Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 27 of 204
Found at i:9866587 original size:21 final size:21
Alignment explanation
Indices: 9866563--9866618 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
9866553 AATAGTGGTG
* *
9866563 GCGGTGAGATTAGTTATTGCA
1 GCGGTGAGATTAGATACTGCA
* *
9866584 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGCA
*
9866605 GCGATGAGATTAGA
1 GCGGTGAGATTAGA
9866619 AACAATGGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGCA
Found at i:9871382 original size:9 final size:9
Alignment explanation
Indices: 9871368--9871425 Score: 82
Period size: 9 Copynumber: 6.4 Consensus size: 9
9871358 TTTGGTTAAA
9871368 AATTAACCG
1 AATTAACCG
*
9871377 AATTAATCG
1 AATTAACCG
9871386 AATTAACCG
1 AATTAACCG
9871395 AATTAACCG
1 AATTAACCG
9871404 AATT-ACCGG
1 AATTAACC-G
*
9871413 AATTAACCT
1 AATTAACCG
9871422 AATT
1 AATT
9871426 GAATCATACA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
8 3 0.07
9 38 0.86
10 3 0.07
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:9872962 original size:2 final size:2
Alignment explanation
Indices: 9872955--9872984 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9872945 TATGTAAGAG
*
9872955 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9872985 CACATAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:9873928 original size:17 final size:18
Alignment explanation
Indices: 9873906--9873943 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
9873896 CCGTTTAAAA
*
9873906 AAAGAAAAT-AGAATAAC
1 AAAGAAAATAAAAATAAC
9873923 AAAGAAAATAAAAATAAC
1 AAAGAAAATAAAAATAAC
9873941 AAA
1 AAA
9873944 AAACGAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (18 bp):
AAAGAAAATAAAAATAAC
Found at i:9876428 original size:22 final size:22
Alignment explanation
Indices: 9876400--9876461 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
9876390 TTTATTGTTC
9876400 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
9876422 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
9876444 AGCCATGAGAGCTTAGTA
1 AAACATGAGAGCTTAGTA
9876462 AACCACTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:9878426 original size:423 final size:419
Alignment explanation
Indices: 9877515--9878778 Score: 2140
Period size: 423 Copynumber: 3.0 Consensus size: 419
9877505 GGGAGAATAT
* * *
9877515 TTAGATGGGTTACCTTAGATTCAAAGGATTTATCTCTGTTCTTGGTAAGGAAGTAGGGAGAAGTA
1 TTAGATGGGTTACCTTAGATTCAAAAGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAGTA
* *
9877580 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACCTTTGTGAAGATTTTC
66 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTGTGAAGATTTTC
*
9877645 CCAAATCTGAAAACAAATAA-AGTTGAGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAA
131 CCAAATCTGAAAACAAATAAGA-TTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAA
* *
9877709 AATAATAAATGAAAATATGGGCATTTTTGTTTGCAAAAAAACTTGACTGCCCACTGTGTTTAAGC
195 AATAATAAATGAAAATAT-GGCATTTTTGTCTGCAACAAAACTTGACTGCCCACTGTGTTTAAGC
*
9877774 TGGAGCTTTTA-T-CTCCGATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTCAACTGCACCT
259 TGGAGCTTTTACTCCT-CGATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTTAACTGCACCT
* *
9877837 CACCATTGTTCCTCCAAACACCAACACAGTGTAGGGAAAAAGAATATTCCTTCAAAATTCCATCT
323 CACTATTGTTTCTCCAAACACCAACACAGTGTAGGGAAAAAGAATATTCCTTCAAAATTCCATCT
9877902 CACCATGGTTGATTCTACATCCAAAGGAAGCC
388 CACCATGGTTGATTCTACATCCAAAGGAAGCC
* *
9877934 TTAGATGGGTTACCTTGGATTCAAATGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAGTA
1 TTAGATGGGTTACCTTAGATTCAAAAGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAGTA
*
9877999 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTGTGAAGATTATC
66 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTGTGAAGATTTTC
9878064 CCAAATCTGAAAACAAATAAGATTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAAA
131 CCAAATCTGAAAACAAATAAGATTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAAA
* * *
9878129 ATAATAAATGAAAATATGTGCATTTTTGTCTGTAACAAAACTTGACTGCACACTCTGTTTAAGCT
196 ATAATAAATGAAAATATG-GCATTTTTGTCTGCAACAAAACTTGACTGCCCACTGTGTTTAAGCT
* * *
9878194 GAAGCTTTTACGTACCTCTGGTTGGAAATGAGGCTGGTAGTGAGGTTCAAATTTTTAACTGCACC
260 GGAGCTTTTAC-T-CCTC-GATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTTAACTGCACC
* * *
9878259 TCACTATTGTTTCTCCAAACACCAACACAATGCAGGGAAAAAGAATATTCCTTCAAAATTTCATC
322 TCACTATTGTTTCTCCAAACACCAACACAGTGTAGGGAAAAAGAATATTCCTTCAAAATTCCATC
*
9878324 TCACCATGGTTGATTCTGCATCCAAAGGAAGCC
387 TCACCATGGTTGATTCTACATCCAAAGGAAGCC
*
9878357 TTAGATGGGTTACCTTAGATTCAAAAGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAATA
1 TTAGATGGGTTACCTTAGATTCAAAAGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAGTA
*
9878422 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTATGAAGATTTTC
66 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTGTGAAGATTTTC
*
9878487 CCAAATCTGAAAACAAATAAGGTTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAAA
131 CCAAATCTGAAAACAAATAAGATTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAAA
* *
9878552 ATAATAAATGAAAATATAGGCATTTTTGTCTGCAACAAAACTTGATTGCCCACAGTGTTTAAGCT
196 ATAATAAATGAAAATAT-GGCATTTTTGTCTGCAACAAAACTTGACTGCCCACTGTGTTTAAGCT
* *
9878617 GGAGCTTTTAC-CTTCAATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTTAACTGCACCTCA
260 GGAGCTTTTACTCCTCGATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTTAACTGCACCTCA
*
9878681 CTATTGTTTCTCCAAACACCAACACAGTGTAGGGAAAAAGAGTATTCCTTCAAAATTCCATCTCA
325 CTATTGTTTCTCCAAACACCAACACAGTGTAGGGAAAAAGAATATTCCTTCAAAATTCCATCTCA
9878746 CCATGGTTGATTCTACATCCAAAGGAAGCC
390 CCATGGTTGATTCTACATCCAAAGGAAGCC
9878776 TTA
1 TTA
9878779 ATGAAGCCAT
Statistics
Matches: 793, Mismatches: 44, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
418 1 0.00
419 391 0.49
420 4 0.01
421 1 0.00
422 1 0.00
423 394 0.50
424 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (419 bp):
TTAGATGGGTTACCTTAGATTCAAAAGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAGTA
AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTGTGAAGATTTTC
CCAAATCTGAAAACAAATAAGATTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAAA
ATAATAAATGAAAATATGGCATTTTTGTCTGCAACAAAACTTGACTGCCCACTGTGTTTAAGCTG
GAGCTTTTACTCCTCGATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTTAACTGCACCTCAC
TATTGTTTCTCCAAACACCAACACAGTGTAGGGAAAAAGAATATTCCTTCAAAATTCCATCTCAC
CATGGTTGATTCTACATCCAAAGGAAGCC
Found at i:9884871 original size:7 final size:7
Alignment explanation
Indices: 9884800--9884890 Score: 51
Period size: 7 Copynumber: 12.9 Consensus size: 7
9884790 TATCACTATA
9884800 GTTTAGG
1 GTTTAGG
**
9884807 GTTTTTG
1 GTTTAGG
*
9884814 GTATAGG
1 GTTTAGG
* *
9884821 GTATATG
1 GTTTAGG
9884828 GTTTAGAG
1 GTTTAG-G
*
9884836 G-TTATGT
1 GTTTA-GG
*
9884843 GTTAAGG
1 GTTTAGG
9884850 GTTTATGG
1 GTTTA-GG
*
9884858 CTTTAGG
1 GTTTAGG
9884865 GTTTA-G
1 GTTTAGG
**
9884871 GTTTATA
1 GTTTAGG
9884878 GTTTAGG
1 GTTTAGG
9884885 GTTTAG
1 GTTTAG
9884891 ATTAACTAGT
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
6 6 0.10
7 45 0.73
8 11 0.18
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:9884884 original size:20 final size:21
Alignment explanation
Indices: 9884849--9884890 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
9884839 ATGTGTTAAG
*
9884849 GGTTTATGGCTTTAGGGTTTA
1 GGTTTATAGCTTTAGGGTTTA
9884870 GGTTTATAG-TTTAGGGTTTA
1 GGTTTATAGCTTTAGGGTTTA
9884890 G
1 G
9884891 ATTAACTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.17, C:0.02, G:0.33, T:0.48
Consensus pattern (21 bp):
GGTTTATAGCTTTAGGGTTTA
Found at i:9884928 original size:16 final size:16
Alignment explanation
Indices: 9884907--9884939 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9884897 TAGTGTTTTC
9884907 TAATTTA-TATATTAAT
1 TAATTTATTATA-TAAT
9884923 TAATTTATTATATAAT
1 TAATTTATTATATAAT
9884939 T
1 T
9884940 GTAAAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTATTATATAAT
Found at i:9885192 original size:28 final size:28
Alignment explanation
Indices: 9885161--9885218 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
9885151 AGTGATTTAA
9885161 AATTTTAAAATTAATTTT-AAAAGATTTT
1 AATTTT-AAATTAATTTTAAAAAGATTTT
***
9885189 AATTTTTTTTTAATTTTAAAAAGATTTT
1 AATTTTAAATTAATTTTAAAAAGATTTT
9885217 AA
1 AA
9885219 ACTTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
AATTTTAAATTAATTTTAAAAAGATTTT
Found at i:9885224 original size:27 final size:27
Alignment explanation
Indices: 9885171--9885224 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
9885161 AATTTTAAAA
**
9885171 TTAATTTTAAAAGATTTTAATTTTTTT
1 TTAATTTTAAAAGATTTTAATACTTTT
9885198 TTAATTTTAAAAAGATTTTAA-ACTTTT
1 TTAATTTT-AAAAGATTTTAATACTTTT
9885225 ATTTTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (27 bp):
TTAATTTTAAAAGATTTTAATACTTTT
Found at i:9885224 original size:28 final size:27
Alignment explanation
Indices: 9885171--9885224 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
9885161 AATTTTAAAA
**
9885171 TTAATTTTAAAAGATTTTAATTTTTTT
1 TTAATTTTAAAAGATTTTAAACTTTTT
9885198 TTAATTTTAAAAAGATTTTAAACTTTT
1 TTAATTTT-AAAAGATTTTAAACTTTT
9885225 ATTTTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (27 bp):
TTAATTTTAAAAGATTTTAAACTTTTT
Found at i:9889291 original size:43 final size:43
Alignment explanation
Indices: 9889216--9889373 Score: 208
Period size: 43 Copynumber: 3.7 Consensus size: 43
9889206 AAATATTTTT
* * * * *
9889216 TAAATGTCTTGTTCTTTAGCGGAGTTTGTGGGAAAAGCGCTGC
1 TAAAGGTCTTGTTCTATAGCGGCGTTTATGGGAAAAGCGCCGC
* *
9889259 TAAAGGTCTTGTTTTTTAGCGGCGTTTATGGGAAAAGCGCCGC
1 TAAAGGTCTTGTTCTATAGCGGCGTTTATGGGAAAAGCGCCGC
* * **
9889302 TAAAGGTCTTGTTCTATAACGGCGTTTGTATGAAAAGCGCCGC
1 TAAAGGTCTTGTTCTATAGCGGCGTTTATGGGAAAAGCGCCGC
*
9889345 TAAAGGTCTTGTTCTATAGCGACGTTTAT
1 TAAAGGTCTTGTTCTATAGCGGCGTTTAT
9889374 TTCTAAAAAT
Statistics
Matches: 101, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (43 bp):
TAAAGGTCTTGTTCTATAGCGGCGTTTATGGGAAAAGCGCCGC
Found at i:9889619 original size:43 final size:43
Alignment explanation
Indices: 9889507--9889619 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 43
9889497 AAATATTTTT
* *
9889507 TAAATGTCGTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAAGTCTTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* ** * **
9889550 TAAAGGTCTTGTTCTTTAAAGACGTTTGTGTTAAAAGCGCCGC
1 TAAAAGTCTTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* *
9889593 TAAAATTCTTGTTCTATAGCGGCGTTT
1 TAAAAGTCTTGTTCTTTAGCGGCGTTT
9889620 ATTTTTAAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (43 bp):
TAAAAGTCTTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:9889678 original size:5 final size:5
Alignment explanation
Indices: 9889668--9889693 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
9889658 TGAGCATTCG
9889668 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
9889694 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:9890777 original size:9 final size:9
Alignment explanation
Indices: 9890763--9890799 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
9890753 TATAGTTTGA
9890763 TATTCGAAT
1 TATTCGAAT
9890772 TATTCGAAT
1 TATTCGAAT
*
9890781 TATTCGAGT
1 TATTCGAAT
9890790 TATTCGAAT
1 TATTCGAAT
9890799 T
1 T
9890800 CGAAAGCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:9890870 original size:9 final size:9
Alignment explanation
Indices: 9890853--9890883 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
9890843 TCGAGTTGAT
9890853 TCGAATAAC
1 TCGAATAAC
*
9890862 TCGATTAAC
1 TCGAATAAC
9890871 TCGAATAAC
1 TCGAATAAC
9890880 TCGA
1 TCGA
9890884 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:9891080 original size:2 final size:2
Alignment explanation
Indices: 9891073--9891165 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
9891063 GAAAACAACA
9891073 AG AG AG AG AG 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 AG AG
9891115 AG AG AG AG AG 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 AG AG
9891157 AG AG AG AG A
1 AG AG AG AG A
9891166 CATGGAGATG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9894695 original size:6 final size:6
Alignment explanation
Indices: 9894684--9894711 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
9894674 GTATGGAAAG
9894684 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
9894712 TCGAGGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:9896138 original size:27 final size:28
Alignment explanation
Indices: 9896092--9896214 Score: 151
Period size: 28 Copynumber: 4.5 Consensus size: 28
9896082 CGTGTGAGGT
* *
9896092 AGCCTTTGTGGCGATATATG-AAAAGGA
1 AGCCTTTGTGGCGATCTATGAAAAAAGA
* * *
9896119 AGCCTTTGTAGCAATTTATGAAAAAAGA
1 AGCCTTTGTGGCGATCTATGAAAAAAGA
*
9896147 AGTCTTTGTGGCGATCTATGAAAAAAGA
1 AGCCTTTGTGGCGATCTATGAAAAAAGA
* *
9896175 AGCCTTTGTGGTGATCTAT-AAAAAGGA
1 AGCCTTTGTGGCGATCTATGAAAAAAGA
*
9896202 AGCATTTGTGGCG
1 AGCCTTTGTGGCG
9896215 CACTCTAAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
27 35 0.43
28 47 0.57
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (28 bp):
AGCCTTTGTGGCGATCTATGAAAAAAGA
Found at i:9896198 original size:55 final size:54
Alignment explanation
Indices: 9896095--9896214 Score: 143
Period size: 55 Copynumber: 2.2 Consensus size: 54
9896085 GTGAGGTAGC
* *
9896095 CTTTGTGGCGATATATGAAAAGGAAGCCTTTGTAGCAATTTATGAAAAAAGAAG
1 CTTTGTGGCGATATATGAAAAAGAAGCCTTTGTAGCAATCTATGAAAAAAGAAG
* * ** *
9896149 TCTTTGTGGCGATCTATGAAAAAAGAAGCCTTTGTGGTGATCTAT-AAAAAGGAAG
1 -CTTTGTGGCGATATATG-AAAAAGAAGCCTTTGTAGCAATCTATGAAAAAAGAAG
9896204 CATTTGTGGCG
1 C-TTTGTGGCG
9896215 CACTCTAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
54 1 0.02
55 34 0.61
56 21 0.38
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (54 bp):
CTTTGTGGCGATATATGAAAAAGAAGCCTTTGTAGCAATCTATGAAAAAAGAAG
Found at i:9900378 original size:13 final size:12
Alignment explanation
Indices: 9900355--9900392 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
9900345 TTTTAAAAAT
9900355 AAAAA-ATTTTA
1 AAAAATATTTTA
9900366 AAAAAGTATTTT-
1 AAAAA-TATTTTA
9900378 AAAAATATTTTA
1 AAAAATATTTTA
9900390 AAA
1 AAA
9900393 TTAAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.46
12 8 0.33
13 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
AAAAATATTTTA
Found at i:9900406 original size:15 final size:17
Alignment explanation
Indices: 9900376--9900408 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
9900366 AAAAAGTATT
9900376 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
9900393 TTAAAAA-A-TTTAAAA
1 TTAAAAATATTTTAAAA
9900408 T
1 T
9900409 ATATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:9924620 original size:81 final size:81
Alignment explanation
Indices: 9924515--9924677 Score: 299
Period size: 81 Copynumber: 2.0 Consensus size: 81
9924505 ATTTCTAAGC
* *
9924515 AGATTTGGATCTCACACTTGAAAGGAAACTTTTAAATTAGTTGAAACCATAACATAGGATGCCTT
1 AGATTTGAATCTCACACTTGAAAGGAAACTTTTAAATTAGTTGAAACCATAACATAGGATACCTT
9924580 CAGTTTGCCTTAGTTA
66 CAGTTTGCCTTAGTTA
*
9924596 AGATTTGAATCTCACACTTGAAAGGAAACTTTTAAATTTGTTGAAACCATAACATAGGATACCTT
1 AGATTTGAATCTCACACTTGAAAGGAAACTTTTAAATTAGTTGAAACCATAACATAGGATACCTT
9924661 CAGTTTGCCTTAGTTA
66 CAGTTTGCCTTAGTTA
9924677 A
1 A
9924678 TACTGTGTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (81 bp):
AGATTTGAATCTCACACTTGAAAGGAAACTTTTAAATTAGTTGAAACCATAACATAGGATACCTT
CAGTTTGCCTTAGTTA
Found at i:9950334 original size:6 final size:6
Alignment explanation
Indices: 9950323--9950350 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
9950313 ATAAAAGGAC
9950323 TAAAAT TAAAAT TAAAAT TAAAAT TAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAA
9950351 GGTCATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
TAAAAT
Found at i:9951591 original size:18 final size:18
Alignment explanation
Indices: 9951550--9951593 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
9951540 TATTAGAATT
*
9951550 TTTTTCATAATTATTAATG
1 TTTTT-ATAATTATTAAAG
* *
9951569 GTTTTATAATTTTTAAAG
1 TTTTTATAATTATTAAAG
9951587 TTTTTAT
1 TTTTTAT
9951594 TTTTATTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (18 bp):
TTTTTATAATTATTAAAG
Found at i:9955342 original size:17 final size:17
Alignment explanation
Indices: 9955306--9955339 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9955296 TAAATGAGCT
*
9955306 AATTAGGATTAAATTGG
1 AATTAAGATTAAATTGG
9955323 AATTAAGATATAAATTG
1 AATTAAGAT-TAAATTG
9955340 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (17 bp):
AATTAAGATTAAATTGG
Found at i:9955395 original size:3 final size:3
Alignment explanation
Indices: 9955387--9955449 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
9955377 AATAGTGTAA
9955387 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9955435 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
9955450 TTCGTAGCTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:9956126 original size:23 final size:22
Alignment explanation
Indices: 9956099--9956178 Score: 60
Period size: 21 Copynumber: 3.7 Consensus size: 22
9956089 TTTACCAATC
9956099 AGGCACTTTATGTGTCGTATTTT
1 AGGCAC-TTATGTGTCGTATTTT
** * *
9956122 AGGCACCTCGTATGTCGTA--TC
1 AGGCA-CTTATGTGTCGTATTTT
*
9956143 AGGCACAT-TGTGT-GTCATTTT
1 AGGCACTTATGTGTCGT-ATTTT
9956164 AGGCACTTATGTGTC
1 AGGCACTTATGTGTC
9956179 ATATACTGAT
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
18 2 0.05
19 5 0.12
20 1 0.02
21 14 0.33
22 5 0.12
23 14 0.33
24 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (22 bp):
AGGCACTTATGTGTCGTATTTT
Found at i:9956158 original size:21 final size:21
Alignment explanation
Indices: 9956096--9956158 Score: 54
Period size: 23 Copynumber: 2.9 Consensus size: 21
9956086 GGCTTTACCA
* *
9956096 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACATTGTGTGTCGT
* * * *
9956117 ATTTTAGGCACCTCGTATGTCGT
1 A--TCAGGCACATTGTGTGTCGT
9956140 ATCAGGCACATTGTGTGTC
1 ATCAGGCACATTGTGTGTC
9956159 ATTTTAGGCA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
21 15 0.48
23 16 0.52
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (21 bp):
ATCAGGCACATTGTGTGTCGT
Found at i:9956595 original size:25 final size:25
Alignment explanation
Indices: 9956567--9956617 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
9956557 AATGAAATTG
*
9956567 AGATAGTGAAATATTGCTTATTGAT
1 AGATAGTGAAATATTGCCTATTGAT
9956592 AGATAGTGAAATATTGCCTATTGAT
1 AGATAGTGAAATATTGCCTATTGAT
9956617 A
1 A
9956618 TTAATGATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (25 bp):
AGATAGTGAAATATTGCCTATTGAT
Found at i:9970923 original size:9 final size:9
Alignment explanation
Indices: 9970909--9970939 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
9970899 GTTCAACGAA
9970909 TCGAGTTAT
1 TCGAGTTAT
*
9970918 TCGAGTTAA
1 TCGAGTTAT
9970927 TCGAGTTAT
1 TCGAGTTAT
9970936 TCGA
1 TCGA
9970940 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:9973728 original size:24 final size:24
Alignment explanation
Indices: 9973683--9973744 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
9973673 TCCGGGTTGT
*
9973683 ATAATGGGAAGCTCATAAGAGCC-
1 ATAATGGGAAGTTCATAAGAGCCA
**
9973706 ATAATTGGGAAGTTCATGCGAGCCA
1 ATAA-TGGGAAGTTCATAAGAGCCA
*
9973731 ATAATGGGTAGTTC
1 ATAATGGGAAGTTC
9973745 CGAAGAGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 4 0.12
24 25 0.76
25 4 0.12
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (24 bp):
ATAATGGGAAGTTCATAAGAGCCA
Found at i:9973892 original size:26 final size:25
Alignment explanation
Indices: 9973820--9973893 Score: 94
Period size: 26 Copynumber: 2.9 Consensus size: 25
9973810 GAAGCTTCGG
*
9973820 AGAGCCATTAATGGGAAGCTCACAA
1 AGAGCCATTAACGGGAAGCTCACAA
* *
9973845 AGAGCCTTTAATCAGGAAGCTCACAA
1 AGAGCCATTAA-CGGGAAGCTCACAA
*
9973871 AGAGCCATATAACGGGACGCTCA
1 AGAGCCAT-TAACGGGAAGCTCA
9973894 TAGGAGTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.24
26 28 0.68
27 3 0.07
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (25 bp):
AGAGCCATTAACGGGAAGCTCACAA
Found at i:9979540 original size:14 final size:14
Alignment explanation
Indices: 9979521--9979551 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9979511 TGCTACCATT
9979521 TTACTATTATATTG
1 TTACTATTATATTG
*
9979535 TTACTATTTTATTG
1 TTACTATTATATTG
9979549 TTA
1 TTA
9979552 TTGCTTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (14 bp):
TTACTATTATATTG
Found at i:9979616 original size:30 final size:30
Alignment explanation
Indices: 9979582--9979646 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
9979572 ACTTATTTTA
*
9979582 TTGTTAATTTTGTTATTATTTTAAAGTCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
9979612 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
9979642 TTGTT
1 TTGTT
9979647 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.03, G:0.14, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:9985325 original size:28 final size:26
Alignment explanation
Indices: 9985288--9985340 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
9985278 CTTTTGAATA
9985288 AATAAATTCTCTTTGAGTTTTTCTTTTC
1 AATAAATTCTC-TTGAG-TTTTCTTTTC
*
9985316 AATAATTTCTCTTGAGTTTTCTTTT
1 AATAAATTCTCTTGAGTTTTCTTTT
9985341 AAAAGAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 9 0.38
27 5 0.21
28 10 0.42
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (26 bp):
AATAAATTCTCTTGAGTTTTCTTTTC
Found at i:9985828 original size:20 final size:18
Alignment explanation
Indices: 9985795--9985831 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
9985785 ATCCTTAAAA
9985795 TAAAAGAATAATTTTTAG
1 TAAAAGAATAATTTTTAG
9985813 TAAATAGAAGTAATTTTTA
1 TAAA-AGAA-TAATTTTTA
9985832 AATTAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (18 bp):
TAAAAGAATAATTTTTAG
Found at i:9989518 original size:25 final size:25
Alignment explanation
Indices: 9989490--9989551 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
9989480 GCTGAAGCTC
* *
9989490 TAGTTGCATTTCAAGAGGTGTTTTA
1 TAGTTGCAATTCAAGAGGTATTTTA
9989515 TAGTTGCAATTCAAGAGGTATTTTA
1 TAGTTGCAATTCAAGAGGTATTTTA
9989540 TAGTTGCAATTC
1 TAGTTGCAATTC
9989552 CAGTAAATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (25 bp):
TAGTTGCAATTCAAGAGGTATTTTA
Found at i:9989718 original size:18 final size:19
Alignment explanation
Indices: 9989695--9989735 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
9989685 TAATGGGCTT
9989695 TATAGGATAA-TTTATTGG
1 TATAGGATAATTTTATTGG
9989713 TATAGGATAATTTTTATTGG
1 TATAGGATAA-TTTTATTGG
9989733 TAT
1 TAT
9989736 TTTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.49
Consensus pattern (19 bp):
TATAGGATAATTTTATTGG
Found at i:9991748 original size:18 final size:18
Alignment explanation
Indices: 9991725--9991799 Score: 69
Period size: 18 Copynumber: 3.8 Consensus size: 18
9991715 AATAAGAATT
9991725 TTATTAAATTATATATTA
1 TTATTAAATTATATATTA
*
9991743 TTATTAAATTATATTTTA
1 TTATTAAATTATATATTA
*
9991761 TAGTATTATATATTATGATTTTA
1 T--TATTA-A-ATTAT-ATATTA
*
9991784 TTAGTAAATTCATATA
1 TTATTAAATT-ATATA
9991800 AGAATATTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
18 18 0.38
19 5 0.10
20 8 0.17
21 5 0.10
22 5 0.10
23 7 0.15
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (18 bp):
TTATTAAATTATATATTA
Found at i:9991761 original size:7 final size:7
Alignment explanation
Indices: 9991732--9991776 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
9991722 ATTTTATTAA
9991732 ATTATAT
1 ATTATAT
9991739 ATTAT-T
1 ATTATAT
9991745 ATTA-A-
1 ATTATAT
9991750 ATTATAT
1 ATTATAT
*
9991757 TTTATAGT
1 ATTATA-T
9991765 ATTATAT
1 ATTATAT
9991772 ATTAT
1 ATTAT
9991777 GATTTTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
5 4 0.12
6 6 0.19
7 16 0.50
8 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (7 bp):
ATTATAT
Found at i:9991781 original size:23 final size:23
Alignment explanation
Indices: 9991727--9991789 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
9991717 TAAGAATTTT
* * *
9991727 ATTAAATTATATATTATTATTAA
1 ATTATATTTTATAGTATTATTAA
*
9991750 ATTATATTTTATAGTATTA-TAT
1 ATTATATTTTATAGTATTATTAA
9991772 ATTATGATTTTATTAGTA
1 ATTAT-ATTTTA-TAGTA
9991790 AATTCATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.21
23 22 0.65
24 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (23 bp):
ATTATATTTTATAGTATTATTAA
Found at i:9991830 original size:84 final size:82
Alignment explanation
Indices: 9991655--9991813 Score: 234
Period size: 84 Copynumber: 1.9 Consensus size: 82
9991645 TATTTAAAAA
9991655 TAATTATTTAAATTATATTTTATAGTATTATATATTATGATTTTAATAAATTCATATAAGAATAA
1 TAATTA-TTAAATTATATTTTATAGTATTATATATTATGATTTTAATAAATTCATATAAGAAT--
9991720 GAATTTTATTAAATTATATAT
63 -AATTTTATTAAATTATATAT
9991741 T-ATTATTAAATTATATTTTATAGTATTATATATTATGATTTTATTAGTAAATTCATATAAGAAT
1 TAATTATTAAATTATATTTTATAGTATTATATATTATGATTTTA--A-TAAATTCATATAAGAAT
9991805 -A-TTTATTAA
63 AATTTTATTAA
9991814 CAATTTTATT
Statistics
Matches: 70, Mismatches: 0, Indels: 10
0.88 0.00 0.12
Matches are distributed among these distances:
82 8 0.11
83 1 0.01
84 38 0.54
85 4 0.06
86 2 0.03
87 17 0.24
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (82 bp):
TAATTATTAAATTATATTTTATAGTATTATATATTATGATTTTAATAAATTCATATAAGAATAAT
TTTATTAAATTATATAT
Found at i:10014547 original size:25 final size:26
Alignment explanation
Indices: 10014513--10014561 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
10014503 ACATATTTTC
10014513 TCAAAATTTTACT-AGGGTAAAATCA
1 TCAAAATTTTACTGAGGGTAAAATCA
*
10014538 TCAAAATTTTACTGGGGGTAAAAT
1 TCAAAATTTTACTGAGGGTAAAAT
10014562 AAGGATGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTACTGAGGGTAAAATCA
Found at i:10018810 original size:32 final size:31
Alignment explanation
Indices: 10018767--10018855 Score: 142
Period size: 32 Copynumber: 2.8 Consensus size: 31
10018757 AATATATTTA
*
10018767 TTTTTTAAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTAAAATATTTTTAAAATAC
10018798 TTTTTTTTAATTTTAAAATATTTTTAAAATAC
1 -TTTTTTTAATTTTAAAATATTTTTAAAATAC
10018830 TTTTTTTAATTTTTAAAATAATTTTT
1 TTTTTTTAA-TTTTAAAAT-ATTTTT
10018856 TGGTATTTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 9 0.17
32 39 0.72
33 6 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:10018841 original size:21 final size:21
Alignment explanation
Indices: 10018817--10018856 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
10018807 ATTTTAAAAT
*
10018817 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAATTTTTTTA
10018838 ATTTTTAAAATAATTTTTT
1 ATTTTTAAAATAATTTTTT
10018857 GGTATTTATT
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:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTAAAATAATTTTTTTA
Found at i:10030792 original size:15 final size:16
Alignment explanation
Indices: 10030751--10030801 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 16
10030741 CGTAAGTTCA
10030751 AATTGTTTCTTTAAGTT
1 AATTGTTT-TTTAAGTT
10030768 AATT-TATTTTTAA-TT
1 AATTGT-TTTTTAAGTT
10030783 AATTGTTTTTTGAAGTT
1 AATTGTTTTTT-AAGTT
10030800 AA
1 AA
10030802 AAATAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 11 0.37
16 9 0.30
17 10 0.33
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (16 bp):
AATTGTTTTTTAAGTT
Found at i:10041535 original size:42 final size:42
Alignment explanation
Indices: 10041476--10041600 Score: 241
Period size: 42 Copynumber: 3.0 Consensus size: 42
10041466 ATCAAATCCT
10041476 CAACAGCTGAAAGTGGGTTCGAAAGCTCCGTACCGTCTACTG
1 CAACAGCTGAAAGTGGGTTCGAAAGCTCCGTACCGTCTACTG
10041518 CAACAGCTGAAAGTGGGTTCGAAAGCTCCGTACCGTCTACTG
1 CAACAGCTGAAAGTGGGTTCGAAAGCTCCGTACCGTCTACTG
*
10041560 CAACAGCTGAAAATGGGTTCGAAAGCTCCGTACCGTCTACT
1 CAACAGCTGAAAGTGGGTTCGAAAGCTCCGTACCGTCTACT
10041601 ACGTTACAGT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (42 bp):
CAACAGCTGAAAGTGGGTTCGAAAGCTCCGTACCGTCTACTG
Found at i:10053612 original size:17 final size:18
Alignment explanation
Indices: 10053580--10053615 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
10053570 GAAACCCTAA
10053580 CTTTTTCTCCTTTCTTTCT
1 CTTTTTCT-CTTTCTTTCT
10053599 CTTTTTCT-TTTCTTTCT
1 CTTTTTCTCTTTCTTTCT
10053616 TTCCTTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTTTTCTCTTTCTTTCT
Found at i:10053716 original size:20 final size:20
Alignment explanation
Indices: 10053669--10053734 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
10053659 TTCTATTTCT
*
10053669 TTATTTGTTTTGTTTTAATTA
1 TTATTTATTTTGTTTT-ATTA
10053690 CTTATTTATTTTGTTTTATTA
1 -TTATTTATTTTGTTTTATTA
**
10053711 TTATTTCA-TTTACTTTATTA
1 TTATTT-ATTTTGTTTTATTA
10053731 TTAT
1 TTAT
10053735 AATAATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
20 20 0.50
21 5 0.12
22 15 0.38
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (20 bp):
TTATTTATTTTGTTTTATTA
Found at i:10053810 original size:19 final size:20
Alignment explanation
Indices: 10053768--10053817 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
10053758 ATATTAAGTA
*
10053768 ATACATAT-TTTATTATTAT
1 ATACATATGTATATTATTAT
10053787 ATACATATGTATATTATT-T
1 ATACATATGTATATTATTAT
* *
10053806 TTACACATGTAT
1 ATACATATGTAT
10053818 TCACCAACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (20 bp):
ATACATATGTATATTATTAT
Found at i:10054530 original size:18 final size:17
Alignment explanation
Indices: 10054507--10054542 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
10054497 AAAATAAACA
10054507 TAATTAATTAATTTAAAT
1 TAATTAATTAA-TTAAAT
10054525 TAATTAATTAATTAAAT
1 TAATTAATTAATTAAAT
10054542 T
1 T
10054543 CTTAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTAATTAATTAAAT
Found at i:10056067 original size:3 final size:3
Alignment explanation
Indices: 10056046--10056126 Score: 74
Period size: 3 Copynumber: 26.7 Consensus size: 3
10056036 CAGAACAATG
* * *
10056046 ATA ATA ATGA A-A ATG ATA ATA ATA ATA GTA ATA ATA ATA TTA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
10056091 ATA ACA AAA ATA ATA AAA ATA ATA CTA ATAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT
10056127 TTTTAGAGTT
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
2 2 0.03
3 55 0.89
4 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:10056365 original size:17 final size:18
Alignment explanation
Indices: 10056338--10056371 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10056328 GAAAATAAAT
10056338 AAATAAATAAATCAAACA
1 AAATAAATAAATCAAACA
*
10056356 AAAT-AATAAATGAAAC
1 AAATAAATAAATCAAAC
10056372 TGTTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATAAATAAATCAAACA
Found at i:10057628 original size:23 final size:23
Alignment explanation
Indices: 10057601--10057651 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
10057591 GGGCTAGGGT
*
10057601 TTTTTATTTTAGGTTTGT-AATAA
1 TTTTTATTTTAGGCTTGTAAAT-A
* *
10057624 TTTTTCTTTTGGGCTTGTAAATA
1 TTTTTATTTTAGGCTTGTAAATA
10057647 TTTTT
1 TTTTT
10057652 GGACTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.20, C:0.04, G:0.14, T:0.63
Consensus pattern (23 bp):
TTTTTATTTTAGGCTTGTAAATA
Found at i:10069722 original size:14 final size:15
Alignment explanation
Indices: 10069698--10069728 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
10069688 GCCCACCCAT
10069698 ATTATTATTTTTTAC
1 ATTATTATTTTTTAC
10069713 ATTA-TATTTTTTAC
1 ATTATTATTTTTTAC
10069727 AT
1 AT
10069729 AATTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTATTATTTTTTAC
Found at i:10069735 original size:13 final size:14
Alignment explanation
Indices: 10069703--10069735 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10069693 CCCATATTAT
*
10069703 TATTTTTTACATTA
1 TATTTTTTACATAA
10069717 TATTTTTTACATAA
1 TATTTTTTACATAA
10069731 T-TTTT
1 TATTTT
10069736 AAATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTTACATAA
Found at i:10075894 original size:15 final size:16
Alignment explanation
Indices: 10075876--10075905 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10075866 TATAAATTGT
10075876 TAAAAAATA-AAATTA
1 TAAAAAATACAAATTA
10075891 TAAAAAATACAAATT
1 TAAAAAATACAAATT
10075906 TATTCAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAAATACAAATTA
Found at i:10075908 original size:17 final size:16
Alignment explanation
Indices: 10075863--10075908 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
10075853 TGATAAAATT
10075863 AAATATAAATTGT-TAAA
1 AAATA-AAATT-TATAAA
10075880 AAATAAAA-TTATAAA
1 AAATAAAATTTATAAA
10075895 AAATACAAATTTAT
1 AAATA-AAATTTAT
10075909 TCAAATCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.04
15 10 0.38
16 6 0.23
17 9 0.35
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATAAAATTTATAAA
Found at i:10080476 original size:43 final size:43
Alignment explanation
Indices: 10080428--10080510 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
10080418 TTTCTTCTGT
10080428 TTTGTAGTCTATTGGAAGCTCGATCAGTTGGAACCCTATCAGA
1 TTTGTAGTCTATTGGAAGCTCGATCAGTTGGAACCCTATCAGA
10080471 TTTGTAGTCTATTGGAAGCTCGATCAGTTGGAACCCTATC
1 TTTGTAGTCTATTGGAAGCTCGATCAGTTGGAACCCTATC
10080511 GGAGTCTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (43 bp):
TTTGTAGTCTATTGGAAGCTCGATCAGTTGGAACCCTATCAGA
Found at i:10081826 original size:18 final size:19
Alignment explanation
Indices: 10081781--10081826 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
10081771 CATTATATTA
*
10081781 ATAATA-AATAATTGAATG
1 ATAATATAATAATTAAATG
10081799 ATACATTATAA-AATTAAATG
1 ATA-A-TATAATAATTAAATG
10081819 ATAATATA
1 ATAATATA
10081827 TGATAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 7 0.29
19 2 0.08
20 13 0.54
21 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (19 bp):
ATAATATAATAATTAAATG
Found at i:10082416 original size:2 final size:2
Alignment explanation
Indices: 10082409--10082438 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10082399 TTTTTATTTA
10082409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10082439 GCTAAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10093880 original size:6 final size:6
Alignment explanation
Indices: 10093869--10093898 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
10093859 AAGGAGCTAG
10093869 AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
10093899 TGCATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:10094969 original size:17 final size:18
Alignment explanation
Indices: 10094947--10094987 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
10094937 TTTATAAGAC
*
10094947 AAATT-AATTGTTTTATA
1 AAATTAAATTCTTTTATA
10094964 AAATTAAAATTCTTTTATA
1 AAATT-AAATTCTTTTATA
10094983 AAATT
1 AAATT
10094988 TAATACTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
19 16 0.76
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
AAATTAAATTCTTTTATA
Found at i:10098191 original size:24 final size:24
Alignment explanation
Indices: 10098142--10098191 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
10098132 AGAAGAAGAT
* * * *
10098142 GATGATGATGATGACAACGACGAC
1 GATGATGACGACGACAACAACAAC
10098166 GATGATGACGACGACAACAACAAC
1 GATGATGACGACGACAACAACAAC
10098190 GA
1 GA
10098192 CGACAACGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.20, G:0.26, T:0.12
Consensus pattern (24 bp):
GATGATGACGACGACAACAACAAC
Found at i:10098205 original size:3 final size:3
Alignment explanation
Indices: 10098199--10098233 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
10098189 CGACGACAAC
10098199 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
10098234 CGACGACGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:10098319 original size:3 final size:3
Alignment explanation
Indices: 10098313--10098348 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
10098303 AGAAGAAGAA
10098313 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
10098349 AACAGCAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:10098580 original size:3 final size:3
Alignment explanation
Indices: 10098574--10098644 Score: 79
Period size: 3 Copynumber: 23.7 Consensus size: 3
10098564 AGAAGAAGAA
* * * * * *
10098574 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAC GAC GAC AAC GAT GAC
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
10098622 GAC GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GA
10098645 CAAATATTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.35, C:0.08, G:0.32, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:10098921 original size:3 final size:3
Alignment explanation
Indices: 10098915--10098957 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
10098905 CATTTTCAAC
10098915 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
10098958 AGCAAAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:10099611 original size:65 final size:65
Alignment explanation
Indices: 10099464--10099597 Score: 268
Period size: 65 Copynumber: 2.1 Consensus size: 65
10099454 AAATAGTCAT
10099464 TTATGTATGGTTTAAATTACATTTTAGTCACTAAACTTTAATTTGTTATGAAATGGTCACTAATA
1 TTATGTATGGTTTAAATTACATTTTAGTCACTAAACTTTAATTTGTTATGAAATGGTCACTAATA
10099529 TTATGTATGGTTTAAATTACATTTTAGTCACTAAACTTTAATTTGTTATGAAATGGTCACTAATA
1 TTATGTATGGTTTAAATTACATTTTAGTCACTAAACTTTAATTTGTTATGAAATGGTCACTAATA
10099594 TTAT
1 TTAT
10099598 CGATTTGTTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.46
Consensus pattern (65 bp):
TTATGTATGGTTTAAATTACATTTTAGTCACTAAACTTTAATTTGTTATGAAATGGTCACTAATA
Found at i:10100836 original size:16 final size:16
Alignment explanation
Indices: 10100812--10100846 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10100802 TAATACCCGA
*
10100812 ATAAATAAAAAATATC
1 ATAAATAAAAAATAAC
*
10100828 ATAATTAAAAAATAAC
1 ATAAATAAAAAATAAC
10100844 ATA
1 ATA
10100847 TATTTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAATAAAAAATAAC
Found at i:10101357 original size:28 final size:28
Alignment explanation
Indices: 10101315--10101369 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
10101305 CCGATTTGCT
*
10101315 CCCTCCGTTTCTTTTCTTTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTTTTCTG
*
10101343 CCCTCTGTTTATTTTCTTTTCTTTTCT
1 CCCTCCGTTTATTTTCTTTTCTTTTCT
10101370 ACCGATTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.02, C:0.29, G:0.05, T:0.64
Consensus pattern (28 bp):
CCCTCCGTTTATTTTCTTTTCTTTTCTG
Found at i:10101390 original size:38 final size:37
Alignment explanation
Indices: 10101343--10101414 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 37
10101333 TTCTTTTCTG
* *
10101343 CCCTCTGTTTATTTTCTTTTCTTTTCTACCGATTTGCT
1 CCCTCTGTTTATTCTCATTT-TTTTCTACCGATTTGCT
* * *
10101381 CCCTTTGTTTCTTCTCATTTTTTTCTGCCGATTT
1 CCCTCTGTTTATTCTCATTTTTTTCTACCGATTT
10101415 CCGAGTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 13 0.45
38 16 0.55
ACGTcount: A:0.07, C:0.26, G:0.08, T:0.58
Consensus pattern (37 bp):
CCCTCTGTTTATTCTCATTTTTTTCTACCGATTTGCT
Found at i:10104616 original size:16 final size:16
Alignment explanation
Indices: 10104573--10104607 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
10104563 TGGTTCCTTA
*
10104573 TTAATTATAA-TATAT
1 TTAATAATAATTATAT
10104588 TTAATAATAATTATAT
1 TTAATAATAATTATAT
10104604 TTAA
1 TTAA
10104608 ATATGATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATAATAATTATAT
Found at i:10104738 original size:18 final size:17
Alignment explanation
Indices: 10104710--10104744 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10104700 ATTATTAAGA
*
10104710 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
10104727 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
10104745 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:10104988 original size:45 final size:43
Alignment explanation
Indices: 10104890--10104999 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
10104880 TTTACCATTA
10104890 TGCTATTACACCTCTATTCCA-T---TCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATCAACCAAACACAAGAT
* * ***
10104929 TACTATTACGCCTCTATTCCATTACATCCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACAT-CAACCAAACACAAGA-T
10104974 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
10105000 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 19 0.33
40 1 0.02
43 1 0.02
44 12 0.21
45 25 0.43
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATTACATCAACCAAACACAAGAT
Found at i:10105027 original size:16 final size:16
Alignment explanation
Indices: 10104980--10105029 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
10104970 GATTTGCTAT
* *
10104980 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
10104996 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
10105012 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
10105028 TA
1 TA
10105030 TAGCGAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:10108053 original size:18 final size:19
Alignment explanation
Indices: 10108019--10108055 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
10108009 TGTGCAAAAC
10108019 AAAATTCGGGTAAAACCGAA
1 AAAATTCGGGT-AAACCGAA
10108039 AAAATTCGGGT-AACCGA
1 AAAATTCGGGTAAACCGA
10108056 CCGAATTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (19 bp):
AAAATTCGGGTAAACCGAA
Found at i:10108278 original size:13 final size:13
Alignment explanation
Indices: 10108262--10108286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10108252 CAAGTATTCA
10108262 ACCCAACCCAATT
1 ACCCAACCCAATT
10108275 ACCCAACCCAAT
1 ACCCAACCCAAT
10108287 CATAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:10108403 original size:9 final size:9
Alignment explanation
Indices: 10108389--10108490 Score: 98
Period size: 9 Copynumber: 11.4 Consensus size: 9
10108379 GTAGTGATTC
10108389 AATTCGGTT
1 AATTCGGTT
*
10108398 AATTCGGGT
1 AATTCGGTT
* *
10108407 AATCCGATT
1 AATTCGGTT
10108416 AATTCGGTT
1 AATTCGGTT
*
10108425 AATTCGGGT
1 AATTCGGTT
*
10108434 AATT-GGGT
1 AATTCGGTT
* *
10108442 AATCCGATT
1 AATTCGGTT
*
10108451 AATTCAGTT
1 AATTCGGTT
*
10108460 AATTCGGGT
1 AATTCGGTT
*
10108469 AATTCGGGT
1 AATTCGGTT
*
10108478 AATTCAGTT
1 AATTCGGTT
10108487 AATT
1 AATT
10108491 TTTAACCAAA
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
8 7 0.09
9 68 0.91
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (9 bp):
AATTCGGTT
Found at i:10108449 original size:35 final size:36
Alignment explanation
Indices: 10108389--10108480 Score: 159
Period size: 35 Copynumber: 2.6 Consensus size: 36
10108379 GTAGTGATTC
* *
10108389 AATTCGGTTAATTCGGGTAATCCGATTAATTCGGTT
1 AATTCGGGTAATTCGGGTAATCCGATTAATTCAGTT
10108425 AATTCGGGTAATT-GGGTAATCCGATTAATTCAGTT
1 AATTCGGGTAATTCGGGTAATCCGATTAATTCAGTT
10108460 AATTCGGGTAATTCGGGTAAT
1 AATTCGGGTAATTCGGGTAAT
10108481 TCAGTTAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
35 34 0.64
36 19 0.36
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (36 bp):
AATTCGGGTAATTCGGGTAATCCGATTAATTCAGTT
Found at i:10111226 original size:46 final size:46
Alignment explanation
Indices: 10111173--10111268 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
10111163 TGAAACAAAC
10111173 AAGAATGCACATTGTATGCAAAATAAAGCACAAGCTTTGAAGAGTT
1 AAGAATGCACATTGTATGCAAAATAAAGCACAAGCTTTGAAGAGTT
10111219 AAGAATGCACATTGTATGCAAAATAAAGCACAAGCTTTGAAGAGTT
1 AAGAATGCACATTGTATGCAAAATAAAGCACAAGCTTTGAAGAGTT
10111265 AAGA
1 AAGA
10111269 GAAAACAAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (46 bp):
AAGAATGCACATTGTATGCAAAATAAAGCACAAGCTTTGAAGAGTT
Found at i:10115537 original size:21 final size:21
Alignment explanation
Indices: 10115491--10115537 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
10115481 AATTTAATTT
10115491 TTTTCTTTTATGTTCTTTTGA
1 TTTTCTTTTATGTTCTTTTGA
* * *
10115512 CTTTCTTTT-TTTTCTTCTTTA
1 TTTTCTTTTATGTTCTT-TTGA
10115533 TTTTC
1 TTTTC
10115538 CATTCTCTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTCTTTTATGTTCTTTTGA
Found at i:10117348 original size:17 final size:18
Alignment explanation
Indices: 10117315--10117349 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10117305 TTTAAATGAA
10117315 AACATATTTAACTTTTTT
1 AACATATTTAACTTTTTT
*
10117333 AACATA-TTAGCTTTTTT
1 AACATATTTAACTTTTTT
10117350 GGTCAAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.54
Consensus pattern (18 bp):
AACATATTTAACTTTTTT
Found at i:10117483 original size:16 final size:16
Alignment explanation
Indices: 10117460--10117495 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
10117450 CAAAAATATA
*
10117460 TTTT-TTTTTAAATTT
1 TTTTATTTTTAAATCT
10117475 TTTTATTTTTAAATCT
1 TTTTATTTTTAAATCT
10117491 TTTTA
1 TTTTA
10117496 ATTAATAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTATTTTTAAATCT
Found at i:10118050 original size:34 final size:36
Alignment explanation
Indices: 10117980--10118051 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
10117970 TTGATTTTAT
*
10117980 AAATAAAATAATTATTAATTAAAAATAAAAATTTGA
1 AAATAAAATAATTATTAATTAAAAATAAAAACTTGA
* *
10118016 AAATAATATATTTATTAATT-AAAA-AAAAACTTGA
1 AAATAAAATAATTATTAATTAAAAATAAAAACTTGA
10118050 AA
1 AA
10118052 CAACTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 11 0.33
35 4 0.12
36 18 0.55
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (36 bp):
AAATAAAATAATTATTAATTAAAAATAAAAACTTGA
Found at i:10123436 original size:28 final size:26
Alignment explanation
Indices: 10123405--10123491 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 26
10123395 AATATTAAAT
10123405 ATTATTTTAATATAATATAATATAATTA
1 ATTATTTTAATAT-AT-TAATATAATTA
* *
10123433 ATTA-TTTAA-ATATTGATCTAATTA
1 ATTATTTTAATATATTAATATAATTA
* *
10123457 ATTA-TTTAA-ATATTGATCTAATTA
1 ATTATTTTAATATATTAATATAATTA
*
10123481 ATTGTTTTAAT
1 ATTATTTTAAT
10123492 GAAATTCTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
24 36 0.67
25 7 0.13
26 2 0.04
27 5 0.09
28 4 0.07
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
ATTATTTTAATATATTAATATAATTA
Found at i:10123454 original size:24 final size:24
Alignment explanation
Indices: 10123427--10123483 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
10123417 TAATATAATA
10123427 TAATTAATTATTTAAATATTGATC
1 TAATTAATTATTTAAATATTGATC
10123451 TAATTAATTATTTAAATATTGATC
1 TAATTAATTATTTAAATATTGATC
10123475 TAATTAATT
1 TAATTAATT
10123484 GTTTTAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (24 bp):
TAATTAATTATTTAAATATTGATC
Found at i:10125064 original size:16 final size:16
Alignment explanation
Indices: 10125032--10125066 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
10125022 TAAGTTATAG
10125032 TTTTAATTTCAATATT
1 TTTTAATTTCAATATT
10125048 TTTTGAATTTCAA-ATT
1 TTTT-AATTTCAATATT
10125064 TTT
1 TTT
10125067 AATCCTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTTAATTTCAATATT
Found at i:10133301 original size:30 final size:32
Alignment explanation
Indices: 10133248--10133311 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 32
10133238 ACTAAGTTTC
*
10133248 TAATCAATCTTAATTTCTTCAAGTGTTTGTAT
1 TAATCAATCTTAATTTCTTCAAGTATTTGTAT
10133280 TAATCAATCTTAA-TT-TTCAAGTATTTGTAT
1 TAATCAATCTTAATTTCTTCAAGTATTTGTAT
10133310 TA
1 TA
10133312 TTTATCCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 16 0.52
31 2 0.06
32 13 0.42
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (32 bp):
TAATCAATCTTAATTTCTTCAAGTATTTGTAT
Found at i:10147635 original size:17 final size:19
Alignment explanation
Indices: 10147599--10147635 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
10147589 GAATGGCTAT
*
10147599 TAAAAGATATGTTTTGATA
1 TAAAAGATATGTTTTAATA
10147618 TAAAA-ATA-GTTTTAATA
1 TAAAAGATATGTTTTAATA
10147635 T
1 T
10147636 GCTTTATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (19 bp):
TAAAAGATATGTTTTAATA
Found at i:10150990 original size:7 final size:6
Alignment explanation
Indices: 10150974--10151025 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
10150964 ATTTTCCAGC
* *
10150974 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
10151024 AA
1 AA
10151026 TAGGAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 5 0.12
6 23 0.57
7 7 0.17
8 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:10151009 original size:25 final size:25
Alignment explanation
Indices: 10150979--10151033 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
10150969 CCAGCAAAAA
10150979 TAAAAATGAAAATAA-AATAA-AATAG
1 TAAAAAT--AAATAATAATAATAATAG
10151004 TAAAAATAAATAATAATAATAATAG
1 TAAAAATAAATAATAATAATAATAG
*
10151029 GAAAA
1 TAAAA
10151034 TTAATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 6 0.22
24 5 0.19
25 16 0.59
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (25 bp):
TAAAAATAAATAATAATAATAATAG
Found at i:10158237 original size:34 final size:35
Alignment explanation
Indices: 10158182--10158248 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
10158172 CAAACACCAA
*
10158182 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
10158217 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
10158249 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:10160382 original size:14 final size:14
Alignment explanation
Indices: 10160363--10160392 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10160353 TATACAAATT
*
10160363 AAAGAATTATTAGA
1 AAAGAATTAATAGA
10160377 AAAGAATTAATAGA
1 AAAGAATTAATAGA
10160391 AA
1 AA
10160393 CAACTAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (14 bp):
AAAGAATTAATAGA
Found at i:10166002 original size:19 final size:19
Alignment explanation
Indices: 10165980--10166018 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
10165970 AAACTTTGTT
10165980 TCTAGTTTCTCACTTAAAC
1 TCTAGTTTCTCACTTAAAC
10165999 TCTAGTTTCTCACTTAAAC
1 TCTAGTTTCTCACTTAAAC
10166018 T
1 T
10166019 TTCAGAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (19 bp):
TCTAGTTTCTCACTTAAAC
Found at i:10172899 original size:2 final size:2
Alignment explanation
Indices: 10172892--10172917 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10172882 TGCATTTTCC
10172892 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
10172918 TCTATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10173044 original size:15 final size:17
Alignment explanation
Indices: 10173014--10173045 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
10173004 CCCATGCATT
10173014 TTTTTAATAGATATATG
1 TTTTTAATAGATATATG
10173031 TTTTT-ATA-ATATATG
1 TTTTTAATAGATATATG
10173046 AATATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTTTAATAGATATATG
Found at i:10181647 original size:23 final size:23
Alignment explanation
Indices: 10181621--10181671 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
10181611 TAAGTTTTAA
*
10181621 ATTTAGGATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
10181644 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
10181667 ATTTA
1 ATTTA
10181672 AGAAAAATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:10181648 original size:13 final size:13
Alignment explanation
Indices: 10181630--10181671 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
10181620 AATTTAGGAT
10181630 TATTTAGTGATAA
1 TATTTAGTGATAA
*
10181643 TATTTA--GA-AT
1 TATTTAGTGATAA
10181653 TATTTAGTGATAA
1 TATTTAGTGATAA
10181666 TATTTA
1 TATTTA
10181672 AGAAAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:10184246 original size:26 final size:25
Alignment explanation
Indices: 10184188--10184253 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
10184178 AAGCAAGCAC
*
10184188 TAACGGGAAGCTCACAAAGAACCTT
1 TAACGGGAAGCTCACAAAGAACCTA
*
10184213 TAATCGGGAAGCTCACGAAA-ATCCATA
1 TAA-CGGGAAGCTCAC-AAAGAACC-TA
*
10184240 TAACGGGACGCTCA
1 TAACGGGAAGCTCA
10184254 TAAGAGCTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 3 0.09
26 25 0.71
27 7 0.20
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (25 bp):
TAACGGGAAGCTCACAAAGAACCTA
Found at i:10188229 original size:20 final size:20
Alignment explanation
Indices: 10188204--10188248 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
10188194 TAAGTATTCA
10188204 TTTATATATATT-TATGTATT
1 TTTATA-ATATTATATGTATT
*
10188224 TTTATAATTTTATATGTATT
1 TTTATAATATTATATGTATT
10188244 TTTAT
1 TTTAT
10188249 CGAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTATAATATTATATGTATT
Found at i:10188299 original size:19 final size:19
Alignment explanation
Indices: 10188261--10188301 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
10188251 AAAAATAAAC
* **
10188261 TTTTAAATTTTTTTTTATT
1 TTTTAAAGTTTTTTGAATT
10188280 TTTTAAAGTTTTTTGAATT
1 TTTTAAAGTTTTTTGAATT
10188299 TTT
1 TTT
10188302 AATTTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (19 bp):
TTTTAAAGTTTTTTGAATT
Found at i:10189418 original size:3 final size:3
Alignment explanation
Indices: 10189410--10189459 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
10189400 TGGGTAGTTA
*
10189410 AAG AAG AAG AAG AAG AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG -AG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
10189457 AAG
1 AAG
10189460 GAAAGTAGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10199503 original size:2 final size:2
Alignment explanation
Indices: 10199496--10199526 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10199486 ATCCAAAACC
10199496 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
10199527 CCCTTAGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:10214126 original size:18 final size:18
Alignment explanation
Indices: 10214103--10214145 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
10214093 AAATAGGTTT
10214103 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
10214121 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
10214139 TTAATTA
1 TTAATTA
10214146 CACCTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:10232305 original size:29 final size:30
Alignment explanation
Indices: 10232246--10232306 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
10232236 AAATTTAATA
*
10232246 ATTTATATATAAAAATTAGTAAAAACTAATC
1 ATTTATATAGAAAAATTAGTAAAAAC-AATC
*
10232277 ATTTATATAGAATAAATTCG-AAAAA-AATC
1 ATTTATATAGAA-AAATTAGTAAAAACAATC
10232306 A
1 A
10232307 ACATTTCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 5 0.19
31 16 0.59
32 6 0.22
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (30 bp):
ATTTATATAGAAAAATTAGTAAAAACAATC
Found at i:10232312 original size:32 final size:31
Alignment explanation
Indices: 10232241--10232312 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
10232231 AATTTAAATT
* * * *
10232241 TAATAATTTATATATAAAAATTAGTAAAAAC
1 TAATCATTTATATAGAAAAATTAGAAAAAAA
*
10232272 TAATCATTTATATAGAATAAATTCGAAAAAAA
1 TAATCATTTATATAGAA-AAATTAGAAAAAAA
10232304 TCAA-CATTT
1 T-AATCATTT
10232313 CAAGTTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 15 0.44
32 17 0.50
33 2 0.06
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (31 bp):
TAATCATTTATATAGAAAAATTAGAAAAAAA
Found at i:10233105 original size:23 final size:24
Alignment explanation
Indices: 10233068--10233112 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
10233058 TTTTGTTTAA
*
10233068 ATTTTTTATAGAAATACATAAATT
1 ATTTTTTATAGAAATAAATAAATT
*
10233092 ATTTTTTA-ATAAATAAATAAA
1 ATTTTTTATAGAAATAAATAAA
10233113 CAGCAACAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
ATTTTTTATAGAAATAAATAAATT
Found at i:10247563 original size:12 final size:12
Alignment explanation
Indices: 10247541--10247584 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
10247531 ATCTCTCTCA
*
10247541 AGAAGCAGAAGC
1 AGAAGCCGAAGC
* *
10247553 CGAAGCCGAAGT
1 AGAAGCCGAAGC
10247565 AGAAGCCGAAGC
1 AGAAGCCGAAGC
10247577 AGAAGCCG
1 AGAAGCCG
10247585 TGGTCGGAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.41, C:0.23, G:0.34, T:0.02
Consensus pattern (12 bp):
AGAAGCCGAAGC
Found at i:10247568 original size:18 final size:18
Alignment explanation
Indices: 10247541--10247582 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
10247531 ATCTCTCTCA
10247541 AGAAGCAGAAGCCGAAGC
1 AGAAGCAGAAGCCGAAGC
* *
10247559 CGAAGTAGAAGCCGAAGC
1 AGAAGCAGAAGCCGAAGC
10247577 AGAAGC
1 AGAAGC
10247583 CGTGGTCGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.33, T:0.02
Consensus pattern (18 bp):
AGAAGCAGAAGCCGAAGC
Found at i:10249998 original size:12 final size:12
Alignment explanation
Indices: 10249981--10250005 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10249971 GGTGTTCATT
10249981 CGGTTAACCGAC
1 CGGTTAACCGAC
10249993 CGGTTAACCGAC
1 CGGTTAACCGAC
10250005 C
1 C
10250006 CGAAATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:10253848 original size:89 final size:89
Alignment explanation
Indices: 10253755--10254171 Score: 342
Period size: 89 Copynumber: 4.7 Consensus size: 89
10253745 TTTGATCTGG
* * *
10253755 TGTTGCAATAAATTTTTTTTAATTTTTCGGAATAATTATAAAAATTACAATTTATATAATTTCAT
1 TGTTGCAATAAATTTTTTTT-ATTTTTCGGAATAATTATAATAATTACAATTTATTTCATTTCAT
* * *
10253820 TTTC-ATGGCACTTGGACTTGA-ATA
65 TTTCGA-GGCACTAGGGCTTGAGCTA
* * * * **
10253844 TGTTGTTGCAAT-AATTTTTCTTATTTCT-GAAATAATTATAATAATTATAATTTCCTTCATTTC
1 ---TGTTGCAATAAATTTTTTTTATTTTTCGGAATAATTATAATAATTACAATTTATTTCATTTC
**
10253907 ATTTTCG-GG-ACATTTGGCTTGAGTCTGA
63 ATTTTCGAGGCAC-TAGGGCTTGAG-CT-A
* *
10253935 TGTTGCAAT-AA--GTTTTTATTTTTCGGAATAGTTATAATAATTACAATTTATTTCATTAT-AT
1 TGTTGCAATAAATTTTTTTTATTTTTCGGAATAATTATAATAATTACAATTTATTTCATT-TCAT
10253996 TTTCGAGGCACTAGGGCTTGAGCT-
65 TTTCGAGGCACTAGGGCTTGAGCTA
* * * * * * * *
10254020 TGGTGCTACAATATATTTTTTATTTTCCGAAATAATTATAACAATTACTATTTATTTCATTTCAT
1 TGTTGCAATAA-ATTTTTTTTATTTTTCGGAATAATTATAATAATTACAATTTATTTCATTTCAT
*
10254085 TTTCGAGGCACTAGGGCTTGAG-TT
65 TTTCGAGGCACTAGGGCTTGAGCTA
* * *
10254109 TGGTGCTACA-AGAATTTTTTTTAATTTTT-GGAATAATTATAATATTTA-ATATTCATTTCATT
1 TGTTGC-A-ATA-AATTTTTTTT-ATTTTTCGGAATAATTATAATAATTACA-ATTTATTTCATT
10254171 T
61 T
10254172 TCGGGGAATA
Statistics
Matches: 266, Mismatches: 39, Indels: 42
0.77 0.11 0.12
Matches are distributed among these distances:
85 6 0.02
86 10 0.04
87 40 0.15
88 35 0.13
89 106 0.40
90 43 0.16
91 17 0.06
92 9 0.03
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.47
Consensus pattern (89 bp):
TGTTGCAATAAATTTTTTTTATTTTTCGGAATAATTATAATAATTACAATTTATTTCATTTCATT
TTCGAGGCACTAGGGCTTGAGCTA
Found at i:10253985 original size:176 final size:177
Alignment explanation
Indices: 10253770--10254150 Score: 411
Period size: 176 Copynumber: 2.1 Consensus size: 177
10253760 CAATAAATTT
*
10253770 TTTTTAATTTTTCGGAATAATTATAAAAATTACAATTTATATAATT-TCATTTTC-ATGGCACTT
1 TTTTTAATTTTTCGGAATAATTATAAAAATTACAATTTATATAATTAT-ATTTTCGA-GGCACTA
* * * * *
10253833 GGACTTGA-ATATGTTGTTGCAATA-ATTTTTCT-TATTTCTGAAATAATTATAATAATTA-TAA
64 GGACTTGAGAT-TGGTGCTACAATATATTTTT-TAT-TTTCCGAAATAATTATAACAATTACT-A
*
10253894 TTTCCTTCATTTCATTTTCGGGACATTTGGCTTGAGTCTGATGTTGCAATAAG
125 TTTACTTCATTTCATTTTCGGGACATTTGGCTTGAGTCTGATGTTGCAATAAG
* * * *
10253947 TTTTT-ATTTTTCGGAATAGTTATAATAATTACAATTTATTTCATTATATTTTCGAGGCACTAGG
1 TTTTTAATTTTTCGGAATAATTATAAAAATTACAATTTATATAATTATATTTTCGAGGCACTAGG
* * *
10254011 GCTTGAGCTTGGTGCTACAATATATTTTTTATTTTCCGAAATAATTATAACAATTACTATTTATT
66 ACTTGAGATTGGTGCTACAATATATTTTTTATTTTCCGAAATAATTATAACAATTACTATTTACT
** * * * * * *
10254076 TCATTTCATTTTCGAGG-CACTAGGGCTTGAGTTTGGTGCTACAAGAATTT
131 TCATTTCATTTTCG-GGACA-TTTGGCTTGAGTCTGATGTTGCAATAA--G
10254126 TTTTTAATTTTT-GGAATAATTATAA
1 TTTTTAATTTTTCGGAATAATTATAA
10254151 TATTTAATAT
Statistics
Matches: 170, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
176 109 0.64
177 38 0.22
179 17 0.10
180 6 0.04
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (177 bp):
TTTTTAATTTTTCGGAATAATTATAAAAATTACAATTTATATAATTATATTTTCGAGGCACTAGG
ACTTGAGATTGGTGCTACAATATATTTTTTATTTTCCGAAATAATTATAACAATTACTATTTACT
TCATTTCATTTTCGGGACATTTGGCTTGAGTCTGATGTTGCAATAAG
Found at i:10254302 original size:88 final size:88
Alignment explanation
Indices: 10253769--10254378 Score: 305
Period size: 89 Copynumber: 7.0 Consensus size: 88
10253759 GCAATAAATT
* * * * * * * **
10253769 TTTTTTAATTTTTCGGAATAATTATAAAAATTACAATTTATATAATTTCATTTTCATGGCACTTG
1 TTTTTTACTTTTT-AGAATAATTATAATAACTACTATTTATTTCATTTCATTTTCGGGGCACTTG
* * * * * *
10253834 GACTTGAATAT-GTTGTTGCAATAA
65 GGCTTGATTCTAG-AGCTACAATAA
* * ** *
10253858 -TTTTT-CTTATTTCTGAAATAATTATAATAATTA-TAATTTCCTTCATTTCATTTTCGGGACA-
1 TTTTTTACTT-TTT-AG-AATAATTATAATAACTACT-ATTTATTTCATTTCATTTTCGGGGCAC
* * * *
10253919 TTTGGCTTGAGTCT-GATGTTGCAATAA
62 TTGGGCTTGATTCTAGA-GCTACAATAA
* * * * * * *
10253946 GTTTTTA-TTTTTCGGAATAGTTATAATAATTACAATTTATTTCATTAT-ATTTTCGAGGCACTA
1 TTTTTTACTTTTT-AGAATAATTATAATAACTACTATTTATTTCATT-TCATTTTCGGGGCACTT
* * *
10254009 GGGCTTGA-GCTTGGTGCTACAATATA
64 GGGCTTGATTC-TAGAGCTACAATA-A
** * * * *
10254035 TTTTTTA-TTTTCCGAAATAATTATAACAATTACTATTTATTTCATTTCATTTTCGAGGCACTAG
1 TTTTTTACTTTTTAG-AATAATTATAATAACTACTATTTATTTCATTTCATTTTCGGGGCACTTG
* * *
10254099 GGCTTGAGTT-TGGTGCTACAAGAA
65 GGCTTGA-TTCTAGAGCTACAATAA
* * * * *
10254123 TTTTTTTTAATTTTTGGAATAATTATAAT-A-T-TTA-ATA-TTCATTTCATTTTCGGGG-AATA
1 --TTTTTTACTTTTTAGAATAATTATAATAACTACTATTTATTTCATTTCATTTTCGGGGCACT-
* * * * * * *
10254182 TAGACTTGAGTCTGGTGTTGCAATAA
63 TGGGCTTGATTCTAGAGCTACAATAA
* * * *
10254208 ---ATT--TTTTTGGAATAATTTTAATAACTACTATTTATTTCATTTCATTTT-TGGGCACTTGG
1 TTTTTTACTTTTTAGAATAATTATAATAACTACTATTTATTTCATTTCATTTTCGGGGCACTTGG
10254267 GCTTGATTCT-GAAGCTACAATAA
66 GCTTGATTCTAG-AGCTACAATAA
* * ** *
10254290 TTTTTTACTTTTTAGAATAGTTATAGTAGTTACTATTTGTTTCATTTCATTTTCGGGGCACTTGG
1 TTTTTTACTTTTTAGAATAATTATAATAACTACTATTTATTTCATTTCATTTTCGGGGCACTTGG
* *
10254355 TCTTTATTCTAGAGCTACAATAA
66 GCTTGATTCTAGAGCTACAATAA
10254378 T
1 T
10254379 GATTATAATA
Statistics
Matches: 412, Mismatches: 74, Indels: 71
0.74 0.13 0.13
Matches are distributed among these distances:
78 18 0.04
79 1 0.00
80 3 0.01
81 3 0.01
82 23 0.06
83 15 0.04
84 3 0.01
85 36 0.09
86 2 0.00
87 79 0.19
88 87 0.21
89 119 0.29
90 18 0.04
91 5 0.01
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.46
Consensus pattern (88 bp):
TTTTTTACTTTTTAGAATAATTATAATAACTACTATTTATTTCATTTCATTTTCGGGGCACTTGG
GCTTGATTCTAGAGCTACAATAA
Found at i:10255518 original size:21 final size:21
Alignment explanation
Indices: 10255494--10255534 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10255484 AAAATCGATA
*
10255494 TAATTTTA-TTAATTATTAATT
1 TAATATTACTTAA-TATTAATT
10255515 TAATATTACTTAATATTAAT
1 TAATATTACTTAATATTAAT
10255535 ACGTTAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATATTACTTAATATTAATT
Found at i:10259188 original size:75 final size:75
Alignment explanation
Indices: 10259065--10259217 Score: 270
Period size: 75 Copynumber: 2.0 Consensus size: 75
10259055 TCACCAGAAT
* *
10259065 AAGAGGGAACACTATGAGAACTAGTATTTGTTGGACTAATATCTACTCCATTCTGAGGAATCGAA
1 AAGAGGGAACACTATGAGAACTAGTATTTGTTAGACTAATATCTACTCCATTCTAAGGAATCGAA
10259130 GACCCATTCA
66 GACCCATTCA
* *
10259140 AAGAGGGAATACTATGAGAATTAGTATTTGTTAGACTAATATCTACTCCATTCTAAGGAATCGAA
1 AAGAGGGAACACTATGAGAACTAGTATTTGTTAGACTAATATCTACTCCATTCTAAGGAATCGAA
10259205 GACCCATTCA
66 GACCCATTCA
10259215 AAG
1 AAG
10259218 TACTCGGGCA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (75 bp):
AAGAGGGAACACTATGAGAACTAGTATTTGTTAGACTAATATCTACTCCATTCTAAGGAATCGAA
GACCCATTCA
Found at i:10268063 original size:24 final size:24
Alignment explanation
Indices: 10268013--10268064 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
10268003 AATTAAAGTC
* **
10268013 AAATATATTATGTTAATAAATGTT
1 AAATATATTATCTTAATAAATACT
10268037 AAATATATTATACTT-ATAAATACT
1 AAATATATTAT-CTTAATAAATACT
10268061 AAAT
1 AAAT
10268065 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (24 bp):
AAATATATTATCTTAATAAATACT
Found at i:10282818 original size:18 final size:17
Alignment explanation
Indices: 10282785--10282823 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
10282775 TTTTATAAAT
10282785 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
10282803 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
10282820 TGTG
1 TGTG
10282824 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Done.