Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 102 of 290
Found at i:31555059 original size:28 final size:28
Alignment explanation
Indices: 31555028--31555083 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
31555018 ATAAGTTGAG
31555028 AAAGACTTT-TTTTTGCTCTTTCCATCCA
1 AAAGACTTTGTTTTT-CTCTTTCCATCCA
31555056 AAAGACTTTGTTTTTCTCTTTCCATCCA
1 AAAGACTTTGTTTTTCTCTTTCCATCCA
31555084 CCACCCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.46
Consensus pattern (28 bp):
AAAGACTTTGTTTTTCTCTTTCCATCCA
Found at i:31562667 original size:31 final size:31
Alignment explanation
Indices: 31562611--31562711 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 31
31562601 CTAGTAGGAT
* * * *
31562611 GCGAAGCTAGCGGAAGTGAAACTAGCAGAAA
1 GCGAAGCTAACGGGATTGAAGCTAGCAGAAA
31562642 GCGAAGCTAACGGGATTGAAGCTAGCA-AGAA
1 GCGAAGCTAACGGGATTGAAGCTAGCAGA-AA
* * * *
31562673 GC-AAAC-AAGTGGGATCGAAGCTAGCGGAAA
1 GCGAAGCTAA-CGGGATTGAAGCTAGCAGAAA
*
31562703 GCAAAGCTA
1 GCGAAGCTA
31562712 GCGAGATCGC
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
29 2 0.04
30 22 0.39
31 31 0.55
32 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.32, T:0.11
Consensus pattern (31 bp):
GCGAAGCTAACGGGATTGAAGCTAGCAGAAA
Found at i:31564735 original size:30 final size:30
Alignment explanation
Indices: 31564695--31564755 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
31564685 GGTTAAGAGA
31564695 ATTTTCTAAGTCATTAACAGGAAGGCATAT
1 ATTTTCTAAGTCATTAACAGGAAGGCATAT
* *
31564725 ATTTTGTAAGTTATTAACAGGAAGGCATAT
1 ATTTTCTAAGTCATTAACAGGAAGGCATAT
31564755 A
1 A
31564756 CTTAGCATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (30 bp):
ATTTTCTAAGTCATTAACAGGAAGGCATAT
Found at i:31566644 original size:38 final size:39
Alignment explanation
Indices: 31566576--31566654 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
31566566 ATGAAAAGAT
31566576 AAGAAAAATGCCAAAAAAAAAACTTAAATTTTTTTTAAA
1 AAGAAAAATGCCAAAAAAAAAACTTAAATTTTTTTTAAA
*
31566615 AAGAAAAATGCCAAAAATAAAACTT-AATTTTTTTTAAA
1 AAGAAAAATGCCAAAAAAAAAACTTAAATTTTTTTTAAA
31566653 AA
1 AA
31566655 TGATAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 15 0.38
39 24 0.62
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (39 bp):
AAGAAAAATGCCAAAAAAAAAACTTAAATTTTTTTTAAA
Found at i:31566891 original size:14 final size:14
Alignment explanation
Indices: 31566861--31566889 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31566851 TATATACTAA
31566861 TTATTTTATTTATT
1 TTATTTTATTTATT
31566875 TTATTTTA-TTATT
1 TTATTTTATTTATT
31566888 TT
1 TT
31566890 TAATTTTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTTATTTATT
Found at i:31572619 original size:42 final size:43
Alignment explanation
Indices: 31572463--31572620 Score: 155
Period size: 42 Copynumber: 3.7 Consensus size: 43
31572453 TATGTGTTAT
* * *
31572463 CGTGTAAGACAACGTCTGGGATGTTGGCATCGAT-TTGTGACTTA
1 CGTGTAAGACCACGTCTAGGACGTTGGCATCGATATT-TGA-TTA
* * * *
31572507 CGTGTAAGACCATGTCTAGGACATTGGCATCG-TATATGATTT
1 CGTGTAAGACCACGTCTAGGACGTTGGCATCGATATTTGATTA
**
31572549 CGTGTAAGACC-CTGTCCGGGACAG-TGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-GTCTAGGAC-GTTGGCATCGATATTTGATTA
*
31572592 CATGTAAGACCACGTCT-GGACGTTGGCAT
1 CGTGTAAGACCACGTCTAGGACGTTGGCAT
31572621 TGTACGAGCT
Statistics
Matches: 93, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 38 0.41
43 25 0.27
44 29 0.31
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTAGGACGTTGGCATCGATATTTGATTA
Found at i:31575601 original size:73 final size:73
Alignment explanation
Indices: 31575474--31575616 Score: 232
Period size: 73 Copynumber: 2.0 Consensus size: 73
31575464 TCGACCATGG
** * *
31575474 AGGAAGATAATGACATTGTTGATACCGAAAAATGATTGCCTAAGGGATCGTGCTAGGTACATCTT
1 AGGAAGATAATGACATTGTTGATACCGAAAAACAATTGCCCAAGGGATCATGCTAGGTACATCTT
31575539 CACGCGAT
66 CACGCGAT
* *
31575547 AGGAAGATAATGACATTGTTGATACTGAAAAACAATTGCCCAAGGGGTCATGCTAGGTACATCTT
1 AGGAAGATAATGACATTGTTGATACCGAAAAACAATTGCCCAAGGGATCATGCTAGGTACATCTT
31575612 CACGC
66 CACGC
31575617 CATAATGACG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (73 bp):
AGGAAGATAATGACATTGTTGATACCGAAAAACAATTGCCCAAGGGATCATGCTAGGTACATCTT
CACGCGAT
Found at i:31578364 original size:23 final size:25
Alignment explanation
Indices: 31578325--31578371 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
31578315 CTTTTAAAAT
*
31578325 ACCCTAAATCCT-AAAAAAATAAAG
1 ACCCTAAACCCTAAAAAAAATAAAG
31578349 ACCCT-AACCCTAAAAAAAATAAA
1 ACCCTAAACCCTAAAAAAAATAAA
31578372 AGCCTTAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.60, C:0.23, G:0.02, T:0.15
Consensus pattern (25 bp):
ACCCTAAACCCTAAAAAAAATAAAG
Found at i:31578718 original size:18 final size:18
Alignment explanation
Indices: 31578697--31578732 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31578687 AATTTTTAAT
31578697 ATTTTTTTATAAATTTTA
1 ATTTTTTTATAAATTTTA
*
31578715 ATTTTTTTATAATTTTTA
1 ATTTTTTTATAAATTTTA
31578733 TTTATGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTTTATAAATTTTA
Found at i:31578735 original size:17 final size:17
Alignment explanation
Indices: 31578696--31578751 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 17
31578686 GAATTTTTAA
31578696 TATTTTTTTATAAATTTT
1 TATTTTTTTAT-AATTTT
*
31578714 AATTTTTTTATAATTTT
1 TATTTTTTTATAATTTT
*
31578731 TATTTATGTTTAGAATTTT
1 TATTT-T-TTTATAATTTT
31578750 TA
1 TA
31578752 AAAGTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 10 0.30
18 11 0.33
19 12 0.36
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (17 bp):
TATTTTTTTATAATTTT
Found at i:31579734 original size:16 final size:17
Alignment explanation
Indices: 31579710--31579745 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
31579700 TTTTTCATTT
31579710 TTTTCACACTTCAATCC
1 TTTTCACACTTCAATCC
31579727 TTTT-ACACTTCAATCC
1 TTTTCACACTTCAATCC
31579743 TTT
1 TTT
31579746 CAATATTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTCACACTTCAATCC
Found at i:31579785 original size:11 final size:11
Alignment explanation
Indices: 31579740--31579793 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
31579730 TACACTTCAA
*
31579740 TCCTTTCAATAT
1 TCCTCTCAA-AT
*
31579752 T-CTCTCAAGT
1 TCCTCTCAAAT
*
31579762 TTCTCTCAAAT
1 TCCTCTCAAAT
31579773 TCCTCTCAAAT
1 TCCTCTCAAAT
*
31579784 TCCTTTCAAA
1 TCCTCTCAAA
31579794 GCTCTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
10 2 0.06
11 33 0.92
12 1 0.03
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.43
Consensus pattern (11 bp):
TCCTCTCAAAT
Found at i:31579792 original size:22 final size:21
Alignment explanation
Indices: 31579740--31579793 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
31579730 TACACTTCAA
*
31579740 TCCTTTCAATATTCTCTCAAGT
1 TCCTTTCAA-ATTCTCTCAAAT
* *
31579762 TTCTCTCAAATTCCTCTCAAAT
1 TCCTTTCAAATT-CTCTCAAAT
31579784 TCCTTTCAAA
1 TCCTTTCAAA
31579794 GCTCTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.43
Consensus pattern (21 bp):
TCCTTTCAAATTCTCTCAAAT
Found at i:31579849 original size:15 final size:14
Alignment explanation
Indices: 31579829--31579858 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31579819 GCTCTATTTA
*
31579829 AATTTTTTCTAAAT
1 AATTTTTTTTAAAT
31579843 AATTTTTTTTAAAT
1 AATTTTTTTTAAAT
31579857 AA
1 AA
31579859 AAAAATATTC
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:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTTTTTTTAAAT
Found at i:31580963 original size:7 final size:7
Alignment explanation
Indices: 31580951--31580976 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31580941 TAGTCGATTC
31580951 GTATTTA
1 GTATTTA
31580958 GTATTTA
1 GTATTTA
31580965 GTATTTA
1 GTATTTA
31580972 GTATT
1 GTATT
31580977 ATGTATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:31581516 original size:30 final size:31
Alignment explanation
Indices: 31581479--31581570 Score: 118
Period size: 30 Copynumber: 3.1 Consensus size: 31
31581469 GACGCGGGCT
* *
31581479 CATCAACAATGCCCACATAATCACCGGT-CC
1 CATCAACAGTGCCCACACAATCACCGGTGCC
* * *
31581509 GATCAACAGTGCCCATACAATCACC-ATGCC
1 CATCAACAGTGCCCACACAATCACCGGTGCC
31581539 CATCAACAGTGCCCACACAATCACCGG-GCC
1 CATCAACAGTGCCCACACAATCACCGGTGCC
31581569 CA
1 CA
31581571 GCACTTCGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.33, C:0.40, G:0.13, T:0.14
Consensus pattern (31 bp):
CATCAACAGTGCCCACACAATCACCGGTGCC
Found at i:31582779 original size:20 final size:20
Alignment explanation
Indices: 31582754--31582799 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
31582744 TTGTTAATTT
31582754 CCTGCACCATACATGGCCTC
1 CCTGCACCATACATGGCCTC
31582774 CCTGCACCATACATGGCCTC
1 CCTGCACCATACATGGCCTC
31582794 CCTGCA
1 CCTGCA
31582800 TTTGGCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.46, G:0.15, T:0.20
Consensus pattern (20 bp):
CCTGCACCATACATGGCCTC
Found at i:31585402 original size:126 final size:126
Alignment explanation
Indices: 31585239--31585616 Score: 632
Period size: 125 Copynumber: 3.0 Consensus size: 126
31585229 GCCAAATAGG
* * * *
31585239 AACTACTGTAGAAAAAAAAGCGTCCATGTGGGAGCTTTTTTTAGTACTTTTGCTAATAGTGCATC
1 AACTACTGTAGAAAAAAAA-CGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATC
*
31585304 TTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
65 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
* *
31585366 AACTACTGTAGAAAAAAAATGTCCACGTGAGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
1 AACTACTGTAGAAAAAAAACGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
*
31585431 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAACTATTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
* * *
31585492 AATTACTATAG-AAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
1 AACTACTGTAGAAAAAAAACGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
*
31585556 TGCTTGAAGCATTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
31585617 TACGTCTTCT
Statistics
Matches: 236, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
125 109 0.46
126 108 0.46
127 19 0.08
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (126 bp):
AACTACTGTAGAAAAAAAACGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
Found at i:31585577 original size:125 final size:126
Alignment explanation
Indices: 31585239--31585616 Score: 623
Period size: 126 Copynumber: 3.0 Consensus size: 126
31585229 GCCAAATAGG
* * * * *
31585239 AACTACTGTAGAAAAAAAAGCGTCCATGTGGGAGCTTTTTTTAGTACTTTTGCTAATAGTGCATC
1 AACTACTATAG-AAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATC
*
31585304 TTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
65 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
* ** *
31585366 AACTACTGTAGAAAAAAAATGTCCACGTGAGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
1 AACTACTATAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
*
31585431 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAACTATTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
*
31585492 AATTACTATAG-AAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
1 AACTACTATAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
*
31585556 TGCTTGAAGCATTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
31585617 TACGTCTTCT
Statistics
Matches: 235, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
125 109 0.46
126 115 0.49
127 11 0.05
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (126 bp):
AACTACTATAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
Found at i:31585624 original size:28 final size:28
Alignment explanation
Indices: 31585577--31585640 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
31585567 TTTTTGACAC
*
31585577 TATTTGTTCAGAAACATCTTCTCAAAAT
1 TATTTTTTCAGAAACATCTTCTCAAAAT
* * * *
31585605 TATTTTTTCAGATACGTCTTCTCTAATT
1 TATTTTTTCAGAAACATCTTCTCAAAAT
31585633 TATTTTTT
1 TATTTTTT
31585641 TTGAAACTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.52
Consensus pattern (28 bp):
TATTTTTTCAGAAACATCTTCTCAAAAT
Found at i:31587246 original size:38 final size:38
Alignment explanation
Indices: 31587195--31587269 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
31587185 CCCCAGCTAA
31587195 CCAAAGACTCTGGTGTGATAATTCTCTGAAGATTTTTG
1 CCAAAGACTCTGGTGTGATAATTCTCTGAAGATTTTTG
31587233 CCAAAGACTCTGGTGTGATAATTCTCTGAAGATTTTT
1 CCAAAGACTCTGGTGTGATAATTCTCTGAAGATTTTT
31587270 TGCTTTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (38 bp):
CCAAAGACTCTGGTGTGATAATTCTCTGAAGATTTTTG
Found at i:31588299 original size:67 final size:67
Alignment explanation
Indices: 31588191--31588325 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
31588181 TTTGTGTTGG
31588191 TGGAGATCTCTTTTTATCTACTATTGTGATATAAAAGTTCTGAGAATTTCTATCTATTAAAAATC
1 TGGAGATCTCTTTTTATCTACTATTGTGATATAAAAGTTCTGAGAATTTCTATCTATTAAAAATC
31588256 AT
66 AT
31588258 TGGAGATCTCTTTTTATCTACTATTGTGATATAAAAGTTCTGAGAATTTCTATCTATTAAAAATC
1 TGGAGATCTCTTTTTATCTACTATTGTGATATAAAAGTTCTGAGAATTTCTATCTATTAAAAATC
31588323 AT
66 AT
31588325 T
1 T
31588326 CTTTGAATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (67 bp):
TGGAGATCTCTTTTTATCTACTATTGTGATATAAAAGTTCTGAGAATTTCTATCTATTAAAAATC
AT
Found at i:31589184 original size:2 final size:2
Alignment explanation
Indices: 31589177--31589222 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
31589167 ATGGTACCTC
*
31589177 CA CA CA CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
31589219 CA CA
1 CA CA
31589223 TTGCAGTGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:31590201 original size:5 final size:5
Alignment explanation
Indices: 31590193--31590224 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
31590183 AAAAATAAAA
31590193 TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TT
1 TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TT
31590225 CAGGCAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (5 bp):
TTTGG
Found at i:31591613 original size:39 final size:39
Alignment explanation
Indices: 31591570--31591648 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
31591560 TCATATATAC
31591570 TTGTAAATTTTTTGTACAGATTGATTTAATAAAATTCTA
1 TTGTAAATTTTTTGTACAGATTGATTTAATAAAATTCTA
*
31591609 TTGTAATTTTTTTGTACAGATTGATTTAATAAAATTCTA
1 TTGTAAATTTTTTGTACAGATTGATTTAATAAAATTCTA
31591648 T
1 T
31591649 CATTTACATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (39 bp):
TTGTAAATTTTTTGTACAGATTGATTTAATAAAATTCTA
Found at i:31595296 original size:43 final size:43
Alignment explanation
Indices: 31595248--31595613 Score: 344
Period size: 43 Copynumber: 8.6 Consensus size: 43
31595238 GTAAAAAAAG
*
31595248 CGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAA
* *
31595291 CGCCGCTAAAAAACATGACCTTTAGCGGCGCTTTTACCACAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAA
** **
31595334 CATCGCTAAAGAACATGACCTTTAGCGATGCTTTTCCCACAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAA
* * * * * ** *
31595377 CGCCACTAAAGATCATGATCTTTAGCGACGATTTTTTCAAAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAA
* * * * * *
31595420 CACCGC-AATAGAACA-AACCTTGAGCGACGCTTTTACAACAAA
1 CGCCGCTAA-AGAACATGACCTTTAGCGGCGCTTTTCCCACAAA
* * * *
31595462 TGCCACTAAAGAACATGACCTTTAGCGGTGCTTTTCTCACAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAA
* * * *
31595505 CGCCACTAAAGAACATGACCTTTAGCGGTGCGTTTCCTGA-AAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCC-CACAAA
** * * * * * *
31595548 TTCGGCTATAGACCA-AACCTTTAGCGGTGCTTTTCCTACAAA
1 CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAA
*
31595590 CGCCGCTAAAAAACATGACCTTTA
1 CGCCGCTAAAGAACATGACCTTTA
31595614 AAAAATATTT
Statistics
Matches: 257, Mismatches: 60, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
41 1 0.00
42 61 0.24
43 194 0.75
44 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (43 bp):
CGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAA
Found at i:31595400 original size:86 final size:85
Alignment explanation
Indices: 31595250--31595613 Score: 340
Period size: 85 Copynumber: 4.3 Consensus size: 85
31595240 AAAAAAAGCG
* * * *
31595250 CCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAAACATGACCTTTA
1 CCGCTAAAGAACATGACCTTTAGCGACGCTTTTCCCACAAACGCCACTAAAGAACATGACCTTTA
31595315 GCGGCGCTTTTACCACAAACA
66 GCGGCGCTTTT-CCACAAACA
* * * *
31595336 TCGCTAAAGAACATGACCTTTAGCGATGCTTTTCCCACAAACGCCACTAAAGATCATGATCTTTA
1 CCGCTAAAGAACATGACCTTTAGCGACGCTTTTCCCACAAACGCCACTAAAGAACATGACCTTTA
* * * *
31595401 GCGACGATTTTTTCAAAAACA
66 GCGGCG-CTTTTCCACAAACA
* * * * *
31595422 CCGC-AATAGAACA-AACCTTGAGCGACGCTTTTACAACAAATGCCACTAAAGAACATGACCTTT
1 CCGCTAA-AGAACATGACCTTTAGCGACGCTTTTCCCACAAACGCCACTAAAGAACATGACCTTT
* *
31595485 AGCGGTGCTTTTCTCACAAACG
65 AGCGGCGCTTTTC-CACAAACA
* ** * * ** ** * * *
31595507 CCACTAAAGAACATGACCTTTAGCGGTGCGTTTCCTGA-AAATTCGGCTATAGACCA-AACCTTT
1 CCGCTAAAGAACATGACCTTTAGCGACGCTTTTCC-CACAAACGCCACTAAAGAACATGACCTTT
* *
31595570 AGCGGTGCTTTTCCTACAAACG
65 AGCGGCGCTTTTCC-ACAAACA
*
31595592 CCGCTAAAAAACATGACCTTTA
1 CCGCTAAAGAACATGACCTTTA
31595614 AAAAATATTT
Statistics
Matches: 228, Mismatches: 43, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
84 5 0.02
85 110 0.48
86 108 0.47
87 5 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (85 bp):
CCGCTAAAGAACATGACCTTTAGCGACGCTTTTCCCACAAACGCCACTAAAGAACATGACCTTTA
GCGGCGCTTTTCCACAAACA
Found at i:31595559 original size:128 final size:128
Alignment explanation
Indices: 31595248--31595613 Score: 344
Period size: 128 Copynumber: 2.9 Consensus size: 128
31595238 GTAAAAAAAG
* * * * * * * *
31595248 CGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCC-CACAAACGCCGCTAA-AAAACATGACC
1 CGCCACTAAAGAACATGACCTTTAGCGACG-ATTTCCTCAAAAACACCGC-AATAGAACA-AACC
* * * ** *
31595311 TTTAGCGGCGCTTTTACCACAAACATCGCTAAAGAACATGACCTTTAGCGATGCTTTTCCCACAA
63 TTGAGCGACGCTTTTACAACAAACGCCACTAAAGAACATGACCTTTAGCGATGCTTTTCCCACAA
31595376 A
128 A
* * **
31595377 CGCCACTAAAGATCATGATCTTTAGCGACGATTTTTTCAAAAACACCGCAATAGAACAAACCTTG
1 CGCCACTAAAGAACATGACCTTTAGCGACGATTTCCTCAAAAACACCGCAATAGAACAAACCTTG
* * *
31595442 AGCGACGCTTTTACAACAAATGCCACTAAAGAACATGACCTTTAGCGGTGCTTTTCTCACAAA
66 AGCGACGCTTTTACAACAAACGCCACTAAAGAACATGACCTTTAGCGATGCTTTTCCCACAAA
* * ** * * *
31595505 CGCCACTAAAGAACATGACCTTTAGCGGTGCG-TTTCCT-GAAAATTCGGCTATAGACCAAACCT
1 CGCCACTAAAGAACATGACCTTTAGC-G-ACGATTTCCTCAAAAACACCGCAATAGAACAAACCT
* ** * * * *
31595568 TTAGCGGTGCTTTTCCTACAAACGCCGCTAAAAAACATGACCTTTA
64 TGAGCGACGCTTTTACAACAAACGCCACTAAAGAACATGACCTTTA
31595614 AAAAATATTT
Statistics
Matches: 193, Mismatches: 40, Indels: 9
0.80 0.17 0.04
Matches are distributed among these distances:
128 146 0.76
129 45 0.23
130 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (128 bp):
CGCCACTAAAGAACATGACCTTTAGCGACGATTTCCTCAAAAACACCGCAATAGAACAAACCTTG
AGCGACGCTTTTACAACAAACGCCACTAAAGAACATGACCTTTAGCGATGCTTTTCCCACAAA
Found at i:31597659 original size:20 final size:20
Alignment explanation
Indices: 31597634--31597674 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
31597624 CAAGTGAAAC
31597634 ATAATTTATTCTGAATCAAG
1 ATAATTTATTCTGAATCAAG
*
31597654 ATAATTTATTTTGAATCAAG
1 ATAATTTATTCTGAATCAAG
31597674 A
1 A
31597675 AATAATCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (20 bp):
ATAATTTATTCTGAATCAAG
Found at i:31599544 original size:24 final size:23
Alignment explanation
Indices: 31599482--31599537 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 23
31599472 TTCATCTTCA
31599482 CTCTCTTCTTCTTCCTCCTTCTC
1 CTCTCTTCTTCTTCCTCCTTCTC
*
31599505 CTCTTCTTCTTCTTCCTCGTTCTC
1 CTC-TCTTCTTCTTCCTCCTTCTC
31599529 CTTCTCTTC
1 C-TCTCTTC
31599538 AACTTCCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 3 0.10
24 25 0.83
25 2 0.07
ACGTcount: A:0.00, C:0.45, G:0.02, T:0.54
Consensus pattern (23 bp):
CTCTCTTCTTCTTCCTCCTTCTC
Found at i:31600292 original size:6 final size:6
Alignment explanation
Indices: 31600281--31600310 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
31600271 ATATTTAAGT
31600281 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
31600311 AATTTTAAAT
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:31600867 original size:15 final size:15
Alignment explanation
Indices: 31600846--31600880 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
31600836 TTTAAAAATA
*
31600846 ATTATTTATATTTAT
1 ATTATTTAGATTTAT
*
31600861 CTTATTTAGATTTAT
1 ATTATTTAGATTTAT
31600876 ATTAT
1 ATTAT
31600881 AAAAAAAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
ATTATTTAGATTTAT
Found at i:31600996 original size:21 final size:20
Alignment explanation
Indices: 31600960--31601008 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
31600950 TAAACCCCAA
*
31600960 AGACCA-AACCCCAAATCTT
1 AGACCATAACCCCAAATCCT
*
31600979 AGACCATACACCCTAAATCCT
1 AGACCATA-ACCCCAAATCCT
31601000 AGACCATAA
1 AGACCATAA
31601009 ACCTACACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 6 0.23
20 2 0.08
21 18 0.69
ACGTcount: A:0.43, C:0.35, G:0.06, T:0.16
Consensus pattern (20 bp):
AGACCATAACCCCAAATCCT
Found at i:31601022 original size:13 final size:13
Alignment explanation
Indices: 31600985--31601024 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
31600975 TCTTAGACCA
31600985 TACACCCTAAATCC
1 TACACCCTAAA-CC
* *
31600999 TAGACCATAAACC
1 TACACCCTAAACC
31601012 TACACCCTAAACC
1 TACACCCTAAACC
31601025 CTAACTATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.40, C:0.40, G:0.03, T:0.17
Consensus pattern (13 bp):
TACACCCTAAACC
Found at i:31601452 original size:7 final size:7
Alignment explanation
Indices: 31601403--31601557 Score: 130
Period size: 7 Copynumber: 22.0 Consensus size: 7
31601393 ACCCCTATCC
31601403 CCATAAA
1 CCATAAA
*
31601410 CCTTAAA
1 CCATAAA
**
31601417 TTATAAA
1 CCATAAA
*
31601424 ACATAAA
1 CCATAAA
*
31601431 CAATAAA
1 CCATAAA
*
31601438 TCATAAA
1 CCATAAA
31601445 CCATAAA
1 CCATAAA
*
31601452 CCCTAAA
1 CCATAAA
**
31601459 CTTTAAA
1 CCATAAA
** *
31601466 CCCCAAC
1 CCATAAA
*
31601473 CCTTAAA
1 CCATAAA
31601480 CCATAAA
1 CCATAAA
*
31601487 CCATTAA
1 CCATAAA
31601494 CCATAAA
1 CCATAAA
*
31601501 CCATTAA
1 CCATAAA
31601508 CCATAAA
1 CCATAAA
31601515 CCATAAA
1 CCATAAA
*
31601522 CCATAAT
1 CCATAAA
*
31601529 CCCTAAA
1 CCATAAA
*
31601536 CCCATAAT
1 -CCATAAA
31601544 CCATAAA
1 CCATAAA
*
31601551 CCTTAAA
1 CCATAAA
31601558 ATAGTAACTT
Statistics
Matches: 114, Mismatches: 33, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
7 109 0.96
8 5 0.04
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.21
Consensus pattern (7 bp):
CCATAAA
Found at i:31601958 original size:40 final size:40
Alignment explanation
Indices: 31601909--31602119 Score: 257
Period size: 40 Copynumber: 5.3 Consensus size: 40
31601899 AATTTTTTTT
* * * *
31601909 GCGGTGTTTTTGATAAAA-CGCCGCTAAAGCTTGATCTATA
1 GCGGCGTTTTTCA-AAAAGCGCCGCTAATGCTCGATCTATA
*
31601949 GCGGCGTTTTTCAAAAAGCGCCACTAATTG-TCGA-CTTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAA-TGCTCGATC-TATA
* * *
31601989 GCGGCGTTTTTTAAAAAGCGCTGATAATGCTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
* * *
31602029 GCGGCGTTTTTCTAAAAGCGCCACTAATGCTCGATCGATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
31602069 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
* *
31602109 GTGGCTTTTTT
1 GCGGCGTTTTT
31602120 TATCCAAACT
Statistics
Matches: 146, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
39 7 0.05
40 137 0.94
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
Found at i:31602763 original size:58 final size:57
Alignment explanation
Indices: 31602693--31602810 Score: 141
Period size: 57 Copynumber: 2.1 Consensus size: 57
31602683 AACAAAATGG
* * *
31602693 TGAAAATGGAGAAATGTGAAACATTT-TGAAATGATTATG-GTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAAT-AGAAACATTTGT-AAATGAATATGATTTTTC-CCAAAATGAAAA
* * *
31602751 TGAAAGTGGAGAAATAGAATCATTTGTAAATGAATGTGATTTTTCCCAAAATGAAAA
1 TGAAAATGGAGAAATAGAAACATTTGTAAATGAATATGATTTTTCCCAAAATGAAAA
31602808 TGA
1 TGA
31602811 CTTGGAAATG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
57 32 0.62
58 20 0.38
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (57 bp):
TGAAAATGGAGAAATAGAAACATTTGTAAATGAATATGATTTTTCCCAAAATGAAAA
Found at i:31610132 original size:40 final size:40
Alignment explanation
Indices: 31609934--31610118 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
31609924 CGAATGATGT
* * * *
31609934 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
31609974 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
* *
31610014 CCAGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
31610053 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
31610094 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
31610119 AATGAGTAGC
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
39 2 0.02
40 114 0.90
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:31610136 original size:80 final size:79
Alignment explanation
Indices: 31609986--31610141 Score: 190
Period size: 80 Copynumber: 2.0 Consensus size: 79
31609976 GGACTAAGAT
* * **
31609986 CCGAAGGCATTTGTGCGAGATACTAATTCCAGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTA
31610051 AATCCGGGTTAAGTC
66 AATCC-GGTTAAGTC
* * * *
31610066 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCAGGCTAAGTCCCGAAGGCATTTGAACGAGTTA-C
*
31610129 TATATCCGGTTAA
64 TAAATCCGGTTAA
31610142 ATTCTGAAGG
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
79 10 0.15
80 55 0.85
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTA
AATCCGGTTAAGTC
Found at i:31612204 original size:93 final size:93
Alignment explanation
Indices: 31612090--31612261 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
31612080 CGCCCATAAG
* * *
31612090 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
31612155 ACGAGCTCGGATGCCTAGTTACATTTCA
66 ACGAGCTCGGATGCCTAGTTACATTTCA
* *
31612183 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
31612248 ACGAGTTCGGATGC
66 ACGAGCTCGGATGC
31612262 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATTTCA
Found at i:31612258 original size:46 final size:46
Alignment explanation
Indices: 31612083--31612258 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
31612073 TGTAACCCGC
* *
31612083 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
* * *
31612129 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* * * *
31612179 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
31612222 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA
31612259 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 62 0.58
47 28 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:31627843 original size:7 final size:7
Alignment explanation
Indices: 31627827--31627857 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
31627817 AACACTACCT
*
31627827 CATATGA
1 CATATCA
31627834 CATATCA
1 CATATCA
31627841 CATATCA
1 CATATCA
31627848 CATATCA
1 CATATCA
31627855 CAT
1 CAT
31627858 GTTGATCGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.42, C:0.26, G:0.03, T:0.29
Consensus pattern (7 bp):
CATATCA
Found at i:31628030 original size:45 final size:45
Alignment explanation
Indices: 31627980--31628070 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
31627970 CCAAAAAACG
*
31627980 TGTCACATACATCATGAACTCAGACCATAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
**
31628025 TGTCACATATGTCATGAACTCAGACCACAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
31628070 T
1 T
31628071 CACATAATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (45 bp):
TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
Found at i:31628068 original size:21 final size:21
Alignment explanation
Indices: 31627999--31628074 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
31627989 CATCATGAAC
*
31627999 TCAGACCATAACTCAATGAGT
1 TCAGACCACAACTCAATGAGT
* * **
31628020 TCAGATGTCACATATGTC-ATGAAC
1 TCAGA--CCACA-A-CTCAATGAGT
31628044 TCAGACCACAACTCAATGAGT
1 TCAGACCACAACTCAATGAGT
*
31628065 TCAGATCACA
1 TCAGACCACA
31628075 TAATTCCTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
20 2 0.05
21 19 0.47
22 4 0.10
23 3 0.08
24 10 0.25
25 2 0.05
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (21 bp):
TCAGACCACAACTCAATGAGT
Found at i:31631317 original size:22 final size:22
Alignment explanation
Indices: 31631280--31631323 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31631270 TAGGAATTAG
31631280 GGTGTGTCGTTTTCTCT-TTTT
1 GGTGTGTCGTTTTCTCTCTTTT
*
31631301 GGTGTAGTCTTTTTCTCTCTTTT
1 GGTGT-GTCGTTTTCTCTCTTTT
31631324 CTTTTCCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.02, C:0.16, G:0.20, T:0.61
Consensus pattern (22 bp):
GGTGTGTCGTTTTCTCTCTTTT
Found at i:31632525 original size:9 final size:10
Alignment explanation
Indices: 31632510--31632569 Score: 63
Period size: 9 Copynumber: 6.1 Consensus size: 10
31632500 TGATACGTGG
31632510 GACATGATAT
1 GACATGATAT
31632520 -ACATGAT-T
1 GACATGATAT
*
31632528 GATATGATAT
1 GACATGATAT
31632538 GCACATGATAT
1 G-ACATGATAT
*
31632549 G-TATGATAT
1 GACATGATAT
31632558 GCACATGATAT
1 G-ACATGATAT
31632569 G
1 G
31632570 TATGAAATGC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
8 1 0.02
9 21 0.51
10 2 0.05
11 17 0.41
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (10 bp):
GACATGATAT
Found at i:31632545 original size:20 final size:20
Alignment explanation
Indices: 31632520--31632586 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
31632510 GACATGATAT
31632520 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
31632540 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
31632560 ACATGATATGTATGAAATGC
1 ACATGATATGTATGATATGC
31632580 ACATGAT
1 ACATGAT
31632587 GAATTCATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:31632715 original size:52 final size:51
Alignment explanation
Indices: 31632636--31632771 Score: 215
Period size: 52 Copynumber: 2.7 Consensus size: 51
31632626 AAGGAAGTGC
*
31632636 AAAAGGGCTTATGCCCCAGTTTTTTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
*
31632688 AAAAGGGCTTATGCCCCTGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
31632739 AAAAGGGCTT-TGCCCCAG-TTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAG-GGCT
31632772 AGGCCTCTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
48 5 0.06
49 9 0.11
50 7 0.09
51 25 0.31
52 34 0.43
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:31632734 original size:25 final size:26
Alignment explanation
Indices: 31632636--31632771 Score: 181
Period size: 26 Copynumber: 5.3 Consensus size: 26
31632626 AAGGAAGTGC
*
31632636 AAAAGGGCTTATGCCCCAGTTTTTTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
31632662 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
31632688 AAAAGGGCTTATGCCCCTGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
31632714 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
31632739 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
31632762 AAAAGAGGCT
1 AAAAG-GGCT
31632772 AGGCCTCTAG
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
23 5 0.05
24 7 0.07
25 30 0.31
26 56 0.57
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:31640646 original size:9 final size:10
Alignment explanation
Indices: 31640634--31640690 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
31640624 TACGTGGGAT
31640634 ATGATAT-AC
1 ATGATATGAC
*
31640643 ATGAT-TGAT
1 ATGATATGAC
31640652 ATGATATGCAC
1 ATGATATG-AC
*
31640663 ATGATATG-T
1 ATGATATGAC
31640672 ATGATATGCAC
1 ATGATATG-AC
31640683 ATGATATG
1 ATGATATG
31640691 TATGAAATGC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 2 0.05
11 17 0.44
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (10 bp):
ATGATATGAC
Found at i:31640666 original size:20 final size:20
Alignment explanation
Indices: 31640633--31640707 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
31640623 ATACGTGGGA
31640633 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
31640650 ATATGATATGCACATGATATG
1 -TATGATATGCACATGATATG
31640671 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
31640691 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
31640708 GAATTCATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 43 0.81
21 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:31640668 original size:11 final size:11
Alignment explanation
Indices: 31640652--31640707 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
31640642 CATGATTGAT
31640652 ATGATATGCAC
1 ATGATATGCAC
*
31640663 ATGATATG--T
1 ATGATATGCAC
31640672 ATGATATGCAC
1 ATGATATGCAC
*
31640683 ATGATATG--T
1 ATGATATGCAC
*
31640692 ATGAAATGCAC
1 ATGATATGCAC
31640703 ATGAT
1 ATGAT
31640708 GAATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:31640786 original size:26 final size:26
Alignment explanation
Indices: 31640757--31640816 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
31640747 GAGGAAGTGC
**
31640757 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
31640783 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
31640809 AAAAGGGC
1 AAAAGGGC
31640817 ATAAGCACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:31640908 original size:26 final size:26
Alignment explanation
Indices: 31640879--31641013 Score: 172
Period size: 25 Copynumber: 5.3 Consensus size: 26
31640869 GAGGAAGTGC
31640879 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
31640905 AAAAGGGCTTATG-CCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
31640930 AAAAGGGCTTATGCCCCTGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
31640956 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
31640981 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
31641004 AAAAGAGGCT
1 AAAAG-GGCT
31641014 AGGCCTCCAG
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
23 5 0.05
24 7 0.07
25 52 0.55
26 31 0.33
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:31640916 original size:122 final size:121
Alignment explanation
Indices: 31640699--31640937 Score: 442
Period size: 122 Copynumber: 2.0 Consensus size: 121
31640689 TGTATGAAAT
*
31640699 GCACATGATGAATTCATAAATGCATTAGGTTGGGTTTTTATATGGATGGAGGAAGTGCAAAAGGG
1 GCACATGATGAATTAATAAATGCATTAGGTTGGGTTTTTATATGGATGGAGGAAGTGCAAAAGGG
*
31640764 CTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCATAA
66 CTTATGCCCCAGTTTATTGAAAAGGGCTTATG-CCCAATTTACCGAAAAGGGCATAA
*
31640821 GCACATGATGAATTAATAAATGCATTGGGTTGGGTTTTTATATGGATGGAGGAAGTGCAAAAGGG
1 GCACATGATGAATTAATAAATGCATTAGGTTGGGTTTTTATATGGATGGAGGAAGTGCAAAAGGG
31640886 CTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCAATTTACCGAAAAGGGC
66 CTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCAATTTACCGAAAAGGGC
31640938 TTATGCCCCT
Statistics
Matches: 114, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
121 19 0.17
122 95 0.83
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (121 bp):
GCACATGATGAATTAATAAATGCATTAGGTTGGGTTTTTATATGGATGGAGGAAGTGCAAAAGGG
CTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCAATTTACCGAAAAGGGCATAA
Found at i:31640955 original size:51 final size:51
Alignment explanation
Indices: 31640879--31641013 Score: 206
Period size: 51 Copynumber: 2.7 Consensus size: 51
31640869 GAGGAAGTGC
31640879 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG-CCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAATTTACCG
* *
31640930 AAAAGGGCTTATGCCCCTGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAATTTACCG
31640981 AAAAGGGCTT-TGCCCCAG-TTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAG-GGCT
31641014 AGGCCTCCAG
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
48 5 0.06
49 9 0.11
50 9 0.11
51 56 0.71
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAATTTACCG
Found at i:31654361 original size:31 final size:31
Alignment explanation
Indices: 31654323--31654382 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
31654313 CCTTTTCATA
31654323 TTTCATATTTCATAACACTGGGCCGAAGCTT
1 TTTCATATTTCATAACACTGGGCCGAAGCTT
**
31654354 TTTCATATTTCATATTACTGGGCCGAAGC
1 TTTCATATTTCATAACACTGGGCCGAAGC
31654383 CTTTACTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCTT
Found at i:31654686 original size:25 final size:24
Alignment explanation
Indices: 31654580--31654700 Score: 183
Period size: 24 Copynumber: 5.0 Consensus size: 24
31654570 GCTTTATCAT
*
31654580 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
31654605 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31654628 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
31654652 ATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
31654677 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31654701 CACTTCTTCC
Statistics
Matches: 90, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
23 18 0.20
24 41 0.46
25 31 0.34
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:31654694 original size:49 final size:48
Alignment explanation
Indices: 31654571--31654700 Score: 183
Period size: 49 Copynumber: 2.6 Consensus size: 48
31654561 AGCATAGCTG
*
31654571 CTTTATCATATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAGCC
1 CTTTATC--ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAGCC
*
31654622 CTTT-TAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCA-AAGCC
31654670 CTTTATCATAACTGGGGCATAAGCCCTTTTA
1 CTTTATCATAACTGGGGCATAAGCCCTTTTA
31654701 CACTTCTTCC
Statistics
Matches: 73, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
47 22 0.30
48 21 0.29
49 25 0.34
50 1 0.01
51 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (48 bp):
CTTTATCATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAGCC
Found at i:31654774 original size:20 final size:20
Alignment explanation
Indices: 31654749--31654815 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
31654739 TTACGAATAC
31654749 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
31654769 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* * *
31654789 GTCATATGCATACCATACAT
1 ATCATGTGCATATCATACAT
*
31654809 ACCATGT
1 ATCATGT
31654816 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:31659847 original size:36 final size:36
Alignment explanation
Indices: 31659800--31659872 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
31659790 CTTTCGAGAG
31659800 TAAGAGCAACTGACTCTAGGTTGATTAATTGAAATT
1 TAAGAGCAACTGACTCTAGGTTGATTAATTGAAATT
*
31659836 TAAGAGCAACTGACTCTAGGTTGATTAATTGGAATT
1 TAAGAGCAACTGACTCTAGGTTGATTAATTGAAATT
31659872 T
1 T
31659873 CTTTCTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (36 bp):
TAAGAGCAACTGACTCTAGGTTGATTAATTGAAATT
Found at i:31662326 original size:9 final size:8
Alignment explanation
Indices: 31662295--31662354 Score: 54
Period size: 8 Copynumber: 7.5 Consensus size: 8
31662285 AGTAAAGTTC
31662295 AAAATAAA
1 AAAATAAA
31662303 AAAA-AACA
1 AAAATAA-A
31662311 AATAATAAGA
1 AA-AATAA-A
31662321 AAAAT-AA
1 AAAATAAA
* *
31662328 AATACAAA
1 AAAATAAA
31662336 AAAAT-AA
1 AAAATAAA
31662343 AAAATAAA
1 AAAATAAA
31662351 AAAA
1 AAAA
31662355 CATAAAATCT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
7 13 0.31
8 19 0.45
9 5 0.12
10 5 0.12
ACGTcount: A:0.83, C:0.03, G:0.02, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:31662330 original size:17 final size:16
Alignment explanation
Indices: 31662297--31662354 Score: 66
Period size: 15 Copynumber: 3.6 Consensus size: 16
31662287 TAAAGTTCAA
*
31662297 AATAAAAAAAAACAAAT
1 AATAAAAAAATA-AAAT
31662314 AATAAGAAAAATAAAAT
1 AATAA-AAAAATAAAAT
*
31662331 -ACAAAAAAATAAAA-
1 AATAAAAAAATAAAAT
31662345 AATAAAAAAA
1 AATAAAAAAA
31662355 CATAAAATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 18 0.50
16 3 0.08
17 9 0.25
18 6 0.17
ACGTcount: A:0.83, C:0.03, G:0.02, T:0.12
Consensus pattern (16 bp):
AATAAAAAAATAAAAT
Found at i:31662330 original size:31 final size:32
Alignment explanation
Indices: 31662295--31662362 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 32
31662285 AGTAAAGTTC
* *
31662295 AAAATAAAAAAAAACAAATAATAAGAAAA-AT
1 AAAATAAAAAAAAACAAAAAATAAAAAAACAT
* *
31662326 AAAATACAAAAAAATAAAAAATAAAAAAACAT
1 AAAATAAAAAAAAACAAAAAATAAAAAAACAT
31662358 AAAAT
1 AAAAT
31662363 CTAAATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 25 0.78
32 7 0.22
ACGTcount: A:0.81, C:0.04, G:0.01, T:0.13
Consensus pattern (32 bp):
AAAATAAAAAAAAACAAAAAATAAAAAAACAT
Found at i:31662361 original size:15 final size:14
Alignment explanation
Indices: 31662295--31662362 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 14
31662285 AGTAAAGTTC
31662295 AAAATAAAA-AAAA
1 AAAATAAAATAAAA
*
31662308 ACAAAT--AATAAGA
1 A-AAATAAAATAAAA
31662321 AAAATAAAATACAAA
1 AAAATAAAATA-AAA
31662336 AAAATAAAAAATAAAA
1 AAAAT--AAAATAAAA
31662352 AAACATAAAAT
1 AAA-ATAAAAT
31662363 CTAAATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
12 6 0.13
13 5 0.11
14 8 0.18
15 12 0.27
16 6 0.13
17 8 0.18
ACGTcount: A:0.81, C:0.04, G:0.01, T:0.13
Consensus pattern (14 bp):
AAAATAAAATAAAA
Found at i:31662367 original size:17 final size:16
Alignment explanation
Indices: 31662295--31662361 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 16
31662285 AGTAAAGTTC
31662295 AAAATAAAAAAAA-ACA
1 AAAATAAAAAAAATA-A
*
31662311 AATAATAAGAAAAAT--
1 AA-AATAAAAAAAATAA
31662326 AAAATACAAAAAAATAA
1 AAAATA-AAAAAAATAA
31662343 AAAATAAAAAAACATAA
1 AAAATAAAAAAA-ATAA
31662360 AA
1 AA
31662362 TCTAAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
14 4 0.09
15 9 0.21
16 8 0.19
17 22 0.51
ACGTcount: A:0.82, C:0.04, G:0.01, T:0.12
Consensus pattern (16 bp):
AAAATAAAAAAAATAA
Found at i:31666254 original size:22 final size:22
Alignment explanation
Indices: 31666201--31666256 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 22
31666191 CACGTTCACT
*
31666201 TTTAAGCATATATCACATTACA
1 TTTAAGCATATATCACATAACA
*
31666223 --T-A-TATA-ATCACATAACA
1 TTTAAGCATATATCACATAACA
31666240 TTTAAGCATATATCACA
1 TTTAAGCATATATCACA
31666257 ATTTAGAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 10
0.67 0.08 0.26
Matches are distributed among these distances:
17 10 0.38
18 3 0.12
19 2 0.08
20 2 0.08
21 3 0.12
22 6 0.23
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.34
Consensus pattern (22 bp):
TTTAAGCATATATCACATAACA
Found at i:31667991 original size:22 final size:22
Alignment explanation
Indices: 31667960--31668040 Score: 99
Period size: 22 Copynumber: 3.7 Consensus size: 22
31667950 TACAGGATCA
31667960 CACTTTAGTGCCTCTGTACTTG
1 CACTTTAGTGCCTCTGTACTTG
* * *
31667982 CATTTTAGTGCCTTTCTACTTG
1 CACTTTAGTGCCTCTGTACTTG
* *
31668004 TACTTTAGTGCCTCTGTATTTG
1 CACTTTAGTGCCTCTGTACTTG
**
31668026 CACTACAGTGCCTCT
1 CACTTTAGTGCCTCT
31668041 ACTAGTATTT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.15, C:0.26, G:0.16, T:0.43
Consensus pattern (22 bp):
CACTTTAGTGCCTCTGTACTTG
Found at i:31670046 original size:25 final size:25
Alignment explanation
Indices: 31670018--31670072 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
31670008 TAGAGTTAGG
31670018 AGTTGATT-TGGCAAAAGCTTTCTGA
1 AGTT-ATTATGGCAAAAGCTTTCTGA
* *
31670043 AGTTCTTCATTGCAAAAGCTTTCTGA
1 AGTTATT-ATGGCAAAAGCTTTCTGA
31670069 AGTT
1 AGTT
31670073 CTTCATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 2 0.08
25 4 0.15
26 20 0.77
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (25 bp):
AGTTATTATGGCAAAAGCTTTCTGA
Found at i:31670057 original size:26 final size:26
Alignment explanation
Indices: 31670028--31670079 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
31670018 AGTTGATTTG
31670028 GCAAAAGCTTTCTGAAGTTCTTCATT
1 GCAAAAGCTTTCTGAAGTTCTTCATT
31670054 GCAAAAGCTTTCTGAAGTTCTTCATT
1 GCAAAAGCTTTCTGAAGTTCTTCATT
31670080 CATTATCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (26 bp):
GCAAAAGCTTTCTGAAGTTCTTCATT
Found at i:31677084 original size:29 final size:29
Alignment explanation
Indices: 31677047--31677147 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 29
31677037 CACTAAACCT
* *
31677047 AATCTCATTCATATGGACCGTTAGGCCCA
1 AATCACATTCATATGGACCATTAGGCCCA
*
31677076 AATCACATTCGTAT-GACCCATTAGGCCCA
1 AATCACATTCATATGGA-CCATTAGGCCCA
* * *
31677105 AATTACATTCATACGGCCCATTAGGCCCA
1 AATCACATTCATATGGACCATTAGGCCCA
*
31677134 AATCACAATCATAT
1 AATCACATTCATAT
31677148 ACATGCTTTC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 57 0.95
30 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (29 bp):
AATCACATTCATATGGACCATTAGGCCCA
Found at i:31677398 original size:16 final size:16
Alignment explanation
Indices: 31677358--31677400 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
31677348 GTAGCCAAAC
*
31677358 TTTCACCTTTTCAGCA
1 TTTCAGCTTTTCAGCA
* *
31677374 TTTCGGCTTTTCGGCA
1 TTTCAGCTTTTCAGCA
*
31677390 TTTTAGCTTTT
1 TTTCAGCTTTT
31677401 TGTCATTTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.23, G:0.14, T:0.51
Consensus pattern (16 bp):
TTTCAGCTTTTCAGCA
Found at i:31681753 original size:19 final size:19
Alignment explanation
Indices: 31681718--31681755 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
31681708 TTGCAATTTA
*
31681718 AATTTTTATTTTCTTTTCT
1 AATTTTTATTTTATTTTCT
31681737 AATTTTTCA-TTTATTTTCT
1 AATTTTT-ATTTTATTTTCT
31681756 TCTGACAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTATTTTATTTTCT
Found at i:31684234 original size:31 final size:31
Alignment explanation
Indices: 31684156--31684237 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
31684146 CAGTCTCAAA
*
31684156 ATAT-ACTGGGCTGAAGCC-TTTCATAATTC
1 ATATCACTGGGCTGAAGCCTTTTCAAAATTC
* *
31684185 ATAACACTGGGCCGAAGCCTTTTCAAAATTC
1 ATATCACTGGGCTGAAGCCTTTTCAAAATTC
* *
31684216 ATATCACTGGGTTAAAGCCTTT
1 ATATCACTGGGCTGAAGCCTTT
31684238 ATTGTAAGCG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 3 0.07
30 13 0.30
31 28 0.64
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (31 bp):
ATATCACTGGGCTGAAGCCTTTTCAAAATTC
Found at i:31684476 original size:24 final size:25
Alignment explanation
Indices: 31684449--31684501 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
31684439 GCTTAGCCTC
*
31684449 TTTTAAT-AACTAGGGTAAAGCCCT
1 TTTTAATAAACTAGGGCAAAGCCCT
*
31684473 TTTTGATAAACTAGGGCAAAGCCCT
1 TTTTAATAAACTAGGGCAAAGCCCT
31684498 TTTT
1 TTTT
31684502 GCACTTCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (25 bp):
TTTTAATAAACTAGGGCAAAGCCCT
Found at i:31684573 original size:21 final size:21
Alignment explanation
Indices: 31684548--31684598 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
31684538 TATAATGAGT
*
31684548 ATATCATGTGCATCTCATAAC
1 ATATCATGTGCATATCATAAC
* **
31684569 ATATCAAGTGCATATCATGTC
1 ATATCATGTGCATATCATAAC
31684590 ATATCATGT
1 ATATCATGT
31684599 ATATCAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (21 bp):
ATATCATGTGCATATCATAAC
Found at i:31685674 original size:22 final size:22
Alignment explanation
Indices: 31685646--31685687 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
31685636 TCGGCAAGGG
31685646 AGATGAAAAGAAAGGAAGTAGT
1 AGATGAAAAGAAAGGAAGTAGT
*
31685668 AGATGAAAAGAAAGGGAGTA
1 AGATGAAAAGAAAGGAAGTA
31685688 TTGGTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (22 bp):
AGATGAAAAGAAAGGAAGTAGT
Found at i:31696536 original size:29 final size:29
Alignment explanation
Indices: 31696470--31696593 Score: 155
Period size: 29 Copynumber: 4.3 Consensus size: 29
31696460 GAGTCTACAT
* *
31696470 ACATGCATATGGCCCACTAGG-CT-AATC
1 ACATTCATATGGCCCATTAGGCCTAAATC
* *
31696497 TCATTCATATGGCCCATTTGGCCTAAATC
1 ACATTCATATGGCCCATTAGGCCTAAATC
* *
31696526 ACATTCGTATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCTAAATC
*
31696555 ACATTCATACGGCCCATTAGGCGC-AAATC
1 ACATTCATATGGCCCATTAGGC-CTAAATC
31696584 ACATTCATAT
1 ACATTCATAT
31696594 ACATGCTTTC
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
27 17 0.20
28 2 0.02
29 63 0.76
30 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCTAAATC
Found at i:31700235 original size:27 final size:27
Alignment explanation
Indices: 31700205--31700320 Score: 108
Period size: 27 Copynumber: 4.3 Consensus size: 27
31700195 CAAAATAGTC
* *
31700205 ATTTTACCCTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCAGTA
31700232 ATTTTACACTACAAGGGTATTTCAGTA
1 ATTTTACACTACAAGGGTATTTCAGTA
* ** *
31700259 ATTTTACA-AACTGGGGGTATTTCAATA
1 ATTTTACACTAC-AAGGGTATTTCAGTA
* **** *
31700286 ATTTTACAATTTGCGAGTATTTCAGTA
1 ATTTTACACTACAAGGGTATTTCAGTA
31700313 ATTTTACA
1 ATTTTACA
31700321 AACTGGGGGT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
26 2 0.03
27 73 0.97
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCAGTA
Found at i:31700321 original size:27 final size:27
Alignment explanation
Indices: 31700219--31700403 Score: 189
Period size: 27 Copynumber: 6.9 Consensus size: 27
31700209 TACCCTACAA
* * **
31700219 GGGTATTTCGGTAATTTTACACTAC-AA
1 GGGTATTTCAGTAATTTTACA-AACTGG
31700246 GGGTATTTCAGTAATTTTACAAACTGG
1 GGGTATTTCAGTAATTTTACAAACTGG
* ** *
31700273 GGGTATTTCAATAATTTTACAATTTGC
1 GGGTATTTCAGTAATTTTACAAACTGG
*
31700300 GAGTATTTCAGTAATTTTACAAACTGG
1 GGGTATTTCAGTAATTTTACAAACTGG
* * *
31700327 GGGTATTT-TGATAATTTTACAAATTGA
1 GGGTATTTCAG-TAATTTTACAAACTGG
*
31700354 GGGTATTTCAATAATTTTACAAACCT-G
1 GGGTATTTCAGTAATTTTACAAA-CTGG
31700381 GGGTATTTC-GATAATTTTACAAA
1 GGGTATTTCAG-TAATTTTACAAA
31700404 TCGAGGTCTT
Statistics
Matches: 131, Mismatches: 22, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
26 3 0.02
27 127 0.97
28 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTACAAACTGG
Found at i:31700402 original size:54 final size:54
Alignment explanation
Indices: 31700219--31700409 Score: 251
Period size: 54 Copynumber: 3.5 Consensus size: 54
31700209 TACCCTACAA
* * *
31700219 GGGTATTTCGGTAATTTTAC-ACTACAAGGGTATTTCAGTAATTTTACAAACTGG
1 GGGTATTTCGATAATTTTACAAAT-CGAGGGTATTTCAGTAATTTTACAAACTGG
* * * * *
31700273 GGGTATTTCAATAATTTTACAATTTGCGAGTATTTCAGTAATTTTACAAACTGG
1 GGGTATTTCGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACTGG
* * *
31700327 GGGTATTTTGATAATTTTACAAATTGAGGGTATTTCAATAATTTTACAAACCT-G
1 GGGTATTTCGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAA-CTGG
31700381 GGGTATTTCGATAATTTTACAAATCGAGG
1 GGGTATTTCGATAATTTTACAAATCGAGG
31700410 TCTTAACAAC
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
54 116 0.97
55 4 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (54 bp):
GGGTATTTCGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACTGG
Found at i:31713658 original size:21 final size:19
Alignment explanation
Indices: 31713621--31713675 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
31713611 ATTAGAATGT
*
31713621 AAAAAATTAAATTAAAATA
1 AAAAAATTAAATCAAAATA
31713640 AAAAATATTAAAATCAAAATA
1 AAAAA-ATT-AAATCAAAATA
**
31713661 AAAAAGCTAAATCAA
1 AAAAAATTAAATCAA
31713676 TAAAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 12 0.39
20 4 0.13
21 15 0.48
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAAAATTAAATCAAAATA
Found at i:31716334 original size:13 final size:14
Alignment explanation
Indices: 31716316--31716346 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31716306 GTTAAAATTG
31716316 TAAATT-AGTAAAA
1 TAAATTAAGTAAAA
31716329 TAAATTAAGTAAAA
1 TAAATTAAGTAAAA
31716343 TAAA
1 TAAA
31716347 GAAAACCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (14 bp):
TAAATTAAGTAAAA
Found at i:31724318 original size:16 final size:16
Alignment explanation
Indices: 31724297--31724329 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31724287 TAATTTGCTT
31724297 AAGGCATACTAAGCTA
1 AAGGCATACTAAGCTA
31724313 AAGGCATACTAAGCTA
1 AAGGCATACTAAGCTA
31724329 A
1 A
31724330 GTTAGCTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (16 bp):
AAGGCATACTAAGCTA
Found at i:31728771 original size:28 final size:27
Alignment explanation
Indices: 31728738--31728790 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
31728728 TTAGAATACT
*
31728738 TTAGTTTACTAAAATTACCGAAATACGC
1 TTAGTTT-CTAAAAATACCGAAATACGC
* *
31728766 TTAGTTTGTAAAAATACTGAAATAC
1 TTAGTTTCTAAAAATACCGAAATAC
31728791 CCTCGATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (27 bp):
TTAGTTTCTAAAAATACCGAAATACGC
Found at i:31728777 original size:27 final size:27
Alignment explanation
Indices: 31728747--31728845 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
31728737 TTTAGTTTAC
31728747 TAAAATTACCGAAATACGCTTAG-TTTG
1 TAAAATTACCGAAATAC-CTTAGATTTG
* * * *
31728774 TAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCTTAGATTTG
* * *
31728801 TAAAATTACTGAAATACCTTCGACTTG
1 TAAAATTACCGAAATACCTTAGATTTG
31728828 TAAAATTACC-AAAGTACC
1 TAAAATTACCGAAA-TACC
31728846 CCCGATTTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 6 0.10
27 56 0.90
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.30
Consensus pattern (27 bp):
TAAAATTACCGAAATACCTTAGATTTG
Found at i:31728846 original size:54 final size:54
Alignment explanation
Indices: 31728747--31728853 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
31728737 TTTAGTTTAC
* * *
31728747 TAAAATTACCGAAATACGCTTAGTTTGTAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACGCTTAGCTTGTAAAAATACTCAAATACCCCCGATTTG
* * *
31728801 TAAAATTACTGAAATAC-CTTCGACTTGTAAAATTAC-CAAAGTACCCCCGATTT
1 TAAAATTACCGAAATACGCTTAG-CTTGTAAAAATACTCAAA-TACCCCCGATTT
31728854 ACATAATTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 7 0.16
54 38 0.84
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (54 bp):
TAAAATTACCGAAATACGCTTAGCTTGTAAAAATACTCAAATACCCCCGATTTG
Found at i:31728861 original size:27 final size:27
Alignment explanation
Indices: 31728831--31728892 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
31728821 CGACTTGTAA
*
31728831 AATTACCAAAGTACCCCCGATTTACAT
1 AATTACCAAAGTACCCCCGATTTACAG
*** *
31728858 AATTACCATTTTACCCTCGATTTACAG
1 AATTACCAAAGTACCCCCGATTTACAG
*
31728885 AAGTACCA
1 AATTACCA
31728893 TTTTACCCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTACCAAAGTACCCCCGATTTACAG
Found at i:31728972 original size:27 final size:27
Alignment explanation
Indices: 31728842--31728973 Score: 156
Period size: 27 Copynumber: 4.9 Consensus size: 27
31728832 ATTACCAAAG
* * *
31728842 TACCCCCGATTTACATAATTACCATTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
31728869 TACCCTCGATTTACAGAAGTACCATTT
1 TACCCTCGATTTACAGAATTACTATTT
* * *
31728896 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
31728923 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
31728950 TACCATCGATTTACAAAATTACTA
1 TACCCTCGATTTACAGAATTACTA
31728974 GAATACCCTA
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 92 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTATTT
Found at i:31729021 original size:27 final size:27
Alignment explanation
Indices: 31728964--31729142 Score: 209
Period size: 27 Copynumber: 6.7 Consensus size: 27
31728954 ATCGATTTAC
* * *
31728964 AAAATTACTAGAATACCC-TAGTCTGT
1 AAAATTACCAAAATACCCTTAGTTTGT
* * *
31728990 AAAATTGCTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTAGTTTGT
* * *
31729017 AAAATTACAAAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCTTAGTTTGT
*
31729044 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCTTAGTTTGT
31729071 AAAATTACCAAAATACCAC-TAGTTTGT
1 AAAATTACCAAAATACC-CTTAGTTTGT
* * * *
31729098 GAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCTTAGTTTGT
31729125 AAAATTACCAAAATACCC
1 AAAATTACCAAAATACCC
31729143 CTGATTTACA
Statistics
Matches: 131, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
26 17 0.13
27 113 0.86
28 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTAGTTTGT
Found at i:31729096 original size:81 final size:81
Alignment explanation
Indices: 31728964--31729144 Score: 258
Period size: 81 Copynumber: 2.2 Consensus size: 81
31728954 ATCGATTTAC
* * * * *
31728964 AAAATTACTAGAATA-CCCTAGTCTGTAAAATTGCTAAAATACCCTTGGTTTGTAAAATTACAAA
1 AAAATTACCAAAATACCCCTAGTCTGTAAAATTACCAAAATACCCTTAGTTTGTAAAATTACAAA
31729028 AATACCCTCAATTTGT
66 AATACCCTCAATTTGT
* * **
31729044 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCAC-TAGTTTGTGAAATTACCG
1 AAAATTACCAAAATACCCCTAGTCTGTAAAATTACCAAAATACC-CTTAGTTTGTAAAATTACAA
31729108 AAATACCCTCAATTTGT
65 AAATACCCTCAATTTGT
31729125 AAAATTACCAAAATACCCCT
1 AAAATTACCAAAATACCCCT
31729145 GATTTACAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 13 0.14
81 76 0.84
82 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.30
Consensus pattern (81 bp):
AAAATTACCAAAATACCCCTAGTCTGTAAAATTACCAAAATACCCTTAGTTTGTAAAATTACAAA
AATACCCTCAATTTGT
Found at i:31729159 original size:27 final size:26
Alignment explanation
Indices: 31728964--31729169 Score: 113
Period size: 27 Copynumber: 7.7 Consensus size: 26
31728954 ATCGATTTAC
* *
31728964 AAAATTACTAGAATA-CCCTAG-TCTGT
1 AAAATTACCAAAATACCCCTAGAT-T-T
* * * * *
31728990 AAAATTGCTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCCTAGATT-T
*
31729017 AAAATTACAAAAATA-CCCTCA-ATTTGT
1 AAAATTACCAAAATACCCCT-AGA-TT-T
*
31729044 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGATT-T
* *
31729071 AAAATTACCAAAATACCACTAGTTTGT
1 AAAATTACCAAAATACCCCTAGATT-T
* *
31729098 GAAATTACCGAAATA-CCCTCA-ATTTGT
1 AAAATTACCAAAATACCCCT-AGA-TT-T
31729125 AAAATTACCAAAATACCCCT-GATTT
1 AAAATTACCAAAATACCCCTAGATTT
31729150 ACAAAGTTA-CAGAAATACCC
1 A-AAA-TTACCA-AAATACCC
31729170 TTGACTTTCT
Statistics
Matches: 149, Mismatches: 18, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
25 2 0.01
26 26 0.17
27 112 0.75
28 9 0.06
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (26 bp):
AAAATTACCAAAATACCCCTAGATTT
Found at i:31729165 original size:54 final size:53
Alignment explanation
Indices: 31729012--31729170 Score: 155
Period size: 54 Copynumber: 2.9 Consensus size: 53
31729002 ATACCCTTGG
* * *
31729012 TTTGTAAAATTACAAAAATACCCTCAATTTGTA-AAATTACCA-AAATACCC-CTAG
1 TTTGTAAAATTACCAAAATACCC-CTA-TT-TACAAATTA-CAGAAATACCCTCTAA
* ** *
31729066 TTTGTAAAATTACCAAAATACCACTAGTTTGTGAAATTACCGAAATACCCTC-AA
1 TTTGTAAAATTACCAAAATACCCCTA-TTT-ACAAATTACAGAAATACCCTCTAA
31729120 TTTGTAAAATTACCAAAATACCCCTGATTTACAAAGTTACAGAAATACCCT
1 TTTGTAAAATTACCAAAATACCCCT-ATTTACAAA-TTACAGAAATACCCT
31729171 TGACTTTCTA
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
52 1 0.01
53 8 0.09
54 77 0.88
55 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (53 bp):
TTTGTAAAATTACCAAAATACCCCTATTTACAAATTACAGAAATACCCTCTAA
Found at i:31729220 original size:27 final size:27
Alignment explanation
Indices: 31729181--31729232 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
31729171 TGACTTTCTA
31729181 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
* *
31729208 AAAATTATTGAAATACCCTTGGTTT
1 AAAATTATAGAAATACCATTGGTTT
31729233 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:31729350 original size:27 final size:27
Alignment explanation
Indices: 31729273--31729350 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
31729263 AAATGACTAA
* *
31729273 AATACCCCTAT-TAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* * *
31729300 AA-AGCCCCAGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
31729327 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
31729351 GAATATGCCC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 1 0.03
27 38 0.95
28 1 0.03
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:31730539 original size:25 final size:25
Alignment explanation
Indices: 31730510--31730557 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31730500 TTATAACATG
* * *
31730510 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
31730535 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
31730558 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:31730660 original size:20 final size:20
Alignment explanation
Indices: 31730594--31730660 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
31730584 ATTTTGATAA
*
31730594 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
31730614 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
31730634 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
31730654 ACTTGAT
1 ACATGAT
31730661 GTATTCATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:31730766 original size:24 final size:23
Alignment explanation
Indices: 31730710--31730876 Score: 219
Period size: 24 Copynumber: 7.0 Consensus size: 23
31730700 GAGGAAGTGA
*
31730710 AAAAGGGTTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
31730733 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
31730756 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
31730780 CAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
31730804 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
31730827 AAAAAGGGCTTTTGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTA-T
*
31730852 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
31730876 A
1 A
31730877 TGATAAAGCA
Statistics
Matches: 129, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
23 42 0.33
24 76 0.59
25 11 0.09
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:31730779 original size:47 final size:47
Alignment explanation
Indices: 31730710--31730876 Score: 221
Period size: 47 Copynumber: 3.5 Consensus size: 47
31730700 GAGGAAGTGA
* *
31730710 AAAAGGGTTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
* *
31730756 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
* *
31730804 TAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTA-T
*
31730852 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
31730877 TGATAAAGCA
Statistics
Matches: 107, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
47 64 0.60
48 31 0.29
49 12 0.11
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
Found at i:31730826 original size:71 final size:71
Alignment explanation
Indices: 31730710--31730875 Score: 253
Period size: 71 Copynumber: 2.3 Consensus size: 71
31730700 GAGGAAGTGA
* * *
31730710 AAAAGGGTTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
31730775 GTTATC
66 GTTATC
*
31730781 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
*
31730846 GTTATT
66 GTTATC
*
31730852 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTACGCC-CCAGTTAT
31730876 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
71 76 0.87
72 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (71 bp):
AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
GTTATC
Found at i:31731105 original size:31 final size:31
Alignment explanation
Indices: 31731069--31731132 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
31731059 CGTTTACAGT
31731069 AAAGGCTTC-GGCCTAGTAATATGAAATATGA
1 AAAGGCTTCGGGCC-AGTAATATGAAATATGA
**
31731100 AAAGGCTTCGGGCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGGCCAGTAATATGAAATATGA
31731131 AA
1 AA
31731133 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGGCCAGTAATATGAAATATGA
Found at i:31739312 original size:13 final size:14
Alignment explanation
Indices: 31739294--31739324 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31739284 GTTAAAATTG
31739294 TAAATT-AGTAAAA
1 TAAATTAAGTAAAA
31739307 TAAATTAAGTAAAA
1 TAAATTAAGTAAAA
31739321 TAAA
1 TAAA
31739325 GAAAACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (14 bp):
TAAATTAAGTAAAA
Found at i:31739919 original size:27 final size:28
Alignment explanation
Indices: 31739889--31739946 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
31739879 TGATATTATT
* *
31739889 TAGATTAA-GAAAAACGAAGT-TCGGATC
1 TAGATAAAGGAAAAACAAAGTATCGGA-C
31739916 TAGATAAAGGAAAAACAAAGTATCGGAC
1 TAGATAAAGGAAAAACAAAGTATCGGAC
31739944 TAG
1 TAG
31739947 TCGATTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 7 0.26
28 15 0.56
29 5 0.19
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.19
Consensus pattern (28 bp):
TAGATAAAGGAAAAACAAAGTATCGGAC
Found at i:31741958 original size:6 final size:6
Alignment explanation
Indices: 31741947--31742136 Score: 337
Period size: 6 Copynumber: 31.8 Consensus size: 6
31741937 TATGTTAAAT
* * * *
31741947 ATATAG ATATAG ATATAG ATATAA ATAT-G TTAAAT ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
31741994 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
31742042 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
31742090 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
31742137 TGAACATGGC
Statistics
Matches: 175, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
5 2 0.01
6 173 0.99
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:31743708 original size:19 final size:19
Alignment explanation
Indices: 31743672--31743710 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31743662 TTTCCATCAT
* *
31743672 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
31743691 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
31743710 A
1 A
31743711 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:31744226 original size:27 final size:28
Alignment explanation
Indices: 31744174--31744243 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
31744164 GTGACAGAGT
* *
31744174 CACCAGATACAGATATGTTGTGGCAGTGC
1 CACCAGA-ACAGATATGATGTGGCAGGGC
31744203 CACCAGAACAGATAT-ATGTGGCAGGGC
1 CACCAGAACAGATATGATGTGGCAGGGC
31744230 CACCAGAACAGATA
1 CACCAGAACAGATA
31744244 ATTTATGGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 24 0.62
28 8 0.21
29 7 0.18
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (28 bp):
CACCAGAACAGATATGATGTGGCAGGGC
Found at i:31744261 original size:28 final size:26
Alignment explanation
Indices: 31744174--31744263 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 26
31744164 GTGACAGAGT
31744174 CACCAGATACAGATATGTTGTGGCAGTGC
1 CACCAGA-ACAGATAT-TTGTGGCA-TGC
* *
31744203 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCA-TGC
*
31744230 CACCAGAACAGATAATTTATGGCATAGC
1 CACCAGAACAGAT-ATTTGTGGCAT-GC
31744258 CACCAG
1 CACCAG
31744264 GACGCTTCCT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 23 0.43
28 24 0.44
29 7 0.13
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.19
Consensus pattern (26 bp):
CACCAGAACAGATATTTGTGGCATGC
Found at i:31744416 original size:28 final size:28
Alignment explanation
Indices: 31744369--31744433 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
31744359 AAATTAACCC
* *
31744369 TAGGGGTATAGAGGTCATTTTGCAGACA
1 TAGGGGTATAGAGGTAATTTTACAGACA
*
31744397 TAGGGGTATA-ATGGTAATTTTACATACA
1 TAGGGGTATAGA-GGTAATTTTACAGACA
31744425 TAGGGGTAT
1 TAGGGGTAT
31744434 TCTAGTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTACAGACA
Found at i:31746553 original size:44 final size:42
Alignment explanation
Indices: 31746469--31746627 Score: 123
Period size: 43 Copynumber: 3.8 Consensus size: 42
31746459 TGTGATTTTT
* *
31746469 TGTAAGACCACGTCTGGAACGTTGGCATCG-ACTTCT-ATTTTAC
1 TGTAAGACCACGTCTGGGACATTGGCATCGTA--TCTGA-TTTAC
*
31746512 GTGTAAGACCATGTCTGGGACATTGGCATCGTATCTGATTT--
1 -TGTAAGACCACGTCTGGGACATTGGCATCGTATCTGATTTAC
** * * *
31746553 T-TAAGACCTTGTCTGGGACATTGGCATTGATGTTTGA-TTAC
1 TGTAAGACCACGTCTGGGACATTGGCATCG-TATCTGATTTAC
* * *
31746594 ATGTAAGACCACGTCTAGGACGTTGGCATTGTAT
1 -TGTAAGACCACGTCTGGGACATTGGCATCGTAT
31746628 ATGTTCTCTG
Statistics
Matches: 96, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
39 28 0.29
40 6 0.06
42 3 0.03
43 30 0.31
44 28 0.29
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGTATCTGATTTAC
Found at i:31760153 original size:29 final size:29
Alignment explanation
Indices: 31760120--31760188 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
31760110 TAGGAACAGG
*
31760120 AAATTTCATTAGGATATCTTAGGTTAATT
1 AAATTTCATTAGGATATCTTAGATTAATT
* *
31760149 AAATTTCATTAGGTTATTTTAGATTAATT
1 AAATTTCATTAGGATATCTTAGATTAATT
*
31760178 -AATTTAATTAG
1 AAATTTCATTAG
31760189 TTTAATTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 10 0.28
29 26 0.72
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (29 bp):
AAATTTCATTAGGATATCTTAGATTAATT
Found at i:31761127 original size:13 final size:13
Alignment explanation
Indices: 31761109--31761133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31761099 TAATTTATAT
31761109 GTGTGAAAATTTC
1 GTGTGAAAATTTC
31761122 GTGTGAAAATTT
1 GTGTGAAAATTT
31761134 TATCGTTTGA
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:31762353 original size:43 final size:43
Alignment explanation
Indices: 31762234--31762353 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 43
31762224 CATAGGATTC
31762234 CGATATGTGATT-CGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
* * * *
31762276 CGATTTGTAATTTACGTGTAAGACC-CTATTTGGGACAG-TGGCAT
1 CGATATGTGA-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
* *
31762320 TGATATGTGATTACATGTAAGACCACGTCTGGGA
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGA
31762354 TGTTTGCGTT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
42 8 0.13
43 22 0.35
44 32 0.51
45 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (43 bp):
CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:31766209 original size:47 final size:47
Alignment explanation
Indices: 31766152--31766708 Score: 915
Period size: 47 Copynumber: 11.9 Consensus size: 47
31766142 GTATGGCGTT
*
31766152 ATGGCCGATGTGATGAATATGAAAGTGTATATATGTGATAAGGCCTA
1 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
31766199 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
1 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
31766246 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
1 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
*
31766293 ATGGCCGATGTGATGAATGTGAAAGTGTATATATATGATAAGGCCTA
1 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
*
31766340 ATGGCCGATGTGATGAATATGAAAGTGTATATATGTGATAAGGCCTA
1 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
* *
31766387 ATGGTCGATGTGATGAATATGAAAGTGTATATATGTGATAAGGCCTA
1 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
*
31766434 ATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
1 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
31766481 ATGGCCGATGTGATGAATGTGAAAGTGTATATA--TGATAAGGCCTA
1 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
*
31766526 ATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
1 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
*
31766573 ATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
1 ATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTA
* * * *
31766622 ATGGACGATGTGATGAATGTGAAAGTG--TATATGTGACAGGGCCGA
1 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
* * * * *
31766667 GTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
31766709 TCCCGAAGGG
Statistics
Matches: 479, Mismatches: 25, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
45 81 0.17
47 353 0.74
49 45 0.09
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
Found at i:31766375 original size:25 final size:25
Alignment explanation
Indices: 31766347--31766425 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
31766337 CTAATGGCCG
31766347 ATGTGATGAATATGAAAGTGTATAT
1 ATGTGATGAATATGAAAGTGTATAT
***** * **
31766372 ATGTGAT-AAGGCCTAA-TG-GTCG
1 ATGTGATGAATATGAAAGTGTATAT
31766394 ATGTGATGAATATGAAAGTGTATAT
1 ATGTGATGAATATGAAAGTGTATAT
31766419 ATGTGAT
1 ATGTGAT
31766426 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 8 0.23
23 6 0.17
24 6 0.17
25 15 0.43
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (25 bp):
ATGTGATGAATATGAAAGTGTATAT
Found at i:31772563 original size:32 final size:32
Alignment explanation
Indices: 31772527--31772590 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
31772517 GATCTGAATT
31772527 TTAGATAGTGAGGTTAAAGAATTAAGAAATAA
1 TTAGATAGTGAGGTTAAAGAATTAAGAAATAA
31772559 TTAGATAGTGAGGTTAAAGAATTAAGAAATAA
1 TTAGATAGTGAGGTTAAAGAATTAAGAAATAA
31772591 GAAAATCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (32 bp):
TTAGATAGTGAGGTTAAAGAATTAAGAAATAA
Found at i:31772864 original size:13 final size:13
Alignment explanation
Indices: 31772846--31772870 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31772836 TAATTTATAT
31772846 GTGTGAAAATTTC
1 GTGTGAAAATTTC
31772859 GTGTGAAAATTT
1 GTGTGAAAATTT
31772871 TATCGTTTGA
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:31774048 original size:43 final size:43
Alignment explanation
Indices: 31773929--31774048 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 43
31773919 TAGGATTCTT
* *
31773929 ATATATGATT-CATGTAGGACCACGTCTGGGACATTGGCATCG
1 ATATATGATTACATGTAAGACCACGTCTGGGACAGTGGCATCG
* *
31773971 ATTTATGATTTA-AGTGTAAGACC-CTGTCTAGGACAGTGGCATCG
1 ATATATGA-TTACA-TGTAAGACCAC-GTCTGGGACAGTGGCATCG
* *
31774015 ATATGTGATTACATGTAAGACCACATCTGGGACA
1 ATATATGATTACATGTAAGACCACGTCTGGGACA
31774049 TTAGCGTTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
42 7 0.11
43 24 0.38
44 33 0.52
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (43 bp):
ATATATGATTACATGTAAGACCACGTCTGGGACAGTGGCATCG
Found at i:31775614 original size:46 final size:46
Alignment explanation
Indices: 31775564--31775736 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
31775554 TGGTTGAGCA
*
31775564 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
31775610 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
31775657 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
31775703 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
31775737 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.58
47 29 0.27
48 3 0.03
50 4 0.04
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:31775720 original size:93 final size:93
Alignment explanation
Indices: 31775561--31775731 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
31775551 GGATGGTTGA
* * *
31775561 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACGCCCGAACTCGTTGAGT
31775626 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
31775654 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATACGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACGCCCGAACTCGTTGAGT
31775719 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
31775732 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:31775998 original size:19 final size:20
Alignment explanation
Indices: 31775961--31775998 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
31775951 ATAAGGTGGT
31775961 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
31775981 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
31775999 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Done.