Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000317.1 Hibiscus syriacus cultivar Beakdansim tig00000599_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: 75524
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:347 original size:12 final size:13
Alignment explanation
Indices: 330--358 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
320 CAACTAGCTA
330 GTTTCTGTTTC-T
1 GTTTCTGTTTCTT
342 GTTTCTGTTTCTT
1 GTTTCTGTTTCTT
355 GTTT
1 GTTT
359 ACCTTCAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.14, G:0.17, T:0.69
Consensus pattern (13 bp):
GTTTCTGTTTCTT
Found at i:652 original size:23 final size:22
Alignment explanation
Indices: 624--670 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
614 ATCAAGTACA
* *
624 ATAATATATTAGGTAGCGCTTAT
1 ATAATAAATT-GGTAACGCTTAT
*
647 ATAATAAATTGGTAATGCTTAT
1 ATAATAAATTGGTAACGCTTAT
669 AT
1 AT
671 TGACCTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (22 bp):
ATAATAAATTGGTAACGCTTAT
Found at i:1584 original size:109 final size:113
Alignment explanation
Indices: 1430--1666 Score: 374
Period size: 109 Copynumber: 2.1 Consensus size: 113
1420 TACTTATAAT
*
1430 AAGTATCGACACTTTCAAAAATATCCAGTAGCTCTTTACCGGTTTTGTCATTTCGAGATCGATTT
1 AAGTATCGACACTTTCAAAAATATCCAGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCGATTT
* *
1495 TGTCATA-TTTTACCTGTTATATTGTTATGGATCGATACA-TTTT-TA
66 TGTCATATTTTTACATGTTATATTGTTATGGATCAATACATTTTTATA
* * * * *
1540 AAGTATTGACACTTTC-AACATATCCGGTAGCTCTTTATCGGTTTTGTCATTTCGAGACCGGTTT
1 AAGTATCGACACTTTCAAAAATATCCAGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCGATTT
1604 TGTCATATTTTTACATGTTATATTGTTATGGATCAATACATTTTTATA
66 TGTCATATTTTTACATGTTATATTGTTATGGATCAATACATTTTTATA
1652 AAGTATCGACACTTT
1 AAGTATCGACACTTT
1667 ATTACGATAT
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
109 50 0.43
110 45 0.39
111 4 0.03
112 16 0.14
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (113 bp):
AAGTATCGACACTTTCAAAAATATCCAGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCGATTT
TGTCATATTTTTACATGTTATATTGTTATGGATCAATACATTTTTATA
Found at i:1853 original size:288 final size:289
Alignment explanation
Indices: 1295--1952 Score: 858
Period size: 288 Copynumber: 2.3 Consensus size: 289
1285 TTACTATTGA
* *
1295 TTTTGTCATTTGAGACCGATTTTGTCACA-TTTTACATG-T-TATTGTTATGGATCGATACA-TT
1 TTTTGTCATTTGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCAATACATTT
* * * * *
1356 TTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTTTATTTTAAATTTCAAAAGTGTCGAT
66 TTATAAAGTATCGACACTTTATTGACGATATAACTTCTTCTACTTTAAATTCCAAAAGTGTAGAT
* *
1421 ACTTATAATAAGTATCGACACTTTCAAAAATATCCAGTAGCTCTTTACCGGTTTTGTCATTTCGA
131 ACTTATAATAAGTATCGACACTATCAAAAATATCCAGTAGCGCTTTACCGGTTTTGTCATTTC-A
* * *
1486 GATCGATTTTGTCATATTTTACCTGTTATATTGTTATGGATCGATACATTTTTAAAGTATTGACA
195 GACCGATTTTGTCATATTTTACCTGTTATATTGTTATGGATCGATACATTTTTAAAATATCGACA
* * * *
1551 CTTTCAACATATCCGGTAGCTCTTTATCGG
260 CTCTCAACATATCCGATAGCGCTTTACCGG
*
1581 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCAATACATT
1 TTTTGTCATTT-GAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCAATACATT
1646 TTTATAAAGTATCGACACTTTATT-ACGATAT-ACTTCTTCT-CTTTAAATTCCAAAAGTGTAGA
65 TTTATAAAGTATCGACACTTTATTGACGATATAACTTCTTCTACTTTAAATTCCAAAAGTGTAGA
* * *
1708 TACTTATAATAAAGTATCGACACTATC-AACATATCCGGTAGCGCTTTACCTGTTTTGTCATTT-
130 TACTTATAAT-AAGTATCGACACTATCAAAAATATCCAGTAGCGCTTTACCGGTTTTGTCATTTC
* * *
1771 ATGACCGGTTTTGTCAT-TTGTGTACCTG-T-TATTGTTATTGATCGATATATTTTTATAAAATA
194 A-GACCGATTTTGTCATATT-T-TACCTGTTATATTGTTATGGATCGATACA-TTTT-TAAAATA
* *
1833 TCGACACTCTCAATATATCCGATAGCGCTTTACCTG
254 TCGACACTCTCAACATATCCGATAGCGCTTTACCGG
* * * *
1869 -TTTGTCATTTATAGACCGATTTTATCAT-TTTTTACCTGTTATATTGTTATAGATCAATACATT
1 TTTTGTCATTT-GAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCAATACATT
* *
1932 TCTATAAAGTATCGAAACTTT
65 TTTATAAAGTATCGACACTTT
1953 CAATATATTC
Statistics
Matches: 328, Mismatches: 33, Indels: 22
0.86 0.09 0.06
Matches are distributed among these distances:
286 84 0.26
287 59 0.18
288 111 0.34
289 24 0.07
290 25 0.08
291 25 0.08
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (289 bp):
TTTTGTCATTTGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCAATACATTT
TTATAAAGTATCGACACTTTATTGACGATATAACTTCTTCTACTTTAAATTCCAAAAGTGTAGAT
ACTTATAATAAGTATCGACACTATCAAAAATATCCAGTAGCGCTTTACCGGTTTTGTCATTTCAG
ACCGATTTTGTCATATTTTACCTGTTATATTGTTATGGATCGATACATTTTTAAAATATCGACAC
TCTCAACATATCCGATAGCGCTTTACCGG
Found at i:2067 original size:108 final size:109
Alignment explanation
Indices: 1716--2168 Score: 621
Period size: 108 Copynumber: 4.1 Consensus size: 109
1706 GATACTTATA
* * * *
1716 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTAT-GACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* * * *
1780 TTTGTCATTTGTGTACCTGTTATTGTTATTGATCGATATATTTTT
66 TTTGTCATTT-TTTACCTGTTATTGTTATAGATCAATACATTTTT
* *
1825 ATAAAATATCGACACTCTCAATATATCCGATAGCGCTTTACCTG-TTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
1889 TTTATCATTTTTTACCTGTTATATTGTTATAGATCAATACATTTCT
66 TTTGTCATTTTTTACCTG-T-TATTGTTATAGATCAATACATTTTT
* * *
1935 ATAAAGTATCGAAACTTTCAATATATTCGATAGCGCTTTACCTGTTTTGTCATTTATAGA-CGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
*
1999 TTTGTCATTTTTTACCTGTTATTGTTATAGATCGATACATTTTT
66 TTTGTCATTTTTTACCTGTTATTGTTATAGATCAATACATTTTT
*
2043 ATAAAGTATCGACACTTTCAATATATTCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
2108 TTTGTCATTTTTTTTTTACCTGTTA-TATTATAGAAT-AATA-TTTTTT
66 TTTGTCA----TTTTTTACCTGTTATTGTTATAG-ATCAATACATTTTT
2154 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
2169 AAACCGACAA
Statistics
Matches: 310, Mismatches: 24, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
108 101 0.33
109 67 0.22
110 81 0.26
111 35 0.11
112 10 0.03
113 16 0.05
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.45
Consensus pattern (109 bp):
ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGTCATTTTTTACCTGTTATTGTTATAGATCAATACATTTTT
Found at i:2099 original size:219 final size:219
Alignment explanation
Indices: 1716--2120 Score: 670
Period size: 219 Copynumber: 1.8 Consensus size: 219
1706 GATACTTATA
* *
1716 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATGACCGGTT
1 ATAAAGTATCGAAACTATCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTATGACCGGTT
* *
1781 TTGTCATTTGTGTACCTGTTATTGTTATTGATCGATATATTTTTATAAAATATCGACACTCTCAA
66 TTGTCATTTGTGTACCTGTTATTGTTATAGATCGATACATTTTTATAAAATATCGACACTCTCAA
1846 TATATCCGATAGCGCTTTACCTGTTTGTCATTTATAGACCGATTTTATCATTTTTTACCTGTTAT
131 TATATCCGATAGCGCTTTACCTGTTTGTCATTTATAGACCGATTTTATCATTTTTTACCTGTTAT
1911 ATTGTTATAGATCAATACATTTCT
196 ATTGTTATAGATCAATACATTTCT
* * *
1935 ATAAAGTATCGAAACTTTCAATATATTCGATAGCGCTTTACCTGTTTTGTCATTTATAGA-CGGT
1 ATAAAGTATCGAAACTATCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTAT-GACCGGT
* * *
1999 TTTGTCATTT-TTTACCTGTTATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTCA
65 TTTGTCATTTGTGTACCTGTTATTGTTATAGATCGATACATTTTTATAAAATATCGACACTCTCA
* *
2063 ATATATTCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTT
130 ATATATCCGATAGCGCTTTACCTG-TTTGTCATTTATAGACCGATTTTATCATTTTTT
2121 TTTTACCTGT
Statistics
Matches: 172, Mismatches: 12, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
218 72 0.42
219 98 0.57
220 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.44
Consensus pattern (219 bp):
ATAAAGTATCGAAACTATCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTATGACCGGTT
TTGTCATTTGTGTACCTGTTATTGTTATAGATCGATACATTTTTATAAAATATCGACACTCTCAA
TATATCCGATAGCGCTTTACCTGTTTGTCATTTATAGACCGATTTTATCATTTTTTACCTGTTAT
ATTGTTATAGATCAATACATTTCT
Found at i:3535 original size:13 final size:14
Alignment explanation
Indices: 3504--3541 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
3494 AGAATTTAGG
3504 TTAAAAAATATAAAT
1 TTAAAAAAT-TAAAT
*
3519 TTAAAAAATTATA-
1 TTAAAAAATTAAAT
3532 TTAAAAAATT
1 TTAAAAAATT
3542 TAGAGGGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 3 0.14
15 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAAAATTAAAT
Found at i:8719 original size:18 final size:19
Alignment explanation
Indices: 8696--8738 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
8686 CAATAATCCT
8696 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
8714 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
8734 ATTCC
1 ATTCC
8739 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:8726 original size:20 final size:20
Alignment explanation
Indices: 8701--8738 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
8691 ATCCTATTCC
8701 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
8721 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
8739 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:10208 original size:42 final size:42
Alignment explanation
Indices: 10073--10208 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 42
10063 TTACTTCGCT
* * * *
10073 GCAATAGATTTG-ACATATAGCGGCGTTTTTACAAAAAACGCC
1 GCAATAGATTGGTAAAT-TAGCGGCGTTTATACCAAAAACGCC
* * * * *
10115 GCAATAGAGTGGTAAATTAGCAGCGTTTAAACCATAAACGCT
1 GCAATAGATTGGTAAATTAGCGGCGTTTATACCAAAAACGCC
* *
10157 GCAACAGATTGGTAAATTAGCGGCGTTTATACCACAAACGCC
1 GCAATAGATTGGTAAATTAGCGGCGTTTATACCAAAAACGCC
10199 GCAATAGATT
1 GCAATAGATT
10209 ACACATATAG
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 74 0.96
43 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (42 bp):
GCAATAGATTGGTAAATTAGCGGCGTTTATACCAAAAACGCC
Found at i:10301 original size:41 final size:41
Alignment explanation
Indices: 10242--10341 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 41
10232 TAAAACGCCG
* *
10242 CAATAGTGATAATAAATAGTGGC-GCTTTTAGACAAACACCA
1 CAATAGTTATAATCAATAGTGGCAGCTTTTA-ACAAACACCA
* ** *
10283 CAATAGTTTTAATCAATAGTGGCATTTTTTAACAAACGCCA
1 CAATAGTTATAATCAATAGTGGCAGCTTTTAACAAACACCA
*
10324 CTATAG-TATAATCAATAG
1 CAATAGTTATAATCAATAG
10342 CGACATTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 11 0.22
41 34 0.68
42 5 0.10
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (41 bp):
CAATAGTTATAATCAATAGTGGCAGCTTTTAACAAACACCA
Found at i:10353 original size:41 final size:42
Alignment explanation
Indices: 10267--10352 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 42
10257 ATAGTGGCGC
* * *
10267 TTTTAGACAAACACCACAATAGTTTTAATCAATAGTGGCATT
1 TTTTAGACAAACACCACAATAGTTATAATCAATAGCGACATT
* *
10309 TTTTA-ACAAACGCCACTATAG-TATAATCAATAGCGACATT
1 TTTTAGACAAACACCACAATAGTTATAATCAATAGCGACATT
10349 TTTT
1 TTTT
10353 TTGTATAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 20 0.51
41 14 0.36
42 5 0.13
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.35
Consensus pattern (42 bp):
TTTTAGACAAACACCACAATAGTTATAATCAATAGCGACATT
Found at i:17022 original size:31 final size:31
Alignment explanation
Indices: 16982--17053 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
16972 ATTTTTTTTA
16982 ACCAATTTGATCCAAGAAGACAAGTTCAGGT
1 ACCAATTTGATCCAAGAAGACAAGTTCAGGT
* * * * *
17013 AGCAATTTGATCCATGAAGCCAAGTTTATGT
1 ACCAATTTGATCCAAGAAGACAAGTTCAGGT
17044 ACCAATTTGA
1 ACCAATTTGA
17054 ATCTTAATCC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (31 bp):
ACCAATTTGATCCAAGAAGACAAGTTCAGGT
Found at i:19376 original size:21 final size:21
Alignment explanation
Indices: 19346--19385 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19336 TGGCAGTGAT
19346 AGTGAGAGT-GACAGTGACAGC
1 AGTGAGAGTGGA-AGTGACAGC
*
19367 AGTGATAGTGGAAGTGACA
1 AGTGAGAGTGGAAGTGACA
19386 ATGGAAGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.35, C:0.10, G:0.38, T:0.17
Consensus pattern (21 bp):
AGTGAGAGTGGAAGTGACAGC
Found at i:58517 original size:18 final size:18
Alignment explanation
Indices: 58496--58572 Score: 77
Period size: 18 Copynumber: 4.3 Consensus size: 18
58486 ATATTTACAA
* *
58496 TTATCATATGATTTTTAG
1 TTATCAAATGATTTTCAG
58514 TTATCAAATGATTTTCAG
1 TTATCAAATGATTTTCAG
* *
58532 TTATCAGATG-TTTACAG
1 TTATCAAATGATTTTCAG
* *
58549 TTATCAGAT-TTTTTACAG
1 TTATCAAATGATTTT-CAG
58567 TTATCA
1 TTATCA
58573 TGCATAGATT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
17 18 0.35
18 34 0.65
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (18 bp):
TTATCAAATGATTTTCAG
Found at i:59485 original size:2 final size:2
Alignment explanation
Indices: 59480--59505 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59470 TATATATATA
59480 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
59506 AACAGTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:60414 original size:84 final size:85
Alignment explanation
Indices: 60246--60542 Score: 438
Period size: 85 Copynumber: 3.5 Consensus size: 85
60236 ACATGAATTT
* * * *
60246 TTTATGACGCGCATGTATGACATACATTGCGTGTCATTGAAGCCCCCGTCATAAATTAAGATGAC
1 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCACCGTCATAAATTAAGATGAC
60311 ACACATTTGTGCGTCATAAA
66 ACACATTTGTGCGTCATAAA
60331 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAG-CACCGTCATAAATTAAGATGAC
1 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCACCGTCATAAATTAAGATGAC
60395 ACACATTTGTGCGTCATAAA
66 ACACATTTGTGCGTCATAAA
* * * * *
60415 TTTATGACACGTATGTATAACTTACATTACGCGTCATTGAAGCCCCCGTCATAAATCT--GCTTG
1 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCACCGTCATAAAT-TAAG-ATG
* *
60478 ACATACATTTGTGTGTCATAAA
64 ACACACATTTGTGCGTCATAAA
* *
60500 TTTATGACACGCATATATGACTTACATTGCGTGTCATTGAAGC
1 TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGC
60543 ACACATCATT
Statistics
Matches: 193, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
84 81 0.42
85 111 0.58
86 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (85 bp):
TTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCACCGTCATAAATTAAGATGAC
ACACATTTGTGCGTCATAAA
Found at i:60606 original size:2 final size:2
Alignment explanation
Indices: 60599--60635 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
60589 TTTCGGAAAT
60599 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60636 GTAGATCGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65823 original size:18 final size:18
Alignment explanation
Indices: 65800--65839 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
65790 GACTCCATTA
65800 ATATTAACTCTTTACTGG
1 ATATTAACTCTTTACTGG
65818 ATATTAACTCTTTACTGG
1 ATATTAACTCTTTACTGG
65836 ATAT
1 ATAT
65840 CATTTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (18 bp):
ATATTAACTCTTTACTGG
Found at i:68042 original size:45 final size:45
Alignment explanation
Indices: 67991--68077 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
67981 TAGTAACGAC
* *
67991 AATAATGTTTG-TGGTATTAGTTTCAGAATTTATCTAGACTATGAA
1 AATAATGTTTGCT-GTATTAGTCTCAAAATTTATCTAGACTATGAA
* *
68036 AATAATGTTTGCTGTATTAGTCTCAAAATTTGTCTATACTAT
1 AATAATGTTTGCTGTATTAGTCTCAAAATTTATCTAGACTAT
68078 TGTCGTGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 36 0.97
46 1 0.03
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (45 bp):
AATAATGTTTGCTGTATTAGTCTCAAAATTTATCTAGACTATGAA
Found at i:69289 original size:54 final size:54
Alignment explanation
Indices: 69224--69395 Score: 224
Period size: 54 Copynumber: 3.2 Consensus size: 54
69214 GGCGTTCGCA
*
69224 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTAACGCAGAAGAAGTCTTCAGT
1 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTAACGCAAAAGAAGTCTTCAGT
* *
69278 TAAGGCTTGGGCACGGCTTATTCATCCAGAACTAACGCAAAAGAAGTCTTCAGT
1 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTAACGCAAAAGAAGTCTTCAGT
** * * * *
69332 TAAGGCGTGGGCACGATTTATCCATCCCGAGCT-ACTGTAAAAGAA-TC-TCTACT
1 TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTAAC-GCAAAAGAAGTCTTC-AGT
69385 TAAGGCGTGGG
1 TAAGGCGTGGG
69396 AACTTATTCA
Statistics
Matches: 105, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
52 2 0.02
53 17 0.16
54 86 0.82
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (54 bp):
TAAGGCGTGGGCACGGCTTATTCATCCAGAGCTAACGCAAAAGAAGTCTTCAGT
Done.