Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 193 of 202
Found at i:58813999 original size:2 final size:2
Alignment explanation
Indices: 58813992--58814022 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
58813982 TGTATGTATG
*
58813992 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58814023 GTGTGTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58814770 original size:2 final size:2
Alignment explanation
Indices: 58814763--58814808 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
58814753 TTGGACTTTG
58814763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58814805 TA TA
1 TA TA
58814809 AAAGCTTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58815288 original size:30 final size:25
Alignment explanation
Indices: 58815253--58815318 Score: 69
Period size: 30 Copynumber: 2.4 Consensus size: 25
58815243 GCAATTAGAC
58815253 CTAAATTTTGAAATATAAAAAGTAAAAGGA
1 CTAAATTTTGAAA-A-AAAAAGT--AA-GA
58815283 CTAAATTCCTTGAAAAAAAAAGTAAGA
1 CTAAATT--TTGAAAAAAAAAGTAAGA
58815310 CTAAATTTT
1 CTAAATTTT
58815319 AATGTACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
25 2 0.06
27 9 0.26
28 2 0.06
30 14 0.41
31 1 0.03
32 6 0.18
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.29
Consensus pattern (25 bp):
CTAAATTTTGAAAAAAAAAGTAAGA
Found at i:58815945 original size:29 final size:29
Alignment explanation
Indices: 58815903--58815961 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
58815893 TGTTGGTAAA
58815903 TATGGGACCCAAAATAATTCTATTTCAAG
1 TATGGGACCCAAAATAATTCTATTTCAAG
58815932 TATGGGACCCAAAATAATTCTATTTCAAG
1 TATGGGACCCAAAATAATTCTATTTCAAG
58815961 T
1 T
58815962 CATGCTTCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (29 bp):
TATGGGACCCAAAATAATTCTATTTCAAG
Found at i:58824636 original size:15 final size:16
Alignment explanation
Indices: 58824608--58824637 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
58824598 TCAAAAAATA
58824608 AATAAAATAATCATAC
1 AATAAAATAATCATAC
58824624 AATAAAA-AATCATA
1 AATAAAATAATCATA
58824638 TAAAAATAAT
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:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (16 bp):
AATAAAATAATCATAC
Found at i:58824739 original size:19 final size:21
Alignment explanation
Indices: 58824701--58824739 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
58824691 ATTCAAAACC
*
58824701 AATTAATTTATAAAATATAAT
1 AATTAATTTATAAAAAATAAT
58824722 AATT-ATTT-TAAAAAATAA
1 AATTAATTTATAAAAAATAA
58824740 ATTTTGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTAATTTATAAAAAATAAT
Found at i:58828047 original size:93 final size:95
Alignment explanation
Indices: 58827930--58828121 Score: 289
Period size: 95 Copynumber: 2.0 Consensus size: 95
58827920 ACTATTTGGC
* * * * *
58827930 AGTTAAGTTTGGCTTCAATTTTCAATTTGGTACTTGAATT-TTTTT-TGCCAATTTGGTACATGA
1 AGTTAAGTTTGGCTTCAATCTTCAATTTGGCACCTAAATTCTTTTTGTCCCAATTTGGTACATGA
* *
58827993 GTTTGGCCACAATGTTCATTTTGGTACCTG
66 GTTTGGCCAAAATGTTCATTTTGGTACCTA
*
58828023 AGTTGAGTTTGGCTTCAATCTTCAATTTGGCACCTAAATTCTTTTTGTCCCAATTTGGTACATGA
1 AGTTAAGTTTGGCTTCAATCTTCAATTTGGCACCTAAATTCTTTTTGTCCCAATTTGGTACATGA
*
58828088 GTTTGGCTAAAATGTTCATTTTGGTACCTA
66 GTTTGGCCAAAATGTTCATTTTGGTACCTA
58828118 AGTT
1 AGTT
58828122 TTTTTGTTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 35 0.40
94 5 0.06
95 48 0.55
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (95 bp):
AGTTAAGTTTGGCTTCAATCTTCAATTTGGCACCTAAATTCTTTTTGTCCCAATTTGGTACATGA
GTTTGGCCAAAATGTTCATTTTGGTACCTA
Found at i:58830391 original size:21 final size:19
Alignment explanation
Indices: 58830336--58830387 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
58830326 GGCCACATTT
*
58830336 CAATTGGTTTTTTTAACGG
1 CAATGGGTTTTTTTAACGG
*
58830355 TAATGGGTTTTTTTAACGG
1 CAATGGGTTTTTTTAACGG
*
58830374 CAATGAGTTTTTTT
1 CAATGGGTTTTTTT
58830388 TTAAATGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (19 bp):
CAATGGGTTTTTTTAACGG
Found at i:58832441 original size:56 final size:56
Alignment explanation
Indices: 58832381--58832489 Score: 173
Period size: 56 Copynumber: 1.9 Consensus size: 56
58832371 AGTAGTTACG
* *
58832381 TTAGAAATCAAATTGATAAAATATAATACCCCATAATAATATCCTATTATATCCCA
1 TTAGAAATCAAATTGATAAAAGATAATACCCCATAATAATATCCTATAATATCCCA
* * *
58832437 TTAGAAATCAAATTGTTAAGAGATAATATCCCATAATAATATCCTATAATATC
1 TTAGAAATCAAATTGATAAAAGATAATACCCCATAATAATATCCTATAATATC
58832490 TGTTAGAGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.33
Consensus pattern (56 bp):
TTAGAAATCAAATTGATAAAAGATAATACCCCATAATAATATCCTATAATATCCCA
Found at i:58833815 original size:31 final size:29
Alignment explanation
Indices: 58833764--58833823 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
58833754 CAATTAGTGG
*
58833764 CTTAAATAAAAACTTAAATTATTTAATGA
1 CTTAAATAAAAACTTAAATTATTCAATGA
*
58833793 CTTAAATGAAAAATTTTAAATTATTCAATGA
1 CTTAAAT-AAAAA-CTTAAATTATTCAATGA
58833824 ATTTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 7 0.26
30 5 0.19
31 15 0.56
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (29 bp):
CTTAAATAAAAACTTAAATTATTCAATGA
Found at i:58842394 original size:4 final size:4
Alignment explanation
Indices: 58842387--58842453 Score: 134
Period size: 4 Copynumber: 16.8 Consensus size: 4
58842377 ATGCATGCAT
58842387 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
58842435 TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TAT
58842454 ACAGACCATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 63 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:58843009 original size:217 final size:217
Alignment explanation
Indices: 58842412--58843048 Score: 996
Period size: 213 Copynumber: 3.0 Consensus size: 217
58842402 GTATGTATGT
* * * * * * *
58842412 ATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATACAGACCATATTTACCATTAACA
1 ATGTATGTATATATATATGTAGGTATGCATGTATGTATGTATACACACCATATTTTCCATCAACA
* * *
58842477 ATAACACCTAACAATGAGAGTACCATATGGGAGAAAAAACATGCATAGGTTGGTCACCATTTGAA
66 AGAACACCTAACAATGAGAGTACCATATGGGAGAAGAAACATGTATAGGTTGGTCACCATTTGAA
*
58842542 TCAATGCCTATAAGAAATCAAAGGCATATGCTATCAACTGCAGGCCTATTTAGCCATGACTTTTC
131 ACAATGCCTATAAGAAATCAAAGGCATATGCTATCAACTGCAGGCCTATTTAGCCATGACTTTTC
58842607 TCCTAACATATTTACCACCAAC
196 TCCTAACATATTTACCACCAAC
* * *
58842629 A-G---GTATATATACATGTAGGTATGCATGTATGTGTGTATACACACCATATTTTCCGTCAACA
1 ATGTATGTATATATATATGTAGGTATGCATGTATGTATGTATACACACCATATTTTCCATCAACA
58842690 AGAACACCTAACAATGAGAGTACCATATGGGAGAAGAAACATGTATAGGTTGGTCACCATTTGAA
66 AGAACACCTAACAATGAGAGTACCATATGGGAGAAGAAACATGTATAGGTTGGTCACCATTTGAA
*
58842755 ACAATGCCGATAAGAAATCAAAGGCATATGCTATCAACTGCAGGCCTATTTAGCCATGACTTTTC
131 ACAATGCCTATAAGAAATCAAAGGCATATGCTATCAACTGCAGGCCTATTTAGCCATGACTTTTC
58842820 TCCTAACATATTTACCACCAAC
196 TCCTAACATATTTACCACCAAC
* *
58842842 ATGTATATATATATATATGTAGGTATGCATGTATGTATGTATACACACCATATTTTCCATCGACA
1 ATGTATGTATATATATATGTAGGTATGCATGTATGTATGTATACACACCATATTTTCCATCAACA
* * * *
58842907 AGAACACCTAACAATGAGAGTACCATATGGGAGAAGAAACATGTATAGGTCGGTGCACTAATTAA
66 AGAACACCTAACAATGAGAGTACCATATGGGAGAAGAAACATGTATAGGTTGGT-CACCATTTGA
** *
58842972 AACAATGCCTATAAGAAATCAAAGGCAT-TAATATCAACTGCAGGCCTATTTAGCAATGACTTTT
130 AACAATGCCTATAAGAAATCAAAGGCATATGCTATCAACTGCAGGCCTATTTAGCCATGACTTTT
* *
58843036 GTCTTAACATATT
195 CTCCTAACATATT
58843049 CATCGATATA
Statistics
Matches: 385, Mismatches: 30, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
213 197 0.51
214 1 0.00
216 1 0.00
217 152 0.39
218 34 0.09
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (217 bp):
ATGTATGTATATATATATGTAGGTATGCATGTATGTATGTATACACACCATATTTTCCATCAACA
AGAACACCTAACAATGAGAGTACCATATGGGAGAAGAAACATGTATAGGTTGGTCACCATTTGAA
ACAATGCCTATAAGAAATCAAAGGCATATGCTATCAACTGCAGGCCTATTTAGCCATGACTTTTC
TCCTAACATATTTACCACCAAC
Found at i:58843965 original size:14 final size:13
Alignment explanation
Indices: 58843946--58843975 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
58843936 GAAAAGTGAG
58843946 AAAAAAAGAAAAGA
1 AAAAAAAG-AAAGA
58843960 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
58843973 AAA
1 AAA
58843976 TTGGAGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAGA
Found at i:58853943 original size:29 final size:28
Alignment explanation
Indices: 58853906--58853970 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
58853896 AGGGTCCCTT
* *
58853906 TAAAAAAAATTATAAAAT-GTAATACAA
1 TAAAAAAAAATATAAAATAGTAATAAAA
* *
58853933 TAAAATAAAAATATATACTAGTAATAAAA
1 TAAAA-AAAAATATAAAATAGTAATAAAA
58853962 TAAAAAAAA
1 TAAAAAAAA
58853971 TTGGAGCCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 5 0.16
28 14 0.44
29 13 0.41
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (28 bp):
TAAAAAAAAATATAAAATAGTAATAAAA
Found at i:58855544 original size:11 final size:11
Alignment explanation
Indices: 58855530--58855570 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
58855520 TATTTTCTCC
58855530 CTATTTTGCTA
1 CTATTTTGCTA
*
58855541 CTATTTTACTA
1 CTATTTTGCTA
* *
58855552 TTATGTTGCTA
1 CTATTTTGCTA
58855563 CTATTTTG
1 CTATTTTG
58855571 TCGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:58855641 original size:30 final size:30
Alignment explanation
Indices: 58855607--58855669 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
58855597 ACTTATTTTA
58855607 TTGTTAAATTTGTTATTATTTTAAAGGCAT
1 TTGTTAAATTTGTTATTATTTTAAAGGCAT
* *
58855637 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAAATTTGTTATTATTTTAAAGGCAT
58855667 TTG
1 TTG
58855670 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.16, T:0.56
Consensus pattern (30 bp):
TTGTTAAATTTGTTATTATTTTAAAGGCAT
Found at i:58855774 original size:18 final size:18
Alignment explanation
Indices: 58855751--58855790 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
58855741 GAAATATTTA
*
58855751 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
58855769 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
58855787 TTTT
1 TTTT
58855791 AAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:58858357 original size:10 final size:10
Alignment explanation
Indices: 58858344--58858368 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
58858334 AAACATAAGC
58858344 TATTTCTGAT
1 TATTTCTGAT
58858354 TATTTCTGAT
1 TATTTCTGAT
58858364 TATTT
1 TATTT
58858369 GAGGTTAACT
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:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (10 bp):
TATTTCTGAT
Found at i:58871246 original size:3 final size:3
Alignment explanation
Indices: 58871238--58871278 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
58871228 ATATGTGCAG
*
58871238 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
58871279 TCAATAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:58872349 original size:24 final size:24
Alignment explanation
Indices: 58872322--58872368 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
58872312 CTGGGTCTTG
*
58872322 TTTGTTGGTTTGGGCCCGAGCATA
1 TTTGTTGGCTTGGGCCCGAGCATA
* *
58872346 TTTGTTTGCTTGGGCCCGGGCAT
1 TTTGTTGGCTTGGGCCCGAGCAT
58872369 TATTGGGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.34, T:0.38
Consensus pattern (24 bp):
TTTGTTGGCTTGGGCCCGAGCATA
Found at i:58872865 original size:50 final size:50
Alignment explanation
Indices: 58872811--58873085 Score: 223
Period size: 50 Copynumber: 5.5 Consensus size: 50
58872801 CGGGGAAACC
* ** *
58872811 AGATCTGCCGTCGTAGCTTCAATCTATTCCACCGCACCGTCAGGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTATTCCATTGCACTGTCAGGGAAGTA
* * * * * ** * * *
58872861 AGATCTGCTGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGAAAACT-
1 AGATCCGCCGTCGTAGCTTCAATCTATTCCATTGCACTGTCAGG-GAAGTA
* *
58872911 AGATCCGCCGTCGTAGCTTCAAGCTATTCCATTGCACTG-CTAAGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTATTCCATTGCACTGTC-AGGGAAGTA
* * * ** * * ***
58872961 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACC
1 AGATCCGCCGTCGTAGCTTCAATCTATTCCATTGCACTGTCAGGGAAGTA
* * *
58873011 AGATCCGCCGTCGTAGCTTCAATCTATTCCACTACACTG-CTAAGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTATTCCATTGCACTGTC-AGGGAAGTA
* *
58873061 AGATCCGCCGTTGTGGCTTCAATCT
1 AGATCCGCCGTCGTAGCTTCAATCT
58873086 TNNNNNNNNN
Statistics
Matches: 169, Mismatches: 51, Indels: 10
0.73 0.22 0.04
Matches are distributed among these distances:
49 5 0.03
50 160 0.95
51 4 0.02
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (50 bp):
AGATCCGCCGTCGTAGCTTCAATCTATTCCATTGCACTGTCAGGGAAGTA
Found at i:58872958 original size:100 final size:100
Alignment explanation
Indices: 58872793--58873086 Score: 446
Period size: 100 Copynumber: 2.9 Consensus size: 100
58872783 TTTGTTCAAC
* * * * *
58872793 TGCAATGTCGGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTATTCCACCGCACCG-TCAGGGA
1 TGCAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCT-AAGGA
* *
58872857 AGTAAGATCTGCTGTTGTGGCTTCAATCTTTTAAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAAT
* * * *
58872893 TGCAATGTCAGGAAAACTAGATCCGCCGTCGTAGCTTCAAGCTATTCCATTGCACTGCTAAGGAA
1 TGCAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAA
*
58872958 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAAT
* *
58872993 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTACACTGCTAAGGAA
1 TGCAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAA
58873058 GTAAGATCCGCCGTTGTGGCTTCAATCTT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTT
58873087 NNNNNNNNNN
Statistics
Matches: 175, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
100 174 0.99
101 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (100 bp):
TGCAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAAT
Found at i:58873858 original size:129 final size:129
Alignment explanation
Indices: 58873402--58874376 Score: 1295
Period size: 132 Copynumber: 7.5 Consensus size: 129
58873392 NNNAATCATT
* * *
58873402 GGCTTCAATGTACTCCTCTGTAACCACAGGGAGGTAAAA-TCTGCCGTCTTTGATCTGCTCCACT
1 GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTC-ACCATCTTTGATCTGCTCCACT
* *
58873466 ACTGCTTAGGGAGACAAGATCTAAAATCTTCAATCTATTCCGCTGCTGTCCAGGGA-AGTAGAAT
65 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGC--T-CAGGGAGA-TAGAAT
* *
58873530 CATT
126 TATC
* * *
58873534 GGCTTCAATGTACTCCACTGTAACTAC-GATGAGGTAAAA-TCTACCGTCTTTGATCTGCTCCAC
1 GGCTTCAATGTACTCCACTGTAACCACAG-GGAGGTAAAATTC-ACCATCTTTGATCTGCTCCAC
*
58873597 TACTGCTTAGGGAGACAAGATCTAAAATCTTCAATCTATTCTGCTACTG-TCTAGGGA-AGTAGA
64 TACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTC--C-ACTGCTC-AGGGAGA-TAGA
* *
58873660 ATCATT
124 ATTATC
* * * * * * * *
58873666 GGCTTCAATGTACTCTACTATAACTAC-GATGAGGTAAAATCCGCCATATTTGATCTGCCCCACT
1 GGCTTCAATGTACTCCACTGTAACCACAG-GGAGGTAAAATTCACCATCTTTGATCTGCTCCACT
*
58873730 ACTGCTTAAGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGATAGAATTATC
65 ACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGATAGAATTATC
58873795 GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTA
1 GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTA
*
58873860 CTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGATAGAATTATC
66 CTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGATAGAATTATC
*
58873924 GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATATTTGATCTGCTCCACTA
1 GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTA
* * *
58873989 CTGCTTAAGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTA
66 CTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCAC---TGCTCAGGGAGATAGAATTA
58874054 TC
128 TC
* * * * *
58874056 GGCTTTAATGTACTCCACTATAACCAC-GAGGAGGTAAAA-TCTGCCATATTTGATCTGCCCCAC
1 GGCTTCAATGTACTCCACTGTAACCACAG-GGAGGTAAAATTC-ACCATCTTTGATCTGCTCCAC
* *
58874119 TACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGATAGAATTAT
64 TACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGATAGAATTAT
58874184 C
129 C
*
58874185 GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTACTCCACTA
1 GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTA
* *
58874250 CTGTTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCTCAGGGA-AGTAGAATT
66 CTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCA---CTGCTCAGGGAGA-TAGAATT
58874314 ATC
127 ATC
* ** * * *
58874317 GGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTC
1 GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTC
58874377 TACTGTCGAT
Statistics
Matches: 770, Mismatches: 53, Indels: 40
0.89 0.06 0.05
Matches are distributed among these distances:
129 351 0.46
130 8 0.01
131 6 0.01
132 400 0.52
133 1 0.00
134 1 0.00
135 3 0.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (129 bp):
GGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTA
CTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGATAGAATTATC
Found at i:58873895 original size:261 final size:258
Alignment explanation
Indices: 58873395--58874376 Score: 1307
Period size: 261 Copynumber: 3.8 Consensus size: 258
58873385 NNNNNNNNNN
* * ** * *
58873395 AATCATTGGCTTCAATGTACTCCTCTGTAACCACAGGGAGGTAAAATCTGCCGTCTTTGATCTGC
1 AATCATCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATATTTGATCTGC
* * *
58873460 TCCACTACTGCTTAGGGAGACAAGATCTAAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGT
66 TCCACTACTGCTTAAGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGC--T-CAGGGAAGT
* * * * *
58873525 AGAATCATTGGCTTCAATGTACTCCACTGTAACTACGATGAGGTAAAATCTACCGTCTTTGATCT
128 AGAATTATCGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTACCATCTTTGATCT
*
58873590 GCTCCACTACTGCTTAGGGAGACAAGATCTAAAATCTTCAATCTATTCTGCTACTG-TCTAGGGA
193 GCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTC--C-ACTGCTC-AGGGA
58873654 -AGTAG
254 GA-TAG
* * * * * *
58873659 AATCATTGGCTTCAATGTACTCTACTATAACTAC-GATGAGGTAAAATCCGCCATATTTGATCTG
1 AATCATCGGCTTCAATGTACTCCACTGTAACCACAG-GGAGGTAAAATCCACCATATTTGATCTG
*
58873723 CCCCACTACTGCTTAAGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGG-AGATA
65 CTCCACTACTGCTTAAGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAAG-TA
58873787 GAATTATCGGCTTCAATGTACTCCACTGTAACCAC-AGGGAGGTAAAAT-TCACCATCTTTGATC
129 GAATTATCGGCTTCAATGTACTCCACTGTAACCACGA-GGAGGTAAAATCT-ACCATCTTTGATC
*
58873850 TGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGAT
192 TGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGAT
58873915 AG
257 AG
* *
58873917 AATTATCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATATTTGATCTGC
1 AATCATCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATATTTGATCTGC
* *
58873982 TCCACTACTGCTTAAGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGG-AGA
66 TCCACTACTGCTTAAGGAGACAAGATCTGAAATCTTCAATCTATTCCAC---TGCTCAGGGAAG-
* * * *
58874046 TAGAATTATCGGCTTTAATGTACTCCACTATAACCACGAGGAGGTAAAATCTGCCATATTTGATC
127 TAGAATTATCGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTACCATCTTTGATC
* * *
58874111 TGCCCCACTACTGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGAT
192 TGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGAT
58874176 AG
257 AG
* * * *
58874178 AATTATCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTAC
1 AATCATCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATATTTGATCTGC
* * *
58874243 TCCACTACTGTTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCTCAGGGAAGT
66 TCCACTACTGCTTAAGGAGACAAGATCTGAAATCTTCAATCTATTCCA---CTGCTCAGGGAAGT
* ** *
58874308 AGAATTATCGGCTTCAATGTACTCCACTGCAACTTCA-G-GGAGGTAAAATCCGCCATCTTCGAT
128 AGAATTATCGGCTTCAATGTACTCCACTGTAAC--CACGAGGAGGTAAAATCTACCATCTTTGAT
58874371 CTGCTC
191 CTGCTC
58874377 TACTGTCGAT
Statistics
Matches: 650, Mismatches: 50, Indels: 39
0.88 0.07 0.05
Matches are distributed among these distances:
258 114 0.18
259 5 0.01
260 4 0.01
261 414 0.64
262 6 0.01
263 3 0.00
264 104 0.16
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (258 bp):
AATCATCGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATATTTGATCTGC
TCCACTACTGCTTAAGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAAGTAGA
ATTATCGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCTACCATCTTTGATCTGCT
CCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTCAGGGAGATAG
Found at i:58875630 original size:8 final size:7
Alignment explanation
Indices: 58875586--58875627 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
58875576 TAAGGCTCTC
58875586 CATTTTT
1 CATTTTT
58875593 -ACTTTTT
1 CA-TTTTT
58875600 CATTTTT
1 CATTTTT
58875607 CA-TTTT
1 CATTTTT
58875613 CATCTTTT
1 CAT-TTTT
58875621 CATTTTT
1 CATTTTT
58875628 TCACATCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 7 0.23
7 16 0.52
8 8 0.26
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:58878377 original size:19 final size:20
Alignment explanation
Indices: 58878353--58878396 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
58878343 TAGAGGTGTT
* *
58878353 TAATGCATATG-ATGGAATG
1 TAATGCAAATGCATGAAATG
58878372 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
58878392 -AATGC
1 TAATGC
58878397 CTAAAGAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:58880581 original size:3 final size:3
Alignment explanation
Indices: 58880573--58880613 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
58880563 ATATGTGCAG
*
58880573 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
58880614 TCAATAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:58881685 original size:24 final size:24
Alignment explanation
Indices: 58881658--58881704 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
58881648 CTGGGTCTTG
*
58881658 TTTGTTGGTTTGGGCCCAGGCATA
1 TTTGTTGGCTTGGGCCCAGGCATA
* *
58881682 TTTGTTTGCTTGGGCCCGGGCAT
1 TTTGTTGGCTTGGGCCCAGGCAT
58881705 TATTGGGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.34, T:0.38
Consensus pattern (24 bp):
TTTGTTGGCTTGGGCCCAGGCATA
Found at i:58886291 original size:75 final size:75
Alignment explanation
Indices: 58886168--58886319 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
58886158 GTACACCATA
58886168 TATCCTCCAGTTGTATGAAGTACACCCTTTTGAAAGTTCATATTAGAGCATAAGAAAGGAATATG
1 TATCCTCCAGTTGTATGAAGTACACCCTTTTGAAAGTTCATATTAGAGCATAAGAAAGGAATATG
58886233 AGAAACTATG
66 AGAAACTATG
58886243 TATCCTCCAGTTGTATGAAGTACACCCTTTTGAAAGTTCATATTAGAGCATAAGAAAGGAATATG
1 TATCCTCCAGTTGTATGAAGTACACCCTTTTGAAAGTTCATATTAGAGCATAAGAAAGGAATATG
58886308 AGAAACTATG
66 AGAAACTATG
58886318 TA
1 TA
58886320 AAATATTTCA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (75 bp):
TATCCTCCAGTTGTATGAAGTACACCCTTTTGAAAGTTCATATTAGAGCATAAGAAAGGAATATG
AGAAACTATG
Found at i:58900147 original size:3 final size:3
Alignment explanation
Indices: 58900139--58900191 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
58900129 TCTGGCATTG
58900139 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
58900187 ATA AT
1 ATA AT
58900192 TTTATATTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:58900568 original size:31 final size:31
Alignment explanation
Indices: 58900522--58900662 Score: 106
Period size: 31 Copynumber: 4.5 Consensus size: 31
58900512 TTTTGGGTCT
* *
58900522 ATTTCGGTTCCTAAACTTGACACTTTTTCCTA
1 ATTT-GGTACCTAAACTTGACACGTTTTCCTA
* *
58900554 ATTTGGTACCTAAACTTGACACTTTTTCTTA
1 ATTTGGTACCTAAACTTGACACGTTTTCCTA
* * * **** ***
58900585 AGTCGGTACTTAAACTT-TTGGGGGGTCC-A
1 ATTTGGTACCTAAACTTGACACGTTTTCCTA
* *
58900614 ATTTGGTACCTGAACTTGACTCGTTTTCCTA
1 ATTTGGTACCTAAACTTGACACGTTTTCCTA
58900645 ATTTGGTACCTAATACTT
1 ATTTGGTACCTAA-ACTT
58900663 TTTTTTTTGA
Statistics
Matches: 80, Mismatches: 26, Indels: 6
0.71 0.23 0.05
Matches are distributed among these distances:
29 14 0.17
30 6 0.08
31 52 0.65
32 8 0.10
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.41
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACGTTTTCCTA
Found at i:58900650 original size:91 final size:92
Alignment explanation
Indices: 58900462--58900662 Score: 239
Period size: 91 Copynumber: 2.2 Consensus size: 92
58900452 TTAATATAAT
* * * *** *
58900462 ATTTGGTACTTGAACTCGACACTTTTTTCTAATCCGGTACTTAAACTTTTTTTTGGGTCTATTTC
1 ATTTGGTACCTAAACTTGACACTTTTTTCTAATCCGGTACTTAAACTTTTTGGGGGGTCAATTTC
* *
58900527 GGTTCCTAAACTTGACACTTTTTCCTA
66 GGTACCTAAACTTGACACGTTTTCCTA
58900554 ATTTGGTACCTAAACTTGACAC-TTTTTCTTAAGT-CGGTACTTAAAC-TTTTGGGGGGTCCAAT
1 ATTTGGTACCTAAACTTGACACTTTTTTC-TAA-TCCGGTACTTAAACTTTTTGGGGGGT-CAAT
* *
58900616 TT-GGTACCTGAACTTGACTCGTTTTCCTA
63 TTCGGTACCTAAACTTGACACGTTTTCCTA
58900645 ATTTGGTACCTAATACTT
1 ATTTGGTACCTAA-ACTT
58900663 TTTTTTTTGA
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
91 50 0.53
92 43 0.46
93 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (92 bp):
ATTTGGTACCTAAACTTGACACTTTTTTCTAATCCGGTACTTAAACTTTTTGGGGGGTCAATTTC
GGTACCTAAACTTGACACGTTTTCCTA
Found at i:58905217 original size:19 final size:19
Alignment explanation
Indices: 58905195--58905235 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
58905185 CAAATAATTT
*
58905195 AAAAATTATAAAATA-TTCA
1 AAAAATTA-AAAAAAGTTCA
58905214 AAAAATTAAAAAAAGTTCA
1 AAAAATTAAAAAAAGTTCA
58905233 AAA
1 AAA
58905236 TTCAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAATTAAAAAAAGTTCA
Found at i:58905238 original size:26 final size:27
Alignment explanation
Indices: 58905204--58905274 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
58905194 TAAAAATTAT
*
58905204 AAAATATTCAAAAAATTAAAAAAAGTTC
1 AAAA-ATTCAAAAAAATAAAAAAAGTTC
* *
58905232 -AAAATTCAAAAAAATATAAATAGTTC
1 AAAAATTCAAAAAAATAAAAAAAGTTC
58905258 ATAAAAATTCAAAAAAA
1 --AAAAATTCAAAAAAA
58905275 CAGCATGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 20 0.54
27 3 0.08
29 14 0.38
ACGTcount: A:0.66, C:0.07, G:0.03, T:0.24
Consensus pattern (27 bp):
AAAAATTCAAAAAAATAAAAAAAGTTC
Found at i:58912047 original size:29 final size:28
Alignment explanation
Indices: 58912002--58912070 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 28
58911992 AATAAACACC
*
58912002 AAAATTTTATTTTAAAAATAAAAAATAA
1 AAAAATTTATTTTAAAAATAAAAAATAA
58912030 AAAAATTTATTTTAAAAATAAAAAATAA
1 AAAAATTTATTTTAAAAATAAAAAATAA
*
58912058 AAAATATATATTT
1 AAAA-ATTTATTT
58912071 ATTATATTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 31 0.82
29 7 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAAATTTATTTTAAAAATAAAAAATAA
Found at i:58915515 original size:22 final size:21
Alignment explanation
Indices: 58915469--58915515 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
58915459 CACTAATTCT
* *
58915469 TAATCTAATCGATTTGAACAT
1 TAATCTAATCGATTTGAAAAA
*
58915490 TAATCTAATCTGATTTTAAAAA
1 TAATCTAATC-GATTTGAAAAA
58915512 TAAT
1 TAAT
58915516 ACAACAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (21 bp):
TAATCTAATCGATTTGAAAAA
Found at i:58915987 original size:28 final size:30
Alignment explanation
Indices: 58915956--58916022 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
58915946 CTTTAAAAAA
* *
58915956 AAAAACTTA-ACAA-TTTAGTAACTTAAAT
1 AAAAACTTAGAAAATTTTAATAACTTAAAT
*
58915984 AAAAACTTATGAAAATTTTAATGACTTAAAT
1 AAAAACTTA-GAAAATTTTAATAACTTAAAT
58916015 AAAAACTT
1 AAAAACTT
58916023 TCGAATAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 9 0.27
30 3 0.09
31 21 0.64
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAAACTTAGAAAATTTTAATAACTTAAAT
Found at i:58916011 original size:31 final size:31
Alignment explanation
Indices: 58915967--58916040 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
58915957 AAAACTTAAC
* *
58915967 AATTTAGTAACTTAAATAAAAACTTAT-GAA-
1 AATTTAATGACTTAAATAAAAACTT-TCGAAT
58915997 AATTTTAATGACTTAAATAAAAACTTTCGAAT
1 AA-TTTAATGACTTAAATAAAAACTTTCGAAT
58916029 AATTTAATGACT
1 AATTTAATGACT
58916041 ATTTTATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 3 0.08
31 34 0.87
32 2 0.05
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (31 bp):
AATTTAATGACTTAAATAAAAACTTTCGAAT
Found at i:58918984 original size:14 final size:15
Alignment explanation
Indices: 58918950--58918987 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
58918940 ATCTTTAAAG
58918950 GAGAAGAAAGAAAAAA
1 GAGAA-AAAGAAAAAA
58918966 GAGAAAAAGAAAAAA
1 GAGAAAAAGAAAAAA
58918981 -AGAAAAA
1 GAGAAAAA
58918988 AAATTTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 7 0.32
15 10 0.45
16 5 0.23
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAGAAAAAGAAAAAA
Found at i:58918988 original size:8 final size:8
Alignment explanation
Indices: 58918956--58918989 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
58918946 AAAGGAGAAG
58918956 AAAG-AAA
1 AAAGAAAA
*
58918963 AAAGAGAA
1 AAAGAAAA
58918971 AAAGAAAA
1 AAAGAAAA
58918979 AAAGAAAA
1 AAAGAAAA
58918987 AAA
1 AAA
58918990 ATTTAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:58919031 original size:17 final size:17
Alignment explanation
Indices: 58919002--58919034 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
58918992 TTAAAGAATG
58919002 AAAGAGAAGGAAAAAAA
1 AAAGAGAAGGAAAAAAA
58919019 AAAGAAGAA-GAAAAAA
1 AAAG-AGAAGGAAAAAA
58919035 TTGTGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAGAGAAGGAAAAAAA
Found at i:58919530 original size:378 final size:379
Alignment explanation
Indices: 58919055--58919809 Score: 1370
Period size: 378 Copynumber: 2.0 Consensus size: 379
58919045 ATGATAGGAC
58919055 CCACTGCTTTAAATGAAATAATTTAAAAATCCACATCATCACTCTTTTTGTAATTTAACGGCACG
1 CCACTGCTTTAAATGAAATAATTTAAAAATCCACATCATCACTCTTTTTGTAATTTAACGGCACG
58919120 ATGATTTAAAAAATAAATTTGAATAATTTAATAATTAAATTAAATTATTTTATAGTTTAGTGATC
66 ATGATTTAAAAAATAAATTTGAATAATTTAATAATTAAATTAAATTATTTTATAGTTTAGTGATC
58919185 AAAATAAAAATACGCTAAAAGTTTAGTGAGTATTAAGGCAATATACCC-TTTTTTCTCTTTATAT
131 AAAATAAAAATACGCTAAAAGTTTAGTGAGTATTAAGGCAATATACCCTTTTTTTCTCTTTATAT
58919249 ATATATTTTTATTTTTAAAATATTTTAAAAGAGAATATATAACTTTCACCACATGGCATAAGTAT
196 ATATATTTTTATTTTTAAAATATTTTAAAAGAGAATATATAACTTTCACCACATGGCATAAGTAT
* * *
58919314 GGCATGACAAGTGACAACAAAAATTTGTTACACTTTAACGGTTAAAATTGATCGTCAAAG-AACT
261 GGCATGACAAGTGACAACAAAAATTTGCTACACTTTAACGATTAAAATTGATCATCAAAGTAACT
58919378 TATGACAATTCTAAAGATATTTTTCCTTCGAATGGGCTTTAATTAATTTAAAAAT
326 TATGACAATTCTAAAGATATTTTTCCTTCGAAT-GGCTTTAATTAATTTAAAAAT
* *
58919433 CCACTGCTTTAAATGAAATAATTTAAAAATCCACGTCATCACTTTTTTTGTAATTTAACGGCACG
1 CCACTGCTTTAAATGAAATAATTTAAAAATCCACATCATCACTCTTTTTGTAATTTAACGGCACG
**
58919498 ATGATTTAAAAAATAAATTTGAATAATTTAATAATTAAATTATTTTATTTTATAGTTTAGTGATC
66 ATGATTTAAAAAATAAATTTGAATAATTTAATAATTAAATTAAATTATTTTATAGTTTAGTGATC
58919563 AAAATAAAAATACGCTAAAAGTTTAGTGAGTATTAAGGCAATATACCCTTTTTTTCTCTTTATAT
131 AAAATAAAAATACGCTAAAAGTTTAGTGAGTATTAAGGCAATATACCCTTTTTTTCTCTTTATAT
*
58919628 ATATATTTTTATTTTTTAAATATTTTAAAAGAGAATATATAACTTTCACCACATGGCATAAGTAT
196 ATATATTTTTATTTTTAAAATATTTTAAAAGAGAATATATAACTTTCACCACATGGCATAAGTAT
58919693 GGCATGACAAGTGACAACAAAAATTTGCTACACTTTAACGATTAAAATTGATCATCAAAGAATTT
261 GGCATGACAAGTGACAACAAAAATTTGCTACACTTTAACGATTAAAATTGATCATCAAAG----T
*
58919758 AATTTATGACAATTCTAAAGATATTTTTCCTTCGAATGGCTTTAATTAATTT
322 AACTTATGACAATTCTAAAGATATTTTTCCTTCGAATGGCTTTAATTAATTT
58919810 TTTTAATTAA
Statistics
Matches: 362, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
378 174 0.48
379 137 0.38
383 15 0.04
384 36 0.10
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (379 bp):
CCACTGCTTTAAATGAAATAATTTAAAAATCCACATCATCACTCTTTTTGTAATTTAACGGCACG
ATGATTTAAAAAATAAATTTGAATAATTTAATAATTAAATTAAATTATTTTATAGTTTAGTGATC
AAAATAAAAATACGCTAAAAGTTTAGTGAGTATTAAGGCAATATACCCTTTTTTTCTCTTTATAT
ATATATTTTTATTTTTAAAATATTTTAAAAGAGAATATATAACTTTCACCACATGGCATAAGTAT
GGCATGACAAGTGACAACAAAAATTTGCTACACTTTAACGATTAAAATTGATCATCAAAGTAACT
TATGACAATTCTAAAGATATTTTTCCTTCGAATGGCTTTAATTAATTTAAAAAT
Found at i:58921449 original size:6 final size:6
Alignment explanation
Indices: 58921435--58921466 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
58921425 AACACAGTGG
*
58921435 AGGTAA AGGTGA AGGTGA AGGTGA AGGTGA AG
1 AGGTGA AGGTGA AGGTGA AGGTGA AGGTGA AG
58921467 ATGACAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.47, T:0.16
Consensus pattern (6 bp):
AGGTGA
Found at i:58924868 original size:32 final size:32
Alignment explanation
Indices: 58924827--58924895 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
58924817 TGTATCTTTG
58924827 TTATATATACACACTCATTAATCTCTGTTACA
1 TTATATATACACACTCATTAATCTCTGTTACA
58924859 TTATATATACACACTCATTAATCTCTGTTACA
1 TTATATATACACACTCATTAATCTCTGTTACA
58924891 TTATA
1 TTATA
58924896 ATCTATGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (32 bp):
TTATATATACACACTCATTAATCTCTGTTACA
Found at i:58929365 original size:3 final size:3
Alignment explanation
Indices: 58929357--58929387 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
58929347 AATTTGTTTG
58929357 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
58929388 TCTTAATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:58933280 original size:30 final size:32
Alignment explanation
Indices: 58933244--58933312 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
58933234 AAGTTTTTGT
*
58933244 ATTTTTTGTATATTT-AGAATTTAG-TCTTTA
1 ATTTTTTGTATATTTAAGAATTTAGCCCTTTA
* * *
58933274 ATTTTTTTTATTTTTAAGAATTTAGCCCTTTT
1 ATTTTTTGTATATTTAAGAATTTAGCCCTTTA
58933306 ATTTTTT
1 ATTTTTT
58933313 AAAATTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 13 0.39
31 9 0.27
32 11 0.33
ACGTcount: A:0.23, C:0.06, G:0.07, T:0.64
Consensus pattern (32 bp):
ATTTTTTGTATATTTAAGAATTTAGCCCTTTA
Found at i:58938544 original size:14 final size:15
Alignment explanation
Indices: 58938525--58938553 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
58938515 GTTTCCATTT
58938525 TCTTTCT-TCTTCCC
1 TCTTTCTCTCTTCCC
58938539 TCTTTCTCTCTTCCC
1 TCTTTCTCTCTTCCC
58938554 CTGCAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTCTCTCTTCCC
Found at i:58949644 original size:17 final size:16
Alignment explanation
Indices: 58949622--58949668 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
58949612 CAATTAACTG
58949622 ACAAAATATATAAAAAT
1 ACAAAATA-ATAAAAAT
*
58949639 ACAAAA-AATATAAAT
1 ACAAAATAATAAAAAT
*
58949654 ATAAAATAATAAAAA
1 ACAAAATAATAAAAA
58949669 CGAACAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 12 0.46
16 8 0.31
17 6 0.23
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (16 bp):
ACAAAATAATAAAAAT
Found at i:58952692 original size:19 final size:18
Alignment explanation
Indices: 58952664--58952700 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
58952654 AAGTTGGATG
58952664 TTTTTCTTTTCTTCTCTTT
1 TTTTTCTTTTCTT-TCTTT
*
58952683 TTTTTGTTTTCTTTCTTT
1 TTTTTCTTTTCTTTCTTT
58952701 CTTGTGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTTCTTTCTTT
Found at i:58959036 original size:129 final size:129
Alignment explanation
Indices: 58958802--58959113 Score: 452
Period size: 129 Copynumber: 2.4 Consensus size: 129
58958792 TTAAAAATTT
* * * * *
58958802 ATGTCAGAATGAGATACAC-TTG-ACATGCCATGTGTAACTGT-TTGGTTATTCTATGCATTTTA
1 ATGTCAGAATGAGGTACACATGGCACAT--CATGTGTAACTGTCTT-GTTATTTTGTACATTTTA
* * *
58958864 TCAAAAAGCAAACTGGTCATTTTATTAAAAATCTCATTCATTTCTACTGTTAAGAATTGGTCCTT
63 TCAAAAAGCAAACTGGTCATTCTATTAAAAATCTCATTAATTTCTACTATTAAGAATTGGTCCTT
58958929 GA
128 GA
58958931 ATGTCAGAATGAGGTACACATGGCACATCATGTGTAACTGTCTTGTTATTTTGTACATTTTATCA
1 ATGTCAGAATGAGGTACACATGGCACATCATGTGTAACTGTCTTGTTATTTTGTACATTTTATCA
* *
58958996 AAAAGCAAACTGGTCATTCTATTAAAAGTTTCATTAATTTCTACTATTAAGAATTGGTCCTTGA
66 AAAAGCAAACTGGTCATTCTATTAAAAATCTCATTAATTTCTACTATTAAGAATTGGTCCTTGA
* *
58959060 ATGTCAGAATGAGGTACACATGGCATGA-CATGTGTAACTGTCTAGTTATTTTGT
1 ATGTCAGAATGAGGTACACATGGCA-CATCATGTGTAACTGTCTTGTTATTTTGT
58959114 TAATGTCAGT
Statistics
Matches: 167, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
129 158 0.95
130 5 0.03
131 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (129 bp):
ATGTCAGAATGAGGTACACATGGCACATCATGTGTAACTGTCTTGTTATTTTGTACATTTTATCA
AAAAGCAAACTGGTCATTCTATTAAAAATCTCATTAATTTCTACTATTAAGAATTGGTCCTTGA
Found at i:58961378 original size:25 final size:25
Alignment explanation
Indices: 58961344--58961394 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
58961334 ATATATTATT
*
58961344 ATTTTGAAAT-TAAAAAATATATAAA
1 ATTTTAAAATATAAAAAATA-ATAAA
*
58961369 ATTTTAAAATATAAAAATTAATAAA
1 ATTTTAAAATATAAAAAATAATAAA
58961394 A
1 A
58961395 AATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
ATTTTAAAATATAAAAAATAATAAA
Found at i:58961393 original size:17 final size:18
Alignment explanation
Indices: 58961350--58961399 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
58961340 TATTATTTTG
58961350 AAATTAA-AAAATATATA
1 AAATTAATAAAATATATA
*
58961367 AAATT-TTAAAATATA-A
1 AAATTAATAAAATATATA
*
58961383 AAATTAATAAAAAATAT
1 AAATTAATAAAATATAT
58961400 TTTTACATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATTAATAAAATATATA
Found at i:58963246 original size:21 final size:21
Alignment explanation
Indices: 58963222--58963261 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58963212 TATTTTCTAC
*
58963222 AATTAAAAGTCAAAACCATTA
1 AATTAAAAGGCAAAACCATTA
58963243 AATTAAAAGGCAAAACCAT
1 AATTAAAAGGCAAAACCAT
58963262 GTCGTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.20
Consensus pattern (21 bp):
AATTAAAAGGCAAAACCATTA
Found at i:58972070 original size:16 final size:17
Alignment explanation
Indices: 58972042--58972073 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
58972032 TATCAAATTT
58972042 AAATTATTATTAATATA
1 AAATTATTATTAATATA
58972059 AAATTATT-TTAATAT
1 AAATTATTATTAATAT
58972074 TTTAATGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTATTATTAATATA
Found at i:58973580 original size:16 final size:16
Alignment explanation
Indices: 58973556--58973586 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58973546 TTTTTATTTT
*
58973556 TATATAAAAATAATAA
1 TATAAAAAAATAATAA
58973572 TATAAAAAAATAATA
1 TATAAAAAAATAATA
58973587 TAAACGAGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TATAAAAAAATAATAA
Found at i:58973583 original size:13 final size:14
Alignment explanation
Indices: 58973557--58973590 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
58973547 TTTTATTTTT
58973557 ATATAAAAATAATA
1 ATATAAAAATAATA
58973571 ATATAAAAA-AATA
1 ATATAAAAATAATA
58973584 ATATAAA
1 ATATAAA
58973591 CGAGCCGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATATAAAAATAATA
Found at i:58977682 original size:14 final size:16
Alignment explanation
Indices: 58977663--58977708 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
58977653 ATCTAACCTT
58977663 ATTTTTATA-A-TTTA
1 ATTTTTATATATTTTA
*
58977677 ATTTTTAATATATTTTG
1 ATTTTT-ATATATTTTA
58977694 ATTTTTATAT-TTTTA
1 ATTTTTATATATTTTA
58977709 TAATATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
16 5 0.19
17 9 0.33
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
ATTTTTATATATTTTA
Found at i:58980551 original size:105 final size:101
Alignment explanation
Indices: 58980436--58980634 Score: 299
Period size: 105 Copynumber: 1.9 Consensus size: 101
58980426 TTAAATTTGT
* *
58980436 AGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGACATAGCCCATCTATGGTCTTACACATG
1 AGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGACATAGCCCAGCTATGGTCTT--ACAT-
* *
58980501 TATATATACTGCCATGGTCCAACCATGGTCTTACGTTCAA
63 T-TAAACACTGCCATGGTCCAACCATGGTCTTACGTTCAA
* * *
58980541 AGTGCCATAACCCAGTTATGGTCTTTTCATTAAAATGCCATAGCCCAGCTATGGTCTTACATTTA
1 AGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGACATAGCCCAGCTATGGTCTTACATTTA
58980606 AACACTGCCATGGTCCAACCATGGTCTTA
66 AACACTGCCATGGTCCAACCATGGTCTTA
58980635 TCCGTCAATT
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
101 29 0.33
102 1 0.01
103 4 0.05
105 53 0.61
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (101 bp):
AGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGACATAGCCCAGCTATGGTCTTACATTTA
AACACTGCCATGGTCCAACCATGGTCTTACGTTCAA
Found at i:58980607 original size:33 final size:33
Alignment explanation
Indices: 58980420--58980634 Score: 101
Period size: 33 Copynumber: 6.3 Consensus size: 33
58980410 TGACCTTGCC
* ** * * *
58980420 ATGGTCTTAAATTTGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATTTAAAATGCCATAGCCCAGCT
* * * *
58980453 ATGGTCTTATCA-TCAGAATGACATAGCCCATCT
1 ATGGTCTTA-CATTTAAAATGCCATAGCCCAGCT
* * * * *
58980486 ATGGTCTTACACATGTATATATACTGCCATGGTCCAACC
1 ATGGTCTT--ACAT-T-TA-A-AATGCCATAGCCCAGCT
* * * * *
58980525 ATGGTCTTACGTTCAAAGTGCCATAACCCAGTT
1 ATGGTCTTACATTTAAAATGCCATAGCCCAGCT
*
58980558 ATGGTCTTTTCA-TTAAAATGCCATAGCCCAGCT
1 ATGGTC-TTACATTTAAAATGCCATAGCCCAGCT
* * * *
58980591 ATGGTCTTACATTTAAACACTGCCATGGTCCAACC
1 ATGGTCTTACATTTAAA-A-TGCCATAGCCCAGCT
58980626 ATGGTCTTA
1 ATGGTCTTA
58980635 TCCGTCAATT
Statistics
Matches: 133, Mismatches: 37, Indels: 22
0.69 0.19 0.11
Matches are distributed among these distances:
32 4 0.03
33 74 0.56
34 8 0.06
35 22 0.17
36 2 0.02
37 4 0.03
39 19 0.14
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (33 bp):
ATGGTCTTACATTTAAAATGCCATAGCCCAGCT
Found at i:58983583 original size:16 final size:16
Alignment explanation
Indices: 58983562--58983592 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
58983552 GAAGAGAAGG
58983562 GGTAATGGTACTCTAA
1 GGTAATGGTACTCTAA
58983578 GGTAATGGTACTCTA
1 GGTAATGGTACTCTA
58983593 TGATGTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (16 bp):
GGTAATGGTACTCTAA
Found at i:58983687 original size:17 final size:17
Alignment explanation
Indices: 58983665--58983699 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
58983655 GCTAGGCTTA
*
58983665 AAGCTACCGAGTGGACC
1 AAGCTACCGAATGGACC
*
58983682 AAGCTACCTAATGGACC
1 AAGCTACCGAATGGACC
58983699 A
1 A
58983700 TTTGTGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.29, G:0.23, T:0.14
Consensus pattern (17 bp):
AAGCTACCGAATGGACC
Found at i:58985656 original size:104 final size:103
Alignment explanation
Indices: 58985471--58985661 Score: 267
Period size: 104 Copynumber: 1.8 Consensus size: 103
58985461 CATCTGCCGA
* **
58985471 ATATAATATTCATGTTACTTGCATTGTATCAATTTCAAAATACTACCGAAAATTAAAACTTACCA
1 ATATAATATTCATGTTACTTGCATTGTATCAATTTCAAAATAATACAAAAAATTAAAACTTACCA
* *
58985536 ACAAGTATTGAATGCAGTGACAGTAACGATGGCGGAAT
66 ACAAATATTGAATGCAGCGACAGTAACGATGGCGGAAT
* *
58985574 ATATAAATATTCATGTTATTTGCATTGTATCAATTTCAAAATAATACAAAAAATTTAAAGC-TAC
1 ATAT-AATATTCATGTTACTTGCATTGTATCAATTTCAAAATAATACAAAAAA-TTAAAACTTAC
* **
58985638 CAATAAATATTGGGTGCAGCGACA
64 CAACAAATATTGAATGCAGCGACA
58985662 ATAGTGGAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
103 4 0.05
104 66 0.87
105 6 0.08
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (103 bp):
ATATAATATTCATGTTACTTGCATTGTATCAATTTCAAAATAATACAAAAAATTAAAACTTACCA
ACAAATATTGAATGCAGCGACAGTAACGATGGCGGAAT
Found at i:58988577 original size:40 final size:38
Alignment explanation
Indices: 58988522--58988621 Score: 112
Period size: 40 Copynumber: 2.6 Consensus size: 38
58988512 AAAGTTTTCT
* *
58988522 AACACATTAAAAATATATTAAAAAATAT-TTATATTAAAA
1 AACACA-TATAAATATAATAAAAAATATATTATATT-AAA
* * *
58988561 AACACTACTATAAATATAATAAATATTTTATTATATTAAA
1 AACAC-A-TATAAATATAATAAAAAATATATTATATTAAA
58988601 AACACATATAAATATAATAAA
1 AACACATATAAATATAATAAA
58988622 TATTTTTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
38 15 0.28
39 6 0.11
40 25 0.47
41 7 0.13
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (38 bp):
AACACATATAAATATAATAAAAAATATATTATATTAAA
Found at i:58988611 original size:38 final size:41
Alignment explanation
Indices: 58988550--58988639 Score: 141
Period size: 38 Copynumber: 2.2 Consensus size: 41
58988540 TAAAAAATAT
58988550 TTATATTAAAAAACACTACTATAAATATAATAAATA-TTTTA
1 TTATATT-AAAAACACTACTATAAATATAATAAATATTTTTA
58988591 TTATATTAAAAACAC-A-TATAAATATAATAAATATTTTTA
1 TTATATTAAAAACACTACTATAAATATAATAAATATTTTTA
*
58988630 TTTTATTAAA
1 TTATATTAAA
58988640 TATAATTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
38 17 0.36
39 15 0.32
40 8 0.17
41 7 0.15
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (41 bp):
TTATATTAAAAACACTACTATAAATATAATAAATATTTTTA
Found at i:58991894 original size:63 final size:64
Alignment explanation
Indices: 58991775--58991897 Score: 176
Period size: 63 Copynumber: 1.9 Consensus size: 64
58991765 CAGCTACAAG
* * **
58991775 TTATTCCATCTATAGTTGAATTTGAAGATTTTATTTTATTGGAAACACCTTGACTAATGCCAAA
1 TTATTCCATCTATAGTTGAATTTGAAGATTTTATTTTATTAGAAACACATCCACTAATGCCAAA
* * *
58991839 TTATTCCA-CTATAGTTGATTTTGAAGATTTTATTTTATTAGACATACATCCACTAATGC
1 TTATTCCATCTATAGTTGAATTTGAAGATTTTATTTTATTAGAAACACATCCACTAATGC
58991898 AAACCTATGT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
63 44 0.85
64 8 0.15
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (64 bp):
TTATTCCATCTATAGTTGAATTTGAAGATTTTATTTTATTAGAAACACATCCACTAATGCCAAA
Found at i:58993899 original size:20 final size:18
Alignment explanation
Indices: 58993876--58993916 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
58993866 GCGTATGTAC
58993876 ATATTTACAAACGTAAAAAT
1 ATATTT-CAAAC-TAAAAAT
*
58993896 ATATTTGAAACTAAAAAT
1 ATATTTCAAACTAAAAAT
58993914 ATA
1 ATA
58993917 AAAGTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 4 0.20
20 6 0.30
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATTTCAAACTAAAAAT
Found at i:58996056 original size:88 final size:89
Alignment explanation
Indices: 58995954--58996141 Score: 270
Period size: 88 Copynumber: 2.1 Consensus size: 89
58995944 GGACCTACTA
* *
58995954 TCTTTGATCTACTTCACGCCAGTACATGAAGACACGATCTGTTTTCTTCGACCTACTCCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGACCTACTCCACCACC
* *
58996019 AGTATGGGGAGACAAGATCTG-TT
66 AGTATGGGAAGACAAGATCCGCTT
* * * * *
58996042 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATTTGCTTTCTTTGATCTGCTTCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGACCTACTCCACCACC
*
58996107 AGTATGGGAAGGCAAGATCCGCTT
66 AGTATGGGAAGACAAGATCCGCTT
58996131 TCTTCTGATCT
1 TCTT-TGATCT
58996142 CTGATCTACT
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 76 0.86
89 6 0.07
90 6 0.07
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (89 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGACCTACTCCACCACC
AGTATGGGAAGACAAGATCCGCTT
Found at i:58996124 original size:45 final size:45
Alignment explanation
Indices: 58995927--58996141 Score: 184
Period size: 44 Copynumber: 4.8 Consensus size: 45
58995917 CCACTTCGCT
* * * * * *
58995927 ACCAATATAGGAAGACAGGACCTACTATCTTTGATCTACTTCA-C
1 ACCAGTATGGGAAGACAAGATCTGCTTTCTTTGATCTACTTCACC
* *** * * * * *
58995971 GCCAGTACATGAAGACACGATCTGTTTTCTTCGACCTACTCCACC
1 ACCAGTATGGGAAGACAAGATCTGCTTTCTTTGATCTACTTCACC
*
58996016 ACCAGTATGGGGAGACAAGATCTG-TTTCTTTGATCTACTTCA-C
1 ACCAGTATGGGAAGACAAGATCTGCTTTCTTTGATCTACTTCACC
* *** * *
58996059 GCCAGTACATGAAGACAAGATTTGCTTTCTTTGATCTGCTTCACC
1 ACCAGTATGGGAAGACAAGATCTGCTTTCTTTGATCTACTTCACC
* *
58996104 ACCAGTATGGGAAGGCAAGATCCGCTTTCTTCTGATCT
1 ACCAGTATGGGAAGACAAGATCTGCTTTCTT-TGATCT
58996142 CTGATCTACT
Statistics
Matches: 132, Mismatches: 35, Indels: 6
0.76 0.20 0.03
Matches are distributed among these distances:
43 19 0.14
44 63 0.48
45 44 0.33
46 6 0.05
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (45 bp):
ACCAGTATGGGAAGACAAGATCTGCTTTCTTTGATCTACTTCACC
Found at i:59004230 original size:20 final size:20
Alignment explanation
Indices: 59004205--59004244 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
59004195 TAAAGGTCTT
*
59004205 TAATGCATATGATGTGATGC
1 TAATGCATATGATGCGATGC
59004225 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
59004245 ATGAGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:59007963 original size:20 final size:18
Alignment explanation
Indices: 59007940--59007980 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
59007930 GCGTATGTAC
59007940 ATATTTACAAACGTAAAAAT
1 ATATTT-CAAAC-TAAAAAT
*
59007960 ATATTTGAAACTAAAAAT
1 ATATTTCAAACTAAAAAT
59007978 ATA
1 ATA
59007981 AAAGTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 4 0.20
20 6 0.30
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATTTCAAACTAAAAAT
Found at i:59017980 original size:14 final size:12
Alignment explanation
Indices: 59017955--59018008 Score: 90
Period size: 12 Copynumber: 4.3 Consensus size: 12
59017945 GGCAGCTAAC
59017955 CTTAAAATATCA
1 CTTAAAATATCA
59017967 CTTAACATATATCA
1 CTTAA-A-ATATCA
59017981 CTTAAAATATCA
1 CTTAAAATATCA
59017993 CTTAAAATATCA
1 CTTAAAATATCA
59018005 CTTA
1 CTTA
59018009 TTTAATAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
12 27 0.68
13 2 0.05
14 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (12 bp):
CTTAAAATATCA
Found at i:59018015 original size:26 final size:26
Alignment explanation
Indices: 59017955--59018008 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
59017945 GGCAGCTAAC
59017955 CTTAAAATATCACTTAACATATATCA
1 CTTAAAATATCACTTAACATATATCA
59017981 CTTAAAATATCACTTAA-A-ATATCA
1 CTTAAAATATCACTTAACATATATCA
59018005 CTTA
1 CTTA
59018009 TTTAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 10 0.36
25 1 0.04
26 17 0.61
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (26 bp):
CTTAAAATATCACTTAACATATATCA
Found at i:59019642 original size:6 final size:6
Alignment explanation
Indices: 59019627--59019656 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
59019617 ATTATTTTAA
*
59019627 TATTAT TATTAC TATTAC TATTAC TATTAC
1 TATTAC TATTAC TATTAC TATTAC TATTAC
59019657 ATCATTATTA
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:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (6 bp):
TATTAC
Found at i:59019747 original size:26 final size:26
Alignment explanation
Indices: 59019709--59019762 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
59019699 TTAGTTTCAA
** * *
59019709 ATTTTGTTGTATATGTACATACTTAC
1 ATTTTGTCATATATATACATACGTAC
59019735 ATTTTGTCATATATATACATACGTAC
1 ATTTTGTCATATATATACATACGTAC
59019761 AT
1 AT
59019763 ATTATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.46
Consensus pattern (26 bp):
ATTTTGTCATATATATACATACGTAC
Found at i:59019820 original size:20 final size:19
Alignment explanation
Indices: 59019781--59019825 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
59019771 AATTTATTTG
*
59019781 TATATA-TATTTTTATACT
1 TATATATTATTTATATACT
59019799 TATATATTATTTATATACCT
1 TATATATTATTTATATA-CT
59019819 TATATAT
1 TATATAT
59019826 ATACATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 9 0.38
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATATTATTTATATACT
Found at i:59020272 original size:23 final size:24
Alignment explanation
Indices: 59020246--59020290 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
59020236 ATTACTCGTG
59020246 TTATT-TTTATGCCAT-CATATTCA
1 TTATTGTTT-TGCCATACATATTCA
*
59020269 TTATTGTTTTGCTATACATATT
1 TTATTGTTTTGCCATACATATT
59020291 TTACCATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.56
Consensus pattern (24 bp):
TTATTGTTTTGCCATACATATTCA
Found at i:59020496 original size:107 final size:107
Alignment explanation
Indices: 59020310--59020731 Score: 702
Period size: 107 Copynumber: 4.0 Consensus size: 107
59020300 ATCAAAAGAA
* * * *
59020310 AAGATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTA
1 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGCGCTG
59020375 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTT
* * * *
59020417 AAGATTTTTTAAATAGGGAAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGCGTTG
1 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGCGCTG
*
59020482 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTT
** * *
59020524 AAGATTTTCTAAATAAGGCAATATTTTGTATTTGGAAATTCAAGAAAACGTGCCCTAACGTGCTG
1 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGCGCTG
59020589 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTT
*
59020631 AAGATTTTTTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTG-CCTAACGCGCTG
1 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGCGCTG
*
59020695 GGTTTCGATTTCTCGTTCGACTAAATAGCCAAATATC
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATC
59020732 CTCTTAAAAC
Statistics
Matches: 291, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
106 47 0.16
107 244 0.84
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (107 bp):
AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGCGCTG
GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTT
Found at i:59027502 original size:19 final size:19
Alignment explanation
Indices: 59027478--59027515 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
59027468 TTGATGTTGG
59027478 GGATAATGACTAATAGTTT
1 GGATAATGACTAATAGTTT
59027497 GGATAATGACTAATAGTTT
1 GGATAATGACTAATAGTTT
59027516 TCTTGCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (19 bp):
GGATAATGACTAATAGTTT
Found at i:59033356 original size:3 final size:3
Alignment explanation
Indices: 59033342--59033413 Score: 67
Period size: 3 Copynumber: 24.3 Consensus size: 3
59033332 CCTGTCATTG
* * * *
59033342 TTA TTT TTA TTA TTA TTA -AA CTAA TT- TTA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* *
59033386 TTA TTA TTA TTA TTC TTA TCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
59033414 GTATATCTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
2 3 0.05
3 51 0.91
4 2 0.04
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:59033527 original size:12 final size:12
Alignment explanation
Indices: 59033510--59033543 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
59033500 ATATTTTATA
59033510 ATCTATATACAT
1 ATCTATATACAT
59033522 ATCTATAT--AT
1 ATCTATATACAT
59033532 ATCTATATACAT
1 ATCTATATACAT
59033544 TTTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (12 bp):
ATCTATATACAT
Found at i:59033578 original size:2 final size:2
Alignment explanation
Indices: 59033571--59033622 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
59033561 TATAAAATAC
*
59033571 AT AT AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
59033611 AC AT AC AT AT AT
1 AT AT AT AT AT AT
59033623 CTTTTTACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:59037539 original size:15 final size:15
Alignment explanation
Indices: 59037519--59037547 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59037509 TACAGCAACC
59037519 CCATCCTTATCTCCG
1 CCATCCTTATCTCCG
59037534 CCATCCTTATCTCC
1 CCATCCTTATCTCC
59037548 TCCACCTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.48, G:0.03, T:0.34
Consensus pattern (15 bp):
CCATCCTTATCTCCG
Found at i:59039134 original size:15 final size:14
Alignment explanation
Indices: 59039113--59039148 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
59039103 ATAATCCTTA
*
59039113 ATAATTATCTTAAT
1 ATAATTATCCTAAT
59039127 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
59039142 ATAATTA
1 ATAATTA
59039149 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:59039759 original size:16 final size:16
Alignment explanation
Indices: 59039715--59039760 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
59039705 ATTTTTTCTT
*
59039715 TTTTATTTATTT-TGA
1 TTTTATTTATTTATTA
59039730 TTTTGATTTATTTATTA
1 TTTT-ATTTATTTATTA
59039747 TTTATATTT-TTTAT
1 TTT-TATTTATTTAT
59039761 GCTTTAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 9 0.33
18 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (16 bp):
TTTTATTTATTTATTA
Found at i:59040816 original size:4 final size:4
Alignment explanation
Indices: 59040782--59040859 Score: 72
Period size: 4 Copynumber: 18.5 Consensus size: 4
59040772 CCAAATAAGT
59040782 AATA AAT- AATAA AATA AAGTA AAGT- AATA AATA AAGTA AATA AAGTA
1 AATA AATA AAT-A AATA AA-TA AA-TA AATA AATA AA-TA AATA AA-TA
59040829 AATAA AATAA AATA AATA AATA AAT- AATA AA
1 AAT-A AAT-A AATA AATA AATA AATA AATA AA
59040860 AATTGGGTTG
Statistics
Matches: 66, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
3 7 0.11
4 33 0.50
5 26 0.39
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:59040823 original size:9 final size:9
Alignment explanation
Indices: 59040793--59040852 Score: 72
Period size: 9 Copynumber: 6.8 Consensus size: 9
59040783 ATAAATAATA
59040793 AAATAAAGT
1 AAATAAAGT
59040802 AAAGT-AA-T
1 AAA-TAAAGT
59040810 AAATAAAGT
1 AAATAAAGT
59040819 AAATAAAGT
1 AAATAAAGT
*
59040828 AAATAAAAT
1 AAATAAAGT
59040837 AAAATAAA-T
1 -AAATAAAGT
59040846 AAATAAA
1 AAATAAA
59040853 TAATAAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
7 1 0.02
8 13 0.28
9 24 0.52
10 8 0.17
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.22
Consensus pattern (9 bp):
AAATAAAGT
Found at i:59044775 original size:15 final size:14
Alignment explanation
Indices: 59044754--59044789 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
59044744 ATAATCCTTA
*
59044754 ATAATTATCTTAAT
1 ATAATTATCCTAAT
59044768 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
59044783 ATAATTA
1 ATAATTA
59044790 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:59050574 original size:11 final size:11
Alignment explanation
Indices: 59050539--59050576 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
59050529 TTTGGGAGGG
59050539 AAAT-GAGCGAA
1 AAATCGAGC-AA
59050550 AAA-CGAGCAA
1 AAATCGAGCAA
59050560 AAATCGAGCAA
1 AAATCGAGCAA
59050571 AAATCG
1 AAATCG
59050577 GAGAAGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.55, C:0.16, G:0.21, T:0.08
Consensus pattern (11 bp):
AAATCGAGCAA
Found at i:59054050 original size:13 final size:13
Alignment explanation
Indices: 59054032--59054057 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59054022 TACATGAACA
59054032 TATCATCTTTTTC
1 TATCATCTTTTTC
59054045 TATCATCTTTTTC
1 TATCATCTTTTTC
59054058 CCCAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (13 bp):
TATCATCTTTTTC
Found at i:59056756 original size:46 final size:46
Alignment explanation
Indices: 59056527--59056757 Score: 399
Period size: 46 Copynumber: 5.0 Consensus size: 46
59056517 ACATTGCTAT
* * *
59056527 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
59056573 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCGC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
**
59056619 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCGT
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
59056665 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
59056711 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
59056757 A
1 A
59056758 TTTTGCCATG
Statistics
Matches: 176, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 176 1.00
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:59067487 original size:46 final size:45
Alignment explanation
Indices: 59067420--59067573 Score: 249
Period size: 46 Copynumber: 3.4 Consensus size: 45
59067410 AGTGATAAGC
59067420 GGTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCA
1 GGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCA
*
59067466 GGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCA
1 GGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCA
* *
59067512 AGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCA
1 GGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCA
59067557 GG-GAC-AAGTGATAAGTG
1 GGTGACAAAGTGATAAGTG
59067574 ATCATATGTA
Statistics
Matches: 102, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
43 12 0.12
44 3 0.03
45 22 0.22
46 64 0.63
47 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (45 bp):
GGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCA
Found at i:59070197 original size:24 final size:24
Alignment explanation
Indices: 59070170--59070239 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
59070160 ATAATACGCA
* *
59070170 AAATGATAATACTCATAATAATGC
1 AAATGATAATAATAATAATAATGC
*
59070194 AAATGATAATAATAATAATAAT-A
1 AAATGATAATAATAATAATAATGC
*
59070217 ATAATAATAATAATAATAATAAT
1 A-AATGATAATAATAATAATAAT
59070240 AATATAAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
AAATGATAATAATAATAATAATGC
Found at i:59070205 original size:3 final size:3
Alignment explanation
Indices: 59070199--59070243 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
59070189 AATGCAAATG
59070199 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
59070244 TAAGTAACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:59073738 original size:17 final size:17
Alignment explanation
Indices: 59073713--59073745 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
59073703 TGCTTGACAC
*
59073713 TATAGATATTTAAAAAA
1 TATAAATATTTAAAAAA
59073730 TATAAATATTTAAAAA
1 TATAAATATTTAAAAA
59073746 GAGTAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TATAAATATTTAAAAAA
Found at i:59081421 original size:24 final size:23
Alignment explanation
Indices: 59081379--59081423 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
59081369 AATATATATT
*
59081379 TTTTATTTTTTATTTTTAAAATA
1 TTTTATTTTGTATTTTTAAAATA
*
59081402 TTTTATTTTGTGTTTATTAAAA
1 TTTTATTTTGTATTT-TTAAAA
59081424 AACGGGCCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTATTTTGTATTTTTAAAATA
Found at i:59100634 original size:21 final size:21
Alignment explanation
Indices: 59100592--59100639 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
59100582 CATCCTTATC
* *
59100592 TCCTCCACCCTCACCTGTTAG
1 TCCTCCACCCCCACCTGCTAG
* *
59100613 TTCTCCACCCCCAGCTGCTAG
1 TCCTCCACCCCCACCTGCTAG
59100634 TCCTCC
1 TCCTCC
59100640 GCCACAGTCG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.12, C:0.50, G:0.10, T:0.27
Consensus pattern (21 bp):
TCCTCCACCCCCACCTGCTAG
Found at i:59106183 original size:42 final size:42
Alignment explanation
Indices: 59106132--59106260 Score: 154
Period size: 42 Copynumber: 3.1 Consensus size: 42
59106122 AGCTAAACAA
*
59106132 AAACTCATAAGGGTTGAACGAAAGCTCGTAAGAGCTGAACGG
1 AAACTCATAAGGGTTAAACGAAAGCTCGTAAGAGCTGAACGG
* **
59106174 AAACCCATAAGGGTTAAATAAAAGCTC--AATGGAGCTGAACGG
1 AAACTCATAAGGGTTAAACGAAAGCTCGTAA--GAGCTGAACGG
* * * *
59106216 AAACTCATATGAGTTAAACGAAAGCTCGTGAGAGCTAAACGG
1 AAACTCATAAGGGTTAAACGAAAGCTCGTAAGAGCTGAACGG
59106258 AAA
1 AAA
59106261 GTAAACATGA
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
40 2 0.03
42 69 0.96
44 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.17
Consensus pattern (42 bp):
AAACTCATAAGGGTTAAACGAAAGCTCGTAAGAGCTGAACGG
Found at i:59106235 original size:21 final size:22
Alignment explanation
Indices: 59106194--59106261 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 22
59106184 GGGTTAAATA
*
59106194 AAAGCTCAATG-GAGCTGAACGG
1 AAAGCTC-ATGAGAGCTAAACGG
*
59106216 AAA-CTCAT-ATGAGTTAAAC-G
1 AAAGCTCATGA-GAGCTAAACGG
*
59106236 AAAGCTCGTGAGAGCTAAACGG
1 AAAGCTCATGAGAGCTAAACGG
59106258 AAAG
1 AAAG
59106262 TAAACATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
20 6 0.16
21 22 0.59
22 9 0.24
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.16
Consensus pattern (22 bp):
AAAGCTCATGAGAGCTAAACGG
Found at i:59110516 original size:27 final size:28
Alignment explanation
Indices: 59110473--59110545 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
59110463 TCGTGACAAG
* * * *
59110473 TTTA-AAAAATATGAAAATTTATATAAA
1 TTTATAAAAATATAAAAAATCATAAAAA
59110500 TTTATAAAAAT-TAAAAAATCATAAAAA
1 TTTATAAAAATATAAAAAATCATAAAAA
*
59110527 TTTATAAAAGTAATAAAAA
1 TTTATAAAAAT-ATAAAAA
59110546 CATATTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 26 0.68
28 6 0.16
29 6 0.16
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (28 bp):
TTTATAAAAATATAAAAAATCATAAAAA
Found at i:59110543 original size:36 final size:36
Alignment explanation
Indices: 59110474--59110545 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
59110464 CGTGACAAGT
* * *
59110474 TTAAAAAATATGAAAATTTATATAAATTTATAAAAA
1 TTAAAAAATATAAAAATTTATATAAAGTAATAAAAA
59110510 TTAAAAAATCATAAAAATTTATA-AAAGTAATAAAAA
1 TTAAAAAAT-ATAAAAATTTATATAAAGTAATAAAAA
59110546 CATATTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (36 bp):
TTAAAAAATATAAAAATTTATATAAAGTAATAAAAA
Found at i:59110574 original size:31 final size:30
Alignment explanation
Indices: 59110521--59110598 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
59110511 TAAAAAATCA
*
59110521 TAAAA-ATTTATAAAAGTAATAAAAACATATT
1 TAAAATATTTA-AAAATTAATAAAAACATA-T
* *
59110552 TAAAATATTTAAAAATTTATAAAAACGTAT
1 TAAAATATTTAAAAATTAATAAAAACATAT
*
59110582 TAAAATACTATAAAAAT
1 TAAAATA-TTTAAAAAT
59110599 CATAAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 8 0.20
31 28 0.68
32 5 0.12
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (30 bp):
TAAAATATTTAAAAATTAATAAAAACATAT
Found at i:59110586 original size:20 final size:19
Alignment explanation
Indices: 59110563--59110655 Score: 66
Period size: 19 Copynumber: 4.8 Consensus size: 19
59110553 AAAATATTTA
59110563 AAAATTTATAAAAACGTATT
1 AAAATTTATAAAAACGTA-T
*
59110583 AAAATACTATAAAAA--TCAT
1 AAAAT-TTATAAAAACGT-AT
*
59110602 AAAA-TTATAAAAAAAGTATT
1 AAAATTTAT-AAAAACGTA-T
* * *
59110622 AAAATTGATATAAACTTAT
1 AAAATTTATAAAAACGTAT
*
59110641 AAAAATTATAAAAAC
1 AAAATTTATAAAAAC
59110656 AATATATAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
17 3 0.05
18 5 0.09
19 20 0.35
20 18 0.32
21 11 0.19
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAATTTATAAAAACGTAT
Found at i:59110596 original size:40 final size:39
Alignment explanation
Indices: 59110552--59110655 Score: 99
Period size: 39 Copynumber: 2.6 Consensus size: 39
59110542 AAAACATATT
59110552 TAAAATATTTAAAAATTTATAAAAACGTATTAAAATACTA
1 TAAAATATTTAAAAA-TTATAAAAACGTATTAAAATACTA
* *
59110592 TAAAA-A-TCATAAAATTATAAAAAAAGTATTAAAATTGA-TA
1 TAAAATATTTA-AAAATTAT-AAAAACGTATTAAAA-T-ACTA
* *
59110632 TAAACT-TATAAAAATTATAAAAAC
1 TAAAATATTTAAAAATTATAAAAAC
59110656 AATATATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
38 6 0.12
39 24 0.46
40 20 0.38
41 2 0.04
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (39 bp):
TAAAATATTTAAAAATTATAAAAACGTATTAAAATACTA
Found at i:59110616 original size:11 final size:10
Alignment explanation
Indices: 59110475--59110668 Score: 59
Period size: 9 Copynumber: 19.7 Consensus size: 10
59110465 GTGACAAGTT
59110475 TAAAAAA-TA
1 TAAAAAATTA
* *
59110484 TGAAAATTTA
1 TAAAAAATTA
* *
59110494 TATAAATTTA
1 TAAAAAATTA
59110504 T-AAAAA-T-
1 TAAAAAATTA
*
59110511 TAAAAAATCA
1 TAAAAAATTA
*
59110521 TAAAAATTTA
1 TAAAAAATTA
* *
59110531 T-AAAAGTAA
1 TAAAAAATTA
*
59110540 TAAAAACATATT
1 TAAAAA-AT-TA
*
59110552 TAAAATATT-
1 TAAAAAATTA
*
59110561 TAAAAATTTA
1 TAAAAAATTA
**
59110571 TAAAAACGTA
1 TAAAAAATTA
* *
59110581 TTAAAATACTA
1 -TAAAAAATTA
*
59110592 T-AAAAATCA
1 TAAAAAATTA
59110601 T--AAAATTA
1 TAAAAAATTA
*
59110609 TAAAAAAAGTA
1 T-AAAAAATTA
*
59110620 T-TAAAATTGA
1 TAAAAAATT-A
* *
59110630 TATAAACTTA
1 TAAAAAATTA
59110640 T-AAAAATTA
1 TAAAAAATTA
59110649 TAAAAACAATATA
1 T-AAAA-AAT-TA
59110662 TAAAAAA
1 TAAAAAA
59110669 CTTGAATTGG
Statistics
Matches: 135, Mismatches: 32, Indels: 34
0.67 0.16 0.17
Matches are distributed among these distances:
7 1 0.01
8 13 0.10
9 40 0.30
10 38 0.28
11 28 0.21
12 12 0.09
13 3 0.02
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:59110654 original size:9 final size:9
Alignment explanation
Indices: 59110475--59110654 Score: 87
Period size: 10 Copynumber: 18.7 Consensus size: 9
59110465 GTGACAAGTT
*
59110475 TAAAAAATA
1 TAAAAATTA
*
59110484 TGAAAATTTA
1 T-AAAAATTA
*
59110494 TATAAATTTA
1 TA-AAAATTA
59110504 TAAAAATTA
1 TAAAAATTA
*
59110513 -AAAAATCA
1 TAAAAATTA
59110521 TAAAAATTTA
1 TAAAAA-TTA
* *
59110531 TAAAAGTAA
1 TAAAAATTA
*
59110540 TAAAAACATATT
1 T-AAAA-AT-TA
59110552 TAAAATATT-
1 TAAAA-ATTA
59110561 TAAAAATTTA
1 TAAAAA-TTA
*
59110571 TAAAAACGTA
1 TAAAAA-TTA
*
59110581 TTAAAATACTA
1 -TAAAA-ATTA
*
59110592 TAAAAATCA
1 TAAAAATTA
59110601 T-AAAATTA
1 TAAAAATTA
*
59110609 TAAAAAAAGTA
1 T--AAAAATTA
*
59110620 TTAAAATTGA
1 TAAAAATT-A
*
59110630 TATAAACTTA
1 TA-AAAATTA
59110640 TAAAAATTA
1 TAAAAATTA
59110649 TAAAAA
1 TAAAAA
59110655 CAATATATAA
Statistics
Matches: 132, Mismatches: 23, Indels: 32
0.71 0.12 0.17
Matches are distributed among these distances:
8 15 0.11
9 43 0.33
10 46 0.35
11 26 0.20
12 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:59110661 original size:20 final size:20
Alignment explanation
Indices: 59110602--59110666 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
59110592 TAAAAATCAT
*
59110602 AAAATTATAAAAA-AAGTATT
1 AAAATTATAAAAACAA-TATA
* *
59110622 AAAATTGATATAAAC-TTATA
1 AAAATT-ATAAAAACAATATA
59110642 AAAATTATAAAAACAATATA
1 AAAATTATAAAAACAATATA
59110662 TAAAA
1 -AAAA
59110667 AACTTGAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
19 7 0.19
20 19 0.53
21 10 0.28
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAATTATAAAAACAATATA
Found at i:59111221 original size:17 final size:17
Alignment explanation
Indices: 59111169--59111237 Score: 54
Period size: 19 Copynumber: 3.9 Consensus size: 17
59111159 ATTTTAAATA
*
59111169 ATTTTT-TAAAATTTA-
1 ATTTTTATAATATTTAT
*
59111184 ATTTTTATTAGAGTTTTTAT
1 ATTTTTA-TA-A-TATTTAT
59111204 ATTTTTATAATATTTAT
1 ATTTTTATAATATTTAT
59111221 ATGTTTTTATAAT-TTTA
1 A--TTTTTATAATATTTA
59111238 ATAAGTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
15 6 0.14
17 9 0.20
18 6 0.14
19 16 0.36
20 7 0.16
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
ATTTTTATAATATTTAT
Found at i:59111236 original size:9 final size:9
Alignment explanation
Indices: 59111182--59111295 Score: 54
Period size: 9 Copynumber: 11.9 Consensus size: 9
59111172 TTTTAAAATT
59111182 TAATTTTTA
1 TAATTTTTA
59111191 TTAGAGTTTTTA
1 -TA-A-TTTTTA
59111203 T-ATTTTTA
1 TAATTTTTA
*
59111211 TAATATTTA
1 TAATTTTTA
*
59111220 TATGTTTTTA
1 TA-ATTTTTA
*
59111230 TAATTTTAA
1 TAATTTTTA
*
59111239 TAAGTTTATA
1 TAA-TTTTTA
59111249 TCAA-TTTTA
1 T-AATTTTTA
*
59111258 TTA-TTTTA
1 TAATTTTTA
*
59111266 TTATATTTTTG
1 -TA-ATTTTTA
*
59111277 TGATTTTTTTA
1 T-A-ATTTTTA
59111288 TAATTTTT
1 TAATTTTT
59111296 TAAAGATTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 21
0.70 0.12 0.18
Matches are distributed among these distances:
8 13 0.16
9 28 0.35
10 17 0.21
11 16 0.20
12 6 0.08
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (9 bp):
TAATTTTTA
Found at i:59111246 original size:27 final size:27
Alignment explanation
Indices: 59111196--59111249 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
59111186 TTTTATTAGA
*
59111196 GTTTTTATATTTTTATAATATTTATAT
1 GTTTTTATATTTTAATAATATTTATAT
*
59111223 GTTTTTATAATTTTAATAA-GTTTATAT
1 GTTTTTAT-ATTTTAATAATATTTATAT
59111250 CAATTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (27 bp):
GTTTTTATATTTTAATAATATTTATAT
Found at i:59111275 original size:19 final size:20
Alignment explanation
Indices: 59111186--59111295 Score: 65
Period size: 19 Copynumber: 5.8 Consensus size: 20
59111176 AAAATTTAAT
* *
59111186 TTTTATTAGAGTTTTTAT-A
1 TTTTATTATAATTTTTATGA
*
59111205 -TTT-TTATAATATTTAT-A
1 TTTTATTATAATTTTTATGA
* *
59111222 TGTTT-TTATAATTTTAATAA
1 T-TTTATTATAATTTTTATGA
* *
59111242 GTTTA-TATCAA-TTTTATTA
1 TTTTATTAT-AATTTTTATGA
*
59111261 TTTTATTAT-ATTTTTGTGA
1 TTTTATTATAATTTTTATGA
*
59111280 TTTTTTTATAATTTTT
1 TTTTATTATAATTTTT
59111296 TAAAGATTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
17 11 0.15
18 4 0.06
19 44 0.62
20 12 0.17
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTATTATAATTTTTATGA
Found at i:59112530 original size:11 final size:11
Alignment explanation
Indices: 59112514--59112538 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59112504 CAGATCTACC
59112514 ATTAAAAATTG
1 ATTAAAAATTG
59112525 ATTAAAAATTG
1 ATTAAAAATTG
59112536 ATT
1 ATT
59112539 CTATACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
ATTAAAAATTG
Found at i:59118897 original size:18 final size:20
Alignment explanation
Indices: 59118876--59118916 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
59118866 TTTTTTAGAT
*
59118876 TTTTTTAAA-AT-TTTATAA
1 TTTTTTAAATATATATATAA
59118894 TTTTTTAAATATATATATAA
1 TTTTTTAAATATATATATAA
59118914 TTT
1 TTT
59118917 AGAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTTAAATATATATATAA
Found at i:59118944 original size:27 final size:28
Alignment explanation
Indices: 59118884--59118950 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
59118874 ATTTTTTTAA
*
59118884 AATTTTATAATTTTTTAAATATATATAT
1 AATTTTAAAATTTTTTAAATATATATAT
* *
59118912 AA-TTTAGAATTTTTATAAATAT-T-TTT
1 AATTTTAAAATTTTT-TAAATATATATAT
59118938 AATTTTAAAATTT
1 AATTTTAAAATTT
59118951 ATTTTGATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 4 0.12
27 21 0.62
28 9 0.26
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
AATTTTAAAATTTTTTAAATATATATAT
Found at i:59118982 original size:20 final size:20
Alignment explanation
Indices: 59118931--59118984 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
59118921 TTTTTATAAA
**
59118931 TATTTT-TAATTTTAAAATT
1 TATTTTGTAATTTTTGAATT
*
59118950 TATTTTG-ATTTTTTGAATT
1 TATTTTGTAATTTTTGAATT
*
59118969 TTTTTTGTAATTTTTG
1 TATTTTGTAATTTTTG
59118985 TTGAAAGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (20 bp):
TATTTTGTAATTTTTGAATT
Found at i:59120674 original size:15 final size:14
Alignment explanation
Indices: 59120654--59120687 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
59120644 AATCATTAAC
*
59120654 AATTATCTTAATATT
1 AATTATCCTAATA-T
59120669 AATTATCCTAATAT
1 AATTATCCTAATAT
59120683 AATTA
1 AATTA
59120688 AAATAGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTATCCTAATAT
Found at i:59124294 original size:29 final size:29
Alignment explanation
Indices: 59124262--59124319 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
59124252 GCTAGGGAGA
*
59124262 AAGGGAAAGCACGCAATTCAATCTAATCC
1 AAGGGAAAGCACACAATTCAATCTAATCC
* *
59124291 AAGGGAAAGCACACAATTTAATCTGATCC
1 AAGGGAAAGCACACAATTCAATCTAATCC
59124320 TCAGTTACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.19
Consensus pattern (29 bp):
AAGGGAAAGCACACAATTCAATCTAATCC
Found at i:59125918 original size:15 final size:14
Alignment explanation
Indices: 59125897--59125932 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
59125887 ATAATCCTTA
*
59125897 ATAATTATCTTAAT
1 ATAATTATCCTAAT
59125911 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
59125926 ATAATTA
1 ATAATTA
59125933 AAATAGAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:59127390 original size:19 final size:19
Alignment explanation
Indices: 59127362--59127403 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
59127352 TCATCAATTA
59127362 ATTTAATAAT-ATTACTATT
1 ATTTAATAATCA-TACTATT
* *
59127381 ATTTATTAATCATATTATT
1 ATTTAATAATCATACTATT
59127400 ATTT
1 ATTT
59127404 GTATTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTAATAATCATACTATT
Found at i:59140119 original size:19 final size:17
Alignment explanation
Indices: 59140095--59140138 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 17
59140085 ATAGTCTTTG
59140095 TTATTATCATTATTTTTA
1 TTATTAT-ATTATTTTTA
59140113 TTTATTAATATTATTTTTA
1 -TTATT-ATATTATTTTTA
59140132 TTATTAT
1 TTATTAT
59140139 TGTCAATGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.08
18 5 0.21
19 15 0.62
20 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTATATTATTTTTA
Found at i:59143685 original size:41 final size:41
Alignment explanation
Indices: 59143628--59144001 Score: 424
Period size: 41 Copynumber: 8.6 Consensus size: 41
59143618 CATTGAATGT
*
59143628 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
*
59143669 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
59143710 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
* * *
59143751 AAGGGGTTGCTAACTGATCGAAAAGGGATTGCTAACTACAGATTCCCTGAATCACTGATCGAA
1 AAGGGGTTGCTAA--G-T-G--CA--GATT-C---C--CCGA----AT----CACTGATCGAA
* * *
59143814 AAGGGGTTGCTAATTGTAGATTCCCCGAATCATTGATCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
*
59143855 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
* * *
59143896 AAAGGGTTGCTAAGTGCAGATTCCCCTAATCATTGATCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
* *
59143937 AAGGGGTTGCTAAGTGCAGATTCTCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
59143978 AAGGGGTTGCTAAGTGCAGATTCC
1 AAGGGGTTGCTAAGTGCAGATTCC
59144002 TCGAGGGGTT
Statistics
Matches: 290, Mismatches: 21, Indels: 44
0.82 0.06 0.12
Matches are distributed among these distances:
41 239 0.82
43 1 0.00
44 1 0.00
45 2 0.01
47 1 0.00
49 7 0.02
50 1 0.00
51 1 0.00
53 1 0.00
54 1 0.00
55 7 0.02
57 1 0.00
59 2 0.01
60 1 0.00
63 24 0.08
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCGAA
Done.