Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004516.1 Hibiscus syriacus cultivar Beakdansim tig00009959_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: 75819
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:1502 original size:21 final size:21
Alignment explanation
Indices: 1476--1518 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1466 AATCTTACAT
1476 GGGGGTATCGGTACCCTCTTG
1 GGGGGTATCGGTACCCTCTTG
1497 GGGGGTATCGGTACCCTCTTG
1 GGGGGTATCGGTACCCTCTTG
1518 G
1 G
1519 CAATCTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.23, G:0.40, T:0.28
Consensus pattern (21 bp):
GGGGGTATCGGTACCCTCTTG
Found at i:8044 original size:12 final size:11
Alignment explanation
Indices: 8012--8042 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
8002 TAATATACCC
8012 TTTAATTTCAT
1 TTTAATTTCAT
8023 TTCTAATTTCAT
1 TT-TAATTTCAT
8035 TTTAATTT
1 TTTAATTT
8043 TCTCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTAATTTCAT
Found at i:14864 original size:179 final size:178
Alignment explanation
Indices: 14564--14929 Score: 498
Period size: 179 Copynumber: 2.1 Consensus size: 178
14554 GGTAGATCAG
* * * * *
14564 ATCGAGGAACGTTGATTCATTCTACTTTTTTCAGGGAATATTGAATCAAGGCAGATTTCTTCCAC
1 ATCGAGGAACATTGATTCATTCCACTTTCTTCAGGGAATATTGAATCAAGGAAAATTTCTTCCAC
* * * * * *
14629 TGTTCCTCGGGGAAGATTAAATCTTGAAAGAGAGGGATTTGTTCCACTTTTTCTTGAGGGAAAAT
66 TATTCCTCAGGGAAGATCAAATCTTGAAAGAGAGGGATCTATTCCACTTATTCTTGAGGGAAAAT
* * * *
14694 CAGATCTGGAGATGTTAATTCATTCTATTGTTCTTTAGGGAAGATTGA
131 CAGATCTGGAGACGTTAATTCATTCCACTGTTCTTCAGGGAAGATTGA
* *
14742 ATCGAGGAGCATTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCAAGGAAAATTTGTTCCA
1 ATCGAGGAACATTGATTCATTCCACT-TTCTTCAGGGAATATTGAATCAAGGAAAATTTCTTCCA
* * * * **
14807 TTATTCCTCAGGGAAGATCAAATCTTGAAATATATGGATCTATTCTGCTTATTCTTGAGGGAAAA
65 CTATTCCTCAGGGAAGATCAAATCTTGAAAGAGAGGGATCTATTCCACTTATTCTTGAGGGAAAA
* *
14872 TCAGATCTGGGGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGA
130 TCAGATCTGGAGACGTTAATTCATTCCACTGTTCTTCAGGGAAGATTGA
14921 ATCGAGGAA
1 ATCGAGGAA
14930 GACTTGTTCC
Statistics
Matches: 161, Mismatches: 26, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
178 23 0.14
179 138 0.86
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (178 bp):
ATCGAGGAACATTGATTCATTCCACTTTCTTCAGGGAATATTGAATCAAGGAAAATTTCTTCCAC
TATTCCTCAGGGAAGATCAAATCTTGAAAGAGAGGGATCTATTCCACTTATTCTTGAGGGAAAAT
CAGATCTGGAGACGTTAATTCATTCCACTGTTCTTCAGGGAAGATTGA
Found at i:15051 original size:134 final size:134
Alignment explanation
Indices: 14753--15052 Score: 370
Period size: 134 Copynumber: 2.2 Consensus size: 134
14743 TCGAGGAGCA
* * * * * * * *
14753 TTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCAAGGAAAATTTGTTCCATTATTCCTCAG
1 TTGATTAATTCCACTATTCTTCAGGAAAGATTGAATCAAGGAAAACTTGTTCCAGTATTACTAAG
* * * *
14818 GGAAGATCAAATCTTGAAATATATGGATCTATTCTGCTTATTCTTGAGGGAAAATCAGATCTGGG
66 AGAAGATCAAATCTTGAAAGAGAGGGATCTATTCTGCTTATTCTTGAGGGAAAATCAGATCTGGG
14883 GACG
131 GACG
* * * * * *
14887 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCAGTGTTACTAAG
1 TTGATTAATTCCACTATTCTTCAGGAAAGATTGAATCAAGGAAAACTTGTTCCAGTATTACTAAG
* * *
14952 AGAATATCAAATCTTGAAAGAGAGGGTTCTATTCCT-CTTCTTCTTGAGGGAAAATCAGATCTGG
66 AGAAGATCAAATCTTGAAAGAGAGGGATCTATT-CTGCTTATTCTTGAGGGAAAATCAGATCTGG
15016 GGACG
130 GGACG
*
15021 TTGATTAATTCTACTATTCCTT-AGGAAAGATT
1 TTGATTAATTCCACTATT-CTTCAGGAAAGATT
15053 TTATCGAGTT
Statistics
Matches: 145, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
134 140 0.97
135 5 0.03
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (134 bp):
TTGATTAATTCCACTATTCTTCAGGAAAGATTGAATCAAGGAAAACTTGTTCCAGTATTACTAAG
AGAAGATCAAATCTTGAAAGAGAGGGATCTATTCTGCTTATTCTTGAGGGAAAATCAGATCTGGG
GACG
Found at i:15645 original size:42 final size:41
Alignment explanation
Indices: 15553--15653 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
15543 AGGTCTTATT
* * * *
15553 GATGGCCCGAAAGACTTATCATCTTGCTCGAAAGGCTTATA
1 GATGGCCTGAAAGACTTATCATCATGCTCGAAAGACTTACA
* * * * *
15594 GATGACCTGAAGGATTTACTCATCATGTTCGAAAGACTTACC
1 GATGGCCTGAAAGACTTA-TCATCATGCTCGAAAGACTTACA
15636 GATGGCCTGAAAGACTTA
1 GATGGCCTGAAAGACTTA
15654 CCGATGGCCC
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
41 14 0.30
42 33 0.70
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
GATGGCCTGAAAGACTTATCATCATGCTCGAAAGACTTACA
Found at i:15649 original size:20 final size:20
Alignment explanation
Indices: 15623--15675 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
15613 TCATCATGTT
15623 CGAAAGACTTACCGATGGCC
1 CGAAAGACTTACCGATGGCC
*
15643 TGAAAGACTTACCGATGGCC
1 CGAAAGACTTACCGATGGCC
*
15663 CGAAGGACTTACC
1 CGAAAGACTTACC
15676 AATTATGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (20 bp):
CGAAAGACTTACCGATGGCC
Found at i:16061 original size:233 final size:231
Alignment explanation
Indices: 15644--17147 Score: 2099
Period size: 233 Copynumber: 6.5 Consensus size: 231
15634 CCGATGGCCT
* * *
15644 GAAAGACTTACCGATGGCCCGAAGGACTTACCAATTATGGAAATAATTTACTAGGTAAGAAGCTT
1 GAAAGACTTACTGATGGCCCGAAGGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTT
* * *
15709 TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTCAAGAGA
66 TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAAA
* * *
15774 CATGTGAAAACATCCTGCCAAAAGGTCTTATGGATGGCCTGAAGGACCTATCATCTTGCTCCAAA
131 CATGTGAAAACATCCTGCC-GAAGGTCTTATGGATGGCC-GAAGGACTTATCATCTTGCTCGAAA
*
15839 GACTTATAGATGACCCGAAGTATTTAAGCATCATGCTC
194 GACTTATAGATGACCCGAAGGATTTAAGCATCATGCTC
* ** *
15877 GAAAGACATACTGATGGCCCGAAGGACTTACCAATTCTAAAAATAATTTATTAGGTAAGAAACTT
1 GAAAGACTTACTGATGGCCCGAAGGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTT
*
15942 TTCTTACTTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAAA
66 TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAAA
* * * * * *
16007 CATGTGAAAACATCCTGTCCAAAGGTCTTATAGATGGTCCAAATGATTTATCATCTTGCTTGAAA
131 CATGTGAAAACATCCTG-CCGAAGGTCTTATGGATGG-CCGAAGGACTTATCATCTTGCTCGAAA
* * * ** *
16072 GAATTATATATGACCCAAAAAATTTAAGCATCATGCTT
194 GACTTATAGATGACCCGAAGGATTTAAGCATCATGCTC
* *
16110 GAAAGACTTACTGATGGCCCGAAAGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAGACTT
1 GAAAGACTTACTGATGGCCCGAAGGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTT
* * * *
16175 TTCTTAC-ATT-AAAAAATT-AATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTTGAGAAA
66 TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAAA
* *
16237 CATGTGAAAACATCTTGCCTGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAA
131 CATGTGAAAACATCCTGCC-GAAGGTCTTATGGATGG-CCGAAGGACTTATCATCTTGCTCGAAA
* * *
16302 GACTTATAGATAACCCGAAGAATTTAAACATCATGCTC
194 GACTTATAGATGACCCGAAGGATTTAAGCATCATGCTC
*
16340 GAAAGACTTACTGATGGCCCGAAGGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACAT
1 GAAAGACTTACTGATGGCCCGAAGGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTT
*
16405 TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTC-A-AAT
66 TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAA-
* * * * * *
16468 GACATGTGAAAGCATCCCGCCCGAATGTCTTTTGGATGGCTCGAAGAACTTATCATCTTGCTTGA
130 -ACATGTGAAAACATCCTG-CCGAAGGTCTTATGGATGGC-CGAAGGACTTATCATCTTGCTCGA
** * *
16533 AAGACTTACGGATGACTCGATGGATTTAAGCATCATGCTC
192 AAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTC
* *
16573 G-AA-ACTTACTGATGGCCCGCCCGAACGACTTACCAATTATGGAAATAATTTACTAGGTAAGAA
1 GAAAGACTTACTGAT-G---GCCCGAAGGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAA
* ** *
16636 ACTTTTCTTATTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATATTACTCATTTTTCGA
62 ACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGA
* *
16701 GAAACATGTGAAAACATCCTGCCCGAAGTTCTTATGGATGGGCCGAAGGACTTATCATATTGCTC
127 GAAACATGTGAAAACATCCTG-CCGAAGGTCTTATGGAT-GGCCGAAGGACTTATCATCTTGCTC
* * *
16766 GAAAGATTTACAGATGACCCGAAGGATTTAAGCATCATGCTT
190 GAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTC
* *
16808 AAAAGACTTACTGATGGCTCGAAGGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTT
1 GAAAGACTTACTGATGGCCCGAAGGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTT
* *
16873 TTCTTACTTTTAAAAAATTTCAATTTTCAGATTTAACTGAGAAACCTTTCTCATTTTTCGAGAAA
66 TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAAA
* *
16938 CATGTGAAAACATCCTATCCGAAGGTCTTATGGATGGCCCGAAGGACCTATCATCTTGCTCGAAA
131 CATGTGAAAACATCCT-GCCGAAGGTCTTATGGATGG-CCGAAGGACTTATCATCTTGCTCGAAA
* *
17003 GACTTATAGATGACCTGAAGGATTTAAACATCATGCTC
194 GACTTATAGATGACCCGAAGGATTTAAGCATCATGCTC
* * ** * *
17041 GAAAGACTTACTGATGGCCCGAATGACTTACTAATTCTACAAATGA-TTACTAGTTAAGAAACTT
1 GAAAGACTTACTGATGGCCCGAAGGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTT
17105 TTCTTACTTTTCAAAAATTTCAATATTT-AGATTTAAATGAGAA
66 TTCTTACTTTTCAAAAATTTCAAT-TTTCAGATTTAAATGAGAA
17148 TTTTTTTTCT
Statistics
Matches: 1126, Mismatches: 123, Indels: 45
0.87 0.10 0.03
Matches are distributed among these distances:
229 2 0.00
230 194 0.17
231 21 0.02
232 70 0.06
233 626 0.56
234 6 0.01
235 188 0.17
236 7 0.01
237 12 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (231 bp):
GAAAGACTTACTGATGGCCCGAAGGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTT
TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAAA
CATGTGAAAACATCCTGCCGAAGGTCTTATGGATGGCCGAAGGACTTATCATCTTGCTCGAAAGA
CTTATAGATGACCCGAAGGATTTAAGCATCATGCTC
Found at i:16361 original size:42 final size:41
Alignment explanation
Indices: 16263--16369 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 41
16253 GCCTGAAGGT
* * * *
16263 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGA
1 CTTATAGATGGCCCGAAGAACTTAACATCATGCTCAAAAGA
** * *
16304 CTTATAGATAACCCGAAGAATTTAAACATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGAACTT-AACATCATGCTCAAAAGA
*
16346 CTTACT-GATGGCCCGAAGGACTTA
1 CTTA-TAGATGGCCCGAAGAACTTA
16370 CCAATTCTGG
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
41 19 0.37
42 32 0.62
43 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGAACTTAACATCATGCTCAAAAGA
Found at i:16840 original size:468 final size:464
Alignment explanation
Indices: 15644--17152 Score: 2115
Period size: 468 Copynumber: 3.2 Consensus size: 464
15634 CCGATGGCCT
* * *
15644 GAAAGACTTACCGATGGCCCGAAGGACTTACCAATTATGGAAATAATTTACTAGGTAAGAAGCTT
1 GAAAGACTTACTGATGGCCCGAAAGACTTACCAATTATGGAAATAATTTACTAGGTAAGAAACTT
* *
15709 TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTCAAGAGA
66 TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAA-TTTTCTCATTTTTCGAGAAA
* * *
15774 CATGTGAAAACATCCTGCCAAAAGGTCTTATGGAT-GGCCTGAAGGACCTATCATCTTGCTCCAA
130 CATGTGAAAACATCCTGCCAGAAGGTCTTATGGATGGGCC-GAAGGACTTATCATCTTGCTCAAA
* *
15838 AGACTTATAGATGACCCGAAGTATTTAAGCATCATGCTCGAAAGACATACTGATGGCCCGAAGGA
194 AGACTTATAGATGACCCGAAGAATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGA
** *
15903 CTTACCAATTCTAAAAATAATTTATTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTT
259 CTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTT
* *
15968 TTAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAAACATGTGAAAACATCCTGTCCAAAGGT
324 TCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAAACATGTGAAAACATCCTGTCCGAAGGT
* * * * * * **
16033 CTTATAGATGG-TCCAA-ATGATTTATCATCTTGCTTGAAAGAATTATATATGACCCAAAAAATT
389 CTTATGGATGGCTCGAAGA--ACTTATCATCTTGCTTGAAAGACTTATAGATGA-CCGAAGGATT
*
16096 TAAGCATCATGCTT
451 TAAGCATCATGCTC
* *
16110 GAAAGACTTACTGATGGCCCGAAAGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAGACTT
1 GAAAGACTTACTGATGGCCCGAAAGACTTACCAATTATGGAAATAATTTACTAGGTAAGAAACTT
* * * * *
16175 TTCTTAC-ATT-AAAAAATT-AATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTTGAGAAA
66 TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAA-TTTTCTCATTTTTCGAGAAA
* * *
16237 CATGTGAAAACATCTTGCCTGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAA
130 CATGTGAAAACATCCTGCCAGAAGGTCTTATGGATGGGCCGAAGGACTTATCATCTTGCTCAAAA
* *
16302 GACTTATAGATAACCCGAAGAATTTAAACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
195 GACTTATAGATGACCCGAAGAATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
*
16367 TTACCAATTCTGGAAATAATTTACTAGGTAAGAAACATTTCTTACTTTTCAAAAATTTCAATTTT
260 TTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTT
* * * * *
16432 CAGATTTAAATGAGAAACTTTTCTCATTTTTC-A-AATGACATGTGAAAGCATCCCGCCCGAATG
325 CAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAA--ACATGTGAAAACATCCTGTCCGAAGG
* ** *
16495 TCTTTTGGATGGCTCGAAGAACTTATCATCTTGCTTGAAAGACTTACGGATGACTCGATGGATTT
388 TCTTATGGATGGCTCGAAGAACTTATCATCTTGCTTGAAAGACTTATAGATGAC-CGAAGGATTT
16560 AAGCATCATGCTC
452 AAGCATCATGCTC
*
16573 G-AA-ACTTACTGATGGCCCGCCCGAACGACTTACCAATTATGGAAATAATTTACTAGGTAAGAA
1 GAAAGACTTACTGAT-G---GCCCGAAAGACTTACCAATTATGGAAATAATTTACTAGGTAAGAA
* *
16636 ACTTTTCTTATTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATATTACTCATTTTTCGA
62 ACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAAT-TTTCTCATTTTTCGA
* * *
16701 GAAACATGTGAAAACATCCTGCCCGAAGTTCTTATGGATGGGCCGAAGGACTTATCATATTGCTC
126 GAAACATGTGAAAACATCCTGCCAGAAGGTCTTATGGATGGGCCGAAGGACTTATCATCTTGCTC
* * * * ** *
16766 GAAAGATTTACAGATGACCCGAAGGATTTAAGCATCATGCTTAAAAGACTTACTGATGGCTCGAA
191 AAAAGACTTATAGATGACCCGAAGAATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAA
*
16831 GGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTTTTCTTACTTTTAAAAAATTTCAA
256 GGACTTACCAATTCTGGAAATAATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAA
* *
16896 TTTTCAGATTTAACTGAGAAACCTTTCTCATTTTTCGAGAAACATGTGAAAACATCCTATCCGAA
321 TTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAAACATGTGAAAACATCCTGTCCGAA
* * * *
16961 GGTCTTATGGATGGCCCGAAGGACCTATCATCTTGCTCGAAAGACTTATAGATGACCTGAAGGAT
386 GGTCTTATGGATGGCTCGAAGAACTTATCATCTTGCTTGAAAGACTTATAGATGACC-GAAGGAT
*
17026 TTAAACATCATGCTC
450 TTAAGCATCATGCTC
* * * ** * *
17041 GAAAGACTTACTGATGGCCCGAATGACTTACTAATTCTACAAATGA-TTACTAGTTAAGAAACTT
1 GAAAGACTTACTGATGGCCCGAAAGACTTACCAATTATGGAAATAATTTACTAGGTAAGAAACTT
*
17105 TTCTTACTTTTCAAAAATTTCAATATTT-AGATTTAAATGAGAATTTTT
66 TTCTTACTTTTCAAAAATTTCAAT-TTTCAGATTTAAATGAGAAATTTT
17153 TTTCTCATTT
Statistics
Matches: 925, Mismatches: 98, Indels: 42
0.87 0.09 0.04
Matches are distributed among these distances:
461 12 0.01
462 5 0.01
463 324 0.35
464 16 0.02
465 111 0.12
466 96 0.10
467 8 0.01
468 337 0.36
469 4 0.00
470 12 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (464 bp):
GAAAGACTTACTGATGGCCCGAAAGACTTACCAATTATGGAAATAATTTACTAGGTAAGAAACTT
TTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAATTTTCTCATTTTTCGAGAAAC
ATGTGAAAACATCCTGCCAGAAGGTCTTATGGATGGGCCGAAGGACTTATCATCTTGCTCAAAAG
ACTTATAGATGACCCGAAGAATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACT
TACCAATTCTGGAAATAATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTC
AGATTTAAATGAGAAACCTTTCTCATTTTTCGAGAAACATGTGAAAACATCCTGTCCGAAGGTCT
TATGGATGGCTCGAAGAACTTATCATCTTGCTTGAAAGACTTATAGATGACCGAAGGATTTAAGC
ATCATGCTC
Found at i:17023 original size:41 final size:42
Alignment explanation
Indices: 16964--17063 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
16954 ATCCGAAGGT
* * * *
16964 CTTATGGATGGCCCGAAGGACCT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACCTAAACATCATGCTCGAAAGA
* **
17005 CTTATAGATGACCTGAAGGATTTAAACATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACCTAAACATCATGCTCGAAAGA
*
17047 CTTACT-GATGGCCCGAA
1 CTTA-TAGATGACCCGAA
17064 TGACTTACTA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
41 18 0.38
42 29 0.60
43 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGACCTAAACATCATGCTCGAAAGA
Found at i:22261 original size:20 final size:21
Alignment explanation
Indices: 22219--22258 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
22209 AATCTTACAT
22219 GGGGGTATCGGTACCCTCTTG
1 GGGGGTATCGGTACCCTCTTG
22240 GGGGGTATCGGTACCCTCT
1 GGGGGTATCGGTACCCTCT
22259 GGGCAATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.25, G:0.38, T:0.28
Consensus pattern (21 bp):
GGGGGTATCGGTACCCTCTTG
Found at i:23692 original size:23 final size:22
Alignment explanation
Indices: 23645--23726 Score: 103
Period size: 23 Copynumber: 3.7 Consensus size: 22
23635 AGACCCCATG
***
23645 GGGGGTATCGGTA-CCCTCCTG
1 GGGGGTATCGGTACCCCTCAAA
23666 GGGGGTATCGGTACCCACTCAAA
1 GGGGGTATCGGTACCC-CTCAAA
*
23689 GGGGGAATCGGTACCCCTTCAAA
1 GGGGGTATCGGTACCCC-TCAAA
23712 GGGGGTATCGGTACC
1 GGGGGTATCGGTACC
23727 TCCTGCACCA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
21 13 0.25
22 3 0.06
23 37 0.70
ACGTcount: A:0.20, C:0.26, G:0.35, T:0.20
Consensus pattern (22 bp):
GGGGGTATCGGTACCCCTCAAA
Found at i:29662 original size:17 final size:18
Alignment explanation
Indices: 29625--29665 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29615 TTGACCGGTT
29625 TTGACCCGACCCGACCCG
1 TTGACCCGACCCGACCCG
* *
29643 TTGACCCGATCTGA-CCG
1 TTGACCCGACCCGACCCG
29660 TTGACC
1 TTGACC
29666 GTTGACCGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.17, C:0.41, G:0.22, T:0.20
Consensus pattern (18 bp):
TTGACCCGACCCGACCCG
Found at i:29722 original size:29 final size:29
Alignment explanation
Indices: 29680--29836 Score: 147
Period size: 29 Copynumber: 5.4 Consensus size: 29
29670 ACCGAGTGAC
* **
29680 ATTTTAGGAA-TTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTTAATTCGAAA-AAGTGCT
** *
29709 ATTTTGGGAA-TTAATTCGAAATGTGTGAT
1 ATTTTGGGAATTTAATTCGAAA-AAGTGCT
* *
29738 ATTTTAGGAATTTAATTCGAAAAAGTGTT
1 ATTTTGGGAATTTAATTCGAAAAAGTGCT
* * *
29767 ATCTTGAGAATTTAATTCGAAAAAGTGTT
1 ATTTTGGGAATTTAATTCGAAAAAGTGCT
* * *
29796 ATCTTGAGAATTTAATTCGAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAGTGCT
*
29825 ATTTTGGTAATT
1 ATTTTGGGAATT
29837 ATTTTAAAAA
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
29 101 0.90
30 11 0.10
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCGAAAAAGTGCT
Found at i:29853 original size:58 final size:57
Alignment explanation
Indices: 29680--29857 Score: 173
Period size: 58 Copynumber: 3.1 Consensus size: 57
29670 ACCGAGTGAC
* * ** *
29680 ATTTTAGGAA-TTAATTCGAAATGGGTGCTATTTTGGGAATTAATTCGAAATGTGTGAT
1 ATTTGAGGAATTTAATTCGAAA-AGGTGCTATTTT-GGAATTAATTCGAAAAATGTGTT
* * * *
29738 ATTTTAGGAATTTAATTCGAAAAAGTGTTATCTTGAGAATTTAATTCGAAAAA-GTGTT
1 ATTTGAGGAATTTAATTCGAAAAGGTGCTATTTTG-GAA-TTAATTCGAAAAATGTGTT
* **
29796 ATCTTGA-GAATTTAATTCGAAAAGGTGCTATTTTGGTAATTATTTTAAAAAATGTGTT
1 AT-TTGAGGAATTTAATTCGAAAAGGTGCTATTTTGG-AATTAATTCGAAAAATGTGTT
29854 ATTT
1 ATTT
29858 CTGTAAATTG
Statistics
Matches: 100, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
57 14 0.14
58 61 0.61
59 25 0.25
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (57 bp):
ATTTGAGGAATTTAATTCGAAAAGGTGCTATTTTGGAATTAATTCGAAAAATGTGTT
Found at i:30980 original size:117 final size:117
Alignment explanation
Indices: 30766--31057 Score: 419
Period size: 117 Copynumber: 2.5 Consensus size: 117
30756 GGAAGTATTT
* * *
30766 CAGGCTCCTTTGTTGTGTCCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGTTTCTGG
1 CAGGCTCCTTTGTTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
* * *
30831 GGAACCTACACATTGTACTGATTGGAGTGACTGGATGGGGAA-GTTATTACTG
66 GGAACCTACACATTGTACTGATTGGAGCGACTGGAT-AGAAACGTTATTACTG
*
30883 CAGGCTCCTTTGTTGTGTGCTTAGGGAAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGTTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
* *
30948 GGAACCTACACATTGTAGTGA-TGGAAGCGACTGGATAGAAACGTTATTACTT
66 GGAACCTACACATTGTACTGATTGG-AGCGACTGGATAGAAACGTTATTACTG
* ** *
31000 TAGGCTCCTCAGCTT-CGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
1 CAGGCTCCTTTG-TTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
31058 TTCGGGAAAA
Statistics
Matches: 158, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
116 6 0.04
117 150 0.95
118 2 0.01
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.33
Consensus pattern (117 bp):
CAGGCTCCTTTGTTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
GGAACCTACACATTGTACTGATTGGAGCGACTGGATAGAAACGTTATTACTG
Found at i:37179 original size:13 final size:13
Alignment explanation
Indices: 37161--37201 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
37151 TTGACCGGTT
37161 TTGACCCGACCCG
1 TTGACCCGACCCG
37174 TTGACCCGACCC-
1 TTGACCCGACCCG
37186 --GACCCGA-CCG
1 TTGACCCGACCCG
37196 TTGACC
1 TTGACC
37202 GAGTGACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.08
10 7 0.28
12 4 0.16
13 12 0.48
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.15
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:37251 original size:29 final size:27
Alignment explanation
Indices: 37209--37357 Score: 127
Period size: 29 Copynumber: 5.1 Consensus size: 27
37199 ACCGAGTGAC
*
37209 ATTTTGAGAATTAATTCAAAATGGGTGCT
1 ATTTTGGGAATTAATTCAAAA--GGTGCT
*
37238 ATTTTGGGAATTAATTCGAAAAGGGTGAT
1 ATTTTGGGAATTAATTC-AAAA-GGTGCT
**
37267 ATTTTGGGAATTTAATTCAAAAAAATGCT
1 ATTTTGGGAA-TTAATTC-AAAAGGTGCT
**
37296 ATTTTGATAATTTAATTCGAAAAGGTGCT
1 ATTTTGGGAA-TTAATTC-AAAAGGTGCT
* * *
37325 ATTTTGGTAATTATTTTAAAAATGGTGCT
1 ATTTTGGGAATTA-ATTCAAAA-GGTGCT
37354 ATTT
1 ATTT
37358 CTGTAAAATA
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
28 7 0.07
29 80 0.78
30 15 0.15
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (27 bp):
ATTTTGGGAATTAATTCAAAAGGTGCT
Found at i:37354 original size:58 final size:59
Alignment explanation
Indices: 37204--37357 Score: 165
Period size: 58 Copynumber: 2.7 Consensus size: 59
37194 CGTTGACCGA
* * *
37204 GTGACATTTTGAGAA-TTAATTC-AAAATGGGTGCTATTTTGGGAATTAATTCGAAAAGG
1 GTGATATTTTGGGAATTTAATTCAAAAAT-GGTGCTATTTTGAGAATTAATTCGAAAAGG
** *
37262 GTGATATTTTGGGAATTTAATTCAAAAA-AATGCTATTTTGATAATTTAATTCGAAAA-G
1 GTGATATTTTGGGAATTTAATTCAAAAATGGTGCTATTTTGAGAA-TTAATTCGAAAAGG
* * * *
37320 GTGCTATTTTGGTAA-TTATTTTAAAAATGGTGCTATTT
1 GTGATATTTTGGGAATTTAATTCAAAAATGGTGCTATTT
37358 CTGTAAAATA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
57 10 0.12
58 47 0.59
59 19 0.24
60 4 0.05
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (59 bp):
GTGATATTTTGGGAATTTAATTCAAAAATGGTGCTATTTTGAGAATTAATTCGAAAAGG
Found at i:38495 original size:117 final size:117
Alignment explanation
Indices: 38284--38572 Score: 420
Period size: 117 Copynumber: 2.5 Consensus size: 117
38274 AGTATTTCAG
* *
38284 GCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGA
1 GCTCCTTTGTTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGA
* * * *
38349 ACCTATACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTACTGCAA
66 ACCTACACATTGTAGTGATTGGAGCGACTGGATAGAGAAGTTATTACTGCAA
* *
38401 GCTCCTTTGTTGTGTGCTTAGGGAAAGTCCTTACTGGTGTACAGGTGGGTGTATGGTTCTGGGGA
1 GCTCCTTTGTTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGA
* * *
38466 ACCTACACATTGTAGTGA-TGGAAGCGACTGGATAGAGACGTTATTATTGCAG
66 ACCTACACATTGTAGTGATTGG-AGCGACTGGATAGAGAAGTTATTACTGCAA
** *
38518 GCTCCTCGGCTT-CGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
1 GCTCCTTTG-TTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
38573 TTCGGGAAAA
Statistics
Matches: 154, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
116 3 0.02
117 149 0.97
118 2 0.01
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (117 bp):
GCTCCTTTGTTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGA
ACCTACACATTGTAGTGATTGGAGCGACTGGATAGAGAAGTTATTACTGCAA
Found at i:41880 original size:12 final size:12
Alignment explanation
Indices: 41865--41895 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
41855 AAACAAGGAC
*
41865 CAAAACACAAAA
1 CAAAAAACAAAA
41877 CAAAAAACAAAA
1 CAAAAAACAAAA
41889 CAAAAAA
1 CAAAAAA
41896 GCACAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAAACAAAA
Found at i:54143 original size:45 final size:45
Alignment explanation
Indices: 54116--54204 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
54106 ATCTGGAGAT
* * * *
54116 GTTGATTCATTCTATTGTTCTTTAGGGAAGATTGAATCAAGGAAC
1 GTTGATTCATTCCACTGTTCTTCAGGGAAAATTGAATCAAGGAAC
* *
54161 GTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCATGGAA
1 GTTGATTCATTCCACTGTTCTTCAGGGAAAATTGAATCAAGGAA
54205 AATTTGTTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (45 bp):
GTTGATTCATTCCACTGTTCTTCAGGGAAAATTGAATCAAGGAAC
Found at i:54282 original size:179 final size:179
Alignment explanation
Indices: 53946--54331 Score: 495
Period size: 179 Copynumber: 2.2 Consensus size: 179
53936 AGGGATATAC
* * * * * *
53946 TCCACTGTTTCTTCAGGGTAGA-TCAGATCGAGGAATGTTGATTCATTCTACTATTTTTCAGGGA
1 TCCACTG-TTCTTCAGGGAAGATTGA-ATCAAGGAACGTTGATTCATTCCACTATTCTTCAGGGA
* * * * * * *
54010 TTATTGAATCAAGGAAGATTTGTTCCACTGTTCCTCGGGGAATATTAAATCTTGAAAGAGAGGGA
64 ATATTGAATCAAGGAAAATTTGTTCCACTATTCCTCAGGGAAGATCAAATCTTGAAAGAGAAGGA
* * * *
54075 TTTGTTCCACTTCTTCTTGAGGGAAAATTAGATCTGGAGATGTTGATTCAT
129 TCTATTACACTTATTCTTGAGGGAAAATTAGATCTGGAGATGTTGATTCAT
* * * *
54126 TCTATTGTTCTTTAGGGAAGATTGAATCAAGGAACGTTGATTCATTCCACTGTTCTTCAGGGAAT
1 TCCACTGTTCTTCAGGGAAGATTGAATCAAGGAACGTTGATTCATTCCACTATTCTTCAGGGAAT
* * * *
54191 ATTGAATCATGGAAAATTTGTTCCATTATTCCTCAGGGAAGATCAAATCTTGAAAGGGAATGATC
66 ATTGAATCAAGGAAAATTTGTTCCACTATTCCTCAGGGAAGATCAAATCTTGAAAGAGAAGGATC
** *
54256 TATTATGCTTATTCTTGAGGGAAAATTAGATCTGGGGATGTTGATTCAT
131 TATTACACTTATTCTTGAGGGAAAATTAGATCTGGAGATGTTGATTCAT
54305 TCCACTGTTCTTCAGGGAAGATTGAAT
1 TCCACTGTTCTTCAGGGAAGATTGAAT
54332 TGAGGAAGAA
Statistics
Matches: 174, Mismatches: 31, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
179 167 0.96
180 7 0.04
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (179 bp):
TCCACTGTTCTTCAGGGAAGATTGAATCAAGGAACGTTGATTCATTCCACTATTCTTCAGGGAAT
ATTGAATCAAGGAAAATTTGTTCCACTATTCCTCAGGGAAGATCAAATCTTGAAAGAGAAGGATC
TATTACACTTATTCTTGAGGGAAAATTAGATCTGGAGATGTTGATTCAT
Found at i:54373 original size:134 final size:134
Alignment explanation
Indices: 54159--54466 Score: 352
Period size: 134 Copynumber: 2.3 Consensus size: 134
54149 GAATCAAGGA
* * * * *
54159 ACGTTGATTCATTCCACTGTTCTTCAGGGAATATTGAATCATGGAAAATTTGTTCCATTATTCCT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCATGGAAAATTTATTACACTATTACT
* * * * ** *
54224 CAGGGAAGATCAAATCTTGAAAGGGAATGATCTATTATGCTTATTCTTGAGGGAAAATTAGATCT
66 CAAGGAAGATCAAATCTTAAAAGAGAAGGATCTATTACACTTATTCTTGAGGGAAAATCAGATCT
54289 GGGG
131 GGGG
* * *
54293 ATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATTGA-GGAAGAA-TTATTACACTGTTA
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAA-TCATGGAA-AATTTATTACACTATTA
* * * * *
54356 CTCAAGGAATATCAAATCTTAAAAGAGAGGGTTCTATTCCACTTTTTCTTGAGGGAAAATCAGAT
64 CTCAAGGAAGATCAAATCTTAAAAGAGAAGGATCTATTACACTTATTCTTGAGGGAAAATCAGAT
54421 CTGGGG
129 CTGGGG
* * * *
54427 ACGTTGATTTATTCCACTATTCCTT-AGGAAAGATTTAATC
1 ACGTTGATTCATTCCACTGTT-CTTCAGGGAAGATTGAATC
54467 GAGTTCAATT
Statistics
Matches: 145, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
133 1 0.01
134 137 0.94
135 7 0.05
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (134 bp):
ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCATGGAAAATTTATTACACTATTACT
CAAGGAAGATCAAATCTTAAAAGAGAAGGATCTATTACACTTATTCTTGAGGGAAAATCAGATCT
GGGG
Found at i:55059 original size:42 final size:42
Alignment explanation
Indices: 54964--55065 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 42
54954 AGGTCTTATG
* * * *
54964 GATGGCTCGAAAGACTTA-TCATCTTGCTCGAAAGGATTATA
1 GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGGATTACA
* * * *
55005 GATGACCTGAAGGATTTACTCATCATGCTCGAAA-GACTTACC
1 GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGGA-TTACA
55047 GATGGCCCGAAGGACTTAC
1 GATGGCCCGAAGGACTTAC
55066 CAATTATGGA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 15 0.31
42 33 0.69
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGGATTACA
Found at i:55195 original size:233 final size:233
Alignment explanation
Indices: 54774--56571 Score: 2093
Period size: 233 Copynumber: 7.6 Consensus size: 233
54764 ATATGACTCA
* * ** * * *
54774 AAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCTTGAAGGACTTACTAATTTTGGAAGT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTATGGAAAT
* * * * *
54839 AGTTTACTAAGAAACTTTGGAAATCATTTTCTCACTTTTCAAAAACTTCAATTTTCAGATTTAAA
66 AATTTACTAGGTAA-----GAAA-C-TTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAA
* * * * *
54904 TGAGAAAATTTTCTCAGTTTTCTAAAAACAAT-CGAAAACA-CCTTG-TCTGAAGGTCTTATGGA
124 TGAGAAACTTTTCTCATTTTTCGAGAAAC-ATGTGAAAACATCC-TGCTC-GAAGGTCTTATGGA
* * *
54966 TGGCTCGAAAGACTTATCATCTTGCTCGAAAGGA-TTATAGATGACCTG
186 TGGCTCGAAGGACTTATCATCTTGCTCGAAA-GACTTACAGATGACCCG
** *
55014 AAGGATTTACTCATCATGCTCGAAAGACTTACCGATGGCCCGAAGGACTTACCAATTATGGAAAT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTATGGAAAT
* *
55079 AATTTACTAGGTAAGAAACTTTTCTTAATTTTCAAAAATTTCAATTTTCAGATTTAAATTAGAAA
66 AATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAA
* * * * *
55144 CTTTTCTCATTTTTCAAGAGACACGTGAAAACATCCTGCTCGAAAGTCTTATGGATAGC-CTGAA
131 CTTTTCTCATTTTTCGAGAAACATGTGAAAACATCCTGCTCGAAGGTCTTATGGATGGCTC-GAA
* *
55208 GGACCTATCATCTTGCTCCAAAGACTTACAGATGACCCG
195 GGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCG
* * * * *
55247 AAGGATTAAAGCATCATGCTCG-AA-ACATACTGATGGCCCGAAAGACTTACCAATTCTAGAAAT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTATGGAAAT
* * *
55310 AATTTATTAGGTAAGAAATTTTTCTTACTTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAA
66 AATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAA
* * * * * *
55375 CCTTTCTCATTTTTTGAGAAACATGTGAAAACATCTTGCCCGAAGGTCTTATAGATGG-TCCAAA
131 CTTTTCTCATTTTTCGAGAAACATGTGAAAACATCCTGCTCGAAGGTCTTATGGATGGCT-CGAA
* * * * * * *
55439 TGACTAATCATCTTGCTTGAAATAATTACATATGACCCA
195 GGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCG
** * *
55478 AAATATTTAAGCATCATGCTTGAAAGAGTTACTGATGGCCCGAAGGACTTACCAATTATGGAAAT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTATGGAAAT
* ** * *
55543 AATTTACTAGGTAAGAGACTTTTCTTACTTTAAAAAAAATTCAATTTTCATATTTAAATGAGAAA
66 AATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAA
* * * * *
55608 CCTTTCTCATTTTTTGAGAAACATGTGAAAACATCCTGCTTGAATGTCTTATGGATGGCCCGAAG
131 CTTTTCTCATTTTTCGAGAAACATGTGAAAACATCCTGCTCGAAGGTCTTATGGATGGCTCGAAG
* *
55673 GACTTATCATCTTGCTCGAAATACTTATAGATGACCCG
196 GACTTATCATCTTGCTCGAAAGACTTACAGATGACCCG
* * ** * * *
55711 AAGAATTTAAACATCATTTTTGAAAAGACTTACTGATGGCCCGAAGGACTTACCAATTCTGAAAA
1 AAGGATTTAAGCATCATGCTCG-AAAGACTTACTGATGGCCCGAAGGACTTACCAATTATGGAAA
*
55776 TAATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAGTTTCAATTTTCAGATTTAAATGAGAA
65 TAATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAA
* * * * *
55841 ACTTTTCTCATTTTTCGA-AAGACATGTGAAAGCATCCTGCCCGAATGTCTTTTGGATGGCTCAA
130 ACTTTTCTCATTTTTCGAGAA-ACATGTGAAAACATCCTGCTCGAAGGTCTTATGGATGGCTCGA
* * * * *
55905 AGAACTTATCATCTTACTCGGAAGACTTACGGATGACTCG
194 AGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCG
*
55945 AAGGATTTAAGCATCATGCTCG-AA-ACTTACTGATGGTCCGAAGGACTTACCAATTATGGAAAT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTATGGAAAT
* *
56008 AATTTGCTAGGTAAGAAACTTTTCTTATTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAA
66 AATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAA
* *
56073 -TATTTCTCA-TTTTCGAGAAACATGTGAAAACATCCTGCCCGAAGTTCTTATGGATGGGC-CGA
131 CT-TTTCTCATTTTTCGAGAAACATGTGAAAACATCCTGCTCGAAGGTCTTATGGAT-GGCTCGA
* *
56135 AGGATTTATCATATTGCTCGAAAGACTTACAGATGACCCG
194 AGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCG
*
56175 AAGGATTTAAGCATCATGCTCGAAAGACTTAAC-GATGGCTCGAAGGACTTAACGATGGCTTGAA
1 AAGGATTTAAGCATCATGCTCGAAAGACTT-ACTGATGGCCCGAAGGACTT-AC-----C----A
*
56239 GGACTTAACAATTCTGGAAATAATTTACTAGGTAAGAAACTTTTCTTACTTTTTAAAAATTTCAA
55 --A-TT----A---TGGAAATAATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAA
* * *
56304 TTTTCAGATTTAACTGAGAAAGC-TTTCTCATTTTTTGAGAAACATGTGAAAACATCCT-ATCTG
110 TTTTCAGATTTAAATGAGAAA-CTTTTCTCATTTTTCGAGAAACATGTGAAAACATCCTGCTC-G
* * * **
56367 AAGGTCTTATGGATGGCCCGAAGGACCTATCATCTTGCTCGAAAGACTTATAGATGACTTG
173 AAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCG
* * *
56428 AAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACCAATTCTGGAAAT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTATGGAAAT
* * *
56493 GATTTACTAGGTAAGAAAATTTTCTTACTTTTCAAAAATTTCAATATTT-AGATTTAAATGAGAT
66 AATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAAT-TTTCAGATTTAAATGAGAA
**
56557 TTTTTTCTCATTTTT
130 ACTTTTCTCATTTTT
56572 TAACTTATAA
Statistics
Matches: 1340, Mismatches: 172, Indels: 99
0.83 0.11 0.06
Matches are distributed among these distances:
230 97 0.07
231 304 0.23
232 30 0.02
233 413 0.31
234 209 0.16
235 4 0.00
238 1 0.00
240 70 0.05
241 1 0.00
242 1 0.00
243 1 0.00
244 1 0.00
245 2 0.00
247 1 0.00
249 1 0.00
252 83 0.06
253 121 0.09
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (233 bp):
AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTATGGAAAT
AATTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAA
CTTTTCTCATTTTTCGAGAAACATGTGAAAACATCCTGCTCGAAGGTCTTATGGATGGCTCGAAG
GACTTATCATCTTGCTCGAAAGACTTACAGATGACCCG
Found at i:56217 original size:20 final size:20
Alignment explanation
Indices: 56192--56247 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
56182 TAAGCATCAT
*
56192 GCTCGAAAGACTTAACGATG
1 GCTCGAAGGACTTAACGATG
56212 GCTCGAAGGACTTAACGATG
1 GCTCGAAGGACTTAACGATG
*
56232 GCTTGAAGGACTTAAC
1 GCTCGAAGGACTTAAC
56248 AATTCTGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (20 bp):
GCTCGAAGGACTTAACGATG
Found at i:63063 original size:13 final size:13
Alignment explanation
Indices: 63045--63069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63035 ACATCCATAA
63045 TAAATCCAAACAG
1 TAAATCCAAACAG
63058 TAAATCCAAACA
1 TAAATCCAAACA
63070 CATTAAAAAG
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:0.56, C:0.24, G:0.04, T:0.16
Consensus pattern (13 bp):
TAAATCCAAACAG
Found at i:64565 original size:13 final size:14
Alignment explanation
Indices: 64547--64581 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
64537 ATGGGCAATT
64547 TTTGAAAACCAA-G
1 TTTGAAAACCAAGG
64560 TTTGAAAACCAAGG
1 TTTGAAAACCAAGG
64574 TTTGAAAA
1 TTTGAAAA
64582 TCAATACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (14 bp):
TTTGAAAACCAAGG
Found at i:64619 original size:19 final size:19
Alignment explanation
Indices: 64579--64615 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
64569 CAAGGTTTGA
*
64579 AAATCAATACAACACAATT
1 AAATCAATAAAACACAATT
64598 AAATCAA-AAAACACAATT
1 AAATCAATAAAACACAATT
64616 TAAAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (19 bp):
AAATCAATAAAACACAATT
Found at i:65059 original size:21 final size:22
Alignment explanation
Indices: 65035--65114 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
65025 ACCCCGTGAA
**
65035 GGGTATCGGTA-CCCTCCTAGG
1 GGGTATCGGTACCCCTCAAAGG
*
65056 GGGTATCGGTAGCCACTCAAAGG
1 GGGTATCGGTA-CCCCTCAAAGG
*
65079 GGGAATCGGTACCCCTTCAAAGG
1 GGGTATCGGTACCCC-TCAAAGG
*
65102 GGGTATCGATACC
1 GGGTATCGGTACC
65115 TCCTACACCA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
21 11 0.22
22 3 0.06
23 35 0.71
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.20
Consensus pattern (22 bp):
GGGTATCGGTACCCCTCAAAGG
Found at i:69639 original size:21 final size:21
Alignment explanation
Indices: 69613--69655 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
69603 AATCTTACAT
69613 GGGGGTATCGGTACCCTCTTG
1 GGGGGTATCGGTACCCTCTTG
69634 GGGGGTATCGGTACCCTCTTG
1 GGGGGTATCGGTACCCTCTTG
69655 G
1 G
69656 CAATCTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.23, G:0.40, T:0.28
Consensus pattern (21 bp):
GGGGGTATCGGTACCCTCTTG
Done.