Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012143.1 Kokia drynarioides strain JFW-HI SEQ_127142, 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: 183158
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 125 characters in sequence are not A, C, G, or T
Found at i:2574 original size:63 final size:64
Alignment explanation
Indices: 2493--2621 Score: 224
Period size: 63 Copynumber: 2.0 Consensus size: 64
2483 GCATAAGTAA
*
2493 GACTAAAAAATGTCCTAAAAGAACAAACAAAAACTTTTAAAAGTGAAAACTTATTTTAAAAAAT
1 GACTAAAAAATGTCCTAAAAGAACAAACAAAAACTTCTAAAAGTGAAAACTTATTTTAAAAAAT
* *
2557 GACT-AAAAATGTTCTAAAAGAGCAAACAAAAACTTCTAAAAGTGAAAACTTATTTTAAAAAAT
1 GACTAAAAAATGTCCTAAAAGAACAAACAAAAACTTCTAAAAGTGAAAACTTATTTTAAAAAAT
2620 GA
1 GA
2622 AAACCTAACA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
63 58 0.94
64 4 0.06
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (64 bp):
GACTAAAAAATGTCCTAAAAGAACAAACAAAAACTTCTAAAAGTGAAAACTTATTTTAAAAAAT
Found at i:3452 original size:10 final size:10
Alignment explanation
Indices: 3423--3452 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
3413 GGTTAAATGA
3423 CATGTTTTGG
1 CATGTTTTGG
3433 CATGTATTTGG
1 CATGT-TTTGG
3444 CATGTTTTG
1 CATGTTTTG
3453 TGCAAGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.13, C:0.10, G:0.27, T:0.50
Consensus pattern (10 bp):
CATGTTTTGG
Found at i:10662 original size:23 final size:23
Alignment explanation
Indices: 10636--10682 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
10626 GAGGGCATTC
10636 TAAATCAGATGATCTAGGACCAT
1 TAAATCAGATGATCTAGGACCAT
*
10659 TAAATTAGATGATCTAGGACCAT
1 TAAATCAGATGATCTAGGACCAT
10682 T
1 T
10683 CTCGAAACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (23 bp):
TAAATCAGATGATCTAGGACCAT
Found at i:15489 original size:6 final size:6
Alignment explanation
Indices: 15478--15502 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15468 TTTTTGTATA
15478 TATATG TATATG TATATG TATATG T
1 TATATG TATATG TATATG TATATG T
15503 TTCTTGCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:20647 original size:24 final size:24
Alignment explanation
Indices: 20615--20669 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
20605 ACAAAACTGC
20615 TTCCACTTTCTCAAATTCATTGGT
1 TTCCACTTTCTCAAATTCATTGGT
20639 TTCCACTTTCTCAAATTCATTGGT
1 TTCCACTTTCTCAAATTCATTGGT
20663 TTCCACT
1 TTCCACT
20670 GCTTCTCCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.45
Consensus pattern (24 bp):
TTCCACTTTCTCAAATTCATTGGT
Found at i:26506 original size:6 final size:6
Alignment explanation
Indices: 26495--26519 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
26485 TCCGGGACTC
26495 CTGTTG CTGTTG CTGTTG CTGTTG C
1 CTGTTG CTGTTG CTGTTG CTGTTG C
26520 CGACTCTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.32, T:0.48
Consensus pattern (6 bp):
CTGTTG
Found at i:38120 original size:8 final size:8
Alignment explanation
Indices: 38107--38135 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
38097 GAATATCATT
38107 TTTTTTTC
1 TTTTTTTC
38115 TTTTTTTC
1 TTTTTTTC
38123 TTTTTTT-
1 TTTTTTTC
38130 TTTTTT
1 TTTTTT
38136 ACTTCATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (8 bp):
TTTTTTTC
Found at i:42373 original size:69 final size:68
Alignment explanation
Indices: 42265--42412 Score: 235
Period size: 69 Copynumber: 2.2 Consensus size: 68
42255 ATGTAACACA
* *
42265 TTTTTATTCACCAAAAAAAAAACTAGGTGCATATAGTAATTAAATAGATTCTCCATATCTACAA-
1 TTTTTATTCACCAAAAAAAAAACTAGATGCATATAGTAATTAAATAGATTCTCCACATCTACAAT
42329 TTT
66 TTT
* *
42332 TTTTTATTCACCAAAAAAAAAAAGTTAGATGCATATAGTAATTAAATAGATTCTCCACATCTATA
1 TTTTTATTCACC-AAAAAAAAAA-CTAGATGCATATAGTAATTAAATAGATTCTCCACATCTACA
42397 ATTTT
64 ATTTT
42402 TTTTTATTCAC
1 TTTTTATTCAC
42413 ATTGTCGATA
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
67 12 0.16
68 10 0.14
69 38 0.51
70 14 0.19
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (68 bp):
TTTTTATTCACCAAAAAAAAAACTAGATGCATATAGTAATTAAATAGATTCTCCACATCTACAAT
TTT
Found at i:44467 original size:21 final size:21
Alignment explanation
Indices: 44443--44483 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44433 TGAGGTTAAA
44443 GATTCAAGA-TTTAGGATTTAG
1 GATTCAAGATTTTA-GATTTAG
*
44464 GATTCGAGATTTTAGATTTA
1 GATTCAAGATTTTAGATTTA
44484 TGGTTTAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (21 bp):
GATTCAAGATTTTAGATTTAG
Found at i:44686 original size:21 final size:21
Alignment explanation
Indices: 44657--44712 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
44647 AATCCAAACA
* * * *
44657 TAAACCTCAAACTTTTAATCT
1 TAAATCTCAAACCTTCAATAT
44678 TAAATCTCAAACCTTCAATAT
1 TAAATCTCAAACCTTCAATAT
*
44699 TAAATTCTTAAACC
1 TAAA-TCTCAAACC
44713 CTAAATCTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATCTCAAACCTTCAATAT
Found at i:45140 original size:18 final size:18
Alignment explanation
Indices: 45105--45140 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45095 TTATTTTAAT
*
45105 TATAAAATATATTTAAAA
1 TATAAAATATATTAAAAA
*
45123 TATAAAATTTATTAAAAA
1 TATAAAATATATTAAAAA
45141 AAATCGAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAAAATATATTAAAAA
Found at i:47316 original size:7 final size:7
Alignment explanation
Indices: 47304--47348 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
47294 TGTTTTCTAC
47304 CCTCTTT
1 CCTCTTT
47311 CCTCTTT
1 CCTCTTT
47318 CCTCTTT
1 CCTCTTT
47325 CCTCTTT
1 CCTCTTT
47332 CCTCTTT
1 CCTCTTT
47339 CCTCTTT
1 CCTCTTT
47346 CCT
1 CCT
47349 TCACTTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
CCTCTTT
Found at i:54287 original size:134 final size:133
Alignment explanation
Indices: 54039--54304 Score: 417
Period size: 134 Copynumber: 2.0 Consensus size: 133
54029 ATACAGATTT
* * *
54039 TTTTTTTTTTTTTGCTCTGCTTTTAGCAAAAATATAGAATATGAAATGTGTGGGGGTAATTTAGA
1 TTTTTTTTTTTTTGCTCTGCTTTTAGCAAAAATATAGAACATGAAAAGTGTGGAGGTAATTTAGA
* * *
54104 ACTATTACTTCCATGTTTTTTTATTTAGAACAGGTAGAACACGAGTCTGATTGCATTTTGAATTG
66 ACTATTACTTACATGTTTTTTTATTTAGAACAGGTAGAACACGAATCTGATAGCATTTTGAATTG
54169 CAA
131 CAA
* **
54172 TTTTTTTTTTTTTGCTCTGCTTTTAGCCAAAATATAGGGCATGAAAAAAGTGTGGAGGTAATTTA
1 TTTTTTTTTTTTTGCTCTGCTTTTAGCAAAAATATAGAACATG--AAAAGTGTGGAGGTAATTTA
*
54237 GAGCTATTACTTACATG-TTTTTTATTTAGAACAGGTAGAACACGAATCTGATAGCATTTTGAAT
64 GAACTATTACTTACATGTTTTTTTATTTAGAACAGGTAGAACACGAATCTGATAGCATTTTGAAT
54301 TGCA
129 TGCA
54305 TTTCCTTGGA
Statistics
Matches: 121, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
133 39 0.32
134 49 0.40
135 33 0.27
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.41
Consensus pattern (133 bp):
TTTTTTTTTTTTTGCTCTGCTTTTAGCAAAAATATAGAACATGAAAAGTGTGGAGGTAATTTAGA
ACTATTACTTACATGTTTTTTTATTTAGAACAGGTAGAACACGAATCTGATAGCATTTTGAATTG
CAA
Found at i:58362 original size:13 final size:13
Alignment explanation
Indices: 58344--58369 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58334 ATTAAATTAT
58344 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
58357 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
58370 TAATTAGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:58951 original size:18 final size:18
Alignment explanation
Indices: 58909--58952 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
58899 GTTTGAATTT
58909 ATTTTATTTCAGATTTAA
1 ATTTTATTTCAGATTTAA
* *
58927 ATATTATTTC-GATTTTTA
1 ATTTTATTTCAGA-TTTAA
58945 ATTTTATT
1 ATTTTATT
58953 ATTTTTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (18 bp):
ATTTTATTTCAGATTTAA
Found at i:64576 original size:18 final size:18
Alignment explanation
Indices: 64553--64589 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
64543 TTTGTGATCA
64553 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
64571 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
64589 A
1 A
64590 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:68227 original size:20 final size:21
Alignment explanation
Indices: 68204--68254 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
68194 ATTAATTATT
*
68204 TATAAAATT-TAATTTGAATA
1 TATAAAATTATAATTTAAATA
*
68224 TAT-AAATTATATTTTAAATA
1 TATAAAATTATAATTTAAATA
68244 T-TAAAA-TATAA
1 TATAAAATTATAA
68255 CCATTTCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TATAAAATTATAATTTAAATA
Found at i:68550 original size:95 final size:93
Alignment explanation
Indices: 68437--68611 Score: 269
Period size: 95 Copynumber: 1.9 Consensus size: 93
68427 CATAAAAAAT
* * * *
68437 TTAACTAATTAATTAATTGCATATCCAAGTTTTAATAAAAAGTTAGATTAAAATCCACATAAATT
1 TTAACTAATTAATCAATTGCAAATCCAAGTTCTAATAAAAA-ATAGATT-AAATCCACATAAATT
*
68502 TTGAATATTTTGTTATACTTAATTAACTAA
64 TTGAATATTTTATTATACTTAATTAACTAA
* *
68532 TTAATTAATTAATCAATTGCAAATCCAAGTTCTAATAAAAAATATATTAAATCCACATAAATTTT
1 TTAACTAATTAATCAATTGCAAATCCAAGTTCTAATAAAAAATAGATTAAATCCACATAAATTTT
68597 GAATATTTTATTATA
66 GAATATTTTATTATA
68612 TTATTATAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 31 0.42
94 5 0.07
95 37 0.51
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.41
Consensus pattern (93 bp):
TTAACTAATTAATCAATTGCAAATCCAAGTTCTAATAAAAAATAGATTAAATCCACATAAATTTT
GAATATTTTATTATACTTAATTAACTAA
Found at i:68878 original size:40 final size:37
Alignment explanation
Indices: 68812--68888 Score: 109
Period size: 40 Copynumber: 2.0 Consensus size: 37
68802 ACATAATTAT
* *
68812 ATAAAATAAAAATAATTTAATATTATTTTATTAATAA
1 ATAAAATAAAAATAATTAAATATTATTTCATTAATAA
68849 ATAAATATACAAAATAATTCAAATATTATTTCATTAATAA
1 ATAAA-ATA-AAAATAATT-AAATATTATTTCATTAATAA
68889 TTTTAGTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
37 5 0.14
38 3 0.09
39 9 0.26
40 18 0.51
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (37 bp):
ATAAAATAAAAATAATTAAATATTATTTCATTAATAA
Found at i:73541 original size:15 final size:17
Alignment explanation
Indices: 73511--73552 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
73501 TAGTAATAAT
73511 ATAATTTTATTATTTTA
1 ATAATTTTATTATTTTA
*
73528 ATAA-TTTA-TATTTTT
1 ATAATTTTATTATTTTA
73543 ATAAATTTTA
1 AT-AATTTTA
73553 AAAGATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATAATTTTATTATTTTA
Found at i:73549 original size:16 final size:17
Alignment explanation
Indices: 73510--73550 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
73500 ATAGTAATAA
*
73510 TATAATTTTATTATTTT
1 TATAAATTTATTATTTT
*
73527 AAT-AATTTA-TATTTT
1 TATAAATTTATTATTTT
73542 TATAAATTT
1 TATAAATTT
73551 TAAAAGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 8 0.40
16 10 0.50
17 2 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATAAATTTATTATTTT
Found at i:75723 original size:15 final size:16
Alignment explanation
Indices: 75692--75733 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
75682 TATATTTTTA
75692 TTAATAATTTTATTATT
1 TTAATAA-TTTATTATT
75709 TTAATAATTTA-TATT
1 TTAATAATTTATTATT
*
75724 TTTATAATTT
1 TTAATAATTT
75734 TTAGATGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 13 0.54
16 4 0.17
17 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAATAATTTATTATT
Found at i:76687 original size:25 final size:25
Alignment explanation
Indices: 76670--76720 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
76660 AAAATTATAA
*
76670 TATTAAAATTTTAAAAAATAAAAAC
1 TATTAAAATATTAAAAAATAAAAAC
76695 TATTAAAATATTAAAGATAATAAAAA
1 TATTAAAATATTAAA-A-AATAAAAA
76721 AAATGGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.61
26 1 0.04
27 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
TATTAAAATATTAAAAAATAAAAAC
Found at i:76706 original size:8 final size:8
Alignment explanation
Indices: 76658--76719 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
76648 TTTTAAAATC
76658 TAAAA-AT
1 TAAAATAT
*
76665 TATAATAT
1 TAAAATAT
*
76673 TAAAATTT
1 TAAAATAT
*
76681 TAAAAAAT
1 TAAAATAT
*
76689 AAAAACTAT
1 TAAAA-TAT
76698 TAAAATAT
1 TAAAATAT
*
76706 TAAAGATAA
1 TAAA-ATAT
76715 TAAAA
1 TAAAA
76720 AAAATGGTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
7 4 0.09
8 26 0.60
9 13 0.30
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (8 bp):
TAAAATAT
Found at i:77734 original size:31 final size:31
Alignment explanation
Indices: 77668--77734 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
77658 AATAACCCAG
* *
77668 TGACTTAAATAAAAACTTTTATATAGTTCAG
1 TGACTTAAATAAAAACTTTTATATAGCTCAA
*
77699 TGACTTAAATGAAAA-TTTTCGA-ATAGCTCAA
1 TGACTTAAATAAAAACTTTT--ATATAGCTCAA
77730 TGACT
1 TGACT
77735 ATTTTGTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 4 0.13
31 26 0.84
32 1 0.03
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTATATAGCTCAA
Found at i:78304 original size:105 final size:105
Alignment explanation
Indices: 78122--78330 Score: 409
Period size: 105 Copynumber: 2.0 Consensus size: 105
78112 GATATAATTA
*
78122 TGCAAATATAACTTCACTTGCCTTAGGTTGGTGGTTCAAGTCCCCCTTCACTCAAGTAACTTCAT
1 TGCAAATATAACTTCACTTGCCTCAGGTTGGTGGTTCAAGTCCCCCTTCACTCAAGTAACTTCAT
78187 AATTTTTCTCATTCTCTATATTGACACTTCTTTTTTAAGT
66 AATTTTTCTCATTCTCTATATTGACACTTCTTTTTTAAGT
78227 TGCAAATATAACTTCACTTGCCTCAGGTTGGTGGTTCAAGTCCCCCTTCACTCAAGTAACTTCAT
1 TGCAAATATAACTTCACTTGCCTCAGGTTGGTGGTTCAAGTCCCCCTTCACTCAAGTAACTTCAT
78292 AATTTTTCTCATTCTCTATATTGACACTTCTTTTTTAAG
66 AATTTTTCTCATTCTCTATATTGACACTTCTTTTTTAAG
78331 CTTTGTAGAT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.41
Consensus pattern (105 bp):
TGCAAATATAACTTCACTTGCCTCAGGTTGGTGGTTCAAGTCCCCCTTCACTCAAGTAACTTCAT
AATTTTTCTCATTCTCTATATTGACACTTCTTTTTTAAGT
Found at i:80178 original size:99 final size:99
Alignment explanation
Indices: 80007--80205 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
79997 TCATCTATAT
80007 ATTGGGTTAAAAGAAGGAAGATTCAAGAAGGGGCATAATCCAAGGGACCATAAGGTTCAAAGAAT
1 ATTGGGTTAAAAGAAGGAAGATTCAAGAAGGGGCATAATCCAAGGGACCATAAGGTTCAAAGAAT
80072 TCAGCAAACAGACCCTTTTTCCGCCTTGGGTTCC
66 TCAGCAAACAGACCCTTTTTCCGCCTTGGGTTCC
80106 ATTGGGTTAAAAGAAGGAAGATTCAAGAAGGGGCATAATCCAAGGGACCATAAGGTTCAAAGAAT
1 ATTGGGTTAAAAGAAGGAAGATTCAAGAAGGGGCATAATCCAAGGGACCATAAGGTTCAAAGAAT
80171 TCAGCAAACAGACCCTTTTTCCGCCTTGGGTTCC
66 TCAGCAAACAGACCCTTTTTCCGCCTTGGGTTCC
80205 A
1 A
80206 CCCCATATCT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (99 bp):
ATTGGGTTAAAAGAAGGAAGATTCAAGAAGGGGCATAATCCAAGGGACCATAAGGTTCAAAGAAT
TCAGCAAACAGACCCTTTTTCCGCCTTGGGTTCC
Found at i:82554 original size:49 final size:47
Alignment explanation
Indices: 82438--82554 Score: 114
Period size: 49 Copynumber: 2.5 Consensus size: 47
82428 AAAAACTAAT
* * * *
82438 AAAT-TATTAAAAAT-TATAAAATTAATAAAATATATTTAAATATAA
1 AAATATATTAAAATTATATAAAAATAATAAAAAATATATAAATATAA
* * *
82483 AAATGTATTAAAATTCTAATAAAAATCATAAAAAATCATATAAATTATAA
1 AAATATATTAAAATTAT-ATAAAAATAATAAAAAAT-ATATAAA-TATAA
82533 AAA-ATATTAAAATTGATATAAA
1 AAATATATTAAAATT-ATATAAA
82555 CTTATAACAA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
45 4 0.07
46 9 0.15
47 1 0.02
48 15 0.25
49 21 0.36
50 9 0.15
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (47 bp):
AAATATATTAAAATTATATAAAAATAATAAAAAATATATAAATATAA
Found at i:83024 original size:10 final size:9
Alignment explanation
Indices: 82972--83022 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
82962 TTTTTATGTT
82972 TTTTTATAA
1 TTTTTATAA
82981 TTTTTATAA
1 TTTTTATAA
* *
82990 GCTTATATTAA
1 -TTTTTA-TAA
*
83001 TTTTAAT-A
1 TTTTTATAA
83009 TTTTTATAA
1 TTTTTATAA
83018 TTTTT
1 TTTTT
83023 TACAATTCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
8 7 0.21
9 16 0.48
10 7 0.21
11 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:84671 original size:23 final size:23
Alignment explanation
Indices: 84604--84671 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
84594 AAATATGTAC
84604 TATATTAAATAAA-AAAAT-TAGTT
1 TATA-TAAATAAATAAAATATA-TT
* * *
84627 TAAAT-TATAAGTAAAATGATATT
1 TATATAAATAAATAAAAT-ATATT
84650 TATATAAATAAATAAAATATAT
1 TATATAAATAAATAAAATATAT
84672 AAACAATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
21 4 0.11
22 6 0.17
23 13 0.37
24 12 0.34
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
TATATAAATAAATAAAATATATT
Found at i:85632 original size:12 final size:12
Alignment explanation
Indices: 85606--85656 Score: 59
Period size: 12 Copynumber: 4.1 Consensus size: 12
85596 AAATAACTAA
*
85606 AATATGATAAAAT
1 AATAT-ATAATAT
85619 AATATATAATAT
1 AATATATAATAT
85631 AATATAT-ATAT
1 AATATATAATAT
85642 ATATATATATATAT
1 A-ATATATA-ATAT
85656 A
1 A
85657 TGTGAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
11 5 0.15
12 19 0.56
13 5 0.15
14 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
AATATATAATAT
Found at i:85637 original size:2 final size:2
Alignment explanation
Indices: 85620--85657 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
85610 TGATAAAATA
85620 AT AT AT A- AT AT A- 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
85658 GTGAATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:87316 original size:18 final size:17
Alignment explanation
Indices: 87293--87330 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
87283 TTTTTTAGAA
87293 TTTTAAAAAATTATAAAT
1 TTTTAAAAAA-TATAAAT
*
87311 TTTTAAAATATATAAAT
1 TTTTAAAAAATATAAAT
87328 TTT
1 TTT
87331 GAAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAAAAAATATAAAT
Found at i:87330 original size:16 final size:17
Alignment explanation
Indices: 87291--87335 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
87281 TATTTTTTAG
*
87291 AATTTTAAAAAATTATA
1 AATTTTAAAATATTATA
87308 AATTTTTAAAATA-TATA
1 AA-TTTTAAAATATTATA
*
87325 AATTTTGAAAT
1 AATTTTAAAAT
87336 TTTTATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.32
17 8 0.32
18 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTTTAAAATATTATA
Found at i:88350 original size:110 final size:110
Alignment explanation
Indices: 88157--88365 Score: 355
Period size: 110 Copynumber: 1.9 Consensus size: 110
88147 ATTATCTATT
* * *
88157 AGTTAAAATCACAATTCAATGAGGGCAAAAAGGTCATTTCCCAAATTTTTGAAGACTTTTACTGA
1 AGTTAAAATCACAATTCAATGAGGGCAAAAAGGTCATTTCCCAAATTCTTGAAGACTTCTACCGA
88222 TACTTGTTGAACAAGTATCGGTAGTTGTCAAGTCGGTAGATTCAG
66 TACTTGTTGAACAAGTATCGGTAGTTGTCAAGTCGGTAGATTCAG
* * *
88267 AGTTAAAATCACAATTCAATGAGGGCAAAAAGGTCATTTCCTAAATTCTTGCAGACTTCTACCGG
1 AGTTAAAATCACAATTCAATGAGGGCAAAAAGGTCATTTCCCAAATTCTTGAAGACTTCTACCGA
*
88332 TACTTGTTGAACAAGTATCGGTAGTTTTCAAGTC
66 TACTTGTTGAACAAGTATCGGTAGTTGTCAAGTC
88366 AATAAATAGT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 92 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (110 bp):
AGTTAAAATCACAATTCAATGAGGGCAAAAAGGTCATTTCCCAAATTCTTGAAGACTTCTACCGA
TACTTGTTGAACAAGTATCGGTAGTTGTCAAGTCGGTAGATTCAG
Found at i:88450 original size:21 final size:21
Alignment explanation
Indices: 88396--88450 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
88386 TGCAGACCTT
* *
88396 TACCGATATAAATGATAGTTC
1 TACCGATATAAGTGACAGTTC
**
88417 TACCGATGCAAGTGACAGTTC
1 TACCGATATAAGTGACAGTTC
88438 TACCGATATAAGT
1 TACCGATATAAGT
88451 ATTACTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (21 bp):
TACCGATATAAGTGACAGTTC
Found at i:89199 original size:53 final size:53
Alignment explanation
Indices: 89133--89475 Score: 409
Period size: 53 Copynumber: 6.5 Consensus size: 53
89123 TCCACATTTG
* **
89133 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTTGT
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCGTGATAGGATTCAT
* * * * **
89186 GTAACTCAGGATGACACAAAGTCATCGAACCTTTAATCCATGATAGGATTTGT
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCGTGATAGGATTCAT
* * *
89239 GTAACTCACGATGACACAAAGTCATCGGACCCTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCGTGATAGGATTCAT
* *
89292 ATAACTCACGATGACACAGAGTCATC-GACCTTTAATTCGTGATAGGATTCAT
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCGTGATAGGATTCAT
* * * * * * *
89344 ATGACTCACAATGACACAGAGTCATCAGAACTTTAATTCGTGATAGGGTTCAT
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCGTGATAGGATTCAT
*** * * * * *
89397 ATAACTCACGATGATGTAGAGTCATTGGACCTTTAATTCGTAATAGAATTCAT
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCGTGATAGGATTCAT
*
89450 ATAACTCACGATGACACATAGTCATC
1 ATAACTCACGATGACACAAAGTCATC
89476 AAACTTTTTT
Statistics
Matches: 254, Mismatches: 35, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
52 47 0.19
53 207 0.81
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (53 bp):
ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCGTGATAGGATTCAT
Found at i:89427 original size:158 final size:159
Alignment explanation
Indices: 89133--89475 Score: 438
Period size: 158 Copynumber: 2.2 Consensus size: 159
89123 TCCACATTTG
** * **
89133 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTTGTGTAACTCAGGAT
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCATATAACTCACAAT
** *
89198 GACACAAAGTCATCGAACCTTTAATCCATGATAGGATTTGTGTAACTCACGATGACACAAAGTCA
66 GACACAAAGTCATCGAACCTTTAATCCATGATAGGATTCATATAACTCACGATGACACAAAGTCA
*
89263 TCGGACCCTTAATCCGTAATAGGATTCAT
131 TCGGACCCTTAATCCGTAATAGAATTCAT
* * * *
89292 ATAACTCACGATGACACAGAGTCATC-GACCTTTAATTCGTGATAGGATTCATATGACTCACAAT
1 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCATATAACTCACAAT
* * * * *** *
89356 GACACAGAGTCATCAGAA-CTTTAATTCGTGATAGGGTTCATATAACTCACGATGATGTAGAGTC
66 GACACAAAGTCATC-GAACCTTTAATCCATGATAGGATTCATATAACTCACGATGACACAAAGTC
* * *
89420 ATTGGACCTTTAATTCGTAATAGAATTCAT
130 ATCGGACCCTTAATCCGTAATAGAATTCAT
*
89450 ATAACTCACGATGACACATAGTCATC
1 ATAACTCACGATGACACAAAGTCATC
89476 AAACTTTTTT
Statistics
Matches: 158, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
158 130 0.82
159 28 0.18
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (159 bp):
ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCATATAACTCACAAT
GACACAAAGTCATCGAACCTTTAATCCATGATAGGATTCATATAACTCACGATGACACAAAGTCA
TCGGACCCTTAATCCGTAATAGAATTCAT
Found at i:90223 original size:75 final size:75
Alignment explanation
Indices: 90100--90249 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
90090 AAATTAATCC
*
90100 CTGGGTTAGCTAGATTAAGCTGATACGAACTCAAAAACATAAAAATTACTAAAAATGGACGAAGA
1 CTGGGTTAGCTAGATTAAGCTGATACGAACTCAAAAACATAAAAATTACTAAAAATGAACGAAGA
90165 TTTCTTACTA
66 TTTCTTACTA
90175 CTGGGTTAGCTAGATTAAGCTGATACGAACTCAAAAACATAAAAATTACTAAAAATGAACGAAGA
1 CTGGGTTAGCTAGATTAAGCTGATACGAACTCAAAAACATAAAAATTACTAAAAATGAACGAAGA
90240 TTTCTTACTA
66 TTTCTTACTA
90250 AAAAACATAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (75 bp):
CTGGGTTAGCTAGATTAAGCTGATACGAACTCAAAAACATAAAAATTACTAAAAATGAACGAAGA
TTTCTTACTA
Found at i:91959 original size:29 final size:29
Alignment explanation
Indices: 91927--92082 Score: 138
Period size: 30 Copynumber: 5.3 Consensus size: 29
91917 TTTACCCTCG
*
91927 AACTTCTCTAAAATTACATTTGACTCCCA
1 AACTTCTCCAAAATTACATTTGACTCCCA
* *
91956 AACTTTTCCAAAATTACATTTTGACCCCCA
1 AACTTCTCCAAAATTACA-TTTGACTCCCA
*
91986 AACTTC-CCAAAATTACATTTTGACTTCCA
1 AACTTCTCCAAAATTACA-TTTGACTCCCA
* ** *
92015 AACTTTTCCAAAATTATGTTTTAAC-CCCTA
1 AACTTCTCCAAAATTA-CATTTGACTCCC-A
* * *
92045 AACTT-TCATAAAATTACATTTTAATCCCTA
1 AACTTCTC-CAAAATTACATTTGACTCCC-A
92075 AACTTCTC
1 AACTTCTC
92083 TAAAGTCACA
Statistics
Matches: 104, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
29 50 0.48
30 52 0.50
31 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
AACTTCTCCAAAATTACATTTGACTCCCA
Found at i:91977 original size:59 final size:58
Alignment explanation
Indices: 91927--92124 Score: 193
Period size: 59 Copynumber: 3.4 Consensus size: 58
91917 TTTACCCTCG
*
91927 AACTTCTCTAAAATTACATTTGACTCCCAAACTTTTCCAAAATTACATTTTGACCCCCA
1 AACTTCTCTAAAATTACATTTGACTCCCAAACTTTTCCAAAATTACATTTT-AACCCCA
* * **
91986 AACTTC-CCAAAATTACATTTTGACTTCCAAACTTTTCCAAAATTATGTTTTAACCCCTA
1 AACTTCTCTAAAATTACA-TTTGACTCCCAAACTTTTCCAAAATTACATTTTAACCCC-A
* * * * * * **
92045 AACTT-TCATAAAATTACATTTTAATCCCTAAACTTCTCTAAAGTCACATTTTAACCTTA
1 AACTTCTC-TAAAATTACATTTGACTCCC-AAACTTTTCCAAAATTACATTTTAACCCCA
* * *
92104 AAATTATCTAAAATTAAATTT
1 AACTTCTCTAAAATTACATTT
92125 TAACCTTTAA
Statistics
Matches: 114, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
58 15 0.13
59 67 0.59
60 32 0.28
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (58 bp):
AACTTCTCTAAAATTACATTTGACTCCCAAACTTTTCCAAAATTACATTTTAACCCCA
Found at i:91986 original size:30 final size:30
Alignment explanation
Indices: 91927--92188 Score: 180
Period size: 29 Copynumber: 8.9 Consensus size: 30
91917 TTTACCCTCG
* *
91927 AACTTCTCTAAAATTACA-TTTGACTCCC-A
1 AACTTTTCCAAAATTACATTTTGAC-CCCTA
*
91956 AACTTTTCCAAAATTACATTTTGACCCCCA
1 AACTTTTCCAAAATTACATTTTGACCCCTA
* *
91986 AAC-TTCCCAAAATTACATTTTGACTTCC-A
1 AACTTTTCCAAAATTACATTTTGAC-CCCTA
** *
92015 AACTTTTCCAAAATTATGTTTTAACCCCTA
1 AACTTTTCCAAAATTACATTTTGACCCCTA
* * *
92045 AAC-TTTCATAAAATTACATTTTAATCCCTA
1 AACTTTTC-CAAAATTACATTTTGACCCCTA
* * * * * *
92075 AACTTCTCTAAAGTCACATTTT-AACCTTA
1 AACTTTTCCAAAATTACATTTTGACCCCTA
* * * * * * *
92104 AAATTATCTAAAATTAAATTTT-AACCTTT
1 AACTTTTCCAAAATTACATTTTGACCCCTA
*
92133 AAC-TTTCCTAAAATTACATTTTCACCCCTA
1 AACTTTTCC-AAAATTACATTTTGACCCCTA
* **
92163 AAATTTTCCAAAATTATGTTTTGACC
1 AACTTTTCCAAAATTACATTTTGACC
92189 TCATATTCTC
Statistics
Matches: 188, Mismatches: 35, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
28 3 0.02
29 91 0.48
30 86 0.46
31 8 0.04
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (30 bp):
AACTTTTCCAAAATTACATTTTGACCCCTA
Found at i:92165 original size:59 final size:58
Alignment explanation
Indices: 91933--92178 Score: 171
Period size: 59 Copynumber: 4.2 Consensus size: 58
91923 CTCGAACTTC
* * * * *
91933 TCTAAAATTACATTTGACTCCC-AAACTTTTCC-AAAATTACATTTTGACCCCCAAACTT
1 TCTAAAATTAAATTTTAATCCCTAAAC-TTTCCTAAAATTACATTTT-ACCCCTAAAATT
* * * * * ** *
91991 CCCAAAATTACATTTTGACTTCC-AAACTTTTCC-AAAATTATGTTTTAACCCCTAAACTT
1 TCTAAAATTAAATTTT-AATCCCTAAAC-TTTCCTAAAATTACATTTT-ACCCCTAAAATT
* * * * *
92050 TCATAAAATTACATTTTAATCCCTAAAC-TTCTCTAAAGTCACATTTTAACCTTAAAATT
1 TC-TAAAATTAAATTTTAATCCCTAAACTTTC-CTAAAATTACATTTTACCCCTAAAATT
* *
92109 ATCTAAAATTAAATTTTAA-CCTTTAACTTTCCTAAAATTACATTTTCACCCCTAAAATTT
1 -TCTAAAATTAAATTTTAATCCCTAAACTTTCCTAAAATTACATTTT-ACCCCTAAAA-TT
*
92169 TCCAAAATTA
1 TCTAAAATTA
92179 TGTTTTGACC
Statistics
Matches: 152, Mismatches: 27, Indels: 17
0.78 0.14 0.09
Matches are distributed among these distances:
58 35 0.23
59 87 0.57
60 30 0.20
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (58 bp):
TCTAAAATTAAATTTTAATCCCTAAACTTTCCTAAAATTACATTTTACCCCTAAAATT
Found at i:97239 original size:14 final size:14
Alignment explanation
Indices: 97220--97247 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
97210 TATATTAGTA
97220 TTTTCTATTCTATT
1 TTTTCTATTCTATT
97234 TTTTCTATTCTATT
1 TTTTCTATTCTATT
97248 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:101570 original size:27 final size:27
Alignment explanation
Indices: 101537--101601 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
101527 TGAAAATTTT
101537 AATTAATTGATATGAGTTATCAAATTA
1 AATTAATTGATATGAGTTATCAAATTA
101564 AATTAATTGATATGAGTTATCAAATTA
1 AATTAATTGATATGAGTTATCAAATTA
101591 AATTAATTGAT
1 AATTAATTGAT
101602 TTAGACTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (27 bp):
AATTAATTGATATGAGTTATCAAATTA
Found at i:101875 original size:69 final size:69
Alignment explanation
Indices: 101814--101942 Score: 168
Period size: 69 Copynumber: 1.9 Consensus size: 69
101804 TACAATGATG
* * * *
101814 ACTAGATGAATGTATAATTGATTAAAACTCTTAAAATTACTTACACACTATAATATCATTACATC
1 ACTAGAAGAATGTACAATTGATCAAAACTCTTAAAATTACTTACACACTACAATATCATTACATC
101879 AATA
66 AATA
* * * * * *
101883 ATTAGAAGAATGTACAATTGATCAATATTCTTGAAATTATTTGCACACTACAATATCATT
1 ACTAGAAGAATGTACAATTGATCAAAACTCTTAAAATTACTTACACACTACAATATCATT
101943 TCATTTGTAC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
69 50 1.00
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.36
Consensus pattern (69 bp):
ACTAGAAGAATGTACAATTGATCAAAACTCTTAAAATTACTTACACACTACAATATCATTACATC
AATA
Found at i:108726 original size:42 final size:42
Alignment explanation
Indices: 108652--108763 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
108642 GCTTTCTTGC
* ** * *
108652 CAACTATACAAAAAATTCATCCAACTGGACGAGTTTTTATGAT
1 CAACTATACAAAAAATTCACCCAACTAAACGAGATTTCATG-T
*
108695 -AATTATACAAAAAATTCACCCAACTAAACGAGATTTCATGT
1 CAACTATACAAAAAATTCACCCAACTAAACGAGATTTCATGT
*
108736 CAACTATGCAAAAAA-TCAACCCAACTAA
1 CAACTATACAAAAAATTC-ACCCAACTAA
108764 CTAGACATTT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
41 3 0.05
42 56 0.95
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (42 bp):
CAACTATACAAAAAATTCACCCAACTAAACGAGATTTCATGT
Found at i:110392 original size:4 final size:4
Alignment explanation
Indices: 110383--110407 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
110373 TCAATCTGTG
110383 TCAT TCAT TCAT TCAT TCAT TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT T
110408 TATTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCAT
Found at i:121448 original size:3 final size:3
Alignment explanation
Indices: 121440--121469 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
121430 TACTACAATT
121440 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
121470 TAATTCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:123274 original size:15 final size:15
Alignment explanation
Indices: 123237--123268 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
123227 ACTTTCATAC
123237 ATATTTATTTATCAA
1 ATATTTATTTATCAA
123252 ATATTTATTTATCAA
1 ATATTTATTTATCAA
123267 AT
1 AT
123269 TATTATGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTATTTATCAA
Found at i:132675 original size:2 final size:2
Alignment explanation
Indices: 132668--132710 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
132658 TTCCTTCTTT
132668 TA TA TA TA 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 TA TA TA TA
132710 T
1 T
132711 TAAATTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:140609 original size:57 final size:57
Alignment explanation
Indices: 140521--140633 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
140511 TGATCCTACC
*
140521 AAGGTTTCTGGAACTAAGAGACCATCCCCTGAATGTCCCGTGAGCCCCTGGCAATGG
1 AAGGTTTCTGGAACTAAGAGACCATCCCCTGAATGTCCCGTGAGCCCCTCGCAATGG
*
140578 AAGGTTTCTGGAACTAAGAGACCATCCCCTGAATGTCCTGTGAGCCCCTCGCAATG
1 AAGGTTTCTGGAACTAAGAGACCATCCCCTGAATGTCCCGTGAGCCCCTCGCAATG
140634 CCAATCTCCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (57 bp):
AAGGTTTCTGGAACTAAGAGACCATCCCCTGAATGTCCCGTGAGCCCCTCGCAATGG
Found at i:142396 original size:12 final size:11
Alignment explanation
Indices: 142367--142395 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
142357 CTAAATAGAG
142367 TTTTTTTGTTT
1 TTTTTTTGTTT
142378 TTTTTTTGTTT
1 TTTTTTTGTTT
142389 TTTTTTT
1 TTTTTTT
142396 TTCATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:142403 original size:19 final size:19
Alignment explanation
Indices: 142366--142403 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
142356 TCTAAATAGA
*
142366 GTTTTTTTGTTTTTTTTTT
1 GTTTTTTTGTTTTTATTTT
142385 GTTTTTTT-TTTTTCATTTT
1 GTTTTTTTGTTTTT-ATTTT
142404 AAATGCGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.87
Consensus pattern (19 bp):
GTTTTTTTGTTTTTATTTT
Found at i:144302 original size:213 final size:212
Alignment explanation
Indices: 143935--144360 Score: 807
Period size: 213 Copynumber: 2.0 Consensus size: 212
143925 TACCACCTGC
143935 TCCTCTTCAAAGTGATTCATATCCCTCAGCCTTACCTTTGGATTTGAGGTTAAGTCTCTGAAGAA
1 TCCTCTTCAAAGTGATTCATATCCCTCAGCCTTACCTTTGGATTTGAGGTTAAGTCTCTGAAGAA
* ** *
144000 CTAAAGTTGTATGCGACTTGTAACCTAGGATTAGAATTATTCTGTATGTATACTCGTATATTTGA
66 CTAAAGTTGTATGCGACTCGTAACCTAGGATTAGAATTATAATGTATGTATACTCATATATTTGA
144065 CACTGATTTCCTTTTTATTTAAACACTAAACCCAACTTAATACTATGGTTTTTTTATCTTTAATT
131 CACTGATTTCCTTTTTATTTAAACACTAAACCCAACTTAATACTATGG-TTTTTTATCTTTAATT
144130 CATCCAACAGTTCATATA
195 CATCCAACAGTTCATATA
144148 TCCTCTTCAAAGTGATTCATATCCCTCAGCCTTACCTTTGGATTTGAGGTTAAGTCTCTGAAGAA
1 TCCTCTTCAAAGTGATTCATATCCCTCAGCCTTACCTTTGGATTTGAGGTTAAGTCTCTGAAGAA
144213 CTAAAGTTGTATGCGACTCGTAACCTAGGATTAGAATTATAATGTATGTATACTCATATATTTGA
66 CTAAAGTTGTATGCGACTCGTAACCTAGGATTAGAATTATAATGTATGTATACTCATATATTTGA
144278 CACTGATTTCCTTTTTATTTAAACACTAAACCCAACTTAATACTATGGTTTTTTATCTTTAATTC
131 CACTGATTTCCTTTTTATTTAAACACTAAACCCAACTTAATACTATGGTTTTTTATCTTTAATTC
144343 ATCCAACAGTTCATATA
196 ATCCAACAGTTCATATA
144360 T
1 T
144361 GAATCATTGA
Statistics
Matches: 209, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
212 35 0.17
213 174 0.83
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (212 bp):
TCCTCTTCAAAGTGATTCATATCCCTCAGCCTTACCTTTGGATTTGAGGTTAAGTCTCTGAAGAA
CTAAAGTTGTATGCGACTCGTAACCTAGGATTAGAATTATAATGTATGTATACTCATATATTTGA
CACTGATTTCCTTTTTATTTAAACACTAAACCCAACTTAATACTATGGTTTTTTATCTTTAATTC
ATCCAACAGTTCATATA
Found at i:147288 original size:32 final size:32
Alignment explanation
Indices: 147247--147316 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
147237 AATACAGCAT
147247 GAAGTATAATAGAAATCATAAAAATAGTTACG
1 GAAGTATAATAGAAATCATAAAAATAGTTACG
147279 GAAGTATAATAGAAATCATAAAAATAGTTACG
1 GAAGTATAATAGAAATCATAAAAATAGTTACG
147311 GAAGTA
1 GAAGTA
147317 CATAAGCTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.24
Consensus pattern (32 bp):
GAAGTATAATAGAAATCATAAAAATAGTTACG
Found at i:151819 original size:22 final size:22
Alignment explanation
Indices: 151794--151836 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
151784 GAAAGACACT
151794 TGATATTGATTATGAAGAGACC
1 TGATATTGATTATGAAGAGACC
151816 TGATATTGATTATGAAGAGAC
1 TGATATTGATTATGAAGAGAC
151837 ATACTCTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (22 bp):
TGATATTGATTATGAAGAGACC
Found at i:154335 original size:2 final size:2
Alignment explanation
Indices: 154328--154353 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
154318 GTTGTATGTA
154328 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
154354 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:161146 original size:44 final size:44
Alignment explanation
Indices: 161083--161174 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
161073 CGGGCCATAC
161083 AAAACCCAGCCAAAATCTTAGCTCCCACTGCTGAACACCTGGAA
1 AAAACCCAGCCAAAATCTTAGCTCCCACTGCTGAACACCTGGAA
161127 AAAACCCAGCCAAAATCTTAGCTCCCACTGCTGAACACCTGGAA
1 AAAACCCAGCCAAAATCTTAGCTCCCACTGCTGAACACCTGGAA
161171 AAAA
1 AAAA
161175 TGGGATCTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.39, C:0.33, G:0.13, T:0.15
Consensus pattern (44 bp):
AAAACCCAGCCAAAATCTTAGCTCCCACTGCTGAACACCTGGAA
Found at i:180755 original size:43 final size:43
Alignment explanation
Indices: 180691--180817 Score: 161
Period size: 43 Copynumber: 3.0 Consensus size: 43
180681 ACTACAAGAA
* *
180691 AACA-GGTTTTTAGCGGTGCTTTTTCCACAAACGCCGCTAAAG
1 AACATGGTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAG
*
180733 AACATGGTCTTTAGTGGCGCTTTTAT-CACAAACGCCGCTAAAG
1 AACATGGTCTTTAGCGGCGCTTTT-TCCACAAACGCCGCTAAAG
* * *
180776 AACATGATCTTTAGCGGC-ATTTTTCCCATAAACGCCGCTAAA
1 AACATGGTCTTTAGCGGCGCTTTTT-CCACAAACGCCGCTAAA
180818 ATTAACAGAT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
41 1 0.01
42 8 0.11
43 64 0.86
44 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (43 bp):
AACATGGTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAG
Done.