Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 2 of 255
Found at i:349744 original size:97 final size:95
Alignment explanation
Indices: 349523--349847 Score: 578
Period size: 95 Copynumber: 3.4 Consensus size: 95
349513 AAGATCTGTA
349523 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
349588 TAGTCAGGGAGGTAAAATCTGCCCTCTTCG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
*
349618 ATCTTCAATCTATTCCACTACCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
349683 TAGTCACATGGAGGTAAAATCTGCCATCTTCG
66 TAGT--CAGGGAGGTAAAATCTGCCATCTTCG
*
349715 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCATTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* *
349780 TAGTCAGGGAGGTAAAATCTGCCATATTTG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
349810 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAG
349848 GATCTGTTTT
Statistics
Matches: 220, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
95 129 0.59
97 91 0.41
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTCAGGGAGGTAAAATCTGCCATCTTCG
Found at i:349908 original size:95 final size:94
Alignment explanation
Indices: 349523--349908 Score: 395
Period size: 95 Copynumber: 4.0 Consensus size: 94
349513 AAGATCTGTA
** **
349523 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAG-TATCGGCTTCAATCCACTCCACAA
* * *
349588 TAGTCAGGGAGGTAAAATCTGCCCTCTTCG
65 TAGTCAGGAAGGCAAAATCTGCCATCTTCG
* ** **
349618 ATCTTCAATCTATTCCACTACCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAG-TATCGGCTTCAATCCACTCCACAA
*
349683 TAGTCACATGG-AGGTAAAATCTGCCATCTTCG
65 TAGT--CA-GGAAGGCAAAATCTGCCATCTTCG
** ***
349715 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCATTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAG-TATCGGCTTCAATCCACTCCACAA
* * * *
349780 TAGTCAGGGAGGTAAAATCTGCCATATTTG
65 TAGTCAGGAAGGCAAAATCTGCCATCTTCG
**
349810 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAG-G-ATCTGTTTTTCAATCCACTTCCTA
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTATC-G-GCTTCAATCCAC-TCC-A
** *
349873 CCAATA-T-AGGAAGGCAGGATCTGCTATCTTCG
62 -CAATAGTCAGGAAGGCAAAATCTGCCATCTTCG
349905 ATCT
1 ATCT
349909 ACTTCACACC
Statistics
Matches: 262, Mismatches: 20, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
92 3 0.01
93 1 0.00
94 11 0.04
95 152 0.58
96 2 0.01
97 91 0.35
98 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (94 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTATCGGCTTCAATCCACTCCACAAT
AGTCAGGAAGGCAAAATCTGCCATCTTCG
Found at i:349920 original size:44 final size:44
Alignment explanation
Indices: 349872--350545 Score: 598
Period size: 44 Copynumber: 15.2 Consensus size: 44
349862 TCCACTTCCT
* *
349872 ACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTACTTCAC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
349916 ACCAATATATGAATACAAGATCTGCTTTTTTGCGATCTACTTCACC
1 ACCAATATAGGAAGACAAGATCTGCTATCTT-CGATCTACTTCA-C
* * * *
349962 ACCAGTATGGGAAGACAAGATCTGC-ATCTTGGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
350004 TATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
350049 GCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * *
350094 ACCAATATGGGAAGACAAGATCTGC-ATCTTGGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
350136 TATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * * *
350181 GCCAATACATGAAGACCAGATCTGCTTTCTGCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * *
350226 ACCAATATGGGAAGACAAGATCTGC-ATCGTCGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* *
350268 TACCAATATAGGAAGATC-GGACCTGCTATCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGA-CAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
350313 GCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* *
350358 ACCAA-ATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * *
350399 TACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
350444 GCCAATACATGAAGACAAGATCTACTTTCTGT-GATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCT-TCGATCTACTTC-AC
* * *
350489 ACCAATATGGGAAGACAAGATCTGCAATCTTCAATCTA-TTCCAC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTT-CAC
350533 TACCAAATATAGG
1 -ACC-AATATAGG
350546 GAGATAGAGT
Statistics
Matches: 493, Mismatches: 111, Indels: 50
0.75 0.17 0.08
Matches are distributed among these distances:
41 1 0.00
42 8 0.02
43 89 0.18
44 265 0.54
45 101 0.20
46 29 0.06
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (44 bp):
ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
Found at i:350139 original size:132 final size:132
Alignment explanation
Indices: 349861--350552 Score: 1118
Period size: 132 Copynumber: 5.2 Consensus size: 132
349851 CTGTTTTTCA
** * * *
349861 ATCCACTTCCTACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTACTTCACACCAATATAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * *
349926 GAATACAAGATCTGCTTTTTTGCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCT
66 GAAGACAAGATCTGC-TTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCT
*
349991 TGG
130 TCG
*
349994 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
350059 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
*
350124 GG
131 CG
*
350126 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
350191 GAAGACCAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
350256 CG
131 CG
*
350258 ATCCACTTCCTACCAATATAGGAAGATCGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
350323 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAA-ATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
350387 CG
131 CG
* *
350389 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
350454 GAAGACAAGATCTACTTTCTGTGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCAATCT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCT
*
350519 TCA
130 TCG
* *
350522 ATCTA-TTCCACTACCAAATATAGGGAGATAG
1 ATCCACTT-C-CTACC-AATATAGGAAGATAG
350553 AGTTATCGGC
Statistics
Matches: 529, Mismatches: 25, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
131 125 0.24
132 301 0.57
133 84 0.16
134 5 0.01
135 14 0.03
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (132 bp):
ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
CG
Found at i:350672 original size:46 final size:46
Alignment explanation
Indices: 350498--350681 Score: 117
Period size: 46 Copynumber: 4.0 Consensus size: 46
350488 CACCAATATG
* *
350498 GGAAGACAAGATCTGCAATCTTCAATCTATTCCACTACCAAATATA
1 GGAAGACAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACA
* * * * ** * * *
350544 GGGAGATAGAGTTAT-C-GGCTTCAATCTACTCCACTG--TAGTCACA
1 GGAAGACA-AGATCTGCAATCTTCAATCTATTCCACTGCCAAAT-ACA
* ** * * * * *
350588 GGGAGGTAAAATCTGCCATCTTCGATCTGCTT-CGCTGCCAAATACA
1 GGAAGACAAGATCTGCAATCTTCAATCT-ATTCCACTGCCAAATACA
* *
350634 GGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACA
1 GGAAGACAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACA
350680 GG
1 GG
350682 GAGATAGAGT
Statistics
Matches: 99, Mismatches: 31, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
43 5 0.05
44 10 0.10
45 30 0.30
46 48 0.48
47 6 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (46 bp):
GGAAGACAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACA
Found at i:350714 original size:45 final size:45
Alignment explanation
Indices: 350517--350849 Score: 128
Period size: 45 Copynumber: 7.4 Consensus size: 45
350507 GATCTGCAAT
* * * * *
350517 CTTCAATCTATTCCACTACCAAATATAGGGAGATAGAGTTATCGG
1 CTTCAATCTACTCCACTGCCAGATACAGGGAGATAGAGTTATCAG
* * * * ** *
350562 CTTCAATCTACTCCACTG-TAG-TCACAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGCCAGAT-ACAGGGAGATAGAGT-TATCAG
* * * * * * ** * * *
350607 CTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCA-AGATCTGCAAT
1 CTTCAATCTACTCCACTGCCAGATACAGGGAGATAGAGTTAT-C-AG
* *
350653 CTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGG
1 CTTCAATCTACTCCACTGCCAGATACAGGGAGATAGAGTTATCAG
* ** * * * *
350698 CTTCAATGTACTCCACTG-TTG-T-CAGGGAGGTAAAATT-TGCCAT
1 CTTCAATCTACTCCACTGCCAGATACAGGGAGATAGAGTTAT--CAG
* * * * * * *
350741 CTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCA-AGA-TCTGAT-AT
1 CTTCAATCTACTCCACTGCCAGATACAGG-GAG-ATAGAGT-T-ATCAG
* *
350787 CTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGG
1 CTTCAATCTACTCCACTGCCAGATACAGGGAGATAGAGTTATCAG
*
350832 CTTCAATGTACTCCACTG
1 CTTCAATCTACTCCACTG
350850 TTGTCAGGGA
Statistics
Matches: 200, Mismatches: 68, Indels: 40
0.65 0.22 0.13
Matches are distributed among these distances:
41 1 0.00
42 12 0.06
43 16 0.08
44 17 0.09
45 73 0.37
46 70 0.35
47 10 0.05
49 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (45 bp):
CTTCAATCTACTCCACTGCCAGATACAGGGAGATAGAGTTATCAG
Found at i:350790 original size:134 final size:134
Alignment explanation
Indices: 350504--350926 Score: 733
Period size: 134 Copynumber: 3.1 Consensus size: 134
350494 TATGGGAAGA
* * *
350504 CAAGATCTGCAATCTTCAATCTATTCCACTACCAAATATAGGGAGATAGAGTTATCGGCTTCAAT
1 CAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGCTTCAAT
* *
350569 CTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACA
66 GTACTCCACTGTTGT--CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACA
*
350634 GGAAGG
129 GGAAAG
350640 CAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGCTTCAAT
1 CAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGCTTCAAT
*
350705 GTACTCCACTGTTGTCAGGGAGGTAAAATTTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGG
66 GTACTCCACTGTTGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGG
350770 AAAG
131 AAAG
350774 CAAGATCTG-ATATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGCTTCAA
1 CAAGATCTGCA-ATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGCTTCAA
350838 TGTACTCCACTGTTGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAG
65 TGTACTCCACTGTTGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAG
350903 GAAAG
130 GAAAG
350908 CAAGATCTG-ATATCTTCAA
1 CAAGATCTGCA-ATCTTCAA
350927 CCAGCTCTGC
Statistics
Matches: 278, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
133 1 0.00
134 202 0.73
136 75 0.27
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27
Consensus pattern (134 bp):
CAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGCTTCAAT
GTACTCCACTGTTGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGG
AAAG
Found at i:351020 original size:86 final size:86
Alignment explanation
Indices: 350874--351223 Score: 547
Period size: 86 Copynumber: 4.1 Consensus size: 86
350864 AAATCTGCCA
* * * *
350874 TCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTGATATCTTCAACCAGCTCTGCTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTA
350939 CAAACGAGAGAGGCAAGGTTTG
65 CAAACGAGAGAGGCAAGGTTTG
* *
350961 TCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
*
351026 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
* *
351047 TCTTCGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
*
351112 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
* * *
351133 TCTTCTATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAACTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
* * *
351198 GACCGAGAGAGGCAAGGTTTA
66 AAACGAGAGAGGCAAGGTTTG
351219 TCTTC
1 TCTTC
351224 AATTTTCACT
Statistics
Matches: 245, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
86 225 0.92
87 20 0.08
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.26
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
AAACGAGAGAGGCAAGGTTTG
Found at i:351083 original size:42 final size:42
Alignment explanation
Indices: 350949--351169 Score: 98
Period size: 42 Copynumber: 5.2 Consensus size: 42
350939 CAAACGAGAG
* * *
350949 AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGA
1 AGGCAAGGTTTGTCTTCAATCTGCTTCACTGTCAATGCAGGA
* * * * * *
350991 AGGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAA-AC-GAGA
1 AGGCAAGGT-T--TGTCTTCAATCTGCTTC-ACTGTCAATGCAG-GA
* *
351034 GTGGCAAGGTTTGTCTTCGATCTGCTTCACTGTCAATGCAGGA
1 -AGGCAAGGTTTGTCTTCAATCTGCTTCACTGTCAATGCAGGA
* * * * * *
351077 AGGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAA-AC-GAGA
1 AGGCAAGGT-T--TGTCTTCAATCTGCTTC-ACTGTCAATGCAG-GA
* * *
351120 GTGGCAAGGTTTGTCTTCTATCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTCTTCAATCTGCTTCACTGTCAATGCAGGA
351163 AGGCAAG
1 AGGCAAG
351170 ATCTGATAAC
Statistics
Matches: 124, Mismatches: 35, Indels: 40
0.62 0.18 0.20
Matches are distributed among these distances:
41 25 0.20
42 33 0.27
43 16 0.13
44 25 0.20
45 25 0.20
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (42 bp):
AGGCAAGGTTTGTCTTCAATCTGCTTCACTGTCAATGCAGGA
Found at i:355373 original size:19 final size:20
Alignment explanation
Indices: 355349--355392 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
355339 CGTGAAAGTC
* *
355349 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
355368 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
355388 -AATGC
1 TAATGC
355393 CAAAAGAAAC
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:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:366725 original size:18 final size:19
Alignment explanation
Indices: 366702--366739 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
366692 GGAAGCAAGC
*
366702 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
366720 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
366739 A
1 A
366740 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:370116 original size:15 final size:14
Alignment explanation
Indices: 370097--370124 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
370087 GAAAATAACA
370097 AAAAAATCATATTT
1 AAAAAATCATATTT
370111 AAAAAATCATATTT
1 AAAAAATCATATTT
370125 TTTTCCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAAAATCATATTT
Found at i:373461 original size:33 final size:33
Alignment explanation
Indices: 373420--373487 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
373410 GTACTAATGG
373420 AAAAAAGTTGTGATTCAAGTAGCAACTTTGTCA
1 AAAAAAGTTGTGATTCAAGTAGCAACTTTGTCA
373453 AAAAAAGTTGTGATTCAAGTAGCAACTTTGTCA
1 AAAAAAGTTGTGATTCAAGTAGCAACTTTGTCA
373486 AA
1 AA
373488 CTTCAATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (33 bp):
AAAAAAGTTGTGATTCAAGTAGCAACTTTGTCA
Found at i:375619 original size:37 final size:36
Alignment explanation
Indices: 375578--375767 Score: 105
Period size: 37 Copynumber: 5.0 Consensus size: 36
375568 ATTTCCTGTT
*
375578 GCGATTGTCATTTTTACGGTTTGCTCGATTTAAGATA
1 GCGATT-TCATTTTTACGGTTCGCTCGATTTAAGATA
* ** * * * *
375615 GCGATCTTCGATATTCTAACAATTCACTTGATTTAATATC
1 GCGAT-TTC-AT-TT-TTACGGTTCGCTCGATTTAAGATA
375655 GCGACTTTCATTTTTACGGTTCGCTCGATTTAAGATA
1 GCGA-TTTCATTTTTACGGTTCGCTCGATTTAAGATA
* * * * * *
375692 ACAATCTTCAATATTCTAACAGTTC-CTTCGATTTAAAACCA
1 GCGAT-TTC-AT-TT-TTACGGTTCGC-TCGATTTAAGA-TA
* *
375733 -CGGTTGTCATTTTTACTGTTCGCTCGATTTAAGAT
1 GCGATT-TCATTTTTACGGTTCGCTCGATTTAAGAT
375768 CACGACCTTC
Statistics
Matches: 113, Mismatches: 27, Indels: 27
0.68 0.16 0.16
Matches are distributed among these distances:
36 1 0.01
37 46 0.41
38 10 0.09
39 10 0.09
40 44 0.39
41 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (36 bp):
GCGATTTCATTTTTACGGTTCGCTCGATTTAAGATA
Found at i:375648 original size:40 final size:38
Alignment explanation
Indices: 375604--375727 Score: 101
Period size: 40 Copynumber: 3.2 Consensus size: 38
375594 CGGTTTGCTC
*
375604 GATTTAAGATAGCGATCTTCGATATTCTAACAATTCACTT
1 GATTTAAGATAGCGATCTTC-ATATTCTAACAGTTC-CTT
* * * * *
375644 GATTTAATATCGCGA-CTTTCAT-TT-TTACGGTTCGCTC
1 GATTTAAGATAGCGATC-TTCATATTCTAACAGTTC-CTT
* *
375681 GATTTAAGATAACAATCTTCAATATTCTAACAGTTCCTT
1 GATTTAAGATAGCGATCTTC-ATATTCTAACAGTTCCTT
375720 CGATTTAA
1 -GATTTAA
375728 AACCACGGTT
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
37 22 0.34
38 5 0.08
39 7 0.11
40 30 0.47
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (38 bp):
GATTTAAGATAGCGATCTTCATATTCTAACAGTTCCTT
Found at i:375818 original size:77 final size:76
Alignment explanation
Indices: 375583--375824 Score: 277
Period size: 77 Copynumber: 3.1 Consensus size: 76
375573 CTGTTGCGAT
* * *
375583 TGTCATTTTTACGGTTTGCTCGATTTAAGATAGCGATCTTCGATATTCTAACAATTCACTTGATT
1 TGTCATTTTTACGGTTCGCTCGATTTAAGATA-CGATCTTCGATATTCTAACAGTTCATTTGATT
*
375648 TAATATCGCGAC
65 TAATATCGCGGC
* * * * *
375660 TTTCATTTTTACGGTTCGCTCGATTTAAGATAACAATCTTCAATATTCTAACAGTTCCTTCGATT
1 TGTCATTTTTACGGTTCGCTCGATTTAAGAT-ACGATCTTCGATATTCTAACAGTTCATTTGATT
* * * *
375725 TAAAACCACGGT
65 TAATATCGCGGC
* * * * *
375737 TGTCATTTTTACTGTTCGCTCGATTTAAGATCACGACCTTCGATATTCTAGCAGTTCGTTTAATT
1 TGTCATTTTTACGGTTCGCTCGATTTAAGAT-ACGATCTTCGATATTCTAACAGTTCATTTGATT
* *
375802 TAATATTGTGGC
65 TAATATCGCGGC
375814 TGTCATTTTTA
1 TGTCATTTTTA
375825 TGGTCCATTT
Statistics
Matches: 135, Mismatches: 29, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
77 134 0.99
78 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (76 bp):
TGTCATTTTTACGGTTCGCTCGATTTAAGATACGATCTTCGATATTCTAACAGTTCATTTGATTT
AATATCGCGGC
Found at i:382581 original size:45 final size:46
Alignment explanation
Indices: 382514--382637 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
382504 CATATGACCT
*
382514 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
382557 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
382603 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
382638 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:382620 original size:46 final size:45
Alignment explanation
Indices: 382514--382748 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
382504 CATATGACCT
*
382514 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
382557 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
382603 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
382640 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
382677 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
382714 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
382749 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:382641 original size:37 final size:37
Alignment explanation
Indices: 382599--382775 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
382589 AGCTGAAGCT
* **
382599 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
382636 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
382673 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
382710 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
382747 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
382776 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:388100 original size:13 final size:13
Alignment explanation
Indices: 388055--388101 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
388045 TCCAATCTCA
*
388055 TTGAACCCCGAAC
1 TTGAACCCTGAAC
*
388068 TTGAAACCTGAACC
1 TTGAACCCTGAA-C
388082 TTGAACCCTGAAC
1 TTGAACCCTGAAC
*
388095 TCGAACC
1 TTGAACC
388102 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.19
Consensus pattern (13 bp):
TTGAACCCTGAAC
Found at i:388211 original size:7 final size:7
Alignment explanation
Indices: 388143--388198 Score: 69
Period size: 7 Copynumber: 8.1 Consensus size: 7
388133 ATTTTTTTAA
388143 CTTGAAC
1 CTTGAAC
*
388150 CCTGAAC
1 CTTGAAC
*
388157 CTAGAAC
1 CTTGAAC
* *
388164 C-TCAGC
1 CTTGAAC
388170 CTTGAAC
1 CTTGAAC
388177 CTTGAAC
1 CTTGAAC
388184 CTTGAAC
1 CTTGAAC
388191 CTTGAAC
1 CTTGAAC
388198 C
1 C
388199 CAAACCTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 3 0.08
7 37 0.93
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.23
Consensus pattern (7 bp):
CTTGAAC
Found at i:388245 original size:21 final size:19
Alignment explanation
Indices: 388221--388271 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
388211 CAAAAGGCCA
388221 AGTTTATGGTTCAAGGTTTAG
1 AGTTTA-GGTTCAAGG-TTAG
* *
388242 AGTTTAGGGTTTAAGGTTCG
1 AGTTTA-GGTTCAAGGTTAG
388262 AGTTTAGGTT
1 AGTTTAGGTT
388272 TAGGTTCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 4 0.15
20 9 0.33
21 14 0.52
ACGTcount: A:0.22, C:0.04, G:0.31, T:0.43
Consensus pattern (19 bp):
AGTTTAGGTTCAAGGTTAG
Found at i:388282 original size:25 final size:27
Alignment explanation
Indices: 388236--388286 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
388226 ATGGTTCAAG
*
388236 GTTTAGAGTTTAGGGTTTAAGGTTCGA
1 GTTTAGAGTTTAGGGTTCAAGGTTCGA
388263 GTTTAG-GTTTA-GGTTCAAGGTTCG
1 GTTTAGAGTTTAGGGTTCAAGGTTCG
388287 GATTCTGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
26 5 0.22
27 6 0.26
ACGTcount: A:0.20, C:0.06, G:0.33, T:0.41
Consensus pattern (27 bp):
GTTTAGAGTTTAGGGTTCAAGGTTCGA
Found at i:390640 original size:23 final size:23
Alignment explanation
Indices: 390612--390698 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 23
390602 TTTATCGATT
* * *
390612 AGGCACTTTATGTGTCGTATTTT
1 AGGCACCTCATGTGTCGTATTTC
*
390635 AGGCACCTCGTGTGTCGTATTTC
1 AGGCACCTCATGTGTCGTATTTC
*
390658 AGGCACCTCGTGTGTCGTA--TC
1 AGGCACCTCATGTGTCGTATTTC
* *
390679 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCATGTGTCGTAT
390699 ACTGATCAGG
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
21 18 0.32
23 38 0.68
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (23 bp):
AGGCACCTCATGTGTCGTATTTC
Found at i:390680 original size:21 final size:21
Alignment explanation
Indices: 390635--390698 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
390625 GTCGTATTTT
390635 AGGCACCTCGTGTGTCGTATTTC
1 AGGCACCTCGTGTGTCGTA--TC
390658 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCGTGTGTCGTATC
* **
390679 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCGTGTGTCGTAT
390699 ACTGATCAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.50
23 19 0.50
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (21 bp):
AGGCACCTCGTGTGTCGTATC
Found at i:392631 original size:18 final size:18
Alignment explanation
Indices: 392598--392691 Score: 122
Period size: 18 Copynumber: 5.4 Consensus size: 18
392588 AAGGTTTTCT
392598 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
392613 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
*
392631 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
* *
392649 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
* *
392667 TATTGATGATAGTGGCGC
1 TATTGATGATAGTGACGA
392685 TATTGAT
1 TATTGAT
392692 CGTGACCTTG
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 60 0.83
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.36
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:393333 original size:29 final size:30
Alignment explanation
Indices: 393299--393361 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
393289 TAGCAAAAGG
*
393299 TAAAATTATACTTT-ACCCCTTAAAAATGA
1 TAAAATTATAATTTAACCCCTTAAAAATGA
* * *
393328 TAAAATTATAATTTAATCCTTTAAAAATTA
1 TAAAATTATAATTTAACCCCTTAAAAATGA
393358 TAAA
1 TAAA
393362 GATATAGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (30 bp):
TAAAATTATAATTTAACCCCTTAAAAATGA
Found at i:396408 original size:71 final size:71
Alignment explanation
Indices: 396298--396438 Score: 255
Period size: 71 Copynumber: 2.0 Consensus size: 71
396288 AGTAACCCAG
396298 TTATTAGCGTGTTTCTGTTTTAGTCACCCTGATTTAAAAAAATTTATTTTAATCATTAACGTTAT
1 TTATTAGCGTGTTTCTGTTTTAGTCACCCTGATTTAAAAAAATTTATTTTAATCATTAACGTTAT
396363 TGACAA
66 TGACAA
* * *
396369 TTATTAGCGTGTTTTTGTTTTGGTCACCCTGATTTAAAAAATTTTATTTTAATCATTAACGTTAT
1 TTATTAGCGTGTTTCTGTTTTAGTCACCCTGATTTAAAAAAATTTATTTTAATCATTAACGTTAT
396434 TGACA
66 TGACA
396439 TTTGATATTT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (71 bp):
TTATTAGCGTGTTTCTGTTTTAGTCACCCTGATTTAAAAAAATTTATTTTAATCATTAACGTTAT
TGACAA
Found at i:397826 original size:32 final size:32
Alignment explanation
Indices: 397790--397850 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
397780 AAAAATATAC
397790 ATTAAATGTTGAGCTTGTTAGAAATTTTCAAT
1 ATTAAATGTTGAGCTTGTTAGAAATTTTCAAT
*
397822 ATTAAATGTTGAGCTTGTTAGAATTTTTC
1 ATTAAATGTTGAGCTTGTTAGAAATTTTC
397851 TAACATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (32 bp):
ATTAAATGTTGAGCTTGTTAGAAATTTTCAAT
Found at i:403687 original size:18 final size:18
Alignment explanation
Indices: 403664--403706 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
403654 CAATAGGTTT
403664 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
403682 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
403700 TTAATTA
1 TTAATTA
403707 CACCTTGAAC
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:414621 original size:18 final size:18
Alignment explanation
Indices: 414598--414633 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
414588 AAGCTGCTTG
414598 AGCTATTAAGCAAGTCGA
1 AGCTATTAAGCAAGTCGA
414616 AGCTATTAAGCAAGTCGA
1 AGCTATTAAGCAAGTCGA
414634 CTTTGAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (18 bp):
AGCTATTAAGCAAGTCGA
Found at i:418166 original size:6 final size:6
Alignment explanation
Indices: 418120--418153 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
418110 CAGTTGTCAG
*
418120 ATATCT ATATCT ATATCT ATTTCT ATATCT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATATCT ATAT
418154 ATAATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (6 bp):
ATATCT
Found at i:438524 original size:36 final size:36
Alignment explanation
Indices: 438477--438547 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
438467 CCTCAAAAAG
438477 ATAGTTTAGTTAACTAGAACTTAACCTAGTTAACCC
1 ATAGTTTAGTTAACTAGAACTTAACCTAGTTAACCC
438513 ATAGTTTAGTTAACTAGAACTTAACCTAGTTAACC
1 ATAGTTTAGTTAACTAGAACTTAACCTAGTTAACC
438548 TAAACTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (36 bp):
ATAGTTTAGTTAACTAGAACTTAACCTAGTTAACCC
Found at i:438554 original size:20 final size:20
Alignment explanation
Indices: 438483--438546 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
438473 AAAGATAGTT
438483 TAGTTAACTAGAACTTAACC
1 TAGTTAACTAGAACTTAACC
* * *
438503 TAGTTAACCCA-TAGTT----
1 TAGTTAA-CTAGAACTTAACC
438519 TAGTTAACTAGAACTTAACC
1 TAGTTAACTAGAACTTAACC
438539 TAGTTAAC
1 TAGTTAAC
438547 CTAAACTTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 2 0.06
16 10 0.31
20 18 0.56
21 2 0.06
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.33
Consensus pattern (20 bp):
TAGTTAACTAGAACTTAACC
Found at i:444947 original size:29 final size:28
Alignment explanation
Indices: 444876--444932 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
444866 TGGGTTAAAT
*
444876 ATTAAATTTATATATAAATTTTTATTTA
1 ATTAAATTTATATATAAATTTTAATTTA
444904 ATTACAATTTAATATATAAATTTTAATTT
1 ATTA-AATTT-ATATATAAATTTTAATTT
444933 GATGTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 17 0.65
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTAAATTTATATATAAATTTTAATTTA
Found at i:448466 original size:16 final size:18
Alignment explanation
Indices: 448445--448477 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
448435 ATTTAATTAT
448445 ATATAA-TAA-ATTGTTC
1 ATATAATTAATATTGTTC
448461 ATATAATTAATATTGTT
1 ATATAATTAATATTGTT
448478 TACAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (18 bp):
ATATAATTAATATTGTTC
Found at i:455683 original size:8 final size:8
Alignment explanation
Indices: 455661--455716 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
455651 CAATAAATAC
455661 TTTAAAAA
1 TTTAAAAA
455669 TTATAAAAA
1 TT-TAAAAA
455678 TTTAAAAA
1 TTTAAAAA
455686 TTT--AAA
1 TTTAAAAA
*
455692 TTTAAATA
1 TTTAAAAA
455700 TTTATGAAAA
1 TTTA--AAAA
455710 -TTAAAAA
1 TTTAAAAA
455717 AAGGACAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
6 6 0.15
7 4 0.10
8 17 0.41
9 11 0.27
10 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
TTTAAAAA
Found at i:455694 original size:14 final size:14
Alignment explanation
Indices: 455661--455703 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
455651 CAATAAATAC
455661 TTTAAAAATTATAAAAA
1 TTTAAAAATT-T--AAA
455678 TTTAAAAATTTAAA
1 TTTAAAAATTTAAA
*
455692 TTTAAATATTTA
1 TTTAAAAATTTA
455704 TGAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 14 0.56
16 1 0.04
17 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAAAAATTTAAA
Found at i:459151 original size:25 final size:23
Alignment explanation
Indices: 459116--459162 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
459106 GTGTTTGATA
*
459116 TTTTTTTTAATATGGTACTTGTG
1 TTTTTTTTAATATGGCACTTGTG
*
459139 TTTTTTATCTAATGTGGCACTTGT
1 TTTTTT-T-TAATATGGCACTTGT
459163 ATTTAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 1 0.05
25 13 0.65
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (23 bp):
TTTTTTTTAATATGGCACTTGTG
Found at i:472973 original size:34 final size:34
Alignment explanation
Indices: 472935--473004 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
472925 TTGGTTTGAC
*
472935 TTGTTAGATATATATGTGTCCGACATTGATATGT
1 TTGTTAGATATATAAGTGTCCGACATTGATATGT
* *
472969 TTGTTAGATATGTAAGTGTCCGACGTTGATATGT
1 TTGTTAGATATATAAGTGTCCGACATTGATATGT
473003 TT
1 TT
473005 ATGTTCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.44
Consensus pattern (34 bp):
TTGTTAGATATATAAGTGTCCGACATTGATATGT
Found at i:474795 original size:29 final size:30
Alignment explanation
Indices: 474732--474795 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
474722 ATCTCAAAAC
*
474732 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTATGATTT-ATGTGCAATTG
* * *
474763 TATACATGAACTTTGATTT-TGTGTAATTT
1 TATACATGAACTATGATTTATGTGCAATTG
474792 TATA
1 TATA
474796 TGTAAAACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (30 bp):
TATACATGAACTATGATTTATGTGCAATTG
Found at i:475035 original size:29 final size:30
Alignment explanation
Indices: 474992--475064 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
474982 CCACAATCAG
* **
474992 AGTTTCATGTGTACAATTGTAC-TAAATTAA
1 AGTTT-ATGTATACAATTAAACATAAATTAA
475022 AGTTTATGTATACAATTAAACATTAAATTAA
1 AGTTTATGTATACAATTAAACA-TAAATTAA
*
475053 AATTTATGTATA
1 AGTTTATGTATA
475065 ATTTTGAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 13 0.35
30 5 0.14
31 19 0.51
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (30 bp):
AGTTTATGTATACAATTAAACATAAATTAA
Found at i:482969 original size:15 final size:15
Alignment explanation
Indices: 482946--482976 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
482936 TTTAAATTTT
*
482946 ATTTTAAAAATTATA
1 ATTTAAAAAATTATA
482961 ATTTAAAAAATTATA
1 ATTTAAAAAATTATA
482976 A
1 A
482977 AAAAAATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTTAAAAAATTATA
Found at i:483027 original size:17 final size:18
Alignment explanation
Indices: 482993--483039 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
482983 TTCTTCTGAC
**
482993 ATTTAAAAAATCTGTAAA
1 ATTTAAAAAAAATGTAAA
483011 ATTTAAAAAAAAT-TAAA
1 ATTTAAAAAAAATGTAAA
*
483028 ATGTAAAAAAAA
1 ATTTAAAAAAAA
483040 AACTTATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (18 bp):
ATTTAAAAAAAATGTAAA
Found at i:485497 original size:3 final size:3
Alignment explanation
Indices: 485489--485519 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
485479 ATTTATTTAT
485489 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
485520 CTACATATAG
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:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:489767 original size:55 final size:53
Alignment explanation
Indices: 489669--489868 Score: 192
Period size: 55 Copynumber: 3.7 Consensus size: 53
489659 TTAAGGATAC
*
489669 CATGTAAGACCATG-CTAAGGCATGGCAATTGGTAAGGTT-TATAAGGCAAGGAAAT
1 CATGTAAGACCATGTC-AAGACATGGC-ATTGGTAA-GTTCTATAAGGCAAGG-AAT
* * * *
489724 CATGTAAGACCATGTAAAGACACGGCATTGATAAGTTACTATAAGGCAAAGG-TT
1 CATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT-CTATAAGGC-AAGGAAT
* * ** * *
489778 CCATGTAAGACCATGCCAAGGCATAACATTGGTGAGTTC-ATAAGGCAAGGATAC
1 -CATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCTATAAGGCAAGGA-AT
*
489832 CATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 CATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT
489869 TCAAAAGGAT
Statistics
Matches: 117, Mismatches: 21, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
52 4 0.03
53 41 0.35
54 9 0.08
55 59 0.50
56 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (53 bp):
CATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCTATAAGGCAAGGAAT
Found at i:489867 original size:108 final size:110
Alignment explanation
Indices: 489668--489868 Score: 289
Period size: 108 Copynumber: 1.8 Consensus size: 110
489658 TTTAAGGATA
* ** * *
489668 CCATGTAAGACCATGCTAAGGCATGGCAATTGGTAAGGTTTATAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATAACAATTGGTAAGGTTCATAAGGCAAGGAAACCATGTAAGA
*
489733 CCATGTAAAGACACGGCATTGATAAGTTACTATAAGGCAAAGGTT
66 CCATGTAAAGACACGGCAATGATAAGTTACTATAAGGCAAAGGTT
* *
489778 CCATGTAAGACCATGCCAAGGCATAAC-ATTGGTGA-GTTCATAAGGCAAGGATACCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATAACAATTGGTAAGGTTCATAAGGCAAGGAAACCATGTAAGA
* * *
489841 CCATGTCAAGACATGGCAATGGTAAGTT
66 CCATGTAAAGACACGGCAATGATAAGTT
489869 TCAAAAGGAT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
108 49 0.61
109 7 0.09
110 24 0.30
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATAACAATTGGTAAGGTTCATAAGGCAAGGAAACCATGTAAGA
CCATGTAAAGACACGGCAATGATAAGTTACTATAAGGCAAAGGTT
Found at i:490105 original size:16 final size:16
Alignment explanation
Indices: 490084--490114 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
490074 ATAAATTTGA
490084 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
490100 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
490115 AGTGAAGAAG
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:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:498342 original size:47 final size:49
Alignment explanation
Indices: 498220--498398 Score: 214
Period size: 47 Copynumber: 3.8 Consensus size: 49
498210 TGTAACCCGC
* * *
498220 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GC-GTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCAGTTCACAT
*
498266 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATG-C-AGTTCACAT
* *
498316 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA--CATTTCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCAGTTCACAT
*
498360 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATG
498399 TTCAACCATC
Statistics
Matches: 115, Mismatches: 7, Indels: 19
0.82 0.05 0.13
Matches are distributed among these distances:
43 3 0.03
44 5 0.04
45 1 0.01
46 37 0.32
47 58 0.50
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCAGTTCACAT
Found at i:498388 original size:94 final size:93
Alignment explanation
Indices: 498228--498398 Score: 297
Period size: 94 Copynumber: 1.8 Consensus size: 93
498218 GCCCATAAGT
* *
498228 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
498293 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
498321 GAACTCGGACTCAACTCAACGAGTTCGGACATTTCACATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGAC-GTTCACATCCATAAGTGAACTCGGACTCAACTCA
498386 ACGAGTTCGGATG
65 ACGAGTTCGGATG
498399 TTCAACCATC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 28 0.38
94 45 0.62
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:500368 original size:55 final size:53
Alignment explanation
Indices: 500231--500438 Score: 215
Period size: 55 Copynumber: 3.8 Consensus size: 53
500221 ATCCTTTTGA
* * *
500231 AACTTACCATTGCCATGTCTTGACATGGTTTTACATGGTATCCTTGCCTTATG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATG
* * *
500284 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGG-AACCTTTGCCTTATAG
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACC-TTGCCTTAT-G
* * **
500338 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-G
1 -AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATG
* * *
500391 AAACCTTGCCAATTGCCATGCCTT-AGCATGGTCTTACATGGTATCCTT
1 -AA-CTTACCAA-TGCCATGTCTTGA-CATGGTCTTACATGGTAACCTT
500439 AAACCCTAAT
Statistics
Matches: 129, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
52 3 0.02
53 45 0.35
54 8 0.06
55 71 0.55
56 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATG
Found at i:500375 original size:108 final size:110
Alignment explanation
Indices: 500231--500431 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 110
500221 ATCCTTTTGA
* * *
500231 AACTTACCATTGCCATGTCTTGACATGGTTTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
*
500294 -TGCCATGCCTTGGCATGGTCTTACATGGAACCTTTGCCTTATAGT
65 TTGCCATGCCTTAGCATGGTCTTACATGGAACCTTTGCCTTATAGT
* * **
500339 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTGCCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
500404 TGCCATGCCTTAGCATGGTCTTACATGG
66 TGCCATGCCTTAGCATGGTCTTACATGG
500432 TATCCTTAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.59
109 6 0.07
110 27 0.33
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTAGCATGGTCTTACATGGAACCTTTGCCTTATAGT
Found at i:501956 original size:18 final size:18
Alignment explanation
Indices: 501933--501969 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
501923 TGGTTAAGCT
501933 AACCCAAGGATTAATTTG
1 AACCCAAGGATTAATTTG
501951 AACCCAAGGATTAATTTG
1 AACCCAAGGATTAATTTG
501969 A
1 A
501970 TCAATTAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (18 bp):
AACCCAAGGATTAATTTG
Found at i:504646 original size:28 final size:27
Alignment explanation
Indices: 504606--504714 Score: 103
Period size: 28 Copynumber: 3.9 Consensus size: 27
504596 CTGCACAATT
*
504606 GATGTCTT-GCACACTAAGTGCTATACCG
1 GATGT-TTCGCACACTAAGTGCCAT-CCG
*
504634 GATGTTTCGCACACTAAGTGCCATCCTC
1 GATGTTTCGCACACTAAGTGCCATCC-G
** **
504662 GATACTTCGCACACTAAGTGCCATTTTG
1 GATGTTTCGCACACTAAGTGCCA-TCCG
* *
504690 GATGTTTCGCATACTAAGTGTCATC
1 GATGTTTCGCACACTAAGTGCCATC
504715 ATCAATACTT
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
27 5 0.08
28 60 0.91
29 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (27 bp):
GATGTTTCGCACACTAAGTGCCATCCG
Found at i:504700 original size:56 final size:56
Alignment explanation
Indices: 504614--504790 Score: 225
Period size: 56 Copynumber: 3.2 Consensus size: 56
504604 TTGATGTCTT
* ** *
504614 GCACACTAAGTGCTATACCGGATGTTTCGCACACTAAGTGCCATCCTCGATACTTC
1 GCACACTAAGTGCCATTTCGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTC
* * * *
504670 GCACACTAAGTGCCATTTTGGATGTTTCGCATACTAAGTGTCATCATCAATACTTC
1 GCACACTAAGTGCCATTTCGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTC
** *
504726 ATACACT--GTGTCATTTCGGATGTCTT-GCACACTAAGTGCCATCCTCAATACTTC
1 GCACACTAAGTGCCATTTCGGATGT-TTCGCACACTAAGTGCCATCCTCAATACTTC
504780 GCACACTAAGT
1 GCACACTAAGT
504791 CCCGTTCGTT
Statistics
Matches: 101, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
54 44 0.44
55 2 0.02
56 55 0.54
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (56 bp):
GCACACTAAGTGCCATTTCGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTC
Found at i:504774 original size:54 final size:55
Alignment explanation
Indices: 504632--504787 Score: 199
Period size: 54 Copynumber: 2.8 Consensus size: 55
504622 AGTGCTATAC
* *
504632 CGGATGTTTCGCACACTAAGTGCCATCCTCGATACTTCGCACACTAAGTGCCATTT
1 CGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTCACACACT-AGTGCCATTT
* * * * * *
504688 TGGATGTTTCGCATACTAAGTGTCATCATCAATACTTCATACACT-GTGTCATTT
1 CGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTCACACACTAGTGCCATTT
*
504742 CGGATGTCTT-GCACACTAAGTGCCATCCTCAATACTTCGCACACTA
1 CGGATGT-TTCGCACACTAAGTGCCATCCTCAATACTTCACACACTA
504788 AGTCCCGTTC
Statistics
Matches: 84, Mismatches: 14, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
54 44 0.52
55 2 0.02
56 38 0.45
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (55 bp):
CGGATGTTTCGCACACTAAGTGCCATCCTCAATACTTCACACACTAGTGCCATTT
Found at i:509593 original size:25 final size:24
Alignment explanation
Indices: 509543--509595 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
509533 TAATATTCAA
509543 TATATATAATTTATAGAATTGCAT
1 TATATATAATTTATAGAATTGCAT
* *
509567 TATATCTAATATTATTAGATTTG-AT
1 TATATATAAT-TTA-TAGAATTGCAT
509592 TATA
1 TATA
509596 ATTGAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 9 0.36
26 7 0.28
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (24 bp):
TATATATAATTTATAGAATTGCAT
Found at i:515059 original size:4 final size:4
Alignment explanation
Indices: 515050--515076 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
515040 TGTAAACATC
515050 CTTT CTTT CTTT CTTT CTTT CTTT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTT
515077 CTTCTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:518832 original size:17 final size:18
Alignment explanation
Indices: 518795--518832 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
518785 AATCCTATGC
518795 TATGCAAACCCTATGTGT
1 TATGCAAACCCTATGTGT
* *
518813 TATGCGAACCC-ATTTGT
1 TATGCAAACCCTATGTGT
518830 TAT
1 TAT
518833 TGTGATCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (18 bp):
TATGCAAACCCTATGTGT
Found at i:522447 original size:15 final size:15
Alignment explanation
Indices: 522416--522462 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
522406 TCATTCATTT
**
522416 AATATTT-TAAATTA
1 AATATTTATAAAAAA
522430 AATATTTATAAAAAA
1 AATATTTATAAAAAA
*
522445 AATATTGATAAATAAA
1 AATATTTATAAA-AAA
522461 AA
1 AA
522463 CAAAACATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 7 0.25
15 16 0.57
16 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
AATATTTATAAAAAA
Found at i:523168 original size:27 final size:26
Alignment explanation
Indices: 523137--523199 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 26
523127 GATATGGGTG
*
523137 AAAAAAATTATATAACAAATATATTTAT
1 AAAAAAATTAAATAA-AAA-ATATTTAT
*
523165 AAAAAAAATTAAATAATAAATATTTAT
1 -AAAAAAATTAAATAAAAAATATTTAT
523192 AAAAAAAT
1 AAAAAAAT
523200 ATTTAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 8 0.25
27 8 0.25
28 2 0.06
29 14 0.44
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (26 bp):
AAAAAAATTAAATAAAAAATATTTAT
Found at i:523170 original size:29 final size:27
Alignment explanation
Indices: 523137--523198 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 27
523127 GATATGGGTG
*
523137 AAAAAAATTATATAACAAATATATTTATA
1 AAAAAAATTAAATAA-AAA-ATATTTATA
*
523166 AAAAAAATTAAATAATAAATATTTATA
1 AAAAAAATTAAATAAAAAATATTTATA
523193 AAAAAA
1 AAAAAA
523199 TATTTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 15 0.48
28 2 0.06
29 14 0.45
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAAAAATTAAATAAAAAATATTTATA
Found at i:523199 original size:14 final size:14
Alignment explanation
Indices: 523137--523208 Score: 64
Period size: 14 Copynumber: 5.3 Consensus size: 14
523127 GATATGGGTG
*
523137 AAAAAAAT-TATAT
1 AAAAAAATATTTAT
*
523150 AACAAATATATTTAT
1 AA-AAAAATATTTAT
523165 AAAAAAA-A-TTA-
1 AAAAAAATATTTAT
523176 AATAATAAATATTTAT
1 AA-AA-AAATATTTAT
523192 AAAAAAATATTTA-
1 AAAAAAATATTTAT
523205 AAAA
1 AAAA
523209 TTAAATGAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
11 2 0.04
12 5 0.10
13 10 0.20
14 19 0.39
15 11 0.22
16 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAAAAATATTTAT
Found at i:523506 original size:15 final size:16
Alignment explanation
Indices: 523476--523508 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
523466 GTGGACGGAG
523476 GGGGACGGTGGGGGAA
1 GGGGACGGTGGGGGAA
*
523492 GGGGACTGT-GGGGAA
1 GGGGACGGTGGGGGAA
523507 GG
1 GG
523509 TATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.18, C:0.06, G:0.67, T:0.09
Consensus pattern (16 bp):
GGGGACGGTGGGGGAA
Found at i:528266 original size:3 final size:3
Alignment explanation
Indices: 528258--528289 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
528248 CTTAAGCTCT
528258 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
528290 TTTTTGTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:528700 original size:28 final size:28
Alignment explanation
Indices: 528668--528723 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
528658 GAAAGGCTAA
528668 AATGACTTTTTCTTTGTAAATTTAAAGG
1 AATGACTTTTTCTTTGTAAATTTAAAGG
528696 AATGACTTTTTCTTTGTAAATTTAAAGG
1 AATGACTTTTTCTTTGTAAATTTAAAGG
528724 GTTGAAGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (28 bp):
AATGACTTTTTCTTTGTAAATTTAAAGG
Found at i:531316 original size:21 final size:20
Alignment explanation
Indices: 531257--531316 Score: 50
Period size: 22 Copynumber: 2.8 Consensus size: 20
531247 CCCTCCTTCC
*
531257 TGTTAAATATTTAACAATAATTT
1 TGTTAAATA--TAA-AATAATTG
531280 TGTTAAAT-TACGAAATAAATTG
1 TGTTAAATATA--AAAT-AATTG
531302 TGTTAAATATAAAAT
1 TGTTAAATATAAAAT
531317 TGAAAGGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
20 2 0.06
21 7 0.22
22 13 0.41
23 10 0.31
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (20 bp):
TGTTAAATATAAAATAATTG
Found at i:536519 original size:33 final size:33
Alignment explanation
Indices: 536477--536539 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
536467 AACCGGGTTA
536477 GATTAAATTGGTGCTAAGAAGATTATCCTTTCG
1 GATTAAATTGGTGCTAAGAAGATTATCCTTTCG
536510 GATTAAATTGGTGCTAAGAAGATTATCCTT
1 GATTAAATTGGTGCTAAGAAGATTATCCTT
536540 ACGGCTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (33 bp):
GATTAAATTGGTGCTAAGAAGATTATCCTTTCG
Found at i:544613 original size:2 final size:2
Alignment explanation
Indices: 544606--544648 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
544596 GAAAACTTAC
544606 AT AT AT AT A- AT AT AT AT AT -T AT AT AT AT ACT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
544647 AT
1 AT
544649 CAATTTCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:544620 original size:9 final size:8
Alignment explanation
Indices: 544606--544648 Score: 63
Period size: 7 Copynumber: 5.5 Consensus size: 8
544596 GAAAACTTAC
544606 ATATATAT
1 ATATATAT
544614 A-ATATAT
1 ATATATAT
544621 ATAT-TAT
1 ATATATAT
544628 ATATATACT
1 ATATATA-T
544637 ATATATAT
1 ATATATAT
544645 ATAT
1 ATAT
544649 CAATTTCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 14 0.44
8 10 0.31
9 8 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (8 bp):
ATATATAT
Found at i:544622 original size:11 final size:11
Alignment explanation
Indices: 544606--544647 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
544596 GAAAACTTAC
544606 ATATATATAAT
1 ATATATATAAT
*
544617 ATATATATTAT
1 ATATATATAAT
544628 ATATATACT-AT
1 ATATATA-TAAT
544639 ATATATATA
1 ATATATATA
544648 TCAATTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 1 0.04
11 26 0.93
12 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATATATAAT
Found at i:552594 original size:71 final size:71
Alignment explanation
Indices: 552514--552648 Score: 243
Period size: 71 Copynumber: 1.9 Consensus size: 71
552504 CAAGTTGCCC
*
552514 AAAATAAATCTTAATTAAAACCTAAAATAGTGTAAACCTAAAATAACTCAAGAAACTCAAGTTAG
1 AAAATAAATCTTAATTAAAACCTAAAATAGTCTAAACCTAAAATAACTCAAGAAACTCAAGTTAG
552579 TTACCT
66 TTACCT
* *
552585 AAAATAAATCTTAATTAAAACCTAAAATAGTCTAAACCTAAAATAACTCGAGAAATTCAAGTTA
1 AAAATAAATCTTAATTAAAACCTAAAATAGTCTAAACCTAAAATAACTCAAGAAACTCAAGTTA
552649 TATGAACTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.27
Consensus pattern (71 bp):
AAAATAAATCTTAATTAAAACCTAAAATAGTCTAAACCTAAAATAACTCAAGAAACTCAAGTTAG
TTACCT
Found at i:552710 original size:34 final size:34
Alignment explanation
Indices: 552670--552747 Score: 147
Period size: 34 Copynumber: 2.3 Consensus size: 34
552660 AATTATCTAA
552670 AACTAAAATGATCTGAACTCGAATTAACTCAACT
1 AACTAAAATGATCTGAACTCGAATTAACTCAACT
552704 AACTAAAATGATCTGAACTCGAATTAACTCAACT
1 AACTAAAATGATCTGAACTCGAATTAACTCAACT
552738 AACTTAAAAT
1 AAC-TAAAAT
552748 CTAATTCAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 37 0.86
35 6 0.14
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (34 bp):
AACTAAAATGATCTGAACTCGAATTAACTCAACT
Found at i:552741 original size:19 final size:19
Alignment explanation
Indices: 552685--552741 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
552675 AAATGATCTG
552685 AACTCGAATTAACTCAACT
1 AACTCGAATTAACTCAACT
* *
552704 AACT--AA--AA-TGATCT
1 AACTCGAATTAACTCAACT
552718 GAACTCGAATTAACTCAACT
1 -AACTCGAATTAACTCAACT
552738 AACT
1 AACT
552742 TAAAATCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
17 4 0.14
19 10 0.36
20 4 0.14
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (19 bp):
AACTCGAATTAACTCAACT
Found at i:552908 original size:22 final size:23
Alignment explanation
Indices: 552864--552910 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
552854 TGTCCCAAAA
*
552864 AAAGTTATAAAAATCATCTTTAT
1 AAAGTTATAAAAATCATCATTAT
*
552887 AAAGTTATAAAAATTAT-ATTAT
1 AAAGTTATAAAAATCATCATTAT
552909 AA
1 AA
552911 GCATAAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAGTTATAAAAATCATCATTAT
Found at i:561791 original size:43 final size:43
Alignment explanation
Indices: 561743--561825 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
561733 TTACGCTTGG
561743 AACCATTTGCTCTTCTACGTTGCTTTAAAGTACCTATGTTTGC
1 AACCATTTGCTCTTCTACGTTGCTTTAAAGTACCTATGTTTGC
561786 AACCATTTGCTCTTCTACGTTGCTTTAAAGTACCTATGTT
1 AACCATTTGCTCTTCTACGTTGCTTTAAAGTACCTATGTT
561826 CGATGCGTAT
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:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (43 bp):
AACCATTTGCTCTTCTACGTTGCTTTAAAGTACCTATGTTTGC
Found at i:565245 original size:30 final size:30
Alignment explanation
Indices: 565165--565245 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
565155 CAGGAGGCTC
* * * *
565165 ATCAGGTGGTGGGGGAGGAACTTGTTCATT
1 ATCAGGAGGTGGTGGAGGAATTTGTTCAGT
* *
565195 ATCAGGAGGAGGTGGTGGAATTTGTTCAGT
1 ATCAGGAGGTGGTGGAGGAATTTGTTCAGT
565225 ATCAGGAGGTGGTGGAGGAAT
1 ATCAGGAGGTGGTGGAGGAAT
565246 CCACTCCTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.23, C:0.07, G:0.42, T:0.27
Consensus pattern (30 bp):
ATCAGGAGGTGGTGGAGGAATTTGTTCAGT
Found at i:574309 original size:21 final size:21
Alignment explanation
Indices: 574268--574310 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
574258 TGTATTTTCA
* *
574268 TAATTTTTTTACAAGTGTGTC
1 TAATGTTTTTACAAGTATGTC
574289 TAATGTTTTTACCAA-TATGTC
1 TAATGTTTTTA-CAAGTATGTC
574310 T
1 T
574311 TTATCTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.51
Consensus pattern (21 bp):
TAATGTTTTTACAAGTATGTC
Found at i:581433 original size:4 final size:4
Alignment explanation
Indices: 581418--581465 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
581408 CTGCAAATTT
* *
581418 CATA CTTA CATA CAT- -ATA TATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
581464 CA
1 CA
581466 GATTCCCTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
2 2 0.05
4 37 0.95
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (4 bp):
CATA
Found at i:582789 original size:72 final size:72
Alignment explanation
Indices: 582635--582772 Score: 197
Period size: 72 Copynumber: 1.9 Consensus size: 72
582625 TATTTTTGAT
* **
582635 TTGCCAAACCTCTTGCAACTAACTCATTTAGACTTGTCGATGAACCAATTGAGTGGACAAATTCC
1 TTGCGAAACCTCTTGCAACTAACTCATTTAGACTTGTCGAACAACCAATTGAGTGGACAAATTCC
582700 AAGATCA
66 AAGATCA
* * * *
582707 TTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTC-ACACAACCAATTGAGTGGACAAGTTC
1 TTGCGAAACCTCTTGCAACTAACTCATTTAGACTTGTCGA-ACAACCAATTGAGTGGACAAATTC
582771 CA
65 CA
582773 TTGTCAATTC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 1 0.02
72 57 0.98
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (72 bp):
TTGCGAAACCTCTTGCAACTAACTCATTTAGACTTGTCGAACAACCAATTGAGTGGACAAATTCC
AAGATCA
Found at i:586021 original size:18 final size:17
Alignment explanation
Indices: 586000--586033 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
585990 TTTTAAGAAA
586000 ATTATTTATTTATTTTTT
1 ATTATTTA-TTATTTTTT
586018 ATTATTTATTATTTTT
1 ATTATTTATTATTTTT
586034 CAATTTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTATTTATTATTTTTT
Found at i:592250 original size:17 final size:17
Alignment explanation
Indices: 592228--592262 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
592218 GTGGTGCCAC
592228 TTGACCAACCGGCAACA
1 TTGACCAACCGGCAACA
592245 TTGACCAACCGGCAACA
1 TTGACCAACCGGCAACA
592262 T
1 T
592263 CAGCTGTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.14
Consensus pattern (17 bp):
TTGACCAACCGGCAACA
Found at i:600582 original size:15 final size:16
Alignment explanation
Indices: 600557--600587 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
600547 GCAACAACTT
600557 AGAGCGGAGGCAGCAG
1 AGAGCGGAGGCAGCAG
600573 AGAG-GGAGGCAGCAG
1 AGAGCGGAGGCAGCAG
600588 CTACAGCGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.16, G:0.52, T:0.00
Consensus pattern (16 bp):
AGAGCGGAGGCAGCAG
Found at i:602602 original size:21 final size:21
Alignment explanation
Indices: 602572--602611 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
602562 GTGGTGAAAA
602572 TTTATTTTTTTAA-AATAAAT
1 TTTATTTTTTTAAGAATAAAT
602592 TTTATTTTTTTTAAGAATAA
1 TTTA-TTTTTTTAAGAATAA
602612 TAATTTCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTATTTTTTTAAGAATAAAT
Found at i:604619 original size:30 final size:30
Alignment explanation
Indices: 604577--604652 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
604567 CGGAGATTTT
*
604577 GCAGGCGACGATGATGTTGTTGGAGAACTC
1 GCAGGGGACGATGATGTTGTTGGAGAACTC
*
604607 GC-GGGAGGCGATGATGTTGTTGGAGAACTC
1 GCAGGG-GACGATGATGTTGTTGGAGAACTC
604637 GCAGGGGACGATGATG
1 GCAGGGGACGATGATG
604653 AAGGAGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 2 0.05
30 36 0.88
31 3 0.07
ACGTcount: A:0.22, C:0.14, G:0.42, T:0.21
Consensus pattern (30 bp):
GCAGGGGACGATGATGTTGTTGGAGAACTC
Found at i:608121 original size:3 final size:3
Alignment explanation
Indices: 608086--608156 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
608076 TTCATTTTTC
* *
608086 TCT TCT TCAT TC- TGT TCC TCT TCCT TC- TCT TCT TCT TCCT T-T TCT
1 TCT TCT TC-T TCT TCT TCT TCT T-CT TCT TCT TCT TCT T-CT TCT TCT
* *
608131 TCT TCT TCC TCC TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
608157 AGACTCATCC
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
2 5 0.09
3 42 0.75
4 9 0.16
ACGTcount: A:0.01, C:0.38, G:0.01, T:0.59
Consensus pattern (3 bp):
TCT
Found at i:608122 original size:30 final size:30
Alignment explanation
Indices: 608086--608153 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
608076 TTCATTTTTC
* *
608086 TCTTCTTCATTCTGTTCCTCTTCCTTCTCT
1 TCTTCTTCATTCTCTTCCTCTTCCTCCTCT
* * *
608116 TCTTCTTCCTTTTCTTCTTCTTCCTCCTCT
1 TCTTCTTCATTCTCTTCCTCTTCCTCCTCT
608146 TCTTCTTC
1 TCTTCTTC
608154 TTCAGACTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.01, C:0.38, G:0.01, T:0.59
Consensus pattern (30 bp):
TCTTCTTCATTCTCTTCCTCTTCCTCCTCT
Found at i:608136 original size:18 final size:18
Alignment explanation
Indices: 608085--608156 Score: 74
Period size: 18 Copynumber: 3.8 Consensus size: 18
608075 TTTCATTTTT
608085 CTCTTCTTCATTCTGTTCCTC
1 CTCTTCTTC-TTC--TTCCTC
* *
608106 TTCCTTC-TCTTCTTCTTC
1 CT-CTTCTTCTTCTTCCTC
*
608124 CTTTTCTTCTTCTTCCTC
1 CTCTTCTTCTTCTTCCTC
608142 CTCTTCTTCTTCTTC
1 CTCTTCTTCTTCTTC
608157 AGACTCATCC
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
17 3 0.07
18 30 0.70
20 3 0.07
21 3 0.07
22 4 0.09
ACGTcount: A:0.01, C:0.39, G:0.01, T:0.58
Consensus pattern (18 bp):
CTCTTCTTCTTCTTCCTC
Found at i:610738 original size:21 final size:21
Alignment explanation
Indices: 610712--610761 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
610702 CTTCTTGCTC
610712 CTCTTCATCATCCCCATCCTT
1 CTCTTCATCATCCCCATCCTT
*
610733 CTCTTCATCATCTCCATCCTT
1 CTCTTCATCATCCCCATCCTT
*
610754 TTCTTCAT
1 CTCTTCAT
610762 GCTCCTCCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.14, C:0.42, G:0.00, T:0.44
Consensus pattern (21 bp):
CTCTTCATCATCCCCATCCTT
Found at i:612966 original size:16 final size:16
Alignment explanation
Indices: 612922--612966 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
612912 CATATTGATT
*
612922 TTTTTGAATTTTTATA
1 TTTTTGAATTTTTAAA
* *
612938 TTTTTTAAATTTTAAA
1 TTTTTGAATTTTTAAA
612954 TTTTTGAATTTTT
1 TTTTTGAATTTTT
612967 TTTGTAACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (16 bp):
TTTTTGAATTTTTAAA
Found at i:613340 original size:30 final size:28
Alignment explanation
Indices: 613282--613343 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 28
613272 TACAAGCTAT
**
613282 TTTTAAAAATTAATAACCATTTAAATTA
1 TTTTAAAAATTAATAACCATACAAATTA
*
613310 TTTTAAAAATTATATTAACTATACAAATTA
1 TTTTAAAAATTA-A-TAACCATACAAATTA
613340 TTTT
1 TTTT
613344 TTTAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 12 0.41
29 1 0.03
30 16 0.55
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTTAAAAATTAATAACCATACAAATTA
Found at i:614243 original size:15 final size:15
Alignment explanation
Indices: 614223--614253 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
614213 CTATCATCTT
614223 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
614238 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
614253 T
1 T
614254 TACAACGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (15 bp):
TAACTGCTAACAGAC
Found at i:614287 original size:20 final size:20
Alignment explanation
Indices: 614262--614303 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
614252 CTTACAACGG
*
614262 TACAACGGTTTTGACTATAT
1 TACAACGGCTTTGACTATAT
*
614282 TACAACTGCTTTGACTATAT
1 TACAACGGCTTTGACTATAT
614302 TA
1 TA
614304 ACTCTAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
TACAACGGCTTTGACTATAT
Found at i:617693 original size:18 final size:18
Alignment explanation
Indices: 617660--617694 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
617650 ACCAGCAGAT
* *
617660 GGCATACTGACTTGTTGG
1 GGCATACTAACCTGTTGG
617678 GGCATACTAACCTGTTG
1 GGCATACTAACCTGTTG
617695 TGGAGAGCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (18 bp):
GGCATACTAACCTGTTGG
Found at i:618956 original size:15 final size:15
Alignment explanation
Indices: 618936--618966 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
618926 CTATCATCTT
618936 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
618951 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
618966 T
1 T
618967 TACAACGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (15 bp):
TAACTGCTAACAGAC
Found at i:619000 original size:20 final size:20
Alignment explanation
Indices: 618975--619016 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
618965 CTTACAACGG
*
618975 TACAACGGTTTTGACTATAT
1 TACAACGGCTTTGACTATAT
*
618995 TACAACTGCTTTGACTATAT
1 TACAACGGCTTTGACTATAT
619015 TA
1 TA
619017 ACTCTAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
TACAACGGCTTTGACTATAT
Found at i:623540 original size:15 final size:14
Alignment explanation
Indices: 623483--623542 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
623473 TATATACTTG
623483 TAATTAAAATATAAT
1 TAATTAAAAT-TAAT
* * *
623498 TAATCATAATTATT
1 TAATTAAAATTAAT
*
623512 TAATTAAATTTTAAT
1 TAATTAAA-ATTAAT
623527 TAATTAAAAGTTAAT
1 TAATTAAAA-TTAAT
623542 T
1 T
623543 GCAATTAACA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
14 9 0.26
15 26 0.74
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
TAATTAAAATTAAT
Found at i:638202 original size:19 final size:19
Alignment explanation
Indices: 638162--638202 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
638152 TTTTTTATAT
**
638162 TTTTCCGTAAAAAATAGTA
1 TTTTCCGTAAAAAATAAAA
*
638181 TTTTCCTTAAAAAATAAAA
1 TTTTCCGTAAAAAATAAAA
638200 TTT
1 TTT
638203 AAAATTAAAC
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:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTTCCGTAAAAAATAAAA
Found at i:640667 original size:15 final size:16
Alignment explanation
Indices: 640639--640668 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
640629 CTGAGTCAGC
640639 TTTCTATGGAACTGAG
1 TTTCTATGGAACTGAG
640655 TTTCTAT-GAACTGA
1 TTTCTATGGAACTGA
640669 CTCAGTGATT
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:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (16 bp):
TTTCTATGGAACTGAG
Found at i:647696 original size:17 final size:18
Alignment explanation
Indices: 647674--647712 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
647664 AATCGAATCG
647674 AATTATTC-AATTATTTA
1 AATTATTCGAATTATTTA
* *
647691 AATTATTCGAGTTATTTG
1 AATTATTCGAATTATTTA
647709 AATT
1 AATT
647713 TTGAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (18 bp):
AATTATTCGAATTATTTA
Found at i:647841 original size:19 final size:20
Alignment explanation
Indices: 647797--647860 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
647787 AAAAAAAATC
647797 AAATAATTTTTTAAAAGTTCA
1 AAATAA-TTTTTAAAAGTTCA
*
647818 CAATAATTTTTAAAA-TTCA
1 AAATAATTTTTAAAAGTTCA
* *
647837 AAAT-ATTTATAAAAATTTCA
1 AAATAATTT-TTAAAAGTTCA
647857 AAAT
1 AAAT
647861 TTATATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 4 0.11
19 12 0.32
20 17 0.45
21 5 0.13
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATAATTTTTAAAAGTTCA
Found at i:647868 original size:24 final size:23
Alignment explanation
Indices: 647839--647897 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
647829 AAAATTCAAA
*
647839 ATATTTATAAAAATTTCAAAATTT
1 ATATTTAAAAAAATTT-AAAATTT
647863 ATATTTAAAAAAATTTAAAATTT
1 ATATTTAAAAAAATTTAAAATTT
*
647886 -TA-TAAAAAAAAT
1 ATATTTAAAAAAAT
647898 ATATAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 9 0.27
22 2 0.06
23 7 0.21
24 15 0.45
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATTTAAAAAAATTTAAAATTT
Found at i:647894 original size:20 final size:20
Alignment explanation
Indices: 647829--647895 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
647819 AATAATTTTT
*
647829 AAAATTCAAAATATTTAT--A
1 AAAATTTAAAAT-TTTATAAA
647848 AAAATTTCAAAATTTATATTTAAA
1 AAAATTT-AAAATTT-TA--TAAA
647872 AAAATTTAAAATTTTATAAA
1 AAAATTTAAAATTTTATAAA
647892 AAAA
1 AAAA
647896 ATATATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
19 8 0.20
20 15 0.37
22 3 0.07
23 7 0.17
24 8 0.20
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATTTAAAATTTTATAAA
Found at i:651365 original size:12 final size:12
Alignment explanation
Indices: 651348--651374 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
651338 ATTTGATTAA
651348 AAAATTTAGTTT
1 AAAATTTAGTTT
651360 AAAATTTAGTTT
1 AAAATTTAGTTT
651372 AAA
1 AAA
651375 TTCGTCCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (12 bp):
AAAATTTAGTTT
Found at i:651969 original size:6 final size:6
Alignment explanation
Indices: 651924--651959 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
651914 GGCCAAATTT
*
651924 CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CATTTC
1 CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC CCTTTC
651960 TTTTCCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (6 bp):
CCTTTC
Found at i:653865 original size:23 final size:24
Alignment explanation
Indices: 653830--653880 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
653820 ACAAGGTAAG
*
653830 AAAAGAAATAAAG-AAATAAAAGA
1 AAAAGAAACAAAGAAAATAAAAGA
*
653853 AAAAGGAACAAAGAAAATAAAAGA
1 AAAAGAAACAAAGAAAATAAAAGA
653877 AAAA
1 AAAA
653881 AATTAAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (24 bp):
AAAAGAAACAAAGAAAATAAAAGA
Found at i:653888 original size:23 final size:21
Alignment explanation
Indices: 653827--653888 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 21
653817 AGAACAAGGT
653827 AAGAAAAGAAATAAAGAAATAA
1 AAGAAAA-AAATAAAGAAATAA
*
653849 AAGAAAAAGGAACAAAGAAAATAA
1 AAGAAAAA--AATAAAG-AAATAA
653873 AAGAAAAAAATTAAAG
1 AAGAAAAAAA-TAAAG
653889 TGTTCAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 1 0.03
22 9 0.26
23 10 0.29
24 14 0.41
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.08
Consensus pattern (21 bp):
AAGAAAAAAATAAAGAAATAA
Found at i:657868 original size:20 final size:21
Alignment explanation
Indices: 657843--657883 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
657833 TTAAGTATCA
657843 AATTG-AAAAATCTGCAATGT
1 AATTGAAAAAATCTGCAATGT
*
657863 AATTGAAAAAATGTGCAATGT
1 AATTGAAAAAATCTGCAATGT
657884 TTCAAGACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.29
Consensus pattern (21 bp):
AATTGAAAAAATCTGCAATGT
Found at i:663759 original size:21 final size:21
Alignment explanation
Indices: 663730--663784 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
663720 TGACTTTTTA
663730 AAGGTATGGGTAGATATGGGC
1 AAGGTATGGGTAGATATGGGC
*
663751 AATGTATGGGTAGATATGGGC
1 AAGGTATGGGTAGATATGGGC
663772 AAGGTATGGGTAG
1 AAGGTATGGGTAG
663785 CTTCTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.04, G:0.42, T:0.25
Consensus pattern (21 bp):
AAGGTATGGGTAGATATGGGC
Found at i:664526 original size:38 final size:38
Alignment explanation
Indices: 664475--664552 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
664465 TATACCTGCT
664475 CACTATACTAACTGCTTGTGAAATATCGGGCTTGTACA
1 CACTATACTAACTGCTTGTGAAATATCGGGCTTGTACA
*
664513 CACTATACTAACTGCTTGTGAAATATCGGGTTTGTACA
1 CACTATACTAACTGCTTGTGAAATATCGGGCTTGTACA
664551 CA
1 CA
664553 TCACTGCATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (38 bp):
CACTATACTAACTGCTTGTGAAATATCGGGCTTGTACA
Found at i:665168 original size:12 final size:12
Alignment explanation
Indices: 665151--665176 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
665141 AAAACGTGAT
665151 CTTCACATCAAG
1 CTTCACATCAAG
665163 CTTCACATCAAG
1 CTTCACATCAAG
665175 CT
1 CT
665177 GAACTAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.35, G:0.08, T:0.27
Consensus pattern (12 bp):
CTTCACATCAAG
Found at i:679789 original size:33 final size:35
Alignment explanation
Indices: 679752--679848 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
679742 ATAGTTATAT
679752 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
679785 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
679820 --AAATATTTAAAATTTATATTTTATATATT
1 TTAAATATTTAAAA--TATAATTTATATATT
679849 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 7 0.14
35 10 0.20
37 5 0.10
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:680089 original size:13 final size:13
Alignment explanation
Indices: 680033--680096 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
680023 TAAACCAAAA
*
680033 TTTTCAAAATCAC
1 TTTTCAAAAGCAC
* *
680046 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
*
680059 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
*
680072 TTTTCAAGAGCAC
1 TTTTCAAAAGCAC
680085 TTTTCAAAAGCA
1 TTTTCAAAAGCA
680097 TTGCCAAACT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 5 0.12
13 32 0.78
14 4 0.10
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.34
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:684267 original size:9 final size:9
Alignment explanation
Indices: 684253--684320 Score: 82
Period size: 9 Copynumber: 7.6 Consensus size: 9
684243 ATAAGTATAA
*
684253 AATTAATCG
1 AATTAACCG
684262 AATTAACCG
1 AATTAACCG
**
684271 AATTAATTG
1 AATTAACCG
*
684280 AAGTAACCG
1 AATTAACCG
*
684289 AATTAAGCG
1 AATTAACCG
*
684298 AATTACCCG
1 AATTAACCG
684307 AATTAACCG
1 AATTAACCG
684316 AATTA
1 AATTA
684321 TTTGTATAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 48 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:684276 original size:18 final size:18
Alignment explanation
Indices: 684253--684320 Score: 91
Period size: 18 Copynumber: 3.8 Consensus size: 18
684243 ATAAGTATAA
684253 AATTAATCGAATTAACCG
1 AATTAATCGAATTAACCG
* *
684271 AATTAATTGAAGTAACCG
1 AATTAATCGAATTAACCG
* *
684289 AATTAAGCGAATTACCCG
1 AATTAATCGAATTAACCG
*
684307 AATTAACCGAATTA
1 AATTAATCGAATTA
684321 TTTGTATAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.26
Consensus pattern (18 bp):
AATTAATCGAATTAACCG
Found at i:690164 original size:7 final size:7
Alignment explanation
Indices: 690149--690215 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
690139 AATTAGTTGT
*
690149 TTTAGGG
1 TTTATGG
690156 TTTATGG
1 TTTATGG
690163 -TTAGTGG
1 TTTA-TGG
*
690170 TTTAGGG
1 TTTATGG
690177 TTTATGG
1 TTTATGG
*
690184 -TTAGTAG
1 TTTA-TGG
*
690191 TTTAGGG
1 TTTATGG
690198 TTTATGG
1 TTTATGG
690205 -TTAGTGG
1 TTTA-TGG
690212 TTTA
1 TTTA
690216 GGATTTTAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
6 9 0.19
7 29 0.62
8 9 0.19
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.49
Consensus pattern (7 bp):
TTTATGG
Found at i:690175 original size:21 final size:21
Alignment explanation
Indices: 690149--690217 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
690139 AATTAGTTGT
690149 TTTAGGGTTTATGGTTAGTGG
1 TTTAGGGTTTATGGTTAGTGG
*
690170 TTTAGGGTTTATGGTTAGTAG
1 TTTAGGGTTTATGGTTAGTGG
690191 TTTAGGGTTTATGGTTAGTGG
1 TTTAGGGTTTATGGTTAGTGG
690212 TTTAGG
1 TTTAGG
690218 ATTTTAGGGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TTTAGGGTTTATGGTTAGTGG
Found at i:690321 original size:19 final size:18
Alignment explanation
Indices: 690299--690357 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
690289 TGGTTAGTTA
690299 ATTAAATTAGGGTTATTCG
1 ATTAAATTAGGGTTATT-G
* *
690318 ATTAAATGAGCGTTAATTG
1 ATTAAATTAGGGTT-ATTG
*
690337 ATTAATTTAGGGTTAATTG
1 ATTAAATTAGGGTT-ATTG
690356 AT
1 AT
690358 ACATAATGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 31 0.91
20 3 0.09
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.42
Consensus pattern (18 bp):
ATTAAATTAGGGTTATTG
Found at i:690748 original size:125 final size:126
Alignment explanation
Indices: 690479--690976 Score: 890
Period size: 127 Copynumber: 4.0 Consensus size: 126
690469 TTAGGTTAAT
690479 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
1 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
** *
690544 TTTGGAAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAATAGTTCGTAGAAAAATAATTC
66 TTCAGAAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGTTCGTAGAAAAATAATTC
*
690605 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGTTTCAAGCAGGATGCACTGTCAGCAAAAT
1 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
*
690670 TTC-GAAAAAAGCTCCCACGTGGACGTGCTTTTGCTACAGTAGTTCGTAGAAAAATAATTC
66 TTCAGAAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGTTCGTAGAAAAATAATTC
*
690730 TGAGTAGACGTTTTTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
1 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
*
690795 TTCAGAAAAAAAGCTCCCACGTGGAGGCGCTTTTGCTACAGTAGTTCGTAGAAAAATAATTC
66 TTCAG-AAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGTTCGTAGAAAAATAATTC
*
690857 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAGCGCTTCAAGCAGGATGCACTGTCAGCAAAAT
1 TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
**
690922 TTCAGAAAAAAAATCCCACGTGGACGCGCTTTTGCTACAGTAGTTCGTAGAAAAA
66 TTCAGAAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGTTCGTAGAAAAA
690977 CTGAGGCTAT
Statistics
Matches: 357, Mismatches: 13, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
125 121 0.34
126 114 0.32
127 122 0.34
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (126 bp):
TGAGTAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAAT
TTCAGAAAAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGTTCGTAGAAAAATAATTC
Found at i:692426 original size:21 final size:20
Alignment explanation
Indices: 692400--692448 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
692390 ATTAAATTAA
692400 AAAATTAAATTTGCATAAAT
1 AAAATTAAATTTGCATAAAT
*
692420 GAAAATTAAATTTTCATAAAT
1 -AAAATTAAATTTGCATAAAT
692441 -AAATTAAA
1 AAAATTAAA
692449 GTATCACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 8 0.30
21 19 0.70
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (20 bp):
AAAATTAAATTTGCATAAAT
Done.