATTATTATTTAT
*
2657842 ATTTATTATTATCTAT
1 A-TTATTATTATTTAT
2657858 ATTATTATTA-TTATT
1 ATTATTATTATTTA-T
2657873 ATTATT
1 ATTATT
2657879 TAATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 2 0.06
15 17 0.52
16 14 0.42
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTATTATTATTTAT
Found at i:2657890 original size:31 final size:31
Alignment explanation
Indices: 2657827--2657890 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
2657817 TTTTGTCTGG
* *
2657827 ATTATTATTATTTATATTTATTATTATCTAT
1 ATTATTATTATTTATATTTATTAATATATAT
2657858 ATTATTATTA-TTAT-TATTATTTAATATATAT
1 ATTATTATTATTTATAT-TTA-TTAATATATAT
2657889 AT
1 AT
2657891 ATATAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 7 0.24
31 21 0.72
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTATTATTATTTATATTTATTAATATATAT
Found at i:2659527 original size:19 final size:18
Alignment explanation
Indices: 2659503--2659539 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2659493 AATAACTTCC
2659503 ATGTTGGTTCTTAATGTTA
1 ATGTTGGTT-TTAATGTTA
*
2659522 ATGTTGGTTTTATTGTTA
1 ATGTTGGTTTTAATGTTA
2659540 TTCTAGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.57
Consensus pattern (18 bp):
ATGTTGGTTTTAATGTTA
Found at i:2661122 original size:17 final size:17
Alignment explanation
Indices: 2661094--2661135 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2661084 CAGAGCATGG
*
2661094 GGGTACAAAACATGTA-
1 GGGTAGAAAACATGTAT
2661110 GGTGTAGAAAACATGTAT
1 GG-GTAGAAAACATGTAT
2661128 GGGTAGAA
1 GGGTAGAA
2661136 CTGTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.40, C:0.07, G:0.31, T:0.21
Consensus pattern (17 bp):
GGGTAGAAAACATGTAT
Found at i:2670856 original size:16 final size:15
Alignment explanation
Indices: 2670837--2670951 Score: 88
Period size: 16 Copynumber: 7.1 Consensus size: 15
2670827 CATCTCTTAT
*
2670837 TTTTTTTCTCTTTTTC
1 TTTTTTT-TCTTCTTC
2670853 TTTTCTTTCTCATT-TTC
1 TTTT-TTT-TC-TTCTTC
* *
2670870 ATTTTTTTGTTCTTC
1 TTTTTTTTCTTCTTC
* *
2670885 GTTTTCATTTTCTTTTTT
1 -TTTT--TTTTCTTCTTC
2670903 TATTTTTTTCTTCTTC
1 T-TTTTTTTCTTCTTC
*
2670919 TATTTTTTCTTCTTC
1 TTTTTTTTCTTCTTC
2670934 TGTTTTTTTCTTCTTC
1 T-TTTTTTTCTTCTTC
2670950 TT
1 TT
2670952 ATAATATATA
Statistics
Matches: 81, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
14 2 0.02
15 19 0.23
16 34 0.42
17 13 0.16
18 13 0.16
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTTTTCTTCTTC
Found at i:2670856 original size:17 final size:18
Alignment explanation
Indices: 2670835--2670900 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 18
2670825 TTCATCTCTT
*
2670835 ATTTTTTTTCTCTTTTTC
1 ATTTTTTTTCTCATTTTC
*
2670853 -TTTTCTTTCTCATTTTC
1 ATTTTTTTTCTCATTTTC
*
2670870 ATTTTTTTGTTCTTCGTTTTC
1 A-TTTTTT-TTC-TCATTTTC
2670891 ATTTTCTTTT
1 ATTTT-TTTT
2670901 TTTATTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 15 0.38
19 5 0.13
20 9 0.23
21 10 0.26
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTTTTTTCTCATTTTC
Found at i:2670877 original size:27 final size:25
Alignment explanation
Indices: 2670847--2670924 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 25
2670837 TTTTTTTCTC
*
2670847 TTTTTCTTTTCTTTCTCATTTTCATT
1 TTTTTTTTTTCTTT-TCATTTTCATT
* *
2670873 TTTTTGTTCTTCGTTTTCATTTTCTTTT
1 TTTTT-TTTTTC-TTTTCATTTTC-ATT
2670901 TTTATTTTTTTCTTCTTCTATTTT
1 TTT-TTTTTTTCTT-TTC-ATTTT
2670925 TTCTTCTTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
26 5 0.12
27 14 0.33
28 16 0.38
29 7 0.17
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (25 bp):
TTTTTTTTTTCTTTTCATTTTCATT
Found at i:2670927 original size:31 final size:30
Alignment explanation
Indices: 2670838--2670951 Score: 93
Period size: 31 Copynumber: 3.5 Consensus size: 30
2670828 ATCTCTTATT
* * *
2670838 TTTTTTCTCTTTTTCTTTTCTTTCTCATTTTCA
1 TTTTTT-TCTTCTTCTTTT-TTTCT-TTTTTTA
*
2670871 TTTTTTTGTTCTTCGTTTTCATTTTCTTTTTTTA
1 TTTTTTTCTTCTTC--TTT--TTTTCTTTTTTTA
* * *
2670905 TTTTTTTCTTCTTCTATTTTTTCTTCTTCTG
1 TTTTTTTCTTCTTCT-TTTTTTCTTTTTTTA
2670936 TTTTTTTCTTCTTCTT
1 TTTTTTTCTTCTTCTT
2670952 ATAATATATA
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
30 1 0.01
31 25 0.37
32 7 0.10
33 8 0.12
34 21 0.31
35 5 0.07
36 1 0.01
ACGTcount: A:0.04, C:0.18, G:0.03, T:0.75
Consensus pattern (30 bp):
TTTTTTTCTTCTTCTTTTTTTCTTTTTTTA
Found at i:2672047 original size:6 final size:6
Alignment explanation
Indices: 2672036--2672066 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2672026 ACACTTGTAT
2672036 CATGAC CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC CATGAC C
2672067 TATGGCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:2683113 original size:16 final size:16
Alignment explanation
Indices: 2683089--2683123 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2683079 ATGTTAAGTT
*
2683089 ATATGTAACGCAAATA
1 ATATATAACGCAAATA
*
2683105 ATATATAACGTAAATA
1 ATATATAACGCAAATA
2683121 ATA
1 ATA
2683124 AATTGACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.29
Consensus pattern (16 bp):
ATATATAACGCAAATA
Found at i:2687158 original size:81 final size:81
Alignment explanation
Indices: 2687065--2687555 Score: 456
Period size: 81 Copynumber: 6.1 Consensus size: 81
2687055 CTGTTTGAAA
* * * * *
2687065 TAAAAGATTAATTGCCTAGCTTTGAATTTAATAGAAATGTGTTAAATATACCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGAATTTGACAGAAAGGTGTCAAATATACCAGTTAGATGAAAG
*
2687130 GTTAAATAACTTTGAG
66 GTTAAATGACTTTGAG
* * * * * *
2687146 TAAAAGATTAATTGCCTAACTGTGCATTTGACAGAAAGATATCAAATATGCCAGTAAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGAATTTGACAGAAAGGTGTCAAATATACCAGTTAGATGAAAG
* *
2687211 GTTAAATGCCTTCGAG
66 GTTAAATGACTTTGAG
* ** * *
2687227 TAAAAGATTAA-TACCTATATGTGCATTTGACAGAAAGGTGTCAAATATGA-TAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGAATTTGACAGAAAGGTGTCAAATAT-ACCAGTTAGATGAAA
* *
2687290 GGTAAAATGCCTTTGAG
65 GGTTAAATGACTTTGAG
* * * * *
2687307 TAAAAGATTAATTACCTAGCTATGAATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGAATTTGACAGAAAGGTGTCAAATATACCAGTTAGATGAAAG
*
2687372 ATTAAAT-ACTTTGAG
66 GTTAAATGACTTTGAG
* * * * * ***
2687387 TAAAAGATTGATTGCCTAGCTATGCATTTGGCAGAAAGGTGT-TAATCATGGAAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGAATTTGACAGAAAGGTGTCAAAT-ATACCAGTTAGATGAAA
* * *
2687451 CGCTAAATGCCTTTGAG
65 GGTTAAATGACTTTGAG
* * * * * * * *
2687468 TTAACA-ATTAAATGCCCAGCTGTGTATTTGGA-AGAAAGGTGAC-AATCATGCAAGCTAGATGA
1 -TAAAAGATTAATTGCCTAGCTGTGAATTT-GACAGAAAGGTGTCAAAT-ATACCAGTTAGATGA
* *
2687530 AAGGTTAAATGCCTTTGAT
63 AAGGTTAAATGACTTTGAG
2687549 TAAAAGA
1 TAAAAGA
2687556 CTATATGTTT
Statistics
Matches: 339, Mismatches: 62, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
79 2 0.01
80 137 0.40
81 195 0.58
82 5 0.01
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.30
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGAATTTGACAGAAAGGTGTCAAATATACCAGTTAGATGAAAG
GTTAAATGACTTTGAG
Found at i:2687415 original size:161 final size:157
Alignment explanation
Indices: 2687065--2687555 Score: 502
Period size: 161 Copynumber: 3.0 Consensus size: 157
2687055 CTGTTTGAAA
* * * * *
2687065 TAAAAGATTAATTGCCTAGCTTTGAATTTAATAGAAATGTGTTAAATAT-ACCAGTTAGATGAAA
1 TAAAAGATT-ATTGCCTAGCTATGCATTTGACAGAAAGGTG-TAAATATGA--AGTTAGATGAAA
** * * * * *
2687129 GGTTAAATAACTTTGAGTAAAAGATTAATTGCCTAACTGTGCATTTGACAGAAAGATATCAAATA
62 GG-TAAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGAATTTGA-AGAAAGGTGTCAATTA
* *
2687194 TGCCAGTAAGATGAAAGGTTAAATGCCTTCGAG
125 TGCCAGTTAGATGAAAGGTTAAATGCCTTTGAG
* * ** *
2687227 TAAAAGATTAATACCTATATGTGCATTTGACAGAAAGGTGTCAAATATGATAGTTAGATGAAAGG
1 TAAAAGATTATTGCCTAGCTATGCATTTGACAGAAAGGTGT-AAATATGA-AGTTAGATGAAAGG
* *
2687292 TAAAATGCCTTTGAGTAAAAGATTAATTACCTAGCTATGAATTTGATAGAAAGGTGTCAATTATG
64 T-AAATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGAATTTGA-AGAAAGGTGTCAATTATG
* *
2687357 CCAGTTAGATGAAAGATTAAAT-ACTTTGAG
127 CCAGTTAGATGAAAGGTTAAATGCCTTTGAG
* *
2687387 TAAAAGATTGATTGCCTAGCTATGCATTTGGCAGAAAGGTGTTAATCATGGAAGTTAGATGAAAC
1 TAAAAGATT-ATTGCCTAGCTATGCATTTGACAGAAAGGTGTAAAT-AT-GAAGTTAGATGAAA-
* * * * * * *
2687452 GCTAAATGCCTTTGAGTTAACA-ATTAAATGCCCAGCTGTGTATTTGGAAGAAAGGTGACAATCA
62 GGTAAATGCCTTTGAG-TAAAAGATTAATTGCCTAGCTGTGAATTT-GAAGAAAGGTGTCAATTA
* * *
2687516 TGCAAGCTAGATGAAAGGTTAAATGCCTTTGAT
125 TGCCAGTTAGATGAAAGGTTAAATGCCTTTGAG
2687549 TAAAAGA
1 TAAAAGA
2687556 CTATATGTTT
Statistics
Matches: 274, Mismatches: 45, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
160 20 0.07
161 221 0.81
162 33 0.12
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.30
Consensus pattern (157 bp):
TAAAAGATTATTGCCTAGCTATGCATTTGACAGAAAGGTGTAAATATGAAGTTAGATGAAAGGTA
AATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGAATTTGAAGAAAGGTGTCAATTATGCCAG
TTAGATGAAAGGTTAAATGCCTTTGAG
Found at i:2700852 original size:95 final size:94
Alignment explanation
Indices: 2700702--2700882 Score: 249
Period size: 95 Copynumber: 1.9 Consensus size: 94
2700692 GATACTAAAA
* * *
2700702 AGAAAGTATTGATAGCATGGATTCCAGAATGCCAAAATGGTATCGATACTAAAAGAGAGTATCGG
1 AGAAAGTATTGATACCATGAATTACAGAATGCCAAAATGGTATCGATACTAAAAGAGAGTATCGG
2700767 TACCATAATATAGTAA-TATCGGTACTGAG
66 TACCATAATATAG-AAGTATCGGTACTGAG
* * * *
2700796 AGAAAGATATTGATACCATGAATTACAGAATG-TAGAAATGGTATCGATATTGAAAGAGGGTATC
1 AGAAAG-TATTGATACCATGAATTACAGAATGCCA-AAATGGTATCGATACTAAAAGAGAGTATC
*
2700860 GGTACCATAGTATAGAAGTATCG
64 GGTACCATAATATAGAAGTATCG
2700883 ATAACATGGT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
94 9 0.12
95 67 0.88
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (94 bp):
AGAAAGTATTGATACCATGAATTACAGAATGCCAAAATGGTATCGATACTAAAAGAGAGTATCGG
TACCATAATATAGAAGTATCGGTACTGAG
Found at i:2701421 original size:81 final size:81
Alignment explanation
Indices: 2701286--2701857 Score: 792
Period size: 81 Copynumber: 7.1 Consensus size: 81
2701276 CTGCTTTAAA
*
2701286 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAATGTGTCAAATATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAAATATGCCAGTTAGATGAAAG
*
2701351 GTTAAATGCCTTTTAG
66 GTTAAATGCCTTTGAG
* *
2701367 TAAAAGATTAATTGCTTAGTTGTGCATTTGACAGAAAGGTGTCAAATATGCCAGTTGGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAAATATGCCAGTTAGATGAAAG
2701432 GTTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* ** *
2701448 TAAAATATTAATTGCCTAGTTGTGCATTTGACAGAAATATGTCAAATATGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAAATATGCCAGTTAGATGAAAG
* *
2701513 ATTAAATGCCTTTGAC
66 GTTAAATGCCTTTGAG
* *
2701529 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAACGGTGTCAAATATTCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAAATATGCCAGTTAGATGAAAG
2701594 GTTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* * * *
2701610 TAAATGATTAATTGTCTAGCTT-TGCATTTGACAAAAAGGTGT-AAATTATGCCAATTAGATGAA
1 TAAAAGATTAATTGCCTAG-TTGTGCATTTGACAGAAAGGTGTCAAA-TATGCCAGTTAGATGAA
* *
2701673 AAGTTAAATGCCTTTGAT
64 AGGTTAAATGCCTTTGAG
* * * *
2701691 TAAAAGATTAATTGCCTAGTTGTGCATTTGCCATAAAGGTGTC-AATCATGTCAGTTATATGAAA
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAAAT-ATGCCAGTTAGATGAAA
*
2701755 GGCTAAATGCCTTTGAG
65 GGTTAAATGCCTTTGAG
* ** * * * * *
2701772 TTAAAGATTAAAAGCCTAGTTGTGCATTTGGCATAAATGTGTC-AATCATGCAAGTTAGAAGAAA
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAAAT-ATGCCAGTTAGATGAAA
*
2701836 GGTTAAATGCCTTTGGG
65 GGTTAAATGCCTTTGAG
2701853 TAAAA
1 TAAAA
2701858 AGACTAAATG
Statistics
Matches: 436, Mismatches: 50, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
80 6 0.01
81 428 0.98
82 2 0.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGTCAAATATGCCAGTTAGATGAAAG
GTTAAATGCCTTTGAG
Found at i:2706307 original size:27 final size:26
Alignment explanation
Indices: 2706275--2706386 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
2706265 ATTATTATCG
2706275 TTTTACAATATAAGGGTATTTTCATAA
1 TTTTAC-ATATAAGGGTATTTTCATAA
** * *
2706302 TTTTACCCCATAATGATATTTTCATAA
1 TTTTA-CATATAAGGGTATTTTCATAA
*
2706329 TTTTACCTCATAAGGGTATTTTCATAA
1 TTTTACAT-ATAAGGGTATTTTCATAA
** *
2706356 TTTTACATATCAAAAGTATTGTCATAA
1 TTTTACATAT-AAGGGTATTTTCATAA
2706383 TTTT
1 TTTT
2706387 TCATCCAAGT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
26 4 0.06
27 66 0.93
28 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (26 bp):
TTTTACATATAAGGGTATTTTCATAA
Found at i:2706381 original size:54 final size:54
Alignment explanation
Indices: 2706284--2706386 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
2706274 GTTTTACAAT
* * *
2706284 ATAAGGGTATTTTCATAATTTTACCCCATAATGATATTTTCATAATTTTACCTC
1 ATAAGGGTATTTTCATAATTTTACACCATAAAGATATTGTCATAATTTTACCTC
*
2706338 ATAAGGGTATTTTCATAATTTTACA-TATCAAA-AGTATTGTCATAATTTT
1 ATAAGGGTATTTTCATAATTTTACACCAT-AAAGA-TATTGTCATAATTTT
2706387 TCATCCAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
53 3 0.07
54 40 0.93
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.45
Consensus pattern (54 bp):
ATAAGGGTATTTTCATAATTTTACACCATAAAGATATTGTCATAATTTTACCTC
Found at i:2709596 original size:24 final size:24
Alignment explanation
Indices: 2709544--2709605 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 24
2709534 GTATTCTATC
*
2709544 ATAAAT-TTAATTT-TTAAAATAA
1 ATAAATATTAATTTAATAAAATAA
* **
2709566 ATTAATATTAATTTAATAAAATTT
1 ATAAATATTAATTTAATAAAATAA
2709590 ATAAATAATT-ATTTAA
1 ATAAAT-ATTAATTTAA
2709606 CTATTTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 5 0.16
23 7 0.22
24 17 0.53
25 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATAAATATTAATTTAATAAAATAA
Found at i:2710336 original size:3 final size:3
Alignment explanation
Indices: 2710330--2710368 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2710320 TCACCCGAAA
*
2710330 TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2710369 GTTGCAGGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2718146 original size:8 final size:7
Alignment explanation
Indices: 2718118--2718238 Score: 76
Period size: 7 Copynumber: 17.4 Consensus size: 7
2718108 ACTCGAAAAG
*
2718118 AAATGAA
1 AAATAAA
2718125 AAATAGACA
1 AAATA-A-A
2718134 AAATAGAA
1 AAATA-AA
2718142 AAATAAA
1 AAATAAA
2718149 AAATAAA
1 AAATAAA
2718156 AAATAAA
1 AAATAAA
*
2718163 AAAGGAAA
1 AAA-TAAA
* **
2718171 TAGGAAA
1 AAATAAA
2718178 AAA-AAA
1 AAATAAA
2718184 AAA-AAA
1 AAATAAA
2718190 AAA-AAA
1 AAATAAA
*
2718196 AAAAAAA
1 AAATAAA
*
2718203 AAAGAAA
1 AAATAAA
2718210 AAA-AAA
1 AAATAAA
2718216 GGAAA-AAA
1 --AAATAAA
2718224 AAA-AAA
1 AAATAAA
2718230 AAA-AAA
1 AAATAAA
2718236 AAA
1 AAA
2718239 AAGGAAAAAA
Statistics
Matches: 101, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
6 36 0.36
7 40 0.40
8 17 0.17
9 8 0.08
ACGTcount: A:0.85, C:0.01, G:0.08, T:0.06
Consensus pattern (7 bp):
AAATAAA
Found at i:2718173 original size:43 final size:38
Alignment explanation
Indices: 2718125--2718336 Score: 155
Period size: 36 Copynumber: 5.3 Consensus size: 38
2718115 AAGAAATGAA
2718125 AAATAGACAAAATAGAAAAATAAAAAATAAAAAATAAAAAAGG
1 AAATAGA-AAAA-AGAAAAA-AAAAAA-AAAAAA-AAAAAAGG
* *
2718168 AAATAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
1 AAATA-GAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAGG
*
2718207 AAA-A-AAAAAGGAAAAAAAAAAAAAAAAAAAAAAAGG
1 AAATAGAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAGG
*
2718243 AAA-A-AAAGAAA-AAAAAAAGGAATAAAAGGAAAAAAAAAGGG
1 AAATAGAAA-AAAGAAAAAAA--AA-AAAA--AAAAAAAAAAGG
* * * * *
2718284 AAAAAGAGAAAAAAGAGAAAAAGAAAGAAAAAAGAATAAGGG
1 --AAATAGAAAAAAGA-AAAAA-AAAAAAAAAAAAAAAAAGG
*
2718326 AAATTGAAAAA
1 AAATAGAAAAA
2718337 GGGCTAAAGA
Statistics
Matches: 143, Mismatches: 12, Indels: 31
0.77 0.06 0.17
Matches are distributed among these distances:
36 43 0.30
37 2 0.01
38 3 0.02
39 14 0.10
40 15 0.10
41 17 0.12
42 16 0.11
43 12 0.08
44 9 0.06
45 6 0.04
46 5 0.03
47 1 0.01
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (38 bp):
AAATAGAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAGG
Found at i:2718246 original size:20 final size:19
Alignment explanation
Indices: 2718140--2718316 Score: 135
Period size: 18 Copynumber: 8.8 Consensus size: 19
2718130 GACAAAATAG
*
2718140 AAAAATAAAAAATAAAAAATA
1 AAAAAGAAAAAA-AAAAAA-A
*
2718161 AAAAAGGAAATAGGAAAAAAAA
1 AAAAA-GAAA-A-AAAAAAAAA
2718183 AAAAA-AAAAAAAAAAAAA
1 AAAAAGAAAAAAAAAAAAA
**
2718201 AAAAAG-AAAAAAAAAGGA
1 AAAAAGAAAAAAAAAAAAA
2718219 AAAAA-AAAAAAAAAAAAA
1 AAAAAGAAAAAAAAAAAAA
*
2718237 AAAAGGAAAAAAAGAAAAAA
1 AAAAAGAAAAAAA-AAAAAA
* *
2718257 AAAAGGAATAAAAGGAAAAAA
1 AAAAAGAA-AAAA-AAAAAAA
**
2718278 AAAGGGAAAAAGAGAAAAAAGA
1 AAAAAGAAAAA-A-AAAAAA-A
2718300 GAAAAAGAAAGAAAAAA
1 -AAAAAGAAA-AAAAAA
2718317 GAATAAGGGA
Statistics
Matches: 130, Mismatches: 13, Indels: 25
0.77 0.08 0.15
Matches are distributed among these distances:
18 42 0.32
19 8 0.06
20 20 0.15
21 29 0.22
22 13 0.10
23 15 0.12
24 3 0.02
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAAAAAAAAAAA
Found at i:2718261 original size:11 final size:11
Alignment explanation
Indices: 2718174--2718319 Score: 131
Period size: 11 Copynumber: 13.3 Consensus size: 11
2718164 AAGGAAATAG
2718174 GAAAAAAAAAA
1 GAAAAAAAAAA
2718185 -AAAAAAAAAA
1 GAAAAAAAAAA
*
2718195 AAAAAAAAAAA
1 GAAAAAAAAAA
*
2718206 GAAAAAAAAAG
1 GAAAAAAAAAA
2718217 GAAAAAAAAAA
1 GAAAAAAAAAA
2718228 -AAAAAAAAAA
1 GAAAAAAAAAA
2718238 -AAAGGAAAAAAA
1 GAAA--AAAAAAA
2718250 GAAAAAAAAAA
1 GAAAAAAAAAA
* * *
2718261 G-GAATAAAAG
1 GAAAAAAAAAA
*
2718271 GAAAAAAAAAGG
1 GAAAAAAAAA-A
2718283 GAAAAAGAGAAAA
1 GAAAAA-A-AAAA
* *
2718296 -AAGAGAAAAA
1 GAAAAAAAAAA
*
2718306 GAAAGAAAAAA
1 GAAAAAAAAAA
2718317 GAA
1 GAA
2718320 TAAGGGAAAT
Statistics
Matches: 112, Mismatches: 14, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
10 34 0.30
11 54 0.48
12 17 0.15
13 4 0.04
14 3 0.03
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:2718280 original size:1 final size:1
Alignment explanation
Indices: 2718175--2718260 Score: 118
Period size: 1 Copynumber: 86.0 Consensus size: 1
2718165 AGGAAATAGG
* **
2718175 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAGGAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** *
2718240 AGGAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAA
2718261 GGAATAAAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:2718280 original size:33 final size:33
Alignment explanation
Indices: 2718146--2718260 Score: 142
Period size: 35 Copynumber: 3.3 Consensus size: 33
2718136 ATAGAAAAAT
*
2718146 AAAAAATAAAAAATAAAAAAGGAAATAGGAAAAAAAAA
1 AAAAAA-AAAAAA-AAAAAA--AAA-AGGAAAAAAAAG
*
2718184 AAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAGG
1 AAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAA-G
2718218 AAAAAAAAAAAAAAAAAAAAAAAGG-AAAAAAAG
1 -AAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAAG
2718251 AAAAAAAAAA
1 AAAAAAAAAA
2718261 GGAATAAAAG
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
32 10 0.14
33 11 0.15
34 10 0.14
35 23 0.32
36 6 0.08
37 6 0.08
38 6 0.08
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.03
Consensus pattern (33 bp):
AAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAAG
Found at i:2718295 original size:17 final size:18
Alignment explanation
Indices: 2718174--2718318 Score: 77
Period size: 17 Copynumber: 8.0 Consensus size: 18
2718164 AAGGAAATAG
*
2718174 GAAAAA-AA-AAAAAAAA
1 GAAAAAGAAGAAAAAAGA
* * *
2718190 AAAAAAAAAAAAAAAAGA
1 GAAAAAGAAGAAAAAAGA
*
2718208 -AAAAAAAAGGAAAAAA-A
1 GAAAAAGAA-GAAAAAAGA
* * *
2718225 AAAAAAAAAAAAAAAAGGA
1 GAAAAAGAAGAAAAAA-GA
* *
2718244 AAAAAAGAA-AAAAAAAA
1 GAAAAAGAAGAAAAAAGA
* *
2718261 GGAATAAAAGGAAAAAAAAAGG
1 -G-A-AAAA-GAAGAAAAAAGA
2718283 GAAAAAG-AGAAAAAAGA
1 GAAAAAGAAGAAAAAAGA
2718300 GAAAAAGAAAGAAAAAAGA
1 GAAAAAG-AAGAAAAAAGA
2718319 ATAAGGGAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 23
0.76 0.08 0.17
Matches are distributed among these distances:
16 5 0.05
17 33 0.31
18 28 0.27
19 24 0.23
20 5 0.05
21 4 0.04
22 6 0.06
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (18 bp):
GAAAAAGAAGAAAAAAGA
Found at i:2718679 original size:19 final size:19
Alignment explanation
Indices: 2718657--2718694 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2718647 TTGTAAAAAT
2718657 TCCAATTTCCTCATTTCAA
1 TCCAATTTCCTCATTTCAA
2718676 TCCAATTTCCTCATTTCAA
1 TCCAATTTCCTCATTTCAA
2718695 GCCCCAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (19 bp):
TCCAATTTCCTCATTTCAA
Found at i:2720396 original size:134 final size:134
Alignment explanation
Indices: 2720150--2720914 Score: 873
Period size: 134 Copynumber: 5.7 Consensus size: 134
2720140 TGTAGATCTA
* * *
2720150 ATATTCCCTTCAGAATAAGTAGAACA-AGTCCCTCT-GTTCTAAGATTTGATATTCCCTAAGTGA
1 ATATTCCCTTCAGAAGAAGTAGAACATA-TCCCTCTCTTTC-AAGATTTGATATTCCCTGAGTGA
* * * * *
2720213 CAGTGGAACAAGTCTGCCCCGATTTAATCTTCCGTGAGTGACAGTGGAATGGATCAACTCCTTCA
64 CAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCTCA
2720278 AATATG
129 AATATG
* *
2720284 ATATTCTCTTCAGAAGAAGTAGAACATGTCCCTCT-TTTCTAAGATTTGATATTCCCTGAGTGAC
1 ATATTCCCTTCAGAAGAAGTAGAACATATCCCTCTCTTTC-AAGATTTGATATTCCCTGAGTGAC
** * * *
2720348 AAAGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCCCTTAA
65 AGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCTCAA
2720413 ATATG
130 ATATG
* * ** ** * *
2720418 ATATCCCCTTTAGAA-AAAAAGGAACAGGTCCATTTCTTTCAAGATTTGATATTCCCTGAGTGAC
1 ATATTCCCTTCAGAAGAAGTA-GAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGAC
* *
2720482 AGCGGAATAAGTCTGCCCCGATTCAATCTTCCCTAAGTGACAGCGGAATGGATCAACTACCCT-A
65 AGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACT-CCCTCA
*
2720546 GATATG
129 AATATG
** *
2720552 ATATTCCCTTCA-AGAGAAGCGGAACATATCCCTCTCTTTCAAGATTTGTTATTCCCTGAGTGAT
1 ATATTCCCTTCAGA-AGAAGTAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGA-
* * * * *
2720616 TA-CGAAACAAGTCTGCCCCGATTCAATCTTCCCTAAGTGAGAGCGGAATGGATTAACTCCC-CT
64 CAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCTC-
** *
2720679 GGATCTG
128 AAATATG
* * * * *
2720686 ATATCCCCTTTAGAAGAAGCAAAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTGACA
1 ATATTCCCTTCAGAAGAAGTAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACA
* * * * ** * *
2720751 GTGGAACAAGTCTTCCCTGATTCAATCTTCCTTGAGTGACAATGGAATGGATCAACTCCCCCATA
66 GCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCTCAAA
2720816 TATG
131 TATG
* * * *
2720820 ATATTCCCTTCACAAGAAGTGGAACATATCCCTCTCTTCCAAGATTAGATATTCCCT-ATGTGAC
1 ATATTCCCTTCAGAAGAAGTAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGA-GTGAC
* * *
2720884 AGCGGAATAAGTATGCCCTGATTCAATCTTC
65 AGCGGAACAAGTCTGCCCCGATTCAATCTTC
2720915 TCTATATAAC
Statistics
Matches: 539, Mismatches: 79, Indels: 26
0.84 0.12 0.04
Matches are distributed among these distances:
133 9 0.02
134 517 0.96
135 13 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (134 bp):
ATATTCCCTTCAGAAGAAGTAGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACA
GCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCTCAAA
TATG
Found at i:2720958 original size:402 final size:402
Alignment explanation
Indices: 2720219--2720962 Score: 969
Period size: 402 Copynumber: 1.9 Consensus size: 402
2720209 GTGACAGTGG
* * * * *
2720219 AACAAGTCTGCCCCGATTTAATCTTCCGTGAGTGACAGTGGAATGGATCAACTCCTTCAAATATG
1 AACAAGTCTGCCCCGATTCAATCTTCCCTAAGTGACAGCGGAATGGATCAACTCCCTCAAATATG
* * * * * *
2720284 ATATTCTCTTCAGAAGAAGTAGAACATGTCCCTCTTTTCTAAGATTTGATATTCCCTGAGTGACA
66 ATATCCCCTTCAGAAGAAGCAAAACATATCCATCTTTTCTAAGATTTGATATTCCCTGAGTGACA
**
2720349 AAGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCCCTTAAA
131 AAGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCCCCCAAA
* * * * * *
2720414 TATGATATCCCCTTTAGAAAAAAAGGAACAGGTCCATTTCTTTCAAGATTTGATATTCCCTGAGT
196 TATGATATCCCCTTCACAAAAAAAGGAACAGATCCATCTCTTCCAAGATTAGATATTCCCTGAGT
* * * **
2720479 GACAGCGGAATAAGTCTGCCCCGATTCAATCTTCCCTAAGTGACAGCGGAATGGATCAACTACCC
261 GACAGCGGAATAAGTATGCCCCGATTCAATCTTCCCTAAGTAACAGCGAAATAAATCAACTACCC
*
2720544 TAGATATGATATTCCCTTCAAGAGAAGCGGAACATATCCCTCTCTTTCAAGATTTGTTATTCCCT
326 CAGATATGATATTCCCTTCAAGAGAAGCGGAACATATCCCTCTCTTTCAAGATTTGTTATTCCCT
2720609 GAGTGATTACGA
391 GAGTGATTACGA
* * ** *
2720621 AACAAGTCTGCCCCGATTCAATCTTCCCTAAGTGAGAGCGGAATGGATTAACTCCC-CTGGATCT
1 AACAAGTCTGCCCCGATTCAATCTTCCCTAAGTGACAGCGGAATGGATCAACTCCCTC-AAATAT
*
2720685 GATATCCCCTTTAGAAGAAGCAAAACATATCCATCTCTTTC-AAGATTTGATATTCCCTGAGTGA
65 GATATCCCCTTCAGAAGAAGCAAAACATATCCATCT-TTTCTAAGATTTGATATTCCCTGAGTGA
** * * * *
2720749 CAGTGGAACAAGTCTTCCCTGATTCAATCTTCCTTGAGTGACAATGGAATGGATCAACTCCCCCA
129 CAAAGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCCCCCA
* * * ** * *
2720814 TATATGATATTCCCTTCACAAGAAGTGGAACATATCCCTCTCTTCCAAGATTAGATATTCCCT-A
194 AATATGATATCCCCTTCACAAAAAAAGGAACAGATCCATCTCTTCCAAGATTAGATATTCCCTGA
* *
2720878 TGTGACAGCGGAATAAGTATGCCCTGATTCAATCTTCTCTATA-TAACA-CTGAAATAAATCAAC
259 -GTGACAGCGGAATAAGTATGCCCCGATTCAATCTTCCCTA-AGTAACAGC-GAAATAAATCAAC
*
2720941 -ATCCCCAGATCTGATATTCCCT
321 TA-CCCCAGATATGATATTCCCT
2720963 GAGTGATAGC
Statistics
Matches: 289, Mismatches: 47, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
401 4 0.01
402 280 0.97
403 5 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (402 bp):
AACAAGTCTGCCCCGATTCAATCTTCCCTAAGTGACAGCGGAATGGATCAACTCCCTCAAATATG
ATATCCCCTTCAGAAGAAGCAAAACATATCCATCTTTTCTAAGATTTGATATTCCCTGAGTGACA
AAGGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAACGGAATGGATCAACTCCCCCAAA
TATGATATCCCCTTCACAAAAAAAGGAACAGATCCATCTCTTCCAAGATTAGATATTCCCTGAGT
GACAGCGGAATAAGTATGCCCCGATTCAATCTTCCCTAAGTAACAGCGAAATAAATCAACTACCC
CAGATATGATATTCCCTTCAAGAGAAGCGGAACATATCCCTCTCTTTCAAGATTTGTTATTCCCT
GAGTGATTACGA
Found at i:2721109 original size:3 final size:3
Alignment explanation
Indices: 2721101--2721142 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
2721091 TTGCCTGAAA
*
2721101 TAT TAT TAT TAT TAT TAT TCT TAT TATT TAT T-T TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT T
2721143 TTGTTGCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.12
3 27 0.79
4 3 0.09
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:2730328 original size:14 final size:15
Alignment explanation
Indices: 2730295--2730327 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2730285 TGTTGGATGT
2730295 TTTTGGATTGTTTTA
1 TTTTGGATTGTTTTA
2730310 TTTTGGA-TGTTTATA
1 TTTTGGATTGTTT-TA
2730325 TTT
1 TTT
2730328 GTTATGGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.15, C:0.00, G:0.18, T:0.67
Consensus pattern (15 bp):
TTTTGGATTGTTTTA
Found at i:2734292 original size:17 final size:17
Alignment explanation
Indices: 2734270--2734310 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2734260 GACCCTCTGA
2734270 ATATTTTAAATTATTAT
1 ATATTTTAAATTATTAT
*
2734287 ATATTTTAAATTTTTAT
1 ATATTTTAAATTATTAT
*
2734304 GTATTTT
1 ATATTTT
2734311 TTATTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATATTTTAAATTATTAT
Found at i:2738658 original size:2 final size:2
Alignment explanation
Indices: 2738653--2738716 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
2738643 TCTCTCTCTC
* *
2738653 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2738695 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
2738717 CTTTATAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2739241 original size:3 final size:3
Alignment explanation
Indices: 2739235--2739271 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2739225 TTAATTTTTT
2739235 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2739272 CTTCATTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2742053 original size:24 final size:24
Alignment explanation
Indices: 2742010--2742081 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
2742000 CTTTCCCCCT
*
2742010 TGAGATTAGAT-ATGCCAAAGTTG
1 TGAGGTTAGATCATGCCAAAGTTG
*
2742033 TGAGGTTAGATCATGCCAAAGTTC
1 TGAGGTTAGATCATGCCAAAGTTG
2742057 TGAGGTTAGATCATGCCAAAGTTG
1 TGAGGTTAGATCATGCCAAAGTTG
2742081 T
1 T
2742082 TTCTCAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 10 0.22
24 35 0.78
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (24 bp):
TGAGGTTAGATCATGCCAAAGTTG
Found at i:2747396 original size:20 final size:20
Alignment explanation
Indices: 2747351--2747397 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2747341 TCAATGCTAC
*
2747351 AAGAACAATATGGATACTTG
1 AAGAACAATATGGATACTGG
*
2747371 AAGAACAATATTGATACTGG
1 AAGAACAATATGGATACTGG
*
2747391 ATGAACA
1 AAGAACA
2747398 GTAGCGGTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (20 bp):
AAGAACAATATGGATACTGG
Found at i:2747840 original size:64 final size:64
Alignment explanation
Indices: 2747736--2747895 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 64
2747726 GAATAAATTG
* * *** * * ** * *
2747736 AACATCAAATACATTTCATGCTTCGATGCACTCTCTATGCATCGATGCACT-TGGGTTTTATTAA
1 AACATCAAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAAGCTATT-TTAA
* *
2747800 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAAGCTATTTTCA
1 AACATCAAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAAGCTATTTTAA
* *
2747864 AACATCAAATGCATTTTATGCATTGATGCACA
1 AACATCAAATGCATTTCATGCATCGATGCACA
2747896 CTTGGTGCAC
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
64 75 0.95
65 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (64 bp):
AACATCAAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAAGCTATTTTAA
Found at i:2755131 original size:20 final size:20
Alignment explanation
Indices: 2755086--2755132 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2755076 TCAATGATAC
*
2755086 AAGAACAATATGGATACTTG
1 AAGAACAATATGGATACTGG
*
2755106 AAGAACAATATTGATACTGG
1 AAGAACAATATGGATACTGG
*
2755126 ATGAACA
1 AAGAACA
2755133 GTAGCGGTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (20 bp):
AAGAACAATATGGATACTGG
Found at i:2761209 original size:16 final size:16
Alignment explanation
Indices: 2761180--2761220 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2761170 CATTTTTTTA
2761180 ATAAA-TAA-ACGAAC
1 ATAAACTAACACGAAC
2761194 ATAAACTAACACGAAC
1 ATAAACTAACACGAAC
*
2761210 ATAAACGAACA
1 ATAAACTAACA
2761221 AAATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 5 0.21
15 3 0.12
16 16 0.67
ACGTcount: A:0.61, C:0.20, G:0.07, T:0.12
Consensus pattern (16 bp):
ATAAACTAACACGAAC
Found at i:2761296 original size:10 final size:10
Alignment explanation
Indices: 2761283--2761349 Score: 71
Period size: 10 Copynumber: 6.4 Consensus size: 10
2761273 GTTCATTTAA
2761283 AACATAAACG
1 AACATAAACG
2761293 AACATAAACG
1 AACATAAACG
**
2761303 AACACGAACG
1 AACATAAACG
2761313 AACATAAACG
1 AACATAAACG
2761323 AACACAATAAACG
1 -A-AC-ATAAACG
**
2761336 AATGTAAACG
1 AACATAAACG
2761346 AACA
1 AACA
2761350 ACACAAACAC
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
10 34 0.74
11 2 0.04
12 3 0.07
13 7 0.15
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
AACATAAACG
Found at i:2761357 original size:23 final size:23
Alignment explanation
Indices: 2761283--2761357 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
2761273 GTTCATTTAA
*
2761283 AACATAAACGAACATAAACG---
1 AACACAAACGAACATAAACGAAC
*
2761303 AACACGAACGAACATAAACGAAC
1 AACACAAACGAACATAAACGAAC
* **
2761326 -ACAATAAACGAATGTAAACGAAC
1 AAC-ACAAACGAACATAAACGAAC
2761349 AACACAAAC
1 AACACAAAC
2761358 ACACACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
20 18 0.42
22 2 0.05
23 21 0.49
24 2 0.05
ACGTcount: A:0.59, C:0.23, G:0.11, T:0.08
Consensus pattern (23 bp):
AACACAAACGAACATAAACGAAC
Found at i:2761631 original size:14 final size:14
Alignment explanation
Indices: 2761612--2761671 Score: 93
Period size: 14 Copynumber: 4.1 Consensus size: 14
2761602 GCCTTCTATT
2761612 CGAACATAAATGAA
1 CGAACATAAATGAA
2761626 CGAACATAAATGAA
1 CGAACATAAATGAA
*
2761640 GGAACATAAATGAA
1 CGAACATAAATGAA
2761654 CGAACATATAATCGAA
1 CGAACATA-AAT-GAA
2761670 CG
1 CG
2761672 TTCACGAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
14 34 0.81
15 3 0.07
16 5 0.12
ACGTcount: A:0.53, C:0.15, G:0.17, T:0.15
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:2764360 original size:22 final size:22
Alignment explanation
Indices: 2764342--2764383 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2764332 TCGTTGATCG
2764342 GACAGTTGACCG-CCATTGACC
1 GACAGTTGACCGACCATTGACC
*
2764363 GACTGTTGACCGACCATTGAC
1 GACAGTTGACCGACCATTGAC
2764384 TTTTTTCGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (22 bp):
GACAGTTGACCGACCATTGACC
Found at i:2767589 original size:46 final size:46
Alignment explanation
Indices: 2767439--2767590 Score: 118
Period size: 45 Copynumber: 3.3 Consensus size: 46
2767429 CTTCTCTTCA
* ** * *
2767439 TGAAGGTTAAATCTAAAAAAGTAGGTTGATTTGCTTCC-TCGTCTCTTTC
1 TGAAGGTTAAATCT-AAAAACTTTG-TGATTTGCTTCCATC--ATCTTTG
*
2767488 TGAAGGTCAAATCT-AAAACTCTTG-G-TTTGC-TCCATCATCTATTCG
1 TGAAGGTTAAATCTAAAAACT-TTGTGATTTGCTTCCATCATCT-TT-G
* *
2767533 TGGAGATTAAATCTAAAAACTTTGATGATTTGCTTCCATCAT-TTTG
1 TGAAGGTTAAATCTAAAAACTTTG-TGATTTGCTTCCATCATCTTTG
2767579 TGAAGGTTAAAT
1 TGAAGGTTAAAT
2767591 ATGAAAAATT
Statistics
Matches: 83, Mismatches: 11, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
43 3 0.04
44 5 0.06
45 21 0.25
46 18 0.22
47 8 0.10
48 7 0.08
49 21 0.25
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (46 bp):
TGAAGGTTAAATCTAAAAACTTTGTGATTTGCTTCCATCATCTTTG
Found at i:2769218 original size:18 final size:19
Alignment explanation
Indices: 2769191--2769229 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
2769181 CCCTTTTTTA
2769191 TTTTTATTTCTCTC-TCTT
1 TTTTTATTTCTCTCTTCTT
*
2769209 TTTTTGTTTCTCTCTTCTT
1 TTTTTATTTCTCTCTTCTT
2769228 TT
1 TT
2769230 ATACCTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTTTATTTCTCTCTTCTT
Found at i:2773856 original size:2 final size:2
Alignment explanation
Indices: 2773849--2773879 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2773839 TTAGATCCGA
2773849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2773880 CTAGTGCACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2775327 original size:22 final size:22
Alignment explanation
Indices: 2775299--2775351 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
2775289 TCAAGCCTAG
2775299 TACATCAACTATGGCATAATTA
1 TACATCAACTATGGCATAATTA
2775321 TACATCAACTATGGCATAATTA
1 TACATCAACTATGGCATAATTA
2775343 TACATCAAC
1 TACATCAAC
2775352 CCACAACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (22 bp):
TACATCAACTATGGCATAATTA
Found at i:2778437 original size:2 final size:2
Alignment explanation
Indices: 2778426--2778463 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2778416 TTCAGATGAC
*
2778426 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2778464 TCATTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.