Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2664
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: 105428
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:4368 original size:3 final size:3
Alignment explanation
Indices: 4353--4403 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
4343 TACCTGTTAA
* *
4353 TGT TGT CGT TGT TGT TGT TGT TGC TGT TGT TGT TGT TGTT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG-T TGT TGT
4399 TGT TG
1 TGT TG
4404 CTGCTGCTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.00, C:0.04, G:0.33, T:0.63
Consensus pattern (3 bp):
TGT
Found at i:4576 original size:2 final size:2
Alignment explanation
Indices: 4565--4593 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4555 CAAAAGAACT
4565 TA TA -A 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
4594 AACTTTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5127 original size:20 final size:19
Alignment explanation
Indices: 5082--5127 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
5072 TATTATTTAA
*
5082 ATTAATTTATAAAATAAAT
1 ATTAATTTATAAAAAAAAT
5101 ATT-ATTTATAAAAAATAAT
1 ATTAATTTATAAAAAA-AAT
*
5120 TTTAATTT
1 ATTAATTT
5128 TTTTATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 11 0.48
19 8 0.35
20 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTAATTTATAAAAAAAAT
Found at i:5140 original size:32 final size:32
Alignment explanation
Indices: 5100--5165 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 32
5090 ATAAAATAAA
*
5100 TATTATTTATAAAAAATAA-TTTTAATTTTTT
1 TATTATTTATAAAAAATAACTTTTAAATTTTT
* **
5131 TATTAATTTATTATTAATAACTTTTAAATTTTT
1 TATT-ATTTATAAAAAATAACTTTTAAATTTTT
5164 TA
1 TA
5166 AAAAAAATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 4 0.14
32 12 0.41
33 13 0.45
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (32 bp):
TATTATTTATAAAAAATAACTTTTAAATTTTT
Found at i:6166 original size:8 final size:8
Alignment explanation
Indices: 6148--6273 Score: 59
Period size: 8 Copynumber: 15.6 Consensus size: 8
6138 AAATATACGA
6148 AAATAATAT
1 AAAT-ATAT
6157 AAATATAT
1 AAATATAT
*
6165 AAATATTTTT
1 AAATA--TAT
*
6175 AAA-ATTT
1 AAATATAT
*
6182 ATATAATAT
1 AAAT-ATAT
6191 AAAT-TAT
1 AAATATAT
*
6198 TAATATAT
1 AAATATAT
*
6206 ATA-ATAT
1 AAATATAT
6213 AAATATAT
1 AAATATAT
6221 -AATACT-T
1 AAATA-TAT
6228 AAATAT-T
1 AAATATAT
*
6235 -ATTATATT
1 AAATATA-T
*
6243 AAATACAT
1 AAATATAT
6251 AAAATAATAT
1 -AAAT-ATAT
6261 AAATATAT
1 AAATATAT
*
6269 GAATA
1 AAATA
6274 AAAAAATTAA
Statistics
Matches: 91, Mismatches: 13, Indels: 27
0.69 0.10 0.21
Matches are distributed among these distances:
6 4 0.04
7 24 0.26
8 32 0.35
9 23 0.25
10 8 0.09
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (8 bp):
AAATATAT
Found at i:6209 original size:22 final size:22
Alignment explanation
Indices: 6181--6224 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
6171 TTTTAAAATT
6181 TATATAATATAAAT-TATTAATA
1 TATATAATATAAATATA-TAATA
6203 TATATAATATAAATATATAATA
1 TATATAATATAAATATATAATA
6225 CTTAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATAATATAAATATATAATA
Found at i:6230 original size:15 final size:14
Alignment explanation
Indices: 6186--6252 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 14
6176 AAATTTATAT
6186 AATATA-AATTATTA
1 AATATATAA-TATTA
6200 ATATATATAATA-TA
1 A-ATATATAATATTA
6214 AATATATAATACTTA
1 AATATATAATA-TTA
*
6229 AATATTATTATATTA
1 AATA-TATAATATTA
*
6244 AATACATAA
1 AATATATAA
6253 AATAATATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
13 10 0.22
14 7 0.16
15 20 0.44
16 8 0.18
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATATAATATTA
Found at i:6276 original size:22 final size:22
Alignment explanation
Indices: 6184--6273 Score: 67
Period size: 22 Copynumber: 3.9 Consensus size: 22
6174 TAAAATTTAT
*
6184 ATAATATAAAT-TATTAATATAT
1 ATAATATAAATATA-TAATATAA
6206 ATAATATAAATATATAATACTTAA
1 ATAATATAAATATATAATA--TAA
* * *
6230 ATATTATTATATTAAATACATA-AA
1 ATAATA-TA-AATATATA-ATATAA
6254 ATAATATAAATATATGAATA
1 ATAATATAAATATAT-AATA
6274 AAAAAATTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
22 24 0.44
23 5 0.09
24 14 0.26
25 2 0.04
26 6 0.11
27 3 0.06
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (22 bp):
ATAATATAAATATATAATATAA
Found at i:7973 original size:5 final size:5
Alignment explanation
Indices: 7971--8004 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
7961 TTCTTTTTCT
* *
7971 TTTTC TTTTA TTTTC TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
8005 TTTCATCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:7986 original size:10 final size:10
Alignment explanation
Indices: 7971--8004 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
7961 TTCTTTTTCT
7971 TTTTCTTTTA
1 TTTTCTTTTA
7981 TTTTCTTTTA
1 TTTTCTTTTA
*
7991 TTTTATTTTA
1 TTTTCTTTTA
8001 TTTT
1 TTTT
8005 TTTCATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:7994 original size:15 final size:15
Alignment explanation
Indices: 7965--8004 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
7955 CAATTTTTCT
*
7965 TTTTCTTTTTCTTTTA
1 TTTTC-TTTTATTTTA
7981 TTTTCTTTTATTTTA
1 TTTTCTTTTATTTTA
*
7996 TTTTATTTT
1 TTTTCTTTT
8005 TTTCATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTATTTTA
Found at i:9299 original size:24 final size:25
Alignment explanation
Indices: 9267--9327 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 25
9257 TTGTATAATT
9267 TTTTAAAATATAAAAAAATTATA-A
1 TTTTAAAATATAAAAAAATTATAGA
9291 TTTTAAAATAT--AAAAATTATAGA
1 TTTTAAAATATAAAAAAATTATAGA
* *
9314 TATTAAAATTTAAA
1 TTTTAAAATATAAA
9328 CTTTAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 10 0.31
23 10 0.31
24 11 0.34
25 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
TTTTAAAATATAAAAAAATTATAGA
Found at i:9308 original size:22 final size:23
Alignment explanation
Indices: 9267--9327 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
9257 TTGTATAATT
9267 TTTTAAAATATAAAAAAATTATA-A
1 TTTTAAAATAT--AAAAATTATAGA
9291 TTTTAAAATATAAAAATTATAGA
1 TTTTAAAATATAAAAATTATAGA
* *
9314 TATTAAAATTTAAA
1 TTTTAAAATATAAA
9328 CTTTAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 10 0.29
23 13 0.38
24 11 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTTAAAATATAAAAATTATAGA
Found at i:9447 original size:17 final size:16
Alignment explanation
Indices: 9427--9479 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
9417 AATTAATAGT
9427 TAAATTTATTTAATAAA
1 TAAATTT-TTTAATAAA
9444 TAAATATTTTTAATAAA
1 TAAAT-TTTTTAATAAA
* * *
9461 AAAATATTTTAATGAA
1 TAAATTTTTTAATAAA
9477 TAA
1 TAA
9480 GAAGCTCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 11 0.35
17 18 0.58
18 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TAAATTTTTTAATAAA
Found at i:9473 original size:16 final size:17
Alignment explanation
Indices: 9435--9470 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
9425 GTTAAATTTA
*
9435 TTTAATAAATAAATATT
1 TTTAATAAAAAAATATT
9452 TTTAATAAAAAAATATT
1 TTTAATAAAAAAATATT
9469 TT
1 TT
9471 AATGAATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAATAAAAAAATATT
Found at i:10844 original size:3 final size:3
Alignment explanation
Indices: 10838--10877 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
10828 TGAAAAAAAT
10838 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10878 AAGTTGGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12355 original size:2 final size:2
Alignment explanation
Indices: 12350--12379 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12340 TGACACACAA
*
12350 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12380 TACAATAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12533 original size:11 final size:11
Alignment explanation
Indices: 12517--12541 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12507 ATATTCAAAA
12517 ATAATTTAAAT
1 ATAATTTAAAT
12528 ATAATTTAAAT
1 ATAATTTAAAT
12539 ATA
1 ATA
12542 TTAATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATAATTTAAAT
Found at i:12555 original size:17 final size:19
Alignment explanation
Indices: 12533--12569 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12523 TAAATATAAT
12533 TTAAA-TATAT-TAATATA
1 TTAAATTATATATAATATA
*
12550 TTAAATTTTATATAATATA
1 TTAAATTATATATAATATA
12569 T
1 T
12570 ATTATTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAATTATATATAATATA
Found at i:14731 original size:19 final size:18
Alignment explanation
Indices: 14683--14807 Score: 60
Period size: 18 Copynumber: 6.6 Consensus size: 18
14673 TCGTTTTCAT
*
14683 ATTTATATATTTTT--AT
1 ATTTATATATTTTTAAAA
14699 ATGTTATA-ATTTTTTAAAA
1 AT-TTATATA-TTTTTAAAA
*
14718 ATATTATATATTTTTATAA
1 AT-TTATATATTTTTAAAA
* * *
14737 ATTTTTTTATTTTTATAA
1 ATTTATATATTTTTAAAA
* *
14755 TTTATAATATATAAATTTTAATAC
1 ATT-T-ATATAT---TTTTAA-AA
*
14779 ATTTATATA-TTTTAATAC
1 ATTTATATATTTTTAA-AA
14797 ATTTATATATT
1 ATTTATATATT
14808 CATATCGTAT
Statistics
Matches: 86, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
16 3 0.03
17 10 0.12
18 34 0.40
19 20 0.23
20 5 0.06
22 5 0.06
23 6 0.07
24 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (18 bp):
ATTTATATATTTTTAAAA
Found at i:14790 original size:18 final size:18
Alignment explanation
Indices: 14764--14807 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
14754 ATTTATAATA
*
14764 TATAAATTTTAATACATT
1 TATATATTTTAATACATT
14782 TATATATTTTAATACATT
1 TATATATTTTAATACATT
14800 TATATATT
1 TATATATT
14808 CATATCGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATATTTTAATACATT
Found at i:14857 original size:17 final size:17
Alignment explanation
Indices: 14817--14865 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
14807 TCATATCGTA
* *
14817 TTTATATTATTTTTTAT
1 TTTATATTATATTATAT
* *
14834 GTCATATTATATTATAT
1 TTTATATTATATTATAT
*
14851 TTTATATTTTATTAT
1 TTTATATTATATTAT
14866 CATTATTATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATATTATATTATAT
Found at i:14863 original size:22 final size:22
Alignment explanation
Indices: 14818--14883 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
14808 CATATCGTAT
* * **
14818 TTATATTATTTTTTATGTCATA
1 TTATATTATATTTTATATTTTA
14840 TTATATTATATTTTATATTTTA
1 TTATATTATATTTTATATTTTA
14862 TTATCATTATTATTTT-TATTTT
1 TTAT-ATTA-TATTTTATATTTT
14884 TTTACTTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 22 0.58
23 10 0.26
24 6 0.16
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (22 bp):
TTATATTATATTTTATATTTTA
Found at i:19578 original size:19 final size:18
Alignment explanation
Indices: 19546--19583 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19536 TATTATTATT
19546 TTTAATAAAATTAATTAAA
1 TTTAATAAAATTAA-TAAA
19565 TTTAA-AAAATTTAATAAA
1 TTTAATAAAA-TTAATAAA
19583 T
1 T
19584 AATATATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTAATAAAATTAATAAA
Found at i:19784 original size:15 final size:15
Alignment explanation
Indices: 19764--19794 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19754 TATAAAATTA
19764 ATTTAATTTATTTTT
1 ATTTAATTTATTTTT
19779 ATTTAATTTATTTTT
1 ATTTAATTTATTTTT
19794 A
1 A
19795 CATGCATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTAATTTATTTTT
Found at i:19986 original size:24 final size:24
Alignment explanation
Indices: 19942--20011 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
19932 AATTTAAAAA
19942 ATTT-TAAAATCTAATTTATTT-TT
1 ATTTATAAAAT-TAATTTATTTATT
19965 ATTTATAAAATTAATTTAATTTATT
1 ATTTATAAAATTAATTT-ATTTATT
* *
19990 -TTTATGAAATTTATTT-TTTATT
1 ATTTATAAAATTAATTTATTTATT
20012 TTATTGTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 6 0.14
23 10 0.24
24 24 0.57
25 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (24 bp):
ATTTATAAAATTAATTTATTTATT
Found at i:23999 original size:66 final size:70
Alignment explanation
Indices: 23862--24006 Score: 176
Period size: 69 Copynumber: 2.1 Consensus size: 70
23852 TAAAACCCTT
**
23862 TTAAATTTAATTTTTTATTTTAAAAAAATAATTAATATTTTAATTTATTAATGTAAAATTTTTAA
1 TTAAATTTAATTTTTTA-TTTAAAAAAATAATTAATACATTAATTTATTAATGTAAAATTTTTAA
23927 AGTTAA
65 AGTTAA
* * *
23933 TTAAATATT-ATTTTTTA-TTAAAATAATAATTAATACATT-A-TTATTTAT-TAAACTTTTTAA
1 TTAAAT-TTAATTTTTTATTTAAAAAAATAATTAATACATTAATTTATTAATGTAAAATTTTTAA
*
23993 ATTTAA
65 AGTTAA
23999 TT-AATTTA
1 TTAAATTTA
24007 TAAAAAAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
64 2 0.03
65 3 0.05
66 18 0.27
67 7 0.11
68 1 0.02
69 19 0.29
71 14 0.21
72 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (70 bp):
TTAAATTTAATTTTTTATTTAAAAAAATAATTAATACATTAATTTATTAATGTAAAATTTTTAAA
GTTAA
Found at i:24127 original size:14 final size:15
Alignment explanation
Indices: 24108--24155 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
24098 ATATTTGTAA
24108 AAAAAATCTATTT-T
1 AAAAAATCTATTTAT
*
24122 AAAAAATAT-TTTAT
1 AAAAAATCTATTTAT
*
24136 AAAAAACCTATTTAT
1 AAAAAATCTATTTAT
24151 GAAAA
1 -AAAA
24156 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 3 0.11
14 16 0.57
15 5 0.18
16 4 0.14
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (15 bp):
AAAAAATCTATTTAT
Found at i:24497 original size:17 final size:18
Alignment explanation
Indices: 24465--24499 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
24455 TTAAACCAAA
24465 TAAAAGATTAATTTAAGT
1 TAAAAGATTAATTTAAGT
*
24483 TAAAAGCTT-ATTTAAGT
1 TAAAAGATTAATTTAAGT
24500 ACAAACTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (18 bp):
TAAAAGATTAATTTAAGT
Found at i:25057 original size:15 final size:15
Alignment explanation
Indices: 25039--25071 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
25029 AATTGTAAAA
25039 ATAAA-TTTTATCTTT
1 ATAAATTTTTAT-TTT
25054 ATAAATTTTTATTTT
1 ATAAATTTTTATTTT
25069 ATA
1 ATA
25072 CGTAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
ATAAATTTTTATTTT
Found at i:25498 original size:15 final size:14
Alignment explanation
Indices: 25456--25507 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
25446 ATTATATATT
25456 TTATATAAATTTTA
1 TTATATAAATTTTA
*
25470 ATATATTAATAATTTATA
1 TTATA-T-A-AATTT-TA
25488 TTATATAAATTTTA
1 TTATATAAATTTTA
*
25502 ATATAT
1 TTATAT
25508 TTATTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 11 0.35
15 6 0.19
16 2 0.06
17 6 0.19
18 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:25650 original size:2 final size:2
Alignment explanation
Indices: 25643--25684 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
25633 TCTTACAGTT
25643 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
25685 AAGTCTGGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30284 original size:21 final size:20
Alignment explanation
Indices: 30249--30287 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
30239 TGTTTGGACT
*
30249 AAAATAAGAAAAGAAAAAGA
1 AAAATAAAAAAAGAAAAAGA
30269 AAAATAAAACAAAGAAAAA
1 AAAATAAAA-AAAGAAAAA
30288 TGGATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (20 bp):
AAAATAAAAAAAGAAAAAGA
Found at i:30512 original size:194 final size:195
Alignment explanation
Indices: 30171--30531 Score: 503
Period size: 194 Copynumber: 1.9 Consensus size: 195
30161 CATTGACATC
* * * *
30171 GACAAAGAAATTATTAAATTTCACAAATAAATTTTATAAGATAACATATATCTTTAAGTTTAACT
1 GACAAAGAAATAATTAAATTTCACAAACAAAATTTATAAAATAACATATATCTTTAAGTTTAACT
*
30236 CTATGTTTGGACTAAAATAAGAAAAGAAAAAGAAAAATAAAACAAAGAAAAATGGATTTCTTTCT
66 CTATGTTTGGACTAAAATAAGAAAAGAAAAAGAAAAATAAAACAAAGAAAAATGGATTCCTTTCT
* *
30301 TTTATTGGGGTAA-TTTTTTTATCCAAGGGAAAGTAAGGAGAGTTGAGTATCTCTTGTATTCATT
131 CTTATTGGGATAATTTTTTTTATCCAAGGGAAAGTAAGGAGAGTTGAGTATCTCTTGTATTCATT
* * *
30365 GACAATGAAATAATTAAATTTCACAAACAAAATTTGTAAAATAACATATATTTTTAAGTTTAACT
1 GACAAAGAAATAATTAAATTTCACAAACAAAATTTATAAAATAACATATATCTTTAAGTTTAACT
* * ** ** * *
30430 TTATGTTTGGATTAAGGTAA-AGAAAGGCAAAGTAAAGTAAAACAAAGAAAAA-GAGATTCCTTT
66 CTATGTTTGGACTAAAATAAGA-AAAGAAAAAGAAAAATAAAACAAAGAAAAATG-GATTCCTTT
* *
30493 CTCTTGTTTGGATAATTTTTTTTATCCAAGGGAAAGTAA
129 CTCTTATTGGGATAATTTTTTTTATCCAAGGGAAAGTAA
30532 AAGGAGTTAA
Statistics
Matches: 144, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
193 2 0.01
194 119 0.83
195 23 0.16
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (195 bp):
GACAAAGAAATAATTAAATTTCACAAACAAAATTTATAAAATAACATATATCTTTAAGTTTAACT
CTATGTTTGGACTAAAATAAGAAAAGAAAAAGAAAAATAAAACAAAGAAAAATGGATTCCTTTCT
CTTATTGGGATAATTTTTTTTATCCAAGGGAAAGTAAGGAGAGTTGAGTATCTCTTGTATTCATT
Found at i:31710 original size:10 final size:9
Alignment explanation
Indices: 31672--31717 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 9
31662 GTGAATCTAA
31672 ATATTTTTT
1 ATATTTTTT
31681 ATA-TTTTT
1 ATATTTTTT
*
31689 AT-TTTATT
1 ATATTTTTT
31697 ATAATTTTTT
1 AT-ATTTTTT
31707 ATAATTTTTT
1 AT-ATTTTTT
31717 A
1 A
31718 ATTAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 13 0.41
9 3 0.09
10 16 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
ATATTTTTT
Found at i:35146 original size:29 final size:27
Alignment explanation
Indices: 35114--35167 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 27
35104 ATATTAGTAT
*
35114 ATTATATTTATATAATTTTTTATATTTTA
1 ATTATATTTA-A-AATATTTTATATTTTA
35143 ATTATATTTAAAATATTTTATATTT
1 ATTATATTTAAAATATTTTATATTT
35168 ATATAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.54
28 1 0.04
29 10 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTATATTTAAAATATTTTATATTTTA
Found at i:35174 original size:20 final size:20
Alignment explanation
Indices: 35135--35174 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
35125 ATAATTTTTT
*
35135 ATATTTTAATTATATTTAAA
1 ATATTTTAATTATATATAAA
35155 ATATTTTATATT-TATATAAA
1 ATATTTTA-ATTATATATAAA
35175 TTTTGATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTTTAATTATATATAAA
Found at i:35236 original size:25 final size:24
Alignment explanation
Indices: 35185--35238 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
35175 TTTTGATACA
*
35185 TTAATAATTTATATTATATAAATT
1 TTAATAATATATATTATATAAATT
*
35209 TTAA-AATATATATTTATACTATATT
1 TTAATAATATATA-TTATA-TAAATT
35234 TTAAT
1 TTAAT
35239 TATTTTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 7 0.28
24 9 0.36
25 9 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATAATATATATTATATAAATT
Found at i:35711 original size:18 final size:17
Alignment explanation
Indices: 35688--35723 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
35678 TTATAAGTTG
*
35688 AAATAAAATTTTTATAAA
1 AAATAAAAATTTTA-AAA
35706 AAATAAAAATTTTAAAA
1 AAATAAAAATTTTAAAA
35723 A
1 A
35724 TAAAATTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAAAATTTTAAAA
Found at i:41542 original size:15 final size:15
Alignment explanation
Indices: 41522--41556 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
41512 AACCAAGCAA
41522 ATATACATAATATAC
1 ATATACATAATATAC
*
41537 ATATACATAATATAT
1 ATATACATAATATAC
41552 ATATA
1 ATATA
41557 TATATACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATACATAATATAC
Found at i:42208 original size:2 final size:2
Alignment explanation
Indices: 42201--42226 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42191 GAAATGAAGG
42201 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
42227 AGGAAAAGAG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:47070 original size:21 final size:21
Alignment explanation
Indices: 47045--47085 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
47035 ATTAAATTGA
47045 TAAAAT-CTTTAAATTATTAAT
1 TAAAATACTTTAAA-TATTAAT
*
47066 TAAAATATTTTAAATATTAA
1 TAAAATACTTTAAATATTAA
47086 AAATAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAATACTTTAAATATTAAT
Found at i:47093 original size:21 final size:22
Alignment explanation
Indices: 47052--47093 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
47042 TGATAAAATC
*
47052 TTTAAATTATTAATTAAAATAT
1 TTTAAATTATTAATAAAAATAT
47074 TTTAAA-TATTAA-AAATAATA
1 TTTAAATTATTAATAAA-AATA
47094 AATATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.56
22 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAATTATTAATAAAAATAT
Found at i:47102 original size:17 final size:17
Alignment explanation
Indices: 47076--47117 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
47066 TAAAATATTT
47076 TAAATA-TTAA-AAATAA
1 TAAATATTTAATAAA-AA
47092 TAAATATTTAATAAAAA
1 TAAATATTTAATAAAAA
*
47109 TATATATTT
1 TAAATATTT
47118 TAGTTAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 14 0.61
18 3 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATATTTAATAAAAA
Found at i:47331 original size:9 final size:9
Alignment explanation
Indices: 47317--47341 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
47307 AGAATTTATG
47317 AATTTAAAT
1 AATTTAAAT
47326 AATTTAAAT
1 AATTTAAAT
47335 AATTTAA
1 AATTTAA
47342 CTGATCTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTTAAAT
Found at i:47463 original size:17 final size:17
Alignment explanation
Indices: 47441--47508 Score: 50
Period size: 16 Copynumber: 4.0 Consensus size: 17
47431 TAAAAAAAAT
47441 TATTTAATATATATTAA
1 TATTTAATATATATTAA
* *
47458 TATTT-ATATATTTTTA
1 TATTTAATATATATTAA
* * *
47474 TAATTAAATTTAAATTAA
1 T-ATTTAATATATATTAA
*
47492 -ATTTATTATTATATTAA
1 TATTTAATA-TATATTAA
47509 ATAAATCGTG
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
16 15 0.41
17 15 0.41
18 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTAATATATATTAA
Found at i:47491 original size:11 final size:12
Alignment explanation
Indices: 47470--47502 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
47460 TTTATATATT
47470 TTTATAATTAAA
1 TTTATAATTAAA
47482 TTTA-AATTAAA
1 TTTATAATTAAA
*
47493 TTTATTATTA
1 TTTATAATTA
47503 TATTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTATAATTAAA
Found at i:48132 original size:37 final size:38
Alignment explanation
Indices: 48089--48169 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
48079 ATTTAGGTAT
48089 AATTATATAAACATA-ATTTATAAAATAT-AA-AATATA
1 AATTATATAAACATATATTT-TAAAATATAAATAATATA
* *
48125 ATATTATATAAATATATATTTTAAAATTTAAATAATATA
1 A-ATTATATAAACATATATTTTAAAATATAAATAATATA
48164 AATTAT
1 AATTAT
48170 TAATGAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
36 1 0.03
37 20 0.51
38 11 0.28
39 7 0.18
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (38 bp):
AATTATATAAACATATATTTTAAAATATAAATAATATA
Found at i:48322 original size:32 final size:31
Alignment explanation
Indices: 48286--48350 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
48276 TTTCTTATTT
48286 AAATATATTTTTATAATTAATATTAAAAATTA
1 AAATATATTTTTAT-ATTAATATTAAAAATTA
* *
48318 AAATATATTTTTATATTAATATTTATAATTA
1 AAATATATTTTTATATTAATATTAAAAATTA
48349 AA
1 AA
48351 TTTTAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 17 0.55
32 14 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
AAATATATTTTTATATTAATATTAAAAATTA
Found at i:49207 original size:16 final size:18
Alignment explanation
Indices: 49182--49215 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
49172 TTTTTTTTTA
49182 AAAAAGTTTA-TTTATTT
1 AAAAAGTTTATTTTATTT
49199 AAAAA-TTTATTTTATTT
1 AAAAAGTTTATTTTATTT
49216 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
AAAAAGTTTATTTTATTT
Found at i:49229 original size:20 final size:21
Alignment explanation
Indices: 49188--49229 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
49178 TTTAAAAAAG
**
49188 TTTATTTATTTAAAAATTTAT
1 TTTATTTATTTAAAAAAATAT
49209 TTTATTT-TTTAAAAAAATAT
1 TTTATTTATTTAAAAAAATAT
49229 T
1 T
49230 AAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATTTATTTAAAAAAATAT
Found at i:49254 original size:18 final size:19
Alignment explanation
Indices: 49233--49268 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
49223 AAATATTAAA
*
49233 ATATTAA-ATTTTATTTTT
1 ATATTAATATTATATTTTT
49251 ATATTAATATTATATTTT
1 ATATTAATATTATATTTT
49269 ATAAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATATTAATATTATATTTTT
Found at i:49308 original size:17 final size:18
Alignment explanation
Indices: 49262--49328 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 18
49252 TATTAATATT
49262 ATATTTTATAAATAAATTTAA
1 ATATTTTA-AAATAAA-TT-A
49283 ATATTTTTTAAAATAAA-TA
1 ATA--TTTTAAAATAAATTA
*
49302 ATATTTTAAATTAAATTA
1 ATATTTTAAAATAAATTA
*
49320 ATAATTTAA
1 ATATTTTAA
49329 TTTATAAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 11 0.27
18 10 0.24
19 4 0.10
20 1 0.02
21 3 0.07
22 7 0.17
23 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATTTTAAAATAAATTA
Found at i:51907 original size:22 final size:22
Alignment explanation
Indices: 51879--51921 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
51869 AAATATGATT
51879 ATAATATA-ATAAAATATAAAAA
1 ATAATATATAT-AAATATAAAAA
*
51901 ATAATATATATATATATAAAA
1 ATAATATATATAAATATAAAA
51922 TAAAAATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATATATATAAATATAAAAA
Found at i:52474 original size:22 final size:22
Alignment explanation
Indices: 52446--52528 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 22
52436 TTTTATTACA
52446 TTATAATTATATTTAAAATATT
1 TTATAATTATATTTAAAATATT
52468 TTATAATTATATATTAATAAT-TT
1 TTATAATTATAT-TTAA-AATATT
* * *
52491 ATATTATATAAATTTTAAAATATT
1 TTATAAT-TATA-TTTAAAATATT
*
52515 TATATATTTATATT
1 T-TATAATTATATT
52529 ATGCTCATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
22 12 0.25
23 16 0.33
24 15 0.31
25 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATAATTATATTTAAAATATT
Found at i:52505 original size:15 final size:14
Alignment explanation
Indices: 52463--52501 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
52453 TATATTTAAA
*
52463 ATATTTTATAATTAT
1 ATATTATATAATT-T
52478 ATATTA-ATAATTT
1 ATATTATATAATTT
52491 ATATTATATAA
1 ATATTATATAA
52502 ATTTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 7 0.32
14 10 0.45
15 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATTATATAATTT
Found at i:55433 original size:14 final size:14
Alignment explanation
Indices: 55412--55446 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
55402 TAATATTTAA
55412 TAAA-TTTAAAATT
1 TAAATTTTAAAATT
*
55425 TAAATTTTAATATT
1 TAAATTTTAAAATT
55439 TAAATTTT
1 TAAATTTT
55447 TATTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAAATTTTAAAATT
Found at i:56190 original size:21 final size:19
Alignment explanation
Indices: 56152--56206 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
56142 ATTGTTGATC
56152 TAAT-TAAAA-AA-TATTT
1 TAATATAAAATAATTATTT
*
56168 AAATATAAAATATATTATTT
1 TAATATAAAATA-ATTATTT
*
56188 TAATATTAAATAATTATTT
1 TAATATAAAATAATTATTT
56207 ATTTTAGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.09
17 5 0.16
18 1 0.03
19 8 0.25
20 15 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATATAAAATAATTATTT
Found at i:56192 original size:20 final size:19
Alignment explanation
Indices: 56163--56207 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
56153 AATTAAAAAA
56163 TATTTAAATATAAAATATAT
1 TATTTAAATATAAAATA-AT
* *
56183 TATTTTAATATTAAATAAT
1 TATTTAAATATAAAATAAT
56202 TATTTA
1 TATTTA
56208 TTTTAGTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTAAATATAAAATAAT
Found at i:56330 original size:12 final size:11
Alignment explanation
Indices: 56307--56340 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
56297 AGATCTTATT
56307 AATT-ATAAAA
1 AATTAATAAAA
56317 AATTAATGAAAA
1 AATTAAT-AAAA
56329 AATTAATAAAA
1 AATTAATAAAA
56340 A
1 A
56341 TCCTAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.18
11 7 0.32
12 11 0.50
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AATTAATAAAA
Found at i:59598 original size:5 final size:5
Alignment explanation
Indices: 59583--59730 Score: 53
Period size: 5 Copynumber: 29.8 Consensus size: 5
59573 TAGTAATTAA
* *
59583 TATATT TATAT TATAT T-TA- TATAT TTTAT TATAT TATAAT TGTATT
1 TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TATA-T
* * * * * * * *
59629 TAAAG TATTT TATTAT TATA- TAAAT TTTAA GATATT TATGT TATAT TATA-
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T TATAT TATAT TATAT
* *
59679 TATTT TA-AT TAT-T T-TTT TAATAT TATAT T-TAT GTA-AT TATAT TAATAT
1 TATAT TATAT TATAT TATAT T-ATAT TATAT TATAT -TATAT TATAT T-ATAT
59727 TATA
1 TATA
59731 AATTTTAATC
Statistics
Matches: 103, Mismatches: 23, Indels: 33
0.65 0.14 0.21
Matches are distributed among these distances:
3 2 0.02
4 22 0.21
5 54 0.52
6 25 0.24
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:59616 original size:29 final size:30
Alignment explanation
Indices: 59583--59644 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
59573 TAGTAATTAA
*
59583 TATATT-TATATTATATTTATA-TATTTTAT
1 TATATTATA-ATTATATTTAAAGTATTTTAT
*
59612 TATATTATAATTGTATTTAAAGTATTTTAT
1 TATATTATAATTATATTTAAAGTATTTTAT
59642 TAT
1 TAT
59645 TATATAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (30 bp):
TATATTATAATTATATTTAAAGTATTTTAT
Found at i:60037 original size:27 final size:28
Alignment explanation
Indices: 59985--60037 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
59975 TTTTTTATTG
* * *
59985 AAAAAGTTTAAATAAAAGTATTAATTTA
1 AAAAAATTTAAATAAAAATATAAATTTA
60013 AAAAAATTTAAATAAAAATA-AAATT
1 AAAAAATTTAAATAAAAATATAAATT
60038 AATTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAAAATTTAAATAAAAATATAAATTTA
Found at i:60046 original size:16 final size:16
Alignment explanation
Indices: 60004--60048 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
59994 AAATAAAAGT
60004 ATTAATTTAAAA-AAA
1 ATTAATTTAAAATAAA
* * *
60019 TTTAAATAAAAATAAA
1 ATTAATTTAAAATAAA
60035 ATTAATTTAAAATA
1 ATTAATTTAAAATA
60049 TGAACTTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAATTTAAAATAAA
Found at i:60233 original size:16 final size:16
Alignment explanation
Indices: 60186--60234 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
60176 ATTTTTTTAT
60186 ATTTTTAATTAA-ATTA
1 ATTTTTAATTAATA-TA
* * *
60202 AATTTAAATAAATATA
1 ATTTTTAATTAATATA
60218 ATTTTTAATTAATATA
1 ATTTTTAATTAATATA
60234 A
1 A
60235 AATTTAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTTTAATTAATATA
Found at i:60240 original size:16 final size:16
Alignment explanation
Indices: 60189--60241 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
60179 TTTTTATATT
*
60189 TTTAATTAA-ATTAAA
1 TTTAATTAATATAAAA
* **
60204 TTTAAATAAATATAATT
1 TTT-AATTAATATAAAA
60221 TTTAATTAATATAAAA
1 TTTAATTAATATAAAA
60237 TTTAA
1 TTTAA
60242 ATTTTATTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 3 0.10
16 20 0.69
17 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAATTAATATAAAA
Found at i:62056 original size:27 final size:29
Alignment explanation
Indices: 62006--62061 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
61996 TATATTTATT
*
62006 TTTTTAAAATTTTTTTTGTATAATTAAAAA
1 TTTTTAAAA-TTTTTTTGCATAATTAAAAA
62036 TTTTTAAAA-TTTTTT-CATAATTAAAA
1 TTTTTAAAATTTTTTTGCATAATTAAAA
62062 GTTATTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 10 0.40
28 6 0.24
30 9 0.36
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (29 bp):
TTTTTAAAATTTTTTTGCATAATTAAAAA
Found at i:66512 original size:23 final size:23
Alignment explanation
Indices: 66451--66512 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
66441 AGGTTGGTTT
*
66451 AATTCAATT-TAAATTATTATTTA
1 AATTTAATTATAAA-TATTATTTA
*
66474 AA--TAA-TATAAAAATTATTTA
1 AATTTAATTATAAATATTATTTA
66494 AATTTAATTATAAATATTA
1 AATTTAATTATAAATATTA
66513 ATATAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 11 0.34
21 6 0.19
22 3 0.09
23 12 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTAATTATAAATATTATTTA
Found at i:67143 original size:5 final size:5
Alignment explanation
Indices: 67122--67155 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
67112 AATTATTTAC
67122 AAGAA AAGAA GAGAGAA AAGAA AAGAA AAGAA AA
1 AAGAA AAGAA -A-AGAA AAGAA AAGAA AAGAA AA
67156 TATTGCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 21 0.78
6 2 0.07
7 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:69377 original size:2 final size:2
Alignment explanation
Indices: 69372--69433 Score: 62
Period size: 2 Copynumber: 33.5 Consensus size: 2
69362 ATAAAAAATT
*
69372 TA TA TA -A TA TA CA TA TA TA TA TA TA TA TA TA TA -A TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
69411 -A AA TA TA TA TA AA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
69434 TTTAAATATA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
1 5 0.10
2 45 0.90
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:69416 original size:27 final size:26
Alignment explanation
Indices: 69372--69432 Score: 81
Period size: 25 Copynumber: 2.3 Consensus size: 26
69362 ATAAAAAATT
*
69372 TATATAAT-ATACATATATATATATATA
1 TATATAATAATACA-A-ATATATATAAA
69399 TATATAATAATA-AAATATATATAAA
1 TATATAATAATACAAATATATATAAA
69424 TATATAATA
1 TATATAATA
69433 TTTTAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 19 0.59
26 1 0.03
27 9 0.28
28 3 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
TATATAATAATACAAATATATATAAA
Found at i:69578 original size:20 final size:21
Alignment explanation
Indices: 69553--69594 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
69543 TCCACAGGAA
69553 AATCTTTAATAGTT-AGACAC
1 AATCTTTAATAGTTAAGACAC
69573 AATCTTTAATAGTTAAGACAC
1 AATCTTTAATAGTTAAGACAC
69594 A
1 A
69595 TTATGCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (21 bp):
AATCTTTAATAGTTAAGACAC
Found at i:71052 original size:3 final size:3
Alignment explanation
Indices: 71022--71071 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
71012 CCAATAAATA
* * *
71022 AAT AAT TAT AAT TAT AACT -AT TAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
71067 AAT AA
1 AAT AA
71072 ATCATACCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 1 0.03
3 38 0.95
4 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:71374 original size:101 final size:101
Alignment explanation
Indices: 71199--71384 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 101
71189 GCATACCATA
* *
71199 AAAGCTAAACAAGTATTTTTCTCGATTAGGATCCAAAACTACCACGAAACTAAAAAACCAATTAT
1 AAAGCTAAAAAAGTAATTTTCTCGATTAGGATCCAAAACTACCACGAAACTAAAAAACCAATTAT
71264 ACTATTGTTTTGATACATATCAGCATCAAAGCCCTT
66 ACTATTGTTTTGATACATATCAGCATCAAAGCCCTT
* * * ** * *
71300 AAAGCTAAAAAAGTAATTTTCTC-AGTTAGGATCCAAGACTACCATGAAACTGATCAACCGATTC
1 AAAGCTAAAAAAGTAATTTTCTCGA-TTAGGATCCAAAACTACCACGAAACTAAAAAACCAATTA
*
71364 TACTGTTGTTTTGATACATAT
65 TACTATTGTTTTGATACATAT
71385 AAGCTAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
100 1 0.01
101 73 0.99
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (101 bp):
AAAGCTAAAAAAGTAATTTTCTCGATTAGGATCCAAAACTACCACGAAACTAAAAAACCAATTAT
ACTATTGTTTTGATACATATCAGCATCAAAGCCCTT
Found at i:71584 original size:103 final size:102
Alignment explanation
Indices: 71392--71597 Score: 385
Period size: 103 Copynumber: 2.0 Consensus size: 102
71382 TATAAGCTAA
71392 AAAACAAGCAAGCACTCTCAATCATAAATCGCACCCTCCATCCCCAGATTCAAACCCGGCAACCC
1 AAAACAAGCAAGCACTCTCAATCATAAATCGCACCCTCCATCCCCAGATTCAAACCCGGCAACCC
71457 AAAGTTGAAATCTTTCTAACTGTAAAGTCAATTATAC
66 AAAGTTGAAATCTTTCTAACTGTAAAGTCAATTATAC
* *
71494 AAAACAAGCAAGCACTCTCAATCATAAATCGCACCCTCCATCGCCCAGATTCAAAGCCGGGAACC
1 AAAACAAGCAAGCACTCTCAATCATAAATCGCACCCTCCATC-CCCAGATTCAAACCCGGCAACC
71559 CAAAGTTGAAATCTTTCTAACTGTAAAGTCAATTATAC
65 CAAAGTTGAAATCTTTCTAACTGTAAAGTCAATTATAC
71597 A
1 A
71598 CTAATCTTCC
Statistics
Matches: 101, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
102 42 0.42
103 59 0.58
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.21
Consensus pattern (102 bp):
AAAACAAGCAAGCACTCTCAATCATAAATCGCACCCTCCATCCCCAGATTCAAACCCGGCAACCC
AAAGTTGAAATCTTTCTAACTGTAAAGTCAATTATAC
Found at i:72311 original size:25 final size:25
Alignment explanation
Indices: 72271--72335 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
72261 TCTACTGTAT
72271 ATAATAATAT-TAAAATATTATAA-AA
1 ATAATAATATAT-AAATATT-TAATAA
72296 ATAATAATATATAAAT-TTTAATAA
1 ATAATAATATATAAATATTTAATAA
* *
72320 AT-ATATTTTATAAATA
1 ATAATAATATATAAATA
72336 AATATTAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
23 14 0.40
24 6 0.17
25 14 0.40
26 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATAATATATAAATATTTAATAA
Found at i:72317 original size:14 final size:14
Alignment explanation
Indices: 72300--72343 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
72290 ATAAAAATAA
*
72300 TAATATATAAATTT
1 TAATAAATAAATTT
*
72314 TAATAAATATATTT
1 TAATAAATAAATTT
*
72328 T-ATAAATAAATAT
1 TAATAAATAAATTT
72341 TAA
1 TAA
72344 GATACATGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATAAATAAATTT
Found at i:73501 original size:2 final size:2
Alignment explanation
Indices: 73496--73526 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
73486 GCTCTCTTTA
73496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73527 GGGCATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78125 original size:22 final size:22
Alignment explanation
Indices: 78084--78127 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
78074 AAGCTCGATC
**
78084 AAATTAAATTTAAATTTAATAT
1 AAATTAAATTTAAAAATAATAT
*
78106 AAATTAATTTTAAAAATAATAT
1 AAATTAAATTTAAAAATAATAT
78128 TAATATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATTAAATTTAAAAATAATAT
Found at i:79241 original size:23 final size:24
Alignment explanation
Indices: 79191--79261 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
79181 AAAATTAGCC
* *
79191 ATCAATTTTAACAAACAACAAGCT
1 ATCAATTTTAACAAACAAAAAGCA
* *
79215 ATCATTTTTAATAAACAAAAAG-A
1 ATCAATTTTAACAAACAAAAAGCA
*
79238 ATCACAATTTTTGACAAACAAAAA
1 AT--CAA-TTTTAACAAACAAAAA
79262 AAGAACCACC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 2 0.05
24 19 0.51
25 2 0.05
26 14 0.38
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.27
Consensus pattern (24 bp):
ATCAATTTTAACAAACAAAAAGCA
Found at i:79289 original size:29 final size:28
Alignment explanation
Indices: 79231--79289 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
79221 TTTAATAAAC
*
79231 AAAAAGAATCACAATTTTTGACAAACAA
1 AAAAAGAACCACAATTTTTGACAAACAA
* * *
79259 AAAAAGAACCACCATTTTTGGCAAACTA
1 AAAAAGAACCACAATTTTTGACAAACAA
79287 AAA
1 AAA
79290 GGGTAGCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.54, C:0.17, G:0.08, T:0.20
Consensus pattern (28 bp):
AAAAAGAACCACAATTTTTGACAAACAA
Found at i:82723 original size:20 final size:21
Alignment explanation
Indices: 82669--82724 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
82659 AAAATTCTCA
**
82669 AATGTATCGATACAAAG-ATC
1 AATGTATCGATACATTGAATC
82689 AATGTATCGATACATTGAAT-
1 AATGTATCGATACATTGAATC
82709 AATGTATCGATACATT
1 AATGTATCGATACATT
82725 TCCTTGGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (21 bp):
AATGTATCGATACATTGAATC
Found at i:84946 original size:19 final size:18
Alignment explanation
Indices: 84918--84980 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
84908 AAACCGTAAA
*
84918 TGTATTGATACATAAGTGT
1 TGTATCGATACATAAGT-T
84937 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
*
84950 TGTATTGATACATAAGTTT
1 TGTATCGATACATAAG-TT
84969 TGTATCGATACA
1 TGTATCGATACA
84981 ATGTATCGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 10 0.29
15 2 0.06
17 2 0.06
19 21 0.60
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:84957 original size:32 final size:32
Alignment explanation
Indices: 84916--84986 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
84906 ACAAACCGTA
84916 AATGTATTGATACATAAGTGTTGTATCGATAC
1 AATGTATTGATACATAAGTGTTGTATCGATAC
*
84948 AATGTATTGATACATAAGTTTTGTATCGATAC
1 AATGTATTGATACATAAGTGTTGTATCGATAC
84980 AATGTAT
1 AATGTAT
84987 CGCTACGAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.39
Consensus pattern (32 bp):
AATGTATTGATACATAAGTGTTGTATCGATAC
Found at i:85035 original size:20 final size:20
Alignment explanation
Indices: 85010--85065 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
85000 CTGCCAAGGA
85010 AATGTATCGATACATT-ACTC
1 AATGTATCGATACATTGA-TC
85030 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
85050 TTTGTATCGATACATT
1 AATGTATCGATACATT
85066 TGGAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:88500 original size:33 final size:33
Alignment explanation
Indices: 88463--88529 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
88453 TTCAACGATT
88463 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
88496 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
88529 T
1 T
88530 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:88501 original size:13 final size:13
Alignment explanation
Indices: 88483--88507 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88473 CATAAAATGT
88483 TGTATCGATACAA
1 TGTATCGATACAA
88496 TGTATCGATACA
1 TGTATCGATACA
88508 TATTTTTTTG
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:88659 original size:52 final size:52
Alignment explanation
Indices: 88603--88731 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
88593 CACTGATCTT
* * * *
88603 TGTATCAATACATGCAGGAAAATTTGCCGAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
88655 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
88707 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
88732 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:93604 original size:13 final size:13
Alignment explanation
Indices: 93586--93610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93576 CAAAAAAATA
93586 TGTATCGATACAT
1 TGTATCGATACAT
93599 TGTATCGATACA
1 TGTATCGATACA
93611 ACATTTTATA
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:93625 original size:33 final size:33
Alignment explanation
Indices: 93564--93630 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
93554 AGTAGCTTAA
*
93564 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATATATCGATAC
* ***
93597 ATTGTATCGATACAACATTTTATATATCGATAC
1 ATTGTATCGATACAAAAAAATATATATCGATAC
93630 A
1 A
93631 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATATATCGATAC
Found at i:94606 original size:49 final size:48
Alignment explanation
Indices: 94520--94664 Score: 168
Period size: 49 Copynumber: 3.0 Consensus size: 48
94510 TATTGGACTT
* * * * *
94520 AAGGTGTCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATATG-
1 AAGGTGCCAATATGCTGATTCAAGGCCAG-TATATTGGACTTAAA-AGGC
*
94569 AAGGTGCCAATATGCTGATTTAAGGCCAGTGATATTGGACTT-AAAGGC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGT-ATATTGGACTTAAAAGGC
* *
94617 AAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGGCTTAAAAGG
1 AAGGTGCCAATATGCTGATTCAAGGCC-AGTATATTGGACTTAAAAGG
94665 AGACGCCACC
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
47 2 0.02
48 39 0.47
49 42 0.51
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (48 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGTATATTGGACTTAAAAGGC
Found at i:94636 original size:48 final size:46
Alignment explanation
Indices: 94434--94661 Score: 207
Period size: 48 Copynumber: 4.8 Consensus size: 46
94424 AAAAGGATGT
* * * *
94434 CAATGTGCTGATTCAAGGCCAACTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G--AAGGTGC
*
94486 CAA-ATGCTGATTCAAGGCCAGCTATATTGGACTT----AAGGTGT
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGGTGC
* * *
94527 CAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-GAAGGTGC
*
94576 CAATATGCTGATTTAAGGCCAG-TGATATTGGACTTAAAGGCAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCT-ATATTGGACTTAAA-G-AAGGTGC
* *
94624 CAATATGCTGATTCAAGGCCAACTATATTGGGCTTAAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
94662 AGGAGACGCC
Statistics
Matches: 148, Mismatches: 17, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
41 9 0.06
42 28 0.19
47 2 0.01
48 43 0.29
49 36 0.24
51 27 0.18
52 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (46 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGGTGC
Found at i:94661 original size:97 final size:92
Alignment explanation
Indices: 94434--94661 Score: 273
Period size: 97 Copynumber: 2.4 Consensus size: 92
94424 AAAAGGATGT
*
94434 CAATGTGCTGATTCAAGGCCAACTACATTGAACTTAAAGATGGAAAAGGTGCCAAATGCTGATTC
1 CAATGTGCTGATTCAAGGCCAACTACATTGGACTTAAAGATGG-AAAGGTGCCAAATGCTGATTC
*
94499 AAGGCCAGCTATATTGGACTTAAGGTGT
65 AAGGCCAGCTATATTGGACTTAAGGTGC
* * * *
94527 CAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATAT-G-AAGGTGCCAATATGCTGATTT
1 CAATGTGCTGATTCAAGGCCAACTACATTGGACTTAAAGATGGAAAGGTGCCAA-ATGCTGATTC
94590 AAGGCCAG-TGATATTGGACTTAAAGGCAAGGTGC
65 AAGGCCAGCT-ATATTGGACTT------AAGGTGC
* * *
94624 CAATATGCTGATTCAAGGCCAACTATATTGGGCTTAAA
1 CAATGTGCTGATTCAAGGCCAACTACATTGGACTTAAA
94662 AGGAGACGCC
Statistics
Matches: 116, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
90 11 0.09
91 28 0.24
92 1 0.01
93 37 0.32
97 39 0.34
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAACTACATTGGACTTAAAGATGGAAAGGTGCCAAATGCTGATTCA
AGGCCAGCTATATTGGACTTAAGGTGC
Found at i:94752 original size:60 final size:59
Alignment explanation
Indices: 94705--94993 Score: 203
Period size: 59 Copynumber: 4.9 Consensus size: 59
94695 AGGTTTGCAT
* * *
94705 CACTGACTTGTGGGCTTTT-AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
** *
94763 CACTAACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGC
1 CACTAACTTGTGGGCTTTT-AAAAGGGTGCCACTAACTTGTGGGCTT---TTG-AAAAGGGTGC
* * * * * ** *
94827 TA-TAGAGTTGTGAGCTTTGGAAAA-GATGCCACCGACTTGTGGGC-TTCGAAAAAGGGTGC
1 CACTA-ACTTGTGGGCTTT-TAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAAAGGGTGC
* * * * * ***
94886 CACTGATTTGTGGGC-TTT-GAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAATGC
1 CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
* * *** * *
94943 CACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGACTTTTGAA
1 CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAA
94994 GGGTGATAAA
Statistics
Matches: 183, Mismatches: 35, Indels: 25
0.75 0.14 0.10
Matches are distributed among these distances:
56 2 0.01
57 39 0.21
58 25 0.14
59 46 0.25
60 25 0.14
62 1 0.01
63 20 0.11
64 25 0.14
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (59 bp):
CACTAACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAAAGGGTGC
Found at i:94764 original size:30 final size:30
Alignment explanation
Indices: 94705--94993 Score: 263
Period size: 30 Copynumber: 9.7 Consensus size: 30
94695 AGGTTTGCAT
*
94705 CACTGACTTGTGGGCTTTT--AAAGGTTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
94733 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
*
94763 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
* ** *
94793 CACTAACTTGTGGGCTTAAAAAGAAAAAGAGTGC
1 CACTGACTTGTGGGCTT---TTG-AAAAGGGTGC
* * * * *
94827 TA-TAGAGTTGTGAGCTTTGGAAAA-GATGC
1 CACT-GACTTGTGGGCTTTTGAAAAGGGTGC
* *
94856 CACCGACTTGTGGGC-TTCGAAAAAGGGTGC
1 CACTGACTTGTGGGCTTTTG-AAAAGGGTGC
* *
94886 CACTGATTTGTGGGC-TTTG--AAGGTTGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
***
94913 CACTGACTTGTGGGCTTTTGAAAAAAATGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
***
94943 CACTGACTTGTGGGC-TTTGAAAAATATGC
1 CACTGACTTGTGGGCTTTTGAAAAGGGTGC
*
94972 CACTGACTTGTGGACTTTTGAA
1 CACTGACTTGTGGGCTTTTGAA
94994 GGGTGATAAA
Statistics
Matches: 218, Mismatches: 29, Indels: 26
0.80 0.11 0.10
Matches are distributed among these distances:
27 21 0.10
28 26 0.12
29 44 0.20
30 104 0.48
31 1 0.00
33 2 0.01
34 20 0.09
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (30 bp):
CACTGACTTGTGGGCTTTTGAAAAGGGTGC
Found at i:96435 original size:1 final size:1
Alignment explanation
Indices: 96431--96549 Score: 112
Period size: 1 Copynumber: 119.0 Consensus size: 1
96421 CCGGACCCCC
* * * * * * * *
96431 TTTTTTTGTTTTTGTTTGTTTTTTTTTGTTTTTGTTTTTTTTTGTTTTTTTTTTGTTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * * * *
96496 TTTTTTCATTTTTTTGTTTTTTTTTTTGTTTTTTTGTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
96550 GGAGGACGCC
Statistics
Matches: 91, Mismatches: 27, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 91 1.00
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.88
Consensus pattern (1 bp):
T
Found at i:96454 original size:20 final size:18
Alignment explanation
Indices: 96431--96550 Score: 136
Period size: 18 Copynumber: 6.4 Consensus size: 18
96421 CCGGACCCCC
96431 TTTTTTTGTTTTTGTTTGTT
1 TTTTTTTGTTTTT-TTT-TT
96451 TTTTTTTGTTTTTGTTTTT
1 TTTTTTTGTTTTT-TTTTT
*
96470 TTTTGTTT-TTTTTTTGTT
1 TTTT-TTTGTTTTTTTTTT
*
96488 TTTTTTTGTTTTTTCATTT
1 TTTTTTTGTTTTTT-TTTT
* *
96507 TTTTGTT-TTTTTTTTTG
1 TTTTTTTGTTTTTTTTTT
96524 TTTTTTTGTTTTTTTTTT
1 TTTTTTTGTTTTTTTTTT
96542 GTTTTTTTG
1 -TTTTTTTG
96551 GAGGACGCCG
Statistics
Matches: 87, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
17 11 0.13
18 29 0.33
19 27 0.31
20 20 0.23
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.88
Consensus pattern (18 bp):
TTTTTTTGTTTTTTTTTT
Found at i:96486 original size:37 final size:36
Alignment explanation
Indices: 96431--96546 Score: 164
Period size: 37 Copynumber: 3.2 Consensus size: 36
96421 CCGGACCCCC
*
96431 TTTTTTTG-TTTTTGTTTGTTTTTTTTTGTTTTTGTT
1 TTTTTTTGTTTTTTTTTTGTTTTTTTTTGTTTTT-TT
*
96467 TTTTTTTGTTTTTTTTTTGTTTTTTTTTGTTTTTTCA
1 TTTTTTTGTTTTTTTTTTGTTTTTTTTTGTTTTTT-T
*
96504 TTTTTTTGTTTTTTTTTT-TGTTTTTTTGTTTTTTT
1 TTTTTTTGTTTTTTTTTTGTTTTTTTTTGTTTTTTT
96539 TTTGTTTT
1 TTT-TTTT
96547 TTTGGAGGAC
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
35 3 0.04
36 28 0.38
37 42 0.58
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.88
Consensus pattern (36 bp):
TTTTTTTGTTTTTTTTTTGTTTTTTTTTGTTTTTTT
Found at i:96489 original size:47 final size:45
Alignment explanation
Indices: 96431--96549 Score: 175
Period size: 47 Copynumber: 2.6 Consensus size: 45
96421 CCGGACCCCC
* *
96431 TTTTTTTGTTTTTGTTTGTTTTTTTTTGTTTTTGTTTTTTTTTGTTT
1 TTTTTTTGTTTTTTTTTGTTTTTTTTT-TTTTTGTTTTTTTTT-TTG
*
96478 TTTTTTTGTTTTTTTTTGTTTTTTCATTTTTTTGTTTTTTTTTTTG
1 TTTTTTTGTTTTTTTTTGTTTTTT-TTTTTTTTGTTTTTTTTTTTG
96524 TTTTTTTGTTTTTTTTTTGTTTTTTT
1 TTTTTTTG-TTTTTTTTTGTTTTTTT
96550 GGAGGACGCC
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
46 10 0.15
47 54 0.82
48 2 0.03
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.88
Consensus pattern (45 bp):
TTTTTTTGTTTTTTTTTGTTTTTTTTTTTTTTGTTTTTTTTTTTG
Found at i:96547 original size:37 final size:35
Alignment explanation
Indices: 96431--96547 Score: 153
Period size: 36 Copynumber: 3.2 Consensus size: 35
96421 CCGGACCCCC
* *
96431 TTTTTTTGTTTTTGTTTGTTTTTTTTTGTTTTTGTT
1 TTTTTTTGTTTTT-TTTTTTTTTTTTTGTTTTTTTT
**
96467 TTTTTTTGTTTTTTTTTTGTTTTTTTTTGTTTTTTCA
1 TTTTTTTG-TTTTTTTTT-TTTTTTTTTGTTTTTTTT
96504 TTTTTTTGTTTTTTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTGTTTTTTTTTTT-TTTTTTTGTTTTTTTT
96540 TTGTTTTT
1 TT-TTTTT
96548 TTGGAGGACG
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
35 2 0.03
36 36 0.51
37 33 0.46
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.88
Consensus pattern (35 bp):
TTTTTTTGTTTTTTTTTTTTTTTTTTGTTTTTTTT
Done.