Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007106.1 Hibiscus syriacus cultivar Beakdansim tig00018569_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: 89029
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:3836 original size:23 final size:23
Alignment explanation
Indices: 3810--3870 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
3800 CTCGTATAAA
3810 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
3833 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
3856 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
3871 TATAAAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:6681 original size:215 final size:214
Alignment explanation
Indices: 6310--6743 Score: 841
Period size: 215 Copynumber: 2.0 Consensus size: 214
6300 AGTCAGCATG
*
6310 TTAACGTCCAACTTAGACGATCATCATTTTTTTAACAGAAAATGATGATTTGGAACATATAAATA
1 TTAACGTCCAACTTAGACGATCATCATTTTTTTAACAGAAAATGACGATTTGGAACATATAAATA
6375 CTCGAATGATCATTTGTAATTTTTAATATTGAGGGATCCAACAAAATAACATCCTATGGTCGATC
66 CTCGAATGATCATTTGTAATTTTTAATATTGAGGGATCCAACAAAATAACATCCTATGGTCGATC
6440 AATCATTTTATAACTTTTAATAATTATGAGACTCAACAGAACAACACCCTGTAATCGGCTGACCA
131 AATCATTTTATAACTTTTAATAATTATGAGACTCAACAGAACAACACCCTGTAATCGGCTGACCA
6505 TTTGTGTATTTTACCCTTT
196 TTTGTGTATTTTACCCTTT
6524 TTAACGTCCAACTTAGACGATCATCATTTTTTTAACAGAAAATGACGATTTGGAACATATAAATA
1 TTAACGTCCAACTTAGACGATCATCATTTTTTTAACAGAAAATGACGATTTGGAACATATAAATA
*
6589 CTCGAATGATCATTTTGTAATTTTTAATATTGAGGGATCCAACAAAATAACATCTTATGGTCGAT
66 CTCGAATGATCA-TTTGTAATTTTTAATATTGAGGGATCCAACAAAATAACATCCTATGGTCGAT
6654 CAATCATTTTATAACTTTTAATAATTATGAGACTCAACAGAACAACACCCTGTAATCGGCTGACC
130 CAATCATTTTATAACTTTTAATAATTATGAGACTCAACAGAACAACACCCTGTAATCGGCTGACC
6719 ATTTGTGTATTTTACCCTTT
195 ATTTGTGTATTTTACCCTTT
6739 TTAAC
1 TTAAC
6744 TGCCAACGCC
Statistics
Matches: 217, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
214 76 0.35
215 141 0.65
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (214 bp):
TTAACGTCCAACTTAGACGATCATCATTTTTTTAACAGAAAATGACGATTTGGAACATATAAATA
CTCGAATGATCATTTGTAATTTTTAATATTGAGGGATCCAACAAAATAACATCCTATGGTCGATC
AATCATTTTATAACTTTTAATAATTATGAGACTCAACAGAACAACACCCTGTAATCGGCTGACCA
TTTGTGTATTTTACCCTTT
Found at i:7197 original size:35 final size:35
Alignment explanation
Indices: 7150--7245 Score: 122
Period size: 35 Copynumber: 2.7 Consensus size: 35
7140 AACACAATCA
* **
7150 TCAATTACATTCTAAACCCCAAATTCCAAAATGTT
1 TCAATTATATTCTAAACCCCAAATTCCAAAATACT
* *
7185 TCAATTATATTCTAAACCTCAAATTCTAAAATACT
1 TCAATTATATTCTAAACCCCAAATTCCAAAATACT
*
7220 TCAATTATATGCCT-AACCCCAAATTC
1 TCAATTATAT-TCTAAACCCCAAATTC
7246 ATAATCCATT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
35 51 0.96
36 2 0.04
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.33
Consensus pattern (35 bp):
TCAATTATATTCTAAACCCCAAATTCCAAAATACT
Found at i:7634 original size:147 final size:148
Alignment explanation
Indices: 7413--7693 Score: 449
Period size: 147 Copynumber: 1.9 Consensus size: 148
7403 TCAATTCAGA
* * *
7413 TTATAAAATAGTTGACTTAATTTTTTTTTTCGATTTGAGTTTATAAAATTTAAATTAAGTCGAGT
1 TTATAAAATAGTTGACTTAA--TATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAAT
* *
7478 TGAAATGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATCATATTATAATATTATT
64 TGAAATGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATT
7543 TGATTCTAATTCAGTTCCGT
129 TGATTCTAATTCAGTTCCGT
7563 TTATAAAATAGTTGACTTGAA-ATTTTTTCGATTTGAGTTTAT-AAATTTAAATCAAGTCGAATT
1 TTATAAAATAGTTGACTT-AATATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATT
* * *
7626 GAATTGAATTTTCGAGTTTGTTTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTT
65 GAAATGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTT
7691 GAT
130 GAT
7694 AATTTAAATA
Statistics
Matches: 122, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
147 82 0.67
148 20 0.16
150 18 0.15
151 2 0.02
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (148 bp):
TTATAAAATAGTTGACTTAATATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTG
AAATGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTG
ATTCTAATTCAGTTCCGT
Found at i:8278 original size:17 final size:17
Alignment explanation
Indices: 8256--8289 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
8246 TTCATGTTCA
8256 TTTATTAAGATGCACAC
1 TTTATTAAGATGCACAC
8273 TTTATTAAGATGCACAC
1 TTTATTAAGATGCACAC
8290 GTAGTGCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (17 bp):
TTTATTAAGATGCACAC
Found at i:8412 original size:55 final size:55
Alignment explanation
Indices: 8308--8630 Score: 488
Period size: 55 Copynumber: 5.9 Consensus size: 55
8298 TATACGATAG
* * * * *
8308 TTCACCAACTCATGATGAATTCCGTGG-GTTGCACACATCGTGCATGTACGTTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGGTTA
* *
8362 TTCATCAACTCATGATAAATTCTGTGGATTTGCACACATAGTGCTTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGGTTA
*
8417 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGGTTA
* *
8472 TTCATCAACTCATGATTAATTCCATGGATTTGCACACATAGTG-TCTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCT-TGTACGGTTA
* * * *
8527 TTCATCAAATCATGATGAATTCTGTGAATTTGCACACATAGTGCTTGTACGATTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGGTTA
*
8582 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCCTGTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTA
8631 GTACACATAT
Statistics
Matches: 243, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
54 24 0.10
55 218 0.90
56 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (55 bp):
TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCTTGTACGGTTA
Found at i:10409 original size:35 final size:34
Alignment explanation
Indices: 10352--10447 Score: 93
Period size: 35 Copynumber: 2.8 Consensus size: 34
10342 ATGGATTATG
* * *
10352 AATTTGGGGTTGGATATGTAATTGATGTATTTTAA
1 AATTTGGGGTT-AAAATATAATTGATGTATTTTAA
* * * **
10387 AATTTGAGGTTTAGAATATAATTGAAGTATTTTGG
1 AATTTG-GGGTTAAAATATAATTGATGTATTTTAA
*
10422 AATTTGGGGTTAAAATGTAATTGATG
1 AATTTGGGGTTAAAATATAATTGATG
10448 ATTGTGTTAC
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
34 16 0.33
35 28 0.58
36 4 0.08
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (34 bp):
AATTTGGGGTTAAAATATAATTGATGTATTTTAA
Found at i:13162 original size:119 final size:118
Alignment explanation
Indices: 13049--13279 Score: 324
Period size: 119 Copynumber: 1.9 Consensus size: 118
13039 AAAAACATGA
** *
13049 TTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAATGGCAAAAGAGGGCCAAAAACTAATC
1 TTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAATGAAAAAAGAGGGCC-AAAACTAA-A
13114 A-TTTTATGAAATTATAAAAATTAGG-GACC-TAATTATAAATATTAAAAAAAAGTG
64 AGTTTTATGAAATTATAAAAATTAGGAG-CCTTAATTATAAATA-TAAAAAAAAGTG
* * * * *
13168 TTAAATTTAATTCAAAATTGGATGAATTAATAAGAGAACTTAAAAAAGAGGGTCAAAACTAAAAG
1 TTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAATGAAAAAAGAGGGCCAAAACTAAAAG
*
13233 TTTTATGAAATTATAAAAATTAGGAGCCTTAATTGTAAATATAAAAA
66 TTTTATGAAATTATAAAAATTAGGAGCCTTAATTATAAATATAAAAA
13280 TTAGGGGTCC
Statistics
Matches: 100, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
117 1 0.01
118 40 0.40
119 59 0.59
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (118 bp):
TTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAATGAAAAAAGAGGGCCAAAACTAAAAG
TTTTATGAAATTATAAAAATTAGGAGCCTTAATTATAAATATAAAAAAAAGTG
Found at i:13275 original size:28 final size:28
Alignment explanation
Indices: 13235--13314 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 28
13225 ACTAAAAGTT
13235 TTATGAAATTATAAAAATTAGGAG-CCTTAA
1 TTAT-AAA-TATAAAAATTAGGAGTCC-TAA
* *
13265 TTGTAAATATAAAAATTAGGGGTCCTAA
1 TTATAAATATAAAAATTAGGAGTCCTAA
* *
13293 TTATAAATACAAAAATTTGGAG
1 TTATAAATATAAAAATTAGGAG
13315 GCTTTGAGCG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
28 35 0.81
29 5 0.12
30 3 0.07
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (28 bp):
TTATAAATATAAAAATTAGGAGTCCTAA
Found at i:17903 original size:26 final size:26
Alignment explanation
Indices: 17874--17937 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
17864 TATTGTATTG
17874 TAATGTAATGTAGGAGTTAA-TGTTTC
1 TAATGTAATGTAGGAGTTAATTG-TTC
* *
17900 TAATGTGATGTAGGTGTTAATTGTTC
1 TAATGTAATGTAGGAGTTAATTGTTC
*
17926 TAATTTAATGTA
1 TAATGTAATGTA
17938 ATCTATTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 31 0.94
27 2 0.06
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.45
Consensus pattern (26 bp):
TAATGTAATGTAGGAGTTAATTGTTC
Found at i:18316 original size:23 final size:23
Alignment explanation
Indices: 18286--18333 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
18276 ATGACAAGGC
18286 AAAATAGTAAACTGGGACCCTTT
1 AAAATAGTAAACTGGGACCCTTT
* *
18309 AAAATAGTAGATTGGGACCCTTT
1 AAAATAGTAAACTGGGACCCTTT
18332 AA
1 AA
18334 TATATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (23 bp):
AAAATAGTAAACTGGGACCCTTT
Found at i:18340 original size:2 final size:2
Alignment explanation
Indices: 18333--18367 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
18323 GGACCCTTTA
18333 AT AT AT AT AT 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 AT AT AT AT AT A
18368 ATAAAACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19082 original size:23 final size:22
Alignment explanation
Indices: 19051--19098 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
19041 TAAATTTTAT
19051 ATAAATTTAAATTTTTTAAAATA
1 ATAAATTTAAATTTTTTAAAA-A
*
19074 ATAATTTTAAATTTTTTAAAAA
1 ATAAATTTAAATTTTTTAAAAA
19096 ATA
1 ATA
19099 TAAATGTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTTAAATTTTTTAAAAA
Found at i:19647 original size:21 final size:20
Alignment explanation
Indices: 19621--19673 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
19611 CCGAAAATGT
* *
19621 TAAAAATATTAATGTTTTAAG
1 TAAAAATATTAATATTTT-AC
*
19642 TAAAAATAATAATATTTTAC
1 TAAAAATATTAATATTTTAC
*
19662 CAAAAATATTAA
1 TAAAAATATTAA
19674 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
TAAAAATATTAATATTTTAC
Found at i:20241 original size:11 final size:10
Alignment explanation
Indices: 20178--20242 Score: 67
Period size: 10 Copynumber: 6.2 Consensus size: 10
20168 ATTCATTTTT
*
20178 TAAAAATAAA
1 TAAAAATGAA
*
20188 TAAAAATACAA
1 TAAAAAT-GAA
20199 TAAAAATGAA
1 TAAAAATGAA
20209 TTAAAAATGAA
1 -TAAAAATGAA
* *
20220 TAAAATTTAA
1 TAAAAATGAA
20230 TAAAAATGTAA
1 TAAAAATG-AA
20241 TA
1 TA
20243 TAAAGCTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
10 23 0.50
11 23 0.50
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (10 bp):
TAAAAATGAA
Found at i:20242 original size:21 final size:20
Alignment explanation
Indices: 20178--20242 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
20168 ATTCATTTTT
* *
20178 TAAAAATAAATAAAAATACAA
1 TAAAAATGAATAAAAAT-GAA
20199 TAAAAATGAATTAAAAATGAA
1 TAAAAATGAA-TAAAAATGAA
* *
20220 TAAAATTTAATAAAAATGTAA
1 TAAAAATGAATAAAAATG-AA
20241 TA
1 TA
20243 TAAAGCTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.21
21 23 0.61
22 7 0.18
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (20 bp):
TAAAAATGAATAAAAATGAA
Found at i:20846 original size:16 final size:16
Alignment explanation
Indices: 20810--20851 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
20800 AATCTTTCAA
20810 AAATATATTAAATTTAT
1 AAATAT-TTAAATTTAT
*
20827 AAATTTTTAAA-TTAT
1 AAATATTTAAATTTAT
20842 AAAATATTTA
1 -AAATATTTA
20852 TTATTATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATATTTAAATTTAT
Found at i:22447 original size:21 final size:21
Alignment explanation
Indices: 22396--22446 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
22386 TCAACATTCG
22396 AATATAAAATTTAAAAATCAA
1 AATATAAAATTTAAAAATCAA
* * *
22417 AATGTAAAATTTAATAATTCAT
1 AATATAAAATTTAA-AAATCAA
22439 AATATAAA
1 AATATAAA
22447 TAATCAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (21 bp):
AATATAAAATTTAAAAATCAA
Found at i:22885 original size:20 final size:22
Alignment explanation
Indices: 22848--22888 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
22838 TTAATAAAAT
*
22848 AATAATATTTTTTAAATATTAA
1 AATAATATTATTTAAATATTAA
22870 AATAAT-TTATTT-AATATTA
1 AATAATATTATTTAAATATTA
22889 TTTATATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATAATATTATTTAAATATTAA
Found at i:22986 original size:15 final size:15
Alignment explanation
Indices: 22960--22995 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
22950 TTATTATATT
22960 TTATTA-AAATAAAA
1 TTATTATAAATAAAA
22974 TTATTATAAATAAAA
1 TTATTATAAATAAAA
22989 TTATTAT
1 TTATTAT
22996 TTATTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATTATAAATAAAA
Found at i:23013 original size:42 final size:42
Alignment explanation
Indices: 22967--23054 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
22957 ATTTTATTAA
*
22967 AATAAAATTATTATAAATAAAATTA-TTATTTATTAAAATAAG
1 AATAAAA-TATTATAAATAAAACTATTTATTTATTAAAATAAG
* * * * *
23009 AATAATATATTATTAATTATACTATTTATTTATTAAAATAAT
1 AATAAAATATTATAAATAAAACTATTTATTTATTAAAATAAG
23051 AATA
1 AATA
23055 TTGTTAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 13 0.33
42 26 0.67
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (42 bp):
AATAAAATATTATAAATAAAACTATTTATTTATTAAAATAAG
Found at i:23021 original size:22 final size:20
Alignment explanation
Indices: 22964--23091 Score: 68
Period size: 21 Copynumber: 6.2 Consensus size: 20
22954 TATATTTTAT
*
22964 TAAAATAA-AATTATTATAAA
1 TAAAATAATTATTATTA-AAA
*
22984 TAAAATTATTATTTATTAAAA
1 TAAAATAATTA-TTATTAAAA
*
23005 TAAGAATAATATATTATT-AAT
1 TAA-AATAAT-TATTATTAAAA
* * *
23026 TATACTATTTATTTATTAAAA
1 TAAAATAATTA-TTATTAAAA
*
23047 T--AATAA-TATTGTTAAAA
1 TAAAATAATTATTATTAAAA
* *
23064 TATTAAAAAATATAATATTAAAA
1 TA--AAATAAT-TATTATTAAAA
23087 TAAAA
1 TAAAA
23092 ATATTATATT
Statistics
Matches: 82, Mismatches: 14, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
17 9 0.11
18 2 0.02
19 5 0.06
20 16 0.20
21 21 0.26
22 16 0.20
23 13 0.16
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAAATAATTATTATTAAAA
Found at i:23088 original size:23 final size:25
Alignment explanation
Indices: 23039--23088 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
23029 ACTATTTATT
* *
23039 TATTAAAATAATAATATTGTTAAAA
1 TATTAAAATAATAATAATATTAAAA
23064 TATTAAAA-AAT-ATAATATTAAAA
1 TATTAAAATAATAATAATATTAAAA
23087 TA
1 TA
23089 AAAATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 3 0.13
25 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
TATTAAAATAATAATAATATTAAAA
Found at i:23239 original size:29 final size:29
Alignment explanation
Indices: 23207--23276 Score: 99
Period size: 28 Copynumber: 2.4 Consensus size: 29
23197 ATCTTATCTA
*
23207 AATAAAAGTATAATATTATA-TATTATAAT
1 AATAAAA-TATAATATTATATTATTAAAAT
*
23236 AATAAAATATTATATTATATTATTAAAAT
1 AATAAAATATAATATTATATTATTAAAAT
23265 AAT-AAATATAAT
1 AATAAAATATAAT
23277 TTAATAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.51
29 18 0.49
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (29 bp):
AATAAAATATAATATTATATTATTAAAAT
Found at i:23249 original size:21 final size:21
Alignment explanation
Indices: 23225--23265 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23215 TATAATATTA
23225 TATATTATAATAATAAAATAT
1 TATATTATAATAATAAAATAT
* *
23246 TATATTATATTATTAAAATA
1 TATATTATAATAATAAAATA
23266 ATAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATATTATAATAATAAAATAT
Found at i:23254 original size:26 final size:29
Alignment explanation
Indices: 23206--23276 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 29
23196 TATCTTATCT
23206 AAATAAAAGTATAATATTATATATTA-TA
1 AAATAAAAGTATAATATTATATATTATTA
*
23234 ATAATAAAA-TATTATA-T-TATATTATTA
1 A-AATAAAAGTATAATATTATATATTATTA
*
23261 AAATAATAAATATAAT
1 AAATAA-AAGTATAAT
23277 TTAATAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 12 0.32
27 6 0.16
28 12 0.32
29 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (29 bp):
AAATAAAAGTATAATATTATATATTATTA
Found at i:23286 original size:26 final size:27
Alignment explanation
Indices: 23206--23287 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 27
23196 TATCTTATCT
*
23206 AAATAA-AAGTATAATATT-ATATATTA
1 AAATAATAAATATAATATTAATA-ATTA
* * *
23232 TAATAATAAAATATTATATTATATTATTA
1 AAATAAT-AAATATAATATTA-ATAATTA
23261 AAATAATAAATATAAT-TTAATAATTA
1 AAATAATAAATATAATATTAATAATTA
23287 A
1 A
23288 TATTTTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
26 12 0.27
27 3 0.07
28 18 0.40
29 10 0.22
30 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
AAATAATAAATATAATATTAATAATTA
Found at i:26791 original size:3 final size:3
Alignment explanation
Indices: 26769--26817 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
26759 TTGTAATATT
* * *
26769 TAA TAA TAT TAA TAA CAA TAA TAA TAA TAAA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
26815 TAA
1 TAA
26818 ATATATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:26827 original size:8 final size:7
Alignment explanation
Indices: 26785--26829 Score: 51
Period size: 6 Copynumber: 6.7 Consensus size: 7
26775 TATTAATAAC
26785 AATAAT-
1 AATAATA
26791 AATAATA
1 AATAATA
26798 AATAAT-
1 AATAATA
*
26804 GATAAT-
1 AATAATA
26810 AATAATA
1 AATAATA
26817 AATATATA
1 AATA-ATA
26825 AATAA
1 AATAA
26830 GATGGGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 16 0.47
7 11 0.32
8 7 0.21
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (7 bp):
AATAATA
Found at i:27088 original size:17 final size:17
Alignment explanation
Indices: 27066--27124 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
27056 TTGAACAAGC
27066 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
27083 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
27102 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
27119 TCTTCT
1 TCTTCT
27125 TCTTCAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 4 0.12
19 10 0.29
20 2 0.06
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.49
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:27143 original size:39 final size:36
Alignment explanation
Indices: 27066--27135 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
27056 TTGAACAAGC
27066 TCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGT
27102 TCTTCTCATTGTGAACTTCTTCTTCTTCAGATGA
1 TCTTCTCATTGTGAACTTCTTCTTCTTCAGATGA
27136 CGAGTTCTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (36 bp):
TCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGT
Found at i:27149 original size:39 final size:36
Alignment explanation
Indices: 27070--27157 Score: 131
Period size: 36 Copynumber: 2.4 Consensus size: 36
27060 ACAAGCTCTT
*
27070 CTCATTGTGAACTTCTTCTTCTTCAGATGAGTTCTT
1 CTCATTGTGAACTTCTTCTTCTTCAGATGAGTTCTG
27106 CTCATTGTGAACTTCTTCTTCTTCAGATGACGAGTTCTG
1 CTCATTGTGAACTTCTTCTTCTTCAGAT---GAGTTCTG
*
27145 CTCATTATGAACT
1 CTCATTGTGAACT
27158 CTACCTGGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 28 0.60
39 19 0.40
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (36 bp):
CTCATTGTGAACTTCTTCTTCTTCAGATGAGTTCTG
Found at i:27299 original size:113 final size:113
Alignment explanation
Indices: 27099--27457 Score: 454
Period size: 113 Copynumber: 3.2 Consensus size: 113
27089 TCTTCAGATG
* ** * * *
27099 AGTTCTTCTCATTGTGAACTTCTTCTT-CTTC-AGATGACGAGTTCTGCTCATTATGAACTCTAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCATTATGAACTCTAA
* * * * *
27162 CTGGCAATGTTGATCCATCAAATGATGAAATTAAACAAAAGGTTGAACA
65 CTGGTAATGCTGATCCATCGAATGATGAAATTAAGCAAAAAGTTGAACA
* * * *
27211 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATCATGAACTCGAAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
* *
27276 TGGTAATGCTGATCCATTGAATGATG-AATTCAAGCAAAAATTTGAACA
66 TGGTAATGCTGATCCATCGAATGATGAAATT-AAGCAAAAAGTTGAACA
* *
27324 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTGTCATTATGAACTCTAAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
* * ** * *
27389 TGGTACTGCTGTTCCGCCGAGTGATGAATTTAAGCAAAAAGTTGAACA
66 TGGTAATGCTGATCCATCGAATGATGAAATTAAGCAAAAAGTTGAACA
27437 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
27458 TCTCTGGAAA
Statistics
Matches: 212, Mismatches: 31, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
112 29 0.14
113 179 0.84
114 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
TGGTAATGCTGATCCATCGAATGATGAAATTAAGCAAAAAGTTGAACA
Found at i:27452 original size:73 final size:73
Alignment explanation
Indices: 27364--27527 Score: 184
Period size: 73 Copynumber: 2.2 Consensus size: 73
27354 TCTTTAGATG
* * ** * * * *
27364 AGTTCTTGTCATTATGAACTCTAACTGGTACTGCTGTTCCGCCGAGTGATGAATTTAAGCAAAAA
1 AGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCACCAAATGATGAATTTAAGCAAAAA
27429 GTTGAACA
66 GTTGAACA
* ** * * * *
27437 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCACCAAATGATGAATTTAAGCAAAAA
27502 GTTGAACA
66 GTTGAACA
*
27510 AATTCTTCTCATTATGAA
1 AGTTCTTCTCATTATGAA
27528 TTTCTTCTTC
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCACCAAATGATGAATTTAAGCAAAAA
GTTGAACA
Found at i:27500 original size:186 final size:184
Alignment explanation
Indices: 27283--27644 Score: 472
Period size: 186 Copynumber: 2.0 Consensus size: 184
27273 AACTGGTAAT
** * *
27283 GCTGATCCATTGAATGATGAATTCAAGCAAAAATTTGAACAAGTTCTTCTCATTATGAACTTCTT
1 GCTGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTT
* * * ** * * * *
27348 CTTCCTTCTTTAGATGAGTTCTTGTCATTATGAACTCTAACTGGTACTGCTGTTCCGCCGAGTGA
66 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TAACTGGAAAAGCTGATCCACCAAATGA
*
27413 TGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
130 TGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAA-TTTCTCTGGAAAA
* ** * *
27469 GCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTT
1 GCTGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTT
** * *
27534 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGGAAAAGTTGATCCATCAAATGAT
66 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTAACTGGAAAAGCTGATCCACCAAATGAT
* * *
27599 GGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCT
131 GAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCT
27645 TCTTCCTTCT
Statistics
Matches: 150, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
184 5 0.03
185 55 0.37
186 90 0.60
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (184 bp):
GCTGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTT
CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTAACTGGAAAAGCTGATCCACCAAATGAT
GAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTCTGGAAAA
Found at i:27558 original size:113 final size:113
Alignment explanation
Indices: 27437--28267 Score: 1053
Period size: 113 Copynumber: 7.2 Consensus size: 113
27427 AAGTTGAACA
27437 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
* *
27502 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
27550 AGTTCTTCTCATTATGAACTTT-TCTGGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
*
27614 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAA------CTT-CTTC-T--TCCTTCTTCAGATG
*
27672 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
* * *
27737 GTTGAACAAATTTTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * * *
27785 AGTTCTTCTCATTATGAACTTTTTCTGGAAAATGTTGATCCATCGAATGATGAATTCGAGCAAAA
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAA-GCTGATCCATCAAATGATGGATTTGAGCAAAA
* * * *
27850 AGTTGAATAAGTTCTTCTCGTTATGAACTTATTCTTCCTTCTTCAGATG
65 GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * * *
27899 AGTTCTTCTCATTATGAACTCTAC-CTGGCAATA-CTGATCCATCGAATGATGAATTCGAGCAAA
1 AGTTCTTCTCATTATGAACT-TTCTCTGG-AAAAGCTGATCCATCAAATGATGGATTTGAGCAAA
* *
27962 AAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATG
64 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * ** *
28012 AGTTCTTCTCATTATGAACTCAT-TCTGGAAATA-TTGATGCCGATCTATCTCTTTCTGCGATAG
1 AGTTCTTCTCATTATGAACT-TTCTCTGGAAA-AGCTGAT-CC-ATC-A------AAT--GATGG
* * * *
28075 AGTCGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATA
53 ATTTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * *
28135 AGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGGTCCATCAAGTGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
*
28200 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
28248 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
28268 CTACCTGGTA
Statistics
Matches: 642, Mismatches: 46, Indels: 60
0.86 0.06 0.08
Matches are distributed among these distances:
112 119 0.19
113 206 0.32
114 97 0.15
115 8 0.01
116 4 0.01
117 2 0.00
118 2 0.00
119 4 0.01
120 2 0.00
121 3 0.00
122 40 0.06
123 108 0.17
124 47 0.07
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:27893 original size:349 final size:343
Alignment explanation
Indices: 27436--28275 Score: 1097
Period size: 349 Copynumber: 2.4 Consensus size: 343
27426 AAAGTTGAAC
27436 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAA-GCTGATCCATCAAATGATGGATTTGAGCAAA
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAATGCTGATCCATC-AATGATGGATTTGAGCAAA
* *
27500 AGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
** * * * *
27565 GAACT-TTTCTGG-AAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCT
130 GAACTCTACCTGGCAAAA-CTGATCCATCAAATGATGAATTCGAGCAAAAAGTTGAACAAATTCT
* *
27628 TCTCATTATGAATTTCTTCTTCCTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
194 TCTCATTATGAA------CTT-ATTC-T--TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * * * *
27693 TTTCTGGAAA-AGCTGAT-CC-ATC-A-AAT-GATGGATTTGAGCAAAAGGTTGAACAAATTTTT
249 ATTCTGGAAATA-CTGATGCCGATCTATAATCGATAGAGTCGAGCAAAAGGTTGAACAAACTCTT
*
27752 CTCATTATGAATTTCTTCTTCCTTCTTCAGAT
313 CTCATTATGAACTTCTTCTT-CTTCTTCAGAT
* * * * *
27784 GAGTTCTTCTCATTATGAACTTTTTCTGGAAAATGTTGATCCATCGAATGATGAATTCGAGCAAA
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAATGCTGATCCATC-AATGATGGATTTGAGCAAA
* * * *
27849 AAGTTGAATAAGTTCTTCTCGTTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * *
27914 GAACTCTACCTGGCAATACTGATCCATCGAATGATGAATTCGAGCAAAAAGTTGAACAAGTTCTT
130 GAACTCTACCTGGCAAAACTGATCCATCAAATGATGAATTCGAGCAAAAAGTTGAACAAATTCTT
27979 CTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCATTCTGGAAAT
195 CTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCATTCTGGAAAT
* ** *
28044 ATTGATGCCGATCTATCTCTTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGCTCTTCTCATT
260 ACTGATGCCGATCTA-----TAAT-CGATAGAGTCGAGCAAAAGGTTGAACAAACTCTTCTCATT
28109 ATGAACTTCTTCTTCTTCTTCAGAT
319 ATGAACTTCTTCTTCTTCTTCAGAT
*
28134 AAGTTCTTCTCATTATGAACTTTCTCTGG-AAATGCTGGTCCATCAAGTGATGGATTTGAGCAAA
1 AAGTTCTTCTCATTATGAACTTTCTCTGGAAAATGCTGATCCATCAA-TGATGGATTTGAGCAAA
*
28198 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
28263 GAACTCTACCTGG
130 GAACTCTACCTGG
28276 TAATGCTGAT
Statistics
Matches: 431, Mismatches: 45, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
340 47 0.11
341 3 0.01
342 4 0.01
343 4 0.01
344 3 0.01
348 33 0.08
349 193 0.45
350 95 0.22
351 49 0.11
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (343 bp):
AAGTTCTTCTCATTATGAACTTTCTCTGGAAAATGCTGATCCATCAATGATGGATTTGAGCAAAA
GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
AACTCTACCTGGCAAAACTGATCCATCAAATGATGAATTCGAGCAAAAAGTTGAACAAATTCTTC
TCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCATTCTGGAAATA
CTGATGCCGATCTATAATCGATAGAGTCGAGCAAAAGGTTGAACAAACTCTTCTCATTATGAACT
TCTTCTTCTTCTTCAGAT
Found at i:28314 original size:463 final size:455
Alignment explanation
Indices: 27437--28285 Score: 1140
Period size: 463 Copynumber: 1.8 Consensus size: 455
27427 AAGTTGAACA
* * * *
27437 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTACTCTGGAAAAGCTGATCCATCAAATGATGAATTCGAGCAAAAA
* *
27502 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * *
27567 ACTTTTCTGGAAAAGTTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTC
131 ACTATTCTGGAAAAGTTGATCCATCAAATGATAGAGTCGAGCAAAAGGTTGAACAAACTCTTCTC
* *
27632 ATTATGAATTTCTTCTTCCTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
196 ATTATGAA-----TCTTCCTTCTT-ATCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTC
* *
27697 TGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTTTTCTCATTATGA
255 TGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAACTCTTCTCATTATGA
* * ** *
27762 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAATGTTGATCCA
320 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAATGCTGATCCA
**
27827 TCGAATGATGAATTCGAGCAAAAAGTTGAATAAGTTCTTCTCGTTATGAACTTATTCTTCCTTCT
385 -CGAATGATGAAAACGAGCAAAAAGTTGAATAAGTTCTTCTCGTTATGAACTTATTCTTCCTTCT
27892 TCAGATG
449 TCAGATG
* *
27899 AGTTCTTCTCATTATGAACTCTAC-CTGGCAATA-CTGATCCATCGAATGATGAATTCGAGCAAA
1 AGTTCTTCTCATTATGAACT-TACTCTGG-AAAAGCTGATCCATCAAATGATGAATTCGAGCAAA
*
27962 AAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
64 AAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
**
28027 GAACTCATTCTGGAAATA-TTGATGCCGATCTATCTCTTTCTGCGATAGAGTCGAGCAAAAGGTT
129 GAACT-ATTCTGGAAA-AGTTGAT-CC-ATC-A------AAT--GATAGAGTCGAGCAAAAGGTT
*
28091 GAACAAGCTCTTCTCATTATGAA-CTT-CTTC-T-T-CTTCTTCAGATAAGTTCTTCTCATTATG
181 GAACAAACTCTTCTCATTATGAATCTTCCTTCTTATCCTTCTTCAGATAAGTTCTTCTCATTATG
* * * *
28151 AACTTTCTCTGGAAATGCTGGTCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
246 AACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAACTCTTC
*
28216 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGG-TAAT
311 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAAT
28280 GCTGAT
376 GCTGAT
28286 GACCCGAAGA
Statistics
Matches: 341, Mismatches: 31, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
462 125 0.37
463 160 0.47
464 4 0.01
465 3 0.01
466 2 0.01
467 4 0.01
468 3 0.01
472 1 0.00
474 39 0.11
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (455 bp):
AGTTCTTCTCATTATGAACTTACTCTGGAAAAGCTGATCCATCAAATGATGAATTCGAGCAAAAA
GTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTATTCTGGAAAAGTTGATCCATCAAATGATAGAGTCGAGCAAAAGGTTGAACAAACTCTTCTC
ATTATGAATCTTCCTTCTTATCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA
AGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCT
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAATGCTGATCCACGAATG
ATGAAAACGAGCAAAAAGTTGAATAAGTTCTTCTCGTTATGAACTTATTCTTCCTTCTTCAGATG
Found at i:28409 original size:76 final size:76
Alignment explanation
Indices: 28283--28513 Score: 390
Period size: 76 Copynumber: 3.0 Consensus size: 76
28273 TGGTAATGCT
* ** *
28283 GATGACCCGAAGATTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
28348 TAGGACTTACA
66 TAGGACTTACA
28359 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
28424 TAGGACTTACA
66 TAGGACTTACA
* * *
28435 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGTACTA
1 GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
*
28500 CAGGACTTACA
66 TAGGACTTACA
28511 GAT
1 GAT
28514 ATGGGAAATA
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 147 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (76 bp):
GATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
TAGGACTTACA
Found at i:28815 original size:164 final size:165
Alignment explanation
Indices: 28517--28842 Score: 546
Period size: 164 Copynumber: 2.0 Consensus size: 165
28507 TACAGATATG
* * *
28517 GGAAATAGTTTACTAAGTAAGAAACTATGGAAATCGTTTTCTTACTATTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTTC
** *
28582 AGAAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTCAAAATAACATGTTAAT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTGTTCAAAATAACATGTTAAT
*
28647 TGGGTAACATGCCCCAATCTCAAGATAATGCTGTT
131 TGGGTAACATGACCCAATCTCAAGATAATGCTGTT
*
28682 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTTC
* * *
28747 -GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTGTTCAAAATATCATGTTGAT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTGTTCAAAATAACATGTTAAT
28811 TGGGTAACATGACCCAATCTCAAGATAATGCT
131 TGGGTAACATGACCCAATCTCAAGATAATGCT
28843 CATTCTTGTG
Statistics
Matches: 150, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
164 89 0.59
165 61 0.41
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (165 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTATTCAACAATTTCATTTTC
AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTGTTCAAAATAACATGTTAAT
TGGGTAACATGACCCAATCTCAAGATAATGCTGTT
Found at i:29375 original size:22 final size:22
Alignment explanation
Indices: 29350--29404 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
29340 AATAAAGCTT
29350 TCATCTTTGAAAAGAAAATCTA
1 TCATCTTTGAAAAGAAAATCTA
* *
29372 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAAAATCTA
29394 TCATCTTTGAA
1 TCATCTTTGAA
29405 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:32269 original size:109 final size:108
Alignment explanation
Indices: 31966--32403 Score: 619
Period size: 109 Copynumber: 4.0 Consensus size: 108
31956 TCATGCAGTT
* * * * * * *
31966 CATCTTTTAATTCCAATGATTGG-TTCTGTGGTTCCTATCGAACCAGATCAGATAACTCAAAGAA
1 CATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
* * * *
32030 CACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGAAAATT
66 CACTTCCAGAAGATGCTATTGGG--T-C----TTCTACTATGAGCACATG
32080 CATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
1 CATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
* *
32145 CCCTTCTAGAAGATGCTATTGGGTCTTCTACTATGAGCACATG
66 CACTTCCAGAAGATGCTATTGGGTCTTCTACTATGAGCACATG
*
32188 CATCTTTCAAATCCAATGATTGGTTTTTGGGGTCTAATACCAAACCAGATCAGATAACTCAAAGA
1 CATCTTTCAAATCCAATGATTGGTTTTTGGGGT-TCATACCAAACCAGATCAGATAACTCAAAGA
* *
32253 ACACTTCTAAAAGATGCTATTGGGTCTTCTACTATGAGCACATG
65 ACACTTCCAGAAGATGCTATTGGGTCTTCTACTATGAGCACATG
*
32297 GATCTTTCAAATCCAATGATTGGTTTTT-GGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
1 CATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
* *
32361 CACTTCCAGAAGATGTTATTGGGTCTTATACTATGAGCACATG
66 CACTTCCAGAAGATGCTATTGGGTCTTCTACTATGAGCACATG
32404 GCACTTGCTC
Statistics
Matches: 300, Mismatches: 22, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
107 70 0.23
108 51 0.17
109 99 0.33
112 1 0.00
113 1 0.00
114 21 0.07
115 57 0.19
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (108 bp):
CATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGGGTCTTCTACTATGAGCACATG
Found at i:32374 original size:216 final size:220
Alignment explanation
Indices: 32006--32403 Score: 633
Period size: 216 Copynumber: 1.8 Consensus size: 220
31996 GTTCCTATCG
*
32006 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGGG-CTCC---TTTCTACCAT
*
32071 GAGAAAATTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAA
62 GAGAAAATGCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAA
* * *
32136 CTCAAAGAACCCTTCTAGAAGATGCTATTGGGTCTTCTACTATGAGCACATGCATCTTTCAAATC
127 CTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTATACTATGAGCACATGCATCTTTCAAATC
32201 CAATGATTGGTTTTTGGGGTCTAATACCA
192 CAATGATTGGTTTTTGGGGTCTAATACCA
* * *
32230 AACCAGATCAGATAACTCAAAGAACACTTCTAAAAGATGCTATTGGG-T-C-TTCTACTATGAGC
1 AACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGGGCTCCTTTCTACCATGAGA
* *
32292 ACATGGATCTTTCAAATCCAATGATTGGTTTTT-GGGTTCATACCAAACCAGATCAGATAACTCA
66 AAATGCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
*
32356 AAGAACACTTCCAGAAGATGTTATTGGGTCTTATACTATGAGCACATG
131 AAGAACACTTCCAGAAGATGCTATTGGGTCTTATACTATGAGCACATG
32404 GCACTTGCTC
Statistics
Matches: 163, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
216 75 0.46
217 41 0.25
221 1 0.01
222 1 0.01
224 45 0.28
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (220 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGGGCTCCTTTCTACCATGAGA
AAATGCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
AAGAACACTTCCAGAAGATGCTATTGGGTCTTATACTATGAGCACATGCATCTTTCAAATCCAAT
GATTGGTTTTTGGGGTCTAATACCA
Found at i:37746 original size:14 final size:14
Alignment explanation
Indices: 37700--37760 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
37690 AAAGCAAACA
*
37700 TAAAAATACAAATG
1 TAAAAATGCAAATG
* *
37714 CAAAGATGCCAAATG
1 TAAAAATG-CAAATG
* *
37729 TAAACATGCAATTG
1 TAAAAATGCAAATG
*
37743 TAAAAATGTAAATG
1 TAAAAATGCAAATG
37757 TAAA
1 TAAA
37761 TTATTTAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
14 25 0.68
15 12 0.32
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (14 bp):
TAAAAATGCAAATG
Found at i:40111 original size:20 final size:19
Alignment explanation
Indices: 40072--40113 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
40062 TTTCCTCGAT
40072 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
40091 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
40111 ATT
1 ATT
40114 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:40129 original size:120 final size:117
Alignment explanation
Indices: 39985--40217 Score: 281
Period size: 120 Copynumber: 2.0 Consensus size: 117
39975 TATATTAGTT
* * * *
39985 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAA-GGACTTCTAGGTGCC
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAAGTGCC
* *
40049 TTAAGACAGCTCTTTTCCTCGATATTAAAAAATAAATAAATAATTAAAACAATTAA
66 TTAAGACAGC-CCTTT-CTCAATATT-AAAAATAAATAAAT-ATTAAAACAATTAA
** * * *
40105 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATTAGAAAATGGACATCCAATTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAAGTGC
* * *
40169 TTTAAGACTGCCCTTTCTTAATATTAAAAATAAATAAATATTAAAACAA
65 CTTAAGACAGCCCTTTCTCAATATTAAAAATAAATAAATATTAAAACAA
40218 GATTAAAATA
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
117 10 0.10
118 14 0.14
119 13 0.13
120 42 0.43
121 18 0.19
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (117 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAAGTGCC
TTAAGACAGCCCTTTCTCAATATTAAAAATAAATAAATATTAAAACAATTAA
Found at i:42111 original size:2 final size:2
Alignment explanation
Indices: 42048--42093 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
42038 AAGGAGGATC
42048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42090 AT AT
1 AT AT
42094 GATTTTCTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43810 original size:20 final size:20
Alignment explanation
Indices: 43785--43823 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
43775 AAACATAGAT
43785 TGTGGCGTTCCACGCTAATA
1 TGTGGCGTTCCACGCTAATA
43805 TGTGGCGTTCCACGCTAAT
1 TGTGGCGTTCCACGCTAAT
43824 TTATCATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (20 bp):
TGTGGCGTTCCACGCTAATA
Found at i:51194 original size:14 final size:14
Alignment explanation
Indices: 51172--51202 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
51162 CTAAAAAAAC
*
51172 AAATTTAATTTTTA
1 AAATCTAATTTTTA
51186 AAATCTAATTTTTA
1 AAATCTAATTTTTA
51200 AAA
1 AAA
51203 GATCCCGTCT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATCTAATTTTTA
Found at i:52974 original size:108 final size:108
Alignment explanation
Indices: 52789--53369 Score: 437
Period size: 108 Copynumber: 5.2 Consensus size: 108
52779 CATGACTAAA
* * *
52789 ATGCAAAAACACGCCT-AAATA-AGGGGACTAAACATAAAATATTCCAAAAATATATATAACATG
1 ATGCAAAAACACG-CTAAAATATGGGGGACTAAACA-AAAATA-TCCCAAAACATATATAACATG
*
52852 CATGAAAATGGGTAAATAACAACTTTGGTCCCTACAAGTGACCAAC
63 CATGAAAAAGGGTAAATAACAACTTTGGTCCCTACAAGTGACCAAC
*
52898 ATGCAAAAGCACGCTAAAATATGGGGGACTAAACAACAAATATCCCAAAA-ATATATAACATGCA
1 ATGCAAAAACACGCTAAAATATGGGGGACTAAACAA-AAATATCCCAAAACATATATAACATGCA
* * *
52962 TGAAAAAGGGTAAATAACAACTTTGGT-CATCGCAGGTGACCAAC
65 TGAAAAAGGGTAAATAACAACTTTGGTCCCT-ACAAGTGACCAAC
* * * * ****** * * * * *
53006 ATGTAAAAACGCGCTAAACTATGGGAGACCTATGTGTGATTTTACCATAAACTTCCCCTATAAAA
1 ATGCAAAAACACGCTAAAATATGGGGGA-CTAAACAAAAATATCCCA-AAA-----CATATATAA
* *** ** * * *
53071 CCCAT-CAGTCCAAAAATATTAAAATAA-AA-TTAAATAATCACTACACA-TGACTAAA
59 --CATGCA-T-GAAAAAGGGT-AAATAACAACTT---TGGTCCCTACA-AGTGACCAAC
* * * *
53126 ATGCAAAAACACGCCT-AAATAAGGGGGGACTATACAGAAAATATTCCAAAAATATATATAACAT
1 ATGCAAAAACACG-CTAAAAT-ATGGGGGACTAAACA-AAAATA-TCCCAAAACATATATAACAT
* *
53190 GCATGAAAATGGGTAAATAATAACTTTGGTCCCTACAAGTGACCAAC
62 GCATGAAAAAGGGTAAATAACAACTTTGGTCCCTACAAGTGACCAAC
*
53237 ATGCAAAAACACGCTAAACTATGGGGGACTAAACAACAAATATCCCAAAA-ATATATAACATGCA
1 ATGCAAAAACACGCTAAAATATGGGGGACTAAACAA-AAATATCCCAAAACATATATAACATGCA
* * * *
53301 TGAAAACGGGTAAATAACAACTTTGGT-CATCGCAAGTGACCAAT
65 TGAAAAAGGGTAAATAACAACTTTGGTCCCT-ACAAGTGACCAAC
* *
53345 ATGCAAAAACGCGCTAAACTATGGG
1 ATGCAAAAACACGCTAAAATATGGG
53370 AGACCCATAT
Statistics
Matches: 367, Mismatches: 72, Indels: 67
0.73 0.14 0.13
Matches are distributed among these distances:
107 4 0.01
108 156 0.43
109 39 0.11
110 38 0.10
111 30 0.08
112 6 0.02
113 7 0.02
114 6 0.02
115 8 0.02
116 8 0.02
117 6 0.02
118 8 0.02
119 6 0.02
120 28 0.08
121 14 0.04
122 3 0.01
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (108 bp):
ATGCAAAAACACGCTAAAATATGGGGGACTAAACAAAAATATCCCAAAACATATATAACATGCAT
GAAAAAGGGTAAATAACAACTTTGGTCCCTACAAGTGACCAAC
Found at i:53355 original size:339 final size:338
Alignment explanation
Indices: 52737--53415 Score: 1198
Period size: 339 Copynumber: 2.0 Consensus size: 338
52727 AAATTACTAA
* *
52737 ATCAGTCCAGAAATATTAAAATTAAATTAAATAATCACTACACATGACTAAAATGCAAAAACACG
1 ATCAGTCCAAAAATATTAAAATAAAATTAAATAATCACTACACATGACTAAAATGCAAAAACACG
*
52802 CCTAAATAAGGGGACTAAACATAAAATATTCCAAAAATATATATAACATGCATGAAAATGGGTAA
66 CCTAAATAAGGGGACTAAACAGAAAATATTCCAAAAATATATATAACATGCATGAAAATGGGTAA
*
52867 ATAACAACTTTGGTCCCTACAAGTGACCAACATGCAAAAGCACGCTAAAATATGGGGGACTAAAC
131 ATAACAACTTTGGTCCCTACAAGTGACCAACATGCAAAAACACGCTAAAATATGGGGGACTAAAC
*
52932 AACAAATATCCCAAAAATATATAACATGCATGAAAAAGGGTAAATAACAACTTTGGTCATCGCAG
196 AACAAATATCCCAAAAATATATAACATGCATGAAAAAGGGTAAATAACAACTTTGGTCATCGCAA
* * *
52997 GTGACCAACATGTAAAAACGCGCTAAACTATGGGAGACCTATGTGTGATTTTACCATAAACTTCC
261 GTGACCAACATGCAAAAACGCGCTAAACTATGGGAGACCCATATGTGATTTTACCATAAACTTCC
*
53062 CCTA-TAAAACCC
326 CCTACGAAAACCC
53074 ATCAGTCCAAAAATATTAAAATAAAATTAAATAATCACTACACATGACTAAAATGCAAAAACACG
1 ATCAGTCCAAAAATATTAAAATAAAATTAAATAATCACTACACATGACTAAAATGCAAAAACACG
*
53139 CCTAAATAAGGGGGGACTATACAGAAAATATTCCAAAAATATATATAACATGCATGAAAATGGGT
66 CCTAAATAA--GGGGACTAAACAGAAAATATTCCAAAAATATATATAACATGCATGAAAATGGGT
* *
53204 AAATAATAACTTTGGTCCCTACAAGTGACCAACATGCAAAAACACGCTAAACTATGGGGGACTAA
129 AAATAACAACTTTGGTCCCTACAAGTGACCAACATGCAAAAACACGCTAAAATATGGGGGACTAA
*
53269 ACAACAAATATCCCAAAAATATATAACATGCATGAAAACGGGTAAATAACAACTTTGGTCATCGC
194 ACAACAAATATCCCAAAAATATATAACATGCATGAAAAAGGGTAAATAACAACTTTGGTCATCGC
* *
53334 AAGTGACCAATATGCAAAAACGCGCTAAACTATGGGAGACCCATATGTGATTTTACCCTAAACTT
259 AAGTGACCAACATGCAAAAACGCGCTAAACTATGGGAGACCCATATGTGATTTTACCATAAACTT
53399 CCCCTACGAAAACCC
324 CCCCTACGAAAACCC
53414 AT
1 AT
53416 TTTTGTTTTT
Statistics
Matches: 324, Mismatches: 15, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
337 72 0.22
339 243 0.75
340 9 0.03
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (338 bp):
ATCAGTCCAAAAATATTAAAATAAAATTAAATAATCACTACACATGACTAAAATGCAAAAACACG
CCTAAATAAGGGGACTAAACAGAAAATATTCCAAAAATATATATAACATGCATGAAAATGGGTAA
ATAACAACTTTGGTCCCTACAAGTGACCAACATGCAAAAACACGCTAAAATATGGGGGACTAAAC
AACAAATATCCCAAAAATATATAACATGCATGAAAAAGGGTAAATAACAACTTTGGTCATCGCAA
GTGACCAACATGCAAAAACGCGCTAAACTATGGGAGACCCATATGTGATTTTACCATAAACTTCC
CCTACGAAAACCC
Found at i:54312 original size:12 final size:12
Alignment explanation
Indices: 54297--54339 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
54287 TAAACATTAA
*
54297 AATTATAATTAT
1 AATTATAATAAT
54309 AATTAGATAATAAT
1 AATT--ATAATAAT
*
54323 AATAATAATAAT
1 AATTATAATAAT
54335 AATTA
1 AATTA
54340 AAAATTATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 16 0.62
14 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
AATTATAATAAT
Found at i:54432 original size:3 final size:3
Alignment explanation
Indices: 54424--54452 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54414 TGGTACTCTC
54424 CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
54453 GTATACAACC
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:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:54824 original size:47 final size:48
Alignment explanation
Indices: 54765--54856 Score: 118
Period size: 47 Copynumber: 1.9 Consensus size: 48
54755 TTTTTTATAT
*
54765 TTAGTTTTTATG-TTATAGTATTCATGTTTAAT-ATTTTTATATTATGTA
1 TTAGTTTTTATGTTTATA-TATT-ATCTTTAATGATTTTTATATTATGTA
* *
54813 TTAG-TTTTATGTTTTTATATTATCTTTAATGTTTTTTATATTAT
1 TTAGTTTTTATGTTTATATATTATCTTTAATGATTTTTATATTAT
54857 ATTTCATTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
46 8 0.21
47 23 0.59
48 8 0.21
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (48 bp):
TTAGTTTTTATGTTTATATATTATCTTTAATGATTTTTATATTATGTA
Found at i:54827 original size:26 final size:29
Alignment explanation
Indices: 54764--54835 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 29
54754 TTTTTTTATA
*
54764 TTTA-GTTTTTATGTTATAGTATTCATGT
1 TTTATGTTTTTATATTATAGTATTCATGT
* *
54792 TTAATATTTTTATATTAT-GTATT-A-GT
1 TTTATGTTTTTATATTATAGTATTCATGT
54818 TTTATGTTTTTATATTAT
1 TTTATGTTTTTATATTAT
54836 CTTTAATGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 18 0.47
27 1 0.03
28 8 0.21
29 11 0.29
ACGTcount: A:0.25, C:0.01, G:0.10, T:0.64
Consensus pattern (29 bp):
TTTATGTTTTTATATTATAGTATTCATGT
Found at i:58778 original size:19 final size:21
Alignment explanation
Indices: 58746--58784 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
58736 ATATAATATG
58746 ATTTAAGTTGAATAAATTTAA
1 ATTTAAGTTGAATAAATTTAA
*
58767 ATTTAA-TT-AATAATTTTA
1 ATTTAAGTTGAATAAATTTA
58785 TTTTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTTAAGTTGAATAAATTTAA
Found at i:64064 original size:18 final size:18
Alignment explanation
Indices: 64041--64075 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
64031 TTCCATCCGG
*
64041 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
64059 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
64076 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:65398 original size:13 final size:13
Alignment explanation
Indices: 65380--65404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65370 TGGTCAACGG
65380 GTCAACGGGTCGA
1 GTCAACGGGTCGA
65393 GTCAACGGGTCG
1 GTCAACGGGTCG
65405 GGTCGGGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:65408 original size:18 final size:18
Alignment explanation
Indices: 65385--65425 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
65375 AACGGGTCAA
65385 CGGGTCGAGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
*
65403 CGGGTCGGGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
65421 CGGGT
1 CGGGT
65426 AAACGGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGAGTCAACGGGT
Found at i:65414 original size:31 final size:31
Alignment explanation
Indices: 65377--65453 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
65367 CAATGGTCAA
* *
65377 CGGGTCAACGGGTCGAGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGAGTAAACGGGTCAGGT
*
65408 CGGGTCAACGGGTCGGGTAAACGGGTCAGGT
1 CGGGTCAACGGGTCGAGTAAACGGGTCAGGT
* *
65439 CAGGTAAACGGGTCG
1 CGGGTCAACGGGTCG
65454 GGTCGGGTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.19, C:0.21, G:0.44, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGAGTAAACGGGTCAGGT
Found at i:65419 original size:13 final size:13
Alignment explanation
Indices: 65403--65440 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
65393 GTCAACGGGT
65403 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
65416 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
*
65429 CGGGTCAGGTCA
1 CGGGTCGGGTCA
65441 GGTAAACGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.18, C:0.21, G:0.45, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:65439 original size:18 final size:18
Alignment explanation
Indices: 65418--65461 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
65408 CGGGTCAACG
65418 GGTCGGGTAAACGGGTCA
1 GGTCGGGTAAACGGGTCA
* *
65436 GGTCAGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCA
65454 GGTCGGGT
1 GGTCGGGT
65462 TGTGACCGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.48, T:0.18
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCA
Found at i:77931 original size:83 final size:81
Alignment explanation
Indices: 77829--78136 Score: 341
Period size: 83 Copynumber: 3.7 Consensus size: 81
77819 AATACTAGCA
* * *
77829 TTTGGTGTTCGAACCTGAGACCTTTAGGAATAGCAACCATTCATTTAACCATTTGACAACGAATG
1 TTTGGTGTTCGAACCTGAGACCTCTAGGAATAACAACCATTCCTTTAACCATTTGACAACGAATG
77894 TTCAAATACACTACAATC
66 TTCAAATAC-CTA-AATC
* * * * *
77912 TTTGGTGTTCGAACATGAGACCTCTAGGAATAACAACCATTCCTTAAATCATTTGATAATGAATG
1 TTTGGTGTTCGAACCTGAGACCTCTAGGAATAACAACCATTCCTTTAACCATTTGACAACGAATG
*
77977 TCCAAATACCCTAAAGTC
66 TTCAAATA-CCTAAA-TC
* * * * * **
77995 TATGGTGTTCAAACTTGAGACCTCTAGGAATAACAATCATTCCTTTAACCATTTGGCTGCGAATG
1 TTTGGTGTTCGAACCTGAGACCTCTAGGAATAACAACCATTCCTTTAACCATTTGACAACGAATG
* *
78060 CTCAAATACCTTAGAGTC
66 TTCAAATACC-TA-AATC
** *
78078 ACTGGTG-TCTGAACCTGAGACCTCT-GAGAATAACAACCATTCCTTTAATCATTTGACAA
1 TTTGGTGTTC-GAACCTGAGACCTCTAG-GAATAACAACCATTCCTTTAACCATTTGACAA
78137 TGAAAGCCCA
Statistics
Matches: 187, Mismatches: 32, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
82 7 0.04
83 178 0.95
84 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (81 bp):
TTTGGTGTTCGAACCTGAGACCTCTAGGAATAACAACCATTCCTTTAACCATTTGACAACGAATG
TTCAAATACCTAAATC
Found at i:78025 original size:166 final size:166
Alignment explanation
Indices: 77831--78140 Score: 419
Period size: 166 Copynumber: 1.9 Consensus size: 166
77821 TACTAGCATT
* * * *
77831 TGGTGTTCGAACCTGAGACCTTTAGGAATAGCAACCATTCATTTAACCATTTGACAACGAATGTT
1 TGGTGTTCAAACCTGAGACCTCTAGGAATAACAACCATTCATTTAACCATTTGACAACGAATGCT
**
77896 CAAATACAC-TACAATCTTTGGTGT-TCGAACATGAGACCTCT-AGGAATAACAACCATTCCTTA
66 CAAATAC-CTTACAATCACTGGTGTCT-GAACATGAGACCTCTGA-GAATAACAACCATTCCTTA
*
77958 AATCATTTGATAATGAATGTCCAAATACCCTAAAGTCTA
128 AATCATTTGACAATGAATGTCCAAATACCCTAAAGTCTA
* * * * **
77997 TGGTGTTCAAACTTGAGACCTCTAGGAATAACAATCATTCCTTTAACCATTTGGCTGCGAATGCT
1 TGGTGTTCAAACCTGAGACCTCTAGGAATAACAACCATTCATTTAACCATTTGACAACGAATGCT
* * * *
78062 CAAATACCTTAGAGTCACTGGTGTCTGAACCTGAGACCTCTGAGAATAACAACCATTCCTTTAAT
66 CAAATACCTTACAATCACTGGTGTCTGAACATGAGACCTCTGAGAATAACAACCATTCCTTAAAT
78127 CATTTGACAATGAA
131 CATTTGACAATGAA
78141 AGCCCAAACC
Statistics
Matches: 124, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
165 1 0.01
166 121 0.98
167 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (166 bp):
TGGTGTTCAAACCTGAGACCTCTAGGAATAACAACCATTCATTTAACCATTTGACAACGAATGCT
CAAATACCTTACAATCACTGGTGTCTGAACATGAGACCTCTGAGAATAACAACCATTCCTTAAAT
CATTTGACAATGAATGTCCAAATACCCTAAAGTCTA
Done.