Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008745.1 Hibiscus syriacus cultivar Beakdansim tig00111834_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: 1915556
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:235049 original size:21 final size:21
Alignment explanation
Indices: 235009--235056 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
234999 CCTGCGGAGA
*
235009 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
* *
235030 TGGCATATGAAGTTGAGGGCT
1 TGGCATATGAACTGGAGGGCT
*
235051 GGGCAT
1 TGGCAT
235057 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.12, G:0.40, T:0.27
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:236822 original size:34 final size:32
Alignment explanation
Indices: 236779--236858 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 32
236769 TTAATAATTC
* *
236779 TAAATAAATAATAATTATACA-AATATTATTTTAA
1 TAAAAAAATAATAATT-TACATAA-A-TATATTAA
236813 TAAAAAAATAAT-ATTTACATAAATATATTAA
1 TAAAAAAATAATAATTTACATAAATATATTAA
*
236844 TATAAAATATAATAA
1 TA-AAAAAATAATAA
236859 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 9 0.22
32 14 0.35
33 6 0.15
34 11 0.28
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAAATAATAATTTACATAAATATATTAA
Found at i:240945 original size:29 final size:29
Alignment explanation
Indices: 240843--240940 Score: 72
Period size: 29 Copynumber: 3.3 Consensus size: 29
240833 GTTTGGAATG
* *
240843 AATAGTCGAGTGATCATTTTATAACTTTT
1 AATAGTCGAGAGACCATTTTATAACTTTT
* * ** * *
240872 AATAGTCGAGAGACTTAATAGAGTAACATTC
1 AATAGTCGAGAGAC-CATTTTA-TAACTTTT
* *
240903 CATAGTC-AAAGGACCATTTTATAACTTTT
1 AATAGTCGAGA-GACCATTTTATAACTTTT
240932 AATAGTCGA
1 AATAGTCGA
240941 CGGACTTAAT
Statistics
Matches: 48, Mismatches: 17, Indels: 7
0.67 0.24 0.10
Matches are distributed among these distances:
29 24 0.50
30 9 0.19
31 15 0.31
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (29 bp):
AATAGTCGAGAGACCATTTTATAACTTTT
Found at i:247065 original size:38 final size:36
Alignment explanation
Indices: 246983--247065 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 36
246973 AATATAATTT
246983 TAAATACAACAAACTTACAATAAGTATTAAATGGTAA
1 TAAATA-AACAAACTTACAATAAGTATTAAATGGTAA
*
247020 -ATGATAAACAAA-TTACAATAACTGATATTAAATGGTAA
1 TA-AATAAACAAACTTACAATAA--G-TATTAAATGGTAA
247058 TAAATAAA
1 TAAATAAA
247066 ATTAACTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
35 9 0.23
36 7 0.18
37 4 0.10
38 18 0.46
39 1 0.03
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.28
Consensus pattern (36 bp):
TAAATAAACAAACTTACAATAAGTATTAAATGGTAA
Found at i:247102 original size:34 final size:33
Alignment explanation
Indices: 247063--247147 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
247053 GGTAATAAAT
*
247063 AAAATTAACTAAAATACATTAACAA-AAAGTCCAAC
1 AAAATTAAC-AAAATAAATTAA-AATAAA-TCCAAC
*
247098 AAATTTAACAAAATAAATTAAAATAAATCCAAC
1 AAAATTAACAAAATAAATTAAAATAAATCCAAC
**
247131 AAAATTAATGAAATAAA
1 AAAATTAACAAAATAAA
247148 GTAAGTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
33 22 0.50
34 14 0.32
35 8 0.18
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.22
Consensus pattern (33 bp):
AAAATTAACAAAATAAATTAAAATAAATCCAAC
Found at i:247184 original size:14 final size:14
Alignment explanation
Indices: 247165--247197 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
247155 TTAAATGATA
247165 AATAAAAAAAGTAC
1 AATAAAAAAAGTAC
*
247179 AAT-AAAAAAGTCC
1 AATAAAAAAAGTAC
247192 AATAAA
1 AATAAA
247198 CAACTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.70, C:0.09, G:0.06, T:0.15
Consensus pattern (14 bp):
AATAAAAAAAGTAC
Found at i:249394 original size:12 final size:12
Alignment explanation
Indices: 249377--249424 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
249367 AAAAAAATTA
249377 ATTAAATAAAAT
1 ATTAAATAAAAT
*
249389 ATTAAATAAATT
1 ATTAAATAAAAT
* *
249401 A-AAAACAAAAT
1 ATTAAATAAAAT
*
249412 ATTAAATATAAT
1 ATTAAATAAAAT
249424 A
1 A
249425 AAATATACAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:249414 original size:23 final size:23
Alignment explanation
Indices: 249384--249427 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
249374 TTAATTAAAT
249384 AAAATATTAAATA-AATTAAAAAC
1 AAAATATTAAATATAA-TAAAAAC
249407 AAAATATTAAATATAATAAAA
1 AAAATATTAAATATAATAAAA
249428 TATACATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAATATTAAATATAATAAAAAC
Found at i:249637 original size:18 final size:18
Alignment explanation
Indices: 249614--249653 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
249604 TTTAGGCCTG
249614 GCCTGGGCCTGTTTAAAA
1 GCCTGGGCCTGTTTAAAA
249632 GCCT-GGCCTGTTTAAAA
1 GCCTGGGCCTGTTTAAAA
249649 GCCTG
1 GCCTG
249654 TTTAAAAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (18 bp):
GCCTGGGCCTGTTTAAAA
Found at i:249652 original size:12 final size:12
Alignment explanation
Indices: 249637--249670 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
249627 TAAAAGCCTG
249637 GCCTGTTTAAAA
1 GCCTGTTTAAAA
249649 GCCTGTTTAAAA
1 GCCTGTTTAAAA
249661 GCCTGTTTAA
1 GCCTGTTTAA
249671 CAATAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (12 bp):
GCCTGTTTAAAA
Found at i:251168 original size:20 final size:21
Alignment explanation
Indices: 251143--251183 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
251133 ATATGATGTT
251143 CTTTAT-TAAATTTAATTTTA
1 CTTTATATAAATTTAATTTTA
* *
251163 CTTTATATAATTTTACTTTTA
1 CTTTATATAAATTTAATTTTA
251184 TAAGAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (21 bp):
CTTTATATAAATTTAATTTTA
Found at i:251185 original size:16 final size:15
Alignment explanation
Indices: 251155--251186 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
251145 TTATTAAATT
251155 TAATTTTACTTTATA
1 TAATTTTACTTTATA
251170 TAATTTTACTTT-TA
1 TAATTTTACTTTATA
251184 TAA
1 TAA
251187 GAATTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATTTTACTTTATA
Found at i:259764 original size:13 final size:13
Alignment explanation
Indices: 259746--259781 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
259736 GCATCTTTTT
259746 ATATTTTTTATTA
1 ATATTTTTTATTA
* *
259759 ATATTTTTTTTTT
1 ATATTTTTTATTA
259772 ATATTTTTTA
1 ATATTTTTTA
259782 AAATTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
ATATTTTTTATTA
Found at i:261006 original size:23 final size:23
Alignment explanation
Indices: 260980--261023 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
260970 ACTCAACGTA
260980 TAATTGTAAATTAGTTAAAATTT
1 TAATTGTAAATTAGTTAAAATTT
* *
261003 TAATTTTAAATTATTTAAAAT
1 TAATTGTAAATTAGTTAAAAT
261024 AACATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (23 bp):
TAATTGTAAATTAGTTAAAATTT
Found at i:295876 original size:2 final size:2
Alignment explanation
Indices: 295871--295910 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
295861 ATACACACAC
295871 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
295911 CAAAGAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:296668 original size:12 final size:12
Alignment explanation
Indices: 296651--296718 Score: 59
Period size: 12 Copynumber: 5.7 Consensus size: 12
296641 ATAATTGTAT
296651 ATTTTATTTTTA
1 ATTTTATTTTTA
296663 ATTTTATTTTTA
1 ATTTTATTTTTA
* *
296675 A-TTT-TTATTC
1 ATTTTATTTTTA
296685 ATTTTATTAATTTA
1 ATTTTATT--TTTA
* * *
296699 GTCTTAATTTTA
1 ATTTTATTTTTA
296711 ATTTTATT
1 ATTTTATT
296719 CAATATAACC
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
10 5 0.12
11 6 0.14
12 24 0.57
14 7 0.17
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (12 bp):
ATTTTATTTTTA
Found at i:296678 original size:19 final size:19
Alignment explanation
Indices: 296642--296681 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
296632 AATATCGATA
296642 TAATTGTATATTTTATTTT
1 TAATTGTATATTTTATTTT
*
296661 TAATTTTAT-TTTTAATTTT
1 TAATTGTATATTTT-ATTTT
296680 TA
1 TA
296682 TTCATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TAATTGTATATTTTATTTT
Found at i:296967 original size:2 final size:2
Alignment explanation
Indices: 296960--296989 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
296950 AACTACAATA
296960 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
296990 GTTATAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:311141 original size:17 final size:18
Alignment explanation
Indices: 311113--311152 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
311103 ACATAATTAT
311113 AATTATAATAAAAAATAA
1 AATTATAATAAAAAATAA
**
311131 AATTA-AATAAAATGTAA
1 AATTATAATAAAAAATAA
311148 AATTA
1 AATTA
311153 CGAGATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (18 bp):
AATTATAATAAAAAATAA
Found at i:312411 original size:2 final size:2
Alignment explanation
Indices: 312404--312501 Score: 113
Period size: 2 Copynumber: 53.0 Consensus size: 2
312394 CCGACCCGAT
312404 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
312446 TA -A TA TT TA TA TA T- TA -A T- TA TA TA TA TA -A TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
312482 TA TA TT TA TA T- TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
312502 AAAATATTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
1 8 0.10
2 75 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:312850 original size:32 final size:32
Alignment explanation
Indices: 312800--312871 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
312790 CAACTTAAGG
*
312800 GGGCAAAACATAATTAATCATAAAAAATGAGA
1 GGGCAAAACATAACTAATCATAAAAAATGAGA
** * *
312832 GGGCAAAGTATAACTAATCATAGAAAATGAGG
1 GGGCAAAACATAACTAATCATAAAAAATGAGA
312864 GGGCAAAA
1 GGGCAAAA
312872 TTAAAATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.17
Consensus pattern (32 bp):
GGGCAAAACATAACTAATCATAAAAAATGAGA
Found at i:315449 original size:70 final size:70
Alignment explanation
Indices: 315368--315525 Score: 255
Period size: 70 Copynumber: 2.3 Consensus size: 70
315358 ATACATTTTT
*
315368 ATAAAGTATCGACACTTTATTGA-TGCTATAACTTATTTTCTTTTAAATTCCAAAAGTGTCGATA
1 ATAAAGTATCGACACTTTATTGACT-CTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATA
315432 CTTATA
65 CTTATA
* * **
315438 ATAAAGTATCGACACTTTATTGACTCTATAACTTCTTCTGTTTTAAATTTTAAAAGTGTCGATAC
1 ATAAAGTATCGACACTTTATTGACTCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATAC
315503 TTATA
66 TTATA
315508 ATAAAGTATCGACACTTT
1 ATAAAGTATCGACACTTT
315526 CAACATATCC
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
70 81 0.99
71 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (70 bp):
ATAAAGTATCGACACTTTATTGACTCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATAC
TTATA
Found at i:315759 original size:182 final size:181
Alignment explanation
Indices: 315438--315818 Score: 593
Period size: 182 Copynumber: 2.1 Consensus size: 181
315428 GATACTTATA
* * * *
315438 ATAAAGTATCGACACTTTATTGACTCTATAACTTCTTCTGTTTTAAATTTTAAAAGTGTCGATAC
1 ATAAAGTATCGACACTTTATTGACGCTATAACTTATTCTCTTTTAAATTCTAAAAGTGTCGATAC
* * * *
315503 TTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGAGA
66 TTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTAGAGA
* *
315568 CCGGTTTTGTCATATTTTTACATGTTATATTATTGTGGATCGATACATTTTT
131 CCAGTTTTGTCAT-TTTTTACATGTTATATTATTATGGATCGATACATTTTT
*
315620 ATAAAGTATCGATACTTTATT-AGCGCTATAACTTATTCTCTTTTAAATTCTAAAAGTGTCGATA
1 ATAAAGTATCGACACTTTATTGA-CGCTATAACTTATTCTCTTTTAAATTCTAAAAGTGTCGATA
*
315684 CTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTATAG
65 CTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTAGAG
* * *
315749 ATCAGTTTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
130 ACCAGTTTTGTCATTTTTTACATGTTATATTATTATGGATCGATACATTTTT
*
315801 ATAAAGTATCGTCACTTT
1 ATAAAGTATCGACACTTT
315819 CAATATATCC
Statistics
Matches: 181, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
181 52 0.29
182 129 0.71
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (181 bp):
ATAAAGTATCGACACTTTATTGACGCTATAACTTATTCTCTTTTAAATTCTAAAAGTGTCGATAC
TTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTAGAGA
CCAGTTTTGTCATTTTTTACATGTTATATTATTATGGATCGATACATTTTT
Found at i:315929 original size:112 final size:112
Alignment explanation
Indices: 315690--316150 Score: 737
Period size: 111 Copynumber: 4.1 Consensus size: 112
315680 GATACTTATA
* * * * *
315690 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTATAGATCAGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
315755 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
315801 ATAAAGTATCGTCACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
315866 TTTGTCATTTTTTTATCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
315913 ATAAAGTATCGACACTTTCAATGTATCCGGTAGCGCTTTACATGTTTTATCATTTATATACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
315978 TTTGTCATTTTTTTA-CTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
316024 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACTTGTTTTGTCATTTATAGATCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
316089 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
316136 ATAAAGTATTGACAC
1 ATAAAGTATCGACAC
316151 AAACCGACAA
Statistics
Matches: 324, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
111 169 0.52
112 155 0.48
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:316078 original size:223 final size:223
Alignment explanation
Indices: 315690--316150 Score: 737
Period size: 223 Copynumber: 2.1 Consensus size: 223
315680 GATACTTATA
* *
315690 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTATAGATCAGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCAGTTTTATCATTTATAGACCAGT
*
315755 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGTCACTTTC
66 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTC
* *
315820 AATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTATCTG
131 AATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACCTG
*
315885 TTATATTGTTATGGATCGATACATTTTT
196 TTATATTGTTATGGATCAATACATTTTT
* ** * *
315913 ATAAAGTATCGACACTTTCAATGTATCCGGTAGCGCTTTA-CATGTTTTATCATTTATATACCGG
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCA-GTTTTATCATTTATAGACCAG
315977 TTTTGTCATTTTTTTA-CTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
65 TTTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
* * * *
316041 TCAATATATCCGGTAGCGTTTTACTTGTTTTGTCATTTATAGATCGATTTTGTCATTTTTTTACC
129 TCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACC
*
316106 TGTTATATTGTTATGGATCAATATATTTTT
194 TGTTATATTGTTATGGATCAATACATTTTT
*
316136 ATAAAGTATTGACAC
1 ATAAAGTATCGACAC
316151 AAACCGACAA
Statistics
Matches: 219, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
222 2 0.01
223 210 0.96
224 7 0.03
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (223 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCAGTTTTATCATTTATAGACCAGT
TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTC
AATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACCTG
TTATATTGTTATGGATCAATACATTTTT
Found at i:318235 original size:25 final size:24
Alignment explanation
Indices: 318193--318239 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
318183 CTCATTATTA
*
318193 TTTAAAACATATTATTGATAAAATT
1 TTTAAAAAATATTATTGA-AAAATT
318218 TTTAAAAAATA-TATTTGAAAAA
1 TTTAAAAAATATTA-TTGAAAAA
318240 GCATAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (24 bp):
TTTAAAAAATATTATTGAAAAATT
Found at i:320448 original size:3 final size:3
Alignment explanation
Indices: 320440--320530 Score: 137
Period size: 3 Copynumber: 30.3 Consensus size: 3
320430 TTTTTATCCA
* * *
320440 TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
320488 TAT TAT TAT TAT TAT TAT TTT TAT TTT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
320531 TATCATTAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:322137 original size:17 final size:18
Alignment explanation
Indices: 322112--322164 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
322102 GGATATTTTT
322112 AAATAAATATAATTTTGA
1 AAATAAATATAATTTTGA
* *
322130 AAAT-AATAGAATTAT-A
1 AAATAAATATAATTTTGA
* *
322146 AATTAAATATATTTTTGA
1 AAATAAATATAATTTTGA
322164 A
1 A
322165 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATAAATATAATTTTGA
Found at i:333301 original size:20 final size:18
Alignment explanation
Indices: 333276--333333 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 18
333266 CTTGAAGAAA
333276 AAAAAACAACAACAAAAAAC
1 AAAAAA-AA-AACAAAAAAC
* *
333296 AAAAAAGAAAAAAAAAAAAG
1 -AAAAA-AAAAACAAAAAAC
333316 AAAAAAAAAACGAAAAAA
1 AAAAAAAAAAC-AAAAAA
333334 GGGGGTCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 8 0.25
21 7 0.22
22 1 0.03
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAACAAAAAAC
Found at i:333306 original size:13 final size:13
Alignment explanation
Indices: 333273--333332 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
333263 ATGCTTGAAG
333273 AAAA-AAAAACAA
1 AAAAGAAAAACAA
*
333285 CAACA-AAAAACAA
1 -AAAAGAAAAACAA
*
333298 AAAAGAAAAAAAA
1 AAAAGAAAAACAA
333311 AAAAGAAAAA-AA
1 AAAAGAAAAACAA
*
333323 AAACGAAAAA
1 AAAAGAAAAA
333333 AGGGGGTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
12 14 0.33
13 28 0.67
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAACAA
Found at i:333325 original size:32 final size:33
Alignment explanation
Indices: 333273--333334 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
333263 ATGCTTGAAG
*
333273 AAAAAAAAACAACAACAAAAAAC-AAAAAAGAAA
1 AAAAAAAAAC-ACAAAAAAAAACGAAAAAAGAAA
*
333306 AAAAAAAAAGA-AAAAAAAAACGAAAAAAG
1 AAAAAAAAACACAAAAAAAAACGAAAAAAG
333335 GGGGTCAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 9 0.35
32 8 0.31
33 9 0.35
ACGTcount: A:0.85, C:0.08, G:0.06, T:0.00
Consensus pattern (33 bp):
AAAAAAAAACACAAAAAAAAACGAAAAAAGAAA
Found at i:333333 original size:1 final size:1
Alignment explanation
Indices: 333273--333325 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
333263 ATGCTTGAAG
* * * * * *
333273 AAAAAAAAACAACAACAAAAAACAAAAAAGAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
333326 CGAAAAAAGG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.89, C:0.08, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:333333 original size:13 final size:13
Alignment explanation
Indices: 333274--333325 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
333264 TGCTTGAAGA
*
333274 AAAAAAAACAACAAC
1 AAAAAAAA-AA-AAG
333289 AAAAAACAAAAAAG
1 AAAAAA-AAAAAAG
333303 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
333316 AAAAAAAAAA
1 AAAAAAAAAA
333326 CGAAAAAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
13 17 0.49
14 8 0.23
15 8 0.23
16 2 0.06
ACGTcount: A:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:333690 original size:19 final size:19
Alignment explanation
Indices: 333662--333698 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
333652 GTTCAACTTA
*
333662 TTGGAGATTCAATTTATTT
1 TTGGAAATTCAATTTATTT
333681 TTGGAAATTCAATTTATT
1 TTGGAAATTCAATTTATT
333699 CTTTTCTATT
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:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (19 bp):
TTGGAAATTCAATTTATTT
Found at i:334538 original size:52 final size:52
Alignment explanation
Indices: 334459--334617 Score: 284
Period size: 52 Copynumber: 3.1 Consensus size: 52
334449 CAAACATTAA
334459 ACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-G
1 ACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
*
334510 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTGG
1 A-CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
*
334563 ACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGG
1 ACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
334615 ACA
1 ACA
334618 AAATCAAGTA
Statistics
Matches: 103, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 1 0.01
52 100 0.97
53 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (52 bp):
ACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
Found at i:335459 original size:119 final size:119
Alignment explanation
Indices: 335248--335779 Score: 891
Period size: 119 Copynumber: 4.5 Consensus size: 119
335238 TTAGCAAAGA
*
335248 CTTGAATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
1 CTTGAATTCATCAATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAACTCGT
335313 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
66 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
**
335367 CTTGAATTCATCAAACTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAACTCGT
1 CTTGAATTCATCAATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAACTCGT
*
335432 CAGCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
66 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
*
335486 CTTGAATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGT
1 CTTGAATTCATCAATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAACTCGT
335551 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
66 CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* *
335605 CTTGAATTCATC-ACTTGATGGATCATTCTTTTCCAG-AGAA-AGTTCATAATGAGAAGAA--C-
1 CTTGAATTCATCAATTTGATGGATCA-TCATTTCCAGAAGAAGAGTTCATAATGAGAAGAACTCG
*
335664 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTG
65 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* ** *
335719 CTTGAATTCATC-ATTTGATGGAACATCATCCCCAGCAGAA-AGTTCATAATGAGAAGAACTC
1 CTTGAATTCATCAATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAACTC
335780 ATCTGGAGAA
Statistics
Matches: 392, Mismatches: 17, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
113 7 0.02
114 99 0.25
115 1 0.00
116 1 0.00
117 18 0.05
118 15 0.04
119 251 0.64
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.28
Consensus pattern (119 bp):
CTTGAATTCATCAATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAACTCGT
CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
Found at i:335942 original size:3 final size:3
Alignment explanation
Indices: 335934--336021 Score: 133
Period size: 3 Copynumber: 29.7 Consensus size: 3
335924 TTTTTATCCA
* *
335934 TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
335982 TAT TAT TTT TAT TTT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
336022 AATATATAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
2 2 0.03
3 74 0.97
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:337619 original size:17 final size:18
Alignment explanation
Indices: 337594--337646 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
337584 GGATATTTTT
337594 AAATAAATATAATTTTGA
1 AAATAAATATAATTTTGA
* *
337612 AAAT-AATAGAATTAT-A
1 AAATAAATATAATTTTGA
* *
337628 AATTAAATATATTTTTGA
1 AAATAAATATAATTTTGA
337646 A
1 A
337647 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATAAATATAATTTTGA
Found at i:342873 original size:22 final size:21
Alignment explanation
Indices: 342833--342883 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
342823 TTATATTTTC
* *
342833 AATTTTGTAAAAAATTATATA
1 AATTTTTTAAAAAAATATATA
342854 AATTTTTTAAAGAAAATATATA
1 AATTTTTTAAA-AAAATATATA
*
342876 AATATTTT
1 AATTTTTT
342884 CCAACTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
AATTTTTTAAAAAAATATATA
Found at i:343048 original size:18 final size:19
Alignment explanation
Indices: 343025--343067 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
343015 AAGTAATCCT
*
343025 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGATAATCTTAC
343043 ATTCCCACTGATAATCTTAC
1 ATT-CCACTGATAATCTTAC
343063 ATTCC
1 ATTCC
343068 GTGAACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:347636 original size:49 final size:49
Alignment explanation
Indices: 347574--347670 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
347564 CATAAAGAGA
347574 AAAAAACATAAAATGAATTCTATTGACTATATAACAGTAAAAGATACAG
1 AAAAAACATAAAATGAATTCTATTGACTATATAACAGTAAAAGATACAG
347623 AAAAAACATAAAATGAATTCTATTGACTATATAACAGTAAAAGATACA
1 AAAAAACATAAAATGAATTCTATTGACTATATAACAGTAAAAGATACA
347671 CAGTTACAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.56, C:0.10, G:0.09, T:0.25
Consensus pattern (49 bp):
AAAAAACATAAAATGAATTCTATTGACTATATAACAGTAAAAGATACAG
Found at i:351828 original size:22 final size:22
Alignment explanation
Indices: 351794--351842 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
351784 ATAATTATTT
351794 AAAAAATTAAAT-AAAAATACAA
1 AAAAAATTAAATAAAAAATA-AA
* *
351816 AAAACATTTAATAAAAAATAAA
1 AAAAAATTAAATAAAAAATAAA
351838 AAAAA
1 AAAAA
351843 TTAGCTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATAAA
Found at i:368291 original size:6 final size:5
Alignment explanation
Indices: 368264--368306 Score: 59
Period size: 5 Copynumber: 8.0 Consensus size: 5
368254 GAAAGCCAAG
368264 CCGAC CCGAC CCGAC CCGAC CACGAC CACGAC CACGAC CCGAC
1 CCGAC CCGAC CCGAC CCGAC C-CGAC C-CGAC C-CGAC CCGAC
368307 ACGGACGGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 20 0.54
6 17 0.46
ACGTcount: A:0.26, C:0.56, G:0.19, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:368804 original size:6 final size:6
Alignment explanation
Indices: 368793--368831 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
368783 TCTCGTCTCG
368793 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
368832 AATAATAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:374672 original size:23 final size:21
Alignment explanation
Indices: 374634--374676 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
374624 TTAATTATTT
374634 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
374655 AAAAACATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
374676 A
1 A
374677 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:384155 original size:18 final size:18
Alignment explanation
Indices: 384132--384166 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
384122 CTTTTAATAG
384132 ATTTGTTTAGATTTATTC
1 ATTTGTTTAGATTTATTC
*
384150 ATTTGTTTATATTTATT
1 ATTTGTTTAGATTTATT
384167 TTGACCTTTA
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:0.03, G:0.09, T:0.66
Consensus pattern (18 bp):
ATTTGTTTAGATTTATTC
Found at i:386578 original size:2 final size:2
Alignment explanation
Indices: 386573--386598 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
386563 ATATGTGTGA
386573 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
386599 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:395912 original size:13 final size:13
Alignment explanation
Indices: 395894--395918 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
395884 TTAATAATAG
395894 CTTAATCTCTACC
1 CTTAATCTCTACC
395907 CTTAATCTCTAC
1 CTTAATCTCTAC
395919 TACCTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (13 bp):
CTTAATCTCTACC
Found at i:396587 original size:69 final size:69
Alignment explanation
Indices: 396440--396595 Score: 179
Period size: 69 Copynumber: 2.3 Consensus size: 69
396430 TCTGCCCTTG
* * * **
396440 AGAGTTTAAATTCCCTTAAAAGTTTAGATCTTTCTTCCAATCAATTGTCGGGGGATATTGCAACC
1 AGAGTTTAACTTCCCTTGAAAGTTTAGATCTTTCTTCCAACCAATTGTCGGGAAATATTGCAACC
396505 ATTA
66 ATTA
** * * *
396509 AGAACTTAACTTCCCTTGAAAGTTTAGATCTTTCTTCCAACCAATTTTCGGGAAAT-TTGTCGAT
1 AGAGTTTAACTTCCCTTGAAAGTTTAGATCTTTCTTCCAACCAATTGTCGGGAAATATTG-CAAC
* *
396573 CTTTC
65 CATTA
*
396578 AGAGTTTAACATCCCTTG
1 AGAGTTTAACTTCCCTTG
396596 TGATGTTGAG
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
68 3 0.04
69 68 0.96
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (69 bp):
AGAGTTTAACTTCCCTTGAAAGTTTAGATCTTTCTTCCAACCAATTGTCGGGAAATATTGCAACC
ATTA
Found at i:399483 original size:21 final size:23
Alignment explanation
Indices: 399447--399488 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
399437 ACTTAAAAAT
399447 ATTTTATTTTCGAAAA-ACCACC
1 ATTTTATTTTCGAAAATACCACC
*
399469 ATTTT-TTTTCTAAAATACCA
1 ATTTTATTTTCGAAAATACCA
399489 AAAAAACCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTTATTTTCGAAAATACCACC
Found at i:404504 original size:23 final size:23
Alignment explanation
Indices: 404458--404505 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
404448 TCGATTCGTC
* *
404458 TAATATTTATAAATATATTTATT
1 TAATATTTATAAACATATTCATT
* *
404481 TAATATTTGTAAACATGTTCATT
1 TAATATTTATAAACATATTCATT
404504 TA
1 TA
404506 TACGATTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (23 bp):
TAATATTTATAAACATATTCATT
Found at i:404952 original size:2 final size:2
Alignment explanation
Indices: 404945--404973 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
404935 TCTTCACCAA
404945 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
404974 TTTCAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:405470 original size:28 final size:28
Alignment explanation
Indices: 405423--405476 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
405413 TTATGATATT
405423 TAAAAAAACTCTAAATTCTTCTAAAATCA
1 TAAAAAAACTCTAAATTCTT-TAAAATCA
405452 TAAAAAAA-TCTTAAA-TCTTTAAAAT
1 TAAAAAAACTC-TAAATTCTTTAAAAT
405477 ACCTAATTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.25
28 6 0.25
29 12 0.50
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (28 bp):
TAAAAAAACTCTAAATTCTTTAAAATCA
Found at i:406583 original size:20 final size:19
Alignment explanation
Indices: 406542--406593 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
406532 AAAATTATTT
* *
406542 AAAATTTTTAAAAAAACAC
1 AAAATTTTTGAAATAACAC
*
406561 AAAATTTTTGAAATAGCACC
1 AAAATTTTTGAAATAACA-C
*
406581 AAAA-CTTTGAAAT
1 AAAATTTTTGAAAT
406594 CCCTCATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.29
Consensus pattern (19 bp):
AAAATTTTTGAAATAACAC
Found at i:410926 original size:26 final size:25
Alignment explanation
Indices: 410896--410972 Score: 62
Period size: 26 Copynumber: 3.3 Consensus size: 25
410886 CAAATAGTTA
410896 CTGTTCATGTAGTTCATGGAGGAAGG
1 CTGTTCATGTAGTTCAT-GAGGAAGG
*
410922 CTGTTCGA-ATAGTT-A--A-G-A--
1 CTGTTC-ATGTAGTTCATGAGGAAGG
410940 CTGTTCATGTAGTTCATGAAGGAAGG
1 CTGTTCATGTAGTTCATG-AGGAAGG
410966 CTGTTCA
1 CTGTTCA
410973 AATAGTTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 20
0.64 0.03 0.33
Matches are distributed among these distances:
17 1 0.03
18 11 0.28
19 1 0.03
20 1 0.03
21 1 0.03
22 2 0.05
23 1 0.03
24 1 0.03
25 1 0.03
26 18 0.46
27 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (25 bp):
CTGTTCATGTAGTTCATGAGGAAGG
Found at i:410963 original size:44 final size:44
Alignment explanation
Indices: 410857--411005 Score: 214
Period size: 44 Copynumber: 3.5 Consensus size: 44
410847 ATTACTTCCC
* *
410857 GTTCATGCAGCTCATGAAGGAAGGTTGTTCAAATAGTT---ACT
1 GTTCATGTAGCTCATGAAGGAAGGCTGTTCAAATAGTTAAGACT
* * *
410898 GTTCATGTAGTTCATGGAGGAAGGCTGTTCGAATAGTTAAGACT
1 GTTCATGTAGCTCATGAAGGAAGGCTGTTCAAATAGTTAAGACT
*
410942 GTTCATGTAGTTCATGAAGGAAGGCTGTTCAAATAGTTAAGACT
1 GTTCATGTAGCTCATGAAGGAAGGCTGTTCAAATAGTTAAGACT
*
410986 GTTCATGTAGCTCACGAAGG
1 GTTCATGTAGCTCATGAAGG
411006 CTGTTCGGGT
Statistics
Matches: 96, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
41 33 0.34
44 63 0.66
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (44 bp):
GTTCATGTAGCTCATGAAGGAAGGCTGTTCAAATAGTTAAGACT
Found at i:412693 original size:23 final size:23
Alignment explanation
Indices: 412663--412729 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
412653 TTTATTTTAG
412663 TTTACGTTCATTTATTGTGTACA
1 TTTACGTTCATTTATTGTGTACA
* **
412686 TTTACGTT-AGTTCATTTGTGTTTA
1 TTTACGTTCA-TTTA-TTGTGTACA
*
412710 TTTACGTTCGTTTATTGTGT
1 TTTACGTTCATTTATTGTGT
412730 TTGTTTACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 1 0.03
23 17 0.47
24 18 0.50
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.57
Consensus pattern (23 bp):
TTTACGTTCATTTATTGTGTACA
Found at i:412731 original size:23 final size:23
Alignment explanation
Indices: 412658--412737 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
412648 TTTCATTTAT
*
412658 TTTAGTTTACGTTCATTTATTGTG
1 TTTA-TTTACGTTCGTTTATTGTG
** * *
412682 TACATTTACGTTAGTTCATTTGTG
1 TTTATTTACGTTCGTTTA-TTGTG
412706 TTTATTTACGTTCGTTTATTGTG
1 TTTATTTACGTTCGTTTATTGTG
*
412729 TTTGTTTAC
1 TTTATTTAC
412738 ATCCGTTCAT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
23 24 0.53
24 21 0.47
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.57
Consensus pattern (23 bp):
TTTATTTACGTTCGTTTATTGTG
Found at i:412744 original size:23 final size:23
Alignment explanation
Indices: 412701--412744 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
412691 GTTAGTTCAT
* *
412701 TTGTGTTTATTTACGTTCGTTTA
1 TTGTGTTTATTTACATCCGTTTA
*
412724 TTGTGTTTGTTTACATCCGTT
1 TTGTGTTTATTTACATCCGTT
412745 CATTTATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.59
Consensus pattern (23 bp):
TTGTGTTTATTTACATCCGTTTA
Found at i:412746 original size:47 final size:48
Alignment explanation
Indices: 412649--412754 Score: 126
Period size: 47 Copynumber: 2.2 Consensus size: 48
412639 AAAATCTATT
* *
412649 TTCATTTAT-TTTAGTTTACGTTCATTTATTGTGTACATTTACGTTAG
1 TTCATTTATGTTTAGTTTACGTTCATTTATTGTGTACATTTACATCAG
* * *** *
412696 TTCATTTGTGTTTA-TTTACGTTCGTTTATTGTGTTTGTTTACATCCG
1 TTCATTTATGTTTAGTTTACGTTCATTTATTGTGTACATTTACATCAG
412743 TTCATTTATGTT
1 TTCATTTATGTT
412755 CGTTCATCAT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 45 0.92
48 4 0.08
ACGTcount: A:0.17, C:0.11, G:0.14, T:0.58
Consensus pattern (48 bp):
TTCATTTATGTTTAGTTTACGTTCATTTATTGTGTACATTTACATCAG
Found at i:415300 original size:60 final size:60
Alignment explanation
Indices: 415198--415312 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
415188 AGTTTCTAAA
*
415198 CTTTTAAATGTTCCAATTTCATCCCTAAACTACGACTATCATTCTAAACTAGTCCTCAAG
1 CTTTTAAATGTTCCAATTTCATCCCCAAACTACGACTATCATTCTAAACTAGTCCTCAAG
* * * * *
415258 CTTTTGAATGTTTCAATTTCATCCCCAAATTATGACCT-TCATTCTAAATTAGTCC
1 CTTTTAAATGTTCCAATTTCATCCCCAAACTACGA-CTATCATTCTAAACTAGTCC
415313 CAACACATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 46 0.96
61 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (60 bp):
CTTTTAAATGTTCCAATTTCATCCCCAAACTACGACTATCATTCTAAACTAGTCCTCAAG
Found at i:415567 original size:60 final size:62
Alignment explanation
Indices: 415471--415649 Score: 176
Period size: 60 Copynumber: 3.0 Consensus size: 62
415461 GAATTTGGGG
* * * *
415471 ATAAAATTGGAATATTCAAAAGTTT-GGGA-TCAATTTAGAAAAGGGGGTCATAGTTTAGGG-
1 ATAAAATTAGAATATTCAAAAGTTTAAGGACT-AATTTAGAAAAGAGGGTTATAGTTTAGGGA
* * * * * * *
415531 AT-AAATTAGAATTTTTAAAAGTTTTAGGACTGATTTAG-AATGTGAGTTATAGTTT-GGGA
1 ATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAAGAGGGTTATAGTTTAGGGA
*
415590 ATAAAATTGGAATATTCAAAAGTTTAAGGACTAATTTA-AAATA-AGGGTTATAGTTTAGGG
1 ATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAA-AGAGGGTTATAGTTTAGGG
415650 GCATGTGATA
Statistics
Matches: 95, Mismatches: 17, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
58 3 0.03
59 34 0.36
60 54 0.57
61 4 0.04
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (62 bp):
ATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAAGAGGGTTATAGTTTAGGGA
Found at i:425822 original size:3 final size:3
Alignment explanation
Indices: 425814--425843 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
425804 AAGATAATCA
425814 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
425844 GTGTTACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:426356 original size:22 final size:23
Alignment explanation
Indices: 426328--426371 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
426318 TATACGATAA
*
426328 AATTTCAAGGTGGACAC-CATAG
1 AATTTCAAGGTGAACACGCATAG
*
426350 AATTTCAGGGTGAACACGCATA
1 AATTTCAAGGTGAACACGCATA
426372 CATTAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (23 bp):
AATTTCAAGGTGAACACGCATAG
Found at i:433934 original size:23 final size:23
Alignment explanation
Indices: 433904--433950 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
433894 ACTGGGTTGG
433904 TTTTGGGCCC-AGATTTGTTTTGT
1 TTTTGGGCCCGAG-TTTGTTTTGT
433927 TTTTGGGCCCGAGTTTGTTTTGT
1 TTTTGGGCCCGAGTTTGTTTTGT
433950 T
1 T
433951 GGGCTTGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.06, C:0.13, G:0.28, T:0.53
Consensus pattern (23 bp):
TTTTGGGCCCGAGTTTGTTTTGT
Found at i:434064 original size:2 final size:2
Alignment explanation
Indices: 434045--434083 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
434035 CCCATTTTTC
* *
434045 AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
434084 AAAGTTCCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:436720 original size:17 final size:18
Alignment explanation
Indices: 436700--436738 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
436690 ATTATATTAG
436700 TAAAAT-ATTAAATAAAA
1 TAAAATGATTAAATAAAA
* *
436717 TAAAATGCTTAAATAAAT
1 TAAAATGATTAAATAAAA
436735 TAAA
1 TAAA
436739 TACATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAATGATTAAATAAAA
Found at i:437536 original size:31 final size:30
Alignment explanation
Indices: 437465--437537 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 30
437455 AAAATTTTGG
* *
437465 TCAGTGACCAAA-ATGTAAATTTTAAAAGT
1 TCAGTGACCAAAGATATAAATTTTAAAAAT
*
437494 TCAGTGGCCAAAGATATAAATTTTGAAAAAT
1 TCAGTGACCAAAGATATAAATTTT-AAAAAT
437525 TCAGTGACCAAAG
1 TCAGTGACCAAAG
437538 TGGTAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 11 0.29
30 10 0.26
31 17 0.45
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (30 bp):
TCAGTGACCAAAGATATAAATTTTAAAAAT
Found at i:437546 original size:30 final size:29
Alignment explanation
Indices: 437465--437547 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 29
437455 AAAATTTTGG
* *
437465 TCAGTGACCAAAATGTAAATTTTAAAAGT
1 TCAGTGACCAAAGTGTAAATTTTAAAAAT
* *
437494 TCAGTGGCCAAAGATATAAATTTTGAAAAAT
1 TCAGTGACCAAAG-TGTAAATTTT-AAAAAT
437525 TCAGTGACCAAAGTGGT-AATTTT
1 TCAGTGACCAAAGT-GTAAATTTT
437548 CTCAAAAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 11 0.24
30 16 0.36
31 18 0.40
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (29 bp):
TCAGTGACCAAAGTGTAAATTTTAAAAAT
Found at i:446326 original size:23 final size:21
Alignment explanation
Indices: 446292--446336 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
446282 ATGAACATGA
446292 AGATTTTAATTATAATTTATAAT
1 AGATTTTAATTA-AATTTA-AAT
*
446315 AGATTTTCATTAAATTTAAAT
1 AGATTTTAATTAAATTTAAAT
446336 A
1 A
446337 TGTATTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 6 0.29
23 11 0.52
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (21 bp):
AGATTTTAATTAAATTTAAAT
Found at i:447170 original size:262 final size:264
Alignment explanation
Indices: 446705--447246 Score: 745
Period size: 262 Copynumber: 2.1 Consensus size: 264
446695 TAGAGTCACA
* *
446705 TTGCAATATGAAATA-TTATCATTTTATAAAATAAAAGTGATTGCGCCTAAAGTATTATAAAAGT
1 TTGCAATATGAAATATTTATCATTTTAAAAAATAAAAGTGATTGCACCTAAAGTATTATAAAAGT
* * *** * * *
446769 TTTAGTCGATGGAGTCTTGGCGTTCCCCATGACAATCAAATATGTTAAGAGCACAAAGTATTACG
66 TTTAGTCCATGGAGCCTTAAAGTTCCCCAAGACAATCAAATAGGTTAAGAACACAAAGTATTACG
* * * * *
446834 ATTAGCCAAAATAAAAACGGTTGTACCCTAGAATATCTCGATTCTAAAGGAAATAGGTCGCGACT
131 ATTAGCCAAAATAAAAACGATTGCACCCCAGAATATCACGATTCTAAAGGAAATAGATCGCGACT
* * *
446899 TGTAATGTCAATTTGTGTATTAATAGAATAGATTGTGCCCAGAGTATCATGTCCCC-AAAGAAAG
196 TGTAATGTCAACTTGTGTATTAATAGAATAGATTGCGCCCAGAGTATCATGACCCCAAAAGAAAG
446963 AACG
261 AACG
446967 TTGCAATATGAAATATTTATCATTTTAAAAAATAAAAGTGATTGCACCTAAAGTATTATGAAAA-
1 TTGCAATATGAAATATTTATCATTTTAAAAAATAAAAGTGATTGCACCTAAAGTATTAT-AAAAG
*
447031 TTTTAG-CCATGGAGCCTTAAAGTTCCCCAAGACAATCAAATAGGTTAAGAACACAAAGTATTAT
65 TTTTAGTCCATGGAGCCTTAAAGTTCCCCAAGACAATCAAATAGGTTAAGAACACAAAGTATTAC
** ** * *
447095 GATTAGGTAAAATGGAAACGATTGCGCCCCAGAATATCAC-AGTTCTAAA-GAAGATAGATTGCG
130 GATTAGCCAAAATAAAAACGATTGCACCCCAGAATATCACGA-TTCTAAAGGAA-ATAGATCGCG
* *
447158 ACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCGCCTAGAGTGTCATGACCCCAAAAGA
193 ACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCGCCCAGAGTATCATGACCCCAAAAGA
*
447223 AAGCACG
258 AAGAACG
* *
447230 TTGCAATCTGGAATATT
1 TTGCAATATGAAATATT
447247 ATGAAAGTTT
Statistics
Matches: 245, Mismatches: 30, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
261 4 0.02
262 164 0.67
263 73 0.30
264 4 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (264 bp):
TTGCAATATGAAATATTTATCATTTTAAAAAATAAAAGTGATTGCACCTAAAGTATTATAAAAGT
TTTAGTCCATGGAGCCTTAAAGTTCCCCAAGACAATCAAATAGGTTAAGAACACAAAGTATTACG
ATTAGCCAAAATAAAAACGATTGCACCCCAGAATATCACGATTCTAAAGGAAATAGATCGCGACT
TGTAATGTCAACTTGTGTATTAATAGAATAGATTGCGCCCAGAGTATCATGACCCCAAAAGAAAG
AACG
Found at i:451633 original size:14 final size:15
Alignment explanation
Indices: 451602--451638 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
451592 AGTAAAATTC
451602 AAAA-TATTTAAATA
1 AAAATTATTTAAATA
*
451616 AAAATTATTTATATA
1 AAAATTATTTAAATA
451631 AAAATTAT
1 AAAATTAT
451639 ATATGTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTATTTAAATA
Found at i:454641 original size:29 final size:29
Alignment explanation
Indices: 454599--454662 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
454589 CAGATTTCAT
454599 ATAAAACGATGAATTTCACTGCTGAGAAA
1 ATAAAACGATGAATTTCACTGCTGAGAAA
454628 ATAAAACGATGAATTTCACTGCTGAGAAA
1 ATAAAACGATGAATTTCACTGCTGAGAAA
454657 ATAAAA
1 ATAAAA
454663 TAAAGGGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.23
Consensus pattern (29 bp):
ATAAAACGATGAATTTCACTGCTGAGAAA
Found at i:465820 original size:2 final size:2
Alignment explanation
Indices: 465813--465846 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
465803 TTTTTAATTA
465813 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
465847 TAAGTCCACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:470680 original size:24 final size:24
Alignment explanation
Indices: 470653--470707 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
470643 ATCAAAAGAC
** *
470653 AGAGAAAAAACATGTTACGAAAGT
1 AGAGAAAAAACATACTACAAAAGT
*
470677 AGAGAAAAAACATACTATAAAAGT
1 AGAGAAAAAACATACTACAAAAGT
470701 AGAGAAA
1 AGAGAAA
470708 TTCGTGTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.60, C:0.07, G:0.18, T:0.15
Consensus pattern (24 bp):
AGAGAAAAAACATACTACAAAAGT
Found at i:476409 original size:9 final size:9
Alignment explanation
Indices: 476397--476428 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
476387 AAAAATAATA
476397 TAATTTTTT
1 TAATTTTTT
476406 TAA-TTTTT
1 TAATTTTTT
476414 TAATTTTTT
1 TAATTTTTT
476423 TAATTT
1 TAATTT
476429 ACAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TAATTTTTT
Found at i:477099 original size:2 final size:2
Alignment explanation
Indices: 477092--477150 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
477082 GCAACACAAG
477092 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
477134 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
477151 ATAAAGGGCG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:477480 original size:123 final size:123
Alignment explanation
Indices: 477261--477508 Score: 460
Period size: 123 Copynumber: 2.0 Consensus size: 123
477251 ACCTTCACTA
*
477261 AACTACGACGTTTTTATAAATTATGTTTAAAATACACTAATGTGGCGTTTGGTTTACTAAACTTT
1 AACTACGACGTTTTTATAAATTATGTTTAAAATACACTAATGTGGCGTTTGGTTCACTAAACTTT
477326 CCCATGTTTGATTCAAGTTTTCAAATGAGGAATTGAAATCCAATTCCATCAAGGATGG
66 CCCATGTTTGATTCAAGTTTTCAAATGAGGAATTGAAATCCAATTCCATCAAGGATGG
* *
477384 AACTACGACGTTTTTATAAATTATGTTTAAGATACACTAATGTGGCGTTTGGTTCACTAAATTTT
1 AACTACGACGTTTTTATAAATTATGTTTAAAATACACTAATGTGGCGTTTGGTTCACTAAACTTT
*
477449 CCCATGTTTGGTTCAAGTTTTCAAATGAGGAATTGAAATCCAATTCCATCAAGGATGG
66 CCCATGTTTGATTCAAGTTTTCAAATGAGGAATTGAAATCCAATTCCATCAAGGATGG
477507 AA
1 AA
477509 AGTAAATTTC
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 121 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (123 bp):
AACTACGACGTTTTTATAAATTATGTTTAAAATACACTAATGTGGCGTTTGGTTCACTAAACTTT
CCCATGTTTGATTCAAGTTTTCAAATGAGGAATTGAAATCCAATTCCATCAAGGATGG
Found at i:480856 original size:32 final size:32
Alignment explanation
Indices: 480792--480880 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 32
480782 TAGAAAATAT
** * *
480792 AAAATAATCATTAAATTTTATTGAACTCTTAC
1 AAAATAATCATTAAATTTTATCCAAATATTAC
*
480824 AAAATAATCATTATATTTTATCCAAATATTAC
1 AAAATAATCATTAAATTTTATCCAAATATTAC
* **
480856 AAATTTGTCATTAAA-TTTAT-CAAAT
1 AAAATAATCATTAAATTTTATCCAAAT
480881 TCTTATACTC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
30 5 0.10
31 5 0.10
32 38 0.79
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (32 bp):
AAAATAATCATTAAATTTTATCCAAATATTAC
Found at i:482559 original size:2 final size:2
Alignment explanation
Indices: 482547--482584 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
482537 TAATTTATCC
482547 TA TA CTA 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 TA TA T
482585 GATTATACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:484466 original size:2 final size:2
Alignment explanation
Indices: 484453--484486 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
484443 TCTTTGACAG
484453 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
484487 GATTATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:493366 original size:17 final size:17
Alignment explanation
Indices: 493339--493377 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
493329 AATTTATAAT
493339 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
493355 TAATTATAAATAATATC
1 TAATTATAAATAATATC
493372 TAATTA
1 TAATTA
493378 ATTTGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:495303 original size:6 final size:6
Alignment explanation
Indices: 495292--495316 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
495282 TAGTTATTTT
495292 ATTTAA ATTTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
495317 ATATATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:501295 original size:18 final size:20
Alignment explanation
Indices: 501267--501303 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
501257 ATAATTTGTG
501267 TATCGAATAATTA-TCGATA
1 TATCGAATAATTAGTCGATA
501286 TATC-AATAATTAGTCGAT
1 TATCGAATAATTAGTCGAT
501304 TTAATGTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (20 bp):
TATCGAATAATTAGTCGATA
Found at i:502830 original size:16 final size:16
Alignment explanation
Indices: 502809--502844 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
502799 GTTGGCAAAG
502809 GCGCGTTCCCGGGGAT
1 GCGCGTTCCCGGGGAT
502825 GCGCGTTCCCGGGGAT
1 GCGCGTTCCCGGGGAT
502841 GCGC
1 GCGC
502845 TTTACCCGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.06, C:0.33, G:0.44, T:0.17
Consensus pattern (16 bp):
GCGCGTTCCCGGGGAT
Found at i:506874 original size:128 final size:128
Alignment explanation
Indices: 506646--507520 Score: 1542
Period size: 128 Copynumber: 6.9 Consensus size: 128
506636 TAATCGGAGT
*
506646 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATATTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
* *
506711 CGTTGTCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
506774 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
506839 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
****
506902 ACTGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
506967 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
507030 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
507095 CATTGCCCTATTATGTCACTCATGT-CCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
507157 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTA-TTCGTTAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
507221 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* ***
507284 TC-AAGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
507348 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* ***
507411 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
*
507475 TCATTGCCTTATTATGTCACTCATGTCCCTCGGGGACACTAGATAT
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATAT
507521 CAGTAAATCA
Statistics
Matches: 721, Mismatches: 23, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
126 81 0.11
127 204 0.28
128 436 0.60
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:507992 original size:32 final size:32
Alignment explanation
Indices: 507923--508019 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 32
507913 AAATTTAATG
507923 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAA-TTTGAATA-TATAATTTATATTTTAAAT
* * * *
507957 TTAAATTTGAATATATTATTTTTATTTTTATT
1 TTAAATTTGAATATATAATTTATATTTTAAAT
*
507989 TTAAATTTCGAATA-ATAATTTGTATTTTAAA
1 TTAAATTT-GAATATATAATTTATATTTTAAA
508020 AATATTTATC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
32 36 0.67
33 13 0.24
34 5 0.09
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (32 bp):
TTAAATTTGAATATATAATTTATATTTTAAAT
Found at i:508566 original size:21 final size:21
Alignment explanation
Indices: 508536--508629 Score: 154
Period size: 21 Copynumber: 4.5 Consensus size: 21
508526 TATGGTATAA
*
508536 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
508557 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
508578 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
508599 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
508620 AACCCTGCGG
1 AACCCTGCGG
508630 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.21, C:0.27, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:508659 original size:21 final size:21
Alignment explanation
Indices: 508633--508680 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
508623 CCTGCGGAGA
*
508633 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
508654 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
508675 GGGCAT
1 TGGCAT
508681 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:510410 original size:16 final size:16
Alignment explanation
Indices: 510389--510419 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
510379 CAAAAAAAAT
*
510389 TAATAATTCTAAATAA
1 TAATAATTATAAATAA
510405 TAATAATTATAAATA
1 TAATAATTATAAATA
510420 TTATTTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATTATAAATAA
Found at i:510441 original size:32 final size:31
Alignment explanation
Indices: 510398--510474 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 31
510388 TTAATAATTC
*
510398 TAAATAATAATAATT-ATAAATATTATTTTAATA
1 TAAAAAATAATAATTAATAAATA-TA--TTAATA
*
510431 -AAAAAATAATATTTACATAAATATATTAATA
1 TAAAAAATAATAATTA-ATAAATATATTAATA
510462 TAAAAAATAATAA
1 TAAAAAATAATAA
510475 CTATTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
31 6 0.16
32 23 0.61
33 2 0.05
34 7 0.18
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAATAATAATTAATAAATATATTAATA
Found at i:511024 original size:2 final size:2
Alignment explanation
Indices: 511017--511044 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
511007 GTTTGGTGTA
511017 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
511045 TATCAGATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:511753 original size:19 final size:19
Alignment explanation
Indices: 511729--511775 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
511719 TTTCATTTTG
511729 TAAAATGTTATTTTTTTCA
1 TAAAATGTTATTTTTTTCA
511748 TAAAATGTTATTTTTTTCA
1 TAAAATGTTATTTTTTTCA
511767 TAAAATGTT
1 TAAAATGTT
511776 TAGGTAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (19 bp):
TAAAATGTTATTTTTTTCA
Found at i:512924 original size:49 final size:50
Alignment explanation
Indices: 512847--512954 Score: 200
Period size: 49 Copynumber: 2.2 Consensus size: 50
512837 TAGAAAAGGA
512847 GAAACAGATCAAGACGTTTCACAACACAGATCATGC-AAACTGAAGATGAT
1 GAAA-AGATCAAGACGTTTCACAACACAGATCATGCAAAACTGAAGATGAT
512897 GAAAAGATCAAGACGTTTCACAACACAGATCATGCAAAACTGAAGATGAT
1 GAAAAGATCAAGACGTTTCACAACACAGATCATGCAAAACTGAAGATGAT
512947 GAAAAGAT
1 GAAAAGAT
512955 TAAAAACAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
49 31 0.54
50 26 0.46
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (50 bp):
GAAAAGATCAAGACGTTTCACAACACAGATCATGCAAAACTGAAGATGAT
Found at i:521585 original size:23 final size:23
Alignment explanation
Indices: 521541--521602 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
521531 TGTTGTACGC
*
521541 TTATCTCTG-C-TTGTTTACACGT
1 TTATCTCTGTCTTTGTGT-CACGT
521563 TTATCAT-TGTCTTTGTGTCACGT
1 TTATC-TCTGTCTTTGTGTCACGT
521586 TTATCTCTGTCTTTGTG
1 TTATCTCTGTCTTTGTG
521603 GCATGTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
22 8 0.23
23 22 0.63
24 5 0.14
ACGTcount: A:0.11, C:0.19, G:0.16, T:0.53
Consensus pattern (23 bp):
TTATCTCTGTCTTTGTGTCACGT
Found at i:521610 original size:23 final size:23
Alignment explanation
Indices: 521558--521610 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
521548 TGCTTGTTTA
*
521558 CACGTTTATCATTGTCTTTGTGT
1 CACGTTTATCATTGTCTTTGTGG
521581 CACGTTTATC-TCTGTCTTTGTGG
1 CACGTTTATCAT-TGTCTTTGTGG
*
521604 CATGTTT
1 CACGTTT
521611 TTTGATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.51
Consensus pattern (23 bp):
CACGTTTATCATTGTCTTTGTGG
Found at i:525640 original size:2 final size:2
Alignment explanation
Indices: 525633--525689 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
525623 ACATATAAGA
525633 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
525675 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
525690 CTAATACACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:526366 original size:15 final size:15
Alignment explanation
Indices: 526346--526375 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
526336 ATCTTTTGAT
526346 TTTAAGATAACTTAA
1 TTTAAGATAACTTAA
526361 TTTAAGATAACTTAA
1 TTTAAGATAACTTAA
526376 GCTCTCCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
TTTAAGATAACTTAA
Found at i:537836 original size:20 final size:20
Alignment explanation
Indices: 537811--537848 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
537801 ATTTCAGGCA
537811 GGGAGTATCAATACTGCCAG
1 GGGAGTATCAATACTGCCAG
*
537831 GGGAGTATCAATATTGCC
1 GGGAGTATCAATACTGCC
537849 CCTACAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (20 bp):
GGGAGTATCAATACTGCCAG
Found at i:542209 original size:36 final size:36
Alignment explanation
Indices: 542162--542230 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
542152 CTTGTACGAA
542162 CTCATTTCTCATTTTCATGTGGCTATTTTATCATTT
1 CTCATTTCTCATTTTCATGTGGCTATTTTATCATTT
542198 CTCATTTCTCATTTTCATGTGGCTATTTTATCA
1 CTCATTTCTCATTTTCATGTGGCTATTTTATCA
542231 AATTTCTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.17, C:0.20, G:0.09, T:0.54
Consensus pattern (36 bp):
CTCATTTCTCATTTTCATGTGGCTATTTTATCATTT
Found at i:546119 original size:32 final size:32
Alignment explanation
Indices: 546078--546141 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
546068 TGCAAGATGA
546078 AGGCGGAAAAAGAAAGGAAATATAGAAATAGT
1 AGGCGGAAAAAGAAAGGAAATATAGAAATAGT
546110 AGGCGGAAAAAGAAAGGAAATATAGAAATAGT
1 AGGCGGAAAAAGAAAGGAAATATAGAAATAGT
546142 TGTTAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.56, C:0.03, G:0.28, T:0.12
Consensus pattern (32 bp):
AGGCGGAAAAAGAAAGGAAATATAGAAATAGT
Found at i:549783 original size:16 final size:16
Alignment explanation
Indices: 549762--549794 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
549752 CAAAGCTTAA
*
549762 TCGAACCAATCTGAGG
1 TCGAACCAATCAGAGG
549778 TCGAACCAATCAGAGG
1 TCGAACCAATCAGAGG
549794 T
1 T
549795 GAAGATCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (16 bp):
TCGAACCAATCAGAGG
Found at i:556191 original size:20 final size:21
Alignment explanation
Indices: 556148--556188 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
556138 GTTTCCAATT
556148 TCGCAACGTGAATAGTAAAAA
1 TCGCAACGTGAATAGTAAAAA
556169 TCGCAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
556189 TCGTAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAACGTGAATAGTAAAAA
Found at i:556565 original size:20 final size:20
Alignment explanation
Indices: 556544--556670 Score: 182
Period size: 20 Copynumber: 6.3 Consensus size: 20
556534 CATATATTCA
*
556544 TTGCGATTTTACTATTCACA
1 TTGCGATTTTACTATTCACG
* *
556564 TTGCAATTTCACTATTCACG
1 TTGCGATTTTACTATTCACG
*
556584 TTGCGATTTCACTATTCACG
1 TTGCGATTTTACTATTCACG
556604 TTGCGATTTTACTATTCACG
1 TTGCGATTTTACTATTCACG
* *
556624 TTGCGATTTTATTATTCATG
1 TTGCGATTTTACTATTCACG
*
556644 TTGCGATTTTTACTATTTACG
1 TTGCGA-TTTTACTATTCACG
556665 TTGCGA
1 TTGCGA
556671 AATTTGAAAC
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
20 79 0.82
21 17 0.18
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTACTATTCACG
Found at i:560333 original size:2 final size:2
Alignment explanation
Indices: 560326--560361 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
560316 TAAAATCAAT
560326 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
560362 GGTGAATCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:562072 original size:19 final size:20
Alignment explanation
Indices: 562033--562074 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
562023 CAAATCTTAA
* *
562033 TCCAACCGTCATCGGTCATC
1 TCCAACCATCATCGATCATC
562053 TCCAACCATCATC-ATCATC
1 TCCAACCATCATCGATCATC
562072 TCC
1 TCC
562075 GAACGATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.24, C:0.43, G:0.07, T:0.26
Consensus pattern (20 bp):
TCCAACCATCATCGATCATC
Found at i:564709 original size:4 final size:4
Alignment explanation
Indices: 564700--564748 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
564690 ATACAAGGAC
* * *
564700 ACAT ACAT ACAT ACAT ACAT GCA- AGCTT ACAA ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT A-CAT ACAT ACAT ACAT ACAT ACAT
564748 A
1 A
564749 TGAATCATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
4 36 0.97
5 1 0.03
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:565564 original size:44 final size:44
Alignment explanation
Indices: 565496--565583 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
565486 GATTCAGCGT
* *
565496 CTGTTTCTTAATCTATTGACAATATATACATTTTGCACATGCAA
1 CTGTTTCTTAATCTATTGACAATATATACATTTTACACACGCAA
* * *
565540 CTGTTTCTTAGTCTATTGAGAATATATACGTTTTACACACGCAA
1 CTGTTTCTTAATCTATTGACAATATATACATTTTACACACGCAA
565584 TTGATCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (44 bp):
CTGTTTCTTAATCTATTGACAATATATACATTTTACACACGCAA
Found at i:566840 original size:18 final size:19
Alignment explanation
Indices: 566817--566859 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
566807 AACTTAAAAA
*
566817 TTAAATTAACTC-GATAAT
1 TTAAATTAACTCAAATAAT
566835 TTAAATTAACTCAAATAAT
1 TTAAATTAACTCAAATAAT
566854 TTAAAT
1 TTAAAT
566860 AAGTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (19 bp):
TTAAATTAACTCAAATAAT
Found at i:568769 original size:2 final size:2
Alignment explanation
Indices: 568665--568756 Score: 175
Period size: 2 Copynumber: 45.5 Consensus size: 2
568655 ATAAAAAAGT
568665 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
568708 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
568750 TA TA TA T
1 TA TA TA T
568757 TAATTGAATA
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 87 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:572841 original size:31 final size:31
Alignment explanation
Indices: 572803--572872 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
572793 CAGAGTTAAT
572803 GTAACAAATCCGACATGCATGGATGTTTTGG
1 GTAACAAATCCGACATGCATGGATGTTTTGG
572834 GTAACAAATCCGACATGCATGGATGTTTTGG
1 GTAACAAATCCGACATGCATGGATGTTTTGG
572865 GTAACAAA
1 GTAACAAA
572873 AGGGAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (31 bp):
GTAACAAATCCGACATGCATGGATGTTTTGG
Found at i:574282 original size:35 final size:37
Alignment explanation
Indices: 574211--574283 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 37
574201 GTTGAAAAAT
* *
574211 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATAATTTCTTTAAAAAAATTAAAATCATAAA
*
574248 ATTTATATAATTT-TTT-ACAAAATTGAAAAT-ATAAA
1 ATTTATATAATTTCTTTAAAAAAATT-AAAATCATAAA
574283 A
1 A
574284 ATATTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 13 0.41
36 7 0.22
37 12 0.38
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
ATTTATATAATTTCTTTAAAAAAATTAAAATCATAAA
Found at i:592384 original size:23 final size:23
Alignment explanation
Indices: 592358--592409 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
592348 GGAATCGATA
*
592358 CCCCCCTTGAAGGGGAACTAATT
1 CCCCCCTTGAAGGGGAACCAATT
* *
592381 CCCCCTTTGAAGGGGAACCGATT
1 CCCCCCTTGAAGGGGAACCAATT
592404 CCCCCC
1 CCCCCC
592410 ACAGGGGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.19
Consensus pattern (23 bp):
CCCCCCTTGAAGGGGAACCAATT
Found at i:594034 original size:18 final size:18
Alignment explanation
Indices: 593999--594036 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
593989 AGAATAGCAC
*
593999 GAGGAACAAACTCCACCA
1 GAGGAACAAACACCACCA
*
594017 GAGGAACAAACACGACCA
1 GAGGAACAAACACCACCA
594035 GA
1 GA
594037 TGATCAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.29, G:0.21, T:0.03
Consensus pattern (18 bp):
GAGGAACAAACACCACCA
Found at i:598541 original size:14 final size:14
Alignment explanation
Indices: 598524--598561 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
598514 TTGTCTATAT
598524 GCAGAGATTTTTAC
1 GCAGAGATTTTTAC
598538 GCAGAGATTTTTAC
1 GCAGAGATTTTTAC
598552 GCAGAGATTT
1 GCAGAGATTT
598562 ATTTACATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (14 bp):
GCAGAGATTTTTAC
Found at i:598626 original size:4 final size:4
Alignment explanation
Indices: 598617--598647 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
598607 TTCAACTATG
598617 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
598648 ACATGCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:606888 original size:15 final size:15
Alignment explanation
Indices: 606860--606895 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
606850 TGTTATTACT
606860 AAAAATATTCAAAAA
1 AAAAATATTCAAAAA
606875 AAGAAATA-TCAAAAA
1 AA-AAATATTCAAAAA
606890 AAAAAT
1 AAAAAT
606896 GATAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 11 0.55
16 5 0.25
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAAATATTCAAAAA
Found at i:608284 original size:18 final size:18
Alignment explanation
Indices: 608261--608313 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
608251 AAAAGAAAAA
608261 AAAAATAAATAAATAAAT
1 AAAAATAAATAAATAAAT
*
608279 AAAAATAAGT-AATAAATT
1 AAAAATAAATAAATAAA-T
608297 AAAAAT-AA-AAATAAAT
1 AAAAATAAATAAATAAAT
608313 A
1 A
608314 GTAATAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 2 0.06
17 13 0.42
18 16 0.52
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAAATAAATAAATAAAT
Found at i:608335 original size:30 final size:28
Alignment explanation
Indices: 608271--608325 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
608261 AAAAATAAAT
608271 AAATAAATAAAAATAAGTAATAAATTAA
1 AAATAAATAAAAATAAGTAATAAATTAA
608299 AAATAAA-AATAAAT-AGTAATAATATTA
1 AAATAAATAA-AAATAAGTAATAA-ATTA
608326 TATATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (28 bp):
AAATAAATAAAAATAAGTAATAAATTAA
Found at i:608389 original size:36 final size:36
Alignment explanation
Indices: 608333--608517 Score: 189
Period size: 38 Copynumber: 5.1 Consensus size: 36
608323 TTATATATAT
* *
608333 AAACGTTTTCAAAAAC-ATATAATATATAAATTTTTA
1 AAACGTTTT-AAAAACTATATATTATATAAATTTTCA
* *
608369 AAATGTTTTAAAAACTATATATTATATATATTTTCA
1 AAACGTTTTAAAAACTATATATTATATAAATTTTCA
* *
608405 AAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCA
1 AAA-CG-TTTTAAAAACTATATATTATATAAA--TTTTCA
* * * * *
608445 TAACATTTTCAAAAGTATATATTATAT--ATTTTAA
1 AAACGTTTTAAAAACTATATATTATATAAATTTTCA
608479 AAACGTTTTCAAAAACTATATATTATAT-AATTTTCA
1 AAACGTTTT-AAAAACTATATATTATATAAATTTTCA
608515 AAA
1 AAA
608518 AAATATATTT
Statistics
Matches: 124, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
34 12 0.10
35 22 0.18
36 38 0.31
37 1 0.01
38 43 0.35
40 8 0.06
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
AAACGTTTTAAAAACTATATATTATATAAATTTTCA
Done.