Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012300.1 Kokia drynarioides strain JFW-HI SEQ_127301, 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: 251787
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 272 characters in sequence are not A, C, G, or T
Found at i:741 original size:17 final size:17
Alignment explanation
Indices: 716--790 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
706 TTTTAATTTT
*
716 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
733 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
* * * *
750 ATTCAAACTCAAAATGA
1 ATTTAAATTTAAAATAA
*
767 ATTTGAATTTAAAATAA
1 ATTTAAATTTAAAATAA
784 ATTTAAA
1 ATTTAAA
791 CTTATTTAAA
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:764 original size:34 final size:34
Alignment explanation
Indices: 726--792 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
716 ATTTTAATTT
*
726 AAAATAAATTTAAATTTAAAGTAAATTCAAACTC
1 AAAATAAATTTAAATTTAAAATAAATTCAAACTC
* * *
760 AAAATGAATTTGAATTTAAAATAAATTTAAACT
1 AAAATAAATTTAAATTTAAAATAAATTCAAACT
793 TATTTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.34
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATTCAAACTC
Found at i:1290 original size:3 final size:3
Alignment explanation
Indices: 1282--1320 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1272 ATGCTTTCTT
1282 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1321 AAGCATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5604 original size:14 final size:14
Alignment explanation
Indices: 5576--5613 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5566 ACTGTCGTTT
*
5576 TTATTTT-AGTTAA
1 TTATTTTAATTTAA
*
5589 TTTTTTTAATTTAA
1 TTATTTTAATTTAA
5603 TTATTTTAATT
1 TTATTTTAATT
5614 AAGATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TTATTTTAATTTAA
Found at i:6459 original size:12 final size:12
Alignment explanation
Indices: 6436--6483 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
6426 ACTGTTTTGA
*
6436 TGTTGTTATTTT
1 TGTTGTTGTTTT
*
6448 TGTTGCTGTTTT
1 TGTTGTTGTTTT
*
6460 TGTTGTTATTTT
1 TGTTGTTGTTTT
*
6472 TATTGTTGTTTT
1 TGTTGTTGTTTT
6484 GCTATTATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.06, C:0.02, G:0.19, T:0.73
Consensus pattern (12 bp):
TGTTGTTGTTTT
Found at i:6463 original size:24 final size:24
Alignment explanation
Indices: 6427--6518 Score: 87
Period size: 24 Copynumber: 3.8 Consensus size: 24
6417 TATATTTTTA
6427 CTGTTTTGATGTTGTTATTTTTGTTG
1 CTGTTTT--TGTTGTTATTTTTGTTG
*
6453 CTGTTTTTGTTGTTATTTTTATTG
1 CTGTTTTTGTTGTTATTTTTGTTG
* * * ***
6477 TTG-TTTTGCTATTATTTTTGCCA
1 CTGTTTTTGTTGTTATTTTTGTTG
*
6500 CTGTTTTGGTTGTTATTTT
1 CTGTTTTTGTTGTTATTTT
6519 GATTGTTTGG
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
23 16 0.30
24 30 0.57
26 7 0.13
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.66
Consensus pattern (24 bp):
CTGTTTTTGTTGTTATTTTTGTTG
Found at i:6470 original size:47 final size:47
Alignment explanation
Indices: 6419--6534 Score: 126
Period size: 47 Copynumber: 2.5 Consensus size: 47
6409 TTTGGTGCTA
* * *** *
6419 TATTTTTACTGTTTTGATGTTGTTATTTTTGTTGCTGTTTTTGTTGT
1 TATTTTTATTGTTTTGATGTTATTATTTTTGCCACTGTTTTGGTTGT
* *
6466 TATTTTTATTGTTGTT-TTGCTATTATTTTTGCCACTGTTTTGGTTGT
1 TATTTTTATTGTT-TTGATGTTATTATTTTTGCCACTGTTTTGGTTGT
* *
6513 TATTTTGATTGTTTGGATGTTA
1 TATTTTTATTGTTTTGATGTTA
6535 ATTTTATGTA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.11, C:0.05, G:0.19, T:0.65
Consensus pattern (47 bp):
TATTTTTATTGTTTTGATGTTATTATTTTTGCCACTGTTTTGGTTGT
Found at i:15983 original size:4 final size:4
Alignment explanation
Indices: 15974--16032 Score: 82
Period size: 4 Copynumber: 14.8 Consensus size: 4
15964 AAACAAGAAT
* * * *
15974 ATAG ATAG ATAG ACAG ACAG ACAG ACAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
16022 ATAG ATAG ATA
1 ATAG ATAG ATA
16033 TAGAGAGAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.19
Consensus pattern (4 bp):
ATAG
Found at i:30054 original size:23 final size:22
Alignment explanation
Indices: 30020--30064 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
30010 GGCTCAATGG
30020 GATTTTTATTGTAGTGTGAAGGA
1 GATTTTTATTGT-GTGTGAAGGA
*
30043 GATTTTGT-TTGTGTTTGAAGGA
1 GATTTT-TATTGTGTGTGAAGGA
30065 TTAGGCTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 10 0.50
24 1 0.05
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (22 bp):
GATTTTTATTGTGTGTGAAGGA
Found at i:47310 original size:26 final size:23
Alignment explanation
Indices: 47264--47309 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
47254 ATTAGGTACA
47264 TCATCCACAACATGAGAATTATT
1 TCATCCACAACATGAGAATTATT
*
47287 TCATCCATAACATGAGAATTATT
1 TCATCCACAACATGAGAATTATT
47310 AGGCAACTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
TCATCCACAACATGAGAATTATT
Found at i:50181 original size:7 final size:7
Alignment explanation
Indices: 50165--50198 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
50155 TTAACAGCTT
50165 TAACTAC
1 TAACTAC
*
50172 TAACTGC
1 TAACTAC
50179 TAACATAC
1 TAAC-TAC
50187 TAACTAC
1 TAACTAC
50194 TAACT
1 TAACT
50199 TCAGCTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (7 bp):
TAACTAC
Found at i:50189 original size:15 final size:14
Alignment explanation
Indices: 50165--50198 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
50155 TTAACAGCTT
*
50165 TAACTACTAACTGC
1 TAACTACTAACTAC
50179 TAACATACTAACTAC
1 TAAC-TACTAACTAC
50194 TAACT
1 TAACT
50199 TCAGCTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (14 bp):
TAACTACTAACTAC
Found at i:53426 original size:18 final size:18
Alignment explanation
Indices: 53403--53452 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
53393 TTTTGGTTGC
53403 TATTTTTTGCTGTTTTGA
1 TATTTTTTGCTGTTTTGA
* *
53421 TATTTTTTACTGTTTTGG
1 TATTTTTTGCTGTTTTGA
*
53439 TTTTTTTTGCTGTT
1 TATTTTTTGCTGTT
53453 ATTTTTGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.08, C:0.06, G:0.16, T:0.70
Consensus pattern (18 bp):
TATTTTTTGCTGTTTTGA
Found at i:53459 original size:12 final size:12
Alignment explanation
Indices: 53442--53493 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
53432 GTTTTGGTTT
*
53442 TTTTTGCTGTTA
1 TTTTTGCTGCTA
*
53454 TTTTTGCTACTA
1 TTTTTGCTGCTA
* * *
53466 TTATTGTTGTTA
1 TTTTTGCTGCTA
*
53478 TTTTTACTGCTA
1 TTTTTGCTGCTA
53490 TTTT
1 TTTT
53494 GCTATTTTTG
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.13, C:0.10, G:0.12, T:0.65
Consensus pattern (12 bp):
TTTTTGCTGCTA
Found at i:53478 original size:24 final size:22
Alignment explanation
Indices: 53443--53545 Score: 63
Period size: 24 Copynumber: 4.7 Consensus size: 22
53433 TTTTGGTTTT
*
53443 TTTTGCTGTTATTTTTGCTACTA
1 TTTTGTTGTTATTTTTG-TACTA
*
53466 TTATTGTTGTTA-TTTT-TACTGC
1 TT-TTGTTGTTATTTTTGTACT-A
* * *
53488 TATT-TTGCTATTTTTGT--TG
1 TTTTGTTGTTATTTTTGTACTA
*
53507 TTTTGTTGTTATTTTTGCTGCTA
1 TTTTGTTGTTATTTTTG-TACTA
*
53530 TCTTGGTTGTTATTTT
1 T-TTTGTTGTTATTTT
53546 GGTTGTTTGG
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
19 3 0.05
20 17 0.27
21 11 0.18
22 2 0.03
23 8 0.13
24 21 0.34
ACGTcount: A:0.11, C:0.09, G:0.16, T:0.65
Consensus pattern (22 bp):
TTTTGTTGTTATTTTTGTACTA
Found at i:53549 original size:12 final size:12
Alignment explanation
Indices: 53501--53552 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
53491 TTTGCTATTT
*
53501 TTGTTGTTTT-G
1 TTGTTATTTTGG
*
53512 TTGTTATTTTTG
1 TTGTTATTTTGG
* * *
53524 CTGCTATCTTGG
1 TTGTTATTTTGG
53536 TTGTTATTTTGG
1 TTGTTATTTTGG
53548 TTGTT
1 TTGTT
53553 TGGATGTTAG
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
11 9 0.28
12 23 0.72
ACGTcount: A:0.06, C:0.06, G:0.23, T:0.65
Consensus pattern (12 bp):
TTGTTATTTTGG
Found at i:53855 original size:31 final size:31
Alignment explanation
Indices: 53813--53886 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
53803 ATGGGTCAGA
53813 TCGGGTCGGGCTCGGGCTTGATTTCTATAAT
1 TCGGGTCGGGCTCGGGCTTGATTTCTATAAT
*
53844 TCGGGTTGGGCTCGGGCTTGATTTCTATAAT
1 TCGGGTCGGGCTCGGGCTTGATTTCTATAAT
53875 TCGGGTCGGGCT
1 TCGGGTCGGGCT
53887 TGGATAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.11, C:0.19, G:0.35, T:0.35
Consensus pattern (31 bp):
TCGGGTCGGGCTCGGGCTTGATTTCTATAAT
Found at i:66107 original size:4 final size:4
Alignment explanation
Indices: 66098--66134 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
66088 AACTCCCAAG
66098 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
66135 AGTAATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:69323 original size:20 final size:21
Alignment explanation
Indices: 69300--69358 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
69290 TTTTTGTTTT
* *
69300 AATT-AGGTTTTGGGTTTTAA
1 AATTAAGGTTTTAGATTTTAA
69320 AATTAAGG-TTTAGATTTTAA
1 AATTAAGGTTTTAGATTTTAA
69340 AATTAAGGTTTTAGTATTT
1 AATTAAGGTTTTAG-ATTT
69359 ATTTTATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 22 0.65
21 8 0.24
22 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (21 bp):
AATTAAGGTTTTAGATTTTAA
Found at i:69715 original size:23 final size:25
Alignment explanation
Indices: 69673--69718 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
69663 TGCTGTCTTT
*
69673 ATTTTATTTACATATTAATTTTAAG
1 ATTTTATTTACATATAAATTTTAAG
69698 ATTTT-TTTA-ATATAAATTTTA
1 ATTTTATTTACATATAAATTTTA
69719 CTTTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 4 0.20
25 5 0.25
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTTTATTTACATATAAATTTTAAG
Found at i:70325 original size:15 final size:15
Alignment explanation
Indices: 70305--70348 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
70295 GTTGAGGCCG
*
70305 GTGCTTTCGTGGGTA
1 GTGCTTACGTGGGTA
* *
70320 GTGCTTGCGTGGGCA
1 GTGCTTACGTGGGTA
70335 GTGCTTACGTGGGT
1 GTGCTTACGTGGGT
70349 GATGATGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.16, G:0.43, T:0.34
Consensus pattern (15 bp):
GTGCTTACGTGGGTA
Found at i:71859 original size:11 final size:11
Alignment explanation
Indices: 71843--71909 Score: 51
Period size: 11 Copynumber: 6.8 Consensus size: 11
71833 TTAATTAAAT
71843 TATAAAAATAA
1 TATAAAAATAA
71854 TAT-AAAATAA
1 TATAAAAATAA
* *
71864 T-TAAATATTA
1 TATAAAAATAA
*
71874 TTTAAAAATAA
1 TATAAAAATAA
71885 T-T---AAT--
1 TATAAAAATAA
71890 TATAAAAATAA
1 TATAAAAATAA
71901 TATAAAAAT
1 TATAAAAAT
71910 TAAAATTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
5 1 0.02
6 1 0.02
7 3 0.07
9 4 0.09
10 15 0.34
11 20 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:71859 original size:18 final size:18
Alignment explanation
Indices: 71824--71906 Score: 67
Period size: 16 Copynumber: 5.1 Consensus size: 18
71814 CATAAAAAAT
71824 ATTA-AAAAATTAAT-TAA
1 ATTATAAAAA-TAATATAA
71841 ATTATAAAAATAATATAA
1 ATTATAAAAATAATATAA
** *
71859 A--ATAATTA-AATAT-T
1 ATTATAAAAATAATATAA
71873 ATT-TAAAAATAAT-T-A
1 ATTATAAAAATAATATAA
71888 ATTATAAAAATAATATAA
1 ATTATAAAAATAATATAA
71906 A
1 A
71907 AATTAAAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
14 1 0.02
15 13 0.25
16 18 0.35
17 9 0.17
18 11 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTATAAAAATAATATAA
Found at i:71866 original size:31 final size:31
Alignment explanation
Indices: 71817--71885 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
71807 CTATTCACAT
*
71817 AAAA-AATATTAAAAAATTAATTA-AATTATA
1 AAAATAATATTAAAAAATTAAATATAATT-TA
*
71847 AAAATAATA-TAAAATAATTAAATATTATTTA
1 AAAATAATATTAAAA-AATTAAATATAATTTA
71878 AAAATAAT
1 AAAATAAT
71886 TAATTATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 9 0.26
31 22 0.65
32 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAATAATATTAAAAAATTAAATATAATTTA
Found at i:72784 original size:23 final size:23
Alignment explanation
Indices: 72758--72803 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
72748 CTAAAATGAA
72758 TTTTTTTTTGTAATTGGGTGACT
1 TTTTTTTTTGTAATTGGGTGACT
72781 TTTTTTTTTGTAATTGGGTGACT
1 TTTTTTTTTGTAATTGGGTGACT
72804 ATCTTTGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.04, G:0.22, T:0.61
Consensus pattern (23 bp):
TTTTTTTTTGTAATTGGGTGACT
Found at i:73150 original size:25 final size:24
Alignment explanation
Indices: 73090--73160 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 24
73080 CAATCTACAG
*
73090 TTTCATGGCTTTTTTTTTTCTATAT
1 TTTCATGG-TTTTTTTTGTCTATAT
73115 TTT--TGCAGTTTTGTTTTGTCTATAT
1 TTTCATG--GTTTT-TTTTGTCTATAT
73140 TTTCATGGTTTTCATTTTGTC
1 TTTCATGGTTTT--TTTTGTC
73161 CACTTTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
23 2 0.05
24 4 0.11
25 23 0.61
26 7 0.18
27 2 0.05
ACGTcount: A:0.11, C:0.11, G:0.13, T:0.65
Consensus pattern (24 bp):
TTTCATGGTTTTTTTTGTCTATAT
Found at i:74344 original size:173 final size:172
Alignment explanation
Indices: 74019--74377 Score: 474
Period size: 173 Copynumber: 2.1 Consensus size: 172
74009 TCTGTTATGT
* * * *
74019 AACATTGGTTTTTTTTTTTTAATATACTGGTATGATTACATAGTAGTATCTGTTCATACTTTTTT
1 AACATTGGTTTTTTTTTTTAAATATACTGGTATAATTACATAGTAGTATATGTTCATACTTTCTT
* * *
74084 AAATCTTTGACAACGCACACACACCTTGCACACACAAGTGCTCAAACCCGGATCTCTTAGGATGA
66 AAATATTTGACAACG-ACACACACCTTGCACACACAAGTGCTCAAACCCGGATCTCCTAAGATGA
*** *
74149 ACATCATCCTCTTTTTCACTGGAGCCACTCGTTG-GTTTCATGG
130 ACATCATCCTCTTAACCACTGGAGACACTCGTTGAG-TTCATGG
* * *
74192 AACATTAGTTTTTTTTTTTGAATATATACTGGTGTAATTACATGGTAGTATATGTTCATACTTTC
1 AACATTGGTTTTTTTTTTT-AA-ATATACTGGTATAATTACATAGTAGTATATGTTCATACTTTC
* * *
74257 TTAACTATTTGACAACG-CACACACCTTGCACACA-AAGGTGCTCGAACCC-GAGTCTCCTAATA
64 TTAAATATTTGACAACGACACACACCTTGCACACACAA-GTGCTCAAACCCGGA-TCTCCTAAGA
*
74319 TGAACATCATCCTCTTAACCACTGGAGACACTCGTTGAGTTCATGT
127 TGAACATCATCCTCTTAACCACTGGAGACACTCGTTGAGTTCATGG
74365 AACATTGGTTTTT
1 AACATTGGTTTTT
74378 GAATTAATTG
Statistics
Matches: 162, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
172 4 0.02
173 104 0.64
174 2 0.01
175 52 0.32
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (172 bp):
AACATTGGTTTTTTTTTTTAAATATACTGGTATAATTACATAGTAGTATATGTTCATACTTTCTT
AAATATTTGACAACGACACACACCTTGCACACACAAGTGCTCAAACCCGGATCTCCTAAGATGAA
CATCATCCTCTTAACCACTGGAGACACTCGTTGAGTTCATGG
Found at i:75551 original size:31 final size:29
Alignment explanation
Indices: 75516--75574 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
75506 TTTTTTTTAA
75516 TCGAATCAAGTGAAATGAAATTCGAGTTGAG
1 TCGAATCAAGTGAAAT--AATTCGAGTTGAG
** *
75547 TCGAATCGGGTGAAATTATTCGAGTTGA
1 TCGAATCAAGTGAAATAATTCGAGTTGA
75575 ATTAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.44
31 14 0.56
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (29 bp):
TCGAATCAAGTGAAATAATTCGAGTTGAG
Found at i:79736 original size:31 final size:31
Alignment explanation
Indices: 79673--79736 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
79663 ATACTTTAAT
* *
79673 TTGATCAATTTTAGTTCTTGTACTTTTTGAA
1 TTGATCAATTTTAGTTCTTGTACTATTCGAA
79704 TTGATCAATTTTA-TTCATTGTA-TGATTCGAA
1 TTGATCAATTTTAGTTC-TTGTACT-ATTCGAA
79735 TT
1 TT
79737 TTGAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.53
Consensus pattern (31 bp):
TTGATCAATTTTAGTTCTTGTACTATTCGAA
Found at i:87924 original size:22 final size:22
Alignment explanation
Indices: 87884--87926 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
87874 AAATATTTTC
**
87884 TAAAATTAAATATTTTAATTAG
1 TAAAATTAAATATAATAATTAG
87906 TAAAATTAAATATAATAATTA
1 TAAAATTAAATATAATAATTA
87927 ATAATGTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAAATTAAATATAATAATTAG
Found at i:88815 original size:29 final size:29
Alignment explanation
Indices: 88773--88843 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 29
88763 ATCGGAGTTA
* * *
88773 AAAATGAGACTTTTTGGA-TACCTGGGAGC
1 AAAATGGGAATTTTTGGACT-CATGGGAGC
* *
88802 AAAATGGTAA-TTTTGGACTCATGGGGGC
1 AAAATGGGAATTTTTGGACTCATGGGAGC
88830 AAAATGGGAATTTT
1 AAAATGGGAATTTT
88844 GGGGAAGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 23 0.68
29 11 0.32
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (29 bp):
AAAATGGGAATTTTTGGACTCATGGGAGC
Found at i:88973 original size:30 final size:31
Alignment explanation
Indices: 88939--89049 Score: 124
Period size: 30 Copynumber: 3.7 Consensus size: 31
88929 TTTGGACATC
* * *
88939 CGAGGGT-AAAAGGGTAATTTTTTAGAGTTT
1 CGAGGGTAAAAATGGTAATTTTTGAAAGTTT
*
88969 CGA-GGTCAAAAAT-GAAATTTTTGAAAG-TT
1 CGAGGGT-AAAAATGGTAATTTTTGAAAGTTT
*
88998 CGGGGGT-AAAATGGTAATTTTTGAAAGTTT
1 CGAGGGTAAAAATGGTAATTTTTGAAAGTTT
*
89028 CGAGGTTAAAAATGGTAATTTT
1 CGAGGGTAAAAATGGTAATTTT
89050 GGGAATTTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
28 5 0.07
29 20 0.30
30 24 0.36
31 18 0.27
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (31 bp):
CGAGGGTAAAAATGGTAATTTTTGAAAGTTT
Found at i:88988 original size:59 final size:59
Alignment explanation
Indices: 88884--89041 Score: 162
Period size: 59 Copynumber: 2.7 Consensus size: 59
88874 AGATAACCAG
* * * * *
88884 GGGTAAAATGGTAATTTTTAGAAA-ATT-G-GGATCAAAAACGGAATTTTTGGACA-TCCGA
1 GGGTAAAAGGGTAATTTTT-GAAAGTTTCGAGG-TCAAAAATGAAATTTTT-GAAAGTCCGA
* * * *
88942 GGGTAAAAGGGTAATTTTTTAGAGTTTCGAGGTCAAAAATGAAATTTTTGAAAGTTCGG
1 GGGTAAAAGGGTAATTTTTGAAAGTTTCGAGGTCAAAAATGAAATTTTTGAAAGTCCGA
* *
89001 GGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTTAAAAATG
1 GGGTAAAAGGGTAATTTTTGAAAGTTTCGAGGTCAAAAATG
89042 GTAATTTTGG
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
57 2 0.02
58 23 0.28
59 56 0.67
60 2 0.02
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (59 bp):
GGGTAAAAGGGTAATTTTTGAAAGTTTCGAGGTCAAAAATGAAATTTTTGAAAGTCCGA
Found at i:89050 original size:30 final size:31
Alignment explanation
Indices: 88946--89049 Score: 124
Period size: 29 Copynumber: 3.5 Consensus size: 31
88936 ATCCGAGGGT
* * * *
88946 AAAAGGGTAATTTTTTAGAGTTTCGAGGTCA
1 AAAATGGTAATTTTTGAAAGTTTCGAGGTTA
* * *
88977 AAAAT-GAAATTTTTGAAAG-TTCGGGGGT-
1 AAAATGGTAATTTTTGAAAGTTTCGAGGTTA
89005 AAAATGGTAATTTTTGAAAGTTTCGAGGTTA
1 AAAATGGTAATTTTTGAAAGTTTCGAGGTTA
89036 AAAATGGTAATTTT
1 AAAATGGTAATTTT
89050 GGGAATTTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 5 0.08
29 19 0.32
30 18 0.30
31 18 0.30
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (31 bp):
AAAATGGTAATTTTTGAAAGTTTCGAGGTTA
Found at i:101620 original size:30 final size:30
Alignment explanation
Indices: 101576--101656 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
101566 TTCGTGAACA
* * *
101576 TTAAACAAATGAATATGAATACACATAACT
1 TTAAATAAACGAATATGAACACACATAACT
*
101606 TTAAATAAACGAATATAAACACACATAACT
1 TTAAATAAACGAATATGAACACACATAACT
* *
101636 TTAAATAAACTAACATGAACA
1 TTAAATAAACGAATATGAACA
101657 AAAAATTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.25
Consensus pattern (30 bp):
TTAAATAAACGAATATGAACACACATAACT
Found at i:105998 original size:2 final size:2
Alignment explanation
Indices: 105991--106029 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
105981 AATAATAAAT
105991 TA TA TA 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 TA TA TA T
106030 TTTAAACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:120923 original size:24 final size:24
Alignment explanation
Indices: 120896--120944 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
120886 ATACAAAGAT
* *
120896 AAAATTGT-AATTTGATCTCTTTAA
1 AAAATT-TCAATTTAATCCCTTTAA
120920 AAAATTTCAATTTAATCCCTTTAA
1 AAAATTTCAATTTAATCCCTTTAA
120944 A
1 A
120945 CTTCTAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (24 bp):
AAAATTTCAATTTAATCCCTTTAA
Found at i:147181 original size:5 final size:5
Alignment explanation
Indices: 147173--147206 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
147163 GGTATGGGTT
*
147173 TTTTT TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
147207 TAATAGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (5 bp):
TTTTG
Found at i:148211 original size:10 final size:10
Alignment explanation
Indices: 148196--148220 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
148186 TAGTTTTTAG
148196 ACATAGAACA
1 ACATAGAACA
148206 ACATAGAACA
1 ACATAGAACA
148216 ACATA
1 ACATA
148221 TCATATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.08, T:0.12
Consensus pattern (10 bp):
ACATAGAACA
Found at i:155504 original size:29 final size:28
Alignment explanation
Indices: 155450--155504 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
155440 ATTATATTGT
* ** *
155450 TGTTTTGGTGTTGTTTTTTTTTTTTTAC
1 TGTTTTGGTGCTGTTTTTGCTGTTTTAC
155478 TGTTTTGGTTGCTGTTTTTGCTGTTTT
1 TGTTTTGG-TGCTGTTTTTGCTGTTTT
155505 GGTGCTGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 8 0.36
29 14 0.64
ACGTcount: A:0.02, C:0.05, G:0.22, T:0.71
Consensus pattern (28 bp):
TGTTTTGGTGCTGTTTTTGCTGTTTTAC
Found at i:155516 original size:43 final size:43
Alignment explanation
Indices: 155469--155562 Score: 161
Period size: 43 Copynumber: 2.2 Consensus size: 43
155459 GTTGTTTTTT
* *
155469 TTTTTTTACTGTTTTGGTTGCTGTTTTTGCTGTTTTGGTGCTG
1 TTTTTTTACTGTTTTGGTTGCTGTTTTTACTGTTTTGATGCTG
155512 TTTTTTTACTGTTTTGGTTGCTGTTTTTACTGTTTTGATGCTG
1 TTTTTTTACTGTTTTGGTTGCTGTTTTTACTGTTTTGATGCTG
155555 TTATTTTT
1 TT-TTTTT
155563 GTTGTTGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
43 43 0.90
44 5 0.10
ACGTcount: A:0.05, C:0.09, G:0.21, T:0.65
Consensus pattern (43 bp):
TTTTTTTACTGTTTTGGTTGCTGTTTTTACTGTTTTGATGCTG
Found at i:155553 original size:20 final size:21
Alignment explanation
Indices: 155471--155556 Score: 122
Period size: 21 Copynumber: 4.1 Consensus size: 21
155461 TGTTTTTTTT
155471 TTTTTACTGTTTTGGTTGCTG
1 TTTTTACTGTTTTGGTTGCTG
*
155492 TTTTTGCTGTTTTGG-TGCTG
1 TTTTTACTGTTTTGGTTGCTG
155512 TTTTTTTACTGTTTTGGTTGCTG
1 --TTTTTACTGTTTTGGTTGCTG
*
155535 TTTTTACTGTTTT-GATGCTG
1 TTTTTACTGTTTTGGTTGCTG
155555 TT
1 TT
155557 ATTTTTGTTG
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
20 13 0.22
21 27 0.46
22 14 0.24
23 5 0.08
ACGTcount: A:0.05, C:0.09, G:0.23, T:0.63
Consensus pattern (21 bp):
TTTTTACTGTTTTGGTTGCTG
Found at i:155568 original size:23 final size:22
Alignment explanation
Indices: 155469--155589 Score: 108
Period size: 23 Copynumber: 5.5 Consensus size: 22
155459 GTTGTTTTTT
*
155469 TTTTTTTACTGTTTTGGTTGCTG
1 TTTTTTTGCTGTTTT-GTTGCTG
*
155492 --TTTTTGCTGTTTTGGTGCTG
1 TTTTTTTGCTGTTTTGTTGCTG
*
155512 TTTTTTTACTGTTTTGGTTGCTG
1 TTTTTTTGCTGTTTT-GTTGCTG
* *
155535 --TTTTTACTGTTTTGATGCTG
1 TTTTTTTGCTGTTTTGTTGCTG
*
155555 TTATTTTTGTTGTTGTT-TTGCTG
1 TT-TTTTTGCTGTT-TTGTTGCTG
155578 TTATTTTTGCTG
1 TT-TTTTTGCTG
155590 CTATTTTGGT
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
20 12 0.15
21 25 0.30
22 12 0.15
23 31 0.38
24 2 0.02
ACGTcount: A:0.05, C:0.08, G:0.22, T:0.64
Consensus pattern (22 bp):
TTTTTTTGCTGTTTTGTTGCTG
Found at i:155573 original size:12 final size:12
Alignment explanation
Indices: 155550--155608 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
155540 ACTGTTTTGA
155550 TGCTGTTATTTT
1 TGCTGTTATTTT
* *
155562 TGTTGTT-GTTT
1 TGCTGTTATTTT
155573 TGCTGTTATTTT
1 TGCTGTTATTTT
*
155585 TGCTGCTATTTT
1 TGCTGTTATTTT
* *
155597 GGTTGTTATTTT
1 TGCTGTTATTTT
155609 ATTTATTTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 9 0.24
12 29 0.76
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.66
Consensus pattern (12 bp):
TGCTGTTATTTT
Found at i:155576 original size:43 final size:42
Alignment explanation
Indices: 155472--155579 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 42
155462 GTTTTTTTTT
* * *
155472 TTTTACTGTTTTGGTTGCTGTTTTTGCTGTTTTGGTGCTGTTT
1 TTTTA-TGTTTTGGTTGCTGTTTTTACTGTTTTGATGCTGTTA
155515 TTTTACTGTTTTGGTTGCTGTTTTTACTGTTTTGATGCTGTTA
1 TTTTA-TGTTTTGGTTGCTGTTTTTACTGTTTTGATGCTGTTA
*
155558 TTTT-TGTTGTTGTTTTGCTGTT
1 TTTTATGTT-TTG-GTTGCTGTT
155580 ATTTTTGCTG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
41 4 0.07
42 3 0.05
43 52 0.88
ACGTcount: A:0.05, C:0.08, G:0.23, T:0.64
Consensus pattern (42 bp):
TTTTATGTTTTGGTTGCTGTTTTTACTGTTTTGATGCTGTTA
Found at i:155596 original size:23 final size:23
Alignment explanation
Indices: 155550--155608 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
155540 ACTGTTTTGA
* * *
155550 TGCTGTTATTTTTGTTGTTGTTT
1 TGCTGTTATTTTTGCTGCTATTT
155573 TGCTGTTATTTTTGCTGCTATTT
1 TGCTGTTATTTTTGCTGCTATTT
*
155596 TGGTTGTTATTTT
1 T-GCTGTTATTTT
155609 ATTTATTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 21 0.68
24 10 0.32
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.66
Consensus pattern (23 bp):
TGCTGTTATTTTTGCTGCTATTT
Found at i:156175 original size:6 final size:6
Alignment explanation
Indices: 156164--156190 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
156154 GGATGCTTAG
156164 AATCAT AATCAT AATCAT AATCAT AAT
1 AATCAT AATCAT AATCAT AATCAT AAT
156191 TTTAGGGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
AATCAT
Found at i:162252 original size:14 final size:14
Alignment explanation
Indices: 162233--162262 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
162223 GAATAGATTT
162233 TTAATTAAATAAAA
1 TTAATTAAATAAAA
*
162247 TTAATTAATTAAAA
1 TTAATTAAATAAAA
162261 TT
1 TT
162263 TTTAAACCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTAAATAAAA
Found at i:164029 original size:18 final size:18
Alignment explanation
Indices: 163988--164041 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
163978 TTTTTTCAAT
*
163988 TTTAATTAATTTAAAATTA
1 TTTAATTAA-TTAAATTTA
*
164007 -CTAATTAATTAAATTTA
1 TTTAATTAATTAAATTTA
164024 TTTAATTAA--AAATTTA
1 TTTAATTAATTAAATTTA
164040 TT
1 TT
164042 CTCATCCCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 9 0.29
17 8 0.26
18 14 0.45
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTAATTAATTAAATTTA
Found at i:170794 original size:39 final size:40
Alignment explanation
Indices: 170741--170820 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
170731 AAGAGGTATG
*
170741 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
* * *
170781 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAATGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
170820 T
1 T
170821 TGAGTGCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
Found at i:175669 original size:39 final size:39
Alignment explanation
Indices: 175625--175708 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
175615 TGGGACAAGT
*
175625 CTCTTCCAAGAGGTAT-GTCCAATATGAAAAGGATTGTGA
1 CTCTTCCAAGAGGTATCATCCAATATG-AAAGGATTGTGA
* * * *
175664 CTCTT-CAATAGGTGTCCATCCAATTTGAAAGGGTTGTGA
1 CTCTTCCAAGAGGTAT-CATCCAATATGAAAGGATTGTGA
175703 CTCTTC
1 CTCTTC
175709 AAAAGGTGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
38 8 0.22
39 21 0.57
40 8 0.22
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (39 bp):
CTCTTCCAAGAGGTATCATCCAATATGAAAGGATTGTGA
Found at i:175709 original size:39 final size:40
Alignment explanation
Indices: 175642--175721 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
175632 AAGAGGTATG
*
175642 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
* *
175682 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
175721 T
1 T
175722 TGAGTGCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
Found at i:179847 original size:33 final size:33
Alignment explanation
Indices: 179787--179849 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
179777 CCAAAATGAT
*
179787 CAAAATGTAAAATTAATTGAAACCTAAAATCAA
1 CAAAATGTAAAATTAATCGAAACCTAAAATCAA
179820 CAAAATTGTAAAATTAACTCG-AA-CTAAAAT
1 CAAAA-TGTAAAATTAA-TCGAAACCTAAAAT
179850 GACTCGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 12 0.44
34 13 0.48
35 2 0.07
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.25
Consensus pattern (33 bp):
CAAAATGTAAAATTAATCGAAACCTAAAATCAA
Found at i:182080 original size:6 final size:6
Alignment explanation
Indices: 182069--182108 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
182059 GGGACTTAGC
*
182069 ACACAT ACACAT ACACAT ACATAT ACACAT ACACAT ACAC
1 ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACAC
182109 CTATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (6 bp):
ACACAT
Found at i:182101 original size:24 final size:24
Alignment explanation
Indices: 182069--182117 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
182059 GGGACTTAGC
182069 ACACATACACATACACATACATAT
1 ACACATACACATACACATACATAT
* *
182093 ACACATACACATACACCTATATAT
1 ACACATACACATACACATACATAT
182117 A
1 A
182118 TAGGTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (24 bp):
ACACATACACATACACATACATAT
Found at i:182127 original size:10 final size:10
Alignment explanation
Indices: 182112--182136 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
182102 CATACACCTA
182112 TATATATAGG
1 TATATATAGG
182122 TATATATAGG
1 TATATATAGG
182132 TATAT
1 TATAT
182137 GGCAGTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (10 bp):
TATATATAGG
Found at i:185965 original size:25 final size:25
Alignment explanation
Indices: 185936--185995 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
185926 ACAGAGTTTA
185936 ACTGAAATATTATTTTCCAAATTTG
1 ACTGAAATATTATTTTCCAAATTTG
185961 ACTGAAATATTATTTTCCAAATTTG
1 ACTGAAATATTATTTTCCAAATTTG
185986 ACTGAAATAT
1 ACTGAAATAT
185996 GAGTCGTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (25 bp):
ACTGAAATATTATTTTCCAAATTTG
Found at i:188221 original size:32 final size:32
Alignment explanation
Indices: 188185--188248 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
188175 TTCTAATAAC
188185 TATGGTTTGGAATGCTATATTTTTAATTTCTT
1 TATGGTTTGGAATGCTATATTTTTAATTTCTT
188217 TATGGTTTGGAATGCTATATTTTTAATTTCTT
1 TATGGTTTGGAATGCTATATTTTTAATTTCTT
188249 CTTCGGGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.56
Consensus pattern (32 bp):
TATGGTTTGGAATGCTATATTTTTAATTTCTT
Found at i:202241 original size:22 final size:22
Alignment explanation
Indices: 202185--202246 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
202175 ATAGATTGAA
202185 ATAAATATAATATAATT-AAATT
1 ATAAATATAATAT-ATTCAAATT
* *
202207 AAAAATTAAAATATATTCAAATT
1 ATAAA-TATAATATATTCAAATT
*
202230 -TAAATCATAATACATTC
1 ATAAAT-ATAATATATTC
202247 TTAAAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 1 0.03
22 19 0.59
23 12 0.38
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAATATAATATATTCAAATT
Found at i:203148 original size:28 final size:28
Alignment explanation
Indices: 203116--203170 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
203106 CGTACATTTG
*
203116 GAATTTAGTCTC-ATACTTTTATTTTTAA
1 GAATTTAGTCCCTATACTTTT-TTTTTAA
*
203144 GAATTTAGTCCCTTTACTTTTTTTTTA
1 GAATTTAGTCCCTATACTTTTTTTTTA
203171 TTTGAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.56
Consensus pattern (28 bp):
GAATTTAGTCCCTATACTTTTTTTTTAA
Found at i:205890 original size:15 final size:15
Alignment explanation
Indices: 205869--205920 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
205859 GTTTGATAAA
205869 TTGAAAAATTAAGT-
1 TTGAAAAATTAAGTG
205883 TCTGAAAAA-TAAGTG
1 T-TGAAAAATTAAGTG
* *
205898 TTGAAAATTTAAGTA
1 TTGAAAAATTAAGTG
205913 TT-AAAAAT
1 TTGAAAAAT
205921 CTAAATACTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 17 0.53
15 15 0.47
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (15 bp):
TTGAAAAATTAAGTG
Found at i:209107 original size:21 final size:21
Alignment explanation
Indices: 209081--209124 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
209071 CAATTTGTTC
209081 ATTTGAAGGTTAAGTTTCCTG
1 ATTTGAAGGTTAAGTTTCCTG
209102 ATTTGAAGGTTAAGTTTCCTG
1 ATTTGAAGGTTAAGTTTCCTG
209123 AT
1 AT
209125 CTTCAGGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (21 bp):
ATTTGAAGGTTAAGTTTCCTG
Found at i:213549 original size:50 final size:49
Alignment explanation
Indices: 213446--213553 Score: 121
Period size: 51 Copynumber: 2.2 Consensus size: 49
213436 TACAAAAAAT
* *
213446 AAAACTAAATTACACAATGTATAAATATTGAGAGTTAATTTTTTAGAATC
1 AAAACTAAATTACACAATATATAAATATTGAGAGTTAATTTTTTAG-ACC
* * **
213496 AAAACTAAATTGACACAATATATTAATGTTGAGAGTTTTTTTTTCTAG-CC
1 AAAACTAAATT-ACACAATATATAAATATTGAGAGTTAATTTTT-TAGACC
213546 AAAA-TAAA
1 AAAACTAAA
213554 ATTAATATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
49 4 0.08
50 16 0.32
51 27 0.54
52 3 0.06
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.36
Consensus pattern (49 bp):
AAAACTAAATTACACAATATATAAATATTGAGAGTTAATTTTTTAGACC
Found at i:222814 original size:133 final size:134
Alignment explanation
Indices: 222544--222942 Score: 727
Period size: 133 Copynumber: 3.0 Consensus size: 134
222534 GTTCCTATTC
*
222544 TACCTAAGTGATTTTGCTGCAAAATTTTCCATTAACCCAAACAGGAAACAACCAAGAACAG--AA
1 TACCTAAGTAATTTTGCTGCAAAATTTTCCATTAACCCAAACAGGAAACAACCAAGAACAGAAAA
222607 TGTAAAAAACATGCACTTGGGGGTGACATAT--ACAGAATATGGGTGTTGACTACAAATTTAAGA
66 TGTAAAAAACATGCACTTGGGGGTGACATATGAACAGAATATGGGTGTTGACTACAAATTTAAGA
222670 GGCT
131 GGCT
* *
222674 TACCTAAGTAATTTTGCTGCAAAATTTTCCATTAACCCAAACAGGAAACAACCAGGAGCAGAAAA
1 TACCTAAGTAATTTTGCTGCAAAATTTTCCATTAACCCAAACAGGAAACAACCAAGAACAGAAAA
222739 TGTAAAAAACATGCACTT-GGGGTGACATATGAACAGAATATGGGTGTTGACTACAAATTTAAGA
66 TGTAAAAAACATGCACTTGGGGGTGACATATGAACAGAATATGGGTGTTGACTACAAATTTAAGA
222803 GGCT
131 GGCT
*
222807 TACCTAAGTAATTTTGCTGCAAAATTTTCCATTAACCCAAACAAGAAACAACCAAGAACAGAAAA
1 TACCTAAGTAATTTTGCTGCAAAATTTTCCATTAACCCAAACAGGAAACAACCAAGAACAGAAAA
222872 TGTAAAAAACATGCACTTGGGGGTGACATATGAACAGAATATGGGTGTTGACTACAAATTTAAGA
66 TGTAAAAAACATGCACTTGGGGGTGACATATGAACAGAATATGGGTGTTGACTACAAATTTAAGA
222937 GGCT
131 GGCT
222941 TA
1 TA
222943 TGATTTGATA
Statistics
Matches: 258, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
130 58 0.22
131 12 0.05
132 20 0.08
133 116 0.45
134 52 0.20
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (134 bp):
TACCTAAGTAATTTTGCTGCAAAATTTTCCATTAACCCAAACAGGAAACAACCAAGAACAGAAAA
TGTAAAAAACATGCACTTGGGGGTGACATATGAACAGAATATGGGTGTTGACTACAAATTTAAGA
GGCT
Found at i:229561 original size:32 final size:32
Alignment explanation
Indices: 229444--229561 Score: 159
Period size: 32 Copynumber: 3.8 Consensus size: 32
229434 ATGATTACAA
* *
229444 ATTGACAACTCTTACGAGCATACAGTTCACAG
1 ATTGACAGCTCTTACGAGCATACTGTTCACAG
* *
229476 ATTGACAGCTCTTACGAGCATACTATTCATAG
1 ATTGACAGCTCTTACGAGCATACTGTTCACAG
* *
229508 ATTGA-TG-TGTTACGAGCATACTGTTCACAG
1 ATTGACAGCTCTTACGAGCATACTGTTCACAG
*
229538 ATTGACAGCTCTTACGAGTATACT
1 ATTGACAGCTCTTACGAGCATACT
229562 ATTTACTGAG
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
30 25 0.34
31 2 0.03
32 46 0.63
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (32 bp):
ATTGACAGCTCTTACGAGCATACTGTTCACAG
Found at i:238310 original size:20 final size:21
Alignment explanation
Indices: 238285--238328 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
238275 TTTAACCTCA
238285 TTTATAA-T-TTATATTAATTT
1 TTTATAATTGTTATA-TAATTT
238305 TTTATAATTGTTATATAATTT
1 TTTATAATTGTTATATAATTT
238326 TTT
1 TTT
238329 TTTTTTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 10 0.45
22 5 0.23
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTATAATTGTTATATAATTT
Found at i:238329 original size:22 final size:20
Alignment explanation
Indices: 238285--238328 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
238275 TTTAACCTCA
238285 TTTATAATTTATATTAATTT
1 TTTATAATTTATATTAATTT
238305 TTTATAATTGT-TATATAATTT
1 TTTATAATT-TATAT-TAATTT
238326 TTT
1 TTT
238329 TTTTTTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTATAATTTATATTAATTT
Found at i:240846 original size:2 final size:2
Alignment explanation
Indices: 240841--240867 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
240831 ACAATCCTTA
240841 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
240868 AGAGTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:244182 original size:12 final size:12
Alignment explanation
Indices: 244161--244195 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
244151 AAATTCATAA
*
244161 TTTAACTTTTTC
1 TTTAATTTTTTC
244173 TTTAATTTTTT-
1 TTTAATTTTTTC
244184 TTTAATTTTTTC
1 TTTAATTTTTTC
244196 CCTCATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTAATTTTTTC
Found at i:244651 original size:60 final size:58
Alignment explanation
Indices: 244531--244701 Score: 191
Period size: 60 Copynumber: 2.9 Consensus size: 58
244521 TTTGGTACCA
* * * * **
244531 GAGTTTGGCTTCAATGTTCAATTTGATACTTGA-TTTTTTTGTCCCAATTTAGTGCAT
1 GAGTTTGGCTTCAATATTCAATTTGGTACTTGAGTTTTTTTATCCCAATTAAGCACAT
* * *
244588 GAGTTTGACTTCAATATTCAAATTGGTATTTGAGCTTTCTTTTATCCCAATTAAGCACAT
1 GAGTTTGGCTTCAATATTCAATTTGGTACTTGAG-TTT-TTTTATCCCAATTAAGCACAT
** *
244648 GAGTTTGGCTTTGATATTCAATTTGGTACTTGAGTTTTTTCTAGTTCCAATTAA
1 GAGTTTGGCTTCAATATTCAATTTGGTACTTGAGTTTTTT-TA-TCCCAATTAA
244702 AGTACTTATG
Statistics
Matches: 94, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
57 28 0.30
58 3 0.03
59 8 0.09
60 55 0.59
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (58 bp):
GAGTTTGGCTTCAATATTCAATTTGGTACTTGAGTTTTTTTATCCCAATTAAGCACAT
Found at i:249638 original size:25 final size:25
Alignment explanation
Indices: 249604--249654 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
249594 CCATACAAAT
249604 GCTAAACATGTTCGGTTTCTTGATA
1 GCTAAACATGTTCGGTTTCTTGATA
249629 GCTAAACATGTTCGGTTTCTTGATA
1 GCTAAACATGTTCGGTTTCTTGATA
249654 G
1 G
249655 AACACAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (25 bp):
GCTAAACATGTTCGGTTTCTTGATA
Done.