Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold211
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: 2157208
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 20444 characters in sequence are not A, C, G, or T
File 4 of 15
Found at i:365556 original size:5 final size:5
Alignment explanation
Indices: 365541--365607 Score: 56
Period size: 5 Copynumber: 14.2 Consensus size: 5
365531 TATTTAAAAA
* *
365541 TATATT TATAT TATAT TATAT TTTA- TATAT TATAT TTTAAT TAT-T T-TA-
1 TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT
365589 TATAT TATA- TA-AT TATAT T
1 TATAT TATAT TATAT TATAT T
365608 TAAAATTATT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
3 3 0.06
4 11 0.22
5 28 0.56
6 8 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TATAT
Found at i:365567 original size:23 final size:24
Alignment explanation
Indices: 365540--365608 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 24
365530 ATATTTAAAA
365540 ATATATTTATATTATATTATATTTT
1 ATATA-TTATATTATATTATATTTT
* *
365565 ATATATTATATTTTAAT-TATTTT
1 ATATATTATATTATATTATATTTT
365588 ATATATTATA-TA-ATTATATTT
1 ATATATTATATTATATTATATTT
365609 AAAATTATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 2 0.05
22 6 0.15
23 16 0.41
24 10 0.26
25 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATATTATATTATATTATATTTT
Found at i:365577 original size:30 final size:32
Alignment explanation
Indices: 365541--365616 Score: 104
Period size: 30 Copynumber: 2.5 Consensus size: 32
365531 TATTTAAAAA
*
365541 TATATTTAT-ATTATATTATATTTTATAT-AT
1 TATATTTATAATTATATTATATATTATATAAT
*
365571 TATATTT-TAATTATTTTATATATTATATAAT
1 TATATTTATAATTATATTATATATTATATAAT
*
365602 TATATTTAAAATTAT
1 TATATTTATAATTAT
365617 TAAATTTATG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.03
30 24 0.60
31 9 0.22
32 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (32 bp):
TATATTTATAATTATATTATATATTATATAAT
Found at i:365605 original size:8 final size:7
Alignment explanation
Indices: 365540--365606 Score: 60
Period size: 7 Copynumber: 10.6 Consensus size: 7
365530 ATATTTAAAA
365540 ATATATT
1 ATATATT
365547 -TATA-T
1 ATATATT
365552 -TATATT
1 ATATATT
*
365558 ATATTTT
1 ATATATT
365565 ATATATT
1 ATATATT
365572 ATAT-TT
1 ATATATT
365578 -TA-ATT
1 ATATATT
365583 AT-T-TT
1 ATATATT
365588 ATATATT
1 ATATATT
365595 ATATAATT
1 ATAT-ATT
365603 ATAT
1 ATAT
365607 TTAAAATTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
5 13 0.26
6 9 0.18
7 21 0.42
8 7 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
ATATATT
Found at i:365615 original size:20 final size:20
Alignment explanation
Indices: 365550--365616 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 20
365540 ATATATTTAT
* *
365550 ATTATATTA-TATTTTATAT
1 ATTATATAATTATTTTATAA
*
365569 ATTATATTTTAATTATTTTATAT
1 ATTATA---TAATTATTTTATAA
365592 ATTATATAATTATATTTA-AA
1 ATTATATAATTAT-TTTATAA
365612 ATTAT
1 ATTAT
365617 TAAATTTATG
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
19 6 0.15
20 13 0.32
21 4 0.10
22 2 0.05
23 16 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATATAATTATTTTATAA
Found at i:372812 original size:20 final size:20
Alignment explanation
Indices: 372761--372814 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
372751 AATTATTTAA
372761 TTAAATATTAAATAAAT-AATT
1 TTAAATA-T-AATAAATAAATT
*
372782 TT--AT-TATTAAATAAATT
1 TTAAATATAATAAATAAATT
372799 TTAAATATAATAAATA
1 TTAAATATAATAAATA
372815 TTTAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
16 6 0.22
17 7 0.26
19 4 0.15
20 8 0.30
21 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAATATAATAAATAAATT
Found at i:372827 original size:17 final size:17
Alignment explanation
Indices: 372762--372834 Score: 50
Period size: 17 Copynumber: 4.5 Consensus size: 17
372752 ATTATTTAAT
372762 TAAATA-TTAAAT-AAA
1 TAAATATTTAAATAAAA
* *
372777 T-AAT-TTTATTATTAAA
1 TAAATATTTA-AATAAAA
*
372793 TAAAT-TTTAAATATAA
1 TAAATATTTAAATAAAA
372809 TAAATATTT-AATAAAAA
1 TAAATATTTAAAT-AAAA
*
372826 TATATATTT
1 TAAATATTT
372835 GATTAAATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 6 0.13
15 3 0.07
16 16 0.35
17 21 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATATTTAAATAAAA
Found at i:374259 original size:21 final size:20
Alignment explanation
Indices: 374235--374275 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
374225 AATTGAGTAC
374235 GATAAATAATTATCTCCTAAA
1 GATAAATAATTATCT-CTAAA
374256 GATAAATAATTATCTCTAAA
1 GATAAATAATTATCTCTAAA
374276 ACTTTTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (20 bp):
GATAAATAATTATCTCTAAA
Found at i:375291 original size:21 final size:21
Alignment explanation
Indices: 375265--375304 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
375255 TATTAAAAAT
375265 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
375286 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
375305 AATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:375528 original size:29 final size:30
Alignment explanation
Indices: 375491--375565 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
375481 TTTTAATTTT
*
375491 TTAATTAAATTTTTATATTTTT-ATTATAC
1 TTAAATAAATTTTTATATTTTTAATTATAC
*
375520 TTAAATAAATTTTTA-ATTTTTAAATTATAT
1 TTAAATAAATTTTTATATTTTT-AATTATAC
*
375550 TTAAATAAGTTTTTAT
1 TTAAATAAATTTTTAT
375566 TTAAAATAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.15
29 14 0.35
30 20 0.50
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (30 bp):
TTAAATAAATTTTTATATTTTTAATTATAC
Found at i:375999 original size:2 final size:2
Alignment explanation
Indices: 375992--376037 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
375982 TTAGTAATAA
375992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
376034 AT AT
1 AT AT
376038 TGCAAATGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:376795 original size:25 final size:24
Alignment explanation
Indices: 376762--376815 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
376752 TTATCTGAGG
*
376762 TTTAATTTTATTAAATTATATTAT-
1 TTTAATTTTATTAAAGTAT-TTATA
*
376786 TTTAATTTTTTTTAAAGTATTTATA
1 TTTAA-TTTTATTAAAGTATTTATA
376811 TTTAA
1 TTTAA
376816 CTCTCATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTAATTTTATTAAAGTATTTATA
Found at i:377108 original size:7 final size:8
Alignment explanation
Indices: 377086--377118 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
377076 TAAAATTATT
377086 ATTAAAAA
1 ATTAAAAA
377094 ATTAAAAA
1 ATTAAAAA
377102 ATTAAAAA
1 ATTAAAAA
377110 ATTAAAAA
1 ATTAAAAA
377118 A
1 A
377119 AATTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATTAAAAA
Found at i:377188 original size:25 final size:27
Alignment explanation
Indices: 377160--377223 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 27
377150 ATAGTTAAAT
*
377160 TTAAATAAAAATATT-ATTTTA-TTAA
1 TTAAATAAAAATATTAAATTTATTTAA
*
377185 TTAAATAATAAT-TTAAATTTATTTAA
1 TTAAATAAAAATATTAAATTTATTTAA
*
377211 TTAAA-AAATATAT
1 TTAAATAAAAATAT
377224 CACTATTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
24 2 0.06
25 20 0.62
26 10 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAATAAAAATATTAAATTTATTTAA
Found at i:377720 original size:16 final size:15
Alignment explanation
Indices: 377695--377728 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
377685 TTTAAATTAT
377695 TTTTATTTTGAATGA
1 TTTTATTTTGAATGA
*
377710 TTTTATGTTTGAATTA
1 TTTTAT-TTTGAATGA
377726 TTT
1 TTT
377729 CGATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (15 bp):
TTTTATTTTGAATGA
Found at i:377895 original size:6 final size:6
Alignment explanation
Indices: 377880--377908 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
377870 TACTCAAATT
377880 AATT-A AATTAA AATTAA AATTAA AATTAA
1 AATTAA AATTAA AATTAA AATTAA AATTAA
377909 TAGGTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATTAA
Found at i:379148 original size:23 final size:23
Alignment explanation
Indices: 379120--379174 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
379110 TTATCCATAA
379120 AAATTTAAATTATTTTTA-AATT
1 AAATTTAAATTATTTTTATAATT
*
379142 AATATTTATA-TATTTTTATAATT
1 AA-ATTTAAATTATTTTTATAATT
379165 AAATTTAAAT
1 AAATTTAAAT
379175 AAAAATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AAATTTAAATTATTTTTATAATT
Found at i:381051 original size:15 final size:15
Alignment explanation
Indices: 381033--381142 Score: 54
Period size: 15 Copynumber: 7.4 Consensus size: 15
381023 AATTTTTAAA
381033 ATATAATATAAATAT
1 ATATAATATAAATAT
** * *
381048 ATATTTTAAAAATTT
1 ATATAATATAAATAT
*
381063 ATATGATATAAAT-T
1 ATATAATATAAATAT
381077 AT-TAATAAATAAATATTT
1 ATATAAT--ATAAATA--T
381095 ATATAAATATATAAT-T
1 ATAT-AATATA-AATAT
* *
381111 TTATAATATAATTAT
1 ATATAATATAAATAT
381126 A-ATAA-A-AAATA-
1 ATATAATATAAATAT
381137 ATATAA
1 ATATAA
381143 ATTATTAAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
11 1 0.01
12 8 0.11
13 4 0.05
14 9 0.12
15 34 0.47
16 4 0.05
18 6 0.08
19 4 0.05
20 3 0.04
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (15 bp):
ATATAATATAAATAT
Found at i:381141 original size:42 final size:47
Alignment explanation
Indices: 381058--381144 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 47
381048 ATATTTTAAA
*
381058 AATTTATATGATATAAATTATTAATAAATAAATATTTATATAAATATAT
1 AATTTATATAATATAAATTATTAATAAATAAATA--TATATAAATATAT
381107 AATTT-TATAATAT-AATTA-TAATAAA-AAATA-ATATAAAT
1 AATTTATATAATATAAATTATTAATAAATAAATATATATAAAT
381145 TATTAAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
42 8 0.22
45 5 0.14
46 7 0.19
47 5 0.14
48 7 0.19
49 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (47 bp):
AATTTATATAATATAAATTATTAATAAATAAATATATATAAATATAT
Found at i:381267 original size:8 final size:8
Alignment explanation
Indices: 381254--381417 Score: 66
Period size: 8 Copynumber: 19.0 Consensus size: 8
381244 AAGTTAGATA
381254 ATTTATAT
1 ATTTATAT
381262 ATTTATATT
1 ATTTATA-T
*
381271 ATTTTATTAA
1 A-TTTA-TAT
381281 ATTTATTAT
1 ATTTA-TAT
*
381290 ATCGTAATTAT
1 AT--TTA-TAT
*
381301 ATTTAAAAT
1 ATTT-ATAT
381310 ATTT-TAT
1 ATTTATAT
*
381317 GTTTATAT
1 ATTTATAT
381325 AAATTTTAATAT
1 --A-TTT-ATAT
*
381337 ATTAATA-
1 ATTTATAT
*
381344 ATTTAAAT
1 ATTTATAT
* *
381352 ATATAAAT
1 ATTTATAT
*
381360 -TTTAAAAT
1 ATTT-ATAT
381368 ATTTATAT
1 ATTTATAT
381376 ATTTATATT
1 ATTTATA-T
*
381385 ATTTTTAT
1 ATTTATAT
381393 ATTATATTAT
1 ATT-TA-TAT
381403 ATTT-TAT
1 ATTTATAT
381410 ATTTATAT
1 ATTTATAT
381418 TTATATTTAT
Statistics
Matches: 122, Mismatches: 16, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
7 19 0.16
8 41 0.34
9 32 0.26
10 13 0.11
11 13 0.11
12 4 0.03
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (8 bp):
ATTTATAT
Found at i:381358 original size:31 final size:32
Alignment explanation
Indices: 381320--381380 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
381310 ATTTTATGTT
*
381320 TATATAAATTTTAATATATTAATA-ATTTAAA
1 TATATAAATTTTAAAATATTAATATATTTAAA
*
381351 TATATAAATTTTAAAATATTTATATATTTA
1 TATATAAATTTTAAAATATTAATATATTTA
381381 TATTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATAAATTTTAAAATATTAATATATTTAAA
Found at i:381382 original size:6 final size:6
Alignment explanation
Indices: 381373--381431 Score: 79
Period size: 6 Copynumber: 10.2 Consensus size: 6
381363 AAAATATTTA
*
381373 TATATT TATA-T TATTTT TATA-T TATA-T TATATTT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATA-TT TATATT TATATT
381419 TATATT TATATT T
1 TATATT TATATT T
381432 CATGGGTGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
5 14 0.29
6 29 0.60
7 5 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:381407 original size:18 final size:18
Alignment explanation
Indices: 381366--381430 Score: 66
Period size: 17 Copynumber: 3.7 Consensus size: 18
381356 AAATTTTAAA
*
381366 ATATTTATATATT-TA-T
1 ATATTTTTATATTATATT
381382 ATTATTTTTATATTATATT
1 A-TATTTTTATATTATATT
381401 ATA-TTTTATATTTATATT
1 ATATTTTTATA-TTATATT
*
381419 -TATATTTATATT
1 ATATTTTTATATT
381431 TCATGGGTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
16 1 0.02
17 22 0.52
18 17 0.40
19 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATTTTTATATTATATT
Found at i:384537 original size:20 final size:21
Alignment explanation
Indices: 384499--384538 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
384489 ACATGAGGAA
* *
384499 CTTATTTTACTCTATTCTTCT
1 CTTATTTTACTCAACTCTTCT
384520 CTTA-TTTACTCAACTCTTC
1 CTTATTTTACTCAACTCTTC
384539 ATTTATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (21 bp):
CTTATTTTACTCAACTCTTCT
Found at i:386836 original size:54 final size:55
Alignment explanation
Indices: 386757--387008 Score: 248
Period size: 54 Copynumber: 4.7 Consensus size: 55
386747 ACCCCCACTT
* * * * *
386757 CTGATGGGATCATTACT-GAAGATCAAATTTCTAGAAGA-GAATTAACCTTCACCC
1 CTGATAGGATGATTACTGGAA-ATCAAAATTCTAGAAAAGGAATCAACCTTCACCC
* ** *
386811 CTGATAGGATGATTGCTGGAAATCAAAATTCTA-AAAAGGAATCAAGTTTTACCC
1 CTGATAGGATGATTACTGGAAATCAAAATTCTAGAAAAGGAATCAACCTTCACCC
* * * **
386865 CTGACAGGATGATTGCTGGAAATCAAAATTCTA-AAAAGGAATCAAGCTTCACAG
1 CTGATAGGATGATTACTGGAAATCAAAATTCTAGAAAAGGAATCAACCTTCACCC
* * *
386919 CTGATAGGATGATTACTGGGAATCAAAACTCTCG-AAAGGAATCAACCCTT-ACCC
1 CTGATAGGATGATTACTGGAAATCAAAATTCTAGAAAAGGAATCAA-CCTTCACCC
* * *
386973 CTAATAGGATCG-TTACTGTAAATCAAATTTCTAGAA
1 CTGATAGGAT-GATTACTGGAAATCAAAATTCTAGAA
387009 GGGAATTAAG
Statistics
Matches: 164, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
53 3 0.02
54 153 0.93
55 8 0.05
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (55 bp):
CTGATAGGATGATTACTGGAAATCAAAATTCTAGAAAAGGAATCAACCTTCACCC
Found at i:387120 original size:54 final size:54
Alignment explanation
Indices: 387041--387144 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
387031 TTGCAATACT
* * * * *
387041 GGAAATCTAATTTCTAGAAGGGAATCAACCTCTACTTCTGATGGGATCATGATG
1 GGAAATCAAATTACTAGAAGCGAATCAACCTCCACTTCTGATGGAATCATGATG
* *
387095 GGAAATCAAATTACTAGAAGCGAATCAACTTCCATTTCTGATGGAATCAT
1 GGAAATCAAATTACTAGAAGCGAATCAACCTCCACTTCTGATGGAATCAT
387145 TTCTAGAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (54 bp):
GGAAATCAAATTACTAGAAGCGAATCAACCTCCACTTCTGATGGAATCATGATG
Found at i:387154 original size:54 final size:54
Alignment explanation
Indices: 387042--387168 Score: 139
Period size: 54 Copynumber: 2.4 Consensus size: 54
387032 TGCAATACTG
* * * * *
387042 GAAATCTAATTTCTAGAAGGGAATCAACCTCTACTTCTGATGGGATCATGATGG
1 GAAATCAAATTTCTAGAAGCGAATCAACCTCCACTTCTGATGGAATCATGATGA
* * * * *
387096 GAAATCAAATTACTAGAAGCGAATCAACTTCCATTTCTGATGGAATCAT-TTCTA
1 GAAATCAAATTTCTAGAAGCGAATCAACCTCCACTTCTGATGGAATCATGAT-GA
*
387150 GAAATCAAGTTTCTAGAAG
1 GAAATCAAATTTCTAGAAG
387169 GGAAGCTACC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 1 0.02
54 59 0.98
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (54 bp):
GAAATCAAATTTCTAGAAGCGAATCAACCTCCACTTCTGATGGAATCATGATGA
Found at i:390871 original size:14 final size:14
Alignment explanation
Indices: 390852--390890 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
390842 CCATATGCTC
* *
390852 AAGAAAAATATAAA
1 AAGAAAAAGAAAAA
390866 AAGAAAAAGAAAAA
1 AAGAAAAAGAAAAA
*
390880 AAGAAGAAGAA
1 AAGAAAAAGAA
390891 GAGTAAAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (14 bp):
AAGAAAAAGAAAAA
Found at i:390889 original size:20 final size:20
Alignment explanation
Indices: 390852--390890 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
390842 CCATATGCTC
* *
390852 AAGAAAAATATAAAAAGAAA
1 AAGAAAAAAAGAAAAAGAAA
*
390872 AAGAAAAAAAGAAGAAGAA
1 AAGAAAAAAAGAAAAAGAA
390891 GAGTAAAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
AAGAAAAAAAGAAAAAGAAA
Found at i:393257 original size:11 final size:11
Alignment explanation
Indices: 393241--393310 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
393231 TATTTTTGTG
393241 TATTTATATTA
1 TATTTATATTA
*
393252 TATTTATGTTA
1 TATTTATATTA
* *
393263 TTTTTTAAATTA
1 -TATTTATATTA
*
393275 TATTTTAAATT-
1 TA-TTTATATTA
*
393286 T-TTTATTTTA
1 TATTTATATTA
*
393296 TTTTTATATTA
1 TATTTATATTA
393307 TATT
1 TATT
393311 CAAAATTACT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 6 0.13
10 1 0.02
11 23 0.50
12 16 0.35
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (11 bp):
TATTTATATTA
Found at i:393296 original size:21 final size:20
Alignment explanation
Indices: 393262--393301 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
393252 TATTTATGTT
393262 ATTTTTTAAATTATATTTTAA
1 ATTTTTTAAATTAT-TTTTAA
**
393283 ATTTTTTATTTTATTTTTA
1 ATTTTTTAAATTATTTTTA
393302 TATTATATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTTTAAATTATTTTTAA
Found at i:393317 original size:32 final size:33
Alignment explanation
Indices: 393254--393317 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
393244 TTATATTATA
**
393254 TTTATGTTATTTTTTAAATTATATTTTAAATTT
1 TTTATGTTATTTTTTAAATTATATTCAAAATTT
* *
393287 TTTATTTTA-TTTTTATATTATATTCAAAATT
1 TTTATGTTATTTTTTAAATTATATTCAAAATT
393318 ACTAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (33 bp):
TTTATGTTATTTTTTAAATTATATTCAAAATTT
Found at i:394617 original size:9 final size:9
Alignment explanation
Indices: 394598--394627 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
394588 AAATTTTATT
394598 TTTTATATAA
1 TTTT-TATAA
394608 TTTTTATAA
1 TTTTTATAA
394617 TTTTTATAA
1 TTTTTATAA
394626 TT
1 TT
394628 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:394630 original size:22 final size:22
Alignment explanation
Indices: 394597--394652 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
394587 AAAATTTTAT
*
394597 TTTTTAT-A-TAATTTTTATAA
1 TTTTTATAATTAATTTTTAAAA
394617 TTTTTATAATTAA-TTTTAAAA
1 TTTTTATAATTAATTTTTAAAA
*
394638 TATTTTTTAATTAAT
1 T-TTTTATAATTAAT
394653 AAATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 7 0.23
21 9 0.30
22 14 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTATAATTAATTTTTAAAA
Found at i:394664 original size:22 final size:23
Alignment explanation
Indices: 394613--394664 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
394603 TATAATTTTT
*
394613 ATAATTTTTATAATTAATTTTAAA
1 ATAATTTTTATAATTAA-TTAAAA
394637 AT-ATTTTT-TAATTAA-TAAATA
1 ATAATTTTTATAATTAATTAAA-A
394658 ATAATTT
1 ATAATTT
394665 AAATTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 3 0.12
21 3 0.12
22 11 0.44
23 6 0.24
24 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATAATTTTTATAATTAATTAAAA
Found at i:394882 original size:19 final size:19
Alignment explanation
Indices: 394858--394901 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
394848 TTTTAAATTT
394858 TTTATTTAAATAGATTTA-A
1 TTTATTTAAAT-GATTTATA
*
394877 TTTATTTAAATTATTTATA
1 TTTATTTAAATGATTTATA
394896 TTTATT
1 TTTATT
394902 AATTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTATTTAAATGATTTATA
Found at i:395279 original size:22 final size:24
Alignment explanation
Indices: 395267--395316 Score: 70
Period size: 21 Copynumber: 2.2 Consensus size: 24
395257 AGAAAAAATT
395267 AATAAAATATAAAAAAATAATTTG
1 AATAAAATATAAAAAAATAATTTG
*
395291 AAT-AAA-AT-AAAAAATAATTTA
1 AATAAAATATAAAAAAATAATTTG
395312 AATAA
1 AATAA
395317 TTAATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 15 0.62
22 3 0.12
23 3 0.12
24 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (24 bp):
AATAAAATATAAAAAAATAATTTG
Found at i:395395 original size:3 final size:3
Alignment explanation
Indices: 395387--395420 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
395377 TATCTATAAT
395387 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
395421 GAAATTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:395544 original size:18 final size:18
Alignment explanation
Indices: 395521--395558 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
395511 TTATTCATAC
395521 ATATATACATATATATGT
1 ATATATACATATATATGT
* *
395539 ATATATAGATATGTATGT
1 ATATATACATATATATGT
395557 AT
1 AT
395559 GTATGTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (18 bp):
ATATATACATATATATGT
Found at i:395563 original size:12 final size:14
Alignment explanation
Indices: 395533--395570 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
395523 ATATACATAT
*
395533 ATATGTATATATAG
1 ATATGTATGTATAG
395547 ATATGTATGTAT-G
1 ATATGTATGTATAG
395560 -TATGTATGTAT
1 ATATGTATGTAT
395571 TCAATGCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 1 0.04
14 11 0.48
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (14 bp):
ATATGTATGTATAG
Found at i:396159 original size:2 final size:2
Alignment explanation
Indices: 396154--396183 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
396144 GAACTCATAA
396154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
396184 TCACTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:396334 original size:20 final size:21
Alignment explanation
Indices: 396305--396344 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
396295 ATAAAATATA
396305 ATATTATAAATTTT-TATTAG
1 ATATTATAAATTTTATATTAG
*
396325 ATATTTTAAATTTTATATTA
1 ATATTATAAATTTTATATTA
396345 TTAAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
ATATTATAAATTTTATATTAG
Found at i:396362 original size:17 final size:15
Alignment explanation
Indices: 396325--396353 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
396315 TTTTTATTAG
396325 ATATT-TTAAATTTT
1 ATATTATTAAATTTT
396339 ATATTATTAAATTTT
1 ATATTATTAAATTTT
396354 TTTACTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTATTAAATTTT
Found at i:396369 original size:34 final size:34
Alignment explanation
Indices: 396305--396369 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
396295 ATAAAATATA
* **
396305 ATATTATAAATTTTTATTAGATATTTTAAATTTT
1 ATATTATAAATTTTTATTACATATCATAAATTTT
*
396339 ATATTATTAAATTTTT-TTACTTATCATAAAT
1 ATATTA-TAAATTTTTATTACATATCATAAAT
396370 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
34 17 0.65
35 9 0.35
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (34 bp):
ATATTATAAATTTTTATTACATATCATAAATTTT
Found at i:396459 original size:22 final size:21
Alignment explanation
Indices: 396420--396463 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
396410 AATTATATTT
396420 ATTTAAATCATAAAAATTAAA
1 ATTTAAATCATAAAAATTAAA
396441 ATTTAAAAT-ATAAACAATTAAA
1 ATTT-AAATCATAAA-AATTAAA
396463 A
1 A
396464 CCTAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTTAAATCATAAAAATTAAA
Found at i:396523 original size:25 final size:23
Alignment explanation
Indices: 396466--396565 Score: 84
Period size: 25 Copynumber: 4.3 Consensus size: 23
396456 AATTAAAACC
*
396466 TAATTATTTAATTTTAAATTCAAT
1 TAATTAATT-ATTTTAAATTCAAT
*
396490 TAATATAATTATTTTATAATTTAATT
1 TAAT-TAATTATTTTA-AATTCAA-T
**
396516 TAATTAATTATTAAAAAATT-AAT
1 TAATTAATTATT-TTAAATTCAAT
396539 TAA-TAA-TATTTT-AATT-AAT
1 TAATTAATTATTTTAAATTCAAT
396558 TAATTAAT
1 TAATTAAT
396566 CGAAGGAATG
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
19 10 0.16
20 3 0.05
21 4 0.06
22 3 0.05
23 4 0.06
24 12 0.19
25 22 0.34
26 6 0.09
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTAATTATTTTAAATTCAAT
Found at i:396523 original size:30 final size:29
Alignment explanation
Indices: 396466--396523 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
396456 AATTAAAACC
*
396466 TAATTATTTAATTTTAAATTCAATTAATA
1 TAATTATTTAAATTTAAATTCAATTAATA
*
396495 TAATTATTTTATAATTT-AATTTAATTAAT
1 TAATTA-TTTA-AATTTAAATTCAATTAAT
396524 TATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 15 0.60
31 4 0.16
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
TAATTATTTAAATTTAAATTCAATTAATA
Found at i:396524 original size:4 final size:4
Alignment explanation
Indices: 396482--396565 Score: 50
Period size: 4 Copynumber: 20.8 Consensus size: 4
396472 TTTAATTTTA
* *
396482 AATT CAATT AATAT AATT ATTT TA-T AATTT AATTT AATT AATT -ATT
1 AATT -AATT AAT-T AATT AATT AATT AA-TT AA-TT AATT AATT AATT
** *
396528 AAAA AATT AATT AA-T AA-T ATTTT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT A-ATT AATT AATT AATT AAT
396566 CGAAGGAATG
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
3 10 0.16
4 35 0.56
5 18 0.29
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:396912 original size:21 final size:20
Alignment explanation
Indices: 396886--396941 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
396876 AAATCATTTA
396886 ATTTAATTTAAATTATTCTTT
1 ATTTAATTTAAATTATT-TTT
**
396907 ATTTAATAAAAATTATTTTT
1 ATTTAATTTAAATTATTTTT
396927 ATTTAATTT-AATTAT
1 ATTTAATTTAAATTAT
396942 AAATATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.19
20 10 0.32
21 15 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTAATTTAAATTATTTTT
Found at i:397010 original size:18 final size:19
Alignment explanation
Indices: 396979--397016 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
396969 TTTAATATTA
396979 TTTTAAATGATAATATAAAT
1 TTTTAAAT-ATAATATAAAT
*
396999 TTTTAAAT-TAATTTAAAT
1 TTTTAAATATAATATAAAT
397017 ATGATTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTTAAATATAATATAAAT
Found at i:397153 original size:13 final size:13
Alignment explanation
Indices: 397135--397263 Score: 55
Period size: 13 Copynumber: 10.3 Consensus size: 13
397125 GTAATTTTAA
397135 ATATAATATAATT
1 ATATAATATAATT
397148 ATATAATATAA--
1 ATATAATATAATT
* *
397159 AAATAAT-TAA-A
1 ATATAATATAATT
*
397170 ATATTATATAA-T
1 ATATAATATAATT
*
397182 AAATTAAT-TAATT
1 ATA-TAATATAATT
*
397195 AAATAA-AT--TT
1 ATATAATATAATT
397205 ATATAATATAAATT
1 ATATAATAT-AATT
*
397219 ATAAATATATAAAATT
1 AT--ATA-ATATAATT
397235 -TAT-ATATAATAT
1 ATATAATATAAT-T
* *
397247 TTTTAATATAATT
1 ATATAATATAATT
397260 ATAT
1 ATAT
397264 TACATATAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 30
0.68 0.09 0.23
Matches are distributed among these distances:
10 10 0.11
11 19 0.21
12 13 0.15
13 25 0.28
14 11 0.12
15 1 0.01
16 7 0.08
17 3 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATAATATAATT
Found at i:397180 original size:27 final size:28
Alignment explanation
Indices: 397139--397216 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 28
397129 TTTTAAATAT
397139 AATATAATTATATAATATAAAAATAATTA
1 AATA-AATTATATAATATAAAAATAATTA
* *
397168 AA-ATATTATATAATA-AATTAATTAATTA
1 AATAAATTATATAATATAA--AAATAATTA
397196 AATAAATTTATATAATATAAA
1 AATAAA-TTATATAATATAAA
397217 TTATAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
26 2 0.05
27 11 0.27
28 11 0.27
29 5 0.12
30 10 0.24
31 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AATAAATTATATAATATAAAAATAATTA
Found at i:397222 original size:22 final size:22
Alignment explanation
Indices: 397197--397262 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
397187 AATTAATTAA
397197 ATAAATTTATATAATATAAATT
1 ATAAATTTATATAATATAAATT
* * * *
397219 ATAAATATATAAAATTTATA-T
1 ATAAATTTATATAATATAAATT
397240 ATAATATTT-T-TAATAT-AATT
1 ATAA-ATTTATATAATATAAATT
397260 ATA
1 ATA
397263 TTACATATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 1 0.03
20 8 0.24
21 6 0.18
22 19 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAATTTATATAATATAAATT
Found at i:397231 original size:30 final size:30
Alignment explanation
Indices: 397127--397240 Score: 89
Period size: 31 Copynumber: 3.8 Consensus size: 30
397117 AAAATGTTGT
*
397127 AATTTTAAATATAATATAA-TTATATAATATA
1 AATTATAAATAT-ATA-AATTTATATAATATA
*
397158 AA-AAT-AAT-TA-AAATATTATAT-A-ATA
1 AATTATAAATATATAAAT-TTATATAATATA
* *
397183 AATTAATTAATTAAATAAATTTATATAATATA
1 AATT-A-TAAATATATAAATTTATATAATATA
397215 AATTATAAATATATAAAATTTATATA
1 AATTATAAATATAT-AAATTTATATA
397241 TAATATTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
25 7 0.11
26 2 0.03
27 8 0.12
28 2 0.03
29 5 0.08
30 15 0.23
31 19 0.29
32 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
AATTATAAATATATAAATTTATATAATATA
Found at i:397241 original size:15 final size:16
Alignment explanation
Indices: 397197--397242 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
397187 AATTAATTAA
397197 ATAAATTTATATA-AT
1 ATAAATTTATATATAT
*
397212 ATAAA-TTATAAATAT
1 ATAAATTTATATATAT
397227 ATAAAATTTATATATA
1 AT-AAATTTATATATA
397243 ATATTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 6 0.23
15 9 0.35
16 3 0.12
17 8 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAATTTATATATAT
Found at i:397653 original size:15 final size:15
Alignment explanation
Indices: 397633--397661 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
397623 ATTTAAATAA
397633 TAATTTAAATTAAAT
1 TAATTTAAATTAAAT
397648 TAATTTAAATTAAA
1 TAATTTAAATTAAA
397662 ATATTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATTTAAATTAAAT
Found at i:398959 original size:15 final size:16
Alignment explanation
Indices: 398929--398963 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
398919 ATTTACAAAA
398929 TTTAAAACCAAAATTT
1 TTTAAAACCAAAATTT
*
398945 TTTAAAATC-AAATTT
1 TTTAAAACCAAAATTT
398960 TTTA
1 TTTA
398964 TCACTCGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTAAAACCAAAATTT
Found at i:400104 original size:34 final size:35
Alignment explanation
Indices: 400021--400112 Score: 91
Period size: 34 Copynumber: 2.6 Consensus size: 35
400011 TTCAATTTTA
**
400021 AATTAATATATATAACGAAAATAAAATTTAAATATTT
1 AATTAATATAT-TAAC-AAAATAAAATTTAAATAAAT
* *
400058 AATT-ATAAATTAA-AAATATATAATTTAAA-AAAT
1 AATTAATATATTAACAAA-ATAAAATTTAAATAAAT
*
400091 AATTAATATATTAACTAAATAA
1 AATTAATATATTAACAAAATAA
400113 TAATAATAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
33 9 0.20
34 22 0.49
35 5 0.11
36 5 0.11
37 4 0.09
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (35 bp):
AATTAATATATTAACAAAATAAAATTTAAATAAAT
Found at i:400125 original size:37 final size:37
Alignment explanation
Indices: 400050--400125 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 37
400040 AATAAAATTT
* * *
400050 AAATATTTAATTATAAATTAAAAATATATAATTTAAA
1 AAATAATTAATTATAAACTAAAAATATATAATTAAAA
*
400087 AAATAATTAATATATTAACTAAATAATA-ATAA-TAAAA
1 AAATAATTAAT-TATAAACTAAA-AATATATAATTAAAA
400124 AA
1 AA
400126 GCAGCCTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
37 16 0.48
38 13 0.39
39 4 0.12
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (37 bp):
AAATAATTAATTATAAACTAAAAATATATAATTAAAA
Found at i:400977 original size:7 final size:8
Alignment explanation
Indices: 400961--400985 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
400951 TTTAAAAAAT
400961 AAATTAAA
1 AAATTAAA
400969 AAATTAAA
1 AAATTAAA
400977 AAATTAAA
1 AAATTAAA
400985 A
1 A
400986 TCCATGTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATTAAA
Found at i:404596 original size:272 final size:272
Alignment explanation
Indices: 404110--404659 Score: 1046
Period size: 272 Copynumber: 2.0 Consensus size: 272
404100 TGGAGTCGTG
404110 CCTCTTGGGACTTACTGTGAAAAATTAAGGCCTTAATCAATAGTTCTATGGTTCTTAAATTTGTA
1 CCTCTTGGGACTTACTGTGAAAAATTAAGGCCTTAATCAATAGTTCTATGGTTCTTAAATTTGTA
*
404175 TGATAATACTGTGAATTTGTATTGCTGAATCAGTAGAAAGCTTATGTTTTTGATGAATGTTATCA
66 TGATAATACTGTGAATTTGTATTGCTGAATCAGTAGAAAGCCTATGTTTTTGATGAATGTTATCA
404240 ATCGATTTATTGTATCCATAATCTTTCCACTCTAATTTCCTGATTGAATTGCCAAACTGATGGTT
131 ATCGATTTATTGTATCCATAATCTTTCCACTCTAATTTCCTGATTGAATTGCCAAACTGATGGTT
* *
404305 GTCCTTGTTGCTTCTTCAATATGATGTTTCTTAGGCTTACATTTTTCTGTTAATTGGATAAGCTT
196 GTCCTTGTTGCTTCTTCAATATGATGTTTCTTAAGCTCACATTTTTCTGTTAATTGGATAAGCTT
404370 AGTGATTTCTTC
261 AGTGATTTCTTC
*
404382 CCTCTTGGGACTTACTGTGAAAAATTAAGGCCTTAATCAATGGTTCTATGGTTCTTAAATTTGTA
1 CCTCTTGGGACTTACTGTGAAAAATTAAGGCCTTAATCAATAGTTCTATGGTTCTTAAATTTGTA
*
404447 TGATGATACTGTGAATTTGTATTGCTGAATCAGTAGAAAGCCTATGTTTTTGATGAATGTTATCA
66 TGATAATACTGTGAATTTGTATTGCTGAATCAGTAGAAAGCCTATGTTTTTGATGAATGTTATCA
404512 ATCGATTTATTGTATCCATAATCTTTCCACTCTAATTTCCTGATTGAATTGCCAAACTGATGGTT
131 ATCGATTTATTGTATCCATAATCTTTCCACTCTAATTTCCTGATTGAATTGCCAAACTGATGGTT
*
404577 GTTCTTGTTGCTTCTTCAATATGATGTTTCTTAAGCTCACATTTTTCTGTTAATTGGATAAGCTT
196 GTCCTTGTTGCTTCTTCAATATGATGTTTCTTAAGCTCACATTTTTCTGTTAATTGGATAAGCTT
404642 AGTGATTTCTTC
261 AGTGATTTCTTC
404654 CCTCTT
1 CCTCTT
404660 TCAGGTGGTT
Statistics
Matches: 272, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
272 272 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (272 bp):
CCTCTTGGGACTTACTGTGAAAAATTAAGGCCTTAATCAATAGTTCTATGGTTCTTAAATTTGTA
TGATAATACTGTGAATTTGTATTGCTGAATCAGTAGAAAGCCTATGTTTTTGATGAATGTTATCA
ATCGATTTATTGTATCCATAATCTTTCCACTCTAATTTCCTGATTGAATTGCCAAACTGATGGTT
GTCCTTGTTGCTTCTTCAATATGATGTTTCTTAAGCTCACATTTTTCTGTTAATTGGATAAGCTT
AGTGATTTCTTC
Found at i:408538 original size:19 final size:20
Alignment explanation
Indices: 408514--408560 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
408504 ATAAAATAAA
408514 ATAAAAAT-TTAAT-TTAAT
1 ATAAAAATATTAATATTAAT
408532 -TATAAAATATTAATATTAAT
1 ATA-AAAATATTAATATTAAT
408552 ATAAAAATA
1 ATAAAAATA
408561 ATTTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 5 0.20
19 5 0.20
20 11 0.44
21 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAAATATTAATATTAAT
Found at i:408602 original size:6 final size:6
Alignment explanation
Indices: 408581--408645 Score: 69
Period size: 6 Copynumber: 10.7 Consensus size: 6
408571 ATTTTAATAT
* * * *
408581 ATTTAA ATAATAA ATTTAA ATTATAA A-ATCA AGTTAA ATTTAA ATTTAA
1 ATTTAA AT-TTAA ATTTAA ATT-TAA ATTTAA ATTTAA ATTTAA ATTTAA
408630 ATTTAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTT
408646 TAAAATTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 3 0.06
6 37 0.76
7 9 0.18
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:408951 original size:18 final size:17
Alignment explanation
Indices: 408906--408953 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
408896 TAAAATCATA
408906 TATTTATATTT-T-TTT
1 TATTTATATTTATATTT
408921 TATTTAGTA-TTATATTT
1 TATTTA-TATTTATATTT
408938 TATGTTATATTTATAT
1 TAT-TTATATTTATAT
408954 CATATAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 3 0.11
17 8 0.29
18 9 0.32
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (17 bp):
TATTTATATTTATATTT
Found at i:411809 original size:27 final size:27
Alignment explanation
Indices: 411772--411841 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
411762 ATATGCCATT
* *
411772 ATTTTTGACAAATAAAAAGAAACCACC
1 ATTTTTTACAAACAAAAAGAAACCACC
* * * *
411799 ATTTTTTACAAACACAAAGTAACTACT
1 ATTTTTTACAAACAAAAAGAAACCACC
411826 ATTTTTTACAAACAAA
1 ATTTTTTACAAACAAA
411842 TTGTGGTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (27 bp):
ATTTTTTACAAACAAAAAGAAACCACC
Found at i:413755 original size:21 final size:22
Alignment explanation
Indices: 413717--413762 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
413707 ATCTGTTGAA
* **
413717 ACTCCACTTGTTTTGGAGTA-T
1 ACTCCACCTGTTACGGAGTACT
413738 ACTCCACCTGTTACGGAGTACT
1 ACTCCACCTGTTACGGAGTACT
413760 ACT
1 ACT
413763 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (22 bp):
ACTCCACCTGTTACGGAGTACT
Found at i:416323 original size:27 final size:26
Alignment explanation
Indices: 416294--416379 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 26
416284 ATTTTGTAAT
* * *
416294 AAAAATTAACCACAAATTTTGACAAAT
1 AAAAA-TAACCACTATTTTTGACAAAC
*
416321 AAAAAGAAACCACTATTTTTGACAAAC
1 AAAAA-TAACCACTATTTTTGACAAAC
416348 ACAAAATAACCACTATTTTTGACAAAC
1 A-AAAATAACCACTATTTTTGACAAAC
416375 AAAAA
1 AAAAA
416380 GTAATTTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 4 0.08
27 44 0.85
28 4 0.08
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.23
Consensus pattern (26 bp):
AAAAATAACCACTATTTTTGACAAAC
Found at i:417800 original size:6 final size:6
Alignment explanation
Indices: 417789--417830 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
417779 TAATTTAAAA
**
417789 AAATTT AAATTT TTATTT AAATTT AAATTT -AA-TT AAATTT AA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AA
417831 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
4 2 0.07
5 4 0.13
6 24 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:417810 original size:18 final size:18
Alignment explanation
Indices: 417789--417838 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 18
417779 TAATTTAAAA
*
417789 AAATTTAAATTTTTATTT
1 AAATTTAAATTTTTAATT
417807 AAATTTAAA--TTTAATT
1 AAATTTAAATTTTTAATT
*
417823 AAATTTAATTTTTTAA
1 AAATTTAAATTTTTAA
417839 AAATTATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 14 0.50
18 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTTAAATTTTTAATT
Found at i:420563 original size:26 final size:27
Alignment explanation
Indices: 420519--420607 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
420509 CATTTGTAAT
* * * *
420519 AAAAATTAACCACAAATTTTGACAAAT
1 AAAAAGTAACCACTATTTTTGACAAAC
*
420546 AAAAAGAAACCACTATTTTTGACAAAC
1 AAAAAGTAACCACTATTTTTGACAAAC
*
420573 ACAAA-TAACCACTATTTTTGACAAAC
1 AAAAAGTAACCACTATTTTTGACAAAC
420599 AAAAAGTAA
1 AAAAAGTAA
420608 TTTTTATTGA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 24 0.45
27 29 0.55
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.24
Consensus pattern (27 bp):
AAAAAGTAACCACTATTTTTGACAAAC
Found at i:422022 original size:6 final size:6
Alignment explanation
Indices: 422011--422052 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
422001 TAATTTAAAA
**
422011 AAATTT AAATTT TTATTT AAATTT AAATTT -AA-TT AAATTT AA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AA
422053 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
4 2 0.07
5 4 0.13
6 24 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:422032 original size:18 final size:18
Alignment explanation
Indices: 422011--422060 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 18
422001 TAATTTAAAA
*
422011 AAATTTAAATTTTTATTT
1 AAATTTAAATTTTTAATT
422029 AAATTTAAA--TTTAATT
1 AAATTTAAATTTTTAATT
*
422045 AAATTTAATTTTTTAA
1 AAATTTAAATTTTTAA
422061 AAATTATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 14 0.50
18 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTTAAATTTTTAATT
Found at i:422618 original size:25 final size:25
Alignment explanation
Indices: 422568--422620 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
422558 TATATTAGTA
*
422568 TTTAATATATATTATTATTTATTAT
1 TTTAATATATATTAATATTTATTAT
*
422593 TTTAATATA-GTTAATATTTATGTAT
1 TTTAATATATATTAATATTTAT-TAT
422618 TTT
1 TTT
422621 TTTATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (25 bp):
TTTAATATATATTAATATTTATTAT
Found at i:422831 original size:15 final size:16
Alignment explanation
Indices: 422801--422833 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
422791 ATTTTAAAAA
422801 TAAAATTAATTAAATT
1 TAAAATTAATTAAATT
*
422817 TAAATTTAATT-AATT
1 TAAAATTAATTAAATT
422832 TA
1 TA
422834 TAATCGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATTAATTAAATT
Found at i:423034 original size:16 final size:17
Alignment explanation
Indices: 423004--423080 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 17
422994 TAAATTATCG
**
423004 ATTTAATTATTAAA-TT
1 ATTTAATTAAAAAATTT
423020 ATTTAATTAAAAAATTTT
1 ATTTAATTAAAAAA-TTT
* *
423038 AATATTAAATATAATAA-TT
1 -AT-TTAATTA-AAAAATTT
423057 ATTTAA-TAAAAATATTT
1 ATTTAATTAAAAA-ATTT
423074 ATTTAAT
1 ATTTAAT
423081 AAATTTCTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
15 3 0.06
16 15 0.31
17 12 0.25
18 4 0.08
19 4 0.08
20 6 0.12
21 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAATTAAAAAATTT
Found at i:423070 original size:17 final size:17
Alignment explanation
Indices: 423050--423083 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
423040 TATTAAATAT
423050 AATAATTATTTAATAAA
1 AATAATTATTTAATAAA
*
423067 AATATTTATTTAATAAA
1 AATAATTATTTAATAAA
423084 TTTCTGTTAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAATTATTTAATAAA
Found at i:423332 original size:35 final size:33
Alignment explanation
Indices: 423293--423370 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 33
423283 ATTAATTTAA
423293 AATAATTTTTATATTAATATTTATAATTAAATTTTAAT
1 AATAATTTTT-TATTAATATTTA-AATTAAA---TAAT
* *
423331 AA-AATATTTTATTATTATTTAAATTAAATAAT
1 AATAATTTTTTATTAATATTTAAATTAAATAAT
423363 AATAATTT
1 AATAATTT
423371 AAATTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
32 6 0.17
33 4 0.11
35 7 0.19
36 11 0.31
37 6 0.17
38 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
AATAATTTTTTATTAATATTTAAATTAAATAAT
Found at i:423336 original size:25 final size:25
Alignment explanation
Indices: 423308--423426 Score: 79
Period size: 25 Copynumber: 4.8 Consensus size: 25
423298 TTTTTATATT
423308 AATATTTATAATTAAATTTTAATAA
1 AATATTTATAATTAAATTTTAATAA
* * *
423333 AATATTT-T-ATTATTATTTAAATTA
1 AATATTTATAATTA-AATTTTAATAA
* * *
423357 AATAATAATAATTTAAATTATAA-AA
1 AATATTTATAA-TTAAATTTTAATAA
*
423382 AATTTATTTA-AATTAAA-TTTAATAT
1 AA--TATTTATAATTAAATTTTAATAA
423407 AA-ATTTATTAAATTAAATTT
1 AATATTTA-T-AATTAAATTT
423427 AAGGACGATC
Statistics
Matches: 70, Mismatches: 13, Indels: 21
0.67 0.12 0.20
Matches are distributed among these distances:
22 5 0.07
23 4 0.06
24 18 0.26
25 26 0.37
26 10 0.14
27 7 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AATATTTATAATTAAATTTTAATAA
Found at i:423370 original size:20 final size:20
Alignment explanation
Indices: 423347--423399 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
423337 TTTTATTATT
423347 ATTTAAATTAAATAATAA-TA
1 ATTTAAATTAAATAA-AATTA
*
423367 ATTTAAATTATAA-AAAATTT
1 ATTTAAATTA-AATAAAATTA
423387 ATTTAAATTAAAT
1 ATTTAAATTAAAT
423400 TTAATATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 23 0.79
21 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTAAATTAAATAAAATTA
Found at i:423411 original size:16 final size:15
Alignment explanation
Indices: 423381--423427 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 15
423371 AAATTATAAA
*
423381 AAATTTATTTAAATT
1 AAATTTATATAAATT
423396 AAATTTA-AT--A-T
1 AAATTTATATAAATT
423407 AAATTTAT-TAAATT
1 AAATTTATATAAATT
423421 AAATTTA
1 AAATTTA
423428 AGGACGATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
11 9 0.33
12 1 0.04
13 1 0.04
14 9 0.33
15 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTTATATAAATT
Found at i:423420 original size:35 final size:35
Alignment explanation
Indices: 423310--423420 Score: 84
Period size: 36 Copynumber: 3.0 Consensus size: 35
423300 TTTATATTAA
*
423310 TATTTATAATTAAATTTTAATA-AAATATT-TT-ATTAT
1 TATTTA-AATTAAA-TTTAATATAAAT-TTATTAAAT-T
* **
423346 TATTTAAATTAAATAATAATAATTTAAATTATAAAAAATT
1 TATTTAAATTAAAT--T--TAATATAAATT-TATTAAATT
423386 TATTTAAATTAAATTTAATATAAATTTATTAAATT
1 TATTTAAATTAAATTTAATATAAATTTATTAAATT
423421 AAATTTAAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
34 1 0.02
35 14 0.23
36 17 0.28
38 6 0.10
39 5 0.08
40 15 0.25
41 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (35 bp):
TATTTAAATTAAATTTAATATAAATTTATTAAATT
Found at i:423427 original size:25 final size:24
Alignment explanation
Indices: 423369--423428 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 24
423359 TAATAATAAT
423369 TTAAATTATAAAAAATTTATTTAAA
1 TTAAATT-TAAAAAATTTATTTAAA
423394 TTAAATTTAATATAAATTTA-TTAAA
1 TTAAATTTAA-A-AAATTTATTTAAA
423419 TTAAATTTAA
1 TTAAATTTAA
423429 GGACGATCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 3 0.09
25 23 0.70
26 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAAATTTAAAAAATTTATTTAAA
Found at i:423499 original size:6 final size:6
Alignment explanation
Indices: 423488--423512 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
423478 GACTGTGAGG
423488 GAGAGT GAGAGT GAGAGT GAGAGT G
1 GAGAGT GAGAGT GAGAGT GAGAGT G
423513 CCTGTATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GAGAGT
Found at i:426577 original size:17 final size:17
Alignment explanation
Indices: 426552--426587 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
426542 ATAAAAAATT
*
426552 AATAAAATATTATATAA
1 AATAAAATATGATATAA
*
426569 AATATAATATGATATAA
1 AATAAAATATGATATAA
426586 AA
1 AA
426588 AAATAACAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AATAAAATATGATATAA
Found at i:426730 original size:19 final size:17
Alignment explanation
Indices: 426700--426738 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
426690 ACACAATAAT
*
426700 AATATAAAAAATTTATA
1 AATATAAAAAATATATA
426717 AATATAATATAAATATATA
1 AATATAA-A-AAATATATA
426736 AAT
1 AAT
426739 CTTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATATAAAAAATATATA
Found at i:428544 original size:2 final size:2
Alignment explanation
Indices: 428491--428530 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
428481 TGACAGAGCT
* * *
428491 TA TA TA TA TA TA TA TA TA TA TA AA AA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
428531 CACACACATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:432612 original size:17 final size:17
Alignment explanation
Indices: 432590--432627 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
432580 CCACGTAGCT
432590 GATGTGTTACTACTTTA
1 GATGTGTTACTACTTTA
432607 GATGTGTTACTACTTTA
1 GATGTGTTACTACTTTA
432624 GATG
1 GATG
432628 ACTAGCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.45
Consensus pattern (17 bp):
GATGTGTTACTACTTTA
Found at i:432682 original size:3 final size:3
Alignment explanation
Indices: 432674--432705 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
432664 GATCTAACGA
*
432674 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
432706 AAGGCATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:433046 original size:2 final size:2
Alignment explanation
Indices: 433041--433072 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
433031 TTAAATCTAC
433041 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
433073 CACACATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:435478 original size:3 final size:3
Alignment explanation
Indices: 435470--435496 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
435460 CTCATTTCTC
435470 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
435497 GTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:439978 original size:38 final size:39
Alignment explanation
Indices: 439895--439983 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 39
439885 TTAAATCACA
* *
439895 TTTTATATT-ATA-AAAATTATTTTATTTAAATTTAAAT
1 TTTTATATTAATATAAAAATATATTATTTAAATTTAAAT
* *
439932 TATAATATTAATATAAAAATATATT-TTTAATATTT-AAT
1 TTTTATATTAATATAAAAATATATTATTTAA-ATTTAAAT
439970 TTTTATATTAATAT
1 TTTTATATTAATAT
439984 TAGATTTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
37 7 0.16
38 23 0.53
39 13 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (39 bp):
TTTTATATTAATATAAAAATATATTATTTAAATTTAAAT
Found at i:440319 original size:30 final size:30
Alignment explanation
Indices: 440283--440342 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
440273 TCGTCTTCTG
*
440283 CTTCTTCTATTGTTCACTGCCTTCGCACTT
1 CTTCTTCTATTATTCACTGCCTTCGCACTT
440313 CTTCTTCTATTATTCACTGCCTTCGCACTT
1 CTTCTTCTATTATTCACTGCCTTCGCACTT
440343 TAGCCTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.12, C:0.33, G:0.08, T:0.47
Consensus pattern (30 bp):
CTTCTTCTATTATTCACTGCCTTCGCACTT
Found at i:446239 original size:31 final size:31
Alignment explanation
Indices: 446204--446263 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
446194 TTGCTATAAA
**
446204 GACTGAATTCTATGCCATTGGGACTCAAGGT
1 GACTGAATTCTATGCCATCAGGACTCAAGGT
* *
446235 GACTGTATTCTATGTCATCAGGACTCAAG
1 GACTGAATTCTATGCCATCAGGACTCAAG
446264 ATGAGTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (31 bp):
GACTGAATTCTATGCCATCAGGACTCAAGGT
Found at i:447876 original size:17 final size:17
Alignment explanation
Indices: 447849--447889 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
447839 TTTAAAAATA
447849 ATTAAATATAT-TT-AT
1 ATTAAATATATATTCAT
447864 ATTAAATATATATTCAT
1 ATTAAATATATATTCAT
*
447881 ATTTAATAT
1 ATTAAATAT
447890 TTATATTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.48
16 2 0.09
17 10 0.43
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAAATATATATTCAT
Found at i:449719 original size:25 final size:23
Alignment explanation
Indices: 449678--449734 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 23
449668 ACTCAAACAA
*
449678 TTATAAATA-TATTATATTTTAT
1 TTATAAATATTTTTATATTTTAT
449700 TATATCAAATATTTTTATATTTTAT
1 T-TAT-AAATATTTTTATATTTTAT
449725 TTATAAATAT
1 TTATAAATAT
449735 AATAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 1 0.03
23 9 0.29
24 8 0.26
25 13 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATAAATATTTTTATATTTTAT
Found at i:453848 original size:20 final size:21
Alignment explanation
Indices: 453823--453861 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
453813 ATTAGTCCTT
*
453823 AAAATAAATATTT-TTTTAAA
1 AAAATAAAGATTTATTTTAAA
453843 AAAATAAAGATTTATTTTA
1 AAAATAAAGATTTATTTTA
453862 GTATAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
AAAATAAAGATTTATTTTAAA
Found at i:454818 original size:17 final size:17
Alignment explanation
Indices: 454784--454839 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
454774 GGTGATGTTT
***
454784 GGCTAAGGTAAGCCTTA
1 GGCTAAGGTAAATTTTA
*
454801 GGCTAAGGTGAATTTTA
1 GGCTAAGGTAAATTTTA
*
454818 -GTTAAGGTAAATTTTA
1 GGCTAAGGTAAATTTTA
*
454834 GTCTAA
1 GGCTAA
454840 AAATGAAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (17 bp):
GGCTAAGGTAAATTTTA
Found at i:454825 original size:16 final size:16
Alignment explanation
Indices: 454804--454835 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
454794 AGCCTTAGGC
*
454804 TAAGGTGAATTTTAGT
1 TAAGGTAAATTTTAGT
454820 TAAGGTAAATTTTAGT
1 TAAGGTAAATTTTAGT
454836 CTAAAAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (16 bp):
TAAGGTAAATTTTAGT
Found at i:454961 original size:16 final size:16
Alignment explanation
Indices: 454937--454973 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
454927 AAGCTTGGGC
*
454937 TAAAATGAGTCTTGGT
1 TAAAGTGAGTCTTGGT
*
454953 TAAAGTGAGTTTTGGT
1 TAAAGTGAGTCTTGGT
454969 TAAAG
1 TAAAG
454974 GTGACCAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (16 bp):
TAAAGTGAGTCTTGGT
Found at i:457773 original size:2 final size:2
Alignment explanation
Indices: 457768--457812 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
457758 CTCTTCATAC
* *
457768 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
457810 AT A
1 AT A
457813 AAGCAACAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:457787 original size:14 final size:14
Alignment explanation
Indices: 457768--457812 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
457758 CTCTTCATAC
*
457768 ATATATATATATAT
1 ATATATATGTATAT
457782 ATATATATGTATAT
1 ATATATATGTATAT
457796 ATATATATGTATAT
1 ATATATATGTATAT
457810 ATA
1 ATA
457813 AAGCAACAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (14 bp):
ATATATATGTATAT
Found at i:458562 original size:15 final size:15
Alignment explanation
Indices: 458542--458579 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
458532 GGCCATTATG
458542 GTTTCCTCATTGATA
1 GTTTCCTCATTGATA
458557 GTTTCCTCATTGATA
1 GTTTCCTCATTGATA
458572 GTTTCCTC
1 GTTTCCTC
458580 TAATTCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.16, C:0.24, G:0.13, T:0.47
Consensus pattern (15 bp):
GTTTCCTCATTGATA
Found at i:459599 original size:19 final size:18
Alignment explanation
Indices: 459574--459641 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
459564 AATTCAACGA
459574 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
459592 TGTTGTATCGAT--ATAA-
1 T-TTGTATCGATACATAAG
459608 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
459624 TATTATATCGATACATAA
1 T-TTGTATCGATACATAA
459642 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 9 0.21
15 4 0.10
17 4 0.10
18 1 0.02
19 24 0.57
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:459612 original size:32 final size:32
Alignment explanation
Indices: 459576--459636 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
459566 TTCAACGATT
* *
459576 TGTATCGATACATAAGTGTTGTATCGATATAA
1 TGTATCGATACATAAGTATTATATCGATATAA
459608 TGTATCGATACATAAGTATTATATCGATA
1 TGTATCGATACATAAGTATTATATCGATA
459637 CATAATTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTATATCGATATAA
Found at i:462872 original size:19 final size:20
Alignment explanation
Indices: 462836--462874 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
462826 ACGACAAATA
* *
462836 TTTAATAATTTTAGTTTAAT
1 TTTAAAAATATTAGTTTAAT
462856 TTTAAAAATATTA-TTTAAT
1 TTTAAAAATATTAGTTTAAT
462875 AATATTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTAAAAATATTAGTTTAAT
Found at i:462904 original size:33 final size:30
Alignment explanation
Indices: 462833--462909 Score: 75
Period size: 33 Copynumber: 2.4 Consensus size: 30
462823 GTTACGACAA
462833 ATATTTAATAATTTTAGTTTAATTTTAAAAAT
1 ATATTTAATAATTTTAGTTTAATTTT--AAAT
462865 ATTATTTAATAATATTTAAGTATTATATTTT-AAT
1 A-TATTTAATAAT-TTT-AGT-TTA-ATTTTAAAT
*
462899 ATATTTTATAA
1 ATATTTAATAA
462910 ATAATATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
32 1 0.03
33 20 0.51
34 7 0.18
35 3 0.08
36 3 0.08
37 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
ATATTTAATAATTTTAGTTTAATTTTAAAT
Found at i:462916 original size:24 final size:24
Alignment explanation
Indices: 462889--462942 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
462879 TTTAAGTATT
*
462889 ATATTTTAATATATTTTA-TAAATA
1 ATATTTTAATATATTATATTAAA-A
**
462913 ATATTTTCTTATATTATATTAAAA
1 ATATTTTAATATATTATATTAAAA
462937 ATATTT
1 ATATTT
462943 ATAAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
ATATTTTAATATATTATATTAAAA
Found at i:462972 original size:36 final size:37
Alignment explanation
Indices: 462903--462990 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 37
462893 TTTAATATAT
* * * *
462903 TTTATAAATAATATTTTCTTATATTATATTAAAA-ATA
1 TTTATAAATAATAATTACTTATATAATAATAAAATA-A
462940 TTTATAAATAATAATTAC-TATATAATAATAAAATAA
1 TTTATAAATAATAATTACTTATATAATAATAAAATAA
**
462976 TTTATATTTAATAAT
1 TTTATAAATAATAAT
462991 ACATCAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
36 27 0.61
37 17 0.39
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (37 bp):
TTTATAAATAATAATTACTTATATAATAATAAAATAA
Found at i:462974 original size:22 final size:22
Alignment explanation
Indices: 462949--462991 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
462939 ATTTATAAAT
462949 AATAA-TTACTATATAATAATAA
1 AATAATTTA-TATATAATAATAA
*
462971 AATAATTTATATTTAATAATA
1 AATAATTTATATATAATAATA
462992 CATCAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAATTTATATATAATAATAA
Found at i:463014 original size:31 final size:30
Alignment explanation
Indices: 462966--463053 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 30
462956 ACTATATAAT
462966 AATAAAATAATTTATATTTAATAATACA-TCAA
1 AATAAAA-AA-TTATATTTAATAATACATTC-A
*
462998 AATAAAAAACTTATATTTAATAATTCATTCA
1 AATAAAAAA-TTATATTTAATAATACATTCA
* *
463029 ATTACAAAAATTATATTCAATAATA
1 AATA-AAAAATTATATTTAATAATA
463054 TAATATAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
31 35 0.71
32 14 0.29
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (30 bp):
AATAAAAAATTATATTTAATAATACATTCA
Found at i:465328 original size:13 final size:13
Alignment explanation
Indices: 465310--465334 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
465300 CATAAAATGT
465310 TGTATCGATACAA
1 TGTATCGATACAA
465323 TGTATCGATACA
1 TGTATCGATACA
465335 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:465417 original size:13 final size:13
Alignment explanation
Indices: 465399--465423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
465389 ATTACTCAAA
465399 TGTATCGATACAT
1 TGTATCGATACAT
465412 TGTATCGATACA
1 TGTATCGATACA
465424 CCGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:465488 original size:52 final size:52
Alignment explanation
Indices: 465432--465552 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
465422 CACCGATCTT
*
465432 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
465484 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
465536 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
465553 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:468972 original size:17 final size:19
Alignment explanation
Indices: 468930--468979 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
468920 CAATAAGGCG
468930 ATGTATCGATACATAAGTGA
1 ATGTATCGATACAT-AGTGA
*
468950 ATGTATCGATACAT-G-GC
1 ATGTATCGATACATAGTGA
468967 ATGTATCGATACA
1 ATGTATCGATACA
468980 GGACCATGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 14 0.48
18 1 0.03
20 14 0.48
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (19 bp):
ATGTATCGATACATAGTGA
Found at i:469032 original size:20 final size:20
Alignment explanation
Indices: 469007--469079 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
468997 GAAAGGAAAT
469007 TGTATCGATACATTTTTCAA
1 TGTATCGATACATTTTTCAA
*
469027 TGTATCGATACATTTTTCAT
1 TGTATCGATACATTTTTCAA
*
469047 TGTATCGATATATTTTTCAA
1 TGTATCGATACATTTTTCAA
*
469067 TGTATTGATACAT
1 TGTATCGATACAT
469080 CTAGTTAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (20 bp):
TGTATCGATACATTTTTCAA
Found at i:472309 original size:20 final size:20
Alignment explanation
Indices: 472260--472316 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
472250 GTAAAAAGAT
*
472260 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTCA
*
472280 AGAATATATCGATACATTCA
1 AGAATGTATCGATACATTCA
*
472300 TA-CATGTATCGATACAT
1 -AGAATGTATCGATACAT
472317 CTGGGTACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTCA
Found at i:473163 original size:20 final size:22
Alignment explanation
Indices: 473133--473173 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
473123 ACATCTAAAT
*
473133 AGCCAATGTT-CATGTATTTTG
1 AGCCAATGTTCCATGCATTTTG
473154 AGCC-ATGTTCCATGCATTTT
1 AGCCAATGTTCCATGCATTTT
473174 AACTTGTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (22 bp):
AGCCAATGTTCCATGCATTTTG
Found at i:473930 original size:24 final size:21
Alignment explanation
Indices: 473887--473930 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
473877 CCACTAAACG
*
473887 ATTTTTCTAAATTTTCTGAAT
1 ATTTTTCTAAAATTTCTGAAT
473908 ATTTTTCCTAATAATTTCATGAA
1 ATTTTT-CTAA-AATTTC-TGAA
473931 ATTCCCTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 4 0.21
23 5 0.26
24 4 0.21
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.52
Consensus pattern (21 bp):
ATTTTTCTAAAATTTCTGAAT
Found at i:474041 original size:25 final size:25
Alignment explanation
Indices: 474007--474057 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
473997 AGTTTGACAT
*
474007 ACCCTTTACTTTATGTGTCCTGCCA
1 ACCCTTTACTTCATGTGTCCTGCCA
*
474032 ACCCTTTACTTCATGTGTTCTGCCA
1 ACCCTTTACTTCATGTGTCCTGCCA
474057 A
1 A
474058 GTAGCGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.18, C:0.31, G:0.12, T:0.39
Consensus pattern (25 bp):
ACCCTTTACTTCATGTGTCCTGCCA
Found at i:476594 original size:26 final size:24
Alignment explanation
Indices: 476565--476612 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
476555 TATCGTATAA
476565 ATATAATAAAAAATAATTAATATATG
1 ATATAATAAAAAAT--TTAATATATG
*
476591 ATATAATATAAAATTTAATATA
1 ATATAATAAAAAATTTAATATA
476613 AATGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
26 13 0.62
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATAATAAAAAATTTAATATATG
Done.