Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold147
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: 880509
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.26
Warning! 187686 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:224487 original size:18 final size:18
Alignment explanation
Indices: 224466--224510 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
224456 TTTATCATTT
224466 TATTTTTATTTGATTAAA
1 TATTTTTATTTGATTAAA
*
224484 TATTAATT-TTTGATTAAA
1 TATT-TTTATTTGATTAAA
224502 T-TTTTTATT
1 TATTTTTATT
224511 CAACTTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 2 0.09
17 4 0.17
18 15 0.65
19 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (18 bp):
TATTTTTATTTGATTAAA
Found at i:224669 original size:27 final size:31
Alignment explanation
Indices: 224615--224684 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 31
224605 TAAGCTTCAG
*
224615 TTTTTATAAATTAAAATTGTTTATTTTTTATA
1 TTTTTATAAATT-AAATTGTTTATTTTTTAAA
224647 TTTTTATAAATT-AA-T-TTTA-TTTTTAAA
1 TTTTTATAAATTAAATTGTTTATTTTTTAAA
224674 TCTTTTA-AAAT
1 T-TTTTATAAAT
224685 CATAGTTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 12 0.33
28 9 0.25
29 1 0.03
30 2 0.06
32 12 0.33
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (31 bp):
TTTTTATAAATTAAATTGTTTATTTTTTAAA
Found at i:228113 original size:4 final size:4
Alignment explanation
Indices: 228104--228138 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
228094 ACCAGCTCTC
228104 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
228139 TATGTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:228798 original size:2 final size:2
Alignment explanation
Indices: 228791--228820 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
228781 TTGTTAATTA
228791 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
228821 TCAGTGCCTT
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:229431 original size:6 final size:6
Alignment explanation
Indices: 229420--229446 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
229410 CCTTCCATTA
229420 CATTTC CATTTC CATTTC CATTTC CAT
1 CATTTC CATTTC CATTTC CATTTC CAT
229447 GTCCTACTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (6 bp):
CATTTC
Found at i:231704 original size:2 final size:2
Alignment explanation
Indices: 231697--231722 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
231687 CGACCTACCA
231697 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
231723 TTCTTTGTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:232649 original size:3 final size:3
Alignment explanation
Indices: 232641--232671 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
232631 TGTGAGAAAT
232641 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
232672 GATAATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:233697 original size:2 final size:2
Alignment explanation
Indices: 233690--233714 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
233680 ACTCAAACAA
233690 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 A
233715 CAAAAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:234879 original size:16 final size:16
Alignment explanation
Indices: 234858--234889 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
234848 GGTTGGCCTT
234858 TTCTTTTCTCCAGAGA
1 TTCTTTTCTCCAGAGA
234874 TTCTTTTCTCCAGAGA
1 TTCTTTTCTCCAGAGA
234890 AGAAGGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (16 bp):
TTCTTTTCTCCAGAGA
Found at i:235492 original size:7 final size:7
Alignment explanation
Indices: 235480--235521 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
235470 AGTTTAAGAT
235480 AAATTTA
1 AAATTTA
235487 AAATTTA
1 AAATTTA
235494 AAATTTA
1 AAATTTA
235501 AAATTT-
1 AAATTTA
*
235507 AATTTTA
1 AAATTTA
235514 AAATTTA
1 AAATTTA
235521 A
1 A
235522 GTTTAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
AAATTTA
Found at i:235513 original size:13 final size:13
Alignment explanation
Indices: 235479--235527 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
235469 AAGTTTAAGA
235479 TAAATTTAAAATT
1 TAAATTTAAAATT
235492 TAAAATTTAAAATT
1 T-AAATTTAAAATT
*
235506 TAATTTTAAAATT
1 TAAATTTAAAATT
*
235519 TAAGTTTAA
1 TAAATTTAA
235528 TTAAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
13 20 0.61
14 13 0.39
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:236453 original size:17 final size:16
Alignment explanation
Indices: 236414--236453 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
236404 ATATACTATA
236414 TTTATATTTAAAATTT
1 TTTATATTTAAAATTT
*
236430 TGATATATTTAAATATTT
1 T-TTATATTTAAA-ATTT
236448 TTTATA
1 TTTATA
236454 GTAATCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTATATTTAAAATTT
Found at i:240987 original size:71 final size:71
Alignment explanation
Indices: 240902--241044 Score: 198
Period size: 71 Copynumber: 2.0 Consensus size: 71
240892 TTAACGCACA
* * * * * *
240902 TTGAATCTTTCTTTGGTTTGAGAGACCTAATATGTTGGGAAGAAGGTAGAGGGAAGAC-GGTACA
1 TTGAACCTTTCTTTGGTTCGAGAGAACTAATAGGTTGGGAAAAAGGTAGAGGGAAAACAGG-ACA
240966 TAAATTG
65 TAAATTG
* *
240973 TTGAACCTTTCTTTGGTTCGAGAGAAGTAATAGGTTGGGAAAAAGGTAGAGGGAAAACAGGGCAT
1 TTGAACCTTTCTTTGGTTCGAGAGAACTAATAGGTTGGGAAAAAGGTAGAGGGAAAACAGGACAT
241038 AAATTG
66 AAATTG
241044 T
1 T
241045 CCATATCAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 61 0.97
72 2 0.03
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (71 bp):
TTGAACCTTTCTTTGGTTCGAGAGAACTAATAGGTTGGGAAAAAGGTAGAGGGAAAACAGGACAT
AAATTG
Found at i:253048 original size:9 final size:9
Alignment explanation
Indices: 253034--253125 Score: 63
Period size: 9 Copynumber: 10.2 Consensus size: 9
253024 TGTTGGACTA
253034 TTTAATAAT
1 TTTAATAAT
253043 TTTAATAA-
1 TTTAATAAT
253051 TTT-ATATAT
1 TTTAATA-AT
253060 TTT-ATAAT
1 TTTAATAAT
*
253068 ATTATAATATT
1 -TT-TAATAAT
253079 ATTTAATATAT
1 -TTTAATA-AT
253090 TTT-AT-A-
1 TTTAATAAT
253096 TTTATATAAAT
1 TTTA-AT-AAT
253107 TTTAAT-AT
1 TTTAATAAT
253115 TTTAATAAT
1 TTTAATAAT
253124 TT
1 TT
253126 ATATTATATA
Statistics
Matches: 69, Mismatches: 2, Indels: 24
0.73 0.02 0.25
Matches are distributed among these distances:
6 3 0.04
7 4 0.06
8 16 0.23
9 22 0.32
10 12 0.17
11 12 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAATAAT
Found at i:253080 original size:16 final size:16
Alignment explanation
Indices: 253047--253172 Score: 57
Period size: 14 Copynumber: 8.5 Consensus size: 16
253037 AATAATTTTA
*
253047 ATAATTTATATATTTT
1 ATAATTTATATATATT
253063 ATAATATTATA-ATATT
1 ATAAT-TTATATATATT
* *
253079 AT--TTAATATATTTT
1 ATAATTTATATATATT
253093 AT-ATTTATATA-A--
1 ATAATTTATATATATT
*
253105 AT--TTTA-ATATTTT
1 ATAATTTATATATATT
253118 AATAATTTATAT-TA-T
1 -ATAATTTATATATATT
253133 ATAAATTT-TATA-A-T
1 AT-AATTTATATATATT
253147 ATATATTTATATTATATT
1 ATA-ATTTATA-TATATT
*
253165 ATATTTTA
1 ATAATTTA
253173 ATTGTTTTAT
Statistics
Matches: 85, Mismatches: 8, Indels: 33
0.67 0.06 0.26
Matches are distributed among these distances:
10 3 0.04
11 4 0.05
12 2 0.02
13 5 0.06
14 22 0.26
15 15 0.18
16 18 0.21
17 12 0.14
18 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAATTTATATATATT
Found at i:253154 original size:72 final size:73
Alignment explanation
Indices: 253034--253170 Score: 192
Period size: 72 Copynumber: 1.9 Consensus size: 73
253024 TGTTGGACTA
* *
253034 TTTAATAATTTTAATAATTTATATATTTTATAATATTATAATATTATTTA-ATATATTTTATATT
1 TTTAATAATTTTAATAATTTATATATTATATAATATTATAATATTATTTATAT-TATATTATATT
253098 TATATAAAT
65 TATATAAAT
*
253107 TTTAAT-ATTTTAATAA-TT-TATATTATATAAATTTTATAATATATATTTATATTATATTATAT
1 TTTAATAATTTTAATAATTTATATATTATAT-AATATTATAATAT-TATTTATATTATATTATAT
253169 TT
64 TT
253171 TAATTGTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
70 9 0.16
71 14 0.24
72 27 0.47
73 8 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (73 bp):
TTTAATAATTTTAATAATTTATATATTATATAATATTATAATATTATTTATATTATATTATATTT
ATATAAAT
Found at i:253162 original size:34 final size:32
Alignment explanation
Indices: 253053--253168 Score: 95
Period size: 34 Copynumber: 3.7 Consensus size: 32
253043 TTTAATAATT
* * *
253053 TATATATTT-TATAATATTATA-ATATTATTTA
1 TATATATTTATATTATATTATATAAATT-TTAA
253084 -ATATATTT-TA-TAT-TTATATAAATTTTAA
1 TATATATTTATATTATATTATATAAATTTTAA
*
253112 TAT-T-TTAATAATTTATATTATATAAATTTTATAA
1 TATATATTTAT-A-TTATATTATATAAA-TTT-TAA
253146 TATATATTTATATTATATTATAT
1 TATATATTTATATTATATTATAT
253169 TTTAATTGTT
Statistics
Matches: 69, Mismatches: 5, Indels: 19
0.74 0.05 0.20
Matches are distributed among these distances:
27 2 0.03
28 10 0.14
29 9 0.13
30 10 0.14
31 3 0.04
32 9 0.13
33 3 0.04
34 17 0.25
35 2 0.03
36 4 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TATATATTTATATTATATTATATAAATTTTAA
Found at i:253167 original size:18 final size:18
Alignment explanation
Indices: 253052--253172 Score: 63
Period size: 18 Copynumber: 6.6 Consensus size: 18
253042 TTTTAATAAT
*
253052 TTATATATTT-TATAATA
1 TTATATATTTATATTATA
* *
253069 TTATAATATTATTTAATATA
1 TTAT-ATATT-TATATTATA
* *
253089 TTTTATATTTATA-TAAA
1 TTATATATTTATATTATA
*
253106 TTTTAATATTTTAATAATTTATA
1 TTAT-ATA-TTT-AT-A-TTATA
* *
253129 TTATATA--AATTTTATA
1 TTATATATTTATATTATA
*
253145 ATATATATTTATATTATA
1 TTATATATTTATATTATA
253163 TTATAT-TTTA
1 TTATATATTTA
253173 ATTGTTTTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
16 11 0.14
17 15 0.19
18 25 0.31
19 9 0.11
20 10 0.12
21 1 0.01
22 3 0.04
23 6 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATATATTTATATTATA
Found at i:253740 original size:29 final size:29
Alignment explanation
Indices: 253683--253740 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
253673 TCAATAGTTT
**
253683 AAATTTAAAAATTTATTTAATATTTTAAA
1 AAATTTAAAAATTTATTTAATATAATAAA
253712 AAATTTAAAAAATTTAATTTAA-A-AATAAA
1 AAATTT-AAAAATTT-ATTTAATATAATAAA
253741 CTTAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 10 0.40
30 9 0.36
31 6 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
AAATTTAAAAATTTATTTAATATAATAAA
Found at i:253895 original size:17 final size:17
Alignment explanation
Indices: 253866--253931 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
253856 GTGGTAAATC
*
253866 ATTTTTTT-TAAAATTA
1 ATTTTTTTAAAAAATTA
*
253882 ATATTTTTAAAAAATTA
1 ATTTTTTTAAAAAATTA
*
253899 ATTTTTTTAAAAGTATTA
1 ATTTTTTTAAAA-AATTA
*
253917 ATTTTTTTATAAAAT
1 ATTTTTTTAAAAAAT
253932 ATCAAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
16 7 0.17
17 20 0.48
18 15 0.36
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTTTTAAAAAATTA
Found at i:253939 original size:20 final size:19
Alignment explanation
Indices: 253866--253952 Score: 69
Period size: 18 Copynumber: 4.8 Consensus size: 19
253856 GTGGTAAATC
253866 ATTTTTTT-TAAAAT-T-A
1 ATTTTTTTATAAAATATAA
* *
253882 ATATTTTTA-AAAA-ATTA
1 ATTTTTTTATAAAATATAA
* *
253899 ATTTTTTTA-AAAGTATTA
1 ATTTTTTTATAAAATATAA
253917 ATTTTTTTATAAAATATCAA
1 ATTTTTTTATAAAATAT-AA
*
253937 ATTTTTATATATAAAT
1 ATTTTTTTATA-AAAT
253953 TTATAATATA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
16 12 0.21
17 12 0.21
18 13 0.22
19 6 0.10
20 11 0.19
21 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (19 bp):
ATTTTTTTATAAAATATAA
Found at i:253961 original size:15 final size:16
Alignment explanation
Indices: 253922--253963 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
253912 TATTAATTTT
*
253922 TTTATAAAATATCAAA
1 TTTATAATATATCAAA
*
253938 TTT-TTATATAT-AAA
1 TTTATAATATATCAAA
253952 TTTATAATATAT
1 TTTATAATATAT
253964 TTTTTACCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 6 0.27
15 13 0.59
16 3 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTATAATATATCAAA
Found at i:255287 original size:4 final size:4
Alignment explanation
Indices: 255280--255306 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
255270 TTTCTTTAAT
255280 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
255307 GTTTTTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:270015 original size:27 final size:27
Alignment explanation
Indices: 269950--270020 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
269940 AAACAAGCCT
* * *
269950 CCATATTTGACAAATACAAAGGAAATTA
1 CCATTTTTGACAAACACAAA-GAAATCA
269978 CCATTTTTGACAAACACAAA-ATAATCA
1 CCATTTTTGACAAACACAAAGA-AATCA
270005 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
270021 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAATCA
Found at i:271943 original size:21 final size:22
Alignment explanation
Indices: 271905--271950 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
271895 ATCTGTTGAA
* **
271905 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
271926 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
271948 ACT
1 ACT
271951 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:274598 original size:24 final size:27
Alignment explanation
Indices: 274525--274595 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
274515 AAACAAGCCT
* *
274525 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
274553 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
274580 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
274596 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:275329 original size:80 final size:80
Alignment explanation
Indices: 275204--275354 Score: 221
Period size: 80 Copynumber: 1.9 Consensus size: 80
275194 CCACCAAATC
* * * *
275204 ACCTTTGCATCCATTTTCAACATTAAATTTAGTGGCTTTACCTTTTAATCATTTAGTCAACAATG
1 ACCTTTGCACCCATTTTCAAAATTAAATTTAGTGGCTTTACCTTTTAACCATCTAGTCAACAATG
275269 GCAAACCACTAATTT
66 GCAAACCACTAATTT
* * * *
275284 ACCTTTGCACCCATTTTCAAAATTAATTTTGGTGGCTTTATCTTTTAACCATCTATTCAACAATG
1 ACCTTTGCACCCATTTTCAAAATTAAATTTAGTGGCTTTACCTTTTAACCATCTAGTCAACAATG
*
275349 GTAAAC
66 GCAAAC
275355 TATCAAATCA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 62 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (80 bp):
ACCTTTGCACCCATTTTCAAAATTAAATTTAGTGGCTTTACCTTTTAACCATCTAGTCAACAATG
GCAAACCACTAATTT
Found at i:279535 original size:19 final size:18
Alignment explanation
Indices: 279464--279536 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
279454 ACAGTGTAAC
* *
279464 CGTACACGTAAAGAGTAT
1 CGTATACGTAAACAGTAT
* *
279482 CTGTATACGTGAACAATAT
1 C-GTATACGTAAACAGTAT
*
279501 CCATATACGTAAACAGTACT
1 -CGTATACGTAAACAGTA-T
279521 CGTATACGTAAACAGT
1 CGTATACGTAAACAGT
279537 GCCTCGACAA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
18 1 0.02
19 41 0.93
20 2 0.05
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (18 bp):
CGTATACGTAAACAGTAT
Found at i:281302 original size:23 final size:22
Alignment explanation
Indices: 281260--281303 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
281250 ATTTAATTTT
* *
281260 AATTTTAATTTTTAAGTTAAAG
1 AATTATAATTTTTAAATTAAAG
281282 AATTATAATTATTTAAATTAAA
1 AATTATAATT-TTTAAATTAAA
281304 TTAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
AATTATAATTTTTAAATTAAAG
Found at i:282366 original size:2 final size:2
Alignment explanation
Indices: 282359--282411 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
282349 TTGTTTAACC
* *
282359 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
282401 TA TA TA T- TA TA
1 TA TA TA TA TA TA
282412 GCATGGTCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:299518 original size:28 final size:27
Alignment explanation
Indices: 299484--299539 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
299474 TTCTATTTTT
299484 TAAATAAATATTTTA-CTTTTATTGTATA
1 TAAATAAAT-TTTTATCTTTTATT-TATA
*
299512 TAAATAAATTTTTATTTTTTATTTATA
1 TAAATAAATTTTTATCTTTTATTTATA
299539 T
1 T
299540 TTAAATGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
TAAATAAATTTTTATCTTTTATTTATA
Found at i:300591 original size:2 final size:2
Alignment explanation
Indices: 300584--300613 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
300574 TTAACTATTG
300584 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
300614 GTTGAATTCA
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:308095 original size:2 final size:2
Alignment explanation
Indices: 308088--308123 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
308078 ACGTCGGTTA
308088 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
308124 GAATCCCAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:314348 original size:20 final size:20
Alignment explanation
Indices: 314323--314426 Score: 89
Period size: 20 Copynumber: 5.5 Consensus size: 20
314313 AATTTGATAA
314323 TTTATATATTTATATAATAT
1 TTTATATATTTATATAATAT
314343 TTTATATATTT-TATTAA-AT
1 TTTATATATTTATA-TAATAT
* * *
314362 TATA-ATTATTTTTAAAATAT
1 TTTATA-TATTTATATAATAT
314382 TTTATATATTTATA-AAT-T
1 TTTATATATTTATATAATAT
*
314400 TTAATATA-TTA-ATAAT-T
1 TTTATATATTTATATAATAT
314417 TTTAATATAT
1 TTT-ATATAT
314427 AAACCTTTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 17
0.75 0.06 0.18
Matches are distributed among these distances:
16 1 0.01
17 9 0.13
18 14 0.20
19 17 0.24
20 28 0.40
21 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATATATTTATATAATAT
Found at i:314365 original size:27 final size:28
Alignment explanation
Indices: 314335--314409 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 28
314325 TATATATTTA
314335 TATAATATTTT-ATATATTTTAT-TAAAT
1 TATAATATTTTAATATATTTTATAT-AAT
* *
314362 TATAATTATTTTTAAAATATTTTATATATT
1 TATAA-TA-TTTTAATATATTTTATATAAT
314392 TATAA-ATTTTAATATATT
1 TATAATATTTTAATATATT
314410 AATAATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 16 0.39
28 3 0.07
29 4 0.10
30 17 0.41
31 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TATAATATTTTAATATATTTTATATAAT
Found at i:314381 original size:39 final size:38
Alignment explanation
Indices: 314326--314414 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 38
314316 TTGATAATTT
*
314326 ATATATTTATATAATATTTTATATATTTTATTAAATTATA
1 ATATATTTATAAAATATTTTATATA-TTTA-TAAATTATA
* *
314366 AT-TATTTTTAAAATATTTTATATATTTATAAATTTTA
1 ATATATTTATAAAATATTTTATATATTTATAAATTATA
*
314403 ATATATTAATAA
1 ATATATTTATAA
314415 TTTTTAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
37 10 0.23
38 11 0.26
39 20 0.47
40 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (38 bp):
ATATATTTATAAAATATTTTATATATTTATAAATTATA
Found at i:314395 original size:30 final size:30
Alignment explanation
Indices: 314323--314396 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
314313 AATTTGATAA
*
314323 TTTATATATTTAT-ATAATATTTTATATAT
1 TTTATATATTTATAATAATATTTTAAATAT
* *
314352 TTTAT-TAAATTATAATTAT-TTTTAAAATAT
1 TTTATAT-ATTTATAATAATATTTT-AAATAT
314382 TTTATATATTTATAA
1 TTTATATATTTATAA
314397 ATTTTAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.03
29 14 0.38
30 21 0.57
31 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTATATATTTATAATAATATTTTAAATAT
Found at i:317611 original size:26 final size:28
Alignment explanation
Indices: 317575--317631 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
317565 AATATATGCA
317575 TAGCTACTTTA-TTAAGA-GATACTTCC
1 TAGCTACTTTATTTAAGATGATACTTCC
**
317601 TAGCTACTTTATTTGTGATGATACTTCC
1 TAGCTACTTTATTTAAGATGATACTTCC
317629 TAG
1 TAG
317632 GTTGGTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 11 0.41
27 4 0.15
28 12 0.44
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (28 bp):
TAGCTACTTTATTTAAGATGATACTTCC
Found at i:319615 original size:10 final size:10
Alignment explanation
Indices: 319600--319641 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
319590 AAATATATTT
319600 AATTTTTTAA
1 AATTTTTTAA
319610 AATTTTTTAA
1 AATTTTTTAA
**
319620 AA-CATTTAA
1 AATTTTTTAA
319629 AATATTTTTAA
1 AAT-TTTTTAA
319640 AA
1 AA
319642 AATAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 7 0.27
10 12 0.46
11 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:319696 original size:27 final size:26
Alignment explanation
Indices: 319628--319697 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
319618 AAAACATTTA
*
319628 AAATATTTTTAAAAAATAAATTTTTAT
1 AAATA-TTTTAAAAAATAAATTATTAT
** *
319655 ATTTATATTT-AAAAATATATTGATTAT
1 AAATAT-TTTAAAAAATAAATT-ATTAT
319682 AAATATTTTAAAAAAT
1 AAATATTTTAAAAAAT
319698 TCAAAATAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 14 0.41
27 20 0.59
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
AAATATTTTAAAAAATAAATTATTAT
Found at i:321020 original size:14 final size:16
Alignment explanation
Indices: 320980--321037 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
320970 TCTAATATGG
* *
320980 TTATTTATTTTATTAT
1 TTATTTATATTAATAT
* *
320996 TTAAATAATATTAA-AT
1 TT-ATTTATATTAATAT
321012 TT-TTTATATTAATAT
1 TTATTTATATTAATAT
321027 TTATTTATATT
1 TTATTTATATT
321038 TTATATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 8 0.24
15 4 0.12
16 14 0.42
17 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTTATATTAATAT
Found at i:321039 original size:23 final size:22
Alignment explanation
Indices: 321006--321068 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
320996 TTAAATAATA
321006 TTAAAT-T-TTTTATATTAATAT
1 TTAAATATATTTTATATTAA-AT
**
321027 TTATTTATATTTTATATTAAAT
1 TTAAATATATTTTATATTAAAT
321049 TTAAATATATTTT-TATTAAA
1 TTAAATATATTTTATATTAAA
321069 AATAATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.31
22 14 0.39
23 11 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTAAATATATTTTATATTAAAT
Found at i:326069 original size:2 final size:2
Alignment explanation
Indices: 326062--326090 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
326052 ACTAACCGAA
326062 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
326091 AACTACAACA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:328609 original size:17 final size:16
Alignment explanation
Indices: 328584--328632 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
328574 TATATCGTAA
328584 TTATA-TTTAAAATATT
1 TTATATTTTAAAA-ATT
328600 TTATATTTTATAAAATT
1 TTATATTTTA-AAAATT
* *
328617 TTATATATTAATAATT
1 TTATATTTTAAAAATT
328633 CGTATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 10 0.34
17 16 0.55
18 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATTTTAAAAATT
Found at i:329717 original size:14 final size:13
Alignment explanation
Indices: 329700--329742 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 13
329690 TAATTATAAA
329700 AATATATAAATATT
1 AATATA-AAATATT
329714 AATATAAAATAATTTT
1 AATATAAAAT-A--TT
329730 AATATAAAATATT
1 AATATAAAATATT
329743 TTTAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 6 0.23
14 7 0.27
15 1 0.04
16 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATATAAAATATT
Found at i:329731 original size:39 final size:39
Alignment explanation
Indices: 329688--329763 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
329678 TTTATTTAAA
* *
329688 TTTAATTATAAAA-ATATATAAATATTAATATAAAATAAT
1 TTTAA-TATAAAATATATATAAATAATAAAATAAAATAAT
* *
329727 TTTAATATAAAATATTTTTAAATAATAAAATAAAATA
1 TTTAATATAAAATATATATAAATAATAAAATAAAATA
329764 TTTGAACTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 7 0.22
39 25 0.78
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (39 bp):
TTTAATATAAAATATATATAAATAATAAAATAAAATAAT
Found at i:329756 original size:18 final size:16
Alignment explanation
Indices: 329712--329759 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
329702 TATATAAATA
329712 TTAATATAAAATAATT
1 TTAATATAAAATAATT
*
329728 TTAATATAAAATATTT
1 TTAATATAAAATAATT
329744 TTAAATAATAAAATAA
1 TT-AAT-ATAAAATAA
329760 AATATTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 17 0.61
17 3 0.11
18 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAATATAAAATAATT
Found at i:330693 original size:18 final size:18
Alignment explanation
Indices: 330659--330694 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
330649 CAAACCAAAA
* *
330659 TTTTTGGTTGATTTATTT
1 TTTTTGGTTCATATATTT
330677 TTTTTGGTTCATATATTT
1 TTTTTGGTTCATATATTT
330695 ACATTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.03, G:0.14, T:0.69
Consensus pattern (18 bp):
TTTTTGGTTCATATATTT
Found at i:331049 original size:20 final size:21
Alignment explanation
Indices: 331026--331065 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
331016 TAAATTTAAT
331026 TAATATATT-ATTTATAAAAA
1 TAATATATTAATTTATAAAAA
* *
331046 TAATATTTTAATTTTTAAAA
1 TAATATATTAATTTATAAAA
331066 TTTATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATATTAATTTATAAAAA
Found at i:332123 original size:71 final size:72
Alignment explanation
Indices: 332007--332221 Score: 326
Period size: 72 Copynumber: 3.0 Consensus size: 72
331997 CATCTTTTGA
*
332007 AATATTCACACCAATTTATAAGTTATTATTTATTTTAATTTATTAAAAAT-TCACAGATTACAAG
1 AATATTCACACTAATTTATAAGTTATTATTTATTTTAATTTATTAAAAATCTCACAGATTACAAG
332071 TAATGCT
66 TAATGCT
* * * *
332078 AATATTCACACTAATTCATAAGTTATTATTTATTTTAATTTATTAAAAGTCTCACAAATTATAAG
1 AATATTCACACTAATTTATAAGTTATTATTTATTTTAATTTATTAAAAATCTCACAGATTACAAG
*
332143 TAATACT
66 TAATGCT
* * *
332150 AATATTCA-AGTCAATTTATAAGTTATTATTTATTTTAATTTATTGAAAATCTCATAGATTACAA
1 AATATTCACACT-AATTTATAAGTTATTATTTATTTTAATTTATTAAAAATCTCACAGATTACAA
332214 GTAATGCT
65 GTAATGCT
332222 GACACTTACA
Statistics
Matches: 128, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
71 49 0.38
72 79 0.62
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.43
Consensus pattern (72 bp):
AATATTCACACTAATTTATAAGTTATTATTTATTTTAATTTATTAAAAATCTCACAGATTACAAG
TAATGCT
Found at i:333157 original size:10 final size:10
Alignment explanation
Indices: 333127--333164 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
333117 TTTATTTTAT
333127 TATTTAAA-A
1 TATTTAAATA
333136 TATTTAAAATA
1 TATTT-AAATA
333147 TATTTAAATA
1 TATTTAAATA
333157 TATATTAA
1 TAT-TTAA
333165 TCTTTTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.19
10 11 0.42
11 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TATTTAAATA
Found at i:333672 original size:2 final size:2
Alignment explanation
Indices: 333667--333696 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
333657 GTAGTGTGTG
333667 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
333697 CACACATACA
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):
TA
Found at i:333756 original size:3 final size:3
Alignment explanation
Indices: 333748--333788 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
333738 TTAATAGTTT
*
333748 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
333789 GCCTTCTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:334446 original size:2 final size:2
Alignment explanation
Indices: 334439--334464 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
334429 TCTTTCCTCC
334439 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
334465 TATTTGCATG
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:336521 original size:2 final size:2
Alignment explanation
Indices: 336514--336539 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
336504 ACTTCTGTTG
336514 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
336540 TGGGAAGGGC
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:338702 original size:2 final size:2
Alignment explanation
Indices: 338695--338728 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
338685 TCCTGTTTGA
*
338695 AT AT AT AT AT AT AT AT AT AT AT -T AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
338729 AATTTAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:339638 original size:2 final size:2
Alignment explanation
Indices: 339631--339657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
339621 TTTAATTAGC
339631 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 A
339658 CAGAGGCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:339942 original size:9 final size:9
Alignment explanation
Indices: 339928--339988 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 9
339918 TTAATTTAAG
339928 TTTATATAT
1 TTTATATAT
339937 TTTATA-ATT
1 TTTATATA-T
*
339946 TTTATATAA
1 TTTATATAT
339955 TTTATAT-T
1 TTTATATAT
*
339963 TTT-GATAT
1 TTTATATAT
339971 TTTAT-T-T
1 TTTATATAT
*
339978 TTTATTTAT
1 TTTATATAT
339987 TT
1 TT
339989 AAATTATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
7 8 0.19
8 10 0.24
9 23 0.55
10 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (9 bp):
TTTATATAT
Found at i:339951 original size:18 final size:17
Alignment explanation
Indices: 339928--339988 Score: 72
Period size: 16 Copynumber: 3.6 Consensus size: 17
339918 TTAATTTAAG
339928 TTTATATATTTTATAATT
1 TTTATATATTTTAT-ATT
*
339946 TTTATATAATTTATATT
1 TTTATATATTTTATATT
*
339963 TTT-GATATTTTAT-TT
1 TTTATATATTTTATATT
*
339978 TTTATTTATTT
1 TTTATATATTT
339989 AAATTATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 5 0.14
16 13 0.35
17 6 0.16
18 13 0.35
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTATATATTTTATATT
Found at i:339964 original size:16 final size:16
Alignment explanation
Indices: 339919--339982 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
339909 AGTAAAATTT
*
339919 TAATTTA-AGTTTATA
1 TAATTTATATTTTATA
*
339934 TATTTTATAATTTTTATA
1 TAATTTAT-A-TTTTATA
339952 TAATTTATATTTT-TGA
1 TAATTTATATTTTAT-A
* *
339968 TATTTTATTTTTTAT
1 TAATTTATATTTTAT
339983 TTATTTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
15 7 0.18
16 16 0.41
17 3 0.08
18 13 0.33
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TAATTTATATTTTATA
Found at i:342592 original size:6 final size:6
Alignment explanation
Indices: 342581--342619 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
342571 TTTTTTAATT
*
342581 TAAAAA TAAAAA TAAAATA TAAAAA TTAATAA TAAAAA T
1 TAAAAA TAAAAA TAAAA-A TAAAAA -TAAAAA TAAAAA T
342620 TCTCTAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (6 bp):
TAAAAA
Found at i:342620 original size:13 final size:13
Alignment explanation
Indices: 342580--342620 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
342570 ATTTTTTAAT
342580 TTAAAAATAAAAA
1 TTAAAAATAAAAA
342593 -TAAAATATAAAAA
1 TTAAAA-ATAAAAA
*
342606 TTAATAATAAAAA
1 TTAAAAATAAAAA
342619 TT
1 TT
342621 CTCTAAATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 5 0.20
13 16 0.64
14 4 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TTAAAAATAAAAA
Found at i:346896 original size:21 final size:22
Alignment explanation
Indices: 346872--346923 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
346862 TATATAATTT
346872 AAAAAATAAAATAAATAA-ATA
1 AAAAAATAAAATAAATAATATA
** **
346893 AAAATTTAAAATATGTAATATA
1 AAAAAATAAAATAAATAATATA
346915 AAAATAATA
1 AAAA-AATA
346924 TATTTCGAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 14 0.61
22 7 0.30
23 2 0.09
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAAATAAAATAAATAATATA
Found at i:346912 original size:28 final size:28
Alignment explanation
Indices: 346867--346921 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
346857 ATTTTTATAT
346867 AATTTAAAAAATAAAATA-AATAAATAAA
1 AATTTAAAAAATAAAATATAA-AAATAAA
* **
346895 AATTTAAAATATGTAATATAAAAATAA
1 AATTTAAAAAATAAAATATAAAAATAA
346922 TATATTTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (28 bp):
AATTTAAAAAATAAAATATAAAAATAAA
Found at i:347133 original size:23 final size:22
Alignment explanation
Indices: 347079--347133 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
347069 TTTATTCTAT
*
347079 TATTATATCTATAAAAAATTAA
1 TATTATATATATAAAAAATTAA
347101 TATT-TAATATATTAATAAAATT-A
1 TATTAT-ATATA-TAA-AAAATTAA
347124 TATTATATAT
1 TATTATATAT
347134 TTTATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 1 0.04
22 8 0.29
23 12 0.43
24 7 0.25
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTATATATATAAAAAATTAA
Found at i:348931 original size:2 final size:2
Alignment explanation
Indices: 348926--348950 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
348916 GTGTGTGTGA
348926 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 A
348951 AAAGTTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:354060 original size:27 final size:27
Alignment explanation
Indices: 353976--354061 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
353966 ATACTTAGTA
*
353976 ATTTATATATTTATATTAAATTTTTATAT
1 ATTT-TATATTTATA-TAAATTTTAATAT
* * *
354005 -TTTTCACA-TCATAATCAAA-TTTAAAAT
1 ATTTT-ATATTTAT-AT-AAATTTTAATAT
354032 ATTTTATATTTATATAAATTTTAATAT
1 ATTTTATATTTATATAAATTTTAATAT
354059 ATT
1 ATT
354062 AATAATTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 14
0.68 0.11 0.22
Matches are distributed among these distances:
26 3 0.07
27 25 0.57
28 16 0.36
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTTTATATTTATATAAATTTTAATAT
Found at i:354066 original size:18 final size:17
Alignment explanation
Indices: 354032--354086 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
354022 AATTTAAAAT
354032 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
354049 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
354066 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
*
354081 AATTTA
1 ATTTTA
354087 AAATATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.09
14 2 0.06
15 5 0.15
16 7 0.21
17 7 0.21
18 6 0.18
19 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:354080 original size:32 final size:33
Alignment explanation
Indices: 354029--354092 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
354019 TCAAATTTAA
* * *
354029 AATATTTTATATTTATATAAATTTTAATATATT
1 AATAATTTATATTTATATAAAATTTAAAATATT
354062 AATAATTTATA-TTATATAAAATTTAAAATAT
1 AATAATTTATATTTATATAAAATTTAAAATAT
354093 ATAAATACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
AATAATTTATATTTATATAAAATTTAAAATATT
Found at i:354084 original size:16 final size:16
Alignment explanation
Indices: 354042--354097 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
354032 ATTTTATATT
354042 TATAT-AAATTT-TAA
1 TATATAAAATTTATAA
*
354056 TATATTAATAATTTATAT
1 TATA-TAA-AATTTATAA
*
354074 TATATAAAATTTAAAA
1 TATATAAAATTTATAA
354090 TATATAAA
1 TATATAAA
354098 TACAAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 4 0.11
15 1 0.03
16 16 0.46
17 8 0.23
18 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATATAAAATTTATAA
Found at i:354084 original size:33 final size:34
Alignment explanation
Indices: 354028--354099 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 34
354018 ATCAAATTTA
* *
354028 AAATATTTTATATTTATATAAATTT-TAATATAT
1 AAATAATTTATATTTATATAAATTTAAAATATAT
*
354061 TAATAATTTATA-TTATATAAAATTTAAAATATAT
1 AAATAATTTATATTTATAT-AAATTTAAAATATAT
354095 AAATA
1 AAATA
354100 CAAATTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 6 0.18
33 16 0.48
34 11 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
AAATAATTTATATTTATATAAATTTAAAATATAT
Found at i:354564 original size:16 final size:16
Alignment explanation
Indices: 354521--354562 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
354511 AATTTAAATA
354521 AAATTATTTAATTATTT
1 AAATTATTTAA-TATTT
*
354538 AATTTAATTTAA-ATTT
1 AAATT-ATTTAATATTT
354554 AAATTATTT
1 AAATTATTT
354563 TATTCAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.18
16 8 0.36
17 4 0.18
18 6 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATTATTTAATATTT
Found at i:354906 original size:21 final size:22
Alignment explanation
Indices: 354867--354908 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
354857 GTTTAAATCT
*
354867 TATTTGATTTAATTTTTTTATC
1 TATTTGATTTAATTATTTTATC
*
354889 TATTT-ATTTCATTATTTTAT
1 TATTTGATTTAATTATTTTAT
354909 TTATCCATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTTGATTTAATTATTTTATC
Found at i:354909 original size:17 final size:16
Alignment explanation
Indices: 354889--354943 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
354879 TTTTTTTATC
354889 TATTTATTTCATTATTT
1 TATTTA-TTCATTATTT
*
354906 TATTTATCCATGTATTT
1 TATTTATTCAT-TATTT
*
354923 CATTTA-T-A-TATTT
1 TATTTATTCATTATTT
354936 TATTTATT
1 TATTTATT
354944 TAAAAACGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 10 0.31
14 1 0.03
15 1 0.03
16 4 0.12
17 16 0.50
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.65
Consensus pattern (16 bp):
TATTTATTCATTATTT
Found at i:354921 original size:25 final size:24
Alignment explanation
Indices: 354878--354926 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
354868 ATTTGATTTA
* *
354878 ATTTTTTTATCTATTTATTTCATT
1 ATTTTTTTATCCATGTATTTCATT
354902 ATTTTATTTATCCATGTATTTCATT
1 ATTTT-TTTATCCATGTATTTCATT
354927 TATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.65
Consensus pattern (24 bp):
ATTTTTTTATCCATGTATTTCATT
Found at i:354934 original size:25 final size:25
Alignment explanation
Indices: 354883--354935 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
354873 ATTTAATTTT
* * *
354883 TTTATCTATTTATTTCATTATTTTA
1 TTTATCCATGTATTTCATTATTATA
354908 TTTATCCATGTATTTCATT-TATATA
1 TTTATCCATGTATTTCATTAT-TATA
354933 TTT
1 TTT
354936 TATTTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTATCCATGTATTTCATTATTATA
Found at i:354956 original size:21 final size:20
Alignment explanation
Indices: 354930--354985 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
354920 TTTCATTTAT
354930 ATATTTTATTTATTTAA-AA
1 ATATTTTATTTATTTAATAA
354949 ACGTATTTTATTTATTTAATAA
1 A--TATTTTATTTATTTAATAA
*
354971 ATTTTTTATTTATTT
1 ATATTTTATTTATTT
354986 TTAGCATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 1 0.03
20 13 0.39
21 16 0.48
22 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
ATATTTTATTTATTTAATAA
Found at i:359185 original size:2 final size:2
Alignment explanation
Indices: 359178--359210 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
359168 GTAGGACCCT
359178 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
359211 TTGGTAAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:359753 original size:19 final size:19
Alignment explanation
Indices: 359716--359755 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
359706 TAAATTAAAA
*
359716 ATAATTAATAATTATTTTT
1 ATAATTAAAAATTATTTTT
359735 ATAATATAAAAATTATTTTT
1 ATAAT-TAAAAATTATTTTT
359755 A
1 A
359756 AAAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAATTAAAAATTATTTTT
Found at i:359897 original size:21 final size:22
Alignment explanation
Indices: 359867--359907 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
359857 AAATAAATTT
*
359867 TTTTATAAAT-TTTTATTTTTA
1 TTTTAAAAATATTTTATTTTTA
359888 TTTTAAAAATATTTTATTTT
1 TTTTAAAAATATTTTATTTT
359908 GTAGTGCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTAAAAATATTTTATTTTTA
Found at i:361211 original size:12 final size:12
Alignment explanation
Indices: 361162--361215 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
361152 ATACTTTTTA
361162 TTATTATCAGATAT
1 TTATTAT-A-ATAT
*
361176 TTATTATAATTAA
1 TTATTATAA-TAT
**
361189 TTAAAATAATAT
1 TTATTATAATAT
361201 TTATTATAATAT
1 TTATTATAATAT
361213 TTA
1 TTA
361216 CAATTATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 16 0.48
13 10 0.30
14 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
TTATTATAATAT
Found at i:362203 original size:46 final size:46
Alignment explanation
Indices: 362136--362242 Score: 214
Period size: 46 Copynumber: 2.3 Consensus size: 46
362126 AAATGATAAG
362136 GGTACAGTGTCATAAAGAGCCTAGTACTTTTGATGGAGGTGGTCCT
1 GGTACAGTGTCATAAAGAGCCTAGTACTTTTGATGGAGGTGGTCCT
362182 GGTACAGTGTCATAAAGAGCCTAGTACTTTTGATGGAGGTGGTCCT
1 GGTACAGTGTCATAAAGAGCCTAGTACTTTTGATGGAGGTGGTCCT
362228 GGTACAGTGTCATAA
1 GGTACAGTGTCATAA
362243 TAATATTTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (46 bp):
GGTACAGTGTCATAAAGAGCCTAGTACTTTTGATGGAGGTGGTCCT
Found at i:365554 original size:14 final size:14
Alignment explanation
Indices: 365535--365576 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
365525 TTAATAATAT
365535 TAAATATAATTATA
1 TAAATATAATTATA
365549 TAAATATAAATATAATA
1 TAAATAT-AAT-T-ATA
365566 TAAAT-TAATTA
1 TAAATATAATTA
365577 ATTAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 1 0.04
14 8 0.32
15 6 0.24
16 2 0.08
17 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:365596 original size:30 final size:28
Alignment explanation
Indices: 365562--365636 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
365552 ATATAAATAT
*
365562 AATATAAATTAATTAATTAAAATATGATAC
1 AATATAAATT-ATTAATCAAAATAT-ATAC
* *
365592 AATATGAATT-TATATATCAAAATATATAT
1 AATATAAATTAT-TA-ATCAAAATATATAC
365621 AATATAAATTATTAAT
1 AATATAAATTATTAAT
365637 ATATGAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 3 0.08
29 16 0.42
30 19 0.50
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (28 bp):
AATATAAATTATTAATCAAAATATATAC
Found at i:365650 original size:18 final size:17
Alignment explanation
Indices: 365605--365663 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
365595 ATGAATTTAT
*
365605 ATATCAAAATATATAT-A
1 ATAT-AAAATTTATATAA
365622 ATAT-AAA-TTAT-TAA
1 ATATAAAATTTATATAA
365636 TATATGAAAATTTATATAA
1 -ATAT-AAAATTTATATAA
365655 ATATAAAAT
1 ATATAAAAT
365664 ATAATATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 4 0.11
15 7 0.20
17 12 0.34
18 8 0.23
19 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
ATATAAAATTTATATAA
Found at i:365671 original size:20 final size:20
Alignment explanation
Indices: 365530--365682 Score: 61
Period size: 20 Copynumber: 7.3 Consensus size: 20
365520 GATATTTAAT
*
365530 AATATTAAATATAATTATATA
1 AATATAAAATATAA-TATATA
365551 AATAT-AAATATAATATA-A
1 AATATAAAATATAATATATA
* * * *
365569 ATTAATTAATTAAAATATGATA
1 AAT-ATAAAATATAATAT-ATA
* *
365591 CAATAT-GAAT-TTATATATCAA
1 -AATATAAAATATAATATAT--A
365612 AATATATATAATATAA-ATTATTA
1 AATATA-A-AATATAATA-TA-TA
365635 ATATATGAAAAT-T--TATATA
1 A-ATAT-AAAATATAATATATA
365654 AATATAAAATATAATATAATAA
1 AATATAAAATATAATAT-AT-A
365676 AATATAA
1 AATATAA
365683 CGAATATGAC
Statistics
Matches: 101, Mismatches: 10, Indels: 41
0.66 0.07 0.27
Matches are distributed among these distances:
17 5 0.05
18 8 0.08
19 11 0.11
20 31 0.31
21 12 0.12
22 12 0.12
23 11 0.11
24 9 0.09
25 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (20 bp):
AATATAAAATATAATATATA
Found at i:365674 original size:10 final size:10
Alignment explanation
Indices: 365537--365682 Score: 51
Period size: 10 Copynumber: 14.7 Consensus size: 10
365527 AATAATATTA
365537 AATATAAT-T
1 AATATAATAT
365546 -ATATAAATAT
1 AATAT-AATAT
365556 AAATATAATAT
1 -AATATAATAT
365567 AA-ATTAAT-T
1 AATA-TAATAT
*
365576 AATTAAAATAT
1 AA-TATAATAT
* *
365587 GATACAATAT
1 AATATAATAT
*
365597 GAATTTATATAT
1 -AATATA-ATAT
*
365609 CAAAATATATAT
1 -AATATA-ATAT
365621 AATATAA-AT
1 AATATAATAT
*
365630 TAT-TAATAT
1 AATATAATAT
*
365639 -ATGAAAAT-T
1 AAT-ATAATAT
*
365648 TATATAA-AT
1 AATATAATAT
*
365657 -ATAAAATAT
1 AATATAATAT
*
365666 AATATAATAA
1 AATATAATAT
365676 AATATAA
1 AATATAA
365683 CGAATATGAC
Statistics
Matches: 104, Mismatches: 16, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
8 14 0.13
9 20 0.19
10 37 0.36
11 16 0.15
12 17 0.16
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (10 bp):
AATATAATAT
Found at i:367315 original size:2 final size:2
Alignment explanation
Indices: 367308--367339 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
367298 AAGACATCAC
367308 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
367340 AAATACCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:367803 original size:25 final size:26
Alignment explanation
Indices: 367775--367829 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
367765 ATTTTTTATT
** *
367775 TTTTTAAATATTTATAT-ATAATATA
1 TTTTTAAATATAAATATAAAAATATA
*
367800 TTTTTAGATATAAATATAAAAATATA
1 TTTTTAAATATAAATATAAAAATATA
367826 TTTT
1 TTTT
367830 ATTTAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTTTAAATATAAATATAAAAATATA
Found at i:375782 original size:2 final size:2
Alignment explanation
Indices: 375775--375805 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
375765 ATCATATCTT
*
375775 AC AC AC AC AC AC AC AC AC AC AC AC GC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
375806 AGGAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:382068 original size:17 final size:19
Alignment explanation
Indices: 382047--382106 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
382037 GATAAGAATT
382047 TATATTATTTGAAT-TAAAA
1 TATA-TATTTGAATATAAAA
*
382066 TATAAATATTGAATATAAAA
1 TATATAT-TTGAATATAAAA
382086 -ATATATTTG-ATAT-AAA
1 TATATATTTGAATATAAAA
382102 TATAT
1 TATAT
382107 TAAATTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 3 0.08
17 8 0.22
18 5 0.14
19 15 0.42
20 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
TATATATTTGAATATAAAA
Found at i:383248 original size:35 final size:36
Alignment explanation
Indices: 383209--383279 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
383199 CTTCTGACCC
*
383209 ATGCATCCTAAAGAGATCTCACAT-CATGGTGGGTT
1 ATGCATCCTAAAGAGATCCCACATCCATGGTGGGTT
383244 ATGCATCCTAAAGAGATCCCACATCCATGGTGGGTT
1 ATGCATCCTAAAGAGATCCCACATCCATGGTGGGTT
383280 TTGAACCTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 23 0.68
36 11 0.32
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (36 bp):
ATGCATCCTAAAGAGATCCCACATCCATGGTGGGTT
Found at i:383853 original size:2 final size:2
Alignment explanation
Indices: 383848--383874 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
383838 ATATATACAA
383848 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
383875 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:384699 original size:2 final size:2
Alignment explanation
Indices: 384692--384727 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
384682 TTATACATAC
384692 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
384728 TGAAGGCGTT
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:387018 original size:2 final size:2
Alignment explanation
Indices: 387013--387045 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
387003 TGTGTTTGTA
387013 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
387046 CCTGAGTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:387863 original size:23 final size:23
Alignment explanation
Indices: 387837--387882 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
387827 TTTTTTTTCC
*
387837 CCTAACTATTGTTATCTATCCCG
1 CCTAACCATTGTTATCTATCCCG
387860 CCTAACCATTGTTATCTATCCCG
1 CCTAACCATTGTTATCTATCCCG
387883 TCTTTAAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.33, G:0.09, T:0.37
Consensus pattern (23 bp):
CCTAACCATTGTTATCTATCCCG
Found at i:390004 original size:137 final size:137
Alignment explanation
Indices: 389758--390033 Score: 498
Period size: 137 Copynumber: 2.0 Consensus size: 137
389748 CGTTCTGTCA
*
389758 AATTTCAATAATATGGTTCAAAATCAGTTTTGGGTAAAAATAAAAAGGCTTAAATCTGATAATGC
1 AATTTCAATAATATGGCTCAAAATCAGTTTTGGGTAAAAATAAAAAGGCTTAAATCTGATAATGC
*
389823 TAGAGATTATTTCAACTATCTCTTATCTGACTACTTTAAAAGAGAGGGAATAATTCATGAGTCCT
66 TAGAGATTATTTCAACTATCTCTTATCTGACTACTTTAAAAGAGAGAGAATAATTCATGAGTCCT
389888 CCTGTGT
131 CCTGTGT
* * *
389895 AATTTCAATAATATGGCTCACAATCAGTTTTGGGTAAAAATAAAGAGGTTTAAATCTGATAATGC
1 AATTTCAATAATATGGCTCAAAATCAGTTTTGGGTAAAAATAAAAAGGCTTAAATCTGATAATGC
*
389960 TAGAGATTATTTCAACTATCTCTTATCTGACTACTTTAAAAGAGAGAGAATAATTCATGAGTCTT
66 TAGAGATTATTTCAACTATCTCTTATCTGACTACTTTAAAAGAGAGAGAATAATTCATGAGTCCT
390025 CCTGTGT
131 CCTGTGT
390032 AA
1 AA
390034 ATACCCCGCA
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 133 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (137 bp):
AATTTCAATAATATGGCTCAAAATCAGTTTTGGGTAAAAATAAAAAGGCTTAAATCTGATAATGC
TAGAGATTATTTCAACTATCTCTTATCTGACTACTTTAAAAGAGAGAGAATAATTCATGAGTCCT
CCTGTGT
Found at i:393387 original size:21 final size:20
Alignment explanation
Indices: 393363--393418 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 20
393353 TTTCTTGCAA
393363 CAAGTA-TAAGCATTTTAGTTT
1 CAAGTAGTAA-CA-TTTAGTTT
393384 CAAGTAAGTAACATTTAGTTT
1 CAAGT-AGTAACATTTAGTTT
393405 CAAGTACGTAACAT
1 CAAGTA-GTAACAT
393419 GCCGTACCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.03
21 25 0.78
22 3 0.09
23 3 0.09
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (20 bp):
CAAGTAGTAACATTTAGTTT
Found at i:397100 original size:2 final size:2
Alignment explanation
Indices: 397093--397117 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
397083 GATTTTTAAA
397093 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
397118 TCAAATTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:401712 original size:7 final size:8
Alignment explanation
Indices: 401696--401729 Score: 54
Period size: 7 Copynumber: 4.5 Consensus size: 8
401686 TTATATTTAA
401696 TATAATAT
1 TATAATAT
401704 TATAA-AT
1 TATAATAT
401711 TATAATAT
1 TATAATAT
401719 T-TAATAT
1 TATAATAT
401726 TATA
1 TATA
401730 TAAAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 14 0.58
8 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TATAATAT
Found at i:401713 original size:27 final size:26
Alignment explanation
Indices: 401682--401740 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
401672 ACTATCTTAT
*
401682 ATTATTATATTTAATATAATATTATAA
1 ATTATTATATTTAATATAATA-TAAAA
* *
401709 ATTATAATATTTAATATTATATAAAA
1 ATTATTATATTTAATATAATATAAAA
401735 ATTATT
1 ATTATT
401741 GGATAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTATTATATTTAATATAATATAAAA
Found at i:401714 original size:15 final size:15
Alignment explanation
Indices: 401680--401729 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
401670 TGACTATCTT
*
401680 ATATTATTATATTT-
1 ATATTATAATATTTA
401694 A-A-TATAATATTATA
1 ATATTATAATATT-TA
401708 A-ATTATAATATTTA
1 ATATTATAATATTTA
401722 ATATTATA
1 ATATTATA
401730 TAAAAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 8 0.26
13 2 0.06
14 6 0.19
15 15 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTATAATATTTA
Found at i:402453 original size:14 final size:14
Alignment explanation
Indices: 402434--402461 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
402424 AAATCTGATA
402434 AATGTTATTAAAAT
1 AATGTTATTAAAAT
402448 AATGTTATTAAAAT
1 AATGTTATTAAAAT
402462 GTAAATTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
AATGTTATTAAAAT
Found at i:408546 original size:21 final size:22
Alignment explanation
Indices: 408494--408546 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
408484 AATTAAAATA
* *
408494 AATTTTATTGTTATATAATTAT
1 AATTTTATTGTAATATAATAAT
408516 AATTTT-TTGTAATATAA-AAT
1 AATTTTATTGTAATATAATAAT
*
408536 TATTTTATTGT
1 AATTTTATTGT
408547 TGAATTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.26
21 14 0.52
22 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (22 bp):
AATTTTATTGTAATATAATAAT
Found at i:408633 original size:15 final size:15
Alignment explanation
Indices: 408610--408665 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
408600 AAGCAGTAAA
*
408610 TTAAATTAATAAAAT
1 TTAATTTAATAAAAT
*
408625 TTAATTTAA-ATAAT
1 TTAATTTAATAAAAT
* *
408639 TTGATTGTATATAATAT
1 TTAATT-TA-ATAAAAT
408656 TTAATTTAAT
1 TTAATTTAAT
408666 TTTAATTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
14 9 0.28
15 12 0.38
16 3 0.09
17 8 0.25
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (15 bp):
TTAATTTAATAAAAT
Found at i:408671 original size:6 final size:6
Alignment explanation
Indices: 408650--408683 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
408640 TGATTGTATA
408650 TAATATT TAA-TT TAATTT TAATTT TAATTT TAAT
1 TAAT-TT TAATTT TAATTT TAATTT TAATTT TAAT
408684 GAAAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 18 0.69
7 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TAATTT
Found at i:409563 original size:20 final size:20
Alignment explanation
Indices: 409538--409581 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
409528 GAGTTTAAAT
* * *
409538 AATTTAATTTTTTAAAATTA
1 AATTTAAATTTTAAAAATAA
409558 AATTTAAATTTTAAAAATAA
1 AATTTAAATTTTAAAAATAA
409578 AATT
1 AATT
409582 CAATCAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTTAAATTTTAAAAATAA
Found at i:410442 original size:18 final size:18
Alignment explanation
Indices: 410419--410456 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
410409 AACGTGATTT
410419 ATTTTT-TAATATTATATA
1 ATTTTTATAATATTA-ATA
*
410437 ATTTTTATAGTATTAATA
1 ATTTTTATAATATTAATA
410455 AT
1 AT
410457 AAATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTTTATAATATTAATA
Found at i:410472 original size:28 final size:29
Alignment explanation
Indices: 410431--410489 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
410421 TTTTTAATAT
* * *
410431 TATATAATTTTTATAGTATTAATAATAAA
1 TATATAATTATTATAATATAAATAATAAA
*
410460 TATATAA-TATTATAATATAAATATTAAA
1 TATATAATTATTATAATATAAATAATAAA
410488 TA
1 TA
410490 ATATGTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
TATATAATTATTATAATATAAATAATAAA
Found at i:410479 original size:13 final size:13
Alignment explanation
Indices: 410451--410489 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
410441 TTATAGTATT
*
410451 AATAATAAATATA
1 AATATTAAATATA
410464 TAATATTATAATATA
1 -AATATTA-AATATA
410479 AATATTAAATA
1 AATATTAAATA
410490 ATATGTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 13 0.57
15 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATTAAATATA
Found at i:417629 original size:79 final size:79
Alignment explanation
Indices: 417498--417858 Score: 401
Period size: 79 Copynumber: 4.6 Consensus size: 79
417488 TAAAACCCGA
* * *
417498 GGTTGAAGCATCCCCGATTGTGAAAAATAGATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCC
417563 CTCGAAAATAACGG
66 CTCGAAAATAACGG
* * *
417577 GGTTGGAGTATCCCCAATTGTGAAAAATCGATGTTTTGAAAATAAAACCGAGGTTGGAGTATTCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCC
* *
417642 CTTGGAAATAACGG
66 CTCGAAAATAACGG
* * * * * * *
417656 GGTTGGAGTAT-CCCTATTATGAAAAATCAAT-ATTTCAGAAAT-AAAGCTAGGGTTGGAGTATC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGA-AAATAAAATCGA-GGTTGGAGTATC
*
417718 CCCTCGAAAATAACAG
64 CCCTCGAAAATAACGG
* * * * *
417734 GGTTGGAGTGT-CCCGATGGTGAAAAATGGATATTTTGAAAATAAAATTG-GGATTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAAATCGAGG-TTGGAGTATCC
*
417797 TCTCGAAAATAACGG
65 CCTCGAAAATAACGG
** * * *
417812 GGTTTGG-GTATCCTTGATTATGAAAAATCGGTGTTTTAAAAATAAAA
1 GG-TTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAAA
417859 ACATCGATGC
Statistics
Matches: 234, Mismatches: 41, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
77 11 0.05
78 103 0.44
79 120 0.51
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCC
CTCGAAAATAACGG
Found at i:417729 original size:78 final size:77
Alignment explanation
Indices: 417518--417857 Score: 344
Period size: 78 Copynumber: 4.3 Consensus size: 77
417508 TCCCCGATTG
* * * *
417518 TGAAAAATAGATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGG
1 TGAAAAATCGATATTTTGAAAATAAACTAG-GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGG
* *
417583 AGTATCCCCAATTG
65 AGTAT-CCCTATTA
* * * * *
417597 TGAAAAATCGATGTTTTGAAAATAAAAC-CGAGGTTGGAGTATTCCCTTGGAAATAACGGGGTTG
1 TGAAAAATCGATATTTTGAAAAT-AAACTAG-GGTTGGAGTATCCCCTCGAAAATAACGGGGTTG
417661 GAGTATCCCTATTA
64 GAGTATCCCTATTA
* * *
417675 TGAAAAATCAATA-TTTCAGAAATAAAGCTAGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTG
1 TGAAAAATCGATATTTTGA-AAATAAA-CTAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTG
* * **
417739 GAGTGTCCCGATGG
64 GAGTATCCCTATTA
* * * *
417753 TGAAAAATGGATATTTTGAAAATAAAATTGGGATTGGAGTATCCTCTCGAAAATAACGGGGTTTG
1 TGAAAAATCGATATTTTGAAAATAAACTAGGG-TTGGAGTATCCCCTCGAAAATAACGGGG-TTG
*
417818 G-GTATCCTTGATTA
64 GAGTATCCCT-ATTA
* * *
417832 TGAAAAATCGGTGTTTTAAAAATAAA
1 TGAAAAATCGATATTTTGAAAATAAA
417858 AACATCGATG
Statistics
Matches: 218, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
77 11 0.05
78 110 0.50
79 94 0.43
80 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (77 bp):
TGAAAAATCGATATTTTGAAAATAAACTAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGA
GTATCCCTATTA
Found at i:417832 original size:157 final size:157
Alignment explanation
Indices: 417549--417840 Score: 421
Period size: 156 Copynumber: 1.9 Consensus size: 157
417539 ATAAAATCGA
* * *
417549 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTTTT
1 GGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTT
* *
417614 GAAAATAAAACCGAGGTTGGAGTATTCCCTTGGAAATAACGGGGTTGGAGTATCCCTATTATGAA
66 GAAAATAAAACCGAGGTTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCTATTATGAA
417679 AAATCAATATTTCAGAAATAAAGCTAG
131 AAATCAATATTTCAGAAATAAAGCTAG
* * *
417706 GGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTGT-CCCGATGGTGAAAAATGGATATTTT
1 GGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTT
** *
417770 GAAAATAAAATTG-GGATTGGAGTA-TCCTCTCGAAAATAACGGGGTTTGG-GTATCCTTGATTA
66 GAAAATAAAACCGAGG-TTGGAGTATTCC-CTCGAAAATAACGGGG-TTGGAGTATCCCT-ATTA
417832 TGAAAAATC
127 TGAAAAATC
417841 GGTGTTTTAA
Statistics
Matches: 120, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
155 5 0.04
156 61 0.51
157 54 0.45
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (157 bp):
GGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTT
GAAAATAAAACCGAGGTTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCTATTATGAA
AAATCAATATTTCAGAAATAAAGCTAG
Found at i:417855 original size:157 final size:158
Alignment explanation
Indices: 417498--417858 Score: 428
Period size: 157 Copynumber: 2.3 Consensus size: 158
417488 TAAAACCCGA
* * * * * * *
417498 GGTTGAAGCATCCCCGATTGTGAAAAATAGATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCC
1 GGTTGGAGTATCCCTGATTATGAAAAATCGATGTTTTAAAAATAAAATAGAGGTTGGAGTATCCC
* * *
417563 CTCGAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATCGATGTTTTGAAAATAAAACCGA
66 CTCGAAAATAACAGGGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTTGAAAATAAAACCGA
* *
417628 GGTTGGAGTATTCCCTTGGAAATAACGG
131 GGTTGGAGTATTCCCTCGAAAATAACGG
* * * * *
417656 GGTTGGAGTATCCCT-ATTATGAAAAATCAATATTTCAGAAATAAAGCTAG-GGTTGGAGTATCC
1 GGTTGGAGTATCCCTGATTATGAAAAATCGATGTTTTAAAAATAAA-ATAGAGGTTGGAGTATCC
* * * **
417719 CCTCGAAAATAACAGGGTTGGAGTGT-CCCGATGGTGAAAAATGGATATTTTGAAAATAAAATTG
65 CCTCGAAAATAACAGGGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTTGAAAATAAAACCG
417783 -GGATTGGAGTA-TCCTCTCGAAAATAACGG
130 AGG-TTGGAGTATTCC-CTCGAAAATAACGG
* *
417812 GGTTTGG-GTATCCTTGATTATGAAAAATCGGTGTTTTAAAAATAAAA
1 GG-TTGGAGTATCCCTGATTATGAAAAATCGATGTTTTAAAAATAAAA
417859 ACATCGATGC
Statistics
Matches: 169, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
155 5 0.03
156 61 0.36
157 89 0.53
158 14 0.08
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (158 bp):
GGTTGGAGTATCCCTGATTATGAAAAATCGATGTTTTAAAAATAAAATAGAGGTTGGAGTATCCC
CTCGAAAATAACAGGGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTTGAAAATAAAACCGA
GGTTGGAGTATTCCCTCGAAAATAACGG
Found at i:422922 original size:26 final size:26
Alignment explanation
Indices: 422886--422936 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
422876 GATTCGAAGA
*
422886 TGAAAGTTAGATTATGAGTGCGTATT
1 TGAAAGTTAGAATATGAGTGCGTATT
* *
422912 TGAATGTTAGAATATGAGTGTGTAT
1 TGAAAGTTAGAATATGAGTGCGTAT
422937 CTCATTGCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.27, T:0.39
Consensus pattern (26 bp):
TGAAAGTTAGAATATGAGTGCGTATT
Found at i:423209 original size:17 final size:18
Alignment explanation
Indices: 423176--423209 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
423166 CATAAGTGTC
*
423176 AAAAATAAATAATTCAAG
1 AAAAATAAATAAATCAAG
423194 AAAAATAAA-AAATCAA
1 AAAAATAAATAAATCAA
423210 AGCCAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAATAAATAAATCAAG
Found at i:427235 original size:3 final size:3
Alignment explanation
Indices: 427227--427261 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
427217 TTTTTCCCCA
*
427227 TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
427262 CTGCCCTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:428742 original size:11 final size:11
Alignment explanation
Indices: 428725--428782 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
428715 AATTTTTACC
428725 TAAATTAAAAT
1 TAAATTAAAAT
*
428736 CAAATT-AAAT
1 TAAATTAAAAT
* *
428746 TTAATAAAAAT
1 TAAATTAAAAT
*
428757 GAAATTAAAAAT
1 TAAATT-AAAAT
428769 TAAATTAAATAT
1 TAAATTAAA-AT
428781 TA
1 TA
428783 CGATTCAACT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
10 7 0.19
11 15 0.42
12 14 0.39
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (11 bp):
TAAATTAAAAT
Found at i:428782 original size:12 final size:12
Alignment explanation
Indices: 428725--428782 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
428715 AATTTTTACC
428725 TAAATT-AAAAT
1 TAAATTAAAAAT
*
428736 CAAATT--AAAT
1 TAAATTAAAAAT
*
428746 TTAA-TAAAAAT
1 TAAATTAAAAAT
*
428757 GAAATTAAAAAT
1 TAAATTAAAAAT
*
428769 TAAATTAAATAT
1 TAAATTAAAAAT
428781 TA
1 TA
428783 CGATTCAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 1 0.03
10 6 0.16
11 11 0.30
12 19 0.51
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (12 bp):
TAAATTAAAAAT
Found at i:429599 original size:21 final size:22
Alignment explanation
Indices: 429565--429606 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
429555 ATAACTTAAC
429565 ATATTTTAATATTTATATTATA
1 ATATTTTAATATTTATATTATA
*
429587 ATATTTT-ATATTTTTATTAT
1 ATATTTTAATATTTATATTAT
429607 TTATATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATATTTTAATATTTATATTATA
Done.