Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 113 of 125
Found at i:34870638 original size:60 final size:61
Alignment explanation
Indices: 34870386--34870648 Score: 236
Period size: 60 Copynumber: 4.3 Consensus size: 61
34870376 GTCGACTATT
* * * * * ** *
34870386 GCATGGCCAACACAAAAAAAATTAATTTTTTTA-CGAGATAAAAAAGGAGGTGTAAGCCATA
1 GCATGACCAACACAAAAAAATTTGATTTTTTTATCGAGACAAAAAAGG-GATGTCGGCCATG
* * * *
34870447 GCATGGCCAACACAAAAAAAAATTTGAATTTTTTATCTA-AC-AAAAAGGGAGTGTCGACCATG
1 GCATGACCAACAC--AAAAAAATTTGATTTTTTTATCGAGACAAAAAAGGGA-TGTCGGCCATG
** * *
34870509 GCATGACCAACACTCAAAAATTTGA-TTTTTTATTC-AGA-TAAAAAGGGGTGTCGGCCAT-
1 GCATGACCAACACAAAAAAATTTGATTTTTTTA-TCGAGACAAAAAAGGGATGTCGGCCATG
* *
34870567 GCGATGGCCAACACAAAAAAATTTGATTTTTTTATC-AGACAAAAAAGGGATGTCGGTCATG
1 GC-ATGACCAACACAAAAAAATTTGATTTTTTTATCGAGACAAAAAAGGGATGTCGGCCATG
*
34870628 GCCTGACCAACATCAAAAAAA
1 GCATGACCAACA-CAAAAAAA
34870649 ATTGTCAGAT
Statistics
Matches: 167, Mismatches: 23, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
58 2 0.01
59 42 0.25
60 53 0.32
61 24 0.14
62 26 0.16
63 18 0.11
64 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (61 bp):
GCATGACCAACACAAAAAAATTTGATTTTTTTATCGAGACAAAAAAGGGATGTCGGCCATG
Found at i:34887070 original size:32 final size:33
Alignment explanation
Indices: 34887034--34887100 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
34887024 TTTTGTTTTA
*
34887034 TTTTTTTCTCATTT-TCCGATGAATGCAGTT-AT
1 TTTTTTTCT-ATTTGTCCAATGAATGCAGTTGAT
* *
34887066 TTTTTTTCTTTTTGTTCAATGAATGCAGTTGAT
1 TTTTTTTCTATTTGTCCAATGAATGCAGTTGAT
34887099 TT
1 TT
34887101 CTTTCTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 3 0.10
32 23 0.77
33 4 0.13
ACGTcount: A:0.18, C:0.12, G:0.13, T:0.57
Consensus pattern (33 bp):
TTTTTTTCTATTTGTCCAATGAATGCAGTTGAT
Found at i:34887363 original size:2 final size:2
Alignment explanation
Indices: 34887356--34887381 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34887346 TGTCTTTGCG
34887356 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
34887382 TTTTCCCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:34899569 original size:41 final size:41
Alignment explanation
Indices: 34899524--34899603 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
34899514 CTTAAAATTC
*
34899524 ATACAACAATATTGTATCACATATTGTACTATTATTAATAT
1 ATACAACAATATAGTATCACATATTGTACTATTATTAATAT
* *
34899565 ATACAACAATATAGTATCACATATTGTTCTATTGTTAAT
1 ATACAACAATATAGTATCACATATTGTACTATTATTAAT
34899604 TTAATTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.41
Consensus pattern (41 bp):
ATACAACAATATAGTATCACATATTGTACTATTATTAATAT
Found at i:34903351 original size:22 final size:22
Alignment explanation
Indices: 34903326--34903368 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
34903316 AACAATTCAG
34903326 CACGCTGCGCAGTCTCGGCGCA
1 CACGCTGCGCAGTCTCGGCGCA
34903348 CACGCTGCGCAGTCTCGGCGC
1 CACGCTGCGCAGTCTCGGCGC
34903369 TAGCTTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.12, C:0.42, G:0.33, T:0.14
Consensus pattern (22 bp):
CACGCTGCGCAGTCTCGGCGCA
Found at i:34913110 original size:21 final size:21
Alignment explanation
Indices: 34913070--34913109 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
34913060 ATATTAAAAA
34913070 TTTGGTTCAATTAATTTTTTG
1 TTTGGTTCAATTAATTTTTTG
*
34913091 TTTGGTTCAA-TATTTTTTT
1 TTTGGTTCAATTAATTTTTT
34913110 TCGGATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.65
Consensus pattern (21 bp):
TTTGGTTCAATTAATTTTTTG
Found at i:34913619 original size:23 final size:22
Alignment explanation
Indices: 34913586--34913638 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
34913576 AATAATTAAT
*
34913586 TTTAATTGTAATTA-TATAAATA
1 TTTACTTGTAATTAGT-TAAATA
*
34913608 TATTACTTGTAATTAGTTACATA
1 T-TTACTTGTAATTAGTTAAATA
34913631 TTTACTTG
1 TTTACTTG
34913639 ACATTGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.30
23 18 0.67
24 1 0.04
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.51
Consensus pattern (22 bp):
TTTACTTGTAATTAGTTAAATA
Found at i:34923542 original size:44 final size:44
Alignment explanation
Indices: 34923469--34923554 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
34923459 TCTTACTAAA
*
34923469 AACCAACACAATAGATTAAGTTCTAAGCAAAACCAA-AAAACAAT
1 AACCAACACAATAAATTAAGTTCTAAGCAAAA-CAAGAAAACAAT
*
34923513 AACCAACACAATAAATTGAAGTTGT-AGCAAAACAAGAAAACA
1 AACCAACACAATAAATT-AAGTTCTAAGCAAAACAAGAAAACA
34923555 TCTTAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
43 3 0.08
44 29 0.76
45 6 0.16
ACGTcount: A:0.57, C:0.19, G:0.09, T:0.15
Consensus pattern (44 bp):
AACCAACACAATAAATTAAGTTCTAAGCAAAACAAGAAAACAAT
Found at i:34925613 original size:15 final size:15
Alignment explanation
Indices: 34925593--34925623 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
34925583 AAAATTGAGC
34925593 AACTAAAGATAATTA
1 AACTAAAGATAATTA
34925608 AACTAAAGATAATTA
1 AACTAAAGATAATTA
34925623 A
1 A
34925624 TTACATCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
AACTAAAGATAATTA
Found at i:34937815 original size:41 final size:38
Alignment explanation
Indices: 34937720--34937818 Score: 92
Period size: 41 Copynumber: 2.6 Consensus size: 38
34937710 AGCAATAGAG
* *
34937720 TGACACCCAGTGTCTCATCG-GCCTAGCCGAAGTAAAG
1 TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAA
** ** * *
34937757 TGGTACCCAGTACCTCATCGAATCTATCCGAAGTAAAATAA
1 TGACACCCAGTGTCTCATCGAACCTAGCCGAAGT--AA-AA
34937798 TGACACCCAGTGTCTCATCGA
1 TGACACCCAGTGTCTCATCGA
34937819 CTCAAGGTCG
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
37 16 0.35
38 10 0.22
40 2 0.04
41 18 0.39
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (38 bp):
TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAA
Found at i:34937946 original size:6 final size:6
Alignment explanation
Indices: 34937937--34937965 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
34937927 TTAATTCTAA
34937937 TTTCAC TTTCAC TTTCAC TTTCAC TTTCA
1 TTTCAC TTTCAC TTTCAC TTTCAC TTTCA
34937966 ATTTTGATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTCAC
Found at i:34940918 original size:24 final size:24
Alignment explanation
Indices: 34940890--34940946 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
34940880 TAGAGTAATA
* *
34940890 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
34940914 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
34940938 AGAGTTTAA
1 AGAGTTTAA
34940947 TTGAAAGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:34940947 original size:24 final size:24
Alignment explanation
Indices: 34940906--34940952 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
34940896 TGACTCAAAT
34940906 AAATAAACAGAGTTTAATTGAAAC
1 AAATAAACAGAGTTTAATTGAAAC
34940930 AAATAAACAGAGTTTAATTGAAA
1 AAATAAACAGAGTTTAATTGAAA
34940953 GATTATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (24 bp):
AAATAAACAGAGTTTAATTGAAAC
Found at i:34942156 original size:24 final size:24
Alignment explanation
Indices: 34942103--34942164 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
34942093 GTTAATTTTT
* *
34942103 TTATTAAAGT-TATTATTTAATAA
1 TTATTAAAATATAATATTTAATAA
* *
34942126 TTAATTAAAATATAATATTTTATTA
1 TT-ATTAAAATATAATATTTAATAA
*
34942151 TTATTATAATATAA
1 TTATTAAAATATAA
34942165 ATAAAAGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 2 0.06
24 18 0.56
25 12 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTATTAAAATATAATATTTAATAA
Found at i:34943189 original size:16 final size:18
Alignment explanation
Indices: 34943164--34943200 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
34943154 ATATGGGACA
*
34943164 AAAATGAGAA-TGATGTG
1 AAAATGAGAATTGAAGTG
34943181 AAAAT-AGAATTGAAGTG
1 AAAATGAGAATTGAAGTG
34943198 AAA
1 AAA
34943201 TTTGATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (18 bp):
AAAATGAGAATTGAAGTG
Found at i:34945720 original size:16 final size:16
Alignment explanation
Indices: 34945685--34945719 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
34945675 TCCCCGTTTA
*
34945685 TTTTCTAATTTCAATT
1 TTTTCTAATTCCAATT
34945701 TTTTCT-ATTCCAATT
1 TTTTCTAATTCCAATT
34945716 TTTT
1 TTTT
34945720 TTCACTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTCTAATTCCAATT
Found at i:34946011 original size:22 final size:23
Alignment explanation
Indices: 34945963--34946012 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
34945953 TTTATTTGAT
* * *
34945963 AAAATATTTTGATATTATAAATT
1 AAAATATTTTGAAAATATAAATG
*
34945986 AAAATATTTT-AAAATATAAGTG
1 AAAATATTTTGAAAATATAAATG
34946008 AAAAT
1 AAAAT
34946013 TGATAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (23 bp):
AAAATATTTTGAAAATATAAATG
Found at i:34946126 original size:20 final size:20
Alignment explanation
Indices: 34946101--34946139 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34946091 ATAATTTTAA
*
34946101 AATCAAGTTAAAATGATTTC
1 AATCAAGTTAAAATCATTTC
34946121 AATCAAGTTAAAATCATTT
1 AATCAAGTTAAAATCATTT
34946140 TAACACTTTA
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:0.08, T:0.36
Consensus pattern (20 bp):
AATCAAGTTAAAATCATTTC
Found at i:34950646 original size:23 final size:23
Alignment explanation
Indices: 34950608--34950655 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
34950598 TCTTTTATTG
* *
34950608 ATGTTTATA-CTTTTTTGGTGAAA
1 ATGTTTATACCCTTTTAGGT-AAA
34950631 ATGTTTATACCCTTTTAGGTAAA
1 ATGTTTATACCCTTTTAGGTAAA
34950654 AT
1 AT
34950656 TTTTGATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (23 bp):
ATGTTTATACCCTTTTAGGTAAA
Found at i:34951946 original size:29 final size:29
Alignment explanation
Indices: 34951860--34952027 Score: 99
Period size: 29 Copynumber: 5.7 Consensus size: 29
34951850 CAAATGGAGT
* * * *
34951860 CAAAAATGTAATTTTTAGATGCCCGGGGG
1 CAAAAAGGTAATTTTTGGATACTCGGGGG
* * **
34951889 TAAAACGGTAA-TTTTGGATACTTTAGGGG
1 CAAAAAGGTAATTTTTGGATAC-TCGGGGG
*
34951918 CAAAACGGTAATTTTTGGATACTCGGGGGG
1 CAAAAAGGTAATTTTTGGATACTC-GGGGG
* * * *
34951948 TAAAAAATGTAATTTTTGGACA-TCCGAGGG
1 -CAAAAAGGTAATTTTTGGATACT-CGGGGG
* * * * *
34951978 TAAAATA-ATAATTTTTTGAAACTCGGAGG
1 CAAAA-AGGTAATTTTTGGATACTCGGGGG
*
34952007 CAAAAATGTAATTTTTGGATA
1 CAAAAAGGTAATTTTTGGATA
34952028 TTTAGGGGTA
Statistics
Matches: 105, Mismatches: 26, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
28 9 0.09
29 57 0.54
30 21 0.20
31 18 0.17
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.32
Consensus pattern (29 bp):
CAAAAAGGTAATTTTTGGATACTCGGGGG
Found at i:34951981 original size:30 final size:31
Alignment explanation
Indices: 34951925--34952025 Score: 104
Period size: 29 Copynumber: 3.4 Consensus size: 31
34951915 GGGCAAAACG
* *
34951925 GTAATTTTTGGATACTCGGGGGGTAAAAAAT
1 GTAATTTTTGGAAACTCGGAGGGTAAAAAAT
* *
34951956 GTAATTTTTGGACA-TCCGAGGGTAAAATAA-
1 GTAATTTTTGGAAACTCGGAGGGTAAAA-AAT
* *
34951986 -TAATTTTTTGAAACTCGGA-GG-CAAAAAT
1 GTAATTTTTGGAAACTCGGAGGGTAAAAAAT
34952014 GTAATTTTTGGA
1 GTAATTTTTGGA
34952026 TATTTAGGGG
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
27 2 0.03
28 3 0.05
29 23 0.40
30 15 0.26
31 15 0.26
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.34
Consensus pattern (31 bp):
GTAATTTTTGGAAACTCGGAGGGTAAAAAAT
Found at i:34952040 original size:29 final size:29
Alignment explanation
Indices: 34952008--34952359 Score: 241
Period size: 30 Copynumber: 11.9 Consensus size: 29
34951998 ACTCGGAGGC
34952008 AAAAATGTAATTTTTGGATA-TTTAGGGGT
1 AAAAATGTAATTTTTGGA-AGTTTAGGGGT
* * * *
34952037 -AAAATGTTAGTTTTTAGATGTTTGGGGGT
1 AAAAATG-TAATTTTTGGAAGTTTAGGGGT
* * *
34952066 AAAAAAGTAATTTTTGGAAG-TTCGAGGT
1 AAAAATGTAATTTTTGGAAGTTTAGGGGT
* *
34952094 CAAAAATGTAATTTTTGTGAAG-TTCGAGG-
1 -AAAAATGTAATTTTTG-GAAGTTTAGGGGT
* * ** *
34952123 ATCAAATGGTATTTTTTGGAAGTTCGGGGGC
1 A-AAAAT-GTAATTTTTGGAAGTTTAGGGGT
* * *
34952154 AAAAATTTGATTTTTGGAAGGTTTAAGGGT
1 AAAAATGTAATTTTTGGAA-GTTTAGGGGT
* * *
34952184 AAAATTGTAATTTTTGGAAGTTTAGAGGC
1 AAAAATGTAATTTTTGGAAGTTTAGGGGT
* * * *
34952213 AAAATTTTGATTTTTGGAAAGTTTAAGGGT
1 AAAAATGTAATTTTTGG-AAGTTTAGGGGT
*
34952243 -AAAATGTAATTTTTGTGAAG-TTCGAGGGT
1 AAAAATGTAATTTTTG-GAAGTTTAG-GGGT
* * *
34952272 TAAAATGCAATTTTTGAAAAGTTTAGGGGT
1 AAAAATGTAATTTTTG-GAAGTTTAGGGGT
* *
34952302 TAAAATGTAAATTTTGAGAAGTTTAGGGGT
1 AAAAATGTAATTTTTG-GAAGTTTAGGGGT
* * *
34952332 CAAAATATGATTTTTGGATAGTTTAGGG
1 AAAAATGTAATTTTTGGA-AGTTTAGGG
34952360 ACTTTTTGGG
Statistics
Matches: 256, Mismatches: 51, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
28 15 0.06
29 103 0.40
30 134 0.52
31 4 0.02
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTTAGGGGT
Found at i:34952118 original size:30 final size:29
Alignment explanation
Indices: 34951950--34952287 Score: 155
Period size: 29 Copynumber: 11.6 Consensus size: 29
34951940 TCGGGGGGTA
*
34951950 AAAAATGTAATTTTTGGACA-TCCGAGGGT-
1 AAAAATGTAATTTTTGGA-AGTTCGA-GGTC
* * **
34951979 -AAAATAATAATTTTTTGAAACTCGGAGG-C
1 AAAAAT-GTAATTTTTGGAAGTTC-GAGGTC
* * *
34952008 AAAAATGTAATTTTTGGATATTTAGGGGT-
1 AAAAATGTAATTTTTGGA-AGTTCGAGGTC
* * * * *
34952037 -AAAATGTTAGTTTTTAGATGTTTGGGGGT-
1 AAAAATG-TAATTTTTGGAAG-TTCGAGGTC
*
34952066 AAAAAAGTAATTTTTGGAAGTTCGAGGTC
1 AAAAATGTAATTTTTGGAAGTTCGAGGTC
34952095 AAAAATGTAATTTTTGTGAAGTTCGAGGATC
1 AAAAATGTAATTTTTG-GAAGTTCGAGG-TC
* * *
34952126 --AAATGGTATTTTTTGGAAGTTCGGGGGC
1 AAAAAT-GTAATTTTTGGAAGTTCGAGGTC
* * **
34952154 AAAAATTTGATTTTTGGAAGGTTTAAGGGT-
1 AAAAATGTAATTTTTGGAA-GTTCGA-GGTC
* *
34952184 AAAATTGTAATTTTTGGAAGTTTAGAGG-C
1 AAAAATGTAATTTTTGGAAG-TTCGAGGTC
* * * **
34952213 AAAATTTTGATTTTTGGAAAGTTTAAGGGT-
1 AAAAATGTAATTTTTGG-AAGTTCGA-GGTC
34952243 -AAAATGTAATTTTTGTGAAGTTCGAGGGT-
1 AAAAATGTAATTTTTG-GAAGTTCGA-GGTC
* *
34952272 TAAAATGCAATTTTTG
1 AAAAATGTAATTTTTG
34952288 AAAAGTTTAG
Statistics
Matches: 237, Mismatches: 47, Indels: 49
0.71 0.14 0.15
Matches are distributed among these distances:
28 19 0.08
29 134 0.57
30 80 0.34
31 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTCGAGGTC
Found at i:34952141 original size:59 final size:57
Alignment explanation
Indices: 34952009--34952356 Score: 240
Period size: 59 Copynumber: 5.9 Consensus size: 57
34951999 CTCGGAGGCA
* * * * * * **
34952009 AAAATGTAATTTTTGGATATTTAGGGGT--AAAATGTTAGTTTTTAGATGTTTGGGGGT
1 AAAATGTAATTTTTGGA-AGTTCGAGGTCAAAAATG-TAATTTTTGGAAGTTTAAGGGT
* ** *
34952066 AAAAAAGTAATTTTTGGAAGTTCGAGGTCAAAAATGTAATTTTTGTGAAGTTCGAGGAT
1 -AAAATGTAATTTTTGGAAGTTCGAGGTCAAAAATGTAATTTTTG-GAAGTTTAAGGGT
* * * * * *
34952125 CAAATGGTATTTTTTGGAAGTTCGGGGGCAAAAATTTGATTTTTGGAAGGTTTAAGGGT
1 AAAAT-GTAATTTTTGGAAGTTCGAGGTCAAAAATGTAATTTTTGGAA-GTTTAAGGGT
* * * *
34952184 AAAATTGTAATTTTTGGAAGTTTAGAGG-CAAAATTTTGATTTTTGGAAAGTTTAAGGGT
1 AAAA-TGTAATTTTTGGAAG-TTCGAGGTCAAAAATGTAATTTTTGG-AAGTTTAAGGGT
* * * *
34952243 AAAATGTAATTTTTGTGAAGTTCGAGGGT-TAAAATGCAATTTTTGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTTG-GAAGTTCGA-GGTCAAAAATGTAATTTTTG-GAAGTTTAAGGG-T
* * *
34952303 AAAATGTAAATTTTGAGAAGTTTAGGGGTCAAAATATG--ATTTTTGGATAGTTTA
1 AAAATGTAATTTTTG-GAAG-TTCGAGGTCAAAA-ATGTAATTTTTGGA-AGTTTA
34952357 GGGACTTTTT
Statistics
Matches: 234, Mismatches: 39, Indels: 32
0.77 0.13 0.10
Matches are distributed among these distances:
57 7 0.03
58 44 0.19
59 131 0.56
60 43 0.18
61 6 0.03
62 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.39
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAGTTCGAGGTCAAAAATGTAATTTTTGGAAGTTTAAGGGT
Found at i:34952712 original size:15 final size:15
Alignment explanation
Indices: 34952692--34952722 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
34952682 ATCGAATGCA
34952692 TAAATAACCCAATTT
1 TAAATAACCCAATTT
34952707 TAAATAACCCAATTT
1 TAAATAACCCAATTT
34952722 T
1 T
34952723 TGAAACACGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATAACCCAATTT
Found at i:34953999 original size:11 final size:11
Alignment explanation
Indices: 34953994--34954025 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
34953984 TAATTAAATT
34953994 TAAATTTAAAA
1 TAAATTTAAAA
*
34954005 TAAATTCAAAA
1 TAAATTTAAAA
34954016 TAAATTTAAA
1 TAAATTTAAA
34954026 TTTATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:34954008 original size:17 final size:17
Alignment explanation
Indices: 34953987--34954055 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 17
34953977 TAATTTTTAA
*
34953987 TTAAATTTAAATTTAAA-
1 TTAAATTTAAA-ATAAAT
* *
34954004 ATAAATTCAAAATAAAT
1 TTAAATTTAAAATAAAT
* *
34954021 TTAAATTTATATTAAAT
1 TTAAATTTAAAATAAAT
* *
34954038 TCAAACTTAAAATAAAT
1 TTAAATTTAAAATAAAT
34954055 T
1 T
34954056 AAAAAATGGG
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
16 4 0.10
17 36 0.90
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:34954020 original size:28 final size:28
Alignment explanation
Indices: 34953988--34954042 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
34953978 AATTTTTAAT
34953988 TAAATTTAAATTTAAAATAAATTCAAAA
1 TAAATTTAAATTTAAAATAAATTCAAAA
* *
34954016 TAAATTTAAATTTATATTAAATTCAAA
1 TAAATTTAAATTTAAAATAAATTCAAA
34954043 CTTAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAATTTAAATTTAAAATAAATTCAAAA
Found at i:34954053 original size:28 final size:28
Alignment explanation
Indices: 34953988--34954060 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
34953978 AATTTTTAAT
*
34953988 TAAATTTAAATTTAAAATAAATTCAAAA
1 TAAATATAAATTTAAAATAAATTCAAAA
* * * *
34954016 TAAATTTAAATTTATATTAAATTCAAACT
1 TAAATATAAATTTAAAATAAATTCAAA-A
*
34954045 TAAA-ATAAATTAAAAA
1 TAAATATAAATTTAAAA
34954061 ATGGGTTCTC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
28 33 0.89
29 4 0.11
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (28 bp):
TAAATATAAATTTAAAATAAATTCAAAA
Found at i:34954758 original size:105 final size:108
Alignment explanation
Indices: 34954573--34954790 Score: 302
Period size: 105 Copynumber: 2.0 Consensus size: 108
34954563 ATGTGCAACC
*
34954573 ATCATGATTGCATTTGAGTCATGTCGAATTTTTTTTTGAAAAGCCTCGACTTTTATTTTAAAAAT
1 ATCATGATTGCATTTGAATCATGTCGAA-TTTTTTTTGAAAAGCCTCGACTTTTATTTTAAAAAT
* *
34954638 AAAAAATTGAGTCGTCACCAATTA-TTTAACTAAGTGTGATTGG
65 AAAAAATTGAATCGTCACCAATAATTTTAACTAAGTGTGATTGG
*
34954681 ATCATGATTGCATTTGAATCATG-CTGAA-TTTTTTT-AAAAG-TTCTGACTTTTATTTTAAAAA
1 ATCATGATTGCATTTGAATCATGTC-GAATTTTTTTTGAAAAGCCTC-GACTTTTATTTTAAAAA
** * *
34954742 TTGAAAATTGAATCGTCACCAATAATTTTAATTAGGTGTGATTGG
64 TAAAAAATTGAATCGTCACCAATAATTTTAACTAAGTGTGATTGG
34954787 ATCA
1 ATCA
34954791 CCTTAAAATA
Statistics
Matches: 99, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
104 2 0.02
105 43 0.43
106 28 0.28
107 1 0.01
108 25 0.25
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (108 bp):
ATCATGATTGCATTTGAATCATGTCGAATTTTTTTTGAAAAGCCTCGACTTTTATTTTAAAAATA
AAAAATTGAATCGTCACCAATAATTTTAACTAAGTGTGATTGG
Found at i:34957835 original size:11 final size:11
Alignment explanation
Indices: 34957819--34957933 Score: 167
Period size: 11 Copynumber: 10.5 Consensus size: 11
34957809 TTGCCAAAGT
34957819 TATTAGATTTA
1 TATTAGATTTA
*
34957830 TATTAGATTTG
1 TATTAGATTTA
*
34957841 TATTATATTTA
1 TATTAGATTTA
34957852 TATTAGATTTA
1 TATTAGATTTA
34957863 TATTAGATTTA
1 TATTAGATTTA
*
34957874 TATTAGATTTG
1 TATTAGATTTA
* *
34957885 TGTTATATTTA
1 TATTAGATTTA
*
34957896 TATTATATTTA
1 TATTAGATTTA
*
34957907 TTTTAGATTTA
1 TATTAGATTTA
34957918 TATTAGATTTA
1 TATTAGATTTA
34957929 TATTA
1 TATTA
34957934 CTGTCTTTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 92 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (11 bp):
TATTAGATTTA
Found at i:34957867 original size:44 final size:44
Alignment explanation
Indices: 34957819--34957933 Score: 194
Period size: 44 Copynumber: 2.6 Consensus size: 44
34957809 TTGCCAAAGT
34957819 TATTAGATTTATATTAGATTTGTATTATATTTATATTAGATTTA
1 TATTAGATTTATATTAGATTTGTATTATATTTATATTAGATTTA
* *
34957863 TATTAGATTTATATTAGATTTGTGTTATATTTATATTATATTTA
1 TATTAGATTTATATTAGATTTGTATTATATTTATATTAGATTTA
* *
34957907 TTTTAGATTTATATTAGATTTATATTA
1 TATTAGATTTATATTAGATTTGTATTA
34957934 CTGTCTTTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (44 bp):
TATTAGATTTATATTAGATTTGTATTATATTTATATTAGATTTA
Found at i:34959037 original size:23 final size:22
Alignment explanation
Indices: 34959007--34959127 Score: 75
Period size: 23 Copynumber: 5.3 Consensus size: 22
34958997 GCTGAGAAAA
34959007 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
* *
34959029 CCAGTAAGCATACATAGTGCAAT
1 -CAGTAAGCACACACAGTGCAAT
* * * * *
34959052 CAGTAGGTGA-ATATAGCGCAAAT
1 CAGTAAG-CACACACAGTGC-AAT
* *
34959075 CAGTAGGCACACA-AGATGCGAAA
1 CAGTAAGCACACACAG-TGC-AAT
* *
34959098 CAGTAAGCACACAAAGTGCAAAA
1 CAGTAAGCACACACAGTGC-AAT
34959121 CAGTAAG
1 CAGTAAG
34959128 TGCGCTAGCG
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
22 16 0.20
23 62 0.77
24 2 0.03
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.15
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:34962772 original size:16 final size:18
Alignment explanation
Indices: 34962733--34962766 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34962723 TAAGTTTATA
34962733 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
34962750 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
34962767 AATTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:34965373 original size:20 final size:21
Alignment explanation
Indices: 34965345--34965384 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
34965335 ATAAAAGAAA
*
34965345 AATTCAATTTTATT-GGTTTC
1 AATTCAATTTGATTAGGTTTC
*
34965365 AATTGAATTTGATTAGGTTT
1 AATTCAATTTGATTAGGTTT
34965385 GATAATAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.53
Consensus pattern (21 bp):
AATTCAATTTGATTAGGTTTC
Found at i:34970483 original size:12 final size:12
Alignment explanation
Indices: 34970450--34970484 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
34970440 ATAGTTATAG
*
34970450 ATTATTATTATT
1 ATTATTATTGTT
34970462 ATTATTATTGTT
1 ATTATTATTGTT
*
34970474 ATTATAATTGT
1 ATTATTATTGT
34970485 AAAGCAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (12 bp):
ATTATTATTGTT
Found at i:34971240 original size:11 final size:11
Alignment explanation
Indices: 34971224--34971327 Score: 154
Period size: 11 Copynumber: 9.5 Consensus size: 11
34971214 TTGCCAAAGT
34971224 TATTAGATTTA
1 TATTAGATTTA
*
34971235 TATTAGATTTG
1 TATTAGATTTA
*
34971246 TATTATATTTA
1 TATTAGATTTA
34971257 TATTAGATTTA
1 TATTAGATTTA
34971268 TATTAGATTTA
1 TATTAGATTTA
*
34971279 TATTAGATTTG
1 TATTAGATTTA
* *
34971290 TGTTATATTTA
1 TATTAGATTTA
*
34971301 TTTTAGATTTA
1 TATTAGATTTA
34971312 TATTAGATTTA
1 TATTAGATTTA
34971323 TATTA
1 TATTA
34971328 CTGTCTTTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 82 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.58
Consensus pattern (11 bp):
TATTAGATTTA
Found at i:34971272 original size:44 final size:44
Alignment explanation
Indices: 34971224--34971327 Score: 190
Period size: 44 Copynumber: 2.4 Consensus size: 44
34971214 TTGCCAAAGT
34971224 TATTAGATTTATATTAGATTTGTATTATATTTATATTAGATTTA
1 TATTAGATTTATATTAGATTTGTATTATATTTATATTAGATTTA
* *
34971268 TATTAGATTTATATTAGATTTGTGTTATATTTATTTTAGATTTA
1 TATTAGATTTATATTAGATTTGTATTATATTTATATTAGATTTA
34971312 TATTAGATTTATATTA
1 TATTAGATTTATATTA
34971328 CTGTCTTTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.58
Consensus pattern (44 bp):
TATTAGATTTATATTAGATTTGTATTATATTTATATTAGATTTA
Found at i:34974678 original size:3 final size:3
Alignment explanation
Indices: 34974670--34974702 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
34974660 TGATTTGATT
34974670 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
34974703 CAAAGCAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:34976967 original size:11 final size:11
Alignment explanation
Indices: 34976951--34977031 Score: 117
Period size: 11 Copynumber: 7.4 Consensus size: 11
34976941 GTTGCCAAAT
*
34976951 TATTAGATTTA
1 TATTATATTTA
* *
34976962 TATTAGATTTG
1 TATTATATTTA
34976973 TATTATATTTA
1 TATTATATTTA
34976984 TATTATATTTA
1 TATTATATTTA
34976995 TATTATATTTA
1 TATTATATTTA
* *
34977006 TTTTAGATTTA
1 TATTATATTTA
34977017 TATTATATTTA
1 TATTATATTTA
34977028 TATT
1 TATT
34977032 GGTGCTTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (11 bp):
TATTATATTTA
Found at i:34981823 original size:14 final size:15
Alignment explanation
Indices: 34981800--34981828 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34981790 AGAGTATAGT
34981800 AAAATATTAAAAAAA
1 AAAATATTAAAAAAA
34981815 AAAAT-TTAAAAAAA
1 AAAATATTAAAAAAA
34981829 GATACATGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATATTAAAAAAA
Found at i:34982769 original size:11 final size:11
Alignment explanation
Indices: 34982753--34982823 Score: 61
Period size: 11 Copynumber: 6.5 Consensus size: 11
34982743 GTTGCCAAAT
34982753 TATTAGATTTA
1 TATTAGATTTA
*
34982764 TATTAGATTTG
1 TATTAGATTTA
* ***
34982775 TTTTATCCTTA
1 TATTAGATTTA
**
34982786 TATTTTATTTA
1 TATTAGATTTA
*
34982797 TTTTAGATTTA
1 TATTAGATTTA
*
34982808 TTTTAGATTTA
1 TATTAGATTTA
34982819 TATTA
1 TATTA
34982824 CTGTCTTTTT
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
11 46 1.00
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (11 bp):
TATTAGATTTA
Found at i:34982820 original size:33 final size:33
Alignment explanation
Indices: 34982759--34982822 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
34982749 AAATTATTAG
* **
34982759 ATTTATATTAGATTTGTTTTATCCTTATATTTT
1 ATTTATATTAGATTTATTTTAGACTTATATTTT
* *
34982792 ATTTATTTTAGATTTATTTTAGATTTATATT
1 ATTTATATTAGATTTATTTTAGACTTATATT
34982823 ACTGTCTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (33 bp):
ATTTATATTAGATTTATTTTAGACTTATATTTT
Found at i:34983688 original size:153 final size:154
Alignment explanation
Indices: 34983469--34983771 Score: 484
Period size: 153 Copynumber: 2.0 Consensus size: 154
34983459 TAATTATAAG
* *
34983469 ATTGAAGAGTGTTTTGAAAACTTTTGAAAAGGGATATCCGATTTGCATGAATTACGAAAATCACA
1 ATTGAAGAGTGTTTCGAAAACTTTTGAAAAGGGATATCCGATTCGCATGAATTACGAAAATCACA
34983534 CTTAACACGTTAAAGCGCGATTCCTCGAAGTTTTCACACGAAAGGACATTGCCTCGTTTTAAAAT
66 CTTAACACGTTAAAGCGCGATTCCTCGAAGTTTTCACACGAAAGGACATTGCCTCGTTTTAAAAT
*
34983599 TATTCGTGATATAGATATATAAAA
131 TATTCGTAATATAGATATATAAAA
* *
34983623 ATTGAAG-GATGTTTCGAAAACTTTTGAAGA-GGATATTCGATTCGCATGAATTACGAAAATCAC
1 ATTGAAGAG-TGTTTCGAAAACTTTTGAAAAGGGATATCCGATTCGCATGAATTACGAAAATCAC
* ** * *
34983686 ACTTAATACGTTAAAGCGCGATTTTTCGGAGTTTTCACACGACAGGACATTGCCTCGTTTTAAAA
65 ACTTAACACGTTAAAGCGCGATTCCTCGAAGTTTTCACACGAAAGGACATTGCCTCGTTTTAAAA
*
34983751 TTATTTGTAATATAGATATAT
130 TTATTCGTAATATAGATATAT
34983772 GTTTTGAGAA
Statistics
Matches: 137, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
153 111 0.81
154 26 0.19
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (154 bp):
ATTGAAGAGTGTTTCGAAAACTTTTGAAAAGGGATATCCGATTCGCATGAATTACGAAAATCACA
CTTAACACGTTAAAGCGCGATTCCTCGAAGTTTTCACACGAAAGGACATTGCCTCGTTTTAAAAT
TATTCGTAATATAGATATATAAAA
Found at i:34984320 original size:29 final size:28
Alignment explanation
Indices: 34984287--34984512 Score: 130
Period size: 29 Copynumber: 7.8 Consensus size: 28
34984277 TTGACTTCTA
34984287 GGGGTAAAAATGTAATTTTTGGTGAAATT
1 GGGGTAAAAATGTAA-TTTTGGTGAAATT
* *
34984316 AGGGTCAAAAATGGAATTTT-G-GAAAGTTT
1 GGGGT-AAAAATGTAATTTTGGTGAAA--TT
** *
34984345 GGAGGTAAAACGGTAATTTTTGGTGAAATC
1 GG-GGTAAAAATGTAA-TTTTGGTGAAATT
34984375 GGGGTTAAAAATG-AGATTTT-G-GAAAGTTT
1 GGGG-TAAAAATGTA-ATTTTGGTGAAA--TT
34984404 GGGGGT-AAAATGGTAATTTTGGTGAAATT
1 -GGGGTAAAAAT-GTAATTTTGGTGAAATT
* *
34984433 AGGGTTAAAAATG-AGATTTT--AGAAAGTT
1 -GGGGTAAAAATGTA-ATTTTGGTGAAA-TT
34984461 CGGGAGT-AAAATGGTAATTTTGGTGAAATT
1 -GGG-GTAAAAAT-GTAATTTTGGTGAAATT
* *
34984491 GGGGTTAAAAATGGAATCTTGG
1 GGGG-TAAAAATGTAATTTTGG
34984513 AAAGTTCGGG
Statistics
Matches: 153, Mismatches: 18, Indels: 52
0.69 0.08 0.23
Matches are distributed among these distances:
27 12 0.08
28 19 0.12
29 64 0.42
30 45 0.29
31 9 0.06
32 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (28 bp):
GGGGTAAAAATGTAATTTTGGTGAAATT
Found at i:34984425 original size:117 final size:120
Alignment explanation
Indices: 34984287--34984636 Score: 434
Period size: 117 Copynumber: 3.0 Consensus size: 120
34984277 TTGACTTCTA
* *
34984287 GGGGTAAAAAT-GTAATTTTTGGTGAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTTGGAGGT
1 GGGGTAAAAATGGTAACTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGGAGGT
*
34984351 AAAACGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAG-ATTTTGGAAAGTTTG
66 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGAATTTTGGAAAGTTTG
* *
34984405 GGGGT-AAAATGGTAA-TTTTGGTGAAATTAGGGTTAAAAAT-GAGATTTTAGAAAGTTCGG-GA
1 GGGGTAAAAATGGTAACTTTTGGTGAAATTAGGGTTAAAAATGGA-ATTTTGGAAAGTTTGGAG-
* * *
34984466 GTAAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATG-GAATCTTGGAAAGTTCG
64 GTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGAATTTTGGAAAGTTTG
* * ** * *
34984521 GGAGT-AAAATGGTAACTTTTAGAAAAATCAGGGTTAAAAATGGAATTTTGGAAA-TTTTGAGGG
1 GGGGTAAAAATGGTAACTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGGA-GG
** * *
34984584 TAAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAAT-AGAATTTTGAAAAGTT
65 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGAATTTTGGAAAGTT
34984637 CGAGGTCAAA
Statistics
Matches: 201, Mismatches: 21, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
115 1 0.00
116 58 0.29
117 96 0.48
118 46 0.23
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (120 bp):
GGGGTAAAAATGGTAACTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGGAGGT
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGAATTTTGGAAAGTTTG
Found at i:34984452 original size:58 final size:59
Alignment explanation
Indices: 34984287--34984636 Score: 422
Period size: 59 Copynumber: 6.0 Consensus size: 59
34984277 TTGACTTCTA
* *
34984287 GGGGTAAAAAT-GTAATTTTTGGTGAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTTG
1 GGGGT-AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
* * *
34984346 GAGGTAAAACGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-GAGATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGA-ATTTTGGAAAGTTTG
* * *
34984405 GGGGTAAAATGGTAA-TTTTGGTGAAATTAGGGTTAAAAAT-GAGATTTTAGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGA-ATTTTGGAAAGTTTG
* ** * *
34984463 GGAGTAAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATGGAATCTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
* * * ** *
34984521 GGAGTAAAATGGTAACTTTTAGAAAAATCAGGGTTAAAAATGGAATTTTGGAAATTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
* ** * *
34984580 AGGGTAAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATAGAATTTTGAAAAGTT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTT
34984637 CGAGGTCAAA
Statistics
Matches: 257, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
58 111 0.43
59 146 0.57
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTG
Found at i:34984528 original size:29 final size:32
Alignment explanation
Indices: 34984454--34984535 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 32
34984444 TGAGATTTTA
*
34984454 GAAAGTTCGGGAGT-AAAATGGTAATTTTGGT
1 GAAAGTTCGGGAGTAAAAATGGTAATCTTGGT
34984485 GAAA-TT-GGG-GTTAAAAATGG-AATCTT-G-
1 GAAAGTTCGGGAG-TAAAAATGGTAATCTTGGT
34984512 GAAAGTTCGGGAGT-AAAATGGTAA
1 GAAAGTTCGGGAGTAAAAATGGTAA
34984536 CTTTTAGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
27 4 0.09
28 11 0.25
29 15 0.34
30 10 0.23
31 4 0.09
ACGTcount: A:0.37, C:0.04, G:0.32, T:0.28
Consensus pattern (32 bp):
GAAAGTTCGGGAGTAAAAATGGTAATCTTGGT
Found at i:34984693 original size:58 final size:58
Alignment explanation
Indices: 34984621--34984734 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 58
34984611 GGTTAAAAAT
34984621 AGAATTTTGAAAAGTTCGAGGTCAAAATAGTAA-TTTTGGAAGTTTCGAGG-TCAAAAGC
1 AGAATTTTGAAAAGTTCGAGGTCAAAATAG-AATTTTTGGAAGTTTCG-GGATCAAAAGC
* * * *
34984679 AGAATTTTGGAAAGTTTGGGGTCAAAATAGAATTTTTTGAAGTTTCGGGATCAAAA
1 AGAATTTTGAAAAGTTCGAGGTCAAAATAGAATTTTTGGAAGTTTCGGGATCAAAA
34984735 TATAATTTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 4 0.08
58 46 0.92
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.32
Consensus pattern (58 bp):
AGAATTTTGAAAAGTTCGAGGTCAAAATAGAATTTTTGGAAGTTTCGGGATCAAAAGC
Found at i:34984715 original size:29 final size:28
Alignment explanation
Indices: 34984557--34984747 Score: 127
Period size: 29 Copynumber: 6.6 Consensus size: 28
34984547 ATCAGGGTTA
* *
34984557 AAAATGGAATTTTGGAAATTTTGAGGGT-
1 AAAATAGAATTTTGGAAAGTTTG-GGGTC
* * ** * *
34984585 AAAATGGTAATTTTTGGAAAAATCAGGGTTA
1 AAAATAG-AA-TTTTGG-AAAGTTTGGGGTC
* * *
34984616 AAAATAGAATTTTGAAAAGTTCGAGGTC
1 AAAATAGAATTTTGGAAAGTTTGGGGTC
*
34984644 AAAATAGTAATTTTGG-AAGTTTCGAGGTC
1 AAAATAG-AATTTTGGAAAGTTT-GGGGTC
*
34984673 AAAAGCAGAATTTTGGAAAGTTTGGGGTC
1 AAAA-TAGAATTTTGGAAAGTTTGGGGTC
* *
34984702 AAAATAGAATTTTTTG-AAGTTTCGGGATC
1 AAAATAGAA-TTTTGGAAAGTTT-GGGGTC
*
34984731 AAAATATAATTTCTGGA
1 AAAATAGAATTT-TGGA
34984748 CAGCTCAGGA
Statistics
Matches: 130, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
28 39 0.30
29 61 0.47
30 19 0.15
31 11 0.08
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (28 bp):
AAAATAGAATTTTGGAAAGTTTGGGGTC
Found at i:34987691 original size:17 final size:17
Alignment explanation
Indices: 34987666--34987744 Score: 72
Period size: 17 Copynumber: 4.6 Consensus size: 17
34987656 TAAATAAATT
*
34987666 TAAACTTAAATTTATAA
1 TAAATTTAAATTTATAA
*
34987683 TAAATTT-AATTTTTAAA
1 TAAATTTAAATTTAT-AA
* *
34987700 TAGATTTAAACTTA-ATA
1 TAAATTTAAATTTATA-A
* *
34987717 TAAACTTAAATTTAAAA
1 TAAATTTAAATTTATAA
34987734 TAAATTTAAAT
1 TAAATTTAAAT
34987745 CTTGCTGGGC
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
16 7 0.14
17 37 0.76
18 5 0.10
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:34987727 original size:40 final size:40
Alignment explanation
Indices: 34987654--34987731 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
34987644 ACATTATAAA
*
34987654 TTTAAATAAATTTAAACTTAAATTTATAATAAATTTAATT
1 TTTAAATAAATTTAAACTTAAATATATAATAAATTTAATT
*
34987694 TTTAAATAGATTTAAACTT-AATATA-AACTTAAATTTAA
1 TTTAAATAAATTTAAACTTAAATATATAA--TAAATTTAA
34987732 AATAAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 2 0.06
39 5 0.15
40 27 0.79
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (40 bp):
TTTAAATAAATTTAAACTTAAATATATAATAAATTTAATT
Found at i:34987743 original size:23 final size:22
Alignment explanation
Indices: 34987650--34987743 Score: 67
Period size: 23 Copynumber: 4.5 Consensus size: 22
34987640 TTGGACATTA
34987650 TAAATTT-AAATAAATTTAAACT
1 TAAATTTAAAATAAATTTAAA-T
*
34987672 TAAATTTATAATAAATTT-AAT
1 TAAATTTAAAATAAATTTAAAT
*
34987693 T---TTT-AAATAGATTTAAACT
1 TAAATTTAAAATAAATTTAAA-T
* * *
34987712 T-AATATAAACTTAAATTTAAAA
1 TAAATTTAAA-ATAAATTTAAAT
34987734 TAAATTTAAA
1 TAAATTTAAA
34987744 TCTTGCTGGG
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
17 8 0.14
18 5 0.09
19 2 0.04
21 4 0.07
22 12 0.21
23 25 0.45
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (22 bp):
TAAATTTAAAATAAATTTAAAT
Found at i:34998260 original size:16 final size:17
Alignment explanation
Indices: 34998221--34998261 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
34998211 ATAATATAAA
*
34998221 TATAATTTCATCATTTT
1 TATAATTTTATCATTTT
*
34998238 AAT-ATTTTAT-ATTTT
1 TATAATTTTATCATTTT
34998253 TATAATTTT
1 TATAATTTT
34998262 TACAGGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 7 0.35
16 11 0.55
17 2 0.10
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
TATAATTTTATCATTTT
Found at i:34999172 original size:24 final size:24
Alignment explanation
Indices: 34999158--34999204 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
34999148 ACCACCAGCT
* *
34999158 CCTACTCCACCACCAGCGCCACCG
1 CCTACACCACCACCAGCACCACCG
34999182 CCTACACCACCACCAGCACCACC
1 CCTACACCACCACCAGCACCACC
34999205 AAATCCACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.60, G:0.09, T:0.06
Consensus pattern (24 bp):
CCTACACCACCACCAGCACCACCG
Found at i:34999201 original size:12 final size:12
Alignment explanation
Indices: 34999164--34999205 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
34999154 AGCTCCTACT
*
34999164 CCACCACCAGCG
1 CCACCACCAGCA
*
34999176 CCACCGCCTA-CA
1 CCACCACC-AGCA
34999188 CCACCACCAGCA
1 CCACCACCAGCA
34999200 CCACCA
1 CCACCA
34999206 AATCCACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.29, C:0.60, G:0.10, T:0.02
Consensus pattern (12 bp):
CCACCACCAGCA
Found at i:34999212 original size:9 final size:9
Alignment explanation
Indices: 34999208--34999305 Score: 85
Period size: 9 Copynumber: 10.9 Consensus size: 9
34999198 CACCACCAAA
*
34999208 TCCACCAAG
1 TCCACCGAG
*
34999217 TCCACCGAC
1 TCCACCGAG
34999226 TCCACCG-G
1 TCCACCGAG
*
34999234 TTCCACCAAG
1 -TCCACCGAG
*
34999244 TCCACCGAC
1 TCCACCGAG
34999253 TCCACCG-G
1 TCCACCGAG
*
34999261 TTCCACCAAG
1 -TCCACCGAG
*
34999271 TCCACCGAC
1 TCCACCGAG
34999280 TCCACCG-G
1 TCCACCGAG
*
34999288 TTCCACCAAG
1 -TCCACCGAG
34999298 TCCACCGA
1 TCCACCGA
34999306 ATCCTCCGGT
Statistics
Matches: 70, Mismatches: 13, Indels: 12
0.74 0.14 0.13
Matches are distributed among these distances:
9 67 0.96
10 3 0.04
ACGTcount: A:0.23, C:0.48, G:0.14, T:0.14
Consensus pattern (9 bp):
TCCACCGAG
Found at i:34999221 original size:27 final size:27
Alignment explanation
Indices: 34999208--34999330 Score: 219
Period size: 27 Copynumber: 4.6 Consensus size: 27
34999198 CACCACCAAA
34999208 TCCACCAAGTCCACCGACTCCACCGGT
1 TCCACCAAGTCCACCGACTCCACCGGT
34999235 TCCACCAAGTCCACCGACTCCACCGGT
1 TCCACCAAGTCCACCGACTCCACCGGT
34999262 TCCACCAAGTCCACCGACTCCACCGGT
1 TCCACCAAGTCCACCGACTCCACCGGT
* *
34999289 TCCACCAAGTCCACCGAATCCTCCGGT
1 TCCACCAAGTCCACCGACTCCACCGGT
*
34999316 TCCTCCAAGTCCACC
1 TCCACCAAGTCCACC
34999331 CAAACCACCA
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.22, C:0.48, G:0.14, T:0.16
Consensus pattern (27 bp):
TCCACCAAGTCCACCGACTCCACCGGT
Found at i:34999348 original size:54 final size:54
Alignment explanation
Indices: 34999236--34999357 Score: 154
Period size: 54 Copynumber: 2.3 Consensus size: 54
34999226 TCCACCGGTT
* * ** ****
34999236 CCACCAAGTCCACCGACTCCACCGGTTCCACCAAGTCCACCGACTCCACCGGTT
1 CCACCAAGTCCACCGAATCCACCGGTTCCACCAAGTCCACCCAAACCACCACCA
* *
34999290 CCACCAAGTCCACCGAATCCTCCGGTTCCTCCAAGTCCACCCAAACCACCACCA
1 CCACCAAGTCCACCGAATCCACCGGTTCCACCAAGTCCACCCAAACCACCACCA
34999344 CCACCAAGTCCACC
1 CCACCAAGTCCACC
34999358 TACACCACCA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.25, C:0.50, G:0.11, T:0.13
Consensus pattern (54 bp):
CCACCAAGTCCACCGAATCCACCGGTTCCACCAAGTCCACCCAAACCACCACCA
Found at i:35018304 original size:13 final size:13
Alignment explanation
Indices: 35018283--35018316 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
35018273 TTGGAATCTT
*
35018283 GATAGAATCTAAA
1 GATAAAATCTAAA
*
35018296 GATAAAATCTAAT
1 GATAAAATCTAAA
35018309 GATAAAAT
1 GATAAAAT
35018317 TGAACTCGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (13 bp):
GATAAAATCTAAA
Found at i:35028204 original size:15 final size:16
Alignment explanation
Indices: 35028174--35028206 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
35028164 TCTGGGAAAA
*
35028174 AATTAAGAGAAAATAG
1 AATTAAAAGAAAATAG
35028190 AATTAAAAG-AAATAG
1 AATTAAAAGAAAATAG
35028205 AA
1 AA
35028207 AATAGAGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (16 bp):
AATTAAAAGAAAATAG
Found at i:35035811 original size:24 final size:24
Alignment explanation
Indices: 35035775--35035832 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
35035765 AAATAAAAAT
* *
35035775 AATTTTATTTAAAT-TTAATTATAA
1 AATTATATATAAATATTAA-TATAA
* *
35035799 AATTATATATAAATATTCATATGA
1 AATTATATATAAATATTAATATAA
35035823 AATTATATAT
1 AATTATATAT
35035833 TTTAATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
AATTATATATAAATATTAATATAA
Found at i:35043073 original size:2 final size:2
Alignment explanation
Indices: 35043066--35043111 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
35043056 CTAAATATTT
35043066 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
35043108 -C TC T
1 TC TC T
35043112 TCTTCCCCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:35047469 original size:6 final size:6
Alignment explanation
Indices: 35047458--35047508 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
35047448 GCCTACATAC
* * * *
35047458 ATACAT ATACAT ATACGT ATGTC-T ATACAT AAACAT ATACAC ATACAT
1 ATACAT ATACAT ATACAT AT-ACAT ATACAT ATACAT ATACAT ATACAT
35047506 ATA
1 ATA
35047509 AAACAGGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
5 1 0.03
6 34 0.94
7 1 0.03
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (6 bp):
ATACAT
Found at i:35053153 original size:4 final size:4
Alignment explanation
Indices: 35053129--35053169 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
35053119 AGATGGTTAA
* * *
35053129 TATG TATA TATG TATG AATG TATG TATG TATC TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
35053170 GTAGTTTCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:35057474 original size:90 final size:89
Alignment explanation
Indices: 35057348--35057590 Score: 221
Period size: 90 Copynumber: 2.7 Consensus size: 89
35057338 GATATTTGGG
* * *
35057348 AAGTTTAGAGGCTAAAATGTGATTTTTTAAAAGTTTGAGATTC-AAATTTAAATTTTTGGAAAGT
1 AAGTTTAGAGGCTAAAATGTGATTTTTTAAAAGTTTGAGAGTCAAAATGT-AATTATTGGAAAGT
*
35057412 TTGGAGGTCAAATCAGCATTTCTAGA
65 TT-GAGGACAAATCAGCATTTCTAGA
* * * *
35057438 AAGTTTAG-GGGTCAAAATGTGA-TTTTTATAATGTTTGGGGGTCAAAATGTAATTATTGGAAAG
1 AAGTTTAGAGGCT-AAAATGTGATTTTTTA-AAAGTTTGAGAGTCAAAATGTAATTATTGGAAAG
* * * *
35057501 TTTGAGGACAAATCCGAATTT-TTGG
64 TTTGAGGACAAATCAGCATTTCTAGA
** * * * *
35057526 AAGGGTAGGGGC-ACAATGTGATTTTTTGAAA-TATT-AGAGGTCAAAATGTAATTTTTGGAAAG
1 AAGTTTAGAGGCTAAAATGTGATTTTTTAAAAGT-TTGAGA-GTCAAAATGTAATTATTGGAAAG
35057588 TTT
64 TTT
35057591 AAGGGTCAAA
Statistics
Matches: 125, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
86 2 0.02
87 37 0.30
88 13 0.10
89 26 0.21
90 42 0.34
91 5 0.04
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.37
Consensus pattern (89 bp):
AAGTTTAGAGGCTAAAATGTGATTTTTTAAAAGTTTGAGAGTCAAAATGTAATTATTGGAAAGTT
TGAGGACAAATCAGCATTTCTAGA
Found at i:35057504 original size:30 final size:30
Alignment explanation
Indices: 35057398--35057612 Score: 151
Period size: 30 Copynumber: 7.3 Consensus size: 30
35057388 TTCAAATTTA
35057398 AATTTTTGGAAAGTTT-GGAGGTC-AAATCAG-
1 AATTTTTGGAAAGTTTAGG-GGTCAAAAT--GT
* * *
35057428 CATTTCTAGAAAGTTTAGGGGTCAAAATGT
1 AATTTTTGGAAAGTTTAGGGGTCAAAATGT
* ** * *
35057458 GATTTTTATAATGTTTGGGGGTCAAAATGT
1 AATTTTTGGAAAGTTTAGGGGTCAAAATGT
* * *
35057488 AATTATTGGAAAGTTT-GAGGAC-AAATCCG-
1 AATTTTTGGAAAGTTTAGGGGTCAAAAT--GT
** *
35057517 AATTTTTGG-AAGGGTAGGGG-CACAATGT
1 AATTTTTGGAAAGTTTAGGGGTCAAAATGT
* * *
35057545 GATTTTTTGAAA-TATTAGAGGTCAAAATGT
1 AATTTTTGGAAAGT-TTAGGGGTCAAAATGT
*
35057575 AATTTTTGGAAAGTTTAAGGGTCAAAATGT
1 AATTTTTGGAAAGTTTAGGGGTCAAAATGT
35057605 AATTTTTG
1 AATTTTTG
35057613 AAAAATTGGG
Statistics
Matches: 143, Mismatches: 30, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
27 1 0.01
28 16 0.11
29 26 0.18
30 93 0.65
31 7 0.05
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTAGGGGTCAAAATGT
Found at i:35057638 original size:59 final size:58
Alignment explanation
Indices: 35057575--35057733 Score: 153
Period size: 59 Copynumber: 2.7 Consensus size: 58
35057565 GTCAAAATGT
* * **
35057575 AATTTTTGGAAAGTTTAAGGGTCAAAATGTAATTTTTGAAAAATTGGGGGCCAAATTTG
1 AATTTCTGAAAAGTTT-AGGGTCAAAATGTAATTTTTGAAAAATTGGGGGCCAAATCCG
* * * * *
35057634 AATTTCT-AAAAATTTAGAAGTCAAAATGTAATTTTTAGAACATTTGGGGGTCAAATCCG
1 AATTTCTGAAAAGTTTAG-GGTCAAAATGTAATTTTT-GAAAAATTGGGGGCCAAATCCG
* *
35057693 AATGTCTGAAAAGTTT-GAGGT-AAAAGTGTGATTTTTGAAAA
1 AATTTCTGAAAAGTTTAG-GGTCAAAA-TGTAATTTTTGAAAA
35057734 GTTAAGGAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
57 2 0.02
58 31 0.38
59 42 0.51
60 7 0.09
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (58 bp):
AATTTCTGAAAAGTTTAGGGTCAAAATGTAATTTTTGAAAAATTGGGGGCCAAATCCG
Found at i:35057666 original size:58 final size:58
Alignment explanation
Indices: 35057595--35057733 Score: 156
Period size: 59 Copynumber: 2.4 Consensus size: 58
35057585 AAGTTTAAGG
** *
35057595 GTCAAAATGTAATTTTTGAAAAATTGGGGGCCAAATTTGAATTTCT-AAAAATTTAGAA
1 GTCAAAATGTAATTTTTGAAAAATTGGGGGCCAAATCCGAATGTCTGAAAAATTT-GAA
* * * * *
35057653 GTCAAAATGTAATTTTTAGAACATTTGGGGGTCAAATCCGAATGTCTGAAAAGTTTGAG
1 GTCAAAATGTAATTTTT-GAAAAATTGGGGGCCAAATCCGAATGTCTGAAAAATTTGAA
*
35057712 GT-AAAAGTGTGATTTTTGAAAA
1 GTCAAAA-TGTAATTTTTGAAAA
35057734 GTTAAGGAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
58 25 0.37
59 36 0.53
60 7 0.10
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (58 bp):
GTCAAAATGTAATTTTTGAAAAATTGGGGGCCAAATCCGAATGTCTGAAAAATTTGAA
Found at i:35057689 original size:29 final size:30
Alignment explanation
Indices: 35057429--35057688 Score: 133
Period size: 30 Copynumber: 8.8 Consensus size: 30
35057419 TCAAATCAGC
* * *
35057429 ATTTCTAGAAAGTTTAGGGGTCAAAATGTG
1 ATTTTTAGAAAATTTAGGGGTCAAAATGTA
* ** *
35057459 ATTTTTATAATGTTTGGGGGTCAAAATGTA
1 ATTTTTAGAAAATTTAGGGGTCAAAATGTA
* * * * *
35057489 ATTATTGGAAAGTTT-GAGGAC-AAATCCG-A
1 ATTTTTAGAAAATTTAGGGGTCAAAAT--GTA
* *** * *
35057518 ATTTTT-GGAAGGGTAGGGG-CACAATGTG
1 ATTTTTAGAAAATTTAGGGGTCAAAATGTA
* *
35057546 ATTTTTTG-AAATATTAGAGGTCAAAATGTA
1 ATTTTTAGAAAAT-TTAGGGGTCAAAATGTA
* * *
35057576 ATTTTTGGAAAGTTTAAGGGTCAAAATGTA
1 ATTTTTAGAAAATTTAGGGGTCAAAATGTA
* * * *
35057606 ATTTTT-GAAAAATT-GGGGGCCAAATTTGA
1 ATTTTTAGAAAATTTAGGGGTCAAAATGT-A
* **
35057635 ATTTCTA-AAAATTTAGAAGTCAAAATGTA
1 ATTTTTAGAAAATTTAGGGGTCAAAATGTA
* *
35057664 ATTTTTAGAACATTTGGGGGTCAAA
1 ATTTTTAGAAAATTTAGGGGTCAAA
35057689 TCCGAATGTC
Statistics
Matches: 171, Mismatches: 46, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
27 1 0.01
28 27 0.16
29 47 0.27
30 93 0.54
31 3 0.02
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35
Consensus pattern (30 bp):
ATTTTTAGAAAATTTAGGGGTCAAAATGTA
Found at i:35061501 original size:17 final size:18
Alignment explanation
Indices: 35061468--35061503 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
35061458 ATATTTCAAG
*
35061468 ATTATCATCTTTGAGAAA
1 ATTATCATCTTTCAGAAA
35061486 ATTATC-TCTTTCAGAAA
1 ATTATCATCTTTCAGAAA
35061503 A
1 A
35061504 CCAACTCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (18 bp):
ATTATCATCTTTCAGAAA
Found at i:35065292 original size:148 final size:145
Alignment explanation
Indices: 35065111--35065495 Score: 449
Period size: 146 Copynumber: 2.6 Consensus size: 145
35065101 TTTTGGTTTT
* * * *
35065111 TTTTAAATAATTTTGAAATAAAAGTTTTA-ATTTTTTTAGCACAATAGTGATTTTCTTTTAAAAA
1 TTTT-AATTATTTTGAAATAAAAG-TTTAGA-TTTTTAAGTA-AATAATGATTTTCTTTTAAAAA
* *
35065175 AGAGAAAGTTTAGATTTTTAAAAAATAAAAATCT-ATTTTTAGTTATTTTAAAGAAAAAATTTAA
62 AGAGAAAG-TTATATTTTT-AAAAATAAAAATATGATTTTTAGTTATTTTAAA-AAAAAATTTAA
* *
35065239 CTTTTTAATAAAATTT-TGATA
124 ATTTTTAACAAAATTTATGATA
* *
35065260 TTTTAATTATTTCGAAATAAAAGTTTAGATTTTTAAGTTAAATAATTATTTT-TTTTAAAAAAGA
1 TTTTAATTATTTTGAAATAAAAGTTTAGATTTTTAAG-TAAATAATGATTTTCTTTTAAAAAAGA
* * *
35065324 AAAAG-TATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAAAAAAGTTTAAATTTTT
65 GAAAGTTATATTTTTAAAAATAAAAATATGATTTTTAGTTATTTTAAAAAAAAATTTAAATTTTT
* * *
35065388 AACAAAGTTTAAATGTTT
130 AACAAAATTT--ATGATA
* *
35065406 TTTTAATTATTTTGAAATAAAAATTTAGATTTTTAAGTAAAATATTGATTTTC-TTTAAAAAAGA
1 TTTTAATTATTTTGAAATAAAAGTTTAGATTTTTAAGT-AAATAATGATTTTCTTTTAAAAAAGA
*
35065470 GAAAAATTATATTTTTAAAAATAAAA
65 G-AAAGTTATATTTTTAAAAATAAAA
35065496 GTTTTGATTT
Statistics
Matches: 204, Mismatches: 22, Indels: 21
0.83 0.09 0.09
Matches are distributed among these distances:
143 36 0.18
144 25 0.12
145 1 0.00
146 76 0.37
147 24 0.12
148 38 0.19
149 4 0.02
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (145 bp):
TTTTAATTATTTTGAAATAAAAGTTTAGATTTTTAAGTAAATAATGATTTTCTTTTAAAAAAGAG
AAAGTTATATTTTTAAAAATAAAAATATGATTTTTAGTTATTTTAAAAAAAAATTTAAATTTTTA
ACAAAATTTATGATA
Found at i:35065341 original size:21 final size:21
Alignment explanation
Indices: 35065311--35065357 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
35065301 ATAATTATTT
35065311 TTTTTAAAAAAGAAAAAGTATA
1 TTTTTAAAAAAGAAAAA-TATA
* *
35065333 TTTTT-AAAAATAAAAATATG
1 TTTTTAAAAAAGAAAAATATA
35065353 TTTTT
1 TTTTT
35065358 TAGTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 10 0.43
22 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (21 bp):
TTTTTAAAAAAGAAAAATATA
Found at i:35066119 original size:20 final size:21
Alignment explanation
Indices: 35066081--35066120 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35066071 ATAATTTTTA
* *
35066081 TTTATTTTTATTCCATATTTG
1 TTTATTTTCATGCCATATTTG
35066102 TTTATTTTCATGCC-TATTT
1 TTTATTTTCATGCCATATTT
35066121 ATATTTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTATTTTCATGCCATATTTG
Found at i:35070724 original size:16 final size:16
Alignment explanation
Indices: 35070700--35070733 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
35070690 ATTCTATGGC
35070700 CTTGAACTCCTTTTTA
1 CTTGAACTCCTTTTTA
*
35070716 CTTGCACTCCTTTTTA
1 CTTGAACTCCTTTTTA
35070732 CT
1 CT
35070734 CAATTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.29, G:0.06, T:0.50
Consensus pattern (16 bp):
CTTGAACTCCTTTTTA
Found at i:35070832 original size:177 final size:178
Alignment explanation
Indices: 35070535--35070884 Score: 693
Period size: 177 Copynumber: 2.0 Consensus size: 178
35070525 AATCCTCCCA
35070535 TTACTTGCACTCCTTTTTACTCAATTACTTTCTCTCTTATAACTTTTACCCCCCCCCCCAACCAA
1 TTACTTGCACTCCTTTTTACTCAATTACTTTCTCTCTTATAACTTTTACCCCCCCCCCCAACCAA
35070600 TGATGCAAACTTGATAATTACTCTTATTAAGGATTTAAGGGAGCCTGCTCTGTTTTTACTCAAAT
66 TGATGCAAACTTGATAATTACTCTTATTAAGGATTTAAGGGAGCCTGCTCTGTTTTTACTCAAAT
35070665 TATGTTCATTTCATGTTGTTAGTAGATTCTATGGCCTTGAACTCCTTT
131 TATGTTCATTTCATGTTGTTAGTAGATTCTATGGCCTTGAACTCCTTT
35070713 TTACTTGCACTCCTTTTTACTCAATTACTTTCTCTCTTATAACTTTTA-CCCCCCCCCCAACCAA
1 TTACTTGCACTCCTTTTTACTCAATTACTTTCTCTCTTATAACTTTTACCCCCCCCCCCAACCAA
35070777 TGATGCAAACTTGATAATTACTCTTATTAAGGATTTAAGGGAGCCTGCTCTGTTTTTACTCAAAT
66 TGATGCAAACTTGATAATTACTCTTATTAAGGATTTAAGGGAGCCTGCTCTGTTTTTACTCAAAT
35070842 TATGTTCATTTCATGTTGTTAGTAGATTCTATGGCCTTGAACT
131 TATGTTCATTTCATGTTGTTAGTAGATTCTATGGCCTTGAACT
35070885 GCTTCTGGGT
Statistics
Matches: 172, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
177 124 0.72
178 48 0.28
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (178 bp):
TTACTTGCACTCCTTTTTACTCAATTACTTTCTCTCTTATAACTTTTACCCCCCCCCCCAACCAA
TGATGCAAACTTGATAATTACTCTTATTAAGGATTTAAGGGAGCCTGCTCTGTTTTTACTCAAAT
TATGTTCATTTCATGTTGTTAGTAGATTCTATGGCCTTGAACTCCTTT
Found at i:35076908 original size:6 final size:6
Alignment explanation
Indices: 35076897--35076926 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35076887 TACACCCCAG
*
35076897 AAGGAA AAGGAA AAGGAA AAGGAA ATGGAA
1 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA
35076927 TGGGATTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (6 bp):
AAGGAA
Found at i:35078468 original size:15 final size:14
Alignment explanation
Indices: 35078443--35078472 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
35078433 TTCCTAGGCT
35078443 GCTGGTCAGCTTGA
1 GCTGGTCAGCTTGA
35078457 GCTGGCTCAGCTTGA
1 GCTGG-TCAGCTTGA
35078472 G
1 G
35078473 ATTTGCTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (14 bp):
GCTGGTCAGCTTGA
Found at i:35095041 original size:15 final size:15
Alignment explanation
Indices: 35095004--35095044 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
35094994 TTTTTCCGCA
*
35095004 GCTTCTGCAGCGGCT
1 GCTTCTGCTGCGGCT
**
35095019 GCAGCTGCTGCGGCT
1 GCTTCTGCTGCGGCT
35095034 GCTTCTGCTGC
1 GCTTCTGCTGC
35095045 TTCTTGTGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.34, G:0.34, T:0.27
Consensus pattern (15 bp):
GCTTCTGCTGCGGCT
Found at i:35096812 original size:22 final size:19
Alignment explanation
Indices: 35096771--35096813 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 19
35096761 TTAATTTAAA
35096771 TATTATTTAAATACATATT
1 TATTATTTAAATACATATT
35096790 TATTACTTTATAATACAATATT
1 TATTA-TTTA-AATAC-ATATT
35096812 TA
1 TA
35096814 AAATAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 5 0.24
22 7 0.33
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATTTAAATACATATT
Found at i:35101968 original size:23 final size:24
Alignment explanation
Indices: 35101929--35101973 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
35101919 TTTAGTAGAA
35101929 AAAATGAAAATATTATTATTTTTT
1 AAAATGAAAATATTATTATTTTTT
35101953 AAAA-GAAAAT-TGTATTATTTT
1 AAAATGAAAATAT-TATTATTTT
35101974 AAAAATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 15 0.75
24 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (24 bp):
AAAATGAAAATATTATTATTTTTT
Found at i:35105598 original size:20 final size:21
Alignment explanation
Indices: 35105563--35105602 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
35105553 TAATAATTTG
*
35105563 ATTGTTGAATTCTATAATATA
1 ATTGTTGAATTATATAATATA
35105584 ATTGTT-AATTATATAATAT
1 ATTGTTGAATTATATAATAT
35105603 TAAGTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (21 bp):
ATTGTTGAATTATATAATATA
Found at i:35105931 original size:19 final size:20
Alignment explanation
Indices: 35105887--35105931 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
35105877 TTTAAATTTG
35105887 TCATGATGTAAGGAACAAATA
1 TCAT-ATGTAAGGAACAAATA
*
35105908 T-ATATGTAAGGAAC-ATTA
1 TCATATGTAAGGAACAAATA
35105926 TCATAT
1 TCATAT
35105932 TGAAATTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.18
19 15 0.68
20 2 0.09
21 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (20 bp):
TCATATGTAAGGAACAAATA
Found at i:35110475 original size:25 final size:24
Alignment explanation
Indices: 35110446--35110508 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
35110436 ATAAAAATTT
*
35110446 GATATAATTTTTTAAAATTTATAAA
1 GATATAATTTTTTAAAA-TGATAAA
* *
35110471 GATATAATCTATTAAAATGATAAA
1 GATATAATTTTTTAAAATGATAAA
* *
35110495 GTTATATTTTTTTA
1 GATATAATTTTTTA
35110509 TCGTAAAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 16 0.52
25 15 0.48
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (24 bp):
GATATAATTTTTTAAAATGATAAA
Found at i:35110500 original size:24 final size:25
Alignment explanation
Indices: 35110446--35110500 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
35110436 ATAAAAATTT
* * *
35110446 GATATAATTTTTTAAAATTTATAAA
1 GATATAATCTATTAAAATTGATAAA
35110471 GATATAATCTATTAAAA-TGATAAA
1 GATATAATCTATTAAAATTGATAAA
*
35110495 GTTATA
1 GATATA
35110501 TTTTTTTATC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (25 bp):
GATATAATCTATTAAAATTGATAAA
Found at i:35111852 original size:20 final size:21
Alignment explanation
Indices: 35111827--35111873 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
35111817 ATAACTTTAT
35111827 AATTTTTAAAGGATTAAA-T-C
1 AATTTTTAAAGG-TTAAAGTGC
*
35111847 AATTTTTAGAGGTTAAAGTGC
1 AATTTTTAAAGGTTAAAGTGC
35111868 AATTTT
1 AATTTT
35111874 ACTTGTACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 12 0.50
21 7 0.29
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (21 bp):
AATTTTTAAAGGTTAAAGTGC
Found at i:35142801 original size:20 final size:17
Alignment explanation
Indices: 35142766--35142808 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 17
35142756 GAAATTTAGT
35142766 TTTTTTGTTTTTTTATA
1 TTTTTTGTTTTTTTATA
35142783 TTTTTTGTTTTATTATTATA
1 TTTTTTG-TTT-TT-TTATA
35142803 TTTTTT
1 TTTTTT
35142809 AATTAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.30
18 3 0.13
19 2 0.09
20 11 0.48
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (17 bp):
TTTTTTGTTTTTTTATA
Found at i:35145475 original size:39 final size:39
Alignment explanation
Indices: 35145430--35145507 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
35145420 TATCAAAATG
35145430 GACTTGAAGACAATAATTGGGTTCAAGATCTGTATAGCA
1 GACTTGAAGACAATAATTGGGTTCAAGATCTGTATAGCA
*
35145469 GACTTGAAGACAATAATTGGGTTCGAGATCTGTATAGCA
1 GACTTGAAGACAATAATTGGGTTCAAGATCTGTATAGCA
35145508 CCATTGAACG
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:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (39 bp):
GACTTGAAGACAATAATTGGGTTCAAGATCTGTATAGCA
Found at i:35145685 original size:84 final size:84
Alignment explanation
Indices: 35145565--35145965 Score: 493
Period size: 84 Copynumber: 4.7 Consensus size: 84
35145555 AATGACACTA
* *
35145565 TCACTAATGAAAGAAGCAATCAACATAATACAGTTGTTGTGGAAAAGGGCATCGAAATGCCTATC
1 TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCGAAATGCCTATC
35145630 ATTAGCTATGATGAAACCG
66 ATTAGCTATGATGAAACCG
* *
35145649 TCACTAATGAAAGAAGCAATCAACATAATATGGTTGTTGCGGAAAATGGCATCGAAACGCCTATG
1 TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCG-AA-----ATG
* * * *
35145714 TCTATCATTAGTTATGACGAAACTG
60 CCTATCATTAGCTATGATGAAACCG
*
35145739 TCATTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCGAAATGCCTAAT
1 TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCGAAATGCCT-AT
**
35145804 -ATTAG-TCATGATGAAAATG
65 CATTAGCT-ATGATGAAACCG
* * *
35145823 TCACTAATGAAAGAAGCAATCAACTTAATATAGTTGTTGCAGAAGAGGGCAAT-GAAATGCCTAT
1 TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGC-ATCGAAATGCCTAT
* * *
35145887 CATTAGCTTTGTTGAAACCA
65 CATTAGCTATGATGAAACCG
* * * * * *
35145907 TTACTAATGAAAGAAGCAATCAACCTAATATAGTTGATGTGGATAAGGGCTTCGAAATG
1 TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCGAAATG
35145966 TCTTCTAACT
Statistics
Matches: 274, Mismatches: 31, Indels: 24
0.83 0.09 0.07
Matches are distributed among these distances:
83 4 0.01
84 186 0.68
85 7 0.03
89 2 0.01
90 75 0.27
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (84 bp):
TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCGAAATGCCTATC
ATTAGCTATGATGAAACCG
Found at i:35148019 original size:24 final size:24
Alignment explanation
Indices: 35147960--35148056 Score: 74
Period size: 24 Copynumber: 4.1 Consensus size: 24
35147950 TTGATTGCTG
*
35147960 TTTTGATGCTATTTTT-TTATTA-
1 TTTTGATGCTATTTTTATTGTTAT
* * *
35147982 CTTTGGTGTTATTTTTATTGTTAT
1 TTTTGATGCTATTTTTATTGTTAT
* * *
35148006 TTTTTATTCTATTTTT-TCTATTAT
1 TTTTGATGCTATTTTTAT-TGTTAT
* * *
35148030 TTTTGCTGCTGTTTTGATTGTTAT
1 TTTTGATGCTATTTTTATTGTTAT
35148054 TTT
1 TTT
35148057 GATTGTTTGA
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
22 13 0.24
23 6 0.11
24 35 0.64
25 1 0.02
ACGTcount: A:0.13, C:0.06, G:0.11, T:0.69
Consensus pattern (24 bp):
TTTTGATGCTATTTTTATTGTTAT
Found at i:35155084 original size:7 final size:7
Alignment explanation
Indices: 35155072--35155106 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
35155062 TATAAATGGG
35155072 AGAGTGA
1 AGAGTGA
35155079 AGAGTGA
1 AGAGTGA
35155086 AGAGTGA
1 AGAGTGA
35155093 AGAGTGA
1 AGAGTGA
35155100 AGAGTGA
1 AGAGTGA
35155107 GGGGATGGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (7 bp):
AGAGTGA
Found at i:35155378 original size:25 final size:26
Alignment explanation
Indices: 35155331--35155380 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
35155321 ATTAAATATT
*
35155331 TTCTTTTGTATTTTTTATTTTTCACA
1 TTCTTTTGTATTTTTTATCTTTCACA
35155357 TTCTTTT-TATTTTTCT-TCTTTCAC
1 TTCTTTTGTATTTTT-TATCTTTCAC
35155381 CAACTCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.70
Consensus pattern (26 bp):
TTCTTTTGTATTTTTTATCTTTCACA
Found at i:35157525 original size:19 final size:19
Alignment explanation
Indices: 35157503--35157539 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35157493 TGTTGATATG
35157503 ATTTGAAATTTTATTGTTT
1 ATTTGAAATTTTATTGTTT
* *
35157522 ATTTGAATTTTTGTTGTT
1 ATTTGAAATTTTATTGTT
35157540 GTTGTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.65
Consensus pattern (19 bp):
ATTTGAAATTTTATTGTTT
Found at i:35172922 original size:15 final size:15
Alignment explanation
Indices: 35172902--35172944 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
35172892 GTAAATTTTC
35172902 AAATATAAGTGACTA
1 AAATATAAGTGACTA
* *
35172917 AAATATAATCTGAGTA
1 AAATATAA-GTGACTA
*
35172933 AAATAAAAGTGA
1 AAATATAAGTGA
35172945 TTATTTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.26
Consensus pattern (15 bp):
AAATATAAGTGACTA
Found at i:35176736 original size:14 final size:14
Alignment explanation
Indices: 35176717--35176755 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
35176707 TAACAAATAA
* *
35176717 TTTTAAAATTATTT
1 TTTTAAAATAAATT
35176731 TTTTAAATATAAATT
1 TTTTAAA-ATAAATT
35176746 TTTTAAAATA
1 TTTTAAAATA
35176756 CAAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAAATAAATT
Found at i:35176917 original size:2 final size:2
Alignment explanation
Indices: 35176910--35176963 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
35176900 TAATTGTTTC
35176910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35176952 AT AT AT AT AT AT
1 AT AT AT AT AT AT
35176964 GAGAATCATC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35177868 original size:22 final size:22
Alignment explanation
Indices: 35177825--35177868 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
35177815 AATTGGAAAT
*
35177825 AATAATTTTATTATTTCAAAAA
1 AATAATTTTATAATTTCAAAAA
*
35177847 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-ATAATTTCAAAA
35177869 TTATTTATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTATAATTTCAAAAA
Found at i:35180649 original size:15 final size:17
Alignment explanation
Indices: 35180619--35180655 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
35180609 ATATTAAAAT
35180619 ATAATTTCACTATTTTA
1 ATAATTTCACTATTTTA
*
35180636 ATAATTT-A-TATTTTT
1 ATAATTTCACTATTTTA
35180651 ATAAT
1 ATAAT
35180656 CTTTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 1 0.05
17 7 0.37
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
ATAATTTCACTATTTTA
Found at i:35185776 original size:16 final size:16
Alignment explanation
Indices: 35185741--35185782 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
35185731 TTTAATATTT
35185741 AATAATA-AAAATTAA
1 AATAATATAAAATTAA
* *
35185756 TATAATATAATATTAA
1 AATAATATAAAATTAA
*
35185772 AATAAAATAAA
1 AATAATATAAA
35185783 TTTTTTTCTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATAATATAAAATTAA
Found at i:35192794 original size:17 final size:18
Alignment explanation
Indices: 35192769--35192815 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
35192759 TAAAAATTCT
35192769 AAAATT-TATATTTTTAAA
1 AAAATTATATA-TTTTAAA
35192787 AAAATTATAATAATTTTAAA
1 AAAATTAT-AT-ATTTTAAA
35192807 AAAATTATA
1 AAAATTATA
35192816 AATAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.23
19 2 0.08
20 17 0.65
21 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTATATATTTTAAA
Found at i:35192808 original size:21 final size:21
Alignment explanation
Indices: 35192780--35192821 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
35192770 AAATTTATAT
35192780 TTTTAAAAAAATTAT-AATAA
1 TTTTAAAAAAATTATAAATAA
35192800 TTTTAAAAAAATTATAAATAA
1 TTTTAAAAAAATTATAAATAA
35192821 T
1 T
35192822 ATATAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTAAAAAAATTATAAATAA
Found at i:35194347 original size:15 final size:16
Alignment explanation
Indices: 35194311--35194350 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
35194301 AGTAAAAATA
35194311 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
35194328 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
35194343 TATAATTT
1 TATAATTT
35194351 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:35195974 original size:21 final size:23
Alignment explanation
Indices: 35195931--35195977 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
35195921 TTTCTCTTGC
*
35195931 TTTTTTTAAGGTTAGAGTTTTGT
1 TTTTTTTAAGGTTAGAGTATTGT
*
35195954 TTTTTTTAA-G-TAGGGTATTGT
1 TTTTTTTAAGGTTAGAGTATTGT
35195975 TTT
1 TTT
35195978 AATCTTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 12 0.55
22 1 0.05
23 9 0.41
ACGTcount: A:0.17, C:0.00, G:0.21, T:0.62
Consensus pattern (23 bp):
TTTTTTTAAGGTTAGAGTATTGT
Found at i:35196294 original size:36 final size:37
Alignment explanation
Indices: 35196219--35196308 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 37
35196209 TATAAATCAT
* *
35196219 AACCCTAACCCTAAAAAGGTAAAATTTGACTTTTAAA
1 AACCCTAACCCTAAAAAGGCAAAATTTGACTTTAAAA
* *
35196256 AACCCTAACCCTAAAAA-GCAAAGTTTTACTTTAAAA
1 AACCCTAACCCTAAAAAGGCAAAATTTGACTTTAAAA
**
35196292 AACCCTAATACTAAAAA
1 AACCCTAACCCTAAAAA
35196309 AAGAAAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 30 0.64
37 17 0.36
ACGTcount: A:0.49, C:0.21, G:0.06, T:0.24
Consensus pattern (37 bp):
AACCCTAACCCTAAAAAGGCAAAATTTGACTTTAAAA
Found at i:35196309 original size:37 final size:37
Alignment explanation
Indices: 35196219--35196319 Score: 114
Period size: 36 Copynumber: 2.7 Consensus size: 37
35196209 TATAAATCAT
* * *
35196219 AACCCTAACCCTAAAAAGGTAAAATTTGACTTTTAAA
1 AACCCTAACCCTAAAAAAGCAAAATTTGACTTTAAAA
* *
35196256 AACCCTAACCCT-AAAAAGCAAAGTTTTACTTTAAAA
1 AACCCTAACCCTAAAAAAGCAAAATTTGACTTTAAAA
** *
35196292 AACCCTAATACTAAAAAAAGAAAAATTT
1 AACCCTAACCCT-AAAAAAGCAAAATTT
35196320 CAAGTGATGT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
36 29 0.55
37 12 0.23
38 12 0.23
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (37 bp):
AACCCTAACCCTAAAAAAGCAAAATTTGACTTTAAAA
Found at i:35200982 original size:45 final size:45
Alignment explanation
Indices: 35200911--35201000 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
35200901 AAATCTACAT
* * *
35200911 TTATTGTGAAACTTTTTATTGCGTATGTATCACGAATTATTGTAA
1 TTATTGTAAAACTCTTCATTGCGTATGTATCACGAATTATTGTAA
* *
35200956 TTATTGTAAAACTCTTCATTGTGTATGTATCACGAGTTATTGTAA
1 TTATTGTAAAACTCTTCATTGCGTATGTATCACGAATTATTGTAA
35201001 AATTCTTCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.46
Consensus pattern (45 bp):
TTATTGTAAAACTCTTCATTGCGTATGTATCACGAATTATTGTAA
Found at i:35201008 original size:36 final size:36
Alignment explanation
Indices: 35200956--35201349 Score: 515
Period size: 36 Copynumber: 11.0 Consensus size: 36
35200946 ATTATTGTAA
*
35200956 TTATTGTAAAACTCTTCATTGTGTATGTATCACGAG
1 TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
* * *
35200992 TTATTGTAAAATTCTTCATTGTGTAAGTATCAAGAG
1 TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
* * **
35201028 TTATTGTGAAACTCTTCTTTGCATAGGTATCACGAG
1 TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
*
35201064 TTATTGTAAAACTCTTCATTGTGTATGTATCACGAG
1 TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
* * *
35201100 TTATTGTAAAATTCTTCATTGTGTAAGTATCAAGAG
1 TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
* * **
35201136 TTATTGTGAAACTCTTCTTTGCATAGGTATCACGAG
1 TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
*
35201172 TTATTGTAAAACTCTTCATTGTGTATGTATCACGAG
1 TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
* * *
35201208 TTATTGTAAAATTCTTCATTGTGTAAGTATCAAGAG
1 TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
* **
35201244 TTATTGTGAAACTCTTCATTGCATAGGTATCACGAG
1 TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
* * *
35201280 TTATTGTAAAACTTTTCATTGCGTAGGTTTCACGAG
1 TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
* *
35201316 TTA---TAAAACTCTTCATTGCGTAGGTATCATGAG
1 TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
35201349 T
1 T
35201350 GCGTAAGTAT
Statistics
Matches: 312, Mismatches: 46, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
33 28 0.09
36 284 0.91
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (36 bp):
TTATTGTAAAACTCTTCATTGTGTAGGTATCACGAG
Found at i:35201080 original size:108 final size:108
Alignment explanation
Indices: 35200956--35201349 Score: 686
Period size: 108 Copynumber: 3.7 Consensus size: 108
35200946 ATTATTGTAA
35200956 TTATTGTAAAACTCTTCATTGTGTATGTATCACGAGTTATTGTAAAATTCTTCATTGTGTAAGTA
1 TTATTGTAAAACTCTTCATTGTGTATGTATCACGAGTTATTGTAAAATTCTTCATTGTGTAAGTA
35201021 TCAAGAGTTATTGTGAAACTCTTCTTTGCATAGGTATCACGAG
66 TCAAGAGTTATTGTGAAACTCTTCTTTGCATAGGTATCACGAG
35201064 TTATTGTAAAACTCTTCATTGTGTATGTATCACGAGTTATTGTAAAATTCTTCATTGTGTAAGTA
1 TTATTGTAAAACTCTTCATTGTGTATGTATCACGAGTTATTGTAAAATTCTTCATTGTGTAAGTA
35201129 TCAAGAGTTATTGTGAAACTCTTCTTTGCATAGGTATCACGAG
66 TCAAGAGTTATTGTGAAACTCTTCTTTGCATAGGTATCACGAG
35201172 TTATTGTAAAACTCTTCATTGTGTATGTATCACGAGTTATTGTAAAATTCTTCATTGTGTAAGTA
1 TTATTGTAAAACTCTTCATTGTGTATGTATCACGAGTTATTGTAAAATTCTTCATTGTGTAAGTA
*
35201237 TCAAGAGTTATTGTGAAACTCTTCATTGCATAGGTATCACGAG
66 TCAAGAGTTATTGTGAAACTCTTCTTTGCATAGGTATCACGAG
* * * * * * *
35201280 TTATTGTAAAACTTTTCATTGCGTAGGTTTCACGAGTTA---TAAAACTCTTCATTGCGTAGGTA
1 TTATTGTAAAACTCTTCATTGTGTATGTATCACGAGTTATTGTAAAATTCTTCATTGTGTAAGTA
*
35201342 TCATGAGT
66 TCAAGAGT
35201350 GCGTAAGTAT
Statistics
Matches: 277, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
105 27 0.10
108 250 0.90
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (108 bp):
TTATTGTAAAACTCTTCATTGTGTATGTATCACGAGTTATTGTAAAATTCTTCATTGTGTAAGTA
TCAAGAGTTATTGTGAAACTCTTCTTTGCATAGGTATCACGAG
Found at i:35201354 original size:17 final size:17
Alignment explanation
Indices: 35201332--35201366 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
35201322 AACTCTTCAT
*
35201332 TGCGTAGGTATCATGAG
1 TGCGTAAGTATCATGAG
35201349 TGCGTAAGTATCATGAG
1 TGCGTAAGTATCATGAG
35201366 T
1 T
35201367 TATTGTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.31
Consensus pattern (17 bp):
TGCGTAAGTATCATGAG
Found at i:35201496 original size:36 final size:36
Alignment explanation
Indices: 35201349--35201498 Score: 237
Period size: 36 Copynumber: 4.2 Consensus size: 36
35201339 GTATCATGAG
* *
35201349 TGCGTAAGTATCATGAGTTATTGTGAAACTCTTCAT
1 TGCGTAGGTATCACGAGTTATTGTGAAACTCTTCAT
* *
35201385 TGCATAGGTATCACGAGTTATTGTGAAACTCTTTAT
1 TGCGTAGGTATCACGAGTTATTGTGAAACTCTTCAT
*
35201421 TGCATAGGTATCACGAGTTATTGTGAAACTCTTCAT
1 TGCGTAGGTATCACGAGTTATTGTGAAACTCTTCAT
* *
35201457 TGCGTAGGTATCACGAATTATTGTAAAACTCTTCAT
1 TGCGTAGGTATCACGAGTTATTGTGAAACTCTTCAT
35201493 TGCGTA
1 TGCGTA
35201499 TGATAAACTT
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 106 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.37
Consensus pattern (36 bp):
TGCGTAGGTATCACGAGTTATTGTGAAACTCTTCAT
Found at i:35201515 original size:57 final size:56
Alignment explanation
Indices: 35201446--35201559 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 56
35201436 AGTTATTGTG
*
35201446 AAACTCTTCATTGCGTAGGTATCACGAATTATTGTAAAACTCTTCATTGCGTATGAT
1 AAACTCTTCATTGAGTAGGTATCACGAATTATTGTAAAACTCTTCATTGCGTA-GAT
* * * *
35201503 AAACTTTTCATTGAGTAGGTATCATGAGTTATTGTGAAACTCTTCATTGCGTAGAT
1 AAACTCTTCATTGAGTAGGTATCACGAATTATTGTAAAACTCTTCATTGCGTAGAT
35201559 A
1 A
35201560 TCACGAATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
56 4 0.08
57 48 0.92
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.38
Consensus pattern (56 bp):
AAACTCTTCATTGAGTAGGTATCACGAATTATTGTAAAACTCTTCATTGCGTAGAT
Found at i:35201532 original size:129 final size:129
Alignment explanation
Indices: 35201252--35201627 Score: 387
Period size: 129 Copynumber: 3.0 Consensus size: 129
35201242 AGTTATTGTG
* * * * * *
35201252 AAACTCTTCATTGCATAGGTATCACGAGTTATTGTAAAACTTTTCATTGCGTAGGTTTCACGAGT
1 AAACTCTTCATTGCATAGGTATCACGAGTTATTGTGAAACTCTTCATTGCATAGATATCACGAAT
* * * * * * * * *
35201317 TA---TAAAACTCTTCATTGCGTAGGTATCATG-AGTGC-GT--AAGT-ATCA-TGAGTTATTG-
66 TATTGTAAAACGCTTCATTGCATAAGTATCACGAATTACTGTAAAACTCTTCATTGCG-TA-TGA
35201372 T
129 T
* * *
35201373 GAAACTCTTCATTGCATAGGTATCACGAGTTATTGTGAAACTCTTTATTGCATAGGTATCACGAG
1 -AAACTCTTCATTGCATAGGTATCACGAGTTATTGTGAAACTCTTCATTGCATAGATATCACGAA
* * * * *
35201438 TTATTGTGAAACTCTTCATTGCGTAGGTATCACGAATTATTGTAAAACTCTTCATTGCGTATGAT
65 TTATTGTAAAACGCTTCATTGCATAAGTATCACGAATTACTGTAAAACTCTTCATTGCGTATGAT
* * *
35201503 AAACTTTTCATTG-AGTAGGTATCATGAGTTATTGTGAAACTCTTCATTGCGTAGATATCACGAA
1 AAACTCTTCATTGCA-TAGGTATCACGAGTTATTGTGAAACTCTTCATTGCATAGATATCACGAA
* *
35201567 TTATTGTAAAACGCTTCATTGCATAAGTATCACTAGTTACTGTAAAACTCTTCATTGCGTA
65 TTATTGTAAAACGCTTCATTGCATAAGTATCACGAATTACTGTAAAACTCTTCATTGCGTA
35201628 GGTATCACAA
Statistics
Matches: 217, Mismatches: 26, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
122 62 0.29
125 26 0.12
126 2 0.01
127 2 0.01
128 1 0.00
129 115 0.53
130 6 0.03
131 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (129 bp):
AAACTCTTCATTGCATAGGTATCACGAGTTATTGTGAAACTCTTCATTGCATAGATATCACGAAT
TATTGTAAAACGCTTCATTGCATAAGTATCACGAATTACTGTAAAACTCTTCATTGCGTATGAT
Found at i:35201706 original size:108 final size:108
Alignment explanation
Indices: 35201503--35201713 Score: 280
Period size: 108 Copynumber: 2.0 Consensus size: 108
35201493 TGCGTATGAT
* **
35201503 AAACTTTTCATTGAGTAGGTATCATGAGTTATTGTGAAACTCTTCATTGCGTAGATATCACGAAT
1 AAACTCTTCATTGAGTAGGTATCACAAGTTATTGTGAAACTCTTCATTGCGTAGATATCACGAAT
*
35201568 TATTGTAAAACGCTTCATTGCATAAGTATCACTAGTTACTGTA
66 TATTGTAAAACGCTTCATTGCATAAGTATCACAAGTTACTGTA
* * * * * *
35201611 AAACTCTTCATTGCGTAGGTATCACAAGTTATTGTGAAACTTTTCATTGTGTAGGTATCATGAGT
1 AAACTCTTCATTGAGTAGGTATCACAAGTTATTGTGAAACTCTTCATTGCGTAGATATCACGAAT
* * **
35201676 TATTGTAAAACTCTTTATTGTGT-AGTTATCACAAGTTA
66 TATTGTAAAACGCTTCATTGCATAAG-TATCACAAGTTA
35201714 ATTGAATGTC
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
107 2 0.02
108 86 0.98
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (108 bp):
AAACTCTTCATTGAGTAGGTATCACAAGTTATTGTGAAACTCTTCATTGCGTAGATATCACGAAT
TATTGTAAAACGCTTCATTGCATAAGTATCACAAGTTACTGTA
Found at i:35201713 original size:36 final size:36
Alignment explanation
Indices: 35201503--35201713 Score: 235
Period size: 36 Copynumber: 5.9 Consensus size: 36
35201493 TGCGTATGAT
* * ** *
35201503 AAACTTTTCATTGAGTAGGTATCATGAGTTATTGTG
1 AAACTCTTCATTGCGTAGGTATCACAAGTTATTGTA
*
35201539 AAACTCTTCATTGCGTAGATATCACGAA-TTATTGTA
1 AAACTCTTCATTGCGTAGGTATCAC-AAGTTATTGTA
* * * * *
35201575 AAACGCTTCATTGCATAAGTATCACTAGTTACTGTA
1 AAACTCTTCATTGCGTAGGTATCACAAGTTATTGTA
*
35201611 AAACTCTTCATTGCGTAGGTATCACAAGTTATTGTG
1 AAACTCTTCATTGCGTAGGTATCACAAGTTATTGTA
* * **
35201647 AAACTTTTCATTGTGTAGGTATCATGAGTTATTGTA
1 AAACTCTTCATTGCGTAGGTATCACAAGTTATTGTA
* * *
35201683 AAACTCTTTATTGTGTAGTTATCACAAGTTA
1 AAACTCTTCATTGCGTAGGTATCACAAGTTA
35201714 ATTGAATGTC
Statistics
Matches: 145, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
35 1 0.01
36 143 0.99
37 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (36 bp):
AAACTCTTCATTGCGTAGGTATCACAAGTTATTGTA
Found at i:35201936 original size:131 final size:133
Alignment explanation
Indices: 35201698--35201949 Score: 447
Period size: 131 Copynumber: 1.9 Consensus size: 133
35201688 CTTTATTGTG
35201698 TAGTTATCACAAGTTAATTGAATGTCAGCTTAGTTGAGAAAAATTATTTATATATATTTTTTAAA
1 TAGTTATCACAAGTTAATTGAATGTCAGCTTAGTTGAGAAAAATTATTTATATATATTTTTTAAA
*
35201763 TGATGACTAATCAGTGGCGTATCTAGGGGGCTGACAAGGGCCTCGATTCTCCTTAATTGGATGTC
66 TGATGACTAATCAGTGGCGTATCTAAGGGGCTGACAAGGGCCTCGATTCTCCTTAATTGGATGTC
35201828 GTA
131 GTA
*
35201831 TAGTTATCACAAGTTAATTGGATGTCAGCTTAGTTGAGAAAAATTA-TT-TATATATTTTTTAAA
1 TAGTTATCACAAGTTAATTGAATGTCAGCTTAGTTGAGAAAAATTATTTATATATATTTTTTAAA
*
35201894 TGATGACTAATCAGTGGTGTATCTAAGGGGCTGAC-AGAGGCCTCGATTCTCCTTAA
66 TGATGACTAATCAGTGGCGTATCTAAGGGGCTGACAAG-GGCCTCGATTCTCCTTAA
35201950 AATGGAAAAT
Statistics
Matches: 115, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
130 2 0.02
131 66 0.57
132 2 0.02
133 45 0.39
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (133 bp):
TAGTTATCACAAGTTAATTGAATGTCAGCTTAGTTGAGAAAAATTATTTATATATATTTTTTAAA
TGATGACTAATCAGTGGCGTATCTAAGGGGCTGACAAGGGCCTCGATTCTCCTTAATTGGATGTC
GTA
Found at i:35203990 original size:11 final size:11
Alignment explanation
Indices: 35203976--35204001 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35203966 TTTTCAATTG
35203976 TTTTTTTTTCT
1 TTTTTTTTTCT
35203987 TTTTTTTTTCT
1 TTTTTTTTTCT
35203998 TTTT
1 TTTT
35204002 CAATTCTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:35211616 original size:2 final size:2
Alignment explanation
Indices: 35211609--35211640 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35211599 GCTTCCATGG
35211609 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35211641 TTACCCTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35211783 original size:2 final size:2
Alignment explanation
Indices: 35211776--35211802 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35211766 TATACATGTT
35211776 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
35211803 GTATGTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35212856 original size:3 final size:3
Alignment explanation
Indices: 35212844--35212883 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
35212834 GTGCAGTTTG
*
35212844 ATA A-A ATA ATA ATA ATA ATA ATA AGA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
35212884 CAGTAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:35214012 original size:10 final size:8
Alignment explanation
Indices: 35213987--35214069 Score: 76
Period size: 9 Copynumber: 9.1 Consensus size: 8
35213977 TTAAATGTTT
35213987 TTTTTATA
1 TTTTTATA
35213995 TATTTTATGA
1 T-TTTTAT-A
35214005 TTTATTATA
1 TTT-TTATA
35214014 TTTTTATA
1 TTTTTATA
35214022 TATTTTATGAA
1 T-TTTTAT--A
35214033 TTTTTATAA
1 TTTTTAT-A
35214042 TTTTTATA
1 TTTTTATA
35214050 TTTTTCATGA
1 TTTTT-AT-A
35214060 GTTTTTATA
1 -TTTTTATA
35214069 T
1 T
35214070 AATTTTTACA
Statistics
Matches: 66, Mismatches: 0, Indels: 18
0.79 0.00 0.21
Matches are distributed among these distances:
8 14 0.21
9 30 0.45
10 15 0.23
11 7 0.11
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.66
Consensus pattern (8 bp):
TTTTTATA
Done.