Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 1 of 210
Found at i:672 original size:20 final size:20
Alignment explanation
Indices: 647--698 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
637 AAGGATATGC
*
647 AATCTTAGATATGATTTTGT
1 AATCTTAGAGATGATTTTGT
667 AATCTTAGAGATGATTTTGT
1 AATCTTAGAGATGATTTTGT
687 AATCTTAGAGAT
1 AATCTTAGAGAT
699 TTAATTTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (20 bp):
AATCTTAGAGATGATTTTGT
Found at i:708 original size:21 final size:20
Alignment explanation
Indices: 647--708 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
637 AAGGATATGC
* *
647 AATCTTAGATATGATTTTGT
1 AATCTTAGAGATGAATTTGT
*
667 AATCTTAGAGATGATTTTGT
1 AATCTTAGAGATGAATTTGT
*
687 AATCTTAGAGATTTAATTTGT
1 AATCTTAGAGA-TGAATTTGT
708 A
1 A
709 GATACCCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
20 30 0.79
21 8 0.21
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (20 bp):
AATCTTAGAGATGAATTTGT
Found at i:1014 original size:3 final size:3
Alignment explanation
Indices: 1006--1041 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
996 TGTTATTAAG
* *
1006 TTA TTA TTA TTG TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1042 CTATATATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:6296 original size:44 final size:44
Alignment explanation
Indices: 6232--6519 Score: 244
Period size: 44 Copynumber: 6.5 Consensus size: 44
6222 GCAGATCAGT
* *
6232 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
*
6277 GAAGATGCAGATCTTGTCTTACC-ATACTGGTAGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTT-CCTATATTGGTAGCGAAGTAGATC
* * * * * *
6321 GAAGAAAGCAGATCTTGTCTTCATGTATTTG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * * *
6365 GAAGAAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * * * *
6408 AAAGATGTAGATCTTGTCTT-CTCATACTAGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCT-ATATTGGTAGCGAAGTAGATC
* * * * * * *
6452 GAAGAAAGCAGATTTTGTCTTCATGTATTGG-CGTGAAGTATATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* *
6496 AAAGATAGCAGATCTTGCCTTCCT
1 GAAGAT-GCAGATCTTGTCTTCCT
6520 GCACTGACAG
Statistics
Matches: 192, Mismatches: 42, Indels: 19
0.76 0.17 0.08
Matches are distributed among these distances:
42 2 0.01
43 53 0.28
44 92 0.48
45 44 0.23
46 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (44 bp):
GAAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
Found at i:6473 original size:131 final size:133
Alignment explanation
Indices: 6232--6519 Score: 447
Period size: 131 Copynumber: 2.2 Consensus size: 133
6222 GCAGATCAGT
*
6232 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCAAAGATGCAGATCTTGTCTT
* *
6297 ACCATACTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTTGCGTGAAGTAG
66 ACCATACTAGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
6362 ATC
131 ATC
* *
6365 GAAGA-AGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCAAAGATGTAGATCTTGTCTT
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCAAAGATGCAGATCTTGTCTT
* *
6428 -CTCATACTAGTGGCGAAGTAGATCGAAGAAAGCAGATTTTGTCTTCATGTATTGGCGTGAAGTA
66 AC-CATACTAGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTA
*
6492 TATC
130 GATC
* * *
6496 AAAGATAGCAGATCTTGCCTTCCT
1 GAAGATAGCAGATCCTGTCTTCCT
6520 GCACTGACAG
Statistics
Matches: 141, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
130 1 0.01
131 93 0.66
132 42 0.30
133 5 0.04
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (133 bp):
GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCAAAGATGCAGATCTTGTCTT
ACCATACTAGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
ATC
Found at i:6601 original size:44 final size:44
Alignment explanation
Indices: 6553--6867 Score: 138
Period size: 44 Copynumber: 7.2 Consensus size: 44
6543 AGACACCAAC
6553 CTTGCCTCCCTGGGTTGCAGCGGAGCAAGCTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAAGCTAAAAATAGCAGAT
* **** * * * * * * * *
6597 CTTGCCTTCCTGCACCGACAACGAAGC-AGATCGAAGACACCA-AC
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAAGCT-AAAAATAGCAGAT
* * * *
6641 CTTGCCTCCATGGGTTGCAGGGGAGCAGGCTAAAAATAGTAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAAGCTAAAAATAGCAGAT
* * **** * * * * * * *
6685 CTTGCATTCCTGCACCGACAGCGAAGC-AGATCGAATACACCAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAAGCT-AAAAATAGCAGAT
* *
6729 CTTGCCTCCCTGGGTTGCAGTGGAGCAGGCTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAAGCTAAAAATAGCAGAT
* **** * * * * * * *
6773 CTTGCCTTCCTGTACCGACAGCGAAGC-AGATCGAAGACACCA-AC
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAAGCT-AAAAATAGCAGAT
6817 CTTGCCTCCCTGGGTTGCAGCGGAGCAAGCTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAAGCTAAAAATAGCAGAT
6861 CTTGCCT
1 CTTGCCT
6868 TCCTACACCG
Statistics
Matches: 171, Mismatches: 88, Indels: 24
0.60 0.31 0.08
Matches are distributed among these distances:
43 39 0.23
44 93 0.54
45 39 0.23
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGGAGCAAGCTAAAAATAGCAGAT
Found at i:6917 original size:88 final size:88
Alignment explanation
Indices: 6500--6894 Score: 673
Period size: 88 Copynumber: 4.5 Consensus size: 88
6490 TATATCAAAG
*
6500 ATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG
6565 GGTTGCAGCGGAGCAAGCTAAAA
66 GGTTGCAGCGGAGCAAGCTAAAA
* *
6588 ATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAACCTTGCCTCCATG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG
* *
6653 GGTTGCAGGGGAGCAGGCTAAAA
66 GGTTGCAGCGGAGCAAGCTAAAA
* * * *
6676 ATAGTAGATCTTGCATTCCTGCACCGACAGCGAAGCAGATCGAATACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG
* *
6741 GGTTGCAGTGGAGCAGGCTAAAA
66 GGTTGCAGCGGAGCAAGCTAAAA
*
6764 ATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG
6829 GGTTGCAGCGGAGCAAGCTAAAA
66 GGTTGCAGCGGAGCAAGCTAAAA
*
6852 ATAGCAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGA
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
6895 TGACCCCAGC
Statistics
Matches: 286, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 286 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTG
GGTTGCAGCGGAGCAAGCTAAAA
Found at i:6970 original size:44 final size:44
Alignment explanation
Indices: 6905--7114 Score: 271
Period size: 44 Copynumber: 4.8 Consensus size: 44
6895 TGACCCCAGC
*
6905 CCTATCTCCCTGGTCAGCAGTGAAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGAAATAGGTTGAAGATTGTGAAT
* * *
6949 CCTATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGAAATAGGTTGAAGATTGTGAAT
** * * *
6993 TATATCTCCCTGGGCAGCAGTGAAATAGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGAAATAGGTTGAAGATTGTGA-AT
*
7037 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGAAATAGGTTGAAGATTGTGAAT
* * *
7081 CCTATCTCCCTAAG-CAGCAGTGGAGTAGGTTGAA
1 CCTATCTCCCT-GGTCAGCAGTGAAATAGGTTGAA
7115 TATAGCAGAT
Statistics
Matches: 143, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
43 1 0.01
44 140 0.98
45 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGAAATAGGTTGAAGATTGTGAAT
Found at i:8274 original size:3 final size:3
Alignment explanation
Indices: 8266--8330 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
8256 TGTTATTAAG
* *
8266 TTA TTA TTA TTA TTG TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
8314 CTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
8331 NNNNNNNNNN
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:11214 original size:19 final size:19
Alignment explanation
Indices: 11183--11221 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
11173 TATGTATAAT
11183 TACATCAAATTAAAATTTA
1 TACATCAAATTAAAATTTA
11202 TACAT-AAATTTAAAATTTA
1 TACATCAAA-TTAAAATTTA
11221 T
1 T
11222 CCCTTAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
TACATCAAATTAAAATTTA
Found at i:13094 original size:22 final size:22
Alignment explanation
Indices: 13069--13113 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
13059 TTCATGGAAA
13069 ATGTCTATAAGCTATATGGTAT
1 ATGTCTATAAGCTATATGGTAT
13091 ATGTCTATAAGCTATATGGTAT
1 ATGTCTATAAGCTATATGGTAT
13113 A
1 A
13114 CCAGATTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (22 bp):
ATGTCTATAAGCTATATGGTAT
Found at i:16407 original size:22 final size:21
Alignment explanation
Indices: 16381--16421 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
16371 CAATATAACC
16381 ACAAAAAATAAAGAAGTTCATA
1 ACAAAAAATAAAGAA-TTCATA
**
16403 ACAAAATTTAAAGAATTCA
1 ACAAAAAATAAAGAATTCA
16422 AAAAGAGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.61, C:0.10, G:0.07, T:0.22
Consensus pattern (21 bp):
ACAAAAAATAAAGAATTCATA
Found at i:17527 original size:21 final size:21
Alignment explanation
Indices: 17501--17559 Score: 79
Period size: 19 Copynumber: 2.9 Consensus size: 21
17491 TCAAAAAATA
17501 TTTTTATTCTTTTTTTTTATG
1 TTTTTATTCTTTTTTTTTATG
*
17522 TTTTTATTC-TTTTGTTT-TG
1 TTTTTATTCTTTTTTTTTATG
17541 TTTTTATT-TTTATTTTTTA
1 TTTTTATTCTTT-TTTTTTA
17560 GAACAAACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 12 0.36
20 12 0.36
21 9 0.27
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.81
Consensus pattern (21 bp):
TTTTTATTCTTTTTTTTTATG
Found at i:18522 original size:6 final size:6
Alignment explanation
Indices: 18511--18536 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
18501 ATAATAAAAT
18511 AAAAGA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AA
18537 GAAAACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:18546 original size:21 final size:21
Alignment explanation
Indices: 18506--18590 Score: 73
Period size: 21 Copynumber: 3.9 Consensus size: 21
18496 AGTGCATAAT
* *
18506 AAAATAAAAGAAAAAGAAAAAG
1 AAAA-AAAAGAAAAACAAAAAC
18528 AAAAAGAAAG-AAAACAAAAAC
1 AAAAA-AAAGAAAAACAAAAAC
* *
18549 TAAAAAAAGTAAAACAAAAAAC
1 AAAAAAAAGAAAAAC-AAAAAC
*
18571 AAAAACAAAAAAAATACAAA
1 AAAAA-AAAGAAAA-ACAAA
18591 CGAAAATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
20 4 0.08
21 19 0.37
22 18 0.35
23 9 0.17
24 2 0.04
ACGTcount: A:0.81, C:0.07, G:0.07, T:0.05
Consensus pattern (21 bp):
AAAAAAAAGAAAAACAAAAAC
Found at i:18547 original size:22 final size:21
Alignment explanation
Indices: 18506--18584 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 21
18496 AGTGCATAAT
*
18506 AAAATAAAAGAAAA-AGAAAAAG
1 AAAA-AAAAGAAAACA-AAAAAC
18528 AAAAAGAAAGAAAAC-AAAAAC
1 AAAAA-AAAGAAAACAAAAAAC
*
18549 TAAAAAAAGTAAAACAAAAAAC
1 AAAAAAAAG-AAAACAAAAAAC
*
18571 AAAAACAAAAAAAA
1 AAAAA-AAAGAAAA
18585 TACAAACGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 4 0.08
21 15 0.31
22 26 0.54
23 3 0.06
ACGTcount: A:0.82, C:0.06, G:0.08, T:0.04
Consensus pattern (21 bp):
AAAAAAAAGAAAACAAAAAAC
Found at i:18567 original size:13 final size:13
Alignment explanation
Indices: 18538--18582 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
18528 AAAAAGAAAG
18538 AAAACAAAAACTAA
1 AAAACAAAAAC-AA
18552 AAAA-AGTAAAACAA
1 AAAACA--AAAACAA
18566 AAAACAAAAACAA
1 AAAACAAAAACAA
18579 AAAA
1 AAAA
18583 AATACAAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 12 0.43
14 10 0.36
15 6 0.21
ACGTcount: A:0.82, C:0.11, G:0.02, T:0.04
Consensus pattern (13 bp):
AAAACAAAAACAA
Found at i:18602 original size:28 final size:28
Alignment explanation
Indices: 18538--18596 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
18528 AAAAAGAAAG
*
18538 AAAACAAAAACTAAAAAAAGTAAAACAA
1 AAAACAAAAACTAAAAAAAATAAAACAA
*
18566 AAAACAAAAAC-AAAAAAAATACAAACGA
1 AAAACAAAAACTAAAAAAAATA-AAACAA
18594 AAA
1 AAA
18597 TAAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.80, C:0.12, G:0.03, T:0.05
Consensus pattern (28 bp):
AAAACAAAAACTAAAAAAAATAAAACAA
Found at i:25906 original size:21 final size:20
Alignment explanation
Indices: 25865--25908 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
25855 ACCCCTGCAG
* * *
25865 TTTGAAAATTTGTATCTTTT
1 TTTGAAAAATTCTATATTTT
*
25885 TTTGAAAAATTCTATATGTT
1 TTTGAAAAATTCTATATTTT
25905 TTTG
1 TTTG
25909 GTTTAGCCCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (20 bp):
TTTGAAAAATTCTATATTTT
Found at i:27611 original size:23 final size:23
Alignment explanation
Indices: 27548--27613 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
27538 TAAGACAAGG
*
27548 GTGGACGACACACCCTAATAGAA
1 GTGGACGACACACCCTAGTAGAA
* *
27571 GTGGATGACACACCCTAGTAGGA
1 GTGGACGACACACCCTAGTAGAA
*
27594 GTGGACGGCACACCCTAGTA
1 GTGGACGACACACCCTAGTA
27614 TTCCTACTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.27, T:0.15
Consensus pattern (23 bp):
GTGGACGACACACCCTAGTAGAA
Found at i:28014 original size:12 final size:12
Alignment explanation
Indices: 27997--28021 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27987 TGCAAATGAA
27997 TCATTTCCATTT
1 TCATTTCCATTT
28009 TCATTTCCATTT
1 TCATTTCCATTT
28021 T
1 T
28022 TGGAAGCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:33569 original size:28 final size:29
Alignment explanation
Indices: 33534--33592 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
33524 ATTCAGGTTG
33534 AAAAATGAGTGAAAAGTGA-GTAGTTGCA
1 AAAAATGAGTGAAAAGTGAGGTAGTTGCA
33562 AAAAATGAGTGAAAAGTGAGGTAGTTGCA
1 AAAAATGAGTGAAAAGTGAGGTAGTTGCA
33591 AA
1 AA
33593 GTTTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 19 0.63
29 11 0.37
ACGTcount: A:0.47, C:0.03, G:0.29, T:0.20
Consensus pattern (29 bp):
AAAAATGAGTGAAAAGTGAGGTAGTTGCA
Found at i:34506 original size:15 final size:15
Alignment explanation
Indices: 34486--34515 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34476 AACAATTTGC
34486 TCTTTTGGGTTATAA
1 TCTTTTGGGTTATAA
34501 TCTTTTGGGTTATAA
1 TCTTTTGGGTTATAA
34516 AACAAACCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (15 bp):
TCTTTTGGGTTATAA
Found at i:36604 original size:17 final size:17
Alignment explanation
Indices: 36561--36594 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
36551 AACTGTCACA
36561 TGAATTAAATTAATTTT
1 TGAATTAAATTAATTTT
36578 TGAATTAAATTAATTTT
1 TGAATTAAATTAATTTT
36595 ATAGTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TGAATTAAATTAATTTT
Found at i:40053 original size:45 final size:45
Alignment explanation
Indices: 39984--40156 Score: 174
Period size: 45 Copynumber: 3.9 Consensus size: 45
39974 TACTGAGAAT
* * * **
39984 CATTGATTATAAAGGTGGTTGCTATATGCTAATTCCACCGGGTAC
1 CATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGAAAC
* * *
40029 CATTAATTATAAAGGTGGTTGCTATGTGTTGACTCCACCGGAAAT
1 CATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGAAAC
* *
40074 CATTGAA-AATAAAGGTGGTTGCTATGTGCTGATTCCACC-GAATAT
1 CATT-AATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGAA-AC
* * * *
40119 AATTGATTATAAGGGTGG-TGCCATGTGCTGA-TCCACCG
1 CATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACCG
40157 TGTAACGATT
Statistics
Matches: 108, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
43 6 0.06
44 16 0.15
45 84 0.78
46 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32
Consensus pattern (45 bp):
CATTAATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGAAAC
Found at i:40136 original size:90 final size:88
Alignment explanation
Indices: 39981--40156 Score: 226
Period size: 90 Copynumber: 2.0 Consensus size: 88
39971 GTGTACTGAG
** ** *
39981 AATCATTGATTATAAAGGTGGTTGCTATATGCTAATTCCACCGGGTACCATTAATTATAAAGGTG
1 AATCATTGAAAATAAAGGTGGTTGCTATATGCTAATTCCACCGAATACAATTAATTATAAAGGTG
* *
40046 GTTGCTATGTGTTGACTCCACCGGA
66 G-TGCCATGTGCTGA-TCCACCGGA
* * * * *
40071 AATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCACCGAATATAATTGATTATAAGGGTG
1 AATCATTGAAAATAAAGGTGGTTGCTATATGCTAATTCCACCGAATACAATTAATTATAAAGGTG
40136 GTGCCATGTGCTGATCCACCG
66 GTGCCATGTGCTGATCCACCG
40157 TGTAACGATT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
88 7 0.09
89 11 0.15
90 56 0.76
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (88 bp):
AATCATTGAAAATAAAGGTGGTTGCTATATGCTAATTCCACCGAATACAATTAATTATAAAGGTG
GTGCCATGTGCTGATCCACCGGA
Found at i:46575 original size:26 final size:26
Alignment explanation
Indices: 46546--46609 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
46536 TACCGCCAGC
46546 AAAATTTTGACGA-TTTT-ACCCTTGAT
1 AAAATTTTGA-GACTTTTGACCCTTG-T
* * *
46572 AAAATTATGATACTTTTGCCCCTTGT
1 AAAATTTTGAGACTTTTGACCCTTGT
46598 AAAATTTTGAGA
1 AAAATTTTGAGA
46610 AAATATGTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 1 0.03
26 24 0.77
27 6 0.19
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (26 bp):
AAAATTTTGAGACTTTTGACCCTTGT
Found at i:48635 original size:23 final size:22
Alignment explanation
Indices: 48609--48652 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
48599 AATTGACTAA
48609 GTGT-AATTGAATAATGAATATAG
1 GTGTGAATTGAAT--TGAATATAG
48632 GTGTGGAATTGAATTGAATAT
1 GTGT-GAATTGAATTGAATAT
48653 CGACTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGAATTGAATTGAATATAG
Found at i:49788 original size:33 final size:33
Alignment explanation
Indices: 49773--49838 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
49763 TGGTAAATGT
*
49773 CTAGATGAAAATATGCTTGTGATCATAAAAGGG
1 CTAGATGAAAATATGCTTGAGATCATAAAAGGG
49806 CTAGATGAAAATATGCTTGTA-ATCATAAAAGGG
1 CTAGATGAAAATATGCTTG-AGATCATAAAAGGG
49839 TGGTAAGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (33 bp):
CTAGATGAAAATATGCTTGAGATCATAAAAGGG
Found at i:56367 original size:11 final size:12
Alignment explanation
Indices: 56351--56383 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
56341 TGGTTCCTTT
56351 ATTTTATTTT-C
1 ATTTTATTTTCC
56362 ATTTTATTTTCC
1 ATTTTATTTTCC
*
56374 TTTTTATTTT
1 ATTTTATTTT
56384 ATTCTAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTATTTTCC
Found at i:64090 original size:10 final size:11
Alignment explanation
Indices: 64075--64103 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
64065 ATTTGTTTCC
64075 TTTATTTTA-T
1 TTTATTTTATT
64085 TTTATTTTATT
1 TTTATTTTATT
64096 TTTATTTT
1 TTTATTTT
64104 CCTATGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:77051 original size:50 final size:50
Alignment explanation
Indices: 76976--77173 Score: 202
Period size: 50 Copynumber: 3.8 Consensus size: 50
76966 TTTCATGTAC
* * * * **
76976 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
77026 TGCCCATGTCATGTCCCAGACATGGTCTTATA-GGGTACCTCTCATCTCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGG-ACCTCTCATATCGG
* *
77076 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG
*
77131 ATGCCAAT-TCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGT-CATGTCCCAGACATGGTCTTACATGGGACCTCT
77174 TTACCCAAAT
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
49 2 0.02
50 75 0.61
51 3 0.02
53 2 0.02
55 2 0.02
56 38 0.31
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:77119 original size:100 final size:104
Alignment explanation
Indices: 76976--77161 Score: 247
Period size: 100 Copynumber: 1.8 Consensus size: 104
76966 TTTCATGTAC
* * ** *
76976 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCAT-A-TC-GG-TGCCCATGT-C
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATGACTCAGGATGCCAAT-TCC
77036 ATGTCCCAGACATGGTCTTATAGGGTACCTCTCATCTCGG
65 ATGTCCCAGACATGGTCTTATAGGGTACCTCTCATCTCGG
* *
77076 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAATTC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATGA-CTC-AGGATGCCAATTC
77141 CATGTCCCAGACATGGTCTTA
64 CATGTCCCAGACATGGTCTTA
77162 CATGGGATCT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
100 39 0.54
101 1 0.01
103 2 0.03
105 3 0.04
106 27 0.38
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (104 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATGACTCAGGATGCCAATTCCA
TGTCCCAGACATGGTCTTATAGGGTACCTCTCATCTCGG
Found at i:88299 original size:88 final size:88
Alignment explanation
Indices: 88150--88329 Score: 306
Period size: 88 Copynumber: 2.0 Consensus size: 88
88140 CTTTCTTAAC
* *
88150 TAAAAATTAATTATTTCATAGTACAGAATTCAGATAATACTCTCGTTTATTTATTTTGAAAATAA
1 TAAAAACTAATTATTTCATAGTACAGAATTCAGATAATAATCTCGTTTATTTATTTTGAAAATAA
88215 ACTCATTCAGGATTCTAAAAATA
66 ACTCATTCAGGATTCTAAAAATA
* * *
88238 TAAAAACTAATTATTTCATAGTACAGAATTCGGATAATAATCTCGTTTATTTCTTTTGAAAATAG
1 TAAAAACTAATTATTTCATAGTACAGAATTCAGATAATAATCTCGTTTATTTATTTTGAAAATAA
*
88303 ACTCATTCAGGATTCTAGAAATA
66 ACTCATTCAGGATTCTAAAAATA
88326 TAAA
1 TAAA
88330 TTTTATCTCA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (88 bp):
TAAAAACTAATTATTTCATAGTACAGAATTCAGATAATAATCTCGTTTATTTATTTTGAAAATAA
ACTCATTCAGGATTCTAAAAATA
Found at i:88923 original size:45 final size:45
Alignment explanation
Indices: 88785--88957 Score: 167
Period size: 45 Copynumber: 3.9 Consensus size: 45
88775 TAGACAATGG
* * * *
88785 ATCAGCACATAGC-ACCACCCTTATAGTTAATGATA-CTCGGTGGA
1 ATCAGCACACAACAACCACCTTTATAATTAATGATACCT-GGTGGA
* * **
88829 ATCA--ACACATAGAACCCACCTTCATAATTAAT-AGTACCCAGTGGA
1 ATCAGCACACA-ACAA-CCACCTTTATAATTAATGA-TACCTGGTGGA
88874 ATCAGCACACAACAACCACCTTTATAATTAATGATACCTGGTGGA
1 ATCAGCACACAACAACCACCTTTATAATTAATGATACCTGGTGGA
* * * *
88919 ATCAGTAGACAACAACCACCTTTATAATCAATGGTACCT
1 ATCAGCACACAACAACCACCTTTATAATTAATGATACCT
88958 AGTACACGTA
Statistics
Matches: 105, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
42 4 0.04
44 6 0.06
45 85 0.81
46 5 0.05
47 5 0.05
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.24
Consensus pattern (45 bp):
ATCAGCACACAACAACCACCTTTATAATTAATGATACCTGGTGGA
Found at i:88956 original size:90 final size:89
Alignment explanation
Indices: 88785--88956 Score: 206
Period size: 90 Copynumber: 1.9 Consensus size: 89
88775 TAGACAATGG
* * * *
88785 ATCAGCACATAGCACCACCCTTATAGTTAATGATACTCGGTGGAATCAACACATAGAACCCACCT
1 ATCAGCACACAACACCACCCTTATAATTAATGATACTCGGTGGAATCAACACATACAACCCACCT
*
88850 TCATAATTAATAGTACCCAGTGGA
66 TCATAATCAATAGTACCCAGTGGA
* *
88874 ATCAGCACACAACAACCACCTTTATAATTAATGATAC-CTGGTGGAATCAGTAGACA-ACAA-CC
1 ATCAGCACACAAC-ACCACCCTTATAATTAATGATACTC-GGTGGAATCA--ACACATACAACCC
* *
88936 ACCTTTATAATCAATGGTACC
62 ACCTTCATAATCAATAGTACC
88957 TAGTACACGT
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
89 12 0.17
90 51 0.73
91 3 0.04
92 4 0.06
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (89 bp):
ATCAGCACACAACACCACCCTTATAATTAATGATACTCGGTGGAATCAACACATACAACCCACCT
TCATAATCAATAGTACCCAGTGGA
Found at i:96022 original size:50 final size:50
Alignment explanation
Indices: 95906--96100 Score: 171
Period size: 50 Copynumber: 3.9 Consensus size: 50
95896 GATAATAACA
* * * * * * **
95906 TGCCAAAGCCATGTCCCAGACATGGTATTACATGGGACATTTC-T-TGCAC
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATAT-CGG
* * **
95955 TGCCAATGCCATATCCTAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATATCGG
* ** * *
96005 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATATCGG
* * *
96055 TGCCAACGCCATGTCCCAAACATGGTCTTACATTG-GACCTCTCATA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACA-TGAGACCTCTCATA
96101 ATCTCAATAA
Statistics
Matches: 116, Mismatches: 27, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
49 34 0.29
50 80 0.69
51 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:106004 original size:50 final size:50
Alignment explanation
Indices: 105925--106028 Score: 127
Period size: 50 Copynumber: 2.1 Consensus size: 50
105915 TTGAGGTTAG
* * * * *
105925 GAGAGGTCCCACATAAGACCATGTTTGGGACTTGGCCTTGGCACCGAGAT
1 GAGAGGTCCCACATAAGACCATGTCTGGGACATGGCATGGGAACCGAGAT
* * * *
105975 GAGAGGTCCCCCGTAAGACTATGTCTGGGACATGGCATGGGAACCGATAT
1 GAGAGGTCCCACATAAGACCATGTCTGGGACATGGCATGGGAACCGAGAT
106025 GAGA
1 GAGA
106029 ACTCTCATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.26, C:0.22, G:0.32, T:0.20
Consensus pattern (50 bp):
GAGAGGTCCCACATAAGACCATGTCTGGGACATGGCATGGGAACCGAGAT
Found at i:106344 original size:20 final size:20
Alignment explanation
Indices: 106319--106357 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
106309 TGAGTTATTT
106319 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
106339 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
106358 GAAAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:106909 original size:17 final size:19
Alignment explanation
Indices: 106887--106923 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
106877 AGGCAAATAA
106887 ATTTT-ATATTA-TGAGAT
1 ATTTTAATATTAGTGAGAT
*
106904 ATTTTAATTTTAGTGAGAT
1 ATTTTAATATTAGTGAGAT
106923 A
1 A
106924 GGGTCAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (19 bp):
ATTTTAATATTAGTGAGAT
Found at i:113582 original size:50 final size:50
Alignment explanation
Indices: 113521--113651 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 50
113511 GAGATCCCGT
* * ** **
113521 GTAAAACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTTCCC-C
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGA-ACTCCCAC
* * *
113571 GTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAACTCCCAC
* *
113621 GTAAGACCATGTTTGGGACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
113652 TGTTATTATC
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 4 0.06
50 64 0.94
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAACTCCCAC
Found at i:117236 original size:36 final size:36
Alignment explanation
Indices: 117196--117268 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
117186 ATCGTCCCCA
117196 GTCAAGCGGCTTTAAGATCCAATCTTAATAGCAGGT
1 GTCAAGCGGCTTTAAGATCCAATCTTAATAGCAGGT
117232 GTCAAGCGGCTTTAAGATCCAATCTTAATAGCAGGT
1 GTCAAGCGGCTTTAAGATCCAATCTTAATAGCAGGT
117268 G
1 G
117269 AAACCGGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (36 bp):
GTCAAGCGGCTTTAAGATCCAATCTTAATAGCAGGT
Found at i:140289 original size:5 final size:5
Alignment explanation
Indices: 140279--140304 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
140269 TATACATTGT
140279 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
140305 CTGTAATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:143123 original size:42 final size:43
Alignment explanation
Indices: 143070--143209 Score: 115
Period size: 42 Copynumber: 3.3 Consensus size: 43
143060 CTAGCACAAA
**
143070 CGCCGCTAAAGAGTAAGACCTTTAGCGGCGCTTTAGTG-GAAG
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTAGTGAGAAG
** * * *
143112 CGCCGCTAAAGACCCTGATCTTTAGCGGCGTTTTTGTGAGAAG
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTAGTGAGAAG
* * * ** *
143155 TGCCGCTAAAG-CTTCATGATCTTTAGCGGCG-TTTTCTGAAAAAG
1 CGCCGCTAAAGAC--CAAGACCTTTAGCGGCGCTTTAGTG-AGAAG
143199 CGCCGCTAAAG
1 CGCCGCTAAAG
143210 GTCATGGTCT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
42 32 0.39
43 20 0.24
44 30 0.37
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (43 bp):
CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTAGTGAGAAG
Found at i:143229 original size:43 final size:42
Alignment explanation
Indices: 143002--143296 Score: 207
Period size: 44 Copynumber: 6.8 Consensus size: 42
142992 ACGCCGCTAA
* ** *
143002 CTTTAGCGGCGTTTTTAGAAATAAACGCCGCTAAAGGTGTTGGT
1 CTTTAGCGGCGTTTTT-GAAA-AAGCGCCGCTAAAGGTCATGAT
* ** * * * *
143046 CTATAGCGGCGCTACTAGCACAAA-CGCCGCTAAAGAGT-AAGAC
1 CTTTAGCGGCG-TTTTTG-AAAAAGCGCCGCTAAAG-GTCATGAT
* * *** ** *
143089 CTTTAGCGGCGCTTTAGTGGAAGCGCCGCTAAAGACCCTGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAAGGTCATGAT
* * * *
143131 CTTTAGCGGCGTTTTTGTGAGAAGTGCCGCTAAAGCTTCATGAT
1 CTTTAGCGGCGTTTTTG-AAAAAGCGCCGCTAAAG-GTCATGAT
*
143175 CTTTAGCGGCGTTTTCTGAAAAAGCGCCGCTAAAGGTCATGGT
1 CTTTAGCGGCGTTTT-TGAAAAAGCGCCGCTAAAGGTCATGAT
* * *
143218 CTATAGCGGCGTTTTTGGGAAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTTT--GAAAAAGCGCCGCTAAAGGTCATGAT
* **
143262 CTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAG
1 CTTTAGCGGCGTTT-TTGAAAAAGCGCCGCTAAAG
143297 TTAGCGACGC
Statistics
Matches: 200, Mismatches: 40, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
41 2 0.01
42 32 0.16
43 72 0.36
44 87 0.44
45 7 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAAGGTCATGAT
Found at i:143286 original size:87 final size:85
Alignment explanation
Indices: 143070--143296 Score: 226
Period size: 87 Copynumber: 2.6 Consensus size: 85
143060 CTAGCACAAA
* * * *
143070 CGCCGCTAAAGAGT-AAGACCTTTAGCGGCGCTTTAGTGG-AAGCGCCGCTAAAGACCCTGATCT
1 CGCCGCTAAAGCGTCATGATCTTTAGCGGCG-TTT-GTGGAAAGCGCCGCTAAAGACCATGATCT
* * *
143133 TTAGCGGCGTTTTTGTGAGAAG
64 ATAGCGGCGTTTTTGGGAAAAG
* * * * ** *
143155 TGCCGCTAAAGCTTCATGATCTTTAGCGGCGTTTTCTGAAAAAGCGCCGCTAAAGGTCATGGTCT
1 CGCCGCTAAAGCGTCATGATCTTTAGCGGCG-TTTGTG-GAAAGCGCCGCTAAAGACCATGATCT
143220 ATAGCGGCGTTTTTGGGAAAAAG
64 ATAGCGGCGTTTTTGGG-AAAAG
* *
143243 CGCCGCTAAAG-GTCTTGGTCTTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAG
1 CGCCGCTAAAGCGTCATGATCTTTAGCGGCGTTTGT-GG-AAAGCGCCGCTAAAG
143297 TTAGCGACGC
Statistics
Matches: 115, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
85 13 0.11
86 21 0.18
87 67 0.58
88 14 0.12
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (85 bp):
CGCCGCTAAAGCGTCATGATCTTTAGCGGCGTTTGTGGAAAGCGCCGCTAAAGACCATGATCTAT
AGCGGCGTTTTTGGGAAAAG
Found at i:143854 original size:87 final size:87
Alignment explanation
Indices: 143748--143941 Score: 230
Period size: 87 Copynumber: 2.2 Consensus size: 87
143738 ATGCTGTTCT
* * * * * *
143748 GCTTCCCTCGTTGCAGCCTCTAATTCCCTCGCTGCTGCATCTGCTTTAAGCTGCT-GTTGGAGTT
1 GCTTCTCTCGATGCTGCCTCTAATTCCCTCGCTGCCGCATCTACTTTAAGCTG-TAGCTGGAGTT
143812 CTTCATA-CTTTCGTTGAACCTCA
65 CTTCATATCTTT-GTTGAACCTCA
* ** * * *
143835 GCTTCTCTCGCTGCTGCCTCTGCTTCTCTCGTTGCCGCATCTACTTTAAGTTGTAGCTGGAGTTC
1 GCTTCTCTCGATGCTGCCTCTAATTCCCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGTTC
*
143900 TTCATATCTTTTTTGAACCTCA
66 TTCATATCTTTGTTGAACCTCA
*
143922 GCTTCTCTCGATGTTGCCTC
1 GCTTCTCTCGATGCTGCCTC
143942 CACTTTAAGT
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
86 1 0.01
87 86 0.95
88 4 0.04
ACGTcount: A:0.12, C:0.30, G:0.18, T:0.39
Consensus pattern (87 bp):
GCTTCTCTCGATGCTGCCTCTAATTCCCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGTTC
TTCATATCTTTGTTGAACCTCA
Found at i:156085 original size:15 final size:15
Alignment explanation
Indices: 156065--156102 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
156055 TTGAAATTAA
156065 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
156080 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
156095 CCCTAAAT
1 CCCTAAAT
156103 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:156572 original size:41 final size:40
Alignment explanation
Indices: 156503--156805 Score: 165
Period size: 41 Copynumber: 7.4 Consensus size: 40
156493 GGCGCTCGGC
** * *
156503 AAAAACGCCGCTAAAGGTAAATACATTAGCGACGCTTAAAT
1 AAAAACGCCGCTAAAGACAGAGA-ATTAGCGACGCTTAAAT
* * * * * **
156544 ACAAACGCCGCTGAAGACAAGAGAATTAGTGGCGCTCAGTT
1 AAAAACGCCGCTAAAGAC-AGAGAATTAGCGACGCTTAAAT
* * **
156585 AGAAACGCCGCTAAAGATCCGAGAATTAGCGACGCTTGTAT
1 AAAAACGCCGCTAAAGA-CAGAGAATTAGCGACGCTTAAAT
* * * * * *
156626 AAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCATAGAC
1 AAAAACGCCGCTAAAGA-CAGAGAATTAGCGACGCTTAAAT
* * * * *
156667 AAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTTAGAC
1 AAAAACGCCGCTAAAGA-CAGAGAATTAGCGACGCTTAAAT
* * * * * * ** *
156708 GAAATCGCCGCTAAAGATCGGGGAATTAGTGGCGCTTTCAC
1 AAAAACGCCGCTAAAGA-CAGAGAATTAGCGACGCTTAAAT
* * * * * * *
156749 AAAAACGCCGCGAAAGATCGGAGCATTAGCGGCACTTACAC
1 AAAAACGCCGCTAAAGA-CAGAGAATTAGCGACGCTTAAAT
156790 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
156806 GTTTAAAAAA
Statistics
Matches: 213, Mismatches: 47, Indels: 4
0.81 0.18 0.02
Matches are distributed among these distances:
41 209 0.98
42 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGACAGAGAATTAGCGACGCTTAAAT
Found at i:156643 original size:82 final size:80
Alignment explanation
Indices: 156526--156805 Score: 262
Period size: 82 Copynumber: 3.4 Consensus size: 80
156516 AAGGTAAATA
* * *
156526 CATTAGCGACGCTTAA-ATACAAACGCCGCTGAAGACAAGAGAATTAGTGGCGC-TCAGTTAGAA
1 CATTAGCGACGCTTAACA-A-AAACGCCGCTAAAGAC-AGAGAATTAGTGGCGCTTCAG-CAAAA
156589 ACGCCGCTAAAGATCCGAG
62 ACGCCGCTAAAGATCCGAG
* * * * * * *
156608 AATTAGCGACGCTTGTATAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCAT-AGACAAAAA
1 CATTAGCGACGCTT-AACAAAAACGCCGCTAAAGA-CAGAGAATTAGTGGCGCTTCAG-CAAAAA
156672 CGCCGCTAAAGATCCGAG
63 CGCCGCTAAAGATCCGAG
* * * * *
156690 CATTAGCGGCGCTTAGACGAAATCGCCGCTAAAGATCGGGGAATTAGTGGCGCTTTCA-CAAAAA
1 CATTAGCGACGCTTA-ACAAAAACGCCGCTAAAGA-CAGAGAATTAGTGGCGC-TTCAGCAAAAA
* *
156754 CGCCGCGAAAGATCGGAG
63 CGCCGCTAAAGATCCGAG
* *
156772 CATTAGCGGCACTTACACAAAAACGCCGCTAAAG
1 CATTAGCGACGCTTA-ACAAAAACGCCGCTAAAG
156806 GTTTAAAAAA
Statistics
Matches: 164, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
82 157 0.96
83 5 0.03
84 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.16
Consensus pattern (80 bp):
CATTAGCGACGCTTAACAAAAACGCCGCTAAAGACAGAGAATTAGTGGCGCTTCAGCAAAAACGC
CGCTAAAGATCCGAG
Found at i:174694 original size:29 final size:29
Alignment explanation
Indices: 174662--174774 Score: 167
Period size: 29 Copynumber: 3.9 Consensus size: 29
174652 AAGGCATTCA
*
174662 TTTAACTGAGATAGCCACAAAGGCTTCCT
1 TTTAACTAAGATAGCCACAAAGGCTTCCT
*
174691 TTTAACTAAGATAGCCACAAAGACATT-CT
1 TTTAACTAAGATAGCCACAAAGGC-TTCCT
*
174720 TTTAACTAAGATAGCCAAAAAGGCTTCCT
1 TTTAACTAAGATAGCCACAAAGGCTTCCT
174749 TTTAAC-AGAGATAGCCACAAAGGCTT
1 TTTAACTA-AGATAGCCACAAAGGCTT
174775 TCTGTAACAC
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
28 3 0.04
29 71 0.93
30 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (29 bp):
TTTAACTAAGATAGCCACAAAGGCTTCCT
Found at i:174732 original size:58 final size:58
Alignment explanation
Indices: 174656--174770 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
174646 TTCCATAAGG
* *
174656 CATTCATTTAACTGAGATAGCCACAAAGGCTTCCTTTTAACTA-AGATAGCCACAAAGA
1 CATTCATTTAACTAAGATAGCCAAAAAGGCTTCCTTTTAAC-AGAGATAGCCACAAAGA
*
174714 CATTCTTTTAACTAAGATAGCCAAAAAGGCTTCCTTTTAACAGAGATAGCCACAAAG
1 CATTCATTTAACTAAGATAGCCAAAAAGGCTTCCTTTTAACAGAGATAGCCACAAAG
174771 GCTTTCTGTA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
57 1 0.02
58 52 0.98
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (58 bp):
CATTCATTTAACTAAGATAGCCAAAAAGGCTTCCTTTTAACAGAGATAGCCACAAAGA
Found at i:184627 original size:20 final size:20
Alignment explanation
Indices: 184602--184640 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
184592 TGAGTTATTT
184602 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
184622 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
184641 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:185439 original size:13 final size:12
Alignment explanation
Indices: 185420--185446 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
185410 GGAGACTTTA
185420 ACGAAAAAATTT
1 ACGAAAAAATTT
185432 ACGAAAAAATTT
1 ACGAAAAAATTT
185444 ACG
1 ACG
185447 GATCTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (12 bp):
ACGAAAAAATTT
Found at i:192628 original size:42 final size:42
Alignment explanation
Indices: 192518--192676 Score: 156
Period size: 43 Copynumber: 3.7 Consensus size: 42
192508 AACTCGTACA
** * * *
192518 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCAAATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACAGGTAATCATAT-ACG
* * *
192561 ATGCCACTATCCCAGACAGGGTCTTACAGGTAATCATATACG
1 ATGCCAATGTCCCAGACATGGTCTTACAGGTAATCATATACG
* ** * *
192603 ACGCCAATGTCCCAGACATGGTCTTACACATAAATCTTAAACCG
1 ATGCCAATGTCCCAGACATGGTCTTACAGGT-AATCATATA-CG
* *
192647 ATGCCAACGTCCCAGACATGGTTTTACAGG
1 ATGCCAATGTCCCAGACATGGTCTTACAGG
192677 ATATCACATT
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
42 28 0.29
43 40 0.42
44 27 0.28
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACAGGTAATCATATACG
Found at i:193783 original size:13 final size:13
Alignment explanation
Indices: 193765--193791 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
193755 CACAAACGAT
193765 AAAATTTTCACAC
1 AAAATTTTCACAC
193778 AAAATTTTCACAC
1 AAAATTTTCACAC
193791 A
1 A
193792 TATAAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:197920 original size:566 final size:567
Alignment explanation
Indices: 196837--197969 Score: 2259
Period size: 566 Copynumber: 2.0 Consensus size: 567
196827 ATCAATCACA
196837 TAAGAAAAATAGGCTTCGCATCCCTTTTTCACATAATTCAGAGCTTTCATTACAGATATCACAAC
1 TAAGAAAAATAGGCTTCGCATCCCTTTTTCACATAATTCAGAGCTTTCATTACAGATATCACAAC
196902 TGGAAACCCTTTCAGATCACTAGACTCAATTCGGATTATCTCATCATTCTTGCATCTCAAATCAA
66 TGGAAACCCTTTCAGATCACTAGACTCAATTCGGATTATCTCATCATTCTTGCATCTCAAATCAA
196967 TAGTTTTTTGTTTGCAATTCACAATAGCATCGTGCAAAGTTAACCAATCCATACCCAGAATTATA
131 TAGTTTTTTGTTTGCAATTCACAATAGCATCGTGCAAAGTTAACCAATCCATACCCAGAATTATA
197032 TCAAATTTATCAAAAGGTAATAGCATCAGATTAGCCAGAAAACAGATATCTCGAATCATCAATGG
196 TCAAATTTATCAAAAGGTAATAGCATCAGATTAGCCAGAAAACAGATATCTCGAATCATCAATGG
197097 ACAATTCTTGCATACTTTATGAACCAAGACACACCGGCCTAAGGGGTTTGATTCTCTAGTCACAA
261 ACAATTCTTGCATACTTTATGAACCAAGACACACCGGCCTAAGGGGTTTGATTCTCTAGTCACAA
197162 ACTCAGTAGACTCTACAGGAAAAGTCTTGCTGGATACTAAATTCATGCATATGTAAGAATGAGTA
326 ACTCAGTAGACTCTACAGGAAAAGTCTTGCTGGATACTAAATTCATGCATATGTAAGAATGAGTA
197227 TATCTCAGATCAATCAAATCAACAATAGTAGTATCATAAAGAAGGAAAGTACCAGTAACGACATC
391 TATCTCAGATCAATCAAATCAACAATAGTAGTATCATAAAGAAGGAAAGTACCAGTAACGACATC
197292 TGGAGATGAGGCTTCTTCGCGAGCACGAATAGCGTATACTCGAGCAGGTGCTCTGGCCTCGGACC
456 TGGAGATGAGGCTTCTTCGCGAGCACGAATAGCGTATACTCGAGCAGGTGCTCTGGCCTCGGACC
197357 TCACAGCTATATTGTTGGTTGTTCTCTGACTCCCACTCATATTCTCG
521 TCACAGCTATATTGTTGGTTGTTCTCTGACTCCCACTCATATTCTCG
197404 TAAGAAAAAT-GGCTTCGCATCCCTTTTTCACATAATTCAGAGCTTTCATTACAGATATCACAAC
1 TAAGAAAAATAGGCTTCGCATCCCTTTTTCACATAATTCAGAGCTTTCATTACAGATATCACAAC
197468 TGGAAACCCTTTCAGATCACTAGACTCAATTCGGATTATCTCATCATTCTTGCATCTCAAATCAA
66 TGGAAACCCTTTCAGATCACTAGACTCAATTCGGATTATCTCATCATTCTTGCATCTCAAATCAA
197533 TAGTTTTTTGTTTGCAATTCACAATAGCATCGTGCAAAGTTAACCAATCCATACCCAGAATTATA
131 TAGTTTTTTGTTTGCAATTCACAATAGCATCGTGCAAAGTTAACCAATCCATACCCAGAATTATA
197598 TCAAATTTATCAAAAGGTAATAGCATCAGATTAGCCAGAAAACAGATATCTCGAATCATCAATGG
196 TCAAATTTATCAAAAGGTAATAGCATCAGATTAGCCAGAAAACAGATATCTCGAATCATCAATGG
197663 ACAATTCTTGCATACTTTATGAACCAAGACACACCGGCCTAAGGGGTTTGATTCTCTAGTCACAA
261 ACAATTCTTGCATACTTTATGAACCAAGACACACCGGCCTAAGGGGTTTGATTCTCTAGTCACAA
197728 ACTCAGTAGACTCTACAGGAAAAGTCTTGCTGGATACTAAATTCATGCATATGTAAGAATGAGTA
326 ACTCAGTAGACTCTACAGGAAAAGTCTTGCTGGATACTAAATTCATGCATATGTAAGAATGAGTA
197793 TATCTCAGATCAATCAAATCAACAATAGTAGTATCATAAAGAAGGAAAGTACCAGTAACGACATC
391 TATCTCAGATCAATCAAATCAACAATAGTAGTATCATAAAGAAGGAAAGTACCAGTAACGACATC
197858 TGGAGATGAGGCTTCTTCGCGAGCACGAATAGCGTATACTCGAGCAGGTGCTCTGGCCTCGGACC
456 TGGAGATGAGGCTTCTTCGCGAGCACGAATAGCGTATACTCGAGCAGGTGCTCTGGCCTCGGACC
197923 TCACAGCTATATTGTTGGTTGTTCTCTGACTCCCACTCATATTCTCG
521 TCACAGCTATATTGTTGGTTGTTCTCTGACTCCCACTCATATTCTCG
197970 GCACCTCTGG
Statistics
Matches: 566, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
566 556 0.98
567 10 0.02
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (567 bp):
TAAGAAAAATAGGCTTCGCATCCCTTTTTCACATAATTCAGAGCTTTCATTACAGATATCACAAC
TGGAAACCCTTTCAGATCACTAGACTCAATTCGGATTATCTCATCATTCTTGCATCTCAAATCAA
TAGTTTTTTGTTTGCAATTCACAATAGCATCGTGCAAAGTTAACCAATCCATACCCAGAATTATA
TCAAATTTATCAAAAGGTAATAGCATCAGATTAGCCAGAAAACAGATATCTCGAATCATCAATGG
ACAATTCTTGCATACTTTATGAACCAAGACACACCGGCCTAAGGGGTTTGATTCTCTAGTCACAA
ACTCAGTAGACTCTACAGGAAAAGTCTTGCTGGATACTAAATTCATGCATATGTAAGAATGAGTA
TATCTCAGATCAATCAAATCAACAATAGTAGTATCATAAAGAAGGAAAGTACCAGTAACGACATC
TGGAGATGAGGCTTCTTCGCGAGCACGAATAGCGTATACTCGAGCAGGTGCTCTGGCCTCGGACC
TCACAGCTATATTGTTGGTTGTTCTCTGACTCCCACTCATATTCTCG
Found at i:199022 original size:30 final size:30
Alignment explanation
Indices: 198963--199021 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
198953 GCTTTTTGAA
* * *
198963 AATATTTACAAAAAGAGGTATCTAATTTTT
1 AATATTTACAAAAAGAGGCAACCAATTTTT
198993 AATATTTACAAAAAGA-GCAACCAATTTTT
1 AATATTTACAAAAAGAGGCAACCAATTTTT
199022 TTAAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCAACCAATTTTT
Found at i:215807 original size:12 final size:12
Alignment explanation
Indices: 215790--215814 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
215780 ATCTACCGAG
215790 CATTAGAGAAGA
1 CATTAGAGAAGA
215802 CATTAGAGAAGA
1 CATTAGAGAAGA
215814 C
1 C
215815 TGAATCCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.12, G:0.24, T:0.16
Consensus pattern (12 bp):
CATTAGAGAAGA
Found at i:238217 original size:50 final size:51
Alignment explanation
Indices: 238106--238351 Score: 187
Period size: 50 Copynumber: 4.8 Consensus size: 51
238096 TTAAGGGAAT
* *
238106 GAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAAGTTGTGA
1 GAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGC---ACTGAAG--ATGA
*
238162 GAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGGCACTG-AGATGA
1 GAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAAGATGA
* * * * * *
238212 GAGGTCCC-CTGTAAGACGATGTTTGGGACATGTCATGGGCACCG-ATATGA
1 GAGGTCCCAC-GTAAGACCATGTCTGGGACATGGCATTGGCACTGAAGATGA
** * * * * * * *
238262 GAACTCCCATGTAAGACCATATATAGGATATGGCATTGGCA--GCACATGA
1 GAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAAGATGA
* ** * * *
238311 AACATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 GAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
238352 TGTTATTATC
Statistics
Matches: 158, Mismatches: 29, Indels: 13
0.79 0.14 0.06
Matches are distributed among these distances:
48 1 0.01
49 39 0.25
50 74 0.47
52 2 0.01
53 3 0.02
56 39 0.25
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (51 bp):
GAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAAGATGA
Found at i:241610 original size:20 final size:20
Alignment explanation
Indices: 241582--241620 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
241572 TCGAGTAGGA
*
241582 ATATCGATACCTTAGGAAAG
1 ATATCGATACCTTAAGAAAG
*
241602 ATATTGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
241621 TGTATCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAG
Found at i:243904 original size:20 final size:21
Alignment explanation
Indices: 243855--243904 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
243845 TATTGATCAA
*
243855 GTATCGATA-ATTTTCTTAAG
1 GTATCGATATATTTTCCTAAG
243875 GTATCGATATA-TTTCCTAAG
1 GTATCGATATATTTTCCTAAG
243895 GTATCGATAT
1 GTATCGATAT
243905 TCTTGCTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (21 bp):
GTATCGATATATTTTCCTAAG
Found at i:245389 original size:137 final size:137
Alignment explanation
Indices: 245230--245493 Score: 411
Period size: 137 Copynumber: 1.9 Consensus size: 137
245220 CTATTTTAGA
* * **
245230 TACCTTGTGAATTCGGCTAGACTCAAATTTGGGTAAAAATGGTTAATTTGCATGTTTTGGGCTCA
1 TACCTTGAGAATTCGGCTAGACTCAAATTTGGGTAAAAATGGTTAATTTGCATGGTTTCAGCTCA
* * * *
245295 GGGATTAAATTGAATAAAAGTAAAATTTTAGGGGAAATTTTATAAAAATGTGAAAAATGACTCAA
66 GAGATTAAATTAAATAAAAGTAAAACTTTAGGGGAAATTTTATAAAAATGTAAAAAATGACTCAA
245360 TTTTGGG
131 TTTTGGG
* * *
245367 TACCTTGAGTATTCGGGTAGACTCAATTTTGGGTAAAAATGGTTAATTTGCATGGTTTCAGCTCA
1 TACCTTGAGAATTCGGCTAGACTCAAATTTGGGTAAAAATGGTTAATTTGCATGGTTTCAGCTCA
* *
245432 GAGATTAAATTAAATAAAAGTAAAACTTTAGGGGCAATTTTGTAAAAATGTAAAAAATGACT
66 GAGATTAAATTAAATAAAAGTAAAACTTTAGGGGAAATTTTATAAAAATGTAAAAAATGACT
245494 AGATTGCATA
Statistics
Matches: 114, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
137 114 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.34
Consensus pattern (137 bp):
TACCTTGAGAATTCGGCTAGACTCAAATTTGGGTAAAAATGGTTAATTTGCATGGTTTCAGCTCA
GAGATTAAATTAAATAAAAGTAAAACTTTAGGGGAAATTTTATAAAAATGTAAAAAATGACTCAA
TTTTGGG
Found at i:249585 original size:50 final size:50
Alignment explanation
Indices: 249525--249666 Score: 212
Period size: 50 Copynumber: 2.8 Consensus size: 50
249515 CAAAATACCA
* * * *
249525 TTTGTAGACAAGCCACCACCGGTTTGCAGATAAACTGCCACTGATAACAC
1 TTTGTAGACAAGCCACCACTGATATGCAGATATACTGCCACTGATAACAC
* **
249575 TTTGTGGACAAGCCACCACTGATATGCAGATATACTGGTACTGATAACAC
1 TTTGTAGACAAGCCACCACTGATATGCAGATATACTGCCACTGATAACAC
*
249625 TTTGTAGACAAGCCACCACTAATATGCAGATATACTGCCACT
1 TTTGTAGACAAGCCACCACTGATATGCAGATATACTGCCACT
249667 TACTTCCTCC
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 81 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (50 bp):
TTTGTAGACAAGCCACCACTGATATGCAGATATACTGCCACTGATAACAC
Found at i:252452 original size:14 final size:14
Alignment explanation
Indices: 252433--252470 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
252423 ATTCATTAAC
252433 ATTATTATTAATCT
1 ATTATTATTAATCT
*
252447 ATTATTATTAATTT
1 ATTATTATTAATCT
252461 ATTATTATTA
1 ATTATTATTA
252471 TTACCACCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTATTATTAATCT
Found at i:252455 original size:17 final size:16
Alignment explanation
Indices: 252433--252473 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
252423 ATTCATTAAC
252433 ATTATTATTAATCTATT
1 ATTATTATTAAT-TATT
*
252450 ATTATTAATTTATTATT
1 ATTATT-ATTAATTATT
252467 ATTATTA
1 ATTATTA
252474 CCACCGCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.73
18 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATTATTAATTATT
Found at i:252462 original size:11 final size:13
Alignment explanation
Indices: 252422--252470 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
252412 CTTTTTTTAC
252422 TATTCATTAAC-AT
1 TATT-ATTAACTAT
252435 TATTATTAATCTAT
1 TATTATTAA-CTAT
*
252449 TATTATTAATTTAT
1 TATTATTAA-CTAT
252463 TATTATTA
1 TATTATTA
252471 TTACCACCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 5 0.15
13 5 0.15
14 23 0.70
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTATTAACTAT
Found at i:253109 original size:18 final size:17
Alignment explanation
Indices: 253082--253116 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
253072 GATTATTGCT
253082 CTTATGTGTATTGTATTG
1 CTTATGTGTATT-TATTG
*
253100 CTTATTTGTATTTATTG
1 CTTATGTGTATTTATTG
253117 ATTCTTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (17 bp):
CTTATGTGTATTTATTG
Found at i:254309 original size:20 final size:20
Alignment explanation
Indices: 254281--254318 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
254271 TGTAACTCTT
*
254281 GTGTGCGAGGTCGTGTGCCC
1 GTGTACGAGGTCGTGTGCCC
254301 GTGTACGAGGTCGTGTGC
1 GTGTACGAGGTCGTGTGC
254319 TAGGTCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.21, G:0.45, T:0.26
Consensus pattern (20 bp):
GTGTACGAGGTCGTGTGCCC
Found at i:270527 original size:18 final size:19
Alignment explanation
Indices: 270501--270538 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
270491 TAAAGTCCAT
* *
270501 AAAATTCCA-AATCTTAAA
1 AAAAATCCACAATCGTAAA
270519 AAAAATCCACAATCGTAAA
1 AAAAATCCACAATCGTAAA
270538 A
1 A
270539 GAAACATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (19 bp):
AAAAATCCACAATCGTAAA
Found at i:270772 original size:17 final size:17
Alignment explanation
Indices: 270750--270783 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
270740 ATGGTCATAT
*
270750 CGATGCATATTTGAAAA
1 CGATGCACATTTGAAAA
*
270767 CGATGCACATTTTAAAA
1 CGATGCACATTTGAAAA
270784 AGTTCCTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (17 bp):
CGATGCACATTTGAAAA
Found at i:274797 original size:24 final size:24
Alignment explanation
Indices: 274770--274826 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
274760 TTACAATACG
274770 AATATTTTTAATTAAAAAGGAACA-
1 AATATTTTTAATT-AAAAGGAACAC
* *
274794 AATAATTTTTTATTCAAAGGAACAC
1 AAT-ATTTTTAATTAAAAGGAACAC
*
274819 AATGTTTT
1 AATATTTT
274827 AAAAATGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (24 bp):
AATATTTTTAATTAAAAGGAACAC
Found at i:275148 original size:16 final size:17
Alignment explanation
Indices: 275116--275149 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
275106 TATAGACTTT
*
275116 AAAAGTATAGAATTGTG
1 AAAACTATAGAATTGTG
275133 AAAACTATAG-ATTGTG
1 AAAACTATAGAATTGTG
275149 A
1 A
275150 CACTAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (17 bp):
AAAACTATAGAATTGTG
Found at i:292713 original size:22 final size:23
Alignment explanation
Indices: 292671--292718 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
292661 CAAATCAGAG
292671 TTCAAGCTTCAGCATATTGTTCT
1 TTCAAGCTTCAGCATATTGTTCT
* *
292694 TTCAAGTTTCA-CGTATTGTTCT
1 TTCAAGCTTCAGCATATTGTTCT
292716 TTC
1 TTC
292719 CAAACCTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (23 bp):
TTCAAGCTTCAGCATATTGTTCT
Found at i:297527 original size:31 final size:31
Alignment explanation
Indices: 297478--297545 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
297468 TACTCCATAG
*
297478 TTTTTT-ATTTGAATTTTTATGAACTTTTATA
1 TTTTTTAATTTGAATTTTTAT-AACTTTTAAA
* *
297509 TTTTTTAATTTTAA-TTTTATAATTTTTAAA
1 TTTTTTAATTTGAATTTTTATAACTTTTAAA
*
297539 TTATTTA
1 TTTTTTA
297546 TTGACATGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 14 0.44
31 12 0.38
32 6 0.19
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.66
Consensus pattern (31 bp):
TTTTTTAATTTGAATTTTTATAACTTTTAAA
Found at i:297531 original size:14 final size:15
Alignment explanation
Indices: 297492--297534 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
297482 TTATTTGAAT
297492 TTTTATGAACTTTTATA
1 TTTTAT-AA-TTTTATA
*
297509 TTTTTTAATTTTA-A
1 TTTTATAATTTTATA
297523 TTTTATAATTTT
1 TTTTATAATTTT
297535 TAAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.50
15 5 0.21
16 2 0.08
17 5 0.21
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTATAATTTTATA
Found at i:298374 original size:18 final size:19
Alignment explanation
Indices: 298335--298377 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
298325 AGTGAGTAAG
*
298335 TATGATAATTGAATATATT
1 TATGATAATAGAATATATT
298354 TATGA-AATAGAATATGA-T
1 TATGATAATAGAATAT-ATT
298372 TATGAT
1 TATGAT
298378 TATTGAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (19 bp):
TATGATAATAGAATATATT
Found at i:302185 original size:14 final size:14
Alignment explanation
Indices: 302166--302194 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
302156 GGGTTGTGTG
302166 TACATTAATATAAT
1 TACATTAATATAAT
302180 TACATTAATATAAT
1 TACATTAATATAAT
302194 T
1 T
302195 TCGGTAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TACATTAATATAAT
Found at i:307757 original size:22 final size:22
Alignment explanation
Indices: 307727--307770 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
307717 TTTGGTATTT
307727 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
307749 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
307771 TGGTTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:308741 original size:30 final size:30
Alignment explanation
Indices: 308683--308741 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
308673 TTAGAAATGT
* *
308683 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
308713 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
308742 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:312075 original size:15 final size:16
Alignment explanation
Indices: 312057--312095 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
312047 TCTTTTCTCG
*
312057 CTTTCTTTT-CATTTT
1 CTTTCTTTTGAATTTT
312072 CTTT-TTTTGAATTTT
1 CTTTCTTTTGAATTTT
312087 CTTTCTTTT
1 CTTTCTTTT
312096 TTTCATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 13 0.62
16 4 0.19
ACGTcount: A:0.08, C:0.15, G:0.03, T:0.74
Consensus pattern (16 bp):
CTTTCTTTTGAATTTT
Found at i:312091 original size:19 final size:20
Alignment explanation
Indices: 312062--312115 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
312052 TCTCGCTTTC
*
312062 TTTTCATTTTCTTTTTTTGAA
1 TTTTC-TTTTCTTTTTTTCAA
*
312083 TTTTC-TTTCTTTTTTTCAT
1 TTTTCTTTTCTTTTTTTCAA
312102 TTTTCTTTTCTTTT
1 TTTTCTTTTCTTTT
312116 GTATTTTCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 17 0.57
20 8 0.27
21 5 0.17
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTTCAA
Found at i:314521 original size:22 final size:23
Alignment explanation
Indices: 314493--314545 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 23
314483 CCGTATACAA
*
314493 TTTTTTTCTTTTTTTTTC--AAT
1 TTTTTTTCATTTTTTTTCAAAAT
*
314514 TTTTTTTTATTTTTTTTCAAAAT
1 TTTTTTTCATTTTTTTTCAAAAT
314537 TTTTTTTCA
1 TTTTTTTCA
314546 CGAGTCTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 16 0.59
23 11 0.41
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTTCATTTTTTTTCAAAAT
Found at i:314872 original size:21 final size:21
Alignment explanation
Indices: 314846--314908 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
314836 TTGGTATTTG
314846 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
314867 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
314888 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
314909 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:315724 original size:30 final size:30
Alignment explanation
Indices: 315666--315724 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
315656 TTGAAAATGT
* *
315666 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
315696 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
315725 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:316864 original size:19 final size:20
Alignment explanation
Indices: 316840--316880 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
316830 GCCCAAGCTC
*
316840 CTAATGCAATGA-TAAAATG
1 CTAATGAAATGACTAAAATG
316859 CTAATGAAATGACCTAAAATG
1 CTAATGAAATGA-CTAAAATG
316880 C
1 C
316881 CACTAACTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (20 bp):
CTAATGAAATGACTAAAATG
Found at i:331461 original size:49 final size:50
Alignment explanation
Indices: 331397--331520 Score: 155
Period size: 50 Copynumber: 2.5 Consensus size: 50
331387 CAAAGCTATG
* * *
331397 TCCCAGACATAGTCTTACATGGGATGTT-TCCTGTAC-TGCCAATGCCATA
1 TCCCAGACATGGTCTTACATGGGATGTTCTCATAT-CGTGCCAATGCCATA
* * *
331446 TCCCAGATATGGTCTTACATGGGA-GTTCTCATATCGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGGGATGTTCTCATATC-GTGCCAATGCCATA
331496 TCCCAGACATGGTCTTACATGGGAT
1 TCCCAGACATGGTCTTACATGGGAT
331521 CTCATCACCC
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
48 4 0.06
49 26 0.41
50 34 0.53
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.30
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGATGTTCTCATATCGTGCCAATGCCATA
Found at i:331501 original size:50 final size:49
Alignment explanation
Indices: 331384--331520 Score: 161
Period size: 49 Copynumber: 2.8 Consensus size: 49
331374 GAATATAATA
* * * * *
331384 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCCTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATATAC
* *
331433 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATAT-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCATATAC
*
331481 GGTGCCCATGCCATGTCCCAGACATGGTCTTACATGGGAT
1 --TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT
331521 CTCATCACCC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 4 0.05
49 36 0.49
50 34 0.46
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATATAC
Found at i:337318 original size:50 final size:50
Alignment explanation
Indices: 337187--337320 Score: 119
Period size: 50 Copynumber: 2.7 Consensus size: 50
337177 TACTGCTAAT
* * * ** * *
337187 GCCATATCCCAGATATGGTCTTACATGGG-GTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGAAAAGGTCTTACATGGGACCTCTCATATCGGTGCCAAC
* * * * * *
337236 GCCATGTCCCTGACATGGTCTTAC-GGGAGACCTCTCATCTCGTTGCCAAC
1 GCCATGTCCCAGAAAAGGTCTTACATGG-GACCTCTCATATCGGTGCCAAC
*
337286 GCCATGTTCCAGAAAAGGTCTTACATGGGACCTCT
1 GCCATGTCCCAGAAAAGGTCTTACATGGGACCTCT
337321 AATTGTCTCA
Statistics
Matches: 67, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
48 2 0.03
49 22 0.33
50 41 0.61
51 2 0.03
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGAAAAGGTCTTACATGGGACCTCTCATATCGGTGCCAAC
Found at i:344984 original size:51 final size:51
Alignment explanation
Indices: 344929--345036 Score: 144
Period size: 51 Copynumber: 2.1 Consensus size: 51
344919 TGAAAGGGAT
*
344929 TGCCTCTGAATCTCCACTTTCTATCTCTACTCAGCCACTACCATCTATTGC
1 TGCCTCTGAATCTCCACTTTCCATCTCTACTCAGCCACTACCATCTATTGC
* * * * * * *
344980 TGCCTCTGGATCTTCATTTTCCATCTCTAGTCAGTCACTACCCTCTATTGT
1 TGCCTCTGAATCTCCACTTTCCATCTCTACTCAGCCACTACCATCTATTGC
345031 TGCCTC
1 TGCCTC
345037 AGGATATCCA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.17, C:0.35, G:0.10, T:0.38
Consensus pattern (51 bp):
TGCCTCTGAATCTCCACTTTCCATCTCTACTCAGCCACTACCATCTATTGC
Found at i:363457 original size:41 final size:42
Alignment explanation
Indices: 363398--363485 Score: 135
Period size: 41 Copynumber: 2.1 Consensus size: 42
363388 ATAAAAGTGC
*
363398 ATTC-AGGGATACCAAAGTATAAACAGGGGCACATATGTCCA
1 ATTCAAGGGATACCAAAGTACAAACAGGGGCACATATGTCCA
* *
363439 ATTCAAGGG-TACCGAAGTACAAACAGGGGCACATATGTGCA
1 ATTCAAGGGATACCAAAGTACAAACAGGGGCACATATGTCCA
363480 ATTCAA
1 ATTCAA
363486 CAATATTCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 39 0.91
42 4 0.09
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (42 bp):
ATTCAAGGGATACCAAAGTACAAACAGGGGCACATATGTCCA
Found at i:368660 original size:22 final size:22
Alignment explanation
Indices: 368595--368667 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
368585 GACAAGCCAC
* * * *
368595 CACTGATTTGCAGTTAAATTGC
1 CACTGATTTACAGATAAACTGT
368617 CACTGATTTACAGATAAACTGT
1 CACTGATTTACAGATAAACTGT
368639 CACTGATTTACAGATAAACTGT
1 CACTGATTTACAGATAAACTGT
*
368661 CATTGAT
1 CACTGAT
368668 AACATTGATG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (22 bp):
CACTGATTTACAGATAAACTGT
Found at i:368853 original size:18 final size:18
Alignment explanation
Indices: 368819--368854 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
368809 ACATGCCCTC
*
368819 ATAATCACTTATCACATA
1 ATAATCACTTATAACATA
*
368837 ATAATCACTTTTAACATA
1 ATAATCACTTATAACATA
368855 CTTTTCACAA
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:0.44, C:0.19, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATCACTTATAACATA
Found at i:373429 original size:22 final size:21
Alignment explanation
Indices: 373377--373431 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
373367 ACTTGTGATT
*
373377 ATTATGATTATTGATATGATGAG
1 ATTAT-ATT-TTGATATGACGAG
*
373400 ATTGATATTTTGATATGTACGTG
1 ATT-ATATTTTGATATG-ACGAG
373423 ATTATATTT
1 ATTATATTT
373432 GTCTTGATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 14 0.50
23 12 0.43
24 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (21 bp):
ATTATATTTTGATATGACGAG
Found at i:374768 original size:15 final size:15
Alignment explanation
Indices: 374750--374780 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
374740 GCAATATGAA
374750 AACTTGAGGTATGTG
1 AACTTGAGGTATGTG
*
374765 AACTTGTGGTATGTG
1 AACTTGAGGTATGTG
374780 A
1 A
374781 TTTTCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.35
Consensus pattern (15 bp):
AACTTGAGGTATGTG
Found at i:377843 original size:8 final size:8
Alignment explanation
Indices: 377830--377855 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
377820 ATTTATCAGC
377830 TTTTATTA
1 TTTTATTA
377838 TTTTATTA
1 TTTTATTA
377846 TTTTATTA
1 TTTTATTA
377854 TT
1 TT
377856 CCCAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTATTA
Found at i:378741 original size:15 final size:15
Alignment explanation
Indices: 378723--378753 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
378713 AGTGATCGAA
*
378723 AAAATACAGAAAAAT
1 AAAATACAAAAAAAT
378738 AAAATACAAAAAAAT
1 AAAATACAAAAAAAT
378753 A
1 A
378754 GATTAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAATACAAAAAAAT
Found at i:385123 original size:49 final size:49
Alignment explanation
Indices: 385006--385191 Score: 214
Period size: 49 Copynumber: 3.8 Consensus size: 49
384996 GGGTAAAGAG
* * * * *
385006 ATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCG-ATATGATAAC
1 ATCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAGA-AAC
* *
385057 -TCCCATGTAAGATCATATCTGGGATATGACATTGGCAGTACAAGAAAC
1 ATCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAAC
* * *
385105 ATCCCATGTAAGACCATATTTGGGATATGGCATTCGCAATACAAGAAAC
1 ATCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAAC
* * *
385154 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
385192 TGTTATTATC
Statistics
Matches: 116, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
48 4 0.03
49 80 0.69
50 32 0.28
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (49 bp):
ATCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAAC
Found at i:396811 original size:180 final size:181
Alignment explanation
Indices: 396501--396859 Score: 711
Period size: 180 Copynumber: 2.0 Consensus size: 181
396491 TATTTTTCTT
396501 AAAATATCCTTGTCTCAAGAAATCAACGTGTCACATTCAATATGTTAGGACACAACATATTGAAT
1 AAAATATCCTTGTCTCAAGAAATCAACGTGTCACATTCAATATGTTAGGACACAACATATTGAAT
396566 CCCCAATGACAAATTTTATTTTGTTTGATTAAAGATCAATTCTCGATTGTTAGATTTAACGAAGA
66 CCCCAATGACAAATTTTATTTTGTTTGATTAAAGATCAATTCTCGATTGTTAGATTTAACGAAGA
396631 AAATCGGAACCCAAATCGTTAGAGCTTAATCTTCTCGAAAATCCTAAATTA
131 AAATCGGAACCCAAATCGTTAGAGCTTAATCTTCTCGAAAATCCTAAATTA
396682 AAAATAT-CTTGTCTCAAGAAATCAACGTGTCACATTCAATATGTTAGGACACAACATATTGAAT
1 AAAATATCCTTGTCTCAAGAAATCAACGTGTCACATTCAATATGTTAGGACACAACATATTGAAT
396746 CCCCAATGACAAATTTTATTTTGTTTGATTAAAGATCAATTCTCGATTGTTAGATTTAACGAAGA
66 CCCCAATGACAAATTTTATTTTGTTTGATTAAAGATCAATTCTCGATTGTTAGATTTAACGAAGA
396811 AAATCGGAACCCAAATCGTTAGAGCTTAATCTTCTCGAAAATCCTAAAT
131 AAATCGGAACCCAAATCGTTAGAGCTTAATCTTCTCGAAAATCCTAAAT
396860 ACGAGTATTA
Statistics
Matches: 178, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
180 171 0.96
181 7 0.04
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (181 bp):
AAAATATCCTTGTCTCAAGAAATCAACGTGTCACATTCAATATGTTAGGACACAACATATTGAAT
CCCCAATGACAAATTTTATTTTGTTTGATTAAAGATCAATTCTCGATTGTTAGATTTAACGAAGA
AAATCGGAACCCAAATCGTTAGAGCTTAATCTTCTCGAAAATCCTAAATTA
Found at i:397394 original size:18 final size:18
Alignment explanation
Indices: 397359--397401 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
397349 AATAGGTACA
*
397359 ATAATAATAATATATAAT
1 ATAATAATAAGATATAAT
397377 ATAATAATAACGAT-TAAT
1 ATAATAATAA-GATATAAT
*
397395 ACAATAA
1 ATAATAA
397402 GAATGTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (18 bp):
ATAATAATAAGATATAAT
Found at i:398835 original size:44 final size:44
Alignment explanation
Indices: 398728--398839 Score: 125
Period size: 44 Copynumber: 2.5 Consensus size: 44
398718 CAGCTTTAAT
* * * *
398728 CTGCTCCACTGCAACCTCAGGGAGATAAGATATGCCATCTTCGAT
1 CTGCTCCACTGCAA-CTTAGGGAGATAAGATATGCAATCTTCAAC
* ** * *
398773 CTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCAAC
1 CTGCTCCACTGCAACTTAGGGAGATAAGATATGCAATCTTCAAC
*
398817 CTGCTCCGCTGCAACTTAGGGAG
1 CTGCTCCACTGCAACTTAGGGAG
398840 GCAAGGCTGG
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
44 43 0.80
45 11 0.20
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTAGGGAGATAAGATATGCAATCTTCAAC
Found at i:398906 original size:88 final size:87
Alignment explanation
Indices: 398808--399133 Score: 289
Period size: 88 Copynumber: 3.7 Consensus size: 87
398798 AAGATATGTA
* ** * * **
398808 ATTTTCAACCTGCTCCGCTGCAACTTAGGGAGGCAAGGCTGGTGTCTTCAATCTGCTTCACTGTT
1 ATTTT-AACCTACTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCAATCTGCTCCACTGAC
398873 AGTACAGGAAGGCAAGATCTGCT
65 AGTACAGGAAGGCAAGATCTGCT
* * * *
398896 ATCTTTAACCTACTCCGCTGCCACCGACGGG-GGCAAGGCTAGTGTCTTCGATCTACTCCACT-A
1 AT-TTTAACCTACTCCGCTGCAACCCA-GGGAGGCAAGGCTAGTGTCTTCAATCTGCTCCACTGA
* * ** * *
398959 CAGCT-TAGGGAGATAAGATCTACA
64 CAG-TACAGGAAGGCAAGATCTGCT
* * * * ** * * * *
398983 ATTTTCAACCTCCTCCGCTCCAACCCAGGGAGGCAAGGCTGGTATCTTTGATATGCTTCGCTGCC
1 ATTTT-AACCTACTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCAATCTGCTCCACTGAC
*
399048 GGTACAGGAAGGCAAGATCTGCT
65 AGTACAGGAAGGCAAGATCTGCT
* * * *
399071 ATTTTTAACCTACTCCGCTGTAACTCAGGGAGTCAAGGCTAGTGTCTTCAGTCTGCTCCACTG
1 A-TTTTAACCTACTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCAATCTGCTCCACTG
399134 CAACCTAGGG
Statistics
Matches: 182, Mismatches: 48, Indels: 16
0.74 0.20 0.07
Matches are distributed among these distances:
86 6 0.03
87 59 0.32
88 107 0.59
89 10 0.05
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (87 bp):
ATTTTAACCTACTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCAATCTGCTCCACTGACA
GTACAGGAAGGCAAGATCTGCT
Found at i:399056 original size:175 final size:175
Alignment explanation
Indices: 398765--399132 Score: 499
Period size: 175 Copynumber: 2.1 Consensus size: 175
398755 AGATATGCCA
* ** * *
398765 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCAACCTGCTCCGCTGCA
1 TCTTCGATCTGCTCCACTACAGCTTAGGGAGATAAGATATACAATTTTCAACCTCCTCCGCTCCA
** * * **
398830 ACTTAGGGAGGCAAGGCTGGTGTCTTCAATCTGCTTCACTGTTAGTACAGGAAGGCAAGATCTGC
66 ACCCAGGGAGGCAAGGCTGGTATCTTCAATATGCTTCACTGCCAGTACAGGAAGGCAAGATCTGC
*
398895 TATCTTTAACCTACTCCGCTGCCAC-CGACGGG-GGCAAGGCTAGTG
131 TATCTTTAACCTACTCCGCTGCAACTC-A-GGGAGGCAAGGCTAGTG
* *
398940 TCTTCGATCTACTCCACTACAGCTTAGGGAGATAAGATCTACAATTTTCAACCTCCTCCGCTCCA
1 TCTTCGATCTGCTCCACTACAGCTTAGGGAGATAAGATATACAATTTTCAACCTCCTCCGCTCCA
** * *
399005 ACCCAGGGAGGCAAGGCTGGTATCTTTGATATGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGC
66 ACCCAGGGAGGCAAGGCTGGTATCTTCAATATGCTTCACTGCCAGTACAGGAAGGCAAGATCTGC
* * *
399070 TATTTTTAACCTACTCCGCTGTAACTCAGGGAGTCAAGGCTAGTG
131 TATCTTTAACCTACTCCGCTGCAACTCAGGGAGGCAAGGCTAGTG
399115 TCTTC-AGTCTGCTCCACT
1 TCTTCGA-TCTGCTCCACT
399133 GCAACCTAGG
Statistics
Matches: 168, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
174 4 0.02
175 163 0.97
176 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (175 bp):
TCTTCGATCTGCTCCACTACAGCTTAGGGAGATAAGATATACAATTTTCAACCTCCTCCGCTCCA
ACCCAGGGAGGCAAGGCTGGTATCTTCAATATGCTTCACTGCCAGTACAGGAAGGCAAGATCTGC
TATCTTTAACCTACTCCGCTGCAACTCAGGGAGGCAAGGCTAGTG
Found at i:399262 original size:78 final size:78
Alignment explanation
Indices: 399131--399364 Score: 240
Period size: 78 Copynumber: 2.9 Consensus size: 78
399121 GTCTGCTCCA
*
399131 CTGCAACCTAGGGAGGCAAGACTGGTGTTTTTGATATGCTTCGCTGTCAGTACAGGAAGGCAAGA
1 CTGCAACCCAGGGAGGCAAGACTGGTGTTTTTGATATGCTTCGCTGTCAGTACAGGAAGGCAAGA
399196 TCTGCCTGCTCTG
66 TCTGCCTGCTCTG
* * *
399209 CTGCAACCCAGGGAGGCAATG-CTGGT-TTCTTTGATCTGCTTCGTTGTCGGTACAGGAAGGCAA
1 CTGCAACCCAGGGAGGCAA-GACTGGTGTT-TTTGATATGCTTCGCTGTCAGTACAGGAAGGCAA
**
399272 GATCTGCTATCTTTAGTTTGCTCCA
64 GATCTGC---C-------TGCTCTG
* * * *
399297 CTGCAACCTAGGGAGGCAAGACTGGTGTCTTCGA-ATTGCTTTGCTGTCAGTACAGGAAGGCAAG
1 CTGCAACCCAGGGAGGCAAGACTGGTGTTTTTGATA-TGCTTCGCTGTCAGTACAGGAAGGCAAG
399361 ATCT
65 ATCT
399365 ACTATTTTCA
Statistics
Matches: 128, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
77 2 0.02
78 61 0.48
79 1 0.01
81 1 0.01
87 1 0.01
88 61 0.48
89 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (78 bp):
CTGCAACCCAGGGAGGCAAGACTGGTGTTTTTGATATGCTTCGCTGTCAGTACAGGAAGGCAAGA
TCTGCCTGCTCTG
Found at i:399463 original size:88 final size:88
Alignment explanation
Indices: 399208--399463 Score: 307
Period size: 88 Copynumber: 2.9 Consensus size: 88
399198 TGCCTGCTCT
* * * *
399208 GCTGCAACCCAGGGAGGCAATGCTGGTTTCTTTGATCTGCTTCGTTGTCGGTACAGGAAGGCAAG
1 GCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTAATCTGCTTCGCTGTCGGTACAGGAAGGCAAG
* *** *
399273 ATCTGCTATCTTTAGTTTGCTCC
66 ATCTGCTATCTTCAACCTGATCC
* * * * * *
399296 ACTGCAACCTAGGGAGGCAAGACTGGTGTCTTCGAAT-TGCTTTGCTGTCAGTACAGGAAGGCAA
1 GCTGCAACCCAGGGAGGCAAGGCTGGTGTCTT-TAATCTGCTTCGCTGTCGGTACAGGAAGGCAA
* *
399360 GATCTACTATTTTCAACCTGATCC
65 GATCTGCTATCTTCAACCTGATCC
* ** *
399384 GCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTTATCTGCTTCGCTACCGGTACAAGAAGGCAAG
1 GCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTAATCTGCTTCGCTGTCGGTACAGGAAGGCAAG
399449 ATCTGCTATCTTCAA
66 ATCTGCTATCTTCAA
399464 TAATCTTTTC
Statistics
Matches: 137, Mismatches: 29, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
87 2 0.01
88 133 0.97
89 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (88 bp):
GCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTAATCTGCTTCGCTGTCGGTACAGGAAGGCAAG
ATCTGCTATCTTCAACCTGATCC
Found at i:401701 original size:25 final size:27
Alignment explanation
Indices: 401650--401716 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
401640 AAGAAAATCC
*
401650 AAAAGAAT-GAAAGAATAATTATTTCA
1 AAAAGAATGGAAAGAATAATTATCTCA
*
401676 AAAAGAATGGAAA-AAT-ATTGTCTCA
1 AAAAGAATGGAAAGAATAATTATCTCA
*
401701 AAAATGAATGCAAAGA
1 AAAA-GAATGGAAAGA
401717 TGTATTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 11 0.31
26 19 0.54
27 5 0.14
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.22
Consensus pattern (27 bp):
AAAAGAATGGAAAGAATAATTATCTCA
Found at i:407055 original size:3 final size:3
Alignment explanation
Indices: 407047--407079 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
407037 ATGTAGGTAC
407047 AAT AAT AAT AAT AAT ATAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
407080 GATTAATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:407074 original size:18 final size:18
Alignment explanation
Indices: 407051--407098 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
407041 AGGTACAATA
407051 ATAATAATAAT-ATATAAT
1 ATAATAATAATGAT-TAAT
407069 ATAATAATAATGATTAAT
1 ATAATAATAATGATTAAT
* *
407087 ACAATAAGAATG
1 ATAATAATAATG
407099 TAAAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (18 bp):
ATAATAATAATGATTAAT
Found at i:407093 original size:21 final size:21
Alignment explanation
Indices: 407044--407093 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
407034 TATATGTAGG
407044 TACAATAATAATAATAATATA
1 TACAATAATAATAATAATATA
*
407065 TA-ATATAATAATAATGAT-TAA
1 TACA-ATAATAATAATAATAT-A
407086 TACAATAA
1 TACAATAA
407094 GAATGTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 22 0.88
22 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (21 bp):
TACAATAATAATAATAATATA
Found at i:413845 original size:27 final size:27
Alignment explanation
Indices: 413778--414012 Score: 253
Period size: 27 Copynumber: 8.7 Consensus size: 27
413768 TTACCCTATG
* ** *
413778 GGGTATTTCGGTAATTTTACCTTTC-G
1 GGGTATTTCGATAATTTTACCCATCAA
* *
413804 GGGTATTTC-AGTAATTTTATCCATCGA
1 GGGTATTTCGA-TAATTTTACCCATCAA
* *
413831 GGGTGTTTCGATAATTTTACCCTTCAA
1 GGGTATTTCGATAATTTTACCCATCAA
* *
413858 GGGTATTTTCG-TAATTTTACTCATCGA
1 GGGTA-TTTCGATAATTTTACCCATCAA
* *
413885 GGGTATTTCGGTAATTTTACCCTTCAA
1 GGGTATTTCGATAATTTTACCCATCAA
413912 GGGTATTTCGATAATTTTACCCATCAA
1 GGGTATTTCGATAATTTTACCCATCAA
413939 GGGTATTTCGATAATTTTACCCATCAA
1 GGGTATTTCGATAATTTTACCCATCAA
* * * *
413966 GTGTATTTTGGTAATTTTACCCTTC-A
1 GGGTATTTCGATAATTTTACCCATCAA
* *
413992 GGTGTATTTCGGTAATCTTAC
1 GG-GTATTTCGATAATTTTAC
414013 AACCTTTTTG
Statistics
Matches: 178, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
26 27 0.15
27 145 0.81
28 6 0.03
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACCCATCAA
Found at i:415680 original size:25 final size:25
Alignment explanation
Indices: 415646--415695 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
415636 TGAACCTCTG
415646 ACCTCCTTACCACACCTGTGACGCC
1 ACCTCCTTACCACACCTGTGACGCC
* *
415671 ACCTGCTTACCACACCTGTGTCGCC
1 ACCTCCTTACCACACCTGTGACGCC
415696 TCCTTGCCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.18, C:0.46, G:0.14, T:0.22
Consensus pattern (25 bp):
ACCTCCTTACCACACCTGTGACGCC
Found at i:418678 original size:27 final size:27
Alignment explanation
Indices: 418499--418683 Score: 155
Period size: 27 Copynumber: 6.9 Consensus size: 27
418489 TATAACAGTC
* **
418499 ATTTTACACTATGGA-GGTATTCCGATA
1 ATTTTAC-CTATCGAGGGTATTTTGATA
* *
418526 ATTTTACCCT-TCGGGGGTATTTTGGTA
1 ATTTTA-CCTATCGAGGGTATTTTGATA
* *
418553 ATTTTACCCATCAAGGGTATTTT-AGTA
1 ATTTTACCTATCGAGGGTATTTTGA-TA
*
418580 ATTTTACCTTTC-AGTGGTATTTTGATA
1 ATTTTACCTATCGAG-GGTATTTTGATA
* *
418607 ATTTTATCTATCGAGGGTATTTTAATA
1 ATTTTACCTATCGAGGGTATTTTGATA
* * * *
418634 ATTTTACCCT-TTGGGGGTATTTCGGTA
1 ATTTTA-CCTATCGAGGGTATTTTGATA
*
418661 ATTTTACCTATCAAGGGTATTTT
1 ATTTTACCTATCGAGGGTATTTT
418684 AGTAATTATA
Statistics
Matches: 125, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
26 9 0.07
27 110 0.88
28 6 0.05
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (27 bp):
ATTTTACCTATCGAGGGTATTTTGATA
Found at i:418683 original size:54 final size:54
Alignment explanation
Indices: 418523--418690 Score: 230
Period size: 54 Copynumber: 3.1 Consensus size: 54
418513 AGGTATTCCG
* *
418523 ATAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCCATCAAGGGTATTTTA
1 ATAATTTTACCCTTTGGGGGTATTTTGGTAATTTTACCTATCAAGGGTATTTTA
* * * * * *
418577 GTAATTTTA-CCTTTCAGTGGTATTTTGATAATTTTATCTATCGAGGGTATTTTA
1 ATAATTTTACCCTTT-GGGGGTATTTTGGTAATTTTACCTATCAAGGGTATTTTA
*
418631 ATAATTTTACCCTTTGGGGGTATTTCGGTAATTTTACCTATCAAGGGTATTTTA
1 ATAATTTTACCCTTTGGGGGTATTTTGGTAATTTTACCTATCAAGGGTATTTTA
*
418685 GTAATT
1 ATAATT
418691 ATAATCGGCT
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
53 4 0.04
54 87 0.91
55 5 0.05
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46
Consensus pattern (54 bp):
ATAATTTTACCCTTTGGGGGTATTTTGGTAATTTTACCTATCAAGGGTATTTTA
Found at i:418690 original size:81 final size:81
Alignment explanation
Indices: 418522--418683 Score: 193
Period size: 81 Copynumber: 2.0 Consensus size: 81
418512 GAGGTATTCC
* * ** *
418522 GATAATTTTACCCT-TCGGGGGTATTTTGGTAATTTTACCCATCAAGGGTATTTTAGTAATTTTA
1 GATAATTTTA-TCTATCGAGGGTATTTTAATAATTTTACCCATCAAGGGTATTTCAGTAATTTTA
*
418586 CCTTTCAGTGGTATTTT
65 CCTATCAGTGGTATTTT
* *** *
418603 GATAATTTTATCTATCGAGGGTATTTTAATAATTTTACCCTTTGGGGGTATTTCGGTAATTTTAC
1 GATAATTTTATCTATCGAGGGTATTTTAATAATTTTACCCATCAAGGGTATTTCAGTAATTTTAC
418668 CTATCAAG-GGTATTTT
66 CTATC-AGTGGTATTTT
418684 AGTAATTATA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
80 2 0.03
81 64 0.94
82 2 0.03
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (81 bp):
GATAATTTTATCTATCGAGGGTATTTTAATAATTTTACCCATCAAGGGTATTTCAGTAATTTTAC
CTATCAGTGGTATTTT
Found at i:418941 original size:27 final size:27
Alignment explanation
Indices: 418919--419118 Score: 165
Period size: 27 Copynumber: 7.4 Consensus size: 27
418909 GAGGTATTCC
418919 GATAATTTTACCCTTCGGGGGTATTTT
1 GATAATTTTACCCTTCGGGGGTATTTT
* * **
418946 GGTAATTTTACCCATCAAGGGTATTTT
1 GATAATTTTACCCTTCGGGGGTATTTT
* * *
418973 -AGTAATTTTACCTTTCAGTGGTATTTT
1 GA-TAATTTTACCCTTCGGGGGTATTTT
* *
419000 GATAATTTTA-TCTATCGAGGGTATTTT
1 GATAATTTTACCCT-TCGGGGGTATTTT
* * *
419027 AATAATTTTACCCTTTGGGGGTATTTC
1 GATAATTTTACCCTTCGGGGGTATTTT
* **
419054 GGTAATTTTA-CCTATCAAGGGTATTTT
1 GATAATTTTACCCT-TCGGGGGTATTTT
** *
419081 -AGTAATTTTACCCTTCGGGTTTATTTC
1 GA-TAATTTTACCCTTCGGGGGTATTTT
*
419108 GATAATCTTAC
1 GATAATTTTAC
419119 AACCTTTCTG
Statistics
Matches: 133, Mismatches: 32, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
26 4 0.03
27 122 0.92
28 7 0.05
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (27 bp):
GATAATTTTACCCTTCGGGGGTATTTT
Found at i:418969 original size:54 final size:54
Alignment explanation
Indices: 418921--419099 Score: 268
Period size: 54 Copynumber: 3.3 Consensus size: 54
418911 GGTATTCCGA
*
418921 TAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCCATCAAGGGTATTTTAG
1 TAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCTATCAAGGGTATTTTAG
* * * * * * *
418975 TAATTTTACCTTTCAGTGGTATTTTGATAATTTTATCTATCGAGGGTATTTTAA
1 TAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCTATCAAGGGTATTTTAG
* *
419029 TAATTTTACCCTTTGGGGGTATTTCGGTAATTTTACCTATCAAGGGTATTTTAG
1 TAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCTATCAAGGGTATTTTAG
419083 TAATTTTACCCTTCGGG
1 TAATTTTACCCTTCGGG
419100 TTTATTTCGA
Statistics
Matches: 107, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 107 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.45
Consensus pattern (54 bp):
TAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCTATCAAGGGTATTTTAG
Found at i:419022 original size:81 final size:81
Alignment explanation
Indices: 418919--419097 Score: 211
Period size: 81 Copynumber: 2.2 Consensus size: 81
418909 GAGGTATTCC
* ** *
418919 GATAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCCATCAAGGGTATTTTAGTAATTTTAC
1 GATAATTTTACCCTTCGAGGGTATTTTAATAATTTTACCCATCAAGGGTATTTCAGTAATTTTAC
*
418984 CTTTC-AGTGGTATTTT
66 CTATCAAG-GGTATTTT
* * *** *
419000 GATAATTTTA-TCTATCGAGGGTATTTTAATAATTTTACCCTTTGGGGGTATTTCGGTAATTTTA
1 GATAATTTTACCCT-TCGAGGGTATTTTAATAATTTTACCCATCAAGGGTATTTCAGTAATTTTA
419064 CCTATCAAGGGTATTTT
65 CCTATCAAGGGTATTTT
419081 -AGTAATTTTACCCTTCG
1 GA-TAATTTTACCCTTCG
419098 GGTTTATTTC
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
80 3 0.04
81 75 0.91
82 4 0.05
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.45
Consensus pattern (81 bp):
GATAATTTTACCCTTCGAGGGTATTTTAATAATTTTACCCATCAAGGGTATTTCAGTAATTTTAC
CTATCAAGGGTATTTT
Found at i:419027 original size:397 final size:397
Alignment explanation
Indices: 418294--419087 Score: 1588
Period size: 397 Copynumber: 2.0 Consensus size: 397
418284 TGCCAATCAC
418294 ATAATCGGCTAAAAGCCATTAGTGGGTCCACAGTCGTCTCATGCGACCCGTGCGACCCTCACATA
1 ATAATCGGCTAAAAGCCATTAGTGGGTCCACAGTCGTCTCATGCGACCCGTGCGACCCTCACATA
418359 TCAATCACTTCCTCCAATACAAGATCATAACCCCATGCAGTATGTCATGTATGCTGTATGATATG
66 TCAATCACTTCCTCCAATACAAGATCATAACCCCATGCAGTATGTCATGTATGCTGTATGATATG
418424 CTCAGAATCAGTCATATATATATCTTAAAACAAGTCGGTCATACACACATTTCAATTCCTAGGGG
131 CTCAGAATCAGTCATATATATATCTTAAAACAAGTCGGTCATACACACATTTCAATTCCTAGGGG
418489 TATAACAGTCATTTTACACTATGGAGGTATTCCGATAATTTTACCCTTCGGGGGTATTTTGGTAA
196 TATAACAGTCATTTTACACTATGGAGGTATTCCGATAATTTTACCCTTCGGGGGTATTTTGGTAA
418554 TTTTACCCATCAAGGGTATTTTAGTAATTTTACCTTTCAGTGGTATTTTGATAATTTTATCTATC
261 TTTTACCCATCAAGGGTATTTTAGTAATTTTACCTTTCAGTGGTATTTTGATAATTTTATCTATC
418619 GAGGGTATTTTAATAATTTTACCCTTTGGGGGTATTTCGGTAATTTTACCTATCAAGGGTATTTT
326 GAGGGTATTTTAATAATTTTACCCTTTGGGGGTATTTCGGTAATTTTACCTATCAAGGGTATTTT
418684 AGTAATT
391 AGTAATT
418691 ATAATCGGCTAAAAGCCATTAGTGGGTCCACAGTCGTCTCATGCGACCCGTGCGACCCTCACATA
1 ATAATCGGCTAAAAGCCATTAGTGGGTCCACAGTCGTCTCATGCGACCCGTGCGACCCTCACATA
418756 TCAATCACTTCCTCCAATACAAGATCATAACCCCATGCAGTATGTCATGTATGCTGTATGATATG
66 TCAATCACTTCCTCCAATACAAGATCATAACCCCATGCAGTATGTCATGTATGCTGTATGATATG
418821 CTCAGAATCAGTCATATATATATCTTAAAACAAGTCGGTCATACACACATTTCAATTCCTAGGGG
131 CTCAGAATCAGTCATATATATATCTTAAAACAAGTCGGTCATACACACATTTCAATTCCTAGGGG
418886 TATAACAGTCATTTTACACTATGGAGGTATTCCGATAATTTTACCCTTCGGGGGTATTTTGGTAA
196 TATAACAGTCATTTTACACTATGGAGGTATTCCGATAATTTTACCCTTCGGGGGTATTTTGGTAA
418951 TTTTACCCATCAAGGGTATTTTAGTAATTTTACCTTTCAGTGGTATTTTGATAATTTTATCTATC
261 TTTTACCCATCAAGGGTATTTTAGTAATTTTACCTTTCAGTGGTATTTTGATAATTTTATCTATC
419016 GAGGGTATTTTAATAATTTTACCCTTTGGGGGTATTTCGGTAATTTTACCTATCAAGGGTATTTT
326 GAGGGTATTTTAATAATTTTACCCTTTGGGGGTATTTCGGTAATTTTACCTATCAAGGGTATTTT
419081 AGTAATT
391 AGTAATT
419088 TTACCCTTCG
Statistics
Matches: 397, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
397 397 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (397 bp):
ATAATCGGCTAAAAGCCATTAGTGGGTCCACAGTCGTCTCATGCGACCCGTGCGACCCTCACATA
TCAATCACTTCCTCCAATACAAGATCATAACCCCATGCAGTATGTCATGTATGCTGTATGATATG
CTCAGAATCAGTCATATATATATCTTAAAACAAGTCGGTCATACACACATTTCAATTCCTAGGGG
TATAACAGTCATTTTACACTATGGAGGTATTCCGATAATTTTACCCTTCGGGGGTATTTTGGTAA
TTTTACCCATCAAGGGTATTTTAGTAATTTTACCTTTCAGTGGTATTTTGATAATTTTATCTATC
GAGGGTATTTTAATAATTTTACCCTTTGGGGGTATTTCGGTAATTTTACCTATCAAGGGTATTTT
AGTAATT
Found at i:419113 original size:81 final size:80
Alignment explanation
Indices: 418919--419118 Score: 208
Period size: 81 Copynumber: 2.5 Consensus size: 80
418909 GAGGTATTCC
* *
418919 GATAATTTTACCCTTCGGGGGTATTTTGGTAATTTTACCCATCAAGGGTATTTTAGTAATTTTAC
1 GATAATTTTACCCTTC-GGGGTATTTTGATAATTTTACCCATCAAGGGTATTTCAGTAATTTTAC
*
418984 CTTTCAGTGGTATTTT
65 CTATCAGTGGTATTTT
* * * *** *
419000 GATAATTTTA-TCTATCGAGGGTATTTTAATAATTTTACCCTTTGGGGGTATTTCGGTAATTTTA
1 GATAATTTTACCCT-TCG-GGGTATTTTGATAATTTTACCCATCAAGGGTATTTCAGTAATTTTA
419064 CCTATCAAG-GGTATTTT
64 CCTATC-AGTGGTATTTT
* * *
419081 -AGTAATTTTACCCTTCGGGTTTATTTCGATAATCTTAC
1 GA-TAATTTTACCCTTCGGG-GTATTTTGATAATTTTAC
419119 AACCTTTCTG
Statistics
Matches: 98, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
80 6 0.06
81 88 0.90
82 4 0.04
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (80 bp):
GATAATTTTACCCTTCGGGGTATTTTGATAATTTTACCCATCAAGGGTATTTCAGTAATTTTACC
TATCAGTGGTATTTT
Found at i:420286 original size:22 final size:23
Alignment explanation
Indices: 420238--420288 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
420228 GACTTCTTTA
420238 CCACACCTGTGATGCCACCTCCTTG
1 CCACACCTGTGATGCCA-C-CCTTG
*
420263 CCACACCTGTGTTGCCA-CCTTG
1 CCACACCTGTGATGCCACCCTTG
420285 CCAC
1 CCAC
420289 TACACCACAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 9 0.36
25 16 0.64
ACGTcount: A:0.16, C:0.45, G:0.16, T:0.24
Consensus pattern (23 bp):
CCACACCTGTGATGCCACCCTTG
Done.