Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003430.1 Hibiscus syriacus cultivar Beakdansim tig00007228_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: 63510
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:8367 original size:29 final size:30
Alignment explanation
Indices: 8330--8392 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
8320 AAATTTTTGA
*
8330 TAGTGACCAAAATATAAAATTT-AAAAGTT
1 TAGTAACCAAAATATAAAATTTAAAAAGTT
* *
8359 TAGTAACCAAAGTATAAACTTTAGAAAAGTT
1 TAGTAACCAAAATATAAAATTTA-AAAAGTT
8390 TAG
1 TAG
8393 GGACTAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 19 0.66
31 10 0.34
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (30 bp):
TAGTAACCAAAATATAAAATTTAAAAAGTT
Found at i:9219 original size:29 final size:31
Alignment explanation
Indices: 9186--9254 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 31
9176 AAATTTTAGA
*
9186 TAGTGACCAAAATATAAA-TTTTG-AAAGTT
1 TAGTGACCAAAATATAAACTTTAGAAAAGTT
*
9215 TAGTGA--AAAGTATAAACTTTAGAAAAGTT
1 TAGTGACCAAAATATAAACTTTAGAAAAGTT
9244 TAAG-GACCAAA
1 T-AGTGACCAAA
9255 GAGGTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
27 9 0.27
28 4 0.12
29 15 0.45
30 2 0.06
31 3 0.09
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (31 bp):
TAGTGACCAAAATATAAACTTTAGAAAAGTT
Found at i:9647 original size:851 final size:853
Alignment explanation
Indices: 8003--10558 Score: 4105
Period size: 851 Copynumber: 3.0 Consensus size: 853
7993 CGGAGTTAGA
* *
8003 CAAAGTTCATAATG-TTTTCATGTGTCGATGCTTAGAAAGTATCGATC-AGATCCTTCAAATGTC
1 CAAAGTTCATAATGTTTTTCATGTGTCGATGCTTAGAAAGTATCGATCGA-ATCATTCACATGTC
*
8066 ATTGCATCAGAGGAAATTGAGATCCCAGATTTGACTTATGAAGAAGAACCAATACGGATATTGGA
65 ATTGCATCAGAGGAAATTGAGATCCCAGATTTGACTTATGAAGAAGAACCAATACGGATATTGGC
* * * *
8131 TCGATAAATCAAATAATTGTGTAGCAAGACGATTACAGTAGTCAAAGTGCTTTGGC-AAATCATA
130 TCGAGAAATCAAATAACTATGTAGCAAGACGATTACACTAGTCAAAGTGCTTTGGCAAAATCATA
* * * *
8195 AAGTCGAGGACGCTACATAGG-AAGAGAGTAGGACATGAGGAAACAATATTCACATCTCTTCACT
195 AAGTCGAGGACGCTACTTAGGAAAGAGAGTAGGACATGAGGAAGCAATATCCACACCTCTTCACT
*
8259 ACAGGTAAGTCTTAAAATTTGATGACGAATTTTATTTAACAGGGGAGAGTTGTAATACCCTAAAT
260 ACAGGTATGTCTTAAAATTTGATGACGAATTTTATTTAACAGGGGAGAGTTGTAATACCCTAAAT
* * * *
8324 TTTTGATAGTGACCAAAATATAAAATTTAAAAGTTTAGTAACCAAAGTATAAACTTTAGAAAAGT
325 TTTAGATAGTGACCAAAATATAAATTTTGAAAGTTTAGTGA--AAAGTATAAACTTTAGAAAAGT
* *
8389 TTAGGGACTAAAGTGGTAATTTTAAAAAGTTACATTTTTACCCTCGTAAATAAATAGTTATAAAG
388 TTAGGGACCAAAGAGGTAATTTTAAAAAGTTACATTTTT-CCCTCGTAAATAAATAGTTATAAAG
* * *
8454 CGTTGAAGTTTGAGGAAAGATTTAGTAAATCGGATCAAATAGAAAATTTAGGAAAATCTGAAGGA
452 CGTTGAAGTTTGAGGAAAGATTCAGTAAATCGGATCGAATAGAAAATTCAGGAAAATCTGAAGGA
* *
8519 TGATAAATTAT-AATTAAAACTATTATTTCCATATTTTAAAATGTTGGAAAATTATATAAATCTT
517 TGATAAATT-TGAATTAAAAATATTATTTCCACATTTTAAAATGTT-GAAAATTATATAAATCTT
* * *
8583 TGGATTTGAGGATTTAATTCCATGATTAATTTGGACTGTTGGATTAAAGTGGGAAGATTGTAGTT
580 TGGATTTGAGGATTTAATTCCATAATTAATTTGGACTGTTGGATTAAAGTGGCAAGATTGTAATT
* * * *
8648 TTTGGAGAAAGGCAAGGGCAAATCGATAAAGTAAGATTTTGTTTGATCATATTTGACTTTAAGTA
645 TTTGGATAAAGGCAAGGGCAAATCGATAAAGTAAGATTTTGTTTGTTCATATTTGACTTTAGGAA
* * * *
8713 GATGATAAGGTTGAGTTGCCTTGGTTTGATGGTAAATATGAAGTTTCATTAAGCGTAAATTGGTA
710 GATGATAAGGTTGAGGTGTCTTGGTTTGATGGTAAATATGAAGTTTCATTAAGGGTAAATTGGTC
*
8778 TTTTCCCAATTAAATGAATTTAATATTCATTAAAGTTTAAATTAAAGATAAATTAGCATGAAATT
775 TTTTCCTAATTAAATGAATTTAATATTCATTAAAGTTTAAATTAAAGATAAATTAGCATGAAATT
8843 AGTCTAAAATTCAT
840 AGTCTAAAATTCAT
8857 CAAAGTTCATAATGTTTTTCATGTGTCGATGCTTAGAAAGTATCGATCGAATCATTCACATGTCA
1 CAAAGTTCATAATGTTTTTCATGTGTCGATGCTTAGAAAGTATCGATCGAATCATTCACATGTCA
* *
8922 TTGCATCAGAGGAAATTGAGATCCCATATTTGACTTATTAAGAAGAACCAATACGGATATTGGCT
66 TTGCATCAGAGGAAATTGAGATCCCAGATTTGACTTATGAAGAAGAACCAATACGGATATTGGCT
* *
8987 TGAGAAATCAAATAACTATTTAGCAAGACGATTACACTAGTCAAAGTGCTTTGGCAAAATCATAA
131 CGAGAAATCAAATAACTATGTAGCAAGACGATTACACTAGTCAAAGTGCTTTGGCAAAATCATAA
9052 AGTCGAGGACGCTACTTAGGAAAGAGAGTAGGACATGAGGAAGCAATATCCACACCTCTTCACTA
196 AGTCGAGGACGCTACTTAGGAAAGAGAGTAGGACATGAGGAAGCAATATCCACACCTCTTCACTA
* *
9117 CAGGTATGTCTTAAAATTTGATGACAAATTTTATTTAACTGGGGAGAGTTG-AATACCCTAAATT
261 CAGGTATGTCTTAAAATTTGATGACGAATTTTATTTAACAGGGGAGAGTTGTAATACCCTAAATT
9181 TTAGATAGTGACCAAAATATAAATTTTGAAAGTTTAGTGAAAAGTATAAACTTTAGAAAAGTTTA
326 TTAGATAGTGACCAAAATATAAATTTTGAAAGTTTAGTGAAAAGTATAAACTTTAGAAAAGTTTA
* * * * *
9246 AGGACCAAAGAGGTAATTTTAAAAAGTTACATTTTTGCCATCGGAAATAAATAGTTATCAAGCGA
391 GGGACCAAAGAGGTAATTTTAAAAAGTTACATTTTT-CCCTCGTAAATAAATAGTTATAAAGCGT
* * *
9311 TAAAGTTTGAGGAAAGATTCAGTAAATCGGATCGAATAAAAAATTCAGGAAAATTTGAAGGATGA
455 TGAAGTTTGAGGAAAGATTCAGTAAATCGGATCGAATAGAAAATTCAGGAAAATCTGAAGGATGA
*
9376 TAAATTTGAAATAAAAATATT-TTT-CACATTTTAAAATGTTGAAAAATTATAT-AATCTTTGGA
520 TAAATTTGAATTAAAAATATTATTTCCACATTTTAAAATGTTG-AAAATTATATAAATCTTTGGA
* *
9438 TTTGAGGATTTAATTCGATAATTAATTTGGACTATTGGATTAAAGTGGCAAGATTGTACATTTTT
584 TTTGAGGATTTAATTCCATAATTAATTTGGACTGTTGGATTAAAGTGGCAAGATTGTA-ATTTTT
* * * * *
9503 -TATAAAGTCAAGGGAAAATCGATAAAGTAAGATTTTGTTTGTTTATATTTGACTTTAGGAAGAC
648 GGATAAAGGCAAGGGCAAATCGATAAAGTAAGATTTTGTTTGTTCATATTTGACTTTAGGAAGAT
*
9567 GATAAGGTTGAGGTGTCTTGGTTTGATGGTAAATATAAAGTTTCATTAAGGGTAAATTGGTCTTT
713 GATAAGGTTGAGGTGTCTTGGTTTGATGGTAAATATGAAGTTTCATTAAGGGTAAATTGGTCTTT
*
9632 TCCTAATTAAATGAATTTAATATTCATTAAAGTTTAAATTAAAGATAAATTAGCATTAAATTAGT
778 TCCTAATTAAATGAATTTAATATTCATTAAAGTTTAAATTAAAGATAAATTAGCATGAAATTAGT
9697 CTAAAATTCAT
843 CTAAAATTCAT
* *
9708 CAAAGTTCATAATGTTTTTCATGTGTCGATGCTTAGAAAGTATCGATCGGATCTTTCACATGTCA
1 CAAAGTTCATAATGTTTTTCATGTGTCGATGCTTAGAAAGTATCGATCGAATCATTCACATGTCA
* *
9773 TTACATTAGAGGAAATTGAGATCCCAGATTTGACTTATGAAGAAGAACCAATACGGATATTGGCT
66 TTGCATCAGAGGAAATTGAGATCCCAGATTTGACTTATGAAGAAGAACCAATACGGATATTGGCT
* * *
9838 CGAGAAATCAAATAACCATGTAGCAAGACGATTACATTAGTCAAAGTCCTTTGGCAAAATCATAA
131 CGAGAAATCAAATAACTATGTAGCAAGACGATTACACTAGTCAAAGTGCTTTGGCAAAATCATAA
* * *
9903 AATCGAGGACGCTACTTAAGAAAGAGAGTAGGACATGAGAAAGCAATATCCACACCTCTTCACTA
196 AGTCGAGGACGCTACTTAGGAAAGAGAGTAGGACATGAGGAAGCAATATCCACACCTCTTCACTA
* * *
9968 CAGGTATGTCTTAAAATTTGATGATGAATTTTATTTAACGGGGGAGAGTTGTAATACTCTAAATT
261 CAGGTATGTCTTAAAATTTGATGACGAATTTTATTTAACAGGGGAGAGTTGTAATACCCTAAATT
* * ** *
10033 TTAGATAGTGACC-AAATACAAATTTTGAAAGTTTACTGGCCAAGTATAAACTTTGGAAAAGTTT
326 TTAGATAGTGACCAAAATATAAATTTTGAAAGTTTAGT-GAAAAGTATAAACTTTAGAAAAGTTT
*
10097 AGGGACCAAAGAGGTAATTTTAAAAAGTTACA-TTTTCCCTCGTAAATAAATAGTTATAAAGTGT
390 AGGGACCAAAGAGGTAATTTTAAAAAGTTACATTTTTCCCTCGTAAATAAATAGTTATAAAGCGT
*
10161 TGAAGTTTGAGGAAAGATTCAGTAAATCGGATCGAATAGAAAATTCAGTAAAATCTGAAGGATGA
455 TGAAGTTTGAGGAAAGATTCAGTAAATCGGATCGAATAGAAAATTCAGGAAAATCTGAAGGATGA
*
10226 TAAATTAGAATTAAAAATATTATTTCCACA-TTTAAAATGTTTGAAAATTATATAAATCTTTGGA
520 TAAATTTGAATTAAAAATATTATTTCCACATTTTAAAATG-TTGAAAATTATATAAATCTTTGGA
*
10290 TTTGAGGATTTAATTCCATACTTAATTTGGACTGTTGGATTAAAGTGGCAAGATTGTAATTTTTG
584 TTTGAGGATTTAATTCCATAATTAATTTGGACTGTTGGATTAAAGTGGCAAGATTGTAATTTTTG
* *
10355 GATAAAGGCAAGGGCAAATCGATAAAGTAAGATTTTGTTTGTTCATGTTTGACTTTAGGAAGATT
649 GATAAAGGCAAGGGCAAATCGATAAAGTAAGATTTTGTTTGTTCATATTTGACTTTAGGAAGATG
* * * *
10420 ATATGGTTGAGGTGTCTTGGTTTGATGGTAAATATGCAGTTTCATTAAGGGTAAATTGGCCTTTC
714 ATAAGGTTGAGGTGTCTTGGTTTGATGGTAAATATGAAGTTTCATTAAGGGTAAATTGGTCTTTT
* * *
10485 CCT-ATTAAATAAATTTAATATTCACTATAGTTTAAATTAAAGATAAATTAGCATGAAATTAGTC
779 CCTAATTAAATGAATTTAATATTCATTAAAGTTTAAATTAAAGATAAATTAGCATGAAATTAGTC
10549 TAAAATTCAT
844 TAAAATTCAT
10559 GCCAATTTGT
Statistics
Matches: 1574, Mismatches: 114, Indels: 31
0.92 0.07 0.02
Matches are distributed among these distances:
850 103 0.07
851 669 0.43
852 302 0.19
853 4 0.00
854 172 0.11
855 157 0.10
856 78 0.05
857 89 0.06
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (853 bp):
CAAAGTTCATAATGTTTTTCATGTGTCGATGCTTAGAAAGTATCGATCGAATCATTCACATGTCA
TTGCATCAGAGGAAATTGAGATCCCAGATTTGACTTATGAAGAAGAACCAATACGGATATTGGCT
CGAGAAATCAAATAACTATGTAGCAAGACGATTACACTAGTCAAAGTGCTTTGGCAAAATCATAA
AGTCGAGGACGCTACTTAGGAAAGAGAGTAGGACATGAGGAAGCAATATCCACACCTCTTCACTA
CAGGTATGTCTTAAAATTTGATGACGAATTTTATTTAACAGGGGAGAGTTGTAATACCCTAAATT
TTAGATAGTGACCAAAATATAAATTTTGAAAGTTTAGTGAAAAGTATAAACTTTAGAAAAGTTTA
GGGACCAAAGAGGTAATTTTAAAAAGTTACATTTTTCCCTCGTAAATAAATAGTTATAAAGCGTT
GAAGTTTGAGGAAAGATTCAGTAAATCGGATCGAATAGAAAATTCAGGAAAATCTGAAGGATGAT
AAATTTGAATTAAAAATATTATTTCCACATTTTAAAATGTTGAAAATTATATAAATCTTTGGATT
TGAGGATTTAATTCCATAATTAATTTGGACTGTTGGATTAAAGTGGCAAGATTGTAATTTTTGGA
TAAAGGCAAGGGCAAATCGATAAAGTAAGATTTTGTTTGTTCATATTTGACTTTAGGAAGATGAT
AAGGTTGAGGTGTCTTGGTTTGATGGTAAATATGAAGTTTCATTAAGGGTAAATTGGTCTTTTCC
TAATTAAATGAATTTAATATTCATTAAAGTTTAAATTAAAGATAAATTAGCATGAAATTAGTCTA
AAATTCAT
Found at i:14267 original size:26 final size:26
Alignment explanation
Indices: 14231--14280 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
14221 GAATATAAGG
14231 TACATGAGTTTAAGGTGCACACTAAA
1 TACATGAGTTTAAGGTGCACACTAAA
*
14257 TACATGAGTTTAAGGTGCATACTA
1 TACATGAGTTTAAGGTGCACACTA
14281 GGCACAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (26 bp):
TACATGAGTTTAAGGTGCACACTAAA
Found at i:14527 original size:18 final size:18
Alignment explanation
Indices: 14504--14554 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
14494 TTAATCTGTG
14504 TCTGATAACTGTAAAACA
1 TCTGATAACTGTAAAACA
14522 TCTGATAACTGTAAAACA
1 TCTGATAACTGTAAAACA
* * *
14540 TATAATATCTGTAAA
1 TCTGATAACTGTAAA
14555 CATTCATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (18 bp):
TCTGATAACTGTAAAACA
Found at i:16004 original size:47 final size:47
Alignment explanation
Indices: 15935--16028 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
15925 TATAGAGGAT
15935 TGTATTTCTAAGTTTTAAAGGTATTGAATGGATAATAATTAGTTTAA
1 TGTATTTCTAAGTTTTAAAGGTATTGAATGGATAATAATTAGTTTAA
15982 TGTATTTCTAAGTTTTAAAGGTATTGAATGGATAATAATTAGTTTAA
1 TGTATTTCTAAGTTTTAAAGGTATTGAATGGATAATAATTAGTTTAA
16029 GTAATTGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (47 bp):
TGTATTTCTAAGTTTTAAAGGTATTGAATGGATAATAATTAGTTTAA
Found at i:16253 original size:64 final size:64
Alignment explanation
Indices: 16182--16344 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 64
16172 ATTGTTCAAG
* *
16182 GTGTATCGATGCACATGAAGTGCATCGATGCACTCATTTAAAATAAAAACATCGAATGCCA-TCA
1 GTGTATCGATGCACA-GAAGTGCATCGATGCACCCACTTAAAATAAAAACATCGAATGCCATTCA
* * * ** *
16246 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGGGATTTA
1 GTGTATCGATGCAC-AGAAGTGCATCGATGCACCCACTTAAAATAAAAACATCGAATGCCATTCA
*
16311 -TGTATCGATGCATAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCACAGA-AGTGCATCGATGCACCC
16345 GTCAAGGGAT
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 2 0.02
64 81 0.94
65 3 0.03
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAGAAGTGCATCGATGCACCCACTTAAAATAAAAACATCGAATGCCATTCA
Found at i:17019 original size:23 final size:23
Alignment explanation
Indices: 16987--17045 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
16977 ATCTTATATG
*
16987 GCACTACGGTGTAATTCTACACA
1 GCACTTCGGTGTAATTCTACACA
* ***
17010 GCACTTCGGTGGAATTCTACGTG
1 GCACTTCGGTGTAATTCTACACA
17033 GCACTTCGGTGTA
1 GCACTTCGGTGTA
17046 TTTATATGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (23 bp):
GCACTTCGGTGTAATTCTACACA
Found at i:23795 original size:23 final size:23
Alignment explanation
Indices: 23727--23787 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
23717 CAATCTTATA
*
23727 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
23750 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
23773 TTGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
23788 TTTATACGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:27696 original size:24 final size:24
Alignment explanation
Indices: 27620--27708 Score: 116
Period size: 24 Copynumber: 3.9 Consensus size: 24
27610 CAGCTAATAA
27620 TTTGCACCGAAGTGCCACATAA-T
1 TTTGCACCGAAGTGCCACATAAGT
* *
27643 TGT-C-CCGAAG-GACCACAT-AGG
1 TTTGCACCGAAGTG-CCACATAAGT
27664 TTTGCACCGAAGTGCCACATAAGT
1 TTTGCACCGAAGTGCCACATAAGT
27688 TTTGCACCGAAGTGCCACATA
1 TTTGCACCGAAGTGCCACATA
27709 TTTATCCCGA
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.04
21 14 0.25
22 2 0.04
23 14 0.25
24 24 0.43
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (24 bp):
TTTGCACCGAAGTGCCACATAAGT
Found at i:28037 original size:14 final size:14
Alignment explanation
Indices: 28018--28057 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28008 AATGTGAAGT
28018 AATCCCTGCA-AATA
1 AATCCCTGCATAA-A
28032 AATCCCTGCATAAA
1 AATCCCTGCATAAA
*
28046 AATCTCTGCATA
1 AATCCCTGCATA
28058 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (14 bp):
AATCCCTGCATAAA
Found at i:36454 original size:24 final size:24
Alignment explanation
Indices: 36382--36462 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
36372 TCGTAATTTA
*
36382 CACCGAAGTGCCACATAA-TTGT-
1 CACCGAAGTGCCACATAAGTTTTG
*
36404 C-CCGAAG-GACCACAT-AGGTTTG
1 CACCGAAGTG-CCACATAAGTTTTG
36426 CACCGAAGTGCCACATAAGTTTTG
1 CACCGAAGTGCCACATAAGTTTTG
36450 CACCGAAGTGCCA
1 CACCGAAGTGCCA
36463 TATTTTTCCC
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
20 2 0.04
21 14 0.28
22 2 0.04
23 12 0.24
24 20 0.40
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (24 bp):
CACCGAAGTGCCACATAAGTTTTG
Found at i:42424 original size:11 final size:12
Alignment explanation
Indices: 42401--42433 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
42391 TAACATATTC
42401 TTATATCATCAT
1 TTATATCATCAT
42413 TTATAT-ATCAT
1 TTATATCATCAT
42424 TTATACTCAT
1 TTATA-TCAT
42434 TCACAATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 7 0.37
13 2 0.11
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATATCATCAT
Found at i:42949 original size:22 final size:20
Alignment explanation
Indices: 42903--42949 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
42893 CGATGTTGCC
*
42903 TGGTATCGATACCCTTAACA
1 TGGTATCGATACACTTAACA
*
42923 TGGTATCGATACTACTATACCA
1 TGGTATCGATAC-ACT-TAACA
42945 TGGTA
1 TGGTA
42950 CTGATACCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 2 0.09
22 9 0.39
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (20 bp):
TGGTATCGATACACTTAACA
Found at i:44919 original size:12 final size:12
Alignment explanation
Indices: 44902--44932 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
44892 GAAATTCACC
44902 TTAACTTTTCCA
1 TTAACTTTTCCA
44914 TTAACTTTTCCA
1 TTAACTTTTCCA
44926 TTAACTT
1 TTAACTT
44933 CATTATGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAACTTTTCCA
Found at i:45551 original size:2 final size:2
Alignment explanation
Indices: 45546--45605 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
45536 AAGAAATAAG
45546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45588 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
45606 AGATTAAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49170 original size:12 final size:11
Alignment explanation
Indices: 49149--49206 Score: 56
Period size: 9 Copynumber: 5.7 Consensus size: 11
49139 GAAATAAGTA
49149 ATATAT-ATAT
1 ATATATAATAT
49159 ATATATACATAT
1 ATATATA-ATAT
*
49171 ACATATAATA-
1 ATATATAATAT
49181 ATA-ATAATA-
1 ATATATAATAT
49190 ATA-ATAATAT
1 ATATATAATAT
49200 ATA-ATAA
1 ATATATAA
49207 AACGTAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
9 15 0.35
10 15 0.35
11 3 0.07
12 10 0.23
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATATAATAT
Found at i:49183 original size:3 final size:3
Alignment explanation
Indices: 49175--49206 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
49165 ACATATACAT
49175 ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA A
49207 AACGTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:50871 original size:56 final size:56
Alignment explanation
Indices: 50751--51334 Score: 750
Period size: 56 Copynumber: 10.7 Consensus size: 56
50741 CCCACTATCA
* * * *
50751 ATACGAAAATTCATATACTTATTATGACTTTCTTAG-CTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * * *
50806 ATACAGAAATTCATAAACTTAATATAAATTTCTTAGTTTTTGCACTCAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
50862 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* ** *
50917 ATAAGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACTGTGCTC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* *
50973 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TATTGAACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* *
51028 GTACGAAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * * *
51083 GTACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTTCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * *
51139 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTTTCACACACAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * * * ** * ** *
51195 ATATGAAAAATCATATACTCGTTATGAATTTCTTAGTTTCTGCACACGCAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
*
51251 ATAC-GAAATTCATAAACTTATTATGAATTTCTTAGTTTTT--ATAC--A-----C
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
51297 --ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTT
51335 GTACACACGG
Statistics
Matches: 475, Mismatches: 50, Indels: 18
0.87 0.09 0.03
Matches are distributed among these distances:
44 2 0.00
45 35 0.07
46 1 0.00
51 1 0.00
53 3 0.01
55 212 0.45
56 221 0.47
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (56 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
Found at i:50882 original size:111 final size:110
Alignment explanation
Indices: 50751--51341 Score: 765
Period size: 111 Copynumber: 5.4 Consensus size: 110
50741 CCCACTATCA
* * * *
50751 ATACGAAAATTCATATACTTATTATGACTTTCTTAGCTTTGCACACAAAGTGCCCATACAGAAAT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATAC-GAAAT
* * *
50816 TCATAAACTTAATATAAATTTCTTAGTTTTTGCACTCAAAGTGCCC
65 TCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
*
50862 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATAAGGAAAT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCAT-ACGAAAT
** *
50927 TCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACTGTGCTC
65 TCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * *
50973 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTATTGAACACAAAGTGCCCGTACGAAAAT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACG-AAAT
51038 TCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCC
65 TCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * * *
51083 GTACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTTTCACACACAGTGCCCATACGAAAA
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCCATACG-AAA
* *
51148 TTCATAAACTTATTATGAATTTCTTAGTTTTTTCACACACAGTGCCC
64 TTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
* * * * ** ** *
51195 ATATGAAAAATCATATACTCGTTATGAATTTCTTAGTTTCTGCACACGCAGTGTCCATACGAAAT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTT-TGCACACAAAGTGCCCATACGAAAT
*
51260 TCATAAACTTATTATGAATTTCTTAGTTTTT--ATAC--A-----C
65 TCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
*
51297 --ACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGTACACA
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
51342 CGGTGCCATT
Statistics
Matches: 428, Mismatches: 47, Indels: 22
0.86 0.09 0.04
Matches are distributed among these distances:
99 6 0.01
100 31 0.07
102 1 0.00
107 1 0.00
109 3 0.01
110 52 0.12
111 270 0.63
112 64 0.15
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (110 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAATT
CATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCC
Found at i:51306 original size:45 final size:44
Alignment explanation
Indices: 51255--51344 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 44
51245 GTGTCCATAC
51255 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTTATACACACG
1 GAAATTCATAAACTTATTATGAATTTCTTAG-TTTTATACACACG
*
51300 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTGTACACACG
1 GAAATTCATAAACTTATTATGAATTTCTTAGTTTTATACACACG
51344 G
1 G
51345 TGCCATTTGG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 13 0.30
45 31 0.70
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (44 bp):
GAAATTCATAAACTTATTATGAATTTCTTAGTTTTATACACACG
Found at i:51797 original size:20 final size:20
Alignment explanation
Indices: 51751--51800 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
51741 GTAATCAATG
*
51751 GTATCGATACCCTCTCTATA
1 GTATCGATACCCTCTCTACA
51771 GTATCGATACCCTCCTCT-CA
1 GTATCGATACCCT-CTCTACA
*
51791 GTCTCGATAC
1 GTATCGATAC
51801 TAATTGCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.32
Consensus pattern (20 bp):
GTATCGATACCCTCTCTACA
Found at i:56396 original size:54 final size:54
Alignment explanation
Indices: 56328--56953 Score: 720
Period size: 54 Copynumber: 11.6 Consensus size: 54
56318 GATGCTCACG
* ** * **
56328 TAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTTTGCGGGTTGCACACA
1 TAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGAATTGCACACA
* *
56382 TAGTACCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACATA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACA
* *
56436 CAGT--CTGTACGGTTATTCATCAACTCATGATGAATTCCCTGAATTTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAA-TTGCACACA
* * * ** ** *
56489 TAGTGCATGTACAGTTATTTATCAACTCATGATGAATTTTGTGGGTTGTACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACA
** * * *
56543 TAGTGATTGCACGGTTATTCATCAACTCATGATGAATTCTGTGAGTTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACA
* * *
56597 TAGTGTCTGTACGGTTATTCATCAACTCATGATGAATTTCATGAATTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACA
* * * * *
56651 TAGTGCTTGTACGATTATT-ATCAACTTATGATGAATTCTGTGGATTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACA
* * * *
56704 TAGTGCATGTACGGTTATTCATCAACCCATGATAAATTCCGTGAATTACACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACA
** * * * *
56758 TAGTGCCTGTACAATTATTGATCAACTCATGATGAATTTCATGAATTGCATACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACA
* * * * * *
56812 TAGTGCCTATACGATTATTCATCAACTTATGATGAATTCCATGAATTGTACATA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACA
* * * * *
56866 TAGTACATGTACGGTTATTCATCAACTTATGATGAATTTCGTGAATTACACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACA
* *
56920 TAGTGCATGTACGGTTATTCATCAACTTATGATG
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATG
56954 TGTGGGTTAC
Statistics
Matches: 487, Mismatches: 80, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
52 38 0.08
53 57 0.12
54 359 0.74
55 33 0.07
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (54 bp):
TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACA
Found at i:56674 original size:161 final size:160
Alignment explanation
Indices: 56348--56953 Score: 770
Period size: 161 Copynumber: 3.8 Consensus size: 160
56338 ACGGTAGTTC
* * *
56348 ATCAACTCATGATGAATTTTGCGGGTTGCACACATAGTACCTGTACGGTTATTCATCAACTCATG
1 ATCAACTCATGATGAATTCTGTGGATTGCACACATAGTA-CTGTACGGTTATTCATCAACTCATG
* ** * *
56413 ATGAATTCCGTGAATT--GCACATACAGTCTGTACGGTTATTCATCAACTCATGATGAATTCCCT
65 ATGAATTCCGTGAATTACACACATAGTGTCTGTACGGTTATTCATCAACTCATGATGAATTTCAT
56476 GAATTTGCACACATAGTGCATGTAC-AGTTATTT
130 GAA-TTGCACACATAGTGCATGTACGA-TTA-TT
* * * * *
56509 ATCAACTCATGATGAATTTTGTGGGTTGTACACATAGTGATTGCACGGTTATTCATCAACTCATG
1 ATCAACTCATGATGAATTCTGTGGATTGCACACATAGT-ACTGTACGGTTATTCATCAACTCATG
* * *
56574 ATGAATTCTGTGAGTTGCACACATAGTGTCTGTACGGTTATTCATCAACTCATGATGAATTTCAT
65 ATGAATTCCGTGAATTACACACATAGTGTCTGTACGGTTATTCATCAACTCATGATGAATTTCAT
*
56639 GAATTGCACACATAGTGCTTGTACGATTATT
130 GAATTGCACACATAGTGCATGTACGATTATT
* * *
56670 ATCAACTTATGATGAATTCTGTGGATTGCACACATAGTGCATGTACGGTTATTCATCAACCCATG
1 ATCAACTCATGATGAATTCTGTGGATTGCACACATAGTAC-TGTACGGTTATTCATCAACTCATG
* * ** *
56735 ATAAATTCCGTGAATTACACACATAGTGCCTGTACAATTATTGATCAACTCATGATGAATTTCAT
65 ATGAATTCCGTGAATTACACACATAGTGTCTGTACGGTTATTCATCAACTCATGATGAATTTCAT
* * *
56800 GAATTGCATACATAGTGCCTATACGATTATT
130 GAATTGCACACATAGTGCATGTACGATTATT
* ** * * * *
56831 CATCAACTTATGATGAATTCCATGAATTGTACATATAGTACATGTACGGTTATTCATCAACTTAT
1 -ATCAACTCATGATGAATTCTGTGGATTGCACACATAGTAC-TGTACGGTTATTCATCAACTCAT
* *
56896 GATGAATTTCGTGAATTACACACATAGTG-CATGTACGGTTATTCATCAACTTATGATG
64 GATGAATTCCGTGAATTACACACATAGTGTC-TGTACGGTTATTCATCAACTCATGATG
56954 TGTGGGTTAC
Statistics
Matches: 393, Mismatches: 45, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
161 217 0.55
162 130 0.33
163 46 0.12
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (160 bp):
ATCAACTCATGATGAATTCTGTGGATTGCACACATAGTACTGTACGGTTATTCATCAACTCATGA
TGAATTCCGTGAATTACACACATAGTGTCTGTACGGTTATTCATCAACTCATGATGAATTTCATG
AATTGCACACATAGTGCATGTACGATTATT
Found at i:56759 original size:215 final size:213
Alignment explanation
Indices: 56345--56945 Score: 774
Period size: 215 Copynumber: 2.8 Consensus size: 213
56335 TATACGGTAG
* * *
56345 TTCATCAACTCATGATGAATTTTGCGGGTTGCACACATAGTACCTGTACGGTTATTCATCAACTC
1 TTCATCAACTCATGATGAA-TTTGTGAGTTGCACACATAGTGCCTGTACGGTTATTCATCAACTC
* * * **
56410 ATGATGAATTCCGTGAATTGCACATACAGTCTGTACGGTTATTCATCAACTCATGATGAATTCCC
65 ATGATGAATTCCATGAATTGCACATATAGTCTGTACGGTTATTCATCAACTTATGATGAATTCTG
* * * * ** ** **
56475 TGAATTTGCACACATAGTGCATGTACAGTTATTTATCAACTCATGATGAATTTTGTGGGTTGTAC
130 TGAA-TTGCACACATAGTGCATGTACGGTTATTCATCAACCCATGATAAATTCCGTGAATTACAC
* **
56540 ACATAGTGATTGCACGGTTA
194 ACATAGTGACTGCACAATTA
*
56560 TTCATCAACTCATGATGAATTCTGTGAGTTGCACACATAGTGTCTGTACGGTTATTCATCAACTC
1 TTCATCAACTCATGATGAATT-TGTGAGTTGCACACATAGTGCCTGTACGGTTATTCATCAACTC
* * *
56625 ATGATGAATTTCATGAATTGCACACATAGTGCTTGTACGATTATT-ATCAACTTATGATGAATTC
65 ATGATGAATTCCATGAATTGCACATATAGT-C-TGTACGGTTATTCATCAACTTATGATGAATTC
*
56689 TGTGGATTGCACACATAGTGCATGTACGGTTATTCATCAACCCATGATAAATTCCGTGAATTACA
128 TGTGAATTGCACACATAGTGCATGTACGGTTATTCATCAACCCATGATAAATTCCGTGAATTACA
* *
56754 CACATAGTGCCTGTACAATTA
193 CACATAGTGACTGCACAATTA
* * * * * * *
56775 TTGATCAACTCATGATGAATTTCATGAATTGCATACATAGTGCCTATACGATTATTCATCAACTT
1 TTCATCAACTCATGATGAATTT-GTGAGTTGCACACATAGTGCCTGTACGGTTATTCATCAACTC
*
56840 ATGATGAATTCCATGAATTGTACATATAGTACATGTACGGTTATTCATCAACTTATGATGAATT-
65 ATGATGAATTCCATGAATTGCACATATAGT-C-TGTACGGTTATTCATCAACTTATGATGAATTC
*
56904 TCGTGAATTACACACATAGTGCATGTACGGTTATTCATCAAC
128 T-GTGAATTGCACACATAGTGCATGTACGGTTATTCATCAAC
56946 TTATGATGTG
Statistics
Matches: 336, Mismatches: 44, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
214 3 0.01
215 244 0.73
216 78 0.23
217 11 0.03
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (213 bp):
TTCATCAACTCATGATGAATTTGTGAGTTGCACACATAGTGCCTGTACGGTTATTCATCAACTCA
TGATGAATTCCATGAATTGCACATATAGTCTGTACGGTTATTCATCAACTTATGATGAATTCTGT
GAATTGCACACATAGTGCATGTACGGTTATTCATCAACCCATGATAAATTCCGTGAATTACACAC
ATAGTGACTGCACAATTA
Found at i:60083 original size:56 final size:56
Alignment explanation
Indices: 59967--60459 Score: 688
Period size: 56 Copynumber: 8.9 Consensus size: 56
59957 ATCAATACAA
* * * * *
59967 AAATTCATATACTTAGTATGACTTTCTTAG-CTTTGCACACAAAGTGCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
* * *
60022 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCTCGCAAAGTGCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
* * * *
60078 AAATTCATAAACTTATTATGAATTTCTTAGTTTTT-CACACAAAATGTCCATAAGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
*
60133 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCTCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
* * * *
60189 AAATTCATAAACTTATTATAAATTTCTTAGTTTTTGCACACATAGTGCCTATACGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
* * * *
60245 AAATTCATAAACTCATTAGGAATTTTTTAGTTTTTGCACACACAGTGCACATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
* * * *
60301 AAATTCATAAACTCATTATGAATTTTTTAGTTTTTGCACACACAGTGTCTATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
* * *
60357 AAATTCATAAA-TTATTATGAATTTCTTAGTTTTTGCAAACACGGTGCCCATACGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
* *
60412 AAATTCATTAACTTATTATGAATTTCTTAG-TTTTGCACACACGGTGCC
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCC
60460 ATTTGGTAAT
Statistics
Matches: 393, Mismatches: 42, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
55 141 0.36
56 252 0.64
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.37
Consensus pattern (56 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
Found at i:60118 original size:111 final size:111
Alignment explanation
Indices: 59967--60452 Score: 677
Period size: 111 Copynumber: 4.4 Consensus size: 111
59957 ATCAATACAA
* * * * *
59967 AAATTCATATACTTAGTATGACTTTCTTAGCTTTGCACACAAAGTGCCCATACGGAAATTCATAA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTCACACAAAGTGCCCATACGGAAATTCATAA
* * *
60032 ACTTATTATGAATTTCTTAGTTTTTGCTCGCAAAGTGCCCATACGG
66 ACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
* * *
60078 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTCACACAAAATGTCCATAAGGAAATTCATAA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTCACACAAAGTGCCCATACGGAAATTCATAA
*
60143 ACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCTCATACGG
66 ACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
* * * *
60189 AAATTCATAAACTTATTATAAATTTCTTAGTTTTTGCACACATAGTGCCTATACGAAAATTCATA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTT-CACACAAAGTGCCCATACGGAAATTCATA
* * * *
60254 AACTCATTAGGAATTTTTTAGTTTTTGCACACACAGTGCACATACGG
65 AACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
* * * * *
60301 AAATTCATAAACTCATTATGAATTTTTTAGTTTTTGCACACACAGTGTCTATACGGAAATTCATA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTT-CACACAAAGTGCCCATACGGAAATTCATA
* * *
60366 AA-TTATTATGAATTTCTTAGTTTTTGCAAACACGGTGCCCATACGA
65 AACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
* *
60412 AAATTCATTAACTTATTATGAATTTCTTAGTTTTGCACACA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTCACACA
60453 CGGTGCCATT
Statistics
Matches: 334, Mismatches: 40, Indels: 3
0.89 0.11 0.01
Matches are distributed among these distances:
110 6 0.02
111 201 0.60
112 127 0.38
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (111 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTTTCACACAAAGTGCCCATACGGAAATTCATAA
ACTTATTATGAATTTCTTAGTTTTTGCACACACAGTGCCCATACGG
Found at i:60333 original size:223 final size:222
Alignment explanation
Indices: 59961--60452 Score: 716
Period size: 223 Copynumber: 2.2 Consensus size: 222
59951 CCTACTATCA
* * * * * *
59961 ATACAAAAATTCATATACTTAGTATGACTTTCTTAGCTTTGCACACAAAGTGCCCATACGGAAAT
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAAT
* * * * *
60026 TCATAAACTTATTATGAATTTCTTAGTTTTTGCTCGCAAAGTGCCCATACGGAAATTCATAAACT
66 TCATAAACTCATTAGGAATTTCTTAGTTTTTGCACACAAAGTGCACATACGGAAATTCATAAACT
*
60091 TATTATGAATTTCTTAGTTTTT-CACACAAAATGTCCATAAGGAAATTCATAAACTTATTATGAA
131 CATTATGAATTTCTTAGTTTTTGCACACAAAATGTCCATAAGGAAATTCATAAA-TTATTATGAA
* *
60155 TTTCTTAGTTTTTGCACACACAGTGCTC
195 TTTCTTAGTTTTTGCAAACACAGTGCCC
* * * *
60183 ATACGGAAATTCATAAACTTATTATAAATTTCTTAGTTTTTGCACACATAGTGCCTATACGAAAA
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCCATACGAAAA
* *
60248 TTCATAAACTCATTAGGAATTTTTTAGTTTTTGCACACACAGTGCACATACGGAAATTCATAAAC
65 TTCATAAACTCATTAGGAATTTCTTAGTTTTTGCACACAAAGTGCACATACGGAAATTCATAAAC
* * * * *
60313 TCATTATGAATTTTTTAGTTTTTGCACACACAGTGTCTATACGGAAATTCATAAATTATTATGAA
130 TCATTATGAATTTCTTAGTTTTTGCACACAAAATGTCCATAAGGAAATTCATAAATTATTATGAA
*
60378 TTTCTTAGTTTTTGCAAACACGGTGCCC
195 TTTCTTAGTTTTTGCAAACACAGTGCCC
*
60406 ATACGAAAATTCATTAACTTATTATGAATTTCTTAGTTTTGCACACA
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
60453 CGGTGCCATT
Statistics
Matches: 239, Mismatches: 29, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
222 41 0.17
223 171 0.72
224 27 0.11
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (222 bp):
ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAAT
TCATAAACTCATTAGGAATTTCTTAGTTTTTGCACACAAAGTGCACATACGGAAATTCATAAACT
CATTATGAATTTCTTAGTTTTTGCACACAAAATGTCCATAAGGAAATTCATAAATTATTATGAAT
TTCTTAGTTTTTGCAAACACAGTGCCC
Done.