Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006999.1 Hibiscus syriacus cultivar Beakdansim tig00018055_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: 83537
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:19705 original size:22 final size:21
Alignment explanation
Indices: 19663--19706 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
19653 TATTAGCCAT
* * *
19663 TAAAAGACCCCACATAGCTGG
1 TAAAAGACCCCAAAAACCTGG
19684 TAAAAGCACCCCAAAAACCTGG
1 TAAAAG-ACCCCAAAAACCTGG
19706 T
1 T
19707 TTGACCCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.41, C:0.30, G:0.16, T:0.14
Consensus pattern (21 bp):
TAAAAGACCCCAAAAACCTGG
Found at i:21609 original size:15 final size:16
Alignment explanation
Indices: 21591--21625 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
21581 GTGGCAGATC
*
21591 AAAATCTAG-ACGGGA
1 AAAATCCAGAACGGGA
21606 AAAATCCAGAACGGGA
1 AAAATCCAGAACGGGA
21622 AAAA
1 AAAA
21626 AAGATTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.54, C:0.14, G:0.23, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:27058 original size:28 final size:28
Alignment explanation
Indices: 27025--27087 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
27015 TCTAAAACCG
* *
27025 ATAAATTACATCATAAACTTCAAAC-CAT
1 ATAAATTACACCATAAACTCCAAACTC-T
* *
27053 ATAAATTATACCATAATCTCCAAACTCT
1 ATAAATTACACCATAAACTCCAAACTCT
27081 ATAAATT
1 ATAAATT
27088 TTTATCTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAAATTACACCATAAACTCCAAACTCT
Found at i:28021 original size:287 final size:285
Alignment explanation
Indices: 27488--28086 Score: 739
Period size: 287 Copynumber: 2.1 Consensus size: 285
27478 GCCCTTAATT
** *
27488 TTTTTTGTAATTTACTCCAAACCCTATAAAGCACATCATAAATTTCATTTTAAACCCTATAGATT
1 TTTTTTGTAATTTACTCCAAACCCTATAAAGCACATCATAAACGTCATTTCAAACCCTATAGATT
* * *
27553 ATATCATAATCTCCAAACCTTATAAACTTTTATTCACAAACTTTAAAAATGAATGAAATTTATCC
66 ATATCATAATCTCCAAACCATATAAAATTTTATTAACAAACTTTAAAAATGAATGAAATTTATCC
* * * * *
27618 AATTTGCTATTAATTTCAGTTTTACATTTACAATTGTTTTAATTTGATCCTCATGTGTTGTTTAA
131 AATTTACTATTAATTTCAGCTTCACATTTACAATTGTTTCAATTTGATCCTCA-GTGTTATTTAA
* * *
27683 ATTATTTAAATTTTAGTTTATAATTTCACATTTGTTCAATTTAGTCCTTAAAAGTCTATTTTTAT
195 ATTATTTAAATTTCAGTTTACAATTTCACATTTGTTCAATTTAGTCCTTAAAAGTATATTTTTAT
* *
27748 CCTAAATTAGCCCATAATTATTTATA
260 CATAAATTAGCACATAATTATTTATA
* *
27774 TTTTTTGTAATTTACTCCAAACCCTATAAATCACATCATAAACGTCATTTCAAACCTTATCA-AT
1 TTTTTTGTAATTTACTCCAAACCCTATAAAGCACATCATAAACGTCATTTCAAACCCTAT-AGAT
* * *** *
27838 TATATCAT-ATC-CCTAAACCATATAAAATTTTGTTAACAAGCTTTTGTAATGAATGCAATTTAA
65 TATATCATAATCTCC-AAACCATATAAAATTTTATTAACAAACTTTAAAAATGAATGAAATTT-A
* * * *
27901 TCCATTTTTATTATTAA-TTCAAGCTTCACATTTTAC-TTTGTTTCAGTTTGATCCCTGC-GTGT
128 TCCA-ATTTACTATTAATTTC-AGCTTCACA-TTTACAATTGTTTCAATTTGAT-CCT-CAGTGT
* * ** *
27963 TATTTAATTTATTTAAATTTCAGTTTGCAATTTCATGTTT-TCTCAATTTAGTCCTTAAAATTAT
188 TATTTAAATTATTTAAATTTCAGTTTACAATTTCACATTTGT-TCAATTTAGTCCTTAAAAGTAT
*
28027 ATTTTTATCATAAATTAGCACATAATTATTTCTA
252 ATTTTTATCATAAATTAGCACATAATTATTTATA
28061 -TTTTT-TAATTTACTCCAAACCCTATA
1 TTTTTTGTAATTTACTCCAAACCCTATA
28087 CAATTACAAT
Statistics
Matches: 270, Mismatches: 34, Indels: 19
0.84 0.11 0.06
Matches are distributed among these distances:
284 2 0.01
285 62 0.23
286 79 0.29
287 118 0.44
288 8 0.03
289 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (285 bp):
TTTTTTGTAATTTACTCCAAACCCTATAAAGCACATCATAAACGTCATTTCAAACCCTATAGATT
ATATCATAATCTCCAAACCATATAAAATTTTATTAACAAACTTTAAAAATGAATGAAATTTATCC
AATTTACTATTAATTTCAGCTTCACATTTACAATTGTTTCAATTTGATCCTCAGTGTTATTTAAA
TTATTTAAATTTCAGTTTACAATTTCACATTTGTTCAATTTAGTCCTTAAAAGTATATTTTTATC
ATAAATTAGCACATAATTATTTATA
Found at i:28974 original size:3 final size:3
Alignment explanation
Indices: 28956--28996 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
28946 TAACCAGGAA
*
28956 ATT ATT -TT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28997 CGATAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:29576 original size:13 final size:12
Alignment explanation
Indices: 29533--29598 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 12
29523 ACTTTCTATA
*
29533 TTAATTATAATCC
1 TTAATTATAAT-T
29546 TTATATTATAACTT
1 TTA-ATTATAA-TT
29560 TTAATTATAATT
1 TTAATTATAATT
29572 ATTAAATTA-AATT
1 -TT-AATTATAATT
*
29585 TTATTATATAATT
1 TTAAT-TATAATT
29598 T
1 T
29599 AGTTATTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
11 2 0.04
12 6 0.13
13 21 0.47
14 15 0.33
15 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAATTATAATT
Found at i:29580 original size:27 final size:25
Alignment explanation
Indices: 29533--29592 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 25
29523 ACTTTCTATA
* *
29533 TTAATTATAATCCTTATATTATAACTT
1 TTAATTATAATCATTAAATTA-AA-TT
*
29560 TTAATTATAATTATTAAATTAAATT
1 TTAATTATAATCATTAAATTAAATT
29585 TT-ATTATA
1 TTAATTATA
29593 TAATTTAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.20
25 4 0.13
26 2 0.07
27 18 0.60
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (25 bp):
TTAATTATAATCATTAAATTAAATT
Found at i:29720 original size:2 final size:2
Alignment explanation
Indices: 29713--29759 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
29703 TAAAATTTTA
29713 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
29755 A- AT AT
1 AT AT AT
29760 GAATTTATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30043 original size:34 final size:33
Alignment explanation
Indices: 29977--30056 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 33
29967 CTCCAGGGTG
*
29977 TGTATAATGTATAATGTATGCAAAATTCATTAA
1 TGTATAATGTATAATGTATGCAAAATTAATTAA
* ** *
30010 TGTATAATGTATGTATGTATTTATAATTAATTAA
1 TGTATAATGTAT-AATGTATGCAAAATTAATTAA
*
30044 CGTATAATGTATA
1 TGTATAATGTATA
30057 TTATGAATTG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 12 0.31
34 27 0.69
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (33 bp):
TGTATAATGTATAATGTATGCAAAATTAATTAA
Found at i:30099 original size:37 final size:36
Alignment explanation
Indices: 30007--30215 Score: 122
Period size: 34 Copynumber: 6.0 Consensus size: 36
29997 CAAAATTCAT
* * *
30007 TAATGTATAATGTATGTATGTATTTATAAT-TA-AT-
1 TAATGTATAATGTATGTATGAATTGAT-ATGTATGTA
* *
30041 TAACGTATAATGTATATTATGAATTGATATGTATGTA
1 TAATGTATAATGTAT-GTATGAATTGATATGTATGTA
* *
30078 TAATGTATAATGATATGTATGAATTGATGTTTATGTA
1 TAATGTATAATG-TATGTATGAATTGATATGTATGTA
*
30115 -AA-GTGT-ATGTATGTAT-AA-TG-TATGTATGTA
1 TAATGTATAATGTATGTATGAATTGATATGTATGTA
* * * * *
30145 TAGTGTATGTATCTAT-AATGTA-TG-TATGTATG-A
1 TAATGTAT-AATGTATGTATGAATTGATATGTATGTA
* *
30178 TAATGATATGCATGTATGTATGATATTGA-ACGTATGTA
1 TAATG-TAT-AATGTATGTATGA-ATTGATATGTATGTA
30216 CATATGATAA
Statistics
Matches: 136, Mismatches: 23, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
30 8 0.06
31 3 0.02
32 5 0.04
33 14 0.10
34 44 0.32
35 17 0.12
36 4 0.03
37 37 0.27
38 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (36 bp):
TAATGTATAATGTATGTATGAATTGATATGTATGTA
Found at i:30127 original size:4 final size:4
Alignment explanation
Indices: 30118--30199 Score: 64
Period size: 4 Copynumber: 20.5 Consensus size: 4
30108 TTATGTAAAG
* * *
30118 TGTA TGTA TGTA T-AA TGTA TGTA TGTA --TA GTGTA TGTA TCTA T-AA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -TGTA TGTA TGTA TGTA
*
30163 TGTA TGTA TGTA TGATAA TGATA TGCA TGTA TGTA TG
1 TGTA TGTA TGTA TG-T-A TG-TA TGTA TGTA TGTA TG
30200 ATATTGAACG
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
2 2 0.03
3 4 0.06
4 47 0.73
5 6 0.09
6 5 0.08
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.45
Consensus pattern (4 bp):
TGTA
Found at i:30129 original size:15 final size:15
Alignment explanation
Indices: 30080--30175 Score: 108
Period size: 15 Copynumber: 6.4 Consensus size: 15
30070 TGTATGTATA
30080 ATGTATAATGATATGT
1 ATGTATAATG-TATGT
* *
30096 ATGAATTGATGT-T-T
1 ATGTA-TAATGTATGT
30110 ATGTA-AAGTGTATGT
1 ATGTATAA-TGTATGT
30125 ATGTATAATGTATGT
1 ATGTATAATGTATGT
*
30140 ATGTATAGTGTATGT
1 ATGTATAATGTATGT
*
30155 ATCTATAATGTATGT
1 ATGTATAATGTATGT
30170 ATGTAT
1 ATGTAT
30176 GATAATGATA
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
12 1 0.01
13 3 0.04
14 6 0.09
15 46 0.69
16 7 0.10
17 4 0.06
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (15 bp):
ATGTATAATGTATGT
Found at i:30135 original size:11 final size:10
Alignment explanation
Indices: 30067--30171 Score: 56
Period size: 11 Copynumber: 10.2 Consensus size: 10
30057 TTATGAATTG
30067 ATATGTATGT
1 ATATGTATGT
*
30077 ATAATGTATAAT
1 AT-ATGTAT-GT
*
30089 GATATGTATGA
1 -ATATGTATGT
30100 AT-TG-ATGT
1 ATATGTATGT
* *
30108 TTATGTAAAGT
1 ATATGT-ATGT
*
30119 GTATGTATGT
1 ATATGTATGT
30129 ATAATGTATG-
1 AT-ATGTATGT
30139 -TATGTATAGT
1 ATATGTAT-GT
* *
30149 GTATGTATCT
1 ATATGTATGT
30159 ATAATGTATGT
1 AT-ATGTATGT
30170 AT
1 AT
30172 GTATGATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
8 10 0.14
9 6 0.08
10 10 0.14
11 37 0.51
12 7 0.10
13 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (10 bp):
ATATGTATGT
Found at i:30187 original size:15 final size:15
Alignment explanation
Indices: 30084--30187 Score: 56
Period size: 15 Copynumber: 6.7 Consensus size: 15
30074 TGTATAATGT
30084 ATAATGATATGTATG
1 ATAATGATATGTATG
* * *
30099 A-ATTGATGTTTATG
1 ATAATGATATGTATG
30113 -TAAAGTG-TATGTATG
1 AT-AA-TGATATGTATG
30128 TATAATG-TATGTATG
1 -ATAATGATATGTATG
* *
30143 TATAGTG-TATGTATCT
1 -ATAATGATATGTAT-G
30159 ATAATGTATGTATGTATG
1 ATAATG-A--TATGTATG
30177 ATAATGATATG
1 ATAATGATATG
30188 CATGTATGTA
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
14 10 0.14
15 40 0.58
16 4 0.06
17 2 0.03
18 6 0.09
19 7 0.10
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.44
Consensus pattern (15 bp):
ATAATGATATGTATG
Found at i:30362 original size:2 final size:2
Alignment explanation
Indices: 30317--30349 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30307 ATACTTTATT
30317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30350 GGACAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30395 original size:16 final size:16
Alignment explanation
Indices: 30374--30405 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
30364 TATACTTTAT
30374 ATATATAAGTATATAC
1 ATATATAAGTATATAC
30390 ATATATAAGTATATAC
1 ATATATAAGTATATAC
30406 TTATTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
ATATATAAGTATATAC
Found at i:30629 original size:2 final size:2
Alignment explanation
Indices: 30622--30665 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
30612 CATTCGTCGC
30622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30663 AT A
1 AT A
30666 ATTGTTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30639 original size:151 final size:153
Alignment explanation
Indices: 30383--30663 Score: 340
Period size: 151 Copynumber: 1.8 Consensus size: 153
30373 TATATATAAG
* * * *
30383 TATATACATATATAAGTATATACTTATTTATAATTTATGCATAAGTATAATGTACATAATATATA
1 TATATACATATATAAGTATATACCTATTTATAATGTAGGCATAAGCATAATGTACATAATATATA
* ** *
30448 CATGCATCGTATTATCATAACATTCATCGTGCATATTATATATATACATATATAT-TATA-ATTA
66 CATGCATCATAACATCATAACATTCATCAT-CATATTATATATATACATATATATATATATATTA
30511 AGTACAATGTACAAAATATACTTT
130 AGTACAATGTACAAAATATACTTT
* * *
30535 TATATATATA-ATAAGTATATACCTATTTATAATGTAGGCATTAGCATAATGTACATTATATATA
1 TATATACATATATAAGTATATACCTATTTATAATGTAGGCATAAGCATAATGTACATAATATATA
* ** *
30599 CATGCATCAATAACATTCGTCGCATAT-AT-AT-ATATATATATATATATATATATATATATATA
66 CATGCATC-ATAACA-TCATAACAT-TCATCATCATAT-TATATATATACATATATATATATATA
30661 TTA
127 TTA
30664 TAATTGTTTT
Statistics
Matches: 108, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
150 4 0.04
151 74 0.69
152 17 0.16
153 12 0.11
154 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (153 bp):
TATATACATATATAAGTATATACCTATTTATAATGTAGGCATAAGCATAATGTACATAATATATA
CATGCATCATAACATCATAACATTCATCATCATATTATATATATACATATATATATATATATTAA
GTACAATGTACAAAATATACTTT
Found at i:33370 original size:30 final size:30
Alignment explanation
Indices: 33305--33498 Score: 194
Period size: 30 Copynumber: 6.4 Consensus size: 30
33295 ACTCAGTGAT
* * * *
33305 TTAAGGGACTAAAATAGCAAAAAACAGGAAC
1 TTAAAGGACTAAAATAAC-AAAAATAGAAAC
* *
33336 TTAAAGGACTAAAATAATAAAAATAGAAAT
1 TTAAAGGACTAAAATAACAAAAATAGAAAC
*
33366 TTAAAGGACCAAAATAACAAAAATAGAAAC
1 TTAAAGGACTAAAATAACAAAAATAGAAAC
* * * *
33396 TTAAAAGATTAAAATAGCAAAAATAGGAA-
1 TTAAAGGACTAAAATAACAAAAATAGAAAC
* * *
33425 TATAAAAGACCAAAATAACAAAAA-CGAAAAC
1 T-TAAAGGACTAAAATAACAAAAATAG-AAAC
* * *
33456 TCAAAGGACTAAAATAGCAAAAATAGAAAG
1 TTAAAGGACTAAAATAACAAAAATAGAAAC
33486 TTAAAGGACTAAA
1 TTAAAGGACTAAA
33499 TTGGTATTAA
Statistics
Matches: 133, Mismatches: 26, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
29 2 0.02
30 114 0.86
31 17 0.13
ACGTcount: A:0.61, C:0.10, G:0.13, T:0.16
Consensus pattern (30 bp):
TTAAAGGACTAAAATAACAAAAATAGAAAC
Found at i:33409 original size:60 final size:59
Alignment explanation
Indices: 33303--33494 Score: 222
Period size: 60 Copynumber: 3.2 Consensus size: 59
33293 TCACTCAGTG
* * * * **
33303 ATTTAAGGGACTAAAATAGCAAAAAACAGGAACTTAAAGGACTAAAATAATAAAAATAGAA
1 ATTTAAAGGACCAAAATAAC-AAAAA-AGAAACTTAAAGGACTAAAATAGCAAAAATAGAA
* * *
33364 ATTTAAAGGACCAAAATAACAAAAATAGAAACTTAAAAGATTAAAATAGCAAAAATAGGA
1 ATTTAAAGGACCAAAATAACAAAAA-AGAAACTTAAAGGACTAAAATAGCAAAAATAGAA
* * * *
33424 ATATAAAAGACCAAAATAACAAAAACGAAAACTCAAAGGACTAAAATAGCAAAAATAGAA
1 ATTTAAAGGACCAAAATAACAAAAAAG-AAACTTAAAGGACTAAAATAGCAAAAATAGAA
*
33484 AGTTAAAGGAC
1 ATTTAAAGGAC
33495 TAAATTGGTA
Statistics
Matches: 110, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
59 1 0.01
60 92 0.84
61 17 0.15
ACGTcount: A:0.61, C:0.10, G:0.13, T:0.16
Consensus pattern (59 bp):
ATTTAAAGGACCAAAATAACAAAAAAGAAACTTAAAGGACTAAAATAGCAAAAATAGAA
Found at i:33440 original size:90 final size:91
Alignment explanation
Indices: 33314--33490 Score: 225
Period size: 90 Copynumber: 2.0 Consensus size: 91
33304 TTTAAGGGAC
* * * * *
33314 TAAAATAGCAAAAAACAGGAACTTAAAGGACTAAAATAATAAAAATAG-AAATTTAAAGGACCAA
1 TAAAATAGCAAAAAACAGGAACTTAAAAGACCAAAATAACAAAAA-AGAAAACTCAAAGGACCAA
33378 AATAACAAAAATAGAAACTTAAAAGAT
65 AATAACAAAAATAGAAACTTAAAAGAT
* * *
33405 TAAAATAGC-AAAAATAGGAA-TATAAAAGACCAAAATAACAAAAACGAAAACTCAAAGGACTAA
1 TAAAATAGCAAAAAACAGGAACT-TAAAAGACCAAAATAACAAAAAAGAAAACTCAAAGGACCAA
* *
33468 AATAGCAAAAATAGAAAGTTAAA
65 AATAACAAAAATAGAAACTTAAA
33491 GGACTAAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
89 2 0.03
90 63 0.85
91 9 0.12
ACGTcount: A:0.63, C:0.10, G:0.11, T:0.16
Consensus pattern (91 bp):
TAAAATAGCAAAAAACAGGAACTTAAAAGACCAAAATAACAAAAAAGAAAACTCAAAGGACCAAA
ATAACAAAAATAGAAACTTAAAAGAT
Found at i:34962 original size:3 final size:3
Alignment explanation
Indices: 34954--34993 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
34944 AAAATAACAT
*
34954 TAA TAA TAA TAAA TAA TAA TAA TAA TAA TCA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34994 ATATAATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:34969 original size:19 final size:19
Alignment explanation
Indices: 34945--34982 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
34935 AATGTAAACA
*
34945 AAATAACATTAATAATAAT
1 AAATAACAATAATAATAAT
*
34964 AAATAATAATAATAATAAT
1 AAATAACAATAATAATAAT
34983 CATAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATAACAATAATAATAAT
Found at i:34999 original size:9 final size:10
Alignment explanation
Indices: 34955--35001 Score: 64
Period size: 9 Copynumber: 5.0 Consensus size: 10
34945 AAATAACATT
34955 AATAATAATA
1 AATAATAATA
34965 AATAATAAT-
1 AATAATAATA
34974 AATAATAAT-
1 AATAATAATA
*
34983 CATAATAATA
1 AATAATAATA
34993 AAT-ATAATA
1 AATAATAATA
35002 TTTTTTGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 23 0.68
10 11 0.32
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (10 bp):
AATAATAATA
Found at i:35153 original size:22 final size:20
Alignment explanation
Indices: 35058--35154 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
35048 CATTTTACTC
*
35058 AAATATAAATTCATAATAAT
1 AAATATAAATTTATAATAAT
* **
35078 ATATATGTA-TTATAAT--T
1 AAATATAAATTTATAATAAT
35095 AAATATAAATTTAT-A-AAT
1 AAATATAAATTTATAATAAT
*
35113 AAATAT--ATTTATATTTAAT
1 AAATATAAATTTATA-ATAAT
35132 CAAATATAAATTTATAAATAAT
1 -AAATATAAATTTAT-AATAAT
35154 A
1 A
35155 TATTATTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 19
0.67 0.10 0.22
Matches are distributed among these distances:
16 6 0.10
17 8 0.14
18 11 0.19
19 9 0.16
20 12 0.21
21 1 0.02
22 10 0.17
23 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (20 bp):
AAATATAAATTTATAATAAT
Found at i:35165 original size:37 final size:38
Alignment explanation
Indices: 35051--35180 Score: 153
Period size: 38 Copynumber: 3.4 Consensus size: 38
35041 AATACTGCAT
* * *
35051 TTTACTCAAATATAAATTCAT-AATAATATA-TATGTA
1 TTTAATCAAATATAAATTTATAAATAATATATTATATA
*
35087 TTATAATTAAATATAAATTTATAAATAAATATATT-TATA
1 TT-TAATCAAATATAAATTTATAAAT-AATATATTATATA
35126 TTTAATCAAATATAAATTTATAAATAATATATTAT-TA
1 TTTAATCAAATATAAATTTATAAATAATATATTATATA
35163 TTTCAAT-AGAATATAAAT
1 TTT-AATCA-AATATAAAT
35181 CCATAAGTAA
Statistics
Matches: 82, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
36 2 0.02
37 30 0.37
38 38 0.46
39 11 0.13
40 1 0.01
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (38 bp):
TTTAATCAAATATAAATTTATAAATAATATATTATATA
Found at i:35196 original size:38 final size:38
Alignment explanation
Indices: 35134--35218 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
35124 TATTTAATCA
** * *
35134 AATATAAATTTATAAATAATATATT-ATTATTTCAATAG
1 AATATAAATCCATAAATAACATATTCA-AATTTCAATAG
*
35172 AATATAAATCCATAAGTAACATATTCAAATTTCAATAG
1 AATATAAATCCATAAATAACATATTCAAATTTCAATAG
35210 AATATAAAT
1 AATATAAAT
35219 ATTCTCCCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
38 40 0.98
39 1 0.02
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.38
Consensus pattern (38 bp):
AATATAAATCCATAAATAACATATTCAAATTTCAATAG
Found at i:35214 original size:76 final size:75
Alignment explanation
Indices: 35051--35218 Score: 175
Period size: 76 Copynumber: 2.2 Consensus size: 75
35041 AATACTGCAT
* **
35051 TTTACTCAAATATAAATTCATAATAATATATATGTATTATAATTAAATATAAATTTATAAATAAA
1 TTTAATCAAATATAAATTCATAATAATATATATGTATTATAATTAAATATAAATCCATAAATAAA
* * *
35116 TATATTTATA
66 CATATTCAAA
* *
35126 TTTAATCAAATATAAATTTATAAATAATATATTAT-TATT-TCAA-TAGAATATAAATCCATAAG
1 TTTAATCAAATATAAATTCAT-AATAATATA-TATGTATTAT-AATTA-AATATAAATCCATAAA
35188 T-AACATATTCAAA
62 TAAACATATTCAAA
35201 TTTCAAT-AGAATATAAAT
1 TTT-AATCA-AATATAAAT
35219 ATTCTCCCTA
Statistics
Matches: 79, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
75 35 0.44
76 41 0.52
77 3 0.04
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (75 bp):
TTTAATCAAATATAAATTCATAATAATATATATGTATTATAATTAAATATAAATCCATAAATAAA
CATATTCAAA
Found at i:41060 original size:14 final size:15
Alignment explanation
Indices: 41036--41064 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41026 AACTTAAGCG
41036 TCTTCTTCTTTTTTT
1 TCTTCTTCTTTTTTT
41051 TCTT-TTCTTTTTTT
1 TCTTCTTCTTTTTTT
41065 AATTTCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TCTTCTTCTTTTTTT
Found at i:46477 original size:38 final size:38
Alignment explanation
Indices: 46435--46519 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
46425 AGATAGACAA
* * *
46435 TTAGGATTATTAGTTATTTTTAGGGTTTAAATCTAAGG
1 TTAGGATTATAAGTAATCTTTAGGGTTTAAATCTAAGG
*
46473 TTAGGATTATAAGTAATCTTTAGGGTTTACATCTAAGG
1 TTAGGATTATAAGTAATCTTTAGGGTTTAAATCTAAGG
*
46511 CTAGGATTA
1 TTAGGATTA
46520 GAACTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (38 bp):
TTAGGATTATAAGTAATCTTTAGGGTTTAAATCTAAGG
Found at i:47678 original size:31 final size:31
Alignment explanation
Indices: 47643--47704 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
47633 CAGAACGTGT
47643 GCATGTCAATATCATTAGGACAGAGAGACTA
1 GCATGTCAATATCATTAGGACAGAGAGACTA
* *
47674 GCATGTTAATATCATTAGGACAGAGGGACTA
1 GCATGTCAATATCATTAGGACAGAGAGACTA
47705 TCAACTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (31 bp):
GCATGTCAATATCATTAGGACAGAGAGACTA
Found at i:48833 original size:11 final size:11
Alignment explanation
Indices: 48811--48848 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
48801 GTAACAGTTC
48811 AATAA-AATTT
1 AATAATAATTT
*
48821 AATAATTATTT
1 AATAATAATTT
48832 AATAATAATTT
1 AATAATAATTT
48843 AATAAT
1 AATAAT
48849 CATGAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AATAATAATTT
Found at i:54245 original size:20 final size:20
Alignment explanation
Indices: 54220--54258 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
54210 TACTAGTTTT
54220 TTTTTTTTTC-TTTCTCTGTA
1 TTTTTTTTTCGTTT-TCTGTA
54240 TTTTTTTTTCGTTTTCTGT
1 TTTTTTTTTCGTTTTCTGT
54259 TTCTGTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.03, C:0.13, G:0.08, T:0.77
Consensus pattern (20 bp):
TTTTTTTTTCGTTTTCTGTA
Found at i:54254 original size:26 final size:24
Alignment explanation
Indices: 54216--54264 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
54206 TTGGTACTAG
54216 TTTTTTTTTTTTTCT-TTCTCTGTA
1 TTTTTTTTTTTTTCTGTT-TCTGTA
54240 TTTTTTTTTCGTTTTCTGTTTCTGT
1 TTTTTTTTT--TTTTCTGTTTCTGT
54265 CTCTTCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.41
26 11 0.50
27 2 0.09
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.78
Consensus pattern (24 bp):
TTTTTTTTTTTTTCTGTTTCTGTA
Found at i:54760 original size:3 final size:3
Alignment explanation
Indices: 54752--54830 Score: 106
Period size: 3 Copynumber: 26.7 Consensus size: 3
54742 TTAATATATT
* * *
54752 TAA TAA TAA TAG TAA -AA AAA TAA TAA TAA TAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
54799 TAA TAT TAA TTA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
54831 TGGATAAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55349 original size:113 final size:113
Alignment explanation
Indices: 55121--55788 Score: 1086
Period size: 113 Copynumber: 5.9 Consensus size: 113
55111 AGATAATATC
* * *
55121 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTT
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
55185 TCATTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATT-ATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*
55234 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
55299 TCATTACGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
* *
55347 AAACAAAAAGTTGAACAAGTTCTTCTTATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
55412 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
55460 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * * * *
55525 TCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTC
66 TCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*** * *
55573 AGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
55638 TCATTATGAACTTTCTCTGGTAATGTTGATCCACCAAATGATGAATTT
66 TCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
*
55686 AAACAAAAAGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
55751 TCATTATGAACTTTCTCTGGCAATGAATGATCCATCAA
66 TCATTATGAACTTTCTCTGGTAATG-TTGATCCATCAA
55789 GTGGATTTGA
Statistics
Matches: 516, Mismatches: 37, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
113 445 0.86
114 71 0.14
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
Found at i:56669 original size:83 final size:83
Alignment explanation
Indices: 56419--57024 Score: 1002
Period size: 83 Copynumber: 7.3 Consensus size: 83
56409 ACTATGAGCC
* * *
56419 AATTTATCTTCCAAATTCAATGATTG-TTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
56483 CAGAAGATGCTATTGGCA
66 CAGAAGATGCTATTGGCA
* * * * *
56501 AATTCATCTTCTAAATTCGATGATTG-TTCTG-CTAAACCAGGTCAGATAACTCAAAGAACACTT
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTC-CAATCAGATCAGATAACTCAAAGAACACTT
56564 CCAGAAGATGCTATTGGCA
65 CCAGAAGATGCTATTGGCA
* * * * *
56583 AATTCATCTTCCAAATTCAATGCTTGGTTCTGTCAAACCAGGTCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
*
56648 CAGAAGATGCTATTGGTA
66 CAGAAGATGCTATTGGCA
*
56666 AATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
56731 CAGAAGATGCTATTGGCA
66 CAGAAGATGCTATTGGCA
*
56749 AATTCATCTTCCAAATTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
56814 CAGAAGATGCTATTGGCA
66 CAGAAGATGCTATTGGCA
* *
56832 AATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCATATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
56897 CAGAAGATGCTATTGGCA
66 CAGAAGATGCTATTGGCA
*
56915 AATTCATCTTCTAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
1 AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
56980 CAGAAGATGCTATTGGCA
66 CAGAAGATGCTATTGGCA
*
56998 AATTCATCTTCCAAATTCAATGCTTGA
1 AATTCATCTTCCAAATTCAATGATTGA
57025 ACTGGGATAT
Statistics
Matches: 496, Mismatches: 25, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
81 1 0.00
82 97 0.20
83 397 0.80
84 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.30
Consensus pattern (83 bp):
AATTCATCTTCCAAATTCAATGATTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
CAGAAGATGCTATTGGCA
Found at i:57781 original size:19 final size:16
Alignment explanation
Indices: 57759--57804 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 16
57749 AATAGAAAAG
57759 AATAAATTGAATTTCCAAA
1 AATAAATTGAATTT-C--A
*
57778 AATAAATTGACTTTCA
1 AATAAATTGAATTTCA
57794 AATAAATTGAA
1 AATAAATTGAA
57805 CTTGAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.44
18 1 0.04
19 13 0.52
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (16 bp):
AATAAATTGAATTTCA
Found at i:58166 original size:18 final size:19
Alignment explanation
Indices: 58140--58176 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
58130 TTTCTTTTTC
*
58140 TTCTCTTTTTTTTT-TATT
1 TTCTATTTTTTTTTCTATT
58158 TTCTATTTTTTTTTCTATT
1 TTCTATTTTTTTTTCTATT
58177 CTCTTCAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (19 bp):
TTCTATTTTTTTTTCTATT
Found at i:68782 original size:13 final size:15
Alignment explanation
Indices: 68760--68796 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
68750 TTTGACATAA
68760 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
68772 AAATAAAATACTTGC
1 AAATAAAATACTTGC
68787 AAATAAAATA
1 AAATAAAATA
68797 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:68835 original size:18 final size:17
Alignment explanation
Indices: 68787--68837 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
68777 AAATACTTGC
*
68787 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
68805 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
68823 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
68838 TGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:70988 original size:3 final size:3
Alignment explanation
Indices: 70971--71092 Score: 116
Period size: 3 Copynumber: 42.3 Consensus size: 3
70961 GATTAATATT
*
70971 TAA TAA TAG TAAA TAA TAA TAA TAA -AA TAA TAA TAA TAA -AA -AA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
71014 TAA TAA -AT TAA TAA TAA TAA TAA -AA TAA TAA TGA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
71060 T-A TAA TAA GGTAA TAA T-A TAT TAA TAA -AA TAA T
1 TAA TAA TAA --TAA TAA TAA TAA TAA TAA TAA TAA T
71093 GGATAAAAAA
Statistics
Matches: 99, Mismatches: 10, Indels: 20
0.77 0.08 0.16
Matches are distributed among these distances:
2 15 0.15
3 79 0.80
4 2 0.02
5 3 0.03
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:71000 original size:14 final size:14
Alignment explanation
Indices: 70971--71091 Score: 110
Period size: 14 Copynumber: 8.9 Consensus size: 14
70961 GATTAATATT
*
70971 TAATAATAGT-AAA
1 TAATAATAATAAAA
70984 TAATAATAATAAAA
1 TAATAATAATAAAA
70998 TAATAATAATAAAA
1 TAATAATAATAAAA
*
71012 -AATAATAA-ATTAA
1 TAATAATAATA-AAA
71025 TAATAATAATAAAA
1 TAATAATAATAAAA
*
71039 TAATAATGAT--AA
1 TAATAATAATAAAA
* *
71051 TAATATTAATATAA
1 TAATAATAATAAAA
* *
71065 TAAGGTAATAATATAT
1 TAA--TAATAATAAAA
71081 TAATAA-AATAA
1 TAATAATAATAA
71092 TGGATAAAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
12 11 0.12
13 23 0.25
14 44 0.48
15 1 0.01
16 12 0.13
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:71000 original size:24 final size:23
Alignment explanation
Indices: 70973--71092 Score: 118
Period size: 23 Copynumber: 5.0 Consensus size: 23
70963 TTAATATTTA
*
70973 ATAATAGTAAATAATAATAATAA-A
1 ATAATAAT-AATAATAA-AATAATA
70997 ATAATAATAATAA-AAAATAATAA
1 ATAATAATAATAATAAAATAAT-A
71020 ATTAATAATAATAATAAAATAATA
1 A-TAATAATAATAATAAAATAATA
* * *
71044 ATGATAATAATATTAATATAATA
1 ATAATAATAATAATAAAATAATA
71067 AGGTAATAATATATTAATAAAATAAT
1 A--TAATAATA-A-TAATAAAATAAT
71093 GGATAAAAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
21 5 0.06
22 2 0.02
23 27 0.33
24 21 0.26
25 15 0.19
26 1 0.01
27 10 0.12
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (23 bp):
ATAATAATAATAATAAAATAATA
Found at i:71001 original size:11 final size:11
Alignment explanation
Indices: 70982--71092 Score: 82
Period size: 11 Copynumber: 9.3 Consensus size: 11
70972 AATAATAGTA
70982 AATAATAATAAT
1 AATAATAA-AAT
70994 AA-AATAATAAT
1 AATAATAA-AAT
71005 AATAA-AAAAT
1 AATAATAAAAT
71015 AATAAATTAATAAT
1 AAT-AA-TAA-AAT
71029 AATAATAAAAT
1 AATAATAAAAT
*
71040 AATAATGATAAT
1 AATAAT-AAAAT
* *
71052 AATATTAATAT
1 AATAATAAAAT
71063 AATAAGGTAATAAT
1 AATAA--TAA-AAT
71077 ATATTAATAAAAT
1 A-A-TAATAAAAT
71090 AAT
1 AAT
71093 GGATAAAAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
10 6 0.07
11 32 0.39
12 17 0.21
13 11 0.13
14 12 0.15
15 1 0.01
16 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:73412 original size:2 final size:2
Alignment explanation
Indices: 73405--73440 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
73395 AATAATTTTG
73405 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
73441 GCAACATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73760 original size:20 final size:21
Alignment explanation
Indices: 73735--73786 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
73725 TTTTCCCAAT
*
73735 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
73755 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
73776 TCGCAATGCGA
1 TCGCAATGCGA
73787 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:73800 original size:20 final size:20
Alignment explanation
Indices: 73775--73888 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
73765 AATTGGGAAA
*
73775 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
73795 ATCGCAATGCAATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
73815 ATCGCAATGCAATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
73836 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
73856 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
73876 TTCGCAACGCGAT
1 ATCGCAACGCGAT
73889 TTACTTAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:73819 original size:61 final size:61
Alignment explanation
Indices: 73754--73887 Score: 137
Period size: 61 Copynumber: 2.2 Consensus size: 61
73744 GAATAAGTAA
** * * * *
73754 ATCGCAACGCGAAT-TGGGAAAATCGCAATGCGATACTGACTATCGCAATGCAATACTTACT
1 ATCGCAACGCGAATAT-ACAAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACT
* * * *
73815 ATCGCAATGC-AATAATACAAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGAAT-ATACAAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACT
*
73876 TTCGCAACGCGA
1 ATCGCAACGCGA
73888 TTTACTTAGC
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
60 3 0.05
61 53 0.91
62 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (61 bp):
ATCGCAACGCGAATATACAAAATCGCAACGAGATACTGACTATCGCAACGCAATACTGACT
Found at i:74459 original size:18 final size:19
Alignment explanation
Indices: 74380--74459 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
74370 TTCGAGAATG
74380 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
74400 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
74416 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* *
74433 AAAAACGCAACGCGAAA-C
1 AAAATCGCAACGCGAAATA
74451 AAAATCGCA
1 AAAATCGCA
74460 TTGCGAATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
14 7 0.15
16 5 0.11
17 4 0.09
18 9 0.19
19 14 0.30
20 8 0.17
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:74482 original size:19 final size:20
Alignment explanation
Indices: 74455--74541 Score: 112
Period size: 18 Copynumber: 4.5 Consensus size: 20
74445 CGAAACAAAA
*
74455 TCGCATTGCGAATTTT-ATT
1 TCGCGTTGCGAATTTTCATT
74474 TCGCGTTGCG-ATTTTCA-T
1 TCGCGTTGCGAATTTTCATT
*
74492 TCGCGTTGCG-ATTTTTATT
1 TCGCGTTGCGAATTTTCATT
74511 TCGCGGTTGCG-ATTTTCATT
1 TCGC-GTTGCGAATTTTCATT
74531 TCGCGTTGCGA
1 TCGCGTTGCGA
74542 TTGTCTGGTC
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
18 22 0.36
19 21 0.34
20 18 0.30
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTTCATT
Found at i:74501 original size:37 final size:39
Alignment explanation
Indices: 74455--74541 Score: 142
Period size: 37 Copynumber: 2.3 Consensus size: 39
74445 CGAAACAAAA
*
74455 TCGCATTGCGAATTTTATTTCGC-GTTGCGATTTTCA-T
1 TCGCGTTGCGAATTTTATTTCGCGGTTGCGATTTTCATT
*
74492 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGAATTTTATTTCGCGGTTGCGATTTTCATT
74531 TCGCGTTGCGA
1 TCGCGTTGCGA
74542 TTGTCTGGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 21 0.46
38 13 0.28
39 12 0.26
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.45
Consensus pattern (39 bp):
TCGCGTTGCGAATTTTATTTCGCGGTTGCGATTTTCATT
Found at i:74542 original size:19 final size:19
Alignment explanation
Indices: 74455--74637 Score: 131
Period size: 20 Copynumber: 10.1 Consensus size: 19
74445 CGAAACAAAA
*
74455 TCGCATTGCGAATTTT-ATT
1 TCGCGTTGCG-ATTTTCATT
74474 TCGCGTTGCGATTTTCA-T
1 TCGCGTTGCGATTTTCATT
*
74492 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
74511 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
74531 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
74547 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
74564 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
74578 CCTCG-TGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
74596 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
74616 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
74636 TC
1 TC
74638 AACCAAAAGA
Statistics
Matches: 131, Mismatches: 17, Indels: 32
0.73 0.09 0.18
Matches are distributed among these distances:
13 5 0.04
14 13 0.10
15 3 0.02
16 1 0.01
17 3 0.02
18 23 0.18
19 37 0.28
20 45 0.34
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:74554 original size:39 final size:38
Alignment explanation
Indices: 74474--74554 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 38
74464 GAATTTTATT
* **
74474 TCGC-GTTGCGATTTTCATTCGCGTTGCGATTTTTATT
1 TCGCGGTTGCGATTTTCATTCGCGTTGCGATTTCTAGG
74511 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTGTCT-GG
1 TCGCGGTTGCGATTTTCA-TTCGCGTTGCGATT-TCTAGG
74550 TCGCG
1 TCGCG
74555 ATAGTCATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 4 0.11
38 13 0.34
39 19 0.50
40 2 0.05
ACGTcount: A:0.09, C:0.21, G:0.27, T:0.43
Consensus pattern (38 bp):
TCGCGGTTGCGATTTTCATTCGCGTTGCGATTTCTAGG
Found at i:74563 original size:33 final size:32
Alignment explanation
Indices: 74526--74610 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 32
74516 GTTGCGATTT
** *
74526 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCCCTCGT-GCGATAG
74559 TCATTTCGCGTTGCGATTCCCTCGTGCGATAG
1 TCATTTCGCGTTGCGATTCCCTCGTGCGATAG
74591 TCATTTCCGCGTTGCGATTC
1 TCATTT-CGCGTTGCGATTC
74611 TCATTATCTC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
32 13 0.27
33 35 0.73
ACGTcount: A:0.12, C:0.26, G:0.26, T:0.36
Consensus pattern (32 bp):
TCATTTCGCGTTGCGATTCCCTCGTGCGATAG
Found at i:75207 original size:14 final size:14
Alignment explanation
Indices: 75188--75223 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
75178 ATTGTTTAAT
75188 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
75202 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
75216 TGATTTGT
1 TGATTTGT
75224 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:75428 original size:19 final size:19
Alignment explanation
Indices: 75400--75528 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
75390 ACGAAATTAA
*
75400 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
75419 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
* *
75435 CTCG--TTGCAATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
75452 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
75466 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
75485 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
75500 -TCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
75516 TTCGCATTGCGAT
1 TTCGCATTGCGAT
75529 AGTAATTTCC
Statistics
Matches: 80, Mismatches: 13, Indels: 34
0.63 0.10 0.27
Matches are distributed among these distances:
12 6 0.08
14 22 0.28
16 6 0.08
17 12 0.15
19 34 0.43
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:75441 original size:33 final size:31
Alignment explanation
Indices: 75399--75528 Score: 188
Period size: 33 Copynumber: 4.1 Consensus size: 31
75389 CACGAAATTA
*
75399 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
1 ATTCTCGTTGCGATTTTCATTTCGCATTGCG
*
75430 ATTCCCTCGTTGCAATTTTCATTTCGCATTGCG
1 ATT--CTCGTTGCGATTTTCATTTCGCATTGCG
**
75463 AAATTAGCGTTGCGATTTTCATTTCGCATTGCG
1 --ATTCTCGTTGCGATTTTCATTTCGCATTGCG
75496 ATTCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATTCTCGTTGCGATTTTCATTTCGCATTGCG
75527 AT
1 AT
75529 AGTAATTTCC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 34 0.39
33 51 0.58
35 3 0.03
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.42
Consensus pattern (31 bp):
ATTCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:75481 original size:66 final size:64
Alignment explanation
Indices: 75398--75527 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 64
75388 ACACGAAATT
*
75398 AATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGCG
1 AATTAGCGTTGCGATTTTCATTTCGCATTGCGATT--CTCGTTGCAATTTTCATTTCGCATTGCG
75463 A
64 A
*
75464 AATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 AATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCGTTGCAATTTTCATTTCGCATTGCGA
75528 TAGTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 28 0.45
66 34 0.55
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (64 bp):
AATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCGTTGCAATTTTCATTTCGCATTGCGA
Found at i:77828 original size:12 final size:12
Alignment explanation
Indices: 77811--77835 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
77801 TCTTCGGGGA
77811 CTTTTTCTTCTT
1 CTTTTTCTTCTT
77823 CTTTTTCTTCTT
1 CTTTTTCTTCTT
77835 C
1 C
77836 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:78041 original size:24 final size:24
Alignment explanation
Indices: 78007--78060 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
77997 CTGAAACATC
* * *
78007 ATCAAAATCCGTGTATTGGCCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
78031 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
78055 ATCAAA
1 ATCAAA
78061 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:79162 original size:19 final size:19
Alignment explanation
Indices: 79104--79178 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 19
79094 ATTCATTTGA
*
79104 CTATCGCAACGCAAAAATGG
1 CTATCGCAACGC-GAAATGG
79124 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCG-AAATGG
79144 CTATCGCAACGCGAAATGG
1 CTATCGCAACGCGAAATGG
*
79163 CTATCGCAACGAGAAA
1 CTATCGCAACGCGAAA
79179 ATCGCAATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
19 21 0.40
20 31 0.60
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (19 bp):
CTATCGCAACGCGAAATGG
Found at i:79168 original size:39 final size:40
Alignment explanation
Indices: 79104--79180 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
79094 ATTCATTTGA
*
79104 CTATCGCAACGCAAAAATGGCTATCGCAACGCGAAAATGG
1 CTATCGCAACGCAAAAATGGCTATCGCAACGAGAAAATGG
*
79144 CTATCGCAACGC-GAAATGGCTATCGCAACGAGAAAAT
1 CTATCGCAACGCAAAAATGGCTATCGCAACGAGAAAAT
79181 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 23 0.66
40 12 0.34
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (40 bp):
CTATCGCAACGCAAAAATGGCTATCGCAACGAGAAAATGG
Found at i:79223 original size:14 final size:14
Alignment explanation
Indices: 79204--79257 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
79194 GAAAATCGCA
79204 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
79218 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
79235 CATTGTGATTTTCTCG
1 --TTGCGATTTTCTCG
79251 TTGCGAT
1 TTGCGAT
79258 AGCCATTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.11, C:0.19, G:0.20, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:79223 original size:33 final size:33
Alignment explanation
Indices: 79186--79256 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
79176 AAAATCGCAA
79186 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** ** *
79219 TGCGATTTTCATTTCGCATTGTGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
79252 TGCGA
1 TGCGA
79257 TAGCCATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:79265 original size:33 final size:33
Alignment explanation
Indices: 79199--79276 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
79189 GAAATGAAAA
***
79199 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
79232 TCGCATTGTGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
79265 TCGCGTTGCGAT
1 TCGCATTGCGAT
79277 AGTTTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:81276 original size:20 final size:19
Alignment explanation
Indices: 81241--81307 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
81231 GAAACTTAAA
81241 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
81260 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
81280 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
81299 ATCGCAACG
1 ATCGCAACG
81308 ACAAATCGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:81315 original size:13 final size:13
Alignment explanation
Indices: 81297--81351 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 13
81287 TGCGAAATGA
81297 AAATCGCAACGAC
1 AAATCGCAACGAC
*
81310 AAATCGCAACGCAAATG
1 AAATCGCAACG---A-C
81327 AAATCGCAACGAC
1 AAATCGCAACGAC
81340 AAAATCGCAACG
1 -AAATCGCAACG
81352 CGAAAACACA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 11 0.31
14 12 0.34
16 1 0.03
17 11 0.31
ACGTcount: A:0.47, C:0.27, G:0.16, T:0.09
Consensus pattern (13 bp):
AAATCGCAACGAC
Found at i:81333 original size:30 final size:33
Alignment explanation
Indices: 81280--81356 Score: 124
Period size: 31 Copynumber: 2.4 Consensus size: 33
81270 GGAAATGGCT
*
81280 ATCGCAATGCGAAATGAAAATCGCAACGAC-AA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
81312 ATCGCAACGC-AAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
81343 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
81357 ACACAAATCG
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 13 0.31
31 17 0.40
32 12 0.29
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:81405 original size:14 final size:14
Alignment explanation
Indices: 81386--81443 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
81376 TTTCATTTCG
81386 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
81400 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
81416 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
81432 CGTTGCGATTTT
1 CGTTGCGATTTT
81444 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:81450 original size:33 final size:33
Alignment explanation
Indices: 81369--81459 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
81359 ACAAATCGCA
*
81369 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
81402 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
81434 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
81460 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:81494 original size:19 final size:19
Alignment explanation
Indices: 81444--81486 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
81434 TTGCGATTTT
*
81444 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTG-GATAGC
*
81463 CATTTCCGCGTTGGATAGT
1 CATTTCCGCGTTGGATAGC
81482 CATTT
1 CATTT
81487 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (19 bp):
CATTTCCGCGTTGGATAGC
Found at i:81991 original size:18 final size:18
Alignment explanation
Indices: 81965--82009 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
81955 GTCGATCAGA
*
81965 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
81983 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
82001 TGATGGCTC
1 TGATGGCTC
82010 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Done.