Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011972.1 Kokia drynarioides strain JFW-HI SEQ_126970, whole genome shotgun sequence
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: 54884
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Warning! 106 characters in sequence are not A, C, G, or T
Found at i:3979 original size:15 final size:16
Alignment explanation
Indices: 3936--3971 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
3926 GCTAAATATG
3936 AAAAACATGAAAGACA
1 AAAAACATGAAAGACA
3952 AAAAACATGAAAGACA
1 AAAAACATGAAAGACA
3968 AAAA
1 AAAA
3972 CATAAAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.72, C:0.11, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAACATGAAAGACA
Found at i:4844 original size:48 final size:45
Alignment explanation
Indices: 4779--4868 Score: 119
Period size: 48 Copynumber: 1.9 Consensus size: 45
4769 GAAATTATTA
* *
4779 TGGTTTTCTTCAAAATGAAAATTAAAATAGAGAAAATGTAAAATGAATG
1 TGGTTTTCTCCAAAATGAAAATGAAAAT---GAAAATG-AAAATGAATG
4828 TGGTTTTC-CCAAAATGAAAATGAAAATGAAAATGAAAATGA
1 TGGTTTTCTCCAAAATGAAAATGAAAATGAAAATGAAAATGA
4869 GAAATGAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 7 0.18
45 7 0.18
48 17 0.44
49 8 0.21
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.28
Consensus pattern (45 bp):
TGGTTTTCTCCAAAATGAAAATGAAAATGAAAATGAAAATGAATG
Found at i:4849 original size:6 final size:6
Alignment explanation
Indices: 4838--4876 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
4828 TGGTTTTCCC
4838 AAAATG AAAATG AAAATG AAAATG AAAATG AGAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AAAATG A-AAATG AA
4877 TTCATTTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:18250 original size:41 final size:41
Alignment explanation
Indices: 18188--18319 Score: 183
Period size: 41 Copynumber: 3.2 Consensus size: 41
18178 TTGTATAAAT
* * *
18188 GGAAGACTTATGTATCGAAATGAGAATGAGATTATGAATAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAA
* *
18229 GGAAGACTCATGTCTCAAAATGAGAATGAGATTTTGATTAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAA
* * *
18270 GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTTAAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATT-AA
18312 GGAAGACT
1 GGAAGACT
18320 TTTGACTCGA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 70 0.88
42 10 0.12
ACGTcount: A:0.40, C:0.08, G:0.26, T:0.26
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAA
Found at i:20104 original size:22 final size:21
Alignment explanation
Indices: 20053--20104 Score: 50
Period size: 25 Copynumber: 2.2 Consensus size: 21
20043 TACATTTATT
*
20053 ACATGCTTGTTTGTTGTTGAA
1 ACATGCTTGTTTGTTGTGGAA
20074 ATGTTCATGCTTGTTTGTTGTAGGAA
1 A----CATGCTTGTTTGTTGT-GGAA
20100 ACATG
1 ACATG
20105 AAACGTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 9
0.71 0.03 0.26
Matches are distributed among these distances:
21 1 0.04
22 4 0.16
25 16 0.64
26 4 0.16
ACGTcount: A:0.21, C:0.10, G:0.25, T:0.44
Consensus pattern (21 bp):
ACATGCTTGTTTGTTGTGGAA
Found at i:20253 original size:23 final size:22
Alignment explanation
Indices: 20205--20256 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
20195 ATTAATAACA
* *
20205 ATAAT-AATAAATTTATTAATG
1 ATAATAAATAAATTAATAAATG
20226 ATAATAAATAATATTAATAAATG
1 ATAATAAATAA-ATTAATAAATG
*
20249 TTAATAAA
1 ATAATAAA
20257 AAAAAGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 5 0.19
22 5 0.19
23 16 0.62
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAATAAATAAATTAATAAATG
Found at i:21361 original size:29 final size:29
Alignment explanation
Indices: 21318--21687 Score: 236
Period size: 30 Copynumber: 12.8 Consensus size: 29
21308 CTCAATTGTA
* * *
21318 CAAAAATTACTTTTTTACCCCCGAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
*
21347 CAAAAATTCCATTTTGACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
* * *
21376 CAAAAATTCCATTTTT-CACATTGAAACTTT
1 CAAAAATTCCATTTTTAC-CCTCG-AACTTC
*
21406 CAAAAATTCCATTTTTAACCTCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCG-AACTTC
* * *
21436 CAAAAATTACA-ATTT----T-G-AC-CC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
*
21457 CAAAAATTCCATTTTTAACCC-CAAGACTTC
1 CAAAAATTCCATTTTT-ACCCTCGA-ACTTC
*
21487 CAAAAATTCCATTTTTACCCTCGAACCTC
1 CAAAAATTCCATTTTTACCCTCGAACTTC
*
21516 CAAAAATTCCTTTTTTGA-CCTCGAGACTTC
1 CAAAAATTCCATTTTT-ACCCTCGA-ACTTC
* *
21546 CAAAAATTCCATTTTTTTCCAC-CGAACCT-
1 CAAAAATTCCA-TTTTTACC-CTCGAACTTC
* * * * *
21575 CTATATTTCCCATTTTTGACCC-CAAAACTTT
1 CAAAAATT-CCATTTTT-ACCCTC-GAACTTC
* *
21606 CAAAAGTACCA-TTTTACCCTCGAA-TGTC
1 CAAAAATTCCATTTTTACCCTCGAACT-TC
*
21634 TAAAAATTCCATTTTTAACCCT-GAACTTTC
1 CAAAAATTCCATTTTT-ACCCTCGAAC-TTC
* *
21664 CCAAAATTACCA-TTTTGCCCTCGA
1 CAAAAATT-CCATTTTTACCCTCGA
21688 GGATCCAAAA
Statistics
Matches: 266, Mismatches: 44, Indels: 61
0.72 0.12 0.16
Matches are distributed among these distances:
21 11 0.04
22 5 0.02
24 1 0.00
25 1 0.00
27 1 0.00
28 16 0.06
29 105 0.39
30 108 0.41
31 17 0.06
32 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCTCGAACTTC
Found at i:21413 original size:59 final size:57
Alignment explanation
Indices: 21340--21561 Score: 210
Period size: 59 Copynumber: 3.9 Consensus size: 57
21330 TTTTACCCCC
21340 GAACTTCCAAAAATTCCATTTTGACCCTCGA-ACTTCCAAAAATTCCATTTTTCACATT
1 GAACTTCCAAAAATTCCATTTTGACCCTCGAGACTTCCAAAAATTCCATTTTT-AC-TT
* * * * * *
21398 GAAACTTTCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTACA--ATT--TT
1 G-AACTTCCAAAAATTCCATTTTGACCCTCGAGACTTCCAAAAATTCCATTTTTACTT
* * * *
21452 G-AC-CCCAAAAATTCCATTTTTAACCC-CAAGACTTCCAAAAATTCCATTTTTACCCTC
1 GAACTTCCAAAAATTCCA-TTTTGACCCTCGAGACTTCCAAAAATTCCATTTTTA--CTT
* *
21509 GAACCTCCAAAAATTCCTTTTTTGA-CCTCGAGACTTCCAAAAATTCCATTTTT
1 GAACTTCCAAAAATTCC-ATTTTGACCCTCGAGACTTCCAAAAATTCCATTTTT
21562 TTCCACCGAA
Statistics
Matches: 133, Mismatches: 18, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
51 28 0.21
52 9 0.07
53 2 0.02
54 3 0.02
57 2 0.02
58 7 0.05
59 67 0.50
60 15 0.11
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (57 bp):
GAACTTCCAAAAATTCCATTTTGACCCTCGAGACTTCCAAAAATTCCATTTTTACTT
Found at i:21488 original size:21 final size:21
Alignment explanation
Indices: 21435--21480 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
21425 CTCGAAACTT
* * *
21435 CCAAAAATTACAATTTTGACC
1 CCAAAAATTCCATTTTTAACC
21456 CCAAAAATTCCATTTTTAACC
1 CCAAAAATTCCATTTTTAACC
21477 CCAA
1 CCAA
21481 GACTTCCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.28, G:0.02, T:0.28
Consensus pattern (21 bp):
CCAAAAATTCCATTTTTAACC
Found at i:21510 original size:81 final size:80
Alignment explanation
Indices: 21375--21523 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 80
21365 CCTCGAACTT
* *** * *
21375 CCAAAAATTCCATTTTTCACATTGAAACTTTCAAAAATTCCATTTTTAACCTCGAAACTTCCAAA
1 CCAAAAATTCCATTTTTAACACCCAAACTTCCAAAAATTCCATTTTTAACCTCG-AACCTCCAAA
21440 AATTACAATTTTGACC
65 AATTACAATTTTGACC
*
21456 CCAAAAATTCCATTTTTAAC-CCCAAGACTTCCAAAAATTCCATTTTTACCCTCGAACCTCCAAA
1 CCAAAAATTCCATTTTTAACACCCAA-ACTTCCAAAAATTCCATTTTTAACCTCGAACCTCCAAA
21520 AATT
65 AATT
21524 CCTTTTTTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
80 15 0.25
81 45 0.75
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (80 bp):
CCAAAAATTCCATTTTTAACACCCAAACTTCCAAAAATTCCATTTTTAACCTCGAACCTCCAAAA
ATTACAATTTTGACC
Found at i:28679 original size:100 final size:100
Alignment explanation
Indices: 28506--28755 Score: 376
Period size: 100 Copynumber: 2.5 Consensus size: 100
28496 GCACCATGAA
* *
28506 ACATGACGGGAAAGATCTAAGATCGCAACGGTGGATCCAGTTTCGCAAAGATACAAAAGGGAAGA
1 ACATGACGGGAAAGATCTAAGACCGCAACGGTGGATCCAGTATCGCAAAGATACAAAAGGGAAGA
* *
28571 GTTTAAGTCGTAACGGCTAACCTTATACCTTAAAG
66 GTTTAAGTCGTAACAGCGAACCTTATACCTTAAAG
* * * *
28606 ACATGACGGGAAAGATTTAAGACCGCAATGGCGGATCCAGTATCGCAAAGATACGAAAGGGAAGA
1 ACATGACGGGAAAGATCTAAGACCGCAACGGTGGATCCAGTATCGCAAAGATACAAAAGGGAAGA
* * *
28671 GTTTAAGTCGTATCAGCGAACCTTGTACCTTAGAG
66 GTTTAAGTCGTAACAGCGAACCTTATACCTTAAAG
* *
28706 ACATGACGGGAAAGATCTAAG-CCGCAACGGTGGATCCAGTACCGCGAAGA
1 ACATGACGGGAAAGATCTAAGACCGCAACGGTGGATCCAGTATCGCAAAGA
28756 CATGAAGGGA
Statistics
Matches: 134, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
99 25 0.19
100 109 0.81
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (100 bp):
ACATGACGGGAAAGATCTAAGACCGCAACGGTGGATCCAGTATCGCAAAGATACAAAAGGGAAGA
GTTTAAGTCGTAACAGCGAACCTTATACCTTAAAG
Found at i:28757 original size:49 final size:49
Alignment explanation
Indices: 28704--29028 Score: 207
Period size: 49 Copynumber: 6.6 Consensus size: 49
28694 TGTACCTTAG
* * ** *
28704 AGACATGACGGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCGCGA
1 AGACATGAAGGGAAAGATCTAAGTCGCAACGGCAGATCCAGTACCACGA
* * * *
28753 AGACATGAAGGGAAAAATCTAAGTCGCAACGGTAGACCCAGTACCATGA
1 AGACATGAAGGGAAAGATCTAAGTCGCAACGGCAGATCCAGTACCACGA
* * * * * *
28802 AGACA-CAAGGGAAAGGTTTAAGTCGCAATGGCAGA-CCTAGTACCTCAA
1 AGACATGAAGGGAAAGATCTAAGTCGCAACGGCAGATCC-AGTACCACGA
* * *
28850 AGACATAAAGGGAAAGATCT-AGATCGCAACGGCAGATCCAGTACTACAA
1 AGACATGAAGGGAAAGATCTAAG-TCGCAACGGCAGATCCAGTACCACGA
* * * * * * *
28899 AGATACA-AAAGGGAAAGGTTTAAGTTGTAACGGC-GAACC-GTGAACCTCAGA
1 AG--ACATGAAGGGAAAGATCTAAGTCGCAACGGCAGATCCAGT--ACCAC-GA
* * * *
28950 AGACAAGAAGGAAAAGATTTAAG-CTGCAACAGC-GAATCCAGTACCACGA
1 AGACATGAAGGGAAAGATCTAAGTC-GCAACGGCAG-ATCCAGTACCACGA
** * *
28999 AGATTTGAAAGGGAAAGGTTTAAGTCGCAA
1 AGACATG-AAGGGAAAGATCTAAGTCGCAA
29029 TGGCGAACCC
Statistics
Matches: 217, Mismatches: 43, Indels: 31
0.75 0.15 0.11
Matches are distributed among these distances:
47 2 0.01
48 40 0.18
49 93 0.43
50 68 0.31
51 12 0.06
52 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (49 bp):
AGACATGAAGGGAAAGATCTAAGTCGCAACGGCAGATCCAGTACCACGA
Found at i:28854 original size:97 final size:98
Alignment explanation
Indices: 28743--28923 Score: 240
Period size: 97 Copynumber: 1.8 Consensus size: 98
28733 CGGTGGATCC
* * * **
28743 AGTACCGCGAAGACATGAAGGGAAAAATCTA-AGTCGCAACGGTAGACCCAGTACCATGAAG-AC
1 AGTACCGCAAAGACATAAAGGGAAAAATCTAGA-TCGCAACGGCAGACCCAGTACCACAAAGAAC
*
28806 ACAAGGGAAAGGTTTAAGTCGCAATGGCAGACCT
65 AAAAGGGAAAGGTTTAAGTCGCAATGGCAGACCT
* * * *
28840 AGTACCTCAAAGACATAAAGGGAAAGATCTAGATCGCAACGGCAGATCCAGTACTACAAAGATAC
1 AGTACCGCAAAGACATAAAGGGAAAAATCTAGATCGCAACGGCAGACCCAGTACCACAAAGA-AC
28905 AAAAGGGAAAGGTTTAAGT
65 AAAAGGGAAAGGTTTAAGT
28924 TGTAACGGCG
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
97 50 0.70
98 1 0.01
99 20 0.28
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (98 bp):
AGTACCGCAAAGACATAAAGGGAAAAATCTAGATCGCAACGGCAGACCCAGTACCACAAAGAACA
AAAGGGAAAGGTTTAAGTCGCAATGGCAGACCT
Found at i:29035 original size:50 final size:49
Alignment explanation
Indices: 28561--29037 Score: 190
Period size: 49 Copynumber: 9.7 Consensus size: 49
28551 CAAAGATACA
* * **
28561 AAAGGG-AAGAGTTTAAGTCGTAACGGCTAACCTTA-TACCTTAAAGACATG
1 AAAGGGAAAG-GTTTAAGTCGCAACGGCGAACC--AGTACCACAAAGACATG
* * * * * * * * *
28611 -ACGGGAAAGATTTAAGACCGCAATGGCGGATCCAGTATCGCAAAGATACG
1 AAAGGGAAAGGTTTAAG-TCGCAACGGC-GAACCAGTACCACAAAGACATG
* * * * ** *
28661 AAAGGG-AAGAGTTTAAGTCGTATCAGCGAACCTTGTACCTTAGAGACATG
1 AAAGGGAAAG-GTTTAAGTCGCAACGGCGAACC-AGTACCACAAAGACATG
* * * * * * * *
28711 -ACGGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCGCGAAGACATG
1 AAAGGGAAAGGTTTAAGTCGCAACGG-CGAACCAGTACCACAAAGACATG
** * * * **
28760 -AAGGGAAAAATCTAAGTCGCAACGGTAGACCCAGTACCATGAAGACA--
1 AAAGGGAAAGGTTTAAGTCGCAACGG-CGAACCAGTACCACAAAGACATG
* * *
28807 CAAGGGAAAGGTTTAAGTCGCAATGGC-AGACCTAGTACCTCAAAGACAT-
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGA-ACC-AGTACCACAAAGACATG
* * * * * **
28856 AAAGGGAAAGATCT-AGATCGCAACGGCAGATCCAGTACTACAAAGATACA
1 AAAGGGAAAGGTTTAAG-TCGCAACGGC-GAACCAGTACCACAAAGACATG
* * * *
28906 AAAGGGAAAGGTTTAAGTTGTAACGGCGAACC-GTGAACCTCAGAAGACAAG
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCAGT--ACCACA-AAGACATG
* * * * **
28957 -AAGGAAAAGATTTAAG-CTGCAACAGCGAATCCAGTACCACGAAGATTTG
1 AAAGGGAAAGGTTTAAGTC-GCAACGGCGAA-CCAGTACCACAAAGACATG
*
29006 AAAGGGAAAGGTTTAAGTCGCAATGGCGAACC
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGAACC
29038 CGATACCTTA
Statistics
Matches: 311, Mismatches: 90, Indels: 53
0.69 0.20 0.12
Matches are distributed among these distances:
46 1 0.00
47 2 0.01
48 37 0.12
49 124 0.40
50 121 0.39
51 24 0.08
52 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (49 bp):
AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCAGTACCACAAAGACATG
Found at i:29243 original size:101 final size:101
Alignment explanation
Indices: 29123--29304 Score: 253
Period size: 101 Copynumber: 1.8 Consensus size: 101
29113 GATCAAAACT
* *
29123 ACAATGGCAAGTCTTTATCTC-CTTGAAGTTACAGCAAGAGAAAGATGAAGCTTT-AACATCAAT
1 ACAATAGCAAGTCTTTATCTCTC-TGAAGTTACAGCAAGAGAAAGATGAAG-TTTCAACATCAAA
29186 TCCTATCC-TCTTGAAGTTGCAGTAAAGTCGGATTAAAA
64 TCCTA-CCTTCTTGAAGTTGCAGTAAAGTCGGATTAAAA
* ** * *
29224 ACAATAGCAAGTCTTTATCTTTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAACATCAAATC
1 ACAATAGCAAGTCTTTATCTCTCTGAAGTTACAGCAAGAGAAAGATGAAGTTTCAACATCAAATC
29289 CTACCTTCTTGAAGTT
66 CTACCTTCTTGAAGTT
29305 ACAGCGAAGT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
100 5 0.07
101 65 0.92
102 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (101 bp):
ACAATAGCAAGTCTTTATCTCTCTGAAGTTACAGCAAGAGAAAGATGAAGTTTCAACATCAAATC
CTACCTTCTTGAAGTTGCAGTAAAGTCGGATTAAAA
Found at i:29440 original size:39 final size:39
Alignment explanation
Indices: 29386--29612 Score: 169
Period size: 39 Copynumber: 5.8 Consensus size: 39
29376 CTACATCGTT
29386 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
1 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
* *
29425 AACCAATCTCTTACCCCGAGCCTAGGGCAGAT--TGA--
1 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
* * *** *
29460 AGCCATTTGATCTTTTACCCCGAGCCTATAGCAGACCATCATC
1 AACCA----ATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
* * * *
29503 AACCAATCTCTTACCCCGAGCCAGAGGCAGATTA-CAGCC
1 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCA-TC
** * * * *
29542 ATTCGATCTCTTACCCCGAGCTTGGGGTAGATCATCGTC
1 AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
* * *
29581 AACCAAACTCTTACTCCGATCAC-GGGGCAGAT
1 AACCAATCTCTTACCCCGAGC-CTGGGGCAGAT
29613 TGTGATTATC
Statistics
Matches: 142, Mismatches: 35, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
35 4 0.03
37 2 0.01
38 2 0.01
39 127 0.89
40 1 0.01
41 2 0.01
43 4 0.03
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (39 bp):
AACCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
Found at i:29610 original size:78 final size:78
Alignment explanation
Indices: 29391--29614 Score: 283
Period size: 78 Copynumber: 2.9 Consensus size: 78
29381 TCGTTAACCA
29391 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCTA-GGGCAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCC-AGGGGCAG
*
29455 ATTGAAGCCATTTG
65 ATTGAAGCCATTCG
* *** * *
29469 ATCTTTTACCCCGAGCCTATAGCAGACCATCATCAACCAATCTCTTACCCCGAGCCAGAGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCAGGGGCAGA
29534 TT-ACAGCCATTCG
66 TTGA-AGCCATTCG
* * * * * *
29547 ATCTCTTACCCCGAGCTTGGGGTAGATCATCGTCAACCAAACTCTTACTCCGA-TCACGGGGCAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCA-GGGGCAG
29611 ATTG
65 ATTG
29615 TGATTATCCA
Statistics
Matches: 123, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
77 4 0.03
78 119 0.97
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.23
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCAGGGGCAGA
TTGAAGCCATTCG
Found at i:30678 original size:205 final size:205
Alignment explanation
Indices: 29684--30598 Score: 1430
Period size: 205 Copynumber: 4.5 Consensus size: 205
29674 ACTCAAAGGG
* * *
29684 GAGCAAATCTTCAAATCCCAGCTTCTTGATAAGACATTGAGAAGCAGGTCGAAGCAATAAAAGGT
1 GAGCAAATCTTCAAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
* *
29749 CAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCG
66 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
*
29814 AATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCA
131 AATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCA
*
29879 TGCTC-----
196 CGCTCGATGT
* * *
29884 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCACTAAAAGGT
1 GAGCAAATCTTCAAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
* * *
29949 AAACTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGATAAGCG
66 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
30014 AATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCA
131 AATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCA
*
30079 CACTCGATGT
196 CGCTCGATGT
* * * *
30089 GAGCAAATCTTCAAACCCTAG-TTTTCTGATGAGAAACTGAGAAGAAGGTCGAAGCAATAAAAGG
1 GAGCAAATCTTCAAACCCCAGCTTCT-TGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGG
30153 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
65 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
* * * * *
30218 GAATTGAAACAAACGACGTGGTCGTCTTCTTGATGAGATACTAAGAAGAAGAGCAAATCAAACCC
130 GAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCC
*
30283 ACGCTTGATGT
195 ACGCTCGATGT
*
30294 GAGCAAATCTTCAAACCCCAG-TTTTCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGG
1 GAGCAAATCTTCAAACCCCAGCTTCT-TGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGG
30358 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
65 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
* * *
30423 GAATTGAAACAAACAACGCGGTCGTCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCC
130 GAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCC
30488 ACGCTCGATGT
195 ACGCTCGATGT
* * * * *
30499 GAGTAAATCTTCGAACCCCAGCTTCTTGTTGAGACATTGAGAAGTAGGTCGAAGCAATAAAAGGT
1 GAGCAAATCTTCAAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
* * * *
30564 TAGCTTCCTGATGAAATACGGGGAAGTGAACCAAA
66 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAA
30599 ACCATCTTCC
Statistics
Matches: 660, Mismatches: 48, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
200 187 0.28
204 2 0.00
205 468 0.71
206 3 0.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (205 bp):
GAGCAAATCTTCAAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
AATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCA
CGCTCGATGT
Found at i:32861 original size:29 final size:29
Alignment explanation
Indices: 32820--33360 Score: 438
Period size: 29 Copynumber: 18.4 Consensus size: 29
32810 AAACTGTCAG
*
32820 AAAATTACATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
* *** *
32849 AAAATTCCATTTTCGACCCTAAAAATTCCA
1 AAAATTCCATTTT-TACCCCCGAACTTCCA
32879 AAAATTCCATTTTTGA-CCCCGAACTTCCA
1 AAAATTCCATTTTT-ACCCCCGAACTTCCA
** * *
32908 AAAATTCCATTTTTA-CCCTAAATTTCAA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
*
32936 AAAATTCCATTTTTGA-CACCGAAACTTCCA
1 AAAATTCCATTTTT-ACCCCCG-AACTTCCA
* *
32966 AAAATTCCATTTTTACCCTC-AATCTTCTA
1 AAAATTCCATTTTTACCCCCGAA-CTTCCA
* *** *
32995 AAAATTACCATTTTAACCCTAAAATTTCCA
1 AAAATT-CCATTTTTACCCCCGAACTTCCA
33025 AAAATTCCATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
* **
33054 AAAATTCCATTTTTGACCTCAAAACTTCCA
1 AAAATTCCATTTTT-ACCCCCGAACTTCCA
* * **
33084 AAAATTCCAATTTTATCCCTAAACTTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
* * *
33113 AAAATTCCATTTTTGA-CCTCGAGACTGCAA
1 AAAATTCCATTTTT-ACCCCCGA-ACTTCCA
* ** * *
33143 AAAATTTCATTTTTACCCTTGAACCTACA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
* *
33172 AAAATTCAATTTGTGA-CCCCGAGACTTCCA
1 AAAATTCCATTT-TTACCCCCGA-ACTTCCA
* * *
33202 AAAATTTCATTTTTTCCCCCGAACCTCCA
1 AAAATTCCATTTTTACCCCCGAACTTCCA
33231 AAAATTCCATTTTTGA-CCCCGAGACTTCCA
1 AAAATTCCATTTTT-ACCCCCGA-ACTTCCA
* * *
33261 AAAATTCCATTTTTACCCCCAAACCT-CT
1 AAAATTCCATTTTTACCCCCGAACTTCCA
*
33289 AAAATTACCATTTTTGA-CCCCGAAACTTTCA
1 AAAATT-CCATTTTT-ACCCCCG-AACTTCCA
* * * *
33320 AAAGTACCA-TTTTACCCTCGAA-TGTCTA
1 AAAATTCCATTTTTACCCCCGAACT-TCCA
33348 AAAATTCCATTTT
1 AAAATTCCATTTT
33361 AAACCCTAAA
Statistics
Matches: 408, Mismatches: 79, Indels: 50
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.00
28 45 0.11
29 181 0.44
30 174 0.43
31 7 0.02
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCCGAACTTCCA
Found at i:32880 original size:30 final size:29
Alignment explanation
Indices: 32841--33396 Score: 353
Period size: 30 Copynumber: 18.9 Consensus size: 29
32831 TTTACCCCCG
32841 AACTTCCAAAAATTCCATTTTCGACCCTAA
1 AACTTCCAAAAATTCCATTTT-GACCCTAA
* **
32871 AAATTCCAAAAATTCCATTTTTGACCC-CG
1 AACTTCCAAAAATTCCA-TTTTGACCCTAA
*
32900 AACTTCCAAAAATTCCATTTTTACCCT-A
1 AACTTCCAAAAATTCCATTTTGACCCTAA
* * *
32928 AATTTCAAAAAATTCCATTTTTGACACC-GA
1 AACTTCCAAAAATTCCA-TTTTGAC-CCTAA
* *
32958 AACTTCCAAAAATTCCATTTTTACCCTCA
1 AACTTCCAAAAATTCCATTTTGACCCTAA
* * *
32987 ATCTTCTAAAAATTACCATTTTAACCCTAA
1 AACTTCCAAAAATT-CCATTTTGACCCTAA
* * ***
33017 AATTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTGACCCTAA
33046 AACTTCCAAAAATTCCATTTTTGA-CCTCAA
1 AACTTCCAAAAATTCCA-TTTTGACCCT-AA
33076 AACTTCCAAAAATTCCAATTTT-ATCCCT-A
1 AACTTCCAAAAATTCC-ATTTTGA-CCCTAA
*
33105 AACTTCCAAAAATTCCATTTTTGA-CCTCGA
1 AACTTCCAAAAATTCCA-TTTTGACCCT-AA
* * * * * **
33135 GACTGCAAAAAATTTCATTTTTACCCTTG
1 AACTTCCAAAAATTCCATTTTGACCCTAA
* * * **
33164 AACCTACAAAAATTCAATTTGTGACCCCGA
1 AACTTCCAAAAATTCCATTT-TGACCCTAA
* * ** ***
33194 GACTTCCAAAAATTTCATTTTTTCCCCCG
1 AACTTCCAAAAATTCCATTTTGACCCTAA
* **
33223 AACCTCCAAAAATTCCATTTTTGACCCCGA
1 AACTTCCAAAAATTCCA-TTTTGACCCTAA
* * **
33253 GACTTCCAAAAATTCCATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTGACCCTAA
* * **
33282 AACCT-CTAAAATTACCATTTTTGACCCCGA
1 AACTTCCAAAAATT-CCA-TTTTGACCCTAA
* * * **
33312 AACTTTCAAAAGTACCATTTT-ACCCTCG
1 AACTTCCAAAAATTCCATTTTGACCCTAA
* *
33340 AA-TGTCTAAAAATTCCATTTTAAACCCT-A
1 AACT-TCCAAAAATTCCATTTT-GACCCTAA
*
33369 AACTTTCCCAAAATTACCATTTTG-CCCT
1 AAC-TTCCAAAAATT-CCATTTTGACCCT
33397 CGAGGATCCA
Statistics
Matches: 411, Mismatches: 87, Indels: 57
0.74 0.16 0.10
Matches are distributed among these distances:
27 1 0.00
28 55 0.13
29 155 0.38
30 179 0.44
31 21 0.05
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTGACCCTAA
Found at i:32899 original size:59 final size:58
Alignment explanation
Indices: 32820--33360 Score: 547
Period size: 59 Copynumber: 9.2 Consensus size: 58
32810 AAACTGTCAG
* * * *
32820 AAAATTACATTTTT-ACCCCCGAACTTCCAAAAATTCCATTTTCGACCCTAAAAATTCCA
1 AAAATTCCATTTTTGA-CCCCGAACTTCCAAAAATTCCATTTT-TACCCTCAAACTTCCA
* *
32879 AAAATTCCATTTTTGACCCCGAACTTCCAAAAATTCCATTTTTACCCT-AAATTTCAA
1 AAAATTCCATTTTTGACCCCGAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCA
* * *
32936 AAAATTCCATTTTTGACACCGAAACTTCCAAAAATTCCATTTTTACCCTCAATCTTCTA
1 AAAATTCCATTTTTGACCCCG-AACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCA
* ** * * *
32995 AAAATTACCA-TTTTAACCCTAAAATTTCCAAAAATTCCATTTTTACCCCCGAACTTCCA
1 AAAATT-CCATTTTTGACCC-CGAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCA
** *
33054 AAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCAATTTTATCCCT-AAACTTCCA
1 AAAATTCCATTTTTGACC-CCGAACTTCCAAAAATTCCATTTTTA-CCCTCAAACTTCCA
* * * * ** * *
33113 AAAATTCCATTTTTGACCTCGAGACTGCAAAAAATTTCATTTTTACCCTTGAACCTACA
1 AAAATTCCATTTTTGACCCCGA-ACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCA
* * * * * * *
33172 AAAATTCAATTTGTGACCCCGAGACTTCCAAAAATTTCATTTTTTCCCCCGAACCTCCA
1 AAAATTCCATTTTTGACCCCGA-ACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCA
* * *
33231 AAAATTCCATTTTTGACCCCGAGACTTCCAAAAATTCCATTTTTACCCCCAAACCT-CT
1 AAAATTCCATTTTTGACCCCGA-ACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCA
* * * * *
33289 AAAATTACCATTTTTGACCCCGAAACTTTCAAAAGTACCA-TTTTACCCTCGAA-TGTCTA
1 AAAATT-CCATTTTTGACCCCG-AACTTCCAAAAATTCCATTTTTACCCTCAAACT-TCCA
33348 AAAATTCCATTTT
1 AAAATTCCATTTT
33361 AAACCCTAAA
Statistics
Matches: 413, Mismatches: 55, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
57 27 0.07
58 66 0.16
59 311 0.75
60 9 0.02
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCCCGAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCA
Found at i:33417 original size:59 final size:58
Alignment explanation
Indices: 33289--33419 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 58
33279 CCAAACCTCT
* * *
33289 AAAATTACCATTTTTGACCCCGAAACTTTCAAAAGTACCATTTTACCCTCGAATGTCTA
1 AAAATTACCA-TTTTAAACCCGAAACTTTCAAAAGTACCATTTTACCCTCGAAGGTCTA
* * * *
33348 AAAATT-CCATTTTAAACCCTAAACTTTCCCAAAATTACCATTTTGCCCTCG-AGGATC-C
1 AAAATTACCATTTTAAACCCGAAACTTT--CAAAAGTACCATTTTACCCTCGAAGG-TCTA
33406 AAAATTACCATTTT
1 AAAATTACCATTTT
33420 GCCCCTCGGG
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
57 15 0.25
58 11 0.18
59 35 0.57
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.33
Consensus pattern (58 bp):
AAAATTACCATTTTAAACCCGAAACTTTCAAAAGTACCATTTTACCCTCGAAGGTCTA
Found at i:33761 original size:96 final size:96
Alignment explanation
Indices: 33656--33837 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
33646 AAAACTTTAA
* * *
33656 AATCGAGGCAATA-TTCTTTTAT-TTCGAGTT-TAAAAAATTTGCGCCTTAACTTACTAGATGCA
1 AATCGAGGCAATATTTC-CTTATCTTCGA-TTCT-AAAAATTTACGCCTTAACTTACTAGATACA
**
33718 ATTTTTCTTCAAATCGAAATAATCGAATACCTTT
63 ACCTTTCTTCAAATCGAAATAATCGAATACCTTT
* * *
33752 AATCGAGGCAATGTTTCCTTATCTTCGATTCTAAGAATTTACGCCTTAACTTACTAGGTACAACC
1 AATCGAGGCAATATTTCCTTATCTTCGATTCTAAAAATTTACGCCTTAACTTACTAGATACAACC
*
33817 TTTCTTCAAATCGAGATAATC
66 TTTCTTCAAATCGAAATAATC
33838 AAACATCCTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
96 65 0.88
97 9 0.12
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATCTTCGATTCTAAAAATTTACGCCTTAACTTACTAGATACAACC
TTTCTTCAAATCGAAATAATCGAATACCTTT
Found at i:34812 original size:14 final size:15
Alignment explanation
Indices: 34788--34816 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34778 ATCACGTCAA
34788 TAAATAATTAAAAAT
1 TAAATAATTAAAAAT
34803 TAAA-AATTAAAAAT
1 TAAATAATTAAAAAT
34817 ACAAAATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAATAATTAAAAAT
Found at i:35660 original size:16 final size:17
Alignment explanation
Indices: 35639--35671 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35629 CCATAAAATC
35639 CATAC-TAAAATCAAAA
1 CATACTTAAAATCAAAA
*
35655 CATACTTAAAATTAAAA
1 CATACTTAAAATCAAAA
35672 TGTCTGAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
CATACTTAAAATCAAAA
Found at i:45440 original size:27 final size:27
Alignment explanation
Indices: 45404--45463 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
45394 AATTTCCAAC
*
45404 TAATGATTGTTTCCTTTGATCTTCTTTT
1 TAAT-ATTGTTTCCTTTGATCCTCTTTT
45432 TAATATTGTTTCCTTTGATCCTCTTTT
1 TAATATTGTTTCCTTTGATCCTCTTTT
45459 TAATA
1 TAATA
45464 GAATTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.18, C:0.15, G:0.08, T:0.58
Consensus pattern (27 bp):
TAATATTGTTTCCTTTGATCCTCTTTT
Found at i:46262 original size:146 final size:154
Alignment explanation
Indices: 46076--46403 Score: 442
Period size: 146 Copynumber: 2.2 Consensus size: 154
46066 AACAAACGGT
46076 TAGCTTCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC-
1 TAGCTTCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCA
* * ** *
46140 GAATTGAAAC-A-A-AC-GACATCTTCTTGATGAGATATTGAGAAGAAGAAC-AA-CCCACCCTC
66 G-ATTGAAACAAGACACGGACATCTTCCTGATGAGATACTGAGAAGAAGAACAAATCAAACCCAC
46199 G-ATG-TGAACAAATCTTCGAACCC
130 GCATGATGAACAAATCTTCGAACCC
* *
46222 TAGCTTCCTGATAAGATACTGAGAAGT-GAACCAAATTCGTCTTCCTGTTGAGATACAGAGAAGC
1 TAGCTTCCTGATGAGATACTGAGAAGTAG-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
* *
46286 AGATTGAAACAAATGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCC
65 AGATTGAAAC-AA-GACACGGACATCTTCCTGATGAGATACTGAGAAGAAGAACAAATCAAACCC
* *
46351 ACGCTTGATGAACAAATCTTCTAACCC
128 ACGCATGATGAACAAATCTTCGAACCC
*
46378 CAGCTTCCTGATGAGATACTGAGAAG
1 TAGCTTCCTGATGAGATACTGAGAAG
46404 CAGGTCGAAG
Statistics
Matches: 157, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
145 1 0.01
146 68 0.43
147 1 0.01
148 1 0.01
150 1 0.01
151 2 0.01
152 30 0.19
153 2 0.01
154 7 0.04
155 2 0.01
156 42 0.27
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (154 bp):
TAGCTTCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCA
GATTGAAACAAGACACGGACATCTTCCTGATGAGATACTGAGAAGAAGAACAAATCAAACCCACG
CATGATGAACAAATCTTCGAACCC
Found at i:46945 original size:19 final size:18
Alignment explanation
Indices: 46898--46990 Score: 91
Period size: 18 Copynumber: 5.2 Consensus size: 18
46888 ATTTTAATTC
*
46898 ATTTTGAGTTTAAATTTA
1 ATTTTAAGTTTAAATTTA
* *
46916 ATTTAAAGTTTAAACTTTT
1 ATTTTAAGTTTAAA-TTTA
*
46935 CTTTTAAGTTTAAATTTA
1 ATTTTAAGTTTAAATTTA
* *
46953 A-ATTAAGTTTAAAATTA
1 ATTTTAAGTTTAAATTTA
*
46970 ATTTGAA-TTTAAAATTTA
1 ATTTTAAGTTT-AAATTTA
46988 ATT
1 ATT
46991 AATTTAAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
17 18 0.30
18 27 0.45
19 15 0.25
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (18 bp):
ATTTTAAGTTTAAATTTA
Found at i:46958 original size:5 final size:6
Alignment explanation
Indices: 46906--46988 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
46896 TCATTTTGAG
*** *
46906 TTTAAA TTT-AA TTTAAA GTTTAAA CTTTTCT TTTAAG TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA
* * *
46955 -TTAAG TTTAAA ATT-AA TTTGAA TTTAAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA
46989 TTAATTTAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
5 13 0.22
6 32 0.54
7 14 0.24
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:46960 original size:17 final size:17
Alignment explanation
Indices: 46904--46998 Score: 88
Period size: 17 Copynumber: 5.5 Consensus size: 17
46894 ATTCATTTTG
46904 AGTTTAAATTTAATTTAA
1 AGTTTAAATTTAATTT-A
**
46922 AGTTTAAACTTTTCTTTTA
1 AGTTTAAA--TTTAATTTA
*
46941 AGTTTAAATTTAAATTA
1 AGTTTAAATTTAATTTA
*
46958 AGTTTAAAATTAATTTGA
1 AGTTTAAATTTAATTT-A
46976 A-TTTAAAATTTAA-TTA
1 AGTTT-AAATTTAATTTA
46992 A-TTTAAA
1 AGTTTAAA
46999 AAAGTCCATT
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.05
16 5 0.08
17 25 0.38
18 17 0.26
19 9 0.14
20 6 0.09
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (17 bp):
AGTTTAAATTTAATTTA
Found at i:47027 original size:15 final size:14
Alignment explanation
Indices: 46992--47030 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
46982 AATTTAATTA
* *
46992 ATTTAAAAAAGTCC
1 ATTTACAAATGTCC
47006 ATTTACAAATGTCC
1 ATTTACAAATGTCC
47020 ACTTTACAAAT
1 A-TTTACAAAT
47031 CCAAATTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (14 bp):
ATTTACAAATGTCC
Found at i:47780 original size:36 final size:36
Alignment explanation
Indices: 47702--47824 Score: 92
Period size: 36 Copynumber: 3.4 Consensus size: 36
47692 ATTAATGATG
* * * *
47702 TTAATAAT-ATAAATTATAATAAATAATAATAATAATA
1 TTAATAATAATAAATAACAATAATTAATAAT-AT-CTA
* * *
47739 GTAATAATAATAAATAAC-A-AATTTATAATAATGGTA
1 TTAATAATAATAAATAACAATAATTAATAAT-AT-CTA
*
47775 TTAATAGAT-ATTAATAACAATAATTAATAATATCTA
1 TTAATA-ATAATAAATAACAATAATTAATAATATCTA
47811 TTAATAATTAATAA
1 TTAATAA-TAATAA
47825 TTATTATTAA
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
35 1 0.01
36 35 0.51
37 16 0.24
38 16 0.24
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.37
Consensus pattern (36 bp):
TTAATAATAATAAATAACAATAATTAATAATATCTA
Found at i:47806 original size:10 final size:10
Alignment explanation
Indices: 47793--47841 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
47783 TATTAATAAC
47793 AATAATTAAT
1 AATAATTAAT
*
47803 AAT-ATCTATT
1 AATAAT-TAAT
47813 AATAATTAAT
1 AATAATTAAT
* *
47823 AATTATTATT
1 AATAATTAAT
47833 AATAATTAA
1 AATAATTAA
47842 AAAAAAAGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.87
11 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (10 bp):
AATAATTAAT
Found at i:47818 original size:20 final size:20
Alignment explanation
Indices: 47793--47841 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
47783 TATTAATAAC
47793 AATAATTAATAA-TATCTATT
1 AATAATTAATAATTAT-TATT
47813 AATAATTAATAATTATTATT
1 AATAATTAATAATTATTATT
47833 AATAATTAA
1 AATAATTAA
47842 AAAAAAAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATTAATAATTATTATT
Found at i:47838 original size:3 final size:3
Alignment explanation
Indices: 47703--47825 Score: 61
Period size: 3 Copynumber: 39.3 Consensus size: 3
47693 TTAATGATGT
* *
47703 TAA TAA T-A TAAA TTA TAA TAAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* * * ** * * *
47749 TAAA TAA CAA -AT TTA TAA TAA TGG TAT TAA TAGA TAT TAA TAA CAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
* *
47795 TAA TTAA TAA TATC TAT TAA TAA TTAA TAA T
1 TAA -TAA TAA TA-A TAA TAA TAA -TAA TAA T
47826 TATTATTAAT
Statistics
Matches: 90, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
2 3 0.03
3 68 0.76
4 19 0.21
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:48757 original size:59 final size:58
Alignment explanation
Indices: 48664--48873 Score: 187
Period size: 58 Copynumber: 3.6 Consensus size: 58
48654 CCTTGGAGGT
* * *
48664 CCCCCAAACTTCCAAAAA-TCCCATTTTTAACCCCAAAACT-TCTAAAAATTCTATTTTTA
1 CCCCCAAACTTCCAAAAATTACCA-TTTT-ACCCCCAAA-TGTCTAAAAATTCCATTTTTA
* * *
48723 CCCCCAAACTTCCAAAAATTACCATTTTACCCCCAGATGTCCAAAAATTCCATTTTCGA
1 CCCCCAAACTTCCAAAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTT-TA
** * * *
48782 CTTCGAAAC-TCTC-AAAATTATCC-TTTTACCCCCGAATGTCTAAAAATTCCCTTTTTA
1 CCCCCAAACTTC-CAAAAATTA-CCATTTTACCCCCAAATGTCTAAAAATTCCATTTTTA
* * * *
48839 ACCCTAAATTTTCCCAAAATTACCATTTTACCCCC
1 CCCCCAAA-CTTCCAAAAATTACCATTTTACCCCC
48874 GAGAATCCAA
Statistics
Matches: 123, Mismatches: 19, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
57 6 0.05
58 62 0.50
59 51 0.41
60 4 0.03
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (58 bp):
CCCCCAAACTTCCAAAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTTTA
Found at i:48765 original size:29 final size:29
Alignment explanation
Indices: 48718--48901 Score: 96
Period size: 29 Copynumber: 6.3 Consensus size: 29
48708 AAAATTCTAT
*
48718 TTTTACCCCCAAACT-TCCAAAAATTACCA
1 TTTTACCCCCAGA-TGTCCAAAAATTACCA
48747 TTTTACCCCCAGATGTCCAAAAATT-CCA
1 TTTTACCCCCAGATGTCCAAAAATTACCA
** * **
48775 TTTTCGACTTCGA-AACTCTC-AAAATTATCC-
1 TTTT--ACCCCCAGATGTC-CAAAAATTA-CCA
* * *
48805 TTTTACCCCC-GAATGTCTAAAAATTCCCT
1 TTTTACCCCCAG-ATGTCCAAAAATTACCA
* * * * *
48834 TTTTAACCCTAAATTTTCCCAAAATTACCA
1 TTTTACCCCCAGA-TGTCCAAAAATTACCA
*
48864 TTTTACCCCCGAGA-ATCC-AAAATTACCA
1 TTTTACCCCC-AGATGTCCAAAAATTACCA
*
48892 TTTTGCCCCC
1 TTTTACCCCC
48902 GGGTATCCGA
Statistics
Matches: 116, Mismatches: 26, Indels: 27
0.69 0.15 0.16
Matches are distributed among these distances:
28 32 0.28
29 52 0.45
30 28 0.24
31 4 0.03
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (29 bp):
TTTTACCCCCAGATGTCCAAAAATTACCA
Found at i:48775 original size:28 final size:28
Alignment explanation
Indices: 48664--48778 Score: 133
Period size: 29 Copynumber: 4.0 Consensus size: 28
48654 CCTTGGAGGT
*
48664 CCCCCAAACTTCCAAAAATCCCATTTTTAA
1 CCCCCAAACTTCCAAAAATTCCA-TTTT-A
* * *
48694 CCCCAAAACTTCTAAAAATTCTATTTTTA
1 CCCCCAAACTTCCAAAAATTCCA-TTTTA
48723 CCCCCAAACTTCCAAAAATTACCATTTTA
1 CCCCCAAACTTCCAAAAATT-CCATTTTA
*
48752 CCCCCAGA-TGTCCAAAAATTCCATTTT
1 CCCCCAAACT-TCCAAAAATTCCATTTT
48779 CGACTTCGAA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
28 8 0.11
29 41 0.55
30 26 0.35
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (28 bp):
CCCCCAAACTTCCAAAAATTCCATTTTA
Found at i:51520 original size:15 final size:15
Alignment explanation
Indices: 51500--51528 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
51490 ACTATATATG
51500 AAAAACATAAAAGAC
1 AAAAACATAAAAGAC
51515 AAAAACATAAAAGA
1 AAAAACATAAAAGA
51529 TATAATAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.10, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAACATAAAAGAC
Found at i:54320 original size:17 final size:17
Alignment explanation
Indices: 54298--54360 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
54288 TTGGAAATTG
*
54298 AATTTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
54315 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
*
54332 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
*
54349 AAATTAAATTTA
1 AATTTAAATTTA
54361 GAAAAGTCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:54420 original size:15 final size:15
Alignment explanation
Indices: 54400--54441 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
54390 CAAAAGTCCA
54400 AATTACAAATGGCCC
1 AATTACAAATGGCCC
* *
54415 AGTTACAGATGGCCC
1 AATTACAAATGGCCC
*
54430 AAATACAAATGG
1 AATTACAAATGG
54442 TTCAATTATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (15 bp):
AATTACAAATGGCCC
Done.