Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 3 of 120
Found at i:882293 original size:19 final size:20
Alignment explanation
Indices: 882256--882293 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
882246 TTTTTTAAAA
882256 ATAAAAATTTTGAAATTTTT
1 ATAAAAATTTTGAAATTTTT
*
882276 ATAAATATTTTG-AATTTT
1 ATAAAAATTTTGAAATTTT
882294 GAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
ATAAAAATTTTGAAATTTTT
Found at i:882299 original size:18 final size:18
Alignment explanation
Indices: 882258--882329 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
882248 TTTTAAAAAT
* *
882258 AAAAATTTTGAAATTTTT
1 AAAATTTTTGAAATTTTG
882276 ATAAATATTTTG-AATTTTG
1 A-AAAT-TTTTGAAATTTTG
* **
882295 AAAATTATTGAGTTTTTG
1 AAAATTTTTGAAATTTTG
* *
882313 AATATTTTTGTAATTTT
1 AAAATTTTTGAAATTTT
882330 TGTTGAGAGA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
17 4 0.10
18 22 0.54
19 10 0.24
20 5 0.12
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (18 bp):
AAAATTTTTGAAATTTTG
Found at i:882303 original size:19 final size:20
Alignment explanation
Indices: 882256--882299 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
882246 TTTTTTAAAA
* *
882256 ATAAAAATTTTGAAATTTTT
1 ATAAATATTTTGAAATTTTG
882276 ATAAATATTTTG-AATTTTG
1 ATAAATATTTTGAAATTTTG
882295 A-AAAT
1 ATAAAT
882300 TATTGAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 7 0.32
20 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (20 bp):
ATAAATATTTTGAAATTTTG
Found at i:885672 original size:19 final size:20
Alignment explanation
Indices: 885629--885674 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
885619 CGAAAAATGA
*
885629 TTTCTGGAAAATGACTTATT
1 TTTCTGGAAAATGACTAATT
885649 TTTCTGGAAAA-G-CTAATAT
1 TTTCTGGAAAATGACTAAT-T
885668 TTTCTGG
1 TTTCTGG
885675 TGTTTGGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 9 0.38
20 11 0.46
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (20 bp):
TTTCTGGAAAATGACTAATT
Found at i:892504 original size:12 final size:12
Alignment explanation
Indices: 892489--892519 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
892479 ATAAAAATAG
892489 TAATTAGTTAGT
1 TAATTAGTTAGT
892501 TAATTAGTTAGT
1 TAATTAGTTAGT
*
892513 TAGTTAG
1 TAATTAG
892520 ATTAAGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (12 bp):
TAATTAGTTAGT
Found at i:895674 original size:31 final size:31
Alignment explanation
Indices: 895639--895764 Score: 118
Period size: 31 Copynumber: 4.2 Consensus size: 31
895629 TATACTATTC
* * * *
895639 GGTACTTAAATTTAATATTTTTTCTTAATTT
1 GGTACCTAAACTTGATACTTTTTCTTAATTT
*
895670 GGTACCTAAACTT--T--TTTTGGTC-CAATTT
1 GGTACCTAAACTTGATACTTTT--TCTTAATTT
* * *
895698 GATACCCAAACTTGACACTTTTTCTTAATTT
1 GGTACCTAAACTTGATACTTTTTCTTAATTT
*
895729 GGTACCTAAACTTGATACTTTTTCTTAAGTT
1 GGTACCTAAACTTGATACTTTTTCTTAATTT
895760 GGTAC
1 GGTAC
895765 TTAAGCTTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
27 4 0.05
28 16 0.21
29 3 0.04
30 2 0.03
31 48 0.62
32 4 0.05
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (31 bp):
GGTACCTAAACTTGATACTTTTTCTTAATTT
Found at i:895801 original size:60 final size:60
Alignment explanation
Indices: 895724--895836 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
895714 ACTTTTTCTT
* * * * *
895724 AATTTGGTACCTAAACTTGA-TACTTTTTCTTAAGTTGGTACTTAAGCTTTTTTGGGATCC
1 AATTTGATACCTAAACTTAACT-CTTTTTCCTAACTTGGTACCTAAGCTTTTTTGGGATCC
* *
895784 AATTTGATACCTGAACTTAACTCTTTTTCCTAACTTGGTACCTAATCTTTTTT
1 AATTTGATACCTAAACTTAACTCTTTTTCCTAACTTGGTACCTAAGCTTTTTT
895837 TTTTGTTTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 44 0.98
61 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (60 bp):
AATTTGATACCTAAACTTAACTCTTTTTCCTAACTTGGTACCTAAGCTTTTTTGGGATCC
Found at i:895801 original size:91 final size:90
Alignment explanation
Indices: 895639--895828 Score: 245
Period size: 90 Copynumber: 2.1 Consensus size: 90
895629 TATACTATTC
* * * * *
895639 GGTACTTAAATTTAATATTTTTTCTTAATTTGGTACCTAAACTTTTTTTGGTCCAATTTGATACC
1 GGTACCTAAACTTAATACTTTTTCTTAAGTTGGTACCTAAACTTTTTTGGGTCCAATTTGATACC
* * *
895704 CAAACTTGACACTTTTTCTTAATTT
66 CAAACTTAACACTTTTTCCTAACTT
* * *
895729 GGTACCTAAACTTGATACTTTTTCTTAAGTTGGTACTTAAGCTTTTTTGGGATCCAATTTGATAC
1 GGTACCTAAACTTAATACTTTTTCTTAAGTTGGTACCTAAACTTTTTTGGG-TCCAATTTGATAC
** *
895794 CTGAACTTAACTCTTTTTCCTAACTT
65 CCAAACTTAACACTTTTTCCTAACTT
895820 GGTACCTAA
1 GGTACCTAA
895829 TCTTTTTTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
90 43 0.51
91 42 0.49
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (90 bp):
GGTACCTAAACTTAATACTTTTTCTTAAGTTGGTACCTAAACTTTTTTGGGTCCAATTTGATACC
CAAACTTAACACTTTTTCCTAACTT
Found at i:904091 original size:50 final size:50
Alignment explanation
Indices: 904032--904135 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
904022 GACACAAAGG
904032 ACATGACTCATACATAAAGGACATAAGCAGATAAGGAGGAATCTGCTTTT
1 ACATGACTCATACATAAAGGACATAAGCAGATAAGGAGGAATCTGCTTTT
904082 ACATGACTCATACATAAAGGACATAAGCAGATAAGGAGGAATCTGCTTTT
1 ACATGACTCATACATAAAGGACATAAGCAGATAAGGAGGAATCTGCTTTT
904132 ACAT
1 ACAT
904136 TAACCTATCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.24
Consensus pattern (50 bp):
ACATGACTCATACATAAAGGACATAAGCAGATAAGGAGGAATCTGCTTTT
Found at i:912357 original size:50 final size:50
Alignment explanation
Indices: 912282--912385 Score: 199
Period size: 50 Copynumber: 2.1 Consensus size: 50
912272 AGATAGGTTA
912282 ATGTAAAAGCAGATTCCTCCTTATCTGCTTATGTCATTTATGTATGAGTC
1 ATGTAAAAGCAGATTCCTCCTTATCTGCTTATGTCATTTATGTATGAGTC
*
912332 ATGTAAAAGCAGATTCCTCCTTATCTGCTTATGTCCTTTATGTATGAGTC
1 ATGTAAAAGCAGATTCCTCCTTATCTGCTTATGTCATTTATGTATGAGTC
912382 ATGT
1 ATGT
912386 CCTTTGTGTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (50 bp):
ATGTAAAAGCAGATTCCTCCTTATCTGCTTATGTCATTTATGTATGAGTC
Found at i:912943 original size:50 final size:50
Alignment explanation
Indices: 912868--912971 Score: 190
Period size: 50 Copynumber: 2.1 Consensus size: 50
912858 AGATAGGTTA
*
912868 ATGTAAAAGCAGATTCCTCCTTATCTGCTTATGTCCTTTATGTATGAGTC
1 ATGTAAAAGCAGATTCATCCTTATCTGCTTATGTCCTTTATGTATGAGTC
*
912918 ATGTAAAAGTAGATTCATCCTTATCTGCTTATGTCCTTTATGTATGAGTC
1 ATGTAAAAGCAGATTCATCCTTATCTGCTTATGTCCTTTATGTATGAGTC
912968 ATGT
1 ATGT
912972 CATTTGTGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (50 bp):
ATGTAAAAGCAGATTCATCCTTATCTGCTTATGTCCTTTATGTATGAGTC
Found at i:920185 original size:50 final size:50
Alignment explanation
Indices: 920110--920208 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
920100 GATAGGTTAA
920110 TGTAAAAGCAGATTCCTCCTTATCTGCTTATGTCCTTTATGTATGAGTCT
1 TGTAAAAGCAGATTCCTCCTTATCTGCTTATGTCCTTTATGTATGAGTCT
920160 TGTAAAAGCAGATTCCTCCTTATCTGCTTATGTCCTTTATGTATGAGTC
1 TGTAAAAGCAGATTCCTCCTTATCTGCTTATGTCCTTTATGTATGAGTC
920209 ATGTCCTGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.41
Consensus pattern (50 bp):
TGTAAAAGCAGATTCCTCCTTATCTGCTTATGTCCTTTATGTATGAGTCT
Found at i:922435 original size:18 final size:18
Alignment explanation
Indices: 922412--922458 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
922402 GTTATAAAAA
922412 ATATTATATTAATTATAT
1 ATATTATATTAATTATAT
*
922430 ATATTAAATAATAATTATAT
1 ATATT--ATATTAATTATAT
*
922450 GT-TTATATT
1 ATATTATATT
922459 TATATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 4 0.17
18 5 0.21
19 2 0.08
20 13 0.54
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATATTATATTAATTATAT
Found at i:928003 original size:67 final size:68
Alignment explanation
Indices: 927912--928039 Score: 204
Period size: 67 Copynumber: 1.9 Consensus size: 68
927902 CTTTTGGGAC
* *
927912 AAAAGCATTCCTAAACAAGATGCTTTTTGAGAGAAAGAGTAC-TCTCTCAAGCCAAAAATTAGCC
1 AAAAGCATTCCTAAACAAGATGCTTTTTGAGAGAAAAAATACTTCTCTCAAGCCAAAAATTAGCC
927976 AAT
66 AAT
* * *
927979 AAAAGCATTCCTAAATAAGCTGCTTTTTGAGAGAAAAAATACTTCTCTCAAGCTAAAAATT
1 AAAAGCATTCCTAAACAAGATGCTTTTTGAGAGAAAAAATACTTCTCTCAAGCCAAAAATT
928040 GACCCAAAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
67 38 0.69
68 17 0.31
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (68 bp):
AAAAGCATTCCTAAACAAGATGCTTTTTGAGAGAAAAAATACTTCTCTCAAGCCAAAAATTAGCC
AAT
Found at i:941121 original size:23 final size:22
Alignment explanation
Indices: 941095--941154 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 22
941085 TAGTTTCGAA
*
941095 ACAAATATATATTACATTTACAT
1 ACAAATATATATT-CAATTACAT
941118 ACAAATATATA-TCAATTACAT
1 ACAAATATATATTCAATTACAT
941139 A-AATATATATATTCAA
1 ACAA-ATATATATTCAA
941155 ATATAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.06
21 16 0.47
22 5 0.15
23 11 0.32
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
ACAAATATATATTCAATTACAT
Found at i:942686 original size:40 final size:40
Alignment explanation
Indices: 942631--942707 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
942621 TAGGAAGTAA
942631 GAGAAAAAAAAATGATAGCTGGACACAACAATCAATTAGT
1 GAGAAAAAAAAATGATAGCTGGACACAACAATCAATTAGT
942671 GAGAAAAAAAAATGATAGCTGGACACAACAATCAATT
1 GAGAAAAAAAAATGATAGCTGGACACAACAATCAATT
942708 GGTGCATCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.53, C:0.13, G:0.17, T:0.17
Consensus pattern (40 bp):
GAGAAAAAAAAATGATAGCTGGACACAACAATCAATTAGT
Found at i:948035 original size:23 final size:23
Alignment explanation
Indices: 948009--948055 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
947999 TATTGAAAAG
948009 ATAAAATGATTGAAGACTCATCA
1 ATAAAATGATTGAAGACTCATCA
948032 ATAAAATGATTGAAGACTCATCA
1 ATAAAATGATTGAAGACTCATCA
948055 A
1 A
948056 GTTGCATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (23 bp):
ATAAAATGATTGAAGACTCATCA
Found at i:950580 original size:14 final size:14
Alignment explanation
Indices: 950561--950587 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
950551 TAAACTTTTA
950561 ATTCGGTTAATTCT
1 ATTCGGTTAATTCT
950575 ATTCGGTTAATTC
1 ATTCGGTTAATTC
950588 AGTCAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (14 bp):
ATTCGGTTAATTCT
Found at i:953223 original size:44 final size:44
Alignment explanation
Indices: 953168--953271 Score: 208
Period size: 44 Copynumber: 2.4 Consensus size: 44
953158 TAACAAAATG
953168 TTAGTAACAATTAATAATTAATAATTTGATATAATTTGATAATT
1 TTAGTAACAATTAATAATTAATAATTTGATATAATTTGATAATT
953212 TTAGTAACAATTAATAATTAATAATTTGATATAATTTGATAATT
1 TTAGTAACAATTAATAATTAATAATTTGATATAATTTGATAATT
953256 TTAGTAACAATTAATA
1 TTAGTAACAATTAATA
953272 CAATTAACAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (44 bp):
TTAGTAACAATTAATAATTAATAATTTGATATAATTTGATAATT
Found at i:953374 original size:16 final size:16
Alignment explanation
Indices: 953355--953403 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
953345 AATTTAATAC
953355 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
953371 AATTTTGATAACAATT
1 AATTTTAATAACAATT
953387 AATTTTAATAACAATT
1 AATTTTAATAACAATT
953403 A
1 A
953404 GNNNNNNNNN
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:954236 original size:61 final size:61
Alignment explanation
Indices: 954112--954237 Score: 148
Period size: 61 Copynumber: 2.1 Consensus size: 61
954102 TTTCCTTTTC
* * * * ** *
954112 AAAACTTCTAAATTTAAAATTAAAATGGCAAATTTTATAAATATTTAAAGCTAAGTTTTTT
1 AAAACTACTAAAATTAAAATTAAAATGACAAATTTTATAAACATTTAAAGCTAAACTTATT
*
954173 AAAACTACTTAAAATTAAAATT-AAATGACAAATTTTATAAACA-TTATAGGCTAAACTTATT
1 AAAACTAC-TAAAATTAAAATTAAAATGACAAATTTTATAAACATTTA-AAGCTAAACTTATT
954234 AAAA
1 AAAA
954238 TTTTAAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 3 0.05
61 40 0.73
62 12 0.22
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.37
Consensus pattern (61 bp):
AAAACTACTAAAATTAAAATTAAAATGACAAATTTTATAAACATTTAAAGCTAAACTTATT
Found at i:958755 original size:20 final size:20
Alignment explanation
Indices: 958701--958755 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
958691 ATCACTGCGT
* *
958701 AATACAGAAGTTGAAAAATGAG
1 AATA-AGAA-TTGAAAAAAGAA
958723 AATAA-AATATGAAAAAAGAA
1 AATAAGAAT-TGAAAAAAGAA
958743 AATAAGAATTGAA
1 AATAAGAATTGAA
958756 TGACAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 1 0.03
20 20 0.69
21 4 0.14
22 4 0.14
ACGTcount: A:0.64, C:0.02, G:0.16, T:0.18
Consensus pattern (20 bp):
AATAAGAATTGAAAAAAGAA
Found at i:961162 original size:20 final size:20
Alignment explanation
Indices: 961125--961184 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
961115 TTTTTTAAAA
*
961125 TATAAAT-TTTA-AAATTTT
1 TATAAATATTTAGAATTTTT
961143 TATAAATATTTAGAATTTTT
1 TATAAATATTTAGAATTTTT
* *
961163 GA-AAATTATTTTGAATTCTTT
1 TATAAA-TATTTAGAATT-TTT
961184 T
1 T
961185 TGTAATCTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 7 0.21
19 7 0.21
20 17 0.50
21 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (20 bp):
TATAAATATTTAGAATTTTT
Found at i:961168 original size:19 final size:19
Alignment explanation
Indices: 961125--961162 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
961115 TTTTTTAAAA
*
961125 TATAAAT-TTTAAAATTTT
1 TATAAATATTTAGAATTTT
961143 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
961162 T
1 T
961163 GAAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:965328 original size:2 final size:2
Alignment explanation
Indices: 965283--965320 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
965273 ACAGATGGAT
*
965283 AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
965321 CTGAGAGAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:974589 original size:20 final size:20
Alignment explanation
Indices: 974549--974585 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
974539 TGAAGCCAGA
*
974549 AAAAGAAAAAGAAAAATAGG
1 AAAAGAAAAAGAAAAAAAGG
974569 AAAAG-AAAAGAAAAAAA
1 AAAAGAAAAAGAAAAAAA
974586 AGGAGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (20 bp):
AAAAGAAAAAGAAAAAAAGG
Found at i:983372 original size:51 final size:52
Alignment explanation
Indices: 983305--983412 Score: 132
Period size: 51 Copynumber: 2.1 Consensus size: 52
983295 TGTGAAATAG
* * * * *
983305 AGAAATATGAAACATTTGGAAA-TGATTATGGTTTTCTCTAAAATGAAAATGA
1 AGAAATATGAAACATTTGGAAATTAATT-TGATTTTCTCGAAAAAGAAAAAGA
*
983357 AGAAAT-TGAATCATTTGGAAATTAATTTGATTTTCTCGAAAAAGAAAAAGA
1 AGAAATATGAAACATTTGGAAATTAATTTGATTTTCTCGAAAAAGAAAAAGA
983408 A-AAAT
1 AGAAAT
983413 GACTTGAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 4 0.08
51 35 0.71
52 10 0.20
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (52 bp):
AGAAATATGAAACATTTGGAAATTAATTTGATTTTCTCGAAAAAGAAAAAGA
Found at i:988506 original size:15 final size:15
Alignment explanation
Indices: 988457--988507 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
988447 GTACCTTAGG
988457 TTACGTTTTAGTCAT
1 TTACGTTTTAGTCAT
* **
988472 TTATG-TTT-GAAAT
1 TTACGTTTTAGTCAT
988485 GTTACGTTTTAGTCAT
1 -TTACGTTTTAGTCAT
988501 TTACGTT
1 TTACGTT
988508 ATCATGCTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 3 0.11
14 7 0.26
15 14 0.52
16 3 0.11
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.53
Consensus pattern (15 bp):
TTACGTTTTAGTCAT
Found at i:988682 original size:24 final size:25
Alignment explanation
Indices: 988636--988683 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
988626 AATCCCTATA
*
988636 TTTTTTTCATTTTAAGTAGTTTAAT
1 TTTTTTTCATTTTAAGTACTTTAAT
* *
988661 TTTTTTTC-TTTTATGTTCTTTAA
1 TTTTTTTCATTTTAAGTACTTTAA
988684 ACTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (25 bp):
TTTTTTTCATTTTAAGTACTTTAAT
Found at i:988829 original size:14 final size:14
Alignment explanation
Indices: 988812--988845 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
988802 TCATCATTTG
988812 CCTATAACCAAAAC
1 CCTATAACCAAAAC
*
988826 CCTATAATCAAAAC
1 CCTATAACCAAAAC
988840 CC-ATAA
1 CCTATAA
988846 ACTCATACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:990047 original size:15 final size:16
Alignment explanation
Indices: 990022--990051 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
990012 TAAATTCTTT
990022 TTTGAATTTTATTATC
1 TTTGAATTTTATTATC
990038 TTTG-ATTTTATTAT
1 TTTGAATTTTATTAT
990052 TTTCGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTGAATTTTATTATC
Found at i:996404 original size:49 final size:49
Alignment explanation
Indices: 996347--996441 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
996337 CAGCTCGCAT
996347 GGGTTTGCAAGCAATGCTTAGGGAGCTGGTCCAAAAGTGTGCCCGAGGC
1 GGGTTTGCAAGCAATGCTTAGGGAGCTGGTCCAAAAGTGTGCCCGAGGC
*
996396 GGGTTTGCAAGCAATGCTTAGGGTGCTGGTCCAAAAGTGTGCCCGA
1 GGGTTTGCAAGCAATGCTTAGGGAGCTGGTCCAAAAGTGTGCCCGA
996442 TGAATTGACT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (49 bp):
GGGTTTGCAAGCAATGCTTAGGGAGCTGGTCCAAAAGTGTGCCCGAGGC
Found at i:998999 original size:6 final size:6
Alignment explanation
Indices: 998988--999023 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
998978 TGTACCATGG
998988 CCCAAC CCCAAC CCCAAC CCCAAC CCCAAC CCCAAC
1 CCCAAC CCCAAC CCCAAC CCCAAC CCCAAC CCCAAC
999024 ATAGCATAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAC
Found at i:1002658 original size:12 final size:12
Alignment explanation
Indices: 1002641--1002667 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1002631 AAGTAATCTT
1002641 CCACTTCTTTAA
1 CCACTTCTTTAA
1002653 CCACTTCTTTAA
1 CCACTTCTTTAA
1002665 CCA
1 CCA
1002668 AATAAGAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (12 bp):
CCACTTCTTTAA
Found at i:1008700 original size:15 final size:15
Alignment explanation
Indices: 1008659--1008693 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1008649 TCTAATTTTG
*
1008659 ATTAATGTTTAATTA
1 ATTAATGTTTAATGA
1008674 ATTAATGTTTAATGA
1 ATTAATGTTTAATGA
1008689 ATTAA
1 ATTAA
1008694 GATTTAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (15 bp):
ATTAATGTTTAATGA
Found at i:1010565 original size:8 final size:8
Alignment explanation
Indices: 1010508--1010566 Score: 52
Period size: 8 Copynumber: 7.2 Consensus size: 8
1010498 TGCATAAGTG
1010508 TATATATAT
1 TATA-ATAT
1010517 TATAAATAT
1 TAT-AATAT
1010526 T-TAA-AGT
1 TATAATA-T
*
1010533 TAAAATA-
1 TATAATAT
1010540 TATATATAT
1 TATA-ATAT
1010549 TATAATAT
1 TATAATAT
1010557 TATAATAT
1 TATAATAT
1010565 TA
1 TA
1010567 AAACTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
6 1 0.02
7 7 0.17
8 20 0.48
9 13 0.31
10 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
TATAATAT
Found at i:1010663 original size:17 final size:17
Alignment explanation
Indices: 1010641--1010689 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
1010631 AAAAAGAAGG
*
1010641 AGAGAAAGAAACGAAAC
1 AGAGAAGGAAACGAAAC
*
1010658 AGAGAAGGAAACGAAAT
1 AGAGAAGGAAACGAAAC
1010675 AGAGAAGGAAA-GAAA
1 AGAGAAGGAAACGAAA
1010690 GAAAAGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 4 0.13
17 26 0.87
ACGTcount: A:0.63, C:0.06, G:0.29, T:0.02
Consensus pattern (17 bp):
AGAGAAGGAAACGAAAC
Found at i:1011570 original size:41 final size:40
Alignment explanation
Indices: 1011524--1011658 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 40
1011514 GACGTCGAGT
* *
1011524 CGATGAGACACTGGGTATCAATTTATTACTTC-GTATTAATT
1 CGATGAGACACTGGGTGTCAATTTATTACTTCAGT-TTAA-C
* * *
1011565 TGATGAGGCACTGGGTGCCAA--T-TTACTTCAGTTTAAC
1 CGATGAGACACTGGGTGTCAATTTATTACTTCAGTTTAAC
** *
1011602 CGATGAGACACTGGGTGTCAATTTATTACTTCAAATTATC
1 CGATGAGACACTGGGTGTCAATTTATTACTTCAGTTTAAC
*
1011642 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
1011659 CCAAACTGGT
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
37 18 0.23
38 11 0.14
39 4 0.05
40 28 0.36
41 17 0.22
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTTATTACTTCAGTTTAAC
Found at i:1011827 original size:20 final size:20
Alignment explanation
Indices: 1011802--1011841 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1011792 TTGAATATGG
1011802 TATGGATAAAGCAATTGCAT
1 TATGGATAAAGCAATTGCAT
1011822 TATGGATAAAGCAATTGCAT
1 TATGGATAAAGCAATTGCAT
1011842 AAATGAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (20 bp):
TATGGATAAAGCAATTGCAT
Found at i:1015650 original size:23 final size:24
Alignment explanation
Indices: 1015618--1015668 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1015608 GAGGAGTTAA
1015618 TTTTAAATTTTATTAGTTAA-TTT
1 TTTTAAATTTTATTAGTTAAGTTT
* * *
1015641 TTTTATATTTTTTTATTTAAGTTT
1 TTTTAAATTTTATTAGTTAAGTTT
1015665 TTTT
1 TTTT
1015669 TCTTTGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTAAATTTTATTAGTTAAGTTT
Found at i:1027332 original size:65 final size:67
Alignment explanation
Indices: 1027170--1027335 Score: 212
Period size: 65 Copynumber: 2.5 Consensus size: 67
1027160 CTTGCATTGC
* **
1027170 TGCTGATTTATGTTGTCCAAAGCTAGACATATTAGTGGTGTAATAACTATTTAATGCTTTGTTTT
1 TGCTGATTTATGTTGTCCAAAGCTAGACATATTAATGGTGT-ATAACTATTTAATGCCCTGTTTT
*
1027235 GTT
65 ATT
* * ** *
1027238 TGTTGATTTATGTTGTCCAAAGCCAGACATATTAATGGTGT-T-GTTGTTTAATGCCCTGTTTTA
1 TGCTGATTTATGTTGTCCAAAGCTAGACATATTAATGGTGTATAACTATTTAATGCCCTGTTTTA
1027301 TT
66 TT
1027303 TGCTGATTTATGTTGTCCAAAG-TAGGACATATT
1 TGCTGATTTATGTTGTCCAAAGCTA-GACATATT
1027336 GATTTCGTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 1 0.01
65 46 0.53
66 1 0.01
68 38 0.44
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (67 bp):
TGCTGATTTATGTTGTCCAAAGCTAGACATATTAATGGTGTATAACTATTTAATGCCCTGTTTTA
TT
Found at i:1027708 original size:72 final size:70
Alignment explanation
Indices: 1027560--1027697 Score: 195
Period size: 72 Copynumber: 1.9 Consensus size: 70
1027550 GGACTGATAG
*
1027560 AGGGAAGATAATTTAAGAAATGGAAAATGGCTTTGCAGAGGTTCAGAAGTGTTGATCAAAGTTTA
1 AGGGAAGATAATTTAAGAAATGGAAAATGGCTTTGCAGAGGTTCAGAAGGGTTGATCAAAGTTTA
1027625 AACAA
66 AACAA
* * * * **
1027630 AGGGAAGATATTTTGAAGAAGTGGAAAAATGGCTTTGCGGAGGTTCGGAAGGGTTGATCGGAGTT
1 AGGGAAGATAATTT-AAGAAATGG-AAAATGGCTTTGCAGAGGTTCAGAAGGGTTGATCAAAGTT
1027695 TAA
64 TAA
1027698 GAATGAGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
70 13 0.22
71 8 0.14
72 38 0.64
ACGTcount: A:0.36, C:0.07, G:0.31, T:0.26
Consensus pattern (70 bp):
AGGGAAGATAATTTAAGAAATGGAAAATGGCTTTGCAGAGGTTCAGAAGGGTTGATCAAAGTTTA
AACAA
Found at i:1030248 original size:2 final size:2
Alignment explanation
Indices: 1030241--1030269 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1030231 CTTTCCTATC
1030241 TA 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 TA T
1030270 GATAAAATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1030636 original size:44 final size:44
Alignment explanation
Indices: 1030551--1030637 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
1030541 AATAAAAGAG
* *
1030551 TTATTAATTAAAACAATGAATTAAGAAACTAGAAAATAATATGT
1 TTATTAATTAAAACAATGAATTAAGAAACTAAAAAAAAATATGT
* *
1030595 TTATTAATTAACAAC-ATTAATTAA-AAATTTAAAAAAAAATATG
1 TTATTAATTAA-AACAATGAATTAAGAAA-CTAAAAAAAAATATG
1030638 AAATAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 3 0.08
44 31 0.84
45 3 0.08
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (44 bp):
TTATTAATTAAAACAATGAATTAAGAAACTAAAAAAAAATATGT
Found at i:1037543 original size:17 final size:16
Alignment explanation
Indices: 1037518--1037556 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1037508 CTAATACTAA
*
1037518 AATAAATAAATTAAAG
1 AATAAATAAACTAAAG
*
1037534 AATAACATAAACTAAAT
1 AATAA-ATAAACTAAAG
1037551 AATAAA
1 AATAAA
1037557 CAACTAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (16 bp):
AATAAATAAACTAAAG
Found at i:1037652 original size:24 final size:24
Alignment explanation
Indices: 1037625--1037689 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
1037615 AAGGATAATA
*
1037625 ATAAATAAAATAATAAAACCAAAT
1 ATAAATAAAATAATAAAAACAAAT
* *
1037649 AT-AATGAATATAATAAAAATAAAT
1 ATAAAT-AAAATAATAAAAACAAAT
1037673 A-AAAT-AAATAATAAAAA
1 ATAAATAAAATAATAAAAA
1037690 GAAAAAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 11 0.31
23 3 0.09
24 21 0.60
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (24 bp):
ATAAATAAAATAATAAAAACAAAT
Found at i:1042725 original size:21 final size:20
Alignment explanation
Indices: 1042676--1042725 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1042666 ATGCAAAAAT
* *
1042676 TAAATAAATATTAAAAATAT
1 TAAATAAAAATTAAAAATAC
*
1042696 TAAATTAAAAATTAAAAATGGC
1 TAAA-TAAAAATTAAAAAT-AC
1042718 TAAATAAA
1 TAAATAAA
1042726 TGAAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 17 0.68
22 4 0.16
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (20 bp):
TAAATAAAAATTAAAAATAC
Found at i:1044701 original size:39 final size:40
Alignment explanation
Indices: 1044567--1044703 Score: 163
Period size: 39 Copynumber: 3.5 Consensus size: 40
1044557 TGTTTTTGAA
* * *
1044567 TATTGCGAAATATGCTTGAATGTTATGTGATTATATGA-G
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGATG
* * ** *
1044606 TATTGTGATATGTGCTTGAACATTATGTAATTATATGAT-
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGATG
*
1044645 TATTGTGATATATGCTTAAATGTTATGCGATTATAT-ATG
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGATG
*
1044684 TAATGTGATATATGCTTAAA
1 TATTGTGATATATGCTTAAA
1044704 AGTGAACATG
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
38 2 0.02
39 81 0.98
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (40 bp):
TATTGTGATATATGCTTAAATGTTATGTGATTATATGATG
Found at i:1055921 original size:16 final size:15
Alignment explanation
Indices: 1055900--1055929 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1055890 ATTCACCCTA
1055900 AATATTGATTTAATTT
1 AATATTG-TTTAATTT
1055916 AATATTGTTTAATT
1 AATATTGTTTAATT
1055930 ATTTAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
AATATTGTTTAATTT
Found at i:1057271 original size:25 final size:25
Alignment explanation
Indices: 1057237--1057286 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1057227 TTTAAAGTAT
1057237 TAGGGTTTTTCCATTGATGAATATG
1 TAGGGTTTTTCCATTGATGAATATG
1057262 TAGGGTTTTTCCATTGATGAATATG
1 TAGGGTTTTTCCATTGATGAATATG
1057287 CTTGAAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (25 bp):
TAGGGTTTTTCCATTGATGAATATG
Found at i:1058551 original size:16 final size:18
Alignment explanation
Indices: 1058518--1058551 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1058508 TAGAAATTTT
1058518 GATTAGAATTGATAAAAG
1 GATTAGAATTGATAAAAG
1058536 GATTA-AATTG-TAAAAG
1 GATTAGAATTGATAAAAG
1058552 AAACTATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
GATTAGAATTGATAAAAG
Found at i:1060680 original size:25 final size:25
Alignment explanation
Indices: 1060642--1060697 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1060632 CACACCACAA
* *
1060642 CTCGTATGAGCTTC-CTAATTTGCAG
1 CTCGTATGAACTTCTC-AATTTACAG
*
1060667 CTCGTATGAACTTCTCGATTTACAG
1 CTCGTATGAACTTCTCAATTTACAG
1060692 CTCGTA
1 CTCGTA
1060698 AGAGCATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (25 bp):
CTCGTATGAACTTCTCAATTTACAG
Found at i:1060711 original size:25 final size:25
Alignment explanation
Indices: 1060683--1060731 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1060673 TGAACTTCTC
* *
1060683 GATTTACAGCTCGTAAGAGCATACT
1 GATTCACAACTCGTAAGAGCATACT
* *
1060708 GATTCATAACTCGTATGAGCATAC
1 GATTCACAACTCGTAAGAGCATAC
1060732 ATGAATATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (25 bp):
GATTCACAACTCGTAAGAGCATACT
Found at i:1071273 original size:19 final size:20
Alignment explanation
Indices: 1071236--1071275 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1071226 TCAAGGTAGA
*
1071236 ATATGATTGCTTTGGTCTGC
1 ATATGATTGCTTTAGTCTGC
*
1071256 ATATGATT-CTTTATTCTGC
1 ATATGATTGCTTTAGTCTGC
1071275 A
1 A
1071276 GACTGAAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.47
Consensus pattern (20 bp):
ATATGATTGCTTTAGTCTGC
Found at i:1076242 original size:17 final size:17
Alignment explanation
Indices: 1076213--1076245 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1076203 TGAATAAAAA
1076213 AATAATAATTTTTTTTG
1 AATAATAATTTTTTTTG
1076230 AATAA-AATATTTTTTT
1 AATAATAAT-TTTTTTT
1076246 ATATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
AATAATAATTTTTTTTG
Found at i:1076251 original size:10 final size:11
Alignment explanation
Indices: 1076235--1076267 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
1076225 TTTTGAATAA
1076235 AATATTTTTTT
1 AATATTTTTTT
1076246 -ATATTTTTTT
1 AATATTTTTTT
1076256 AATAATTTTTTT
1 AAT-ATTTTTTT
1076268 TAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 2 0.10
12 8 0.40
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
AATATTTTTTT
Found at i:1076364 original size:27 final size:27
Alignment explanation
Indices: 1076326--1076392 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
1076316 CCTATTAGGT
1076326 AGGCGCCAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
1076353 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
1076380 AGGCGCCAATGAA
1 AGGCGCCAATGAA
1076393 TATTGTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.31, C:0.24, G:0.33, T:0.12
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCACAGAG
Found at i:1076491 original size:21 final size:21
Alignment explanation
Indices: 1076462--1076505 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1076452 TGGATTAGTA
*
1076462 TTTTGTATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
1076483 TTTTATATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
1076504 TT
1 TT
1076506 GTGTTTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
TTTTATATGAATATTGTAATT
Found at i:1076636 original size:16 final size:16
Alignment explanation
Indices: 1076593--1076636 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1076583 AAAATCAAAT
*
1076593 AAAATTTAATTATATA
1 AAAATTAAATTATATA
* *
1076609 AAAGTTACATTATATA
1 AAAATTAAATTATATA
1076625 AAAATTAAATTA
1 AAAATTAAATTA
1076637 GTTAACAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTAAATTATATA
Found at i:1076712 original size:38 final size:38
Alignment explanation
Indices: 1076669--1076750 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
1076659 AAAAAGTCAG
*
1076669 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATAATTTTTAATTTTT
*
1076707 TTATAATTAAACTTTTAATAAGATAATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATAATTTTTAATTTTT
1076745 TTATAA
1 TTATAA
1076751 ACTTTATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATAATTTTTAATTTTT
Found at i:1076885 original size:60 final size:60
Alignment explanation
Indices: 1076783--1076904 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
1076773 ATATTAAACT
* * * * * *
1076783 AAACACAACAACTTATAGCTTAATCCTAAATTATTAATAAATTAAATTTTA-AATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATT-AATTATAGAATAATTAC
*
1076843 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAGAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAGAATAATTAC
1076903 AA
1 AA
1076905 TATTCATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 6 0.11
60 48 0.89
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAGAATAATTAC
Found at i:1076932 original size:8 final size:8
Alignment explanation
Indices: 1076919--1077076 Score: 79
Period size: 8 Copynumber: 18.4 Consensus size: 8
1076909 CATACAAAAA
1076919 ATTACAAT
1 ATTACAAT
1076927 ATTACAAT
1 ATTACAAT
* * *
1076935 ATATCCCGAC
1 AT-T-ACAAT
1076945 ATTACAAT
1 ATTACAAT
*
1076953 ATTCATACAAA
1 A-T--TACAAT
1076964 ATTACAAT
1 ATTACAAT
1076972 ATTACAAT
1 ATTACAAT
*
1076980 ATTCATACAAA
1 A-T--TACAAT
1076991 ATTACAAT
1 ATTACAAT
1076999 ATTACAAT
1 ATTACAAT
*
1077007 ATTCATACAAA
1 A-T--TACAAT
*
1077018 ATTATAAT
1 ATTACAAT
1077026 ATTACAAT
1 ATTACAAT
*
1077034 ATTCATACAAA
1 A-T--TACAAT
1077045 ATTACAAT
1 ATTACAAT
1077053 ATT-C-AT
1 ATTACAAT
* *
1077059 A-TAAAAA
1 ATTACAAT
1077066 ATTACAAT
1 ATTACAAT
1077074 ATT
1 ATT
1077077 CATACAAAAT
Statistics
Matches: 113, Mismatches: 20, Indels: 34
0.68 0.12 0.20
Matches are distributed among these distances:
5 1 0.01
6 3 0.03
7 3 0.03
8 68 0.60
9 6 0.05
10 8 0.07
11 24 0.21
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.34
Consensus pattern (8 bp):
ATTACAAT
Found at i:1076969 original size:19 final size:19
Alignment explanation
Indices: 1076966--1077159 Score: 120
Period size: 19 Copynumber: 10.1 Consensus size: 19
1076956 CATACAAAAT
*
1076966 TACAATATTACAATATTCA
1 TACAAAATTACAATATTCA
1076985 TACAAAATTACAATA-T--
1 TACAAAATTACAATATTCA
* *
1077001 TACAATATTCATACAAAATT-A
1 TACAA-AAT--TACAATATTCA
*
1077022 T--AATATTACAATATTCA
1 TACAAAATTACAATATTCA
1077039 TACAAAATTACAATATTCATA
1 TACAAAATTACAATATTC--A
*
1077060 TAAAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
1077079 TACAAAA-TACAA-ATCTAA
1 TACAAAATTACAATAT-TCA
*
1077097 AACTATAAA-TACAAATTTAATT-A
1 TAC-A-AAATTAC-AA--T-ATTCA
* *
1077120 TAAAATAATTACAATATTAA
1 TACAA-AATTACAATATTCA
1077140 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
1077159 T
1 T
1077160 TGGCGCCTCT
Statistics
Matches: 139, Mismatches: 15, Indels: 42
0.71 0.08 0.21
Matches are distributed among these distances:
16 13 0.09
17 6 0.04
18 11 0.08
19 61 0.44
20 13 0.09
21 22 0.16
22 5 0.04
23 5 0.04
24 1 0.01
25 2 0.01
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:1076981 original size:27 final size:27
Alignment explanation
Indices: 1076945--1077076 Score: 213
Period size: 27 Copynumber: 5.1 Consensus size: 27
1076935 ATATCCCGAC
1076945 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
1076972 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
*
1076999 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
1077026 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
1077053 ATT-C-ATA-T-A-A-AAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
1077074 ATT
1 ATT
1077077 CATACAAAAT
Statistics
Matches: 103, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
21 14 0.14
22 1 0.01
23 1 0.01
24 1 0.01
25 3 0.03
26 1 0.01
27 82 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:1077109 original size:67 final size:61
Alignment explanation
Indices: 1076999--1077156 Score: 167
Period size: 67 Copynumber: 2.5 Consensus size: 61
1076989 AAATTACAAT
* * **
1076999 ATTACAATATTCATACAAAATTATAATATTACAATATTCATACAAAATTACAATATTCATATAAA
1 ATTACAATATTCATACAAAATTACAATATTAAAATATAAATAC-AAATT--AA-ATT-ATA-AAA
1077064 AA
60 AA
* *
1077066 ATTACAATATTCATACAAAA-TACAA-ATCTAAAACTATAAATACAAATTTAATTATAAAATA
1 ATTACAATATTCATACAAAATTACAATAT-TAAAA-TATAAATACAAATTAAATTATAAAAAA
*
1077127 ATTACAATATTAATACAAAATTACAATATT
1 ATTACAATATTCATACAAAATTACAATATT
1077157 CATTGGCGCC
Statistics
Matches: 80, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
61 23 0.29
62 9 0.11
63 5 0.06
64 1 0.01
65 2 0.03
66 13 0.16
67 27 0.34
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (61 bp):
ATTACAATATTCATACAAAATTACAATATTAAAATATAAATACAAATTAAATTATAAAAAA
Found at i:1077232 original size:27 final size:27
Alignment explanation
Indices: 1077155--1077221 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
1077145 AATTACAATA
1077155 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
1077182 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
1077209 TTCATTGGCGCCT
1 TTCATTGGCGCCT
1077222 ACCTGATAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.13, C:0.33, G:0.22, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:1078211 original size:1 final size:1
Alignment explanation
Indices: 1078205--1078233 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1078195 AAGTTTCTTC
1078205 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1078234 GTTGTTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1079329 original size:22 final size:22
Alignment explanation
Indices: 1079271--1079352 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
1079261 AAGTGAAGGT
* **
1079271 AGAGCTTAGTACGTGAAACATG
1 AGAGCTTAGTACGTTAGCCATG
1079293 AGAGCTTAGTACGTTAGCCATG
1 AGAGCTTAGTACGTTAGCCATG
1079315 AGAGCTTAGTACGTTAGCCATG
1 AGAGCTTAGTACGTTAGCCATG
* * *
1079337 AGGGTTTAGTTCGTTA
1 AGAGCTTAGTACGTTA
1079353 AACATGGGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (22 bp):
AGAGCTTAGTACGTTAGCCATG
Found at i:1081812 original size:25 final size:23
Alignment explanation
Indices: 1081784--1081836 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
1081774 ATAATTTTAG
1081784 AATTTTTTTAAGATTTAAATAATAT
1 AATTTTTTTAAGATTT--ATAATAT
*
1081809 AA-TTTTTTAGGATTTATAATAT
1 AATTTTTTTAAGATTTATAATAT
1081831 AATTTT
1 AATTTT
1081837 AGAAAGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 9 0.35
23 3 0.12
24 12 0.46
25 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.55
Consensus pattern (23 bp):
AATTTTTTTAAGATTTATAATAT
Found at i:1081827 original size:22 final size:23
Alignment explanation
Indices: 1081787--1081836 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
1081777 ATTTTAGAAT
1081787 TTTTTTAAGATTTAAATAATATAA
1 TTTTTTAAGATTT-AATAATATAA
*
1081811 TTTTTTAGGATTT-ATAATATAA
1 TTTTTTAAGATTTAATAATATAA
1081833 TTTT
1 TTTT
1081837 AGAAAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 13 0.52
24 12 0.48
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (23 bp):
TTTTTTAAGATTTAATAATATAA
Found at i:1088383 original size:19 final size:19
Alignment explanation
Indices: 1088359--1088409 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
1088349 TTAAATTGAT
1088359 AATAATTTTATCTCA-TTTA
1 AATAATTTTAT-TCACTTTA
1088378 AATAATTTGT-TTCACTTTA
1 AATAATTT-TATTCACTTTA
1088397 ATATAATTTTATT
1 A-ATAATTTTATT
1088410 TTAAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 3 0.11
19 15 0.54
20 10 0.36
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (19 bp):
AATAATTTTATTCACTTTA
Found at i:1088592 original size:16 final size:15
Alignment explanation
Indices: 1088571--1088621 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
1088561 TACCAAACCT
1088571 AAATGACTCGAACATG
1 AAATGACTCGAAC-TG
* *
1088587 AAATGATTCAAACTCG
1 AAATGACTCGAACT-G
1088603 AAATGACTCGAACTTG
1 AAATGACTCGAAC-TG
1088619 AAA
1 AAA
1088622 CTAACCCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.22
Consensus pattern (15 bp):
AAATGACTCGAACTG
Found at i:1092392 original size:13 final size:12
Alignment explanation
Indices: 1092369--1092394 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1092359 CAATATGAAG
1092369 TTGACAAAAAAA
1 TTGACAAAAAAA
1092381 TTGACAAAAAAA
1 TTGACAAAAAAA
1092393 TT
1 TT
1092395 TAAAATGACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (12 bp):
TTGACAAAAAAA
Found at i:1105227 original size:12 final size:12
Alignment explanation
Indices: 1105210--1105235 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1105200 TTTGTCTCGG
1105210 TCCGTACAACTT
1 TCCGTACAACTT
1105222 TCCGTACAACTT
1 TCCGTACAACTT
1105234 TC
1 TC
1105236 TGGAGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.35, G:0.08, T:0.35
Consensus pattern (12 bp):
TCCGTACAACTT
Found at i:1113153 original size:8 final size:8
Alignment explanation
Indices: 1113140--1113166 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1113130 CAGCCTCTAC
1113140 AAAAAACA
1 AAAAAACA
1113148 AAAAAACA
1 AAAAAACA
1113156 AAAAAACA
1 AAAAAACA
1113164 AAA
1 AAA
1113167 CTTGAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:1118499 original size:31 final size:29
Alignment explanation
Indices: 1118464--1118522 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1118454 ATTGTCATGT
1118464 TTGAGTTGGCAAAATTTGGCAACAAATTATC
1 TTGAGTT-G-AAAATTTGGCAACAAATTATC
* *
1118495 TTGAGTTGTAATTTTGGCAACAAATTAT
1 TTGAGTTGAAAATTTGGCAACAAATTAT
1118523 TTTGGGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 18 0.69
30 1 0.04
31 7 0.27
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (29 bp):
TTGAGTTGAAAATTTGGCAACAAATTATC
Found at i:1124012 original size:21 final size:22
Alignment explanation
Indices: 1123977--1124024 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1123967 CAAATGTGTT
1123977 AAAATTATTAATTAAAAATAA-A
1 AAAATTATTAATT-AAAATAAGA
*
1123999 AAAATTATT-TTTAAAATAAGA
1 AAAATTATTAATTAAAATAAGA
1124020 AAAAT
1 AAAAT
1124025 GTGTTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 8 0.33
22 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATTATTAATTAAAATAAGA
Found at i:1124014 original size:20 final size:22
Alignment explanation
Indices: 1123977--1124024 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 22
1123967 CAAATGTGTT
1123977 AAAATTATTAATTAAAAATAA-A
1 AAAATTATT-ATTAAAAATAAGA
*
1123999 AAAATTATT-TTTAAAATAAGA
1 AAAATTATTATTAAAAATAAGA
1124020 AAAAT
1 AAAAT
1124025 GTGTTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 6 0.25
22 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATTATTATTAAAAATAAGA
Found at i:1124405 original size:43 final size:43
Alignment explanation
Indices: 1124357--1124707 Score: 315
Period size: 43 Copynumber: 8.0 Consensus size: 43
1124347 TCAAAAGTAC
* * *
1124357 TTCTCAAAATCATTTTTCAAAAGCATTTTTTACAAGAACTTCT
1 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGAACTTCT
*
1124400 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGCACTTCT
1 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGAACTTCT
**
1124443 TTCTCAAAATTTTTTTTCGAAAGCACTTTTTAAAA-ACACTTCT
1 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGA-ACTTCT
* * *
1124486 TTCTCAAAATTATTTTTTGAAAGCACTTTTTAAAAG--C-AC-
1 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGAACTTCT
* * * * *
1124525 TTCTCAAAAGCA--ATGCTAAA-CACTCAAATCTTAAACCA-AACTTTTCAAAAGT
1 TTCTCAAAATCATTTTTCGAAAGCACT----TTTTAAA--AGAAC--TTC-----T
* *
1124577 ACTTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGTACTTCT
1 --TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGAACTTCT
* *
1124622 TTCTCAAAATCATTTTTCGAAAACACTTTTTAAAAGCACTTCT
1 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGAACTTCT
* *
1124665 TTCTCAAAATCAATTTTCGAAAGCACTTTTTAAAAGCACTTCT
1 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGAACTTCT
1124708 CAAAAGCAAT
Statistics
Matches: 254, Mismatches: 29, Indels: 50
0.76 0.09 0.15
Matches are distributed among these distances:
36 4 0.02
37 4 0.02
39 10 0.04
40 7 0.03
41 1 0.00
42 1 0.00
43 193 0.76
45 1 0.00
46 1 0.00
50 3 0.01
51 1 0.00
52 2 0.01
53 6 0.02
54 11 0.04
56 5 0.02
57 4 0.02
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (43 bp):
TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGAACTTCT
Found at i:1124521 original size:13 final size:13
Alignment explanation
Indices: 1124462--1124536 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
1124452 TTTTTTTTCG
1124462 AAAGCACTTTTTA
1 AAAGCACTTTTTA
*
1124475 AAAACACTTCTTTCTCA
1 AAAGCAC-T-TTT-T-A
** * *
1124492 AAATTATTTTTTG
1 AAAGCACTTTTTA
1124505 AAAGCACTTTTTA
1 AAAGCACTTTTTA
* *
1124518 AAAGCACTTCTCA
1 AAAGCACTTTTTA
1124531 AAAGCA
1 AAAGCA
1124537 ATGCTAAACA
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
13 32 0.68
14 2 0.04
15 6 0.13
16 2 0.04
17 5 0.11
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.36
Consensus pattern (13 bp):
AAAGCACTTTTTA
Found at i:1124661 original size:13 final size:13
Alignment explanation
Indices: 1124564--1124715 Score: 67
Period size: 13 Copynumber: 11.1 Consensus size: 13
1124554 CTTAAACCAA
* *
1124564 ACTTTTCAAAAGT
1 ACTTTTTAAAAGC
* * *
1124577 ACTTCTCAAAATC
1 ACTTTTTAAAAGC
1124590 A-TTTTTCAAAAGC
1 ACTTTTT-AAAAGC
*
1124603 ACTTTTTAAAAGT
1 ACTTTTTAAAAGC
*
1124616 ACTTCTTTCTCAAAATC
1 AC-T-TTT-T-AAAAGC
1124633 A-TTTTTCGAAAA-C
1 ACTTTTT--AAAAGC
1124646 ACTTTTTAAAAGC
1 ACTTTTTAAAAGC
*
1124659 ACTTCTTTCTCAAAATC
1 AC-T-TTT-T-AAAAGC
* **
1124676 AATTTTCGAAAGC
1 ACTTTTTAAAAGC
1124689 ACTTTTTAAAAGC
1 ACTTTTTAAAAGC
* *
1124702 ACTTCTCAAAAGC
1 ACTTTTTAAAAGC
1124715 A
1 A
1124716 ATGCTAAACT
Statistics
Matches: 106, Mismatches: 20, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
12 7 0.07
13 56 0.53
14 19 0.18
15 10 0.09
16 3 0.03
17 11 0.10
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (13 bp):
ACTTTTTAAAAGC
Found at i:1124700 original size:179 final size:179
Alignment explanation
Indices: 1124400--1124724 Score: 569
Period size: 179 Copynumber: 1.8 Consensus size: 179
1124390 AAGAACTTCT
* **
1124400 TTCTCAAAATCATTTTTCGAAAGCACTTTTTAAAAGCACTTCTTTCTCAAAATTTTTTTTCGAAA
1 TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGCACTTCTTTCTCAAAATCATTTTTCGAAA
* * * *
1124465 GCACTTTTTAAAAACACTTCTTTCTCAAAATTATTTTTTGAAAGCACTTTTTAAAAGCACTTCTC
66 ACACTTTTTAAAAACACTTCTTTCTCAAAATCAATTTTCGAAAGCACTTTTTAAAAGCACTTCTC
1124530 AAAAGCAATGCTAAACACTCAAATCTTAAACCAAACTTTTCAAAAGTAC
131 AAAAGCAATGCTAAACACTCAAATCTTAAACCAAACTTTTCAAAAGTAC
*
1124579 TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGTACTTCTTTCTCAAAATCATTTTTCGAAA
1 TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGCACTTCTTTCTCAAAATCATTTTTCGAAA
*
1124644 ACACTTTTTAAAAGCACTTCTTTCTCAAAATCAATTTTCGAAAGCACTTTTTAAAAGCACTTCTC
66 ACACTTTTTAAAAACACTTCTTTCTCAAAATCAATTTTCGAAAGCACTTTTTAAAAGCACTTCTC
1124709 AAAAGCAATGCTAAAC
131 AAAAGCAATGCTAAAC
1124725 TAACCCTAAG
Statistics
Matches: 137, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
179 137 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (179 bp):
TTCTCAAAATCATTTTTCAAAAGCACTTTTTAAAAGCACTTCTTTCTCAAAATCATTTTTCGAAA
ACACTTTTTAAAAACACTTCTTTCTCAAAATCAATTTTCGAAAGCACTTTTTAAAAGCACTTCTC
AAAAGCAATGCTAAACACTCAAATCTTAAACCAAACTTTTCAAAAGTAC
Found at i:1128332 original size:18 final size:18
Alignment explanation
Indices: 1128309--1128364 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
1128299 ATAAACACCA
1128309 AAAAATTATTTTAAAAAT
1 AAAAATTATTTTAAAAAT
*
1128327 AAAAATAATTTTAAAAAT
1 AAAAATTATTTTAAAAAT
* *
1128345 --TAA-TATTTTAAAATT
1 AAAAATTATTTTAAAAAT
1128360 AAAAA
1 AAAAA
1128365 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 10 0.32
16 2 0.06
17 2 0.06
18 17 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATTATTTTAAAAAT
Found at i:1133021 original size:33 final size:33
Alignment explanation
Indices: 1132983--1133056 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
1132973 TTCCTTTTGA
* * * ** *
1132983 AAATCAAGAGTTTTTTGTTGTATTTGTTGTTGG
1 AAATCAAGAGTTTGTCGTTGTATCTACTGTTGC
*
1133016 AAATCAATAGTTTGTCGTTGTATCTACTGTTGC
1 AAATCAAGAGTTTGTCGTTGTATCTACTGTTGC
1133049 AAATCAAG
1 AAATCAAG
1133057 CAGATTAGCT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.43
Consensus pattern (33 bp):
AAATCAAGAGTTTGTCGTTGTATCTACTGTTGC
Found at i:1135296 original size:19 final size:18
Alignment explanation
Indices: 1135247--1135302 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
1135237 ATTTGTTCCT
1135247 AATTAAACTCTAAAAGATA
1 AATTAAA-TCTAAAAGATA
** *
1135266 AA-TAAAGATAAAAGCTGA
1 AATTAAATCTAAAAGAT-A
*
1135284 AATTAAATCTAAAAAATA
1 AATTAAATCTAAAAGATA
1135302 A
1 A
1135303 TCCTAACAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
17 7 0.25
18 9 0.32
19 12 0.43
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.23
Consensus pattern (18 bp):
AATTAAATCTAAAAGATA
Found at i:1138121 original size:30 final size:31
Alignment explanation
Indices: 1138097--1138155 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
1138087 GTAAATACTC
*
1138097 AAAATTTGAGGGGTTAA-AATGTAAATATAA
1 AAAATTTGAAGGGTTAATAATGTAAATATAA
*
1138127 AAAATTTGAAGGGTTAATAGTGTAAATAT
1 AAAATTTGAAGGGTTAATAATGTAAATAT
1138156 TTTAAGGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.32
Consensus pattern (31 bp):
AAAATTTGAAGGGTTAATAATGTAAATATAA
Found at i:1140724 original size:53 final size:54
Alignment explanation
Indices: 1140661--1140768 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
1140651 ATTGGTACAA
1140661 GAATTAAATTGTAAAGCATG-AAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1 GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1140714 GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1 GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
1140768 G
1 G
1140769 CATGCATGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 20 0.37
54 34 0.63
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (54 bp):
GAATTAAATTGTAAAGCATGTAAAAACATTATGCGAAAAGTGTAAAAGTGATAT
Found at i:1141537 original size:44 final size:44
Alignment explanation
Indices: 1141477--1141564 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
1141467 ATTGACTATA
1141477 AAGGTGGTTGTTATGTGATGATTCCACCGAGTATCAT-TTATTAT
1 AAGGTGGTTGTTATGTGATGATTCCACCGAGTATC-TGTTATTAT
* *
1141521 AAGGTGGTTGTTATGTGCTGATTCCACCGTGTATCTGTTATTAT
1 AAGGTGGTTGTTATGTGATGATTCCACCGAGTATCTGTTATTAT
1141565 TCCGAAGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.98
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.42
Consensus pattern (44 bp):
AAGGTGGTTGTTATGTGATGATTCCACCGAGTATCTGTTATTAT
Found at i:1153345 original size:2 final size:2
Alignment explanation
Indices: 1153338--1153370 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1153328 TCTGCCTTTC
1153338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1153371 ATACTTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1165784 original size:5 final size:5
Alignment explanation
Indices: 1165774--1165803 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1165764 GCTGGGGGCA
*
1165774 ATTGT ATTGT ATTGT ATTGT ATTGT GTTGT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
1165804 CTGTACACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (5 bp):
ATTGT
Found at i:1168833 original size:22 final size:22
Alignment explanation
Indices: 1168808--1168850 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1168798 TTTTAAAATA
* *
1168808 TAAAAAATAGGGACTAAATTTC
1 TAAAAAACAAGGACTAAATTTC
*
1168830 TAAAATACAAGGACTAAATTT
1 TAAAAAACAAGGACTAAATTT
1168851 TTAATTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (22 bp):
TAAAAAACAAGGACTAAATTTC
Found at i:1172979 original size:27 final size:27
Alignment explanation
Indices: 1172944--1172997 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1172934 GAAGCAACTT
* * *
1172944 TCTCGCTGTTGTTGGCTTCGTGTTGAA
1 TCTCACTGTTGTTCGCTTCATGTTGAA
1172971 TCTCACTGTTGTTCGCTTCATGTTGAA
1 TCTCACTGTTGTTCGCTTCATGTTGAA
1172998 GTTCGAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.44
Consensus pattern (27 bp):
TCTCACTGTTGTTCGCTTCATGTTGAA
Found at i:1182151 original size:224 final size:222
Alignment explanation
Indices: 1181728--1182255 Score: 681
Period size: 224 Copynumber: 2.3 Consensus size: 222
1181718 CCTGAAGAAC
* * *
1181728 TAGTGGCGTTTCTAAAAAA-ACGTCGTAAAAGAACATAATTAGTGGCGTTTA-TTGTAAGCACCG
1 TAGTGGCGTTTTTAAAAAACAC--CGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCG
* *
1181791 CAAAATACCTTAACCAAAACGCAGCGTTGGTTCAATTGTATATTAGAATTCGTGGCGTTTTTTAT
64 CAAAATACCTT----AAAACGAAGCGTTGGTTCAATTGTATATTAGAATTCGTGGCGTTTTCTAT
*
1181856 AAAAAACGCCGCGAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGA
125 -AAAAACGCCGCAAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGA
*
1181921 AAACGCACCGTTTTATCTTGAGGTAGATTAATAT
189 AAACGCACCGTTTCATCTTGAGGTAGATTAATAT
* * * *
1181955 TAGTGGCATTTTTAAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTGGATGTGCCACA
1 TAGTGGCGTTTTTAAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCGCA
* *
1182020 AAATACCTTAAAACGAATGGGTTGGGGTT-TATTGTGATATTAGACATT-GTGGCGTTTTCTAT-
66 AAATACCTTAAAACGAA-GCGTT--GGTTCAATTGT-ATATTAGA-ATTCGTGGCGTTTTCTATA
* * ** *
1182082 AAAACGCCGCAAAAGAATAGTATTAGTGGCGTTT-TCGGTAAAGCGCCGCAAATATCTTAATGAA
126 AAAACGCCGCAAAAGAATAGTATTAGCGGCGTTTAAC-AAAAAGCGCCGCAAATATCTTAAGGAA
* *
1182146 AACGCACCGTTTCGTCTTGAGGTAGATTAGTAT
190 AACGCACCGTTTCATCTTGAGGTAGATTAATAT
* * *
1182179 TAGTGGCGTTTTTAGAAAAACGCCGTAAAAGAACATGATTAGTGGCGTTTATTTTTATGCGCCGC
1 TAGTGGCGTTTTTA-AAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCGC
1182244 AAAATACCTTAA
65 AAAATACCTTAA
1182256 CCAAAACGCA
Statistics
Matches: 265, Mismatches: 27, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
223 8 0.03
224 103 0.39
225 61 0.23
226 53 0.20
227 38 0.14
228 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (222 bp):
TAGTGGCGTTTTTAAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTGTATGCGCCGCA
AAATACCTTAAAACGAAGCGTTGGTTCAATTGTATATTAGAATTCGTGGCGTTTTCTATAAAAAC
GCCGCAAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAAACGCA
CCGTTTCATCTTGAGGTAGATTAATAT
Found at i:1182303 original size:114 final size:113
Alignment explanation
Indices: 1181723--1182303 Score: 427
Period size: 114 Copynumber: 5.1 Consensus size: 113
1181713 TAAAACCTGA
* * * * *
1181723 AGAACTAGTGGCGTTTCTAAAAAAACGTCGTAAAAGAACATAATTAGTGGCGTTTA-TTGTAAGC
1 AGAATTAGTGGCGTTT-TTAAAAAACGCCGTAAAAGAACATGATTAGTGGCGTTTATTTGAAAGC
* ** *
1181787 ACCGCAAAATACCTTAACCAAAACGCAGCG-TTGG-TTCAATTGTATATT
65 GCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGA-GGTATATT
* ** * * ****
1181835 AGAATTCGTGGCGTTTTTTATAAAAAACGCCGCGAAAGAATA-GTATTAGCGGCGTTTAACAAAA
1 AGAATTAGTGGCG--TTTT-TAAAAAACGCCGTAAAAGAACATG-ATTAGTGGCGTTTATTTGAA
* ** * ** * *
1181899 AGCGCCGC-AAATATCTTAAGGAAAACGCACCGTTTTATCTTGAGGTAGATT
62 AGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATT
* * * * * *
1181950 A-ATATTAGTGGCATTTTTAAAAAACACCGTAAAAGAACATAATTAGTGGCGTTTATTTGGATGT
1 AGA-ATTAGTGGCGTTTTTAAAAAACGCCGTAAAAGAACATGATTAGTGGCGTTTATTTGAAAGC
* * * * * *
1182014 GCCACAAAATACCTT----AAAACGAATGGGTTGGGGTTT-ATTGTGATATT
65 GCCGCAAAATACCTTAACCAAAACGCA-GCGTTTGGTTTTGA-GGT-ATATT
* * * **
1182061 AGACATT-GTGGCGTTTTCTATAAAACGCCGCAAAAGAATA-GTATTAGTGGCGTTT-TCGGTAA
1 AGA-ATTAGTGGCGTTTT-TAAAAAACGCCGTAAAAGAACATG-ATTAGTGGCGTTTATTTG-AA
* ** * * * *
1182123 AGCGCCGC-AAATATCTTAATGAAAACGCACCGTTTCGTCTTGAGGTAGATT
62 AGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATT
* ** *
1182174 AGTATTAGTGGCGTTTTTAGAAAAACGCCGTAAAAGAACATGATTAGTGGCGTTTATTTTTATGC
1 AGAATTAGTGGCGTTTTTA-AAAAACGCCGTAAAAGAACATGATTAGTGGCGTTTATTTGAAAGC
*
1182239 GCCGCAAAATACCTTAACCAAAACGCAGCATTTGGTTTTGAGGTATATT
65 GCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATT
1182288 AGAATTAGTGGCGTTT
1 AGAATTAGTGGCGTTT
1182304 ACGATAAAAC
Statistics
Matches: 349, Mismatches: 93, Indels: 52
0.71 0.19 0.11
Matches are distributed among these distances:
109 8 0.02
110 7 0.02
111 24 0.07
112 94 0.27
113 67 0.19
114 114 0.33
115 33 0.09
116 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (113 bp):
AGAATTAGTGGCGTTTTTAAAAAACGCCGTAAAAGAACATGATTAGTGGCGTTTATTTGAAAGCG
CCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATT
Found at i:1182337 original size:188 final size:188
Alignment explanation
Indices: 1182103--1182503 Score: 658
Period size: 188 Copynumber: 2.1 Consensus size: 188
1182093 AAAGAATAGT
* * *
1182103 ATTAGTGGCGTTTTCGGTAAAGCGCCGCAAATATCTTAATGAAAACGCACCGTTTCGTCTTGAGG
1 ATTAGTGGCGTTTACGGTAAAACGCCGCAAATATCTTAACGAAAACGCACCGTTTCGTCTTGAGG
* * *
1182168 TAGATTAGTATTAGTGGCGTTTTTAGAAAAACGCCGTAAAAGAACATGATTAGTGGCGTTTATTT
66 TAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
** *
1182233 TTATGCGCCGCAAAATACCTTAACCAAAACGCAGCATTTGGTTTTGAGGTATATTAGA
131 GGAAGCGCCGCAAAATACCTTAACCAAAACGCAGCATTTGGTTTTGAGGTATATTAGA
* *
1182291 ATTAGTGGCGTTTACGATAAAACGCCGCAAATATCTTAACGAAAACGCACCGTTTGGTCTTGAGG
1 ATTAGTGGCGTTTACGGTAAAACGCCGCAAATATCTTAACGAAAACGCACCGTTTCGTCTTGAGG
1182356 TAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
66 TAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
* ** *
1182421 GGAAGCGCCGCAAAATGCCTTAACCAAAACGCAGTGTTTGGTTTTGATGTATATTAGA
131 GGAAGCGCCGCAAAATACCTTAACCAAAACGCAGCATTTGGTTTTGAGGTATATTAGA
*
1182479 ATTAGTGGCGTTTATGGTAAAACGC
1 ATTAGTGGCGTTTACGGTAAAACGC
1182504 TGCTAAAGAA
Statistics
Matches: 196, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
188 196 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (188 bp):
ATTAGTGGCGTTTACGGTAAAACGCCGCAAATATCTTAACGAAAACGCACCGTTTCGTCTTGAGG
TAGATTAATATTAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
GGAAGCGCCGCAAAATACCTTAACCAAAACGCAGCATTTGGTTTTGAGGTATATTAGA
Found at i:1182347 original size:74 final size:75
Alignment explanation
Indices: 1182238--1182377 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 75
1182228 TATTTTTATG
* * *
1182238 CGCCGCAAAATACCTTAACCAAAACGCAGCATTTGGTTTTGAGGTATATTAGA-ATTAGTGGCGT
1 CGCCGCAAAATACCTTAACCAAAACGCACCATTTGGTCTTGAGGTAGATTA-ATATTAGTGGCGT
1182302 TTACGATAAAA
65 TTACGATAAAA
* * *
1182313 CGCCGC-AAATATCTTAACGAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
1 CGCCGCAAAATACCTTAACCAAAACGCACCATTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
1182377 T
66 T
1182378 TTAAAAAAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
73 1 0.02
74 51 0.88
75 6 0.10
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (75 bp):
CGCCGCAAAATACCTTAACCAAAACGCACCATTTGGTCTTGAGGTAGATTAATATTAGTGGCGTT
TACGATAAAA
Found at i:1182387 original size:74 final size:75
Alignment explanation
Indices: 1182238--1182396 Score: 196
Period size: 74 Copynumber: 2.1 Consensus size: 75
1182228 TATTTTTATG
* * *
1182238 CGCCGCAAAATACCTTAACCAAAACGCAGCATTTGGTTTTGAGGTATATTAGAATTAGTGGCGTT
1 CGCCGCAAAATACCTTAACCAAAACGCACCATTTGGTCTTGAGGTAGATTAGAATTAGTGGCGTT
* *
1182303 TACGATAAAA
66 TACAAAAAAA
* * *
1182313 CGCCGC-AAATATCTTAACGAAAACGCACCGTTTGGTCTTGAGGTAGATTA-ATATTAGTGGCGT
1 CGCCGCAAAATACCTTAACCAAAACGCACCATTTGGTCTTGAGGTAGATTAGA-ATTAGTGGCGT
**
1182376 TTTTAAAAAAA
65 TTACAAAAAAA
*
1182387 CGCCGTAAAA
1 CGCCGCAAAA
1182397 GAACATAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
73 1 0.01
74 61 0.86
75 9 0.13
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (75 bp):
CGCCGCAAAATACCTTAACCAAAACGCACCATTTGGTCTTGAGGTAGATTAGAATTAGTGGCGTT
TACAAAAAAA
Found at i:1182512 original size:114 final size:113
Alignment explanation
Indices: 1182313--1182530 Score: 246
Period size: 114 Copynumber: 1.9 Consensus size: 113
1182303 TACGATAAAA
*
1182313 CGCCGCAAATATCTTAACGAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTTT
1 CGCCGCAAATATCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTTT
* *
1182378 TTAAAAAAACGCCGTAAAAGAACA-TAATTAGTGGCGTTTATTTGGAAG
66 ATAAAAAAACGCCGTAAAAGAACAGT-ATTAGCGGCGTTTATTTGGAAG
** * * *
1182426 CGCCGCAAA-ATGCCTTAACCAAAACGCAGTGTTTGGTTTTGATGTATATTAGA-ATTAGTGGCG
1 CGCCGCAAATAT--CTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTA-ATATTAGTGGCG
*** * *
1182489 TTTATGGTAAAACGCTGCT-AAAGAATAGTATTAGCGGCGTTT
63 TTTATAAAAAAACGCCG-TAAAAGAACAGTATTAGCGGCGTTT
1182531 TCGGTAAAGC
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
112 2 0.02
113 9 0.10
114 73 0.84
115 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (113 bp):
CGCCGCAAATATCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAATATTAGTGGCGTTT
ATAAAAAAACGCCGTAAAAGAACAGTATTAGCGGCGTTTATTTGGAAG
Found at i:1182929 original size:7 final size:7
Alignment explanation
Indices: 1182919--1182969 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
1182909 GGTTTATGGA
1182919 TTAGGGG
1 TTAGGGG
1182926 TTAGGGG
1 TTAGGGG
*
1182933 TTATGGG
1 TTAGGGG
1182940 TTAGGGG
1 TTAGGGG
1182947 TTAGGGG
1 TTAGGGG
1182954 TTA--GG
1 TTAGGGG
1182959 TTAGGGG
1 TTAGGGG
1182966 TTAG
1 TTAG
1182970 ATGTTAAGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 5 0.12
7 35 0.88
ACGTcount: A:0.16, C:0.00, G:0.51, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:1182938 original size:21 final size:20
Alignment explanation
Indices: 1182912--1182969 Score: 91
Period size: 21 Copynumber: 2.9 Consensus size: 20
1182902 GATTTAAGGT
1182912 TTATGGATTAGGGGTTAGGGG
1 TTATGG-TTAGGGGTTAGGGG
1182933 TTATGGGTTAGGGGTTAGGGG
1 TTAT-GGTTAGGGGTTAGGGG
1182954 TTA-GGTTAGGGGTTAG
1 TTATGGTTAGGGGTTAG
1182970 ATGTTAAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.36
21 21 0.58
22 2 0.06
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.34
Consensus pattern (20 bp):
TTATGGTTAGGGGTTAGGGG
Found at i:1182983 original size:33 final size:33
Alignment explanation
Indices: 1182924--1182991 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
1182914 ATGGATTAGG
* *
1182924 GGTTAGGGGTTATGGGTTAGGGGTTAGGGGTTA
1 GGTTAGGGGTTATGGGTTAAGAGTTAGGGGTTA
* *
1182957 GGTTAGGGGTTA-GATGTTAAGAGTTAGGGTTTA
1 GGTTAGGGGTTATG-GGTTAAGAGTTAGGGGTTA
1182990 GG
1 GG
1182992 ATTTATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.34
Consensus pattern (33 bp):
GGTTAGGGGTTATGGGTTAAGAGTTAGGGGTTA
Found at i:1183080 original size:7 final size:7
Alignment explanation
Indices: 1183068--1183164 Score: 88
Period size: 7 Copynumber: 13.9 Consensus size: 7
1183058 TAAATAAGTT
1183068 TTAGGGG
1 TTAGGGG
1183075 TTAGGGG
1 TTAGGGG
*
1183082 TTAGAGG
1 TTAGGGG
* *
1183089 TCATGGG
1 TTAGGGG
*
1183096 TTAAGGGT
1 TT-AGGGG
1183104 TTA-GGG
1 TTAGGGG
*
1183110 TTAAGGG
1 TTAGGGG
**
1183117 TTAAAGG
1 TTAGGGG
**
1183124 TTAAAGG
1 TTAGGGG
1183131 TTAGGGG
1 TTAGGGG
*
1183138 TTAAGGG
1 TTAGGGG
1183145 TTAGGGG
1 TTAGGGG
1183152 TTAGGGG
1 TTAGGGG
1183159 TTAGGG
1 TTAGGG
1183165 ATTGGGTTAT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
6 5 0.07
7 65 0.87
8 5 0.07
ACGTcount: A:0.23, C:0.01, G:0.46, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Found at i:1183098 original size:21 final size:21
Alignment explanation
Indices: 1183068--1183164 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
1183058 TAAATAAGTT
1183068 TTAGGGGTTAGGGGTTAGAGG
1 TTAGGGGTTAGGGGTTAGAGG
* * *
1183089 TCATGGGTTAAGGGTTTAG-GG
1 TTAGGGGTT-AGGGGTTAGAGG
* ** *
1183110 TTAAGGGTTAAAGGTTAAAGG
1 TTAGGGGTTAGGGGTTAGAGG
* *
1183131 TTAGGGGTTAAGGGTTAGGGG
1 TTAGGGGTTAGGGGTTAGAGG
1183152 TTAGGGGTTAGGG
1 TTAGGGGTTAGGG
1183165 ATTGGGTTAT
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
20 5 0.08
21 47 0.78
22 8 0.13
ACGTcount: A:0.23, C:0.01, G:0.46, T:0.30
Consensus pattern (21 bp):
TTAGGGGTTAGGGGTTAGAGG
Found at i:1183322 original size:95 final size:96
Alignment explanation
Indices: 1183125--1183319 Score: 225
Period size: 95 Copynumber: 2.0 Consensus size: 96
1183115 GGTTAAAGGT
* * * * *
1183125 TAAAGGTTAGGGGTTAAGGGTTAGGGGTTAGGGGTTAGGGATTGGGTTATGGTTTAAGGTTTAGA
1 TAAAGTTTAGGGGTTAAGGGTTAGGGGTTAGGGGTTAGGGATCGGGTTAGGGATTAAGATTTAGA
* * * * *
1183190 TTAATTAGTGTTTTTTATTTTATATATTAAA
66 TTAATTAGTCTTATTTAATTAACATATTAAA
* * *
1183221 TAAAGTTTAGGGGTT-AGTGGTTA-GGGTTATGGGTT-TGGAGTCGGGTTAGGGATTAAGATTTG
1 TAAAGTTTAGGGGTTAAG-GGTTAGGGGTTAGGGGTTAGGGA-TCGGGTTAGGGATTAAGATTTA
1183283 GATTAATTAGTACTTATTTAATTAACATATTAAA
64 GATTAATTAGT-CTTATTTAATTAACATATTAAA
1183317 TAA
1 TAA
1183320 GTTCTTTATA
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
94 3 0.04
95 41 0.49
96 39 0.47
ACGTcount: A:0.28, C:0.02, G:0.29, T:0.41
Consensus pattern (96 bp):
TAAAGTTTAGGGGTTAAGGGTTAGGGGTTAGGGGTTAGGGATCGGGTTAGGGATTAAGATTTAGA
TTAATTAGTCTTATTTAATTAACATATTAAA
Found at i:1183409 original size:14 final size:14
Alignment explanation
Indices: 1183390--1183416 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1183380 GATATGCAAT
1183390 ATATAATAATTTGA
1 ATATAATAATTTGA
1183404 ATATAATAATTTG
1 ATATAATAATTTG
1183417 GAATTGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
ATATAATAATTTGA
Found at i:1183456 original size:20 final size:20
Alignment explanation
Indices: 1183418--1183458 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1183408 AATAATTTGG
**
1183418 AATTGTAAAAATTGTAAAAA
1 AATTGTAAAAATTACAAAAA
*
1183438 AATTGTCAAAATTACAAAAA
1 AATTGTAAAAATTACAAAAA
1183458 A
1 A
1183459 TAAAATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (20 bp):
AATTGTAAAAATTACAAAAA
Found at i:1183479 original size:8 final size:8
Alignment explanation
Indices: 1183466--1183498 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1183456 AAATAAAATG
1183466 AAAATAAA
1 AAAATAAA
1183474 AAAAT-AA
1 AAAATAAA
1183481 AAAATAAA
1 AAAATAAA
1183489 AAAACTAAA
1 AAAA-TAAA
1183498 A
1 A
1183499 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.30
8 11 0.48
9 5 0.22
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:1183486 original size:15 final size:16
Alignment explanation
Indices: 1183466--1183498 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1183456 AAATAAAATG
1183466 AAAATAAAAAAA-TAA
1 AAAATAAAAAAACTAA
1183481 AAAATAAAAAAACTAA
1 AAAATAAAAAAACTAA
1183497 AA
1 AA
1183499 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAATAAAAAAACTAA
Found at i:1184877 original size:10 final size:10
Alignment explanation
Indices: 1184862--1184886 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1184852 TCGAAAATTG
1184862 CAAAATTGTT
1 CAAAATTGTT
1184872 CAAAATTGTT
1 CAAAATTGTT
1184882 CAAAA
1 CAAAA
1184887 CCATGTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (10 bp):
CAAAATTGTT
Found at i:1188154 original size:52 final size:46
Alignment explanation
Indices: 1188023--1188171 Score: 133
Period size: 48 Copynumber: 3.0 Consensus size: 46
1188013 NNNNNNNNNN
1188023 AAAATTTATATATTACATTACTTAAATATATATATGTTAATATTTTT
1 AAAATTTATATATTACATTACTTAAATATATAT-TGTTAATATTTTT
* *
1188070 ACAATTTA-AT-TTAACTTATTAC-TAATACATATATTGTTCGAATATAATTTTTT
1 AAAATTTATATATT-AC--ATTACTTAA-ATATATATTGTT---A-AT-A-TTTTT
*
1188123 AAAATTTATATATTACATTACTTAAATATATATTTTTAAGTATATTTT
1 AAAATTTATATATTACATTACTTAAATATATATTGTTAA-TAT-TTTT
1188171 A
1 A
1188172 GATGTCTTAC
Statistics
Matches: 82, Mismatches: 5, Indels: 29
0.71 0.04 0.25
Matches are distributed among these distances:
45 2 0.02
46 4 0.05
47 15 0.18
48 19 0.23
49 2 0.02
50 1 0.01
51 2 0.02
52 16 0.20
53 15 0.18
54 4 0.05
55 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (46 bp):
AAAATTTATATATTACATTACTTAAATATATATTGTTAATATTTTT
Found at i:1188243 original size:13 final size:13
Alignment explanation
Indices: 1188225--1188276 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
1188215 TTTTACTCTT
*
1188225 AATATATTACTTG
1 AATATATTACTTA
1188238 AATATATTACTTA
1 AATATATTACTTA
*
1188251 AATAAATTACTTA
1 AATATATTACTTA
*
1188264 AATACATTACTTA
1 AATATATTACTTA
1188277 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (13 bp):
AATATATTACTTA
Found at i:1188301 original size:53 final size:53
Alignment explanation
Indices: 1188244--1188379 Score: 200
Period size: 53 Copynumber: 2.6 Consensus size: 53
1188234 CTTGAATATA
**
1188244 TTACTTAAATAAATTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
1 TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
* ** * *
1188297 TTACTTAAATATGTTACTCAGTTACATTAATTACTAAAATTTGGTTAAATTTT
1 TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
*
1188350 TTACTTAAATATGTTACTTGAATACATTAC
1 TTACTTAAATATGTTACTTAAATACATTAC
1188380 CCGCTATAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 71 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (53 bp):
TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
Found at i:1188548 original size:9 final size:9
Alignment explanation
Indices: 1188524--1188773 Score: 130
Period size: 9 Copynumber: 28.8 Consensus size: 9
1188514 TATGTACAAG
1188524 AACTTACAT
1 AACTTACAT
* *
1188533 AATTTACAC
1 AACTTACAT
*
1188542 AACTTACTT
1 AACTTACAT
*
1188551 AACCTACAT
1 AACTTACAT
1188560 AACTTACAT
1 AACTTACAT
1188569 AA--TACA-
1 AACTTACAT
1188575 AAGCTTACAT
1 AA-CTTACAT
* *
1188585 AACTAAAAT
1 AACTTACAT
* *
1188594 AGCTTACAC
1 AACTTACAT
1188603 AACTTACAT
1 AACTTACAT
1188612 AACTTACAT
1 AACTTACAT
*
1188621 AACTTACAG
1 AACTTACAT
* *
1188630 AAGTTATAT
1 AACTTACAT
1188639 AA--TACAT
1 AACTTACAT
* *
1188646 AA-TAACGTAC
1 AACTTAC--AT
1188656 AACTTACAT
1 AACTTACAT
*
1188665 AACATACAT
1 AACTTACAT
* **
1188674 TACTTTGAT
1 AACTTACAT
1188683 AACTTACAT
1 AACTTACAT
*
1188692 AAGTTACAT
1 AACTTACAT
*
1188701 AA--TACAC
1 AACTTACAT
*
1188708 AAC-TGCAT
1 AACTTACAT
** *
1188716 AGTTTACTT
1 AACTTACAT
*
1188725 AA--TACAA
1 AACTTACAT
1188732 AACTTACAT
1 AACTTACAT
1188741 AACTT--AT
1 AACTTACAT
*
1188748 ACACGTACAT
1 A-ACTTACAT
*
1188758 AACCTACAT
1 AACTTACAT
*
1188767 AATTTAC
1 AACTTAC
1188774 TTAATACATA
Statistics
Matches: 177, Mismatches: 49, Indels: 30
0.69 0.19 0.12
Matches are distributed among these distances:
6 2 0.01
7 24 0.14
8 9 0.05
9 131 0.74
10 8 0.05
11 3 0.02
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:1194347 original size:66 final size:65
Alignment explanation
Indices: 1194240--1194410 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
1194230 GAGCAAATTA
* * * *
1194240 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
1194304 G
65 G
* *
1194305 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
1194370 G
65 G
* * ** *
1194371 CAGCAGCTTAAAGCAGATACAGCAGTAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
1194411 CGGCAGCTAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 85 0.93
67 4 0.04
ACGTcount: A:0.42, C:0.19, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:1194446 original size:21 final size:21
Alignment explanation
Indices: 1194401--1194491 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
1194391 AGCAGTAAGA
* * * *
1194401 GAAGCAGAGGCGGCAGCTAGA
1 GAAGCAGAGGCTGCAACGAGG
* *
1194422 GAAGTACAGGCTGCAACGAGG
1 GAAGCAGAGGCTGCAACGAGG
* *
1194443 GAAGCAGAGCCT-AAAGCGAGG
1 GAAGCAGAGGCTGCAA-CGAGG
*
1194464 GAAGCAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCTGCAACGAGG
1194485 GAAGCAG
1 GAAGCAG
1194492 GGCAGAGTCA
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.04
21 52 0.95
22 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.42, T:0.05
Consensus pattern (21 bp):
GAAGCAGAGGCTGCAACGAGG
Found at i:1195229 original size:22 final size:22
Alignment explanation
Indices: 1195201--1195243 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1195191 CTACGGCGCT
*
1195201 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
1195223 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
1195244 GTTATGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:1198670 original size:26 final size:25
Alignment explanation
Indices: 1198622--1198697 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 25
1198612 TTTCTCACCT
1198622 AATTTTACCC-CAATAAAATTTTGAC
1 AATTTTACCCTC-ATAAAATTTTGAC
1198647 AATTTTACCCTCAGTAAAATTTTGAC
1 AATTTTACCCTCA-TAAAATTTTGAC
* *
1198673 GATTTTACCACTGATAAAATTTTGA
1 AATTTTACC-CTCATAAAATTTTGA
1198698 GAAAATTCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
25 11 0.24
26 32 0.70
27 3 0.07
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (25 bp):
AATTTTACCCTCATAAAATTTTGAC
Found at i:1199034 original size:24 final size:25
Alignment explanation
Indices: 1198979--1199047 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 25
1198969 TTCGTTCATT
*
1198979 TGTGGTGTAATATGAAAGAAAAAGCTTT
1 TGTGGTGTAATATG-AA-AAAAAGC-TC
1199007 TGTGGTGTAATATGAAAAAAAGC-C
1 TGTGGTGTAATATGAAAAAAAGCTC
* *
1199031 TGTGGCGGAATATGAAA
1 TGTGGTGTAATATGAAA
1199048 GGAATGTCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 15 0.39
26 7 0.18
27 2 0.05
28 14 0.37
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (25 bp):
TGTGGTGTAATATGAAAAAAAGCTC
Found at i:1200448 original size:20 final size:20
Alignment explanation
Indices: 1200405--1200453 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1200395 CAAAATATAA
1200405 ATAAATAAATTTCTAAAAAT
1 ATAAATAAATTTCTAAAAAT
*
1200425 -TAAATTAAATTT-TAAATAT
1 ATAAA-TAAATTTCTAAAAAT
*
1200444 ATAAAAAAAT
1 ATAAATAAAT
1200454 ATGTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAATAAATTTCTAAAAAT
Found at i:1201121 original size:30 final size:28
Alignment explanation
Indices: 1201041--1201121 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
1201031 CCCTTCAATG
* *
1201041 TTTACAGATTCTATCAATTTAGTCATAA
1 TTTACAAATTCTATCAATTTAGCCATAA
* *
1201069 TTCTAAAAAATCTA-CAAATTTAGCCATCAA
1 TT-TACAAATTCTATC-AATTTAGCCAT-AA
*
1201099 CTTTACACATTCTATCAATTTAG
1 -TTTACAAATTCTATCAATTTAG
1201122 TTTTATTTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
28 3 0.07
29 18 0.44
30 17 0.41
31 3 0.07
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (28 bp):
TTTACAAATTCTATCAATTTAGCCATAA
Done.