Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000630.1 Hibiscus syriacus cultivar Beakdansim tig00001226_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: 61833
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1864 original size:198 final size:195
Alignment explanation
Indices: 1432--2129 Score: 721
Period size: 198 Copynumber: 3.5 Consensus size: 195
1422 ATATGCATTT
* * * * *
1432 AACCGGTATATTTATACCGGTAACATTGCAAATTTACCTATTGCATTATAATTATTAGTTTCGTT
1 AACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTTGTTTCGAT
*
1497 GTTTTTTA-GATCGATACAATTTTAAATGTATCAACACTTTATGT-TTGCACCTCGTTGGGCATT
66 G-TTTTTAGGATCGATACAATTTTAAATGTATCGACACTTTAT-TCTTGCACCTCGTTGGG---T
* * * * *
1560 CCTAATTCATTCTGGAAAAAAGTAGCGACACAAACTATAAAGGTGTCGATACATTATTTAGACAT
126 --T--TTCATTATGGAAAAAAGTATCGACACAAA-T-TAAAAGTGTCGATACTTTATTT-GACCT
1625 ATTTTCTCATAA
184 ATTTTCTCATAA
* * * * *
1637 AACCGATATGTTTATACCGGGTACATTGTAAATTTACCTATAACATTGTAATT-TTTGTTTCGAT
1 AACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTTGTTTCGAT
1701 GTTTTTAGGATCGATACAATTTTAAATGTATCGACA-TGTTATTCTTGCACCTCGTTGGGTTTTC
66 GTTTTTAGGATCGATACAATTTTAAATGTATCGACACT-TTATTCTTGCACCTCGTTGGGTTTTC
*
1765 ATTATGGACAAAATGTATCGACACAAATTACACAAGTGTCGATACTTTATTCTGACCTATTTTCT
130 ATTATGGA-AAAAAGTATCGACACAAATTA-A-AAGTGTCGATACTTTATT-TGACCTATTTTCT
1830 CATAA
191 CATAA
* * * * **
1835 AACCGGTAAATTTAAACCGGTTACATTGTAAATTGATCTATTACATTATAATTATCGGTTTCGAT
1 AACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTTGTTTCGAT
* * * * * *
1900 GTTTTT-GTGATCGATAAAATTTTAAATGTATCGACACTTTATGCGTGAACCT-GTTTGTGATTT
66 GTTTTTAG-GATCGATACAATTTTAAATGTATCGACACTTTATTCTTGCACCTCG-TTGGGTTTT
* * * *
1963 C-TTTTGGAAAAAAATATCGACACAAACTTAAAAAGTGTCGATACTTTATGTTGACCTGTTTTAT
129 CATTATGGAAAAAAGTATCGACACAAA-TT-AAAAGTGTCGATACTTTAT-TTGACCTATTTTCT
* *
2027 AAT-T
191 CATAA
* * * ** *
2031 AACCGGTATATGTATACTGGTTACATTGTTAATTTAAATATTACATTATAATTTTTTGTTTCGAT
1 AACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTTGTTTCGAT
* * *
2096 GTTTTTGGGGTCGATAC-TTTTTGAAAATGTATCG
66 GTTTTTAGGATCGATACAATTTT--AAATGTATCG
2130 TCACATATTC
Statistics
Matches: 421, Mismatches: 55, Indels: 42
0.81 0.11 0.08
Matches are distributed among these distances:
195 4 0.01
196 69 0.16
197 69 0.16
198 104 0.25
199 64 0.15
200 1 0.00
201 1 0.00
203 8 0.02
204 56 0.13
205 45 0.11
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (195 bp):
AACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTTGTTTCGAT
GTTTTTAGGATCGATACAATTTTAAATGTATCGACACTTTATTCTTGCACCTCGTTGGGTTTTCA
TTATGGAAAAAAGTATCGACACAAATTAAAAGTGTCGATACTTTATTTGACCTATTTTCTCATAA
Found at i:4985 original size:199 final size:199
Alignment explanation
Indices: 4637--6684 Score: 2849
Period size: 199 Copynumber: 10.2 Consensus size: 199
4627 AGACATTTGG
*
4637 TTATAATTATGGTTTTCGATTTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA-
1 TTATAATTAT-GTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAT
* *
4701 GTGCACTTGGTTTTGAAATACATTATGGACCAAAAGTATCGACACTT-TCTCGATTTGTGTCGAT
65 GTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGT-TTGATTTGTGTCGAT
* * ** * * ***
4765 ACTTTTTGTACATCGGTTTTCTCAAAAACCAATATATTTAGACCGATTATATTTCTAATTTACCT
129 ACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCT
4830 ATTACA
194 ATTACA
*
4836 TTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTA-
1 TTATAATTAT-GTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAT
*
4900 GTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCGATA
65 GTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATA
4965 CTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTA
130 CTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTA
5030 TTACA
195 TTACA
* * *
5035 TTATAATTATGTTTTTTGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACAC-TTTTAT
1 TTATAATTATG-TTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAT
*
5099 GTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCT-ATTTGTGTCGAT
65 GTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTT-TGATTTGTGTCGAT
* * * *
5163 ACTGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTG-CTAATTTACC
129 ACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACA-TGAATAATTTACC
5227 TATTACA
193 TATTACA
* *
5234 TTATAATTATGGTTTTTGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTA-
1 TTATAATTAT-GTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAT
* * * * * *
5298 GTGCACTTAGTTTTGAAATACATTATGGGCAAAAAGTATCGACACTTGTTCGA-TTGTGTCAATA
65 GTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATA
*
5362 CTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTA
130 CTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTA
5427 TTACA
195 TTACA
* *
5432 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACAC-TTTTAT
1 TTATAATTATG-TTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAT
* * *
5496 GTGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGATACTTCTTCT-ATTTGTGTCGAT
65 GTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTT-TGATTTGTGTCGAT
* * * * * ***
5560 ACTGTTTGTATACCTGTTTTCTCAAAAATCGGTATATTTAGACCGATTATATTTCTAATTTACCT
129 ACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCT
5625 ATTACA
194 ATTACA
5631 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA-
1 TTATAATTAT-GTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAT
* *
5695 GTGCACTTGGTTTTGAAATACATTTTAGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATA
65 GTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATA
* *
5760 CTTTTTTTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCATTTACATGAATAATTTACCTA
130 CTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTA
5825 TTACA
195 TTACA
* *
5830 TTAT-ATT-T-TTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACAC-TTTTATG
1 TTATAATTATGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTATG
* * *
5891 TGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTCTTCT-ATTTGTGTTGATA
66 TGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTT-TGATTTGTGTCGATA
* * * * * ***
5955 CTGTTTGTACGCCTGTTTTCTCAAAAACTGGTATATTTAGACCGGTTATATTTCTAATTTACCTA
130 CTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTA
6020 TTACA
195 TTACA
* *
6025 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACTCTTGTTACAAATGTATCGACACTTGTTAC
1 TTATAATTAT-GTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC---TT--
*
6090 AAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACAC
60 ---T-T-T----A-----T-GTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACAC
* * *
6155 TTGTTCGATTTGTTTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGT
110 TTGTTTGATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGT
6220 TTACATGAATAATTTACCTATTACA
175 TTACATGAATAATTTACCTATTACA
*
6245 TTATAATTATGTTTTTCGATGTTTTTGGGGA-CGACACTTGTTTTAAATGTATCGACAC-TTTTA
1 TTATAATTATG-TTTTCGATGTTTTT-GGGATCGACACTTGTTATAAATGTATCGACACTTTTTA
* * * * *
6308 TGTGCACTTGGTTCTGAAATACATTATGGACCAAAAGTATCAACATTTGTTCT-ATGTGTGTCGA
64 TGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTT-TGATTTGTGTCGA
* * * * ***
6372 TACTGTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTTCTAATTTACC
128 TACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACC
6437 TATTACA
193 TATTACA
6444 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA-
1 TTATAATTAT-GTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAT
* *
6508 GTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACTTGTTAGATTTGTGTCGATA
65 GTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATA
* * *
6573 CTTTTTGTACACATGTTTTCTCAAAAATCGGTATATTTAGACCTTTTACATGAATAATTTACCTA
130 CTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTA
6638 TTACA
195 TTACA
*
6643 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTT
1 TTATAATTATG-TTTTCGATGTTTTTGGGATCGACACTTGTT
6685 TTATTTGTGT
Statistics
Matches: 1651, Mismatches: 146, Indels: 104
0.87 0.08 0.05
Matches are distributed among these distances:
194 5 0.00
195 166 0.10
196 4 0.00
197 10 0.01
198 183 0.11
199 1075 0.65
200 23 0.01
203 1 0.00
205 1 0.00
208 1 0.00
209 2 0.00
210 2 0.00
211 1 0.00
214 1 0.00
216 1 0.00
219 2 0.00
220 169 0.10
221 4 0.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (199 bp):
TTATAATTATGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTATG
TGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATAC
TTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTAT
TACA
Found at i:6078 original size:21 final size:21
Alignment explanation
Indices: 6054--6105 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
6044 TGTTTTTGGG
*
6054 ATCGACTCTTGTTACAAATGT
1 ATCGACACTTGTTACAAATGT
6075 ATCGACACTTGTTACAAATGT
1 ATCGACACTTGTTACAAATGT
6096 ATCGACACTT
1 ATCGACACTT
6106 TTTAGTGCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (21 bp):
ATCGACACTTGTTACAAATGT
Found at i:6237 original size:220 final size:220
Alignment explanation
Indices: 5855--6304 Score: 699
Period size: 220 Copynumber: 2.0 Consensus size: 220
5845 TGTTTTCGGG
**
5855 ATCGACACTTGTTTTAAATGTATCGACACTTTTATGTGCACTTGGTTCTGAAATACATTCTGGAC
1 ATCGACACTTGTTACAAATGTATCGACACTTTTATGTGCACTTGGTTCTGAAATACATTCTGGAC
* * *
5920 CAAAAGTATCGACACTTCTTCTATTTGTGTTGATACTGTTTGTACGCCTGTTTTCTCAAAAACTG
66 AAAAAGTATCGACACTTCTTCGATTTGTGTTGATACTGTTTGTACACCTGTTTTCTCAAAAACTG
* ***
5985 GTATATTTAGACCGGTTATATTTCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTT
131 GTATATTTAGACCGGTTACATGAATAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTT
*
6050 T-GGGATCGACTCTTGTTACAAATGT
196 TGGGGA-CGACACTTGTTACAAATGT
*
6075 ATCGACACTTGTTACAAATGTATCGACACTTTT-TAGTGCACTTGGTTTTGAAATACATTCTGGA
1 ATCGACACTTGTTACAAATGTATCGACACTTTTAT-GTGCACTTGGTTCTGAAATACATTCTGGA
* *
6139 CAAAAAGTATCGACACTTGTTCGATTTGT-TTCGATACTTTTTGTACACCTGTTTTCTCAAAAAC
65 CAAAAAGTATCGACACTTCTTCGATTTGTGTT-GATACTGTTTGTACACCTGTTTTCTCAAAAAC
* *
6203 TGGTATATTTAGACCGTTTACATGAATAATTTACCTATTACATTATAATTATGTTTTTCGATGTT
129 TGGTATATTTAGACCGGTTACATGAATAATTTACCTATTACATTATAATTATGGTTTTCGATGTT
**
6268 TTTGGGGACGACACTTGTTTTAAATGT
194 TTTGGGGACGACACTTGTTACAAATGT
6295 ATCGACACTT
1 ATCGACACTT
6305 TTATGTGCAC
Statistics
Matches: 210, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
219 3 0.01
220 203 0.97
221 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (220 bp):
ATCGACACTTGTTACAAATGTATCGACACTTTTATGTGCACTTGGTTCTGAAATACATTCTGGAC
AAAAAGTATCGACACTTCTTCGATTTGTGTTGATACTGTTTGTACACCTGTTTTCTCAAAAACTG
GTATATTTAGACCGGTTACATGAATAATTTACCTATTACATTATAATTATGGTTTTCGATGTTTT
TGGGGACGACACTTGTTACAAATGT
Found at i:6435 original size:813 final size:795
Alignment explanation
Indices: 4637--6687 Score: 3380
Period size: 813 Copynumber: 2.6 Consensus size: 795
4627 AGACATTTGG
* * *
4637 TTATAATTATGGTTTTCGAT-TTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTT-T
1 TTATAATTATGTTTTTCGATGTTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTAT
* * *
4700 AGTGCACTTGGTTTTGAAATACATTATGGACCAAAAGTATCGACACTTTCTCGATTTGTGTCGAT
66 -GTGCACTTGGTTCTGAAATACATTATGGACCAAAAGTATCGACA-TTTTTCTATTTGTGTCGAT
* * * **
4765 ACTTTTTGTACATCGGTTTTCTCAAAAACCAATATATTTAGACCGATTATATTTCTAATTTACCT
129 ACTGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGATTATATTTCTAATTTACCT
* *
4830 ATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACT
194 ATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACT
* *
4895 TTTTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGT
259 TTTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACTTGTTTGATTTGTGT
*
4960 CGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTT
324 CGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCATTTACATGAATAATTT
*
5025 ACCTATTACATTATAATTATGTTTTTTGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGA
389 ACCTATTACATTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGA
* *
5090 CACTTTTATGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTT
454 CACTTTTATGTGCACTTGGTTCTGAAATACATTCTGGACAAAAAGTATCGACACTTCTTCTATTT
5155 GTGTCGATACTGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTA
519 GTGTCGATACTGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTA
*
5220 ATTTACCTATTACATTATAATTATGGTTTTTGATGTTTTTGGGATCGACACTTGTTACAAATGTA
584 ATTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTA
*
5285 TCGACACTTTTTAGTGCACTTAGTTTTGAAATACATTATGGGCAAAAAGTATCGACACTTGTTCG
649 TCGACACTTTTTAGTGCACTTAGTTTTGAAATACATTATGGACAAAAAGTATCGACACTTGTTCG
5350 ATTGTGTCAATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGA
714 ATTGTGTCAATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGA
5415 ATAATTTACCTATTACA
779 ATAATTTACCTATTACA
5432 TTATAATTATGTTTTTCGATG-TTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTAT
1 TTATAATTATGTTTTTCGATGTTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTAT
* * *
5496 GTGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGATACTTCTTCTATTTGTGTCGATA
66 GTGCACTTGGTTCTGAAATACATTATGGACCAAAAGTATCGACA-TTTTTCTATTTGTGTCGATA
* *
5561 CTGTTTGTATACCTGTTTTCTCAAAAATCGGTATATTTAGACCGATTATATTTCTAATTTACCTA
130 CTGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGATTATATTTCTAATTTACCTA
5626 TTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTT
195 TTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTT
*
5691 TTTAGTGCACTTGGTTTTGAAATACATTTTAGACCAAAAGTATCGACACTTGTTTGATTTGTGTC
260 TTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACTTGTTTGATTTGTGTC
*
5756 GATACTTTTTTTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCATTTACATGAATAATTTA
325 GATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCATTTACATGAATAATTTA
5821 CCTATTACATTAT-A-T-T-TTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGAC
390 CCTATTACATTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGAC
*
5882 ACTTTTATGTGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTCTTCTATTTG
455 ACTTTTATGTGCACTTGGTTCTGAAATACATTCTGGACAAAAAGTATCGACACTTCTTCTATTTG
* * * *
5947 TGTTGATACTGTTTGTACGCCTGTTTTCTCAAAAACTGGTATATTTAGACCGGTTATATTTCTAA
520 TGTCGATACTGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAA
6012 TTTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACTCTTGTTACAAATGTAT
585 TTTACCTATTACATTATAATTATGGTTTTCGATG-TTTT----T-G------G--------G-AT
* *
6077 CGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACAA
629 CGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTAGTTTTGAAATACATTATGGACAA
* * * *
6142 AAAGTATCGACACTTGTTCGATTTGTTTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTGGT
694 AAAGTATCGACACTTGTTCGA-TTGTGTCAATACTTTTTGTACACATGTTTTCTCAAAAACCGGT
6207 ATATTTAGACCGTTTACATGAATAATTTACCTATTACA
758 ATATTTAGACCGTTTACATGAATAATTTACCTATTACA
*
6245 TTATAATTATGTTTTTCGATGTTTTTGGGGA-CGACACTTGTTTTAAATGTATCGACACTTTTAT
1 TTATAATTATGTTTTTCGATGTTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTAT
* *
6309 GTGCACTTGGTTCTGAAATACATTATGGACCAAAAGTATCAACATTTGTTCTATGTGTGTCGATA
66 GTGCACTTGGTTCTGAAATACATTATGGACCAAAAGTATCGACATTT-TTCTATTTGTGTCGATA
* *
6374 CTGTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTTCTAATTTACCTA
130 CTGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGATTATATTTCTAATTTACCTA
6439 TTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTT
195 TTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTT
*
6504 TTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACTTGTTAGATTTGTGTC
260 TTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACTTGTTTGATTTGTGTC
* * *
6569 GATACTTTTTGTACACATGTTTTCTCAAAAATCGGTATATTTAGACCTTTTACATGAATAATTTA
325 GATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCATTTACATGAATAATTTA
6634 CCTATTACATTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTA
390 CCTATTACATTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTA
6688 TTTGTGTCGA
Statistics
Matches: 1171, Mismatches: 55, Indels: 38
0.93 0.04 0.03
Matches are distributed among these distances:
791 200 0.17
792 5 0.00
793 1 0.00
794 1 0.00
795 376 0.32
796 2 0.00
797 1 0.00
803 1 0.00
811 1 0.00
812 87 0.07
813 451 0.39
814 9 0.01
815 1 0.00
816 1 0.00
817 34 0.03
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (795 bp):
TTATAATTATGTTTTTCGATGTTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTAT
GTGCACTTGGTTCTGAAATACATTATGGACCAAAAGTATCGACATTTTTCTATTTGTGTCGATAC
TGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGATTATATTTCTAATTTACCTAT
TACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTT
TTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCG
ATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCATTTACATGAATAATTTAC
CTATTACATTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACA
CTTTTATGTGCACTTGGTTCTGAAATACATTCTGGACAAAAAGTATCGACACTTCTTCTATTTGT
GTCGATACTGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAAT
TTACCTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATC
GACACTTTTTAGTGCACTTAGTTTTGAAATACATTATGGACAAAAAGTATCGACACTTGTTCGAT
TGTGTCAATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAAT
AATTTACCTATTACA
Found at i:6614 original size:398 final size:398
Alignment explanation
Indices: 4637--6687 Score: 3326
Period size: 398 Copynumber: 5.1 Consensus size: 398
4627 AGACATTTGG
* * * *
4637 TTATAATTATGGTTTTCGATTTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTT-TA
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTAT-
* * *
4701 GTGCACTTGGTTTTGAAATACATTATGGACCAAAAGTATCGACACTT-TCTCGATTTGTGTCGAT
65 GTGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTCT-TCTATTTGTGTCGAT
* * * ** *
4765 ACTTTTTGTACATCGGTTTTCTCAAAAACCAATATATTTAGACCGATTATATTTCTAATTTACCT
129 ACTGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTTCTAATTTACCT
*
4830 ATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACT
194 ATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACT
*
4895 TTTTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGT
259 TTTTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCGATTTGTGT
4960 CGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTT
324 CGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTT
5025 ACCTATTACA
389 ACCTATTACA
*
5035 TTATAATTATGTTTTTTGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTATG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTATG
* * *
5100 TGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCTATTTGTGTCGATAC
66 TGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTCTTCTATTTGTGTCGATAC
*
5165 TGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTAT
131 TGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTTCTAATTTACCTAT
*
5230 TACATTATAATTATGGTTTTTGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTT
196 TACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTT
* * * *
5295 TTAGTGCACTTAGTTTTGAAATACATTATGGGCAAAAAGTATCGACACTTGTTCGA-TTGTGTCA
261 TTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCGATTTGTGTCG
*
5359 ATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTAC
326 ATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTAC
5424 CTATTACA
391 CTATTACA
5432 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTATG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTATG
*
5497 TGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGATACTTCTTCTATTTGTGTCGATAC
66 TGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTCTTCTATTTGTGTCGATAC
* * *
5562 TGTTTGTATACCTGTTTTCTCAAAAATCGGTATATTTAGACCGATTATATTTCTAATTTACCTAT
131 TGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTTCTAATTTACCTAT
*
5627 TACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTT
196 TACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTT
* * * *
5692 TTAGTGCACTTGGTTTTGAAATACATTTTAGACCAAAAGTATCGACACTTGTTTGATTTGTGTCG
261 TTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCGATTTGTGTCG
* *
5757 ATACTTTTTTTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCATTTACATGAATAATTTAC
326 ATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTAC
5822 CTATTACA
391 CTATTACA
5830 TTAT-A-T-T-TTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTATG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTATG
*
5891 TGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTCTTCTATTTGTGTTGATAC
66 TGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTCTTCTATTTGTGTCGATAC
* *
5956 TGTTTGTACGCCTGTTTTCTCAAAAACTGGTATATTTAGACCGGTTATATTTCTAATTTACCTAT
131 TGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTTCTAATTTACCTAT
6021 TACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACTCTTGTTACAAATGTATCGACACTTG
196 TACATTATAATTATGGTTTTCGATG-TTTT----T-G------G--------G-ATCGACACTTG
6086 TTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCG
240 TTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCG
* *
6151 ACACTTGTTCGATTTGTTTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGA
305 ACACTTGTTCGATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGA
6216 CCGTTTACATGAATAATTTACCTATTACA
370 CCGTTTACATGAATAATTTACCTATTACA
*
6245 TTATAATTATGTTTTTCGATGTTTTTGGGGA-CGACACTTGTTTTAAATGTATCGACACTTTTAT
1 TTATAATTATGTTTTTCGATG-TTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTAT
* * * * *
6309 GTGCACTTGGTTCTGAAATACATTATGGACCAAAAGTATCAACATTTGTTCTATGTGTGTCGATA
65 GTGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTCTTCTATTTGTGTCGATA
*
6374 CTGTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTTCTAATTTACCTA
130 CTGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTTCTAATTTACCTA
*
6439 TTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTT
195 TTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTT
* * *
6504 TTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACTTGTTAGATTTGTGTC
260 TTTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCGATTTGTGTC
* * *
6569 GATACTTTTTGTACACATGTTTTCTCAAAAATCGGTATATTTAGACCTTTTACATGAATAATTTA
325 GATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTA
6634 CCTATTACA
390 CCTATTACA
6643 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTA
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTA
6688 TTTGTGTCGA
Statistics
Matches: 1543, Mismatches: 80, Indels: 60
0.92 0.05 0.04
Matches are distributed among these distances:
394 202 0.13
395 5 0.00
396 1 0.00
397 387 0.25
398 568 0.37
399 4 0.00
400 1 0.00
406 1 0.00
407 1 0.00
413 1 0.00
414 2 0.00
415 165 0.11
416 1 0.00
417 1 0.00
418 5 0.00
419 190 0.12
420 8 0.01
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (398 bp):
TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTATG
TGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTCTTCTATTTGTGTCGATAC
TGTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTTCTAATTTACCTAT
TACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTT
TTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTCGATTTGTGTCG
ATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTAC
CTATTACA
Found at i:9304 original size:15 final size:15
Alignment explanation
Indices: 9280--9321 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
9270 AGGAGGTTGT
9280 GGTTGAGAAGAGCTG
1 GGTTGAGAAGAGCTG
* *
9295 GGTTGGGAAGAGGTG
1 GGTTGAGAAGAGCTG
9310 GGTTGAGAAGAG
1 GGTTGAGAAGAG
9322 ATTTGAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.52, T:0.19
Consensus pattern (15 bp):
GGTTGAGAAGAGCTG
Found at i:10012 original size:199 final size:199
Alignment explanation
Indices: 9672--10968 Score: 2218
Period size: 199 Copynumber: 6.5 Consensus size: 199
9662 TTTTTAATTT
** * * *
9672 AAACCGGTATATTTAGACCAATTATATTGTTAATTTACCTATTATATTATAATTATGATTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
*
9737 TTTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* *
9802 CATTCTGGACCAAAAGTATCGACACTTGCTCGATTTGTGTCGATACTTTTTGTACACTTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTGTACACCTGTTTTC
9867 TCAA
196 TCAA
* *
9871 AAACCGGTATATTTAGACCGGTTATATTTCTAATTTACCTATTACATTATAATTATGGTTTTTGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
* *
9936 TGTTTTTGGGATCGACAATTGTTATAAATGTATCGACACTTTTTAGTGAACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* * * * *
10001 CATTCTGGACCAAAAGTATCAACACTTGTTTGATTTGTGTCGATATTTTTTTTACACATGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTGTACACCTGTTTTC
10066 TCAA
196 TCAA
* *
10070 AAACTGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCAA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
*
10135 TGTTTTTGGGATCGACACTTGTTATAAATCTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* *
10200 CATTCTGGACCAAAAGTATCGACACTTGTTAGATTTGTGTCGATACTTTTTGTACACCGGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTGTACACCTGTTTTC
10265 TCAA
196 TCAA
*
10269 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGTTTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
* *
10334 TGTTTTTGGGATCGACACTTGTTACAAATGTATCGATAC-TTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* *
10398 CATTCTGGACAAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTGTACACCGGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTGTACACCTGTTTTC
10463 TCAA
196 TCAA
* * * *
10467 AATCCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACTTTATAATTATAGTTTTCAA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
*
10532 TGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* *
10597 CATTCTGGACAAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTGTATACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTGTACACCTGTTTTC
10662 TCAA
196 TCAA
* *
10666 AAACTGGTATATTTAGACCGGTTATATTTCTAATTTACCTATTACATTATAATTATGGTTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
*
10731 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACGTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* * * *
10796 CATTCTGAACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACTTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTGTACACCTGTTTTC
10861 TCAA
196 TCAA
10865 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
10930 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
10969 ATAAGTTTAC
Statistics
Matches: 1036, Mismatches: 61, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
198 190 0.18
199 846 0.82
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (199 bp):
AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
CATTCTGGACCAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTGTACACCTGTTTTC
TCAA
Found at i:10810 original size:596 final size:597
Alignment explanation
Indices: 9672--10968 Score: 2245
Period size: 596 Copynumber: 2.2 Consensus size: 597
9662 TTTTTAATTT
** * *
9672 AAACCGGTATATTTAGACCAATTATATTGTTAATTTACCTATTATATTATAATTATGATTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGATTTTCGA
*
9737 TTTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* **
9802 CATTCTGGACCAAAAGTATCGACACTTGCTCGATTTGTGTCGATACTTTTTGTACACTTGTTTTC
131 CATTCTGGACAAAAAGTATCGACACTTGCTCGATTTGTGTCGATACTTTTTGTACACCGGTTTTC
* *
9867 TCAAAAACCGGTATATTTAGACCGGTTATATTTCTAATTTACCTATTACATTATAATTATGGTTT
196 TCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATAGTTT
** *
9932 TTGATGTTTTTGGGATCGACAATTGTTATAAATGTATCGACACTTTTTAGTGAACTTGGTTTTGA
261 TCAATGTTTTTGGGATCGACAATTGTTACAAATGTATCGACACTTTTTAGTGAACTTGGTTTTGA
* * * *
9997 AATACATTCTGGACCAAAAGTATCAACACTTGTTTGATTTGTGTCGATATTTTTTTTACACATGT
326 AATACATTCTGGACAAAAAGTATCAACACTTGTTCGATTTGTGTCGATACTTTTTGTACACATGT
10062 TTTCTCAAAAACTGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATG
391 TTTCTCAAAAACTGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATG
*
10127 GTTTTCAATGTTTTTGGGATCGACACTTGTTATAAATCTATCGACACTTTTTAGTGCACTTGGTT
456 GTTTTCAATGTTTTTGGGATCGACACTTGTTATAAATCTATCGACACGTTTTAGTGCACTTGGTT
*
10192 TTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTAGATTTGTGTCGATACTTTTTGTACAC
521 TTGAAATACATTCTGAACCAAAAGTATCGACACTTGTTAGATTTGTGTCGATACTTTTTGTACAC
10257 CGGTTTTCTCAA
586 CGGTTTTCTCAA
*
10269 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGTTTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGATTTTCGA
* *
10334 TGTTTTTGGGATCGACACTTGTTACAAATGTATCGATAC-TTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
*
10398 CATTCTGGACAAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTGTACACCGGTTTTC
131 CATTCTGGACAAAAAGTATCGACACTTGCTCGATTTGTGTCGATACTTTTTGTACACCGGTTTTC
* *
10463 TCAAAATCCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACTTTATAATTATAGTTT
196 TCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATAGTTT
* *
10528 TCAATGTTTTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGA
261 TCAATGTTTTTGGGATCGACAATTGTTACAAATGTATCGACACTTTTTAGTGAACTTGGTTTTGA
* * *
10593 AATACATTCTGGACAAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTGTATACCTGT
326 AATACATTCTGGACAAAAAGTATCAACACTTGTTCGATTTGTGTCGATACTTTTTGTACACATGT
*
10658 TTTCTCAAAAACTGGTATATTTAGACCGGTTATATTTCTAATTTACCTATTACATTATAATTATG
391 TTTCTCAAAAACTGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATG
* *
10723 GTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACGTTTTAGTGCACTTGGTT
456 GTTTTCAATGTTTTTGGGATCGACACTTGTTATAAATCTATCGACACGTTTTAGTGCACTTGGTT
* *
10788 TTGAAATACATTCTGAACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACAC
521 TTGAAATACATTCTGAACCAAAAGTATCGACACTTGTTAGATTTGTGTCGATACTTTTTGTACAC
**
10853 TTGTTTTCTCAA
586 CGGTTTTCTCAA
*
10865 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGATTTTCGA
10930 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
10969 ATAAGTTTAC
Statistics
Matches: 660, Mismatches: 40, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
596 564 0.85
597 96 0.15
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (597 bp):
AAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGATTTTCGA
TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
CATTCTGGACAAAAAGTATCGACACTTGCTCGATTTGTGTCGATACTTTTTGTACACCGGTTTTC
TCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATAGTTT
TCAATGTTTTTGGGATCGACAATTGTTACAAATGTATCGACACTTTTTAGTGAACTTGGTTTTGA
AATACATTCTGGACAAAAAGTATCAACACTTGTTCGATTTGTGTCGATACTTTTTGTACACATGT
TTTCTCAAAAACTGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATG
GTTTTCAATGTTTTTGGGATCGACACTTGTTATAAATCTATCGACACGTTTTAGTGCACTTGGTT
TTGAAATACATTCTGAACCAAAAGTATCGACACTTGTTAGATTTGTGTCGATACTTTTTGTACAC
CGGTTTTCTCAA
Found at i:11361 original size:18 final size:19
Alignment explanation
Indices: 11314--11362 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
11304 TTACATTTAC
*
11314 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAATCGT
*
11333 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCGT
11352 ATAC-AAATTAA
1 ATACAAAATTAA
11363 CCATGCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:12867 original size:21 final size:18
Alignment explanation
Indices: 12829--12867 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12819 TTCTCCTCAT
12829 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
12847 TTCCTCCATCTTCTCTTC
1 TTCCTCCATCTTTTCTTC
12865 TTC
1 TTC
12868 AAATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:14907 original size:19 final size:20
Alignment explanation
Indices: 14860--14908 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
14850 CATTTATACA
14860 ACCTA-AAATATCATTTTCT
1 ACCTATAAATATCATTTTCT
*
14879 ACATAT-AATATCATTTT-T
1 ACCTATAAATATCATTTTCT
14897 ACCTATAAATAT
1 ACCTATAAATAT
14909 TAACTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (20 bp):
ACCTATAAATATCATTTTCT
Found at i:15533 original size:182 final size:181
Alignment explanation
Indices: 15291--16647 Score: 1404
Period size: 182 Copynumber: 7.6 Consensus size: 181
15281 TACGCGTACT
* * * * *
15291 TATTAAAGTATCGACACATTCAACATATTCGGTATCTATTTACCGGTTTTGTCA-TTTTGAGAAC
1 TATTAAATTATCGACACTTTCAACAT-TTCGGTAACT-TTTTCCGGTTTTGTCATTTTTGAGACC
* *
15355 GGTTTTATCATATTTTTACCTGTTATATTGTTTTGGATCGATACATTTTCATAAAGTGTCGACAC
64 AGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* * *
15420 TTTTTAAGCGTTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
129 TTTTTAAGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAA
*
15473 TATTAAATTATCGACACTTTCAACATGTTCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACCT
1 TATTAAATTATCGACACTTTCAACAT-TTCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACCA
* * * *
15538 GTTTTATCATATTTTTACCTGTTATATTGGTAAGGATCGATACATTCTAATAAAGTGTCGACACT
65 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
15603 TTTTAAGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAA
130 TTTTAAGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAA
* * * * *
15655 TATTAAATTATCGACACTTTCAATATATCTGGTAACTTTTTACGTTTTTTTCATTTTTGAGACCA
1 TATTAAATTATCGACACTTTCAACATTTC-GGTAACTTTTTCCGGTTTTGTCATTTTTGAGACCA
*
15720 GTTTTATCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACT
65 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
* ** * * * *
15785 TTTT-A--G-TTTAA----TT-TC--AGAAAGTGTC-GATACT-T--ATATTAA
130 TTTTAAGCGCTATAACTTCTTCTCTTTTAAA-T-TCAAAAAGTGTCGATACTAA
* ** * * ** * ** * * *
15824 -ATT--ATTGA-C-AC-TTTCAACATA-TCCGGTGTCGTTTTACTAGTTTTGTCAATTTCGGGAC
1 TATTAAATT-ATCGACACTTTCA-ACATTTCGGTAAC-TTTTTCCGGTTTTGTCATTTTTGAGAC
** * ** ** *
15882 TTGTTTTATCATATTTTTACCTGTTATATTGTTGTGGATCGATATTTTTTTTTAAAGTATCGACA
63 CAGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACA
* * * * *
15947 CTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
128 CTTTTTAAGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAA
* * * * * * * *
16001 TATTAAATTATTGACACTTTCAATATATCCGGTAGCGTTTTACTGATTTTGTCAATTTTGAGA-C
1 TATTAAATTATCGACACTTTCAACAT-TTCGGTAAC-TTTTTCCGGTTTTGTCATTTTTGAGACC
* *
16065 ATGTTTTATCATATTTTTATCTGTTATATTGTTATGGATTGATACATTTTCATAAAGTGTCGACA
64 A-GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACA
* * * * * *
16130 CTTTTTAAGCGCAATAATTTTTTCTCTTTTAAATTCAGAAAGTATCGATACTTA
128 CTTTTTAAGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAA
* * * * *
16184 TATTAAATTATCGACACTTTTAACATATCCGGTAACTTTTTTCGGTTTTTTCATTTTTGAGACCT
1 TATTAAATTATCGACACTTTCAACAT-TTCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACCA
* * *
16249 GTTTTATCATATTTTTACCTGTTACATTGGTAAT-GATCGATATATTTTCATAAAGTGTCGACAC
65 GTTTTATCATATTTTTACCTGTTATATT-GTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* *
16313 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTAA
129 TTTTTAAGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAA
* * *
16366 TATTAAATTATCGACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGTCCA
1 TATTAAATTATCGACACTTTCAACAT-TTCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACCA
* * ** *
16431 GTTTTATCATATTTTTACCTGATATATTGTTGTGGATCG--ACATTTTTTTTAAAGTATCGACAC
65 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACA-TTTTCATAAAGTGTCGACAC
* * * * *
16494 TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
129 TTTTTAAGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAA
* * * * *
16547 TATTAAATTATCGACACTCT-ACACATATCCGGTAGCGTTTTACCGGTTTTGTCA-TTTTGGGAC
1 TATTAAATTATCGACACTTTCA-ACAT-TTCGGTAAC-TTTTTCCGGTTTTGTCATTTTTGAGAC
* * * * * *
16610 CGGTTTTGTCATGTTTGTACCTGTAATATTGCTATGGA
63 CAGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
16648 GTTATCCATT
Statistics
Matches: 992, Mismatches: 146, Indels: 75
0.82 0.12 0.06
Matches are distributed among these distances:
163 4 0.00
164 83 0.08
165 5 0.01
166 4 0.00
167 2 0.00
168 7 0.01
169 6 0.01
171 4 0.00
172 6 0.01
173 8 0.01
174 7 0.01
175 4 0.00
177 5 0.01
178 7 0.01
179 2 0.00
180 6 0.01
181 161 0.16
182 501 0.51
183 170 0.17
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (181 bp):
TATTAAATTATCGACACTTTCAACATTTCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACCAG
TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTT
TTTAAGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAA
Found at i:15924 original size:164 final size:163
Alignment explanation
Indices: 15628--15950 Score: 423
Period size: 164 Copynumber: 2.0 Consensus size: 163
15618 CTTCTTCTCT
* * *
15628 TTTAAATTCAAAAAGTGTCGATACTAATATTAAATTATCGACACTTTCAATATATCTGGTAACTT
1 TTTAAATTCAAAAAGTGTCGATACTAATATTAAATTATCGACACTTTCAACATATCCGGTAACGT
* * *
15693 TTTACGTTTTTTTCATTTTTGAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTATAGATC
66 TTTACGTTTTTGTCAATTTCGAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTATAGATC
*
15758 GATACATTTTCATAAAGTGTCGACACTTTTTAG
131 GATACATTTTCATAAAGTATCGACACTTTTTAG
* * * * **
15791 TTTAATTTCAGAAAGTGTCGATACTTATATTAAATTATTGACACTTTCAACATATCCGGTGTCGT
1 TTTAAATTCAAAAAGTGTCGATACTAATATTAAATTATCGACACTTTCAACATATCCGGTAACGT
* ** * *
15856 TTTAC-TAGTTTTGTCAATTTCGGGACTTGTTTTATCATATTTTTACCTGTTATATTGTTGTGGA
66 TTTACGT--TTTTGTCAATTTCGAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTATAGA
** **
15920 TCGATATTTTTTTTTAAAGTATCGACACTTT
129 TCGATACATTTTCATAAAGTATCGACACTTT
15951 ATAGGCGCTA
Statistics
Matches: 136, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
162 1 0.01
163 61 0.45
164 74 0.54
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (163 bp):
TTTAAATTCAAAAAGTGTCGATACTAATATTAAATTATCGACACTTTCAACATATCCGGTAACGT
TTTACGTTTTTGTCAATTTCGAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTATAGATC
GATACATTTTCATAAAGTATCGACACTTTTTAG
Found at i:16613 original size:20 final size:21
Alignment explanation
Indices: 16588--16626 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
16578 GTAGCGTTTT
16588 ACCGGTTTTGTCAT-TTTGGG
1 ACCGGTTTTGTCATGTTTGGG
16608 ACCGGTTTTGTCATGTTTG
1 ACCGGTTTTGTCATGTTTG
16627 TACCTGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.10, C:0.15, G:0.28, T:0.46
Consensus pattern (21 bp):
ACCGGTTTTGTCATGTTTGGG
Found at i:18727 original size:34 final size:34
Alignment explanation
Indices: 18688--18753 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
18678 ATACCCGAAC
* * *
18688 TAAAATTAATCCGACTAAAACCCAAACTGAAAGG
1 TAAAATTAACCCAACCAAAACCCAAACTGAAAGG
* *
18722 TAAAATTAACCCAACCATAACCTAAACTGAAA
1 TAAAATTAACCCAACCAAAACCCAAACTGAAA
18754 TTGTTTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.08, T:0.18
Consensus pattern (34 bp):
TAAAATTAACCCAACCAAAACCCAAACTGAAAGG
Found at i:18891 original size:65 final size:66
Alignment explanation
Indices: 18777--18906 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 66
18767 TATTAATTTC
18777 AGCTTCACCTGTTACAATTGTTATGATTTCATCCCTATTATTTAATTTAATTAATTTTCAATTTT
1 AGCTTCACCTGTTACAATTGTTATGATTTCATCCCTATTATTTAATTTAATTAATTTTCAATTTT
18842 T
66 T
* *
18843 AGCTTCACCCT-TTACAATTGTTTTTATTTCAT-CCTATTATTTAATTTAATTAATTTTCAATTT
1 AGCTTCA-CCTGTTACAATTGTTATGATTTCATCCCTATTATTTAATTTAATTAATTTTCAATTT
18906 T
65 T
18907 ATGTTTGTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
65 32 0.52
66 26 0.43
67 3 0.05
ACGTcount: A:0.27, C:0.15, G:0.05, T:0.53
Consensus pattern (66 bp):
AGCTTCACCTGTTACAATTGTTATGATTTCATCCCTATTATTTAATTTAATTAATTTTCAATTTT
T
Found at i:19026 original size:143 final size:142
Alignment explanation
Indices: 18845--19116 Score: 474
Period size: 143 Copynumber: 1.9 Consensus size: 142
18835 CAATTTTTAG
* *
18845 CTTCACCCTTTACAATTGTTTTTATTTCATCCTATTATTTAATTTAATTAATTTTCAATTTTATG
1 CTTCACCCTTTACAATTGTTTTGATTTCATCATATTATTTAATTTAATTAATTTTCAATTTTATG
* *
18910 TTTGTTCAATTTAATCTTTAAAGTTATTCTTTTATCAAAATTGACTCATAATTATTTTTATTTTT
66 TTTATTCAATTT-ATCCTTAAAGTTATTCTTTTATCAAAATTGACTCATAATTATTTTTATTTTT
18975 TATGATTTGGAGT
130 TATGATTTGGAGT
*
18988 CTTCA-CCTGTTACAATTGTTTTGATTTCATCATGTTATTTAATTTAATTAATTTTCAATTTTAT
1 CTTCACCCT-TTACAATTGTTTTGATTTCATCATATTATTTAATTTAATTAATTTTCAATTTTAT
19052 GTTTATTCAATTTATCCTTAAAGTTATTCTTTTATCAAAATTGACTCATAATTATTTTTATTTTT
65 GTTTATTCAATTTATCCTTAAAGTTATTCTTTTATCAAAATTGACTCATAATTATTTTTATTTTT
19117 ATTTATAATT
Statistics
Matches: 123, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
142 54 0.44
143 69 0.56
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.55
Consensus pattern (142 bp):
CTTCACCCTTTACAATTGTTTTGATTTCATCATATTATTTAATTTAATTAATTTTCAATTTTATG
TTTATTCAATTTATCCTTAAAGTTATTCTTTTATCAAAATTGACTCATAATTATTTTTATTTTTT
ATGATTTGGAGT
Found at i:19396 original size:13 final size:13
Alignment explanation
Indices: 19378--19404 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19368 AATGAACCGA
19378 CTTAAAATTGATC
1 CTTAAAATTGATC
19391 CTTAAAATTGATC
1 CTTAAAATTGATC
19404 C
1 C
19405 GAACTAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (13 bp):
CTTAAAATTGATC
Found at i:23925 original size:24 final size:24
Alignment explanation
Indices: 23896--23946 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
23886 AAATTTTTCT
23896 TCATCATTTTTTGCATCAAATTTG
1 TCATCATTTTTTGCATCAAATTTG
23920 TCATCATTTTTTGCATCAAATTTG
1 TCATCATTTTTTGCATCAAATTTG
23944 TCA
1 TCA
23947 AGATTATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (24 bp):
TCATCATTTTTTGCATCAAATTTG
Found at i:23926 original size:27 final size:26
Alignment explanation
Indices: 23886--23945 Score: 88
Period size: 24 Copynumber: 2.3 Consensus size: 26
23876 ATAACAAAGA
*
23886 AAATTTTTCTTCATCATTTTTTGCATC
1 AAATTTGTC-TCATCATTTTTTGCATC
23913 AAATTTG--TCATCATTTTTTGCATC
1 AAATTTGTCTCATCATTTTTTGCATC
23937 AAATTTGTC
1 AAATTTGTC
23946 AAGATTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 24 0.80
27 6 0.20
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.52
Consensus pattern (26 bp):
AAATTTGTCTCATCATTTTTTGCATC
Found at i:34674 original size:257 final size:253
Alignment explanation
Indices: 34224--34739 Score: 948
Period size: 257 Copynumber: 2.0 Consensus size: 253
34214 AGAAGTGAAG
34224 AAACAATTTGAAGCTGGTTTTCTTACGGTGGCCAAATATCCTGAGTGGGTAAATATTATCCCGTG
1 AAACAATTTGAAGCTGGTTTTCTTACGGTGGCCAAATATCCTGAGTGGGTAAATATTATCCCGTG
34289 CGAAGAAGGATGGGAAAAGTGCGAATGTGTGTCGACTATGAGATCTTAACAGAGCCAGTCCGAAG
66 CGAAGAAGGATGGGAAAAGTGCGAATGTGTGTCGACTATGAGATCTTAACAGAGCCAGTCCGAAG
34354 GATAATTTCCTTTGCCTCACATAGATATGCTGGTAGACAACACTGCCGGAAATTCCTTATTTTTA
131 GATAATTTCCTTTGCCTCACATAGATATGCTGGTAGACAACACTGCCGGAAATTCCTTATTTTTA
34419 -TT-TGGATGGATTCTCCGGCTTCAATCAAATTAAAATGCACCCTGAAGATATGGAGA
196 TTTATGGATGGATTCTCCGGCTTCAATCAAATTAAAATGCACCCTGAAGATATGGAGA
34475 AAACAATTTGAAGCTGGTTTTCTTACGGTGGCCAAATATCCTGAGTGGGTAGCAAATATTATCCC
1 AAACAATTTGAAGCTGGTTTTCTTACGGTGGCCAAATATCCTGAGTGGGT---AAATATTATCCC
34540 AGTGCCGAAGAAGGATGGG-AAAGTGCGAATGTGTGTCGACTATAGAGATCTTAACAGAGCCAGT
63 -GTG-CGAAGAAGGATGGGAAAAGTGCGAATGTGTGTCGACTAT-GAGATCTTAACAGAGCCAGT
34604 CCGAAGGATAACTTTCCTTTGCCTCACATAGATATGCTGGTAGACAACACTGCCGGAAATTCCTT
125 CCGAAGGATAA-TTTCCTTTGCCTCACATAGATATGCTGGTAGACAACACTGCCGGAAATTCCTT
34669 ATTTTTATTTATGGATGGATTCTCCGGCTTCAATCAAATTAAAATGCACCCTGAAGATATGGAGA
189 ATTTTTATTTATGGATGGATTCTCCGGCTTCAATCAAATTAAAATGCACCCTGAAGATATGGAGA
34734 AAACAA
1 AAACAA
34740 CGTTTATCAC
Statistics
Matches: 256, Mismatches: 0, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
251 50 0.20
254 12 0.05
255 27 0.11
256 45 0.18
257 60 0.23
258 2 0.01
259 60 0.23
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (253 bp):
AAACAATTTGAAGCTGGTTTTCTTACGGTGGCCAAATATCCTGAGTGGGTAAATATTATCCCGTG
CGAAGAAGGATGGGAAAAGTGCGAATGTGTGTCGACTATGAGATCTTAACAGAGCCAGTCCGAAG
GATAATTTCCTTTGCCTCACATAGATATGCTGGTAGACAACACTGCCGGAAATTCCTTATTTTTA
TTTATGGATGGATTCTCCGGCTTCAATCAAATTAAAATGCACCCTGAAGATATGGAGA
Found at i:37419 original size:1 final size:1
Alignment explanation
Indices: 37415--37485 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
37405 TGAAAAAGAT
* * * * * * * * *
37415 AAAAAAAGAACAAAAAAAAGAACAAAAAAAAGAACAAAAAAAAAGAACAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
37480 AGAAAA
1 AAAAAA
37486 GGAGGATTCA
Statistics
Matches: 50, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:37429 original size:25 final size:22
Alignment explanation
Indices: 37407--37485 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
37397 CTTGAAAATG
37407 AAAAAGATAAAAAAAGAACAAAAA
1 AAAAAGA-AAAAAAAGAAC-AAAA
*
37431 AAAGAACAAAAAAAAGAACAAAA
1 AAA-AAGAAAAAAAAGAACAAAA
37454 AAAAAGAACAAAAAA-AGA-AAAA
1 AAAAAGAA-AAAAAAGA-ACAAAA
37476 AAAAAGAAAA
1 AAAAAGAAAA
37486 GGAGGATTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
21 2 0.04
22 17 0.34
23 14 0.28
24 14 0.28
25 3 0.06
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.01
Consensus pattern (22 bp):
AAAAAGAAAAAAAAGAACAAAA
Found at i:37432 original size:12 final size:12
Alignment explanation
Indices: 37415--37483 Score: 115
Period size: 12 Copynumber: 5.8 Consensus size: 12
37405 TGAAAAAGAT
37415 AAAAAAAGAACA
1 AAAAAAAGAACA
37427 AAAAAAAGAACA
1 AAAAAAAGAACA
37439 AAAAAAAGAACAA
1 AAAAAAAGAAC-A
37452 AAAAAAAGAAC-
1 AAAAAAAGAACA
37463 AAAAAAAGAA-A
1 AAAAAAAGAACA
37474 AAAAAAAGAA
1 AAAAAAAGAA
37484 AAGGAGGATT
Statistics
Matches: 55, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
11 20 0.36
12 23 0.42
13 12 0.22
ACGTcount: A:0.86, C:0.06, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAACA
Found at i:37447 original size:24 final size:23
Alignment explanation
Indices: 37407--37483 Score: 113
Period size: 24 Copynumber: 3.3 Consensus size: 23
37397 CTTGAAAATG
*
37407 AAAAAG-ATAAAAAAAGAACAAA
1 AAAAAGAACAAAAAAAGAACAAA
37429 AAAAAGAACAAAAAAAAGAACAAAA
1 AAAAAGAAC-AAAAAAAGAAC-AAA
37454 AAAAAGAACAAAAAAAGAA-AAA
1 AAAAAGAACAAAAAAAGAACAAA
37476 AAAAAGAA
1 AAAAAGAA
37484 AAGGAGGATT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
22 17 0.33
23 1 0.02
24 21 0.41
25 12 0.24
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.01
Consensus pattern (23 bp):
AAAAAGAACAAAAAAAGAACAAA
Found at i:37484 original size:11 final size:11
Alignment explanation
Indices: 37415--37485 Score: 97
Period size: 11 Copynumber: 6.1 Consensus size: 11
37405 TGAAAAAGAT
37415 AAAAAAAGAACA
1 AAAAAAAGAA-A
37427 AAAAAAAGAACA
1 AAAAAAAGAA-A
37439 AAAAAAAGAACAA
1 AAAAAAAG-A-AA
*
37452 AAAAAAAGAAC
1 AAAAAAAGAAA
37463 AAAAAAAGAAA
1 AAAAAAAGAAA
37474 AAAAAAAGAAA
1 AAAAAAAGAAA
37485 A
1 A
37486 GGAGGATTCA
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
11 23 0.42
12 21 0.38
13 10 0.18
14 1 0.02
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:37568 original size:45 final size:45
Alignment explanation
Indices: 37483--37568 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
37473 AAAAAAAAGA
* * *
37483 AAAGGAGGATTCAAGATGAAAACTCGAGAAGGGCGTCTTGAAACC
1 AAAGGAGGATTCAAGATGAAAACCCGAGAAGAGCGGCTTGAAACC
*
37528 AAAGGAGGCA-TCAAGTTGAAAACCCGCA-AAGAGCGGCTTGA
1 AAAGGAGG-ATTCAAGATGAAAACCCG-AGAAGAGCGGCTTGA
37569 GTTTTAAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
45 33 0.94
46 2 0.06
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.14
Consensus pattern (45 bp):
AAAGGAGGATTCAAGATGAAAACCCGAGAAGAGCGGCTTGAAACC
Found at i:38564 original size:37 final size:37
Alignment explanation
Indices: 38514--38592 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
38504 ATTGAAGATA
38514 TTGAAGCATGAAGATGAGAATGACTAGTTTGGTGATC
1 TTGAAGCATGAAGATGAGAATGACTAGTTTGGTGATC
*
38551 TTGAAGCATGAAGATGAGGATGACTAGTTTGGTGATC
1 TTGAAGCATGAAGATGAGAATGACTAGTTTGGTGATC
38588 TTGAA
1 TTGAA
38593 AAGATTGATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (37 bp):
TTGAAGCATGAAGATGAGAATGACTAGTTTGGTGATC
Found at i:38911 original size:54 final size:54
Alignment explanation
Indices: 38811--39365 Score: 662
Period size: 54 Copynumber: 10.0 Consensus size: 54
38801 GTGAAGCAGA
** * * **
38811 AGAAGATTATTCGAGTTCTATACTCCCTGAAAGAAAGAGAGAGCGAACCCGTTTGC
1 AGAAGATCGTTCGAGTTC-CTACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAAGC
* *
38867 AGAAGATCGTTCGAGTTCTTACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAGC
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
* *
38921 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCATAAGT
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
*
38975 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAGC
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
* * *
39029 ATAAGATCATTCGAGTTCCTACTCCCTAAAGAAAGATGGAGCGAACCCGTAAGC
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
* * *
39083 AGAAAATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAGG
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
* * * *
39137 AGAACATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCTGAAAGC
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
* * * *
39191 AGAAGATCGTTTGAGTTCCTACACCCTAATTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCGTA
1 AGAAGATCGTTCGAGTTCCTACTCCCTAA-----A------GAA---AGAGGGAGCGAACCCGTA
39256 AGC
52 AGC
* *
39259 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAATCCGTAGGC
1 AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
* * * * *
39313 AAAAGAT-TTTCGAGTTCCATACTCCTTAGAGAAAGAGGGATCGAACCCGTAAG
1 AGAAGATCGTTCGAGTTCC-TACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
39366 AAGATATTCG
Statistics
Matches: 435, Mismatches: 49, Indels: 32
0.84 0.09 0.06
Matches are distributed among these distances:
53 10 0.02
54 350 0.80
55 8 0.02
56 16 0.04
57 2 0.00
59 1 0.00
63 1 0.00
65 2 0.00
68 45 0.10
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (54 bp):
AGAAGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
Found at i:39241 original size:68 final size:68
Alignment explanation
Indices: 39152--39287 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
39142 ATTGTTCGAG
* *
39152 TTCCTACTCCCTAAAGAAAGAGGGAGCGAACCTGAAAGCAGAAGATCGTTTGAGTTCCTACACCC
1 TTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAGCAGAAGATCGTTCGAGTTCCTACACCC
39217 TAA
66 TAA
* * *
39220 TTCCTACTCCCTAAAGAAAGAGGGAGTGAACCCGTAAGCAGAAGATCGTTCGAGTTCCTACTCCC
1 TTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAGCAGAAGATCGTTCGAGTTCCTACACCC
39285 TAA
66 TAA
39288 AGAAAGAGGG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (68 bp):
TTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAGCAGAAGATCGTTCGAGTTCCTACACCC
TAA
Found at i:39441 original size:55 final size:55
Alignment explanation
Indices: 39381--39514 Score: 196
Period size: 55 Copynumber: 2.4 Consensus size: 55
39371 ATTCGAGTTC
* **
39381 TATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTTGAGTCT
1 TATACTCTCTGAAGGAATAGGGAGCAGACACGATTATTGAAGATTGTTCCAGTCT
* * *
39436 TATACTCTCTGAAGAAATAGGGAGCAGATACGTTTATTGAAGATTGTTCCAGTCT
1 TATACTCTCTGAAGGAATAGGGAGCAGACACGATTATTGAAGATTGTTCCAGTCT
* *
39491 CATACCCTCTGAAGGAATAGGGAG
1 TATACTCTCTGAAGGAATAGGGAG
39515 TGTACATGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 70 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (55 bp):
TATACTCTCTGAAGGAATAGGGAGCAGACACGATTATTGAAGATTGTTCCAGTCT
Found at i:39705 original size:3 final size:3
Alignment explanation
Indices: 39697--39732 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
39687 TTGTCCGGGA
39697 TAT TAT TAT TAT TAT TA- TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
39733 ATAATAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39719 original size:8 final size:8
Alignment explanation
Indices: 39696--39730 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
39686 TTTGTCCGGG
39696 ATATTATT
1 ATATTATT
39704 ATTATTATT
1 A-TATTATT
39713 ATATTATT
1 ATATTATT
*
39721 ATTTTATT
1 ATATTATT
39729 AT
1 AT
39731 TAATAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
ATATTATT
Found at i:39719 original size:11 final size:11
Alignment explanation
Indices: 39697--39732 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
39687 TTGTCCGGGA
39697 TATTATTATTAT
1 TATTA-TATTAT
39709 TATTATATTAT
1 TATTATATTAT
*
39720 TATTTTATTAT
1 TATTATATTAT
39731 TA
1 TA
39733 ATAATAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTATATTAT
Found at i:40948 original size:12 final size:12
Alignment explanation
Indices: 40931--40963 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
40921 ATAACTAATA
40931 ATTAAATATTAT
1 ATTAAATATTAT
*
40943 ATTAAATAATAT
1 ATTAAATATTAT
40955 ATTAAATAT
1 ATTAAATAT
40964 ATTTATGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTAAATATTAT
Found at i:42876 original size:28 final size:28
Alignment explanation
Indices: 42817--42880 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
42807 ATATTTTAAA
* *
42817 TTTAAATTT-GAATAATATTATTTTTTTTAT
1 TTTAAATTTCGAATAATA-TA--ATTTATAT
*
42847 TTTAAATTTCGAATAATATAATTTGTAT
1 TTTAAATTTCGAATAATATAATTTATAT
42875 TTTAAA
1 TTTAAA
42881 AACATTTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 12 0.39
30 11 0.35
31 8 0.26
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (28 bp):
TTTAAATTTCGAATAATATAATTTATAT
Found at i:43487 original size:21 final size:21
Alignment explanation
Indices: 43399--43492 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
43389 TATGGTATAA
*
43399 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
43420 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
*
43441 AA-CATGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
43462 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
43483 AACCCTGCGG
1 AACCCTGCGG
43493 AGATGGCCTA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 3 0.04
21 62 0.93
22 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:45314 original size:30 final size:34
Alignment explanation
Indices: 45250--45328 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 34
45240 AAAATAATTC
* *
45250 TAAATAAATAATAATTATATAAATATTATTTTA-A
1 TAAA-AAATAATAATTACATAAATATTATTTAATA
*
45284 TAAAAAATAATATTTACATAAATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
45316 TAAAAAATAATAA
1 TAAAAAATAATAA
45329 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 3 0.08
32 15 0.38
33 18 0.45
34 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:49614 original size:6 final size:6
Alignment explanation
Indices: 49603--49651 Score: 82
Period size: 6 Copynumber: 8.2 Consensus size: 6
49593 ATTAACACCT
49603 TTTGCA TTTGCA TTTGCA TTTGCA TTTGGCA TTTGCA TTTGCA -TTGCA
1 TTTGCA TTTGCA TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA TTTGCA
49651 T
1 T
49652 ATATTTGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.12
6 30 0.73
7 6 0.15
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.49
Consensus pattern (6 bp):
TTTGCA
Found at i:49636 original size:19 final size:18
Alignment explanation
Indices: 49603--49651 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
49593 ATTAACACCT
49603 TTTGCATTTGCATTTGCA
1 TTTGCATTTGCATTTGCA
49621 TTTGCATTTGGCATTTGCA
1 TTTGCATTT-GCATTTGCA
49640 TTTGCA-TTGCAT
1 TTTGCATTTGCAT
49652 ATATTTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.13
18 11 0.37
19 15 0.50
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.49
Consensus pattern (18 bp):
TTTGCATTTGCATTTGCA
Found at i:51972 original size:21 final size:18
Alignment explanation
Indices: 51947--52002 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 18
51937 CATCATAAAG
51947 AGAAAGAATAGAAATGTAGAA
1 AGAAAGAAT-GAAA-G-AGAA
51968 AGAAAGAATGAAAGAGAA
1 AGAAAGAATGAAAGAGAA
*
51986 AGAAA-AA-GAAAAAGAA
1 AGAAAGAATGAAAGAGAA
52002 A
1 A
52003 AAAATAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
16 9 0.26
17 2 0.06
18 9 0.26
19 1 0.03
20 4 0.12
21 9 0.26
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (18 bp):
AGAAAGAATGAAAGAGAA
Found at i:53159 original size:123 final size:123
Alignment explanation
Indices: 52940--53261 Score: 355
Period size: 123 Copynumber: 2.6 Consensus size: 123
52930 ATTGGAGAAA
* * * * * * * *
52940 AAGAATAAGCGGTGCTAGAACATGAAGCATTCTACGATCTTGAAGC--ATACGATCCAAGAGGTC
1 AAGAATAAGCGATGCCAGAACATGAAGCATTCCATGATCGTGAAACAGATA-G-TCTAAGAGATC
*
53003 AGAATGGATGAAGGAAGAAATTGTAATATTTCCTTGTGACGTTATCAGTAACCCGTCAGG
64 AGAATGGATGAAGGAAGAAATTGTAATATTTCCTTGTGACGTTATCAGTAACCCATCAGG
* * *
53063 AAGAATACA-CGATGACCA-AATATGAAGCATTCCATGATCTTGAAATAGATAGTCTAAGAGATC
1 AAGAATA-AGCGATG-CCAGAACATGAAGCATTCCATGATCGTGAAACAGATAGTCTAAGAGATC
* * * * * *
53126 AGAATGAATGAAGGAATAAATTGTAATATTTCCTTGTGATGTTGTCAGTAACCTATCCGG
64 AGAATGGATGAAGGAAGAAATTGTAATATTTCCTTGTGACGTTATCAGTAACCCATCAGG
* ** * * * *
53186 AAGAATAAGTGATGCCAGAACATGAAGCATTCTGTGATCGTGTAGCAGATGGTCTAAGAAATCAG
1 AAGAATAAGCGATGCCAGAACATGAAGCATTCCATGATCGTGAAACAGATAGTCTAAGAGATCAG
53251 AATGGATGAAG
66 AATGGATGAAG
53262 AACACTTTCT
Statistics
Matches: 166, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
122 4 0.02
123 155 0.93
124 4 0.02
125 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.25
Consensus pattern (123 bp):
AAGAATAAGCGATGCCAGAACATGAAGCATTCCATGATCGTGAAACAGATAGTCTAAGAGATCAG
AATGGATGAAGGAAGAAATTGTAATATTTCCTTGTGACGTTATCAGTAACCCATCAGG
Found at i:53694 original size:125 final size:125
Alignment explanation
Indices: 53469--53837 Score: 535
Period size: 125 Copynumber: 3.0 Consensus size: 125
53459 AAGTTATGAT
* * *
53469 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACGAGATTCAGATCAAGGAGGCATAAA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGAGGCATGAA
* * * *
53534 GAATGAGCCTTATAATTTGAGGTGATGGGGGATTTTGAAGGCCCGTACAAGTATAATACA
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACA
* * *
53594 ATGTTGGGGTACGA-TAAAACCCACATCATGTTGAGATGACAACATTCAGACCAAGGAGGCATGA
1 ATGTTGGGGCACGACT-GAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGAGGCATGA
* * *
53658 AGAATGAGCCTTACAAGTTGAGGTGATGGGGCATTTTGAAGGCCCATACCAGTATAAGATA
65 AGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACA
* * * *
53719 ATGTTGGGGCATGACTGAACCCACATCATGTCGAGATGACAAGATTCAGACCGAGAAGGCATTG-
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGAGGCA-TGA
* *
53783 AGAATGAGCCTTACGATTTGAGGTGTTGGGGCATTTTGAAGGCCCGTACCAGTAT
65 AGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTAT
53838 GAGATAATAT
Statistics
Matches: 217, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
124 1 0.00
125 213 0.98
126 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.24
Consensus pattern (125 bp):
ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGAGGCATGAA
GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACA
Found at i:55185 original size:34 final size:34
Alignment explanation
Indices: 55002--56160 Score: 1709
Period size: 34 Copynumber: 33.8 Consensus size: 34
54992 AAGTCAATCC
*
55002 TAAGCCTTCACCAG-AGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCA-CAGAAGAGTAGTGAAGC--ACCATCT
* *
55038 GAAGCCTTCACCAG-AGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCA-CAGAAGAGTAGTGAAGC--ACCATCT
* * * *
55074 GAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGC--ACCATCT
* * * *
55110 GAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGC--ACCATCT
*
55146 GAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
* * *
55180 CAAGCCTTCACATAAGAGTAGTGAAGCGCCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
*
55214 CAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
* *
55248 CAAGCCTTCATAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
*
55282 CAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
*
55316 TAAGCCTTCACAGAAAAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
55350 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
55384 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
*
55418 CAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
* *
55452 CAAGCCTTCACAGAAGAGTAGTGAAACACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
55486 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
* * *
55520 CAAGCCTTCACAGAAGAGTATTGAAGAACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
* *
55554 CAAGCCTTCACACAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
* *
55588 TAAGCCTTCACAGAAGAGTAGTGAAGTACCGTCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
55622 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
*
55656 TAAGCCTTCATAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
* * *
55690 CAAGCCTTTATAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
55724 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
* *
55758 TAAGCATTCATAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
*
55792 TAAGCCTTCACAGAAGAGTAGTGGAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
*
55826 TAAGCCTTCACAGAAGAGTAGTGAAGCATCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
* *
55860 TAAGCCTTCACAGAAGAGTAGTGGAGCACCATAT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
*
55894 TAAGCCTTCACAGAAGAGTAGTGGAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
55928 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
*
55962 TAAGCCTTCACAGAAAAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
* * *
55996 TAAGCCTTCATAGAAGAGTAGTGGAA-CATCATAT
1 TAAGCCTTCACAGAAGAGTAGT-GAAGCACCATCT
56030 TAAGCCTTCACA-AAGTAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAG-AGTAGTGAAGCACCATCT
*
56064 TAAGCCTTCACCA-AAGAGTAGTGAAGCAATCATCT
1 TAAGCCTTCA-CAGAAGAGTAGTGAAGC-ACCATCT
*
56099 TAAGCCTTCACAGAGGAGTAGTGAAGCACCATCT
1 TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
*
56133 TAAGCTTTCACCA-AAGAGTAGTGAAGCA
1 TAAGCCTTCA-CAGAAGAGTAGTGAAGCA
56161 AATCCATCCA
Statistics
Matches: 1053, Mismatches: 62, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
33 6 0.01
34 879 0.83
35 41 0.04
36 127 0.12
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (34 bp):
TAAGCCTTCACAGAAGAGTAGTGAAGCACCATCT
Found at i:60073 original size:6 final size:6
Alignment explanation
Indices: 60064--60089 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
60054 CATTGTCATT
60064 TCTTCA TCTTCA TCTTCA TCTTCA TC
1 TCTTCA TCTTCA TCTTCA TCTTCA TC
60090 ATTTGAGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCA
Found at i:60191 original size:18 final size:18
Alignment explanation
Indices: 60139--60182 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 18
60129 ACCAATCTTT
60139 TTTCTTCTTTTC--CAT-
1 TTTCTTCTTTTCTTCATC
*
60154 TTCCTTCTTTTCTTCATC
1 TTTCTTCTTTTCTTCATC
60172 TTTCTTCTTTT
1 TTTCTTCTTTT
60183 GTTCTTCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 11 0.46
17 3 0.12
18 10 0.42
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTCTTCTTTTCTTCATC
Done.