Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005042.1 Hibiscus syriacus cultivar Beakdansim tig00011317_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: 101477
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1174 original size:40 final size:42
Alignment explanation
Indices: 1129--1215 Score: 144
Period size: 40 Copynumber: 2.1 Consensus size: 42
1119 GAAATTCTAA
1129 ATATTTAAATAAAAATTATTTCTATACAAA-TTCATCG-T-AT
1 ATATTTAAATAAAAATTATTTCTATA-AAACTTCATCGATAAT
1169 ATATTTAAATAAAAATTATTTCTATAAAACTTCATCGATAAT
1 ATATTTAAATAAAAATTATTTCTATAAAACTTCATCGATAAT
1211 ATATT
1 ATATT
1216 AATTTATTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
39 3 0.07
40 33 0.75
41 1 0.02
42 7 0.16
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (42 bp):
ATATTTAAATAAAAATTATTTCTATAAAACTTCATCGATAAT
Found at i:3680 original size:18 final size:18
Alignment explanation
Indices: 3657--3697 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3647 GAGGCCATTA
3657 AATTAA-AAAAACAACAAT
1 AATTAATAAAAA-AACAAT
*
3675 AATTAATAAAGAAACAAT
1 AATTAATAAAAAAACAAT
3693 AATTA
1 AATTA
3698 CCCATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.22
Consensus pattern (18 bp):
AATTAATAAAAAAACAAT
Found at i:5897 original size:33 final size:32
Alignment explanation
Indices: 5829--5903 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 32
5819 TAACAGTAAT
* * *
5829 AAAATAAAATAAAAATAAGAAGTACAAAAAAA
1 AAAAAAAAATAAAAATAAAAAATACAAAAAAA
* **
5861 AAAAAAAAATAAATAATAAAAAATACTAAATTA
1 AAAAAAAAATAAA-AATAAAAAATACAAAAAAA
5894 AAAAAAAAAT
1 AAAAAAAAAT
5904 CAACTTTTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 12 0.33
33 24 0.67
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (32 bp):
AAAAAAAAATAAAAATAAAAAATACAAAAAAA
Found at i:6562 original size:3 final size:3
Alignment explanation
Indices: 6544--6601 Score: 64
Period size: 3 Copynumber: 18.3 Consensus size: 3
6534 GCCTGCAAAA
6544 AAT AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAAT AAAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT
*
6591 ATAT AAA AAT A
1 A-AT AAT AAT A
6602 TTTTTGTAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 2 0.04
3 34 0.69
4 13 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:10624 original size:89 final size:84
Alignment explanation
Indices: 10436--10741 Score: 271
Period size: 87 Copynumber: 3.5 Consensus size: 84
10426 AAAATTAATT
* **
10436 AAATTAGAGGCCTAAATTATAAAGTAAAAAGTGAGATTAAAAAAATTAGGGGCATCAGTTAAAAG
1 AAATTAGAGGCCTCAATTATAAAGTAAAAAGTGAGATTAAAAAAATTAGGGGCATCAAATAAAAG
10501 ATAAAAAGTGAGATTAAAA
66 ATAAAAAGTGAGATTAAAA
* * * *
10520 AAATTAGGGGCCTCAATTATAAAGTTGGAAAAGTGAGATTGAAAATAAATTAGGGGCCTTAAATA
1 AAATTAGAGGCCTCAATTATAAAG-T-AAAAAGTGAGATT-AAAA-AAATTAGGGGCATCAAATA
* * *
10585 TAAAGGTTAAAAGCAT-A-ATTGAAA
62 -AAAGATAAAAAG--TGAGATTAAAA
* * * **
10609 AAATTAGAGCCCTCAATTATAAATGTAAAAAATGATATTAAAAAAATTAGGAATC-TCAATTATA
1 AAATTAGAGGCCTCAATTATAAA-GTAAAAAGTGAGATTAAAAAAATTAGG-GGCATCAA--ATA
*
10673 AAA-AGTAAAAAGTGAGATTACAA
62 AAAGA-TAAAAAGTGAGATTAAAA
* ** *
10696 AAATTAGGGGATTCAATTATAAAAATAAAAAGT-AGAATTAAAAAAA
1 AAATTAGAGGCCTCAATTAT-AAAGTAAAAAGTGAG-ATTAAAAAAA
10742 AGTAAAAGTC
Statistics
Matches: 177, Mismatches: 29, Indels: 29
0.75 0.12 0.12
Matches are distributed among these distances:
84 22 0.12
85 2 0.01
86 25 0.14
87 56 0.32
88 31 0.18
89 38 0.21
90 2 0.01
91 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.25
Consensus pattern (84 bp):
AAATTAGAGGCCTCAATTATAAAGTAAAAAGTGAGATTAAAAAAATTAGGGGCATCAAATAAAAG
ATAAAAAGTGAGATTAAAA
Found at i:10653 original size:43 final size:42
Alignment explanation
Indices: 10436--10741 Score: 287
Period size: 43 Copynumber: 7.1 Consensus size: 42
10426 AAAATTAATT
* *
10436 AAATTAGAGGCCTAAATTATAAAGTAAAAAGTGAGATTAAAA
1 AAATTAGGGGCCTCAATTATAAAGTAAAAAGTGAGATTAAAA
* *
10478 AAATTAGGGGCATCAGTTA-AAAGATAAAAAGTGAGATTAAAA
1 AAATTAGGGGCCTCAATTATAAAG-TAAAAAGTGAGATTAAAA
*
10520 AAATTAGGGGCCTCAATTATAAAGTTGGAAAAGTGAGATTGAAAA
1 AAATTAGGGGCCTCAATTATAAAG-T-AAAAAGTGAGATT-AAAA
* * * *
10565 TAAATTAGGGGCCTTAAATATAAAGGTTAAAAGCAT-A-ATTGAAA
1 -AAATTAGGGGCCTCAATTATAAA-GTAAAAAG--TGAGATTAAAA
* * * *
10609 AAATTAGAGCCCTCAATTATAAATGTAAAAAATGATATTAAAA
1 AAATTAGGGGCCTCAATTATAAA-GTAAAAAGTGAGATTAAAA
*** *
10652 AAATTAGGAATCTCAATTATAAAAAGTAAAAAGTGAGATTACAA
1 AAATTAGGGGCCTCAATTAT--AAAGTAAAAAGTGAGATTAAAA
** *
10696 AAATTAGGGGATTCAATTATAAAAATAAAAAGT-AGAATTAAAA
1 AAATTAGGGGCCTCAATTAT-AAAGTAAAAAGTGAG-ATTAAAA
10739 AAA
1 AAA
10742 AGTAAAAGTC
Statistics
Matches: 218, Mismatches: 33, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
41 5 0.02
42 53 0.24
43 73 0.33
44 47 0.22
45 15 0.07
46 23 0.11
47 2 0.01
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.25
Consensus pattern (42 bp):
AAATTAGGGGCCTCAATTATAAAGTAAAAAGTGAGATTAAAA
Found at i:16220 original size:27 final size:28
Alignment explanation
Indices: 16168--16222 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
16158 ATTGAATCAA
16168 AGTTCATATAAAATTTTGAGATTTATCC
1 AGTTCATATAAAATTTTGAGATTTATCC
16196 AGTTCATATAAAA-TTTGAGATTTATCC
1 AGTTCATATAAAATTTTGAGATTTATCC
16223 CCATTATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (28 bp):
AGTTCATATAAAATTTTGAGATTTATCC
Found at i:18397 original size:20 final size:21
Alignment explanation
Indices: 18355--18398 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
18345 TGACCTCAAC
18355 TTCTCCCAATTTCTTCGTCAT
1 TTCTCCCAATTTCTTCGTCAT
*
18376 TTCTCCCAATTTC-TCTTCAT
1 TTCTCCCAATTTCTTCGTCAT
18396 TTC
1 TTC
18399 CACGCTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.14, C:0.34, G:0.02, T:0.50
Consensus pattern (21 bp):
TTCTCCCAATTTCTTCGTCAT
Found at i:25424 original size:17 final size:17
Alignment explanation
Indices: 25402--25434 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25392 AGTTTGATAA
*
25402 AAAATTATTTATTTTTT
1 AAAATTATATATTTTTT
25419 AAAATTATATATTTTT
1 AAAATTATATATTTTT
25435 CTATATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAAATTATATATTTTTT
Found at i:41944 original size:3 final size:3
Alignment explanation
Indices: 41936--42033 Score: 144
Period size: 3 Copynumber: 32.7 Consensus size: 3
41926 TTATTTATTA
*
41936 AAT AAT AAT AAT ATAT ATT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* **
41981 AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42029 AAT AA
1 AAT AA
42034 ATTTAAATGA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.02
3 80 0.94
4 3 0.04
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:42320 original size:76 final size:76
Alignment explanation
Indices: 42159--42522 Score: 638
Period size: 76 Copynumber: 4.8 Consensus size: 76
42149 GATGGAAATG
* *
42159 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTTGAAAACATCAAAAAG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTGAAAACATCAAAAAG
42224 CTCCCGAAGGCTT
64 CTCCCGAAGGCTT
* *
42237 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
42302 CCCGAAGGCTT
66 CCCGAAGGCTT
42313 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
42378 CCCGAAGGCTT
66 CCCGAAGGCTT
*
42389 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
*
42454 CACGAAGGCTT
66 CCCGAAGGCTT
* *
42465 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCA
42523 TGCACTGAAG
Statistics
Matches: 275, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
76 233 0.85
78 42 0.15
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:42524 original size:45 final size:45
Alignment explanation
Indices: 42456--42567 Score: 188
Period size: 45 Copynumber: 2.4 Consensus size: 45
42446 AAAAAGCTCA
* *
42456 CGAAGGCTTTTTGGAAACATCATGCACTGGAGGACTTACAGATGACC
1 CGAAGGC--TTTGAAAACATCATGCACTGAAGGACTTACAGATGACC
42503 CGAAGGCTTTGAAAACATCATGCACTGAAGGACTTACAGATGACC
1 CGAAGGCTTTGAAAACATCATGCACTGAAGGACTTACAGATGACC
42548 CGAAGGCTTTGAAAACATCA
1 CGAAGGCTTTGAAAACATCA
42568 AAAAGCTCCC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
45 56 0.89
47 7 0.11
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (45 bp):
CGAAGGCTTTGAAAACATCATGCACTGAAGGACTTACAGATGACC
Found at i:42526 original size:121 final size:121
Alignment explanation
Indices: 42378--42643 Score: 469
Period size: 121 Copynumber: 2.2 Consensus size: 121
42368 TCAAAAAGCT
* * *
42378 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTAAAAC
1 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
*
42443 ATCAAAAAGCTCACGAAGGCTTTTTGGAAACATCATGCACTGGAGGACTTACAGATGA
64 ATCAAAAAGCTCACGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
42501 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
*
42566 CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
66 CAAAAAGCTCACGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
42622 CCCGAAGGCTTTGAAAACATCA
1 CCCGAAGGCTTTGAAAACATCA
42644 AAAAGCTCCC
Statistics
Matches: 138, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
121 129 0.93
123 9 0.07
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (121 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
CAAAAAGCTCACGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:42539 original size:197 final size:197
Alignment explanation
Indices: 42302--42719 Score: 764
Period size: 197 Copynumber: 2.1 Consensus size: 197
42292 TCAAAAAGAT
* *
42302 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
42367 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
64 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
* * *
42432 GTTTTTAAAACATCAAAAAGCTCACGAAGGCTTTTTGGAAACATCATGCACTGGAGGACTTACAG
129 GCTTTGAAAACATCAAAAAGCTCACGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
42497 ATGA
194 ATGA
42501 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
42566 CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC
66 CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC
*
42631 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
131 TTTGAAAACATCAAAAAGCTCACGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
42696 GA
196 GA
42698 CCCGAAGGCTTTGAAAACATCA
1 CCCGAAGGCTTTGAAAACATCA
42720 AAAAGCTCCC
Statistics
Matches: 213, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
197 204 0.96
199 9 0.04
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (197 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACAT
CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC
TTTGAAAACATCAAAAAGCTCACGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
GA
Found at i:42738 original size:273 final size:275
Alignment explanation
Indices: 42226--42773 Score: 1001
Period size: 273 Copynumber: 2.0 Consensus size: 275
42216 TCAAAAAGCT
*
42226 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGC-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
42291 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
65 ATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
*
42356 GTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
130 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
* *
42421 ATGACCCGAAGGTTTTTAAAACATCAAAAAGCTCACGAAGGC-TTTTTGGAAACATCATGCACTG
195 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCACGAAGGCTTTTTTGGAAACATCATGCACTG
*
42485 GAGGACTTACAGATGA
260 AAGGACTTACAGATGA
42501 CCCGAAGGC-TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
1 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
*
42565 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
66 TCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
42630 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
131 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
* *
42695 TGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGGAGGCTTTTTTGGAAACATCATGCACTGA
196 TGACCCGAAGGCTTTGAAAACATCAAAAAGCTCACGAAGGCTTTTTTGGAAACATCATGCACTGA
42760 AGGACTTACAGATG
261 AGGACTTACAGATG
42774 TGAGAAATAG
Statistics
Matches: 264, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
273 219 0.83
274 36 0.14
275 9 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (275 bp):
CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
TCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
TGACCCGAAGGCTTTGAAAACATCAAAAAGCTCACGAAGGCTTTTTTGGAAACATCATGCACTGA
AGGACTTACAGATGA
Found at i:42800 original size:77 final size:76
Alignment explanation
Indices: 42501--42773 Score: 505
Period size: 76 Copynumber: 3.6 Consensus size: 76
42491 TTACAGATGA
*
42501 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
42564 ATCAAAAAGCT
66 ATCAAAAAGCT
42575 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
42640 ATCAAAAAGCT
66 ATCAAAAAGCT
42651 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
42716 ATCAAAAAGCT
66 ATCAAAAAGCT
*
42727 CCCGGAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 CCCGAAGGC-TTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
42774 TGAGAAATAG
Statistics
Matches: 194, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
74 9 0.05
76 148 0.76
77 37 0.19
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:43901 original size:54 final size:54
Alignment explanation
Indices: 43819--43930 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
43809 CGAATAGCAG
**
43819 GTTCGTAAAACATTTAACAGTGCATTCATCCTTTCCTGTAGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTAACAGCACATTCATCCTTTCCTGTAGCTTCTGCTCAGAT
* ** *
43873 GTTCGTAAAACATTTGAC-GACACATTCATCCTTTTTTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTAACAG-CACATTCATCCTTTCCTGTAGCTTCTGCTCAGAT
43927 GTTC
1 GTTC
43931 TCAATCATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
53 1 0.02
54 50 0.98
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTAACAGCACATTCATCCTTTCCTGTAGCTTCTGCTCAGAT
Found at i:46228 original size:114 final size:114
Alignment explanation
Indices: 46028--46253 Score: 344
Period size: 114 Copynumber: 2.0 Consensus size: 114
46018 GATCATGCAG
* * * * * *
46028 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATCGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
46093 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTAATTCCACTATGAGCAAA
* * *
46142 TTCATCTTTAAAATCCAATGATTGGTTTTTAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATCGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
46207 ACACTTCCAGAAGATGCTATTGGGTCTCTTTAATTCCACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTAATTCCACTATGAGCA
46254 CATGGCACTT
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (114 bp):
TTCATCTTTAAAATCCAATGATCGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTAATTCCACTATGAGCAAA
Found at i:48318 original size:11 final size:11
Alignment explanation
Indices: 48302--48336 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
48292 TCAATTTTCC
48302 TTTTTCTTCTT
1 TTTTTCTTCTT
*
48313 TTTTTCCTTTTT
1 TTTTT-CTTCTT
48325 TTTTTCTTCTT
1 TTTTTCTTCTT
48336 T
1 T
48337 CTTTGCTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:48641 original size:2 final size:2
Alignment explanation
Indices: 48634--48687 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
48624 ACAACAAAGG
48634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48676 AT AT AT AT AT AT
1 AT AT AT AT AT AT
48688 TAAAGGATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53199 original size:2 final size:2
Alignment explanation
Indices: 53192--53227 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
53182 ATTATTTTAA
53192 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53228 GACTAAGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54028 original size:14 final size:15
Alignment explanation
Indices: 54011--54048 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
54001 TTGTGGTCTG
54011 TTTCTTGTTTT-TTT
1 TTTCTTGTTTTCTTT
*
54025 TTTCTTTTTTTCTTT
1 TTTCTTGTTTTCTTT
54040 TTTC-TGTTT
1 TTTCTTGTTT
54049 CTGTATCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (15 bp):
TTTCTTGTTTTCTTT
Found at i:54486 original size:3 final size:3
Alignment explanation
Indices: 54478--54595 Score: 173
Period size: 3 Copynumber: 38.7 Consensus size: 3
54468 TTATTTATTA
*
54478 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* *
54525 AAT AAT AAT AAT TAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
54573 AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
54596 ATTTAAATGA
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
3 97 0.94
4 6 0.06
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:57712 original size:28 final size:27
Alignment explanation
Indices: 57672--57725 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
57662 AAATTTGAAT
*
57672 ATTTTATGTATTTATTTTGACTAAAAAC
1 ATTTTAAGTATTTATTTTGA-TAAAAAC
57700 ATTTTAAGTATTTATTTTGATAAAAA
1 ATTTTAAGTATTTATTTTGATAAAAA
57726 GATAAACTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (27 bp):
ATTTTAAGTATTTATTTTGATAAAAAC
Found at i:57875 original size:22 final size:23
Alignment explanation
Indices: 57833--57877 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
57823 AATAGTATTA
57833 TTACTTTGTCAAATTTGTTTTTGG
1 TTACTTTGTC-AATTTGTTTTTGG
*
57857 TTACTTTGTC-ATTTTTTTTTG
1 TTACTTTGTCAATTTGTTTTTG
57878 CTTAATTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
24 10 0.50
ACGTcount: A:0.13, C:0.09, G:0.13, T:0.64
Consensus pattern (23 bp):
TTACTTTGTCAATTTGTTTTTGG
Found at i:62419 original size:36 final size:37
Alignment explanation
Indices: 62344--62425 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
62334 CCCCATTACA
*
62344 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACC
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACC
* *
62380 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAATC
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACC
62416 A-TTTTCAAAG
1 ATTTTTCAAAG
62426 TTGGTTGTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 9 0.21
36 13 0.31
37 20 0.48
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACC
Found at i:71322 original size:21 final size:20
Alignment explanation
Indices: 71258--71322 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
71248 ACTTCGACTA
* *
71258 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTTCAAAT
* ** *
71278 TTGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATTTTC-AAAT
71299 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGA-TTTTCAAAT
71320 TCG
1 TCG
71323 TTGCGATAGT
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
20 12 0.36
21 18 0.55
22 3 0.09
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTTCAAAT
Found at i:71339 original size:40 final size:44
Alignment explanation
Indices: 71283--71380 Score: 150
Period size: 44 Copynumber: 2.3 Consensus size: 44
71273 CATATTTGCA
* *
71283 TTGCGATAGTCGAAGTTCGC-ATTG-CGATTT-TT-CAAATTCG
1 TTGCGATAGTCCAAGTTCGCGATAGTCGATTTATTCCAAATTCG
71323 TTGCGATAGTCCAAGTTCGCGATAGTCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGATAGTCGATTTATTCCAAATTCG
71367 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
71381 AATCGCAACG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
40 19 0.37
41 3 0.06
42 6 0.12
43 2 0.04
44 22 0.42
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (44 bp):
TTGCGATAGTCCAAGTTCGCGATAGTCGATTTATTCCAAATTCG
Found at i:71381 original size:19 final size:20
Alignment explanation
Indices: 71282--71381 Score: 60
Period size: 19 Copynumber: 4.8 Consensus size: 20
71272 ACATATTTGC
* *
71282 ATTGCGATAGTCGAAGTTCG
1 ATTGCGATAGTCCAAATTCG
** *
71302 CATTGCGATTTTTCAAATTCG
1 -ATTGCGATAGTCCAAATTCG
*
71323 -TTGCGATAGTCCAAGTTCGCG
1 ATTGCGATAGTCCAAATT--CG
* *
71344 ATAGTCGATTTATTCCAAATTCG
1 ATTG-CGA--TAGTCCAAATTCG
71367 -TTGCGATAGTCCAAA
1 ATTGCGATAGTCCAAA
71382 ATCGCAACGA
Statistics
Matches: 59, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
19 21 0.36
21 20 0.34
22 4 0.07
23 5 0.08
25 9 0.15
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
ATTGCGATAGTCCAAATTCG
Found at i:71481 original size:6 final size:6
Alignment explanation
Indices: 71470--71494 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
71460 GACACGTATT
71470 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
71495 TGACGACGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:72305 original size:19 final size:19
Alignment explanation
Indices: 72244--72370 Score: 119
Period size: 19 Copynumber: 6.3 Consensus size: 19
72234 CGTTGCGATT
*
72244 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
* *
72263 TTGTAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
72286 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
72305 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
72324 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
72347 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
72366 TTGGA
1 TTGGA
72371 AAATTGCATT
Statistics
Matches: 88, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
19 42 0.48
21 28 0.32
23 18 0.20
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:72339 original size:61 final size:61
Alignment explanation
Indices: 72244--72370 Score: 218
Period size: 61 Copynumber: 2.1 Consensus size: 61
72234 CGTTGCGATT
*
72244 TTGGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
* * *
72305 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
72366 TTGGA
1 TTGGA
72371 AAATTGCATT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (61 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
Found at i:72357 original size:42 final size:40
Alignment explanation
Indices: 72293--72371 Score: 140
Period size: 42 Copynumber: 1.9 Consensus size: 40
72283 AACTTCGACT
72293 ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAA
72333 ATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAA
1 ATCGCAA--CGAACTTGGACTATCGCAACGAATTTGGAA
72372 AATTGCATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 7 0.19
42 30 0.81
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (40 bp):
ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAA
Found at i:72405 original size:21 final size:21
Alignment explanation
Indices: 72379--72426 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
72369 GAAAATTGCA
72379 TTGCGATAGTCGATGTTCGCG
1 TTGCGATAGTCGATGTTCGCG
72400 TTGCGATAGTCGATGTTCGCG
1 TTGCGATAGTCGATGTTCGCG
72421 TTGCGA
1 TTGCGA
72427 ATCTAGAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.15, C:0.19, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGCGATAGTCGATGTTCGCG
Found at i:74672 original size:24 final size:24
Alignment explanation
Indices: 74645--74691 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
74635 TTTTTATATA
*
74645 TAATAATATTAAATATTTAATTAT
1 TAATAATATTAAATATTAAATTAT
* *
74669 TAATAATTTTATATATTAAATTA
1 TAATAATATTAAATATTAAATTA
74692 AGCTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATATTAAATATTAAATTAT
Found at i:77098 original size:30 final size:30
Alignment explanation
Indices: 77020--77177 Score: 144
Period size: 30 Copynumber: 5.4 Consensus size: 30
77010 TAAAATTAAC
* * *
77020 AGAAATTTAAAGGGCTAAAATAGCAAAAA-
1 AGAAACTTAAATGACTAAAATAGCAAAAAT
* * *
77049 A-AAA-TTAAAGGACTGAAATAGAAAAAAT
1 AGAAACTTAAATGACTAAAATAGCAAAAAT
*
77077 AGAAACTTAGCA-GACTAAAATAGCAAAAAT
1 AGAAACTTA-AATGACTAAAATAGCAAAAAT
* *
77107 AGAAACTTAAATGACTAAAATAGCAAACAC
1 AGAAACTTAAATGACTAAAATAGCAAAAAT
** * * *
77137 AGAAACTTAACGGGCCAAAATAGCAAAAAC
1 AGAAACTTAAATGACTAAAATAGCAAAAAT
*
77167 ATAAACTTAAA
1 AGAAACTTAAA
77178 GGGATAAACA
Statistics
Matches: 108, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
27 20 0.19
28 4 0.04
29 5 0.05
30 78 0.72
31 1 0.01
ACGTcount: A:0.58, C:0.12, G:0.13, T:0.16
Consensus pattern (30 bp):
AGAAACTTAAATGACTAAAATAGCAAAAAT
Found at i:77141 original size:60 final size:58
Alignment explanation
Indices: 77000--77179 Score: 177
Period size: 60 Copynumber: 3.1 Consensus size: 58
76990 AAGTATTTAC
* * *
77000 AGGACTAAAATA-AAATTAACAGAAATTTAA-AGGGCTAAAATAGCAAAAAAAAA-TTAA
1 AGGACTAAAATAGAAA-AAACAGAAACTTAACA-GACTAAAATAGCAAAAAAAAACTTAA
* * *
77057 AGGACTGAAATAGAAAAAATAGAAACTTAGCAGACTAAAATAGCAAAAATAGAAACTTAA
1 AGGACTAAAATAGAAAAAACAGAAACTTAACAGACTAAAATAGCAAAAA-A-AAACTTAA
* * * * * *
77117 ATGACTAAAATAGCAAACACAGAAACTTAACGGGCCAAAATAGCAAAAACATAAACTTAA
1 AGGACTAAAATAGAAAAAACAGAAACTTAACAGACTAAAATAGCAAAAA-A-AAACTTAA
77177 AGG
1 AGG
77180 GATAAACAGT
Statistics
Matches: 100, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
57 37 0.37
58 5 0.05
59 3 0.03
60 55 0.55
ACGTcount: A:0.58, C:0.12, G:0.14, T:0.17
Consensus pattern (58 bp):
AGGACTAAAATAGAAAAAACAGAAACTTAACAGACTAAAATAGCAAAAAAAAACTTAA
Found at i:77869 original size:21 final size:21
Alignment explanation
Indices: 77844--77897 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
77834 AAATAGAGAG
77844 AGAGCTCAAGAGCTTTCAACC
1 AGAGCTCAAGAGCTTTCAACC
*
77865 AGAGCTCAAGAGCTTTCAGCC
1 AGAGCTCAAGAGCTTTCAACC
*
77886 GGAGCTCCAAGA
1 AGAGCT-CAAGA
77898 AAACGGCGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (21 bp):
AGAGCTCAAGAGCTTTCAACC
Found at i:78662 original size:17 final size:17
Alignment explanation
Indices: 78635--78684 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
78625 GGATTATGCT
78635 TGTATCTGGGCTTCAATG
1 TGTA-CTGGGCTTCAATG
78653 TGTACTGGGCTTCAATG
1 TGTACTGGGCTTCAATG
*
78670 TGTACTGGGCCTCAA
1 TGTACTGGGCTTCAA
78685 GTGATGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 27 0.87
18 4 0.13
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (17 bp):
TGTACTGGGCTTCAATG
Found at i:78754 original size:3 final size:3
Alignment explanation
Indices: 78735--78796 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
78725 ATATGTAATT
*
78735 TAA TAA -AA -AA T-A TAA TAA TAA TAA TAA -ATA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
*
78777 TAA TAA TAA TAA AAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
78797 TTTTTAATAG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 7 0.14
3 44 0.86
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:78761 original size:21 final size:21
Alignment explanation
Indices: 78735--78782 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
78725 ATATGTAATT
78735 TAATAAAAAATATAATAATAA
1 TAATAAAAAATATAATAATAA
* *
78756 TAATAAATATTATAATAATAA
1 TAATAAAAAATATAATAATAA
78777 TAATAA
1 TAATAA
78783 TAATAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATAAAAAATATAATAATAA
Found at i:80312 original size:13 final size:13
Alignment explanation
Indices: 80277--80313 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
80267 AGAAAATGGT
*
80277 AAAATCATGACCC
1 AAAATCATGTCCC
80290 AAAATCATGTCCC
1 AAAATCATGTCCC
80303 AAAATCATGTC
1 AAAATCATGTC
80314 TCCGGTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (13 bp):
AAAATCATGTCCC
Found at i:80564 original size:15 final size:14
Alignment explanation
Indices: 80516--80565 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
80506 TAATATTTTT
80516 ATTTAAAAAGAATGA
1 ATTTAAAAA-AATGA
**
80531 ATTTATAAAAAATTT
1 ATTTA-AAAAAATGA
80546 ATTTAGAAAAAATGA
1 ATTTA-AAAAAATGA
80561 ATTTA
1 ATTTA
80566 TTAAATTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 25 0.86
16 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (14 bp):
ATTTAAAAAAATGA
Found at i:91602 original size:18 final size:18
Alignment explanation
Indices: 91567--91605 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
91557 CGAGGGTTAT
*
91567 ATAGTGGTCCTTTGGGAC
1 ATAGTGGTCATTTGGGAC
91585 ATAGTGGTCATTCT-GGAC
1 ATAGTGGTCATT-TGGGAC
91603 ATA
1 ATA
91606 TATAGTGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (18 bp):
ATAGTGGTCATTTGGGAC
Found at i:94274 original size:23 final size:23
Alignment explanation
Indices: 94246--94308 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
94236 GACATTTATA
*
94246 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTTAGGTGCAATTCTACG
*
94269 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTAGGTGCAATTCTACG
94292 TGGCACTTAGGTG-AATT
1 TGGCACTTAGGTGCAATT
94309 TATACGAGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 4 0.11
23 34 0.89
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:98111 original size:19 final size:19
Alignment explanation
Indices: 98087--98136 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
98077 ATGCAATTAT
*
98087 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAA
98106 TGCATCGATGCATAAGGAA
1 TGCATCGATGCATAAGGAA
98125 TGCATCGATGCA
1 TGCATCGATGCA
98137 CATGTTAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAA
Found at i:98145 original size:24 final size:22
Alignment explanation
Indices: 98087--98182 Score: 82
Period size: 19 Copynumber: 4.6 Consensus size: 22
98077 ATGCAATTAT
*
98087 TGCATCGATG--C-ATAAGGAG
1 TGCATCGATGCACTATAAGGAA
98106 TGCATCGATG--C-ATAAGGAA
1 TGCATCGATGCACTATAAGGAA
* *
98125 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCAC-T-ATAAGGAA
*
98149 TGCATCGATACACTAT-A-GAA
1 TGCATCGATGCACTATAAGGAA
98169 TGCATCGATGCACT
1 TGCATCGATGCACT
98183 GCAAGGGGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
19 28 0.43
20 15 0.23
21 2 0.03
22 1 0.02
23 1 0.02
24 18 0.28
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (22 bp):
TGCATCGATGCACTATAAGGAA
Found at i:100710 original size:12 final size:12
Alignment explanation
Indices: 100677--100724 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
100667 TTTCTGAATT
100677 CGGTACTGTTCA
1 CGGTACTGTTCA
* * *
100689 TGGCAATGTTCA
1 CGGTACTGTTCA
100701 CGGTACTGTTCATA
1 CGGTACTGTTC--A
100715 CGGTACTGTT
1 CGGTACTGTT
100725 TATACCTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 17 0.61
14 11 0.39
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (12 bp):
CGGTACTGTTCA
Found at i:100719 original size:14 final size:14
Alignment explanation
Indices: 100700--100729 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
100690 GGCAATGTTC
100700 ACGGTACTGTTCAT
1 ACGGTACTGTTCAT
*
100714 ACGGTACTGTTTAT
1 ACGGTACTGTTCAT
100728 AC
1 AC
100730 CTTATTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (14 bp):
ACGGTACTGTTCAT
Done.