Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 57 of 91
Found at i:13036501 original size:95 final size:96
Alignment explanation
Indices: 13036344--13036525 Score: 260
Period size: 95 Copynumber: 1.9 Consensus size: 96
13036334 ATATCAAAGA
*
13036344 GGTAGTATCGATACCACGATAAGGGGTATCGATACCAAGAAACATTGAATCTAATTTTGGTATCG
1 GGTAGTATCGATACCACGATAAGGGGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCG
* *
13036409 ATACCGGTAGGGGGTATCAGTACCATAGTAG
66 ATACCAGAAGGGGGTATCAGTACCATAGTAG
* * * * * *
13036440 GGTAGTATCGATACCATGGTAA-GGGTATCGATACCAGGCAACATCGAA-CATATTTTTGGTATT
1 GGTAGTATCGATACCACGATAAGGGGTATCGATACCAAGAAACATCGAATC-TAATTTTGGTATC
13036503 GATACCAGAAGGGGGTATCAGTA
65 GATACCAGAAGGGGGTATCAGTA
13036526 ATATAGTATA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
94 1 0.01
95 55 0.72
96 20 0.26
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (96 bp):
GGTAGTATCGATACCACGATAAGGGGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCG
ATACCAGAAGGGGGTATCAGTACCATAGTAG
Found at i:13036563 original size:95 final size:95
Alignment explanation
Indices: 13036347--13036568 Score: 232
Period size: 95 Copynumber: 2.3 Consensus size: 95
13036337 TCAAAGAGGT
* * * *
13036347 AGTATCGATACCACGATAAGGGGTATCGATACCAAGAAACATTGAATCTAATTTTGGTATCGATA
1 AGTATCGATACCAGGGTAA-GAGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCGATA
* * * * *
13036412 CCGGTAGGGGGTATCAGTACCATAGTAGGGT
65 CCAGAAGGGGGTATCAGTAACATAGTAGAGA
* * * * * *
13036443 AGTATCGATACCATGGTAAGGGTATCGATACCAGGCAACATCGAA-CATATTTTTGGTATTGATA
1 AGTATCGATACCAGGGTAAGAGTATCGATACCAAGAAACATCGAATC-TAATTTTGGTATCGATA
* *
13036507 CCAGAAGGGGGTATCAGTAATATAGTATAGA
65 CCAGAAGGGGGTATCAGTAACATAGTAGAGA
* *
13036538 AGTATCGGTATCAGGGT-AGTAGTATCGATAC
1 AGTATCGATACCAGGGTAAG-AGTATCGATAC
13036569 TATGGAGCAA
Statistics
Matches: 106, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
94 3 0.03
95 86 0.81
96 17 0.16
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (95 bp):
AGTATCGATACCAGGGTAAGAGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCGATAC
CAGAAGGGGGTATCAGTAACATAGTAGAGA
Found at i:13036862 original size:18 final size:18
Alignment explanation
Indices: 13036839--13036876 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
13036829 TGCATGCTAT
13036839 AATAGTTATAGTTGAAGA
1 AATAGTTATAGTTGAAGA
13036857 AATAGTTATAGTTGAAGA
1 AATAGTTATAGTTGAAGA
13036875 AA
1 AA
13036877 AAAAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (18 bp):
AATAGTTATAGTTGAAGA
Found at i:13037657 original size:137 final size:136
Alignment explanation
Indices: 13037404--13037728 Score: 458
Period size: 137 Copynumber: 2.4 Consensus size: 136
13037394 AAGGATTAGT
* * * *
13037404 AGGCCTAACTGTGCATATGACA-AAAAGGTGTCATTTATACTAGTTAGATGAAAGACTAGGTGTC
1 AGGCCTAAATGTGAATATGACAGAAAA-GTGTCATTTATGCCAGTTAGATGAAAGACTAGGTGTC
* *
13037468 TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCACTTATGCCAGTTAGATGAAAGTCTAAGT
65 TTTGAGGCATAACTGTGCATATGACAGAAAGGTGTCACTTATGCCAGTTAGATGAAAGACTAAGT
*
13037533 TTCTTTG
130 GTCTTTG
*
13037540 AGGCCTAAATGTGAATATGACAGAAAAGTGTCATTTATGCCAGTT-GATGAAAGACTATGTGTCT
1 AGGCCTAAATGTGAATATGACAGAAAAGTGTCATTTATGCCAGTTAGATGAAAGACTAGGTGTCT
* *
13037604 TTGAGGCATAACTGTGCATATATGACAGAAAGGTGTCATTTATGTCAGTTAGATGAAAGACTAAG
66 TTGAGGCATAACTGTGC--ATATGACAGAAAGGTGTCACTTATGCCAGTTAGATGAAAGACTAAG
13037669 TGTCTTTG
129 TGTCTTTG
** * * *
13037677 AGGCCTAGTTGTGCAAT-TGACAGAAATGTGTCAATTATGCCAGTTACATGAA
1 AGGCCTAAATGTG-AATATGACAGAAAAGTGTCATTTATGCCAGTTAGATGAA
13037729 CGGTTAAGTA
Statistics
Matches: 169, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
135 34 0.20
136 36 0.21
137 91 0.54
138 8 0.05
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (136 bp):
AGGCCTAAATGTGAATATGACAGAAAAGTGTCATTTATGCCAGTTAGATGAAAGACTAGGTGTCT
TTGAGGCATAACTGTGCATATGACAGAAAGGTGTCACTTATGCCAGTTAGATGAAAGACTAAGTG
TCTTTG
Found at i:13037746 original size:68 final size:69
Alignment explanation
Indices: 13037404--13037728 Score: 453
Period size: 68 Copynumber: 4.8 Consensus size: 69
13037394 AAGGATTAGT
* * * *
13037404 AGGCCTAACTGTGC-ATATGACAAAAAGGTGTCATTTATACTAGTTAGATGAAAGACTAGGTGTC
1 AGGCCTAACTGTGCAATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
13037468 TTTG
66 TTTG
* * *
13037472 AGGCCTAACTGTGC-ATATGACAGAAAGGTGTCACTTATGCCAGTTAGATGAAAGTCTAAGTTTC
1 AGGCCTAACTGTGCAATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
13037536 TTTG
66 TTTG
* * *
13037540 AGGCCTAAATGTG-AATATGACAGAAAAGTGTCATTTATGCCAGTT-GATGAAAGACTATGTGTC
1 AGGCCTAACTGTGCAATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
13037603 TTTG
66 TTTG
* *
13037607 AGGCATAACTGTGCATATATGACAGAAAGGTGTCATTTATGTCAGTTAGATGAAAGACTAAGTGT
1 AGGCCTAACTGTGCA-ATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGT
13037672 CTTTG
65 CTTTG
** * * *
13037677 AGGCCTAGTTGTGCAAT-TGACAGAAATGTGTCAATTATGCCAGTTACATGAA
1 AGGCCTAACTGTGCAATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
13037729 CGGTTAAGTA
Statistics
Matches: 228, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
67 30 0.13
68 134 0.59
69 31 0.14
70 33 0.14
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (69 bp):
AGGCCTAACTGTGCAATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
TTTG
Found at i:13038542 original size:81 final size:81
Alignment explanation
Indices: 13037678--13038545 Score: 1153
Period size: 81 Copynumber: 10.7 Consensus size: 81
13037668 GTGTCTTTGA
* *
13037678 GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTACATGAACGGTTAAGTACCGT
1 GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
13037743 TGAGTAAAAGAAAAAT
66 TGAGTAAAAGAAAAAT
** * * * * *
13037759 GGCCTAACTATGCAATTGACATAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGCACCGT
1 GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
13037824 TGAGTAAAAGAAAAAT
66 TGAGTAAAAGAAAAAT
* * * *
13037840 GTCCTAGTTGTACAATTGACAGAAATGTGTCAATTATACCAGTTAGATGAACGGTTAAGTACCGT
1 GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
13037905 TGAGTAAAAGAAAAAT
66 TGAGTAAAAGAAAAAT
** * * * ** * * *
13037921 ATCCTAGCTGTGAAATTGATAGAAGGGTATTAATTATGCCAGTTAGATGAATTGTTAAGTACCGT
1 GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
*
13037986 TGAGTAGAAGAAAAAT
66 TGAGTAAAAGAAAAAT
* * * * *
13038002 GGCCTAGTTGTGCAATTGGCAGAAAGGTATCAATTATGCCAGTTAGATGAACGGTTAAGTACCAT
1 GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
*
13038067 TGAGTAGAAGAAAAAT
66 TGAGTAAAAGAAAAAT
* * * * *
13038083 GGCCTAGTTGTGCAATTGACATAAATGTGTTAATTATGCTAATTAGAGGAATGGTTAAGTACCGT
1 GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
13038148 TGAGTAAAAGAAAAAT
66 TGAGTAAAAGAAAAAT
* * * * *
13038164 GGCCTAGTTGTGCAATTGACAAAAATGTTTCAAATTATGCTAGTTAGATGAATGGTTAAGTATCA
1 GGCCTAGTTGTGCAATTGACAGAAATGTGTC-AATTATGCCAGTTAGATGAATGGTTAAGTACCG
13038229 TTGAGTAAAAGAAAAAT
65 TTGAGTAAAAGAAAAAT
** * * * * * * *
13038246 GTTCTAGCTGTGCTATTGACAAAAAGGTGTCAATTATGCCAATTAGATGAATAGTTAAGTACTGT
1 GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
*
13038311 TGAGTAAAACAAAAAT
66 TGAGTAAAAGAAAAAT
* *
13038327 GGCCTAGTTGTGTAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
1 GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
*
13038392 TGAGTATAAGAAAAAT
66 TGAGTAAAAGAAAAAT
* * * * * *
13038408 GGCCTAGATATGCAATTGACATAAATGTGTCAATTATGCCAGTTAGATTAATGTTTAAGTATCGT
1 GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
13038473 TGAGTAAAAGAAAAAT
66 TGAGTAAAAGAAAAAT
* * * *
13038489 GGCCTAGTTGGGCAATTGATAGAAATGTTTCAATTATGCCAGTTAGACGAAT-GTTAA
1 GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAA
13038546 ACACTGTTGA
Statistics
Matches: 684, Mismatches: 102, Indels: 3
0.87 0.13 0.00
Matches are distributed among these distances:
80 4 0.01
81 609 0.89
82 71 0.10
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (81 bp):
GGCCTAGTTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGT
TGAGTAAAAGAAAAAT
Found at i:13038608 original size:2 final size:2
Alignment explanation
Indices: 13038601--13038628 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13038591 TGAAGAGATG
13038601 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13038629 TGTATAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13042123 original size:162 final size:163
Alignment explanation
Indices: 13041897--13042223 Score: 647
Period size: 162 Copynumber: 2.0 Consensus size: 163
13041887 CCCAAGGGTT
13041897 ATCTTAGGTCCATAAGTAATTACCAGCTTGATCAGAGCTAAACCTCCACACTCCACCCTACCCAG
1 ATCTTAGGTCCATAAGTAATTACCAGCTTGATCAGAGCTAAACCTCCACACTCCACCCTACCCAG
13041962 ATAATGTCCTAATAAAATAGTTCAACTAGTAACTAGTAGATCCCATGATCCATGAATCAAGAACA
66 ATAATGTCCTAATAAAATAGTTCAACTAGTAACTAGTAGATCCCATGATCCATGAATCAAGAACA
13042027 A-TATATTTTCCAGTGAAAATAGTAATCAGAGA
131 ATTATATTTTCCAGTGAAAATAGTAATCAGAGA
13042059 ATCTTAGGTCCATAAGTAATTACCAGCTTGATCAGAGCTAAACCTCCACACTCCACCCTACCCAG
1 ATCTTAGGTCCATAAGTAATTACCAGCTTGATCAGAGCTAAACCTCCACACTCCACCCTACCCAG
13042124 ATAATGTCCTAATAAAATAGTTCAACTAGTAACTAGTAGATCCCATGATCCATGAATCAAGAACA
66 ATAATGTCCTAATAAAATAGTTCAACTAGTAACTAGTAGATCCCATGATCCATGAATCAAGAACA
13042189 ATTATATTTTCCAGTGAAAATAGTAATCAGAGA
131 ATTATATTTTCCAGTGAAAATAGTAATCAGAGA
13042222 AT
1 AT
13042224 ACATACAATG
Statistics
Matches: 164, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 131 0.80
163 33 0.20
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (163 bp):
ATCTTAGGTCCATAAGTAATTACCAGCTTGATCAGAGCTAAACCTCCACACTCCACCCTACCCAG
ATAATGTCCTAATAAAATAGTTCAACTAGTAACTAGTAGATCCCATGATCCATGAATCAAGAACA
ATTATATTTTCCAGTGAAAATAGTAATCAGAGA
Found at i:13050006 original size:77 final size:78
Alignment explanation
Indices: 13049914--13050067 Score: 215
Period size: 77 Copynumber: 2.0 Consensus size: 78
13049904 TTGAATTAAG
*
13049914 TAAACTCTTATTTAATTAATTCAAATTAAAAATCCATTAAAA-ACTTATAATCCA-AATTACA-C
1 TAAACTCTTATTTAATTAATTCAAACTAAAAATCCATTAAAAGACTTATAAT-CATAATTACATC
13049976 TATTTAATGTTTATT
65 T-TTTAATGTTTATT
* * * *
13049991 TAAACTCTTATTTAATTATTTCAAACTAAATATCCATTAAAAGAGTTTTAATCATAATTACATTC
1 TAAACTCTTATTTAATTAATTCAAACTAAAAATCCATTAAAAGACTTATAATCATAATTACA-TC
13050056 TTTTAATGTTTA
65 TTTTAATGTTTA
13050068 CTTACTATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
77 41 0.60
78 14 0.21
79 11 0.16
80 2 0.03
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.44
Consensus pattern (78 bp):
TAAACTCTTATTTAATTAATTCAAACTAAAAATCCATTAAAAGACTTATAATCATAATTACATCT
TTTAATGTTTATT
Found at i:13054770 original size:22 final size:22
Alignment explanation
Indices: 13054742--13054784 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13054732 ATTGGTTATT
* *
13054742 ATATATGATGTTTATCATGAAA
1 ATATATGACGTTTACCATGAAA
13054764 ATATATGACGTTTACCATGAA
1 ATATATGACGTTTACCATGAA
13054785 TGTTATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATATGACGTTTACCATGAAA
Found at i:13058274 original size:98 final size:96
Alignment explanation
Indices: 13058167--13058494 Score: 229
Period size: 98 Copynumber: 3.3 Consensus size: 96
13058157 ACAATATTTT
*
13058167 TTCAAAATAAAAAATTCTAACAAATTTATTTAATCAAAATAATAATTTATAACAAATATTAATTT
1 TTCAAAATAAAAAATTCTAACAAAATTATTTAATCAAAATAATAATTTATAACAAATATTAATTT
13058232 CTCATCATAAAAAATTGTGACAAGTAATATTCG
66 CTCAT-ATAAAAAATTGTGACAA-TAATATTCG
* * * * * * * *
13058265 TTCATAATAACAAAATGC-AACAAAATGATTTAGTCACAATAACAAGTTAAATTTAGTCAAAGTA
1 TTCAAAATAA-AAAATTCTAACAAAATTATTTAATCAAAATAATAA-TT---TATA-ACAAA-T-
** * *** * ** *
13058329 AACAATTATGTCA-A-ATTTATTTCGTCCCAAT-AT-TTTG
58 ATTAATT-TCTCATATAAAAAATT-GTGACAATAATATTCG
* * *
13058366 -TCAAAATAAAAAATTGTGACAAATTTATTTAATCAAAATAACT-ATTTATAACAAATATTAATT
1 TTCAAAATAAAAAATTCTAACAAAATTATTTAATCAAAATAA-TAATTTATAACAAATATTAATT
* *
13058429 TCTCATTATAAAAAATTATGACAAATAATATTCT
65 TCTCA-TATAAAAAATTGTGAC-AATAATATTCG
* * *
13058463 TTCACAATAACAAATTGTAACAAAATTATTTA
1 TTCAAAATAAAAAATTCTAACAAAATTATTTA
13058495 GTCACAGTAA
Statistics
Matches: 165, Mismatches: 46, Indels: 38
0.66 0.18 0.15
Matches are distributed among these distances:
92 4 0.02
93 5 0.03
94 4 0.02
95 11 0.07
96 5 0.03
97 2 0.01
98 58 0.35
99 15 0.09
100 28 0.17
101 3 0.02
102 5 0.03
103 9 0.05
104 7 0.04
105 5 0.03
106 4 0.02
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.35
Consensus pattern (96 bp):
TTCAAAATAAAAAATTCTAACAAAATTATTTAATCAAAATAATAATTTATAACAAATATTAATTT
CTCATATAAAAAATTGTGACAATAATATTCG
Found at i:13058474 original size:198 final size:198
Alignment explanation
Indices: 13058136--13058500 Score: 597
Period size: 198 Copynumber: 1.8 Consensus size: 198
13058126 AAATAAAAAT
* *
13058136 TTATGTCAAATTTATTTTGTCACAATATTTTTTCAAAATAAAAAATTCTAACAAATTTATTTAAT
1 TTATGTCAAATTTATTTCGTCACAATATTTTGTCAAAATAAAAAATTCTAACAAATTTATTTAAT
* *
13058201 CAAAATAATAATTTATAACAAATATTAATTTCTCATCATAAAAAATTGTGACAAGTAATATTCGT
66 CAAAATAATAATTTATAACAAATATTAATTTCTCATCATAAAAAATTATGACAAATAATATTCGT
*
13058266 TCATAATAACAAAATGCAACAAAATGATTTAGTCACAATAACAAGTTAAATTTAGTCAAAGTAAA
131 TCACAATAACAAAATGCAACAAAATGATTTAGTCACAATAACAAGTTAAATTTAGTCAAAGTAAA
13058331 CAA
196 CAA
* * *
13058334 TTATGTCAAATTTATTTCGTCCCAATATTTTGTCAAAATAAAAAATTGTGACAAATTTATTTAAT
1 TTATGTCAAATTTATTTCGTCACAATATTTTGTCAAAATAAAAAATTCTAACAAATTTATTTAAT
* *
13058399 CAAAATAACT-ATTTATAACAAATATTAATTTCTCATTATAAAAAATTATGACAAATAATATTCT
66 CAAAATAA-TAATTTATAACAAATATTAATTTCTCATCATAAAAAATTATGACAAATAATATTCG
* * *
13058463 TTCACAATAACAAATTGTAACAAAATTATTTAGTCACA
130 TTCACAATAACAAAATGCAACAAAATGATTTAGTCACA
13058501 GTAAAAAAAA
Statistics
Matches: 153, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
198 152 0.99
199 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (198 bp):
TTATGTCAAATTTATTTCGTCACAATATTTTGTCAAAATAAAAAATTCTAACAAATTTATTTAAT
CAAAATAATAATTTATAACAAATATTAATTTCTCATCATAAAAAATTATGACAAATAATATTCGT
TCACAATAACAAAATGCAACAAAATGATTTAGTCACAATAACAAGTTAAATTTAGTCAAAGTAAA
CAA
Found at i:13058595 original size:18 final size:18
Alignment explanation
Indices: 13058574--13058617 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
13058564 TGTAATATGT
13058574 CTTTTTTGTCACGAAAAC
1 CTTTTTTGTCACGAAAAC
* *
13058592 CTTTTTT-TCATGAAAAT
1 CTTTTTTGTCACGAAAAC
*
13058609 ATTTTTTGT
1 CTTTTTTGT
13058618 TTGATGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (18 bp):
CTTTTTTGTCACGAAAAC
Found at i:13073967 original size:19 final size:19
Alignment explanation
Indices: 13073943--13073981 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
13073933 TGCTAGTTAA
13073943 AGGTC-AAAGTCAAATGGTC
1 AGGTCAAAAGTC-AATGGTC
13073962 AGGTCAAAAGTCAATGGTC
1 AGGTCAAAAGTCAATGGTC
13073981 A
1 A
13073982 AAAGGGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (19 bp):
AGGTCAAAAGTCAATGGTC
Found at i:13077854 original size:32 final size:31
Alignment explanation
Indices: 13077801--13077866 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
13077791 TTAAAAACTG
* *
13077801 TAAAAAAATTATAAATGAAAACATAATTTAA
1 TAAAAAAATTATAAATGAAAACAAAATTCAA
* * *
13077832 TAAAATAATTCATATATTAAAACAAAATTCAA
1 TAAAAAAATT-ATAAATGAAAACAAAATTCAA
13077864 TAA
1 TAA
13077867 TGTCGTACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (31 bp):
TAAAAAAATTATAAATGAAAACAAAATTCAA
Found at i:13080521 original size:63 final size:61
Alignment explanation
Indices: 13080422--13080541 Score: 150
Period size: 63 Copynumber: 1.9 Consensus size: 61
13080412 GTGCTAAACT
* * **
13080422 TGCACTAAGCTTACGCTCTAGTGCTGATCTGGATATGACACATAAGGTCATGTGCCCACCACC
1 TGCACTAAGATTACACTCTAGTGCTGATAAGGATATGACACATAAGGT--TGTGCCCACCACC
* * * *
13080485 TGCACTAGGATTACACTCTAGTGTTGATAAGGATATGATACATATGGTTGTGCCCAC
1 TGCACTAAGATTACACTCTAGTGCTGATAAGGATATGACACATAAGGTTGTGCCCAC
13080542 TACATGCAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 9 0.18
63 40 0.82
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (61 bp):
TGCACTAAGATTACACTCTAGTGCTGATAAGGATATGACACATAAGGTTGTGCCCACCACC
Found at i:13087790 original size:2 final size:2
Alignment explanation
Indices: 13087783--13087844 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
13087773 ACATACATAC
13087783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13087825 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
13087845 TAGTAGTTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13092383 original size:19 final size:17
Alignment explanation
Indices: 13092359--13092402 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
13092349 ATTTACCCAA
13092359 AACTAATAATATAAAACCT
1 AACTAATAAT-T-AAACCT
13092378 AACTAAATAATTAAACCT
1 AACT-AATAATTAAACCT
13092396 AGACTAA
1 A-ACTAA
13092403 CCTCACCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.39
19 8 0.35
20 6 0.26
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (17 bp):
AACTAATAATTAAACCT
Found at i:13092395 original size:18 final size:20
Alignment explanation
Indices: 13092359--13092402 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
13092349 ATTTACCCAA
13092359 AACT-AATAATATAAAACCT
1 AACTAAATAATATAAAACCT
13092378 AACTAAATAAT-T-AAACCT
1 AACTAAATAATATAAAACCT
13092396 AGACTAA
1 A-ACTAA
13092403 CCTCACCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.30
19 10 0.43
20 6 0.26
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (20 bp):
AACTAAATAATATAAAACCT
Found at i:13093624 original size:55 final size:55
Alignment explanation
Indices: 13093555--13093879 Score: 283
Period size: 55 Copynumber: 6.0 Consensus size: 55
13093545 CGAATGAGGA
* * *
13093555 GTCTGCTCCCTATTCGTTCAGTAAGTATAAGACTCGAACAATCTTCAGCAAACGT
1 GTCTGCTCCCTATTCATTCAGGAAGTATAAGACTCGAACAATCTTCAACAAACGT
* * * ***
13093610 GTCTTCTCCCTATTCAATCAGGGAA-TATAAGACTCAAACAATCTTTGGCAAACGT
1 GTCTGCTCCCTATTCATTCA-GGAAGTATAAGACTCGAACAATCTTCAACAAACGT
* * * * * *
13093665 GTATGCTCCCTATTTATTCAGGGAGTATAAAACTCGAACAATCTTCAATAAACGG
1 GTCTGCTCCCTATTCATTCAGGAAGTATAAGACTCGAACAATCTTCAACAAACGT
* *
13093720 GTCTGCTCCCTATTCATTCAGGGAGTAT-AGAACTCGAACAATCTTCAACAAATGT
1 GTCTGCTCCCTATTCATTCAGGAAGTATAAG-ACTCGAACAATCTTCAACAAACGT
* ** * * * *
13093775 GTCCGCTCCCTATTTC-TTC-GGAGAGTATGGGACTTGAACAATCTTCGACGAACTT
1 GTCTGCTCCCTA-TTCATTCAGGA-AGTATAAGACTCGAACAATCTTCAACAAACGT
* * *
13093830 GTCCT-CTCCTTATTCTTTCA-GAGAGTATAGGACT----CAATCTTCAACAAACG
1 GT-CTGCTCCCTATTCATTCAGGA-AGTATAAGACTCGAACAATCTTCAACAAACG
13093880 AGTTTGCTTC
Statistics
Matches: 222, Mismatches: 39, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
51 13 0.06
54 9 0.04
55 192 0.86
56 8 0.04
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (55 bp):
GTCTGCTCCCTATTCATTCAGGAAGTATAAGACTCGAACAATCTTCAACAAACGT
Found at i:13093932 original size:37 final size:36
Alignment explanation
Indices: 13093882--13093989 Score: 153
Period size: 37 Copynumber: 2.9 Consensus size: 36
13093872 AACAAACGAG
13093882 TTTGCTTCACTACTCTTCCGTGAAGGCTTATAGATGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTA-AGATGA
*
13093919 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAG-ATGA
* * * *
13093956 ATTGCTTAACTTCTCTTTCGTGAAGGCTTAAGAT
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
13093990 TGACCTGTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
36 3 0.05
37 61 0.95
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (36 bp):
TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATGA
Found at i:13095312 original size:8 final size:8
Alignment explanation
Indices: 13095287--13095426 Score: 95
Period size: 8 Copynumber: 17.6 Consensus size: 8
13095277 CTTTTATTTC
*
13095287 TTTTTCTT
1 TTTTTCAT
13095295 TTTTCATCAT
1 TTTT--TCAT
13095305 TTTTTCAT
1 TTTTTCAT
13095313 TTTTT--T
1 TTTTTCAT
13095319 TCTCTTTCATT
1 T-T-TTTCA-T
13095330 TTTTTCAT
1 TTTTTCAT
13095338 TTTTT-ATTT
1 TTTTTCA--T
*
13095347 TTTCTTCTT
1 TTT-TTCAT
13095356 TTTTTCA-
1 TTTTTCAT
13095363 TTTTTC-T
1 TTTTTCAT
13095370 TTTCTTC--
1 TTT-TTCAT
13095377 TTTTTC--
1 TTTTTCAT
13095383 -TTTTCAT
1 TTTTTCAT
13095390 TTTTTCATT
1 TTTTTCA-T
13095399 TTTTTCAT
1 TTTTTCAT
13095407 TTTTTCA-
1 TTTTTCAT
13095414 TTTTTCAT
1 TTTTTCAT
13095422 TTTTT
1 TTTTT
13095427 ATATTTCTTC
Statistics
Matches: 111, Mismatches: 3, Indels: 36
0.74 0.02 0.24
Matches are distributed among these distances:
5 5 0.05
6 5 0.05
7 21 0.19
8 47 0.42
9 21 0.19
10 10 0.09
11 2 0.02
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:13095345 original size:61 final size:60
Alignment explanation
Indices: 13095278--13095412 Score: 168
Period size: 62 Copynumber: 2.2 Consensus size: 60
13095268 CTTTTATTTC
*
13095278 TTTTATTTCTTT-TTC-TTTTTTCATCATT-TTTTCATTTTTTTTCTCTTTCATTTTTTTCATT
1 TTTTATTT-TTTCTTCTTTTTTTCATCATTCTTTTC-TTCTTTTTCT-TTTCA-TTTTTTCATT
**
13095339 TTTTATTTTTTCTTCTTTTTTTCATTTTTCTTTTCTTCTTTTTCTTTTCATTTTTTCATTT
1 TTTTATTTTTTCTTCTTTTTTTCATCATTCTTTTCTTCTTTTTCTTTTCATTTTTTCA-TT
13095400 TTTTCATTTTTTC
1 TTTT-ATTTTTTC
13095413 ATTTTTCATT
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
60 11 0.17
61 22 0.33
62 28 0.42
63 5 0.08
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (60 bp):
TTTTATTTTTTCTTCTTTTTTTCATCATTCTTTTCTTCTTTTTCTTTTCATTTTTTCATT
Found at i:13095409 original size:6 final size:7
Alignment explanation
Indices: 13095330--13095425 Score: 69
Period size: 7 Copynumber: 13.7 Consensus size: 7
13095320 CTCTTTCATT
13095330 TTTTTCA
1 TTTTTCA
*
13095337 TTTTTTA
1 TTTTTCA
13095344 TTTTTTC-
1 -TTTTTCA
*
13095351 TTCTT--
1 TTTTTCA
13095356 TTTTTCA
1 TTTTTCA
*
13095363 TTTTTCT
1 TTTTTCA
13095370 TTTCTTC-
1 TTT-TTCA
13095377 TTTTTC-
1 TTTTTCA
13095383 -TTTTCA
1 TTTTTCA
13095389 TTTTTTCA
1 -TTTTTCA
13095397 TTTTTTTCA
1 --TTTTTCA
13095406 TTTTTTCA
1 -TTTTTCA
13095414 TTTTTCA
1 TTTTTCA
13095421 TTTTT
1 TTTTT
13095426 TATATTTCTT
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
5 9 0.12
6 7 0.09
7 30 0.39
8 22 0.29
9 8 0.11
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCA
Found at i:13095418 original size:60 final size:61
Alignment explanation
Indices: 13095315--13095439 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 61
13095305 TTTTTCATTT
* *
13095315 TTTTTCTCTTTCATTTTTTTCATTTTTTATTTTTTCTTCTTTTTTTCA-TTTTTCT-TTTCTTC
1 TTTTTCTCTTTCATTTTTTTCATTTTTTA--TTTT-TTCTATTTTTCATTTTTTATATTTCTTC
13095377 TTTTTCT-TTTCA-TTTTTTCATTTTTTTCATTTTTTC-ATTTTTCATTTTTTATATTTCTTC
1 TTTTTCTCTTTCATTTTTTTCA-TTTTTT-ATTTTTTCTATTTTTCATTTTTTATATTTCTTC
13095437 TTT
1 TTT
13095440 AAGCGAAATA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
58 7 0.12
59 9 0.16
60 22 0.39
61 11 0.19
62 8 0.14
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (61 bp):
TTTTTCTCTTTCATTTTTTTCATTTTTTATTTTTTCTATTTTTCATTTTTTATATTTCTTC
Found at i:13095419 original size:51 final size:51
Alignment explanation
Indices: 13095287--13095424 Score: 160
Period size: 51 Copynumber: 2.7 Consensus size: 51
13095277 CTTTTATTTC
*
13095287 TTTTTC-TTTTTTCATCATTTTTTCA-TTTT-TTTTCTCTTTCATTTTTTTCAT
1 TTTTTCATTTTTT--TCATTTTTTCATTTTTCTTTTCTCTTT-ATTCTTTTCAT
*
13095338 TTTTT-ATTTTTTCTTCTTTTTTTCATTTTTCTTTTCTTCTTT-TTCTTTTCAT
1 TTTTTCA-TTTTT-TTCATTTTTTCATTTTTCTTTTC-TCTTTATTCTTTTCAT
13095390 TTTTTCATTTTTTTCATTTTTTCATTTTTCATTTT
1 TTTTTCATTTTTTTCATTTTTTCATTTTTC-TTTT
13095425 TTATATTTCT
Statistics
Matches: 76, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
51 32 0.42
52 32 0.42
53 7 0.09
54 5 0.07
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (51 bp):
TTTTTCATTTTTTTCATTTTTTCATTTTTCTTTTCTCTTTATTCTTTTCAT
Found at i:13095435 original size:51 final size:50
Alignment explanation
Indices: 13095301--13095425 Score: 62
Period size: 44 Copynumber: 2.7 Consensus size: 50
13095291 TCTTTTTTCA
* * *
13095301 TCATTTTTTCATTTTTTT--TCTCTTTCATTTTT-TTCATTTTTTATTTTTTCT
1 TCATTTTTTCATTTTTTTCAT-TTTTTCATTTTTCTT--TTCTTTATTTCTT-T
*
13095352 TCTTTTTTTCA--TTTTTC-TTTTCTTC-TTTTTCTTTTC---A-TT-TTT
1 TCATTTTTTCATTTTTTTCATTTT-TTCATTTTTCTTTTCTTTATTTCTTT
13095394 TCATTTTTTTCA-TTTTTTCA-TTTTTCATTTTT
1 TCA-TTTTTTCATTTTTTTCATTTTTTCATTTTT
13095426 TATATTTCTT
Statistics
Matches: 63, Mismatches: 4, Indels: 21
0.72 0.05 0.24
Matches are distributed among these distances:
42 3 0.05
43 13 0.21
44 16 0.25
45 1 0.02
48 2 0.03
49 12 0.19
50 6 0.10
51 10 0.16
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (50 bp):
TCATTTTTTCATTTTTTTCATTTTTTCATTTTTCTTTTCTTTATTTCTTT
Found at i:13107287 original size:19 final size:17
Alignment explanation
Indices: 13107263--13107306 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
13107253 ATTTACCCAA
13107263 AACTAATAATATAAAACCT
1 AACTAATAAT-T-AAACCT
13107282 AACTAAATAATTAAACCT
1 AACT-AATAATTAAACCT
13107300 AGACTAA
1 A-ACTAA
13107307 CCTCACCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.39
19 8 0.35
20 6 0.26
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (17 bp):
AACTAATAATTAAACCT
Found at i:13107299 original size:18 final size:20
Alignment explanation
Indices: 13107263--13107306 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
13107253 ATTTACCCAA
13107263 AACT-AATAATATAAAACCT
1 AACTAAATAATATAAAACCT
13107282 AACTAAATAAT-T-AAACCT
1 AACTAAATAATATAAAACCT
13107300 AGACTAA
1 A-ACTAA
13107307 CCTCACCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.30
19 10 0.43
20 6 0.26
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (20 bp):
AACTAAATAATATAAAACCT
Found at i:13115001 original size:93 final size:93
Alignment explanation
Indices: 13114891--13115076 Score: 345
Period size: 93 Copynumber: 2.0 Consensus size: 93
13114881 GTCAATGAGA
*
13114891 TGCTTGGTTCGACTGATGAAAACGAACCATAGCAGGTTGTTGCATTAATAATTTCCTTTTCTACA
1 TGCTTGGTTCGACTGATGAAAACGAACCATAGCAGGTTGTTGCACTAATAATTTCCTTTTCTACA
13114956 TTCAAATAGTGAGTCATGCATGTGTATG
66 TTCAAATAGTGAGTCATGCATGTGTATG
*
13114984 TGCTTGGTTCGACTGATGAAAACGAACCATTGCAGGTTGTTGCACTAATAATTTCCTTTTCTACA
1 TGCTTGGTTCGACTGATGAAAACGAACCATAGCAGGTTGTTGCACTAATAATTTCCTTTTCTACA
*
13115049 TTCACATAGTGAGTCATGCATGTGTATG
66 TTCAAATAGTGAGTCATGCATGTGTATG
13115077 CTTTATCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (93 bp):
TGCTTGGTTCGACTGATGAAAACGAACCATAGCAGGTTGTTGCACTAATAATTTCCTTTTCTACA
TTCAAATAGTGAGTCATGCATGTGTATG
Found at i:13117223 original size:2 final size:2
Alignment explanation
Indices: 13117216--13117243 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13117206 TTCAAAAATA
13117216 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13117244 TATTATTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13117578 original size:338 final size:328
Alignment explanation
Indices: 13116915--13117591 Score: 933
Period size: 356 Copynumber: 2.0 Consensus size: 328
13116905 TTAAGTTTAA
* *
13116915 CTAGGATAGTTGTTAAATAAAATGTTCATTTTAGAAATTATGTTGTAAATTAAAGATATAGTATT
1 CTAGGATAGTTGTTAAATAAAATGTTCATTTTAGAAATTATGTTGTAAATTAAAAATATAATATT
*
13116980 TAAATTATGTTTACACTTATTAATACTATGATATATAAAATATATCAACTTAAATAAAAATATAA
66 TAAATTATATTTACACTTATTAATACTATGATATATAAAATATATCAACTTAAATAAAAATATAA
** * *
13117045 AAAGTTTTAAAATAACTTATTAATAATATTTTTCTATATAAAATATTTTATTCAAGAAAAAAAAT
131 AAAGTTTTAAAATAACCCAATAATAATATTTTTATATATAAAATATTTTATTCAAGAAAAAAAAT
* * *
13117110 ACATTTCAATACTTTTTGACATTTGAATTTTAAAATAATATTTTGATTATTTCGTTTAACTACAA
196 ACATTTCAATACTTTTTAACATTTGAAATTCAAAATAATATTTTGATTATTTCGTTTAACTACAA
* *
13117175 TCACTCAATAATATATTTATCTTTTTAACCATTCAAAAATAATATATATATATATATATATATAT
261 TCACTCAATAATATATTTATCCTTTTAACC--TC-------A-ATACATATATATATATATATAT
13117240 ATATTATTATTAT
316 ATATTATTATTAT
13117253 CTAGGATAGTTGTTAAATAAAATGTTCATTTTAGAAATTATGTTGTAAATTAAAAATATAATATT
1 CTAGGATAGTTGTTAAATAAAATGTTCATTTTAGAAATTATGTTGTAAATTAAAAATATAATATT
13117318 TAAATTATATTTACACTTATTAATACTATGATATATAAAATATATCAACCTAAATTATAATAAAA
66 TAAATTATATTTACACTTATTAATACTATGATATATAAAATATATCAA-C----TTA-AATAAAA
*
13117383 ATATAAAAAAAAGTTTTAAGATAACCCAATAATAATATTTTATATATATATATATATATAATATT
125 ATAT---AAAAAGTTTTAAAATAACCCAATAATAATA---T-T-T-T-TATATATA-A-AATATT
13117448 TTATTCAAGAAAAAAAATACATTTCAATACTTTTTAACATTTGAAATTCAAAATAATATTTTGAT
178 TTATTCAAGAAAAAAAATACATTTCAATACTTTTTAACATTTGAAATTCAAAATAATATTTTGAT
* *
13117513 TATTTCGTTTAACTGCAATCACTCAATAATATATTTATCCTTTTAACCATACAA-AAATAATATA
243 TATTTCGTTTAACTACAATCACTCAATAATATATTTATCCTTTTAACC-T-CAATACAT-ATATA
13117577 TATATATATATATAT
305 TATATATATATATAT
13117592 ATATATATAT
Statistics
Matches: 304, Mismatches: 15, Indels: 30
0.87 0.04 0.09
Matches are distributed among these distances:
338 110 0.36
339 1 0.00
343 3 0.01
344 11 0.04
347 29 0.10
348 21 0.07
349 1 0.00
350 1 0.00
351 1 0.00
352 1 0.00
353 1 0.00
354 7 0.02
355 2 0.01
356 115 0.38
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (328 bp):
CTAGGATAGTTGTTAAATAAAATGTTCATTTTAGAAATTATGTTGTAAATTAAAAATATAATATT
TAAATTATATTTACACTTATTAATACTATGATATATAAAATATATCAACTTAAATAAAAATATAA
AAAGTTTTAAAATAACCCAATAATAATATTTTTATATATAAAATATTTTATTCAAGAAAAAAAAT
ACATTTCAATACTTTTTAACATTTGAAATTCAAAATAATATTTTGATTATTTCGTTTAACTACAA
TCACTCAATAATATATTTATCCTTTTAACCTCAATACATATATATATATATATATATATTATTAT
TAT
Found at i:13117579 original size:2 final size:2
Alignment explanation
Indices: 13117572--13117614 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
13117562 TACAAAAATA
13117572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13117614 A
1 A
13117615 AAAAACTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13117685 original size:18 final size:18
Alignment explanation
Indices: 13117662--13117702 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
13117652 CTATAATAAA
13117662 AATAAAAA-ATATGATTAT
1 AATAAAAATATAT-ATTAT
*
13117680 AATAAAAATATATTTTAT
1 AATAAAAATATATATTAT
13117698 AATAA
1 AATAA
13117703 CCCACTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AATAAAAATATATATTAT
Found at i:13118174 original size:17 final size:17
Alignment explanation
Indices: 13118152--13118200 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
13118142 ATTTCTAAAC
13118152 AATAATTTTTAAAATAT
1 AATAATTTTTAAAATAT
* *
13118169 AATAATATTT-CAA-AT
1 AATAATTTTTAAAATAT
*
13118184 AAT-TTTTTTAAAATAT
1 AATAATTTTTAAAATAT
13118200 A
1 A
13118201 TATTAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
14 4 0.16
15 7 0.28
16 5 0.20
17 9 0.36
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
AATAATTTTTAAAATAT
Found at i:13118202 original size:33 final size:33
Alignment explanation
Indices: 13118138--13118200 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 33
13118128 TATATTTTTC
13118138 TAATATTTCTAAACAATAATTTTTAAAATATAA
1 TAATATTTCTAAACAATAATTTTTAAAATATAA
* *
13118171 TAATATTTC-AAATAAT-TTTTTTAAAATATA
1 TAATATTTCTAAACAATAATTTTTAAAATATA
13118201 TATTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 13 0.46
32 6 0.21
33 9 0.32
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (33 bp):
TAATATTTCTAAACAATAATTTTTAAAATATAA
Found at i:13118225 original size:19 final size:19
Alignment explanation
Indices: 13118201--13118237 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13118191 TTAAAATATA
13118201 TATTAAAAATAGAATTTAT
1 TATTAAAAATAGAATTTAT
*
13118220 TATTAAAATTAGAATTTA
1 TATTAAAAATAGAATTTA
13118238 AAGAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
TATTAAAAATAGAATTTAT
Found at i:13129056 original size:24 final size:24
Alignment explanation
Indices: 13128982--13129114 Score: 142
Period size: 24 Copynumber: 5.5 Consensus size: 24
13128972 TAATGTTTTA
* *
13128982 TCTGATTT-TCGATTTGAATTATGT
1 TCTGATTTCT-GATCTGAATTCTGT
* * *
13129006 TATGATTTCTGATTTGAATTATGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
13129030 TCTGATTTTTGATCTGAATTCTAT
1 TCTGATTTCTGATCTGAATTCTGT
*
13129054 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
13129078 TATGATATCTGATATGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
13129102 TTTGATTTCTGAT
1 TCTGATTTCTGAT
13129115 ATCTCTATTT
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
24 92 0.99
25 1 0.01
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.53
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:13129069 original size:12 final size:12
Alignment explanation
Indices: 13129008--13129114 Score: 65
Period size: 12 Copynumber: 8.9 Consensus size: 12
13128998 AATTATGTTA
*
13129008 TGATTTCTGATT
1 TGATTTCTGATC
* * *
13129020 TGAATTATGTTC
1 TGATTTCTGATC
*
13129032 TGATTTTTGATC
1 TGATTTCTGATC
*
13129044 TGAATTCT-ATTC
1 TGATTTCTGA-TC
13129056 TGATTTCTGATC
1 TGATTTCTGATC
* *
13129068 TGGA-TTCTGTTA
1 T-GATTTCTGATC
* *
13129080 TGATATCTGATA
1 TGATTTCTGATC
* * *
13129092 TGAATTCTGTTT
1 TGATTTCTGATC
13129104 TGATTTCTGAT
1 TGATTTCTGAT
13129115 ATCTCTATTT
Statistics
Matches: 71, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
11 3 0.04
12 65 0.92
13 3 0.04
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (12 bp):
TGATTTCTGATC
Found at i:13131440 original size:63 final size:64
Alignment explanation
Indices: 13131292--13131453 Score: 188
Period size: 63 Copynumber: 2.5 Consensus size: 64
13131282 ATTGTTCATG
* *
13131292 GTGTATCGATGCAAATGA-AGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCAAA-GATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
* * ** *
13131356 GTGAATCGATGCACAAG-TAGTGCATCGATGCACCCCCTT-AAATATAAACATCGAATGGGATTT
1 GTGTATCGATGCA-AAGATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCA-TC
13131419 A
64 A
* *
13131420 -TGTATCGATTCATAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCAAAGATAGTGCATCGATGCACCC
13131454 GTCAAGGGAT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
62 2 0.02
63 46 0.55
64 34 0.40
65 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCAAAGATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:13132137 original size:23 final size:23
Alignment explanation
Indices: 13132092--13132137 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13132082 CAATCTTATA
*
13132092 TGGCACTATGGTGCAATTCTACG
1 TGGCACTATGGTGCAATTATACG
*
13132115 TGGCACT-TCGGTGCATTTATACG
1 TGGCACTAT-GGTGCAATTATACG
13132138 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTATGGTGCAATTATACG
Found at i:13138298 original size:63 final size:63
Alignment explanation
Indices: 13138141--13138302 Score: 159
Period size: 63 Copynumber: 2.5 Consensus size: 63
13138131 ATTGTTCAAG
* * *
13138141 GTGTATCGATGCACATGA-AGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCA-A-GATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCA
* ** * * * * *
13138205 GTGTATCGATGCAAAAGTAGTATATTGATGCACCCCCTT-AAATACAAACATTGAATGAGATTTA
1 GTGTATCGATGCAAGA-TAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACA-TCA
13138269 -TGTATCGATGCATAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCA-AGATAGTGCATCGATGCACCC
13138303 GTCAAGGGAT
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
62 1 0.01
63 45 0.57
64 33 0.42
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (63 bp):
GTGTATCGATGCAAGATAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCA
Found at i:13138928 original size:23 final size:23
Alignment explanation
Indices: 13138893--13138945 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
13138883 TTGGCATATG
* * *
13138893 TATATGATTCTTAAGGA-ATTTT
1 TATATGGTCCTTAAGGACATTCT
*
13138915 CTATATGGTCCTTAGGGACATTCT
1 -TATATGGTCCTTAAGGACATTCT
13138939 TATATGG
1 TATATGG
13138946 CACTACGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.43
Consensus pattern (23 bp):
TATATGGTCCTTAAGGACATTCT
Found at i:13138970 original size:23 final size:23
Alignment explanation
Indices: 13138943--13138995 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
13138933 CATTCTTATA
*
13138943 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAACTCTACG
*
13138966 TGGCACTTCGGTGCAACTCTACG
1 TGGCACTACGGTGCAACTCTACG
*
13138989 TGACACT
1 TGGCACT
13138996 TTGGTTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAACTCTACG
Found at i:13142146 original size:15 final size:17
Alignment explanation
Indices: 13142116--13142148 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13142106 CTTATTTTAA
13142116 TTTTTGATATACTATTT
1 TTTTTGATATACTATTT
13142133 TTTTTGAT-TA-TATTT
1 TTTTTGATATACTATTT
13142148 T
1 T
13142149 GGTCAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (17 bp):
TTTTTGATATACTATTT
Found at i:13144560 original size:18 final size:18
Alignment explanation
Indices: 13144537--13144594 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
13144527 GCAAAAAGAA
13144537 AAAAAGAGAATATGTAAC
1 AAAAAGAGAATATGTAAC
* *
13144555 AAAAAGATAA-AAG-AA-
1 AAAAAGAGAATATGTAAC
*
13144570 AAAAATAGAATATGTAAC
1 AAAAAGAGAATATGTAAC
13144588 AAAAAGA
1 AAAAAGA
13144595 TAAAAGAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 8 0.26
16 4 0.13
17 4 0.13
18 15 0.48
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (18 bp):
AAAAAGAGAATATGTAAC
Found at i:13144568 original size:33 final size:33
Alignment explanation
Indices: 13144530--13144612 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 33
13144520 AGAAATAGCA
*
13144530 AAAAGAAAAAAAGAGAATATGTAACAAAAAGAT
1 AAAAGAAAAAAAAAGAATATGTAACAAAAAGAT
*
13144563 AAAAGAAAAAAATAGAATATGTAACAAAAAGAT
1 AAAAGAAAAAAAAAGAATATGTAACAAAAAGAT
13144596 AAAAGAAAAAAAAAGAA
1 AAAAGAAAAAAAAAGAA
13144613 AAAATATATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.11
Consensus pattern (33 bp):
AAAAGAAAAAAAAAGAATATGTAACAAAAAGAT
Found at i:13144636 original size:36 final size:35
Alignment explanation
Indices: 13144555--13144657 Score: 88
Period size: 33 Copynumber: 3.0 Consensus size: 35
13144545 AATATGTAAC
* * * *
13144555 AAAAAGATAAAAGA-AAAAAATAG-AATATGTA-A
1 AAAAAGAAAAAAGAGAAAAAAAAGAAAAATATATA
*
13144587 CAAAAAGATAAAAGA-AAAAAAAAGAAAAAATATATA
1 -AAAAAGAAAAAAGAGAAAAAAAAG-AAAAATATATA
* *
13144623 AAAAAGAAAAAAAGAGAAAAGAAAGAGAAATATAT
1 AAAAAG-AAAAAAGAGAAAAAAAAGAAAAATATAT
13144658 CAAACACTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 22 0.37
35 12 0.20
36 17 0.29
37 8 0.14
ACGTcount: A:0.75, C:0.01, G:0.13, T:0.12
Consensus pattern (35 bp):
AAAAAGAAAAAAGAGAAAAAAAAGAAAAATATATA
Found at i:13144649 original size:11 final size:10
Alignment explanation
Indices: 13144596--13144652 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 10
13144586 ACAAAAAGAT
13144596 AAAAGA-AAA
1 AAAAGAGAAA
13144605 AAAA-AG-AA
1 AAAAGAGAAA
* * *
13144613 AAAATATATA
1 AAAAGAGAAA
13144623 AAAA-AGAAA
1 AAAAGAGAAA
13144632 AAAAGAGAAA
1 AAAAGAGAAA
13144642 AGAAAGAGAAA
1 A-AAAGAGAAA
13144653 TATATCAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 7 0.18
9 12 0.31
10 11 0.28
11 9 0.23
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (10 bp):
AAAAGAGAAA
Found at i:13146699 original size:55 final size:55
Alignment explanation
Indices: 13146629--13147426 Score: 686
Period size: 55 Copynumber: 14.6 Consensus size: 55
13146619 TTTTTTTTTG
* *
13146629 GAAACTAAGTATGATTTTTAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAA
1 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
** * * * *
13146684 GAAGTTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAA
1 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
* * * *
13146739 GAAACTAATTCTGATTTTCAAAAGTTTCTTGACGATTTTCAAATGAGTTTTTAAA
1 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
13146794 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAG-TATTTAAA
1 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCT-TTTAAA
* * * * *
13146849 GAAACTAATTCTGATTTTCAAAAGTTTCTTGACGATTTTCAAGTGAGTTTTTAAA
1 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
* * * * * * * *
13146904 GAAACTAAG-CATGACTTTCAGAAGTTTATTAATGATTTTTTAAATGATCTTTCAAA
1 GAAACTAAGTC-TGATTTTTAGAAGTTTCTTGACGA-TTTTCAAATGAGCTTTTAAA
** * * *
13146960 GAGGCTAAGTATGATTTTTCATAAGTTTCTTGACGATTTTCAAATTAG-TTTGTAAA
1 GAAACTAAGTCTGATTTTT-AGAAGTTTCTTGACGATTTTCAAATGAGCTTT-TAAA
* * *
13147016 GAAATTAAGTCTGATTTTTAGAAGTTTCTTAACGATTTTCAAATGA-ATTTTAAA
1 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
* * * * * * * *
13147070 GAAACTAAATCTGATTTTCAGTAGTTTCTT-TCTGATTTTTAAAAGAACTTTCAAA
1 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGAC-GATTTTCAAATGAGCTTTTAAA
* * * ** * * *
13147125 GAAATTAAG-CATAATATTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAAA
1 GAAACTAAGTC-TGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
* * ** * * *
13147178 GAAACAAAGTCTAATTTTTAGGGGTTTCTTGATG-TTTTCAATTGA-ATTTTAAA
1 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
* * ** * * *
13147231 GAAGCTAAGCCT-ATTTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAAA
1 GAAACTAAGTCTGA-TTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
* * * ** *
13147284 GAAGCTAAGCCTAATTTTTAGGGGTTTATTGACGATTTTCAAATGAGCTTTTAAA
1 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
* * * * * * * * * *
13147339 GAAACTAGGTCTTATTTTCAAAAGTGTCTTGATGTTTTTTAAATGAACTTTCAAA
1 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
* * * *
13147394 GAAATTAAGTTTGATTTTCAGAGGTTTCTTGAC
1 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGAC
13147427 ATAATTAATT
Statistics
Matches: 613, Mismatches: 113, Indels: 34
0.81 0.15 0.04
Matches are distributed among these distances:
52 1 0.00
53 129 0.21
54 66 0.11
55 349 0.57
56 56 0.09
57 12 0.02
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (55 bp):
GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAA
Found at i:13147198 original size:53 final size:54
Alignment explanation
Indices: 13146629--13147530 Score: 554
Period size: 55 Copynumber: 16.7 Consensus size: 54
13146619 TTTTTTTTTG
* * ** ** *
13146629 GAAACTAAGTATGATTTTTAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGA-ATTTTAAA
** * * ** * * *
13146684 GAAGTTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGA-ATTTTAAA
* * * *** * *
13146739 GAAACTAATTCTGATTTTCAAAAGTTTCTTGACGATTTTCAAATGAGTTTTTAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGA-ATTTTAAA
* ** * *
13146794 GAAACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAATGAGTATTTAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGAAT-TTTAAA
* * * *** * * *
13146849 GAAACTAATTCTGATTTTCAAAAGTTTCTTGACGATTTTCAAGTGAGTTTTTAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGA-ATTTTAAA
* * * ** * * *
13146904 GAAACTAAG-CATGACTTTCAGAAGTTTATTAATGATTTTTTAAATG-ATCTTTCAAA
1 GAAACTAAGTC-TAATTTTTAGGGGTTTCTTGATGA-TTTTCAAATGAAT-TTT-AAA
** * * *** * * *
13146960 GAGGCTAAGTATGATTTTTCATAAGTTTCTTGACGATTTTCAAATTAGTTTGTAAA
1 GAAACTAAGTCTAATTTTT-AGGGGTTTCTTGATGATTTTCAAATGAATTT-TAAA
* * ** * *
13147016 GAAATTAAGTCTGATTTTTAGAAGTTTCTTAACGATTTTCAAATGAATTTTAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGAATTTTAAA
* * * ** ** * * *
13147070 GAAACTAAATCTGATTTTCAGTAGTTTCTTTCTGATTTTTAAAAGAACTTTCAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGAA-TTTTAAA
* * *
13147125 GAAATTAAG-CATAATATTTAGGGGTTTCTTGATG-TTTTCAAATGAATTTGAAA
1 GAAACTAAGTC-TAATTTTTAGGGGTTTCTTGATGATTTTCAAATGAATTTTAAA
* *
13147178 GAAACAAAGTCTAATTTTTAGGGGTTTCTTGATG-TTTTCAATTGAATTTTAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGAATTTTAAA
* * * *
13147231 GAAGCTAAGCCTATTTTTTAGGGGTTTCTTGATG-TTTTCAAATGAATTTGAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGAATTTTAAA
* * * * *
13147284 GAAGCTAAGCCTAATTTTTAGGGGTTTATTGACGATTTTCAAATGAGCTTTTAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGA-ATTTTAAA
* * * *** * * * *
13147339 GAAACTAGGTCTTATTTTCAAAAGTGTCTTGATGTTTTTTAAATGAACTTTCAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGAA-TTTTAAA
* * * * * * * *
13147394 GAAATTAAGTTTGATTTTCAGAGGTTTCTTGA-CA---T--AATTAATTTAAAA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGAATTTTAAA
* ** * * *
13147442 GAAAGTAAACCTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGAATTTTATA
1 GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGAATTTTAAA
* *
13147495 GAAGA-TAAGCCTAATGTTTAGGGGTTTCTTGATGAT
1 GAA-ACTAAGTCTAATTTTTAGGGGTTTCTTGATGAT
13147531 AACTGTAAAC
Statistics
Matches: 692, Mismatches: 131, Indels: 49
0.79 0.15 0.06
Matches are distributed among these distances:
48 33 0.05
49 5 0.01
51 2 0.00
53 168 0.24
54 70 0.10
55 347 0.50
56 53 0.08
57 14 0.02
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.41
Consensus pattern (54 bp):
GAAACTAAGTCTAATTTTTAGGGGTTTCTTGATGATTTTCAAATGAATTTTAAA
Found at i:13148137 original size:144 final size:142
Alignment explanation
Indices: 13147652--13148206 Score: 649
Period size: 144 Copynumber: 3.9 Consensus size: 142
13147642 AACAATATAA
* * * *
13147652 TAAGTCCTTCGAGCCATCCATAAGACCATCGGGCTGGATGTTTTCAACATTTCCTTTGCTCAATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCT-GATATTTTCAACATTTCCTTTGCTCGATT
* * *
13147717 CACAACACTTCGAATCAGCAATG-CCCATCAGAGGGGTTAACATTTCATATTGCTCCATTCACAA
65 CACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATATTGCTCGATTCAC-A
13147781 CACTTTGAATCAACT
129 -ACTTTGAATCAACT
* * * ** * *
13147796 GATGTCTTTCGGGCCATTTATAAGACATTCGGGCCGAATATTTTCAACATTTCCTTTGCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCTG-ATATTTTCAACATTTCCTTTGCTCGATT
* * * ** * *
13147861 CACAATACTTTGAATCAGCAACACTTCACCAGAGGGGTTAACATATCCTATTGCTCGATTC-C-A
65 CACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATATTGCTCGATTCACAA
13147924 -----AATCAACT
130 CTTTGAATCAACT
* * * * *
13147932 TAAATCCTTTGGGCCATCCATAATACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGC-TGATATTTTCAACATTTCCTTTGCTCGATT
* *
13147997 CACAACACTTCGAATCAACAACGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAT
65 CACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATATTGCTCGATTCACA-
*
13148062 ACTTTGAATCAGCT
129 ACTTTGAATCAACT
* **
13148076 TTAGTCCTTCGGGCCATTTATAAGACCTTCGGGCATGATATTTTCAACATTTCCTTTGCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGC-TGATATTTTCAACATTTCCTTTGCTCGATT
* * * * * *
13148141 CACAACACTTCAAATCAGCAACGCCCTACCAAAGGGGTTAACATTTAATGTTACTCGATTCACAA
65 CACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATATTGCTCGATTCACAA
13148206 C
130 C
13148207 ACTTCAAATC
Statistics
Matches: 344, Mismatches: 56, Indels: 23
0.81 0.13 0.05
Matches are distributed among these distances:
136 114 0.33
137 2 0.01
139 1 0.00
141 1 0.00
143 3 0.01
144 192 0.56
145 31 0.09
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (142 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCTGATATTTTCAACATTTCCTTTGCTCGATTC
ACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTCATATTGCTCGATTCACAAC
TTTGAATCAACT
Found at i:13148179 original size:280 final size:280
Alignment explanation
Indices: 13147664--13148184 Score: 789
Period size: 280 Copynumber: 1.9 Consensus size: 280
13147654 AGTCCTTCGA
*
13147664 GCCATCCATAAGACCATCGGGCTGGATGTTTTCAACATTTCCTTTGCTCAATTCACAACACTTCG
1 GCCATCCATAAGACCATCGGGCAGGATGTTTTCAACATTTCCTTTGCTCAATTCACAACACTTCG
* * *
13147729 AATCAGCAATGCCCATCAGAGGGGTTAACATTTCATATTGCTCCATTCACAACACTTTGAATCAA
66 AATCAACAACGCCCACCAGAGGGGTTAACATTTCATATTGCTCCATTCACAACACTTTGAATCAA
*
13147794 CTGATGTCTTTCGGGCCATTTATAAGACATTCGGGCCGAATATTTTCAACATTTCCTTTGCTCGA
131 CTGATGTCCTTCGGGCCATTTATAAGACATTCGGGCCGAATATTTTCAACATTTCCTTTGCTCGA
* ** * *
13147859 TTCACAATACTTTGAATCAGCAACACTTCACCAGAGGGGTTAACATATCCTATTGCTCGATTCCA
196 TTCACAACACTTCAAATCAGCAACACCTCACCAAAGGGGTTAACATATCCTATTGCTCGATTCCA
13147924 AATCAACTTAAATCCTTTGG
261 AATCAACTTAAATCCTTTGG
* * *
13147944 GCCATCCATAATACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATTCACAACACTTCG
1 GCCATCCATAAGACCATCGGGCAGGATGTTTTCAACATTTCCTTTGCTCAATTCACAACACTTCG
* * *
13148009 AATCAACAACGCCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCAC-ATACTTTGAATCA
66 AATCAACAACG-CCCACCAGAGGGGTTAACATTTCATATTGCTCCATTCACAACACTTTGAATCA
* * * *
13148073 GCT-TTAGTCCTTCGGGCCATTTATAAGACCTTCGGGCATG-ATATTTTCAACATTTCCTTTGCT
130 ACTGAT-GTCCTTCGGGCCATTTATAAGACATTCGGGC-CGAATATTTTCAACATTTCCTTTGCT
*
13148136 CGATTCACAACACTTCAAATCAGCAACGCC-CTACCAAAGGGGTTAACAT
193 CGATTCACAACACTTCAAATCAGCAACACCTC-ACCAAAGGGGTTAACAT
13148185 TTAATGTTAC
Statistics
Matches: 216, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
279 2 0.01
280 177 0.82
281 37 0.17
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (280 bp):
GCCATCCATAAGACCATCGGGCAGGATGTTTTCAACATTTCCTTTGCTCAATTCACAACACTTCG
AATCAACAACGCCCACCAGAGGGGTTAACATTTCATATTGCTCCATTCACAACACTTTGAATCAA
CTGATGTCCTTCGGGCCATTTATAAGACATTCGGGCCGAATATTTTCAACATTTCCTTTGCTCGA
TTCACAACACTTCAAATCAGCAACACCTCACCAAAGGGGTTAACATATCCTATTGCTCGATTCCA
AATCAACTTAAATCCTTTGG
Found at i:13148268 original size:22 final size:22
Alignment explanation
Indices: 13148240--13148310 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
13148230 CTGGCCATCA
13148240 GTAAGTCTTTCGAGCCTGAAGT
1 GTAAGTCTTTCGAGCCTGAAGT
* *
13148262 GTAAGTCCTTC-AGGCCAT-CA--
1 GTAAGTCTTTCGA-GCC-TGAAGT
* *
13148282 GTAAGTCTTTCGAGCATGATGT
1 GTAAGTCTTTCGAGCCTGAAGT
13148304 GTAAGTC
1 GTAAGTC
13148311 GTTTGGGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 1 0.03
20 12 0.32
21 2 0.05
22 21 0.57
23 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (22 bp):
GTAAGTCTTTCGAGCCTGAAGT
Found at i:13148291 original size:42 final size:42
Alignment explanation
Indices: 13148232--13148337 Score: 151
Period size: 42 Copynumber: 2.5 Consensus size: 42
13148222 AAGTTATTCT
*
13148232 GGCCATCAGTAAGTCTTTCGAGCCTGAAGTGTAAGTCCTTCA
1 GGCCATCAGTAAGTCTTTCGAGCATGAAGTGTAAGTCCTTCA
* * **
13148274 GGCCATCAGTAAGTCTTTCGAGCATGATGTGTAAGTCGTTTG
1 GGCCATCAGTAAGTCTTTCGAGCATGAAGTGTAAGTCCTTCA
13148316 GGCCATCTA-TAAGTCTTTCGAG
1 GGCCATC-AGTAAGTCTTTCGAG
13148338 AAAGATGATA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 57 0.98
43 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (42 bp):
GGCCATCAGTAAGTCTTTCGAGCATGAAGTGTAAGTCCTTCA
Found at i:13152236 original size:21 final size:21
Alignment explanation
Indices: 13152211--13152253 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13152201 ATGACCGTTG
*
13152211 AATAAAAGTTTCAAAATTCTT
1 AATAAAAGTTTCAAAACTCTT
*
13152232 AATAAAAGTTTCCAAACTCTT
1 AATAAAAGTTTCAAAACTCTT
13152253 A
1 A
13152254 CAAAGTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (21 bp):
AATAAAAGTTTCAAAACTCTT
Found at i:13158301 original size:45 final size:44
Alignment explanation
Indices: 13158219--13158484 Score: 178
Period size: 45 Copynumber: 6.4 Consensus size: 44
13158209 CACGTTTATC
* * ****
13158219 ATGCA-CCATTATGCATTTTCAATTATAGCATACTTTTATGTTGGTA
1 ATGCACCCA-TATGCA-TTTCAATT-TGGCATCCTTTTATGCCAATA
13158265 ATGCACCCATATGCATTTCAACTTTGGCATCCTTTTATGCCAATA
1 ATGCACCCATATGCATTTCAA-TTTGGCATCCTTTTATGCCAATA
* *
13158310 ATGCACCCATATGCA-TT--A--T----T-CTTTTATGTCGATA
1 ATGCACCCATATGCATTTCAATTTGGCATCCTTTTATGCCAATA
* * * *
13158344 ATGCACCTATATGCATTTCAACTTTGGCATCATTTCATGCAAATA
1 ATGCACCCATATGCATTTCAA-TTTGGCATCCTTTTATGCCAATA
* *
13158389 ATGCACCCATATGCA-TT--A--T----T-CTTTTATGTCGATA
1 ATGCACCCATATGCATTTCAATTTGGCATCCTTTTATGCCAATA
* * *
13158423 ATGCACCCATATGCATTTCAGCTTTGGCGTCCTTTCATGCCAATA
1 ATGCACCCATATGCATTTCA-ATTTGGCATCCTTTTATGCCAATA
13158468 ATGCACCCATATGCATT
1 ATGCACCCATATGCATT
13158485 ATTCTTTTAT
Statistics
Matches: 172, Mismatches: 24, Indels: 49
0.70 0.10 0.20
Matches are distributed among these distances:
34 50 0.29
35 6 0.03
37 1 0.01
39 2 0.01
40 2 0.01
42 2 0.01
44 6 0.03
45 87 0.51
46 13 0.08
47 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (44 bp):
ATGCACCCATATGCATTTCAATTTGGCATCCTTTTATGCCAATA
Found at i:13158334 original size:34 final size:34
Alignment explanation
Indices: 13158296--13158494 Score: 146
Period size: 34 Copynumber: 5.2 Consensus size: 34
13158286 CTTTGGCATC
13158296 CTTTTATGCCAATAATGCACCCATATGCATTATT
1 CTTTTATGCCAATAATGCACCCATATGCATTATT
* * *
13158330 CTTTTATGTCGATAATGCACCTATATGCATTTCAACTTT
1 CTTTTATGCCAATAATGCACCCATATGCA-TT--A--TT
*
13158369 GGCATCATTTCATGCAAATAATGCACCCATATGCATTATT
1 --C-T--TTT-ATGCCAATAATGCACCCATATGCATTATT
* *
13158409 CTTTTATGTCGATAATGCACCCATATGCATTTCAGCTTT
1 CTTTTATGCCAATAATGCACCCATATGCA-TT-A---TT
13158448 GGCGTCCTTTCATGCCAATAATGCACCCATATGCATTATT
1 --C-T--TTT-ATGCCAATAATGCACCCATATGCATTATT
13158488 CTTTTAT
1 CTTTTAT
13158495 TTATTTGTTC
Statistics
Matches: 131, Mismatches: 12, Indels: 44
0.70 0.06 0.24
Matches are distributed among these distances:
34 49 0.37
35 10 0.08
36 1 0.01
37 3 0.02
38 2 0.02
39 4 0.03
40 4 0.03
41 2 0.02
42 3 0.02
43 1 0.01
44 10 0.08
45 42 0.32
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.39
Consensus pattern (34 bp):
CTTTTATGCCAATAATGCACCCATATGCATTATT
Found at i:13158389 original size:79 final size:79
Alignment explanation
Indices: 13158251--13158494 Score: 416
Period size: 79 Copynumber: 3.1 Consensus size: 79
13158241 TTATAGCATA
* * *
13158251 CTTTTATGTTGGTAATGCACCCATATGCATTTCAACTTTGGCATCCTTTTATGCCAATAATGCAC
1 CTTTTATGTCGATAATGCACCCATATGCATTTCAACTTTGGCATCCTTTCATGCCAATAATGCAC
13158316 CCATATGCATTATT
66 CCATATGCATTATT
* * *
13158330 CTTTTATGTCGATAATGCACCTATATGCATTTCAACTTTGGCATCATTTCATGCAAATAATGCAC
1 CTTTTATGTCGATAATGCACCCATATGCATTTCAACTTTGGCATCCTTTCATGCCAATAATGCAC
13158395 CCATATGCATTATT
66 CCATATGCATTATT
* *
13158409 CTTTTATGTCGATAATGCACCCATATGCATTTCAGCTTTGGCGTCCTTTCATGCCAATAATGCAC
1 CTTTTATGTCGATAATGCACCCATATGCATTTCAACTTTGGCATCCTTTCATGCCAATAATGCAC
13158474 CCATATGCATTATT
66 CCATATGCATTATT
13158488 CTTTTAT
1 CTTTTAT
13158495 TTATTTGTTC
Statistics
Matches: 154, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 154 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (79 bp):
CTTTTATGTCGATAATGCACCCATATGCATTTCAACTTTGGCATCCTTTCATGCCAATAATGCAC
CCATATGCATTATT
Found at i:13159020 original size:19 final size:20
Alignment explanation
Indices: 13158996--13159040 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
13158986 GTTTCAAAAT
**
13158996 GGTATCAATAC-CTTCCTTC
1 GGTATCAATACTCCCCCTTC
*
13159015 GGTATCGATACTCCCCCTTC
1 GGTATCAATACTCCCCCTTC
13159035 GGTATC
1 GGTATC
13159041 GATGCTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.18, C:0.33, G:0.16, T:0.33
Consensus pattern (20 bp):
GGTATCAATACTCCCCCTTC
Found at i:13162948 original size:27 final size:27
Alignment explanation
Indices: 13162897--13162950 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
13162887 GGTACTTCTA
* **
13162897 GTCATTTTACACTTCAAGGGTATTTTG
1 GTCATTATACACTTCAAGGAAATTTTG
13162924 GTCATTATACACTTCAAGGAAATTTTG
1 GTCATTATACACTTCAAGGAAATTTTG
13162951 TAATTTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (27 bp):
GTCATTATACACTTCAAGGAAATTTTG
Found at i:13167705 original size:27 final size:28
Alignment explanation
Indices: 13167661--13167716 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
13167651 AGGGTTTAGA
13167661 GGTACTTTGAGTCATTTTACACTTCAAG
1 GGTACTTTGAGTCATTTTACACTTCAAG
*
13167689 GGTATTTTG-GTCATTTTACACTTCAAG
1 GGTACTTTGAGTCATTTTACACTTCAAG
13167716 G
1 G
13167717 CAATTCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (28 bp):
GGTACTTTGAGTCATTTTACACTTCAAG
Found at i:13169817 original size:138 final size:138
Alignment explanation
Indices: 13169564--13169817 Score: 375
Period size: 138 Copynumber: 1.8 Consensus size: 138
13169554 TTGAAATAGA
* *
13169564 AATTCACAAACTCATTATGAATTCCATGGATGCACACATAGTGCAGAAAGTAAACATAGTACTGA
1 AATTCACAAACTCATTATGAATACCATGGATGCACACATAGTACAGAAAGTAAACATAGTACTGA
* **
13169629 TACAAAAATGCACTGTTATGCATTAAACAAAATCGATCGAAAACTTTTATACATAATTGTTTGTC
66 TACAAAAATGCACCGTTATGCATTAAACAAAATCGATCGAAAACAATTATACATAATTGTTTGTC
13169694 AAAATGGT
131 AAAATGGT
* * *
13169702 AATTCACAAACTCATTATGAATACCATGGTTGCACATC-TAGTACCGAAAGTACACATAGTACTG
1 AATTCACAAACTCATTATGAATACCATGGATGCACA-CATAGTACAGAAAGTAAACATAGTACTG
* * * * *
13169766 ATACGAAAATGCACCGTTATGCATTATACAAATTTGATCGATAACAATTATA
65 ATACAAAAATGCACCGTTATGCATTAAACAAAATCGATCGAAAACAATTATA
13169818 TACAATTTAT
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
138 101 0.99
139 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (138 bp):
AATTCACAAACTCATTATGAATACCATGGATGCACACATAGTACAGAAAGTAAACATAGTACTGA
TACAAAAATGCACCGTTATGCATTAAACAAAATCGATCGAAAACAATTATACATAATTGTTTGTC
AAAATGGT
Found at i:13175347 original size:2 final size:2
Alignment explanation
Indices: 13175340--13175368 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13175330 CATTCTTTGA
13175340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13175369 ACACATCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13176153 original size:138 final size:138
Alignment explanation
Indices: 13175905--13176160 Score: 363
Period size: 138 Copynumber: 1.9 Consensus size: 138
13175895 ACCTAAGTGA
** * * * *
13175905 TGAAATGGAAATTCACAAACTTGTTATGAATTCCATGGATGTACACATAGTGTCGAAAGTACACA
1 TGAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACACA
* *
13175970 TAGTACTGATACGAAAATGCATCGTTATGCATTAAAAATAATCGATCGATAACTTTTATACATAA
66 TAGTACTGATACAAAAATGCAACGTTATGCATTAAAAATAATCGATCGATAACTTTTATACATAA
13176035 TTGTATAT
131 TTGTATAT
* * *
13176043 TGAAATGGTAATTCACAAACTCATTATGAATACCATGGTTGCGCATC-TAGTGCCAAAAGTACAC
1 TGAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACA-CATAGTGCCAAAAGTACAC
* *
13176107 ATAGTACTGATACAAAAATGCAACGTTTTGCATTAATCAA-AATCGATCGATAAC
65 ATAGTACTGATACAAAAATGCAACGTTATGCATTAA-AAATAATCGATCGATAAC
13176161 CATTATATAC
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
138 100 0.97
139 3 0.03
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (138 bp):
TGAAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACACA
TAGTACTGATACAAAAATGCAACGTTATGCATTAAAAATAATCGATCGATAACTTTTATACATAA
TTGTATAT
Found at i:13179090 original size:21 final size:20
Alignment explanation
Indices: 13179051--13179092 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
13179041 ATTATTTTTT
*
13179051 TATTTTTTTATTATAAAATA
1 TATTTTTTTAATATAAAATA
*
13179071 TATTTTTATTAATATTAAATA
1 TATTTTT-TTAATATAAAATA
13179092 T
1 T
13179093 CAAGTAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTTTAATATAAAATA
Found at i:13179770 original size:2 final size:2
Alignment explanation
Indices: 13179763--13179795 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13179753 ACTTTAGGTC
13179763 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
13179796 GAGGAAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13181141 original size:9 final size:10
Alignment explanation
Indices: 13181118--13181146 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
13181108 TTTATTTTTG
13181118 AAAATTTTAT
1 AAAATTTTAT
13181128 AAAATTTTAT
1 AAAATTTTAT
13181138 -AAATTTTAT
1 AAAATTTTAT
13181147 TTAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AAAATTTTAT
Found at i:13183239 original size:8 final size:7
Alignment explanation
Indices: 13183228--13183304 Score: 63
Period size: 7 Copynumber: 11.1 Consensus size: 7
13183218 ACATGAAAAC
13183228 AATAAAT
1 AATAAAT
13183235 GAATAAAT
1 -AATAAAT
13183243 AGATAAAT
1 A-ATAAAT
*
13183251 AATATAT
1 AATAAAT
*
13183258 AAAATAAT
1 AATA-AAT
13183266 -ATAAAT
1 AATAAAT
13183272 AAT-AAT
1 AATAAAT
*
13183278 AATATAT
1 AATAAAT
*
13183285 AATATAT
1 AATAAAT
13183292 -AT-AAT
1 AATAAAT
13183297 AATAAAT
1 AATAAAT
13183304 A
1 A
13183305 TATACTATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
5 2 0.04
6 13 0.23
7 26 0.46
8 16 0.28
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (7 bp):
AATAAAT
Found at i:13183367 original size:7 final size:7
Alignment explanation
Indices: 13183249--13183391 Score: 104
Period size: 7 Copynumber: 20.1 Consensus size: 7
13183239 AAATAGATAA
13183249 ATAATAT
1 ATAATAT
13183256 ATAA-A-
1 ATAATAT
13183261 ATAATAT
1 ATAATAT
13183268 A-AATAAT
1 ATAAT-AT
13183275 AATAATAT
1 -ATAATAT
13183283 ATAATAT
1 ATAATAT
13183290 AT-ATA-
1 ATAATAT
*
13183295 ATAATAA
1 ATAATAT
13183302 ATATATACT
1 ATA-ATA-T
13183311 ATAATAT
1 ATAATAT
13183318 ATAAGACTAT
1 AT-A-A-TAT
13183328 ATAATAT
1 ATAATAT
13183335 AT-ATCAT
1 ATAAT-AT
*
13183342 ATACTAT
1 ATAATAT
13183349 ATAAATACT
1 AT-AATA-T
13183358 ATAATAT
1 ATAATAT
13183365 ATAATAT
1 ATAATAT
*
13183372 AAAATA-
1 ATAATAT
13183378 AT-ATAT
1 ATAATAT
*
13183384 AGAATAT
1 ATAATAT
13183391 A
1 A
13183392 GTGTATATTA
Statistics
Matches: 112, Mismatches: 6, Indels: 36
0.73 0.04 0.23
Matches are distributed among these distances:
5 9 0.08
6 15 0.13
7 53 0.47
8 19 0.17
9 11 0.10
10 5 0.04
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:13183382 original size:52 final size:52
Alignment explanation
Indices: 13183251--13183382 Score: 136
Period size: 52 Copynumber: 2.6 Consensus size: 52
13183241 ATAGATAAAT
13183251 AATATATAA-A-ATAATAT-AAATAATAATAATATATAATATATATAATAATA
1 AATATATAATATATAATATAAAATAAT-ATAATATATAATATATATAATAATA
* *
13183301 AATATATACTATA-ATATATAAGACT-ATATAATATAT-ATCATATACT-AT-ATA
1 AATATATAATATATA-ATATAA-AATAATATAATATATAAT-ATATA-TAATAATA
13183352 AATACTATAATATATAATATAAAATAATATA
1 AATA-TATAATATATAATATAAAATAATATA
13183383 TAGAATATAG
Statistics
Matches: 68, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
50 8 0.12
51 13 0.19
52 40 0.59
53 5 0.07
54 2 0.03
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (52 bp):
AATATATAATATATAATATAAAATAATATAATATATAATATATATAATAATA
Found at i:13183389 original size:12 final size:11
Alignment explanation
Indices: 13183240--13183389 Score: 90
Period size: 12 Copynumber: 13.1 Consensus size: 11
13183230 TAAATGAATA
*
13183240 AATAGATAAAT
1 AATATATAAAT
13183251 AATATATAAAAT
1 AATATAT-AAAT
*
13183263 AATATAAATAAT
1 AATATATA-AAT
*
13183275 AATA-ATATAT
1 AATATATAAAT
13183285 AATATATATAAT
1 AATATATA-AAT
* *
13183297 AATAAATATAT
1 AATATATAAAT
* *
13183308 ACTATAATATAT
1 AATAT-ATAAAT
*
13183320 AAGACTATATAAT
1 AATA-TATA-AAT
*
13183333 -ATATATCATAT
1 AATATAT-AAAT
*
13183344 ACTATATAAAT
1 AATATATAAAT
* *
13183355 ACTATAATATAT
1 AATAT-ATAAAT
13183367 AATATA-AAAT
1 AATATATAAAT
13183377 AATATATAGAAT
1 AATATATA-AAT
13183389 A
1 A
13183390 TAGTGTATAT
Statistics
Matches: 108, Mismatches: 19, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
10 15 0.14
11 32 0.30
12 58 0.54
13 3 0.03
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (11 bp):
AATATATAAAT
Found at i:13183391 original size:47 final size:45
Alignment explanation
Indices: 13183259--13183391 Score: 135
Period size: 47 Copynumber: 2.9 Consensus size: 45
13183249 ATAATATATA
* *
13183259 AAATAATATAA-ATAATAATAATATATAATATATATAATA-ATAAAT
1 AAATACTATAATAT-ATAATAA-ATATAATATATATAATATATATAT
* * * *
13183304 ATATACTATAATATATAAGACTATATAATATATATCATATACTATAT
1 AAATACTATAATATATAATA-AATATAATATATATAATATA-TATAT
* *
13183351 AAATACTATAATATATAATATAAAATAATATATAGAATATA
1 AAATACTATAATATATAATA-AATATAATATATATAATATA
13183392 GTGTATATTA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
45 30 0.42
46 3 0.04
47 38 0.54
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (45 bp):
AAATACTATAATATATAATAAATATAATATATATAATATATATAT
Found at i:13183404 original size:54 final size:52
Alignment explanation
Indices: 13183237--13183407 Score: 157
Period size: 56 Copynumber: 3.1 Consensus size: 52
13183227 CAATAAATGA
* *
13183237 ATAAATAGATAAATA-AT-ATATAAAATAATATAAATAATAATAATATATAATAT
1 ATAAATA-ATAAATATATAATATAAAATAATATATATAAT-AT-ATATATATTAT
* *
13183290 ATATAATAATAAATATATACTATAATATATAAGACTATATAATATATATCATATACTAT
1 ATA-AATAATAAATATATAATATAA-A-ATAATA-TATATAATATATAT-ATAT--TAT
* * *
13183349 ATAAATACTATAATATATAATATAAAATAATATATAGAATATAGTGTATATTAT
1 ATAAATAATA-AATATATAATATAAAATAATATATATAATATA-TATATATTAT
13183403 ATAAA
1 ATAAA
13183408 AAAATAACCC
Statistics
Matches: 98, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
53 10 0.10
54 14 0.14
55 5 0.05
56 19 0.19
57 17 0.17
58 14 0.14
59 19 0.19
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (52 bp):
ATAAATAATAAATATATAATATAAAATAATATATATAATATATATATATTAT
Found at i:13184291 original size:14 final size:14
Alignment explanation
Indices: 13184264--13184312 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
13184254 ATGTTTAAGC
13184264 CAAAATTGAAGTATA
1 CAAAATT-AAGTATA
13184279 CAAAATTAAGTATA
1 CAAAATTAAGTATA
13184293 -AAAATTTAAGT-TA
1 CAAAA-TTAAGTATA
*
13184306 TAAAATT
1 CAAAATT
13184313 TATTTAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.25
14 17 0.53
15 7 0.22
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (14 bp):
CAAAATTAAGTATA
Found at i:13187065 original size:39 final size:38
Alignment explanation
Indices: 13187009--13187138 Score: 122
Period size: 39 Copynumber: 3.3 Consensus size: 38
13186999 TGTACACCCA
*
13187009 GTAAGGGCTTACACTATGCACAAAGCAGAGGAGCCTGAG
1 GTAAGGACTTAC-CTATGCACAAAGCAGAGGAGCCTGAG
* * *
13187048 GTAAGGTCTTATCCTATGTACAAAGCAGGGGAGCCTGCA-
1 GTAAGGACTTA-CCTATGCACAAAGCAGAGGAGCCTG-AG
* * *
13187087 ATAAGGACTTACCCTGA-GCACAAAGTC-TAGGAGCCTGCG
1 GTAAGGACTTA-CCT-ATGCACAAAG-CAGAGGAGCCTGAG
13187126 GTAAGGACTTACC
1 GTAAGGACTTACC
13187139 CTGAATACAA
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
38 2 0.03
39 69 0.92
40 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (38 bp):
GTAAGGACTTACCTATGCACAAAGCAGAGGAGCCTGAG
Found at i:13187139 original size:39 final size:39
Alignment explanation
Indices: 13187077--13187165 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
13187067 ACAAAGCAGG
** * ** *
13187077 GGAGCCTGCAATAAGGACTTACCCTGAGCACAAAGTCTA
1 GGAGCCTGCGGTAAGGACTTACCCTGAACACAAAACCGA
*
13187116 GGAGCCTGCGGTAAGGACTTACCCTGAATACAAAACCGA
1 GGAGCCTGCGGTAAGGACTTACCCTGAACACAAAACCGA
13187155 GGAGCCTGCGG
1 GGAGCCTGCGG
13187166 AAAGCGATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.16
Consensus pattern (39 bp):
GGAGCCTGCGGTAAGGACTTACCCTGAACACAAAACCGA
Found at i:13187375 original size:16 final size:15
Alignment explanation
Indices: 13187356--13187393 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
13187346 GAAATATACA
13187356 ATAAATCATATATCAG
1 ATAAATCATAT-TCAG
*
13187372 ATAAATCATGTTCAG
1 ATAAATCATATTCAG
13187387 A-AAATCA
1 ATAAATCA
13187394 GGTATTGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 5 0.24
16 10 0.48
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (15 bp):
ATAAATCATATTCAG
Found at i:13192119 original size:39 final size:39
Alignment explanation
Indices: 13192062--13192223 Score: 173
Period size: 39 Copynumber: 4.2 Consensus size: 39
13192052 TATACACCCA
* *
13192062 GTAAGGGCTTACCCTGTGCACAAAGTAGAGGAGCCTACG
1 GTAAGGACTTACCCTGAGCACAAAGTAGAGGAGCCTACG
* * * * * * *
13192101 GTAAGGTCTTATCTTGTGCACAAAGTAGAGGAACCTGCA
1 GTAAGGACTTACCCTGAGCACAAAGTAGAGGAGCCTACG
* *
13192140 GTAAGGACTTACCCTGAGCACAAACTCGAGGAGCCTGA-G
1 GTAAGGACTTACCCTGAGCACAAAGTAGAGGAGCCT-ACG
* * * *
13192179 GTAAGGACTTACCCAGAGCACAAAGTCGATGAGCCTGCG
1 GTAAGGACTTACCCTGAGCACAAAGTAGAGGAGCCTACG
13192218 GTAAGG
1 GTAAGG
13192224 TCTTGCAAGT
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 102 1.00
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.19
Consensus pattern (39 bp):
GTAAGGACTTACCCTGAGCACAAAGTAGAGGAGCCTACG
Found at i:13192200 original size:78 final size:78
Alignment explanation
Indices: 13192060--13192223 Score: 195
Period size: 78 Copynumber: 2.1 Consensus size: 78
13192050 CATATACACC
* * * * * ** *
13192060 CAGTAAGGGCTTACCCTGTGCACAAAGTAGAGGAGCCTACGGTAAGGTCTTATCTTGTGCACAAA
1 CAGTAAGGACTTACCCTGAGCACAAACTAGAGGAGCCTACGGTAAGGACTTACCCAGAGCACAAA
13192125 GTAGAGGAACCTG
66 GTAGAGGAACCTG
*
13192138 CAGTAAGGACTTACCCTGAGCACAAACTCGAGGAGCCTGA-GGTAAGGACTTACCCAGAGCACAA
1 CAGTAAGGACTTACCCTGAGCACAAACTAGAGGAGCCT-ACGGTAAGGACTTACCCAGAGCACAA
* * *
13192202 AGTCGATGAGCCTG
65 AGTAGAGGAACCTG
*
13192216 CGGTAAGG
1 CAGTAAGG
13192224 TCTTGCAAGT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 71 0.99
79 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.18
Consensus pattern (78 bp):
CAGTAAGGACTTACCCTGAGCACAAACTAGAGGAGCCTACGGTAAGGACTTACCCAGAGCACAAA
GTAGAGGAACCTG
Found at i:13193601 original size:29 final size:30
Alignment explanation
Indices: 13193537--13193597 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
13193527 ATTTGGATCC
* *
13193537 AAATTTAATCAAAATTTCACTTTGGTCCAT
1 AAATTTAATCAAAATTTCAATTTAGTCCAT
* *
13193567 GAATTTAATTAAAA-TTCAATTTAGTCC-T
1 AAATTTAATCAAAATTTCAATTTAGTCCAT
13193595 AAA
1 AAA
13193598 ATTTTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
28 3 0.12
29 11 0.42
30 12 0.46
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (30 bp):
AAATTTAATCAAAATTTCAATTTAGTCCAT
Found at i:13199536 original size:24 final size:24
Alignment explanation
Indices: 13199504--13199560 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
13199494 CAAAAGAAGA
*
13199504 AGAAGAAACACCGTCCTAATTTTG
1 AGAAGAAACACCATCCTAATTTTG
13199528 AGAAGAAACACCATCCTAATTTTG
1 AGAAGAAACACCATCCTAATTTTG
*
13199552 AGAAAAAAC
1 AGAAGAAAC
13199561 TATTTTACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (24 bp):
AGAAGAAACACCATCCTAATTTTG
Found at i:13200353 original size:16 final size:15
Alignment explanation
Indices: 13200343--13200378 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
13200333 TATTTACATT
13200343 ACTTGACATTTATCTG
1 ACTTGACATTTA-CTG
13200359 ACTTGACATTTACCTG
1 ACTTGACATTTA-CTG
13200375 ACTT
1 ACTT
13200379 ATATATTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (15 bp):
ACTTGACATTTACTG
Found at i:13200512 original size:21 final size:21
Alignment explanation
Indices: 13200477--13200543 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
13200467 TTTAAATGTT
*
13200477 ATAA-TAAAATATTAATTATG
1 ATAATTAACATATTAATTATG
*
13200497 ATAATTAA-ATTCTTAA--AT-
1 ATAATTAACA-TATTAATTATG
*
13200515 ATACTTAACATATTAATTATG
1 ATAATTAACATATTAATTATG
13200536 ATAATTAA
1 ATAATTAA
13200544 TATACTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 7 0.19
21 15 0.41
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (21 bp):
ATAATTAACATATTAATTATG
Found at i:13200564 original size:14 final size:15
Alignment explanation
Indices: 13200543--13200618 Score: 97
Period size: 13 Copynumber: 5.3 Consensus size: 15
13200533 ATGATAATTA
13200543 ATATACTTTATATTT
1 ATATACTTTATATTT
13200558 A-ATAC-TTATATTT
1 ATATACTTTATATTT
13200571 ATATACTTTATATTT
1 ATATACTTTATATTT
*
13200586 A-ATAC-TAATATTT
1 ATATACTTTATATTT
*
13200599 ATATAATTTAATATTT
1 ATATACTTT-ATATTT
13200615 ATAT
1 ATAT
13200619 CCAAACACTT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
13 17 0.32
14 15 0.28
15 11 0.21
16 10 0.19
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATACTTTATATTT
Found at i:13200574 original size:28 final size:28
Alignment explanation
Indices: 13200543--13200673 Score: 129
Period size: 28 Copynumber: 4.5 Consensus size: 28
13200533 ATGATAATTA
*
13200543 ATATACTTTATATTTAATACTTATATTT
1 ATATACTTTATATTTAATACTAATATTT
13200571 ATATACTTTATATTTAATACTAATATTT
1 ATATACTTTATATTTAATACTAATATTT
* * * *
13200599 ATATAATTTAATATTTATATCCAAACACTTT
1 ATATACTTT-ATATTTA-ATACTAATA-TTT
* *
13200630 AT-TACTTTATATTAAATATATATATATATAT
1 ATATACTTTATATTTAATA-CTA-ATAT-T-T
13200661 ATATACTTTATAT
1 ATATACTTTATAT
13200674 ATGTATATAA
Statistics
Matches: 84, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
28 37 0.44
29 15 0.18
30 14 0.17
31 8 0.10
32 10 0.12
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (28 bp):
ATATACTTTATATTTAATACTAATATTT
Found at i:13201101 original size:4 final size:4
Alignment explanation
Indices: 13201092--13201315 Score: 448
Period size: 4 Copynumber: 56.0 Consensus size: 4
13201082 AAAATTTAAA
13201092 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13201140 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13201188 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13201236 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13201284 TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
13201316 ATGAATGTTA
Statistics
Matches: 220, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 220 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:13201347 original size:2 final size:2
Alignment explanation
Indices: 13201340--13201423 Score: 125
Period size: 2 Copynumber: 41.5 Consensus size: 2
13201330 AATATGATGC
13201340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
13201382 AT AT AT AT AT AT AT AT AT ACT -T AT ACT TT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT A
13201424 AAGTACCAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
1 1 0.01
2 72 0.96
3 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13201734 original size:2 final size:2
Alignment explanation
Indices: 13201729--13201905 Score: 136
Period size: 2 Copynumber: 89.0 Consensus size: 2
13201719 ATTAATACAT
* * *
13201729 TA TA TA TA TA TA TA TA TT TA T- TA -A TA TA -A AA GTA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
13201769 TA TA -A GTA TA TA TA TA TA TA CT- TA TT TA AA TA TA CA TA TA AA
1 TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * *
13201811 AA TGG TA TA -A GTA TA -A GTA TA TA TA TA AA GTA TA AA TA -A TA
1 TA T-A TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA
13201852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13201894 TA TA TA TA TA TA
1 TA TA TA TA TA TA
13201906 AGTTCTAGTA
Statistics
Matches: 141, Mismatches: 19, Indels: 30
0.74 0.10 0.16
Matches are distributed among these distances:
1 8 0.06
2 126 0.89
3 7 0.05
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:13201743 original size:25 final size:26
Alignment explanation
Indices: 13201681--13201746 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 26
13201671 ATGATGCATG
13201681 TATATATAT-TATA-TAATGCACATTA
1 TATATATATATATATTAAT-CACATTA
**
13201706 TACT-TATGCATATATTAAT-ACATTA
1 TA-TATATATATATATTAATCACATTA
13201731 TATATATATATATATT
1 TATATATATATATATT
13201747 TATTAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
24 1 0.03
25 23 0.70
26 5 0.15
27 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (26 bp):
TATATATATATATATTAATCACATTA
Found at i:13202007 original size:18 final size:20
Alignment explanation
Indices: 13201970--13202013 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
13201960 TAATATAAAG
13201970 TATATAAGAATATAAGTATA
1 TATATAAGAATATAAGTATA
*
13201990 TATATAA-ACTATAA-TATA
1 TATATAAGAATATAAGTATA
*
13202008 GATATA
1 TATATA
13202014 TATAAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 6 0.27
20 7 0.32
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (20 bp):
TATATAAGAATATAAGTATA
Found at i:13202014 original size:20 final size:20
Alignment explanation
Indices: 13201937--13202015 Score: 63
Period size: 22 Copynumber: 3.8 Consensus size: 20
13201927 TAGGTATATA
* *
13201937 ATAATATAAAGTATAAAAGTAT
1 ATAATAT-AA-TATATAAGAAT
13201959 ATAATATAAAGTATATAAGAAT
1 ATAATAT-AA-TATATAAGAAT
*
13201981 ATAAGTAT-ATATATAA-ACT
1 ATAA-TATAATATATAAGAAT
13202000 ATAATATAGATATATA
1 ATAATATA-ATATATA
13202016 TAAAGTTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
18 3 0.06
19 6 0.12
20 14 0.27
21 1 0.02
22 24 0.47
23 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (20 bp):
ATAATATAATATATAAGAAT
Found at i:13202058 original size:41 final size:39
Alignment explanation
Indices: 13202013--13202089 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
13202003 ATATAGATAT
* *
13202013 ATATAAAGTTTTAGTATAAAGTATATATACATATATAATTA
1 ATATAAAGTATAAGTAT-AAGTATAT-TACATATATAATTA
* *
13202054 ATATAAAGTATAAGTATACGTATATTATATATATAA
1 ATATAAAGTATAAGTATAAGTATATTACATATATAA
13202090 AAAGTATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 10 0.31
40 7 0.22
41 15 0.47
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (39 bp):
ATATAAAGTATAAGTATAAGTATATTACATATATAATTA
Found at i:13202072 original size:30 final size:31
Alignment explanation
Indices: 13201822--13202097 Score: 148
Period size: 30 Copynumber: 8.7 Consensus size: 31
13201812 ATGGTATAAG
13201822 TATAAGTATATATATAAAGTATAA-ATA-ATA
1 TATAA-TATATATATAAAGTATAATATACATA
* *
13201852 TATATATATATATATATA-TATATATATATATA
1 TATA-ATATATATATAAAGTATA-ATATACATA
*
13201884 TATATATATATATATATA-TATAAGT-T-C-TA
1 TATA-ATATATATATAAAGTATAA-TATACATA
* *
13201913 GTATGAAGTATATATAGGTATA-TAATAATATAAAGTA
1 -TAT-AA-TATATATA--TAAAGT-ATAATATACA-TA
* *
13201950 TAAAAGTATATAATATAAAGTAT-ATA-AGA-A
1 TATAA-TATAT-ATATAAAGTATAATATACATA
* *
13201980 TATAAGTATATATATAAACTATAATATAGATA
1 TATAA-TATATATATAAAGTATAATATACATA
* *
13202012 TATATAAAGTTTTAGTATAAAGTAT-ATATACATA
1 TATA-ATA--TATA-TATAAAGTATAATATACATA
*
13202046 TATAAT-TA-ATATAAAGTATAAGTATACGTA
1 TATAATATATATATAAAGTATAA-TATACATA
* *
13202076 TATTATATATATAAAAAGTATA
1 TATAATATATATATAAAGTATA
13202098 TAAGCATATA
Statistics
Matches: 201, Mismatches: 17, Indels: 54
0.74 0.06 0.20
Matches are distributed among these distances:
28 10 0.05
29 18 0.09
30 47 0.23
31 20 0.10
32 45 0.22
33 11 0.05
34 25 0.12
35 18 0.09
36 5 0.02
37 2 0.01
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.39
Consensus pattern (31 bp):
TATAATATATATATAAAGTATAATATACATA
Found at i:13202099 original size:41 final size:40
Alignment explanation
Indices: 13201956--13202100 Score: 93
Period size: 41 Copynumber: 3.5 Consensus size: 40
13201946 AGTATAAAAG
* *
13201956 TATATA-ATATAAAGTATATAAGAATATAAGTATA-TATAT
1 TATATATATAAAAAGTATATAA-AGTATAAGTATAGTATAT
* * * * *
13201995 AAACTATAATATAGATA-TATATAAAGTTTTAGTATAAAGTATA-
1 -TA-TAT-ATATAAAAAGTATATAAAGTATAAGTAT--AGTATAT
* * *
13202038 TATACATAT-ATAATTAATATAAAGTATAAGTATACGTATAT
1 TATATATATAAAAAGT-ATATAAAGTATAAGTATA-GTATAT
13202079 TATATATATAAAAAGTATATAA
1 TATATATATAAAAAGTATATAA
13202101 GCATATAAAG
Statistics
Matches: 78, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
39 2 0.03
40 11 0.14
41 42 0.54
42 13 0.17
43 6 0.08
44 4 0.05
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (40 bp):
TATATATATAAAAAGTATATAAAGTATAAGTATAGTATAT
Found at i:13202108 original size:19 final size:17
Alignment explanation
Indices: 13202079--13202127 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
13202069 ATACGTATAT
*
13202079 TATATATATAAA-AAGTA
1 TATACATATAAAGAA-TA
13202096 TATAAGCATATAAAGAATA
1 TAT-A-CATATAAAGAATA
13202115 TATACATATAAAG
1 TATACATATAAAG
13202128 TACTGTAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 12 0.43
18 2 0.07
19 12 0.43
20 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (17 bp):
TATACATATAAAGAATA
Found at i:13202272 original size:28 final size:25
Alignment explanation
Indices: 13202236--13202291 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 25
13202226 ATATATGCGT
*
13202236 TACATTTATATTATATACATATACATA
1 TACATTTATACTATATAC-TATA-ATA
13202263 TACATATTATACTATATACTATAATA
1 TACAT-TTATACTATATACTATAATA
13202289 TAC
1 TAC
13202292 TATGCGGGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.22
27 9 0.33
28 12 0.44
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (25 bp):
TACATTTATACTATATACTATAATA
Found at i:13202285 original size:12 final size:11
Alignment explanation
Indices: 13202249--13202294 Score: 53
Period size: 10 Copynumber: 4.3 Consensus size: 11
13202239 ATTTATATTA
13202249 TATACATATAC
1 TATACATATAC
13202260 ATATACATAT--
1 -TATACATATAC
13202270 TATACTATATAC
1 TATAC-ATATAC
13202282 TATA-ATATAC
1 TATACATATAC
13202292 TAT
1 TAT
13202295 GCGGGGCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.16
10 13 0.42
12 13 0.42
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (11 bp):
TATACATATAC
Found at i:13203427 original size:16 final size:15
Alignment explanation
Indices: 13203401--13203430 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
13203391 TTAAATCATT
13203401 TTTATTTTTATTTTG
1 TTTATTTTTATTTTG
13203416 TTTATGTTTTATTTT
1 TTTAT-TTTTATTTT
13203431 AGCCACTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTATTTTTATTTTG
Found at i:13203631 original size:30 final size:30
Alignment explanation
Indices: 13203596--13203667 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
13203586 TTTGGATAAT
13203596 TTATATTTTAGTTCTAATTGTACGGGTTTA
1 TTATATTTTAGTTCTAATTGTACGGGTTTA
*
13203626 TTATATTTTAGTTCTAATTGTATGGGTTTA
1 TTATATTTTAGTTCTAATTGTACGGGTTTA
13203656 TTATATTTTAGT
1 TTATATTTTAGT
13203668 GTTTAAAATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.24, C:0.04, G:0.15, T:0.57
Consensus pattern (30 bp):
TTATATTTTAGTTCTAATTGTACGGGTTTA
Found at i:13206840 original size:150 final size:150
Alignment explanation
Indices: 13206559--13206857 Score: 465
Period size: 150 Copynumber: 2.0 Consensus size: 150
13206549 AGAATTCGTT
* *
13206559 GCTTCAACAGAGAATTCTTGTGAAGAATATAAAGCACAAAATGATGGAAAAGGAAATCCAAGCAG
1 GCTTCAACAGAGAATTCATGTGAAGAACATAAAGCACAAAATGATGGAAAAGGAAATCCAAGCAG
*
13206624 AAGGGCTTTCATGAATGTAATCCGAGACTGGCCCATGAGTTTAGGAATGGATGGGGCAGATACAG
66 AAGGGCTTTCATGAATGTAATCCGAGACTGGCCCATGAGTTTAGGAATGAATGGGGCAGATACAG
13206689 CCATGAAGACACCTCAAACG
131 CCATGAAGACACCTCAAACG
* * ** *
13206709 GCTTTAACAGAGAATTCATGTGAAGAACATAAGGCTTAAAATGATGGAAAAGGAAATCCAAGCCG
1 GCTTCAACAGAGAATTCATGTGAAGAACATAAAGCACAAAATGATGGAAAAGGAAATCCAAGCAG
* * * *
13206774 AAGGG-TTTCCATGAATGTAATCCGAGACTGGCCCGTGGGTTTATGAATGAATGGGGCAGATGCA
66 AAGGGCTTT-CATGAATGTAATCCGAGACTGGCCCATGAGTTTAGGAATGAATGGGGCAGATACA
*
13206838 GCCTTGAAGACACCTCAAAC
130 GCCATGAAGACACCTCAAAC
13206858 ACCTATATCA
Statistics
Matches: 135, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
149 3 0.02
150 132 0.98
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.20
Consensus pattern (150 bp):
GCTTCAACAGAGAATTCATGTGAAGAACATAAAGCACAAAATGATGGAAAAGGAAATCCAAGCAG
AAGGGCTTTCATGAATGTAATCCGAGACTGGCCCATGAGTTTAGGAATGAATGGGGCAGATACAG
CCATGAAGACACCTCAAACG
Found at i:13207951 original size:99 final size:99
Alignment explanation
Indices: 13207831--13208032 Score: 323
Period size: 99 Copynumber: 2.0 Consensus size: 99
13207821 TTATAATATT
* * *
13207831 ATATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGGAATTGGTTAAACGCCCCGACTTTATGG
1 ATATCTATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGG
13207896 ATAAAATTCAGCTAGCATGATAAAGGTGATTATA
66 ATAAAATTCAGCTAGCATGATAAAGGTGATTATA
* * *
13207930 ATATCTATACAATAAAGCTTGAGGTGTCCCTCTAAAGCAATTGGTTAAACGCCCTGGCTTTATGG
1 ATATCTATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGG
* * *
13207995 GTAAGATTCAGCTAGCGTGATAAAGGTGATTATA
66 ATAAAATTCAGCTAGCATGATAAAGGTGATTATA
13208029 ATAT
1 ATAT
13208033 TGAGATGTCC
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (99 bp):
ATATCTATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGG
ATAAAATTCAGCTAGCATGATAAAGGTGATTATA
Found at i:13209828 original size:85 final size:85
Alignment explanation
Indices: 13209689--13209941 Score: 337
Period size: 85 Copynumber: 3.0 Consensus size: 85
13209679 TCCCAACCTA
* * * *
13209689 TTACATCATAGCTCAAGGAGAGAAGGGCTATATGTCAACCAAAACCTTCAAGTTCGATTACATTC
1 TTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTC
*
13209754 AACTCAAGGACATATTAAAT
66 AACTCAAGGACATATCAAAT
* *
13209774 TTACAACATAGCTCAAGGCGATAAGGGCTATCTATCAACCAAAACCTTCGAGTTCGATTACATTC
1 TTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTC
*
13209839 AACTCAAGGGCATATCAAAT
66 AACTCAAGGACATATCAAAT
* * ** * *
13209859 TTACAACATAGCTTAAGTCGAGAAAAGCTATCTGTCAA-CAAAAACTATCGAGTTCGATTCCATT
1 TTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCT-TCGAGTTCGATTACATT
* * *
13209923 CATCTCGATGACATATCAA
65 CAACTCAAGGACATATCAA
13209942 CCGCATGGTA
Statistics
Matches: 147, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
84 7 0.05
85 140 0.95
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.26
Consensus pattern (85 bp):
TTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTC
AACTCAAGGACATATCAAAT
Found at i:13210703 original size:22 final size:20
Alignment explanation
Indices: 13210678--13210720 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
13210668 TGTGTTACGT
*
13210678 TTATATTATATACATATACATA
1 TTATACTATATAC-TATA-ATA
13210700 TTATACTATATACTATAATA
1 TTATACTATATACTATAATA
13210720 T
1 T
13210721 ACTATGCAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 4 0.20
22 12 0.60
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATACTATATACTATAATA
Found at i:13210721 original size:17 final size:16
Alignment explanation
Indices: 13210685--13210725 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
13210675 CGTTTATATT
13210685 ATATAC-ATATACATA
1 ATATACTATATACATA
*
13210700 TTATACTATATACTATA
1 ATATACTATATAC-ATA
13210717 ATATACTAT
1 ATATACTAT
13210726 GCAGGGCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 5 0.23
16 6 0.27
17 11 0.50
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATACTATATACATA
Found at i:13212291 original size:12 final size:13
Alignment explanation
Indices: 13212269--13212297 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
13212259 CGAATCAAGT
13212269 TTTTAAATTTTAA
1 TTTTAAATTTTAA
13212282 TTTT-AATTTTAA
1 TTTTAAATTTTAA
13212294 TTTT
1 TTTT
13212298 CACAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:13223811 original size:28 final size:28
Alignment explanation
Indices: 13223780--13223835 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
13223770 TATTTTCCCT
13223780 TTATTTCTTTACATTCACATTAACTAAC
1 TTATTTCTTTACATTCACATTAACTAAC
13223808 TTATTTCTTTACATTCACATTAACTAAC
1 TTATTTCTTTACATTCACATTAACTAAC
13223836 AAAAAATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.46
Consensus pattern (28 bp):
TTATTTCTTTACATTCACATTAACTAAC
Found at i:13230068 original size:18 final size:19
Alignment explanation
Indices: 13230033--13230069 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
13230023 CACAGAATGT
13230033 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
13230053 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
13230070 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:13231525 original size:48 final size:49
Alignment explanation
Indices: 13231457--13231550 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 49
13231447 AATATTTCTC
* * * * * *
13231457 TTAGGGTGAAAATTCTAAAGGGCGCACTAAGTTGAAGAA-AAAAAATGT
1 TTAGAGTGAAAACTCGAAAGGGCACACTAAATTGAAAAATAAAAAATGT
*
13231505 TTAGAGTGAAAACTCGAAAGGGCACTCTAAATTGAAAAATAAAAAA
1 TTAGAGTGAAAACTCGAAAGGGCACACTAAATTGAAAAATAAAAAA
13231551 GAAAAACCAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 32 0.84
49 6 0.16
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (49 bp):
TTAGAGTGAAAACTCGAAAGGGCACACTAAATTGAAAAATAAAAAATGT
Found at i:13234108 original size:2 final size:2
Alignment explanation
Indices: 13234101--13234127 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13234091 TCTTTATAAT
13234101 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13234128 TGTCGTAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13234965 original size:2 final size:2
Alignment explanation
Indices: 13234958--13234984 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13234948 AATTATAACA
13234958 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
13234985 ATGAATGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13236109 original size:40 final size:40
Alignment explanation
Indices: 13236041--13236161 Score: 165
Period size: 40 Copynumber: 3.1 Consensus size: 40
13236031 GTAATATCTG
*
13236041 CACCGTAGTGC--TACACATAAGGTTGTGCCCACCATATA
1 CACCGTAGTGCATTACACATAAGGTCGTGCCCACCATATA
*
13236079 CACCGTAGTGCATTAAACATAAGGTCGTGCCCACCATATA
1 CACCGTAGTGCATTACACATAAGGTCGTGCCCACCATATA
* * * * *
13236119 CAGCATAGTACATTACACATAAGGTCGTGGCCAACATATA
1 CACCGTAGTGCATTACACATAAGGTCGTGCCCACCATATA
13236159 CAC
1 CAC
13236162 TTAGTGTCCT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 11 0.15
40 61 0.85
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (40 bp):
CACCGTAGTGCATTACACATAAGGTCGTGCCCACCATATA
Found at i:13237099 original size:30 final size:31
Alignment explanation
Indices: 13237046--13237111 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
13237036 CATTCACATT
* * * *
13237046 TTTTCCAAAATTATCGAATTGGTCCCCTAAC
1 TTTTCAAAAATTATCAAAATGGTCCCCAAAC
*
13237077 TTTTCAAAAATTA-CAAAATGGTCCCCAAAT
1 TTTTCAAAAATTATCAAAATGGTCCCCAAAC
13237107 TTTTC
1 TTTTC
13237112 TAAGGCTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (31 bp):
TTTTCAAAAATTATCAAAATGGTCCCCAAAC
Found at i:13244692 original size:24 final size:24
Alignment explanation
Indices: 13244665--13244836 Score: 118
Period size: 24 Copynumber: 7.2 Consensus size: 24
13244655 ATTGATATTG
13244665 ATTAGTGCATTTGTGCACTCCTAT
1 ATTAGTGCATTTGTGCACTCCTAT
* *
13244689 ATTAGTGCATTTGTGCACTCATGT
1 ATTAGTGCATTTGTGCACTCCTAT
* * * *
13244713 ATCAGTG-TTTTCATGCACTCCTAA
1 ATTAGTGCATTT-GTGCACTCCTAT
* * * *
13244737 ATTAGTGCAATTGAGCACTCATGT
1 ATTAGTGCATTTGTGCACTCCTAT
* * ***
13244761 ATTAGTGTGA-ATACACACTCCTAT
1 ATTAGTG-CATTTGTGCACTCCTAT
* *
13244785 A-TAGTGCACTTGTGCACTCCGAT
1 ATTAGTGCATTTGTGCACTCCTAT
* **
13244808 ATTAATGC-TTTGTGCACTCCCGT
1 ATTAGTGCATTTGTGCACTCCTAT
13244831 ATTAGT
1 ATTAGT
13244837 ACCATTGGGT
Statistics
Matches: 109, Mismatches: 34, Indels: 11
0.71 0.22 0.07
Matches are distributed among these distances:
22 1 0.01
23 35 0.32
24 70 0.64
25 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.37
Consensus pattern (24 bp):
ATTAGTGCATTTGTGCACTCCTAT
Found at i:13244780 original size:48 final size:47
Alignment explanation
Indices: 13244679--13244803 Score: 146
Period size: 48 Copynumber: 2.6 Consensus size: 47
13244669 GTGCATTTGT
* * *
13244679 GCACTCCTATATTAGTGCATTTGTGCACTCATGTATCAGTGTTTTCA
1 GCACTCCTATATTAGTGCAATTGTGCACTCATGTATCAGTGTATACA
* * *
13244726 TGCACTCCTAAATTAGTGCAATTGAGCACTCATGTATTAGTGTGAATACA
1 -GCACTCCTATATTAGTGCAATTGTGCACTCATGTATCAGTGT--ATACA
*
13244776 -CACTCCTATA-TAGTGCACTTGTGCACTC
1 GCACTCCTATATTAGTGCAATTGTGCACTC
13244804 CGATATTAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
47 16 0.24
48 47 0.71
50 3 0.05
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (47 bp):
GCACTCCTATATTAGTGCAATTGTGCACTCATGTATCAGTGTATACA
Found at i:13244802 original size:23 final size:23
Alignment explanation
Indices: 13244776--13244827 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
13244766 TGTGAATACA
* *
13244776 CACTCCTATA-TAGTGCACTTGTG
1 CACTCCGATATTAATGC-CTTGTG
*
13244799 CACTCCGATATTAATGCTTTGTG
1 CACTCCGATATTAATGCCTTGTG
13244822 CACTCC
1 CACTCC
13244828 CGTATTAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (23 bp):
CACTCCGATATTAATGCCTTGTG
Found at i:13249386 original size:23 final size:23
Alignment explanation
Indices: 13249360--13249404 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
13249350 ATTTAGTGCA
13249360 TTTGTACACTCCTGTATCAGTGG
1 TTTGTACACTCCTGTATCAGTGG
* *
13249383 TTTGTGCACTCCTGTATTAGTG
1 TTTGTACACTCCTGTATCAGTG
13249405 TATTTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (23 bp):
TTTGTACACTCCTGTATCAGTGG
Found at i:13249417 original size:24 final size:23
Alignment explanation
Indices: 13249352--13249427 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 23
13249342 CGATCTTAAT
13249352 TTAGTGCATTTGT-ACACTCCTGTA
1 TTAGTG-ATTTGTGA-ACTCCTGTA
* * *
13249376 TCAGTGGTTTGTGCACTCCTGTA
1 TTAGTGATTTGTGAACTCCTGTA
*
13249399 TTAGTGTATTTGTGAACTCATGTA
1 TTAGTG-ATTTGTGAACTCCTGTA
13249423 TTAGT
1 TTAGT
13249428 CCCTTCGTGC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 19 0.44
24 24 0.56
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (23 bp):
TTAGTGATTTGTGAACTCCTGTA
Found at i:13249441 original size:24 final size:24
Alignment explanation
Indices: 13249386--13249441 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
13249376 TCAGTGGTTT
* ** *
13249386 GTGCACTCCTGTATTAGTGTATTT
1 GTGCACTCATGTATTAGTCCATTC
* *
13249410 GTGAACTCATGTATTAGTCCCTTC
1 GTGCACTCATGTATTAGTCCATTC
13249434 GTGCACTC
1 GTGCACTC
13249442 TTAAATTAGG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (24 bp):
GTGCACTCATGTATTAGTCCATTC
Found at i:13255093 original size:17 final size:16
Alignment explanation
Indices: 13255052--13255093 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
13255042 AAATATCTTT
13255052 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
13255068 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
13255085 TAAAA-AATT
1 TAAAATAATT
13255094 GATCTGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Done.