Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 14 of 26
Found at i:2306084 original size:11 final size:11
Alignment explanation
Indices: 2306066--2306117 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
2306056 TTATAATTCT
2306066 TTTA-ATTAAA
1 TTTATATTAAA
*
2306076 TTTATATTATA
1 TTTATATTAAA
2306087 TTTATATTATAA
1 TTTATATTA-AA
*
2306099 TTATATTTTAAA
1 TT-TATATTAAA
2306111 TTTATAT
1 TTTATAT
2306118 ATTTAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 7 0.20
13 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTATATTAAA
Found at i:2306344 original size:2 final size:2
Alignment explanation
Indices: 2306337--2306366 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2306327 AGAAGTGCTA
2306337 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
2306367 TGTTTATTTG
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:2306548 original size:6 final size:6
Alignment explanation
Indices: 2306523--2306556 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
2306513 AATTGTGGGT
*
2306523 AGGAAA AGGGAAA AGAAAA AGGAAA AGGAAA AGG
1 AGGAAA A-GGAAA AGGAAA AGGAAA AGGAAA AGG
2306557 TTGCCGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
AGGAAA
Found at i:2308736 original size:25 final size:24
Alignment explanation
Indices: 2308708--2308776 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
2308698 AATTTTTATT
2308708 TAAATTTAATTATATAAATATAATA
1 TAAATTTAATT-TATAAATATAATA
** * * *
2308733 TAAAAATAATTTTTAAATTTTAATC
1 TAAATTTAATTTATAAA-TATAATA
2308758 T-AATTTAATTTATAAATAT
1 TAAATTTAATTTATAAATAT
2308777 TTTTGTTTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
23 2 0.06
24 17 0.50
25 15 0.44
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAATTTAATTTATAAATATAATA
Found at i:2309110 original size:14 final size:14
Alignment explanation
Indices: 2309091--2309120 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2309081 TAGGTGGGAA
2309091 TATTATTATTAAAT
1 TATTATTATTAAAT
*
2309105 TATTATTATTTAAT
1 TATTATTATTAAAT
2309119 TA
1 TA
2309121 ATACTTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATTATTAAAT
Found at i:2310220 original size:2 final size:2
Alignment explanation
Indices: 2310213--2310244 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2310203 AATCCAAACG
*
2310213 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2310245 GTTAATGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2310441 original size:2 final size:2
Alignment explanation
Indices: 2310434--2310479 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2310424 GACATAAAGC
2310434 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 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
2310476 AG AG
1 AG AG
2310480 TTACGTATTG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2311158 original size:22 final size:22
Alignment explanation
Indices: 2311111--2311158 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2311101 TTAAGCTTTT
* * *
2311111 AAATATATTATGATAAATAATG
1 AAATAAATTATGACAAATAATA
2311133 AAATAAATTATGTACAAAT-ATA
1 AAATAAATTATG-ACAAATAATA
2311155 AAAT
1 AAAT
2311159 TACTTAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (22 bp):
AAATAAATTATGACAAATAATA
Found at i:2311982 original size:21 final size:22
Alignment explanation
Indices: 2311953--2311994 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2311943 AAATTAATAA
*
2311953 AACTAAAATTTATATTATTTTT
1 AACTAAAATATATATTATTTTT
*
2311975 AACT-AAATATATTTTATTTT
1 AACTAAAATATATATTATTTT
2311995 AGTTGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
AACTAAAATATATATTATTTTT
Found at i:2312492 original size:16 final size:16
Alignment explanation
Indices: 2312471--2312502 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2312461 CTTTAAAAAT
2312471 TCATAAATTACTCAAC
1 TCATAAATTACTCAAC
*
2312487 TCATAAATTATTCAAC
1 TCATAAATTACTCAAC
2312503 CAAATAAAAT
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:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (16 bp):
TCATAAATTACTCAAC
Found at i:2315091 original size:13 final size:13
Alignment explanation
Indices: 2315073--2315097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2315063 TCTTAAGATC
2315073 TTATTTTTTTATT
1 TTATTTTTTTATT
2315086 TTATTTTTTTAT
1 TTATTTTTTTAT
2315098 ATCTTAAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTATTTTTTTATT
Found at i:2320863 original size:13 final size:13
Alignment explanation
Indices: 2320845--2320869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2320835 AGAACACTTA
2320845 TGTATCGATACAT
1 TGTATCGATACAT
2320858 TGTATCGATACA
1 TGTATCGATACA
2320870 ACACTTATGT
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:2320864 original size:32 final size:32
Alignment explanation
Indices: 2320818--2320888 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
2320808 AGCTTCGTAG
*
2320818 CGATACATTATATCGATAGAACACTTATGTAT
1 CGATACATTATATCGATACAACACTTATGTAT
*
2320850 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTATATCGATACAACACTTATGTAT
2320882 CGATACA
1 CGATACA
2320889 ATTACTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTATATCGATACAACACTTATGTAT
Found at i:2320887 original size:19 final size:19
Alignment explanation
Indices: 2320828--2320910 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
2320818 CGATACATTA
*
2320828 TATCGATAGAACACTTATG
1 TATCGATACAACACTTATG
2320847 TATCGAT---ACA--T-TG
1 TATCGATACAACACTTATG
2320860 TATCGATACAACACTTATG
1 TATCGATACAACACTTATG
* *
2320879 TATCGATACAATTACTGTTTG
1 TATCGATACAA-CACT-TATG
2320900 TATCGATACAA
1 TATCGATACAA
2320911 ATTGTTGAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
13 9 0.17
14 1 0.02
16 6 0.11
18 1 0.02
19 20 0.37
20 3 0.06
21 14 0.26
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (19 bp):
TATCGATACAACACTTATG
Found at i:2320903 original size:21 final size:19
Alignment explanation
Indices: 2320857--2320910 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
2320847 TATCGATACA
2320857 TTGTATCGATACAACACTT
1 TTGTATCGATACAACACTT
* *
2320876 ATGTATCGATACAATTACTGT
1 TTGTATCGATACAA-CACT-T
2320897 TTGTATCGATACAA
1 TTGTATCGATACAA
2320911 ATTGTTGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACAACACTT
Found at i:2323063 original size:37 final size:37
Alignment explanation
Indices: 2323020--2323096 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
2323010 TTCATATATT
2323020 TGTAAGAAGGTATTTAACCTTTTTACAACTTATATGG
1 TGTAAGAAGGTATTTAACCTTTTTACAACTTATATGG
* *
2323057 TGTAAGAAGGTTTTTAACCTTTTTGCAACTTATATGG
1 TGTAAGAAGGTATTTAACCTTTTTACAACTTATATGG
2323094 TGT
1 TGT
2323097 CTTGTCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (37 bp):
TGTAAGAAGGTATTTAACCTTTTTACAACTTATATGG
Found at i:2324179 original size:53 final size:53
Alignment explanation
Indices: 2324099--2324206 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
2324089 TAACAAGTGA
*
2324099 CATTGATATTAACTCACCGAGTTATATGAGTTTTTCACTATATTCATTTTAGT
1 CATTGATATCAACTCACCGAGTTATATGAGTTTTTCACTATATTCATTTTAGT
2324152 CATTGATATCAACTCACCGAGTTATATGAGTTTTTCACTATATTCATTTTAGT
1 CATTGATATCAACTCACCGAGTTATATGAGTTTTTCACTATATTCATTTTAGT
2324205 CA
1 CA
2324207 CTACAGCAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.44
Consensus pattern (53 bp):
CATTGATATCAACTCACCGAGTTATATGAGTTTTTCACTATATTCATTTTAGT
Found at i:2324980 original size:16 final size:16
Alignment explanation
Indices: 2324959--2325036 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 16
2324949 ATATTAAAAT
2324959 TTAAATTATAAATTTA
1 TTAAATTATAAATTTA
*
2324975 TTAAA-TAT-TA-TT-
1 TTAAATTATAAATTTA
* *
2324987 TT-AATTATATATTAA
1 TTAAATTATAAATTTA
2325002 TTAAATT-TAAA--T-
1 TTAAATTATAAATTTA
2325014 TTAAATT-TAAATTTAA
1 TTAAATTATAAATTT-A
2325030 TTAAATT
1 TTAAATT
2325037 GTTTGATCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
11 2 0.04
12 16 0.33
13 4 0.08
14 3 0.06
15 8 0.16
16 16 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATTATAAATTTA
Found at i:2324995 original size:27 final size:27
Alignment explanation
Indices: 2324956--2325036 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
2324946 TAAATATTAA
2324956 AATTTAAATTATAAATTTATTAAATATT
1 AATTTAAATTATAAATTTATTAAAT-TT
* * *
2324984 -ATTTTAATTATATATTAATTAAATTT
1 AATTTAAATTATAAATTTATTAAATTT
2325010 AAATTTAAATT-TAAATTTAATTAAATT
1 -AATTTAAATTATAAATTT-ATTAAATT
2325037 GTTTGATCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 2 0.05
27 26 0.59
28 16 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AATTTAAATTATAAATTTATTAAATTT
Found at i:2325013 original size:6 final size:6
Alignment explanation
Indices: 2325002--2325029 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2324992 TATATATTAA
2325002 TTAAAT TTAAAT TTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAA
2325030 TTAAATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:2332427 original size:45 final size:45
Alignment explanation
Indices: 2332378--2332464 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 45
2332368 ATTTAACACA
2332378 AATTAAAAATCTATATAAACTTAAACCCAAA-CTCAATTAAAATCG
1 AATTAAAAATCTATATAAACTTAAACCCAAATC-CAATTAAAATCG
* *
2332423 AATTAAAAATCTCTATAAACTTAAATCCAAATCCAATTAAAA
1 AATTAAAAATCTATATAAACTTAAACCCAAATCCAATTAAAA
2332465 AAATAACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 38 0.97
46 1 0.03
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (45 bp):
AATTAAAAATCTATATAAACTTAAACCCAAATCCAATTAAAATCG
Found at i:2333707 original size:18 final size:17
Alignment explanation
Indices: 2333658--2333715 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
2333648 GATATATTTT
2333658 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
2333674 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
2333689 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
2333707 TAAATATTT
1 TAAA-ATTT
2333716 TAAACATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 5 0.14
15 7 0.20
16 1 0.03
17 6 0.17
18 12 0.34
19 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:2334235 original size:22 final size:22
Alignment explanation
Indices: 2334204--2334245 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2334194 TTTAAAAAAT
*
2334204 TATTTTTATA-CTAATATTTATA
1 TATTTATATAGCTAA-ATTTATA
2334226 TATTTATATAGCTAAATTTA
1 TATTTATATAGCTAAATTTA
2334246 AATAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTTATATAGCTAAATTTATA
Found at i:2335971 original size:12 final size:12
Alignment explanation
Indices: 2335950--2335982 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2335940 ATCAAATGTA
2335950 TCAAATTCATAT
1 TCAAATTCATAT
*
2335962 TCATATTCATAT
1 TCAAATTCATAT
2335974 TCAAATTCA
1 TCAAATTCA
2335983 AAGTGAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (12 bp):
TCAAATTCATAT
Found at i:2337403 original size:22 final size:22
Alignment explanation
Indices: 2337353--2337407 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2337343 AATTAATAAA
* *
2337353 AAATTAAAATATATTTTATATT
1 AAATTTAAATATATTTTACATT
2337375 AATATTTAAATAT-TTTTACATTT
1 AA-ATTTAAATATATTTTACA-TT
2337398 AAATTTAAAT
1 AAATTTAAAT
2337408 TAAAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTAAATATATTTTACATT
Found at i:2354206 original size:26 final size:25
Alignment explanation
Indices: 2354152--2354212 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
2354142 CTAGTAAAAA
**
2354152 TTAAATTAAATTATTATATTTAATT
1 TTAAATTAAATTATTATATTTAAAC
**
2354177 TTAAATTTGATTATTTATATTTAAAC
1 TTAAATTAAATTA-TTATATTTAAAC
2354203 TTAAATTAAA
1 TTAAATTAAA
2354213 AAATATTGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
TTAAATTAAATTATTATATTTAAAC
Found at i:2354592 original size:18 final size:18
Alignment explanation
Indices: 2354510--2354594 Score: 56
Period size: 18 Copynumber: 4.9 Consensus size: 18
2354500 ATATTCATAT
*
2354510 ATTTTAAT-TATATTTAAA
1 ATTTTAATATATATAT-AA
* * *
2354528 ATATTATATATTTAAATAA
1 ATTTTA-ATATATATATAA
2354547 ATTTTAATAT-T-T-T-A
1 ATTTTAATATATATATAA
*
2354561 ATAATTAATA-ATATATAA
1 AT-TTTAATATATATATAA
2354579 ATTTTAATATATATAT
1 ATTTTAATATATATAT
2354595 TTATATTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
14 3 0.06
15 8 0.16
16 1 0.02
17 8 0.16
18 18 0.35
19 9 0.18
20 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTAATATATATATAA
Found at i:2355517 original size:2 final size:2
Alignment explanation
Indices: 2355510--2355541 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2355500 TTCTTAACAT
*
2355510 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2355542 AACTGAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2356244 original size:32 final size:30
Alignment explanation
Indices: 2356208--2356295 Score: 77
Period size: 32 Copynumber: 2.8 Consensus size: 30
2356198 TAATTTATTT
*
2356208 TTTTAACCTTAATTAATATATATTATATAAAA
1 TTTTAACATTAA-TAATATATATTATAT-AAA
** *
2356240 TTTTATTTATTAATAATTTATATTATATAAA
1 TTTTA-ACATTAATAATATATATTATATAAA
* *
2356271 TTTTAATATATATATATTATATATT
1 TTTTAACAT-TA-ATAATATATATT
2356296 TTATCATATT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 3 0.07
31 10 0.22
32 29 0.63
33 4 0.09
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTTAACATTAATAATATATATTATATAAA
Found at i:2356265 original size:16 final size:16
Alignment explanation
Indices: 2356216--2356265 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
2356206 TTTTTTAACC
*
2356216 TTAATTAATATATATTA
1 TTAA-TAATTTATATTA
2356233 TATAA-AATTT-TATTTA
1 T-TAATAATTTATA-TTA
2356249 TTAATAATTTATATTA
1 TTAATAATTTATATTA
2356265 T
1 T
2356266 ATAAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
15 5 0.18
16 17 0.61
17 3 0.11
18 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATAATTTATATTA
Found at i:2356275 original size:16 final size:16
Alignment explanation
Indices: 2356226--2356295 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
2356216 TTAATTAATA
2356226 TATATTATATAAAATTT
1 TATATTATAT-AAATTT
*
2356243 TAT-TTAT-TAATAATT
1 TATATTATATAA-ATTT
2356258 TATATTATATAAATTT
1 TATATTATATAAATTT
* *
2356274 TA-ATATATATATATTA
1 TATAT-TATATAAATTT
2356290 TATATT
1 TATATT
2356296 TTATCATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
14 2 0.05
15 9 0.20
16 25 0.57
17 8 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATTATATAAATTT
Found at i:2356291 original size:23 final size:21
Alignment explanation
Indices: 2356253--2356298 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
2356243 TATTTATTAA
*
2356253 TAATTTATATTATATAAATTT
1 TAATATATATTATATAAATTT
*
2356274 TAATATATATATATTATATATTT
1 TAATATATAT-TA-TATAAATTT
2356297 TA
1 TA
2356299 TCATATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 2 0.10
23 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATATATTATATAAATTT
Found at i:2356304 original size:23 final size:24
Alignment explanation
Indices: 2356249--2356298 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
2356239 ATTTTATTTA
*
2356249 TTAATA-ATTTATATTATATAAATT
1 TTAATATATATATATTATAT-AATT
2356273 TTAATATATATATATTATAT-ATT
1 TTAATATATATATATTATATAATT
2356296 TTA
1 TTA
2356299 TCATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 6 0.25
25 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAATATATATATATTATATAATT
Found at i:2361254 original size:26 final size:26
Alignment explanation
Indices: 2361222--2361294 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
2361212 AAAGCTTGTT
2361222 TTATTATTTTTAATAATATTAAAATA
1 TTATTATTTTTAATAATATTAAAATA
* * * *
2361248 TTATTATTTATATTAATATTTATATA
1 TTATTATTTTTAATAATATTAAAATA
* **
2361274 TTTTTATAATTAA-AATATTAA
1 TTATTATTTTTAATAATATTAA
2361295 TTCAAAATAG
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
25 7 0.19
26 30 0.81
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATTATTTTTAATAATATTAAAATA
Found at i:2361260 original size:12 final size:12
Alignment explanation
Indices: 2361245--2361281 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2361235 TAATATTAAA
2361245 ATATTATTATTT
1 ATATTATTATTT
*
2361257 ATATTAATATTT
1 ATATTATTATTT
2361269 ATA-TATT-TTT
1 ATATTATTATTT
2361279 ATA
1 ATA
2361282 ATTAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 6 0.26
11 3 0.13
12 14 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTATTATTT
Found at i:2361275 original size:20 final size:20
Alignment explanation
Indices: 2361237--2361293 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
2361227 ATTTTTAATA
2361237 ATATTAAAATATTATTATTT
1 ATATTAAAATATTATTATTT
*
2361257 ATATTAATAT-TTATATATTTTT
1 ATATTAAAATATTAT-TA--TTT
2361279 ATAATTAAAATATTA
1 AT-ATTAAAATATTA
2361294 ATTCAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 4 0.13
20 11 0.37
22 5 0.17
23 7 0.23
24 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTAAAATATTATTATTT
Found at i:2363660 original size:20 final size:19
Alignment explanation
Indices: 2363602--2363660 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
2363592 GATTTTATTT
2363602 AAATTATTAATTA-ATAATAA
1 AAATT-TTAATTATATAAT-A
*
2363622 AAATTTTAATTATAAAATA
1 AAATTTTAATTATATAATA
*
2363641 AAATTTTAATATATTTAATA
1 AAATTTTAAT-TATATAATA
2363661 TTATTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTTAATTATATAATA
Found at i:2364224 original size:31 final size:30
Alignment explanation
Indices: 2364189--2364246 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2364179 TATTGATATG
*
2364189 TATTAATATATTTTAATATATTATTTAAATT
1 TATTAATAT-TTTTAAAATATTATTTAAATT
*
2364220 TATTAATATTTTTAAAATATTTTTTAA
1 TATTAATATTTTTAAAATATTATTTAA
2364247 TATATAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TATTAATATTTTTAAAATATTATTTAAATT
Found at i:2364266 original size:24 final size:25
Alignment explanation
Indices: 2364230--2364276 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2364220 TATTAATATT
*
2364230 TTTAAAATATTTTTTAATATATAAA
1 TTTAAAATATTTTTAAATATATAAA
*
2364255 TTTATAAT-TTTTTAAATATATA
1 TTTAAAATATTTTTAAATATATA
2364277 TTATATATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTAAAATATTTTTAAATATATAAA
Found at i:2365288 original size:23 final size:22
Alignment explanation
Indices: 2365262--2365331 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 22
2365252 AATTTTTTTA
2365262 AAATTTTAATTATAAAAATATAT
1 AAATTTTAATTATAAAAATA-AT
*
2365285 AAATATTAA-TATAAAAATAAT
1 AAATTTTAATTATAAAAATAAT
2365306 --ATTTTAATAATATAACAAATAAT
1 AAATTTTAAT--TATAA-AAATAAT
2365329 AAA
1 AAA
2365332 ATTAATTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 6 0.15
21 2 0.05
22 15 0.38
23 15 0.38
25 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATTTTAATTATAAAAATAAT
Found at i:2372788 original size:22 final size:21
Alignment explanation
Indices: 2372762--2372805 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2372752 TAAACATGAG
*
2372762 ATATAAATATAAAATTTTTTAA
1 ATATAAA-ATAAAATCTTTTAA
*
2372784 ATATATAATAAAATCTTTTAA
1 ATATAAAATAAAATCTTTTAA
2372805 A
1 A
2372806 AAAATTAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATAAAATAAAATCTTTTAA
Found at i:2380694 original size:37 final size:37
Alignment explanation
Indices: 2380638--2380709 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
2380628 TCCAAGATTG
* * *
2380638 TAGCTTAAACTTTCGATAATTATTTCTCTATGTTCCA
1 TAGCTTAAACTTTCAATAATGATTCCTCTATGTTCCA
* *
2380675 TAGCTTGAACTTTTAATAATGATTCCTCTATGTTC
1 TAGCTTAAACTTTCAATAATGATTCCTCTATGTTC
2380710 TATATGTGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (37 bp):
TAGCTTAAACTTTCAATAATGATTCCTCTATGTTCCA
Found at i:2384032 original size:24 final size:22
Alignment explanation
Indices: 2383979--2384032 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 22
2383969 TTAATTTATT
* *
2383979 TTTAAGTATAATTTTTTTTCAA
1 TTTAATTAAAATTTTTTTTCAA
* *
2384001 ATTCATTAAAATTTATTTATTCAA
1 TTTAATTAAAATTT-TTT-TTCAA
2384025 TTTAATTA
1 TTTAATTA
2384033 GTGATCAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 10 0.42
23 3 0.12
24 11 0.46
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAATTAAAATTTTTTTTCAA
Found at i:2384090 original size:5 final size:5
Alignment explanation
Indices: 2384081--2384128 Score: 60
Period size: 5 Copynumber: 9.0 Consensus size: 5
2384071 TAAATCATTC
*
2384081 AAATA TAATA AAATAA AAATAA AAATAA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAAT-A AAAT-A AAAT-A AAATA AAATA AAATA AAATA
2384129 TAATTAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
5 23 0.57
6 17 0.43
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:2384101 original size:6 final size:6
Alignment explanation
Indices: 2384090--2384131 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
2384080 CAAATATAAT
2384090 AAAATA AAAATA AAAATA AAAAT- AAAAT- AAAATA AAATATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA-ATA A
2384132 TTAAATTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 10 0.29
6 20 0.59
7 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:2384103 original size:11 final size:11
Alignment explanation
Indices: 2384087--2384128 Score: 68
Period size: 12 Copynumber: 3.8 Consensus size: 11
2384077 ATTCAAATAT
2384087 AATAAAATAAA
1 AATAAAATAAA
2384098 AATAAAAATAAA
1 AAT-AAAATAAA
2384110 AATAAAAT-AA
1 AATAAAATAAA
2384120 AATAAAATA
1 AATAAAATA
2384129 TAATTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.34
11 8 0.28
12 11 0.38
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:2384567 original size:21 final size:21
Alignment explanation
Indices: 2384526--2384567 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2384516 AAATTCTTAT
*
2384526 TTAATATAATAAAAATTAAAA
1 TTAATATAATAAAAATAAAAA
*
2384547 TTAATTTAA-AAATAATAAAAA
1 TTAATATAATAAA-AATAAAAA
2384568 AATAATTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAATATAATAAAAATAAAAA
Found at i:2389189 original size:22 final size:20
Alignment explanation
Indices: 2389164--2389204 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
2389154 GTATTAATTT
*
2389164 ATCAATTTTAAAATTAAATTAG
1 ATCAAATTT-AAA-TAAATTAG
2389186 ATCAAATTTAAATAAATTA
1 ATCAAATTTAAATAAATTA
2389205 TTTACTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (20 bp):
ATCAAATTTAAATAAATTAG
Found at i:2390985 original size:29 final size:30
Alignment explanation
Indices: 2390935--2391000 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
2390925 TTAAAATTTT
*
2390935 TAAATAT-ATAAAATATTTTAAATAAAATTA
1 TAAATATAATAAAATATTATAAAT-AAATTA
*
2390965 T-AATATAATAAAATA-TATAAATATATTA
1 TAAATATAATAAAATATTATAAATAAATTA
2390993 TAAATATA
1 TAAATATA
2391001 TGAATTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 6 0.19
29 17 0.53
30 9 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
TAAATATAATAAAATATTATAAATAAATTA
Found at i:2394340 original size:2 final size:2
Alignment explanation
Indices: 2394333--2394374 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2394323 ATGGGAATTA
**
2394333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GC 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
2394375 CCATTTGTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2396226 original size:18 final size:18
Alignment explanation
Indices: 2396199--2396237 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2396189 ACTGTTGAAT
*
2396199 CAAATACAAGTTCAAATG
1 CAAATACAAGTACAAATG
*
2396217 CAAATGCAAGTACAAATG
1 CAAATACAAGTACAAATG
2396235 CAA
1 CAA
2396238 TTGCTATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (18 bp):
CAAATACAAGTACAAATG
Found at i:2398164 original size:4 final size:4
Alignment explanation
Indices: 2398157--2398184 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2398147 CCACTAAAAA
2398157 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2398185 GATAATCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:2398564 original size:26 final size:26
Alignment explanation
Indices: 2398494--2398567 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
2398484 ATTTTATTTA
* * *
2398494 TTTATATTATTATTAATTGTTTATATAT
1 TTTATATT-TTAATAATT-TATATAAAT
* *
2398522 TTTAAATATT-ATAAATTTATATAAAT
1 TTTATATTTTAAT-AATTTATATAAAT
2398548 TTTATATTTTAATAATTTAT
1 TTTATATTTTAATAATTTAT
2398568 TTTATTTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
26 23 0.62
27 8 0.22
28 6 0.16
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (26 bp):
TTTATATTTTAATAATTTATATAAAT
Found at i:2398948 original size:18 final size:19
Alignment explanation
Indices: 2398925--2398968 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
2398915 TTTTTTTTAC
* *
2398925 AAAAAAGGAAGAGAAAGA-
1 AAAAAAAGAAGAAAAAGAG
*
2398943 AAAAAAAGAGGAAAAAGAG
1 AAAAAAAGAAGAAAAAGAG
2398962 AAAAAAA
1 AAAAAAA
2398969 ATTATGTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAGAAAAAGAG
Found at i:2399035 original size:13 final size:13
Alignment explanation
Indices: 2399019--2399044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2399009 AATATTATAA
2399019 ATTTATATATATT
1 ATTTATATATATT
2399032 ATTTATATATATT
1 ATTTATATATATT
2399045 TTAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTATATATATT
Found at i:2400928 original size:9 final size:10
Alignment explanation
Indices: 2400898--2400928 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2400888 ATAATCTTTT
2400898 AAAAAATATA
1 AAAAAATATA
2400908 AAAAAATATA
1 AAAAAATATA
2400918 AAAAAAT-TA
1 AAAAAATATA
2400927 AA
1 AA
2400929 CATATTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAAATATA
Found at i:2401473 original size:3 final size:3
Alignment explanation
Indices: 2401465--2401499 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2401455 TGACGTTTAC
2401465 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2401500 AATATTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2406696 original size:16 final size:16
Alignment explanation
Indices: 2406684--2406717 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2406674 ATTTATATTT
2406684 AATTATAAATATATAA
1 AATTATAAATATATAA
*
2406700 AATTATTAATATA-AA
1 AATTATAAATATATAA
2406715 AAT
1 AAT
2406718 ATTTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTATAAATATATAA
Found at i:2407949 original size:17 final size:17
Alignment explanation
Indices: 2407918--2407957 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2407908 AATAAAGACT
* *
2407918 AAAACTCCAATTAATTA
1 AAAACTACAACTAATTA
*
2407935 TAAACTACAACTAATTA
1 AAAACTACAACTAATTA
2407952 AAAACT
1 AAAACT
2407958 TAATTAACAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAACTACAACTAATTA
Found at i:2409616 original size:33 final size:32
Alignment explanation
Indices: 2409553--2409620 Score: 75
Period size: 34 Copynumber: 2.1 Consensus size: 32
2409543 ATAACGTAAC
* * *
2409553 AAAATATAAATTTTAATATATTATTGATAAATA
1 AAAATATAAATTTAAATATAATATTCATAAA-A
*
2409586 AAAATATTTAATTTAAATATAATA-TCATAAAA
1 AAAATA-TAAATTTAAATATAATATTCATAAAA
2409618 AAA
1 AAA
2409621 CTTAATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
32 4 0.13
33 12 0.40
34 14 0.47
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (32 bp):
AAAATATAAATTTAAATATAATATTCATAAAA
Found at i:2410464 original size:24 final size:25
Alignment explanation
Indices: 2410411--2410467 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
2410401 AATTTTTTAA
2410411 AAAAATT-TTATTTAAATTAAAAAT
1 AAAAATTATTATTTAAATTAAAAAT
** * *
2410435 TTAAATTATTATTTAAA-TATATAT
1 AAAAATTATTATTTAAATTAAAAAT
2410459 AAAAATTAT
1 AAAAATTAT
2410468 AAAAAATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAAATTATTATTTAAATTAAAAAT
Found at i:2412266 original size:30 final size:28
Alignment explanation
Indices: 2412219--2412278 Score: 93
Period size: 30 Copynumber: 2.1 Consensus size: 28
2412209 ACGCCATAAT
*
2412219 AATAATAATAATATTTTTAAAAATTTAA
1 AATAATAATAATATTTTTAAAAAATTAA
2412247 AATAATTAATAATTATTTTTAAAAAATTAA
1 AATAA-TAATAA-TATTTTTAAAAAATTAA
2412277 AA
1 AA
2412279 ATATTTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 5 0.17
29 6 0.21
30 18 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
AATAATAATAATATTTTTAAAAAATTAA
Found at i:2412272 original size:31 final size:28
Alignment explanation
Indices: 2412219--2412281 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 28
2412209 ACGCCATAAT
*
2412219 AATAATAATAATATTTTTAAAAATTTAA
1 AATAATAATAATATTTTTAAAAATTAAA
2412247 AATAATTAATAATTATTTTTAAAAAATTAAA
1 AATAA-TAATAA-TATTTTT-AAAAATTAAA
2412278 AATA
1 AATA
2412282 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 5 0.16
29 6 0.19
30 7 0.23
31 13 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AATAATAATAATATTTTTAAAAATTAAA
Found at i:2412283 original size:20 final size:21
Alignment explanation
Indices: 2412242--2412292 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 21
2412232 TTTTTAAAAA
*
2412242 TTTAAAATAATTAATAATTATT
1 TTTAAAA-AATTAATAAATATT
2412264 TTTAAAAAATTAA-AAATATT
1 TTTAAAAAATTAATAAATATT
2412284 TTTAAAAAA
1 TTTAAAAAA
2412293 ATTTTAGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 15 0.54
21 6 0.21
22 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAAAAAATTAATAAATATT
Found at i:2412293 original size:21 final size:22
Alignment explanation
Indices: 2412242--2412295 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
2412232 TTTTTAAAAA
* *
2412242 TTTAAAATAATTAATAATTATT
1 TTTAAAAAAATTAATAAATATT
2412264 TTT-AAAAAATTAA-AAATATT
1 TTTAAAAAAATTAATAAATATT
2412284 TTTAAAAAAATT
1 TTTAAAAAAATT
2412296 TTAGGGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 9 0.31
21 17 0.59
22 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAAAAAAATTAATAAATATT
Found at i:2412342 original size:15 final size:16
Alignment explanation
Indices: 2412322--2412355 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2412312 TTTGTAAGAG
*
2412322 TTATTTTT-TAAAATT
1 TTATTTTTAAAAAATT
2412337 TTATTTTTAAAAAATT
1 TTATTTTTAAAAAATT
2412353 TTA
1 TTA
2412356 GATGATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTTTTAAAAAATT
Found at i:2412384 original size:32 final size:32
Alignment explanation
Indices: 2412348--2412424 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
2412338 TATTTTTAAA
* *
2412348 AAATTTTAGATGATATTTATCAT-AATACTATT
1 AAATTTAAGATAATATTTATC-TCAATACTATT
* * *
2412380 AAATTAAAAATAATATTTATCTCAATATTATT
1 AAATTTAAGATAATATTTATCTCAATACTATT
2412412 AAATTTAAGATAA
1 AAATTTAAGATAA
2412425 AAAATTATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
31 1 0.03
32 36 0.97
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (32 bp):
AAATTTAAGATAATATTTATCTCAATACTATT
Found at i:2412453 original size:3 final size:3
Alignment explanation
Indices: 2412445--2412478 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2412435 TATAACAATG
2412445 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2412479 TAAACGCACC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2413010 original size:23 final size:22
Alignment explanation
Indices: 2412952--2413013 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
2412942 AATTGAGTTA
* **
2412952 TAATTTAAAAGTTTACATATTTT
1 TAATTT-AAAGTTTAAATAGATT
*
2412975 TTATTTAAA-TTTAAATAGATT
1 TAATTTAAAGTTTAAATAGATT
2412996 TAATTTGAAAGTTTAAAT
1 TAATTT-AAAGTTTAAAT
2413014 TATTATTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 14 0.44
22 6 0.19
23 12 0.38
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (22 bp):
TAATTTAAAGTTTAAATAGATT
Found at i:2413099 original size:15 final size:15
Alignment explanation
Indices: 2413079--2413119 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
2413069 TATTACATAG
2413079 TAATTCAAATTGAAT
1 TAATTCAAATTGAAT
2413094 TAATTCAAATTGAAT
1 TAATTCAAATTGAAT
*
2413109 CAATTCAAATT
1 TAATTCAAATT
2413120 AAAAAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (15 bp):
TAATTCAAATTGAAT
Found at i:2413524 original size:3 final size:3
Alignment explanation
Indices: 2413516--2413544 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2413506 ATTAGATTTT
2413516 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2413545 GAGTTGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2413820 original size:2 final size:2
Alignment explanation
Indices: 2413813--2413848 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2413803 CATTGCACTG
2413813 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
2413849 GTATGTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2414771 original size:28 final size:28
Alignment explanation
Indices: 2414723--2414781 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
2414713 TTTTATTTAT
2414723 ATTTTTAATATATCTTAAAAA-TAAAATA
1 ATTTTTAATATATCTTAAAAATTAAAA-A
* *
2414751 ATTTTTAATTTA-CTTGTAAAATTAAAAA
1 ATTTTTAATATATCTT-AAAAATTAAAAA
2414779 ATT
1 ATT
2414782 ATACCATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 19 0.70
29 5 0.19
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (28 bp):
ATTTTTAATATATCTTAAAAATTAAAAA
Found at i:2418533 original size:20 final size:20
Alignment explanation
Indices: 2418496--2418534 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2418486 CTAATATTTT
*
2418496 TAATCAACAAAACTTAATTA
1 TAATCAACAAAAATTAATTA
2418516 TAAT-AACAAAAATATAATT
1 TAATCAACAAAAAT-TAATT
2418535 TTACATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (20 bp):
TAATCAACAAAAATTAATTA
Found at i:2420889 original size:2 final size:2
Alignment explanation
Indices: 2420882--2420928 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2420872 AATCTTACCT
2420882 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2420924 TA TA T
1 TA TA T
2420929 GTATGACAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2422778 original size:2 final size:2
Alignment explanation
Indices: 2422767--2422798 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2422757 ATTGTTTTAT
2422767 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2422799 TAAAATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2422938 original size:3 final size:3
Alignment explanation
Indices: 2422917--2422959 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
2422907 AAGTTAAATA
* *
2422917 TAT TAT TAC TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2422960 TTAAAGTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2424845 original size:23 final size:23
Alignment explanation
Indices: 2424802--2424846 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2424792 AGTCATTTTA
* *
2424802 CAATATATAATATTTGGTAATTT
1 CAATATATAATATATGATAATTT
2424825 CAATATATATATATAT-ATAATT
1 CAATATATA-ATATATGATAATT
2424847 ATTTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (23 bp):
CAATATATAATATATGATAATTT
Found at i:2424926 original size:18 final size:18
Alignment explanation
Indices: 2424903--2424937 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2424893 AATAATTTTG
*
2424903 ATATATATTTATCAATAA
1 ATATATAATTATCAATAA
2424921 ATATATAATTATCAATA
1 ATATATAATTATCAATA
2424938 TATGATTTAA
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:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATAATTATCAATAA
Found at i:2425215 original size:27 final size:26
Alignment explanation
Indices: 2425185--2425271 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 26
2425175 ATTTTAATTG
2425185 AATTTAATATAAATAAATAAAAATATT
1 AATTTAATATAAATAAATAAAAATA-T
*
2425212 AATTTAAT-TAAAAAATATAAAAATAAT
1 AATTTAATATAAATAA-ATAAAAAT-AT
* * *
2425239 ATTTTATAAATTAAATTAAATAATAATAT
1 AATTTA-ATA-TAAA-TAAATAAAAATAT
2425268 AATT
1 AATT
2425272 GGGTCAAGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
26 6 0.12
27 22 0.46
28 2 0.04
29 5 0.10
30 11 0.23
31 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
AATTTAATATAAATAAATAAAAATAT
Found at i:2433074 original size:2 final size:2
Alignment explanation
Indices: 2433067--2433105 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2433057 TAGAACCGAC
2433067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2433106 TTTTAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2434973 original size:2 final size:2
Alignment explanation
Indices: 2434966--2434994 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2434956 AGTTGTCTTC
2434966 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 A
2434995 AACAAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2438404 original size:2 final size:2
Alignment explanation
Indices: 2438397--2438435 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
2438387 AAAGGCAAAT
2438397 TA TA TA TA TA TA TA TA TA TA -A T- TA -A T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2438435 T
1 T
2438436 GTGTATAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.12
2 29 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2438867 original size:14 final size:14
Alignment explanation
Indices: 2438850--2438894 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
2438840 ATTAAAAATC
2438850 TAAATACTAAATTT
1 TAAATACTAAATTT
**
2438864 TAAATTTTAAATTT
1 TAAATACTAAATTT
* *
2438878 TGAATCCTAAATTT
1 TAAATACTAAATTT
2438892 TAA
1 TAA
2438895 TCCCGAACTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (14 bp):
TAAATACTAAATTT
Found at i:2439524 original size:15 final size:15
Alignment explanation
Indices: 2439462--2439526 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
2439452 ATTTTTTCAT
2439462 TATATAAATATTAAA
1 TATATAAATATTAAA
*
2439477 TATATTAAA-ATTTTAA
1 TATA-TAAATA-TTAAA
*
2439493 -ATACAAATA-TAATA
1 TATATAAATATTAA-A
*
2439507 TATATATATATTAAA
1 TATATAAATATTAAA
2439522 TATAT
1 TATAT
2439527 CGAATCATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
13 2 0.05
14 4 0.10
15 22 0.56
16 11 0.28
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TATATAAATATTAAA
Found at i:2440405 original size:2 final size:2
Alignment explanation
Indices: 2440361--2440394 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2440351 ATGGCACTAA
2440361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2440395 ACATGTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2441537 original size:34 final size:36
Alignment explanation
Indices: 2441499--2441586 Score: 110
Period size: 37 Copynumber: 2.5 Consensus size: 36
2441489 TCAAACTTTC
*
2441499 TTGACATCCCACGACTCTCT-T-TAATC-AAATTATG
1 TTGACATCCCACGACTCT-TATATAATCAAAACTATG
* *
2441533 TTGACATCCCACGACTCTTATATAATCAAAAACTCTT
1 TTGACATCCCACGACTCTTATATAATC-AAAACTATG
2441570 TTGACATCCCACGACTC
1 TTGACATCCCACGACTC
2441587 ATGATTGCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
33 1 0.02
34 19 0.40
35 5 0.11
37 22 0.47
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.32
Consensus pattern (36 bp):
TTGACATCCCACGACTCTTATATAATCAAAACTATG
Found at i:2441583 original size:37 final size:33
Alignment explanation
Indices: 2441487--2441586 Score: 114
Period size: 34 Copynumber: 2.8 Consensus size: 33
2441477 AACTCAACAA
2441487 AATCAAACTTTCTTGACATCCCACGACTCTCTTT
1 AATCAAACTTT-TTGACATCCCACGACTCTCTTT
2441521 AATCAAA-TTATGTTGACATCCCACGACTCT-TATAT
1 AATCAAACTT-T-TTGACATCCCACGACTCTCT-T-T
2441556 AATCAAAAACTCTTTTGACATCCCACGACTC
1 AATC--AAACT-TTTTGACATCCCACGACTC
2441587 ATGATTGCTT
Statistics
Matches: 58, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
33 3 0.05
34 27 0.47
35 5 0.09
37 20 0.34
38 2 0.03
39 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (33 bp):
AATCAAACTTTTTGACATCCCACGACTCTCTTT
Found at i:2442296 original size:30 final size:29
Alignment explanation
Indices: 2442262--2442320 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
2442252 CAGGAATGAA
*
2442262 TGAATTTATAA-TAACATTTTTAAAATTTTG
1 TGAATTTAAAATTAA-A-TTTTAAAATTTTG
2442292 TGAATTTAAAATTTAAATTTTAAAATTTT
1 TGAATTTAAAA-TTAAATTTTAAAATTTT
2442321 AAGATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 22 0.85
31 1 0.04
32 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (29 bp):
TGAATTTAAAATTAAATTTTAAAATTTTG
Found at i:2443563 original size:17 final size:19
Alignment explanation
Indices: 2443541--2443577 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
2443531 GAGTTGAATT
2443541 ATTTTTTTAA-ATTT-AAA
1 ATTTTTTTAATATTTGAAA
2443558 ATTTTTTTAATATTTGAAA
1 ATTTTTTTAATATTTGAAA
2443577 A
1 A
2443578 GATTTTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 4 0.22
19 4 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTTTTTTAATATTTGAAA
Found at i:2447178 original size:18 final size:18
Alignment explanation
Indices: 2447155--2447197 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
2447145 TAAAAATTGA
*
2447155 AAAAAAATGGTAATTATG
1 AAAAAAATGGTAATTAAG
2447173 AAAAAAA-GGTAATTAAG
1 AAAAAAATGGTAATTAAG
*
2447190 ATAAAAAT
1 AAAAAAAT
2447198 TGCAGCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (18 bp):
AAAAAAATGGTAATTAAG
Found at i:2447521 original size:15 final size:16
Alignment explanation
Indices: 2447490--2447522 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2447480 AATTTTTTAA
2447490 ATATAGATTTGATATT
1 ATATAGATTTGATATT
*
2447506 ATATTGATTT-ATATT
1 ATATAGATTTGATATT
2447521 AT
1 AT
2447523 TCTATATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (16 bp):
ATATAGATTTGATATT
Found at i:2448017 original size:6 final size:6
Alignment explanation
Indices: 2447991--2448033 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
2447981 ATAGATTATT
* * *
2447991 ATATAG ACATTG ATATGG ATATAG ATATAG ATATAG ATATAG A
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG A
2448034 GATAATTACA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:2450231 original size:3 final size:3
Alignment explanation
Indices: 2450223--2450254 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2450213 AAAGAAAATG
2450223 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2450255 TTTAAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2451381 original size:20 final size:20
Alignment explanation
Indices: 2451358--2451397 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2451348 TTTTTGTTTG
* *
2451358 AATTTTTATTTTTTTTATTA
1 AATTTGTATTATTTTTATTA
*
2451378 AATTTGTGTTATTTTTATTA
1 AATTTGTATTATTTTTATTA
2451398 TAATCGAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
AATTTGTATTATTTTTATTA
Found at i:2453096 original size:21 final size:21
Alignment explanation
Indices: 2453070--2453111 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2453060 TATGTTATTT
2453070 TTATTT-AAAATAAATTAATTA
1 TTATTTGAAAA-AAATTAATTA
*
2453091 TTATTTGAAAAAAATTGATTA
1 TTATTTGAAAAAAATTAATTA
2453112 AATGAAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
TTATTTGAAAAAAATTAATTA
Found at i:2455491 original size:18 final size:18
Alignment explanation
Indices: 2455468--2455515 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
2455458 ATTATTAAAT
* *
2455468 TTAAAAATTACTCATTTC
1 TTAAAAATTACACACTTC
*
2455486 TTAAAAAAATTTCACACTTC
1 TT--AAAAATTACACACTTC
2455506 TTAAAAATTA
1 TTAAAAATTA
2455516 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 9 0.38
20 15 0.62
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAAATTACACACTTC
Found at i:2455495 original size:20 final size:20
Alignment explanation
Indices: 2455470--2455512 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2455460 TATTAAATTT
* *
2455470 AAAAATTACTCATTTCTTAA
1 AAAAATTACACACTTCTTAA
*
2455490 AAAAATTTCACACTTCTTAA
1 AAAAATTACACACTTCTTAA
2455510 AAA
1 AAA
2455513 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATTACACACTTCTTAA
Found at i:2462100 original size:38 final size:39
Alignment explanation
Indices: 2462022--2462100 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 39
2462012 ATTACAATAT
* * * *
2462022 AATTTTTAAAATAATTAAATTATTACCACCCTTAATTTA
1 AATTTTAAAAATAATTAAATAATTACCAACCTTAAATTA
**
2462061 AATTTTAAAAATAATTAAATAATTA-CAATTTTAAATTA
1 AATTTTAAAAATAATTAAATAATTACCAACCTTAAATTA
2462099 AA
1 AA
2462101 AGTTAAAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 11 0.32
39 23 0.68
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (39 bp):
AATTTTAAAAATAATTAAATAATTACCAACCTTAAATTA
Found at i:2462107 original size:38 final size:39
Alignment explanation
Indices: 2462029--2462108 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 39
2462019 TATAATTTTT
* * * **
2462029 AAAATAATTAAATTATTACCACCCTTAATTTAAATTTTA
1 AAAATAATTAAATAATTACCAACCTTAAATTAAAAGTTA
**
2462068 AAAATAATTAAATAATTA-CAATTTTAAATTAAAAGTTA
1 AAAATAATTAAATAATTACCAACCTTAAATTAAAAGTTA
2462106 AAA
1 AAA
2462109 CTAAATATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
38 17 0.50
39 17 0.50
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (39 bp):
AAAATAATTAAATAATTACCAACCTTAAATTAAAAGTTA
Found at i:2462512 original size:29 final size:30
Alignment explanation
Indices: 2462473--2462534 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
2462463 TGGTTCAAAA
2462473 TAATAATATTTTAATAATTTATTT-TAAAT
1 TAATAATATTTTAATAATTTATTTATAAAT
* *
2462502 TAATATTATTTTAATAATTTGTTTATAAAT
1 TAATAATATTTTAATAATTTATTTATAAAT
2462532 TAA
1 TAA
2462535 AAACACGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TAATAATATTTTAATAATTTATTTATAAAT
Found at i:2465794 original size:96 final size:96
Alignment explanation
Indices: 2465651--2465835 Score: 343
Period size: 96 Copynumber: 1.9 Consensus size: 96
2465641 TCGTAGCCGT
*
2465651 AGAGAGGATTTTGTGCACAAAACATGTTTGTCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
1 AGAGAGGATTTTGTGCACAAAACATGTTTGCCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
2465716 ATGTGAGATGCTTTGAAGGATTCTTTGCCTA
66 ATGTGAGATGCTTTGAAGGATTCTTTGCCTA
* *
2465747 AGAGAGGATTTTGTGCATAAAACATGTTTGCCAAAATGTCTTATAGACAGAATTGCTTTGTTTAG
1 AGAGAGGATTTTGTGCACAAAACATGTTTGCCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
2465812 ATGTGAGATGCTTTGAAGGATTCT
66 ATGTGAGATGCTTTGAAGGATTCT
2465836 GTTTTAAGTT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 86 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (96 bp):
AGAGAGGATTTTGTGCACAAAACATGTTTGCCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
ATGTGAGATGCTTTGAAGGATTCTTTGCCTA
Found at i:2466379 original size:29 final size:29
Alignment explanation
Indices: 2466313--2466379 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
2466303 AATAAAGACT
*
2466313 CAAAGCATAGTAAATATAACCTCATAAAG
1 CAAAGCATTGTAAATATAACCTCATAAAG
*
2466342 CAAAGCATTGTAAATATAACCTTATAAAG
1 CAAAGCATTGTAAATATAACCTCATAAAG
*
2466371 CATAGCATT
1 CAAAGCATT
2466380 ATGTAGATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.25
Consensus pattern (29 bp):
CAAAGCATTGTAAATATAACCTCATAAAG
Found at i:2470422 original size:96 final size:96
Alignment explanation
Indices: 2470279--2470463 Score: 343
Period size: 96 Copynumber: 1.9 Consensus size: 96
2470269 TCGTAGCCGT
*
2470279 AGAGAGGATTTTGTGCACAAAACATGTTTGTCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
1 AGAGAGGATTTTGTGCACAAAACATGTTTGCCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
2470344 ATGTGAGATGCTTTGAAGGATTCTTTGCCTA
66 ATGTGAGATGCTTTGAAGGATTCTTTGCCTA
* *
2470375 AGAGAGGATTTTGTGCATAAAACATGTTTGCCAAAATGTCTTATAGACAGAATTGCTTTGTTTAG
1 AGAGAGGATTTTGTGCACAAAACATGTTTGCCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
2470440 ATGTGAGATGCTTTGAAGGATTCT
66 ATGTGAGATGCTTTGAAGGATTCT
2470464 GTTTTAAGTT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 86 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (96 bp):
AGAGAGGATTTTGTGCACAAAACATGTTTGCCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
ATGTGAGATGCTTTGAAGGATTCTTTGCCTA
Found at i:2471007 original size:29 final size:29
Alignment explanation
Indices: 2470941--2471007 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
2470931 AATAAAGACT
*
2470941 CAAAGCATAGTAAATATAACCTCATAAAG
1 CAAAGCATTGTAAATATAACCTCATAAAG
*
2470970 CAAAGCATTGTAAATATAACCTTATAAAG
1 CAAAGCATTGTAAATATAACCTCATAAAG
*
2470999 CATAGCATT
1 CAAAGCATT
2471008 ATGTAGATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.25
Consensus pattern (29 bp):
CAAAGCATTGTAAATATAACCTCATAAAG
Found at i:2475050 original size:96 final size:96
Alignment explanation
Indices: 2474907--2475091 Score: 343
Period size: 96 Copynumber: 1.9 Consensus size: 96
2474897 TCGTAGCCGT
*
2474907 AGAGAGGATTTTGTGCACAAAACATGTTTGTCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
1 AGAGAGGATTTTGTGCACAAAACATGTTTGCCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
2474972 ATGTGAGATGCTTTGAAGGATTCTTTGCCTA
66 ATGTGAGATGCTTTGAAGGATTCTTTGCCTA
* *
2475003 AGAGAGGATTTTGTGCATAAAACATGTTTGCCAAAATGTCTTATAGACAGAATTGCTTTGTTTAG
1 AGAGAGGATTTTGTGCACAAAACATGTTTGCCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
2475068 ATGTGAGATGCTTTGAAGGATTCT
66 ATGTGAGATGCTTTGAAGGATTCT
2475092 GTTTTAAGTT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 86 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (96 bp):
AGAGAGGATTTTGTGCACAAAACATGTTTGCCAAAATGTCTCATAGACAGAATTGCTTTGTTTAG
ATGTGAGATGCTTTGAAGGATTCTTTGCCTA
Found at i:2475635 original size:29 final size:29
Alignment explanation
Indices: 2475569--2475635 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
2475559 AATAAAGACT
*
2475569 CAAAGCATAGTAAATATAACCTCATAAAG
1 CAAAGCATTGTAAATATAACCTCATAAAG
*
2475598 CAAAGCATTGTAAATATAACCTTATAAAG
1 CAAAGCATTGTAAATATAACCTCATAAAG
*
2475627 CATAGCATT
1 CAAAGCATT
2475636 ATGTAGATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.25
Consensus pattern (29 bp):
CAAAGCATTGTAAATATAACCTCATAAAG
Found at i:2481267 original size:7 final size:7
Alignment explanation
Indices: 2481257--2481287 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2481247 ACAAACCAGA
2481257 AAAAAAC
1 AAAAAAC
2481264 AAAAAAC
1 AAAAAAC
2481271 AAAAAA-
1 AAAAAAC
2481277 AAAAAAC
1 AAAAAAC
2481284 AAAA
1 AAAA
2481288 GAAATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:2481280 original size:13 final size:14
Alignment explanation
Indices: 2481257--2481287 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
2481247 ACAAACCAGA
2481257 AAAAAACAAAAAAC
1 AAAAAACAAAAAAC
2481271 AAAAAA-AAAAAAC
1 AAAAAACAAAAAAC
2481284 AAAA
1 AAAA
2481288 GAAATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAACAAAAAAC
Found at i:2481538 original size:2 final size:2
Alignment explanation
Indices: 2481531--2481570 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2481521 AGTACTCAAG
2481531 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
2481571 GTAACAAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2483058 original size:22 final size:21
Alignment explanation
Indices: 2483027--2483082 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
2483017 TTTATATTAA
2483027 AAATAT-ATTTATATAAATTAT
1 AAATATAATTTATATAAA-TAT
* *
2483048 AATTATAATTTTTTATAAATAT
1 AAATATAA-TTTATATAAATAT
*
2483070 AAATATATTTTAT
1 AAATATAATTTAT
2483083 CACTCCTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 9 0.32
22 10 0.36
23 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATATAATTTATATAAATAT
Found at i:2483478 original size:12 final size:11
Alignment explanation
Indices: 2483441--2483491 Score: 66
Period size: 12 Copynumber: 4.4 Consensus size: 11
2483431 TAAAGAAAAT
2483441 ATAATTATATA
1 ATAATTATATA
*
2483452 ATAGTTATATGA
1 ATAATTATAT-A
2483464 ATAATATATATA
1 ATAAT-TATATA
2483476 ATAAATTATATA
1 AT-AATTATATA
2483488 ATAA
1 ATAA
2483492 ATACATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 11 0.31
12 16 0.46
13 8 0.23
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (11 bp):
ATAATTATATA
Found at i:2484088 original size:24 final size:23
Alignment explanation
Indices: 2484029--2484090 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
2484019 AAACTTTATA
* *
2484029 TATATTTTTATATTTTAATAATT
1 TATATATTTATATTTTAACAATT
* * *
2484052 TATTTTATATATATTTTAACACGTT
1 TA-TATATTTATATTTTAACA-ATT
2484077 TATATATTTATATT
1 TATATATTTATATT
2484091 CGATTCGTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 2 0.07
24 24 0.80
25 4 0.13
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (23 bp):
TATATATTTATATTTTAACAATT
Found at i:2484736 original size:51 final size:52
Alignment explanation
Indices: 2484606--2484744 Score: 163
Period size: 51 Copynumber: 2.7 Consensus size: 52
2484596 TCTGGAAAGA
* * * * *
2484606 AAATGTATCAATACATTTTTCATTGTATCAATACATTCTAGGTTTTTGACTC
1 AAATATATCAATACATTATTCATTGTATCGATACATTCTAAGTTTTTGACCC
* * ** *
2484658 AAATATATCAAAACATTCTTTTTTGTATTGATACATTCTAAG-TTTTGACCC
1 AAATATATCAATACATTATTCATTGTATCGATACATTCTAAGTTTTTGACCC
* *
2484709 AAATATATCGATACATTATTCAATGTATCGATACAT
1 AAATATATCAATACATTATTCATTGTATCGATACAT
2484745 GTAGGCAAAT
Statistics
Matches: 71, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
51 37 0.52
52 34 0.48
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.42
Consensus pattern (52 bp):
AAATATATCAATACATTATTCATTGTATCGATACATTCTAAGTTTTTGACCC
Found at i:2487729 original size:80 final size:80
Alignment explanation
Indices: 2487607--2487767 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
2487597 TAAATATTTC
*
2487607 GTATCAAGTACTGAAAAGATACTAACACGGAACATTACTTTTTTTATTTTTGTAAACAACTTTTA
1 GTATCAAGTACTGAAAAGATACCAACACGGAACATTACTTTTTTTATTTTTGTAAACAACTTTTA
2487672 AAACATGAATACATG
66 AAACATGAATACATG
2487687 GTATCAAGTACTGAAAAGATACCAACACGGAACATTACTTTTTTTATTTTTGTAAACAACTTTTA
1 GTATCAAGTACTGAAAAGATACCAACACGGAACATTACTTTTTTTATTTTTGTAAACAACTTTTA
2487752 AAACATGAATACATG
66 AAACATGAATACATG
2487767 G
1 G
2487768 AATATTACTG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (80 bp):
GTATCAAGTACTGAAAAGATACCAACACGGAACATTACTTTTTTTATTTTTGTAAACAACTTTTA
AAACATGAATACATG
Found at i:2489263 original size:38 final size:41
Alignment explanation
Indices: 2489162--2489244 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
2489152 AGGATAAGTA
2489162 AATTGTCTTAACCCAAGTATTCTTAAGTGTTTTGATTTCTC
1 AATTGTCTTAACCCAAGTATTCTTAAGTGTTTTGATTTCTC
2489203 AATTGTCTTAACCCAAGTATTCTTAAGTGTTTTGATTTCTC
1 AATTGTCTTAACCCAAGTATTCTTAAGTGTTTTGATTTCTC
2489244 A
1 A
2489245 TGTTTAACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (41 bp):
AATTGTCTTAACCCAAGTATTCTTAAGTGTTTTGATTTCTC
Found at i:2489924 original size:32 final size:32
Alignment explanation
Indices: 2489879--2489944 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
2489869 AATCGGAGGT
* *
2489879 AGAAGTTCCGGTTTCATCTACAAACTAAACGC
1 AGAAGTTCCGGTTTCAACTACAAACCAAACGC
* *
2489911 AGAAGTTCTGGTTTCAACTACAAACCAAAGGC
1 AGAAGTTCCGGTTTCAACTACAAACCAAACGC
2489943 AG
1 AG
2489945 GATCAAACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (32 bp):
AGAAGTTCCGGTTTCAACTACAAACCAAACGC
Found at i:2490034 original size:2 final size:2
Alignment explanation
Indices: 2490027--2490052 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2490017 CAGTCATAGC
2490027 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
2490053 TGGGTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2490174 original size:2 final size:2
Alignment explanation
Indices: 2490169--2490194 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2490159 TTTTATGTTT
2490169 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
2490195 GCTATGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2490715 original size:2 final size:2
Alignment explanation
Indices: 2490708--2490746 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2490698 CTTTTCTTAT
*
2490708 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2490747 GCTACGCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.