Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008694.1 Hibiscus syriacus cultivar Beakdansim tig00111723_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: 1352611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:218893 original size:113 final size:114
Alignment explanation
Indices: 218745--218966 Score: 383
Period size: 113 Copynumber: 2.0 Consensus size: 114
218735 GATCATGCAG
* * *
218745 TTCATCTTTCAATTCTAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
218810 ACACTTCCA-AAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
*
218858 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
218923 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGA
66 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGA
218967 TAACGTGGCA
Statistics
Matches: 102, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
113 70 0.69
114 32 0.31
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (114 bp):
TTCATCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
Found at i:219324 original size:19 final size:17
Alignment explanation
Indices: 219296--219344 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
219286 AAAATAAAAG
*
219296 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
219315 AATAAATTGAA-TTTCA
1 AATAAATTGAATTTTCA
219331 AATAAATTGAATTT
1 AATAAATTGAATTT
219345 AGAGAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 12 0.43
17 2 0.07
18 4 0.14
19 10 0.36
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:219714 original size:13 final size:13
Alignment explanation
Indices: 219693--219743 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 13
219683 TCTTGACCCC
219693 CTCTTTTTTCTTT
1 CTCTTTTTTCTTT
219706 CTCTCTTTTT-TTT
1 CTCT-TTTTTCTTT
219719 CT-TTTTTTCTTT
1 CTCTTTTTTCTTT
*
219731 TTCATTTTTTCTT
1 CTC-TTTTTTCTT
219744 CAAGCGTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 9 0.27
14 14 0.42
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (13 bp):
CTCTTTTTTCTTT
Found at i:219718 original size:17 final size:17
Alignment explanation
Indices: 219696--219732 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
219686 TGACCCCCTC
219696 TTTTTTCTTTCTCTCTT
1 TTTTTTCTTTCTCTCTT
* *
219713 TTTTTTCTTTTTTTCTT
1 TTTTTTCTTTCTCTCTT
219730 TTT
1 TTT
219733 CATTTTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTCTTTCTCTCTT
Found at i:227086 original size:15 final size:15
Alignment explanation
Indices: 227063--227094 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
227053 AAAATAATGC
227063 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
227078 AATGCATGTATGCAA
1 AATGAATGTATGCAA
227093 AA
1 AA
227095 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:231110 original size:103 final size:104
Alignment explanation
Indices: 230907--231130 Score: 256
Period size: 103 Copynumber: 2.1 Consensus size: 104
230897 ATTATAATTA
*
230907 TGAAAAATATATATTAATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGA
1 TGAAAAATA-A-A-TAATTTATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGA
* * * * *
230972 AAATGACTTCTAGGTGCCTTAAGACAACTCTTTTCTTTGATAT
63 AAATGACATCCAGGTACCTTAAGACAACTCCTTTC-TTAATAT
** *
231015 T-AAAAATAAATAATTTATATA-ATTTATAAATAGGATATTTATTTATTTAAAAATATTAGAAAA
1 TGAAAAATAAATAATTTATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAA
* ** **
231078 TGGACATCCAGTTATTTTAAGAC-TGTCCTTTCTTAATAT
66 T-GACATCCAGGTACCTTAAGACAACTCCTTTCTTAATAT
231117 TGAAAAATAAATAA
1 TGAAAAATAAATAA
231131 ATATTAAAAC
Statistics
Matches: 100, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
102 7 0.07
103 57 0.57
104 26 0.26
105 1 0.01
106 1 0.01
107 7 0.07
108 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (104 bp):
TGAAAAATAAATAATTTATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAA
TGACATCCAGGTACCTTAAGACAACTCCTTTCTTAATAT
Found at i:231216 original size:2 final size:2
Alignment explanation
Indices: 231204--231237 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
231194 TATTATTTAT
*
231204 TA TA TA AA 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
231238 ACTAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:232607 original size:3 final size:3
Alignment explanation
Indices: 232599--232651 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
232589 ATATTGTTTG
* *
232599 TAA TAA TAA TATA TAA TAA TAAA TAA -AA TTA TAA TAA T-A TAT TAA
1 TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
232644 TAA TAA TA
1 TAA TAA TA
232652 TTGAAAACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:232616 original size:10 final size:10
Alignment explanation
Indices: 232601--232648 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
232591 ATTGTTTGTA
232601 ATAATAATAT
1 ATAATAATAT
*
232611 ATAATAATAA
1 ATAATAATAT
232621 ATAA-AAT-T
1 ATAATAATAT
232629 ATAATAATAT
1 ATAATAATAT
232639 ATTAATAATA
1 A-TAATAATA
232649 ATATTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 15 0.45
11 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATAATAT
Found at i:241223 original size:33 final size:33
Alignment explanation
Indices: 241186--241262 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
241176 TTTCGTATAT
*
241186 GCATTC-GAAAACACTTGATTATATTGTTATGTC
1 GCATTCAG-AAACACTTGATTATATTGATATGTC
* *
241219 GCATTCAGAAATACTTGATTATATTGATATGTT
1 GCATTCAGAAACACTTGATTATATTGATATGTC
*
241252 ACATTCAGAAA
1 GCATTCAGAAA
241263 TATTTAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 38 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (33 bp):
GCATTCAGAAACACTTGATTATATTGATATGTC
Found at i:241263 original size:33 final size:33
Alignment explanation
Indices: 241198--241264 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
241188 ATTCGAAAAC
* *
241198 ACTTGATTATATTGTTATGTCGCATTCAGAAAT
1 ACTTGATTATATTGATATGTCACATTCAGAAAT
*
241231 ACTTGATTATATTGATATGTTACATTCAGAAAT
1 ACTTGATTATATTGATATGTCACATTCAGAAAT
241264 A
1 A
241265 TTTAATATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (33 bp):
ACTTGATTATATTGATATGTCACATTCAGAAAT
Found at i:243217 original size:42 final size:41
Alignment explanation
Indices: 243131--243223 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 41
243121 TGTCAAAATG
* * * * **
243131 GTATCGATACTGAAAGAGAGTATCGGTACCATATTGTAGTA
1 GTATCGATACTGAAAGAAAGTACCGGTACCATAGTATAAAA
* *
243172 GTATCGATACTGAGAGAAAGATACCGGTACTATAGTATAAAA
1 GTATCGATACTGAAAGAAAG-TACCGGTACCATAGTATAAAA
243214 GTATCGATAC
1 GTATCGATAC
243224 AATGGTAGGG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 18 0.42
42 25 0.58
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27
Consensus pattern (41 bp):
GTATCGATACTGAAAGAAAGTACCGGTACCATAGTATAAAA
Found at i:243715 original size:26 final size:26
Alignment explanation
Indices: 243647--243908 Score: 185
Period size: 26 Copynumber: 11.0 Consensus size: 26
243637 CTAAAATGAA
243647 TCCATAAATGAAATGCATGAAAGGA-
1 TCCATAAATGAAATGCATGAAAGGAT
* *
243672 TGCAT---T--AAGGCATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGAT
*
243693 TCCATAAATGAAATGCATAAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGAT
*
243719 ACCATAAATGAAATGCATGAAAGGA-
1 TCCATAAATGAAATGCATGAAAGGAT
* *
243744 TGCAT---T--AAGGCATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGAT
*
243765 GCCATAAATGAAATGCATGAAAGGA-
1 TCCATAAATGAAATGCATGAAAGGAT
* * *
243790 TACAT---T--AAGGCATGAAAGAAT
1 TCCATAAATGAAATGCATGAAAGGAT
* *
243811 GCCATAAATGAAATGTATGAAAGGA-
1 TCCATAAATGAAATGCATGAAAGGAT
* * * *
243836 TGCAT---T--AAGGAATGAAAGAAT
1 TCCATAAATGAAATGCATGAAAGGAT
* *
243857 GCTATAAATGAAATGCATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGAT
*
243883 GCCATAAATGAAATGCATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGAT
243909 ACATTAAGGC
Statistics
Matches: 179, Mismatches: 34, Indels: 47
0.69 0.13 0.18
Matches are distributed among these distances:
20 49 0.27
21 12 0.07
22 4 0.02
24 4 0.02
25 13 0.07
26 97 0.54
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.21
Consensus pattern (26 bp):
TCCATAAATGAAATGCATGAAAGGAT
Found at i:243726 original size:72 final size:72
Alignment explanation
Indices: 243648--243792 Score: 272
Period size: 72 Copynumber: 2.0 Consensus size: 72
243638 TAAAATGAAT
*
243648 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAAATGAAATGCATAA
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGCATAA
243713 AAGGATA
66 AAGGATA
*
243720 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGCATGA
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGCATAA
243785 AAGGATA
66 AAGGATA
243792 C
1 C
243793 ATTAAGGCAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (72 bp):
CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGCATAA
AAGGATA
Found at i:243762 original size:46 final size:46
Alignment explanation
Indices: 243720--243884 Score: 285
Period size: 46 Copynumber: 3.6 Consensus size: 46
243710 TAAAAGGATA
*
243720 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATG
*
243766 CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGAATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATG
* *
243812 CCATAAATGAAATGTATGAAAGGATGCATTAAGGAATGAAAGAATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATG
*
243858 CTATAAATGAAATGCATGAAAGGATGC
1 CCATAAATGAAATGCATGAAAGGATGC
243885 CATAAATGAA
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 112 1.00
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.21
Consensus pattern (46 bp):
CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATG
Found at i:243802 original size:118 final size:118
Alignment explanation
Indices: 243648--243942 Score: 405
Period size: 118 Copynumber: 2.5 Consensus size: 118
243638 TAAAATGAAT
* *
243648 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAAATGAAATGCATAA
1 CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAATGAAATGCATAA
* * ** *
243713 AAGGATACCATAAATGAAATGCATGAAAG-GATGCAT-TAAGGCATGAAAGGATG
66 AAGGAT-CCATAAA-GAAATGAAAGAAAGCGATAAATGAAAGGCATGAAAGGATG
* * *
243766 CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGAATGCCATAAATGAAATGTATGA
1 CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAATGAAATGCATAA
* * * * * *
243831 AAGGATGCATTAAGGAATGAAAGAATGCTATAAATGAAATGCATGAAAGGATG
66 AAGGATCCATAAAGAAATGAAAGAAAGCGATAAATGAAAGGCATGAAAGGATG
*
243884 CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGACATAAATGAAAT
1 CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAATGAAAT
243943 TAACGAATAA
Statistics
Matches: 157, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
116 10 0.06
117 9 0.06
118 138 0.88
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.21
Consensus pattern (118 bp):
CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAATGAAATGCATAA
AAGGATCCATAAAGAAATGAAAGAAAGCGATAAATGAAAGGCATGAAAGGATG
Found at i:243831 original size:72 final size:72
Alignment explanation
Indices: 243753--243908 Score: 181
Period size: 72 Copynumber: 2.2 Consensus size: 72
243743 ATGCATTAAG
* * * *
243753 GCATGAAAGGATGCCATAAATGAAATGCATGAAAG-GATACAT-TAAGGCATGAAAGAATGCCAT
1 GCATGAAAGGATG-CATAAA-GAAATGAAAGAAAGCGATAAATGAAAGGCATGAAAGAATGCCAT
243816 AAATGAAAT
64 AAATGAAAT
* * * * * * *
243825 GTATGAAAGGATGCATTAAGGAATGAAAGAATGCTATAAATGAAATGCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCATAAAGAAATGAAAGAAAGCGATAAATGAAAGGCATGAAAGAATGCCATAA
243890 ATGAAAT
66 ATGAAAT
243897 GCATGAAAGGAT
1 GCATGAAAGGAT
243909 ACATTAAGGC
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
70 10 0.14
71 10 0.14
72 50 0.71
ACGTcount: A:0.47, C:0.09, G:0.24, T:0.21
Consensus pattern (72 bp):
GCATGAAAGGATGCATAAAGAAATGAAAGAAAGCGATAAATGAAAGGCATGAAAGAATGCCATAA
ATGAAAT
Found at i:243916 original size:72 final size:72
Alignment explanation
Indices: 243799--243942 Score: 227
Period size: 72 Copynumber: 2.0 Consensus size: 72
243789 ATACATTAAG
* *
243799 GCATGAAAGAATGCCATAAATGAAATGTATGAAAGGATGCATTAAGGAATGAAAGAATG-CTATA
1 GCATGAAAGAATGCCATAAATGAAATGCATGAAAGGATACATTAAGGAATGAAAGAATGAC-ATA
243863 AATGAAAT
65 AATGAAAT
* * *
243871 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGACATAA
1 GCATGAAAGAATGCCATAAATGAAATGCATGAAAGGATACATTAAGGAATGAAAGAATGACATAA
243936 ATGAAAT
66 ATGAAAT
243943 TAACGAATAA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 65 0.98
73 1 0.02
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.21
Consensus pattern (72 bp):
GCATGAAAGAATGCCATAAATGAAATGCATGAAAGGATACATTAAGGAATGAAAGAATGACATAA
ATGAAAT
Found at i:244472 original size:81 final size:82
Alignment explanation
Indices: 244329--244528 Score: 230
Period size: 81 Copynumber: 2.5 Consensus size: 82
244319 TGTTATAATA
* * * * *
244329 TAAAAGATT-AATGACCTAACTGTGTATTTGACAGGAAGGTGTCAATCGTGCCAGTTAGATGAAA
1 TAAAAGATTAAAAGACCTAACTGTGTATTTGACAGAAAGGTGTCAATCATGCCAATTAAATGAAA
*
244393 GGTTAAATACCTTTGAG
66 GGTTAAATACATTTGAG
* *
244410 TAAAAGATTAAAAG-CCTAATTGTG-ATTTTGGCAGAAAGGTGTCAATCATGCCAATTAAATGAA
1 TAAAAGATTAAAAGACCTAACTGTGTA-TTTGACAGAAAGGTGTCAATCATGCCAATTAAATGAA
*
244473 AGGTTAAATACATTTGGG
65 AGGTTAAATACATTTGAG
* * * *
244491 TAAAAGACTAAATGTCC-AAC-GATGTATTTGGCAGAAAG
1 TAAAAGATTAAAAGACCTAACTG-TGTATTTGACAGAAAG
244529 ATGCCAATAA
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
80 2 0.02
81 94 0.92
82 6 0.06
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (82 bp):
TAAAAGATTAAAAGACCTAACTGTGTATTTGACAGAAAGGTGTCAATCATGCCAATTAAATGAAA
GGTTAAATACATTTGAG
Found at i:244553 original size:81 final size:82
Alignment explanation
Indices: 244381--244553 Score: 185
Period size: 81 Copynumber: 2.1 Consensus size: 82
244371 CAATCGTGCC
* * *
244381 AGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAAAAGCCTAATTGTGATTTTGGCAGAA
1 AGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGACTAAAAGCCTAAATGTGATTTTGGCAGAA
* * * *
244446 AGGTGTCAATCATGCCA
66 AGATGCCAATAATGCAA
* * *
244463 A-TTAAATGAAAGGTTAAATACATTTGGGTAAAAGACTAAATGTCC-AACGATGT-A-TTTGGCA
1 AGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGACTAAAAG-CCTAA--ATGTGATTTTGGCA
244524 GAAAGATGCCAATAATG-AA
63 GAAAGATGCCAATAATGCAA
*
244543 AGTTGGATGAA
1 AGTTAGATGAA
244554 TGATTAATTT
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
80 2 0.03
81 66 0.88
82 4 0.05
83 3 0.04
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (82 bp):
AGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGACTAAAAGCCTAAATGTGATTTTGGCAGAA
AGATGCCAATAATGCAA
Found at i:244657 original size:2 final size:2
Alignment explanation
Indices: 244650--244698 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
244640 CCATAAATGA
244650 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
244692 AT AT AT A
1 AT AT AT A
244699 ATAATGCATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:247884 original size:81 final size:81
Alignment explanation
Indices: 247714--247862 Score: 217
Period size: 81 Copynumber: 1.8 Consensus size: 81
247704 GACATAATTG
* * *
247714 TGTATTTGATAGAAATGTGTCAATCATGACAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
1 TGTATTTGGTAGAAAGGTGTCAATCATGACAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAG
*
247779 ACTGAAAGCCTAACTC
66 ACTGAAAGCCTAACGC
** * * *
247795 TGCCTTTGGTAGAAAGGTTTCAATCATGCCAGTTAGATGAAAGGTTAAATACATTTGGGTAAAAG
1 TGTATTTGGTAGAAAGGTGTCAATCATGACAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAG
247860 ACT
66 ACT
247863 AAATTTCTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 60 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (81 bp):
TGTATTTGGTAGAAAGGTGTCAATCATGACAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAG
ACTGAAAGCCTAACGC
Found at i:247890 original size:81 final size:81
Alignment explanation
Indices: 247714--247891 Score: 207
Period size: 81 Copynumber: 2.2 Consensus size: 81
247704 GACATAATTG
* *
247714 TGTATTT-GATAGAAATGTGTCAATCATGACAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAA
1 TGTATTTGGA-AGAAAGGTGTCAATCATGACAGTTAGATGAAAGGTTAAATACATTTGAGTAAAA
*
247778 GACTGAAAGCCTAACTC
65 GACTGAAAGCCTAACGC
** * * * *
247795 TGCCTTTGGTAGAAAGGTTTCAATCATGCCAGTTAGATGAAAGGTTAAATACATTTGGGTAAAAG
1 TGTATTTGGAAGAAAGGTGTCAATCATGACAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAG
** *
247860 ACT-AAATTTCTAACGG
66 ACTGAAA-GCCTAACGC
*
247876 TTTATTTGGAAGAAAG
1 TGTATTTGGAAGAAAG
247892 ATGCCAATAA
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
80 3 0.04
81 75 0.95
82 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (81 bp):
TGTATTTGGAAGAAAGGTGTCAATCATGACAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAG
ACTGAAAGCCTAACGC
Found at i:247915 original size:81 final size:81
Alignment explanation
Indices: 247744--247916 Score: 186
Period size: 81 Copynumber: 2.1 Consensus size: 81
247734 CAATCATGAC
* * * *
247744 AGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGACTGAAAGCCTAACTCTGCCTTTGGTAGAA
1 AGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGACTGAAAGCCTAACGCTGCATTTGGAAGAA
* ** * *
247809 AGGTTTCAATCATGCC
66 AGATGCCAATAATGCA
* ** * **
247825 AGTTAGATGAAAGGTTAAATACATTTGGGTAAAAGACT-AAATTTCTAACGGTTTATTTGGAAGA
1 AGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGACTGAAA-GCCTAACGCTGCATTTGGAAGA
247889 AAGATGCCAATAATGCA
65 AAGATGCCAATAATGCA
*
247906 AGTTGGATGAA
1 AGTTAGATGAA
247917 GGATTAATTG
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
80 3 0.04
81 72 0.96
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.29
Consensus pattern (81 bp):
AGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGACTGAAAGCCTAACGCTGCATTTGGAAGAA
AGATGCCAATAATGCA
Found at i:248020 original size:2 final size:2
Alignment explanation
Indices: 248013--248045 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
248003 CCATAAATGA
248013 AT AT 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 AT AT A
248046 ACAGTGCATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:259358 original size:14 final size:15
Alignment explanation
Indices: 259341--259377 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
259331 AATAGTTTTG
259341 AGAAAAA-CGGCTGA
1 AGAAAAAGCGGCTGA
*
259355 AGAAAAAGTGGCTGA
1 AGAAAAAGCGGCTGA
259370 AGAAAAAG
1 AGAAAAAG
259378 TTGCTGCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.54, C:0.08, G:0.30, T:0.08
Consensus pattern (15 bp):
AGAAAAAGCGGCTGA
Found at i:259377 original size:15 final size:15
Alignment explanation
Indices: 259349--259383 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
259339 TGAGAAAAAC
259349 GGCTGAAGAAAAAGT
1 GGCTGAAGAAAAAGT
259364 GGCTGAAGAAAAAGT
1 GGCTGAAGAAAAAGT
*
259379 TGCTG
1 GGCTG
259384 CTAGACTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.34, T:0.17
Consensus pattern (15 bp):
GGCTGAAGAAAAAGT
Found at i:259557 original size:77 final size:79
Alignment explanation
Indices: 259462--259610 Score: 212
Period size: 77 Copynumber: 1.9 Consensus size: 79
259452 TAATAAAAAA
** *
259462 TCTTATTTAATTAGTTCAAATTAAATATCCATT-AAAGACTTATAATCTGAATTATAATC-TTTA
1 TCTTATTTAATTAGTTCAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTTTTA
259525 ATGTTTATTTAAAC
66 ATGTTTATTTAAAC
* * * * *
259539 TCTTATTTAATTATTTCAAATTAAATATCGATTAAAAGAGTTGTAATCAAAATTACATTCTTTTA
1 TCTTATTTAATTAGTTCAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTTTTA
259604 ATGTTTA
66 ATGTTTA
259611 CTTATTATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 31 0.50
78 20 0.32
79 11 0.18
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (79 bp):
TCTTATTTAATTAGTTCAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTTTTA
ATGTTTATTTAAAC
Found at i:262120 original size:33 final size:32
Alignment explanation
Indices: 262079--262161 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 32
262069 AGAAAATATA
*
262079 ATGTGCATTCAAAAATACTTGATTATATTGAT
1 ATGTGCATTCGAAAATACTTGATTATATTGAT
262111 ATGTCGCATTCGAAAATACTTGATTATATTGAT
1 ATGT-GCATTCGAAAATACTTGATTATATTGAT
*
262144 ATGTTACATTCGAAAATA
1 ATG-TGCATTCGAAAATA
262162 TTTAATATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
32 4 0.09
33 42 0.89
34 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (32 bp):
ATGTGCATTCGAAAATACTTGATTATATTGAT
Found at i:263128 original size:16 final size:16
Alignment explanation
Indices: 263104--263145 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
263094 TGATATTAAG
263104 AAAAA-AAATAAAAGA
1 AAAAATAAATAAAAGA
*
263119 AAAAATAAAT-AAAGT
1 AAAAATAAATAAAAGA
263134 AAAAATATAATA
1 AAAAATA-AATA
263146 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (16 bp):
AAAAATAAATAAAAGA
Found at i:264580 original size:83 final size:84
Alignment explanation
Indices: 264370--264587 Score: 246
Period size: 85 Copynumber: 2.6 Consensus size: 84
264360 GGTGTCATCA
* * * *
264370 AGCTGAATGGAATCGAACTCGACA-AT-TTTCGTTGACAGATAGCCCTTCTTTCCTTGAGCTATG
1 AGCTGAATGTAATCGAACTCGA-AGGTCTTT-GTTGACAGATAACCCTTCTTGCCTTGAGCTATG
** *
264433 CTGTAAATTTGATTTACCTCTG
64 CTACAAATTTGATGTA-CTCTG
* * * *
264455 AGTTGAATGTAATCGAACTCGAAGGTCTTTGATGATAGATAACCCTTCTTGCCTTGAGTTATGCT
1 AGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCT
*
264520 ACAAATTATG-TGT-CTTTG
66 ACAAATT-TGATGTACTCTG
* *
264538 AGCTGAGTGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTT
1 AGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTT
264588 TGAGTTGGAT
Statistics
Matches: 113, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
83 49 0.43
84 1 0.01
85 58 0.51
86 5 0.04
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (84 bp):
AGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGCT
ACAAATTTGATGTACTCTG
Found at i:265630 original size:36 final size:36
Alignment explanation
Indices: 265578--265696 Score: 166
Period size: 36 Copynumber: 3.3 Consensus size: 36
265568 ATTCAAAGAT
*
265578 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
*
265614 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * *
265650 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
265687 TTTGTTTCAA
1 TTTGTTTCAA
265697 ATAAAACATA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
36 42 0.58
37 30 0.42
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
Found at i:265675 original size:37 final size:36
Alignment explanation
Indices: 265590--265681 Score: 130
Period size: 37 Copynumber: 2.5 Consensus size: 36
265580 TGTTTCAAGG
* * * *
265590 GAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
265626 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
*
265663 GAAACTGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
265682 TGAAATTTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 23 0.46
37 27 0.54
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:266648 original size:31 final size:32
Alignment explanation
Indices: 266583--266676 Score: 136
Period size: 31 Copynumber: 2.9 Consensus size: 32
266573 ATTCCCAAAG
* *
266583 ATGCCCCAATATTCGATGTTGAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
* *
266615 ATGCCCCAACATTTGATTTTAAATCT-AAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
266646 ATGCCCCAACATTTGATGTTGAATCTTCAAA
1 ATGCCCCAACATTTGATGTTGAATC-TCAAA
266677 GATGCCCTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
31 28 0.52
32 23 0.43
33 3 0.06
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATCTCAAAAA
Found at i:267479 original size:69 final size:69
Alignment explanation
Indices: 267364--267501 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 69
267354 TGTCTCTCTC
267364 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
267429 TCAT
66 TCAT
* *
267433 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
267498 TCAT
66 TCAT
267502 AGTTTGAATC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
TCAT
Found at i:267590 original size:13 final size:12
Alignment explanation
Indices: 267574--267637 Score: 74
Period size: 13 Copynumber: 4.8 Consensus size: 12
267564 TTTTTTTCAA
267574 TTTTCTTTTGTTT
1 TTTTCTTTT-TTT
267587 TTTTCTCTTTTTAT
1 TTTTCT-TTTTT-T
267601 TTTCTCTTTGTTTT
1 TTT-TCTTT-TTTT
267615 TTTTCTTTTTTT
1 TTTTCTTTTTTT
267627 TTTCTCTTTTT
1 TTT-TCTTTTT
267638 GTTCTGATTG
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.15
13 20 0.43
14 13 0.28
15 6 0.13
ACGTcount: A:0.02, C:0.12, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:267614 original size:26 final size:27
Alignment explanation
Indices: 267573--267635 Score: 103
Period size: 26 Copynumber: 2.4 Consensus size: 27
267563 TTTTTTTTCA
267573 ATTTTCT-TTTGTTTTTTTCTCTTTTT
1 ATTTTCTCTTTGTTTTTTTCTCTTTTT
267599 ATTTTCTCTTTGTTTTTTT-TCTTTTT
1 ATTTTCTCTTTGTTTTTTTCTCTTTTT
*
267625 TTTTTCTCTTT
1 ATTTTCTCTTT
267636 TTGTTCTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 24 0.69
27 11 0.31
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.81
Consensus pattern (27 bp):
ATTTTCTCTTTGTTTTTTTCTCTTTTT
Found at i:270734 original size:19 final size:18
Alignment explanation
Indices: 270697--270771 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 18
270687 ACGTGAGAAT
270697 AATAAATAA-AACAAGAAAA
1 AATAAA-AATAACAA-AAAA
270716 AATAGAAAATAACAAAAAA
1 AATA-AAAATAACAAAAAA
** *
270735 CGTAAAAAATAATAAAAAA
1 AAT-AAAAATAACAAAAAA
270754 TAATAAAAATAAACAAAA
1 -AATAAAAAT-AACAAAA
270772 TGAATAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 30 0.67
20 15 0.33
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.13
Consensus pattern (18 bp):
AATAAAAATAACAAAAAA
Found at i:270751 original size:9 final size:9
Alignment explanation
Indices: 270739--270780 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
270729 AAAAAACGTA
270739 AAAAATAAT
1 AAAAATAAT
270748 AAAAAATAAT
1 -AAAAATAAT
270758 AAAAATAA-
1 AAAAATAAT
270766 ACAAAATGAAT
1 A-AAAAT-AAT
270777 AAAA
1 AAAA
270781 TGTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 1 0.03
9 13 0.45
10 14 0.48
11 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (9 bp):
AAAAATAAT
Found at i:270777 original size:19 final size:19
Alignment explanation
Indices: 270739--270780 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
270729 AAAAAACGTA
270739 AAAAATAATAAAAAATAAT
1 AAAAATAATAAAAAATAAT
*
270758 AAAAATAA-ACAAAATGAAT
1 AAAAATAATAAAAAAT-AAT
270777 AAAA
1 AAAA
270781 TGTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAAATAATAAAAAATAAT
Found at i:271005 original size:16 final size:17
Alignment explanation
Indices: 270971--271030 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 17
270961 TGATATTAAG
270971 AAAA-AAAATAATAGAA
1 AAAATAAAATAATAGAA
*
270987 AAAATAAAATAA-AGTA
1 AAAATAAAATAATAGAA
* *
271003 AAAATATAATATATATAA
1 AAAATAAAATA-ATAGAA
271021 ATAAATAAAA
1 A-AAATAAAA
271031 ACAAAAATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 17 0.49
17 8 0.23
18 3 0.09
19 7 0.20
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAATAAAATAATAGAA
Found at i:271135 original size:8 final size:8
Alignment explanation
Indices: 271122--271186 Score: 67
Period size: 8 Copynumber: 8.1 Consensus size: 8
271112 AGAAAAATTA
*
271122 ATACATCT
1 ATACATAT
271130 ATACATAT
1 ATACATAT
*
271138 ATATATAT
1 ATACATAT
*
271146 ATATATAT
1 ATACATAT
*
271154 ATATATAT
1 ATACATAT
*
271162 ATATATAT
1 ATACATAT
*
271170 ATATATAT
1 ATACATAT
*
271178 ATATATAT
1 ATACATAT
271186 A
1 A
271187 AATATAAGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 55 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (8 bp):
ATACATAT
Found at i:271141 original size:2 final size:2
Alignment explanation
Indices: 271129--271203 Score: 116
Period size: 2 Copynumber: 38.0 Consensus size: 2
271119 TTAATACATC
*
271129 TA TA CA 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
* *
271171 TA TA TA TA TA TA TA TA AA TA TA -A GA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
271204 ATAAAAAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:271226 original size:22 final size:23
Alignment explanation
Indices: 271186--271232 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
271176 ATATATATAT
*
271186 AAATATAAGATATATATAATAAAA
1 AAATATAAGATATAAATAA-AAAA
271210 AAATAT-A-ATATAAATAAAAAA
1 AAATATAAGATATAAATAAAAAA
271231 AA
1 AA
271233 GAGGAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 9 0.41
23 1 0.05
24 6 0.27
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (23 bp):
AAATATAAGATATAAATAAAAAA
Found at i:271227 original size:19 final size:19
Alignment explanation
Indices: 271176--271231 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
271166 ATATATATAT
* *
271176 ATATATATATAAAT-ATAAG
1 ATATA-ATATAAATAAAAAA
271195 ATAT-ATAT-AATAAAAAA
1 ATATAATATAAATAAAAAA
271212 ATATAATATAAATAAAAAA
1 ATATAATATAAATAAAAAA
271231 A
1 A
271232 AGAGGAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 3 0.09
17 11 0.34
18 4 0.12
19 14 0.44
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
ATATAATATAAATAAAAAA
Found at i:276885 original size:36 final size:36
Alignment explanation
Indices: 276848--277248 Score: 367
Period size: 36 Copynumber: 11.0 Consensus size: 36
276838 GTTGAGGTTC
* * * * *
276848 TAGGTAAACGATCTTAAGGAAGACTGGGTTGGTTTC
1 TAGGGAAACAATCTTAAGGAAGACTAGATTGGTTTA
* * * *
276884 TAGGGAAACAATTTTAAGAAAGAGTA-ACTCGAGGTTTA
1 TAGGGAAACAATCTTAAGGAAGACTAGA-T--TGGTTTA
*
276922 TAGGGAAACATTCTTAAGGAAGACTA-ATTTGAGTTTA
1 TAGGGAAACAATCTTAAGGAAGACTAGA-TTG-GTTTA
* *
276959 TAGGGAAACAATCTTAAAGAATACTAGATTGGTTTA
1 TAGGGAAACAATCTTAAGGAAGACTAGATTGGTTTA
* *
276995 TAGGGAAACAATATTAAGGAAGACTAGGTTGGTTTA
1 TAGGGAAACAATCTTAAGGAAGACTAGATTGGTTTA
* *
277031 TAGGGAAA-AATATTAAGAAAGACTAGATTGGTTTA
1 TAGGGAAACAATCTTAAGGAAGACTAGATTGGTTTA
* * *
277066 TAGGTAAACAATCTTAAGGAATACTAGGTTGGTTTA
1 TAGGGAAACAATCTTAAGGAAGACTAGATTGGTTTA
* * * *
277102 TAGGGAAATAATTTTAAGGAAGATTAGATTGGTTTC
1 TAGGGAAACAATCTTAAGGAAGACTAGATTGGTTTA
* * * * * *
277138 TAGGGAAACAGTCTTAGGGAATAATTTGAGTTGTGTTTT
1 TAGGGAAACAATCTTAAGGAA-GACTAGA-TTG-GTTTA
* * * *
277177 TAGGGGAAACAGTCTTAAAGAAGCCTAGGTTGGTTTA
1 TA-GGGAAACAATCTTAAGGAAGACTAGATTGGTTTA
* * * *
277214 TAGGGAAATAGTCTTAAAGAAGGCTAGATTGGTTT
1 TAGGGAAACAATCTTAAGGAAGACTAGATTGGTTT
277249 CCACGAAAAA
Statistics
Matches: 301, Mismatches: 54, Indels: 20
0.80 0.14 0.05
Matches are distributed among these distances:
35 32 0.11
36 166 0.55
37 42 0.14
38 36 0.12
39 8 0.03
40 17 0.06
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.31
Consensus pattern (36 bp):
TAGGGAAACAATCTTAAGGAAGACTAGATTGGTTTA
Found at i:276892 original size:107 final size:106
Alignment explanation
Indices: 276749--277147 Score: 381
Period size: 107 Copynumber: 3.7 Consensus size: 106
276739 TAGAGCAATT
** * *
276749 AATCTTAAGG-AGACTAGGTTGAGGTTCCTAGGGAAACAATCTTAAGGAA-ATTAGGTTAGATTC
1 AATCTTAAGGAAGACTAGGTT--GGTTTATAGGGAAACAATTTTAAGGAAGATTAGGTTAGTTTC
* * * *
276812 TTGGGAAACGATTTTATGACAGACAAGTTGAGGTTCTAGGTAAAC
64 TAGGGAAAC-ATTTTAAGA-AGACAAGTTGAGTTTATAGGTAAAC
* * * * * ** * *
276857 GATCTTAAGGAAGACTGGGTTGGTTTCTAGGGAAACAATTTTAAGAAAGAGTAACTCGAGGTTTA
1 AATCTTAAGGAAGACTAGGTTGGTTTATAGGGAAACAATTTTAAGGAAGATTAGGT-TA-GTTTC
* *
276922 TAGGGAAACATTCTTAAGGAAGACTAATTTGAGTTTATAGGGAAAC
64 TAGGGAAACATT-TTAA-GAAGAC-AAGTTGAGTTTATAGGTAAAC
* * * * * * *
276968 AATCTTAAAGAATACTAGATTGGTTTATAGGGAAACAATATTAAGGAAGACTAGGTTGGTTTATA
1 AATCTTAAGGAAGACTAGGTTGGTTTATAGGGAAACAATTTTAAGGAAGATTAGGTTAGTTTCTA
* * *
277033 GGGAAAAATATTAAGAAAGACTAGATTG-GTTTATAGGTAAAC
66 GGGAAACATTTTAAG-AAGACAAG-TTGAGTTTATAGGTAAAC
* * * *
277075 AATCTTAAGGAATACTAGGTTGGTTTATAGGGAAATAATTTTAAGGAAGATTAGATTGGTTTCTA
1 AATCTTAAGGAAGACTAGGTTGGTTTATAGGGAAACAATTTTAAGGAAGATTAGGTTAGTTTCTA
277140 GGGAAACA
66 GGGAAACA
277148 GTCTTAGGGA
Statistics
Matches: 239, Mismatches: 43, Indels: 19
0.79 0.14 0.06
Matches are distributed among these distances:
107 104 0.44
108 25 0.10
109 28 0.12
110 18 0.08
111 64 0.27
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (106 bp):
AATCTTAAGGAAGACTAGGTTGGTTTATAGGGAAACAATTTTAAGGAAGATTAGGTTAGTTTCTA
GGGAAACATTTTAAGAAGACAAGTTGAGTTTATAGGTAAAC
Found at i:277077 original size:71 final size:72
Alignment explanation
Indices: 276777--277248 Score: 398
Period size: 72 Copynumber: 6.5 Consensus size: 72
276767 TTGAGGTTCC
* * * * * * * * *
276777 TAGGGAAACAATCTTAAGGAA-ATTAGGTTAGATTCTTGGGAAACGATTTTATGACAGACAAG-T
1 TAGGGAAACAATCTTAAGGAAGACTAGGTTGGTTTATAGGGAAACAATTTTAAGAAAGACTAGAT
* *
276840 TGAGGTTC
66 TG-GTTTA
* * * * *
276848 TAGGTAAACGATCTTAAGGAAGACTGGGTTGGTTTCTAGGGAAACAATTTTAAGAAAGAGTA-AC
1 TAGGGAAACAATCTTAAGGAAGACTAGGTTGGTTTATAGGGAAACAATTTTAAGAAAGACTAGA-
*
276912 TCGAGGTTTA
65 T--TGGTTTA
* ** * *
276922 TAGGGAAACATTCTTAAGGAAGACTAATTTGAGTTTATAGGGAAACAATCTTAA-AGAATACTAG
1 TAGGGAAACAATCTTAAGGAAGACTAGGTTG-GTTTATAGGGAAACAATTTTAAGA-AAGACTAG
276986 ATTGGTTTA
64 ATTGGTTTA
* *
276995 TAGGGAAACAATATTAAGGAAGACTAGGTTGGTTTATAGGGAAA-AATATTAAGAAAGACTAGAT
1 TAGGGAAACAATCTTAAGGAAGACTAGGTTGGTTTATAGGGAAACAATTTTAAGAAAGACTAGAT
277059 TGGTTTA
66 TGGTTTA
* * * * *
277066 TAGGTAAACAATCTTAAGGAATACTAGGTTGGTTTATAGGGAAATAATTTTAAGGAAGATTAGAT
1 TAGGGAAACAATCTTAAGGAAGACTAGGTTGGTTTATAGGGAAACAATTTTAAGAAAGACTAGAT
*
277131 TGGTTTC
66 TGGTTTA
* * * * * * * * *
277138 TAGGGAAACAGTCTTAGGGAATAATTTGAGTTGTGTTTTTAGGGGAAACAGTCTTAA-AGAAGCC
1 TAGGGAAACAATCTTAAGGAA-GACTAG-GTTG-GTTTATA-GGGAAACAATTTTAAGA-AAGAC
*
277202 TAGGTTGGTTTA
61 TAGATTGGTTTA
* * * * *
277214 TAGGGAAATAGTCTTAAAGAAGGCTAGATTGGTTT
1 TAGGGAAACAATCTTAAGGAAGACTAGGTTGGTTT
277249 CCACGAAAAA
Statistics
Matches: 324, Mismatches: 62, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
71 83 0.26
72 85 0.26
73 41 0.13
74 36 0.11
75 35 0.11
76 44 0.14
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.31
Consensus pattern (72 bp):
TAGGGAAACAATCTTAAGGAAGACTAGGTTGGTTTATAGGGAAACAATTTTAAGAAAGACTAGAT
TGGTTTA
Found at i:282296 original size:18 final size:18
Alignment explanation
Indices: 282250--282289 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
282240 TTTCTGAGAG
* *
282250 AATTAAAATATGTGAATA
1 AATTAGAATCTGTGAATA
282268 AATTAGAATCTGTGAATA
1 AATTAGAATCTGTGAATA
282286 AATT
1 AATT
282290 GTAATCTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (18 bp):
AATTAGAATCTGTGAATA
Found at i:292893 original size:34 final size:34
Alignment explanation
Indices: 292797--293842 Score: 838
Period size: 34 Copynumber: 31.8 Consensus size: 34
292787 TGATTTGGAA
* *
292797 CACACTTACTTTGAAGTGACGATGATC-TTG-A-G
1 CACACTTACTTGGAAGTGGCGATG-TCTTTGTAGG
* * * * * * *
292829 CATATTTGCTTGCAAGTGACTATGTCTTTGTGGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
*
292863 CACACTTACTTGGAATTGGCGATGTCTTTGT-GG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
* * * * *
292896 ATACACTTACTTGGAAATGGAGATTCTCTTTGTTGG
1 -CACACTTACTTGGAAGTGGCGA-TGTCTTTGTAGG
* *
292932 CACACTTACTTCGAAGTGGTGATGTCTTTGTAGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
* * *
292966 CACACTTACTTGAAAGTGGTGATGCCTTTGTAGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
* ** *
293000 CATACTTACTTGGAAGTGGTAATGTCTTTGTGGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
** * * * *
293034 CACACTTTGTTTGAAGTGGTTG-TATCTTTGCAGG
1 CACACTTACTTGGAAGTGG-CGATGTCTTTGTAGG
* *
293068 CATACTTACTTGGAAGTGGC-AGTATCTTTGTAGG
1 CACACTTACTTGGAAGTGGCGA-TGTCTTTGTAGG
293102 CACACTTACTTGGAAGTGGCGATGTC-TTG-A-G
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
* *
293133 CAAACTTACTTGGACA-TGGCGATGTCTTTGTGGG
1 CACACTTACTTGGA-AGTGGCGATGTCTTTGTAGG
* * * *
293167 CACACTTACTTGGAAGTGGCAAAT-T-TTTTTTGC
1 CACACTTACTTGGAAGTGGC-GATGTCTTTGTAGG
**
293200 CACACTTACTTGGAAGTGATGATGTC-TTG-A-G
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
*
293231 CACACTTACTTGGAAGTGACGATGTC-TTG-A-G
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
* *
293262 CACACTTACTTGG-AGTGGAGATGTCTTTGTAGA
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
*
293295 CACACTTACTCGGAAGTGGCGATGTCTTTGTAGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
** * *
293329 --CAC--AC-T-GAAGTGATGATGTCTTTATGGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
* ** *
293357 CAGAGATACTTGGAAGTGGC-AGTATCTTTGTAGG
1 CACACTTACTTGGAAGTGGCGA-TGTCTTTGTAGG
* * *
293391 CACACTTACTTTGAAGTTGCAATG--TTTG-A-G
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
* * * *
293421 CACACTTTCTTGCAAGTGGCAATGTCTTTCTAGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
*
293455 CACAATTACTTGGAAGTGGCGATGTCTTTGTAGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
* * *
293489 CACACATACTT---AGTGTCGATGTCTTTGTGGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
*
293520 CACACTTACTTGGAAGTGGC-AGTATCTTTGTAGG
1 CACACTTACTTGGAAGTGGCGA-TGTCTTTGTAGG
*
293554 --CAC--ACTTGGAAGTTGCGATG--TTTG-A-G
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
* *
293580 CACACTTTCTTGGAAGTGGCGATGTCTTTCTAGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
*
293614 CACACTTACTTGGAAGTGGCGATGTCTTTGTGGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
* * * *
293648 AACACTTACTTCGAAGTGG-TAGTATCTTTGTAGG
1 CACACTTACTTGGAAGTGGCGA-TGTCTTTGTAGG
* * * *
293682 CACACTTACTTGGAAGTCGCAATATCCTTGTAGG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
* * *
293716 CACACTTACTTGGAGGTGGC-AGTATCTTTGTATG
1 CACACTTACTTGGAAGTGGCGA-TGTCTTTGTAGG
* ** * * *
293750 CACAATTACTTGGAAGT-GATAGTATCTTTGTCGA
1 CACACTTACTTGGAAGTGGCGA-TGTCTTTGTAGG
* *
293784 CACACTTGCTTGGAAGTGGCGATGTATTTGT-GAG
1 CACACTTACTTGGAAGTGGCGATGTCTTTGTAG-G
*
293818 AACA-TATACTTGGAAGTGGC-ATGTC
1 CACACT-TACTTGGAAGTGGCGATGTC
293843 GTTAACCAGA
Statistics
Matches: 818, Mismatches: 142, Indels: 107
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.00
27 1 0.00
28 25 0.03
30 62 0.08
31 102 0.12
32 47 0.06
33 58 0.07
34 486 0.59
35 34 0.04
36 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (34 bp):
CACACTTACTTGGAAGTGGCGATGTCTTTGTAGG
Found at i:293228 original size:98 final size:96
Alignment explanation
Indices: 292797--293698 Score: 390
Period size: 98 Copynumber: 9.2 Consensus size: 96
292787 TGATTTGGAA
* * * * * *
292797 CACACTTACTTTGAAGTGACGATGATCTTGAGCATATTTGCTTGCAAGTGACTATGTCTTTGTGG
1 CACACTTACTTGGAAGTGACGATG-TCTTGAGCAAACTTACTTGGAAGTGACGATGTC--T-TGG
* * * *
292862 GCACACTTACTTGGAATTGGC-GATGTCTTTGTGGA
62 GCACACTTACTTGGAAGTGGCAGA-ATCTTTGTAGC
* * * * * * **
292897 TACACTTACTTGGAAATGGA-GATTCTCTTTGTTGGCACACTTACTTCGAAGTGGTGATGTCTTT
1 CACACTTACTTGGAAGT-GACGA-TGTC-TTG--AGCAAACTTACTTGGAAGTGACGATGTC-TT
* * *
292961 GTAGGCACACTTACTTGAAAGTGG-TG-ATGCCTTTGTAGG
60 G--GGCACACTTACTTGGAAGTGGCAGAAT--CTTTGTAGC
* *** * * ** * *
293000 CATACTTACTTGGAAGTGGTAATGTCTTTGTGGGCACACTTTGTTTGAAGTG--GTTGTATCTTT
1 CACACTTACTTGGAAGTGACGATGTC--T-TGAGCAAACTTACTTGGAAGTGACGATG--TC-TT
* * *
293063 GCAGGCATACTTACTTGGAAGTGGCAGTATCTTTGTAGG
60 G--GGCACACTTACTTGGAAGTGGCAGAATCTTTGTAGC
* *
293102 CACACTTACTTGGAAGTGGCGATGTCTTGAGCAAACTTACTTGGACA-TGGCGATGTCTTTGTGG
1 CACACTTACTTGGAAGTGACGATGTCTTGAGCAAACTTACTTGGA-AGTGACGATGTC--T-TGG
* * *
293166 GCACACTTACTTGGAAGTGGCA-AATTTTTTTTGC
62 GCACACTTACTTGGAAGTGGCAGAATCTTTGTAGC
* * *
293200 CACACTTACTTGGAAGTGATGATGTCTTGAGCACACTTACTTGGAAGTGACGATGTCTTGAGCAC
1 CACACTTACTTGGAAGTGACGATGTCTTGAGCAAACTTACTTGGAAGTGACGATGTCTTGGGCAC
* *
293265 ACTTACTTGG-AGTGG-AGATGTCTTTGTAGA
66 ACTTACTTGGAAGTGGCAGA-ATCTTTGTAGC
* * *
293295 CACACTTACTCGGAAGTGGCGATGTCTTTGTAGGC--AC--AC-T-GAAGTGATGATGTCTTTAT
1 CACACTTACTTGGAAGTGACGATGTC-TTG-A-GCAAACTTACTTGGAAGTGACGATGTC--T-T
* ** * *
293354 GGGCAGAGATACTTGGAAGTGGCAGTATCTTTGTAGG
60 GGGCACACTTACTTGGAAGTGGCAGAATCTTTGTAGC
* * * * * * * *
293391 CACACTTACTTTGAAGTTG-CAATGT-TTGAGCACACTTTCTTGCAAGTGGCAATGTCTTTCTAG
1 CACACTTACTTGGAAG-TGACGATGTCTTGAGCAAACTTACTTGGAAGTGACGATGTC--T-TGG
* * *
293454 GCACAATTACTTGGAAGTGGC-GATGTCTTTGTAGG
62 GCACACTTACTTGGAAGTGGCAGA-ATCTTTGTAGC
* * * * * *
293489 CACACATACTT---AGTGTCGATGTCTTTGTGGGCACACTTACTTGGAAGTGGC-AGTATCTTTG
1 CACACTTACTTGGAAGTGACGATGTC--T-TGAGCAAACTTACTTGGAAGTGACGA-TGTC-TTG
* *
293550 TAGG--CAC--ACTTGGAAGTTGC-G-ATGTTTG-AG-
61 --GGCACACTTACTTGGAAGTGGCAGAATCTTTGTAGC
* * * * *
293580 CACACTTTCTTGGAAGTGGCGATGTCTTTCTAGGCACACTTACTTGGAAGTGGCGATGTCTTTGT
1 CACACTTACTTGGAAGTGACGATGTC-TT-GA-GCAAACTTACTTGGAAGTGACGATGTC--T-T
* * * * *
293645 GGGAACACTTACTTCGAAGTGGTAGTATCTTTGTAGG
60 GGGCACACTTACTTGGAAGTGGCAGAATCTTTGTAGC
293682 CACACTTACTTGGAAGT
1 CACACTTACTTGGAAGT
293699 CGCAATATCC
Statistics
Matches: 632, Mismatches: 105, Indels: 128
0.73 0.12 0.15
Matches are distributed among these distances:
91 9 0.01
92 18 0.03
93 10 0.02
94 53 0.08
95 81 0.13
96 45 0.07
97 11 0.02
98 127 0.20
99 66 0.10
100 31 0.05
101 16 0.03
102 97 0.15
103 64 0.10
104 4 0.01
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (96 bp):
CACACTTACTTGGAAGTGACGATGTCTTGAGCAAACTTACTTGGAAGTGACGATGTCTTGGGCAC
ACTTACTTGGAAGTGGCAGAATCTTTGTAGC
Found at i:293640 original size:353 final size:355
Alignment explanation
Indices: 292862--293687 Score: 910
Period size: 353 Copynumber: 2.3 Consensus size: 355
292852 GTCTTTGTGG
* * * *
292862 GCACACTTACTTGGAATTGGCGATGTCTTTGT-GGATACACTTACTTGGAAATGGAGATTCTCTT
1 GCACACTTACTTGGAAGTGGCGATGTCTTT-TAGG-CACACTTACTTGGAAGTGGAGA-TGTCTT
* * *
292926 TGTTGGCACACTTACTTCGAAGTGGTGATGTCTTTGTAGGCACACTTACTTGAAAGTGGTGATGC
63 TGTAGACACACTTACTTCGAAGTGG-GATGTCTTTGTAGG--CAC--AC-TGAAAGTGATGATGC
* * * * * * **
292991 CTTTGTAGGCATACTTACTTGGAAGTGGTAATGTCTTTGTGGGCACACTTTGTTTGAAGTGGTTG
122 CTTTATAGGCAGACATACTTGGAAGTGGCAATATCTTTGTAGGCACACTTACTTTGAA--GGTTG
* * * * * *
293056 TATCTTTGCAGGCATACTTACTTGGAAGTGGCAGTATCTTTGTAGGCACACTTACTTGGAAGTGG
185 AATCTTTGCAGGCACACTTACTTGCAAGTGGCAATATCTTTCTAGGCACAATTACTTGGAAGTGG
*
293121 CGATGTCTTGAGCAAACTTACTTGGACATGGCGATGTCTTTGTGGGCACACTTACTTGGAAGTGG
250 CGATGTCTTGAGCAAACATACTT-GACATGGCGATGTCTTTGTGGGCACACTTACTTGGAAGTGG
* * * *
293186 CAAATTTTTTTTGCCACACTTACTTGGAAGTGATGATGTCTTGA
314 CAAATCTTTGTAG-CACAC-TACTTGGAAGTGACGATGTCTTGA
* *
293230 GCACACTTACTTGGAAGTGACGATGTC-TTGA-GCACACTTACTTGG-AGTGGAGATGTCTTTGT
1 GCACACTTACTTGGAAGTGGCGATGTCTTTTAGGCACACTTACTTGGAAGTGGAGATGTCTTTGT
* *
293292 AGACACACTTAC-TCGGAAGTGGCGATGTCTTTGTAGGCACACTG-AAGTGATGATGTCTTTATG
66 AGACACACTTACTTC-GAAGTGG-GATGTCTTTGTAGGCACACTGAAAGTGATGATGCCTTTATA
* * *
293355 GGCAGAGATACTTGGAAGTGGCAGTATCTTTGTAGGCACACTTACTTTGAA-GTTGCAATGTTTG
129 GGCAGACATACTTGGAAGTGGCAATATCTTTGTAGGCACACTTACTTTGAAGGTTG-AATCTTTG
* *
293419 -A-GCACACTTTCTTGCAAGTGGCAATGTCTTTCTAGGCACAATTACTTGGAAGTGGCGATGTCT
193 CAGGCACACTTACTTGCAAGTGGCAATATCTTTCTAGGCACAATTACTTGGAAGTGGCGATGTC-
* * * *
293482 TTGTAGGCACACATACTT-A-GTGTCGATGTCTTTGTGGGCACACTTACTTGGAAGTGGCAGTAT
257 TTG-A-GCAAACATACTTGACATGGCGATGTCTTTGTGGGCACACTTACTTGGAAGTGGCA-AAT
*
293545 CTTTGTAG-GCAC-ACTTGGAAGTTG-CGATGT-TTGA
319 CTTTGTAGCACACTACTTGGAAG-TGACGATGTCTTGA
* *
293579 GCACACTTTCTTGGAAGTGGCGATGTCTTTCTAGGCACACTTACTTGGAAGTGGCGATGTCTTTG
1 GCACACTTACTTGGAAGTGGCGATGTCTTT-TAGGCACACTTACTTGGAAGTGGAGATGTCTTTG
* * *
293644 TGGGA-ACACTTACTTCGAAGTGGTAGTATCTTTGTAGGCACACT
65 T-AGACACACTTACTTCGAAGTGGGA-TGTCTTTGTAGGCACACT
293688 TACTTGGAAG
Statistics
Matches: 395, Mismatches: 48, Indels: 45
0.81 0.10 0.09
Matches are distributed among these distances:
349 29 0.07
350 16 0.04
351 3 0.01
352 18 0.05
353 140 0.35
354 20 0.05
355 7 0.02
356 10 0.03
357 57 0.14
358 2 0.01
359 2 0.01
361 3 0.01
362 2 0.01
363 39 0.10
364 7 0.02
365 12 0.03
366 1 0.00
367 2 0.01
368 25 0.06
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (355 bp):
GCACACTTACTTGGAAGTGGCGATGTCTTTTAGGCACACTTACTTGGAAGTGGAGATGTCTTTGT
AGACACACTTACTTCGAAGTGGGATGTCTTTGTAGGCACACTGAAAGTGATGATGCCTTTATAGG
CAGACATACTTGGAAGTGGCAATATCTTTGTAGGCACACTTACTTTGAAGGTTGAATCTTTGCAG
GCACACTTACTTGCAAGTGGCAATATCTTTCTAGGCACAATTACTTGGAAGTGGCGATGTCTTGA
GCAAACATACTTGACATGGCGATGTCTTTGTGGGCACACTTACTTGGAAGTGGCAAATCTTTGTA
GCACACTACTTGGAAGTGACGATGTCTTGA
Found at i:293679 original size:128 final size:125
Alignment explanation
Indices: 293454--293688 Score: 371
Period size: 128 Copynumber: 1.9 Consensus size: 125
293444 GTCTTTCTAG
* *
293454 GCACAATTACTTGGAAGTGGCGATGTCTTTGTAGGCACACATACTTAGTGTCGATGTCTTTGTGG
1 GCACAATTACTTGGAAGTGGCGATGTCTTTCTAGGCACACATACTTAGTGGCGATGTCTTTGTGG
* *
293519 GCACACTTACTTGGAAGTGGCAGTATCTTTGTAGGCACACTTGGAAGTTGCGATGTTTGA
66 GAACACTTACTTCGAAGTGGCAGTATCTTTGTAGGCACACTTGGAAGTTGCGATGTTTGA
* * *
293579 GCACACTTTCTTGGAAGTGGCGATGTCTTTCTAGGCACACTTACTTGGAAGTGGCGATGTCTTTG
1 GCACAATTACTTGGAAGTGGCGATGTCTTTCTAGGCACACATACTT---AGTGGCGATGTCTTTG
*
293644 TGGGAACACTTACTTCGAAGTGGTAGTATCTTTGTAGGCACACTT
63 TGGGAACACTTACTTCGAAGTGGCAGTATCTTTGTAGGCACACTT
293689 ACTTGGAAGT
Statistics
Matches: 99, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
125 42 0.42
128 57 0.58
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (125 bp):
GCACAATTACTTGGAAGTGGCGATGTCTTTCTAGGCACACATACTTAGTGGCGATGTCTTTGTGG
GAACACTTACTTCGAAGTGGCAGTATCTTTGTAGGCACACTTGGAAGTTGCGATGTTTGA
Found at i:297857 original size:15 final size:15
Alignment explanation
Indices: 297837--297866 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
297827 ACTAGTATCA
297837 ACTTTATTTAATGCT
1 ACTTTATTTAATGCT
297852 ACTTTATTTAATGCT
1 ACTTTATTTAATGCT
297867 TTTACTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (15 bp):
ACTTTATTTAATGCT
Found at i:299910 original size:20 final size:21
Alignment explanation
Indices: 299885--299937 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 21
299875 TTGAAGAAGA
299885 TATCGATAC-TGAAATGGGGG
1 TATCGATACATGAAATGGGGG
299905 TATCGATACCAAATGAAATGGGGG
1 TATCGATA-C--ATGAAATGGGGG
*
299929 TATTGATAC
1 TATCGATAC
299938 CATTATCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 8 0.29
21 1 0.04
23 1 0.04
24 18 0.64
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.26
Consensus pattern (21 bp):
TATCGATACATGAAATGGGGG
Found at i:299921 original size:24 final size:24
Alignment explanation
Indices: 299894--299939 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
299884 ATATCGATAC
299894 TGAAATGGGGGTATCGATACCAAA
1 TGAAATGGGGGTATCGATACCAAA
*
299918 TGAAATGGGGGTATTGATACCA
1 TGAAATGGGGGTATCGATACCA
299940 TTATCAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.11, G:0.30, T:0.24
Consensus pattern (24 bp):
TGAAATGGGGGTATCGATACCAAA
Found at i:300637 original size:23 final size:23
Alignment explanation
Indices: 300582--300637 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
300572 GTCGAGGGTT
** * **
300582 CTATGTGGTCCTTCGGGATAATC
1 CTATGTGGTTATTCGGGACAAAA
300605 CTATGTGGTTATTCGGGACAAAA
1 CTATGTGGTTATTCGGGACAAAA
300628 CTATGTGGTT
1 CTATGTGGTT
300638 TTTCAGGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (23 bp):
CTATGTGGTTATTCGGGACAAAA
Found at i:310650 original size:20 final size:21
Alignment explanation
Indices: 310625--310723 Score: 76
Period size: 21 Copynumber: 4.6 Consensus size: 21
310615 TTGTGCTTCA
310625 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-AG
* *
310645 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAAAG
* *
310667 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAAAG
* * * *
310688 TGCACCGATGCTCGCCTTGAATG
1 TGCATCGAT--ACACCTTGAAAG
310711 TGCATCGATACAC
1 TGCATCGATACAC
310724 AAGGCCATGC
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
20 11 0.18
21 19 0.31
22 13 0.21
23 18 0.30
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAAAG
Found at i:310715 original size:44 final size:42
Alignment explanation
Indices: 310625--310723 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 42
310615 TTGTGCTTCA
*
310625 TGCATCGATACACCTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATGCATCCTTGAATG
*
310667 TGCATCGATACACCATGAA-GGTGCACCGATGC-TCGCCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATGCAT--CCTTGAATG
310711 TGCATCGATACAC
1 TGCATCGATACAC
310724 AAGGCCATGC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
42 15 0.29
43 12 0.24
44 24 0.47
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATGCATCCTTGAATG
Found at i:310740 original size:43 final size:42
Alignment explanation
Indices: 310643--310744 Score: 118
Period size: 44 Copynumber: 2.4 Consensus size: 42
310633 TACACCTAAC
* *
310643 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGA
* *
310685 AGGTGCACCGATGC-TCGCCTTGAATGTGCATCGATACACAAGGCC
1 A-GTGCATCGATGCAT--CCTTGAATGTGCATCGATACACAAGG-A
310730 A-TGCATCGATGCATC
1 AGTGCATCGATGCATC
310745 AGTCGGGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
42 3 0.06
43 21 0.42
44 25 0.50
45 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (42 bp):
AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGA
Found at i:312651 original size:14 final size:15
Alignment explanation
Indices: 312626--312654 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
312616 TTGTTTTTTA
312626 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
312641 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
312655 AAATGTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:313147 original size:19 final size:19
Alignment explanation
Indices: 313123--313161 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
313113 TAACAAATTA
313123 AGTTTAAATGAATTT-TAAG
1 AGTTT-AATGAATTTCTAAG
*
313142 AGTTTAATGATTTTCTAAG
1 AGTTTAATGAATTTCTAAG
313161 A
1 A
313162 ATATTCGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (19 bp):
AGTTTAATGAATTTCTAAG
Found at i:317296 original size:23 final size:23
Alignment explanation
Indices: 317270--317372 Score: 109
Period size: 23 Copynumber: 4.5 Consensus size: 23
317260 TATGTGGTCC
317270 TTCGGGACAAACCTATATGGCCT
1 TTCGGGACAAACCTATATGGCCT
317293 TTCGGGACAAACCTATATGGTCC-
1 TTCGGGACAAACCTATATGG-CCT
* * * * *
317316 TTCTGGACAATCCTATGTGGTCA
1 TTCGGGACAAACCTATATGGCCT
* * * *
317339 TTCAGGACAAAACTATGTGGTCT
1 TTCGGGACAAACCTATATGGCCT
317362 TTCGGGACAAA
1 TTCGGGACAAA
317373 TATGTGGCAC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.01
23 66 0.96
24 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
TTCGGGACAAACCTATATGGCCT
Found at i:317331 original size:46 final size:46
Alignment explanation
Indices: 317259--317372 Score: 147
Period size: 46 Copynumber: 2.5 Consensus size: 46
317249 GTCGAGGGTT
* * *
317259 CTATGTGGTCCTTCGGGACAAACCTATATGGCCTTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAACCTATATGGCCATTCAGGACAAAA
* * * * *
317305 CTATATGGTCCTTCTGGACAATCCTATGTGGTCATTCAGGACAAAA
1 CTATGTGGTCCTTCGGGACAAACCTATATGGCCATTCAGGACAAAA
*
317351 CTATGTGGTCTTTCGGGACAAA
1 CTATGTGGTCCTTCGGGACAAA
317373 TATGTGGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 56 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (46 bp):
CTATGTGGTCCTTCGGGACAAACCTATATGGCCATTCAGGACAAAA
Found at i:319108 original size:163 final size:164
Alignment explanation
Indices: 318935--319398 Score: 454
Period size: 163 Copynumber: 2.8 Consensus size: 164
318925 GTTGGAAGAT
* *
318935 TTTTTCATGGATTCATCACACAAAAAACCATTACCTTTATTTTTATTTGATATTAAAAATAATAT
1 TTTTTCATGGATTC-TCACACAAAAAACCATTGCCTTGATTTTTATTTGATATTAAAAATAATAT
* * *
319000 AATATAATATTAATATTTCTTTAAAAAACATTCGAATAAAAATGGTA-CATTTTATATGAACAAT
65 AATATAATATTAATATTTCTTTAAAAAACATTAGAATAAAAATGGTACCTTTTTGTATGAACAAT
** * *
319064 CCTCAGAAACACGC-TTCTTTTATAATCGGGAGAC
130 CCTCAGAAACACGCTTTCCATAATAATCGAGAGAC
** * * * *
319098 TTTTTCATGGATTTCTCACACAAAAATGCATTGTCTTGATTTTTAATTAATATTAAAAAATAAGA
1 TTTTTCATGGA-TTCTCACACAAAAAACCATTGCCTTGATTTTTATTTGATATT-AAAAATAATA
* * * * * ** *
319163 TAATA-ATATCTTAAAATTTC--TATAAAA-ATTAAAATAAAAATGCTATTTTTTTGTACGAACA
64 TAATATA-ATATTAATATTTCTTTAAAAAACATTAGAATAAAAATGGTACCTTTTTGTATGAACA
* * *** * *
319224 ATCTTTAGAAGTGCGCTTTCCATAATAGTTGAGAGAC
128 ATCCTCAGAAACACGCTTTCCATAATAATCGAGAGAC
* **
319261 TTTTTCATGAATTCCTCACACAAATGACCATTGCCTTGATTTTTATTTGATATTAAAAATAATAT
1 TTTTTCATGGATT-CTCACACAAAAAACCATTGCCTTGATTTTTATTTGATATTAAAAATAATAT
* * * * *
319326 ACTATTATATTCATGTTTCTTTTAAAAAAAAACATTAGAATAAAAAGGGTACCTTTTTGTATGAA
65 AATATAATATTAATATTTC-TTT---AAAAAACATTAGAATAAAAATGGTACCTTTTTGTATGAA
*
319391 AAATCCTC
126 CAATCCTC
319399 TAATATGTGC
Statistics
Matches: 233, Mismatches: 54, Indels: 22
0.75 0.17 0.07
Matches are distributed among these distances:
161 15 0.06
162 52 0.22
163 101 0.43
164 28 0.12
165 1 0.00
168 5 0.02
169 31 0.13
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (164 bp):
TTTTTCATGGATTCTCACACAAAAAACCATTGCCTTGATTTTTATTTGATATTAAAAATAATATA
ATATAATATTAATATTTCTTTAAAAAACATTAGAATAAAAATGGTACCTTTTTGTATGAACAATC
CTCAGAAACACGCTTTCCATAATAATCGAGAGAC
Found at i:324581 original size:13 final size:13
Alignment explanation
Indices: 324563--324596 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
324553 TGTCATAATC
324563 TATGACGCGAATT
1 TATGACGCGAATT
*
324576 TATGACGCGTATT
1 TATGACGCGAATT
324589 TATGACGC
1 TATGACGC
324597 TCATTGCGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (13 bp):
TATGACGCGAATT
Found at i:324683 original size:57 final size:58
Alignment explanation
Indices: 324589--324703 Score: 142
Period size: 57 Copynumber: 2.0 Consensus size: 58
324579 GACGCGTATT
* * * * **
324589 TATGACGCTCATTGCGCATCATTGAAGCCCCCGTCATA-AATGAAGATGACACACATG
1 TATGACGCTCATTACGCATCATTGAAGCACACATCATATAAAAAAGATGACACACATG
**
324646 TATGACGCTCATTACGTGTCATTGAAGCACACATCATATTAAAAAAGATGACACACAT
1 TATGACGCTCATTACGCATCATTGAAGCACACATCATA-TAAAAAAGATGACACACAT
324704 TCTTGTGTCG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 32 0.67
59 16 0.33
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (58 bp):
TATGACGCTCATTACGCATCATTGAAGCACACATCATATAAAAAAGATGACACACATG
Found at i:328859 original size:15 final size:16
Alignment explanation
Indices: 328830--328860 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
328820 TTTGATATTA
328830 TGATTTACTGATTTAT
1 TGATTTACTGATTTAT
328846 TGATTTACTG-TTTAT
1 TGATTTACTGATTTAT
328861 GAACTATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (16 bp):
TGATTTACTGATTTAT
Found at i:332928 original size:21 final size:21
Alignment explanation
Indices: 332902--332941 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
332892 CAGAACCCCA
*
332902 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
332923 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
332942 TCAAAGGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:336814 original size:22 final size:21
Alignment explanation
Indices: 336772--336811 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
336762 GAGTTTGTTT
336772 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
336793 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
336812 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:342615 original size:4 final size:4
Alignment explanation
Indices: 342606--342642 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
342596 AATAAGAAAC
*
342606 AATA AATA AATA AATA AATAA AATA GATA AATA AATA
1 AATA AATA AATA AATA AAT-A AATA AATA AATA AATA
342643 TCAAGGCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:342635 original size:17 final size:17
Alignment explanation
Indices: 342609--342642 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
342599 AAGAAACAAT
342609 AAATAAATAAATAAATA
1 AAATAAATAAATAAATA
*
342626 AAATAGATAAATAAATA
1 AAATAAATAAATAAATA
342643 TCAAGGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAAATAAATAAATA
Found at i:343068 original size:12 final size:13
Alignment explanation
Indices: 343041--343071 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
343031 TTAGGTATCT
343041 AATAAAAAATTAA
1 AATAAAAAATTAA
343054 AATAAAAAATT-A
1 AATAAAAAATTAA
343066 AATAAA
1 AATAAA
343072 TTTAACCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAAAAATTAA
Found at i:346617 original size:42 final size:42
Alignment explanation
Indices: 346536--346677 Score: 110
Period size: 42 Copynumber: 3.4 Consensus size: 42
346526 ATTTTTCTAC
** *
346536 CTTTATAATTGAGATTCTTAATTTTTGTAATCCCACA-TTTCA
1 CTTTATAATTGAGGCTCTTAATTTTT-TAATCCCACATTTTAA
* ***
346578 TTTTATAATTGAGGCTCTTAATTTTTTCAATCTTGCATTTTAA
1 CTTTATAATTGAGGCTCTTAATTTTTT-AATCCCACATTTTAA
* * ** ** *
346621 CTTTAAAATTTAGGC-CTTAATTTTTTTAATTTCAGTTTTTAC
1 CTTTATAATTGAGGCTCTTAA-TTTTTTAATCCCACATTTTAA
346663 CTTTAT-ATTGAGGCT
1 CTTTATAATTGAGGCT
346678 TATCAATTTT
Statistics
Matches: 78, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
41 8 0.10
42 48 0.62
43 22 0.28
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.51
Consensus pattern (42 bp):
CTTTATAATTGAGGCTCTTAATTTTTTAATCCCACATTTTAA
Found at i:348965 original size:60 final size:60
Alignment explanation
Indices: 348864--348997 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
348854 AATATAGGGT
* * * * *
348864 AAAGTATAC-AAATGGTCCCTCGGCTATAGGGTGATGTTTTGTTGAGTCACT-CGACTATTA
1 AAAGT-TACAAAATGGTCCCTCGACTATAGGATGATGCTTTGTTCAG-CACTCCGACAATTA
* * * *
348924 AAAGTTACAAAATGGTCCTTCGACTATAGGATGTTGCTTTGTTCAGCCCTCCTACAATTA
1 AAAGTTACAAAATGGTCCCTCGACTATAGGATGATGCTTTGTTCAGCACTCCGACAATTA
348984 AAAGTTACAAAATG
1 AAAGTTACAAAATG
348998 ATTACCCGAC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 6 0.10
60 57 0.90
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCTCGACTATAGGATGATGCTTTGTTCAGCACTCCGACAATTA
Found at i:349272 original size:59 final size:60
Alignment explanation
Indices: 349209--349354 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 60
349199 AACATAATAA
* * *
349209 ATAGTC-AGGTGACTATTTTGTAACTTTTAATGGTCG-GGGACTCAATAAAACAACATCCT
1 ATAGTCGAGG-GACTATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACACCCT
* * * * * * * *
349268 ATAGTCGAAGGACCACTTTATATCTTTTAATAGTCGAGGGACTTAACAAAGCATCACCCT
1 ATAGTCGAGGGACTATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACACCCT
349328 ATAGTCGAGGGACTATTTGTGT-ACTTT
1 ATAGTCGAGGGACTATTT-TGTAACTTT
349355 ACCCTAAAAT
Statistics
Matches: 68, Mismatches: 16, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
59 27 0.40
60 39 0.57
61 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (60 bp):
ATAGTCGAGGGACTATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACACCCT
Found at i:352102 original size:60 final size:60
Alignment explanation
Indices: 352028--352164 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 60
352018 ATAATCGGGT
*
352028 GACCATTTTGTAACTTTTAATAATCG-GAGAACTTAACAAAGCAAT-ACCCTATAGTTGAAG
1 GACCATTTTGTAACTTTTAATAATCGAG-GAACTTAACAAAGC-ATCACCCTATAGTCGAAG
* * * * *
352088 GACCATTTTTTAACTTTTAATAGTCGAGGGACTTAACAAAGCATCACTCTATAGTCGAGG
1 GACCATTTTGTAACTTTTAATAATCGAGGAACTTAACAAAGCATCACCCTATAGTCGAAG
352148 GACCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
352165 ACCCTAGTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
59 2 0.03
60 62 0.93
61 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAATCGAGGAACTTAACAAAGCATCACCCTATAGTCGAAG
Found at i:355063 original size:21 final size:22
Alignment explanation
Indices: 355037--355096 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 22
355027 GGCAAGGTGT
*
355037 ATCGATGCACATTCAATG-TGC
1 ATCGATGCACATTCAAAGATGC
*
355058 ATCGATGCACATGTTAAAGAATGC
1 ATCGATGCACAT-TCAAAG-ATGC
355082 ATCGATGCAC-TTCAA
1 ATCGATGCACATTCAA
355097 GGGGAAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 12 0.36
22 7 0.21
23 1 0.03
24 13 0.39
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (22 bp):
ATCGATGCACATTCAAAGATGC
Found at i:359727 original size:2 final size:2
Alignment explanation
Indices: 359720--359765 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
359710 CTACATGGTT
359720 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
359762 TA TA
1 TA TA
359766 GAGAGAGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:361429 original size:21 final size:21
Alignment explanation
Indices: 361404--361443 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
361394 TTTTATTTTA
361404 TTTATTTATTTGAGAATTAGG
1 TTTATTTATTTGAGAATTAGG
361425 TTTATTTATTTGAGAATTA
1 TTTATTTATTTGAGAATTA
361444 TGACGCTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (21 bp):
TTTATTTATTTGAGAATTAGG
Found at i:368153 original size:3 final size:3
Alignment explanation
Indices: 368145--368367 Score: 140
Period size: 3 Copynumber: 75.0 Consensus size: 3
368135 TACCATTACC
* *
368145 ATT ATT ATT -TT ATT ACTT -TT ATT -CT ATT ATT GTT ATT ATT ATCT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
* * * *
368189 -TT -TT CATT ATT ATT ACT ACT ATT ATT ATT ATC ATT -TT ATT ACT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
368232 A-C ATT AAT GTT ATT ATT ATA ATT ATTT ATT ATT ATCCT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT AT--T ATT ATT ATT
* * * *
368279 ATT ATT ATT ATT ATT ATT ATT ATC ATC ATT -TT GTT ACT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
368325 ATT ATT ATT ACT ACT CTT ATTT ATT ATT AAT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
368368 TCAAATTACC
Statistics
Matches: 173, Mismatches: 32, Indels: 30
0.74 0.14 0.13
Matches are distributed among these distances:
2 15 0.09
3 145 0.84
4 11 0.06
5 2 0.01
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:368316 original size:85 final size:87
Alignment explanation
Indices: 368194--368353 Score: 216
Period size: 85 Copynumber: 1.9 Consensus size: 87
368184 TATCTTTTTC
* *
368194 ATTATTATTACTACTATTATTATTATCATTTTATTACTACATTAATGTTATTATTA-TA-ATTAT
1 ATTATTATTACTACTATTATTATCATCATTTTATTACTACATTAATATTATTATTACTACATTAT
368257 TTATTATTATCCTAGTATTATT
66 TTATTATTATCCTAGTATTATT
* * * ** * *
368279 ATTATTATTATTATTATTATTATCATCATTTTGTTACTATTTTATTATTATTATTACTACTCTTA
1 ATTATTATTACTACTATTATTATCATCATTTTATTACTACATTAATATTATTATTACTAC-ATTA
368344 TTTATTATTA
65 TTTATTATTA
368354 ATATTACTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 48 0.76
86 2 0.03
88 13 0.21
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (87 bp):
ATTATTATTACTACTATTATTATCATCATTTTATTACTACATTAATATTATTATTACTACATTAT
TTATTATTATCCTAGTATTATT
Found at i:368351 original size:22 final size:22
Alignment explanation
Indices: 368195--368368 Score: 69
Period size: 22 Copynumber: 8.1 Consensus size: 22
368185 ATCTTTTTCA
* *
368195 TTATTATTACTACTATTATTAT
1 TTATTATTAATACTACTATTAT
*
368217 TATCATT-TTATTACTAC-ATTA-
1 T-T-ATTATTAATACTACTATTAT
* * *
368238 ATGTTATTATTA-TA--ATTAT
1 TTATTATTAATACTACTATTAT
* *
368257 TTATTATT-ATCCTAGTATTA-
1 TTATTATTAATACTACTATTAT
* * *
368277 TTATTATTATTATTATTATTAT
1 TTATTATTAATACTACTATTAT
* * ** *
368299 TATCATCATT-TTGTTACTATTTT
1 T-T-ATTATTAATACTACTATTAT
* *
368322 ATTATTATTATTACTACTCTTAT
1 -TTATTATTAATACTACTATTAT
*
368345 TTATTATTAATATTACTATTAT
1 TTATTATTAATACTACTATTAT
368367 TT
1 TT
368369 CAAATTACCA
Statistics
Matches: 115, Mismatches: 24, Indels: 26
0.70 0.15 0.16
Matches are distributed among these distances:
18 5 0.04
19 12 0.10
20 15 0.13
21 12 0.10
22 32 0.28
23 30 0.26
24 9 0.08
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (22 bp):
TTATTATTAATACTACTATTAT
Found at i:370877 original size:139 final size:139
Alignment explanation
Indices: 370529--370996 Score: 504
Period size: 139 Copynumber: 3.4 Consensus size: 139
370519 TTTAATTTAG
* *
370529 ATTCGAATTACATAATTTATTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTT
1 ATTCGAATTAAATAATTAATTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCC-TT
* * * *
370594 TTTTCAAATGTAATCCTTAAA-TTTGGCTGAATTCTTAATTTGGTCCTCACTTTTGCTCGAGGTT
65 TTTTCAAATATAGTCCTTAAATTTTGG-TGAATTATTAATTTGGTCCTCGCTTTTGCTCGAGGTT
*
370658 CCACTTTAATT
129 CCACTTTAATC
* *
370669 ATTCGAATCAAATAATTAATTAAAATTAATTAGGATTAATAATAGAGCCTTCACTTTAGGCCTTT
1 ATTCGAATTAAATAATTAATTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTT
* * *
370734 TTTCAAATTTAGTCCTTAAATTTTGGTGAATTATTAATTTGATCCTCGCTTTTGCTCGAGGTTTC
66 TTTCAAATATAGTCCTTAAATTTTGGTGAATTATTAATTTGGTCCTCGCTTTTGCTCGAGGTTCC
370799 ACTTTAATC
131 ACTTTAATC
* * * * * *
370808 ATTCGAATTAAATAATTGATTAAAATTAAATAAG-TTAATATTTAGAGCCTCCAATTTA-G-ATT
1 ATTCGAATTAAATAATTAATTAAAATTAATTAGGATTAATA-TTAGAGCCTTCACTTTAGGCCTT
** * * * *
370870 TAATTTCACAA-ATAG-CCTTTTATTTTAGGAGAATTTTTGATTTGGTCCTCGCTTTTGCTTGAG
65 T--TTTCA-AATATAGTCCTTAAATTTT-GGTGAATTATTAATTTGGTCCTCGCTTTTGCTCGAG
* *
370933 GTTCCATTTTGA-C
126 GTTCCACTTTAATC
* * * * *
370946 TATTCG-ACTCAATAATTTATTAAAAGATGACTT-GGATTAATATTAGAGCCT
1 -ATTCGAATTAAATAATTAATT-AAA-ATTAATTAGGATTAATATTAGAGCCT
370997 AGTTTTTTAG
Statistics
Matches: 281, Mismatches: 37, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
137 3 0.01
138 29 0.10
139 174 0.62
140 75 0.27
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (139 bp):
ATTCGAATTAAATAATTAATTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTT
TTTCAAATATAGTCCTTAAATTTTGGTGAATTATTAATTTGGTCCTCGCTTTTGCTCGAGGTTCC
ACTTTAATC
Found at i:391931 original size:8 final size:8
Alignment explanation
Indices: 391918--391957 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
391908 TATAAACAAG
391918 AAAAGAAA
1 AAAAGAAA
391926 AAAAGAAA
1 AAAAGAAA
*
391934 ACAA-AAA
1 AAAAGAAA
*
391941 GAAAGAAA
1 AAAAGAAA
391949 AAAAGAAA
1 AAAAGAAA
391957 A
1 A
391958 TTGAAATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 5 0.19
8 22 0.81
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:391941 original size:11 final size:11
Alignment explanation
Indices: 391923--391957 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
391913 ACAAGAAAAG
391923 AAAAAAAGAAA
1 AAAAAAAGAAA
*
391934 ACAAAAAGAAA
1 AAAAAAAGAAA
391945 GAAAAAAAGAAA
1 -AAAAAAAGAAA
391957 A
1 A
391958 TTGAAATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:391951 original size:12 final size:12
Alignment explanation
Indices: 391919--391956 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
391909 ATAAACAAGA
391919 AAAGAAAAAAAG
1 AAAGAAAAAAAG
*
391931 AAA-ACAAAAAG
1 AAAGAAAAAAAG
391942 AAAGAAAAAAAG
1 AAAGAAAAAAAG
391954 AAA
1 AAA
391957 ATTGAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:393206 original size:20 final size:19
Alignment explanation
Indices: 393145--393206 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
393135 CAATAGAAGG
393145 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
*
393164 CGTTCGA-AAGGGAGAAGAA--
1 -GTTC-ATAA-TGAGAAGAACT
393183 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
393203 GTTC
1 GTTC
393207 GACCTTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
17 9 0.26
18 6 0.18
20 10 0.29
21 9 0.26
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:393354 original size:115 final size:116
Alignment explanation
Indices: 393102--393521 Score: 505
Period size: 117 Copynumber: 3.6 Consensus size: 116
393092 TTATAGATTT
* * * *
393102 AATCCATCGT-AGAAGGAGGAT-GATTGTCAATTCCAATAGAAGGGTTCATAATGAGAAGAACTC
1 AATCCATCGTAAAAAGAAGG-TGGATCGTCATTTCCAATAGAAGGGTTCATAATGAGAAGAACTC
* *
393165 GTTCGAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTTCTC
65 GTCCGAAA--GAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGCTC
* *
393219 AATCCATCAT-AGAAGAAGGTGGATCGTCATTTCCAATAGAAGGGTTCATAATGAGAAGAACTCG
1 AATCCATCGTAAAAAGAAGGTGGATCGTCATTTCCAATAGAAGGGTTCATAATGAGAAGAACTCG
* * *
393283 TCCGAACA-AGAAGAAGTTCATAATTAGAAGAACTAGTTCGACCTCTTGCTC
66 TCCGAA-AGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGCTC
*
393334 AATCCATCGTAAAAAG-AGGTGGATCGTCATTT-CAATAGAAGGGTTCATAACGAGAAGAACTCG
1 AATCCATCGTAAAAAGAAGGTGGATCGTCATTTCCAATAGAAGGGTTCATAATGAGAAGAACTCG
* * * * *
393397 TCCAAAGAGGGAGAATAAGTTCATAATGAAAAGAACTTCTTCAACCTTTTGCTC
66 TCCGAA-A--GAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGCTC
* * * * *
393451 AAATTCATC--ACAAAAGTAGGTGGATCGACATTTCCAATTGAAGGGTTCATAATGAGAAGAAGT
1 -AATCCATCGTA-AAAAGAAGGTGGATCGTCATTTCCAATAGAAGGGTTCATAATGAGAAGAACT
393514 CGTCCGAA
64 CGTCCGAA
393522 GCGATCGTTG
Statistics
Matches: 266, Mismatches: 27, Indels: 18
0.86 0.09 0.06
Matches are distributed among these distances:
114 36 0.14
115 64 0.24
116 6 0.02
117 104 0.39
118 23 0.09
119 33 0.12
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (116 bp):
AATCCATCGTAAAAAGAAGGTGGATCGTCATTTCCAATAGAAGGGTTCATAATGAGAAGAACTCG
TCCGAAAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGCTC
Found at i:393676 original size:3 final size:3
Alignment explanation
Indices: 393670--393886 Score: 178
Period size: 3 Copynumber: 72.3 Consensus size: 3
393660 CCATTACCAA
*
393670 TAT TAT T-T TAT TACT T-T TAT CA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * ** *
393713 CAT T-T TAT TAT TA- CAT TAT TGC TAT TAT TAT AAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * *
393757 TAT CCTAT TAT TAT TAT TAC TAT TAT TAT CAT TTT TAT TAT T-T TAT
1 TAT --TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
393803 TAT TAT TAT AAT TAT TATT TAT TATT TAT TAG TGT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * *
393849 TAT TAT TAC TCT TATT TAT TAT TAA TAT TAC TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
393887 TCAAATTACC
Statistics
Matches: 168, Mismatches: 32, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
2 12 0.07
3 139 0.83
4 14 0.08
5 3 0.02
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:393683 original size:23 final size:22
Alignment explanation
Indices: 393651--393705 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
393641 TGTAATCACC
*
393651 ATTTTTTTACCATTACCAATATT
1 ATTTTATTACCATTACC-ATATT
** *
393674 ATTTTATTACTTTTATCATATT
1 ATTTTATTACCATTACCATATT
393696 ATTATTATTA
1 ATT-TTATTA
393706 TTATTATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTATTACCATTACCATATT
Found at i:393894 original size:22 final size:22
Alignment explanation
Indices: 393792--393887 Score: 61
Period size: 22 Copynumber: 4.4 Consensus size: 22
393782 TTATCATTTT
* * * *
393792 TATTATTTTATTATTATTATAAT
1 TATTA-TTTATAATTAATATTAC
* *
393815 TATTATTTATTATT--TATTAG
1 TATTATTTATAATTAATATTAC
* * *
393835 TGTTATTTTATTATTATTATTAC
1 TATTA-TTTATAATTAATATTAC
* *
393858 TCTTATTTATTATTAATATTAC
1 TATTATTTATAATTAATATTAC
393880 TATTATTT
1 TATTATTT
393888 CAAATTACCA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.13
21 9 0.14
22 32 0.51
23 14 0.22
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTATTTATAATTAATATTAC
Found at i:396801 original size:84 final size:83
Alignment explanation
Indices: 396605--397259 Score: 727
Period size: 84 Copynumber: 7.8 Consensus size: 83
396595 GATTTGCATA
* * * * * * * *
396605 TGAGTTGAATGTAATCGAACTCGAAGGTATTTATTGACAAATAACCCTTCTCGCCTTGAGTTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
* * *
396670 TTGTAAATTGGATACGCCTC
66 TTGCAAA-T-GATGCGCCTT
* * * * * * * *
396690 AGAGCTTAATGTAATCGAACTCAAAGGTCTTTAATTGGCAAATAACCATTCTTTCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
* *
396755 GTTACAAATGATGCACCTT
65 GTTGCAAATGATGCGCCTT
* *
396774 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACTCTTCTTACCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
*
396839 GTTACAAATGATGCGCCTT
65 GTTGCAAATGATGCGCCTT
* *
396858 TGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
*
396923 GTTGCAAATGATGCTCCTT
65 GTTGCAAATGATGCGCCTT
* * *
396942 TGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTGTTGGCAGATATA-TCTTCTTACCTTGAGCTA
1 TGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATA-ACCCTTCTTGCCTTGAGCTA
* * *
397006 TGCTGTAAATGATGTGCCTT
64 TGTTGCAAATGATGCGCCTT
* * * ** * * * *
397026 CGAGCTGAGTGTAATCAAACTTGAAGGTCTTTGTTGATATATAACCCTTCTAGCCATGAGTTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
* *
397091 TTGTAAATGATGTGCCTT
66 TTGCAAATGATGCGCCTT
* * * * *
397109 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTGGCAGAGAGCACTTCTTACCTTGAGCTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
* *
397174 ATGCAAATGATGTGCCTT
66 TTGCAAATGATGCGCCTT
* ** * * *
397192 TGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGATAAATAACCCTTCTCGCCTTGAGTTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
397257 TTG
66 TTG
397260 TACTTGGCTG
Statistics
Matches: 485, Mismatches: 81, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
82 1 0.00
83 166 0.34
84 254 0.52
85 31 0.06
86 33 0.07
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (83 bp):
TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
TTGCAAATGATGCGCCTT
Found at i:397544 original size:64 final size:62
Alignment explanation
Indices: 397391--397554 Score: 176
Period size: 64 Copynumber: 2.6 Consensus size: 62
397381 TGAAGTTGAG
* *
397391 CTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCC--ATGAACTGTTTTACCAAATTGGT
1 CTTTGAGTT-GATATCCTTCGTTGTGAAGTTGAAATCCAAATGAACAGTTTCACCAAATTGGT
* * * *
397452 -TTTGAACTGGATATCCTTCATCGTGAAGTTGAAATCCAATATTGAGTA-AGTTTCACCAAATT-
1 CTTTG-AGTTGATATCCTTCGTTGTGAAGTTGAAATCCAA-A-TGA--ACAGTTTCACCAAATTG
397514 GT
61 GT
*
397516 CTTTGAGTTGATATCCTTTGTTGTGAAGTTGAAATCCAA
1 CTTTGAGTTGATATCCTTCGTTGTGAAGTTGAAATCCAA
397555 GGGTTGAATT
Statistics
Matches: 84, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
60 30 0.36
61 2 0.02
63 1 0.01
64 34 0.40
65 16 0.19
66 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (62 bp):
CTTTGAGTTGATATCCTTCGTTGTGAAGTTGAAATCCAAATGAACAGTTTCACCAAATTGGT
Found at i:397695 original size:121 final size:124
Alignment explanation
Indices: 397567--397920 Score: 480
Period size: 121 Copynumber: 2.9 Consensus size: 124
397557 GTTGAATTGA
* *
397567 TGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTTGTCATGAAGT
1 TGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCGTCGTGAAGT
* * * **
397632 TGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTAAAATCCAATCTTGAG-T-AA-GT
66 TGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATAAAGATGAATGT
* * * *
397688 TGGTTGTGGGCACAATATCCTTTGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGT
1 TGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCGTCGTGAAGT
* * * *
397753 TGAGCCTCGAATTGGATATCTTTTGTCGTGAAGTTGAAATCTAATATAAAGATGAATGT
66 TGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATAAAGATGAATGT
* * * * * * *
397812 TGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATAGATGGCTCCTTCATTGTAAAGT
1 TGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCGTCGTGAAGT
*
397877 TGAGCCTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAA
66 TGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
397921 GGGTTGTTTC
Statistics
Matches: 199, Mismatches: 31, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
121 101 0.51
122 1 0.01
123 2 0.01
124 95 0.48
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (124 bp):
TGCTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCGTCGTGAAGT
TGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATATAAAGATGAATGT
Found at i:398009 original size:54 final size:54
Alignment explanation
Indices: 397883--398035 Score: 216
Period size: 54 Copynumber: 2.7 Consensus size: 54
397873 AAGTTGAGCC
* * *
397883 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAAGGGTTGTTTCACCAAATTGGTT
1 TTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAA------TTTCACAAAATTGGCT
*
397943 TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATTTCACAAAATTGGCT
1 TTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATTTCACAAAATTGGCT
397997 TTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAAT
1 TTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAAT
398036 CTCGAGTAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
54 52 0.59
60 36 0.41
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (54 bp):
TTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATTTCACAAAATTGGCT
Found at i:399570 original size:20 final size:20
Alignment explanation
Indices: 399545--399582 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
399535 TTTACTTCAC
399545 TTTTTCCTT-TGTTTTTCTCT
1 TTTTTCCTTCT-TTTTTCTCT
399565 TTTTTCCTTCTTTTTTCT
1 TTTTTCCTTCTTTTTTCT
399583 TTTGTTCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTTCCTTCTTTTTTCTCT
Found at i:405315 original size:14 final size:14
Alignment explanation
Indices: 405298--405351 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
405288 TATTCGATTG
*
405298 ATTTATTTTTTGTT
1 ATTTAATTTTTGTT
*
405312 ATTTAAATTTTTGTC
1 ATTT-AATTTTTGTT
* *
405327 ATTTAAATTTGGTT
1 ATTTAATTTTTGTT
*
405341 ATTTTATTTTT
1 ATTTAATTTTT
405352 CCTTTAAATT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (14 bp):
ATTTAATTTTTGTT
Found at i:405324 original size:15 final size:15
Alignment explanation
Indices: 405304--405336 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
405294 ATTGATTTAT
*
405304 TTTTTGTTATTTAAA
1 TTTTTGTCATTTAAA
405319 TTTTTGTCATTTAAA
1 TTTTTGTCATTTAAA
405334 TTT
1 TTT
405337 GGTTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTTGTCATTTAAA
Found at i:405969 original size:139 final size:139
Alignment explanation
Indices: 405701--406157 Score: 654
Period size: 139 Copynumber: 3.3 Consensus size: 139
405691 ATTCAAATTG
* *
405701 AATAATTGATTAAAATTAATTAGGATTAATATTCGATCCTTCACTTTAGGCCTTTTTCTCAAACT
1 AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTTTTC-CAAACT
* *
405766 TAGTCCTTAAATTTAGGTAAATTCTTAATTTGGTTTTCACTTTTGCTCAA-GTTTCCACTTTAAT
65 TAGTCCTTAAATTTAGGTGAATTCTTAATTTGGTTTTCGCTTTTGCTCAAGGTTT-CACTTTAAT
405830 TATTCGAATCA
129 TATTCGAATCA
405841 AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTTTTCCAAACTT
1 AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTTTTCCAAACTT
* * *
405906 AGTCCTTAAATTTAGGTGAATTCTTAATTTGGTCCTT-GCTTTTGCTCAAGGTTTTACTGTAATT
66 AGTCCTTAAATTTAGGTGAATTCTTAATTTGGT-TTTCGCTTTTGCTCAAGGTTTCACTTTAATT
*
405970 ATTTGAATCA
130 ATTCGAATCA
* * *
405980 AATAATTGATTAAAATGAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTTTT-TAAATTT
1 AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTTTTCCAAACTT
* * * *
406044 AGTCCTTAAATTTAGGTGAATTCTTAATTTGATTTTCGCTTTTGCTCGAGGTTCCACTTTAATCA
66 AGTCCTTAAATTTAGGTGAATTCTTAATTTGGTTTTCGCTTTTGCTCAAGGTTTCACTTTAATTA
* **
406109 TTCAAATTG
131 TTCGAATCA
* *
406118 CATAATTGATTAAATTTGAA-TAGG-TTAATATTTAGAGCCT
1 AATAATTGATTAAAATT-AATTAGGATTAATA-TTAGAGCCT
406158 CCATTTTATA
Statistics
Matches: 287, Mismatches: 25, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
137 8 0.03
138 92 0.32
139 125 0.44
140 62 0.22
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (139 bp):
AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTTTTCCAAACTT
AGTCCTTAAATTTAGGTGAATTCTTAATTTGGTTTTCGCTTTTGCTCAAGGTTTCACTTTAATTA
TTCGAATCA
Found at i:406215 original size:277 final size:278
Alignment explanation
Indices: 405701--406227 Score: 715
Period size: 277 Copynumber: 1.9 Consensus size: 278
405691 ATTCAAATTG
* * *
405701 AATAATTGATTAAAATTAATTAGGATTAATATTCGATCCTTCACTTTAGGCCTTTTTCTCAAACT
1 AATAATTGATTAAAATGAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTTTTCTCAAACT
* * *
405766 TAGTCCTTAAATTTAGGTAAATTCTTAATTTGGTTTTCACTTTTGCTCAAGTTTCCACTTTAATT
66 TAGTCCTTAAATTTAGGTAAATTCTTAATTTGATTTTCACTTTTGCTCAAGGTTCCACTTTAATC
* * *
405831 ATTCGAATCAAATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTT
131 ATTCAAATCAAATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAGGACTTT
* **
405896 TTCCAAACTTAGTCCTTAAATTTAGGTGAATTCTTAATTTGGTCCTTGCTTTTGCTCAAGGTTTT
196 TTCCAAAC-TAGTCCTTAAATTTAGGAGAATTCTTAATTTGGTCCTAACTTTTGCTCAAGGTTTT
405961 ACTGTAATTATTTGAATCA
260 ACTGTAATTATTTGAATCA
*
405980 AATAATTGATTAAAATGAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTTTT-T-AAATT
1 AATAATTGATTAAAATGAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTTTTCTCAAACT
* * *
406043 TAGTCCTTAAATTTAGGTGAATTCTTAATTTGATTTTCGCTTTTGCTCGAGGTTCCACTTTAATC
66 TAGTCCTTAAATTTAGGTAAATTCTTAATTTGATTTTCACTTTTGCTCAAGGTTCCACTTTAATC
*** * * * *
406108 ATTCAAATTGCATAATTGATTAAATTTGAA-TAGG-TTAATATTTAGAGCCTCCATTTTA-TATT
131 ATTCAAATCAAATAATTGATTAAAATT-AATTAGGATTAATA-TTAGAGCCTCCACTTTAGGACT
* * * *
406170 TAATTTCACAAA-TAGTCCTTTATTTTAGGAGAATTTTTGATTTGGTCCTAACTTTTGC
194 T--TTTC-CAAACTAGTCCTTAAATTTAGGAGAATTCTTAATTTGGTCCTAACTTTTGC
406228 CCGAAGTTCC
Statistics
Matches: 216, Mismatches: 27, Indels: 12
0.85 0.11 0.05
Matches are distributed among these distances:
276 8 0.04
277 143 0.66
278 7 0.03
279 58 0.27
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.44
Consensus pattern (278 bp):
AATAATTGATTAAAATGAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTTTTTCTCAAACT
TAGTCCTTAAATTTAGGTAAATTCTTAATTTGATTTTCACTTTTGCTCAAGGTTCCACTTTAATC
ATTCAAATCAAATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACTTTAGGACTTT
TTCCAAACTAGTCCTTAAATTTAGGAGAATTCTTAATTTGGTCCTAACTTTTGCTCAAGGTTTTA
CTGTAATTATTTGAATCA
Found at i:409556 original size:17 final size:18
Alignment explanation
Indices: 409542--409580 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
409532 AAAAAAAATC
409542 AGTTTCAGGAAAAAATTA
1 AGTTTCAGGAAAAAATTA
*
409560 AGTTTCA-GACGAAAATTA
1 AGTTTCAGGA-AAAAATTA
409578 AGT
1 AGT
409581 GTTTACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (18 bp):
AGTTTCAGGAAAAAATTA
Found at i:409556 original size:18 final size:18
Alignment explanation
Indices: 409533--409567 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
409523 TAATAATATA
*
409533 AAAAAAATCAGTTTCAGG
1 AAAAAAATAAGTTTCAGG
*
409551 AAAAAATTAAGTTTCAG
1 AAAAAAATAAGTTTCAG
409568 ACGAAAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (18 bp):
AAAAAAATAAGTTTCAGG
Found at i:409916 original size:20 final size:20
Alignment explanation
Indices: 409891--409933 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
409881 TCTAAAGGCT
409891 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
409911 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
409931 CAT
1 CAT
409934 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:417561 original size:21 final size:21
Alignment explanation
Indices: 417537--417577 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
417527 ATGTTTTCAC
*
417537 CTTTCACTTTCTATCTTTTTA
1 CTTTCACTTTCTATCATTTTA
*
417558 CTTTTACTTTCTATCATTTT
1 CTTTCACTTTCTATCATTTT
417578 CTTCTCCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (21 bp):
CTTTCACTTTCTATCATTTTA
Found at i:422320 original size:12 final size:12
Alignment explanation
Indices: 422303--422327 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
422293 GTGTTTTTGC
422303 TTATTAAGTTAT
1 TTATTAAGTTAT
422315 TTATTAAGTTAT
1 TTATTAAGTTAT
422327 T
1 T
422328 ATGTGTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TTATTAAGTTAT
Found at i:423529 original size:21 final size:21
Alignment explanation
Indices: 423481--423529 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
423471 TTGCAATGAG
*
423481 CCCTAAACCATAAATCTTAAA
1 CCCTAAACCATAAACCTTAAA
* * **
423502 TCATAAACTTTAAACCTTAAA
1 CCCTAAACCATAAACCTTAAA
423523 CCCTAAA
1 CCCTAAA
423530 TACTAAACTT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (21 bp):
CCCTAAACCATAAACCTTAAA
Found at i:423563 original size:28 final size:28
Alignment explanation
Indices: 423505--423565 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
423495 TCTTAAATCA
*
423505 TAAACTTTAAACCTTAAACCCTAAATAC
1 TAAACTTTAAACCTTAAACCCTAAACAC
** *
423533 TAAACTTTAAATTTTAAACCCTAAACCC
1 TAAACTTTAAACCTTAAACCCTAAACAC
423561 TAAAC
1 TAAAC
423566 CCTTATTCCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.30
Consensus pattern (28 bp):
TAAACTTTAAACCTTAAACCCTAAACAC
Found at i:427135 original size:11 final size:11
Alignment explanation
Indices: 427119--427183 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
427109 TGAAGAGAGT
*
427119 TCGAGCTTGAA
1 TCGAGCTTCAA
427130 TCGAGC-TCAAAA
1 TCGAGCTTC--AA
427142 TCGAGCTTCAA
1 TCGAGCTTCAA
*
427153 TCGAGC-TCGAGTC
1 TCGAGCTTC-A--A
427166 TCGAGCTTCAA
1 TCGAGCTTCAA
427177 TCGAGCT
1 TCGAGCT
427184 CCTGAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 3 0.07
11 22 0.50
12 8 0.18
13 9 0.20
14 2 0.05
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (11 bp):
TCGAGCTTCAA
Found at i:427174 original size:24 final size:23
Alignment explanation
Indices: 427115--427184 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
427105 AGCTTGAAGA
*
427115 GAGTTCGAGCTTGAATCGAGCTC
1 GAGTTCGAGCTTCAATCGAGCTC
* **
427138 AAAATCGAGCTTCAATCGAGCTC
1 GAGTTCGAGCTTCAATCGAGCTC
427161 GAGTCTCGAGCTTCAATCGAGCTC
1 GAGT-TCGAGCTTCAATCGAGCTC
427185 CTGAATTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (23 bp):
GAGTTCGAGCTTCAATCGAGCTC
Found at i:431632 original size:43 final size:43
Alignment explanation
Indices: 431585--431669 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
431575 CAACTTCTTA
* * *
431585 TGTGAAGAATCAAGCGAAAGGTTTTCACTGATCTAACTCTTTC
1 TGTGAAGAATCAAGCGAAAGGTTGTCACCGATCCAACTCTTTC
* ** *
431628 TGTGAAGGATTGAGTGAAAGGTTGTCACCGATCCAACTCTTT
1 TGTGAAGAATCAAGCGAAAGGTTGTCACCGATCCAACTCTTT
431670 TTTTGAATGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (43 bp):
TGTGAAGAATCAAGCGAAAGGTTGTCACCGATCCAACTCTTTC
Found at i:433116 original size:5 final size:5
Alignment explanation
Indices: 433049--433123 Score: 57
Period size: 5 Copynumber: 14.6 Consensus size: 5
433039 CTTAAACCCC
*
433049 CTTTT CATTTT CTTTT -ATTT -TTTT CTTATT -TTTT CTATTT CTATTT
1 CTTTT C-TTTT CTTTT CTTTT CTTTT CTT-TT CTTTT CT-TTT CT-TTT
* *
433095 ATTTT CCTTTT CCTTT CTTTT CTTTT CTT
1 CTTTT -CTTTT CTTTT CTTTT CTTTT CTT
433124 GACATATGAC
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
4 8 0.14
5 29 0.50
6 21 0.36
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (5 bp):
CTTTT
Found at i:436499 original size:20 final size:19
Alignment explanation
Indices: 436470--436509 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
436460 TTGTAGAGAG
*
436470 GAAAGCGAAACGAATAAAA
1 GAAAGCGAAACAAATAAAA
*
436489 GAAATGCGAAATAAATAAAA
1 GAAA-GCGAAACAAATAAAA
436509 G
1 G
436510 TGAAATGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.62, C:0.07, G:0.20, T:0.10
Consensus pattern (19 bp):
GAAAGCGAAACAAATAAAA
Found at i:437767 original size:2 final size:2
Alignment explanation
Indices: 437760--437809 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
437750 GCTTATTAAC
437760 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
437802 AT AT AT AT
1 AT AT AT AT
437810 GTCATGAAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:443547 original size:21 final size:21
Alignment explanation
Indices: 443521--443561 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
443511 TTTAAAAAAA
*
443521 AAAAAAAAAAAAAAGGCAAAC
1 AAAAAAAAAAAAAAGCCAAAC
*
443542 AAAAAAAACAAAAAGCCAAA
1 AAAAAAAAAAAAAAGCCAAA
443562 ATTTCAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.80, C:0.12, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAAAGCCAAAC
Found at i:450962 original size:22 final size:20
Alignment explanation
Indices: 450911--450981 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 20
450901 TGCAAAAATG
* * *
450911 GTATCAATATCATAGGAGG-
1 GTATCGATACCATAGTAGGA
*
450930 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTA-GG-A
* *
450952 GTATCGATACCATGGTAGGG
1 GTATCGATACCATAGTAGGA
450972 GTATCGATAC
1 GTATCGATAC
450982 TAAGGAGCCA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 13 0.31
20 12 0.29
21 2 0.05
22 15 0.36
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (20 bp):
GTATCGATACCATAGTAGGA
Found at i:450977 original size:20 final size:21
Alignment explanation
Indices: 450928--450981 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
450918 TATCATAGGA
*
450928 GGGTATCGGTACCATAGTATG
1 GGGTATCGATACCATAGTATG
* *
450949 GTAGTATCGATACCATGGTA-G
1 G-GGTATCGATACCATAGTATG
450970 GGGTATCGATAC
1 GGGTATCGATAC
450982 TAAGGAGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.36
21 3 0.11
22 15 0.54
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (21 bp):
GGGTATCGATACCATAGTATG
Found at i:451496 original size:24 final size:24
Alignment explanation
Indices: 451468--451513 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
451458 ATCGGCATGA
*
451468 AAGGATGCCATAGCTGAAATGCAT
1 AAGGATGCCATAGCTAAAATGCAT
451492 AAGGATGCCATAGCTAAAATGC
1 AAGGATGCCATAGCTAAAATGC
451514 GTATGGGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (24 bp):
AAGGATGCCATAGCTAAAATGCAT
Found at i:457640 original size:20 final size:19
Alignment explanation
Indices: 457608--457658 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
457598 TGATTCAATC
*
457608 AGTATCG-TACCGAATGGGG
1 AGTATCGATACCGAA-GGGA
457627 AGTATCGATACCGAAGGGA
1 AGTATCGATACCGAAGGGA
457646 AGGTATCGATACC
1 A-GTATCGATACC
457659 ATTTTGAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (19 bp):
AGTATCGATACCGAAGGGA
Found at i:458223 original size:45 final size:45
Alignment explanation
Indices: 458159--458279 Score: 215
Period size: 45 Copynumber: 2.7 Consensus size: 45
458149 AATTAATGAA
458159 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* * *
458204 CAAAAGAATATTGCATATGGGTGCATCATCGGCATGAAAGGATGT
1 CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
458249 CAAAAGAATAATGCATATGGGTGCATTATCG
1 CAAAAGAATAATGCATATGGGTGCATTATCG
458280 ACATAAGAGT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (45 bp):
CAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
Done.