Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 1 of 34
Found at i:462 original size:61 final size:61
Alignment explanation
Indices: 333--461 Score: 156
Period size: 63 Copynumber: 2.1 Consensus size: 61
323 AGCAAATTTG
* *
333 GGTTTTTACTAATGCAGTAAAATAAGAGTTGCGATTACAAAGGGAAAAAAATTAGGCTTTA
1 GGTTTTTACTAATGCAGTAAAATAAGAGTTGCGATAAAAAAGGGAAAAAAATTAGGCTTTA
* * *
394 GGTTTTTACTAATGCTAAAG-AAAATAATAGTTGCGACTAAAAAAGGG-AAAAACTTAGG-TTTT
1 GGTTTTTACTAATGC---AGTAAAATAAGAGTTGCGA-TAAAAAAGGGAAAAAAATTAGGCTTTA
456 GGTTTT
1 GGTTTT
462 AGGTGAGTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
61 15 0.25
62 9 0.15
63 25 0.42
64 10 0.17
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.32
Consensus pattern (61 bp):
GGTTTTTACTAATGCAGTAAAATAAGAGTTGCGATAAAAAAGGGAAAAAAATTAGGCTTTA
Found at i:783 original size:21 final size:19
Alignment explanation
Indices: 743--790 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
733 ATAATAATAA
*
743 ATTATTTAAAAATTAATTT
1 ATTATATAAAAATTAATTT
*
762 ATTATATATAAATTAATTT
1 ATTATATAAAAATTAATTT
781 -TTATTATAAA
1 ATTA-TATAAA
791 TATAGGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTATATAAAAATTAATTT
Found at i:1022 original size:16 final size:16
Alignment explanation
Indices: 993--1026 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
983 TTTGAACTCG
* *
993 AAAAGGCTCGAACCCA
1 AAAAGGCCCAAACCCA
1009 AAAAGGCCCAAACCCA
1 AAAAGGCCCAAACCCA
1025 AA
1 AA
1027 TAAGCTCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.32, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAGGCCCAAACCCA
Found at i:1429 original size:16 final size:16
Alignment explanation
Indices: 1400--1446 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1390 ATTGATTATG
* *
1400 GGTTTGCATCATTTTA
1 GGTTTGAATTATTTTA
*
1416 GGTTT-AAGTTATTTTT
1 GGTTTGAA-TTATTTTA
1432 GGTTTGAATTATTTT
1 GGTTTGAATTATTTT
1447 GGATTTAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 23 0.88
17 2 0.08
ACGTcount: A:0.19, C:0.04, G:0.19, T:0.57
Consensus pattern (16 bp):
GGTTTGAATTATTTTA
Found at i:1446 original size:32 final size:32
Alignment explanation
Indices: 1400--1468 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
1390 ATTGATTATG
* * *
1400 GGTTTGCATCATTTTAGG-TTTAAGTTATTTTT
1 GGTTTGAATCATTTT-GGATTTAAGATACTTTT
* *
1432 GGTTTGAATTATTTTGGATTTAGGATACTTTT
1 GGTTTGAATCATTTTGGATTTAAGATACTTTT
1464 GGTTT
1 GGTTT
1469 TAAGTCATCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 2 0.06
32 29 0.94
ACGTcount: A:0.19, C:0.04, G:0.22, T:0.55
Consensus pattern (32 bp):
GGTTTGAATCATTTTGGATTTAAGATACTTTT
Found at i:11713 original size:33 final size:33
Alignment explanation
Indices: 11637--11768 Score: 148
Period size: 33 Copynumber: 4.1 Consensus size: 33
11627 TTTAGTGGCA
*
11637 TTTCTTTTCAAAATCCACAACTCCATGGCAACCTT
1 TTTCTTTT-AAAGTCCACAACTCCATGGCAACC-T
* **
11672 TTTCTTTTAAAGTCCATAACTCTGTGGCAACCT
1 TTTCTTTTAAAGTCCACAACTCCATGGCAACCT
*
11705 TTTCTTTTAAAGTCCACAACTCCGTGGC-ACC-
1 TTTCTTTTAAAGTCCACAACTCCATGGCAACCT
* *
11736 ---CTTTTAAAGTCCATAACTCCATGGCATCCT
1 TTTCTTTTAAAGTCCACAACTCCATGGCAACCT
11766 TTT
1 TTT
11769 AAGTCCACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
28 23 0.28
29 2 0.02
32 3 0.04
33 27 0.33
34 20 0.24
35 8 0.10
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.36
Consensus pattern (33 bp):
TTTCTTTTAAAGTCCACAACTCCATGGCAACCT
Found at i:11780 original size:27 final size:27
Alignment explanation
Indices: 11708--12975 Score: 1416
Period size: 27 Copynumber: 46.4 Consensus size: 27
11698 GCAACCTTTT
*
11708 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
* *
11736 CTTTTAAAGTCCATAACTCCATGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
*
11764 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATC
* *
11791 CTTTTAAGTCCA-ACACTCCAGTAGCACC
1 CTTTTAAGTCCACA-ACTCC-GTGGCATC
* *
11819 CTTTTAAGTCCA-ACACTCTGTGGCACC
1 CTTTTAAGTCCACA-ACTCCGTGGCATC
* * *
11846 CTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCATC
11873 CTTTTAAAGTCCACAACTCCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
* * * *
11901 CCTTTAAGTCCATAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATC
11928 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATC
* * * * *
11955 TTTTTAAAGTTCACAATCTCAGTGGTACC
1 CTTTT-AAGTCCACAA-CTCCGTGGCATC
* *
11984 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATC
* * * *
12011 CTTTAAAGTCTACGACTCTGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCATC
*
12037 TTTTTTAAAGTCCACAACTCCGTGGCATC
1 -CTTTT-AAGTCCACAACTCCGTGGCATC
* *
12066 CTTTTGAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATC
*
12093 CTTTTTAAGTCCACAACTCCATGGCA-C
1 C-TTTTAAGTCCACAACTCCGTGGCATC
*
12120 TCTTTTAAAG-CCTACAACTTCGTGGCATC
1 -CTTTT-AAGTCC-ACAACTCCGTGGCATC
12149 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCAT-C
* * * **
12177 CTTTAAAGTCCATAATTTTGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATC
*
12204 CTTTTTAAGTCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCATC
* * * *
12232 CTATAAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATC
*
12259 CTTTTAAAGTCCACAACTCCGTAGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
12287 CTTTTAAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCATC
* *
12313 CATTTTAAGTTCACAACT-CGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCATC
12340 CTTTTAAAGTCCACAACTCCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
* * *
12368 CTTTTAAGTCCATAACTTCGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCA-TC
** * *
12396 CTTTTAAGTTAACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCATC
* * * *
12423 CTTTTAAAGCCCATAATTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
* *
12451 TTTTTAAGTCCATAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATC
* *
12478 CTTTTAAGTCCATAACTTCGTGGCA--
1 CTTTTAAGTCCACAACTCCGTGGCATC
12503 ---TT--GTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATC
*
12525 CTTTTAAAGTCCATAACTCCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
12553 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATC
12580 CTTTTAAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCATC
12606 CTTTTTAAAGTCCACAACTCCGTGGCATC
1 C-TTTT-AAGTCCACAACTCCGTGGCATC
* *
12635 CTTTTAAAGTCTACAACTCCATGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
*
12663 CTTTTAAGTCCATAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATC
* *
12690 CCTTTAAGTCCACAACTCTGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATC
*
12717 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
*
12745 CTTTTAAAGTCCACAACTCCGTGGCGTC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
*
12773 CTTTTAAAGTCCACAACTTCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
12801 CTTTTAAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCATC
* * * * * * *
12827 TCGTTAAAATCTATAACTCCATTGCATC
1 -CTTTTAAGTCCACAACTCCGTGGCATC
* *
12855 CTTTTAAAGTCCACAACTCTGTGGTATC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
*
12883 CTTTTAAGTCCACAACTCTGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATC
12910 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCATC
* *
12937 CTTTTAAAGTCCACAACTCCATGGTATC
1 CTTTT-AAGTCCACAACTCCGTGGCATC
*
12965 CTTTAAAGTCC
1 CTTTTAAGTCC
12976 TTTTAAGTCC
Statistics
Matches: 1070, Mismatches: 130, Indels: 81
0.84 0.10 0.06
Matches are distributed among these distances:
20 16 0.01
22 2 0.00
25 2 0.00
26 18 0.02
27 532 0.50
28 483 0.45
29 17 0.02
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCATC
Found at i:11793 original size:55 final size:55
Alignment explanation
Indices: 11708--12975 Score: 1415
Period size: 55 Copynumber: 23.2 Consensus size: 55
11698 GCAACCTTTT
* *
11708 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCATAACTCCATGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* *
11764 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCA-ACACTCCAGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACA-ACTCC-GTGGCATC
* * *
11819 CTTTTAAGTCCA-ACACTCTGTGGCACCC-TTTAAAGTCCACAACTCCGTGGTACC
1 CTTTTAAGTCCACA-ACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* * *
11873 CTTTTAAAGTCCACAACTCCGTGGCATCCC-TTT-AAGTCCATAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCA-CCCTTTTAAAGTCCACAACTCCGTGGCATC
* * * * * *
11928 CTTTTAAGTCCACAACTCCGTGGCATCTTTTTAAAGTTCACAATCTCAGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAA-CTCCGTGGCATC
* * * *
11984 CTTTTAAGTCCACAACTCTGTGGCACCC-TTTAAAGTCTACGACTCTGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* * * *
12037 TTTTTTAAAGTCCACAACTCCGTGGCATCCTTTT-GAGTCCACAACTCCGTGGCACC
1 -CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* * *
12093 CTTTTTAAGTCCACAACTCCATGGCACTCTTTTAAAG-CCTACAACTTCGTGGCATC
1 C-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCC-ACAACTCCGTGGCATC
* * **
12149 CTTTTAAGTCCACAACTCCGTGGCATCCC-TTTAAAGTCCATAATTTTGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAAGTCCACAACTCCGTGGCATC
* * *
12204 CTTTTTAAGTCCACAACTCCGTGGCACCC-TATAAAGTCCACAACTCTGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* *
12259 CTTTTAAAGTCCACAACTCCGTAGCATCCTTTT-AAGTCCACAACTCCGTGGCA-C
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
*
12313 CATTTTAAGTTCACAACT-CGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
1 C-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* * ** * *
12368 CTTTTAAGTCCATAACTTCGTGGCACCCCTTTT-AAGTTAACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAAGTCCACAACTCCGTGGCATC
* * * * * * *
12423 CTTTTAAAGCCCATAATTCTGTGGCA-TCTTTTTAAGTCCATAACTCCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* *
12478 CTTTTAAGTCCATAACTTCGTGGCA-----TT---GTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* *
12525 CTTTTAAAGTCCATAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
*
12580 CTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* * * *
12635 CTTTTAAAGTCTACAACTCCATGGCATCCTTTT-AAGTCCATAACTCCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* * * *
12690 CCTTTAAGTCCACAACTCTGTGGCATCCTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
** *
12745 CTTTTAAAGTCCACAACTCCGTGGCGTCCTTTTAAAGTCCACAACTTCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* * * * * * *
12801 CTTTTAAGTCCACAACTCCGTGGCACTC-GTTAAAATCTATAACTCCATTGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* * * *
12855 CTTTTAAAGTCCACAACTCTGTGGTATCCTTTT-AAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
* * *
12910 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCATGGTATC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
*
12965 CTTTAAAGTCC
1 CTTTTAAGTCC
12976 TTTTAAGTCC
Statistics
Matches: 1044, Mismatches: 123, Indels: 91
0.83 0.10 0.07
Matches are distributed among these distances:
47 24 0.02
48 19 0.02
50 2 0.00
53 17 0.02
54 231 0.22
55 549 0.53
56 202 0.19
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (55 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATC
Found at i:12514 original size:20 final size:20
Alignment explanation
Indices: 12485--12523 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12475 ATCCTTTTAA
* *
12485 GTCCATAACTTCGTGGCATT
1 GTCCACAACTCCGTGGCATT
12505 GTCCACAACTCCGTGGCAT
1 GTCCACAACTCCGTGGCAT
12524 CCTTTTAAAG
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:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (20 bp):
GTCCACAACTCCGTGGCATT
Found at i:12956 original size:28 final size:28
Alignment explanation
Indices: 12505--12975 Score: 667
Period size: 28 Copynumber: 17.1 Consensus size: 28
12495 TCGTGGCATT
12505 GTCCACAACTCCGTGGCATCCTTTTAAA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
*
12533 GTCCATAACTCCGTGGCATCCTTTT-AA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
12560 GTCCACAACTCCGTGGCATCCTTTT-AA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
12587 GTCCACAACTCCGTGGCA-CCTTTTTAAA
1 GTCCACAACTCCGTGGCATCC-TTTTAAA
12615 GTCCACAACTCCGTGGCATCCTTTTAAA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
* *
12643 GTCTACAACTCCATGGCATCCTTTT-AA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
* *
12670 GTCCATAACTCCGTGGCATCCCTTT-AA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
*
12697 GTCCACAACTCTGTGGCATCCTTTTAAA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
*
12725 GTCCACAACTCTGTGGCATCCTTTTAAA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
*
12753 GTCCACAACTCCGTGGCGTCCTTTTAAA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
*
12781 GTCCACAACTTCGTGGCATCCTTTT-AA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
*
12808 GTCCACAACTCCGTGGCA--CTCGTTAAA
1 GTCCACAACTCCGTGGCATCCT-TTTAAA
* * * * *
12835 ATCTATAACTCCATTGCATCCTTTTAAA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
* *
12863 GTCCACAACTCTGTGGTATCCTTTT-AA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
*
12890 GTCCACAACTCTGTGGCATCCTTTT-AA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
12917 GTCCACAACTCCGTGGCATCCTTTTAAA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
* *
12945 GTCCACAACTCCATGGTATCC-TTTAAA
1 GTCCACAACTCCGTGGCATCCTTTTAAA
12972 GTCC
1 GTCC
12976 TTTTAAGTCC
Statistics
Matches: 400, Mismatches: 34, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
25 2 0.00
26 4 0.01
27 193 0.48
28 197 0.49
29 4 0.01
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (28 bp):
GTCCACAACTCCGTGGCATCCTTTTAAA
Found at i:12988 original size:37 final size:38
Alignment explanation
Indices: 12935--13012 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 38
12925 CTCCGTGGCA
*
12935 TCCTTTTAAAGTCCACAACTCCATGGTATCCTTTAAAG
1 TCCTTTTAAAGTCCACAACTCCATGGCATCCTTTAAAG
* *
12973 TCCTTTT-AAGTCCACAACTCCATGGCATTCTTTTAAG
1 TCCTTTTAAAGTCCACAACTCCATGGCATCCTTTAAAG
13010 TCC
1 TCC
13013 ACAAGTCAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 30 0.81
38 7 0.19
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (38 bp):
TCCTTTTAAAGTCCACAACTCCATGGCATCCTTTAAAG
Found at i:13043 original size:28 final size:28
Alignment explanation
Indices: 13011--13835 Score: 418
Period size: 32 Copynumber: 28.1 Consensus size: 28
13001 TCTTTTAAGT
*
13011 CCACAAGTCAGTGGCACCCTTCCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* **
13039 CCACAAGTCATTGGCACCCCTTTTTAAGC
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGC
*
13068 CCACAAGTTAGTGGCACCC-TTCTAAAGC
1 CCACAAGTCAGTGGCACCCTTTC-AAAGC
* *
13096 CCATAAATCAGTGGCACCCCTTTCAAAGC
1 CCACAAGTCAGTGGCA-CCCTTTCAAAGC
* * *
13125 CTACAAGTCAGTGGCATCCTTTCAAAGT
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
** *
13153 CCACAAACCAGTGGCACCTTTTCGAAAGC
1 CCACAAGTCAGTGGCACCCTTTC-AAAGC
13182 CCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
13210 CCGCAAGTCAATGGCA-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
13237 CCACAAGTCAGTAGCA-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * *
13264 CCACAAGTTAGTGGTAACTCATTTCAAAGC
1 CCACAAGTCAGTGG-CAC-CCTTTCAAAGC
* ** **
13294 CGACACAAGTCGGTGGCA--AGTT-AGTG-
1 C--CACAAGTCAGTGGCACCCTTTCAAAGC
* *** ** ** **
13320 GCACCTTTCA-AAGC-CCACAAGTCAGTGGC
1 CCACAAGTCAGTGGCACC-C-TTTCA-AAGC
* *** * *
13349 ACCACTTTCAAAGCCTACAAGTTAG-TGGC-ATCAAAGT
1 -CCA----C-AAG--T-C-AG-TGGCACCCTTTCAAAGC
* ** * *
13386 CTACAAAACCAGTGGCACCTTTTTGAAAGC
1 CCAC-AAGTCAGTGGCACC-CTTTCAAAGC
**
13416 CCACAAGTCAGTGGCACTTTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* *
13444 CCACAAATTAGTGGCA-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
*
13471 CCATAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
13499 CCACAAGTCAGTGGCA-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
13526 CCACAAGTCAGTGGCA-CCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGC
* * *
13553 CCACAAGTTAGTGGTAACTCATTTCAAAGC
1 CCACAAGTCAGTGG-CAC-CCTTTCAAAGC
* **
13583 CGACACAAGTCGGTGGCAACTTATTTCAAAGC
1 C--CACAAGTCAGTGGC-AC-CCTTTCAAAGC
** *
13615 CTACACAAGTTGGTGGCAACCCATTTGAAAGC
1 C--CACAAGTCAGTGGC-ACCC-TTTCAAAGC
* *
13647 CCACATAAGTCGGTGGCAACCCATTTGAAAGC
1 CCAC--AAGTCAGTGGC-ACCC-TTTCAAAGC
**
13679 CCACAAGTTGGTGGCAACCCTTTTCAAAGCC
1 CCACAAGTCAGTGGC-ACCC-TTTCAAAG-C
* *
13710 CACACAAGTCGGTGGCAACCCATTTGAAAGC
1 C-CACAAGTCAGTGGC-ACCC-TTTCAAAGC
**
13741 CCACAAGTTGGTGGCAACCCTTTTCAAAGCC
1 CCACAAGTCAGTGGC-ACCC-TTTCAAAG-C
* * * *
13772 CACACAAGTCGGTGGGAACCTCTCTCAAAACC
1 C-CACAAGTCAGT-GGCACC-CTTTC-AAAGC
* *
13804 CGCACAAGTCAGTGGGAACCCTTTTAAAGC
1 C-CACAAGTCAGT-GGCACCCTTTCAAAGC
13834 CC
1 CC
13836 GCACAAGTTG
Statistics
Matches: 629, Mismatches: 118, Indels: 99
0.74 0.14 0.12
Matches are distributed among these distances:
23 2 0.00
24 5 0.01
26 1 0.00
27 127 0.20
28 139 0.22
29 81 0.13
30 90 0.14
31 10 0.02
32 155 0.25
33 6 0.01
34 1 0.00
36 2 0.00
37 2 0.00
38 4 0.01
39 1 0.00
40 1 0.00
41 2 0.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (28 bp):
CCACAAGTCAGTGGCACCCTTTCAAAGC
Found at i:13072 original size:57 final size:55
Alignment explanation
Indices: 13011--13775 Score: 583
Period size: 57 Copynumber: 13.1 Consensus size: 55
13001 TCTTTTAAGT
* * **
13011 CCACAAGTCAGTGGCACCCTTCCAAAGCCCACAAGTCATTGGCACCCCTTTTTAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA--CCTTTCAAAGC
* * *
13068 CCACAAGTTAGTGGCACCC-TTCTAAAGCCCATAAATCAGTGGCACCCCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTC-AAAGCCCACAAGTCAGTGGCA--CCTTTCAAAGC
* * * **
13125 CTACAAGTCAGTGGCATCCTTTCAAAGTCCACAAACCAGTGGCACCTTTTCGAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC-TTTC-AAAGC
* *
13182 CCACAAGTCAGTGGCACCCTTTCAAAGCCCGCAAGTCAATGGCACCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGC
* * *
13237 CCACAAGTCAGTAGCA-CCTTTCAAAGCCCACAAGTTAGTGGTAACTCATTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG-CAC-C-TTTCAAAGC
*
13294 CGACACAAGTCGGTGGCAAGTTAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACCACTTTCA
1 C--CACAAGTCAGTGGC-----A----C-CCTTTCAAAGCCCACAAGTCAGTGGCA-C-CTTTCA
13359 AAGC
52 AAGC
* * * * ** *
13363 CTACAAGTTAGTGGCA-----TCAAAGTCTACAAAACCAGTGGCACCTTTTTGAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCAC-AAGTCAGTGGCACC--TTTCAAAGC
** * *
13416 CCACAAGTCAGTGGCACTTTTTCAAAGCCCACAAATTAGTGGCACCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGC
*
13471 CCATAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGC
* *
13526 CCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTTAGTGGTAACTCATTTCAAAGC
1 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG-CAC-C-TTTCAAAGC
* ** ** *
13583 CGACACAAGTCGGTGGCAACTTATTTCAAAGCCTACACAAGTTGGTGGCAACCCATTTGAAAGC
1 C--CACAAGTCAGTGGC-AC-CCTTTCAAAGCC--CACAAGTCAGTGGC-A-CC-TTTCAAAGC
* * **
13647 CCACATAAGTCGGTGGCAACCCATTTGAAAGCCCACAAGTTGGTGGCAACCCTTTTCAAAGCC
1 CCAC--AAGTCAGTGGC-ACCC-TTTCAAAGCCCACAAGTCAGTGGC-A-CC-TTTCAAAG-C
* * **
13710 CACACAAGTCGGTGGCAACCCATTTGAAAGCCCACAAGTTGGTGGCAACCCTTTTCAAAGC
1 C-CACAAGTCAGTGGC-ACCC-TTTCAAAGCCCACAAGTCAGTGGC-A-CC-TTTCAAAGC
13771 CCACA
1 CCACA
13776 CAAGTCGGTG
Statistics
Matches: 598, Mismatches: 64, Indels: 89
0.80 0.09 0.12
Matches are distributed among these distances:
51 1 0.00
52 10 0.02
53 32 0.05
54 46 0.08
55 99 0.17
56 12 0.02
57 157 0.26
58 12 0.02
59 25 0.04
60 5 0.01
61 2 0.00
62 95 0.16
63 2 0.00
64 51 0.09
65 1 0.00
67 11 0.02
69 11 0.02
70 26 0.04
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (55 bp):
CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGC
Found at i:13348 original size:38 final size:42
Alignment explanation
Indices: 13267--13349 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 42
13257 TCAAAGCCCA
*
13267 CAAGTTAGTGGTAACTCATTTCAAAGCCGACACAAGTCGGTGG
1 CAAGTTAGTGGTAACTCATTTCAAAGCC-ACACAAGTCAGTGG
*
13310 CAAGTTAGTGG-CAC-C-TTTCAAAGCC-CACAAGTCAGTGG
1 CAAGTTAGTGGTAACTCATTTCAAAGCCACACAAGTCAGTGG
13348 CA
1 CA
13350 CCACTTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
38 14 0.37
40 10 0.26
41 1 0.03
42 2 0.05
43 11 0.29
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (42 bp):
CAAGTTAGTGGTAACTCATTTCAAAGCCACACAAGTCAGTGG
Found at i:13558 original size:289 final size:293
Alignment explanation
Indices: 13014--13601 Score: 884
Period size: 289 Copynumber: 2.0 Consensus size: 293
13004 TTTAAGTCCA
* * **
13014 CAAGTCAGTGGCACCCTTCCAAAGCCCACAAGTCATTGGCACCCCTTTTTAAGCCCACAAGTTAG
1 CAAGTCAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGGCACCACTTTCAAAGCCCACAAGTTAG
* * *
13079 TGGCACCCTTCTAAAGCCCATAAATCAGTGGCACCCCTTTCAAAGCCTACAAGTCAGTGGCATCC
66 TGGCA--C-TCTAAAGCACATAAACCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGCATCC
*
13144 TTTCAAAGTCCACAAACCAGTGGCACCTTTTCGAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
128 TTTCAAAGCCCACAAACCAGTGGCACCTTTTCGAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
*
13209 CCCGCAAGTCAATGGCACCTTTCAAAGCCCACAAGTCAGTAGCACCTTTCAAAGCCCACAAGTTA
193 CCCACAAGTCAATGGCACCTTTCAAAGCCCACAAGTCAGTAGCACCTTTCAAAGCCCACAAGTTA
13274 GTGGTAACTCATTTCAAAGCCGACACAAGTCGGTGG
258 GTGGTAACTCATTTCAAAGCCGACACAAGTCGGTGG
* * *
13310 CAAGTTAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACCACTTTCAAAGCCTACAAGTTAG
1 CAAGTCAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGGCACCACTTTCAAAGCCCACAAGTTAG
** * *
13374 TGGCA-TC-AAAGTCTACA-AAACCAGTGGCACCTTTTTGAAAGCCCACAAGTCAGTGGCA-CTT
66 TGGCACTCTAAAG-C-ACATAAACCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGCATC-C
** *
13435 TTTCAAAGCCCACAAATTAGTGGCACC-TTTC-AAAGCCCATAAGTCAGTGGCACCCTTTCAAAG
128 TTTCAAAGCCCACAAACCAGTGGCACCTTTTCGAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* *
13498 CCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTTA
193 CCCACAAGTCAATGGCACCTTTCAAAGCCCACAAGTCAGTAGCACCTTTCAAAGCCCACAAGTTA
13563 GTGGTAACTCATTTCAAAGCCGACACAAGTCGGTGG
258 GTGGTAACTCATTTCAAAGCCGACACAAGTCGGTGG
13599 CAA
1 CAA
13602 CTTATTTCAA
Statistics
Matches: 268, Mismatches: 21, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
289 132 0.49
290 9 0.03
291 63 0.24
292 2 0.01
295 50 0.19
296 12 0.04
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.21
Consensus pattern (293 bp):
CAAGTCAGTGGCACCCTTCCAAAGCCCACAAGTCAGTGGCACCACTTTCAAAGCCCACAAGTTAG
TGGCACTCTAAAGCACATAAACCAGTGGCACCCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTT
CAAAGCCCACAAACCAGTGGCACCTTTTCGAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCC
ACAAGTCAATGGCACCTTTCAAAGCCCACAAGTCAGTAGCACCTTTCAAAGCCCACAAGTTAGTG
GTAACTCATTTCAAAGCCGACACAAGTCGGTGG
Found at i:13684 original size:94 final size:85
Alignment explanation
Indices: 13310--13786 Score: 373
Period size: 94 Copynumber: 5.5 Consensus size: 85
13300 AAGTCGGTGG
* * ** * *
13310 CAAGTTAGTGGC-A-CC-TTTCAAAGCCCACAAGTCAGTGGCACCACTTTCAAAGCCTACAAGTT
1 CAAGTCAGTGGCAACCCATTTCAAAGCCCACAAGTCGGTGGCA-CTTTTTCAAAGCCCACAAGTC
* *
13372 AGTGGCA----TCAAAGTCTA
65 AGTGGCACCTTTCAAAGCCCA
** ** * * * *
13389 CAAAACCAGTGGC-ACCTTTTTGAAAGCCCACAAGTCAGTGGCACTTTTTCAAAGCCCACAAATT
1 C-AAGTCAGTGGCAACCCATTTCAAAGCCCACAAGTCGGTGGCACTTTTTCAAAGCCCACAAGTC
13453 AGTGGCACCTTTCAAAGCCCA
65 AGTGGCACCTTTCAAAGCCCA
* * *
13474 TAAGTCAGTGGC-ACCC-TTTCAAAGCCCACAAGTCAGTGGCAC-CTTTCAAAGCCCACAAGTCA
1 CAAGTCAGTGGCAACCCATTTCAAAGCCCACAAGTCGGTGGCACTTTTTCAAAGCCCACAAGTCA
13536 GTGGCACCTTTCAAAGCCCA
66 GTGGCACCTTTCAAAGCCCA
* * *
13556 CAAGTTAGTGGTAACTCATTTCAAAGCCGACACAAGTCGGTGGCAACTTATTTCAAAGCCTACAC
1 CAAGTCAGTGGCAACCCATTTCAAAGCC--CACAAGTCGGTGGC-ACTT-TTTCAAAGCC--CAC
** *
13621 AAGTTGGTGGCAACCCATTTGAAAGCCCA
60 AAGTCAGTGGC-A-CC-TTTCAAAGCCCA
* * * *
13650 CATAAGTCGGTGGCAACCCATTTGAAAGCCCACAAGTTGGTGGCAACCCTTTTCAAAGCCCACAC
1 C--AAGTCAGTGGCAACCCATTTCAAAGCCCACAAGTCGGTGGC-A-CTTTTTCAAAG-CC-CAC
* *
13715 AAGTCGGTGGCAACCCATTTGAAAGCCCA
60 AAGTCAGTGGC-A-CC-TTTCAAAGCCCA
** *
13744 CAAGTTGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGG
1 CAAGTCAGTGGCAACCCATTTCAAAG-CC-CACAAGTCGGTGG
13787 GAACCTCTCT
Statistics
Matches: 333, Mismatches: 40, Indels: 35
0.82 0.10 0.09
Matches are distributed among these distances:
79 1 0.00
80 9 0.03
81 25 0.08
82 70 0.21
83 28 0.08
84 22 0.07
85 8 0.02
86 13 0.04
87 2 0.01
89 10 0.03
91 12 0.04
92 23 0.07
93 4 0.01
94 80 0.24
95 4 0.01
96 22 0.07
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (85 bp):
CAAGTCAGTGGCAACCCATTTCAAAGCCCACAAGTCGGTGGCACTTTTTCAAAGCCCACAAGTCA
GTGGCACCTTTCAAAGCCCA
Found at i:13710 original size:62 final size:61
Alignment explanation
Indices: 13396--13917 Score: 441
Period size: 62 Copynumber: 8.7 Consensus size: 61
13386 CTACAAAACC
* * * ** *
13396 AGTGGC-ACCTTTTTGAAAG-CC-CACAAGTCAGTGGC-ACTTTTTCAAAGCCCACAAATT
1 AGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACAAGTT
* * *
13453 AGTGGC-A-CC-TTTCAAAG-CC-CATAAGTCAGTGGC-ACCCTTTCAAAGCCCACAAGTC
1 AGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACAAGTT
*
13508 AGTGGC-A-CC-TTTCAAAG-CC-CACAAGTCAGTGGC-A-CCTTTCAAAGCCCACAAGTT
1 AGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACAAGTT
* * * * **
13562 AGTGGTAACTCATTTCAAAGCCGACACAAGTCGGTGGCAACTTATTTCAAAGCCTACACAAGTT
1 AGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAAC-CCTTTCAAAGCC--CACAAGTT
* * * * *
13626 GGTGGCAACCCATTTGAAAGCCCACATAAGTCGGTGGCAACCCATTTGAAAGCCCACAAGTT
1 AGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCC-TTTCAAAGCCCACAAGTT
* *
13688 GGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTGAAAGCCCACAAGTT
1 AGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCC-TTTCAAAGCCCACAAGTT
* * * * *
13750 GGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGGAACCTCTCTCAAAACCCGCACAAGTC
1 AGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACC-CTTTC-AAAGCC-CACAAGTT
* * * * ** * **
13814 AGTGGGAACCCTTTT-AAAGCCCGCACAAGTTGGTGGCATCGTTTTTCAAAAGTCCACACTTTT
1 AGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAAC-CCTTTC-AAAGCCCACA-AGTT
* * ** *
13877 GGTGGCAACCCTTTTTAAAGCCCACGTAAGTCAGTGGCAAC
1 AGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAAC
13918 TTTTTTCAAA
Statistics
Matches: 394, Mismatches: 54, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
54 24 0.06
55 74 0.19
56 2 0.01
57 15 0.04
58 1 0.00
59 13 0.03
60 1 0.00
62 124 0.31
63 49 0.12
64 91 0.23
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (61 bp):
AGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACAAGTT
Found at i:13800 original size:94 final size:91
Alignment explanation
Indices: 13411--13851 Score: 419
Period size: 94 Copynumber: 4.9 Consensus size: 91
13401 CACCTTTTTG
* * * *
13411 AAAGCCCACAAGTCAGTGGC-A-CTTTTTCAAAGCCCACA-AA-TTAGTGGC-A-CCTTTCAAAG
1 AAAGCCCACAAGTCGGTGGCAACCTCTTTCAAAGCCCACACAAGTCAGTGGCAACCCTTTGAAAG
* **
13470 CCCATAAGTCAGTGGC-ACCC-TTTC
66 CCCACAAGTTGGTGGCAACCCATTTC
* *
13494 AAAGCCCACAAGTCAGTGGC-A-C-CTTTCAAAG-CC-CACAAGTCAGTGGC-A-CCTTTCAAAG
1 AAAGCCCACAAGTCGGTGGCAACCTCTTTCAAAGCCCACACAAGTCAGTGGCAACCCTTTGAAAG
* * *
13552 CCCACAAGTTAGTGGTAACTCATTTC
66 CCCACAAGTTGGTGGCAACCCATTTC
* * * **
13578 AAAGCCGACACAAGTCGGTGGCAACTTATTTCAAAGCCTACACAAGTTGGTGGCAACCCATTTGA
1 AAAGCC--CACAAGTCGGTGGCAACCTCTTTCAAAGCCCACACAAGTCAGTGGCAACCC-TTTGA
* *
13643 AAGCCCACATAAGTCGGTGGCAACCCATTTG
63 AAGCCCAC--AAGTTGGTGGCAACCCATTTC
* *
13674 AAAGCCCACAAGTTGGTGGCAACC-CTTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTGAA
1 AAAGCCCACAAGTCGGTGGCAACCTC-TTTCAAAGCCCACACAAGTCAGTGGCAACCC-TTTGAA
*
13738 AGCCCACAAGTTGGTGGCAACCCTTTTC
64 AGCCCACAAGTTGGTGGCAACCCATTTC
* * * * * *
13766 AAAGCCCACACAAGTCGGTGGGAACCTCTCTCAAAACCCGCACAAGTCAGTGGGAACCCTTTTAA
1 AAAG-CC-CACAAGTCGGTGGCAACCTCTTTCAAAGCCCACACAAGTCAGTGGCAACCCTTTGAA
13831 AGCCCGCACAAGTTGGTGGCA
64 AG-CC-CACAAGTTGGTGGCA
13852 TCGTTTTTCA
Statistics
Matches: 302, Mismatches: 34, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
80 2 0.01
81 4 0.01
82 39 0.13
83 25 0.08
84 10 0.03
86 13 0.04
87 1 0.00
89 8 0.03
90 1 0.00
91 12 0.04
92 23 0.08
93 11 0.04
94 115 0.38
95 16 0.05
96 22 0.07
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (91 bp):
AAAGCCCACAAGTCGGTGGCAACCTCTTTCAAAGCCCACACAAGTCAGTGGCAACCCTTTGAAAG
CCCACAAGTTGGTGGCAACCCATTTC
Found at i:13908 original size:95 final size:92
Alignment explanation
Indices: 13434--13917 Score: 356
Period size: 94 Copynumber: 5.3 Consensus size: 92
13424 CAGTGGCACT
* * * * * **
13434 TTTTCAAAGCCCACAAATTAGTGGC-A-CC-TTTCAAAGCCCATAAGTCAGTGGC-ACCC-TTTC
1 TTTTAAAAGCCCACAAGTCAGTGGCAACCCATTTGAAAGCCCACAAGTTGGTGGCAACCCTTTTC
**
13494 AAAG-CC-CACAAGTCAGTGGC-A-CC
66 AAAGCCCACACAAGTTGGTGGCAACCC
* * * * * *
13517 -TTTCAAAGCCCACAAGTCAGTGGC-A-CC-TTTCAAAGCCCACAAGTTAGTGGTAACTCATTTC
1 TTTTAAAAGCCCACAAGTCAGTGGCAACCCATTTGAAAGCCCACAAGTTGGTGGCAACCCTTTTC
* * *
13578 AAAGCCGACACAAGTCGGTGGCAA-CT
66 AAAGCCCACACAAGTTGGTGGCAACCC
* ** *
13604 TATTTCAAAGCCTACACAAGTTGGTGGCAACCCATTTGAAAGCCCACATAAGTCGGTGGCAACCC
1 T-TTTAAAAGCC--CACAAGTCAGTGGCAACCCATTTGAAAGCCCAC--AAGTTGGTGGCAACCC
* *
13669 ATTTGAAAG-CC-CACAAGTTGGTGGCAACCC
61 TTTTCAAAGCCCACACAAGTTGGTGGCAACCC
* *
13699 TTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTGAAAGCCCACAAGTTGGTGGCAACCCTTT
1 TTTTAAAAG-CC-CACAAGTCAGTGGCAACCCATTTGAAAGCCCACAAGTTGGTGGCAACCCTTT
* *
13764 TCAAAGCCCACACAAGTCGGTGGGAACCTC
64 TCAAAGCCCACACAAGTTGGTGGCAACC-C
* * * * * * **
13794 TCTCAAAACCCGCACAAGTCAGTGGGAACCC-TTTTAAAGCCCGCACAAGTTGGTGGCATCGTTT
1 TTTTAAAAGCC-CACAAGTCAGTGGCAACCCATTTGAAAG-CC-CACAAGTTGGTGGCAACCCTT
* **
13858 TTCAAAAGTCCACAC-TTTTGGTGGCAACCC
63 TTC-AAAGCCCACACAAGTTGGTGGCAACCC
*
13888 TTTTTAAAGCCCACGTAAGTCAGTGGCAAC
1 TTTTAAAAGCCCAC--AAGTCAGTGGCAAC
13918 TTTTTTCAAA
Statistics
Matches: 330, Mismatches: 47, Indels: 36
0.80 0.11 0.09
Matches are distributed among these distances:
82 46 0.14
83 3 0.01
84 8 0.02
85 1 0.00
86 13 0.04
87 2 0.01
89 10 0.03
91 12 0.04
92 23 0.07
93 14 0.04
94 113 0.34
95 55 0.17
96 30 0.09
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (92 bp):
TTTTAAAAGCCCACAAGTCAGTGGCAACCCATTTGAAAGCCCACAAGTTGGTGGCAACCCTTTTC
AAAGCCCACACAAGTTGGTGGCAACCC
Found at i:13914 original size:32 final size:30
Alignment explanation
Indices: 13395--13927 Score: 371
Period size: 32 Copynumber: 17.7 Consensus size: 30
13385 TCTACAAAAC
* *
13395 CAGTGGC-ACCTTTTTGAAAGCCCACAAGT
1 CAGTGGCAACCCTTTTCAAAGCCCACAAGT
* *
13424 CAGTGGC-A-CTTTTTCAAAGCCCACAAAT
1 CAGTGGCAACCCTTTTCAAAGCCCACAAGT
* *
13452 TAGTGGC-A-CC-TTTCAAAGCCCATAAGT
1 CAGTGGCAACCCTTTTCAAAGCCCACAAGT
13479 CAGTGGC-ACCC-TTTCAAAGCCCACAAGT
1 CAGTGGCAACCCTTTTCAAAGCCCACAAGT
13507 CAGTGGC-A-CC-TTTCAAAGCCCACAAGT
1 CAGTGGCAACCCTTTTCAAAGCCCACAAGT
13534 CAGTGGC-A-CC-TTTCAAAGCCCACAAGT
1 CAGTGGCAACCCTTTTCAAAGCCCACAAGT
* * * *
13561 TAGTGGTAACTCATTTCAAAGCCGACACAAGT
1 CAGTGGCAACCCTTTTCAAAGCC--CACAAGT
* *
13593 CGGTGGCAA-CTTATTTCAAAGCCTACACAAGT
1 CAGTGGCAACCCT-TTTCAAAGCC--CACAAGT
** * *
13625 TGGTGGCAACCCATTTGAAAGCCCACATAAGT
1 CAGTGGCAACCCTTTTCAAAGCCCAC--AAGT
* * *
13657 CGGTGGCAACCCATTTGAAAGCCCACAAGT
1 CAGTGGCAACCCTTTTCAAAGCCCACAAGT
**
13687 TGGTGGCAACCCTTTTCAAAGCCCACACAAGT
1 CAGTGGCAACCCTTTTCAAAG-CC-CACAAGT
* * *
13719 CGGTGGCAACCCATTTGAAAGCCCACAAGT
1 CAGTGGCAACCCTTTTCAAAGCCCACAAGT
**
13749 TGGTGGCAACCCTTTTCAAAGCCCACACAAGT
1 CAGTGGCAACCCTTTTCAAAG-CC-CACAAGT
* * * *
13781 CGGTGGGAA-CCTCTCTCAAAACCCGCACAAGT
1 CAGTGGCAACCCT-TTTC-AAAGCC-CACAAGT
*
13813 CAGTGGGAACCCTTTT-AAAGCCCGCACAAGT
1 CAGTGGCAACCCTTTTCAAAG-CC-CACAAGT
** * ** * **
13844 TGGTGGCATCGTTTTTCAAAAGTCCACACTTT
1 CAGTGGCAACCCTTTTC-AAAGCCCACA-AGT
** *
13876 TGGTGGCAACCCTTTTTAAAGCCCACGTAAGT
1 CAGTGGCAACCCTTTTCAAAGCCCAC--AAGT
**
13908 CAGTGGCAACTTTTTTCAAA
1 CAGTGGCAACCCTTTTCAAA
13928 TCACTACTTT
Statistics
Matches: 420, Mismatches: 61, Indels: 43
0.80 0.12 0.08
Matches are distributed among these distances:
27 73 0.17
28 53 0.13
29 9 0.02
30 63 0.15
31 41 0.10
32 169 0.40
33 12 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (30 bp):
CAGTGGCAACCCTTTTCAAAGCCCACAAGT
Found at i:19105 original size:19 final size:20
Alignment explanation
Indices: 19081--19121 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
19071 ATTTTGTTAC
19081 TTTATTTCTTAAT-TTTAAT
1 TTTATTTCTTAATATTTAAT
* *
19100 TTTATTTTTTATTATTTAAT
1 TTTATTTCTTAATATTTAAT
19120 TT
1 TT
19122 ACATCTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTTCTTAATATTTAAT
Found at i:23482 original size:33 final size:34
Alignment explanation
Indices: 23424--23488 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
23414 CAAGAAAATG
*
23424 TATCGATACATTACTCAAATGTATCGATACATTA
1 TATCGATACACTACTCAAATGTATCGATACATTA
*
23458 TATCGATACACTA-TGAAATGTATCGATACAT
1 TATCGATACACTACTCAAATGTATCGATACAT
23489 ACAGGCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (34 bp):
TATCGATACACTACTCAAATGTATCGATACATTA
Found at i:37369 original size:4 final size:4
Alignment explanation
Indices: 37362--37458 Score: 53
Period size: 4 Copynumber: 24.8 Consensus size: 4
37352 CCGCAAAAAA
* * **
37362 AAAC AAAC AAAC AAAAC AAAAC AAAA AAAG TGAC AAA- AAA- AAAC AAAC
1 AAAC AAAC AAAC -AAAC -AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC
* * *
37410 AAAAC AAA- AGAA- AAAA AAAC AAA- AAAA AAAC AAAC GAAC AAAC -AAC
1 -AAAC AAAC A-AAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC
37456 AAA
1 AAA
37459 AAGGGTCCGG
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
3 15 0.20
4 47 0.63
5 13 0.17
ACGTcount: A:0.79, C:0.15, G:0.04, T:0.01
Consensus pattern (4 bp):
AAAC
Found at i:37407 original size:36 final size:36
Alignment explanation
Indices: 37358--37461 Score: 126
Period size: 36 Copynumber: 2.9 Consensus size: 36
37348 TCCTCCGCAA
*
37358 AAAAAAACAAACAAACAAAACAAAACAAAAAAAGTGAC
1 AAAAAAA-AAACAAACAAAACAAAACAAAAAAAG-AAC
*
37396 -AAAAAAAAACAAACAAAACAAAAGAAAAAAA-AAC
1 AAAAAAAAAACAAACAAAACAAAACAAAAAAAGAAC
*
37430 AAAAAAAAAACAAAC-GAAC-AAACAACAAAAAG
1 AAAAAAAAAACAAACAAAACAAAACAA-AAAAAG
37462 GGTCCGGATG
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
33 5 0.08
34 10 0.17
35 14 0.24
36 24 0.41
37 6 0.10
ACGTcount: A:0.80, C:0.14, G:0.05, T:0.01
Consensus pattern (36 bp):
AAAAAAAAAACAAACAAAACAAAACAAAAAAAGAAC
Found at i:37440 original size:26 final size:26
Alignment explanation
Indices: 37356--37460 Score: 83
Period size: 26 Copynumber: 4.2 Consensus size: 26
37346 CGTCCTCCGC
* *
37356 AAAAAAAAAC-AAA-CAAACAAAACA
1 AAAAAAAAACAAAAGAAAAAAAAACA
* **
37380 AAACAAAAA-AAGTGACAAAAAAAA-A
1 AAAAAAAAACAAAAGA-AAAAAAAACA
* *
37405 CAAACAAAACAAAAGAAAAAAAAACA
1 AAAAAAAAACAAAAGAAAAAAAAACA
* * *
37431 AAAAAAAAACAAACGAACAAACAACA
1 AAAAAAAAACAAAAGAAAAAAAAACA
37457 AAAA
1 AAAA
37461 GGGTCCGGAT
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
24 9 0.15
25 15 0.25
26 37 0.61
ACGTcount: A:0.81, C:0.14, G:0.04, T:0.01
Consensus pattern (26 bp):
AAAAAAAAACAAAAGAAAAAAAAACA
Found at i:38926 original size:30 final size:30
Alignment explanation
Indices: 38885--39349 Score: 481
Period size: 30 Copynumber: 16.1 Consensus size: 30
38875 ATTCCTCACC
* *
38885 TTTCAAAAGCCCACAAGTTAGTGGCACCCTT
1 TTTC-AAAGCCCACAAGTCAGTGGCAACCTT
* *
38916 TTTCAAAGCCCACAAGTTAGCT-GC-ATCTT
1 TTTCAAAGCCCACAAGTCAG-TGGCAACCTT
38945 TTTCAAAGCCCACAAGTCAGTGGCAACC--
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT
* *
38973 -TTCAAAGGCCACAAGTCAGTGGCACCCTT
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT
* *
39002 TTTCAAAGCCCACAAGTTAGTGGC-ATCTT
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT
*
39031 TTTCAAAGCCCACAAATCAGTGGCAACC--
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT
* * *
39059 -ATCAAAGCCCACAAATCAGTGGCACCCTT
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT
*
39088 TTTCAAAGCCCACAAGTTAGTGGCAACC--
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT
*
39116 -TTCAAAGCCCACAAATCAGTGGC-ACCTT
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT
39144 TTTCCAAAGCCCACAAGTCAGTGGCAACC--
1 TTT-CAAAGCCCACAAGTCAGTGGCAACCTT
* *
39173 -TTCGAAAGCCCACAAGTTAGTGGCACCCTT
1 TTTC-AAAGCCCACAAGTCAGTGGCAACCTT
39203 TTTCAAAGCCCACAAGTCAGTGGCAACC--
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT
*
39231 -TTCAAAAGCCCACAAGTCAGTGGCACCCTT
1 TTTC-AAAGCCCACAAGTCAGTGGCAACCTT
* * *
39261 TTTCGAAGCCCACAAGTCAATGGC-ATCTT
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT
* * *
39290 TTCCAAAGCCCACAAGCCAGCGGCAACC-T
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT
* * * *
39319 TCT-AAAGTCCACAACTCCGTGGC-ACCTT
1 TTTCAAAGCCCACAAGTCAGTGGCAACCTT
39347 TTT
1 TTT
39350 TCTTTTTAAA
Statistics
Matches: 364, Mismatches: 45, Indels: 53
0.79 0.10 0.11
Matches are distributed among these distances:
26 3 0.01
27 78 0.21
28 66 0.18
29 75 0.21
30 128 0.35
31 14 0.04
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (30 bp):
TTTCAAAGCCCACAAGTCAGTGGCAACCTT
Found at i:38994 original size:86 final size:86
Alignment explanation
Indices: 38890--39351 Score: 614
Period size: 86 Copynumber: 5.3 Consensus size: 86
38880 TCACCTTTCA
*
38890 AAAGCCCACAAGTTAGTGGCACCCTTTTTCAAAGCCCACAAGTTAGCT-GCATCTTTTTCAAAGC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTTAG-TGGCATCTTTTTCAAAGC
38954 CCACAAGTCAGTGGCAACCTTC
65 CCACAAGTCAGTGGCAACCTTC
*
38976 AAAGGCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTTCAAAGCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTTCAAAGCC
* *
39041 CACAAATCAGTGGCAACCATC
66 CACAAGTCAGTGGCAACCTTC
* * *
39062 AAAGCCCACAAATCAGTGGCACCCTTTTTCAAAGCCCACAAGTTAGTGGCAAC--CTTCAAAGCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTTCAAAGCC
*
39125 CACAAATCAGTGGC-ACCTTTTTCC
66 CACAAGTCAGTGGCAACC---TT-C
* *
39149 AAAGCCCACAAGTCAGTGGCAACC---TTCGAAAGCCCACAAGTTAGTGGCACCCTTTTTCAAAG
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC-AAAGCCCACAAGTTAGTGGCA-TCTTTTTCAAAG
39211 CCCACAAGTCAGTGGCAACCTTC
64 CCCACAAGTCAGTGGCAACCTTC
* * * *
39234 AAAAGCCCACAAGTCAGTGGCACCCTTTTTCGAAGCCCACAAGTCAATGGCATCTTTTCCAAAGC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTTCAAAGC
* *
39299 CCACAAGCCAGCGGCAACCTTC
65 CCACAAGTCAGTGGCAACCTTC
* * * *
39321 TAAAGTCCACAACTCCGTGGCACCTTTTTTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTTTC
39352 TTTTTAAAGC
Statistics
Matches: 335, Mismatches: 27, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
83 3 0.01
84 26 0.08
85 23 0.07
86 157 0.47
87 80 0.24
88 40 0.12
89 6 0.02
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.22
Consensus pattern (86 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTTCAAAGCC
CACAAGTCAGTGGCAACCTTC
Found at i:39018 original size:57 final size:56
Alignment explanation
Indices: 38882--39347 Score: 453
Period size: 57 Copynumber: 8.1 Consensus size: 56
38872 GACATTCCTC
* *
38882 ACCTTTCAAAAGCCCACAAGTTAGTGGCACCCTTTTTCAAAGCCCACAAGTTAGCT-GCA
1 ACCTTTC-AAAGCCCACAAGTCAGTGGCACCC--TTTCAAAGCCCACAAGTCAG-TGGCA
* * * *
38941 TCTTTTTCAAAGCCCACAAGTCAGTGGCAACC-TTCAAAGGCCACAAGTCAGTGGCA
1 AC-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * ** *
38997 CCCTTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTTCAAAGCCCACAAATCAGTGGCA
1 ACC--TTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
39056 ACC-ATCAAAGCCCACAAATCAGTGGCACCCTTTTTCAAAGCCCACAAGTTAGTGGCA
1 ACCTTTCAAAGCCCACAAGTCAGTGGCACCC--TTTCAAAGCCCACAAGTCAGTGGCA
* *
39113 ACC-TTCAAAGCCCACAAATCAGTGGCACCTTTTTCCAAAGCCCACAAGTCAGTGGCA
1 ACCTTTCAAAGCCCACAAGTCAGTGGCACC-CTTT-CAAAGCCCACAAGTCAGTGGCA
*
39170 ACC-TTCGAAAGCCCACAAGTTAGTGGCACCCTTTTTCAAAGCCCACAAGTCAGTGGCA
1 ACCTTTC-AAAGCCCACAAGTCAGTGGCACCC--TTTCAAAGCCCACAAGTCAGTGGCA
* *
39228 ACC-TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTTCGAAGCCCACAAGTCAATGGCA
1 ACCTTTC-AAAGCCCACAAGTCAGTGGCACCC--TTTCAAAGCCCACAAGTCAGTGGCA
* * * * * * * *
39286 TCTTTTCCAAAGCCCACAAGCCAGCGGCAACC-TTCTAAAGTCCACAACTCCGTGGC-
1 ACCTTT-CAAAGCCCACAAGTCAGTGGCACCCTTTC-AAAGCCCACAAGTCAGTGGCA
39342 ACCTTT
1 ACCTTT
39348 TTTCTTTTTA
Statistics
Matches: 347, Mismatches: 44, Indels: 35
0.81 0.10 0.08
Matches are distributed among these distances:
55 2 0.01
56 52 0.15
57 117 0.34
58 98 0.28
59 73 0.21
60 5 0.01
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.22
Consensus pattern (56 bp):
ACCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:39401 original size:68 final size:70
Alignment explanation
Indices: 39316--39556 Score: 303
Period size: 68 Copynumber: 3.5 Consensus size: 70
39306 CCAGCGGCAA
*
39316 CCTTCTAAAGTCCACAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTC
1 CCTTCTAAAGTCCACAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCTATGGCACTC
39381 -TTTT
66 TTTTT
* * * *
39385 CCTTCT-AAGTCCACAACTCCGTGGCATCTTTCTTCTTTTTAAAGCCTACAACTCTATGGCGCTC
1 CCTTCTAAAGTCCACAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCTATGGCACTC
39449 TTTTT
66 TTTTT
* * * * *
39454 CCTTTTTAAAGCCCACAACTCTGTGGCA-CTCTTTTTCCTTTT-AAGCCCACAACTCCATGGCAC
1 CC-TTCTAAAGTCCACAACTCCGTGGCACCT-TTTTTCTTTTTAAAGCCCACAACTCTATGGCAC
39517 TCTTTTT
64 TCTTTTT
* * * *
39524 CCTT-TTAAGTCCACAACTCTGTGACACCCTTTT
1 CCTTCTAAAGTCCACAACTCCGTGGCACCTTTTT
39557 AAGCCCACAA
Statistics
Matches: 150, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
68 76 0.51
69 15 0.10
70 32 0.21
71 27 0.18
ACGTcount: A:0.20, C:0.32, G:0.11, T:0.37
Consensus pattern (70 bp):
CCTTCTAAAGTCCACAACTCCGTGGCACCTTTTTTCTTTTTAAAGCCCACAACTCTATGGCACTC
TTTTT
Found at i:39505 original size:34 final size:35
Alignment explanation
Indices: 39316--39556 Score: 269
Period size: 34 Copynumber: 7.0 Consensus size: 35
39306 CCAGCGGCAA
* * *
39316 CCTTCTAAAGTCCACAACTCCGTGGCAC-CTTTTTT
1 CCTTTTAAAGCCCACAACTCTGTGGCACTC-TTTTT
*
39351 CTTTTTAAAGCCCACAACTCTGTGGCACTC-TTTT
1 CCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
* * *
39385 CCTTCT-AAGTCCACAACTCCGTGGCA-TCTTTCTT
1 CCTTTTAAAGCCCACAACTCTGTGGCACTCTTT-TT
* * * *
39419 CTTTTTAAAGCCTACAACTCTATGGCGCTCTTTTT
1 CCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
39454 CCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 CC-TTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
**
39490 CCTTTT-AAGCCCACAACTCCATGGCACTCTTTTT
1 CCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
* * *
39524 CCTTTT-AAGTCCACAACTCTGTGACACCCTTTT
1 CCTTTTAAAGCCCACAACTCTGTGGCACTCTTTT
39557 AAGCCCACAA
Statistics
Matches: 174, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.01
33 20 0.11
34 68 0.39
35 46 0.26
36 38 0.22
ACGTcount: A:0.20, C:0.32, G:0.11, T:0.37
Consensus pattern (35 bp):
CCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
Found at i:39556 original size:104 final size:104
Alignment explanation
Indices: 39316--39556 Score: 328
Period size: 104 Copynumber: 2.3 Consensus size: 104
39306 CCAGCGGCAA
* * *
39316 CCTTCTAAAGTCCACAACTCCGTGGCA-CCTTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACT
1 CCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTTCCTTTTTAAAGCCCACAACTCTGTGGCACT
* *
39380 CTTTTCCTTCTAAGTCCACAACTCCGTGGCATCTTTCTT
66 CTTTTCCTTCTAAGCCCACAACTCCATGGCATCTTTCTT
* * * *
39419 CTTTTTAAAG-CCTACAACTCTATGGCGCTCTTTTTCCTTTTTAAAGCCCACAACTCTGTGGCAC
1 CCTTTTAAAGTCC-ACAACTCTGTGGCACCCTTTTTCCTTTTTAAAGCCCACAACTCTGTGGCAC
*
39483 TCTTTTTCCTTTTAAGCCCACAACTCCATGGCACTCTTT-TT
65 TC-TTTTCCTTCTAAGCCCACAACTCCATGGCA-TCTTTCTT
*
39524 CCTTTT-AAGTCCACAACTCTGTGACACCCTTTT
1 CCTTTTAAAGTCCACAACTCTGTGGCACCCTTTT
39557 AAGCCCACAA
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
102 2 0.02
103 19 0.16
104 56 0.47
105 36 0.31
106 5 0.04
ACGTcount: A:0.20, C:0.32, G:0.11, T:0.37
Consensus pattern (104 bp):
CCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTTCCTTTTTAAAGCCCACAACTCTGTGGCACT
CTTTTCCTTCTAAGCCCACAACTCCATGGCATCTTTCTT
Found at i:39578 original size:27 final size:28
Alignment explanation
Indices: 39524--39598 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
39514 CACTCTTTTT
* *
39524 CCTTTTAAGTCCACAACTCTGTGACA-C
1 CCTTTTAAGCCCACAAGTCTGTGACACC
*
39551 CCTTTTAAGCCCACAAGT-TGGTGGCACC
1 CCTTTTAAGCCCACAAGTCT-GTGACACC
*
39579 CCTTTCAAAGCCCACAAGTC
1 CCTTT-TAAGCCCACAAGTC
39599 AGTGGCAACC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 6 0.15
29 12 0.30
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (28 bp):
CCTTTTAAGCCCACAAGTCTGTGACACC
Found at i:39593 original size:29 final size:28
Alignment explanation
Indices: 39557--39627 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
39547 ACACCCTTTT
*
39557 AAGCCCACAAGTTGGTGGCACCCCTTTC-A
1 AAGCCCACAAGTTGGTGGCAACCC--TCAA
**
39586 AAGCCCACAAGTCAGTGGCAACCCTCAA
1 AAGCCCACAAGTTGGTGGCAACCCTCAA
*
39614 AAGCACACAAGTTG
1 AAGCCCACAAGTTG
39628 ATACAACCCT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
27 2 0.06
28 12 0.34
29 21 0.60
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.15
Consensus pattern (28 bp):
AAGCCCACAAGTTGGTGGCAACCCTCAA
Found at i:39789 original size:43 final size:43
Alignment explanation
Indices: 39728--40143 Score: 292
Period size: 43 Copynumber: 8.9 Consensus size: 43
39718 TCTTTAAAAC
* *
39728 CCAATATCGCTTGCCTTGAATCAGCATATTGACACCTTGAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGAAGT
* * *
39771 CCAATATCGCTGGTCTTGAATCAGCACATTGGCACCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGAAGT
* *
39814 CCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG--------AAGT
* * *
39866 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGAAGT
* *
39909 CCAATATCGCTGGCTTTGAATCAGCATATTAGCACCTTTGTCATCTTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG---------AAGT
* * * * *
39962 CCAATGTCACTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTGAAGT
* *
40011 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG--------AAGT
* * * * * *
40063 CCAATGTCGTTGGCCTTGAATTAGCACATTGGCAACTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGAAGT
*
40106 CTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
40144 CGTCATCTTT
Statistics
Matches: 291, Mismatches: 48, Indels: 68
0.71 0.12 0.17
Matches are distributed among these distances:
43 142 0.49
44 6 0.02
45 1 0.00
49 33 0.11
51 4 0.01
52 69 0.24
53 32 0.11
57 1 0.00
58 2 0.01
59 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (43 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGAAGT
Found at i:39884 original size:52 final size:52
Alignment explanation
Indices: 39806--40250 Score: 421
Period size: 52 Copynumber: 8.9 Consensus size: 52
39796 ACATTGGCAC
* * *
39806 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCAT
*
39858 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-------C--
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCAT
* * * *
39901 CTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTAGCACCTTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCAT
* *
39953 CTTTTAAGTCCAATGTCACTAGCCTTGAATCAGCACATTGGCACC--T-TCAT
1 C-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCAT
* * *
40003 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCAT
* * *
40055 CTTTAAGACCAATGTCGTTGGCCTTGAATTAGCACATTGGCA--------A-
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCAT
* * * *
40098 CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCAT
** * * * *
40150 CTTTAAAACCCAATGTCGTTGGCCTTGAATCAGCACGTTGGCA-TTCTTCTCAT
1 CTTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT-TTGTCAT
* * * * *
40203 CTTCAAGTCTAATGTCGCTGACCATGAATCAGCACATTGACATCCTTT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTT
40251 TTCTCATCTT
Statistics
Matches: 315, Mismatches: 52, Indels: 51
0.75 0.12 0.12
Matches are distributed among these distances:
43 73 0.23
44 1 0.00
45 1 0.00
49 38 0.12
50 6 0.02
51 3 0.01
52 114 0.36
53 78 0.25
54 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (52 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCAT
Found at i:39885 original size:95 final size:95
Alignment explanation
Indices: 39771--40192 Score: 619
Period size: 95 Copynumber: 4.4 Consensus size: 95
39761 ACCTTGAAGT
* * *
39771 CCAATATCGCTGGTCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGTTGGCCTTGAATC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATC
39836 AGCATATTGGCACCTTTGTCATCTTTAAGA
66 AGCATATTGGCACCTTTGTCATCTTTAAGA
*
39866 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCTTTGAATC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATC
* *
39931 AGCATATTAGCACCTTTGTCATCTTTTAAGT
66 AGCATATTGGCACCTTTGTCATC-TTTAAGA
* *
39962 CCAATGTCACTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCT
*
40027 TGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGA
60 TGAATCAGCATATTGGCACCTTTGTCATCTTTAAGA
* * * *
40063 CCAATGTCGTTGGCCTTGAATTAGCACATTGGCAACTTTAAGTCTAATATCGCTGGCCTTGAATC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATC
* *
40128 AGCATATTGGCACCTTCGTCATCTTTAAAA
66 AGCATATTGGCACCTTTGTCATCTTTAAGA
* *
40158 CCCAATGTCGTTGGCCTTGAATCAGCACGTTGGCA
1 -CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
40193 TTCTTCTCAT
Statistics
Matches: 296, Mismatches: 23, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
95 139 0.47
96 70 0.24
100 1 0.00
101 36 0.12
102 50 0.17
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (95 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATC
AGCATATTGGCACCTTTGTCATCTTTAAGA
Found at i:40036 original size:197 final size:196
Alignment explanation
Indices: 39767--40250 Score: 654
Period size: 197 Copynumber: 2.5 Consensus size: 196
39757 TGACACCTTG
* * *
39767 AAGTCCAATATCGCTGGTCTTGAATCAGCACATTGGCA---C--CTTTAAGTCCAATATCGTTGG
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCCAATATCGCTGG
39827 CCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCA
66 CCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCA
* * *
39892 CATTGGCACCTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTAGCACCTTTGTCATCTTT
131 CATTGGCAACTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTCGTCATCTTT
*
39957 T
196 A
* *
39958 AAGTCCAATGTCACTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTG
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTTTAAGTCCAATATCGCTG
* * *
40023 GCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTTGAATTAGC
65 GCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGC
* *
40088 ACATTGGCAACTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTT
130 ACATTGGCAACTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTCGTCATCTT
40153 TA
195 TA
** * * * * *
40155 AAACCCAATGTCGTTGGCCTTGAATCAGCACGTTGGCATTCTTCTCATCTTCAAGTCTAATGTCG
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--C-T-TCATCTTTAAGTCCAATATCG
* * * *
40220 CTGACCATGAATCAGCACATTGACATCCTTT
62 CTGGCCTTGAATCAGCATATTGGCA-CCTTT
40251 TTCTCATCTT
Statistics
Matches: 254, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
191 34 0.13
195 1 0.00
197 174 0.69
198 1 0.00
199 1 0.00
200 38 0.15
201 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (196 bp):
AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCCAATATCGCTGG
CCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCA
CATTGGCAACTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTCGTCATCTTT
A
Found at i:40219 original size:148 final size:144
Alignment explanation
Indices: 39955--40241 Score: 333
Period size: 148 Copynumber: 2.0 Consensus size: 144
39945 TTTGTCATCT
* **
39955 TTTAAGTCCAATGTCACTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
1 TTTAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAACCCAATATCG
* * * * * * *
40020 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTTGAATT
66 CTGGCCTTGAATCAGCACATTGGCGCCTTTCTCATCTTCAAGACCAATGTCGCTGACCATGAATC
40085 AGCACATTGGCAAC
131 AGCACATTGGCAAC
* * * *
40099 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAAACCCAAT
1 TTTAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACC-T--TCATCTTT-AAACCCAAT
* * * ** * *
40164 GTCGTTGGCCTTGAATCAGCACGTTGGC-ATTCTTCTCATCTTCAAGTCTAATGTCGCTGACCAT
62 ATCGCTGGCCTTGAATCAGCACATTGGCGCCT-TTCTCATCTTCAAGACCAATGTCGCTGACCAT
40228 GAATCAGCACATTG
126 GAATCAGCACATTG
40242 ACATCCTTTT
Statistics
Matches: 117, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
144 38 0.32
145 1 0.01
147 9 0.08
148 69 0.59
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (144 bp):
TTTAAGTCCAATATCACTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAACCCAATATCG
CTGGCCTTGAATCAGCACATTGGCGCCTTTCTCATCTTCAAGACCAATGTCGCTGACCATGAATC
AGCACATTGGCAAC
Found at i:41053 original size:13 final size:13
Alignment explanation
Indices: 41035--41059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41025 ATTACTCAAA
41035 TGTATCGATACAT
1 TGTATCGATACAT
41048 TGTATCGATACA
1 TGTATCGATACA
41060 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:41112 original size:52 final size:52
Alignment explanation
Indices: 41068--41248 Score: 317
Period size: 52 Copynumber: 3.5 Consensus size: 52
41058 CACTGATCTT
* *
41068 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATACAGGCAAATTTGCCAAGATGTATCGATACACTATGAAA
*
41120 TGTATCGATACATGCAGGCAAATTTGCCAAGATGTATCGATACACTATGAAA
1 TGTATCGATACATACAGGCAAATTTGCCAAGATGTATCGATACACTATGAAA
* *
41172 TGTATCGATACATACAGGCAAATTTGCCTAGATGTATCGATACATTATGAAA
1 TGTATCGATACATACAGGCAAATTTGCCAAGATGTATCGATACACTATGAAA
41224 TGTATCGATACATACAGGCAAATTT
1 TGTATCGATACATACAGGCAAATTT
41249 TCATATTTCG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATACAGGCAAATTTGCCAAGATGTATCGATACACTATGAAA
Found at i:43405 original size:24 final size:26
Alignment explanation
Indices: 43378--43428 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
43368 ACCAAAATTT
43378 TATTCAT-T-GGGGACACTCCAACCC
1 TATTCATCTAGGGGACACTCCAACCC
*
43402 TATTCCTCTAAGGGGACACTCCAACCC
1 TATTCATCT-AGGGGACACTCCAACCC
43429 CGTTTTCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 1 0.04
27 16 0.70
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (26 bp):
TATTCATCTAGGGGACACTCCAACCC
Found at i:50157 original size:13 final size:13
Alignment explanation
Indices: 50139--50164 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50129 ACACCAAAGT
50139 ATGTATCGATACA
1 ATGTATCGATACA
50152 ATGTATCGATACA
1 ATGTATCGATACA
50165 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:50180 original size:33 final size:33
Alignment explanation
Indices: 50120--50184 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
50110 TAGCCAAACT
* * *
50120 TGTATCGATACACCAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAATATGCATCGATACAA
50153 TGTATCGATACACAAAAA-ATTGCATCGATACA
1 TGTATCGATACACAAAAATA-TGCATCGATACA
50185 TTGACTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGCATCGATACAA
Found at i:52847 original size:13 final size:13
Alignment explanation
Indices: 52829--52854 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52819 TACACCAAGT
52829 ATGTATCGATACA
1 ATGTATCGATACA
52842 ATGTATCGATACA
1 ATGTATCGATACA
52855 CAAATAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:52852 original size:32 final size:33
Alignment explanation
Indices: 52811--52874 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
52801 TAGCCAAACT
*
52811 TGTATCGATACACCAAGT-A-TGTATCGATACAA
1 TGTATCGATACA-CAAATAATTGTATCGATACAA
52843 TGTATCGATACACAAATAATTGTATCGATACA
1 TGTATCGATACACAAATAATTGTATCGATACA
52875 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.14
32 13 0.45
33 12 0.41
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAATAATTGTATCGATACAA
Found at i:55110 original size:21 final size:21
Alignment explanation
Indices: 55077--55121 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
55067 TTGCAAGATG
*
55077 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
55099 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
55119 AAA
1 AAA
55122 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:56944 original size:15 final size:15
Alignment explanation
Indices: 56924--56962 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
56914 TAAAAATGTC
*
56924 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
56939 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
56954 CCAAATGAA
1 CAAAATGAA
56963 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:59052 original size:13 final size:13
Alignment explanation
Indices: 59034--59059 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59024 ACATTTTTCC
59034 TTGTATCGATACA
1 TTGTATCGATACA
59047 TTGTATCGATACA
1 TTGTATCGATACA
59060 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:59853 original size:39 final size:39
Alignment explanation
Indices: 59802--59879 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
59792 TCATTCGACT
59802 TCATCTACTATCCAACACTTGAGATATTCGATTGGCTCA
1 TCATCTACTATCCAACACTTGAGATATTCGATTGGCTCA
*
59841 TCATCTACTATCCAACACTTGAGATATTTGATTGGCTCA
1 TCATCTACTATCCAACACTTGAGATATTCGATTGGCTCA
59880 CGCTTTTGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (39 bp):
TCATCTACTATCCAACACTTGAGATATTCGATTGGCTCA
Found at i:61317 original size:20 final size:20
Alignment explanation
Indices: 61292--61343 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
61282 TACAAGCCAA
** *
61292 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTGG
61312 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
61331 TGTATCGATACAA
1 TGTATCGATACAA
61344 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:61349 original size:19 final size:18
Alignment explanation
Indices: 61292--61349 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
61282 TACAAGCCAA
*
61292 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA--TTTGG
*
61312 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
61331 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
61350 CTACTGCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.58
20 12 0.36
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:62075 original size:20 final size:20
Alignment explanation
Indices: 62052--62092 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
62042 TTTATTAATA
62052 ATTCTCCCCCTTAATCAAGT
1 ATTCTCCCCCTTAATCAAGT
*
62072 ATTCTCCCTCTTAATCAAGT
1 ATTCTCCCCCTTAATCAAGT
62092 A
1 A
62093 ATTCATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.32, G:0.05, T:0.37
Consensus pattern (20 bp):
ATTCTCCCCCTTAATCAAGT
Found at i:63915 original size:13 final size:13
Alignment explanation
Indices: 63897--63922 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63887 ATAATCACCC
63897 TGTATCGATACAA
1 TGTATCGATACAA
63910 TGTATCGATACAA
1 TGTATCGATACAA
63923 GGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:66022 original size:15 final size:15
Alignment explanation
Indices: 66002--66032 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
65992 ATTTCGTTTG
*
66002 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
66017 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
66032 G
1 G
66033 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:67865 original size:21 final size:21
Alignment explanation
Indices: 67836--67880 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
67826 AAGTTTTCAT
*
67836 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
67856 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
67878 TTT
1 TTT
67881 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:70122 original size:13 final size:13
Alignment explanation
Indices: 70104--70129 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
70094 CAATTTTTTG
70104 TGTATCGATACAT
1 TGTATCGATACAT
70117 TGTATCGATACAT
1 TGTATCGATACAT
70130 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:70144 original size:32 final size:33
Alignment explanation
Indices: 70084--70147 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
70074 TACAAGCCAA
** *
70084 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
70117 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
70148 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:71609 original size:13 final size:13
Alignment explanation
Indices: 71591--71616 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71581 TACACCAAGT
71591 ATGTATCGATACA
1 ATGTATCGATACA
71604 ATGTATCGATACA
1 ATGTATCGATACA
71617 GAAATAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:73050 original size:41 final size:41
Alignment explanation
Indices: 72964--73053 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
72954 CCTCTTTTAG
* **
72964 GCTTTATCAGTTTTGTCCTAGCCAACCTTTCTAATTAATTG
1 GCTTTATCAGTTTCGTCCTAGCCAACCTTTCTAATTAATAA
*
73005 GCTTTATCAGTTTCGTCCTAGCCAACCTCTT-TAACTT-GTAA
1 GCTTTATCAGTTTCGTCCTAGCCAACCT-TTCTAA-TTAATAA
73046 GCTTTATC
1 GCTTTATC
73054 TATTTTGCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 39 0.91
42 4 0.09
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (41 bp):
GCTTTATCAGTTTCGTCCTAGCCAACCTTTCTAATTAATAA
Found at i:73133 original size:41 final size:41
Alignment explanation
Indices: 73076--73913 Score: 300
Period size: 41 Copynumber: 20.6 Consensus size: 41
73066 GCTAACCCCT
* * * *
73076 CAACCTTTCTACCTTGTTGGCTTTATCAGTTTTACCTTGTC
1 CAACCTCTCTAACTTGTTGGCTTTATCAGTTTTGCCTTGGC
*
73117 CAACCTCTCTAACTTGTTGGCTTTATCAGTTTTGCCTCGGC
1 CAACCTCTCTAACTTGTTGGCTTTATCAGTTTTGCCTTGGC
* * * * * * *
73158 CAACC-CTACTAACCTATTGGTTTTAACAGTTTCGCCCTAGC
1 CAACCTCT-CTAACTTGTTGGCTTTATCAGTTTTGCCTTGGC
* * * * *
73199 CAACCAT-TTTAACCTATTGACTTTATCAGTTTTGCATTGGC
1 CAACC-TCTCTAACTTGTTGGCTTTATCAGTTTTGCCTTGGC
*
73240 CAACCT-TCTAACTTATTGGCTTTATCAGTTTTGGCCTAT--C
1 CAACCTCTCTAACTTGTTGGCTTTATCAGTTTT-GCCT-TGGC
* ** *
73280 CAACCTCTCTAACTAGTTGGCTTTATTGGTTTTGCCTTGTC
1 CAACCTCTCTAACTTGTTGGCTTTATCAGTTTTGCCTTGGC
* * **
73321 TAACC-CTTTTAACTTGTTGATTTTATC-GATTTTGCCTTGGC
1 CAACCTC-TCTAACTTGTTGGCTTTATCAG-TTTTGCCTTGGC
* * *
73362 CAACCCCTCTAA-TTGTTGGCTTTATC-GATTTCGTCC-TAGC
1 CAACCTCTCTAACTTGTTGGCTTTATCAG-TTTTG-CCTTGGC
* *** * * *
73402 CAACCCCTCTAACTTGTTGGCTTTATTTTTTTTACCCTGGT
1 CAACCTCTCTAACTTGTTGGCTTTATCAGTTTTGCCTTGGC
* * * *
73443 TAACCACAT-TAACATGTTGGCTTTATC-GATTTCGCCTTGGC
1 CAACCTC-TCTAACTTGTTGGCTTTATCAG-TTTTGCCTTGGC
* * *
73484 CAAGCC-CTCTAGCTTATTGG-TTTA-AAGGTTTTG-CTGTGGC
1 CAA-CCTCTCTAACTTGTTGGCTTTATCA-GTTTTGCCT-TGGC
* * * * * * * *
73524 CGACC-C-CTAACTTGCTAGCTTTGT-TGTTTTCACCTTAGT
1 CAACCTCTCTAACTTGTTGGCTTTATCAGTTTT-GCCTTGGC
* * * * * * * **
73563 TAACC-CTTTTAACATGTAGACTTTATCA-TTTCGCCCTGAT
1 CAACCTC-TCTAACTTGTTGGCTTTATCAGTTTTGCCTTGGC
* * * ** * *
73603 CACCCT-TTTAA-TCTATTAACTTTATCAGTTTTG-CTTAAGT
1 CAACCTCTCTAACT-TGTTGGCTTTATCAGTTTTGCCTT-GGC
* * * * ** * *
73643 CTACCCCTTTAACGTGTTGGCTTTATCAGTTTCACCCTAGC
1 CAACCTCTCTAACTTGTTGGCTTTATCAGTTTTGCCTTGGC
* * * * *
73684 CAACC-CTTCTAACTTATTGGTTTTATC-GGTTT-CATCGTGC
1 CAACCTC-TCTAACTTGTTGGCTTTATCAGTTTTGCCTTG-GC
* * * * * *
73724 CAACCCCTATAACTAGTTGACTTTATC-GATTTTGCGC-TAGT
1 CAACCTCTCTAACTTGTTGGCTTTATCAG-TTTTGC-CTTGGC
* * *
73765 CAACCTCTTTAACATT-TTGGCTTTATC-GATTTCGCCATGGC
1 CAACCTCTCTAAC-TTGTTGGCTTTATCAG-TTTTGCCTTGGC
* * * * * * * **
73806 CAACCCCTTTAACTTGTTGGTTTTATTAATTTTTCCCTAAC
1 CAACCTCTCTAACTTGTTGGCTTTATCAGTTTTGCCTTGGC
* * **
73847 CAATCC-CTCTAACTTGTTGGCTTTATTAGTTTTGCCCTAAC
1 CAA-CCTCTCTAACTTGTTGGCTTTATCAGTTTTGCCTTGGC
* *
73888 CAACCCCTCTAACTTGTTGACTTTAT
1 CAACCTCTCTAACTTGTTGGCTTTAT
73914 TGGCTTCACC
Statistics
Matches: 598, Mismatches: 151, Indels: 96
0.71 0.18 0.11
Matches are distributed among these distances:
38 13 0.02
39 34 0.06
40 138 0.23
41 401 0.67
42 12 0.02
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.41
Consensus pattern (41 bp):
CAACCTCTCTAACTTGTTGGCTTTATCAGTTTTGCCTTGGC
Found at i:73447 original size:122 final size:122
Alignment explanation
Indices: 73090--73507 Score: 345
Period size: 122 Copynumber: 3.4 Consensus size: 122
73080 CTTTCTACCT
* * * * *
73090 TGTTGGCTTTATC-AGTTTTACCTTGTCCAACCTCTCTAACTTGTTGGCTTTATCAGTTT-TGCC
1 TGTTGACTTTATCGA-TTTTGCCTTGGCCAACC-CTCTAACTTATTGGCTTTATCAGTTTCGGCC
* * *** * * * * *
73153 TCGGCCAA-CCCTACTAACCTA-TTGGTTTTAACAGTTTCGCCCTAG-CCAACCATTTTAACC
64 T-AGCCAACCCCT-CTAA-CTAGTTGGCTTTATTGGTTT-TCCCTGGTCTAACCCTTTTAACA
* * * *
73213 TATTGACTTTATC-AGTTTTGCATTGGCCAACCTTCTAACTTATTGGCTTTATCAGTTTTGGCCT
1 TGTTGACTTTATCGA-TTTTGCCTTGGCCAACCCTCTAACTTATTGGCTTTATCAGTTTCGGCCT
* * * * *
73277 ATCCAACCTCTCTAACTAGTTGGCTTTATTGGTTTTGCCTTGTCTAACCCTTTTAACT
65 AGCCAACCCCTCTAACTAGTTGGCTTTATTGGTTTTCCCTGGTCTAACCCTTTTAACA
* * *
73335 TGTTGATTTTATCGATTTTGCCTTGGCCAACCCCTCTAA-TTGTTGGCTTTATC-GATTTCGTCC
1 TGTTGACTTTATCGATTTTGCCTTGGCCAA-CCCTCTAACTTATTGGCTTTATCAG-TTTCGGCC
* ** *
73398 TAGCCAACCCCTCTAACTTGTTGGCTTTATTTTTTTTACCCTGGT-TAACCAC-ATTAACA
64 TAGCCAACCCCTCTAACTAGTTGGCTTTATTGGTTTT-CCCTGGTCTAACC-CTTTTAACA
* * *
73457 TGTTGGCTTTATCGATTTCGCCTTGGCCAAGCCCTCTAGCTTATTGG-TTTA
1 TGTTGACTTTATCGATTTTGCCTTGGCCAA-CCCTCTAACTTATTGGCTTTA
73508 AAGGTTTTGC
Statistics
Matches: 242, Mismatches: 43, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
121 8 0.03
122 180 0.74
123 54 0.22
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.41
Consensus pattern (122 bp):
TGTTGACTTTATCGATTTTGCCTTGGCCAACCCTCTAACTTATTGGCTTTATCAGTTTCGGCCTA
GCCAACCCCTCTAACTAGTTGGCTTTATTGGTTTTCCCTGGTCTAACCCTTTTAACA
Found at i:73867 original size:82 final size:79
Alignment explanation
Indices: 73645--73872 Score: 213
Period size: 81 Copynumber: 2.8 Consensus size: 79
73635 GCTTAAGTCT
* * * *
73645 ACCCCTTTAACGTGTTGGCTTTATCAGTTTCACCCTAGCCAACCCTTCTAACTTATTGGTTTTAT
1 ACCCCTTTAACTTGTTGGCTTTATCAATTTTACCCTAGCCAACCC-TCTAACTT-TTGGCTTTAT
* * *
73710 CGGTTTCATCGTGCCA
64 CGATTTCACCATGCCA
* * * * * * * *
73726 ACCCCTATAACTAGTTGACTTTATCGATTTTGCGCTAGTCAACCTCTTTAACATTTTGGCTTTAT
1 ACCCCTTTAACTTGTTGGCTTTATCAATTTTACCCTAGCCAACC-CTCTAAC-TTTTGGCTTTAT
*
73791 CGATTTCGCCATGGCCA
64 CGATTTCACCAT-GCCA
* * * *
73808 ACCCCTTTAACTTGTTGGTTTTATTAATTTTTCCCTAACCAATCCCTCTAACTTGTTGGCTTTAT
1 ACCCCTTTAACTTGTTGGCTTTATCAATTTTACCCTAGCCAA-CCCTCTAACTT-TTGGCTTTAT
73873 TAGTTTTGCC
Statistics
Matches: 115, Mismatches: 27, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
81 58 0.50
82 55 0.48
83 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.40
Consensus pattern (79 bp):
ACCCCTTTAACTTGTTGGCTTTATCAATTTTACCCTAGCCAACCCTCTAACTTTTGGCTTTATCG
ATTTCACCATGCCA
Found at i:73926 original size:41 final size:41
Alignment explanation
Indices: 73805--73926 Score: 127
Period size: 41 Copynumber: 3.0 Consensus size: 41
73795 TTCGCCATGG
* ** ** **
73805 CCAACCCCTTTAACTTGTTGGTTTTATTAATTTTTCCCTAA
1 CCAACCCCTCTAACTTGTTGACTTTATTAGCTTCACCCTAA
* * * **
73846 CCAATCCCTCTAACTTGTTGGCTTTATTAGTTTTGCCCTAA
1 CCAACCCCTCTAACTTGTTGACTTTATTAGCTTCACCCTAA
*
73887 CCAACCCCTCTAACTTGTTGACTTTATTGGCTTCACCCTA
1 CCAACCCCTCTAACTTGTTGACTTTATTAGCTTCACCCTA
73927 GTTAACTTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.20, C:0.29, G:0.10, T:0.41
Consensus pattern (41 bp):
CCAACCCCTCTAACTTGTTGACTTTATTAGCTTCACCCTAA
Found at i:76114 original size:25 final size:25
Alignment explanation
Indices: 76070--76155 Score: 106
Period size: 24 Copynumber: 3.5 Consensus size: 25
76060 TATAATTAAA
* *
76070 TAAAAAAACTA-CTCACTTTTTACT
1 TAAAAAAATTATCTCACTTTTTATT
*
76094 TAAAAAAATTATC-CACATTTTATT
1 TAAAAAAATTATCTCACTTTTTATT
*
76118 TAGAAAAATT-TCTCACCTTTTTATT
1 TAAAAAAATTATCTCA-CTTTTTATT
76143 TAAAAAAATTATC
1 TAAAAAAATTATC
76156 AATCTTTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.04
24 30 0.58
25 18 0.35
26 2 0.04
ACGTcount: A:0.43, C:0.15, G:0.01, T:0.41
Consensus pattern (25 bp):
TAAAAAAATTATCTCACTTTTTATT
Found at i:76162 original size:25 final size:24
Alignment explanation
Indices: 76070--76170 Score: 98
Period size: 24 Copynumber: 4.1 Consensus size: 24
76060 TATAATTAAA
* *
76070 TAAAAAAACTA-CTCACTTTTTACT
1 TAAAAAAATTATC-CACTTTTTATT
*
76094 TAAAAAAATTATCCACATTTTATT
1 TAAAAAAATTATCCACTTTTTATT
*
76118 TAGAAAAATT-TCTCACCTTTTTATT
1 TAAAAAAATTATC-CA-CTTTTTATT
*
76143 TAAAAAAATTATCAATCTTTTTAATT
1 TAAAAAAATTATCCA-CTTTTT-ATT
76169 TA
1 TA
76171 TTATTTATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
23 2 0.03
24 30 0.47
25 25 0.39
26 7 0.11
ACGTcount: A:0.42, C:0.14, G:0.01, T:0.44
Consensus pattern (24 bp):
TAAAAAAATTATCCACTTTTTATT
Found at i:76163 original size:24 final size:25
Alignment explanation
Indices: 76087--76170 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
76077 ACTACTCACT
* *
76087 TTTTACTTAAAAAAATTATCCA-CA
1 TTTTATTTAAAAAAATTATCAATCA
* * * *
76111 TTTTATTTAGAAAAATT-TCTCACCT
1 TTTTATTTAAAAAAATTATC-AATCA
*
76136 TTTTATTTAAAAAAATTATCAATCT
1 TTTTATTTAAAAAAATTATCAATCA
76161 TTTTAATTTA
1 TTTT-ATTTA
76171 TTATTTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.04
24 17 0.34
25 24 0.48
26 7 0.14
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (25 bp):
TTTTATTTAAAAAAATTATCAATCA
Found at i:78857 original size:2 final size:2
Alignment explanation
Indices: 78852--78894 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
78842 TACACACGCG
* * *
78852 CA CA CA CA CA CA CA CA CG CG CA CA TA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
78894 C
1 C
78895 GCACCTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.49, G:0.05, T:0.02
Consensus pattern (2 bp):
CA
Found at i:78866 original size:18 final size:18
Alignment explanation
Indices: 78843--78894 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
78833 TCTCAACCTT
*
78843 ACACACGCGCACACACAC
1 ACACACACGCACACACAC
* *
78861 ACACACACGCGCACATAC
1 ACACACACGCACACACAC
*
78879 ACACACACACACACAC
1 ACACACACGCACACAC
78895 GCACCTAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.42, C:0.48, G:0.08, T:0.02
Consensus pattern (18 bp):
ACACACACGCACACACAC
Found at i:78868 original size:20 final size:20
Alignment explanation
Indices: 78843--78888 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
78833 TCTCAACCTT
78843 ACACACGCGCACACACACAC
1 ACACACGCGCACACACACAC
*
78863 ACACACGCGCACATACACAC
1 ACACACGCGCACACACACAC
78883 ACACAC
1 ACACAC
78889 ACACACGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.48, G:0.09, T:0.02
Consensus pattern (20 bp):
ACACACGCGCACACACACAC
Found at i:94772 original size:28 final size:28
Alignment explanation
Indices: 94701--95662 Score: 1104
Period size: 28 Copynumber: 34.5 Consensus size: 28
94691 CACCAACTTG
* * *
94701 TGTGGGCTTTAGAGAAAGTTGCCACCGACTT
1 TGTGGGCTTT-GA-AAGGATGCCACTGAC-T
* **
94732 ATGTGTGCTTTGAAAAAATGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
*
94761 TGTGGGCTTTGAAATGG-TGCCACTAACT
1 TGTGGGCTTTGAAA-GGATGCCACTGACT
* *
94789 TGTGGGCTTTGAACA-TAGGCCACTGACT
1 TGTGGGCTTTGAA-AGGATGCCACTGACT
94817 TGTGGGCTTTTGAAAGGATGCCACTGACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
* * *
94846 TATGAGC---G---GG-TGTCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
94867 TGTGGGCTTTGAAAGGGTGCTAGTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
94895 TATGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
94923 TGTGGGCTTTGAAAGGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
94951 TATGGGCTTTGAACGGATGCCACTTACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
94979 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
95007 TGTGGGCTTT-AAACGGATGCCACTTACT
1 TGTGGGCTTTGAAA-GGATGCCACTGACT
*
95035 TGTCGGCTTTGGAAA-GATGCCACTGACT
1 TGTGGGCTTT-GAAAGGATGCCACTGACT
** *
95063 TGTGGGCTTT-AAAAAAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
95091 TGTGGG-TTTGGAAAAGATGCCGCTGACT
1 TGTGGGCTTT-GAAAGGATGCCACTGACT
* * *
95119 TGTGGGTTTTGAAAGAATGCCAAT-AGCT
1 TGTGGGCTTTGAAAGGATGCCACTGA-CT
95147 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
95175 TGTGGGCTTTG-AAGCGATGCCACTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
*
95203 TCT-GGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
95230 TGTGGACTTTGAAAGGATGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
95258 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
95286 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
95314 TGTGGGCTTTGAAGAGG-TGCCACTGACT
1 TGTGGGCTTTGAA-AGGATGCCACTGACT
* *
95342 TGTGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
95370 TGTGGACTTTGAAAGGATGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
95398 TGTAGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
95426 TGTGGGCTTTG-AAGAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
95454 TATGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
95482 TGTGGGCTTTG-AAGAAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
95510 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
95538 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
95566 TGTGGACTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
95594 TGTGGACTTTG-AAGAGATGCCACTAACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
* * *
95622 TGTGGGTTTTGAAAGGATGTCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
95650 TATGGGCTTTGAA
1 TGTGGGCTTTGAA
95663 GAAATGAACG
Statistics
Matches: 807, Mismatches: 87, Indels: 76
0.83 0.09 0.08
Matches are distributed among these distances:
21 15 0.02
22 2 0.00
24 1 0.00
25 1 0.00
26 3 0.00
27 50 0.06
28 660 0.82
29 49 0.06
30 15 0.02
31 2 0.00
32 9 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:109704 original size:20 final size:20
Alignment explanation
Indices: 109681--109753 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
109671 CAATTCAAAA
109681 TATCGATACATGTTGCAATG
1 TATCGATACATGTTGCAATG
****
109701 TATCGATACATGAAAAAGATG
1 TATCGATACATGTTGCA-ATG
109722 TATCGATACATGTTGCAATG
1 TATCGATACATGTTGCAATG
109742 TATCGATACATG
1 TATCGATACATG
109754 AAAAAGATGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
TATCGATACATGTTGCAATG
Found at i:109724 original size:21 final size:21
Alignment explanation
Indices: 109698--109773 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
109688 ACATGTTGCA
109698 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
109719 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
109739 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
109760 ATGTATCGATACAT
1 ATGTATCGATACAT
109774 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:109732 original size:41 final size:41
Alignment explanation
Indices: 109681--109773 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
109671 CAATTCAAAA
109681 TATCGATACATGTTGCAATGTATCGATACATGAAAAAGATG
1 TATCGATACATGTTGCAATGTATCGATACATGAAAAAGATG
109722 TATCGATACATGTTGCAATGTATCGATACATGAAAAAGATG
1 TATCGATACATGTTGCAATGTATCGATACATGAAAAAGATG
109763 TATCGATACAT
1 TATCGATACAT
109774 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
TATCGATACATGTTGCAATGTATCGATACATGAAAAAGATG
Found at i:109830 original size:13 final size:13
Alignment explanation
Indices: 109812--109837 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
109802 TACAGCAAGT
109812 ATGTATCGATACA
1 ATGTATCGATACA
109825 ATGTATCGATACA
1 ATGTATCGATACA
109838 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:112084 original size:21 final size:21
Alignment explanation
Indices: 112051--112095 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
112041 TTGCAAGTTG
*
112051 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
112073 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
112093 AAA
1 AAA
112096 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:116014 original size:20 final size:20
Alignment explanation
Indices: 115935--116014 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
115925 AATGTCCAAA
*
115935 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
115955 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
115980 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
116000 TTGTATCGATACATT
1 ATGTATCGATACATT
116015 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:116018 original size:13 final size:13
Alignment explanation
Indices: 116000--116038 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
115990 ACATTTTTCT
116000 TTGTATCGATACA
1 TTGTATCGATACA
116013 TTGTATCGATACA
1 TTGTATCGATACA
*
116026 CTGTATCGATACA
1 TTGTATCGATACA
116039 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:118509 original size:20 final size:20
Alignment explanation
Indices: 118486--118558 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
118476 CAATTCAAAA
118486 TATCGATACATGTTGCAATG
1 TATCGATACATGTTGCAATG
****
118506 TATCGATACATGAAAAAGATG
1 TATCGATACATGTTGCA-ATG
118527 TATCGATACATGTTGCAATG
1 TATCGATACATGTTGCAATG
118547 TATCGATACATG
1 TATCGATACATG
118559 AAAAAGATGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
TATCGATACATGTTGCAATG
Found at i:118529 original size:21 final size:21
Alignment explanation
Indices: 118503--118578 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
118493 ACATGTTGCA
118503 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
118524 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
118544 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
118565 ATGTATCGATACAT
1 ATGTATCGATACAT
118579 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:118537 original size:41 final size:41
Alignment explanation
Indices: 118486--118578 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
118476 CAATTCAAAA
118486 TATCGATACATGTTGCAATGTATCGATACATGAAAAAGATG
1 TATCGATACATGTTGCAATGTATCGATACATGAAAAAGATG
118527 TATCGATACATGTTGCAATGTATCGATACATGAAAAAGATG
1 TATCGATACATGTTGCAATGTATCGATACATGAAAAAGATG
118568 TATCGATACAT
1 TATCGATACAT
118579 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
TATCGATACATGTTGCAATGTATCGATACATGAAAAAGATG
Found at i:118635 original size:13 final size:13
Alignment explanation
Indices: 118617--118642 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
118607 TACAGCAAGT
118617 ATGTATCGATACA
1 ATGTATCGATACA
118630 ATGTATCGATACA
1 ATGTATCGATACA
118643 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:122104 original size:26 final size:26
Alignment explanation
Indices: 122048--122105 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
122038 TGTGACATGT
* *
122048 AATAAACAATTATATAAGAAACCTTA
1 AATAAACAAATATATAAGAAACATTA
*
122074 AATAAATAAATATA-AAGAAACATATA
1 AATAAACAAATATATAAGAAACAT-TA
*
122100 CATAAA
1 AATAAA
122106 ATATCAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (26 bp):
AATAAACAAATATATAAGAAACATTA
Found at i:124189 original size:13 final size:13
Alignment explanation
Indices: 124171--124195 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
124161 CACAGCCAGA
124171 TGTATCGATACAT
1 TGTATCGATACAT
124184 TGTATCGATACA
1 TGTATCGATACA
124196 AGCTTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:124226 original size:20 final size:20
Alignment explanation
Indices: 124182--124235 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
124172 GTATCGATAC
124182 ATTGTATCGATACA-AGCTT
1 ATTGTATCGATACATAGCTT
124201 ATTGTATCGATACATA-CTT
1 ATTGTATCGATACATAGCTT
124220 AATTGTATCGATACAT
1 -ATTGTATCGATACAT
124236 GAAATTGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
ATTGTATCGATACATAGCTT
Found at i:132913 original size:13 final size:13
Alignment explanation
Indices: 132895--132920 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
132885 CACATCCAGA
132895 TGTATCGATACAT
1 TGTATCGATACAT
132908 TGTATCGATACAT
1 TGTATCGATACAT
132921 GCTCATTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:132929 original size:19 final size:18
Alignment explanation
Indices: 132905--132956 Score: 72
Period size: 16 Copynumber: 2.9 Consensus size: 18
132895 TGTATCGATA
132905 CATTGTATCGATACATGCT
1 CATTGTATCGATACATG-T
132924 CATTGTATCGATACA--T
1 CATTGTATCGATACATGT
*
132940 AATTGTATCGATACATG
1 CATTGTATCGATACATG
132957 AAGTTGGCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 15 0.50
19 15 0.50
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (18 bp):
CATTGTATCGATACATGT
Found at i:134093 original size:19 final size:20
Alignment explanation
Indices: 134048--134098 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
134038 GAGCCCAAAA
*
134048 GTATCGATACATATTGCTTT
1 GTATCGATACATATTGCATT
* *
134068 ATATCGATACAT-TTTCATT
1 GTATCGATACATATTGCATT
134087 GTATCGATACAT
1 GTATCGATACAT
134099 GAAAAATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
GTATCGATACATATTGCATT
Found at i:134109 original size:20 final size:20
Alignment explanation
Indices: 134084--134122 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
134074 ATACATTTTC
*
134084 ATTGTATCGATACATGAAAA
1 ATTGTATCAATACATGAAAA
134104 ATTGTATCAATACATGAAA
1 ATTGTATCAATACATGAAA
134123 CTGGCAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (20 bp):
ATTGTATCAATACATGAAAA
Found at i:134166 original size:13 final size:13
Alignment explanation
Indices: 134148--134174 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
134138 CTACCATTGT
134148 TTGTATCGATACA
1 TTGTATCGATACA
134161 TTGTATCGATACA
1 TTGTATCGATACA
134174 T
1 T
134175 AGTAAAATGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:140250 original size:13 final size:14
Alignment explanation
Indices: 140229--140265 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
140219 AAGGATCTTA
140229 GTATCGATACA-TT
1 GTATCGATACATTT
*
140242 GTATTGATA-ATTT
1 GTATCGATACATTT
140255 GTATCGATACA
1 GTATCGATACA
140266 AGGGCACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 1 0.05
13 18 0.90
14 1 0.05
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (14 bp):
GTATCGATACATTT
Found at i:142048 original size:20 final size:20
Alignment explanation
Indices: 142023--142063 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
142013 GGAGCGACTG
142023 TTTTATAAAAGAGATTATTT
1 TTTTATAAAAGAGATTATTT
*
142043 TTTTATGAAAGAGATTATTT
1 TTTTATAAAAGAGATTATTT
142063 T
1 T
142064 GGAAACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTTATAAAAGAGATTATTT
Found at i:146148 original size:16 final size:16
Alignment explanation
Indices: 146127--146164 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
146117 TTGATCTTTC
146127 AAAAAAA-GATTTCTAG
1 AAAAAAATGATTTC-AG
*
146143 AAAAAAATGTTTTCAG
1 AAAAAAATGATTTCAG
146159 AAAAAA
1 AAAAAA
146165 CTATATGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.61, C:0.05, G:0.11, T:0.24
Consensus pattern (16 bp):
AAAAAAATGATTTCAG
Found at i:147810 original size:19 final size:20
Alignment explanation
Indices: 147786--147837 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
147776 ACGATTGAGT
* *
147786 ATGTATCGATACAATG-AAC
1 ATGTATCGATACAAAGCAAA
147805 ATGTATCGATACAAAGCAAA
1 ATGTATCGATACAAAGCAAA
147825 ATGTATCGATACA
1 ATGTATCGATACA
147838 TCTTGATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAAA
Found at i:149855 original size:21 final size:20
Alignment explanation
Indices: 149808--149865 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
149798 CGTATCGATA
**
149808 CAATGTATCGATACATGATT
1 CAATGTATCGATACATGACC
*
149828 CAATGTATCGATACATTACC
1 CAATGTATCGATACATGACC
149848 CAAATGTATCGATACATG
1 C-AATGTATCGATACATG
149866 CATGCAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (20 bp):
CAATGTATCGATACATGACC
Found at i:154093 original size:20 final size:21
Alignment explanation
Indices: 154063--154102 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
154053 ATCTGGGTTT
154063 TTCAGATGTATCGATACATTA
1 TTCAGATGTATCGATACATTA
154084 TTCA-ATGTATCGATACATT
1 TTCAGATGTATCGATACATT
154103 CTGGAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (21 bp):
TTCAGATGTATCGATACATTA
Found at i:155575 original size:21 final size:21
Alignment explanation
Indices: 155549--155625 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
155539 AAATTATCCA
155549 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
* *
155570 AATGTATTGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
155591 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
155612 AATGTATCGATACA
1 AATGTATCGATACA
155626 GGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:155685 original size:19 final size:19
Alignment explanation
Indices: 155661--155715 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
155651 AATTCAACAA
155661 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
155680 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
155699 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
155716 TTAGCTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:155773 original size:13 final size:13
Alignment explanation
Indices: 155755--155780 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
155745 CATTTTTCTG
155755 TGTATCGATACAT
1 TGTATCGATACAT
155768 TGTATCGATACAT
1 TGTATCGATACAT
155781 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:155777 original size:33 final size:33
Alignment explanation
Indices: 155735--155801 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
155725 GCCAAGGAAA
***
155735 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
155768 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
155801 T
1 T
155802 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:158210 original size:27 final size:28
Alignment explanation
Indices: 158175--158243 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
158165 TTCACAATCA
* * **
158175 GGGACACTCCAAGCCCGTTA-ATCATCG
1 GGGATACTCCAACCCCGTTATATCAGAG
*
158202 GGGATACTCCAACCCCGTTATTTCAGAG
1 GGGATACTCCAACCCCGTTATATCAGAG
158230 GGGATACTCCAACC
1 GGGATACTCCAACC
158244 TCGACTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.20
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATATCAGAG
Found at i:158286 original size:51 final size:50
Alignment explanation
Indices: 158229--158398 Score: 205
Period size: 52 Copynumber: 3.3 Consensus size: 50
158219 TTATTTCAGA
* ***
158229 GGGGATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACC-CGATTTTATTTCCAAAATACCAATTTTTCATAATC
* * * * *
158280 GGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCGA-TTTTATTTCCAAAATACCAATTTTTC-ATAATC
*
158332 GGGGATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAAC-CCGATTTTATTTCC-AAAATACCAATTTTTCATAATC
158384 GGGGATACTCCAACC
1 GGGGATACTCCAACC
158399 TCGTTATTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
50 2 0.02
51 35 0.35
52 46 0.46
53 17 0.17
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:158413 original size:28 final size:28
Alignment explanation
Indices: 158381--158462 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 28
158371 ATTTTTCACA
*
158381 ATCGGGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
158409 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
158437 --CGAGGGAACACTCCAACCCCGTTATT
1 ATCG-GGG-ATACTCCAACCCCGTTATT
158463 ATCTCCAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 43 0.90
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:158472 original size:211 final size:211
Alignment explanation
Indices: 158088--158472 Score: 571
Period size: 211 Copynumber: 1.8 Consensus size: 211
158078 CTAACTTCGA
* *
158088 TTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAA
1 TTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACACCAATTTTATTTCCAAAA
158153 AACACCAATTTCTTCACAATCAGGGACACTCCAAGCCCGTTAATCATCGGGGATACTCCAACCCC
66 AACACCAATTTCTTCACAATCAGGGACACTCCAAGCCCGTTAATCATCGGGGATACTCCAACCCC
* * * * *
158218 GTTATTTCAGAGGGGATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTTTCATAATCGGG
131 GTTACTTCAGAGGGAACACTCCAACCCCGACTTTATCTCCAAAATATTGATTTTTCATAATCGGG
158283 GATACTCCAACCCCAG
196 GATACTCCAACCCCAG
* *
158299 TTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACACCGATTTTATTTCC-AA
1 TTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACTCCAACACCAATTTTATTTCCAAA
* * * *
158363 AAATACCAATTT-TTCACAATCGGGGATACTCCAA-CCTCGTTATTTCATCGGGGATACTCCAAC
65 AAACACCAATTTCTTCACAATCAGGGACACTCCAAGCC-CGTTA-ATCATCGGGGATACTCCAAC
* *
158426 CCCGTTACTTCCGAGGGAACACTCCAACCCCG-TTATTATCTCCAAAA
128 CCCGTTACTTCAGAGGGAACACTCCAACCCCGACT-TTATCTCCAAAA
158473 CATTAAATTT
Statistics
Matches: 155, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
209 2 0.01
210 26 0.17
211 93 0.60
212 34 0.22
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (211 bp):
TTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACACCAATTTTATTTCCAAAA
AACACCAATTTCTTCACAATCAGGGACACTCCAAGCCCGTTAATCATCGGGGATACTCCAACCCC
GTTACTTCAGAGGGAACACTCCAACCCCGACTTTATCTCCAAAATATTGATTTTTCATAATCGGG
GATACTCCAACCCCAG
Found at i:169612 original size:13 final size:13
Alignment explanation
Indices: 169594--169619 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
169584 ACAAAGATCC
169594 ATGTATCGATACA
1 ATGTATCGATACA
169607 ATGTATCGATACA
1 ATGTATCGATACA
169620 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:169615 original size:33 final size:33
Alignment explanation
Indices: 169573--169639 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
169563 AAAATTTCCA
***
169573 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
169606 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
169639 A
1 A
169640 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:169683 original size:19 final size:18
Alignment explanation
Indices: 169659--169726 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
169649 CAGTAGCTAA
169659 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
*
169678 TTATGTATTGATAC--A-
1 TTATGTATCGATACAAAC
169693 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
169710 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
169727 TTGTTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:169703 original size:32 final size:32
Alignment explanation
Indices: 169662--169724 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
169652 TAGCTAATTA
* *
169662 TGTATCGATACAATACTTATGTATTGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
169694 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
169725 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:170629 original size:55 final size:55
Alignment explanation
Indices: 170545--171341 Score: 1067
Period size: 55 Copynumber: 14.3 Consensus size: 55
170535 ATAAAGTGTC
* * * * * *
170545 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
170600 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
170655 TCCTGCTCTTTGAAGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
170710 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGGG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * * **
170765 TCCTGCTCTTTGGGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
*
170826 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTG-GATGGGCTTTAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTG-TGGGCTTT----G-AAAGGTG
* *
170885 TCCAGCTCTTTGAGGACTG-AAGGTGCCACCCACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
170939 TCCTGCTCTCTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
170994 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
171049 TCCTGCTCTTTGAGGACTGGAAA-ATGTCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
171104 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
171159 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
171214 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
171269 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
171324 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
171342 AAAAAGCGGA
Statistics
Matches: 681, Mismatches: 37, Indels: 48
0.89 0.05 0.06
Matches are distributed among these distances:
53 2 0.00
54 34 0.05
55 537 0.79
56 16 0.02
59 44 0.06
60 25 0.04
61 18 0.03
64 5 0.01
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:170732 original size:26 final size:26
Alignment explanation
Indices: 170703--170790 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
170693 GTGGGCTTTA
170703 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** *
170729 AAAGGTG-CCACCAACTTGTGTGGG-CTTTG
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC--TG
* *
170758 AAAGGGGTCCTGCTCTTTGGGGACTA
1 AAAGGTGTCCTGCTCTTTGGGGACTG
170784 AAAGGTG
1 AAAGGTG
170791 CCACCAGCTT
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
25 3 0.07
26 17 0.37
27 6 0.13
28 6 0.13
29 11 0.24
30 3 0.07
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:170759 original size:29 final size:29
Alignment explanation
Indices: 170679--170762 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
170669 GACTGGAAAA
*
170679 TGCCACCAACTTGTGTGGGCTTTAAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGG
** *
170708 TGTCCTGC-TCTT-TG-GGGAC--TGAAAGG
1 TG-CCACCAACTTGTGTGGG-CTTTGAAAGG
170734 TGCCACCAACTTGTGTGGGCTTTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGG
170763 GGTCCTGCTC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
25 3 0.07
26 11 0.27
27 6 0.15
28 6 0.15
29 12 0.29
30 3 0.07
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGG
Found at i:171016 original size:27 final size:27
Alignment explanation
Indices: 170986--171071 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
170976 TGTGGGCTTT
170986 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
171013 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
171041 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
171068 GAAA
1 GAAA
171072 ATGTCACCAA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:178203 original size:20 final size:20
Alignment explanation
Indices: 178175--178249 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
178165 TCATACCCTG
178175 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
178195 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
178215 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
178235 ATGTATCGATACATT
1 ATGTATCGATACATT
178250 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:178242 original size:40 final size:39
Alignment explanation
Indices: 178175--178252 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
178165 TCATACCCTG
* *
178175 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
178215 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
178253 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:192275 original size:15 final size:15
Alignment explanation
Indices: 192255--192300 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 15
192245 CCGTTACACC
192255 CAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAA
*
192270 CAAAAAAAAACAAAA
1 CAAAAAAAAAAAAAA
192285 CAAAAAAACAAAAAAA
1 CAAAAAAA-AAAAAAA
192301 AAATAGCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 22 0.79
16 6 0.21
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAAAAAA
Found at i:192289 original size:23 final size:23
Alignment explanation
Indices: 192258--192302 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
192248 TTACACCCAA
192258 AAAAAAAAAAAACAAAAAAAAAC
1 AAAAAAAAAAAACAAAAAAAAAC
*
192281 AAAACAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAACAAAAAAAAA
192303 ATAGCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAAACAAAAAAAAAC
Found at i:192312 original size:15 final size:13
Alignment explanation
Indices: 192255--192313 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
192245 CCGTTACACC
192255 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
*
192268 -AACAAAAAAAAA
1 CAAAAAAAAAAAA
*
192280 CAAAACAAAAAAA
1 CAAAAAAAAAAAA
*
192293 CAAAAAAAAAATAG
1 CAAAAAAAAAA-AA
192307 CAAAAAA
1 CAAAAAA
192314 TAGAAGGGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
12 11 0.28
13 20 0.51
14 8 0.21
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.02
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:192313 original size:1 final size:1
Alignment explanation
Indices: 192256--192303 Score: 60
Period size: 1 Copynumber: 48.0 Consensus size: 1
192246 CGTTACACCC
* * * *
192256 AAAAAAAAAAAAAACAAAAAAAAACAAAACAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
192304 TAGCAAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:193577 original size:29 final size:28
Alignment explanation
Indices: 193534--194360 Score: 754
Period size: 32 Copynumber: 27.4 Consensus size: 28
193524 GAATGTTCAT
193534 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
193562 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
193591 CTCTTTCAAAGCCCACAAATCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
193619 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
193647 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
193675 CTCCTTTCAAAGCCTACAAGTTAGTGGTA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
193704 CTCTTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
193733 CTCTTTTTAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
193762 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
193791 CTCCTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
193820 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
193849 CCCTTTCAAAGCCCACAACTCATTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
193877 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
193905 CTCCTTTCAAAGCCCACAAGCCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
193934 CTCTTTTCAGAGCCCACAAGTCGGTGGCAA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGC-A
*
193964 CCCATTTCAAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTC-AAAG-CC-CACAAGTCAGTGGC-A
* * *
193997 CCCATTCCAAAGCCCACACAAGTCGGCGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* *
194029 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* *
194061 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* *
194093 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
*
194125 CCCATTTCAAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTC-AAAG-CC-CACAAGTCAGTGGC-A
*
194158 CCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
*
194190 CCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* *
194222 CCCATTTCAAAACCCACAAAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCAC--AAGTCAGTGGC-A
* *
194254 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* *
194286 CTCATTTCAAAGCCCACATAAGTCGGTGGCAA
1 C-CCTTTCAAAGCCCAC--AAGTCAGTGGC-A
*
194318 CCCATTTAAAAGCCCATGCAAGTCAGTGGCAA
1 CCC-TTTCAAAGCCCA--CAAGTCAGTGGC-A
194350 CCCTTTTCAAA
1 CCC-TTTCAAA
194361 TCACCATATT
Statistics
Matches: 733, Mismatches: 47, Indels: 34
0.90 0.06 0.04
Matches are distributed among these distances:
28 130 0.18
29 237 0.32
30 12 0.02
31 8 0.01
32 284 0.39
33 58 0.08
34 4 0.01
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:194140 original size:161 final size:161
Alignment explanation
Indices: 193948--194352 Score: 695
Period size: 161 Copynumber: 2.5 Consensus size: 161
193938 TTTCAGAGCC
*
193948 CACAAGTCGGTGGCAACCCATTTCAAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
194013 CACAAGTCGGCGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCAC
66 CACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAACCCAC
*
194078 ACAAGTCGGTGGCAACCCATTCCAAAGCCCA
131 AAAAGTCGGTGGCAACCCATTCCAAAGCCCA
194109 CACAAGTCGGTGGCAACCCATTTCAAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
194174 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAACCCAC
66 CACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAACCCAC
194239 AAAAGTCGGTGGCAACCCATTCCAAAGCCCA
131 AAAAGTCGGTGGCAACCCATTCCAAAGCCCA
* * *
194270 CACAAGTCGGTGGCAACTCATTTC-AAAGCCCACATAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
194334 TGCAAGTCAGTGGCAACCC
66 CACAAGTCGGTGGCAACCC
194353 TTTTCAAATC
Statistics
Matches: 232, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
160 54 0.23
161 178 0.77
ACGTcount: A:0.32, C:0.35, G:0.19, T:0.15
Consensus pattern (161 bp):
CACAAGTCGGTGGCAACCCATTTCAAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
CACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAACCCAC
AAAAGTCGGTGGCAACCCATTCCAAAGCCCA
Found at i:194915 original size:20 final size:20
Alignment explanation
Indices: 194887--194961 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
194877 TCATACCCTG
194887 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
194907 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
194927 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
194947 ATGTATCGATACATT
1 ATGTATCGATACATT
194962 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Done.