Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007951.1 Hibiscus syriacus cultivar Beakdansim tig00110374_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: 657610
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:187852 original size:6 final size:6
Alignment explanation
Indices: 187841--187886 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
187831 TAAATAAATC
* * *
187841 CTAATT CTAATT CAAATC CTAATT CTAATT CTAAGT CTAATT CTAA
1 CTAATT CTAATT CTAATT CTAATT CTAATT CTAATT CTAATT CTAA
187887 ATAAATGTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (6 bp):
CTAATT
Found at i:187859 original size:18 final size:19
Alignment explanation
Indices: 187835--187886 Score: 81
Period size: 18 Copynumber: 2.8 Consensus size: 19
187825 ATTACGTAAA
187835 TAAATCCTAATTCTAATTC
1 TAAATCCTAATTCTAATTC
187854 -AAATCCTAATTCTAATTC
1 TAAATCCTAATTCTAATTC
*
187872 TAAGT-CTAATTCTAA
1 TAAATCCTAATTCTAA
187887 ATAAATGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 28 0.90
19 3 0.10
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAATCCTAATTCTAATTC
Found at i:187986 original size:26 final size:26
Alignment explanation
Indices: 187957--188029 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 26
187947 ATTTAAATTT
*
187957 ATTAAAATTTAATTAATTTTAATAGA
1 ATTAAAATTTAATTAATTTTAATAAA
* * * *
187983 ATTATAATTAAATTATAATTTATTAAA
1 ATTAAAATTTAATTA-ATTTTAATAAA
* *
188010 AATAATAATTTAAGTAATTT
1 ATTAA-AATTTAATTAATTT
188030 AATTTGTTTA
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
26 13 0.37
27 14 0.40
28 8 0.23
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (26 bp):
ATTAAAATTTAATTAATTTTAATAAA
Found at i:190480 original size:37 final size:37
Alignment explanation
Indices: 190430--190510 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
190420 AATCCGTAAT
**
190430 GCTAATTACCGATATAGGTAAACAGTACTATCGCAAC
1 GCTAATTACCGATATAGGTAAACACAACTATCGCAAC
*
190467 GCTAATTATCGATATAGGTAAACACAACTATCGCAAC
1 GCTAATTACCGATATAGGTAAACACAACTATCGCAAC
*
190504 GCGAATT
1 GCTAATT
190511 TCACAAATCG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (37 bp):
GCTAATTACCGATATAGGTAAACACAACTATCGCAAC
Found at i:190651 original size:20 final size:20
Alignment explanation
Indices: 190626--190674 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
190616 TCGGTAATTA
*
190626 GCGTTGCGGATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
190646 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
*
190666 GTGTTGCGA
1 GCGTTGCGA
190675 TAGTACTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:190672 original size:77 final size:77
Alignment explanation
Indices: 190561--190731 Score: 270
Period size: 77 Copynumber: 2.2 Consensus size: 77
190551 ATTCAATTTG
** * **
190561 TGAAAATAACGTTACGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTA
1 TGAAAATCGCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCAATAATTA
*
190626 GCGTTGCGGATT
66 GCATTGCGGATT
* *
190638 TGAAAATCGCGTTGCGAATTTGAAAATCGTGTTGCGATAGTACTGTTTACCTATATCAATGATTA
1 TGAAAATCGCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCAATAATTA
190703 GCATTGCGGATT
66 GCATTGCGGATT
190715 TGAAAATCGCGTTGCGA
1 TGAAAATCGCGTTGCGA
190732 TAGTACTGTT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 86 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (77 bp):
TGAAAATCGCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCAATAATTA
GCATTGCGGATT
Found at i:190710 original size:57 final size:57
Alignment explanation
Indices: 190649--190788 Score: 217
Period size: 57 Copynumber: 2.5 Consensus size: 57
190639 GAAAATCGCG
* *
190649 TTGCGAATTTGAAAATCGTGTTGCGATAGTACTGTTTACCTATATCAATGATTAGCA
1 TTGCGGATTTGAAAATCGTGTTGCGATAGTACTGTTTACCTATATCAATAATTAGCA
* ** *
190706 TTGCGGATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCG
1 TTGCGGATTTGAAAATCGTGTTGCGATAGTACTGTTTACCTATATCAATAATTAGCA
*
190763 TTGCGGATTTAAAAATCGTGTTGCGA
1 TTGCGGATTTGAAAATCGTGTTGCGA
190789 ATTTGAAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 75 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (57 bp):
TTGCGGATTTGAAAATCGTGTTGCGATAGTACTGTTTACCTATATCAATAATTAGCA
Found at i:190787 original size:20 final size:20
Alignment explanation
Indices: 190760--190808 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
190750 TCGGTAATTA
*
190760 GCGTTGCGGATTTAAAAATC
1 GCGTTGCGAATTTAAAAATC
* *
190780 GTGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTAAAAATC
190800 GCGTTGCGA
1 GCGTTGCGA
190809 TAGTACTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (20 bp):
GCGTTGCGAATTTAAAAATC
Found at i:190787 original size:77 final size:77
Alignment explanation
Indices: 190706--190887 Score: 310
Period size: 77 Copynumber: 2.4 Consensus size: 77
190696 ATGATTAGCA
* *
190706 TTGCGGATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGGAT
1 TTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTACGGAT
*
190771 TTAAAAATCGTG
66 TTAAAAATCGCG
190783 TTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTACGGAT
1 TTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTACGGAT
190848 TTAAAAATCGCG
66 TTAAAAATCGCG
* *
190860 TCGCAAATTTGGAAAATCGCGTTGCGAT
1 TTGCGAATTT-GAAAATCGCGTTGCGAT
190888 TTTCGAAACT
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 82 0.83
78 17 0.17
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (77 bp):
TTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTACGGAT
TTAAAAATCGCG
Found at i:190818 original size:134 final size:134
Alignment explanation
Indices: 190572--190860 Score: 488
Period size: 134 Copynumber: 2.2 Consensus size: 134
190562 GAAAATAACG
*
190572 TTACGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGGAT
1 TTACGGATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGGAT
* * *
190637 TTGAAAATCGCGTTGCGAATTTGAAAATCGTGTTGCGATAGTACTGTTTACCTATATCAATGATT
66 TTAAAAATCGCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCAATAATT
190702 AGCA
131 AGCA
*
190706 TTGCGGATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGGAT
1 TTACGGATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGGAT
* **
190771 TTAAAAATCGTGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATT
66 TTAAAAATCGCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCAATAATT
*
190836 AGCG
131 AGCA
*
190840 TTACGGATTTAAAAATCGCGT
1 TTACGGATTTGAAAATCGCGT
190861 CGCAAATTTG
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
134 144 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (134 bp):
TTACGGATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGGAT
TTAAAAATCGCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCAATAATT
AGCA
Found at i:190895 original size:21 final size:21
Alignment explanation
Indices: 190851--190910 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
190841 TACGGATTTA
* * *
190851 AAAATCGCGTCGCAAATTTGG
1 AAAATCGCGTTGCGAATTTCG
*
190872 AAAATCGCGTTGCGATTTTCG
1 AAAATCGCGTTGCGAATTTCG
*
190893 AAACT-GCGTTGCGAATTT
1 AAAATCGCGTTGCGAATTT
190911 ATTGGTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 12 0.36
21 21 0.64
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (21 bp):
AAAATCGCGTTGCGAATTTCG
Found at i:191067 original size:18 final size:19
Alignment explanation
Indices: 191028--191074 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
191018 AAATATTATA
*
191028 AAATTAAATATTCAATCAT
1 AAATTAAATATTCAATAAT
191047 AAATT-AATATT-AATAATT
1 AAATTAAATATTCAATAA-T
*
191065 AAATGAAATA
1 AAATTAAATA
191075 ATATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.17
18 11 0.46
19 9 0.38
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (19 bp):
AAATTAAATATTCAATAAT
Found at i:191867 original size:35 final size:35
Alignment explanation
Indices: 191828--191903 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
191818 GTTAAAATTT
* *
191828 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
191863 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
191898 AATTGA
1 AATTGA
191904 GGACTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:192563 original size:31 final size:31
Alignment explanation
Indices: 192528--192605 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
192518 CAGTTACGTC
192528 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACGGACTAAATGTTG
* *
192559 GGGGATCATATTGAAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACGGACTAAATGTTG
* **
192590 GGAGACTGTATTGCAA
1 GGGGACCATATTGCAA
192606 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGCAAACGGACTAAATGTTG
Found at i:192739 original size:25 final size:24
Alignment explanation
Indices: 192674--192747 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 24
192664 TACTTTACCC
*
192674 TATTATTTATTGGTTTTTATT-ATT
1 TATTATTTATT-GTTTTTATTGTTT
*
192698 AATT-TTATATATGTTTTTATTGTTT
1 TATTATT-TAT-TGTTTTTATTGTTT
192723 TATTATTTATTGTTTTTTATTGTTT
1 TATTATTTATTG-TTTTTATTGTTT
192748 CTTTATAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
23 2 0.05
24 17 0.40
25 21 0.50
26 2 0.05
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (24 bp):
TATTATTTATTGTTTTTATTGTTT
Found at i:192900 original size:7 final size:7
Alignment explanation
Indices: 192888--192917 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
192878 TATAATTAAA
192888 ATTGAAT
1 ATTGAAT
192895 ATTGAAT
1 ATTGAAT
192902 ATTGAAT
1 ATTGAAT
192909 ATTGAAT
1 ATTGAAT
192916 AT
1 AT
192918 AATTAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (7 bp):
ATTGAAT
Found at i:193492 original size:31 final size:31
Alignment explanation
Indices: 193457--193516 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
193447 ACAATCTCCC
*
193457 AACATTTAGTATGTTTTCAATATGGTCCCCA
1 AACATTTAGTATGTTTGCAATATGGTCCCCA
*
193488 AACATTTAGTCTGTTTGCAATATGGTCCC
1 AACATTTAGTATGTTTGCAATATGGTCCC
193517 TGATGTAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (31 bp):
AACATTTAGTATGTTTGCAATATGGTCCCCA
Found at i:197020 original size:16 final size:16
Alignment explanation
Indices: 196993--197141 Score: 203
Period size: 16 Copynumber: 9.4 Consensus size: 16
196983 GGTATTACCC
196993 GACCTG-TTTCAACCT
1 GACCTGTTTTCAACCT
197008 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
197024 GA-ATGTTTTCAACCT
1 GACCTGTTTTCAACCT
197039 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
197055 GACATGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
197071 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
*
197087 GACCTGTTTTCAATCT
1 GACCTGTTTTCAACCT
* *
197103 GACCTATTTTTAACCT
1 GACCTGTTTTCAACCT
* *
197119 GACTTGTTTTTAACCT
1 GACCTGTTTTCAACCT
*
197135 GATCTGT
1 GACCTGT
197142 AAATGATTCG
Statistics
Matches: 118, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
15 20 0.17
16 98 0.83
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.41
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:197451 original size:23 final size:24
Alignment explanation
Indices: 197411--197461 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
197401 ATGCAAAAGA
197411 AAATTGATATAATATAATTTATAT
1 AAATTGATATAATATAATTTATAT
* *
197435 AAATT-ATATAGTTTAATTTATAT
1 AAATTGATATAATATAATTTATAT
197458 AAAT
1 AAAT
197462 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
AAATTGATATAATATAATTTATAT
Found at i:197995 original size:35 final size:33
Alignment explanation
Indices: 197974--198123 Score: 129
Period size: 33 Copynumber: 4.7 Consensus size: 33
197964 TTTATATTAA
197974 TAAATTAATATATAGTTTATATATACTAATGAAC
1 TAAA-TAATATATAGTTTATATATACTAATGAAC
* *
198008 TATATAATATATAGTTTGTATATAC-------C
1 TAAATAATATATAGTTTATATATACTAATGAAC
* * *
198034 -ATATACTATATAGGTTATATATACTAATGAAC
1 TAAATAATATATAGTTTATATATACTAATGAAC
* **
198066 TATATAATATATAGTTTATATATACTATAT-AGTT
1 TAAATAATATATAGTTTATATATACTA-ATGA-AC
*
198100 TATATAATATATAGTTTATATATA
1 TAAATAATATATAGTTTATATATA
198124 ATGTATAGTT
Statistics
Matches: 97, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
25 21 0.22
26 1 0.01
32 1 0.01
33 45 0.46
34 29 0.30
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (33 bp):
TAAATAATATATAGTTTATATATACTAATGAAC
Found at i:198043 original size:25 final size:25
Alignment explanation
Indices: 198009--198057 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
197999 CTAATGAACT
* *
198009 ATATAATATATAGTTTGTATATACC
1 ATATAATATATAGGTTATATATACC
*
198034 ATATACTATATAGGTTATATATAC
1 ATATAATATATAGGTTATATATAC
198058 TAATGAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (25 bp):
ATATAATATATAGGTTATATATACC
Found at i:198055 original size:18 final size:18
Alignment explanation
Indices: 198034--198180 Score: 112
Period size: 18 Copynumber: 8.4 Consensus size: 18
198024 TGTATATACC
198034 ATATACTATATAGGTTAT
1 ATATACTATATAGGTTAT
*
198052 ATATACTA-AT--G-AACT
1 ATATACTATATAGGTTA-T
* *
198067 ATATAATATATAGTTTAT
1 ATATACTATATAGGTTAT
198085 ATATACTATATA-GTT-T
1 ATATACTATATAGGTTAT
* *
198101 ATATAATATATAGTTTAT
1 ATATACTATATAGGTTAT
* * *
198119 ATATAATGTATAGTTTAT
1 ATATACTATATAGGTTAT
*
198137 ATATACCATATA-GTCTAT
1 ATATACTATATAGGT-TAT
* *
198155 ATAGT-TTATATAGTTTAT
1 ATA-TACTATATAGGTTAT
198173 ATATACTA
1 ATATACTA
198181 ATAAACTATA
Statistics
Matches: 101, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
14 1 0.01
15 9 0.09
16 14 0.14
17 8 0.08
18 66 0.65
19 3 0.03
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (18 bp):
ATATACTATATAGGTTAT
Found at i:198055 original size:58 final size:58
Alignment explanation
Indices: 197982--198166 Score: 229
Period size: 58 Copynumber: 3.3 Consensus size: 58
197972 AATAAATTAA
*
197982 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATATACCATATAC
1 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACCATATAC
* * *
198040 TATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTATATAG
1 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACCATATAC
* * ** *
198098 T-T-TA-TATA-ATATA-TAGTTTA-TATATAATGTATAGTTTATATATACCATATAGTC
1 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACCATATA--C
198152 TATATAGTTTATATA
1 TATATAGTTTATATA
198167 GTTTATATAT
Statistics
Matches: 108, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
52 29 0.27
53 4 0.04
54 6 0.06
55 3 0.03
56 4 0.04
57 4 0.04
58 58 0.54
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (58 bp):
TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACCATATAC
Found at i:198109 original size:34 final size:34
Alignment explanation
Indices: 198034--198175 Score: 146
Period size: 34 Copynumber: 4.1 Consensus size: 34
198024 TGTATATACC
* * **
198034 ATATACTATATAGGTTATATATACTA-AT-GAACT
1 ATATAATATATAGTTTATATATACTATATAG-TTT
198067 ATATAATATATAGTTTATATATACTATATAGTTT
1 ATATAATATATAGTTTATATATACTATATAGTTT
* *
198101 ATATAATATATAGTTTATATATAATGTATAGTTT
1 ATATAATATATAGTTTATATATACTATATAGTTT
* * *
198135 ATATATACCATATAGTCTATATAGT-TTATATAGTTT
1 ATATA-A-TATATAGTTTATATA-TACTATATAGTTT
198171 ATATA
1 ATATA
198176 TACTAATAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
33 24 0.26
34 40 0.43
35 2 0.02
36 27 0.29
37 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (34 bp):
ATATAATATATAGTTTATATATACTATATAGTTT
Found at i:198177 original size:11 final size:9
Alignment explanation
Indices: 198073--198175 Score: 81
Period size: 9 Copynumber: 11.7 Consensus size: 9
198063 AACTATATAA
198073 TATATAGTT
1 TATATAGTT
*
198082 TATATA-TAC
1 TATATAGT-T
198091 TATATAGTT
1 TATATAGTT
*
198100 TATATA--A
1 TATATAGTT
198107 TATATAGTT
1 TATATAGTT
*
198116 TATATA-TAA
1 TATATAGT-T
*
198125 TGTATAGTT
1 TATATAGTT
*
198134 TATATA-TAC
1 TATATAGT-T
* *
198143 CATATAGTC
1 TATATAGTT
198152 TATATAGTT
1 TATATAGTT
198161 TATATAGTT
1 TATATAGTT
198170 TATATA
1 TATATA
198176 TACTAATAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
7 6 0.08
8 3 0.04
9 62 0.84
10 3 0.04
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.50
Consensus pattern (9 bp):
TATATAGTT
Found at i:198261 original size:9 final size:9
Alignment explanation
Indices: 198239--198310 Score: 51
Period size: 9 Copynumber: 7.7 Consensus size: 9
198229 TAAATTATAC
198239 TATATAGTA
1 TATATAGTA
*
198248 CATATAGTTTA
1 TATATAG--TA
198259 TATATA-TAA
1 TATATAGT-A
198268 TATATAGTA
1 TATATAGTA
*
198277 TATA-AATA
1 TATATAGTA
198285 TCAACTATAGTA
1 T--A-TATAGTA
198297 TATATA-TA
1 TATATAGTA
198305 TATATA
1 TATATA
198311 TATGTCATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
8 13 0.25
9 22 0.43
10 3 0.06
11 9 0.18
12 4 0.08
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (9 bp):
TATATAGTA
Found at i:198332 original size:2 final size:2
Alignment explanation
Indices: 198234--198313 Score: 56
Period size: 2 Copynumber: 37.5 Consensus size: 2
198224 ATATGTAAAT
* *
198234 TA TA CTA TA TA GTA CA TA TA GTT TA TA TA TA TA -A TA TA TA GTA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
*
198277 TA TA AA TA TCA -A CTA TA GTA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA -TA TA -TA TA TA TA TA TA TA TA TA T
198314 GTCATATGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
1 2 0.03
2 50 0.79
3 11 0.17
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:198352 original size:33 final size:31
Alignment explanation
Indices: 198306--198366 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 31
198296 ATATATATAT
198306 ATATATATGTCATATGTAAACTATATAGTTTAC
1 ATATATATGTCATATGTAAA-T-TATAGTTTAC
198339 ATATATA-GTTCATATGTAAATTATAGTT
1 ATATATATG-TCATATGTAAATTATAGTT
198367 CATATGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 7 0.26
32 2 0.07
33 18 0.67
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (31 bp):
ATATATATGTCATATGTAAATTATAGTTTAC
Found at i:198365 original size:18 final size:18
Alignment explanation
Indices: 198342--198457 Score: 90
Period size: 18 Copynumber: 6.0 Consensus size: 18
198332 AGTTTACATA
198342 TATAGTTCATATGTAAAT
1 TATAGTTCATATGTAAAT
198360 TATAGTTCATATGTAAATATT
1 TATAGTTCATATGT-AA-A-T
* *
198381 AACTATAGTTTATATGTAAAC
1 ---TATAGTTCATATGTAAAT
*
198402 TATAGTT-AGTATATAAATT
1 TATAGTTCA-TATGTAAA-T
* *
198421 ATATAGTTTATATGTAAAC
1 -TATAGTTCATATGTAAAT
*
198440 TATAGTTCATATATAAAT
1 TATAGTTCATATGTAAAT
198458 ATCAACCTTA
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
17 1 0.01
18 43 0.54
19 2 0.03
20 15 0.19
21 2 0.03
22 1 0.01
23 2 0.03
24 13 0.16
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.44
Consensus pattern (18 bp):
TATAGTTCATATGTAAAT
Found at i:198434 original size:80 final size:75
Alignment explanation
Indices: 198317--198459 Score: 205
Period size: 80 Copynumber: 1.8 Consensus size: 75
198307 TATATATGTC
* * *
198317 ATATGTAAACTATATAGTTTACATATATAGTTCATATGTAAATTATAGTTCATATGTAAATATTA
1 ATATGTAAACTATATAGTTTAAATATATAGTTCATATGTAAACTATAGTTCATATATAAATATTA
198382 ACTATAGTTT
66 ACTATAGTTT
*
198392 ATATGTAAACTATAGTTAGTATATAAATTATATAGTTTATATGTAAACTATAGTTCATATATAAA
1 ATATGTAAACTATA--TAGT-T-TAAA-TATATAGTTCATATGTAAACTATAGTTCATATATAAA
198457 TAT
61 TAT
198460 CAACCTTAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
75 14 0.24
77 4 0.07
78 1 0.02
79 3 0.05
80 37 0.63
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (75 bp):
ATATGTAAACTATATAGTTTAAATATATAGTTCATATGTAAACTATAGTTCATATATAAATATTA
ACTATAGTTT
Found at i:198435 original size:38 final size:37
Alignment explanation
Indices: 198287--198457 Score: 149
Period size: 38 Copynumber: 4.5 Consensus size: 37
198277 TATAAATATC
*
198287 AACTATAG-TATATATATATATATATA-TGTCATATGTA
1 AACTATAGTTATATATAAAT-TATATAGT-TCATATGTA
*
198324 AACTATA--TAGT-T-TACA-TATATAGTTCATATGTA
1 AACTATAGTTA-TATATAAATTATATAGTTCATATGTA
* * *
198357 AATTATAGTTCATATGTAAATATTAACTATAGTTTATATGTA
1 AACTATAGTT-ATATAT-AA-ATT-A-TATAGTTCATATGTA
*
198399 AACTATAGTTAGTATATAAATTATATAGTTTATATGTA
1 AACTATAGTTA-TATATAAATTATATAGTTCATATGTA
198437 AACTATAGTTCATATATAAAT
1 AACTATAGTT-ATATATAAAT
198458 ATCAACCTTA
Statistics
Matches: 114, Mismatches: 6, Indels: 27
0.78 0.04 0.18
Matches are distributed among these distances:
33 21 0.18
34 1 0.01
35 5 0.04
36 5 0.04
37 9 0.08
38 35 0.31
39 3 0.03
40 4 0.04
41 4 0.04
42 27 0.24
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (37 bp):
AACTATAGTTATATATAAATTATATAGTTCATATGTA
Found at i:198475 original size:80 final size:75
Alignment explanation
Indices: 198317--198475 Score: 203
Period size: 80 Copynumber: 2.1 Consensus size: 75
198307 TATATATGTC
* * * *
198317 ATATGTAAACTATATAGTTTACATATATAGTTCATATGTAAATTATAGTTCATATGTAAATATTA
1 ATATGTAAACTATATAGTTTAAATATATAGTTCATATGTAAACTATAGTTCATATATAAATATCA
*
198382 ACTATAGTTT
66 ACTATAGTAT
*
198392 ATATGTAAACTATAGTTAGTATATAAATTATATAGTTTATATGTAAACTATAGTTCATATATAAA
1 ATATGTAAACTATA--TAGT-T-TAAA-TATATAGTTCATATGTAAACTATAGTTCATATATAAA
198457 TATCAACCT-TAGTAT
61 TATCAA-CTATAGTAT
198472 ATAT
1 ATAT
198476 ATTTATATAT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
75 14 0.19
77 4 0.06
78 1 0.01
79 3 0.04
80 48 0.67
81 2 0.03
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.43
Consensus pattern (75 bp):
ATATGTAAACTATATAGTTTAAATATATAGTTCATATGTAAACTATAGTTCATATATAAATATCA
ACTATAGTAT
Found at i:198571 original size:31 final size:32
Alignment explanation
Indices: 198514--198573 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
198504 ATAATTCATA
*
198514 TATATAGTAATACATTTATAAATTGTATAGTT
1 TATATAGTAATACATATATAAATTGTATAGTT
* *
198546 TATATA-TAATTCATATATAATTTGTATA
1 TATATAGTAATACATATATAAATTGTATA
198574 TAAACTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (32 bp):
TATATAGTAATACATATATAAATTGTATAGTT
Found at i:198651 original size:2 final size:2
Alignment explanation
Indices: 198644--198752 Score: 64
Period size: 2 Copynumber: 53.5 Consensus size: 2
198634 TTATACATGG
* * *
198644 TA TA TA TA GTT TA TA T- TT TA TA CA TA -A TA TA TA TA TA CTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
198686 TA GTT TA TA TA TA TA -A TA CA TA TA CTT TA TA TA TA AA CTA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
*
198728 TA GTT TA TA T- TA TA TA TA TA TA TA T
1 TA -TA TA TA TA TA TA TA TA TA TA TA T
198753 TAGTTGTTTT
Statistics
Matches: 82, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
1 4 0.05
2 71 0.87
3 7 0.09
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:198664 original size:27 final size:28
Alignment explanation
Indices: 198601--198694 Score: 95
Period size: 27 Copynumber: 3.4 Consensus size: 28
198591 ATATAGTTCA
* *
198601 ATAGTTCATATATAA-ACTATATAGTATT
1 ATAGTTTATACATAATA-TATATAGTATT
**
198629 ATAGTTTATACATGGTATATATAGT-TT
1 ATAGTTTATACATAATATATATAGTATT
*
198656 ATATTTTATACATAATATATATA-TACTAT
1 ATAGTTTATACATAATATATATAGTA-T-T
198685 ATAGTTTATA
1 ATAGTTTATA
198695 TATATAATAC
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
26 1 0.02
27 22 0.41
28 20 0.37
29 11 0.20
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (28 bp):
ATAGTTTATACATAATATATATAGTATT
Found at i:198685 original size:9 final size:8
Alignment explanation
Indices: 198644--198752 Score: 64
Period size: 9 Copynumber: 13.4 Consensus size: 8
198634 TTATACATGG
198644 TATATATA
1 TATATATA
*
198652 GTTTATAT-
1 -TATATATA
* *
198660 TTTATACA
1 TATATATA
198668 TA-ATATA
1 TATATATA
198675 TATATACTA
1 TATATA-TA
*
198684 TATAGTTTA
1 TATA-TATA
198693 TATATATA
1 TATATATA
*
198701 -ATACATA
1 TATATATA
*
198708 TACTTTATA
1 TA-TATATA
*
198717 TATAAACTA
1 TATATA-TA
*
198726 TATAGTTTA
1 TATA-TATA
198735 TAT-TATA
1 TATATATA
198742 TATATATA
1 TATATATA
198750 TAT
1 TAT
198753 TAGTTGTTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
7 24 0.31
8 17 0.22
9 35 0.45
10 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.50
Consensus pattern (8 bp):
TATATATA
Found at i:198687 original size:29 final size:29
Alignment explanation
Indices: 198644--198717 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
198634 TTATACATGG
*
198644 TATATATAGTTTATATTTTATACATA-ATA
1 TATATATACTTTATATTTTATACATATA-A
* * *
198673 TATATATACTATATAGTTTATATATATAA
1 TATATATACTTTATATTTTATACATATAA
*
198702 TACATATACTTTATAT
1 TATATATACTTTATAT
198718 ATAAACTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 36 0.97
30 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (29 bp):
TATATATACTTTATATTTTATACATATAA
Found at i:198718 original size:42 final size:44
Alignment explanation
Indices: 198671--198752 Score: 132
Period size: 42 Copynumber: 1.9 Consensus size: 44
198661 TTATACATAA
*
198671 TATATATATACTATATAGTTTATA-TATATA-ATACATATACTT
1 TATATATAAACTATATAGTTTATATTATATATATACATATACTT
*
198713 TATATATAAACTATATAGTTTATATTATATATATATATAT
1 TATATATAAACTATATAGTTTATATTATATATATACATAT
198753 TAGTTGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 23 0.64
43 6 0.17
44 7 0.19
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (44 bp):
TATATATAAACTATATAGTTTATATTATATATATACATATACTT
Found at i:199380 original size:216 final size:213
Alignment explanation
Indices: 198837--199583 Score: 1134
Period size: 216 Copynumber: 3.5 Consensus size: 213
198827 ATGAGTATAA
* * *
198837 TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTTGATTCGAT--C-CATTTTGTGTTGTTT
1 TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTCATATTGTGTTGTTT
*
198899 AATATATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTTATTTGC
66 AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
**
198964 ACCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTAAATTGG-CCATAACTTTTTAAATG
131 ATATGAAATTGACCCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATG
199028 GGTATAATTTAGTACTTT
196 GGTATAATTTAGTACTTT
*
199046 TTT-TATTAATTTTAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT--T-TTGTGTTGTTT
1 TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTCATATTGTGTTGTTT
199107 AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
66 AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
* * *
199172 ATTTGAAACTGACCCGTACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATG
131 ATATGAAATTGACCCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATG
*
199237 GGTACAATTTAGTACTTT
196 GGTATAATTTAGTACTTT
* * * *
199255 TTTGTATTAATTTCAACATCACAATTTAAAATTATTTTGATTTGATCCCTCATCAAAGTGTGTTG
1 TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTCAT---ATTGTGTTG
* *
199320 TTTAATTTATTTAAA-TTTTATTTGTAATTTCATATTTTTTTCAATTTAGTCCTCCAAATTTTAT
63 TTTAATATATTTAAATTTTTATTTGTAATTTCATA-TTTGTTCAATTTAGTCCTCCAAATTTTAT
* * * *
199384 TTGCATATGAAATTAATCCATACTTATTACTTAATTCTATTTTTTAATTGGCCCATAACTTTTTA
127 TTGCATATGAAATTGACCCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTA
*
199449 AATGGGTATAATTTAGTATTTT
192 AATGGGTATAATTTAGTACTTT
* * *
199471 TTTGTATTAATTTCAACTTCACAATTTAAAATTATTTCGATTTGATCCCTCATCATTATGTATTG
1 TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTCAT-A-T-TGTGTTG
*
199536 TTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
63 TTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
199584 ATTATTAAAT
Statistics
Matches: 492, Mismatches: 31, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
208 157 0.32
209 41 0.08
210 43 0.09
212 1 0.00
214 1 0.00
215 19 0.04
216 211 0.43
217 19 0.04
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (213 bp):
TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTCATATTGTGTTGTTT
AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
ATATGAAATTGACCCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATG
GGTATAATTTAGTACTTT
Found at i:200691 original size:19 final size:20
Alignment explanation
Indices: 200659--200698 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
200649 GAATTTTATG
*
200659 TTAGGGGAGTAAACTTAAAT
1 TTAGGGGAGTAAACTAAAAT
200679 TTAGGGG-GTAAACTAAAAT
1 TTAGGGGAGTAAACTAAAAT
200698 T
1 T
200699 CCATAAGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (20 bp):
TTAGGGGAGTAAACTAAAAT
Found at i:204368 original size:9 final size:9
Alignment explanation
Indices: 204354--204387 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
204344 GAAATCGATT
204354 AATTAACCG
1 AATTAACCG
*
204363 AATTAACTG
1 AATTAACCG
204372 AATTAACCG
1 AATTAACCG
204381 AAATTAA
1 -AATTAA
204388 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:204712 original size:186 final size:185
Alignment explanation
Indices: 204393--204783 Score: 649
Period size: 186 Copynumber: 2.1 Consensus size: 185
204383 ATTAAATTTT
* * *
204393 AAATTTTAAATATATTGTATATAACATATGGGCTTAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
*
204458 TTTAAAATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAACTTATATAAAATTT
66 TTTAAAATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAACTTATATAAAATTT
*
204523 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTGAATTAAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTGAATT-AAA
204579 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* * *
204644 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAAATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAACTTATATAAAATTT
** *
204709 TTATTTTATAATTATATATTATTTAAATTAATTATAATGTTTTTTTTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTGAATTAAA
* *
204764 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
204784 AATTAAAAAT
Statistics
Matches: 192, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
184 8 0.04
185 13 0.07
186 171 0.89
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAAATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAACTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTGAATTAAA
Found at i:206642 original size:34 final size:30
Alignment explanation
Indices: 206604--206672 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
206594 TTGATATAAC
206604 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
206638 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
206667 AATTTA
1 AATTTA
206673 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:206683 original size:29 final size:30
Alignment explanation
Indices: 206613--206672 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
206603 CAATTTAAGG
206613 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
206644 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
206673 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:206780 original size:22 final size:23
Alignment explanation
Indices: 206752--206794 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
206742 AGGGTGTCAA
206752 AGTGCATCCATGCACC-TGCACT
1 AGTGCATCCATGCACCATGCACT
*
206774 AGTGCATCGATGCACCATGCA
1 AGTGCATCCATGCACCATGCA
206795 TTGTATCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (23 bp):
AGTGCATCCATGCACCATGCACT
Found at i:206854 original size:20 final size:20
Alignment explanation
Indices: 206829--206906 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
206819 AATGTAATTA
206829 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
206849 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
***
206869 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTTCT
*
206890 TTGCATCGATGCATCCT
1 GTGCATCGATGCATCCT
206907 GTTGTGTATC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
20 35 0.69
21 16 0.31
ACGTcount: A:0.18, C:0.28, G:0.22, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:206922 original size:41 final size:41
Alignment explanation
Indices: 206850--206930 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
206840 CATCCTTCTG
*
206850 TGCATCGATGCATCCTTCTGTGCATCGATGCATC-AAGGCTT
1 TGCATCGATGCATCCTTCTGTGCATCCATGCA-CGAAGGCTT
*
206891 TGCATCGATGCATCCTGT-TGTGTATCCATGCACGAAGGCT
1 TGCATCGATGCATCCT-TCTGTGCATCCATGCACGAAGGCT
206931 GCAACAACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
40 1 0.03
41 34 0.94
42 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (41 bp):
TGCATCGATGCATCCTTCTGTGCATCCATGCACGAAGGCTT
Found at i:210370 original size:63 final size:63
Alignment explanation
Indices: 210240--210377 Score: 161
Period size: 63 Copynumber: 2.2 Consensus size: 63
210230 GGGGGGTATG
* * **
210240 AGAGTCAGCATTATCAATATTATTTTTCGACCTTGGTAAAAGTTCAGGCTATTGGGTAGTATG
1 AGAGTCAGCATTATCAATATTATTTTCCGACCTTGGTAAAAGTTCAGGCTATTGGATAGTACA
* * * * * *
210303 AGAGTCAGCGTTATCAGTATTGTTTTCCGACTTTGGTAAAGGTTCAGGCTGTT-GATACGTACA
1 AGAGTCAGCATTATCAATATTATTTTCCGACCTTGGTAAAAGTTCAGGCTATTGGATA-GTACA
*
210366 AGAGTCACCATT
1 AGAGTCAGCATT
210378 GTTTGAAGAC
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
62 3 0.05
63 59 0.95
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (63 bp):
AGAGTCAGCATTATCAATATTATTTTCCGACCTTGGTAAAAGTTCAGGCTATTGGATAGTACA
Found at i:216339 original size:2 final size:2
Alignment explanation
Indices: 216332--216366 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
216322 ATTTACAACT
216332 TA 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 TA T
216367 TTTTAAACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:218522 original size:20 final size:19
Alignment explanation
Indices: 218495--218537 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
218485 GTATTGAACT
* *
218495 CTTAGTATTGATATTTTAC
1 CTTAGTATCGATACTTTAC
218514 CTTAGGTATCGATACTTTAC
1 CTTA-GTATCGATACTTTAC
218534 CTTA
1 CTTA
218538 TTATTACTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (19 bp):
CTTAGTATCGATACTTTAC
Found at i:221050 original size:19 final size:19
Alignment explanation
Indices: 221023--221080 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
221013 TATTAAGATT
*
221023 TAAATTTTTAAAAATAGGA
1 TAAAATTTTAAAAATAGGA
*
221042 TAAAATTTT---ACTAGGA
1 TAAAATTTTAAAAATAGGA
*
221058 TTCAAACTTTTAAAAATAGGA
1 -T-AAAATTTTAAAAATAGGA
221079 TA
1 TA
221081 GAGTTCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 6 0.20
17 1 0.03
18 7 0.23
19 9 0.30
20 1 0.03
21 6 0.20
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.36
Consensus pattern (19 bp):
TAAAATTTTAAAAATAGGA
Found at i:221114 original size:37 final size:36
Alignment explanation
Indices: 221016--221116 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 36
221006 TTCGTATTAT
*
221016 TAAGATTTAAATTTTTAAAAATAGGATAAAATTTTAC
1 TAAGATTTAAA-TTTTAAAAATAGGATAAAATTCTAC
* * * *
221053 TAGGATTCAAACTTTTAAAAATAGGATAGAGTTCTAC
1 TAAGATTTAAA-TTTTAAAAATAGGATAAAATTCTAC
* *
221090 TAAGATTTAAATTCCTAAAGATAGGAT
1 TAAGATTTAAATT-TTAAAAATAGGAT
221117 CTACAAGCAC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 2 0.04
37 51 0.96
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (36 bp):
TAAGATTTAAATTTTAAAAATAGGATAAAATTCTAC
Found at i:227023 original size:72 final size:75
Alignment explanation
Indices: 226931--227091 Score: 188
Period size: 72 Copynumber: 2.2 Consensus size: 75
226921 ATACAGATGA
* * * * *
226931 TTATCTCACTCAAATTTGTTTTTCTTAAAATATA-CTTTGTCTCACTTGACACTGTTTT-TCTCG
1 TTATTTCACTCAAATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGACACCGTTTTCACTCG
226994 AAA-AAAG-AT
65 AAAGAAAGCAT
* *
227003 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCG
1 TTATTTCACTCAA-ATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGACACCGTTTTCACTCG
*
227067 AAAGAAGGCAT
65 AAAGAAAGCAT
227078 TTCATTTCACTCAA
1 TT-ATTTCACTCAA
227092 TGCTATTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
71 1 0.01
72 48 0.64
73 8 0.11
74 3 0.04
75 4 0.05
76 11 0.15
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (75 bp):
TTATTTCACTCAAATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGACACCGTTTTCACTCGA
AAGAAAGCAT
Found at i:227164 original size:39 final size:39
Alignment explanation
Indices: 227105--227256 Score: 117
Period size: 39 Copynumber: 3.6 Consensus size: 39
227095 TATTTTTTTA
* **
227105 AGAAAATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAAATTTTGTCTCCCTTGAGATAGTTTCCCTCGAAAC
* * *
227144 AGAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAAC
1 AGAAAATTTTGTCTCCCTTGAGATAGTTTCCCTCG-AAAC
*
227184 ATTTCCCTTGAAATTATTTT-TCTCTCTCCTGAGATAGTTTCCCTCGAAAC
1 A--------GAAA--ATTTTGTCTC-C-CTTGAGATAGTTTCCCTCGAAAC
227234 AGAAAATTTTGTCTCCCTTGAGA
1 AGAAAATTTTGTCTCCCTTGAGA
227257 CAATTTCTCT
Statistics
Matches: 88, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
39 35 0.40
40 11 0.12
41 4 0.05
42 4 0.05
48 4 0.05
49 4 0.05
50 11 0.12
51 15 0.17
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (39 bp):
AGAAAATTTTGTCTCCCTTGAGATAGTTTCCCTCGAAAC
Found at i:227342 original size:105 final size:104
Alignment explanation
Indices: 227176--227494 Score: 500
Period size: 105 Copynumber: 3.1 Consensus size: 104
227166 ACAGTTTCTC
* * *
227176 TTGAAAACATTTCCCTTGAAATTATTTTTCTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGATTTTTATCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
* *
227241 TTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACA
66 TTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
227280 TTGAAAACATTTCCCTTGAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-TTTTTATCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
227345 TTTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
227385 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGATTTTTATCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
227447 TTTATCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
227486 TTGAAAACA
1 TTGAAAACA
227495 ATTTAACGAA
Statistics
Matches: 202, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
101 48 0.24
103 1 0.00
104 53 0.26
105 100 0.50
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGATTTTTATCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:227441 original size:36 final size:36
Alignment explanation
Indices: 227394--227469 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
227384 ATTGAAAACA
* * *
227394 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
227430 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
227466 TTTC
1 TTTC
227470 TCTCCAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:227774 original size:105 final size:104
Alignment explanation
Indices: 227589--228036 Score: 663
Period size: 105 Copynumber: 4.3 Consensus size: 104
227579 TCGAGAATAG
* *
227589 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCAAGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
227654 ACCGCTGCTTATCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
227694 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
227759 ACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
227799 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
227864 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* * * *
227899 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
227964 A-CGACTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCG-CTGCTTGTCAAC-AACAACTTCCCAATT-CAGAGCCA
* *
228005 ATTTCAACTTCACGACGGAGGATATTGGACTC
1 ATTTCAACTTCACAACGAAGGATATTGGACTC
228037 GGAACAATGC
Statistics
Matches: 316, Mismatches: 20, Indels: 13
0.91 0.06 0.04
Matches are distributed among these distances:
99 2 0.01
100 79 0.25
101 4 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 185 0.59
106 36 0.11
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (104 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
Found at i:228635 original size:37 final size:37
Alignment explanation
Indices: 228575--228645 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
228565 ACACATTTTC
* *
228575 GTTCTATTAGGATTCAAACTCCTAAAAATAGGATAGA
1 GTTCTACTAAGATTCAAACTCCTAAAAATAGGATAGA
* * *
228612 GTTCTACTAAGATTTAAATTCCTAAAGATAGGAT
1 GTTCTACTAAGATTCAAACTCCTAAAAATAGGAT
228646 CCACAACCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (37 bp):
GTTCTACTAAGATTCAAACTCCTAAAAATAGGATAGA
Found at i:229028 original size:18 final size:17
Alignment explanation
Indices: 228989--229030 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
228979 ATTATATGGA
228989 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
229005 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
229023 TATTATTA
1 TATTATTA
229031 AATGTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 11 0.50
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:240339 original size:60 final size:60
Alignment explanation
Indices: 240271--240407 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
240261 TAAAGTGCAC
* * * *
240271 AAATAGTCCCCCGCCTACATGATGTTACTTTGTTGAGTC-CT-TAGACTATTAAAAGTTATA
1 AAATAGTCCCCCGACTACAAGATGTTACTTTGTTGAGTCACTCT--ACTACTAAAAGTTACA
* * *
240331 AAATAGTCCCCCGATTATAAGATGTTCCTTTGTTGAGTCACTCTACTACTAAAAGTTACA
1 AAATAGTCCCCCGACTACAAGATGTTACTTTGTTGAGTCACTCTACTACTAAAAGTTACA
*
240391 AAAT-GATCACCCGACTA
1 AAATAG-TCCCCCGACTA
240408 TTCATTATGT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 1 0.02
60 61 0.94
61 2 0.03
62 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (60 bp):
AAATAGTCCCCCGACTACAAGATGTTACTTTGTTGAGTCACTCTACTACTAAAAGTTACA
Found at i:246858 original size:6 final size:6
Alignment explanation
Indices: 246847--246907 Score: 122
Period size: 6 Copynumber: 10.2 Consensus size: 6
246837 CACGTATTAT
246847 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
246895 CACGAC CACGAC C
1 CACGAC CACGAC C
246908 CGAGACGGGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:252710 original size:21 final size:21
Alignment explanation
Indices: 252684--252724 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
252674 TTGAAATCTG
*
252684 CCTTGTTCAGCCATAATTTTC
1 CCTTGTTCAACCATAATTTTC
252705 CCTTGTTCAACCATAATTTT
1 CCTTGTTCAACCATAATTTT
252725 ACTGAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.07, T:0.44
Consensus pattern (21 bp):
CCTTGTTCAACCATAATTTTC
Found at i:264219 original size:2 final size:2
Alignment explanation
Indices: 264214--264245 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
264204 TTTCCGCGCA
264214 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
264246 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:266526 original size:23 final size:23
Alignment explanation
Indices: 266500--266548 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
266490 GAAAATTCCC
266500 AATCCATAAAT-TTCAATCCCTAA
1 AATCC-TAAATATTCAATCCCTAA
*
266523 AATCCTAAATATTCAATCCCTTA
1 AATCCTAAATATTCAATCCCTAA
266546 AAT
1 AAT
266549 TCCTTTGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (23 bp):
AATCCTAAATATTCAATCCCTAA
Found at i:267298 original size:13 final size:14
Alignment explanation
Indices: 267282--267314 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
267272 ATTAACGTTC
267282 TAAATTATTT-TTT
1 TAAATTATTTATTT
*
267295 TAAAATATTTATTT
1 TAAATTATTTATTT
267309 TAAATT
1 TAAATT
267315 CAAAACATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TAAATTATTTATTT
Found at i:267582 original size:24 final size:25
Alignment explanation
Indices: 267546--267603 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
267536 ATATGTTAAC
*
267546 TTAAAAATGTTTTA-TATTAACTTA
1 TTAAAAATATTTTATTATTAACTTA
*
267570 TTAAATATATTTTATTATTAACTTAA
1 TTAAAAATATTTTATTATTAACTT-A
267596 TTTAAAAA
1 -TTAAAAA
267604 AATATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 12 0.43
25 9 0.32
26 1 0.04
27 6 0.21
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (25 bp):
TTAAAAATATTTTATTATTAACTTA
Found at i:268197 original size:17 final size:17
Alignment explanation
Indices: 268170--268208 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
268160 AATTTACAAT
*
268170 TAATT-TAAATAATATC
1 TAATTATAAATAATATA
268186 TAATTATAAATAATATA
1 TAATTATAAATAATATA
268203 TAATTA
1 TAATTA
268209 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATA
Found at i:268284 original size:11 final size:11
Alignment explanation
Indices: 268268--268292 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
268258 AATATTGATT
268268 TGGGTTTTAAA
1 TGGGTTTTAAA
268279 TGGGTTTTAAA
1 TGGGTTTTAAA
268290 TGG
1 TGG
268293 ATTAGGCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (11 bp):
TGGGTTTTAAA
Found at i:268337 original size:9 final size:9
Alignment explanation
Indices: 268323--268348 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
268313 TATATTTAAA
268323 GGTTAATTC
1 GGTTAATTC
268332 GGTTAATTC
1 GGTTAATTC
268341 GGTTAATT
1 GGTTAATT
268349 AACCGATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (9 bp):
GGTTAATTC
Found at i:272263 original size:30 final size:30
Alignment explanation
Indices: 272216--272292 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
272206 AAATACATAA
* *
272216 ATACAGT-AATCAAATATCATATAAAAAAT
1 ATACAGTAAATCAGATATCAGATAAAAAAT
*
272245 ATACAGTAAATCAGATATCAGATAAACAAT
1 ATACAGTAAATCAGATATCAGATAAAAAAT
* *
272275 ATTCAGGAAATCAGATAT
1 ATACAGTAAATCAGATAT
272293 TGTCTCGTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 7 0.17
30 35 0.83
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (30 bp):
ATACAGTAAATCAGATATCAGATAAAAAAT
Found at i:279483 original size:14 final size:14
Alignment explanation
Indices: 279464--279493 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
279454 CATTTTTGAA
279464 AGGAGATCTAGATG
1 AGGAGATCTAGATG
*
279478 AGGAGATCTATATG
1 AGGAGATCTAGATG
279492 AG
1 AG
279494 AACAATGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (14 bp):
AGGAGATCTAGATG
Found at i:280939 original size:31 final size:31
Alignment explanation
Indices: 280901--280963 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
280891 CCCAAGAGTT
280901 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
1 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
*
280932 TGGGAGTTCCTAGTGAGAATGACATATTGAA
1 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
280963 T
1 T
280964 TCACCAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.29
Consensus pattern (31 bp):
TGGGAGTTCCTAGTGAGAAGGACATATTGAA
Found at i:285187 original size:12 final size:12
Alignment explanation
Indices: 285165--285204 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
285155 AATTTGAATC
285165 AATAA-AATAAT
1 AATAACAATAAT
285176 AATAACAATAAT
1 AATAACAATAAT
* *
285188 AACAACAACAAT
1 AATAACAATAAT
285200 AATAA
1 AATAA
285205 TAATTTGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (12 bp):
AATAACAATAAT
Found at i:298386 original size:17 final size:17
Alignment explanation
Indices: 298364--298396 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
298354 TTTCTAAAAT
*
298364 AAAAGATAATAATTAAA
1 AAAAGAAAATAATTAAA
298381 AAAAGAAAATAATTAA
1 AAAAGAAAATAATTAA
298397 TTAAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAAGAAAATAATTAAA
Found at i:300211 original size:13 final size:13
Alignment explanation
Indices: 300179--300218 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
300169 GAACCATTTT
300179 TAAAAT-AAA-AA
1 TAAAATAAAATAA
*
300190 TGAAA-AAAATAA
1 TAAAATAAAATAA
300202 TAAAATAAAATAA
1 TAAAATAAAATAA
300215 TAAA
1 TAAA
300219 TAGAGAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 7 0.29
12 6 0.25
13 11 0.46
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
TAAAATAAAATAA
Found at i:303074 original size:10 final size:10
Alignment explanation
Indices: 303059--303088 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
303049 AGTGTGCTAC
303059 AAATAAAATG
1 AAATAAAATG
303069 AAATAAAATG
1 AAATAAAATG
*
303079 AAATGAAATG
1 AAATAAAATG
303089 GGTCGCCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (10 bp):
AAATAAAATG
Found at i:303800 original size:41 final size:41
Alignment explanation
Indices: 303736--303817 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
303726 ATTTGCTCGG
* * *
303736 TCGTTTTCCATGTCAATGCCATAGAAATCTTCCGGAAATAT
1 TCGTTTTCCATATCAATGACATAGAAATCTTCCGAAAATAT
*
303777 TCGTTTTCCATATGAATGACATAGAAATCTTCCGAAAATAT
1 TCGTTTTCCATATCAATGACATAGAAATCTTCCGAAAATAT
303818 AAGCTCATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (41 bp):
TCGTTTTCCATATCAATGACATAGAAATCTTCCGAAAATAT
Found at i:309309 original size:36 final size:35
Alignment explanation
Indices: 309248--309334 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 35
309238 TTTAGATATG
* *
309248 TACTTTTCTATTTCAGTTCATATCATTGCAAAAT-TA
1 TACTTTTCT-TTTCAGTTCAGATCATTGC-AAATCAA
*
309284 TACTTTTCTTTTCGAAG-TCAGATCATTTCAAATCAA
1 TACTTTTCTTTTC--AGTTCAGATCATTGCAAATCAA
309320 TACTTTTCTTGTTCA
1 TACTTTTCTT-TTCA
309335 TATAAGATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
35 9 0.20
36 30 0.68
37 5 0.11
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (35 bp):
TACTTTTCTTTTCAGTTCAGATCATTGCAAATCAA
Found at i:311510 original size:18 final size:18
Alignment explanation
Indices: 311487--311521 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
311477 CGGTGGTTAA
311487 AGGTCAAATTAATAGATG
1 AGGTCAAATTAATAGATG
311505 AGGTCAAATTAATAGAT
1 AGGTCAAATTAATAGAT
311522 TTTATACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.29
Consensus pattern (18 bp):
AGGTCAAATTAATAGATG
Found at i:316446 original size:14 final size:13
Alignment explanation
Indices: 316423--316468 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
316413 TGAATTTGAA
316423 TAAAAAATAACTT
1 TAAAAAATAACTT
316436 TAAAAATATAACTT
1 TAAAAA-ATAACTT
* *
316450 TACAAAATAACAT
1 TAAAAAATAACTT
316463 TAAAAA
1 TAAAAA
316469 TAATTCACGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAAAAATAACTT
Found at i:316997 original size:21 final size:21
Alignment explanation
Indices: 316958--317003 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
316948 ATGAAACTTG
* *
316958 GCGGGCTAGGAATATAACCCT
1 GCGGGCTAGGAATACAACCCA
*
316979 GCGGGCTAGGAATGCAACCCA
1 GCGGGCTAGGAATACAACCCA
317000 GCGG
1 GCGG
317004 AGATGGCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (21 bp):
GCGGGCTAGGAATACAACCCA
Found at i:319820 original size:23 final size:23
Alignment explanation
Indices: 319777--319821 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
319767 TAATATTTTA
**
319777 TTTTAAATAATTTATCTTTATAT
1 TTTTAAATAATTTATAATTATAT
*
319800 TTTTAACTAATTTATAATTATA
1 TTTTAAATAATTTATAATTATA
319822 CGTAGAGTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTAAATAATTTATAATTATAT
Found at i:320289 original size:21 final size:21
Alignment explanation
Indices: 320260--320312 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
320250 ATTCTGACTA
320260 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
320281 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
320302 TCGCAATGCGA
1 TCGCATTGCGA
320313 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:320327 original size:20 final size:20
Alignment explanation
Indices: 320302--320413 Score: 129
Period size: 20 Copynumber: 5.5 Consensus size: 20
320292 TTTTCCTAAT
320302 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
320322 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
320343 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
320363 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
320383 TCGCAATGCAAAT-C-TGAATA
1 TCGCAATGCGAATACGT-AA-A
320403 TCGCAATGCGA
1 TCGCAATGCGA
320414 TTTACATAGC
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 58 0.75
21 15 0.19
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:320375 original size:61 final size:60
Alignment explanation
Indices: 320302--320415 Score: 183
Period size: 61 Copynumber: 1.9 Consensus size: 60
320292 TTTTCCTAAT
* *
320302 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCAAATCT-GAAAATCGCAATGCGATTACGTAAA
* *
320363 TCGCAATGCGAATACGTAAATCGCAATGCAAATCTGAATATCGCAATGCGATT
1 TCGCAATGCGAATACGTAAATCGCAACGCAAATCTGAAAATCGCAATGCGATT
320416 TACATAGCGT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 17 0.35
61 32 0.65
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAACGCAAATCTGAAAATCGCAATGCGATTACGTAAA
Found at i:320615 original size:22 final size:22
Alignment explanation
Indices: 320590--320651 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
320580 GGCGACATCC
320590 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
320612 GTCCCCA----CGACGATAA-CA
1 GTCCCCATCTCCGACGA-AATCA
* *
320630 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
320652 TTCACGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
21 2 0.06
22 14 0.44
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:322965 original size:20 final size:20
Alignment explanation
Indices: 322940--323063 Score: 143
Period size: 20 Copynumber: 6.5 Consensus size: 20
322930 AGAATAGTTT
*
322940 ACTATCGCAATACGAAAATG
1 ACTATCGCAATGCGAAAATG
*
322960 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
322980 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
322996 A--ATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
323014 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
**
323034 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
323054 ACTATCGCAA
1 ACTATCGCAA
323064 CGAAAGAATC
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
14 7 0.08
16 3 0.03
17 4 0.05
18 4 0.05
20 70 0.80
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:323012 original size:34 final size:34
Alignment explanation
Indices: 322963--323084 Score: 136
Period size: 34 Copynumber: 3.4 Consensus size: 34
322953 GAAAATGACT
* *
322963 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
* *
322997 ATCGCAATGCAAAAATGACTATCGCAATGTGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
**
323035 CTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
323071 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
323085 TGAAAATCGC
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
34 38 0.52
36 3 0.04
37 5 0.07
38 3 0.04
40 24 0.33
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:323061 original size:74 final size:74
Alignment explanation
Indices: 322940--323080 Score: 228
Period size: 74 Copynumber: 1.9 Consensus size: 74
322930 AGAATAGTTT
*
322940 ACTATCGCAATACGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAAT
1 ACTATCGCAATACGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
323005 GCAAAAATG
66 GCAAAAATG
** * **
323014 ACTATCGCAATGTGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAAT
1 ACTATCGCAATACGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
323079 GC
66 GC
323081 GAAATGAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (74 bp):
ACTATCGCAATACGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
GCAAAAATG
Found at i:323153 original size:20 final size:20
Alignment explanation
Indices: 323108--323156 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
323098 GCGATTCTCT
323108 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTTG
* *
323128 CATTGCGATAGTC-ATTTTCG
1 CGTTGCGATAGTCAAATTT-G
323148 CGTTGCGAT
1 CGTTGCGAT
323157 TTTGTTGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTTG
Found at i:323201 original size:33 final size:34
Alignment explanation
Indices: 323128--323220 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 34
323118 GTCAAATTTG
* * *
323128 CATTGCGATAGTCATTTTCGCGTTGCGATTTTGT
1 CATTGCGATAGTCATTTTCGCATTGCGATTCTCT
** **
323162 TGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CATTGCGATAGTCATTTTCGCATTGCGATTCTCT
*
323195 CATTGCGATAGTCATTTTCGCGTTGC
1 CATTGCGATAGTCATTTTCGCATTGC
323221 AATAGTCTTT
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
33 26 0.57
34 20 0.43
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (34 bp):
CATTGCGATAGTCATTTTCGCATTGCGATTCTCT
Found at i:323225 original size:20 final size:20
Alignment explanation
Indices: 323197--323240 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
323187 GATTCTCTCA
*
323197 TTGCGATAGTCATTTTCGCG
1 TTGCAATAGTCATTTTCGCG
*
323217 TTGCAATAGTCTTTTTCGCG
1 TTGCAATAGTCATTTTCGCG
323237 TTGC
1 TTGC
323241 GATTTTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.43
Consensus pattern (20 bp):
TTGCAATAGTCATTTTCGCG
Found at i:323768 original size:18 final size:19
Alignment explanation
Indices: 323729--323770 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
323719 TTCACCTGTC
323729 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
323750 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
323768 ATC
1 ATC
323771 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:325419 original size:34 final size:33
Alignment explanation
Indices: 325331--325425 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
325321 AAAACAGACT
* ** *
325331 ATCGCAACGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
325365 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
325398 ATCGCAATGCGAAAATGAAAATCGCAAC
1 ATCGCAATGCG-AAATGAAAATCGCAAC
325426 ACGAAACTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:325457 original size:19 final size:19
Alignment explanation
Indices: 325435--325522 Score: 71
Period size: 19 Copynumber: 4.8 Consensus size: 19
325425 CACGAAACTA
*
325435 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
325454 ATTTTCGCATTACGA--TTC
1 A-TTTCGCATTGCGATTTTC
* *
325472 A-CTCG--TTGTGATTTTC
1 ATTTCGCATTGCGATTTTC
325488 ATTGT-GCATTGCGATTTTC
1 ATT-TCGCATTGCGATTTTC
*
325507 ATTTCACATTGCGATT
1 ATTTCGCATTGCGATT
325523 CTCTCGTTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
14 4 0.08
16 7 0.13
17 1 0.02
18 6 0.11
19 24 0.45
20 11 0.21
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:325542 original size:52 final size:53
Alignment explanation
Indices: 325443--325542 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 53
325433 TAATTTCGCG
* ** **
325443 TTGCGATTTTCATTTTCGCATTACGATTCACTCGTTGTGATTTTCATTGTGCA
1 TTGCGATTTTCATTTTCACATTACGATTCACTCGTTGCAATAGTCATTGTGCA
* *
325496 TTGCGATTTTCA-TTTCACATTGCGATTCTCTCGTTGCAATAGTCATT
1 TTGCGATTTTCATTTTCACATTACGATTCACTCGTTGCAATAGTCATT
325543 TCCGAGTTGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
52 28 0.70
53 12 0.30
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCATTTTCACATTACGATTCACTCGTTGCAATAGTCATTGTGCA
Found at i:325553 original size:53 final size:54
Alignment explanation
Indices: 325442--325555 Score: 126
Period size: 52 Copynumber: 2.1 Consensus size: 54
325432 CTAATTTCGC
* ** ** *
325442 GTTGCGATTTTCATTTTCGCATTACGATTCACTCGTTGTGATTTTCATTGTGCA
1 GTTGCGATTTTCATTTTCACATTACGATTCACTCGTTGCAATAGTCATTGTCCA
* *
325496 -TTGCGATTTTCA-TTTCACATTGCGATTCTCTCGTTGCAATAGTCATT-TCCGA
1 GTTGCGATTTTCATTTTCACATTACGATTCACTCGTTGCAATAGTCATTGTCC-A
325548 GTTGCGAT
1 GTTGCGAT
325556 AGTCAATTCC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
51 2 0.04
52 29 0.58
53 19 0.38
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (54 bp):
GTTGCGATTTTCATTTTCACATTACGATTCACTCGTTGCAATAGTCATTGTCCA
Found at i:325557 original size:20 final size:20
Alignment explanation
Indices: 325528--325615 Score: 99
Period size: 20 Copynumber: 4.4 Consensus size: 20
325518 CGATTCTCTC
*
325528 GTTGCAATAGTCATTTCCGA
1 GTTGCGATAGTCATTTCCGA
*
325548 GTTGCGATAGTCAATTCCGTA
1 GTTGCGATAGTCATTTCCG-A
* *
325569 -TTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTCCGA
*
325588 GTTGCGATAGTCATATT-CGC
1 GTTGCGATAGTCAT-TTCCGA
325608 GTTGCGAT
1 GTTGCGAT
325616 TTCCGCGTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
20 56 0.95
21 3 0.05
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGA
Found at i:325592 original size:40 final size:41
Alignment explanation
Indices: 325529--325605 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
325519 GATTCTCTCG
325529 TTGCAATAGTCATTTCCGAGTTGCGATAGTCA-ATTCCGTA
1 TTGCAATAGTCATTTCCGAGTTGCGATAGTCATATTCCGTA
* * *
325569 TTGCGATAGTCATTTTCGTGTTGCGATAGTCATATTC
1 TTGCAATAGTCATTTCCGAGTTGCGATAGTCATATTC
325606 GCGTTGCGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (41 bp):
TTGCAATAGTCATTTCCGAGTTGCGATAGTCATATTCCGTA
Found at i:325613 original size:40 final size:38
Alignment explanation
Indices: 325527--325615 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 38
325517 GCGATTCTCT
*
325527 CGTTGCAATAGTCATTTCCGAGTTGCGATAGTCAATTC
1 CGTTGCGATAGTCATTTCCGAGTTGCGATAGTCAATTC
* *
325565 CGTATTGCGATAGTCATTTTCGTGTTGCGATAGTCATATTC
1 CG--TTGCGATAGTCATTTCCGAGTTGCGATAGTCA-ATTC
325606 GCGTTGCGAT
1 -CGTTGCGAT
325616 TTCCGCGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
38 2 0.05
40 36 0.82
41 4 0.09
42 2 0.05
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (38 bp):
CGTTGCGATAGTCATTTCCGAGTTGCGATAGTCAATTC
Found at i:327834 original size:14 final size:14
Alignment explanation
Indices: 327815--327841 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
327805 TCTCGTGGCA
327815 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
327829 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
327842 TTTCTTCTTC
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:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:328108 original size:24 final size:24
Alignment explanation
Indices: 328057--328108 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
328047 ATCTGAGTAT
** *
328057 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
328081 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
328105 TGAC
1 TGAC
328109 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:328968 original size:20 final size:19
Alignment explanation
Indices: 328955--329043 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 19
328945 CAGAATCTCG
*
328955 TTGCGATTTACAGATTCGCA
1 TTGCGATTTAC-GAATCGCA
328975 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACG-AATCGCA
*
328995 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACG-AATCGCA
329015 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACG-AATCGCA
329035 TTGCGATTT
1 TTGCGATTT
329044 TCCAAATTCG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 1 0.02
20 64 0.98
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (19 bp):
TTGCGATTTACGAATCGCA
Found at i:328979 original size:40 final size:40
Alignment explanation
Indices: 328955--329043 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
328945 CAGAATCTCG
*
328955 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTAC-GTATTCGCATTGCGATTCACGTAATCGCA
*
328995 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCATTGCGATTCACGTAATCGCA
329035 TTGCGATTT
1 TTGCGATTT
329044 TCCAAATTCG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 1 0.02
40 47 0.98
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACGTATTCGCATTGCGATTCACGTAATCGCA
Found at i:329019 original size:60 final size:62
Alignment explanation
Indices: 328955--329077 Score: 171
Period size: 60 Copynumber: 2.0 Consensus size: 62
328945 CAGAATCTCG
* **
328955 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTAA-TCGCATTGCGA-TTTACGTATTCGCA
1 TTGCGATTTAC-GTAATCGCATTGCGATTTACCAAATTCGCATTGCGATTTTACGTATTCGCA
* *
329015 TTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACCAAATTCGCATTGCGATTTTACGTATTCGCA
329077 T
1 T
329078 ACGTAAATCG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 1 0.02
60 29 0.53
61 10 0.18
62 15 0.27
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (62 bp):
TTGCGATTTACGTAATCGCATTGCGATTTACCAAATTCGCATTGCGATTTTACGTATTCGCA
Found at i:329059 original size:21 final size:21
Alignment explanation
Indices: 328955--329065 Score: 86
Period size: 20 Copynumber: 5.5 Consensus size: 21
328945 CAGAATCTCG
* *
328955 TTGCGA-TTTACAGATTCGCA
1 TTGCGATTTTCCAAATTCGCA
* **
328975 TTGCGATTTACGTAA-TCGCA
1 TTGCGATTTTCCAAATTCGCA
* **
328995 TTGCGA-TTTACGTATTCGCA
1 TTGCGATTTTCCAAATTCGCA
* **
329015 TTGCGATTTACGTAA-TCGCA
1 TTGCGATTTTCCAAATTCGCA
*
329035 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCA
329056 TTGCGATTTT
1 TTGCGATTTT
329066 ACGTATTCGC
Statistics
Matches: 68, Mismatches: 19, Indels: 7
0.72 0.20 0.07
Matches are distributed among these distances:
19 3 0.04
20 45 0.66
21 20 0.29
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:336305 original size:14 final size:14
Alignment explanation
Indices: 336286--336319 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
336276 TTCTCATAGG
336286 CTTTTCTTCAAATC
1 CTTTTCTTCAAATC
336300 CTTTTCTTCAAATC
1 CTTTTCTTCAAATC
336314 CTTTTC
1 CTTTTC
336320 ATATTGTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.53
Consensus pattern (14 bp):
CTTTTCTTCAAATC
Found at i:336821 original size:41 final size:41
Alignment explanation
Indices: 336764--336845 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
336754 ATTTTCTCGG
* *
336764 TCGTTTTCCATGTCAATGACATAGATATCTTCCAGAAATAT
1 TCGTTTTCCATATCAATGACATAGAAATCTTCCAGAAATAT
*
336805 TCGTTTTCCATATCAATGACATAGAAATCTTCCGGAAATAT
1 TCGTTTTCCATATCAATGACATAGAAATCTTCCAGAAATAT
336846 AAGCTCATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (41 bp):
TCGTTTTCCATATCAATGACATAGAAATCTTCCAGAAATAT
Found at i:348819 original size:29 final size:29
Alignment explanation
Indices: 348776--348887 Score: 179
Period size: 29 Copynumber: 3.8 Consensus size: 29
348766 CTCACCTAAC
348776 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
348806 TAAATGATGTAAGCAATGACATCATTACT
1 TAAATGATGTAAGCAATGACATCATTACT
* *
348835 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTACT
* *
348864 TAAATTATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
348888 ATTTAGTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 73 0.95
30 4 0.05
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:352274 original size:15 final size:15
Alignment explanation
Indices: 352254--352283 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
352244 CTTTCTCATA
352254 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
352269 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
352284 CCAGCCTCGT
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:0.13, C:0.00, G:0.33, T:0.53
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:353575 original size:29 final size:29
Alignment explanation
Indices: 353499--353581 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
353489 CTCACCTAAC
* *
353499 TAAATTGATGTAAGCAATGAAATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
* *
353529 TAAATGATGTAAACAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
353558 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
353582 ATTTAGTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 42 0.91
30 4 0.09
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:358371 original size:139 final size:138
Alignment explanation
Indices: 357685--358451 Score: 985
Period size: 139 Copynumber: 5.6 Consensus size: 138
357675 CATGTGAAGA
* * * * * *
357685 CGCGTTTTAGGGGGCGTGCTTTCTCTTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATG
1 CGCGTTTCAAGGGGCGCGCCTTCTATTATTTTT-TCAGAGAATATGTTATAATTGCCCTATTATG
* *** *
357750 TGAGTCATGTCCCTGGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAAAG
65 TGACTCATGTCCCCCAGGGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACGCAACAAAG
*
357815 TGATGAAAG
130 TGGTGAAAG
* * *
357824 ACGTGTTTCAAGGGGCGCGTCTTCCATTATTTTGTT-AGAGAATATGTTATAATTGCCCTATTAT
1 -CGCGTTTCAAGGGGCGCGCCTTCTATTATTTT-TTCAGAGAATATGTTATAATTGCCCTATTAT
* * * ** ***
357888 GTGAGTCATGTCCTCGAGGGCACTATTCATGTCAATACCTATCATGTTTGAGGGGATATAACAAA
64 GTGACTCATGTCCCCCAGGGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACGCAACAAA
*
357953 GTAGTGAAAG
129 GTGGTGAAAG
** * * *
357963 TACGTCT-AAGGGGTCGTGCCTT-TCATTATTTTTTCATAGAATATGTTATAATTGCCCTATTAT
1 CGCGTTTCAAGGGG-CGCGCCTTCT-ATTATTTTTTCAGAGAATATGTTATAATTGCCCTATTAT
* *
358026 GTGACTCATGT-CCCCAGGGCACTATTCATGTCGGTACTTATCATGTTTGAGGGGACGCAATAAA
64 GTGACTCATGTCCCCCAGGGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACGCAACAAA
358090 GTGGTGAAAG
129 GTGGTGAAAG
* * *
358100 CGCGTTTC-AGGTGGAGCGCCTCCT-TTATTTTGTCAGAGAATATGTTATAATTGCCCTATTATG
1 CGCGTTTCAAGG-GGCGCGCCTTCTATTATTTTTTCAGAGAATATGTTATAATTGCCCTATTATG
* *
358163 TGACTCATGTCCCCC-TGGCACTATTCATGTCGGTACCTATCATGTTAGAGGGGACGCAACAAAG
65 TGACTCATGTCCCCCAGGGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACGCAACAAAG
358227 TGGTGAAAG
130 TGGTGAAAG
* *
358236 CGCGTTTCAAGGGGCGTGCCTTCTATTATTTTTTCAGAGAATATGTTATAATTTCCCTATTATGT
1 CGCGTTTCAAGGGGCGCGCCTTCTATTATTTTTTCAGAGAATATGTTATAATTGCCCTATTATGT
*
358301 GACTCATGTCCCCCCAGGGCACTATTCATGTCGGTGCCTATCATGTTTGAGGGGACGCAACAAAG
66 GACTCATGT-CCCCCAGGGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACGCAACAAAG
358366 TGGTGAAAG
130 TGGTGAAAG
* * * * * * *
358375 TGTGTATT--AGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATGATCGCCCTATTATG
1 CGCGT-TTCAAGGGGCGCGCCTTCTATTATTTTTTCAGAGAATATGTTATAATTGCCCTATTATG
358438 TGACTCATGTCCCC
65 TGACTCATGTCCCC
358452 GGGGTCGCAA
Statistics
Matches: 548, Mismatches: 66, Indels: 29
0.85 0.10 0.05
Matches are distributed among these distances:
136 118 0.22
137 131 0.24
138 120 0.22
139 152 0.28
140 26 0.05
141 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (138 bp):
CGCGTTTCAAGGGGCGCGCCTTCTATTATTTTTTCAGAGAATATGTTATAATTGCCCTATTATGT
GACTCATGTCCCCCAGGGCACTATTCATGTCGGTACCTATCATGTTTGAGGGGACGCAACAAAGT
GGTGAAAG
Found at i:359020 original size:14 final size:13
Alignment explanation
Indices: 358997--359042 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
358987 TGAATTTGAA
358997 TAAAAAATAACTT
1 TAAAAAATAACTT
359010 TAAAAATATAACTT
1 TAAAAA-ATAACTT
* *
359024 TATAAAATAACAT
1 TAAAAAATAACTT
359037 TAAAAA
1 TAAAAA
359043 TAATTCACGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAAAAATAACTT
Found at i:359550 original size:21 final size:20
Alignment explanation
Indices: 359513--359577 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
359503 AAAACCATAT
*
359513 GGGCTAGGCATGA-AACCTGGC
1 GGGCTAGGAAT-ATAACCT-GC
*
359534 GGGCTAGGAATATAACCCTTC
1 GGGCTAGGAATATAA-CCTGC
*
359555 GGGCTAGGAATGTAACCCTGC
1 GGGCTAGGAATATAA-CCTGC
359576 GG
1 GG
359578 AGATGGCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 34 0.89
22 3 0.08
ACGTcount: A:0.25, C:0.23, G:0.34, T:0.18
Consensus pattern (20 bp):
GGGCTAGGAATATAACCTGC
Found at i:359661 original size:42 final size:42
Alignment explanation
Indices: 359555--359661 Score: 97
Period size: 42 Copynumber: 2.5 Consensus size: 42
359545 ATAACCCTTC
* * *
359555 GGGCTAGGAATGTAACCCTGCGGAGATGGCATATGAACTGGT
1 GGGCTAGGAATGTACCCCTGTGGAGATGGCATATGAACTGGA
** * * * * * *
359597 GGGCTTTGCATATGCCCTTGTGGAGATGGCATTTGAATTGGA
1 GGGCTAGGAATGTACCCCTGTGGAGATGGCATATGAACTGGA
* *
359639 GGGCTGGGTATGTACCCCTGTGG
1 GGGCTAGGAATGTACCCCTGTGG
359662 CATCATCATC
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.20, C:0.17, G:0.36, T:0.27
Consensus pattern (42 bp):
GGGCTAGGAATGTACCCCTGTGGAGATGGCATATGAACTGGA
Found at i:373789 original size:10 final size:11
Alignment explanation
Indices: 373763--373793 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
373753 AGTGTGCTAC
373763 AAATAAAATGA
1 AAATAAAATGA
373774 AAATAAAATG-
1 AAATAAAATGA
373784 AAATAAAATG
1 AAATAAAATG
373794 TAATGGGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (11 bp):
AAATAAAATGA
Found at i:374502 original size:41 final size:40
Alignment explanation
Indices: 374445--374522 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 40
374435 ATTTGCTCGA
* *
374445 TCGTTTTCCATGTCAATGACATAGATATCTTCCAGAAATAT
1 TCGTTTTCCATATCAATGACATAGAAATCTTCC-GAAATAT
374486 TCGTTTTCCATATCAATGACATAGAAATCTTCCGAAA
1 TCGTTTTCCATATCAATGACATAGAAATCTTCCGAAA
374523 GTATAAGCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 4 0.11
41 31 0.89
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (40 bp):
TCGTTTTCCATATCAATGACATAGAAATCTTCCGAAATAT
Found at i:383900 original size:19 final size:19
Alignment explanation
Indices: 383876--383913 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
383866 TTTTACAAGT
383876 CATTACAATAAAATCCTTA
1 CATTACAATAAAATCCTTA
383895 CATTACAATAAAATCCTTA
1 CATTACAATAAAATCCTTA
383914 AATTCCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (19 bp):
CATTACAATAAAATCCTTA
Found at i:385789 original size:29 final size:29
Alignment explanation
Indices: 385746--385857 Score: 188
Period size: 29 Copynumber: 3.8 Consensus size: 29
385736 CTCACCTAAC
385746 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
385776 TAAATGATGTAAGCAATGACATCATTACT
1 TAAATGATGTAAGCAATGACATCATTACT
* *
385805 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTACT
*
385834 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
385858 ATTTAGTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 74 0.95
30 4 0.05
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:387503 original size:15 final size:15
Alignment explanation
Indices: 387479--387551 Score: 103
Period size: 15 Copynumber: 4.9 Consensus size: 15
387469 TTGATTTTCC
387479 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
387494 GGAATTTGAATTACT
1 GGAAAATGAATTACT
387509 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
387524 GGAATTTGAATT-CT
1 GGAAAATGAATTACT
387538 GGAAAATGAATTAC
1 GGAAAATGAATTAC
387552 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.24
15 37 0.76
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (15 bp):
GGAAAATGAATTACT
Done.