Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008863.1 Hibiscus syriacus cultivar Beakdansim tig00112095_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: 108283
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1330 original size:3 final size:3
Alignment explanation
Indices: 1312--1441 Score: 156
Period size: 3 Copynumber: 42.7 Consensus size: 3
1302 ATATATAGTT
* *
1312 TAA TATA TAT TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA T-A TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1357 TAA TAA TAA TAG TAAA TAA TAA TAA TAA TAA TAA TAC TAG TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1403 TAA TAA TAA TAAA TAAA TAA -AA TAC TAA TAA TAA TAA TA
1 TAA TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TA
1442 TGGATAAAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.04
3 95 0.86
4 12 0.11
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1457 original size:25 final size:25
Alignment explanation
Indices: 1338--1405 Score: 52
Period size: 25 Copynumber: 2.7 Consensus size: 25
1328 TAATAATGAT
*
1338 AATAATAATAATAATATAAT-AATAA
1 AATACTAATAATAATA-AATAAATAA
*
1363 TAATAGTAAATAATAAT-AAT-AATAA
1 -AATACT-AATAATAATAAATAAATAA
*
1388 TAATACTAGTAATAATAA
1 -AATACTAATAATAATAA
1406 TAATAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 8 0.22
25 15 0.41
26 5 0.14
27 9 0.24
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (25 bp):
AATACTAATAATAATAAATAAATAA
Found at i:1866 original size:50 final size:49
Alignment explanation
Indices: 1812--1938 Score: 155
Period size: 50 Copynumber: 2.5 Consensus size: 49
1802 CCCTACGTGG
* * * *
1812 CGTATAGCGAGGATCAGGGGGCGCGTTATACCCACGTGGCGTCAGATCAC
1 CGTATAGCGCGG-TCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
* * *
1862 CGTATATCGCGGGGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAG
1 CGTATAGCGC-GGTCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
*
1912 CATATAGCGCGGTGCAGGGGGCGCGCT
1 CGTATAGCGCGGT-CAGGGGGCGCGCT
1939 TTTCTACTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 2 0.03
50 61 0.94
51 2 0.03
ACGTcount: A:0.20, C:0.28, G:0.37, T:0.16
Consensus pattern (49 bp):
CGTATAGCGCGGTCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
Found at i:5078 original size:4 final size:4
Alignment explanation
Indices: 5069--5108 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
5059 GACATAAAGA
*
5069 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-AT ACAC ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
5109 AATATACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:16053 original size:32 final size:32
Alignment explanation
Indices: 16007--16071 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
15997 TACTCCTAAA
16007 AGACCCCCTTACTCACCAGAAACCCATAAACT
1 AGACCCCCTTACTCACCAGAAACCCATAAACT
*
16039 AGACGCCCTTACTCACCAGAAACCCATAAACT
1 AGACCCCCTTACTCACCAGAAACCCATAAACT
16071 A
1 A
16072 ATTCATCTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.38, G:0.08, T:0.15
Consensus pattern (32 bp):
AGACCCCCTTACTCACCAGAAACCCATAAACT
Found at i:17400 original size:44 final size:45
Alignment explanation
Indices: 17296--17411 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 45
17286 TTAATTCTTG
* * *
17296 ATTTCCAAACTATAAAATAATATTTATATTAATTTCGAAAATCAAA
1 ATTTCAAAACTATATAAT-ATATTTATATTAATTTCGAAAAACAAA
* * *
17342 ATTTCAAAACTATATAATATATTTATATTATTTTC-AAAAACCAT
1 ATTTCAAAACTATATAATATATTTATATTAATTTCGAAAAACAAA
*
17386 ATTTCAAAATTATATAATATATTTAT
1 ATTTCAAAACTATATAATATATTTAT
17412 GACTCTTCAG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
44 31 0.49
45 16 0.25
46 16 0.25
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.42
Consensus pattern (45 bp):
ATTTCAAAACTATATAATATATTTATATTAATTTCGAAAAACAAA
Found at i:17842 original size:133 final size:133
Alignment explanation
Indices: 17504--18037 Score: 570
Period size: 133 Copynumber: 4.0 Consensus size: 133
17494 ATCGAATATG
* * * * * * **
17504 AAAAAGGGATATGCTCTACTGCTCTTCAGGGAAGATCAGATTTGGAAAGTTTTGACTCACTCCAC
1 AAAAATGGATATGCTCCACTGCTCTTCAGGGAAGATCAGATCTAGAAAGTTTTGATTCATTCTGC
* * * **
17569 TACT-TTTAAGGGAAGATTGAATTGGGGTAGATTTGCTCCACTGCTCTTCAGGGAAGATCAAATC
66 TGCTCTTCAA-GGAAGATTGAATCGGGGTAGATTTATTCCACTGCTCTTCAGGGAAGATCAAATC
17633 T-GA
130 TAGA
* * * * * *
17636 GAAAATGGATATGCTCCACTACTCTTCAGTGAAGACCAGATCTGGAAAATTTTGATTCATT-TCG
1 AAAAATGGATATGCTCCACTGCTCTTCAGGGAAGATCAGATCTAGAAAGTTTTGATTCATTCT-G
* * * * *
17700 CTGCTCTTCAAGAAAGATTGAATCAGGGTAGATTTGTTGCACTGCTCTTCAGGGAAGATTAAATC
65 CTGCTCTTCAAGGAAGATTGAATCGGGGTAGATTTATTCCACTGCTCTTCAGGGAAGATCAAATC
17765 TAGA
130 TAGA
* * * *
17769 AAAAAAGGATATGCTCCACTGTTATTCAGGGAAGATCATATCTAGAAAGTTTTGATTCATTCTGC
1 AAAAATGGATATGCTCCACTGCTCTTCAGGGAAGATCAGATCTAGAAAGTTTTGATTCATTCTGC
* * * * * *
17834 TGCTCTTCATGGAAGATTGAATCGGGGTATATTTATTCCACTTCTCTTTAAGGAATATCAAATCT
66 TGCTCTTCAAGGAAGATTGAATCGGGGTAGATTTATTCCACTGCTCTTCAGGGAAGATCAAATCT
*
17899 AGG
131 AGA
* * * * * * *
17902 GAAAATGGATACGTTCCACTTCTCTTTAGGGAAGATCGGATCTAGAAAGTTTTGATTCATTATGC
1 AAAAATGGATATGCTCCACTGCTCTTCAGGGAAGATCAGATCTAGAAAGTTTTGATTCATTCTGC
* * * * * * * * *
17967 TGCTCTTCAAGGATGAATGAATTGGGGCAGATTTATTACATTTCTCTTCAGGGAAGATTAGATCT
66 TGCTCTTCAAGGAAGATTGAATCGGGGTAGATTTATTCCACTGCTCTTCAGGGAAGATCAAATCT
18032 AGA
131 AGA
18035 AAA
1 AAA
18038 TTTTGATTCA
Statistics
Matches: 330, Mismatches: 68, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
132 104 0.32
133 225 0.68
134 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (133 bp):
AAAAATGGATATGCTCCACTGCTCTTCAGGGAAGATCAGATCTAGAAAGTTTTGATTCATTCTGC
TGCTCTTCAAGGAAGATTGAATCGGGGTAGATTTATTCCACTGCTCTTCAGGGAAGATCAAATCT
AGA
Found at i:18102 original size:87 final size:87
Alignment explanation
Indices: 17914--18113 Score: 208
Period size: 87 Copynumber: 2.3 Consensus size: 87
17904 AAATGGATAC
* * * **
17914 GTTCCACTTCTCTTTAGGGAAGATCGGATCTAGAAAGTTTTGATTCATTATGCTGCTCTTCAAGG
1 GTTCCACTTCTCTTCAGGGAAGATCAGATCTAGAAAATTTTGATTCATTACACTGCTCTTCAAGG
* * *
17979 ATGAATGAATTGGGGCAGATTT
66 AAGAATAAATCGGGGCAGATTT
* * * * * *
18001 ATTACATTTCTCTTCAGGGAAGATTAGATCTAGAAAATTTTGATTCATTCCACTGTTCTTC-AGA
1 GTTCCACTTCTCTTCAGGGAAGATCAGATCTAGAAAATTTTGATTCATTACACTGCTCTTCAAG-
* *
18065 GAAGATTAAATCGGGGTAGATTT
65 GAAGAATAAATCGGGGCAGATTT
18088 GTTCCACTAT-TCTTCAGAGG-AGATCA
1 GTTCCACT-TCTCTTCAG-GGAAGATCA
18114 AATATGAAAA
Statistics
Matches: 90, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
86 2 0.02
87 85 0.94
88 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (87 bp):
GTTCCACTTCTCTTCAGGGAAGATCAGATCTAGAAAATTTTGATTCATTACACTGCTCTTCAAGG
AAGAATAAATCGGGGCAGATTT
Found at i:19459 original size:21 final size:20
Alignment explanation
Indices: 19435--19492 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
19425 TCTTGAACCC
*
19435 TTTTTATTTTACTTTTCTCTT
1 TTTTTCTTTTA-TTTTCTCTT
*
19456 TTTTCCTCCTTT-TTTTCTCTT
1 TTTT--TCTTTTATTTTCTCTT
19477 TTTTTCTTTTATTTTC
1 TTTTTCTTTTATTTTC
19493 CCCCTTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 5 0.16
20 5 0.16
21 17 0.55
23 4 0.13
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTCTTTTATTTTCTCTT
Found at i:19477 original size:10 final size:10
Alignment explanation
Indices: 19447--19492 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
19437 TTTATTTTAC
19447 TTTTCTCTTT
1 TTTTCTCTTT
*
19457 TTTCCTCCTTT
1 TTTTCT-CTTT
19468 TTTTCTCTTT
1 TTTTCTCTTT
19478 TTTTCT-TTT
1 TTTTCTCTTT
19487 ATTTTC
1 -TTTTC
19493 CCCCTTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 3 0.09
10 20 0.62
11 9 0.28
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:28296 original size:15 final size:15
Alignment explanation
Indices: 28278--28320 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
28268 ACATTTTGAA
28278 TGTTTTGGATTTGTG
1 TGTTTTGGATTTGTG
* * *
28293 TGTTTTAGATATGTT
1 TGTTTTGGATTTGTG
28308 TGTTTTGGATTTG
1 TGTTTTGGATTTG
28321 AATGGTTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (15 bp):
TGTTTTGGATTTGTG
Found at i:36020 original size:21 final size:21
Alignment explanation
Indices: 35994--36043 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
35984 GTTGATGGTT
*
35994 TTATGTGGTCATTCGGGATAA
1 TTATGTGGTCATTCGGGACAA
* *
36015 TTATGTGGTCCTTTGGGACAA
1 TTATGTGGTCATTCGGGACAA
36036 TTATGTGG
1 TTATGTGG
36044 CACTTCAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.10, G:0.30, T:0.40
Consensus pattern (21 bp):
TTATGTGGTCATTCGGGACAA
Found at i:36071 original size:23 final size:23
Alignment explanation
Indices: 36041--36085 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
36031 GACAATTATG
36041 TGGCACTTCAGTGCAAACCTATT
1 TGGCACTTCAGTGCAAACCTATT
36064 TGGCACTTCAGTGCAAACCTAT
1 TGGCACTTCAGTGCAAACCTAT
36086 GTGGTCATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (23 bp):
TGGCACTTCAGTGCAAACCTATT
Found at i:44586 original size:7 final size:7
Alignment explanation
Indices: 44570--44599 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
44560 ATAAAACAAA
44570 ATAA-AT
1 ATAACAT
44576 ATAACAT
1 ATAACAT
44583 ATAACAT
1 ATAACAT
44590 ATAACAT
1 ATAACAT
44597 ATA
1 ATA
44600 CTATACTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (7 bp):
ATAACAT
Found at i:44725 original size:45 final size:45
Alignment explanation
Indices: 44646--44763 Score: 166
Period size: 45 Copynumber: 2.6 Consensus size: 45
44636 TTAAACCTTG
* *
44646 ATTTCCAAACTATA-CATATATTTATATTACTTTCAAAAACCAAA
1 ATTTCAAAACTATATAATATATTTATATTACTTTCAAAAACCAAA
* *
44690 ATTTCAAAACTATATAATATATTTATATTATTTTCAAAAACCATA
1 ATTTCAAAACTATATAATATATTTATATTACTTTCAAAAACCAAA
* *
44735 TTTTCAAAACTATATATATATATATATAT
1 ATTTCAAAACTATATA-ATATATTTATAT
44764 ATATATATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 13 0.20
45 42 0.64
46 11 0.17
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.42
Consensus pattern (45 bp):
ATTTCAAAACTATATAATATATTTATATTACTTTCAAAAACCAAA
Found at i:44752 original size:2 final size:2
Alignment explanation
Indices: 44745--44773 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44735 TTTTCAAAAC
44745 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 T
44774 TATTTATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45889 original size:16 final size:17
Alignment explanation
Indices: 45852--45896 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
45842 GTTTATGAGA
45852 GAATTGGAATCTGTGAAG
1 GAATTGGAATCTGT-AAG
45870 GAATTGGAATCTGT-AG
1 GAATTGGAATCTGTAAG
45886 GAATTGGAATC
1 GAATTGGAATC
45897 CAATTCCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.33, C:0.07, G:0.31, T:0.29
Consensus pattern (17 bp):
GAATTGGAATCTGTAAG
Found at i:46656 original size:37 final size:38
Alignment explanation
Indices: 46577--46658 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
46567 TTCACCCTAA
*
46577 ACCCGAACCTGACCCGAATATCACACTTAAAAAAACCCG
1 ACCCG-ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
46616 ACCCGACCCGACCCGAATATCATACTT-AAAAAACCCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
46653 ACCCGA
1 ACCCGA
46659 ACAAAATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 16 0.39
38 20 0.49
39 5 0.12
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.12
Consensus pattern (38 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:46794 original size:249 final size:249
Alignment explanation
Indices: 46342--46882 Score: 815
Period size: 249 Copynumber: 2.2 Consensus size: 249
46332 TATTTTTCCT
***
46342 GAATATCACACTTAAAAAAAACCCGATCCGACTTTACCCGAATATCACACTTAAAAAACCCGACC
1 GAATATCACACTTAAAAAAAACCCGATCCGACCCGACCCGAATATCACACTTAAAAAACCCGA-C
* * *
46407 CGACTCGAACAAAATAAGGTTTCATCCGACCCGAATATATGAATTAGAAATTCGACCCGACCCGA
65 C-ACTCGAACAAAATAAAGTTTCATCCGACCCAAATATATGAATTAGAAATCCGACCCGACCCGA
*
46472 CCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCTGACCCGACCCGAAT
129 CCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGAAT
* *
46537 TATATATATTTTCAGGTCGGTCCGGTTTTTTTCACCCTAAACCCG-A-ACCTGACCC
194 TATATATATTTTCAGGTCGGTCCAG-TTTTTTCACCCTAAACCCGAACACCCGACCC
* *
46592 GAATATCACACTT-AAAAAAACCCGACCCGACCCGACCCGAATATCATACTTAAAAAACCCGA-C
1 GAATATCACACTTAAAAAAAACCCGATCCGACCCGACCCGAATATCACACTTAAAAAACCCGACC
46655 -C-CGAACAAAATAAAGTTTCATCTGACCCGACCCAAATATATGAATTAGAAATCCGACCCGACC
66 ACTCGAACAAAATAAAGTTTCA--T---CCGACCCAAATATATGAATTAGAAATCCGACCCGACC
*
46718 CGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
126 CGACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
*
46783 AATTATATATATTTTCGGGTCGGTCCAGTTTTTTCACCCTAAACCCGAACCCGACCCGACCC
191 AATTATATATATTTTCAGGTCGGTCCAGTTTTTTCACCCTAAACCCGAA--C-ACCCGACCC
*
46845 GAATATCACACTTAAAAAAAACCTGATCCGACCCGACC
1 GAATATCACACTTAAAAAAAACCCGATCCGACCCGACC
46883 AAAATAAAGT
Statistics
Matches: 265, Mismatches: 15, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
244 18 0.07
245 1 0.00
246 1 0.00
247 1 0.00
248 19 0.07
249 169 0.64
250 13 0.05
253 21 0.08
254 22 0.08
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.23
Consensus pattern (249 bp):
GAATATCACACTTAAAAAAAACCCGATCCGACCCGACCCGAATATCACACTTAAAAAACCCGACC
ACTCGAACAAAATAAAGTTTCATCCGACCCAAATATATGAATTAGAAATCCGACCCGACCCGACC
CAAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGAATTA
TATATATTTTCAGGTCGGTCCAGTTTTTTCACCCTAAACCCGAACACCCGACCC
Found at i:52170 original size:15 final size:15
Alignment explanation
Indices: 52146--52193 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
52136 ACATTACCCT
* *
52146 CCCCGCATCCGCCCG
1 CCCCGAATCCGCTCG
52161 CCCCGAATCCGCTCG
1 CCCCGAATCCGCTCG
52176 CCCC-ACATCCGCTCG
1 CCCCGA-ATCCGCTCG
52191 CCC
1 CCC
52194 AGCTAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 1 0.03
15 29 0.97
ACGTcount: A:0.10, C:0.62, G:0.17, T:0.10
Consensus pattern (15 bp):
CCCCGAATCCGCTCG
Found at i:56279 original size:4 final size:4
Alignment explanation
Indices: 56270--56312 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
56260 CAATGCATGT
*
56270 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATGA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
56313 GTTAAACAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:61007 original size:3 final size:3
Alignment explanation
Indices: 60999--61075 Score: 82
Period size: 3 Copynumber: 25.3 Consensus size: 3
60989 ATGTTATTTA
* * * * * *
60999 TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT AAT AAT AAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
61047 TAT TAT TAT TAT TAT TAA TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
61076 TAATATTACA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 64 0.96
4 3 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:61587 original size:15 final size:15
Alignment explanation
Indices: 61555--61594 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
61545 GCAAAGAAAC
61555 AGAAAAGAAAAAAAAA
1 AGAAAAG-AAAAAAAA
*
61571 AGAAAAGAAAAAGAA
1 AGAAAAGAAAAAAAA
*
61586 AGAAGAGAA
1 AGAAAAGAA
61595 GCTTACCGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAAAAAA
Found at i:62492 original size:22 final size:21
Alignment explanation
Indices: 62459--62500 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
62449 AAATATATAA
62459 TAATAATAA-TTTATATATTTT
1 TAATAATAATTTTA-ATATTTT
*
62480 TAATAAATTATTTTAATATTT
1 TAAT-AATAATTTTAATATTT
62501 ATTTTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATAATAATTTTAATATTTT
Found at i:63699 original size:9 final size:9
Alignment explanation
Indices: 63685--63709 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
63675 TTACATGTAA
63685 ATTTAAATT
1 ATTTAAATT
63694 ATTTAAATT
1 ATTTAAATT
63703 ATTTAAA
1 ATTTAAA
63710 AGCATGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTTAAATT
Found at i:73855 original size:13 final size:13
Alignment explanation
Indices: 73839--73883 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
73829 TAATAATAAA
73839 AAAAAGAGAAAAG
1 AAAAAGAGAAAAG
*
73852 AAAAAAAGAAAAG
1 AAAAAGAGAAAAG
*
73865 --AAAGAAAAAAG
1 AAAAAGAGAAAAG
73876 AAAAAGAG
1 AAAAAGAG
73884 GGGTCAAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.35
13 17 0.65
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAAAG
Found at i:73868 original size:9 final size:8
Alignment explanation
Indices: 73837--73880 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
73827 AATAATAATA
73837 AAAAAAAG
1 AAAAAAAG
*
73845 -AGAAAAG
1 AAAAAAAG
73852 AAAAAAAG
1 AAAAAAAG
73860 AAAAGAAAG
1 AAAA-AAAG
73869 -AAAAAAG
1 AAAAAAAG
73876 AAAAA
1 AAAAA
73881 GAGGGGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 10 0.32
8 17 0.55
9 4 0.13
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:73880 original size:7 final size:7
Alignment explanation
Indices: 73838--73880 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
73828 ATAATAATAA
73838 AAAAAAG
1 AAAAAAG
*
73845 AGAAAAG
1 AAAAAAG
73852 AAAAAAAG
1 -AAAAAAG
73860 AAAAGAAAG
1 -AAA-AAAG
73869 AAAAAAG
1 AAAAAAG
73876 AAAAA
1 AAAAA
73881 GAGGGGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 15 0.47
8 13 0.41
9 4 0.12
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:75156 original size:83 final size:83
Alignment explanation
Indices: 75017--75408 Score: 624
Period size: 83 Copynumber: 4.7 Consensus size: 83
75007 ACATTAGCTG
*
75017 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
75082 AAACCAATCATTGAATTT
66 AAACCAATCATTGAATTT
*
75100 GAAAGATGAATGTGCTCATAGCATCTTCTGTAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* *
75165 AAACCAGTTATTGAATTT
66 AAACCAATCATTGAATTT
*
75183 GGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGT
1 -GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
*
75248 AAAACTAATCATTGAATTT
65 AAAACCAATCATTGAATTT
* * *
75267 GGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
75332 AAACCAATCATTGAATTT
66 AAACCAATCATTGAATTT
* * *
75350 GAAAGAAAT-AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 GAAAG--ATGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
75409 AATTTGGTTT
Statistics
Matches: 284, Mismatches: 20, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
83 161 0.57
84 82 0.29
85 3 0.01
86 38 0.13
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
AAACCAATCATTGAATTT
Found at i:75291 original size:167 final size:167
Alignment explanation
Indices: 75015--75408 Score: 639
Period size: 167 Copynumber: 2.3 Consensus size: 167
75005 AAACATTAGC
75015 TGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGG
1 TGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGG
* * *
75080 TAAAACCAATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGTAAGTGTTCTTTGAG
66 TAAAACCAATCATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAG
* *
75145 TTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATT
131 TTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
75182 TGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGG
1 TGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGG
* *
75247 TAAAACTAATCATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAG
66 TAAAACCAATCATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAG
75312 TTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
131 TTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
* * * *
75349 T-GAAAGAAAT-AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 TGGAAAG--ATGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCT
75409 AATTTGGTTT
Statistics
Matches: 212, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
166 5 0.02
167 165 0.78
168 4 0.02
169 38 0.18
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (167 bp):
TGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGG
TAAAACCAATCATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAG
TTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
Found at i:76535 original size:226 final size:221
Alignment explanation
Indices: 76138--76792 Score: 849
Period size: 226 Copynumber: 3.0 Consensus size: 221
76128 GCAAAGATTT
*
76138 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAG-AGTTCATAATGAGAAGAACTCATCT-AAG
* *
76203 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATG
64 AAGGA-GAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATG
* * * *
76268 GATTATCTTTTCCAGTTCG-AGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTC
128 GATCAACTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTC
76332 ATAATGAGAAGAATTTGTTCAACCTTTTGCTC
190 ATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* ** *
76364 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATTTAAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AAGAGTTCATAATGAGAAGAACTCATCT-AAG
76429 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATG
64 AAGG-AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATG
*
76494 GATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCA
128 GATCAACTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCA
* *
76559 TAATGAGAAGAATTTGTTCAGCTTTTTGCTC
191 TAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
76590 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCT----
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTAAGA
* * *
76651 ----GAAG-A----ATAATGAGAATAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGG
65 AGGAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGA
** *
76707 TCAGTTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATC---AGGAGAAGAAGAAGTTCATAAT
130 TCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAAT
** *
76769 GAGAAGAGCTTATTCAACCTTTTG
195 GAGAAGAATTTGTTCAACCTTTTG
76793 AATGACTCTA
Statistics
Matches: 390, Mismatches: 34, Indels: 30
0.86 0.07 0.07
Matches are distributed among these distances:
206 37 0.09
207 3 0.01
210 25 0.06
211 60 0.15
215 1 0.00
216 4 0.01
224 1 0.00
226 257 0.66
227 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (221 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTAAGAA
GGAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGAT
CAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATG
AGAAGAATTTGTTCAACCTTTTGCTC
Found at i:76657 original size:113 final size:113
Alignment explanation
Indices: 76138--76656 Score: 813
Period size: 113 Copynumber: 4.6 Consensus size: 113
76128 GCAAAGATTT
* *
76138 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
76203 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * **** *
76251 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAATAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
76316 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * **** * *
76364 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATTTAAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
76429 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
76477 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
76542 AATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
76590 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
76655 AA
66 AA
76657 TAATGAGAAT
Statistics
Matches: 380, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 380 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:76692 original size:98 final size:97
Alignment explanation
Indices: 76558--76746 Score: 324
Period size: 98 Copynumber: 1.9 Consensus size: 97
76548 GAAGAAGTTC
*
76558 ATAATGAGAAGAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCTAGA
1 ATAATGAGAAGAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGA
76623 GAAAGTTCATAATGAGAAGAACTCATCTGAAGA
66 G-AAGTTCATAATGAGAAGAACTCATCTGAAGA
* * **
76656 ATAATGAGAATAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGGTCAGTTTTTCCAGA
1 ATAATGAGAAGAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGA
76721 GAAGTTCATAATGAGAAGAACTCATC
66 GAAGTTCATAATGAGAAGAACTCATC
76747 AGGAGAAGAA
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
97 25 0.29
98 61 0.71
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (97 bp):
ATAATGAGAAGAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGA
GAAGTTCATAATGAGAAGAACTCATCTGAAGA
Found at i:76775 original size:17 final size:17
Alignment explanation
Indices: 76720--76775 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
76710 GTTTTTCCAG
76720 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
*
76737 AGAA-CTCATCAGGA-GAAGA
1 AGAAGTTCAT-A--ATG-AGA
76756 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
76773 AGA
1 AGA
76776 GCTTATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 2 0.06
19 9 0.29
20 4 0.13
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (17 bp):
AGAAGTTCATAATGAGA
Found at i:77031 original size:3 final size:3
Alignment explanation
Indices: 77023--77090 Score: 86
Period size: 3 Copynumber: 23.3 Consensus size: 3
77013 ATGTTATTTA
* * *
77023 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT AAT TA- TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
77070 TAT TAT TAT TAA TA- TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
77091 TAATATTACA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 4 0.07
3 52 0.93
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:77097 original size:18 final size:18
Alignment explanation
Indices: 77026--77098 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 18
77016 TTATTTATAT
* * *
77026 TATTATTATTATTATTAT
1 TATTAATATAATTATTAA
*
77044 TATTATTATAATTA-T-A
1 TATTAATATAATTATTAA
*
77060 -ATT-ATATAATTATTAT
1 TATTAATATAATTATTAA
77076 TATTAATAT-ATTATTTAA
1 TATTAATATAATTA-TTAA
77094 TATTA
1 TATTA
77099 CAAGCCCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
14 8 0.18
15 4 0.09
17 8 0.18
18 25 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTAATATAATTATTAA
Found at i:77599 original size:15 final size:15
Alignment explanation
Indices: 77567--77606 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
77557 GCAAAGAAAC
77567 AGAAAAGAAAAAAAAA
1 AGAAAAG-AAAAAAAA
*
77583 AGAAAAGAAAAAGAA
1 AGAAAAGAAAAAAAA
*
77598 AGAAGAGAA
1 AGAAAAGAA
77607 GTTTACCGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAAAAAA
Found at i:90559 original size:29 final size:30
Alignment explanation
Indices: 90526--90583 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
90516 CCTTTGGTTT
90526 TAGTTTAGTATCTAACGTTT-ATTTCGTTC
1 TAGTTTAGTATCTAACGTTTCATTTCGTTC
* * **
90555 TAGTTTGGTGTCTAATTTTTCATTTCGTT
1 TAGTTTAGTATCTAACGTTTCATTTCGTT
90584 ACTCATTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.17, C:0.12, G:0.16, T:0.55
Consensus pattern (30 bp):
TAGTTTAGTATCTAACGTTTCATTTCGTTC
Found at i:97126 original size:10 final size:10
Alignment explanation
Indices: 97111--97135 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
97101 CGATTATATG
97111 TGTTCATTTA
1 TGTTCATTTA
97121 TGTTCATTTA
1 TGTTCATTTA
97131 TGTTC
1 TGTTC
97136 GAACAGAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.60
Consensus pattern (10 bp):
TGTTCATTTA
Found at i:97409 original size:10 final size:10
Alignment explanation
Indices: 97394--97437 Score: 61
Period size: 10 Copynumber: 4.1 Consensus size: 10
97384 TTTTTTGTGT
97394 TGTTCGTTTA
1 TGTTCGTTTA
97404 TGTTCGTTTA
1 TGTTCGTTTA
97414 TTGAGTTCGTTTA
1 -T--GTTCGTTTA
97427 TGTTCGTTTA
1 TGTTCGTTTA
97437 T
1 T
97438 TGTTTTCGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 20 0.65
11 1 0.03
12 1 0.03
13 9 0.29
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:97421 original size:13 final size:12
Alignment explanation
Indices: 97395--97451 Score: 59
Period size: 13 Copynumber: 4.9 Consensus size: 12
97385 TTTTTGTGTT
97395 GTTCGTTTA-T-
1 GTTCGTTTATTG
97405 GTTCGTTTATTG
1 GTTCGTTTATTG
97417 AGTTCGTTTA-T-
1 -GTTCGTTTATTG
97428 GTTCGTTTATTG
1 GTTCGTTTATTG
*
97440 TTTTCGTTTATT
1 -GTTCGTTTATT
97452 TATTAAATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
10 18 0.45
11 2 0.05
12 1 0.03
13 19 0.47
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.61
Consensus pattern (12 bp):
GTTCGTTTATTG
Found at i:97423 original size:23 final size:23
Alignment explanation
Indices: 97395--97450 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
97385 TTTTTGTGTT
97395 GTTCGTTTATGTTCGTTTATTGA
1 GTTCGTTTATGTTCGTTTATTGA
*
97418 GTTCGTTTATGTTCGTTTATTGT
1 GTTCGTTTATGTTCGTTTATTGA
*
97441 TTTCGTTTAT
1 GTTCGTTTAT
97451 TTATTAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.61
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTTATTGA
Done.