Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 125 of 240
Found at i:38855500 original size:34 final size:33
Alignment explanation
Indices: 38855462--38855608 Score: 77
Period size: 34 Copynumber: 4.3 Consensus size: 33
38855452 ATTAATATTA
38855462 TACATAACTTACATAACTTACAACTTACATAACT
1 TACATAACTTACATAA-TTACAACTTACATAACT
*** * * *
38855496 TACATTTTTTTA-ATTATT-CGTAAATTACACAACT
1 TACA-TAACTTACATAATTAC--AACTTACATAACT
* * * * *
38855530 TACTTAATTTTCATAATAAATAACTTACATAACT
1 TACATAACTTACATAAT-TACAACTTACATAACT
*
38855564 TAC--AACTTACATAACTTATATGACTTACATAACT
1 TACATAACTTACATAA-TTACA--ACTTACATAACT
*
38855598 TACATAGCTTA
1 TACATAACTTA
38855609 ACTATACTTA
Statistics
Matches: 83, Mismatches: 19, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
32 13 0.16
33 7 0.08
34 54 0.65
35 4 0.05
36 5 0.06
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (33 bp):
TACATAACTTACATAATTACAACTTACATAACT
Found at i:38855501 original size:236 final size:232
Alignment explanation
Indices: 38855091--38855550 Score: 751
Period size: 236 Copynumber: 2.0 Consensus size: 232
38855081 TACATATCAT
* *
38855091 TTAATTAATTAATATACATAAATTACATAAGTTACATTAATATTATACATAAATTACATAACTTA
1 TTAATTAATTAATAAACATAAATTACATAAATTACATTAATATTATACATAAATTACATAACTTA
* *
38855156 ATTAATTAATATTATGCATAACTTGCATTAATATTATACATAAATTACATAACTTAATTAATTAA
66 ATTAATTAATATTATACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAA
38855221 TATTATACATAACTTACATAACTTACAACTTACATAACTTACATTTTTATAATTATTCATAAATT
131 TATTATACATAACTTACATAACTTACAACTTACATAACTTACATTTTTATAATTATTCATAAATT
*
38855286 ACATAACTTACATTAATATT-ATACATAAATTACATAAC
196 ACACAACTTAC-TTAATATTCATA-ATAAATTACATAAC
38855324 TTAATTAATTAATAAACATAAATTACATAACTAATTACATTAATATTATACATAAATTACATAAC
1 TTAATTAATTAATAAACATAAATTACAT-A--AATTACATTAATATTATACATAAATTACATAAC
** * * *
38855389 TTTGTTAATTAATATTATACATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAAT
63 TTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAAT
* *
38855454 TAATATTATACATAACTTACATAACTTACAACTTACATAACTTACATTTTTTTAATTATTCGTAA
128 TAATATTATACATAACTTACATAACTTACAACTTACATAACTTACATTTTTATAATTATTCATAA
*
38855519 ATTACACAACTTACTTAATTTTCATAATAAAT
193 ATTACACAACTTACTTAATATTCATAATAAAT
38855551 AACTTACATA
Statistics
Matches: 210, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
233 27 0.13
234 1 0.00
235 13 0.06
236 169 0.80
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (232 bp):
TTAATTAATTAATAAACATAAATTACATAAATTACATTAATATTATACATAAATTACATAACTTA
ATTAATTAATATTATACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAA
TATTATACATAACTTACATAACTTACAACTTACATAACTTACATTTTTATAATTATTCATAAATT
ACACAACTTACTTAATATTCATAATAAATTACATAAC
Found at i:38855509 original size:56 final size:56
Alignment explanation
Indices: 38855213--38855511 Score: 173
Period size: 56 Copynumber: 5.1 Consensus size: 56
38855203 CATAACTTAA
38855213 TTAATTAATATTATACATAACTTACATAACTTACAACTTACATAACTTACATTTT-
1 TTAATTAATATTATACATAACTTACATAACTTACAACTTACATAACTTACATTTTG
* * ** * ***
38855268 TATAATTATTCATAAATTACATAACTTACATTAA--TATTA--TACATAAATTACA-TAAC
1 T-TAATTAAT-AT-TA-TACATAACTTACA-TAACTTACAACTTACATAACTTACATTTTG
* * * * *
38855324 TTAATTAATTAATAAACATAAATTACATAACTAATTACATTAATATTATACATAAATTACATAAC
1 TTAATTAA-TATTATACATAACTTACATAAC---TTAC----A-ACT-TACATAACTTACAT---
38855389 TTTG
53 TTTG
* * * * * * *
38855393 TTAATTAATATTATACATAACTTACATTAATATTA-TACTTAAATTACATA-AGTTAG
1 TTAATTAATATTATACATAACTTACA-TAA-CTTACAACTTACATAACTTACATTTTG
*
38855449 TTAATTAATATTATACATAACTTACATAACTTACAACTTACATAACTTACATTTTT
1 TTAATTAATATTATACATAACTTACATAACTTACAACTTACATAACTTACATTTTG
38855505 TTAATTA
1 TTAATTA
38855512 TTCGTAAATT
Statistics
Matches: 179, Mismatches: 37, Indels: 55
0.66 0.14 0.20
Matches are distributed among these distances:
52 3 0.02
53 11 0.06
54 4 0.02
55 23 0.13
56 60 0.34
57 4 0.02
58 4 0.02
59 14 0.08
60 10 0.06
61 2 0.01
62 1 0.01
65 13 0.07
67 3 0.02
68 15 0.08
69 12 0.07
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.41
Consensus pattern (56 bp):
TTAATTAATATTATACATAACTTACATAACTTACAACTTACATAACTTACATTTTG
Found at i:38855591 original size:18 final size:16
Alignment explanation
Indices: 38855551--38855601 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
38855541 CATAATAAAT
38855551 AACTTACATAACTTAC
1 AACTTACATAACTTAC
*
38855567 AACTTACATAACTTAT
1 AACTTACATAACTTAC
38855583 ATGACTTACATAACTTAC
1 A--ACTTACATAACTTAC
38855601 A
1 A
38855602 TAGCTTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 16 0.52
18 15 0.48
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:38861130 original size:65 final size:66
Alignment explanation
Indices: 38861028--38861173 Score: 197
Period size: 65 Copynumber: 2.2 Consensus size: 66
38861018 GAGGTAACAT
* *
38861028 CGAGAGAAGTTGAGGTTCAAAAAAGATATGAAAAACTCCAGCTACAGCTTAAAGCAGATGCAGCA
1 CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAAAACTCCAGCAACAGCTTAAAGCAGATGCAGCA
38861093 G
66 G
* * * *
38861094 CGAGAGAAGCT-AGGTTCAATGAAAG-TATGAAGAACTCCAGCAACAGCTTAGAGCAGATGCGGC
1 CGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAAAACTCCAGCAACAGCTTAAAGCAGATGCAGC
38861157 AG
65 AG
* *
38861159 CAAGAGAAGCAGAGG
1 CGAGAGAAGCTGAGG
38861174 CGGCAGCGAG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
65 53 0.76
66 17 0.24
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.14
Consensus pattern (66 bp):
CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAAAACTCCAGCAACAGCTTAAAGCAGATGCAGCA
G
Found at i:38861217 original size:21 final size:21
Alignment explanation
Indices: 38861145--38861256 Score: 98
Period size: 21 Copynumber: 5.3 Consensus size: 21
38861135 AACAGCTTAG
* * * *
38861145 AGCAGATGCGGCAGCAAGAGA
1 AGCAGAGGCTGCAGCGAGGGA
* *
38861166 AGCAGAGGCGGCAGCGAGAGA
1 AGCAGAGGCTGCAGCGAGGGA
* *
38861187 AGTACAGGCTGCAGCGAGGGA
1 AGCAGAGGCTGCAGCGAGGGA
* ** **
38861208 AGCAAAGGCTATAATGAGGGA
1 AGCAGAGGCTGCAGCGAGGGA
*
38861229 AGTAGAGGCTGCAGCGAGGGA
1 AGCAGAGGCTGCAGCGAGGGA
38861250 AGCAGAG
1 AGCAGAG
38861257 CAGCGTCAAA
Statistics
Matches: 72, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.35, C:0.16, G:0.42, T:0.07
Consensus pattern (21 bp):
AGCAGAGGCTGCAGCGAGGGA
Found at i:38861630 original size:43 final size:43
Alignment explanation
Indices: 38861564--38861752 Score: 191
Period size: 43 Copynumber: 4.4 Consensus size: 43
38861554 ATCTGCCAAA
* * ** *
38861564 TTTAGTGGCGTTTTTGGTCAAAGCGCCACTAAAGATAAGGGTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCACTAAAGATCAGGGTC
** * *
38861607 TTTAGCGGCGTTTGTGGAAAAAGCACCACTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCACTAAAGATCAGGGTC
* * *
38861650 TTTAGCGGCGTTTGTGGGGAAAGTGCCGCTATAGATCAGGGTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCACTAAAGATCAGGGTC
* * * * *
38861693 TATT-GCGACGTTTGAGGGGAAAGCGCCGCTAAAGATTAGGTTC
1 T-TTAGCGGCGTTTGTGGGGAAAGCGCCACTAAAGATCAGGGTC
* *
38861736 TATAGTGGCGTTTGTGG
1 TTTAGCGGCGTTTGTGG
38861753 TCGAAGCGCC
Statistics
Matches: 120, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
42 1 0.01
43 117 0.98
44 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGGAAAGCGCCACTAAAGATCAGGGTC
Found at i:38861716 original size:86 final size:86
Alignment explanation
Indices: 38861564--38861941 Score: 259
Period size: 86 Copynumber: 4.4 Consensus size: 86
38861554 ATCTGCCAAA
* * * * * * *
38861564 TTTAGTGGCGTTTTTGGTC-AAAGCGCCACTAAAGATAAGGGTCT-TTAGCGGCGTTTGTGGAAA
1 TTTAGCGGCGTTTGTGG-CGAAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTGAGGGAA
* *
38861627 AAGCACCACTAAAGATCATGGTC
64 AAGCGCCGCTAAAGATCATGGTC
* * * *
38861650 TTTAGCGGCGTTTGTGGGGAAAGTGCCGCTATAGATCAGGGTCTATTGCGACGTTTGAGGGGAAA
1 TTTAGCGGCGTTTGTGGCGAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGGAAAA
*
38861715 GCGCCGCTAAAGATTA-GGTTC
66 GCGCCGCTAAAGATCATGG-TC
* * * * * *
38861736 TATAGTGGCGTTTGTGGTCG-AAGCGCCGTTATAGATCAAGGTCTATTGCGGCTTTTGAGAGAAA
1 TTTAGCGGCGTTTGTGG-CGAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGGAAA
* * * *
38861800 AACGCCGCTAAAGACCCTGATC
65 AGCGCCGCTAAAGATCATGGTC
** * ** * * * * ** **
38861822 TTTAGCGGCACTTCTCCCAAAAACGTCGCTAAAGATCAGGGTCT-TTAGCGGCGCTTCCA--CTA
1 TTTAGCGGCGTTTGTGGCGAAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCG-TTTGAGGGAA
* * *
38861884 AAGCGCCGCTAAAGGTCTTAGTC
64 AAGCGCCGCTAAAGATCATGGTC
* *
38861907 TTCAGCGGCGTTTGT-GCTAGAAGCGCCGCTATAGA
1 TTTAGCGGCGTTTGTGGCGA-AAGCGCCGCTATAGA
38861942 CCAACACCTT
Statistics
Matches: 221, Mismatches: 62, Indels: 19
0.73 0.21 0.06
Matches are distributed among these distances:
84 2 0.01
85 46 0.21
86 166 0.75
87 7 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGGCGAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAGGGAAAA
GCGCCGCTAAAGATCATGGTC
Found at i:38861760 original size:43 final size:42
Alignment explanation
Indices: 38861570--38861792 Score: 167
Period size: 43 Copynumber: 5.2 Consensus size: 42
38861560 CAAATTTAGT
* * * * *
38861570 GGCGTTTTTGGTCAAAGCGCCACTAAAGATAAGGGTCTTTAGC
1 GGCGTTTGTGG-CGAAGCGCCGCTAAAGATCAGGGTCTATAGC
** * * * *
38861613 GGCGTTTGTGGAAAAAGCACCACTAAAGATCATGGTCTTTAGC
1 GGCGTTTGTGG-CGAAGCGCCGCTAAAGATCAGGGTCTATAGC
* * * *
38861656 GGCGTTTGTGGGGAAAGTGCCGCTATAGATCAGGGTCTATTGC
1 GGCGTTTGTGGCG-AAGCGCCGCTAAAGATCAGGGTCTATAGC
* * * * * *
38861699 GACGTTTGAGGGGAAAGCGCCGCTAAAGATTAGGTTCTATAGT
1 GGCGTTTGTGGCG-AAGCGCCGCTAAAGATCAGGGTCTATAGC
* * * *
38861742 GGCGTTTGTGGTCGAAGCGCCGTTATAGATCAAGGTCTATTGC
1 GGCGTTTGTGG-CGAAGCGCCGCTAAAGATCAGGGTCTATAGC
*
38861785 GGCTTTTG
1 GGCGTTTG
38861793 AGAGAAAAAC
Statistics
Matches: 144, Mismatches: 34, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
43 143 0.99
44 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (42 bp):
GGCGTTTGTGGCGAAGCGCCGCTAAAGATCAGGGTCTATAGC
Found at i:38861844 original size:43 final size:42
Alignment explanation
Indices: 38861797--38861897 Score: 112
Period size: 43 Copynumber: 2.4 Consensus size: 42
38861787 CTTTTGAGAG
** *
38861797 AAAAACGCCGCTAAAGACCCTGATCTTTAGCGGCACTTCTCCC
1 AAAAACGCCGCTAAAGACCAGGATCTTTAGCGGCACTTC-CAC
* * * *
38861840 AAAAACGTCGCTAAAGATCAGGGTCTTTAGCGGCGCTTCCAC
1 AAAAACGCCGCTAAAGACCAGGATCTTTAGCGGCACTTCCAC
* *
38861882 TAAAGCGCCGCTAAAG
1 AAAAACGCCGCTAAAG
38861898 GTCTTAGTCT
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 15 0.31
43 33 0.69
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCAGGATCTTTAGCGGCACTTCCAC
Found at i:38862079 original size:21 final size:21
Alignment explanation
Indices: 38862054--38862097 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
38862044 ATCTGCGGCG
* *
38862054 CTAAAAAGCGTCGCTAAAGGC
1 CTAAAAAGCGCCGCTAAAAGC
*
38862075 CTAAAAAGTGCCGCTAAAAGC
1 CTAAAAAGCGCCGCTAAAAGC
38862096 CT
1 CT
38862098 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (21 bp):
CTAAAAAGCGCCGCTAAAAGC
Found at i:38862369 original size:34 final size:34
Alignment explanation
Indices: 38862331--38862397 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
38862321 CTGTAAGCCG
*
38862331 TAACCATAAATCT-TAAACCCTAAACTATAAACCA
1 TAACCACAAA-CTGTAAACCCTAAACTATAAACCA
* * *
38862365 TAACCCCAAACTGTAAACCTTAAACTCTAAACC
1 TAACCACAAACTGTAAACCCTAAACTATAAACC
38862398 CATCAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.22
Consensus pattern (34 bp):
TAACCACAAACTGTAAACCCTAAACTATAAACCA
Found at i:38862375 original size:20 final size:20
Alignment explanation
Indices: 38862346--38862383 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38862336 ATAAATCTTA
*
38862346 AACCCTAAACTATAAACCAT
1 AACCCCAAACTATAAACCAT
*
38862366 AACCCCAAACTGTAAACC
1 AACCCCAAACTATAAACC
38862384 TTAAACTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.34, G:0.03, T:0.16
Consensus pattern (20 bp):
AACCCCAAACTATAAACCAT
Found at i:38862603 original size:13 final size:14
Alignment explanation
Indices: 38862572--38862604 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
38862562 ACCCTAAAGT
38862572 CTAAACCATAAATC
1 CTAAACCATAAATC
*
38862586 ATAAACCAT-AATC
1 CTAAACCATAAATC
38862599 CTAAAC
1 CTAAAC
38862605 TATATCTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAAACCATAAATC
Found at i:38863293 original size:114 final size:113
Alignment explanation
Indices: 38863154--38863700 Score: 419
Period size: 114 Copynumber: 4.8 Consensus size: 113
38863144 CTAATTGTGG
* *
38863154 GATATAGCGGCGTTTT-ATAGTAAGCGTCGCTAACGCCTCTATAGGTCAAGCTGGAACGATGCGT
1 GATATAGCGGCGTTTTCA-AGTAAGCGCCGCTAACGCCTCTATAGGTCAAGCCGGAACGATGCGT
*
38863218 TTTGGTCAAAATTTTTGCGTCGCCTCTAT-GGAAGCGCCACTAAAAGCTAA
65 TTTGGTCAAAATTTTTGCG-CGCTTCTATAGGAAGCGCCACTAAAAGC-AA
* ** * * * * * ** * *
38863268 TATATAGCGGCGTTTTCGGGTAAGCGCCTCTAACGGCGCTATAGCTAAAGATGAAACGTTGCGTT
1 GATATAGCGGCGTTTTCAAGTAAGCGCCGCTAACGCCTCTATAGGTCAAGCCGGAACGATGCGTT
* * * * * * * * ** *
38863333 TCGGTTTAAAATGTTT-CAGC-ATTTTTTAGTTAAGCGCCGCTAATTGCGA
66 TTGG-TCAAAATTTTTGC-GCGCTTCTATAG-GAAGCGCCACTAAAAGCAA
** * * *
38863382 GATATAGCAACATTTTCAAGTAAGCGCCACTAATGCCTCTATAGGTCAAGCCGGAACGATGCGTT
1 GATATAGCGGCGTTTTCAAGTAAGCGCCGCTAACGCCTCTATAGGTCAAGCCGGAACGATGCGTT
*
38863447 TTGGTCAAAATTTTTGCGACGCTTC-AGTA-GAAGCACCACTAAAAGCTAA
66 TTGGTCAAAATTTTTGCG-CGCTTCTA-TAGGAAGCGCCACTAAAAGC-AA
* ** * * * * * * *
38863496 TATATAGCGGCGTTTTCGTGTAAGCGCCGCTAACGGCACTATAGCTCAAGACGAAACGTTGCATT
1 GATATAGCGGCGTTTTCAAGTAAGCGCCGCTAACGCCTCTATAGGTCAAGCCGGAACGATGCGTT
* * * * * * * ** *
38863561 TCGGTTTAAAATTTTTTG-GCG-TTTTTTAGTAGAGCGTCGCTAATTGCGA
66 TTGG-TCAAAA-TTTTTGCGCGCTTCTATAGGA-AGCGCCACTAAAAGCAA
* *
38863610 GATATAGCGGTGTTTTCAAGTAAGCGCCGCTAACGCCTCTATAGGTCAAGCCGGAACGATGCATT
1 GATATAGCGGCGTTTTCAAGTAAGCGCCGCTAACGCCTCTATAGGTCAAGCCGGAACGATGCGTT
38863675 TTGGTCAAAAATTTTATG-GCGCTTCT
66 TTGGTC-AAAATTTT-TGCGCGCTTCT
38863701 GCTAAAAGCT
Statistics
Matches: 324, Mismatches: 91, Indels: 35
0.72 0.20 0.08
Matches are distributed among these distances:
113 34 0.10
114 238 0.73
115 46 0.14
116 6 0.02
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (113 bp):
GATATAGCGGCGTTTTCAAGTAAGCGCCGCTAACGCCTCTATAGGTCAAGCCGGAACGATGCGTT
TTGGTCAAAATTTTTGCGCGCTTCTATAGGAAGCGCCACTAAAAGCAA
Found at i:38863488 original size:228 final size:226
Alignment explanation
Indices: 38863073--38863840 Score: 904
Period size: 228 Copynumber: 3.4 Consensus size: 226
38863063 AAAATTTTTG
* *
38863073 CGGCGCTATAGCTCAAGACGAAACGTTGACTTTCGGTTTAAAGTTTTCCAGTGTTTTTTAGTTAA
1 CGGCGCTATAGCTCAAGACGAAACGTTG-CTTTCGGTTTAAAATTTT-CAGCGTTTTTTAGTTAA
* * *
38863138 GCGCCGCTAATTGTGGGATATAGCGGCGTTTT-ATAGTAAGCGTCGCTAACGCCTCTATAGGTCA
64 GCGCCGCTAATTGCGAGATATAGCGGCGTTTTCA-AGTAAGCGCCGCTAACGCCTCTATAGGTCA
* * * *
38863202 AGCTGGAACGATGCGTTTTGGTCAAAATTTTTGCGTCGCCTCTATGGAAGCGCCACTAAAAGCTA
128 AGCCGGAACGATGCGTTTTGGTCAAAATTTTTGCGACGCCTCTATAGAAGCACCACTAAAAGCTA
*
38863267 ATATATAGCGGCGTTTTCGGGTAAGCGCCTCTAA
193 ATATATAGCGGCGTTTTCGGGTAAGCGCCGCTAA
* * *
38863301 CGGCGCTATAGCTAAAGATGAAACGTTGCGTTTCGGTTTAAAATGTTTCAGCATTTTTTAGTTAA
1 CGGCGCTATAGCTCAAGACGAAACGTTGC-TTTCGGTTTAAAAT-TTTCAGCGTTTTTTAGTTAA
** * * *
38863366 GCGCCGCTAATTGCGAGATATAGCAACATTTTCAAGTAAGCGCCACTAATGCCTCTATAGGTCAA
64 GCGCCGCTAATTGCGAGATATAGCGGCGTTTTCAAGTAAGCGCCGCTAACGCCTCTATAGGTCAA
*
38863431 GCCGGAACGATGCGTTTTGGTCAAAATTTTTGCGACGCTTC-AGTAGAAGCACCACTAAAAGCTA
129 GCCGGAACGATGCGTTTTGGTCAAAATTTTTGCGACGCCTCTA-TAGAAGCACCACTAAAAGCTA
*
38863495 ATATATAGCGGCGTTTTCGTGTAAGCGCCGCTAA
193 ATATATAGCGGCGTTTTCGGGTAAGCGCCGCTAA
* **
38863529 CGGCACTATAGCTCAAGACGAAACGTTGCATTTCGGTTTAAAATTTTTTGGCGTTTTTTAG-TAG
1 CGGCGCTATAGCTCAAGACGAAACGTTGC-TTTCGGTTTAAAA-TTTTCAGCGTTTTTTAGTTA-
* *
38863593 AGCGTCGCTAATTGCGAGATATAGCGGTGTTTTCAAGTAAGCGCCGCTAACGCCTCTATAGGTCA
63 AGCGCCGCTAATTGCGAGATATAGCGGCGTTTTCAAGTAAGCGCCGCTAACGCCTCTATAGGTCA
* *
38863658 AGCCGGAACGATGCATTTTGGTCAAAAATTTTATG-G-CG-CT-TCT----G-----CTAAAAGC
128 AGCCGGAACGATGCGTTTTGGTC-AAAATTTT-TGCGACGCCTCTATAGAAGCACCACTAAAAGC
* * * * * * * **
38863710 TGATATCTAGCGGCTTTTTTGTGTAAGCGTCGTTGT
191 TAATATATAGCGGCGTTTTCGGGTAAGCGCCGCTAA
* ** *
38863746 CGGTGCTATAGCTCAAGACGAAACGTTGCATTTCGGTTTAAAATTTTTTGGCGTTATTTAGTTAA
1 CGGCGCTATAGCTCAAGACGAAACGTTGC-TTTCGGTTTAAAA-TTTTCAGCGTTTTTTAGTTAA
* * *
38863811 GCGCCACGAATT-CTGGGATATAGCGGCGTT
64 GCGCCGCTAATTGC-GAGATATAGCGGCGTT
38863841 GTCTACAACC
Statistics
Matches: 476, Mismatches: 53, Indels: 33
0.85 0.09 0.06
Matches are distributed among these distances:
216 1 0.00
217 118 0.25
218 2 0.00
222 1 0.00
226 1 0.00
227 5 0.01
228 332 0.70
229 14 0.03
230 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (226 bp):
CGGCGCTATAGCTCAAGACGAAACGTTGCTTTCGGTTTAAAATTTTCAGCGTTTTTTAGTTAAGC
GCCGCTAATTGCGAGATATAGCGGCGTTTTCAAGTAAGCGCCGCTAACGCCTCTATAGGTCAAGC
CGGAACGATGCGTTTTGGTCAAAATTTTTGCGACGCCTCTATAGAAGCACCACTAAAAGCTAATA
TATAGCGGCGTTTTCGGGTAAGCGCCGCTAA
Found at i:38863915 original size:217 final size:217
Alignment explanation
Indices: 38863485--38863915 Score: 503
Period size: 217 Copynumber: 2.0 Consensus size: 217
38863475 AGAAGCACCA
38863485 CTAAAAGCTAATATATAGCGGCGTTTTCGTGTAAGCGCCGCTAACGGCACTATAGCTCAAGACGA
1 CTAAAAGCTAATATATAGCGGCGTTTTCGTGTAAGCGCCGCTAACGGCACTATAGCTCAAGACGA
* * * *
38863550 AACGTTGCATTTCGGTTTAAAATTTTTTGGCGTTTTTTAGTAGAGCGTCGCTAATTGCGAGATAT
66 AACGTTGCATTTCGGTTTAAAATTTTTTGGCGTTATTTAGTAGAGCGCCACGAATTGCGAGATAT
* * * * * *
38863615 AGCGGTGTTTTCAAGTAAGCGCCGCTAACGCCTCTATAGGTCAAGCCGGAACGATGCATTTTGGT
131 AGCGGCGTTGTCAAGCAACCGCCGCTAACGCCTCTATACGTCAAGCCGAAACGATGCATTTTGGT
*
38863680 CAAAAATTTTATGGCGCTTCTG
196 CAAAAATTTTACGGCGCTTCTG
* * * * * * ** **
38863702 CTAAAAGCTGATATCTAGCGGCTTTTTTGTGTAAGCGTCGTTGTCGGTGCTATAGCTCAAGACGA
1 CTAAAAGCTAATATATAGCGGCGTTTTCGTGTAAGCGCCGCTAACGGCACTATAGCTCAAGACGA
*
38863767 AACGTTGCATTTCGGTTTAAAATTTTTTGGCGTTATTTAGTTA-AGCGCCACGAATT-CTGGGAT
66 AACGTTGCATTTCGGTTTAAAATTTTTTGGCGTTATTTAG-TAGAGCGCCACGAATTGC-GAGAT
* ** * * *
38863830 ATAGCGGCGTTGTCTA-CAACCGCCGCTATTGGCTTTATACGTCAAGACC-AAAC-ATTGCGTTT
129 ATAGCGGCGTTGTCAAGCAACCGCCGCTAACGCCTCTATACGTCAAG-CCGAAACGA-TGCATTT
* * *
38863892 TGGTTAAGATATTTTGCGGCGCTT
192 TGGTCAA-AAATTTTACGGCGCTT
38863916 TTTATAAAAT
Statistics
Matches: 178, Mismatches: 31, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
215 1 0.01
216 39 0.22
217 136 0.76
218 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (217 bp):
CTAAAAGCTAATATATAGCGGCGTTTTCGTGTAAGCGCCGCTAACGGCACTATAGCTCAAGACGA
AACGTTGCATTTCGGTTTAAAATTTTTTGGCGTTATTTAGTAGAGCGCCACGAATTGCGAGATAT
AGCGGCGTTGTCAAGCAACCGCCGCTAACGCCTCTATACGTCAAGCCGAAACGATGCATTTTGGT
CAAAAATTTTACGGCGCTTCTG
Found at i:38864802 original size:20 final size:19
Alignment explanation
Indices: 38864761--38864802 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
38864751 GTCATTTCAC
*
38864761 TGTTGTATTATTATTATTT
1 TGTTGTATTATTATTATAT
38864780 TGTTGTTATTGATTA-TATAT
1 TGTTG-TATT-ATTATTATAT
38864800 TGT
1 TGT
38864803 ATAACTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (19 bp):
TGTTGTATTATTATTATAT
Found at i:38865376 original size:40 final size:38
Alignment explanation
Indices: 38865323--38865398 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 38
38865313 CGCTATCTAA
*
38865323 AAAACGCCGCTAAAAATCGAGTATTAGCGACGCTTTTCTG
1 AAAACGCCGCTAAAAAT-GAGCATTAGCGACG-TTTTCTG
* *
38865363 AAAACGCCTCTAAAAATGAGCATTAGCGGCGTTTTC
1 AAAACGCCGCTAAAAATGAGCATTAGCGACGTTTTC
38865399 CAAAAAGCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 5 0.15
39 12 0.36
40 16 0.48
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (38 bp):
AAAACGCCGCTAAAAATGAGCATTAGCGACGTTTTCTG
Found at i:38865517 original size:41 final size:41
Alignment explanation
Indices: 38865456--38865642 Score: 250
Period size: 41 Copynumber: 4.6 Consensus size: 41
38865446 TTTTTTGGGA
* * **
38865456 TTTAGCGGCGTTTTTTAAGAAGCGCCGCTAAAGACCCAAG-C
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAAG-CTCTGGTC
* * *
38865497 ATTAGCGGCGTTTCTGAAGAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAAGCTCTGGTC
* *
38865538 TTTAGCGGCGTTTTTGAATAAGCGCAGCTAAAGCTCTGGTC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAAGCTCTGGTC
* *
38865579 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGTTCTGGTC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAAGCTCTGGTC
*
38865620 TTTAGCGGCGTTTTTGAACAAGC
1 TTTAGCGGCGTTTTTGAAGAAGC
38865643 ACCACTAGAA
Statistics
Matches: 128, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 3 0.02
41 125 0.98
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAAGCTCTGGTC
Found at i:38866010 original size:15 final size:15
Alignment explanation
Indices: 38865967--38866022 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
38865957 GGGATTATGA
*
38865967 TTTAAGGGTT-GGGA
1 TTTAAGGGTTAGGGG
* *
38865981 TTTAAGGTTTCGGGG
1 TTTAAGGGTTAGGGG
*
38865996 TTAAAGGGTTAGGGG
1 TTTAAGGGTTAGGGG
*
38866011 TTTAGGGGTTAG
1 TTTAAGGGTTAG
38866023 ACGTGTTAGG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
14 9 0.26
15 25 0.74
ACGTcount: A:0.20, C:0.02, G:0.43, T:0.36
Consensus pattern (15 bp):
TTTAAGGGTTAGGGG
Found at i:38866288 original size:21 final size:21
Alignment explanation
Indices: 38866216--38866296 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 21
38866206 GAGTTCATAT
38866216 TTTAAGGTTTAAGGAGTAT-AGA
1 TTTAAGGTTTAAGG-GT-TGAGA
* * * * *
38866238 TTTAGGGATTATGGATTAGCGA
1 TTTAAGGTTTAAGGGTT-GAGA
*
38866260 -TTATGGTTTAAGGGTTGAGA
1 TTTAAGGTTTAAGGGTTGAGA
*
38866280 TTTAAGGTTTAGGGGTT
1 TTTAAGGTTTAAGGGTT
38866297 AGGGGTTTAG
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
20 4 0.09
21 27 0.61
22 13 0.30
ACGTcount: A:0.27, C:0.01, G:0.32, T:0.40
Consensus pattern (21 bp):
TTTAAGGTTTAAGGGTTGAGA
Found at i:38866305 original size:15 final size:15
Alignment explanation
Indices: 38866285--38866313 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38866275 TGAGATTTAA
38866285 GGTTTAGGGGTTAGG
1 GGTTTAGGGGTTAGG
38866300 GGTTTAGGGGTTAG
1 GGTTTAGGGGTTAG
38866314 ATGTTATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.52, T:0.34
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:38866334 original size:36 final size:36
Alignment explanation
Indices: 38866264--38866344 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
38866254 TAGCGATTAT
* *
38866264 GGTTTAAGGGTTGAGATTTAAGGTTTAGGGGTTAGG
1 GGTTTAAGGGTTGAGATTTAAGGTTTAAGAGTTAGG
* * *
38866300 GGTTTAGGGGTT-AGATGTTATGGTTTAAGAGTTAGA
1 GGTTTAAGGGTTGAGAT-TTAAGGTTTAAGAGTTAGG
*
38866336 GATTTAAGG
1 GGTTTAAGG
38866345 TTTAAGGATT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
35 4 0.11
36 33 0.89
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.37
Consensus pattern (36 bp):
GGTTTAAGGGTTGAGATTTAAGGTTTAAGAGTTAGG
Found at i:38868855 original size:10 final size:10
Alignment explanation
Indices: 38868840--38868870 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
38868830 TGTGGTGGAC
*
38868840 TTGCTTGACT
1 TTGCTTAACT
38868850 TTGCTTAACT
1 TTGCTTAACT
38868860 TTGCTTAACT
1 TTGCTTAACT
38868870 T
1 T
38868871 ACATTATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.13, T:0.52
Consensus pattern (10 bp):
TTGCTTAACT
Found at i:38870664 original size:15 final size:16
Alignment explanation
Indices: 38870641--38870671 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
38870631 ATTTATCATA
38870641 GAAATAAATATTATTT
1 GAAATAAATATTATTT
38870657 GAAA-AAATATTATTT
1 GAAATAAATATTATTT
38870672 TTTTAAAAGA
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:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
GAAATAAATATTATTT
Found at i:38870819 original size:43 final size:42
Alignment explanation
Indices: 38870688--38870911 Score: 242
Period size: 43 Copynumber: 5.3 Consensus size: 42
38870678 AAGATATATT
** *
38870688 TTTAGCGGCGTTT-TCAGAAAAGCGTCGCTAAAGGTCTAT--TC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA-GTCT-TGGTC
* * * ** *
38870729 TATAGCGGCATTTGTGTG--AAGCGTTGCTAAAAGTATTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCT-AAAGTCTTGGTC
* * *
38870770 TTTAGCGGCGTTTGTGGGAAAATCGTCGCTGAATGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCT-AAAGTCTTGGTC
38870813 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA-GTCTTGGTC
*
38870856 TTTAGCGGCGTTTGTGGGAATAGCGCCGCTAAAGATCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG-TCTTGGTC
38870899 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
38870912 ATTTATAAAA
Statistics
Matches: 157, Mismatches: 18, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.01
40 12 0.08
41 31 0.20
42 5 0.03
43 108 0.69
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.33
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGTCTTGGTC
Found at i:38871020 original size:22 final size:22
Alignment explanation
Indices: 38870992--38871033 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
38870982 TAGCAGCGCT
*
38870992 AAAAACGCCGCTAAAGGCCTAA
1 AAAAACGCCGCTAAAAGCCTAA
38871014 AAAAACGCCGCTAAAAGCCT
1 AAAAACGCCGCTAAAAGCCT
38871034 GTTTTGGTGT
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:0.45, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
AAAAACGCCGCTAAAAGCCTAA
Found at i:38871540 original size:9 final size:9
Alignment explanation
Indices: 38871526--38871555 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
38871516 ATTTTGTATT
38871526 AATATTTTA
1 AATATTTTA
38871535 AATATTTTA
1 AATATTTTA
38871544 AATATTTCTA
1 AATATTT-TA
38871554 AA
1 AA
38871556 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (9 bp):
AATATTTTA
Found at i:38873802 original size:26 final size:26
Alignment explanation
Indices: 38873773--38873829 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
38873763 TGCTGAACAT
* **
38873773 AATTAAAATATATTAATTTATTTAAA
1 AATTAAAATATAATAATCAATTTAAA
* *
38873799 AATTCAAATATAATAATCAATTTTAA
1 AATTAAAATATAATAATCAATTTAAA
38873825 AATTA
1 AATTA
38873830 TAATTAAAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTAAAATATAATAATCAATTTAAA
Found at i:38882613 original size:27 final size:26
Alignment explanation
Indices: 38882550--38882613 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
38882540 AAAAATATTG
*
38882550 TAAATATATACAAATTATACAAATGA
1 TAAATATATTCAAATTATACAAATGA
* * * *
38882576 CATACTTTATTCAAATTATACAATTGA
1 TA-AATATATTCAAATTATACAAATGA
38882603 TTAAATATATT
1 -TAAATATATT
38882614 AATTAATACA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
26 1 0.04
27 26 0.93
28 1 0.04
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (26 bp):
TAAATATATTCAAATTATACAAATGA
Found at i:38882760 original size:23 final size:24
Alignment explanation
Indices: 38882727--38882771 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
38882717 AGTAAAAAGT
38882727 GAAATGAAAATGAAATTAAAATTG
1 GAAATGAAAATGAAATTAAAATTG
38882751 GAAATG-AAATGAAATTAAAAT
1 GAAATGAAAATGAAATTAAAAT
38882772 GAAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (24 bp):
GAAATGAAAATGAAATTAAAATTG
Found at i:38882777 original size:11 final size:11
Alignment explanation
Indices: 38882721--38882778 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
38882711 AAATAAAGTA
*
38882721 AAAAGTGAAATG
1 AAAA-TGAAATT
38882733 AAAATGAAATT
1 AAAATGAAATT
38882744 AAAATTGGAAA-T
1 AAAA-T-GAAATT
*
38882756 GAAATGAAATT
1 AAAATGAAATT
38882767 AAAATGAAATT
1 AAAATGAAATT
38882778 A
1 A
38882779 TATTTAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 4 0.10
11 23 0.57
12 9 0.22
13 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (11 bp):
AAAATGAAATT
Found at i:38882860 original size:22 final size:22
Alignment explanation
Indices: 38882830--38882898 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
38882820 GAACTTTTTT
*
38882830 ATTGAAATGAAATGAAATTAAA
1 ATTGGAATGAAATGAAATTAAA
*
38882852 ATTGGAATGAAATGAAATTCAA
1 ATTGGAATGAAATGAAATTAAA
*
38882874 ATT-GAATAGAAATTGAAATGAAA
1 ATTGGAAT-GAAA-TGAAATTAAA
38882897 AT
1 AT
38882899 ATAATTAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
21 4 0.10
22 27 0.66
23 10 0.24
ACGTcount: A:0.55, C:0.01, G:0.16, T:0.28
Consensus pattern (22 bp):
ATTGGAATGAAATGAAATTAAA
Found at i:38882864 original size:11 final size:11
Alignment explanation
Indices: 38882830--38882896 Score: 59
Period size: 11 Copynumber: 6.1 Consensus size: 11
38882820 GAACTTTTTT
38882830 ATTGAAATGAA
1 ATTGAAATGAA
*
38882841 A-TGAAATTAAA
1 ATTGAAA-TGAA
*
38882852 ATTGGAATGAA
1 ATTGAAATGAA
*
38882863 A-TGAAATTCAA
1 ATTGAAA-TGAA
38882874 ATTG-AATAGAA
1 ATTGAAAT-GAA
38882885 ATTGAAATGAA
1 ATTGAAATGAA
38882896 A
1 A
38882897 ATATAATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
10 10 0.23
11 25 0.57
12 9 0.20
ACGTcount: A:0.55, C:0.01, G:0.16, T:0.27
Consensus pattern (11 bp):
ATTGAAATGAA
Found at i:38882879 original size:17 final size:17
Alignment explanation
Indices: 38882839--38882896 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
38882829 TATTGAAATG
*
38882839 AAATGAAATTA-AAATTG
1 AAATGAAA-TAGAAATTC
*
38882856 GAATGAAAT-GAAATTC
1 AAATGAAATAGAAATTC
*
38882872 AAATTG-AATAGAAATTG
1 AAA-TGAAATAGAAATTC
38882889 AAATGAAA
1 AAATGAAA
38882897 ATATAATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 13 0.39
17 20 0.61
ACGTcount: A:0.57, C:0.02, G:0.16, T:0.26
Consensus pattern (17 bp):
AAATGAAATAGAAATTC
Found at i:38883121 original size:16 final size:16
Alignment explanation
Indices: 38883081--38883170 Score: 51
Period size: 16 Copynumber: 5.6 Consensus size: 16
38883071 GCTTAAAAAG
*
38883081 AAATCAAATGAAATTA
1 AAATAAAATGAAATTA
* *
38883097 AAGTAAAATGAGATTA
1 AAATAAAATGAAATTA
* *
38883113 AAATGAAAT-AAA-CA
1 AAATAAAATGAAATTA
*
38883127 AAATTCAAATGAAATTTA
1 AAA-TAAAATGAAA-TTA
*
38883145 AAA-AGAAATTGAAATGA
1 AAATA-AAA-TGAAATTA
*
38883162 TAATAAAAT
1 AAATAAAAT
38883171 TGACATGACA
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
14 4 0.07
15 7 0.13
16 24 0.44
17 10 0.18
18 10 0.18
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.24
Consensus pattern (16 bp):
AAATAAAATGAAATTA
Found at i:38883244 original size:6 final size:6
Alignment explanation
Indices: 38883198--38883260 Score: 53
Period size: 6 Copynumber: 11.2 Consensus size: 6
38883188 AAGTGAAATG
* * * * *
38883198 AAATTA TAATTT AAATT- AAATTC AAATT- AAATGA GAA--A AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
38883242 AAATTA AAATTA AAATTA A
1 AAATTA AAATTA AAATTA A
38883261 GTTTTAATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 3 0.06
5 9 0.19
6 35 0.74
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (6 bp):
AAATTA
Found at i:38883610 original size:33 final size:34
Alignment explanation
Indices: 38883573--38883647 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
38883563 TTGATTTGAA
* * *
38883573 AAATTTTAAA-GAGAAAAAAATTGAACTTAAATG
1 AAATTTAAAATGAGAAAAAAATTGAAATAAAATG
*
38883606 AAATTTAAAATGAGAAAAAAATTTAAATAAAATG
1 AAATTTAAAATGAGAAAAAAATTGAAATAAAATG
38883640 AAATTTAA
1 AAATTTAA
38883648 TTGAAGAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 9 0.24
34 28 0.76
ACGTcount: A:0.61, C:0.01, G:0.09, T:0.28
Consensus pattern (34 bp):
AAATTTAAAATGAGAAAAAAATTGAAATAAAATG
Found at i:38883626 original size:34 final size:33
Alignment explanation
Indices: 38883573--38883670 Score: 106
Period size: 34 Copynumber: 2.8 Consensus size: 33
38883563 TTGATTTGAA
* * *
38883573 AAATTTTAAAGAGAAAAAAATTGAACTTAAATG
1 AAATTTAAAAGAGAAAAAAATTGAAATAAAATG
*
38883606 AAATTTAAAATGAGAAAAAAATTTAAATAAAATG
1 AAATTTAAAA-GAGAAAAAAATTGAAATAAAATG
*
38883640 AAATTTAATTGAAGAAGAAAAAATTTGAAAT
1 AAATTTAA---AAG-AGAAAAAAATTGAAAT
38883671 TCAAATAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
33 9 0.17
34 28 0.52
36 1 0.02
37 16 0.30
ACGTcount: A:0.60, C:0.01, G:0.11, T:0.28
Consensus pattern (33 bp):
AAATTTAAAAGAGAAAAAAATTGAAATAAAATG
Found at i:38883810 original size:39 final size:39
Alignment explanation
Indices: 38883767--38883841 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
38883757 AGTTTTAACT
* *
38883767 AAAAAAAGTGAA-ATTGAAATAAAATTGAAATGAAATTAG
1 AAAAAAAATGAATA-TGAAAAAAAATTGAAATGAAATTAG
38883806 AAAAAAAATGAATATGAAAAAAAATTGAAATGAAAT
1 AAAAAAAATGAATATGAAAAAAAATTGAAATGAAAT
38883842 GAATTGTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.21
Consensus pattern (39 bp):
AAAAAAAATGAATATGAAAAAAAATTGAAATGAAATTAG
Found at i:38883814 original size:17 final size:18
Alignment explanation
Indices: 38883794--38883836 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
38883784 AATAAAATTG
38883794 AAATGAAATTA-GAAAAA
1 AAATGAAATTATGAAAAA
38883811 AAATG-AA-TATGAAAAA
1 AAATGAAATTATGAAAAA
38883827 AAATTGAAAT
1 AAA-TGAAAT
38883837 GAAATGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.09
16 11 0.50
17 7 0.32
18 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (18 bp):
AAATGAAATTATGAAAAA
Found at i:38883829 original size:56 final size:56
Alignment explanation
Indices: 38883767--38883885 Score: 161
Period size: 56 Copynumber: 2.1 Consensus size: 56
38883757 AGTTTTAACT
38883767 AAAAAAAGTGAAATTGAAATAAAAT-TGAAATGAAATTAGAAA-AAAAATGAATATGA
1 AAAAAAAGTGAAA-TGAAATAAAATGTGAAATGAAATTAGAAACAAAAATGAA-ATGA
* * * * *
38883823 AAAAAAATTGAAATGAAATGAATTGTGAAATGAAATTAGAAACTAAATTGAAATGA
1 AAAAAAAGTGAAATGAAATAAAATGTGAAATGAAATTAGAAACAAAAATGAAATGA
38883879 AAAAAAA
1 AAAAAAA
38883886 AAGTGACAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
55 9 0.16
56 40 0.71
57 7 0.12
ACGTcount: A:0.63, C:0.01, G:0.14, T:0.22
Consensus pattern (56 bp):
AAAAAAAGTGAAATGAAATAAAATGTGAAATGAAATTAGAAACAAAAATGAAATGA
Found at i:38883864 original size:12 final size:11
Alignment explanation
Indices: 38883775--38883880 Score: 76
Period size: 11 Copynumber: 9.5 Consensus size: 11
38883765 CTAAAAAAAG
38883775 TGAAATTGAAA
1 TGAAATTGAAA
*
38883786 TAAAATTGAAA
1 TGAAATTGAAA
38883797 TGAAATTAGAAA
1 TGAAATT-GAAA
* *
38883809 -AAAAATGAATA
1 TGAAATTGAA-A
**
38883820 TGAAA-AAAAA
1 TGAAATTGAAA
38883830 TTGAAA-TGAAA
1 -TGAAATTGAAA
*
38883841 TGAATTGTGAAA
1 TGAAAT-TGAAA
38883853 TGAAATTAGAAA
1 TGAAATT-GAAA
38883865 CT-AAATTGAAA
1 -TGAAATTGAAA
38883876 TGAAA
1 TGAAA
38883881 AAAAAAAGTG
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
10 9 0.12
11 39 0.52
12 26 0.35
13 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.15, T:0.25
Consensus pattern (11 bp):
TGAAATTGAAA
Found at i:38886503 original size:89 final size:90
Alignment explanation
Indices: 38886409--38886642 Score: 260
Period size: 90 Copynumber: 2.6 Consensus size: 90
38886399 TTAATAAAAC
* * * *
38886409 AAATATATAATTTGAAAAAAAAATAATACGCAAC-AAATGAAATTTACAGATACAAGAAAATAAA
1 AAATATAAAATTTGAAAAACAAATAATAC-CAACTAAATTAAATTTACAGATACAACAAAATAAA
* * *
38886473 AACA-TTCTATAATATTAATACACGA
65 AACAGATCGATAAAATTAATACACGA
** *
38886498 AAATATAAAATTT-AAACAACAAATAATA-CAGACTAAATTAAATTTACAGACCCAACAAAATAC
1 AAATATAAAATTTGAAA-AACAAATAATACCA-ACTAAATTAAATTTACAGATACAACAAAATAA
* *
38886561 AAACAGATGGGTAAAATTAATACACGA
64 AAACAGATCGATAAAATTAATACACGA
* * * **
38886588 AAATATAAAATTCGAACAACAAATAATACAAACTAAATTTGATTTACAGATACAA
1 AAATATAAAATTTGAAAAACAAATAATACCAACTAAATTAAATTTACAGATACAA
38886643 AAATAATACA
Statistics
Matches: 120, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
87 2 0.02
88 5 0.04
89 51 0.43
90 59 0.49
91 3 0.03
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (90 bp):
AAATATAAAATTTGAAAAACAAATAATACCAACTAAATTAAATTTACAGATACAACAAAATAAAA
ACAGATCGATAAAATTAATACACGA
Found at i:38888961 original size:18 final size:17
Alignment explanation
Indices: 38888919--38888996 Score: 72
Period size: 17 Copynumber: 4.5 Consensus size: 17
38888909 ATTTATAATT
*
38888919 TGAATATGA-AATGAAA
1 TGAAAATGAGAATGAAA
38888935 TTG-AAATGAGAATGAGAA
1 -TGAAAATGAGAATGA-AA
*
38888953 TGAAAATGAGAATGATA
1 TGAAAATGAGAATGAAA
38888970 TGAAAATG-GAAATGAATA
1 TGAAAATGAG-AATGAA-A
*
38888988 TGAATATGA
1 TGAAAATGA
38888997 AATCAATTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
16 6 0.12
17 23 0.45
18 22 0.43
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.24
Consensus pattern (17 bp):
TGAAAATGAGAATGAAA
Found at i:38888972 original size:23 final size:21
Alignment explanation
Indices: 38888922--38888999 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 21
38888912 TATAATTTGA
*
38888922 ATATGAAATGAAATTGAAATG
1 ATATGAAATGAAAATGAAATG
*
38888943 AGAATGAGAATGAAAATGAGAATG
1 A-TATGA-AATGAAAATGA-AATG
*
38888967 ATATGAAAATGGAAATGAATATG
1 ATATG-AAATGAAAATGAA-ATG
38888990 AATATGAAAT
1 -ATATGAAAT
38889000 CAATTGTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
21 1 0.02
22 5 0.11
23 30 0.64
24 11 0.23
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
ATATGAAATGAAAATGAAATG
Found at i:38888972 original size:29 final size:29
Alignment explanation
Indices: 38888927--38888999 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
38888917 TTTGAATATG
*
38888927 AAATGAAATTGAAATGAGAAT-GAGAATGA
1 AAATGAAATTGAAATGAAAATGGA-AATGA
*
38888956 AAATGAGAA-TGATATGAAAATGGAAATGA
1 AAATGA-AATTGAAATGAAAATGGAAATGA
*
38888985 ATATG-AATATGAAAT
1 AAATGAAAT-TGAAAT
38889000 CAATTGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
27 2 0.06
29 30 0.83
30 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.22, T:0.23
Consensus pattern (29 bp):
AAATGAAATTGAAATGAAAATGGAAATGA
Found at i:38888990 original size:6 final size:5
Alignment explanation
Indices: 38888919--38888999 Score: 63
Period size: 6 Copynumber: 14.2 Consensus size: 5
38888909 ATTTATAATT
*
38888919 TGAATA TGAAA TGAAA TTGAAA TGAGAA TGAGAA TGAAAA TGAGAA TGATA
1 TGAA-A TGAAA TGAAA -TGAAA TGA-AA TGA-AA TG-AAA TGA-AA TGAAA
38888970 TGAAAA TGGAAA TGAATA TGAATA TGAAA T
1 TG-AAA T-GAAA TGAA-A TGAA-A TGAAA T
38889000 CAATTGTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
5 18 0.27
6 46 0.70
7 2 0.03
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (5 bp):
TGAAA
Found at i:38891492 original size:14 final size:14
Alignment explanation
Indices: 38891473--38891519 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
38891463 TCCTTACACA
38891473 TTAAAATATAAATT
1 TTAAAATATAAATT
* **
38891487 TTAAAAT-TACACA
1 TTAAAATATAAATT
*
38891500 TTAAAACATAAATT
1 TTAAAATATAAATT
38891514 TTAAAA
1 TTAAAA
38891520 ACTTATAAAC
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAAAATATAAATT
Found at i:38891504 original size:27 final size:27
Alignment explanation
Indices: 38891466--38891519 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
38891456 TATACAATCC
*
38891466 TTACACATTAAAATATAAATTTTAAAA
1 TTACACATTAAAACATAAATTTTAAAA
38891493 TTACACATTAAAACATAAATTTTAAAA
1 TTACACATTAAAACATAAATTTTAAAA
38891520 ACTTATAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (27 bp):
TTACACATTAAAACATAAATTTTAAAA
Found at i:38897305 original size:20 final size:18
Alignment explanation
Indices: 38897258--38897306 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
38897248 CAAGATAAAC
38897258 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
38897275 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
38897295 ATTAAATTAATA
1 ATTAAATTAATA
38897307 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:38908232 original size:188 final size:183
Alignment explanation
Indices: 38907885--38908239 Score: 557
Period size: 188 Copynumber: 1.9 Consensus size: 183
38907875 GAAGGAGTTG
38907885 ATACTTTAATGTCACTTTCCATAGTTTGTTTAAAGATGAATAAAGTTGCATACCCCAATTCCAAA
1 ATACTTTAATGTCACTTTCCATAGTTTGTTTAAAGATGAATAAAGTTGCATACCCCAATTCCAAA
** * * *
38907950 TTGACTCTCTTTGCAATATACTCTCAAAATCATTATAATCAAACCCAACTAGAAAGTTCCTCTCC
66 TCAACTCTCTTTGCAATATACTCTCAAAATCATTATAACCAAACCCAACTAGAAAGTTACTCCCC
* *
38908015 GCCAAACTATAGAACAAAAAAACAGAAAAAAAGAAAATATTGAAAAAACTTTT
131 GCCAAACTACAAAACAAAAAAACAGAAAAAAAGAAAATATTGAAAAAACTTTT
*
38908068 ATACTTTAATGTCACTTTCCATAGTTTGTTTAAAGATGAATAAAGTTGCATACCCCAATTCCAAC
1 ATACTTTAATGTCACTTTCCATAGTTTGTTTAAAGATGAATAAAGTTGCATACCCCAATTCCAAA
* * *
38908133 TCAACAATCTTCTCTCTGCAATATGCTCTCAAAATCATTATAACCAAACCTACCTAGAAAGTTAC
66 TCAAC--TC-TCT-T-TGCAATATACTCTCAAAATCATTATAACCAAACCCAACTAGAAAGTTAC
*
38908198 TCCCCGCCAAACTACAAAACAAAAAAAGAGAAAAAAAGAAAA
126 TCCCCGCCAAACTACAAAACAAAAAAACAGAAAAAAAGAAAA
38908240 AGAAAAAATT
Statistics
Matches: 155, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
183 67 0.43
185 2 0.01
186 3 0.02
187 1 0.01
188 82 0.53
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (183 bp):
ATACTTTAATGTCACTTTCCATAGTTTGTTTAAAGATGAATAAAGTTGCATACCCCAATTCCAAA
TCAACTCTCTTTGCAATATACTCTCAAAATCATTATAACCAAACCCAACTAGAAAGTTACTCCCC
GCCAAACTACAAAACAAAAAAACAGAAAAAAAGAAAATATTGAAAAAACTTTT
Found at i:38911396 original size:14 final size:14
Alignment explanation
Indices: 38911374--38911404 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38911364 GAGAACTTAG
38911374 TTTAAGCTTATGTT
1 TTTAAGCTTATGTT
*
38911388 TTTAGGCTTATGTT
1 TTTAAGCTTATGTT
38911402 TTT
1 TTT
38911405 GGATTGCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.16, T:0.61
Consensus pattern (14 bp):
TTTAAGCTTATGTT
Found at i:38918794 original size:13 final size:14
Alignment explanation
Indices: 38918772--38918821 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
38918762 ATTTTACCCT
38918772 AAACCTTGAA-CTC
1 AAACCTTGAACCTC
* *
38918785 AAATCTTGAACCTT
1 AAACCTTGAACCTC
*
38918799 AAACCTTGAATCTC
1 AAACCTTGAACCTC
*
38918813 AAACTTTGA
1 AAACCTTGA
38918822 GGTTCAGGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 9 0.30
14 21 0.70
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (14 bp):
AAACCTTGAACCTC
Found at i:38921203 original size:18 final size:18
Alignment explanation
Indices: 38921169--38921215 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
38921159 GTATTCAAAA
*
38921169 TTATTATTTT-AATTTTTT
1 TTATT-TTTTAAAATTTTT
38921187 TTATTTTTTAAAATTTTT
1 TTATTTTTTAAAATTTTT
*
38921205 ATATCTTTTTA
1 TTAT-TTTTTA
38921216 GATTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTTTTTAAAATTTTT
Found at i:38921250 original size:16 final size:16
Alignment explanation
Indices: 38921227--38921260 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
38921217 ATTGTTTTAG
38921227 AACTTTTAAAT-TTTT
1 AACTTTTAAATATTTT
38921242 AACTATTTAAATATTTT
1 AACT-TTTAAATATTTT
38921259 AA
1 AA
38921261 AAAAATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 7 0.41
17 6 0.35
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
AACTTTTAAATATTTT
Found at i:38925632 original size:6 final size:6
Alignment explanation
Indices: 38925621--38925648 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
38925611 AGTTTCACAT
38925621 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
38925649 AGTATATGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTA
Found at i:38927252 original size:13 final size:13
Alignment explanation
Indices: 38927234--38927266 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
38927224 TAGCACAATT
38927234 GGGAAATCAGCAA
1 GGGAAATCAGCAA
*
38927247 GGGAAATCAGTAA
1 GGGAAATCAGCAA
38927260 GGGAAAT
1 GGGAAAT
38927267 GGGAAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.45, C:0.09, G:0.33, T:0.12
Consensus pattern (13 bp):
GGGAAATCAGCAA
Found at i:38929852 original size:20 final size:20
Alignment explanation
Indices: 38929827--38929864 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38929817 GCCCCGTTTC
*
38929827 ACTAAAGCTTTTATACGCCT
1 ACTAAAGCTTCTATACGCCT
38929847 ACTAAAGCTTCTATACGC
1 ACTAAAGCTTCTATACGC
38929865 ACCGTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (20 bp):
ACTAAAGCTTCTATACGCCT
Found at i:38938964 original size:11 final size:11
Alignment explanation
Indices: 38938950--38938990 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
38938940 TGTTTTCTCC
38938950 CTATTTTGCTA
1 CTATTTTGCTA
*
38938961 CTATTTTACTA
1 CTATTTTGCTA
* *
38938972 TTATGTTGCTA
1 CTATTTTGCTA
38938983 CTATTTTG
1 CTATTTTG
38938991 TTATTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:38939063 original size:30 final size:30
Alignment explanation
Indices: 38939027--38939088 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
38939017 ACTTATTTTA
38939027 TTGTTAATTTTATTATTATTTTAAAAGCAT
1 TTGTTAATTTTATTATTATTTTAAAAGCAT
* * *
38939057 TTGTTAATTTTGTTATTATTTTAGAAGTAT
1 TTGTTAATTTTATTATTATTTTAAAAGCAT
38939087 TT
1 TT
38939089 ACTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAAGCAT
Found at i:38943553 original size:20 final size:21
Alignment explanation
Indices: 38943520--38943583 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 21
38943510 CAGCTCCTTT
* *
38943520 AGCTCGTTTCAGCTCCAA-TC
1 AGCTCATTTGAGCTCCAATTC
38943540 AGCTCATTTGAGCT-CAATTC
1 AGCTCATTTGAGCTCCAATTC
* *
38943560 AGCTCATTCGAGCT-CAATTT
1 AGCTCATTTGAGCTCCAATTC
38943580 AGCT
1 AGCT
38943584 TTCTATCAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.08
20 36 0.92
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (21 bp):
AGCTCATTTGAGCTCCAATTC
Found at i:38943574 original size:30 final size:30
Alignment explanation
Indices: 38943517--38943583 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
38943507 TTCCAGCTCC
**
38943517 TTTAGCTCGTTTCAGCTCCAATCAGCTC-A
1 TTTAGCTCAATTCAGCTCCAATCAGCTCAA
*
38943546 TTTGAGCTCAATTCAGCT-CATTCGAGCTCAA
1 TTT-AGCTCAATTCAGCTCCAATC-AGCTCAA
38943577 TTTAGCT
1 TTTAGCT
38943584 TTCTATCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 7 0.22
30 21 0.66
31 4 0.12
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (30 bp):
TTTAGCTCAATTCAGCTCCAATCAGCTCAA
Found at i:38947149 original size:16 final size:16
Alignment explanation
Indices: 38947124--38947158 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38947114 ATTTAATCCC
* *
38947124 TAATACTAAAACTATT
1 TAATAATAAAAATATT
38947140 TAATAATAAAAATATT
1 TAATAATAAAAATATT
38947156 TAA
1 TAA
38947159 AATCTTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAATAAAAATATT
Found at i:38947311 original size:4 final size:4
Alignment explanation
Indices: 38947302--38947356 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
38947292 CCGTGCGCGA
** *
38947302 CTTT CTTT CTCC CTTT CTTT -TCTT -TTT CTTT CTTT TTTT CTTT CTTTT
1 CTTT CTTT CTTT CTTT CTTT CT-TT CTTT CTTT CTTT CTTT CTTT C-TTT
38947350 CTTT CTT
1 CTTT CTT
38947357 AATTTGCATG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
3 3 0.07
4 35 0.83
5 4 0.10
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:38947337 original size:9 final size:9
Alignment explanation
Indices: 38947314--38947356 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
38947304 TTCTTTCTCC
38947314 CTTTCTTTT
1 CTTTCTTTT
*
38947323 CTTTTTCTTT
1 CTTTCT-TTT
38947333 CTTT-TTTT
1 CTTTCTTTT
38947341 CTTTCTTTT
1 CTTTCTTTT
38947350 CTTTCTT
1 CTTTCTT
38947357 AATTTGCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 7 0.23
9 17 0.55
10 7 0.23
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
CTTTCTTTT
Found at i:38949575 original size:22 final size:21
Alignment explanation
Indices: 38949549--38949599 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
38949539 AAGAGGTTTC
*
38949549 TAAATTTTTTTTGAAGTTTCAA
1 TAAATTTTTCTTG-AGTTTCAA
* *
38949571 TAAATATTTCTTGAGTTTTAA
1 TAAATTTTTCTTGAGTTTCAA
*
38949592 TGAATTTT
1 TAAATTTT
38949600 CAGAAAATAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55
Consensus pattern (21 bp):
TAAATTTTTCTTGAGTTTCAA
Found at i:38951561 original size:27 final size:27
Alignment explanation
Indices: 38951513--38951564 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
38951503 AAAAACATTT
*
38951513 ATATACATGATATCAATTTATTCAAAA
1 ATATACATGATATCAATATATTCAAAA
38951540 ATATACATGATATTC-ATATATTCAA
1 ATATACATGATA-TCAATATATTCAA
38951565 TATATATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (27 bp):
ATATACATGATATCAATATATTCAAAA
Found at i:38958798 original size:26 final size:26
Alignment explanation
Indices: 38958748--38958799 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
38958738 ATTATACACA
*
38958748 AAAACAATTTTAAAATACTACGTATG
1 AAAACAATTTTAAAATAATACGTATG
*
38958774 AAAA-AATTTTAAAAGTAATATGTATG
1 AAAACAATTTTAAAA-TAATACGTATG
38958800 TACATATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.33
Consensus pattern (26 bp):
AAAACAATTTTAAAATAATACGTATG
Found at i:38971750 original size:31 final size:31
Alignment explanation
Indices: 38971712--38971770 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
38971702 CTGTGGAAAG
38971712 AAAAAAAATAGGGTTCTTTCTTTTATTTAGA
1 AAAAAAAATAGGGTTCTTTCTTTTATTTAGA
38971743 AAAAAAAATAGGGTTCTTTCTTTTATTT
1 AAAAAAAATAGGGTTCTTTCTTTTATTT
38971771 TATTTTTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (31 bp):
AAAAAAAATAGGGTTCTTTCTTTTATTTAGA
Found at i:38992559 original size:128 final size:128
Alignment explanation
Indices: 38992328--38992580 Score: 452
Period size: 128 Copynumber: 2.0 Consensus size: 128
38992318 TGCATGCTTC
* *
38992328 CTTAATCGCCAACACTTTTGCACTAGAGGCATCGACATTAACTTCAACACTCCTGAATATGGTGC
1 CTTAATCGCCAACACTTTTGCAATAGAGGCATCAACATTAACTTCAACACTCCTGAATATGGTGC
*
38992393 ACTCTATCGAGCTGAAGGCCTCACCCTTTTATATTTTTTCTTCAATCTAAAACAATTAGAAAA
66 ACTCTATCGAGCTGAAGGCCTCACCCTTTTATACTTTTTCTTCAATCTAAAACAATTAGAAAA
* * *
38992456 CTTAATTGCCAACACTTTTGCAATAGAGGCATCAACATTAACTTCAACACTCCTGACTGTGGTGC
1 CTTAATCGCCAACACTTTTGCAATAGAGGCATCAACATTAACTTCAACACTCCTGAATATGGTGC
38992521 ACTCTATCGAGCTGAAGGCCTCACCCTTTTATACTTTTTCTTCAATCTAAAACAATTAGA
66 ACTCTATCGAGCTGAAGGCCTCACCCTTTTATACTTTTTCTTCAATCTAAAACAATTAGA
38992581 GAATCTGGAA
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 119 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (128 bp):
CTTAATCGCCAACACTTTTGCAATAGAGGCATCAACATTAACTTCAACACTCCTGAATATGGTGC
ACTCTATCGAGCTGAAGGCCTCACCCTTTTATACTTTTTCTTCAATCTAAAACAATTAGAAAA
Found at i:38993095 original size:31 final size:31
Alignment explanation
Indices: 38993059--38993130 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
38993049 ATATTAAAAC
38993059 TATACATGAACTTTGAACTAATGTTG-AATGT
1 TATACATGAACTTTGAACTAATG-TGCAATGT
*
38993090 TATACATGAACTTTGAACTAATGTGCAATTT
1 TATACATGAACTTTGAACTAATGTGCAATGT
*
38993121 TATATATGAA
1 TATACATGAA
38993131 ATTTAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (31 bp):
TATACATGAACTTTGAACTAATGTGCAATGT
Found at i:39002239 original size:301 final size:301
Alignment explanation
Indices: 39001697--39002298 Score: 1105
Period size: 301 Copynumber: 2.0 Consensus size: 301
39001687 ATGAAACATC
*
39001697 ATTGTTTGATCCTTGAAACATTATGAAAATTGTTTAATCATTGGAACATTTAACAGACTTTCAAC
1 ATTGTTTGATCCTTGAAACATTATGAAAATTGTTTAATCATTGGAACATTTAACAGACTTTAAAC
39001762 ATTATACTTACATTAAATCAACAAATTGCATGTCTATTGTCACTCTTTTCTTTTACATACACTTG
66 ATTATACTTACATTAAATCAACAAATTGCATGTCTATTGTCACTCTTTTCTTTTACATACACTTG
* * *
39001827 ACATATATGTCGAAACCGTTTTTTTGAAAACAAAAATTTTGTTGTCGACTTTAAAAATAAAATTG
131 ACATATATGTCGAAACCGGTTTTTTGAAAACAAAAATTTTGTTGCCGACTTTAAAAATAAAACTG
* *
39001892 GAGTCGCCACCGATCCTTTATTAAGGTGTGATCGGCTCATCTTAAAAATTATTTTGGTCTACGAA
196 GAGTCGCCACCGATCCTTTATTAAGGTGTGATCGGCTCACCTTAAAAATTATTTTAGTCTACGAA
*
39001957 TTTTGAGAAAACGAGTTCGGGAGTCAGTTACGTACGAGGAA
261 TTTTGAGAAAACGAGTTCGGGAATCAGTTACGTACGAGGAA
* *
39001998 ATTGTTTGATCCTTGGAACATTATGAAAATTGTTTGATCATTGGAACATTTAACAGACTTTAAAC
1 ATTGTTTGATCCTTGAAACATTATGAAAATTGTTTAATCATTGGAACATTTAACAGACTTTAAAC
39002063 ATTATACTTACATTAAATCAACAAATTGCATGTCTATTGTCACTCTTTTCTTTTACATACACTTG
66 ATTATACTTACATTAAATCAACAAATTGCATGTCTATTGTCACTCTTTTCTTTTACATACACTTG
* *
39002128 ATATATATGTCGAAATCGGTTTTTTGAAAACAAAAATTTTGTTGCCGACTTTAAAAATAAAACTG
131 ACATATATGTCGAAACCGGTTTTTTGAAAACAAAAATTTTGTTGCCGACTTTAAAAATAAAACTG
39002193 GAGTCGCCACCGATCCTTTATTAAGGTGTGATCGGCTCACCTTAAAAATTATTTTAGTCTACGAA
196 GAGTCGCCACCGATCCTTTATTAAGGTGTGATCGGCTCACCTTAAAAATTATTTTAGTCTACGAA
39002258 TTTTGAGAAAACGAGTTCGGGAATCAGTTACGTACGAGGAA
261 TTTTGAGAAAACGAGTTCGGGAATCAGTTACGTACGAGGAA
39002299 GGGTTAGCAC
Statistics
Matches: 290, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
301 290 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (301 bp):
ATTGTTTGATCCTTGAAACATTATGAAAATTGTTTAATCATTGGAACATTTAACAGACTTTAAAC
ATTATACTTACATTAAATCAACAAATTGCATGTCTATTGTCACTCTTTTCTTTTACATACACTTG
ACATATATGTCGAAACCGGTTTTTTGAAAACAAAAATTTTGTTGCCGACTTTAAAAATAAAACTG
GAGTCGCCACCGATCCTTTATTAAGGTGTGATCGGCTCACCTTAAAAATTATTTTAGTCTACGAA
TTTTGAGAAAACGAGTTCGGGAATCAGTTACGTACGAGGAA
Found at i:39009450 original size:23 final size:23
Alignment explanation
Indices: 39009420--39009467 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
39009410 ATGATTTGAG
*
39009420 TATATTTTTTATACTATAATTGT
1 TATATTTTTTATACGATAATTGT
*
39009443 TATATTTTTTATACGGTAATTGT
1 TATATTTTTTATACGATAATTGT
39009466 TA
1 TA
39009468 ATTGAGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.58
Consensus pattern (23 bp):
TATATTTTTTATACGATAATTGT
Found at i:39015501 original size:43 final size:42
Alignment explanation
Indices: 39015345--39015493 Score: 151
Period size: 42 Copynumber: 3.5 Consensus size: 42
39015335 TGTGATTTCG
*
39015345 TGTAAGACCACGTCTGGGACGATGGCATCGGTT-TGA-GATTTACA
1 TGTAAGACCACGTCTGGGACAATGGCATC--TTAT-ATGA-TTACA
* * * *
39015389 TGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTACG
1 TGTAAGACCACGTCTGGGACAATGGCATCTTATATGATTACA
** *
39015431 TGTAAGACC-CTGTCTAAGACAATGGCATCATTATTTGATTACA
1 TGTAAGACCAC-GTCTGGGACAATGGCATC-TTATATGATTACA
39015474 TGTAAGACCACGTCTGGGAC
1 TGTAAGACCACGTCTGGGAC
39015494 GTTGGCATTA
Statistics
Matches: 86, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
42 30 0.35
43 29 0.34
44 27 0.31
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACAATGGCATCTTATATGATTACA
Found at i:39019048 original size:123 final size:120
Alignment explanation
Indices: 39018910--39019207 Score: 386
Period size: 123 Copynumber: 2.5 Consensus size: 120
39018900 TTCATACTCA
* * * *
39018910 ATTTTTTCCTTTTATTTGTTGAATAATTGTACTAAAAGATTTTATCGTAGTTTTTCAATTTTTTC
1 ATTTTTTCCCTTTATTTGTTGAATGATTGTACCAAAAGATTCTATCGTAGTTTTTCAATTTTTTC
* * * *
39018975 AAATAATTCAAAACAAAATTTACACCGTTTACTTTAGCCCTTTACTTACATTTTACCC
66 AAACAATT--AAA-AAAATTTACACCATTTACTTTAGCCATTTACTTACATATTACCC
** * *
39019033 ATTTTTTCCCTTTATTTGTTGAATGATTGTACCAAAAGATTCTATCACAATTTTCCAATTTTTTC
1 ATTTTTTCCCTTTATTTGTTGAATGATTGTACCAAAAGATTCTATCGTAGTTTTTCAATTTTTTC
** * * *
39019098 AAACCCTTAAAAAAATTTACACTATTTACTTTAGTCATTTCCTTACATATTACCC
66 AAACAATTAAAAAAATTTACACCATTTACTTTAGCCATTTACTTACATATTACCC
*
39019153 -TTTTTT--CTGTATTTGTTGAATGATTGTACCAAAAGATTCTATCGTAGTTTTTCAA
1 ATTTTTTCCCTTTATTTGTTGAATGATTGTACCAAAAGATTCTATCGTAGTTTTTCAA
39019208 ACACTTCTAA
Statistics
Matches: 153, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
117 44 0.29
119 6 0.04
120 38 0.25
121 3 0.02
123 62 0.41
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.46
Consensus pattern (120 bp):
ATTTTTTCCCTTTATTTGTTGAATGATTGTACCAAAAGATTCTATCGTAGTTTTTCAATTTTTTC
AAACAATTAAAAAAATTTACACCATTTACTTTAGCCATTTACTTACATATTACCC
Found at i:39022259 original size:26 final size:26
Alignment explanation
Indices: 39022178--39022260 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
39022168 GATGAACACG
* **
39022178 TGTGTAGTACTATGTGAAGGCTACTA
1 TGTGTAATACTAAATGAAGGCTACTA
* *
39022204 CGTGT-ATCAATAAAT-AATGG-TCAC-A
1 TGTGTAAT-ACTAAATGAA-GGCT-ACTA
39022229 TGTGTAATACTAAATGAAGGCTACTA
1 TGTGTAATACTAAATGAAGGCTACTA
39022255 TGTGTA
1 TGTGTA
39022261 CTGAAAAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
25 19 0.44
26 24 0.56
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.33
Consensus pattern (26 bp):
TGTGTAATACTAAATGAAGGCTACTA
Found at i:39022276 original size:51 final size:50
Alignment explanation
Indices: 39022178--39022348 Score: 182
Period size: 51 Copynumber: 3.4 Consensus size: 50
39022168 GATGAACACG
* *
39022178 TGTGTAGTACTATGTGAAGGCTACTACGTGTA-TCAATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACTGAA-AAAT-TTGGTCACA
* ** * **
39022229 TGTGTAATACTAAATGAAGGCTACTATGTGTACTGAAAAGATTTGGTCATG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACTGAAAA-ATTTGGTCACA
* * * * * *
39022280 TGAGTAGTACTATGTGAAGGCTACTACGTGGACCGTAAAACTTGATCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACTGAAAAATTTGGTCACA
39022330 TGTGTAGTACTATGTGAAG
1 TGTGTAGTACTATGTGAAG
39022349 ACTAGTATGT
Statistics
Matches: 97, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
50 25 0.26
51 67 0.69
52 5 0.05
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTACTGAAAAATTTGGTCACA
Found at i:39026077 original size:9 final size:9
Alignment explanation
Indices: 39026050--39026092 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
39026040 AAAAAAAAAT
*
39026050 TCGAGTTAAT
1 TCGA-TTAAC
*
39026060 TCGAATAAC
1 TCGATTAAC
39026069 TCGATTAAC
1 TCGATTAAC
*
39026078 TCGAATAAC
1 TCGATTAAC
39026087 TCGATT
1 TCGATT
39026093 TGTTTAACTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 24 0.86
10 4 0.14
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (9 bp):
TCGATTAAC
Found at i:39026081 original size:18 final size:18
Alignment explanation
Indices: 39026050--39026092 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
39026040 AAAAAAAAAT
*
39026050 TCGAGTTAATTCGAATAAC
1 TCGA-TTAACTCGAATAAC
39026069 TCGATTAACTCGAATAAC
1 TCGATTAACTCGAATAAC
39026087 TCGATT
1 TCGATT
39026093 TGTTTAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (18 bp):
TCGATTAACTCGAATAAC
Found at i:39026482 original size:5 final size:5
Alignment explanation
Indices: 39026472--39026496 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39026462 TTTGGATTCC
39026472 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
39026497 ACTAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:39026972 original size:7 final size:7
Alignment explanation
Indices: 39026960--39026984 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39026950 ACAACTTAAT
39026960 ATATATA
1 ATATATA
39026967 ATATATA
1 ATATATA
39026974 ATATATA
1 ATATATA
39026981 ATAT
1 ATAT
39026985 TATTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATA
Found at i:39027265 original size:82 final size:82
Alignment explanation
Indices: 39027128--39027289 Score: 288
Period size: 82 Copynumber: 2.0 Consensus size: 82
39027118 TCACCCAAAT
* * *
39027128 GAGTATTGCTATTCAGTTGGTGCTTGTGCACACTATTTAGAGTGCTCGAGTATTTTTCATGTATT
1 GAGTACTGCTATTCACTTGGTGCTTGTGCACACTATTTAGAGTGCTCGAGTATTTTTCATGTATC
39027193 CGTTCATTGTTTCATTG
66 CGTTCATTGTTTCATTG
*
39027210 GAGTACTGCTATTCACTTGGTGCTTGTGCACACTATTTAGAGTGTTCGAGTATTTTTCATGTATC
1 GAGTACTGCTATTCACTTGGTGCTTGTGCACACTATTTAGAGTGCTCGAGTATTTTTCATGTATC
39027275 CGTTCATTGTTTCAT
66 CGTTCATTGTTTCAT
39027290 GTTCGTTAAC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (82 bp):
GAGTACTGCTATTCACTTGGTGCTTGTGCACACTATTTAGAGTGCTCGAGTATTTTTCATGTATC
CGTTCATTGTTTCATTG
Found at i:39032266 original size:25 final size:25
Alignment explanation
Indices: 39032236--39032288 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
39032226 GAACATAGAA
* *
39032236 GCTAAGAGCTGTTGATGGAGTATAG
1 GCTAAGAGCTGGTGACGGAGTATAG
39032261 GCTAAGAGCTGGTGACGGAGTATAG
1 GCTAAGAGCTGGTGACGGAGTATAG
39032286 GCT
1 GCT
39032289 TAGTATTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.26, C:0.11, G:0.38, T:0.25
Consensus pattern (25 bp):
GCTAAGAGCTGGTGACGGAGTATAG
Found at i:39037544 original size:25 final size:24
Alignment explanation
Indices: 39037516--39037573 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
39037506 AGCTTCCCGA
*
39037516 TATTGGCTCATTTGAACCTTCCTAT
1 TATTGGCTCATATG-ACCTTCCTAT
* *
39037541 TATTGGCTCGTATGAGCTTCCTAT
1 TATTGGCTCATATGACCTTCCTAT
*
39037565 TAATGGCTC
1 TATTGGCTC
39037574 TCCGGAGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.41
Consensus pattern (24 bp):
TATTGGCTCATATGACCTTCCTAT
Found at i:39037565 original size:24 final size:24
Alignment explanation
Indices: 39037533--39037661 Score: 75
Period size: 25 Copynumber: 5.2 Consensus size: 24
39037523 TCATTTGAAC
39037533 CTTCCTATTATTGGCTCGTATGAG
1 CTTCCTATTATTGGCTCGTATGAG
* **
39037557 CTTCCTATTAATGGCTC-TCCGGAG
1 CTTCCTATTATTGGCTCGT-ATGAG
** * **
39037581 CTTCCGGTTACATGGCTCACATGAG
1 CTTCCTATTA-TTGGCTCGTATGAG
* *
39037606 CTTCC-AGTTATGTGGCTCGAAAGAG
1 CTTCCTA-TTAT-TGGCTCGTATGAG
*
39037631 CTTCTTATT-TATGTGCTCGTATGAG
1 CTTCCTATTAT-TG-GCTCGTATGAG
39037656 CATTCC
1 C-TTCC
39037662 CGAATATAAA
Statistics
Matches: 79, Mismatches: 18, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
23 1 0.01
24 30 0.38
25 44 0.56
26 4 0.05
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (24 bp):
CTTCCTATTATTGGCTCGTATGAG
Found at i:39039876 original size:50 final size:50
Alignment explanation
Indices: 39039798--39039989 Score: 213
Period size: 50 Copynumber: 3.8 Consensus size: 50
39039788 ATTTGGGTAA
* * *
39039798 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* *
39039848 AGAGGTCCCATGTAAGACCATGTCTGGGACGTGGCGTTGGTACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
** * * * *
39039898 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
** * * * * * *
39039948 AGAACTCTCATGTAAGTCCATATCTAGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
39039990 GTACAAGAAA
Statistics
Matches: 119, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 119 1.00
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
Found at i:39044546 original size:20 final size:20
Alignment explanation
Indices: 39044517--39044555 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39044507 ATATTTTCTG
*
39044517 GTAAATCATTTTACAGAAAA
1 GTAAAACATTTTACAGAAAA
*
39044537 GTAAAACATTTTCCAGAAA
1 GTAAAACATTTTACAGAAA
39044556 TCATTTTACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (20 bp):
GTAAAACATTTTACAGAAAA
Found at i:39044562 original size:14 final size:14
Alignment explanation
Indices: 39044539--39044578 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39044529 ACAGAAAAGT
*
39044539 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
39044553 AAATCATTTTACGG
1 AAAACATTTTACAG
39044567 AAAACATTTTAC
1 AAAACATTTTAC
39044579 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:39050406 original size:25 final size:25
Alignment explanation
Indices: 39050282--39050500 Score: 132
Period size: 25 Copynumber: 8.8 Consensus size: 25
39050272 ATATCACAGA
* * *
39050282 AAGCTCATGTGAACCATGTAA-CGGT
1 AAGCTCATGAGAGCCAT-TAATCGGG
* * * *
39050307 AAGCTCATAAAAGACA-TAATCAGG
1 AAGCTCATGAGAGCCATTAATCGGG
*
39050331 AAGCTCATGTA-AGCCAAT-ATCGGG
1 AAGCTCATG-AGAGCCATTAATCGGG
* * **
39050355 AAGATC-CGAAGAGCCATTAATTTGG
1 AAGCTCATG-AGAGCCATTAATCGGG
* *
39050380 AAGCTCATGAGAACCATTTATCGGG
1 AAGCTCATGAGAGCCATTAATCGGG
* *
39050405 AAGCTC-TGGAGAGCTAATT-ATCAGG
1 AAGCTCAT-GAGAGC-CATTAATCGGG
* *
39050430 AAGCTCAT-ACGAGCCA-TAAACGGA
1 AAGCTCATGA-GAGCCATTAATCGGG
*
39050454 AAGCTCAAGAGAGCCATTAATCGGG
1 AAGCTCATGAGAGCCATTAATCGGG
*
39050479 AAGCTCTTGAGAGCCATATAAT
1 AAGCTCATGAGAGCCAT-TAAT
39050501 GATATGCTCA
Statistics
Matches: 146, Mismatches: 34, Indels: 27
0.71 0.16 0.13
Matches are distributed among these distances:
23 6 0.04
24 49 0.34
25 82 0.56
26 9 0.06
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (25 bp):
AAGCTCATGAGAGCCATTAATCGGG
Found at i:39058610 original size:3 final size:3
Alignment explanation
Indices: 39058602--39058650 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
39058592 AATGTTACCT
* *
39058602 TTC TTC TTC TTC TTC TTC TTC TTC TTG TT- TTC TTC TCTA TTC TT-
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC
39058646 TTC TT
1 TTC TT
39058651 TTTTTTTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:39058622 original size:15 final size:14
Alignment explanation
Indices: 39058601--39058650 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
39058591 AAATGTTACC
39058601 TTTCTTCTTCTTCT
1 TTTCTTCTTCTTCT
*
39058615 TCTTCTTCTTCTTGT
1 T-TTCTTCTTCTTCT
*
39058630 TTTCTTCTCTATTCT
1 TTTCTTCT-TCTTCT
39058645 TTTCTT
1 TTTCTT
39058651 TTTTTTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTCTTCTTCTTCT
Found at i:39064544 original size:12 final size:12
Alignment explanation
Indices: 39064527--39064551 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39064517 TTAGTAGGTG
39064527 TCGAACAAACCA
1 TCGAACAAACCA
39064539 TCGAACAAACCA
1 TCGAACAAACCA
39064551 T
1 T
39064552 TCAATATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.32, G:0.08, T:0.12
Consensus pattern (12 bp):
TCGAACAAACCA
Found at i:39066906 original size:26 final size:26
Alignment explanation
Indices: 39066875--39066928 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
39066865 AACAAATTGA
*
39066875 AAATAA-ATTAAAAAAAATGTATACTT
1 AAATAACACTAAAAAAAATGTA-ACTT
* *
39066901 AAATAACACTAAGATAAATGTAACTT
1 AAATAACACTAAAAAAAATGTAACTT
39066927 AA
1 AA
39066929 TAAGCAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28
Consensus pattern (26 bp):
AAATAACACTAAAAAAAATGTAACTT
Found at i:39067082 original size:22 final size:22
Alignment explanation
Indices: 39067034--39067092 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
39067024 AAATGGTAGT
* *
39067034 AAAATAGTGAAAAAAACAAGAAG
1 AAAATAAT-AAAAAAACAAGAAA
39067057 AAAATAATAAAAAAAC-AGCAAA
1 AAAATAATAAAAAAACAAG-AAA
39067079 AAAAGTAA-AAAAAA
1 AAAA-TAATAAAAAA
39067093 GTAGGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 2 0.06
22 20 0.62
23 10 0.31
ACGTcount: A:0.76, C:0.05, G:0.10, T:0.08
Consensus pattern (22 bp):
AAAATAATAAAAAAACAAGAAA
Found at i:39077834 original size:21 final size:21
Alignment explanation
Indices: 39077810--39077853 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
39077800 GAAAAAGATA
39077810 CAATTTTTGAGTTTAACAAAG
1 CAATTTTTGAGTTTAACAAAG
*
39077831 CAATTTTTGAGTTTGACAAAG
1 CAATTTTTGAGTTTAACAAAG
39077852 CA
1 CA
39077854 TGTTTGGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (21 bp):
CAATTTTTGAGTTTAACAAAG
Found at i:39090486 original size:16 final size:16
Alignment explanation
Indices: 39090462--39090498 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
39090452 GGTGTGACTT
*
39090462 TTAACACCAAACAAAA
1 TTAAGACCAAACAAAA
39090478 TTAAGACCAAACAAAA
1 TTAAGACCAAACAAAA
39090494 TTAAG
1 TTAAG
39090499 TCTATGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.19, G:0.05, T:0.16
Consensus pattern (16 bp):
TTAAGACCAAACAAAA
Found at i:39090918 original size:25 final size:24
Alignment explanation
Indices: 39090864--39090920 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 24
39090854 ATATACAATT
*
39090864 TGTTAAACATGCATGGGGTGGATA
1 TGTTAAACATGCATGGAGTGGATA
39090888 --TT--ACATGCATGGAGTGGGATA
1 TGTTAAACATGCATGGAGT-GGATA
39090909 TGTTAAACATGC
1 TGTTAAACATGC
39090921 TTATGTGTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
20 12 0.44
21 5 0.19
22 2 0.07
23 2 0.07
25 6 0.22
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (24 bp):
TGTTAAACATGCATGGAGTGGATA
Found at i:39096644 original size:29 final size:27
Alignment explanation
Indices: 39096606--39096660 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
39096596 GTGATTAAAT
39096606 AAAATCGACA-CAAGCAAAATTTAAAAGAA
1 AAAATCGACAGCAAG--AAA-TTAAAAGAA
*
39096635 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
39096661 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 3 0.12
29 9 0.38
30 4 0.17
ACGTcount: A:0.62, C:0.11, G:0.13, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:39098620 original size:21 final size:22
Alignment explanation
Indices: 39098591--39098641 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
39098581 TCTCTCTAGC
*
39098591 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
39098612 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
39098634 TTT-ATTTT
1 TTTCATTTT
39098642 TCTCTTCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:39098647 original size:21 final size:21
Alignment explanation
Indices: 39098603--39098663 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
39098593 TCCTTTTCGC
39098603 CTTTTTCATTTTCATTTTCTT
1 CTTTTTCATTTTCATTTTCTT
39098624 CTTTTTCACTTTT-ATTTT-TCT
1 CTTTTTCA-TTTTCATTTTCT-T
* * *
39098645 CTTCTTCTTTTTCTTTTTC
1 CTTTTTCATTTTCATTTTC
39098664 CTCACTTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 5 0.15
21 24 0.73
22 4 0.12
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (21 bp):
CTTTTTCATTTTCATTTTCTT
Found at i:39103312 original size:44 final size:44
Alignment explanation
Indices: 39103143--39103357 Score: 134
Period size: 45 Copynumber: 4.8 Consensus size: 44
39103133 TTCCGAAGTG
* * * * *
39103143 ATGCCATACTATCTTTCAACTATAGTATTAT-TCATATC-GGATTTA
1 ATGCCATAGTATCTTTAAACTATGGTCTT-TCTCAT-TCAGG-TATA
* * * * *
39103188 ATGTCATAGTATCTTTCAACTATGGTCTTAT-ACATTTATAGTATA
1 ATGCCATAGTATCTTTAAACTATGGTCTT-TCTCATTCA-GGTATA
* * * * * *
39103233 ATACCTTAGTTTCTTTTAACTATGGTCTTAT-TCATTCCGGTTTA
1 ATGCCATAGTATCTTTAAACTATGGTCTT-TCTCATTCAGGTATA
*
39103277 ATGCCATAGTATCTTTAAACTGTGGTCTTTCTCATTTCAGGTATA
1 ATGCCATAGTATCTTTAAACTATGGTCTTTCTCA-TTCAGGTATA
* * * *
39103322 ATTCCATCGTACCTTTCAA-TCATGGTCTTTCTCATT
1 ATGCCATAGTATCTTTAAACT-ATGGTCTTTCTCATT
39103358 TCTCAATCCA
Statistics
Matches: 135, Mismatches: 30, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
43 1 0.01
44 35 0.26
45 98 0.73
46 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (44 bp):
ATGCCATAGTATCTTTAAACTATGGTCTTTCTCATTCAGGTATA
Found at i:39104177 original size:27 final size:26
Alignment explanation
Indices: 39104131--39104181 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
39104121 TTTTCTTTTG
*
39104131 TTTATTTTATTTTATCTTAACTTAACT
1 TTTATTTTATTTAATCTTAA-TTAACT
39104158 TTTATTTTAATTTAAT-TTAATTAA
1 TTTATTTT-ATTTAATCTTAATTAA
39104182 AACACATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 4 0.18
27 12 0.55
28 6 0.27
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTATTTTATTTAATCTTAATTAACT
Found at i:39111022 original size:17 final size:18
Alignment explanation
Indices: 39110995--39111028 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
39110985 AATAATGTGC
39110995 ATAATAAAATTAAAATGT
1 ATAATAAAATTAAAATGT
39111013 ATAA-AAAATTAAAATG
1 ATAATAAAATTAAAATG
39111029 AAGGTTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
ATAATAAAATTAAAATGT
Found at i:39111500 original size:313 final size:311
Alignment explanation
Indices: 39110825--39111482 Score: 973
Period size: 313 Copynumber: 2.1 Consensus size: 311
39110815 TTGATTATTG
** * * * *
39110825 TTAAAATGGAAAGACTAAAATATGCTCAAATAACAT-AACTTATTTTAATTATGAAAGGGTGGTT
1 TTAAAAT--AAAGACTAAAATATAATAAAAAAACATAAAC-TAATTTAATTATAAAAGGGTGGTT
* *
39110889 CTGTAATTTACCTAATTGAGTTGGTACCCGGTTGACTCATGACACCAACATAGTTAGGAGCTTAA
63 CTATAATTTACCTAATCGAGTTGGTACCCGGTTGACTCATGACACCAACATAGTTAGGAGCTTAA
*
39110954 ATAATAGTATAGATATACAATTATTGGAAATAATAATGTGCATAATAAAATTAAAATGTATAAAA
128 ATAATAGTATAGATATACAATTATTGGAAATAATAATGTGCACAATAAAATTAAAATGTATAAAA
* *
39111019 AATTAAAATGAAGGTTTAGCTGAGTGGTAAATTAAAGACATTACTATTGCAATTGATTCAAATTC
193 AATTAAAATAAAGGTTTAGCTGAGTGGTAAATTAAAGACATTACTAATGCAATTGATTCAAATTC
39111084 AAACCTTACTATATGCATATTTCTATTGTTTTTTAAAATAAAAAGACTTATCTC
258 AAACCTTACTATATGCATATTTCTATTGTTTTTTAAAATAAAAAGACTTATCTC
** * * * * *
39111138 TTAAAATGAAAAGACTAAAATATCCTCAAATAACATAACCTATTTTAATTATAAAAGTGTGGTTC
1 TTAAAAT--AAAGACTAAAATATAATAAAAAAACATAAACTAATTTAATTATAAAAGGGTGGTTC
* * *
39111203 TATAATTTACCTAATCGAGTTGGTACTCGGTTGACTCGTGACACCAACTTAGTTAGGAGCTTAAA
64 TATAATTTACCTAATCGAGTTGGTACCCGGTTGACTCATGACACCAACATAGTTAGGAGCTTAAA
39111268 TAATAGTATAGATATACAATTATTGGAAATAATAATGTGCACAATAAAATTAAAATGTATAAAAA
129 TAATAGTATAGATATACAATTATTGGAAATAATAATGTGCACAATAAAATTAAAATGTATAAAAA
*
39111333 TATTAAAATAAAGGTTTAGCTGAGTGGTAAGTTAAAGACATTACTAATGCAATTGATTCAAATTC
194 -ATTAAAATAAAGGTTTAGCTGAGTGGTAAATTAAAGACATTACTAATGCAATTGATTCAAATTC
* *
39111398 AAACCTTTCTATATGCATATTTCTATTGTTTTTTTTTAAAATAAAAAGGCTTATCTC
258 AAACCTTACTATATGCATATTTCTATTG---TTTTTTAAAATAAAAAGACTTATCTC
* *
39111455 TTAAAAT-TATAC-AAAAT-TAATAAAAAAA
1 TTAAAATAAAGACTAAAATATAATAAAAAAA
39111483 TTTAAATACA
Statistics
Matches: 318, Mismatches: 22, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
312 7 0.02
313 186 0.58
314 93 0.29
317 32 0.10
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (311 bp):
TTAAAATAAAGACTAAAATATAATAAAAAAACATAAACTAATTTAATTATAAAAGGGTGGTTCTA
TAATTTACCTAATCGAGTTGGTACCCGGTTGACTCATGACACCAACATAGTTAGGAGCTTAAATA
ATAGTATAGATATACAATTATTGGAAATAATAATGTGCACAATAAAATTAAAATGTATAAAAAAT
TAAAATAAAGGTTTAGCTGAGTGGTAAATTAAAGACATTACTAATGCAATTGATTCAAATTCAAA
CCTTACTATATGCATATTTCTATTGTTTTTTAAAATAAAAAGACTTATCTC
Found at i:39111657 original size:19 final size:18
Alignment explanation
Indices: 39111630--39111667 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
39111620 TTAAAACAAG
39111630 TTTTTTAAAATAAT-TTAT
1 TTTTTTAAAA-AATATTAT
39111648 TTTTTATAAAAAATATTAT
1 TTTTT-TAAAAAATATTAT
39111667 T
1 T
39111668 AAAATTTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTTAAAAAATATTAT
Found at i:39113769 original size:19 final size:20
Alignment explanation
Indices: 39113745--39113848 Score: 79
Period size: 20 Copynumber: 5.3 Consensus size: 20
39113735 CACTTACATG
39113745 CCCCTGTTTGTACTT-GGTA
1 CCCCTGTTTGTACTTCGGTA
* *
39113764 CCCCTGATTGCACTTAC-GT-
1 CCCCTGTTTGTACTT-CGGTA
* *
39113783 GCCCTGTTTGTACTTCGATA
1 CCCCTGTTTGTACTTCGGTA
* * * ** *
39113803 CCCTTGATTGCACTTTTGTG
1 CCCCTGTTTGTACTTCGGTA
*
39113823 CCCCTGTTTGTACTTCAGTA
1 CCCCTGTTTGTACTTCGGTA
39113843 CCCCTG
1 CCCCTG
39113849 ATTGCACTTA
Statistics
Matches: 61, Mismatches: 20, Indels: 7
0.69 0.23 0.08
Matches are distributed among these distances:
18 1 0.02
19 26 0.43
20 34 0.56
ACGTcount: A:0.12, C:0.31, G:0.18, T:0.38
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:39113786 original size:39 final size:40
Alignment explanation
Indices: 39113731--39113859 Score: 190
Period size: 39 Copynumber: 3.3 Consensus size: 40
39113721 TTATTGAATA
*
39113731 ATTGCACTTACATGCCCCTGTTTGTACTT-GGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* *
39113770 ATTGCACTTACGTG-CCCTGTTTGTACTTCGATACCCTTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
** *
39113809 ATTGCACTTTTGTGCCCCTGTTTGTACTTCAGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
39113849 ATTGCACTTAC
1 ATTGCACTTAC
39113860 ATACTTCGAA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
38 14 0.18
39 33 0.42
40 31 0.40
ACGTcount: A:0.16, C:0.29, G:0.17, T:0.38
Consensus pattern (40 bp):
ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
Found at i:39114361 original size:13 final size:13
Alignment explanation
Indices: 39114340--39114369 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39114330 TTGTCTTGAT
*
39114340 ATGTTATGTTTGG
1 ATGTAATGTTTGG
39114353 ATGTAATGTTTGG
1 ATGTAATGTTTGG
39114366 ATGT
1 ATGT
39114370 TAATTGTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (13 bp):
ATGTAATGTTTGG
Found at i:39116161 original size:22 final size:22
Alignment explanation
Indices: 39116133--39116201 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
39116123 CGAACTCTAG
39116133 GTTACATGCAAACCCTATATAT
1 GTTACATGCAAACCCTATATAT
** **
39116155 GTTACATGTGAATTCTATACATAT
1 GTTACATGCAAACCCTAT--ATAT
* *
39116179 GTTATATACAAACCCTATATAT
1 GTTACATGCAAACCCTATATAT
39116201 G
1 G
39116202 ATATATGCGA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
22 19 0.54
24 16 0.46
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
GTTACATGCAAACCCTATATAT
Found at i:39116214 original size:22 final size:22
Alignment explanation
Indices: 39116133--39116214 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
39116123 CGAACTCTAG
*
39116133 GTTACATGCAAACCCTATATAT
1 GTTATATGCAAACCCTATATAT
* ** **
39116155 GTTACATGTGAATTCTATACATAT
1 GTTATATGCAAACCCTAT--ATAT
*
39116179 GTTATATACAAACCCTATATAT
1 GTTATATGCAAACCCTATATAT
* *
39116201 GATATATGCGAACC
1 GTTATATGCAAACC
39116215 ATCATACATG
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
22 29 0.64
24 16 0.36
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (22 bp):
GTTATATGCAAACCCTATATAT
Found at i:39131484 original size:7 final size:7
Alignment explanation
Indices: 39131472--39131508 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
39131462 ATTATTTTAC
39131472 TTTTAAT
1 TTTTAAT
39131479 TTTTAAT
1 TTTTAAT
39131486 TTTTAAT
1 TTTTAAT
*
39131493 TTTTTAT
1 TTTTAAT
*
39131500 TTTTTAT
1 TTTTAAT
39131507 TT
1 TT
39131509 AATAACTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTAAT
Found at i:39131496 original size:15 final size:15
Alignment explanation
Indices: 39131454--39131505 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
39131444 TTATGCTCCC
39131454 ATTTTATAATTATTTT-
1 ATTTT-TAATT-TTTTA
*
39131470 ACTTTTAA-TTTTTA
1 ATTTTTAATTTTTTA
39131484 ATTTTTAATTTTTTA
1 ATTTTTAATTTTTTA
*
39131499 TTTTTTA
1 ATTTTTA
39131506 TTTAATAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 4 0.13
14 8 0.26
15 15 0.48
16 4 0.13
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTTAATTTTTTA
Found at i:39131502 original size:6 final size:7
Alignment explanation
Indices: 39131466--39131508 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
39131456 TTTATAATTA
*
39131466 TTTTACT
1 TTTTATT
*
39131473 TTTAATT
1 TTTTATT
*
39131480 TTTAATT
1 TTTTATT
*
39131487 TTTAATT
1 TTTTATT
39131494 TTTTATT
1 TTTTATT
39131501 TTTTATT
1 TTTTATT
39131508 T
1 T
39131509 AATAACTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTATT
Found at i:39135630 original size:23 final size:22
Alignment explanation
Indices: 39135604--39135676 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
39135594 CTATATGACT
*
39135604 TTTGTGGCATAATCTGAATGGCC
1 TTTGTGGCATAATCTG-TTGGCC
* * *
39135627 TTTGTGGCACATTCTGTTTAGCC
1 TTTGTGGCATAATCTG-TTGGCC
39135650 TTTGTGGC-TAATTCTGTTGGCC
1 TTTGTGGCATAA-TCTGTTGGCC
39135672 TTTGT
1 TTTGT
39135677 AGAGTACTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 11 0.27
23 30 0.73
ACGTcount: A:0.14, C:0.18, G:0.25, T:0.44
Consensus pattern (22 bp):
TTTGTGGCATAATCTGTTGGCC
Found at i:39144489 original size:27 final size:27
Alignment explanation
Indices: 39144459--39144511 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
39144449 TCGGAGAATA
39144459 AATATTATCCCAAAGAGATTAAGGATG
1 AATATTATCCCAAAGAGATTAAGGATG
39144486 AATATTATCCCAAAGAGATTAAGGAT
1 AATATTATCCCAAAGAGATTAAGGAT
39144512 ATCATATGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.26
Consensus pattern (27 bp):
AATATTATCCCAAAGAGATTAAGGATG
Found at i:39144875 original size:57 final size:55
Alignment explanation
Indices: 39144787--39144961 Score: 215
Period size: 57 Copynumber: 3.1 Consensus size: 55
39144777 ATAGAAATGG
*
39144787 TGAAAATGAGAAATAGGGAATCATTTGGAAATTATTATGGTTTTCTCCAAAATGAAAA
1 TGAAAATGAGAAAT--GGAATCATTT-GAAATGATTATGGTTTTCTCCAAAATGAAAA
* * * *
39144845 TGAAAATGGAGAAATGGAAACATTTAGAAATGATTAGGGTTTTGTCCAAAATGATAA
1 TGAAAAT-GAGAAATGGAATCATTT-GAAATGATTATGGTTTTCTCCAAAATGAAAA
* * *
39144902 TGAAAATAGAGAAATGGAATCATTTGAAAATGAATGTGGTTTTCTACAAAATGAAAA
1 TGAAAAT-GAGAAATGGAATCATTTG-AAATGATTATGGTTTTCTCCAAAATGAAAA
39144959 TGA
1 TGA
39144962 CCTGAAAATT
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
56 1 0.01
57 86 0.85
58 7 0.07
59 7 0.07
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.29
Consensus pattern (55 bp):
TGAAAATGAGAAATGGAATCATTTGAAATGATTATGGTTTTCTCCAAAATGAAAA
Found at i:39160199 original size:25 final size:24
Alignment explanation
Indices: 39160169--39160259 Score: 62
Period size: 24 Copynumber: 3.8 Consensus size: 24
39160159 AATTTTGCTA
39160169 TAAATAAAATTTTAAAAAATAAATT
1 TAAATAAAATTTTAAAAAAT-AATT
* * *
39160194 TAAATATATTTTTATAAAATTTAA-T
1 TAAATAAAATTTTA-AAAA-ATAATT
* *
39160219 T-AATTAAATTATT-TAAAATAATT
1 TAAATAAAATT-TTAAAAAATAATT
* *
39160242 GAAATAAAAATTTAAAAA
1 TAAATAAAATTTTAAAAA
39160260 TTTTAACATA
Statistics
Matches: 48, Mismatches: 12, Indels: 13
0.66 0.16 0.18
Matches are distributed among these distances:
22 3 0.06
23 6 0.12
24 16 0.33
25 16 0.33
26 6 0.12
27 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
TAAATAAAATTTTAAAAAATAATT
Found at i:39161457 original size:66 final size:66
Alignment explanation
Indices: 39161353--39161482 Score: 215
Period size: 66 Copynumber: 2.0 Consensus size: 66
39161343 CGTTTATTTA
* *
39161353 TTTTATTTTTTAAATATTAATTAATGATATATGACGATTTCTTAGCTTCACCTATTAAATAATTA
1 TTTTATTTTTTAAATATCAATTAATGATATATGACGATTTCTTAGCTTCACCTATCAAATAATTA
39161418 T
66 T
* * *
39161419 TTTTATTTTTTAAATATCAATTAATGATATATGTCGATTTTTTAGCTTCACCTCTCAAATAATT
1 TTTTATTTTTTAAATATCAATTAATGATATATGACGATTTCTTAGCTTCACCTATCAAATAATT
39161483 GTCAACTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (66 bp):
TTTTATTTTTTAAATATCAATTAATGATATATGACGATTTCTTAGCTTCACCTATCAAATAATTA
T
Done.