Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005480.1 Hibiscus syriacus cultivar Beakdansim tig00012566_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: 84554
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:7114 original size:18 final size:17
Alignment explanation
Indices: 7091--7128 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
7081 AATATTTGTT
7091 TTTTAATTTATTTAAGTA
1 TTTTAATTTATTTAA-TA
7109 TTTTAATTTATTTAATA
1 TTTTAATTTATTTAATA
7126 TTT
1 TTT
7129 ACTTATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTAATTTATTTAATA
Found at i:9168 original size:3 final size:3
Alignment explanation
Indices: 9160--9185 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9150 ACCTACTTAG
9160 GAC GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GA
9186 TGATGGTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:9458 original size:35 final size:33
Alignment explanation
Indices: 9418--9502 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 33
9408 GTATTTCAGT
9418 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
9453 TAATTTTGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
9488 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
9503 TAAAATTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
33 2 0.04
34 1 0.02
35 26 0.58
36 1 0.02
37 2 0.04
38 13 0.29
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:13224 original size:23 final size:23
Alignment explanation
Indices: 13144--13225 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 23
13134 CACCACAGCT
* * * *
13144 CGTATAAATACACCGAAGTGCCG
1 CGTAGAAATGCACCAAAGTGCCA
* *
13167 CTTAGAAATGCACCATAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* *
13190 CGTAGGATTGCACCAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
13213 CGTAGAAATGCAC
1 CGTAGAAATGCAC
13226 GTGCCATATA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:20887 original size:22 final size:25
Alignment explanation
Indices: 20843--20900 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 25
20833 ATTTAATTTT
20843 TTTTAAAAAATAAACTTATTTTAAA
1 TTTTAAAAAATAAACTTATTTTAAA
*
20868 TTTTAAATAA-AAA-TTA-TTTAAA
1 TTTTAAAAAATAAACTTATTTTAAA
* *
20890 TATTCAAAAAT
1 TTTTAAAAAAT
20901 TAAATATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 13 0.46
23 3 0.11
24 3 0.11
25 9 0.32
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTTAAAAAATAAACTTATTTTAAA
Found at i:20929 original size:47 final size:47
Alignment explanation
Indices: 20878--20967 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 47
20868 TTTTAAATAA
*
20878 AAATTATT-TAAATATTCAAAAATTAAATA-TAAAAATACTAAAAAATT
1 AAATTATTATAAAAATTCAAAAA--AAATATTAAAAATACTAAAAAATT
* * *
20925 AAATTATTATAAAAATTGAATAAACATATTAAAAATACTAAAA
1 AAATTATTATAAAAATTCAAAAAAAATATTAAAAATACTAAAA
20968 TTATTATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
46 4 0.11
47 22 0.59
48 11 0.30
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (47 bp):
AAATTATTATAAAAATTCAAAAAAAATATTAAAAATACTAAAAAATT
Found at i:21164 original size:25 final size:25
Alignment explanation
Indices: 21130--21178 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
21120 TTCTTACTAT
21130 ATTAATCGAGATTTACAAAATTTAA
1 ATTAATCGAGATTTACAAAATTTAA
* *
21155 ATTAGTCGAGATTTACAAATTTTA
1 ATTAATCGAGATTTACAAAATTTA
21179 GGTTAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (25 bp):
ATTAATCGAGATTTACAAAATTTAA
Found at i:21324 original size:26 final size:25
Alignment explanation
Indices: 21295--21347 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
21285 AAGGTTTGAC
21295 TAATTCAAAAATTATTAAGACTCGAT
1 TAATTCAAAAATTA-TAAGACTCGAT
* ** *
21321 TAATTTAAATTTTATAATACTCGAT
1 TAATTCAAAAATTATAAGACTCGAT
21346 TA
1 TA
21348 TTCCAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (25 bp):
TAATTCAAAAATTATAAGACTCGAT
Found at i:21595 original size:24 final size:24
Alignment explanation
Indices: 21560--21606 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
21550 TTTAAATTAA
* *
21560 TTTTTAATATTTGTATA-TTTTAC
1 TTTTTAAAATTTGAATACTTTTAC
21583 TTTTTGAAAATTTGAATACTTTTA
1 TTTTT-AAAATTTGAATACTTTTA
21607 TATTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTTAAAATTTGAATACTTTTAC
Found at i:22052 original size:2 final size:2
Alignment explanation
Indices: 22047--22112 Score: 75
Period size: 2 Copynumber: 33.5 Consensus size: 2
22037 AATCATTGAT
* *
22047 TA TA TA TA TA TT TA AA TCA TGA TA TA TA TA TA TA TA TA TA -A T-
1 TA TA TA TA TA TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA TA
22089 TA TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22113 TATGAAAACT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
1 3 0.05
2 48 0.87
3 4 0.07
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:22368 original size:2 final size:2
Alignment explanation
Indices: 22361--22394 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22351 AGGGTTTCAC
22361 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22395 GGAAAACTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23102 original size:21 final size:21
Alignment explanation
Indices: 23078--23117 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23068 TTTAAATTTT
23078 TTATATAAAATTTAAAAAAAA
1 TTATATAAAATTTAAAAAAAA
* *
23099 TTATATATATTTTAAAAAA
1 TTATATAAAATTTAAAAAA
23118 TAAAAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTATATAAAATTTAAAAAAAA
Found at i:25608 original size:38 final size:38
Alignment explanation
Indices: 25558--25635 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
25548 AAACACTTAG
*
25558 AAAATTCCTTCCAAACTCGTTCTTTCCGGTGATAGAGA
1 AAAATTCATTCCAAACTCGTTCTTTCCGGTGATAGAGA
* *
25596 AAAATTCATTCCAAATTCGTTCTTTTCGGTGATAGAGA
1 AAAATTCATTCCAAACTCGTTCTTTCCGGTGATAGAGA
25634 AA
1 AA
25636 GGCAAGATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (38 bp):
AAAATTCATTCCAAACTCGTTCTTTCCGGTGATAGAGA
Found at i:26147 original size:19 final size:19
Alignment explanation
Indices: 26125--26168 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
26115 TATTTGTAGG
26125 TTCCAATACAATTTGCAGA
1 TTCCAATACAATTTGCAGA
26144 TTCCAATACAATTTGCAGA
1 TTCCAATACAATTTGCAGA
26163 TTCCAA
1 TTCCAA
26169 AAAGAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (19 bp):
TTCCAATACAATTTGCAGA
Found at i:28746 original size:21 final size:22
Alignment explanation
Indices: 28722--28768 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
28712 CTTTTCATCA
*
28722 AAAGGA-TAAGTCCTTTAATTG
1 AAAGGATTAAGTCCTTTAATCG
*
28743 AAA-GATTAAGTCCTTTCATCG
1 AAAGGATTAAGTCCTTTAATCG
28764 AAAGG
1 AAAGG
28769 TCTTAACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 19 0.86
22 1 0.05
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (22 bp):
AAAGGATTAAGTCCTTTAATCG
Found at i:29541 original size:22 final size:22
Alignment explanation
Indices: 29516--29574 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
29506 TAGTTTTTAT
*
29516 AAATTCTAAACTTTAGAATCTA
1 AAATCCTAAACTTTAGAATCTA
29538 AAATCCTAAACTTTAGAATCTA
1 AAATCCTAAACTTTAGAATCTA
29560 AAATCCTAAACTTTA
1 AAATCCTAAACTTTA
29575 AACAAGGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (22 bp):
AAATCCTAAACTTTAGAATCTA
Found at i:33551 original size:24 final size:24
Alignment explanation
Indices: 33524--33596 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
33514 GTAAACGGAG
*
33524 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* * * *
33548 ATATAAGATATCAGAACAAAATCC
1 ATATCAGAAATCAGAACAGAATTC
33572 ATATCAGAAATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
33596 A
1 A
33597 GGTAATGTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.53, C:0.16, G:0.10, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:36373 original size:21 final size:21
Alignment explanation
Indices: 36347--36387 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36337 GATAGTCGTG
36347 AATCGACG-AAAAACCAACGAA
1 AATCGA-GTAAAAACCAACGAA
*
36368 AATCGAGTTAAAACCAACGA
1 AATCGAGTAAAAACCAACGA
36388 TACTTCCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.54, C:0.22, G:0.15, T:0.10
Consensus pattern (21 bp):
AATCGAGTAAAAACCAACGAA
Found at i:45527 original size:347 final size:346
Alignment explanation
Indices: 44799--45823 Score: 1996
Period size: 347 Copynumber: 3.0 Consensus size: 346
44789 TTTGTTGCCA
*
44799 TTCATAATCTAGCTGTTCATTTCAATCCCCATAAAGATTAAAGGGCACAACTAGAGCATAGTTTC
1 TTCATAATCTAGCTGTTCATTTCAATCCCCATAAAGAATAAAGGGCACAACTAGAGCATAGTTTC
*
44864 TGCAGTAGCTTTCCATCTTTAAGTACATAAAATTCTATGCTACACAGACATATGATCCCTCAACT
66 TGCAGTAGCTTTCCATCTTTAAGTACATAAAATTCTATGCTACACAAACATATGATCCCTCAACT
44929 TTATCTTTTATTTTTTCTATCCTGAAAGAAATGACTTCTAGCATGGCTTCAATAGGCAAATAAAA
131 TTATCTTTTATTTTTTCTATCCTGAAAGAAATGACTTCTAGCATGGCTTCAATAGGCAAATAAAA
44994 AACAGAATTACTTGGCTTAAGCACAAGATTATTTAACCTCTAGTTTTATGTAAGCCATTCATAGG
196 AACAGAATTACTTGGCTTAAGCACAAGATTATTTAACCTCTAGTTTTATGTAAGCCATTCATAGG
45059 AGAAACACCATAAATTAACAACCTCTGCAGTGAATAACGGGATGATTGAGAAAATAACAGACTAA
261 AGAAACACCATAAATTAACAACCTCTGCAGTGAATAACGGGATGATTGAGAAAATAACAGACTAA
* *
45124 ACCAATAAAGATTCTATGCAG
326 ACCAATAAAGATTCTATGAAC
*
45145 TTCATTATCTAGCTGTTCATTTCAATCCCCATAAAGAATAAAGGGCACAACTAGAGCATAGTTTC
1 TTCATAATCTAGCTGTTCATTTCAATCCCCATAAAGAATAAAGGGCACAACTAGAGCATAGTTTC
45210 TGCAGTAGCTTTCCATCTTTAAGTACATAAAATTCTATGCTACACAAACATATGATCCCTCAACT
66 TGCAGTAGCTTTCCATCTTTAAGTACATAAAATTCTATGCTACACAAACATATGATCCCTCAACT
45275 TTATCTTTTATTTTTTCTATCCTGAAAGAAATGACTTCTAGCATGGCTTCAATAGGCAAATAAAA
131 TTATCTTTTATTTTTTCTATCCTGAAAGAAATGACTTCTAGCATGGCTTCAATAGGCAAAT-AAA
45340 AAACAGAATTACTTGGCTTAAGCACAAGATTATTTAACCTCTAGTTTTATGTAAGCCATTCATAG
195 AAACAGAATTACTTGGCTTAAGCACAAGATTATTTAACCTCTAGTTTTATGTAAGCCATTCATAG
45405 GAGAAACACCATAAATTAACAACCTCTGCAGTGAATAACGGGATGATTGAGAAAATAACAGACTA
260 GAGAAACACCATAAATTAACAACCTCTGCAGTGAATAACGGGATGATTGAGAAAATAACAGACTA
45470 AACCAATAAAGATTCTATGAAC
325 AACCAATAAAGATTCTATGAAC
45492 TTCATAATCTAGCTGTTCATTTCAATCCCCATAAAGAATAAAGGGCACAACTAGAGCATAGTTTC
1 TTCATAATCTAGCTGTTCATTTCAATCCCCATAAAGAATAAAGGGCACAACTAGAGCATAGTTTC
45557 TGCAGTAGCTTTCCATCTTTAAGTACATAAAATTCTATGCTACACAAACATATGATCCCTCAACT
66 TGCAGTAGCTTTCCATCTTTAAGTACATAAAATTCTATGCTACACAAACATATGATCCCTCAACT
45622 TTATCTTTTATTTTTTCTATCCTGAAAGAAATGACTTCTAGCATGGCTTCAATAGGCAAATAAAA
131 TTATCTTTTATTTTTTCTATCCTGAAAGAAATGACTTCTAGCATGGCTTCAATAGGCAAATAAAA
45687 AACAGAATTACTTGGCTTAAGCACAAGATTATTTAACCTCTAGTTTTATGTAAGCCATTCATAGG
196 AACAGAATTACTTGGCTTAAGCACAAGATTATTTAACCTCTAGTTTTATGTAAGCCATTCATAGG
45752 AGAAACACCATAAATTAACAACCTCTGCAGTGAATAACGGGATGATTGAGAAAATAACAGACTAA
261 AGAAACACCATAAATTAACAACCTCTGCAGTGAATAACGGGATGATTGAGAAAATAACAGACTAA
45817 ACCAATA
326 ACCAATA
45824 GCATGGAGTA
Statistics
Matches: 672, Mismatches: 6, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
346 329 0.49
347 343 0.51
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.30
Consensus pattern (346 bp):
TTCATAATCTAGCTGTTCATTTCAATCCCCATAAAGAATAAAGGGCACAACTAGAGCATAGTTTC
TGCAGTAGCTTTCCATCTTTAAGTACATAAAATTCTATGCTACACAAACATATGATCCCTCAACT
TTATCTTTTATTTTTTCTATCCTGAAAGAAATGACTTCTAGCATGGCTTCAATAGGCAAATAAAA
AACAGAATTACTTGGCTTAAGCACAAGATTATTTAACCTCTAGTTTTATGTAAGCCATTCATAGG
AGAAACACCATAAATTAACAACCTCTGCAGTGAATAACGGGATGATTGAGAAAATAACAGACTAA
ACCAATAAAGATTCTATGAAC
Found at i:49551 original size:31 final size:30
Alignment explanation
Indices: 49516--49593 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 30
49506 TCAAAAAACA
* *
49516 TAAGTTTTGATCACTTACATTATTGTTTTAT
1 TAAGTTTTG-TCACTTACATTATCGTTTAAT
*
49547 TAAGTTTTTGTCACTTACGTTATCGTTTAAT
1 TAAG-TTTTGTCACTTACATTATCGTTTAAT
49578 TAAGTTTTGGTCACTT
1 TAAGTTTT-GTCACTT
49594 GGACGTTGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 4 0.10
31 33 0.79
32 5 0.12
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.53
Consensus pattern (30 bp):
TAAGTTTTGTCACTTACATTATCGTTTAAT
Found at i:49782 original size:35 final size:34
Alignment explanation
Indices: 49736--49813 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 34
49726 AAGCAATATA
*
49736 TTAAAA-A-TTAATATGTGTACTAGTTTGATGTTT
1 TTAAAATATTTAATATGTGTACTAGTTTAAT-TTT
*
49769 TTAAAATATTTAATATGTTTACTAGTTTAATTTT
1 TTAAAATATTTAATATGTGTACTAGTTTAATTTT
*
49803 TTTAAATATTT
1 TTAAAATATTT
49814 GCTAACATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 6 0.15
34 14 0.35
35 20 0.50
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.54
Consensus pattern (34 bp):
TTAAAATATTTAATATGTGTACTAGTTTAATTTT
Found at i:51995 original size:15 final size:16
Alignment explanation
Indices: 51975--52004 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51965 TAATTGAAGT
51975 TCAAGA-CTAAAAATG
1 TCAAGATCTAAAAATG
51990 TCAAGATCTAAAAAT
1 TCAAGATCTAAAAAT
52005 CGAGTTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.23
Consensus pattern (16 bp):
TCAAGATCTAAAAATG
Found at i:52362 original size:11 final size:11
Alignment explanation
Indices: 52328--52363 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
52318 AAAATAATTA
52328 AAATAACAAAT
1 AAATAACAAAT
52339 AAA-AACAACAT
1 AAATAACAA-AT
52350 AAATAACAAAT
1 AAATAACAAAT
52361 AAA
1 AAA
52364 AATAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 5 0.22
11 13 0.57
12 5 0.22
ACGTcount: A:0.75, C:0.11, G:0.00, T:0.14
Consensus pattern (11 bp):
AAATAACAAAT
Found at i:52373 original size:22 final size:22
Alignment explanation
Indices: 52328--52373 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
52318 AAAATAATTA
*
52328 AAATAACAAATAAAAACAACAT
1 AAATAACAAATAAAAACAAAAT
*
52350 AAATAACAAATAAAAATAAAAT
1 AAATAACAAATAAAAACAAAAT
52372 AA
1 AA
52374 GTACAAGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (22 bp):
AAATAACAAATAAAAACAAAAT
Found at i:53381 original size:78 final size:78
Alignment explanation
Indices: 53282--53594 Score: 300
Period size: 78 Copynumber: 4.1 Consensus size: 78
53272 CGCTGCGAAC
* * * * ** *
53282 TCTTATGTTTCGAGAGAAACTATCTCAAGCTAGATAAAATATTATATTTCGAGGGGAACTATCTC
1 TCTTCTGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCTCCTATTTCGAGGGAAACTATCTC
*
53347 AAGCGAGACAAAA
66 AAGCGAGATAAAA
* * * * * * *
53360 TCTTCTGTTTCGAGGGAAACTATATCAAACGAGACAAAATCT--TCTTT--A--AAAACAATCTT
1 TCTTCTGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCTCCTATTTCGAGGGAAACTATCTC
* ** * *
53419 GAGTAAAATGAAATG
66 AAGCGAGAT-AAA-A
* * * * *
53434 TCTTCT-TTT-GAGTAAAAATTGTCTCAAGCGAGACAAAATCTCCTGTTTCAAGGGAAACTATCT
1 TCTTCTGTTTCGAG-AGAAACTATCTCAAGCGAGACAAAATCTCCTATTTCGAGGGAAACTATCT
53497 CAAGCGAGATAAAA
65 CAAGCGAGATAAAA
* *
53511 TCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACAAAATCTCCTATTTCGAGAGAAACTATCTC
1 TCTTCTGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCTCCTATTTCGAGGGAAACTATCTC
53576 AAGCGAGATAAAA
66 AAGCGAGATAAAA
53589 TCTTCT
1 TCTTCT
53595 TTATAAACAA
Statistics
Matches: 184, Mismatches: 40, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
72 14 0.08
73 28 0.15
74 7 0.04
75 4 0.02
76 4 0.02
77 7 0.04
78 104 0.57
79 16 0.09
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (78 bp):
TCTTCTGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCTCCTATTTCGAGGGAAACTATCTC
AAGCGAGATAAAA
Found at i:53590 original size:39 final size:39
Alignment explanation
Indices: 53287--53591 Score: 244
Period size: 39 Copynumber: 7.9 Consensus size: 39
53277 CGAACTCTTA
* * * **
53287 TGTTTCGAGAGAAACTATCTCAAGCTAGATAAAATATTA
1 TGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCTCC
* * * *
53326 TATTTCGAGGGGAACTATCTCAAGCGAGACAAAATCTTC
1 TGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCTCC
* * *
53365 TGTTTCGAGGGAAACTATATCAAACGAGACAAAATCT--
1 TGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCTCC
* * ** ** * ** * *
53402 TCTTT--A-A-AAACAATCTTGAGTAAAATGAAATGTCT
1 TGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCTCC
* * * * *
53437 TCTTTTGAGTAAAAATTGTCTCAAGCGAGACAAAATCTCC
1 TGTTTCGAG-AGAAACTATCTCAAGCGAGACAAAATCTCC
* * * *
53477 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCTCC
*
53516 TGTTTCGAGGGAAACTATCTCAAGCGAGACAAAATCTCC
1 TGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCTCC
* *
53555 TATTTCGAGAGAAACTATCTCAAGCGAGATAAAATCT
1 TGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCT
53592 TCTTTATAAA
Statistics
Matches: 208, Mismatches: 51, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
33 15 0.07
35 6 0.03
37 5 0.02
39 160 0.77
40 22 0.11
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (39 bp):
TGTTTCGAGAGAAACTATCTCAAGCGAGACAAAATCTCC
Found at i:53643 original size:190 final size:190
Alignment explanation
Indices: 53287--53660 Score: 588
Period size: 190 Copynumber: 2.0 Consensus size: 190
53277 CGAACTCTTA
* * *
53287 TGTTTCGAGAGAAACTATCTCAAGCTAGATAAAATATTATATTTCGAGGGGAACTATCTCAAGCG
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATATTATATTTCGAGGGAAACTATCTCAAGCG
* * *
53352 AGACAAAATCTTCTGTTTCGAGGGAAACTATATCAAACGAGACAAAATCTTCTTTAAAAACAATC
66 AGACAAAATCTCCTATTTCGAGAGAAACTATATCAAACGAGACAAAATCTTCTTTAAAAACAATC
53417 TTGAGTAAAATGAAATGTCTTCTTTTGAGTAAAAATTGTCTCAAGCGAGACAAAATCTCC
131 TTGAGTAAAATGAAATGTCTTCTTTTGAGTAAAAATTGTCTCAAGCGAGACAAAATCTCC
* * * *
53477 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCG
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATATTATATTTCGAGGGAAACTATCTCAAGCG
* * * *
53542 AGACAAAATCTCCTATTTCGAGAGAAACTATCTCAAGCGAGATAAAATCTTCTTTATAAACAATC
66 AGACAAAATCTCCTATTTCGAGAGAAACTATATCAAACGAGACAAAATCTTCTTTAAAAACAATC
* *
53607 TTGAGT-GAATGGAATGTCTTCTTTTGAGTAAAAAATTGTCTCAAGCGAGACAAA
131 TTGAGTAAAATGAAATGTCTTCTTTTGAGT-AAAAATTGTCTCAAGCGAGACAAA
53661 TCTTGTTTTA
Statistics
Matches: 167, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
189 21 0.13
190 146 0.87
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (190 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATATTATATTTCGAGGGAAACTATCTCAAGCG
AGACAAAATCTCCTATTTCGAGAGAAACTATATCAAACGAGACAAAATCTTCTTTAAAAACAATC
TTGAGTAAAATGAAATGTCTTCTTTTGAGTAAAAATTGTCTCAAGCGAGACAAAATCTCC
Found at i:53768 original size:78 final size:77
Alignment explanation
Indices: 53572--53819 Score: 296
Period size: 78 Copynumber: 3.3 Consensus size: 77
53562 AGAGAAACTA
* * *
53572 TCTCAAGCGAGATAAAATCTTC-TTT-AT--AAACAATCTTGAGTG-AATGGAATGTCTTCTTTT
1 TCTCAAGCGAGAAAAAATCTTCTTTTAATAAAAACAATCTTGAGTGAAATGAAATGTCTTGTTTT
53632 GAGTAAAAAATTG
66 GAGT-AAAAATTG
* * * *
53645 TCTCAAGCGAG-ACAAATCTTGTTTTAAGAAAAACAA-CATGTAGTGAAATGAAATGTCTTGTTT
1 TCTCAAGCGAGAAAAAATCTTCTTTTAATAAAAACAATCTTG-AGTGAAATGAAATGTCTTGTTT
53708 TGAGTAAAAATTG
65 TGAGTAAAAATTG
* *
53721 TCTCAAGCGAGAAAAAAATCTTCTTTTAATAAAAACAATCTTGAGTGAAAT-AAATCTTATTGTT
1 TCTCAAGCGAG-AAAAAATCTTCTTTTAATAAAAACAATCTTGAGTGAAATGAAAT-GTCTTGTT
* *
53785 TCGAGTAAAAACTG
64 TTGAGTAAAAATTG
*
53799 TCTCAAGCGAGACAAAATCTT
1 TCTCAAGCGAGAAAAAATCTT
53820 TTGTTTGAAG
Statistics
Matches: 149, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
72 7 0.05
73 14 0.09
74 1 0.01
75 3 0.02
76 29 0.19
77 33 0.22
78 59 0.40
79 3 0.02
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (77 bp):
TCTCAAGCGAGAAAAAATCTTCTTTTAATAAAAACAATCTTGAGTGAAATGAAATGTCTTGTTTT
GAGTAAAAATTG
Found at i:53927 original size:65 final size:65
Alignment explanation
Indices: 53821--53951 Score: 192
Period size: 65 Copynumber: 2.0 Consensus size: 65
53811 CAAAATCTTT
* * **
53821 TGTTTGAAGGGAAACTATCTCAAGAGAGACATAATTCGTTTCAAGGAAAACGTTCTCAAAGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACAATCTCAAAGTTTA
* *
53886 TGTTTCAAGGGAAACTCTCTCAAGAGAGACAAAACTT-GTTTCAAGGGAAACAATCTCAAAGTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTCGTTTCAAGGAAAACAATCTCAAAGTTT
53950 A
65 A
53951 T
1 T
53952 CAATTTTGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 57 0.97
66 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (65 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACAATCTCAAAGTTTA
Found at i:54133 original size:36 final size:37
Alignment explanation
Indices: 54093--54163 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
54083 TGAGATTAAT
54093 TTTGTTTTAAAGAAAA-TTGTCTCCACCGAGACGAAA
1 TTTGTTTTAAAGAAAACTTGTCTCCACCGAGACGAAA
* * *
54129 TTTGTTTTTAAGAAAACTTGTCTCGAGCGAGACGA
1 TTTGTTTTAAAGAAAACTTGTCTCCACCGAGACGA
54164 CCCTTTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 15 0.48
37 16 0.52
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (37 bp):
TTTGTTTTAAAGAAAACTTGTCTCCACCGAGACGAAA
Found at i:57888 original size:30 final size:30
Alignment explanation
Indices: 57854--57921 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
57844 AAACTTACTT
* *
57854 AAAATAATTAAAATAAC-AAATAAAAAACTA
1 AAAATAATAAAAACAACAAAATAAAAAA-TA
* *
57884 AAAATAGTAAAAACAACATAAATAACAAATA
1 AAAATAATAAAAACAACA-AAATAAAAAATA
57915 AAAATAA
1 AAAATAA
57922 AATAAGTACA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 14 0.45
31 8 0.26
32 9 0.29
ACGTcount: A:0.74, C:0.07, G:0.01, T:0.18
Consensus pattern (30 bp):
AAAATAATAAAAACAACAAAATAAAAAATA
Found at i:58637 original size:33 final size:33
Alignment explanation
Indices: 58590--58719 Score: 143
Period size: 37 Copynumber: 3.8 Consensus size: 33
58580 ATTGTTGTGG
*
58590 GTGGAAGAAGGAAACATGGAATGGTGGAAGGTA
1 GTGGAAAAAGGAAACATGGAATGGTGGAAGGTA
*
58623 GTGGAAAAAAGAAACATGGAATGGTGGAAGGAAGGTA
1 GTGGAAAAAGGAAACATGGAATGGT----GGAAGGTA
* *
58660 GTGGAAAAAGGAAACATGGAATGGTAGAAGGTTG
1 GTGGAAAAAGGAAACATGGAATGGTGGAAGG-TA
* * * *
58694 GTGGAGACATGAAACATGGGATGGTG
1 GTGGAAAAAGGAAACATGGAATGGTG
58720 TAGGGCTGAG
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
33 28 0.34
34 22 0.27
37 32 0.39
ACGTcount: A:0.40, C:0.04, G:0.40, T:0.16
Consensus pattern (33 bp):
GTGGAAAAAGGAAACATGGAATGGTGGAAGGTA
Found at i:58656 original size:37 final size:36
Alignment explanation
Indices: 58590--58690 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 36
58580 ATTGTTGTGG
*
58590 GTGGAAGAAGGAAACATGGAATGGT---GGAAGGTA
1 GTGGAAAAAGGAAACATGGAATGGTGAAGGAAGGTA
*
58623 GTGGAAAAAAGAAACATGGAATGGTGGAAGGAAGGTA
1 GTGGAAAAAGGAAACATGGAATGGT-GAAGGAAGGTA
58660 GTGGAAAAAGGAAACATGGAATGGTAGAAGG
1 GTGGAAAAAGGAAACATGGAATGGT-GAAGG
58691 TTGGTGGAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
33 23 0.38
37 37 0.62
ACGTcount: A:0.44, C:0.03, G:0.40, T:0.14
Consensus pattern (36 bp):
GTGGAAAAAGGAAACATGGAATGGTGAAGGAAGGTA
Found at i:59545 original size:20 final size:21
Alignment explanation
Indices: 59499--59550 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
59489 CAGGGTTTTA
* *
59499 AGTTAGAGGTTAAGGGTTAATG
1 AGTTAGA-GTTTAGGGCTAATG
59521 A-TTAGAGTTTAGGGCTAA-G
1 AGTTAGAGTTTAGGGCTAATG
59540 AGTTAGAGTTT
1 AGTTAGAGTTT
59551 GGGGTTCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 19 0.70
21 5 0.19
22 1 0.04
ACGTcount: A:0.31, C:0.02, G:0.33, T:0.35
Consensus pattern (21 bp):
AGTTAGAGTTTAGGGCTAATG
Found at i:61104 original size:18 final size:19
Alignment explanation
Indices: 61069--61105 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
61059 CACAGAATGT
61069 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
61089 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
61106 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:66277 original size:44 final size:43
Alignment explanation
Indices: 66214--66314 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 43
66204 CACCTACCAC
*
66214 CATTAATGTTAAATGATATATGAAGTGAATTCAATTCTTATCA
1 CATTAATGTTAAATGATATATGAAGTGAATACAATTCTTATCA
*
66257 TCATTAAT-TTGAAATTATATATGAAGTGAATACAATTCTTATCA
1 -CATTAATGTT-AAATGATATATGAAGTGAATACAATTCTTATCA
66301 CTATTAATG-TAAAT
1 C-ATTAATGTTAAAT
66315 CATAAAGTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
43 7 0.13
44 45 0.87
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (43 bp):
CATTAATGTTAAATGATATATGAAGTGAATACAATTCTTATCA
Found at i:66638 original size:43 final size:44
Alignment explanation
Indices: 66576--66673 Score: 117
Period size: 43 Copynumber: 2.2 Consensus size: 44
66566 ACCTATCACT
* * * *
66576 ATTAATGTGAGATGATATATGAAATGAATATAATTGTTACCACC
1 ATTAATATGAAATGATATATGAAATAAATATAATTCTTACCACC
* * * *
66620 ATTAATTTGAAAT-ATATATGAAGTAAATATAATTCTTATCACT
1 ATTAATATGAAATGATATATGAAATAAATATAATTCTTACCACC
66663 ATTAATATGAA
1 ATTAATATGAA
66674 TCATAAAGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
43 35 0.76
44 11 0.24
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (44 bp):
ATTAATATGAAATGATATATGAAATAAATATAATTCTTACCACC
Found at i:66995 original size:206 final size:206
Alignment explanation
Indices: 66423--67026 Score: 550
Period size: 206 Copynumber: 3.0 Consensus size: 206
66413 ATCTACCAAT
* * * * *
66423 ATTAATATGAAATGATATATGAAATGAATAAAATTATTATCACCATTAATGTG---AAT-AAGTT
1 ATTAATTTGAAAT-ATATATGAAATAAATACAATTCTTATCACCATTAATATGAATAATAAAGTT
* * * * * *
66484 AAAGAATATTCACTCATAACTTTAATTCATGGTCATATA-TTTTTCTTTAATTTATGATC-ATAA
65 AAA-AAAATTCACTCATAAC-TTAATTTA-GATAATA-ACTTTTTGTTTAATTTATGA-CAACAA
* * * * * * *
66547 CATT-AGTTG--GTAAA-A-A-A--TCACCTA-TCACTATTAATGTGAGATGATATATGAAATGA
125 CTTTAATTTGTAGAAAATAGACATTTCACCTACTAATTATTAATGTGAAATGATATATGAAGTGA
* * *
66603 ATATAATTGTTACCACC
190 ATACAATTCTTATCACC
* * * *
66620 ATTAATTTGAAATATATATGAAGTAAATATAATTCTTATCACTATTAATATGAATCATAAAGTTA
1 ATTAATTTGAAATATATATGAAATAAATACAATTCTTATCACCATTAATATGAATAATAAAGTTA
* * * *
66685 AAAAAATTCACTCATAACTTAATTTAGATCATAACTTTTTGTTTGATTTATGGCCACAACTTTAA
66 AAAAAATTCACTCATAACTTAATTTAGATAATAACTTTTTGTTTAATTTATGACAACAACTTTAA
** *
66750 TTTGTAGAAAATCTACATTTCACCTACTAATT-TTAATGTGAAATGATATATGAAGTGAACACAA
131 TTTGTAGAAAATAGACATTTCACCTACTAATTATTAATGTGAAATGATATATGAAGTGAATACAA
66814 TTCTTATCACC
196 TTCTTATCACC
*
66825 ATTAATTTGAAATA-ATATGTAAAATAAATACAATTCTTATCACCATTAATGTGAATAATAAAGT
1 ATTAATTTGAAATATATATG--AAATAAATACAATTCTTATCACCATTAATATGAATAATAAAGT
** * * *
66889 T-GTAAAATTTACTCATAATTTTAATTTATGGTAATAA--TTTTGTTTTAATTTATGACAACAAC
64 TAAAAAAATTCACTCATAA-CTTAATTTA-GATAATAACTTTTTG-TTTAATTTATGACAACAAC
* * * * * *
66951 TTTAA-TTGATAGGAAATAGACCTTTCAGCTAC-CATTATTAATGTGAAAAGATATATAAAGTGA
126 TTTAATTTG-TAGAAAATAGACATTTCACCTACTAATTATTAATGTGAAATGATATATGAAGTGA
67014 ATACAATTCTTAT
190 ATACAATTCTTAT
67027 TACTATTATT
Statistics
Matches: 335, Mismatches: 50, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
196 35 0.10
197 39 0.12
198 11 0.03
199 17 0.05
200 12 0.04
202 1 0.00
203 1 0.00
204 5 0.01
205 83 0.25
206 125 0.37
207 6 0.02
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (206 bp):
ATTAATTTGAAATATATATGAAATAAATACAATTCTTATCACCATTAATATGAATAATAAAGTTA
AAAAAATTCACTCATAACTTAATTTAGATAATAACTTTTTGTTTAATTTATGACAACAACTTTAA
TTTGTAGAAAATAGACATTTCACCTACTAATTATTAATGTGAAATGATATATGAAGTGAATACAA
TTCTTATCACC
Found at i:67042 original size:162 final size:161
Alignment explanation
Indices: 66825--67365 Score: 530
Period size: 164 Copynumber: 3.3 Consensus size: 161
66815 TCTTATCACC
* * * * * *
66825 ATTAATTTGAAATA-ATATGTAAAATAAATACAATTCTTATCACCATTAATGTGAATAATAAAGT
1 ATTAATGTGAAA-AGATATATAAAGTGAATACAATTCTTATCACTATTAATGTGAATCATAAAGT
* * * * *
66889 T-GTAAAATTTACTCATAATTTTAATTTATGGTAATAATTTTGTTTTAATTTATGACAACAACTT
65 TAG-AAAATTCACTCATAACTTTAATTTATGGTCATAATTTTTTTTTAATTTATGACCACAACTT
66953 TAATTGATAGGAAATAGACCTTTCAGCTACCATT
129 TAATTGATA-GAAATAGACCTTTCAGCTACCATT
* *
66987 ATTAATGTGAAAAGATATATAAAGTGAATACAATTCTTATTACTATTATTGTGAATCATAAAGTT
1 ATTAATGTGAAAAGATATATAAAGTGAATACAATTCTTATCACTATTAATGTGAATCATAAAGTT
** * *
67052 AAAGAAAATTCACTC--AACTTTAATTTATAATCATAATTTTTTCTTTTATTTTATGACCACAAT
66 --AGAAAATTCACTCATAACTTTAATTTATGGTCATAA-TTTTT-TTTTAATTTATGACCACAAC
* * **
67115 TTTAATTGATAAAAAATTGACCTTTCA-CTTGTCATT
127 TTTAATTGAT-AGAAATAGACCTTTCAGC-TACCATT
* * *
67151 ATTAATGT-AAAATGATATATCAAGTG-ATACAGTTCTTATCA-TAATTAATATGAATCATAAAG
1 ATTAATGTGAAAA-GATATATAAAGTGAATACAATTCTTATCACT-ATTAATGTGAATCATAAAG
* * * *
67213 TTAAAGAAAATTCACTTATAACTTTAATTTACGGTCATAACGTTTTCTTTAATTTATGACCACAA
64 TT--AGAAAATTCACTCATAACTTTAATTTATGGTCATAA-TTTTTTTTTAATTTATGACCACAA
* **
67278 CTTTAATTGGTAGAAACCGACC-TT--GCTACCATT
126 CTTTAATTGATAGAAATAGACCTTTCAGCTACCATT
* * * * * *
67311 GTTAATGTGAAATGATATATGAAGTGAATTCAATTGTTA-CTACTATTAATTTGAA
1 ATTAATGTGAAAAGATATATAAAGTGAATACAATTCTTATC-ACTATTAATGTGAA
67366 GTGATATATG
Statistics
Matches: 314, Mismatches: 48, Indels: 35
0.79 0.12 0.09
Matches are distributed among these distances:
160 25 0.08
161 25 0.08
162 76 0.24
163 63 0.20
164 101 0.32
165 24 0.08
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (161 bp):
ATTAATGTGAAAAGATATATAAAGTGAATACAATTCTTATCACTATTAATGTGAATCATAAAGTT
AGAAAATTCACTCATAACTTTAATTTATGGTCATAATTTTTTTTTAATTTATGACCACAACTTTA
ATTGATAGAAATAGACCTTTCAGCTACCATT
Found at i:67606 original size:43 final size:43
Alignment explanation
Indices: 67512--67620 Score: 130
Period size: 43 Copynumber: 2.5 Consensus size: 43
67502 CCCTTTCACC
* * *
67512 TATCACTATTAATGTGAAATAATATATGAAGTGAACAAAATTCT
1 TATCACCATTAATGTGAAAT-ATATATAAAATGAACAAAATTCT
* * * * *
67556 TACCACCATTAATTTGAAATATATATAAAATGAATACAATTTT
1 TATCACCATTAATGTGAAATATATATAAAATGAACAAAATTCT
67599 TATCACCATTAATGTG-AATATA
1 TATCACCATTAATGTGAAATATA
67621 AAGTTAAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 6 0.11
43 32 0.58
44 17 0.31
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (43 bp):
TATCACCATTAATGTGAAATATATATAAAATGAACAAAATTCT
Found at i:67687 original size:738 final size:727
Alignment explanation
Indices: 66259--67774 Score: 1886
Period size: 738 Copynumber: 2.1 Consensus size: 727
66249 TCTTATCATC
* *
66259 ATTAATTTGAAATTATATATGAAGTGAATACAATTCTTATCACTATTAATGTAAATCATAAAGTT
1 ATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACTATTAATGTAAATCATAAAGTT
** ** *
66324 AAAGAAAATTCACTCATTACTTTAATTTATTGTTGCAATTTTTCTTTAACTTATGATCACAACTT
66 AAAGAAAATTCACTCA-TACTTTAATTTATAATCACAATTTTTCTTTAACTTATGACCACAACTT
** * *
66389 TAATTAGTAGGAAATTGACCTTTCATCTACCAATATTAATATGAAATGATATATGAAATGAATAA
130 TAATTAGTAAAAAATTGACCTTTCATCTACCAATATTAATATAAAATGATATATCAAATGAATAA
* * * *
66454 AATTATTATCACCATTAATGTGAATAAGTTAAAGAATATTCACTCATAACTTTAATTCATGGTCA
195 AATTATTATCACAATTAATATGAATAAGTTAAAGAAAATTCACTCATAACTTTAATTCACGGTCA
* * * * *
66519 TATATTTTTCTTTAATTTATGATCATAACATTAGTTGGTAAAAAATCACCTATCACTATTAATGT
260 TATAGTTTTCTTTAATTTATGACCACAACATTAATTGGTAAAAAACCACCTATCACTATTAATGT
* *
66584 GAGATGATATATGAAATGAATATAATTGTTACCACCATTAATTTGAAATATATATGAAGTAAATA
325 GAAATGATATATGAAATGAATATAATTGTTACCACCATTAATTTGAAATATATATGAAATAAATA
* * * *
66649 TAATTCTTATCACTATTAATATGAATCATAAAGTTAAAAAAATTCACTCATAACTTAATTTAGAT
390 CAATTCTTATCACTATTAACATGAATCACAAAGTTAAAAAAATCCACTCATAACTTAATTTAGAT
* * * * *
66714 CATAACTTTTTGTTTGATTTATGGCCACAACTTTAATTTGTAGAAAATCTACATTTCACCTACTA
455 CATAACTTTTTCTTTAATTTATGACCACAACTTTAATTGGTAGAAAATCGACATTTCACCTACTA
* * * * *
66779 ATTTTAATGTGAAATGATATATGAAGTGAACACAATTCTTATCACCATTAATTTGAAATAATATG
520 ATATTAATGTGAAATAATATATGAAGTGAACAAAATTCTTACCACCATTAATTTGAAATAATATA
** * * *
66844 TAAAATAAATACAATTCTTATCACCATTAATGTGAATAATAAAGTTGTAAAATTTACTCATAATT
585 TAAAATAAATACAATTCTTATCACCATTAATGTGAATAATAAAGTTAAAAAATTCAATCATAACT
* * *
66909 TTAATTTATGGTAATAATTTTGTTTTAATTTATGACAACAACTTTAATTGATAGGAAATAGACCT
650 TTAATTTACGGTAATAATTTTGTTTTAATTTATGACAACAACTTTAATTAATAAGAAATAGACCT
*
66974 TTCAGCTACCATT
715 TTCACCTACCATT
* * * * *
66987 ATTAATGTGAAAAGATATATAAAGTGAATACAATTCTTATTACTATTATTGTGAATCATAAAGTT
1 ATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACTATTAATGTAAATCATAAAGTT
* ** *
67052 AAAGAAAATTCACTCA-ACTTTAATTTATAATCATAATTTTTTCTTTTATTTTATGACCACAATT
66 AAAGAAAATTCACTCATACTTTAATTTATAATCACAA-TTTTTC-TTTAACTTATGACCACAACT
** * * *
67116 TTAATT-GATAAAAAATTGACCTTTCA-CTTGTCATTATTAATGTAAAATGATATATCAAGTG-A
129 TTAATTAG-TAAAAAATTGACCTTTCATC-TACCAATATTAATATAAAATGATATATCAAATGAA
* * * * * *
67178 TACAGTTCTTATCATAATTAATATGAATCATAAAGTTAAAGAAAATTCACTTATAACTTTAATTT
192 TAAAATTATTATCACAATTAATATG-A--AT-AAGTTAAAGAAAATTCACTCATAACTTTAATTC
* *
67243 ACGGTCATA-ACGTTTTCTTTAATTTATGACCACAACTTTAATTGGT-AGAAACCGACCT-TGCT
253 ACGGTCATATA-GTTTTCTTTAATTTATGACCACAACATTAATTGGTAAAAAACC-ACCTAT-C-
* * * * *
67305 ACCATTGTTAATGTGAAATGATATATGAAGTGAAT-TCAATTGTTACTACTATTAATTTGAAGTG
314 A-C--TATTAATGTGAAATGATATATGAAATGAATAT-AATTGTTACCACCATTAATTTGAAAT-
* *
67369 ATATATGAAATGAATACAATTCTTATCA-TCATTAACATGAATCACAAAGTTAAAAAAATCCATT
374 ATATATGAAATAAATACAATTCTTATCACT-ATTAACATGAATCACAAAGTTAAAAAAATCCACT
* * * ** *
67433 CATAATTTTATTTTATAGTCATAACTTTTTCTTTAATTTATGACCATGACTTTAATTGGTAGGAA
438 CATAA-CTTAATTTAGA-TCATAACTTTTTCTTTAATTTATGACCACAACTTTAATTGGTAGAAA
* * *
67498 ATCGCCCTTTCACCTA-TCACTATTAATGTGAAATAATATATGAAGTGAACAAAATTCTTACCAC
501 ATCGACATTTCACCTACT-AATATTAATGTGAAATAATATATGAAGTGAACAAAATTCTTACCAC
* *
67562 CATTAATTTGAAAT-ATATATAAAATGAATACAATTTTTATCACCATTAATGTGAAT-ATAAAGT
565 CATTAATTTGAAATAATATATAAAATAAATACAATTCTTATCACCATTAATGTGAATAATAAAGT
* * *
67625 TAAAAAAATTCAATCATAACTTTAATTTACGGTCATCATTTTTTCTTTAATTTATGACAACAACT
630 T-AAAAAATTCAATCATAACTTTAATTTACGGTAATAATTTTGT-TTTAATTTATGACAACAACT
* * *
67690 TTAGTTAATAAGAAATTGATCTTTCACCTACCATT
693 TTAATTAATAAGAAATAGACCTTTCACCTACCATT
* * *
67725 ATTGATGTGAAATGATATATGAAGTGAATATAATTCTTATCACCATTAAT
1 ATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACTATTAAT
67775 ATATGGTGGT
Statistics
Matches: 667, Mismatches: 98, Indels: 36
0.83 0.12 0.04
Matches are distributed among these distances:
726 15 0.02
727 28 0.04
728 139 0.21
730 9 0.01
731 73 0.11
732 1 0.00
733 1 0.00
734 1 0.00
735 51 0.08
736 68 0.10
737 81 0.12
738 200 0.30
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (727 bp):
ATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACTATTAATGTAAATCATAAAGTT
AAAGAAAATTCACTCATACTTTAATTTATAATCACAATTTTTCTTTAACTTATGACCACAACTTT
AATTAGTAAAAAATTGACCTTTCATCTACCAATATTAATATAAAATGATATATCAAATGAATAAA
ATTATTATCACAATTAATATGAATAAGTTAAAGAAAATTCACTCATAACTTTAATTCACGGTCAT
ATAGTTTTCTTTAATTTATGACCACAACATTAATTGGTAAAAAACCACCTATCACTATTAATGTG
AAATGATATATGAAATGAATATAATTGTTACCACCATTAATTTGAAATATATATGAAATAAATAC
AATTCTTATCACTATTAACATGAATCACAAAGTTAAAAAAATCCACTCATAACTTAATTTAGATC
ATAACTTTTTCTTTAATTTATGACCACAACTTTAATTGGTAGAAAATCGACATTTCACCTACTAA
TATTAATGTGAAATAATATATGAAGTGAACAAAATTCTTACCACCATTAATTTGAAATAATATAT
AAAATAAATACAATTCTTATCACCATTAATGTGAATAATAAAGTTAAAAAATTCAATCATAACTT
TAATTTACGGTAATAATTTTGTTTTAATTTATGACAACAACTTTAATTAATAAGAAATAGACCTT
TCACCTACCATT
Found at i:67716 original size:206 final size:207
Alignment explanation
Indices: 67151--67774 Score: 722
Period size: 206 Copynumber: 3.0 Consensus size: 207
67141 ACTTGTCATT
* * * * * **
67151 ATTAATGTAAAATGATATATCAAGTG-ATACAGTTCTTATCATAATTAATATGAATCATAAAGTT
1 ATTAATTTGAAATGATATATAAAATGAATACAATTCTTATCACCATTAATATGAATCATAAAGTT
* * *
67215 AAAGAAAATTCACTTATAACTTTAATTTACGGTCATAACGTTTTCTTTAATTTATGACCACAACT
66 AAA-AAAATTCAATCATAACTTTAATTTACGGTCATAACTTTTTCTTTAATTTATGACCACAACT
* * * *
67280 TTAATTGGT-AGAAACCGACCTTGCTACC-AT--TGTTAATGTGAAATGATATATGAAGTGAATT
130 TTAATTGGTAAGAAATCGACCTTTC-ACCTATCATATTAATGTGAAATGATATATGAAGTGAATA
* * * *
67341 CAATTGTTACTACT
194 AAATTCTTACCACC
* * * * *
67355 ATTAATTTGAAGTGATATATGAAATGAATACAATTCTTATCATCATTAACATGAATCACAAAGTT
1 ATTAATTTGAAATGATATATAAAATGAATACAATTCTTATCACCATTAATATGAATCATAAAGTT
* * * * ** **
67420 AAAAAAATCCATTCATAATTTTATTTTATAGTCATAACTTTTTCTTTAATTTATGACCATGACTT
66 AAAAAAATTCAATCATAACTTTAATTTACGGTCATAACTTTTTCTTTAATTTATGACCACAACTT
* * * *
67485 TAATTGGTAGGAAATCGCCCTTTCACCTATCACTATTAATGTGAAATAATATATGAAGTGAACAA
131 TAATTGGTAAGAAATCGACCTTTCACCTATCA-TATTAATGTGAAATGATATATGAAGTGAATAA
67550 AATTCTTACCACC
195 AATTCTTACCACC
* *
67563 ATTAATTTGAAAT-ATATATAAAATGAATACAATTTTTATCACCATTAATGTGAAT-ATAAAGTT
1 ATTAATTTGAAATGATATATAAAATGAATACAATTCTTATCACCATTAATATGAATCATAAAGTT
* * *
67626 AAAAAAATTCAATCATAACTTTAATTTACGGTCATCATTTTTTCTTTAATTTATGACAACAACTT
66 AAAAAAATTCAATCATAACTTTAATTTACGGTCATAACTTTTTCTTTAATTTATGACCACAACTT
* ** * * * * *
67691 TAGTTAATAAGAAATTGATCTTTCACCTACCATTATTGATGTGAAATGATATATGAAGTGAATAT
131 TAATTGGTAAGAAATCGACCTTTCACCTATCA-TATTAATGTGAAATGATATATGAAGTGAATAA
*
67756 AATTCTTATCACC
195 AATTCTTACCACC
67769 ATTAAT
1 ATTAAT
67775 ATATGGTGGT
Statistics
Matches: 351, Mismatches: 63, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
204 84 0.24
205 50 0.14
206 131 0.37
207 37 0.11
208 49 0.14
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (207 bp):
ATTAATTTGAAATGATATATAAAATGAATACAATTCTTATCACCATTAATATGAATCATAAAGTT
AAAAAAATTCAATCATAACTTTAATTTACGGTCATAACTTTTTCTTTAATTTATGACCACAACTT
TAATTGGTAAGAAATCGACCTTTCACCTATCATATTAATGTGAAATGATATATGAAGTGAATAAA
ATTCTTACCACC
Found at i:68418 original size:24 final size:24
Alignment explanation
Indices: 68391--68437 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
68381 TCACTTATAA
**
68391 CTTTAATTTATGGTCATAACTTTT
1 CTTTAATTTATGACCATAACTTTT
*
68415 CTTTAATTTTTGACCATAACTTT
1 CTTTAATTTATGACCATAACTTT
68438 AATTGGTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (24 bp):
CTTTAATTTATGACCATAACTTTT
Found at i:68461 original size:164 final size:165
Alignment explanation
Indices: 68239--68593 Score: 545
Period size: 164 Copynumber: 2.2 Consensus size: 165
68229 AACTTCATGA
* * *
68239 TCATATCTTTTTCTTTAATTTATGACCACAACTTTAATTTGTAAGAAATTGACCTTTCACCTATC
1 TCATAACTTTTTCTTTAATTTATGACCACAACTTTAATTGGTAAGAAATTAACCTTTCACCTATC
* * * *
68304 ATTATTAATGTGAAATGATATATGAAGTGAATATAGTTCTTATCACCATTAATGTGAATCATAAA
66 ACTATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACCATTAATGTAAATCATAAA
*
68369 GTTACGA-AAAATTCACTTATAACTTTAATTTATGG
131 GTTA-AATAAAATTCACTTATAACTTTAATTTATGG
* * *
68404 TCATAAC-TTTTCTTTAATTTTTGACCATAACTTTAATTGGT-AGAAAATTAACCTTTCATCTAT
1 TCATAACTTTTTCTTTAATTTATGACCACAACTTTAATTGGTAAG-AAATTAACCTTTCACCTAT
* *
68467 CACTATTAATGTGAAATTATATATGAAGTGAATACAATTTTTATCACCATTAATGTAAATCATAA
65 CACTATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACCATTAATGTAAATCATAA
68532 AGTTAAATAAAATTCACTTATAACTTTAATTTATGG
130 AGTTAAATAAAATTCACTTATAACTTTAATTTATGG
*
68568 TCGTAACTTTTTCTTTAATTTATGAC
1 TCATAACTTTTTCTTTAATTTATGAC
68594 AATATCGATA
Statistics
Matches: 172, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
163 3 0.02
164 146 0.85
165 23 0.13
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (165 bp):
TCATAACTTTTTCTTTAATTTATGACCACAACTTTAATTGGTAAGAAATTAACCTTTCACCTATC
ACTATTAATGTGAAATGATATATGAAGTGAATACAATTCTTATCACCATTAATGTAAATCATAAA
GTTAAATAAAATTCACTTATAACTTTAATTTATGG
Found at i:75996 original size:21 final size:20
Alignment explanation
Indices: 75966--76025 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 20
75956 GTCCTTCAGG
75966 ATATAGTGGTCATTCGGGAC
1 ATATAGTGGTCATTCGGGAC
* **
75986 ATATCAGTGGTCCTTCTAGAC
1 ATAT-AGTGGTCATTCGGGAC
76007 --ATAGTGGTCATTCGGGAC
1 ATATAGTGGTCATTCGGGAC
76025 A
1 A
76026 AATATTCAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
18 13 0.41
19 2 0.06
20 4 0.12
21 13 0.41
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (20 bp):
ATATAGTGGTCATTCGGGAC
Found at i:76011 original size:39 final size:39
Alignment explanation
Indices: 75948--76025 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
75938 GTCGAGGGAT
*
75948 TATCAGTGGTCCTTCAGGATATAGTGGTCATTCGGGACA
1 TATCAGTGGTCCTTCAGGACATAGTGGTCATTCGGGACA
75987 TATCAGTGGTCCTTCTA-GACATAGTGGTCATTCGGGACA
1 TATCAGTGGTCCTTC-AGGACATAGTGGTCATTCGGGACA
76026 AATATTCAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
39 36 0.97
40 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (39 bp):
TATCAGTGGTCCTTCAGGACATAGTGGTCATTCGGGACA
Found at i:76025 original size:18 final size:18
Alignment explanation
Indices: 75952--76025 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
75942 AGGGATTATC
* * *
75952 AGTGGTCCTTCAGGATAT
1 AGTGGTCATTCGGGACAT
75970 AGTGGTCATTCGGGACATAT
1 AGTGGTCATTCGGGAC--AT
* **
75990 CAGTGGTCCTTCTAGACAT
1 -AGTGGTCATTCGGGACAT
76009 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
76026 AATATTCAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
18 27 0.61
19 2 0.05
20 2 0.05
21 13 0.30
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:82789 original size:18 final size:18
Alignment explanation
Indices: 82734--82790 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
82724 GTGGTCCTTT
* **
82734 ACATAGTGGTCTTTCGAA
1 ACATAGTGGTCATTCGGG
* * *
82752 ACATAGTGATCCTTCTGG
1 ACATAGTGGTCATTCGGG
82770 ACATAGTGGTCATTCGGG
1 ACATAGTGGTCATTCGGG
82788 ACA
1 ACA
82791 AATATTCATG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (18 bp):
ACATAGTGGTCATTCGGG
Done.