Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007095.1 Hibiscus syriacus cultivar Beakdansim tig00018537_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: 73494
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4564 original size:218 final size:218
Alignment explanation
Indices: 4183--4619 Score: 811
Period size: 218 Copynumber: 2.0 Consensus size: 218
4173 ACGGAGAGAA
4183 GTAACCGTAAATTGAAAAACAGTATGCCAAAACAACCGAGAGCAGTAAAGGAGCGATCTCACCAG
1 GTAACCGTAAATTGAAAAACAGTATGCCAAAACAACCGAGAGCAGTAAAGGAGCGATCTCACCAG
4248 ATTTGAAAAACAAAGAGCCAAACAAGGAGTAGCAGAGAAACAGGACGCAAAGACGCAGCCTGAAA
66 ATTTGAAAAACAAAGAGCCAAACAAGGAGTAGCAGAGAAACAGGACGCAAAGACGCAGCCTGAAA
* *
4313 TCGAAGGAGCTAACCGACAATCAACCAGAGTGCAGAGATCACCAAACTGTGCTGAGGCCAAGCAA
131 TCGAAGGAGCAAACCGACAATCAACCAGAGTGCAGAGATCAACAAACTGTGCTGAGGCCAAGCAA
4378 AGGAGCCACTTCACTTCGACAAG
196 AGGAGCCACTTCACTTCGACAAG
4401 GTAACCGTAAATTGAAAAACAGTATGCCAAAACAACCGAGAGCAGTAAAGGAGCGATCTCACCAG
1 GTAACCGTAAATTGAAAAACAGTATGCCAAAACAACCGAGAGCAGTAAAGGAGCGATCTCACCAG
* *
4466 ATTTGAAAAACGAAGAGCCAAACAAGGAGTAGCAGAGAAATAGGACGCAAAGACGCAGCCTGAAA
66 ATTTGAAAAACAAAGAGCCAAACAAGGAGTAGCAGAGAAACAGGACGCAAAGACGCAGCCTGAAA
* * *
4531 TCGAAGGAGCAAACCGACAATCAACCGGAGTGCAGAGATCAACGAACTGTGCTGAGGCTAAGCAA
131 TCGAAGGAGCAAACCGACAATCAACCAGAGTGCAGAGATCAACAAACTGTGCTGAGGCCAAGCAA
4596 AGGAGCCACTTCACTTCGACAAG
196 AGGAGCCACTTCACTTCGACAAG
4619 G
1 G
4620 ATTAGGAGCG
Statistics
Matches: 212, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
218 212 1.00
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (218 bp):
GTAACCGTAAATTGAAAAACAGTATGCCAAAACAACCGAGAGCAGTAAAGGAGCGATCTCACCAG
ATTTGAAAAACAAAGAGCCAAACAAGGAGTAGCAGAGAAACAGGACGCAAAGACGCAGCCTGAAA
TCGAAGGAGCAAACCGACAATCAACCAGAGTGCAGAGATCAACAAACTGTGCTGAGGCCAAGCAA
AGGAGCCACTTCACTTCGACAAG
Found at i:5068 original size:29 final size:29
Alignment explanation
Indices: 4972--5051 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
4962 ATTCTACAGT
*
4972 GACCAAAGAGGTCGCCATGCACGCCCAAC
1 GACCAAGGAGGTCGCCATGCACGCCCAAC
5001 GACCAAGGAGGTCGCCATGCACGCCCAAC
1 GACCAAGGAGGTCGCCATGCACGCCCAAC
5030 GACCAAGGAGGTCGCCATGCAC
1 GACCAAGGAGGTCGCCATGCAC
5052 TCGGGGCGAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.29, C:0.36, G:0.28, T:0.07
Consensus pattern (29 bp):
GACCAAGGAGGTCGCCATGCACGCCCAAC
Found at i:5130 original size:19 final size:20
Alignment explanation
Indices: 5096--5142 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
5086 GCATGGGTGG
5096 GGGGAGATCAGTGCATGCAT
1 GGGGAGATCAGTGCATGCAT
5116 GGGGAGATC-GTGCATGCAT
1 GGGGAGATCAGTGCATGCAT
5135 GGGGAGAT
1 GGGGAGAT
5143 TGGTGCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.23, C:0.13, G:0.45, T:0.19
Consensus pattern (20 bp):
GGGGAGATCAGTGCATGCAT
Found at i:5154 original size:16 final size:16
Alignment explanation
Indices: 5111--5163 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
5101 GATCAGTGCA
*
5111 TGCATGGGGAGATCGTG
1 TGCAAGGGGAGATCG-G
* *
5128 CATGCATGGGGAGATTGG
1 --TGCAAGGGGAGATCGG
5146 TGCAAGGGGAGATCGG
1 TGCAAGGGGAGATCGG
5162 TG
1 TG
5164 ACCAAAGAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 16 0.52
18 1 0.03
19 14 0.45
ACGTcount: A:0.21, C:0.11, G:0.47, T:0.21
Consensus pattern (16 bp):
TGCAAGGGGAGATCGG
Found at i:5230 original size:29 final size:30
Alignment explanation
Indices: 5182--5241 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
5172 GCGGGAGCTG
*
5182 CATGTGTAGGTCGCCGTGGAGTCCCGGCGA
1 CATGTGTAGGTCGCCATGGAGTCCCGGCGA
5212 CATG-GTAGGTCGCCATGGAGTCCCGGCGA
1 CATGTGTAGGTCGCCATGGAGTCCCGGCGA
5241 C
1 C
5242 CAAGCTGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.18
Consensus pattern (30 bp):
CATGTGTAGGTCGCCATGGAGTCCCGGCGA
Found at i:5358 original size:65 final size:65
Alignment explanation
Indices: 5254--5392 Score: 206
Period size: 65 Copynumber: 2.1 Consensus size: 65
5244 AGCTGTGGAG
* * * * *
5254 TCCTGCACCACGCCCAAAATTTAACCCTATCCCTCATGCATGCGTTGCATCCATAGCTGGGAGAT
1 TCCTGCATCACGACCAAAATTTAACCATATCACTCATGCATACGTTGCATCCATAGCTGGGAGAT
** *
5319 TCCTGCATCACGACCAAGCTTTAACCATATCACTCATGCATACGTTTCATCCATAGCTGGGAGAT
1 TCCTGCATCACGACCAAAATTTAACCATATCACTCATGCATACGTTGCATCCATAGCTGGGAGAT
5384 TCCTGCATC
1 TCCTGCATC
5393 CGTAGCTGCA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (65 bp):
TCCTGCATCACGACCAAAATTTAACCATATCACTCATGCATACGTTGCATCCATAGCTGGGAGAT
Found at i:5816 original size:21 final size:21
Alignment explanation
Indices: 5791--5834 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5781 AATCTAGTTA
5791 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
5812 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
5833 AT
1 AT
5835 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:6350 original size:17 final size:17
Alignment explanation
Indices: 6328--6389 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
6318 AGATAATTTC
6328 TGTTTAAAAAAATATTG
1 TGTTTAAAAAAATATTG
* *
6345 TGTTTAAAAATATTTAGTG
1 TGTTTAAAAA-A-ATATTG
*
6364 TTGTTTTAAAAAAATATTT
1 -TG-TTTAAAAAAATATTG
6383 TGTTTAA
1 TGTTTAA
6390 TTTATATTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 15 0.42
18 3 0.08
19 7 0.19
20 3 0.08
21 8 0.22
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.48
Consensus pattern (17 bp):
TGTTTAAAAAAATATTG
Found at i:6393 original size:22 final size:23
Alignment explanation
Indices: 6350--6393 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
6340 TATTGTGTTT
**
6350 AAAAATATTTAGTGTTGTTTTAA
1 AAAAATATTTAGTGTTAATTTAA
*
6373 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
6394 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTGTTAATTTAA
Found at i:6644 original size:22 final size:22
Alignment explanation
Indices: 6619--6666 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
6609 TCATATTATT
*
6619 ATTAAATCATTAATATCAAATC
1 ATTAAATCAATAATATCAAATC
* * *
6641 ATTAGATTAATAATATTAAATC
1 ATTAAATCAATAATATCAAATC
6663 ATTA
1 ATTA
6667 TTAGTAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTAAATCAATAATATCAAATC
Found at i:6674 original size:20 final size:21
Alignment explanation
Indices: 6629--6678 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
6619 ATTAAATCAT
*
6629 TAATATCAAATCATTAGATTAA
1 TAATATTAAATCATTA-ATTAA
*
6651 TAATATTAAATCATT-ATTAG
1 TAATATTAAATCATTAATTAA
6671 TAATATTA
1 TAATATTA
6679 GTAATAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 12 0.46
22 14 0.54
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (21 bp):
TAATATTAAATCATTAATTAA
Found at i:9708 original size:17 final size:18
Alignment explanation
Indices: 9626--9714 Score: 65
Period size: 17 Copynumber: 4.8 Consensus size: 18
9616 GATAGTAATG
*
9626 ATTAGTAATAATGAAATT
1 ATTAATAATAATGAAATT
* **
9644 ATTATTAAT-ATTTAATT
1 ATTAATAATAATGAAATT
* *
9661 ATTTGATAGTAATATTAGTAATT
1 A-TT-A-A-TAATAAT-GAAATT
9684 ATTAATAATAATGAAATT
1 ATTAATAATAATGAAATT
9702 A-TAATAATAATGA
1 ATTAATAATAATGA
9715 TTTACTAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
17 19 0.33
18 16 0.28
19 7 0.12
20 1 0.02
21 5 0.09
22 3 0.05
23 6 0.11
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (18 bp):
ATTAATAATAATGAAATT
Found at i:9931 original size:12 final size:12
Alignment explanation
Indices: 9916--9947 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
9906 CATTATAATG
9916 ATTTAATAATAA
1 ATTTAATAATAA
*
9928 ATTTAATAATGA
1 ATTTAATAATAA
9940 ATTTAATA
1 ATTTAATA
9948 TTTAATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
ATTTAATAATAA
Found at i:9934 original size:20 final size:22
Alignment explanation
Indices: 9889--9947 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 22
9879 TAACCATAAA
*
9889 AATGATTTGATAATAATCATTAT
1 AATGATTTAATAATAA-CATTAT
9912 AATGATTTAATAATAA-ATTTAAT
1 AATGATTTAATAATAACA-TT-AT
9935 AATGAATTTAATA
1 AATG-ATTTAATA
9948 TTTAATGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 1 0.03
22 2 0.06
23 21 0.66
24 8 0.25
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (22 bp):
AATGATTTAATAATAACATTAT
Found at i:9998 original size:26 final size:25
Alignment explanation
Indices: 9969--10188 Score: 191
Period size: 26 Copynumber: 8.6 Consensus size: 25
9959 GATGATTTAG
9969 TAATGATTTGATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
9995 TAATGATTTGATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
10021 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
* * * *
10047 TAATGATTTA-AATATTTAATGAT-T
1 TAATGATTTATAATA-ATCATTATAA
* *
10071 TGATGATTTAGTAATGAT--TTGATAA
1 TAATGATTTA-TAATAATCATT-ATAA
* *
10096 TAATCA-TTATAATAATGATT-TAA
1 TAATGATTTATAATAATCATTATAA
*
10119 TAATAATCATTATAATAATCATTATAA
1 TAATGAT--TTATAATAATCATTATAA
* *
10146 TAATGATTTAATAATAATGATTTGATAG
1 TAATGATTT-ATAATAATCA-TT-ATAA
10174 TAATGATTTAGTAAT
1 TAATGATTTA-TAAT
10189 GATTAGTAAT
Statistics
Matches: 161, Mismatches: 17, Indels: 30
0.77 0.08 0.14
Matches are distributed among these distances:
23 15 0.09
24 18 0.11
25 15 0.09
26 85 0.53
27 12 0.07
28 16 0.10
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.44
Consensus pattern (25 bp):
TAATGATTTATAATAATCATTATAA
Found at i:10067 original size:113 final size:110
Alignment explanation
Indices: 9884--10182 Score: 432
Period size: 113 Copynumber: 2.7 Consensus size: 110
9874 TCAATTAACC
*
9884 ATAAAAATGATTTGATAATAATCA-T-T-ATAATGATTTAATAATAA-ATT-TAATAATGAATTT
1 ATAATAATGATTTGATAATAATCATTATAATAATGATTT-ATAATAATATTATAATAATG-ATTT
9944 AATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATT
64 AATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATT
9991 ATAATAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATTT
1 ATAATAATGATTTGATAATAATCATTATAATAATGATTTA-TAATAAT-ATTATAATAATGATTT
10056 AAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATT
64 -AATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATT
* *
10104 ATAATAATGATTTAATAATAATCATTATAATAATCA-TTATAATAATGATTTAATAATAATGATT
1 ATAATAATGATTTGATAATAATCATTATAATAATGATTTATAATAAT-A-TT-ATAATAATGATT
* *
10168 TGATA-GTAATGATTT
63 TAATATTTAATGATTT
10183 AGTAATGATT
Statistics
Matches: 176, Mismatches: 6, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
107 23 0.13
108 1 0.01
109 2 0.01
110 16 0.09
111 17 0.10
112 15 0.09
113 102 0.58
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (110 bp):
ATAATAATGATTTGATAATAATCATTATAATAATGATTTATAATAATATTATAATAATGATTTAA
TATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATT
Found at i:10228 original size:60 final size:60
Alignment explanation
Indices: 10160--10909 Score: 398
Period size: 60 Copynumber: 12.6 Consensus size: 60
10150 GATTTAATAA
10160 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
* * *
10220 TAATGATTTGATATTAATGATTTAGCAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
10280 TAATGATTTGATAGTAATGA-TTAG---T-A--A-TAATAAT----TTATTATTAATATT
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
* *
10328 TAATGATTTGATACTAATGATTTAGTAATGGTTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
10388 TAATGATTTGATAGTAATGA-TTAG---T-A--A-TAATAAT----TTATTATTAATATT
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
* * * * * ** *
10436 TAATGATTTAATATTAATGATTTAGTAATGATTTGATAGTAATG-ATTTACGACTTGAACAATGA
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAG-TAATAATGAAATTATTA-TT-AA-TAT--
*
10500 A
60 T
* * * * * * * * * *
10501 CAATG-TTTAGTTCAATTAACCAT-ATTTTCGTTA-CATAACTAGTAATGAAATTA-TAATAATG
1 TAATGATTT-GAT--AGT-A--ATGA-TTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-
10562 ATT
58 ATT
* * * * * * ** * * *
10565 TAGT-A-ATGATTAGTAAT-A-AT-GAAATTATTATTAAT-ATTTAATGA-T-TTGATA-G
1 TAATGATTTGA-TAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
* * * * *
10617 TAATGA-TT--TAGTAATGATTAGTATATTTAATGATTTGATAATAATGATTAGTAATGATTAAT
1 TAATGATTTGATAGTAATGA-T--T-TA-GTAATGATTAG-TAATAATGA--AATTATTATTAAT
*
10679 ATAA
58 AT-T
* * *
10683 TAATTTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAATAATGAAATTAT
1 TAA-TGA-T-TTGATA-GTAATGA-TT--TAGTAATGA-TTAG-------TAATAATGAAATTAT
10748 TATTAATATT
51 TATTAATATT
* * * *
10758 TAATGATTTGATATTAATGATTTAATAATAATTAGTAATAATAAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
10818 TAATGATTTGATAGTAATGA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATT
1 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
10876 TAATGATTTGATATTAATGATTTAGTAATGATTA
1 TAATGATTTGATAGTAATGATTTAGTAATGATTA
10910 AATAGTAATG
Statistics
Matches: 533, Mismatches: 83, Indels: 149
0.70 0.11 0.19
Matches are distributed among these distances:
48 64 0.12
49 8 0.02
50 7 0.01
51 1 0.00
52 19 0.04
53 6 0.01
54 3 0.01
55 11 0.02
56 17 0.03
57 6 0.01
58 44 0.08
59 44 0.08
60 159 0.30
61 4 0.01
62 6 0.01
63 4 0.01
64 10 0.02
65 5 0.01
66 7 0.01
67 10 0.02
68 17 0.03
69 7 0.01
70 12 0.02
71 14 0.03
72 13 0.02
73 9 0.02
74 2 0.00
75 3 0.01
76 12 0.02
78 9 0.02
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (60 bp):
TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:10452 original size:14 final size:14
Alignment explanation
Indices: 10388--10484 Score: 65
Period size: 14 Copynumber: 6.7 Consensus size: 14
10378 TATTAATATT
*
10388 TAATGATTTGATAG
1 TAATGATTTAATAG
*
10402 TAATGATTAGTAATAA
1 TAATGATT--TAATAG
* *
10418 TAATTTATTATTAATATT
1 TAA-TGA-T-TTAATA-G
*
10436 TAATGATTTAATAT
1 TAATGATTTAATAG
10450 TAATGA-TT--TAG
1 TAATGATTTAATAG
*
10461 TAATGATTTGATAG
1 TAATGATTTAATAG
10475 TAATGATTTA
1 TAATGATTTA
10485 CGACTTGAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
11 8 0.12
12 2 0.03
13 2 0.03
14 27 0.40
15 6 0.09
16 8 0.12
17 9 0.13
18 4 0.06
19 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (14 bp):
TAATGATTTAATAG
Found at i:10467 original size:440 final size:432
Alignment explanation
Indices: 9995--11298 Score: 1127
Period size: 440 Copynumber: 3.0 Consensus size: 432
9985 ATCATTATAA
* * * * *
9995 TAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTA-AA
1 TAATGATTTGATATTAATGATT-TAGTAATGATTTAGTAGTAATGATT-TAATAATGA--TACAA
10059 TATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATA
62 TATTTAATGATTTGAT-ATTTAGTAAT-ATTTG-TAATAA-CATTATAATAATGATTTAATAATA
* * *
10124 ATCATTATAATAATCATTATAATAATGATTTAATAATAATGATTTGATAGTAATGATTTAGTAAT
123 ATGATTATAATAATCATTATAATAATGA-TTAATATTAAT-ATTTAATAGTAATGATTTAGTAAT
* *
10189 GATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGCAATGATTA
186 GATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAATAATGATTTAGTAATGATTA
*
10254 GTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAATAATAATTTAT
251 GTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATAATAATTTAT
* *
10318 TATTAATATTTAATGATTTGATACTAATGATTTAGTAATGGTTAGTAATAATGAAATTATTATTA
316 TATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAAT-AAATTATTATTA
10383 ATATTTAATGATTTGATAGTAATGATTAGTAATAATAATTTATTATTAATATT
380 ATATTTAATGATTTGATAGTAATGATTAGTAATAATAATTTATTATTAATATT
* ** *
10436 TAATGATTTAATATTAATGATTTAGTAATGATTT-GATAGTAATGATTTACGACTTGA-ACAATG
1 TAATGATTTGATATTAATGATTTAGTAATGATTTAG-TAGTAATGATTTAATA-ATGATACAAT-
** * * *** ** * * * *
10499 A-ACAATG-TTTAGTTCAATTAACCATATTT-TCGTTACATAACTAGTAATGAAATT-ATAATAA
63 ATTTAATGATTT-GAT-ATTTAGTAATATTTGTAATAACATTA-TAATAATG-ATTTAATAATAA
* * * *
10560 TGATT-TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAAT-G-ATTTGA--TAGTAA
124 TGATTATAATAATCATTA-TAATAATG--ATTAATATTAATATTTAATAGTA-ATGATTTAGTAA
* *
10620 TGATT--TAGTAATG-----ATTAGT-ATATTTAATGATTTGATAATAATGA-TTAGTAATGATT
185 TGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAATAATGATTTAGTAATGATT
* *
10676 AAT-ATAAT-AATTTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAATAA
250 AGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGT-A--A-TAATAA
* *
10739 TGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAATAATAATTAGTAATAATAAAA
311 T----TTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAAT-AAA
10804 TTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATAATTTATTAT
371 TTATTATTAATATTT-A--A--TGAT--T--TGA-TAGTAATGATTAGTAATAATAATTTATTAT
10869 TAATATT
426 TAATATT
* *
10876 TAATGATTTGATATTAATGATTTAGTAATGATTAAATAGTAATGATTTACGACTTGAACAATGA-
1 TAATGATTTGATATTAATGATTTAGTAATGATTTAGTAGTAATGATTTA--A--T----AATGAT
* ** * ** * * *
10940 ACAATGTTTGGTTCAATTAACCATATTTTCGTTACATAACTAGTAATGAA-ATTATAATAATGAT
58 ACAATATTT-AAT-GATT--TGATA-TTTAG-TA-AT-ATTTGTAAT-AACATTATAATAATGAT
* * * *
11004 TTAGT-AT--TGATTAGTAATAATC---A-AATTATTATTAATATTTAATAATTTAATATTAATG
114 TTAATAATAATGATTA-TAATAATCATTATAATAATGATTAATA-TTAAT-ATTTAATAGTAATG
* * *
11062 ATTTAATAATGATTAGTAATAATGAAATTAGTATTAATATTTAATGATTTGATAGTAATGATTTA
176 ATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAATAATGATTTA
*
11127 GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAT
241 GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAAT
* * * * * * * *
11192 GATTAGTAATAATGAA-A-TT-ATTA-TTAATATTTAATGATTT-GATAGTATGATTAGTAATAA
306 AATAATTTATTATTAATATTTAATGATTTGATA-TTAATGATTTAG-TA--ATGATTAGTAATAA
* *
11252 TAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAT
367 TAAATTATTATTAATATTTAATGATTTGATAGTAATGA-TTAGTAAT
11299 GATTTGATAG
Statistics
Matches: 689, Mismatches: 98, Indels: 150
0.74 0.10 0.16
Matches are distributed among these distances:
421 35 0.05
422 10 0.01
423 14 0.02
424 24 0.03
425 6 0.01
426 7 0.01
430 77 0.11
431 1 0.00
432 11 0.02
433 2 0.00
434 18 0.03
435 39 0.06
436 12 0.02
437 10 0.01
438 15 0.02
439 8 0.01
440 105 0.15
441 19 0.03
442 8 0.01
443 11 0.02
445 1 0.00
446 6 0.01
447 17 0.02
448 14 0.02
449 4 0.01
450 10 0.01
451 34 0.05
452 19 0.03
453 35 0.05
454 17 0.02
455 5 0.01
456 1 0.00
458 8 0.01
459 25 0.04
460 14 0.02
461 6 0.01
462 41 0.06
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (432 bp):
TAATGATTTGATATTAATGATTTAGTAATGATTTAGTAGTAATGATTTAATAATGATACAATATT
TAATGATTTGATATTTAGTAATATTTGTAATAACATTATAATAATGATTTAATAATAATGATTAT
AATAATCATTATAATAATGATTAATATTAATATTTAATAGTAATGATTTAGTAATGATTAGTAAT
AATGAAATTATTATTAATATTTAATGATTTGATAATAATGATTTAGTAATGATTAGTAATAATGA
AATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATAATAATTTATTATTAATATT
TAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATAAATTATTATTAATATTTAATGA
TTTGATAGTAATGATTAGTAATAATAATTTATTATTAATATT
Found at i:10586 original size:13 final size:12
Alignment explanation
Indices: 10550--10686 Score: 52
Period size: 11 Copynumber: 10.9 Consensus size: 12
10540 TAGTAATGAA
10550 ATTATAATAATG
1 ATTATAATAATG
*
10562 ATT-TAGTAATG
1 ATTATAATAATG
10573 ATTAGTAATAATG
1 ATTA-TAATAATG
*
10586 AAATTATTATTAAT-
1 --ATTA-TAATAATG
*
10600 ATT-TAATGAT-
1 ATTATAATAATG
*
10610 -TTGATAGTAATG
1 ATT-ATAATAATG
*
10622 ATT-TAGTAATG
1 ATTATAATAATG
10633 ATTAGTATATTTAATG
1 ATTA-TA-A--TAATG
10649 ATTTGATAATAATG
1 A-TT-ATAATAATG
* *
10663 ATTAGTAATGATT
1 ATTA-TAATAATG
*
10676 AATATAATAAT
1 ATTATAATAAT
10687 TTATTATTAA
Statistics
Matches: 96, Mismatches: 13, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
9 2 0.02
10 5 0.05
11 26 0.27
12 13 0.14
13 22 0.23
14 6 0.06
15 10 0.10
16 7 0.07
17 4 0.04
18 1 0.01
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (12 bp):
ATTATAATAATG
Found at i:10622 original size:14 final size:14
Alignment explanation
Indices: 10603--10665 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
10593 TATTAATATT
10603 TAATGATTTGATAG
1 TAATGATTTGATAG
10617 TAATGA-TT--TAG
1 TAATGATTTGATAG
* *
10628 TAATGATTAGTATATT
1 TAATGATTTG-ATA-G
*
10644 TAATGATTTGATAA
1 TAATGATTTGATAG
10658 TAATGATT
1 TAATGATT
10666 AGTAATGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
11 9 0.22
12 1 0.03
13 2 0.05
14 14 0.35
15 5 0.12
16 9 0.22
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:10645 original size:41 final size:40
Alignment explanation
Indices: 10598--10681 Score: 141
Period size: 41 Copynumber: 2.1 Consensus size: 40
10588 ATTATTATTA
* *
10598 ATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGT
1 ATATTTAATGATTTGATAATAATGA-TTAGTAATGATTAAT
10639 ATATTTAATGATTTGATAATAATGATTAGTAATGATTAAT
1 ATATTTAATGATTTGATAATAATGATTAGTAATGATTAAT
10679 ATA
1 ATA
10682 ATAATTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 17 0.41
41 24 0.59
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (40 bp):
ATATTTAATGATTTGATAATAATGATTAGTAATGATTAAT
Found at i:10706 original size:98 final size:101
Alignment explanation
Indices: 10553--10853 Score: 351
Period size: 98 Copynumber: 2.9 Consensus size: 101
10543 TAATGAAATT
*
10553 ATAATAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT
1 ATAATAATGATTTAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGT
10618 AATGATTTAGTAATGATTAGTATATTTAATGATTTG
66 AATGATTTAGTAATGATTAGTATATTTAATGATTTG
*
10654 ATAATAATGA-TTAGTAATGATTAAT-ATAAT-AATTTATTATTAATATTTAATGATTTGATAGT
1 ATAATAATGATTTAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGT
*
10716 AATGATTTAGTAATGATTAATAATGAAATTATTATTAAT-ATTTAATG
66 AATGATTTAGTAATGA-T--T-A-G-TA-TA-T-TTAATGA-TT--TG
* * * *
10763 ATTTGATATTAATGATTTAATAATAATTAGTAATAATAAAATTATTATTAATATTTAATGATTTG
1 A--T-A-A-TAATGATTTAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTG
10828 ATAGTAATGA-TTAGTAATGATTAGTA
61 ATAGTAATGATTTAGTAATGATTAGTA
10854 ATAATAATTT
Statistics
Matches: 172, Mismatches: 8, Indels: 31
0.82 0.04 0.15
Matches are distributed among these distances:
98 47 0.27
99 6 0.03
100 14 0.08
101 11 0.06
102 1 0.01
103 1 0.01
104 1 0.01
105 2 0.01
106 2 0.01
107 7 0.04
109 3 0.02
110 1 0.01
111 2 0.01
112 2 0.01
113 2 0.01
114 6 0.03
115 13 0.08
116 15 0.09
117 36 0.21
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.46
Consensus pattern (101 bp):
ATAATAATGATTTAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGT
AATGATTTAGTAATGATTAGTATATTTAATGATTTG
Found at i:10844 original size:10 final size:10
Alignment explanation
Indices: 10829--10855 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
10819 AATGATTTGA
10829 TAGTAATGAT
1 TAGTAATGAT
10839 TAGTAATGAT
1 TAGTAATGAT
10849 TAGTAAT
1 TAGTAAT
10856 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:10879 original size:21 final size:22
Alignment explanation
Indices: 10855--10904 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
10845 TGATTAGTAA
10855 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
10876 TAATGATTTGATATTAATGATT
1 TAATAATTTGATATTAATGATT
*
10898 TAGTAAT
1 TAATAAT
10905 GATTAAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:10905 original size:25 final size:25
Alignment explanation
Indices: 10876--10924 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
10866 TATTAATATT
** *
10876 TAATGATTTGATATTAATGATTTAG
1 TAATGATTAAATAGTAATGATTTAG
10901 TAATGATTAAATAGTAATGATTTA
1 TAATGATTAAATAGTAATGATTTA
10925 CGACTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (25 bp):
TAATGATTAAATAGTAATGATTTAG
Found at i:11046 original size:22 final size:22
Alignment explanation
Indices: 11021--11070 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
11011 TGATTAGTAA
*
11021 TAATCAAATTATTATTAAT-ATT
1 TAAT-AAATTAATATTAATGATT
*
11043 TAATAATTTAATATTAATGATT
1 TAATAAATTAATATTAATGATT
11065 TAATAA
1 TAATAA
11071 TGATTAGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TAATAAATTAATATTAATGATT
Found at i:11057 original size:21 final size:21
Alignment explanation
Indices: 11029--11298 Score: 102
Period size: 21 Copynumber: 13.0 Consensus size: 21
11019 AATAATCAAA
11029 TTATTATTAATATTTAATAAT
1 TTATTATTAATATTTAATAAT
*
11050 TTAATATTAATGATTTAATAA-
1 TTATTATTAAT-ATTTAATAAT
* * * *
11071 TGATTAGTAATA-ATGA-AA-
1 TTATTATTAATATTTAATAAT
* *
11089 TTAGTATTAATATTTAATGAT
1 TTATTATTAATATTTAATAAT
* *
11110 TTGA-TAGTAATGATTTAGTAA-
1 TT-ATTATTAAT-ATTTAATAAT
* * * *
11131 TGATTAGTAATA-ATGA-AA-
1 TTATTATTAATATTTAATAAT
*
11149 TTATTATTAATATTTAATGAT
1 TTATTATTAATATTTAATAAT
*
11170 TTGA-TATTAATGATTTAGTAA-
1 TT-ATTATTAAT-ATTTAATAAT
* * * *
11191 TGATTAGTAATA-ATGA-AA-
1 TTATTATTAATATTTAATAAT
*
11209 TTATTATTAATATTTAATGAT
1 TTATTATTAATATTTAATAAT
* * *
11230 TTGATAGTATGATTAGTAATAATAAT
1 TT-AT--TATTAATA-T-TTAATAAT
*
11256 TTATTATTAATATTTAATGAT
1 TTATTATTAATATTTAATAAT
*
11277 TTGA-TATTAATGATTTAGTAAT
1 TT-ATTATTAAT-ATTTAATAAT
11299 GATTTGATAG
Statistics
Matches: 180, Mismatches: 46, Indels: 45
0.66 0.17 0.17
Matches are distributed among these distances:
18 35 0.19
19 10 0.06
20 8 0.04
21 67 0.37
22 37 0.21
23 6 0.03
24 6 0.03
25 3 0.02
26 8 0.04
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (21 bp):
TTATTATTAATATTTAATAAT
Found at i:11063 original size:285 final size:275
Alignment explanation
Indices: 10557--11302 Score: 880
Period size: 285 Copynumber: 2.6 Consensus size: 275
10547 GAAATTATAA
*
10557 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
* * * **
10622 ATTTAGTAATGATTAGTATATTTAATGATTTGATAATAATGATTAGTAATGATTAATATAATAAT
66 ATTTAGTAATGATTAGAATATGTAATGATTTGATAACAATGACAAGTAATGATTAATATAATAAT
* * * * *
10687 TTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAATAATGAAATTATTATT
131 TTATTAATAATATGTAATGAATTGATAATAATGATTTAGTAATGATTAATAATCAAATTATTATT
* * *
10752 AATATTTAATGATTTGATATTAATGATTTAATAATAATTAGTAATAATAAAATTATTATTAATAT
196 AATATTTAATAATTTAATATTAATGATTTAATAATAATTAGTAATAATAAAATTAGTATTAATAT
10817 TTAATGATTTGATAG
261 TTAATGATTTGATAG
*
10832 TAATGA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
* *
10895 ATTTAGTAATGATTA-AATA-GTAATGATTTACGACTTGAACAATGAACAATGT-TTGGTTCAAT
66 ATTTAGTAATGATTAGAATATGTAATGATTT--GA--T-AACAATG-ACAA-GTAATGATT-AAT
* * *
10957 -TAACCATATTTTCGTTACATAACTA-GTAATGAAATT-ATAATAATGATTTAGTATTGATTAGT
123 AT-A--ATAATTT-ATTA-ATAA-TATGTAATG-AATTGATAATAATGATTTAGTAATGA-T--T
*
11019 AATAATCAAATTATTATTAATATTTAATAATTTAATATTAATGATTTAATAATGATTAGTAATAA
178 AATAATCAAATTATTATTAATATTTAATAATTTAATATTAATGATTTAATAATAATTAGTAATAA
*
11084 TGAAATTAGTATTAATATTTAATGATTTGATAG
243 TAAAATTAGTATTAATATTTAATGATTTGATAG
11117 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
* * * ** * *
11182 ATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGT-ATGATTAG
66 ATTTAGTAATGATTAG-AAT-ATGTAATGA-T-TTGATA-ACAATGA---CA-AGTAATGATTAA
* * * *
11246 TAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATT
122 T-ATAATAATTTATTAATAATATGTAATGAATTGATAATAATGATTTAGTAATGATT
11303 TGATAGTAAT
Statistics
Matches: 397, Mismatches: 39, Indels: 61
0.80 0.08 0.12
Matches are distributed among these distances:
271 9 0.02
272 3 0.01
273 51 0.13
274 21 0.05
275 7 0.02
276 6 0.02
277 7 0.02
278 6 0.02
280 6 0.02
281 3 0.01
282 27 0.07
283 6 0.02
284 1 0.00
285 99 0.25
286 27 0.07
287 77 0.19
288 5 0.01
289 14 0.04
290 3 0.01
291 14 0.04
292 3 0.01
293 2 0.01
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.45
Consensus pattern (275 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
ATTTAGTAATGATTAGAATATGTAATGATTTGATAACAATGACAAGTAATGATTAATATAATAAT
TTATTAATAATATGTAATGAATTGATAATAATGATTTAGTAATGATTAATAATCAAATTATTATT
AATATTTAATAATTTAATATTAATGATTTAATAATAATTAGTAATAATAAAATTAGTATTAATAT
TTAATGATTTGATAG
Found at i:11065 original size:14 final size:15
Alignment explanation
Indices: 11035--11069 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
11025 CAAATTATTA
11035 TTAATATTTAATAAT
1 TTAATATTTAATAAT
*
11050 TTAATA-TTAATGAT
1 TTAATATTTAATAAT
11064 TTAATA
1 TTAATA
11070 ATGATTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAATATTTAATAAT
Found at i:11071 original size:11 final size:12
Alignment explanation
Indices: 11057--11206 Score: 52
Period size: 11 Copynumber: 12.5 Consensus size: 12
11047 AATTTAATAT
11057 TAATGATT-TAA
1 TAATGATTATAA
11068 TAATGATTAGTAA
1 TAATGATTA-TAA
*
11081 TAATGAAATTAGTAT
1 TAATG--ATTA-TAA
11096 TAAT-ATT-TAA
1 TAATGATTATAA
* *
11106 TGAT--TTGATAG
1 TAATGATT-ATAA
*
11117 TAATGATT-TAG
1 TAATGATTATAA
11128 TAATGATTAGTAA
1 TAATGATTA-TAA
*
11141 TAATGAAATTATTAT
1 TAATG--ATTA-TAA
11156 TAAT-ATT-TAA
1 TAATGATTATAA
* *
11166 TGAT--TTGATAT
1 TAATGATT-ATAA
*
11177 TAATGATT-TAG
1 TAATGATTATAA
11188 TAATGATTAGTAA
1 TAATGATTA-TAA
11201 TAATGA
1 TAATGA
11207 AATTATTATT
Statistics
Matches: 107, Mismatches: 14, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
9 4 0.04
10 10 0.09
11 39 0.36
12 6 0.06
13 27 0.25
15 21 0.20
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (12 bp):
TAATGATTATAA
Found at i:11090 original size:60 final size:60
Alignment explanation
Indices: 10997--11302 Score: 449
Period size: 60 Copynumber: 5.3 Consensus size: 60
10987 GAAATTATAA
* * * *
10997 TAATGATTTAGTATTGATTAGTAATAATCAAATTATTATTAATATTTAATAATTTAATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
* * *
11057 TAATGATTTAATAATGATTAGTAATAATGAAATTAGTATTAATATTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
11117 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
11177 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTT-A--A--TG--AT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
*
11230 T--TGA--TAGT-ATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
11284 TAATGATTTAGTAATGATT
1 TAATGATTTAGTAATGATT
11303 TGATAGTAAT
Statistics
Matches: 223, Mismatches: 11, Indels: 25
0.86 0.04 0.10
Matches are distributed among these distances:
47 17 0.08
48 16 0.07
49 4 0.02
50 1 0.00
51 3 0.01
52 2 0.01
53 3 0.01
54 3 0.01
55 2 0.01
56 3 0.01
57 1 0.00
58 4 0.02
59 7 0.03
60 157 0.70
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (60 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
Found at i:11107 original size:35 final size:35
Alignment explanation
Indices: 11068--11230 Score: 114
Period size: 35 Copynumber: 5.2 Consensus size: 35
11058 AATGATTTAA
11068 TAATGATTAGTAATAATGAAATTAGTATTAATATT
1 TAATGATTAGTAATAATGAAATTAGTATTAATATT
* * *
11103 TAATGATT--TGAT-A-GTAA-T-G-ATT--TA-G
1 TAATGATTAGTAATAATGAAATTAGTATTAATATT
*
11128 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTAGTATTAATATT
* * *
11163 TAATGATT--TGAT-AT-TAA-T-G-ATT--TA-G
1 TAATGATTAGTAATAATGAAATTAGTATTAATATT
*
11188 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTAGTATTAATATT
11223 TAATGATT
1 TAATGATT
11231 TGATAGTATG
Statistics
Matches: 93, Mismatches: 15, Indels: 40
0.63 0.10 0.27
Matches are distributed among these distances:
25 16 0.17
26 4 0.04
27 6 0.06
28 9 0.10
29 6 0.06
30 4 0.04
31 5 0.05
32 9 0.10
33 6 0.06
34 4 0.04
35 24 0.26
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTAGTATTAATATT
Found at i:11270 original size:47 final size:49
Alignment explanation
Indices: 11185--11298 Score: 187
Period size: 47 Copynumber: 2.3 Consensus size: 49
11175 ATTAATGATT
11185 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
11234 TAGT-ATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
11281 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
11299 GATTTGATAG
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
47 30 0.49
48 19 0.31
49 12 0.20
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.47
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:11286 original size:14 final size:14
Alignment explanation
Indices: 11270--11317 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
11260 TATTAATATT
*
11270 TAATGATTTGATAT
1 TAATGATTTGATAG
11284 TAATGA-TT--TAG
1 TAATGATTTGATAG
11295 TAATGATTTGATAG
1 TAATGATTTGATAG
11309 TAATGATTT
1 TAATGATTT
11318 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:11299 original size:25 final size:25
Alignment explanation
Indices: 11270--11318 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
11260 TATTAATATT
*
11270 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
11295 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
11319 CGACTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:11318 original size:47 final size:46
Alignment explanation
Indices: 11185--11318 Score: 130
Period size: 47 Copynumber: 2.8 Consensus size: 46
11175 ATTAATGATT
*
11185 TAGTAATGATTAGTAATAATGAAATT-ATTATTAATATTTAATGATTTGA
1 TAGT-ATGATTAGTAATAAT---ATTGATTAGTAATATTTAATGATTTGA
* *
11234 TAGTATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGA
1 TAGTATGATTAGTAATAAT-ATTGATTAGTAATATTTAATGATTTGA
* *
11281 TATTAATGATTTAGTAATGAT-TTGA-TAGTAATGATTTA
1 TAGT-ATGA-TTAGTAATAATATTGATTAGTAAT-ATTTA
11319 CGACTTGAAC
Statistics
Matches: 77, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
46 10 0.13
47 34 0.44
48 19 0.25
49 14 0.18
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (46 bp):
TAGTATGATTAGTAATAATATTGATTAGTAATATTTAATGATTTGA
Found at i:11340 original size:394 final size:395
Alignment explanation
Indices: 10639--11399 Score: 1275
Period size: 394 Copynumber: 1.9 Consensus size: 395
10629 AATGATTAGT
* * * * *
10639 ATATTTAATGATTTGATAATAATGATTAGTAATGATTAATATAATAATTTATTATTAATATTTAA
1 ATATTTAATAATTTAATAATAATGATTAATAATGATTAATATAATAAATTAGTATTAATATTTAA
10704 TGATTTGATAGTAATGATTTAGTAATGATTAATAATGAAATTATTATTAATATTTAATGATTTGA
66 TGATTTGATAGTAATGATTTAGTAATGATTAATAATGAAATTATTATTAATATTTAATGATTTGA
10769 TATTAATGATTTAATAATAATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTA
131 TATTAATGATTTAATAATAATTAGTAATAATAAAATTATTATTAATATTTAA-GA-TTGATA-T-
10834 ATGATTAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTT
192 ATGATTAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTT
10899 AGTAATGATTAAATAGTAATGATTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACCAT
257 AGTAATGATTAAATAGTAATGATTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACCAT
10964 ATTTTCGTTACATAACTAGTAATGAAATTATAATAATGATTTAGTATTGATTAGTAATAATCAAA
322 ATTTTCGTTACATAACTAGTAATGAAATTATAATAATGATTTAGTATTGATTAGTAATAATCAAA
11029 TTATTATTA
387 TTATTATTA
* *
11038 ATATTTAATAATTTAATATTAATGATTTAATAATGATTAGTAATAATGAAATTAGTATTAATATT
1 ATATTTAATAATTTAATAATAATGA-TTAATAATGATTAAT-ATAAT-AAATTAGTATTAATATT
11103 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
63 TAATGATTTGATAGTAATGATTTAGTAATGA-T--TAATAATGAAATTATTATTAATATTTAATG
* * *
11168 ATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTT-A-A-TGAT
125 ATTTGATATTAATGATTTAATAATAATTAGTAATAATAAAATTATTATTAATATTTAAGATTGAT
11230 -T-TGA-TAGT-ATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGAT
190 ATATGATTAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGAT
**
11291 TTAGTAATGATTTGATAGTAATGATTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACC
255 TTAGTAATGATTAAATAGTAATGATTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACC
11356 ATATTTTCGTTACATAACTAGTAATGAAATTATAATAATGATTT
320 ATATTTTCGTTACATAACTAGTAATGAAATTATAATAATGATTT
11400 GATACTAAAA
Statistics
Matches: 344, Mismatches: 12, Indels: 17
0.92 0.03 0.05
Matches are distributed among these distances:
394 160 0.47
395 4 0.01
396 3 0.01
398 1 0.00
399 22 0.06
400 17 0.05
401 5 0.01
402 47 0.14
403 1 0.00
404 1 0.00
405 83 0.24
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (395 bp):
ATATTTAATAATTTAATAATAATGATTAATAATGATTAATATAATAAATTAGTATTAATATTTAA
TGATTTGATAGTAATGATTTAGTAATGATTAATAATGAAATTATTATTAATATTTAATGATTTGA
TATTAATGATTTAATAATAATTAGTAATAATAAAATTATTATTAATATTTAAGATTGATATATGA
TTAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
ATGATTAAATAGTAATGATTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACCATATTT
TCGTTACATAACTAGTAATGAAATTATAATAATGATTTAGTATTGATTAGTAATAATCAAATTAT
TATTA
Found at i:12336 original size:23 final size:23
Alignment explanation
Indices: 12310--12354 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12300 AAAATTACAA
*
12310 AAATAATAAAATTTATTTAAATC
1 AAATAATAAAATTAATTTAAATC
* *
12333 AAATAATATAGTTAATTTAAAT
1 AAATAATAAAATTAATTTAAAT
12355 AATAATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATAATAAAATTAATTTAAATC
Found at i:13666 original size:22 final size:22
Alignment explanation
Indices: 13641--13689 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
13631 ACAACTAATA
13641 AACTATTCTTTAATATAACT-TT
1 AACTATTCTTTAATATAA-TGTT
13663 AACTATTCTTTAATATAATGTT
1 AACTATTCTTTAATATAATGTT
13685 AACTA
1 AACTA
13690 ATAAACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (22 bp):
AACTATTCTTTAATATAATGTT
Found at i:13667 original size:30 final size:29
Alignment explanation
Indices: 13633--13758 Score: 97
Period size: 30 Copynumber: 4.4 Consensus size: 29
13623 TCCCTTAAAC
13633 AACTAATAAACTATTCTTT-A-AT-A--T
1 AACTAATAAACTATTCTTTAATATAATTT
*
13657 AACT--TTAACTATTCTTTAATATAATGTT
1 AACTAATAAACTATTCTTTAATATAAT-TT
* *
13685 AACTAATAAACTATTTTTTAATATAACTTA
1 AACTAATAAACTATTCTTTAATATAA-TTT
* *
13715 AACTAATAAA-TGTTTTTTAATTATAATTT
1 AACTAATAAACTATTCTTTAA-TATAATTT
*
13744 ATTACTAAAAAACTA
1 A--ACTAATAAACTA
13759 ATTAACTAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
22 12 0.15
23 1 0.01
24 6 0.07
25 1 0.01
28 5 0.06
29 12 0.15
30 34 0.42
31 9 0.11
32 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (29 bp):
AACTAATAAACTATTCTTTAATATAATTT
Found at i:13731 original size:29 final size:30
Alignment explanation
Indices: 13663--13741 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
13653 ATATAACTTT
* *
13663 AACTATTCTTTAATATAATGTTAACTAATA
1 AACTATTTTTTAATATAATGTAAACTAATA
13693 AACTATTTTTTAATATAACT-TAAACTAATA
1 AACTATTTTTTAATATAA-TGTAAACTAATA
*
13723 AA-TGTTTTTTAATTATAAT
1 AACTATTTTTTAA-TATAAT
13742 TTATTACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
29 10 0.23
30 33 0.75
31 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (30 bp):
AACTATTTTTTAATATAATGTAAACTAATA
Found at i:14035 original size:29 final size:29
Alignment explanation
Indices: 14002--14095 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 29
13992 TGTTTTACCC
14002 TAATTTATAATAATAAACTAATTAACTAA
1 TAATTTATAATAATAAACTAATTAACTAA
* *
14031 TAATTTATAACAATAAACTAATTTAAATAA
1 TAATTTATAATAATAAACTAA-TTAACTAA
* *
14061 TTATTCTTTTATATAACTTAAACTAATTAACTAA
1 -TAAT-TTATA-ATAA--TAAACTAATTAACTAA
14095 T
1 T
14096 TTTTTTATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 20 0.38
30 7 0.13
31 3 0.06
32 4 0.08
33 4 0.08
34 7 0.13
35 8 0.15
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATTTATAATAATAAACTAATTAACTAA
Found at i:14054 original size:18 final size:18
Alignment explanation
Indices: 14001--14055 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
13991 TTGTTTTACC
*
14001 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
14019 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
14031 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
14048 CTAATTTA
1 CTAATTTA
14056 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:14084 original size:35 final size:31
Alignment explanation
Indices: 14044--14107 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 31
14034 TTTATAACAA
14044 TAAACTAATTTAAATAATTATTCTTTTATATAACT
1 TAAACTAA-TTAAATAA-T-TT-TTTTATATAACT
*
14079 TAAACTAATTAACTAATTTTTTTATATAA
1 TAAACTAATTAAATAATTTTTTTATATAA
14108 TATAAATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 10 0.36
32 2 0.07
33 1 0.04
34 7 0.25
35 8 0.29
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (31 bp):
TAAACTAATTAAATAATTTTTTTATATAACT
Found at i:14701 original size:29 final size:29
Alignment explanation
Indices: 14647--14702 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
14637 CGTTGGACAT
*
14647 CGGGCGTGCATGGCGTCCTTATAGGACGC
1 CGGGCGTGCATGGCGACCTTATAGGACGC
14676 CGGGCGTGCATGGCGACC-TATAAGGAC
1 CGGGCGTGCATGGCGACCTTAT-AGGAC
14703 CCTATAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.18, C:0.27, G:0.38, T:0.18
Consensus pattern (29 bp):
CGGGCGTGCATGGCGACCTTATAGGACGC
Found at i:15012 original size:19 final size:19
Alignment explanation
Indices: 14988--15040 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
14978 CTGATTAGCC
*
14988 CAACTAACCAAAAACAACT
1 CAACTAACCAGAAACAACT
*
15007 CAACTAACTAGAAACAACT
1 CAACTAACCAGAAACAACT
15026 CAACTAACCAGAAAC
1 CAACTAACCAGAAAC
15041 GGTTATAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.55, C:0.30, G:0.04, T:0.11
Consensus pattern (19 bp):
CAACTAACCAGAAACAACT
Found at i:20778 original size:31 final size:26
Alignment explanation
Indices: 20690--20762 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
20680 CTACTAAGTT
* * *
20690 TTACGTTAGAAGCATTAACTCATACA
1 TTACATTAGAAACATTAACTCTTACA
20716 TTACATTAGAAACATTAACTCTTACA
1 TTACATTAGAAACATTAACTCTTACA
20742 TTACATTAGAAACATTAACTC
1 TTACATTAGAAACATTAACTC
20763 CTATATTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (26 bp):
TTACATTAGAAACATTAACTCTTACA
Found at i:20802 original size:37 final size:36
Alignment explanation
Indices: 20737--20807 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
20727 ACATTAACTC
* * *
20737 TTACATTACATTAGAAACATTAACTCCTATATTATA
1 TTACATCACATTAAAAACATTAACTCCTACATTATA
20773 TTACATCACATTAAAAAGCATTAACTCCTACATTA
1 TTACATCACATTAAAAA-CATTAACTCCTACATTA
20808 CATAACAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 15 0.48
37 16 0.52
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (36 bp):
TTACATCACATTAAAAACATTAACTCCTACATTATA
Found at i:30916 original size:3 final size:3
Alignment explanation
Indices: 30908--30946 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
30898 TATTTTAATT
30908 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30947 ATACAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31525 original size:14 final size:14
Alignment explanation
Indices: 31506--31536 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31496 GAGAGGAATG
*
31506 AAAAAACCAGAAAA
1 AAAAAACAAGAAAA
31520 AAAAAACAAGAAAA
1 AAAAAACAAGAAAA
31534 AAA
1 AAA
31537 GAGAACTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAACAAGAAAA
Found at i:33525 original size:18 final size:18
Alignment explanation
Indices: 33502--33540 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
33492 TATCTAAAAA
33502 TGGTTATGACAGGGTAAT
1 TGGTTATGACAGGGTAAT
33520 TGGTTATGACAGGGTAAT
1 TGGTTATGACAGGGTAAT
33538 TGG
1 TGG
33541 ATGTTGTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.33
Consensus pattern (18 bp):
TGGTTATGACAGGGTAAT
Found at i:33934 original size:13 final size:13
Alignment explanation
Indices: 33899--33926 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33889 TTGAAGAGAC
33899 TATCAATTTTCAT
1 TATCAATTTTCAT
33912 TATCAATTTTCAT
1 TATCAATTTTCAT
33925 TA
1 TA
33927 CTATTTTTAG
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:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (13 bp):
TATCAATTTTCAT
Found at i:34408 original size:59 final size:58
Alignment explanation
Indices: 34330--34502 Score: 233
Period size: 60 Copynumber: 2.9 Consensus size: 58
34320 TGAAAGTTAG
*
34330 AATGATTAAAATATGAGTAATTTGAAAGTTAAGTAATTAATTTAAAAAAATTAAACCTC
1 AATGATTAAATTA-GAGTAATTTGAAAGTTAAGTAATTAATTTAAAAAAATTAAACCTC
* * * *
34389 GATGATTAAATTAGAAGTAATTTGAAAATTAAGTAATTAAATTAAAAAAAATTAAACTTC
1 AATGATTAAATTAG-AGTAATTTGAAAGTTAAGTAATT-AATTTAAAAAAATTAAACCTC
* *
34449 AATGATTAAATTAGGAGTAATTTGAAAG-TAAGTAATTAAATT-AAGAAATTAAAC
1 AATGATTAAATTA-GAGTAATTTGAAAGTTAAGTAATTAATTTAAAAAAATTAAAC
34503 TTCAGTGACC
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
57 11 0.11
58 4 0.04
59 42 0.42
60 43 0.43
61 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (58 bp):
AATGATTAAATTAGAGTAATTTGAAAGTTAAGTAATTAATTTAAAAAAATTAAACCTC
Found at i:34432 original size:13 final size:13
Alignment explanation
Indices: 34414--34501 Score: 52
Period size: 13 Copynumber: 6.2 Consensus size: 13
34404 AGTAATTTGA
34414 AAATTAAGTAATT
1 AAATTAAGTAATT
**
34427 AAATTAAAAAAAATT
1 AAATT--AAGTAATT
*
34442 AAACTTCAA-TGATT
1 AAA-TT-AAGTAATT
34456 AAATTAGGAGTAATTT
1 AAATTA--AGTAA-TT
*
34472 GAAAGTAAGTAATT
1 -AAATTAAGTAATT
*
34486 AAATTAAGAAATT
1 AAATTAAGTAATT
34499 AAA
1 AAA
34502 CTTCAGTGAC
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
12 1 0.02
13 21 0.36
14 9 0.16
15 18 0.31
16 4 0.07
17 5 0.09
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (13 bp):
AAATTAAGTAATT
Found at i:34461 original size:29 final size:29
Alignment explanation
Indices: 34368--34461 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
34358 TTAAGTAATT
* * *
34368 AATTTAAAAAAATTAAACCTCGATGATTA
1 AATTAAAAAAAATTAAACTTCAATGATTA
** * * *
34397 AATTAGAAGTAATTTGAAAATT-AAGTAATTA
1 AATTA-AAAAAAATT-AAACTTCAA-TGATTA
34428 AATTAAAAAAAATTAAACTTCAATGATTA
1 AATTAAAAAAAATTAAACTTCAATGATTA
34457 AATTA
1 AATTA
34462 GGAGTAATTT
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
29 19 0.40
30 15 0.31
31 14 0.29
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.33
Consensus pattern (29 bp):
AATTAAAAAAAATTAAACTTCAATGATTA
Found at i:34468 original size:60 final size:59
Alignment explanation
Indices: 34330--34506 Score: 250
Period size: 59 Copynumber: 3.0 Consensus size: 59
34320 TGAAAGTTAG
* * * * *
34330 AATGATTAAAATATGAGTAATTTGAAAGTTAAGTAATTAATTTAAAAAAATTAAACCTC
1 AATGATTAAATTAGGAGTAATTTGAAAATTAAGTAATTAAATTAAAAAAATTAAACTTC
* *
34389 GATGATTAAATTAGAAGTAATTTGAAAATTAAGTAATTAAATTAAAAAAAATTAAACTTC
1 AATGATTAAATTAGGAGTAATTTGAAAATTAAGTAATTAAATT-AAAAAAATTAAACTTC
* *
34449 AATGATTAAATTAGGAGTAATTTG-AAAGTAAGTAATTAAATT-AAGAAATTAAACTTC
1 AATGATTAAATTAGGAGTAATTTGAAAATTAAGTAATTAAATTAAAAAAATTAAACTTC
34506 A
1 A
34507 GTGACCAAAA
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
57 15 0.14
59 54 0.51
60 37 0.35
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.33
Consensus pattern (59 bp):
AATGATTAAATTAGGAGTAATTTGAAAATTAAGTAATTAAATTAAAAAAATTAAACTTC
Found at i:36787 original size:31 final size:31
Alignment explanation
Indices: 36703--36889 Score: 155
Period size: 31 Copynumber: 6.0 Consensus size: 31
36693 GTCGAGGGTT
* * *
36703 TACCTATGTTCTACGGAACACATAGACAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * *
36734 TTACATATG-TCTTTCGGGACATATGGACAGTA
1 -TACCTATGTTC-TACGGAACATATGGACAGTA
36766 TACCTATGTTCTACGGAACATATGGACA-TAA
1 TACCTATGTTCTACGGAACATATGGACAGT-A
* * *
36797 TTACCTACG-TCTTTCGGGACATATGGACAGTA
1 -TACCTATGTTC-TACGGAACATATGGACAGTA
* * *
36829 TACCTATGTTCTAAGGAACATATGGGCAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTA
* ** * *
36860 TACCTAGGTTCTTTGGGACCTATGGACAGT
1 TACCTATGTTCTACGGAACATATGGACAGT
36890 TGCCGAGGTT
Statistics
Matches: 124, Mismatches: 24, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
30 1 0.01
31 73 0.59
32 49 0.40
33 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:36809 original size:63 final size:63
Alignment explanation
Indices: 36703--36889 Score: 254
Period size: 63 Copynumber: 3.0 Consensus size: 63
36693 GTCGAGGGTT
* * * * *
36703 TACCTATGTTCTACGGAACACATAGACAGAATTACATATGTCTTTCGGGACATATGGACAGTA
1 TACCTATGTTCTACGGAACATATGGACATAATTACCTACGTCTTTCGGGACATATGGACAGTA
36766 TACCTATGTTCTACGGAACATATGGACATAATTACCTACGTCTTTCGGGACATATGGACAGTA
1 TACCTATGTTCTACGGAACATATGGACATAATTACCTACGTCTTTCGGGACATATGGACAGTA
* * * *
36829 TACCTATGTTCTAAGGAACATATGGGCAGT--TTACCTAGGTTCTTT-GGGACCTATGGACAGT
1 TACCTATGTTCTACGGAACATATGGACA-TAATTACCTACG-TCTTTCGGGACATATGGACAGT
36890 TGCCGAGGTT
Statistics
Matches: 113, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
62 23 0.20
63 89 0.79
64 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (63 bp):
TACCTATGTTCTACGGAACATATGGACATAATTACCTACGTCTTTCGGGACATATGGACAGTA
Found at i:37581 original size:21 final size:21
Alignment explanation
Indices: 37555--37594 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
37545 TTACGAAAGT
37555 ACTGTAGCAGTACATCGATGC
1 ACTGTAGCAGTACATCGATGC
*
37576 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTACATCGAT
37595 ACACAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTACATCGATGC
Found at i:45516 original size:33 final size:34
Alignment explanation
Indices: 45474--45538 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
45464 AGAAGGAAAG
* *
45474 AATTTATAAAATTCCAAGGGACAAAA-TAGACAT
1 AATTTATAAAATTCCAAGAGAAAAAATTAGACAT
*
45507 AATTTATAAAATTTCAAGAGAAAAAATTAGAC
1 AATTTATAAAATTCCAAGAGAAAAAATTAGAC
45539 GTTCAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (34 bp):
AATTTATAAAATTCCAAGAGAAAAAATTAGACAT
Found at i:49584 original size:4 final size:5
Alignment explanation
Indices: 49563--49611 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
49553 CAACGGTCAA
* *
49563 CGGGT CGGGT CGGGT C-GGT C-GGT CGGGT C-GAT C-GAT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT
49609 CGG
1 CGG
49612 TTGGGTTGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 15 0.38
5 25 0.62
ACGTcount: A:0.04, C:0.22, G:0.53, T:0.20
Consensus pattern (5 bp):
CGGGT
Found at i:49586 original size:13 final size:13
Alignment explanation
Indices: 49565--49617 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
49555 ACGGTCAACG
49565 GGTCGGGTCGGGTC
1 GGTC-GGTCGGGTC
49579 GGTCGGTCGGGTC
1 GGTCGGTCGGGTC
* *
49592 GATCGATCGGGTC
1 GGTCGGTCGGGTC
*
49605 GGGTCGGTTGGGT
1 -GGTCGGTCGGGT
49618 TGGGTCAGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
13 20 0.61
14 13 0.39
ACGTcount: A:0.04, C:0.19, G:0.53, T:0.25
Consensus pattern (13 bp):
GGTCGGTCGGGTC
Found at i:49586 original size:18 final size:18
Alignment explanation
Indices: 49563--49612 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
49553 CAACGGTCAA
*
49563 CGGGTCGGGTCGGGTCGGT
1 CGGGTCGGGTC-GGTCGAT
*
49582 C-GGTCGGGTCGATCGAT
1 CGGGTCGGGTCGGTCGAT
49599 CGGGTCGGGTCGGT
1 CGGGTCGGGTCGGT
49613 TGGGTTGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 6 0.22
18 20 0.74
19 1 0.04
ACGTcount: A:0.04, C:0.22, G:0.52, T:0.22
Consensus pattern (18 bp):
CGGGTCGGGTCGGTCGAT
Found at i:55991 original size:262 final size:262
Alignment explanation
Indices: 55526--56053 Score: 1013
Period size: 262 Copynumber: 2.0 Consensus size: 262
55516 TACTTTAAAA
55526 TAAGGTCCATGTCACCAAAATAAAGTCAACCTGAATGATAAAAACATTACAATATCTGAAAGGGG
1 TAAGGTCCATGTCACCAAAATAAAGTCAACCTGAATGATAAAAACATTACAATATCTGAAAGGGG
55591 GAAAACATTTTCGAAAGGTGAGCTAGGCTCAGTGTGTCCCAATATTACCTTAAAATCACAATAGG
66 GAAAACATTTTCGAAAGGTGAGCTAGGCTCAGTGTGTCCCAATATTACCTTAAAATCACAATAGG
*
55656 TACATTAATCAAATCATAGTCCAGTAAATCTCATAAATTCATAAAAGAGTTTAACTTTTGAAAAT
131 TACATTAATCAAATCATAGTCCAGTAAATCTCATAAATTCATAAAAGAGTTTAACTTTCGAAAAT
55721 CATAGTTTAAACTCTTTTCTTGTACACCATCAGTAATTTCCAAAACTATTTTCCATATAGCTTAC
196 CATAGTTTAAACTCTTTTCTTGTACACCATCAGTAATTTCCAAAACTATTTTCCATATAGCTTAC
55786 TC
261 TC
*
55788 TAAGGTCCATGTCACCAAAATAAAGTCAACCTGAATGATAAAAATATTACAGA-ATCTGAAAGGG
1 TAAGGTCCATGTCACCAAAATAAAGTCAACCTGAATGATAAAAACATTACA-ATATCTGAAAGGG
55852 GGAAAACATTTTCGAAAGGTGAGCTAGGCTCAGTGTGTCCCAATATTACCTTAAAATCACAATAG
65 GGAAAACATTTTCGAAAGGTGAGCTAGGCTCAGTGTGTCCCAATATTACCTTAAAATCACAATAG
*
55917 GTACATTAATCAAATCATAGTCCAGTAAATCTCATAAATTTATAAAAGAGTTTAACTTTCGAAAA
130 GTACATTAATCAAATCATAGTCCAGTAAATCTCATAAATTCATAAAAGAGTTTAACTTTCGAAAA
55982 TCATAGTTTAAACTCTTTTCTTGTACACCATCAGTAATTTCCAAAACTATTTTCCATATAGCTTA
195 TCATAGTTTAAACTCTTTTCTTGTACACCATCAGTAATTTCCAAAACTATTTTCCATATAGCTTA
56047 CTC
260 CTC
56050 TAAG
1 TAAG
56054 CACACAGCAA
Statistics
Matches: 262, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
262 261 1.00
263 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (262 bp):
TAAGGTCCATGTCACCAAAATAAAGTCAACCTGAATGATAAAAACATTACAATATCTGAAAGGGG
GAAAACATTTTCGAAAGGTGAGCTAGGCTCAGTGTGTCCCAATATTACCTTAAAATCACAATAGG
TACATTAATCAAATCATAGTCCAGTAAATCTCATAAATTCATAAAAGAGTTTAACTTTCGAAAAT
CATAGTTTAAACTCTTTTCTTGTACACCATCAGTAATTTCCAAAACTATTTTCCATATAGCTTAC
TC
Found at i:57056 original size:19 final size:19
Alignment explanation
Indices: 57023--57065 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
57013 CGAGTCAGAT
* *
57023 CGGTTCGGACTGGTCAAAC
1 CGGTTCGAACCGGTCAAAC
57042 CGGTTCGAACCGGTCAAAC
1 CGGTTCGAACCGGTCAAAC
57061 CGGTT
1 CGGTT
57066 TTCAGTCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.28, G:0.30, T:0.21
Consensus pattern (19 bp):
CGGTTCGAACCGGTCAAAC
Found at i:62742 original size:21 final size:21
Alignment explanation
Indices: 62716--62756 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
62706 CGAAGCCACA
*
62716 GGATTCGGGTTCTGGGCAGTC
1 GGATTCGGGGTCTGGGCAGTC
62737 GGATTCGGGGTCTGGGCAGT
1 GGATTCGGGGTCTGGGCAGT
62757 ACCGAAGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.17, G:0.46, T:0.27
Consensus pattern (21 bp):
GGATTCGGGGTCTGGGCAGTC
Found at i:62837 original size:14 final size:14
Alignment explanation
Indices: 62818--62847 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
62808 ACCAGTCTTC
62818 ATGGTTTCAATCTA
1 ATGGTTTCAATCTA
62832 ATGGTTTCAATCTA
1 ATGGTTTCAATCTA
62846 AT
1 AT
62848 AGCTATGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (14 bp):
ATGGTTTCAATCTA
Found at i:66916 original size:22 final size:22
Alignment explanation
Indices: 66869--66916 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
66859 CGTCTCGACT
**
66869 TAAAAAATTAATTAATTATATT
1 TAAAAAATTAATTAATTATAAA
*
66891 TAAAAAATTAATTGATTCA-AAA
1 TAAAAAATTAATTAATT-ATAAA
66913 TAAA
1 TAAA
66917 TTCTGACTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAAAAATTAATTAATTATAAA
Found at i:67552 original size:23 final size:23
Alignment explanation
Indices: 67522--67569 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
67512 TATAGTAGTC
67522 TCAATTTATCACTTTTTCTTTTA
1 TCAATTTATCACTTTTTCTTTTA
67545 TCAATTTATCACTTTTTCTTTTA
1 TCAATTTATCACTTTTTCTTTTA
67568 TC
1 TC
67570 GTATTTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (23 bp):
TCAATTTATCACTTTTTCTTTTA
Found at i:68422 original size:24 final size:24
Alignment explanation
Indices: 68393--68444 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
68383 AGATAAACTT
68393 AATAGATTAGAGGAAATATTATTA
1 AATAGATTAGAGGAAATATTATTA
*
68417 AATAGATTAGAGTAAATATTATTA
1 AATAGATTAGAGGAAATATTATTA
68441 AATA
1 AATA
68445 AACGTCGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (24 bp):
AATAGATTAGAGGAAATATTATTA
Done.