Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004105.1 Hibiscus syriacus cultivar Beakdansim tig00008979_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: 262281
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:213850 original size:28 final size:28
Alignment explanation
Indices: 213789--213842 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
213779 CAATATATCC
* *
213789 GATAGCGGTTTATCGGTTTTATCATAAT
1 GATACCGGTTTACCGGTTTTATCATAAT
213817 GATACCGGTTTACCGGTTTTATCATA
1 GATACCGGTTTACCGGTTTTATCATA
213843 TTTTTACCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (28 bp):
GATACCGGTTTACCGGTTTTATCATAAT
Found at i:215182 original size:213 final size:213
Alignment explanation
Indices: 214811--215239 Score: 804
Period size: 213 Copynumber: 2.0 Consensus size: 213
214801 TGAAAAGAAA
*
214811 TATCAGTAGAGCCGAATCGATCGGAAGCTCCGGAGGTGTTTCTAATGGCGGAAACAGCGACGGCG
1 TATCAGTAGAGCCGAATCGATCGGAAGCTCAGGAGGTGTTTCTAATGGCGGAAACAGCGACGGCG
*
214876 GCGGAGGGATGAGTCGGAGCGGCAGCAATGGTACTAGTTTCGGTTGTTCATCGAAACTTAGCTTC
66 GCGGAGGGATGAGGCGGAGCGGCAGCAATGGTACTAGTTTCGGTTGTTCATCGAAACTTAGCTTC
214941 AGAGATCATATATTGACTTACACTCAAAGATACCTTGCTGCCGATGCGGTAGAAGAGGCGGCGGC
131 AGAGATCATATATTGACTTACACTCAAAGATACCTTGCTGCCGATGCGGTAGAAGAGGCGGCGGC
215006 GGAAGCGGTACACACTCC
196 GGAAGCGGTACACACTCC
* *
215024 TATCAGTAGAGCCGTATCGATCGGAAGCTCAGGAGGTGTTTCTAATGGCGGAAACAGCGACGGTG
1 TATCAGTAGAGCCGAATCGATCGGAAGCTCAGGAGGTGTTTCTAATGGCGGAAACAGCGACGGCG
215089 GCGGAGGGATGAGGCGGAGCGGCAGCAATGGTACTAGTTTCGGTTGTTCATCGAAACTTAGCTTC
66 GCGGAGGGATGAGGCGGAGCGGCAGCAATGGTACTAGTTTCGGTTGTTCATCGAAACTTAGCTTC
* *
215154 AGAGATCATATATTGACTTACGCTCAAAGATACCTTGCTGCCGATGCGGTAGAAGAGGCGGCGTC
131 AGAGATCATATATTGACTTACACTCAAAGATACCTTGCTGCCGATGCGGTAGAAGAGGCGGCGGC
215219 GGAAGCGGTACACACTCC
196 GGAAGCGGTACACACTCC
215237 TAT
1 TAT
215240 GAATAACCGC
Statistics
Matches: 210, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
213 210 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (213 bp):
TATCAGTAGAGCCGAATCGATCGGAAGCTCAGGAGGTGTTTCTAATGGCGGAAACAGCGACGGCG
GCGGAGGGATGAGGCGGAGCGGCAGCAATGGTACTAGTTTCGGTTGTTCATCGAAACTTAGCTTC
AGAGATCATATATTGACTTACACTCAAAGATACCTTGCTGCCGATGCGGTAGAAGAGGCGGCGGC
GGAAGCGGTACACACTCC
Found at i:218811 original size:51 final size:51
Alignment explanation
Indices: 218712--219269 Score: 557
Period size: 51 Copynumber: 10.8 Consensus size: 51
218702 AAAGAAGCAC
* * * * *
218712 AGGGGTGTCTTCAGACATGCTCCAGT-GGAAGAAGATACCGAGCAAGCAGA
1 AGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGATATCGAACAAGCAGA
* * *
218762 GGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGAAACCGAACAAGCAGA
1 AGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGATATCGAACAAGCAGA
* * *
218813 ATGGGTGTCTTCAGACATGTTCCGGTAGGAAGAGGATATCAAACAAGCAGA
1 AGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGATATCGAACAAGCAGA
* * * * *
218864 AGGGGTTTCTTAAGACATGTTCCAGTGGGAAGAGGGTATCGAACAAGCATA
1 AGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGATATCGAACAAGCAGA
* * *
218915 TGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGAAACCGAACAAGCAGA
1 AGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGATATCGAACAAGCAGA
* * * *
218966 ATGGGTGTCTTCAGACATGTTCCGGTAGGAAGAGGATTTCAAACAAGCAGA
1 AGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGATATCGAACAAGCAGA
* * * *
219017 AGGGGTGTCTTAAGACATGTTCCAGTGGGAAGAGGGTATCGAACAAGCATA
1 AGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGATATCGAACAAGCAGA
* *
219068 TGGGGTGTCTTCAGACATGTTCCGGTGGGAGGAGGATATCGAACAAGCAG-
1 AGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGATATCGAACAAGCAGA
* * * * * * * *
219118 AGGGTGTGTCTTCAAACTTCAGTCATGTTCCAGT-AGAAGGAGCACATTGAATAAACAGA
1 AGGG-GTG---T----CTTCAGACATGTTCCGGTGGGAA-GAGGATATCGAACAAGCAGA
* * * * * * * * *
219177 TGGGATGTTTTCAAACATGTTTCAGTGGGAGGAGGATATTGAACAAGTAGA
1 AGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGATATCGAACAAGCAGA
* * * *
219228 A-GGGTGTCTTCAGTCATGTTCCAGTGGGAGGACGATATCGAA
1 AGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGATATCGAA
219270 TGAAGAACAG
Statistics
Matches: 416, Mismatches: 80, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
50 60 0.14
51 315 0.76
52 2 0.00
54 1 0.00
55 1 0.00
57 2 0.00
58 32 0.08
59 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (51 bp):
AGGGGTGTCTTCAGACATGTTCCGGTGGGAAGAGGATATCGAACAAGCAGA
Found at i:219016 original size:153 final size:153
Alignment explanation
Indices: 218712--219131 Score: 691
Period size: 153 Copynumber: 2.8 Consensus size: 153
218702 AAAGAAGCAC
* * * * * * * *
218712 AGGGGTGTCTTCAGACATGCTCCAGT-GGAAGAAGATACCGAGCAAGCAGAGGGGGTGTCTTCAG
1 AGGGGTGTCTTAAGACATGTTCCAGTGGGAAGAGGGTATCGAACAAGCATATGGGGTGTCTTCAG
218776 ACATGTTCCGGTGGGAAGAGGAAACCGAACAAGCAGAATGGGTGTCTTCAGACATGTTCCGGTAG
66 ACATGTTCCGGTGGGAAGAGGAAACCGAACAAGCAGAATGGGTGTCTTCAGACATGTTCCGGTAG
218841 GAAGAGGATATCAAACAAGCAGA
131 GAAGAGGATATCAAACAAGCAGA
*
218864 AGGGGTTTCTTAAGACATGTTCCAGTGGGAAGAGGGTATCGAACAAGCATATGGGGTGTCTTCAG
1 AGGGGTGTCTTAAGACATGTTCCAGTGGGAAGAGGGTATCGAACAAGCATATGGGGTGTCTTCAG
218929 ACATGTTCCGGTGGGAAGAGGAAACCGAACAAGCAGAATGGGTGTCTTCAGACATGTTCCGGTAG
66 ACATGTTCCGGTGGGAAGAGGAAACCGAACAAGCAGAATGGGTGTCTTCAGACATGTTCCGGTAG
*
218994 GAAGAGGATTTCAAACAAGCAGA
131 GAAGAGGATATCAAACAAGCAGA
219017 AGGGGTGTCTTAAGACATGTTCCAGTGGGAAGAGGGTATCGAACAAGCATATGGGGTGTCTTCAG
1 AGGGGTGTCTTAAGACATGTTCCAGTGGGAAGAGGGTATCGAACAAGCATATGGGGTGTCTTCAG
* * * *
219082 ACATGTTCCGGTGGGAGGAGGATATCGAACAAGCAG-AGGGTGTGTCTTCA
66 ACATGTTCCGGTGGGAAGAGGAAACCGAACAAGCAGAATGG-GTGTCTTCA
219132 AACTTCAGTC
Statistics
Matches: 251, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
152 26 0.10
153 225 0.90
ACGTcount: A:0.30, C:0.16, G:0.33, T:0.21
Consensus pattern (153 bp):
AGGGGTGTCTTAAGACATGTTCCAGTGGGAAGAGGGTATCGAACAAGCATATGGGGTGTCTTCAG
ACATGTTCCGGTGGGAAGAGGAAACCGAACAAGCAGAATGGGTGTCTTCAGACATGTTCCGGTAG
GAAGAGGATATCAAACAAGCAGA
Found at i:219746 original size:20 final size:21
Alignment explanation
Indices: 219695--219750 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
219685 ATATATATTT
219695 GAATAATAAACTATTCCATTG
1 GAATAATAAACTATTCCATTG
*
219716 GAATAAAAAACTATTCCATTG
1 GAATAATAAACTATTCCATTG
219737 G-ATAATAAACTATT
1 GAATAATAAACTATT
219751 GCTGATTGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 12 0.36
21 21 0.64
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.32
Consensus pattern (21 bp):
GAATAATAAACTATTCCATTG
Found at i:223753 original size:21 final size:21
Alignment explanation
Indices: 223711--223753 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
223701 TTTATGGGCT
*
223711 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
223732 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
223753 A
1 A
223754 ATGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:224474 original size:103 final size:103
Alignment explanation
Indices: 224290--224816 Score: 964
Period size: 103 Copynumber: 5.1 Consensus size: 103
224280 GTAGAGGGTC
224290 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
224355 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
224393 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
224458 TTGATCATTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
224496 TATGTGATCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
224561 TTGATCCTTGACATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
** *
224599 TATGTGGTCCTTCTAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
224664 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
224702 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
224767 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
224805 TATGTGGTCCTT
1 TATGTGGTCCTT
224817 ATGAACATTA
Statistics
Matches: 405, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 405 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:224866 original size:23 final size:23
Alignment explanation
Indices: 224833--224895 Score: 101
Period size: 23 Copynumber: 2.7 Consensus size: 23
224823 ATTATTATAT
224833 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
224856 GGCACTCCGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
224879 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
224896 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.29, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:230981 original size:21 final size:21
Alignment explanation
Indices: 230939--230981 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
230929 TTTCTGGGCT
*
230939 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
230960 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
230981 A
1 A
230982 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:231034 original size:20 final size:20
Alignment explanation
Indices: 231009--231046 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
230999 GAACGCTAGA
*
231009 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
231029 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
231047 TAAAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:232059 original size:103 final size:103
Alignment explanation
Indices: 231525--232051 Score: 973
Period size: 103 Copynumber: 5.1 Consensus size: 103
231515 GTAGAGGGTC
231525 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
231590 TTGATCCCTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
231628 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
231693 TTGATCCTTGGCATATGTATATGATTCTTAAGGAAAGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
231731 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATGC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
231796 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
231834 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
231899 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
231937 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
232002 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
232040 TATGTGGTCCTT
1 TATGTGGTCCTT
232052 ATGGACATTA
Statistics
Matches: 408, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 408 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:232101 original size:23 final size:23
Alignment explanation
Indices: 232070--232130 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
232060 TATTATATGG
232070 CACTACGGTGCAATTCTACGCGA
1 CACTACGGTGCAATTCTACGCGA
* * *
232093 CACTCCGGTGCAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCGA
232116 CACTTA-GGTGCAATT
1 CAC-TACGGTGCAATT
232131 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGA
Found at i:233071 original size:22 final size:23
Alignment explanation
Indices: 233045--233096 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 23
233035 AATGAAAGTG
233045 TTTTTCTAAGTTAAAGATTATTT
1 TTTTTCTAAGTTAAAGATTATTT
*
233068 TTTTCTCATAAGTTAGAGATTATTT
1 TTTT-TC-TAAGTTAAAGATTATTT
233093 TTTT
1 TTTT
233097 CTCATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 4 0.15
24 2 0.08
25 20 0.77
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.58
Consensus pattern (23 bp):
TTTTTCTAAGTTAAAGATTATTT
Found at i:233082 original size:25 final size:25
Alignment explanation
Indices: 233051--233103 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
233041 AGTGTTTTTC
233051 TAAGTTAAAGATTATTTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
*
233076 TAAGTTAGAGATTATTTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
233101 TAA
1 TAA
233104 TAAATTAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (25 bp):
TAAGTTAAAGATTATTTTTTTCTCA
Found at i:239857 original size:24 final size:24
Alignment explanation
Indices: 239728--239850 Score: 151
Period size: 24 Copynumber: 5.1 Consensus size: 24
239718 TCTGATTTTC
*
239728 GACATGAATTCTGATCTGATACTT
1 GACATGGATTCTGATCTGATACTT
239752 GACATGGATTCTGATCTGATA-TCT
1 GACATGGATTCTGATCTGATACT-T
* *
239776 AACATGGATTCTGATATGATACTT
1 GACATGGATTCTGATCTGATACTT
* *
239800 GACTTGGATTCTGATCTGTTACTT
1 GACATGGATTCTGATCTGATACTT
* *
239824 GACCT-GATTTCTGATATGATACTT
1 GACATGGA-TTCTGATCTGATACTT
239848 GAC
1 GAC
239851 CTGATTTATG
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.03
24 82 0.95
25 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (24 bp):
GACATGGATTCTGATCTGATACTT
Found at i:239873 original size:24 final size:24
Alignment explanation
Indices: 239787--239860 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
239777 ACATGGATTC
* *
239787 TGATATGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
239811 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
239835 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
239859 TG
1 TG
239861 TTTTGATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:250807 original size:17 final size:19
Alignment explanation
Indices: 250785--250824 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
250775 AACACGTAAA
*
250785 AAAAATAAA-ATAAT-AAT
1 AAAAATAAACAAAATGAAT
250802 AAAAATAAACAAAATGAAT
1 AAAAATAAACAAAATGAAT
250821 AAAA
1 AAAA
250825 TGTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 4 0.20
19 7 0.35
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (19 bp):
AAAAATAAACAAAATGAAT
Found at i:250810 original size:26 final size:27
Alignment explanation
Indices: 250738--250816 Score: 74
Period size: 26 Copynumber: 2.9 Consensus size: 27
250728 CAAACGTGAG
* *
250738 AATAATAAATAAAACA-AGAAAAAATGA
1 AATAAT-AATAAAACATAAAAAAAATAA
*
250765 AA-AATAACAAAACACGTAAAAAAAATAA
1 AATAATAATAAAACA--TAAAAAAAATAA
*
250793 AATAATAATAAAA-ATAAACAAAAT
1 AATAATAATAAAACATAAAAAAAAT
250817 GAATAAAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
25 8 0.19
26 12 0.28
27 2 0.05
28 12 0.28
29 9 0.21
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (27 bp):
AATAATAATAAAACATAAAAAAAATAA
Found at i:251006 original size:11 final size:10
Alignment explanation
Indices: 250988--251018 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
250978 CATGATATTA
250988 AGAAAAAAAT
1 AGAAAAAAAT
250998 AGAAAAAAAT
1 AGAAAAAAAT
251008 AGAAAAAAAT
1 AGAAAAAAAT
251018 A
1 A
251019 AATAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AGAAAAAAAT
Found at i:251103 original size:43 final size:40
Alignment explanation
Indices: 251024--251127 Score: 109
Period size: 43 Copynumber: 2.5 Consensus size: 40
251014 AAATAAATAA
*
251024 ATTAAAAATATAATATATATAAATAAAAACAAAAATAGAAT
1 ATTAAGAATAT-ATATATATAAATAAAAACAAAAATAGAAT
* * *
251065 ATTAAGAATATATATATATATATATAAACGTATAAAATATAAT
1 ATTAAGAATATATATATATAAATAAAAAC--A-AAAATAGAAT
* * *
251108 ATTATGAAAAAATATATATA
1 ATTAAGAATATATATATATA
251128 CATAGCAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 16 0.30
41 10 0.19
42 1 0.02
43 26 0.49
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (40 bp):
ATTAAGAATATATATATATAAATAAAAACAAAAATAGAAT
Found at i:251213 original size:13 final size:13
Alignment explanation
Indices: 251195--251221 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
251185 GATATAAGAT
251195 ATATATAATAAAA
1 ATATATAATAAAA
251208 ATATATAATAAAA
1 ATATATAATAAAA
251221 A
1 A
251222 AAAAGAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATATATAATAAAA
Found at i:251255 original size:21 final size:20
Alignment explanation
Indices: 251201--251263 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
251191 AGATATATAT
251201 AATAAAAATATATAATAAAA
1 AATAAAAATATATAATAAAA
*
251221 AA-AAAGAGGA-ATATAGTAAATA
1 AATAAA-A--ATATATAATAAA-A
251243 AATAAAAATATATAATTAAAA
1 AATAAAAATATATAA-TAAAA
251264 TATATATAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 15 0.44
22 9 0.26
23 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (20 bp):
AATAAAAATATATAATAAAA
Found at i:251264 original size:19 final size:19
Alignment explanation
Indices: 251201--251265 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 19
251191 AGATATATAT
*
251201 AATAAAAATATATAATAAAA
1 AATAAAAATATATAAT-TAA
* *
251221 AAAAAGAGGAATATAGTAAAT-A
1 AATAA-A--AATATA-TAATTAA
251243 AATAAAAATATATAATTAA
1 AATAAAAATATATAATTAA
251262 AATA
1 AATA
251266 TATATAGGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
18 4 0.11
19 11 0.31
20 4 0.11
21 2 0.06
22 5 0.14
23 6 0.17
24 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (19 bp):
AATAAAAATATATAATTAA
Found at i:252815 original size:110 final size:108
Alignment explanation
Indices: 252589--252855 Score: 307
Period size: 110 Copynumber: 2.5 Consensus size: 108
252579 AGTATTGTTC
* * *
252589 CGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTG--GAACTGGGAAATTATTTGTTG
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGACTCTGAAGAACTGGAAAATTATTTGTTG
* *
252651 ACAGTCAGCCGCCCATTCGCTGTGAAGTTGAGCTTGTGTTATCT
65 ACAATCAGCCACCCATTCGCTGTGAAGTTGAGCTTGTGTTATCT
* * *
252695 CGAGTTCAATATTCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAGACT-GAAAAGTTGTTTGT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAA-GA-ACTGGAAAA-TTATTTGT
* * * *
252759 TGACAATCAGTCACCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCT
63 TGACAATCAGCCACCCATTCGCTGTGAAGTTGAGCTTGTGTTATCT
*
252805 TGAGTCCAATATCCCTT-GCTGTGAAGTTGAAATT-AGCTCTG-A-AACTGGAAA
1 CGAGTCCAATAT-CCTTCGCTGTGAAGTTGAAATTGA-CTCTGAAGAACTGGAAA
252856 GCCCCTTCGC
Statistics
Matches: 137, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
106 38 0.28
107 6 0.04
109 8 0.06
110 82 0.60
111 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (108 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAGAACTGGAAAATTATTTGTTGA
CAATCAGCCACCCATTCGCTGTGAAGTTGAGCTTGTGTTATCT
Found at i:253729 original size:65 final size:67
Alignment explanation
Indices: 253589--253734 Score: 190
Period size: 65 Copynumber: 2.2 Consensus size: 67
253579 CTAAAGGGAA
** *
253589 ACAAAATTTTGTTTTAAGGGAAATAAATTTGAATATTTTGTGTTTCAAGAGAAACTGTCTCAATG
1 ACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAATG
253654 GAG
65 GAG
* * *
253657 ACAAAATTTGTTTTAGGGGAAATAAATTCAAAGA-TTT-TGTTTCGAGGGAAACTGTCTCAA-GA
1 ACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAATG-
253719 GAG
65 GAG
*
253722 ACGAAATTTGTTT
1 ACAAAATTTGTTT
253735 CAAGAGAGAC
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 1 0.01
65 36 0.51
66 3 0.04
67 24 0.34
68 6 0.09
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (67 bp):
ACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAATGG
AG
Found at i:253860 original size:36 final size:36
Alignment explanation
Indices: 253813--254003 Score: 186
Period size: 36 Copynumber: 5.5 Consensus size: 36
253803 ATATTCAAAT
253813 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* **
253849 AATTTGTTTCAAGGGAAACTGCCTCAAGAGAGATGA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * *
253885 AATTTATTTCAAGGGAAA-TGTTTTC-A-A-TG----
1 AATTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAA
* * *
253914 -TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
1 AATT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
253950 AATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
1 AA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
253987 AA-TTCTTTCAAGGGAAA
1 AATTTGTTTCAAGGGAAA
254004 TGTTTTCAAT
Statistics
Matches: 125, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
28 2 0.02
29 15 0.12
30 3 0.02
32 1 0.01
33 1 0.01
34 1 0.01
35 17 0.14
36 52 0.42
37 31 0.25
38 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:253885 original size:101 final size:102
Alignment explanation
Indices: 253734--254036 Score: 299
Period size: 101 Copynumber: 3.0 Consensus size: 102
253724 GAAATTTGTT
* * ** * * * *
253734 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGACTAAAGGGAGATGAAATTTGTTTCAAATA
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGACTCAAGAGAGATGAAATTTATTTCAAAGA
*
253799 AAACATATTCAAATAATT-TGTTTCAAGGGAAACTGTC
66 AAACATATTC-AATAATTATGTTTCAAGAGAAACTGTC
* * *
253836 TCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGCCTCAAGAGAGATGAAATTTATTTCAAGGG
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGACTCAAGAGAGATGAAATTTATTTCAAAGA
** * **
253900 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTC
66 AAACATATTCAATAATTATGTTTCAAGAGAAACTGTC
* * * * * *
253937 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACT-ATCTCAAGAGAGA-CAAAATTCTTTCAAGG
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGA-CTCAAGAGAGATGAAATTTATTTCAAAG
* ** * **
254000 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGT
65 AAAACATATTCAATAATTATGTTTCAAGAGAAACTGT
254037 GCGAGATAAA
Statistics
Matches: 176, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
100 5 0.03
101 127 0.72
102 44 0.25
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (102 bp):
TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGACTCAAGAGAGATGAAATTTATTTCAAAGA
AAACATATTCAATAATTATGTTTCAAGAGAAACTGTC
Found at i:253969 original size:37 final size:35
Alignment explanation
Indices: 253918--254003 Score: 118
Period size: 37 Copynumber: 2.4 Consensus size: 35
253908 TCAATGTTTA
* * *
253918 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA--T
253955 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
*
253990 TCTTTCAAGGGAAA
1 TGTTTCAAGGGAAA
254004 TGTTTTCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 14 0.31
37 31 0.69
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
Found at i:255736 original size:26 final size:25
Alignment explanation
Indices: 255694--255753 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
255684 TTTTTCTTCA
* *
255694 ATTTTC-CTTTGTTTTTTCTCTTTTT
1 ATTTTCTCTTTGCTTTTTCTC-TCTT
*
255719 ATTTTCTCTTTGCTTTTTTTCTCTT
1 ATTTTCTCTTTGCTTTTTCTCTCTT
255744 -TTTTCTCTTT
1 ATTTTCTCTTT
255754 TTGTTCTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.32
25 9 0.29
26 12 0.39
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (25 bp):
ATTTTCTCTTTGCTTTTTCTCTCTT
Found at i:255738 original size:15 final size:13
Alignment explanation
Indices: 255695--255747 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
255685 TTTTCTTCAA
*
255695 TTTTC-CTTTGTT
1 TTTTCTCTTTTTT
*
255707 TTTTCTCTTTTTA
1 TTTTCTCTTTTTT
255720 TTTTCTCTTTGCTTT
1 TTTTCTCTTT--TTT
255735 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
255748 CTCTTTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 5 0.14
13 18 0.51
15 12 0.34
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:255742 original size:28 final size:25
Alignment explanation
Indices: 255694--255746 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 25
255684 TTTTTCTTCA
255694 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
255719 ATTTTCTCTTTGCTTTTTTTCTCTTTTT
1 ATTTTC-CTTTG--TTTTTTCTCTTTTT
255747 TCTCTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
28 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:256987 original size:7 final size:7
Alignment explanation
Indices: 256975--257007 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
256965 TGAAATGTAG
256975 ATGCAAA
1 ATGCAAA
256982 ATGCAAA
1 ATGCAAA
256989 ATGCAAA
1 ATGCAAA
256996 ATGCAAA
1 ATGCAAA
257003 ATGCA
1 ATGCA
257008 TGAAATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGCAAA
Found at i:258831 original size:25 final size:25
Alignment explanation
Indices: 258773--258837 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
258763 GTAAACATGA
258773 GAATAATAAATAAAACAAGAAAAAAT
1 GAATAAT-AATAAAACAAGAAAAAAT
*
258799 GGAA-AATAATAAAACACGTAAAAAAT
1 -GAATAATAATAAAACAAG-AAAAAAT
*
258825 -AATAATAAAAAAA
1 GAATAATAATAAAA
258838 TAAAAATAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.06
25 19 0.56
26 10 0.29
27 3 0.09
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (25 bp):
GAATAATAATAAAACAAGAAAAAAT
Found at i:258837 original size:14 final size:14
Alignment explanation
Indices: 258818--258858 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
258808 TAAAACACGT
258818 AAAAAATAATAATA
1 AAAAAATAATAATA
*
258832 AAAAAATAAAAATA
1 AAAAAATAATAATA
*
258846 ACAAAATGAATAA
1 AAAAAAT-AATAA
258859 AATGTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (14 bp):
AAAAAATAATAATA
Found at i:259088 original size:28 final size:29
Alignment explanation
Indices: 259040--259106 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
259030 ATATTAAGAA
**
259040 AAAAATAGAA-A-A-AAATAAAATAAAGT
1 AAAAATAGAATATATAAATAAAATAAAAC
*
259066 AAAAATATAATATATAAAT-AAATAAAAC
1 AAAAATAGAATATATAAATAAAATAAAAC
259094 AAAAATAGAATAT
1 AAAAATAGAATAT
259107 TAAGAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 9 0.26
27 1 0.03
28 20 0.59
29 4 0.12
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (29 bp):
AAAAATAGAATATATAAATAAAATAAAAC
Found at i:259117 original size:39 final size:38
Alignment explanation
Indices: 259074--259157 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 38
259064 GTAAAAATAT
259074 AATATATAAATAAATAAAACA-AAAATAGAATATTAAGAA
1 AATATAT-AATAAA-AAAACATAAAATAGAATATTAAGAA
*** *
259113 AATATAT-ATAAAAACGTATAAAATATAATATTAAGAA
1 AATATATAATAAAAAAACATAAAATAGAATATTAAGAA
259150 AATATATA
1 AATATATA
259158 TACATAGCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
36 3 0.08
37 29 0.74
39 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.27
Consensus pattern (38 bp):
AATATATAATAAAAAAACATAAAATAGAATATTAAGAA
Found at i:259153 original size:16 final size:16
Alignment explanation
Indices: 259095--259155 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
259085 AAATAAAACA
*
259095 AAAATAGAATATTAAG
1 AAAATATAATATTAAG
**
259111 AAAATATATATAAAAACG
1 AAAATATA-ATATTAA-G
259129 TATAAAATATAATATTAAG
1 ---AAAATATAATATTAAG
259148 AAAATATA
1 AAAATATA
259156 TATACATAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
16 15 0.43
17 5 0.14
18 1 0.03
19 1 0.03
20 5 0.14
21 8 0.23
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.28
Consensus pattern (16 bp):
AAAATATAATATTAAG
Found at i:259200 original size:6 final size:6
Alignment explanation
Indices: 259189--259222 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
259179 TTAATACATC
* *
259189 TATACA TATACA TATACA TATATA TATATA TATA
1 TATACA TATACA TATACA TATACA TATACA TATA
259223 ATAAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (6 bp):
TATACA
Found at i:259231 original size:8 final size:8
Alignment explanation
Indices: 259220--259254 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
259210 ATATATATAT
259220 ATAATAAA
1 ATAATAAA
259228 ATAATATAA
1 ATAATA-AA
259237 TATAATAAA
1 -ATAATAAA
259246 ATAATAAA
1 ATAATAAA
259254 A
1 A
259255 AATGAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.60
9 4 0.16
10 6 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
ATAATAAA
Found at i:259236 original size:13 final size:13
Alignment explanation
Indices: 259218--259299 Score: 62
Period size: 13 Copynumber: 6.4 Consensus size: 13
259208 ATATATATAT
259218 ATATAATAAAATA
1 ATATAATAAAATA
*
259231 ATATAATATAATA
1 ATATAATAAAATA
*
259244 AAATAATAAAA-A
1 ATATAATAAAATA
* * *
259256 AT-GAATATAGTA
1 ATATAATAAAATA
*
259268 A-ATAAATAAAAAA
1 ATAT-AATAAAATA
*
259281 ATATAATTAAATA
1 ATATAATAAAATA
259294 TATATA
1 -ATATA
259300 TATATATATG
Statistics
Matches: 51, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
11 5 0.10
12 4 0.08
13 35 0.69
14 7 0.14
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (13 bp):
ATATAATAAAATA
Found at i:259302 original size:18 final size:18
Alignment explanation
Indices: 259194--259307 Score: 57
Period size: 18 Copynumber: 6.6 Consensus size: 18
259184 ACATCTATAC
* * *
259194 ATATACATATACATATAT
1 ATATATATATAAATAAAT
259212 ATATATATAT-AATAAA-
1 ATATATATATAAATAAAT
259228 ATA-ATATAATATAATAAA-
1 ATATATAT-ATA-AATAAAT
* *
259246 ATA-ATA-AAAAATGAAT
1 ATATATATATAAATAAAT
*
259262 ATAGTA-A-ATAAATAAAA
1 ATA-TATATATAAATAAAT
* *
259279 AAATATA-ATTAAATATAT
1 ATATATATA-TAAATAAAT
259297 ATATATATATA
1 ATATATATATA
259308 TGAGAAGAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 18
0.71 0.11 0.17
Matches are distributed among these distances:
15 9 0.12
16 12 0.16
17 16 0.21
18 37 0.49
19 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
ATATATATATAAATAAAT
Found at i:261344 original size:16 final size:17
Alignment explanation
Indices: 261323--261357 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
261313 TTACTATTCA
261323 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
261339 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
261356 CG
1 CG
261358 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Done.