Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008823.1 Hibiscus syriacus cultivar Beakdansim tig00111993_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: 1111368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:180782 original size:34 final size:34
Alignment explanation
Indices: 180733--180836 Score: 100
Period size: 40 Copynumber: 2.9 Consensus size: 34
180723 GCGATTTTCA
*
180733 TTTCGCATTGTGATTTTCTAGTTGCGATAGCCAT
1 TTTCGCGTTGTGATTTTCTAGTTGCGATAGCCAT
* *
180767 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGTGA-TTTTC---T--AGTTGCGATAGCCAT
* **
180807 TTTCGCGTTGTGATTTCCCCGTTGCGATAG
1 TTTCGCGTTGTGATTTTCTAGTTGCGATAG
180837 TCAAATGAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
34 20 0.36
35 5 0.09
38 1 0.02
39 4 0.07
40 26 0.46
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.42
Consensus pattern (34 bp):
TTTCGCGTTGTGATTTTCTAGTTGCGATAGCCAT
Found at i:180810 original size:20 final size:20
Alignment explanation
Indices: 180754--180811 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
180744 GATTTTCTAG
**
180754 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGAA
***
180774 TTGCGATTTTTCA-TTTCGAA
1 TTGCGA-TAGCCATTTTCGAA
180794 TTGCGATAGCCATTTTCG
1 TTGCGATAGCCATTTTCG
180812 CGTTGTGATT
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
19 3 0.11
20 22 0.79
21 3 0.11
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGAA
Found at i:181154 original size:20 final size:20
Alignment explanation
Indices: 181110--181181 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
181100 ATAGTCAGTA
* **
181110 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACTTAT
181131 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
181151 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
181171 TCGCATTGCGA
1 TCGCATTGCGA
181182 ATTAGGAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 37 0.77
21 11 0.23
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:181937 original size:24 final size:24
Alignment explanation
Indices: 181910--181963 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
181900 GTATTCAAAA
*
181910 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
181934 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
181958 TTTGAT
1 TTTGAT
181964 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:182155 original size:12 final size:12
Alignment explanation
Indices: 182138--182162 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
182128 ATATAATCCT
182138 GAAGAAGAAAAA
1 GAAGAAGAAAAA
182150 GAAGAAGAAAAA
1 GAAGAAGAAAAA
182162 G
1 G
182163 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:184500 original size:33 final size:33
Alignment explanation
Indices: 184454--184580 Score: 195
Period size: 33 Copynumber: 3.8 Consensus size: 33
184444 GGAAATTACT
184454 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
184487 ATCGCAATACGAAATGAAAATCGCAACGCA-A-A
1 ATCGCAATGCGAAATGAAAATCGCAACG-AGAGA
* *
184519 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
184553 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
184581 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
32 2 0.02
33 81 0.95
34 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:184566 original size:66 final size:66
Alignment explanation
Indices: 184455--184587 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
184445 GAAATTACTA
184455 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGCAAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGCAAAT
184520 T
66 T
* * *
184521 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGCAAAT
184586 T
66 T
184587 T
1 T
184588 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGCAACGCAAAT
T
Found at i:184612 original size:14 final size:14
Alignment explanation
Indices: 184595--184684 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
184585 TTTAATTTCG
184595 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
184609 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
184628 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
184642 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
184661 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
184675 CGTTGCGATT
1 CGTTGCGATT
184685 TTCATTTCGC
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
16 6 0.10
17 6 0.10
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:184631 original size:33 final size:33
Alignment explanation
Indices: 184580--184702 Score: 219
Period size: 33 Copynumber: 3.7 Consensus size: 33
184570 AAATCGCAAC
* *
184580 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
184613 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
184646 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
184679 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
184703 AGTACTTTTT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:184633 original size:19 final size:19
Alignment explanation
Indices: 184609--184702 Score: 91
Period size: 19 Copynumber: 5.5 Consensus size: 19
184599 GCGATTCTCT
184609 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
184628 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
184642 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
184661 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
184675 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
184694 CATTGCGAT
1 CGTTGCGAT
184703 AGTACTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
14 20 0.33
16 6 0.10
17 6 0.10
19 28 0.47
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:184828 original size:14 final size:14
Alignment explanation
Indices: 184809--184845 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
184799 CATCAATTAA
184809 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
184823 ACAAATCACCTTTT
1 ACAAATCAACTTTT
184837 ACAAATCAA
1 ACAAATCAA
184846 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:186268 original size:21 final size:21
Alignment explanation
Indices: 186202--186268 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
186192 GTGAATCGGG
*
186202 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
186222 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
186244 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
186265 CTCT
1 CTCT
186269 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:186718 original size:91 final size:90
Alignment explanation
Indices: 186542--186726 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
186532 ATTTCAAACT
* *
186542 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTGTAGC
186607 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
186635 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTGTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTGTAGCA
*
186699 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
186726 T
1 T
186727 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTGTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:188446 original size:20 final size:19
Alignment explanation
Indices: 188411--188518 Score: 100
Period size: 20 Copynumber: 5.8 Consensus size: 19
188401 TCTTTTGGTT
*
188411 GAAATGAAAATTGCAACGA
1 GAAATGAAAATCGCAACGA
* *
188430 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
188451 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGA
188470 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
188489 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
188503 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
188519 TGCGATTTTG
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
14 11 0.15
16 2 0.03
17 2 0.03
19 27 0.38
20 28 0.39
21 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:188475 original size:19 final size:19
Alignment explanation
Indices: 188411--188523 Score: 110
Period size: 19 Copynumber: 6.1 Consensus size: 19
188401 TCTTTTGGTT
* *
188411 GAAATGAAAATTGCAACGA
1 GAAATGAAAATCGCAACGC
*
188430 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
188450 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
188470 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
188487 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
188503 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
188522 GA
1 GA
188524 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 30 0.39
20 29 0.38
21 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:188552 original size:19 final size:19
Alignment explanation
Indices: 188519--188563 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
188509 AAAATCGCAA
*
188519 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
188538 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
188557 TGCGATT
1 TGCGATT
188564 CTCTCGTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:189181 original size:21 final size:20
Alignment explanation
Indices: 189135--189188 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
189125 CGATAGTAAG
* *
189135 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
*
189155 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCT
189175 AATTCGCATTGCGA
1 -ATTCGCATTGCGA
189189 ATTATGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACCT
Found at i:189221 original size:20 final size:21
Alignment explanation
Indices: 189178--189250 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
189168 TTTTCCTAAT
* *
189178 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
*
189199 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
189219 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
189240 TCGCATTGCGA
1 TCGCAATGCGA
189251 TAGTCATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 18 0.40
21 27 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:189279 original size:41 final size:41
Alignment explanation
Indices: 189114--189272 Score: 135
Period size: 41 Copynumber: 3.9 Consensus size: 41
189104 GGCGCTATGT
* * * * * *
189114 AAATCGCATTGCGATAGTAAGATTCACATTGCGATTTACG-
1 AAATCGCATTGCGATAGTCATAATCGCATTGCGAATTAGGA
* * ** * *
189154 TATTCGCATTGCGATTTTCCTAATTCGCATTGCGAATTATGA
1 AAATCGCATTGCGATAGTCATAA-TCGCATTGCGAATTAGGA
* *
189196 AAATCGCAATGCGAATACGT-A-AATCGCAATGCGAATTAGGA
1 AAATCGCATTGCG-ATA-GTCATAATCGCATTGCGAATTAGGA
*
189237 AAATCGCATTGCGATAGTCATAATCGCGTTGCGAAT
1 AAATCGCATTGCGATAGTCATAATCGCATTGCGAAT
189273 CTGGAAACTG
Statistics
Matches: 91, Mismatches: 22, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
39 2 0.02
40 19 0.21
41 55 0.60
42 12 0.13
43 2 0.02
44 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (41 bp):
AAATCGCATTGCGATAGTCATAATCGCATTGCGAATTAGGA
Found at i:189523 original size:19 final size:19
Alignment explanation
Indices: 189499--189535 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
189489 ATCTATTACA
189499 AATATTAAATATAATAAAT
1 AATATTAAATATAATAAAT
**
189518 AATATTATTTATAATAAA
1 AATATTAAATATAATAAA
189536 ACTTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATTAAATATAATAAAT
Found at i:189534 original size:22 final size:22
Alignment explanation
Indices: 189509--189599 Score: 55
Period size: 19 Copynumber: 4.1 Consensus size: 22
189499 AATATTAAAT
189509 ATAATAAATAATATTATTTATA
1 ATAATAAATAATATTATTTATA
* * *
189531 ATAAAACTTAATATTATTATTTTAAA
1 AT--AA-TAAATAATATTA-TTTATA
*
189557 ATATTAAAATAAT-TTATTTAT-
1 ATAAT-AAATAATATTATTTATA
* *
189578 -TATTAAATATTATT-TTTATA
1 ATAATAAATAATATTATTTATA
189598 AT
1 AT
189600 TTTATTAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
19 11 0.21
20 6 0.11
21 1 0.02
22 6 0.11
23 4 0.08
24 8 0.15
25 10 0.19
26 7 0.13
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATAAATAATATTATTTATA
Found at i:189602 original size:49 final size:50
Alignment explanation
Indices: 189505--189603 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
189495 TACAAATATT
*
189505 AAATATAATAAATAATATTATTTATAATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATAATAAAACTTAATATTATAATTTTA
* * * *
189555 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTA-TAATAAA-ACTTAATATTATAATTTTA
189604 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 7 0.17
49 27 0.64
50 8 0.19
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATAATAAAACTTAATATTATAATTTTA
Found at i:189709 original size:90 final size:86
Alignment explanation
Indices: 189553--189722 Score: 200
Period size: 88 Copynumber: 1.9 Consensus size: 86
189543 ATTATTATTT
* * * * *
189553 TAAAATATTAAAATAATTTATTTATTATTAAATATTATTTTTATAATTTTATTAATAAAAATATT
1 TAAAATATTAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTATATTAATAAAAATATT
*
189618 AATATTGGTATATTTTAGTGAAA
66 -A-ATTAGTATATTTTAGTGAAA
* *
189641 TAAAATATTATAAATTATATTAATTATTTATTAAAGTAATAGTGTTAT-ATTATATT-TTAAAAA
1 TAAAATATTA-AAATAAT-TTAATTA-TTATTAAA-TAATAGTGTTATAATTATATTAATAAAAA
189704 TATTAATTAGTATATTTTA
62 TATTAATTAGTATATTTTA
189723 AATATCTTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 23 0.33
89 7 0.10
90 16 0.23
91 15 0.21
92 9 0.13
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (86 bp):
TAAAATATTAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTATATTAATAAAAATATT
AATTAGTATATTTTAGTGAAA
Found at i:189778 original size:28 final size:27
Alignment explanation
Indices: 189738--189828 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 27
189728 CTTTACTAAA
189738 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATATAAA-AATATTAT
189767 -TCATTATTAAATATATAAAAAATTTATTAT
1 AT-ATTATTAAATATAT-AAAAA--TATTAT
*
189797 ATATTATTAAA-ATA-AAAAATATAAT
1 ATATTATTAAATATATAAAAATATTAT
*
189822 ATCTTAT
1 ATATTAT
189829 ATTATTATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
25 11 0.20
27 5 0.09
28 13 0.24
29 10 0.18
30 15 0.27
31 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATTATTAAATATATAAAAATATTAT
Found at i:189795 original size:30 final size:28
Alignment explanation
Indices: 189738--189828 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 28
189728 CTTTACTAAA
*
189738 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATATAAAAAATATTAT
189767 -TCATTATTAAATATATAAAAAATTTATTAT
1 AT-ATTATTAAATATATAAAAAA--TATTAT
*
189797 ATATTATT-AA-A-ATAAAAAATATAAT
1 ATATTATTAAATATATAAAAAATATTAT
*
189822 ATCTTAT
1 ATATTAT
189829 ATTATTATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
25 11 0.20
27 8 0.15
28 17 0.31
29 6 0.11
30 12 0.22
31 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATTATTAAATATATAAAAAATATTAT
Found at i:189881 original size:22 final size:23
Alignment explanation
Indices: 189856--189899 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
189846 GATTATTTTA
189856 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
189878 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
189900 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:189890 original size:30 final size:30
Alignment explanation
Indices: 189757--189905 Score: 97
Period size: 32 Copynumber: 5.1 Consensus size: 30
189747 AAATATATAA
189757 ATAATATTATTCATTATTA-AATATATAAAAA-
1 ATAATATTA-T-ATTATTATAATAT-TAAAAAT
* * *
189788 AT-TTATTATA-TATTATTAAAATAAAAAAT
1 ATAATATTATATTATTA-TAATATTAAAAAT
189817 ATAATATCTTATATTATTATAATA-T---AAT
1 ATAATA--TTATATTATTATAATATTAAAAAT
* *
189845 -T--GATTATTTTA-TATAATATTAAAAAT
1 ATAATATTATATTATTATAATATTAAAAAT
189871 ATAATATTATATTATTATAAATATTAATAAAT
1 ATAATATTATATTATTAT-AATATTAA-AAAT
189903 ATA
1 ATA
189906 TTTTAAATAT
Statistics
Matches: 91, Mismatches: 10, Indels: 33
0.68 0.07 0.25
Matches are distributed among these distances:
22 7 0.08
23 8 0.09
25 1 0.01
26 3 0.03
27 7 0.08
28 9 0.10
29 15 0.16
30 10 0.11
31 10 0.11
32 16 0.18
33 5 0.05
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
ATAATATTATATTATTATAATATTAAAAAT
Found at i:189904 original size:22 final size:22
Alignment explanation
Indices: 189860--189916 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
189850 ATTTTATATA
* *
189860 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
189881 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
189903 ATATTTTAAATATT
1 ATATTATAAATATT
189917 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:189915 original size:52 final size:51
Alignment explanation
Indices: 189795--189916 Score: 133
Period size: 52 Copynumber: 2.3 Consensus size: 51
189785 AAAATTTATT
* **
189795 ATATATTATTAAA-ATAAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
189847 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
189901 ATATATTTTAAATATT
1 ATATATTTTAAATATT
189917 TTAATAATTA
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
51 3 0.05
52 24 0.40
53 8 0.13
54 23 0.38
55 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:190157 original size:42 final size:41
Alignment explanation
Indices: 190105--190224 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 41
190095 ATGAATTACG
* *
190105 TTTCGGAAAACGAATTACGTGAAACAAACACGGTAAAACATT
1 TTTCGAAAAACGAATTACGTAAAACAAACACGG-AAAACATT
*
190147 TTTCGAAAAACGAATTACGTAAAACGAACACAGGAAAACATT
1 TTTCGAAAAACGAATTACGTAAAACAAACAC-GGAAAACATT
* * *
190189 TTCCGAAGAACGAATTACATAAAACAAACAC-GAAAA
1 TTTCGAAAAACGAATTACGTAAAACAAACACGGAAAA
190225 TTTGGAGAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 5 0.07
42 63 0.90
43 2 0.03
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.18
Consensus pattern (41 bp):
TTTCGAAAAACGAATTACGTAAAACAAACACGGAAAACATT
Found at i:196467 original size:60 final size:60
Alignment explanation
Indices: 196403--196519 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
196393 GTTAGAGTTG
* * * * * * *
196403 AGGGATGAAATTGAAATGTTTAGAAGTTTGAGGAT-TAATTTAGAGTGAATGTCATAATTT
1 AGGGATGAAAATAAAATATTTAAAAGTTTGAGGATCAAATTCA-AATGAATGTCATAATTT
*
196463 AGGGATGAAAATAAAATATTTAAAAGTTTGATGATCAAATTCAAATGAATGTCATAA
1 AGGGATGAAAATAAAATATTTAAAAGTTTGAGGATCAAATTCAAATGAATGTCATAA
196520 ATTGGAGACA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 43 0.90
61 5 0.10
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.33
Consensus pattern (60 bp):
AGGGATGAAAATAAAATATTTAAAAGTTTGAGGATCAAATTCAAATGAATGTCATAATTT
Found at i:197476 original size:15 final size:14
Alignment explanation
Indices: 197456--197485 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
197446 TTAATTAACT
197456 TTTTTTAATAACTAA
1 TTTTTTAATAA-TAA
197471 TTTTTTAATAATAA
1 TTTTTTAATAATAA
197485 T
1 T
197486 CAAATCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTTTAATAATAA
Found at i:202345 original size:8 final size:8
Alignment explanation
Indices: 202334--202371 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
202324 AAAGAGAAGA
202334 AGAGAGGG
1 AGAGAGGG
202342 AGAGAGGG
1 AGAGAGGG
202350 AGAGAGGG
1 AGAGAGGG
*
202358 AGAGAGAG
1 AGAGAGGG
202366 AGAGAG
1 AGAGAG
202372 AGACAGAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Found at i:202372 original size:8 final size:8
Alignment explanation
Indices: 202326--202379 Score: 58
Period size: 8 Copynumber: 7.0 Consensus size: 8
202316 AGAAAAGAAA
202326 AGAGA-AG
1 AGAGAGAG
202333 A-AGAGAG
1 AGAGAGAG
*
202340 GGAGAGAG
1 AGAGAGAG
*
202348 GGAGAGAG
1 AGAGAGAG
*
202356 GGAGAGAG
1 AGAGAGAG
202364 AGAGAGAG
1 AGAGAGAG
*
202372 AGACAGAG
1 AGAGAGAG
202380 GAACCTTAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 36 0.86
ACGTcount: A:0.46, C:0.02, G:0.52, T:0.00
Consensus pattern (8 bp):
AGAGAGAG
Found at i:202374 original size:6 final size:6
Alignment explanation
Indices: 202326--202379 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
202316 AGAAAAGAAA
* * *
202326 AGAGA- AGA-AG AGAGGG AGAGAG GGAGAG AGGGAG AGAGAG AGAGAG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
*
202372 AGACAG AG
1 AGAGAG AG
202380 GAACCTTAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
4 1 0.03
5 6 0.15
6 33 0.82
ACGTcount: A:0.46, C:0.02, G:0.52, T:0.00
Consensus pattern (6 bp):
AGAGAG
Found at i:203248 original size:18 final size:17
Alignment explanation
Indices: 203218--203251 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
203208 GAAGATTGCG
*
203218 TTCACAACGATCGTCGC
1 TTCACAACCATCGTCGC
203235 TTCAGCAACCATCGTCG
1 TTCA-CAACCATCGTCG
203252 AGGTAACACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (17 bp):
TTCACAACCATCGTCGC
Found at i:206352 original size:20 final size:20
Alignment explanation
Indices: 206327--206364 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
206317 ATGTGAAATT
206327 TGTCCCGAATG-ACCTATGTA
1 TGTCCCGAA-GAACCTATGTA
206347 TGTCCCGAAGAACCTATG
1 TGTCCCGAAGAACCTATG
206365 AACCCTCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
TGTCCCGAAGAACCTATGTA
Found at i:212040 original size:20 final size:20
Alignment explanation
Indices: 211998--212072 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
211988 ATATTTGATA
*
211998 TTTT-TTAACTTTATATTATAT
1 TTTTATTAA-TTT-TATTACAT
212019 TTTTATTGAATTTTATT-CAT
1 TTTTATT-AATTTTATTACAT
*
212039 TTTTAATTCATTTTATTACAT
1 TTTT-ATTAATTTTATTACAT
* *
212060 ATTTATTTATTTT
1 TTTTATTAATTTT
212073 TTAAAAAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
20 22 0.48
21 17 0.37
22 5 0.11
23 2 0.04
ACGTcount: A:0.27, C:0.05, G:0.01, T:0.67
Consensus pattern (20 bp):
TTTTATTAATTTTATTACAT
Found at i:212047 original size:11 final size:10
Alignment explanation
Indices: 212017--212073 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
212007 TTTATATTAT
*
212017 ATTTTTATTG
1 ATTTTTATTC
*
212027 AATTTTATTC
1 ATTTTTATTC
212037 ATTTTTAATTC
1 ATTTTT-ATTC
212048 A-TTTTATTAC
1 ATTTTTATT-C
* *
212058 ATATTTATTT
1 ATTTTTATTC
212068 ATTTTT
1 ATTTTT
212074 TAAAAAAGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 3 0.08
10 24 0.63
11 11 0.29
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:213579 original size:21 final size:22
Alignment explanation
Indices: 213555--213598 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
213545 AAACATTTTC
213555 TTAAGATAATAAAA-ATTTATT
1 TTAAGATAATAAAATATTTATT
* *
213576 TTAATATAGTAAAATATTTATT
1 TTAAGATAATAAAATATTTATT
213598 T
1 T
213599 ATTCAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAAATATTTATT
Found at i:215190 original size:3 final size:3
Alignment explanation
Indices: 215175--215223 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
215165 CTGTATTTAT
*
215175 TAA TAA T-A GAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
215219 TAA TA
1 TAA TA
215224 TTTAAATGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 3 0.07
3 36 0.88
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:215758 original size:17 final size:17
Alignment explanation
Indices: 215736--215769 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
215726 TTGAACAAGC
215736 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
215753 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
215770 CGACCTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (17 bp):
TCTTCTCATTATGAACT
Found at i:216179 original size:113 final size:113
Alignment explanation
Indices: 215752--217285 Score: 1797
Period size: 113 Copynumber: 13.4 Consensus size: 113
215742 CATTATGAAC
** ** * *
215752 TTCTTCTCATTATGAACTCGAC-CTGTCAATGCTGATCCATTGAATGATGAATTTAAGCAAAAAG
1 TTCTTCTCATTATGAACT-TTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAG
* * *
215816 GTTGAACAAATTCTTCTCATTATGAACATCTTCTTACTTCTTCAGATGAG
64 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * ***
215866 TTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATGCTGATCTATCTCCTTCTGTGATAGAATT
1 TTCTTCTCATTATGAACTTTCTCTGG--AA----ATGCTGATCCA--T-C--GAATGAT-GAATT
* * * * *
215931 -ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-C-TCTTCAAATAAG
54 CAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* *
215988 TTCTTCTCATTATGAAC--T-TCTGGAAAAT-TTGATCCATCGAATGATGAATTCAAACAAAAGG
1 TTCTTCTCATTATGAACTTTCTCTGG-AAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGG
* *
216049 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAG
65 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * *
216098 TTCTTCTCATTATGAACTTGAC-CTGGTAATGATGATCCATCGAATGATGAATTCAAGCGAAAA-
1 TTCTTCTCATTATGAACTT-TCTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAG
216161 GTTGAACAAGTTCTTCTCATTATGAACTT-TTGCTTCCTTCTTCAGATGAG
64 GTTGAACAAGTTCTTCTCATTATGAACTTCTT-CTTCCTTCTTCAGATGAG
* *
216211 TTCTTCTCATTATGAACTTGAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA-
1 TTCTTCTCATTATGAACTT-TCTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAG
*
216274 GTTGAACAATTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
64 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* *
216324 TTCTTCTCATTATGAACTTGAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA-
1 TTCTTCTCATTATGAACTT-TCTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAG
216387 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
64 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* *
216437 TTCTTCTCATTATGAACTTGAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA-
1 TTCTTCTCATTATGAACTT-TCTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAG
*
216500 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTACTTCTTCAGATGAG
64 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * * **
216550 TTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCGAGTGATGGATTTGAGCAAAAGGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGGT
*
216615 TGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* *** *
216663 TTCTTCTCCTTATGAACTTTCTCTGGAAATG-TGTATGCTAATCTATCTCCTTCTG-TGATAGAG
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTG-AT-C----C-A--T-CGAATGATG--A-AT
* *
216726 TCATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAG
53 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * ** **
216786 TTCTTTTCATTATGAACTTTCTCTGGAAATGCTGATCCATC-AAGTGATGGATTTGATAAAAAGG
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAA-TGATGAATTCAAGCAAAAGG
*
216850 TTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
65 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * * **
216899 TTCTTCTCATTATGAACTTTCTCTGGAAATACTGATCCATCGAGTGATGGATTTGAGCAAAAGGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGGT
* *
216964 TGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * *
217012 TTCTTCTCATTATGAACTTTCTCTGGAAAT-TTGATCCATC-AAGTGATGGATTTGAA-CAAAAG
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAA-TGAT-GAATTCAAGCAAAAG
* * *
217074 GTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATAAG
64 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
** * **
217124 TTCTTCTCATTATGAACTTTCTCTGGAAATTTTGATCCATC-AAGTGATGGATTTGAGCAAAAGG
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAA-TGATGAATTCAAGCAAAAGG
* *
217188 TTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAG
65 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
** * **
217237 TTCTTCTCATTATGAACTCGAC-CTGGTAATGCTGATCCATTAAATGATG
1 TTCTTCTCATTATGAACT-TTCTCTGGAAATGCTGATCCATCGAATGATG
217286 GATTTGAACT
Statistics
Matches: 1273, Mismatches: 97, Indels: 101
0.87 0.07 0.07
Matches are distributed among these distances:
107 5 0.00
108 45 0.04
110 28 0.02
111 2 0.00
112 156 0.12
113 798 0.63
114 37 0.03
115 3 0.00
116 1 0.00
117 1 0.00
118 5 0.00
119 6 0.00
120 11 0.01
121 3 0.00
122 32 0.03
123 44 0.03
124 84 0.07
125 7 0.01
126 5 0.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGGT
TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:220566 original size:114 final size:114
Alignment explanation
Indices: 220358--220573 Score: 360
Period size: 114 Copynumber: 1.9 Consensus size: 114
220348 ATGTAGTTCA
* * * *
220358 TCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTTAAAGAACAC
1 TCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
*
220423 TTCCAGAAGATGCTATTGGGTCTCATTATTTCTACTATGAGCAAATTCG
66 TTCCAGAAGATGCTATTGGGGCTCATTATTTCTACTATGAGCAAATTCG
* *
220472 TCTTTCAAATCCAATGATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGAACAC
1 TCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
*
220537 TTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
66 TTCCAGAAGATGCTATTGGGGCTCATTATTTCTACTA
220574 CGAGAACGTG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 94 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (114 bp):
TCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTGGGGCTCATTATTTCTACTATGAGCAAATTCG
Found at i:222743 original size:10 final size:9
Alignment explanation
Indices: 222726--222802 Score: 66
Period size: 9 Copynumber: 8.1 Consensus size: 9
222716 CAATTTCTCC
222726 TTCTTTTTT
1 TTCTTTTTT
222735 TTCCTTTTTT
1 TT-CTTTTTT
222745 TTCTTTTTT
1 TTCTTTTTT
* *
222754 TGCTTTGCTT
1 TTCTTT-TTT
222764 TTCTTTTTTCT
1 TTC-TTTTT-T
222775 TTCTTTCTTT
1 TTCTTT-TTT
*
222785 TT-TTTTTG
1 TTCTTTTTT
*
222793 TTGTTTTTT
1 TTCTTTTTT
222802 T
1 T
222803 CAAGTATAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
8 4 0.07
9 23 0.41
10 20 0.36
11 9 0.16
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:225047 original size:12 final size:12
Alignment explanation
Indices: 225028--225077 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
225018 GTAAAAATGA
225028 AAATGTAAATAC
1 AAATGTAAATAC
* *
225040 AAACGTAAAAAATGC
1 AAATGT---AAATAC
225055 AAATGTAAATAC
1 AAATGTAAATAC
225067 AAATGTAAATA
1 AAATGTAAATA
225078 TGTGAATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 21 0.68
15 10 0.32
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.22
Consensus pattern (12 bp):
AAATGTAAATAC
Found at i:225050 original size:27 final size:27
Alignment explanation
Indices: 225020--225075 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
225010 GTAATTATGT
225020 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGTAAATACAAACGTA
* *
225047 AAAAATGCAAATGTAAATACAAATGTA
1 AAAAATGAAAATGTAAATACAAACGTA
225074 AA
1 AA
225076 TATGTGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGTAAATACAAACGTA
Found at i:225169 original size:7 final size:7
Alignment explanation
Indices: 225135--225176 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
225125 ATAAAAGTAT
225135 AAATGCA
1 AAATGCA
* *
225142 CAATGAA
1 AAATGCA
225149 AAATGCA
1 AAATGCA
225156 AAGATGCA
1 AA-ATGCA
225164 AAATGC-
1 AAATGCA
225170 AAATGCA
1 AAATGCA
225177 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:227711 original size:20 final size:22
Alignment explanation
Indices: 227686--227746 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 22
227676 ATTTAAACAT
*
227686 ATAAAATTAAA-ATATAAA-TA
1 ATAAAATTAAATATAAAAAGTA
227706 ATAAAATTAAATATAAAAAGTA
1 ATAAAATTAAATATAAAAAGTA
227728 ATAAAACTTATAAT-TAAAA
1 ATAAAA-TTA-AATATAAAA
227747 TTGGTGACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 11 0.31
21 6 0.17
22 8 0.22
23 8 0.22
24 3 0.08
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAAAATTAAATATAAAAAGTA
Found at i:229010 original size:3 final size:3
Alignment explanation
Indices: 228995--229060 Score: 84
Period size: 3 Copynumber: 22.7 Consensus size: 3
228985 CTGTATTTAT
* *
228995 TAA TAA T-A GAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
229042 TAA T-A TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TA
229061 TTTAAATGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 48 0.87
4 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:229217 original size:2 final size:2
Alignment explanation
Indices: 229210--229240 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
229200 TCAGCTGCCT
229210 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 T
229241 TGTCTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:233190 original size:25 final size:25
Alignment explanation
Indices: 233162--233222 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
233152 ACACCTATAT
233162 ATGAATCATATCAATTTTTTATTAC
1 ATGAATCATATCAATTTTTTATTAC
233187 ATGAATCATATCAATTTTTTATTAC
1 ATGAATCATATCAATTTTTTATTAC
233212 ATGAATCATAT
1 ATGAATCATAT
233223 AAGTTTAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (25 bp):
ATGAATCATATCAATTTTTTATTAC
Found at i:242185 original size:19 final size:19
Alignment explanation
Indices: 242161--242208 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
242151 ATTCGAGTAA
242161 AAACCTGCACCGTAGTGCT
1 AAACCTGCACCGTAGTGCT
242180 AAACCTGCACCGTAGTGCT
1 AAACCTGCACCGTAGTGCT
242199 AAACCTGCAC
1 AAACCTGCAC
242209 TAAGCTTACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (19 bp):
AAACCTGCACCGTAGTGCT
Found at i:242683 original size:24 final size:24
Alignment explanation
Indices: 242651--242696 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
242641 AGTCTTTCTG
242651 ATGATGTATAAAACATCTATGTTC
1 ATGATGTATAAAACATCTATGTTC
242675 ATGATGTATAAAACATCTATGT
1 ATGATGTATAAAACATCTATGT
242697 ACAATGTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTTC
Found at i:244966 original size:288 final size:288
Alignment explanation
Indices: 244450--245028 Score: 1158
Period size: 288 Copynumber: 2.0 Consensus size: 288
244440 ATGTTCAGCT
244450 TTCACCTGTTGACACGTCAGACATGTAGCAACAAACTCAGAAATTACCCAGCCACCAAAATCGAC
1 TTCACCTGTTGACACGTCAGACATGTAGCAACAAACTCAGAAATTACCCAGCCACCAAAATCGAC
244515 TATTTACATCCTTATACATCTTACTCGTGCTTGGATGCATAGTCAGTAGACTATAATATGCCTCA
66 TATTTACATCCTTATACATCTTACTCGTGCTTGGATGCATAGTCAGTAGACTATAATATGCCTCA
244580 GAACTAATATTTTTCTTTATCTCATCAACATGTGAAATGCATATTCTTCCTAAATAATACAGACA
131 GAACTAATATTTTTCTTTATCTCATCAACATGTGAAATGCATATTCTTCCTAAATAATACAGACA
244645 ACCATCAGACTTGACTTCAAAGTCTTTAGTCTCACTTTTTTCCACCAGTGAAATCTTTTCCTTTG
196 ACCATCAGACTTGACTTCAAAGTCTTTAGTCTCACTTTTTTCCACCAGTGAAATCTTTTCCTTTG
244710 TATCTTTATTATCTGATCTAGAAACATC
261 TATCTTTATTATCTGATCTAGAAACATC
244738 TTCACCTGTTGACACGTCAGACATGTAGCAACAAACTCAGAAATTACCCAGCCACCAAAATCGAC
1 TTCACCTGTTGACACGTCAGACATGTAGCAACAAACTCAGAAATTACCCAGCCACCAAAATCGAC
244803 TATTTACATCCTTATACATCTTACTCGTGCTTGGATGCATAGTCAGTAGACTATAATATGCCTCA
66 TATTTACATCCTTATACATCTTACTCGTGCTTGGATGCATAGTCAGTAGACTATAATATGCCTCA
244868 GAACTAATATTTTTCTTTATCTCATCAACATGTGAAATGCATATTCTTCCTAAATAATACAGACA
131 GAACTAATATTTTTCTTTATCTCATCAACATGTGAAATGCATATTCTTCCTAAATAATACAGACA
244933 ACCATCAGACTTGACTTCAAAGTCTTTAGTCTCACTTTTTTCCACCAGTGAAATCTTTTCCTTTG
196 ACCATCAGACTTGACTTCAAAGTCTTTAGTCTCACTTTTTTCCACCAGTGAAATCTTTTCCTTTG
244998 TATCTTTATTATCTGATCTAGAAACATC
261 TATCTTTATTATCTGATCTAGAAACATC
245026 TTC
1 TTC
245029 TTTACCTTTA
Statistics
Matches: 291, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
288 291 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (288 bp):
TTCACCTGTTGACACGTCAGACATGTAGCAACAAACTCAGAAATTACCCAGCCACCAAAATCGAC
TATTTACATCCTTATACATCTTACTCGTGCTTGGATGCATAGTCAGTAGACTATAATATGCCTCA
GAACTAATATTTTTCTTTATCTCATCAACATGTGAAATGCATATTCTTCCTAAATAATACAGACA
ACCATCAGACTTGACTTCAAAGTCTTTAGTCTCACTTTTTTCCACCAGTGAAATCTTTTCCTTTG
TATCTTTATTATCTGATCTAGAAACATC
Found at i:246607 original size:20 final size:18
Alignment explanation
Indices: 246567--246603 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
246557 TGATCTCGTT
246567 TTTTTTCTCAATCACTAA
1 TTTTTTCTCAATCACTAA
*
246585 TTTTTTCTTAATCACTAA
1 TTTTTTCTCAATCACTAA
246603 T
1 T
246604 ATTTCCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTTTCTCAATCACTAA
Found at i:246608 original size:17 final size:18
Alignment explanation
Indices: 246570--246612 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
246560 TCTCGTTTTT
*
246570 TTTCTCAATCACTAATTT
1 TTTCTCAATCACTAATTA
*
246588 TTTCTTAATCACTAA-TA
1 TTTCTCAATCACTAATTA
246605 TTTC-CAAT
1 TTTCTCAAT
246613 TTATCCACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 5 0.23
18 14 0.64
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCTCAATCACTAATTA
Found at i:254277 original size:21 final size:22
Alignment explanation
Indices: 254227--254280 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
254217 TGATTGAATC
254227 AGTATCGATACC--GATGAGGT
1 AGTATCGATACCAGGATGAGGT
254247 AGTATCGATACCAGGATGAGG-
1 AGTATCGATACCAGGATGAGGT
* *
254268 GGTATTGATACCA
1 AGTATCGATACCA
254281 AGAAACATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 12 0.40
21 11 0.37
22 7 0.23
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (22 bp):
AGTATCGATACCAGGATGAGGT
Found at i:254468 original size:95 final size:95
Alignment explanation
Indices: 254269--254444 Score: 219
Period size: 95 Copynumber: 1.9 Consensus size: 95
254259 AGGATGAGGG
* ** * * *
254269 GTATTGATACCAAGAAACATCGAATGTAATTTTGGTATCGATACCGGTAGGGGTTATCAGTACCA
1 GTATCGATACCAAGAAACATCGAACATAATTTTGGTATCGATACCCGAAGGGGGTATCAGTACCA
* * *
254334 TAGTAGAGTAGTTTCGATACCATAGTAAGG
66 TAGTAGAGAAGTATCGATACCATAGTAAGA
* * *
254364 GTATCGATACCAAGCAACATTGAACATATTTTTGGTATCGATACCCGAAGGGGGTATC-GATACC
1 GTATCGATACCAAGAAACATCGAACATAATTTTGGTATCGATACCCGAAGGGGGTATCAG-TACC
*
254428 ATAGTATAGAAGTATCG
65 ATAGTAGAGAAGTATCG
254445 GTACTAGTGT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
94 1 0.01
95 67 0.99
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (95 bp):
GTATCGATACCAAGAAACATCGAACATAATTTTGGTATCGATACCCGAAGGGGGTATCAGTACCA
TAGTAGAGAAGTATCGATACCATAGTAAGA
Found at i:255252 original size:68 final size:67
Alignment explanation
Indices: 255075--255530 Score: 562
Period size: 68 Copynumber: 6.8 Consensus size: 67
255065 AAAAGATCAA
* *
255075 GAGGCCTAAATGTGCATATGACAG-AAGGTGTCAATTATGCCAGTTAGATAAAAGACTAAGTGTC
1 GAGGCCT-AATATGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTC
255139 TTT
65 TTT
* ** *
255142 GAGTCCT-GCA--CATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTTAGTGTCT
1 GAGGCCTAATATGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTCT
255204 TT
66 TT
** * * *
255206 GAGGCCTAATTACACATATGAGAGAAAGGTGTCAATTATTCTAGTTAGATGAAAGACTAAGTGTC
1 GAGGCCTAA-TATGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTC
255271 TTT
65 TTT
* * * *
255274 GAGGCCTAACTATGCATATGACAGAAAGGTGTCATTTATGACAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAA-TATGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTC
255339 TTT
65 TTT
* * * *
255342 GAGGCCTAACTGTGTATATCACTGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTC
1 GAGGCCTAA-TATGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTC
255407 TTT
65 TTT
* * * *
255410 GAGGCCTAATAGTGCATATTACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGT-TC
1 GAGGCCTAATA-TGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGT-
255474 CTTT
64 CTTT
* * * * *
255478 GAGGCCTAACTGTGTATATGACAGAAAGATGTCATTTATGACAGTTAGATGAA
1 GAGGCCTAA-TATGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
255531 CAGTAAAGTA
Statistics
Matches: 337, Mismatches: 44, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
63 10 0.03
64 47 0.14
66 1 0.00
67 8 0.02
68 270 0.80
69 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (67 bp):
GAGGCCTAATATGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTCT
TT
Found at i:255438 original size:204 final size:200
Alignment explanation
Indices: 255075--255530 Score: 632
Period size: 204 Copynumber: 2.3 Consensus size: 200
255065 AAAAGATCAA
* * * * *
255075 GAGGCCTAAATGTGCATATGACAG-AAGGTGTCAATTATGCCAGTTAGATAAAAGACTAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGACAGTTAGATGAAAGACTAAGTGCC
* * * *
255139 TTTGAGTCCTGCACATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTTAGTGTCT
66 TTTGAGGCCTGAACATATCACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTCT
* *
255204 TTGAGGCCTAATTACACATATGAGAGAAAGGTGTCAATTATTCTAGTTAGATGAAAGACTAAGTG
131 TTGAGGCCTAATTACACATATGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGACTAAGT-
255269 T-CTTT
195 TCCTTT
* *
255274 GAGGCCTAACTATGCATATGACAGAAAGGTGTCATTTATGACAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGACAGTTAGATGAAAGACTAAGTGCC
*
255339 TTTGAGGCCT-AACTGTGTATATCACTGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAG
66 TTTGAGGCCTGAAC-----ATATCACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAG
** * * *
255403 TGTCTTTGAGGCCTAA-TAGTGCATATTACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGC
126 TGTCTTTGAGGCCTAATTA-CACATATGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGAC
255467 TAAGTTCCTTT
190 TAAGTTCCTTT
* *
255478 GAGGCCTAACTGTGTATATGACAGAAAGATGTCATTTATGACAGTTAGATGAA
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGACAGTTAGATGAA
255531 CAGTAAAGTA
Statistics
Matches: 227, Mismatches: 22, Indels: 11
0.87 0.08 0.04
Matches are distributed among these distances:
199 24 0.11
200 44 0.19
203 3 0.01
204 156 0.69
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (200 bp):
GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGACAGTTAGATGAAAGACTAAGTGCC
TTTGAGGCCTGAACATATCACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTCT
TTGAGGCCTAATTACACATATGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGACTAAGTT
CCTTT
Found at i:255817 original size:80 final size:81
Alignment explanation
Indices: 255499--255826 Score: 442
Period size: 81 Copynumber: 4.1 Consensus size: 81
255489 GTGTATATGA
* * * * *
255499 CAGAAAGATGTCATTTATGACAGTTAGATGAACAGTAAAGTACCGTTGAGTAAAATAAAAATGGC
1 CAGAAAGGTGTCAATTATGACAGTTAGATGAACAGTTAAGTACCATTGAGTAAAAGAAAAATGGC
*
255564 CTAGTTGTGCAATTGG
66 CTAGCTGTGCAATTGG
* * * * * * * *
255580 TAGAAAGGTTTCATTTATGATAGTTAGATTAACGGTTAAGTATCGTTGAGTAAAAGAAAAATGGC
1 CAGAAAGGTGTCAATTATGACAGTTAGATGAACAGTTAAGTACCATTGAGTAAAAGAAAAATGGC
*
255645 CTAGTTGTGCAATTGG
66 CTAGCTGTGCAATTGG
* * * * *
255661 CAGAAATGTGTCAATTATGCCAGTTATATTAACAGTTAAGTACCATTGAGTAAAAGAAAAATGAC
1 CAGAAAGGTGTCAATTATGACAGTTAGATGAACAGTTAAGTACCATTGAGTAAAAGAAAAATGGC
* *
255726 ATAGCTATGCAATTGG
66 CTAGCTGTGCAATTGG
*
255742 CAGAAAGGTGTCAATTATGCCAGTTAGATGAACA-TTAAGTACCATTGAGTAAAAGAAAAATGGC
1 CAGAAAGGTGTCAATTATGACAGTTAGATGAACAGTTAAGTACCATTGAGTAAAAGAAAAATGGC
255806 CTAGCTGTGCAATTGG
66 CTAGCTGTGCAATTGG
255822 CAGAA
1 CAGAA
255827 TAATGTATTG
Statistics
Matches: 218, Mismatches: 29, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
80 48 0.22
81 170 0.78
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (81 bp):
CAGAAAGGTGTCAATTATGACAGTTAGATGAACAGTTAAGTACCATTGAGTAAAAGAAAAATGGC
CTAGCTGTGCAATTGG
Found at i:255971 original size:45 final size:44
Alignment explanation
Indices: 255904--255995 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 44
255894 TTATAAAGGC
* *
255904 AAAGGTAAACATAATATCAAAGGCAGGAAAGGATGCCATAAATG
1 AAAGGTAAACATAATATAAAAGGCAGGAAAGGATGACATAAATG
* * *
255948 AAAGGTAAA-ATAATGTATAAAAGGCATGTAAGGATGACATAATTG
1 AAAGGTAAACATAA--TATAAAAGGCAGGAAAGGATGACATAAATG
255993 AAA
1 AAA
255996 TGCATATAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 4 0.10
44 9 0.22
45 28 0.68
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.20
Consensus pattern (44 bp):
AAAGGTAAACATAATATAAAAGGCAGGAAAGGATGACATAAATG
Found at i:258606 original size:2 final size:2
Alignment explanation
Indices: 258599--258628 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
258589 GGTGCACATA
258599 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
258629 TAAGTATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:267410 original size:25 final size:25
Alignment explanation
Indices: 267366--267439 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 25
267356 GACACCTATG
*
267366 GTGCAATTCTACGAGACACTTTTAA
1 GTGCAATTCTACGAGACACTTTCAA
* * * *
267391 GTGCAATTTTATGAGGCACTTTCGA
1 GTGCAATTCTACGAGACACTTTCAA
** *
267416 GTGCAAACCTACGAGGCACTTTCA
1 GTGCAATTCTACGAGACACTTTCA
267440 CGTGTAAATT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (25 bp):
GTGCAATTCTACGAGACACTTTCAA
Found at i:271526 original size:51 final size:52
Alignment explanation
Indices: 271421--271543 Score: 153
Period size: 51 Copynumber: 2.4 Consensus size: 52
271411 GGTCCATATT
* * *
271421 ATCCATGT-GGGTATCTTGAAGGCTCATATCAGCATGAAAAAGATAGAAGAA
1 ATCCATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAAAA
*
271472 ATCCATGTGGGGTATCTTGAAGGCTCACATCAGCATG-AAATGACA-AAAATA
1 ATCCATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAAA-A
* * *
271523 ATCCATATGGGGCATTTTGAA
1 ATCCATGTGGGGTATCTTGAA
271544 AGTTCATGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
50 3 0.05
51 33 0.52
52 27 0.43
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (52 bp):
ATCCATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAAAA
Found at i:273191 original size:40 final size:40
Alignment explanation
Indices: 273136--273425 Score: 422
Period size: 40 Copynumber: 7.3 Consensus size: 40
273126 GACATTTCAT
273136 TCAAGATT-TTTTTCCTTGAAACAGAAGATTTTATCTCGC
1 TCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGC
*
273175 TCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGA
1 TCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGC
*
273215 TCAATATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGC
1 TCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGC
** * * *
273255 TTGAGATAG-TTTCCCTCGAAACAGAAGATTTTATCTCGC
1 TCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGC
273294 TCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGC
1 TCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGC
* *
273334 TCAAGATTGTTTTTCCTTGAAATATAAGATTTTATCTCGC
1 TCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGC
** * * *
273374 TTGAGATAGTTTTTCCTTGAAATAGAAGATTTTATCTCAC
1 TCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGC
* *
273414 TTAAGATAGTTT
1 TCAAGATTGTTT
273426 CTCACGAAAC
Statistics
Matches: 227, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
39 42 0.19
40 185 0.81
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (40 bp):
TCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGC
Found at i:273203 original size:23 final size:23
Alignment explanation
Indices: 273177--273245 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
273167 TATCTCGCTC
273177 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
* * *
273200 AAGA-T-TTTAT-CTCG-ATC--
1 AAGATTGTTTTTCCTTGAAACAG
*
273217 AATATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
273240 AAGATT
1 AAGATT
273246 TTATCTCGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 3 0.09
18 1 0.03
19 6 0.19
20 6 0.19
21 6 0.19
22 1 0.03
23 9 0.28
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAG
Found at i:273434 original size:159 final size:158
Alignment explanation
Indices: 273136--273436 Score: 485
Period size: 159 Copynumber: 1.9 Consensus size: 158
273126 GACATTTCAT
273136 TCAAGATTTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGA
1 TCAAGATTTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGA
* * * *
273201 AGATTTTATCTCGATCAATATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
66 AGATTTTATCTCGATCAAGATAGTTTTTCCTTGAAACAGAAGATTTTATCTCACTTAAGATAGTT
*
273266 TCCCTCGAAACAGAAGATTTTATCTCGC
131 TCCCACGAAACAGAAGATTTTATCTCGC
* *
273294 TCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAATAT
1 TCAAGATT-TTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAG
* ** *
273359 AAGATTTTATCTCGCTTGAGATAGTTTTTCCTTGAAATAGAAGATTTTATCTCACTTAAGATAGT
65 AAGATTTTATCTCGATCAAGATAGTTTTTCCTTGAAACAGAAGATTTTATCTCACTTAAGATAGT
*
273424 TTCTCACGAAACA
130 TTCCCACGAAACA
273437 AAAAAAAACT
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
158 8 0.06
159 122 0.94
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (158 bp):
TCAAGATTTTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGA
AGATTTTATCTCGATCAAGATAGTTTTTCCTTGAAACAGAAGATTTTATCTCACTTAAGATAGTT
TCCCACGAAACAGAAGATTTTATCTCGC
Found at i:273436 original size:119 final size:119
Alignment explanation
Indices: 273144--273425 Score: 449
Period size: 119 Copynumber: 2.4 Consensus size: 119
273134 ATTCAAGATT
273144 TTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTA
1 TTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCC-TGAAACAGAAGATTTTA
*
273209 TCTCGATCAATATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAG
65 TCTCGATCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAG
* *
273264 -TTTCCCTCGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTA
1 TTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCC-TGAAACAGAAGATTTTA
* * *
273328 TCTCGCTCAAGATTGTTTTTCCTTGAAATATAAGATTTTATCTCGCTTGAGATAG
65 TCTCGATCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAG
* * * *
273383 TTTTTCCTTGAAATAGAAGATTTTATCTCACTTAAGATAGTTT
1 TTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTT
273426 CTCACGAAAC
Statistics
Matches: 149, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
119 113 0.76
120 36 0.24
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (119 bp):
TTTTTCCTTGAAACAGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTGAAACAGAAGATTTTAT
CTCGATCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAG
Found at i:273832 original size:3 final size:3
Alignment explanation
Indices: 273826--273857 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
273816 ATATTATAAA
273826 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
273858 ATTTACATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:278754 original size:42 final size:42
Alignment explanation
Indices: 278695--278892 Score: 202
Period size: 42 Copynumber: 4.7 Consensus size: 42
278685 ATTTACTATA
* * *
278695 GATGTTGCCGATGATCAGGATGTTGTAGTGAAAGTTATTATG
1 GATGTTGTCGATGATCAGGATGTTGTAGCGAAAGTTATTGTG
* *
278737 GATGTTGTCGATGATCA-GATTTCTATAGCGAAAGTTATTGTG
1 GATGTTGTCGATGATCAGGATGT-TGTAGCGAAAGTTATTGTG
* * *
278779 GATGTTATCGATGATCAAGG-TGTTGTAGCGGAAGTTACTGTG
1 GATGTTGTCGATGATC-AGGATGTTGTAGCGAAAGTTATTGTG
* * * * * *
278821 GATGTTGTCGATGATCAGGGTGTTGCAACGGAGGTTACTGTG
1 GATGTTGTCGATGATCAGGATGTTGTAGCGAAAGTTATTGTG
* * * *
278863 GATGTTTTCAATTATCAGGGTGTTGTAGCG
1 GATGTTGTCGATGATCAGGATGTTGTAGCG
278893 GAGGTTACTA
Statistics
Matches: 133, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 7 0.05
42 122 0.92
43 3 0.02
44 1 0.01
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (42 bp):
GATGTTGTCGATGATCAGGATGTTGTAGCGAAAGTTATTGTG
Found at i:278863 original size:84 final size:84
Alignment explanation
Indices: 278703--278906 Score: 227
Period size: 84 Copynumber: 2.4 Consensus size: 84
278693 TAGATGTTGC
* * *
278703 CGATGATC-AGGATGTTGTAGTGAAAGTTATTATGGATGTTGTCGATGATCAGATTTCTATAGCG
1 CGATGATCAAGG-TGTTGTAGCGGAAGTTACTATGGATGTTGTCGATGATCAGATTTCTATAGCG
*
278767 AAAGTTATTGTGGATGTTAT
65 AAAGTTACTGTGGATGTTAT
* *
278787 CGATGATCAAGGTGTTGTAGCGGAAGTTACTGTGGATGTTGTCGATGATCAGGGTGTTGC-A-A-
1 CGATGATCAAGGTGTTGTAGCGGAAGTTACTATGGATGTTGTCGATGATCA-GAT-TT-CTATAG
* * *
278849 CGGAGGTTACTGTGGATGTTTT
63 CGAAAGTTACTGTGGATGTTAT
* * * *
278871 CAATTATCAGGGTGTTGTAGCGGAGGTTACTATGGA
1 CGATGATCAAGGTGTTGTAGCGGAAGTTACTATGGA
278907 CTTTGTAGAT
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
84 92 0.90
85 6 0.06
86 3 0.03
87 1 0.01
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.35
Consensus pattern (84 bp):
CGATGATCAAGGTGTTGTAGCGGAAGTTACTATGGATGTTGTCGATGATCAGATTTCTATAGCGA
AAGTTACTGTGGATGTTAT
Found at i:279462 original size:51 final size:52
Alignment explanation
Indices: 279352--279480 Score: 165
Period size: 51 Copynumber: 2.5 Consensus size: 52
279342 AAAATGTATT
*
279352 ACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAAGATTAGCACTTA
1 ACACATACTTACACCGATGTAAGTGAATAAAATAAAAAAAGATTAGCACTTA
** *
279404 ACACATACTTACATTGATGTAAGTGAATGAAAT-AAAAAAG-TGT-GTCACTTA
1 ACACATACTTACACCGATGTAAGTGAATAAAATAAAAAAAGAT-TAG-CACTTA
* *
279455 ATACATACTTACACCAATGTAAGTGA
1 ACACATACTTACACCGATGTAAGTGA
279481 TGTTATGTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
50 2 0.03
51 36 0.54
52 29 0.43
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (52 bp):
ACACATACTTACACCGATGTAAGTGAATAAAATAAAAAAAGATTAGCACTTA
Found at i:281955 original size:21 final size:22
Alignment explanation
Indices: 281929--281971 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
281919 CCAGGACAGG
*
281929 GAGTATCGGTAC-TCTTTTAAT
1 GAGTATCGGTACTTCCTTTAAT
281950 GAGTATCGGTACTTCCTTTAAT
1 GAGTATCGGTACTTCCTTTAAT
281972 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (22 bp):
GAGTATCGGTACTTCCTTTAAT
Found at i:284105 original size:13 final size:13
Alignment explanation
Indices: 284087--284111 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
284077 CTTCTTCTTG
284087 TTTTTTTTCTTCA
1 TTTTTTTTCTTCA
284100 TTTTTTTTCTTC
1 TTTTTTTTCTTC
284112 CTTCACCATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTTCTTCA
Found at i:286437 original size:22 final size:23
Alignment explanation
Indices: 286412--286470 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 23
286402 AAAACCATAA
**
286412 ATATAAATTGTAAATATAAAA-G
1 ATATAAATACTAAATATAAAATG
*
286434 ATATGAATACTAAATATAAAATG
1 ATATAAATACTAAATATAAAATG
286457 ATATAAATACTAAA
1 ATATAAATACTAAA
286471 ATTACTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (23 bp):
ATATAAATACTAAATATAAAATG
Found at i:286638 original size:17 final size:16
Alignment explanation
Indices: 286599--286659 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
286589 AAATTATAAA
286599 AATATGAATATGTATAT
1 AATAT-AATATGTATAT
*
286616 GTATATAATATAGTATAT
1 -AATATAATAT-GTATAT
* *
286634 AATATGATATGATACAT
1 AATATAATATG-TATAT
286651 AATA-AATAT
1 AATATAATAT
286660 AATAATATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
16 5 0.14
17 21 0.58
18 10 0.28
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (16 bp):
AATATAATATGTATAT
Found at i:286638 original size:29 final size:28
Alignment explanation
Indices: 286594--286667 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
286584 AATACAAATT
* *
286594 ATAAAAATATGAATATGTATATG-TATATA
1 ATAAATATAT-AATATG-ATATGATACATA
*
286623 ATATAGTATATAATATGATATGATACATA
1 ATA-AATATATAATATGATATGATACATA
286652 ATAAATATAATAATAT
1 ATAAATAT-ATAATAT
286668 AAAAATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 9 0.24
29 24 0.63
30 5 0.13
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (28 bp):
ATAAATATATAATATGATATGATACATA
Found at i:286765 original size:2 final size:2
Alignment explanation
Indices: 286758--286787 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
286748 ATGTAAAGAT
286758 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
286788 ATAAAACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:286983 original size:17 final size:17
Alignment explanation
Indices: 286947--286980 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
286937 AACAAAACAC
*
286947 AAAAATAAAGATAAATT
1 AAAAATAAAAATAAATT
286964 AAAAATAAAAATGAAAT
1 AAAAATAAAAAT-AAAT
286981 AAATAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAAATAAAAATAAATT
Found at i:296613 original size:18 final size:18
Alignment explanation
Indices: 296587--296663 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
296577 CCGGGTCACA
296587 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
296605 ACCCAACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
296622 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
296636 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
296654 ACCCGACCCG
1 ACCCGACCCG
296664 TTGACTGTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
13 12 0.24
18 39 0.76
ACGTcount: A:0.18, C:0.51, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:296626 original size:13 final size:13
Alignment explanation
Indices: 296610--296668 Score: 64
Period size: 13 Copynumber: 4.2 Consensus size: 13
296600 CGTTGACCCA
*
296610 ACCCGACCCGTTT
1 ACCCGACCCGTTG
296623 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTT-----G
296641 ACCCGACCCGTTG
1 ACCCGACCCGTTG
296654 ACCCGACCCGTTG
1 ACCCGACCCGTTG
296667 AC
1 AC
296669 TGTTGATCCG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 28 0.70
18 12 0.30
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.15
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:296628 original size:31 final size:31
Alignment explanation
Indices: 296591--296668 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
296581 GTCACAACCC
296591 GACCCGACCCGTTGACCCAACCCGACCCGTT
1 GACCCGACCCGTTGACCCAACCCGACCCGTT
* *
296622 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCAACCCGACCCGTT
296653 GACCCGACCCGTTGAC
1 GACCCGACCCGTTGAC
296669 TGTTGATCCG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCAACCCGACCCGTT
Found at i:299146 original size:48 final size:48
Alignment explanation
Indices: 299094--299225 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
299084 AATATTTTAC
*
299094 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
299142 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
299190 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
299226 CTGATTTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:299232 original size:24 final size:24
Alignment explanation
Indices: 299111--299225 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
299101 TCGATTTGAT
299111 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
299135 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
299159 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
299183 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
299206 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
299226 CTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:299248 original size:24 final size:24
Alignment explanation
Indices: 299162--299235 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
299152 ACATGGATTC
* * *
299162 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
299186 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
299210 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
299234 TG
1 TG
299236 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:301425 original size:18 final size:18
Alignment explanation
Indices: 301399--301475 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
301389 ACCGGTCACA
301399 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
301417 ACCCAACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
301434 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
301448 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
301466 ACCCGACCCG
1 ACCCGACCCG
301476 TTGACTGTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
13 12 0.24
18 39 0.76
ACGTcount: A:0.18, C:0.51, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:301438 original size:13 final size:13
Alignment explanation
Indices: 301422--301480 Score: 64
Period size: 13 Copynumber: 4.2 Consensus size: 13
301412 CGTTGACCCA
*
301422 ACCCGACCCGTTT
1 ACCCGACCCGTTG
301435 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTT-----G
301453 ACCCGACCCGTTG
1 ACCCGACCCGTTG
301466 ACCCGACCCGTTG
1 ACCCGACCCGTTG
301479 AC
1 AC
301481 TGTTGACCCG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 28 0.70
18 12 0.30
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.15
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:301442 original size:31 final size:31
Alignment explanation
Indices: 301403--301480 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
301393 GTCACAACCC
301403 GACCCGACCCGTTGACCCAACCCGACCCGTT
1 GACCCGACCCGTTGACCCAACCCGACCCGTT
* *
301434 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCAACCCGACCCGTT
301465 GACCCGACCCGTTGAC
1 GACCCGACCCGTTGAC
301481 TGTTGACCCG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCAACCCGACCCGTT
Found at i:301468 original size:8 final size:8
Alignment explanation
Indices: 301457--301503 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
301447 GACCCGACCC
301457 GACCCGTT
1 GACCCGTT
301465 GACCC---
1 GACCCGTT
301470 GACCCGTT
1 GACCCGTT
*
301478 GA-CTGTT
1 GACCCGTT
301485 GACCCGTT
1 GACCCGTT
301493 GA-CCGTT
1 GACCCGTT
301500 GACC
1 GACC
301504 GGAGTTGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
5 5 0.16
7 13 0.41
8 14 0.44
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:301490 original size:15 final size:15
Alignment explanation
Indices: 301457--301503 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
301447 GACCCGACCC
*
301457 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
*
301470 GACCCGTTGACTGTT
1 GACCCGTTGACCGTT
301485 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
301500 GACC
1 GACC
301504 GGAGTTGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.38
15 18 0.62
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:303954 original size:48 final size:48
Alignment explanation
Indices: 303902--304033 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
303892 AATATTTTAC
*
303902 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
303950 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
303998 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
304034 CTGATTTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:304040 original size:24 final size:24
Alignment explanation
Indices: 303919--304033 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
303909 TCGATTTGAT
303919 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
303943 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
303967 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
303991 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
304014 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
304034 CTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:304056 original size:24 final size:24
Alignment explanation
Indices: 303970--304043 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
303960 ACATGGATTC
* * *
303970 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
303994 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
304018 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
304042 TG
1 TG
304044 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:305527 original size:14 final size:14
Alignment explanation
Indices: 305508--305579 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
305498 GTGAAATTAT
305508 AATTATTTAAATAA
1 AATTATTTAAATAA
*
305522 AATTATTTATATAA
1 AATTATTTAAATAA
*
305536 AA--ATTCATAGATAA
1 AATTATT--TAAATAA
*
305550 TA-TATTTAAATAA
1 AATTATTTAAATAA
*
305563 AACTTATTTATATAA
1 AA-TTATTTAAATAA
305578 AA
1 AA
305580 ATTTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
12 3 0.06
13 7 0.15
14 22 0.47
15 15 0.32
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (14 bp):
AATTATTTAAATAA
Found at i:305578 original size:42 final size:41
Alignment explanation
Indices: 305506--305597 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 41
305496 AAGTGAAATT
305506 ATAAT-TATTTAAATAAAATTATTTATATAAAAATTCATAG
1 ATAATATATTTAAATAAAATTATTTATATAAAAATTCATAG
* *
305546 ATAATATATTTAAATAAAACTTATTTATATAAAAATTTATCG
1 ATAATATATTTAAATAAAA-TTATTTATATAAAAATTCATAG
305588 ATAATATATT
1 ATAATATATT
305598 ATTTTATTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 5 0.10
41 13 0.27
42 30 0.62
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (41 bp):
ATAATATATTTAAATAAAATTATTTATATAAAAATTCATAG
Found at i:310986 original size:13 final size:13
Alignment explanation
Indices: 310968--311004 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
310958 CCCCTATTCC
*
310968 TTAATTAAACTAA
1 TTAATTAAACCAA
310981 TTAATTAAACCAA
1 TTAATTAAACCAA
310994 TTAATTAAACC
1 TTAATTAAACC
311005 TGATGCAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (13 bp):
TTAATTAAACCAA
Found at i:314347 original size:46 final size:45
Alignment explanation
Indices: 314277--314363 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
314267 CATTTGACTC
* * *
314277 TTCTTCTTTTCTTCTAAACCGTTAGTGGTTTGCTGCTAAGCTATA
1 TTCTTCTCTTCTTCCAAACCGTTAGTGGTTTGCTCCTAAGCTATA
*
314322 TTCTTCATCTTCTTCCAAACTGTTAGTGGTTTGCTCCTAAGC
1 TTCTTC-TCTTCTTCCAAACCGTTAGTGGTTTGCTCCTAAGC
314364 ATAGCTCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 6 0.16
46 31 0.84
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (45 bp):
TTCTTCTCTTCTTCCAAACCGTTAGTGGTTTGCTCCTAAGCTATA
Found at i:315256 original size:32 final size:31
Alignment explanation
Indices: 315213--315317 Score: 92
Period size: 32 Copynumber: 3.4 Consensus size: 31
315203 GGCCTGGAAA
315213 GCCTA-CCAAGAAAGTTGCTCGGGGCCAAGGG
1 GCCTACCCAAGAAAGTT-CTCGGGGCCAAGGG
* *
315244 GCCTACCCAAGAAGGATCTCGAGGGCCCCAA--G
1 GCCTACCCAAGAAAGTTCTCG-GGG--CCAAGGG
** *
315276 GCCTACCCAAGAAA-TATCTCGGGGCCTCGGA
1 GCCTACCCAAGAAAGT-TCTCGGGGCCAAGGG
315307 GCCTACCCAAG
1 GCCTACCCAAG
315318 GGTCGCCTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
29 2 0.03
31 23 0.38
32 31 0.52
34 4 0.07
ACGTcount: A:0.27, C:0.32, G:0.29, T:0.12
Consensus pattern (31 bp):
GCCTACCCAAGAAAGTTCTCGGGGCCAAGGG
Found at i:324627 original size:198 final size:199
Alignment explanation
Indices: 324178--324770 Score: 873
Period size: 198 Copynumber: 2.9 Consensus size: 199
324168 AATAAAAACG
* * *
324178 AAGATATTCATGAACAGGCCAAGCCATTTTCAGATTCCATACAACAGAAAACAAGCCTTGAAACA
1 AAGATATTCATGAACAGGCCAAGCCATTTTCAGATTCCATACAACTGAAAACAAGGCTTGAAGCA
* *
324243 AGATGCTGTGATTCACCAAAAATCGCAAAGCCAAGGACACCCTTGAAGGGTAAATCGAAGAATGA
66 AGATGCTGTGAATCACCAAAAATTGCAAAGCCAAGGACACCCTTGAAGGGTAAATCGAAG-A-GA
* * *
324308 GTTGTCCGTAAAGAAAGGGTCCAACAGCCGGCAACATCTCTTCCTTGGCTCACAAGAAACTGTAA
129 --TG-CCGTAAAGCAAGGGTCCAACAGCCAGCAAAATCTCTTCCTTGGCTCACAAGAAACTGTAA
*
324373 CTCAAAATG
191 CTCAAAATA
*
324382 AAGATATTCATGAACAGGCCAAACCATTTTCAGATTCCATACAACTGAAAACAAGGCTTGAAGCA
1 AAGATATTCATGAACAGGCCAAGCCATTTTCAGATTCCATACAACTGAAAACAAGGCTTGAAGCA
*
324447 AGATGCTGTGAATCACCAAAAATTGCAAAGCCAAGGACACGCTTGAAGGGTAAATCGAAGA-ATG
66 AGATGCTGTGAATCACCAAAAATTGCAAAGCCAAGGACACCCTTGAAGGGTAAATCGAAGAGATG
* *
324511 CCGTAAAGCAAGGGTCCAACAGCCAGCAAAATCTCTTCCTTGTCTCACAAGAAACTGTAACTCGA
131 CCGTAAAGCAAGGGTCCAACAGCCAGCAAAATCTCTTCCTTGGCTCACAAGAAACTGTAACTCAA
324576 AATA
196 AATA
* * *
324580 AAGATATTCATGAACAGGCCAAGCCATTTTCAGATTCCGTGCAACTGAAAACAAGGCTTGAAGCG
1 AAGATATTCATGAACAGGCCAAGCCATTTTCAGATTCCATACAACTGAAAACAAGGCTTGAAGCA
* * * *
324645 AGATGCTGTGAATCATCAAAAATTGCAAAGCCAAGTACACCCTTGAAGCGTCAATCGAAAATGAG
66 AGATGCTGTGAATCACCAAAAATTGCAAAGCCAAGGACACCCTTGAAGGGTAAATCG--AA-GAG
* * * * *
324710 GTGGCCATAAAGCAGGGGTCCAACAGCCAACAATATCTCTTCCTTGGCTCACAAGAAACTG
128 AT-GCCGTAAAGCAAGGGTCCAACAGCCAGCAAAATCTCTTCCTTGGCTCACAAGAAACTG
324771 CAGAAACCGT
Statistics
Matches: 356, Mismatches: 28, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
198 176 0.49
199 2 0.01
200 2 0.01
201 3 0.01
202 1 0.00
203 54 0.15
204 118 0.33
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (199 bp):
AAGATATTCATGAACAGGCCAAGCCATTTTCAGATTCCATACAACTGAAAACAAGGCTTGAAGCA
AGATGCTGTGAATCACCAAAAATTGCAAAGCCAAGGACACCCTTGAAGGGTAAATCGAAGAGATG
CCGTAAAGCAAGGGTCCAACAGCCAGCAAAATCTCTTCCTTGGCTCACAAGAAACTGTAACTCAA
AATA
Found at i:325014 original size:78 final size:77
Alignment explanation
Indices: 324885--325228 Score: 463
Period size: 78 Copynumber: 4.4 Consensus size: 77
324875 AATTTTAGCA
** *
324885 TAGAGAACAAGATAGGTGAAGAAGAGGGCGATGATCATCATCAGCATCTCGGGCTAGAGTCTCAG
1 TAGAGAATGAGATTGGTGAAGAAGAGGGCGATGATCATCATCAGCATCTCGGGCTAGAGTCTCAG
* **
324950 TTTCAGGATAATG
66 TCTCA-GATACCG
* * * *
324963 TAGAGAATGAGATTAGTGAAGAAGAGGGCAATGGTCTTCATCAGCATCTCGGGCTAGAGTCTCAG
1 TAGAGAATGAGATTGGTGAAGAAGAGGGCGATGATCATCATCAGCATCTCGGGCTAGAGTCTCAG
325028 TCTCATGATACCG
66 TCTCA-GATACCG
* * * *
325041 TAGAGAATGAGATTGATGAAGAAGAGGGTGATGATCATCATCAGCATCTCGGGCTATATTCTCAG
1 TAGAGAATGAGATTGGTGAAGAAGAGGGCGATGATCATCATCAGCATCTCGGGCTAGAGTCTCAG
* *
325106 TCTCAAATACCA
66 TCTCAGATACCG
* * * *
325118 TAGAGAATGAGATTGGTGAAGAAGAAGGTGATGATCATCATCAGCATCTCAGGCTAGACTCTCAG
1 TAGAGAATGAGATTGGTGAAGAAGAGGGCGATGATCATCATCAGCATCTCGGGCTAGAGTCTCAG
* *
325183 TCTCAAGTTACTG
66 TCTC-AGATACCG
325196 TAGAGAATGAGATTGGTGAAGAAGAGGGCGATG
1 TAGAGAATGAGATTGGTGAAGAAGAGGGCGATG
325229 CGGCAGCATC
Statistics
Matches: 233, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
77 69 0.30
78 164 0.70
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (77 bp):
TAGAGAATGAGATTGGTGAAGAAGAGGGCGATGATCATCATCAGCATCTCGGGCTAGAGTCTCAG
TCTCAGATACCG
Found at i:325185 original size:155 final size:156
Alignment explanation
Indices: 324901--325228 Score: 469
Period size: 155 Copynumber: 2.1 Consensus size: 156
324891 ACAAGATAGG
* * **
324901 TGAAGAAGAGGGCGATGATCATCATCAGCATCTCGGGCTAGAGTCTCAGTTTCAGGATAATGTAG
1 TGAAGAAGAGGGCGATGATCATCATCAGCATCTCGGGCTAGAGTCTCAGTCTCAGAATAACATAG
* * * * *
324966 AGAATGAGATTAGTGAAGAAGAGGGCAATGGTCTTCATCAGCATCTCGGGCTAGAGTCTCAGTCT
66 AGAATGAGATTAGTGAAGAAGAAGGCAATGATCATCATCAGCATCTCAGGCTAGACTCTCAGTCT
*
325031 CATGATACCGTAGAGAATGAGATTGA
131 CAAGATACCGTAGAGAATGAGATTGA
* * * *
325057 TGAAGAAGAGGGTGATGATCATCATCAGCATCTCGGGCTATATTCTCAGTCTCA-AATACCATAG
1 TGAAGAAGAGGGCGATGATCATCATCAGCATCTCGGGCTAGAGTCTCAGTCTCAGAATAACATAG
* **
325121 AGAATGAGATTGGTGAAGAAGAAGGTGATGATCATCATCAGCATCTCAGGCTAGACTCTCAGTCT
66 AGAATGAGATTAGTGAAGAAGAAGGCAATGATCATCATCAGCATCTCAGGCTAGACTCTCAGTCT
* * *
325186 CAAGTTACTGTAGAGAATGAGATTGG
131 CAAGATACCGTAGAGAATGAGATTGA
325212 TGAAGAAGAGGGCGATG
1 TGAAGAAGAGGGCGATG
325229 CGGCAGCATC
Statistics
Matches: 151, Mismatches: 21, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
155 101 0.67
156 50 0.33
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (156 bp):
TGAAGAAGAGGGCGATGATCATCATCAGCATCTCGGGCTAGAGTCTCAGTCTCAGAATAACATAG
AGAATGAGATTAGTGAAGAAGAAGGCAATGATCATCATCAGCATCTCAGGCTAGACTCTCAGTCT
CAAGATACCGTAGAGAATGAGATTGA
Found at i:326198 original size:153 final size:153
Alignment explanation
Indices: 325920--326225 Score: 497
Period size: 153 Copynumber: 2.0 Consensus size: 153
325910 CGAACAAGAA
* * * *
325920 GAAGAAGACGAAGACGAAGAAGAAAGGATCTTAAGCAGCCATGAATGTCAGCAAGAGGTTGAGGG
1 GAAGAAGAAGAAAAAGAAAAAGAAAGGATCTTAAGCAGCCATGAATGTCAGCAAGAGGTTGAGGG
* * *
325985 TAAGGAAGAAACTATCCAACCCATGTGTTGCCTCCATACAAATTTGCATCCAGAAGGTGATCAGG
66 TAAGGAAGAAACCATCCAACCCATGTGTTGCCACCAGACAAATTTGCATCCAGAAGGTGATCAGG
326050 GTGAAGAAGAACAAGAAGATGAC
131 GTGAAGAAGAACAAGAAGATGAC
*
326073 GAAGAAGAAGAAAAAGAAAAAGAAAGGAGT-TTAAGCAGCCATGAATGTCAGCAAGAGTTTGAGG
1 GAAGAAGAAGAAAAAGAAAAAGAAAGGA-TCTTAAGCAGCCATGAATGTCAGCAAGAGGTTGAGG
* * *
326137 GTAAGGAAGAAACCCTCCAACCGATGTGTTGCCAGCAGACAAATTTGCATCCAGAAGGTGATCAG
65 GTAAGGAAGAAACCATCCAACCCATGTGTTGCCACCAGACAAATTTGCATCCAGAAGGTGATCAG
326202 GGTGAAGAAGAACAAGAAGATGAC
130 GGTGAAGAAGAACAAGAAGATGAC
326226 CGCGACGAAT
Statistics
Matches: 141, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
153 140 0.99
154 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.28, T:0.16
Consensus pattern (153 bp):
GAAGAAGAAGAAAAAGAAAAAGAAAGGATCTTAAGCAGCCATGAATGTCAGCAAGAGGTTGAGGG
TAAGGAAGAAACCATCCAACCCATGTGTTGCCACCAGACAAATTTGCATCCAGAAGGTGATCAGG
GTGAAGAAGAACAAGAAGATGAC
Found at i:326249 original size:153 final size:154
Alignment explanation
Indices: 325917--326278 Score: 496
Period size: 153 Copynumber: 2.3 Consensus size: 154
325907 TGACGAACAA
**
325917 GAAGAAGAAGACGAAGACGAAGAAGAAAGGA-TCTTAAGCAGCCATGAATGTCAGCAAGAGGTTG
1 GAAGAAGAAGAAAAAGA--AAGAAGAAAGGAGT-TTAAGCAGCCATGAATGTCAGCAAGAGGTTG
* * *
325981 AGGGTAAGGAAGAAACTATCCAACCCATGTGTTGCCTCCATACAAATTTGCATCCAGAAGGTGAT
63 AGGGTAAGGAAGAAACCATCCAACCCATGTGTTGCCACCAGACAAATTTGCATCCAGAAGGTGAT
326046 CAGGGTGAAGAAGAACAAGAAGATGAC
128 CAGGGTGAAGAAGAACAAGAAGATGAC
*
326073 GAAGAAGAAGAAAAAGAAA-AAGAAAGGAGTTTAAGCAGCCATGAATGTCAGCAAGAGTTTGAGG
1 GAAGAAGAAGAAAAAGAAAGAAGAAAGGAGTTTAAGCAGCCATGAATGTCAGCAAGAGGTTGAGG
* * *
326137 GTAAGGAAGAAACCCTCCAACCGATGTGTTGCCAGCAGACAAATTTGCATCCAGAAGGTGATCAG
66 GTAAGGAAGAAACCATCCAACCCATGTGTTGCCACCAGACAAATTTGCATCCAGAAGGTGATCAG
326202 GGTGAAGAAGAACAAGAAGATGACC
131 GGTGAAGAAGAACAAGAAGATGA-C
* * * *** * *
326227 G-CGACGAATACGGAGATGAAGAAGAAAGGAGCTTAAGCACCCATGAATGTCA
1 GAAGAAGAAGAAAAAGA--AAGAAGAAAGGAGTTTAAGCAGCCATGAATGTCA
326279 TGAAGCCAAT
Statistics
Matches: 184, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
153 133 0.72
154 5 0.03
155 2 0.01
156 44 0.24
ACGTcount: A:0.41, C:0.16, G:0.28, T:0.15
Consensus pattern (154 bp):
GAAGAAGAAGAAAAAGAAAGAAGAAAGGAGTTTAAGCAGCCATGAATGTCAGCAAGAGGTTGAGG
GTAAGGAAGAAACCATCCAACCCATGTGTTGCCACCAGACAAATTTGCATCCAGAAGGTGATCAG
GGTGAAGAAGAACAAGAAGATGAC
Found at i:332617 original size:27 final size:27
Alignment explanation
Indices: 332559--332618 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
332549 ATACCTTTTT
332559 AATATTTTAATTAAAAATACTAATAAA
1 AATATTTTAATTAAAAATACTAATAAA
* * *
332586 TATATTTTAATTTAAAATATTCAA-AAA
1 AATATTTTAATTAAAAATACT-AATAAA
332613 AATATT
1 AATATT
332619 GATTTCCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (27 bp):
AATATTTTAATTAAAAATACTAATAAA
Found at i:339956 original size:12 final size:12
Alignment explanation
Indices: 339939--339971 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
339929 TGATAGTGGA
339939 AAAGGTGATCCT
1 AAAGGTGATCCT
*
339951 AAAGGTGATTCT
1 AAAGGTGATCCT
339963 AAAGGTGAT
1 AAAGGTGAT
339972 AAAAAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.27
Consensus pattern (12 bp):
AAAGGTGATCCT
Found at i:340152 original size:33 final size:33
Alignment explanation
Indices: 340110--340172 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
340100 TTTTTGTCTT
*
340110 CTTGTGGTGGCTTCCATGTCTTGTACTTTTCTC
1 CTTGTGGTGGCTTCCACGTCTTGTACTTTTCTC
340143 CTTGTGGTGGCTTCCACGTCTTGTACTTTT
1 CTTGTGGTGGCTTCCACGTCTTGTACTTTT
340173 ATTTATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.06, C:0.24, G:0.22, T:0.48
Consensus pattern (33 bp):
CTTGTGGTGGCTTCCACGTCTTGTACTTTTCTC
Found at i:346254 original size:24 final size:24
Alignment explanation
Indices: 346218--346264 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
346208 AACTGGCACA
* * *
346218 TAGAATTTGCACCGAAGTGCCACG
1 TAGAATATACACCAAAGTGCCACG
346242 TAGAATATACACCAAAGTGCCAC
1 TAGAATATACACCAAAGTGCCAC
346265 AAATATTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (24 bp):
TAGAATATACACCAAAGTGCCACG
Found at i:346297 original size:23 final size:23
Alignment explanation
Indices: 346271--346339 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
346261 CCACAAATAT
*
346271 TTGTCCCAAAGGACCACGTAGAA
1 TTGTCCCGAAGGACCACGTAGAA
* *
346294 TTGTCCCGAAGAACCACATAGAA
1 TTGTCCCGAAGGACCACGTAGAA
*
346317 TTGTCCCGAAGGACCGCGTAGAA
1 TTGTCCCGAAGGACCACGTAGAA
346340 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.17
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACGTAGAA
Found at i:365655 original size:25 final size:25
Alignment explanation
Indices: 365619--365739 Score: 81
Period size: 25 Copynumber: 5.0 Consensus size: 25
365609 GAGTCGAGGG
*
365619 TTCTACGCGGTCATTTGGGACAAAT
1 TTCTACGTGGTCATTTGGGACAAAT
* *
365644 TTCTACGTGGTCTTTTGGGATAAA-
1 TTCTACGTGGTCATTTGGGACAAAT
** * * ** *
365668 -AATATGTGGTCCTTCAGGAC-TA-
1 TTCTACGTGGTCATTTGGGACAAAT
* *
365690 TTCTACGTGGTCATTCGAGACAAAT
1 TTCTACGTGGTCATTTGGGACAAAT
*
365715 TTCTACGTGGTTC-TTTGAGACAAAT
1 TTCTACGTGG-TCATTTGGGACAAAT
365740 CTACATGGCA
Statistics
Matches: 73, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
22 1 0.01
23 27 0.37
24 1 0.01
25 42 0.58
26 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (25 bp):
TTCTACGTGGTCATTTGGGACAAAT
Found at i:371248 original size:138 final size:137
Alignment explanation
Indices: 371000--371282 Score: 352
Period size: 138 Copynumber: 2.1 Consensus size: 137
370990 CACTGAAGTG
* * * *
371000 TCGAAATGGAAATTCACAAACTTATTATCAATTCCATGGATGCACACATAGTGCCAAAAGTACAC
1 TCGAAATGGAAATTCACAAACTCAATATCAATACCATGGATGCACACATAGTACCAAAAGTACAC
* ***
371065 ACAATACTGAAACGAAAATGCACCATTATGCATTAAACAAAATCGATCGATAACTTTTATATACA
66 ACAATACTGAAACAAAAATGCACCATTATGCATTAAACAAAATCGATCGATAACCAATATATACA
371130 TATGTATA
131 -ATGTATA
** * ** *
371138 TCGAAATGGTGATTCACAAACTCAATATGAATACCAT-GATTGCACATTTAGTACCGAAAGTACA
1 TCGAAATGGAAATTCACAAACTCAATATCAATACCATGGA-TGCACACATAGTACCAAAAGTACA
* * * ***
371202 CATAGTACTGATACAAAAATGCATTGTTATGCATTAAACAAAATCGATCGATAACCAATATATAC
65 CACAATACTGAAACAAAAATGCACCATTATGCATTAAACAAAATCGATCGATAACCAATATATAC
*
371267 AATGTATG
130 AATGTATA
371275 TCGAAATG
1 TCGAAATG
371283 CACCAATTAC
Statistics
Matches: 123, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
137 16 0.13
138 107 0.87
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (137 bp):
TCGAAATGGAAATTCACAAACTCAATATCAATACCATGGATGCACACATAGTACCAAAAGTACAC
ACAATACTGAAACAAAAATGCACCATTATGCATTAAACAAAATCGATCGATAACCAATATATACA
ATGTATA
Found at i:378882 original size:22 final size:22
Alignment explanation
Indices: 378852--378916 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
378842 GTATCGGTAC
* *
378852 CTATCCTATGGTATCTATACTT
1 CTATACTATGGTATCGATACTT
378874 CTATACTATGGTATCGATACTT
1 CTATACTATGGTATCGATACTT
378896 CTATACTATGGTATCGATACT
1 CTATACTATGGTATCGATACT
378917 CCCTTCATCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (22 bp):
CTATACTATGGTATCGATACTT
Found at i:381017 original size:23 final size:25
Alignment explanation
Indices: 380991--381048 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
380981 ACAAAACTAT
380991 GTGGTCCTTC-GG-AATAATTATAC
1 GTGGTCCTTCGGGAAATAATTATAC
* * *
381014 GTGGTCCTTCGGGAAATATTTCTGC
1 GTGGTCCTTCGGGAAATAATTATAC
381039 GTGGTCCTTC
1 GTGGTCCTTC
381049 AGGACAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 10 0.33
24 2 0.07
25 18 0.60
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (25 bp):
GTGGTCCTTCGGGAAATAATTATAC
Found at i:381072 original size:71 final size:71
Alignment explanation
Indices: 380940--381073 Score: 173
Period size: 71 Copynumber: 1.9 Consensus size: 71
380930 TCGAGGATTC
* * **
380940 TACGTGGTCCTTCGGGACAAATTTCTAATTGGTCCTTCAGTACAAAACTATGTGGTCCTTCGGAA
1 TACGTGGTCCTTCGGGACAAATTTCTAAGTGGTCCTTCAGGACAAAACTACATGGTCCTTCGGAA
381005 TAATTA
66 TAATTA
** *
381011 TACGTGGTCCTTCGGGA-AATATTTCTGCGTGGTCCTTCAGGACAAATCTACATGG-CACTTCGG
1 TACGTGGTCCTTCGGGACAA-ATTTCTAAGTGGTCCTTCAGGACAAAACTACATGGTC-CTTCGG
381074 TACAAATTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
70 3 0.06
71 51 0.94
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (71 bp):
TACGTGGTCCTTCGGGACAAATTTCTAAGTGGTCCTTCAGGACAAAACTACATGGTCCTTCGGAA
TAATTA
Found at i:382837 original size:23 final size:23
Alignment explanation
Indices: 382789--382839 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
382779 AAGGACTGTG
* *
382789 TAGAATTGTTCCGAAGGACCATA
1 TAGAATTGTCCCGAAGGACCACA
*
382812 TAGAATTGTCCCGAAGGACCGCA
1 TAGAATTGTCCCGAAGGACCACA
382835 TAGAA
1 TAGAA
382840 CCCTCGACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCACA
Found at i:397329 original size:239 final size:237
Alignment explanation
Indices: 396879--397397 Score: 704
Period size: 239 Copynumber: 2.2 Consensus size: 237
396869 TTAAGTGATA
* *
396879 TTAAAAAAATGAGAAAGAC-ATTTCCAAAGTTTCCCATTTAGTATTTTAGAAAATGAAATTTTTG
1 TTAAAAAAATGAGAAAG-CGATTTCCAAAGTTTCTCATTTAGTATTTTAGAAAATGAAATTTTTA
* *
396943 AAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGGCCTTCGGGCCATTAGTAAGTTAT
65 AAAAGTAAGAAAACGATTTCCAAAGTTTATTACTTAGTAAGGCCTTCGGGCCATCAGTAAGTTAT
* * ** * *
397008 TCTAGCACGATGATTAAATCATTCGGGTCATATGTAAGTCTTTCGAGCAAGATGATGAGTTCTTC
130 TCGAGCAAGAAAATTAAATCATTCGGGTCATATGTAAGGCTTTCGAGCAAGATGATAAGTTCTTC
* ** *
397073 GTGCCAACCACAAGACCTTCGGGCAGGATGTTTTCAGGTGATT
195 GGGCCAACCACAAGACCTTCGGGCAGGATGTTTTCACATGAAT
**
397116 TTCAAAATGATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAATTTTT
1 TT-AAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTA-TTTTAGAAAATGAAATTTTT
* *
397181 AAAAAGTAAGAAAGCGATTTCCAAAGTTTATTACTTAGTAAGTCCTTCGGGCCATCAGTAAGTCT
64 AAAAAGTAAGAAAACGATTTCCAAAGTTTATTACTTAGTAAGGCCTTCGGGCCATCAGTAAGT-T
* *
397246 -TTCGAGCAAGAAAATTAAATTC-TTCGGGTCATCTGTTAGGCTTTCGAGCAAGATGATAAG-TC
128 ATTCGAGCAAGAAAATTAAA-TCATTCGGGTCATATGTAAGGCTTTCGAGCAAGATGATAAGTTC
* ** *
397308 TTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAAT
192 -TTCGGGCCAACCACAAGACCTTCGGGCAGGATGTTTTCACATGAAT
* * * *
397355 TTAAAAAAATGAGAAAGTGATTTTCAAAGTTTCTTACTTAGTA
1 TTAAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTA
397398 AGTCCTTCAG
Statistics
Matches: 246, Mismatches: 30, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
237 3 0.01
238 73 0.30
239 167 0.68
240 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (237 bp):
TTAAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTAGAAAATGAAATTTTTAA
AAAGTAAGAAAACGATTTCCAAAGTTTATTACTTAGTAAGGCCTTCGGGCCATCAGTAAGTTATT
CGAGCAAGAAAATTAAATCATTCGGGTCATATGTAAGGCTTTCGAGCAAGATGATAAGTTCTTCG
GGCCAACCACAAGACCTTCGGGCAGGATGTTTTCACATGAAT
Found at i:397546 original size:177 final size:177
Alignment explanation
Indices: 397181--397565 Score: 506
Period size: 177 Copynumber: 2.2 Consensus size: 177
397171 TGAAATTTTT
* * * * *
397181 AAAAAG-TAAGAAAGCGATTTCCAAAGTTTATTACTTAGTAAGTCCTTCGGGCCATCAGTAAGTC
1 AAAAAGATGAGAAAGTGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAATAAGTC
* ** *
397245 TTTCGAGCAAGAAAATTAAATTCTTCGGGTCATCTGTTAGGCTTTCGAGCAAGATGATAAGTCTT
66 TTTCGAGCAAGAAAATTAAATCCTTCAAGTCATCTGTAAGGCTTTCGAGCAAGATGATAAGTCTT
* * * * *
397310 TCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATTT
131 TCGGGACATCCATAAGACCTTCGGGTAAGATGTTCTCACATGAATTC
* * *
397357 AAAAAAATGAGAAAGTGATTTTCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATTAATAAGTC
1 AAAAAGATGAGAAAGTGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAATAAGTC
** * * *
397422 TTTCGAG-AATGATGATTAAATCCTTCAAGTCATTTGTAAGTCTTTCGATCAAGATGATAAGTC-
66 TTTCGAGCAA-GAAAATTAAATCCTTCAAGTCATCTGTAAGGCTTTCGAGCAAGATGATAAGTCT
* * *
397485 TTCGGGACATCCATAAGACCTTTGGGTAAGATGTTCTCACGTGGTATTC
130 TTCGGGACATCCATAAGACCTTCGGGTAAGATGTTCTCACAT-GAATTC
397534 AAAAAGATGAGAAAGTGATTTCCAAAGTTTCT
1 AAAAAGATGAGAAAGTGATTTCCAAAGTTTCT
397566 CATTTAGAAT
Statistics
Matches: 179, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
176 43 0.24
177 136 0.76
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (177 bp):
AAAAAGATGAGAAAGTGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAATAAGTC
TTTCGAGCAAGAAAATTAAATCCTTCAAGTCATCTGTAAGGCTTTCGAGCAAGATGATAAGTCTT
TCGGGACATCCATAAGACCTTCGGGTAAGATGTTCTCACATGAATTC
Found at i:397738 original size:415 final size:417
Alignment explanation
Indices: 396957--397805 Score: 1166
Period size: 415 Copynumber: 2.0 Consensus size: 417
396947 GTAAGAAAAC
* * * * *
396957 GATTTCCAAAGTTTCTTACTTAGTAAGGCCTTCGGGCCATTAGTAAGTTATTCTAGCACGATGAT
1 GATTTTCAAAGTTTCTTACTTAGTAAGGCCTTCAGGCCATTAATAAGTTATTCGAGAACGATGAT
** * * *
397022 TAAATCATTCGGGTCATATGTAAGTCTTTCGAGCAAGATGATGAGTTCTTCGTGCCAACCACAAG
66 TAAATCATTCAAGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTTCTTCGGGACAACCACAAG
* * * * *
397087 ACCTTCGGGCAGGATGTTTTCAGGTGATTTTCAAAATGATGAGAAAGCGATTTCCAAAGTTTCTC
131 ACCTTCGGGCAAGATGTTCTCACGTGATATTCAAAAAGATGAGAAAGCGATTTCCAAAGTTTCTC
* * * *
397152 ATTTAGTATTTTTAGAAAATGAAATTTTTAAAAAGTAAGAAAGCGATTTCCAAAGTTTATTACTT
196 ATTTAGAATTTTCAGAAAATGAAATTCTTAAAAAGCAAGAAAGCGATTTCCAAAGTTTATTACTT
* * *
397217 AGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGAAAATTAAATTCTTCGGGTCATCTGT
261 AATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGAAAATTAAATCCTTCGAGTCATCTGT
* * ** * *
397282 TAGGCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTC
326 CAGGCTTGCGAGCAAGATGATAAGTCAATCAGGCCATCCGTAAGACCTTCGGGTAGGATGATTTC
397347 ACATGAA-TTTAAAAAAATGAGAAAGT
391 ACATGAACTTTAAAAAAATGAGAAAGT
* *
397373 GATTTTCAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATTAATAAGTCT-TTCGAGAATGATGA
1 GATTTTCAAAGTTTCTTACTTAGTAAGGCCTTCAGGCCATTAATAAGT-TATTCGAGAACGATGA
* * * * *
397437 TTAAATCCTTCAAGTCATTTGTAAGTCTTTCGATCAAGATGATAAG-TCTTCGGGACATCCATAA
65 TTAAATCATTCAAGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTTCTTCGGGACAACCACAA
* * * *
397501 GACCTTTGGGTAAGATGTTCTCACGTGGTATTCAAAAAGATGAGAAAGTGATTTCCAAAGTTTCT
130 GACCTTCGGGCAAGATGTTCTCACGTGATATTCAAAAAGATGAGAAAGCGATTTCCAAAGTTTCT
* *
397566 CATTTAGAATTTTCAGAAAATGAAATTCTTGAAAAGCAAGAAAGTGATTTCCAAAGTTTCA-TAC
195 CATTTAGAATTTTCAGAAAATGAAATTCTTAAAAAGCAAGAAAGCGATTTCCAAAGTTT-ATTAC
* * ** * * *
397630 TTAATAAGTCCTTCGGGGCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGAGTTATTT
259 TTAATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGAAAATTAAATCCTTCGAGTCATCT
* * *
397695 GTCAGGCTTGCGAGCAAGATGATAAGTCAATCATGCTATCCGTAAGACCTTTGGGTAGGATGATT
324 GTCAGGCTTGCGAGCAAGATGATAAGTCAATCAGGCCATCCGTAAGACCTTCGGGTAGGATGATT
*
397760 TCACATTAACTTTTAAAAAAATGAGAAAGT
389 TCACATGAAC-TTTAAAAAAATGAGAAAGT
*
397790 GATTTTTAAAGTTTCT
1 GATTTTCAAAGTTTCT
397806 CATTTAGTGT
Statistics
Matches: 376, Mismatches: 53, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
415 245 0.65
416 96 0.26
417 35 0.09
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (417 bp):
GATTTTCAAAGTTTCTTACTTAGTAAGGCCTTCAGGCCATTAATAAGTTATTCGAGAACGATGAT
TAAATCATTCAAGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTTCTTCGGGACAACCACAAG
ACCTTCGGGCAAGATGTTCTCACGTGATATTCAAAAAGATGAGAAAGCGATTTCCAAAGTTTCTC
ATTTAGAATTTTCAGAAAATGAAATTCTTAAAAAGCAAGAAAGCGATTTCCAAAGTTTATTACTT
AATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGAAAATTAAATCCTTCGAGTCATCTGT
CAGGCTTGCGAGCAAGATGATAAGTCAATCAGGCCATCCGTAAGACCTTCGGGTAGGATGATTTC
ACATGAACTTTAAAAAAATGAGAAAGT
Found at i:398046 original size:473 final size:473
Alignment explanation
Indices: 397416--400010 Score: 3089
Period size: 473 Copynumber: 5.5 Consensus size: 473
397406 AGGCCATTAA
* ** * * *
397416 TAAGTCTTTCGAGAATGATGATTAAATCCTTCAAGTCATTTGTAAGTCTTTCGATCAAGATGATA
1 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATA
** * * * * * *
397481 AGT-CTTCGGGACATCCATAAGACCTTT-GGGTAAGATGTTCTCACGTGGTATTCAAAAAGATGA
66 AGTCCTTCATGCCATCCATAAGA-CTTTCGGGCAGGATGTTTTCACGTGATTTTCAAAAAGATGA
* * *
397544 GAAAGTGATTTCCAAAGTTTCTCATTTAGAATTTTCAGAAAATGAAATTCTTGAAAAGCAAGAAA
130 GAAAG-AATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTCTTGAAAAGTAAGAAA
397609 GTGATTTCCAAAGTTTCATACTTAATAAGTCCTTCGGGGCATCAGTAAGTCTTTCGAGCATGATG
194 GTGATTTCCAAAGTTTCATACTTAATAAGTCCTTCGGGGCATCAGTAAGTCTTTCGAGCATGATG
* * * * *
397674 ATTAAATCCTTTGAGTTATTTGTCAGGCTTGCGAGCAAGATGATAAGTCAATCATGCTATCCGTA
259 ATTAAATCCTTCGAGTCATCTGTCAGGCTTTCGAGCAAGATGATAAGTCAATCATGCCATCCGTA
* * * **
397739 AGACCTTTGGGTAGGATGATTTCACATTAACTTTTAAAAAAATGAGAAAGTGATTTTTAAAGTTT
324 AGACCTTCGGGTAGGATGTTTTCACATGAACTTTTAAAAAAATGAGAAAGTGATTTCCAAAGTTT
*
397804 CTCATTTAGTGTTTTTAGAAAATGAAATTTTTGAAAAGTAAAAAAGCAATTTCCAAAGTTTCTTA
389 CTCATTTAGTGTTTTTAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTA
397869 CTTAGTAAGCCATT-ATCAG
454 CTTAGTAAGCCATTGATCAG
*
397888 TACGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATA
1 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATA
* *** *
397953 TA-TCCTTCATTCCATCCATAAGACTTTCATACAGGATGTTTTCACGTGATTTTCAAAAAGATAA
66 -AGTCCTTCATGCCATCCATAAGACTTTCGGGCAGGATGTTTTCACGTGATTTTCAAAAAGATGA
* * *
398017 GAAAGTAATTTCCAAAGTTCCTCATTTAGAATTTTCAGAAAATGAAATTCTTGAAAAGCAAGAAA
130 GAAAG-AATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTCTTGAAAAGTAAGAAA
*
398082 GTGATTTCCAAAGTTTCATACTTAATAAGTCCTTCGGGGCATCAGTAAGTCTTTCAAGCATGATG
194 GTGATTTCCAAAGTTTCATACTTAATAAGTCCTTCGGGGCATCAGTAAGTCTTTCGAGCATGATG
* * * *
398147 ATTAAATCCTTCGAGTTATTTGTCAGGCTTGCGAGCAAGATGATAAGTCAATCATGCTATCCGTA
259 ATTAAATCCTTCGAGTCATCTGTCAGGCTTTCGAGCAAGATGATAAGTCAATCATGCCATCCGTA
* * *
398212 AGACCTTTGGGTAGGATGATTTCACATGAACTTTAAAAAAAATGAGAAAGTGATTTCCAAAGTTT
324 AGACCTTCGGGTAGGATGTTTTCACATGAACTTTTAAAAAAATGAGAAAGTGATTTCCAAAGTTT
* *
398277 CTCATTTAGTGTTTTTACAAAATGAAATTTTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTA
389 CTCATTTAGTGTTTTTAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTA
398342 CTTAGTAAGCCATT-ATCAG
454 CTTAGTAAGCCATTGATCAG
* * *
398361 TACGTCTTTCAAGCATGATGATTAAATCCTTCCGGTCATCTGTAAGTCTTTCAAGCAAGATGATA
1 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATA
* * * **
398426 TGTCCTTCGTTCCATCCATAAGACTTTCATGCAGGATGTTTTCACGTGATTTTCAAAAAGATGAG
66 AGTCCTTCATGCCATCCATAAGACTTTCGGGCAGGATGTTTTCACGTGATTTTCAAAAAGATGAG
* * * *
398491 AAAACGAA-CTCCAAAGTTTCTAATTTAGTATTTTCAGAAAATAAAATTTTTGAAAAGTAAGAAA
131 -AAA-GAATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTCTTGAAAAGTAAGAAA
* * * * * * *
398555 GTGGTTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGCAAGTCTTTTGGGCATGATG
194 GTGATTTCCAAAGTTTCATACTTAATAAGTCCTTCGGGGCATCAGTAAGTCTTTCGAGCATGATG
* * * ** * *
398620 ATTAAATCCTTCGGGTCATCTGTCAGGCTTTTGAGTAAGATGATAAGTCCTTCAGGCCATCTGTA
259 ATTAAATCCTTCGAGTCATCTGTCAGGCTTTCGAGCAAGATGATAAGTCAATCATGCCATCCGTA
* * *
398685 AGACCATCAGGTAGGATGTTTTCACATGAA--TTTAAAAAAATGAGAAAGCGATTTCCAAAGTTT
324 AGACCTTCGGGTAGGATGTTTTCACATGAACTTTTAAAAAAATGAGAAAGTGATTTCCAAAGTTT
* * * **
398748 CTCATTTATTGTTTTCAGAAAATGAAATTTTTGAAATGTAAGAAAGTGATTTCCAAAGTTTCTTA
389 CTCATTTAGTGTTTTTAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTA
398813 CTTAGTAAGTCC-TTCGGGCCATCAG
454 CTTAGTAAG-CCATT---G--ATCAG
* * * * *
398838 TAAGTCTTTTGAGCATGATGATTAAATACGTCGTGTCATCTGTAAGTCTTTCGAGCAAGATGATA
1 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATA
* * * *
398903 AGTCCTTCGA-GCCATCCATAAGACCTTCGGGCAAGATGTTTTCATGTGGTTTTCAAAAAGATGA
66 AGTCCTTC-ATGCCATCCATAAGACTTTCGGGCAGGATGTTTTCACGTGATTTTCAAAAAGATGA
** *
398967 GAAAG---TTCCAAA-TATTCTCATTTAGTATTTTCTTAAAATGAAATTCTTGAAAAATAAGAAA
130 GAAAGAATTTCCAAAGT-TTCTCATTTAGTATTTTCAGAAAATGAAATTCTTGAAAAGTAAGAAA
* *
399028 GAGATTTCCAAAGTTTCATACTT-ATAAGTCATTCGGGGCATCAGTAAGTCTTTCGAGCATGATG
194 GTGATTTCCAAAGTTTCATACTTAATAAGTCCTTCGGGGCATCAGTAAGTCTTTCGAGCATGATG
* * * * *
399092 ATTAAATCTTTCGAGTCATCTGTTAGGCTTTTGAGCAAGATGATAAGTCATTCAGGCCATCCGTA
259 ATTAAATCCTTCGAGTCATCTGTCAGGCTTTCGAGCAAGATGATAAGTCAATCATGCCATCCGTA
* *
399157 AGACCTTCGAGTAGGATGTTTTCACATGAAC-TTTAAAAAAACTGAGAAAGTGATTTTCAAAGTT
324 AGACCTTCGGGTAGGATGTTTTCACATGAACTTTTAAAAAAA-TGAGAAAGTGATTTCCAAAGTT
* * *
399221 TCTCATTCAGTGTTTTTAG---A--AAA----TGCAAAGTAAGAAAGCGATTTCCAAAGTTTCTT
388 TCTCATTTAGTGTTTTTAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTT
*
399277 ACTTAGTAAGTCATTTGGGCCATCAG
453 ACTTAGTAAGCCA-TT--G--ATCAG
*
399303 TAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATA
1 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATA
* *
399368 AGTCCTTTTGGCAATCCATAAGACCTTCGGGCAATCCATAAGACCTTCGGGCAAGATGTTTTCAC
66 AGTCC---T-----T-CAT--G-----C---C-ATCCATAAGACTTTCGGGCAGGATGTTTTCAC
* * *
399433 ATGATTTTCAAAAAGATGAGAAAGAGATTTCCAAAGTTTCTCATTTATTATTTTCAAAAAATGAA
111 GTGATTTTCAAAAAGATGAGAAAGA-ATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAA
* * * * *
399498 ATTTTTGAAAAGTAAGAAAGTGGTTTCCAAAG-TT--T-CTTACTAAGTCCTTCGGGCCATTAGT
175 ATTCTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCATACTTAATAAGTCCTTCGGGGCATCAGT
* * * * * * *
399559 AAGTCTTTCTAGCATGATGATTAAATTCTTCGGGTCATATCTCAGGATTTCAAGCAAGATGATAA
240 AAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTCAGGCTTTCGAGCAAGATGATAA
* * * *
399624 GTC-CT-TTGGACCACCCGTACGACCTTCGGGTAGGATGTTTTCACATGAA-TTTTAAAAAAATG
305 GTCAATCAT-G-CCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAACTTTTAAAAAAATG
* * * *
399686 AGAAAGTGATTTCCAAAGATTCTCATTTAGTGTTTTCAAAAAATGAAATTTTTGAAAACTAAGAA
368 AGAAAGTGATTTCCAAAGTTTCTCATTTAGTGTTTTTAGAAAATGAAATTTTTGAAAAGTAAGAA
* *
399751 AGCAATTTCCAAATTTTCTTACTTAGTAAGTCCTTTGGGCCATCAG
433 AGCAATTTCCAAAGTTTCTTACTTAGTAAG-CCATT--G--ATCAG
** * * * * * * *
399797 TAAACCTTTTGAGTATGATGATTGAATCCTTTGGGTTATCTCTCAA-TCTTTCGAGCAAGATGAT
1 TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGT-AAGTCTTTCAAGCAAGATGAT
* ** * * *
399861 ATGTCCTTCGGGCCATCTATAAGACTTTTGGGCAGGATGTTTTCACGTGATTTTCAAAAAAATGA
65 AAGTCCTTCATGCCATCCATAAGACTTTCGGGCAGGATGTTTTCACGTGATTTTCAAAAAGATGA
* * * * * * *
399926 GAAAGTGATTTCCAAAGTTTTTCAGTTAGTATTTTCAGAGAAT-AAATTTTTAAAAATTAAGAAA
130 GAAAG-AATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTCTTGAAAAGTAAGAAA
*
399990 GCGATTTCCAAAGTTTCATAC
194 GTGATTTCCAAAGTTTCATAC
400011 CCAGTAGACT
Statistics
Matches: 1857, Mismatches: 201, Indels: 125
0.85 0.09 0.06
Matches are distributed among these distances:
464 1 0.00
465 114 0.06
466 2 0.00
468 1 0.00
469 3 0.00
471 101 0.05
472 187 0.10
473 794 0.43
474 125 0.07
475 3 0.00
476 5 0.00
477 118 0.06
478 1 0.00
481 1 0.00
483 1 0.00
484 1 0.00
485 95 0.05
486 124 0.07
488 3 0.00
489 60 0.03
490 4 0.00
491 1 0.00
494 109 0.06
495 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (473 bp):
TAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATA
AGTCCTTCATGCCATCCATAAGACTTTCGGGCAGGATGTTTTCACGTGATTTTCAAAAAGATGAG
AAAGAATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTCTTGAAAAGTAAGAAAGT
GATTTCCAAAGTTTCATACTTAATAAGTCCTTCGGGGCATCAGTAAGTCTTTCGAGCATGATGAT
TAAATCCTTCGAGTCATCTGTCAGGCTTTCGAGCAAGATGATAAGTCAATCATGCCATCCGTAAG
ACCTTCGGGTAGGATGTTTTCACATGAACTTTTAAAAAAATGAGAAAGTGATTTCCAAAGTTTCT
CATTTAGTGTTTTTAGAAAATGAAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACT
TAGTAAGCCATTGATCAG
Done.