Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004290.1 Hibiscus syriacus cultivar Beakdansim tig00009412_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: 130140
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:540 original size:38 final size:39
Alignment explanation
Indices: 497--572 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 39
487 GCGGTGTTTG
* *
497 TAACAAAAATACCACTAAAT-ACTTGACTTTTTGCGACA
1 TAACAAAAATACCACTAAATAACCTAACTTTTTGCGACA
** *
535 TAACAAAAATGTCGCTAAATAACCTAACTTTTTGCGAC
1 TAACAAAAATACCACTAAATAACCTAACTTTTTGCGAC
573 GTTTGTTAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 17 0.53
39 15 0.47
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (39 bp):
TAACAAAAATACCACTAAATAACCTAACTTTTTGCGACA
Found at i:1133 original size:2 final size:2
Alignment explanation
Indices: 1126--1150 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1116 TTAGTGAGAC
1126 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1151 CAGTAATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8292 original size:20 final size:20
Alignment explanation
Indices: 8264--8322 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
8254 CACTGAATAT
8264 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
8284 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
8303 -TGCCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
8322 T
1 T
8323 AATCCCTCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
20 16 0.50
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:9293 original size:26 final size:26
Alignment explanation
Indices: 9257--9315 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
9247 TTTCAAATAT
9257 GAACTCTATTTCAAAATTCCATTCAA
1 GAACTCTATTTCAAAATTCCATTCAA
* *
9283 GAACTTTATTTTAAAATTCCATTCAA
1 GAACTCTATTTCAAAATTCCATTCAA
9309 GAACTCT
1 GAACTCT
9316 TAATCTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (26 bp):
GAACTCTATTTCAAAATTCCATTCAA
Found at i:10118 original size:21 final size:21
Alignment explanation
Indices: 10091--10142 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
10081 TATGTTTATT
* *
10091 AAAAAATATTATTTTATTCAA
1 AAAAAATATGATTTAATTCAA
* *
10112 TAAAAATAGGGATTTAATTCAA
1 AAAAAATA-TGATTTAATTCAA
10134 AAAAAATAT
1 AAAAAATAT
10143 ATATATAGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (21 bp):
AAAAAATATGATTTAATTCAA
Found at i:11956 original size:44 final size:45
Alignment explanation
Indices: 11835--11957 Score: 160
Period size: 45 Copynumber: 2.8 Consensus size: 45
11825 ATAAATTTTT
* *
11835 TTACCATTTA-TCTCATAAACTTGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTATTC-CATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * * *
11880 TTACCATTTGTTTCATAAGCTCGTAAGTTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
*
11925 TTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTT
11958 GCATGCTTAC
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 24 0.36
45 42 0.63
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:14263 original size:23 final size:23
Alignment explanation
Indices: 14233--14277 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
14223 TTGGTCATCG
*
14233 TCTAAATTTTTTAGTATTACAAT
1 TCTAAATTTTTGAGTATTACAAT
*
14256 TCTAAATTTTTGGGTATTACAA
1 TCTAAATTTTTGAGTATTACAA
14278 ATCATTCGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (23 bp):
TCTAAATTTTTGAGTATTACAAT
Found at i:19676 original size:13 final size:13
Alignment explanation
Indices: 19658--19685 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19648 TGAACTCTCC
19658 CCTATTAATCCAA
1 CCTATTAATCCAA
19671 CCTATTAATCCAA
1 CCTATTAATCCAA
19684 CC
1 CC
19686 CAATATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (13 bp):
CCTATTAATCCAA
Found at i:25267 original size:61 final size:59
Alignment explanation
Indices: 25198--25312 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 59
25188 TATCATATGT
* * * *
25198 TCCTAAACTATGA-TCCTCATTTTAAATTAATCCTTAAATTTTTTTAATATTCTAACTTCC
1 TCCTAAACTATAACT-CTCATTCTAAATTAATCCTTAAA-CTTTTGAATATTCTAACTTCC
* *
25258 TCCTCAAACTATAACTTTCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAA
1 TCCT-AAACTATAACTCTCATTCTAAATTAATCCTTAAACTTTTGAATATTCTAA
25313 TTTCATCCCC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 18 0.38
61 28 0.60
62 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.44
Consensus pattern (59 bp):
TCCTAAACTATAACTCTCATTCTAAATTAATCCTTAAACTTTTGAATATTCTAACTTCC
Found at i:25942 original size:60 final size:58
Alignment explanation
Indices: 25791--25958 Score: 153
Period size: 60 Copynumber: 2.8 Consensus size: 58
25781 AGTATATACA
* * *
25791 TATAGTTTCGGATGAAATTGAAATA-TTAAACAGTTTAGGA-TCAATTTAGAATGAATGT
1 TATAGTTTAGGATGAAATTGAAATATTTAAA-AGTTTAAGACT-AATTTAGAATCAATGT
* * * ** *
25849 CATAATTTGAGGGTGAAATTGAAACGTTCAAAAGTTTGAAGACTAATTTAGAATC-ATAGT
1 TATAGTTT-AGGATGAAATTGAAATATTTAAAAGTTT-AAGACTAATTTAGAATCAAT-GT
* *
25909 TATAGTTTAAGGATGAAATTAAAATATTTAAAAGCTTAAGAACTAATTTA
1 TATAGTTT-AGGATGAAATTGAAATATTTAAAAGTTTAAG-ACTAATTTA
25959 AAATAAAAAT
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
58 6 0.07
59 23 0.27
60 56 0.65
61 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (58 bp):
TATAGTTTAGGATGAAATTGAAATATTTAAAAGTTTAAGACTAATTTAGAATCAATGT
Found at i:30381 original size:19 final size:19
Alignment explanation
Indices: 30334--30385 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
30324 ATACAATTTT
* * *
30334 TATTTTTTTATATTATTAT
1 TATTATTTTATATTTTTAC
* *
30353 TTTTAATTTATATTTTTAC
1 TATTATTTTATATTTTTAC
30372 TATTATTTTA-ATTT
1 TATTATTTTATATTT
30386 AAAATTAATA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTATTTTATATTTTTAC
Found at i:31273 original size:4 final size:4
Alignment explanation
Indices: 31264--31290 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
31254 AATATTCTCA
31264 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
31291 GAAAAGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:31848 original size:37 final size:36
Alignment explanation
Indices: 31807--31878 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
31797 CATAAAATGA
31807 GTTTGCTTCACTAATCTTCCGTGAAGGCTTACAGATG
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTA-AGATG
* *
31844 GTTTGTTTCACTACTCTTCCGTGAAGGCTTAAGAT
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGAT
31879 TGACCTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (36 bp):
GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGATG
Found at i:31888 original size:37 final size:37
Alignment explanation
Indices: 31813--31890 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
31803 ATGAGTTTGC
***
31813 TTCACTAATCTTCCGTGAAGGCTTACAGATGGTTTGT
1 TTCACTAATCTTCCGTGAAGGCTTACAGATGACCTGT
*
31850 TTCACTACTCTTCCGTGAAGGCTTA-AGATTGACCTGT
1 TTCACTAATCTTCCGTGAAGGCTTACAGA-TGACCTGT
31887 TTCA
1 TTCA
31891 AATGTCCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 3 0.08
37 33 0.92
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (37 bp):
TTCACTAATCTTCCGTGAAGGCTTACAGATGACCTGT
Found at i:32846 original size:23 final size:23
Alignment explanation
Indices: 32793--32843 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
32783 GATAATTTAA
*
32793 AAATAATAATATTTCAAATAAGT
1 AAATAATAAGATTTCAAATAAGT
* *
32816 AAATAATAAGATTTTAAA-AATT
1 AAATAATAAGATTTCAAATAAGT
32838 AAATAA
1 AAATAA
32844 ATATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
AAATAATAAGATTTCAAATAAGT
Found at i:32854 original size:19 final size:19
Alignment explanation
Indices: 32769--32855 Score: 61
Period size: 19 Copynumber: 4.4 Consensus size: 19
32759 TATAATATTA
* *
32769 TTTAAAATTAAATAGATAA
1 TTTAAAATTAAATAAATAT
*
32788 TTTAAAAAT-AAT-AATAT
1 TTTAAAATTAAATAAATAT
* * *
32805 TTCAAATAAGTAAATAATAAGAT
1 TT-TAA-AATTAAAT-A-AATAT
32828 TTTAAAAATTAAATAAATAT
1 TTT-AAAATTAAATAAATAT
32848 TTTAAAAT
1 TTTAAAAT
32856 ATTTTCATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
17 5 0.10
18 5 0.10
19 16 0.31
20 10 0.19
21 1 0.02
22 7 0.13
23 8 0.15
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTAAAATTAAATAAATAT
Found at i:32925 original size:24 final size:23
Alignment explanation
Indices: 32856--32925 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
32846 ATTTTAAAAT
32856 ATTTTCATAATAT-TATAAATATAA
1 ATTTT-ATAATATATATAAATA-AA
* * *
32880 TTTTTAGAATA-ATTTAATATAAA
1 ATTTTATAATATATATAA-ATAAA
32903 ATTTTATAATTATATATAAATAA
1 ATTTTATAA-TATATATAAATAA
32926 TTATTTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
23 18 0.50
24 13 0.36
25 5 0.14
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (23 bp):
ATTTTATAATATATATAAATAAA
Found at i:34868 original size:30 final size:30
Alignment explanation
Indices: 34814--34874 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
34804 GTAAACTATA
*
34814 AGTTTAGTAGTTAAACTATTATTTTTGTTCT
1 AGTTTAGTACTTAAACTATTATTTTT-TTCT
* *
34845 AGTTTGGTACTTAAA-TTTTATTTTTTTCT
1 AGTTTAGTACTTAAACTATTATTTTTTTCT
34874 A
1 A
34875 AAAGAATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 9 0.33
31 13 0.48
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (30 bp):
AGTTTAGTACTTAAACTATTATTTTTTTCT
Found at i:37785 original size:3 final size:3
Alignment explanation
Indices: 37777--37805 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
37767 TCGATTCCAA
37777 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
37806 ATAACAGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42038 original size:59 final size:60
Alignment explanation
Indices: 41934--42047 Score: 169
Period size: 59 Copynumber: 1.9 Consensus size: 60
41924 TGATCCATAA
*
41934 ACTTTTAAATATTCTAATTTTATCCCGAAACTATGACTATTATTCTAAATTAGTCTTCAG
1 ACTTTTAAATATTCTAATTTCATCCCGAAACTATGACTATTATTCTAAATTAGTCTTCAG
* * *
41994 ACTTTTGAATATT-TCATTTCATCCCTAAACTATGAC-ATTCATTCTAAATTAGTC
1 ACTTTTAAATATTCTAATTTCATCCCGAAACTATGACTATT-ATTCTAAATTAGTC
42048 CCTAAACTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 3 0.06
59 34 0.69
60 12 0.24
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.43
Consensus pattern (60 bp):
ACTTTTAAATATTCTAATTTCATCCCGAAACTATGACTATTATTCTAAATTAGTCTTCAG
Found at i:42057 original size:59 final size:58
Alignment explanation
Indices: 41931--42082 Score: 164
Period size: 59 Copynumber: 2.6 Consensus size: 58
41921 AATTGATCCA
* * * * *
41931 TAAACTTTTAAATATTCTAATTTTATCCCGAAACTATGACTATTATTCTAAATTAGTCT
1 TAAACTTTTGAATATT-TCATTTCATCCCTAAACTATGACTATTATTCTAAATTAGTCC
*
41990 TCAGACTTTTGAATATTTCATTTCATCCCTAAACTATGAC-ATTCATTCTAAATTAGTCCC
1 T-AAACTTTTGAATATTTCATTTCATCCCTAAACTATGACTATT-ATTCTAAATTAGT-CC
* *
42050 TAAACTTTTTGAATACTCCAATTTCAT-CCTAAA
1 TAAAC-TTTTGAATATTTC-ATTTCATCCCTAAA
42083 TTATATATAT
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
58 3 0.04
59 37 0.47
60 32 0.41
61 7 0.09
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (58 bp):
TAAACTTTTGAATATTTCATTTCATCCCTAAACTATGACTATTATTCTAAATTAGTCC
Found at i:42345 original size:29 final size:29
Alignment explanation
Indices: 42269--42397 Score: 134
Period size: 29 Copynumber: 4.4 Consensus size: 29
42259 AGACGGTCTT
*
42269 AGTTTAAGGGTGAAATTAGAATAATCAAA
1 AGTTTAAGGATGAAATTAGAATAATCAAA
*
42298 AGTTTAAGGGTGAAATTAGAATAATCAAA
1 AGTTTAAGGATGAAATTAGAATAATCAAA
* * * *
42327 AGTTTAAGGATTAATTTAGAATGTGAGTC-AT
1 AGTTTAAGGATGAAATTAGAA--T-AATCAAA
* * * *
42358 ACTTTAGGGATAAAATTAGAATATTCAAA
1 AGTTTAAGGATGAAATTAGAATAATCAAA
42387 AGTTTAAGGAT
1 AGTTTAAGGAT
42398 CAATTTAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.04
29 58 0.70
31 19 0.23
32 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (29 bp):
AGTTTAAGGATGAAATTAGAATAATCAAA
Found at i:42386 original size:60 final size:60
Alignment explanation
Indices: 42310--42423 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
42300 TTTAAGGGTG
* * *
42310 AAATTAGAATAATCAAAAGTTTAAGGATTAATTTAGAATGTGAGTCATACTTTAGGGATA
1 AAATTAGAATAATCAAAAGTTTAAGGATCAATTTAAAATGAGAGTCATACTTTAGGGATA
* * *
42370 AAATTAGAATATTCAAAAGTTTAAGGATCAATTTAAAATGAGAGTTATAGTTTA
1 AAATTAGAATAATCAAAAGTTTAAGGATCAATTTAAAATGAGAGTCATACTTTA
42424 AGGAAATATG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (60 bp):
AAATTAGAATAATCAAAAGTTTAAGGATCAATTTAAAATGAGAGTCATACTTTAGGGATA
Found at i:43484 original size:40 final size:38
Alignment explanation
Indices: 43440--43522 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 38
43430 TATTGAACAT
* * *
43440 AAAATATTACGAAGAATATAATATTTTCGATTGTCAACCG
1 AAAATATTACGAACAATATAACATTTTC-AGT-TCAACCG
* * *
43480 AAAATGTTATGAACAATGTAACATTTTCAGTTCAACCG
1 AAAATATTACGAACAATATAACATTTTCAGTTCAACCG
43518 AAAAT
1 AAAAT
43523 GTTGAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 12 0.32
39 2 0.05
40 23 0.62
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (38 bp):
AAAATATTACGAACAATATAACATTTTCAGTTCAACCG
Found at i:47721 original size:132 final size:133
Alignment explanation
Indices: 47493--47761 Score: 504
Period size: 132 Copynumber: 2.0 Consensus size: 133
47483 AGTGTATTTG
*
47493 CAACTAGCTTTCCAAATAATTTTAGTGAGGAGGAGGAGGAGTTTTTTTTTTTTTTTTAATTGTCA
1 CAACTAGCTTTCCAAATAATTTTAGTGAGGAGGAGGAGGAG-TTTTTTTTTATTTTTAATTGTCA
*
47558 CGTAACACTTTAACTAATGGAGTTAATGGTCGAGGGACCAAAATTAAACGGATTGATAATGTAAG
65 CGTAACACTTTAACTAATGGAGTTAACGGTCGAGGGACCAAAATTAAACGGATTGATAATGTAAG
47623 GGAC
130 GGAC
47627 CAACTAGCTTTCCAAATAATTTTAGTGAGGAGGAGGAGGA-TTTTTTTTTATTTTTAATTGTCAC
1 CAACTAGCTTTCCAAATAATTTTAGTGAGGAGGAGGAGGAGTTTTTTTTTATTTTTAATTGTCAC
47691 GTAACACTTTAACTAATGGAGTTAACGGTCGAGGGACCAAAATTAAACGGATTGATAATGTAAGG
66 GTAACACTTTAACTAATGGAGTTAACGGTCGAGGGACCAAAATTAAACGGATTGATAATGTAAGG
47756 GAC
131 GAC
47759 CAA
1 CAA
47762 ACGCACTTAA
Statistics
Matches: 133, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
132 93 0.70
134 40 0.30
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (133 bp):
CAACTAGCTTTCCAAATAATTTTAGTGAGGAGGAGGAGGAGTTTTTTTTTATTTTTAATTGTCAC
GTAACACTTTAACTAATGGAGTTAACGGTCGAGGGACCAAAATTAAACGGATTGATAATGTAAGG
GAC
Found at i:49779 original size:31 final size:31
Alignment explanation
Indices: 49657--49779 Score: 185
Period size: 31 Copynumber: 4.0 Consensus size: 31
49647 GAGTCGAGGG
*
49657 TTACCTATGTTCTTTGGGACATATGGACT-A
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* *
49687 TTTACCTATGTTCTTTGGGACATATGGACTGT
1 -TTACCTATGTTCTTCGGGACATATGGACTGA
49719 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* *
49750 TTACCTAGGTTCTTCGGGACCTATGGACTG
1 TTACCTATGTTCTTCGGGACATATGGACTG
49780 GTCCTTTGGG
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
31 86 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGA
Found at i:49993 original size:31 final size:31
Alignment explanation
Indices: 49958--50054 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
49948 TATGTTACAG
49958 ATTACCTATGTTCTTCGGGACATATGGACAA
1 ATTACCTATGTTCTTCGGGACATATGGACAA
* * * *
49989 ATTACCTATGTCCTTTGGGACATATGAACAG
1 ATTACCTATGTTCTTCGGGACATATGGACAA
* * * *
50020 GTTACCTATGTTATTCGGGATATATGGACAT
1 ATTACCTATGTTCTTCGGGACATATGGACAA
50051 ATTA
1 ATTA
50055 TTATATGAGC
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (31 bp):
ATTACCTATGTTCTTCGGGACATATGGACAA
Found at i:54384 original size:40 final size:39
Alignment explanation
Indices: 54348--54421 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
54338 AAATCATACC
*
54348 TAAAA-TTTAGTTTGTGTTTCATTTTA-TATCTCATCAT
1 TAAAACTTTAGTTTGTGCTTCATTTTAGTATCTCATCAT
*
54385 TAAAAGCTTTAGTTTTTGCTTCATTTTAGTATCTCAT
1 TAAAA-CTTTAGTTTGTGCTTCATTTTAGTATCTCAT
54422 TGTTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 5 0.16
39 19 0.59
40 8 0.25
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (39 bp):
TAAAACTTTAGTTTGTGCTTCATTTTAGTATCTCATCAT
Found at i:55546 original size:12 final size:12
Alignment explanation
Indices: 55529--55553 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55519 AAAGAAAGGG
55529 AATATATCAATT
1 AATATATCAATT
55541 AATATATCAATT
1 AATATATCAATT
55553 A
1 A
55554 GTGTTTATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AATATATCAATT
Found at i:63826 original size:29 final size:31
Alignment explanation
Indices: 63748--63827 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
63738 CTTTAATGAT
*
63748 TTAACAGTTCAATGGTATAATTGAAACATAAA
1 TTAAAAGTTCAATGGTATAATTG-AACATAAA
* * *
63780 TT-AAAGTTCAGTGCTATAATTG-ATA-AAA
1 TTAAAAGTTCAATGGTATAATTGAACATAAA
*
63808 TTAAAAGTTTAATGGTATAA
1 TTAAAAGTTCAATGGTATAA
63828 ACGATATAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
28 5 0.12
29 16 0.40
31 17 0.43
32 2 0.05
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (31 bp):
TTAAAAGTTCAATGGTATAATTGAACATAAA
Found at i:65153 original size:12 final size:12
Alignment explanation
Indices: 65130--65166 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
65120 GTATTATTAT
65130 ATTTACAAAAAAA
1 ATTTA-AAAAAAA
65143 ATTTAAAAAAAA
1 ATTTAAAAAAAA
65155 ATTTAAAAAAAA
1 ATTTAAAAAAAA
65167 GGAACTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 19 0.79
13 5 0.21
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
ATTTAAAAAAAA
Found at i:65440 original size:31 final size:30
Alignment explanation
Indices: 65405--65474 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
65395 TTTTGCTAAC
* * *
65405 ATTTGTTCTTAAGGGCTCAATTTTTTTCAAT
1 ATTTGTTATGAAGGGCTCAA-TCTTTTCAAT
* *
65436 ATTTGTTATGAGGGGTTCAATCTTTTCAAT
1 ATTTGTTATGAAGGGCTCAATCTTTTCAAT
*
65466 ATTTTTTAT
1 ATTTGTTAT
65475 TAGGTGCATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.23, C:0.10, G:0.14, T:0.53
Consensus pattern (30 bp):
ATTTGTTATGAAGGGCTCAATCTTTTCAAT
Found at i:67569 original size:63 final size:63
Alignment explanation
Indices: 67475--67603 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 63
67465 TTGGTGGCAT
* * * **
67475 TGCAAATTCATCCCCTTCACGGTAGTCGTCAGGGCCTAAGTCGTAATCAGATTCCGGTGGAAG
1 TGCAAACTCATCCCCTCCACGGTAGTAGTCAGGGCCTAAGTCGTAATCAGAGACCGGTGGAAG
* * * *
67538 TGCAAACTCATCTCCTCCACGGTGGTAGTCAGGGCCTAGGTCGTAATCGGAGACCGGTGGAAG
1 TGCAAACTCATCCCCTCCACGGTAGTAGTCAGGGCCTAAGTCGTAATCAGAGACCGGTGGAAG
67601 TGC
1 TGC
67604 GAAATCCGCC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (63 bp):
TGCAAACTCATCCCCTCCACGGTAGTAGTCAGGGCCTAAGTCGTAATCAGAGACCGGTGGAAG
Found at i:67741 original size:87 final size:87
Alignment explanation
Indices: 67527--67713 Score: 225
Period size: 87 Copynumber: 2.1 Consensus size: 87
67517 GTAATCAGAT
* * * ** * * * *
67527 TCCGGTGGAAGTGCAAACTCATCTCC-TCCACGGTGGTAGTCAGGGCCTAGGTCGTAATCGGAGA
1 TCCGGTGGCACTGCAAATTCATCTCCAT-CACCATCGTAGTCAGGGCCTAAGTCGAAATCGAAGA
67591 CCGGTGGAAGTGCGAAATCCGCC
65 CCGGTGGAAGTGCGAAATCCGCC
**
67614 TCCGGTGGCACTGCAAATTCATCTCCATCACCATCGTAGTCAGGGCCTAAGTCGAAATCGAATTC
1 TCCGGTGGCACTGCAAATTCATCTCCATCACCATCGTAGTCAGGGCCTAAGTCGAAATCGAAGAC
*
67679 GGGTGGAAGTGCGAAATCCGCC
66 CGGTGGAAGTGCGAAATCCGCC
*
67701 -CTTGGTGGCACTG
1 TC-CGGTGGCACTG
67714 TAATTGTATC
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
86 1 0.01
87 83 0.98
88 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.21
Consensus pattern (87 bp):
TCCGGTGGCACTGCAAATTCATCTCCATCACCATCGTAGTCAGGGCCTAAGTCGAAATCGAAGAC
CGGTGGAAGTGCGAAATCCGCC
Found at i:76388 original size:87 final size:85
Alignment explanation
Indices: 76252--76494 Score: 265
Period size: 87 Copynumber: 2.8 Consensus size: 85
76242 ATGGGAGACT
* * *
76252 TGGTAGTAGGCAGGGCCTAAGCCGTAATCGGAGTCCGGTGGAAGTGCGAAATCCACCATTGGTGG
1 TGGTAGTAGTCAGGGCCTAAGTCATAATCGGAGTCCGGTGGAAGTGCGAAATCC-CC-TTGGTGG
76317 CACTACAAATTCATCTCCTTCA
64 CACTACAAATTCATCTCCTTCA
* * * *
76339 TGGTAGTAGTCAGGGCCTAAGTCATAATCGGAGTCCGGCGGAAGAGCGAACTCCGCTTCCGGTGG
1 TGGTAGTAGTCAGGGCCTAAGTCATAATCGGAGTCCGGTGGAAGTGCGAAATCCCCTT--GGTGG
* *
76404 CAATGCAAATTCATCTCCTTCA
64 CACTACAAATTCATCTCCTTCA
** * * * *
76426 CCG-ACGTAGTCAGGGCCTAAGTCGA-AATCGAATTCGGGTGGAAGTGCGAAATCCGCCCTTAGT
1 TGGTA-GTAGTCAGGGCCTAAGTC-ATAATCGGAGTCCGGTGGAAGTGCGAAAT-C-CCCTTGGT
76489 GGCACT
62 GGCACT
76495 GTAATTGTAT
Statistics
Matches: 130, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
85 2 0.02
86 2 0.02
87 120 0.92
88 2 0.02
89 4 0.03
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (85 bp):
TGGTAGTAGTCAGGGCCTAAGTCATAATCGGAGTCCGGTGGAAGTGCGAAATCCCCTTGGTGGCA
CTACAAATTCATCTCCTTCA
Found at i:84281 original size:3 final size:3
Alignment explanation
Indices: 84275--84340 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
84265 TTATTTTTTT
* * *
84275 ATA ATA ATA ATA TATA TATA ATA ATT ATA ATA ATA ATA ATT ATG ATA
1 ATA ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
84322 ATA ATT ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
84341 AATGGGTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 48 0.87
4 7 0.13
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:84919 original size:113 final size:113
Alignment explanation
Indices: 84581--85430 Score: 1299
Period size: 113 Copynumber: 7.5 Consensus size: 113
84571 TTAAATAAGC
* * *
84581 TCTTCTCATTATGAACTTCTTCTTTCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * * * * *
84646 AAAGGTTGATCCATCAAGTGATGAATTTGAATCAAAAGGTTAAACAAGT
66 AAAAGCTGATCCATCAAGTGATGGATTTG-AGCAAAAGGTTGAACAAAT
* * * *
84695 TCTTCTCATTATGAACTTCTTCTTTCTCCTTCAGATGAGTTTTTCTCATTATGAACTTTTTTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTCTCTG
84760 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
65 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
* * ***
84809 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTTATTATGAACTCGAAT-TG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTG
*
84873 GAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
65 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
* * *
84922 TCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
84987 AGAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAAT
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
*
85035 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
85100 CAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
*
85148 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
85213 CAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
* *
85261 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * * ** *
85326 CAAAGCTGATCCATCAAATGATGAATTCAAGCAAAA-GTTGAACAAGT
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
* *
85373 TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
85431 CTTCTTCCTT
Statistics
Matches: 690, Mismatches: 43, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
112 67 0.10
113 467 0.68
114 123 0.18
115 33 0.05
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
Found at i:85414 original size:40 final size:40
Alignment explanation
Indices: 85370--85469 Score: 182
Period size: 40 Copynumber: 2.5 Consensus size: 40
85360 AAGTTGAACA
85370 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATG
1 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATG
85410 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATG
1 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATG
* *
85450 AGTTCTTCTCATTTTGAACT
1 AGTTCTTCTTATTATGAACT
85470 CTAACTGACA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.18, C:0.22, G:0.10, T:0.50
Consensus pattern (40 bp):
AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:85455 original size:20 final size:20
Alignment explanation
Indices: 85392--85457 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
85382 TATGAACTTC
85392 TTCTTCCTTCTTCAGATGAG
1 TTCTTCCTTCTTCAGATGAG
* **
85412 TTCTT-CTTATT-ATGAACT-TC
1 TTCTTCCTTCTTCA-G-A-TGAG
85432 TTCTTCCTTCTTCAGATGAG
1 TTCTTCCTTCTTCAGATGAG
85452 TTCTTC
1 TTCTTC
85458 TCATTTTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 1 0.03
19 7 0.21
20 18 0.53
21 7 0.21
22 1 0.03
ACGTcount: A:0.15, C:0.24, G:0.11, T:0.50
Consensus pattern (20 bp):
TTCTTCCTTCTTCAGATGAG
Found at i:86463 original size:91 final size:92
Alignment explanation
Indices: 86192--86469 Score: 443
Period size: 92 Copynumber: 3.0 Consensus size: 92
86182 CGATCATGCA
* * * *
86192 ATTCATCTTT-TAATTCCAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAATTCAAA
1 ATTCATCTTTCAAATT-CAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAA
*
86256 GAACACTTCCAGAAGATGCTATGATCAC
65 GAACACTTCCAGAAGATGCTATGAGCAC
* *
86284 ATTCATCTTCCAAATTCAATGATTAGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 ATTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAG
86349 AACACTTCCAGAAGATGCTATGAGCAC
66 AACACTTCCAGAAGATGCTATGAGCAC
** *
86376 ATTCATCTTTCAAATTCAATGATTGGTTCTG-GGTTTTTACCAAACCAAATCAGATAACTCAAAG
1 ATTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAG
86440 AACACTTCCAGAAGATGCTATGAGCAC
66 AACACTTCCAGAAGATGCTATGAGCAC
86467 ATT
1 ATT
86470 GCATTTGTTC
Statistics
Matches: 173, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
91 60 0.35
92 109 0.63
93 4 0.02
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (92 bp):
ATTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATGAGCAC
Found at i:86499 original size:91 final size:89
Alignment explanation
Indices: 86203--86499 Score: 353
Period size: 92 Copynumber: 3.2 Consensus size: 89
86193 TTCATCTTTT
* * * *
86203 AATTCCAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAATTCAAAGAACACTTCCAG
1 AATT-CAATGTTTGG-TCTG-GGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
* *
86268 AAGATGCTATGATCACATTCATCTTCC
63 AAGATGCTATGAGCACATTCATTTTCC
* *
86295 AAATTCAATGATTAGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 -AATTCAATG-TTTGGTCTG-GGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
*
86360 AAGATGCTATGAGCACATTCATCTTTCA
63 AAGATGCTATGAGCACATTCAT-TTTCC
* ** *
86388 AATTCAATGATTGGTTCTGGGTTTTTACCAAACCAAATCAGATAACTCAAAGAACACTTCCAGAA
1 AATTCAATGTTTGG-TCTGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
86453 GATGCTATGAGCACATTGCATTTGTTCC
65 GATGCTATGAGCACATT-CA-TT-TTCC
* *
86481 AGTT-AATGTTTGGACTGGG
1 AATTCAATGTTTGGTCTGGG
86500 ATATCACAGT
Statistics
Matches: 179, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
91 67 0.37
92 96 0.54
93 16 0.09
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (89 bp):
AATTCAATGTTTGGTCTGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
ATGCTATGAGCACATTCATTTTCC
Found at i:87842 original size:9 final size:9
Alignment explanation
Indices: 87828--87883 Score: 67
Period size: 9 Copynumber: 5.9 Consensus size: 9
87818 CTTGACCCTT
87828 TTTTTTTTC
1 TTTTTTTTC
*
87837 TTTTTTTCC
1 TTTTTTTTC
*
87846 TTTTTTTCC
1 TTTTTTTTC
87855 TTTTTTTTC
1 TTTTTTTTC
87864 TCTTTTCTTTC
1 T-TTTT-TTTC
87875 TTTTCTTTT
1 TTTT-TTTT
87884 TCTCTCTAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
9 26 0.62
10 10 0.24
11 6 0.14
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:87847 original size:20 final size:20
Alignment explanation
Indices: 87824--87887 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 20
87814 TCACCTTGAC
*
87824 CCTTTTTTTTTTCTTTTTTT
1 CCTTTTTTTTTTCTTTTTCT
87844 CCTTTTTTTCCTTT-TTTTTCT
1 CCTTTTTTT--TTTCTTTTTCT
*
87865 CTTTTCTTTCTTTTCTTTTTCT
1 CCTTT-TTT-TTTTCTTTTTCT
87887 C
1 C
87888 TCTAAGCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 9 0.24
21 13 0.35
22 14 0.38
23 1 0.03
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (20 bp):
CCTTTTTTTTTTCTTTTTCT
Found at i:87849 original size:18 final size:19
Alignment explanation
Indices: 87828--87878 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
87818 CTTGACCCTT
87828 TTTTTTTTCTTTTTTTC-C
1 TTTTTTTTCTTTTTTTCTC
*
87846 TTTTTTTCCTTTTTTTTCTC
1 TTTTTTTTC-TTTTTTTCTC
*
87866 TTTTCTTTCTTTT
1 TTTTTTTTCTTTT
87879 CTTTTTCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.29
19 12 0.43
20 8 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTTCTTTTTTTCTC
Found at i:95220 original size:15 final size:15
Alignment explanation
Indices: 95197--95228 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
95187 TGAAATGAAT
95197 AATGAATGTATGTAA
1 AATGAATGTATGTAA
*
95212 AATGCATGTATGTAA
1 AATGAATGTATGTAA
95227 AA
1 AA
95229 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (15 bp):
AATGAATGTATGTAA
Found at i:100211 original size:19 final size:19
Alignment explanation
Indices: 100187--100225 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
100177 TTTCTGTCTC
*
100187 TCTCGG-TCTGTCTTCTCTT
1 TCTCGGTTCT-TCCTCTCTT
100206 TCTCGGTTCTTCCTCTCTT
1 TCTCGGTTCTTCCTCTCTT
100225 T
1 T
100226 TTTTTCTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.00, C:0.33, G:0.13, T:0.54
Consensus pattern (19 bp):
TCTCGGTTCTTCCTCTCTT
Found at i:100636 original size:12 final size:12
Alignment explanation
Indices: 100621--100646 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
100611 ATTATTATTA
100621 TTATTTATTTTT
1 TTATTTATTTTT
100633 TTATTTATTTTT
1 TTATTTATTTTT
100645 TT
1 TT
100647 TAATAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTATTTATTTTT
Found at i:100653 original size:3 final size:3
Alignment explanation
Indices: 100647--100704 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
100637 TTATTTTTTT
* * *
100647 TAA TAA TAA TAA T-A TATA TATA TAA TAA TTA TGA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
100693 TAA TAA TAA TAA
1 TAA TAA TAA TAA
100705 AATGGGTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
2 2 0.04
3 39 0.81
4 7 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:100688 original size:15 final size:14
Alignment explanation
Indices: 100649--100704 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 14
100639 ATTTTTTTTA
100649 ATAATAATAATATAT
1 ATAATAATAAT-TAT
100664 ATATATAATAATTAT
1 ATA-ATAATAATTAT
100679 GATAATAATAATTAT
1 -ATAATAATAATTAT
100694 AATAATAATAA
1 -ATAATAATAA
100705 AATGGGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
15 27 0.71
16 11 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
ATAATAATAATTAT
Found at i:103361 original size:113 final size:112
Alignment explanation
Indices: 103154--103372 Score: 325
Period size: 112 Copynumber: 1.9 Consensus size: 112
103144 ATTTTGGGGT
* * *
103154 AATAATAGTGGCGTTTTTTTGAAAAACACGTCACAATAGGTCCATCTATAGTGGTGTTTATTGGA
1 AATAATAGTGGCGTTTTTTTGAAAAACACGTCACAATAGGTCCATCTATAATGGCGTTTATTAGA
103219 AAACGCCACTATATATATACTTTTTTTTGGCATTTTTTTGGGCTATGC
66 AAACGCCACTATATATATACTTTTTTTTGG-ATTTTTTTGGGCTATGC
* * *
103267 AATAATAGTGGCGGTTTTTTT-TAAAA-ACGTCGCAATAGGTCTATCTATAATGGCGTTTATTAG
1 AATAATAGTGGC-GTTTTTTTGAAAAACACGTCACAATAGGTCCATCTATAATGGCGTTTATTAG
* *
103330 AAAAGCGCCACTATATATATATTTTTTTTTGGGTTTTTTTGGG
65 AAAA-CGCCACTATATATATACTTTTTTTTGGATTTTTTTGGG
103373 GGCGGTCGCG
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
112 46 0.48
113 42 0.44
114 8 0.08
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.41
Consensus pattern (112 bp):
AATAATAGTGGCGTTTTTTTGAAAAACACGTCACAATAGGTCCATCTATAATGGCGTTTATTAGA
AAACGCCACTATATATATACTTTTTTTTGGATTTTTTTGGGCTATGC
Found at i:114447 original size:2 final size:2
Alignment explanation
Indices: 114440--114473 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
114430 CTAAGTAAAG
114440 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
114474 GTTTAATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115006 original size:15 final size:15
Alignment explanation
Indices: 114986--115015 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
114976 TAATTAAATT
114986 ATTTAAAAAAATTTA
1 ATTTAAAAAAATTTA
*
115001 ATTTAAAAACATTTA
1 ATTTAAAAAAATTTA
115016 TCACAATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAAAAAAATTTA
Found at i:122264 original size:21 final size:21
Alignment explanation
Indices: 122220--122265 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
122210 CGAAGTACCG
* **
122220 CATATATCTTCCAAAGGATTA
1 CATATATCTCCCAAAGGACCA
*
122241 CATATATGTCCCAAAGGACCA
1 CATATATCTCCCAAAGGACCA
122262 CATA
1 CATA
122266 GAACCCTCGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (21 bp):
CATATATCTCCCAAAGGACCA
Found at i:127105 original size:21 final size:21
Alignment explanation
Indices: 127066--127109 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
127056 CAAATTTATT
127066 AAATTTTAAAGGAATAATAATA
1 AAATTTTAAAGGAATAAT-ATA
**
127088 AAATTTTAATTGAA-AATATA
1 AAATTTTAAAGGAATAATATA
127108 AA
1 AA
127110 TAAAATATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 3 0.15
22 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (21 bp):
AAATTTTAAAGGAATAATATA
Found at i:128591 original size:21 final size:21
Alignment explanation
Indices: 128562--128614 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
128552 GGTAGAGTGT
* **
128562 TACCTAAAATGTTATTTTTTC
1 TACCTAAAATGTTAATTTCGC
*
128583 TACCGAAAATGTTAATTTCGC
1 TACCTAAAATGTTAATTTCGC
128604 TACCTAAAATG
1 TACCTAAAATG
128615 AATATTTCCG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (21 bp):
TACCTAAAATGTTAATTTCGC
Done.