Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008520.1 Hibiscus syriacus cultivar Beakdansim tig00111387_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: 519447
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:140379 original size:30 final size:30
Alignment explanation
Indices: 140345--140422 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
140335 ATAAGCTATA
140345 TGATACGATCT-ATATGATTACATGCACATG
1 TGATA-GATCTGATATGATTACATGCACATG
* *
140375 TGATATATGTGATATGATTACATGCACATG
1 TGATAGATCTGATATGATTACATGCACATG
* *
140405 TGATATATGTGATATGAT
1 TGATAGATCTGATATGAT
140423 ATAAACCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 3 0.07
30 42 0.93
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.37
Consensus pattern (30 bp):
TGATAGATCTGATATGATTACATGCACATG
Found at i:140498 original size:33 final size:33
Alignment explanation
Indices: 140456--140520 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
140446 TATGAAGATG
140456 GATCTATGAGATCATACAAGAATGTTACACAAT
1 GATCTATGAGATCATACAAGAATGTTACACAAT
*
140489 GATCTATGAGATCATACAAGAATGTTATACAA
1 GATCTATGAGATCATACAAGAATGTTACACAA
140521 GCTACATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (33 bp):
GATCTATGAGATCATACAAGAATGTTACACAAT
Found at i:143468 original size:18 final size:18
Alignment explanation
Indices: 143445--143479 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
143435 ATATAGGTCT
*
143445 TATTATATATGTGTTGCC
1 TATTATATATCTGTTGCC
143463 TATTATATATCTGTTGC
1 TATTATATATCTGTTGC
143480 ACTGTTCCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.51
Consensus pattern (18 bp):
TATTATATATCTGTTGCC
Found at i:153777 original size:24 final size:24
Alignment explanation
Indices: 153750--153796 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
153740 GTTAGAAGGT
153750 CTTTACACC-GAATATGTTGCAAGC
1 CTTTACACCTGAAT-TGTTGCAAGC
* *
153774 CTTTTCACCTGAATTGTTTCAAG
1 CTTTACACCTGAATTGTTGCAAG
153797 TCGTCGGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (24 bp):
CTTTACACCTGAATTGTTGCAAGC
Found at i:163965 original size:29 final size:29
Alignment explanation
Indices: 163918--163979 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
163908 TGTTAGATGG
* *
163918 CGAACTTGAACTTACAAAATTTCAGGGGA
1 CGAACTTAAACTTACAAAATTTCAAGGGA
* * *
163947 CGAACTTAAATTTATAAAATTTTAAGGGA
1 CGAACTTAAACTTACAAAATTTCAAGGGA
163976 CGAA
1 CGAA
163980 AACAAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (29 bp):
CGAACTTAAACTTACAAAATTTCAAGGGA
Found at i:173439 original size:24 final size:24
Alignment explanation
Indices: 173412--173462 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
173402 GCAATTTGGT
173412 TTGGTATTTTCTAACAAATCTAAC
1 TTGGTATTTTCTAACAAATCTAAC
173436 TTGGTATTTTCTAACAAATCTAAC
1 TTGGTATTTTCTAACAAATCTAAC
173460 TTG
1 TTG
173463 AGGCTCTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (24 bp):
TTGGTATTTTCTAACAAATCTAAC
Found at i:176960 original size:20 final size:20
Alignment explanation
Indices: 176935--176972 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
176925 GAACGCTAGA
176935 GGGGAATCGATACCCCCAGG
1 GGGGAATCGATACCCCCAGG
* *
176955 GGGGAATTGATTCCCCCA
1 GGGGAATCGATACCCCCA
176973 TAATAGAAAA
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:0.29, G:0.32, T:0.16
Consensus pattern (20 bp):
GGGGAATCGATACCCCCAGG
Found at i:177634 original size:103 final size:103
Alignment explanation
Indices: 177455--177775 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
177445 GTAGAGGGTC
*
177455 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
177520 TTTATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
177558 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
177623 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
* *
177661 TACGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGGAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
177726 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
177764 TATGTGGTCCTT
1 TATGTGGTCCTT
177776 ATGGACATTA
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:177825 original size:23 final size:23
Alignment explanation
Indices: 177792--177854 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
177782 ATTATTATAT
*
177792 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
177815 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
177838 GGCACTTAGGTGCAATT
1 GGCACTTCGGTGCAATT
177855 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:183932 original size:21 final size:21
Alignment explanation
Indices: 183890--183932 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
183880 TTTCTGGGCT
* *
183890 AGGGGAATCGATACCCATTCA
1 AGGGAAATCGATACCCACTCA
*
183911 AGGGAAATCGATACCCCCTCA
1 AGGGAAATCGATACCCACTCA
183932 A
1 A
183933 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (21 bp):
AGGGAAATCGATACCCACTCA
Found at i:184800 original size:103 final size:103
Alignment explanation
Indices: 184472--184792 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
184462 GTAGAGGGTC
* *
184472 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
184537 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
* *
184575 TATGTGGCCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
184640 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
184678 TACGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
184743 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
184781 TATGTGGTCCTT
1 TATGTGGTCCTT
184793 ATGGACATTA
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:184858 original size:23 final size:23
Alignment explanation
Indices: 184808--184871 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
184798 CATTATTATA
184808 TGGCACTACGGTGCAATTCTAAC
1 TGGCACTACGGTGCAATTCTAAC
* *
184831 CGGCACTCCGGTGCAATTCT-AC
1 TGGCACTACGGTGCAATTCTAAC
184853 GTGGCACTTA-GGTGCAATT
1 -TGGCAC-TACGGTGCAATT
184872 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 2 0.06
23 32 0.91
24 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTAAC
Found at i:190192 original size:12 final size:12
Alignment explanation
Indices: 190175--190203 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
190165 ATTTTCTTCA
190175 TTCTTCTTGTCC
1 TTCTTCTTGTCC
190187 TTCTTCTTGTCC
1 TTCTTCTTGTCC
190199 TTCTT
1 TTCTT
190204 TTCTTCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.31, G:0.07, T:0.62
Consensus pattern (12 bp):
TTCTTCTTGTCC
Found at i:192744 original size:23 final size:23
Alignment explanation
Indices: 192644--192741 Score: 65
Period size: 25 Copynumber: 4.0 Consensus size: 23
192634 ATATAAATAC
* * *
192644 TTAACTTAAATTTATAATATTTT
1 TTAAATTAACTTTAAAATATTTT
192667 TTATATATTAACTTTAAAA-ATATTT
1 TTA-A-ATTAACTTTAAAATAT-TTT
* *
192692 TTATATTAACTTATTAAATATTTCATT
1 TTAAATTAACTT-TAAAATA-TT--TT
192719 ATTAAATTAA-TTTAAAATATTTT
1 -TTAAATTAACTTTAAAATATTTT
192742 ATTTATTATT
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
23 13 0.22
24 7 0.12
25 20 0.34
26 7 0.12
27 4 0.07
28 8 0.14
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAAATTAACTTTAAAATATTTT
Found at i:192895 original size:57 final size:60
Alignment explanation
Indices: 192782--192925 Score: 156
Period size: 57 Copynumber: 2.4 Consensus size: 60
192772 TAAAATATTT
* *
192782 TAAAGTTAAGATAAAAATAAATATATTTAATAATCTAAATTAATAATACAATATATTTAG
1 TAAAGTTAAGATAAAAATAAATATATTTAAAAATCTAAATTAATAATAAAATATATTTAG
* *
192842 TAAA-TTAAGAT-AAAATATATA-ATTTGAAAAAT-TATAA-TAATAATAAAATATATTT-T
1 TAAAGTTAAGATAAAAATAAATATATTT-AAAAATCTA-AATTAATAATAAAATATATTTAG
* *
192898 TAAAAGTTTAGATAAGAATAAAATATAT
1 T-AAAGTTAAGATAAAAAT-AAATATAT
192926 ATTTTTAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
56 1 0.01
57 26 0.37
58 22 0.31
59 11 0.16
60 8 0.11
61 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (60 bp):
TAAAGTTAAGATAAAAATAAATATATTTAAAAATCTAAATTAATAATAAAATATATTTAG
Found at i:192931 original size:33 final size:33
Alignment explanation
Indices: 192847--192934 Score: 103
Period size: 31 Copynumber: 2.8 Consensus size: 33
192837 TTTAGTAAAT
* *
192847 TAAG-ATAAAATATATAATTTGAAAAATTATAA
1 TAAGAATAAAATATATATTTTTAAAAATTATAA
* *
192879 TAATAAT-AAA-ATATATTTTTAAAAGTT-TAGA
1 TAAGAATAAAATATATATTTTTAAAAATTATA-A
192910 TAAGAATAAAATATATATTTTTAAA
1 TAAGAATAAAATATATATTTTTAAA
192935 TTAAAATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
30 2 0.04
31 21 0.45
32 9 0.19
33 15 0.32
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (33 bp):
TAAGAATAAAATATATATTTTTAAAAATTATAA
Found at i:192957 original size:17 final size:16
Alignment explanation
Indices: 192935--192982 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
192925 TATTTTTAAA
192935 TTAAAATAAAAAATATT
1 TTAAAATAAAAAATA-T
192952 TTAAAATAAAAAA-AT
1 TTAAAATAAAAAATAT
*
192967 TTAAATTAAATAAATA
1 TTAAAATAAA-AAATA
192983 ATAAATGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 10 0.36
16 4 0.14
17 14 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAAATAAAAAATAT
Found at i:192958 original size:23 final size:25
Alignment explanation
Indices: 192909--192963 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
192899 AAAAGTTTAG
* *
192909 ATAAGAATAAAATATATATTTTTAA
1 ATAAAAATAAAATATATATTTTAAA
*
192934 ATTAAAATAAAA-A-ATATTTTAAA
1 ATAAAAATAAAATATATATTTTAAA
192957 ATAAAAA
1 ATAAAAA
192964 AATTTAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 15 0.58
24 1 0.04
25 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
ATAAAAATAAAATATATATTTTAAA
Found at i:192969 original size:15 final size:15
Alignment explanation
Indices: 192935--192981 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
192925 TATTTTTAAA
192935 TTAAAATAAAAAATATT
1 TTAAAATAAAAAA-A-T
192952 TTAAAATAAAAAAAT
1 TTAAAATAAAAAAAT
* *
192967 TTAAATTAAATAAAT
1 TTAAAATAAAAAAAT
192982 AATAAATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.50
16 1 0.04
17 13 0.46
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAAATAAAAAAAT
Found at i:193550 original size:57 final size:58
Alignment explanation
Indices: 193460--193569 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 58
193450 TTCTCTTAGT
* * *
193460 TTCTAAAGAATAAAAAAAAAACAATCTGAAAGTATGACGGTCAAGACTCAATTATCGG
1 TTCTAAAGAATAAAAAAAAAACAATCTAAAAGTATGAAGATCAAGACTCAATTATCGG
* * * *
193518 TTCTAAAGAAT-CAAAAAATACAATTTAAAAGTATGAAGATTAAGACTCAATT
1 TTCTAAAGAATAAAAAAAAAACAATCTAAAAGTATGAAGATCAAGACTCAATT
193570 CTCACGATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 34 0.76
58 11 0.24
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (58 bp):
TTCTAAAGAATAAAAAAAAAACAATCTAAAAGTATGAAGATCAAGACTCAATTATCGG
Found at i:193673 original size:13 final size:12
Alignment explanation
Indices: 193654--193689 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
193644 TTAATATTGT
193654 AAAAAGAAAATA
1 AAAAAGAAAATA
193666 ATAAAAGAAAATA
1 A-AAAAGAAAATA
193679 AAGAAAGAAAA
1 AA-AAAGAAAA
193690 ACAGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 20 0.91
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATA
Found at i:195819 original size:52 final size:52
Alignment explanation
Indices: 195741--195843 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
195731 TTATAATATT
195741 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
195793 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
195844 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:200413 original size:52 final size:52
Alignment explanation
Indices: 200335--200437 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
200325 TTATAATATT
*
200335 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGAAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
* *
200387 CTTGTAATTAGTTGAAATCCTCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGAAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
200438 TGTCCAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGAAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:204217 original size:29 final size:29
Alignment explanation
Indices: 204174--204285 Score: 188
Period size: 29 Copynumber: 3.8 Consensus size: 29
204164 CTCACCTAAC
204174 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
204204 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
204233 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
204262 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
204286 ATTTAGTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 75 0.95
30 4 0.05
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:209013 original size:29 final size:29
Alignment explanation
Indices: 208970--209081 Score: 188
Period size: 29 Copynumber: 3.8 Consensus size: 29
208960 CTCACCTAAC
208970 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
209000 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
209029 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
209058 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
209082 ATTTAGTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 75 0.95
30 4 0.05
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:211463 original size:33 final size:33
Alignment explanation
Indices: 211408--211488 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
211398 TTGAAATTAG
*
211408 TCACTACCG-TTTATTAAAATAATCATTTTGAC
1 TCACTATCGTTTTATTAAAATAATCATTTTGAC
*
211440 TCACTATCGTTTTATTAATATAATCATTTTGAC
1 TCACTATCGTTTTATTAAAATAATCATTTTGAC
211473 TCACTATCGTTTTATT
1 TCACTATCGTTTTATT
211489 TTAGAACAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 8 0.17
33 38 0.83
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (33 bp):
TCACTATCGTTTTATTAAAATAATCATTTTGAC
Found at i:212141 original size:16 final size:16
Alignment explanation
Indices: 212120--212174 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
212110 CTTAAACTTA
*
212120 AAAAAAACACAAACTC
1 AAAAAAACTCAAACTC
*
212136 AAAAAAATTCAAACTC
1 AAAAAAACTCAAACTC
*
212152 AAAAAAACTCAAATTC
1 AAAAAAACTCAAACTC
212168 AAAAAAA
1 AAAAAAA
212175 ATTCAAGAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.69, C:0.18, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAACTCAAACTC
Found at i:213934 original size:7 final size:7
Alignment explanation
Indices: 213918--213947 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
213908 CATAATTGGA
213918 TTTAGGG
1 TTTAGGG
*
213925 TTTAGAG
1 TTTAGGG
213932 TTTAGGG
1 TTTAGGG
213939 TTTAGGG
1 TTTAGGG
213946 TT
1 TT
213948 CATTACAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:217659 original size:24 final size:24
Alignment explanation
Indices: 217632--217689 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
217622 TAGTTAATGC
* *
217632 ATCGATGCACATATTACTGAGTGT
1 ATCGATGCACATACTACAGAGTGT
217656 ATCGATGCACATACTACAGAGTGT
1 ATCGATGCACATACTACAGAGTGT
*
217680 ACCGATGCAC
1 ATCGATGCAC
217690 TTCAAAGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (24 bp):
ATCGATGCACATACTACAGAGTGT
Found at i:218790 original size:2 final size:2
Alignment explanation
Indices: 218783--218815 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
218773 TAGGAATTTG
218783 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
218816 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:227399 original size:31 final size:31
Alignment explanation
Indices: 227364--227426 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
227354 CAGGTCAATA
*
227364 TGGGTCAAGTCAAGACCGGATCAGTTGATTT
1 TGGGTCAAGTCAAGACCAGATCAGTTGATTT
* * * *
227395 TGGGTCAGGTTAATACCAGATCGGTTGATTT
1 TGGGTCAAGTCAAGACCAGATCAGTTGATTT
227426 T
1 T
227427 CGGTTAGGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (31 bp):
TGGGTCAAGTCAAGACCAGATCAGTTGATTT
Found at i:227875 original size:18 final size:19
Alignment explanation
Indices: 227839--227877 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
227829 AAGTAAACTT
*
227839 TATATTATTTTTATTATAAA
1 TATAATATTTTTA-TATAAA
227859 TATAATATTTTTA-ATAAA
1 TATAATATTTTTATATAAA
227877 T
1 T
227878 TATCAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATAATATTTTTATATAAA
Found at i:228056 original size:16 final size:16
Alignment explanation
Indices: 227952--228118 Score: 88
Period size: 16 Copynumber: 10.6 Consensus size: 16
227942 ATTTCAATAT
* *
227952 GTTCAGGTTGCTTTTG
1 GTTCGGGTTGCTTTCG
* ***
227968 GGTCGGGTTAAATTCG
1 GTTCGGGTTGCTTTCG
*
227984 GTTCGGGTTACTTTCG
1 GTTCGGGTTGCTTTCG
* * ***
228000 GATCGAGTTAAAATTCG
1 GTTCGGGTT-GCTTTCG
* *
228017 GTT-GAGTTTCTTTCG
1 GTTCGGGTTGCTTTCG
* * *
228032 GTTCAGGTTGTTTTTG
1 GTTCGGGTTGCTTTCG
** *
228048 GTTCGGGTTAATTTCA
1 GTTCGGGTTGCTTTCG
*
228064 GTTTGGGTTGCTTTCG
1 GTTCGGGTTGCTTTCG
*
228080 GTTCGGGTT--TTTCA
1 GTTCGGGTTGCTTTCG
* *
228094 GTTTGGGTTGCTTTTG
1 GTTCGGGTTGCTTTCG
228110 GTTCGGGTT
1 GTTCGGGTT
228119 AATTTCAGTT
Statistics
Matches: 110, Mismatches: 37, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
14 12 0.11
15 7 0.06
16 84 0.76
17 7 0.06
ACGTcount: A:0.10, C:0.12, G:0.32, T:0.46
Consensus pattern (16 bp):
GTTCGGGTTGCTTTCG
Found at i:228095 original size:30 final size:31
Alignment explanation
Indices: 228037--228129 Score: 143
Period size: 30 Copynumber: 3.0 Consensus size: 31
228027 TTTCGGTTCA
*
228037 GGTTGTTTTTGGTTCGGGTTAATTTCAGTTTG
1 GGTTGCTTTTGGTTCGGGTT-ATTTCAGTTTG
*
228069 GGTTGCTTTCGGTTCGGGTT-TTTCAGTTTG
1 GGTTGCTTTTGGTTCGGGTTATTTCAGTTTG
228099 GGTTGCTTTTGGTTCGGGTTAATTTCAGTTT
1 GGTTGCTTTTGGTTCGGGTT-ATTTCAGTTT
228130 CGATTCGAGT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
30 29 0.52
32 27 0.48
ACGTcount: A:0.08, C:0.10, G:0.31, T:0.52
Consensus pattern (31 bp):
GGTTGCTTTTGGTTCGGGTTATTTCAGTTTG
Found at i:232693 original size:22 final size:23
Alignment explanation
Indices: 232662--232706 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
232652 TCATGGATTA
232662 ATTTAATTAAAA-TTAAAAATAT
1 ATTTAATTAAAATTTAAAAATAT
*
232684 ATTTATTTAAAATTTAAAAATAT
1 ATTTAATTAAAATTTAAAAATAT
232707 TAAATCAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTAATTAAAATTTAAAAATAT
Found at i:236757 original size:123 final size:118
Alignment explanation
Indices: 236537--236773 Score: 420
Period size: 123 Copynumber: 2.0 Consensus size: 118
236527 AACCCAATTT
236537 AATTATATATAAAATAGAGGGGTTGGTGAGGGGAAGAGCGTGAAGATGAAGAGGAAATGGGGGGG
1 AATTATATATAAAATAGAGGGGTTGGTGAGGGGAAGAGCGTGAAGATGAAGAGGAAATGGGGGGG
236602 GTAGGTGGGAGATGTGGCCTTGCTTTGTAGTTGAACTTCAAACCTACCTTTTA
66 GTAGGTGGGAGATGTGGCCTTGCTTTGTAGTTGAACTTCAAACCTACCTTTTA
236655 AATTATATATAAAATAGAGGGGGTTGGTGAGGGGAAGAGCGTGAAGATGAAGATGGGGAAATGGG
1 AATTATATATAAAATAGA-GGGGTTGGTGAGGGGAAGAGCGTGAAGATGAAGA---GGAAATGGG
*
236720 GTGTGGTAGGTGGGAGATGTGGCCTTGCTTTGTAGTTGAACTTCAAACCTACCT
62 G-GGGGTAGGTGGGAGATGTGGCCTTGCTTTGTAGTTGAACTTCAAACCTACCT
236774 ACCCTTTTCT
Statistics
Matches: 113, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
118 18 0.16
119 34 0.30
122 10 0.09
123 51 0.45
ACGTcount: A:0.29, C:0.08, G:0.36, T:0.26
Consensus pattern (118 bp):
AATTATATATAAAATAGAGGGGTTGGTGAGGGGAAGAGCGTGAAGATGAAGAGGAAATGGGGGGG
GTAGGTGGGAGATGTGGCCTTGCTTTGTAGTTGAACTTCAAACCTACCTTTTA
Found at i:237142 original size:2 final size:2
Alignment explanation
Indices: 237135--237176 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
237125 ATAAATACTA
237135 AT AT AT AT AT AT AT -T 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
237176 A
1 A
237177 ATTTTCTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:237234 original size:20 final size:21
Alignment explanation
Indices: 237197--237238 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
237187 TAAGAGTACA
*
237197 ATATAGAAATAATTTAAATTT
1 ATATAGAAATAATATAAATTT
*
237218 ATATA-AAATTATATAAATTT
1 ATATAGAAATAATATAAATTT
237238 A
1 A
237239 AAAACGGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATAGAAATAATATAAATTT
Found at i:238878 original size:55 final size:55
Alignment explanation
Indices: 238818--239274 Score: 641
Period size: 55 Copynumber: 8.3 Consensus size: 55
238808 ATTTCGTGGT
* *
238818 TGCACAC-ATAGTGCATGTATGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
1 TGCACACGA-AGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* * * *
238873 TGCACACGAAGTGCCTATACAGTGATTTATCCACTCAGGATGAATTCCGTTAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* * *
238928 TGCACACGAAGTACCTGTACGGTGATTCATCCACTCAGGATGAATTTCATG-A-A
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
*
238981 TGCAAACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* * * *
239036 TGCACATGAAGTGCCTGTACGGTGATTTATCCACTTAGGATGAATTCCATGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* * * *
239091 TGCACACAAAGTGCCTATACGTTGATTCATCCACTCAGGATGAATTTCGTGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* * * **
239146 TGCACACGAAGTGCATCTACGGTGATTCATCCACTCATGATGAATTTTGTGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* *
239201 TGCATACGAAGTGCCTGTATGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* *
239256 TGCACACAAAGTGCATGTA
1 TGCACACGAAGTGCCTGTA
239275 GTACACATAG
Statistics
Matches: 353, Mismatches: 46, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
53 48 0.14
54 2 0.01
55 302 0.86
56 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (55 bp):
TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
Found at i:239119 original size:163 final size:165
Alignment explanation
Indices: 238827--239269 Score: 683
Period size: 163 Copynumber: 2.7 Consensus size: 165
238817 TTGCACACAT
* *
238827 AGTGCATGTATGGTGATTCATCCACTCAGGATGAATTCCGTGAATATGCACACGAAGTGCCTATA
1 AGTGCATGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATATGCACACGAAGTGCCTGTA
* * * * *
238892 CAGTGATTTATCCACTCAGGATGAATTCCGTTAATATGCACACGAAGTACCTGTACGGTGATTCA
66 CGGTGATTTATCCACTCAGGATGAATTCCGTGAATATGCACACAAAGTGCCTATACGGTGATTCA
238957 TCCACTCAGGATGAATTTCATG-A-ATGCAAACGA
131 TCCACTCAGGATGAATTTCATGAATATGCAAACGA
* *
238990 AGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATATGCACATGAAGTGCCTGTA
1 AGTGCATGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATATGCACACGAAGTGCCTGTA
* * *
239055 CGGTGATTTATCCACTTAGGATGAATTCCATGAATATGCACACAAAGTGCCTATACGTTGATTCA
66 CGGTGATTTATCCACTCAGGATGAATTCCGTGAATATGCACACAAAGTGCCTATACGGTGATTCA
* *
239120 TCCACTCAGGATGAATTTCGTGAATATGCACACGA
131 TCCACTCAGGATGAATTTCATGAATATGCAAACGA
* * ** *
239155 AGTGCATCTACGGTGATTCATCCACTCATGATGAATTTTGTGAATATGCATACGAAGTGCCTGTA
1 AGTGCATGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATATGCACACGAAGTGCCTGTA
* *
239220 TGGTGATTCATCCACTCAGGATGAATTCCGTGAATATGCACACAAAGTGC
66 CGGTGATTTATCCACTCAGGATGAATTCCGTGAATATGCACACAAAGTGC
239270 ATGTAGTACA
Statistics
Matches: 253, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
163 139 0.55
164 1 0.00
165 113 0.45
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (165 bp):
AGTGCATGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATATGCACACGAAGTGCCTGTA
CGGTGATTTATCCACTCAGGATGAATTCCGTGAATATGCACACAAAGTGCCTATACGGTGATTCA
TCCACTCAGGATGAATTTCATGAATATGCAAACGA
Found at i:245174 original size:2 final size:2
Alignment explanation
Indices: 245167--245210 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
245157 GGTACAAGTG
245167 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
245209 AT
1 AT
245211 GTTTACATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:251250 original size:302 final size:302
Alignment explanation
Indices: 250704--251309 Score: 1203
Period size: 302 Copynumber: 2.0 Consensus size: 302
250694 TCTAGGTAGA
250704 AATGTGTTTTCTGGGCATAATTATCGATACTATTTCAAGAGTATTTAAGGGAATTAAAAGTATCG
1 AATGTGTTTTCTGGGCATAATTATCGATACTATTTCAAGAGTATTTAAGGGAATTAAAAGTATCG
250769 GTACTTATATAAAGTATCGAAACTTTTACAGAAATATCGATACTCTTGGGCTAGTATCGATACTT
66 GTACTTATATAAAGTATCGAAACTTTTACAGAAATATCGATACTCTTGGGCTAGTATCGATACTT
250834 TCAGACTCTTTTGGGCAAAAAGGATCGTATATAAGGGAATTAGACCTGAGGTACCCCAATACTTC
131 TCAGACTCTTTTGGGCAAAAAGGATCGTATATAAGGGAATTAGACCTGAGGTACCCCAATACTTC
250899 AGTATATCATCAAATAAGACTACAAGTGAAAATATTACGATGTTTAATTCAAACATAGAAACCAA
196 AGTATATCATCAAATAAGACTACAAGTGAAAATATTACGATGTTTAATTCAAACATAGAAACCAA
250964 ATTATTAGGGTGACATAAAACTAGCATTGGTTGATGCTTGAG
261 ATTATTAGGGTGACATAAAACTAGCATTGGTTGATGCTTGAG
*
251006 AATGTGTTTTCTGGGTATAATTATCGATACTATTTCAAGAGTATTTAAGGGAATTAAAAGTATCG
1 AATGTGTTTTCTGGGCATAATTATCGATACTATTTCAAGAGTATTTAAGGGAATTAAAAGTATCG
251071 GTACTTATATAAAGTATCGAAACTTTTACAGAAATATCGATACTCTTGGGCTAGTATCGATACTT
66 GTACTTATATAAAGTATCGAAACTTTTACAGAAATATCGATACTCTTGGGCTAGTATCGATACTT
251136 TCAGACTCTTTTGGGCAAAAAGGATCGTATATAAGGGAATTAGACCTGAGGTACCCCAATACTTC
131 TCAGACTCTTTTGGGCAAAAAGGATCGTATATAAGGGAATTAGACCTGAGGTACCCCAATACTTC
251201 AGTATATCATCAAATAAGACTACAAGTGAAAATATTACGATGTTTAATTCAAACATAGAAACCAA
196 AGTATATCATCAAATAAGACTACAAGTGAAAATATTACGATGTTTAATTCAAACATAGAAACCAA
251266 ATTATTAGGGTGACATAAAACTAGCATTGGTTGATGCTTGAG
261 ATTATTAGGGTGACATAAAACTAGCATTGGTTGATGCTTGAG
251308 AA
1 AA
251310 ATAATCCAGA
Statistics
Matches: 303, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
302 303 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (302 bp):
AATGTGTTTTCTGGGCATAATTATCGATACTATTTCAAGAGTATTTAAGGGAATTAAAAGTATCG
GTACTTATATAAAGTATCGAAACTTTTACAGAAATATCGATACTCTTGGGCTAGTATCGATACTT
TCAGACTCTTTTGGGCAAAAAGGATCGTATATAAGGGAATTAGACCTGAGGTACCCCAATACTTC
AGTATATCATCAAATAAGACTACAAGTGAAAATATTACGATGTTTAATTCAAACATAGAAACCAA
ATTATTAGGGTGACATAAAACTAGCATTGGTTGATGCTTGAG
Found at i:258872 original size:20 final size:21
Alignment explanation
Indices: 258847--258939 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
258837 TTTTCCCAAT
*
258847 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
258867 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
258888 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
258908 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
258929 TCGCAATGCGA
1 TCGCAATGCGA
258940 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:258892 original size:41 final size:41
Alignment explanation
Indices: 258847--258939 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
258837 TTTTCCCAAT
258847 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
258888 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
258929 TCGCAATGCGA
1 TCGCAATGCGA
258940 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:258952 original size:41 final size:41
Alignment explanation
Indices: 258866--259000 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
258856 GAATAAGTAA
** *
258866 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
258907 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
258948 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
258989 TTCGCAACGCGA
1 ATCGCAACGCGA
259001 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:258953 original size:20 final size:20
Alignment explanation
Indices: 258928--259021 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
258918 AATTGGGAAA
*
258928 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
258948 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
*
258969 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
258989 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
259009 TTCGCAACGCGAT
1 ATCGCAACGCGAT
259022 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:259596 original size:19 final size:19
Alignment explanation
Indices: 259536--259616 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
259526 TTCGAGAATG
259536 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
259556 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
259572 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
259589 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
259608 AAAATCGCA
1 AAAATCGCA
259617 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:259634 original size:19 final size:19
Alignment explanation
Indices: 259612--259796 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
259602 GAAACCAAAA
*
259612 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
259631 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
259650 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
259669 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
259689 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
259705 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
259722 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
259736 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
259755 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
259775 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
259795 TC
1 TC
259797 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:259689 original size:39 final size:38
Alignment explanation
Indices: 259612--259796 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
259602 GAAACCAAAA
*
259612 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
259650 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
259689 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
259722 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
259755 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
259795 TC
1 TC
259797 AACCAAAAGA
Statistics
Matches: 124, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:259773 original size:20 final size:20
Alignment explanation
Indices: 259739--259796 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
259729 GCGATTCTCT
**
259739 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
259759 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
259779 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
259797 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:261875 original size:21 final size:21
Alignment explanation
Indices: 261851--261917 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
261841 TCATTCCTCG
261851 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
261872 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
261893 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
261914 AGAG
1 AGAG
261918 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:261875 original size:42 final size:42
Alignment explanation
Indices: 261795--261917 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
261785 GCTCGACTTG
* * * * * * *
261795 CCTATCATCCCTCAAGAGTCCACTTCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
261837 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
261879 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
261918 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:263296 original size:14 final size:14
Alignment explanation
Indices: 263277--263312 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
263267 ATTGTTTAAT
263277 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
263291 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
263305 TGATTTGT
1 TGATTTGT
263313 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:263513 original size:19 final size:19
Alignment explanation
Indices: 263491--263575 Score: 72
Period size: 19 Copynumber: 4.7 Consensus size: 19
263481 CGAAATTAAA
263491 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
263510 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
263525 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
263543 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
263562 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
263576 GGACATTAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
14 9 0.18
16 3 0.06
17 3 0.06
19 26 0.51
20 10 0.20
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:267132 original size:20 final size:20
Alignment explanation
Indices: 267104--267181 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
267094 ATTCATTTGA
267104 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
267124 CTATTGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
267144 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
267164 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
267182 CGCATTGCGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:267201 original size:14 final size:14
Alignment explanation
Indices: 267184--267210 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
267174 GAGAAAATCG
267184 CATTGCGATTTTCT
1 CATTGCGATTTTCT
267198 CATTGCGATTTTC
1 CATTGCGATTTTC
267211 ATTTCGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (14 bp):
CATTGCGATTTTCT
Found at i:267220 original size:19 final size:19
Alignment explanation
Indices: 267193--267229 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
267183 GCATTGCGAT
*
267193 TTTCTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
267212 TTTCGCATTGCGATTTTC
1 TTTCGCATTGCGATTTTC
267230 TCGTTACGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.14, T:0.51
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:267223 original size:33 final size:33
Alignment explanation
Indices: 267181--267258 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
267171 AACGAGAAAA
* ***
267181 TCGCATTGCGATTTTCTCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCATTACGATAGCCATT
*
267214 TCGCATTGCGATTTTCTCGTTACGATAGCCATT
1 TCGCATTGCGATTTTCTCATTACGATAGCCATT
*
267247 TCGCGTTGCGAT
1 TCGCATTGCGAT
267259 AGTCTGTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCATTACGATAGCCATT
Found at i:269286 original size:20 final size:19
Alignment explanation
Indices: 269251--269316 Score: 89
Period size: 20 Copynumber: 3.5 Consensus size: 19
269241 GAAACTTAAA
269251 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
269270 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* *
269290 ATCGCAATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
269308 ATCGCAACG
1 ATCGCAACG
269317 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 8 0.20
19 16 0.39
20 17 0.41
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:269325 original size:14 final size:14
Alignment explanation
Indices: 269306--269362 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
269296 ATGCGAAATG
269306 AAATCGCAACGACA
1 AAATCGCAACGACA
*
269320 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
269336 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
269352 AAATCGCAACG
1 AAATCGCAACG
269363 CGAAACACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:269334 original size:32 final size:32
Alignment explanation
Indices: 269290--269367 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
269280 GGAAATGGCT
*
269290 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
269322 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
269354 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
269368 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:269396 original size:19 final size:18
Alignment explanation
Indices: 269374--269468 Score: 82
Period size: 19 Copynumber: 5.7 Consensus size: 18
269364 GAAACACAAA
269374 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
269393 TCGCGTTGCGA-TT--TG
1 TCGCATTGCGATTTCATT
269408 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
269424 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
269440 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
269457 TCGCATTGCGAT
1 TCGCATTGCGAT
269469 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
13 6 0.10
14 8 0.13
15 7 0.11
16 8 0.13
17 6 0.10
18 10 0.16
19 16 0.26
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:269412 original size:13 final size:14
Alignment explanation
Indices: 269396--269452 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
269386 TTTCATTTCG
269396 CGTTGCGA-TTTGT
1 CGTTGCGATTTTGT
*
269409 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
269425 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
269441 CGTTGCGATTTT
1 CGTTGCGATTTT
269453 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.22
14 12 0.32
16 8 0.22
18 9 0.24
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:269440 original size:32 final size:33
Alignment explanation
Indices: 269379--269468 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
269369 ACAAATCGCA
*
269379 TTGCGATTTTCATTTCGCGTTGCGA-TTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
269411 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
269443 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
269469 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 17 0.31
32 19 0.35
33 19 0.35
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:269504 original size:20 final size:20
Alignment explanation
Indices: 269453--269496 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
269443 TTGCGATTTT
* *
269453 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGTGATAGC
*
269472 CATTTCCGCGTTGTGATAGT
1 CATTTCCGCGTTGTGATAGC
269492 CATTT
1 CATTT
269497 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCCGCGTTGTGATAGC
Found at i:270004 original size:18 final size:18
Alignment explanation
Indices: 269978--270022 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
269968 GTCGATCAGA
*
269978 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
269996 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
270014 TGATGGCTC
1 TGATGGCTC
270023 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:271362 original size:20 final size:20
Alignment explanation
Indices: 271337--271374 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
271327 AATAGTTTCT
271337 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
271357 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
271375 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:271654 original size:22 final size:22
Alignment explanation
Indices: 271629--271672 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
271619 GATTTAGATA
271629 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
271651 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
271673 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:271885 original size:20 final size:20
Alignment explanation
Indices: 271860--271953 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
271850 GATTATGTAT
*
271860 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
271880 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
* *** * *
271900 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTAAG
* *
271921 TATCGCATTGCGATAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
271941 TATCGCATTGCGA
1 TATCGCGTTGCGA
271954 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:271954 original size:20 final size:20
Alignment explanation
Indices: 271840--271954 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
271830 CGCTTTGAAA
*
271840 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * *
271861 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
271881 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * ** * *
271901 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTAAGT
271922 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
271942 ATCGCATTGCGAT
1 ATCGCATTGCGAT
271955 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:271972 original size:21 final size:21
Alignment explanation
Indices: 271943--272035 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
271933 ATAGTAAGTA
271943 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
271964 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
271984 TCGCATTGCTATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
272005 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
272025 TCGCATTGCGA
1 TCGCATTGCGA
272036 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:271973 original size:41 final size:41
Alignment explanation
Indices: 271882--272016 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
271872 AAAGTCAGTA
* * * ** *
271882 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
271922 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
271964 TCGCGTTGCGAT-TTACTTATTCGCATTGCTATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
272005 TCGCGTTGCGAT
1 TCGCGTTGCGAT
272017 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:272017 original size:41 final size:41
Alignment explanation
Indices: 271943--272035 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
271933 ATAGTAAGTA
271943 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
271984 TCGCATTGCTATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
272025 TCGCATTGCGA
1 TCGCATTGCGA
272036 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:272587 original size:129 final size:130
Alignment explanation
Indices: 272345--272613 Score: 380
Period size: 129 Copynumber: 2.1 Consensus size: 130
272335 TCAATTTGCA
* * * * * * *
272345 ATGGAGAGGGGTGGAGAGGC-AGAGTTTCAATCCAAGCAGGAACTATCGTCGGTGTTCAGGCGTC
1 ATGGA-AGGGGTGGAGCGGCGA-AATTTTAACCCAGGCAGGAACTATCGTCGGTGATCAAGCGTC
* **
272409 TCAGTTTTTGTGGACAATGTTTGTAGGAGAATCCATCACCAGATGCTCAAGGAATCTTTTCCGAT
64 TCAGTTTTTGTGGACAATGTTAGTAGGAGAATCCATCACCAGACACTCAAGGAATCTTTTCCGAT
272474 GT
129 GT
*
272476 AT-GAAGGGGTGGAGCGGCGAAATTTTAACCCAGGCAGGAGCTATCGTCGGTGATCAAGCGTCTC
1 ATGGAAGGGGTGGAGCGGCGAAATTTTAACCCAGGCAGGAACTATCGTCGGTGATCAAGCGTCTC
* * *
272540 AGTTTTTGTGGACAATGTTAGTAGGAGAATCCATCACCGGACACTCAAGGAATCTTTTCTGATTT
66 AGTTTTTGTGGACAATGTTAGTAGGAGAATCCATCACCAGACACTCAAGGAATCTTTTCCGATGT
272605 ATGGAAGGG
1 ATGGAAGGG
272614 TCTTAGACAC
Statistics
Matches: 122, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
129 111 0.91
130 9 0.07
131 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (130 bp):
ATGGAAGGGGTGGAGCGGCGAAATTTTAACCCAGGCAGGAACTATCGTCGGTGATCAAGCGTCTC
AGTTTTTGTGGACAATGTTAGTAGGAGAATCCATCACCAGACACTCAAGGAATCTTTTCCGATGT
Found at i:274125 original size:29 final size:29
Alignment explanation
Indices: 274083--274139 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
274073 AGTGGAGTTG
274083 TTTGTCGACCAGACAACTGTCAAATTGCT
1 TTTGTCGACCAGACAACTGTCAAATTGCT
274112 TTTGTCGACCAGACAACTGTCAAATTGC
1 TTTGTCGACCAGACAACTGTCAAATTGC
274140 AAAAGACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (29 bp):
TTTGTCGACCAGACAACTGTCAAATTGCT
Found at i:285731 original size:26 final size:26
Alignment explanation
Indices: 285701--285754 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
285691 GTCATGCAAC
*
285701 AACAAAACCTAGAAAAGATAAACAAA
1 AACAAAAACTAGAAAAGATAAACAAA
* * *
285727 AACAAAAACTAGTAAAGCTATACAAA
1 AACAAAAACTAGAAAAGATAAACAAA
285753 AA
1 AA
285755 TAAAGAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.67, C:0.15, G:0.07, T:0.11
Consensus pattern (26 bp):
AACAAAAACTAGAAAAGATAAACAAA
Found at i:291531 original size:10 final size:10
Alignment explanation
Indices: 291508--291545 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
291498 GACTATTATC
291508 TTTTATGAGTT
1 TTTTATGAG-T
291519 TTTTATGAGT
1 TTTTATGAGT
291529 TTTTATGAGGT
1 TTTTATGA-GT
291540 TTTTAT
1 TTTTAT
291546 CATCCGTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.63
Consensus pattern (10 bp):
TTTTATGAGT
Found at i:292486 original size:30 final size:31
Alignment explanation
Indices: 292443--292502 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
292433 ATTTATATTA
*
292443 GGGAGCAATCTTGAACACT-TAAAATTTTAGT
1 GGGAGCAAACTTGAAC-CTATAAAATTTTAGT
*
292474 GGGA-CAAACTTGAACTTATAAAATTTTAG
1 GGGAGCAAACTTGAACCTATAAAATTTTAG
292503 AAAGATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 21 0.81
31 4 0.15
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (31 bp):
GGGAGCAAACTTGAACCTATAAAATTTTAGT
Found at i:297430 original size:20 final size:20
Alignment explanation
Indices: 297344--297594 Score: 122
Period size: 20 Copynumber: 12.6 Consensus size: 20
297334 AATGACCAAC
* *
297344 AAATTCGCAACGCG-ATCTC
1 AAATTCGCAACGCGAATTTT
* * **
297363 AAATTTGCAACGCGAACTCC
1 AAATTCGCAACGCGAATTTT
* * **
297383 AATTTCGCAACTC-AACTTCC
1 AAATTCGCAACGCGAA-TTTT
297403 AAATTCGCAACGCGAATTTGT
1 AAATTCGCAACGCGAATTT-T
* *
297424 AAA-TCGCAACGTGAATCTGT
1 AAATTCGCAACGCGAAT-TTT
* *
297444 AAA-TCGCAACGAG-ATTTCC
1 AAATTCGCAACGCGAATTT-T
297463 AAATTCGCAACGCG-ATTTT
1 AAATTCGCAACGCGAATTTT
*
297482 CAAATTCGCAACACTGAATTTT
1 -AAATTCGCAACGC-GAATTTT
*
297504 AAATTCGCAACTCG-ATTTCT
1 AAATTCGCAACGCGAATTT-T
* * *
297524 GAATTTGTAACGCGAATTTT
1 AAATTCGCAACGCGAATTTT
*** *
297544 GTTTTCGCAACTCG-ATTTT
1 AAATTCGCAACGCGAATTTT
* ** *
297563 CTAATTCGCAATACAAATTTT
1 -AAATTCGCAACGCGAATTTT
*
297584 AATTTCGCAAC
1 AAATTCGCAAC
297595 AGGTTTTAGT
Statistics
Matches: 179, Mismatches: 39, Indels: 27
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.01
19 29 0.16
20 116 0.65
21 28 0.16
22 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (20 bp):
AAATTCGCAACGCGAATTTT
Found at i:297463 original size:60 final size:62
Alignment explanation
Indices: 297399--297543 Score: 165
Period size: 60 Copynumber: 2.4 Consensus size: 62
297389 GCAACTCAAC
*
297399 TTCCAAATTCGCAACGCGAATTTGT-AAA-TCGCAAC-GTGAATCTGTAAA-TCGCAACGAGAT
1 TTCCAAATTCGCAACGCGAATTT-TCAAATTCGCAACACTGAAT-TGTAAATTCGCAACGAGAT
* **
297459 TTCCAAATTCGCAACGCG-ATTTTCAAATTCGCAACACTGAATTTTAAATTCGCAACTCGAT
1 TTCCAAATTCGCAACGCGAATTTTCAAATTCGCAACACTGAATTGTAAATTCGCAACGAGAT
** * *
297520 TTCTGAATTTGTAACGCGAATTTT
1 TTCCAAATTCGCAACGCGAATTTT
297544 GTTTTCGCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
58 1 0.01
59 7 0.10
60 30 0.42
61 29 0.40
62 5 0.07
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (62 bp):
TTCCAAATTCGCAACGCGAATTTTCAAATTCGCAACACTGAATTGTAAATTCGCAACGAGAT
Found at i:297514 original size:41 final size:40
Alignment explanation
Indices: 297344--297594 Score: 140
Period size: 40 Copynumber: 6.3 Consensus size: 40
297334 AATGACCAAC
* * * * * **
297344 AAATTCGCAACGCGA-TCTCAAATTTGCAACGCGAACTCC
1 AAATTCGCAACTCGATTTTCAAATTCGCAACACGAATTTT
* * * * *
297383 AATTTCGCAACTCAACTTCCAAATTCGCAACGCGAATTTGT
1 AAATTCGCAACTCGATTTTCAAATTCGCAACACGAATTT-T
* *
297424 AAA-TCGCAACGT-GAATCTGT-AAA-TCGC-A-ACGAGATTTCC
1 AAATTCGCAAC-TCG-AT-TTTCAAATTCGCAACACGA-ATTT-T
*
297463 AAATTCGCAACGCGATTTTCAAATTCGCAACACTGAATTTT
1 AAATTCGCAACTCGATTTTCAAATTCGCAACAC-GAATTTT
* * * *
297504 AAATTCGCAACTCGA-TTTCTGAATTTGTAACGCGAATTTT
1 AAATTCGCAACTCGATTTTC-AAATTCGCAACACGAATTTT
*** * * *
297544 GTTTTCGCAACTCGATTTTCTAATTCGCAATACAAATTTT
1 AAATTCGCAACTCGATTTTCAAATTCGCAACACGAATTTT
*
297584 AATTTCGCAAC
1 AAATTCGCAAC
297595 AGGTTTTAGT
Statistics
Matches: 161, Mismatches: 36, Indels: 29
0.71 0.16 0.13
Matches are distributed among these distances:
38 5 0.03
39 25 0.16
40 87 0.54
41 35 0.22
42 7 0.04
43 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (40 bp):
AAATTCGCAACTCGATTTTCAAATTCGCAACACGAATTTT
Found at i:297582 original size:40 final size:40
Alignment explanation
Indices: 297466--297594 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
297456 GATTTCCAAA
* * *
297466 TTCGCAACGCGATTTTCAAATTCGCAACACTGAATTTTAAA
1 TTCGCAACTCGATTTTCTAATTCGCAACAC-GAATTTTAAT
* * * **
297507 TTCGCAACTCGA-TTTCTGAATTTGTAACGCGAATTTTGTT
1 TTCGCAACTCGATTTTCT-AATTCGCAACACGAATTTTAAT
* *
297547 TTCGCAACTCGATTTTCTAATTCGCAATACAAATTTTAAT
1 TTCGCAACTCGATTTTCTAATTCGCAACACGAATTTTAAT
297587 TTCGCAAC
1 TTCGCAAC
297595 AGGTTTTAGT
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 46 0.65
41 25 0.35
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (40 bp):
TTCGCAACTCGATTTTCTAATTCGCAACACGAATTTTAAT
Found at i:299140 original size:21 final size:19
Alignment explanation
Indices: 299096--299150 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
299086 TCTGAAACTT
*
299096 AAAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
*
299115 AAAATCGCAATGCGAATTTGG
1 AAAATCGCAATGCGAA-AT-G
*
299136 AAAATCACAATGCGA
1 AAAATCGCAATGCGA
299151 TTTACATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 15 0.48
20 1 0.03
21 15 0.48
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.16
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:299604 original size:22 final size:22
Alignment explanation
Indices: 299573--299619 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
299563 GAGATAGACG
299573 GATTTCGTCGGAGATGGGGACA
1 GATTTCGTCGGAGATGGGGACA
*
299595 GATTTTGTCGGAGATGGGGACA
1 GATTTCGTCGGAGATGGGGACA
299617 GAT
1 GAT
299620 GTCGCCATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.11, G:0.40, T:0.26
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACA
Found at i:299803 original size:20 final size:20
Alignment explanation
Indices: 299774--299822 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
299764 TAAACGCGCT
*
299774 TTGCGAATTTAACTTTTATG
1 TTGCGAATTTAACTTATATG
* * *
299794 TTGTGAATTTGACTTATGTG
1 TTGCGAATTTAACTTATATG
299814 TTGCGAATT
1 TTGCGAATT
299823 ATAGATTCGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.20, T:0.49
Consensus pattern (20 bp):
TTGCGAATTTAACTTATATG
Found at i:299861 original size:21 final size:21
Alignment explanation
Indices: 299837--299879 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
299827 ATTCGCGTTT
299837 AATTCAGAAAATCACAACGCG
1 AATTCAGAAAATCACAACGCG
* *
299858 AATTCAGAAAATCGCAATGCG
1 AATTCAGAAAATCACAACGCG
299879 A
1 A
299880 TTTACATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (21 bp):
AATTCAGAAAATCACAACGCG
Found at i:302796 original size:30 final size:30
Alignment explanation
Indices: 302762--302824 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
302752 GTTATATGAG
* *
302762 CTATGTGATAAAGGTATGGAAATGATATGT
1 CTATGTGATAAAGGTATGAAAATAATATGT
302792 CTATGTGATAAAGGTATGAAAATAATATGT
1 CTATGTGATAAAGGTATGAAAATAATATGT
302822 CTA
1 CTA
302825 CGCGATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGAAAATAATATGT
Found at i:303698 original size:21 final size:22
Alignment explanation
Indices: 303672--303714 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
303662 GTAGCAGTAA
*
303672 TGTAGCA-GGGTATCGGTTCCC
1 TGTAGCAGGGGAATCGGTTCCC
303693 TGTAGCAGGGGAATCGGTTCCC
1 TGTAGCAGGGGAATCGGTTCCC
303715 CTCAAGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.16, C:0.23, G:0.35, T:0.26
Consensus pattern (22 bp):
TGTAGCAGGGGAATCGGTTCCC
Found at i:303786 original size:22 final size:21
Alignment explanation
Indices: 303761--303806 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 21
303751 AGCAGGGCAA
303761 TGTTCACGGTATTGTTCATTAC
1 TGTTCACGGTATTGTTCA-TAC
303783 TGTTCACGGTATTGTTCATAC
1 TGTTCACGGTATTGTTCATAC
303804 TGT
1 TGT
303807 ATTTTACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (21 bp):
TGTTCACGGTATTGTTCATAC
Found at i:305424 original size:20 final size:22
Alignment explanation
Indices: 305399--305438 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
305389 AGTCGTATAT
305399 AGCCG-TCGGGGAT-ATTTTGG
1 AGCCGTTCGGGGATGATTTTGG
*
305419 AGCCGTTTGGGGATGATTTT
1 AGCCGTTCGGGGATGATTTT
305439 CTACTCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.15, C:0.12, G:0.38, T:0.35
Consensus pattern (22 bp):
AGCCGTTCGGGGATGATTTTGG
Found at i:305556 original size:17 final size:17
Alignment explanation
Indices: 305516--305568 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
305506 CGTTGTAGCC
*
305516 AGGGGTATAGATACCCCT
1 AGGGGTATAGATA-CCAT
* *
305534 GGGGGGTATCGATACCAT
1 -AGGGGTATAGATACCAT
305552 AGGGGTATAGATACCAT
1 AGGGGTATAGATACCAT
305569 CCGAGCAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 15 0.52
18 3 0.10
19 11 0.38
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (17 bp):
AGGGGTATAGATACCAT
Found at i:305886 original size:21 final size:21
Alignment explanation
Indices: 305862--305901 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
305852 ATATTTAATG
305862 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
305883 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
305902 CCAATTGGTA
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:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:307554 original size:3 final size:3
Alignment explanation
Indices: 307546--307586 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
307536 TACCTTCTCA
* *
307546 TTC TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
307587 CCTTTCCTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:308959 original size:21 final size:21
Alignment explanation
Indices: 308933--308974 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
308923 CCACGATAGG
308933 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTACCCCTTCATA
*
308954 GGGTATCGGTACTCCTTCATA
1 GGGTATCGGTACCCCTTCATA
308975 AAATTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (21 bp):
GGGTATCGGTACCCCTTCATA
Found at i:310509 original size:23 final size:23
Alignment explanation
Indices: 310483--310541 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
310473 ATTCTACGTA
310483 GTCCTTCGAGACATTTCTACAAG
1 GTCCTTCGAGACATTTCTACAAG
* *
310506 GTCCTTC-AGGACA--TCTATATG
1 GTCCTTCGA-GACATTTCTACAAG
*
310527 GTCCTTCGGGACATT
1 GTCCTTCGAGACATT
310542 CTATGTGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
21 17 0.59
22 1 0.03
23 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (23 bp):
GTCCTTCGAGACATTTCTACAAG
Found at i:310529 original size:21 final size:22
Alignment explanation
Indices: 310459--310545 Score: 70
Period size: 23 Copynumber: 3.9 Consensus size: 22
310449 GGTTCTATGC
* **
310459 GGTCATTCAGGACAATTCTACGT
1 GGTCCTTCAGGAC-ATTCTATAT
* * *
310482 AGTCCTTC-GAGACATTTCTACAA
1 GGTCCTTCAG-GACA-TTCTATAT
310505 GGTCCTTCAGGACA-TCTATAT
1 GGTCCTTCAGGACATTCTATAT
*
310526 GGTCCTTCGGGACATTCTAT
1 GGTCCTTCAGGACATTCTAT
310546 GTGACACTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
21 18 0.35
22 7 0.13
23 26 0.50
24 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (22 bp):
GGTCCTTCAGGACATTCTATAT
Found at i:310809 original size:6 final size:6
Alignment explanation
Indices: 310798--310875 Score: 68
Period size: 6 Copynumber: 13.2 Consensus size: 6
310788 TTAAATGGAT
* * * *
310798 TAATGA TAATGA -AATGA TAATGA TAGTGA TAGTGA TAGTGA TAAGGA
1 TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA TAATGA
* * ** *
310845 TAAGGA TAATAA TGTTGA TGATGA TAATGA T
1 TAATGA TAATGA TAATGA TAATGA TAATGA T
310876 GGTATATGTG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
5 5 0.08
6 56 0.92
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (6 bp):
TAATGA
Found at i:310846 original size:18 final size:18
Alignment explanation
Indices: 310798--310840 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
310788 TTAAATGGAT
* *
310798 TAATGATAATGA-AATGA
1 TAATGATAGTGATAGTGA
310815 TAATGATAGTGATAGTGA
1 TAATGATAGTGATAGTGA
*
310833 TAGTGATA
1 TAATGATA
310841 AGGATAAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (18 bp):
TAATGATAGTGATAGTGA
Found at i:314728 original size:33 final size:33
Alignment explanation
Indices: 314670--314780 Score: 153
Period size: 28 Copynumber: 3.5 Consensus size: 33
314660 CTTTATTTTG
* *
314670 TTCGGGTCGGGTCGGG-TTTTTTAAGTGTGATG
1 TTCGGGTCGAGTCGGGTTTTTTTAAGTGTGATA
314702 TTCGGGTCGAGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGAGTCGGGTTTTTTTAAGTGTGATA
314735 TTCGGGT----T-GGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGAGTCGGGTTTTTTTAAGTGTGATA
*
314763 TTCGGGTCTAGTCGGGTT
1 TTCGGGTCGAGTCGGGTT
314781 CGAGTTTAGG
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
28 27 0.38
29 1 0.01
32 16 0.23
33 27 0.38
ACGTcount: A:0.12, C:0.09, G:0.36, T:0.43
Consensus pattern (33 bp):
TTCGGGTCGAGTCGGGTTTTTTTAAGTGTGATA
Found at i:315342 original size:44 final size:44
Alignment explanation
Indices: 315279--315362 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
315269 ATTTGACATG
*
315279 TCTGCGAACCAAACAGAATATGAAATTGGATTCCAATTCCATTT
1 TCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCCATTT
* *
315323 TCTGCCAACCAAACAGAATATGTAATTGGATTTCAATTCC
1 TCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCC
315363 TGACAGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (44 bp):
TCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCCATTT
Found at i:315373 original size:17 final size:18
Alignment explanation
Indices: 315351--315397 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
315341 TATGTAATTG
*
315351 GATTTCAATTCC-TGACA
1 GATTTCAATTCCTTCACA
315368 GATTTCAATTCCTTCACA
1 GATTTCAATTCCTTCACA
*
315386 GATTCCAATTCC
1 GATTTCAATTCC
315398 CTCATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:316569 original size:20 final size:20
Alignment explanation
Indices: 316544--316592 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
316534 GTTCGAACAC
316544 AATATTTATAGAACTATTTA
1 AATATTTATAGAACTATTTA
316564 AATATTTATAGAACTATTTA
1 AATATTTATAGAACTATTTA
316584 AATATTTAT
1 AATATTTAT
316593 TATCAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
AATATTTATAGAACTATTTA
Found at i:321816 original size:32 final size:29
Alignment explanation
Indices: 321762--321831 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 29
321752 AAAAAACAAG
*
321762 AAAATAAAAATGATAATAAAAAAAAAATA
1 AAAATAAAAATGATAAGAAAAAAAAAATA
* **
321791 CAAATAAAAATGATTAGAGAGAAAAATTAATA
1 AAAATAAAAATGA-TA-AGA-AAAAAAAAATA
321823 AAAATAAAA
1 AAAATAAAA
321832 TATTTAAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 12 0.36
30 2 0.06
31 2 0.06
32 17 0.52
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (29 bp):
AAAATAAAAATGATAAGAAAAAAAAAATA
Found at i:323349 original size:10 final size:11
Alignment explanation
Indices: 323311--323354 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 11
323301 CAAAAAGAGA
323311 AATAAATAAAT
1 AATAAATAAAT
*
323322 AACAAATAATATT
1 AATAAATAA-A-T
323335 AATAAATAAAT
1 AATAAATAAAT
323346 -ATAAATAAA
1 AATAAATAAA
323355 ATATATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 9 0.31
11 9 0.31
12 2 0.07
13 9 0.31
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:323390 original size:35 final size:35
Alignment explanation
Indices: 323351--323448 Score: 126
Period size: 35 Copynumber: 2.7 Consensus size: 35
323341 TAAATATAAA
*
323351 TAAAATATATTTTAAAAAACTATATATAT-AAATTT
1 TAAAATGT-TTTTAAAAAACTATATATATAAAATTT
*
323386 TAAAATGTTTTTTAAAAACATATATATATAAAATTT
1 TAAAATGTTTTTAAAAAAC-TATATATATAAAATTT
*
323422 CAAAATTGTTTTTTAAAAAACTATATA
1 TAAAA-TG-TTTTTAAAAAACTATATA
323449 CTTTTAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
34 10 0.18
35 16 0.29
36 10 0.18
37 8 0.15
38 11 0.20
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (35 bp):
TAAAATGTTTTTAAAAAACTATATATATAAAATTT
Found at i:323432 original size:37 final size:35
Alignment explanation
Indices: 323360--323448 Score: 119
Period size: 37 Copynumber: 2.5 Consensus size: 35
323350 ATAAAATATA
* *
323360 TTTTAAAAAAC-TATATATATAAATTTTAAAATGT
1 TTTTTAAAAACATATATATATAAATTTCAAAATGT
323394 TTTTTAAAAACATATATATATAAAATTTCAAAATTGT
1 TTTTTAAAAACATATATATAT-AAATTTCAAAA-TGT
323431 TTTTTAAAAA-ACTATATA
1 TTTTTAAAAACA-TATATA
323449 CTTTTAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
34 10 0.20
35 9 0.18
36 11 0.22
37 19 0.39
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (35 bp):
TTTTTAAAAACATATATATATAAATTTCAAAATGT
Found at i:323541 original size:37 final size:37
Alignment explanation
Indices: 323488--323677 Score: 231
Period size: 37 Copynumber: 5.1 Consensus size: 37
323478 TATAATATTA
* *
323488 AAAAATGTTTTAAAAATTAAATATTATATAAGTTTTC
1 AAAAATGTTTTTAAAATTATATATTATATAAGTTTTC
**
323525 AAAAATGTTTTTAAAATTATATATTATATATTTTTTC
1 AAAAATGTTTTTAAAATTATATATTATATAAGTTTTC
* * *
323562 AAAAATATTTTT-AAACTATATATTATATAATTTTTC
1 AAAAATGTTTTTAAAATTATATATTATATAAGTTTTC
* *
323598 AAAAATGCTTTTAAAATCTATTTATTATATAAGTTTTC
1 AAAAATGTTTTTAAAAT-TATATATTATATAAGTTTTC
* **
323636 -AAAATGTTTTAAAAATTATATAGCATATAAATGTTTTC
1 AAAAATGTTTTTAAAATTATATATTATAT-AA-GTTTTC
323674 AAAA
1 AAAA
323678 TTATATATTA
Statistics
Matches: 131, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
36 41 0.31
37 63 0.48
38 24 0.18
39 3 0.02
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (37 bp):
AAAAATGTTTTTAAAATTATATATTATATAAGTTTTC
Found at i:331996 original size:4 final size:4
Alignment explanation
Indices: 331963--332012 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
331953 AGCCAGTACC
* * * * *
331963 ATAT ACAT ATAC ATAC ATAT ACAT ACAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
332011 AT
1 AT
332013 TATCTCTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (4 bp):
ATAT
Found at i:332004 original size:10 final size:10
Alignment explanation
Indices: 331963--332012 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
331953 AGCCAGTACC
331963 ATATACATAT
1 ATATACATAT
*
331973 ACATACATAT
1 ATATACATAT
*
331983 ACATACATAT
1 ATATACATAT
*
331993 ATATATATAT
1 ATATACATAT
*
332003 ATATATATAT
1 ATATACATAT
332013 TATCTCTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATACATAT
Found at i:332012 original size:6 final size:6
Alignment explanation
Indices: 331963--332012 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
331953 AGCCAGTACC
* * * * *
331963 ATATAC ATATAC ATACAT ATACAT ACATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
332011 AT
1 AT
332013 TATCTCTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (6 bp):
ATATAT
Found at i:332056 original size:17 final size:17
Alignment explanation
Indices: 332034--332068 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
332024 GTTTATTTGT
332034 CTCCATCTTTACCTCCC
1 CTCCATCTTTACCTCCC
332051 CTCCATCTTTACCTCCC
1 CTCCATCTTTACCTCCC
332068 C
1 C
332069 CACTTGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.54, G:0.00, T:0.34
Consensus pattern (17 bp):
CTCCATCTTTACCTCCC
Found at i:350271 original size:45 final size:45
Alignment explanation
Indices: 350222--350529 Score: 420
Period size: 45 Copynumber: 6.8 Consensus size: 45
350212 ATTCTAACAT
* * *
350222 CTTTTATATTGATAATGCACCCATATGTATTTCAACTATATTATA
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAATATA
* ** *
350267 CTTTTATGTTGATAATGTACCCATATATATTTCAACCATAATATA
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAATATA
*
350312 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAATATA
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAATATA
* * *
350357 CTTTTATGTTGATAATGTACCCATATACATTTCAACCATAATATA
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAATATA
* * **
350402 CTTTTATGTTGATAATGTACCCATATGCATTATCAACTCTAGCATA
1 CTTTTATGTTGATAATGCACCCATATGCATT-TCAACTATAATATA
* * *
350448 CTTTTCTGTTGATAA-GACACCCATATGCATTTCAACTCTAGTATA
1 CTTTTATGTTGATAATG-CACCCATATGCATTTCAACTATAATATA
*
350493 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACT
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACT
350530 CTGGCATCCT
Statistics
Matches: 238, Mismatches: 22, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
45 200 0.84
46 38 0.16
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (45 bp):
CTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAATATA
Found at i:350503 original size:136 final size:135
Alignment explanation
Indices: 350222--350528 Score: 456
Period size: 136 Copynumber: 2.3 Consensus size: 135
350212 ATTCTAACAT
* * * *
350222 CTTTTATATTGATAATGCACCCATATGTATTTCAACTATATTATACTTTTATGTTGATAATGTAC
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACCATAATATACTTTTATGTTGATAATGTAC
* *
350287 CCATATATATTTCAACCATAATATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATA
66 CCATATACATTTCAACCATAACATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATA
350352 ATATA
131 ATATA
* *
350357 CTTTTATGTTGATAATGTACCCATATACATTTCAACCATAATATACTTTTATGTTGATAATGTAC
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACCATAATATACTTTTATGTTGATAATGTAC
* *
350422 CCATATGCATTATCAACTC-TAGCATACTTTTCTGTTGATAA-GACACCCATATGCATTTCAACT
66 CCATATACATT-TCAAC-CATAACATACTTTTCTGTTGATAATG-CACCCATATGCATTTCAACT
* *
350485 CTAGTATA
128 ATAATATA
*
350493 CTTTTCTGTTGATAATGCACCCATATGCATTTCAAC
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAAC
350529 TCTGGCATCC
Statistics
Matches: 154, Mismatches: 15, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
135 69 0.45
136 84 0.55
137 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (135 bp):
CTTTTATGTTGATAATGCACCCATATGCATTTCAACCATAATATACTTTTATGTTGATAATGTAC
CCATATACATTTCAACCATAACATACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATA
ATATA
Found at i:350553 original size:45 final size:45
Alignment explanation
Indices: 350230--350568 Score: 321
Period size: 45 Copynumber: 7.5 Consensus size: 45
350220 ATCTTTTATA
* * * * *
350230 TTGATAATGCACCCATATGTATTTCAACTATATTATACTTTTATG
1 TTGATAATGCACCCATATGCATTTCAACTCTAGTATCCTTTCATG
* ** * *
350275 TTGATAATGTACCCATATATATTTCAAC-CATAATATACTTTTC-TG
1 TTGATAATGCACCCATATGCATTTCAACTC-TAGTAT-CCTTTCATG
* * * *
350320 TTGATAATGCACCCATATGCATTTCAACTATAATATACTTTTATG
1 TTGATAATGCACCCATATGCATTTCAACTCTAGTATCCTTTCATG
* * * * *
350365 TTGATAATGTACCCATATACATTTCAAC-CATAATATACTTTTATG
1 TTGATAATGCACCCATATGCATTTCAACTC-TAGTATCCTTTCATG
* * *
350410 TTGATAATGTACCCATATGCATTATCAACTCTAGCATACTTTTC-TG
1 TTGATAATGCACCCATATGCATT-TCAACTCTAGTAT-CCTTTCATG
*
350456 TTGATAA-GACACCCATATGCATTTCAACTCTAGTATACTTTTC-TG
1 TTGATAATG-CACCCATATGCATTTCAACTCTAGTAT-CCTTTCATG
* *
350501 TTGATAATGCACCCATATGCATTTCAACTCTGGCATCCTTTCATG
1 TTGATAATGCACCCATATGCATTTCAACTCTAGTATCCTTTCATG
** *
350546 TCAATAATGCACCAATATGCATT
1 TTGATAATGCACCCATATGCATT
350569 ATTCTTTTAT
Statistics
Matches: 252, Mismatches: 31, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
44 8 0.03
45 205 0.81
46 35 0.14
47 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.39
Consensus pattern (45 bp):
TTGATAATGCACCCATATGCATTTCAACTCTAGTATCCTTTCATG
Found at i:350624 original size:79 final size:79
Alignment explanation
Indices: 350506--350656 Score: 221
Period size: 79 Copynumber: 1.9 Consensus size: 79
350496 TTCTGTTGAT
* * ** *
350506 AATGCACCCATATGCATTTCAACTCTGGCATCCTTTCATGTCAATAATGCACCAATATGCATTAT
1 AATGCACCCATATACATTTCAACTATAACATCCTTTCATGACAATAATGCACCAATATGCATTAT
350571 TCTTTTATGCTGAC
66 TCTTTTATGCTGAC
* * * *
350585 AATGTACCCATATACATTTCAGCTATAACATTCTTTCATGACAATAATGCACCCATATGCATTAT
1 AATGCACCCATATACATTTCAACTATAACATCCTTTCATGACAATAATGCACCAATATGCATTAT
350650 TCTTTTA
66 TCTTTTA
350657 CATTTGTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (79 bp):
AATGCACCCATATACATTTCAACTATAACATCCTTTCATGACAATAATGCACCAATATGCATTAT
TCTTTTATGCTGAC
Found at i:351095 original size:22 final size:21
Alignment explanation
Indices: 351046--351101 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
351036 CTGGCCCTTA
* *
351046 GGTATCGATACCCCTGCTTAT
1 GGTATCGATACCCCTGATTAG
351067 GGTATCGATACTACCCT-ATTAG
1 GGTATCGATAC--CCCTGATTAG
351089 GGTATCGATACCC
1 GGTATCGATACCC
351102 TCTTCATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 2 0.06
21 11 0.35
22 14 0.45
23 4 0.13
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (21 bp):
GGTATCGATACCCCTGATTAG
Found at i:351166 original size:20 final size:19
Alignment explanation
Indices: 351141--351213 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 19
351131 TGATGTAGCT
351141 TGGTATCGATACCCTCACCA
1 TGGTATCGATACCC-CACCA
*
351161 TGGTATCGATACCCCTATGCTA
1 TGGTATCGATACCCC-A--CCA
* *
351183 TGGTACCGATACCCCCGCCA
1 TGGTATCGATA-CCCCACCA
351203 -GGTATCGATAC
1 TGGTATCGATAC
351214 ACATATTAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 1 0.02
19 10 0.23
20 17 0.39
22 12 0.27
23 4 0.09
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (19 bp):
TGGTATCGATACCCCACCA
Found at i:351172 original size:95 final size:94
Alignment explanation
Indices: 351065--351268 Score: 225
Period size: 95 Copynumber: 2.1 Consensus size: 94
351055 ACCCCTGCTT
* * ** *
351065 ATGGTATCGATACTACCCTAT-TAGGGTATCGATACCCTCTTCATGTATCGATATCGA-A-ATTA
1 ATGGTATCGATAC--CCCTATCTAGGGTACCGATACCCCCGCCAGGTATCGATA-C-ACATATTA
* * **
351127 GCTTTGATGTAGCTTGGTATCGATACCCTCACC
62 GATTCGATGTAGAATGGTATCGATACCCTCACC
*
351160 ATGGTATCGATACCCCTATGCTATGGTACCGATACCCCCGCCAGGTATCGATACACATATTAGAT
1 ATGGTATCGATACCCCTAT-CTAGGGTACCGATACCCCCGCCAGGTATCGATACACATATTAGAT
** *
351225 TCGATGTTTAATGGTATCGATACCCTTACC
65 TCGATGTAGAATGGTATCGATACCCTCACC
351255 ATGGTATCGATACC
1 ATGGTATCGATACC
351269 ACATTGCTTG
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
93 7 0.08
94 2 0.02
95 83 0.90
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (94 bp):
ATGGTATCGATACCCCTATCTAGGGTACCGATACCCCCGCCAGGTATCGATACACATATTAGATT
CGATGTAGAATGGTATCGATACCCTCACC
Found at i:352725 original size:19 final size:19
Alignment explanation
Indices: 352677--352728 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
352667 TATACATGAG
*
352677 TTAACTATTACTTTATAAA
1 TTAACTATTATTTTATAAA
*
352696 TTAACCATTATTTTATAAA
1 TTAACTATTATTTTATAAA
352715 TTAACTATTATTTT
1 TTAACTATTATTTT
352729 TCTGTATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAACTATTATTTTATAAA
Found at i:353131 original size:28 final size:28
Alignment explanation
Indices: 353099--353194 Score: 192
Period size: 28 Copynumber: 3.4 Consensus size: 28
353089 TTAGTCGTTG
353099 CTTTTAACTTCAAATTTTCAAATATGCA
1 CTTTTAACTTCAAATTTTCAAATATGCA
353127 CTTTTAACTTCAAATTTTCAAATATGCA
1 CTTTTAACTTCAAATTTTCAAATATGCA
353155 CTTTTAACTTCAAATTTTCAAATATGCA
1 CTTTTAACTTCAAATTTTCAAATATGCA
353183 CTTTTAACTTCA
1 CTTTTAACTTCA
353195 TTTAGTCCAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 68 1.00
ACGTcount: A:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (28 bp):
CTTTTAACTTCAAATTTTCAAATATGCA
Done.